U.S. patent application number 16/015955 was filed with the patent office on 2019-03-21 for mhc multimers, methods for their generation, labeling and use.
The applicant listed for this patent is Dako Denmark A/S. Invention is credited to Liselotte Brix, Katja Brunstedt, Kivin Jacobsen, Tina Jakobsen, Jesper Lohse, Henrik Pedersen, Jorgen Scholler.
Application Number | 20190085048 16/015955 |
Document ID | / |
Family ID | 40225718 |
Filed Date | 2019-03-21 |
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United States Patent
Application |
20190085048 |
Kind Code |
A1 |
Brix; Liselotte ; et
al. |
March 21, 2019 |
MHC Multimers, Methods for Their Generation, Labeling and Use
Abstract
The present invention describes novel methods to generate MHC
multimers and methods to improve existing and new MHC multimers.
The invention also describes improved methods for the use of MHC
multimers in analysis of T-cells in samples including diagnostic
and prognostic methods. Furthermore, the use of MHC multimers in
therapy are described, e.g. anti-tumour and anti-virus therapy,
including isolation of antigen specific T-cells capable of
inactivation or elimination of undesirable targeT-cells or
isolation of specific T-cells capable of regulation of other immune
cells.
Inventors: |
Brix; Liselotte; (Bagsv.ae
butted.rd, DK) ; Pedersen; Henrik; (Lynge, DK)
; Jakobsen; Tina; (Ballerup, DK) ; Scholler;
Jorgen; (Lyngby, DK) ; Lohse; Jesper;
(Copenhagen NV, DK) ; Brunstedt; Katja; (Lyngby,
DK) ; Jacobsen; Kivin; (Hvalso, DK) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Dako Denmark A/S |
Glostrup |
|
DK |
|
|
Family ID: |
40225718 |
Appl. No.: |
16/015955 |
Filed: |
June 22, 2018 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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12644554 |
Dec 22, 2009 |
10030065 |
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16015955 |
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PCT/DK08/50167 |
Jul 3, 2008 |
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12644554 |
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60929583 |
Jul 3, 2007 |
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60929581 |
Jul 3, 2007 |
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60292586 |
May 22, 2001 |
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60929582 |
Jul 3, 2007 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61K 47/61 20170801;
A61K 47/6425 20170801; A61K 47/665 20170801; C07K 14/70539
20130101; B82Y 5/00 20130101; A61P 31/00 20180101; A61K 38/00
20130101 |
International
Class: |
C07K 14/74 20060101
C07K014/74; A61K 47/66 20060101 A61K047/66; A61K 47/64 20060101
A61K047/64; B82Y 5/00 20060101 B82Y005/00 |
Foreign Application Data
Date |
Code |
Application Number |
Jul 3, 2007 |
DK |
PA 2007 00972 |
Jul 3, 2007 |
DK |
PA 2007 00973 |
Jul 3, 2007 |
DK |
PA 2007 00974 |
Jul 3, 2007 |
DK |
PA 2007 00975 |
Claims
1. An MHC multimer comprising (a-b-P).sub.n, wherein n>1,
wherein a and b together form a functional MHC protein capable of
binding peptide P, when P is present, wherein (a-b-P) is an
MHC-peptide complex formed when the peptide P binds to the
functional MHC protein, wherein each MHC-peptide complex is
associated with one or more multimerization domains, and wherein
one or more detectable labelling molecules selected from the group
consisting of DNA and RNA are attached to the MHC-peptide complex
or to the one or more multimerization domains.
2. The MHC multimer according to claim 1, wherein said one or more
detectable labelling molecules uniquely designate the MHC
multimer.
3. The MHC multimer according to claim 1, wherein the one or more
labelling molecules are covalently attached to the MHC
multimer.
4. The MHC multimer according to claim 1, wherein the one or more
labelling molecules are non-covalently attached to the MHC
multimer.
5. The MHC multimer according to claim 1, wherein the one or more
labelling molecules are attached directly to the MHC multimer.
6. The MHC multimer according to claim 5, wherein the one or more
labelling molecules are attached directly to the MHC complex via
the heavy chain, .beta.2m, or peptide.
7. The MHC multimer according to claim 5, wherein the one or more
labelling molecules are attached directly to the one or more
multimerization domains.
8. The MHC multimer according to claim 1, wherein the one or more
labelling molecules are conjugated to a linker.
9. The MHC multimer according to claim 8, wherein the linker
attaches the detectable labelling molecule to the one or more
multimerization domains.
10. The MHC multimer according to claim 1, wherein one or more of
the n MHC-peptide complexes are covalently linked to the one or
more multimerization domains.
11. The MHC multimer according to claim 1, wherein the one or more
multimerization domains comprise a polymer, to which is optionally
attached one or more scaffolds.
12. The MHC multimer according to claim 11, wherein the polymer
comprises a polysaccharide.
13. The MHC multimer according to claim 12, wherein the
polysaccharide is one or more dextran moieties.
14. The MHC multimer according to claim 1, wherein the MHC
complexes comprise chemically modified MHC complexes.
15. The MHC multimer according to claim 14, wherein the chemically
modified MHC complexes comprise one or more types of
cross-linkers.
16. The MHC multimer according to claim 15, wherein the
cross-linkers are one or more chemical cross linkers.
17. A composition comprising a plurality of MHC multimers according
to claim 1.
18. A method for generating the MHC multimer according to claim 1,
said method comprising the steps of: providing one or more
MHC-peptide complexes; providing one or more multimerization
domains; and reacting said one or more MHC-peptide complexes and
said one or more multimerization domains, thereby generating the
MHC multimer according to claim 1.
Description
[0001] This application is a continuation of U.S. application Ser.
No. 12/644,554, filed 22 Dec. 2009, which is a continuation of PCT
Appl. No. PCT/DK2008/050167, filed 3 Jul. 2008, which claims the
priority of U.S. Prov. Appl. No. 60/929,583, filed 3 Jul. 2007, and
U.S. Prov. Appl. No. 60/929,581, filed 3 Jul. 2007, and U.S. Prov.
Appl. No. 60/929,586, filed 3 Jul. 2007, and U.S. Prov. Appl. No.
60/929,582, filed 3 Jul. 2007, which PCT application also claims
the priority of Danish Appl. No. PA 2007 00974, filed 3 Jul. 2007,
and Danish Appl. No. PA 2007 00972, filed 3 Jul. 2007, and Danish
Appl. No. PA 2007 00975, filed 3 Jul. 2007, and Danish Appl. No. PA
2007 00973, filed 3 Jul. 2007. Each of the aforementioned
applications is hereby incorporated by reference in its
entirety.
[0002] Further, all patent and non-patent references cited in this
application are hereby incorporated by reference in their entirety.
All patent and non-patent references cited in U.S. 60/929,583, U.S.
60/929,586, U.S. 60/929,582, U.S. 60/929,581, PA 2007 00972, PA
2007 00975 and PA 2007 00973 are hereby incorporated by reference
in their entirety.
BACKGROUND
[0003] Biochemical interactions between peptide epitope specific
membrane molecules encoded by the Major Histocompatibility Complex
(MHC, in humans HLA) and T-cell receptors (TCR) are required to
elicit specific immune responses. This requires activation of
T-cells by presentation to the T-cells of peptides against which a
T-cell response should be raised. The peptides are presented to the
T-cells by the MHC complexes.
The Immune Response
[0004] The immune response is divided into two parts termed the
innate immune response and the adaptive immune response. Both
responses work together to eliminate pathogens (antigens). Innate
immunity is present at all times and is the first line of defence
against invading pathogens. The immediate response by means of
pre-existing elements, i.e. various proteins and phagocytic cells
that recognize conserved features on the pathogens, is important in
clearing and control of spreading of pathogens. If a pathogen is
persistent in the body and thus only partially cleared by the
actions of the innate immune system, the adaptive immune system
initiate a response against the pathogen. The adaptive immune
system is capable of eliciting a response against virtually any
type of pathogen and is unlike the innate immune system capable of
establishing immunological memory.
[0005] The adaptive response is highly specific to the particular
pathogen that activated it but it is not so quickly launched as the
innate when first encountering a pathogen. However, due to the
generation of memory cells, a fast and more efficient response is
generated upon repeated exposure to the same pathogen. The adaptive
response is carried out by two distinct sets of lymphocytes, the
B-cells producing antibodies leading to the humoral or antibody
mediated immune response, and the T-cells leading to the cell
mediated immune response.
[0006] T-cells express a clonotypic T-cell receptor (TCR) on the
surface. This receptor enable the T-cell to recognize peptide
antigens bound to major histocompatibility complex (MHC) molecules,
called human leukocyte antigens (HLA) in man. Depending on the type
of pathogen, being intracellular or extracellular, the antigenic
peptides are bound to MHC class I or MHC class II, respectively.
The two classes of MHC complexes are recognized by different
subsets of T-cells; Cytotoxic CD8+ T-cells recognizing MHC class I
and CD4+ helper cells recognizing MHC class II. In general, TCR
recognition of MHC-peptide complexes result in T-cell activation,
clonal expansion and differentiation of the T-cells into effector,
memory and regulatory T-cells.
[0007] B-cells express a membrane bound form of immunoglobulin (Ig)
called the B-cell receptor (BCR). The BCR recognizes an epitope
that is part of an intact three dimensional antigenic molecule.
Upon BCR recognition of an antigen the BCR:antigen complex is
internalized and fragments from the internalized antigen is
presented in the context of MHC class II on the surface of the
B-cell to CD4+ helper T-cells (Th). The specific Th cell will then
activate the B-cell leading to differentiation into an antibody
producing plasma cell.
[0008] A very important feature of the adaptive immune system is
its ability to distinguish between self and non-self antigens, and
preferably respond against non-self. If the immune system fails to
discriminate between the two, specific immune responses against
self-antigens are generated. These autoimmune reactions can lead to
damage of self-tissue.
[0009] The adaptive immune response is initiated when antigens are
taken up by professional antigen presenting cells such as dendritic
cells, Macrophages, Langerhans cells and B-cells. These cells
present peptide fragments, resulting from the degradation of
proteins, in the context of MHC class II proteins (Major
Histocompatibility Complex) to helper T-cells. The T helper cells
then mediate help to B-cells and antigen specific cytotoxic
T-cells, both of which have received primary activation signals via
their BCR respective TCR. The help from the Th-cell is mediated by
means of soluble mediators e.g. cytokines.
[0010] In general the interactions between the various cells of the
cellular immune response is governed by receptor-ligand
interactions directly between the cells and by production of
various soluble reporter substances e.g. cytokines by activated
cells.
[0011] The function of the immune system is to protect the body
against foreign invaders or aberrant self-molecules (e. g.
parasites, bacteria, viruses and cancer). Such threats can normally
be eliminated or neutralised efficiently by the immune system. To
administrate this potential, the immune system must discriminate
normal molecules in the healthy body from the presence of foreign
or aberrant self-molecules, which can be expressed during genesis
of diseases e. g. cancer. Ideally, foreign or aberrant molecules
should be eliminated, while the body itself should be left
unharmed. One major hallmark of the immune system is therefore one
of specificity i. e. the ability to discriminate between various
targets and in particular to distinguish between self and non-self.
The specific- or adaptive-immune system involves a large number of
different cell types. Immune responses develop from an orchestral
interplay of antigen-processing/presenting cells and effector
cells. The central effector cells are lymphocytes, with a major
subdivision into B- and T-cells representing humoral and cellular
responses, respectively. Both cell populations use receptors, which
in their genome are encoded in many bits and pieces allowing
enormous recombinatorial receptor diversity. Each B- or T-cell
carries one, and only one, of these receptors which recognise their
tiny but unique fragments of the universe. All human lymphocytes
combined divide the entire universe into two major groups of
targets: a group of self-antigens that are tolerated by the immune
system and a group of non-self or aberrant antigens that can elicit
a response. The overall specificity of the immune system is
generated, regulated and co-ordinated through processes controlling
individual lymphocytes. Deleting, or inactivating a lymphocyte
clone removes the corresponding specificity from the repertoire.
Activation and propagation of a lymphocyte clone enhances the
corresponding specificity- and allows the immune system to respond
quickly and strongly toward the antigen.
[0012] The cells of the immune system include the following:
Lymphocytes are a type of white blood cells found in the blood and
many other parts of the body. Types of lymphocytes include B-cells,
T-cells, and Natural Killer (NK) cells.
[0013] The B- and T-cells recognise and respond specifically to
aberrant substances, thus being a part of the specific immune
system. B-cells (or B-lymphocytes) mature into plasma cells that
secrete antibodies (immunoglobulins), the proteins that recognise
and attach to foreign substances known as antigens. Each type of
B-cell produces one specific antibody, which recognises one
specific epitope on the antigen. The T-cells recognise and respond
towards aberrant substances by interaction with antigen presenting
cells (APC) that display antigens in form of "non-self" (or
aberrant) peptides in context of MHC molecules. Each T-cell clone
expresses one unique specificity of T-cell receptors (TCR), which
recognise one specific peptide/MHC epitope.
[0014] T-cells comprise two major subpopulations. Cytolytic T-cells
directly attack infected, foreign, or cancerous cells displaying
foreign or aberrant forms of endogenous peptides in context of MHC
Class I molecules (described below). "Helper" T-cells that are
activated by foreign exogenous peptides in MHC Class II molecules,
contribute to regulation of the immune response by signalling other
immune system defenders. T-cells also work by producing proteins
called lymphokines.
[0015] NK cells produce powerful chemical substances that bind to
and kill any foreign invader. They attack without first having to
recognise a specific antigen, thus being an immune cell type that
also relate to the innate immune system.
[0016] Monocytes are white blood cells that are able to swallow and
digest microscopic organisms and particles in a process known as
phagocytosis and antigen processing.
[0017] Dendritic cells (DC) are of particular interest as they
present peptide epitopes in a "professional way" which leads to
effective activation of T-cells. The professional APC express a
variety of co-stimulatory molecules that ligate with a variety of
counter receptors expressed on the T-cells.
[0018] Cells in the immune system secrete two types of proteins,
namely antibodies and cytokines. Specific antibodies match epitopes
on specific antigens, fitting together much the way a key fits a
lock. Conventional vaccine approaches, in particular, work through
activation of helper T-cells and B-cells leading to secretion of
antigen specific antibodies. Cytokines are substances produced by
some immune cells to communicate with other cells. Types of
cytokines include lymphokines, interferons, interleukins, and
colony-stimulating factors.
[0019] Antigen-Recognition by B- and T-Cells.
[0020] B- and T-cells use entirely different mechanisms to
recognise their targets. B-cells recognise soluble antigens, and
since they can secrete their receptors as antibodies, they can
potentially interact with antigen throughout the fluid phase of the
extra-cellular space. In sharp contrast, the T-cell receptor is
always membrane-bound and it only recognises antigen, which is
presented on the membrane of an antigen-presenting cell (APC). In
other words, T-cell recognition involves a direct physical
interaction between two cells; a T-cell and an APC. B- and T-cells
also differ with respect to what they recognise. B-cells can
recognise organic substances of almost any kind, whereas T-cells
predominantly recognise proteins (as a biological target, proteins
are particularly important since they constitute the structural and
functional basis of all life). B-cells recognise the
three-dimensional structure of proteins as illustrated by their
ability to distinguish between native and denatured proteins. In
contrast, T-cells cannot distinguish between native and denatured
proteins.
[0021] Today, we know that T-cells only recognise antigenic
peptides presented in association with MHC molecules on the surface
of APC's. In general, cytotoxic T-cells recognise short peptides
(corresponding in general to 8-11 residues), the amino and
carboxy-termini of which are deeply embedded within the MHC Class I
molecule (i. e. the peptide length is restricted). In comparison,
helper T-cells tend to recognise longer peptides (corresponding in
general to 13-30 residues) with amino and carboxy terminal ends
extending out of the MHC Class II molecule.
[0022] MHC Restriction and T-Cell Immunity.
[0023] T-cells determine the reactivity and specificity of the
adaptive immune system, including the activity of B-cells. It is
therefore appropriate to focus the attention on these cells.
T-cells can only recognise a given antigen, when it is presented in
the context of a particular MHC molecule. They are "educated"
during ontogeny and further activated during the first priming in
processes designed to develop T-cells carrying receptors specific
for a particular antigen-MHC molecule combination. These T-cells
are subsequently only able to recognise the same antigen-MHC
molecule combination. This phenomenon is known as "MHC
restriction". Another immune phenomenon; that of "responder
status", is also determined by the MHC molecules. Individuals of
one MHC haplotype will respond to some antigens, and not to others.
Other individuals with other MHC haplotypes will respond
differently. These two phenomena are of obvious importance for any
rational immune manipulation. As mentioned, we now know that MHC
molecules control them both. These molecules have specifically
evolved for the purpose of antigen presentation. Our current
understanding of antigen presentation can be summarised as follows.
Firstly, the foreign substance, the antigen, is taken up by APC's.
An intracellular pool of antigenic peptides is generated through
proteolytic fragmentation of all the protein available to the cell
(which can include both normal cell proteins ("self-proteins") and
antigens ("non-self proteins") from infective organisms. This pool
of peptides is offered to the MHC molecules of the individual and
sampled according to length and sequence; some are bound, while
others are ignored (the MHC molecule is said to perform
"determinant selection"). Subsequently, MHC molecules protect the
selected peptides against further degradation, transport them to
the surface of the APC and display them for T-cell scrutiny.
Antigenic peptides from "non-self proteins" are, in contrast to
peptides from "self-proteins", recognised by T-cells that
consequently can become activated.
[0024] A plurality of receptors is involved in antigen specific
activation of immune cells. Several ligand-receptor interactions
related to control this network of cells are complex, in comparison
to more "conventional" ligand-receptor models comprising simple
hormone-receptor interaction e. g. insulin and IR. For example,
full activation of T-cells acquires simultaneous signalling through
a variety of receptors in addition to TCR signalling. The binding
energy yielded from ligation of multiple membrane molecules
expressed on APC and T-cells, ensure a close physical contact
between the involved cells. One of the most important additional
receptors related to activation of T-cells is CD28 molecules, which
bind proteins of the B7 family expressed on professional APCs.
Other known examples of regulatory receptors expressed on T-cells
are a variety of NK receptors (NKR), which comprise both inhibitory
and activating isoforms. The balance between expressed forms of
activating and inhibiting NKRs is believed to determine a threshold
for activation of specific T-cells.
[0025] It has recently been reported that molecular interactions
between many of the receptors and ligands involved in this cellular
interplay, including TCR and MHC molecules, are unstable i. e. of
low affinity. By example, it has been measured that monovalent MHC
molecule-TCR interaction has an affinity constant of Ko=10 uM with
a dissociation constant less than a minute. Molecular interaction
of CD28 and B7 protein has an affinity constant of same level. In
comparison, the stability and affinity of complexes formed by
high-affinity interactions e. g. hormone ligand-receptor binding
(insulin/IR) and antibody-antigen binding, are significantly higher
(affinity constant KD in the range of 0.1-10 nM).
[0026] The plurality of proteins related to activation of T-cells
do, however, not only stabilise cellular contact between APC and
T-cells, they also contribute to a variety of signalling events
required for activation of T-cells. It is-orchestrated actions of
these signalling events that determines the activation of T-cells.
For example, it has been shown that naive cytolytic T-cells require
at least two signals for activation. The first signal is delivered
through ligation of MHC molecules (expressed on APCs) to TCRs on
T-cells. The second signal is delivered through co-stimulatory
molecules from e. g. B7 protein family, which ligate with the CD28
receptor on T-cells.
[0027] The genes located in the human MHC locus (HLA locus) encode
a set of highly polymorph membrane proteins that sample peptides in
intracellular compartments and present such peptide epitopes on
surfaces of APCs to scrutinising T-cells. The extensive genetic
polymorphism of the MHC locus is the background for the unique
genetic finger print of the immune system in individuals and
defines the repertoire of antigenic peptide epitopes which the
human population is capable of recognising and responds to.
[0028] Two subtypes of MHC molecules exist, MHC Class I and II
molecules. These subtypes correspond to two subsets of
T-lymphocytes: 1) CD8+ cytotoxic T-cells, which usually recognize
peptides presented by MHC Class I molecules, and kill infected or
mutated T-cells, and 2) CD4+ helper T-cells, which usually
recognise peptides presented by MHC Class II molecules, and
regulate the responses of other cells of the immune system. MHC
Class I molecules consist of a 43,000 MW transmembrane glycoprotein
(the a chain) non-covalently associated with a 12,000 MW
non-glycosylated protein (the light (.beta.) chain, also known as
.beta.2-microglobulin). MHC Class II molecules have an overall
structure similar to MHC Class I molecules although the domain
distribution is different. The MHC Class II molecule consists of
two non-covalently associated trans-membrane glycoproteins of
approximately 34,000 and 29,000 MW. The detailed structures of MHC
Class I and II molecules have been solved at the X-ray
crystallography level. The most interesting part of the MHC
molecule structure is the "upper" part that shows a unique
peptide-binding groove consisting of two alpha helixes forming the
walls of the groove and eight beta-pleated sheaths forming the
floor of the groove.
[0029] The peptides are the essential target structures in
recognition of "non-self" by the adaptive immune system and, one
could say, the group of MHC molecules comprises a port to the
immune system, thus being a major player in determining penetrance
and spreading of human diseases.
[0030] MHC molecules of other higher vertebrate species exert
identical biological functions as those of HLA in man.
[0031] The MHC locus is extremely polymorphic i. e. many different
versions (alleles, allotypes) exist in the population, but each
individual has only inherited two of these (one from the father and
one from the mother). It is also polygenic i. e. several MHC
encoding loci exist in the genome allowing for simultaneous
expression of several isotypes. Importantly, the majority of the
polymorphic residues points towards the peptide binding groove
affecting its size, shape and functionality. Peptide-MHC
interactions are specific, albeit broad, allowing the binding of
many unrelated peptides to each MHC allotype. The polymorphism
dictates the specificity of peptide binding and the biological
consequence of this is that each individual in the population
educates and shapes a unique T-cell repertoire.
[0032] A variety of relatively invariant MHC Class I molecule like
molecules have been identified. This group comprises CDId, HLA E,
HLA G, HLA H, HLA F, MIC A, MIC B, ULBP-1, ULBP-2, and ULBP-3.
These non-classical molecules have a tissue distribution and
functions distinct from HLA A, B and C. Some of them comprise only
a heavy chain protein i. e. do not associate with .beta.2m
molecules and peptides. As described previously, the immune
responses develop from an orchestral interplay of
antigen-processing/presenting cells and effector cells.
[0033] Monomer and soluble forms of cognate as well as modified MHC
molecules e. g. single chain protein with peptide, heavy and light
chains fused into one construct, have been produced in bacteria as
well as eucaryotic cells. Recent advances in recombinant technology
and in vitro protein folding methods have provided efficient
protocols for large-scale production of multimeric MHC molecules,
which bind with high avidity to appropriate T-cell receptors.
[0034] NK Cells and MHC Molecules.
[0035] NK cells remained mysterious until recently. These cells
were defined by their ability to lyse certain tumours in the
absence of prior stimulation. NK cell activity is regulated by a
number of ligands including MHC molecule. NK cells recognise MHC
Class I molecules through surface receptors that deliver an
inhibitory signal. Thus, NK cells can lyse targeT-cells that have
lost expression of MHC molecules. It is well known that tumour
cells often reduce or loose their expression of MHC molecules
presumably due to a selective pressure from cytotoxic T-cells that
recognise tumour associated antigens (peptides) in context of MHC
molecules. The ability of NK cells to discriminate between normal
and tumour cells is then explained by the "missing-self
hypothesis". However, NK cells are not simply equipped with
receptors that recognise a broad spectrum of MHC molecules. The
complexity of NK receptors is also reflected by expression of
different isoforms, some of which are activating whereas others are
inhibitory. Interestingly, 5-10% of the (alpha beta) T-cells also
express different NK receptors such as KIR, ILT or CD94/NKG2, which
belong to the inhibitory-receptor superfamily. Such receptors can
serve to raise the activation threshold for cellular immune
responses. The balances between stimulating and inhibitory
receptors presumably control the activation of T-cells and NK
cells. Some of the different NK receptors expressed on NK cells and
T-cells recognise broader specificity of MHC Class I molecules,
whereas others recognise more rarely expressed allelic
determinants. Thus, the MHC molecules can be involved in both
stimulation and inhibition of specific immune responses.
[0036] The T-cell receptor (TCR), a member of the immunglobulin
super-family, consists of two non-covalently associated
trans-membrane glycoproteins of approximately 30,000 MW; each
comprising two extra-cellular domains. The two chains form a
dimmer, which associate with a larger protein complex, CD3. The
detailed structures of TCR in association with MHC Class I
molecules have been solved at the X-ray crystallography level.
Recombinant forms of soluble TCRs (consisting of extracellular
domains) have been produced in bacteria and eucaryotic cells. The
specific interplay of specific TCR ligands i. e. immunogenic
peptide/HLA complexes and specific T-cell receptors results in
ligand induced formation of a signalosome composed by the TCR/CD3
complex and its interplay with intracellular pools of tyrosine
kinases (Ick, Fyn, Syk, Zap-70) and adaptors (LAT, TRIM and Grp2).
As described above, the TCRs are expressed clonally and only
appropriate peptide-specific MHC complexes can elicit an immune
response.
[0037] The adaptive immune responses require two signals for
initial activation: one signal provided through the binding of
peptide-MHC on the antigen presenting cell (APC) to the T-cell
receptor (TCR), and a second antigen-independent signal called
co-stimulation. CD28 is a membrane receptor on T-cells that
provides co-stimulatory function when T-cells encounter APCs that
express CD28 ligands, B7-1 (CD80) of B7-2 (CD86). The functions of
CD28 are predominantly to influence signals initiated through the
TCR, which results in qualitative and quantitative changes in the
cascade of events leading to proliferation, cytokine production,
and cell survival. Triggering of naive T-cells without the
co-stimulatory signal can render the T-cells functionally
unresponsive (anergy, apoptosis). CD28 induces greater
proliferation of CD4+ T-cells compared with CD8+ T-cells. Other
members of the CD28 immunoglobulin (Ig) superfamily such as
includes inducible co-stimulator (ICOS) provides co-stimulatory
signals on activated CD4+ and CD8+ T-cells to enhance their
proliferation.
[0038] Lymphocyte responses are regulated by inhibitory as well as
activating signals. CTLA-4 and PD-1 mediated such inhibitory
signals. CTLA-4 has higher affinity for shared ligands B7-1 and
B7-2 compared with CD28, and it is up-regulated upon TCR-CD28
engagement. PD-1 appears to mediate an inhibitory signal, and it is
widely expressed on hematopoietic-derived tissues and on activated
T-cells. Interleukin-2 and co-stimulatory signals are the two most
important factors required for maintenance of continuous cell
division. Although CD28 provides a critical co-stimulatory signal
on naive T-cells, other co-stimulatory molecules in the tumour
necrosis receptor (TNFR) superfamily, such as 4-1BB (CD137), CD27
and OX40 (CD134), provides co-stimulatory signals on activated
T-cells to orient the quality of T-cell response towards cell
survival or apoptosis. Some CD8+ effector T-cells lack CD28
expression. However, these cells express the lectin-like NKG2D
homo-dimer, a receptor for the MHC Class I-like molecules called
MIC. NKG2D serves as a co-stimulatory molecule for CD28-CD8+
T-cells and with combined triggering of TCR/CD3 complexes induced
IL-2 and T-cell proliferation. Expression and function of NKG2D are
selectively up-regulated by the cytokine IL-15. Human NKG2D is
expressed on gamma, delta T-cells, CD8+ T-cells, NK cells, and a
small subset of CD4+ T-cells. The stress-induced MIC A and MIC B
molecules are expressed in the intestinal epithelium as well as in
diverse tumours of epithelial origin. NK cells are able to reject
tumours expressing MHC Class I molecules if the tumour expresses a
ligand for NKG2D, i. e. MIC A or MIC B. A family of receptors
(NKp46, NKp30, NKp44) termed natural cytotoxicity receptors (NCR)
expressed on NK cells are involved in NK-mediated lysis of various
tumours.
MHC-Peptide Complexes
[0039] MHC complexes function as antigenic peptide receptors,
collecting peptides inside the cell and transporting them to the
cell surface, where the MHC-peptide complex can be recognized by
T-lymphocytes. Two classes of classical MHC complexes exist; MHC
class I and II. The most important difference between these two
molecules lies in the protein source from which they obtain their
associated peptides. MHC class I molecules present peptides derived
from endogenous antigens degraded in the cytosol and are thus able
to display fragments of viral proteins and unique proteins derived
from cancerous cells. Almost all nucleated cells express MHC class
I on their surface even though the expression level varies among
different cell types. MHC class II molecules bind peptides derived
from exogenous antigens. Exogenous proteins enter the cells by
endocytosis or phagocytosis, and these proteins are degraded by
proteases in acidified intracellular vesicles before presentation
by MHC class II molecules. MHC class II molecules are only
expressed on professional antigen-presenting cells like B-cells and
macrophages.
[0040] The three-dimensional structure of MHC class I and II
molecules are very similar but important differences exist. MHC
class I molecules consist of two polypeptide chains, a heavy chain,
a, spanning the membrane and a light chain, .beta.2-microglobulin
(.beta.2m). The heavy chain is encoded in the gene complex termed
the major histocompatibility complex (MHC), and its extracellular
portion comprises three domains, .alpha.1, .alpha.2 and .alpha.3.
The .beta.2m chain is not encoded in the MHC gene and consists of a
single domain, which together with the .alpha.3 domain of the heavy
chain make up a folded structure that closely resembles that of the
immunoglobulin. The .alpha.1 and .alpha.2 domains pair to form the
peptide binding cleft, consisting of two segmented .alpha. helices
lying on a sheet of eight .beta.-strands. In humans as well as in
mice three different types of MHC class I molecule exist. HLA-A, B,
C are found in humans while MHC class I molecules in mice are
designated H-2K, H-2D and H-2L. The MHC class II molecule is
composed of two membrane spanning polypeptide chains, .alpha. and
.beta., of similar size (about 30,000 Da). Genes located in the
major histocompatibility complex encode both chains. Each chain
consists of two domains, where .alpha.1 and 31 forms a 9-pocket
peptide-binding cleft, where pocket 1, 4, 6 and 9 are considered as
major peptide binding pockets. The .alpha.2 and .beta.2, like the
.alpha.2 and .beta.2m in the MHC class I molecules, have amino acid
sequence and structural similarities to immunoglobulin constant
domains. In contrast to MHC class I complexes, where the ends of
the antigenic peptide is buried, peptide-ends in MHC class II
complexes are not. HLA-DR, DQ and DP are the human class II
molecules, H-2A, M and E are those of the mice. A remarkable
feature of MHC genes is their polymorphism accomplished by multiple
alleles at each gene. The polygenic and polymorphic nature of MHC
genes is reflected in the peptide-binding cleft so that different
MHC complexes bind different sets of peptides. The variable amino
acids in the peptide binding cleft form pockets where the amino
acid side chains of the bound peptide can be buried. This permits a
specific variant of MHC to bind some peptides better than
others.
SUMMARY OF THE INVENTION
[0041] Measurement of antigen specific T-cells during an immune
response are important parameters in vaccine development,
autologous cancer therapy, transplantation, infectious diseases,
inflammation, autoimmunity, toxicity studies etc. MHC multimers are
crucial reagents in monitoring of antigen specific T-cells. The
present invention describes novel methods to generate MHC multimers
and methods to improve existing and new MHC multimers. The
invention also describes improved methods for the use of MHC
multimers in analysis of T-cells in samples including diagnostic
and prognostic methods. Furthermore the use of MHC multimers in
therapy are described, e.g. anti-tumour and anti-virus therapy,
including isolation of antigen specific T-cells capable of
inactivation or elimination of undesirable targeT-cells or
isolation of specific T-cells capable of regulation of other immune
cells.
MHC Multimers
[0042] Due to the short half-life of the peptide-MHC-T-cell
receptor ternary complex (typically between 10 and 25 seconds), it
is difficult to label specific T-cells with labelled MHC-peptide
complexes, and like-wise, it is difficult to employ such monomers
of MHC-peptide for therapeutic and vaccine purposes because of
their weak binding. In order to circumvent this problem, MHC
multimers have been developed. These are complexes that include
multiple copies of MHC-peptide complexes, providing these complexes
with an increased affinity and half-life of interaction, compared
to that of the monomer MHC-peptide complex. The multiple copies of
MHC-peptide complexes are attached, covalently or non-covalently,
to one or more multimerization domain(s). Known examples of such
MHC multimers include the following: [0043] MHC-dimers: Each MHC
dimer contains two copies of MHC-peptide. IgG is used as one or
more multimerization domain(s), and one of the domains of the MHC
protein is covalently linked to IgG. [0044] MHC-tetramers: Each
MHC-tetramer contains four copies of MHC-peptide, each of which is
biotinylated. The MHC complexes are held together in a complex by
the streptavidin tetramer protein, providing a non-covalent linkage
between a streptavidin monomer and the MHC protein. Tetramers are
described in U.S. Pat. No. 5,635,363. [0045] MHC pentamers: Five
copies of MHC-peptide complexes are multimerised by a
self-assembling coiled-coil domain, to form a MHC pentamer. MHC
pentamers are described in the US patent 2004209295 [0046] MHC
dextramers: A large number of MHC-peptide complexes, typically more
than ten, are attached to a dextran polymer. MHC-dextramers are
described in the patent application WO 02/072631 A2.
Use of MHC Multimers in Flow Cytometry and Related Techniques
[0047] The concentration of antigen specific T-cells in samples
from e.g. peripheral blood can be very low. Flow cytometry and
related methods offer the ability to analyze a large number of
cells and simultaneously identify the few of interest. MHC
multimers have turned out to be very valuable reagents for
detection and characterization of antigen specific T-cells in flow
cytometer experiments. The relative amount of antigen specific
T-cells in a sample can be determined and also the affinity of the
binding of MHC multimer to the T-cell receptor can be
determined.
[0048] The basic function of a flow cytometer is its ability to
analyse and identify fluorochrome labelled entities in a liquid
sample, by means of its excitation, using a light source such as a
laser beam and the light emission from the bound fluorochrome.
[0049] MHC multimers is used as detections molecule for
identification of antigen specific T-cells in flow cytometry, by
labelling the MHC multimer with a specific fluorochrome, which is
detectable, by the flow cytometer used.
[0050] In order to facilitate the identification of a small amount
of cells, the cells can be sub-categorized using antibodies or
other fluorochrome labelled detections molecules directed against
surface markers other than the TCR on the specific T-cells
population. Antibodies or other fluorochrome labelled detections
molecules can also be used to identify cells known not to be
antigen specific T-cells. Both kinds of detections molecules are in
the following referred to as gating reagents. Gating reagents,
helps identify the "true" antigen specific T-cells bound by MHC
multimers by identifying specific subpopulations in a sample, e.g.
T-cells and by excluding cells that for some reason bind MHC
multimers without being antigen specific T-cells. Other cytometry
methods, e.g. fluorescence microscopy and IHC can like flow
cytometry be employed in identification of antigen specific T-cells
in a cell sample using MHC multimers.
Application of MHC Multimers in Immune Monitoring, Diagnostics,
Prognostics, Therapy and Vaccines
[0051] T-cells are pivotal for mounting an adaptive immune
response. It is therefore of importance to be able to measure the
number of specific T-cells when performing a monitoring of a given
immune response. For example in connection with vaccine
development, autologous cancer therapy, transplantation, infectious
diseases, toxicity studies etc.
DETAILED DESCRIPTION OF INVENTION
Design, Generation and Use of MHC Multimers
[0052] As used in the description of this invention, the term "MHC
multimers" will be used interchangeably with the terms MHC'mers and
MHCmers, and will include any number, (larger than one) of
MHC-peptide complexes, held together in a large complex by covalent
or non-covalent interactions between one or more multimerization
domain(s) and one or more MHC-peptide complexes. MHC multimers thus
include MHC-dimers, MHC-tetramers, MHC-tetramers, MHC-pentamers,
MHC-hexamers, as well as organic molecules, cells, membranes,
polymers and particles that comprise two or more MHC-peptide
complexes. Example organic molecule-based multimers include
functionalized cyclic structures such as benzene rings where e.g. a
benzene ring is functionalized and covalently linked to e.g. three
MHC complexes; example cell-based MHC multimers include dendritic
cells and antigen presenting cells (APCs); example membrane-based
MHC multimers include liposomes and micelles carrying MHC-peptide
complexes in their membranes; example polymer-based MHC multimers
include MHC-dextramers (dextran to which a number of MHC-peptide
complexes are covalently or non-covalently attached) and example
particles include beads or other solid supports with MHC complexes
immobilized on the surface. Obviously, any kind of multimerization
domain can be used, including any kind of cell, polymer, protein or
other molecular structure, or particles and solid supports.
[0053] Different approaches to the generation of various types of
MHC multimers are described in U.S. Pat. No. 5,635,363 (Altmann et
al.), patent application WO 02/072631 A2 (Winther et al.), patent
application WO 99/42597, US patent application 2004209295, U.S.
Pat. No. 5,635,363, and is described elsewhere in the present
patent application as well. In brief, MHC multimers can be
generated by first expressing and purifying the individual protein
components of the MHC protein, and then combining the MHC protein
components and the peptide, to form the MHC-peptide complex. Then
an appropriate number of MHC-peptide complexes are linked together
by covalent or non-covalent bonds to one or more multimerization
domain(s). This can be done by chemical reactions between reactive
groups of the multimerization domain (e.g. vinyl sulfone
functionalities on a dextran polymer) and reactive groups on the
MHC protein (e.g. amino groups on the protein surface), or by
non-covalent interaction between a part of the MHC protein (e.g. a
biotinylated peptide component) and the multimerization domain
(e.g. four binding sites for biotin on the strepavidin tetrameric
protein). As an alternative, the MHC multimer can be formed by the
non-covalent association of amino acid helices fused to one
component of the MHC protein, to form a pentameric MHC multimer,
held together by five helices in a coiled-coil structure making up
the multimerization domain(s).
[0054] Appropriate chemical reactions for the covalent coupling of
MHC and the multimerization domain(s) include nucleophilic
substitution by activation of electrophiles (e.g. acylation such as
amide formation, pyrazolone formation, isoxazolone formation;
alkylation; vinylation; disulfide formation), addition to
carbon-hetero multiple bonds (e.g. alkene formation by reaction of
phosphonates with aldehydes or ketones; arylation; alkylation of
arenes/hetarenes by reaction with alkyl boronates or enolethers),
nucleophilic substitution using activation of nucleophiles (e.g.
condensations; alkylation of aliphatic halides or tosylates with
enolethers or enamines), and cycloadditions.
[0055] Appropriate molecules, capable of providing non covalent
interactions between the one or more multimerization domain and the
MHC-peptide complex, involve the following molecule pairs and
molecules: streptavidin/biotin, avidin/biotin, antibody/antigen,
DNA/DNA, DNA/PNA, DNA/RNA, PNA/PNA, LNA/DNA, leucine zipper e.g.
Fos/Jun, IgG dimeric protein, IgM multivalent protein, acid/base
coiled-coil helices, chelate/metal ion-bound chelate, streptavidin
(SA) and avidin and derivatives thereof, biotin, immunoglobulins,
antibodies (monoclonal, polyclonal, and recombinant), antibody
fragments and derivatives thereof, leucine zipper domain of AP-1
(jun and fos), hexa-his (metal chelate moiety), hexa-hat GST
(glutathione S-transferase) glutathione affinity,
Calmodulin-binding peptide (CBP), STREP-TAG.RTM., Cellulose Binding
Domain, Maltose Binding Protein, S-Peptide Tag, Chitin Binding Tag,
Immuno-reactive Epitopes, Epitope Tags, E2Tag, HA Epitope Tag, Myc
Epitope, FLAG Epitope, AU1 and AU5 Epitopes, Glu-Glu Epitope, KT3
Epitope, IRS Epitope, Btag Epitope, Protein Kinase-C Epitope, VSV
Epitope, lectins that mediate binding to a diversity of compounds,
including carbohydrates, lipids and proteins, e.g. Con A (Canavalia
ensiformis) or WGA (wheat germ agglutinin) and tetranectin or
Protein A or G (antibody affinity). Combinations of such binding
entities are also comprised. In particular, when the MHC complex is
tagged, the multimerization domain(s) can be an "anti-tag". By
"anti-tag" is meant an antibody binding to the tag and any other
molecule capable of binding to such tag.
[0056] The MHC multimers can be used in a number of applications,
including analyses such as flow cytometry, immunohistochemistry
(IHC), and ELISA-like analyses, and can be used for diagnostic,
prognostic or therapeutic purposes including autologous cancer
therapy or vaccines such as HIV vaccine or cancer vaccine. The MHC
multimers can be labelled with one or more fluorophores and used in
flow cytometry. MHC multimers can be used to label T-cells carrying
specific T-cell receptors (TCR). For IHC, the MHC multimers can be
labelled with chromophores, in order to specifically stain specific
T-cells carrying TCRs that specifically bind the MHC multimer in
question.
[0057] ELISA and ELISA-like analyses can be performed with MHC
multimers that are labelled with e.g. chromophores, fluorophores or
enzymes. For the purpose of making cancer vaccines or other types
of vaccines it can be desirable to employ MHC multimers that
comprise a polymer such as dextran, or that are cell-based (e.g.
specialized dendritic cells such as described by Banchereau and
Palucka, Nature Reviews, Immunology, 2005, vol. 5, p. 296-306).
[0058] In one embodiment the multimerization domain(s) in the
present invention is preferable less than 1,000 Da (small molecule
scaffold). In another embodiment the multimerization domain(s) is
preferable between 1,000 Da and 10,000 Da (small molecule scaffold,
small peptides, small polymers). In another embodiment the
multimerization domain(s) is between 10,000 Da and 100,000 Da
(Small molecule scaffold, polymers e.g. dextran, streptavidin, IgG,
pentamer structure). In another embodiment the multimerization
domain(s) is preferable between 100,000 Da and 1,000,000 Da (Small
molecule scaffold, polymers e.g. dextran, streptavidin, IgG,
pentamer structure). In another embodiment the multimerization
domain(s) is preferable larger than 1,000,000 Da (Small molecule
scaffold, polymers e.g. dextran, streptavidin, IgG, pentamer
structure, cells, liposomes, artificial lipid bi layers,
polystyrene beads and other beads.
[0059] In one preferred embodiment the MHC multimer is between
50,000 Da and 1,000,000 Da, such as from 50,000 Da to 980,000; for
example from 50,000 Da to 960,000; such as from 50,000 Da to
940,000; for example from 50,000 Da to 920,000; such as from 50,000
Da to 900,000; for example from 50,000 Da to 880,000; such as from
50,000 Da to 860,000; for example from 50,000 Da to 840,000; such
as from 50,000 Da to 820,000; for example from 50,000 Da to
800,000; such as from 50,000 Da to 780,000; for example from 50,000
Da to 760,000; such as from 50,000 Da to 740,000; for example from
50,000 Da to 720,000; such as from 50,000 Da to 700,000; for
example from 50,000 Da to 680,000; such as from 50,000 Da to
660,000; for example from 50,000 Da to 640,000; such as from 50,000
Da to 620,000; for example from 50,000 Da to 600,000; such as from
50,000 Da to 580,000; for example from 50,000 Da to 560,000; such
as from 50,000 Da to 540,000; for example from 50,000 Da to
520,000; such as from 50,000 Da to 500,000; for example from 50,000
Da to 480,000; such as from 50,000 Da to 460,000; for example from
50,000 Da to 440,000; such as from 50,000 Da to 420,000; for
example from 50,000 Da to 400,000; such as from 50,000 Da to
380,000; for example from 50,000 Da to 360,000; such as from 50,000
Da to 340,000; for example from 50,000 Da to 320,000; such as from
50,000 Da to 300,000; for example from 50,000 Da to 280,000; such
as from 50,000 Da to 260,000; for example from 50,000 Da to
240,000; such as from 50,000 Da to 220,000; for example from 50,000
Da to 200,000; such as from 50,000 Da to 180,000; for example from
50,000 Da to 160,000; such as from 50,000 Da to 140,000; for
example from 50,000 Da to 120,000; such as from 50,000 Da to
100,000; for example from 50,000 Da to 80,000; such as from 50,000
Da to 60,000; such as from 100,000 Da to 980,000; for example from
100,000 Da to 960,000; such as from 100,000 Da to 940,000; for
example from 100,000 Da to 920,000; such as from 100,000 Da to
900,000; for example from 100,000 Da to 880,000; such as from
100,000 Da to 860,000; for example from 100,000 Da to 840,000; such
as from 100,000 Da to 820,000; for example from 100,000 Da to
800,000; such as from 100,000 Da to 780,000; for example from
100,000 Da to 760,000; such as from 100,000 Da to 740,000; for
example from 100,000 Da to 720,000; such as from 100,000 Da to
700,000; for example from 100,000 Da to 680,000; such as from
100,000 Da to 660,000; for example from 100,000 Da to 640,000; such
as from 100,000 Da to 620,000; for example from 100,000 Da to
600,000; such as from 100,000 Da to 580,000; for example from
100,000 Da to 560,000; such as from 100,000 Da to 540,000; for
example from 100,000 Da to 520,000; such as from 100,000 Da to
500,000; for example from 100,000 Da to 480,000; such as from
100,000 Da to 460,000; for example from 100,000 Da to 440,000; such
as from 100,000 Da to 420,000; for example from 100,000 Da to
400,000; such as from 100,000 Da to 380,000; for example from
100,000 Da to 360,000; such as from 100,000 Da to 340,000; for
example from 100,000 Da to 320,000; such as from 100,000 Da to
300,000; for example from 100,000 Da to 280,000; such as from
100,000 Da to 260,000; for example from 100,000 Da to 240,000; such
as from 100,000 Da to 220,000; for example from 100,000 Da to
200,000; such as from 100,000 Da to 180,000; for example from
100,000 Da to 160,000; such as from 100,000 Da to 140,000; for
example from 100,000 Da to 120,000; such as from 150,000 Da to
980,000; for example from 150,000 Da to 960,000; such as from
150,000 Da to 940,000; for example from 150,000 Da to 920,000; such
as from 150,000 Da to 900,000; for example from 150,000 Da to
880,000; such as from 150,000 Da to 860,000; for example from
150,000 Da to 840,000; such as from 150,000 Da to 820,000; for
example from 150,000 Da to 800,000; such as from 150,000 Da to
780,000; for example from 150,000 Da to 760,000; such as from
150,000 Da to 740,000; for example from 150,000 Da to 720,000; such
as from 150,000 Da to 700,000; for example from 150,000 Da to
680,000; such as from 150,000 Da to 660,000; for example from
150,000 Da to 640,000; such as from 150,000 Da to 620,000; for
example from 150,000 Da to 600,000; such as from 150,000 Da to
580,000; for example from 150,000 Da to 560,000; such as from
150,000 Da to 540,000; for example from 150,000 Da to 520,000; such
as from 150,000 Da to 500,000; for example from 150,000 Da to
480,000; such as from 150,000 Da to 460,000; for example from
150,000 Da to 440,000; such as from 150,000 Da to 420,000; for
example from 150,000 Da to 400,000; such as from 150,000 Da to
380,000; for example from 150,000 Da to 360,000; such as from
150,000 Da to 340,000; for example from 150,000 Da to 320,000; such
as from 150,000 Da to 300,000; for example from 150,000 Da to
280,000; such as from 150,000 Da to 260,000; for example from
150,000 Da to 240,000; such as from 150,000 Da to 220,000; for
example from 150,000 Da to 200,000; such as from 150,000 Da to
180,000; for example from 150,000 Da to 160,000.
[0060] For all applications, it is important to choose the right
MHC allele as well as a peptide that binds well to the MHC protein.
It is also important that the chosen MHC allele and peptide forms a
MHC-peptide complex that is efficiently and specifically recognized
by the TCR. For applications that involve binding as well as
activation of cells, further restrictions on the choice of MHC and
peptide can apply.
[0061] The peptide P in the MHC-peptide complexe(s) can be any
natural or non-natural peptide capable of being presented by the
MHC complex in question. In one embodiment, the peptide P is a
peptide disclosed in U.S. 60/907,217, the text of which is hereby
incorporated by reference herein in its entirety.
Synthesis of MHC Multimers with Different Multimerization
Domains
The MHC Multimer
[0062] One of the benefits of the MHC multimers of the present
invention is clearly that the MHC multimers overcome low intrinsic
affinities of monomer ligands and counter receptors. It should be
noted, however, that such MHC multimers can have a large variety of
applications that include targeting of high affinity receptors (e.
g. hormone peptide receptors for insulin) on targeT-cells. Taken
together, poly-ligand binding to target T-cells does have
practical, clinical and scientifically uses of immediate commercial
interest.
[0063] Thus, the present invention provides constructs of MHC
molecules, which present multi-valent binding sites for MHC
recognising cells. The constructs of the present invention have
highly advantageous properties and are an important tool with a
broad range of valuable uses.
[0064] Thus, in a first aspect, the present invention relates to
MHC molecule construct comprising one or more multimerization
domain(s) having attached thereto one or more MHC molecules, said
MHC molecules being attached to the one or more multimerization
domain(s) either directly or via one or more binding entities. This
applies i.e. to the MHC molecule and the one or more
multimerization domain(s). The multimerization domain(s) can thus
have attached thereto a MHC molecule or a plurality of MHC
molecules, and/or a multimerization domain or a plurality of
binding entities. When a plurality of MHC molecules is attached to
the multimerization domain(s), the number can only be limited by
the capacity of the multimerization domain(s) or the binding
entity, as the case can be. The number of binding entities can only
be limited by the capacity and nature of the multimerization
domain(s).
[0065] Depending on the use of the MHC multimers of the present
invention, the construct as such can be provided in soluble or
non-soluble form by carefully selecting the multimerization
domain(s). Both the soluble and the non-soluble format display the
advantageous properties.
[0066] A "MHC Class I molecule" as used everywhere herein is
defined as a molecule which comprises 1-3 subunits, including a
heavy chain, a heavy chain combined with a light chain (.beta.2m),
a heavy chain combined with a light chain (D2m) through a flexible
linker, a heavy chain combined with a peptide, a heavy chain
combined with a peptide through a flexible linker, a heavy chains
dimer combined with a peptide, and a heavy chain/P2m dimer with a
peptide through a flexible linker to the heavy or light chain. The
MHC molecule chain can be changed by substitution of single or by
cohorts of native amino acids or by inserts, or deletions to
enhance or impair the functions attributed to said molecule. By
example, it has been shown that substitution of XX with YY in
position nn of human P2m enhance the biochemical stability of MHC
Class I molecule complexes and thus can lead to more efficient
antigen presentation of subdominant peptide epitopes.
[0067] A "MHC Class II molecule" as used everywhere herein is
defined as a molecule which comprises 2-3 subunits including an
a-chain and a P-chain (oc/.beta.-dimer), an axa dimer with a
peptide, and an axa dimer combined with a peptide through a
flexible linker to the a or p chain, an a/p dimer combined through
an interaction by affinity tags e. g. jun-fos, an oc/.beta. dimer
combined through an interaction by affinity tags e.g. jun-fos and
further combined with a peptide through a flexible linker to the a
or .beta. chain. The MHC molecule chains can be changed by
substitution of single or by cohorts of native amino acids or by
inserts, or deletions to enhance or impair the functions attributed
to said molecule.
[0068] MHC Class I like molecules (including non-classical MHC
Class I molecules) include CDId, HLA E, HLA G, HLA F, HLA H, MIC A,
MIC B, ULBP-1, ULBP-2, and ULBP-3.
[0069] MHC Class II like molecules (including non-classical MHC
Class II molecules) include HLA DM, HLA DO, I-A beta2, and I-E
beta2.
[0070] The MHC molecule can suitably be a vertebrate MHC molecule
such as a human, a mouse, a rat, a porcine, a bovine or an avian
MHC molecule. Such MHC molecules from different species have
different names. E. g. in humans, MHC molecules are denoted HLA.
The person skilled in the art will readily know the name of the MHC
molecules from various species.
[0071] In general, the term "MHC molecule" is intended to include
alleles. By way of example, in humans e. g. HLA A, HLA B, HLA C,
HLA D, HLA E, HLA F, HLA G, HLA H, HLA DR, HLA DQ and HLA DP
alleles are of interest, and in the mouse system, H-2 alleles are
of interest. Likewise, in the rat system RT1-alleles, in the
porcine system SLA-alleles, in the bovine system BoLA, in the avian
system e. g. chicken-B alleles, are of interest.
[0072] The definition of the MHC molecule construct of the present
invention enables various valuable possibilities as regards the MHC
molecules. Thus, examples of valuable MHC multimers are such
wherein at least two of the MHC molecules are different, wherein
the MHC molecules are the same, wherein at least two of the
peptides harboured by the MHC molecules are different, wherein the
peptides harboured by the MHC molecules are the same, wherein the
peptides harboured by the MHC molecules are chemically modified or
synthesised to contain not natural amino acids, or to contain
hydrophilic or hydrophobic groups, wherein the peptides harboured
by the MHC Class I molecules are linked to the MHC Class I heavy
chain by a flexible linker, wherein the peptides harboured by the
MHC Class I molecules are linked to the MHC Class I light chain
(.beta.2m) by a flexible linker, wherein the peptides are harboured
by MHC Class I molecules comprising MHC Class I heavy chain in
association with a light chain (.beta.2m) by a flexible linker,
wherein the peptide harboured by the MHC Class II molecules are
linked to the alpha-chain by a flexible linker, wherein the peptide
harboured by the MHC Class II molecules are linked to the p-chain
by a flexible linker, wherein the MHC Class I molecules are
mutated, wherein the MHC Class II molecules are mutated.
[0073] The above list is not exhaustive in any way, but out-lines a
number of valuable possibilities.
[0074] In particular, if the peptides harboured by a plurality of
MHC molecules are different from each other, such can be used to
detect several types of MHC recognising cells simultaneously. This
can be achieved either by employing one MHC molecule construct with
MHC molecules filled with different peptides, or by employing
several MHC molecule constructs, where each MHC molecule construct
have MHC molecules with the same type of peptide, e. g. one MHC
molecule construct displaying one peptide, and another MHC molecule
construct displaying another peptide.
[0075] In one embodiment of the MHC multimers of the present
invention, the one or more MHC molecules are attached to the
multimerization domain(s) directly. In another embodiment, the one
or more MHC molecules are attached to the multimerization domain(s)
via one or more binding entities.
[0076] When the MHC molecules are attached via one or more binding
entities, each binding entity suitably has attached thereto from 1
to 10, such as from 1 to 8, from 1 to 6, from 1 to 4, from 1 to 3,
or 1 or 2 MHC molecules. However, it is to be understood that the
possible number of MHC molecules depends on the binding entity in
question (i. e. how many MHC molecules that can be attached). Thus,
by choosing the binding entity carefully, it can be possible to
attach more than 10 MHC molecules to each binding entity. However,
it is to be understood that this number can be the average number
of MHC molecules attached to each binding entity. Thus, the number
of MHC molecules can be evenly or unevenly distributed on the
binding entity as the MHC multimers are most often made and
purified with a certain desired weight distribution. Thus, the
average number needs not be an integer, but can be anything between
two integers (i.e. a decimal number), e. g. 2.8, 4.7 or 5.3, to
mention a few, non-limiting examples.
[0077] The total number of MHC molecules of the MHC molecule
construct is in principle unlimited. Thus, the total number of MHC
molecules of the construct can suitably be at least 4, at least 5,
at least 6, at least 7, at least 8, at least 9, at least 10, at
least 12, at least 16, at least 20, at least 24, at least 28, at
least 32, or at least 64. In particular, the total number of MHC
molecules of the construct can be within from 1 to 100000, within
from 1 to 95, within from 1 to 90, within from 1 to 85, within from
1 to 80, within from 1 to 75, within from 1 to 70, within from 1 to
65, within from 1 to 60, within from 1 to 55, within from 1 to 50,
within from 1 to 45, within from 1 to 40, within from 1 to 35,
within from 1 to 30, within from 1 to 25, within from 1 to 20,
within from 1 to 15, within from 1 to 10, within from 1 to 5,
within from 1 to 4, within from 1 to 3, or 1 or 2.
[0078] A non-exhaustive list of possible MHC mono- and multimers
illustrates the possibilities. n indicates the number of MHC
complexes comprised in the multimer:
TABLE-US-00001 a) n = 1, Monomers b) n = 2, Dimers, multimerization
can be based on IgG scaffold, SA with two MHC's, coiled-coil
dimerization e.g. Fos.Jun dimerization c) n = 3, Trimers,
multimerization can be based on SA as scaffold with three MHC's,
TNFalpha-MHC hybrids, triplex DNA-MHC konjugates or other trimer
structures d) n = 4, Tetramers, multimerization can be based on SA
with all four binding sites occupied by MHC molecules or on dimeric
IgA e) n = 5, Pentamers, multimerization can take place around a
pentameric coil-coil structure f) n = 6, Hexamers g) n = 7,
Heptamers h) n = 8-12, Octa- dodecamers, multimerization can take
place using Streptactin i) n = 10, Decamers, multimerization could
take place using IgM j) 1 < n < 100, Dextramers, as
multimerization domain polymers such as polypeptide, polysaccharide
and Dextrans can be used k) 1 < n < 1000, Multimerization
make use of DC, APC, micelles, liposomes, beads, surfaces surfaces
e.g. microtiterplate, tubes, microarray devices, micro-fluidic
systems l) 1 < n, n in billions or trillions or higher,
multimerization take olace on beads, and surfaces e.g.
microtiterplate, tubes, microarray devices, micro-fluidic
systems
[0079] The total number of MHC molecules of the MHC molecule
construct is in principle unlimited. Thus, the total number of MHC
molecules of the construct can suitably be in the range from 100
MHC molecules to 1,000,000 MHC molecules such as from 100 to 1,000
MHC molecules, for example from 1,000 to 5,000 MHC molecules, such
as from 5,000 to 10,000 MHC molecules, for example from 10,000 to
20,000 MHC molecules, such as from 20,000 to 30,000 MHC molecules,
for example from 30,000 to 40,000 MHC molecules, such as from
40,000 to 50,000 MHC molecules, for example from 50,000 to 60,000
MHC molecules, such as from 60,000 to 70,000 MHC molecules, for
example from 70,000 to 80,000 MHC molecules, such as from 80,000 to
90,000 MHC molecules, for example from 90,000 to 100,000 MHC
molecules, such as from 100,000 to 200,000 MHC molecules, for
example from 200,000 to 300,000 MHC molecules, such as from 300,000
to 400,000 MHC molecules, for example from 400,000 to 500,000 MHC
molecules, such as from 500,000 to 600,000 MHC molecules, for
example from 600,000 to 700,000 MHC molecules, such as from 700,000
to 800,000 MHC molecules, for example from 800,000 to 900,000 MHC
molecules, such as from 900,000 to 1,000,000 MHC molecules.
[0080] The number of MHC molecules can be evenly or unevenly
distributed among a plurality of MHC molecule constructs. Thus, the
average number needs not be an integer, but can be any number
between two integers (i.e. a decimal number), e. g. 28. 4, 44.5 or
57.2, to mention a few, non-limiting examples.
[0081] The binding entity is any such suited for attachment of the
MHC molecules, while rendering the MHC molecules capable of binding
to MHC recognising cells. Examples of suitable binding entities are
streptavidin (SA) and avidin and derivatives thereof, biotin,
immunoglobulins, antibodies (monoclonal, polyclonal, and
recombinant), antibody fragments and derivatives thereof, leucine
zipper domain of AP-1 (jun and fos), hexa-his (metal chelate
moiety), hexa-hat GST (glutathione S-tranferase) glutathione
affinity, Calmodulin-binding peptide (CBP), STREP-TAG.RTM.,
Cellulose Binding Domain, Maltose Binding Protein, S-Peptide Tag,
Chitin Binding Tag, Immuno-reactive Epitopes, Epitope Tags, E2Tag,
HA Epitope Tag, Myc Epitope, FLAG Epitope, AU1 and AU5 Epitopes,
Glu-Glu Epitope, KT3 Epitope, IRS Epitope, Btag Epitope, Protein
Kinase-C Epitope, VSV Epitope, lectins that mediate binding to a
diversity of compounds, including carbohydrates, lipids and
proteins, e. g. Con A (Canavalia ensiformis) or WGA (wheat germ
agglutinin) and tetranectin or Protein A or G (antibody affinity)
or coiled-coil polypeptides e.g. leucine zipper.
[0082] Combinations of such binding entities are also comprised.
Non-limiting examples are streptavidin-biotin and jun-fos and other
leucine zipper likestructures. In particular, when the MHC molecule
is tagged, the binding entity can be an "anti-tag". By "anti-tag"
is meant an antibody binding to the tag and any other molecule
capable of binding to such tag.
[0083] The number, density, and nature of the binding entities can
vary for each multimerization domain(s). It is to be understood
that the binding entity can be attached to the multimerization
domain(s) by a linker. Suitable linkers include Calmodulin-binding
peptide (CBP), 6.times.HIS, Protein A, Protein G, biotin, Avidin,
Streptavidin, STREP-TAG.RTM., Cellulose Binding Domain, Maltose
Binding Protein, S-Peptide Tag, Chitin Binding Tag, Immuno-reactive
Epitopes, Epitope Tags, GST tagged proteins, E2Tag, HA Epitope Tag,
Myc Epitope, FLAG Epitope, AU1 and AU5 Epitopes, Glu-Glu Epitope,
KT3 Epitope, IRS Epitope, Btag Epitope, Protein Kinase-C Epitope,
VSV Epitope or any other linker as described elsewhere herein.
[0084] The one or more MHC molecules can suitably be attached to
the binding entity by tags. Examples of tags are given above under
the definition of suitable binding entities. Thus, MHC molecules
being recombinantly tagged or chemically tagged bind specifically
to the binding entity due to high affinity. The recombinant tags of
MHC molecules furthermore allow regio-specific attachment sites in
the constructs. The tags can be located at any part of the MHC
molecule, but it is presently believed that the tags should
preferably be located away from the cell binding part of the MHC
molecule. By way of example, a tagged MHC molecule could be a
recombinant MHC fusion molecule consisting of MHC Class I heavy
chain molecule and a C-terminal target peptide sequence for
enzymatic mono-biotinylation. The C-terminal location of the
affinity tag allows optimal exposure of the N-terminal cell binding
part of the MHC molecule. It is presently believed that target
sequences for biotinylation also can be located at P2M
molecules.
[0085] Chemically biotinylated MHC protein binds to a streptavidin
binding entity. Biotinylated MHC molecule binds to streptavidin
with high affinity. The ratio of MHC molecules per streptavidin is
theoretically 4:1 due to four biotin-binding sites in streptavidin
complexes.
Generation of Components of MHC-Peptide Complexes
[0086] MHC-peptide complexes in multimers of the present invention
can be of any of the below mentioned origins. The list is
non-exhaustive. A complete list would encompass all Chordate
species. By origin is meant that the sequence is identical or
highly homologous to a naturally occurring sequence of the specific
species.
List of Origins:
[0087] Human [0088] Mouse [0089] Primate [0090] Chimpansee [0091]
Gorilla [0092] Orang Utan [0093] Monkey [0094] Macaques [0095]
Porcine (Swine/Pig) [0096] Bovine (Cattle/Antilopes) [0097] Equine
(Horse) [0098] Camelides (Camels) [0099] Ruminants (Deears) [0100]
Canine (Dog) [0101] Feline (Cat) [0102] Bird [0103] Chicken [0104]
Turkey [0105] Fish [0106] Reptiles [0107] Amphibians
[0108] The MHC complexes in MHC multimers of the present invention
may be MHC I complexes, MHC II complexes, MHC like molecule or
other TCR binding molecules as described elsewhere herein. The
polypeptide chains of the MHC complexes can be from the same or
different species. The MHC-peptide complexes may be a natural part
of the MHC multimer, or may be generated separately and then
combined with the multimerization domain.
[0109] Example MHC multimers where the MHC-peptide complexes are a
natural part of the MHC multimer include: [0110] MHC expressing
cells of natural origin like dendritic cells, B-cells, Macrophages,
other professional antigen presenting cells, NK cells, T-cells,
granolycetes, other nucleated cells or any cell naturally
expressing MHC-peptide molecules [0111] Cell or cell lines
transfected with MHC encoding genes, including but not limited to
mammalian cells, bacterial cell, insecT-cells, yeasT-cells [0112]
Hybridoma cell lines [0113] Phages or virions expressing MHC
molecules on their surface. Genes encoding MHC complexes may be
fused to genes encoding surface proteins of the phages thereby
creating a fusion protein enabling the phage to express MHC
molecules on their surface fused to one or more coat proteins
[0114] Liposomes or micelles made from MHC expressing cells
[0115] Individual MHC-peptide complexes may be generated as whole
molecules by elution from cells expressing MHC molecules or the
individual polypeptide chains may be produced separately and then
combined with peptide. Principles for generation of individual MHC
I and MHC II molecules are described below.
Generation of MHC I and MHC II Polypeptide Chains
[0116] MHC class I and/or MHC II can be obtained from a variety of
sources involving different methods: [0117] a) Natural sources by
means of purification from eukaryotic cells naturally expressing
the MHC class I and/or MHC II molecules. [0118] b) MHC molecules
can be generated by recombinant methods e.g. using [0119] a. in
vitro translation of mRNA obtained from cells naturally expressing
MHC I and/or II [0120] b. Expression and isolation of MHC I or MHC
II or any of the polypeptide chains of either complex (HC,
.beta.2m, .alpha.-chain and/or .beta.-chain) from cells transfected
or transformed with genes encoding the MHC molecules or polypeptide
chains. The transfected cells may be of mammalian, yeast, bacterial
or other origin. The genetic material used for
transfection/transformation can be: [0121] i. of natural origin
directly isolated from cells, tissue or organisms expressing MHC I
and/or MHC IImolecules. [0122] ii. Genes amplified from cells
and/or tissue expressing MHC I and/or MHC II molecules. This can be
done by isolation of DNA from cells/tissue expressing MHC molecules
and then amplifying relevant genes encoding HC and/or .beta.2m or
.alpha.-chain and/or .mu.-chain e.g. using PCR. Alternative mRNA
may be isolated and changed into DNA using e.g. reverse
transcriptase or other method known by persons skilled in the art,
and then the relevant genes amplified by PCR. [0123] iii. DNA
syntesized in vitro manufactured by e.g. solid phase protein
synthesis. Synthetic DNA may correspond to the natural DNA sequence
encoding MHC I and/or MHC II or any of the polypeptide chains of
either complex (HC, .beta.2m .alpha.-chain and/or .beta.-chain).
The genes may be modified from the original natural DNA sequence in
order to improve expression of the final protein, increase/decrease
solubility of expressed protein or increase/decrease protein
stability as described elsewhere herein.
[0124] For MHC I molecules, the HC and .beta.2m may be expressed in
separate cells as individual polypeptides or in the same cell as a
fusion protein consisting of HC and .beta.2m connected through a
linker. The peptide of the MHC I-peptide complex may be produced
separately and added during in vitro refolding or expressed
together with HC and/or .beta.2m connected to either chain through
a linker. The genetic material can encode all or only a fragment of
.beta.2m, all or only a fragment of MHC class I heavy chain. Of
special interest are MHC class I heavy chain fragments consisting
of, the complete chain minus the intramembrane domain, a chain
consisting of only the extracellular .alpha.1 and .alpha.2 class I
heavy chain domains, or any .beta.2m and/or heavy chain fragments
containing modified or added designer domain(s) or sequence(s) as
described elsewhere herein.
[0125] For MHC II molecules the .alpha.-chain and .beta.-chain may
be expressed in separate cells as individual polypeptides or in the
same cell as a fusion protein. The peptide of the MHC II-peptide
complex may be produced separately and added following purification
of whole MHC complexes or added during in vitro refolding or
expressed together with .alpha.-chain and/or .beta.-chain connected
to either chain through a linker. The genetic material can encode
all or only a fragment of MHC class II .alpha.- and .beta.-chains.
Of special interest are MHC class II .alpha.- and
.beta.-chain_fragments consisting of, the complete .alpha.- and
.beta.-chains minus the intramembrane domains of either or both
chains; and .alpha.- and .beta.-chains consisting of only the
extracellular domains of either or both, i.e .alpha.1 plus .alpha.2
and .beta.1 plus .beta.2 domains, respectively. The genetic
material can be modified to encode the interesting MHC class II
molecule fragments consisting of domains starting from the amino
terminal in consecutive order, MHC class II .beta.1 plus MHC class
II .alpha.1 plus MHC class I .alpha.3 domains or in alternative
order, MHC class II .alpha.1 plus MHC class II .beta.1 plus MHC
class I .alpha.3 domains. Lastly, the genetic material can encode
any of the above mentioned MHC class II .alpha.- and .beta.-chain
molecules or fragments containing modified or added designer
domain(s) or sequence(s). The genetic material may be fused with
genes encoding other proteins, including proteins usefull in
purification of the expressed polypeptide chains, proteins usefull
in increasing/decreasing solubility of the polypeptide(s), proteins
usefull in detection of polypeptide(s), proteins involved in
coupling of MHC complex to multimerization domains and/or coupling
of labels to MHC complex and/or MHC multimer.
[0126] Example proteins usefull in purification of expressed
polypeptide chain include polyhistidine tag, Polyargenine tag,
STREP-TAG.RTM., STREP-TAG.RTM. II, FLAG tag, S-tag, c-myc,
Calmodulin-binding peptide, Streptavidin binding peptide (SBP-tag),
Cellulose-binding domain, Chitin-binding domain, Glutathione
S-transferase-tag (GST-tag), Maltose-binding protein (MBP),
protein-A, protein-G, AviTag, PinPoint X.sub.a, biotin, antigens,
Bio-tag or any other tag that can bind a specific affinity matrix
usefull in purification of proteins. Example proteins usefull for
detection include enterokinase cleavage site (ECS), hemaglutinin
(HA), Glu-Glu, bacteriophage T/and V5 epitopes, all the above
mentioned tags or any other tag able to be measured in a detection
system.
[0127] Example proteins usefull in increasing solubility of
expressed polypeptide chains include hydrophilic tags such as
transcription anti-termination factor (NusA), E. coli thioredoxin
(TrxA), protein disulfide isomerise I (DsbA), large affinity tags
such as GST, MBP or other proteins or peptides increasing
solubility of protein.
[0128] Once expressed the MHC complexes can be purified directly as
whole MHC or MHC-peptide complexes from MHC expressing cells. The
MHC complexes may be expressed on the surface of cells, and are
then isolated by disruption of the cell membrane using e.g.
detergent followed by purification of the MHC complex as described
elsewhere herein. Alternatively MHC complexes are expressed into
the periplasm and expressing cells are lysed and released MHC
complexes purified.
[0129] Finally, MHC complexes may be purified from the supernatant
of cells secreting expressed proteins into culture supernatant.
[0130] Whole MHC complexes may be purified using standard protein
purification methods known by persons skilled in the art. Briefly,
purification using affinity tags, as described elsewhere herein,
together with affinity chromatography, beads coated with ant-tag
and/or other techniques involving immobilisation of MHC protein to
affinity matrix; size exclusion chromatography using e.g.
gelfiltration, ion exchange or other methods able to separate MHC
molecules from cell and/or cell lysate.
[0131] As an alternative to expression and purification of whole
MHC complexes, the polypeptides chains of MHC can be expressed in
cells, cells lysed, the polypeptides chains isolated by
purification and then refolded in vitro. In one aspect of the
present invention a preferred cell for this type of expression is
E. coli, where MHC polypeptide chains accumulate as insoluble
inclusion bodies in the bacterial cell. In vitro refolding occurs
in a refolding buffer where the polypeptides are added by e.g.
dialysis or dilution. Refolding buffers can be any buffer wherein
the MHC polypeptide chains and peptide are allowed to reconstitute
their native trimer fold. The buffer may contain oxidative and/or
reducing agents thereby creating a redox buffer system helping the
MHC proteins to establish the correct fold. Examples of suitable
refoldings buffer of the present invention include but is not
limited to Ttris-buffer, CAPS buffer, TAPs buffer, PBS buffer,
other phosphate buffer, carbonate buffer and Ches buffer. Chaperone
molecules or other molecules improving correct protein folding may
also be added and likewise agents increasing solubility and
preventing aggregate formation may be added to the buffer. Examples
of such molecules include but is not limited to Arginine, GroE,
HSP70, HSP90, small organic compunds, DnaK, CIpB, proline, glycin
betaine, glycerol, tween, salt, PLURONIC.RTM..
[0132] Both MHC I and MHC II molecules may be generated using any
of the above described procedures. In the present invention a
preferred method is using recombinant expression systems.
[0133] In one embodiment of the present invention E. coli
expression followed by refolding in vitro is preferred for
generation of MHC I molecules. Another preferred embodiment of the
present invention is generation of MHC II complexes made by
coexpression of MHC II .alpha.-chain and .beta.-chain subunits in
baculovirus-infected or stably transfected insecT-cells.
[0134] Using the above described methods MHC I and MHC II molecules
may be generated with or without peptide bound in the peptide
binding groove. Loading of peptide into MHC molecules are described
elsewhere herein.
Generation of Peptide Able to Bind the Peptide Binding Cleft of MHC
I or MHC II
[0135] MHC class I molecules normally binds octa-, nona-, deca- or
ondecamer (8-, 9-, 10,-11-mer) peptides in their peptide binding
groove. The individual MHC class I1 alleles have individual
preferences for the peptide length within the given range. MHC
class II molecules bind peptides most often with a total length of
13-18 amino acids around a 9-mer core motif containing the
important amino acid anchor residues. However the total length is
not strictly defined as for most MHC class I molecules.
[0136] Peptides binding MHC I or MHC II can be derived from a
variety of sources including:
[0137] a) Natural Sources.
[0138] Peptides can be obtained from natural sources by enzymatic
digestion or proteolysis of natural proteins or proteins derived by
in vitro translation of mRNA.
[0139] Peptides may also be eluted from the MHC binding groove.
[0140] b) Recombinant Sources: [0141] As monomeric or multimeric
peptide [0142] Peptides can be produced recombinantly by
transfected cells either as monomeric antigenic peptides or as
multimeric (contatemeric) antigenic peptides. [0143] as part of a
bigger recombinant protein [0144] Binding peptides may also
constitute a part of a bigger recombinant protein e.g. consisting
of: [0145] For MHC class I binding peptides,
Peptide-linker-.beta.2m, .beta.2m being full length or truncated;
Peptide-linker-MHC class 1 heavy chain, the heavy chain being full
length or truncated. Most importantly the truncated class I heavy
chain will consist of the extracellular part i.e the .alpha.1,
.quadrature. .alpha.2, and a domains. The heavy chain fragment may
also only contain the .alpha.1 and .alpha.2 domains, or .alpha.1
domain alone, or any fragment or full length .beta.2m or heavy
chain attached to a designer domain(s) or protein fragment(s).
[0146] For MHC class II binding peptides the recombinant
construction can consist of, Peptide-linker-MHC class 2
.alpha.-chain, full length or truncated; Peptide-linker-MHC class 2
.beta.-chain, full length or truncated; Peptide-linker-MHC class 2
.alpha.-chain-linker-MHC class 2 .beta.-chain, both chains can be
full length or truncated, truncation may involve, omission of
.alpha.- and/or .beta.-chain intermembrane domain, or omission of
.alpha.- and/or .beta.-chain intermembrane plus cytoplasmic
domains. MHC class 2 part of the construction may consist of fused
domains from NH2-terminal, MHC class 2 .beta.1 domain-MHC class 2
.alpha.1 domain-constant .alpha.3 of MHC class 1, or alternatively
of fused domains from NH2-terminal, MHC class 2 .alpha.1 domain-MHC
class 2 .beta.1 domain-constant .alpha.3 of MHC class 1. In both
cases .beta.2m will be associated non-covalently in the folded MHC
complex. .beta.2m can also be covalently associated in the folded
MHC class 2 complex if the following constructs are used from NH2
terminal, MHC class 2 .beta.1 domain-MHC class 2 .alpha.1
domain-constant .alpha.3 of MHC class 1-linker-.beta.2m, or
alternatively of fused domains from NH2-terminal, MHC class 2
.alpha.1 domain-MHC class 2 .beta.1 domain-constant .alpha.3 of MHC
class 1-linker-.beta.2m; the construct may also consist of any of
the above MHC class 2 constructs with added designer domain(s) or
sequence(s).
[0147] c) From Chemical Synthesis
MHC binding peptide can also be chemically synthesized by solid
phase or fluid phase synthesis. Loading of Peptide into the MHC
Complex
[0148] Loading of peptides into the peptide binding cleft of MHC
complexes being either MHC class I or class II can be performed in
a number of ways depending on the source of the peptide and the
MHC. MHC class II molecules can in principle be loaded with
peptides in similar ways as MHC class I.
[0149] a) During MHC Complex Folding [0150] as a free peptide
[0151] MHC class I molecules are most often loaded with peptide
during assembly in vitro by the individual components in a folding
reaction i.e. consisting of purified recombinant heavy chain a with
the purified recombinant 32 microglobulin and a peptide or a
peptide mix. [0152] as part of a recombinant protein construct
[0153] Alternatively the peptide to be folded into the binding
groove can be encoded together with e.g. the .alpha. heavy chain or
fragment hereof by a gene construct having the structure, heavy
chain-flexible linker-peptide. This recombinant molecule is then
folded in vitro with .beta.2-microglobulin.
[0154] b) By Exchange Reaction [0155] in solution [0156] Loading of
desired peptide can also be made by an in vitro exchange reaction
where a peptide already in place in the binding groove are being
exchanged by another peptide species. [0157] "in situ" [0158]
Peptide exchange reactions can also take place when the parent
molecule is attached to other molecules, structures, surfaces,
artificial or natural membranes and nano-particles. [0159] by aided
exchange [0160] This method can be refined by making the parent
construct with a peptide containing a meta-stable amino acid analog
that is split by either light or chemically induction thereby
leaving the parent structure free for access of the desired peptide
in the binding groove. [0161] by in vivo loading [0162] Loading of
MHC class I and II molecules expressed on the cell surface with the
desired peptides can be performed by an exchange reaction.
[0163] Alternatively cells can be transfected by the peptides
themselves or by the mother proteins that are then being processed
leading to an in vivo analogous situation where the peptides are
bound in the groove during the natural cause of MHC expression by
the transfected cells. In the case of professional antigen
presenting cells e.g. dendritic cells, macrophages, Langerhans
cells, the proteins and peptides can be taken up by the cells
themselves by phagocytosis and then bound to the MHC complexes the
natural way and expressed on the cell surface in the correct MHC
context.
Coupling of MHC Complexes and Multimerization Domains
[0164] The coupling of one or more multimerization domains and MHC
complexes can involve the association of an entity X (attached to
or part of the one or more multimerization domain) and an entity Y
(attached to or part of the MHC complex). Thus, the linker that
connects the one or more multimerization domain(s) and the MHC
complex can comprise an XY portion.
[0165] The XY linkage can be covalent, in which case X and Y are
reactive groups. In this case, X can be a nucleophilic group (such
as --NH.sub.2, --OH, --SH, --NH--NH.sub.2), and Y an electrophilic
group (such as CHO, COOH, CO) that react to form a covalent bond
XY; or Y can be a nucleophilic group and X an electrophilic group
that react to form a covalent bond XY. Other possibilities exist,
e.g. either of the reactive groups can be a radical, capable of
reacting with the other reactive group. A number of reactive groups
X and Y, and the bonds that are formed upon reaction of X and Y,
are shown in FIG. 1.
[0166] X and Y can be reactive groups naturally comprised within
the multimerization domain(s) and/or the MHC complex, or they can
be artificially added reactive groups. Thus, linkers comprising
reactive groups can be linked to either of the multimerization
domain(s) and MHC complex; subsequently the introduced reactive
group(s) can be used to covalently link the one or more
multimerization domain(s) and MHC complex.
[0167] Example natural reactive groups of MHC complexes include
amino acid side chains comprising --NH.sub.2, --OH, --SH, and
--NH--. Example natural reactive groups of multimerization domains
include hydroxyls of polysaccharides such as dextrans, but also
include amino acid side chains comprising --NH.sub.2, --OH, --SH,
and --NH-- of polypeptides, when the polypeptide is used as one or
more multimerization domain(s). In some MHC multimers, one of the
polypeptides of the MHC complex (i.e. the .beta.2M, MHC I heavy
chain, MHC II .alpha.-cahin, MHC II .beta.-chain or the antigenic
peptide) is linked by a protein fusion to the one or more
multimerization domain(s). Thus, during the translation of the
fusion protein, an acyl group (reactive group X or Y) and an amino
group (reactive group Y or X) react to form an amide bond. Example
MHC multimers where the bond between the one or more
multimerization domain(s) and the MHC complex is covalent and
results from reaction between natural reactive groups, include
MHC-pentamers (described in US patent 2004209295) and MHC-dimers,
where the linkage between the one or more multimerization domain(s)
and MHC complex is in both cases generated during the translation
of the fusion protein. Another example is MHC multimers where
either of the MHC polypeptide chains are fused to one alpha-helic
of a coiled-coil structure and where the other alpha helic of a
coiled-coil structure is attached to the multimerisation domain.
