U.S. patent application number 12/417097 was filed with the patent office on 2009-09-10 for nucleic acids encoding receptor for il-17 homologous polypeptides and uses thereof.
Invention is credited to Jian Chen, Ellen Filvaroff, Sherman Fong, Audrey Goddard, Paul Godowski, Christopher Grimaldi, Austin Gurney, Kenneth Hillan, Hanzhong Li, Daniel Tumas, Richard Vandlen, Menno VanLookeren, Colin Watanabe, P. Mickey Williams, William I. Wood, Daniel Yansura.
Application Number | 20090227017 12/417097 |
Document ID | / |
Family ID | 28455213 |
Filed Date | 2009-09-10 |
United States Patent
Application |
20090227017 |
Kind Code |
A1 |
Chen; Jian ; et al. |
September 10, 2009 |
NUCLEIC ACIDS ENCODING RECEPTOR FOR IL-17 HOMOLOGOUS POLYPEPTIDES
AND USES THEREOF
Abstract
The present invention is directed to novel polypeptides and to
nucleic acid molecules encoding those polypeptides. Also provided
herein are vectors and host cells comprising those nucleic acid
sequences, chimeric polypeptide molecules comprising the
polypeptides of the present invention fused to heterologous
polypeptide sequences, antibodies which bind to the polypeptides of
the present invention and to methods for producing the polypeptides
of the present invention.
Inventors: |
Chen; Jian; (Princeton,
NJ) ; Filvaroff; Ellen; (San Francisco, CA) ;
Fong; Sherman; (Alameda, CA) ; Goddard; Audrey;
(San Francisco, CA) ; Godowski; Paul; (Burlingame,
CA) ; Grimaldi; Christopher; (San Francisco, CA)
; Gurney; Austin; (Belmont, CA) ; Li;
Hanzhong; (San Mateo, CA) ; Hillan; Kenneth;
(San Francisco, CA) ; Tumas; Daniel; (Orinda,
CA) ; VanLookeren; Menno; (San Francisco, CA)
; Vandlen; Richard; (Hillsborough, CA) ; Watanabe;
Colin; (Moraga, CA) ; Williams; P. Mickey;
(Half Moon Bay, CA) ; Wood; William I.;
(Hillsborough, CA) ; Yansura; Daniel; (Pacifica,
CA) |
Correspondence
Address: |
GOODWIN PROCTER LLP
135 COMMONWEALTH DRIVE
MENLO PARK
CA
94025
US
|
Family ID: |
28455213 |
Appl. No.: |
12/417097 |
Filed: |
April 2, 2009 |
Related U.S. Patent Documents
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Application
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Filing Date |
Patent Number |
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10410374 |
Apr 8, 2003 |
7544482 |
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12417097 |
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09747259 |
Dec 20, 2000 |
6569645 |
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10410374 |
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PCT/US00/23328 |
Aug 24, 2000 |
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09747259 |
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Current U.S.
Class: |
435/358 ;
435/252.33; 435/254.2; 435/320.1; 536/23.5 |
Current CPC
Class: |
C07K 14/54 20130101;
G01N 33/57423 20130101; C07K 14/705 20130101; G01N 33/57415
20130101; A61K 38/00 20130101; G01N 33/57419 20130101; G01N 2500/04
20130101 |
Class at
Publication: |
435/358 ;
536/23.5; 435/320.1; 435/252.33; 435/254.2 |
International
Class: |
C12N 5/06 20060101
C12N005/06; C07H 21/00 20060101 C07H021/00; C12N 15/63 20060101
C12N015/63; C12N 1/21 20060101 C12N001/21; C12N 1/16 20060101
C12N001/16 |
Claims
1-88. (canceled)
89. An isolated nucleic acid having at least 80% nucleic acid
sequence identity to: (a) a nucleic acid sequence encoding the
polypeptide shown in FIG. 12 (SEQ ID NO:12); (b) a nucleic acid
sequence encoding the polypeptide shown in FIG. 12 (SEQ ID NO:12),
lacking its associated signal peptide; (c) the nucleic acid
sequence show in FIG. 11 (SEQ ID NO:11); (d) the full-length coding
sequence of the nucleic acid sequence show in FIG. 11 (SEQ ID
NO:11); or (e) the full-length coding sequence of the cDNA
deposited under ATCC accession number PTA-202; wherein the nucleic
acid having at least 80% sequence identity to the nucleic acid of
(a)-(e) encodes a polypeptide that binds to IL-17E.
90. The isolated nucleic acid of claim 89 having at least 85%
nucleic acid sequence identity to: (a) a nucleic acid sequence
encoding the polypeptide shown in FIG. 12 (SEQ ID NO:12); (b) a
nucleic acid sequence encoding the polypeptide shown in FIG. 12
(SEQ ID NO:12), lacking its associated signal peptide; (c) the
nucleic acid sequence shown in FIG. 11 (SEQ ID NO:11); (d) the
full-length coding sequence of the nucleic acid sequence shown in
FIG. 11 (SEQ ID NO:11); or (e) the full-length coding sequence of
the cDNA deposited under ATCC accession number PTA-202; wherein the
nucleic acid having at least 85% sequence identity to the nucleic
acid of (a)-(e) encodes a polypeptide that binds to IL-17E.
91. The isolated nucleic acid of claim 89 having at least 90%
nucleic acid sequence identity to: (a) a nucleic acid sequence
encoding the polypeptide shown in FIG. 12 (SEQ ID NO:12); (b) a
nucleic acid sequence encoding the polypeptide shown in FIG. 12
(SEQ ID NO:12); lacking its associated signal peptide; (c) the
nucleic acid sequence shown in FIG. 11 (SEQ ID NO:11); (d) the
full-length coding sequence of the nucleic acid sequence shown in
FIG. 11 (SEQ ID NO:11); or (e) the full-length coding sequence of
the cDNA deposited under ATCC accession number PTA-202; wherein the
nucleic acid having at least 90% sequence identity to the nucleic
acid of (a)-(e) encodes a polypeptide that binds to IL-17E.
92. The isolated nucleic acid of claim 89 having at least 95%
nucleic acid sequence identity to: (a) a nucleic acid sequence
encoding the polypeptide shown in FIG. 12 (SEQ ID NO:12); (b) a
nucleic acid sequence encoding the polypeptide shown in FIG. 12
(SEQ ID NO:12), lacking its associated signal peptide; (c) the
nucleic acid sequence shown in FIG. 11 (SEQ ID NO:11); (d) the
full-length coding sequence of the nucleic acid sequence shown in
FIG. 11 (SEQ ID NO:11); or (e) the full-length coding sequence of
the cDNA deposited under ATCC accession number PTA-202; wherein the
nucleic acid having at least 95% sequence identity to the nucleic
acid of (a)-(e) encodes a polypeptide that binds to IL-17E.
93. The isolated nucleic acid of claim 89 having at least 99%
nucleic acid sequence identity to: (a) a nucleic acid sequence
encoding the polypeptide shown in FIG. 12 (SEQ ID NO:12); (b) a
nucleic acid sequence encoding the polypeptide shown in FIG. 12
(SEQ ID NO:12), lacking its associated signal peptide; (c) the
nucleic acid sequence shown in FIG. 11 (SEQ ID NO:11); (d) the
full-length coding sequence of the nucleic acid sequence shown in
FIG. 11 (SEQ ID NO:11); or (e) the full-length coding sequence of
the cDNA deposited under ATCC accession number PTA-202; wherein the
nucleic acid having at least 99% sequence identity to the nucleic
acid of (a)-(e) encodes a polypeptide that binds to IL-17E.
94. A vector comprising the nucleic acid of claim 89.
95. The vector of claim 94, wherein the nucleic acid is operably
linked to control sequences recognized by a host cell transformed
with the vector.
96. An isolated host cell comprising the vector of claim 94.
97. The host cell of claim 96, wherein the cell is a CHO cell, an
E. coli or a yeast cell.
98. An isolated nucleic acid that hybridizes to: (a) a nucleic acid
sequence encoding the polypeptide shown in FIG. 12 (SEQ ID NO:12);
(b) a nucleic acid sequence encoding the polypeptide shown in FIG.
12 (SEQ ID NO:12), lacking its associated signal peptide; (c) the
nucleic acid sequence shown in FIG. 11 (SEQ ID NO:11); (d) the
full-length coding sequence of the nucleic acid sequence shown in
FIG. 11 (SEQ ID NO:11); or (e) the full-length coding sequence of
the cDNA deposited under ATCC accession number PTA-202.
99. The isolated nucleic acid of claim 98, wherein hybridization
occurs under stringent conditions.
100. The isolated nucleic acid of claim 98 which is at least 10
nucleotides, 20 nucleotides, 30 nucleotides, 40 nucleotides, 60
nucleotides, 70 nucleotides, 80 nucleotides or 90 nucleotides in
length.
Description
FIELD OF THE INVENTION
[0001] The present invention relates generally to the
identification and isolation of novel DNA and to the recombinant
production of novel polypeptides having sequence similarity to
interleukin-17 and to interleukin-17 receptor protein, designated
herein as "PRO" polypeptides.
BACKGROUND OF THE INVENTION
[0002] Extracellular proteins play important roles in, among other
things, the formation, differentiation and maintenance of
multicellular organisms. The fate of many individual cells, e.g.,
proliferation, migration, differentiation, or interaction with
other cells, is typically governed by information received from
other cells and/or the immediate environment. This information is
often transmitted by secreted polypeptides (for instance, mitogenic
factors, survival factors, cytotoxic factors, differentiation
factors, neuropeptides, and hormones) which are, in turn, received
and interpreted by diverse cell receptors or membrane-bound
proteins. These secreted polypeptides or signaling molecules
normally pass through the cellular secretory pathway to reach their
site of action in the extracellular environment.
[0003] Secreted proteins have various industrial applications,
including as pharmaceuticals, diagnostics, biosensors and
bioreactors. Most protein drugs available at present, such as
thrombolytic agents, interferons, interleukins, erythropoietins,
colony stimulating factors, and various other cytokines, are
secretory proteins. Their receptors, which are membrane proteins,
also have potential as therapeutic or diagnostic agents.
[0004] Membrane-bound proteins and receptors can play important
roles in, among other things, the formation, differentiation and
maintenance of multicellular organisms. The fate of many individual
cells, e.g., proliferation, migration, differentiation, or
interaction with other cells, is typically governed by information
received from other cells and/or the immediate environment. This
information is often transmitted by secreted polypeptides (for
instance, mitogenic factors, survival factors, cytotoxic factors,
differentiation factors, neuropeptides, and hormones) which are, in
turn, received and interpreted by diverse cell receptors or
membrane-bound proteins. Such membrane-bound proteins and cell
receptors include, but are not limited to, cytokine receptors,
receptor kinases, receptor phosphatases, receptors involved in
cell-cell interactions, and cellular adhesin molecules like
selectins and integrins. For instance, transduction of signals that
regulate cell growth and differentiation is regulated in part by
phosphorylation of various cellular proteins. Protein tyrosine
kinases, enzymes that catalyze that process, can also act as growth
factor receptors. Examples include fibroblast growth factor
receptor and nerve growth factor receptor.
[0005] Similarly to secreted proteins, membrane-bound proteins and
receptor molecules have various industrial applications, including
as pharmaceutical and diagnostic agents. Receptor immunoadhesins,
for instance, can be employed as therapeutic agents to block
receptor-ligand interactions. The membrane-bound proteins can also
be employed for screening of potential peptide or small molecule
inhibitors of the relevant receptor/ligand interaction.
[0006] Efforts are being undertaken by both industry and academia
to identify new, native secreted proteins and native receptor or
membrane-bound proteins. Many efforts are focused on the screening
of mammalian recombinant DNA libraries to identify the coding
sequences for novel secreted proteins. Examples of screening
methods and techniques are described in the literature [see, for
example, Klein et al., Proc. Natl. Acad. Sci., 93:7108-7113 (1996);
U.S. Pat. No. 5,536,637)].
[0007] In this regard, the present invention relates to identifying
novel secreted polypeptides and receptors of the interleukin-17
(IL-17) family which have been shown to be related to
immune-mediated and inflammatory disease. Immune related and
inflammatory diseases are the manifestation or consequence of
fairly complex, often multiple interconnected biological pathways
which in normal physiology are critical to respond to insult or
injury, initiate repair from insult or injury, and mount innate and
acquired defense against foreign organisms. Disease or pathology
occurs when these normal physiological pathways cause additional
insult or injury either as directly related to the intensity of the
response, as a consequence of abnormal regulation or excessive
stimulation, as a reaction to self, or as a combination of
these.
[0008] Though the genesis of these diseases often involves
multistep pathways and often multiple different biological
systems/pathways, intervention at critical points in one or more of
these pathways can have an ameliorative or therapeutic effect.
Therapeutic intervention can occur by either antagonism of a
detrimental process/pathway or stimulation of a beneficial
process/pathway.
[0009] Many immune related diseases are known and have been
extensively studied. Such diseases include immune-mediated
inflammatory diseases (such as rheumatoid arthritis, immune
mediated renal disease, hepatobiliary diseases, inflammatory bowel
disease (IBD), psoriasis, and asthma), non-immune-mediated
inflammatory diseases, infectious diseases, immunodeficiency
diseases, neoplasia, etc.
[0010] T lymphocytes (T cells) are an important component of a
mammalian immune response. T cells recognize antigens which are
associated with a self-molecule encoded by genes within the major
histocompatibility complex (MHC). The antigen may be displayed
together with MHC molecules on the surface of antigen presenting
cells, virus infected cells, cancer cells, grafts, etc. The T cell
system eliminates these altered cells which pose a health threat to
the host mammal. T cells include helper T cells and cytotoxic T
cells. Helper T cells proliferate extensively following recognition
of an antigen-MHC complex on an antigen presenting cell. Helper T
cells also secrete a variety of cytokines, i.e., lymphokines, which
play a central role in the activation of B cells, cytotoxic T cells
and a variety of other cells which participate in the immune
response.
