U.S. patent application number 15/052487 was filed with the patent office on 2016-07-21 for conditionally active chimeric antigen receptors for modified t-cells.
This patent application is currently assigned to BioAtla, LLC. The applicant listed for this patent is BioAtla, LLC. Invention is credited to Jay M. Short.
Application Number | 20160207989 15/052487 |
Document ID | / |
Family ID | 55400578 |
Filed Date | 2016-07-21 |
United States Patent
Application |
20160207989 |
Kind Code |
A1 |
Short; Jay M. |
July 21, 2016 |
CONDITIONALLY ACTIVE CHIMERIC ANTIGEN RECEPTORS FOR MODIFIED
T-CELLS
Abstract
This disclosure relates to a chimeric antigen receptor for
binding with a target antigen. The chimeric antigen receptor
comprises at least one antigen specific targeting region including
a multispecific antibody evolved from a wild-type antibody or a
fragment thereof and having at least one of: (a) a decrease in
activity in the assay at the normal physiological condition
compared to the wild-type antibody or the fragment thereof, and (b)
an increase in activity in the assay under the aberrant condition
compared to the wild-type antibody or the fragment thereof. A
method for using the chimeric antigen receptor and cytotoxic cells
for cancer treatment is also provided. A method for producing the
chimeric antigen receptor is also provided.
Inventors: |
Short; Jay M.; (Del Mar,
CA) |
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Applicant: |
Name |
City |
State |
Country |
Type |
BioAtla, LLC |
San Diego |
CA |
US |
|
|
Assignee: |
BioAtla, LLC
San Diego
CA
|
Family ID: |
55400578 |
Appl. No.: |
15/052487 |
Filed: |
February 24, 2016 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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PCT/US2015/047197 |
Aug 27, 2015 |
|
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15052487 |
|
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62043067 |
Aug 28, 2014 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07K 2317/92 20130101;
C07K 16/18 20130101; A61K 2039/5156 20130101; A61P 35/02 20180101;
C07K 14/7051 20130101; C07K 2317/31 20130101; A61K 2039/572
20130101; C07K 2317/622 20130101; C07K 2317/94 20130101; A61K 35/17
20130101; C12N 15/1058 20130101; A61P 35/00 20180101; A61K 39/3955
20130101; C07K 14/705 20130101; A61K 38/00 20130101; C07K 14/70503
20130101; C07K 14/70521 20130101; A61P 35/04 20180101; C07K
14/70535 20130101; C07K 2319/03 20130101; C07K 2319/02
20130101 |
International
Class: |
C07K 16/18 20060101
C07K016/18; A61K 39/395 20060101 A61K039/395; A61K 35/17 20060101
A61K035/17; C07K 14/725 20060101 C07K014/725; C12N 15/10 20060101
C12N015/10 |
Claims
1. A chimeric antigen receptor for binding with a target antigen,
comprising: i. at least one antigen specific targeting region
evolved from a wild-type protein or a domain thereof and having at
least one of: (a) a decrease in activity in an assay at the normal
physiological condition compared to the antigen specific targeting
region of the wild-type protein or a domain thereof, and (b) an
increase in activity in an assay under the aberrant condition
compared to the antigen specific targeting region of the wild-type
protein or a domain thereof; ii. a transmembrane domain; and iii.
an intracellular signaling domain.
2. The chimeric antigen receptor of claim 1, wherein the antigen
specific targeting region has both (a) a decrease in activity in an
assay at the normal physiological condition compared to the antigen
specific targeting region of the wild-type protein or a domain
thereof, and (b) an increase in activity in an assay under the
aberrant condition compared to the antigen specific targeting
region of the wild-type protein or a domain thereof.
3. The chimeric antigen receptor of claim 1, further comprising an
extracellular spacer domain or at least one co-stimulatory
domain.
4. The chimeric antigen receptor of claim 3, wherein the
extracellular spacer domain is selected from an Fc fragment of an
antibody, a hinge region of an antibody, a CH2 region of an
antibody, a CH3 region of an antibody, an artificial spacer
sequence and combinations thereof.
4. The chimeric antigen receptor of claim 3, wherein the
extracellular spacer domain has a first conformation at the
aberrant condition for the at least one antigen specific targeting
region to bind to the target antigen at a higher binding activity
than a binding activity of a second conformation of a second
conformation of the extracellular spacer domain at the normal
physiological condition.
5. The chimeric antigen receptor of claim 3, wherein the
extracellular spacer domain has an enhanced
ubiquitylation-resistance level at the aberrant condition than at
the normal physiological condition.
6. The chimeric antigen receptor of claim 1, wherein the at least
one antigen specific targeting region comprises two antigen
specific targeting regions that are connected with a linker.
7. The chimeric antigen receptor of claim 6, wherein the two
antigen specific targeting regions each binds with a different
target antigen or a different epitope of the same target
antigen.
8. The chimeric antigen receptor of claim 6, wherein the linker has
a first conformation at the aberrant condition for the at least two
antigen specific targeting regions to bind to the target antigen at
a higher binding activity than a binding activity of a second
conformation of the linker at the normal physiological
condition.
9. The chimeric antigen receptor of claim 1, wherein the at least
one antigen specific targeting region is selected from an antibody,
a fragment of an antibody, a divalent single chain antibody or a
diabody, a ligand, a receptor binding domain of a ligand, a
receptor, a ligand binding domain of a receptor, and an
affibody.
10. The chimeric antigen receptor of claim 9, wherein the antibody
is a multiple specific antibody.
11. The chimeric antigen receptor of claim 1, wherein the
transmembrane domain is selected from an artificial hydrophobic
sequence and transmembrane domains of a Type I transmembrane
protein, an alpha, beta or zeta chain of a T cell receptor, CD28,
CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37,
CD64, CD80, CD86, CD134, CD137, and CD154.
12. The chimeric antigen receptor of claim 1, wherein the
co-stimulatory domain is selected from co-stimulatory domains of
proteins in the TNFR superfamily, CD28, CD 137, CD 134, DaplO,
CD27, CD2, CD5, ICAM-1, LFA-1, Lck, TNFR-I, TNFR-II, Fas, CD30,
CD40, ICOS LIGHT, NKG2C, and B7-H3.
13. The chimeric antigen receptor of claim 1, wherein the
intracellular signaling domain is selected from cytoplasmic
signaling domains of a human CD3 zeta chain, FcyRIII, FcsRI, a
cytoplasmic tail of a Fc receptor, an immunoreceptor tyrosine-based
activation motif (ITAM) bearing cytoplasmic receptors, TCR zeta,
FcR gamma, FcR beta, CD3 gamma, CD3 delta, CD3 epsilon, CD5, CD22,
CD79a, CD79b, and CD66d.
14. The chimeric antigen receptor of claim 1, wherein the normal
physiological condition is selected from one or more of
temperature, pH, osmotic pressure, osmolality, oxidative stress, an
electrolyte concentration, a concentration of a small organic
molecule, a concentration of inorganic molecule, cell types, and
nutrient availability.
15. The chimeric antigen receptor of claim 1, wherein the aberrant
condition is a condition selected from conditions present in a
tumor microenvironment, a brain extracellular fluid, a stem cell
niche, a lymph node, a tonsil, an adenoid, a sinus, and a synovial
fluid.
16. An expression vector, comprising a polynucleotide sequence
encoding the chimeric antigen receptor of claim 1.
17. The expression of claim 16, wherein the expression vector is
selected from lentivirus vectors, gamma retrovirus vectors, foamy
virus vectors, adeno associated virus vectors, adenovirus vectors,
pox virus vectors, herpes virus vectors, engineered hybrid viruses,
and transposon mediated vectors.
18. A genetically engineered cytotoxic cell, comprising a
polynucleotide sequence encoding the chimeric antigen receptor of
claim 1.
19. The genetically engineered cytotoxic cell of claim 17, wherein
the cytotoxic cell is selected from a T cell, natural killer cell,
an activated NK cells, a neutrophil, an eosinophil, a basophil, a
B-cell, a macrophage and a lymphokine-activated killer cell.
20. A method for treating a cancer in a subject, comprising the
steps of: a. introducing an expression vector comprising a
polynucleotide sequence encoding the chimeric antigen receptor of
claim 1 into a cytotoxic cell obtained from the subject to produce
an genetically engineered cytotoxic cell; and b. administering the
genetically engineered cytotoxic cell to the subject.
21. A method for producing a chimeric antigen receptor comprising
at least one antigen specific targeting region, a transmembrane
domain and an intracellular signaling domain, said method
comprising the steps of generating the at least one antigen
specific targeting region from a wild-type protein or a domain
thereof that binds specifically with a target antigen, by: i.
evolving the DNA which encodes the wild-type protein or a domain
thereof using one or more evolutionary techniques to create mutant
DNAs; ii. expressing the mutant DNAs to obtain mutant polypeptides;
iii. subjecting the mutant polypeptides and the wild-type protein
or a domain thereof to an assay under a normal physiological
condition and to an assay under an aberrant condition; and iv.
selecting a conditionally active antigen specific targeting region
from the mutant polypeptides expressed in step (iii) which exhibits
at least one of: (a) a decrease in activity in the assay at the
normal physiological condition compared to the antigen specific
targeting region of the wild-type protein or a domain thereof, and
(b) an increase in activity in the assay under the aberrant
condition compared to the antigen specific targeting region of the
wild-type protein or a domain thereof.
Description
RELATED APPLICATION DATA
[0001] This application claims benefit of U.S. provisional
application No. 62/043,067, filed on Aug. 28, 2014, now expired,
and international application no. PCT/US15/47197, filed on Aug. 27,
2015, and which designates the United States of America, both of
which applications are hereby incorporated by reference in their
entirety.
FIELD OF THE DISCLOSURE
[0002] This disclosure relates to the field of protein evolution.
Specifically, this disclosure relates to a method of generating a
conditionally active chimeric antigen receptor from a wild type
protein. The conditionally active chimeric antigen receptor is
reversibly or irreversibly inactivated at a wild type normal
physiological condition, but is active at an aberrant
condition.
BACKGROUND OF THE DISCLOSURE
[0003] There is a considerable body of literature describing the
potential for evolving proteins for a variety of characteristics,
especially enzymes. For example, enzymes may be evolved to be
stabilized for operation at different conditions such as at an
elevated temperature. In situations where there is an activity
improvement at the elevated temperature, a substantial portion of
the improvement can be attributed to the higher kinetic activity
commonly described by the Q10 rule where it is estimated that in
the case of an enzyme the turnover doubles for every increase of 10
degrees Celsius.
[0004] In addition, there exist examples of natural mutations that
destabilize proteins at their normal operating conditions. Certain
mutants can be active at a lower temperature, but at a reduced
level compared to the wild type proteins. This is also typically
described by a reduction in activity as guided by the Q10 or
similar rules.
[0005] It is desirable to generate useful molecules that are
conditionally activated. For example, it is desirable to generate
molecules that are virtually inactive at wild-type operating
conditions but are active at other than wild-type operating
conditions at a level that is equal to or better than at wild-type
operating conditions, or that are activated or inactivated in
certain microenvironments, or that are activated or inactivated
over time. Besides temperature, other conditions for which the
proteins can be evolved or optimized include pH, osmotic pressure,
osmolality, oxidative stress and electrolyte concentration. Other
desirable properties that can be optimized during evolution include
chemical resistance, and proteolytic resistance.
[0006] Many strategies for evolving or engineering molecules have
been published. However, engineering or evolving a protein to be
inactive or virtually inactive (less than 10% activity and
preferably less than 1% activity) at a wild type operating
condition, while maintaining activity equivalent or better than its
corresponding wild type protein at a condition other than a
wild-type operating condition, requires that destabilizing
mutation(s) co-exist with activity increasing mutations that do not
counter the destabilizing effect. It is expected that
destabilization would reduce the protein's activity greater than
the effects predicted by standard rules such as Q10. Therefore, the
ability to evolve proteins that work efficiently at lower
temperature, for example, while being inactivated under the normal
operating condition for the corresponding wild-type protein,
creates an unexpected new class of proteins.
[0007] Chimeric antigen receptors (CARs) have been used in treating
cancers. US 2013/0280220 discloses methods and compositions
providing improved cells encoding a chimeric antigen receptor that
is specific for two or more antigens, including tumor antigens.
Cells expressing the chimeric antigen receptor may be used in cell
therapy. Such cell therapy may be suitable for any medical
condition, although in specific embodiments the cell therapy is for
cancer, including cancer involving solid tumors.
[0008] The present invention provides engineered conditionally
active chimeric antigen receptors that are inactive or less active
at a normal physiological condition but active at an aberrant
physiological condition.
[0009] Throughout this application, various publications are
referenced by author and date. The disclosures of these
publications are hereby incorporated by reference in their
entireties into this application in order to more fully describe
the state of the art as known to those skilled therein as of the
date of the disclosure described and claimed herein.
BRIEF DESCRIPTION OF THE DRAWINGS
[0010] FIG. 1 depicts a schematic representation of a chimeric
antigen receptor in accordance with one embodiment of the present
invention. ASTR is an antigen-specific targeting region, L is a
linker, ESD is an extracellular spacer domain, TM is a
transmembrane domain, CSD is a co-stimulatory domain, and ISD is an
intracellular signaling domain.
[0011] FIGS. 2 and 3 show that expressing the conditionally active
antibodies of Example 1 as bivalent or monovalent antibodies does
not significantly alter that selectivity of these antibodies under
pH 6.0 and over pH 7.4.
[0012] FIG. 4 is a profile of a size exclusive chromatograph
indicating that the conditionally active antibodies of Example 2 do
not aggregate.
[0013] FIG. 5 shows on and off rates for the conditionally active
antibodies of Example 2 as measured by a surface plasmon resonance
(SPR) assay.
[0014] FIGS. 6A-6B show the selectivity of the conditionally active
antibodies as measured by the SPR assay of Example 2.
[0015] FIG. 7A shows that CAR-T cells had no effect on a population
of CHO cells that do not express the target antigen X1 of the CAR-T
cells. The CAR molecule in the CAR-T cells of this example included
an antibody against target antigen X1, though this antibody was not
conditionally active (Comparative Example A).
[0016] FIG. 7B shows that CAR-T cells reduced the population of
CHO-63 cells that express the target antigen X1 of the CAR-T cells.
These CAR-T cells are the same cells as were used to generate the
data shown in FIG. 7A (Comparative Example A).
[0017] FIG. 8A shows that CAR-T cells had no effect on a population
of CHO cells that do not express the target antigen X1 of the CAR-T
cells. The CAR molecule in the CAR-T cells of this Example 3
included a conditionally active antibody against target antigen
X1.
[0018] FIG. 8B shows that CAR-T cells reduced the population of
CHO-63 cells that express the target antigen X1 of the CAR-T cells
as tested in Example 3. These CAR-T cells are the same cells as
were used to generate the data shown in FIG. 8A.
[0019] FIGS. 9A-9B show cytokine release induced by binding of
CAR-T cells with the target antigen X1, as described in Example
3.
[0020] FIG. 10 shows conditionally active antibodies against target
antigen X2.
[0021] FIG. 11A shows the cytotoxic effect induced by CAR-T cells
binding to Daudi cells that express target antigen X2 and the
cytotoxic effect induced by CAR-T cells on HEK293 cells that do not
express target antigen X2, as described in Example 4.
[0022] FIGS. 12A-12B show cytokine release induced by binding of
CAR-T cells with the target antigen X1, as described in Example
5.
[0023] FIGS. 13A-13B show cytokine release induced by binding of
CAR-T cells with the target antigen X2, as described in Example
5.
[0024] FIG. 14 shows conditionally active antibodies against target
antigen X3 that are suitable for construction of CAR-T cells.
SUMMARY OF THE DISCLOSURE
[0025] In one aspect, the present invention provides a chimeric
antigen receptor (CAR) for binding with a target antigen. The
chimeric antigen receptor comprises at least one antigen specific
targeting region that is evolved from a wild-type protein or a
domain thereof. The CAR further comprises a transmembrane domain
and an intracellular signaling domain. The at least one antigen
specific targeting region has at least one of: (a) a decrease in
activity in an assay at the normal physiological condition compared
to the antigen specific targeting region of the wild-type protein
or a domain thereof, and (b) an increase in activity in an assay
under the aberrant condition compared to the antigen specific
targeting region of the wild-type protein or a domain thereof.
[0026] In another aspect, the present invention provides an
expression vector, including a polynucleotide sequence encoding the
chimeric antigen receptor of the invention. The expression vector
is selected from lentivirus vectors, gamma retrovirus vectors,
foamy virus vectors, adeno associated virus vectors, adenovirus
vectors, pox virus vectors, herpes virus vectors, engineered hybrid
viruses, and transposon mediated vectors.
[0027] In yet another aspect, the present invention provides a
genetically engineered cytotoxic cell that includes a
polynucleotide sequence encoding the chimeric antigen receptor of
the invention. The cytotoxic cell may be a T cell and may be
selected from a naive T cell, a central memory T cell, and an
effector memory T cell.
[0028] In yet another aspect, the present invention provides a
pharmaceutical composition, including the chimeric antigen
receptor, the expression vector, and/or the genetically engineered
cytotoxic cell of the invention, and a pharmaceutically acceptable
excipient.
[0029] In yet another aspect, the present invention provides a
method for treating a cancer in a subject, including the step of
introducing an expression vector including a polynucleotide
sequence encoding the chimeric antigen receptor of the invention
into a cytotoxic cell obtained from the subject to produce a
genetically engineered cytotoxic cell; and administering the
genetically engineered cytotoxic cell to the subject.
[0030] In yet another aspect, the present invention provides a
method for producing a chimeric antigen receptor comprising at
least one antigen specific targeting region, a transmembrane domain
and an intracellular signaling domain. The method comprising the
steps of generating the at least one antigen specific targeting
region from a wild-type protein or a domain thereof that binds
specifically with a target antigen. These steps include (i)
evolving the DNA which encodes the wild-type protein or a domain
thereof using one or more evolutionary techniques to create mutant
DNAs; (ii) expressing the mutant DNAs to obtain mutant
polypeptides; (iii) subjecting the mutant polypeptides and the
wild-type protein or a domain thereof to an assay under a normal
physiological condition and to an assay under an aberrant
condition; and (iv) selecting a conditionally active antigen
specific targeting region from the mutant polypeptides expressed in
step (iii) which exhibits at least one of (a) a decrease in
activity in the assay at the normal physiological condition
compared to the antigen specific targeting region of the wild-type
protein or a domain thereof, and (b) an increase in activity in the
assay under the aberrant condition compared to the antigen specific
targeting region of the wild-type protein or a domain thereof.
[0031] [1] A chimeric antigen receptor for binding with a target
antigen. The chimeric antigen receptor comprises at least two
antigen specific targeting regions connected by a conditional
linker. The conditional linker has a first conformation at an
aberrant condition for the at least two antigen specific targeting
regions to bind to the target antigen at a higher binding activity
than a binding activity of a second conformation of the conditional
linker at a normal physiological condition. The chimeric antigen
receptor further comprises a transmembrane domain and an
intracellular signaling domain.
[0032] [2] A chimeric antigen receptor for binding with a target
antigen. The chimeric antigen receptor comprises at least one
antigen specific targeting region that binds with the target
antigen, a transmembrane domain and an intracellular signaling
domain. The chimeric antigen receptor further comprises an
extracellular spacer domain having a first conformation at an
aberrant condition for the at least one antigen specific targeting
region to bind to the target antigen at a higher binding activity
than a binding activity of a second conformation of a second
conformation of the extracellular spacer domain at a normal
physiological condition.
[0033] [3] A chimeric antigen receptor for binding with a target
antigen. The chimeric antigen receptor comprises at least one
antigen specific targeting region that binds with the target
antigen, a transmembrane domain and an intracellular signaling
domain. The chimeric antigen receptor further comprises an
extracellular spacer domain having an enhanced
ubiquitylation-resistance level at an aberrant condition than at a
normal physiological condition.
[0034] [4] The chimeric antigen receptor of [1-3], wherein the
antigen specific targeting region is evolved from a wild-type
protein or a domain thereof and having at least one of: (a) a
decrease in activity in an assay at the normal physiological
condition compared to the antigen specific targeting region of the
wild-type protein or a domain thereof, and (b) an increase in
activity in an assay under the aberrant condition compared to the
antigen specific targeting region of the wild-type protein or a
domain thereof.
DEFINITIONS
[0035] In order to facilitate understanding of the examples
provided herein, certain frequently occurring methods and/or terms
will be defined herein.
[0036] As used herein in connection with a measured quantity, the
term "about" refers to the normal variation in that measured
quantity that would be expected by the skilled artisan making the
measurement and exercising a level of care commensurate with the
objective of the measurement and the precision of the measuring
equipment used. Unless otherwise indicated, "about" refers to a
variation of +/-10% of the value provided.
[0037] The term "agent" is used herein to denote a chemical
compound, a mixture of chemical compounds, an array of spatially
localized compounds (e.g., a VLSIPS peptide array, polynucleotide
array, and/or combinatorial small molecule array), biological
macromolecule, a bacteriophage peptide display library, a
bacteriophage antibody (e.g., scFv) display library, a polysome
peptide display library, or an extract made from biological
materials such as bacteria, plants, fungi, or animal (particular
mammalian) cells or tissues. Agents are evaluated for potential
enzyme activity by inclusion in screening assays described herein
below. Agents are evaluated for potential activity as conditionally
active biologic therapeutic enzymes by inclusion in screening
assays described herein below.
[0038] The term "amino acid" as used herein refers to any organic
compound that contains an amino group (--NH.sub.2) and a carboxyl
group (--COOH); preferably either as free groups or alternatively
after condensation as part of peptide bonds. The "twenty naturally
encoded polypeptide-forming alpha-amino acids" are understood in
the art and refer to: alanine (ala or A), arginine (arg or R),
asparagine (asn or N), aspartic acid (asp or D), cysteine (cys or
C), gluatamic acid (glu or E), glutamine (gin or Q), glycine (gly
or G), histidine (his or H), isoleucine (ile or I), leucine (leu or
L), lysine (lys or K), methionine (met or M), phenylalanine (phe or
F), proline (pro or P), serine (ser or S), threonine (thr or T),
tryptophan (tip or W), tyrosine (tyr or Y), and valine (val or
V).
[0039] The term "amplification" as used herein means that the
number of copies of a polynucleotide is increased.
[0040] The term "antibody" as used herein refers to intact
immunoglobulin molecules, as well as fragments of immunoglobulin
molecules, such as Fab, Fab', (Fab')2, Fv, and SCA fragments, that
are capable of binding to an epitope of an antigen. These antibody
fragments, which retain some ability to selectively bind to an
antigen (e.g., a polypeptide antigen) of the antibody from which
they are derived, can be made using well known methods in the art
(see, e.g., Harlow and Lane, supra), and are described further, as
follows. Antibodies can be used to isolate preparative quantities
of the antigen by immunoaffinity chromatography. Various other uses
of such antibodies are to diagnose and/or stage disease (e.g.,
neoplasia) and for therapeutic application to treat disease, such
as for example: neoplasia, autoimmune disease, AIDS, cardiovascular
disease, infections, and the like Chimeric, human-like, humanized
or fully human antibodies are particularly useful for
administration to human patients.
[0041] An Fab fragment consists of a monovalent antigen-binding
fragment of an antibody molecule, and can be produced by digestion
of a whole antibody molecule with the enzyme papain, to yield a
fragment consisting of an intact light chain and a portion of a
heavy chain.
[0042] An Fab' fragment of an antibody molecule can be obtained by
treating a whole antibody molecule with pepsin, followed by
reduction, to yield a molecule consisting of an intact light chain
and a portion of a heavy chain. Two Fab' fragments are obtained per
antibody molecule treated in this manner.
[0043] An (Fab')2 fragment of an antibody can be obtained by
treating a whole antibody molecule with the enzyme pepsin, without
subsequent reduction. A (Fab')2 fragment is a dimer of two Fab'
fragments, held together by two disulfide bonds.
[0044] An Fv fragment is defined as a genetically engineered
fragment containing the variable region of a light chain and the
variable region of a heavy chain expressed as two chains.
[0045] The term "antigen" or "Ag" as used herein is defined as a
molecule that provokes an immune response. This immune response may
involve either antibody production, or the activation of specific
immunologically-competent cells, or both. A person skilled in the
art will understand that any macromolecule, including virtually all
proteins or peptides, can serve as an antigen. Furthermore,
antigens can be derived from recombinant or genomic DNA. A person
skilled in the art will understand that any DNA, which includes a
nucleotide sequence or a partial nucleotide sequence encoding a
protein that elicits an immune response therefore encodes an
"antigen" as that term is used herein. Furthermore, one skilled in
the art will understand that an antigen need not be encoded solely
by a full length nucleotide sequence of a gene. It is readily
apparent that the present invention includes, but is not limited
to, the use of partial nucleotide sequences of more than one gene
and that these nucleotide sequences are arranged in various
combinations to elicit the desired immune response. Moreover, a
skilled person will understand that an antigen need not be encoded
by a "gene" at all. It is readily apparent that an antigen can be
generated, synthesized or can be derived from a biological sample.
Such a biological sample can include, but is not limited to a
tissue sample, a tumor sample, a cell or a biological fluid.
[0046] "Antigen loss escape variants" as used herein refer to cells
which exhibit reduced or loss of expression of the target antigen,
which antigens are targeted by the CARs of the invention.
[0047] The term "autoimmune disease" as used herein is defined as a
disorder that results from an autoimmune response. An autoimmune
disease is the result of an inappropriate and excessive response to
a self-antigen. Examples of autoimmune diseases include but are not
limited to, Addison's disease, alopecia greata, ankylosing
spondylitis, autoimmune hepatitis, autoimmune parotitis, Crohn's
disease, diabetes (Type 1), dystrophic epidermolysis bullosa,
epididymitis, glomerulonephritis, Graves' disease, Guillain-Barr
syndrome, Hashimoto's disease, hemolytic anemia, systemic lupus
erythematosus, multiple sclerosis, myasthenia gravis, pemphigus
vulgaris, psoriasis, rheumatic fever, rheumatoid arthritis,
sarcoidosis, scleroderma, Sjogren's syndrome,
spondyloarthropathies, thyroiditis, vasculitis, vitiligo, myxedema,
pernicious anemia, ulcerative colitis, among others.
[0048] The term "autologous," as used herein refers to any material
derived from the same individual to which it is later to be
reintroduced. For example, T cells from a patient may be isolated,
genetically engineered to express a CAR and then reintroduced into
the patient.
[0049] The term "B-cell associated diseases" as used herein include
B-cell immunodeficiencies, autoimmune diseases and/or
excessive/uncontrolled cell proliferation associated with B-cells
(including lymphomas and/or leukemia's). Examples of such diseases,
wherein bispecific CARs of the invention may be used for
therapeutic approaches include but are not limited to systemic
lupus erythematosus (SLE), diabetes, rheumatoid arthritis (RA),
reactive arthritis, multiple sclerosis (MS), pemphigus vulgaris,
celiac disease, Crohn's disease, inflammatory bowel disease,
ulcerative colitis, autoimmune thyroid disease, X-linked
agammaglobulinaemis, pre-B acute lymphoblastic leukemia, systemic
lupus erythematosus, common variable immunodeficiency, chronic
lymphocytic leukemia, diseases associated with selective IgA
deficiency and/or IgG subclass deficiency, B lineage lymphomas
(Hodgkin's lymphoma and/or non-Hodgkin's lymphoma),
immunodeficiency with thymoma, transient hypogammaglobulinemia
and/or hyper IgM syndrome, as well as virally-mediated B-cell
diseases such as EBV mediated lymphoproliferative disease, and
chronic infections in which B-cells participate in the
pathophysiology.
[0050] The term "blood-brain barrier" or "BBB" refers to the
physiological barrier between the peripheral circulation and the
brain and spinal cord which is formed by tight junctions within the
brain capillary endothelial plasma membranes, creating a tight
barrier that restricts the transport of molecules into the brain,
even very small molecules such as urea (60 Daltons). The
blood-brain barrier within the brain, the blood-spinal cord barrier
within the spinal cord, and the blood-retinal barrier within the
retina are contiguous capillary barriers within the central nerve
system (CNS), and are herein collectively referred to as the
"blood-brain barrier" or "BBB." The BBB also encompasses the
blood-cerebral spinal fluid barrier (choroid plexus) where the
barrier is included of ependymal cells rather than capillary
endothelial cells.
[0051] The terms "cancer" and "cancerous" as used herein refer to
or describe the physiological condition in mammals that is
typically characterized by unregulated cell growth. Examples of
cancer include, but are not limited to B-cell lymphomas (Hodgkin's
lymphomas and/or non-Hodgkins lymphomas), brain tumor, breast
cancer, colon cancer, lung cancer, hepatocellular cancer, gastric
cancer, pancreatic cancer, cervical cancer, ovarian cancer, liver
cancer, bladder cancer, cancer of the urinary tract, thyroid
cancer, renal cancer, carcinoma, melanoma, head and neck cancer,
brain cancer, and prostate cancer, including but not limited to
androgen-dependent prostate cancer and androgen-independent
prostate cancer.
[0052] The term "chimeric antigen receptor" or "CAR" or "CARs" as
used herein refers to engineered receptors, which graft antigen
specificity onto a cytotoxic cell, for example T cells, NK cells
and macrophages. The CARs of the invention may include at least one
antigen specific targeting region (ASTR), an extracellular spacer
domain (ESD), a transmembrane domain (TM), one or more
co-stimulatory domains (CSD), and an intracellular signaling domain
(ISD). In an embodiment, the ESD and/or CSD are optional. In
another embodiment, the CAR is a bispecific CAR, which is specific
to two different antigens or epitopes. After the ASTR binds
specifically to a target antigen, the ISD activates intracellular
signaling. For example, the ISD can redirect T cell specificity and
reactivity toward a selected target in a non-MHC-restricted manner,
exploiting the antigen-binding properties of antibodies. The
non-MHC-restricted antigen recognition gives T cells expressing the
CAR the ability to recognize an antigen independent of antigen
processing, thus bypassing a major mechanism of tumor escape.
Moreover, when expressed in T cells, CARs advantageously do not
dimerize with endogenous T cell receptor (TCR) alpha and beta
chains.
[0053] The term "co-express" as used herein refers to simultaneous
expression of two or more genes. Genes may be nucleic acids
encoding, for example, a single protein or a chimeric protein as a
single polypeptide chain. For example, the CARs of the invention
may be co-expressed with a therapeutic control (for example
truncated epidermal growth factor (EGFRt)), wherein the CAR is
encoded by a first polynucleotide chain and the therapeutic control
is encoded by a second polynucleotide chain. In an embodiment, the
first and second polynucleotide chains are linked by a nucleic acid
sequence that encodes a cleavable linker. Alternately, the CAR and
the therapeutic control are encoded by two different
polynucleotides that are not linked via a linker but are instead
encoded by, for example, two different vectors.
[0054] The term "cognate" as used herein refers to a gene sequence
that is evolutionarily and functionally related between species.
For example, but without limitation, in the human genome the human
CD4 gene is the cognate gene to the mouse 3d4 gene, since the
sequences and structures of these two genes indicate that they are
highly homologous and both genes encode a protein which functions
in signaling T cell activation through MHC class II-restricted
antigen recognition.
[0055] The term "conditionally active biologic protein" refers to a
variant, or mutant, of a wild-type protein which is more or less
active than the parent wild-type protein under one or more normal
physiological conditions. This conditionally active protein also
exhibits activity in selected regions of the body and/or exhibits
increased or decreased activity under aberrant, or permissive,
physiological conditions. The term "normal physiological condition"
as used herein refers to one of temperature, pH, osmotic pressure,
osmolality, oxidative stress, electrolyte concentration, a
concentration of a small organic molecule such as glucose, lactic
acid, pyruvate, nutrient components, other metabolites, and the
like, a concentration of another molecule such as oxygen,
carbonate, phosphate, and carbon dioxide, as well as cell types,
and nutrient availability, which would be considered within a
normal range at the site of administration, or at the tissue or
organ at the site of action, to a subject.