MHC complexes are then attached to the multimerisation domian
through interaction of the two alpha-helices. Example coiled-coil
structure include leucine zipper, fos-jun or other coiled coil
structures as described elsewhere herein. Example non-native
reactive groups include reactive groups that are attached to the
one or more multimerization domain(s) or MHC complex, through
association of a linker molecule comprising the reactive group. The
activation of dextran by reaction of the dextran hydroxyls with
divinyl sulfone, introduces a reactive vinyl group that can react
with e.g. amines of the MHC complex, to form an amine that now
links the one or more multimerization domain(s) (the dextran
polymer) and the MHC complex. Reactive vinyl groups may also react
with thiols of the MHC complex. An alternative activation of the
dextran multimerization domain(s) involves a multistep reaction
that results in the decoration of the dextran with maleimide
groups, as described in the patent Siiman et al. U.S. Pat. No.
6,387,622. In this approach, the amino groups of MHC complexes are
converted to --SH groups, capable of reacting with the maleimide
groups of the activated dextran. Alternatively-SH groups of natural
occuring Cysteine or artificial incorporated Cysteine can react
with the maleimide. Thus, in the latter examples, both the reactive
group of the multimerization domain(s) (the maleimide) and the
reactive group of the MHC complex (the thiol) are artificially
introduced.
[0168] Sometimes activating reagents are used in order to make the
reactive groups more reactive. For example, acids such as glutamate
or aspartate can be converted to activated esters by addition of
e.g. carbodiimid and NHS or nitrophenol, or by converting the acid
moiety to a tosyl-activated ester. The activated ester reacts
efficiently with a nucleophile such as --NH.sub.2, --SH, --OH,
etc.
[0169] For the purpose of this invention, the multimerization
domain(s) (including small organic scaffold molecules, proteins,
protein complexes, polymers, beads, liposomes, micelles, cells)
that form a covalent bond with the MHC complexes can be divided
into separate groups, depending on the nature of the reactive group
that the one or more multimerization domain(s) contains. One group
comprise multimerization domain(s) that carry nucleophilic groups
(e.g. --NH.sub.2, --OH, --SH, --CN, --NH--NH.sub.2), exemplified by
polysaccharides, polypeptides comprising e.g. lysine, serine, and
cysteine; another group of multimerization domain(s) carry
electrophilic groups (e.g. --COOH, --CHO, --CO, NHS-ester,
tosyl-activated ester, and other activated esters,
acid-anhydrides), exemplified by polypeptides comprising e.g.
glutamate and aspartate, or vinyl sulfone activated dextran; yet
another group of multimerization domains carry radicals or
conjugated double bonds.
[0170] The one or more multimerization domain(s) appropriate for
this invention can be those that comprise any of the reactive
groups shown in FIG. 1 or that can react with other reactive groups
to form the bonds shown in FIG. 1.
[0171] The MHC complexes can be divided in a similar way, according
to the nature of their reactive groups.
[0172] In another preferred embodiment the linker can be selected
from, but is not limited to, the group consisting of a
disulfide-bridge connecting amino acids, heparin or heparan
sulfate-derived oligosaccharides (glycosoaminoglycans),
bifunctional or chemical cross-linkers, peptide linker, polypeptide
linker, fexible linker, synthetic linker, hydrazones, thioethers,
esters, disulfides and peptide-containing linkers.
[0173] Examples of linkers include but are not limited to a
disulfide-bridge connecting amino acids from both polypeptides;
heparin or heparan sulfate-derived oligosaccharides
(glycosoaminoglycans) connecting both polypeptides; bifunctional or
chemical cross-linkers; and a peptide or polypeptide linker. The
unimolecular protein can also be a chimera or fusion
polypeptide.
[0174] The peptide linker sequence is typically flexibly disposed
in the fusion protein so as to position the V-alpha and V-beta
chains in a configuration which optimally binds an antigen. The
peptide linker preferably predominantly comprises amino acids with
small side chains, such as glycine, alanine and serine, to provide
flexibility. Preferably, about 80 or 90 percent or greater of the
linker sequence comprises glycine, alanine or serine residues,
particularly glycine and serine residues. Preferably, the linker
sequence does not contain any proline residues, which could inhibit
flexibility. The linker sequence is suitably attached to the
C-terminus of the V-alpha chain and the N-terminus of the V-beta
chain of a fusion protein.
[0175] Crosslinkers can be either homobifunctional or
heterobifunctional. Homobifunctional crosslinkers have two
identical reactive groups and often are used in one-step reaction
procedures to crosslink proteins to each other or to stabilize
quaternary structure. Heterobifunctional crosslinkers possess two
different reactive groups that allow for sequential (two-stage)
conjugations, helping to minimize undesirable polymerization or
self-conjugation. Crosslinkers that are amine-reactive at one end
and sulfhydryl-reactive at the other end are especially useful in
this regard.
[0176] The most widely-used heterobifunctional crosslinkers are
those having an amine-reactive succinimidyl ester (i.e., NHS-ester)
at one end and a sulfhydrylreactive group on the other end. The
sulfhydryl-reactive groups are usually maleimides, pyridyl
disulfides and haloacetyls. The NHS-ester reactivity is less stable
in aqueous solution and is usually reacted first in sequential
crosslinking procedures. NHS-esters react with amines to form amide
bonds. Carbodiimides are zero-length crosslinkers and effect direct
coupling between carboxylates (--COOH) and primary amines
(--NH.sub.2).
[0177] Other heterobifunctional reagents have one reactive group
that is photoreactive rather than thermoreactive. This reactivity
allows for specific attachment of the labile thermoreactive group
first; subsequently, conjugation to any adjacent N--H or C--H sites
can be initiated through the photoreactive group by activation with
UV light. Crosslinkers preferably comprise at least two reactive
groups. Functional groups that can be targeted for crosslinking
include primary amines, sulfhydryls, carbonyls, carbohydrates and
carboxylic acids (Table 1). Coupling also can be nonselective using
a photoreactive phenyl azide crosslinker.
TABLE-US-00002 TABLE 1 Reactive Crosslinker Groups and Their
Functional Group Targets Reactive Group Functional Group Aryl Azide
Non-selective (or primary amine) Carbodiimide Amine/Carboxyl
Hydrazide Carbohydrate (oxidized) Hydroxymethyl Phosphine Amine
Imidoester Amine Isocyanate Hydroxyl (non-aqueous) Maleimide
Sulfhydryl NHS-ester Amine PFP-ester Amine Psoralen Thymine
(photoreactive intercalator) Pyridyl Disulfide Sulfhydryl Vinyl
Sulfone Sulfhydryl, amine, hydroxyl
[0178] The linker that connects the one or more multimerization
domain(s) and the MHC complex can comprise an XY portion. Above
different kinds of covalent linkages XY were described. However,
the XY linkage can also be non-covalent.
[0179] Non-covalent XY linkages can comprise natural dimerization
pairs such as antigen-antibody pairs, DNA-DNA interactions, or can
include natural interactions, for example between biotin and
streptavidin. Likewise, the interaction of MHC complexes
(comprising full-length polypeptide chains, including the
transmembrane portion) with the cell membrane of for example
dendritic cells, is an example of a non-covalent XY
interaction.
[0180] Artificial XY examples include XY pairs such as His.sub.6
tag (X) interacting with Ni-NTA (Y) and PNA-PNA,
[0181] A list of dimerization- and multimerization domains,
appropriate for use as XY non-covalent linkers between the
multimerization domain(s) and the MHC complex, can be found
elsewhere in this application.
[0182] The abovementioned dimerization- and multimerization domains
represent specific binding interactions. Another type of
non-covalent interactions involves the non-specific adsorption of
e.g. proteins onto surfaces. As an example, the non-covalent
adsorption of proteins onto glass beads represents this class of XY
interactions.
[0183] A preferred embodiment involving non-covalent interactions
between X and Y are represented by the pentamer structure described
in US patent 2004209295.
[0184] Another preferred embodiment involves the use of antibodies,
with affinity of the surface of MHC opposite to the peptide-binding
groove. Thus, an anti-MHC antibody, with its two binding site, will
bind two MHC complexes and in this way generate a bivalent MHC
multimer. In addition, the antibody can stabilize the MHC complex
through the binding interactions, in which case the MHC multimer is
particularly relevant for MHC class II complexes, as these are less
stable than class I MHC complexes.
[0185] The antibodies mentioned above can be selected from, but is
not limited to, the group consisting of polyclonal antibody,
monoclonal antibody, IgA, IgG, IgM, IgD, IgE, IgG1, IgG2, IgG3,
IgG4, IgA1, IgA2, IgM1, IgM2, humanized antibody, humanized
monoclonal antibody, Chimeric antibody, mouse antibody, rat
antibody, rabbit antibody, human antibody, camel antibody, sheep
antibody, engineered human antibody, epitope-focused antibody,
agonist antibody, antagonist antibody, neutralizing antibody,
naturally-occurring antibody, isolated antibody, monovalent
antibody, bispecific antibody, trispecific antibody, multispecific
antibody, Heteroconjugate antibody, immunoconjugates,
immunoliposomes, labeled antibody, antibody fragment, domain
antibody, nanobody, minibody, maxibody, diabody, fusion
antibody.
[0186] Another preferred embodiment involves use of Streptavidin or
Avidin binding biotin on biotinylated MHC complexes. MHC complexes
can be biotinylated enzymatically e.g. using a biotinylation tag
recognised by BirA enzyme or they can be chemically biotinylated
e.g. using Sulfo-NHS esters of biotin reacting with amino groups or
maleimide activated biotin reacting with --SH groups.
[0187] The Streptavdin or avidin may further be conjugated to a
polymer e.g. dextran as described by Winther et al. in patent WO
02/072631.
[0188] Also included in the present invention is genetically or
chemically modified Streptavidin/Avidin binding natural biotin
and/or chemically or genetically modified biotin; and chemically or
genetically modified biotin binding natural Streptavidin/Avidin or
chemically or genetically Streptavidin/Avidin.
[0189] In the present invention another preferred embodiment
involving non-covalent interactions between X and Y are use of
dimer coiled-coil structures, where one half the coiled structure
are attached to the MHC molecule, e.g. as a fusion protein and the
other half is attached to the multimerization domain. Example
coiled-coil structures include but are not limited to leucine
zippers like Fos-Jun, GCN4 leucine zipper, Fos-Jun like leucine
zippers, heterodimeric coiled coil structures consisting of a basic
peptide and an acidic peptide, heterodimeric coiled coil structures
consisting of a basic peptide and an acidic peptide where Cystein
are added to the C-termini of the acid and base peptides either
directly or through a linker e.g. Gly-Gly, other heterodimeric
coiled-coil structures or homodimeric structures.
Multimerisation Domains
[0190] The MHC multimers of the invention in one embodiment
comprise one or more multimerization domain(s). The multimerization
domain(s) can be a soluble multimerization domain(s) or a not
soluble multimerization domain(s). The multimerization domain(s)
can be any such which enables attachment of the MHC molecules, the
binding entities, and/or the biologically active compounds, while
providing the advantageous properties of the construct.
[0191] Examples of suitable multimerization domain(s)s are
polysaccharides including dextrans, carboxy methyl dextran, dextran
polyaldehyde, carboxymethyl dextran lactone, and cyclodextrins,
pullulans, schizophyllan, scleroglucan, xanthan, gellan,
O-ethylamino guaran, chitins and chitosans indlucing
6-O-carboxymethyl chitin and N-carboxymethyl chitosan, derivatised
cellolosics including carboxymethyl cellulose, carboxymethyl
hydroxyethyl cellulose, hydroxy-ethyl cellulose, 6-amino-6-deoxy
cellulose and O-ethyl-amine cellulose, hydroxylated starch,
hydroxypropyl starch, hydroxyethyl starch, carrageenans, alginates,
and agarose, synthetic polysaccharides including FICOLL.RTM. and
carboxy-methylated FICOLL.RTM., vinyl polymers including poly
(acrylic acid), poly (acryl amides), poly (acrylic esters), poly
(2-hydroxy ethyl methacrylate), poly (methyl methacrylate), poly
(maleic acid), poly (maleic anhydride), poly (acrylamide), poly
(ethyl-co-vinyl acetate), poly (methacrylic acid), poly
(vinyl-alcohol), poly (vinyl alcohol-co-vinyl chloroacetate),
aminated poly (vinyl alcohol), and co block polymers thereof, poly
ethylene glycol (PEG) or polypropylene glycol or poly (ethylene
oxide-co-propylene oxides) comprising polymer backbones including
linear, comb-shaped or StarBurst dendrimers, poly amino acids
including polylysines, polyglutamic acid, polyurethanes, poly
(ethylene imines), pluriol, proteins including peptides,
polypeptides, antigenbinding peptides, albumins, immunoglobulins,
coiled-coil helixes e.g. Fos-Jun or Fos-Jun like or coiled-coiled
dimers/trimers/tetramers/pentamers, Streptavidin, Avidin,
Streptactin, T-cell receptors orther protein receptors and
virus-like proteins (VLP), and polynucleotides, DNA, RNA, PNA, LNA,
oligonucleotides and oligonucleotide dendrimer constructs and small
organic molecules including but not limited to steroids, peptides,
linear or cyclic structures, aromatic structures, aliphatic
structures.
[0192] Also included are cells e.g. dendritic cells, antigen
presenting cell, B-cell, T-cell Macrophages, Kupfer cells,
Langerhans cells, transfected cells expressing MHC comlexes,
hybriddoma cells expressing MHC complexes, YeasT-cells,
insecT-cells, CHO cells, any cell expressing MHC complexes or
MHC-like complexes and cell-like structures e.g. micelles,
liposomes, other structures of MHC and phages e.g. filamentious
phages and viral or viral-like particles.
[0193] Other suitable multimerization domains are solid supports
including but not limited to beads, particulate matters and other
surfaces.
[0194] Also included are self-assembling multimeric structures as
described elsewhere herein.
[0195] Also included in this definition of the multimerization
domain(s) is mixed forms, i.e. one or more multimerization
domain(s) composed of one or more of the above examples. An example
of this is dextran coupled with Streptavidin whereto biotinylated
MHC-peptidecomlexes can bind.
[0196] The choice of multimerization domain(s) depend i.e. on the
application of the MHC molecule construct. Of course, several
parameters can be varied in the above-given examples of
multimerization domain(s), including the length and branching.
Furthermore, the multimerization domain(s) can carry various
substitutions, including such, which can be protected and/or
activated, enabling further derivatisation.
[0197] It is to be understood that the MHC molecule construct of
the invention can further comprise one or more additional
substituents. Such biologically active molecules can be attached to
the construct in order to affect the characteristics of the
constructs, e. g. with respect to binding properties, effects, MHC
molecule specificities, solubility, stability, or detectability.
For instance, spacing could be provided between the MHC molecules,
one or both chromophores of a Fluorescence Resonance Energy
Transfer (FRET) donor/acceptor pair could be inserted, functional
groups could be attached, or groups having a biological activity
could be attached.
[0198] One preferred embodiment of the present invention includes
multimerisation domains made of Streptavidin or Avidin whereto
biotin, biotin-like peptides or other biotin-like molecules can
bind.
[0199] Another preferred embodiment includes dextran whereto
MHC-peptide complexes arebe attached directly through a linker as
described elsewhere herein. The MHC-peptide complexes can also be
attached through a second multimerization domain or an entity as
described elsewhere herein. Examples include but is not limited to
divinylsulfone activated dextran whereto MHC-peptide complexes are
coupled directly e.g. through --SH group(s) or amine(s) in the
MHC-peptide complex, dextran coupled with SA whereto MHC-peptide
complexes are attached through a biotin on the MHC-peptide complex,
dextran with MHC-peptide complexes are attached through a
coiled-coil structure where on .alpha.-helix of a coiled-coil dimer
is coupled to dextran and the other .alpha.-helix is coupled to
MHC-peptide complex e.g. as a fusion protein.
[0200] A preferred embodiment include beads or bead-like structures
having an excluded volume (e.g. polysaccharide beads, polystyrene
beads, magnetic polystyrene beads, polycarbamate beads, or any
other kind of beads that can be dissolved or suspended in aqueous
buffer) that carry electrophilic groups (e.g. divinyl sulfone
activated polysaccharide, polystyrene beads that have been
functionalized with tosyl-activated esters, magnetic polystyrene
beads functionalized with tosyl-activated esters), and where MHC
complexes have been covalently immobilized to these by reaction of
nucleophiles comprised within the MHC complex with the
electrophiles of the beads.
[0201] In another preferred embodiment, the MHC multimers described
immediately above (where the one or more multimerization domain(s)
is a bead) further comprises a flexible or rigid, and water
soluble, linker that allows for the immobilized MHC complexes to
interact efficiently with cells, such as T-cells with affinity for
the MHC complexes. In yet another embodiment, the linker is
cleavable, allowing for release of the MHC complexes from the bead.
If T-cells have been immobilized, by binding to the MHC complexes,
the T-cells can very gently be released by cleavage of this
cleavable linker. Appropriate cleavable linkers are shown in FIG.
2. Most preferably, the linker is cleaved at physiological
conditions, allowing for the integrity of the isolated cells.
[0202] In another preferred embodiment the bead is covalently or
non-covalently coated with MHC multimers or single MHC complexes,
through non-cleavable or cleavable linkers. As an example, the bead
can be coated with streptavidin monomers, which in turn are
associated with biotinylated MHC complexes; or the bead can be
coated with streptavidin tetramers, each of which are associated
with 0, 1, 2, 3, or 4 biotinylated MHC complexes; or the bead can
be coated with MHC-dextramers where e.g. the reactive groups of the
MHC-dextramer (e.g. the divinyl sulfone-activated dextran backbone)
has reacted with nucleophilic groups on the bead, to form a
covalent linkage between the dextran of the dextramer and the
beads.
[0203] A preferred embodiment including self-assembling multimeric
structures are trimer, tetramer or pentamer coiled-coil structures
holding together 3, 4 or 5 MHC complexes. The coiled-coil
structures may be attached to MHC-peptide complex through covalent
or non-covalent.
[0204] In some of the abovementioned embodiments, several
multimerization domains (e.g. streptavidin tetramers bound to
biotinylated MHC complexes) are linked to another multimerization
domain (e.g. the bead). For the purpose of the invention we shall
call both the smaller and the bigger multimerization domain, as
well as the combined multimerization domain, for multimerization
domain.
[0205] In another preferred embodiment the one or more
multimerization domain(s) can be any support capable of binding the
MHC complex. Well-known supports or multimerization domains include
glass, polystyrene, polypropylene, polyethylene, dextran, nylon,
amylases, natural and modified celluloses, polyacrylamides,
gabbros, and magnetite. The nature of the one or more
multimerization domain(s) can be either soluble to some extent or
insoluble for the purposes of the present invention. The support
material can have virtually any possible structural configuration
so long as the coupled molecule is capable of binding to the MHC
complex. The support configuration can be spherical, as in a bead,
or cylindrical, as in the inside surface of a test tube, or the
external surface of a rod. Alternatively, the surface can be flat
such as a sheet, test strip, a membrane, or a plastic surface such
as that on a microtiter plate etc.
[0206] In another preferred embodiment the multimerization
domain(s) can be a polymer or an oligomer or a non-repeating
moiety. The polymer or oligomer moiety can comprise repeat units
consisting of a repeat moiety selected from alkyl (e.g.,
--CH.sub.2--), substituted alkyl (e.g., --CHR--), alkenyl,
substituted alkenyl, alkynyl, substituted alkynyl, phenyl, aryl,
heterocyclic, amine, ether, sulfide, disulfide, hydrazine, and any
of the foregoing substituted with oxygen, sulfur, sulfonyl,
phosphonyl, hydroxyl, alkoxyl, amine, thiol, ether, carbonyl,
carboxyl, ester, amide, alkyl, alkenyl, alkynyl, aryl,
heterocyclic, as well as moieties comprising combinations thereof.
Generally, a non-repeating multifunctional bridge moiety can be a
moiety selected from alkyl, phenyl, aryl, alkenyl, alkynyl,
heterocyclic, amine, ether, sulfide, disulfide, hydrazine, and any
of the foregoing substituted with oxygen, sulfur, sulfonyl,
phosphonyl, hydroxyl, alkoxyl, amine, thiol, ether, carbonyl,
carboxyl, ester, amide, alkyl, alkenyl, alkynyl, aryl,
heterocyclic, and moieties comprising combinations thereof (in each
permutation). A non-repeating moiety can include repeating units
(e.g., methylene) within portions or segments thereof without
repeating as a whole.
[0207] The oligomer (or oligomer moiety) or the polymer (or polymer
moiety), can generally be soluble or insoluble; can generally be a
cross-linked oligomer (or oligomer moiety) or a cross-linked
polymer (or polymer moiety); can generally be a homopolymer or a
copolymer (including polymers having two monomer-repeat-units,
terpolymers and higher-order polymers), including for example
random copolymer moieties and block copolymer moieties; can
generally include one or more ionic monomer moieties such as one or
more anionic monomer moieties; can generally include one or more
hydrophobic monomer moieties; can generally include one or more
hydrophilic monomer moieties; and can generally include any of the
foregoing features in combination.
[0208] The polymer moiety can be soluble or insoluble, existing for
example as dispersed micelles or particles, such as colloidal
particles or (insoluble) macroscopic beads. Polymer moieties can be
hydrophobic, hydrophilic, amphiphilic, uncharged or non-ionic,
negatively or positively charged, or a combination thereof, and can
be organic or inorganic. Inorganic polymers, also referred to as
inorganic multimerization domains in some cases, include silica
(e.g., multi-layered silica), diatomaceous earth, zeolite, calcium
carbonate, talc, and the like.
[0209] Suitable water-soluble polymers include polyethylene glycol
(PEG), monomethoxy-PEG, mono-(C.sub.1-C.sub.10)alkoxy-PEG,
aryloxy-PEG, poly-(N-vinyl pyrrolidone)PEG, tresyl monomethoxy PEG,
PEG propionaldehyde, bis-succinimidyl carbonate PEG, propylene
glycol homopolymers, a polypropylene oxide/ethylene oxide
co-polymer, polyoxyethylated polyols (e.g., glycerol), polyvinyl
alcohol, dextran, cellulose, or other carbohydrate-based polymers.
A conjugate can also comprise a mixture of such water-soluble
polymers.
[0210] Examples of polysaccharides useful in the present invention
include materials from vegetal or animal origin, including
cellulose materials, hemicellulose, alkyl cellulose, hydroxyalkyl
cellulose, carboxymethylcellulose, sulfoethylcellulose, starch,
xylan, amylopectine, chondroitin, hyarulonate, heparin, guar,
xanthan, mannan, galactomannan, chitin, and/or chitosan.
[0211] The type of multimerization domain can also be selected
from, but is not limited to, the group consisting of agarose,
SEPHAROSE.RTM., resin beads, glass beads, pore-glass beads, glass
particles coated with a hydrophobic polymer, chitosan-coated beads,
SH beads, latex beads, spherical latex beads, allele-type beads,
SPA bead, PEG-based resins, PEG-coated bead, PEG-encapsulated bead,
polystyrene beads, magnetic polystyrene beads, glutathione agarose
beads, magnetic bead, paramagnetic beads, protein A and/or protein
G SEPHAROSE.RTM. beads, activated carboxylic acid bead, macroscopic
beads, microscopic beads, insoluble resin beads, silica-based
resins, cellulosic resins, cross-linked agarose beads, polystyrene
beads, cross-linked polyacrylamide resins, beads with iron cores,
metal beads, DYNABEADS.RTM., Polymethylmethacrylate beads activated
with NHS, streptavidin-agarose beads, polypropylene, polyethylene,
dextran, nylon, amylases, natural and modified celluloses,
nitrocellulose, polyacrylamides, gabbros, magnetite, polymers,
oligomers, non-repeating moieties, polyethylene glycol (PEG),
monomethoxy-PEG, mono-(C.sub.1-C.sub.10)alkoxy-PEG, aryloxy-PEG,
poly-(N-vinyl pyrrolidone)PEG, tresyl monomethoxy PEG, PEG
propionaldehyde, bis-succinimidyl carbonate PEG, polystyrene bead
crosslinked with divinylbenzene, propylene glycol homopolymers, a
polypropylene oxide/ethylene oxide co-polymer, polyoxyethylated
polyols (e.g., glycerol), polyvinyl alcohol, dextran, aminodextran,
carbohydrate-based polymers, cross-linked dextran beads,
polysaccharide beads, polycarbamate beads, polyvinylcarbamate,
divinyl sulfone activated polysaccharide, polystyrene beads that
have been functionalized with tosyl-activated esters, magnetic
polystyrene beads functionalized with tosyl-activated esters,
streptavidin beads, streptavidin-monomer coated beads,
streptavidin-tetramer coated beads, Streptavidin Coated Compel
Magnetic beads, avidin coated beads, dextramer coated beads,
divinyl sulfone-activated dextran, Carboxylate-modified bead,
amine-modified beads, antibody coated beads, cellulose beads,
grafted co-poly beads, poly-acrylamide beads, dimethylacrylamide
beads optionally crosslinked with
N--N'-bis-acryloylethylenediamine, hollow fiber membranes,
fluorescent beads, collagen-agarose beads, gelatin beads,
collagen-gelatin beads, collagen-fibronectin-gelatin beads,
collagen beads, chitosan beads, collagen-chitosan beads,
protein-based beads, hydrogel beads, hemicellulose, alkyl
cellulose, hydroxyalkyl cellulose, carboxymethylcellulose,
sulfoethylcellulose, starch, xylan, amylopectine, chondroitin,
hyarulonate, heparin, guar, xanthan, mannan, galactomannan, chitin
and chitosan.
Immuno Active Molecules
[0212] In many applications, it will be advantageous that the MHC
multimer construct further comprises one or more Immuno active
molecules. By the term "Immuno active" is meant that the compound
can affect the binding characteristics or the effects of the MHC
multimer construct. The MHC multimer construct can comprise several
immuno active molecules which can be the same or different.
[0213] Such immuno active molecules can in particular be selected
from the group of biological active molecules including proteins,
co-stimulatory molecules, cell modulating molecules, receptors,
accessory molecules, adhesion molecules, natural ligands, and toxic
molecules, as well as antibodies and recombinant binding molecules
to any of the foregoing, and combinations thereof.
[0214] "Recombinant binding molecules" is intended to mean
molecules such as peptide fragment prepared by recombinant
technology, and which have the ability to mimic the activity (e. g.
up-regulation or down-regulation) of natural molecules, or to
inhibit or block the activity of natural molecules.
[0215] In particular, the Immuno active molecule can be selected
from proteins such as MHC Class I-like proteins like MIC A, MIC B,
CDId, HLA E, HLA F, HLA G, HLA H, ULBP-1, ULBP-2, and ULBP-3,
co-stimulatory molecules such as CD2, CD3, CD4, CD5, CD8, CD9,
CD27, CD28, CD30, CD69, CD134 (OX40), CD137 (4-1BB), CD147, CDw150
(SLAM), CD152 (CTLA-4), CD153 (CD30L), CD40L (CD154), NKG2D, ICOS,
HVEM, HLA Class II, PD-1, Fas (CD95), FasL expressed on T and/or NK
cells, CD40, CD48, CD58, CD70, CD72, B7.1 (CD80), B7.2 (CD86),
B7RP-1, B7-H3, PD-L1, PD-L2, CD134L, CD137L, ICOSL, LIGHT expressed
on APC and/or tumour cells, cell modulating molecules such as CD16,
NKp30, NKp44, NKp46, NKp80, 2B4, KIR, LIR, CD94/NKG2A, CD94/NKG2C
expressed on NK cells, IFN-alpha, IFN-beta, IFN-gamma, IL-1, IL-2,
IL-3, IL-4, IL-6, IL-7, IL-8, IL-10, IL-11, IL-12, IL-15, CSFs
(colony-stimulating factors), vitamin D3, IL-2 toxins, cyclosporin,
FK-506, rapamycin, TGF-beta, clotrimazole, nitrendipine, and
charybdotoxin, accessory molecules such as LFA-1, CD11a/18, CD54
(ICAM-1), CD106 (VCAM), and CD49a, b, c, d, e, f/CD29 (VLA-4),
adhesion molecules such as ICAM-1, ICAM-2, GlyCAM-1, CD34,
anti-LFA-1, anti-CD44, anti-beta7, chemokines, CXCR4, CCR5,
anti-selectin L, anti-selectin E, and anti-selectin P, toxic
molecules selected from toxins, enzymes, antibodies, radioisotopes,
chemiluminescent substances, bioluminescent substances, polymers,
metal particles, and haptens, such as cyclophosphamide,
methrotrexate, Azathioprine, mizoribine, 15-deoxuspergualin,
neomycin, staurosporine, genestein, herbimycin A, Pseudomonas
exotoxin A, saporin, Rituxan, Ricin, gemtuzumab ozogamicin, Shiga
toxin, heavy metals like inorganic and organic mercurials, and
FN18-CRM9, radioisotopes such as incorporated isotopes of iodide,
cobalt, selenium, tritium, and phosphor, and haptens such as DNP,
and digoxiginin, and combinations of any of the foregoing, as well
as antibodies (monoclonal, polyclonal, and recombinant) to the
foregoing, where relevant. Antibody derivatives or fragments
thereof can also be used. The biologically active molecules may
also derive from viral or bacterial proteins or fragments
thereof.
[0216] The immuno active molecule can suitably be attached to the
multimerization domain(s) either directly, thorugh one or more
linkers or via one or more of the binding entities or one or more
multimerization domains as described elsewhere herein. The
immunoactive molecules can aslo be linked to another immunoactive
molecule and then attached to one or more multimerization
domains.
[0217] MHC multimers can be covalently or non-covalently associated
with various molecules: having adjuvant effects; being immune
targets e.g. antigens; having biological activity e.g. enzymes,
regulators of receptor activity, receptor ligands, immune
potentiators, drugs, toxins, co-receptors, proteins and peptides in
general; sugar moieties; lipid groups; nucleic acids including
siRNA; nano particles; small molecules. In the following these
molecules are collectively called biologically active molecules.
Such molecules can be attached to the MHC multimer using the same
principles as those described for attachment of MHC complexes to
multimerisation domains as described elsewhere herein. In brief,
attachment can be done by chemical reactions between reactive
groups on the biologically active molecule and reactive groups of
the multimerisation domain and/or between reactive groups on the
biologically active molecule and reactive groups of the MHC-peptide
complex. Alternatively, attachment is done by non-covalent
interaction between part of the multimerisation domain and part of
the biological active molecule or between part of the MHC-peptide
complex and part of the biological active molecule. In both
covalent and non-covalent attachment of the biologically molecule
to the multimerisation domain a linker molecule can connect the
two. The linker molecule can be covalent or non-covalent attached
to both molecules. Examples of linker molecules are described
elsewhere herein.
[0218] Biological active molecules can be attached repetitively
aiding to recognition by and stimulation of the innate immune
system via Toll or other receptors.
[0219] MHC multimers carrying one or more additional groups can be
used as therapeutic or vaccine reagents.
[0220] An example of a vaccine reagent could be one against HIV. In
this case antigens of the viral particle or the cell membrane
surrounding the particle could be relevant to attach to the MHC
multimer. The resulting MHC multimer e.g. a MHC class I Dextramer
could have additional molecules like HIV gp120, HIV-GAG gp 27,
HSP70, and MHC class II proteins or peptides attached or
combinations thereof.
Immobilization to Multimerization Domain
[0221] In a number of applications, it can be advantageous to
immobilise the MHC molecule construct onto a solid or semi-solid
support. Such support can be any which is suited for
immobilisation, separation etc. Non-limiting examples include
particles, beads, biodegradable particles, sheets, gels, filters,
membranes (e. g. nylon membranes), fibres, capillaries, needles,
microtitre strips, tubes, plates or wells, combs, pipette tips,
micro arrays, chips, slides, or indeed any solid surface material.
The solid or semi-solid support can be labelled, if this is
desired. The support can also have scattering properties or sizes,
which enable discrimination among supports of the same nature, e.
g. particles of different sizes or scattering properties, colour or
intensities.
[0222] Conveniently the support can be made of glass, silica,
latex, plastic or any polymeric material. The support can also be
made from a biodegradable material. Generally speaking, the nature
of the support is not critical and a variety of materials can be
used. The surface of support can be hydrophobic or hydrophilic.
[0223] Preferred are materials presenting a high surface area for
binding of the MHC molecule constructs. Such supports can be for
example be porous or particulate e. g. particles, beads, fibres,
webs, sinters or sieves. Particulate materials like particles and
beads are generally preferred due to their greater binding
capacity. Particularly polymeric beads and particles can be of
interest. Conveniently, a particulate support (e.g. beads or
particles) can be substantially spherical. The size of the
particulate support is not critical, but it can for example have a
diameter of at least 1 um and preferably at least 2 um, and have a
maximum diameter of preferably not more than 10 um and more
preferably not more than 6 urn. For example, particulate supports
having diameters of 2.8 um and 4.5 um will work well. An example of
a particulate support is monodisperse particles, i.e. such which
are substantially uniform in size (e. g. size having a diameter
standard deviation of less than 5%). Such have the advantage that
they provide very uniform reproducibility of reaction.
[0224] Non-magnetic polymer beads can also be applicable. Such are
available from a wide range of manufactures, e. g. Dynal Particles
AS, Qiagen, Amersham Biosciences, Serotec, Seradyne, Merck, Nippon
Paint, Chemagen, Promega, Prolabo, Polysciences, Agowa, and Bangs
Laboratories.
[0225] Another example of a suitable support is magnetic beads or
particles. The term "magnetic" as used everywhere herein is
intended to mean that the support is capable of having a magnetic
moment imparted to it when placed in a magnetic field, and thus is
displaceable under the action of that magnetic field. In other
words, a support comprising magnetic beads or particles can readily
be removed by magnetic aggregation, which provides a quick, simple
and efficient way of separating out the beads or particles from a
solution. Magnetic beads and particles can suitably be paramagnetic
or superparamagnetic. Superparamagnetic beads, magnetic beads and
particles are available from several manufacturers, e. g. Dynal
Biotech ASA (Oslo, Norway, previously Dynal AS, e. g.
DYNABEADS.RTM.@).
[0226] The support can suitably have a functionalised surface.
Different types of functionalisation include making the surface of
the support positively or negatively charged, or hydrophilic or
hydrophobic. This applies in particular to beads and particles.
[0227] The MHC multimers of the present invention can be attached
(immobilised) to the solid or semi-solid support by any method
known in the art for attachment (or immobilisation) to supports. In
particular, the MHC multimers can be immobilised to the support by
way of linkers, spacers or antibodies, or any combination thereof.
Examples of suitable linkers include Calmodulin-binding peptide
(CBP), 6.times.HIS, Protein A, Protein G, biotin, Avidin,
Streptavidin, STREP-TAG.RTM., Cellulose Binding Domain, Maltose
Binding Protein, S-Peptide Tag, Chitin Binding Tag, Immuno-reactive
Epitopes, Epitope Tags, GST tagged proteins, E2Tag, HA Epitope Tag,
Myc Epitope, FLAG Epitope, AU1 and AU5 Epitopes, Glu-Glu Epitope,
KT3 Epitope, IRS Epitope, Btag Epitope, Protein Kinase-C Epitope,
VSV Epitope, "zero length cross-linkers" such as 1-ethyl-3
(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDAC),
homobifunctional cross-linkers such as glutaric dialdehyde,
disuccinimidyl suberate (DSS) dimethyl adipimidate dihydrochloride
(DMA), divinylfulfone (DVS), or bismaleimidohexane, and
heterobifunctional cross-linkers such as 4-(N-maleimidomethyl)
cyclohexane-1-carboxyl hydrazide hydro-chloride (M2C2H),
succinimidyl-4-(N-maleimidomethyl) (SMCC),
N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP), and
N-(gamma-maleimidobutyryloxy) succinimide (GMBS). Examples of
suitable spacers include multifunctional molecules such as diamino
alkanes, dicarboxyls and dihydroxyls. The spacers can additionally
include functionalities such as e. g. ethers, amides, and
amines.
[0228] Examples of suitable antibodies (polyclonal, monoclonal,
recombinant) include antibodies directed against the
multimerization domain(s) and antibodies against the binding
entity. It is to be understood that the MHC multimers can be
attached covalently or reversibly. By "reversibly" is meant that
the attachment can be reversed such that the MHC multimers can be
liberated from the support.
[0229] By way of example, if the multimerization domain(s) is a
dextran molecule, the MHC molecule construct can be immobilised
using anti-dextran antibodies. By way of example, a PNA could be
attached to the MHC molecule construct, and an anti-PNA antibody
could be used for immobilisation.
[0230] It is to be understood that several or only one type of
support can be applied at the same time. Likewise, a support can
have immobilised thereto one or more MHC molecule constructs. The
MHC multimers immobilised onto the support can be the same or
different. E. g. on type of MHC molecule construct can be
immobilised to one type of support, and another type of MHC
molecule construct to another type of support. In principle, the
number of different MHC molecule construct is unlimited.
Alternative MHC Multimers
[0231] In the following alternatives ways to make MHC multimers
compared to traditional methods are described.
[0232] MHC trimers can be generated by attaching three MHC
complexes to the same multimerization domain together with a
labelleling molecule, e.g. 3 MHC complexes attached to SA through
biotin and with a biotinylated labelling molecule attached to the
fourth biotin-binding pocket of SA. Alternatively the MHC complexes
can be covalent linked to SA, e.g. by genetic fusion. The labelling
molecules can be any labelling molecule suitable for direct or
indirect detection, including fluorophores, chromophores or enzymes
as described elsewhere herein.
[0233] MHC dextramers are as described elsewhere made by coupling
MHC complexes to dextran via a streptavidin-biotin interaction. In
principle biotin-streptavidin can be replaced by any dimerization
domain where one half of the dimerization domain is coupled to the
MHC-peptide complex and the other half is coupled to dextran. E.g.
an acidic helix (one half of a coiled-coil dimer) is coupled/fused
to MHC and a basic helix (other half of a coiled-coil dimmer) is
coupled/fused to dextran. Mixing the two results in MHC binding to
dextran by forming a coiled-coil structure between the two.
[0234] MHC dextramers can also be made by covalent coupling of MHC
complexes to the dextran backbone, e.g. by chemical coupling of MHC
complexes to dextran backbones. The MHC complexes can be coupled
through either heavy chain or .beta.2-microglobulin if the MHC
complexes are MHC I or through .alpha.-chain or .beta.-chain if the
MHC complexes are MHC II. MHC complexes can be coupled as folded
complexes comprising heavy chain/beta2microglobulin or
.alpha.-chain/.beta.-chain or either combination together with
peptide in the peptide binding cleft. Alternatively either of the
protein chains can be coupled to dextran and then folded in vitro
together with the other chain of the MHC complex not coupled to
dextran and together with peptide. Direct coupling of MHC complexes
to dextran multimerization domain can be via an amino group or via
a sulphide group. Either group can be a naturally component of the
MHC complex or attached to the MHC complex chemically.
Alternatively a gene encoding an amino or sulphide comprising amino
acid can be fused to the genes of either chain in the MHC
complex.
[0235] Another way to couple MHC complexes to dextran
multimerization domains is to use peptide as a linker between MHC
and dextran. Linker containing antigenic peptide in one end is
coupled to dextran. Antigenic peptide here means a peptide able to
bind MHC complexes in the peptide binding cleft. E.g. 10 or more
antigenic peptides are coupled to one dextran molecule. When MHC
complexes are added to such peptide-dextran construct the MHC
complexes will bind the antigenic peptides and thereby MHC-peptide
complexes are displayed around the dextran multimerization domain.
The antigenic peptides can be identical or different from each
other. Similarly MHC complexes can be either identical or different
from each other as long as they are capable of binding one or more
of the peptides on the dextran multimerization domain.
[0236] MHC complexes can be multimerized by other means than
coupling to one or more multimerization domain(s). One method is to
extend the bound peptide with dimerization domains. One end of the
peptide is extended with dimerization domain A (e.g. acidic helix,
half of a coiled-coil dimer) and the other end is extended with
dimerization domain B (e.g. basic helix, other half of a
coiled-coil dimer). When MHC complexes are loaded/mixed with these
extended peptides the following multimer structure will be formed:
A-MHC-BA-MHC-BA-MHC-B etc. The peptides in the mixture can either
be identical or a mixture of peptides with comparable extended
dimerization domains. Alternatively both ends of a peptide are
extended with the same dimerization domain A and another peptide
(same amino acid sequence or a different amino acid sequence) is
extended with dimerization domain B. When MHC and peptides are
mixed the following structures are formed:
A-MHC-AB-MHC-BA-MHC-AB-MHC-B etc. Multimerization of MHC complexes
by extension of peptides are restricted to MHC II molecules since
the peptide binding groove of MHC I molecules are closed in both
ends thereby limit the size of peptide embedded in the groove and
preventing the peptide from extending out of the groove.
[0237] Another multimerization approach applicable to both MHC I
and MHC II complexes is based on extension of N- and C-terminal of
the MHC complex. For example the N-terminal of the MHC complex is
extended with dimerization domain A and the C-terminal is extended
with dimerization domain B. When MHC complexes are incubated
together they pair with each other and form multimers like:
A-MHC-BA-MHC-BA-MHC-BA-MHC-B etc. Alternatively the N-terminal and
the C-terminal of a MHC complex are both extended with dimerization
domain A and the N-terminal and C-terminal of another preparation
of MHC complex (either the same or a different MHC) are extended
with dimerization domain B. When these to types of MHC complexes
are incubated together multimers will be formed:
A-MHC-AB-MHC-BA-MHC-AB-MHC-B etc.
[0238] In all the above-described examples the extension can be
either chemically coupled to the peptide/MHC complex or introduced
as extension by gene fusion.
[0239] Dimerization domain AB can be any molecule pair able to bind
to each other like: acid/base coiled-coil helices,
antibody-antigen, DNA-DNA, PNA-PNA, DNA-PNA, DNA-RNA, LNA-DNA,
leucine zipper e.g. Fos/Jun, streptavidin-biotin and other molecule
pairs as described elsewhere herein.
Stabilization of Empty MHC Complexes and MHC-Peptide Complexes
[0240] Classical MHC complexes are in nature embedded in the
membrane. A preferred embodiment includes multimers comprising a
soluble form of MHC II or I where the transmembrane and cytosolic
domains of the membrane-anchored MHC complexes are removed. The
removal of the membrane-anchoring parts of the molecules can
influence the stability of the MHC complexes. The stability of MHC
complexes is an important parameter when generating and using MHC
multimers.
[0241] MHC I complexes consist of a single membrane-anchored heavy
chain that contains the complete peptide binding groove and is
stable in the soluble form when complexed with .beta.2m. The
long-term stability is dependent on the binding of peptide in the
peptide-binding groove. Without a peptide in the peptide binding
groove the heavy chain and .beta.2m tend to dissociate. Similarly,
peptides with high affinity for binding in the peptide-binding
groove will typically stabilize the soluble form of the MHC complex
while peptides with low affinity for the peptide-binding groove
will typically have a smaller stabilizing effect.
[0242] In contrast, MHC II complexes consist of two
membrane-anchored chains of almost equal size. When not attached to
the cell membrane the two chains tend to dissociate and are
therefore not stable in the soluble form unless a high affinity
peptide is bound in the peptide-binding groove or the two chains
are held together in another way.
[0243] In nature MHC I molecules consist of a heavy chain combined
with .beta.2m, and a peptide of typically 8-11 amino acids. Herein,
MHC I molecules also include molecules consisting of a heavy chain
and .beta.2m (empty MHC), or a heavy chain combined with a peptide
or a truncated heavy chain comprising .alpha.1 and .alpha.2
subunits combined with a peptide, or a full-length or truncated
heavy chain combined with a full-length or truncated .beta.2m
chain. These MHC I molecules can be produced in E. coli as
recombinant proteins, purified and refolded in vitro (Garboczi et
al., (1992), Proc. Natl. Acad. Sci. 89, 3429-33). Alternatively,
insecT-cell systems or mammalian cell systems can be used. To
produce stable MHC I complexes and thereby generate reliable MHC I
multimers several strategies can be followed. Stabilization
strategies for MHC I complexes are described in the following.
Generation of Covalent Protein-Fusions
[0244] MHC I molecules can be stabilized by introduction of one or
more linkers between the individual components of the MHC I
complex. This could be a complex consisting of a heavy chain fused
with .beta.2m through a linker and a soluble peptide, a heavy chain
fused to .beta.2m through a linker, a heavy chain/.beta.2m dimer
covalently linked to a peptide through a linker to either heavy
chain or .beta.2m, and where there can or can not be a linker
between the heavy chain and .beta.2m, a heavy chain fused to a
peptide through a linker, or the .alpha.1 and .alpha.2 subunits of
the heavy chain fused to a peptide through a linker. In all of
these example protein-fusions, each of the heavy chain, .beta.2m
and the peptide can be truncated.
[0245] The linker could be a flexible linker, e.g. made of glycine
and serine and e.g. between 5-20 residues long. The linker could
also be rigid with a defined structure, e.g. made of amino acids
like glutamate, alanine, lysine, and leucine creating e.g. a more
rigid structure.
[0246] In heavy chain-.beta.2m fusion proteins the COOH terminus of
.beta.2m can be covalently linked to the NH.sub.2 terminus of the
heavy chain, or the NH.sub.2 terminus of .beta.2m can be linked to
the COOH terminus of the heavy chain. The fusion-protein can also
comprise a .beta.2m domain, or a truncated .beta.2m domain,
inserted into the heavy chain, to form a fusion-protein of the form
"heavy chain (first part)-.beta.2m-heavy chain (last part)".
Likewise, the fusion-protein can comprise a heavy chain domain, or
a truncated heavy chain, inserted into the .beta.2m chain, to form
a fusion-protein of the form ".beta.2m(first part)-heavy
chain-.beta.2m(last part)".
[0247] In peptide-.beta.2m fusion proteins the COOH terminus of the
peptide is preferable linked to the NH.sub.2 terminus of .beta.2m
but the peptide can also be linked to the COOH terminal of .beta.2m
via its NH.sub.2 terminus. In heavy chain-peptide fusion proteins
it is preferred to fuse the NH.sub.2 terminus of the heavy chain to
the COOH terminus of the peptide, but the fusion can also be
between the COOH terminus of the heavy chain and the NH.sub.2
terminus of the peptide. In heavy chain-.beta.2m-peptide fusion
proteins the NH.sub.2 terminus of the heavy chain can be fused to
the COOH terminus of .beta.2m and the NH.sub.2 terminus of .beta.2m
can be fused to the COOH terminus of the peptide.
Non-Covalent Stabilization by Binding to an Unnatural Component
[0248] Non-covalent binding of unnatural components to the MHC I
complexes can lead to increased stability. The unnatural component
can bind to both the heavy chain and the .beta.2m, and in this way
promote the assembly of the complex, and/or stabilize the formed
complex. Alternatively, the unnatural component can bind to either
.beta.2m or heavy chain, and in this way stabilize the polypeptide
in its correct conformation, and in this way increase the affinity
of the heavy chain for .beta.2m and/or peptide, or increase the
affinity of .beta.2m for peptide. Here, unnatural components mean
antibodies, peptides, aptamers or any other molecule with the
ability to bind peptides stretches of the MHC complex. Antibody is
here to be understood as truncated or full-length antibodies (of
isotype IgG, IgM, IgA, IgE), Fab, scFv or bi-Fab fragments or
diabodies.
[0249] An example of special interest is an antibody binding the
MHC I molecule by interaction with the heavy chain as well as
.beta.2m. The antibody can be a bispecific antibody that binds with
one arm to the heavy chain and the other arm to the .beta.2m of the
MHC complex. Alternatively the antibody can be monospecific, and
bind at the interface between heavy chain and .beta.2m.
[0250] Another example of special interest is an antibody binding
the heavy chain but only when the heavy chain is correct folded.
Correct folded is here a conformation where the MHC complex is able
to bind and present peptide in such a way that a restricted T-cell
can recognize the MHC-peptide complex and be activated. This type
of antibody can be an antibody like the one produced by the clone
W6/32 (M0736 from Dako, Denmark) that recognizes a conformational
epitope on intact human and some monkey MHC complexes comprising
.beta.2m, heavy chain and peptide.
Generation of Modified Proteins or Protein Components
[0251] One way to improve stability of a MHC I complex am to
increase the affinity of the binding peptide for the MHC complex.
This can be done by mutation/substitution of amino acids at
relevant positions in the peptide, by chemical modifications of
amino acids at relevant positions in the peptide or introduction by
synthesis of non-natural amino acids at relevant positions in the
peptide. Alternatively, mutations, chemical modifications,
insertion of natural or non-natural amino acids or deletions could
be introduced in the peptide binding cleft, i.e. in the binding
pockets that accommodate peptide side chains responsible for
anchoring the peptide to the peptide binding cleft. Moreover,
reactive groups can be introduced into the antigenic peptide;
before, during or upon binding of the peptide, the reactive groups
can react with amino acid residues of the peptide binding cleft,
thus covalently linking the peptide to the binding pocket.
[0252] Mutations, chemical modifications, insertion of natural or
non-natural amino acids or deletions could also be introduced in
the heavy chain and/or .beta.2m at positions outside the
peptide-binding cleft. A preferred embodiment is removal of
"unwanted cysteine residues" in the heavy chain by mutation,
chemical modification, amino acid exchange or deletion. "Unwanted
cysteine residues" is here to be understood as cysteines not
involved in the correct folding of the final MHC I molecule. The
presence of cysteine not directly involved in the formation of
correctly folded MHC I molecules can lead to formation of intra
molecular disulfide bridges resulting in a non correct folded MHC
complex during in vitro refolding. Another method for covalent
stabilization of MHC I complex am to covalently attach a linker
between two of the subunits of the MHC complex. This can be a
linker between peptide and heavy chain or between heavy chain and
beta2microglobulin.
[0253] MHC II complexes consist of a .alpha.-chain and a
.beta.-chain combined with a peptide. It could also be a molecule
only consisting of .alpha.-chain and .beta.-chain (so-called empty
MHC II), a truncated .alpha.-chain (e.g. the .alpha.1 domain)
combined with full-length .beta.-chain either empty or loaded with
a peptide, a truncated .beta.-chain (e.g. the .beta.1 domain)
combined with a full-length .alpha.-chain, either empty or loaded
with a peptide or a truncated .alpha.-chain combined with a
truncated .beta.-chain (e.g. .alpha.1 and .beta.1 domain), either
empty or loaded with a peptide.
[0254] In contrast to MHC I complexes, MHC II complexes are not
easily refolded after denaturation in vitro. Only some MHC II
alleles can be expressed in E. coli and refolded in vitro.
Therefore, preferred expression systems for production of MHC II
molecules are eukaryotic systems where refolding after expression
of protein is not necessary. Preferred expression systems include
stable Drosophila cell transfectants, baculovirus infected
insecT-cells, CHO cells or other mammalian cell lines suitable for
expression of proteins.
[0255] Stabilization of soluble MHC II complexes is even more
important than for MHC I molecules, since both .alpha.- and
.beta.-chain are participants in formation of the peptide binding
groove and tend to dissociate when not embedded in the cell
membrane. Stabilization strategies for MHC II complexes are
described in the following.
Generation of Covalent Protein-Fusions
[0256] MHC II complexes can be stabilized by introduction of one or
more linkers between the individual components of the MHC II
complex. This can be a .alpha./.beta. dimer with a linker between
.alpha.-chain and .beta.-chain; a .alpha./.beta. dimer covalently
linked to the peptide via a linker to either the .alpha.-chain or
.beta.-chain; a .alpha./.beta. dimer, covalently linked by a linker
between the .alpha.-chain and .beta.-chain, and where the dimer is
covalently linked to the peptide; a .alpha./.beta. dimer with a
linker between .alpha.-chain and .beta.-chain, where the dimer is
combined with a peptide covalently linked to either .alpha.-chain
or .beta.-chain.
[0257] The linker can be a flexible linker, e.g. made of glycine
and serine, and is typically between 5-20 residues long, but can be
shorter or longer. The linker can also be more rigid with a more
defined structure, e.g. made of amino acids like glutamate,
alanine, lysine, and leucine.
[0258] The peptides can be linked to the NH.sub.2-- or
COOH-terminus of either .alpha.-chain or .beta.-chain. Of special
interest are peptides linked to the NH.sub.2-terminus of the
.beta.-chain via their COOH-terminus, since the linker required is
shorter than if the peptide is linked to the COOH-terminus of the
.beta.-chain.
[0259] Linkage of .alpha.-chain to .beta.-chain can be via the
COOH-terminus of the .beta.-chain to the NH.sub.2-terminus of the
.alpha.-chain or from the COOH-terminus of the .alpha.-chain to the
NH.sub.2-terminus of the .beta.-chain.
[0260] In a three-molecule fusion protein consisting of
.alpha.-chain, .beta.-chain and peptide a preferred construct is
where one linker connect the COOH-terminus of the .beta.-chain with
the NH.sub.2-terminus of the .alpha.-chain and another linker
connects the COOH-terminal of the peptide with the
NH.sub.2-terminal of the .beta.-chain. Alternatively one linker
joins the COOH-terminus of the .alpha.-chain with the
NH.sub.2-terminus of the .beta.-chain and the second linker joins
the NH.sub.2-terminus of the peptide with the COOH-terminus of the
.beta.-chain. The three peptides of the MHC complex can further be
linked as described above for the three peptides of the MHC
complex, including internal fusion points for the proteins.
Non-Covalent Stabilization by Binding Ligand
[0261] Non-covalent binding of ligands to the MHC II complex can
promote assembly of .alpha.- and .beta.-chain by bridging the two
chains, or by binding to either of the .alpha.- or .beta.-chains,
and in this way stabilize the conformation of a or .beta., that
binds .beta. or .alpha., respectively, and/or that binds the
peptide. Ligands here mean antibodies, peptides, aptamers or any
other molecules with the ability to bind proteins.
[0262] A particular interesting example is an antibody binding the
MHC complex distal to the interaction site with TCR, i.e. distal to
the peptide-binding cleft. An antibody in this example can be any
truncated or full length antibody of any isotype (e.g. IgG, IgM,
IgA or IgE), a bi-Fab fragment or a diabody. The antibody could be
bispecific with one arm binding to the .alpha.-chain and the other
arm binding to the .beta.-chain. Alternatively the antibody could
be monospecific and directed to a sequence fused to the
.alpha.-chain as well as to the .beta.-chain. Alternatively the
antibody is monospecific and binds to a surface of the complex that
involves both the .alpha.- and .beta.-chain, e.g. both the
.alpha.2- and .beta.2-domain or both the .alpha.1- and
.beta.1-domain.
[0263] The antibodies described above can be substituted with any
other ligand that binds at the .alpha.-/.beta.-chain interface,
e.g. peptides and aptamers. The ligand can also bind the peptide,
although, in this case it is important that the ligand does not
interfere with the interaction of the peptide or binding cleft with
the TCR.
Non-Covalent Stabilization by Induced Multimerization
[0264] In nature the anchoring of the .alpha.- and .beta.-chains in
the cell membrane stabilizes the MHC II complexes considerably. As
mentioned above, a similar concept for stabilization of the
.alpha./.beta.-dimer was employed by attachment of the MHC II
chains to the Fc regions of an antibody, leading to a stable
.alpha./.beta.-dimer, where .alpha. and .beta. are held together by
the tight interactions between two Fc domains of an antibody. Other
dimerization domains can be used as well.
[0265] In one other example of special interest MHC II molecules
are incorporated into artificial membrane spheres like liposomes or
lipospheres. MHC II molecules can be incorporated as monomers in
the membrane or as dimers like the MHC II-antibody constructs
describes above. In addition to stabilization of the MHC II complex
an increased avidity is obtained. The stabilization of the dimer
will in most cases also stabilize the trimeric MHC-peptide
complex.
[0266] Induced multimerization can also be achieved by
biotinylation of .alpha.-as well as .beta.-chain and the two chains
brought together by binding to streptavidin. Long flexible linkers
such as extended glycine-serine tracts can be used to extend both
chains, and the chains can be biotinylated at the end of such
extended linkers. Then streptavidin can be used as a scaffold to
bring the chains together in the presence of the peptide, while the
flexible linkers still allow the chains to orientate properly.
Generation of Modified Proteins or Protein Components
[0267] Stability of MHC II complexes can be increased by covalent
modifications of the protein. One method is to increase the
affinity of the peptide for the MHC complex. This can be done by
exchange of the natural amino acids with other natural or
non-natural amino acids at relevant positions in the peptide or by
chemical modifications of amino acids at relevant positions in the
peptide. Alternatively, mutations, chemical modifications,
insertion of natural or non-natural amino acids or deletions can be
introduced in the peptide-binding cleft. Mutations, chemical
modifications, insertion of natural or non-natural amino acids or
deletions can alternatively be introduced in .alpha.- and/or
.beta.-chain at positions outside the peptide-binding cleft.
[0268] In this respect a preferred embodiment is to replace the
hydrophobic transmembrane regions of .alpha.-chain and .beta.-chain
by leucine zipper dimerisation domains (e.g. Fos-Jun leucine
zipper; acid-base coiled-coil structure) to promote assembly of
.alpha.-chain and .beta.-chain.
[0269] Another preferred embodiment is to introduce one or more
cysteine residues by amino acid exchange at the COOH-terminal of
both .alpha.-chain and .beta.-chain, to create disulfide bridges
between the two chains upon assembly of the MHC complex.
[0270] Another embodiment is removal of "unwanted cysteine
residues" in either of the chains by mutation, chemical
modification, amino acid exchange or deletion. "Unwanted cysteine
residues" is here to be understood as cysteines not involved in
correct folding of the MHC II-peptide complex. The presence of
cysteines not directly involved in the formation of correctly
folded MHC II complexes can lead to formation of intra molecular
disulfide bridges and incorrectly folded MHC complexes.
[0271] MHC II complexes can also be stabilized by chemically
linking together the subunits and the peptide. That can be a linker
between peptide and .alpha.-chain, between peptide and
.beta.-chain, between .alpha.-chain and .beta.-chain, and
combination thereof.
[0272] Such linkages can be introduced prior to folding by linking
two of the complex constituents together, then folding this
covalent hetero-dimer in the presence of the third constituent. An
advantage of this method is that it only requires complex formation
between two, rather than three species.
[0273] Another possibility is to allow all three constituents to
fold, and then to introduce covalent cross-links on the folded
MHC-complex, stabilizing the structure. An advantage of this method
is that the two chains and the peptide will be correctly positioned
relatively to each other when the cross linkages are
introduced.
Chemically Modified MHC Complexes
[0274] There are a number of amino acids that are particularly
reactive towards chemical cross linkers. In the following, chemical
reactions are described that are particularly preferable for the
cross-linking or modification of MHC I or MHC II complexes.
[0275] The amino group at the N-terminal of both chains and of the
peptide, as well as amino groups of lysine side chains, are
nucleophilic and can be used in a number of chemical reactions,
including nucleophilic substitution by activation of electrophiles
(e.g. acylation such as amide formation, pyrazolone formation,
isoxazolone formation; alkylation; vinylation; disulfide
formation), addition to carbon-hetero multiple bonds (e.g. alkene
formation by reaction of phosphonates with aldehydes or ketones;
arylation; alkylation of arenes/hetarenes by reaction with alkyl
boronates or enolethers), nucleophilic substitution using
activation of nucleophiles (e.g. condensations; alkylation of
aliphatic halides or tosylates with enolethers or enamines), and
cycloadditions. Example reagents that can be used in a reaction
with the amino groups are activated carboxylic acids such as
NHS-ester, tetra and pentafluoro phenolic esters, anhydrides, acid
chlorides and fluorides, to form stable amide bonds. Likewise,
sulphonyl chlorides can react with these amino groups to form
stable sulphone-amides. Iso-Cyanates can also react with amino
groups to form stable ureas, and isothiocyanates can be used to
introduce thio-urea linkages. Aldehydes, such as formaldehyde and
glutardialdehyde will react with amino groups to form shiff's
bases, than can be further reduced to secondary amines. The
guanidino group on the side chain of arginine will undergo similar
reactions with the same type of reagents. Another very useful amino
acid is cysteine. The thiol on the side chain is readily alkylated
by maleimides, vinyl sulphones and halides to form stable
thioethers, and reaction with other thiols will give rise to
disulphides. Carboxylic acids at the C-terminal of both chains and
peptide, as well as on the side chains of glutamic and aspartic
acid, can also be used to introduce cross-links. They will require
activation with reagents such as carbodiimides, and can then react
with amino groups to give stable amides.
[0276] Thus, a large number of chemistries can be employed to form
covalent cross-links. The crucial point is that the chemical
reagents are bi-functional, being capable of reacting with two
amino acid residues. They can be either homo bi-functional,
possessing two identical reactive moieties, such as
glutardialdehyde or can be hetero bi-functional with two different
reactive moieties, such as GMBS (MaleimidoButyryloxy-Succinimide
ester).
[0277] Alternatively, two or more reagents can be used; i.e. GMBS
can be used to introduce maleimides on the .alpha.-chain, and
iminothiolane can be used to introduce thiols on the .beta.-chain;
the malemide and thiol can then form a thioether link between the
two chains.
[0278] For the present invention some types of cross-links are
particularly useful. The folded MHC-complex can be reacted with
dextrans possessing a large number (up to many hundreds) of vinyl
sulphones. These can react with lysine residues on both the .alpha.
and .beta. chains as well as with lysine residues on the peptide
protruding from the binding site, effectively cross linking the
entire MHC-complex. Such cross linking is indeed a favoured
reaction because as the first lysine residue reacts with the
dextran, the MHC-complex becomes anchored to the dextran favouring
further reactions between the MHC complex and the dextran
multimerization domain. Another great advantage of this dextran
chemistry is that it can be combined with fluorochrome labelling;
i.e. the dextran is reacted both with one or several MHC-complexes
and one or more fluorescent protein such as APC.
[0279] Another valuable approach is to combine the molecular
biological tools described above with chemical cross linkers. As an
example, one or more lysine residues can be inserted into the
.alpha.-chain, juxtaposed with glutamic acids in the .beta.-chain,
where after the introduced amino groups and carboxylic acids are
reacted by addition of carbodiimide. Such reactions are usually not
very effective in water, unless as in this case, the groups are
well positioned towards reaction. This implies that one avoids
excessive reactions that could otherwise end up denaturing or
changing the conformation of the MHC-complex.
[0280] Likewise one or more dextran multimerization domain(s) can
be cross-linked with appropriately modified MHC-complexes; i.e. one
or both chains of the MHC complex can be enriched with lysine
residues, increasing reactivity towards the vinylsulphone dextran.
The lysine's can be inserted at positions opposite the peptide
binding cleft, orienting the MHC-complexes favourably for T-cell
recognition.
[0281] Another valuable chemical tool is to use extended and
flexible cross-linkers. An extended linker will allow the two
chains to interact with little or no strain resulting from the
linker that connects them, while keeping the chains in the vicinity
of each other should the complex dissociate. An excess of peptide
should further favour reformation of dissociated MHC-complex.
Stabilization with One or More Soluble Additives
[0282] Salts, detergents, organic solvent, polymers and any other
soluble additives can be added to increase the stability of MHC
complexes. Of special interest are additives that increase surface
tension of the MHC complex. Examples are sucrose, mannose, glycine,
betaine, alanine, glutamine, glutamic acid and ammonium sulfate.
Glycerol, mannitol and sorbitol are also included in this group
even though they are able to bind polar regions.
[0283] Another group of additives of special interest increases
surface tension of the MHC complex and simultaneously can interact
with charged groups in the protein. Examples are MgSO.sub.4, NaCl,
polyethylenglycol, 2-methyl-2,4-pentanediol and
guanidiniumsulphate.
[0284] Correct formation of MHC complexes is dependent on binding
of peptide in the peptide-binding cleft; the bound peptide appears
to stabilize the complex in its correct conformation. Addition of
molar excess of peptide will force the equilibrium towards
correctly folded MHC-peptide complexes. Likewise, excess .beta.2m
is also expected to drive the folding process in direction of
correctly folded MHC complexes. Therefore peptide identical to the
peptide bound in the peptide-binding cleft and .beta.2m can be
included as stabilizing soluble additives.
[0285] Other additives of special interest for stabilization of MHC
complexes are BSA, fetal and bovine calf serum, and other protein
components in serum with a protein stabilizing effect.
[0286] All of the above mentioned soluble additives could be added
to any solution comprising MHC complexes in order to increase the
stability of the molecule. This can be during the refolding
process, to the formed MHC complex or to a solution of MHC
multimers comprising several MHC complexes.
tcr-binding molecules
[0287] MHC I and MHC II complexes bind to TCRs. However, other
molecules also bind TCR. Some TCR-biding molecules are described in
the following.
Modified MHC I or MHC II Complexes:
[0288] MHC I and MHC II complexes modified in any way as described
above, may bind TCR. Modifications include mutations
(substitutions, deletions or insertions of natural or non-natural
amino acids, or any other organic molecule. The mutations are not
limited to those that increase the stability of the MHC complex,
and could be introduced anywhere in the MHC complex. One example of
special interest is mutations introduced in the .alpha.3 subunit of
MHC I heavy chain. The .alpha.3-subunit interacts with CD8
molecules on the surface of T-cells. To minimize binding of MHC
multimer to CD8 molecules on the surface of non-specific T-cells,
amino acids in .alpha.3 domain involved in the interaction with CD8
may be mutated. Such a mutation may result in altered or abrogated
binding of MHC to CD8 molecules. Another example of special
interest is mutations in areas of the .beta.2-domain of MHC II
molecules responsible for binding CD4 molecules.
[0289] Another embodiment is chemically modified MHC complexes
where the chemical modification could be introduced anywhere in the
complex, e.g. a MHC complex where the peptide in the
peptide-binding cleft has a dinitrophenyl group attached. A
chemical modification of special interest is chemical biotinylation
of any of the three components (.alpha.-chain, .beta.-chain or
peptide) in the MHC-peptide complex. Biotin may be covalent coupled
to primary amines in the MHC-peptide complex, e.g. to Lysine, using
chemical reactions as described elsewhere herein. Particularly
suited for biottinylation reactions are N-hydroxy succinimide
esters.
[0290] Modified MHC complexes could also be MHC I or MHC II fusion
proteins where the fusion protein is not necessarily more stable
than the native protein. Of special interest is MHC complexes fused
with genes encoding an amino acid sequence capable of being
biotinylated with a BirA enzyme (Schatz, P. J., (1993),
Biotechnology 11(10):1138-1143). This biotinylation sequence could
be fused with the COOH-terminal of .beta.2m or the heavy chain of
MHC I molecules or the COOH-terminal of either the .alpha.-chain or
.beta.-chain of MHC II. Other sequences capable of being
enzymatically or chemically modified, may be fused to the NH.sub.2
or COOH-terminal ends of the MHC complex. Both enzymatic and
chemical biotinylation may be carried out in vitro as well as in
vivo.
Non-Classical MHC Complexes and Other MHC-Like Molecules:
[0291] Non-classical MHC complexes include protein products of MHC
Ib and MHC IIb genes. MHC Ib genes encode .beta.2m-associated
cell-surface molecules but show little polymorphism in contrast to
classical MHC class I genes. Protein products of MHC class Ib genes
include HLA-E, HLA-G, HLA-F, HLA-H, MIC A, MIC B, ULBP-1, ULBP-2,
ULBP-3 in humans and H2-M, H2-Q, H2-T and Rae1 in mice.
[0292] Non-classical MHC II molecules (protein products of MHC lib
genes) include HLA-DM, HLA-DO in humans and H2-DM and H2-DO in mice
that are involved in regulation of peptide loading into MHC II
molecules.
[0293] Another MHC-like molecule of special interest is the MHC
I-like molecule CD1. CD1 is similar to MHC I molecules in its
organization of subunits and association with .beta.2m but presents
glycolipids and lipids instead of peptides.
Artificial Molecules Capable of Binding Specific TCRs:
[0294] Of special interest are antibodies that bind TCRs.
Antibodies herein include full length antibodies of isotype IgG,
IgM, IgE, IgA and truncated versions of these, antibody fragments
like Fab fragments and scFv. Antibodies also include antibodies of
antibody fragments displayed on various supramolecular structures
or solid supports, including filamentous phages, yeast, mammalian
cells, fungi, artificial cells or micelles, and beads with various
surface chemistries.
[0295] Another embodiment of special interest is peptides that bind
TCRs. Peptides herein include peptides composed of natural,
non-natural and/or chemically modified amino acids with a length of
8-20 amino acids. The peptides could also be longer than 20 amino
acids or shorter than 8 amino acids. The peptides can or can not
have a defined tertiary structure.
[0296] Aptamers are another preferred group of TCR ligands.
Aptamers are herein understood as natural nucleic acids (e.g. RNA
and DNA) or unnatural nucleic acids (e.g. PNA, LNA, morpholinos)
capable of binding TCR. The aptamer molecules consist of natural or
modified nucleotides in various lengths.
[0297] Other TCR-binding molecules can be ankyrin repeat proteins
or other repeat proteins, Avimers, or small chemical molecules, as
long as they are capable of binding TCR with a dissociation
constant smaller than 10.sup.-3 M.
Technical Applications for MHC Multimers
[0298] MHC multimers as described herein can be used to identify
and isolate specific T-cells in a wide array of applications. In
principle all kind of samples possessing T-cells and/or T-cell
receptors (TCR's) can be analyzed with MHC multimers.
[0299] Technical applications for MHC multimers include but is not
limited to the methods and principles described in the
following.
[0300] MHC multimers can be used to detect T-cells and/or TCR's in
a sample by binding specific TCR's in a given sample. In general
T-cells can be detected as individual cells or as populations of
cells and the sample may be fluid, solid, semifluid or
semisolid.
[0301] Example fluid sample include, but is not limited to, blood,
lymph, cerebrospinal fluid, synovial fluid, sputum, lymph, semen,
fluid cultures of cells, suspensions of solid tissue, fluid samples
with TCR coated beads, fluid samples with soluble TCR's and any
fluid sample containing T-cells and/or TCR's.
[0302] Example solid sample include, but is not limited to, solid
tissue, tissue sections, organ, part of organ or tissue, human
bodies or any part thereof, animal bodies of any part thereof and
cells embedded in a solid matrix, e.g. parafin.
[0303] In the following applications of MHC multimers for detection
of T-cells in fluid are explained.
Flow Cytometry Analysis:
[0304] In one embodiment of the present invention MHC multimers can
be used for detection of individual T-cells in fluid samples using
flow cytometry or flow cytometry-like analysis.
[0305] Liquid cell samples can be analyzed using a flow cytometer,
able to detect and count individual cells passing in a stream
through a laser beam. For identification of specific T-cells using
MHC multimers, cells are stained with fluorescently labeled MHC
multimer by incubating cells with MHC multimer and then forcing the
cells with a large volume of liquid through a nozzle creating a
stream of spaced cells. Each cell passes through a laser beam and
any fluorochrome bound to the cell is excited and thereby
fluoresces. Sensitive photomultipliers detect emitted fluorescence,
providing information about the amount of MHC multimer bound to the
cell. By this method MHC multimers can be used to identify
individual T-cells and/or specific T-cell populations in liquid
samples.
[0306] Cell samples capable of being analyzed by MHC multimers in
flow cytometry analysis include, but is not limited to, blood
samples or fractions thereof, T-cell lines (hybridomas, transfected
cells) and homogenized tissues like spleen, lymph nodes, tumors,
brain or any other tissue comprising T-cells.
[0307] When analyzing blood samples whole blood can be used with or
without lysis of red blood cells prior to analysis on flow
cytometer. Lysing reagent can be added before or after staining
with MHC multimers. When analysing blood samples without lysis of
red blood cells one or more gating reagents may be included to
distinguish lymphocytes from red blood cells. Preferred gating
reagent are marker molecules specific for surface proteins on red
blood cells, enabling subtraction of this cell population from the
remaing cells of the sample. As an example, a fluorochrome labelled
CD45 specific marker molecule e.g. an antibody can be used to set
the trigger discriminator to allow the flow cytometer to
distinguish between red blood corpuscles and stained white blood
cells.
[0308] Alternative to analysis of whole blood, lymphocytes can be
purified before flow cytometry analysis e.g. using standard
procedures like a FICOLL.RTM.-Hypaque gradient. Another possibility
is to isolate T-cells from the blood sample for example by adding
the sample to antibodies or other T-cell specific markers
immobilized on solid support. Marker specific T-cells will then
attached to the solid support and following washing specific
T-cells can be eluted. This purified T-cell population can then be
used for flow cytometry analysis together with MHC multimers.
[0309] T-cells may also be purified from other lymphocytes or blood
cells by rosetting. Human T-cells form spontaneous rosettes with
sheep erythrocytes also called E-rossette formation. E-rossette
formation can be carried out by incubating lymphocytes with sheep
red erythrocytes followed by purification over a density gradient
e.g. a FICOLL.RTM.-Hypaque gradient.
[0310] Instead of actively isolating T-cells unwanted cells like
B-cells, NK cells or other cell populations can be removed prior to
the analysis. A preferred method for removal of unwanted cells is
to incubate the sample with marker molecules specific or one or
more surface proteins on the unwanted cells immobilised unto solid
support. An example include use of beads coated with antibodies or
other marker molecule specific for surface receptors on the
unwanted cells e.g. markers directed against CD19, CD56, CD14, CD15
or others. Briefly beads coated with the specific surface marker(s)
are added to the cell sample. Cells different from the wanted
T-cells with appropriate surface receptors will bind the beads.
Beads are removed by e.g. centrifugation or magnetic withdrawal
(when using magnetic beads) and remaining cell are enriched for
T-cells.
[0311] Another example is affinity chromatography using columns
with material coated with antibodies or other markers specific for
the unwanted cells.
[0312] Alternatively, specific antibodies or markers can be added
to the blood sample together with complement, thereby killing cells
recognized by the antibodies or markers.
[0313] Various gating reagents can be included in the analysis.
Gating reagents here means labeled antibodies or other labelled
marker molecules identifying subsets of cells by binding to unique
surface proteins or intraccellular components or intracellular
secreted components. Preferred gating reagents when using MHC
multimers are antibodies and marker molecules directed against CD2,
CD3, CD4, and CD8 identifying major subsets of T-cells. Other
preferred gating reagents are antibodies and markers against CD11a,
CD14, CD15, CD19, CD25, CD30, CD37, CD49a, CD49e, CD56, CD27, CD28,
CD45, CD45RA, CD45RO, CD45RB, CCR7, CCR5, CD62L, CD75, CD94, CD99,
CD107b, CD109, CD152, CD153, CD154, CD160, CD161, CD178, CDw197,
CDw217, Cd229, CD245, CD247, Foxp3, or other antibodies or marker
molecules recognizing specific proteins unique for different
lymphocytes, lymphocytes populations or other cell populations.
Also included is antibodies and markers directed against
interleukines e.g. IL-2, IL-4, II-6, IL-10, IL-12, IL-21;
Interferones e.g. INF-.gamma., TNF-.alpha., TNF-.beta. or other
cytokine or chemokines.
[0314] Gating reagents can be added before, after or simultaneous
with addition of MHC multimer to the sample.
[0315] Following labelling with MHC multimers and before analysis
on a flow cytometer stained cells can be treated with a fixation
reagent e.g. formaldehyde, ethanol or methanol to cross-link bound
MHC multimer to the cell surface. Stained cells can also be
analyzed directly without fixation.
[0316] The number of cells in a sample can vary. When the
targeT-cells are rare, it is preferable to analyze large amounts of
cells. In contrast, fewer cells are required when looking at T-cell
lines or samples comprising many cells of the targeT-cell type.
[0317] The flow cytometer can in one embodiment be equipped to
separate and collect particular types of cells. This is called cell
sorting. MHC multimers in combination with sorting on a flow
cytometer can be used to isolate antigen specific T-cell
populations. Gating reagents as described above can be including
further specifying the T-cell population to be isolated. Isolated
and collected specific T-cell populations can then be further
manipulated as described elsewhere herein e.g. expanded in vitro.
This can e.g. be useful in autologous cancer therapy.
[0318] Direct determination of the concentration of MHC-peptide
specific T-cells in a sample can be obtained by staining blood
cells or other cell samples with MHC multimers and relevant gating
reagents followed by addition of an exact amount of counting beads
of known concentration. In general, the counting beads are
microparticles with scatter properties that put them in the context
of the cells of interest when registered by a flow cytometer. They
can be either labelled with antibodies, fluorochromes or other
marker molecules or they may be unlabelled. In some embodiments of
the invention, the beads are polystyrene beads with molecules
embedded in the polymer that are fluorescent in most channels of
the flow-cytometer. Inhere the terms "counting bead" and
"microparticle" are used interchangeably.
[0319] The counting beads employed in the methods and compositions
described here should preferably be small, and are preferably
between 0.1 .mu.m and 100 .mu.m, preferably about 5 .mu.m in
diameter. The microparticles should preferably be made of such
material and be of such size as to stay suspended, with minimal
agitation if necessary, in solution or suspension (i.e., once the
sample is added). It should preferably not settle any faster than
the cells of interest in the sample. The material from which the
microparticles are made should be such as to avoid clumping or
aggregation, i.e., the formation of doublets, triplets, quadruplets
and other multiplets. Generally, a final count of counting beads of
at least 1000/.mu.l is preferred but any number can be counted.
[0320] The counting beads should preferably be labelled with one or
more reporter molecule(s), such as one or more fluorescent
molecule(s) (which is described in further detail elsewhere).
Alternatively, or in addition, a microparticle which is
autofluorescent may be employed.
[0321] Counting beads may in one embodiment be selected from the
group consisting of fixed chicken red blood cells, coumarin beads,
liposomes containing a fluorescent dye, FLUORESCEIN.TM. beads,
rhodamine beads, fixed fluorescenT-cells, fluorescenT-cell nuclei,
microorganisms and other beads tagged with a fluorescent dye.
However, particularly advantageous examples of compact particles
that may be used in the invention include microbeads, such as
agarose beads, polyacrylamide beads, polystyrene beads, silica gel
beads, etc.
[0322] Beads or microparticles suitable for use include those which
are used for gel chromatography, for example, gel filtration media
such as SEPHADEX.RTM. .RTM.. Suitable microbeads of this sort
include, but is not limited to, SEPHADEX.RTM. G-10 having a bead
size of 40-120 .mu.m (Sigma Aldrich catalogue number 27, 103-9),
SEPHADEX.RTM. .RTM. G-15 having a bead size of 40-120 .mu.m (Sigma
Aldrich catalogue number 27, 104-7), SEPHADEX.RTM. .RTM. G-25
having a bead size of 20-50 m (Sigma Aldrich catalogue number 27,
106-3), SEPHADEX.RTM. .RTM. G-25 having a bead size of 20-80 m
(Sigma Aldrich catalogue number 27, 107-1), SEPHADEX.RTM. .RTM.
G-25 having a bead size of 50-150 m (Sigma Aldrich catalogue number
27, 109-8), SEPHADEX.RTM. .RTM. G-25 having a bead size of 100-300
m (Sigma Aldrich catalogue number 27, 110-1), SEPHADEX.RTM. .RTM.
G-50 having a bead size of 20-50 .mu.m (Sigma Aldrich catalogue
number 27, 112-8), SEPHADEX.RTM. .RTM. SEPHADEX.RTM. G-50 having a
bead size of 20-80m (Sigma Aldrich catalogue number 27, 113-6),
Sephadex G-50 having a bead size of 50-150 m (Sigma Aldrich
catalogue number 27, 114-4), SEPHADEX.RTM. .RTM. G-50 having a bead
size of 100-300 .mu.m (Sigma Aldrich catalogue number 27, 115-2),
SEPHADEX.RTM. G-75 having a bead size of 20-50 m (Sigma Aldrich
catalogue number 27, 116-0), SEPHADEX.RTM. G-75 having a bead size
of 40-120 .mu.m (Sigma Aldrich catalogue number 27, 117-9),
SEPHADEX.RTM. G-100 having a bead size of 20-50 m (Sigma Aldrich
catalogue number 27, 118-7), SEPHADEX.RTM. G-100 having a bead size
of 40-120 m (Sigma Aldrich catalogue number 27, 119-5),
SEPHADEX.RTM. G-150 having a bead size of 40-120 m (Sigma Aldrich
catalogue number 27, 121-7), and SEPHADEX.RTM. G-200 having a bead
size of 40-120 m (Sigma Aldrich catalogue number 27, 123-3).
[0323] SEPHAROSE.RTM. beads, for example, as used in liquid
chromatography, may also be used. Examples include
Q-SEPHAROSE.RTM., S-SEPHAROSE.RTM. and SP-SEPHAROSE.RTM. beads,
available for example from Amersham Biosciences Europe GmbH
(Freiburg, Germany) as Q SEPHAROSE.RTM. XL (catalogue number
17-5072-01), Q SEPHAROSE.RTM. XL (catalogue number 17-5072-04), Q
SEPHAROSE.RTM. XL (catalogue number 17-5072-60), SP SEPHAROSE.RTM.