[0011] A central event in bot humoral and cell mediated immune
responses is the activation and clonal expansion of helper T cells.
Helper T cell activation is initiated by the interaction of the T
cell receptor (TCR)-CD3 complex with an antigen-MHC on the surface
of an antigen presenting cell. This interaction mediates a cascade
of biochemical events that induce the resting helper T cell to
enter a cell cycle (the G0 to G1 transition) and results in the
expression of a high affinity receptor for IL-2 and sometimes IL4.
The activated T cell progresses through the cycle proliferating and
differentiating into memory cells or effector cells.
[0012] In addition to the signals mediated through the TCR,
activation of T cells involves additional costimulation induced by
cytokines released by the antigen presenting cell or through
interactions with membrane bound molecules on the antigen
presenting cell and the T cell. The cytokines IL-1 and IL-6 have
been shown to provide a costimulatory signal. Also, the interaction
between the B7 molecule expressed on the surface of an antigen
presenting cell and CD28 and CTLA-4 molecules expressed on the T
cell surface effect T cell activation. Activated T cells express an
increased number of cellular adhesion molecules, such as ICAM-1,
integrins, VLA-4, LFA-1, CD56, etc.
[0013] T-cell proliferation in a mixed lymphocyte culture or mixed
lymphocyte reaction (MLR) is an established indication of the
ability of a compound to stimulate the immune system. In many
immune responses, inflammatory cells infiltrate the site of injury
or infection. The migrating cells may be neutrophilic,
eosinophilic, monocytic or lymphocytic as can be determined by
histologic examination of the affected tissues. Current Protocols
in Immunology, ed. John E. Coligan, 1994, John Wiley & Sons,
Inc.
[0014] Immune related diseases could be treated by suppressing the
immune response. Using neutralizing antibodies that inhibit
molecules having immune stimulatory activity would be beneficial in
the treatment of immune-mediated and inflammatory diseases.
Molecules which inhibit the immune response can be utilized
(proteins directly or via the use of antibody agonists) to inhibit
the immune response and thus ameliorate immune related disease.
[0015] Interleukin-17 (IL-17) has been identified as a cellular
ortholog of a protein encoded by the T lymphotropic Herpes virus
Saimiri (HSV) [see, Rouvier et al., J. Immunol., 150(12): 5445-5456
(19993); Yao et al., J. Immunol., 122(12):5483-5486 (1995) and Yao
et al., Immunity, 3(6):811-821 (1995)]. Subsequent characterization
has shown that this protein is a potent cytokine that acts to
induce proinflammatory responses in a wide variety of peripheral
tissues. IL-17 is a homodimeric cytokine of about 32 kDa which is
synthesized and secreted only by CD4.sup.+ activated memory T cells
(reviewed in Fossiez et al., Int. Rev. Immunol. 16: 541-551
[1998]).
[0016] Despite its restricted tissue distribution, IL-17 exhibits
pleitropic biological activities on various types of cells. IL-17
has been found to stimulate the production of many cytokines. It
induces the secretion of IL-6, IL-8, prostaglandin E2, MCP-1 and
G-CSF by adherent cells like fibroblasts, keratinocytes, epithelial
and endothelial cells. IL-17 also has the ability to induce ICAM-1
surface expression, proliferation of T cells, and growth and
differentiation of CD34.sup.+ human progenitors into neutrophils.
IL-17 has also been implicated in bone metabolism, and has been
suggested to play an important role in pathological conditions
characterized by the presence of activated T cells and TNF-.alpha.
production such as rheumatoid arthritis and loosening of bone
implants (Van Bezooijen et al., J. Bone Miner. Res. 14: 1513-1521
[1999]). Activated T cells of synovial tissue derived from
rheumatoid arthritis patients were found to secrete higher amounts
of IL-17 than those derived from normal individuals or
osteoarthritis patients (Chabaud et al., Arthritis Rheum., 42:
963-970 [1999]). It was suggested that this proinflammatory
cytokine actively contributes to synovial inflammation in
rheumatoid arthritis. Apart from its proinflammatory role, IL-17
seems to contribute to the pathology of rheumatoid arthritis by yet
another mechanism. For example, IL-17 has been shown to induce the
expression of osteoclast differentiation factor (ODF) mRNA in
osteoblasts (Kotake et al., J. Clin. Invest., 103: 1345-1352
[1999]). ODF stimulates differentiation of progenitor cells into
osteoclasts, the cells involved in bone resorption. Since the level
of IL-17 is significantly increased in synovial fluid of rheumatoid
arthritis patients, it appears that IL-17 induced osteoclast
formation plays a crucial role in bone resorption in rheumatoid
arthritis. IL-17 is also believed to play a key role in certain
other autoimmune disorders such as multiple sclerosis (Matusevicius
et al., Mult. Scler. 5: 101-104 [1999]). IL-17 has further been
shown, by intracellular signalling, to stimulate Ca.sup.2+ influx
and a reduction in [cAMP].sub.i in human macrophages (Jovanovic et
al., J. Immunol., 160:3513 [1998]). Fibroblasts treated with IL-17
induce the activation of NF-.kappa.B, [Yao et al., Immunity, 3:811
(1995), Jovanovic et al., supra], while macrophages treated with it
activate NF-.kappa.B and mitogen-activated protein kinases
(Shalom-Barek et al., J. Biol. Chem., 273:27467 [1998]).
[0017] Additionally, IL-17 also shares sequence similarity with
mammalian cytokine-like factor 7 that is involved in bone and
cartilage growth. Other proteins with which IL-17 polypeptides
share sequence similarity are human embryo-derived
interleukin-related factor (EDIRF) and interleukin-20.
[0018] Consistent with IL-17's wide-range of effects, the cell
surface receptor for IL-17 has been found to be widely expressed in
many tissues and cell types (Yao et al., Cytokine, 9:794 [1997]).
While the amino acid sequence of the human IL-17 receptor (IL-R)
(866 amino acids) predicts a protein with a single transmembrane
domain and a long, 525 amino acid intracellular domain, the
receptor sequence is unique and is not similar to that of any of
the receptors from the cytokine/growth factor receptor family. This
coupled with the lack of similarity of IL-17 itself to other known
proteins indicates that IL-17 and its receptor may be part of a
novel family of signalling proteins and receptors. It has been
demonstrated that IL-17 activity is mediated through binding to its
unique cell surface receptor, wherein previous studies have shown
that contacting T cells with a soluble form of the IL-17 receptor
polypeptide inhibited T cell proliferation and IL-2 production
induced by PHA, concanavalin A and anti-TCR monoclonal antibody
(Yao et al., J. Immunol., 155:5483-5486 [1995]). As such, there is
significant interest in identifying and characterizing novel
polypeptides having homology to the known cytokine receptors,
specifically IL-17 receptors.
[0019] Recently, we have identified two new proteins termed IL-17B
and IL-17C that are clearly related to IL-17, establishing that
there exists a family of IL-17-like molecules (Li et al., Proc.
Natl. Acad. Sci. (USA), 97(2):773-778 [2000]). Interestingly, they
do not appear to be ligands for IL-17 receptor, suggesting that
there exists other molecules that serve as cognate receptors for
these factors. Interest in this family of molecules has increased
as it has become apparent that IL-17 may contribute to a number of
important medical conditions related to immune function: including
rheumatoid arthritis, immune mediated renal diseases, hepatobiliary
diseases, inflammatory bowel disease, psoriasis, asthma, multiple
sclerosis, atherosclerosis, promotion of tumor growth, or
degenerative joint disease. Given the potential of IL-17 related
molecules to occupy important roles in the control of immune
function, there is an interest in the identification of other
members of this family and the receptors that direct the actions of
these molecules through particular target cell populations. In this
respect, the present invention describes the cloning and
characterization of novel proteins (designated herein as "PRO"
polypeptides) that are similar in amino acid sequence to IL-17, and
active variants thereof, as well as novel interleukin-receptor
molecules which have been shown to interact with the novel IL-17
protein ligands.
SUMMARY OF THE INVENTION
A. Embodiments
[0020] The present invention concerns compositions and methods
useful for the diagnosis and treatment of immune related disease in
mammals, including humans. The present invention is based on the
identification of proteins (including agonist and antagonist
antibodies) which either stimulate or inhibit the immune response
in mammals. Immune related diseases can be treated by suppressing
or enhancing the immune response. Molecules that enhance the immune
response stimulate or potentiate the immune response to an antigen.
Molecules which stimulate the immune response can be used
therapeutically where enhancement of the immune response would be
beneficial. Alternatively, molecules that suppress the immune
response attenuate or reduce the immune response to an antigen
(e.g., neutralizing antibodies) can be used therapeutically where
attenuation of the immune response would be beneficial (e.g.,
inflammation). Accordingly, the PRO polypeptides of the present
invention and agonists and antagonists thereof are also useful to
prepare medicines and medicaments for the treatment of
immune-related and inflammatory diseases. In a specific aspect,
such medicines and medicaments comprise a therapeutically effective
amount of a PRO polypeptide, agonist or antagonist thereof with a
pharmaceutically acceptable carrier. Preferably, the admixture is
sterile.
[0021] In a further embodiment, the invention concerns a method of
identifying agonists of or antagonists to a PRO polypeptide which
comprises contacting the PRO polypeptide with a candidate molecule
and monitoring a biological activity mediated by said PRO
polypeptide. Preferably, the PRO polypeptide is a native sequence
PRO polypeptide. In a specific aspect, the PRO agonist or
antagonist is an anti-PRO antibody.
[0022] In another embodiment, the invention concerns a composition
of matter comprising a PRO polypeptide or an agonist or antagonist
antibody which binds the polypeptide in admixture with a carrier or
excipient. In one aspect, the composition comprises a
therapeutically effective amount of the polypeptide or antibody. In
another aspect, when the composition comprises an immune
stimulating molecule, the composition is useful for: (a) enhancing
infiltration of inflammatory cells into a tissue of a mammal in
need thereof, (b) stimulating or enhancing an immune response in a
mammal in need thereof, (c) increasing the proliferation of
T-lymphocytes in a mammal in need thereof in response to an
antigen, (d) stimulating the activity of T-lymphocytes or (e)
increasing the vascular permeability. In a further aspect, when the
composition comprises an immune inhibiting molecule, the
composition is useful for: (a) decreasing infiltration of
inflammatory cells into a tissue of a mammal in need thereof, (b)
inhibiting or reducing an immune response in a mammal in need
thereof, (c) decreasing the activity of T-lymphocytes or (d)
decreasing the proliferation of T-lymphocytes in a mammal in need
thereof in response to an antigen. In another aspect, the
composition comprises a further active ingredient, which may, for
example, be a further antibody or a cytotoxic or chemotherapeutic
agent. Preferably, the composition is sterile.
[0023] In another embodiment, the invention concerns a method of
treating an immune related disorder in a mammal in need thereof,
comprising administering to the mammal a therapeutically effective
amount of a PRO polypeptide, an agonist thereof, or an antagonist
thereto. In a preferred aspect, the immune related disorder is
selected form the group consisting of: systemic lupus
erythematosis, rheumatoid arthritis, osteoarthritis, juvenile
chronic arthritis, spondyloarthropathies, systemic sclerosis,
idiopathic inflammatory myopathies, Sjogren's syndrome, systemic
vasculitis, sarcoidosis, autoimmune hemolytic anemia, autoimmune
thrombocytopenia, thyroiditis, diabetes mellitus, immune-mediated
renal disease, demyelinating diseases of the central and peripheral
nervous systems such as multiple sclerosis, idiopathic
demyelinating polyneuropathy or Guillain-Barre syndrome, and
chronic inflammatory demyelinating polyneuropathy, hepatobiliary
diseases such as infectious, autoimmune chronic active hepatitis,
primary biliary cirrhosis, granulomatous hepatitis, and sclerosing
cholangitis, inflammatory bowel disease, gluten-sensitive
enteropathy, and Whipple's disease, autoimmune or immune-mediated
skin diseases including bullous skin diseases, erythema multiforme
and contact dermatitis, psoriasis, allergic diseases such as
asthma, allergic rhinitis, atopic dermatitis, food hypersensitivity
and urticaria, immunologic diseases of the lung such as
eosinophilic pneumonias, idiopathic pulmonary fibrosis and
hypersensitivity pneumonitis, transplantation associated diseases
including graft rejection and graft-versus-host-disease.
[0024] In another embodiment, the invention provides an antibody
which specifically binds to any of the above or below described
polypeptides. Optionally, the antibody is a monoclonal antibody,
humanized antibody, antibody fragment or single-chain antibody. In
one aspect, the present invention concerns an isolated antibody
which binds a PRO polypeptide. In another aspect, the antibody
mimics the activity of a PRO polypeptide (an agonist antibody) or
conversely the antibody inhibits or neutralizes the activity of a
PRO polypeptide (an antagonist antibody). In another aspect, the
antibody is a monoclonal antibody, which preferably has nonhuman
complementarity determining region (CDR) residues and human
framework region (FR) residues. The antibody may be labeled and may
be immobilized on a solid support. In a further aspect, the
antibody is an antibody fragment, a monoclonal antibody, a
single-chain antibody, or an anti-idiotypic antibody.
[0025] In yet another embodiment, the present invention provides a
composition comprising an anti-PRO antibody in admixture with a
pharmaceutically acceptable carrier. In one aspect, the composition
comprises a therapeutically effective amount of the antibody.
Preferably, the composition is sterile. The composition may be
administered in the form of a liquid pharmaceutical formulation,
which may be preserved to achieve extended storage stability.
Alternatively, the antibody is a monoclonal antibody, an antibody
fragment, a humanized antibody, or a single-chain antibody.