[0056] The term "aberrant condition" as used herein refers to a
condition that deviates from the normally acceptable range for that
condition. In one aspect, the conditionally active biologic protein
is virtually inactive at a normal physiological condition but is
active at an aberrant condition at a level that is equal or better
than the wild-type protein from which it is derived. For example,
in one aspect, an evolved conditionally active biologic protein is
virtually inactive at body temperature, but is active at lower
temperatures. In another aspect, the conditionally active biologic
protein is reversibly or irreversibly inactivated at the normal
physiological condition. In a further aspect, the wild-type protein
is a therapeutic protein. In another aspect, the conditionally
active biologic protein is used as a drug, or therapeutic agent. In
yet another aspect, the protein is more or less active in highly
oxygenated blood, such as, for example, after passage through the
lung or in the lower pH environments found in the kidney.
[0057] "Conservative amino acid substitutions" refer to the
interchangeability of residues having similar side chains. For
example, a group of amino acids having aliphatic side chains is
glycine, alanine, valine, leucine, and isoleucine; a group of amino
acids having aliphatic-hydroxyl side chains is serine and
threonine; a group of amino acids having amide-containing side
chains is asparagine and glutamine; a group of amino acids having
aromatic side chains is phenylalanine, tyrosine, and tryptophan; a
group of amino acids having basic side chains is lysine, arginine,
and histidine; and a group of amino acids having sulfur-containing
side chains is cysteine and methionine. Preferred conservative
amino acids substitution groups are: valine-leucine-isoleucine,
phenylalanine-tyrosine, lysine-arginine, alanine-valine, and
asparagine-glutamine.
[0058] The term "corresponds to" is used herein to mean that a
polynucleotide sequence is homologous (i.e., is identical, not
strictly evolutionarily related) to all or a portion of a reference
polynucleotide sequence, or that a polypeptide sequence is
identical to a reference polypeptide sequence. In
contradistinction, the term "complementary to" is used herein to
mean that the complementary sequence is homologous to all or a
portion of a reference polynucleotide sequence. For illustration,
the nucleotide sequence "TATAC" corresponds to a reference "TATAC"
and is complementary to a reference sequence "GTATA."
[0059] The term "co-stimulatory ligand" as used herein includes a
molecule on an antigen presenting cell (e.g., dendritic cell, B
cell, and the like) that specifically binds a cognate
co-stimulatory molecule on a T cell, thereby providing a signal
which, in addition to the primary signal provided by, for instance,
by the binding of a TCR/CD3 complex with an MHC molecule loaded
with peptide, mediates a T cell response, including, but not
limited to, proliferation, activation, differentiation, and the
like. A co-stimulatory ligand can include, but is not limited to,
CD7, B7-1 (CD80), B7-2 (CD86), PD-L1, PD-L2, 4-1BBL, OX40L, an
inducible costimulatory ligand (ICOS-L), an intercellular adhesion
molecule (ICAM), CD30L, CD40, CD70, CD83, HLA-G, MICA, MICB, HVEM,
a lymphotoxin beta receptor, 3/TR6, ILT3, ILT4, HVEM, an agonist or
an antibody that binds to a Toll ligand receptor and a ligand that
specifically binds with B7-H3. A co-stimulatory ligand also
encompasses, inter alia, an antibody that specifically binds with a
co-stimulatory molecule present on a T cell, such as, but not
limited to, CD27, CD28, 4-1BB, OX40, CD30, CD40, PD-1, ICOS, a
lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT,
NKG2C, B7-H3, and a ligand that specifically binds with CD83.
[0060] The term "co-stimulatory molecule" as used herein refers to
the cognate binding partner on a T cell that specifically binds
with a co-stimulatory ligand, thereby mediating a co-stimulatory
response by the T cell, such as, but not limited to, proliferation.
Co-stimulatory molecules include, but are not limited to an MHC
class 1 molecule, BTLA and a Toll ligand receptor.
[0061] The term "co-stimulatory signal" as used herein refers to a
signal, which in combination with a primary signal, such as TCR/CD3
ligation, leads to T cell proliferation and/or upregulation or down
regulation of key molecules.
[0062] The term "cytotoxic cell" as used herein means a cell which
can injure or destroy invading microorganisms, tumor cells or other
diseased tissue cells. This term is meant to include natural killer
(NK) cells, activated NK cells, neutrophils, T cells, eosinophils,
basophils, B-cells, macrophages and lymphokine-activated killer
(LAK) cells among other cell types. The cytotoxic cell, through an
antibody, receptor, ligand or fragments/derivatives thereof, is
bound to a target cell to form a stable complex, and stimulates the
cytotoxic cell to destroy the target cell.
[0063] Cytotoxic cells may also include other immune cells with
tumor lytic capabilities including but not limited to natural
killer T cells (Heczey et al., "Invariant NKT cells with chimeric
antigen receptor provide a novel platform for safe and effective
cancer immunotherapy," Blood, vol. 124, pp. 2824-2833, 2014) and
granulocytes. Further, cytotoxic cells may include immune cells
with phagocytic capability including but not limited to macrophages
and granulocytes, cells with stem cell and/or progenitor cell
properties including, but not limited to, hematopoietic
stem/progenitor cells (Zhen et al., "HIV-specific Immunity Derived
From Chimeric Antigen Receptor-engineered Stem Cells," Mol Ther.,
vol. 23, pp. 1358-1367, 2015), embryonic stem cells (ESCs), cord
blood stem cells, and induced pluripotent stem cells (iPSCs)
(Themeli et al., "New cell sources for T cell engineering and
adoptive immunotherapy," Cell Stem Cell., vol. 16, pp. 357-366,
2015). Additionally, cytotoxic cells include "synthetic cells" such
as iPSC-derived T cells (TiPSCs) (Themeli et al., "Generation of
tumor-targeted human T lymphocytes from induced pluripotent stem
cells for cancer therapy," Nat Biotechnol., vol. 31, pp. 928-933,
2013) or iPSC-derived NK cells.
[0064] The term "degrading effective" amount refers to the amount
of enzyme which is required to process at least 50% of the
substrate, as compared to substrate not contacted with the
enzyme.
[0065] The term "directional ligation" refers to a ligation in
which a 5' end and a 3' end of a polynucleotide are different
enough to specify a preferred ligation orientation. For example, an
otherwise untreated and undigested PCR product that has two blunt
ends will typically not have a preferred ligation orientation when
ligated into a cloning vector digested to produce blunt ends in its
multiple cloning site; thus, directional ligation will typically
not be displayed under these circumstances. In contrast,
directional ligation will typically be displayed when a digested
PCR product having a 5' EcoR I-treated end and a 3' BamH I is
ligated into a cloning vector that has a multiple cloning site
digested with EcoR I and BamH I.
[0066] The term "disease targeted by genetically modified cytotoxic
cells" as used herein encompasses the targeting of any cell
involved in any manner in any disease by the genetically modified
cells of the invention, irrespective of whether the genetically
modified cells target diseased cells or healthy cells to effectuate
a therapeutically beneficial result. The genetically modified cells
include but are not limited to genetically modified T cells, NK
cells, and macrophages. The genetically modified cells express the
CARs of the invention, which CARs may target any of the antigens
expressed on the surface of target cells. Examples of antigens
which may be targeted include but are not limited to antigens
expressed on B-cells; antigens expressed on carcinomas, sarcomas,
lymphomas, leukemia, germ cell tumors, and blastomas; antigens
expressed on various immune cells; and antigens expressed on cells
associated with various hematologic diseases, autoimmune diseases,
and/or inflammatory diseases. Other antigens that may be targeted
will be apparent to those of skill in the art and may be targeted
by the CARs of the invention in connection with alternate
embodiments thereof.
[0067] The terms "genetically modified cells", "redirected cells",
"genetically engineered cells" or "modified cells" as used herein
refer to cells that express the CARs of the invention.
[0068] The term "DNA shuffling" is used herein to indicate
recombination between substantially homologous but non-identical
sequences, in some embodiments DNA shuffling may involve crossover
via non-homologous recombination, such as via cer/lox and/or
flp/frt systems and the like. DNA shuffling can be random or
non-random.
[0069] The term "drug" or "drug molecule" refers to a therapeutic
agent including a substance having a beneficial effect on a human
or animal body when it is administered to the human or animal body.
Preferably, the therapeutic agent includes a substance that can
treat, cure or relieve one or more symptoms, illnesses, or abnormal
conditions in a human or animal body or enhance the wellness of a
human or animal body.
[0070] An "effective amount" is an amount of a conditionally active
biologic protein or fragment which is effective to treat or prevent
a condition in a living organism to whom it is administered over
some period of time, e.g., provides a therapeutic effect during a
desired dosing interval.
[0071] The term "electrolyte" as used herein defines a mineral in
the blood or other body fluids that carries a charge. For example,
in one aspect, the normal physiological condition and aberrant
condition can be conditions of "electrolyte concentration". In one
aspect, the electrolyte concentration to be tested is selected from
one or more of ionized calcium, sodium, potassium, magnesium,
chloride, bicarbonate, and phosphate concentration. For example, in
one aspect, normal range of serum calcium is 8.5 to 10.2 mg/dL. In
this aspect, aberrant serum calcium concentration may be selected
from either above or below the normal range, m another example, in
one aspect, normal range of serum chloride is 96-106
milliequivalents per liter (mEq/L). In this aspect, aberrant serum
chloride concentration may be selected from either above or below
the normal range, in another example, in one aspect, a normal range
of serum magnesium is from 1.7-2.2 mg/dL. In this aspect, an
aberrant serum magnesium concentration may be selected from either
above or below the normal range, in another example, in one aspect,
a normal range of serum phosphorus is from 2.4 to 4.1 mg/dL. In
this aspect, aberrant serum phosphorus concentration may be
selected from either above or below the normal range. In another
example, in one aspect, a normal range of serum, or blood, sodium
is from 135 to 145 mEq/L. In this aspect, aberrant serum, or blood,
sodium concentration may be selected from either above or below the
normal range. In another example, in one aspect, a normal range of
serum, or blood, potassium is from 3.7 to 5.2 mEq/L. In this
aspect, aberrant serum, or blood, potassium concentration maybe
selected from either above or below the normal range. In a further
aspect, a normal range of serum bicarbonate is from 20 to 29 mEq/L.
In this aspect, aberrant serum, or blood, bicarbonate concentration
may be selected from either above or below the normal range. In a
different aspect, bicarbonate levels can be used to indicate normal
levels of acidity (pH), in the blood. The term "electrolyte
concentration" may also be used to define the condition of a
particular electrolyte in a tissue or body fluid other than blood
or plasma. In this case, the normal physiological condition is
considered to be the clinically normal range for that tissue or
fluid. In this aspect, aberrant tissue or fluid electrolyte
concentration may be selected from either above or below the normal
range.
[0072] The term "epitope" as used herein refers to an antigenic
determinant on an antigen, such as an enzyme polypeptide, to which
the paratope of an antibody, such as an enzyme-specific antibody,
binds. Antigenic determinants usually consist of chemically active
surface groupings of molecules, such as amino acids or sugar side
chains, and can have specific three-dimensional structural
characteristics, as well as specific charge characteristics. As
used herein "epitope" refers to that portion of an antigen or other
macromolecule capable of forming a binding interaction that
interacts with the variable region binding body of an antibody.
Typically, such binding interaction is manifested as an
intermolecular contact with one or more amino acid residues of a
CDR.
[0073] As used herein, the term "evolution", or "evolving", refers
to using one or more methods of mutagenesis to generate a novel
polynucleotide encoding a novel polypeptide, which novel
polypeptide is itself an improved biological molecule &/or
contributes to the generation of another improved biological
molecule. In a particular non-limiting aspect, the present
disclosure relates to evolution of conditionally active biologic
proteins from a parent wild type protein. In one aspect, for
example, evolution relates to a method of performing both
non-stochastic polynucleotide chimerization and non-stochastic
site-directed point mutagenesis disclosed in U.S. patent
application publication 2009/0130718. More particularly, the
present disclosure provides methods for evolution of conditionally
active biologic enzymes which exhibit reduced activity at normal
physiological conditions compared to a wild-type enzyme parent
molecule, but enhanced activity under one or more aberrant
conditions compared to the antigen specific targeting region of the
wild-type enzyme.
[0074] The terms "fragment", "derivative" and "analog" when
referring to a reference polypeptide include a polypeptide which
retains at least one biological function or activity that is at
least essentially same as that of the reference polypeptide.
Furthermore, the terms "fragment", "derivative" or "analog" are
exemplified by a "pro-form" molecule, such as a low activity
proprotein that can be modified by cleavage to produce a mature
enzyme with significantly higher activity.
[0075] The term "gene" as used herein means the segment of DNA
involved in producing a polypeptide chain; it includes regions
preceding and following the coding region (leader and trailer) as
well as intervening sequences (nitrons) between individual coding
segments (exons).
[0076] The term "heterologous" as used herein means that one
single-stranded nucleic acid sequence is unable to hybridize to
another single-stranded nucleic acid sequence or its complement.
Thus, areas of heterology mean that areas of polynucleotides or
polynucleotides have areas or regions within their sequence which
are unable to hybridize to another nucleic acid or polynucleotide.
Such regions or areas are for example areas of mutations.
[0077] The term "homologous" or "homeologous" as used herein means
that one single-stranded nucleic acid sequence may hybridize to a
complementary single-stranded nucleic acid sequence. The degree of
hybridization may depend on a number of factors including the
amount of identity between the sequences and the hybridization
conditions such as temperature and salt concentrations as discussed
later. Preferably the region of identity is greater than about 5
bp, more preferably the region of identity is greater than 10
bp.
[0078] The benefits of this disclosure extend to "industrial
applications" (or industrial processes), which term is used to
include applications in commercial industry proper (or simply
industry) as well as non-commercial industrial applications (e.g.
biomedical research at a non-profit institution). Relevant
applications include those in areas of diagnosis, medicine,
agriculture, manufacturing, and academia.
[0079] The term "immune cell" as used herein refers to cells of the
mammalian immune system including but not limited to antigen
presenting cells, B-cells, basophils, cytotoxic T cells, dendritic
cells, eosinophils, granulocytes, helper T cells, leukocytes,
lymphocytes, macrophages, mast cells, memory cells, monocytes,
natural killer cells, neutrophils, phagocytes, plasma cells and T
cells.
[0080] The term "immune response" as used herein refers to
immunities including but not limited to innate immunity, humoral
immunity, cellular immunity, immunity, inflammatory response,
acquired (adaptive) immunity, autoimmunity and/or overactive
immunity
[0081] The term "isolated" as used herein means that the material
is removed from its original environment (e.g., the natural
environment if it is naturally occurring). For example, a
naturally-occurring polynucleotide or enzyme present in a living
animal is not isolated, but the same polynucleotide or enzyme,
separated from some or all of the coexisting materials in the
natural system, is isolated. Such polynucleotides could be part of
a vector and/or such polynucleotides or enzymes could be part of a
composition, and still be isolated in that such vector or
composition is not part of its natural environment.
[0082] The term "isolated nucleic acid" as used herein to define a
nucleic acid, e.g., a DNA or RNA molecule, that is not immediately
contiguous with the 5' and 3' flanking sequences with which it
normally is immediately contiguous when present in the naturally
occurring genome of the organism from which it is derived. The term
thus describes, for example, a nucleic acid that is incorporated
into a vector, such as a plasmid or viral vector; a nucleic acid
that is incorporated into the genome of a heterologous cell (or the
genome of a homologous cell, but at a site different from that at
which it naturally occurs); and a nucleic acid that exists as a
separate molecule, e.g., a DNA fragment produced by PCR
amplification or restriction enzyme digestion, or an RNA molecule
produced by in vitro transcription. The term also describes a
recombinant nucleic acid that forms part of a hybrid gene encoding
additional polypeptide sequences that can be used, for example, in
the production of a fusion protein.
[0083] The term "lentivirus" as used herein refers to a genus of
the Retroviridae family Lentiviruses are unique among the
retroviruses in being able to infect non-dividing cells; they can
deliver a significant amount of genetic information into the DNA of
the host cell, so they are one of the most efficient ways to
deliver a gene delivery vector. HIV, SIV, and FIV are all examples
of lentiviruses. Vectors derived from lentiviruses offer the means
to achieve significant levels of gene transfer in vivo.
[0084] The term "ligand" as used herein refers to a molecule, such
as a random peptide or variable segment sequence that is recognized
by a particular receptor. As a person skilled in the art will
recognize, a molecule (or macromolecular complex) can be both a
receptor and a ligand. In general, the binding partner having a
smaller molecular weight is referred to as the ligand and the
binding partner having a greater molecular weight is referred to as
a receptor.
[0085] The term "ligation" as used herein refers to the process of
forming phosphodiester bonds between two double stranded nucleic
acid fragments (Sambrook et al., (1982). Molecular Cloning: A
Laboratory Manual. Cold Spring Harbour Laboratory, Cold Spring
Harbor, N.Y., p. 146; Sambrook et al., Molecular Cloning: a
laboratory manual, 2.sup.nd Ed., Cold Spring Harbor Laboratory
Press, 1989). Unless otherwise provided, ligation may be
accomplished using known buffers and conditions with 10 units of T4
DNA ligase ("ligase") per 0.5 micrograms of approximately equimolar
amounts of the DNA fragments to be ligated.
[0086] The terms "linker" or "spacer" as used herein refer to a
molecule or group of molecules that connects two molecules, such as
a DNA binding protein and a random peptide, and serves to place the
two molecules in a preferred configuration, e.g., so that the
random peptide can bind to a receptor with minimal steric hindrance
from the DNA binding protein. "Linker" (L) or "linker domain" or
"linker region" as used herein refers to an oligo- or polypeptide
region of from about 1 to 100 amino acids in length, which links
together any of the domains/regions of the CARs of the invention.
Linkers may be composed of flexible residues like glycine and
serine so that the adjacent protein domains are free to move
relative to one another. Longer linkers may be used when it is
desirable to ensure that two adjacent domains do not sterically
interfere with one another. Linkers may be cleavable or
non-cleavable. Examples of cleavable linkers include 2A linkers
(for example T2A), 2A-like linkers or functional equivalents
thereof and combinations thereof. In some embodiments, the linkers
include the picornaviral 2A-like linker, CHYSEL sequences of
porcine teschovirus (P2A), Thosea asigna virus (T2A) or
combinations, variants and functional equivalents thereof. Other
linkers will be apparent to those skilled in the art and may be
used in connection with alternate embodiments of the invention.
[0087] The term "mammalian cell surface display" as used herein
refers to a technique whereby a protein or antibody, or a portion
of an antibody, is expressed and displayed on a mammalian host cell
surface for screening purposes; for example, by screening for
specific antigen binding by a combination of magnetic beads and
fluorescence-activated cell sorting. In one aspect, mammalian
expression vectors are used for simultaneous expression of
immunoglobulins as both a secreted and cell surface bound form as
in DuBridge et al., US 2009/0136950. In another aspect, the
techniques are employed for screening a viral vector encoding for a
library of antibodies or antibody fragments that are displayed on
the cell membranes when expressed in a cell as in Gao et al., US
2007/0111260. Whole IgG surface display on mammalian cells is
known. For example, Akamatsuu et al. developed a mammalian cell
surface display vector, suitable for directly isolating IgG
molecules based on their antigen-binding affinity and biological
activity. Using an Epstein-Barr virus-derived episomal vector,
antibody libraries were displayed as whole IgG molecules on the
cell surface and screened for specific antigen binding by a
combination of magnetic beads and fluorescence-activated cell
sorting. Plasmids encoding antibodies with desired binding
characteristics were recovered from sorted cells and converted to a
form suitable for production of soluble IgG. See Akamatsuu et al.
J. Immunol. Methods, vol. 327, pages 40-52, 2007. Ho et al. used
human embryonic kidney 293T cells that are widely used for
transient protein expression for cell surface display of
single-chain Fv antibodies for affinity maturation. Cells
expressing a rare mutant antibody with higher affinity were
enriched 240-fold by a single-pass cell sorting from a large excess
of cells expressing WT antibody with a slightly lower affinity.
Furthermore, a highly enriched mutant was obtained with increased
binding affinity for CD22 after a single selection of a combinatory
library randomizing an intrinsic antibody hotspot. See Ho et al.,
"Isolation of anti-CD22 Fv with high affinity by Fv display on
human cells," Proc Natl Acad Sci USA, vol. 103, pages 9637-9642,
2006.
[0088] B cells specific for an antigen may also be used. Such B
cells may be directly isolated from peripheral blood mononuclear
cells (PBMC) of human donors. Recombinant, antigen-specific
single-chain Fv (scFv) libraries are generated from this pool of B
cells and screened by mammalian cell surface display by using a
Sindbis virus expression system. The variable regions (VRs) of the
heavy chains (HCs) and light chains (LCs) can be isolated from
positive clones and recombinant fully human antibodies produced as
whole IgG or Fab fragments. In this manner, several hypermutated
high-affinity antibodies binding the Q.beta. virus like particle
(VLP), a model viral antigen, as well as antibodies specific for
nicotine can be isolated. See Beerli et al., "Isolation of human
monoclonal antibodies by mammalian cell display," Proc Natl Acad
Sci USA, vol. 105, pages 14336-14341, 2008.
[0089] Yeast cell surface display may also be used in the present
invention, for example, see Kondo and Ueda, "Yeast cell-surface
display-applications of molecular display," Appl. Microbiol.
Biotechnol., vol. 64, pages 28-40, 2004, which describes for
example, a cell-surface engineering system using the yeast
Saccharomyces cerevisiae. Several representative display systems
for the expression in yeast S. cerevisiae are described in Lee et
al, "Microbial cell-surface display," TRENDS in Bitechnol., vol.
21, pages 45-52, 2003. Also Boder and Wittrup, "Yeast surface
display for screening combinatorial polypeptide libraries," Nature
Biotechnol., vol. 15, pages 553, 1997.
[0090] The term "manufacturing" as used herein refers to production
of a protein in a sufficient quantity to permit at least Phase I
clinical testing of a therapeutic protein, or sufficient quantity
for regulatory approval of a diagnostic protein.
[0091] As used herein, the term "microenvironment" means any
portion or region of a tissue or body that has a constant or
temporal, physical or chemical difference from other regions of the
tissue or other regions of the body.
[0092] As used herein, the term "molecular property to be evolved"
includes reference to molecules included of a polynucleotide
sequence, molecules included of a polypeptide sequence, and
molecules included in part of a polynucleotide sequence and in part
of a polypeptide sequence. Particularly relevant--but by no means
limiting--examples of molecular properties to be evolved include
protein activities at specified conditions, such as related to
temperature; salinity; osmotic pressure; pH; oxidative stress, and
concentration of glycerol, DMSO, detergent, and/or any other
molecular species with which contact is made in a reaction
environment. Additional particularly relevant--but by no means
limiting--examples of molecular properties to be evolved include
stabilities--e.g. the amount of a residual molecular property that
is present after a specified exposure time to a specified
environment, such as may be encountered during storage.
[0093] The term "mutations" as used herein means changes in the
sequence of a wild-type nucleic acid sequence or changes in the
sequence of a peptide. Such mutations may be point mutations such
as transitions or transversions. The mutations may be deletions,
insertions or duplications.
[0094] The term "multispecific antibody" as used herein is an
antibody having binding affinities for at least two different
epitopes. Multispecific antibodies can be prepared as full-length
antibodies or antibody fragments (e.g. F(ab').sub.2 bispecific
antibodies). Engineered antibodies may bind to two, three or more
(e.g. four) antigens (see, e.g., US 2002/0004587 A1). One
conditionally active antibody may be engineered to be
multispecific, or two antibodies may be engineered to include a
hetero-dimer that binds to two antigens. Multispecific antibodies
can also be multifunctional.
[0095] As used herein, the degenerate "N,N,G/T" nucleotide sequence
represents 32 possible triplets, where "N" can be A, C, G or T.
[0096] The term "naturally-occurring" as used herein as applied to
the object refers to the fact that an object can be found in
nature. For example, a polypeptide or polynucleotide sequence that
is present in an organism (including viruses) that can be isolated
from a source in nature and which has not been intentionally
modified by man in the laboratory is naturally occurring.
Generally, the term naturally occurring refers to an object as
present in a non-pathological (un-diseased) individual, such as
would be typical for the species.
[0097] As used herein, "normal physiological conditions", or "wild
type operating conditions", are those conditions of temperature,
pH, osmotic pressure, osmolality, oxidative stress and electrolyte
concentration which would be considered within a normal range at
the site of administration, or the site of action, in a
subject.
[0098] As used herein, the term "nucleic acid molecule" is included
of at least one base or one base pair, depending on whether it is
single-stranded or double-stranded, respectively. Furthermore, a
nucleic acid molecule may belong exclusively or chimerically to any
group of nucleotide-containing molecules, as exemplified by, but
not limited to, the following groups of nucleic acid molecules:
RNA, DNA, genomic nucleic acids, non-genomic nucleic acids,
naturally occurring and not naturally occurring nucleic acids, and
synthetic nucleic acids. This includes, by way of non-limiting
example, nucleic acids associated with any organelle, such as the
mitochondria, ribosomal RNA, and nucleic acid molecules included
chimerically of one or more components that are not naturally
occurring along with naturally occurring components.
[0099] Additionally, a "nucleic acid molecule" may contain in part
one or more non-nucleotide-based components as exemplified by, but
not limited to, amino acids and sugars. Thus, by way of example,
but not limitation, a ribozyme that is in part nucleotide-based and
in part protein-based is considered a "nucleic acid molecule".
[0100] The terms "nucleic acid sequence coding for" or a "DNA
coding sequence of or a "nucleotide sequence encoding" as used
herein refer to a DNA sequence which is transcribed and translated
into an enzyme when placed under the control of appropriate
regulatory sequences such as promoters. A "promotor" is a DNA
regulatory region capable of binding RNA polymerase in a cell and
initiating transcription of a downstream (3' direction) coding
sequence. The promoter is part of the DNA sequence. This sequence
region has a start codon at its 3' terminus. The promoter sequence
does include the minimum number of bases where elements necessary
to initiate transcription at levels detectable above background.
However, after the RNA polymerase binds the sequence and
transcription is initiated at the start codon (3' terminus with a
promoter), transcription proceeds downstream in the 3' direction.
Within the promotor sequence will be found a transcription
initiation site (conveniently defined by mapping with nuclease S1)
as well as protein binding domains (consensus sequences)
responsible for the binding of RNA polymerase.
[0101] The term "oligonucleotide" (or synonymously an "oligo")
refers to either a single stranded polydeoxynucleotide or two
complementary polydeoxynucleotide strands which may be chemically
synthesized. Such synthetic oligonucleotides may or may not have a
5' phosphate. Those that do not will not ligate to another
oligonucleotide without adding a phosphate with an ATP in the
presence of a kinase. A synthetic oligonucleotide will ligate to a
fragment that has not been dephosphorylated.
[0102] As used herein, the term "operably linked" refers to a
linkage of polynucleotide elements in a functional relationship. A
nucleic acid is "operably linked" when it is placed into a
functional relationship with another nucleic acid sequence. For
instance, a promoter or enhancer is operably linked to a coding
sequence if it affects the transcription of the coding sequence.
Operably linked means that the DNA sequences being linked are
typically contiguous and, where necessary to join two protein
coding regions, contiguous and in reading frame.
[0103] A coding sequence is "operably linked to" another coding
sequence when RNA polymerase will transcribe the two coding
sequences into a single mRNA, which is then translated into a
single polypeptide having amino acids derived from both coding
sequences. The coding sequences need not be contiguous to one
another so long as the expressed sequences are ultimately processed
to produce the desired protein.
[0104] As used herein the term "parental polynucleotide set" is a
set included of one or more distinct polynucleotide species.
Usually this term is used in reference to a progeny polynucleotide
set which is preferably obtained by mutagenization of the parental
set, in which case the terms "parental", "starting" and "template"
are used interchangeably.
[0105] The term "patient", or "subject", refers to an animal, for
example a mammal, such as a human, who is the object of treatment.
The subject, or patient, may be either male or female.
[0106] As used herein the term "physiological conditions" refers to
temperature, pH, osmotic pressure, ionic strength, viscosity, and
like biochemical parameters which are compatible with a viable
organism, and/or which typically exist intracellularly in a viable
cultured yeast cell or mammalian cell. For example, the
intracellular conditions in a yeast cell grown under typical
laboratory culture conditions are physiological conditions.
Suitable in vitro reaction conditions for in vitro transcription
cocktails are generally physiological conditions. In general, in
vitro physiological conditions include 50-200 mM NaCl or KCl, pH
6.5-8.5, 20-45 degrees C. and 0.001-10 mM divalent cation (e.g.,
Mg.sup.++'', Ca.sup.++); preferably about 150 mM NaCl or KCl, pH
7.2-7.6, 5 mM divalent cation, and often include 0.01-1.0 percent
nonspecific protein (e.g., bovine serum albumin (BSA)). A non-ionic
detergent (Tween, NP-40, Triton X-100) can often be present,
usually at about 0.001 to 2%, typically 0.05-0.2% (v/v). Particular
aqueous conditions may be selected by the practitioner according to
conventional methods. For general guidance, the following buffered
aqueous conditions may be applicable: 10-250 mM NaCl, 5-50 mM Tris
HCl, pH 5-8, with optional addition of divalent cation(s) and/or
metal chelators and/or non-ionic detergents and/or membrane
fractions and/or anti-foam agents and/or scintillants. Normal
physiological conditions refer to conditions of temperature, pH,
osmotic pressure, osmolality, oxidative stress and electrolyte
concentration in vivo in a patient or subject at the site of
administration, or the site of action, which would be considered
within the normal range in a patient.
[0107] Standard convention (5' to 3') is used herein to describe
the sequence of double stranded polynucleotides.
[0108] The term "population" as used herein means a collection of
components such as polynucleotides, portions or polynucleotides or
proteins. A "mixed population" means a collection of components
which belong to the same family of nucleic acids or proteins (i.e.,
are related) but which differ in their sequence (i.e., are not
identical) and hence in their biological activity.
[0109] A molecule having a "pro-form" refers to a molecule that
undergoes any combination of one or more covalent and noncovalent
chemical modifications (e.g. glycosylation, proteolytic cleavage,
dimerization or oligomerization, temperature--induced or pH-induced
conformational change, association with a co-factor, etc.) en route
to attain a more mature molecular form having a property difference
(e.g. an increase in activity) in comparison with the reference
pro-form molecule. When two or more chemical modifications (e.g.
two proteolytic cleavages, or a proteolytic cleavage and a
deglycosylation) can be distinguished en route to the production of
a mature molecule, the reference precursor molecule may be termed a
"pre-pro-form" molecule.
[0110] As used herein, the term "receptor" refers to a molecule
that has an affinity for a given ligand. Receptors can be naturally
occurring or synthetic molecules. Receptors can be employed in an
unaltered state or as aggregates with other species. Receptors can
be attached, covalently or non-covalently, to a binding member,
either directly or via a specific binding substance. Examples of
receptors include, but are not limited to, antibodies, including
monoclonal antibodies and antisera reactive with specific antigenic
determinants (such as on viruses, cells, or other materials), cell
membrane receptors, complex carbohydrates and glycoproteins,
enzymes, and hormone receptors.
[0111] The term "reductive reassortment", as used herein, refers to
the increase in molecular diversity that is accrued through
deletion (and/or insertion) events that are mediated by repeated
sequences.
[0112] The term "restriction site" as used herein refers to a
recognition sequence that is necessary for the manifestation of the
action of a restriction enzyme, and includes a site of catalytic
cleavage. It is appreciated that a site of cleavage may or may not
be contained within a portion of a restriction site that includes a
low ambiguity sequence (i.e. a sequence containing the principal
determinant of the frequency of occurrence of the restriction
site). When an enzyme (e.g. a restriction enzyme) is said to
"cleave" a polynucleotide, it is understood to mean that the
restriction enzyme catalyzes or facilitates a cleavage of a
polynucleotide.