XL (catalogue number 17-5073-01), SP SEPHAROSE.RTM. XL (catalogue
number 17-5073-04) and SP SEPHAROSE.RTM. XL (catalogue number
117-5073-60) etc.
[0324] Other preferred particles for use in the methods and
compositions described here comprise plastic microbeads. While
plastic microbeads are usually solid, they may also be hollow
inside and could be vesicles and other microcarriers. They do not
have to be perfect spheres in order to function in the methods
described here. Plastic materials such as polystyrene,
polyacrylamide and other latex materials may be employed for
fabricating the beads, but other plastic materials such as
polyvinyl chloride, polypropylene and the like may also be used.
Polystyrene is a preferred material. The microparticles include
unlabelled beads, beads with antibodies, fluorochromes or other
small molecules conjugated to the surface or beads with
fluorochromes embedded in the polymer.
[0325] The counting beads are used as reference population to
measure the exact volume of analyzed sample. The sample(s) are
analyzed on a flow cytometer and the amount of MHC-specific T-cell
is determined using e.g. a predefined gating strategy and then
correlating this number to the number of counted counting beads in
the same sample using the following equation:
Concentration of MHC-specific T-cell in sample=(number of
MHC-peptide specific T-cells counted/number of counting beads
counted).times.concentration of counting beads in sample
[0326] MHC multimers, gating reagents and/or counting beads can be
added to the sample simultaneously or one by one in any order and
with incubation and/or washes in between, before and/or after
addition of the various components. Alternatively the MHC
multimers, gating reagents and/or counting beads can be kept in a
container to which the sample may be added directly either during
colletion of sample (e.g. during blood collection) or immediate
prior to sample analysis. The container features a predetermined
quantity of MHC multimers, gating reagents and/or counting beads
and the reagents can be in suspension or alternatively embedded in
a solid or semisolid medium or matrix.
[0327] When embedded in a matrix the matrix is such that it retains
the reagents in the container when dry but releases the reagents
into the sample medium when a sample containing cells of interest
is added to the container. Preferably, the matrix dissolves in the
sample medium to effect release.
[0328] For this purpose, the matrix preferably comprises a
gelatinous, viscous, material, which may be liquid, semi-solid or
gel-like in consistency. Preferably, the matrix is a viscous
liquid.
[0329] The matrix may be substantially free of water, or it may
comprise water. Preferably (although appearing dry) the matrix
contains some water. Preferably less than 30% of the matrix is
water, such as less than 25%, for example less than 20%, such as
less than 15%, for example less than 10% and such as less than 5%.
The matrix may comprise liquid other than water, such as glycerol,
ethylene glycol, propylene glycol or others.
[0330] The matrix may preferably exist as a single contiguous mass,
or it may be attached to the container as a number of separate
pieces. Preferably it is contiguous. Preferably, however, the
matrix is such that during handling or storage no portion of the
matrix effectively detaches from the container to cause loss of
reagents.
[0331] In preferred various embodiments, therefore, the matrix is
water soluble, preferably readily soluble in aqueous media. In one
preferred embodiment, the matrix dissolves when a sample containing
the cells of interest is added into a container comprising the
matrix, or otherwise breaks up in such a manner as to release the
reagents into the sample medium. Preferably, all or substantially
all of the reagents are released into the sample medium such as at
least 75%, for example at least 85%, such as at least 90%, for
example at least 95%, such as at least 99%.
[0332] Preferably, the matrix should comprise a non-oxidising
(reducing) environment in order to avoid any unwanted
redox-reactions. Thus, where a carbohydrate matrix (see below) is
employed, the carbohydrates should be non-reducing. Furthermore the
matrix should preferably be composed such that is does not
crystallise, crack or change phase at any temperature that it may
be subjected to under normal transportation and/or storage.
[0333] It is preferable to use a matrix with low melting point to
avoid crystallization of the matrix. A high molecular weight is
preferable to reduce the osmotic effect on the sample
preparation.
[0334] In preferred embodiments, the matrix is based on a water
soluble sugar mixture. The matrix or embedding medium may comprise
one or more compounds including carbohydrates, polymers, small
proteins or others or any combination thereof.
[0335] Examples of suitable carbohydrates for use in a matrix
include, but are not limited to, saccharose, arabinose, ribulose,
fructose, sorbose, glucose, mannose, gulose, galactose, sucrose,
lactose, maltose, trehalose, raffinose and melizitose. Cellulose as
well as carboxylated or otherwise derivatised cellulose products
may also be employed.
[0336] Examples of suitable polymers for use in a matrix include
polyvinyalcohols, polyethylene glycols, polyethylene imines,
polyacryl amides, polyaziridines, glycols, polyacrylic acids,
esters or derivatives thereof. It should be clear, that block
co-polymers of the aforementioned could also be used.
[0337] Examples of small proteins include BSA other albumins or
protein fragments such as Byco A.
[0338] Mixtures of two or more of the above may also be used. The
components of the matrix may be present in any suitable proportion
consistent with the desirable properties outlined above.
Specifically, we disclose matrices comprising mixtures of
carbohydrates, for example, fructose, trehalose and raffinose.
Thus, the matrix may comprise any two of fructose, trehalose and
raffinose, preferably at a 2:1 ratio, a 1:1 ratio or a 1:2
ratio.
[0339] The matrix may comprise 2:1, 1:1 or 1:2 of fructose and
trehalose. One highly preferred advantageous embodiment is 3 mg of
a 1:1 mixture of fructose and trehalose. The amount of carbohydrate
has been determined as the maximum amount that still allows good
lysing of the sample.
[0340] The matrix may perform other functions, such as providing a
stable and inert medium for preserving the reagents during storage.
For this purpose, other components may also be included.
[0341] These may include any one or more of preservatives,
detergents, fixatives, antioxidants and pH-stabilizers. Examples of
preservatives include bronidix, sodium azide and thiomersal.
Examples of detergents include Tween, Triton, BRIJ.RTM.,
PLURONIC.RTM. and TETRONIC.RTM. as well as derivatives and mixtures
of the aforementioned. Examples of fixatives include vinylsulfone
and glutaraldehyde.
[0342] The matrix may comprise one or more antioxidants, which are
molecules that are radical scavengers. The radicals can e.g. be O-,
N- C- or S-radicals. In some embodiments, the matrix may comprise
scavengers for oxygen-derived radicals such as the superoxide anion
or the hydroxyl radical formed by atmospheric oxygen under
influence of light, heat or other environmental factors. Examples
of such radical scavengers are ascorbic acid, beta-carotene,
bilirubin, butylated hydroxytoluene (BHT), butylated hydroxyanisol
(BHA) tert-butylhydroquinone (TBHQ) d-alpha-tocopherol, trolox and
hydroxyanisol. Examples of pH-stabilizers include Good buffers,
HEPES, MES, phosphate, citrate.
[0343] Staining fluid cell samples with MHC multimers may be
combined with detecting of intracellular substances. The
intracellular substances include, but are not limited to, detection
of soluble factors like interleukins, hormones, proteins, peptides,
DNA, RNA or other intracellular structures. In principle the T-cell
is first labeled with MHC multimer, then fixated and the cell
membrane made permeable using methanol, detergent e.g. saponin,
digitonin, Leucoperm, Tween 20, triton, NP-40 or other agent able
to make the membrane permeable. Then the intracellular substance
can be detected using labeled antibody or other molecules capable
of binding the intracellular substance.
[0344] Example MHC multimer staining combined with detection of
intracellular substances is measurement of activation status of
antigen specific T-cells. Activation status of antigen specific
T-cells can e.g. be measured by detection of the TCR using MHC
multimer combined with measurement of up- or down-regulation of
intracellular molecules e.g. measurement of level of intracellular
interleukines or other soluble factors. The method comprises one or
more of the following steps: 1) MHC multimers and other marker
molecules recognising surface exposed proteins are added to T-cells
sample. Optionally the sample is washed. 2) An reagent able to
block extracellular secretion of cytokine is added, e.g. monensin
that interrupt intracellular transport processes leading to
accumulation of produced soluble factor, e.g. interleukine-2 in the
Golgi complex, 3) Fixation of cell membrane using mild fixator
followed by permeabilization of cell membrane by. e.g. saponine. 4)
Addition of labelled marker specific for the produced soluble
factor to be determined; the labbelled cell samples are analysed
using a flow cytometer.
[0345] An alternative to this procedure is to trap secreted soluble
factors on the surface of the secreting T-cell as described by
Manz, R. et al., Proc. Natl. Acad. Sci. USA 92:1921 (1995).
[0346] Detection of specific T-cells in a sample combined with
simultaneous detection of activation status of T-cells can also be
measured using marker molecules specific for up- or down-regulated
surface exposed receptors together with MHC multimers. The marker
molecule and MHC multimer can be labelled with the same label or
different labelling molecules and added to the sample
simultaneously or sequentially or separately.
Detection of Individual T-Cells in Fluid Samples Using
Microscopy
[0347] Another preferred method for detection of individual T-cells
in fluid samples is using microscopy. Microscopy comprises any type
of microscopy including optical, electron and scanning probe
microscopy, Bright field microscopy, Dark field microscopy, Phase
contrast microscopy, Differential interference contrast microscopy,
Fluorescence microscopy, Confocal laser scanning microscopy, X-ray
microscopy, Transmission electron microscopy, Scanning electron
microscopy, atomic force microscope, Scanning tunneling microscope
and photonic force microscope. This can be done as follows: A
suspension of T-cells are added MHC multimers, the sample washed
and then the amount of MHC multimer bound to each cell are
measured. Bound MHC multimers may be labelled directly or measured
through addition of labelled marker molecules. The sample is then
spread out on a slide or similar in a thin layer able to
distinguish individual cells and labelled cells identified using a
microscope. Depending on the type of label different types of
microscopes may be used, e.g. if fluorescent labels are used a
fluorescent microscope is used for the analysis. For example MHC
multimers can be labeled with a flourochrome or bound MHC multimer
detected with a fluorescent antibody. Cells with bound fluorescent
MHC multimers can then be visualized using e.g. an
immunofluorescence microscope or a confocal fluorescence
microscope.
Immunohistochemistry (IHC)
[0348] MHC multimers can also be used to directly detect T-cells in
solid samples for example solid tissue. In the present invention
solid tissue includes tissue, tissue biopsies, frozen tissue or
frozen tissue biopsies, paraffin embedded tissue or tissue biopsies
and sections of either of the above mentioned.
[0349] IHC is a method where MHC multimers can be used to directly
detect specific T-cells e.g. in sections of solid tissue. In a
preferred embodiment of the present invention sections of fixed or
frozen tissue sample are incubated with MHC multimer allowing MHC
multimer to bind specific T-cells in the tissue. The MHC multimer
may be labelled with a fluorochrome, chromophore, or any other
labelling molecule that can be detected. The labbeling of the MHC
multimer may be directly or through a second marker molecule. As an
example, the MHC multimer can be labelled with a tag that can be
recognized by e.g. a secondary antibody, optionally labelled with
HRP or another label. The bound MHC multimer is then detected by
its fluorescence or absorbance (for fluorophore or chromophore), or
by addition of an enzyme-labelled antibody directed against this
tag, or another component of the MHC multimer (e.g. one of the
protein chains, a label on the one or more multimerization domain).
The enzyme can e.g. be Horseradish Peroxidase (HRP) or Alkaline
Phosphatase (AP), both of which convert a colourless substrate into
a coloured reaction product in situ. This coloured deposit
identifies the binding site of the MHC multimer, and can be
visualized under e.g. a light microscope. The MHC multimer can also
be directly labelled with e.g. HRP or AP, and used in IHC without
an additional antibody.
[0350] A preferred embodiment for detection of T-cells in solid
tissue includes use of tissue embedded in paraffin, from which
tissue sections are made and fixed in formalin before staining.
Antibodies are standard reagents used for staining of
formalin-fixed tissue sections; these antibodies often recognize
linear epitopes. In contrast, most MHC multimers are expected to
recognize a conformational epitope on the TCR. In this case, the
native structure of TCR needs to be at least partly preserved in
the fixed tissue. Fixation of tissue therefore should be
gentle.
[0351] Another preferred embodiment and an alternative to stain
fixed tissue section is staining performed tissue sections from
frozen tissue blocks. In this type of staining fixation is done
after MHC multimer staining.
Immunofluorescence Microscopy
[0352] This is an alternative technical application to IHC where
MHC multimers can be used to identify specific T-cells in sections
of solid tissue. Instead of visualization of bound MHC multimer by
an enzymatic reaction, MHC multimers are labelled with a
flourochrome or bound MHC multimer are detected by a fluorescent
antibody. Cells with bound fluorescent MHC multimers can be
visualized in an immunofluorescence microscope or in a confocal
fluorescence microscope. This method can also be used for detection
of T-cells in fluid samples using the principles described for
detection of T-cells in fluid sample described elsewhere
herein.
Detection of T-Cells in Solid Tissue In Vivo
[0353] MHC multimers may also be used for detection of T-cells in
solid tissue in vivo. For in vivo detection of T-cells labeled MHC
multimers are injected in to the body of the individual to be
investigated. The MHC multimers may be labeled with e.g. a
paramagnetic isotope. Using a magnetic resonance imaging (MRI)
scanner or electron spin resonance (ESR) scanner MHC multimer
binding T-cells can then be measured and localized. In general, any
conventional method for diagnostic imaging visualization can be
utilized. Usually gamma and positron emitting radioisotopes are
used for camera and paramagnetic isotopes for MRI.
Detection of T-Cells Immobilized on Solid Support.
[0354] In a number of applications, it may be advantageous
immobilise the T-cell onto a solid or semi-solid support. Such
support may be any which is suited for immobilisation, separation
etc. Non-limiting examples include particles, beads, biodegradable
particles, sheets, gels, filters, membranes (e. g. nylon
membranes), fibres, capillaries, needles, microtitre strips, tubes,
plates or wells, combs, pipette tips, micro arrays, chips, slides,
or indeed any solid surface material. The solid or semi-solid
support may be labelled, if this is desired. The support may also
have scattering properties or sizes, which enable discrimination
among supports of the same nature, e.g. particles of different
sizes or scattering properties, colour or intensities.
[0355] An example of a method where MHC multimers can be used for
detection of immobilized T-cells is ELISA (Enzyme-Linked
Immunosorbent Assay). ELISA is a binding assay originally used for
detection of antibody-antigen interaction. Detection is based on an
enzymatic reaction, and commonly used enzymes are e.g. HRP and AP.
MHC multimers can be used in ELISA-based assays for analysis of
purified TCR's and T-cells immobilized in wells of a microtiter
plate. The bound MHC multimers can be labelled either by direct
chemical coupling of e.g. HRP or AP to the MHC multimer (e.g. the
one or more multimerization domain or the MHC proteins), or e.g. by
an HRP- or AP-coupled antibody or other marker molecule that binds
to the MHC multimer. Detection of the enzyme-label is then by
addition of a substrate (e.g. colourless) that is turned into a
detectable product (e.g. coloured) by the HRP or AP enzyme.
[0356] Conveniently the support may be made of e.g. glass, silica,
latex, plastic or any polymeric material. The support may also be
made from a biodegradable material. Generally speaking, the nature
of the support is not critical and a variety of materials may be
used. The surface of support may be hydrophobic or hydrophilic.
[0357] Preferred are materials presenting a high surface area for
binding of the T-cells. Such supports may be for example be porous
or particulate e.g. particles, beads, fibres, webs, sinters or
sieves. Particulate materials like particles and beads are
generally preferred due to their greater binding capacity.
Particularly polymeric beads and particles may be of interest.
[0358] Conveniently, a particulate support (e.g. beads or
particles) may be substantially spherical. The size of the
particulate support is not critical, but it may for example have a
diameter of at least 1 .mu.m and preferably at least 2 .mu.m, and
have a maximum diameter of preferably not more than 10 .mu.m and
more preferably not more than 6 .mu.m. For example, particulate
supports having diameters of 2.8 .mu.m and 4.5 .mu.m will work
well. An example of a particulate support is monodisperse
particles, i.e. such which are substantially uniform in size (e. g.
size having a diameter standard deviation of less than 5%). Such
have the advantage that they provide very uniform reproducibility
of reaction. Monodisperse particles, e.g. made of a polymeric
material, produced by the technique described in U.S. Pat. No.
4,336,173 (ref. 25) are especially suitable.
[0359] Non-magnetic polymer beads may also be applicable. Such are
available from a wide range of manufactures, e.g. Dynal Particles
AS, Qiagen, Amersham Biosciences, Serotec, Seradyne, Merck, Nippon
Paint, Chemagen, Promega, Prolabo, Polysciences, Agowa, and Bangs
Laboratories.
[0360] Another example of a suitable support is magnetic beads or
particles. The term "magnetic" as used everywhere herein is
intended to mean that the support is capable of having a magnetic
moment imparted to it when placed in a magnetic field, and thus is
displaceable under the action of that magnetic field. In other
words, a support comprising magnetic beads or particles may readily
be removed by magnetic aggregation, which provides a quick, simple
and efficient way of separating out the beads or particles from a
solution. Magnetic beads and particles may suitably be paramagnetic
or superparamagnetic. Superparamagnetic beads and particles are
e.g. described in EP 0 106 873 (Sintef, ref. 26). Magnetic beads
and particles are available from several manufacturers, e.g. Dynal
Biotech ASA (Oslo, Norway, previously Dynal AS, e.g.
DYNABEADS.RTM.).
[0361] The support may suitably have a functionalised surface.
Different types of functionalisation include making the surface of
the support positively or negatively charged, or hydrophilic or
hydrophobic. This applies in particular to beads and particles.
Various methods therefore are e.g. described in U.S. Pat. No.
4,336,173 (ref. 25), U.S. Pat. No. 4,459,378 (ref. 27) and U.S.
Pat. No. 4,654,267 (ref. 28).
[0362] Immobilized T-cells may be detected in several ways
including: [0363] Direct detection of T-cells directly immobilized
on solid support. [0364] T-cells may be directly immobilized on
solid support e.g. by non-specifically adhesion. Then MHC multimers
are added to the immobilized T-cells thereby allowing specific
T-cells to bind the MHC multimers. Bound MHC multimer may be
measured through label directly attached to the multimer or through
labeled marker molecules. Individual T-cells may be detected if the
method for analysis is able to distinguish individual labeled
cells, e.g. cells are immobilized in a monolayer on a cell culture
well or a glass slide. Following staining with labeled multimer a
digital picture is taken and labeled cells identified and counted.
Alternatively a population of T-cells is detected by measurement of
total signal from all labeled T-cells, e.g. cells are plated to
wells of a microtiter plate, stained with labeled MHC multimer and
total signal from each well are measured. [0365] Direct detection
of T-cells immobilized on solid support through linker molecule
[0366] T-cell can also be immobilized to solid support through a
linker molecule. The linker molecule can be an antibody specific
for the T-cell, the linker can be MHC multimer or the linker can be
any molecule able to bind the T-cells. In any case the linker may
be attached directly to the solid support, the linker may be
attached to the solid support through another linker or the linker
is embedded in a matrix, e.g. a sugar matrix. [0367] Then MHC
multimers are added to the immobilized T-cells thereby allowing
specific T-cells to bind the MHC multimers. Bound MHC multimer may
be measured through label directly attached to the multimer or
through labeled marker molecules. Individual T-cells may be
detected if the method for analysis is able to distinguish
individual labeled cells, e.g. a digital picture is taken and
labeled cells identified and counted. [0368] Alternatively a
population of T-cells is detected by measurement of total signal
from all labeled T-cells. [0369] Phenotyping T-cell sample using
MHC multimer beads. [0370] Different MHC multimers are immobilized
to different beads with different characteristics (e.g. different
size, different fluorescence's or different fluorescence
intensities) where each kind of bead has a specific type of MHC
multimer molecule immobilized. The immobilization may be direct or
through a linker molecule as described above. The amount of bound
T-cells to a specific populations of beads can be analyzed,
thereby, phenotyping the sample. The TCR on the T-cell is defined
by the bead to which it binds. [0371] Direct detection of T-cells
immobilized to solid support in a defined pattern. [0372] Different
MHC multimers are immobilized to a support to form a spatial array
in a defined pattern, where the position specifies the identity of
the MHC multimer immobilized at this position. The immobilization
may be direct or through a linker molecule as described above. Then
a suspension of labeled T-cells are added or passed over the array
of MHC multimers and specific T-cells will bind the immobilized MHC
multimer molecules. The label will thus be located at specific
regions of the array, which will allow identification of the MHC
multimers that bind the cells, and thus, allows the identification
of T-cells with recognition specificity for the immobilized MHC
multimers. Alternatively, the cells can be labelled after they have
been bound to the MHC multimers. The label can be specific for the
type of cell that is expected to bind the MHC multimer (e.g.
anti-CD4 for the labelling of T-helper cells in general, where some
of the T-helper cells can be specific for a Class II MHC complex),
or the label can stain cells in general (e.g. a label that binds
DNA). [0373] In this way T-cells bound to the defined areas of the
support are analyzed, thereby, phenotyping the sample. Each
individual T-cell is defined by the TCR it expose and depending on
these TCRs each entity will bind to different types of MHC multimer
molecules immobilized at defined positions on the solid
support.
MHC Multimers and Cell Sorting
[0374] In another preferred application of the present invention
MHC multimers can be used to isolate particular, TCR-specific
T-cells, either through the use of MHC multimers in flow cytometry
or through the use of MHC complexes or MHC multimers immobilized on
a solid surface, e.g. beads, immunotubes, microtiter plates.
Isolation of specific T-cells using MHC multimers and flow
cytometry are described elsewhere herein.
[0375] T-cells immobilized to solid support in either of the ways
described elsewhere herein can following washing be eluted from the
solid support and treated further. This is a method to sort out
specific T-cells from a population of different T-cells. Specific
T-cells can e.g. be isolated through the use of bead-based MHC
multimers. Bead-based MHC multimers are beads whereto monomer
MHC-peptide complexes or MHC multimers are immobilized either
directly or through a linker. After the cells have been isolated
they can be manipulated in many different ways. The isolated cells
can be activated (to differentiate or proliferate), they can
undergo induced apoptosis, or undesired cells of the isolated cell
population can be removed. Then, the manipulated cell population
can be re-introduced into the patient, or can be introduced into
another patient.
[0376] For some applications it can be a problem if the cell
intracellularizes the MHC multimer during e.g. flow cytometry. When
beads coated with MHC complexes are employed, the size of the bead
eliminates the intracellularization. This can be an advantage for
certain applications.
[0377] A typical cell sorting experiment, based on bead-based MHC
multimers, would comprise some of the steps of the general
procedure outlined in general terms in the following: [0378]
Acquire the sample, e.g. a cell sample from the bone marrow of a
cancer patient. [0379] Block the sample with a protein solution,
e.g. BSA or skim milk. [0380] Block the beads coated with MHC
complexes, with BSA or skim milk. [0381] Mix MHC-coated beads and
the cell sample, and incubate. [0382] Wash the beads with washing
buffer, to remove unbound cells and non-specifically bound cells.
[0383] Isolate the immobilized cells, by either cleavage of the
linker that connects MHC complex and bead; or alternatively,
release the cells by a change in pH, salt-concentration addition of
competitive binder or the like. Preferably, the cells are released
under conditions that do not disrupt the integrity of the cells.
[0384] Manipulate the isolated cells (induce apoptosis,
proliferation or differentiation)
[0385] Other solid supports than beads may be used for sorting out
specific T-cells and examples of such solid supports are given
elsewhere herein. However, the principles for binding, washing,
elution and further manipulation is the same as described for
bead-based sorting.
Microchip MHC Multimer Technology
[0386] A microarray of MHC multimers can be formed, by
immobilization of different MHC multimers or MHC complexes on solid
support, to form a spatial array where the position specifies the
identity of the MHC-peptide complex or specific empty MHC
immobilized at this position. When labelled cells are passed over
the microarray (e.g. blood cells stained with anti-CD8 antibody,
conjugated to APC), the cells carrying TCRs specific for MHC
multimers in the microarray will become immobilized. The label will
thus be located at specific regions of the microarray, which will
allow identification of the MHC multimers that bind the cells, and
thus, allows the identification of e.g. T-cells with recognition
specificity for the immobilized MHC multimers. Alternatively, the
cells can be labelled after they have been bound to the MHC
multimers. The label can be specific for the type of cell that is
expected to bind the MHC multimer (e.g. anti-CD4 for the labelling
of T-helper cells in general, where some of the T-helper cells can
be specific for a class 2 MHC complex), or the label can stain
cells in general (e.g. a label that binds DNA). Alternatively,
cytokine capture antibodies can be co-spotted together with MHC
multimers or MHC complexes on the solid support and the cytokine
secretion from bound antigen specific T-cells analyzed. This is
possible because T-cells are stimulated to secrete cytokines when
recognizing and binding specific MHC-peptide complexes.
[0387] The above-mentioned techniques are not restricted to the
analysis of T-cells and TCRs, but can in principle be applied to
any molecule or cell that binds a MHC-complex.
Indirect Detection of T-Cell Using MHC Multimer
[0388] T-cells in a sample may also be detected indirectly using
MHC multimers. In indirect detection, the number or activity of
T-cells are measured, by detection of events that are the result of
TCR-MHC-peptide complex interaction. Interaction between MHC
multimer and T-cell may stimulate the T-cell resulting in
activation of T-cells, in cell division and proliferation of T-cell
populations or alternatively result in inactivation of T-cells. All
these mechanism can be measured using detection methods able to
detect these events.
[0389] Example measurement of activation include measurement of
secretion of specific soluble factor e.g. cytokine that can be
measured using flow cytometry as described in the section with flow
cytometry, measurement of expression of activation markers e.g.
measurement of expression of CD27 and CD28 and/or other receptors
by e.g. flow cytometry and/or ELISA-like methods and measurement of
T-cell effector function e.g. CD8 T-cell cytotoxicity that can be
measured in cytotoxicity assays like chromium release assay's know
by persons skilled in the art.
[0390] Example measurement of proliferation include but is not
limited to measurement of mRNA, measurement of incorporation of
thymidine or incorporation of other molecules like
bromo-2'-deoxyuridine (BrdU).
[0391] Example measurements of inactivation of T-cells include but
is not limited to measurement of effect of blockade of specifc TCR
and measurement of apoptosis.
Labelling Molecules
[0392] Labelling molecules are molecules that can be detected in a
certain analysis, i.e. the labelling molecules provide a signal
detectable by the used method. The amount of labelling molecules
can be quantified.
[0393] Different principles of labelling and detection exist, based
on the specific property of the labelling molecule. Examples of
different types of labelling are emission of radioactive radiation
(radionuclide, isotopes), absorption of light (e.g. dyes,
chromophores), emission of light after excitation (fluorescence
from fluorochromes), NMR (nuclear magnetic resonance form
paramagnetic molecules) and reflection of light (scatter from e.g.
such as gold-, plastic- or glass-beads/particles of various sizes
and shapes). Alternatively, the labelling molecules can have an
enzymatic activity, by which they catalyze a reaction between
chemicals in the near environment of the labelling molecules,
producing a signal, which include production of light
(chemiluminescence), precipitation of chromophor dyes, or
precipitates that can be detected by an additional layer of
detection molecules. The enzymatic product can deposit at the
location of the enzyme or, in a cell based analysis system, react
with the membrane of the cell or diffuse into the cell to which it
is attached. Examples of labelling molecules and associated
detection principle are shown in table 2 below.
TABLE-US-00003 TABLE 2 Examples of labelling molecules and
associated detection principles. Labelling substance Effect
Assay-principle Fluorochromes emission of light having .sup.
Photometry, a specific spectra Microscopy, spectroscopy PMT,
photographic film, CCD's (Colour-Capture Device or Charge- coupled
device). Radionuclide irradiation, .alpha., or Scintillation
counting, .gamma..quadrature.rays GM-tube, photographic film,
excitation of phosphor-imager screen Enzyme; catalysis of
H.sub.2O.sub.2 .sup. Photometry, HRP, (horseradish reduction using
luminol Microscopy, peroxidase), as Oxygen acceptor, spectroscopy
PMT, peroxidases in resulting in oxidized photographic film, CCD's
general luminal + light (Colour-Capture catalysis of H.sub.2O.sub.2
Device or Charge- reduction using a coupled device), soluble dye,
or Secondary label linked molecule comprising a hapten, such as a
biotin antibody residue as Oxygen acceptor, resulting in
precipitation. The habten can be recognized by a detection
molecule. Particles; gold, Change of scatter, Microscopy,
cytometry, polystyrene beads, reflection and electron microscopy
pollen and other transparency of the PMT's, light detecting
particles associated entity devices, flowcytometry scatter AP
(Alkaline Catalyze a chemical .sup. Photometry, Phosphatase)
conversion of a non- Microscopy, detectable to a spectroscopy
precipitated detectable Secondary label linked molecule, such as a
dye antibody or a hapten Ionophores or Change in absorption .sup.
Photometry, Cytometry, chelating chemical and emission spectrums
spectroscopy compounds binding when binding. to specific ions, e.g.
Change in intensity Ca.sup.2+ Lanthanides Fluorescence .sup.
photometry, cytometry, Phosphorescence spectroscopy Paramagnetic
NMR (Nuclear magnetic resonance) DNA fluorescing Propidium iodide
.sup. Photometry, cytometry, stains Hoechst stain spectroscopy DAPI
AMC DraQ5 .TM. Acridine orange 7-AAD .sup. Photometry; is to be
understood as any method that can be applied to detect the
intensity, analyze the wavelength spectra, and or measure the
accumulation of light derived form a source emitting light of one
or multiple wavelength or spectra.
[0394] Labelling molecules can be used to label MHC multimers as
well as other reagents used together with MHC multimers, e.g.
antibodies, aptamers or other proteins or molecules able to bind
specific structures in another protein, or in sugar, DNA or other
molecules. In the following molecules able to bind a specific
structure in another molecule (protein, sugar, DNA etc.) are named
a marker or marker molecule.
[0395] MHC multimers and/or marker molecules can be used to
positively select the entities they bind or they can be used to
deselect or negatively select the entities they bind.
[0396] Labelling molecules can be attached to a given MHC multimer
or any other protein marker by covalent or non-covalent linkage as
described for attachment of MHC complexes to multimerisation
domains elsewhere herein. The attachment can be directly between
reactive groups in the labelling molecule and reactive groups in
the marker molecule or the attachment can be through a linker
connecting labelling molecule and marker, both as described
elsewhere herein. The linker can be covalently attached to the
labelling molecule and in that case the whole complex consisting of
linker and labelling molecule is regarded as one labelling
molecule. An example of such a molecule is the FLUORESCEIN.TM.
linker molecule shown in FIG. 14. Other types of linkers can be
covalently coupled to one or more labelling molecules such linkers
are described elsewhere herein and in patent application WO
2007/015168 A2 (Lohse (2007).
[0397] When labelling MHC multimers the label can be attached
directly to the multimer either to the MHC complex (heavy chain,
.beta.2m or peptide) or to the one or more multimerization
domain(s). MHC multimers can also be labelled indirectly by binding
one or more marker molecule carrying one or more labels.
[0398] A single labelling molecule on a marker does not always
generate sufficient signal intensity. The signal intensity can be
improved by assembling single label molecules into large
multi-labelling compounds, comprising two or more label molecule
residues. Generation of multi-label compounds can be achived by
covalent or non-covalent, association of labelling molecules with a
major structural molecule. Examples of such structures are
synthetic or natural polymers (e.g. dextramers), proteins (e.g.
streptavidin), or polymers as DNA or PNA. The labelling molecules
in a multi-labelling compound can all be of the same type or can be
a mixture of different labelling molecules.
[0399] Detection principles, such as those listed in Table 2, can
be applied to flow cytometry, stationary cytometry, and batch-based
analysis. Most batch-based approaches can use any of the labelling
substances depending on the purpose of the assay. Flow cytometry
primarily employs fluorescence, whereas stationary cytometry
primarily employs light absorption, e.g. dyes or chromophore
deposit from enzymatic activity. In the following section,
principles involving fluorescence detection will be exemplified for
flow cytometry, and principles involving chromophore detection will
be exemplified in the context of stationary cytometry. However, the
labelling molecules can be applied to any of the analyses described
in this invention.
[0400] In another aspect, the present invention relates to a MHC
molecule construct as defined above further comprising one or more
labelling compounds. A plurality of labelling compounds should
everywhere be interpreted as two or more labelling compounds which
can be the same or different.
[0401] In particular, one or more labelling compounds can be
attached to the one or more multimerization domain(s), or one or
more labelling compounds can be attached to one or more of the
binding entities, or one or more labelling compounds can be
attached to one or more of the MHC molecules, or one or more
labelling compounds can be attached to the one or more
multimerization domain(s) and/or one or more of the binding
entities and/or one or more of the MHC molecules, or one or more
labelling compounds can be attached to the peptide harboured by the
MHC molecule.
[0402] In some applications, it can be advantageous to apply
different MHC multimer constructs, either as a combination or in
individual steps. Such different MHC multimers can be differently
labelled (i. e. by labelling with different labelling compounds)
enabling visualisation of different target MHC recognising cells
individually. For example in one preferred embodiment each MHC
multimer binding MHC multimer is labeled with an individual
label.
[0403] Thus, if several different MHC multimers with different
labelling compounds are present, it is possible simultaneously to
identify more than one specific receptor, if each of the MHC
multimers present a different peptide.
[0404] In another preferred embodiment of the present invention the
different MHC multimers used in same application all have same
label enabling visualization of different target MHC recognizing
cells as a group. Alternatively groups of MHC multimers are labeled
with same label and other groups of MHC multimers in same
preparation are labeled with other labels. MHC multimers identified
by same label can be positively selected as a group or negatively
selected as a group.
[0405] In another preferred embodiment of the present invention
different MHC multimers specific for different TCRs are labeled
with same label thereby identifying subpopulations of MHC
expressing cells for which one or more is also positive for one or
more additional MHC multimers labeled with another label. For
example 6 different MHC multimers (A, B, C, D, E, F) are labeled
using 3 different labels (1, 2, 3) as follows: MHC multimer A, B
and E are labeled with label 1, MHC multimer C, D and E are labeled
with label 2 and MHC multimer B, C and F are labeled with label 3.
Thereby all 6 MHC multimers can be distinguished from each other by
one or more labels: MHC multimer A is labeled with label 1, MHC
multimer B is labeled with label 1 and 3, MHC multimer C is labeled
with label 2 and 3, MHC multimer D is labeled with label 2, MHC
multimer E is labeled with label 1 and 2 and MHC multimer F is
labeled with label 3.
[0406] Using this form for labeling few types of labeling molecules
may be used for labeling many different MHC multimers.
[0407] The above mentioned principles for labeling not only apply
to MHC multimers but are also usefull for other marker
molecules.
[0408] The labelling compound is preferably such which is directly
or indirectly detectable.
[0409] The labelling compound can be any labelling compound
suitable for directly or indirectly detection. By the term
"directly" is meant that the labelling compound can be detected per
se without the need for a secondary compound, i. e. is a "primary"
labelling compound. By the term "indirectly" is meant that the
labelling compound can be detected by using one or more "secondary"
compounds, i. e. the detection is performed by the detection of the
binding of the secondary compound (s) to the primary compound.
[0410] The labelling compound can further be attached via a
suitable linker. Linkers suitable for attachment to labelling
compounds are described elsewhere herein or would be readily known
by the person skilled in the art.
[0411] Examples of such suitable labelling compounds are
fluorescent labels, enzyme labels, radioisotopes, chemiluminescent
labels, bioluminescent labels, polymers, metal particles, haptens,
antibodies, and dyes.
[0412] The labelling compound can suitably be selected from
fluorescent labels such as 5-(and 6)-carboxy-FLUORESCEIN.TM., 5- or
6-carboxyFLUORESCEIN.TM., 6-(FLUORESCEIN.TM.)-5-(and 6)-carboxamido
hexanoic acid, FLUORESCEIN.TM. isothiocyanate (FITC), rhodamine,
tetramethylrhodamine, and dyes such as Cy2, Cy3, and CY5.TM.,
optionally substituted coumarin including AMCA, PerCP,
phycobiliproteins including R-phycoerythrin (RPE) and
allophycoerythrin (APC), Texas Red, Princeston Red, Green
fluorescent protein (GFP) and analogues thereof, and conjugates of
R-phycoerythrin or allophycoerythrin and e. g. CY5.TM. or Texas
Red, and inorganic fluorescent labels based on semiconductor
nanocrystals (like quantum dot and QDOT.RTM.Im nanocrystals), and
time-resolved fluorescent labels based on lanthanides like Eu3+ and
Sm3+, from haptens such as DNP, biotin, and digoxiginin, from
enzymatic labels such as horseradish peroxidase (HRP), alkaline
phosphatase (AP), beta-galactosidase (GAL), glucose-6-phosphate
dehydrogenase, beta-N-acetylglucosaminidase, R-glucuronidase,
invertase, Xanthine Oxidase, firefly luciferase and glucose oxidase
(GO), from luminiscence labels such as luminol, isoluminol,
acridinium esters, 1,2-dioxetanes and pyridopyridazines, and from
radioactivity labels such as incorporated isotopes of iodide,
cobalt, selenium, tritium, and phosphor.
[0413] Radioactive labels can in particular be interesting in
connection with labelling of the peptides harboured by the MHC
molecules.
Labeling Molecules of Particular Utility in Flow Cytometry
[0414] In flow cytometry the typical label is detected by its
fluorescence. Most often a positive detection is based on the
presents of light from a single fluorochrome, but in other
techniques the signal is detected by a shift in wavelength of
emitted light; as in FRET based techniques, where the exited
fluorochrome transfer its energy to an adjacent bound fluorochrome
that emits light, or when using Ca.sup.2+ chelating fluorescent
props, which change the emission (and absorption) spectra upon
binding to calcium.
[0415] Preferably labelling molecules employed in flow cytometry
are illustrated in Table 3a and 3b and described in the
following.
[0416] Simple fluorescent labels: [0417] Fluor dyes, Pacific
Blue.TM., Pacific Orange.TM., Cascade Yellow.TM., [0418] ALEXA
FLUOR.RTM. (AF); [0419] AF405, AF488, AF500, AF514, AF532, AF546,
AF555, AF568, AF594, AF610, AF633, AF635, AF647, AF680, AF700,
AF710, AF750, AF800 [0420] Quantum Dot based dyes, QDOT.RTM.
Nanocrystals (Invitrogen, MolecularProbs) [0421] QDOT.RTM.525,
QDOT.RTM.565, QDOT.RTM.585, QDOT.RTM.605, QDOT.RTM.655,
QDOT.RTM.705, QDOT.RTM.800 [0422] DyLight.TM. Dyes (Pierce) (DL);
[0423] DL549, DL649, DL680, DL800 [0424] FLUORESCEIN.TM. (Flu) or
any derivate of that, ex. FITC [0425] Cy-Dyes; [0426] Cy2, Cy3,
Cy3.5, CY5.TM., CY5.TM.5, Cy7 [0427] Fluorescent Proteins; [0428]
RPE, PerCp, APC [0429] Green fluorescent proteins; [0430] GFP and
GFP derived mutant proteins; BFP, CFP, YFP, DsRed, T1, Dimer2,
mRFP1, MBanana, mOrange, dTomato, tdTomato, mTangerine,
mStrawberry, mCherry [0431] Tandem dyes: [0432] RPE-CY5.TM.,
RPE-CY5.TM.5, RPE-Cy7, RPE-ALEXA FLUOR.RTM. tandem conjugates;
RPE-Alexa610, RPE-TxRed [0433] APC-Aleca600, APC-Alexa610,
APC-Alexa750, APC-CY5.TM., APC-CY5.TM. 0.5 [0434] Multi
fluorochrome assemblies; [0435] Multiple fluorochromes attached to
a polymer molecule, such as a peptide/protein, Dextran,
polysaccharide. [0436] Any combination of the fluorescent dyes
involving in generation of FRET (Fluorescence resonance energy
transfer) based techniques. [0437] Ionophors; ion chelating
fluorescent props [0438] Props that change wavelength when binding
a specific ion, such as Calcium [0439] Props that change intensity
when binding to a specific ion, such as Calcium [0440] Combinations
of fluorochromes on the same marker. Thus, the marker is not
identified by a single fluorochrome but by a code of identification
being a specific combination of fluorochromes, as well as inter
related ratio of intensities. Example: Antibody Ab1 and Ab2, are
conjugated to both FITC and BP but Ab1 have 1 FITC to 1 BP whereas
Ab2 have 2 FITC to 1 BP. Each antibody can then be identified
individually by the relative intensity of each fluorochrome. Any
such combinations of n fluorochromes with m different ratios can be
generated.
TABLE-US-00004 [0440] TABLE 3a Examples of preferable fluorochromes
Fluorophor/Fluorochrome Excitation nm Emission nm
2-(4'-maleimidylanilino)naphthalene-6- 322 417 sulfonic acid,
sodium salt 5-((((2-iodoacetyl)amino)ethyl)amino) 336 490
naphthalene-1-sulfonic acid Pyrene-1-butanoic acid 340 376 ALEXA
FLUOR .RTM. 350 (7-amino-6-sulfonic 346 442 acid-4-methyl
coumarin-3-acetic acid AMCA (7-amino-4-methyl coumarin-3- 353 442
acetic acid 7-hydroxy-4-methyl coumarin-3-acetic acid 360 455
Marina Blue (6,8-difluoro-7-hydroxy-4- 362 459 methyl
coumarin-3-acetic acid 7-dimethylamino-coumarin-4-acetic acid 370
459 Fluorescamin-N-butyl amine adduct 380 464
7-hydroxy-coumarine-3-carboxylic acid 386 448 CascadeBlue
(pyrene-trisulphonic acid 396 410 acetyl azide Cascade Yellow 409
558 Pacific Blue (6,8 difluoro-7-hydroxy 416 451
coumarin-3-carboxylic acid 7-diethylamino-coumarin-3-carboxylic
acid 420 468 N-(((4-azidobenzoyhamino)ethyl)- 4- 426 534
amino-3,6-disulfo-1,8-naphthalimide, dipotassium salt Alexa Fluor
430 434 539 3-perylenedodecanoic acid 440 448
8-hydroxypyrene-1,3,6-trisulfonic acid, 454 511 trisodium salt
12-(N-(7-nitrobenz-2-oxa-1,3-diazol-4- 467 536 yl)amino)dodecanoic
acid N,N'-dimethyl-N-(iodoacetyl)-N'-(7- 478 541
nitrobenz-2-oxa-1,3-diazol-4- yl)ethylenediamine Oregon Green 488
(difluoro carboxy 488 518 FLUORESCEIN .TM.)
5-iodoacetamidoFLUORESCEIN .TM. 492 515 propidium iodide-DNA adduct
493 636 Carboxy FLUORESCEIN .TM. 495 519
TABLE-US-00005 TABLE 3b Examples of preferable fluorochrome
families Fluorochrome family Example fluorochrome ALEXA AF
.RTM.350, AF405, AF430, AF488, AF500, AF514, FLUOR .RTM.(AF) AF532,
AF546, AF555, AF568, AF594, AF610, AF633, AF635, AF647, AF680,
AF700, AF710, AF750, AF800 Quantum Dot QDOT .RTM.525, QDOT
.RTM.565, QDOT .RTM.585, (QDOT .RTM.) QDOT .RTM.605, QDOT .RTM.655,
QDOT .RTM.705, based dyes QDOT .RTM.800 DyLight .TM. Dyes DL549,
DL649, DL680, DL800 (DL) Small fluorescing FITC, Pacific Blue .TM.,
Pacific Orange .TM., Cascade dyes Yellow .TM., Marina blue .TM.,
DSred, DSred-2, 7- AAD, TO-Pro-3, Cy-Dyes Cy2, Cy3, Cy3.5, CY5
.TM., CY5 .TM..5, Cy7 Phycobili Proteins: R-Phycoerythrin (RPE),
PerCP, Allophycocyanin (APC), B-Phycoerythrin, C-Phycocyanin
Fluorescent Proteins (E)GFP and GFP ((enhanced) green fluorescent
protein) derived mutant proteins; BFP,CFP, YFP, DsRed, T1, Dimer2,
mRFP1,MBanana, mOrange, dTomato, tdTomato, mTangerine, mStrawberry,
mCherry Tandem dyes with RPE-CY5 .TM., RPE-CY5 .TM..5, RPE-Cy7,
RPE- RPE ALEXA FLUOR .RTM. tandem conjugates; RPE- Alexa610,
RPE-TxRed Tandem dyes with APC-Aleca600, APC-Alexa 610, APC-Alexa
750, APC APC-CY5 .TM., APC-CY5 .TM..5 Calcium dyes Indo-1-Ca.sup.2+
Indo-2-Ca.sup.2+
[0441] Preferable Labeling Molecules Employed in Stationary
Cytometry and IHC [0442] Enzymatic labelling, as exemplified in
Table 4: [0443] Horseradish peroxidase; reduces peroxides
(H.sub.2O.sub.2), and the signal is generated by the Oxygen
acceptor when being oxidized. [0444] Precipitating dyes; Dyes that
when they are reduced they are soluble, and precipitate when
oxidized, generating a coloured deposit at the site of the
reaction. [0445] Precipitating agent, carrying a chemical residue,
a hapten, for second layer binding of marker molecules, for
amplification of the primary signal. [0446] Luminol reaction,
generating a light signal at the site of reaction. [0447] Other
enzymes, such as Alkaline Phosphatase, capable of converting a
chemical compound from a non-detectable molecule to a precipitated
detectable molecule, which can be coloured, or carries a hapten as
described above. [0448] Fluorescent labels, as exemplified in Table
3a and b; as those described for Flow cytometry are likewise
important for used in stationary cytometry, such as in fluorescent
microscopy.
TABLE-US-00006 [0448] TABLE 4 Example preferable labels for
stationary cytometry Enzyme substrate, Precipitate or Oxygen
acceptor Residue, hapten* for Chromogen/ secondary detection
Binding partner Label precipitating agent layer to hapten HRP
diaminobenzidine Coloured precipitate -- (DAB) HRP 3-amino-9-ethyl-
Coloured precipitate -- carbazole (AEC+) AP Fast red dye Red
precipitate -- HRP biotinyl tyramide Exposed Biotin Streptavidin,
residue avidin HRP FLUORESCEIN .TM. Exposed Anti-Fluorecein
tyramide FLUORESCEIN .TM. Antibody residue "Enzyme" Substrate that
when Primary label; being a Secondary label reacted precipitate
dye, in case the chemiluminescence's, primary label is or exposure
of a a hapten hapten
[0449] In another preferred embodiment the labelling of an antibody
is through linkage to a readily detectable enzyme, such as an
enzyme immunoassay (EIA). The enzyme which is bound to the antibody
will react with an appropriate substrate, preferably a chromogenic
substrate, in such a manner as to produce a chemical moiety that
can be detected, for example, by spectrophotometric, fluorimetric
or by visual means. Enzymes that can be used to detectably label
the antibody include, but are not limited to, malate dehydrogenase,
staphylococcal nuclease, delta-5-steroid isomerase, yeast alcohol
dehydrogenase, alpha-glycerophosphate, dehydrogenase, triose
phosphate isomerase, horseradish peroxidase, alkaline phosphatase,
asparaginase, glucose oxidase, beta-galactosidase, ribonuclease,
urease, catalase, glucose-6-phosphate dehydrogenase, glucoamylase
and acetylcholinesterase. The detection can be accomplished by
colorimetric methods that employ a chromogenic substrate for the
enzyme. Detection can also be accomplished by visual comparison of
the extent of enzymatic reaction of a substrate in comparison with
similarly prepared standards.
[0450] Detection can also be accomplished using any of a variety of
other immunoassays. For example, by radioactively labelling the
antibodies or antibody fragments known as radioimmunoassay (RIA).
The radioactive isotope can be detected by such means as the use of
a gamma counter or a scintillation counter or by
autoradiography.
[0451] It is also possible to label the antibody with a fluorescent
compound. When the fluorescently labelled antibody is exposed to
light of the proper wave length, its presence can then be detected
due to fluorescence. Among the most commonly used fluorescent
labelling compounds are FLUORESCEIN.TM. isothiocyanate, rhodamine,
phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde and
fluorescamine.
[0452] The antibody can also be detectably labelled using
fluorescence emitting metals such as .sup.152Eu, or others of the
lanthanide series. These metals can be attached to the antibody
using such metal chelating groups as diethylenetriaminepentacetic
acid (DTPA) or ethylenediaminetetraacetic acid (EDTA).
[0453] The antibody also can be detectably labelled by coupling it
to a chemiluminescent compound. The presence of the
chemiluminescent-tagged antibody is then determined by detecting
the presence of luminescence that arises during the course of a
chemical reaction. Examples of particularly useful chemiluminescent
labelling compounds are luminol, isoluminol, theromatic acridinium
ester, imidazole, acridinium salt and oxalate ester.
[0454] Likewise, a bioluminescent compound can be used to label the
antibody of the present invention. Bioluminescence is a type of
chemiluminescence found in biological systems in which a catalytic
protein increases the efficiency of the chemiluminescent reaction.
The presence of a bioluminescent protein is determined by detecting
the presence of luminescence. Important bioluminescent compounds
for purposes of labelling are luciferin, luciferase and
aequorin.
[0455] In one embodiment, the peptide P is a peptide disclosed in
U.S. 60/907,217, the text of which is hereby incorporated by
reference herein in its entirety.
[0456] In another preferred embodiment the MHC multimer(s) can be
labelled as described in WO/2007/015168, the text of which is
hereby incorporated by reference herein in its entirety. This
method for labelling of the MHC multimer is described in detail
below.
Linkers
[0457] The instant "linker" is a molecule that may help to join
other atoms, molecules, or functional groups together through
chemical bonds. For example, one of the instant linkers may be
conjugated to a protein as well as to another group such as a
fluorophore, joining those substances together through the
intervening chemical bonds in the linker.
[0458] In some embodiments of the invention, the "linker" comprises
a molecular entity derived from the reaction of at least one amine,
such as a diamine, and a di-carboxylic acid anhydride. In some
embodiments, the amine comprises no more than two ethyleneoxy
(CH.sub.2--CH.sub.2--O) units. For example, the instant "linker"
may comprise an alternating copolymer of such amine and
di-carboxylic acid anhyride-derived units. In some embodiments, the
amine comprises a structural formula with no more than two
methylene units in a row. For example, the amine may comprise a
structural formula such as:
NH.sub.2--CH.sub.2--CH.sub.2--O--CH.sub.2--CH.sub.2--O--CH.sub.2--CH.sub.-
2--NH.sub.2 or
NH.sub.2--CH.sub.2--CH.sub.2--O--CH.sub.2--CH.sub.2--O--CH.sub.2--CH.sub.-
2--O--CH.sub.2--CH.sub.2--NH.sub.2, or other structural formulas in
which a heteroatom is placed after every two methylene units.
[0459] In some embodiments of this invention, the "linker"
comprises at least one monomeric unit referred to herein as "L15."
In other embodiments, the instant "linker" comprises two or more
L15 units arranged in a linear or branched fashion.
[0460] For example, in some embodiments, the linker is a linear
polymer chain comprising two L15 units, called "L30" herein. In yet
other embodiments, the linker comprises a longer linear polymer
comprising several L15 units, and may be called, for example,
"L45," or "L60," "L90," or "L120," or "L300," and so forth herein,
depending on the number of L15 units the polymer chain comprises.
In some embodiments comprising more than one L15 unit, the L15
units may be connected covalently via one or more intervening
chemical bonds.
[0461] In some embodiments of this invention, L15 comprises the
unit shown below in Formula I.
##STR00001##
[0462] In Formula I, R.sub.1 and R.sub.2 may comprise either NH or
O, while R.sub.3 may comprise methyl, ethyl, propyl,
CH.sub.2--O--CH.sub.2, and (CH.sub.2--O--CH.sub.2).sub.2. Further,
when Formula I is conjugated to other groups, atoms, or molecules,
and, for instance, R.sub.1 and/or R.sub.2 is an oxygen, no more
than three consecutively repeating ethyleneoxy
(CH.sub.2--CH.sub.2--O) groups are present.
[0463] Thus, some of the L15 units according to this invention may
have the following molecular structures:
##STR00002##
[0464] Other possible L15 structures not shown above may be
envisioned based upon the choice of R-i, R.sub.2, and R.sub.3
groups.
[0465] In some embodiments, the instant linkers are comprised of a
linear polymer of L15 units in which each L15 unit has the same
molecular formula, for example, that of structural formula II. In
other embodiments, one or more L15 units may differ from the others
in the linker chain. For example, a linker may comprise several
units of formula II, and one or more units comprising one or more
different structures. Such a differing L15 unit may be useful in
attaching a particular atom, group, or molecule at a defined
location in the chain, for example. Because each unit may be added
iteratively to the growing linker chain, such as by solid phase
synthesis, a variety of mixed L15 polymers may be constructed
simply and in a controlled fashion.
[0466] In some embodiments, one or more of the heteroatom groups in
the linker comprises a further substituent. That substituent may
comprise a variety of atoms or functional groups such as a simple
hydrogen atom, a protecting group, or a conjugating group which
serves to attach the linker to a atom, group, or molecule. In some
embodiments, the substituent is a detectable label or another
linker. Attachment via the heteroatom groups to a further linker
forms a branched linker polymer.
Design and Synthesis of Linkers
[0467] The present invention also comprises novel methods of
synthesizing an L15 linker and linear polymers of the L15 linker in
high yield. According to this synthesis method, long linkers of,
for example, L120, L200, L300, or even longer, such as L600 or
L990, may be constructed by consecutive additions of L15 units or
portions of L15 units, for example, on solid phase. Alternatively,
long linkers may be formed by joining two intermediate length
linkers together. Linkers of L30 or larger synthesized according to
this method may comprise individual L15 units of the same or
different molecular structure.
[0468] L15 units according to this invention may be prepared by
contacting a protected amine with a di-carboxylic acid anhydride
and acetic anhydride, resulting in a cyclic imide terminal group,
which may then be opened once the linker reaches its desired
length, for instance by basic aqueous hydrolysis in dioxane using a
tertiary amine such as diisopropylethyl amine. A
3,9,12-trioxa-6,15-d iaza-5-oxo-pentadecanoic acid molecule has
been synthesized from 2,2'-(ethylenedioxy)bis(ethylamine) at about
87-91% yield (see Pieters et al., Bioorg. Med. Chem. Lett. 9: 161-6
(1999)). In contrast, the controlled methods of synthesizing L15
units according to the present invention may provide yields of 96%,
for example.
[0469] The synthesis may be carried out in solution. The amine may
be protected with (Boc).sub.2.theta., monomethoxytrityl (MMT),
benzyloxycarbonyl (Z), or fluorenylmethyloxycarbonyl (Fmoc), or
another suitable protecting group. In some embodiments, the amine
is 2,2'-(ethylenedioxy)bis(ethylamine). In some embodiments, the
amine is present in excess over the di-carboxylic acid anhydride
and acetic anhydride. The addition of the di-carboxylic acid
anhydride may be carried out at a wide range of temperature.
Suitable di-carboxylic acid anhydrides include those from
diglycolic acid, 1,5-dipentanoic acid, 1,4-dibutyric acid, 1,3
dipropanoic acid, and 3,6 dioxaoctane dioic acid, depending on the
desired R.sub.3 group. Subsequent addition of acetic anhydride may
force the product into the cyclic imide form in high yield. The
cyclic imide may be quantitatively opened if desired, for example,
in excess dioxane and di-isopropylethylamine (DIPEA). To initiate
the preparation of an L30 linker, the cyclic imide may be reacted
with another amine. Then, di-carboxylic acid anhydride and acetic
anhydride may be added and the resulting cyclic imide opened. In
some embodiments, the terminal cyclic imide on the linker may be
left unopened in order to serve as a reactive group for the
formation of other bonds such as to reactive groups or other
attachments.
[0470] For example, a 3,9,12-trioxa-6,15-diaza-b-oxo-pentadecanoic
acid-derived L15 monomer may be prepared by protecting one of the
two amine groups of 2,2'-(ethylenedioxy)bis(ethylamine) with
(Boc).sub.2O. After dissolving the mono-protected
2,2'-(ethylenedioxy)bis(ethylamine) in pyridine, diglycolic acid
and then acetic anhydride may be added at high temperature, such as
at about 100.degree. C., to form a cyclic L15 structure. Excess
2,2'-(ethylenedioxy)bis(ethylamine) reacts with the cyclic imide
terminal to form structure 3. To form an L30 linker, an additional
diglycolic acid may be added, and the cyclic terminal opened by
addition of 1,4 dioxane and diisopropylethylamine (DIPEA) in
aqueous solution.
[0471] In some embodiments of the invention in which one or both of
Ri and R.sub.2 are oxygens rather than amine groups, amino-aicohols
or di-alcohols may be substituted for the amine in the reactions
described above. Conditions may also be adjusted to account for the
different reactivities of alcohols and amines. For instance,
reactions may be run at higher temperatures when coupling with
alcohols rather than amines.
[0472] Using the instant methods, large batches, such as 100 g, of
protected L30 linkers may be prepared in pure form by an extractive
work-up using one-liter scale laboratory equipment. The examples
below provide a more detailed description of the synthesis of
exemplary molecules comprising L15 and L30 linkers according to
this invention.
[0473] The same synthetic principles apply to the preparation of
larger linker polymer chains used in some embodiments of this
invention. For example, linkers such as L45, L60, L90, L120, L150,
L200, L300, or even larger, for instance, comprising as many as 40
L15 units, may be prepared by repeating the steps described above
successively: first reacting the cyclic imide of the preceding L15
unit in the growing chain with excess amine, and adding acid
anhydride and then acetic anhydride to build on a further L15 unit.
Once the desired length is achieved, the terminal ring may be
opened. If desired, those successive steps may also be performed on
solid support, which may be convenient in preparing linkers longer
than L30 or L60, for example In fact, compounds of molecular
weights of 8 to 15 KDa may be prepared with the methods of the
present invention because successive synthetic steps are not
inhibited by the growing poly-L15 chains. This is quite unusual for
peptide chemistry.
[0474] Alternatively, to shorten the number of steps needed to
prepare longer linkers, intermediate length linkers such as L30,
for example, can be directly combined together or conjugated
indirectly through an intervening chemical group such as a reactive
group or a detectable label. For instance, a single chromatographic
purification step allows the preparation of high purity Boc-L30,
which may be readily oligomerized to prepare longer linkers such as
L300 at high purity. Even linkers such as L600 and longer such as
L1000 may be prepared by such methods, the only limitations being
the yield of each step and the amount of materials available.
Further, two long linkers may be joined along their chains to form
very long branched linkers comprising, for instance, as many as 10,
20, 40, or even 60 L15 units in total.
[0475] Because it is possible to control the synthesis conditions,
the present invention further comprises linkers and linker
derivatives comprising a homogeneous molecular and structural
formula. A homogeneous molecular formula means herein that the
molecular weight of the linker may be obtained via mass
spectrometry with less than 1% deviation from the expected
molecular weight based upon the synthesis protocol used, in some
embodiments less than 0.1% or even less than 0.01%. This is
possible even with very long linkers such as L300, L600, or L990. A
homogeneous structural formula means herein that the structural
composition of each L15 unit and its location within the linker
chain is controlled by the synthesis protocol used to prepare the
linker. In contrast, many PEG-based linkers comprise a mixture of
lengths and structural formulae. Thus, substances that comprise
those mixed linkers inherently are heterogeneous, regardless of the
purity or homogeneity of the molecules, groups, or atoms to which
the linkers were conjugated.
[0476] Many currently used linkers, such as certain nucleic acid or
nucleic acid analog-based linkers, carry a charge on each monomer
of the chain, for example, from a backbone phosphate or
phosphorothioate group. Such charges may cause those linkers to
aggregate with substances of opposite charge, including the walls
of a plate or vessel, or to attract unwanted metal ions, or to
precipitate in the presence of salts. In contrast, the instant
linkers may be designed such that they carry no charge, or only one
or a few charges at defined locations along the chain. Because one
may control the synthesis of the instant linkers, they may be
designed to place charges at only specific locations or to carry no
charges at all. This allows for a precise modulation of the
location and amount of charge in a given linker and linker
derivative and is a further method of avoiding unwanted aggregation
or tertiary interactions.
[0477] Nevertheless, for some embodiments, the instant linkers may
also be prepared using an uncontrolled polymerization reaction. For
example, a one-pot synthesis may be conducted based upon the
reaction steps above, such as by mixing a diamine in solution with
an excess of di-carboxylic anhydride. The synthesis may also be
terminated, for example, by adding a reagent that would form an end
group, such as an amino acid or fluorophore. Controlling the amount
of such a terminating reagent may help dictate the actual length
distribution of the mixture. Such methods may be useful, for
instance, when absolute length is unimportant, or to generate
linkers of a variety of different lengths at once. The products may
be fractionated by length, for instance by chromatography.
Linker Derivatives
[0478] Linkers of the present invention may be covalently bound to
another atom, group, or molecule to form a "linker derivative."
Linker derivatives may comprise only one linker conjugated to
another atom, group, or molecule, or may comprise multiple linkers
conjugated to more than one of the same atom, group, or molecule,
or conjugated to different atoms, groups, or molecules. The binding
of the atom, group, or molecule may occur at one or more free ends
of the linker, or along its length such as at one of its
heteroatoms. Examples of atoms, groups, or molecules that may be
conjugated to linkers to form linker derivatives include hydrogen
atoms, terminal groups such as protecting groups, methyl groups, or
acetyl groups. Other examples include heavy or radioactive
isotopes, leaving groups; fluorophores; chromophores; enzyme
substrates; antigens; antibodies; other proteins and peptides;
amino acids and amino acid analogs; nucleic acids and nucleic acid
analogs; components of a membrane or a solid support; and other
small or large molecules. Linkers according to this invention may
thus be conjugated to several atoms, groups, or molecules of the
same type, such as multiple fluorophores, or may be conjugated to
different types of groups or molecules, such as a PNA and a
fluorophore or a protein and a solid surface or an acetyl group and
an antibody. The covalent binding may be direct, with no
intervening bonds or atoms, or indirect, with one or more
intervening bonds or atoms. As used herein, any atom, group, or
molecule that is covalently attached to a linker, either directly
or indirectly, is "conjugated to" the linker. Hence, "linker
derivatives" include molecular entities referred to as
"conjugates." Atoms, groups, or molecules may also be
non-covalently attached to the instant linkers or linker
derivatives, for example, by adsorption on a surface,
intercalation, hybridization of complementary nucleic acids or
nucleic acid analogs, or other interactions.
[0479] Atoms, groups, or molecules may be conjugated at one end of
the linker, or the same or different atoms, groups, or molecules
may be placed at both ends. Alternatively, conjugated atoms,
groups, or molecules may be placed between two linkers, for
example, at a defined spacing that prevents unwanted interactions
between them. Hence, linker derivatives such as X-L, L-X, or X-L-X
or L-X-L may be prepared where X represents a directly or
indirectly conjugated atom, group, or molecule and L represents a
linker. Such linker derivatives can also include different atoms,
groups, or molecules, for example, X1-L-X2, or X1-L1-X2-L2 or
L1-X1-L2-X2. An atom, group, or molecule can also be conjugated,
for example, via one of the heteroatoms in the linker. In addition,
several linkers may be conjugated to one linker derivative to form
branched structures. Linkers conjugated to multiple atoms, groups,
or molecules such as color labels or radioactive isotopes are
advantageous, for example, in amplifying signals in detection
assays as an alternative to antibody-based amplification methods
and radioactivity.
Indirect Conjugation
[0480] A linker may be conjugated to another group, atom, or
molecule indirectly through a group that is more reactive with the
anticipated atom, group, or molecule than the linker itself. As
used herein, such groups are called "conjugating groups." In some
embodiments, the linkers are conjugated to carbodiimide-based
conjugating groups. Amino acids may also serve as conjugating
groups. For example, amino acids with amino side chains may be used
to conjugate, for example, fluorophores. The sulfhydryl of cysteine
is also useful as a conjugating group for forming disulfide
crosslinks to other substances. In some embodiments, the linkers
are conjugated to Lys(Cys), which is a C-terminal
lysine-carboxamide with a cysteine amino acid bound to the N of the
lysine side-chain, and which may serve as a conjugating group. The
juxtaposed amine and sulfhydryl groups of this cysteine moiety
unexpectedly provided significantly higher reactivity toward
dextran, for example, than carbodiimide conjugating groups. In some
embodiments, the linker is conjugated to amino groups such as to a
lysine amino acid in which the N is derivatized with
beta-alanine-N,N-diacetic acid. The lysine derivative can be
quantitatively converted into its cyclic N-2,6-Dioxo-morpholino
anhydride form. That form was highly amino reactive under weakly
basic aqueous conditions when compared to previously used amino
reactive groups such as NHS-esters.
[0481] Hence, it may also serve as a conjugating group. One of
ordinary skill in the art may readily envision other conjugating
groups that may be conjugated to the instant linkers in order to
assist in conjugating a variety of substances to the instant
linkers.
Detectable Labels
[0482] In some embodiments, one or more detectable labels are
conjugated to a linker. According to this invention, a "detectable
label" is any molecule or functional group that allows for the
detection of a biological or chemical characteristic or change in a
system, such as the presence of a target substance in the
sample.
[0483] Examples of detectable labels which may be used in the
invention include fluorophores, chromophores,
electrochemiluminescent labels, bioluminescent labels, polymers,
polymer particles, bead or other solid surfaces, gold or other
metal particles or heavy atoms, spin labels, radioisotopes, enzyme
substrates, haptens, antigens, Quantum Dots, aminohexyl, pyrene,
nucleic acids or nucleic acid analogs, or proteins, such as
receptors, peptide ligands or substrates, enzymes, and antibodies
(including antibody fragments).
[0484] Examples of polymer particles labels which may be used in
the invention include micro particles, beads, or latex particles of
polystyrene, PMMA or silica, which can be embedded with fluorescent
dyes, or polymer micelles or capsules which contain dyes, enzymes
or substrates. Examples of metal particles which may be used in the
invention include gold particles and coated gold particles, which
can be converted by silver stains. Examples of haptens that may be
conjugated in some embodiments are fluorophores, myc,
nitrotyrosine, biotin, avidin, streptavidin, 2,4-dinitrophenyl,
digoxigenin, bromodeoxy uridine, sulfonate, acetylaminoflurene,
mercury trintrophonol, and estradiol.
[0485] Examples of enzymes which may be used in the invention
comprise horse radish peroxidase (HRP), alkaline phosphatase (AP),
beta-galactosidase (GAL), glucose-6-phosphate dehydrogenase,
beta-N-acetylglucosaminidase, .beta.-glucuronidase, invertase,
Xanthine Oxidase, firefly luciferase and glucose oxidase (GO).
Examples of commonly used substrates for horse radish peroxidase
(HRP) include 3,3'-diaminobenzidine (DAB), diaminobenzidine with
nickel enhancement, 3-amino-9-ethylcarbazole (AEC), Benzidine
dihydrochloride (BDHC), Hanker-Yates reagent (HYR), Indophane blue
(IB), tetramethylbenzidine (TMB), 4-chloro-1-naphtol (CN),
alpha-naphtol pyronin (.alpha.-NP), o-dianisidine (OD),
5-bromo-4-chloro-3-indolylphosphate (BCIP), Nitro blue tetrazolium
(NBT), 2-(p-iodophenyl)-3-p-nitrophenyl-5-phenyl tetrazolium
chloride (INT), tetranitro blue tetrazolium (TNBT), .delta.-bromo
-chloro-S-indoxyl-beta-D-galactoside/ferro-ferricyanide (BCIG/FF).
Examples of commonly used substrates for Alkaline Phosphatase
include Naphthol-AS-B1-phosphate/fast red TR (NABP/FR),
Naphthol-AS-MX-phosphate/fast red TR (NAMP/FR),
Naphthol-AS-B1-phosphate/fast red TR (NABP/FR),
Naphthol-AS-MX-phosphate/fast red TR (NAMP/FR),
Naphthol-AS-B1-phosphate/new fuschin (NABP/NF), bromochloroindolyl
phosphate/nitroblue tetrazolium (BCIP/NBT), b-Bromo
-chloro-S-indolyl-beta-delta-galactopyranoside (BCIG).
[0486] Examples of luminescent labels which may be used in the
invention include luminol, isoluminol, acridinium esters,
1,2-dioxetanes and pyridopyridazines. Examples of
electrochemiluminescent labels include ruthenium derivatives.
Examples of radioactive labels which may be used in the invention
include radioactive isotopes of iodide, cobalt, selenium, hydrogen,
carbon, sulfur, and phosphorous.
[0487] Some "detectable labels" according to this invention
comprise "colour labels," in which the biological change or event
in the system may be assayed by the presence of a colour, or a
change in colour. Examples of "colour labels" are chromophores,
fluorophores, chemiluminescent compounds, electrochemiluminescent
labels, bioluminescent labels, and enzymes that catalyze a colour
change in a substrate.
[0488] "Fluorophores" as described herein are molecules that emit
detectable electro-magnetic radiation upon excitation with
electro-magnetic radiation at one or more wavelengths. A large
variety of fluorophores are known in the art and are developed by
chemists for use as detectable molecular labels and can be
conjugated to the linkers of the present invention. Examples
include FLUORESCEIN.TM. or its derivatives, such as
FLUORESCEIN.TM.-5-isothiocyanate (FITC), 5-(and
6)-carboxyFLUORESCEIN.TM., 5- or 6-carboxyFLUORESCEIN.TM.,
6-(FLUORESCEIN.TM.)-5-(and 6)-carboxamido hexanoic acid,
FLUORESCEIN.TM. isothiocyanate, rhodamine or its derivatives such
as tetramethylrhodamine and tetramethylrhodamine-5-(and
-6).about.isothiocyanate (TRITC). Other example fluorophores that
could be conjugated to the instant linkers include: coumarin dyes
such as (diethyl-amino)coumarin or
7-amino-4-methylcoumarin-3-acetic acid, succinimidyl ester (AMCA);
sulforhodamine 101 sulfonyl chloride (TexasRed.TM. or TexasRed.TM.
sulfonyl chloride; 5-(and-6)-carboxyrhodamine 101, succinimidyl
ester, also known as 5-(and-6)-carboxy-X-rhodamine, succinimidyl
ester (CXR); lissamine or lissamine derivatives such as lissamine
rhodamine B sulfonyl Chloride (LisR);
5-(and-6)-carboxyFLUORESCEIN.TM., succinimidyl ester (CFI);
FLUORESCEIN.TM.-5-isothiocyanate (FITC);
7-diethylaminocoumarin-3-carboxylic acid, succinimidyl ester
(DECCA); 5-(and-6)-carboxytetramethyl-rhodamine, succinimidyl ester
(CTMR); 7-hydroxycoumarin-3-carboxylic acid, succinimidyl ester
(HCCA); 6->FLUORESCEIN.TM.-5-(and-6)-carboxamidolhexanoic acid
(FCHA);
N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-3-indacenepropionic
acid, succinimidyl ester; also known as 5,7-dimethylBODIPY.TM.
propionic acid, succinimidyl ester (DMBP); "activated
FLUORESCEIN.TM. derivative" (FAP), available from Probes, Inc.;
eosin-5-isothiocyanate (EITC); erythrosin-5-isothiocyanate (ErlTC);
and Cascade.TM. Blue acetylazide (CBAA) (the O-acetylazide
derivative of 1-hydroxy-3,6,8-pyrene-trisulfonic acid). Yet other
potential fluorophores useful in this invention include fluorescent
proteins such as green fluorescent protein and its analogs or
derivatives, fluorescent amino acids such as tyrosine and
tryptophan and their analogs, fluorescent nucleosides, and other
fluorescent molecules such as Cy2, Cy3, Cy 3.5, CY5.TM., CY5.TM.5,
Cy 7, IR dyes, Dyomics dyes, phycoerythrine, Oregon green 488,
pacific blue, rhodamine green, and Alexa dyes. Yet other examples
of fluorescent labels which may be used in the invention include
and conjugates of R-phycoerythrin or allophycoerythrin, inorganic
fluorescent labels such as particles based on semiconductor
material like coated CdSe nanocrystallites.
[0489] A number of the fluorophores above, as well as others, are
available commercially, from companies such as Probes, Inc.
(Eugene, Oreg.), Pierce Chemical Co. (Rockford, Ill.), or
Sigma-Aldrich Co. (St. Louis, Mo.).
[0490] In some embodiments the detection unit may comprise from 1
up to 500 detectable label molecules. In some embodiments, the
detectable label is an enzyme, which may be conjugated to a
polymer, such that the number of enzyme molecules conjugated to
each polymer molecule is, for instance, 1 to 200, 2 to 50, or 2 to
25. In some embodiments, the detectable label is a gold particle, a
radioactive isotope, or a colour label, e.g. a low molecular weight
fluorophore, and the number of detectable labels conjugated to each
polymer molecule is, for instance, 1 to 500, or for instance, 2 to
200. In some embodiments, the detectable label is a protein
fluorophore and the number of detectable labels conjugated to each
polymer molecule is 1-50, 2-20. In some embodiments, the number of
detectable label molecules conjugated to each polymer is 1-200,
2-50, 2-25, or is 10-20, 5-10, or 1-5.
[0491] The detectable label can be detected by numerous methods,
including, for example, reflectance, transmittance, light scatter,
optical rotation, and fluorescence or combinations hereof in the
case of optical labels or by film, scintillation counting, or
phosphorimaging in the case of radioactive labels. See, e.g.,
Larsson, 1988, Immunocytochemistry: Theory and Practice, (CRC
Press, Boca Raton, Fla.); Methods in Molecular Biology, vol. 80
1998, John D. Pound (ed.) (Humana Press, Totowa, N.J.). In some
embodiments, more than one detectable label is employed.
Probes
[0492] Some linker derivatives according to this invention may be
comprise a conjugated "probe" which, as used herein, is a
functional group or molecule which monitors events or changes in a
system, for example, by binding, reacting with, or hybridizing to a
target substance in the system directly or indirectly. An example
of a probe is a nucleic acid or nucleic acid analog capable of
binding to or hybridizing with a particular target sequence. Other
examples include antibodies, such as primary or secondary
antibodies, antigens, enzyme substrates and protein ligands,
haptens, proteins, and peptides.
Antibodies
[0493] In some embodiments, the instant linker derivatives
comprise, for example, at least one polyclonal, monoclonal,
monospecific, polyspecific, humanized, single-chain, chimeric,
synthetic, recombinant, hybrid, mutated, and CDR-grafted
antibodies. Various techniques for producing antibodies and
preparing recombinant antibody molecules are known in the art and
have been described, see, e.g., Kohler and Milstein, (1975) Nature
256:495; Harlow and Lane, Antibodies: a Laboratory Manual, (1988)
(Cold Spring Harbor Press, Cold Spring Harbor, N.Y.). Antibodies
used in the invention may be derived from any mammal species, e.g.,
rat, mouse, goat, guinea pig, donkey, rabbit, horse, lama, camel,
or any avian species e.g., chicken, duck. The origin of the
antibody is defined by the genomic sequence irrespective of the
method of production.
[0494] The antibody may be of any isotype, e.g., IgG, IgM, IgA,
IgD, IgE or any subclass, e.g., IgGI, IgG2, IgG3, IgG4. The skilled
artisan will appreciate that antibodies produced recombinantly, or
by other means, for use in the invention include any antibody
fragment which can still bind antigen, e.g. an Fab, an F(ab).sub.2,
Fv, scFv. In certain embodiments, the antibody, including an
antibody fragment, may be recombinantly engineered to include a
hapten, e.g, a peptide. In certain embodiments the hapten may be a
myc tag. Inclusion of a hapten in an antibody or antibody fragment
facilitates subsequent binding of a binding agent, probe, or
label
[0495] Certain embodiments employ linker derivatives comprising a
primary antibody containing an antigen binding region. Some
embodiments employ linker derivatives comprising a secondary
antibody containing an antigen binding region which specifically
binds to a primary antibody, e.g., the constant region of the
primary antibody. In certain embodiments, the linker derivative is
further conjugated to a polymer. Some embodiments employ linker
derivatives comprising a tertiary antibody containing an antigen
binding region which specifically binds to the secondary antibody,
e.g., a constant region of the secondary antibody, or a hapten
linked to the secondary antibody or a polymer conjugated to the
secondary antibody. In certain embodiments, the tertiary antibody
is further conjugated to a polymer.
Nucleic Acids and Nucleic Acid Analogs
[0496] In some embodiments, the linker is conjugated to at least
one nucleic acid and/or nucleic acid analog. As used herein, a
"nucleic acid" refers to a nucleobase sequence comprising any
oligomer, polymer, or polymer segment, having a backbone formed
solely from RNA or DNA nucleosides and comprising only the bases
adenine (A), cytosine (C), guanine (G), thymine (T), and uracil
(U), wherein an oligomer means a sequence of two or more
nucleobases. Nucleic acids may also be referred to as nucleic
acids.
[0497] Non-natural bases may include, for example, purine-like and
pyrimidine-like molecules, such as those that may interact using
Watson-Crick-type, wobble, or Hoogsteen-type pairing interactions.
Examples include generally any nucleobase referred to elsewhere as
"non-natural" or as an "analog."
[0498] Examples include: halogen-substituted bases,
alkyl-substituted bases, hydroxy-substituted bases, and
thiol-substituted bases, as well as 5-propynyl-uracil,
2-thio-5-propynyl-uracil, 5-methylcytosine, isoguanine,
isocytosine, pseudoisocytosine, 4-thiouracil, 2-thiouracil and
2-thiothymine, inosine, 2-aminopurine, N9-(2-amino-6-chloropurine),
N9-(2,6-diaminopurine), hypoxanthine, N9-(7-deaza-guanine),
N9-(7-deaza-8-aza-guanine) and N8-(7-deaza-8-aza-adenine).
[0499] Yet other examples include bases in which one amino group
with a hydrogen is substituted with a halogen (small "h" below),
such as 2-amino-6-"h"-purines, 6-amino-2-"h"-purines,
6-oxo-2-"h"-purines, 2-oxo-4-"h"-pyrimidines, 2-oxo-6-"h"-purines,
4-oxo-2-"h"-pyrimidines. Those will form two hydrogen bond base
pairs with non-thiolated and thiolated bases; respectively, 2,4
dioxo and 4-oxo-2-thioxo pyrimidines, 2,4 dioxo and 2-oxo-4-thioxo
pyrimidines, 4-amino-2-oxo and 4-amino-2-thioxo pyrimidines,
6-oxo-2-amino and 6-thioxo-2-amino purines, 2-amino-4-oxo and
2-amino-4-thioxo pyrimidines, and 6-oxo-2-amino and
6-thioxo-2-amino purines.
[0500] These and other non-natural bases are described further
below and in the accompanying International Application entitled
"New Non-Natural Base Pairs."
[0501] In other examples, one or more of the H or CH.sub.3 are
independently substituted with a halogen such as Cl or F. In some
embodiments, the following types of base pairs are used: one or
more of Us:A, T:D, C:G, and P:Gs. In some embodiments, T:A and P:G
are used.
[0502] Nucleic acid analogs may also comprise monomer units in
which natural bases A, C, G, T, and U or non-natural bases are
connected to a non-natural backbone unit. Non-natural backbone
units include, for example, those with a backbone other than
ribose-phosphate or deoxyribose-phosphate. For example, in some
embodiments, one or more phosphate oxygens may be replaced by
another molecule, such as sulphur. In other embodiments, a
different sugar or a sugar analog may be used, for example, one in
which a sugar oxygen is replaced by hydrogen or an amine, or an
O-methyl. In yet other embodiments, nucleic acid analogs comprise
synthetic molecules that can bind to a nucleic acid or nucleic acid
analog. For example, a nucleic acid analog may be comprised of
peptide nucleic acids (PNAs), locked nucleic acids (LNAs), or any
derivatized form of a nucleic acid.
[0503] As used herein, "peptide nucleic acid" or "PNA" means any
oligomer or polymer comprising at least one or more PNA subunits
(residues), including, but not limited to, any of the oligomer or
polymer segments referred to or claimed as peptide nucleic acids in
U.S. Pat. Nos. 5,539,082, 5,527,675, 5,623,049, 5,714,331,
5,718,262, 5,736,336, 5,773,571, 5,766,855, 5,786,461, 5,837,459,
5,891,625, 5,972,610, 5,986,053, 6,107,470 6,201,103, 6,228,982 and
6,357,163; all of which are herein incorporated by reference.
[0504] The term PNA also applies to any oligomer or polymer segment
comprising one or more subunits of the nucleic acid mimics
described in the following publications: Lagriffoul et al.,
Bioorganic & Medicinal Chemistry Letters, 4: 1081-1082 (1994);
Petersen et al., Bioorganic & Medicinal Chemistry Letters, 6:
793-796 (1996); Diderichsen et al., Tett. Lett. 37: 475-478 (1996);
Fujii et al., Bioorg. Med. Chem. Lett. 7: 637-627 (1997); Jordan et
al., Bioorg. Med. Chem. Lett. 7: 687-690 (1997); Krotz et al.,
Tett. Lett. 36: 6941-6944 (1995); Lagriffoul et al., Bioorg. Med.