[0026] In a further embodiment, the invention concerns an article
of manufacture, comprising:
(a) a composition of matter comprising a PRO polypeptide or
agonist, antagonist, or an antibody that specifically binds to said
polypeptide thereof; (b) a container containing said composition;
and (c) a label affixed to said container, or a package insert
included in said container referring to the use of said PRO
polypeptide or agonist or antagonist thereof in the treatment of an
immune related disease. The composition may comprise a
therapeutically effective amount of the PRO polypeptide or the
agonist or antagonist thereof.
[0027] In yet another embodiment, the present invention concerns a
method of diagnosing an immune related disease in a mammal,
comprising detecting the level of expression of a gene encoding a
PRO polypeptide (a) in a test sample of tissue cells obtained from
the mammal, and (b) in a control sample of known normal tissue
cells of the same cell type, wherein a higher or lower expression
level in the test sample as compared to the control sample
indicates the presence of immune related disease in the mammal from
which the test tissue cells were obtained.
[0028] In another embodiment, the present invention concerns a
method of diagnosing an immune disease in a mammal, comprising (a)
contacting an anti-PRO antibody with a test sample of tissue cells
obtained from the mammal, and (b) detecting the formation of a
complex between the antibody and a PRO polypeptide, in the test
sample; wherein the formation of said complex is indicative of the
presence or absence of said disease. The detection may be
qualitative or quantitative, and may be performed in comparison
with monitoring the complex formation in a control sample of known
normal tissue cells of the same cell type. A larger quantity of
complexes formed in the test sample indicates the presence or
absence of an immune disease in the mammal from which the test
tissue cells were obtained. The antibody preferably carries a
detectable label. Complex formation can be monitored, for example,
by light microscopy, flow cytometry, fluorimetry, or other
techniques known in the art. The test sample is usually obtained
from an individual suspected of having a deficiency or abnormality
of the immune system.
[0029] In another embodiment, the invention provides a method for
determining the presence of a PRO polypeptide in a sample
comprising exposing a test sample of cells suspected of containing
the PRO polypeptide to an anti-PRO antibody and determining the
binding of said antibody to said cell sample. In a specific aspect,
the sample comprises a cell suspected of containing the PRO
polypeptide and the antibody binds to the cell. The antibody is
preferably detectably labeled and/or bound to a solid support.
[0030] In another embodiment, the present invention concerns an
immune-related disease diagnostic kit, comprising an anti-PRO
antibody and a carrier in suitable packaging. The kit preferably
contains instructions for using the antibody to detect the presence
of the PRO polypeptide. Preferably the carrier is pharmaceutically
acceptable.
[0031] In another embodiment, the present invention concerns a
diagnostic kit, containing an anti-PRO antibody in suitable
packaging. The kit preferably contains instructions for using the
antibody to detect the PRO polypeptide.
[0032] In another embodiment, the invention provides a method of
diagnosing an immune-related disease in a mammal which comprises
detecting the presence or absence or a PRO polypeptide in a test
sample of tissue cells obtained from said mammal, wherein the
presence or absence of the PRO polypeptide in said test sample is
indicative of the presence of an immune-related disease in said
mammal.
[0033] In another embodiment, the present invention concerns a
method for identifying an agonist of a PRO polypeptide
comprising:
(a) contacting cells and a test compound to be screened under
conditions suitable for the induction of a cellular response
normally induced by a PRO polypeptide; and (b) determining the
induction of said cellular response to determine if the test
compound is an effective agonist, wherein the induction of said
cellular response is indicative of said test compound being an
effective agonist.
[0034] In another embodiment, the invention concerns a method for
identifying a compound capable of inhibiting the activity of a PRO
polypeptide comprising contacting a candidate compound with a PRO
polypeptide under conditions and for a time sufficient to allow
these two components to interact and determining whether the
activity of the PRO polypeptide is inhibited. In a specific aspect,
either the candidate compound or the PRO polypeptide is immobilized
on a solid support. In another aspect, the non-immobilized
component carries a detectable label. In a preferred aspect, this
method comprises the steps of:
(a) contacting cells and a test compound to be screened in the
presence of a PRO polypeptide under conditions suitable for the
induction of a cellular response normally induced by a PRO
polypeptide; and (b) determining the induction of said cellular
response to determine if the test compound is an effective
antagonist.
[0035] In another embodiment, the invention provides a method for
identifying a compound that inhibits the expression of a PRO
polypeptide in cells that normally express the polypeptide, wherein
the method comprises contacting the cells with a test compound and
determining whether the expression of the PRO polypeptide is
inhibited. In a preferred aspect, this method comprises the steps
of:
(a) contacting cells and a test compound to be screened under
conditions suitable for allowing expression of the PRO polypeptide;
and (b) determining the inhibition of expression of said
polypeptide.
[0036] In yet another embodiment, the present invention concerns a
method for treating an immune-related disorder in a mammal that
suffers therefrom comprising administering to the mammal a nucleic
acid molecule that codes for either (a) a PRO polypeptide, (b) an
agonist of a PRO polypeptide or (c) an antagonist of a PRO
polypeptide, wherein said agonist or antagonist may be an anti-PRO
antibody. In a preferred embodiment, the mammal is human. In
another preferred embodiment, the nucleic acid is administered via
ex vivo gene therapy. In a further preferred embodiment, the
nucleic acid is comprised within a vector, more preferably an
adenoviral, adeno-associated viral, lentiviral or retroviral
vector.
[0037] In yet another aspect, the invention provides a recombinant
viral particle comprising a viral vector consisting essentially of
a promoter, nucleic acid encoding (a) a PRO polypeptide, (b) an
agonist polypeptide of a PRO polypeptide, or (c) an antagonist
polypeptide of a PRO polypeptide, and a signal sequence for
cellular secretion of the polypeptide, wherein the viral vector is
in association with viral structural proteins. Preferably, the
signal sequence is from a mammal, such as from a native PRO
polypeptide.
[0038] In a still further embodiment, the invention concerns an ex
vivo producer cell comprising a nucleic acid construct that
expresses retroviral structural proteins and also comprises a
retroviral vector consisting essentially of a promoter, nucleic
acid encoding (a) a PRO polypeptide, (b) an agonist polypeptide of
a PRO polypeptide or (c) an antagonist polypeptide of a PRO
polypeptide, and a signal sequence for cellular secretion of the
polypeptide, wherein said producer cell packages the retroviral
vector in association with the structural proteins to produce
recombinant retroviral particles.
[0039] In a still further embodiment, the invention provides a
method for enhancing the infiltration of inflammatory cells from
the vasculature into a tissue of a mammal comprising administering
to said mammal (a) a PRO polypeptide, (b) an agonist of a PRO
polypeptide, or (c) an antagonist of a PRO polypeptide, wherein the
infiltration of inflammatory cells from the vasculature in the
mammal is enhanced.
[0040] In a still further embodiment, the invention provides a
method for decreasing the infiltration of inflammatory cells from
the vasculature into a tissue of a mammal comprising administering
to said mammal (a) a PRO polypeptide, (b) an agonist of a PRO
polypeptide, or (c) an antagonist of a PRO polypeptide, wherein the
infiltration of inflammatory cells from the vasculature in the
mammal is decreased.
[0041] In a still further embodiment, the invention provides a
method of increasing the activity of T-lymphocytes in a mammal
comprising administering to said mammal (a) a PRO polypeptide, (b)
an agonist of a PRO polypeptide, or (c) an antagonist of a PRO
polypeptide, wherein the activity of T-lymphocytes in the mammal is
increased.
[0042] In a still further embodiment, the invention provides a
method of decreasing the activity of T-lymphocytes in a mammal
comprising administering to said mammal (a) a PRO polypeptide, (b)
an agonist of a PRO polypeptide, or (c) an antagonist of a PRO
polypeptide, wherein the activity of T-lymphocytes in the mammal is
decreased.
[0043] In a still further embodiment, the invention provides a
method of increasing the proliferation of T-lymphocytes in a mammal
comprising administering to said mammal (a) a PRO polypeptide, (b)
an agonist of a PRO polypeptide, or (c) an antagonist of a PRO
polypeptide, wherein the proliferation of T-lymphocytes in the
mammal is increased.
[0044] In a still further embodiment, the invention provides a
method of decreasing the proliferation of T-lymphocytes in a mammal
comprising administering to said mammal (a) a PRO polypeptide, (b)
an agonist of a PRO polypeptide, or (c) an antagonist of a PRO
polypeptide, wherein the proliferation of T-lymphocytes in the
mammal is decreased.
[0045] In a still further embodiment, the invention provides a
method of stimulating the proliferation of T-cells comprising
contacting said T-cells with a PRO1031 or PRO10272 polypeptide or
agonist thereof, wherein said T-cell proliferation is
stimulated.
[0046] In a still further embodiment, the invention provides a
method of decreasing the proliferation of T-lymphocytes comprising
contacting said T-lymphocytes with an antagonist of a PRO1031 or
PRO10272 polypeptide, wherein the proliferation of T-lymphocytes is
decreased.
[0047] In a still further embodiment, the invention provides a
method of enhancing the infiltration of inflammatory cells into a
tissue of a mammal comprising administering an effective amount of
a PRO1031 polypeptide or agonist thereof, wherein said infiltration
is enhanced.
[0048] In a still further embodiment, the invention provides a
method of decreasing the infiltration of inflammatory cells into a
tissue of a mammal comprising administering an effective amount of
an antagonist of a PRO1031 polypeptide, wherein said infiltration
is decreased.
[0049] In yet another embodiment, the invention provides a method
for inhibiting angiogenesis induced by a PRO1031 polypeptide or an
agonist thereof in a mammal comprising administering a
therapeutically effective amount of an anti-PRO1031 antibody to the
mammal. Preferably, the mammal is a human, and more preferably the
mammal has a tumor or a retinal disorder.
[0050] In yet another embodiment, the invention provides a method
for stimulating angiogenesis induced by a PRO1031 polypeptide in a
mammal comprising administering a therapeutically effective amount
of a PRO1031 polypeptide or agonist thereof to the mammal.
Preferably, the mammal is a human, and more preferably angiogenesis
would promote tissue regeneration or wound healing.
[0051] In another embodiment, the invention provides a method for
inhibiting angiogenesis in a mammal comprising administering a
therapeutically effective amount of an antagonist of a PRO1031
polypeptide to the mammal, wherein said angiogenesis is
inhibited.
[0052] In still a further embodiment, the invention concerns the
use of a PRO1031 or PRO1122 polypeptide, or an agonist or
antagonist thereof as hereinbefore described, or an anti-PRO1031 or
anti-PRO1122 antibody, for the preparation of a medicament useful
in the treatment of a condition which is responsive to the PRO1031
or PRO1122 polypeptide or an agonist or antagonist thereof (e.g.,
anti-PRO1031 or anti-PRO1122). In a particular aspect, the
invention concerns the use of a PRO1031 or PRO1122 polypeptide, or
an agonist or antagonist thereof in a method for treating a
degenerative cartilaginous disorder.
[0053] In still a further embodiment, the invention relates to a
method of treating a degenerative cartilaginous disorder in a
mammal comprising administering a therapeutically effective amount
of a PRO1031 or PRO1122 polypeptide, agonist, or antagonist
thereof, to said mammal suffering from said disorder.
[0054] In still a further embodiment, the invention relates to a
kit comprising a composition comprising a PRO1031 or PRO1122
polypeptide, or an agonist or antagonist thereof, in admixture with
a pharmaceutically acceptable carrier; a container containing said
composition; and a label affixed to said container, referring to
the use of said composition, in the treatment of a degenerative
cartilaginous disorder.
[0055] In a further embodiment, the invention relates to a method
of detecting a polypeptide designated as A, B, or C in a sample
suspected of containing an A, B, or C polypeptide, said method
comprising contacting said sample with a polypeptide designated
herein as D, E, or F and determining the formation of a A/D, B/D,
C/E or C/F polypeptide conjugate in said sample, wherein the
formation of said conjugate is indicative of the presence of an A,
B, or C polypeptide in said sample and wherein A is a PRO1031
polypeptide (herein also designated IL-17B), B is a PRO10272
polypeptide (herein also designated IL-17B), C is a PRO20110
polypeptide (herein also designated IL-17F), D is a PRO5801
polypeptide (herein also designated IL-17RH1), E is a PRO1
polypeptide (herein known as IL-17R), and F is a PRO20040
polypeptide (herein also designated IL-17RH2). In one aspect of
this embodiment, said sample comprises cells suspected of
expressing said A, B, or C polypeptide.
[0056] In another aspect of this embodiment said D, E, or F
polypeptide is labeled with a detectable label and said D, E, or F
polypeptide is attached to a solid support.
[0057] In yet another embodiment, the invention relates to a method
of detecting a polypeptide designated as D, E, or F in a sample
suspected of containing an D, E, or F polypeptide, said method
comprising contacting said sample with a polypeptide designated
herein as A, B, or C and determining the formation of a A/D, B/D,
C/E, or C/F polypeptide conjugate in said sample, wherein the
formation of said conjugate is indicative of the presence of an A,
B, or C polypeptide in said sample and wherein A is a PRO1031
polypeptide (herein also designated IL-17B), B is a PRO10272
polypeptide (herein also designated IL-17E), C is a PRO20110
polypeptide (herein also designated IL-17F), D is a PRO5801
polypeptide (herein also designated IL-17RH1), E is a PRO1
polypeptide (herein known as IL-17R), and F is a PRO20040
polypeptide (herein also designated IL-17RH2). In one aspect of
this embodiment, said sample comprises cells suspected of
expressing said D, E, or F polypeptide. In another aspect of this
embodiment, said A, B, or C polypeptide is labeled with a
detectable label and said A, B, or C polypeptide is attached to a
solid support.