[0113] As used herein, the term "single-chain antibody" refers to a
polypeptide including a VH domain and a VL domain in polypeptide
linkage, generally liked via a spacer peptide, and which may
include additional amino acid sequences at the amino- and/or
carboxy-termini. For example, a single-chain antibody may include a
tether segment for linking to the encoding polynucleotide. As an
example a scFv is a single-chain antibody. Single-chain antibodies
are generally proteins consisting of one or more polypeptide
segments of at least 10 contiguous amino substantially encoded by
genes of the immunoglobulin superfamily (e.g, see The
Immunoglobulin Gene Superfamily, A. F. Williams and A. N. Barclay,
in Immunoglobulin Genes, T. Honjo, F. W. Alt, and THE. Rabbits,
eds., (1989) Academic press: San Diego, Calif., pp. 361-368, most
frequently encoded by a rodent, non-human primate, avian, porcine
bovine, ovine, goat, or human heavy chain or light chain gene
sequence. A functional single-chain antibody generally contains a
sufficient portion of an immunoglobulin superfamily gene product so
as to retain the property of binding to a specific target molecule,
typically a receptor or antigen (epitope).
[0114] The members of a pair of molecules (e.g., an
antibody-antigen pair and ligand-receptor pair) are said to
"specifically bind" to each other if they bind to each other with
greater affinity than to other, non-specific molecules. For
example, an antibody raised against an antigen to which it binds
more efficiently than to a non-specific protein can be described as
specifically binding to the antigen.
[0115] The term "stimulation" as used herein means a primary
response induced by binding of a stimulatory molecule (e.g., a
TCR/CD3 complex) with its cognate ligand thereby mediating a signal
transduction event, such as, but not limited to, signal
transduction via the TCR/CD3 complex. Stimulation can mediate
altered expression of certain molecules, such as downregulation of
TGF-.beta., and/or reorganization of cytoskeletal structures, and
the like.
[0116] The term "stimulatory molecule" as used herein means a
molecule on a T cell that specifically binds with a cognate
stimulatory ligand present on an antigen presenting cell.
[0117] The term "stimulatory ligand" as used herein means a ligand
that when present on an antigen presenting cell (e.g, a dendritic
cell, a B-cell, and the like) can specifically bind with a cognate
binding partner (referred to herein as a "stimulatory molecule") on
a T cell, thereby mediating a primary response by the T cell,
including, but not limited to, activation, initiation of an immune
response, proliferation, and the like. Stimulatory ligands are
well-known in the art and encompass, inter alia, an MHC Class I
molecule loaded with a peptide, an anti-CD3 antibody, a
superagonist anti-CD28 antibody, and a superagonist anti-CD2
antibody.
[0118] The term "target cell" as used herein refers to cells which
are involved in a disease and can be targeted by the genetically
modified cytotoxic cells of the invention (including but not
limited to genetically modified T cells, NK cells, and
macrophages). Other target cells will be apparent to those skilled
in the art and may be used in connection with alternate embodiments
of the invention.
[0119] The terms "T cell" and "T-lymphocyte" are interchangeable
and used synonymously herein. Examples include, but are not limited
to, naive T cells, central memory T cells, effector memory T cells
and combinations thereof.
[0120] The term "transduction" as used herein refers to the
introduction of a foreign nucleic acid into a cell using a viral
vector. "Transfection" as used herein refers to the introduction of
a foreign nucleic acid into a cell using recombinant DNA
technology. The term "transformation" means the introduction of a
"foreign" (i.e. extrinsic or extracellular) gene, DNA or RNA
sequence to a host cell, so that the host cell will express the
introduced gene or sequence to produce a desired substance, such as
a protein or enzyme coded by the introduced gene or sequence. The
introduced gene or sequence may also be called a "cloned" or
"foreign" gene or sequence, may include regulatory or control
sequences, such as start, stop, promoter, signal, secretion, or
other sequences used by a cell's genetic machinery. The gene or
sequence may include nonfunctional sequences or sequences with no
known function. A host cell that receives and expresses introduced
DNA or RNA has been "transformed" and is a "transformant" or a
"clone." The DNA or RNA introduced to a host cell can come from any
source, including cells of the same genus or species as the host
cell, or cells of a different genus or species
[0121] The term "treating" includes: (1) preventing or delaying the
appearance of clinical symptoms of the state, disorder or condition
developing in an animal that may be afflicted with or predisposed
to the state, disorder or condition but does not yet experience or
display clinical or subclinical symptoms of the state, disorder or
condition; (2) inhibiting the state, disorder or condition (i.e.,
arresting, reducing or delaying the development of the disease, or
a relapse thereof in case of maintenance treatment, of at least one
clinical or subclinical symptom thereof); and/or (3) relieving the
condition (i.e., causing regression of the state, disorder or
condition or at least one of its clinical or subclinical symptoms).
The benefit to a patient to be treated is either statistically
significant or at least perceptible to the patient or to the
physician.
[0122] "Tumor," as used herein refers to all neoplastic cell growth
and proliferation, whether malignant or benign, and all
pre-cancerous and cancerous cells and tissues
[0123] As used herein, the term "tumor microenvironment" refers to
any and all elements of the tumor milieu including elements that
create a structural and or functional environment for the malignant
process to survive and/or expand and/or spread.
[0124] As used herein, the term "variable segment" refers to a
portion of a nascent peptide which includes a random, pseudorandom,
or defined kernal sequence. A "variable segment" refers to a
portion of a nascent peptide which includes a random pseudorandom,
or defined kernal sequence. A variable segment can include both
variant and invariant residue positions, and the degree of residue
variation at a variant residue position may be limited: both
options are selected at the discretion of the practitioner.
Typically, variable segments are about 5 to 20 amino acid residues
in length (e.g., 8 to 10), although variable segments may be longer
and may include antibody portions or receptor proteins, such as an
antibody fragment, a nucleic acid binding protein, a receptor
protein, and the like.
[0125] "Vector", "cloning vector" and "expression vector" as used
herein refer to the vehicle by which a polynucleotide sequence
(e.g. a foreign gene) can be introduced into a host cell, so as to
transform the host and promote expression (e.g. transcription and
translation) of the introduced sequence. Vectors include plasmids,
phages, viruses, etc.
[0126] As used herein, the term "wild-type" means that the
polynucleotide does not include any mutations. A "wild type
protein", "wild-type protein", "wild-type biologic protein", or
"wild type biologic protein", refers to a protein which can be
isolated from nature that will be active at a level of activity
found in nature and will include the amino acid sequence found in
nature. The terms "parent molecule" and "target protein" also refer
to the wild-type protein. The "wild-type protein" preferably has
some desired properties, such as higher binding affinity, or
enzymatic activity, which may be obtained by screening of a library
of proteins for a desired properties, including better stability in
different temperature or pH environments, or improved selectivity
and/or solubility.
[0127] The term "working", as in "working sample", for example, is
simply a sample with which one is working. Likewise, a "working
molecule", for example is a molecule with which one is working.
DETAILED DESCRIPTION
[0128] For illustrative purposes, the principles of the present
invention are described by referencing various exemplary
embodiments. Although certain embodiments of the invention are
specifically described herein, one of ordinary skill in the art
will readily recognize that the same principles are equally
applicable to, and can be employed in other systems and methods.
Before explaining the disclosed embodiments of the present
invention in detail, it is to be understood that the invention is
not limited in its application to the details of any particular
embodiment shown. Additionally, the terminology used herein is for
the purpose of description and not of limitation. Furthermore,
although certain methods are described with reference to steps that
are presented herein in a certain order, in many instances, these
steps may be performed in any order as may be appreciated by one
skilled in the art; the novel method is therefore not limited to
the particular arrangement of steps disclosed herein.
[0129] It must be noted that as used herein and in the appended
claims, the singular forms "a", "an", and "the" include plural
references unless the context clearly dictates otherwise.
Furthermore, the terms "a" (or "an"), "one or more" and "at least
one" can be used interchangeably herein. The terms "comprising",
"including", "having" and "constructed from" can also be used
interchangeably.
[0130] The present disclosure is directed to a chimeric antigen
receptor (CAR) for binding with a target antigen, comprising at
least one antigen specific targeting region evolved from a
wild-type protein or a domain thereof and having at least one of:
(a) a decrease in activity in the assay at the normal physiological
condition compared to the antigen specific targeting region of the
wild-type protein or a domain thereof, and (b) an increase in
activity in the assay under the aberrant condition compared to the
antigen specific targeting region of the wild-type protein or a
domain thereof; a transmembrane domain; and an intracellular
signaling domain. In some embodiments, the chimeric antigen
receptor further includes an extracellular spacer domain or at
least one co-stimulatory domain.
[0131] The CARs of the present invention have at least one of (1)
their affinity to the target antigen reversibly or irreversibly
reduced at the normal physiological condition, and (2) an increased
affinity, in comparison with the same CAR without the conditionally
active antigen specific targeting region. These CARs can direct
cytotoxic cells to a disease site where an aberrant condition is
present, such as a tumor microenvironment or synovial fluid. As a
result of these properties, the CARs can preferentially direct the
cytotoxic cells to a disease site while because of their low
affinity for normal tissue. Such CARs can dramatically reduce
side-effects and allow higher doses of therapeutics to be used to
increase therapeutic efficacy. The CARs are particularly valuable
for development of novel therapeutics that are required for short
or limited periods of time within a subject. Examples of beneficial
applications include systemic treatments at high dosages, as well
as localized treatments at high concentrations.
[0132] The chimeric antigen receptor may include an antigen
specific targeting region that has a decrease in a binding affinity
to the target antigen at a normal physiological condition compared
to the antigen specific targeting region of the wild-type protein
or the domain thereof.
[0133] The chimeric antigen receptor many include an antigen
specific targeting region that has an increase in activity in the
assay under the aberrant condition compared to the antigen specific
targeting region of the wild-type protein or a domain thereof and a
decrease in a binding affinity to the target antigen at a normal
physiological condition compared to the antigen specific targeting
region of the wild-type protein or the domain thereof.
[0134] In any of the foregoing chimeric antigen receptors the
antigen specific targeting region may also have an increase in
selectivity in the assay under the aberrant condition compared to
the antigen specific targeting region of the wild-type protein or a
domain thereof.
[0135] The CAR molecule includes a linker to connect the two
antigen specific targeting regions (FIG. 1). The linker orients the
two antigen specific targeting regions in such a way that the two
antigen specific targeting regions on the CAR-T cells exhibit
improved or optimal activity in binding to the target antigen
(Jensen et al., "Design and implementation of adoptive therapy with
chimeric antigen receptor-modified T cells," Immunol Rev., vol.
257, pp. 127-144, 2014). The linker is thus preferably capable of
adopting a specific conformation which enables improved or optimal
binding of the two antigen specific targeting regions to the target
antigen, thereby increasing the effectiveness of the CAR-T
cells.
[0136] In some embodiments, the linker may be Gly-Ser tandem
repeats in a length of 18-25 amino acids (Grada, "TanCAR: A Novel
Bispecific Chimeric Antigen Receptor for Cancer Immunotherapy,"
Molecular Therapy Nucleic Acids, vol. 2, e105, 2013). This flexible
linker is capable of adopting many different conformations for
improved or optimal presentation of two antigen specific targeting
regions for binding to the target antigen.
[0137] In some embodiments, the linker is capable of adopting
different conformations at a normal physiological condition and an
aberrant condition. Particularly, the linker has a first
conformation at the aberrant condition which is improved or optimal
for presentation of two antigen specific targeting regions for
binding to the target antigen, while the same linker has a second
conformation at the normal physiological condition which is less
effective for presentation of two antigen specific targeting
regions for binding to the target antigen than the first
conformation of the linker under the aberrant condition. Such a
linker may be called a "conditional linker" that allows the two
antigen specific targeting regions to bind to the target antigen at
a higher binding activity at an aberrant condition than at a normal
physiological condition. Therefore, CAR-T cells including such a
conditional linker are more active at an aberrant condition than
the same CAR-T cells at a normal physiological condition.
[0138] Proteins that change conformation at different pH have been
described previously, for example, in Di Russo et al.
("pH-Dependent conformational changes in proteins and their effect
on experimental pK(a)s: the case of Nitrophorin 4," PLoS Comput
Biol., vol. 8, e1002761, 2012). Further, proteins with different
conformations at different temperatures have been described in
Caldwell, "Temperature-induced protein conformational changes in
barley root plasma membrane-enriched microsomes," Plant Physiol.,
vol. 84, pp. 924-929, 1989. The conformation of antibodies being
influenced by pH and/or temperature has been discussed in Gandhi,
"Effect of pH and temperature on conformational changes of a
humanized monoclonal antibody," Master's thesis from University of
Rhode Island, U.S.
[0139] It is within the scope of the present invention to select a
conditional linker to be used in the CAR molecule. The conditional
linker can adopt a first conformation at an aberrant condition,
which is improved or optimal for presenting the two antigen
specific targeting regions for binding to the target antigen, and
adopt a second conformation at a normal physiological condition,
which is suboptimal for presenting the two antigen specific
targeting regions for binding to the target antigen. In some
embodiments, the suboptimal conformation of the linker at the
normal physiological condition produces a CAR molecule having a
binding activity to the target antigen that is less than about 90%,
or about 80%, or about 70%, or about 60%, or about 50%, or about
40%, or about 30%, or about 20%, or about 10%, or about 5% of the
binding activity of the CAR molecule with the improved or optimal
conformation of the linker at the aberrant condition.
[0140] The conditional linker may be generated from a starting
linker selected from 2A linkers, 2A-like linkers, picornaviral
2A-like linkers, a 2A peptide of porcine teschovirus (P2A), and a
2A peptide of those a asigna virus (T2A), as well as variants and
functional equivalents thereof. The starting linker is evolved to
produce mutant proteins; the mutant proteins are then subjected to
an assay at a normal physiological condition and an assay at an
aberrant condition. Proteins having a conditional linker are
selected from the mutant proteins on the basis that the selected
proteins exhibit (a) a conditional linker having a first
conformation at the aberrant condition, which is improved or
optimal for presenting the two antigen specific targeting regions
for binding to the target antigen, and (b) a second conformation of
the conditional linker at the normal physiological condition, which
is suboptimal for presenting the two antigen specific targeting
regions for binding to the target antigen.
[0141] The CAR molecule also includes an extracellular spacer
domain that connects the two antigen specific targeting regions
with the transmembrane domain, which, in turn, connects to the
co-stimulatory domain and the intracellular signaling domain inside
of the T cells (FIG. 1). The extracellular spacer domain is
preferably capable of supporting the antigen specific targeting
regions to recognize and bind to the target antigen on the target
cells (Hudecek et al., "The non-signaling extracellular spacer
domain of chimeric antigen receptors is decisive for in vivo
antitumor activity," Cancer Immunol Res., vol. 3, pp. 125-135,
2015). In some embodiments, the extracellular spacer domain is a
flexible domain, thus allowing the antigen specific targeting
regions to have a structure to optimally recognize the specific
structure and density of the target antigens on a cell such as
tumor cell (Hudecek et al., "The non-signaling extracellular spacer
domain of chimeric antigen receptors is decisive for in vivo
antitumor activity," Cancer Immunol Res., vol. 3, pp. 125-135,
2015). The flexibility of the extracellular spacer domain permits
the extracellular spacer domain to adopt many different
conformations.
[0142] In some embodiments, the extracellular spacer domain is
capable of adopting different conformations at a normal
physiological condition and an aberrant condition. Particularly,
the extracellular spacer domain has a first conformation at the
aberrant condition which is improved or optimal for presentation of
two antigen specific targeting regions for binding to the target
antigen, while the same extracellular spacer domain has a second
conformation at the normal physiological condition which is
suboptimal for presentation of two antigen specific targeting
regions for binding to the target antigen. Such an extracellular
spacer domain may be called a "conditional extracellular spacer
domain" since it enables the two antigen specific targeting regions
to bind to the target antigen at a higher binding activity at the
aberrant condition than at the normal physiological condition.
Therefore, with the conditional extracellular spacer domain, CAR-T
cells may be more active at the aberrant condition than the same
CAR-T cells at the normal physiological condition.
[0143] It is within the scope of the present invention to select a
conditional extracellular spacer domain to be used in the CAR
molecule. In some embodiments, the suboptimal conformation of the
extracellular spacer domain at the normal physiological condition
produces a CAR molecule having a binding activity to the target
antigen that is less than about 90%, or about 80%, or about 70%, or
about 60%, or about 50%, or about 40%, or about 30%, or about 20%,
or about 10%, or about 5% of the CAR molecule with the optimal
conformation for the same extracellular spacer domain at the
aberrant condition.
[0144] It has been discovered that the ubiquitylation-resistant
form for the region including the extracellular spacer domain and
the transmembrane domain can enhance CAR-T cell signaling and thus
augment antitumor activity (Kunii et la, "Enhanced function of
redirected human t cells expressing linker for activation of t
cells that is resistant to ubiquitylation," Human Gene Therapy,
vol. 24, pp. 27-37, 2013). Within this region, the extracellular
spacer domain is outside of the CAR-T cells, and thus is exposed to
different conditions and can potentially be made conditionally
ubiquitylation-resistant.
[0145] It is within the scope of the present invention that the
extracellular spacer domain is conditionally
ubiquitylation-resistant. Particularly, the extracellular spacer
domain of the CAR molecule is more ubiquitylation-resistant at an
aberrant condition than at a normal physiological condition.
Therefore, the CAR-T cells having the conditionally
ubiquitylation-resistant extracellular spacer domain will have
enhanced cytotoxicity at the aberrant condition, relative to their
cytotoxicity at the normal physiological condition.
[0146] The conditionally ubiquitylation-resistant extracellular
spacer domain may be selected to be more ubiquitylation-resistant
at an aberrant pH or aberrant temperature, and less
ubiquitylation-resistant at a normal physiological pH or normal
physiological temperature. In one embodiment, the conditionally
ubiquitylation-resistant extracellular spacer domain is more
ubiquitylation-resistant at a pH of a tumor microenvironment, and
less ubiquitylation-resistant at a normal physiological pH, such as
the pH in human blood plasma at pH 7.2-7.6.
[0147] To produce a conditional extracellular spacer domain, a
starting protein fragment selected from an Fc fragment of an
antibody, a hinge region of an antibody, a CH2 region of an
antibody, and a CH3 region of an antibody, is evolved to produce
mutant proteins. The mutant proteins are subjected to an assay at a
normal physiological condition and an assay at an aberrant
condition. The conditional extracellular spacer domain is selected
from the mutant proteins that exhibit (a) a conditional
extracellular spacer domain that has a first conformation at the
aberrant condition for the antigen specific targeting region to
bind to the target antigen at a higher binding activity and a
second conformation of the conditional extracellular binding domain
at the normal physiological condition for the antigen specific
targeting region to bind to the target antigen at a lower binding
activity than at the aberrant condition, or proteins that are (b)
more ubiquitylation-resistant at the aberrant condition than at the
normal physiological condition.
[0148] Any of the foregoing chimeric antigen receptors may be
configured such that a protein containing the antigen receptor has
an increase in expression level compared to the wild-type protein
or a domain thereof.
[0149] In an alternative embodiment, the present invention provides
a chimeric antigen receptor (CAR) for binding with a target
antigen, including at least one antigen specific targeting region
evolved from a wild-type protein or a domain thereof and having an
increase in selectivity in the assay under the aberrant condition
compared to the antigen specific targeting region of the wild-type
protein or a domain thereof; a transmembrane domain; and an
intracellular signaling domain. In some embodiments, the chimeric
antigen receptor further includes an extracellular spacer domain or
at least one co-stimulatory domain.
[0150] The present disclosure is also directed to methods of
evolving a wild-type protein or a domain thereof to generate a
conditionally active protein that has at least one of: (a) a
decrease in activity in the assay at the normal physiological
condition compared to the antigen specific targeting region of the
wild-type protein or a domain thereof, and (b) an increase in
activity in the assay under the aberrant condition compared to the
antigen specific targeting region of the wild-type protein or a
domain thereof. The conditionally active protein may be engineered
into a CAR.
[0151] The chimeric antigen receptor produced by the method may
include an antigen specific targeting region that has a decrease in
a binding affinity to the target antigen at a normal physiological
condition compared to the antigen specific targeting region of the
wild-type protein or the domain thereof.
[0152] The chimeric antigen receptor produced by the method may
include an antigen specific targeting region that has an increase
in activity in the assay under the aberrant condition compared to
the antigen specific targeting region of the wild-type protein or a
domain thereof and a decrease in a binding affinity to the target
antigen at a normal physiological condition compared to the antigen
specific targeting region of the wild-type protein or the domain
thereof.
[0153] In any of the foregoing chimeric antigen receptors produced
by the method the antigen specific targeting region may also have
an increase in selectivity in the assay under the aberrant
condition compared to the antigen specific targeting region of the
wild-type protein or a domain thereof.
[0154] Any of the foregoing chimeric antigen receptors produced by
the method may be configured such that a protein containing the
antigen receptor has an increase in expression level compared to
the wild-type protein or a domain thereof.
[0155] In an alternative embodiment of the method, the chimeric
antigen receptor (CAR) produced by the method for binding with a
target antigen, includes at least one antigen specific targeting
region evolved from a wild-type protein or a domain thereof and
having an increase in selectivity in the assay under the aberrant
condition compared to the antigen specific targeting region of the
wild-type protein or a domain thereof; a transmembrane domain; and
an intracellular signaling domain. In some embodiments, the
chimeric antigen receptor further includes an extracellular spacer
domain or at least one co-stimulatory domain.
Chimeric Antigen Receptors
[0156] The immune system of mammals, especially humans, has
cytotoxic cells for targeting and destroying diseased tissue and/or
pathogens. Using these cytotoxic cells to remove unwanted tissue
(i.e. target tissue) such as tumors is a promising therapeutic
approach. Other tissues that may be targeted for removal include
glandular (e.g. prostate) hyperplasia, warts, and unwanted fatty
tissue. However, this relatively new therapeutic approach has
achieved only limited success so far. For example, using T cells to
target and destroy tumors has relatively low long term benefits
because the cancer cells may adapted to the new therapy by reducing
expression of surface antigens to reduce the effectiveness of this
therapy. Cancer cells can even dedifferentiate to evade detection
in response to tumor-specific T cells. See Maher, "Immunotherapy of
Malignant Disease Using Chimeric Antigen Receptor Engrafted T
Cells," ISRN Oncology, vol. 2012, article ID 278093, 2012.
[0157] Cytotoxic cells expressing chimeric antigen receptors can
significantly improve the specificity and sensitivity of these
cytotoxic cells. For example, T cells expressing a CAR (CAR-T
cells) are capable of using the CAR to direct the T cells to target
tumor cells expressing a cell surface antigen that specifically
binds to the CAR. Such CAR-T cells can deliver the cytotoxic agent
more selectively to the tumor cells. CAR-T cells can directly
recognize a target molecule and thus are typically not restricted
by polymorphic presenting elements such as human leukocyte antigens
(HLAs). Advantages of this CAR targeting strategy are threefold.
First, since the CAR-T cell function is not dependent upon HLA
status, the same CAR-based approach can in principle be used in all
patients with tumors that express the same target surface antigen.
Second, corruption of antigen processing and presenting machinery
is a common attribute of tumor cells and may facilitate immune
escape. However, this affords no protection against CAR-T cells.
Third, a range of macromolecules can be targeted using this system,
including proteins, carbohydrates, and glycolipids.
[0158] A chimeric antigen receptor of the present invention is a
chimeric artificial protein including at least one antigen specific
targeting region (ASTR), a transmembrane domain (TM), and an
intracellular signaling domain (ISD). In some embodiments, the CAR
may further include an extracellular spacer domain (ESD) and/or a
co-stimulatory domain (CSD). See FIG. 1.
[0159] The ASTR is an extracellular region of the CAR for binding
to a specific target antigen including proteins, carbohydrates, and
glycolipids. In some embodiments, the ASTR includes an antibody,
especially a single-chain antibody, or a fragment thereof. The ASTR
may include a full length heavy chain, an Fab fragment, a single
chain Fv (scFv) fragment, a divalent single chain antibody or a
diabody, each of which are specific to the target antigen.
[0160] The ASTR may also include another protein functional domain
to recognize and bind to the target antigen. Because the target
antigen may have other biological functions, such as acting as a
receptor or a ligand, the ASTR may alternatively include a
functional domain for specifically binding with the antigen. Some
examples of proteins with functional domains include linked
cytokines (which leads to recognition of cells bearing the cytokine
receptor), affibodies, ligand binding domains from naturally
occurring receptors, soluble protein/peptide ligands for a
receptor, for example on a tumor cell. In fact, almost any molecule
that is capable of binding to a given antigen with high affinity
can be used in the ASTR, as will be appreciated by those skilled in
the art.
[0161] In one embodiment, the CAR of the invention includes at
least two ASTRs which target at least two different antigens or two
epitopes on the same antigen. In an embodiment, the CAR includes
three or more ASTRs which target at least three or more different
antigens or epitopes. When a plurality of ASTRs is present in the
CAR, the ASTRs may be arranged in tandem and may be separated by
linker peptides (FIG. 1).
[0162] In one embodiment, the ASTR includes a full-length IgG heavy
chain that is specific for the target antigen and having the
V.sub.H, CH1, hinge, and the CH2 and CH3 (Fc) Ig domains, if the
V.sub.H domain alone is sufficient to confer antigen-specificity
("single-domain antibodies"). If both, the V.sub.H and the V.sub.L
domains are necessary to generate a fully active ASTR, the
V.sub.H-containing CAR and the full-length lambda light chain (IgL)
are both introduced into the same cytotoxic cell to generate an
active ASTR. In another embodiment, each ASTR of the CAR includes
at least two single chain antibody variable fragments (scFv), each
specific for a different target antigen. scFvs, in which the
C-terminus of one variable domain (V.sub.H or V.sub.L) is tethered
to the N-terminus of the other variable domain (V.sub.L or V.sub.H,
respectively) via a polypeptide linker, have been developed without
significantly disrupting antigen binding or specificity of the
binding (Chaudhary et al., "A recombinant single-chain immunotoxin
composed of anti-Tac variable regions and a truncated diphtheria
toxin," Proc. Natl. Acad. Sci., vol. 87, page 9491, 1990; Bedzyk et
al., "Immunological and structural characterization of a high
affinity anti-fluorescein single-chain antibody," J. Biol. Chem.,
vol. 265, page 18615, 1990). These scFvs lack the constant regions
(Fc) present in the heavy and light chains of a native antibody.
The scFvs, specific for at least two different antigens, are
arranged in tandem. In an embodiment, an extracelluar spacer domain
may be linked between the ASTR and the transmembrane domain.
[0163] In another embodiment, an scFv fragment may be fused to all
or a portion of the constant domains of the heavy chain. In a
further embodiment, an ASTR of the CAR includes a divalent (or
bivalent) single-chain variable fragment (di-scFvs, bi-scFvs). In
CARs including di-scFVs, two scFvs each specific for an antigen are
linked together to form a single peptide chain with two V.sub.H and
two V.sub.L regions (Xiong et al., "Development of tumor targeting
anti-MUC-1 multimer: effects of di-scFv unpaired cysteine location
on PEGylation and tumor binding," Protein Engineering Design and
Selection, vol. 19, pages 359-367, 2006; Kufer et al., "A revival
of bispecific antibodies," Trends in Biotechnology, vol. 22, pages
238-244, 2004).
[0164] In yet another embodiment, an ASTR includes a diabody. In a
diabody, the scFvs are created with linker peptides that are too
short for the two variable regions to fold together, driving the
scFvs to dimerize. Still shorter linkers (one or two amino acids)
lead to the formation of trimers, the so-called triabodies or
tribodies. Tetrabodies may also be used in the ASTR.
[0165] When two or more ASTRs are present in a CAR, the ASTRs are
connected to each other covalently on a single polypeptide chain,
through an oligo-or polypeptide linker, an Fc hinge or a membrane
hinge region.
[0166] The antigens targeted by the CAR are present on the surface
or inside of cells in a tissue that targeted for removal, such as
tumors, glandular (e.g. prostate) hyperplasia, warts, and unwanted
fatty tissue. While the surface antigens are more efficiently
recognized and bound by the ASTR of CARs, intracellular antigens
may also be targeted by the CARs. In some embodiments, the target
antigens are preferably specific for cancer, inflammatory disease,
neuronal-disorders, diabetes, cardiovascular disease, or infectious
diseases. Examples of target antigens include antigens expressed by
various immune cells, carcinomas, sarcomas, lymphomas, leukemia,
germ cell tumors, blastomas, and cells associated with various
hematologic diseases, autoimmune diseases, and/or inflammatory
diseases.
[0167] Antigens specific for cancer which may be targeted by the
ASTR include one or more of 4-IBB, 5T4, adenocarcinoma antigen,
alpha-fetoprotein, BAFF, B-lymphoma cell, C242 antigen, CA-125,
carbonic anhydrase 9 (CA-IX), C-MET, CCR4, CD152, CD19, CD20,
CD200, CD22, CD221, CD23 (IgE receptor), CD28, CD30 (TNFRSF8),
CD33, CD4, CD40, CD44 v6, CD51, CD52, CD56, CD74, CD80, CEA,
CNT0888, CTLA-4, DRS, EGFR, EpCAM, CD3, FAP, fibronectin extra
domain-B, folate receptor 1, GD2, GD3 ganglioside, glycoprotein 75,
GPNMB, HER2/neu, HGF, human scatter factor receptor kinase, IGF-1
receptor, IGF-I, IgG1, LI-CAM, IL-13, IL-6, insulin-like growth
factor I receptor, integrin .alpha.5.beta.1, integrin
.alpha..nu..beta.3, MORAb-009, MS4A1, MUC1, mucin CanAg,
N-glycolylneuraminic acid, NPC-1C, PDGF-R a, PDL192,
phosphatidylserine, prostatic carcinoma cells, RANKL, RON, ROR1,
SCH 900105, SDC1, SLAMF7, TAG-72, tenascin C, TGF beta 2,
TGF-.beta., TRAIL-R1, TRAIL-R2, tumor antigen CTAA16.88, VEGF-A,
VEGFR-1, VEGFR2 or vimentin.
[0168] Antigens specific for inflammatory diseases which may be
targeted by the ASTR include one or more of AOC3 (VAP-1), CAM-3001,
CCL11 (eotaxin-1), CD125, CD147 (basigin), CD154 (CD40L), CD2,
CD20, CD23 (IgE receptor), CD25 (a chain of IL-2 receptor), CD3,
CD4, CD5, IFN-a, IFN-.gamma., IgE, IgE Fc region, IL-1, IL-12,
IL-23, IL-13, IL-17, IL-17A, IL-22, IL-4, IL-5, IL-5, IL-6, IL-6
receptor, integrin a4, integrin .sigma.4.beta.7, Lama glama, LFA-1
(CD11a), MEDI-528, myostatin, OX-40, rhuMAb .beta.7, scleroscin,
SOST, TGF beta 1, TNF-a or VEGF-A.
[0169] Antigens specific for neuronal disorders which may be
targeted by the ASTR of the invention include one or more of beta
amyloid or MABT5102A. Antigens specific for diabetes which may be
targeted by the ASTR of the invention include one or more of
L-I.beta. or CD3. Antigens specific for cardiovascular diseases
which may be targeted by the ASTR of the invention include one or
more of C5, cardiac myosin, CD41 (integrin alpha-lib), fibrin II,
beta chain, ITGB2 (CD 18) and sphingosine-1-phosphate.