Chem. Lett. 4: 1081-1082 (1994); Diederichsen, U., Bioorganic &
Medicinal Chemistry Letters, 7: 1743-1746 (1997); Lowe et al., J.
Chem. Soc. Perkin Trans. 1, (1997) 1: 539-546; Lowe et al., J.
Chem. Soc. Perkin Trans. 11: 547-554 (1997); Lowe et al., J. Chem.
Soc. Perkin Trans. 1 1:5 55-560 (1997); Howarth et al., J. Org.
Chem. 62: 5441-5450 (1997); Altmann, K-H et al., Bioorganic &
Medicinal Chemistry Letters, 7/1119-1122 (1997); Diederichsen, U.,
Bioorganic & Med. Chem. Lett., 8: 165-168 (1998); Diederichsen
et al., Angew. Chem. Int. Ed., 37/302-305 (1998); Cantin et al.,
Tett. Lett., 38/4211-4214 (1997); Ciapetti et al., Tetrahedron, 53:
1167-1176 (1997); Lagriffoule et al., Chem. Eur. J., 3: 912-919
(1997); Kumar et al., Organic Letters 3(9): 1269-1272 (2001); and
the Peptide-Based Nucleic Acid Mimics (PENAMs) of Shah et al. as
disclosed in WO96/04000.
[0505] As used herein, the term "locked nucleic acid" or "LNA"
means an oligomer or polymer comprising at least one or more LNA
subunits. As used herein, the term "LNA subunit" means a
ribonucleotide containing a methylene bridge that connects the
2'-oxygen of the ribose with the 4'-carbon. See generally, Kurreck,
Eur. J. Biochem., 270:1628-44 (2003).
Linker Derivatives Comprising Fluorophores
[0506] In some embodiments, linkers may be conjugated to one or
more fluorophores. For example, two fluorophores may be conjugated
to form a fluorophore-linker-Lys(fluorophore)-linker-X derivative.
Similarly, one may prepare longer derivatives in which several
fluorophores are spaced in between linker units of the same or
varying lengths, such as in a
Fluorophore-[linker-Lys(fluorophore)]N-linker-X construct, in which
X is a conjugating group, or another atom, group, or molecule. In
some embodiments, two fluorophores are separated from each other by
at least four L15 units (L90) in order to ensure that the
fluorophores are separated beyond the Foerster Radius (typically
not more than 5 nm) such that quenching due to fluorescence
resonance energy transfer is minimized or eliminated. In some
embodiments, two fluorophores may be separated by four to ten L15
units (L90 to L150), while in others, by four to six L15 units (L90
to L120). In fact, in some embodiments, FLUORESCEIN.TM.s spaced by
at least four L15 units (L90) showed negligible quenching in
aqueous buffers, strongly indicating that the linker adopts an
extended structure in water. In contrast, polyethylene glycol
(PEG)-based spacers may adopt a collapsed, coiled structure in
water.
[0507] Because the linkers of the present invention may allow for
the separation of individual fluorophores such that quenching is
minimized, two or more different types of fluorophores may be
conjugated to one or more linkers to produce amplified or uniquely
coloured signals. For example, 2, 3, 4, or 5 fluorophore groups may
be conjugated to linkers, each spaced at least four L15 units
apart, for example, spaced between four and ten L15 units or four
and six L15 units apart. Some embodiments of this invention
comprise Rhodamine-L-Lys(FLUORESCEIN.TM.)-L-X in which L contains a
sufficient length to avoid quenching of the rhodamine and
FLUORESCEIN.TM. signals, for example, and in which X is another
atom, group, or molecule or a conjugating group. The optimal
spacing for a given fluorophore depends in part upon its size, but
may readily be determined by testing the intensity of the
fluorescent signal at various spacings, for example.
[0508] In some embodiments, a molecule such as a protein may be
conjugated to several linker derivatives which are each conjugated
to a detectable label such as a fluorophore. In conventional
protein fluorescence labelling methods without linkers or with
short linkers, the size of the conjugated protein determines how
far apart the attached fluorophores can be placed, and
consequently, primarily determines the fluorescence intensity. The
same principle applies to other molecules as well. In contrast,
embodiments of the present invention may relieve this size
constraint because the instant linkers can: (1) conjugate to
several fluorophores, (2) maintain an extended structure in
solution that minimizes unwanted interactions between the
individual fluorophores, and (3) conjugate to many types of
proteins and other molecules. Thus, in some embodiments, this
invention may greatly enhance the fluorescence intensity of a
molecule, and may eliminate the need for the extra steps commonly
employed to enhance a signal in a system. For example, attaching
multiple linker derivatives each comprising multiple fluorophores
to an antibody may allow for direct detection of minute quantities
of an antigen without the need for secondary antibody
signal-amplification procedures.
Linker Derivatives with Multiple Conjugated Substances
[0509] Some linker derivatives according to this invention include
different types of conjugated detectable labels. In some
embodiments, linkers are conjugated to two different detectable
labels in which one label serves to monitor a change or event in a
system by binding to or hybridizing with a target, while the other
serves to detect that binding event via a colour change,
radioactivity, or some other detectable signal. For example, a
fluorophore may be combined with a different type of colour label.
Derivatives such as DNP-linker-Lys(Fluorophore)-linker-X have been
prepared. DNP (dinitrophenol) may be recognized by an anti-DNP
antibody while the fluorescent emission provides a second type of
signal, thus providing two alternative labelling methods.
[0510] Further, embodiments of the present invention may comprise
other combinations of atoms, groups, or molecules such as a
detectable label and a solid surface, membrane, protein, or other
large molecule. Attachments may be covalent as well as
non-covalent. Embodiments with more than one type of conjugated
atom, group, or molecule are useful, for example, in
immunoprecipitation or ELIZA assays, in situ detection assays,
multi-layer assays, fluorescent micro-sphere assays, and capture
assays.
[0511] In some embodiments, linkers are conjugated to fluorophores
as well as to probes such as nucleic acids and nucleic acid
analogs. For example, a nucleic acid or nucleic acid analog may be
used to hybridize to a target sequence in a system, while the
fluorophore conjugated to the probe through the linker provides a
means to detect the hybridization. Such bifunctionally labelled
linker derivatives may be useful, for example, in in situ
hybridization assays such as FISH.
[0512] Other linker derivatives according to this invention
comprise multiple nucleic acid or nucleic acid analog conjugates,
optionally further conjugated with other types of detectable
labels. For example, a single linker derivative molecule may
comprise several different nucleic acid or nucleic acid analogs,
each separated from the others by stretches of one or more L15
units. In some embodiments, the different nucleic acid or nucleic
acid analogs are separated from each other by spacings of L120 to
L300, L150 to L300, or L300.
[0513] In some embodiments, linkers are conjugated to fluorophores
or other colour-based labels as well as to PNA or LNA probes.
PNA-containing linker derivatives made according to the present
invention include, for example, X-L-PNA-L-Lys(Cys) comprising
linker derivatives, in which X may be an end-group such as acetyl,
a conjugating group, or a colour label such as a fluorophore or
enzyme substrate such as DNP. Attachment of a fluorophore such as
FLUORESCEIN.TM. may allow simpler purification and analysis of the
derivative. A spacing of L30 or larger between the X group and a
PNA or oligonucleotide is generally a sufficient distance to avoid
steric hindrance between the linker and the hybridization target,
however longer spacing may be used, for example to increase entropy
to further minimize unwanted tertiary interactions or aggregation.
For instance, the distance between the PNA or oligonucleotide and a
Lys(Cys) group may be, for example, up to L300, including from L120
to L300 or from L150 to L300. Spacing between the PNA and other
conjugates may be, for example, from L120 to L300, from L150 to
L300, or L300. Other exemplary PNA-comprising linker derivatives
according to the invention also include multiple fluorophore or
colour label attachments. For example, the derivative
[Flu-L60).sub.2Lys-].sub.2Lys-L30-PNA was prepared and contains
four FLUORESCEIN.TM. linker derivatives (Flu). In other
embodiments, a linear linker derivative may be prepared, conjugated
to PNA and multiple fluorophores. The embodiment
Lys(Flu)-L30-PNA-L30-Lys(Flu)-L90-Lys(Flu)-L90-Lys(Flu) was also
prepared and similarly contains four FLUORESCEIN.TM.s. While
fluorophores conjugated to the same linker derivative can be more
likely to aggregate in solution than fluorophores conjugated to
different linker derivatives, surprisingly, linker derivatives
comprising a PNA probe and several fluorophores spaced by L90
linkers not only gave enhanced signals over others containing
single fluorophores, but also showed a reduced background,
indicating that the high entropy due to the flexible, extended
structure of each L90 linker more than compensated for any
increased tendency for the fluorophores to interact. In some
embodiments, the linker derivatives may also form branched
structures or may specifically hybridize with each other via the
conjugated PNAs so as to amplify the signal.
Cross-Linking Agents
[0514] The linkers of the present invention may also be used as
protein cross-linkers. For example, the instant linkers may be
conjugated with a protein conjugating group such as malemide,
and/or with an antigen, ligand, or substrate for a particular
protein or antibody, and optionally also with a detectable label in
order to visualize the cross-link. For instance, malemide-linker-X
groups have been prepared, in which X represents a reactive group
such as Lys(betaalanine-N.sub.1N diacetic acid), or a specific
ligand, antigen, or substrate of the protein of interest. Such a
linker can be used, for example, to bind to a specific protein or
antibody via the X group, and to cross link to other proteins in
the vicinity of that specific protein via the malemide-linker. A
detectable label may also be conjugated to the linker derivative to
aid in detecting the cross-link. Even relatively short linker
segments such as L30 between a label and a protein ligand may allow
for detection of the label without significant interference from
quenching of a fluorescent label, for example.
[0515] The extended, flexible structure of some of the instant
linkers allows them to assist in the cross-linking of even two
large molecules, such as a fluorescent protein (for example, RPE or
green fluorescent protein) and an antibody. For example, long
linkers according to the present invention may have lengths in
solution of, for instance, 9 nm in the case of L90, or even 30 nm
in the case of L300, or even longer. That length provides
significant freedom for even very large proteins within a
cross-linked complex to adopt their preferred orientations
independently of others within the complex. Thus, the instant
linkers allow for more accurate identification of interacting
proteins because the complex is minimally perturbed by the presence
of the linker.
Surface or Polymer Conjugation
[0516] In some embodiments, the instant linkers may serve to
covalently or non-covalently attach a detectable label or other
atom, group, or molecule to a polymer or a surface such as dextran
or a membrane or an array or a plate. The instant linkers take up
little space in the longitudinal direction. Hence, they may be
useful in coating such surfaces at high density because they can
access relatively narrow spaces or pores in such surfaces. Further,
long linkers may be employed in order to maximize the distance
between the surface and other components of the system, such that
the system is minimally perturbed. For example, linker derivatives
can be prepared for conjugation to dextran in conjunction with
nucleic acids or nucleic acid analogs such as PNA as well as colour
labels such as HRP and one or more fluorophores. Other linker
derivatives can be prepared for conjugation to combinations of
dextran, PNA, and antibodies. Linker derivatives with multiple
conjugated atoms, groups, or molecules may be used to amplify
signals in a variety of ways. For example, minute quantities of
antibodies or antigens may be detected by attaching the antibody or
antigen to a linker derivative comprising multiple fluorophores.
Further, two potentially cross-reactive antigens may be
distinguished by attaching the antigens to linker derivatives
comprising different types of fluorophores. Multi-layer systems may
also be constructed in which certain interacting atoms, groups, or
molecules such as complementary nucleic acids or nucleic acid
analogs or a protein and a ligand are placed in between another
detectable label such as a colour label and a surface or
molecule.
Enhancing the Solubility of Conjugated Substances
[0517] Another surprising feature of some of the instant linkers is
a relatively high solubility despite the presence of relatively few
polar or charged groups. Hence, linkers, for example, those
comprising two or more L15 units in some derivatives, or four or
more L15 units in other derivatives, can also be employed to
enhance the solubility of an atom, group, or molecule in aqueous
solution. For example, an acetyl-L-X group may be used to enhance
the solubility of the atom, group, or molecule X. Surprisingly, PNA
probes with multiple fluorophores spaced via at least four L15
units showed higher water solubility, as well as less aggregation
and less non-specific binding, than those without conjugated
linkers and with only one fluorophore. Further, poly-linker
derivatives of the present invention conjugated to even 50 to 100
bases of PNA as well as to fluorophores did not aggregate and
showed high water solubility.
Other Exemplary Uses of Linker Derivatives
[0518] In yet other embodiments, the instant linkers may be
conjugated to a drug compound, for instance, to increase its
retention, solubility, or to effectively link it to another group
so as to target it to a particular area of the body. For example,
in some embodiments, at least one linker of homogeneous molecular
and structural formula is conjugated to at least one drug
compound.
[0519] The instant linkers are also useful in a variety of
biological and chemical assays. For instance, in capture assays,
steric barriers may be relieved by in effect lifting a probe from a
surface so that it is free in solution to recognize its target. If
the rate of binding between the probe and target is slow relative
to the rate of diffusion, a shorter linker length may be employed.
However, when the rate of binding is rapid compared to the rate of
diffusion in the system, a long linker may be advantageous. Because
the instant linkers may be prepared at precise short or long
lengths, as well as in mixtures of different lengths, depending on
the synthesis method used, the instant linkers provide a uniform
system around which such assays may be designed.
MHC I and MHC II Heavy and Light Chain Sequences
[0520] This is examples of amino acid sequences of full length and
truncated MHC I and MHC II heavy and light chains:
TABLE-US-00007 Example MHC I heavy chain, HLA-A*0201, full length
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAP
WIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYG
CDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAA
HVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEAT
LRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVP
SGQEQRYTCHVQHEGLPKPLTLRWEPSSQPTIPIVGIIAGLVLFGAVITG
AVVAAVMWRRKSSDRKGGSYSQAASSDSAQGSDVSLTACKV Example MHC I heavy
chain, HLA-A*0201, truncated (-transmembrane and cytoplasnic
domain) GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAP
WIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYG
CDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAA
HVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEAT
LRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVP
SGQEQRYTCHVQHEGLPKPLTLRWE Example MHC I light chain, .beta.2m, full
length MSRSVALAVLALLSLSGLEGIQRTPKIQVYSRHPAENGKSNFLNCYVSGF
HQSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYAC
RVNHVTLSQPKIVKWDRDM Example MHC II .alpha.-chain, DRA*0101, full
length IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGR
FASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELR
EPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHY
LPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDAPSPLPETTENVVCALGLT
VGLVGIIIGTIFIIKGVRKSNAAERRGPL Example MHC II .alpha.-chain,
DRA*0101, truncated (-transmembrane and cytoplasmic domain)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGR
FASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELR
EPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHY
LPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDAPSPLPETTE Example MHC II
.beta.-chain, HLA-DRB1*0401, full length
GDTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAV
TELGRPDAEYWNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVT
VYPAKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKTGVVSTGLIQN
GDWTFQTLVMLETVPRSGEVYTCQVEHPSLTSPLTVEWRARSESAQSKML
SGVGGFVLGLLFLGAGLFIYFRNQKGHSGLQPTGFLS Example MHC II .beta.-chain,
HLA-DRB1*0401, truncated (-transmembrane and cytoplasnic domain)
GDTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAV
TELGRPDAEYWNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVT
VYPAKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKTGVVSTGLIQN
GDWTFQTLVMLETVPRSGEVYTCQVEHPSLTSPLTVEWRARSESAQSKM
[0521] The polypeptides a and b can include various polypeptide
variants. Variant a and/or b polypeptides can include a and/or b
polypeptides containing amino acid insertions, deletions or
substitutions, as well as chemical modifications.
[0522] Amino acid substitutions can include conservative and
non-conservative amino acid substitutions. Conservative amino acid
substitutions replace an amino acid with an amino acid of the same
class, whereas non-conservative amino acid substitutions replace an
amino acid with an amino acid of a different class.
Non-conservative substitutions result in a change in the
hydrophobicity of the polypeptide or in the bulk of a residue side
chain. In addition, non-conservative substitutions can make a
substantial change in the charge of the polypeptide, such as
reducing electropositive charges or introducing electronegative
charges. Examples of non-conservative substitutions include a basic
amino acid for a non-polar amino acid, or a polar amino acid for an
acidic amino acid. Amino acid insertions, deletions and
substitutions can be made using random mutagenesis, site-directed
mutagenesis, or other recombinant techniques known in the art.
[0523] Variant a and/or b polypeptides can also be evaluated based
on a predetermined number of conservative amino acid substitutions,
as defined herein below. Conservative amino acid substitution as
used herein relates to the substitution of one amino acid (within a
predetermined group of amino acids) for another amino acid (within
the same group), wherein the amino acids exhibit similar or
substantially similar characteristics.
[0524] Within the meaning of the term "conservative amino acid
substitution" as applied herein, one amino acid may be substituted
for another within the groups of amino acids indicated herein
below: [0525] i) Amino acids having polar side chains (Asp, Glu,
Lys, Arg, His, Asn, Gin, Ser, Thr, Tyr, and Cys,) [0526] ii) Amino
acids having non-polar side chains (Gly, Ala, Val, Leu, Ile, Phe,
Trp, Pro, and Met) [0527] iii) Amino acids having aliphatic side
chains (Gly, Ala Val, Leu, Ile) [0528] iv) Amino acids having
cyclic side chains (Phe, Tyr, Trp, His, Pro) [0529] v) Amino acids
having aromatic side chains (Phe, Tyr, Trp) [0530] vi) Amino acids
having acidic side chains (Asp, Glu) [0531] vii) Amino acids having
basic side chains (Lys, Arg, His) [0532] viii) Amino acids having
amide side chains (Asn, Gin) [0533] ix) Amino acids having hydroxy
side chains (Ser, Thr) [0534] x) Amino acids having
sulphor-containing side chains (Cys, Met), [0535] xi) Neutral,
weakly hydrophobic amino acids (Pro, Ala, Gly, Ser, Thr) [0536]
xii) Hydrophilic, acidic amino acids (Gln, Asn, Glu, Asp), and
[0537] xiii) Hydrophobic amino acids (Leu, Ile, Val)
[0538] Accordingly, a variant polypeptide, or a fragment thereof
according to the present invention, can comprise, within the same
variant of the sequence or fragments thereof, or among different
variants of the sequence or fragments thereof, at least one
substitution, such as a plurality of substitutions introduced
independently of one another.
[0539] It is clear from the above outline that the same variant or
fragment thereof can comprise more than one conservative amino acid
substitution from more than one group of conservative amino acids
as defined herein above.
Positive Control Experiments for the Use of MHC Multimers
[0540] When performing analysis of samples with MHC multimers using
e.g. flow cytometry or other technologies/methods, it is important
to include appropriate positive and negative controls. In addition
to establishing proper conditions for the experiments, positive and
negative control reagents can also be used to evaluate the quality
(e.g. specificity and affinity) and stability (e.g. shelf life) of
produced MHC multimers.
[0541] Positive control experiments may be performed as a control
before analysis of a given sample, simultaneously with analysis of
sample and/or after analysis of sample. The positive control
experiment may be a control of the MHC multimer reagent itself, a
control of the sample analysed or a control of the analysis method
used.
Evaluating MHC Multimer Reagent
[0542] One preferred positive control experiment of the present
invention includes analysis of the, quality, performance,
specificity, stability and integrity of MHC multimer reagents.
Principles and methods for performing this kind of experiments
include but are not limited to: [0543] Evaluation of MHC multimers
ability to bind TCR. The quality of MHC multimer reagents can be
evaluated by analysis of the ability of the MHC multimer reagent to
bind specific TCR. The TCR have to be specific for one or more
MHC-peptide complexes of the multimer and preferable not able to
recognise other MHC-peptide complexes consisting of different MHC
alleles and/or different peptide in the peptide binding cleft.
However TCR's specific for more than one MHC-peptide complex can
also be used. [0544] In one preferred positive control experiment
of the present invention MHC multimer binding to TCR's displayed on
the surface of cells are analysed. In such experiments the positive
control reagent is TCR expressing cells. That includes measurement
of specific MHC multimer binding to specific cell lines (e.g.
T-cell lines) displaying displaying TCRs with appropriate
specificity and affinity for the MHC multimer in question. Example
usefull cell lines are natural T-cell lines, T-cell hybridomas,
cells transfected/transformed with genes encoding specific TCR e.g.
transfected mammalian cells, yeasT-cells, insecT-cells and
bacterial cells and cell like structures displaying TCR including
but not limited to liposomes and micelles. [0545] Another positive
control experiment of the present invention using TCR displayed on
cell surface includes measurement of specific MHC multimer binding
to cells in blood samples, preparations of purified lymphocytes
(HPBMCs) as described elsewhere herein, CSF samples, samples of
lymph, synovial fluid, semen, sputum or other bodily fluids that
contain cells carrying TCR molecules specific for the MHC multimer
in question. [0546] Alternatively MHC multimer binding to
immobilized specific T-cells can be measured e.g. measurement of
MHC multimer binding to T-cells in solid tissue, in sections of
solid tissue, in tissue or in organs inside body and to TCR
expressing cells immobilised on solid support as described
elsewhere herein. [0547] In another positive control experiment of
the present invention MHC multimer binding to TCR's immobilised on
solid support are measured. In such experiments the positive
control reagent is immobilized TCR or TCR in solution that later
are immobilized on solid support. The TCR can be full-length (i.g.
comprise the intracellular- and intra-membrane domains), or can be
truncated (e.g. only comprise the extracellular domains or subunits
of extracellular domains). The TCR may be natural in sequence e.g.
identical in sequence to one or more naturally occurring TCR's, may
be mutated in one or more positions or insertions/deletions of
amino acids can be introduce. Likewise, the TCR can be chemically
or enzymatically modified on one or more amino acids. The TCR may
also be fused with one or more proteins or other molecules. Fusion
with another protein can be made by genetically fusion of the gene
encoding that protein with genes encoding one or both polypeptide
chains of the TCR or encoding part of either chain. An example is
fusion of genes encoding antibody or fragment of antibody e.g. the
constant part with genes encoding TCR. [0548] Protein or other
molecules like carbohydrates, small organic molecules, DNA, RNA,
PNA, lipids, polymers, metals can also be attached to the TCR by
covalent or non-covalent interaction as described for
multimerisation domains elsewhere herein. [0549] The TCR's can be
generated by elution from T-cells or other TCR expressing cells,
generated by recombinant methods known by persons skilled in the
art, by in vitro translation of mRNA obtained from cells expressing
expressing TCR or by chemically synthesis. [0550] Usefull solid
supports for immobilisation of TCR include beads, particles,
biodegradable particles, sheets, gels, filters, membranes (e. g.
nylon membranes), fibres, capillaries, needles, microtitre strips,
tubes, plates or wells, combs, pipette tips, micro arrays, chips,
slides, any other solid support as described elsewhere herein or
indeed any solid surface material. [0551] TCR's can be attached to
the solid support by covalent or non-covalent interaction as
described elsewhere herein for attachment of MHC complexes to solid
support or other multimerization domains. [0552] MHC multimer
binding to TCR or T-cell can be determined directly using labbeled
MHC multimer or a secondary labelling molecule specific for the MHC
multimer or by measurement of effect of binding MHC multimer as
described elsewhere herein. [0553] Alternatively MHC multimer are
first bound to TCR/T-cell, then eluted and subsequently detected
through labelling molecule(s), secondary marker molecules with
labels, by activity of eluted product or by determination of amount
of eluted MHC multimer e.g. determination of protein concentration,
measurement of amount of label (flourecense intensity, enzymatic
activity, ect.) or amount of multimerisation domain (e.g. counting
of cells if multimerisation domain is a cell ect.). [0554] Another
example includes measurement of functional MHC in an assay where
the total protein concentration is measured before functional MHC
is captured, by binding to e.g. immobilized TCR. Then non-binding
MHC is removed by e.g. removing supernatant and concentration of
non-bound protein are measured. If the dissociation constant for
the interaction is known, the amount of total and the amount of
non-bound protein can be determined. From these numbers, the
fraction of functional MHC complex can be determined. [0555]
Usefull methods and principles for measurement of MHC multimer
binding to T-cell and/or TCR are described in the section
"Technical applications for use of MHC multimers" [0556] Evaluation
of MHC multimers ability to bind TCR-like molecules is another type
of positive control experiment. TCR-like molecules are molecules
binding MHC multimers with same specificity as TCR, i.e.
recognising the peptide binding grove part of the MHC-peptide
complex. Examples of TCR-like molecules include but is not limited
to antibodies, antibody fragments, antibody like scaffold proteins,
aptamers or any other molecule able to bind MHC-peptide complexes
in a peptide and MHC alle specific manner. [0557] Binding of MHC
multimers to TCR-like molecules follows the same methods and
principles as described for binding to TCR above. Thus positive
control reagents in such positive control experiments are cells or
cell-like structures expressing TCR-like molecules, TCR-like
molecules immobilised to solid support and/or TCR-like molecules in
solution. [0558] Analysis of conformation of MHC-peptide complex in
MHC multimer. MHC-peptide complexes are only able to be recognised
by specific T-cells if the MHC-peptide complex have the correct
three-dimensional structure i.e. the correct fold and contains both
MHC polypeptide chains and antigenic peptide. Therefore measurement
of the conformation of MHC-peptide complexes in a MHC multimer are
relevant positive control experiments. [0559] One preferred
analysis of conformational correct folded MHC-peptide complexes in
MHC multimers includes use of antibodies or other molecules
recognising structural correct MHC molecules and not unfolded
molecules or MHC molecules that are fallen apart. The antibodies
recognise one or more epitopes on the MHC-peptide complexes that
are only present when the MHC-peptide complex is correct assembled.
An example is the antibody clone W6/32 that recognise all human HLA
I molecules but only when both heavy chain and .beta.2m are
assemblet (Parham et al. (1979). J. Immunol., vol 123, 342-349).
[0560] Molecules usefull for this type of positive control
experiment includes but is not limited to antibody, antibody
fragment e.g. Fab, (Fab).sub.2 Fv, scFV, aptamers, antibody like
molecules, scaffold proteins. Also included are cells and cell-like
structures expressing any of the above described type of molecules
and also viral particles expressing such molecules. [0561]
Antibodies and other molecules recognising a conformational correct
epitope on MHC-peptide complexes can be generated and used in
positive control experiments as described for TCR above. Thus
positive control reagents in such positive control experiments are
cells or cell-like structures expressing molecules recognising
conformational epitopes on MHC molecules, molecules recognising
conformational epitopes on MHC molecules in solution and/or
immobilised to solid support. [0562] A preferred embodiment
includes measurement of MHC multimer binding to beads or other
types of solid support, to which antibodies or molecules that
recognize conformational epitopes on MHC-peptide complexes have
been immobilized. Bound MHC multimer are then detected through a
label on the multimer or through a secondary labelled marker
molecule. An example is measurement of correctly folded MHC in a
quantitative ELISA, e.g. where the MHC binds to immobilized
molecules recognizing the correctly folded complex. [0563] Another
preferred embodiment includes detection of binding of MHC multimers
to cells, cell-like structures, yeast or viral particles displaying
antibodies or other molecules able to recognise conformational
epitopes on MHC-peptide complexes. [0564] Alternative methods to
determine correct conformation of MHC-peptide complexes in MHC
multimers include X-ray Crystallography, circular dichroism and NMR
spectroscopy. [0565] During production of MHC multimers, it can
also be desirable to determine the degree of correctly folded MHC.
The fraction or amount of functional and/or correctly folded MHC
can be tested in a number of different ways, using methods and
principles as described above. [0566] Measurement of presence of
components of MHC multimer e.g. MHC-peptide complex, MHC
polypeptide chains, antigenic peptide and label is another way to
perform a positive control experiment. This type of analysis does
not tell if the MHC multimer is functional but gives information of
the intactness of the multimer. [0567] The presence of MHC-peptide
complex, MHC polypeptide chains, antigenic peptide and/or label on
a multimer may be determined by detection of binding of an antibody
or other molecule to one or more of the components in the MHC
multimer. Examples include measurement of binding of antibodies to
any epitope in MHC-peptide complexes, in MHC I heavy chain, in
.beta.2microglobulin, in MHC II .alpha.-chain or .beta.-chain, in
antigenic peptide, in label, in multimerisation domain, in the
linker connecting MHC-peptide complexes and/or label to
multimerization domain or in tags or other recognising binding any
other part of MHC multimer. [0568] Antibodies and other molecules
recognising components of MHC multimer can be generated and used in
positive control experiments as described for the use of TCR in
positive control experiments above. Thus positive control reagents
in such positive control experiments are cells or cell-like
structures expressing molecules recognising any part of MHC
multimer, soluble molecules recognising any part of MHC multimer
and/or such molecules to solid support. [0569] A preferred
embodiment includes measurement of MHC multimer binding to beads or
other types of solid support, to which antibodies or molecules
recognising components of MHC multimer have been immobilized. Bound
MHC multimer are then detected through a label on the multimer or
through a secondary labelled marker molecule. [0570] Another
preferred embodiment includes detection of binding of MHC multimer
to cells, cell-like structures, yeast or viral particles displaying
antibodies or other molecules able to recognise components of MHC
multimer [0571] Alternatively the presence of MHC-peptide complex,
MHC polypeptide chains, antigenic peptide and/or label in a MHC
multimer can be measured using Mass spectrometry (MS), HPLC, FPLC,
SDS PAGE or other methods that can visualize the individual
components of the MHC multimer due to their different size and/or
chemical and/or physical properties. Prior to analysis it may be
advantageous to split the MHC multimer into its individual
components by e.g. boiling, changeing pH, using detergent ect.
[0572] Above principles for positive control experiments evaluating
MHC multimer reagents are given. However positive control
experiments determining the quality and stability of individual
components of the MHC multimer are also important. Quality and
stability of labelling molecules can be evaluated using methods
measuring their presences e.g. by detection with antibodies or
other molecules able to bind the label or using MS, HPLC, FPLC or
similar methods. Alternatively the activity e.g. fluorescence or
enzymatic activity of the label can be measured.
[0573] The quality and stability of individual MHC-peptide
complexes can be determined using the same principles as described
above for MHC multimers but can also be determined by: [0574]
Measurement of MHC-peptide complex binding using shift assays.
Binding of specific MHC-peptide complexes to soluble TCRs,
antibodies, aptamers or other soluble molecules recognising
MHC-peptide complexes can be measured in so called shift assay. A
shift assay is here an assay detecting a shift in size of a given
MHC-peptide complex. Upon binding another molecule the molecular
weigth of a MHC-peptide complex will increase with the molecular
weight of the molecule bound and this increase in size can be
measured using methods able to separate molecules according to size
including but not limited to SDS PAGE, size exclusion
chromatography and density gradient centrifugation (e.g. CsCl).
Preferable soluble TCR, TCR-like molecules or molecules recognizing
conformational epitopes on the MHC-peptide complexes are used. A
shift in size of a preparation of MHC-peptide complex upon addition
of such molecules will then indicate that the MHC-peptide complex
is present in the sample and correctly folded and is functional.
[0575] An example is measurement of functional MHC complex using a
non-denaturing SDS PAGE gel-shift assay, where functional MHC
complexes bind to soluble TCR (or another molecule that recognize
correctly folded MHC complex), and thereby shifts the TCR to
another position in the gel.
[0576] Depending on the technical method employed for the positive
control experiment one or more of the above described principles
for measurement can be used. For example for flow cytometry
analysis cells, beads or particles are preferred as positive
control reagents since they can be seen as individual populations
during a flow cytometry analysis.
[0577] When using beads or particles as positive controls they are
preferable such that they can be distinguished from T-cells in the
sample e.g. due to different size, different scatter properties
and/or different labelling or labelling intentsity Preferable the
beads or particles are small e.g. with a diameter between 0.1-100
um but can in principle be of any size usefull in a flow cytometer
analysis. The beads or particles may be fluorescent themselves or
coupled to one or more fluorescent molecules as described elsewhere
herein. In principle the same type and same principles of beads and
particles can be used as what is described in relation to counting
beads in flow cytometry experiments, detection of T-cells using
beads with immobilised MHC multimers and bead-based MHC multimers
elsewhere herein.
[0578] When performing positive control experiments using IHC as
analysis method tissue sections or cells immobilized to e.g. glass
plates are preferred as positive controls. Likewise when performing
ELISA or ELISA-like control experiments TCR or T-cell's immobilized
to wells of a microtiter plate or similar are preferred.
Evaluating Sample and Analysis
[0579] Another preferred type of positive control experiments
include evalution of sample and analysis method. Such experiments
determine whether a sample is intact and usefull and/or whether the
analysis method is successful. Such positive controls are
preferably analysed on same sample as used in the MHC multimer
analysis in question. However, another sample from same individual,
a similar sample from another individual or a complete different
sample can also be used. In these latter cases only information of
the quality of analysis methods are determined.
[0580] The positive control can be an internal control and added
into the same sample for which it is a positive control together
with MHC multimer reagent i.e. into same container or it can a
natural part of sample. Alternatively the positive control reagents
are added to a separate container containing the same or a
different sample. In all cases the analysis method is the same as
used for analysis of actual sample with MHC multimer.
[0581] Positive control experiments evaluating analysis method and
or sample include but are not limited to: [0582] Measurement of MHC
multimer binding to beads or other solid supports with immobilised
molecules specific for MHC-peptide complex e.g. specific TCR,
TCR-like molecules, molecules recognizing conformational epitopes
on MHC-peptide complexes, molecules recognizing any epitope on
MHC-peptide complexes or molecules recognizing tag or other
detectable components on the MHC multimer e.g. recognizing
streptavidin or coiled-coil structure. Example of various MHC
multimer tags are described elsewhere herein. [0583] Principles and
methods for measurement of MHC multimer binding to such beads or
solid support are described above in the section "Evaluating MHC
multimer reagent" [0584] This type of control can be used to
evaluate analysis method as well as MHC multimer reagent used.
[0585] Measurement of MHC multimer binding to Cells displaying TCR
or other molecules specific for MHC-peptide complexes or other part
of MHC multimer. [0586] Cells includes T-cells, T-cell lines,
T-cell hybridomas, cells transfected/transformed with genes
encoding TCR, cells transfected/transformed with genes encoding
TCR-like molecules able to recognise MHC-pepitde complexes, cells
displaying other molecules specific for MHC-peptide complexes or
any other part of MHC multimer or cell-like structures displaying
TCR, TCR-like molecules or other molecules able to recognize
MHC-peptide complexes or any other part of MHC multimer. Principles
and methods for measurement of MHC multimer binding to such cells
or cell-like structures are described above in the section
"Evaluating MHC multimer reagent". [0587] This type of control can
be used to evaluate analysis method as well as MHC multimer reagent
used [0588] Measurement of binding positive control MHC multimers
to T-cells and/or TCR in sample. The positive control MHC multimer
include MHC multimers comprising MHC molecule complexed with an
appropriate peptide that allows the MHC multimer to interact
specifically and efficiently with its cognate TCR. The type MHC
multimer can be identical to or different from the MHC multimer
used in the analysis in question, e.g. comprice the same or
different mulimerisation domain. Likewise, the positive MHC
multimer can have the same specificity as the MHC multimer used in
the analysis or it may have specificity for other T-cells in the
sample analysed. [0589] This type of control can be used to
evaluate analysis method as well as the quality of sample. [0590]
Measurement of HLA-type of sample [0591] T-cell from a given donor
are "educated" to recognize only MHC allele's identical to MHC
alleles expressed on cells of that donor, they are self-restricted.
Therefore a given MHC multimer are only recognized by T-cells in a
sample if that sample derive from a donor positive for the same MHC
allele(s) as is in the MHC multimer and of cause if the MHC
complexes of the MHC multimers presents the right peptide. [0592]
MHC multimers of the present invention may feature one or more
different MHC allele's and one or more different MHC multimers may
be applied for analysis of a given sample. In many aspect of the
present invention it is therefore important that the sample derive
from a donor that have MHC alleles corresponding to one or more MHC
alleles of the MHC multimer(s) used for analysis. Positive control
experiments determining whether the sample contains or derive from
a donor with matching MHC allele type can therefore be important
controls. MHC allele determination of a given sample are in the
following called MHC allele typing and includes but is not limited
to: [0593] MHC allele typing using PCR. MHC allele typing can be
determined by amplification of DNA fragments encoding MHC
polypeptide chains by PCR using primers specific for all known MHC
alleles or selected groups of alleles e.g. human alleles, sub
groups of human alleles or few selected alleles. DNA fragments from
a given donor can be obtained by lysing or otherwise disrupting
cells from the sampe to be analysed or from another sample from
that donor. [0594] MHC allele typing using MHC allele specific
antibodies or marker molecules. [0595] Expression of specific MHC
alleles on the surface of a cell can be determined by measuring the
binding of antibodies or other marker molecules specific for one or
more MHC alleles. Binding of antibody or other marker molecules may
be detected directly through a label on the antibody/marker
molecule or through secondary labeled antibodies and marker
molecules. In the following antibodies and other marker molecules
are collectively called marker molecules. [0596] In one preferred
embodiment marker molecules with different specificity are labeled
with same labeling molecule and thereby detected as a pool. In such
a positive control experiment the presence of alleles recognized by
any of the marker molecules used for analysis are determined and
not the presence of individual alleles. The panel of marker
molecules used is matching the MHC alleles in the MHC multimer
preparation used for analysis of sample. [0597] In another
preferred embodiment each marker molecule is labeled with an
individual label. In such a positive control experiment the
presence of alleles recognized by any of the marker molecules used
for analysis are determined and also the presence of individual
alleles. The panel of marker molecules used is matching the MHC
alleles in the MHC multimer preparation used for analysis of
sample. [0598] In another preferred embodiment of the present
invention groups of marker molecules are labeled with same label
and other groups of marker molecules are labeled with other labels.
In such a positive control experiment the presence of alleles
recognized by any of the marker molecules used for analysis are
determined and not the presence of individual alleles. However the
presences of subgroups of MHC alleles may be determined. The panel
of marker molecules used is matching the MHC alleles in the MHC
multimer preparation used for analysis of sample. [0599] In another
preferred embodiment of the present invention marker molecules
specific for different alleles are labeled with same label thereby
identifying subpopulations of MHC expressing cells for which one or
more is positive for one ore more additional marker molecules
labeled with another label. For example 6 different marker
molecules (A, B, C, D, E, F) are labeled using 3 different labels
(1, 2, 3) as follows: marker molecule A, B and E are labeled with
label 1, marker molecule C, D and E are labeled with label 2 and
marker molecule B, C and F are labeled with label 3. Thereby all 6
marker molecules can be distinguished from each other by one or
more labels: marker molecule A is labeled with label 1, marker
molecule B is labeled with label 1 and 3, marker molecule C is
labeled with label 2 and 3, marker molecule D is labeled with label
2, marker molecule E is labeled with label 1 and 2 and marker
molecule F is labeled with label 3. [0600] Using this form for
labeling few types of labeling molecules may be used for labeling
many different marker molecules. [0601] MHC allele typing using MHC
multimers. MHC multimers can also be used for determination of MHC
allele occurrence in a sample. MHC multimers are good positive
controls if they carry common antigenic peptides meaning antigenic
peptides derived from antigenic proteins any donor have been in
contact with and thereby have specific T-cells for. One preferred
type of antigenic peptides are those derived from common pathogens
that most of us have been infected with including but not limited
to proteins from CMV, EBV, influenza and other common viruses and
proteins from common bacteria. [0602] Another preferred type of
antigenic peptides is derived from self proteins, meaning proteins
that we have naturally in our own body. An example of such self
proteins is Melan-A/MART-1. Circulating Melan-A/MART-1 specific
T-cells have been detected with MHC multimers in human healthy
donors (Zippelius et al. (2002). J. Exp. med. Vol 195, 485-494).
[0603] Measurement of binding of MHC multimers carrying common
antigenic epitopes to T-cells in the sample analysed can therefore
be used for MHC allele typing of the sample. Binding of MHC
multimer may be detected directly through a label on the MHC
multimer or through secondary labelled marker molecules or as
described elsewhere herein. [0604] Preferred embodiments for
labeling of MHC multimers used as positive controls are as
described above for labeling antibodies and other marker
molecules.
Minimization of Undesired Binding of the MHC Multimer
[0605] Identification of MHC-peptide specific T-cells can give rise
to background signals due to unwanted binding to cells that do not
carry TCRs. This undesired binding can result from binding to cells
or other material, by various components of the MHC multimer, e.g.
the dextran in a MHC dextramer construct, the labelling molecule
(e.g. FITC), or surface regions of the MHC-peptide complex that do
not include the peptide and the peptide-binding cleft.
[0606] MHC-peptide complexes bind to specific T-cells through
interaction with at least two receptors in the cell membrane of the
T-cell. These two receptors are the T-cell receptor (TCR) and CD8
for MHC I-peptide complexes and TCR and CD4 receptor protein for
MHC II-peptide complexes. Therefore, a particularly interesting
example of undesired binding of a MHC multimer is its binding to
the CD8 or CD4 molecules of T-cells that do not carry a TCR
specific for the actual MHC-peptide complex. The interaction of CD8
or CD4 molecules with the MHC is not very strong; however, because
of the avidity gained from the binding of several MHC complexes of
a MHC multimer, the interaction between the MHC multimer and
several CD8 or CD4 receptors potentially can result in undesired
but efficient binding of the MHC multimer to these T-cells. In an
analytical experiment this would give rise to an unwanted
background signal; in a cell sorting experiment undesired cells
might become isolated. Other particular interesting examples of
undesired binding is binding to lymphoid cells different from
T-cells, e.g. NK-cells, B-cells, monocytes, dendritic cells, and
granulocytes like eosinophils, neutrophils and basophiles.
[0607] Apart from the MHC complex, other components in the MHC
multimer can give rise to unspecific binding. Of special interest
are the multimerization domain, multimerization domain molecules,
and labeling molecules.
[0608] One way to overcome the problem with unwanted binding is to
include negative controls in the experiment and subtract this
signal from signals derived from the analyzed sample, as described
elsewhere in the invention.
[0609] Alternatively, unwanted binding could be minimized or
eliminated during the experiment. Methods to minimize or eliminate
background signals include: [0610] Mutations in areas of the MHC
complex responsible for binding to unwanted cells can be
introduced. Mutations here mean substitution, insertion, and/or
deletion of natural or non-natural amino acids. Sub-domains in the
MHC complex can be responsible for unwanted binding of the MHC
multimer to cells without a TCR specific for the MHC-peptide
complex contained in the MHC multimer. One example of special
interest of the present invention is a small region in the
.alpha.3-domain of the .alpha.-chain of MHC I molecules that is
responsible for binding to CD8 on all cytotoxic T-cells. Mutations
in this area can alter or completely abolish the interaction
between CD8 on cytotoxic T-cells and MHC multimer (Neveu et al.
(2006) Int Immunol. 18, 1139-45). Similarly a sub domain in the
.beta.2 domain of the .beta.-chain of MHC II molecules is
responsible for binding CD4 molecules on all CD4 positive T-cells.
Mutations in this sub domain can alter or completely abolish the
interaction between MHC II and CD4. Another embodiment is to mutate
other areas of MHC I/MHC II complexes that are involved in
interactions with T-cell surface receptors different from TCR, CD8
and CD4, or that bind surface receptors on B-cells, NK cells,
Eosiniophils, Neutrophils, Basophiles, Dendritic cells or
monocytes. [0611] Chemical alterations in areas of the MHC complex
responsible for binding to unwanted cells can be employed in order
to minimize unwanted binding of MHC multimer to irrelevanT-cells.
Chemical alteration here means any chemical modification of one or
more amino acids. Regions in MHC complexes that are of special
interest are as mentioned above the .alpha.3 domain of the
.alpha.-chain in MHC I molecules and .beta.2 domains in the
.beta.-chain of MHC II molecules. Other regions in MHC I/MHC II
molecules that can be chemically modified to decrease the extent of
undesired binding are regions involved in interaction with T-cell
surface receptors different from TCR, CD8 and CD4, or that bind
surface receptors on B-cells, NK cells, Eosiniophils, Neutrophils,
Basophiles, Dendritic cells or monocytes. [0612] Another method to
minimize undesired binding involves the addition of one or more
components of a MHC multimer, predicted to be responsible for the
unwanted binding. The added component is not labeled, or carries a
label different from the label of the MHC multimer used for
analysis. Of special interest is addition of MHC multimers that
contain nonsense peptides, i.e. peptides that interact efficiently
with the MHC protein, but that expectably do not support specific
binding of the MHC multimer to the TCR in question. Another example
of interest is addition of soluble MHC complexes not coupled to one
or more multimerization domain(s), and with or without peptide
bound in the peptide binding cleft. In another embodiment,
individual components of the MHC complex can be added to the
sample, e.g. I .alpha.-chain or subunits of MHC I .alpha.-chain
either folded or unfolded, beta2microglobulin or subunits thereof
either folded or unfolded, .alpha./.beta.-chain of MHC II or
subunits thereof either folded or unfolded. Any of the above
mentioned individual components can also be attached to one or more
multimerization domain(s) identical or different from the one used
in the MHC multimer employed in the analysis. [0613] Of special
interest is also addition of one or more multimerization domain
similar or identical to the one or more multimerization domain used
in the MHC multimer or individual components of the one or more
multimerization domain. [0614] Reagents able to identify specific
cell types either by selection or exclusion can be included in the
analysis to help identify the population of T-cells of interest,
and in this way deselect the signal arising from binding of the MHC
multimer to undesired cells. [0615] Of special interest is the use
of appropriate gating reagents in flow cytometry experiments. Thus,
fluorescent antibodies directed against specific surface markers
can be used for identification of specific subpopulations of cells,
and in this way help to deselect signals resulting from
MHC-multimers binding to undesired cells. [0616] Gating reagents of
special interest that helps identify the subset of T-cells of
interest when using MHC I multimers are reagents binding to CD3 and
CD8 identifying all cytotoxic T-cells. These reagents are
preferably antibodies but can be any labeled molecule capable of
binding CD3 or CD8. Gating reagents directed against CD3 and CD8
are preferably used together. As they stain overlapping cell
populations they are preferably labeled with distinct
fluorochromes. However, they can also be used individually in
separate samples. In experiments with MHC II multimers reagents
binding to CD3 and CD4 identifying T helper cells can be used.
These reagents are preferably antibodies but can be any labeled
molecule capable of binding CD3 or CD4. Gating reagents directed
against CD3 and CD4 are preferable used together. As they stain
overlapping cell populations they are preferably labeled with
distinct fluorochromes. However, they can also be used individually
in separate samples.
[0617] Other gating reagents of special interest in experiments
with any MHC multimer are reagents binding to the cell surface
markers CD2, CD27, CD28, CD45RA, CD45RO, CD62L and CCR7. These
surface markers are unique to T-cells in various differentiation
states. Co staining with either of these reagents or combinations
thereof together with MHC multimers helps to select MHC multimer
binding T-cells expressing a correct TCR. These reagents can also
be combined with reagents directed against CD3, CD4 and/or CD8.
[0618] Another flow cytometric method of special interest to remove
signals from MHC multimer stained cells not expressing the specific
TCR, is to introduce an exclusion gate. Antibodies or other
reagents specific for surface markers unique to the unwanted cells
are labeled with a fluorochrome and added to the test sample
together with the MHC multimer. The number of antibodies or surface
marker specific reagents are not limited to one but can be two,
three, four, five, six, seven, eight, nine, ten or more individual
reagents recognizing different surface markers, all of which are
unique to the unwanted cells. During or after collection of data
all events representing cells labeled with these antibodies are
dumped in the same gate and removed from the dataset. This is
possible because all the antibodies/reagents that bind to the wrong
cells are labeled with the same fluorochrome.
[0619] Reagents of special interest that exclude irrelevanT-cells
include reagents against CD45 expressed on red blood cells, CD19
expressed on B-cells, CD56 expressed on NK cells, CD4 expressed on
T helper cells and CD8 expressed on cytotoxic T-cells, CD14
expressed on monocytes and CD15 expressed on granulocytes and
monocytes.
Negative Control Reagents and Negative Control Experiments for the
Use of MHC Multimers in Flow Cytometry and Related Techniques
[0620] Experiments with MHC multimers require a negative control in
order to determine background staining with MHC multimer.
Background staining can be due to unwanted binding of any of the
individual components of the MHC multimer, e.g., MHC complex or
individual components of the MHC complex, multimerization domain or
label molecules. The unwanted binding can be to any surface or
intracellular protein or other cellular structure of any cell in
the test sample, e.g. undesired binding to B-cells, NK cells or
T-cells. Unwanted binding to certain cells or certain components on
cells can normally be corrected for during the analysis, by
staining with antibodies that bind to unique surface markers of
these specific cells, and thus identifies these as false positives,
or alternatively, that binds to other components of the
targeT-cells, and thus identifies these cells as true positives. A
negative control reagent can be used in any experiment involving
MHC multimers, e.g. flow cytometry analysis, other cytometric
methods, immunohistochemistry (IHC) and ELISA. Negative control
reagents include the following: [0621] MHC complexes or MHC
multimers comprising MHC complexes carrying nonsense peptides. A
nonsense peptide is here to be understood as a peptide that binds
the MHC protein efficiently, but that does not support binding of
the resultant MHC-peptide complex to the desired TCR. An example
nonsense peptide is a peptide with an amino acid sequence different
from the linear sequence of any peptide derived from any known
protein. When choosing an appropriate nonsense peptide the
following points are taken into consideration. The peptide should
ideally have appropriate amino acids at relevant positions that can
anchor the peptide to the peptide-binding groove of the MHC. The
remaining amino acids should ideally be chosen in such a way that
possible binding to TCR (through interactions with the peptide or
peptide-binding site of MHC) are minimized. The peptide should
ideally be soluble in water to make proper folding with MHC alpha
chain and .beta.2m possible in aqueous buffer. The length of the
peptide should ideally match the type and allele of MHC complex.
The final peptide sequence should ideally be taken through a blast
search or similar analysis, to ensure that it is not identical with
any peptide sequence found in any known naturally occurring
proteins. [0622] MHC complexes or MHC multimers comprising MHC
complexes carrying a chemically modified peptide in the
peptide-binding groove. The modification should ideally allow
proper conformation of the MHC-peptide structure, yet should not
allow efficient interaction of the peptide or peptide-binding site
of MHC with the TCR. [0623] MHC complexes or MHC multimers
comprising MHC complexes carrying a naturally occurring peptide
different from the peptide used for analysis of specific T-cells in
the sample. When choosing the appropriate natural peptide the
following should be taken into consideration. The peptide in
complex with the MHC protein should ideally not be likely to bind a
TCR of any T-cell in the sample with such an affinity that it can
be detected with the applied analysis method. The peptide should
ideally be soluble in water to make proper folding with MHC alpha
chain and .beta.2m possible in aqueous buffer. The length of the
peptide should match the type and allele of MHC complex. [0624]
Empty MHC complexes or MHC multimers comprising empty MHC
complexes, meaning any correctly folded MHC complex without a
peptide in the peptide-binding groove. [0625] MHC heavy chain or
MHC multimers comprising MHC heavy chain, where MHC heavy chain
should be understood as full-length MHC I or MHC II heavy chain or
any truncated version of MHC I or MHC II heavy chain. The MHC heavy
chains can be either folded or unfolded. Of special interest is MHC
I alpha chains comprising the .alpha.3 domain that binds CD8
molecules on cytotoxic T-cells. Another embodiment of special
interest is MHC II .beta. chains comprising the .beta.2 domain that
binds CD4 on the surface of helper T-cells. [0626]
Beta2microglobulin or subunits of beta2microglobulin, or MHC
multimers comprising Beta2microglobulin or subunits of
beta2microglobulin, folded or unfolded. [0627] MHC-like complexes
or MHC multimers comprising MHC-like complexes folded or unfolded.
An example could be CD1 molecules that are able to bind peptides in
a peptide-binding groove that can be recognized by T-cells (Russano
et al. (2007). CD1-restricted recognition of exogenous and
self-lipid antigens by duodenal gammadelta+ T lymphocytes. J
Immunol. 178(6):3620-6) [0628] Multimerization domain(s) without
MHC or MHC-like molecules, e.g. dextran, streptavidin, IgG,
coiled-coil-domain liposomes. [0629] Labels, e.g. FITC, PE, APC,
pacific blue, cascade yellow or any other label listed elsewhere
herein.
[0630] Negative controls 1-4 can provide information about
potentially undesired binding of the MHC multimer, through
interaction of a surface of the MHC-peptide complex different from
the peptide-binding groove and its surroundings. Negative control 5
and 6 can provide information about binding through interactions
through the MHC I or MHC II proteins (in the absence of peptide).
Negative control 7 can provide information about binding through
surfaces of the MHC complex that is not unique to the MHC complex.
Negative controls 8 and 9 provide information about potential
undesired interactions between non-MHC-peptide complex components
of the MHC multimer and cell constituents.
Application of MHC Multimers in Immune Monitoring, Diagnostics,
Prognostics, Therapy and Vaccines
[0631] MHC multimers detect antigen specific T-cells of the various
T-cell subsets. T-cells are pivotal for mounting an adaptive immune
response. It is therefore of importance to be able to measure the
number of specific T-cells when performing a monitoring of a given
immune response. Typically, the adaptive immune response is
monitored by measuring the specific antibody response, which is
only one of the effector arms of the immune system. This can lead
to miss-interpretation of the actual clinical immune status.
[0632] In many cases intruders of the organism can hide away inside
the cells, which can not provoke a humoral response. In other
cases, e.g. in the case of certain viruses the intruder mutates
fast, particularly in the genes encoding the proteins that are
targets for the humoral response. Examples include the influenza
and HIV viruses. The high rate of mutagenesis renders the humoral
response unable to cope with the infection. In these cases the
immune system relies on the cellular immune response. When
developing vaccines against such targets one needs to provoke the
cellular response in order to get an efficient vaccine.
[0633] Developing vaccines that should give rise to lifelong
protection is another case where the cellular immune system needs
to be activated. Commonly, various childhood vaccines are expected
to give lifelong protection but will only come to trial many years
after the vaccination has been performed and then there is only to
hope that it actually have created effective immunity.
[0634] Therapeutically cancer vaccines generally rely on cytotoxic
effector T-cells and have short duration of function. Therefore,
continuous monitoring is important. MHC multimers are therefore
very important for immune monitoring of vaccine responses both
during vaccine development, as a means to verify the obtained
immunity for lifelong vaccines and to follow cancer patients under
treatment with therapeutically cancer vaccines.
[0635] The number of antigen specific cytotoxic T-cells can be used
as surrogate markers for the overall wellness of the immune system.
The immune system can be compromised severely by natural causes
such as HIV infections or big traumas or by immuno suppressive
therapy in relation to transplantation. The efficacy of an anti HIV
treatment can be evaluated by studying the number of common
antigen-specific cytotoxic T-cells, specific against for example
Cytomegalovirus (CMV) and Epstein-Barr virus. In this case the
measured T-cells can be conceived as surrogate markers. The
treatment can then be corrected accordingly and a prognosis can be
made.
[0636] A similar situation is found for patients undergoing
transplantation as they are severely immune compromised due to
pharmaceutical immune suppression to avoid organ rejection. The
suppression can lead to outbreak of opportunistic infections caused
by reactivation of otherwise dormant viruses residing in the
transplanted patients or the grafts. This can be the case for CMV
and EBV viruses. Therefore measurement of the number of virus
specific T-cells can be used to give a prognosis for the outcome of
the transplantation and adjustment of the immune suppressive
treatment. Similarly, the BK virus has been implied as a causative
reagent for kidney rejection. Therefore measurement of BK-virus
specific T-cells can have prognostic value.
[0637] In relation to transplantation, the presence of specific
T-cells directed against minor histocompatibility antigens (mHAgs)
is important as they can cause graft versus host reaction/disease
that can develop to a fatal situation for the patient. Again, a
well-adjusted immune suppressive treatment is important. A similar
reaction denoted graft versus cancer is sometimes employed in the
treatment of malignancies of the lymphoid system. It is evident
that such treatment is balancing on the edge of a knife and will
benefit of specific measurement of relevant effector T-cells.
[0638] Due to lack of organs, transplantations across greater
mismatches are increasingly making harsher immune suppressive
treatment more common. This calls for more efficient methods to
monitor the immune status of the patient so that corrective
measures in the treatment can be applied in due cause.
[0639] MHC multimers can be of importance in diagnosis of
infections caused by bacteria, virus and parasites that hide away
inside cells. Serum titers can be very low and direct measurement
of the disease-causing organisms by PCR can be very difficult
because the host cells are not identified or are inaccessible.
Other clinical symptoms of a chronic infection can be
unrecognizable in an otherwise healthy individuals, even though
such persons still are disease-carriers and at risk of becoming
spontaneously ill if being compromised by other diseases or stress.
Likewise, cancers can also be diagnosed early in its development if
increased numbers of cancer specific T-cells can be measured in
circulation, even though the tumor is not yet localized.
[0640] Antigen-specific T helper cells and regulatory T-cells have
been implicated in the development of autoimmune disorders. In most
cases the timing of events leading to autoimmune disease is unknown
and the exact role of the immune cells not clear. Use of MHC
multimers to study these diseases will lead to greater
understanding of the disease-causing scenario and make provisions
for development of therapies and vaccines for these diseases.
[0641] Therapeutically use of MHC multimers can be possible, either
directly or as part of therapeutically vaccines. When performing
autologous cancer therapy it is often recognized that the in vitro
amplified cancer-specific effector T-cells do not home effectively
to the correct target sites but ends up in the lungs. If the
molecules responsible for interaction with the correct homing
receptor can be identified these can be added to the MHC multimer
making a dual, triple or multiple molecular structure that are able
to aid the antigen-specific T-cells home to the correct target, as
the MHC complex will bind to the specific T-cell and the additional
molecules will mediate binding to the targeT-cells.
[0642] In a preferable embodiment, MHC multimers bound to other
functional molecules are employed to directly block, regulate or
kill these cells. The MHC complexes specifically recognize the
target T-cells and direct the action of the other molecules to the
target.
[0643] Derivatives of MHC multimers can be useful as vaccines, as
vaccine components or as engineered intelligent adjuvant. The
possibility of combining MHC complexes that specifically bind
certain T-cells with molecules that trigger, e.g. the humoral
response or the innate immune response, can accelerate vaccine
development and improve the efficiency of vaccines.
[0644] In relation to the use and application of MHC multimers in
immune monitoring, diagnostics, prognostics, therapy and vaccines
several organisms and human proteins are of relevance, comprising
but not limited to virus, bacteria, archaeo, fungi, parasites,
allergens, minor histocompatibility antigens (mHAgs), auto
antigens, cancer associated proteins and other disease associated
proteins. Of special relevance are the following; Adenovirus
(subgropus A-F), BK-virus, CMV (Cytomegalo virus, HHV-5), EBV
(Epstein Barr Virus, HHV-4), HBV (Hepatitis B Virus), HCV
(Hepatitis C virus), HHV-6a and b (Human Herpes Virus-6a and b),
HHV-7, HHV-8, HSV-1 (Herpes simplex virus-1, HHV-1), HSV-2 (HHV-2),
JC-virus, SV-40 (Simian virus 40), VZV (Varizella-Zoster-Virus,
HHV-3), Parvovirus B19, Haemophilus influenza, HIV-1 (Human
immunodeficiency Virus-1), HTLV-1 (Human T-lymphotrophic virus-1),
HPV (Human Papillomavirus), Mycobacterium tuberculosis,
Mycobacterium bovis, Borrelia burgdorferi, Helicobacter pylori,
Streptococcus pneumoniae, Listeria monocytogenes, Histoplasma
capsulatum, Aspergillus fumigatus, Candida albicans, Cryptococcus
neoformans, Pneumocystis carinii, Plasmodium falciparum, Plasmodium
vivax, Plasmodium malariae, Schistosoma mansoni, Schistosoma
japonicum, Schistosoma haematobium, Trypanosoma cruzi, Trypanosoma
rhodesiense, Trypanosoma gambiense, Leishmania donovani, Leishmania
tropica, Birch, Hazel, Elm, Ragweed, Wormwood, Grass, Mould, Dust
Mite, HA-1, HA-8, USP9Y, SMCY, TPR-protein, HB-1Y, GAD64, Collagen,
Survivin, Survivin-2B, Livin/ML-IAP, Bcl-2, Mcl-1, Bcl-X(L),
Mucin-1, NY-ESO-1, Telomerase, CEA, MART-1, HER-2/neu, bcr-abl,
PSA, PSCA, Tyrosinase, p53, hTRT, Leukocyte Proteinase-3, hTRT,
gp100, MAGE antigens, GASC, JMJD2C, JARD2 (JMJ), JHDM3a, WT-1, CA
9, Protein kinases, Collagen, human cartilage glycoprotein 39,
beta-amyloid, Abeta42, APP, Presenilin 1.
In Vivo Diagnostics
[0645] Antigen specific tumor infiltrating lymphocytes can be used
to identify tumor lesions and metastases as the antigen specific
T-cells will migrate/home to the tumor site to exert their help or
immuno modulatory action (CD4+ T helper cells) or cytotoxic killing
of tumor cells expressing the tumor specific/tumor associated
peptide MHC complex (CD8+ T-cells). Likewise identification of
sites of infection tumor lesions can be identified as they
typically attract antigen specific T-cells.
[0646] Localization of tumors and sites of infection can be carried
out using antigen specific T-cells labelled with a paramagnetic
isotope in conjunction with magnetic resonance imaging (MRI) or
electron spin resonance (ESR). In general, any conventional method
for diagnostic imaging visualization can be utilized. Usually gamma
and positron emitting radioisotopes are used for camera and
paramagnetic isotopes for MRI. For peripheral cancer lesion in skin
(e.g. melanoma) fluorescently labelled antigen specific T-cells can
be used likewise.
Therapy and Vaccines
[0647] Therapy and vaccine approaches for manipulation of immune
responses Biological therapy (immunotherapy, biotherapy, or
biological response modifier therapy) is a relatively new type of
treatment and based on knowledge of cellular and molecular
mechanism underlying activation of the human immune system. For
example, the immune system can recognise the difference between
healthy cells and cancer cells in the body and work to eliminate
those that become cancerous. Biological therapies use the body's
immune system, either directly or indirectly, to fight cancer or to
lessen the side effects that can be caused by some cancer
treatments. An important goal of such immunotherapy is boosting of
killing power of immune system cells by stimulation of appropriate
effector cells, such as T-cells.
[0648] Conventional vaccines for infectious diseases, such as
measles, mumps, and tetanus, are effective because they expose the
immune system to weakened versions of the disease. This exposure
causes the immune system to respond by producing antibodies. Once
the immune system has created antibodies, some of the activated
immune cells remember the exposure. Therefore, the next time the
same antigen enters the body, the immune system can respond more
readily to destroy it.
[0649] For cancer treatment, researchers are developing vaccines
that can encourage the immune system to recognise cancer cells.
These vaccines can help the body reject tumours and prevent cancer
from recurring. In contrast to vaccines against infectious
diseases, cancer vaccines are designed to be injected after the
disease is diagnosed, rather than before it develops. By example,
it has been shown that immunisation with DCs loaded with
appropriate peptides from tumour associated antigens (TAAs)
stimulate "tumour specific" T-cells, which in some patients prevent
further progression of the disease and eventually lead to
regression of the disease. This approach takes advantage of the
"professional pathway" of antigen processing/-presentation
performed by DCs. In contrast, injection of soluble tumour TAAs or
soluble MHC molecules comprising appropriate peptides from TAAs
have only proven a limited or no effect, presumably due to low
efficacy of antigen stimulation from soluble antigens. The low
affinity as well as insufficient stimulation of specific T-cells
can explain poor protection obtained by immunisation with soluble
peptide/MHC molecule. Indeed, the low intrinsic affinity of
essential ligand-receptor interactions has implied limited
utilisation of soluble recombinant proteins for stimulation of
specific T-cells.
[0650] As evident from the above, MHC molecules play a very
important role, and thus detection of cells recognising MHC
molecules is of major importance and value. Likewise, several
attempts have been made to manipulate the immune system in a
controllable, efficient and consistent way.
[0651] However, the success has been limited. Thus, finding
substances for immunotherapy that actually works would be a major
step forward for the fight against a number of serious diseases for
which we do not at present have a cure.
[0652] The present invention is related to the major undertaking to
generate compounds comprising MHC molecules to detect and analyse
receptors on MHC recognising cells such as epitope specific T-cell
clones or other immune competent effector cells. It is shown herein
that the increased valences of compounds of the invention produce
surprisingly higher avidity in comparison to oligo-valent complexes
(tetramers) known from the prior art. This allows for quantitative
analysis of even small cell populations by e. g. flow
cytometry.
[0653] The potential and value of the present invention is obvious,
as several reports have demonstrated lack of correlation between
T-cell reactivity in peripheral blood and the course of neoplastic
diseases. For instance, analysis of T-cell activity in tumour
tissues as well as lymphatic tissues can provide better insights on
immunity toward solid tumours.
[0654] Combining the growing genome databases of primary protein
sequences of humans and parasites with the knowledge of how the
immune system handles the molecular information provided by
appropriate ligands will lead to new and powerful strategies for
development of curative vaccines.
[0655] This in turn will improve the possibilities for directed and
efficient immune manipulations against diseases caused by tumour
genesis or infection by pathogenic agent like viruses and bacteria.
HIV is an important example.
[0656] The ability to generate and ligate recombinant MHC molecules
or a variety of mixed ligands to multimerization domain(s) as
envisaged by the present invention, will enable a novel analytical
tool for monitoring immune responses and contribute to a rational
platform for novel therapy and "vaccine" applications. Therapeutic
compositions ("vaccines") that stimulate specific T-cell
proliferation by peptide-specific stimulation are indeed a
possibility within the present invention. Thus, quantitative
analysis and ligand-based detection of specific T-cells that
proliferate by the peptide specific stimulation should be performed
simultaneously to monitor the generated response. Effective methods
to produce a variety of molecules from the group of highly
polymorphic human HLA encoded proteins would lead to advanced
analyses of complex immune responses, which can comprise a variety
of peptide epitope specific T-cell clones. The high avidity-based
flow cytometry and tissue-staining approaches from the state of art
technology disclosed herein will add significantly to the
development of such advanced analysis of T-cell responses.
Further Applications
[0657] The MHC multimers of the present invention have numerous
uses and are a valuable and powerful tool e. g. in the fields of
diagnosis, prognosis, monitoring, stratification, and determining
the status of diseases or conditions as well as in therapy. Thus,
the MHC multimer can be applied in the various methods involving
the detection of MHC recognising cells. Furthermore, the present
invention relates to compositions comprising the MHC multimers in a
solubilising medium. The present invention also relates to
compositions comprising the MHC multimers immobilised onto a solid
or semi-solid support. The MHC multimers are very suitable as
detection systems. Thus, the present invention relates to the use
of the MHC multimers as defined herein as detection systems.
[0658] In another aspect, the present invention relates to the
general use of MHC molecules and multimers of such MHC molecules in
various sample-mounted methods. These methods include diagnostic
methods, prognostic methods, methods for determining the progress
and status of a disease or condition, and methods for the
stratification of a patient.
[0659] The MHC multimers of the present invention are also of value
in testing the expected efficacy of medicaments against or for the
treatment of various diseases. Thus, the present invention relates
to methods of testing the effect of medicaments or treatments, the
methods comprising detecting the binding of the MHC multimers to
MHC recognising cells and establishing the effectiveness of the
medicament or the treatment in question based on the specificity of
the MHC recognising cells. The present invention relates to
therapeutic compositions comprising as active ingredients the MHC
multimers as defined herein.
[0660] An important aspect of the present invention is therapeutic
compositions comprising as active ingredients effective amounts of
MHC recognising cells obtained using the MHC multimers as defined
herein to isolate relevant MHC recognising cells, and expanding
such cells to a clinically relevant number.
[0661] The present invention further relates to methods for
treating, preventing or alleviating diseases, methods for inducing
anergy of cells, as well as to methods for up-regulating,
down-regulating, modulating, stimulating, inhibiting, restoring,
enhancing and/or otherwise manipulating immune responses. The
invention also relates to methods for obtaining MHC recognising
cells using the MHC multimers as described herein.
[0662] Uses in which the MHC multimers of the invention can
suitably be provided in solubilised form include radio immune assay
(RIA), cell bound radioactive ligand assay, flow cytometry and
ELISA. Such assays are readily known to the person skilled in the
art as are the procedures, by which such are carried out.
[0663] Uses in which the MHC multimers of the invention can
suitably be provided immobilised onto a solid or semi-solid support
include flow cytometry, immunomagnetic separation techniques, ex
vivo stimulation of cultured cells, aggregation techniques, lateral
flow devices, ELISA, RIA and cell bound radio ligand assays.
[0664] Thus, the present invention relates in particular to MHC
multimers as defined above for use in flow cytometric methods,
histochemical methods, and cytochemical methods. Accordingly, the
MHC multimers of the invention are suited as detection systems.
[0665] Methods employing the MHC multimers of the invention The MHC
multimers of the invention are a powerful tool in a broad range of
in vitro or ex vivo methods.
[0666] Thus, the present invention relates to methods for detecting
the presence of MHC recognising cells in a sample comprising the
steps of (a) providing a sample suspected of comprising MHC
recognising cells, (b) contacting the sample with a MHC molecule
construct as defined above, and (c) determining any binding of the
MHC molecule construct, which binding indicates the presence of MHC
recognising cells.
[0667] Such methods are a powerful tool in diagnosing various
diseases. Establishing a diagnosis is important in several ways. A
diagnosis gives information about the disease, thus the patient can
be offered a suitable treatment regime. Also, establishing a more
specific diagnosis can give important information about a subtype
of a disease for which a particular treatment will be beneficial
(i. e. various subtypes of diseases can involve display of
different peptides which are recognised by MHC recognising cells,
and thus treatment can be targeted effectively against a particular
subtype). In this way, it can also be possible to gain information
about aberrant cells, which emerge through the progress of the
disease or condition, or to investigate whether and how T-cell
specificity is affected. The binding of the MHC molecule construct
makes possible these options, since the binding is indicative for
the presence of the MHC recognising cells in the sample, and
accordingly the presence of MHC molecules displaying the peptide.
The present invention also relates to methods for monitoring MHC
recognising cells comprising the steps of (a) providing a sample
suspected of comprising MHC recognising cells, (b) contacting the
sample with a MHC molecule construct as defined above, and (c)
determining any binding of the MHC molecule construct, thereby
monitoring MHC recognising cells.
[0668] Such methods are a powerful tool in monitoring the progress
of a disease, e. g. to closely follow the effect of a treatment.
The method can i. a. be used to manage or control the disease in a
better way, to ensure the patient receives the optimum treatment
regime, to adjust the treatment, to confirm remission or
recurrence, and to ensure the patient is not treated with a
medicament which does not cure or alleviate the disease. In this
way, it can also be possible to monitor aberrant cells, which
emerge through the progress of the disease or condition, or to
investigate whether and how T-cell specificity is affected during
treatment. The binding of the MHC molecule construct makes possible
these options, since the binding is indicative for the presence of
the MHC recognising cells in the sample, and accordingly the
presence of MHC molecules displaying the peptide.
[0669] The present invention also relates to methods for
establishing a prognosis of a disease involving MHC recognising
cells comprising the steps of (a) providing a sample suspected of
comprising MHC recognising cells, (b) contacting the sample with a
MHC molecule construct as defined above, and (c) determining any
binding of the MHC molecule construct, thereby establishing a
prognosis of a disease involving MHC recognising cells.
[0670] Such methods are a valuable tool in order to manage
diseases, i. a. to ensure the patient is not treated without
effect, to ensure the disease is treated in the optimum way, and to
predict the chances of survival or cure. In this way, it can also
be possible to gain information about aberrant cells, which emerge
through the progress of the disease or condition, or to investigate
whether and how T-cell specificity is affected, thereby being able
to establish a prognosis.
[0671] The binding of the MHC molecule construct makes possible
these options, since the binding is indicative for the presence of
the MHC recognising cells in the sample, and accordingly the
presence of MHC molecules displaying the peptide.
[0672] The present invention also relates to methods for
determining the status of a disease involving MHC recognising cells
comprising the steps of (a) providing a sample suspected of
comprising MHC recognising cells, (b) contacting the sample with a
MHC molecule construct as defined above, and (c) determining any
binding of the MHC molecule construct, thereby determining the
status of a disease involving MHC recognising cells.
[0673] Such methods are a valuable tool in managing and controlling
various diseases. A disease could, e. g. change from one stage to
another, and thus it is important to be able to determine the
disease status. In this way, it can also be possible to gain
information about aberrant cells which emerge through the progress
of the disease or condition, or to investigate whether and how
T-cell specificity is affected, thereby determining the status of a
disease or condition. The binding of the MHC molecule construct
makes possible these options, since the binding is indicative for
the presence of the MHC recognising cells in the sample, and
accordingly the presence of MHC molecules displaying the
peptide.
[0674] The present invention also relates to methods for the
diagnosis of a disease involving MHC recognising cells comprising
the steps of (a) providing a sample suspected of comprising MHC
recognising cells, (b) contacting the sample with a MHC molecule
construct as defined above, and (c) determining any binding of the
MHC molecule construct, thereby diagnosing a disease involving MHC
recognising cells.
[0675] Such diagnostic methods are a powerful tool in the diagnosis
of various diseases. Establishing a diagnosis is important in
several ways. A diagnosis gives information about the disease, thus
the patient can be offered a suitable treatment regime. Also,
establishing a more specific diagnosis can give important
information about a subtype of a disease for which a particular
treatment will be beneficial (i. e. various subtypes of diseases
can involve display of different peptides which are recognised by
MHC recognising cells, and thus treatment can be targeted
effectively against a particular subtype). Valuable information can
also be obtained about aberrant cells emerging through the progress
of the disease or condition as well as whether and how T-cell
specificity is affected. The binding of the MHC molecule construct
makes possible these options, since the binding is indicative for
the presence of the MHC recognising cells in the sample, and
accordingly the presence of MHC molecules displaying the
peptide.
[0676] The present invention also relates to methods of correlating
cellular morphology with the presence of MHC recognising cells in a
sample comprising the steps of (a) providing a sample suspected of
comprising MHC recognising cells, (b) contacting the sample with a
MHC molecule construct as defined above, and (c) determining any
binding of the MHC molecule construct, thereby correlating the
binding of the MHC molecule construct with the cellular
morphology.
[0677] Such methods are especially valuable as applied in the field
of histochemical methods, as the binding pattern and distribution
of the MHC multimers can be observed directly. In such methods, the
sample is treated so as to preserve the morphology of the
individual cells of the sample. The information gained is important
i. a. in diagnostic procedures as sites affected can be observed
directly.
[0678] The present invention also relates to methods for
determining the effectiveness of a medicament against a disease
involving MHC recognising cells comprising the steps of (a)
providing a sample from a subject receiving treatment with a
medicament, (b) contacting the sample with a MHC molecule construct
as defined herein, and (c) determining any binding of the MHC
molecule construct, thereby determining the effectiveness of the
medicament.
[0679] Such methods are a valuable tool in several ways. The
methods can be used to determine whether a treatment is effectively
combating the disease. The method can also provide information
about aberrant cells which emerge through the progress of the
disease or condition as well as whether and how T-cell specificity
is affected, thereby providing information of the effectiveness of
a medicament in question. The binding of the MHC molecule construct
makes possible these options, since the binding is indicative for
the presence of the MHC recognising cells in the sample, and
accordingly the presence of MHC molecules displaying the
peptide.
[0680] The present invention also relates to methods for
manipulating MHC recognising cells populations comprising the steps
of (a) providing a sample comprising MHC recognising cells, (b)
contacting the sample with a MHC molecule construct immobilised
onto a solid support as defined above, (c) isolating the relevant
MHC recognising cells, and (d) expanding such cells to a clinically
relevant number, with or without further manipulation.
[0681] Such ex vivo methods are a powerful tool to generate
antigen-specific, long-lived human effector T-cell populations
that, when re-introduced to the subject enable killing of
targeT-cells and has a great potential for use in immunotherapy
applications against various types of cancer and infectious
diseases.
[0682] As used everywhere herein, the term "MHC recognising cells"
are intended to mean such which are able to recognise and bind to
MHC molecules. Such MHC recognising cells can also be called MHC
recognising cell clones, targeT-cells, target MHC recognising
cells, target MHC molecule recognising cells, MHC molecule
receptors, MHC receptors, MHC peptide specific receptors, or
peptide-specific cells. The term "MHC recognising cells" is
intended to include all subsets of normal, abnormal and
defecT-cells, which recognise and bind to the MHC molecule.
Actually, it is the receptor on the MHC recognising cell that binds
to the MHC molecule.
[0683] As described above, in diseases and various conditions,
peptides are displayed by means of MHC molecules, which are
recognised by the immune system, and cells targeting such MHC
molecules are produced (MHC recognising cells).
[0684] Thus, the presence of such MHC protein recognising cells is
a direct indication of the presence of MHC molecules displaying the
peptides recognised by the MHC protein recognising cells. The
peptides displayed are indicative and can be involved in various
diseases and conditions.
[0685] For instance, such MHC recognising cells can be involved in
diseases of inflammatory, auto-immune, allergic, viral, cancerous,
infectious, allo- or xenogene (graft versus host and host versus
graft) origin.
[0686] In particular, the MHC recognising cells can be involved in
a chronic inflammatory bowel disease such as Crohn's disease or
ulcerative colitis, sclerosis, type I diabetes, rheumatoid
arthritis, psoriasis, atopic dermatitis, asthma, malignant
melanoma, renal carcinoma, breast cancer, lung cancer, cancer of
the uterus, cervical cancer, prostatic cancer, brain cancer, head
and neck cancer, leukaemia, cutaneous lymphoma, hepatic carcinoma,
colorectal cancer, bladder cancer, rejection-related disease,
Graft-versus-host-related disease, or a viral disease associated
with hepatitis, AIDS, measles, pox, chicken pox, rubella or
herpes.
[0687] In one embodiment, the MHC recognising cells are selected
from subpopulations of CD3+ T-cells, gamma, delta T-cells, alpha,
beta T-cells, CD4+ T-cells, T helper cells, CD8+ T-cells,
Suppressor T-cells, CD8+ cytotoxic T-cells, CTLs, NK cells,
NKT-cells, LAK cells, and MAK.
[0688] In the above-described methods, the sample is preferably
selected from histological material, cytological material, primary
tumours, secondary organ metastasis, fine needle aspirates, spleen
tissue, bone marrow specimens, cell smears, exfoliative cytological
specimens, touch preparations, oral swabs, laryngeal swabs, vaginal
swabs, bronchial lavage, gastric lavage, from the umbilical cord,
and from body fluids such as blood (e. g. from a peripheral blood
mononuclear cell (PBMC) population isolated from blood or from
other blood-derived preparations such as leukopheresis products),
from sputum samples, expectorates, and bronchial aspirates. Such
samples can be used as they are, or they can be subjected to
various purification, decontamination, filtration, or concentration
methods, and/or methods to isolate parts of the sample like
immunomagnetic separation. The sample or part thereof (sample
constituents) can further be treated so as to preserve morphology
or arrest the cells of the sample.
[0689] Such methods for sample treatment are readily known by the
person skilled in the art.
[0690] The MHC molecule construct employed in the methods of the
invention may, as mentioned above, be directly or indirectly
labelled so as to facilitate observation of binding. Thus, the MHC
molecule construct can suitably be labelled so as to enable
observation by inspection in a microscope, by light, by
fluorescence, by electron transmission, or by flow cytometry.
[0691] It is to be understood that one MHC molecule construct can
be employed in the methods as well as several (a plurality of) MHC
multimers (i. e. one or more), depending on the information
desired. The total number of MHC multimers as well as actual
combination of MHC molecules, peptides, optionally biologically
active compounds, and optionally labelling compounds are in
principle unlimited.
[0692] The methods of the invention described above can suitably be
such, wherein the sample to be analysed is mounted on a support.
The support can suitably be a solid or semi-solid surface. Suitable
solid and semi-solid surfaces are readily known in the art, and
include glass slides, beads, particles, membranes, filters, filter
membranes, polymer slides, polymer membranes, chamber slides,
backings, settings, dishes, and petridishes. In particular, the
support can be a glass slide, a membrane, a filter, a polymer
slide, a chamber slide, a dish, or a petridish. The sample or parts
thereof can suitably be grown or cultured directly on the support
prior to analysis.
[0693] However, the cells need not be grown or cultured prior to
analysis. Often the sample will be analysed directly without
culturing. It is to be understood that samples for direct analysis
can undergo the processing procedures described above.
[0694] Thus, the sample may, either directly or after having
undergone one or more processing steps, be analysed in primarily
two major types of methods, in situ methods (in situ analyses) and
in vitro methods (in vitro analyses).