[0058] In still a further embodiment, the invention relates to a
method of linking a bioactive molecule to a cell expressing a
polypeptide designated as A, B, or C, said method comprising
contacting said cell with a polypeptide designated as D, E, or F
that is bound to said bioactive molecule and allowing said A, B, or
C and said D, E, or F polypeptides to bind to one another, thereby
linking said bioactive molecules to said cell, wherein A is a
PRO1031 polypeptide (herein also designated IL-17B), B is a
PRO10272 polypeptide (herein also designated IL-17E), C is a
PRO20110 polypeptide (herein also designated IL-17F), D is a
PRO5801 polypeptide (herein also designated IL-17RH1), E is a PRO1
polypeptide (herein known as IL-17R), and F is a PRO20040
polypeptide (herein also designated IL-17RH2). In one aspect of
this embodiment, said bioactive molecule is a toxin, a radiolabel
or an antibody. In another aspect of this embodiment, said
bioactive molecule causes the death of said cell.
[0059] In a further embodiment, the invention relates to a method
of linking a bioactive molecule to a cell expressing a polypeptide
designated as D, E, or F, said method comprising contacting said
cell with a polypeptide designated as A, B, or C that is bound to
said bioactive molecule and allowing said A, B, or C and said D, E,
or F polypeptides to bind to one another, thereby linking said
bioactive molecules to said cell, wherein A is a PRO1031
polypeptide (herein also designated IL-17B), B is a PRO10272
polypeptide (herein also designated IL-17E), C is a PRO20110
polypeptide (herein also designated IL-17F), D is a PRO5801
polypeptide (herein also designated IL-17RH1), E is a PRO
polypeptide (herein known as IL-17R), and F is a PRO20040
polypeptide (herein also designated IL-17RH2). In one aspect of
this embodiment, said bioactive molecule is a toxin, a radiolabel
or an antibody. In another aspect of this embodiment, said
bioactive molecule causes the death of said cell.
[0060] In still another embodiment, the invention relates to a
method of modulating at least one biological activity of a cell
expressing a polypeptide designated as A, B, or C, said method
comprising contacting said cell with a polypeptide designated as D,
E, or F or an anti-A, anti-B, or anti-C polypeptide antibody,
whereby said D, E, or F polypeptide or anti-A, anti-B, or anti-C
polypeptide antibody binds to said A, B, or C polypeptide, thereby
modulating at least one biological activity of said cell, wherein A
is a PRO1031 polypeptide (herein also designated IL-17B), B is a
PRO10272 polypeptide (herein also designated IL-17E), C is a
PRO20110 polypeptide (herein also designated IL-17F), D is a
PRO5801 polypeptide (herein also designated IL-17RH1), E is a PRO1
polypeptide (herein known as IL-17R), and F is a PRO20040
polypeptide (herein also designated IL-17RH2). In one aspect of
this embodiment, said cell is killed.
[0061] In yet a further embodiment, the invention relates to a
method of modulating at least one biological activity of a cell
expressing a polypeptide designated as D, E, or F, said method
comprising contacting said cell with a polypeptide designated as A,
B, or C or an anti-D, anti-E, or anti-F polypeptide antibody,
whereby said A, B, or C polypeptide or anti-D, anti-E, or anti-F
polypeptide antibody binds to said D, E, or F polypeptide, thereby
modulating at least one biological activity of said cell, wherein A
is a PRO1031 polypeptide (herein also designated IL-17B), B is a
PRO10272 polypeptide (herein also designated IL-17E), C is a
PRO20110 polypeptide (herein also designated IL-17F), D is a
PRO5801 polypeptide (herein also designated IL-17RH1), E is a PRO1
polypeptide (herein known as IL-17R), and F is a PRO20040
polypeptide (herein also designated IL-17RH2). In one aspect of
this embodiment, said cell is killed.
B. Additional Embodiments
[0062] In other embodiments of the present invention, the invention
provides an isolated nucleic acid molecule comprising a nucleotide
sequence that encodes a PRO polypeptide.
[0063] In one aspect, the isolated nucleic acid molecule comprises
a nucleotide sequence having at least about 80% nucleic acid
sequence identity, alternatively at least about 81% nucleic acid
sequence identity, alternatively at least about 82% nucleic acid
sequence identity, alternatively at least about 83% nucleic acid
sequence identity, alternatively at least about 84% nucleic acid
sequence identity, alternatively at least about 85% nucleic acid
sequence identity, alternatively at least about 86% nucleic acid
sequence identity, alternatively at least about 87% nucleic acid
sequence identity, alternatively at least about 88% nucleic acid
sequence identity, alternatively at least about 89% nucleic acid
sequence identity, alternatively at least about 90% nucleic acid
sequence identity, alternatively at least about 91% nucleic acid
sequence identity, alternatively at least about 92% nucleic acid
sequence identity, alternatively at least about 93% nucleic acid
sequence identity, alternatively at least about 94% nucleic acid
sequence identity, alternatively at least about 95% nucleic acid
sequence identity, alternatively at least about 96% nucleic acid
sequence identity, alternatively at least about 97% nucleic acid
sequence identity, alternatively at least about 98% nucleic acid
sequence identity and alternatively at least about 99% nucleic acid
sequence identity to (a) a DNA molecule encoding a PRO polypeptide
having a full-length amino acid sequence as disclosed herein, an
amino acid sequence lacking the signal peptide as disclosed herein,
an extracellular domain of a transmembrane protein, with or without
the signal peptide, as disclosed herein or any other specifically
defined fragment of the full-length amino acid sequence as
disclosed herein, or (b) the complement of the DNA molecule of
(a).
[0064] In other aspects, the isolated nucleic acid molecule
comprises a nucleotide sequence having at least about 80% nucleic
acid sequence identity, alternatively at least about 81% nucleic
acid sequence identity, alternatively at least about 82% nucleic
acid sequence identity, alternatively at least about 83% nucleic
acid sequence identity, alternatively at least about 84% nucleic
acid sequence identity, alternatively at least about 85% nucleic
acid sequence identity, alternatively at least about 86% nucleic
acid sequence identity, alternatively at least about 87% nucleic
acid sequence identity, alternatively at least about 88% nucleic
acid sequence identity, alternatively at least about 89% nucleic
acid sequence identity, alternatively at least about 90% nucleic
acid sequence identity, alternatively at least about 91% nucleic
acid sequence identity, alternatively at least about 92% nucleic
acid sequence identity, alternatively at least about 93% nucleic
acid sequence identity, alternatively at least about 94% nucleic
acid sequence identity, alternatively at least about 95% nucleic
acid sequence identity, alternatively at least about 96% nucleic
acid sequence identity, alternatively at least about 97% nucleic
acid sequence identity, alternatively at least about 98% nucleic
acid sequence identity and alternatively at least about 99% nucleic
acid sequence identity to (a) a DNA molecule comprising the coding
sequence of a full-length PRO polypeptide cDNA as disclosed herein,
the coding sequence of a PRO polypeptide lacking the signal peptide
as disclosed herein, the coding sequence of an extracellular domain
of a transmembrane PRO polypeptide, with or without the signal
peptide, as disclosed herein or the coding sequence of any other
specifically defined fragment of the full-length amino acid
sequence as disclosed herein, or (b) the complement of the DNA
molecule of (a).
[0065] In a further aspect, the invention concerns an isolated
nucleic acid molecule comprising a nucleotide sequence having at
least about 80% nucleic acid sequence identity, alternatively at
least about 81% nucleic acid sequence identity, alternatively at
least about 82% nucleic acid sequence identity, alternatively at
least about 83% nucleic acid sequence identity, alternatively at
least about 84% nucleic acid sequence identity, alternatively at
least about 85% nucleic acid sequence identity, alternatively at
least about 86% nucleic acid sequence identity, alternatively at
least about 87% nucleic acid sequence identity, alternatively at
least about 88% nucleic acid sequence identity, alternatively at
least about 89% nucleic acid sequence identity, alternatively at
least about 90% nucleic acid sequence identity, alternatively at
least about 91% nucleic acid sequence identity, alternatively at
least about 92% nucleic acid sequence identity, alternatively at
least about 93% nucleic acid sequence identity, alternatively at
least about 94% nucleic acid sequence identity, alternatively at
least about 95% nucleic acid sequence identity, alternatively at
least about 96% nucleic acid sequence identity, alternatively at
least about 97% nucleic acid sequence identity, alternatively at
least about 98% nucleic acid sequence identity and alternatively at
least about 99% nucleic acid sequence identity to (a) a DNA
molecule that encodes the same mature polypeptide encoded by any of
the human protein cDNAs deposited with the ATCC as disclosed
herein, or (b) the complement of the DNA molecule of (a).
[0066] Another aspect of the present invention provides an isolated
nucleic acid molecule comprising a nucleotide sequence encoding a
PRO polypeptide which is either transmembrane domain-deleted or
transmembrane domain-inactivated, or is complementary to such
encoding nucleotide sequence, wherein the transmembrane domain(s)
of such polypeptide are disclosed herein. Therefore, soluble
extracellular domains of the herein described PRO polypeptides are
contemplated.
[0067] Another embodiment is directed to fragments of a PRO
polypeptide coding sequence, or the complement thereof, that may
find use as, for example, hybridization probes, for encoding
fragments of a PRO polypeptide that may optionally encode a
polypeptide comprising a binding site for an anti-PRO antibody or
as antisense oligonucleotide probes. Such nucleic acid fragments
are usually at least about 20 nucleotides in length, alternatively
at least about 30 nucleotides in length, alternatively at least
about 40 nucleotides in length, alternatively at least about 50
nucleotides in length, alternatively at least about 60 nucleotides
in length, alternatively at least about 70 nucleotides in length,
alternatively at least about 80 nucleotides in length,
alternatively at least about 90 nucleotides in length,
alternatively at least about 100 nucleotides in length,
alternatively at least about 110 nucleotides in length,
alternatively at least about 120 nucleotides in length,
alternatively at least about 130 nucleotides in length,
alternatively at least about 140 nucleotides in length,
alternatively at least about 150 nucleotides in length,
alternatively at least about 160 nucleotides in length,
alternatively at least about 170 nucleotides in length,
alternatively at least about 180 nucleotides in length,
alternatively at least about 190 nucleotides in length,
alternatively at least about 200 nucleotides in length,
alternatively at least about 250 nucleotides in length,
alternatively at least about 300 nucleotides in length,
alternatively at least about 350 nucleotides in length,
alternatively at least about 400 nucleotides in length,
alternatively at least about 450 nucleotides in length,
alternatively at least about 500 nucleotides in length,
alternatively at least about 600 nucleotides in length,
alternatively at least about 700 nucleotides in length,
alternatively at least about 800 nucleotides in length,
alternatively at least about 900 nucleotides in length and
alternatively at least about 1000 nucleotides in length, wherein in
this context the term "about" means the referenced nucleotide
sequence length plus or minus 10% of that referenced length. It is
noted that novel fragments of a PRO polypeptide-encoding nucleotide
sequence may be determined in a routine manner by aligning the PRO
polypeptide-encoding nucleotide sequence with other known
nucleotide sequences using any of a number of well known sequence
alignment programs and determining which PRO polypeptide-encoding
nucleotide sequence fragment(s) are novel. All of such PRO
polypeptide-encoding nucleotide sequences are contemplated herein.
Also contemplated are the PRO polypeptide fragments encoded by
these nucleotide molecule fragments, preferably those PRO
polypeptide fragments that comprise a binding site for an anti-PRO
antibody.
[0068] In another embodiment, the invention provides an isolated
PRO polypeptide encoded by any of the isolated nucleic acid
sequences hereinabove identified.
[0069] In a certain aspect, the invention concerns an isolated PRO
polypeptide, comprising an amino acid sequence having at least
about 80% amino acid sequence identity, alternatively at least
about 81% amino acid sequence identity, alternatively at least
about 82% amino acid sequence identity, alternatively at least
about 83% amino acid sequence identity, alternatively at least
about 84% amino acid sequence identity, alternatively at least
about 85% amino acid sequence identity, alternatively at least
about 86% amino acid sequence identity, alternatively at least
about 87% amino acid sequence identity, alternatively at least
about 88% amino acid sequence identity, alternatively at least
about 89% amino acid sequence identity, alternatively at least
about 90% amino acid sequence identity, alternatively at least
about 91% amino acid sequence identity, alternatively at least
about 92% amino acid sequence identity, alternatively at least
about 93% amino acid sequence identity, alternatively at least
about 94% amino acid sequence identity, alternatively at least
about 95% amino acid sequence identity, alternatively at least
about 96% amino acid sequence identity, alternatively at least
about 97% amino acid sequence identity, alternatively at least
about 98% amino acid sequence identity and alternatively at least
about 99% amino acid sequence identity to a PRO polypeptide having
a full-length amino acid sequence as disclosed herein, an amino
acid sequence lacking the signal peptide as disclosed herein, an
extracellular domain of a transmembrane protein, with or without
the signal peptide, as disclosed herein or any other specifically
defined fragment of the full-length amino acid sequence as
disclosed herein.
[0070] In a further aspect, the invention concerns an isolated PRO
polypeptide comprising an amino acid sequence having at least about
80% amino acid sequence identity, alternatively at least about 81%
amino acid sequence identity, alternatively at least about 82%
amino acid sequence identity, alternatively at least about 83%
amino acid sequence identity, alternatively at least about 84%
amino acid sequence identity, alternatively at least about 85%
amino acid sequence identity, alternatively at least about 86%
amino acid sequence identity, alternatively at least about 87%
amino acid sequence identity, alternatively at least about 88%
amino acid sequence identity, alternatively at least about 89%
amino acid sequence identity, alternatively at least about 90%
amino acid sequence identity, alternatively at least about 91%
amino acid sequence identity, alternatively at least about 92%
amino acid sequence identity, alternatively at least about 93%
amino acid sequence identity, alternatively at least about 94%
amino acid sequence identity, alternatively at least about 95%
amino acid sequence identity, alternatively at least about 96%
amino acid sequence identity, alternatively at least about 97%
amino acid sequence identity, alternatively at least about 98%
amino acid sequence identity and alternatively at least about 99%
amino acid sequence identity to an amino acid sequence encoded by
any of the human protein cDNAs deposited with the ATCC as disclosed
herein.