[0170] Antigens specific for infectious diseases which may be
targeted by the ASTR of the invention include one or more of
anthrax toxin, CCR5, CD4, clumping factor A, cytomegalovirus,
cytomegalovirus glycoprotein B, endotoxin, Escherichia coli,
hepatitis B surface antigen, hepatitis B virus, HIV-1, Hsp90,
Influenza A hemagglutinin, lipoteichoic acid, Pseudomonas
aeruginosa, rabies virus glycoprotein, respiratory syncytial virus
and TNF-a.
[0171] Further examples of target antigens include surface proteins
found on cancer cells in a specific or amplified fashion, e.g. the
IL-14 receptor, CD19, CD20 and CD40 for B-cell lymphoma, the Lewis
Y and CEA antigens for a variety of carcinomas, the Tag72 antigen
for breast and colorectal cancer, EGF-R for lung cancer, folate
binding protein and the HER-2 protein which is often amplified in
human breast and ovarian carcinomas, or viral proteins, e.g. gp120
and gp41 envelope proteins of HIV, envelope proteins from the
Hepatitis B and C viruses, glycoprotein B and other envelope
glycoproteins of human cytomegalovirus, and the envelope proteins
from oncoviruses such as Kaposi's sarcoma-associated Herpes virus.
Other potential target antigens include CD4, where the ligand is
the HIV gp120 envelope glycoprotein, and other viral receptors, for
example ICAM, which is the receptor for the human rhinovirus, and
the related receptor molecule for poliovirus.
[0172] In another embodiment, the CAR may target antigens that
engage cancer-treating cells, such as NK cells and other cells
mentioned herein, to activate the cancer-treating cells by acting
as immune effector cells. One example of this is a CAR that targets
the CD 16A antigen to engage NK cells to fight CD30-expressing
malignancies. The bispecific, tetravalent AFM13 antibody is an
example of an antibody that can deliver this effect. Further
details of this type of embodiment can be found, for example, in
Rothe, A., et al., "A phase 1 study of the bispecific
anti-CD30/CD16A antibody construct AFM13 in patients with relapsed
or refractory Hodgkin lymphoma," Blood, 25 Jun. 2015, V1. 125, no.
26, pp. 4024-4031.
[0173] The extracellular spacer domain of the CAR is a hydrophilic
region which is located between the ASTR and the transmembrane
domain. In some embodiments, this domain facilitates proper protein
folding for the CAR. The extracellular spacer domain is an optional
component for the CAR. The extracellular spacer domain may include
a domain selected from Fc fragments of antibodies, hinge regions of
antibodies, CH2 regions of antibodies, CH3 regions of antibodies,
artificial spacer sequences or combinations thereof. Examples of
extracellular spacer domains include CD8a hinge, artificial spacers
made of polypeptides which may be as small as, three glycines
(Gly), as well as CH1 and CH3 domains of IgGs (such as human
IgG4).
[0174] The transmembrane domain of the CAR is a region that is
capable of spanning the plasma membrane of the cytotoxic cells. The
transmembrane domain is selected from a transmembrane region of a
transmembrane protein such as, for example, Type I transmembrane
proteins, an artificial hydrophobic sequence or a combination
thereof. Examples of the transmembrane domain include the
transmembrane regions of the alpha, beta or zeta chain of the T
cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16,
CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137, CD154. Synthetic
transmembrane domains may include a triplet of phenylalanine,
tryptophan and valine. Optionally, a short oligo- or polypeptide
linker, preferably between 2 and 10 amino acids in length, may form
the linkage between the transmembrane domain and the intracellular
signaling domain of the CAR. A glycine-serine doublet provides a
particularly suitable linker between the transmembrane domain and
the intracellular signaling domain.
[0175] The CAR of the invention also includes an intracellular
signaling domain. The intracellular signaling domain transduces the
effector function signal and directs the cytotoxic cell to perform
its specialized function, i.e., harming and/or destroying the
target cells. Examples of the intracellular signaling domain
include the chain of the T cell receptor complex or any of its
homologs, e.g., .eta. chain, FcsRly and .beta. chains, MB 1 (Iga)
chain, B29 (Ig) chain, etc., human CD3 zeta chain, CD3 polypeptides
(.DELTA., .delta. and .epsilon.), syk family tyrosine kinases (Syk,
ZAP 70, etc.), src family tyrosine kinases (Lck, Fyn, Lyn, etc.)
and other molecules involved in T cell transduction, such as CD2,
CD5 and CD28. Specifically, the intracellular signaling domain may
be human CD3 zeta chain, FcyRIII, FcsRI, cytoplasmic tails of Fc
receptors, an immunoreceptor tyrosine-based activation motif (ITAM)
bearing cytoplasmic receptors and combinations thereof.
[0176] The intracellular signaling domains used in the CAR may
include intracellular signaling domains of several types of various
other immune signaling receptors, including, but not limited to,
first, second, and third generation T cell signaling proteins
including CD3, B7 family costimulatory, and Tumor Necrosis Factor
Receptor (TNFR) superfamily receptors (Park et al., "Are all
chimeric antigen receptors created equal?" J Clin Oncol., vol. 33,
pp. 651-653, 2015). Additionally intracellular signaling domains
include signaling domains used by NK and NKT cells (Hermanson, et
al., "Utilizing chimeric antigen receptors to direct natural killer
cell activity," Front Immunol., vol. 6, p.195, 2015) such as
signaling domains of NKp30 (B7-H6) (Zhang et al., "An NKp30-based
chimeric antigen receptor promotes T cell effector functions and
antitumor efficacy in vivo," J Immunol., vol. 189, pp. 2290-2299,
2012), and DAP12 (Topfer et al., "DAP12-based activating chimeric
antigen receptor for NK cell tumor immunotherapy," J Immunol., vol.
194, pp. 3201-3212, 2015), NKG2D, NKp44, NKp46, DAP10, and CD3z.
Additionally intracellular signaling domains also includes
signaling domains of human Immunoglobulin receptors that contain
immunoreceptor tyrosine based activation motif (ITAM) such as
FcgammaRI, FcgammaRIIA, FcgammaRIIC, FcgammaRIIIA, FcRL5 (Gillis et
al., "Contribution of Human Fc.gamma.Rs to Disease with Evidence
from Human Polymorphisms and Transgenic Animal Studies," Front
Immunol., vol. 5, p.254, 2014).
[0177] In some embodiments, the intracellular signaling domain
includes a cytoplasmic signaling domain of TCR zeta, FcR gamma, FcR
beta, CD3 gamma, CD3 delta, CD3 epsilon, CD5, CD22, CD79a, CD79b,
or CD66d. It is particularly preferred that the intracellular
signaling domain in the CAR includes a cytoplasmic signaling domain
of human CD3 zeta.
[0178] The CAR of the present invention may include a
co-stimulatory domain, which has the function of enhancing cell
proliferation, cell survival and development of memory cells for
the cytotoxic cells that express the CAR. The CAR of the invention
may include one or more co-stimulatory domains selected from
co-stimulatory domains of proteins in the TNFR superfamily, CD28,
CD137 (4-1BB), CD134 (OX40), DaplO, CD27, CD2, CD7, CD5, ICAM-1,
LFA-1(CD11a/CD18), Lck, TNFR-I, PD-1, TNFR-II, Fas, CD30, CD40,
ICOS LIGHT, NKG2C, B7-H3, or combinations thereof. If the CAR
includes more than one co-stimulatory domain, these domains may be
arranged in tandem, optionally separated by a linker. The
co-stimulatory domain is an intracellular domain that may locate
between the transmembrane domain and the intracellular signaling
domain in the CAR.
[0179] In some embodiments, two or more components of the CAR of
the invention are separated by one or more linkers. For example, in
a CAR including at least two ASTRs, the two ASTRs may be separated
by a linker. Linkers are oligo- or polypeptide regions of from
about 1 to 100 amino acids in length. In some embodiments, the
linkers may be, for example, 5-12 amino acids in length, 5-15 amino
acids in length or 5 to 20 amino acids in length. Linkers may be
composed of flexible residues like glycine and serine so that the
adjacent protein domains are free to move relative to one another.
Longer linkers, for example those longer than 100 amino acids, may
be used in connection with alternate embodiments of the invention,
and may be selected to, for example, ensure that two adjacent
domains do not sterically interfere with one another. Examples of
linkers which may be used in the instant invention include but are
not limited to 2A linkers (for example T2A), 2A-like linkers or
functional equivalents thereof.
Conditionally Active Antigen Specific Targeting Region
[0180] The CARs are chimeric proteins that are generated by fusing
all the different domains discussed above together to form a fusion
protein. The CAR is typically generated by an expression vector
including polynucleotide sequences that encode the different
domains of the CAR. The ASTR of the present invention, which
functions to recognize and bind with an antigen on target cells, is
conditionally active. Specifically, the ASTR is less active or
inactive at a normal physiological condition and active at an
aberrant condition for binding with the target antigen, in
comparison with an ASTR of the corresponding wild-type protein. The
present invention provides a method to generate the conditionally
active ASTR from a wild-type protein or its binding domain
(wild-type ASTR).
[0181] The wild-type protein that suitable to be used in whole or
in part for at least its binding domain for the target antigen, as
an ASTR in the present invention may be discovered by generating a
protein library and screening the library for a protein with a
desired binding affinity to the target antigen. The wild-type
protein may be discovered by screening a cDNA library. A cDNA
library is a combination of cloned cDNA (complementary DNA)
fragments inserted into a collection of host cells, which together
constitute some portion of the transcriptome of the organism. cDNA
is produced from fully transcribed mRNA and therefore contains the
coding sequence for expressed proteins of an organism. The
information in cDNA libraries is a powerful and useful tool for
discovery of proteins with desired properties by screening the
libraries for proteins with the desired binding affinity to the
target antigen.
[0182] In some embodiments where the wild-type proteins are
antibodies, the wild-type antibodies can be discovered by
generating and screening antibody libraries. The antibody libraries
can be either polyclonal antibody libraries or monoclonal antibody
libraries. A polyclonal antibody library against a target antigen
can be generated by direct injection of the antigen into an animal
or by administering the antigen to a non-human animal. The
antibodies so obtained represent a library of polyclonal antibodies
that bind to the antigen. For preparation of monoclonal antibody
libraries, any technique which provides antibodies produced by
continuous cell line cultures can be used. Examples include the
hybridoma technique, the trioma technique, the human B-cell
hybridoma technique, and the EBV-hybridoma technique (see, e.g.,
Cole (1985) in Monoclonal Antibodies and Cancer Therapy, Alan R.
Liss, Inc., pp. 77-96). Techniques described for the generating
single chain antibodies (see, e.g., U.S. Pat. No. 4,946,778) can be
adapted to produce single chain antibody library.
[0183] There are other methods for generation and screening of
antibody libraries for discovery of the wild-type antibody. For
example, fully human antibody display libraries can be utilized.
Such a library is a population of antibodies displayed on the
surface of host cell(s). Preferably, the antibody library is
representative of the human repertoire of antibodies in that they
have the capability of binding to a wide range of antigens. Because
the antibodies are displayed on the surface of cells, the effective
affinity (due to avidity) of each antibody in the library is
increased. Unlike other popular library types, such as phage
display libraries, where avidity of the antibodies for screening
and identification purposes is less desirable, the super avidity
provided by cell surface display in the present invention, is
desirable. Cell surface display libraries enable the identification
of low, medium and high binding affinity antibodies, as well as the
identification of non-immunogenic and weak epitopes in the
screening or selection step.
Generation of Evolved Molecules from Parent Molecule
[0184] The wild-type protein, or its binding domain (wild-type
ASTR) undergoes a process of mutagenesis to produce a population of
mutant polypeptides, which can then be screened to identify a
mutant ASTR with an enhanced binding affinity to the target antigen
at an aberrant condition, and optionally, substantially the same or
a reduction in binding affinity to the target antigen at a normal
physiological condition, in comparison with the wild-type ASTR.
[0185] Any chemical synthetic or recombinant mutagenic method may
be used to generate the population of mutant polypeptides. The
practice of the present invention may employ, unless otherwise
indicated, conventional techniques of cell biology, cell culture,
molecular biology, transgenic biology, microbiology, recombinant
DNA, and immunology, which are within the skill of the art. Such
techniques are explained fully in the literature. See, for example,
Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook,
Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1989);
DNA Cloning, Volumes I and II (D. N. Glover ed., 1985);
Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al.
U.S. Pat. No. 4,683,195; Nucleic Acid Hybridization (B. D. Hames
& S. J. Higgins eds. 1984); Transcription And Translation (B.
D. Hames & S. J. Higgins eds. 1984); Culture Of Animal Cells
(R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And
Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To
Molecular Cloning (1984); the treatise, Methods In Enzymology
(Academic Press, Inc., N.Y.); Gene Transfer Vectors For Mammalian
Cells (J. H. Miller and M. P. Cabs eds., 1987, Cold Spring Harbor
Laboratory); Methods In Enzymnology, Vols. 154 and 155 (Wu et al.
eds.), Immunochemical Methods In Cell And Molecular Biology (Mayer
and Walker, eds., Academic Press, London, 1987); Handbook Of
Experimental Immunology, Volumes 1-IV (D. M. Weir and C. C.
Blackwell, eds., 1986); Manipulating the Mouse Embryo, (Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, N. Y., 1986).
[0186] The disclosure provides for a method for generating a
nucleic acid mutant encoding a mutant polypeptide being
conditionally active, the method including modifying the nucleic
acid by (i) substituting one or more nucleotides for a different
nucleotide, wherein the nucleotide includes a natural or
non-natural nucleotide; (ii) deleting one or more nucleotides,
(iii) adding one or more nucleotides, or (iv) any combination
thereof. In one aspect, the non-natural nucleotide includes
inosine. In another aspect, the method further includes assaying
the polypeptides encoded by the modified nucleic acids for altered
enzyme activity, thereby identifying the modified nucleic acid(s)
encoding a polypeptide having altered enzyme activity. In one
aspect, the modifications of step (a) are made by PCR, error-prone
PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR,
sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis,
recursive ensemble mutagenesis, exponential ensemble mutagenesis,
site-specific mutagenesis, gene reassembly, gene site saturated
mutagenesis, ligase chain reaction, in vitro mutagenesis, ligase
chain reaction, oligonuclteotide synthesis, any DNA-generating
technique and any combination thereof. In another aspect, the
method further includes at least one repetition of the modifying
step.
[0187] The disclosure further provides a method for making a
polynucleotide from two or more nucleic acids, the method
including: (a) identifying regions of identity and regions of
diversity between two or more nucleic acids, wherein at least one
of the nucleic acids includes a nucleic acid of the disclosure; (b)
providing a set of oligonucleotides which correspond in sequence to
at least two of the two or more nucleic acids; and, (c) extending
the oligonucleotides with a polymerase, thereby making the
polynucleotide.
[0188] Any technique of mutagenesis can be employed in various
embodiments of the disclosure. Stochastic or random mutagenesis is
exemplified by a situation in which a parent molecule is mutated
(modified or changed) to yield a set of progeny molecules having
mutation(s) that are not predetermined Thus, in an in vitro
stochastic mutagenesis reaction, for example, there is not a
particular predetermined product whose production is intended;
rather there is an uncertainty--hence randomness--regarding the
exact nature of the mutations achieved, and thus also regarding the
products generated. Stochastic mutagenesis is manifested in
processes such as error-prone PCR and stochastic shuffling, where
the mutation(s) achieved are random or not predetermined. The
variant forms can be generated by error-prone transcription, such
as an error-prone PCR or use of a polymerase which lacks
proof-reading activity (see, Liao (1990) Gene 88: 107-111), of the
first variant form, or, by replication of the first form in a
mutator strain (mutator host cells are discussed in further detail
below, and are generally well known). A mutator strain can include
any mutants in any organism impaired in the functions of mismatch
repair. These include mutant gene products of mutS, mutT, mutH,
mutL, ovrD, dcm, vsr, umuC, umuD, sbcB, recJ, etc. The impairment
is achieved by genetic mutation, allelic replacement, selective
inhibition by an added reagent such as a small compound or an
expressed antisense RNA, or other techniques Impairment can be of
the genes noted, or of homologous genes in any organism.
[0189] Other mutagenesis methods include oligonucleotide-directed
mutagenesis technologies, error-prone polymerase chain reactions
(error-prone PCR) and cassette mutagenesis, in which a specific
region of the parental polynucleotide is replaced with a
synthetically mutagenized oligonucleotide. In these cases, a number
of mutant sites are generated around certain sites in the parental
sequence.
[0190] In oligonucleotide-directed mutagenesis, a short sequence is
replaced with a synthetically mutagenized oligonucleotide. In
oligonucleotide-directed mutagenesis, a short sequence of the
polynucleotide is removed from the polynucleotide using restriction
enzyme digestion and is replaced with a synthetic polynucleotide in
which various bases have been altered from the original sequence.
The polynucleotide sequence can also be altered by chemical
mutagenesis. Chemical mutagens include, for example, sodium
bisulfite, nitrous acid, hydroxylamine, hydrazine or formic acid.
Other agents which are analogues of nucleotide precursors include
nitrosoguanidine, 5-bromouracil, 2-aminopurine, or acridine.
Generally, these agents are added to the PCR reaction in place of
the nucleotide precursor thereby mutating the sequence.
Intercalating agents such as proflavine, acriflavine, quinacrine
and the like can also be used. Random mutagenesis of the
polynucleotide sequence can also be achieved by irradiation with
X-rays or ultraviolet light. Generally, plasmid polynucleotides so
mutagenized are introduced into E. coli and propagated as a pool or
library of hybrid plasmids.
[0191] Error-prone PCR uses low-fidelity polymerization conditions
to introduce a low level of point mutations randomly over a long
sequence. In a mixture of fragments of unknown sequence,
error-prone PCR can be used to mutagenize the mixture.
[0192] In cassette mutagenesis, a sequence block of a single
template is typically replaced by a (partially) randomized
sequence. Reidhaar-Olson J F and Sauer R T: Combinatorial cassette
mutagenesis as a probe of the informational content of protein
sequences. Science 241(4861):53-57, 1988.
[0193] Alternatively, any technique of non-stochastic or non-random
mutagenesis can be employed in various embodiments of the
disclosure. Non-stochastic mutagenesis is exemplified by a
situation in which a parent molecule is mutated (modified or
changed) to yield a progeny molecule having one or more
predetermined mutations. It is appreciated that the presence of
background products in some quantity is a reality in many reactions
where molecular processing occurs, and the presence of these
background products does not detract from the non-stochastic nature
of a mutagenesis process having a predetermined product.
Site-saturation mutagenesis and synthetic ligation reassembly, are
examples of mutagenesis techniques where the exact chemical
structure(s) of the intended product(s) are predetermined.
[0194] One method of site-saturation mutagenesis is disclosed in
U.S. patent application publication 2009/0130718 This method
provides a set of degenerate primers corresponding to codons of a
template polynucleotide, and performs polymerase elongation to
produce progeny polynucleotides, which contain sequences
corresponding to the degenerate primers. The progeny
polynucleotides can be expressed and screened for directed
evolution. Specifically, this is a method for producing a set of
progeny polynucleotides, including the steps of (a) providing
copies of a template polynucleotide, each including a plurality of
codons that encode a template polypeptide sequence; and (b) for
each codon of the template polynucleotide, performing the steps of
(1) providing a set of degenerate primers, where each primer
includes a degenerate codon corresponding to the codon of the
template polynucleotide and at least one adjacent sequence that is
homologous to a sequence adjacent to the codon of the template
polynucleotide; (2) providing conditions allowing the primers to
anneal to the copies of the template polynucleotides; and (3)
performing a polymerase elongation reaction from the primers along
the template; thereby producing progeny polynucleotides, each of
which contains a sequence corresponding to the degenerate codon of
the annealed primer; thereby producing a set of progeny
polynucleotides. Site-saturation mutagenesis relates to the
directed evolution of nucleic acids and screening of clones
containing the evolved nucleic acids for resultant binding activity
of interest.
[0195] Site saturation mutagenesis relates generally to a method
of: 1) preparing a progeny generation of molecule(s) (including a
molecule that is included of a polynucleotide sequence, a molecule
that is included of a polypeptide sequence, and a molecule that is
included in part of a polynucleotide sequence and in part of a
polypeptide sequence), that is mutagenized to achieve at least one
point mutation, addition, deletion, and/or chimerization, from one
or more ancestral or parental generation template(s); 2) screening
the progeny generation molecule(s)--preferably using a high
throughput method--for desired binding affinity to the target
antigen; 3) optionally obtaining &/or cataloguing structural
&/or and functional information regarding the parental &/or
progeny generation molecules; and 4) optionally repeating any of
steps 1) to 3).
[0196] In site saturation mutagenesis, there is generated (e.g.
from a parent polynucleotide template)--in what is termed "codon
site-saturation mutagenesis"--a progeny generation of
polynucleotides, each having at least one set of up to three
contiguous point mutations (i.e. different bases including a new
codon), such that every codon (or every family of degenerate codons
encoding the same amino acid) is represented at each codon
position. Corresponding to--and encoded by--this progeny generation
of polynucleotides, there is also generated a set of progeny
polypeptides, each having at least one single amino acid point
mutation. In a preferred aspect, there is generated--in what is
termed "amino acid site-saturation mutagenesis"-one such mutant
polypeptide for each of the 19 naturally encoded
polypeptide-forming alpha-amino acid substitutions at each and
every amino acid position along the polypeptide. This yields--for
each and every amino acid position along the parental
polypeptide--a total of 20 distinct progeny polypeptides including
the original amino acid, or potentially more than 21 distinct
progeny polypeptides if additional amino acids are used either
instead of or in addition to the 20 naturally encoded amino
acids.
[0197] Other mutagenesis techniques can also be employed which
involve recombination and more specifically a method for preparing
polynucleotides encoding a polypeptide by a method of in vivo
re-assortment of polynucleotide sequences containing regions of
partial homology, assembling the polynucleotides to form at least
one polynucleotide and screening the polynucleotides for the
production of polypeptide(s) having a useful property.
[0198] In another aspect, mutagenesis techniques exploit the
natural property of cells to recombine molecules and/or to mediate
reductive processes that reduce the complexity of sequences and
extent of repeated or consecutive sequences possessing regions of
homology.
[0199] Various mutagenesis techniques can be used alone or in
combination to provide a method for generating hybrid
polynucleotides encoding biologically active hybrid polypeptides.
In accomplishing these and other objects, there has been provided,
in accordance with one aspect of the disclosure, a method for
introducing polynucleotides into a suitable host cell and growing
the host cell under conditions that produce hybrid
polypeptides.
[0200] Chimeric genes have been made by joining 2 polynucleotide
fragments using compatible sticky ends generated by restriction
enzyme(s), where each fragment is derived from a separate
progenitor (or parental) molecule. Another example is the
mutagenesis of a single codon position (i.e. to achieve a codon
substitution, addition, or deletion) in a parental polynucleotide
to generate a single progeny polynucleotide encoding for a single
site-mutagenized polypeptide.
[0201] Further, in vivo site specific recombination systems have
been utilized to generate hybrids of genes, as well as random
methods of in vivo recombination, and recombination between
homologous but truncated genes on a plasmid. Mutagenesis has also
been reported by overlapping extension and PCR.
[0202] Non-random methods have been used to achieve larger numbers
of point mutations and/or chimerizations, for example comprehensive
or exhaustive approaches have been used to generate all the
molecular species within a particular grouping of mutations, for
attributing functionality to specific structural groups in a
template molecule (e.g. a specific single amino acid position or a
sequence included of two or more amino acids positions), and for
categorizing and comparing specific grouping of mutations.
[0203] Any of these or other methods of evolving can be employed in
the present disclosure to generate a new population of mutant
polypeptides (library) from the wild-type protein.
Expression of Evolved Molecules
[0204] The mutant polynucleotides generated from the evolving step
may, or may not be size fractionated on an agarose gel according to
published protocols, inserted into an expression vector, and
transfected into an appropriate host cell to produce the mutant
polypeptides (expression). The expression may use routine molecular
biology techniques. Thus, the expression step can use various known
methods.
[0205] For example, briefly, mutant polynucleotides generated from
the evolving step are then digested and ligated into an expression
vector, such as plasmid DNA using standard molecular biology
techniques. The vector is then transformed into bacteria or other
cells using standard protocols. This can be done in an individual
well of a multi-well tray, such as a 96-well tray for high
throughput expression and screening. The process is repeated for
each mutant polynucleotide.
[0206] Polynucleotides selected and isolated as described are
introduced into a suitable host cell. A suitable host cell is any
cell which is capable of promoting recombination and/or reductive
reassortment. The selected polynucleotides are preferably already
in a vector which includes appropriate control sequences. The host
cell can be a higher eukaryotic cell, such as a mammalian cell, or
a lower eukaryotic cell, such as a yeast cell, or preferably, the
host cell can be a prokaryotic cell, such as a bacterial cell.
Introduction of the construct into the host cell can be effected by
calcium phosphate transfection, DEAE-Dextran mediated transfection,
or electroporation (e.g. Ecker and Davis, 1986, Inhibition of gene
expression in plant cells by expression of antisense RNA, Proc Natl
Acad Sci USA, 83:5372-5376).
[0207] As representative examples of expression vectors which may
be used, there may be mentioned viral particles, baculovirus,
phage, plasmids, phagemids, cosmids, fosmids, bacterial artificial
chromosomes, viral DNA (e.g., vaccinia, adenovirus, foul pox virus,
pseudorabies and derivatives of SV40), P1-based artificial
chromosomes, yeast plasmids, yeast artificial chromosomes, and any
other vectors specific for specific hosts of interest (such as
bacillus, aspergillus and yeast). Thus, for example, the DNA may be
included in any one of a variety of expression vectors for
expressing a polypeptide. Such vectors include chromosomal,
nonchromosomal and synthetic DNA sequences. Large numbers of
suitable vectors are known to those of skill in the art, and are
commercially available. The following vectors are provided by way
of example; Bacterial: pQE vectors (Qiagen), pBluescript plasmids,
pNH vectors, (lambda-ZAP vectors (Stratagene); ptrc99a, pKK223-3,
pDR540, pRIT2T (Pharmacia); Eukaryotic: pXT1, pSGa (Stratagene),
pSVK3, pBPV, .mu.MSG, pSVLSV40 (Pharmacia). However, any other
plasmid or other vector may be used so long as they are replicable
and viable in the host. Low copy number or high copy number vectors
may be employed with the present disclosure.
[0208] The mutant polynucleotide sequence in the expression vector
is operatively linked to an appropriate expression control
sequence(s) (promoter) to direct RNA synthesis. Particular named
bacterial promoters include lad, lacZ, T3, T7, gpt, lambda PR, PL
and trp. Eukaryotic promoters include CMV immediate early, HSV
thymidine kinase, early and late SV40, LTRs from retrovirus, and
mouse metallothionein-1. Selection of the appropriate vector and
promoter is well within the level of ordinary skill in the art. The
expression vector also contains a ribosome binding site for
translation initiation and a transcription terminator. The vector
may also include appropriate sequences for amplifying expression.
Promoter regions can be selected from any desired gene using
chloramphenicol transferase (CAT) vectors or other vectors with
selectable markers. In addition, the expression vectors preferably
contain one or more selectable marker genes to provide a phenotypic
trait for selection of transformed host cells such as dihydrofolate
reductase or neomycin resistance for eukaryotic cell culture, or
such as tetracycline or ampicillin resistance in E. coli.
[0209] Eukaryotic DNA transcription can be increased by inserting
an enhancer sequence into the expression vector Enhancers are
cis-acting sequences of between 10 to 300 bp that increase
transcription by a promoter. Enhancers can effectively increase
transcription when either 5' or 3' to the transcription unit. They
are also effective if located within an intron or within the coding
sequence itself. Typically, viral enhancers are used, including
SV40 enhancers, cytomegalovirus enhancers, polyoma enhancers, and
adenovirus enhancers. Enhancer sequences from mammalian systems are
also commonly used, such as the mouse immunoglobulin heavy chain
enhancer.
[0210] Mammalian expression vector systems also typically include a
selectable marker gene. Examples of suitable markers include, the
dihydrofolate reductase gene (DHFR), the thymidine kinase gene
(TK), or prokaryotic genes conferring drug resistance. The first
two marker genes prefer the use of mutant cell lines that lack the
ability to grow without the addition of thymidine to the growth
medium. Transformed cells can then be identified by their ability
to grow on non-supplemented media. Examples of prokaryotic drug
resistance genes useful as markers include genes conferring
resistance to G418, mycophenolic acid and hygromycin.
[0211] The expression vectors containing the DNA segments of
interest can be transferred into host cells by well-known methods,
depending on the type of cell production hosts. For example,
calcium chloride transfection is commonly utilized for prokaryotic
host cells, whereas calcium phosphate treatment, lipofection, or
electroporation may be used for eukaryotic host cells. Other
methods used to transform mammalian cell production hosts include
the use of polybrene, protoplast fusion, liposomes,
electroporation, and microinjection (see, generally, Sambrook et
al., supra).
[0212] Once the expression vector has been introduced into an
appropriate host, the host is maintained under conditions suitable
for high level expression of the introduced mutant polynucleotide
sequences to produce the mutant polypeptides. The expression vector
is typically replicable in the host organisms either as episomes or
as an integral part of the host chromosomal DNA. Commonly,
expression vectors will contain selection markers, e.g.,
tetracycline or neomycin, to permit detection of those cells
transformed with the desired DNA sequences (see, e.g., U.S. Pat.
No. 4,704,362).
[0213] Therefore, in another aspect of the disclosure, mutant
polynucleotides can be generated by the process of reductive
reassortment. The method involves the generation of constructs
containing consecutive sequences (original encoding sequences),
their insertion into an appropriate vector, and their subsequent
introduction into an appropriate host cell. The reassortment of the
individual molecular identities occurs by combinatorial processes
between the consecutive sequences in the construct possessing
regions of homology, or between quasi-repeated units. The
reassortment process recombines and/or reduces the complexity and
extent of the repeated sequences, and results in the production of
novel molecular species. Various treatments may be applied to
enhance the rate of reassortment. These could include treatment
with ultra-violet light, or DNA damaging chemicals, and/or the use
of host cell lines displaying enhanced levels of "genetic
instability". Thus the reassortment process may involve homologous
recombination or the natural property of quasi-repeated sequences
to direct their own evolution.
[0214] The cells are then propagated and "reductive reassortment"
is effected. The rate of the reductive reassortment process may be
stimulated by the introduction of DNA damage if desired, in vivo
reassortment is focused on "inter-molecular" processes collectively
referred to as "recombination" which in bacteria, is generally
viewed as a "RecA-dependent" phenomenon. The disclosure can rely on
recombination processes of a host cell to recombine and re-assort
sequences, or the cells' ability to mediate reductive processes to
decrease the complexity of quasi-repeated sequences in the cell by
deletion. This process of "reductive reassortment" occurs by an
"intra-molecular", RecA-independent process. The end result is a
reassortment of the molecules into all possible combinations.
[0215] In one aspect, the host organism or cell includes a gram
negative bacterium, a gram positive bacterium or a eukaryotic
organism. In another aspect of the disclosure, the gram negative
bacterium includes Escherichia coli, or Pseudomonas fluorescens. In
another aspect of the disclosure, the gram positive bacterium
include Streptomyces diversa, Lactobacillus gasseri, Lactococcus
lactis, Lactococcus cremoris, or Bacillus subtilis. In another
aspect of the disclosure, the eukaryotic organism includes
Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia
pastoris, Kluyveromyces lactis, Hansenula plymorpha, or Aspergillus
niger. As representative examples of appropriate hosts, there may
be mentioned: bacterial cells, such as E. coli, Streptomyces,
Salmonella typhimurium; fungal cells, such as yeast; insect cells
such as Drosophila S2 and Spodoptera Sf9; animal cells such as CHO,
COS or Bowes melanoma; adenoviruses; and plant cells. The selection
of an appropriate host is deemed to be within the scope of those
skilled in the art from the teachings herein.