[0695] In this context, in situ methods (in situ analyses) are to
be understood as assays, in which the morphology of the sample
cells is essentially preserved. By "essentially preserved" is meant
that the overall morphology is preserved, making it possible to
identify some or all of the structural compositions of the tissue
or cells. Examples are analysis of smears, biopsies, touch
preparations and spreading of the sample onto the support. Samples
can be subjected to i. a. fixation, permeabilisation, or other
processing steps prior to analysis.
[0696] In vitro methods are to be understood as methods, in which
the overall morphology is not preserved. In the case of in vitro
methods, the sample is subjected to a treatment, which disrupts the
morphology of the cell structure. Such treatments are known to the
person skilled in the art and include treatment with organic
solvents, treatment with strong chaotropic reagents such as high
concentrations of guanidine thiocyanate, enzyme treatment,
detergent treatment, bead beating, heat treatment, sonication
and/or application of a French press.
[0697] Histological and cytological materials include biopsies and
other tissue samples. In general, cytology is the study of the
structure of all normal and abnormal components of cells and the
changes, movements, and transformations of such components.
Cytology disciplines include cytogenics, cytochemistry, and
microscopic anatomy. Cells are studied directly in the living state
or are killed (fixed) and prepared by e. g. embedding, sectioning,
or staining for investigation in bright field or electron
microscopes.
[0698] One well-known cytology procedure is the Papanicolaou test
medical procedure used to detect cancer of the uterine cervix. A
scraping, brushing, or smear, is taken from the surface of the
vagina or cervix and is prepared on a slide and stained for
microscopic examination and cytological analysis. The appearance of
the cells determines whether they are normal, suspicious, or
cancerous.
[0699] By histology is generally understood the study of groups of
specialised cells called tissues that are found in most
multi-cellular plants and animals.
[0700] Histologists study the organisation of tissues at all
levels, from the whole organ down to the molecular components of
cells. Animal tissues are for example classified as epithelium,
connective, muscle and nerve tissue. Blood and lymph are sometimes
commonly classified separately as vascular tissue.
[0701] These tissue types are combined in different ways in the
organism to form characteristic organs. The way cells are connected
and organised is sometimes called the morphology of the tissue and
gives valuable information about the state of the cells and the
tissue.
[0702] A variety of techniques are used for histological studies,
including tissue culture, use of various fixatives and stains, the
use of a microtome for preparing thin sections, light microscopy,
electron microscopy, and X-ray diffraction. The histology field
also includes histochemistry, which is the study of the chemical
composition of tissue structures.
[0703] Histological investigation includes study of tissue death
and regeneration and the reaction of tissue to injury or invading
organisms. Because normal tissue has a characteristic appearance,
histologic examination is often utilised to identify diseased
tissue.
[0704] There are in general, two categories of histological
materials. The most common is a fixed, paraffin-embedded tissue
specimen, often archive material. These specimens are fixed,
usually using a formalin-based fixative, dehydrated to xylene,
embedded in paraffin or plastic (e. g. Epon, Araldite, Lowicryl, LR
White or polyacrylamide), sectioned onto a slide, deparaffinised or
otherwise treated, re-hydrated, and stained.
[0705] The second category includes preparations, which are fresh
tissues and/or cells, which generally are not fixed with
aldehyde-based fixatives. Such specimens are either placed directly
on a slide or cover slip, or frozen and sectioned onto slides. Such
specimens are then fixed, usually with an alcohol- or acetone-based
fixative, and stained. These specimens commonly include biopsy
materials, which can be analysed while the surgical procedure is in
progress (frozen sections), cytological preparations (including e.
g. touch preparations and blood smears), and tissues, which are to
be histochemically analysed.
[0706] The method of viewing the stained specimens includes bright
field microscopes or scanners, fluorescent microscopes or scanners,
transmission electron microscope (TEM) or scanning electron
microscope (SEM).
[0707] Immunostaining requires a series of treatment steps
conducted on a tissue section mounted on a slide to highlight by
selective staining certain morphological indicators of disease
states. Typical steps include pre-treatment of the tissue section
to reduce non-specific binding, contacting with specific reagent,
and various visualisation techniques, optionally separated by
washing steps. Counterstaining with e. g. hematoxylin, Ehrlich
staining, Sirius red, Methyl green, methylene blue, and the like,
can also be applied. Incubations at room temperature or at slightly
elevated temperatures, usually around 40.degree. C., can be
applied, and the tissue must be continuously protected from
dehydration.
[0708] In the following, some of the individual steps in a staining
procedure are described.
[0709] Fixatives are needed to preserve cells and tissues in a
reproducible and life-like manner. To achieve this, tissue blocks,
sections, or smears are immersed in a fixative fluid, or in the
case of smears, are dried.
[0710] Fixatives stabilise cells and tissues thereby protecting
them from the rigors of processing and staining techniques.
[0711] Types of fixative include formalin (aqueous formaldehyde)
and neutral buffered formalin (NBF) is among the most commonly
used. Other fixatives include glutaraldehyd, acrolein,
carbodiimide, imidates, benzoequinone, osmic acid and osmium
tetraoxide.
[0712] Fresh biopsy specimens, cytological preparations (including
touch preparations and blood smears), frozen sections and tissues
for immunohistochemical analysis are commonly fixed in organic
solvents, including ethanol, methanol and/or acetone.
[0713] The methods for attaching or mounting sections to slides
include using clean slides and relying on the capillary attraction
and no adhesives. Other techniques include glues like egg-white
glycerine, glycerine-gelatine mixtures, polyvinyl acetate glue,
chrome-alum gelatine and poly lysine coating. Heating or "burning"
of the section as a means of facilitating mounting of the section
should be used with caution, as the tissue can be destroyed.
[0714] To facilitate the specific recognition in fixed tissue, it
is often necessary to retrieve or unmask the targets through
pre-treatment of the specimens to increase reactivity of the
majority of targets.
[0715] Target retrieval includes a variety of methods by which the
availability of the target for interaction with a specific
detection reagent is maximised. The most common techniques are
enzymatic digestion with a proteolytic enzyme (e. g. Protinease,
pronase, pepsin, papain, trypsin or neuraminidase) in an
appropriate buffer or heat induced epitope retrieval (HIER) using
microwave irradiation, heating in a regular oven, autoclaving or
pressure-cooking in an appropriately pH stabilised buffer, usually
comprising EDTA, Tris-HCl, citrate, urea, glycin-HCl or boric
acid.
[0716] The penetration of reagents through the tissue section can
be increased using detergents during pre-treatment of sections or
cytological preparations, or as additives to dilution media and
rinsing buffers.
[0717] Additionally, the signal-to-noise ratio can be increased by
different physical methods, including application of vacuum and
ultrasound, or freezing and thawing of the sections before or
during incubation of the reagents.
[0718] Endogenous biotin binding sites or endogenous enzyme
activity (e. g. phosphatase, catalase or peroxidase) can be removed
as a step in the staining procedure.
[0719] Similarly, blocking of unspecific binding sites with inert
proteins like, HSA, BSA, ovalbumine, fetal calf serum or other
sera, or detergents like Tween20, Triton X-100, Saponin, BRIJ.RTM.
or PLURONIC.RTM. s is widely used.
[0720] Blocking unspecific binding sites in the tissue or cells
with unlabelled and target non-specific versions of the specific
reagents.
[0721] The standard visualisation techniques utilised in
immunocytochemistry can not be used directly for staining of the
receptors, as the binding relies on the low binding strength of MHC
molecules and not the high avidity antibodies or DNA probes
normally used. Also, the polymorph and somewhat sensitive nature of
the MHC molecule distinguishes it from e. g. the monoclonal
antibodies used in immunocytochemistry. On the other hand, in order
to be of practical use, specific receptor staining procedures and
methods used should resemble current methods.
[0722] The present invention surprisingly makes it possible to
stain specific receptors using a methodology which resembles
routine immunocytochemistry procedures.
[0723] The most commonly used detection methods in
immuno-histochemistry are direct visualisation of fluorescence or
gold particles and enzyme mediated colorimetric detection.
[0724] For direct fluorescent studies, the labels can e. g. be
5-(and 6)-carboxyFLUORESCEIN.TM., 5- or 6-carboxyFLUORESCEIN.TM.,
6-(FLUORESCEIN.TM.)-5-(and 6)-carboxamido hexanoic acid,
FLUORESCEIN.TM. isothiocyanate (FITC), rhodamine,
tetra-methylrhodamine, and dyes such as Cy2, Cy3, and CY5.TM.,
optionally substituted coumarin including AMCA, PerCP,
phycobiliproteins including R-phycoerythrin (RPE) and
allophycoerythrin (APC), Texas Red, Princeston Red, Green
fluorescent protein (GFP) and analogues thereof, and conjugates of
R-phycoerythrin or allophycoerythrin and e. g. CY5.TM. or Texas
Red, and inorganic fluorescent labels based on semiconductor
nanocrystals (like quantum dot and QDOT.RTM.TX nanocrystals), and
time-resolved fluorescent labels based on lanthanides like Eu3+ and
Sm3+.
[0725] Colloidal gold or silver can be used as direct labels for
immunocytochemical studies for electron microscopy and light
microscopy. Amplification of the signal can be obtained by further
silver enhancement of the colloidal gold particles.
[0726] The general enzymatic methods use labelled avidin or
streptavidin-biotin (LAB), avidin or streptavidin-biotin complex
(ABC), enzyme anti-enzyme complex (e. g. PAP and APAAP), direct
dextran polymer based antibody-enzyme complex (e. g. DAKO's EPOS);
indirect dextran polymer based antibody-enzyme complex (e. g.
DAKO's EnVision) or double bridge enzyme anti-enzyme complex.
[0727] The enzymatic staining uses enzymatic labels such as horse
radish peroxidase (HRP), alkaline phosphatase (AP),
beta-galactosidase (GAL), glucose-6-phosphate dehydrogenase,
beta-N-acetylglucosaminidase, invertase, Xanthine Oxidase, firefly
luciferase and glucose oxidase (GO).
[0728] Examples of commonly used substrates for horse radish
peroxidase include 3,3'-diaminobenzidine (DAB), diamino-benzidine
with nickel enhancement, 3-amino-9-ethylcarbazole (ABC), Benzidine
dihydrochloride (BDHC), Hanker-Yates reagent (HYR), Indophane blue
(IB), tetramethyl-benzidine (TMB), 4-chloro-l-naphtol (CN),
a-naphtol pyro-nin (a-NP), o-dianisidine (OD),
5-bromo-4-chloro-3-indol-ylphosphate (BCIP), Nitro blue tetrazolium
(NBT), 2-(p-iodophenyl)-3-p-nitrophenyl-5-phenyl tetrazolium
chloride (INT), tetranitro blue tetrazolium (TNBT),
5-bromo-4-chloro-3-indoxyl-beta-D-galactoside/ferro-ferricyanide
(BCIG/FF).
[0729] Examples of commonly used substrates for Alkaline
Phosphatase include Naphthol-AS-B1-phosphate/fast red TR (NABP/FR),
Naphthol-AS-MX-phosphate/fast red TR (NAMP/FR),
Naphthol-AS-BI-phosphate/fast red TR (NABP/FR),
Naphthol-AS-MX-phosphate/fast red TR (NAMP/FR),
Naphthol-AS-BI-phosphate/new fuschin (NABP/NF), bromochloroindolyl
phosphate/nitroblue tetrazolium (BCIP/NBT),
5-Bromo-4-chloro-3-indolyl-b-d-galactopyranoside (BCIG).
[0730] One of the most potent detection systems is the catalysed
reporter deposition (CARD); this amplification method is based on
the deposition of labelled tyramide on tissue through the enzymatic
action of HRP. After HRP-immunostaining, labelled tyramide is
applied and bound near the site of HRP-activity. The bound and
labelled tyramide is then visualised by traditional fluorescence or
colorimetric enzyme mediated detection.
[0731] Automated staining systems have been introduced to reduce
cost, increase uniformity of slide preparation, reduce laborious
routine work and most significantly reduce procedural human
errors.
[0732] The current automated systems can handle any immunochemical
assay including assays relying on immunofluorescence, indirect
immunoassay procedures, enzyme or gold staining methods. They
perform all steps of the immunohistochemical assay irrespective of
complexity or their order, at the prescribed time and
temperature.
[0733] Immunocytochemistry techniques have traditionally used
specific antibodies for identification and visualisation of
specific antigens. The technique is complex, many steps and
molecules with high affinities for specific staining are
needed.
[0734] By the present invention, immunocytochemistry techniques
have been improved to allow identification of the minute quantity
of delicate receptors, which is not based on antibody-antigen
interactions.
[0735] Staining of MHC peptide specific receptors in tissue mounted
on e. g. slides will be a very potent diagnostic tool, enabling
identification of MHC peptide specific receptors, optionally
combined with morphological information, if desired.
[0736] By further combining morphological information with double
staining of specific cells and specific receptors, additional
useful diagnostic information can be obtained.
[0737] Flow cytometric method The MHC multimers of the invention
are suitably used as labelled reagents to identify MHC recognising
cells by flow cytometry. This further allows for the analysis of
additional surface markers like e. g. antibody epitopes expressed
by CD8, CD4, CD3, CD94/NKG2-A/C and KIRs.
[0738] A further advantage of the MHC multimers of the invention is
that by coupling flow cytometric analysis with high-speed cell
sorting, functional assays can be performed on sorted cells without
the need for in vitro expansion of the cells to be analysed.
[0739] In the flow cytometer, different cells can be identified by
their distinct cell morphology like density, shape and size. Tissue
morphology as such is not visible from the data obtained from flow
cytometer as the cells are broken up.
[0740] Flow cytometry is a system for measuring cells, beads or
particles as they move in a liquid stream, in the so-called flow
cell, through a laser or light beam past a sensing area. The
relative light scattering and colour discriminated fluorescence of
the particles is measured.
[0741] A flow cytometer consists in general of a light source, flow
cell, optics to focus light of different colours onto a detector,
signal amplifier and processor and a computer to record and analyse
data.
[0742] Lasers are used as the preferred light source in modern flow
cytometers. The most common laser used is the argon-ion laser. This
produces a major line at 488 nm, which gives a source of blue light
for excitation of e. g. FLUORESCEIN.TM. phycoerythrin, and tandem
conjugates and for propidium iodide used in DNA measurements. In
the flow cell, cells are aligned by hydrodynamic focusing, so that
they pass through the laser beams one at a time.
[0743] Light scatter is utilised to identify the cell or particle
population of interest, while the measurement of fluorescence
intensity provides specific information about individual cells.
[0744] Individual cells held in the stream of fluid are passed
through one or more laser beams. The cells scatter the laser light,
which at the same time make fluorescent dyes emit light at various
frequencies. Photomultiplier tubes (PMT) convert light to
electrical signals and cell data is collected.
[0745] What makes flow cytometry such a powerful technique is its
ability to measure several parameters on many thousands of
individual cells in a very short time, by measurement of their
fluorescence and the way in which they scatter light. As an
example, using blue light for excitation, it is possible to measure
red, green and orange fluorescence and the amount of light
scattered, both forward and at right angles to the beam, on each
cell in a population of thousands.
[0746] Many instruments can measure at least five different
parameters. As all the parameters cannot be combined for display
simultaneously in a correlated fashion, a system called gating is
employed. Regions of interest- or "Gates"-are defined, enabling
selection of specific cell populations for display of further
parameters. A flow cytometer can be used to analyse sub-populations
of cells, which have been fluorescently labelled, with speed and
accuracy. Sorting on the basis of other features, e. g. size, is
also possible.
[0747] Flow cytometry instruments simultaneously generate three
types of data: 1) Forward scatter (FSc) gives the approximate cell
or particle size, 2) Side or Orthogonal scatter (SSc) gives the
cell or particle complexity or granularity, and 3) fluorescent
labelling is used to investigate e. g. cell structure and
function.
[0748] Forward and side scatter are used for preliminary
identification of cells. In a peripheral blood sample, for example,
lymphocyte, monocyte, and granulocyte populations can be defined on
the basis of forward and side scatter. Forward and side scatter are
used to exclude debris and dead cells. Particles, for example, can
be identified by their size and/or their fluorescence.
[0749] Cell or particle populations can be represented on single or
dual parameter histograms. Light scatter and fluorescence signals
can be analysed after linear or logarithmic amplification. Once the
population of cells or particles to be analysed has been
identified, the fluorescence associated with bound antibodies or
dyes is determined after the background fluorescence has been
established.
[0750] Some flow cytometers are able to physically sort cells or
particles into specific populations. This is most commonly done by
electrostatic deflection of charged droplets comprising a cell. The
flow cell is vibrated and causes the liquid stream to break up into
small droplets as it leaves the exit nozzle. At the moment a cell
or particle of interest is inside the droplet currently being
formed, the flow cell is charged-thus charging the droplet. The
stream of droplets then passes through a pair of electrically
charged plates, and droplets that are charged (comprising the cells
or particles of interest) are deflected into a collection
vessel.
[0751] The electric field created between the plates can direct the
cells or particles towards one of several, user-specified
collection receptacles. Uncharged droplets flow into a waste
vessel.
[0752] Analysis of concentrations of cells or subsets of cells,
often referred to as "absolute counting", can be of further
interest for medical diagnostics or monitoring the status of cells
in cell cultures or other biotechnological processes.
[0753] The flow cytometer is able to rapidly screen large numbers
of cells far beyond the capacity of traditional pathological or
cytological methods. The information obtained aids in the
diagnosis, classification, and prognosis of a variety of
diseases.
[0754] The applications to which flow cytometry can be applied have
expanded rapidly from cell sorting, to measurement of cell surface
antigens, and analysis of DNA to aid the interpretation of
malignant disorders.
[0755] Common uses for flow cytometry in the routine clinical
laboratory include immunophenotyping of hematopoietic neoplasms,
immune status evaluation, especially quantificaation of CD4+
T-cells in HIV positive patients, and DNA cell cycle analysis of
solid tumours.
[0756] Different cell populations that compose the hematopoietic
system express distinct different cell surface antigens at various
stages of maturation. By detecting and measuring these expressed
antigens, flow cytometry can aid in the classification of the cell
lineage of leukaemia and lymphoma.
[0757] Although not intended to be an independent diagnostic
modality, flow cytometry is often able to sub-classify
haematopoietic malignancies beyond the capabilities of traditional
morphologic and cytochemical techniques.
[0758] The most common routine uses of flow cytometry have been
measurement of surface antigens (markers) by immuno-fluorescent
labelling using monoclonal antibodies. The markers commonly used
are total B-cells, total T-cells and subsets of T-cells. The
markers for total T-cells, Helper T-cells and suppressor T-cells
have been assigned the cluster differentiation (CD) categories of
CD3, CD4, and CD8, respectively. This spectrum of markers, of which
there are more than 45 in all, are used for clinical classification
of immunodeficiency states, lymphoid leukaemias, autoimmune
diseases and for monitoring their response to therapy.
[0759] For example, CD4 and CD8 measurements are especially useful
to monitor the progression of AIDS, as the CD4+ cells are depleted
by infection by HIV, whereas the CD8+ cells persist. The absolute
number of CD4+ cells is also a marker of progression of HIV
infection to more overt AIDS. The CD4/CD8 ratio can also be used to
assess the success of immunosuppressive therapy with cyclosporin A
in transplant patients.
[0760] For immune status evaluation, typically sub-populations of
lymphocytes are identified and quantified by the flow cytometer by
utilising monoclonal antibodies to various cell surface antigens.
Patients with acquired or congenital immunodeficiency disease and
patients on immunosuppressive drug therapy exhibit characteristic
alterations in lymphocyte populations.
[0761] The typical direct staining procedure for flow cytometry can
include one or several of the following steps besides washing and
mixing steps: Fixation of the cells with e. g. buffered
formaldehyde, permeabilisation, addition of fluorescently labelled
target specific reagent, incubation, centrifugation, aspiration of
the supernatant from the cell pellet, resuspension, dilution and
analysis on flow cytometer.
[0762] Several examples on flow cytometry based detection and
quantitative analysis of proliferating immune subpopulations of in
vitro expanded T-cells in blood samples from patients have been
reported. Well-known examples on antigenic TAA peptides recognised
by T-cell that have been monitored in patients undergoing tumour
specific immune therapy are MART-1 (27-35), gap100 (154-162), and
NY-ESO (157-165). Other interesting MHC molecules include HLA A,
HLA B, HLA C, H-2, DR-alleles and HLA E to detect a variety of
receptors with low intrinsic affinities e. g. peptide specific TCRs
and NK receptors like CD94/NKG2-A/C and KIRs.
[0763] The interaction between peptide/MHC molecule and the
specific counter receptor is driven by a relatively high affinity,
which is essential for the staining function.
[0764] The constructs of the invention are therefore in particular
useful for flow cytometric analysis of even subtle subpopulations
of MHC recognising cells. The increased binding avidity of MHC
multimers of the invention allows detection of MHC recognising
cells expressing low affinity receptors. The augmented interactions
also allow detection of even very small MHC recognising cell
populations in blood samples without the need for in vitro
expansion. It is therefore envisioned that MHC multimers of the
invention are useful for direct monitoring by flow cytometry of all
types of MHC recognising cells in blood samples.
[0765] The poly-ligand MHC multimers of the invention also allow
better separation of specific and unspecific MHC recognising cells
and, thus, augment utilisation of fast flow cell sorting of antigen
specific MHC recognising cells.
[0766] Other techniques Also, it is believed that the MHC multimers
of the invention can suitably be applied in the so-call
"free-floating" techniques.
[0767] In staining procedures using the so-called "free floating
techniques", a tissue section is brought into contact with
different reagents and wash buffers in suspension or freely
floating in appropriate containers, e. g. micro centrifuge
tubes.
[0768] The tissue sections can be transferred from tube to tube
with different reagents and buffers during the staining procedure
using e. g. a "fishing hook like" device, a spatula or a glass
ring.
[0769] The different reagents and buffer can also be changed by
gentle decantation or vacuum suction. Alternatively, containers
with the tissue sections can be emptied into a special staining
net, like the Corning "Netwells" and the tissue section washed
before being transferred back into the tube for the next staining
step.
[0770] All the individual staining procedure steps, including e. g.
fixation, antigen retrieval, washing, incubation with blocking
reagents, immuno-specific reagents and e. g. the enzymatic
catalysed development of the coloured stains, are done while the
tissue section is floating freely or withheld on nets. After
development of the stain, the tissue section is mounted on slides,
dried, before being counterstained and cover slipped before being
analysed in e. g. a microscope.
[0771] Occasionally, the tissue section is mounted on slides
following the critical incubation with the immuno-specific
reagents. The rest of the staining process is then conducted on the
slide mounted tissue sections.
[0772] The free-floating method has been used mainly on thick
tissue sections. It is important that sections never dry out during
the staining process.
[0773] Advantages of the free-floating method include even and good
penetration of the immunohistochemical staining reagents. The
free-floating method allows for high concentrations of reagents and
good mixing.
[0774] Compositions comprising MHC multimers Compositions (kits)
comprising MHC multimers are also an important embodiment of the
present invention. Such compositions can be formulated in a way
making them ready-to-use in hospitals and laboratories.
[0775] They can also be formulated so as to enable the user to
modify or use as desired.
[0776] It is to be understood that the composition can include one
MHC molecule construct or several MHC molecule constructs,
depending on the intended use. The total number of MHC multimers as
well as actual combination of MHC molecules and peptides are in
principle unlimited.
[0777] Thus, the present invention relates to compositions
comprising a MHC molecule construct as defined above and optionally
other components such as buffers and/or visualisation means. The
MHC molecules of the MHC molecule construct can be peptide filled
or peptide free MHC molecules as defined above, or a mixture
thereof. The MHC molecule construct and optionally other components
can be provided in separate containers or in the same
container.
[0778] In one embodiment, the composition of the invention
comprises a MHC molecule construct as defined above in a
solubilising medium. The composition can be such, wherein the MHC
molecule construct comprises peptide filled MHC molecules, or such,
wherein the MHC molecule construct comprises peptide free MHC
molecules. In the latter case, the composition can be such, wherein
peptides to fill the peptide free MHC molecules, and the MHC
molecule construct comprising peptide free MHC molecules are
provided separately.
[0779] In another embodiment, the composition of the invention
comprises a MHC molecule construct as defined above, wherein the
MHC molecule construct is immobilised onto a solid or semi-solid
support. Suitable solid and semi-solid supports are indicated
above. The composition can be such, wherein the MHC molecule
construct comprises peptide filled MHC molecules, or such, wherein
the MHC molecule construct comprises peptide free MHC
molecules.
[0780] In the latter case, the composition can be such, wherein
peptides to fill the peptide free MHC molecules are provided
separately.
[0781] In particular, the MHC multimers can be provided in a form,
wherein the MHC molecules are filled with low affinity peptides.
Thus, it can be possible to exchange these low affinity peptides
with higher affinity peptides for a particular use. This
application can particularly be valuable when providing the
compositions (kits). Filling the MHC molecules with low affinity
peptides has the advantage of stabilising the MHC molecules, while
providing the benefits of peptide free MHC molecules.
[0782] In the following, the production of MHC molecules, peptides,
and MHC multimers is described.
[0783] Production of MHC molecules, peptides and MHC multimers
Herein the production of MHC molecules and i. a. their usage for
well-defined MHC molecules organised as poly-ligand compounds on
one or more multimerization domain(s) (MHC molecule constructs) to
achieve specific binding of the MHC molecule to immune competent
targeT-cells (MHC recognising cells) expressing appropriate T-cell
receptors and NK cell receptors are described.
[0784] Production of MHC molecule Some MHC molecules have proven
very difficult to obtain from natural sources i. e. eukaryotic
cells as they are contaminated or pre-occupied with undesired
peptides during the cellular biosynthesis.
[0785] Recent technological progress allows production of peptide
empty but functional MHC Class I as well as MHC Class II using
appropriate cDNA ligated into a bacterial expression vector. In
vitro folding procedure Oxidized Protein Folding (OPF) allows
production of well-defined MHC Class I molecules. The method can be
of use in any protein production scheme (be it in prokaryotes or
eucaryotes) where the protein (e. g. inclusion bodies) at some
point during the production is solvated in chaotrophic (e. g. urea)
at conditions that do not disrupt established and appropriate
disulphide bonds. Briefly, the OPF method takes advantage of
pre-formed disulphide bonds that guide the denatured MHC molecule
through an efficient and fast folding pathway in buffers with
appropriate conditions (like pH, salinity). By example, peptide
empty and relatively stable MHC Class I molecule is instantly
formed by dilution of denatured heavy chain molecule with
appropriate disulphide bonds in a buffer comprising excess of
functional .beta.2m. This intermediate state of de novo folded MHC
Class I heavy chain is strictly controlled by the presence of P2m.
Subsequent addition of peptide induces molecular changes in the
heavy chain molecule and lead to formation of stable and functional
MHC Class I molecules. Thus, the OPF method allows production of
MHC Class I molecule in two distinct forms, namely a) as a peptide
filled molecule, which is extremely stable and T-cell binding, and
b) as a partially mature, peptide free molecule ("empty" MHC
molecules), which is reasonably stable and readily peptide
receptive. In comparison, conventional folding of bacterial
produced MHC molecule requires presence of both .beta.2m and
peptide and leads, consequently, only to stable peptide filled MHC
molecules.
[0786] Oxidised states of e. g. MHC Class I subunits can, only, be
obtained by biochemical purification, e. g. size exclusion and
ion-exchange chromatography of individual subunits from urea
solubilised bacterial inclusion bodies or from denatured MHC Class
I molecules produced in eukaryotic cells e. g. CHO cells.
[0787] The MHC molecules can also be generated by recombinant
technology to obtain well defined and highly purified components
tagged with an appropriate moiety (e. g. a biotinylation site) for
ligation to the one or more multimerization domain(s) via a binding
entity, like e. g. streptavidin. MHC molecules and MHC-like
molecules are only obtained with difficulty from natural sources,
as they are loaded with many different peptides in intracellular
compartments during biosynthesis. Efficient methods for production
of MHC molecules are also prerequisites to overcome the extreme
polymorphism of the MHC locus. In the human population more than
400 different HLA A, HLA B and HLA C alleles exist, and more that
200 HLA D alleles exist.
[0788] This molecular diversity has as stated above an
immunological purpose, but is a practical obstacle to MHC
production because many different MHC molecules need be generated
and individually optimised, validated, characterised, stored etc.
Recombinant MHC molecules that present well-defined peptides can,
however, be obtained with high efficacy by in vitro folding of
denatured and pre-oxidised subunits (i. e. heavy and light P2M of
MHC Class I molecules, and a, .beta. chains of MHC Class II
molecules) from MHC molecules that have been produced in bacteria
or eukaryotic cells.
[0789] MHC molecules can be obtained by cloning of cDNA encoding
the various molecules of interest following standard procedures, e.
g. as described in Molecular Cloning. Briefly, cDNA is synthesised
from appropriate cell lines using commercial cDNA synthesis kits
(in casu from Pharmacia). For instance, in the case of human cells,
the cells can be derived from the panel of HLA expressing EBV
transformed human B-cell lines from the 12 International
Histocompatibility Workshop Cell Lines Panel Database ("HLA:
Genetic diversity of HLA.
[0790] In the case of HLA A*0201, an appropriate cell line would be
the IHW 9012. The nucleotide sequence corresponding to a desired
MHC (HLA) molecule can be found at public available databases.
Using the appropriate sequence information oligonucleotide primers
can be designed to amplify by the PCR reaction the coding region
encompassing of the relevant mature MHC (HLA) molecule from the
appropriate cDNA. The relevant forward and backward primer set for
the purpose of amplifying is inserted into the Ncol and Hindlll
restriction sites of an appropriate expression vector. Suitable
expression vectors are e. g. obtainable from Novagen (Novagen, Inc,
Madison, Wis., USA).
[0791] The peptides (or peptide antigens) to fill the MHC molecules
can be any length. The peptides should be at least 8-10 amino acid
residues long when associated to MHC Class I molecules. The length
of the peptides associated to MHC Class II molecules are usually
longer than the peptides associated to MHC Class I molecules and
can be e. g. as much as 50 amino acid residues, however, usually
less than about 20 amino acid residues such as less than about 17
amino acid residues. However, it is to be understood that the
above-indicated lengths are by way of example, and should, thus,
not be limiting.
[0792] Since antigenic molecules or tissues are known for a number
of immunopathologies, suitable peptides can be selected using this
information. By way of example, a panel of antigenic peptides from
tumour-associated antigens recognised by specific cytotoxic T-cells
has been identified.
[0793] The amino acid composition can also be obtained by iterative
procedures or by molecular modelling. The rapid and reliable
identification of MHC Class I- and Class II-restricted T-cell
epitopes is essential in various fields of medical research
including the definition of new tumour antigens, auto-antigens or
with respect to infectious diseases. A prerequisite therefore is
the exact knowledge about the molecular interactions within the
MHC-peptide-TCR complex. By means of synthetic combinatorial
peptide libraries a large number of MHC peptide binding motifs have
been revealed with in the last ten years. A common feature of MHC
peptide binding motifs is the presence of anchor residues of the
peptide and pockets of the binding site, which control the strength
of peptide binding to the MHC molecule. More than 500 different MHC
molecules have been found, each of them comprising different
peptide binding motifs. From existing biodatabases comprising
information of binding motifs, a number of algorithms have
developed to predict MHC binding motifs deduced from known
sequences of antigens. One well-known example is the DATABASE OF
MHC LIGANDS AND PEPTIDE MOTIFS "SYFPEITHI", a database comprising
approximately 2000 peptide sequences known to bind Class I and
Class II MHC molecules. The entries are compiled from published
reports. The databases provide a strong tool for identification of
MHC binding motifs in molecules involved in a variety of infections
and cellular transformations. For example HIV/SIV antigens and
tumour-associated antigens have been identified. From the known
sequences of these antigens a number of MHC binding motifs have
been predicted and subsequently verified by peptide binding
analyses. Similar deductions of MHC binding peptides are available
for a variety of disease-associated antigens in e. g. cancer,
malaria and tuberculosis.
[0794] More recent approaches to improve prediction of suitable MHC
Class I peptide epitopes are based on knowledge to digest patterns
of proteosomes that generate the MHC Class I bound peptides in ER.
By example, the NetChop WVVVVWW server produces neural network
predictions for cleavage sites of the human proteasome (http://www.
cbs. dtu. dk/-services/NetChop/). Since the proteasome structure is
quite conserved, it is likely that the server is able to produce
reliable predictions for at least the other mammalian proteasomes.
A similar WVVVVW server is available at http://www.uni-tuebingen.
de/uni/kxi/.
[0795] Analysis by trained artificial networks enables
identification of additional motifs and characteristics that
promote or inhibit cleavage. The tools also enable, in combination
with a predictor of MHC binding capacity, a more complete
prediction of the generation and presentation of peptides on MHC
Class I molecules.
[0796] Peptides can be obtained by solid phase synthesis methods.
The first stage of the technique firstly introduced by Merrifield
(refs. 14 and 15) consists of peptide chain assembly with protected
amino acid derivatives on a polymeric support. The second stage of
the technique is the cleavage of the peptide from the support with
the concurrent cleavage of all side chain protecting groups to give
the crude free peptide. To achieve larger peptides, these processes
can be repeated sequentially.
[0797] For a review of this methodology, including the different
chemical protection schemes and solid and soluble supports, see for
example G. Barany and Fields (refs. 16 and 17).
[0798] A large number of peptides, so-called peptide libraries, can
be obtained by combinatorial peptide synthesis; see e. g. Gordon et
al., R. A. Houghten et al. and G. Jung et al. (refs. 18, 19 and
20). These collections of peptides can contain both natural,
unnatural amino acids and amino acid mimics in the sequences. The
libraries are useful for screening a large number of peptides.
[0799] Other methods for obtaining peptides include enzymatic
fragment ligation, genetic engineering techniques as e. g.
site-directed mutagenesis. Alternatively, the peptides can be
obtained after isolation from natural sources.
[0800] By the present invention, it is possible to bind low
affinity soluble MHC molecules stably to their specific counter
receptors. The process making this possible is described in the
following and comprises associating the MHC molecule to one or more
multimerization domain(s) (which can be chosen to be soluble or
non-soluble, depending on the intended use) to form the MHC
molecule construct, which thus is a poly-ligand (i. e. poly-valent)
compound.
[0801] The plurality of low affinity MHC molecules organised in
this way as multi- or poly-valent molecular complexes compensates
for intrinsic high off-rates related to binding of individual MHC
molecules.
[0802] The MHC multimers of the present invention expressing
multiple low affinity MHC molecules bind to specific receptors on
MHC recognising cells with high avidity. For instance, the monomer
form of soluble HLA Class I dissociates rapidly, whereas a MHC
molecule construct of the invention comprising HLA Class I has
proven far more stable.
[0803] Thus, the present invention further relates to a process for
preparing a MHC molecule construct.
[0804] The process of the invention comprises the steps of (a)
providing a MHC molecule or a MHC molecule subunit, and (b)
associating the MHC molecule or the MHC molecule subunit to one or
more suitable multimerization domain(s) as described herein, or a
suitable multimerization domain(s) and a suitable binding entity as
described herein, thereby obtaining a MHC molecule construct.
[0805] As mentioned, the multimerization domain(s) can be chosen so
as to be soluble or non-soluble.
[0806] More specifically, the process of the present invention
comprises the steps of (a) providing a prokaryotic or eukaryotic
cell comprising one or more genes coding for a tagged or untagged
MHC molecules or MHC molecule subunits, the gene or genes being
expressible in said cell, (b) cultivating the cell under conditions
where the gene is expressed, (c) isolating the MHC molecules or MHC
subunits from the cell under conditions which allow subsequent
purification of the MHC molecules or MHC molecule subunits
generated by the cell, and (d) optionally subjecting the isolated
MHC molecule subunits to a folding treatment prior to or during a
process of association to one or more multimerization domain(s) as
described herein, or a binding entity and one or more
multimerization domain(s) as described herein, thereby obtaining
the MHC molecule construct.
[0807] The MHC molecules can be generated in the same cell or in
different cells. In the latter case, the MHC molecules (which can
very well be two different kinds of molecules, e. g. a heavy chain
of a MHC Class I molecule and a fm) can be combined prior to or
during the time of association to the one or more multimerization
domain(s) (with or without a binding entity).
[0808] HosT-cells comprising appropriate expression vectors can be
prokaryotic or eukaryotic.
[0809] Particularly preferred for production of MHC molecules used
herein is the versatile and high expressive bacterial expression.
By way of example, an E. coli strain e. g. lysogene BL21 (DE3) can
easily be transformed with a cDNA encoding expression vector of
interest and induced to expression of large amounts of
molecules.
[0810] The host cells comprising expression plasmids encoding the
MHC molecules can be of prokaryotic origin (bacteria) or of
eukaryotic origin (yeast, insect or mammalian cells).
[0811] A preferred bacterial production is such which yields high
amounts of denatured subunit molecule e. g. heavy chain and p2m
molecule. Functional MHC molecules can be obtained by in vitro
folding following standard procedures known by persons skilled in
the art. For example, a conventional method describes that
denatured and fully reduced MHC Class I heavy chain molecule
obtained from bacteria regenerates in presence of P2m and
appropriate peptide at physical and chemical conditions that allow
formation of disulphide bonds and establishment of secondary and
tertiary formation of denatured polypeptide chains. Both peptide
and p2m are added in excess in comparison to the amount of folding
heavy chain to compensate for the low affinities of subunit
molecules in the early folding phases. The peptide of interest
should comprise appropriate anchor residues to ensure a sufficient
loading into the peptide-binding site formed by the heavy
chain.
[0812] A more recently developed and preferred method "Oxidised
Folding Protein" (OPF) takes advantage of heavy chain molecules
with pre-formed disulphide bonds, which direct a fast and more
efficient folding of denatured molecules.
[0813] This method describes folding of MHC Class I heavy chains in
presence of P2m alone. A peptide empty and bio-chemically stable
MHC Class I molecule is formed by association of heavy- and light
chain. Subsequent addition of peptides comprising appropriate
anchor residues leads to fast formation of the functional and
stable MHC-peptide complexes.
[0814] Well-defined MHC molecules or MHC molecule subunits can also
be produced in cells encoding appropriate cDNAs.
[0815] Expression vectors comprising such cDNA can be introduced
into host cells using any technique known in the art.
[0816] These techniques include electroporation, calcium-phosphate
mediated transfection, transferrin-polycation mediated DNA
transfer, transfection with naked or encapsulated nucleic acids,
liposome mediated cellular fusion, intracellular transportation of
DNA-coated latex beads, protoplast fusion and viral infection.
[0817] Therapy As mentioned above, the present invention relates in
general to the field of therapy. MHC multimers of the invention are
a powerful tool in various therapeutic applications. In particular,
the MHC multimers of the invention are applicable in in vivo and ex
vivo therapeutic applications as will be apparent from the
following.
[0818] The present invention is also based on the recognition that
it is possible to design a poly-ligand MHC molecule construct so as
to (I) target specific MHC recognising cells, and (II) induce a
response as desired, in specific target MHC recognising cells by
addressing receptors on such cells. It was further recognised that
with such design of MHC molecule/peptide complexes with a given
specificity, it is possible to "add" other stimuli to the
therapeutic composition by incorporating other molecules, which
will affect the activity of the MHC recognising cells. Thus, it is
possible to modulate the activity of specifically targeted MHC
recognising cell clones, while leaving other MHC recognising cell
clones unaffected.
[0819] Furthermore, it is also possible to specifically modulate
the activity of more than one MHC recognising cell clone by
choosing the before-mentioned other molecules appropriately. The
inventions is further based on the recognition that it is possible
to obtain specific MHC recognising cells using the MHC multimers
described herein, to modulate such ex vivo, whereby such cells can
be used for in vivo treatment.
[0820] Accordingly, the present invention provides for methods of
up-regulating, down-regulating, modulate, restoring, enhancing,
and/or stimulate the immune system, as well as methods of inducing
anergy of cells. This can in accordance with the present invention
in general be accomplished in two ways, namely in vivo or ex vivo.
By "in vivo" is meant that an effective amount of an active
substance or ingredient is administered to a subject by any
suitable route, the active substance or ingredient exerting its
effect in the subject. By "ex vivo" (can also be termed "in vitro")
is meant thaT-cells withdrawn from a subject are in some way
affected outside the subject, and then re-introduced to the
subject, thereby achieving a desired response.
[0821] It is to be understood that the therapeutic compositions of
the present invention can comprise one or more MHC multimers as
defined above. As also described above, the MHC molecules of the
construct can be peptide filled, peptide empty or mixtures thereof.
The MHC molecules of each construct can be the same or
different.
[0822] Likewise, the peptides of the MHC molecules can be the same
or different. Likewise, the MHC molecule construct can comprise one
or more biologically active molecules, which can be the same or
different. These expressions are described in the foregoing.
[0823] In particular, the inclusion of biologically active
molecules can be important to initiate a response as desired. As
mentioned above, the immune system is dependent on several
signalling pathways, and thus inclusion of biologically active
molecules, either as part of the MHC construct or alone, can be an
excellent way to control or guide the immune system.
[0824] Thus, the present invention relates generally to the MHC
multimers per se as defined above for use as therapeutic
compositions or medicaments. The present invention also relates to
the MHC multimers as defined herein for use in in vivo therapy and
for use in ex vivo therapy.
[0825] In one aspect, the present invention relates to therapeutic
compositions comprising as an active ingredient a MHC molecule
construct as defined herein.
[0826] In another aspect, the present invention relates to
therapeutic compositions comprising as active ingredient an
effective amount of MHC recognising cells, the MHC recognising
cells being obtainable by bringing a sample from a subject
comprising MHC recognising cells into contact with a MHC molecule
construct as described herein, whereby the MHC recognising cells
become bound to the MHC molecule construct, isolating the bound MHC
molecule construct and the MHC recognising cells, and expanding
such MHC recognising cells to a clinically relevant number.
[0827] The therapeutic compositions can suitably comprise one or
more adjuvants and/or excipients.
[0828] As used herein, the term "adjuvant" refers to an
immunological adjuvant. By this is meant a compound that is able to
enhance or facilitate the immune system's response to the
ingredient in question, thereby inducing an immune response or
series of immune responses in the subject. The adjuvant can
facilitate the effect of the therapeutic composition by forming
depots (prolonging the half-life of the ingredient), provide
additional T-cell help and stimulate cytokine production.
Facilitation of antigen survival and unspecific stimulation by
adjuvants may, in some cases, be required if MHC molecule epitopes
are the only feature in the therapeutic composition recognised by
the immune system.
[0829] Included in the term "immune response" is specific humoral,
i. e. antibody, as well as cellular immune responses, the
antibodies being serologic as well as secretory and pertaining to
the subclasses IgM, IgD, IgG, IgA and IgE as well as all isotypes,
allotypes, and subclasses thereof. The term is further intended to
include other serum or tissue components. The cellular response
includes Type-1 and Type-2 T-helper lymphocytes, cytotoxic T-cells
as well NK cells.
[0830] Examples of suitable adjuvant are those mentioned above, i.
e. saponins such as Quit. A and Qs-21, oil in water emulsions such
as MF59, MPL, PLG, PLGA, aluminium salts, calcium phosphate, water
in oil emulsions such as IFA (Freund's incomplete adjuvant) and CFA
(Freund's complete adjuvant), interleukins such as IL-1 (3, IL-2,
IL-7, IL-12, and INFy, Adju-Phose, glucan, antigen formulation,
biodegradable microparticles, Cholera Holotoxin, liposomes, DDE,
DHEA, DMPC, DMPG, DOC/Alum Complex, Iscoms muramyl peptide,
monophosphoryl lipid A, muramyl tripeptide, and
phospatidylethanolamine In a preferred embodiment, the adjuvant is
selected from saponins such as Quil A and Qs-21, MF59, MPL, PLG,
PLGA, calcium phosphate, and aluminium salts. Examples of suitable
excipients are those mentioned above, i. e. diluents, buffers,
suspending agents, wetting agents, solubilising agents,
pH-adjusting agents, dispersing agents, preserving agents, and/or
colorants. In particular a PBS buffer without calcium ions and
magnesium ions can be suited.
[0831] The therapeutic compositions of the invention can suitably
be applied in the treatment, prevention, stabilisation, or
alleviation of various diseases.
[0832] Diseases of relevance are those mentioned above, i. e.
diseases of inflammatory, auto-immune, allergic, viral, cancerous,
infectious, allo- or xenogene (graft versus host and host versus
graft) origin. In particular, the disease can be a chronic
inflammatory bowel disease such as Crohn's disease or ulcerative
colitis, sclerosis, type I diabetes, rheumatoid arthritis,
psoriasis, atopic dermatitis, asthma, malignant melanoma, renal
carcinoma, breast cancer, lung cancer, cancer of the uterus,
prostatic cancer, brain cancer, head and neck cancer, leukaemia,
cutaneous lymphoma, hepatic carcinoma, colorectal cancer, bladder
cancer, rejection-related disease, Graft-versus-host-related
disease, or a viral disease associated with hepatitis, AIDS,
measles, pox chicken pox, rubella or herpes.
[0833] More specifically, the disease can be of
inflammatory/auto-immune origin, including asthma, hypersensitivity
pneumonitis, interstitial lung disease, sarcoidosis, idiopathic
pulmonary fibrosis, interstitial lung disease associated with Crohn
s Disease or ulcerative colitis or Whipple's disease, interstitial
lung disease associated with Wegeners granulomatosis or
hypersensitivity vasculitis, vasculitis syndromes,
Hennoch-Schonleins purpura, Goodpastures syndrome, Wegeners
granulomatosis, renal diseases such as antibody mediated
glomerulopathia as in acute glomerulonephritis, nephritis
associated with systemic lupus erythematosus, nephritis associated
with other systemic diseases such as Wegeners granulomatosis and
Goodpastures syndrome and mixed connective tissue disease, chronic
interstitial nephritis, chronic glomerulonephritis,
gastrointestinal diseases such as Crohn s Disease, Ulcerative
colitis, coeliac disease, Whipple's disease, collagenous colitis,
eosinophillic colitis, lymphatic colitis, hepatobilliary diseases
such as auto-immune hepatitis, alcohol induced hepatitis,
periportal fibrosis, primary billiary cirrhosis, sclerosing
colangitis, disorders of the central or peripheral nervous system
such as demyelinating disease as multiple sclerosis, acute
disseminated encephalomyelitis, sub-acute sclerosing
panencephalitis, skin disease such as psoriasis, atopic dermatitis,
eczema, allergic skin disease, progressive systemic sclerosis
(scleroderma), exfoliating dermatitis, pemphigus vulgaris, joint
diseases such as rheumatoid arthritis, ankylosing spondylitis,
arthritis associated with psoriasis or inflammatory bowel disease,
muscoloskelletal diseases such as myastenia gravis, polymyositis,
endocrine diseases such as insulin dependent diabetes mellitus,
auto-immune thyroiditis (Hashimoto), thyreotoxicosis, Graves,
diseases of the hematopoetic system such as auto-immune anaemia,
auto-immune thrombocytopenia, cardiovascular diseases such as
cardiomyopathia, vasculitis, cardiovascular disease associated with
systemic diseases as systemic lupus erythematosus, polyarthritis
nodosa, rheumatoid arthritis, scleroderma, sarcoidosis, diseases of
cancerous origin, including malignant melanoma, Sezary's syndrome,
cutaneous T-cell lymphoma, renal cell carcinoma, colorectal cancer,
breast cancer, ovarian cancer, cancer of the uterus, prostatic
cancer, hepatic carcinoma, lung cancer, and sarcoma, diseases,
disorders or conditions of allergic origin.
[0834] The most common allergens, to which allergic reactions
occur, include. inhalation allergens originating i. a. from trees,
grasses, herbs, fungi, house dust mites, storage mites, cockroaches
and animal hair, feathers, and dandruff. Important pollen allergens
from trees, grasses and herbs are such originating from the
taxonomic orders of Fagales, Oleales and Pinales including i. a.
birch (Betula), alder (Alnus), hazel (Corylus), hornbeam (Carpinus)
and olive (Olea), the order of Poales including i. a. grasses of
the genera Lolium, Phleum, Poa, Cynodon, Dactylis and Secale, the
orders of Astrales and Urticales including i. a. herbs of the
genera Ambrosia and Artemisia. Important inhalation allergens from
fungi are i. a. such originating from the genera Alternaria and
Cladosporium. Other important inhalation allergens are those from
house dust mites of the genus Dermatophagoides, storage mites from
the genus Lepidoglyphys destructor, those from cockroaches and
those from mammals such as cat, dog, horse, cow, and bird. Also,
allergic reactions towards stinging or biting insects such as those
from the taxonomic order of Hymenoptera including bees, wasps, and
ants are commonly observed. Specific allergen components are known
to the person skilled in the art and include e. g. Bet v 1 (B.
verrucosa, birch), Aln g 1 (Alnus glutinosa, alder), Cor a 1
(Corylus avelana, hazel) and Car b 1 (Carpinus betulus, hornbeam)
of the Fagales order. Others are Cry j 1 (Pinales), Amb a 1 and 2,
Art v 1 (Asterales), Par j 1 (Urticales), Ole e 1 (Oleaves), Ave e
1, Cyn d 1, Dac g 1, Fes p 1, Hol 1 1, Lol p 1 and 5, Pas n 1, Phl
p 1 and 5, Poa p 1,2 and 5, Sec c 1 and 5, and Sor h 1 (various
grass pollens), Alt a 1 and Cla h 1 (fungi), Der f 1 and 2, Der p 1
and 2 (house dust mites, D. farinae and D. pteronyssinus,
respectively), Lep d 1, Bla g 1 and 2, Per a 1 (cockroaches,
Blatella germanica and Periplaneta americana, respectively), Fel d
1 (cat), Can f 1 (dog), Equ c 1,2 and 3 (horse), Apis m 1 and 2
(honeybee), Ves g 1,2 and 5, Pol a 1,2 and 5 (all wasps) and Sol i
1, 2,3 and 4 (fire ant), to mention the most common.
[0835] The therapeutic compositions of the invention can be
formulated in any suitable way, i. a. depending on the route of
administration, and the amount of active ingredient to be
administered. In particular, the therapeutic compositions of the
invention can be formulated for parenteral administration,
including intravenous, intramuscular, intraarticular, subcutaneous,
intradermal, epicutantous/transdermal, and intra-peritoneal
administration, for infusion, for oral administration, for nasal
administration, for rectal administration, or for topic
administration.
[0836] The MHC molecule construct can suitably be immobilised onto
a solid or semi-solid support. Examples of solid and semi-solid
support are those mentioned above, i. e. particles, beads,
biodegradable particles, sheets, gels, filters, membranes, fibres,
capillaries, needles, microtitre strips, tubes, plates or wells,
combs, pipette tips, micro arrays, and chips. In particular, the
solid support can be selected from particles and beads, preferably
particles and beads, which are polymeric, magnetic or
superparamagnetic. For in vivo therapy, biodegradable particles
will be especially preferred, while for ex vivo therapy,
biodegradable, polymeric, magnetic, paramagnetic or
superparamagnetic particles will be especially preferred.
[0837] As mentioned, the MHC multimers used in the therapeutically
compositions are very interesting molecule poly-ligand compounds
possessing highly appropriate properties for modulation of MHC
recognising cells both in vivo and ex vivo.
[0838] The poly-ligand MHC multimers can, due to the one or more
multimerization domain(s), be loaded with a plurality of
peptide-displaying MHC molecules to ensure high avidity binding to
specific counter receptors.
[0839] It is to be understood that such responses include inducing
anergy leading to apoptosis, up-regulating a response,
down-regulating a response, stimulating a response, modulating a
response, enhancing a response, inhibiting a response, and in any
other way manipulating a response. In this connection, it should be
understood that the MHC molecules/peptides of the construct can be
chosen so as to induce a number of other responses, or activate
signal pathways which results in the production of various
signalling substances which can have a beneficial influence on the
disease to be treated, prevented or alleviated.
[0840] To accomplish this, the MHC molecule construct used in the
composition can suitably comprise heterogeneous or homogeneous MHC
molecules (e. g. displaying different peptides) to elicit one or
more or more functions in the target MHC recognising cells in vivo
and ex vivo.
[0841] Furthermore, this desired effect of the MHC molecule
construct can be enhanced, reduced, inhibited, stimulated or
combined with other effects by the further attachment of
biologically active compounds as described above, thereby
addressing specific MHC recognising cell clones.
[0842] For this, a specific combination of MHC molecule and peptide
can be selected. By way of example, loading co-stimulatory
molecules e. g. B7.1 onto a poly-ligand MHC molecule construct thus
leads to formation of a bi-functional poly-ligand MHC molecule
construct, which (I) is directed to the peptide specific MHC
recognising cell clones of interest and (II) facilitate appropriate
stimulation implying two mandatory signals to initiate an immune
response. Another example is compositions for the treatment of
auto-immune diseases wherein a recombinant toxin, e. g. PE-38, is
also attached to the MHC multimers used.
[0843] By this, it is possible to modulate the response in any way
it would be desired. Therefore, the present invention also relates
to a method of designing a MHC molecule/peptide combination,
resulting in a desired targeT-cell response both in vivo and ex
vivo.
[0844] A variety of diseases, including cancer cause
immunosuppression in the patients. Immunotherapy is an attempt to
stimulate the patient's own immune system to recognise and destroy
cancer cells. The tumour can exert its suppressive influence over
the immune system through several different mechanisms. Although
tumour cells can prime the immune system, tumour escape mechanisms
can induce immunological tolerance to the tumour. There are several
known mechanisms of tumour escaping immune surveillance. For
instance, tumour cells are often inefficient in presenting tumour
antigens to effector T-cells. This can be the result of tumour cell
down-regulation or mutation of MHC molecules, or down-regulation of
co-stimulatory molecules such as B7, or other molecules, such as
TAP, that are important in the antigen presenting pathway.
[0845] Furthermore, tumour cells have been shown to induce
tolerance in T-cells by down-regulating the expression of CD3-zeta
chain in T-cells. Tumour cells can also suppress T-cell activation
by release of inhibitory cytokines, and induce apoptosis in T-cells
through Fas-Fas ligand interaction. Tumour cells also have the
ability to suppress the immune system through release of cytokines
such as IL-12 that inhibits the maturation of immature dendritic
cells into fully mature antigen presenting cells. Inhibitory
factors released by tumour cells have been shown to suppress
granulocyte activation, thus avoiding the killing of tumour cells
by activated granulocytes.
[0846] Common treatment regimes such as chemotherapy and radiation
therapy also suppress immunity in a more general way.
[0847] A variety of different prior art strategies have been
employed in an attempt to restore or enhance the patient's immune
response to tumours, including treatment with monoclonal
antibodies, cancer vaccines, cytokine therapy and adoptive cellular
immunotherapy using dendritic cells or T-cells. Cellular
immunotherapy involving T-cells include CD8+ cytotoxic effector
cells that have the capacity to kill tumour cells. Furthermore, it
has been shown that CD4+ cytokine producing T-cells also play an
important role in maintaining a sustainable anti-tumour cell
activity of cytotoxic CD8 cells. The success, however, of the prior
art methods have been limited.
[0848] In accordance with the above, interesting the MHC multimers
of the therapeutic composition can be such, wherein at least two of
the MHC molecules of the MHC molecule construct used are different,
wherein the MHC molecules of the MHC molecule construct used are
the same, wherein at least two of the peptides harboured by a
plurality MHC molecules of the MHC molecule construct used are
different, wherein the peptides harboured by the MHC molecules of
the MHC molecule construct used are the same, wherein the peptides
harboured by the MHC molecules of the MHC molecule construct used
are chemically modified or synthesised to contain not natural amino
acids, hydrophilic or hydrophobic groups, wherein the peptides
harboured by the MHC Class I molecules of the MHC molecule
construct used are linked to the MHC Class I heavy chain by a
flexible linker, wherein the peptides harboured by the MHC Class I
molecules of the MHC molecule construct used are linked to the MHC
Class I light chain (.beta.2m) by a flexible linker, wherein the
peptides are harboured by MHC Class I molecules of the MHC molecule
construct used comprising of MHC Class I heavy chain in association
with a light chain (2m) by a flexible linker, wherein the peptide
harboured by the MHC Class II molecules of the MHC molecule
construct used are linked to the alfa-chain by a flexible linker,
wherein the peptide harboured by the MHC Class II molecules of the
MHC molecule construct used are linked to the 0-chain by a flexible
linker, wherein the MHC Class I molecules of the MHC molecule
construct used are mutated, wherein the MHC Class II molecules of
the MHC molecule construct used are mutated, wherein the MHC
molecules of the MHC molecule construct used are peptide free MHC
molecules.
[0849] As mentioned above, the MHC molecule construct can comprise
one or more biologically active molecules. Such are defined above.
Particularly preferred biologically compounds will be selected from
MIC A, MIC B, CDId, ULBP-1, ULBP-2, ULBP-3, CD2, CD3, CD4, CD5,
CD8, CD9, CD27, CD28, CD30, CD69, CD134 (OX40), CD137 (4-1BB),
CD147, CDw150 (SLAM), CD152 (CTLA-4), CD153 (CD30L), CD40L (CD154),
NKG2D, ICOS, HVEM, HLA Class II, PD-1, Fas (CD95), FasL, CD40,
CD48, CD58, CD70, CD72, B7.1 (CD80), B7.2 (CD86), B7RP-1, B7-H3,
PD-L1, PD-L2, CD134L, CD137L, ICOSL, LIGHT, CD16, NKp30, NKp44,
NKp46, NKp80, 2B4, KIR, LIR, CD94/NKG2A, and CD94/NKG2C.
[0850] As mentioned the present invention relates to methods for
the treatment of an animal, including a human being, which methods
comprise administering a therapeutic composition as described
herein in an effective amount.
[0851] The treatment can be such which involves up-regulation,
down-regulation, modulation, stimulation, inhibition, restoration,
enhancement and/and otherwise manipulation of immune responses.
This can indeed be accomplished by the compositions of the present
invention. The present invention also relates to methods of
inducing anergy in a cell, by which methods a therapeutic
composition as described herein is administered.
[0852] In a further aspect, the present invention relates to
methods of performing adoptive immunotherapy, which methods
comprise administrating to an animal, including a human being, a
therapeutic composition as described herein.
[0853] As mentioned above, the therapeutic composition of the
invention is suited for in vivo therapy.
[0854] Therapeutic compositions for in vivo therapy can suitably
comprise from 1 to 10 different MHC molecule constructs.
[0855] Thus, the inclusion of two, three, four, five, six or more
different MHC multimers are contemplated and believed to be
advantageous in some cases. Also, it can be advantageous to include
a MHC molecule construct carrying MHC molecules harbouring
different peptides. The amount of each MHC molecule construct
depends on the MHC molecule construct or combination of MHC
multimers in question. Furthermore, the affinity of the MHC
molecule should be taken into consideration. High-affinity, as well
as low affinity peptides can be harboured by the MHC molecules.
This, however, is expected to affect the amount necessary to
generate the desired response and the strength of the desired
response. It is contemplated that the amount of MHC molecule
construct required to induce a systemic immune response will
typically be in the range of from 0.0001 to 10,000 ug/kg/dose, such
as from 0.01 to 1000 ug/kg/dose, from 0.1 to 100 ug/kg/dose, or
from 1 to 10 ug/kg/dose.
[0856] In general, the MHC molecules used should be synergenic with
the receiving subject to avoid or minimise the risk of
alloreactions.
[0857] The administration of the composition of the invention can
be as single doses or as several doses. In certain cases,
administration only once can be sufficient. In general, several
doses should be given with intervals of a day, a week, two weeks, a
month, or several months, etc. For example, a single dose can be
given once, or a dose can be given as a primer, followed by one or
more administration, or a continuous administration regime like up
to four doses per week, followed by one month without
administrations, followed by up to four doses per week (optionally
with increasing amount of the MHC molecule construct), etc.
Optionally different adjuvants or combinations of adjuvants can be
used in the different administrations. These are all examples, and
the optimal administration regime depends on the MHC molecule
construct in question and several other factors. The person skilled
in the art will readily know how to optimise this.
[0858] Of course, other medicaments can be administered
simultaneously in order to enhance or support the treatment.
[0859] In particular, one or more MHC multimers without MHC
molecules attached, but with biologically active molecules attached
can be administered together with the MHC molecule construct to
stimulate, up-regulate, down-regulate, inhibit or enhance other MHC
recognising cell clones than the MHC recognising cell clones
addressed by the MHC molecule construct of the composition. Such
can also be added to promote response to the cell clone addressed.
In particular, such biologically active molecules can be part of
the MHC molecule construct as described in the foregoing.
[0860] Containers for mixing and storage of the therapeutic
composition of the invention can be made of glass or various
polymeric materials. The containers chosen should not adsorb the
product stored. The containers can suitably be ampoules or capped
vials for mono- or multidosage.
[0861] The invention further relates to methods for producing the
therapeutic compositions of the invention, which methods comprise
providing a MHC molecule construct as described herein, and
solubilising or dispersing the MHC molecule construct in a medium
suitable for therapeutic substances, and optionally adding other
adjuvants and/or excipients.
[0862] As mentioned above, the compositions of the present
invention are suited for ex vivo therapy.
[0863] Thus, the present invention relates in particular to
therapeutic compositions comprising as an active ingredient an
effective amount of MHC recognising cells, the MHC recognising
cells being obtained by isolating from a subject MHC recognising
cells using a MHC molecule construct as defined herein, and
expanding such MHC recognising cells to a clinically relevant
number.
[0864] Once the MHC recognising cells have been isolated they may,
if needed, be genetical or in any other appropraite way modified or
manipulated before they are expanded.
[0865] The MHC recognising cells can be isolated in a number of
ways, which are described in more detail in the following.
[0866] In particular: 1) One or more MHC multimers as defined
herein can be brought into contact with a sample from a subject,
whereby the MHC multimers are allowed to bind to MHC recognising
cells in the sample. The MHC multimers can then be recovered from
the sample, whereafter the MHC recognising cells can be liberated
from the MHC multimers and subsequently expanded.
[0867] 2) One or more MHC multimers as defined herein can be
brought into contact with a sample from a subject, whereby the MHC
multimers are allowed to bind to MHC recognising cells in the
sample. The MHC multimers can then be recovered from the sample,
whereafter the MHC recognising cells can be liberated from the MHC
molecule construct and subsequently expanded in the presence of one
or more other MHC molecule constructs.
[0868] 3) One or more MHC multimers as defined herein immobilised
onto a solid or semi-support as defined herein can be brought into
contact with a sample from a subject, whereby the MHC multimers are
allowed to bind to MHC recognising cells in the sample. The MHC
multimers can then be recovered from the sample, whereafter the MHC
recognising cells can be liberated from the MHC multimers and
subsequently expanded.
[0869] 4) One or more MHC multimers as defined herein immobilised
onto a solid or semi-support as defined herein can be brought into
contact with a sample from a subject, whereby the MHC multimers are
allowed to bind to MHC recognising cells in the sample. The MHC
multimers can then be recovered from the sample, whereafter the MHC
recognising cells can be liberated from the MHC multimers and
subsequently expanded in the presence of one or more other MHC
molecule constructs.
[0870] 5) One or more labelled MHC multimers as defined herein
immobilised onto a solid or semi-support as defined herein can be
brought into contact with a sample from a subject, whereby the MHC
multimers are allowed to bind to MHC recognising cells in the
sample. The MHC multimers can then be recovered from the sample,
whereafter the MHC recognising cells can be liberated from the MHC
multimers and subsequently expanded.
[0871] 6) One or more labelled MHC multimers as defined herein
immobilised onto a solid or semi-support as defined herein can be
brought into contact with a sample from a subject, whereby the MHC
multimers are allowed to bind to MHC recognising cells in the
sample. The MHC multimers can then be recovered from the sample,
whereafter the MHC recognising cells can be liberated from the MHC
multimers and subsequently expanded in the presence of one or more
other MHC molecule constructs.
[0872] 7) One or more MHC multimers as defined herein can be
brought into contact with a sample from a subject, whereby the MHC
multimers are allowed to bind to MHC recognising cells in the
sample. Then the sample comprising the MHC recognising cells bound
MHC multimers can be brought into contact with a solid or
semi-solid support as defined herein having immobilised thereon one
or more molecules which are able to bind to the any part of the MHC
recognising cells or MHC molecule construct, whereby the MHC
molecule construct with the bound MHC recognising cells will become
bound to the support. The thus bound MHC multimers with MHC
recognising cells can then be recovered from the sample, whereafter
the MHC recognising cells can be liberated from the MHC multimers
and subsequently expanded.
[0873] 8) One or more labelled MHC multimers as defined herein can
be brought into contact with a sample from a subject, whereby the
MHC multimers are allowed to bind to MHC recognising cells in the
sample.
[0874] Then the sample comprising the MHC recognising cells bound
MHC multimers can be brought into contact with a solid or
semi-solid support as defined herein having immobilised thereon one
or more molecules which are able to bind to the any part of the MHC
recognising cells or MHC molecule construct, whereby the MHC
molecule construct with the bound MHC recognising cells will become
bound to the support. The thus bound MHC multimers with MHC
recognising cells can then be recovered from the sample, whereafter
the MHC recognising cells can be liberated from the MHC multimers
and subsequently expanded in the presence of one or more other MHC
molecule constructs.
[0875] The above list is not exhaustive in any way.
[0876] It is to be understood that the time of contact between the
MHC multimers and the sample will depend on several factors, i. a.
the MHC multimers in question and the conditions under which the
contacting take place. The contact time will be any such
sufficiently to enable binding to the MHC recognising cells to the
MHC molecule construct. The person skilled in the art will readily
know how to optimise this. In general, the sample can and the MHC
molecule construct can be brought into contact for 10 minutes to 2
hours, such as from 20-45 minutes, at a temperature of from
4.degree. C. to 20.degree. C.
[0877] It is to be understood that the MHC recognising cells are
those indicated above.
[0878] It is to be understood that "sample" has the meaning defined
above. In particular, the sample can be peripheral blood
mononuclear cells (PBMC) or other blood-derived preparations such
as leukopheresis products, or bone marrow, spleen or umbilical
cord. Samples can be used as they are, or they can be subjected to
various purification, decontamination, filtration, or concentration
methods, and/or methods to isolate or remove parts of the sample
like immunomagnetic separation.
[0879] The MHC molecule construct with bound MHC recognising cells
can suitably be isolated by use of a magnetic field (if the support
are magnetic particles or beads) (i. e. an immunomagnetic
separation technique), or by use of a cell sorter device such as a
flow cytometer. For the latter isolation procedure, the MHC
multimers can suitably be labelled. If the immobilisation to the
solid or semi-solid support is carried out following contact
between the MHC molecule construct and sample, it is to be
understood that the MHC molecule construct with the MHC recognising
cells can be immobilised using a compound capable of binding
thereto. Such, which are suitable, are indicated above. For
immunomagnetic isolation of MHC recognising cells from larger
sample volumes, disposable blood bags can be applied. Examples of
equipment suited for such purpose are the Isolex@ 300i or
MAXSEP.TM. (D equipment from Baxter Healthcare Corp, or the
CliniMACS from Miltenyi Biotech. The MHC recognising cells can be
liberated from the MHC molecule construct by procedures such as
DNA-linker digested by DNase, temperature-sensitive Elastin-linker
detaching antibodies, release by incubation and other release
mechanisms known to persons skilled in the art.
[0880] The MHC molecule construct can in accordance with the
definitions above comprise one or more biologically active
molecules. Such can be included e. g in order to attract the MHC
recognising cells desired, and to lower or prevent potential
induction of apoptosis resulting from the isolation procedure.
[0881] It is to be understood that the expansion of the cells can
be carried out in the presence of one or more MHC multimers as
defined above. Such used MHC multimers can be the same as used for
capturing the MHC recognising cells or can be different. Such can
in accordance with the definitions above comprise one or more
biologically active molecules. Such biologically active molecules
will further facilitate multiple interactions with the TCR and
co-stimulatory molecules on MHC recognising cells and produce
efficient ex vivo stimulation of MHC recognising cells. The binding
affinity of e. g. co-stimulatory molecules and their ligands is in
the same range as the binding affinity of MHC molecule-peptide
complexes and the TCR (10 uM range).
[0882] The inclusion of such biologically active molecules
facilitates the use of natural molecules as a replacement for
stimulatory antibodies during expansion, since they compensate for
low affinity by introducing multiple binding interactions. In
particular, the MHC recognising cells can be expanded in the
presence of one or more MHC multimers without MHC molecules
attached, but with biologically active molecules attached to
stimulate, up-regulate, down-regulate, inhibit or enhance 1) other
MHC recognising cell clones than the MHC recognising cell clones of
interest as well as 2) the MHC recognising cell clones of interest.
The expansion can further be carried out in the presence of feeder
cells such as dendritic cells or stroma cells.
[0883] It is to be understood that the expansion of the cells can
additionally be carried out in the presence of further compounds,
e. g. such which promote or stimulate expansion of the cells,
inhibit growth of non-relevanT-cells, or select for the desired
cells. Such can e. g. be one or more biologically active molecules
as described above. Such further compounds can also be selected
from cytokines such as lymphokines, interferons, interleukins,
growth factors, and colony-stimulating factors. For example, 11-2
can be added to enhance proliferation of cells, and other cytokines
can be added to induce particular differentiation patterns, if
required. For example, IL-4 triggers differentiation of T-cell
populations into the Th2 subpopulation, and INF-gamma triggers
differentiation into the Thi subpopulation. Of course a suitable
culturing medium and suitable conditions have to be used to expand
and maintain cells.
[0884] Expansion time is usually between 3 and 10 days, but can be
as long as 14 to 20 days, or even longer providing viability and
continued proliferation of cells are maintained.
[0885] In a special aspect, the present invention relates to
methods of obtaining MHC recognising cells comprising, which
methods comprise bringing into contact a MHC molecule construct as
described herein and a sample suspected of comprising MHC
recognising cells under conditions whereby the MHC recognising
cells bind to the MHC molecule construct, and isolating the bound
MHC molecule construct and MHC recognising cells.
[0886] Such methods are e. g. suited for the obtaining the MHC
recognising cells of therapeutic compositions of the invention.
Such methods are further believed to be of value for identifying
new disease-associated peptides, in that random peptides can be
applied as part of the MHC molecule construct, and their binding
effect to MHC recognising cells can be tested. The methods can
suitably be carried out by immunomagnetic separation techniques or
by flow cytometry.
[0887] The invention further relates to methods for producing the
therapeutic compositions of the invention, which methods comprise
obtaining MHC recognising cells using a MHC molecule construct as
described herein, expanding such MHC recognising cells to a
clinically relevant number, formulating the obtained cells in a
medium suitable for administration, and optionally adding adjuvants
and/or excipients.
[0888] The invention further relates to kits for obtaining the MHC
recognising cells. In one embodiment, such kits comprise one or
more MHC protein constructs as defined herein, optionally
immobilised on to a solid or semi-solid support as defined herein.
In another embodiment, such kits comprise one or more MHC protein
constructs as defined herein and means for immobilisation of the
MHC multimers (s) prior to or following binding to the MHC
recognising cells.
[0889] The invention further in general relates to the use of the
MHC molecule construct described herein for ex vivo expansion of
MHC recognising cells. For such ex vivo expansion of cells, the MHC
molecule construct can be provided in soluble form. The MHC
molecule construct can also be provided immobilised onto a solid or
semi-solid support. The solid and semi-solid supports are those
mentioned above. Beads and particles are especially preferred, in
particular polymeric, magnetic or superparamagnetic particles or
beads. In particular, the MHC molecule construct can comprise one
or more of the biologically active compounds as described
above.
[0890] In the following, more specific procedures are described in
the context of cancerous diseases, but the procedures apply equally
well to other diseases.
[0891] It is believed that one strategy to overcome the suppressive
effect of e. g. tumour cells on the immune system would be to
remove the immune relevanT-cells from a subject through standard
apheresis procedures, and to expand and modify these immune cells
ex vivo before re-infusion to the patients. This would not only
remove the suppressive pressure of tumour cells, but also allow for
the rescue of immunocompetenT-cells prior to immunosuppressive
treatment regimens including chemotherapy and radiation
therapy.
[0892] Pheripheral blood T-cells can be removed from a subject, and
placed into culture under conditions that allow the T-cells to
proliferate. Such conditions include growing T-cells with mitogens
or antigens in the presence of cytokines (IL-2) and dendritic cells
as antigen presenting cells. Antigen can be introduced in the
cultures either as protein extracts from tumours, defined protein
antigens or peptides, or as tumour mRNA or DNA transfected into the
dendritic cells. Alternatively, T-cell expansion protocols have
been developed that include the use of stimulatory antibodies such
as anti-CD3 and anti-CD28 antibodies, either in soluble form or
coupled to a solid phase. The advantage of such antibody-based
expansion protocols is that they circumvent the need for feeder
cells and tumour antigens that can not be readily available.
Following ex vivo T-cell-expansion, often in the order of 100-1000
fold, the T-cells are re-infused to the patients in order to
restore or enhance the immune function towards the tumour.
[0893] It is well known that T-cells of the immune system express a
multitude of specificities, and only a limited number of the
available T-cell clones express specificities that are relevant for
the recognition and killing of the tumour cells.
[0894] Most prior art protocols for T-cell expansion do not take
into consideration the antigen specificity of the T-cells for
tumour antigens, and result in a polyclonal expansion of T-cells
which include a multitude of irrelevant T-cell specificities.
Although the expanded T-cells would help restore the immune
function of the patients through production of cytokines, it is
expected that only a fraction of the re-infused T-cells can
recognise and kill tumour cells directly. In addition, polyclonal
expansion of T-cells increases the risk of expanding T-cell clones
with autoimmune specificities.
[0895] The present invention relates in particular to adoptive
immunotherapy using T-cells with known specificities for tumour
antigens. In this aspect of immunotherapy, CD4 and CD8 T-cells
specific for pre-determined tumour antigens can be isolated from
peripheral blood, apheresis products, bone marrow, lymph nodes,
primary tumours, secondary organ metastasis and other tissues by an
immunomagnetic separation procedure or by a flow cytometric
procedure. After optional purification, the cells can be expanded
ex vivo and re-infused to the patients. Such expanded antigen
specific T-cells will have the ability to target tumour cells
directly, and thus be more efficient than polyclonally expanded
T-cells. In addition, the use of antigen specific T-cells would
decrease the potential danger of re-infusing T-cells clones with
autoimmune specificities.
[0896] By the present invention, a support as defined above,
preferably in the form of beads or particles as defined above,
having MHC multimers as defined herein immobilised thereon, can be
applied to aid manipulation and separation of relevanT-cells from a
sample. Thus, a support comprising magnetic particles can readily
be removed by magnetic aggregation, which provides a quick, simple
and efficient way of ex vivo separating bound cells.
[0897] The magnetic particles or beads with the specific T-cells
attached can be removed ex vivo from a sample onto a suitable solid
or semi-solid support by application of a magnetic field e. g.
using a permanent magnet. It is usually sufficient to apply a
magnet to the side of the vessel comprising the sample mixture to
aggregate the particles to the wall of the vessel and to pour away
the remainder of the sample.
[0898] Especially preferred are superparamagnetic particles, as
magnetic aggregation and clumping of the particles during reaction
can be avoided. DYNABEADS.RTM. (Dynal Biotech ASA, Oslo, Norway)
are one particularly suited example.
[0899] In a convenient embodiment, the MHC multimers can be
attached to the support, prior to contact with the sample. Such
attachment can readily be achieved by methods (e. g. coupling
chemistries) well known in the art, and conveniently the MHC
multimers are bound directly to the solid support, for example by
coating. However, the MHC multimers can also be attached via a
spacer, a linker, or an antibody as described above. The MHC
multimers can be covalently or reversibly attached according to
choice.
[0900] Alternatively, as mentioned above, the MHC multimers can
first be brought into contact with the sample, to bind to the
T-cells before being attached to the solid support. In this case,
the solid support can conveniently carry or be provided with a
molecule as described above capable of binding to the MHC molecule
construct thereby capturing the MHC molecule construct.
[0901] Non-limiting examples include antibodies against the binding
entity, antibodies against the one or more multimerization
domain(s), streptavidin or derivatives thereof for use with
biotinylated multimerization domain(s), and anti-leucocyte
antibodies.
[0902] Where more than one type of MHC molecule construct is used
they can be attached to the same or different solid supports. Such
a system using different solid supports is applicable particularly
in the case of a particulate support such as beads or particles.
Thus, different MHC multimers can be attached to different beads or
particles. Such beads or particles can suitably have difference
sizes or properties, which thus enable separation according to the
different MHC molecule constructs.
[0903] In an embodiment where more than one different type of MHC
molecule construct is used, appropriate amounts or ratios at which
the different types of MHC multimers can be used will be readily
determined by a person skilled in the art.
[0904] As mentioned above, cell separation techniques based on
solid phase affinity binding (e. g. immunomagnetic separation
(IMS)) are well known in the art and conditions to achieve this can
readily be determined by the skilled worker in this field. Thus,
for example a solid support carrying anti-leukocyte antibodies can
be brought into contact with the sample. A particulate solid
support may, for example, be added to the sample contained (e. g.
suspended) in an appropriate medium (e. g. a buffer). The support
can then be left in contact with the sample (e. g. incubated) for a
length of time to enable binding to the cells to occur. Conditions
during the step are not critical, and the sample-support mixture
can be incubated at e. g. 4.degree. C. to 20.degree. C. for 10
minutes to 2 hours e. g. 20-45 minutes.
[0905] Antigen specific T-cells usually occur at very low
frequencies. The low frequency of antigen specific T-cells makes
these cells difficult targets for immunomagnetic isolation. In
addition, the binding affinity between MHC-peptide complexes and
the TCR is relatively low (in the order of 10 uM) compared to the
binding affinity of antibodies and their target molecules (in the
range of 10-0.1 nM). The low binding affinity of the MHC-peptide
complexes can be compensated by introducing multiple binding sites
between the solid phase used for cell isolation and the TCR on the
T-cell surface. In the present invention, this is achieved by
conjugating multiple MHC-peptide complexes to poly-ligand
molecules. By coupling multiple such poly-ligand molecules to the
solid phase, the avidity of binding to T-cells is increased to
facilitate efficient isolation of the target T-cells.
[0906] Efficient isolation of antigen specific T-cells can be
achieved by coupling the MHC-conjugated polymer molecules to the
beads or particles prior to the cell isolation step, or indirectly
by mixing soluble MHC multimers with the sample, before introducing
beads or particles which have a binding affinity for the a part of
the MHC molecule construct.
[0907] Following isolation, the T-cells can be cultivated under
conditions that facilitate proliferation and expansion.
[0908] T-cell activation and proliferation depends, as described
above, on two different signals delivered by antigen presenting
cells. The first signal is the antigen specific signal delivered by
MHC-peptide complexes to the TCR. The second signal is an antigen
unspecific signal delivered by co-stimulatory molecules on the
antigen presenting cells. Such co-stimulatory molecules include
B7-1 and B7-2 which interact with interact with the CD28 molecule
on T-cells, and other co-stimulatory molecules such as LFA-3, CD3,
CD40, ICOS, NKG2D, OX40 and CD137.
[0909] As mentioned above, administration of the expanded cells can
be by any convenient route. Typically, the number of cell for each
administration should be about 109-10 cells. The cells can suitably
be administered in a volume of from about 50 ml to about 1 litre,
such as about 50 ml to about 500 ml, about 50 ml to about 250 ml,
about 50 ml to about 150 ml, or about 50 ml to about 100 ml,
depending on the route of administration and the disease to be
treated. The cells can be administered in a single dose or as
several doses. In certain cases, administration only once can be
sufficient. In general, several doses should be given with
intervals of a day, a week, two weeks, a month, or several months,
etc. For example, a single dose can be given once, or a dose can be
given as a primer, followed by one or more administration, or a
continuous administration regime like up to four doses per week,
followed by one month without administrations, followed by up to
four doses per week (sometimes with increasing or decreasing amount
of the cells), etc. Optionally different adjuvants or combinations
of adjuvants can be used in the different administrations. These
are all examples, and the optimal administration regime depends on
the cells in question and several other factors. The person skilled
in the art will readily know how to optimise this. Of course, other
medicaments can be administered simultaneously in order to enhance
or support the treatment.
[0910] In particular, a MHC molecule construct as defined herein,
or one or more MHC multimers without MHC molecules attached, but
with biologically active molecules attached can be administered
together with the therapeutic composition to stimulate,
up-regulate, down-regulate, inhibit or enhance other MHC
recognising cell clones than the MHC recognising cell clones
addressed by the MHC molecule construct of the composition. Such
constructs can optionally be immobilised onto biodegradable
particles.
[0911] Containers for mixing and storage of the therapeutic
composition of the invention can be made of glass or various
polymeric materials. The containers chosen should essentially not
affect the product stored. The containers can suitably be ampoules
or capped vials for mono- or multidosage.
[0912] In a special aspect, the present invention relates to uses
of MHC molecules in histological methods, and uses of MHC molecules
in cytological methods.
[0913] Such methods are sample-mounted methods.