[0071] In a further aspect, the invention concerns an isolated PRO
polypeptide comprising an amino acid sequence scoring at least
about 80% positives, alternatively at least about 81% positives,
alternatively at least about 82% positives, alternatively at least
about 83% positives, alternatively at least about 84% positives,
alternatively at least about 85% positives, alternatively at least
about 86% positives, alternatively at least about 87% positives,
alternatively at least about 88% positives, alternatively at least
about 89% positives, alternatively at least about 90% positives,
alternatively at least about 91% positives, alternatively at least
about 92% positives, alternatively at least about 93% positives,
alternatively at least about 94% positives, alternatively at least
about 95% positives, alternatively at least about 96% positives,
alternatively at least about 97% positives, alternatively at least
about 98% positives and alternatively at least about 99% positives
when compared with the amino acid sequence of a PRO polypeptide
having a full-length amino acid sequence as disclosed herein, an
amino acid sequence lacking the signal peptide as disclosed herein,
an extracellular domain of a transmembrane protein, with or without
the signal peptide, as disclosed herein or any other specifically
defined fragment of the full-length amino acid sequence as
disclosed herein.
[0072] In a specific aspect, the invention provides an isolated PRO
polypeptide without the N-terminal signal sequence and/or the
initiating methionine and is encoded by a nucleotide sequence that
encodes such an amino acid sequence as hereinbefore described.
Processes for producing the same are also herein described, wherein
those processes comprise culturing a host cell comprising a vector
which comprises the appropriate encoding nucleic acid molecule
under conditions suitable for expression of the PRO polypeptide and
recovering the PRO polypeptide from the cell culture.
[0073] Another aspect of the invention provides an isolated PRO
polypeptide which is either transmembrane domain-deleted or
transmembrane domain-inactivated. Processes for producing the same
are also herein described, wherein those processes comprise
culturing a host cell comprising a vector which comprises the
appropriate encoding nucleic acid molecule under conditions
suitable for expression of the PRO polypeptide and recovering the
PRO polypeptide from the cell culture.
[0074] In yet another embodiment, the invention concerns agonists
and antagonists of a native PRO polypeptide as defined herein. In a
particular embodiment, the agonist or antagonist is an anti-PRO
antibody or a small molecule.
[0075] In a further embodiment, the invention concerns a method of
identifying agonists or antagonists to a PRO polypeptide which
comprise contacting the PRO polypeptide with a candidate molecule
and monitoring a biological activity mediated by said PRO
polypeptide. Preferably, the PRO polypeptide is a native PRO
polypeptide.
[0076] In a still further embodiment, the invention concerns a
composition of matter comprising a PRO polypeptide, or an agonist
or antagonist of a PRO polypeptide as herein described, or an
anti-PRO antibody, in combination with a carrier. Optionally, the
carrier is a pharmaceutically acceptable carrier.
[0077] Another embodiment of the present invention is directed to
the use of a PRO polypeptide, or an agonist or antagonist thereof
as hereinbefore described, or an anti-PRO antibody, for the
preparation of a medicament useful in the treatment of a condition
which is responsive to the PRO polypeptide, an agonist or
antagonist thereof or an anti-PRO antibody.
[0078] In additional embodiments of the present invention, the
invention provides vectors comprising DNA encoding any of the
herein described polypeptides. Host cell comprising any such vector
are also provided. By way of example, the host cells may be CHO
cells, E. coli, yeast, or Baculovirus-infected insect cells. A
process for producing any of the herein described polypeptides is
further provided and comprises culturing host cells under
conditions suitable for expression of the desired polypeptide and
recovering the desired polypeptide from the cell culture.
[0079] In other embodiments, the invention provides chimeric
molecules comprising any of the herein described polypeptides fused
to a heterologous polypeptide or amino acid sequence. Example of
such chimeric molecules comprise any of the herein described
polypeptides fused to an epitope tag sequence or a Fc region of an
immunoglobulin.
[0080] In yet another embodiment, the invention provides an
antibody which specifically binds to any of the above or below
described polypeptides. Optionally, the antibody is a monoclonal
antibody, humanized antibody, antibody fragment or single-chain
antibody.
[0081] In yet other embodiments, the invention provides
oligonucleotide probes useful for isolating genomic and cDNA
nucleotide sequences or as antisense probes, wherein those probes
may be derived from any of the above or below described nucleotide
sequences.
BRIEF DESCRIPTION OF THE DRAWINGS
[0082] FIG. 1 shows a nucleotide sequence (SEQ ID NO:1) of a native
sequence PRO1031 cDNA, wherein SEQ ID NO:1 is a clone designated
herein as "DNA59294-1381-1".
[0083] FIG. 2 shows the amino acid sequence (SEQ ID NO:2) derived
from the coding sequence of SEQ ID NO:1 shown in FIG. 1.
[0084] FIG. 3 shows a nucleotide sequence (SEQ ID NO:3) of a native
sequence PRO1122 cDNA, wherein SEQ ID NO:3 is a clone designated
herein as "DNA62377-1381-1".
[0085] FIG. 4 shows the amino acid sequence (SEQ ID NO:4) derived
from the coding sequence of SEQ ID NO:3 shown in FIG. 3.
[0086] FIG. 5 shows a nucleotide sequence (SEQ ID NO:5) of a native
sequence PRO10272 cDNA, wherein SEQ ID NO:5 is a clone designated
herein as "DNA147531-2821".
[0087] FIG. 6 shows the amino acid sequence (SEQ ID NO:6) derived
from the coding sequence of SEQ ID NO:5 shown in FIG. 5.
[0088] FIG. 7 shows a nucleotide sequence (SEQ ID NO:7) of a native
sequence PRO21175 cDNA, wherein SEQ ID NO:7 is a clone designated
herein as "DNA173894-2947".
[0089] FIG. 8 shows the amino acid sequence (SEQ ID NO:8) derived
from the coding sequence of SEQ ID NO:7 shown in FIG. 7.
[0090] FIG. 9 shows a nucleotide sequence (SEQ ID NO:9) of a native
sequence PRO20110 cDNA, wherein SEQ ID NO:9 is a clone designated
herein as "DNA166819".
[0091] FIG. 10 shows the amino acid sequence (SEQ ID NO:10) derived
from the coding sequence of SEQ ID NO:9 shown in FIG. 9.
[0092] FIG. 11 shows a nucleotide sequence (SEQ ID NO:11) of a
native sequence PRO5801 cDNA, wherein SEQ ID NO:11 is a clone
designated herein as "DNA115291-2681".
[0093] FIG. 12 shows the amino acid sequence (SEQ ID NO:12) derived
from the coding sequence of SEQ ID NO:11 shown in FIG. 11.
[0094] FIG. 13 shows a nucleotide sequence (SEQ ID NO:13) of a
native sequence PRO20040 cDNA, wherein SEQ ID NO:13 is a clone
designated herein as "DNA 164625-2890".
[0095] FIG. 14 shows the amino acid sequence (SEQ ID NO:14) derived
from the coding sequence of SEQ ID NO:13 shown in FIG. 13.
[0096] FIG. 15 shows a nucleotide sequence (SEQ ID NO:15) of a
native sequence PRO9877 cDNA, wherein SEQ ID NO:15 is a clone
designated herein as "DNA119502-2789".
[0097] FIG. 16 shows the amino acid sequence (SEQ ID NO:16) derived
from the coding sequence of SEQ ID NO:15 shown in FIG. 15.
[0098] FIG. 17 shows a nucleotide sequence (SEQ ID NO:17) of a
native sequence PRO20026 cDNA, wherein SEQ ID NO:17 is a clone
designated herein as "DNA 154095-2998".
[0099] FIG. 18 shows the amino acid sequence (SEQ ID NO:18) derived
from the coding sequence of SEQ ID NO:17 shown in FIG. 17.
[0100] FIG. 19 shows the alignment of the human IL-17 family
members: h-IL17 [SEQ ID NO:40]; h-1L17B [PRO1031; SEQ ID NO:2];
h-IL17C [PRO1122; SEQ ID NO:4]; h-IL17D [PRO21175; SEQ ID NO:8];
h-ILE [PRO10272; SEQ ID NO:6]; and h-IL17F [PRO20110; SEQ ID
NO:10].
[0101] FIG. 20 shows the relative tissue expression distribution of
the IL-17B ligand PRO1031).
[0102] FIG. 21 shows the relative tissue expression distribution of
the IL-17C ligand (PRO1122).
[0103] FIG. 22 shows the relative tissue expression distribution of
the IL-17D ligand (PRO21175).
[0104] FIG. 23 shows mRNA expression of IL-17E (PRO10272) by RT-PCR
analysis. RNA from the indicated tissues was subjected to RT-PCR
with primers that were designed to amplify the entire coding
sequence of IL-17E. The PCR product was resolved by agarose gel
electrophoresis, transferred to nylon membrane and probed with a
.sup.32P-labeled IL-17E cDNA probe.
[0105] FIG. 24 shows the relative tissue expression distribution of
the IL17F ligand (PRO20110).
[0106] FIG. 25 shows the relative tissue expression distribution of
the IL-17RH1 receptor (PRO5801).
[0107] FIG. 26 shows the relative tissue expression distribution of
the IL-17RH2 receptor (PRO20040).
[0108] FIG. 27 shows the relative tissue expression distribution of
the IL-17RH3 receptor (PRO9877).
[0109] FIG. 28 shows the relative tissue expression distribution of
the IL-17RH4 receptor (PRO20026).
[0110] FIG. 29 shows immunoprecipitation of IL-17R extracellular
domain (ECD) with IL-17, IL-17B (PRO1031) and IL-17C (PRO1122).
His-tagged IL-17R ECD was expressed in 293 cells and metabolically
labeled with .sup.35S as described in EXAMPLE 21. The supernatant
was recovered and Ni-NTA beads were used to affinity precipitate
the His-tagged IL-17R ECD in the supernatant (lane 1). In part A.,
IL-17, IL-17B.Fc and IL-17C.Fc, or control Fc fusion proteins were
incubated with the supernatant and protein-A-agarose beads were
added to precipitate the Fc fusion proteins. For the IL-17
immunoprecipitation reaction, anti-IL17 antibodies were included.
Part B. shows the results of a competitive binding experiment,
wherein immunoprecipitation of IL-17R ECD by L-17 was performed in
the presence of a five-fold excess of IL-17B. His and control
His-tagged proteins. Precipitates in both part A. and B. were
analyzed by electrophoresis on NuPAGE (4-12% Bis-Tris) gels.
Molecular weight markers are indicated on the left of each
panel.
[0111] FIG. 30 shows the alignment of the human IL-17 family
members (h-IL17; h-IL17B; h-IL17C; and h-ILE). The predicted signal
sequences are underlined. Conserved cysteines are indicated by
bullet, and potential N-linked glycosylation sites are boxed.
[0112] FIG. 31 shows mRNA expression of IL-17RH1 receptor
(PRO5801). FIG. 31A shows Northern blot analysis of IL-17RH1
receptor in selected tissues. FIG. 31B shows the quantitative PCR
analysis of IL-17RH1 mRNA expression in selected tissues.
[0113] FIG. 32 shows IL-17E (PRO10272) ligand binding to IL-17RH1
receptor (PRO5801). FIG. 32A shows a comparison of IL-17 and IL-17E
(PRO10272) ligand binding to IL-17R receptor (herein designated
PRO1) and IL-17RH1 receptor (PRO5801). 293 cells were transiently
co-transfected with expression vectors for green fluorescent
protein (GCP) and IL-17R or IL-17RH1 receptors as indicated. Cells
were incubated with IL-17-Fc or IL-17E-Fc protein as indicated and
binding was revealed with PE conjugated anti-human Fc antibody.
FACS curves show PE staining within the co-transfected GFP positive
cell population. In FIG. 32B, His-epitope tagged IL-17RH1 receptor
extracellular domain was incubated with ligand-Fc fusion protein
for members of the human IL-17 family depicted as follows: lane 1,
IL-17RH1-His direct load; lane 2, IL-17; lane 3, IL-17B (PRO1031);
lane 4, IL-17C (PRO1122); and lane 5, IL-17E (PRO10272). Ligand
immunoadhesins were immunoprecipitated with Protein A beads and
bound IL-17RH1 receptor was analyzed by Western Blot analysis with
antibody to the His-epitope tag. The positions of molecular weight
markers (kDa) are indicated on the left.
[0114] FIG. 33 shows the induction of NF-.kappa.B by IL-17E
(PRO10272). FIG. 33 (part A) shows the results of transiently
transfecting human 293 and TK-10 cells with the NF-.kappa.B
responsive luciferase reporter pGL3.ELAM.tk and expression vector
for IL-17E as indicated. Luciferase activity was determined as
indicated in EXAMPLE 22. FIG. 33 (part B) depicts titration of
NF-.kappa.B induction by IL-17E. Human 293 cells were transfected
with the NF-.kappa.B responsive luciferase reporter pGL3.ELAM.tk
and the indicated expression vector for IL-17E as indicated.
[0115] FIG. 34 shows the effect of IL-17E (PRO10272) on IL-8
production. Human TK-10 kidney derived cells lines were incubated
by Elisa. Shown is the level of IL-8 measured minus the level of
IL-8 production observed in the absence of cytokine addition. The
experiments were repeated several times with similar results.