[0216] In addition to eukaryotic microorganisms such as yeast,
mammalian tissue cell culture may also be used to express the
mutant polypeptides of the present invention (see, Winnacker, "From
Genes to Clones," VCH Publishers, N.Y., N.Y. (1987)). Eukaryotic
cells are preferred, because a number of suitable host cell lines
capable of secreting intact immunoglobulins have been developed in
the art, and include the CHO cell lines, various COS cell lines,
HeLa cells, myeloma cell lines, B-cells or hybridomas. Expression
vectors for these cells can include expression control sequences,
such as an origin of replication, a promoter, an enhancer (Queen et
al., Immunol. Rev., vol. 89, page 49, 1986), and necessary
processing information sites, such as ribosome binding sites, RNA
splice sites, polyadenylation sites, and transcriptional terminator
sequences. Preferred expression control sequences are promoters
derived from immunoglobulin genes, cytomegalovirus, SV40,
Adenovirus, Bovine Papilloma Virus, and the like.
[0217] In one embodiment, the eukaryotic host cells are selected
from CHO, HEK293, IM9, DS-1, THP-1, Hep G2, COS, NIH 3T3, C33a,
A549, A375, SK-MEL-28, DU 145, PC-3, HCT 116, Mia PACA-2, ACHN,
Jurkat, MM1, Ovcar 3, HT 1080, Panc-1, U266, 769P, BT-474, Caco-2,
HCC 1954, MDA-MB-468, LnCAP, NRK-49F, and SP2/0 cell lines; and
mouse splenocytes and rabbit PBMC. In one aspect, the mammalian
hoist cell is selected from a CHO or HEK293 cell line. In one
specific aspect, the mammalian host cell is a CHO-S cell line. In
another specific aspect, the mammalian system is a HEK293 cell
line. In another embodiment, the eukaryotic host is a yeast cell
system. In one aspect, the eukaryotic host is selected from S.
cerevisiae yeast cells or picchia yeast cells.
[0218] In another embodiment, mammalian host cells may be created
commercially by a contract research or custom manufacturing
organization. For example, for recombinant antibodies or other
proteins, Lonza (Lonza Group Ltd, Basel, Switzerland) can create
vectors to express these products using the GS Gene Expression
System.TM. technology with either CHOK1SV or NS0 cell production
hosts. Host cells containing the polynucleotides of interest can be
cultured in conventional nutrient media modified as appropriate for
activating promoters, selecting transformants or amplifying genes.
The culture conditions, such as temperature, pH and the like, are
those previously used with the host cell selected for expression,
and will be apparent to the ordinarily skilled artisan.
[0219] As discussed above, expression optimization for the
conditionally active ASTR can be achieved by optimization of
vectors used (vector components, such as promoters, splice sites,
5' and 3' termini and flanking sequences), gene modification of
host cells to reduce gene deletions and rearrangements, evolution
of host cell gene activities by in vivo or in vitro methods of
evolving relevant genes, optimization of host glycosylating enzymes
by evolution of relevant genes, and/or by chromosome wide host cell
mutagenesis and selection strategies to select for cells with
enhanced expression capabilities.
[0220] Protein expression can be induced by a variety of known
methods, and many genetic systems have been published for induction
of protein expression. For example, with appropriate systems, the
addition of an inducing agent will induce protein expression. Cells
are then pelleted by centrifugation and the supernatant removed.
Periplasmic protein can be enriched by incubating the cells with
DNAse, RNAse, and lysozyme. After centrifugation, the supernatant,
containing the new protein, is transferred to a new multi-well tray
and stored prior to assay.
[0221] Cells are typically harvested by centrifugation, disrupted
by physical or chemical means, and the resulting crude extract is
retained for further purification. Microbial cells employed for
expression of proteins can be disrupted by any convenient method,
including freeze-thaw cycling, sonication, mechanical disruption,
or use of cell lysing agents. Such methods are well known to those
skilled in the art. The expressed polypeptide or fragment thereof
can be recovered and purified from recombinant cell cultures by
methods including ammonium sulfate or ethanol precipitation, acid
extraction, anion or cation exchange chromatography,
phosphocellulose chromatography, hydrophobic interaction
chromatography, affinity chromatography, hydroxylapatite
chromatography and lectin chromatography. Protein refolding steps
can be used, as necessary, in completing configuration of the
polypeptide. If desired, high performance liquid chromatography
(HPLC) can be employed for final purification steps. The screening
of a conditionally active ASTR can be aided by the availability of
a convenient high throughput screening or selection process. Cell
surface display expression and screening technology (for example,
as defined above) can be employed to screen mutant proteins for
conditionally active ASTR.
Screening of Mutants to Identify Reversible or Nonreversible
Mutants
[0222] Identifying desirable molecules is most directly
accomplished by measuring protein activity at the permissive
condition and the wild type condition. The mutants with the largest
ratio of activity (permissive/wild type) can then be selected and
permutations of the point mutations are generated by combining the
individual mutations using standard methods. The combined
permutation protein library is then screened for those proteins
displaying the largest differential activity between the permissive
and wild type condition.
[0223] Activity of supernatants can be screened using a variety of
methods, for example using high throughput activity assays, such as
fluorescence assays, to identify protein mutants that are sensitive
at whatever characteristic one desires (temperature, pH, etc). For
example, to screen for temporally sensitive mutants, the enzymatic
or antibody activity of each individual mutant is determined at
lower temperatures (such as 25 degrees Celsius), and at
temperatures which the original protein functions (such as 37
degrees Celsius), using commercially available substrates.
Screening can be carried out in a variety of media such as serum
and BSA, among others. Reactions can initially be performed in a
multi well assay format, such as a 96-well assay, and confirmed
using a different format, such as a 14 ml tube format.
[0224] In one aspect, the method further includes modifying at
least one of the nucleic acids or polypeptides prior to testing the
candidates for conditional biologic activity, in another aspect,
the testing of step (c) further includes testing for improved
expression of the polypeptide in a host cell or host organism, in a
further aspect, the testing of step (c) further includes testing
for enzyme activity within a pH range from about pH 3 to about pH
12. In a further aspect, the testing of step (c) further includes
testing for enzyme activity within a pH range from about pH 5 to
about pH 10. In a further aspect, the testing of step (c) further
includes testing for enzyme activity within a pH range from about
pH 6 to about pH 8. In a further aspect, the testing of step (c)
further includes testing for enzyme activity at pH 6.7 and pH 7.5.
In another aspect, the testing of step (c) further includes testing
for enzyme activity within a temperature range from about 4 degrees
C. to about 55 degrees C. In another aspect, the testing of step
(c) further includes testing for enzyme activity within a
temperature range from about 15 degrees C. to about 47 degrees C.
In another aspect, the testing of step (c) further includes testing
for enzyme activity within a temperature range from about 20
degrees C. to about 40 degrees C. In another aspect, the testing of
step (c) further includes testing for enzyme activity at the
temperatures of 25 degrees C. and 37 degrees C. In another aspect,
the testing of step (c) further includes testing for enzyme
activity under normal osmotic pressure, and aberrant (positive or
negative) osmotic pressure, In another aspect, the testing of step
(c) further includes testing for enzyme activity under normal
electrolyte concentration, and aberrant (positive or negative)
electrolyte concentration. The electrolyte concentration to be
tested is selected from one of calcium, sodium, potassium,
magnesium, chloride, bicarbonate and phosphate concentration, in
another aspect, the testing of step (c) further includes testing
for enzyme activity which results in a stabilized reaction
product.
[0225] In another aspect, the disclosure provides for a purified
antibody that specifically binds to the polypeptide of the
disclosure or a fragment thereof, having enzyme activity. In one
aspect, the disclosure provides for a fragment of the antibody that
specifically binds to a polypeptide having enzyme activity.
Antibodies and Antibody-Based Screening Methods
[0226] The disclosure provides isolated or recombinant antibodies
that specifically bind to an enzyme of the disclosure. These
antibodies can be used to isolate, identify or quantify the enzymes
of the disclosure or related polypeptides. These antibodies can be
used to isolate other polypeptides within the scope the disclosure
or other related enzymes. The antibodies can be designed to bind to
an active site of an enzyme. Thus, the disclosure provides methods
of inhibiting enzymes using the antibodies of the disclosure.
[0227] The antibodies can be used in immunoprecipitation, staining,
immunoaffinity columns, and the like. If desired, nucleic acid
sequences encoding for specific antigens can be generated by
immunization followed by isolation of polypeptide or nucleic acid,
amplification or cloning and immobilization of polypeptide onto an
array of the disclosure. Alternatively, the methods of the
disclosure can be used to modify the structure of an antibody
produced by a cell to be modified, e.g., an antibody's affinity can
be increased or decreased. Furthermore, the ability to make or
modify antibodies can be a phenotype engineered into a cell by the
methods of the disclosure.
[0228] Methods of immunization, producing and isolating antibodies
(polyclonal and monoclonal) are known to those of skill in the art
and described in the scientific and patent literature, see, e.g.,
Coligan, CURRENT PROTOCOLS IN IMMUNOLOGY, Wiley/Greene, NY (1991);
Stites (eds.) BASIC AND CLINICAL IMMUNOLOGY (7th ed.) Lange Medical
Publications, Los Altos, Calif. ("Stites"); Goding, MONOCLONAL
ANTIBODIES: PRINCIPLES AND PRACTICE (2d ed.) Academic Press, New
York, N. Y. (1986); Kohler (1975) "Continuous cultures of fused
cells secreting antibody of predefined specificity", Nature
256:495; Harlow (1988) ANTIBODIES, A LABORATORY MANUAL, Cold Spring
Harbor Publications, New York. Antibodies also can be generated in
vitro, e.g., using recombinant antibody binding site expressing
phage display libraries, in addition to the traditional in vivo
methods using animals. See, e.g., Hoogenboom (1997) "Designing and
optimizing library selection strategies for generating
high-affinity antibodies", Trends Biotechnol. 15:62-70; and Katz
(1997) "Structural and mechanistic determinants of affinity and
specificity of ligands discovered or engineered by phage display",
Annu. Rev. Biophys. Biomol. Struct. 26:27-45.
[0229] Polypeptides or peptides can be used to generate antibodies
which bind specifically to the polypeptides, e.g., the enzymes, of
the disclosure. The resulting antibodies may be used in
immunoaffinity chromatography procedures to isolate or purify the
polypeptide or to determine whether the polypeptide is present in a
biological sample. In such procedures, a protein preparation, such
as an extract, or a biological sample is contacted with an antibody
capable of specifically binding to one of the polypeptides of the
disclosure.
[0230] In immunoaffinity procedures, the antibody is attached to a
solid support, such as a bead or other column matrix. The protein
preparation is placed in contact with the antibody under conditions
in which the antibody specifically binds to one of the polypeptides
of the disclosure. After a wash to remove non-specifically bound
proteins, the specifically bound polypeptides are eluted.
[0231] The ability of proteins in a biological sample to bind to
the antibody may be determined using any of a variety of procedures
familiar to those skilled in the art. For example, binding may be
determined by labeling the antibody with a detectable label such as
a fluorescent agent, an enzymatic label, or a radioisotope.
Alternatively, binding of the antibody to the sample may be
detected using a secondary antibody having such a detectable label
thereon. Particular assays include ELISA assays, sandwich assays,
radioimmunoassays, and Western Blots.
[0232] Polyclonal antibodies generated against the polypeptides of
the disclosure can be obtained by direct injection of the
polypeptides into an animal or by administering the polypeptides to
a non-human animal. The antibody so obtained will then bind the
polypeptide itself. In this manner, even a sequence encoding only a
fragment of the polypeptide can be used to generate antibodies
which may bind to the whole native polypeptide. Such antibodies can
then be used to isolate the polypeptide from cells expressing that
polypeptide.
[0233] For preparation of monoclonal antibodies, any technique
which provides antibodies produced by continuous cell line cultures
can be used. Examples include the hybridoma technique, the trioma
technique, the human B-cell hybridoma technique, and the
EBV-hybridoma technique (see, e.g., Cole (1985) in Monoclonal
Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96).
[0234] Techniques described for the production of single chain
antibodies (see, e.g., U.S. Pat. No. 4,946,778) can be adapted to
produce single chain antibodies to the polypeptides of the
disclosure. Alternatively, transgenic mice may be used to express
humanized antibodies to these polypeptides or fragments thereof.
Antibodies generated against the polypeptides of the disclosure may
be used in screening for similar polypeptides (e.g., enzymes) from
other organisms and samples. In such techniques, polypeptides from
the organism are contacted with the antibody and those polypeptides
which specifically bind the antibody are detected. Any of the
procedures described above may be used to detect antibody
binding.
Screening Methodologies and "On-Line" Monitoring Devices
[0235] In practicing the methods of the disclosure, a variety of
apparatus and methodologies can be used to in conjunction with the
polypeptides and nucleic acids of the disclosure, e.g., to screen
polypeptides for enzyme activity, to screen compounds as potential
modulators, e.g., activators or inhibitors, of an enzyme activity,
for antibodies that bind to a polypeptide of the disclosure, for
nucleic acids that hybridize to a nucleic acid of the disclosure,
to screen for cells expressing a polypeptide of the disclosure and
the like. Arrays, or "Biochips"
[0236] Nucleic acids or polypeptides of the disclosure can be
immobilized to or applied to an array. Arrays can be used to screen
for or monitor libraries of compositions (e.g., small molecules,
antibodies, nucleic acids, etc.) for their ability to bind to or
modulate the activity of a nucleic acid or a polypeptide of the
disclosure. For example, in one aspect of the disclosure, a
monitored parameter is transcript expression of an enzyme gene. One
or more, or, all the transcripts of a cell can be measured by
hybridization of a sample including transcripts of the cell, or,
nucleic acids representative of or complementary to transcripts of
a cell, by hybridization to immobilized nucleic acids on an array,
or "biochip." By using an "array" of nucleic acids on a microchip,
some or all of the transcripts of a cell can be simultaneously
quantified. Alternatively, arrays including genomic nucleic acid
can also be used to determine the genotype of a newly engineered
strain made by the methods of the disclosure. Polypeptide arrays"
can also be used to simultaneously quantify a plurality of
proteins. The present disclosure can be practiced with any known
"array," also referred to as a "microarray" or "nucleic acid array"
or "polypeptide array" or "antibody array" or "biochip," or
variation thereof. Arrays are generically a plurality of "spots" or
"target elements," each target element including a defined amount
of one or more biological molecules, e.g., oligonucleotides,
immobilized onto a defined area of a substrate surface for specific
binding to a sample molecule, e.g., mRNA transcripts.
[0237] In practicing the methods of the disclosure, any known array
and/or method of making and using arrays can be incorporated in
whole or in part, or variations thereof, as described, for example,
in U.S. Pat. Nos. 6,277,628; 6,277,489; 6,261,776; 6,258,606;
6,054,270; 6,048,695; 6,045,996; 6,022,963; 6,013,440; 5,965,452;
5,959,098; 5,856,174; 5,830,645; 5,770,456; 5,632,957; 5,556,752;
5,143,854; 5,807,522; 5,800,992; 5,744,305; 5,700,637; 5,556,752;
5,434,049; see also, e.g., WO 99/51773; WO 99/09217; WO 97/46313;
WO 96/17958; see also, e.g., Johnston (1998) "Gene chips: Array of
hope for understanding gene regulation", Curr. Biol. 8:R171-R174;
Schummer (1997) "Inexpensive Handheld Device for the Construction
of High-Density Nucleic Acid Arrays", Biotechniques 23:1087-1092;
Kern (1997) "Direct hybridization of large-insert genomic clones on
high-density gridded cDNA filter arrays", Biotechniques 23:120-124;
Solinas-Toldo (1997) "Matrix-Based Comparative Genomic
Hybridization: Biochips to Screen for Genomic Imbalances", Genes,
Chromosomes & Cancer20:399-407; Bowtell (1999) "Options
Available--From Start to Finish.about.for Obtaining Expression Data
by Microarray", Nature Genetics Supp. 21:25-32. See also published
U.S. patent applications Nos. 20010018642; 20010019827;
20010016322; 20010014449; 20010014448; 20010012537;
20010008765.
Capillary Arrays
[0238] Capillary arrays, such as the GIGAMATRIX.TM. Diversa
Corporation, San Diego, Calif., can be used in the methods of the
disclosure. Nucleic acids or polypeptides of the disclosure can be
immobilized to or applied to an array, including capillary arrays.
Arrays can be used to screen for or monitor libraries of
compositions (e.g., small molecules, antibodies, nucleic acids,
etc.) for their ability to bind to or modulate the activity of a
nucleic acid or a polypeptide of the disclosure. Capillary arrays
provide another system for holding and screening samples. For
example, a sample screening apparatus can include a plurality of
capillaries formed into an array of adjacent capillaries, wherein
each capillary includes at least one wall defining a lumen for
retaining a sample. The apparatus can further include interstitial
material disposed between adjacent capillaries in the array, and
one or more reference indicia formed within of the interstitial
material. A capillary for screening a sample, wherein the capillary
is adapted for being bound in an array of capillaries, can include
a first wall defining a lumen for retaining the sample, and a
second wall formed of a filtering material, for filtering
excitation energy provided to the lumen to excite the sample. A
polypeptide or nucleic acid, e.g., a ligand, can be introduced into
a first component into at least a portion of a capillary of a
capillary array. Each capillary of the capillary array can include
at least one wall defining a lumen for retaining the first
component. An air bubble can be introduced into the capillary
behind the first component. A second component can be introduced
into the capillary, wherein the second component is separated from
the first component by the air bubble. A sample of interest can be
introduced as a first liquid labeled with a detectable particle
into a capillary of a capillary array, wherein each capillary of
the capillary array includes at least one wall defining a lumen for
retaining the first liquid and the detectable particle, and wherein
the at least one wall is coated with a binding material for binding
the detectable particle to the at least one wall. The method can
further include removing the first liquid from the capillary tube,
wherein the bound detectable particle is maintained within the
capillary, and introducing a second liquid into the capillary tube.
The capillary array can include a plurality of individual
capillaries including at least one outer wall defining a lumen. The
outer wall of the capillary can be one or more walls fused
together. Similarly, the wall can define a lumen that is
cylindrical, square, hexagonal or any other geometric shape so long
as the walls form a lumen for retention of a liquid or sample. The
capillaries of the capillary array can be held together in close
proximity to form a planar structure. The capillaries can be bound
together, by being fused (e.g., where the capillaries are made of
glass), glued, bonded, or clamped side-by-side. The capillary array
can be formed of any number of individual capillaries, for example,
a range from 100 to 4,000,000 capillaries. A capillary array can
form a micro titer plate having about 100,000 or more individual
capillaries bound together.
Engineering Conditionally Active Antibodies
[0239] Conditionally active antibodies may be engineered to
generate multispecific conditionally active antibodies. The
multispecific antibody may be an antibody with polyepitopic
specificity, as described in WO 2013/170168. Multispecific
antibodies include, but are not limited to, an antibody including a
heavy chain variable domain (V.sub.H) and a light chain variable
domain (V.sub.L), where the V.sub.HV.sub.L unit has polyepitopic
specificity, antibodies having two or more V.sub.L and V.sub.H
domains where each V.sub.HV.sub.L unit binds to a different
epitope, antibodies having two or more single variable domains with
each single variable domain binding to a different epitope, and
antibodies including one or more antibody fragments as well as
antibodies including antibody fragments that have been linked
covalently or non-covalently.
[0240] To construct multispecific antibodies, including bispecific
antibodies, antibody fragments having at least one free sulfhydryl
group are obtained. The antibody fragments may be obtained from
full-length conditionally active antibodies. The conditionally
active antibodies may be digested enzymatically to produce antibody
fragments. Exemplary enzymatic digestion methods include, but are
not limited to, pepsin, papain and Lys-C. Exemplary antibody
fragments include, but are not limited to, Fab, Fab', F(ab')2, Fv,
diabodies (Db); tandem diabodies (taDb), linear antibodies (see
U.S. Pat. No. 5,641,870, Example 2; Zapata et al., Protein Eng.,
vol. 8, pages 1057-1062 (1995)); one-armed antibodies, single
variable domain antibodies, minibodies (Olafsen et al (2004)
Protein Eng. Design & Sel., vol. 17, pages 315-323),
single-chain antibody molecules, fragments produced by a Fab
expression library, anti-idiotypic (anti-Id) antibodies,
complementary determining regions (CDRs), and epitope-binding
fragments. Antibody fragments may also be produced using DNA
recombinant technology. The DNA encoding the antibody fragments may
be cloned into plasmid expression vectors or phagemid vectors and
expressed directly in E. Coli. Antibody enzymatic digestion
methods, DNA cloning and recombinant protein expression methods are
well known to those skilled in the art.
[0241] Antibody fragments may be purified using conventional
techniques and may be subjected to reduction to generate a free
thiol group. Antibody fragments having a free thiol group may be
reacted with a cross-linker, for example, bis-maleimide. Such
crosslinked antibody fragments are purified and then reacted with a
second antibody fragment having a free thiol group. The final
product in which two antibody fragments are crosslinked is
purified. In certain embodiments, each antibody fragment is a Fab
and the final product, in which the two Fabs are linked through
bis-maleimide, is referred to herein as bismaleimido-(thio-Fab)2,
or bis-Fab. Such multispecific antibodies and antibody analogs,
including bis-Fabs, can be exploited to quickly synthesize a large
number of antibody fragment combinations, or structural variants of
native antibodies or particular antibody/fragment combinations.
[0242] Multispecific antibodies can be synthesized with modified
cross-linkers such that additional functional moieties may be
attached to the multispecific antibodies. Modified cross-linkers
allow for attachment of any sulfhydryl-reactive moiety. In one
embodiment, N-succinimidyl-S-acetylthioacetate (SATA) is attached
to bis-maleimide to form bis-maleimido-acetylthioacetate (BMata).
After deprotection of the masked thiol group, any functional group
having a sulfhydryl-reactive (or thiol-reactive) moiety may be
attached to the multispecific antibodies.
[0243] Exemplary thiol-reactive reagents include a multifunctional
linker reagent, a capture, i.e. an affinity, label reagent (e.g. a
biotin-linker reagent), a detection label (e.g. a fluorophore
reagent), a solid phase immobilization reagent (e.g. SEPHAROSE.TM.,
polystyrene, or glass), or a drug-linker intermediate. One example
of a thiol-reactive reagent is N-ethyl maleimide (NEM). Such
multispecific antibodies or antibody analogs having modified
cross-linkers may be further reacted with a drug moiety reagent or
other label. Reaction of a multispecific antibody or antibody
analog with a drug-linker intermediate provides a multispecific
antibody-drug conjugate or antibody analog-drug conjugate,
respectively.
[0244] Other techniques for making multispecific antibodies may
also be used in the present invention. References describing these
techniques include: (1) Milstein and Cuello, Nature, vol. 305, page
537 (1983)), WO 93/08829, and Traunecker et al., EMBO J., vol. 10,
page 3655 (1991) on recombinant co-expression of two immunoglobulin
heavy chain-light chain pairs having different specificities; (2)
U.S. Pat. No. 5,731,168 on "knob-in-hole" engineering; (3) WO
2009/089004A1 on engineering electrostatic steering effects for
making antibody Fc-heterodimeric molecules; (4) U.S. Pat. No.
4,676,980, and Brennan et al., Science, vol. 229, page 81 (1985) on
cross-linking two or more antibodies or fragments; (5) Kostelny et
al., J. Immunol., vol. 148, pages 1547-1553 (1992) on using leucine
zippers to produce bi-specific antibodies; (6) Hollinger et al.,
Proc. Natl. Acad. Sci. USA, vol. 90, pages 6444-6448 (1993) on
using "diabody" technology for making bispecific antibody
fragments; (7) Gruber et al., J. Immunol., vol. 152, page 5368
(1994) on using single-chain Fv (sFv) dimers; (8) Tutt et al. J.
Immunol. 147: 60 (1991) on preparing trispecific antibodies; and
(9) US 2006/0025576A1 and Wu et al. Nature Biotechnology, vol. 25,
pages 1290-1297 (2007) on engineered antibodies with three or more
functional antigen binding sites, including "Octopus antibodies" or
"dual-variable domain immunoglobulins" (DVDs).
[0245] Multispecific antibodies of the present invention may also
be generated as described in WO/2011/109726.
[0246] In one embodiment, a conditionally active antibody for
crossing the blood-brain barrier (BBB) is engineered to make a
multispecific antibody (e.g. a bispecific antibody). This
multispecific antibody includes a first antigen binding site which
binds a BBB-R and a second antigen binding site which binds a brain
antigen. At least the first antigen binding site for BBB-R is
conditionally active. A brain antigen is an antigen expressed in
the brain, which can be targeted with an antibody or small
molecule. Examples of such antigens include, without limitation:
beta-secretase 1 (BACE1), amyloid beta (Abeta), epidermal growth
factor receptor (EGFR), human epidermal growth factor receptor 2
(HER2), Tau, apolipoprotein E4 (ApoE4), alpha-synuclein, CD20,
huntingtin, prion protein (PrP), leucine rich repeat kinase 2
(LRRK2), parkin, presenilin 1, presenilin 2, gamma secretase, death
receptor 6 (DR6), amyloid precursor protein (APP), p75 neurotrophin
receptor (p75NTR), and caspase 6. In one embodiment, the antigen is
BACE1.
[0247] The BBB has endogenous transport systems that are mediated
by a BBB receptor (BBB-R), which is a specific receptor that allows
transport of macromolecules across the BBB. For example, an
antibody that can bind to a BBB-R may be transported across BBB
using the endogenous transport systems. Such an antibody may serve
as a vehicle for transport of drugs or other agents across BBB by
using the endogenous BBB receptor mediated transport system that
traverses the BBB. Such antibodies need not have high affinity to a
BBB-R. Antibodies that are not conditionally active antibodies with
low affinities for BBB-R have been described as crossing the BBB
more efficiently than a high affinity antibody, as described in US
2012/0171120.
[0248] Another method for engineering antibodies to enter the brain
is to engineer antibodies to be delivered to the brain via the
central nervous system lymphatic vessels. Thus, the antibodies can
be engineered to bind to or mimic immune cells such as T-cells, or
synovial or cerebrospinal fluids that travel to the central nervous
system via lymphatic vessels. Details of the lymphatic vessels of
the central nervous system are described in, for example, Louveau,
A., et al., "Structural and functional features of central nervous
system lymphatic vessels," Nature523, pp. 337-341, 16 Jul. 2015 and
the articles citing this article that are publicly available as of
the date of filing of this application.
[0249] Unlike traditional antibodies, conditionally active
antibodies are not required to have low affinity for BBB-R to cross
the BBB and remain inside the brain. Conditionally active
antibodies can have high affinity for the BBB-R on the blood side
of the BBB, and little or no affinity on the brain side of the BBB.
Drugs, such as drug conjugates, may be coupled to a conditionally
active antibody to be transported with the antibody across the BBB
into the brain.
[0250] A BBB-R is a transmembrane receptor protein expressed on
brain endothelial cells which is capable of transporting molecules
across the blood-brain barrier. Examples of BBB-R include
transferrin receptor (TfR), insulin receptor, insulin-like growth
factor receptor (IGF-R), low density lipoprotein receptors
including without limitation low density lipoprotein
receptor-related protein 1 (LRP1) and low density lipoprotein
receptor-related protein 8 (LRP8), and heparin-binding epidermal
growth factor-like growth factor (HB-EGF). An exemplary BBB-R
herein is a transferrin receptor (TfR). The TfR is a transmembrane
glycoprotein (with a molecular weight of about 180,000) composed of
two disulphide-bonded sub-units (each of apparent molecular weight
of about 90,000) involved in iron uptake in vertebrates.
[0251] In some embodiments, the present invention provides a
conditionally active antibody generated from a parent or wild-type
antibody against a BBB-R. The conditionally active antibody binds
the BBB-R on the blood side of the BBB, and has a lower affinity to
the BBB-R than the parent or wild-type antibody on the brain side
of the BBB. In some other embodiments, the conditionally active
antibody has affinity to the BBB-R than the wild type or parent
antibody on the blood side of the BBB, and has no affinity to the
BBB-R on the brain side of the BBB.
[0252] Blood plasma is a body fluid that is very different from
brain extracellular fluid (ECF). As discussed by Somjen ("Ions in
the Brain: Normal Function, Seizures, and Stroke," Oxford
University Press, 2004, pages 16 and 33) and Redzic ("Molecular
biology of the blood-brain and the blood-cerebrospinal fluid
barriers: similarities and differences," Fluids and Barriers of the
CNS, vol. 8:3, 2011), the brain extracellular fluid has
significantly less K.sup.+, more Mg.sup.2+ and H.sup.+ than blood
plasma. The differences in ion concentrations between blood plasma
and brain ECF lead to significant differences in osmotic pressure
and osmolality between the two fluids. Table 1 shows the
concentrations of common ions in millimoles for both blood plasma
and brain ECF.
TABLE-US-00001 TABLE 1 Common ions in plasma (arterial plasma) and
brain extracellular fluid (CSF) ARTERIAL PLASMA CSF HUMAN RAT HUMAN
RAT Na.sup.+ 150 148 147 152 K.sup.+ 4.6 5.3 2.9 3.4 Ca, total 2.4
3.1 1.14 1.1 Ca.sup.2+, free 1.4 1.5 1.0 1.0 pCa Mg, total 0.86 0.8
1.15 1.3 Mg.sup.2+, free 0.47 0.44 0.7 0.88 H.sup.+ 0.000039
0.000032 0.000047 0.00005 pH 7.41 7.5 7.3 7.3 Cl.sup.- 99 119
HCO.sub.3.sup.- 26.8 31 23.3 28
[0253] Brain ECF also contains significantly more lactate than
blood plasma and significantly less glucose than blood plasma
(Abi-Saab et al., "Striking Differences in Glucose and Lactate
Levels Between Brain Extracellular Fluid and Plasma in Conscious
Human Subjects: Effects of Hyperglycemia and Hypoglycemia," Journal
of Cerebral Blood Flow & Metabolism, vol. 22, pages 271-279,
2002).
[0254] Thus, there are several physiological conditions that are
different between the two sides of the BBB, such as pH,
concentrations of various substances (such as lactose, glucose, K+,
Mg2+), osmotic pressure and osmolality. For the physiological
condition of pH, human blood plasma has a higher pH than human
brain ECF. For the physiological condition of K+ concentration,
brain ECF has a lower K+ concentration than human blood plasma. For
the physiological condition of Mg2+ concentration, the human brain
ECF has significantly more Mg2+ than human blood plasma. For the
physiological condition of osmotic pressure, the human brain ECF
has an osmotic pressure that is different from that of human blood
plasma. In some embodiments, the physiological conditions of brain
ECF may be the composition, pH, osmotic pressure and osmolality of
brain ECF of patients with a particular neurological disorder,
which may be different from the physiological condition of the
brain ECF of the general population.
[0255] The present invention thus provides a method for evolving a
DNA that encodes a template antibody against a BBB-R to create a
mutant DNA library. The mutant DNA library is then expressed to
obtain mutant antibodies. The mutant antibodies are screened for a
conditionally active antibody that has binds to the BBB-R under at
least one blood plasma physiological condition and has a low or no
affinity to the BBB-R under at least one brain physiological
condition in the brain ECF compared to the template antibody. Thus,
the selected mutant antibody has a low or high affinity to the
BBB-R at the blood plasma side and a low or no affinity to the
BBB-R at the brain ECF side. This selected mutant antibody is
useful as a conditionally active antibody for transport across the
BBB.
[0256] Such a conditionally active antibody is advantageous for
crossing the BBB and remaining in the brain ECF. The low affinity
to the BBB-R at the brain side lowers the rate (or removes) the
conditionally active antibody is transported back across the BBB
out of the brain and back into the blood relative to the template
antibody.