[0914] This aspect of the invention is based on the surprising
recognition that although MHC molecules or multimers of MHC
molecules per se can not be very suited for some applications due
to low intrinsic affinity, they perform unexpectedly well in
sample-mounted applications.
[0915] Thus, in one embodiment, the present invention relates to
the use of MHC molecules in a method for determining the presence
of MHC recognising cells in a sample, wherein the MHC recognising
cells of the sample are mounted on a support.
[0916] Such methods are a powerful tool in diagnosing various
diseases. Establishing a diagnosis is important in several ways. A
diagnosis gives information about the disease, thus the patient can
be offered suitable treatment. Also, establishing a more specific
diagnosis can give important information about a subtype of a
disease for which a particular treatment will be beneficial (i. e.
various subtypes of diseases can involve display of different
peptides which are recognised by MHC recognising cells, and thus
treatment can be targeted effectively against a particular
subtype). In this way, it can also be possible to gain information
about aberrant cells, which emerge through the progress of the
disease or condition, or to investigate whether and how cell
specificity is affected. The binding of the MHC molecule makes
possible these options, since the binding is indicative for the
presence of the MHC recognising cells in the sample, and
accordingly the presence of MHC molecules displaying the
peptide.
[0917] In another embodiment, the present invention relates to the
use of a MHC molecule in a method for monitoring the presence of
MHC recognising cells in a sample, wherein the MHC recognising
cells of the sample are mounted on a support.
[0918] Such methods are a powerful tool in monitoring the progress
of a disease, e. g. to closely follow the effect of a treatment.
The method can i. a. be used to manage or control the disease in a
better way, to ensure the patient receives the optimum treatment,
to adjust the treatment, to confirm remission or recurrence, and to
ensure the patient is not treated with a medicament which does not
cure or alleviate the disease. In this way, it can also be possible
to monitor aberrant cells which emerge through the progress of the
disease or condition, or to investigate whether and how T-cell
specificity is affected. The binding of the MHC molecule makes
possible these options, since the binding is indicative for the
presence of the MHC recognising cells in the sample, and
accordingly the presence of MHC molecules displaying the
peptide.
[0919] In yet another embodiment, the present invention relates to
the use of a MHC molecule in a method for determining the status of
a disease involving MHC recognising cells, in which method the MHC
recognising cells of the sample are mounted on a support.
[0920] Such methods are a valuable tool in managing and controlling
various diseases. A disease could, e. g. change from stage to
another, and thus it is important to be able to determine the
disease status. In this way, it can also be possible to gain
information about aberrant cells which emerge through the progress
of the disease or condition, or to investigate whether and how cell
specificity is affected, thereby determining the status of a
disease or condition. The binding of the MHC molecule makes
possible these options, since the binding is indicative for the
presence of the MHC recognising cells in the sample, and
accordingly the presence of MHC molecules displaying the
peptide.
[0921] In still another embodiment, the present invention relates
to the use of a MHC molecule in a method for establishing a
prognosis of a disease involving MHC recognising cells, in which
method the MHC recognising cells of the sample are mounted on a
support.
[0922] Such methods are a valuable tool in order to manage
diseases, i. a. to ensure the patient is not treated without
effect, to ensure the disease is treated in the optimum way, and to
predict the chances of survival or cure. In this way, it can also
be possible to gain information about aberrant cells, which emerge
through the progress of the disease or condition, or to investigate
whether and how T-cell specificity is affected, thereby being able
to establish a prognosis.
[0923] The binding of the MHC molecule makes possible these
options, since the binding is indicative for the presence of the
MHC recognising cells in the sample, and accordingly the presence
of MHC molecules displaying the peptide.
[0924] The present invention also relates to the use of a MHC
molecule in methods for the diagnosis of a disease involving MHC
recognising cells, in which method the MHC recognising cells of the
sample are mounted on a support.
[0925] Such diagnostic methods are a powerful tool in the diagnosis
of various diseases. Establishing a diagnosis is important in
several ways. A diagnosis gives information about the disease, thus
the patient can be offered suitable treatment. Also, establishing a
more specific diagnosis can give important information about a
subtype of a disease for which a particular treatment will be
beneficial (i. e. various subtypes of diseases can involve display
of different peptides which are recognised by MHC recognising
cells, and thus treatment can be targeted effectively against a
particular subtype). Valuable information can also be obtained
about aberrant cells emerging through the progress of the disease
or condition as well as whether and how T-cell specificity is
affected. The binding of the MHC molecule makes possible these
options, since the binding is indicative for the presence of the
MHC recognising cells in the sample, and accordingly the presence
of MHC molecules displaying the peptide.
[0926] The present invention also relates to the use of a MHC
molecule in methods of correlating cellular morphology with the
presence of MHC recognising cells in a sample.
[0927] Such methods are especially valuable as applied in the field
of histological methods, as the binding pattern and distribution of
the MHC multimers can be observed directly. In such methods, the
sample is treated so as to preserve the morphology of the
individual cells of the sample. The information gained is important
i. a. in diagnostic procedures as sited affected can be viewed
directly.
[0928] As mentioned above, the use of the MHC molecule is in
sample-mounted methods. Thus, the sample is mounted on a support.
The support is selected from a solid or semi-solid surface. In
particular, the support is selected from glass slides, membranes,
filters, polymer slides, chamber slides, dishes, and
petridishes.
[0929] The sample can suitably be selected from histological
material, cytological material, primary tumours, secondary organ
metastasis, fine needle aspirates, spleen tissue, bone marrow
specimens, cell smears, exfoliative cytological specimens, touch
preparations, oral swabs, laryngeal swabs, vaginal swabs, bronchial
lavage, gastric lavage, from the umbilical cord, and from body
fluids such as blood (e. g. from a peripheral blood mononuclear
cell (PBMC) population isolated from blood or from other
blood-derived preparations such as leukopheresis products), from
sputum samples, expectorates, and bronchial aspirates. Such can be
subjected to various treatments.
[0930] The MHC molecule to be used can be a MHC Class I molecule
selected from the group consisting of a heavy chain, a heavy chain
combined with a .beta.2m, a heavy chain combined with a peptide,
and a heavy chains dimer with a peptide; or a MHC Class II molecule
selected from the group consisting of an a/p dimer, an a/dimer with
a peptide, oc/.beta. dimer combined through an affinity tag and a
oc/.beta. dimer combined through an affinity tag with a peptide; or
a MHC Class I like molecule or a MHC Class II like molecule.
[0931] The MHC molecule can suitably be a vertebrate MHC molecule
such as a human, a murine, a rat, a porcine, a bovine or an avian
molecule. The explanation to these molecules given above also
applies here.
[0932] In particular, the MHC molecule to be used can be a human
MHC molecule.
[0933] The MHC molecule to be used can be a peptide free MHC
molecule, or a peptide filled MHC molecule.
[0934] The MHC molecule to be used can suitably be attached to a
binding entity. Suitable binding entities are those described
above, including streptavidin (SA) and avidin and derivatives
thereof, biotin, immunoglobulins, antibodies (monoclonal,
polyclonal, and recombinant), antibody fragments and derivatives
thereof, leucine zipper domain of AP-1 (jun and fos), hexa-his
(metal chelate moiety), hexa-hat GST (glutathione S-tranferase)
glutathione affinity, Calmodulin-binding peptide (CBP),
STREP-TAG.RTM., Cellulose Binding Domain, Maltose Binding Protein,
S-Peptide Tag, Chitin Binding Tag, Immuno-reactive Epitopes,
Epitope Tags, E2Tag, HA Epitope Tag, Myc Epitope, FLAG Epitope, AU1
and AU5 Epitopes, Glu-Glu Epitope, KT3 Epitope, IRS Epitope, Btag
Epitope, Protein Kinase-C Epitope, VSV Epitope, lectins that
mediate binding to a diversity of compounds, including
carbohydrates, lipids and proteins, e. g. Con A (Canavalia
ensiformis) or WGA (wheat germ agglutinin) and tetranectin or
Protein A or G' (antibody affinity). It is to be understood that
the binding entity can be a combination of those mentioned
above.
[0935] For enabling detection of the MHC molecule, the MHC molecule
can further comprise a labelling compound. The labelling compound
is suitably such which is directly or indirectly detectable. Thus,
the labelling compound can be a fluorescent label, an enzyme label,
a radioisotope, a chemiluminescent label, a bioluminescent label, a
polymer, a metal particle, a hapten, an antibody, or a dye. In
particular, the labelling compound can be selected from 5-(and
6)-carboxyFLUORESCEIN.TM., 5- or 6-carboxyFLUORESCEIN.TM.,
6-(FLUORESCEIN.TM.)-5-(and 6)-carboxamido hexanoic acid,
FLUORESCEIN.TM. isothiocyanate (FITC), rhodamine,
tetrameth-ylrhodamine, and dyes such as Cy2, Cy3, and CY5.TM.,
optionally substituted coumarin including AMCA, PerCP,
phycobiliproteins including R-phycoerythrin (RPE) and
allophycoerythrin (APC), Texas Red, Princeston Red, Green
fluorescent protein (GFP) and analogues thereof, and conjugates of
R-phycoerythrin or allophycoerythrin and e. g. CY5.TM. or Texas
Red, and inorganic fluorescent labels based on semiconductor
nanocrystals (like quantum dot and QDOT.RTM. nanocrystals), and
time-resolved fluorescent labels based on lanthanides like Eu3+ and
Sm3+, from haptens such as DNP, biotin, and digoxiginin, or is
selected from enzymatic labels such as horse radish peroxidase
(HRP), alkaline phosphatase (AP), beta-galactosidase (GAL),
glucose-6-phosphate dehydrogenase, beta-N-acetylglucosaminidase,
.beta.-glucuronidase, invertase, Xanthine Oxidase, firefly
luciferase and glucose oxidase (GO), or is selected from
luminiscence labels such as luminol, isoluminol, acridinium esters,
1,2-dioxetanes and pyridopyridazines, or is selected from
radioactivity labels such as incorporated isotopes of iodide,
cobalt, selenium, tritium, and phosphor.
[0936] A labelling compound can be attached to the MHC molecule,
the binding entity, or both to the MHC molecule and the binding
entity.
[0937] Thus, the present invention relates to methods for detecting
the presence of MHC recognising cells in a sample comprising the
steps of (a) providing a sample suspected of comprising MHC
recognising cells mounted on a support, (b) contacting the sample
with a MHC molecule as described herein, and (c) determining any
binding of the MHC molecule, which binding indicates the presence
of MHC recognising cells.
[0938] The invention further relates to methods for monitoring MHC
recognising cells comprising the steps of (a) providing a sample
suspected comprising MHC recognising cells mounted on a support,
(b) contacting the sample with a MHC molecule as described herein,
and (c) determining any binding of the MHC molecule, thereby
monitoring MHC recognising cells.
[0939] The invention also relates to methods for establishing a
prognosis of a disease involving MHC recognising cells comprising
the steps of (a) providing a sample suspected comprising MHC
recognising cells mounted on a support, (b) contacting the sample
with a MHC molecule as described herein, and (c) determining any
binding of the MHC molecule, thereby establishing a prognosis of a
disease involving MHC recognising cells.
[0940] Furthermore, the invention relates to methods for
determining the status of a disease involving MHC recognising cells
comprising the steps of (a) providing a sample suspected comprising
MHC recognising cells mounted on a support, (b) contacting the
sample with a MHC molecule as described herein, and (c) determining
any binding of the MHC molecule, thereby determining the status of
a disease involving molecule recognising cells.
[0941] The present invention also relates to methods of correlating
cellular morphology with the presence of MHC recognising cells in a
sample comprising the steps of (a) providing a sample suspected of
comprising MHC recognising cells mounted on a support, (b)
contacting the sample with a MHC molecule as described herein, and
(c) determining any binding of the MHC molecule, thereby
correlating the binding of the MHC molecule construct with the
cellular morphology.
[0942] Also comprised by this invention are methods for diagnosing
a disease involving MHC recognising cells, comprising the steps of
(a) providing a sample suspected comprising MHC recognising cells
mounted on a support, (b) contacting the sample with a MHC molecule
as described herein, and (c) determining any binding of the MHC
molecule, thereby diagnosing a disease involving MHC recognising
cells.
[0943] The invention also relates to methods for determining the
effectiveness of a medicament against a disease involving MHC
recognising cells comprising the steps of (a) providing a sample
from a subject receiving treatment with a medicament mounted on a
support, (b) contacting the sample with a MHC molecule as described
herein, and (c) determining any binding of the MHC molecule,
thereby determining the effectiveness of the medicament.
[0944] The disease can be of inflammatory, auto-immune, allergic,
viral, cancerous, infectious, allo- or xenogene (graft-versus-host
and host-versus-graft) origin. In particular, the disease can be a
chronic inflammatory bowel disease such as Crohn's disease or
ulcerative colitis, sclerosis, type I diabetes, rheumatoid
arthritis, psoriasis, atopic dermatitis, asthma, malignant
melanoma, renal carcinoma, breast cancer, lung cancer, cancer of
the uterus, cervical cancer, prostatic cancer, brain cancer, head
and neck cancer, leukaemia, cutaneous lymphoma, hepatic carcinoma,
colorectal cancer, bladder cancer, rejection-related disease,
Graft-versus-host-related disease, or a viral disease associated
with hepatitis, AIDS, measles, pox, chicken pox, rubella or
herpes.
[0945] The sample to be subjected to the methods of the invention
can suitably be selected from histological material, cytological
material, primary tumours, secondary organ metastasis, fine needle
aspirates, spleen tissue, bone marrow specimens, cell smears,
exfoliative cytological specimens, touch preparations, oral swabs,
laryngeal swabs, vaginal swabs, bronchial lavage, gastric lavage,
from the umbilical cord, and from body fluids such as blood (e. g.
from a peripheral blood mononuclear cell (PBMC) population isolated
from blood or from other blood-derived preparations such as
leukopheresis products), from sputum samples, expectorates, and
bronchial aspirates. Such can be subjected to various
treatments.
Definitions
[0946] As used everywhere herein, the term "a", "an" or "the" is
meant to be one or more, i. e. at least one.
[0947] Adjuvant: adjuvants are drugs that have few or no
pharmacological effects by themselves, but can increase the
efficacy or potency of other drugs when given at the same time. In
another embodiment, an adjuvant is an agent which, while not having
any specific antigenic effect in itself, can stimulate the immune
system, increasing the response to a vaccine.
[0948] Agonist: agonist as used herein is a substance that binds to
a specific receptor and triggers a response in the cell. It mimics
the action of an endogenous ligand that binds to the same
receptor.
[0949] Antagonist: antagonist as used herein is a substance that
binds to a specific receptor and blocks the response in the cell.
It blocks the action of an endogenous ligand that binds to the same
receptor.
[0950] Antibodies: As used herein, the term "antibody" means an
isolated or recombinant binding agent that comprises the necessary
variable region sequences to specifically bind an antigenic
epitope. Therefore, an antibody is any form of antibody or fragment
thereof that exhibits the desired biological activity, e.g.,
binding the specific target antigen. Antibodies can derive from
multiple species. For example, antibodies include rodent (such as
mouse and rat), rabbit, sheep, camel, and human antibodies.
Antibodies can also include chimeric antibodies, which join
variable regions from one species to constant regions from another
species. Likewise, antibodies can be humanized, that is constructed
by recombinant DNA technology to produce immunoglobulins which have
human framework regions from one species combined with
complementarity determining regions (CDR's) from a another species'
immunoglobulin. The antibody can be monoclonal or polyclonal.
Antibodies can be divided into isotypes (IgA, IgG, IgM, IgD, IgE,
IgG1, IgG2, IgG3, IgG4, IgA1, IgA2, IgM1, IgM2)
[0951] Antibodies: In another embodiment the term "antibody" refers
to an intact antibody, or a fragment of an antibody that competes
with the intact antibody for antigen binding. In certain
embodiments, antibody fragments are produced by recombinant DNA
techniques. In certain embodiments, antibody fragments are produced
by enzymatic or chemical cleavage of intact antibodies. Exemplary
antibody fragments include, but are not limited to, Fab, Fab',
F(ab')2, Fv, and scFv. Exemplary antibody fragments also include,
but are not limited to, domain antibodies, nanobodies, minibodies
((scFv-CH.sub.3).sub.2), maxibodies
((scFv-CH.sub.2--CH.sub.3).sub.2), diabodies (noncovalent dimer of
scFv).
[0952] Antigen presenting cell: An antigen-presenting cell (APC) as
used herein is a cell that displays foreign antigen complexed with
MHC on its surface.
[0953] Antigenic peptide: Any peptide molecule that is bound to or
able to bind into the binding groove of either MHC I or MHC II
molecules.
[0954] Aptamer: the term aptamer as used herein is defined as
oligonucleic acid or peptide molecules that bind a specific target
molecule. Aptamers are usually created by selecting them from a
large random sequence pool, but natural aptamers also exist.
Aptamers can be divided into DNA aptamers, RNA aptamers and peptide
aptamers.
[0955] Avidin: Avidin as used herein is a glycoprotein found in the
egg white and tissues of birds, reptiles and amphibians. It
contains four identical subunits having a combined mass of
67,000-68,000 daltons. Each subunit consists of 128 amino acids and
binds one molecule of biotin.
[0956] Biologically active molecule: A biologically active molecule
is a molecule having itself a biological activity/effect or is able
to induce a biological activity/effect when administered to a
biological system. Biologically active molecules include adjuvants,
immune targets (e.g. antigens), enzymes, regulators of receptor
activity, receptor ligands, immune potentiators, drugs, toxins,
cytotoxic molecules, co-receptors, proteins and peptides in
general, sugar moieties, lipid groups, nucleic acids including
siRNA, nanoparticles, small molecules.
[0957] Bioluminescent: Bioluminescence, as used herein, is the
production and emission of light by a living organism as the result
of a chemical reaction during which chemical energy is converted to
light energy.
[0958] Biotin: Biotin, as used herein, is also known as vitamin H
or B7. Biotin has the chemical formula
C.sub.10H.sub.16N.sub.2O.sub.3S.
[0959] Bispecific antibodies: The term bispecific antibodies as
used herein is defined as monoclonal, preferably but not limited to
human or humanized, antibodies that have binding specificities for
at least two different antigens. The antibody can also be
trispecific or multispecific.
[0960] Carrier: A carrier as used herein can be any type of
molecule that is directly or indirectly associated with the MHC
peptide complex.
[0961] Chelating chemical compound: Chelating chemical compound, as
used herein, is the process of reversible binding of a ligand to a
metal ion, forming a metal complex.
[0962] Chemiluminescent: Chemiluminescence, as used herein, is the
emission of light (luminescence) without emission of heat as the
result of a chemical reaction.
[0963] Chromophore: A chromophore, as used herein, is the part of a
visibly coloured molecule responsible for light absorption over a
range of wavelengths thus giving rise to the colour. By extension
the term can be applied to UV or IR absorbing parts of
molecules.
[0964] CMV: Cytomegalo Virus
[0965] CMV pp65: cytomegalovirus (CMV) internal matrix protein
pp65
[0966] Coiled-coil polypeptide: the term coiled-coil polypeptide as
used herein is a structural motif in proteins, in which 2-7
alpha-helices are coiled together like the strands of a rope
[0967] Counting beads: Beads or particles that can be used as
internal control beads enabling absolute cell count in a
sample.
[0968] Covalent binding: The term covalent binding is used herein
to describe a form of chemical bonding that is characterized by the
sharing of pairs of electrons between atoms.
Attraction-to-repulsion stability that forms between atoms when
they share electrons is known as covalent bonding.
[0969] Crosslinking is the process of chemically joining two or
more molecules by a covalent bond. Crosslinking reagents contain
reactive ends to specific functional groups (primary amines,
sulfhydryls, etc.) on proteins or other molecules.
[0970] Dendritic cell: The term dendritic cell as used herein is a
type of immune cells. Their main function is to process antigen
material and present it on the surface to other cells of the immune
system, thus functioning as antigen-presenting cells.
[0971] Detection: In this invention detection means any method
capable of measuring one molecule bound to another molecule. The
molecules are typically proteins but can be any type of
molecule.
[0972] Detection molecule: A molecule or a complex comprising a
marker molecule and a labeling molecule. A detection molecule can
be both in one molecule.
[0973] Dextran: the term dextran as used herein is is a complex,
branched polysaccharide made of many glucose molecules joined into
chains of varying lengths. The straight chain consists of
.alpha.1->6 glycosidic linkages between glucose molecules, while
branches begin from .alpha.1->3 linkages (and in some cases,
.alpha.1->2 and .alpha.1->4 linkages as well).
[0974] Diabodies: The term "diabodies" refers to small antibody
fragments with two antigen-binding sites, which fragments comprise
a heavy-chain variable domain (VH) connected to a light-chain
variable domain (VL) in the same polypeptide chain (VH-VL). By
using a linker that is too short to allow pairing between the two
domains on the same chain, the domains are forced to pair with the
complementary domains of another chain and create two
antigen-binding sites.
[0975] DNA: The term DNA (Deoxyribonucleic acid) duplex as used
herein is a polymer of simple units called nucleotides, with a
backbone made of sugars and phosphate atoms joined by ester bonds.
Attached to each sugar is one of four types of molecules called
bases.
[0976] DNA duplex: In living organisms, DNA does not usually exist
as a single molecule, but instead as a tightly-associated pair of
molecules. These two long strands entwine like vines, in the shape
of a double helix.
[0977] Electrophilic: electrophile, as used herein, is a reagent
attracted to electrons that participates in a chemical reaction by
accepting an electron pair in order to bond to a nucleophile.
[0978] Enzyme label: enzyme labelling, as used herein, involves a
detection method comprising a reaction catalysed by an enzyme.
[0979] Epitope-focused antibody: Antibodies also include
epitope-focused antibodies, which have at least one minimal
essential binding specificity determinant from a heavy chain or
light chain CDR3 from a reference antibody, methods for making such
epitope-focused antibodies are described in U.S. patent application
Ser. No. 11/040,159, which is incorporated herein by reference in
its entirety.
[0980] Fluorescent: the term fluorescent as used herein is to have
the ability to emit light of a certain wavelength when activated by
light of another wavelength.
[0981] Fluorochromes: fluorochrome, as used herein, is any
fluorescent compound used as a dye to mark e.g. protein with a
fluorescent label.
[0982] Fluorophore: A fluorophore, as used herein, is a component
of a molecule which causes a molecule to be fluorescent.
[0983] Folding: In this invention folding means in vitro or in vivo
folding of proteins in a tertiary structure.
[0984] Fusion antibody: As used herein, the term "fusion antibody"
refers to a molecule in which an antibody is fused to a
non-antibody polypeptide at the N- or C-terminus of the antibody
polypeptide.
[0985] Glycosylated: Glycosylation, as used herein, is the process
or result of addition of saccharides to proteins and lipids.
[0986] Hapten: A residue on a molecule for which there is a
specific molecule that can bind, e.g. an antibody.
[0987] Heteroconjugate antibodies are composed of two covalently
joined antibodies. Such antibodies have, for example, been proposed
to target immune system cells to unwanted cells.
[0988] IgG: IgG as used herein is a monomeric immunoglobulin, built
of two heavy chains and two light chains. Each molecule has two
antigen binding sites.
[0989] Isolated antibody: The term "isolated" antibody as used
herein is an antibody which has been identified and separated
and/or recovered from a component of its natural environment.
[0990] Immuno active molecule: By the term "immuno active molecule"
is meant any compound that as an active part of a MHC multimer, a
solution containing MHC multimers, a therapeutics or a vaccines is
modulating the immuno-activity of the MHC multimer/the solution of
MHC multimer/the therapeutic and/or the vaccine itself or is
modulating the immune system as such. Included in Immuno active
molecules are Biological active molecules.
[0991] Immunoconjugates: The invention also pertains to
immunoconjugates comprising an antibody conjugated to a cytotoxic
agent such as a chemotherapeutic agent, toxin (e.g., an
enzymatically active toxin of bacterial, fungal, plant, or animal
origin, or fragments thereof), or a radioactive isotope (i.e., a
radioconjugate). Enzymatically active toxins and fragments thereof
that can be used include diphtheria A chain, nonbinding active
fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas
aeruginosa), ricin A chain, abrin A chain, modeccin A chain,
alpha-sarcin, Aleurites fordii proteins, dianthin proteins,
Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica
charantia inhibitor, curcin, crotin, sapaonaria officinalis
inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin,
and the tricothecenes. A variety of radionuclides are available for
the production of radioconjugated antibodies. Conjugates of the
antibody and cytotoxic agent are made using a variety of
bifunctional protein-coupling agents such as
N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP),
iminothiolane (IT), bifunctional derivatives of imidoesters (such
as dimethyl adipimidate HCL), active esters (such as disuccinimidyl
suberate), aldehydes (such as glutaraldehyde), bis-azido compounds
(such as bis(p-azidobenzoyl)hexanediamine), bis-diazonium
derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine),
diisocyanates (such as tolyene 2,6-diisocyanate), and bis-active
fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene).
[0992] Influenza MP1: influenza A matrix protein 1
[0993] Ionophore: ionophore, as used herein, is a lipid-soluble
molecule usually synthesized by microorganisms capable of
transporting ions.
[0994] Label: Label herein is used interchangeable with labeling
molecule. Label as described herein is an identifiable substance
that is detectable in an assay and that can be attached to a
molecule creating a labeled molecule. The behavior of the labeled
molecule can then be studied.
[0995] Labelling: Labelling herein means attachment of a label to a
molecule.
[0996] Lanthanide: lanthanide, as used herein, series comprises the
15 elements with atomic numbers 57 through 71, from lanthanum to
lutetium.
[0997] Linker molecule: Linker molecule and linker is used
interchangeable herein. A linker molecule is a molecule that
covalently or non-covalently connects two or more molecules,
thereby creating a larger complex consisting of all molecules
including the linker molecule.
[0998] Liposomes: The term liposome as used herein is defined as a
spherical vesicle with a membrane composed of a phospholipid and
cholesterol bilayer. Liposomes, usually but not by definition,
contain a core of aqueous solution; lipid spheres that contain no
aqueous material are called micelles.
[0999] Immunoliposomes: The antibodies disclosed herein can also be
formulated as immunoliposomes. Liposomes comprising the antibody
are prepared by methods known in the art, such as described in
Epstein et al., Proc. Natl. Acad. Sci. USA 82: 3688 (1985); Hwang
et al., Proc. Natl. Acad. Sci. USA 77: 4030 (1980); and U.S. Pat.
Nos. 4,485,045 and 4,544,545. Particularly useful liposomes can be
generated by the reverse-phase evaporation method with a lipid
composition comprising phosphatidylcholine, cholesterol, and
PEG-derivatized phosphatidylethanolamine (PEG-PE).
[1000] Marker: Marker is used interchangeably with marker molecule
herein. A marker is molecule that specifically associates
covalently or non-covalently with a molecule belonging to or
associated with an entity.
[1001] MHC: Denotes the major histocompatibility complex.
[1002] A "MHC Class I molecule" as used everywhere herein is
defined as a molecule which comprises 1-3 subunits, including a
heavy chain, a heavy chain combined with a light chain
(beta.sub.2m), a heavy chain combined with a light chain
(beta.sub.2m) through a flexible linker, a heavy chain combined
with a peptide, a heavy chain combined with a peptide through a
flexible linker, a heavy chain/beta.sub.2m dimer combined with a
peptide, and a heavy chain/beta.sub.2m dimer with a peptide through
a flexible linker to the heavy or light chain. The MHC molecule
chain can be changed by substitution of single or by cohorts of
native amino acids or by inserts, or deletions to enhance or impair
the functions attributed to said molecule. By example, it has been
shown that substitution of XX with YY in position nn of human
beta.sub.2m enhance the biochemical stability of MHC Class I
molecule complexes and thus can lead to more efficient antigen
presentation of subdominant peptide epitopes.
[1003] MHC complex: MHC complex is herein used interchangeably with
MHC-peptide complex, unless it is specified that the MHC complex is
empty, i.e. is not complexed with peptide.
[1004] MHC Class I like molecules (including non-classical MHC
Class I molecules) include CDld, HLA E, HLA G, HLA F, HLA H, MIC A,
MIC B, ULBP-1, ULBP-2, and ULBP-3.
[1005] A "MHC Class II molecule" as used everywhere herein is
defined as a molecule which comprises 2-3 subunits including an
alpha-chain and a beta-chain (alpha/beta-dimer), an alpha/beta
dimer with a peptide, and an alpha/beta dimer combined with a
peptide through a flexible linker to the alpha or beta chain, an
alpha/beta dimer combined through an interaction by affinity tags
e.g. jun-fos, an alpha/beta dimer combined through an interaction
by affinity tags e.g. jun-fos and further combined with a peptide
through a flexible linker to the alpha or beta chain. The MHC
molecule chains can be changed by substitution of single or by
cohorts of native amino acids or by inserts, or deletions to
enhance or impair the functions attributed to said molecule. Under
circumstances where the alpha-chain and beta-chain have been fused,
to form one subunit, the "MHC Class II molecule" can comprise only
1 subunit.
[1006] MHC Class II like molecules (including non-classical MHC
Class II molecules) include HLA DM, HLA DO, I-A beta2, and I-E
beta2.
[1007] "MHC complexes" and "MHC constructs" are used interchangably
herein.
[1008] "MHC protein" and "MHC molecule" are used interchangably
herein. Accordingly, a functional MHC peptide complex comprises a
MHC protein or MHC molecule associated with a peptide to be
presented for cells or binding partners having an affinity for said
peptide.
[1009] By the terms "MHC complexes" and "MHC multimers" as used
herein are meant such complexes and multimers thereof, which are
capable of performing at least one of the functions attributed to
said complex or multimer. The terms include both classical and
non-classical MHC complexes. The meaning of "classical" and
"non-classical" in connection with MHC complexes is well known to
the person skilled in the art. Non-classical MHC complexes are
subgroups of MHC-like complexes. The term "MHC complex" includes
MHC Class I molecules, MHC Class II molecules, as well as MHC-like
molecules (both Class I and Class II), including the subgroup
non-classical MHC Class I and Class II molecules.
[1010] The MHC molecule can suitably be a vertebrate MHC molecule
such as a human, a mouse, a rat, a porcine, a bovine or an avian
MHC molecule. Such MHC complexes from different species have
different names. E.g. in humans, MHC complexes are denoted HLA. The
person skilled in the art will readily know the name of the MHC
complexes from various species.
[1011] MHC multimer: The terms MHC multimer, MHCmer and MHC'mer
herein are used interchangeably, to denote a complex comprising
more than one MHC-peptide complexes, held together by covalent or
non-covalent bonds.
[1012] MHC molecule: Herein denotes the empty MHC protein, i.e. MHC
protein not complexed with antigenic peptide.
[1013] MHC multimer: The terms MHC multimer, MHCmer and MHC'mer
herein are used interchangeably, to denote a complex comprising
more than one MHC-peptide complexes, held together by covalent or
non-covalent bonds.
[1014] Monoclonal antibodies: Monoclonal antibodies, as used
herein, are antibodies that are identical because they were
produced by one type of immune cell and are all clones of a single
parenT-cell.
[1015] Monovalent antibodies: The antibodies in the present
invention can be monovalent antibodies. Methods for preparing
monovalent antibodies are well known in the art. For example, one
method involves recombinant expression of immunoglobulin light
chain and modified heavy chain. The heavy chain is truncated
generally at any point in the Fc region so as to prevent heavy
chain crosslinking. Alternatively, the relevant cysteine residues
are substituted with another amino acid residue or are deleted so
as to prevent crosslinking. In vitro methods are also suitable for
preparing monovalent antibodies. Digestion of antibodies to produce
fragments thereof, particularly, Fab fragments, can be accomplished
using routine techniques known in the art.
[1016] Multimerization domain: A multimerization domain is a
molecule, a complex of molecules, or a solid support, to which one
or more MHC or MHC-peptide complexes can be attached.
Multimerization domains thus include IgG, streptavidin, micelles,
cells, polymers, beads and other types of solid support, and small
organic molecules carrying reactive groups or carrying chemical
motifs that can bind MHC complexes.
[1017] Nanobodies: Nanobodies as used herein is a type of
antibodies derived from camels, and are much smaller than
traditional antibodies.
[1018] Neutralizing antibodies: neutralizing antibodies as used
herein is an antibody which, on mixture with the homologous
infectious agent, reduces the infectious titer
[1019] NMR: NMR (Nuclear magnetic resonance), as used herein, is a
physical phenomenon based upon the quantum mechanical magnetic
properties of an atom's nucleus. NMR refers to a family of
scientific methods that exploit nuclear magnetic resonance to study
molecules.
[1020] Non-covalent: The term noncovalent bond as used herein is a
type of chemical bond, that does not involve the sharing of pairs
of electrons, but rather involves more dispersed variations of
electromagnetic interactions.
[1021] Nucleic acid duplex: A nucleic acid is a complex,
high-molecular-weight biochemical macromolecule composed of
nucleotide chains that convey genetic information. The most common
nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA).
[1022] Nucleophilic: a nucleophile, as used herein, is a reagent
that forms a chemical bond to its reaction partner (the
electrophile) by donating both bonding electrons.
[1023] "One or more" as used everywhere herein is intended to
include one and a plurality.
[1024] A "peptide free MHC Class I molecule" as used everywhere
herein is meant to be a MHC Class I molecule as defined above with
no peptide.
[1025] A "peptide free MHC Class II molecule" as used everywhere
herein is meant to be a MHC Class II molecule as defined above with
no peptide.
[1026] Such peptide free MHC Class I and II molecules are also
called "empty" MHC Class I and II molecules.
[1027] Pegylated: pegylated, as used herein, is conjugation of
Polyethylene glycol (PEG) to proteins.
[1028] Phosphorylated; phosphorylated, as used herein, is is the
addition of a phosphate (PO.sub.4) group to a protein molecule or a
small molecule.
[1029] "A plurality" as used everywhere herein should be
interpreted as two or more.
[1030] PNA: PNA (Peptide nucleic acid) as used herein is a chemical
similar to DNA or RNA. PNA is not known to occur naturally in
existing life on Earth but is artificially synthesized and used in
some biological research and medical treatments. DNA and RNA have a
deoxyribose and ribose sugar backbone, respectively, whereas PNA's
backbone is composed of repeating N-(2-aminoethyl)-glycine units
linked by peptide bonds. The various purine and pyrimidine bases
are linked to the backbone by methylene carbonyl bonds. PNAs are
depicted like peptides, with the N-terminus at the first (left)
position and the C-terminus at the right.
[1031] Polyclonal antibodies: a polyclonal antibody as used herein
is an antibody that is derived from different B-cell lines. They
are a mixture of immunoglobulin molecules secreted against a
specific antigen, each recognising a different epitope.
[1032] Polymer: the term polymer as used herein is defined as a
compound composed of repeating structural units, or monomers,
connected by covalent chemical bonds.
[1033] Polypeptide: Peptides are the family of short molecules
formed from the linking, in a defined order, of various
.alpha.-amino acids. The link between one amino acid residue and
the next is an amide bond and is sometimes referred to as a peptide
bond. Longer peptides are reffered to as proteins or
polypeptide.
[1034] Polysaccharide: The term polysaccharide as used herein is
defined as polymers made up of many monosaccharides joined together
by glycosidic linkages.
[1035] Radicals: radicals, as used herein, are atomic or molecular
species with unpaired electrons on an otherwise open shell
configuration. These unpaired electrons are usually highly
reactive, so radicals are likely to take part in chemical
reactions.
[1036] Radioactivity: Radioactive decay is the process in which an
unstable atomic nucleus loses energy by emitting radiation in the
form of particles or electromagnetic waves.
[1037] RNA: RNA (Ribonucleic acid) as used herein is a nucleic acid
polymer consisting of nucleotide monomers that plays several
important roles in the processes that translate genetic information
from deoxyribonucleic acid (DNA) into protein products
[1038] Scaffold: A scaffold is typically an organic molecule
carrying reactive groups, capable of reacting with reactive groups
on a MHC-peptide complex. Particularly small organic molecules of
cyclic structure (e.g. functionalized cycloalkanes or
functionalized aromatic ring structures) are termed scaffolds.
[1039] Shift assay: an assay detecting a shift in size of a given
molecule upon binding another molecule.
[1040] Staining: In this invention staining means specific or
unspecific labelling of cells by binding labeled molecules to
defined proteins or other structures on the surface of cells or
inside cells. The cells are either in suspension or part of a
tissue. The labeled molecules can be MHC multimers, antibodies or
similar molecules capable of binding specific structures on the
surface of cells.
[1041] Streptavidin: Streptavidin as used herein is a tetrameric
protein purified from the bacterium Streptomyces avidinii.
Streptavidin is widely use in molecular biology through its
extraordinarily strong affinity for biotin.
[1042] Sugar: Sugars as used herein include monosaccharides,
disaccharides, trisaccharides and the oligosaccharides-comprising
1, 2, 3, and 4 or more monosaccharide units respectively.
FIGURE LEGENDS
[1043] FIG. 1. Reactive groups and the bonds formed upon their
reaction. Shown in A, B and C are reactive groups, relevant for the
present invention, and the bonds that are formed upon their
reaction.
[1044] FIG. 2. Cleavable linkers, conditions for cleaving them and
the resulting products of the cleavage. Shown are cleavable linkers
relevant for the present invention, as well as the conditions that
lead to their cleavage, and the products of the cleavage
reaction.
[1045] FIG. 3. Size exclusion chromatography of folded
HLA-A*0201-.beta.2m-QLFEELQEL peptide-complex. Purification of
HLA-A*0201-.beta.2m-QLFEELQEL (SEQ ID NO:8) peptide-complex by size
exclusion chromatography on a HiLoad 16/60 Superdex 75 column.
Eluted protein was followed by measurement of the absorbance at 280
nm. The elution profile consisted of 4 peaks, corresponding to
aggregated Heavy Chain, correctly folded MHC-complex, .beta.2m and
excess biotin and peptide.
[1046] FIG. 4. MHC-SHIFT Assay. The SHIFT Assay shows that heavy
chain is efficiently biotinylated, since the band corresponding to
biotinylated heavy chain (lane 2) is shifted up-wards upon
incubation with streptavidin.
[1047] Lane 1: Benchmark protein-ladder [1048] Lane 2: Folded
HLA-A*0201-.beta.2m-QLFEELQEL (SEQ ID NO:8) peptide-complex [1049]
Lane 3: Folded HLA-A*0201-.beta.2m-QLFEELQEL (SEQ ID NO:8)
peptide-complex incubated with molar excess Streptavidin.
[1050] FIG. 5. Conformational ELISA. The ELISA is carried out as a
sandwich-ELISA. The ELISA-plate was coated with W6/32
mouse-anti-hHLA-ABC (DAKO M0736) antibody, which recognizes a
conformational epitope on correctly folded MHC-complex. Then MHC
complex in various concentration was added. .beta.2m in various
concentrations was used as negative control. HRP-conjugated rabbit
anti-.beta.2m (DAKO PO174) was used for detection of bound MHC
complex. TMB One-step substrate system (Dako) was used as a
substrate for HRP, and color formation was followed by measurement
of absorbance at 450 nm.
[1051] FIG. 6. Carboxylate-modified beads coupled to TCR and
stained with HLA-A*0201(NLVPMVATV (SEQ ID NO:9))/RPE or
HLA-A*0201(ILKEPVHGV (SEQ ID NO:10))/RPE dextramers. TCR in various
concentrations were coupled to carboxylate-modified beads and then
stained with HLA-A*0201(NLVPMVATV (SEQ ID NO:9))/RPE or
HLA-A*0201(ILKEPVHGV SEQ ID NO:10)/RPE dextramers in a flow
cytometry experiment. A) Histogram showing x-axis: Fluorescence
intensity measured in the RPE channel (FL2), y-axis: events
counted. Events measured in the Region R9 are regarded as negative,
and events measured in Region R10 are regarded as positive. B)
Percentage of positively stained beads is shown for each
preparation of beads. Negative control samples: [1052] 1) Beads
coupled with 10 .mu.g TCR stained with HLA-A*0201(ILKEPVHGV (SEQ ID
NO: 10))/RPE [1053] 2) Beads coupled with 0 .mu.g TCR stained with
HLA-A*0201 (NLVPMVATV (SEQ ID NO:9))/RPE Positive control samples:
[1054] 3) Beads coupled with 2 .mu.g TCR stained with HLA-A*0201
(NLVPMVATV (SEQ ID NO:9))/RPE [1055] 4) Beads coupled with 5 .mu.g
TCR stained with HLA-A*0201 (NLVPMVATV (SEQ ID NO:9))/RPE [1056] 5)
Beads coupled with 10 .mu.g TCR stained with HLA-A*0201(NLVPMVATV
(SEQ ID NO:9))/RPE [1057] 6) Beads coupled with 20 .mu.g TCR
stained with HLA-A*0201(NLVPMVATV (SEQ ID NO:9))/RPE
[1058] FIG. 7. Flow cytometry analysis of human cell samples added
TCR-coated beads. TCR-beads were added into human peripheral whole
blood (A) or HPBMC (B) and then the samples were analysed by flow
cytometry. Region R1 represents TCR-beads; region R2 represents
lymphocyte cell population of interest.
[1059] FIG. 8. Flow cytometry analysis of MHC multimer constructs
carrying nonsense peptides. Human Peripheral Blood Lymphocytes were
FICOLL.RTM. purified from blood from a human donor and stained with
mouse anti-human CD3/PE antibody and mouse anti-human CD8/PB
antibody together with either of the MHC Dextramer molecule
constructs A) HLA-A*0201 (NLVPMVATV (SEQ ID NO:9))/APC, B)
HLA-A*0201 (ILKEPVHGV (SEQ ID NO:10))/APC, C) HLA-A*0201(nonsense
peptide 1)/APC or D) HLA-A*0201 (nonsense peptide 2)/APC. The
staining was analysed on a CyAn ADP flow cytometer. Live-gated and
CD3 positive lymphocytes are shown.
[1060] FIG. 9. Summary of flow cytometry analysis of the binding of
different MHC multimer constructs to specific T-cells in purified
Human Peripheral Blood. Mononuclear Cell samples. Purified HPBMC
were stained with different MHC(peptide) molecules attached to APC
labeled dextran270 multimerization domain and analyzed by flow
cytometry. See example 30 for details on experimental procedures. 5
different MHC(peptide) molecules were investigated. Construct 1:
HLA-A*0201 (GLAGDVSAV (SEQ ID NO:11)), construct 2:
HLA-A*0201(ALIAPVHAV (SEQ ID NO:12)), construct 3: HLA-A*0201
(NLVPMVATV SEQ ID NO:9), construct 4: HLA-A*0201 (GLCTLVAML (SEQ ID
NO:13)) and construct 5: HLA-A*0201(ILKEPVHGV (SEQ ID NO:10)). A
positive staining is symbolized with a (+) and is here defined as
the identification of a distinct CD8 positive and MHC(peptide)
positive population when visualized in a dot plot (se FIG. 8).
Negative staining is symbolized with a (-) and is defined as
absence of a distinct CD8 positive and MHC(peptide) positive
population when visualized in a dot plot. Nt means not determined.
All samples have previously been analyzed for the presence of
T-cells restricted by HLA-A*0201 (NLVPMVATV (SEQ ID NO:9)),
HLA-A*0201 (GLCTLVAML (SEQ ID NO:13)) and HLA-A*0201(ILKEPVHGV) and
these results are shown in italics in the figure (column 2 and
3).
[1061] FIG. 10. Gating strategy for `no-lyse no-wash`-procedure.
Whole blood was stained with MHC multimer, anti-CD8/APC,
anti-CD3/PB and CD45/CY antibody in a no-lyse no-wash procedure.
For further details see text in example 37. During analysis of data
the following gating strategy was used: CD45/PB antibody was used
to set a trigger discriminator to allow the flow cytometer to
distinguish between red blood cells and stained white blood cells.
This was done during data collection by gating on CD45/PB positive
cells in a CD45/PB vs. side scatter dot plot as shown in A. After
data collection and during data analysis CD3 positive cells were
selected by gating CD3/FITC positive cells in a CD3/FITC vs side
scatter plot as shown in B. The final data was illustrated in a MHC
multimer/PE vs CD8/APC plot (see FIG. 11).
[1062] FIG. 11. Identification of CMV-specific T-cells in a blood
sample using `no-lyse no-wash`-procedure. Whole blood from three
different donors were analysed for the presence of CMV-specific
T-cells by flow cytometry using a no-lyse no-wash procedure. Donor
1 was stained with a MHC multimer consisting of PE-conjugated 270
kDa dextran coupled with HLA-A*0201 in complex with
beta2microglobulin and the peptide NLVPMVATV (SEQ ID NO:9) derived
from Human Cytomegalo Virus (HCMV) (left panel) and with a negative
control MHC multimer consisting of PE conjugated 270 kDa dextran
coupled with HLA-A*0201 in complex with beta2microglobulin and the
peptide ILKEPVHGV (SEQ ID NO:10) derived from Human
Immunodeficiency Virus (HIV) (right panel). Donor 2 was stained
with a MHC multimer consisting of PE-conjugated 270 kDa dextran
coupled with HLA-A*0101 in complex with beta2microglobulin and the
peptide VTEHDTLLY (SEQ ID NO:14) derived from Human Cytomegalo
Virus (HCMV) (left panel) and a negative control MHC multimer
consisting of PE-conjugated 270 kDa dextran coupled with HLA-A*0101
in complex with beta2microglobulin and the peptide IVDCLTEMY (SEQ
ID NO:15) derived from ubiquitin specific peptidase 9 (USP9) (right
panel). Donor 3 was stained with twoMHC multimers consisting of PE
conjugated 270 kDa dextran coupled with HLA-B*0207 in complex with
beta2microglobulin and either of the peptides TPRVTGGGAM (SEQ ID
NO:16) (left panel) or RPHERNGFTVL (SEQ ID NO:17) (center panel)
both derived from Human Cytomegalo Virus (HCMV) and with a negative
control MHC multimer consisting of PE-conjugated 270 kDa dextran
coupled with HLA-B*0207 in complex with beta2microglobulin and the
peptide TPGPGVRYPL (SEQ ID NO:18) derived from Human
Immunodeficiency Virus (HIV) (right panel). All samples were also
added Anti-CD45/PB, anti-CD3/FITC and anti-CD8/APC antibodies. The
samples were gated as shown in FIG. 10.
[1063] FIG. 12. Enumeration of specific T-cells using CytoCount.TM.
beads. Whole blood from a human donor were analysed for the
presence of CMV-specific T-cells with MHC multimers by flow
cytometry using a no-lyse no-wash procedure. 2.times.100 .mu.l
donor blood was analysed with two different MHC multimers: A)
PE-conjugated 270 kDa dextran coupled with HLA-A*0101 in complex
with beta2microglobulin and the peptide VTEHDTLLY (SEQ ID NO:14)
derived from Human Cytomegalo Virus (HCMV) and a negative control
construct B) consisting of PE-conjugated 270 kDa dextran coupled
with HLA-A*0101 in complex with beta2microglobulin and the peptide
IVDCLTEMY (SEQ ID NO:15) derived from ubiquitin specific peptidase
9 (USP9). To each sample Anti-CD45/CY, anti-CD3/APC and anti-CD8/PB
antibody was added together with 50 .mu.l CytoCount beads (1028
beads/.mu.l). Following staining for 15 minutes PBS was added to 1
ml and the samples analysed on a CyAn flow cytometer. During
analysis CD45/CY antibody was used to set a trigger discriminator
to allow the flow cytometer to distinguish between red blood cells
and stained white blood cells and CD3/APC antibody was used to gate
for CD3 positive T lymphocytes. Amount of counted beads in sample A
are shown in the histogram C and amount of beads counted in the
negative control sample B are show in histogram D. Concentration of
HLA-A*0101 (VTEHDTLLY SEQ ID NOP14) specific T-cells in the blood
sample was determined as follows: ((count of MHC multimer+CD8+
cells in A.times.concentration of beads.times.dilution factor of
beads)/counted beads C))-((counted MHC multimer+CD8+ cells in
B.times.concentration of beads.times.dilution factor of
beads)/counted beads D)=((1300 cells.times.1028
beads/.mu.l.times.0.05)/67225 beads)-((2 cells.times.1028
beads/.mu.l.times.0.05)/72623 beads)=0.9926 cells/.mu.l=992.6
cells/ml.
[1064] FIG. 13. MHC dextramers can be embedded in a sugar matrix
together with antibodies and used for detection of specific T-cells
in a blood sample. MHC dextramer constructs was embedded in a sugar
matrix together with relevant gating reagents (anti-CD3/Pacific
Blue, anti-CD8/Alexa700 and anti-CD45/Cascade Yellow antibodies)
and the matrix dried. Then EDTA stabilized blood from a human donor
were added and the samples analyzed by flow cytometry. Two
different MHC construct were used HLA-A*0101 (VTEHDTLLY SEQ ID
NO:14)/PE dextramer (A) and the negative control construct
HLA-A*0101 (IVDCLTEMY SEQ ID NO:15)/PE (B). As a control antibodies
and MHC dextramer constructs were used to stain blood from the same
donor following a general staining procedure without embedding the
antibodies and MHC dextramers in a sugar matrix as described
elsewhere herein. (C) Staining with HLA-A*0101 (VTEHDTLLY (SEQ ID
NO:14))/PE dextramer following a normal staining procedure and (D)
Staining with HLA-A*0101 (IVDCLTEMY SEQ ID NO:15)/PE dextramer
following a normal staining procedure.
[1065] FIG. 14. Composition of FLUORESCEIN.TM.-linker molecule. (A)
Schematic representation of an example of a FLUORESCEIN.TM.-linker
molecule. (B) Composition of a L15 linker.
[1066] FIG. 15. Flow cytometry analysis of human blood sample using
MHC dextramers where the MHC molecules are chemically biotinylated.
Human peripheral blood lymphocytes were FICOLL.RTM. purified from a
human donor and stained with either of the MHC dextramer molecule
constructs HLA-A*0201/NLVPMVATV (SEQ ID NO:9)/APC or the negative
control construct HLA-A*0201/GLAGDVSAV (SEQ ID NO:11)/APC together
with mouse-anti-human CD3/PE, mouse-anti-human CD8/PB and
mouse-anti-human CD4/FITC antibodies. Following staining the sample
was analysed on a CyAn flow cytometer. Live-gated and CD3 positive
lymphocytes are shown. Positive staining of T-cells directed
against HLA-A*0201/NLVPMVATV (SEQ ID NO:9) dextramer are shown left
and negative staining with HLA-A*0201/GLAGDVSAV (SEQ ID NO:11) MHC
dextramer is shown right. MHC dextramers were generated as follows:
MHC-peptide complexes were made by in vitro refolding of heavy
chain and .beta.2m together with peptide and then the complexes
were chemically biotinylated. Biotinylated complexes were coupled
to a 270 kDa dextran multimerization domains containing
Streptavidin (SA) and APC.
[1067] FIG. 16. Detection of antigen specific T cells using MHC
multimer constructs simultaneously with activation and
intracellular staining of cytokines. The figures illustrate
IFN-.gamma. versus Pentamer staining of live lymphocytes I a blood
sample from a human donor. PBMCs were incubated with either a
negative control (non-specific) Pentamer (A*0201/EBV (GLCTLVAML
(SEQ ID NO:13))) or a Pentamer specific for the cells of interest
(B*0801/EBV (RAKFKQLL SEQ ID NO:19)), then stimulated with LAC
(non-specific activation) or B*0801/EBV peptide (specific peptide
activation) for 15 hours in the presence of Brefeldin A. Fixation,
permeabilization and staining for IFN-.gamma. were carried out
exactly as detailed in the protocol in example 55.
[1068] FIG. 17. Detection of Borrelia specific T cells in sample
from human donor. Human peripheral blood lymphocytes were
FICOLL.RTM. purified and stained with either of a pool of MHC/APC
dextramer molecule constructs containing peptides derived from
Borrelia antigen Osp A and FlaB or the cells were stained with the
negative control construct HLA-A*0201/GLAGDVSAV (SEQ ID NO:11)/APC.
Both samples were also stained with the antibodies mouse-anti-human
CD3/PB (clone UCHT1 from Dako), mouse-anti-human CD4/FITC (clone
MT310 from Dako) and mouse-anti-human CD8/PE (clone DK25 from
Dako). Following staining the sample was analysed on a CyAn flow
cytometer. Live-gated, CD4 negative and CD3 positive lymphocytes
are shown. Dot plots showing live gated CD3.sup.+/CD4.sup.-
lymphocytes from Borrelia patient stained with (A) Negative Control
MHC Dextramer (HLA-A*0201 (GLAGDVSAV (SEQ ID NO:11)) or (B) pool of
MHC Dextramers containing peptides from Borrelia antigen Osp A and
Fla B pool of MHC Dextramers containing peptides from Borrelia
antigen are shown. 0.05% of the live gated CD3+/CD4.sup.-
lymphocytes are positive for one or more of the MHC Dextramers in
the pool.
[1069] FIG. 18. HLA-typing using HLA-specific antibodies.
[1070] Human peripheral blood lymphocytes were FICOLL.RTM. purified
from two donors, donor 1 and donor 2. Samples of cells from each
donor were stained with PE-labeled anti-HLA-A*02 and anti-HLA-A*03
antibodies respectively and then analysed on a flow cytometer. As a
control unstained cell samples from each donor was also analysed.
Cells were gated using a lymphocyte gate in a FCS/SSC plot and the
presence of PE positive staining was determined in each sample. As
shown by the histogram plots in the figure, donor 1 was positive
for HLA-A*02 and negative for HLA-A*03 and donor 2 was negative for
HLA-A*02 and positive for HLA-A*03.
EXAMPLES
Example 1
[1071] This example describes how to make a MHC class I complex
with a peptide in the peptide binding-groove. The MHC-complex in
this example consisted of light chain .beta.2m, the MHC class I
Heavy Chain allele HLA-A*0201 (a truncated version in which the
intracellular and transmembrane domains have been deleted) and the
peptide QLFEELQEL (SEQ ID NO:8).
[1072] MHC I-complexes consists of 3 components; Light Chain
(.beta.2m), Heavy Chain and a peptide of typically 8-10 amino
acids. In this example MHC-complexes was generated by in vitro
refolding of heavy chain, .beta.2m and peptide in a buffer
comprising reduced and oxidized glutathione. By incubation in this
buffer a non-covalent complex between Heavy Chain, .beta.2m and
peptide was formed. Heavy chain and .beta.2m was expressed as
inclusion bodies in E. coli prior to in vitro refolding following
standard procedures as described in Garboczi et al., (1996), Nature
384, 134-141. Following refolding the MHC complexes was
biotinylated using BirA enzyme able to biotinylate a specific amino
acid residue in a recognition sequence fused to the C-terminal of
the Heavy Chain by genetic fusion. Monomer MHC complexes was then
purified by size exclusion chromatography. [1073] 1. 200 ml of
refolding buffer (100 mM Tris, 400 mM L-arginin-HCL, 2 mM NaEDTA,
0.5 mM oxidized Gluthathione, 5 mM reduced Glutathione, pH 8.0) was
supplied with protease inhibitors PMSF (phenylmethylsulphonyl
fluoride), Pepstatin A and Leupeptin (to a final concentration of 1
mM, 1 mg/I and 1 mg/I, respectively). The refolding buffer was
placed at 10.degree. C. on a stirrer. [1074] 2. 12 mg of peptide
QLFEELQEL (SEQ ID NO:8) was dissolved in DMSO or another suitable
solvent (300-500 .mu.l), and added drop-wise to the refolding
buffer at vigorous stirring. [1075] 3. 4.4 mg of human Light Chain
.beta.2m was added drop-wise to the refolding buffer at vigorous
stirring. [1076] 4. 6.2 mg of Heavy Chain HLA-A*0201 (supplied with
DTT to a concentration of 0.1 mM) was added drop-wise to the
refolding buffer at vigorous stirring. [1077] 5. The folding
reaction was placed at 10.degree. C. at slow stirring for 4-8
hours. [1078] 6. After 4-8 hours, step 3 and 4 was repeated and the
folding reaction is placed at 10.degree. C. at slow stirring O/N.
[1079] 7. Step 3 and 4 was repeated, and the folding reaction is
placed at 10.degree. C. at slow stirring for 6-8 hours. [1080]
Optionally, steps 5-7 can be done in less time, e.g. a total of
0.5-5 hours. [1081] 8. After 6-8 hours the folding reaction was
filtrated through a 0.2 .mu.m filter to remove aggregates. [1082]
9. The folding reaction was concentrated O/N at 10.degree. C.
shaking gently in a suitable concentrator with a 5000 mw cut-off
filter. The folding reaction was concentrated to approximately 5-10
ml. (Optionally the filtrate can be stored at 4.degree. C. and
reused for another folding with the same peptide and heavy chain.)
[1083] 10. The concentrated folding reaction was buffer-exchanged
at least 8 times, into a MHC-buffer (20 mM Tris-HCl, 50 mM NaCl, pH
8.0) and concentrated (at 10.degree. C. in a suitable concentrator
with a 5000 mw cut-off filter) down to approximately 1 ml. [1084]
11. The heavy chain part of the MHC-complex was biotinylated by
mixing the following components: approximately 1000 .mu.l folded
MHC-complex, 100 .mu.l each of Biomix-A, Biomix-B and d-Biotin (all
3 from Biotin Protein Ligase Kit from Avidity, 10 .mu.l birA enzyme
(3 mg/ml, from Biotin Protein Ligase Kit from Avidity, 0.5 .mu.l
Pepstatin A (2 mg/ml) and 0.5 .mu.l Leupeptin (2 mg/ml). The above
was gently mixed and incubated O/N at room temperature. [1085] 12.
The biotinylated and folded MHC-complex solution was centrifuged
for 5 min. at 1700.times.g, room temperature. [1086] 13. Correctly
folded MHC-complex was separated and purified from excess biotin,
excess .beta.2m, excesss heavy chain and aggregates thereoff, by
size exclusion chromatography on a column that separates proteins
in the 10-100 kDa range. Correctly folded monomer MHC-complex was
eluted with a MHC-buffer (20 mM Tris-HCl, 50 mM NaCl, pH 8.0). The
elution profile consisted of 4 peaks, corresponding to aggregated
Heavy Chain, correctly folded monomer MHC-complex, .beta.2m and
excess biotin and peptide (See FIG. 3). [1087] 14. Fractions
comprising the folded MHC-complex were pooled and concentrated to
approximately 1 ml in a suitable concentrator with a 5000 mw
cut-off filter. The protein-concentration was estimated from its
abosorption at 280 nm. [1088] 15. Folded MHC-complex can optionally
be stored stored at -170.degree. C. before further use. [1089] 16.
The grade of biotinylation was analyzed by a SDS PAGE SHIFT-assay
with Streptavidin (FIG. 4) and correct folding was confirmed by
ELISA, using the antibody W6/32 that recognizes correctly folded
MHC-peptide complex as described elsewhere herein.
[1090] The above procedure can be used for folding any MHC I
compexes consisting of any .beta.2m, any heavy chain and any
peptide approx. 8-11 amino acids long. Either of the components can
be truncated or otherwise modified. The above procedure can also be
used for generation of "empty" MHC I complexes consisting of
.beta.2m and heavy chain without peptide.
Example 2
[1091] This example describes how to generate soluble biotinylated
MHC II complexes using a baculovirus expression system, where the
MHC II complex was DR4 consisting of the .alpha.-chain DRA1*0101
and the .beta.-chain DRB1*0401 as described by Svendsen et al.,
(2004), J. Immunol. 173(11):7037-45. Briefly, The hydrophobic
transmembrane regions of the DR.alpha. and DR.beta. chains of DR4
were replaced by leucine zipper dimerization domains from the
transcription factors Fos and Jun to promote DR .alpha./.beta.
assembly. This was done by ligating cytoplasmic cDNA sequences of
DRA1*0101 and DRB1*0401 to fos- and jun-encoding sequences. A birA
site GLNDIFEAQKIEWH (SEQ ID NO:20) was added to the 3' end of the
DRA1*0101-fos template. Covalently bound peptide AGFKGEQGPKGEP (SEQ
ID NO:21) derived from collagen II amino acid 261-273 were
genetically attached by a flexible linker peptide to the N terminus
of the DRp-chain. Finally, the modified DRA1*0101 and DRB1*0401
inserts were cloned into the expression vector pAcAb3. The
pAcAB3-DRA1*0101/DRB1*0401 plasmids were cotransfected with
linearized baculovirus DNA (BD Pharmingen; BaculoGold kit) into Sf9
insecT-cells, according to the manufacturer's instructions.
Following two rounds of plaque purification, clonal virus isolates
were further amplified three times before preparation of
high-titervirus (10.sup.8-10.sup.10/ml). These stocks were used to
infect High Five or serum-free Sf21 insecT-cells (Invitrogen Life
Technologies, Carlsbad, Calif.) for protein production. Spinner
cultures (2-3.times.10.sup.6 cells/ml) were infected at a
multiplicity of infection of 1-3 in a volume of 150 ml per 2 L
spinner flask. Supernatants were harvested and proteinase inhibitor
tablets (Roche, Basel, Switzerland) were added before affinity
purification on MiniLeak-Low columns (Kem-En-Tec) coupled with the
anti-HLA-DR monoclonal antibody L243. HLA-DR4 complexes were eluted
with diethylamine (pH 11) into neutralization buffer (2 M Tris, pH
6.5) and immediately buffer exchanged and concentrated in PBS,
0.01% NaN.sub.3, using Millipore (Bedford, Mass.) concentrators.
The purity of protein was confirmed by SDS-PAGE. The purified DR4
complexes were biotinylated in vitro as described for MHC I
complexes elsewhere herein. These complexes can now be used for
coupling to any dimerization domain, e.g. divynylsulfone activated
dextran 270 coupled with SA and a fluorochrome.
Example 3
[1092] This example describes how to generate empty biotinylated
MHC II complexes using a baculovirus expression system, where the
MHC II complex consists of any .alpha.-chain and any .beta.-chain,
including truncated and otherwise modified versions of the two.
Briefly, The hydrophobic transmembrane regions of the DR.alpha. and
DR.beta. chains of MHC II are replaced by leucine zipper
dimerization domains from the transcription factors Fos and Jun to
promote DR .alpha./.beta. assembly. This is done by ligating
cytoplasmic cDNA sequences of DR.alpha. and DR.beta. to fos- and
jun-encoding sequences. A birA site GLNDIFEAQKIEWH (SEQ ID NO:20)
is added to the 3' end of either the DR.alpha.-fos/DR.alpha.-jun or
the DR.beta.-jun/DR.beta.-fos template. The modified DR.alpha. and
DR.beta. inserts is cloned into the expression vector pAcAb3 and
cotransfected with linearized baculovirus DNA into Sf9
insecT-cells, according to the manufacturer's instructions.
Following rounds of plaque purification, clonal virus isolates is
further amplified before preparation of high-titervirus. These
stocks are used to infect High Five or serum-free Sf21 insecT-cells
(Invitrogen Life Technologies, Carlsbad, Calif.) for protein
production, e.g. as Spinner cultures. Supernatants are harvested
and proteinase inhibitors added before affinity purification, e.g.
using MiniLeak-Low columns (Kem-En-Tec) coupled with anti-MHC II
antibody. The purified MHC II complexes is biotinylated in vitro as
described for MHC I complexes elsewhere herein. These biotinylated
MHC II complexes can now be used for coupling to any dimerization
domain, e.g. divynylsulfone activated dextran 270 coupled with SA
and a fluorochrome.
Example 4
[1093] This example describes how to generate biotinylated MHC II
complexes using a cell based protein expression system, where the
MHC II complex consist of any .alpha.-chain and any .beta.-chain,
including truncated and otherwise modified versions of the two. The
MHC II complex can also have a peptide bound in the peptide binding
cleft. The hydrophobic transmembrane regions of the MHC II
.alpha.-chain and MHC II .beta.-chain are replaced by leucine
zipper dimerization domains from the transcription factors Fos and
Jun to promote a/p chain assembly. This is done by ligating
cytoplasmic cDNA sequences of .alpha.-chain and .beta.-chain to
fos- and jun-encoding sequences. A birA site GLNDIFEAQKIEWH (SEQ ID
NO:20) is added to the 3' end of the DR.alpha.-fos template.
Optionally covalently bound peptide is genetically attached by a
flexible linker peptide to the N terminus of the DRp-chain. The
modified DR.alpha. and DR.beta. inserts is cloned into a suitable
expression vector and transfected into a cell line capable of
protein expression, e.g. insecT-cells, CHO cells or similar.
Transfected cells are grown in culture, supernatants are harvested
and proteinase inhibitors added before affinity purification, e.g.
using a MiniLeak-Low columns (Kem-En-Tec) coupled with anti-MHC II
antibody. Alternatively the expressed MHC II complexes can be
purified by anion- or cation-exchange chromatography. The purified
MHC II complexes is biotinylated in vitro as described for MHC I
complexes elsewhere herein. These biotinylated MHC II complexes can
now be used for coupling to any dimerization domain, e.g.
divynylsulfone activated dextran 270 coupled with SA and a
fluorochrome.
Example 5
[1094] This example describes how an activated
divinylsylfone-dextran(270 kDa)(VS-dex270) was coupled with
streptavidin (SA) and Allophycocyanin (APC). [1095] 1. Streptavidin
(approx. 100 mg SA/ml in 10 mM HEPES, 0.1M NaCl, pH 7.85) was
dialysed with gentle stirring for 2 days against 10 mM HEPES, 0.1M
NaCl, pH 7.85 (20 fold excess volume) at 2-8.degree. C. with 1
buffer change/day. [1096] 2. 5 ml of APC from a homogen suspension
(approx. 10 mg/ml) was centrifuged 40 min. at 3000 rpm. The
supernatant was discharged and the precipitate dissolved in 5 ml of
10 mM HEPES, 0.1M NaCl, pH 7.85. This APC solution was dialysed
with gentle stirring in the dark for 2 days against 10 mM HEPES,
0.1M NaCl, pH 7.85 (20 fold excess volume) at 2-8.degree. C. with 1
buffer change/day. [1097] 3. The APC-solution was concentrated to 1
ml and the concentration measured to 47 g/L at UV 650 nm. The
A650/A278-ratio was measured to 4.2. [1098] 4. The SA-solution was
filtrated through a 0.45 .mu.m filter and the protein concentration
was measured to 61.8 g SA/L at UV 278 nm. [1099] 5. Conjugation:
The reagents was mixed to a total volume of 500 .mu.l in the
following order with 8.1 mol SA/mol Dex and 27 mol APC/mol Dex.:
[1100] a) 90 .mu.l water [1101] b) 160 .mu.l activated VS-dex270
[1102] c) 23 .mu.l SA (61.8 g/L) 8.1 equivalents, [1103] d) 177
.mu.l APC (47 g/L) 27 equivalents, [1104] e) 50 .mu.l of 100 mM
HEPES, 1M NaCl, pH 8 [1105] The reaction was placed in a water bath
with stirring at 30.degree. C. in the dark for 18 hours. [1106] 6.
The coupling was stopped by adding 50 .mu.l 0.1M ethanolamine, pH
8.0. [1107] 7. The conjugate was purified on a Sephacryl S-200
column with 10 mM HEPES, 0.1M NaCl buffer, pH 7.2. [1108] 8. 3
peaks were collected (peak 1: APC-SA-dex270; peak 2: Free APC; peak
3: Free SA). Volume, UV A650 and UV A278 were measured. [1109] 9.
The concentration of dextran270, APC/Dex and SA/Dex were calculated
to 22.4.times.10.sup.-8 M; 3.48 and 9.54 respectively. [1110] 10.
The conjugate were added NaN.sub.3 and BSA to a final concentration
of 15 mM and 1% respectively. The volume was adjusted with 10 mM
HEPES, 0.1M NaCl, pH 7.2 to a final concentration of
16.times.10.sup.-8 M Dex270. [1111] 11. The conjugate were kept at
2-8.degree. C. in dark until further use.
Example 6
[1112] This example describes how an activated
divinylsylfone-dextran(270 kDa)(VS-dex270) was coupled with
streptavidin (SA) and R-phycoerythrin (RPE).
[1113] The coupling procedure described for coupling of SA and APC
to VS-dex270 (as described elsewhere herein) were followed with the
exception that APC were replaced with RPE.
Example 7
[1114] This example describes how to couple an empty MHC or a
MHC-complex to a dextran multimerization domain, to generate a
MHC-dextramer. The MHC-dextramer in this example consisted of
APC-streptavidin (APC-SA)-conjugated 270 kDA dextran and a
biotinylated, folded MHC-complex composed of .beta.2m, HLA-A*0201
heavy chain and the peptide NLVPMVATV (SEQ ID NO:9).
[1115] The APC-SA conjugated 270 kDA dextran contained 3.7
molecules of SA per dextran (each SA can bind 3 MHC-complexes) and
the concentration was 16.times.10.sup.-8 M. The concentration of
the HLA-A*0201/NLVPMVATV (SEQ ID NO:9)-complex was 4 mg/ml (1
.mu.g=20,663 pmol). The molecular concentration of the MHC-complex
was 8.27.times.10.sup.-5M.
[1116] The MHC-complex was attached to the dextran by a
non-covalent Biotin-Streptavidin interaction between the
biotinylated Heavy Chain part of the MHC-complex and the SA,
conjugated to dextran.
[1117] Here follows a protocol for how to produce 1000 .mu.l of a
MHC-dextramer solution with a final concentration of approximately
32.times.10.sup.-9M: [1118] 1. 200 .mu.L 270 kDA
vinylsulfone-activated dextran, corresponding to
3.2.times.10.sup.-11 mol, and 4 .mu.l MHC-complex, corresponding to
3.55.times.10.sup.-10 mol was mixed and incubated at room
temperature in the dark for 30 min. [1119] 2. A buffer of 0.05M
Tris-HCl, 15 mM NaN.sub.3, 1% BSA, pH 7.2 was added to a total
volume of 1000 .mu.l. [1120] 3. The resulting MHC-dextramer
preparation can now be used in flow cytometry eksperiments.
Example 8
[1121] This example describes how the quality of a MHC multimer can
be tested. The MHC multimer is in this example a MHC-dextramer, and
the test involves specific binding of the MHC-dextramer to TCRs
immobilized on beads.
[1122] Recombinant TCRs (CMV3 TCRs; Soluble CMVpp65(NLVPMVATV (SEQ
ID NO:9))-specific TCR protein) specific for the MHC-peptide
complex HLA-A*0201 (NLVPMVATV (SEQ ID NO:9)), where the letters in
parenthesis denote the peptide complexed to the MHC-allel
HLA-A*0201, were obtained from Altor Biosciences. The TCRs were
dimers linked together via an IgG framework.
[1123] The purity of the TCRs were verified by SDS PAGE and was
between 95-100% pure. The quality of the TCRs were verified by
their ability to recognize the relevant MHC-dextramer and not
irrelevant MHC dextramers in ELISA experiments (data not
shown).
[1124] Carboxylate-modified beads were coupled with dimeric TCR
(CMV3 TCRs; Soluble CMVpp65(NLVPMVATV)-specific TCR protein),
incubated with fluorescently labeled MHC-dextramers and the extend
of cell staining analysed by flow cytometry, as follows:
[1125] Immobilization of TCR on carboxylate beads: [1126] 1.
3.times.10.sup.9 Carboxylate-modified beads, Duke Scientific
Corporation, XPR-1536, 4 .mu.m, lot:4394 were washed in 2.times.500
.mu.l Wash buffer 1 (0.05% TETRONIC.RTM. 1307, 0.1M MES-buffer
(2-[N-morpholino]ethanesulfonic acid), pH 6.0), centrifuged 4 min
at 15000 g, and the supernatant was discarded. [1127] 2. 125 .mu.l
EDAC/Sulfo-NHS (50 mM EDAC (1-ethyl-3-(3-dimethylaminopropyl)
carbodiimide), 50 mM Sulfo-NHS, in Wash buffer 1) was added to the
beads, and the suspension incubated at room temperature for 20 min.
[1128] 3. Beads were washed in 2.times.250 .mu.l Wash buffer 1 and
centrifuged 2 min at 15000 g, and the supernatant was discarded.
[1129] 4. TCR was added in various concentrations from 0 .mu.g to
20 .mu.g, and incubated with slow shaking overnight at 4.degree. C.
[1130] 5. Beads were centrifuged 4 min at 15000 g, and the
supernatant discarded. [1131] 6. Beads were washed in 2.times.500
.mu.l Wash buffer 1 and centrifuged 4 min at 1500 g, and the
supernatant was discarded. [1132] 7. 125 .mu.l 20 mM Glycin in Wash
buffer 1 was added, and resuspended beads incubated for 1 hour at
room temperature. [1133] 8. Beads were washed in 2.times.500 .mu.l
phosphate-buffered saline (PBS) pH 7.2, 0.5% TETRONIC.RTM. 1307,
and centrifuged 2 min at 15000 g, and the supernatant was
discarded. [1134] 9. Beads were resuspended in 250 .mu.l PBS pH
7.2, 0.05% TETRONIC.RTM. 1307.
[1135] Bead concentration after resuspension was 1.2.times.10.sup.7
beads/.mu.l. Beads coated with TCR were stored at 2-8.degree. C.
until further use.
[1136] Flow cytometry analysis: [1137] 1. 20 .mu.l beads
(1.2.times.10.sup.7 beads/.mu.l) coated with 0-20 .mu.g TCRs, as
described above were washed in 200 .mu.l Wash buffer 2 (5% FCS,
PBS, pH 7.4). [1138] 2. Beads were centrifuged 3 min at 12000 g,
and the supernatant was discarded, and beads resuspended in 50
.mu.l Wash buffer 2. [1139] 3. 10 .mu.l MHC-dextramers were added,
and samples were incubated 15 min. at room temperature in the dark.
[1140] 4. Samples were washed in 1 ml Wash buffer 2, centrifuged at
300 g for 5 min. The supernatant was discarded, and pellet
resuspended in 0.4 ml PBS pH 7.4, and kept at 4.degree. C. in the
dark until analysis on flow cytometer. [1141] 5. Samples were
analysed by flow cytometry on a CyAn instrument.
[1142] The results are shown in FIG. 6. Beads coated with 2-20
.mu.g TCR all showed positive staining with the specific HLA-A*0201
(NLVPMVATV (SEQ ID NO:9))/RPE and not with an irrelevant
HLA-A*0201(ILKEPVHGV (SEQ ID NO:10))/RPE dextramer. It can be
concluded that carboxylate beads coated with dimeric TCRs can be
used to test the quality of the MHC-dextramers.
Example 9
[1143] This example describes how the quality of a MHC multimer can
be tested. The MHC multimer was in this example a MHC-dextramer,
and the test involved specific binding of the MHC-dextramer to
monomeric and dimeric TCRs immobilized to different kinds of
beads.
[1144] Binding of MHC-dextramer to carboxylated beads coated with
monomeric TCR: [1145] Recombinant monomeric TCRs (CMV3 TCRs;
Soluble CMVpp65(NLVPMVATV (SEQ ID NO:9))-specific TCR protein)
specific for the MHC-peptide complex HLA-A*0201 (NLVPMVATV (SEQ ID
NO:9)), were obtained from Altor Biosciences.
[1146] The purity of the TCRs were verified by SDS PAGE. The
quality of the TCRs were verified by their ability to recognize the
relevant MHC-dextramer and not irrelevant MHC dextramers in ELISA
experiments (data not shown).
[1147] Carboxylate modified beads were coupled with monomeric TCR
(CMV3 TCRs; Soluble CMVpp65(NLVPMVATV (SEQ ID NO:9))-specific TCR
protein), incubated with fluorescently labeled MHC-dextramers and
the extend of cell staining analysed by flow cytometry, as
described in Example 8. 0-20 .mu.g of monomeric TCRs were coupled
to Carboxylate modified beads.
[1148] Flow cytometry analysis of beads coupled with 0-20 .mu.g of
monomeric TCRs showed a slightly stronger signal when stained with
the relevant HLA-A*0201 (NLVPMVATV (SEQ ID NO:9)) dextramer than
with an irrelevant MHC-dextramer (data not shown). It might be
desirable to coat the beads with larger amounts of monomeric TCRs
in order to increase the signal difference between relevant and
irrelevant MHC-dextramer.
[1149] Beads couples with 0 .mu.g of monomeric TCRs showed
identical signal when stained with relevant and irrelevant
MHC-dextramers.
[1150] We conclude that the monomeric TCRs coupled to Carboxylate
modified beads can be used as positive control for the
MHC-dextramer.
[1151] Binding of MHC-dextramer to streptavidin beads coupled with
biotinylated monomeric TCR: Recombinant monomeric, biotinylated
TCRs (CMV3 TCRs; Soluble CMVpp65(NLVPMVATV (SEQ ID NO:9))-specific
TCR protein) specific for the MHC-peptide complex HLA-A*0201
(NLVPMVATV (SEQ ID NO:9)), were obtained from Altor
Biosciences.
[1152] The purity of the TCRs were verified by SDS PAGE. The
quality of the TCRs were verified by their ability to recognize the
relevant MHC-dextramer and not irrelevant MHC dextramers in ELISA
experiments (data not shown).
[1153] Streptavidin beads were coupled with monomeric biotinylated
TCR (CMV3 TCRs; Soluble CMVpp65 (NLVPMVATV)-specific TCR protein),
incubated with fluorescently labeled MHC-dextramers and the extend
of cell staining analysed by flow cytometry.
[1154] Immobilization of TCR on streptavidin beads: [1155] 1.
2.times.10.sup.6 Streptavidin Coated Compel Magnetic beads, Bangs
laboratories, CM01N, lot: 6998, were washed in 2.times.500 .mu.l
phosphate-buffered saline (PBS) pH 7.2 centrifuged 5 min at 15000
g, and then the supernatant was discarded. [1156] 2. Beads were
resuspended in 50 .mu.l PBS pH 7.2. [1157] 3. 0-4 .mu.g TCRs was
added. Incubated at room temperature for 30 min. [1158] 4. Beads
were washed in 2.times.500 .mu.l PBS, pH 7.2. Centrifuged 5 min at
15000 g, and the supernatant was discarded. [1159] 5. Beads were
resuspended in 100 .mu.l PBS pH 7.2.
[1160] Bead concentration after resuspension was 2.times.10.sup.4
beads/.mu.l. Beads coated with TCRs were stored at 2-8.degree. C.
until further use.
[1161] Flow cytometry analysis: [1162] 1. 50 .mu.l streptavidin
beads (.about.1.times.10.sup.6 beads) coated with 0-4 .mu.g TCRs
were added 10 .mu.l MHC-dextramers, and samples were incubated at
4.degree. C. for 1 hour. [1163] 2. 2.times.500 .mu.l PBS pH 7.2 was
added, and samples were centrifuged for 5 min at 15000 g, and
supernatant discarded. [1164] 3. Beads were resuspended in 500
.mu.l PBS pH 7.2 and kept at 4.degree. C. in the dark until
analysis on a flow cytometer. [1165] 4. Samples were analysed by
flow cytometry on a CyAn instrument.
[1166] Beads were stained with HLA-A*0201 (NLVPMVATV (SEQ ID
NO:9))-dextramers specific for the TCR and with irrelevant
MHC-dextramers not able to bind the TCR. Flow cytometry analysis of
beads coupled with >0 .mu.g TCRs showed a slightly stronger
signal when stained with the relevant MHC-dextramer than with the
irrelevant MHC-dextramer (data not shown). The staining intensity
was identical when beads conjugated with 0 .mu.g TCR were stained
with either specific or non-specific MHC-dextramers. We conclude
that the monomeric biotinylated TCRs bound to streptavidin coated
beads can be used as positive control for the MHC-dextramer.
[1167] Binding of MHC-dextramers toamine-modified beads coupled
with monomeric or dimeric TCRs: [1168] Recombinant monomeric or
dimeric TCRs (CMV3 TCRs; Soluble CMVpp65(NLVPMVATV (SEQ ID
NO:9))-specific TCR protein) specific for the MHC-peptide complex
HLA-A*0201 (NLVPMVATV (SEQ ID NO:9)), were obtained from Altor
Biosciences.
[1169] The purity of the TCRs were verified by SDS PAGE. The
quality of the TCRs were verified by their ability to recognize the
relevant MHC-dextramer and not irrelevant MHC dextramers in ELISA
experiments (data not shown).
[1170] Amine-modified beads were coupled with dimeric TCR (CMV3
TCRs; Soluble CMVpp65(NLVPMVATV (SEQ ID NO:9))-specific TCR
protein).
[1171] Immobilization of TCR on amine modified beads: [1172] 1.
3.times.10.sup.9 Amine modified beads, Duke Scentific XPR-1536, 4
.mu.m, lot:4393 were washed in 2.times.500 .mu.l phosphate-buffered
saline (PBS) pH 7.5 centrifuged 4 min at 15000 g, and then the
supernatant was discarded. [1173] 2. Resuspend beads in 0.3 ml PBS
pH 7.5 [1174] 3. 25 .mu.l 20 mM solution of SPDP (N-Succinimidyl
3-(2-pyridyldithio) propionate) in DMSO was added to the beads, and
the suspension incubated at room temperature for 30 min. [1175] 4.