[0116] FIG. 35 depicts the IL-17 family of cytokines and the
complex pattern of overlapping receptor-ligand specificities. From
left to right, FIG. 35 demonstrates that IL-17 ligand binds to the
IL-17 receptor (IL-17R; herein designated PRO1); IL-17B ligand
(PRO1031) binds to the IL-17RH1 receptor (PRO5801); IL-17E ligand
(PRO10272) binds to the IL-17RH1 receptor (PRO5801); IL-17F ligand
(PRO20110) binds to both the IL-17 receptor (IL-17R, herein
designated PRO1) as well as to the IL-17RH2 receptor (PRO20040);
IL-17C ligand (PRO1122) and IL-17D ligand (PRO21175) do not
interact with IL-17R, IL-17RH1 or IL-17RH2 receptors.
[0117] FIG. 36 depicts bar graphs representing the biological
activities of IL-17, IL-17B (PRO1031), and IL-17C (PRO1122). FIG.
36 (part A.) shows human foreskin fibroblast (HFF) cells cultured
with control Fc fusion protein, IL-17, IL-17B.Fc or IL-17C.Fc at
100 ng/ml for 18 hours and the conditioned media were assayed for
IL-6 as described in EXAMPLE 28. FIG. 36 (part B.) shows the human
leukemic cell line, THP-1, which was treated with the same
cytokines (100 ng/ml) as above under the same conditions wherein
the supernatants were assayed for the level of TNF-.alpha. release.
Results are expressed as the mean+/-SE of triplicate determinations
from one representative experiment.
[0118] FIG. 37 shows a time course representing the dependence of
IL-17B (PRO1031) and IL-17C (PRO1122) activated TNF-.alpha. release
from THP-1 cells. In FIG. 37 (part A.), THP-1 cells were incubated
with 100 ng/ml (2.2 nM) of IL-17B.Fc or IL-17C.Fc for 0.5 to 32
hours, the conditioned media harvested, and the TNF-.alpha.
concentration quantitated as described in EXAMPLE 28. In FIG. 37
(part B.), THP-1 cells were treated with the IL-17B.Fc and
IL-17C.Fc at a concentration range from 0 to 120 nM for 18 hours
and the TNF-.alpha. release determined.
[0119] FIG. 38 shows FACS analysis of the binding of IL-17B.Fc and
IL-17C.Fc to THP-1 cells as described in EXAMPLE 29. THP-1 cells
were incubated with IL-17B.Fc (FIG. 38 part A.) or IL-17C.Fc (FIG.
38 part B.) or control Fc fusion proteins in PBS (5% horse serum)
and followed by addition of FITC conjugated anti-Fc secondary
antibodies.
[0120] FIG. 39 shows the effect of IL-17 on articular cartilage.
Cartilage explants were cultured with the indicated concentration
of IL-17 alone (solid) or in the presence of IL-1.alpha. at the
indicated concentration (hatched) or IL-1ra (IL-1 receptor
antagonist, R & D Systems, 1 .mu.g/ml, for 72 hours). Release
of proteoglycans (PG) into the media (top panel) indicates matrix
breakdown. Matrix synthesis was determined by incorporation of
.sup.35S-sulfate into the tissue (bottom panel).
[0121] FIG. 40 shows the effect of IL-17 on the release of nitric
oxide. Explants were treated with IL-17 (10 ng/ml) alone (left
columns) or in the presence of IL-1.alpha. (10 ng/ml) (right
columns). After 48 hours, media was assayed for nitrite
concentration.
[0122] FIG. 41 shows the effect of nitric oxide (NO) on IL-17
induced changes in matrix metabolism. Explants were treated with
IL-17 (5 ng/ml) alone (+) or with an irreversible inhibitor of
nitric oxide synthase, NOS (L-NIO, Caymen Chemical, 0.5 mM). After
72 hours of treatment, media was assayed for nitrite (FIG. 41 part
A.) and proteoglycans (Pgs) (FIG. 41 part B.). FIG. 41 part C.
shows proteoglycan synthesis as determined by incorporation of
.sup.35S-sulphate into the tissue.
[0123] FIG. 42 shows the effect of the inhibition of nitric oxide
(NO) on IL-17 induced changes in proteoglycan (PG) metabolism.
Articular cartilage explants were treated with IL-1.alpha. (5
ng/ml) alone (+) or with inhibitors of NOS (L-NIO or L-NIL) (NIL,
reversible NOS inhibitor, Caymen Chemical) or IL-1ra (IL-1 receptor
antagonist, R & D Systems, 1 .mu.g/ml). After 72 hours of
treatment, media was assayed for nitrite concentration and amount
of proteoglycans. Matrix synthesis was determined by incorporation
of .sup.35S-sulphate into the tissue.
[0124] FIG. 43 shows the effect of IL-17C (PRO1122) on articular
cartilage. Explants were treated with IL-17C at 1% or 0.1% in the
absence (leftmost 3 columns) or presence (rightmost 3 columns) of
IL-1.alpha.(+) (10 ng/ml. Proteoglycan (PG) release and synthesis
are shown as amount above control.
[0125] FIG. 44 shows the relative expression of the human IL-17
family in the mouse model of inflammatory bowel disease [IBD] as
demonstrated by -delta Ct values relative to GAPDH. IL-17 shows
enhanced expression in this mouse model during mild and severe
stages of inflammatory bowel disease. In contrast, IL-17E
(PRO10272) demonstrates a marked decrease in expression during
severe stages of IBD, whereas IL-17B (PRO1031) demonstrates a
moderate decrease in expression in severe IBD.
[0126] FIG. 45 shows a time course study which measures the
relative expression of IL-17D (PRO21175) in a mouse model of stroke
over the first 72 hours. IL-17D expression in the brain
dramatically decreases from the time stroke is induced to the
endpoint of 72 hours.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
I. Definitions
[0127] The terms "PRO polypeptide" and "PRO" as used herein and
when immediately followed by a numerical designation refer to
various polypeptides, wherein the complete designation (i.e.,
PRO/number) refers to specific polypeptide sequences as described
herein. The terms "PRO/number polypeptide" and "PRO/number" wherein
the term "number" is provided as an actual numerical designation as
used herein encompass native sequence polypeptides and polypeptide
variants (which are further defined herein). The PRO polypeptides
described herein may be isolated from a variety of sources, such as
from human tissue types or from another source, or prepared by
recombinant or synthetic methods. The term "PRO polypeptide" refers
to each individual PRO/number polypeptide disclosed herein. All
disclosures in this specification which refer to the "PRO
polypeptide" refer to each of the polypeptides individually as well
as jointly. For example, descriptions of the preparation of,
purification of, derivation of, formation of antibodies to or
against, administration of, compositions containing, treatment of a
disease with, etc., pertain to each polypeptide of the invention
individually. The term "PRO polypeptide" also includes variants of
the PRO/number polypeptides disclosed herein.
[0128] A "native sequence PRO polypeptide" comprises a polypeptide
having the same amino acid sequence as the corresponding PRO
polypeptide derived from nature. Such native sequence PRO
polypeptides can be isolated from nature or can be produced by
recombinant or synthetic means. The term "native sequence PRO
polypeptide" specifically encompasses naturally-occurring truncated
or secreted forms of the specific PRO polypeptide (e.g., an
extracellular domain sequence), naturally-occurring variant forms
(e.g., alternatively spliced forms) and naturally-occurring allelic
variants of the polypeptide. In various embodiments of the
invention, the native sequence PRO polypeptides disclosed herein
are mature or full-length native sequence polypeptides comprising
the full-length amino acids sequences shown in the accompanying
figures. Start and stop codons are shown in bold font and
underlined in the figures. However, while the PRO polypeptide
disclosed in the accompanying figures are shown to begin with
methionine residues designated herein as amino acid position 1 in
the figures, it is conceivable and possible that other methionine
residues located either upstream or downstream from the amino acid
position 1 in the figures may be employed as the starting amino
acid residue for the PRO polypeptides.
[0129] The PRO polypeptide "extracellular domain" or "ECD" refers
to a form of the PRO polypeptide which is essentially free of the
transmembrane and cytoplasmic domains. Ordinarily, a PRO
polypeptide ECD will have less than 1% of such transmembrane and/or
cytoplasmic domains and preferably, will have less than 0.5% of
such domains. It will be understood that any transmembrane domains
identified for the PRO polypeptides of the present invention are
identified pursuant to criteria routinely employed in the art for
identifying that type of hydrophobic domain. The exact boundaries
of a transmembrane domain may vary but most likely by no more than
about 5 amino acids at either end of the domain as initially
identified herein. Optionally, therefore, an extracellular domain
of a PRO polypeptide may contain from about 5 or fewer amino acids
on either side of the transmembrane domain/extracellular domain
boundary as identified in the Examples or specification and such
polypeptides, with or without the associated signal peptide, and
nucleic acid encoding them, are comtemplated by the present
invention.
[0130] The approximate location of the "signal peptides" of the
various PRO polypeptides disclosed herein are shown in the present
specification and/or the accompanying figures. It is noted,
however, that the C-terminal boundary of a signal peptide may vary,
but most likely by no more than about 5 amino acids on either side
of the signal peptide C-terminal boundary as initially identified
herein, wherein the C-terminal boundary of the signal peptide may
be identified pursuant to criteria routinely employed in the art
for identifying that type of amino acid sequence element (e.g.,
Nielsen et al., Prot. Eng., 10:1-6 (1997) and von Heinje et al.,
Nucl. Acids. Res., 14:4683-4690 (1986)). Moreover, it is also
recognized that, in some cases, cleavage of a signal sequence from
a secreted polypeptide is not entirely uniform, resulting in more
than one secreted species. These mature polypeptides, where the
signal peptide is cleaved within no more than about 5 amino acids
on either side of the C-terminal boundary of the signal peptide as
identified herein, and the polynucleotides encoding them, are
contemplated by the present invention.
[0131] "PRO polypeptide variant" means an active PRO polypeptide as
defined above or below having at least about 80% amino acid
sequence identity with a full-length native sequence PRO
polypeptide sequence as disclosed herein, a PRO polypeptide
sequence lacking the signal peptide as disclosed herein, an
extracellular domain of a PRO polypeptide, with or without the
signal peptide, as disclosed herein or any other fragment of a
full-length PRO polypeptide sequence as disclosed herein. Such PRO
polypeptide variants include, for instance, PRO polypeptides
wherein one or more amino acid residues are added, or deleted, at
the N- or C-terminus of the full-length native amino acid sequence.
Ordinarily, a PRO polypeptide variant will have at least about 80%
amino acid sequence identity, alternatively at least about 81%
amino acid sequence identity, alternatively at least about 82%
amino acid sequence identity, alternatively at least about 83%
amino acid sequence identity, alternatively at least about 84%
amino acid sequence identity, alternatively at least about 85%
amino acid sequence identity, alternatively at least about 86%
amino acid sequence identity, alternatively at least about 87%
amino acid sequence identity, alternatively at least about 88%
amino acid sequence identity, alternatively at least about 89%
amino acid sequence identity, alternatively at least about 90%
amino acid sequence identity, alternatively at least about 91%
amino acid sequence identity, alternatively at least about 92%
amino acid sequence identity, alternatively at least about 93%
amino acid sequence identity, alternatively at least about 94%
amino acid sequence identity, alternatively at least about 95%
amino acid sequence identity, alternatively at least about 96%
amino acid sequence identity, alternatively at least about 97%
amino acid sequence identity, alternatively at least about 98%
amino acid sequence identity and alternatively at least about 99%
amino acid sequence identity to a full-length native sequence PRO
polypeptide sequence as disclosed herein, a PRO polypeptide
sequence lacking the signal peptide as disclosed herein, an
extracellular domain of a PRO polypeptide, with or without the
signal peptide, as disclosed herein or any other specifically
defined fragment of a full-length PRO polypeptide sequence as
disclosed herein. Ordinarily, PRO variant polypeptides are at least
about 10 amino acids in length, alternatively at least about 20
amino acids in length, alternatively at least about 30 amino acids
in length, alternatively at least about 40 amino acids in length,
alternatively at least about 50 amino acids in length,
alternatively at least about 60 amino acids in length,
alternatively at least about 70 amino acids in length,
alternatively at least about 80 amino acids in length,
alternatively at least about 90 amino acids in length,
alternatively at least about 100 amino acids in length,
alternatively at least about 150 amino acids in length,
alternatively at least about 200 amino acids in length,
alternatively at least about 300 amino acids in length, or
more.
[0132] "Percent (%) amino acid sequence identity" with respect to
the PRO polypeptide sequences identified herein is defined as the
percentage of amino acid residues in a candidate sequence that are
identical with the amino acid residues in the specific PRO
polypeptide sequence, after aligning the sequences and introducing
gaps, if necessary, to achieve the maximum percent sequence
identity, and not considering any conservative substitutions as
part of the sequence identity. Alignment for purposes of
determining percent amino acid sequence identity can be achieved in
various ways that are within the skill in the art, for instance,
using publicly available computer software such as BLAST, BLAST-2,
ALIGN or Megalign (DNASTAR) software. Those skilled in the art can
determine appropriate parameters for measuring alignment, including
any algorithms needed to achieve maximal alignment over the full
length of the sequences being compared. For purposes herein,
however, % amino acid sequence identity values are generated using
the sequence comparison computer program ALIGN-2, wherein the
complete source code for the ALIGN-2 program is provided in Table 1
below. The ALIGN-2 sequence comparison computer program was
authored by Genentech, Inc. and the source code shown in Table 1
below has been filed with user documentation in the U.S. Copyright
Office, Washington D.C., 20559, where it is registered under U.S.
Copyright Registration No. TXU510087. The ALIGN-2 program is
publicly available through Genentech, Inc., South San Francisco,
Calif. or may be compiled from the source code provided in Table 1
below. The ALIGN-2 program should be compiled for use on a UNIX
operating system, preferably digital UNIX V4.0D. All sequence
comparison parameters are set by the ALIGN-2 program and do not
vary.