[0257] In some other embodiments, the present invention provides a
method for evolving a DNA that encodes a template antibody against
a BBB-R to create a mutant DNA library. The mutant DNA library is
then expressed to obtain mutant antibodies. The mutant antibodies
are screened for a conditionally active antibody that binds to the
BBB-R under at least one blood plasma physiological condition and
little or no affinity to the BBB-R under at least one brain
physiological condition. Thus, the selected mutant antibody has
affinity to the BBB-R at the plasma side and little or no affinity
to the BBB-R at the brain ECF side. This selected mutant antibody
is a conditionally active antibody.
[0258] Such a conditionally active antibody is advantageous in
crossing the BBB and remaining in the brain ECF. After binding to
the BBB-R at the blood plasma side, the conditionally active
antibody is transported across the BBB, and the little to no
affinity to the BBB-R at the brain ECF side means that the
conditionally active antibody is unlikely to be transported out of
the brain.
[0259] The affinity of the conditionally active antibody to a BBB-R
may be measured by its half maximal inhibitory concentration
(IC50), which is a measure of how much of the antibody is needed to
inhibit the binding of a known BBB-R ligand to the BBB-R by 50%. A
common approach is to perform a competitive binding assay, such as
competitive ELISA assy. An exemplary competitive ELISA assay to
measure IC50 on TfR (a BBB-R) is one in which increasing
concentrations of anti-TfR antibody compete against biotinylated
TfR.sup.A for binding to TfR. The anti-TfR antibody competitive
ELISA may be performed in Maxisorp plates (Neptune, N.J.) coated
with 2.5 .mu.g/ml of purified murine TfR extracellular domain in
PBS at 4.degree. C. overnight. Plates are washed with PBS/0.05%
Tween 20 and blocked using Superblock blocking buffer in PBS
(Thermo Scientific, Hudson, N.H.). A titration of each individual
anti-TfR antibody (1:3 serial dilution) is combined with
biotinylated anti-TfR.sup.A (0.5 nM final concentration) and added
to the plate for 1 hour at room temperature. Plates are washed with
PBS/0.05% Tween 20, and HRP-streptavidin (Southern Biotech,
Birmingham) is added to the plate and incubated for 1 hour at room
temperature. Plates are washed with PBS/0.05% Tween 20, and
biotinylated anti-TfR.sup.A bound to the plate is detected using
TMB substrate (BioFX Laboratories, Owings Mills).
[0260] A high IC50 indicates that more of the conditionally active
antibody is required to inhibit binding of the known ligand of a
BBB-R, and thus that the antibody's affinity for that BBB-R is
relatively low. Conversely, a low IC50 indicates that less of the
conditionally active antibody is required to inhibit binding of the
known ligand, and thus that the antibody's affinity for that BBB-R
is relatively high.
[0261] In some embodiments, the IC50 of the conditionally active
antibodies from a BBB-R in the blood plasma may be from about 1 nM
to about 100 .mu.M, or from about 5 nM to about 100 .mu.M, or from
about 50 nM to about 100 .mu.M, or from about 100 nM to about 100
.mu.M, or from about 5 nM to about 10 .mu.M, or from about 30 nM to
about 1 .mu.M, or from about 50 nM to about 1 .mu.M.
Conditionally Active Biologic Proteins for Synovial Fluid
[0262] Joint diseases are a major cause of disability and early
retirement in the industrialized countries. Joint diseases often
lead to damage at a joint which is difficult to repair. Synovial
fluid is a body fluid that is found in the synovial cavity of the
joints (e.g., knee, hip, shoulder) of a human or animal body
between the cartilage and synovium of facing articulating surfaces.
Synovial fluid provides nourishment to the cartilage and also
serves as a lubricant for the joints. The cells of the cartilage
and synovium secrete fluid that serve as a lubricant between the
articulating surfaces. Human synovial fluid includes approximately
85% water. It is derived from the dialysate of blood plasma, which
itself is made up of water, dissolved proteins, glucose, clotting
factors, mineral ions, hormones, etc. Proteins such as albumin and
globulins are present in synovial fluid and are believed to play an
important role in the lubricating the joint area. Some other
proteins are also found in human synovial fluid, including the
glycoproteins such as alpha-1-acid glycoprotein (AGP),
alpha-1-antitrypsin (A1AT) and lubricin.
[0263] Synovial fluid has a composition that is very different from
other parts of the body. Thus, synovial fluid has physiological
conditions that are different from other parts of the body, such as
the blood plasma. For example, synovial fluid has less than about
10 mg/dL of glucose whereas the mean normal glucose level in human
blood plasma is about 100 mg/dL, fluctuating within a range between
70 and 100 mg/dL throughout the day. In addition, the total protein
level in the synovial fluid is about one third of the blood plasma
protein level since large molecules such as proteins do not easily
pass through the synovial membrane into the synovial fluid. It has
also been found that the pH of human synovial fluid is higher than
the pH in human plasma (Jebens et al., "On the viscosity and pH of
synovial fluid and the pH of blood," The Journal of Bone and Joint
Surgery, vol. 41 B, pages 388-400, 1959; Farr et al., "Significance
of the hydrogen ion concentration in synovial fluid in Rheumatoid
Arthritis," Clinical and Experimental Rheumatology, vol. 3, pages
99-104, 1985).
[0264] Thus, the synovial fluid has several physiological
conditions that are different from those of the other parts of
body, such as the physiological conditions in the blood plasma. The
synovial fluid has a pH that is higher than other parts of the
body, especially the blood plasma. The synovial fluid has a lower
concentration of glucose than other parts of the body, such as
blood plasma. The synovial fluid also has a lower concentration of
protein than other parts of the body, such as blood plasma.
[0265] Several antibodies have been used to treat joint disease by
introducing the antibodies into the synovial fluid. For example,
the synovial fluid in an injured joint is known to contain many
factors which have an influence on the progression of
osteoarthritis (see, for example, Fernandes, et al., "The Role of
Cytokines in Osteoarthritis Pathophysiology", Biorheology, vol. 39,
pages 237-246, 2002). Cytokines, such as Interleukin-1 (IL-I) and
Tumor Necrosis Factor-.alpha. (TNF-.alpha.), which are produced by
activated synoviocytes, are known to upregulate matrix
metalloproteinase (MMP) gene expression. Upregulation of MMP leads
to degredation of the matrix and non-matrix proteins in the joints.
Antibodies that neutralize cytokines may stop the progression of
osteoarthritis.
[0266] Using antibodies as drug is a promising strategy for the
treatment of joint diseases. For example, antibodies (such as
antibody against aggrecan or aggrecanase) have been developed to
treat osteoarthritis, which has by far the greatest prevalence
among joint diseases (WO1993/022429A1). An antibody against
acetylated high-mobility group box 1 (HMGB1) has been developed for
diagnosis or treatment of joint diseases that are inflammatory,
autoimmune, neurodegenerative or malignant diseases/disorders, such
as arthritis. This antibody may be used to detect the acetylated
form of HMGB1 in synovial fluid (WO 2011/157905A1). Another
antibody (CD20 antibody) has also been developed to treat damage to
connective tissue and cartilage of the joints.
[0267] However, the antigens of these antibodies are often
expressed in other parts of the body carrying important
physiological functions. Antibodies against these antigens, though
efficacious in treating joint diseases, may also significantly
interfere with the normal physiological functions of these antigens
in other parts of the body. Therefore, severe side effects may be
experienced by patients. It is thus desirable to develop
therapeutics, such as antibodies against cytokines or other
antigens that can preferentially bind to their antigens (proteins
or other macromolecules) at higher affinity in the synovial fluid,
while not binding or only weakly binding to the same antigens in
other parts of the body in order to reduce side effects.
[0268] Such conditionally active biologic proteins may be
conditionally active antibodies. In some embodiments, the present
invention also provides conditionally active biologic proteins that
are proteins other than antibodies. For example, a conditionally
active immune regulator may be developed by the present invention
for preferentially regulating the immune response in the synovial
fluid, which may less or no effect on the immune response at other
parts of the body.
[0269] The conditionally active biologic proteins may be
conditionally active suppressors of cytokine signaling (SOCS). Many
of these SOCS are involved in inhibiting the JAK-STAT signaling
pathway. The conditionally active suppressors of cytokine signaling
can preferentially suppress the cytokine signaling in the synovial
fluid, while not or to a lesser extent suppressing the cytokine
signaling in other parts of the body.
[0270] In some embodiments, the present invention provides a
conditionally active biologic protein derived from a wild-type
biologic protein. The conditionally active biologic protein has a
lower activity under at least one physiological condition in
certain parts of the body such as in blood plasma than the
wild-type biologic protein, and has a higher activity than the
wild-type biologic protein under at least one physiological
condition in the synovial fluid. Such conditionally active biologic
proteins can preferentially function in the synovial fluid, but not
or to a lesser extent act upon other parts of the body.
Consequently, such conditionally active biologic proteins may have
reduced side effects.
[0271] In some embodiments, the conditionally active biologic
proteins are antibodies against an antigen in or exposed to
synovial fluid. Such antigens may be any proteins involved in
immune response/inflammation in a joint disease, though the antigen
is often a cytokine. The conditionally active antibody has a lower
affinity to the antigen than the wild-type antibody for the same
antigen under at least one physiological condition in other parts
of the body (such as blood plasma), while has higher affinity for
the antigen than the wild-type antibody under at least one
physiological condition of synovial fluid. Such conditionally
active antibodies can bind weakly or not at all to the antigen in
other parts of the body, but bind, for example bind strongly and
tightly or bind stronger to the antigen in synovial fluid.
Conditionally Active Biologic Proteins for Tumors
[0272] Cancer cells in a solid tumor are able to form a tumor
microenvironment in their surroundings to support the growth and
metastasis of the cancer cells. A tumor microenvironment is the
cellular environment in which the tumor exists, including
surrounding blood vessels, immune cells, fibroblasts, other cells,
soluble factors, signaling molecules, an extracellular matrix, and
mechanical cues that can promote neoplastic transformation, support
tumor growth and invasion, protect the tumor from host immunity,
foster therapeutic resistance, and provide niches for dormant
metastases to thrive. The tumor and its surrounding
microenvironment are closely related and interact constantly.
Tumors can influence their microenvironment by releasing
extracellular signals, promoting tumor angiogenesis and inducing
peripheral immune tolerance, while the immune cells in the
microenvironment can affect the growth and evolution of cancerous
cells. See Swarts et al. "Tumor Microenvironment Complexity:
Emerging Roles in Cancer Therapy," Cancer Res, vol., 72, pages
2473-2480, 2012.
[0273] The tumor microenvironment is often hypoxic. As the tumor
mass increases, the interior of the tumor grows farther away from
existing blood supply, which leads to difficulties in fully
supplying oxygen to the tumor microenvironment. The partial oxygen
pressure in the tumor environment is below 5 mm Hg in more than 50%
of locally advanced solid tumors, in comparison with a partial
oxygen pressure at about 40 mm Hg in blood plasma. In contrast,
other parts of the body are not hypoxic. The hypoxic environment
leads to genetic instability, which is associated with cancer
progression, via downregulating nucleotide excision repair and
mismatch repair pathways. Hypoxia also causes the upregulation of
hypoxia-inducible factor 1 alpha (HIF1-.alpha.), which induces
angiogenesis, and is associated with poorer prognosis and the
activation of genes associated with metastasis. See Weber et al.,
"The tumor microenvironment," Surgical Oncology, vol. 21, pages
172-177, 2012 and Blagosklonny, "Antiangiogenic therapy and tumor
progression," Cancer Cell, vol. 5, pages 13-17, 2004.
[0274] In addition, tumor cells tend to rely on energy generated
from lactic acid fermentation, which does not require oxygen. So
tumor cells are less likely to use normal aerobic respiration that
does require oxygen. A consequence of using lactic acid
fermentation is that the tumor microenvironment is acidic (pH
6.5-6.9), in contrast to other parts of the body which are
typically either neutral or slightly basic. For example, human
blood plasma has a pH of about 7.4. See Estrella et al., "Acidity
Generated by the Tumor Microenvironment Drives Local Invasion,"
Cancer Research, vol. 73, pages 1524-1535, 2013. The nutrient
availability in the tumor microenvironment is also low due to the
relatively high nutrient demand of the proliferating cancer cells,
in comparison with cells located in other parts of the body.
[0275] Further, the tumor microenvironment also contains many
distinct cell types not commonly found in other parts of the body.
These cell types include endothelial cells and their precursors,
pericytes, smooth muscle cells, Wbroblasts, carcinoma-associated
Wbroblasts, myoWbroblasts, neutrophils, eosinophils, basophils,
mast cells, T and B lymphocytes, natural killer cells and antigen
presenting cells (APC) such as macrophages and dendritic cells
(Lorusso et al., "The tumor microenvironment and its contribution
to tumor evolution toward metastasis," Histochem Cell Biol, vol.
130, pages 1091-1103, 2008).
[0276] Accordingly, the tumor microenvironment has at least several
physiological conditions that are different from those of other
parts of body, such as the physiological conditions in blood
plasma. The tumor microenvironment has a pH (acidic) that is lower
than other parts of the body, especially the blood plasma (pH 7.4).
The tumor microenvironment has a lower concentration of oxygen than
other parts of the body, such as blood plasma. Also, the tumor
microenvironment has a lower nutrient availability than other parts
of the body, especially the blood plasma. The tumor
microenvironment also has some distinct cell types that are not
commonly found in other parts of the body, especially the blood
plasma.
[0277] Some cancer drugs include antibodies that can penetrate into
the tumor microenvironment and act upon the cancer cells therein.
Antibody-based therapy for cancer is well established and has
become one of the most successful and important strategies for
treating patients with haematological malignancies and solid
tumors. There is a broad array of cell surface antigens that are
expressed by human cancer cells that are overexpressed, mutated or
selectively expressed in cancer cells compared with normal tissues.
These cell surface antigens are excellent targets for antibody
cancer therapy.
[0278] Cancer cell surface antigens that may be targeted by
antibodies fall into several different categories. Haematopoietic
differentiation antigens are glycoproteins that are usually
associated with clusters of differentiation (CD) groupings and
include CD20, CD30, CD33 and CD52. Cell surface differentiation
antigens are a diverse group of glycoproteins and carbohydrates
that are found on the surface of both normal and tumor cells.
Antigens that are involved in growth and differentiation signaling
are often growth factors and growth factor receptors. Growth
factors that are targets for antibodies in cancer patients include
CEA2, epidermal growth factor receptor (EGFR; also known as
ERBB1)12, ERBB2 (also known as HER2)13, ERBB3 (REF. 18), MET (also
known as HGFR)19, insulin-like growth factor 1 receptor (IGF1R)20,
ephrin receptor A3 (EPHA3)21, tumor necrosis factor (TNF)-related
apoptosis-inducing ligand receptor 1 (TRAILR1; also known as
TNFRSF10A), TRAILR2 (also known as TNFRSF10B) and receptor
activator of nuclear factor-KB ligand (RANKL; also known as
TNFSF11)22. Antigens involved in angiogenesis are usually proteins
or growth factors that support the formation of new
microvasculature, including vascular endothelial growth factor
(VEGF), VEGF receptor (VEGFR), integrin .alpha.V.beta.3 and
integrin .alpha.5.beta.1 (REF. 10). Tumor stroma and the
extracellular matrix are indispensable support structures for a
tumor. Stromal and extracellular matrix antigens that are
therapeutic targets include fibroblast activation protein (FAP) and
tenascin. See Scott et al., "Antibody therapy of cancer," Nature
Reviews Cancer, vol. 12, pages 278-287, 2012.
[0279] In addition to antibodies, other biologic proteins have also
shown promise in treating cancers. Examples include tumor
suppressors such as Retinoblastoma protein (pRb), p53, pVHL, APC,
CD95, ST5, YPEL3, ST7, and ST14. Some proteins that induce
apoptosis in cancer cells may also be introduced into tumors for
shrinking the size of tumors. There are at least two mechanisms
that can induce apoptosis in tumors: the tumor necrosis
factor-induced mechanism and the Fas-Fas ligand-mediated mechanism.
At least some of the proteins involved in either of the two
apoptotic mechanisms may be introduced to tumors for treatment.
[0280] Cancer stem cells are cancer cells that have the ability to
give rise to all cell types found in a particular cancer sample,
and are therefore tumor-forming. They may generate tumors through
the stem cell processes of self-renewal and differentiation into
multiple cell types. It is believed that cancer stem cells persist
in tumors as a distinct population and cause relapse and metastasis
by giving rise to new tumors. Development of specific therapies
targeted at cancer stem cells may improve the survival and quality
of life of cancer patients, especially for sufferers of metastatic
disease.
[0281] These drugs for treating tumors often interfere with normal
physiological functions in other parts of the body besides tumors.
For example, proteins inducing apoptosis in tumors may also induce
apoptosis in some other parts of the body thus causing side
effects. In embodiments where an antibody is used to treat tumors,
the antigen of the antibody may also be expressed in other parts of
the body where they perform normal physiological functions. For
example, monoclonal antibody bevacizumab (targeting vascular
endothelial growth factor) to stop tumor blood vessel growth. This
antibody can also prevent blood vessel growth or repair in other
parts of the body, thus causing bleeding, poor wound healing, blood
clots, and kidney damage. Development of a conditionally active
biologic protein that concentrates on targeting mainly or solely
tumors is highly desirable for more effective tumor therapies.
[0282] In some embodiments, the present invention provides a
conditionally active biologic protein generated from a wild-type
biologic protein that may be a candidate for tumor treatment. The
conditionally active biologic protein has lower activity under at
least one physiological condition in parts of the body other than
the tumor microenvironment such as blood plasma than the wild-type
biologic protein, while it has higher activity under at least one
physiological condition in the tumor microenvironment than the
wild-type biologic protein. Such conditionally active biologic
proteins can preferentially act upon cancer cells in the tumor
microenvironment for treating tumors, and thus will be less likely
to cause side effects. In the embodiment where the biologic protein
is an antibody against an antigen on the surface of the tumor cells
where the antigen is exposed to the tumor microenvironment, the
conditionally active antibody has lower affinity to the antigen
than the wild-type antibody in other parts of the body, e.g. a
non-tumor microenvironment, while it has higher affinity to the
antigen than the wild-type antibody in the tumor microenvironment.
Such conditionally active antibodies can bind weakly or not at all
to the antigen in other parts of the body, but have greater
binding, or bind strongly and tightly, to the antigen in the tumor
microenvironment.
[0283] In some embodiments, the conditionally active antibody is an
antibody against an immune checkpoint protein, resulting in
inhibition of the immune checkpoints. Such conditionally active
antibodies have at least one of (1) an increased binding affinity
to the immune checkpoint protein in a tumor microenvironment in
comparison to the wild-type antibody from which the conditionally
active antibody is derived, and, (2) a decreased binding affinity
to the immune checkpoint protein in a non-tumor microenvironment in
comparison to the wild-type antibody from which the conditionally
active antibody is derived.
[0284] The immune checkpoints function as endogenous inhibitory
pathways for the immune system to maintain self-tolerance and
modulate the duration and extent of immune response to antigenic
stimulation, i.e., foreign molecules, cells and tissues See
Pardoll, Nature Reviews Cancer, vol. 12, pages 252-264, 2012
Inhibition of immune checkpoints by suppressing one or more
checkpoint proteins can cause super-activation of the immune
system, especially T-cells, thus inducing the immune system to
attack tumors. Checkpoint proteins suitable for the present
invention include CTLA4 and its ligands CD80 and CD86, PD1 and its
ligands PDL1 and PDL2, T cell immunoglobulin and mucin protein-3
(TIM3) and its ligand GALS, B and T lymphocyte attenuator (BTLA)
and its ligand HVEM (herpesvirus entry mediator), receptors such as
killer cell immunoglobulin-like receptor (KIR), lymphocyte
activation gene-3 (LAGS) and adenosine A2a receptor (A2aR), as well
as ligands B7-H3 and B7-H4. Additional suitable immune checkpoint
proteins are described in Pardoll, Nature Reviews Cancer, vol. 12,
pages 252-264, 2012 and Nirschl & Drake, Clin Cancer Res, vol.
19, pages 4917-4924, 2013.
[0285] CTLA-4 and PD1 are two of the best known immune checkpoint
proteins. CTLA-4 can down-regulate pathways of T-cell activation
(Fong et al., Cancer Res. 69(2):609-615, 2009; and Weber, Cancer
Immunol. Immunother, 58:823-830, 2009). Blockading CTLA-4 has been
shown to augment T-cell activation and proliferation Inhibitors of
CTLA-4 include anti-CTLA-4 antibodies. Anti-CTLA-4 antibodies bind
to CTLA-4 and block the interaction of CTLA-4 with its ligands CD80
or CD86 thereby blocking the down-regulation of the immune
responses elicited by the interaction of CTLA-4 with its
ligand.
[0286] The checkpoint protein PD1 is known to suppress the activity
of T cells in peripheral tissues at the time of an inflammatory
response to infection and to limit autoimmunity. An in vitro PD1
blockade can enhance T-cell proliferation and cytokine production
in response to stimulation by specific antigen targets or by
allogeneic cells in mixed lymphocyte reactions. A strong
correlation between PD1 expression and reduced immune response was
shown to be caused by the inhibitory function of PD1, i.e., by
inducing immune checkpoints (Pardoll, Nature Reviews Cancer, 12:
252-264, 2012). A PD1 blockade can be accomplished by a variety of
mechanisms including antibodies that bind PD1 or its ligands, PDL1
or PDL2.
[0287] Past research has discovered antibodies against several
checkpoint proteins (CTLA4, PD1, PD-L1). These antibodies are
effective in treating tumors by inhibiting the immune checkpoints
thereby super-activating the immune system, especially the T-cells,
for attacking tumors (Pardoll, Nature Reviews Cancer, vol. 12,
pages 252-264, 2012). However, the super-activated T-cells may also
attack host cells and/or tissues, resulting in collateral damage to
a patient's body. Thus, therapy based on use of these known
antibodies for inhibition of immune checkpoints is difficult to
manage and the risk to the patient is a serious concern. For
example, an FDA approved antibody against CTLA-4 carries a black
box warning due to its high toxicity.
[0288] The present invention addresses the problem of collateral
damage by super-activated T-cells by providing conditionally active
antibodies against immune checkpoint proteins. These conditionally
active antibodies preferentially activate the immune checkpoints in
a tumor-microenvironment. At the same time, the immune checkpoints
in the non-tumor-microenvironment(s), e.g. normal body tissue, are
not inhibited or are less inhibited by the conditionally active
antibodies such that in the non-tumor microenvironment the
potential for collateral damage to the body is reduced. This goal
is achieved by engineering the conditionally active antibody to be
more active in the tumor microenvironment than in the non-tumor
microenvironment.
[0289] In some embodiments, the conditionally active antibody
against an immune checkpoint protein may have a ratio of binding
activity to an immune checkpoint protein in the
tumor-microenvironment to the binding activity to the same immune
checkpoint protein in a non-tumor microenvironment of at least
about 1.1, or at least about 1.2, or at least about 1.4, or at
least about 1.6, or at least about 1.8, or at least about 2, or at
least about 2.5, or at least about 3, or at least about 5, or at
least about 7, or at least about 8, or at least about 9, or at
least about 10, or at least about 15, or at least about 20. A
typical assay for measuring the binding activity of an antibody is
an ELISA assay.
[0290] Highly immunogenic tumors, such as malignant melanoma, are
most vulnerable to a super-activated immune system achieved by
immune system manipulation. Thus the conditionally active
antibodies against immune checkpoint proteins may be especially
effective for treating such highly immunogenic tumors. However,
other types of tumors are also vulnerable to a super-activated
immune system.
[0291] In some embodiments, the conditionally active antibodies
against the immune checkpoint proteins may be used in combination
therapy. For example, combination therapy may include a
conditionally active antibody against a tumor cell surface molecule
(tumor specific antigen) and a conditionally active antibody
against an immune checkpoint protein. In one embodiment, both the
binding activity of the conditionally active antibody to the tumor
cell surface molecule and the binding activity of the conditionally
active antibody to the immune checkpoint protein may reside in a
single protein, i.e., a bispecific conditionally active antibody as
disclosed herein. In some further embodiments, combination therapy
may include a conditionally active antibody against a tumor cell
surface molecule (tumor specific antigen) and two or more
conditionally active antibodies against two or more different
immune checkpoint proteins. In one embodiment, all of these binding
activities may reside in a single protein, i.e., a multispecific
antibody as disclosed herein.
[0292] Since the conditionally active antibodies are more active in
a tumor microenvironment in comparison with the activity of the
wild-type antibody against the same tumor cell surface molecule or
checkpoint protein from which the conditionally active antibody is
derived, these combination therapies can provide both an enhanced
efficacy and a significant reduction in toxicity. The reduced
toxicity of these conditionally active antibodies, especially the
antibodies against the immune checkpoint proteins, can allow safe
use of potent antibodies, such as ADC antibodies as described
herein, as well as a higher dose of the antibodies.
[0293] In some embodiments, the conditionally active antibodies
against the checkpoint proteins may be in a prodrug form. For
example, the conditionally active antibodies may be prodrugs that
have no desired drug activity before being cleaved and turned into
a drug form. The prodrugs may be cleaved preferentially in a
tumor-microenvironment, either because the enzyme that catalyzes
such cleavage exists preferentially in the tumor-microenvironment
or because the conditionally active antibodies make the cleavage
site more accessible in a tumor microenvironment, in comparison
with the accessibility of the cleavage site in a non-tumor
microenvironment.
Conditionally Active Biologic Proteins for Stem Cell Niches,
Including Tumor Stem Cells
[0294] Stem cells exist in an environment called stem cell niche in
the body, which constitutes a basic unit of tissue physiology,
integrating signals that mediate the response of stem cells to the
needs of organisms. Yet the niche may also induce pathologies by
imposing aberrant functions on stem cells or other targets. The
interplay between stem cells and their niches creates the dynamic
system necessary for sustaining tissues, and for the ultimate
design of stem-cell therapeutics (Scadden, "The stem-cell niche as
an entity of action," Nature, vol. 441, pages 1075-1079, 2006).
Common stem cell niches in vertebrates include the germline stem
cell niche, the hematopoietic stem cell niche, the hair follicle
stem cell niche, the intestinal stem cell niche, and the
cardiovascular stem cell niche.
[0295] The stem cell niche is a specialized environment that is
different from other parts of the body (e.g. blood plasma)
(Drummond-Barbosa, "Stem Cells, Their Niches and the Systemic
Environment: An Aging Network," Genetics, vol. 180, pages
1787-1797, 2008; Fuchs, "Socializing with the Neighbors: Stem Cells
and Their Niche," Cell, vol. 116, pages 769-778, 2004). The stem
cell niche is hypoxic where oxidative DNA damage is reduced. Direct
measurements of oxygen levels have revealed that bone marrow is, in
general, quite hypoxic (.about.1%-2% O2), in comparison to blood
plasma (Keith et al., "Hypoxia-Inducible Factors, Stem Cells, and
Cancer," Cell, vol. 129, pages 465-472, 2007; Mohyeldin et al.,
"Oxygen in Stem Cell Biology: A Critical Component of the Stem Cell
Niche," Cell Stem Cell, vol. 7, pages 150-161, 2010). In addition,
the stem cell niches need to have several other factors to regulate
stem cell characteristics within the niches: extracellular matrix
components, growth factors, cytokines, and factors of the
physiochemical nature of the environment including the pH, ionic
strength (e.g. Ca.sup.2+ concentration) and metabolites.
[0296] Accordingly, the stem cell niche has at least several
physiological conditions that are different from those of the other
parts of body, such as the physiological conditions in the blood
plasma. The stem cell niche has a lower oxygen concentration (1-2%)
than other parts of the body, especially the blood plasma. Other
physiological conditions for the stem cell niche including pH and
ionic strength, may also be different from other parts of the
body.
[0297] Stem cell therapy is an interventional strategy that
introduces new adult stem cells into damaged tissue in order to
treat disease or injury. This strategy depends on the ability of
stem cells to self-renew and give rise to subsequent offspring with
variable degrees of differentiation capacities. Stem cell therapy
offers significant potential for regeneration of tissues that can
potentially replace diseased and damaged areas in the body, with
minimal risk of rejection and side effects. Therefore, delivering a
drug (biologic protein (e.g. antibody) or chemical compound) to the
stem cell niche for influencing the renewal and differentiation of
stem cells is an important part of stem cell therapy.
[0298] There are several examples on how the stem cell niches
influence the renewal and/or differentiation of the stem cells in
mammals. The first is in the skin, where the .beta.-1 integrin is
known to be differentially expressed on primitive cells and to
participate in constrained localization of a stem-cell population
through interaction with matrix glycoprotein ligands. Second, in
the nervous system, the absence of tenascin C alters neural
stem-cell number and function in the subventricular zone. Tenascin
C seems to modulate stem-cell sensitivity to fibroblast growth
factor 2 (FGF2) and bone morphogenetic protein 4 (BMP4), resulting
in increased stem-cell propensity. Third, another matrix protein,
the Arg-Gly-Asp-containing sialoprotein, osteopontin (OPN), has now
been demonstrated to contribute to haematopoietic stem cell
regulation. OPN interacts with several receptors known to be on
haematopoietic stem cells, CD44, and .alpha.4 and .alpha.5.beta.1
integrins. OPN production can vary markedly, particularly with
osteoblast activation. Animals deficient in OPN have an increased
HS-cell number, because a lack of OPN leads to superphysiologic
stem-cell expansion under stimulatory conditions. Therefore, OPN
seems to serve as a constraint on haematopoietic stem cell numbers,
limiting the number of stem cells under homeostatic conditions or
with stimulation. See Scadden, "The stem-cell niche as an entity of
action," Nature, vol. 441, pages 1075-1079, 2006.
[0299] Xie et al. "Autocrine signaling based selection of
combinatorial antibodies that transdifferentiate human stem cells,"
Proc Natl Acad Sci USA, vol. 110, pages 8099-8104, 2013) discloses
a method of using antibodies to influence stem cell
differentiation. The antibodies are agonists for a granulocyte
colony stimulating factor receptor. Unlike the natural
granulocyte-colony stimulating factor that activates cells to
differentiate along a predetermined pathway, the isolated agonist
antibodies transdifferentiated human myeloid lineage CD34+ bone
marrow cells into neural progenitors. Melidoni et al. ("Selecting
antagonistic antibodies that control differentiation through
inducible expression in embryonic stem cells," Proc Natl Acad Sci
USA, vol. 110, pages 17802-17807, 2013) also discloses a method of
using an antibody to interfere the interaction between FGF4 and its
receptor FGFR1.beta., therefore block the autocrine FGF4-mediated
embryonic stem cell differentiation.
[0300] Knowledge of the functions of ligands/receptors in stem cell
differentiation has enabled the strategy of applying biologic
proteins to interfere with these ligands/receptors for the purpose
of regulating or even directing stem cell differentiation. The
ability to control differentiation of genetically unmodified human
stem cells through the administration of antibodies into the stem
cell niche can provide new ex vivo or in vivo approaches to stem
cell-based therapeutics. In some embodiments, the present invention
provides a conditionally active biologic protein generated from a
wild-type biologic protein that is capable of entering the stem
cell niches, including cancer stem cells, to regulate stem cell or
tumor development. The conditionally active biologic protein has
lower activity than the wild-type biologic protein under at least
one physiological condition in other parts of the body, while it
has higher activity than the wild-type biologic protein under at
least one physiological condition in the stem cell niche, for
example the cancer stem cell environment. Such conditionally active
biologic proteins will be less likely to cause side effects and
preferentially act in the stem cell niche to regulate renewal and
differentiation of stem cells. In some embodiments, the
conditionally active biologic proteins are antibodies. Such
conditionally active antibodies can bind weakly or not at all to
their antigens in other parts of the body, but bind strongly and
tightly to the antigens in the stem cell niche.