Beads were washed in 2.times.1 ml PBS comprising 1 mM EDTA, pH 7.5.
Centrifuged 4 min at 15000 g, and the supernatant was discarded.
[1176] 5. Resuspend beads in 0.3 ml PBS comprising 1 mM EDTA, pH
7.5. [1177] 6. 10 mg dithiothritol (DTT) was added, and suspension
incubated at room temperature for 30 min. [1178] 7. Beads were
washed in 2.times.1 ml PBS, pH 7.5. Centrifuged 4 min at 15000 g,
and the supernatant was discarded. [1179] 8. Sedimented beads, were
added a freshly prepared SPDP-derivatized protein prepared
according to the following outlines (step 14-15): [1180] 9. Treat
protein (in this example dimeric TCR) 2-5 mg/ml, in 0.1 ml
carbonate buffer, pH 8 with 10 .mu.l 20 mM solution of SPDP in DMSO
at room temperature for 30 min. [1181] 10. Remove excess reagent by
passing through a small desalting column in PBS pH 7.5, or by rapid
dialyse against PBS pH 7.5. [1182] 11. Add >1 mg SPDS-protein
per 10.sup.9 beads, to the SPDP derivatized and reduced bead
preparation from paragraph 13. 0-1 mg of SPDS-protein per 10.sup.9
beads might be desirable. [1183] 12. Resuspend beads in the
SPDP-protein solution. Incubate with slow shaking overnight at
4.degree. C. [1184] 13. Beads were washed in 2.times.1 ml PBS pH
7.5. Centrifuged 4 min at 15000 g, and the supernatant was
discarded. [1185] 14. Resuspend beads in 250 .mu.l PBS pH 7.5.
[1186] Bead concentration after resuspension was 1.2.times.10.sup.7
beads/l. Beads coated with TCRs were stored at 2-8.degree. C. The
quality of MHC-dextramer can now be analysed by examining the
degree of binding of specific MHC-dextramer to the TCR-coated
beads, versus the binding of irrelevant MHC-dextramer to the TCR
coated beads.
[1187] Various reaction conditions (e.g various protein:bead
ratios) and assay for optimal coupling yield can be explored. The
latter can be done by using an ELISA technique (incubate
protein/bead conjugated with an appropiate anti-protein enzyme
conjugated (e.g. HRP Peroxidase) followed by washing and colour
development with a suitable substrate (e.g. TMB/Peroxide)) or by
flow cytometry (e.g. a fluorescence labelled anti-protein (in this
example MHC multimer HLA-A*0201 (NLVPMVATV (SEQ ID NO:9))) to
assess level of covalently bound protein to amine-modified
beads.
[1188] We conclude that the TCRs coupled to amine-modified beads
coupled can be used as positive controls for the MHC Dextramer as
described in Example 8 and 9.
Example 10
[1189] This example describes how TCR-coated beads can be used as
internal, positive controls when analysing suspensions of Human
Peripheral Blood Mononuclear Cells (HPBMCs), whole blood samples or
any other cell sample of interest. The MHC multimer employed in
this example is a MHC-dextramer.
[1190] In this example TCR-coated carboxylated beads generated as
described in Example 8 were added to a sample comprising either
HPBMCs or whole peripheral blood.
[1191] HPBMCs and TCR-beads were incubated with fluorescently
labelled MHC-dextramers and the extent of cell staining analysed by
flow cytometry according to this general staining procedure: [1192]
1. Transfer 1-3.times.10.sup.6 lymphoid cells (PBMC or splenocytes)
to a 12.times.75 mm polystyrene test tube. Other cells of interest
can be used. Allocate only 2-5.times.10.sup.5 cells per tube when
staining T-cell clones or cell lines due to the high frequency of
antigen-specific T-cells [1193] 2. Add 2 ml 0.01 mol/L PBS
comprising 5% fetal calf serum and centrifuge at 300.times.g for 5
minutes. Remove supernatant and resuspend cells in remaining
liquid. [1194] 3. Add 10 .mu.l of MHC Dextramer and mix gently with
a vortex mixer. Incubate in the dark at room temperature for 10
minutes. [1195] 4. Add an optimally titrated amount of anti-CD8
antibody conjugated with a relevant flourochrome (e.g. Dako clone
DK25 for human lymphocytes or clone YTS169.4/KT15 for mouse
lymphocytes). Incubate in the dark at 2-80.degree. C. for 20 min.
[1196] 5. Add 2 ml of 0.01 mol/L PBS comprising 5% fetal calf serum
and centrifuge at 300.times.g for 5 minutes. [1197] 6. Resuspend
pellet in an appropriate fluid for flow cytometry, e.g. 0.4 ml PBS.
Analyse on a flow cytometer or store at 2-8.degree. C. in the dark
until analysis. Do not store longer than 2 hours before
analysis.
[1198] Human peripheral whole blood and TCR-beads were incubated
with fluorescently labelled MHC-dextramers and the extent of cell
staining analysed by flow cytometry as follows: [1199] 1. Transfer
100 .mu.L whole blood to a 12.times.75 mm polystyrene test tube.
[1200] 2. Add 10 .mu.l of MHC Dextramer and mix with a vortex
mixer. Incubate in the dark at room temperature for 10 minutes.
[1201] 3. Add an optimally titrated amount of anti-CD8 antibody
(e.g. Dako clone DK25) conjugated with a relevant fluorochromes and
mix well. Continue incubation at 2-8.degree. C. in the dark for 20
minutes. [1202] 4. Add 2 mL EasyLyse.TM. working solution (Code No.
S2364) and incubate for 10 minutes. [1203] 5. Centrifuge for 5
minutes at 300.times.g and aspirate supernatant. [1204] 6. Add 2 mL
0.01 mol/L PBS and centrifuge for 5 minutes at 300.times.g and
aspirate supernatant. [1205] 7. Resuspend pellet in an appropriate
fluid for flow cytometry, e.g. 0.4 mL PBS, and analyze on a flow
cytometer or store at 2-8.degree. C. in the dark until analysis. Do
not store longer than 2 hours before analysis.
[1206] FIG. 7 shows examples of TCR-beads added into whole blood or
HPBMC samples.
[1207] In both experiments it is possible, by forward-vs.
side-scatter measurements, to distinguish TCR-beads from cell
populations in the sample. Region R1 is TCR-beads, and region R2 is
lymphocyte cell population of interest in the analysis of MHC
positive T-cells.
[1208] The size and conditions of coating of beads might be
optimized. The size of beads or labeling of beads (e.g. flourescent
labeling) can be optimized to allow separation of cells of interest
in the sample. In this example the forward-vs. side-scatter dot
plot has been used for gating of cell populations of interest.
Other parameters (e.g. fluorescence intensity) for cell populations
of interest can be used.
[1209] Human peripheral whole blood and other cells (e.g. HPBMCs)
can be stained with MHC Dextramers simultaneously with
immuno-phenotyping of relevant antigens. The staining procedure
describes the use of labelled CD8 antibody together with MHC
dextramers; additional antibodies for detection of other
extracellular antigens can be added. Likewise, detection of
intracellular antigens can be performed simultaneously with
MHC-detection (for protocol, see IntraStain procedure, cat no.
K2311, Dako. Additional washing step prior to IntraStain Reagent A
is essential for good results using MHC Dextramers together with
this IntraStain procedure).
Example 11
[1210] This example describes how TCR-coated beads can be used as
internal, positive controls when analysing suspensions of Human
Peripheral Blood Mononuclear Cells (HPBMCs), whole blood samples or
any cell sample of interest. The MHC multimer employed in this
example is a MHC-tetramer.
[1211] In this example TCR-coated beads as described in Example 8
and 9 are added to a sample comprising either HPBMCs or whole
peripheral blood.
[1212] HPBMCs/whole peripheral blood and TCR-beads are incubated
with fluorescently labelled MHC-tetramers and the extent of cell
staining is analysed by flow cytometry according to staining
procedures as described for Tetramers in the product insert by
Beckman Coulter.
[1213] Results can be analysed as in Example 10, and it will be
possible, by forward-vs. side-scatter measurements, to distinguish
TCR-beads from cell populations in the sample.
Example 12
[1214] This example describes how TCR-coated beads can be used as
internal, positive controls when analysing suspensions of Human
Peripheral Blood Mononuclear Cells (HPBMCs), blood samples (red
blood cell depleted) or any cell sample of interest. The MHC
multimer employed in this example is a MHC-pentamer.
[1215] In this example TCR-coated beads as described in Example 8
and 9 are added to a sample comprising either HPBMCs or blood.
[1216] HPBMCs/blood sample and TCR-beads are incubated with
fluorescently labelled MHC-pentamers and the extent of cell
staining is analysed by flow cytometry according to staining
procedures as described for Petramers in the product insert by
Prolmmune. Results can be analysed as in Example 10 and it will be
possible, by forward-vs. side-scatter measurements, to distinguish
TCR-beads from cell populations in the sample.
Example 13
[1217] This example describes how it can be examined whether a MHC
multimer is correctly folded. The MHC multimer is in this example a
MHC-dextramer, and the test involves specific binding of the
MHC-dextramer to antibodies immobilized on beads.
[1218] Beads were coated with the antibody clone W6/32. W6/32 is an
antibody recognizing all human MHC I HLA-A, B and, C alleles but
only when they are in the correct conformation and properly loaded
with antigenic peptide. The protocol for immobilization of proteins
on carboxylate beads described in example 8 was followed. In the
following these W6/32 antibody coated carboxylated beads are
referred to as W/32-beads.
[1219] W6/32-beads were incubated with fluorescently labeled
MHC-dextramers and the extent of cell staining analyzed by flow
cytometry. The staining procedure described in example 8 was
followed.
[1220] W6/32-beads incubated with correctly folded MHC-dextramers
showed efficient staining. Experiments with W6/32-beads incubated
with unfolded heavy chain attached to fluorescently labelled
dextran, or a fluorescently labelled dextran without MHC complex
attached, showed less fluorescence intensity compared to
W6/32-beads incubated with correct folded MHC-dextramer.
[1221] We conclude that beads coupled with the antibody clone W6/32
can be used as positive control for all MHC alleles recognized by
this antibody.
[1222] Other antibodies, or other types of molecules such as DNA
aptamers recognizing correctly folded MHCs or parts of MHC could be
used in similar experiments.
Example 14
[1223] This example describes how the quality of the MHC multimer
can be tested. The MHC multimer in this example is a MHC-dextramer,
and the test involves specific binding of the MHC-dextramer to TCRs
or other MHC-recognizing molecules.
[1224] Experiments can be performed with any kind of TCRs or
MHC-recognizing molecules immobilized on a bead or other solid
support.
[1225] Procedures as described in examples elsewhere herein can be
used, depending on the chemistry of the MHC recognizing molecules
and type of solid support. Procedures for coupling of molecules and
type of solid support can be chosen and optimized according to the
chemistry of the molecules and solid support. Alternatively, the
experiments could be performed without including solid supports,
e.g. by performing immunoprecipitation of formed MHC multimer-TCR
complexes.
Example 15
[1226] This example describes how the quality of a MHC multimer can
be tested. The MHC multimer in this example is a MHC-dextramer, and
the test involves specific binding of the MHC-dextramer to a cell
line that expresses specific TCRs and display these on the cell
surface.
[1227] A transfected Jurkat T-cell line (JT3A) from Altor
Biosciences specific for the MHC complex HLA-A*0201(NLVPMVATV (SEQ
ID NO:9)) was evaluated as positive control for the MHC-dextramer
HLA-A*0201 (NLVPMVATV (SEQ ID NO:9)). The cells were cultured and
treated to express TCR just before evaluation. Under the conditions
used, 20-50% of the cells were expected to express and display TCR.
After stimulation the cells were incubated with fluorescently
labeled MHC-dextramers and the extent of cell staining analyzed by
flow cytometry, as follows: [1228] 1. JT3A cells growing in log
phase were incubated at room temperature for 2-3 hours to express
TCRs (The TCRs are not stable expressed at 37.degree. C.). [1229]
2. After 3 hours cells were centrifuged for 5 min at 400 g, and the
supernatant was discarded. [1230] 3. Cells were washed in PBS pH
7.4+5% FCS, and centrifuged for 5 min at 400 g. The supernatant was
discarded, and cells resuspended in proper volume PBS pH 7.4+5% FCS
for counting in a Burker chamber. [1231] 4. 1.times.10.sup.6 cells
per sample in 100 .mu.l PBS pH 7.4+5% FCS were added to each sample
tube. [1232] 5. 10 .mu.l MHC-dextramers were added. Incubation for
30 min at 4.degree. C. in the dark. [1233] 6. 5 .mu.l anti-CD3 was
added to each sample. Further incubation for 30 min at 4.degree. C.
in the dark. [1234] 7. Samples were washed in 2 ml PBS, centrifuged
for 5 min at 300 g. Supernatant discarded and sample resuspended in
0.4 ml PBS pH 7.4. [1235] 8. Samples were kept at 2-8.degree. C. in
the dark until analysis on flow cytometer. [1236] 9. Samples were
analyzed by flow cytometry on a CyAn instrument.
[1237] Data were analyzed by the Summit software. Stimulated JT3A
cells were stained with the specific MHC-dextramer
HLA-A*0201(NLVPMVATV (SEQ ID NO:9)) and anti-CD3. Another sample of
cells were stained with the irrelevant MHC-dextramer HLA-A*0201
(GILGFVFTL (SEQ ID NO:22)) and anti-CD3. The cells stained with
HLA-A*0201 (GILGFVFTL (SEQ ID NO:22)) had weak signals (low
fluorescent intensity), and therefore regarded as the negative
population. A boundary was introduced in the dot plot, to mark the
negative population. Cells with fluorescence higher than the
negative boundary were hereafter regarded positive. 19% and 0.25%
of the cells were regarded positive when stained with the relevant
and irrelevant MHC-dextramer, respectively. See table below.
TABLE-US-00008 MHC-complex Percentage of positive cells
HLA-A*0201(NLVPMVATV 19% (SEQ ID NO: 9)) HLA-A*0201(GILGFVFTL 0.25%
(SEQ ID NO: 22))
[1238] The results thus correlate well with the expected 20-50%
HLA-A*0201 (NLVPMVATV (SEQ ID NO:9)) positive JT3A cells after
stimulation. We conclude that the transfected JurkaT-cell line
(JT3A) can be used as positive control for the MHC-dextramer.
Example 16
[1239] This example describes how the quality of a MHC multimer can
be tested. The MHC multimer in this example is a MHC-dextramer, and
the test involves specific binding of the MHC-dextramer to cell
preparations expressing TCRs.
[1240] Three different peptide specific T-cell preparations of
Human cytotoxic T lymphocyte lines specific for a viral peptide
were incubated with fluorescently labeled MHC-dextramers and the
extent of cell staining analyzed by flow cytometry. The following
T-cell preparations were examined: (NLV) specific for MHC-dextramer
HLA-A*0201(NLVPMVATV (SEQ ID NO:9)), (IPSI) specific for
MHC-dextramer B*3501(IPSINVHHY (SEQ ID NO:23)) and (GLC) specific
for MHC-dextramer A*0201(GLCLVALM (SEQ ID NO:24)). [1241] 1. Cells
were added 1 ml RPMI and then transfer to a tube with 9 ml RPMI.
Cells were centrifuged for 5 min at 300 g, and the supernatant was
discarded. [1242] 2. Cells were washed in 10 ml PBS pH 7.4+5% FCS,
and centrifuged for 5 min at 300 g, and the supernatant was
discarded. [1243] 3. 1.times.10.sup.6 cells per sample in 100 .mu.l
PBS pH 7.4+5% FCS were added to sample tubes. [1244] 4. 10 .mu.l
MHC Dextramers were added, and incubated at room temperature in the
dark for 10 min. [1245] 5. 5 .mu.l anti-CD3 and anti-CD8 were added
to each sample. Further incubation for 20 min at 4.degree. C. in
the dark. [1246] 6. Samples were washed in 2 ml PBS pH 7.4+5% FCS
and centrifuged for 5 min at 300 g, and the supernatant was
discarded. [1247] 7. Pellets were resuspended in 0.4 ml PBS pH 7.4.
[1248] 8. Samples were kept in the dark at 2-8.degree. C. until
analysis on a flow cytometer. [1249] 9. Samples were analyzed by
flow cytometry on a CyAn instrument.
[1250] Data were analyzed by the Summit software. The cell
preparations were stained with anti-CD3, anti-CD8, the respective
specific MHC-dextramer, or an irrelevant MHC-dextramer. Anti-CD3
positive cells were positively gated and anti-CD8 vs. MHC-dextramer
were depicted in a dot plot. The main population of anti-CD8
positive cells stained with the irrelevant MHC-dextramer was
regarded as negative, and a boundary was introduced in the dot plot
to mark the negative population. Anti-CD8 positive cells with
fluorescence higher than the negative boundary were regarded
positive. In the NLV and IPSI cell preparations, approximately 95%
of the CD8+ cells were positive for the relevant MHC dextramer. 45%
of the CD8.sup.+ GLC cells were positive for relevant MHC
Dextramers, see table below. Cell preparations were not stained by
the irrelevant MHC-dextramer.
[1251] We conclude that the different peptide specific T-cell
preparations can be used as positive controls for the relevant
MHC-dextramer.
TABLE-US-00009 Cell Percentage of preparation MHC-complex positive
cells NLV HLA-A*0201(NLVPMVATV) 97% (SEQ ID NO: 9))
HLA-B*3501(IPSINVHHY 0.02% (SEQ ID NO: 23)) IPSI
HLA-B*3501(IPSINVHHY 95% (SEQ ID NO: 23)) HLA-A*0201(NLVPMVATV
0.01% (SEQ ID NO: 9)) GLC HLA-A*0201(GLCLVALM 45% (SEQ ID NO: 24))
HLA-A*0201(ILKEPVHGV 0.1% (SEQ ID NO: 10))
Example 17
[1252] This example describes how the quality of the MHC multimer
can be tested. The MHC multimer in this example is a MHC-dextramer,
and the test involves specific binding of the MHC-dextramer to cell
lines or other preparations expressing TCRs or MHC-recognizing
molecules.
[1253] Experiments can be performed with any kind of TCRs or
MHC-recognizing molecules displayed on cells (e.g. a cell line or a
cell preparation).
[1254] Procedures as described in Example 15 and 16 can be used
with any kind of TCRs or MHC-recognizing molecules displayed on
cells. Stimulation of cells has to be optimized for the specific
experiments (e.g. stimulation with chemicals and/or temperature to
express the TCR prior to analysis).
[1255] Results can be analyzed as in Example 15 and 16 and cell
preparations stained with relevant MHC-dextramers will extent
higher signal intensity than when stained with irrevant
MHC-dextramers.
Example 18
[1256] This example describes how the quality of the MHC multimer
can be tested. The MHC multimer in this example is a MHC-dextramer,
and the test involves specific binding of the MHC-dextramer to TCRs
or MHC recognizing motifs immobilized or expressed on molecules
detectable in flow cytometry.
[1257] The experiments can be performed with any kind of molecule
detectable in flow cytometry. MHC-recognizing molecules can be
displayed on beads, cells, or other entities that are amenable to
flow cytometry analysis.
[1258] MHC-recognizing molecules can be displayed on entities
amenable in flow cytometry either naturally or artificially (e.g.
chemical coupling). Procedures as described in the above examples
can be applied, depending on the nature of the molecules.
Alternatively procedures optimized for the specific molecule can be
applied.
[1259] Molecules can be stained with flourescently labeled
MHC-dextramers and the extent of cell staining can be analyzed by
flow cytometry. Molecules stained with relevant MHC-dextramers will
extent higher signal intensity than when stained with irrelevant
MHC-dextramers.
Example 19
[1260] This example describes how the quantity of correctly folded
MHC can be determined by ELISA assay. The test involves specific
binding of the MHC to anti-HLA-ABC antibody, clone W6/32. W6/32 is
an antibody recognizing all human MHC I HLA-A, B and C alleles but
only when they are in the correct conformation and properly loaded
with antigenic peptide.
[1261] The ELISA can be carried out as follows. A preparation of
MHC complexes is incubated in wells of a microtiter plate
pre-coated with W6/32 antibody following standard ELISA procedure
regarding washes, blocking ect. A secondary antibody recognizing
MHC (e.g. anti-.beta..sub.2m) is used for visualization. The
secondary antibody can be labbelled, e.g. with Horse raddish
Peroxidase or it can be unlabelled, and a labeled compound specific
for the secondary antibody is then employed (e.g. EnVision System)
before visualization. A compound for visualization is added, e.g.
TMB One-Substrate System when Peroxidase enzyme is the label. The
chromogenic intensity is measured and the result from the ELISA
assay is evaluated. In parallel a standard curve of is generated,
e.g. consisting of various concentrations of correctly folded MHC
complexes. The chromogenic intensity of the tested MHC sample can
now be converted to actual concentrations of correctly folded MHC
using the standard curve. We conclude that the ELISA assay together
with a standard curve can be used to quantify correctly folded
MHC.
Example 20
[1262] This example describes how the quantity of correctly folded
MHC can be determined by ELISA assay. The test involves specific
binding of MHC complexes to a molecule recognizing correctly folded
MHC (e.g. antibody, TCR, aptamers, or other MHC-peptide complex
binding molecules).
[1263] As described elsewhere the quantity of correctly folded MHC
can be measured in an ELISA assay using a molecule specific for
correctly folded MHC complexes either for catching of the testet
MHC complex preparation or for detection of it. The result obtained
from bound MHC complex in the sample tested is correlated to a
standard curve for determination of concentration. The ELISA assay
can be conducted and optimized by various measures depending on the
reagent and enzyme used.
Example 21
[1264] This example describes how the quantity of correctly folded
MHC can be determined by competitive ELISA assay. The test involves
specific binding of MHC complexes to a molecule recognizing
correctly folded MHC (e.g. antibody, TCR, aptamers, or other
MHC-peptide complex binding molecules). The analysis is carried out
as follows. A preparation of correctly folded MHC of known
concentration is immobilized in wells of a microtiter plate. A
mixture of a molecule recognizing correctly folded MHC (e.g. the
antibody W6/32) and soluble MHC complex, comprising a mixture of
correctly and non-correctly folded MHC, is added to the microtiter
plate. The molecules recognizing correctly folded MHC will now
attach to either the immobilized MHC or the correctly folded MHC in
the soluble fraction. The amount of molecules recognizing correctly
folded MHC bound to the immobilized MHC in the microtiter plate is
measured, e.g. by addition of a secondary labeled or unlabeled
antibody specific for the molecule recognizing correctly folded
MHC. Depending on the characteristic of the secondary antibody
visualization is performed. The result of the ELISA assay is
evaluated. The amount of bound molecules specific for correctly
folded MHC complexs is inversely proportional to the quantity of
correctly folded MHC in the soluble fraction. The quantity of
correctly folded MHC in the soluble fraction can be measured using
a standard curve, obtained using known amounts of a pure
preparation of MHC complexes and constant amount of molecules
recognizing correctly folded MHC.
[1265] We conclude that an indirect competitive ELISA can be used
to quantify correctly folded MHC.
Example 22
[1266] This example describes how the quantity of correctly folded
MHC can be determined by competitive ELISA assay. The test involves
specific binding of MHC complexes to a molecule recognizing
correctly folded MHC (e.g. antibody, TCR, aptamers, or other
MHC-peptide complex binding molecules).
[1267] The analysis is carried out as follows. Molecules
recognizing correctly folded MHC are immobilized in wells of a
microtiter plate. A preparation of in vitro folded MHC complexes is
mixed with a known amount of labeled correctly folded MHC and the
mixure added to the microtiter plate. The correctly folded MHC in
the mixture will now compete for binding to the molecules
recognizing correctly folded MHC immobilized in the microtiter
plate. The amount of bound labeled MHC can now be visualized and
measured. The result is inversely proportional to the quantity of
correctly folded MHC in the mixture. The quantity of correctly
folded MHC in the mixture can be measured using a standard curve,
obtained using known amounts of a pure preparation of MHC mixed
with a constant amount of labeled MHC.
Example 23
[1268] This example describes how the quantity of correctly folded
MHC can be determined by competitive ELISA assay. The test involves
specific binding of the MHC to a molecule recognizing correctly
folded MHC (e.g. antibody, TCR, aptamers, or other MHC-peptide
complex binding molecules) or to molecules recognizing MHC,
correctly as well as non-correctly folded (e.g. antibody, TCR,
aptamers, or other MHC-peptide complex binding molecules). [1269]
1. A preparation of MHC complexes are immobilized in a microtiter
plate and incubated with a labeled molecule recognizing MHC,
correctly as well as non-correctly folded (in the following
referred to as recognizing all MHC complexes). [1270] 2. Then an
unlabeled molecule recognizing correctly folded MHC is added in
major excess. These molecules will displace all the MHC recognizing
molecules added in step 1 that binds correctly folded MHC
complexes. [1271] 3. The amount of bound labeled molecule
recognizing all MHC can now be visualized and measured. [1272] 4.
The result is inversely proportional to the quantity of correctly
folded MHC. The quantity of correctly folded MHC can be measured
using a standard curve, obtained using known amounts of a MHC
incubated with labeled molecule recognizing all MHC.
Example 24
[1273] This example describes how the quantity of correctly folded
MHC can be determined. The test involves specific binding of MHC
complexes to anti-HLA-ABC antibody, clone W6/32. In this example
W6/32 antibody is immobilized on magnetic beads. [1274] 1. The
protein concentration in a purified preparation of MHC complexes is
determined by spectofotometric measurement of OD.sub.280. Other
techniques can be used as well, e.g. BCA (bicinchoninic acid) assay
or SDS-PAGE gel. [1275] 2. To measure the proportion of correctly
folded MHC, a sample of the MHC complex preparation is incubated
with W6/32 antibody coated magnetic beads. [1276] 3. After
incubation the beads are sedimented or captured by a magnet and
excess supernatant is withdrawn. [1277] 4. The concentration of
protein in the supernatant is measured as in step 1. [1278] 5. The
proportion of correctly folded MHC complex is calculated as
follows:
[1278] X : Total protein concentration ( step 1 ) ##EQU00001## Y :
Protein concentration after capture of correctly folded MHC ( step
4 ) ##EQU00001.2## % of correct folded MHC = ( 1 - ( Y / X ) ) *
100 % ##EQU00001.3## Ex . X = 10 mg / ml ##EQU00001.4## Y = 2 mg /
ml ##EQU00001.5## % of correct folded MHC = ( 1 - ( 2 mg / ml / 10
mg / ml ) ) * 100 % = 80 % ##EQU00001.6##
[1279] The proportion of correctly folded MHC can be used as
quality parameter, to measure the variation from production to
production of a specific MHC-peptide complex.
Example 25
[1280] This example describes how the quantity of correctly folded
MHC can be determined. The test involves specific binding of MHC
complexes to a molecule recognizing correctly folded MHC (e.g.
antibody, TCR, aptamers, or other MHC-peptide complex binding
molecules). The MHC recognizing molecules can be immobilized to a
solid support (e.g. beads, microtiter plate or gel material).
[1281] 1. The protein concentration in a purified preparation of
MHC complexes is determined by spectofotometric measurement of
OD.sub.280. Other techniques can be used as well, e.g. BCA
(bicinchoninic acid) assay or SDS-PAGE gel. [1282] 2. To measure
the proportion of correctly folded MHC, a sample of the MHC complex
preparation is incubated with a molecule recognizing correctly
folded MHC complex immobilized to a solid support. [1283] 3. After
incubation supernatant is withdrawn. [1284] 4. The concentration of
protein in the supernatant is measured as in step 1. [1285] 5. The
proportion of correctly folded MHC complex is calculated as
follows:
[1285] X : Total protein concentration ( step 1 ) ##EQU00002## Y :
Protein concentration after capture of correctly folded MHC ( step
4 ) ##EQU00002.2## % of correct folded MHC = ( 1 - ( Y / X ) ) *
100 % ##EQU00002.3## Ex . X = 10 mg / ml ##EQU00002.4## Y = 2 mg /
ml ##EQU00002.5## % of correct folded MHC = ( 1 - ( 2 mg / ml / 10
mg / ml ) ) * 100 % = 80 % ##EQU00002.6##
[1286] The proportion of correctly folded MHC can be used as
quality parameter, to measure the variation from production to
production of a specific MHC-peptide complex.
Example 26
[1287] This example describes how the quantity of correctly folded
MHC can be determined. The test involves specific binding of MHC
complexes to anti-HLA-ABC antibody, clone W6/32. In this example
W6/32 antibody is immobilized on magnetic beads. [1288] 1. A
preparation of MHC complexes is incubated with W6/32 antibody
coated magnetic beads and all correctly folded MHCs are thereby
captured. [1289] 2. After incubation the beads are sedimented or
captured by magnet, the supernatant withdrawn and the amount of
non-bound MHC complex (equal to not correctly folded MHC complex)
is determined by ELISA. [1290] 3. To measure the quantity of MHC
complexes in solution before and after incubation with W6/32
antibody coated magnetic beads an ELISA assay is applied. A
microtiter plate is coated with an antibody recognizing all MHC
complexes correct as well as non-correct folded. [1291] 4. Samples
of MHC complex before and after incubation with W6/32 antibody
coated magnetic beads are added to the coated microtiter plate.
[1292] 5. A labeled secondary antibody recognizing MHC (e.g.
anti-.beta..sub.2m) is used for visualization. Alternatively the
secondary antibody is unlabelled, and a labeled molcule specific
for the secondary antibody is employed (e.g. EnVision System)
before visualization. [1293] 6. The proportion between results from
the sample after incubation with W6/32 antibody coated magnetic
beads and the sample before incubation with W6/32 antibody coated
magnetic beads is a measure of the amount of non correct folded MHC
complex and thereby an indirect measure of the amount of correct
folded MHC complex. To obtain exact values for the amount of MHC
complex in each sample a standard curve can be generated.
Example 27
[1294] This example describes how the quantity of correctly folded
MHC in a sample can be determined. The test involves specific
binding of MHC complexes to a molecule recognizing correctly folded
MHC complex (e.g. antibody, TCR, aptamers, or other MHC-peptide
complex binding molecules). The MHC recognizing molecules can be
immobilized to any solid support (e.g. beads, microtiter plate or
gel material). Correctly folded MHC complex in a sample is captured
by addition of the sample to the immobilized MHC-binding molecule,
and then non-bound MHC-complex (equal to not corretly folded MHC
complex) is removed. The proportion of MHC complex in the two
fractions (before and after incubation with immobilized
MHC-specific molecule) can be evaluated by any method capable of
determination of the total amount of MHC complex (folded or
undfodled)
Example 28
[1295] This example describes how the quantity of correctly folded
MHC in a sample can be determined. The test involves specific
binding of MHC complex to a molecule recognizing correctly folded
MHC (e.g. antibody, TCR, aptamers, or other MHC-peptide complex
binding molecules). The specific binding is evaluated by native
protein gel electrophoresis.
[1296] A preparation of in vitro folded and purified MHC complex is
incubated with a molecule recognizing correctly folded MHC, e.g.
the antibody W6/32.
[1297] The product is analysed by native protein gel
electrophoresis (lane 1) together with a sample of in vitro folded
and purified MHC complex not incubated with MHC recognizing
molecule (lane 2), and a sample of the molecule recognizing
correctly folded MHC (lane 3). In the protein gel the different
proteins are separated according to size. The various protein
products are visualized in the gel e.g. by Comassie blue staining,
isotope or chemiluminiscence. In the sample with MHC complex and
MHC-binding molecule correctly folded MHC complex will bind the
MHC-binding molecule and appear in the protein gel as one or more
large bands in the top of the gel. In contrast non-correctly folded
MHC complex will appear as monomer lower in the gel. The fraction
of not correctly folded MHC (lane 1) can now be compared with the
total amount of MHC in the sample (lane 2) and the difference
between the two correlates with the amount of correctly folded MHC
complex in the sample. The results can be evaluated in different
manners to determine the quantity of correctly folded MHC, e.g.
comparison of intensity to the intensity of products of known
concentration.
Example 29
[1298] This example describes how to verify that a MHC-complex is
correctly folded by a sandwich-ELISA assay. W6/32
mouse-anti-HLA-ABC antibody (Dako M0736), that recognizes a
conformational epitope on correctly folded MHC-complex, was used as
coating-antibody. HRP-conjugated rabbit anti-.beta.2m (Dako P0174)
was used for visualization. [1299] 1. Wells of a microtiter plate
was pre-coated with W6/32 antibody (Dako M0736, 5 .mu.g/ml in 0.1M
NaHCO.sub.3, 1 mM MgCl.sub.2, pH 9.8, 50 l/well) following a
standard ELISA procedure regarding washes and blocking etc. [1300]
2. After addition of 50 .mu.l of 0.5M Tris-HCl, 0.1 M NaCl, 0.1%
Tween 20, 0.01% Bronidox, pH 7.2 to each well, 50 .mu.l of a sample
of purified folded MHC-complex (in a concentration of approx. 0.4
mg/ml) was added to two wells in to columns in the microtiter
plate, diluted 2-fold down the column and incubated 2 hours at
4.degree. C. Light chain .beta.2m (0.15 mg/ml in 0.5M Tris-HCl, 0.1
M NaCl, 0.1% Tween 20, 0.01% Bronidox, pH 7.2) was used as a
negative control and the cell-line KG-la, expressing HLA-A*30,
HLA-A*31 and HLA-B*35 heavy chains, was used as positive control
(10.sup.6 cells/well). [1301] 3. After a standard ELISA wash, 50
.mu.l of the detecting antibody; HRP-conjugated rabbit
anti-.beta.2m (Dako PO174), diluted 1:2500 in 1% Skimmed Milk in
0.5M Tris-HCl, 0.1 M NaCl, 0.1% Tween 20, 0.01% Bronidox, pH 7.2
was added to each well. The plate wass incubated 1 hour at
4.degree. C. [1302] 4. After a standard ELISA wash, 50 .mu.l of an
amplifying antibody; HRP-Dextran500-conjugated goat anti-rabbit
(Dako DM0106), diluted 1:2000 in 1% Skimmed Milk in 0.5M Tris-HCl,
0.1 M NaCl, 0.1% Tween 20, 0.01% Bronidox, 1% mouse serum (Dako
X0190) pH 7.2 was added. The plate was incubated 30 min. at
20.degree. C. [1303] 5. After a standard ELISA wash, 50 .mu.l of
Dako S1599 (TMB+Substrat Chromogen) was added to each well for
visualization. [1304] 6. After 10 min. the visualization reaction
was stopped with 50 .mu.l 0.5M H.sub.2SO.sub.4/well. [1305] 7. The
chromogenic intensity was measured at OD.sub.450 and the result
from the ELISA assay evaluated.
[1306] As shown in FIG. 5 the OD.sub.450 values from wells with MHC
complex was more than 6 times higher than OD.sub.450 values from
wells with the negative control .beta.2m. This ELISA procedure can
be used to verify the presence of correctly folded MHC-peptide
complexes in a preparation of MHC complexes.
Example 30
[1307] This example describes the generation and application of
negative controls, where the MHC complex is HLA-A*0201 loaded with
either of the nonsense peptides GLAGDVSAV (SEQ ID NO:11) or
ALIAPVHAV (SEQ ID NO:12) and these MHC complexes are coupled to a
270 kDa dextran multimerization domain. The nonsense peptides have
an amino acid sequence different from the linear sequence of any
peptide derived from any known naturally occurring protein. This
was analyzed by a blast search. The amino acids at position 2 and 9
can serve as anchor residues when binding to HLA-A*0201
molecules.
[1308] Purified MHC (peptide) molecules consisting of the allele
HLA-A*0201, human beta2microglobulin and peptide was generated by
in vitro refolding, purified and biotinylated as described
elsewhere herin. Biotinylated HLA-A*0201(peptide) was mixed with
APC-SA-conjugated 270 kDa dextran in an amount corresponding to a
ratio of three biotinylated HLA-A*0201(peptide) molecules per SA
molecule and incubated for 30 minutes in the dark at room
temperature. The APC-SA-conjugated 270 kDa dextran contained 9
molecules APC and 3.7 molecules SA per dextran molecule. Following
incubation the mixture was diluted into a buffer comprising 0.05M
Tris/HCl, 15 nM NaN.sub.3 and 1% BSA to a final concentration of
3.8.times.10.sup.-8 M dextran. By this procedure the following MHC
multimer constructs were made: [1309] 1) A negative control
construct comprising APC-SA-conjugated 270 kDa dextran and
biotinylated HLA-A*0201 in complex with beta2microglobulin and the
nonsense peptide GLAGDVSAV (SEQ ID NO:11) (nonsense peptide 1).
[1310] 2) A negative control construct comprising APC-SA-conjugated
270 kDa dextran and biotinylated HLA-A*0201 in complex with
beta2microglobulin and the nonsense peptide ALIAPVHAV (SEQ ID
NO:12) (nonsense peptide 2). [1311] 3) A construct comprising
APC-SA-conjugated 270 kDa dextran and biotinylated HLA-A*0201 in
complex with beta2microglobulin and the peptide NLVPMVATV (SEQ ID
NO:9) derived from pp65 protein from human cytomegalovirus (HCMV).
[1312] 4) A construct comprising APC-SA-conjugated 270 kDa dextran
and biotinylated HLA-A*0201 in complex with beta2microglobulin and
the peptide GLCTLVAML (SEQ ID NO:13) derived from BMLF-1 protein
from Epstein Barr virus (EBV). [1313] 5) A construct comprising
APC-SA-conjugated 270 kDa dextran and biotinylated HLA-A*0201 in
complex with beta2microglobulin and the peptide ILKEPVHGV (SEQ ID
NO:10) Reverse Transcriptase from Human Immunodeficiency Virus
(HIV).
[1314] The binding of the HLA-A*0201(peptide)/APC dextran
constructs to Human Peripheral Blood Mononuclear Cells (HPBMC) from
various donors was analyzed by flow cytometry following a standard
flow cytometry protocol. Briefly, HPBMC from the blood of 9
individual donors were isolated, by a standard protocol using
FICOLL.RTM.-Hypaque. 1.times.10.sup.6 purified HPBMC at a
concentration of 2.times.10.sup.7 cells/ml were incubated with 10
.mu.l of one of the HLA-A*0201(peptide)/APC dextran constructs
described above for 10 minutes in the dark at room temperature. 10
.mu.l of each of the antibodies mouse-anti-human CD3/PE (clone
UCHT1 from Dako) and mouse-anti-human CD8/PB (clone DK25 from Dako)
were added and the incubation continued for another 20 minutes at
40.degree. C. in the dark. The samples were then washed by adding 2
ml PBS; pH=7.2 followed by centrifugation for 5 minutes at
200.times.g and the supernatant removed. The cells were then
resuspended in 400-500 .mu.l PBS; pH=7.2 and analyzed on a CYAN ADP
flowcytometer.
[1315] Donor 1-5 were known to have detectable T-cells specific for
HLA-A*0201(NLVPMVATV (SEQ ID NO:9)) and no detectable T-cells
specific for HLA-A*0201(ILKEPVHGV (SEQ ID NO: 10)) while donor 6
were known not to have detectable specific T-cells for either
HLA-A*0201 (NLVPMVATV (SEQ ID NO:9)) nor HLA-A*0201(ILKEPVHGV (SEQ
ID NO:10)). Lymphocytes from these 6 donors were stained with MHC
multimer construct 1, 2, 3, and 5. Donor 1-5 showed positive
staining with MHC multimer construct 3 as expected while no
staining was observed with the either of the negative control MHC
complex constructs 1 and 2 or with MHC complex construct 5. An
example showing the staining patterns for donor 2 is shown in FIG.
8. No specific staining was observed of lymphocytes from donor 6
with either of the MHC multimer constructs.
[1316] Donor 7-8 known to have detectable T-cells specific for
HLA-A*0201 (GLCTLVAML (SEQ ID NO:13)) and no detectable T-cells
recognizing HLA-A*0201(ILKEPVHGV (SEQ ID NO:10)) and donor 9 having
no detectable T-cells specific for either HLA-A*0201(GLCTLVAML (SEQ
ID NO:13)) nor HLA-A*0201(ILKEPVHGV (SEQ ID NO:10)) were all
stained with MHC multimer construct 1, 2, 4, and 5. Donor 7 and 8
demonstrated efficient staining with MHC multimer construct 4 as
expected while no staining was observed with the other MHC multimer
constructs tested. No staining was observed of lymphocytes from
donor 9 with either of the MHC multimer constructs tested. A
summary of the results is shown in FIG. 9.
[1317] In conclusion this experiment demonstrates that the negative
MHC multimer constructs 1 and 2 did not stain any specific T-cells
in lymphocyte preparations from 10 different donors. Donors known
to have specific T-cells for either HLA-A*0201(GLCTLVAML (SEQ ID
NO:13)) or HLA-A*0201(NLVPMVATV (SEQ ID NO:9)) also demonstrated
positive staining with the corresponding MHC multimer constructs 3
and 4. None of the 10 donors were infected with HIV and as expected
did not appear to have T-cells specific for HLA-A*0201 in complex
with the HIV derived peptide ILKEPVHGV (SEQ ID NO:10), and as
expected none of these donors showed staining with MHC multimere
construct 5. MHC multimer construct 1 and 2 are therefore suitable
negative controls when using HLA-A*0201(peptide) multimers for
detection of specific T-cells in Flow Cytometry.
Example 31
[1318] This is an example of how to generate and use negative
controls, where the MHC complex is any MHC I or MHC II complex of
human, mouse, rabbit, rat, swine or monkey origin loaded with a
nonsense peptide. A nonsense peptide is here to be understood as a
peptide having an amino acid sequence different from any peptide
derived from any known naturally occurring protein, and preferably
is not recognized by any T-cell when presented by a MHC complex.
The nonsense peptide has amino acid residues at relevant positions
that anchor the peptide to the peptide-binding groove of the MHC
complex. The MHC(nonsense peptide) complex is coupled to a 270 kDa
dextran multimerization domain.
[1319] Purified MHC(peptide) molecules consisting of the alpha
chain, human beta2microglobulin and peptide is generated by in
vitro refolding, purified and biotinylated as described elsewhere.
Biotinylated MHC(peptide) is mixed with APC-SA-conjugated 270 kDa
dextran in amounts corresponding to a ratio of three biotinylated
MHC(peptide) molecules per SA molecule and incubated for 30 minutes
in the dark at room temperature. The APC-SA-conjugated 270 kDa
dextran contains 9 molecules APC and 3.7 molecules SA per dextran
molecule. Following incubation the mixture is diluted into a buffer
comprising 0.05M Tris/HCl, 15 nM NaN.sub.3 and 1% BSA to a final
concentration of 3.8.times.10.sup.-8 M dextran.
[1320] By this procedure the following MHC complex constructs are
made: [1321] 1. A negative control construct comprising
APC-SA-conjugated 270 kDa dextran and biotinylated alpha chain in
complex with beta2microglobulin and a corresponding nonsense
peptide. A nonsense peptide is here to be understood as a peptide
with an amino acid sequence different from any peptide derived from
any known naturally occurring protein and the nonsense peptide is
not recognized by any T-cell when presented by a MHC complex.
[1322] 2. A construct comprising APC-SA-conjugated 270 kDa dextran
and biotinylated alpha chain in complex with beta2microglobulin and
a peptide derived from a known protein.
[1323] The binding of the MHC(peptide)/APC dextran constructs to
Human Peripheral Blood Mononuclear Cells (HPBMC) from various
donors is analyzed by flow cytometry following a standard flow
cytometry protocol. Briefly, HPBMC from the blood of 9 individual
donors are isolated by a standard protocol using
FICOLL.RTM.-Hypaque. 1.times.10.sup.6 purified HPBMC at a
concentration of 2.times.10.sup.7 cells/ml is incubated with 10
.mu.l of one of the MHC(peptide)/APC dextran constructs described
above for 10 minutes in the dark at room temperature. 10 .mu.l of
each of each of the antibodies mouse-anti-human CD3/PE (clone UCHT1
from Dako) and mouse-anti-human CD8/PB (clone DK25 from Dako) are
added and the incubation continued for another 20 minutes at
4.degree. C. in the dark. The samples are then washed by adding 2
ml PBS; pH=7.2 followed by centrifugation for 5 minutes at
200.times.g and the supernatant removed. The washed cells are
resuspended in 400-500 .mu.l PBS; pH=7.2 and analyzed on a CYAN ADP
flowcytometer.
[1324] The staining patterns of flow cytometry analysis with the
two MHC(peptide)/APC constructs 1 and 2 are compared. There will be
no staining observed with construct 1.
Example 32
[1325] This is an example of how to generate negative controls,
where the MHC complexes is any MHC I or MHC II molecule of human,
mouse, rabbit, rat, swine, monkey or any other origin loaded with a
nonsense peptide and where the MHC(nonsense peptide) complexes are
coupled to any multimerization domain. A nonsense peptide is here
to be understood as a peptide that have an amino acid sequence
different from any peptide derived from any known naturally
occurring protein and cannot be recognized by any T-cell when
presented by a MHC complex. The nonsense peptide carries amino acid
residues at relevant positions that anchor the peptide to the
peptide-binding groove of the MHC complex.
[1326] The MHC(nonsense peptide) complex can be made as described
elsewhere herein, and can then be coupled to one or more relevant
multimerization domain(s). The labeling of the one or more
multimerization domain(s) can be optimized depending on later use
of the negative control e.g. in flow cytometry analysis, IHC, ELISA
or similar.
Example 33
[1327] This example describes the generation of a negative control,
where the MHC complex is HLA-A*0201 coupled to a 270 kDa dextran,
and where the MHC is loaded with the peptide ILAKFLHWL (SEQ ID
NO:25) that have pivaloyl coupled to Lysine at position 4.
ILAKFLHWL (SEQ ID NO:25) is a peptide derived from telomerase and
is known to bind HLA-A*0201. Pivaloyl is a small molecule that
confers high sterical hindrance. Because pivaloyl is placed at a
central position in the peptide it is likely to inhibit or
completely abrogate the interaction with a specific TCR, because
TCR-recognition is normally directed to the middle of the peptide
when bound in the peptide-binding cleft. In the following the
pivaloyl-modified peptide will be designated ILAKPFLHWL.
[1328] Purified HLA-A*0201(ILAKPFLHWL (SEQ ID NO:35)) molecules
consisting of the HLA-A*0201 heavy chain, human beta2microglobulin
and ILAKPFLHWL (SEQ ID NO:35) peptide is generated by in vitro
refolding, purified and biotinylated as described elsewhere herein.
Biotinylated HLA-A*0201(ILAKPFLHWL (SEQ ID NO:35)) molecules are
mixed with flourochrome-SA-conjugated 270 kDa dextran molecules.
The resulting HLA-A*0201(LAKPFLHWL (SEQ ID
NO:35))/flourochrome-carrying dextran molecules can be used as
negative controls in e.g. flow cytometric analysis.
Example 34
[1329] This example describes the generation of a negative control,
where the MHC complex is any MHC I or MHC II molecule of human,
mouse, rabbit, rat, swine, monkey or any other origin loaded with
the peptide ILAKPFLHWL (SEQ ID NO:35) and coupled to any
multimerization domain labeled with fluorochrome, HRP or any other
label. Purified MHC(ILAKPFLHWL (SEQ ID NO:35)) complexes consisting
of the heavy chain, human beta2microglobulin and ILAKPFLHWL peptide
is generated by in vitro refolding, purified and biotinylated as
described elsewhere herein. Biotinylated MHC(ILAKPFLHWL (SEQ ID
NO:35)) complexes are mixed with labeled multimerization domain,
thereby generating MHC(ILAKPFLHWL (SEQ ID NO:35)) multimers. The
MHC(ILAKPFLHWL (SEQ ID NO:35)) multimers mayn be used as negative
controls in e.g. flow cytometric analysis, IHC, ELISA or
similar.
Example 35
[1330] This example describes the generation of a negative control
where the MHC is HLA-A*0201 loaded with the peptide ILKEPVHGV (SEQ
ID NO:10) and coupled to a 270 kDa dextran multimerization domain.
The peptide ILKEPVHGV (SEQ ID NO:10) is derived from HIV.
HLA-A*0201(lLKEPVHGV (SEQ ID NO:10)) complexes are generated,
biotinylated and coupled with a labeled dextran multimerization
domain as described elsewhere herein. Then these
HLA-A*0201(ILKEPVHGV (SEQ ID NO:10))-dextran conjugates are used as
negative controls in experiments with samples from humans that are
HLA-A*0201 positive and not infected by HIV, because it is not
likely that they have T-cell's with a TCR specific for HLA-A*0201
(ILKEPVHGV (SEQ ID NO:10)) in amounts that can be detected by MHC
multimer reagents. The conjugates can also be used as negative
control in samples from humans that are HLA-A*0201 negative or in
samples from other species.
Example 36
[1331] This example describes the generation of a negative control.
CD8 molecules on the surface of cytotoxic T-cells bind MHC I
complexes by interaction with amino acids in the .alpha.3 domain of
the heavy chain. When using MHC multimers this interaction can
result in MHC multimer binding to CD8 positive T-cells that are not
restricted by the MHC(peptide) complex in the MHC multimer. In this
example a proper negative control showing these false positive
cells is described. Such a negative control can consist of MHC I
heavy chain or truncated versions of MHC I heavy chain bound to any
multimerization domain. The heavy chain can be folded or unfolded,
and can have a peptide bound in the peptide binding groove but does
not have to comprise a peptide. A MHC I heavy chain-multimerization
domain can be made in a way similar to what is described for the
generation of MHC I-multimerization domains. Briefly, purified MHC
I heavy chain is expressed as inclusion bodies in E. coli and
purified by general procedures. The heavy chain is refolded in
vitro, purified and biotinylated, or the heavy chain can be
biotinylated directly without refolding. Biotinylated heavy chain
is coupled to any multimerization domain. The multimerization
domain can be labeled with any suitable label or can be unlabeled
depending on later use. Such a negative control can be used in
experiments with MHC I multimers, e.g. in flow cytometry analysis,
IHC, or ELISA.
Example 37
[1332] This example describes how to identify specific T-cells in a
blood sample with MHC multimers using flow cytometry analysis
without lysis of red blood cells and without washing the cells
after staining. MHC complexes in this example consisted of
HLA-A*0201 heavy chain, human beta2microglobulin and different
peptides, and the MHC complexes were coupled to a 270 kDa dextran
multimerization domain. Purified MHC-peptide complexes consisting
of human heavy chain, human beta2microglobulin and peptide were
generated by in vitro refolding, purified and biotinylated as
described elsewhere herein. Biotinylated MHC-peptide complexes were
then coupled to a 270 kDa dextran multimerization domain labelled
with PE by interaction with streptavidin (SA) on the dextran
multimerization domain. The SA-PE-dextran was made as described
elsewhere herein. MHC-peptide complexes were added in an amount
corresponding to a ratio of three MHC-peptide molecules per SA
molecule and each molecule dextran contained 6.1 SA molecule and
3.9 molecules PE. The final concentration of dextran was
3.8.times.10e-8 M. The following constructs were made: [1333] 1. PE
conjugated 270 kDa dextran coupled with HLA-A*0101 in complex with
beta2microglobulin and the peptide VTEHDTLLY (SEQ ID NO:14) derived
from Human Cytomegalo Virus (HCMV). [1334] 2. PE conjugated 270 kDa
dextran coupled with HLA-A*0101 in complex with beta2microglobulin
and the peptide IVDCLTEMY (SEQ ID NO:15) derived from ubiquitin
specific peptidase 9 (USP9). [1335] 3. PE conjugated 270 kDa
dextran coupled with HLA-A*0201 in complex with beta2microglobulin
and the peptide NLVPMVATV (SEQ ID NO:9) derived from Human
Cytomegalo Virus (HCMV). [1336] 4. PE conjugated 270 kDa dextran
coupled with HLA-A*0201 in complex with beta2microglobulin and the
peptide ILKEPVHGV (SEQ ID NO:10) derived from Human
Immunodeficiency Virus (HIV). [1337] 5. PE/SA conjugated 270 kDa
dextran coupled with HLA-B*0207 in complex with beta2microglobulin
and the peptide TPRVTGGGAM (SEQ ID NO:16) derived from Human
Cytomegalo Virus (HCMV). [1338] 6. PE conjugated 270 kDa dextran
coupled with HLA-B*0207 in complex with beta2microglobulin and the
peptide RPHERNGFTVL (SEQ ID NO:17) derived from Human Cytomegalo
Virus (HCMV). [1339] 7. PE conjugated 270 kDa dextran coupled with
HLA-B*0207 in complex with beta2microglobulin and the peptide
TPGPGVRYPL (SEQ ID NO:18) derived from Human Immunodeficiency Virus
(HIV).
[1340] These seven MHC multimer constructs were used for detection
of specific T-cells in flow cytometry analysis using a no-lyse
no-wash procedure. Blood samples from three individual donors were
analyzed. The donors had previously been screened for the presence
of specific T-cells using a general staining procedure including
lysis and wash of the cell sample, and donor one turned out to be
positive for HLA*0201 in complex with the peptide NLVPMVATV (SEQ ID
NO:9), donor two were positive for HLA*0101 in complex with the
peptide VTEHDTLLY (SEQ ID NO:14) and donor three were positive for
HLA-B*0207 in complex with the peptides TPRVTGGGAM (SEQ ID NO:16)
and RPHERNGFTVL (SEQ ID NO:17). In this experiment blood from each
donor were analyzed with the MHC multimer construct they were
supposed to have specific T-cells restricted for and with MHC
multimers of same haplotype but carrying a negative control
peptide. The negative control peptides were either derived from HIV
or the self-protein USP 9. Self-protein here means a naturally
occurring protein in normal cells of a human individual. Normal
healthy donors not infected with HIV are not expected to have
specific T-cells recognizing HIV derived peptides or peptides
derived from self-proteins in complex with any HLA molecule in an
amount detectable with this analysis method.
[1341] The blood was stained as follows: [1342] 100 .mu.l EDTA
stabilized blood were incubated with 5 .mu.l MHC(peptide)/PE
dextran for 5 minutes at room temperature. Anti-CD45/PB,
anti-CD3/FITC and anti-CD8/APC antibody in an amount of 0.4-1.2
.mu.g/sample was added to each tube and the incubation continued
for another 15 minutes. 850 .mu.l PBS; pH=7.2 was added and the
sample analyzed on a CyAn ADP flowcytometry instrument with a speed
of 150 .mu.l/minute. A total of 20.000 CD8 positive cells were
acquired. During analysis CD45/PB antibody was used to set a
trigger discriminator to allow the flow cytometer to distinguish
between red blood cells and stained white blood cells (see FIG.
10A). Furthermore CD3/FITC antibody was used to select CD3 positive
cells in a second gating strategy (see FIG. 10B).
[1343] Blood from donor one showed specific staining with
HLA-A*0201(NLVPMVATV (SEQ ID NO:9)) multimer (construct 3) while no
staining of specific T-cells was observed with the negative control
HLA-A*0201 (ILKEPVHGV (SEQ ID NO: 10)) multimer (construct 4).
Donor two showed specific staining with HLA-A*0101 (VTEHDTLLY (SEQ
ID NO:14)) multimer (construct 1) and no staining was observed with
the negative control HLA-A*0101(IVDCLTEMY (SEQ ID NO:15)) multimer
(construct 2). In blood from donor three a population of T-cells
were stained with HLA-B*0207(TPRVTGGGAM (SEQ ID NO:16)) multimer
(construct 5) and another population with HLA-B*0207(RPHERNGFTVL
(SEQ ID NO:17)) multimer (construct 6) while no specific staining
was observed with the negative control HLA-B*0207(TPGPGVRYPL (SEQ
ID NO:18)) multimer (construct 7). The results are shown in FIG.
11.
[1344] We have shown that MHC multimers of three different
haplotypes can be used to identify specific T-cells in blood
samples from three different donors using an approach without
lysing red blood cells and without wash following staining with MHC
multimer. This method is simple, fast and interfere as little as
possible with cells in the blood sample.
Example 38
[1345] This example describes how to identify specific T-cells in a
blood sample with MHC multimers using flow cytometry analysis
without lysis of red blood cells and without washing cells upon
staining. The MHC complex is here any MHC I or MHC II molecule of
human, rodent, bovine, monkey or any other origin loaded with any
peptide able to bind the peptide-binding cleft of the MHC complex
and where the MHC-peptide complexes are coupled to any
multimerization domain.
[1346] Purified MHC-peptide complexes is generated as described
elsewhere herein and coupled to any multimerization domain labelled
with a fluorescent dye, preferable FITC, PE, APC, pacific blue,
cascade yellow or any other flour chrome. These MHC multimers are
used for detection of specific T-cells by flow cytometry using the
following procedure: [1347] EDTA stabilized blood are incubated
with MHC multimer at room temperature. The amount of blood analyzed
is preferable 50-150 .mu.l but could be any volume ranging from
1-1000 .mu.l. The amount of MHC multimer depends on the multimer
construct and the volumen of blood and should be determined by
titration prior to this type of experiment. The incubation time
with MHC multimer is preferably 5-20 minutes but could be anything
between 0 minutes and 1 hour. Then anti-CD45/CY, anti-CD3/APC and
anti-CD8/PB antibody is added and the incubation continued. The
incubation time is preferably 5-20 minutes but can be anything
between 1 minute and 1 hour. The amount of antibody is preferable
0.4-1.2 .mu.g/100 .mu.l blood but these limits can be extended and
should be determined by titration prior to this kind of
experiments. The antibodies can be labelled with any fluorochrome
as long as the fluorochrome is different from the fluorochrome on
the MHC multimer. Next PBS; pH=7.0-8.0 is added and the sample
analyzed by a flowcytometer. The amount of PBS added is preferable
500-1000 .mu.l but can also be more than 1000 .mu.l and less than
500 .mu.l. During analysis anti-CD45 antibody is used to set a
trigger discriminator to allow the flow cytometer to distinguish
between red blood cells and stained white blood cells. Different
gating strategies can then be applied to analyse data. Preferably
cells are first gated on CD3 positive cells and then for CD8
positive cells, but can also be gated only for CD8 positive cells
of only for CD3 positive cells. Alternatively "dump" gates can be
applied excluding unwanted cells, e.g. B-cells, CD4-positive cells,
NK-cells.
[1348] In the above example MHC multimers are added prior to
antibodies but MHC multimers and antibodies can also be added
simultaneously to the blood sample and incubated for preferably
5-30 minutes but the incubation time can be anything between 1
minute and 2 hours.
[1349] This method can be used to identify specific T-cells in
blood samples fromfdifferent donors using an approach without
lysing red blood cells and without wash following staining with MHC
multimer. This method is simple, fast and interfere as little as
possible with cells in the blood sample
Example 39
[1350] This example illustrates how MHC multimers together with
counting beads was used for exact numeration of MHC-peptide
specific T-cells in a flow cytometry analysis whit no lyses of red
blood cells and no washing steps during or after staining. Counting
beads in this example was CytoCount.TM., Count Control Beads from
Dako that are polystyrene Fluorospheres with a diameter of 5.2
.mu.m. The MHC multimer consisted of HLA-A*0101 heavy chain
complexed with human beta2 microgloblin and a peptide and the
MHC-peptide complexes were coupled to a 270 kDa dextran
multimerization domain labelled with PE. MHC multimers were
generated as described elsewhere herein and the following two
constructs were made: [1351] 1) PE conjugated 270 kDa dextran
coupled with HLA-A*0101 in complex with beta2microglobulin and the
peptide VTEHDTLLY (SEQ ID NO:14) derived from Human Cytomegalo
Virus (HCMV). [1352] 2) PE conjugated 270 kDa dextran coupled with
HLA-A*0101 in complex with beta2microglobulin and the peptide
IVDCLTEMY (SEQ ID NO:15) derived from ubiquitin specific peptidase
9 (USP9).
[1353] Construct 2 is a negative control for construct 1 in this
example and both were used for detection of specific T-cells by
flow cytometry using a no-lyse no-wash procedure: 100 .mu.l of EDTA
stabilized blood from a donor positive for HLA*0101 in complex with
the peptide VTEHDLLY (SEQ ID NO:14) were incubated with 5 .mu.l MHC
multimer for 5 minutes at room temperature. Anti-CD45/CY,
anti-CD3/PB and anti-CD8/APC antibody in an amount of 0.4-1.2
.mu.g/sample was added and the incubation continued for another 15
minutes. 850 .mu.l PBS; pH=7.2 was added together with precise 50
.mu.l CytoCount beads 1028 bead/.mu.l and the sample analyzed on a
CyAn ADP flowcytometry instrument with a speed of 150 .mu.l/minute.
A total of 20.000 CD8 positive cells were acquired. During analysis
CD45/CY antibody was used to set a trigger discriminator to allow
the flow cytometer to distinguish between red blood cells and
stained white blood cells.
[1354] A dot plot was made for each sample showing MHC multimer vs
CD8 positive events (se FIGS. 12 A and B). Based on the negative
control a gate comprising events representing CD8 positive T-cells
specific for MHC multimer was defined. Similarly histogram plots
for each sample was made showing FITC signal vs counts (FIGS. 12 C
and D). In these histograms the amount of beads in the analyzed
sample were identified since the beads in contrast to the cells
emit light in the FITC channel. In principle the beads could be
visualized in any fluorochrome channel because they emit light in
all channels but it was important to visualize the beads in a
channel where there was no interfering signal from labelled
cells.
[1355] The concentration of T-cells specific for HLA-A*0101
(VTEHDTLLY (SEQ ID NO:14)) multimer (construct 1) in the blood
sample were determined using the counting beads as an internal
standard. Events obtained from staining with the negative control
MHC multimer, construct 2, were defined as background signals and
subtracted from the result obtained from staining with construct
1.
[1356] Concentration of HLA-A*0101 (VTEHDTLLY (SEQ ID NO:14))
specific T-cells in the blood sample=((Count of MHC multimer+CD8+
positive cells, construct 1.times.concentration of
beads.times.dilution factor of beads)/counted beads))-((Counted MHC
multimer+CD8+ cells, construct 2.times.concentration of
beads.times.dilution factor of beads)/counted beads)=992.6
cells/ml. (For details se FIG. 12).
[1357] This experiment demonstrated how CytoCount.TM. counting
beads together with MHC multimers could be used to determine the
exact concentration of MHC-peptide specific T-cells in a blood
sample using a no-lyse no-wash method.
Example 40
[1358] This example describes an analysis of specific T-cells in
blood using MHC multimers where MHC multimers together with
antibodies are pre-mixed and embedded in a matrix material to
retain and immobilize the reagents prior to use. In this example
the matrix was composed of Trehalose and Fructose and the MHC
complex consisted of HLA-A*0101 heavy chain complexed with human
beta2microglobulin and peptide. The MHC-peptide complexes were
coupled to a 270 kDa dextran multimerization domain.
[1359] Purified MHC-peptide complexes consisting of heavy chain,
human beta2microglobulin and peptide were generated by in vitro
refolding, purified and biotinylated as described elsewhere herein.
Biotinylated MHC(peptide) complexes were coupled to a 270 kDa
dextran multimerization domain labelled with PE, thereby generating
PE labelled MHC multimers. The following MHC multimer constructs
were made: [1360] 1) PE conjugated 270 kDa dextran coupled with
HLA-A*0101 in complex with beta2microglobulin and the peptide
VTEHDTLLY (SEQ ID NO:14) derived from Human Cytomegalo Virus
(HCMV). [1361] 2) PE conjugated 270 kDa dextran coupled with
HLA-A*0101 in complex with beta2microglobulin and the negative
control peptide IVDCLTEMY (SEQ ID NO:15) derived from ubiquitin
specific peptidase 9 (USP9).
[1362] Tubes with a matrix material to retain and immobilize the
above described MHC multimer constructs together with antibodies
relevant for later flow cytometer analysis were made. The matrix
material was made to retain MHC multimer and antibody in the
container when dry but release them into the sample medium when a
sample comprising cells of interest was added to the tube.
[1363] Experimentally, solutions of 20% Fructose in water and 20%
Trehalose in water were made and mixed in a 1:1 ratio. 15 .mu.l of
this mixture were transferred to two 5 ml Falcon tubes. A premix of
antibodies were made consisting of 40 .mu.l anti-CD8 Alexa700
labelled antibody in a concentration of 25 .mu.g/ml+40 .mu.l
anti-CD3 Pacific Blue labelled antibody in a concentration of 100
.mu.g/ml+160 .mu.l anti-CD45 Cascade Yellow labelled antibody in a
concentration of 200 .mu.g/ml. 12 .mu.l of this mixture were added
to each Falcon tube together with 3 .mu.l of either of the two MHC
multimer constructs. 100 .mu.l butylated hydroxytoluen (BHT) with a
concentration of 99 mg/L were added. The mixtures were dried under
vacuum a 2-8.degree. C. over night. 100 .mu.l EDTA stabilized blood
from a donor with T-cells specific for HLA-A*101 complexed with the
peptide VTEHDTLLY (SEQ ID NO:14) were added to each of the two
tubes. As a control experiment 6 .mu.l of the antibody premix
described above were transferred to two empty 5 ml Falcon tubes
together with 3 .mu.l of either of the MHC multimer constructs and
100 .mu.l blood from the same donor. All four tubes were incubated
for 15 minutes at room temperature. Then 900 .mu.l PBS; pH=7.2 was
added and the sample analyzed on a CyAn ADP flowcytometer
instrument.
[1364] A total of 20.000 CD8 positive cells were acquired for each
sample. During analysis CD45/CY antibody was used to set a trigger
discriminator to allow the flow cytometer to distinguish between
red blood cells and stained white blood cells.
[1365] As expected and shown in FIG. 13 a population of CD8
positive and HLA-A*0101 (VTEHDTLLY (SEQ ID NO:14)) multimer
positive cells were observed in the two samples stained with
construct 1. The amount of specific T-cells detected in the matrix
sample was comparable to the amount of specific T-cells detected in
the control sample without matrix material. No HLA-A*0101(IVDCLTEMY
(SEQ ID NO:15)) multimer specific CD8 positive cells were observed
in the two samples stained with the negative control MHC multimer
construct 2.
[1366] This experiment demonstrates that the MHC multimer
constructs used in this experiment can be embedded in a sugar
matrix and later used for analysis of specific T-cells in a blood
sample and that this method gives results comparable to results
obtained from a no-lyse no-wash staining procedure.
Example 41
[1367] This example describes an analysis of specific T-cells in
blood or other samples with cells in solution using MHC multimers
where MHC multimers together with antibodies are pre-mixed and
embedded in a matrix material to retain and immobilize the reagents
prior to use. In this example the matrix is composed of Trehalose
and Fructose and the MHC multimer is any MHC I, MHC II or MHC like
molecule.
[1368] Tubes with a matrix material to retain and immobilize MHC
multimer constructs together with antibodies relevant for later
flow cytometer analysis are made. The matrix material is made to
retain MHC multimer and antibody in the container when dry but
release them into the sample medium when a sample comprising cells
of interest is added to the tube. The matrix is preferable
water-soluble sugar mixtures but can be any contiguous mass
releasing its components upon addition of aqueous solution. The
matrix embedding medium can comprise one or more compounds
including carbohydrates, polymers, small proteins ect. Examples of
carbohydrates for use in the matrix include saccharose, arabinose,
ribulose, fructose, sorbose, glucose, mannose, gulose, galactose,
sucrose, lactose, maltose, trehalose, raffinose and melizitose.
Examples of suitable polymers for use in matrix include polyvinyl
alcohols, polyethylene glycols, polyethylene imines, polyacryl
amides, polyaziridines, glycols, polyacrylic acids, esters or
derivatives thereof. Examples of small proteins include BSA, other
albumins or protein fragments.
[1369] The matrix-embedding medium is transferred to tubes
preferable 5 ml tubes or other tubes usable in flow cytometry.
Fluorochrome antibodies are added and here means any antibody
useable for gating when analysing samples with T lymphocytes.
Preferable antibodies are directed against CD8, CD4, CD3, CD45,
CD27, CD28, CD45RA, CD45RO and CD62L. Then MHC multimer constructs
are added but can also be added simultaneously with the antibodies
or before the antibodies. Addition of MHC multimer is not
restricted to one type of MHC multimer but several different MHC
multimers can be added to the same tube and thereby embedded in the
same matrix sample. Optionally scavengers for oxygen-derived
radicals can be added. Examples of such radical scavengers are
ascorbic acid, beta-carotene, bilirubin, butylated hydroxytoluene,
butylated hydroxyanisol, tert-butylhydroquinone,
d-alpha-tocopherol, trolox and hydroxyanisol. The matrix mixtures
are then dried under vacuum a 2-8.degree. C. over night.
[1370] Cell samples in solution are added to the dry or semidry
matrix tubes. Cell samples here means any sample comprising
specific T-cells. That is preferable whole blood, homogenized
spleen, lymph nodes, tumors or similar or purified lymphocytes from
any of the above. The samples are incubated at room temperature for
1 minute to 2 hours, preferable 10-30 minutes. They can also be
incubated at 4.degree. C. or 37.degree. C. or any temperature in
between those two. The samples are analyzed on a flowcytometry
instrument.
[1371] As an alternative to the above described method MHC
multimers can be added to the sample after addition of cell sample
thereby only embedding antibodies and not MHC multimer in the
matrix. Similarly only MHC multimer are embedded in the matrix and
antibodies added after addition of cell sample.
[1372] For enumeration of specific T-cells in the samples counting
beads can be embedded in the matrix medium. The beads are then
added before, together with or after adding antibodies and MHC
multimer. Alternatively counting beads are added following
incubation with cell sample. The exact amount of specific T-cells
are determined as described elsewhere herein.
Example 42
[1373] This is an example of how to make and use MHC multimers
consisting of a streptavidin multimerization domain with 3
biotinylated MHC complexs and 1 flourophore molecule attached to
the biotin binding pockets of streptavidin.
[1374] MHC complexs consisting of HLA-A*0201 heavy chain,
beta2microglobulin and NLVPMVATV peptide or the negative control
peptide GLAGDVSAV (SEQ ID NO:11) were generated as described
elsewhere herein. The fluorophore in this example was
FLUORESCEIN.TM.-linker molecules as shown in FIG. 14. Each of these
molecules consist of a linker-biotin molecule mounted with 4
trippel FLUORESCEIN.TM.-linker molecules. The linker-biotin
molecule was here
H-L30-Lys(NH.sub.2)-L30-Lys(NH.sub.2)-L30-Lys(NH2)L300Lys(caproylamidobio-
tin)-NH.sub.2 where L30 was a 30 atom large linker and L300 was a
300 atom large linker. Both L30 and L300 was composed of multiple
L15 linkers with the structure shown in FIG. 14B. Linker-biotin
molecules were generated as follows: Downloaded Boc-L300-Lys(Fmoc)
resin (100 mg) was deprotected and subjected to coupling with
Boc-Lys(2CIZ)-OH, Boc-L30-OH, Boc-Lys(2CIZ)-OH, Boc-L30-OH,
Boc-Lys(2CIZ)-OH then Boc-L30-OH. The resin was Fmoc deprotected
and reacted twice (2.times.2 h) with caproylamido biotin NHS ester
(25 mg in 0.5 mL NMP+25 microL DIPEA). The resin was washed with
TFA and the product cleaved off with TFA:TFMSA:mCresol:thioanisol
(6:2:1:1), 1 mL, precipitated with diethyl ether and purified by
RP-HPLC. MS calculated for C.sub.300H.sub.544N.sub.64O.sub.137S is
7272.009 Da, found 7271.19 Da.
[1375] Alternatively linker-biotin molecule was
H-L60-Lys(NH.sub.2)-L60-Lys(NH.sub.2)-L60-Lys(NH.sub.2)L300Lys(caproylami-
dobiotin)-NH.sub.2 and made from downloaded Boc-L300-Lys(Fmoc)
resin (100 mg), and then prepared analogously to
H-L30-Lys(NH.sub.2)-L30-Lys(NH.sub.2)-L30-Lys(NH.sub.2)L300Lys(caproylami-
dobiotin)-NH.sub.2. MS calculated for
C.sub.360H.sub.652N.sub.76O.sub.167S is 8749.5848 Da and was found
to be 7271.19 Da. Yield 3 mg.
[1376] The trippel FLUORESCEIN.TM.-linker molecules was here
betaalanin-L90-Lys(Flu)-L90-Lys(Flu)-L90-Lys(Flu)-NH.sub.2 where
Lys=Lysine, Flu=FLUORESCEIN.TM. and L90 is a 90 atom linker (se
FIG. 14 for further details). The trippel-FLUORESCEIN.TM.-linker
molecule was generated as follows: Downloaded Boc-Lys(Fmoc) resin,
2 g, was Boc deprotected and subjected to 3.times.coupling with
Boc-L30-OH, Boc-Lys(Fmoc)-OH, 3.times.Boc-L30-OH, Boc-Lys(Fmoc)-OH,
3.times.Boc-L30-OH. The three Fmoc groups were removed and
carboxyFLUORESCEIN.TM., 301 mg, activated with HATU, 274 mg, and
DIPEA, 139 .mu.L, in 8 mL NMP, was added to the resin twice for 30
min. The resin was Boc deprotected and subjected to 2.times.30 min
coupling with beta-alanine-N,N-diacetic acid benzyl ester, followed
by 5 min treatment with 20% piperidine in NMP. The resin was washed
with DCM, then TFA and the product was cleaved off the resin,
precipitated with diethyl ether and purified by RP-HPLC. Yield was
621 mg. MS calculated for C268H402N44O116 is 6096.384 Da, while MS
found was 6096 Da.
[1377] Biotin-linker molecule were coupled together with 4 trippel
FLUORESCEIN.TM.-linker molecules as follows: (500 nmol) was
dissolved in 88 microliter NMP+2 .mu.l pyridine and activated for
10 min at room temperature (conversion to cyclic anhydride) by
addition of 10 .mu.l N,N'diisopropylcarbodiimide. Following
activation the trippel FLUORESCEIN.TM.-linker was precipitated with
diethyl ether and redissolved in 100 microliter NMP comprising 10
nmol biotin-linker. Once dissolved the coupling was initiated by
addition of 5 .mu.l diisopropyl ethyl amine, and was complete after
30 min.
[1378] Streptavidin and FLUORESCEIN.TM.-linker molecules are then
mixed in a molar ration of 1:1 and incubated for/2 hour. Then MHC
complexes are added in 3-fold molar excess in respect to
streptavidin and incubated for another 1/2 hour. Alternatively, MHC
complexes are added first, then FLUORESCEIN.TM.-linker molecules or
MHC complexes are mixed with FLUORESCEIN.TM.-linker molecules
before addition to Streptavidin.
[1379] These MHC multimers are then used to stain CMV specific
T-cells in a flow Cytometry experiment. 1.times.10.sup.6 purified
HPBMC from a donor with T-cells specific for HLA-A*0201(NLVPMVATV
(SEQ ID NO:9)) are incubated with 10 .mu.l of each of the two
HLA-A*0201(peptide)/FLUORESCEIN.TM. constructs described above for
10 minutes in the dark at room temperature with a cell
concentration of 2.times.10.sup.7 cells/ml. 10 .mu.l of
mouse-anti-human CD8/PB (clone DK25 from Dako) are added and the
incubation continued for another 20 minutes at 4.degree. C. in the
dark. The samples are then washed by adding 2 ml PBS; pH=7.2
followed by centrifugation for 5 minutes at 200.times.g and the
supernatant removed. The cells are resuspended in 400-500 .mu.l
PBS; pH=7.2 and analyzed on a flowcytometer.
[1380] In the above described example the FLUORESCEIN.TM.-linker is
as shown in FIG. 14 but the linker molecule can be any linker
molecule as described in patent application WO 2007/015168 A2
(Lohse (2007)) or alternatively chemical biotinylated fluorochrom
can be used instead of FLUORESCEIN.TM.-linker molecules. The MHC
complexes described in this example is a MHC I molecule composed of
HLA-A*0201 heavy chain, beta2microglobulin and NLVPMVATV (SEQ ID
NO:9) peptide but can in principle be any MHC complex or MHC like
molecule as described elsewhere herein.
Example 43
[1381] This is an example of how to make MHC multimers consisting
of a streptavidin multimerization domain with 3 biotinylated MHC
complexs attached to the biotin binding pockets of streptavidin and
how to use such trimer MHC complexs to stain specific T-cells in a
flow cytometry experiment by addition of a biotinylated flourophore
molecule. In this example the fluorophore is FLUORESCEIN.TM. linker
molecules constructed as described elsewhere herein.
[1382] MHC complexs consisting of HLA-A*0201 heavy chain,
beta2microglobulin and peptide are generated as described
elsewhere. MHC complexs are incubated with streptavidin in a molar
ratio of 3:1 for % hour.
[1383] These trimer MHC multimers are then used to stain CMV
specific T-cells in a flow Cytometry experiment. 1.times.10.sup.6
purified HPBMC from a donor with T-cells specific for
HLA-A*0201(NLVPMVATV (SEQ ID NO:9)) are incubated with 10 .mu.l
HLA-A*0201(peptide) multimer construct for 10 minutes in the dark
at room temperature with a cell concentration of 2.times.10.sup.7
cells/ml. Then FLUORESCEIN.TM. linker molecules (as described in
Example 42) are added and incubation continued for 5 minutes. 10
.mu.l mouse-anti-human CD8/PB antibody (clone DK25 from Dako) is
added and the incubation continued for another 20 minutes at
4.degree. C. in the dark. The samples are then washed by addition
of 2 ml PBS; pH=7.2 followed by centrifugation for 5 minutes at
200.times.g and the supernatant removed. Cells are resuspended in
400-500 .mu.l PBS; pH=7.2 and analyzed on a flowcytometer.
[1384] In this example the FLUORESCEIN.TM.-linker is as shown in
FIG. 14 but the linker molecule can be any linker molecule as
described in Lohse, Jesper, (2007), WO 2007/015168 A2 or
alternative chemically biotinylated fluorochrome can be used. The
MHC complexse described in this example is a MHC I molecule
composed of HLA-A*0201 heavy chain, beta2microglobulin and
NLVPMVATV (SEQ ID NO:9) peptide but can in principle be any MHC
complex or MHC like molecule as described elsewhere herein.
Example 44
[1385] This is an example of how to make MHC multimers where the
multimerization domain is dextran and the MHC complexs are
chemically conjugated to the dextran multimerization domain.
[1386] MHC complexs consisting of HLA-A*0201 heavy chain,
beta2microglobulin and NLVPMVATV (SEQ ID NO:9) peptide or the
negative control peptide GLAGDVSAV (SEQ ID NO:11) are generated as
described elsewhere herein. Dextran with a molecular weight of 270
kDa is activated with divinylsulfone. Activated Dextran is then
incubated with MHC and RPE in a 0.05 M NaCHO.sub.3 buffer; pH=9.5
with a molar ratio between MHC and Dextran of 30-60 and a molar
ratio between RPE and dextran of 3-7:1 The mixture is placed in a
water bath at 30.degree. C. for 16 hours. Excess flourochrome, MHC
and dextran are removed by FPLC using a sephacryl S-300 column.
[1387] These MHC/RPE dextramers are then used to stain CMV specific
T-cells in a flow Cytometry experiment. Briefly, 1.times.10.sup.6
purified HPBMC from a donor with T-cells specific for
HLA-A*0201(NLVPMVATV (SEQ ID NO:9)) are incubated with 10 .mu.l of
each of the two HLA-A*0201(peptide)/RPE constructs described above
for 10 minutes in the dark at room temperature with a cell
concentration of 2.times.10.sup.7 cells/ml. 10 .mu.l
mouse-anti-human CD8/PB antibody (clone DK25 from Dako) are added
and the incubation continued for another 20 minutes at 40.degree.
C. in the dark. The samples are then washed by adding 2 ml PBS;
pH=7.2 followed by centrifugation for 5 minutes at 200.times.g and
the supernatant removed. The cells are then resuspended in 400-500
.mu.l PBS; pH=7.2 and analyzed on a flow cytometer.
Example 45
[1388] This is an example of how to make MHC multimers where the
multimerization domain is dextran and MHC complexs are MHC I
molecules chemically conjugated to dextran multimerization domain
and the dextran multimerization domain also have fluorochrome
chemically coupled.
[1389] Human beta2microglobulin is coupled to dextran as follows.
Dextran with a molecular weight of 270 kDa is activated with
divinylsulfone. Activated dextran is incubated with human
beta2microglobulin and RPE in a 0.05 M NaCHO.sub.3 buffer; pH=9.5
with a molar ratio between beta2microglobulin and Dextran of 30-60
and a molar ratio between RPE and dextran of 3-7:1. The molar ratio
of the final product is preferable 4-6 RPE and 15-24
beta2microglobulin per dextran. The mixture is placed in a water
bath at 30.degree. C. for 16 hours. Excess flourochrome,
beta2microglobulin and dextran are removed by FPLC using a
sephacryl S-300 column. The beta2microglobulin-RPE-dextran
construct is then refolded in vitro together with heavy chain and
peptide using the following procedure. 200 ml refolding buffer (100
mM Tris, 400 mM L-arginin-HCL, 2 mM NaEDTA, 0.5 mM oxidized
Gluthathione, 5 mM reduced Glutathione, pH 8.0) supplied with
protease inhibitors PMSF, Pepstatin A and Leupeptin (to a final
concentration of 1 mM, 1 mg/I and 1 mg/I, respectively) is made and
cooled to 10.degree. C. 12 mg NLVPMVATV peptide is dissolved in
DMSO and added to the refolding buffer together with 20-30 mg
beta2microglobulin-RPE-dex and 6 mg HLA-A*0201 heavy chain.