[0133] In situations where ALIGN-2 is employed for amino acid
sequence comparisons, the % amino acid sequence identity of a given
amino acid sequence A to, with, or against a given amino acid
sequence B (which can alternatively be phrased as a given amino
acid sequence A that has or comprises a certain % amino acid
sequence identity to, with, or against a given amino acid sequence
B) is calculated as follows:
100 times the fraction X/Y
where X is the number of amino acid residues scored as identical
matches by the sequence alignment program ALIGN-2 in that program's
alignment of A and B, and where Y is the total number of amino acid
residues in B. It will be appreciated that where the length of
amino acid sequence A is not equal to the length of amino acid
sequence B, the % amino acid sequence identity of A to B will not
equal the % amino acid sequence identity of B to A. As examples of
% amino acid sequence identity calculations using this method,
Tables 2 and 3 demonstrate how to calculate the % amino acid
sequence identity of the amino acid sequence designated "Comparison
Protein" to the amino acid sequence designated "PRO", wherein "PRO"
represents the amino acid sequence of a hypothetical PRO
polypeptide of interest, "Comparison Protein" represents the amino
acid sequence of a polypeptide against which the "PRO" polypeptide
of interest is being compared, and "X, "Y" and "Z" each represent
different hypothetical amino acid residues.
[0134] Unless specifically stated otherwise, all % amino acid
sequence identity values used herein are obtained as described in
the immediately preceding paragraph using the ALIGN-2 computer
program. However, % amino acid sequence identity values may also be
obtained as described below by using the WU-BLAST-2 computer
program (Altschul et al., Methods in Enzymology 266:460-480
(1996)). Most of the WU-BLAST-2 search parameters are set to the
default values. Those not set to default values, i.e., the
adjustable parameters, are set with the following values: overlap
span=1, overlap fraction=0.125, word threshold (T)=11, and scoring
matrix=BLOSUM62. When WU-BLAST-2 is employed, a % amino acid
sequence identity value is determined by dividing (a) the number of
matching identical amino acid residues between the amino acid
sequence of the PRO polypeptide of interest having a sequence
derived from the native PRO polypeptide and the comparison amino
acid sequence of interest (i.e., the sequence against which the PRO
polypeptide of interest is being compared which may be a PRO
variant polypeptide) as determined by WU-BLAST-2 by (b) the total
number of amino acid residues of the PRO polypeptide of interest.
For example, in the statement "a polypeptide comprising an the
amino acid sequence A which has or having at least 80% amino acid
sequence identity to the amino acid sequence B", the amino acid
sequence A is the comparison amino acid sequence of interest and
the amino acid sequence B is the amino acid sequence of the PRO
polypeptide of interest.
[0135] Percent amino acid sequence identity may also be determined
using the sequence comparison program NCBI-BLAST2 (Altschul et al.,
Nucleic Acids Res. 25:3389-3402 (1997)). The NCBI-BLAST2 sequence
comparison program may be downloaded from
http://www.ncbi.nlm.nih.gov or otherwise obtained from the National
Institute of Health, Bethesda, Md. NCBI-BLAST2 uses several search
parameters, wherein all of those search parameters are set to
default values including, for example, unmask=yes, strand=all,
expected occurrences=10, minimum low complexity length=15/5,
multi-pass e-value=0.01, constant for multi-pass=25, dropoff for
final gapped alignment=25 and scoring matrix=BLOSUM62.
[0136] In situations where NCBI-BLAST2 is employed for amino acid
sequence comparisons, the % amino acid sequence identity of a given
amino acid sequence A to, with, or against a given amino acid
sequence B (which can alternatively be phrased as a given amino
acid sequence A that has or comprises a certain % amino acid
sequence identity to, with, or against a given amino acid sequence
B) is calculated as follows:
100 times the fraction X/Y
where X is the number of amino acid residues scored as identical
matches by the sequence alignment program NCBI-BLAST2 in that
program's alignment of A and B, and where Y is the total number of
amino acid residues in B. It will be appreciated that where the
length of amino acid sequence A is not equal to the length of amino
acid sequence B, the % amino acid sequence identity of A to B will
not equal the % amino acid sequence identity of B to A.
[0137] "PRO variant polynucleotide" or "PRO variant nucleic acid
sequence" means a nucleic acid molecule which encodes an active PRO
polypeptide as defined below and which has at least about 80%
nucleic acid sequence identity with a nucleotide acid sequence
encoding a full-length native sequence PRO polypeptide sequence as
disclosed herein, a full-length native sequence PRO polypeptide
sequence lacking the signal peptide as disclosed herein, an
extracellular domain of a PRO polypeptide, with or without the
signal peptide, as disclosed herein or any other fragment of a
full-length PRO polypeptide sequence as disclosed herein.
Ordinarily, a PRO variant polynucleotide will have at least about
80% nucleic acid sequence identity, alternatively at least about
81% nucleic acid sequence identity, alternatively at least about
82% nucleic acid sequence identity, alternatively at least about
83% nucleic acid sequence identity, alternatively at least about
84% nucleic acid sequence identity, alternatively at least about
85% nucleic acid sequence identity, alternatively at least about
86% nucleic acid sequence identity, alternatively at least about
87% nucleic acid sequence identity, alternatively at least about
88% nucleic acid sequence identity, alternatively at least about
89% nucleic acid sequence identity, alternatively at least about
90% nucleic acid sequence identity, alternatively at least about
91% nucleic acid sequence identity, alternatively at least about
92% nucleic acid sequence identity, alternatively at least about
93% nucleic acid sequence identity, alternatively at least about
94% nucleic acid sequence identity, alternatively at least about
95% nucleic acid sequence identity, alternatively at least about
96% nucleic acid sequence identity, alternatively at least about
97% nucleic acid sequence identity, alternatively at least about
98% nucleic acid sequence identity and alternatively at least about
99% nucleic acid sequence identity with a nucleic acid sequence
encoding a full-length native sequence PRO polypeptide sequence as
disclosed herein, a full-length native sequence PRO polypeptide
sequence lacking the signal peptide as disclosed herein, an
extracellular domain of a PRO polypeptide, with or without the
signal sequence, as disclosed herein or any other fragment of a
full-length PRO polypeptide sequence as disclosed herein. Variants
do not encompass the native nucleotide sequence.
[0138] Ordinarily, PRO variant polynucleotides are at least about
30 nucleotides in length, alternatively at least about 60
nucleotides in length, alternatively at least about 90 nucleotides
in length, alternatively at least about 120 nucleotides in length,
alternatively at least about 150 nucleotides in length,
alternatively at least about 180 nucleotides in length,
alternatively at least about 210 nucleotides in length,
alternatively at least about 240 nucleotides in length,
alternatively at least about 270 nucleotides in length,
alternatively at least about 300 nucleotides in length,
alternatively at least about 450 nucleotides in length,
alternatively at least about 600 nucleotides in length,
alternatively at least about 900 nucleotides in length, or
more.
[0139] "Percent (%) nucleic acid sequence identity" with respect to
PRO-encoding nucleic acid sequences identified herein is defined as
the percentage of nucleotides in a candidate sequence that are
identical with the nucleotides in the PRO nucleic acid sequence of
interest, after aligning the sequences and introducing gaps, if
necessary, to achieve the maximum percent sequence identity.
Alignment for purposes of determining percent nucleic acid sequence
identity can be achieved in various ways that are within the skill
in the art, for instance, using publicly available computer
software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR)
software. For purposes herein, however, % nucleic acid sequence
identity values are generated using the sequence comparison
computer program ALIGN-2, wherein the complete source code for the
ALIGN-2 program is provided in Table 1 below. The ALIGN-2 sequence
comparison computer program was authored by Genentech, Inc. and the
source code shown in Table 1 below has been filed with user
documentation in the U.S. Copyright Office, Washington D.C., 20559,
where it is registered under U.S. Copyright Registration No.
TXU510087. The ALIGN-2 program is publicly available through
Genentech, Inc., South San Francisco, Calif. or may be compiled
from the source code provided in Table 1 below. The ALIGN-2 program
should be compiled for use on a UNIX operating system, preferably
digital UNIX V4.0D. All sequence comparison parameters are set by
the ALIGN-2 program and do not vary.
[0140] In situations where ALIGN-2 is employed for nucleic acid
sequence comparisons, the % nucleic acid sequence identity of a
given nucleic acid sequence C to, with, or against a given nucleic
acid sequence D (which can alternatively be phrased as a given
nucleic acid sequence C that has or comprises a certain % nucleic
acid sequence identity to, with, or against a given nucleic acid
sequence D) is calculated as follows:
100 times the fraction W/Z
where W is the number of nucleotides scored as identical matches by
the sequence alignment program ALIGN-2 in that program's alignment
of C and D, and where Z is the total number of nucleotides in D. It
will be appreciated that where the length of nucleic acid sequence
C is not equal to the length of nucleic acid sequence D, the %
nucleic acid sequence identity of C to D will not equal the %
nucleic acid sequence identity of D to C. As examples of % nucleic
acid sequence identity calculations, Tables 4 and 5, demonstrate
how to calculate the % nucleic acid sequence identity of the
nucleic acid sequence designated "Comparison DNA" to the nucleic
acid sequence designated "PRO-DNA", wherein "PRO-DNA" represents a
hypothetical PRO-encoding nucleic acid sequence of interest,
"Comparison DNA" represents the nucleotide sequence of a nucleic
acid molecule against which the "PRO-DNA" nucleic acid molecule of
interest is being compared, and "N", "L" and "V" each represent
different hypothetical nucleotides.
[0141] Unless specifically stated otherwise, all % nucleic acid
sequence identity values used herein are obtained as described in
the immediately preceding paragraph using the ALIGN-2 computer
program. However, % nucleic acid sequence identity values may also
be obtained as described below by using the WU-BLAST-2 computer
program (Altschul et al., Methods in Enzymology 266:460-480
(1996)). Most of the WU-BLAST-2 search parameters are set to the
default values. Those not set to default values, i.e., the
adjustable parameters, are set with the following values: overlap
span=1, overlap fraction=0.125, word threshold (T)=11, and scoring
matrix=BLOSUM62. When WU-BLAST-2 is employed, a % nucleic acid
sequence identity value is determined by dividing (a) the number of
matching identical nucleotides between the nucleic acid sequence of
the PRO polypeptide-encoding nucleic acid molecule of interest
having a sequence derived from the native sequence PRO
polypeptide-encoding nucleic acid and the comparison nucleic acid
molecule of interest (i.e., the sequence against which the PRO
polypeptide-encoding nucleic acid molecule of interest is being
compared which may be a variant PRO polynucleotide) as determined
by WU-BLAST-2 by (b) the total number of nucleotides of the PRO
polypeptide-encoding nucleic acid molecule of interest. For
example, in the statement "an isolated nucleic acid molecule
comprising a nucleic acid sequence A which has or having at least
80% nucleic acid sequence identity to the nucleic acid sequence B",
the nucleic acid sequence A is the comparison nucleic acid molecule
of interest and the nucleic acid sequence B is the nucleic acid
sequence of the PRO polypeptide-encoding nucleic acid molecule of
interest.
[0142] Percent nucleic acid sequence identity may also be
determined using the sequence comparison program NCBI-BLAST2
(Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997)). The
NCBI-BLAST2 sequence comparison program may be downloaded from
http://www.ncbi.nlm.nih.gov or otherwise obtained from the National
Institute of Health, Bethesda, Md. NCBI-BLAST2 uses several search
parameters, wherein all of those search parameters are set to
default values including, for example, unmask=yes, strand=all,
expected occurrences=10, minimum low complexity length=15/5,
multi-pass e-value=0.01, constant for multi-pass=25, dropoff for
final gapped alignment=25 and scoring matrix=BLOSUM62.
[0143] In situations where NCBI-BLAST2 is employed for sequence
comparisons, the % nucleic acid sequence identity of a given
nucleic acid sequence C to, with, or against a given nucleic acid
sequence D (which can alternatively be phrased as a given nucleic
acid sequence C that has or comprises a certain % nucleic acid
sequence identity to, with, or against a given nucleic acid
sequence D) is calculated as follows:
100 times the fraction W/Z
where W is the number of nucleotides scored as identical matches by
the sequence alignment program NCBI-BLAST2 in that program's
alignment of C and D, and where Z is the total number of
nucleotides in D. It will be appreciated that where the length of
nucleic acid sequence C is not equal to the length of nucleic acid
sequence D, the % nucleic acid sequence identity of C to D will not
equal the % nucleic acid sequence identity of D to C.
[0144] In other embodiments, PRO variant polynucleotides are
nucleic acid molecules that encode an active PRO polypeptide and
which are capable of hybridizing, preferably under stringent
hybridization and wash conditions, to nucleotide sequences encoding
a full-length PRO polypeptide as disclosed herein. PRO variant
polypeptides may be those that are encoded by a PRO variant
polynucleotide.
[0145] "Isolated," when used to describe the various polypeptides
disclosed herein, means polypeptide that has been identified and
separated and/or recovered from a component of its natural
environment. Contaminant components of its natural environment are
materials that would typically interfere with diagnostic or
therapeutic uses for the polypeptide, and may include enzymes,
hormones, and other proteinaceous or non-proteinaceous solutes. In
preferred embodiments, the polypeptide will be purified (1) to a
degree sufficient to obtain at least 15 residues of N-terminal or
internal amino acid sequence by use of a spinning cup sequenator,
or (2) to homogeneity by SDS-PAGE under non-reducing or reducing
conditions using Coomassie blue or, preferably, silver stain.
Isolated polypeptide includes polypeptide in situ within
recombinant cells, since at least one component of the PRO
polypeptide natural environment will not be present. Ordinarily,
however, isolated polypeptide will be prepared by at least one
purification step.