[0301] The conditionally active biologic proteins for the synovial
fluid, tumor microenvironment and stem cell niches of the present
invention are generated by a method for evolving a DNA that encodes
a wild-type biologic protein to create a mutant DNA library. The
mutant DNA library is then expressed to obtain mutant proteins. The
mutant proteins are screened for a conditionally active biologic
protein that has a higher activity than the wild-type biologic
protein under at least one physiological condition of a first part
of the body selected from the group consisting of synovial fluid,
tumor microenvironment, and stem cell niches, and has lower
activity than the wild-type biologic protein under at least one
physiological condition at a second part of the body that is
different from the first part of the body. The second part of the
body may be the blood plasma. Such selected mutant biologic
proteins are conditionally active biologic proteins that have high
activity in the first part of the body but low activity in the
second parts of the body.
[0302] Such conditionally active biologic proteins are advantageous
in lowering side effects of the wild-type protein, since the
conditionally active biologic protein has lower activity in the
other parts of the body where the conditionally active biologic
protein is not intended to act. For instance, if the conditionally
active biologic protein is intended to be introduced into the tumor
microenvironment, the fact that the conditionally active biologic
protein has low activity in parts of the body other than the tumor
microenvironment means such conditionally active biologic protein
will be less likely to interfere with normal physiological
functions in parts of the body other than the tumor
microenvironment. At the same time, the conditionally active
biologic protein has high activity in the tumor microenvironment,
which gives the conditionally active biologic protein a higher
efficacy in treating tumors.
[0303] Because of the reduced side effects, the conditionally
active biologic protein will allow a significantly higher dose of
the protein to be safely used, in comparison with the wild-type
biologic protein. This is especially beneficial for an antibody
against a cytokine or a growth factor, because antibodies against
the cytokine or growth factor may interfere with normal
physiological functions of the cytokine or growth factor in other
parts of the body. By using a conditionally active biologic
protein, with reduced side effects, higher doses may be used to
achieve higher efficacy.
[0304] The conditionally active biologic proteins for acting in one
of a synovial fluid, tumor microenvironment, or stem cell niche can
also enable new drug targets to be used. Using traditional biologic
proteins as therapeutics may cause unacceptable side effects. For
example, inhibition of an epidermal growth factor receptor (EGFR)
can very effectively suppress tumor growth. However, a drug
inhibiting EGFR will also suppress growth at the skin and
gastrointestinal (GI) tract. The side effects render EGFR
unsuitable as a tumor drug target. Using a conditionally active
antibody that binds to EGFR at high affinity in only the tumor
microenvironment, but not or at very low affinity at any other
parts of the body, will significantly reduce the side effects and
at the same time suppress tumor growth. In this case, EGFR may
become an effective new tumor drug target by using conditionally
active antibodies.
[0305] In another example, suppressing cytokines is often
beneficial in repairing joint damage. However, suppressing
cytokines in other parts of the body also may suppress the immune
response of the body, causing an immune deficiency. Thus, cytokines
in synovial fluid are not ideal targets for developing traditional
antibody drugs for treatment of joint damage. However, by using
conditionally active antibodies that preferentially bind to
cytokines in the synovial fluid, while not or only weakly to the
same cytokines in other parts of the body, the side effect of
immune deficiency can be dramatically reduced. Therefore, cytokines
in synovial fluid may become suitable targets for repairing joint
damage by using conditionally active antibodies.
Conditionally Active Biologic Proteins for Organs/Tissues
Susceptible to Inflammation
[0306] In some embodiments, the conditionally active biologic
proteins are designed to preferentially act in organs or tissues
that are susceptible to inflammation, such as a lymph node, a
tonsil, an adenoid, and a sinus. Additional organs and tissues that
are susceptible to inflammation may be found in anatomy textbooks
such as Gray's Anatomy by Henry Gray, 41.sup.st edition, 2015,
published by Elsevier.
[0307] These organs and tissues typically exhibit at least one
aberrant condition once they are inflamed. For example, these
inflamed organs and tissues may have higher osmotic pressure and/or
a lower concentration of one or more ions, in comparison with, for
example, the normal physiological conditions of other parts of the
body such as human blood plasma. Further, there may be higher
concentrations of small molecules, lactic acid, cytokines and white
blood cells in such inflamed organs and tissues as compared to the
normal physiological conditions of other parts of the body such as
human blood plasma.
[0308] In some embodiments, the conditionally active biologic
proteins may be produced by the present invention using an aberrant
condition selected from one or more aberrant conditions encountered
in an area of inflammation and a normal physiological condition in
the human blood plasma. Such conditionally active biologic proteins
would thus have a higher activity in the organs/tissues in an
inflammatory state than the activity of the wild-type biologic
protein and lower activity in human blood plasma than the activity
of the wild-type biologic protein. Such conditionally active
biologic proteins can preferentially act in an inflamed region of
the body, but will have little or no activity in a region of the
body that is not inflamed.
Conditionally Active Viral Particles
[0309] Viral particles have long been used as delivery vehicles for
transporting proteins, nucleic acid molecules, chemical compounds
or radioactive isotopes to a target cell or tissue. Viral particles
that are commonly used as delivery vehicles include retoviruses,
adenoviruses, lentivirus, herpes virus, and adeno-associated
viruses. The viral particles recognize their target cells through a
surface protein that serves as a recognition protein for specific
binding to a cellular protein that serves as target protein of the
target cells, often in a ligand-receptor binding system (Lentz,
"The recognition event between virus and host cell receptor: a
target for antiviral agents," J. of Gen. Virol., vol. 71, pages
751-765, 1990). For example, the viral recognition protein may be a
ligand for a receptor on the target cells. The specificity between
a ligand and a receptor allows the viral particles to specifically
recognize and deliver their content a target cell.
[0310] Techniques for developing artificial viral particles from
wild-type viruses are well known to a person skilled in the art.
Known artificial viral particles as delivery vehicles include these
based on retroviruses (see, e.g., WO 90/07936; WO 94/03622; WO
93/25698; WO 93/25234; U.S. Pat. No. 5,219,740; WO 93/11230; WO
93/10218; U.S. Pat. No. 4,777,127; GB Patent No. 2,200,651; EP 0
345 242; and WO 91/02805), alphavirus (e.g., Sindbis virus vectors,
Semliki forest virus (ATCC VR-67; ATCC VR-1247), Ross River virus
(ATCC VR-373; ATCC VR-1246), Venezuelan equine encephalitis virus
(ATCC VR-923; ATCC VR-1250; ATCC VR 1249; ATCC VR-532)), and
adeno-associated viruses (see, e.g., WO 94/12649, WO 93/03769; WO
93/19191; WO 94/28938; WO 95/11984 and WO 95/00655).
[0311] Generally, the artificial viral particles are constructed by
inserting a foreign recognition protein into a virus particle,
often replacing the native recognition protein by recombinant
technology. The foreign recognition protein may be, for example, an
antibody, a receptor, a ligand or a collagen binding domain. The
present invention provides a conditionally active recognition
protein that is inactive or less active for binding to a cell at a
normal physiological condition, and that is active or more active
for binding to a cell at an aberrant condition. The conditionally
active recognition protein can thereby preferentially bind to
target cells of diseased tissue and/or at a disease site based on
the presence of an abnormal condition at that site and avoid or
only minimally bind to the cells of normal tissue where a normal
physiological condition exists. The conditionally active
recognition protein may be expressed and displayed on the surface
of a viral particle.
[0312] In some embodiments, the present invention provides a method
of evolving a wild-type recognition protein and screening for a
conditionally active recognition protein. The conditionally active
recognition protein is less active in binding to a cell than the
wild-type recognition protein under a normal physiological
condition, and more active in binding to a cell than the wild-type
recognition protein under an aberrant condition. Such a
conditionally active recognition protein may be inserted into a
viral particle by well-known recombinant technology to generate a
conditionally active viral particle.
[0313] In another embodiment, the present invention provides a
conditionally active viral particle including a conditionally
active recognition protein, which allows the conditionally active
viral particle to recognize and bind with the target cells of
diseased tissue or at a disease site, but not the cells of normal
tissue. Such a conditionally active viral particle can
preferentially deliver therapeutics within the viral particle to
the disease tissue or disease site, while the conditionally active
viral particle delivers less or does not deliver the therapeutics
to the cells of normal tissue.
[0314] In some embodiments, the target cells at a disease site are
inside a zone or microenvironment with an abnormal pH (e.g., pH
6.5) or an abnormal temperature, in comparison with the pH or
temperature in other parts of the body that are healthy or not
suffering from the particular disease or disease state. In this
embodiment, the conditionally active recognition protein is less
active than a wild-type recognition protein in binding with a
target protein of a target cell at a normal physiological pH or
temperature, and more active than a wild-type recognition protein
in binding with the target protein of a target cell at an abnormal
pH or temperature. In this manner, the recognition protein will
preferentially bind at a site where an abnormal pH or temperature
is encountered thereby delivering a treatment to the site of a
disease.
[0315] In one embodiment, the viral particle may include a
conditionally active antibody of the present invention, and
especially the variable region of an antibody (e.g., Fab, Fab',
Fv). Such a conditionally active antibody can bind to the target
protein (as antigen) of a target cell with lower affinity than a
wild-type antibody under a normal physiological condition which may
be encountered at a location with normal tissue, and a higher
affinity than the wild-type antibody under aberrant condition which
may be encountered at a disease site or diseased tissue. The
conditionally active antibody may be derived from the wild-type
antibody according to the method of the present invention.
[0316] In an embodiment, the target protein on the target cell
includes tyrosine kinase growth factor receptors which are
overexpressed on the cell surfaces in, for example, many tumors.
Exemplary tyrosine kinase growth factors are VEGF receptors, FGF
receptors, PDGF receptors, IGF receptors, EGF receptors, TOP-alpha
receptors, TOP-beta receptors, HB-EGF receptors, ErbB2 receptors,
ErbB3 receptors, and ErbB4 receptors. Conditionally active DNA/RNA
modifying proteins
[0317] DNA/RNA modifying proteins have been discovered as a form of
new genome-engineering tools, particularly one called CRISPR, which
can allow researchers to perform microsurgery on genes, precisely
and easily changing a DNA sequence at exact locations on a
chromosome (genome editing, Mali et al., "Cas9 as a versatile tool
for engineering biology," Nature Methods, vol. 10, pages 957-963,
2013). For example, sickle-cell anemia is caused by a single base
mutation, which can potentially be corrected using DNA/RNA
modifying proteins. The technology may precisely delete or edit
bits of a chromosome, even by changing a single base pair (Makarova
et al., "Evolution and classification of the CRISPR--Cas systems,"
Nature Reviews Microbiology, vol. 9, pages 467-477, 2011).
[0318] Genome editing with CRISPR has the ability to quickly and
simultaneously make multiple genetic changes to a cell. Many human
illnesses, including heart disease, diabetes, and neurological
diseases, are affected by mutations in multiple genes. This
CRISPR-based technology has the potential to reverse the disease
causing mutations and cure these diseases or at least reduce the
severity of these diseases. Genome editing relies on CRISPR
associated (Cas) proteins (a family of enzymes) for cutting the
genomic DNA. Typically, the Cas protein is guided by a small guide
RNA to a targeted region in the genome, where the guide RNA matches
the target region. Because the Cas protein has little or no
sequence specificity, the guide RNA serves as a pointer for the Cas
protein to achieve precise genome editing. In one embodiment, one
Cas protein may be used with multiple guide RNAs to simultaneously
correct multiple gene mutations.
[0319] There are many Cas proteins. Examples include Cas1, Cas2,
Cas3', Cas3'', Cas4, Cas5, Cas6, Cas6e, Cas6f, Cas7, Cas8a1,
Cas8a2, Cas8b, Cas8c, Cas9, Cas10, Cas10d, Csy1, Csy2, Csy3, Cse1,
Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1,
Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx10, Csx16, CsaX, Csx3,
Csx1, Csx15, Csf1, Csf2, Csf3, and Csf4 ((Makarova et al.,
"Evolution and classification of the CRISPR-Cas systems," Nature
Reviews Microbiology, vol. 9, pages 467-477, 2011).
[0320] To conduct genome editing, the Cas protein has to enter the
target cell. Cells in a subject may have a different intracellular
pH inside of the cells. Some cells in diseased tissue have an
abnormal intracellular pH. For example, some tumor cells tend to
have an alkaline intracellular pH of about 7.12-7.65, while cells
in normal tissue have a neutral intracellular pH ranging from
6.99-7.20. See Cardone et al., "The role of disturbed pH dynamics
and the Na(+)/H(+) exchanger in metatasis," Nat. Rev. Cancer, vol.
5, pages 786-795, 2005. In chronic hypoxia, the cells in diseased
tissue have an intracellular pH of about 7.2-7.5, also higher than
the intracellular pH of normal tissue (Rios et al., "Chronic
hypoxia elevates intracellular pH and activates Na+/H+ exchange in
pulmonary arterial smooth muscle cells," American Journal of
Physiology--Lung Cellular and Molecular Physiology, vol. 289, pages
L867-L874, 2005). Further, in ischemia cells, the intracellular pH
is typical in a range of 6.55-6.65, which is lower than the
intracellular pH of normal tissue (Haqberg, "Intracellular pH
during ischemia in skeletal muscle: relationship to membrane
potential, extracellular pH, tissue lactic acid and ATP," Pflugers
Arch., vol. 404, pages 342-347, 1985). More examples of abnormal
intracellular pH in diseased tissue are discussed in Han et al.,
"Fluorescent Indicators for Intracellular pH," Chem Rev., vol. 110,
pages 2709-2728, 2010.
[0321] The present invention provides a method for producing a
conditionally active Cas protein from a wild-type Cas protein,
where the conditionally active Cas protein has at least one of (1)
a decreased enzymatic activity relative to the activity of the
wild-type Cas protein under a normal physiological condition inside
a normal cell, and (2) an increased enzymatic activity relative to
the activity of the wild-type Cas protein under an aberrant
condition inside a target cell such as one of the diseased cells
discussed above. In some embodiments, the normal physiological
condition is an intracellular pH about neutral, and the aberrant
condition is a different intracellular pH that is above or below
neutral. In an embodiment, the aberrant condition is an
intracellular pH of from 7.2 to 7.65 or an intracellular pH of from
6.5-6.8.
[0322] In some embodiments, the conditionally active Cas protein
may be delivered to a target cell using the conditionally active
viral particle of the present invention. The conditionally active
viral particle includes the conditionally active Cas protein and at
least one guide RNA for directing the Cas protein to the location
at which Cas protein will edit the genomic DNA.
[0323] Multispecific antibodies have high selectivity at
preferentially targeting tissues containing all or most of the
targets (antigens) that a multispecific antibody can bind to. For
example, a bispecific antibody provides selectivity for target
cells by displaying greater preference to target cells that express
both of the antigens recognized by the bispecific antibody, in
comparison with non-target cells that may express only one of the
antigens. Therefore, due to the dynamism of the system, there are
more bispecific antibodies being bound to the target cells than
non-target cells at equilibrium.
[0324] The multispecific antibodies engineered herein, or their
antigen-recognition fragments, may be used as the ASTR in the
chimeric antigen receptor of the present invention.
Engineering Cytotoxic Cells
[0325] Once a conditionally active ASTR is identified by the
screening step, the chimeric antigen receptor may be assembled by
ligating the polynucleotide sequences encoding the individual
domains to form a single polynucleotide sequence (the CAR gene,
which encodes the conditionally active CAR). The individual domains
include a conditionally active ASTR, a TM, and an ISD. In some
embodiments, other domains may also be introduced in the CARs,
including an ab ESD and a CSD (FIG. 1). If the conditionally active
CAR is a bispecific CAR, the CAR gene may be, for example, in the
following configuration in the N-terminal to C-terminal direction:
N-terminal signal sequence--ASTR 1--linker--ASTR 2--extracellular
spacer domain--transmembrane domain--co-stimulatory
domain--intracellular signaling domain. In one embodiment, such a
CAR gene may include two or more co-stimulatory domains.
[0326] Alternatively, the polynucleotide sequence encoding the
conditionally active CAR may be in the following configuration in
the N-terminal to C-terminal direction: N-terminal signal
sequence--ASTR 1--linker--ASTR 2--transmembrane
domain--co-stimulatory domain--intracellular signaling domain. In
an embodiment, such a CAR may include two or more co-stimulatory
domains. If a CAR includes more than two ASTRs, the polynucleotide
sequence encoding the CAR may be in the following configuration in
the N-terminal to C-terminal direction: N-terminal signal
sequence--ASTR 1--linker--ASTR 2--linker--(antigen-specific
targeting region).sub.n--transmembrane domain--co-stimulatory
domain--intracellular signaling domain. Such a CAR may further
include an extracellular spacer domain. Each ASTR may be separated
by a linker. In an embodiment, such a CAR may include two or more
co-stimulatory domains.
[0327] The conditionally active CAR is introduced into the
cytotoxic cells by an expression vector. Expression vectors
including a polynucleotide sequence encoding a conditionally active
CAR of the invention are also provided herein. Suitable expression
vectors include lentivirus vectors, gamma retrovirus vectors, foamy
virus vectors, adeno associated virus (AAV) vectors, adenovirus
vectors, engineered hybrid viruses, naked DNA, including but not
limited to transposon mediated vectors, such as Sleeping Beauty,
Piggybak, and Integrases such as Phi31. Some other suitable
expression vectors include Herpes simplex virus (HSV) and
retrovirus expression vectors.
[0328] Adenovirus expression vectors are based on adenoviruses,
which have a low capacity for integration into genomic DNA but a
high efficiency for transfecting host cells. Adenovirus expression
vectors contain adenovirus sequences sufficient to: (a) support
packaging of the expression vector and (b) to ultimately express
the CAR gene in the host cell. The adenovirus genome is a 36 kb,
linear, double stranded DNA, where a foreign DNA sequence (such as
CAR genes) may be inserted to substitute large pieces of adenoviral
DNA in order to make the expression vector of the present invention
(Grunhaus and Horwitz, "Adenoviruses as cloning vectors," Seminars
Virol., vol. 3, pages 237-252, 1992).
[0329] Another expression vector is based on an adeno associated
virus, which takes advantage of the adenovirus coupled systems.
This AAV expression vector has a high frequency of integration into
the host genome. It can even infect nondividing cells, thus making
it useful for delivery of genes into mammalian cells, for example,
in tissue cultures or in vivo. The AAV vector has a broad host
range for infectivity. Details concerning the generation and use of
AAV vectors are described in U.S. Pat. Nos. 5,139,941 and
4,797,368.
[0330] Retrovirus expression vectors are capable of integrating
into the host genome, delivering a large amount of foreign genetic
material, infecting a broad spectrum of species and cell types and
being packaged in special cell lines. The retrovirus vector is
constructed by inserting a nucleic acid (e.g., one encoding the
CAR) into the viral genome at certain locations to produce a virus
that is replication defective. Though the retrovirus vectors are
able to infect a broad variety of cell types, integration and
stable expression of the CAR gene requires the division of host
cells.
[0331] Lentivirus vectors are derived from lentiviruses, which are
complex retroviruses that, in addition to the common retroviral
genes gag, pol, and env, contain other genes with regulatory or
structural function (U.S. Pat. Nos. 6,013,516 and 5,994,136). Some
examples of lentiviruses include the Human Immunodeficiency Viruses
(HIV-1, HIV-2) and the Simian Immunodeficiency Virus (SIV).
Lentivirus vectors have been generated by multiply attenuating the
HIV virulence genes, for example, the genes env, vif, vpr, vpu and
nef are deleted making the vector biologically safe. Lentivirus
vectors are capable of infecting non-dividing cells and can be used
for both in vivo and ex vivo gene transfer and expression of the
CAR gene (U.S. Pat. No. 5,994,136).
[0332] Expression vectors including the conditionally active CAR
gene can be introduced into a host cell by any means known to
person skilled in the art. The expression vectors may include viral
sequences for transfection, if desired. Alternatively, the
expression vectors may be introduced by fusion, electroporation,
biolistics, transfection, lipofection, or the like. The host cell
may be grown and expanded in culture before introduction of the
expression vectors, followed by the appropriate treatment for
introduction and integration of the vectors. The host cells are
then expanded and screened by virtue of a marker present in the
vectors. Various markers that may be used include hprt, neomycin
resistance, thymidine kinase, hygromycin resistance, etc. As used
herein, the terms "cell," "cell line," and "cell culture" may be
used interchangeably. In some embodiments, the host cell is a T
cell, NK cell and NKT cell.
[0333] In another aspect, the present invention also provides
genetically engineered cytotoxic cells which include and stably
express the conditionally active CAR of the invention. In one
embodiment, the genetically engineered cells include T-lymphocytes
(T cells), naive T cells (T.sub.N), memory T cells (for example,
central memory T cells (TC.sub.M), effector memory cells
(T.sub.EM)), natural killer cells, and macrophages capable of
giving rise to therapeutically relevant progeny. In another
embodiment, the genetically engineered cells are autologous cells.
Examples of suitable T cells include CD4.sup.+/CD8.sup.-,
CD4.sup.-/CD8.sup.+, CD4.sup.-/CD8.sup.- or CD4.sup.+/CD8.sup.+ T
cells. The T cells may be a mixed population of CD4.sup.+/CD8.sup.-
and CD4.sup.-/CD8.sup.+ cells or a population of a single clone.
CD4.sup.+ T cells of the invention may also produce IL-2,
IFN-gamma, TNF-alpha and other T cell effector cytokines when
co-cultured in vitro with cells expressing the target antigens (for
example CD20.sup.+ and/or CD 19.sup.+ tumor cells). CD8.sup.+ T
cells of the invention may lyse cells expressing the target
antigen. In some embodiments, T cells may be any one or more of
CD45RA.sup.+ CD62L.sup.+ naive cells, CD45RO CD62I7 central memory
cells, CD62L'' effector memory cells or a combination thereof
(Berger et al., "Adoptive transfer of virus-specific and
tumor-specific T cell immunity," Curr. Opin. Immunol., vol. 21,
pages 224-232, 2009).
[0334] Genetically engineered cytotoxic cells may be produced by
stably transfecting host cells with an expression vector including
the CAR gene of the invention. Additional methods to genetically
engineer the cytotoxic cells using the expression vector include
chemical transformation methods (e.g., using calcium phosphate,
dendrimers, liposomes and/or cationic polymers), non-chemical
transformation methods (e.g., electroporation, optical
transformation, gene electrotransfer and/or hydrodynamic delivery)
and/or particle-based methods (e.g., impalefection, using a gene
gun and/or magnetofection). Transfected cells demonstrating the
presence of a single integrated un-rearranged vector and expressing
the conditionally active CAR may be expanded ex vivo.
[0335] Physical methods for introducing an expression vector into
host cells include calcium phosphate precipitation, lipofection,
particle bombardment, microinjection, electroporation, and the
like. Methods for producing cells including vectors and/or
exogenous nucleic acids are well-known in the art. See, for
example, Sambrook et al. (2001, Molecular Cloning: A Laboratory
Manual, Cold Spring Harbor Laboratory, New York). Chemical methods
for introducing an expression vector into a host cell include
colloidal dispersion systems, such as macromolecule complexes,
nanocapsules, microspheres, beads, and lipid-based systems
including oil-in-water emulsions, micelles, mixed micelles, and
liposomes.
[0336] After the expression vector containing the CAR gene is
introduced into the host cells, the CAR gene will be expressed thus
producing a CAR molecule that can bind to the target antigen. The
produced CAR molecule becomes a transmembrane protein by virtue of
having a transmembrane domain. The host cells will then be
converted to CAR cells such as CAR-T cells. The process for
producing engineered cytotoxic cells with the CAR molecule, for
example CAR-T cells, has been described in, for example,
(Cartellieri et al., "Chimeric antigen receptor-engineered T cells
for immunotherapy of cancer," Journal of Biomedicine and
Biotechnology, vol. 2010, Article ID 956304, 2010; and Ma et al.,
"Versatile strategy for controlling the specificity and activity of
engineered T cells," PNAS, vol. 113, E450-E458, 2016).
[0337] Whether prior to or after genetic modification of the
cytotoxic cells to express a desirable conditionally active CAR,
the cells can be activated and expanded in number using methods as
described, for example, in U.S. Pat. Nos. 6,352,694; 6,534,055;
6,905,680; 6,692,964; 5,858,358; 6,887,466; 6,905,681; 7,144,575;
7,067,318; 7,172,869; 7,232,566; 7,175,843; 5,883,223; 6,905,874;
6,797,514; 6,867,041; and US 20060121005. For example, the T cells
of the invention may be expanded by contact with a surface having
attached thereto an agent that stimulates a CD3/TCR complex
associated signal and a ligand that stimulates a co-stimulatory
molecule on the surface of the T cells. In particular, T cell
populations may be stimulated by contact with an anti-CD3 antibody,
or antigen-binding fragment thereof, or au anti-CD2 antibody
immobilized on a surface, or by contact with a protein kinase C
activator (e.g., bryostatin) in conjunction with a calcium
ionophore. For co-stimulation of an accessory molecule on the
surface of the T cells, a ligand that binds the accessory molecule
is used. For example, T cells can be contacted with an anti-CD3
antibody and an anti-CD28 antibody, under conditions appropriate
for stimulating proliferation of the T cells. To stimulate
proliferation of either CD4.sup.+ T cells or CD8.sup.+ T cells, an
anti-CD3 antibody and an anti-CD28 antibody. Examples of an
anti-CD28 antibody include 9.3, B-T3, XR-CD28 (Diaclone, Besancon,
France) and these can be used in the invention, as can other
methods commonly known in the art (Berg et al., Transplant Proc.
30(8):3975-3977, 1998; Haanen et al., J. Exp. Med. 190(9):13191328,
1999; Garland et al., J. Immunol. Meth. 227(1-2):53-63, 1999).
[0338] In various embodiments, the present invention provides
pharmaceutical compositions including a pharmaceutically acceptable
excipient and a therapeutically effective amount of the
conditionally active CAR of the invention. The conditionally active
CAR in the composition may be any one or more of a polynucleotide
encoding the CAR, a protein including the CAR or genetically
modified cells expressing the CAR protein. The CAR protein may be
in the form of a pharmaceutically acceptable salt. Pharmaceutically
acceptable salts refers to salts which can be used as salts of a
therapeutic protein in the pharmaceutical industry, including for
example, salts of sodium, potassium, calcium and the like, and
amine salts of procaine, dibenzylamine, ethylenediamine,
ethanolamine, methylglucamine, taurine, and the like, as well as
acid addition salts such as hydrochlorides, and basic amino acids
and the like.
[0339] The pharmaceutically acceptable excipient may include any
excipient that is useful in preparing a pharmaceutical composition
that is generally safe, non-toxic, and desirable, and includes
excipients that are acceptable for veterinary use as well as for
human pharmaceutical use. Such excipients may be solid, liquid,
semisolid, or, in the case of an aerosol composition, gaseous. One
type of excipient includes pharmaceutically acceptable carriers,
which may be added to enhance or stabilize the composition, or to
facilitate preparation of the composition. Liquid carriers include
syrup, peanut oil, olive oil, glycerin, saline, alcohols and water.
Solid carriers include starch, lactose, calcium sulfate, dihydrate,
terra alba, magnesium stearate or stearic acid, talc, pectin,
acacia, agar and gelatin. The carrier may also include a sustained
release material such as glyceryl monostearate or glyceryl
distearate, alone or with a wax.
[0340] The pharmaceutically acceptable carriers are determined in
part by the particular composition being administered, as well as
by the particular method used to administer the composition.
Accordingly, there are a wide variety of suitable formulations of
pharmaceutical compositions of the present invention. A variety of
aqueous carriers can be used, e.g., buffered saline and the like.
These solutions are sterile and generally free of undesirable
matter. These compositions may be sterilized by conventional, well
known sterilization techniques. The compositions may contain
pharmaceutically acceptable auxiliary substances as required to
approximate physiological conditions such as pH adjustment agents
and buffering agents, toxicity adjusting agents and the like, for
example, sodium acetate, sodium chloride, potassium chloride,
calcium chloride, sodium lactate and the like. The concentration of
CAR in these formulations can vary widely, and will be selected
primarily based on fluid volumes, viscosities, and body weight in
accordance with the particular mode of administration selected and
the patient's needs.
[0341] In various embodiments, the pharmaceutical compositions
according to the invention may be formulated for delivery via any
suitable route of administration. "Route of administration" may
refer to any administration pathway known in the art, including but
not limited to aerosol, nasal, oral, intravenous, intramuscular,
intraperitoneal, inhalation, transmucosal, transdermal, parenteral,
implantable pump, continuous infusion, topical application,
capsules and/or injections.
[0342] The pharmaceutical compositions according to the invention
can be encapsulated, tableted or prepared in an emulsion or syrup
for oral administration. The pharmaceutical compositions are made
following the conventional techniques of pharmacy involving
milling, mixing, granulation, and compression, when necessary, for
tablet forms; or milling, mixing and filling for hard gelatin
capsule forms. When a liquid carrier is used, the preparation may
be in the form of syrup, elixir, emulsion or an aqueous or
non-aqueous suspension. Such a liquid formulation may be
administered directly p.o. or filled into a soft gelatin
capsule.
[0343] The pharmaceutical compositions may be formulated as: (a)
liquid solutions, such as an effective amount of the packaged
nucleic acid suspended in diluents, such as water, saline or PEG
400; (b) capsules, sachets or tablets, each containing a
predetermined amount of the active ingredient, as liquids, solids,
granules or gelatin; (c) suspensions in an appropriate liquid; and
(d) suitable emulsions. Particularly, suitable dosage forms
include, but are not limited to, tablets, pills, powder, dragees,
capsules, liquids, lozenges, gels, syrups, slurries, suspensions,
etc.
[0344] The solid formulations include suitable solid excipients
such as carbohydrates or protein fillers including, e.g., sugars
such as lactose, sucrose, mannitol, or sorbitol; starch from corn,
wheat, rice, potato, or other plants; cellulose such as methyl
cellulose, hydroxypropyhnethyl cellulose, and sodium
carboxy-methylcellulose; and gums including arabic and tragacanth;
and proteins, e.g., gelatin and collagen. Disintegrating or
solubilizing agents may be added, such as cross-linked polyvinyl
pyrrolidone, agar, alginic acid, or a salt thereof, such as sodium
alginate. Tablet forms can include one or more of lactose, sucrose,
mannitol, sorbitol, calcium phosphates, corn starch, potato starch,
tragacanth, microcrystalline cellulose, acacia, gelatin, colloidal
silicon dioxide, croscannellose sodium, talc, magnesium stearate,
stearic acid, and other excipients, colorants, fillers, binders,
diluents, buffering agents, moistening agents, preservatives,
flavoring agents, dyes, disintegrating agents, and pharmaceutically
acceptable carriers.
[0345] The liquid suspensions include a conditionally active CAR,
in admixture with excipients suitable for the manufacture of
aqueous suspensions. Such excipients include a suspending agent,
such as sodium carboxymethylcellulose, methylcellulose,
hydroxypropylmethylcellulose, sodium alginate,
polyvinylpyrrolidone, gum tragacanth and gum acacia, and dispersing
or wetting agents such as a naturally occurring phosphatide (e.g.,
lecithin), a condensation product of an alkylene oxide with a fatty
acid (e.g., polyoxyethylene stearate), a condensation product of
ethylene oxide with a long chain aliphatic alcohol (e.g.,
heptadecaethylene oxycetanol), a condensation product of ethylene
oxide with a partial ester derived from a fatty acid and a hexitol
(e.g., polyoxyethylene sorbitol mono-oleate), or a condensation
product of ethylene oxide with a partial ester derived from fatty
acid and a hexitol anhydride (e.g., polyoxyethylene sorbitan
mono-oleate). The liquid suspension can also contain one or more
preservatives such as ethyl or n-propyl p-hydroxybenzoate, one or
more coloring agents, one or more flavoring agents and one or more
sweetening agents, such as sucrose, aspartame or saccharin.
Formulations can be adjusted for osmolality.