Incubation at 10.degree. C. for 4-8 hours, then 20-30 mg
beta2microglobulin-RPE-dex and 6 mg HLA-A*0201 heavy chain is added
and incubation continued for 4-8 hours. Another 20-30 mg
beta2microglobulin-RPE-dex and 6 mg HLA-A*0201 heavy chain is added
and incubation continued for 6-8 hours. The folding reaction is
filtrated through a 0.2 .mu.m filter to remove larger aggregates
and then buffer exchanged into a buffer comprising 20 mM Tris-HCl,
50 nM NaCl; pH=8.0 followed by concentration to 1-2 ml sample.
Dextran-RPE-MHC complexs are then separated from excess heavy chain
and peptide by size exclusion chromatography using a sephacryl
S-300, S-400 or sephacryl S-500 column.
[1390] These MHC/RPE dextramers can be used to stain CMV specific
T-cells in a flow Cytometry experiment. Briefly, 1.times.10.sup.6
purified HPBMC from a donor with T-cells specific for
HLA-A*0201(NLVPMVATV (SEQ ID NO:9)) are incubated with 10 .mu.l of
each of the two HLA-A*0201(peptide)/RPE constructs described above
for 10 minutes in the dark at room temperature with a cell
concentration of 2.times.10.sup.7 cells/ml. 10 .mu.l of
mouse-anti-human CD8/PB antibody (clone DK25 from Dako) are added
and the incubation continued for another 20 minutes at 4.degree. C.
in the dark. The samples are then washed by adding 2 ml PBS; pH=7.2
followed by centrifugation for 5 minutes at 200.times.g and the
supernatant removed. The cells are then resuspended in 400-500
.mu.l PBS; pH=7.2 and analyzed on a flowcytometer.
Example 46
[1391] This is an example of how to make and use MHC multimers
where the multimerisation domain is dextran coupled with
Streptavidin and fluorochrome and where the MHC-peptide complex is
chemically biotinylated.
[1392] Purified MHC-peptide complexes constiting of of HLA-A*0201
heavy chain, human beta2microglobulin and either the peptides
NLVPMVATV (SEQ ID NO:9) or GLAGDVSAV (SEQ ID NO:11) are generated
as described elsewhere herein. Briefly, HLA-A*0201 heavy chain and
human beta2microglobulin is expressed separately as inclusion
bodies in E. coli and is then refolded in vitro together with
peptide following standard procedures as described by Garboczi et
al., (1996), Nature 384, 134-141. Following refolding the
MHC-peptide complexes are purified according to size on a
SEPHADEX.RTM. 75 column and buffer exchanged to a buffer containing
100 mm Carbonate, pH=8.0. The MHC-peptide complexes are incubated
with 40-80 .mu.g Biotinamidohexanoic acid N-hydroxysuccinimide
ester (dissolved in DMSO) per milligram MHC-peptide complex and are
incubated at room temperature for 4 hours, end-over-end. Excess
biotin is removed using PD-10 columns (Amersham) and the buffer is
changed to a buffer containing 20 mM Tris, 50 mM NaCl, pH=8.0.
Biotinylated MHC-peptide complexes are then coupled to 270 kDa
dextran multimerization domains containing Streptavidin (SA) and
APC by interaction with SA on the dextran multimerization domains.
The SA-APC-dextran is made as described elsewhere herein.
MHC-peptide complexes are added in an amount corresponding to a
ratio of three MHC-peptide molecules per SA molecule and each
molecule dextran contains 3 SA molecules and 12 molecules APC. The
final concentration of dextran is 3.8.times.10e-8 M.
[1393] The binding of HLA-A*0201(NLVPMVATV (SEQ ID NO:9))/APC and
the HLA-A*0201 (GLAGDVSAV (SEQ ID NO:11))/APC dextran constructs to
Human Peripheral Blood Mononuclear Cells (HPBMC) from two donors is
analyzed by flow cytometry following a standard flow cytometry
protocol. Donor 1 is positive for T-cell's directed against
HLA-A*0201 (NLVPMVATV (SEQ ID NO:9)) complexes and negative for
T-cells with specificity for HLA-A*0201 (GLAGDVSAV (SEQ ID NO: 11))
complexes while donor 2 do not have T-cells specific either
MHC-peptide complex. Briefly, HPBMC from the blood of two human
donors are isolated, by a standard protocol using
FICOLL.RTM.-Hypaque. 1.times.10.sup.6 purified HPBMC from each
donor at a concentration of 2.times.10.sup.7 cells/ml are incubated
with 10 .mu.l of each of the two MHC multimer constructs described
above for 10 minutes in the dark at room temperature. 10 .mu.l of
each of the antibodies mouse-anti-human CD3/PE (clone UCHT1 from
Dako) and mouse-anti-human CD8/PB (clone DK25 from Dako) is added
and the incubation continued for another 20 minutes at 4.degree. C.
in the dark. The samples are then washed by adding 2 ml PBS; pH=7.2
followed by centrifugation for 5 minutes at 200.times.g and the
supernatant removed. The cells are resuspended in 400-500 .mu.l
PBS; pH=7.2 and analyzed on a flowcytometer. Samples from donor 1
will show positive staining with HLA-A*0201(NLVPMVATV (SEQ ID
NO:9))/APC dextran constructs (positive staining here means a
distinguishable group of cells binding anti-CD3/PE, anti-CD8/PB
antibodies and HLA-A*0201 (NLVPMVATV (SEQ ID NO:9))/APC multimers)
while no staining will be observed with A*0201(GLAGDVSAV (SEQ ID
NO:11))/APC dextran multimers. Donor 2 will be negatively stained
with both MHC multimers.
Example 47
[1394] This is an example of how a MHC class 1 complex with a
peptide in the peptide binding-groove was chemically biotinylated,
coupled to a dextran multimerizantion domain containing
Streptavidin (SA) and APC and then used to detect specific T-cells
in a flow cytometry analysis.
[1395] MHC class 1 complexes consisting of light chain human
beta2microglobulin, heavy chain HLA-A0201 and the peptide NLVPMVATV
(SEQ ID NO:9) was generated as described next: [1396] 1. 200 ml of
refolding buffer (100 mM Tris, 400 mM L-arginin-HCL, 2 mM NaEDTA,
0.5 mM oxidized Gluthathione, 5 mM reduced Glutathione, pH 8.0) was
supplied with protease inhibitors PMSF (phenylmethylsulphonyl
fluoride), Pepstatin A and Leupeptin (to a final concentration of 1
mM, 1 mg/I and 1 mg/I, respectively). The refolding buffer was
placed at 10.degree. C. on a stirrer. [1397] 2. 12.3 mg of peptide
NLVPMVATV (SEQ ID NO:9) was dissolved in 400 .mu.l DMSO and added
drop-wise to the refolding buffer at vigorous stirring. [1398] 3.
4.4 mg of human Light Chain .beta.2m was added drop-wise to the
refolding buffer at vigorous stirring. [1399] 4. 6.2 mg of Heavy
Chain HLA-A*0201 (supplied with DTT to a concentration of 0.1 mM)
was added drop-wise to the refolding buffer at vigorous stirring.
[1400] 5. The folding reaction was placed at 10.degree. C. at slow
stirring for approx. 8 hours. [1401] 6. After approx. 8 hours, step
3 and 4 was repeated and the folding reaction was placed at
10.degree. C. at slow stirring O/N. [1402] 7. Step 3 and 4 was
repeated, and the folding reaction is placed at 10.degree. C. at
slow stirring for approx 6 hours. [1403] 8. After approx. 6 hours
the folding reaction was filtrated through a 0.2 .mu.m filter to
remove aggregates. [1404] 9. The folding reaction was concentrated
O/N at 10.degree. C. shaking gently in a Vivacell 250 concentrator
with a 5000 MWCO PES-filter. The folding reaction was concentrated
to approx. 1.5 ml. [1405] 10. Correctly folded MHC-complex was
separated and purified from excess 132m, excesss heavy chain and
aggregates thereoff, by size exclusion chromatography on a 120 ml
Superdex 75 column. Correctly folded monomer MHC-complex was eluted
with a buffer containing 100 mM Carbonat-buffer, pH 8.0 [1406] 11.
Fractions comprising the folded MHC-complex were pooled and
concentrated to 3.24 mg/ml by centrifugation in a Vivaspin6
concentrator with a 5000 MWCO PES-filter. The protein-concentration
was estimated from its abosorption at 280 nm. [1407] 12. Folded
MHC-complex was stored stored at -170.degree. C. before further
use.
[1408] The above MHC class 1 complex was chemically biotinylated as
described next: [1409] 13. 100 .mu.g of the folded MHC-complex (a
buffer containing 100 mM Carbonat-buffer, pH 8.0) and 4 .mu.g (40
.mu.g biotin/mg MHC complex) Sulfo-NHS-LC-Biotin
(sulfosuccinimidyl-6-[biotinamido]hexanoate, PIERCE 21335)
dissolved to 1 mg/ml in water, was incubated at room temperature
for 2.5 hours, end over end. [1410] 14. Excess biotin was removed
using PD-10 columns (Amersham) and the buffer is changed to a
buffer containing 20 mM Tris, 50 mM NaCl, pH=8.0. [1411] 15. The
chemically biotinylated MHC-complex was concentrated by
centrifugation in Vivaspin6 concentrator with a 5000 MWCO
PES-filter and the protein-concentration was estimated from its
abosorption at 280 nm. 10 vol % of a buffer containing 0.05M
Tris/HCl, 15 mM NaN3, 10% BSA, pH 7.2 was added and the final
concentration of MHC-complex was calculated to 0.575 mg/ml.
[1412] The chemically biotinyaleted MHC class 1 complex was
attached to a 270 kDa dextran multimerization domains containing
Streptavidin (SA) and APC by a non-covalent interaction
Biotin_Streptavidin interaction between the chemically biotinylated
MHC complex and the SA on the dextran multimerization domains. The
SA-APC-dextran is made as described elsewhere herein.
[1413] 100 .mu.l of a MHC-dextramer solution with a final
concentration of 32.times.10.sup.-9M was produced as follows:
[1414] 16. 20 .mu.l 270 kDa Vinylsulfone-activated dextran (each
molecule dextran contains 3.7 SA molecules and 9 APC molecules),
corresponding to 3.2.times.10.sup.-12 mol, and 5.98 .mu.l of the
above described MHC-complex, corresponding to 7.1.times.10.sup.-11
mol (6 mol MHC-complex/mol SA), was mixed and incubated at room
temperature in the dark for 30 min. [1415] 17. A buffer of 0.05M
Tris-HCl, 15 mM NaN.sub.3, 1% BSA, pH 7.2 was added to a final
volume of 100 .mu.l. [1416] 18. The resulting MHC-dextramer
preparation was then used in flow cytometry experiments.
[1417] The binding of the above MHC class 1 complex coupled to an
APC dextran construct to Human Peripheral Blood Mononuclear Cells
(HPBMC) from one donor were analyzed by flow cytometry following a
standard flow cytometry protocol. As a negative control a MHC class
1 complex consisting of beta2microglobulin, heavy chain HLA-A0201
and the peptide GLAGDVSAV (SEQ ID NO:11), produced by the same
procedure as described above, were used.
[1418] Briefly, HPBMC from the blood of a human donors were
isolated, by a standard protocol using FICOLL.RTM.-Hypaque.
1.times.10.sup.6 purified HPBMC at a concentration of
2.times.10.sup.7 cells/ml were incubated with 10 .mu.l of each of
the two MHC multimer constructs described above for 10 minutes in
the dark at room temperature. 10 .mu.l of each of the antibodies
mouse-anti-human CD3/PE, mouse-anti-human CD8/PB and
mouse-anti-human CD4/FITC was added and the incubation continued
for another 30 minutes at 40.degree. C. in the dark. The samples
are then washed by adding 2 ml PBS; pH=7.2 followed by
centrifugation for 5 minutes at 200.times.g and the supernatant
removed. The cells was resuspended in 400 .mu.l PBS; pH=7.2 and
analyzed on a flowcytometer. Samples from the donor showed positive
staining with HLA-A*0201 (NLVPMVATV (SEQ ID NO:9))/APC dextran
constructs (positive staining here means a distinguishable group of
cells binding anti-CD3/PE, anti-CD8/PB antibodies and HLA-A*0201
(NLVPMVATV (SEQ ID NO:9))/APC multimers) while no staining was
observed with A*0201 (GLAGDVSAV (SEQ ID NO:11))/APC dextran
multimers. The result is shown in FIG. 15.
Example 48
[1419] This example describes how to make MHC multimers where the
MHC complexes are attached to the mulitmerization domain by
interaction of two alpha-helices and a disulfide bond between the
adjacent cysteine residues.
[1420] The MHC-complex in this example consisted of light chain
.beta.2m, the MHC class I Heavy Chain allele HLA-B*0801 (a
truncated version in which the intracellular and transmembrane
domains have been deleted) fused to alpha-helic and cysteine by
genetic fusion, and the peptide RAKFKQLL (SEQ ID NO:19).
[1421] An alpha-helic sequence
AQLEKELQALEKENAQLEWELQALEKELAQGGCGGSCG (SEQ ID NO:26) comprising a
C-terminal cysteine residue is fused to MHC class I Heavy Chain
allele HLA-B*0801 modified as described elsewhere herein (deletion
of intracellular and transmembran domains and introduction of
recognition site for BirA enzyme) by genetic fusion. This is done
by ligating cytoplasmatic cDNA sequence of the modified HLA-B*0801
to the alpha-helic encoding sequence. The HLA-B*0801-Coil sequence
is cloned into the expression vector pGarboczi and expressed as
inclusion bodies in E. coli prior to in vitro refolding together
with .beta.2m and peptide as described elsewhere herein. Following
refolding the monomer MHC complexes is purified by size exclusion
chromatography as described elsewhere herein.
[1422] The multimerization domain in this example is divinylsulfone
activated dextran 270 (VS-dex270) decorated with peptides
comprising an alpha-helic structure and a cysteine residue for
dislulfid bond, and flourochromes.
[1423] A peptide comprising alpha-helic coil structure, cysteine
residue for disulfide bond, and C-terminal cysteine for thiol
reaction with reactive vinyl groups on dextran is synthesised;
AQLEKELQALEKENAQLEWELQALEKELAQGG(C(tButhio))GGSC (SEQ ID NO:36).
The internal cysteine is protected to direct reaction of C-terminal
thiol to reactive vinyl on dextran.
[1424] VS-dex 270 and peptide is mixed under natural conditions to
promote thiol reaction of the peptide to divinylsulfone on dextran.
Afterwards fluorochrome of choice (e.g. R-phycoerythrine (RPE)) is
added and pH is raised to favour reaction of amines of the
fluorochrome to dextran. The reaction is stopped by adding
nucleophilic reagent such as ethanolamine. The conjugate is
purified by size exclusion chromatography. The internal cysteine is
deprotected. In this example the protection group is
tert-Butylthio, which is deprotected by reducing agents such as
DTT. Immediately prior to assembling to MHC complexes, the reducing
reagent is replaced by a non-reducing reagent, e.g. by buffer
exchange on a spin-column.
[1425] MHC complexes are attached to the mulitmerization domain
through interaction of the two alpha-helices and a disulfide bond
between the adjacent cysteine residues.
[1426] Dextran decorated with deprotected alpha-helic peptides is
mixed, in various molar ratios, with MHC complexes under oxidative
conditions allowing the two alpha-helices to form coiled-coil
structure, and the two adjacent --SH groups of cysteine residues to
form disulfide bonds. Optionally the product is purified by size
exclusion chromatography before use. The product can be used to
stain specific T cells as described elsewhere herein for staining
specific T cells with MHC dextramers.
Example 49
[1427] This example describes how to make MHC multimers where the
MHC complexes are attached to the mulitmerization domain by
interaction of two alpha-helices and a disulfide bond between the
adjacent cysteine residues.
[1428] The MHC-complex in this example consisted of light chain
.beta.2m, the MHC class I Heavy Chain allele HLA-B*0801 (a
truncated version in which the intracellular and transmembrane
domains have been deleted) fused to alpha-helic and cysteine by
genetic fusion, and the peptide RAKFKQLL.
[1429] An alpha-helic sequence
AQLEKELQALEKENAQLEWELQALEKELAQGGCGGSCG (SEQ ID NO:26) comprising a
C-terminal cysteine residue is fused to MHC class I Heavy Chain
allele HLA-B*0801 modified as described elsewhere herein (deletion
of intracellular and transmembran domains and introduction of
recognition site for BirA enzyme) by genetic fusion. This is done
by ligating cytoplasmatic cDNA sequence of the modified HLA-B*0801
to the alpha-helic encoding sequence. The HLA-B*0801-Coil sequence
is cloned into the expression vector pGarboczi and expressed as
inclusion bodies in E. coli prior to in vitro refolding together
with .beta.2m and peptide as described elsewhere herein. Following
refolding the Monomer MHC complexes is purified by size exclusion
chromatography as described elsewhere herein.
[1430] The multimerization domain in this example is divinylsulfone
activated dextran 270 (VS-dex270) decorated with peptides
comprising an alpha-helic structure and a cysteine residue for
dislulfid bond, and flourochromes.
[1431] A peptide comprising alpha-helic coil structure, cysteine
residue for disulfide bond, and C-terminal cysteine for thiol
reaction with reactive vinyl groups on dextran is synthesised;
AQLEKELQALEKENAQLEWELQALEKELAQGG(C(tButhio))GGSC (SEQ ID NO:36).
The internal cysteine is protected to direct reaction of C-terminal
thiol to reactive vinyl on dextran.
[1432] Peptide and VS-dex 270 is mixed in molar ratios 10-50:1 in
10 mM HEPES, 0.1 M NaCl, pH 7 to react thiol of peptide to
divinylsulfone on dextran. Excess of peptide is removed by FPLC
using a sepharyl S-300 column.
[1433] VS-dex 270 decorated with peptides is mixed to fluorochrome
RPE in molar ratio 1:18 in 10 mM HEPES, 0.1 M NaCl, pH 8. The
reaction is stopped by adding 0.1M ethanolamine, pH 8. The
conjugate is purified by size exclusion chromatography using a
sepharyl S-300 column in 10 mM HEPES, 0.1 M NaCl, pH 7.2. The
internal cysteine is deprotected. In this example the protection
group is tert-Butylthio, which is deprotected by reducing agents
such as 0.1 M DTT. Immediately prior to assembling to MHC
complexes, the reducing reagent is replaced by 10 mM HEPES, 0.1 M
NaCl, 15 mM NaN.sub.3, 1% BSA, pH 7.2 by buffer exchange on a
spin-column.
[1434] MHC complexes are attached to the mulitmerization domain
through interaction of the two alpha-helices and a disulfide bond
between the adjacent cysteine residues.
[1435] Dextran decorated with deprotected alpha-helic peptides is
mixed with MHC complexes in molar ratios 1: 10-50 in 0.05 M
Tris-HCl, 15 mM NaN.sub.3, 1% BSA, pH 7.2 allowing the two
alpha-helices to form coiled-coil structure, and the two adjacent
--SH groups of cysteine residues to form disulfide bonds.
Optionally the product is purified by size exclusion chromatography
before use. The product can be used to stain specific T cells as
described elsewhere herein for staining specific T cells with MHC
dextramers.
Example 50
[1436] This example describes how to make MHC multimers where the
MHC complexes are attached to the mulitmerization domain by
interaction of two alpha-helices and a disulfide bond between the
adjacent cysteine residues.
[1437] The MHC-complex in this example consisted of light chain
.beta.2m, the MHC class I Heavy Chain allele HLA-B*0801 (a
truncated version in which the intracellular and transmembrane
domains have been deleted) fused to alpha-helic and cysteine by
genetic fusion, and the peptide RAKFKQLL.
[1438] An alpha-helic sequence
AQLEKELQALEKENAQLEWELQALEKELAQGGCGGSCG (SEQ ID NO:26) comprising a
C-terminal cysteine residue is fused to MHC class I Heavy Chain
allele HLA-B*0801 modified as described elsewhere herein (deletion
of intracellular and transmembran domains and introduction of
recognition site for BirA enzyme) by genetic fusion. This is done
by ligating cytoplasmatic cDNA sequence of the modified HLA-B*0801
to the alpha-helic encoding sequence. The HLA-B*0801-Coil sequence
is cloned into the expression vector pGarboczi and expressed as
inclusion bodies in E. coli prior to in vitro refolding together
with .beta.2m and peptide as described elsewhere herein. Following
refolding the Monomer MHC complexes is purified by size exclusion
chromatography as described elsewhere herein.
[1439] The multimerization domain in this example is divinylsulfone
activated dextran 270 (VS-dex270) decorated with peptides
comprising a alpha-helic structure and a cysteine residue for
dislulfid bond, and flourochromes.
[1440] A peptide comprising alpha-helic coil structure, cysteine
residue for disulfide bond, and C-terminal cysteine for thiol
reaction with reactive vinyl groups on dextran is synthesised;
AQLEKELQALEKENAQLEWELQALEKELAQGG(C(tButhio))GGSC (SEQ ID NO:36).
The internal cysteine is protected to direct reaction of C-terminal
thiol to reactive vinyl on dextran.
[1441] VS-dex 270, peptide and fluorochrome is mixed under natural
conditions to promote reaction of the peptide and fluorochrome
(e.g. allophycocyanin, APC) to divinylsulfone on dextran. The
reaction is stopped by adding nucleophilic reagent such as
ethanolamine. The conjugate is purified by size exclusion
chromatography. The internal cysteine is deprotected. In this
example the protection group is tert-Butylthio, which is
deprotected by reducing agents such as DTT. Immediately prior to
assembling to MHC complexes, the reducing reagent is replaced by a
non-reducing reagent, e.g. by buffer exchange on a spin-column.
[1442] MHC complexes are attached to the mulitmerization domain
through interaction of the two alpha-helices and a disulfide bond
between the adjacent cysteine residues. Dextran decorated with
deprotected alpha-helic peptides is mixed, in various molar ratios,
with MHC complexes under oxidative conditions allowing the two
alpha-helices to form coiled-coil structure, and the two adjacent
--SH groups of cysteine residues to form disulfide bonds. The
product might be purified by size exclusion chromatography before
used to stain specific T cells as described elsewhere herein.
Example 51
[1443] This example describes how to make MHC multimers where the
MHC complexes are chemically conjugated to the mulitmerization
domain by reaction of C-terminal cysteine to divinylsulfone on
dextran.
[1444] The MHC-complex in this example consisted of light chain
.beta.2m, the MHC class I Heavy Chain allele HLA-B*0801 (a
truncated version in which the intracellular and transmembrane
domains have been deleted) fused cysteine by genetic fusion, and
the peptide RAKFKQLL (SEQ ID NO:19).
[1445] A cysteine and glycine (Cys-Gly) residue is added to the
C-terminal of MHC class I Heavy Chain allele HLA-B*0801 modified as
described elsewhere herein (deletion of intracellular and
transmembran domains and introduction of recognition site for BirA
enzyme) by site-directed mutagenesis. The HLA-B*0801-Cys sequence
is cloned into the expression vector pGarboczi and expressed as
inclusion bodies in E. coli prior to in vitro refolding together
with .beta.2m and peptide as described elsewhere herein. Following
refolding the Monomer MHC complexes is purified by size exclusion
chromatography as described elsewhere herein.
[1446] The multimerization domain in this example is divinylsulfone
activated dextran 270 (VS-dex270) as described elsewhere
herein.
[1447] VS-dex 270 and MHC complexes are mixed under natural
conditions to promote thiol reaction of the C-terminal cysteine to
divinylsulfone on dextran. Afterwards fluorochrome of choice (e.g.
RPE) is added and pH is raised to favour reaction of amines of the
fluorochrome to dextran. The reaction is stopped by adding
nucleophilic reagent such as ethanolamine. The conjugate is
purified by size exclusion chromatography before used to stain
specific T cells as described elsewhere herein.
Example 52
[1448] This example describes how to make MHC multimers where the
MHC complexes are chemically conjugated to the mulitmerization
domain by reaction of C-terminal cysteine to divinylsulfone on
dextran.
[1449] The MHC-complex in this example consisted of light chain
.beta.2m, the MHC class I Heavy Chain allele HLA-B*0801 (a
truncated version in which the intracellular and transmembrane
domains have been deleted) fused cysteine by genetic fusion, and
the peptide RAKFKQLL (SEQ ID NO:19).
[1450] A cysteine and glycine (Cys-Gly) residue is added to the
C-terminal of MHC class I Heavy Chain allele HLA-B*0801 modified as
described elsewhere herein (deletion of intracellular and
transmembran domains and introduction of recognition site for BirA
enzyme) by site-directed mutagenesis. The HLA-B*0801-Cys sequence
is cloned into the expression vector pGarboczi and expressed as
inclusion bodies in E. coli prior to in vitro refolding together
with .beta.2m and peptide as described elsewhere herein. Following
refolding the Monomer MHC complexes is purified by size exclusion
chromatography as described elsewhere herein.
[1451] The multimerization domain in this example is divinylsulfone
activated dextran 270 (VS-dex270) as described elsewhere
herein.
[1452] VS-dex 270, MHC complexes and fluorochrome (e.g. APC) are
mixed under natural conditions to promote reaction of the
C-terminal cysteine of the MHC comples and the fluorochrome to
divinylsulfone on dextran. The reaction is stopped by adding
nucleophilic reagent such as ethanolamine. The conjugate is
purified by size exclusion chromatography before used to stain
specific T cells as described elsewhere herein.
Example 53
[1453] This example describes how to make MHC multimers where the
MHC complexes are attached to the mulitmerization domain by
streptavidin-biotin interaction. The MHC-multimer in this example
consist of APC-streptavidin (APC-SA)-conjugated 270 kDa dextran and
a biotinylated, folded MHC-complex composed of .beta.2m, HLA-B*0801
Heavy Chain and the peptide RAKFKQLL (SEQ ID NO:19).
[1454] In this example the HLA-B*0801 contains a C-terminal
cystein, generated as described elsewhere herein (example 51 and
52). After refolding in vitro of .beta.2m, HLA-B*0801 Heavy Chain
and the peptide RAKFKQLL (SEQ ID NO:19), and size exclusion
chromatography, the MHC complex is treated with a --SH specific
biotinylating reagent, e.g.
1-Biotinamido-4-[4'(maleimidomethyl)-clyco-hexanecarboxamido]-butane
(biotin-BMCC). The biotinylated MHC complexes are separated from
excess of biotin by size exclusion chromatography.
[1455] The biotinylated MHC complexes can be assembled to
APC-SA-conjugated dextran or other SA-conjugated dextrans as
described elsewhere herein, and used to stain specific T cells.
Example 54
[1456] This example describes how to make MHC multimers where the
MHC complexes are attached to the mulitmerization domain by
streptavidin-biotin interaction. The MHC-multimer in this example
consist of APC-streptavidin (APC-SA)-conjugated 270 kDa dextran and
a biotinylated, folded MHC-complex composed of .beta.2m, HLA-B*0801
Heavy Chain and the peptide RAKFKQLL (SEQ ID NO:19).
[1457] In this example the .beta.2m contains an N-terminal cystein.
A N-terminal cystein residue is introduced to the .beta.2m by
site-directed mutagenesis. The .beta.2m-Cys is cloned into a vector
and expressed in E. coli prior to in vitro refolding together with
Heavy Chain HLA-B*0801 and peptide as described elsewhere herein.
The MHC complexes are separated by size exclusion chromatography
and treated with a --SH specific biotinylating reagent, e.g.
1-Biotinamido-4-[4'(maleimidomethyl)-clyco-hexanecarboxamido]-butane
(biotin-BMCC). The biotinylated MHC complexes are separated from
excess of biotin by size exclusion chromatography.
[1458] The biotinylated MHC complexes can be assembled to
APC-SA-conjugated dextran or other SA-conjugated dextrans as
described elsewhere herein, and used to stain specific T cells.
Example 55
[1459] This is an example of how MHC multimers may be used for the
detection of antigen specific T-cells simultaneously with
activation of T cells. This example is a combination of i) direct
detection of TCR, using MHC complexes coupled to any
multimerisation as described elsewhere herein to stain antigen
specific T cells, and ii) detection of induced intracellular
cytokine production by addition of fluorophor-labelled
anti-cytokine antibodies by flow cytometry.
[1460] Multicolor immunofluorescent staining with antibodies
against intracellular cytokines and cell surface markers provides a
high resolution method to identify the nature and frequency of
cells which express a particular cytokine(s). In addition to
enabling highly specific and sensitive measurements of several
parameters for individual cells simultaneously, this method has the
capacity for rapid analysis of large numbers of cells which are
required for making statistically significant measurements.
[1461] Production of cytokines plays an important role in the
immune response. Examples include the induction of many antiviral
proteins by IFN-.gamma., the induction of T cell proliferation by
IL-2 and the inhibition of viral gene expression and replication by
TNF-.alpha.. Cytokines are not preformed factors; instead they are
rapidly produced upon relevant stimulation. Intracellular cytokine
staining relies upon the stimulation of T cells in the presence of
an inhibitor of protein transport thus retaining the cytokines
inside the cell.
[1462] Cellular activation to trigger cytokine production generally
results in down-regulation of the T cell receptor. For this reason,
MHC multimer staining is carried out prior to activation to ensure
a good level of staining. The MHC multimers may be internalized
with the T cell receptor during this period, but can still be
detected in permeabilized cells. To analyze the effector function
of antigen-specific T cells, the cells are first stained with MHC
multimers, and then stimulated with antigen. This is followed by
staining with antibodies specific for extracellular epitopes (such
as CD8), then by membrane permeabilization and intracellular
cytokine staining. The following protocol is an example of MHC
multimer co-staining with anti-IFN-.gamma., TNF-.alpha., MIP-1b, or
IL-2.
[1463] Protocol applicable for intracellular staining of IFNg,
TNFa, MIP-1 b, or IL-2: [1464] 1. Prepare peripheral blood cells in
phosphate buffered saline (PBS) at a cell concentration of
2.times.10.sup.7 cells/ml. [1465] 2. Transfer the cell suspension
to individual tubes in 50 .mu.l aliquots. [1466] 3. Add relevant
titrated fluorescently-labeled MHC multimers to the desired tubes,
and incubate for 10 min at 22.degree. C. (nonstimulated
single-color controls should not be stained at this stage). Add 10
.mu.l PBS to remaining tubes. [1467] 4. Add 500 .mu.l PBS to each
tube. Centrifuge at 450.times.g for 5 minutes at 10.degree. C.
[1468] 5. Aspirate supernatant. Agitate to disrupt cell pellets and
resuspend in 200 .mu.l complete RPMI. [1469] 6. Dilute
peptide/antigen stock 1:50 in complete RPMI. Add 2 .mu.l of this
(10 .mu.g/ml (investigate the effect on cytokine response of
titrating your peptide)) to each desired tube. If using Leukocyte
Activation cocktail (LAC) as a control, rapidly thaw this at
37.degree. C. in a water bath and add 0.33 .mu.l of this to each
desired tube. [1470] 7. Place the tubes at 37.degree. C. in a
humidified CO.sub.2 incubator for 15 minutes to 1 hour. [1471] 8.
Add Brefeldin A (10 .mu.g/ml final) to the desired tubes (n.b. LAC
contains Brefeldin A) and return to the incubator. Incubate for 15
hours (the optimal incubation time isvariable and must be
determined). [1472] 9. Remove tubes from the incubator. Centrifuge
at 450.times.g for 5 minutes at 10.degree. C. [1473] 10. Aspirate
supernatant. Resuspend desired cell pellets in 50 .mu.l PBS
containing an optimally titrated amount of anti-CD8 antibody. Add
50 .mu.l PBS to remaining tubes. Note: Single-color controls should
be stained at this stage. If additional phenotyping of samples is
desired, antibodies to other cell surface receptors may also be
added at this time. [1474] 11. Incubate for 20 minutes on ice.
[1475] 12. Add 500 .mu.l PBS to each tube. Centrifuge at
450.times.g for 5 minutes at 10.degree. C. [1476] 13. Aspirate
supernatant. Agitate to disrupt cell pellets. [1477] 14. Add 200
.mu.l 4% paraformaldehyde to each sample tube. Vortex tubes.
Incubate for 20 minutes on ice. This step will fix the cell
morphology of the activated cells. Note: The procedure can be
stopped at this point. Repeat steps 12 and 13. Resuspend the cells
in 100 .mu.l/tube PBS. Cover and store the cells at 4.degree. C.
for up to 3 days. To proceed, repeat steps 12 and 13. Resuspend the
cells in 100 .mu.l/tube permeabilization buffer and proceed to step
16. [1478] 15. Add 200 .mu.l permeabilization buffer to each tube.
[1479] 16. Centrifuge at 450.times.g for 5 minutes at 10.degree. C.
Aspirate supernatant. [1480] 17. Add 100 .mu.l permeabilization
buffer to the sample tubes that are to be stained with
anti-cytokine antibody. Add 100 .mu.l PBS to the remaining tubes
(i.e. Single-color controls). [1481] 18. Incubate for 5 minutes at
room temperature. [1482] 19. Add an optimally titrated amount of
conjugated anti-cytokine antibody to the desired sample tubes and
mix. [1483] 20. Incubate for 20 minutes at room temperature. [1484]
21. Add 200 .mu.l permeabilization buffer to each tube and
centrifuge at 450.times.g for 5 minutes at 10.degree. C. Aspirate
supernatant and agitate tubes to disrupt the cell pellets. [1485]
22. Resuspend the cells in 200 .mu.l fix solution. Vortex tubes. It
is important to vortex well when adding this fixative so that cells
do not clump. [1486] 23. The samples are now ready for data
acquisition and analysis on a flow cytometer but may be stored
overnight at 4.degree. C. in the dark prior to analysis.
[1487] We conclude that the MHC multimer constructs can be used to
detect the presence of specific T cells in the blood simultaneously
with activation and intracellular staining of cytokines.
Example 56
[1488] This is an example of how MHC multimers may be used for the
detection of antigen specific T-cells simultaneously with
activation of T cells. This example is a combination of i) direct
detection of TCR, using MHC complexes coupled as pentamers to stain
antigen specific T cells, and ii) detection of induced
intracellular cytokine production by addition of
fluorophor-labelled anti-cytokine antibodies by flow cytometry. The
antigenic origin is Epstein-Barr Virus (EBV), thus, immune
monitoring of EBV infection PBMCs were incubated with either a
negative control (non-specific) Pentamer (A*0201/EBV (GLCTLVAML
(SEQ ID NO:13))) or a Pentamer specific for the cells of interest
(B*0801/EBV (RAKFKQLL (SEQ ID NO:19))), then stimulated with LAC
(non-specific activation) or B*0801/EBV peptide (specific peptide
activation) for 15 hours in the presence of Brefeldin A. Fixation,
permeabilization and staining for IFN-.gamma. were carried out
exactly as detailed in the protocol outlined in the example
above.
[1489] FIG. 16 illustrates Pentamer (specific or non-specific)
versus intracellular IFN-.gamma. staining after activation with
specific or non-specific antigen.
[1490] This example shows that the MHC multimer constructs can be
used to detect the presence of EBV specific T cells in the blood
simultaneously with activation and intracellular staining of
cytokines.
Example 57
[1491] This is an example of how MHC multimers may be used for the
detection of antigen specific T-cells simultaneously with
activation of T cells. This example is a combination of i) direct
detection of TCR, using MHC complexes coupled as any
multimerisation as described elsewhere herein to stain antigen
specific T cells, and ii) indirect detection of TCR, by detection
of induced intracellular cytokine production by addition of
fluorophor-labelled anti-cytokine antibodies by flow cytometry. The
antigenic origin is Rheumatoid arthritis (RA), thus, immune
monitoring of RA.
[1492] PBMCs are incubated with either a negative control
(non-specific) MHC multimer (HLA-DR4/nonsens) or a MHC multimer
specific for the cells of interest (HLA-DR4/CII(261-273)), then
stimulated with LAC (non-specific activation) or DR4/CII(261-273)
peptide (specific peptide activation) for an optimal period of time
in the presence of Brefeldin A.
[1493] Fixation, permeabilization and staining for IFN-.gamma. are
carried out exactly as detailed in the protocol outlined in the
example above.
[1494] We conclude that the MHC multimer constructs can be used to
detect the presence of Rheumatoid arthritis specific T cells in the
blood simultaneously with activation and intracellular staining of
cytokines.
Example 58
[1495] This is an example of indirect detection of activation of T
cells, by detection of intracellular cytokine production by
addition of fluorophor-labelled anti-cytokine antibodies by flow
cytometry. The MHC multimer used MHC complexes coupled as any
multimerisation as described elsewhere herein. The antigenic origin
is Rheumatoid arthritis (RA), thus, immune monitoring of RA.
[1496] PBMCs stimulated with LAC (non-specific activation) or
DR4/CII(261-273) peptide (specific peptide activation) for an
optimal period of time in the presence of Brefeldin A. Fixation,
permeabilization and staining for IFN-.gamma. are carried out as
detailed in the protocol outlined in the example above. The initial
MHC multimer staining in step 3-5 in the protocol is omitted in
this experiment.
[1497] We conclude that the MHC multimer constructs can be used to
activate Rheumatoid arthritis specific T cells in the blood.
Example 59
[1498] This is an example of how MHC multimers may be used for the
detection of antigen specific T-cells and activation of T cells
[1499] This example is a combination of i) direct detection of TCR,
using MHC complexes coupled as any multimerisation as described
elsewhere herein to stain antigen specific T cells, and ii)
indirect detection of TCR, by detection of induced intracellular
cytokine production by addition of fluorophor-labelled
anti-cytokine antibodies by flow cytometry.
[1500] PBMCs are stimulated with either a negative control
(non-specific) MHC multimer or a MHC multimer specific for the
cells of interest (specific peptide activation) for an optimal
period of time in the presence of Brefeldin A. Fixation,
permeabilization and staining for IFN-.gamma. are carried out as
detailed in the protocol outlined in the example above.
[1501] We conclude that the MHC multimer constructs can activate T
cells. The cytokine production is detected by intracellular
staining in flow cytometric analysis.
Example 60
[1502] This is an example of how MHC multimers may be used for
diagnosis of Lyme Disease in blood samples from humans infected
with Borrelia bacteria.
[1503] In this example the MHC multimer used are MHC complexes
coupled to fluorophor-labelled dextran (Dextramers). The dextramers
are used for direct detection of TCR in flow Cytometry. The antigen
origin is Borrelia, thus, immune monitoring of a Borrelia
infection.
[1504] Lyme disease is caused by infection by Borrelia bacteria.
During acute infection Borrelia specific activated T cells will be
present in increased amounts in an activated state compared to
healthy individuals. The presences of an increased amount of
activated Borrelia specific T cells may thereby act as a surrogate
marker for infection with Borrelia bacterium. MHC multimers
carrying borrelia specific peptides is in this example used to
detect the presence of Borrelia specific T cells in the blood of
patients infected with Borrelia.
[1505] Purified MHC-peptide complexes consisting of HLA-A*0201
heavy chain, human beta2microglobulin and peptide derived from
regions in Outer surface protein A or Flagellin B conserved among
the three species Borrelia Burgdorferi, Borrelia Garinii and
Borrelia Afzelii or a negative control peptide are generated by in
vitro refolding, purified and biotinylated as described elsewhere
herein. Biotinylated MHC-peptide complexes are then coupled to a
270 kDa dextran multimerization domain labelled with APC by
interaction with streptavidin (SA) on the dextran multimerization
domain. The dextran-APC-SA multimerization domain is generated as
described elsewhere herein. MHC-peptide complexes are added in an
amount corresponding to a ratio of three MHC-peptide molecules per
SA molecule and each molecule dextran contains 3.7 SA molecule and
8.95 molecules APC. The final concentration of dextran is
3.8.times.10e-8 M. The following MHC(peptide)/APC dextran
constructs are made: [1506] 1. APC-SA conjugated 270 kDa dextran
coupled with HLA-A*0201 in complex with beta2microglobulin and the
peptide ALIACKQNV (SEQ ID NO:27) derived from OspA. [1507] 2.
APC-SA conjugated 270 kDa dextran coupled with HLA-A*0201 in
complex with beta2microglobulin and the peptide FTKEDTIT (SEQ ID
NO:28) derived from OspA. [1508] 3. APC-SA conjugated 270 kDa
dextran coupled with HLA-A*0201 in complex with beta2microglobulin
and the peptide SIQIEIEQL (SEQ ID NO:29) derived from Fla B [1509]
4. APC-SA conjugated 270 kDa dextran coupled with HLA-A*0201 in
complex with beta2microglobulin and the peptide NLNEVEKVL (SEQ ID
NO:30) derived from Fla B [1510] 5. APC-SA conjugated 270 kDa
dextran coupled with HLA-A*0201 in complex with beta2microglobulin
and the peptide SLAKIENAI (SEQ ID NO:31) derived from Fla B [1511]
6. APC-SA conjugated 270 kDa dextran coupled with HLA-A*0201 in
complex with beta2microglobulin and the non-sense peptide GLAGDVSAV
(SEQ ID NO:11)
[1512] The binding of the above described MHC(peptide)/APC dextran
is used to determine the presence of Osp A or Fla B specific T
cells in the blood from Borrelia infected individuals by flow
cytometry following a standard flow cytometry protocol.
[1513] Blood from a patient with Lyme disease is isolated and 100
ul of this blood is incubated with 10 .mu.l of each of the
MHC(peptide)/APC dextran constructs described above for 10 minutes
in the dark at room temperature. 5 .mu.l of each of each of the
antibodies mouse-anti-human CD3/PB (clone UCHT1 from Dako),
mouse-anti-human CD4/FITC (clone MT310 from Dako) and
mouse-anti-human CD8/PE (clone DK25 from Dako) are added and the
incubation continues for another 20 minutes at 4.degree. C. in the
dark. The samples are then washed by adding 2 ml PBS; pH=7.2
followed by centrifugation for 5 minutes at 300.times.g and the
supernatant removed. The washing step is repeated twice. The washed
cells are resuspended in 400-500 .mu.l PBS+1% BSA; pH=7.2 and
analyzed on flowcytometer.
[1514] The presence of cells labeled with anti-CD3/PB, anti-CD8/PE
and the MHC(peptide)/APC dextran constructs 1, 2, 3, 4 and 5
described above and thereby the presence of Borrelia specific T
cells indicate that the patient are infected with Borrelia
bacteria. Blood analysed with MHC(peptide)/APC dextran construct 6
show no staining of CD3 and CD8 positive cells with this
MHC(peptide)/APC dextran construct. Results are shown in FIG.
17.
[1515] The sensitivity of the above described diagnostic test may
be enhanced by addition of labeled antibodies specific for
activation markers expressed in or on the surface of the Borrelia
specific T cells.
[1516] This example shows that MHC(peptide)/APC dextran constructs
can be used to detect the presence of Borrelia specific T cells in
the blood of patients infected with Borrelia.
Example 61
[1517] The preparation of a Pentamer is described in e.g. (United
States Patent application 20040209295). Briefly, the following
steps lead to a fluorescent Pentamer reagent:
[1518] The following is a detailed example for cloning, expressing,
and purifying a pentameric class I MHC complex, which comprises a
chimeric fusion of .beta.2m with COMP. The chimeric .beta.2m-COMP
protein is expressed in insoluble inclusion bodies in E. coli and
subsequently assembled as pentameric .beta.2m-COMP in vitro. The
pentameric class I MHC peptide complex is then formed in a second
refolding reaction by combining .beta.2m-COMP pentamers and the
human MHC class I .alpha. molecule known as HLA-A*0201, in the
presence of an appropriate synthetic binding peptide representing
the T cell antigen. In this example, a well characterized antigen
derived from Epstein-Barr virus BMLF1 protein, GLCTLVAML (SEQ ID
NO:13) (a.a. 289-297), is used. The resultant complex is labelled
with a fluorescent entity and used as a staining reagent for
detecting antigen-specific T cells from a mixed lymphocyte
population, in a flow cytometry application.
[1519] The strategy involves the sequential cloning into pET-24c
vector of .beta.2m, yielding a construct referred to as pETBMC01,
followed by the insertion of the oligomerisation domain of
cartilage oligomeric matrix protein (COMP) with a biotin acceptor
sequence (BP) for site-specific biotinylation with the
biotin-protein ligase BirA, yielding a construct referred to as
pETBMC02. Thirdly a polyglycine linker is cloned in between
.beta.2m and COMP, yielding a construct referred to as pETBMC03,
and finally, a serine-residue is removed by site-directed
mutagenesis, which serine residue precedes the poly-glycine linker,
to give the final .beta.2m-COMP/pET-24c construct, referred to as
pETBMC04. Removal of the serine residue is carried out to avoid
steric hindrance when the .beta.2m molecule is associated with the
MHC class I chain protein.
[1520] The extracellular portion of .beta.2m comprises of 99 amino
acids (equivalent to Ile1-Met99 of the mature protein) encoded by
74 bp-370 bp of the DNA sequence. This region of the .beta.2m
sequence is amplified from a normal human lymphocyte cDNA library,
by polymerase chain reaction (PCR)
[1521] beta2m PCR product is purified from the above reaction mix
using a QIAquick.RTM. PCR purification kit according to the
manufacturer's instructions (Qiagen). 200 ng of purified PCR
product and 1 .mu.g pET-24c vector (Novagen) are each digested with
BamH I (10 U) and Nde I (10 U) restriction enzymes (New England
Biolabs, NEB) for 4 h at 37 .degree. C., in accordance with the
manufacturer's instructions, and purified.
[1522] The gel-purified insert and vector DNA are ligated at a 1:3
molar ratio (vector:insert, 50 ng: 7.5 ng) using T4 DNA ligase (5
U; Bioline), in T4 DNA ligase buffer (as supplied) for 16 hrs at
16.degree. C.
[1523] The ligation mixtures and appropriate controls are
subsequently transformed into XL1-Blue strain competent E. coli
cells, according to the manufacturer's instructions (Stratagene).
Successful transformants are selected by plating the cells on
Luria-Bertani (LB) agar plates containing 30 .mu.g/ml kanamycin,
and incubating overnight at 37.degree. C.
[1524] A selection of single colonies from the bacterial
transformation plates are screened by PCR with T7 promoter (1
.mu.M) and T7 terminator (1 .mu.M) primers (Sigma Genosys, see
Appendix I for primer sequences), which are complementary to
regions of the pET vector flanking the cloning site. Amplification
is carried out using Taq DNA polymerase (1 U, Bioline) in Taq
reaction buffer (as supplied), supplemented with 2 mM MgSO.sub.4
and 0.2 mM dNTPs, using 25 thermal-cycling reactions as detailed
above. Successful transformants generated a DNA fragment of
approximately 500 bp, ascertained by 1.5% agarose gel
electrophoresis.
[1525] Bacterial transformants that generated the correct size of
PCR products are inoculated into 6 ml of sterile LB-kanamycin
medium and incubated overnight at 37.degree. C. with 200 rpm
shaking. pETBMC01 plasmid DNA is recovered from the bacterial
cultures using a QIAprep..RTM. Spin Mini-prep kit according to the
manufacturer's instructions (Qiagen). The presence of the .beta.2m
fragment in these plasmids is further verified by automated DNA
sequencing.
[1526] The sequence of the oligomerisation domain of COMP is
obtained from the Genbank database (accession #1705995) and a
region encoding the coiled-coil domain (amino acids 21-85) is
selected based on self-association experiments of COMP (Efinov et
al., FEBS Letters 341:54-58 (1994)). A biotin acceptor sequence
`BP`: SLNDIFEAQKIEWHE (SEQ ID NO:32) is incorporated at the C
terminus and an additional 14 amino acid linker, PQPQPKPQPKPEPET
(SEQ ID NO:33) is included to provide a physical separation between
the COMP oligomerising domain and BP.
[1527] The whole region is synthesized using the overlapping
complementary oligonucleotides, and purified COMP-BP and 1 .mu.g
pETBMC01 vector are digested for 4 hrs at 37.degree. C. using Hind
III (10 U) and Xho 1 (10 U) restriction enzymes (NEB), as described
in Section 1.1. The digestion products are purified, ligated,
transformed and PCR screened as in Section 1.1. Plasmids positive
from the screen are purified and sequenced as described in Section
1.1.
[1528] The poly-glycine linker is synthesized by annealing
overlapping oligonucleotides. Since the nucleotide sequence of the
polyGlycine linker only incorporates the 5' overhang of the cut
BamH I restriction site, and the 3' overhang of the cut Hind III
nucleotide recognition motifs, there is no need to digest the
annealed product to produce the complementary single-stranded
overhangs suitable for subsequent ligation. The oligonucleotides
are phosphorylated and annealed as described in Section 1.2.
[1529] pETBMC02 is digested with BamH I (10 U) and Hind III (10 U).
Ligation of the annealed poly-glycine linker into pETBMC02 was as
described previously (Section 1.1), assuming 96 fmoles of annealed
oligonucleotide/.mu.I. The transformation and PCR-screening
reactions are as described in Section 1.1, but in addition, the
presence of an inserted linker is verified by a restriction enzyme
digestion of the PCR screen product to ascertain the presence or
absence of a Sal I restriction site. Successful transformants are
not susceptible to Sal I digestion, given the removal of the site
from the plasmid vector backbone. Purification of pETBMC03 and
automated sequencing is as described elsewhere herein.
[1530] Analysis of X-ray crystallography models of MHC class I
molecules reveal that the C terminus of .beta.2m closely abuts the
.alpha.3 domain of the .alpha. chain. It is therefore desirable to
achieve maximum flexibility at the start of the poly-glycine
linker.
[1531] The extracellular portion of HLA-A*0201 .alpha. chain (EMBL
M84379) comprises of 276 amino acids (equivalent to Gly1-Pro276 of
the mature protein) encoded by bases 73-900 of the messenger RNA
sequence. This region of the A*0201 sequence is amplified from a
normal human lymphocyte cDNA library by PCR, using the primers
A2S#1 and A2S#2 which incorporated Ncol and BamHI restriction sites
respectively. The procedure for cloning the A*0201 insert into Nco
I/BamH I-digested pET-11d vector (Novagen) is essentially as
described for .beta.2m in Section 1.1.
[1532] An identical procedure is carried out to produce either
.beta.2m-COMP or A*0201 .alpha. chain proteins. Plasmid DNA is
transformed into an E. coli expression host strain in preparation
for a large scale bacterial prep. Protein is produced as insoluble
inclusion bodies within the bacterial cells, and is recovered by
sonication. Purified inclusion bodies are solubilised in denaturing
buffer and stored at -80.degree. C. until required.
[1533] Purified plasmid DNA is transformed into the BL21(DE3)pLysS
E. coli strain, which carries a chromosomal copy of the T7 RNA
polymerase required to drive protein expression from pET-based
constructs. Transformations into BL21 (DE3)pLysS competent cells
(Stratagene) are carried out with appropriate controls.
[1534] A single bacterial transformant colony is innoculated into
60 ml sterile LB medium, containing appropriate antibiotics for
selection, and left to stand overnight in a warm room
(.about.24.degree. C.) The resulting overnight culture is added to
6 litres of LB and grown at 37.degree. C. with shaking (.about.240
rpm), up to mid-log phase (OD.sub.600=0.3-0.4). Protein expression
is induced at this stage by addition of 1.0 ml of 1M IPTG to each
flask. The cultures are left for a further 4 h at 37.degree. C.
with shaking, after which the cells are harvested by centrifugation
and the supernatant discarded.
[1535] The bacterial cell pellet is resuspended in ice-cold
balanced salt solution and sonicated (XL series sonicator; Misonix
Inc., USA) in a small glass beaker on ice in order to lyse the
cells and release the protein inclusion bodies. Once the cells are
completely lysed the inclusion bodies are spun down in 50 ml
polycarbonate Oak Ridge centrifuge tubes in a Beckman high-speed
centrifuge (J2 series) at 15,000 rpm for 10 min. The inclusion
bodies are then washed three times in chilled Triton..RTM. wash
This is followed by a final wash in detergent-free wash buffer.
[1536] The resultant purified protein preparation is solubilised in
20-50 ml of 8 M urea buffer, containing 50 mM MES, pH 6.5, 0.1 mM
EDTA and 1 mM DTT, and left on an end-over-end rotator overnight at
4.degree. C. Insoluble particles are removed by centrifugation and
the protein yield is determined using Bradford's protein assay
reagent (Bio-Rad Laboratories) and by comparison with known
standards. Urea-solubilised protein is dispensed in 10 mg aliquots
and stored at -80.degree. C. for future use.
[1537] Assembly of .beta.2m-COMP from the urea-solubilised
inclusion bodies is performed by diluting the protein into 20 mM
CAPS buffer, pH 11.0, containing 0.2 M sodium chloride and 1 mM
EDTA, to give a final protein concentration of 1.5 mg/ml. The
protein is oxidised at room temperature by addition of oxidised and
reduced glutathione to final concentrations of 20 mM and 2 mM,
respectively. Following an overnight incubation, disulphide bond
formation is analysed by non-reducing SDS-PAGE on 10% bis-tricine
gels (Invitrogen).
[1538] The protein mixture is subsequently buffer exchanged into 20
mM Tris, pH 8.0, 50 mM sodium chloride (`S200 buffer`), and
concentrated to a final volume of 4.5 ml, in preparation for
enzymatic biotinylation with BirA (Affinity, Denver, Colo.). 0.5 ml
of 10.times. BirA reaction buffer (as supplied) is added, and
recombinant BirA enzyme at 10 .mu.M final concentration,
supplemented with 10 mM ATP, pH 7.0. A selection of protease
inhibitors is also used to preserve the proteins: 0.2 mM PMSF, 2
.mu.g/ml pepstatin and 2 .mu.g/ml leupeptin. The reaction is left
for 4 hours at room temperature.
[1539] Biotinylated .beta.2m-COMP is purified by size exclusion
chromatography (SEC) on a Superdex.RTM.200 HR 26/60 column
(Amersham Biosciences), running S200 buffer. 500 ml of refolding
buffer is prepared as follows: 100 mM Tris, pH 8.0, 400 mM
Larginine hydrochloride, 2 mM EDTA, 5 mM reduced glutathione and
0.5 mM oxidised glutathione, dissolved in deionised water and left
stirring at 4.degree. C. 15 mg of lyophilised synthetic peptide
GLCTLVAML (SEQ ID NO:13) is dissolved in 0.5 ml dimethylsulfoxide
and added to the refolding buffer whilst stirring. 50 mg of
biotinylated pentameric .beta.2m-COMP and 30 mg of A*0201 .alpha.
chain is added sequentially, injected through a 23 gauge hypodermic
needle directly into the vigorously-stirred buffer, to ensure
adequate dispersion. The refolding mixture is then left stirring
gently for 16 hours at 4.degree. C.
[1540] The protein refolding mixture is subsequently concentrated
from 500 ml to 20 ml using a MiniKros hollow fibre ultrafiltration
cartridge (Spectrum Labs, Rancho Dominguez, Calif.) with a 30 kD
molecular weight cutoff. Further concentration of the complex from
20 ml to 5 ml is carried out in Centricon Plus-20 centrifugal
concentrators (30 kD molecular weight cut-off) according to the
manufacturers instructions, followed by buffer exchange into S200
buffer using disposable PD10 desalting columns (Amersham
Biosciences), according to the manufacturer's instructions. Final
volume is 7.5 ml. The concentrated protein refold mixture is first
purified by SEC on a Superdex.RTM. 200 HR 26/60 gel filtration
chromatography column, as in Section 4.2. Fractions containing
protein complexes in the region of 310 kD is collected.
[1541] Fractions collected from SEC are pooled and subjected to
further purification by anion exchange chromatography on a
MonoQ..RTM. HR 5/5 column (Amersham Biosciences), running a salt
gradient from 0-0.5 M sodium chloride in 20 mM Tris over 15 column
volumes. The dominant peak is collected. Protein recovery is
determined using the Bradford assay.
[1542] Since each streptavidin molecule is able to bind up to 4
biotin entities, final labelling with phycoerythrin (PE)-conjugated
streptavidin is carried out in a molar ratio of 1:0.8, streptavidin
to biotinylated pentamer complex respectively, taking into account
the initial biotinylation efficiency measurement made for
.beta.2m-COMP in Section 4.2. The total required amount of pentamer
complex is subdivided (e.g. into 5 equal amounts) and titrated
successively into streptavidin-PE. The concentration of A*0201
pentamer-streptavidin complex is adjusted to 1 mg/ml with phosphate
buffered saline (PBS), supplemented with 0.01% azide and 1%
BSA.
[1543] This resultant fluorescent Pentamer reagent is stored at
4.degree. C.
Example 62
[1544] This an example of a positive control experiment determining
whether a sample contains or derives from a donor with certain MHC
allele types.
[1545] In the present example the sample is analysed for the
presences of T cells recognizing common pathogen antigens when
bound to the MHC alleles HLA-A*0101, HLA-A*0201 and HLA-B*0702,
thereby indirectly typing the sample for these three MHC
alleles.
[1546] 10.sup.6 HBPMC are stained with a mix of 9 MHC-Dextramers
(3-10 .mu.l of each), carrying antigenic peptides derived from the
antigenic proteins Influenza MP1, EBV BMLF-1 and CMV pp65. 3
different HLA alleles are used HLA-A*0101, HLA-A*0201 and
HLA-B*0702 each carrying peptides derived from the 3 antigenic
proteins. All MHC-Dextramers are all labeled with APC.
[1547] The sample is incubated for 10 min, where after the sample
is stained with 5 .mu.l of each of the antibodies; CD14/FITC,
CD19/FITC, CD3/RPE and CD8/RPE for 20 min. Subsequently, the sample
is washed and applied to flow cytomety analysis. The sample is
analyzed by sequential gating; the lymphocytes are identified using
the scatter parameters, followed by applying an exclusion gate
defined by the CD14/FITC, CD19/FITC positive cells. In the
remaining cell populations the cytotoxic T cell population is
defined by being RPE positive (CD3 and CD8 positive).
[1548] It is now analyzed if there is one or more population(s) of
APC positive cells. If a population of cells is identified we can
conclude that the donor has one or more of the tissue types
HLA-A*0101, HLA-A*0201 and HLA-B*0702. If no population is formed
we can conclude that either the tissue type is diverging from those
in the test reagent, or the donor has no antigen specific cytotoxic
T cells against the Flue-MP1, EBV-BMLF-1, CMV-pp65 antigens.
Example 63
[1549] This an example of a positive control experiment determining
whether a sample contains or derive from a donor with certain MHC
allele types.
[1550] In the present example the sample is analysed for the
presences of T cells recognizing epitopes from the self protein
MART-1 when the epitopes are bound to any MHC allele, thereby
indirectly typing the sample for the applied MHC alleles.
[1551] 10.sup.6 HBPMC are stained with a mix of MHC-Dextramers
(3-10 .mu.l of each), carrying antigenic peptides derived from
MART-1. All MHC-Dextramers are all labeled with APC.
[1552] The sample is incubated for 10 min, where after the sample
is stained with 5 .mu.l of each of the antibodies; CD14/FITC,
CD19/FITC, CD3/RPE and CD8/RPE for 20 min. Subsequently, the sample
is washed and applied to flow cytomety analysis. The sample is
analyzed by sequential gating; the lymphocytes are identified using
the scatter parameters, followed by applying an exclusion gate
defined by the CD14/FITC, CD19/FITC positive cells. In the
remaining cell populations the cytotoxic T cell population is
defined by being RPE positive (CD3 and CD8 positive).
[1553] It is now analyzed if there is one or more population(s) of
APC positive cells. If a population of cells is identified we can
conclude that the donor has one or more of the HLA-types used in
the analysis. If no population is formed we can conclude that
either the tissue type is diverging from those in the test reagent,
or the donor has no antigen specific cytotoxic T cells against the
MART-1 epitopes tested.
Example 64
[1554] This an example of a positive control experiment determining
whether a sample contains or derives from a donor with certain MHC
allele types.
[1555] In the present example the sample is analysed for the
presences of T cells recognizing epitopes from an antigen from a
common pathogen when bound to the MHC alleles HLA-A*0201,
HLA-A*2402 and HLA-B*0702, thereby indirectly typing the sample for
these three MHC alleles.
[1556] The following MHC dextramer constructs were made: [1557] 1.
APC-SA conjugated 270 kDa dextran coupled with HLA-A*0201 in
complex with beta2microglobulin and the peptide NLVPMVATV (SEQ ID
NO:9) derived from CMV pp65. [1558] 2. APC-SA conjugated 270 kDa
dextran coupled with HLA-A*2402 in complex with beta2microglobulin
and the peptide QYDPVAALF (SEQ ID NO:34) derived from CMV pp65.
[1559] 3. APC-SA conjugated 270 kDa dextran coupled with HLA-B*0702
in complex with beta2microglobulin and the peptide TPRVTGGGAM (SEQ
ID NO:16) derived from CMV pp65
[1560] 10.sup.6 HBPMC are stained with a mix of the 3
MHC-Dextramers constructs 1, 2, 3 described above (3-10 .mu.l of
each).
[1561] The sample is incubated for 10 min, where after the sample
is stained with 5 .mu.l of each of the antibodies; CD14/FITC,
CD19/FITC, CD3/RPE and CD8/RPE for 20 min. Subsequently, the sample
is washed and applied to flow cytomety analysis. The sample is
analyzed by sequential gating; the lymphocytes are identified using
the scatter parameters, followed by applying an exclusion gate
defined by the CD14/FITC, CD19/FITC positive cells. In the
remaining cell populations the cytotoxic T cell population is
defined by being RPE positive (CD3 and CD8 positive).
[1562] It is now analyzed if there is one or more population(s) of
APC positive cells. If a population of cells is identified we can
conclude that the donor has one or more of the tissue types
HLA-A*0201, HLA-A*2402 or HLA-B*0702. If no population is formed we
can conclude that either the tissue type is diverging from those in
the test reagent, or the donor has no antigen specific cytotoxic T
cells against the, CMV-pp65 antigen.
Example 65
[1563] This is an example of how to type a sample for the presence
of certain MHC alleles using MHC allele specific antibodies.
[1564] HPBMC from the blood of two donors, donor 1 and 2 were
isolated by a standard protocol using FICOLL.RTM.-Hypaque. A
fraction of the cells from each sample was transferred to two new
tube making a total of 4 tubes. 10 .mu.l PE-labeled antibody
specific for the MHC alleles HLA-A*02 (clone BB7.2 from BD) was
added to one tube for each sample and biotinylated antibody
specific for HLA-A*03 (ab31572 from abcam) was added to the second
tube of each sample. Samples were incubated at 4.degree. C. for 10
minutes in the dark. Then 10 .mu.l SA/PE (R0438 from Dako) was
added to tubes with anti-HLA-A*03 antibody and incubation continued
for another 30 minutes.
[1565] Cells were washed in 2 ml PBS, centrifuged and supernatant
removed. Cells were resuspended I PBS and samples analysed on a
CyAn flow cytometer. As a control unstained cell samples from each
donor was also analysed.
[1566] Cells were gated using a lymphocyte gate in a FCS/SSC plot
and the presence of PE positive staining was determined in each
sample.
[1567] Donor 1 was positive for HLA-A*02 and negative for HLA-A*03
and donor 2 was negative for HLA-A*02 and positive for HLA-A*03.
Results are shown in FIG. 18.
[1568] The results was confirmed in a PCR test using probes
specific for HLA-A*02 and HLA-A*03 (data not shown).
[1569] This example demonstrates that antibodies specific for a
specific HLA allele can be used to determine the HLA type of cells
in a given sample.
Sequence CWU 1
1
361341PRTHomo sapiens 1Gly Ser His Ser Met Arg Tyr Phe Phe Thr Ser
Val Ser Arg Pro Gly1 5 10 15Arg Gly Glu Pro Arg Phe Ile Ala Val Gly
Tyr Val Asp Asp Thr Gln 20 25 30Phe Val Arg Phe Asp Ser Asp Ala Ala
Ser Gln Arg Met Glu Pro Arg 35 40 45Ala Pro Trp Ile Glu Gln Glu Gly
Pro Glu Tyr Trp Asp Gly Glu Thr 50 55 60Arg Lys Val Lys Ala His Ser
Gln Thr His Arg Val Asp Leu Gly Thr65 70 75 80Leu Arg Gly Tyr Tyr
Asn Gln Ser Glu Ala Gly Ser His Thr Val Gln 85 90 95Arg Met Tyr Gly
Cys Asp Val Gly Ser Asp Trp Arg Phe Leu Arg Gly 100 105 110Tyr His
Gln Tyr Ala Tyr Asp Gly Lys Asp Tyr Ile Ala Leu Lys Glu 115 120
125Asp Leu Arg Ser Trp Thr Ala Ala Asp Met Ala Ala Gln Thr Thr Lys
130 135 140His Lys Trp Glu Ala Ala His Val Ala Glu Gln Leu Arg Ala
Tyr Leu145 150 155 160Glu Gly Thr Cys Val Glu Trp Leu Arg Arg Tyr
Leu Glu Asn Gly Lys 165 170 175Glu Thr Leu Gln Arg Thr Asp Ala Pro
Lys Thr His Met Thr His His 180 185 190Ala Val Ser Asp His Glu Ala
Thr Leu Arg Cys Trp Ala Leu Ser Phe 195 200 205Tyr Pro Ala Glu Ile
Thr Leu Thr Trp Gln Arg Asp Gly Glu Asp Gln 210 215 220Thr Gln Asp
Thr Glu Leu Val Glu Thr Arg Pro Ala Gly Asp Gly Thr225 230 235
240Phe Gln Lys Trp Ala Ala Val Val Val Pro Ser Gly Gln Glu Gln Arg
245 250 255Tyr Thr Cys His Val Gln His Glu Gly Leu Pro Lys Pro Leu
Thr Leu 260 265 270Arg Trp Glu Pro Ser Ser Gln Pro Thr Ile Pro Ile
Val Gly Ile Ile 275 280 285Ala Gly Leu Val Leu Phe Gly Ala Val Ile
Thr Gly Ala Val Val Ala 290 295 300Ala Val Met Trp Arg Arg Lys Ser
Ser Asp Arg Lys Gly Gly Ser Tyr305 310 315 320Ser Gln Ala Ala Ser
Ser Asp Ser Ala Gln Gly Ser Asp Val Ser Leu 325 330 335Thr Ala Cys
Lys Val 3402275PRTHomo sapiens 2Gly Ser His Ser Met Arg Tyr Phe Phe
Thr Ser Val Ser Arg Pro Gly1 5 10 15Arg Gly Glu Pro Arg Phe Ile Ala
Val Gly Tyr Val Asp Asp Thr Gln 20 25 30Phe Val Arg Phe Asp Ser Asp
Ala Ala Ser Gln Arg Met Glu Pro Arg 35 40 45Ala Pro Trp Ile Glu Gln
Glu Gly Pro Glu Tyr Trp Asp Gly Glu Thr 50 55 60Arg Lys Val Lys Ala
His Ser Gln Thr His Arg Val Asp Leu Gly Thr65 70 75 80Leu Arg Gly
Tyr Tyr Asn Gln Ser Glu Ala Gly Ser His Thr Val Gln 85 90 95Arg Met
Tyr Gly Cys Asp Val Gly Ser Asp Trp Arg Phe Leu Arg Gly 100 105
110Tyr His Gln Tyr Ala Tyr Asp Gly Lys Asp Tyr Ile Ala Leu Lys Glu
115 120 125Asp Leu Arg Ser Trp Thr Ala Ala Asp Met Ala Ala Gln Thr
Thr Lys 130 135 140His Lys Trp Glu Ala Ala His Val Ala Glu Gln Leu
Arg Ala Tyr Leu145 150 155 160Glu Gly Thr Cys Val Glu Trp Leu Arg
Arg Tyr Leu Glu Asn Gly Lys 165 170 175Glu Thr Leu Gln Arg Thr Asp
Ala Pro Lys Thr His Met Thr His His 180 185 190Ala Val Ser Asp His
Glu Ala Thr Leu Arg Cys Trp Ala Leu Ser Phe 195 200 205Tyr Pro Ala
Glu Ile Thr Leu Thr Trp Gln Arg Asp Gly Glu Asp Gln 210 215 220Thr
Gln Asp Thr Glu Leu Val Glu Thr Arg Pro Ala Gly Asp Gly Thr225 230
235 240Phe Gln Lys Trp Ala Ala Val Val Val Pro Ser Gly Gln Glu Gln
Arg 245 250 255Tyr Thr Cys His Val Gln His Glu Gly Leu Pro Lys Pro
Leu Thr Leu 260 265 270Arg Trp Glu 2753119PRTHomo sapiens 3Met Ser
Arg Ser Val Ala Leu Ala Val Leu Ala Leu Leu Ser Leu Ser1 5 10 15Gly
Leu Glu Gly Ile Gln Arg Thr Pro Lys Ile Gln Val Tyr Ser Arg 20 25
30His Pro Ala Glu Asn Gly Lys Ser Asn Phe Leu Asn Cys Tyr Val Ser
35 40 45Gly Phe His Gln Ser Asp Ile Glu Val Asp Leu Leu Lys Asn Gly
Glu 50 55 60Arg Ile Glu Lys Val Glu His Ser Asp Leu Ser Phe Ser Lys
Asp Trp65 70 75 80Ser Phe Tyr Leu Leu Tyr Tyr Thr Glu Phe Thr Pro
Thr Glu Lys Asp 85 90 95Glu Tyr Ala Cys Arg Val Asn His Val Thr Leu
Ser Gln Pro Lys Ile 100 105 110Val Lys Trp Asp Arg Asp Met
1154229PRTHomo sapiens 4Ile Lys Glu Glu His Val Ile Ile Gln Ala Glu
Phe Tyr Leu Asn Pro1 5 10 15Asp Gln Ser Gly Glu Phe Met Phe Asp Phe
Asp Gly Asp Glu Ile Phe 20 25 30His Val Asp Met Ala Lys Lys Glu Thr
Val Trp Arg Leu Glu Glu Phe 35 40 45Gly Arg Phe Ala Ser Phe Glu Ala
Gln Gly Ala Leu Ala Asn Ile Ala 50 55 60Val Asp Lys Ala Asn Leu Glu
Ile Met Thr Lys Arg Ser Asn Tyr Thr65 70 75 80Pro Ile Thr Asn Val
Pro Pro Glu Val Thr Val Leu Thr Asn Ser Pro 85 90 95Val Glu Leu Arg
Glu Pro Asn Val Leu Ile Cys Phe Ile Asp Lys Phe 100 105 110Thr Pro
Pro Val Val Asn Val Thr Trp Leu Arg Asn Gly Lys Pro Val 115 120
125Thr Thr Gly Val Ser Glu Thr Val Phe Leu Pro Arg Glu Asp His Leu
130 135 140Phe Arg Lys Phe His Tyr Leu Pro Phe Leu Pro Ser Thr Glu
Asp Val145 150 155 160Tyr Asp Cys Arg Val Glu His Trp Gly Leu Asp
Glu Pro Leu Leu Lys 165 170 175His Trp Glu Phe Asp Ala Pro Ser Pro
Leu Pro Glu Thr Thr Glu Asn 180 185 190Val Val Cys Ala Leu Gly Leu
Thr Val Gly Leu Val Gly Ile Ile Ile 195 200 205Gly Thr Ile Phe Ile
Ile Lys Gly Val Arg Lys Ser Asn Ala Ala Glu 210 215 220Arg Arg Gly
Pro Leu2255191PRTHomo sapiens 5Ile Lys Glu Glu His Val Ile Ile Gln
Ala Glu Phe Tyr Leu Asn Pro1 5 10 15Asp Gln Ser Gly Glu Phe Met Phe
Asp Phe Asp Gly Asp Glu Ile Phe 20 25 30His Val Asp Met Ala Lys Lys
Glu Thr Val Trp Arg Leu Glu Glu Phe 35 40 45Gly Arg Phe Ala Ser Phe
Glu Ala Gln Gly Ala Leu Ala Asn Ile Ala 50 55 60Val Asp Lys Ala Asn
Leu Glu Ile Met Thr Lys Arg Ser Asn Tyr Thr65 70 75 80Pro Ile Thr
Asn Val Pro Pro Glu Val Thr Val Leu Thr Asn Ser Pro 85 90 95Val Glu
Leu Arg Glu Pro Asn Val Leu Ile Cys Phe Ile Asp Lys Phe 100 105
110Thr Pro Pro Val Val Asn Val Thr Trp Leu Arg Asn Gly Lys Pro Val
115 120 125Thr Thr Gly Val Ser Glu Thr Val Phe Leu Pro Arg Glu Asp
His Leu 130 135 140Phe Arg Lys Phe His Tyr Leu Pro Phe Leu Pro Ser
Thr Glu Asp Val145 150 155 160Tyr Asp Cys Arg Val Glu His Trp Gly
Leu Asp Glu Pro Leu Leu Lys 165 170 175His Trp Glu Phe Asp Ala Pro
Ser Pro Leu Pro Glu Thr Thr Glu 180 185 1906237PRTHomo sapiens 6Gly
Asp Thr Arg Pro Arg Phe Leu Glu Gln Val Lys His Glu Cys His1 5 10
15Phe Phe Asn Gly Thr Glu Arg Val Arg Phe Leu Asp Arg Tyr Phe Tyr
20 25 30His Gln Glu Glu Tyr Val Arg Phe Asp Ser Asp Val Gly Glu Tyr
Arg 35 40 45Ala Val Thr Glu Leu Gly Arg Pro Asp Ala Glu Tyr Trp Asn
Ser Gln 50 55 60Lys Asp Leu Leu Glu Gln Lys Arg Ala Ala Val Asp Thr
Tyr Cys Arg65 70 75 80His Asn Tyr Gly Val Gly Glu Ser Phe Thr Val
Gln Arg Arg Val Tyr 85 90 95Pro Glu Val Thr Val Tyr Pro Ala Lys Thr
Gln Pro Leu Gln His His 100 105 110Asn Leu Leu Val Cys Ser Val Asn
Gly Phe Tyr Pro Gly Ser Ile Glu 115 120 125Val Arg Trp Phe Arg Asn
Gly Gln Glu Glu Lys Thr Gly Val Val Ser 130 135 140Thr Gly Leu Ile
Gln Asn Gly Asp Trp Thr Phe Gln Thr Leu Val Met145 150 155 160Leu
Glu Thr Val Pro Arg Ser Gly Glu Val Tyr Thr Cys Gln Val Glu 165 170
175His Pro Ser Leu Thr Ser Pro Leu Thr Val Glu Trp Arg Ala Arg Ser
180 185 190Glu Ser Ala Gln Ser Lys Met Leu Ser Gly Val Gly Gly Phe
Val Leu 195 200 205Gly Leu Leu Phe Leu Gly Ala Gly Leu Phe Ile Tyr
Phe Arg Asn Gln 210 215 220Lys Gly His Ser Gly Leu Gln Pro Thr Gly
Phe Leu Ser225 230 2357199PRTHomo sapiens 7Gly Asp Thr Arg Pro Arg
Phe Leu Glu Gln Val Lys His Glu Cys His1 5 10 15Phe Phe Asn Gly Thr
Glu Arg Val Arg Phe Leu Asp Arg Tyr Phe Tyr 20 25 30His Gln Glu Glu
Tyr Val Arg Phe Asp Ser Asp Val Gly Glu Tyr Arg 35 40 45Ala Val Thr
Glu Leu Gly Arg Pro Asp Ala Glu Tyr Trp Asn Ser Gln 50 55 60Lys Asp
Leu Leu Glu Gln Lys Arg Ala Ala Val Asp Thr Tyr Cys Arg65 70 75
80His Asn Tyr Gly Val Gly Glu Ser Phe Thr Val Gln Arg Arg Val Tyr
85 90 95Pro Glu Val Thr Val Tyr Pro Ala Lys Thr Gln Pro Leu Gln His
His 100 105 110Asn Leu Leu Val Cys Ser Val Asn Gly Phe Tyr Pro Gly
Ser Ile Glu 115 120 125Val Arg Trp Phe Arg Asn Gly Gln Glu Glu Lys
Thr Gly Val Val Ser 130 135 140Thr Gly Leu Ile Gln Asn Gly Asp Trp
Thr Phe Gln Thr Leu Val Met145 150 155 160Leu Glu Thr Val Pro Arg
Ser Gly Glu Val Tyr Thr Cys Gln Val Glu 165 170 175His Pro Ser Leu
Thr Ser Pro Leu Thr Val Glu Trp Arg Ala Arg Ser 180 185 190Glu Ser
Ala Gln Ser Lys Met 19589PRTHomo sapiens 8Gln Leu Phe Glu Glu Leu
Gln Glu Leu1 599PRTHuman cytomegalo virus (HCMV) 9Asn Leu Val Pro
Met Val Ala Thr Val1 5109PRTHuman Immunodeficiency virus (HIV)
10Ile Leu Lys Glu Pro Val His Gly Val1 5119PRTArtificial
SequenceSynthetic construct 11Gly Leu Ala Gly Asp Val Ser Ala Val1
5129PRTArtificial SequenceSynthetic construct 12Ala Leu Ile Ala Pro
Val His Ala Val1 5139PRTEpstein-Barr Virus (EBV) 13Gly Leu Cys Thr
Leu Val Ala Met Leu1 5149PRTHuman cytomegalo virus (HCMV) 14Val Thr
Glu His Asp Thr Leu Leu Tyr1 5159PRTHomo sapiens 15Ile Val Asp Cys
Leu Thr Glu Met Tyr1 51610PRTHuman cytomegalo virus (HCMV) 16Thr
Pro Arg Val Thr Gly Gly Gly Ala Met1 5 101711PRTHuman cytomegalo
virus (HCMV) 17Arg Pro His Glu Arg Asn Gly Phe Thr Val Leu1 5
101810PRTHuman Immunodeficiency virus (HIV) 18Thr Pro Gly Pro Gly
Val Arg Tyr Pro Leu1 5 10198PRTEpstein-Barr Virus (EBV) 19Arg Ala
Lys Phe Lys Gln Leu Leu1 52014PRTHomo sapiens 20Gly Leu Asn Asp Ile
Phe Glu Ala Gln Lys Ile Glu Trp His1 5 102113PRTHomo sapiens 21Ala
Gly Phe Lys Gly Glu Gln Gly Pro Lys Gly Glu Pro1 5
10229PRTHaemophilus influenzae 22Gly Ile Leu Gly Phe Val Phe Thr
Leu1 5239PRTHuman cytomegalo virus (HCMV) 23Ile Pro Ser Ile Asn Val
His His Tyr1 5248PRTHuman cytomegalo virus (HCMV) 24Gly Leu Cys Leu
Val Ala Leu Met1 5259PRTHomo sapiens 25Ile Leu Ala Lys Phe Leu His
Trp Leu1 52638PRTArtificial SequenceSynthetic construct 26Ala Gln
Leu Glu Lys Glu Leu Gln Ala Leu Glu Lys Glu Asn Ala Gln1 5 10 15Leu
Glu Trp Glu Leu Gln Ala Leu Glu Lys Glu Leu Ala Gln Gly Gly 20 25
30Cys Gly Gly Ser Cys Gly 35279PRTBorrelia 27Ala Leu Ile Ala Cys
Lys Gln Asn Val1 5288PRTBorrelia 28Phe Thr Lys Glu Asp Thr Ile Thr1
5299PRTBorrelia 29Ser Ile Gln Ile Glu Ile Glu Gln Leu1
5309PRTBorrelia 30Asn Leu Asn Glu Val Glu Lys Val Leu1
5319PRTBorrelia 31Ser Leu Ala Lys Ile Glu Asn Ala Ile1 53215PRTHomo
sapiens 32Ser Leu Asn Asp Ile Phe Glu Ala Gln Lys Ile Glu Trp His
Glu1 5 10 153315PRTCamelus dromedarius 33Pro Gln Pro Gln Pro Lys
Pro Gln Pro Lys Pro Glu Pro Glu Thr1 5 10 15349PRTHuman cytomegalo
virus (HCMV) 34Gln Tyr Asp Pro Val Ala Ala Leu Phe1 5359PRTHomo
sapiensMOD_RES4pivaloyl coupled to lysine 35Ile Leu Ala Lys Phe Leu
His Trp Leu1 53637PRTArtificial SequenceMOD_RES33cystein is
deprotected with tert-ButylthioSynthetic construct 36Ala Gln Leu
Glu Lys Glu Leu Gln Ala Leu Glu Lys Glu Asn Ala Gln1 5 10 15Leu Glu
Trp Glu Leu Gln Ala Leu Glu Lys Glu Leu Ala Gln Gly Gly 20 25 30Cys
Gly Gly Ser Cys 35
* * * * *
References