[0346] The lozenge forms can include the active ingredient in a
flavor, usually sucrose and acacia or tragacanth, as well as
pastilles including the active ingredient in an inert base, such as
gelatin and glycerin or sucrose and acacia emulsions, gels, and the
like containing, in addition to the active ingredient, carriers
known in the art. It is recognized that the conditionally active
CAR, when administered orally, must be protected from digestion.
This is typically accomplished either by complexing the
conditionally active CAR with a composition to render it resistant
to acidic and enzymatic hydrolysis or by packaging the
conditionally active CAR in an appropriately resistant carrier such
as a liposome. Means of protecting proteins from digestion are well
known in the art. The pharmaceutical compositions can be
encapsulated, e.g., in liposomes, or in a formulation that provides
for slow release of the active ingredient.
[0347] The pharmaceutical composition may be formulated as aerosol
formulations (e.g., they can be "nebulized") to be administered via
inhalation. Aerosol formulations can be placed into pressurized
acceptable propellants, such as dichlorodifluoromethane, propane,
nitrogen, and the like. Suitable formulations for rectal
administration include, for example, suppositories, which consist
of the packaged nucleic acid with a suppository base. Suitable
suppository bases include natural or synthetic triglycerides or
paraffin hydrocarbons, in addition, it is also possible to use
gelatin rectal capsules which consist of a combination of the
packaged nucleic acid with a base, including, for example, liquid
triglycerides, polyethylene glycols, and paraffin hydrocarbons.
[0348] The pharmaceutical composition may be formulated for
parenteral administration, such as, for example, by intra-articular
(in the joints), intravenous, intramuscular, intradermal,
intraperitoneal, and subcutaneous routes, include aqueous and
non-aqueous, isotonic sterile injection solutions, which can
contain antioxidants, buffers, bacteriostats, and solutes that
render the formulation isotonic with the blood of the intended
recipient, and aqueous and nonaqueous sterile suspensions that can
include suspending agents, solubilizers, thickening agents,
stabilizers, and preservatives, in the practice of this invention,
compositions can be administered, for example, by intravenous
infusion, orally, topically, intraperitoneally, intravesically or
intrathecally. In one aspect, parenteral modes of administration
are preferred methods of administration for compositions including
the CAR protein or genetically engineered cytotoxic cells. The
compositions may conveniently be administered in unit dosage form
and may be prepared by any of the methods well-known in the
pharmaceutical art, for example as described in Remington's
Pharmaceutical Sciences, Mack Publishing Co. Easton Pa., 18.sup.th
Ed., 1990. Formulations for intravenous administration may contain
a pharmaceutically acceptable carrier such as sterile water or
saline, polyalkylene glycols such as polyethylene glycol, oils of
vegetable origin, hydrogenated naphthalenes and the like.
[0349] The pharmaceutical composition may be administered by at
least one mode selected from parenteral, subcutaneous,
intramuscular, intravenous, intrarticular, intrabronchial,
intraabdominal, intracapsular, intracartilaginous, intracavitary,
intracelial, intracelebellar, intracerebroventricular, intracolic,
intracervical, intragastric, intrahepatic, intramyocardial,
intraosteal, intrapelvic, intrapericardiac, intraperitoneal,
intrapleural, intraprostatic, intrapulmonary, intrarectal,
intrarenal, intraretinal, intraspinal, intrasynovial,
intrathoracic, intrauterine, intravesical, bolus, vaginal, rectal,
buccal, sublingual, intranasal, or transdermal. The method can
optionally further include administering, prior to, concurrently,
or after the conditionally active CAR at least one composition
including an effective amount of at least one compound or protein
selected from at least one of a detectable label or reporter, a TNF
antagonist, an antirheumatic, a muscle relaxant, a narcotic, a
non-steroid anti-inflammatory drug (NSAK)), an analgesic, an
anesthetic, a sedative, a local anesthetic, a neuromuscular
blocker, an antimicrobial, an antipsoriatic, a corticosteriod, an
anabolic steroid, an erythropoietin, an immunization, an
immunoglobulin, an immunosuppressive, a growth hormone, a hormone
replacement drug, a radiopharmaceutical, an antidepressant, an
antipsychotic, a stimulant, an asthma medication, a beta agonist,
an inhaled steroid, an epinephrine or analog thereof, a cytotoxic
or other anti-cancer agent, an anti-metabolite such as
methotrexate, or an antiproliferative agent.
[0350] The types of cancers to be treated with the genetically
engineered cytotoxic cells or pharmaceutical compositions of the
invention include, carcinoma, blastoma, and sarcoma, and certain
leukemia or lymphoid malignancies, benign and malignant tumors, and
malignancies e.g., sarcomas, carcinomas, and melanomas. The cancers
may be non-solid tumors (such as hematological tumors) or solid
tumors. Adult tumors/cancers and pediatric tumors/cancers are also
included.
[0351] Hematologic cancers are cancers of the blood or bone marrow.
Examples of hematological (or hematogenous) cancers include
leukemias, including acute leukemias (such as acute lymphocytic
leukemia, acute myelocytic leukemia, acute myelogenous leukemia and
myeloblastic, promyelocytic, myelomonocytic, monocytic and
erythroleukemia), chronic leukemias (such as chronic myelocytic
(granulocytic) leukemia, chronic myelogenous leukemia, and chronic
lymphocytic leukemia), polycythemia vera, lymphoma, Hodgkin's
disease, non-Hodgkin's lymphoma (indolent and high grade forms),
multiple myeloma, Waldenstrom's macroglobulinemia, heavy chain
disease, myelodysplastic syndrome, hairy cell leukemia and
myelodysplasia.
[0352] Solid tumors are abnormal masses of tissue that usually do
not contain cysts or liquid areas. Solid tumors can be benign or
malignant. Different types of solid tumors are named for the type
of cells that form them (such as sarcomas, carcinomas, and
lymphomas). Examples of solid tumors, such as sarcomas and
carcinomas, include fibrosarcoma, myxosarcoma, liposarcoma,
chondrosarcoma, osteosarcoma, and other sarcomas, synovioma,
mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma,
colon carcinoma, lymphoid malignancy, pancreatic cancer, breast
cancer, lung cancers, ovarian cancer, prostate cancer,
hepatocellular carcinoma, squamous cell carcinoma, basal cell
carcinoma, adenocarcinoma, sweat gland carcinoma, medullary thyroid
carcinoma, papillary thyroid carcinoma, pheochromocytomas sebaceous
gland carcinoma, papillary carcinoma, papillary adenocarcinomas,
medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma,
hepatoma, bile duct carcinoma, choriocarcinoma, Wilms' tumor,
cervical cancer, testicular tumor, seminoma, bladder carcinoma,
melanoma, and CNS tumors (such as a glioma (such as brainstem
glioma and mixed gliomas), glioblastoma (also known as glioblastoma
multiforme) astrocytoma, CNS lymphoma, germinoma, medulloblastoma,
Schwannoma craniopharyogioma, ependymoma, pinealoma,
hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma,
neuroblastoma, retinoblastoma and brain metastases).
[0353] The present invention also provides a medical device,
including at least one CAR protein, a polynucleotide sequence
encoding a CAR, or a host cell expressing a CAR, wherein the device
is suitable for administering the at least one conditionally active
CAR by at least one mode selected from parenteral, subcutaneous,
intramuscular, intravenous, intrarticular, intrabronchial,
intraabdominal, intracapsular, intracartilaginous, intracavitary,
intracelial, intracelebellar, intracerebroventricular, intracolic,
intracervical, intragastric, intrahepatic, intramyocardial,
intraosteal, intrapelvic, intrapericardiac, intraperitoneal,
intrapleural, intraprostatic, intrapulmonary, intrarectal,
intrarenal, intraretinal, intraspinal, intrasynovial,
intrathoracic, intrauterine, intravesical, bolus, vaginal, rectal,
buccal, sublingual, intranasal, or transdermal.
[0354] In a further aspect, the invention provides a kit including
at least one CAR protein, a polynucleotide sequence encoding a CAR,
or a host cell expressing a CAR, in lyophilized form in a first
container, and an optional second container including sterile
water, sterile buffered water, or at least one preservative
selected from the group consisting of phenol, m-cresol, p-cresol,
o-cresol, chlorocresol, benzyl alcohol, phenylmercuric nitrite,
phenoxyethanol, formaldehyde, chlorobutanol, magnesium chloride,
alkylparaben, benzalkonium chloride, benzethonium chloride, sodium
dehydroacetate and thimerosal, or mixtures thereof in an aqueous
diluent. In one aspect, in the kit, the concentration of
conditionally active CAR or a specified portion or variant in the
first container is reconstituted to a concentration of about 0.1
mg/ml to about 500 mg/ml with the contents of the second container.
In another aspect, the second container further includes an
isotonic agent. In another aspect, the second container further
includes a physiologically acceptable buffer. In one aspect, the
disclosure provides a method of treating at least one wild-type
protein mediated condition, including administering to a patient in
need thereof a formulation provided in a kit and reconstituted
prior to administration.
[0355] Also provided is an article of manufacture for human
pharmaceutical or diagnostic use including a packaging material and
a container including a solution or a lyophilized form of at least
one CAR protein, polynucleotide sequence encoding a CAR, or a host
cell expression a CAR. The article of manufacture can optionally
include having the container as a component of a parenteral,
subcutaneous, intramuscular, intravenous, intrarticular,
intrabronchial, intraabdominal, intracapsular, intracartilaginous,
intracavitary, intracelial, intracelebellar,
intracerebroventricular, intracolic, intracervical, intragastric,
intrahepatic, intramyocardial, intraosteal, intrapelvic,
intrapericardiac, intraperitoneal, intrapleural, intraprostatic,
intrapulmonary, intrarectal, intrarenal, intraretinal, intraspinal,
intrasynovial, intrathoracic, intrauterine, intravesical, bolus,
vaginal, rectal, buccal, sublingual, intranasal, or transdermal
delivery device or system.
[0356] In some embodiments, the present invention provides a method
including retrieving cytotoxic cells from a subject, genetically
engineering the cytotoxic cells by introducing a CAR gene of the
present invention into the cytotoxic cells, and administering the
genetically engineered cytotoxic cells to the subject. In some
embodiments, the cytotoxic cells are selected from T cells, naive T
cells, memory T cells, effector T cells, natural killer cells, and
macrophages. In one embodiment, the cytotoxic cells are T
cells.
[0357] In one embodiment, the T cells are obtained from a subject.
T cells can be obtained from a number of sources, including
peripheral blood mononuclear cells, bone marrow, lymph node tissue,
cord blood, thymus tissue, tissue from a site of infection,
ascites, pleural effusion, spleen tissue, and tumors. In certain
embodiments of the present invention, any number of T cell lines
available in the art, may be used. In certain embodiments of the
present invention, T cells can be obtained from blood collected
from a subject using any number of techniques known to the skilled
artisan, such as Ficoll.TM. separation.
[0358] In one preferred embodiment, cells from the circulating
blood of an individual are obtained by apheresis. The apheresis
product typically contains lymphocytes, including T cells,
monocytes, granulocytes, B cells, other nucleated white blood
cells, red blood cells, and platelets. In one embodiment, the cells
collected by apheresis may be washed to remove the plasma fraction
and to place the cells in an appropriate buffer or media for
subsequent processing steps. In one embodiment of the invention,
the cells are washed with phosphate buffered saline (PBS). In an
alternative embodiment, the wash solution lacks calcium and may
lack magnesium or may lack many if not all divalent cations. Again,
surprisingly, initial activation steps in the absence of calcium
lead to magnified activation. As those of ordinary skill in the art
would readily appreciate a washing step may be accomplished by
methods known to those in the art, such as by using a
semi-automated "flow-through" centrifuge (for example, the Cobe
2991 cell processor, the Baxter CytoMate, or the Haemonetics Cell
Saver 5) according to the manufacturer's instructions. After
washing, the cells may be resuspended in a variety of biocompatible
buffers, such as, for example, Ca.sup.2+-free, Mg.sup.2+-free PBS,
PlasmaLyte A, or another saline solution with or without buffer.
Alternatively, the undesirable components of the apheresis sample
may be removed and the cells directly resuspended in culture
media.
[0359] In another embodiment, T cells are isolated from peripheral
blood by lysing the red blood cells and depleting the monocytes,
for example, by centrifugation through a PERCOLL.TM. gradient or by
counter-flow centrifugal elutriation. A specific subpopulation of T
cells, such as CD3.sup.+, CD28.sup.+, CD4.sup.+, CD8.sup.+,
CD45RA.sup.+, and CD45RO.sup.+ T cells, can be further isolated by
positive or negative selection techniques. For example, enrichment
of a T cell population by negative selection can be accomplished
with a combination of antibodies directed to surface markers unique
to the negatively selected cells. One method is cell sorting and/or
selection via negative magnetic immunoadherence or flow cytometry
that uses a cocktail of monoclonal antibodies directed to cell
surface markers present on the cells negatively selected. To enrich
CD4.sup.+ cells by negative selection, a monoclonal antibody
cocktail typically includes antibodies to CD 14, CD20, CD11b, CD
16, HLA-DR, and CD8. In certain embodiments, it may be desirable to
enrich for or positively select for regulatory T cells which
typically express CD4.sup.+, CD25.sup.+, CD62L.sup.hi, GITR.sup.+,
and FoxP3.sup.+.
[0360] For example, in one embodiment, T cells are isolated by
incubation with anti-CD3/anti-CD28 (i.e., 3.times.28)-conjugated
beads, such as DYNABEADS.RTM. M-450 CD3/CD28 T, for a time period
sufficient for positive selection of the desired T cells. In one
embodiment, the time period is about 30 minutes. In a further
embodiment, the time period ranges from 30 minutes to 36 hours or
longer and all integer values there between. In a further
embodiment, the time period is at least 1, 2, 3, 4, 5, or 6 hours.
In yet another preferred embodiment, the time period is 10 to 24
hours. In one preferred embodiment, the incubation time period is
24 hours. For isolation of T cells from patients with leukemia, use
of longer incubation times, such as 24 hours, can increase cell
yield. Longer incubation times may be used to isolate T cells in
any situation where there are few T cells as compared to other cell
types, such in isolating tumor infiltrating lymphocytes (TIL) from
tumor tissue or from immune-compromised individuals. Further, use
of longer incubation times can increase the efficiency of capture
of CD8+ T cells. Thus, by simply shortening or lengthening the time
T cells are allowed to bind to the CD3/CD28 beads and/or by
increasing or decreasing the ratio of beads to T cells (as
described further herein), subpopulations of T cells can be
preferentially selected for or against at culture initiation or at
other time points during the process. Additionally, by increasing
or decreasing the ratio of anti-CD3 and/or anti-CD28 antibodies on
the beads or other surface, subpopulations of T cells can be
preferentially selected for or against at culture initiation or at
other desired time points. The skilled person would recognize that
multiple rounds of selection can also be used in the context of
this invention. In certain embodiments, it may be desirable to
perform the selection procedure and use the "unselected" cells in
the activation and expansion process. "Unselected" cells can also
be subjected to further rounds of selection.
[0361] The obtained cytotoxic cells are then genetically engineered
as described herein. A polynucleotide encoding the CAR, typically
located in an expression vector, is introduced into the cytotoxic
cells such that the cytotoxic cells will express, preferably
stably, the CAR. The polynucleotide encoding the CAR is typically
integrated into the cytotoxic cell host genome. In some
embodiments, the polynucleotide introduction need not result in
integration but rather only transient maintenance of the
polynucleotide introduced may be sufficient. In this way, one could
have a short term effect, where cytotoxic cells could be introduced
into the host and then turned on after a predetermined time, for
example, after the cells have been able to migrate to a particular
site for treatment.
[0362] Depending upon the nature of the cytotoxic cells and the
diseases to be treated, the genetically engineered cytotoxic cells
may be introduced into the subject, e.g. a mammal, in a wide
variety of ways. The genetically engineered cytotoxic cells may be
introduced at the site of the tumor. In one embodiment, the
genetically engineered cytotoxic cells navigate to the cancer or
are modified to navigate to the cancer. The number of genetically
engineered cytotoxic cells that are employed will depend upon a
number of factors such as the circumstances, the purpose for the
introduction, the lifetime of the cells, the protocol to be used.
For example, the number of administrations, the ability of the
cells to multiply, and the stability of the recombinant construct.
The genetically engineered cytotoxic cells may be applied as a
dispersion injected at or near the site of interest. The cells may
be in a physiologically-acceptable medium.
[0363] It should be appreciated that the treatment method is
subject to many variables, such as the cellular response to the
CAR, the efficiency of expression of the CAR by the cytotoxic cells
and, as appropriate, the level of secretion, the activity of the
expressed CAR, the particular need of the subject, which may vary
with time and circumstances, the rate of loss of the cellular
activity as a result of loss of genetically engineered cytotoxic
cells or the expression activity of individual cells, and the like.
Therefore, it is expected that for each individual patient, even if
there were universal cells which could be administered to the
population at large, each patient would be monitored for the proper
dosage for the individual, and such practices of monitoring a
patient are routine in the art.
[0364] The following examples are illustrative, but not limiting,
of the methods of the present disclosure. Other suitable
modifications and adaptations of the variety of conditions and
parameters normally encountered in the field, and which are obvious
to those skilled in the art, are within the scope of this
disclosure.
EXAMPLES
Example 1
Generation of scFv Conditionally Active Antibodies
[0365] Two conditionally active antibodies (CAB-scFv-63.9-4 and
CAB-scFv-63.9-6) for a drug target antigen X1 were expressed as
homodimers with wild type human IgG1 Fc (resulting in bivalent
antibodies CAB-scFv-63.9-4-01 and CAB-scFv-63.9-6-01 in FIGS. 2-3),
as well as heterodimers in the knob-in-hole system resulting in a
monovalent scFv (resulting in monovalent antibodies scFv
CAB-scFv-63.9-4-02 and CAB-scFv-63.9-6-02 in FIGS. 2-3).
[0366] The binding affinities of these antibodies to the drug
target antigen X1 at pH 6.0 and pH 7.4 were measured by the ELISA
assay. As show in FIG. 2, the scFv antibodies showed affinities to
drug target antigen X1 at both pH 6.0 and pH 7.4, which were
comparable to the full bivalent antibodies. Further, the
selectivity of these scFv antibodies at pH 6.0 over pH 7.4 as shown
in FIG. 3 was also comparable to the full bivalent antibodies. This
example demonstrated that the conditionally active antibodies of
the present invention have comparable affinity and selectivity
either as scFv antibodies or full bivalent antibodies. Thus, the
conditionally active antibodies of the present invention may be
inserted as a single DNA chain in a DNA molecule that encodes CAR
in the CAR-T platform of the present invention.
Example 2
scFv Antibodies Against Target Antigen X1 for Constructing CAR-T
Cells
[0367] Conditionally active antibodies for the drug target antigen
X1 were generated by simultaneously screening for selectivity and
affinity, as well as expression level at both pH 6.0 and pH 7.4, in
accordance with one embodiment of the present invention. The
screening was done in serum using a FLAG tag because there were
human antibodies in the serum which might cause false positives for
the screening. The screening buffer was a carbonate buffer (krebs
buffer with ringer--standard buffer but different from PBS). The
generated conditionally active antibodies were found to have a
higher affinity to the drug target antigen X1 at pH 6.0 but lower
affinity to the same drug target antigen X1 at pH 7.4, both in
comparison with the wild-type antibody. Further, these
conditionally active antibodies all have high expression levels as
shown in Table 2 below, with column "Clone" showing the antibodies
and the expression level "mg/ml" being shown in the second
column
[0368] The clones of these antibodies were sent to a service
provider with a requested expression level ("amount ordered",
expected expression levels). However, the actual expression levels
of these antibodies ("amount delivered") were very high and
exceeded the expected expression levels.
TABLE-US-00002 TABLE 2 Conditionally active antibodies with high
expression levels amount amount Clone mg/ml targeted obtained
BAP063.6-hum10F10-FLAG 7 150 294 BAP063.6-HC-H100Y-FLAG 6.6 150 238
BAP063.8-LC046HC04-FLAG 7 200 332.5 BAP063.8-LC062HC02-FLAG 5.8 200
220.4 BAP063.9-13-1-FLAG 5.3 50 123 BAP063.9-29-2-FLAG 4.9 50 102
BAP063.9-45-2-FLAG 5.4 50 129 BAP063.9-13-3-FLAG 5.9 50 130
BAP063.9-21-3-FLAG 5.3 50 17 BAP063.9-21-4-FLAG 7 50 176
BAP063.9-29-4-FLAG 8.2 50 196 BAP063.9-48-3-FLAG 7 50 125
BAP063.9-49-4-FLAG 5.3 50 126 BAP063.9-61-1-FLAG 5.1 50 97
BAP063.9-61-2-FLAG 5 50 92
[0369] The conditionally active antibodies did not show aggregation
in a buffer as demonstrated in FIG. 4, using BAP063.9-13-1 antibody
as an example. The BAP063.9-13-1 antibody was analyzed by size
exclusion chromatography. In FIG. 4, only one peak was detected,
demonstrating little or no aggregation of the antibody.
[0370] The conditionally active antibodies were also assayed using
surface plasmon resonance (SPR) to measure their on and off rates
to the drug target antigen X1. The SPR assay has been known to
measure on and off rates for the conditionally active antibodies.
The SPR assay was performed in the presence of bicarbonate. The in
vivo on and off rate (in animals and humans) of the conditionally
active antibodies is a very important feature for the conditionally
active antibodies.
[0371] It was observed that the conditionally active antibodies
have quick on-rates at pH 6.0 and slower on-rates at pH 7.4, in
comparison with the negative control (BAP063 10F10 which has
similar on-rates at both pH 6.0 and pH 7.4) (FIG. 5). In addition,
raising the temperature from room temperature to 60.degree. C. does
not significantly alter the SPR assay results (FIG. 5). The SPR
assay also showed that these conditionally active antibodies were
highly selective at pH 6.0 as compared to pH 7.4 (FIGS. 6A-6B show
one antibody as an example).
[0372] The conditionally active biological antibodies are
summarized in Table 3. Two of the antibodies were expressed as scFv
(BAP063.9-13.3 and BAP063.9-48.3), which were ready to be inserted
into a CAR in the CAR-T platform. Incubating the antibodies at
60.degree. C. for one hour did not change the affinities of most of
the antibodies ("Thermostability"). In the two columns reporting
data using SPR to measure binding activity at pH 6.0 and pH 7.4
(the last two columns of Table 3), a comparison was made to
"BAP063.6-hum10F10-FLAG" (a negative control, second row in Table
3). The selectivity of these antibodies may be determined by the
differences between the data in the two last columns. The two scFv
antibodies had very high selectivity (75% and 50% at pH 6 over 0%
at pH 7.4).
TABLE-US-00003 TABLE 3 Summary of the conditionally active
antibodies Increased Aggre- binding at gation Thermo- pH 7.4 KD SPR
SPR CAB amount amount (PBS, stability after heat Ka Kd [M] activity
activity Clone scFv mg/ml ordered delivered pH 7.4) (1 h 60.degree.
C.) treatment [M s] [s.sup.-1] pH 6.0 pH 6.0 pH 7.4 BAP063.6- 7 150
294 No 100% No 5.14E+06 8.38E-04 1.63E-10 100% 100% hum10F10-FLAG
BAP063.6- 6.6 150 238 N.D. 2.41E+06 5.12E-03 2.12E-09 80% 40%
HC-H100Y-FLAG BAP063.9- 5.3 50 123 No 100% Yes 1.98E+06 2.88E-03
1.46E-09 100% 75% 13-1-FLAG BAP063.9- 4.9 50 102 No 100% Yes
1.19E+06 2.14E-03 1.79E-09 90% 50% 29-2-FLAG BAP063.9- 5.4 50 129
No reduced Yes 1.53E+06 2.31E-03 1.51E-09 75% 25% 45-2-FLAG
BAP063.9- Yes 5.9 50 130 No 100% Yes 1.42E+06 1.82E-03 1.28E-09 75%
0% 13-3-FLAG BAP063.9- 5.3 50 117 No 100% No 1.53E+06 4.13E-03
2.69E-09 50% 25% 21-3-FLAG BAP063.9- 7 50 176 No 100% No 1.03E+06
3.26E-03 3.16E-09 50% 0% 21-4-FLAG BAP063.9- 8.2 50 196 No 100%
(yes) 1.40E+06 2.21E-03 1.58E-09 75% 0% 29-4-FLAG BAP063.9- Yes 7
50 125 <5% reduced No 8.92E+05 2.33E-03 2.61E-09 50% 0%
48-3-FLAG
Comparative Example A
CAR-T Cells with Non-Conditionally Active Antibody Against Target
Antigen X1
[0373] A non-conditionally active scFv antibody against target
antigen X1 was used to construct CAR-T cells that bind to target
antigen X1 or CHO cells expressing target antigen X1 on the cell
surface (CHO-X1), FIGS. 7A-7B. The non-conditionally active
antibody was used as the ASTR of the CAR molecule that was inserted
into T cells to construct CAR-T cells that can bind to target
antigen X1.
[0374] As a comparison, CHO cells that do not express target
antigen X1 were treated with: (1) T cells not transduced with a CAR
molecule, (2) T cells transduced with a CAR molecule that does not
bind to target antigen X1, and (3) T cells transduced with a CAR
molecule with a non-conditionally active antibody against target
antigen X1 (FIG. 7A). The CHO cell population is indicated by the
cell index (Y-axis in FIG. 7A), with a decrease in cell index
indicating cytotoxicity (cell killing) by the CAR-T cells.
[0375] Referring to FIG. 7A, before addition of the T cells, the
CHO cells showed growth. After addition of the CAR-T cells that
bind to target antigen X1, the cell index initially decreased,
indicating non-specific cytotoxicity of the T cells. However, the
CHO cells resumed growing shortly thereafter. More importantly, the
differences among the three treatments were insignificant,
indicating no significant cytotoxicity to the CHO cells that do not
express target antigen X1 of the CAR-T cells with the
non-conditionally active antibody against target antigen X1.
[0376] CHO cells that express target antigen X1 were then treated
in the same manner as above with: (1) T cells not transduced with a
CAR molecule, (2) T cells transduced with a CAR molecule that does
not bind to target antigen X1, and (3) T cells transduced with a
CAR molecule with a non-conditionally active antibody against
target antigen X1 (FIG. 7B). After addition of the T cells, the
cell index is significantly decreased by the treatment with the
CAR-T cells with the non-conditionally active antibody against
target antigen X1, but not by the other two treatments, indicating
cytotoxicity to the CHO-X1 cells that express target antigen X1 by
the CAR-T cells with the non-conditionally active antibody against
target antigen X1.
Example 3
CAR-T Cells with a Conditionally Active scFv Antibody Against
Target Antigen X1
[0377] A conditionally active scFv antibody against target antigen
X1 was used to construct a CAR molecule. T cells were transduced
with the CAR molecule such that the T cells expressed the CAR
molecule (CAR-T cells). CHO cells expressing target antigen X1
(CHO-63 cells) or regular CHO cells that do not express target
antigen X1 (CHO cells) were separately treated with the CAR-T
cells. Non-transduced T-cells (without the CAR molecule) were used
as a control (FIGS. 8A-8B).
[0378] Referring to FIG. 8A, CHO cells that do not express the
target antigen X1 were treated with the CAR-T cells and
non-transduced T-cells. There was no significant difference between
the two treatments, indicating no cytotoxicity of the CAR-T cells
to the CHO cells. Referring to FIG. 8B where CHO cells expressing
target antigen X1 (CHO-63) were similarly treated, the CAR-T cells
with a conditionally active antibody against target antigen X1
significantly reduced the CHO-63 cell population, in comparison
with non-transduced T-cells. This indicated that CAR-T cells with a
conditionally active antibody against target antigen X1 were
cytotoxic to the CHO-63 cells.
[0379] The CAR-T cells, once bound to target antigen X1, induced
cytotoxicity. This effect was confirmed by measurement of the
levels of the cytokines interferon gamma (INFg) and IL2. The
cytokine data is shown in FIGS. 9A-9B. In FIG. 9A, the binding of
CAR-T cells with target antigen X1 on the CHO-63 cells triggered
significant release of INFg, in comparison with non-transduced T
cells, as shown by the increased cytokine levels that were
observed. Similarly, in FIG. 9B, the binding of CAR-T cells with
target antigen X1 on the CHO-63 cells triggered significant release
of IL2, in comparison with non-transduced T cells, as shown by the
increased cytokine levels that were observed.
Example 4
CAR-T Cells with a Conditionally Active scFv Antibody Against
Target Antigen X2
[0380] Conditionally active scFv antibodies against target antigen
X2 were produced. Their binding activity to target antigen X2 was
measured using an ELISA essay (FIG. 10).
[0381] One of the scFv antibodies shown in FIG. 10, scFv-116101,
was used to construct CAR molecules for producing CAR-T cells
(116101 CAR-T). The constructed CAR-T cells were used to target
Daudi cells that express target antigen X2. The negative controls
were T-cells not transduced with a CAR molecule (non-transduced T
cells) and CAR-T cells transduced with a CAR molecule not capable
of binding to target antigen X2 (non-X2 scFv CAR-T). The results
are shown in FIG. 11A. The ratio of the number of T cells to the
number of Daudi cells in these treatments was 10:1. The CAR-T cells
with the scFv antibody targeting target antigen X2 on the Daudi
cells (116101 CAR-T) induced significant cell death for the Daudi
cells as shown by the higher dead/live cell ratio in FIG. 11A.
[0382] HEK293 cells were treated with the same T cells as were used
to treat the Daudi cells. The results are shown in FIG. 11B. Since
HEK293 cells do not express target antigen X2 on the cell surface,
the CAR-T cells with the scFv antibody targeting target antigen X2
(116101 CAR-T) did not induce significant cell death in the HEK293
cells, as compared with the negative controls (FIG. 11B).
Example 5
Cytokine Release of CAR-T Cells with Antibodies Against Target
Antigens X1 and X2
[0383] The cytokine release induced by binding of CAR-T cells with
target antigens was measured in this example. FIGS. 12A-12B show
INFg and IL2 release after binding of CAR-T cells containing a
conditionally active scFv antibody against target antigen X1 with
CHO-63 cells expressing target antigen X1. After treating the CAR-T
cells with these CHO-63 cells for 24 hours, there was a significant
increase both the INFg and IL2 cytokine levels indicating release
of both INFg and IL2 cytokines, in comparison with controls where
the same CAR-T cells were used to treat CHO cells that do not
express target antigen X1. Further, T cells not transduced with a
CAR molecule and CAR-T cells that did not bind with target antigen
X1 did not result in significant release of INFg and IL2
cytokines.
[0384] FIGS. 13A-13B show INFg and IL cytokine levels after binding
of CAR-T cells containing a conditionally active scFv antibody
against target antigen X2 with Rajib cells and Daudi cells both of
which express target antigen X2. After treating the Rajib cells and
Daudi cells with CAR-T cells for 24 hours, a significant increase
in INFg and IL2 cytokine levels was observed, in comparison with
controls where the same CAR-T cells were used to treat HEK293 cells
that do not express target antigen X2. Further, T cells not
transduced with a CAR molecule and CAR-T cells that did not bind
with target antigen X2 did not significantly increase cytokine
levels thereby indicating a failure to induce significant release
of INFg and IL2 cytokines.
Example 6
Conditionally Active scFv Antibodies Against Target Antigen X3
[0385] Five conditionally active scFv antibodies against target
antigen X3 were selected. The selected conditionally active scFv
antibodies are more active at pH 6.0 than at pH 7.4. These
conditionally active scFv antibodies may be used to construct CAR-T
cells binding to cells expressing target antigen X3.
[0386] It is to be understood, however, that even though numerous
characteristics and advantages of the present invention have been
set forth in the foregoing description, together with details of
the structure and function of the invention, the disclosure is
illustrative only, and changes may be made in detail, especially in
matters of shape, size and arrangement of parts within the
principles of the invention to the full extent indicated by the
broad general meanings of the terms in which the appended claims
are expressed.
* * * * *