[0146] An "isolated" PRO polypeptide-encoding nucleic acid or other
polypeptide-encoding nucleic acid is a nucleic acid molecule that
is identified and separated from at least one contaminant nucleic
acid molecule with which it is ordinarily associated in the natural
source of the polypeptide-encoding nucleic acid. An isolated
polypeptide-encoding nucleic acid molecule is other than in the
form or setting in which it is found in nature. Isolated
polypeptide-encoding nucleic acid molecules therefore are
distinguished from the specific polypeptide-encoding nucleic acid
molecule as it exists in natural cells. However, an isolated
polypeptide-encoding nucleic acid molecule includes
polypeptide-encoding nucleic acid molecules contained in cells that
ordinarily express the polypeptide where, for example, the nucleic
acid molecule is in a chromosomal location different from that of
natural cells.
[0147] The term "control sequences" refers to DNA sequences
necessary for the expression of an operably linked coding sequence
in a particular host organism. The control sequences that are
suitable for prokaryotes, for example, include a promoter,
optionally an operator sequence, and a ribosome binding site.
Eukaryotic cells are known to utilize promoters, polyadenylation
signals, and enhancers.
[0148] Nucleic acid is "operably linked" when it is placed into a
functional relationship with another nucleic acid sequence. For
example, DNA for a presequence or secretory leader is operably
linked to DNA for a polypeptide if it is expressed as a preprotein
that participates in the secretion of the polypeptide; a promoter
or enhancer is operably linked to a coding sequence if it affects
the transcription of the sequence; or a ribosome binding site is
operably linked to a coding sequence if it is positioned so as to
facilitate translation. Generally, "operably linked" means that the
DNA sequences being linked are contiguous, and, in the case of a
secretory leader, contiguous and in reading phase. However,
enhancers do not have to be contiguous. Linking is accomplished by
ligation at convenient restriction sites. If such sites do not
exist, the synthetic oligonucleotide adaptors or linkers are used
in accordance with conventional practice.
[0149] The term "antibody" is used in the broadest sense and
specifically covers, for example, single anti-PRO monoclonal
antibodies (including agonist, antagonist, and neutralizing
antibodies), anti-PRO antibody compositions with polyepitopic
specificity, single chain anti-PRO antibodies, and fragments of
anti-PRO antibodies (see below). The term "monoclonal antibody" as
used herein refers to an antibody obtained from a population of
substantially homogeneous antibodies, i.e., the individual
antibodies comprising the population are identical except for
possible naturally-occurring mutations that may be present in minor
amounts.
[0150] "Stringency" of hybridization reactions is readily
determinable by one of ordinary skill in the art, and generally is
an empirical calculation dependent upon probe length, washing
temperature, and salt concentration. In general, longer probes
require higher temperatures for proper annealing, while shorter
probes need lower temperatures. Hybridization generally depends on
the ability of denatured DNA to reanneal when complementary strands
are present in an environment below their melting temperature. The
higher the degree of desired homology between the probe and
hybridizable sequence, the higher the relative temperature which
can be used. As a result, it follows that higher relative
temperatures would tend to make the reaction conditions more
stringent, while lower temperatures less so. For additional details
and explanation of stringency of hybridization reactions, see
Ausubel et al., Current Protocols in Molecular Biology, Wiley
Interscience Publishers, (1995).
[0151] "Stringent conditions" or "high stringency conditions", as
defined herein, may be identified by those that: (1) employ low
ionic strength and high temperature for washing, for example 0.015
M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl
sulfate at 50.degree. C.; (2) employ during hybridization a
denaturing agent, such as formamide, for example, 50% (v/v)
formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1%
polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with
750 mM sodium chloride, 75 mM sodium citrate at 42.degree. C.; or
(3) employ 50% formamide, 5.times.SSC (0.75 M NaCl, 0.075 M sodium
citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium
pyrophosphate, 5.times.Denhardt's solution, sonicated salmon sperm
DNA (50 .mu.g/ml), 0.1% SDS, and 10% dextran sulfate at 42.degree.
C., with washes at 42.degree. C. in 0.2.times.SSC (sodium
chloride/sodium citrate) and 50% formamide at 55.degree. C.,
followed by a high-stringency wash consisting of 0.1.times.SSC
containing EDTA at 55.degree. C.
[0152] "Moderately stringent conditions" may be identified as
described by Sambrook et al., Molecular Cloning: A Laboratory
Manual, New York: Cold Spring Harbor Press, 1989, and include the
use of washing solution and hybridization conditions (e.g.,
temperature, ionic strength and % SDS) less stringent that those
described above. An example of moderately stringent conditions is
overnight incubation at 37.degree. C. in a solution comprising: 20%
formamide, 5.times.SSC (150 mM NaCl, 15 mM trisodium citrate), 50
mM sodium phosphate (pH 7.6), 5.times.Denhardt's solution, 10%
dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA,
followed by washing the filters in 1.times.SSC at about
37-50.degree. C. The skilled artisan will recognize how to adjust
the temperature, ionic strength, etc. as necessary to accommodate
factors such as probe length and the like.
[0153] The term "epitope tagged" when used herein refers to a
chimeric polypeptide comprising a PRO polypeptide fused to a "tag
polypeptide". The tag polypeptide has enough residues to provide an
epitope against which an antibody can be made, yet is short enough
such that it does not interfere with activity of the polypeptide to
which it is fused. The tag polypeptide preferably also is fairly
unique so that the antibody does not substantially cross-react with
other epitopes. Suitable tag polypeptides generally have at least
six amino acid residues and usually between about 8 and 50 amino
acid residues (preferably, between about 10 and 20 amino acid
residues).
[0154] As used herein, the term "immunoadhesin" designates
antibody-like molecules which combine the binding specificity of a
heterologous protein (an "adhesin") with the effector functions of
immunoglobulin constant domains. Structurally, the immunoadhesins
comprise a fusion of an amino acid sequence with the desired
binding specificity which is other than the antigen recognition and
binding site of an antibody (i.e., is "heterologous"), and an
immunoglobulin constant domain sequence. The adhesin part of an
immunoadhesin molecule typically is a contiguous amino acid
sequence comprising at least the binding site of a receptor or a
ligand. The immunoglobulin constant domain sequence in the
immunoadhesin may be obtained from any immunoglobulin, such as
IgG-1, IgG-2, IgG-3, or IgG-4 subtypes, IgA (including IgA-1 and
IgA-2), IgE, IgD or IgM.
[0155] The term "antagonist" is used in the broadest sense, and
includes any molecule that partially or fully blocks, inhibits, or
neutralizes a biological activity of a native PRO polypeptide
disclosed herein. In a similar manner, the term "agonist" is used
in the broadest sense and includes any molecule that mimics a
biological activity of a native PRO polypeptide disclosed herein.
Suitable agonist or antagonist molecules specifically include
agonist or antagonist antibodies or antibody fragments, fragments
or amino acid sequence variants of native PRO polypeptides,
peptides, antisense oligonucleotides, small organic molecules, etc.
Methods for identifying agonists or antagonists of a PRO
polypeptide may comprise contacting a PRO polypeptide with a
candidate agonist or antagonist molecule and measuring a detectable
change in one or more biological activities normally associated
with the PRO polypeptide.
[0156] "Treatment" refers to both therapeutic treatment and
prophylactic or preventative measures, wherein the object is to
prevent or slow down (lessen) the targeted pathologic condition or
disorder. Those in need of treatment include those already with the
disorder as well as those prone to have the disorder or those in
whom the disorder is to be prevented.
[0157] "Chronic" administration refers to administration of the
agent(s) in a continuous mode as opposed to an acute mode, so as to
maintain the initial therapeutic effect (activity) for an extended
period of time. "Intermittent" administration is treatment that is
not consecutively done without interruption, but rather is cyclic
in nature.
[0158] "Mammal" for purposes of treatment refers to any animal
classified as a mammal, including humans, domestic and farm
animals, and zoo, sports, or pet animals, such as dogs, cats,
cattle, horses, sheep, pigs, goats, rabbits, etc. Preferably, the
mammal is human.
[0159] Administration "in combination with" one or more further
therapeutic agents includes simultaneous (concurrent) and
consecutive administration in any order.
[0160] "Carriers" as used herein include pharmaceutically
acceptable carriers, excipients, or stabilizers which are nontoxic
to the cell or mammal being exposed thereto at the dosages and
concentrations employed. Often the physiologically acceptable
carrier is an aqueous pH buffered solution. Examples of
physiologically acceptable carriers include buffers such as
phosphate, citrate, and other organic acids; antioxidants including
ascorbic acid; low molecular weight (less than about 10 residues)
polypeptide; proteins, such as serum albumin, gelatin, or
immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone;
amino acids such as glycine, glutamine, asparagine, arginine or
lysine; monosaccharides, disaccharides, and other carbohydrates
including glucose, mannose, or dextrins; chelating agents such as
EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming
counterions such as sodium; and/or nonionic surfactants such as
TWEEN.TM., polyethylene glycol (PEG), and PLURONICS.TM..
[0161] "Antibody fragments" comprise a portion of an intact
antibody, preferably the antigen binding or variable region of the
intact antibody. Examples of antibody fragments include Fab, Fab',
F(ab').sub.2, and Fv fragments; diabodies; linear antibodies
(Zapata et al., Protein Eng., 8(10):1057-1062 [1995]); single-chain
antibody molecules; and multispecific antibodies formed from
antibody fragments.
[0162] Papain digestion of antibodies produces two identical
antigen-binding fragments, called "Fab" fragments, each with a
single antigen-binding site, and a residual "Fc" fragment, a
designation reflecting the ability to crystallize readily. Pepsin
treatment yields an F(ab').sub.2 fragment that has two
antigen-combining sites and is still capable of cross-linking
antigen.
[0163] "Fv" is the minimum antibody fragment which contains a
complete antigen-recognition and -binding site. This region
consists of a dimer of one heavy- and one light-chain variable
domain in tight, non-covalent association. It is in this
configuration that the three CDRs of each variable domain interact
to define an antigen-binding site on the surface of the
V.sub.H-V.sub.L dimer. Collectively, the six CDRs confer
antigen-binding specificity to the antibody. However, even a single
variable domain (or half of an Fv comprising only three CDRs
specific for an antigen) has the ability to recognize and bind
antigen, although at a lower affinity than the entire binding
site.
[0164] The Fab fragment also contains the constant domain of the
light chain and the first constant domain (CH1) of the heavy chain.
Fab fragments differ from Fab' fragments by the addition of a few
residues at the carboxy terminus of the heavy chain CH1 domain
including one or more cysteines from the antibody hinge region.
Fab'-SH is the designation herein for Fab' in which the cysteine
residue(s) of the constant domains bear a free thiol group.
F(ab').sub.2 antibody fragments originally were produced as pairs
of Fab' fragments which have hinge cysteines between them. Other
chemical couplings of antibody fragments are also known.
[0165] The "light chains" of antibodies (immunoglobulins) from any
vertebrate species can be assigned to one of two clearly distinct
types, called kappa and lambda, based on the amino acid sequences
of their constant domains.
[0166] Depending on the amino acid sequence of the constant domain
of their heavy chains, immunoglobulins can be assigned to different
classes. There are five major classes of immunoglobulins: IgA, IgD,
IgE, IgG, and IgM, and several of these may be further divided into
subclasses (isotypes), e.g., IgG1, IgG2, IgG3, IgG4, IgA, and
IgA2.
[0167] "Single-chain Fv" or "sFv" antibody fragments comprise the
V.sub.H and V.sub.L domains of antibody, wherein these domains are
present in a single polypeptide chain. Preferably, the Fv
polypeptide further comprises a polypeptide linker between the
V.sub.H and V.sub.L domains which enables the sFv to form the
desired structure for antigen binding. For a review of sFv, see
Pluckthun in The Pharmacology of Monoclonal Antibodies, vol. 113,
Rosenburg and Moore eds., Springer-Verlag, New York, pp. 269-315
(1994).
[0168] The term "diabodies" refers to small antibody fragments with
two antigen-binding sites, which fragments comprise a heavy-chain
variable domain (V.sub.H) connected to a light-chain variable
domain (V.sub.L) in the same polypeptide chain (V.sub.H-V.sub.L).
By using a linker that is too short to allow pairing between the
two domains on the same chain, the domains are forced to pair with
the complementary domains of another chain and create two
antigen-binding sites. Diabodies are described more fully in, for
example, EP 404,097; WO 93/11161; and Hollinger et al., Proc. Natl.
Acad. Sci. USA, 90:6444-6448 (1993).
[0169] An "isolated" antibody is one which has been identified and
separated and/or recovered from a component of its natural
environment. Contaminant components of its natural environment are
materials which would interfere with diagnostic or therapeutic uses
for the antibody, and may include enzymes, hormones, and other
proteinaceous or nonproteinaceous solutes. In preferred
embodiments, the antibody will be purified (1) to greater than 95%
by weight of antibody as determined by the Lowry method, and most
preferably more than 99% by weight, (2) to a degree sufficient to
obtain at least 15 residues of N-terminal or internal amino acid
sequence by use of a spinning cup sequenator, or (3) to homogeneity
by SDS-PAGE under reducing or nonreducing conditions using
Coomassie blue or, preferably, silver stain. Isolated antibody
includes the antibody in situ within recombinant cells since at
least one component of the antibody's natural environment will not
be present. Ordinarily, however, isolated antibody will be prepared
by at least one purification step.
[0170] An antibody that "specifically binds to" or is "specific
for" a particular polypeptide or an epitope on a particular
polypeptide is one that binds to that particular polypeptide or
epitope on a particular polypeptide without substantially binding
to any other polypeptide or polypeptide epitope.
[0171] The word "label" when used herein refers to a detectable
compound or composition which is conjugated directly or indirectly
to the antibody so as to generate a "labeled" antibody. The label
may be detectable by itself (e.g. radioisotope labels or
fluorescent labels) or, in the case of an enzymatic label, may
catalyze chemical alteration of a substrate compound or composition
which is detectable.
[0172] By "solid phase" is meant a non-aqueous matrix to which the
antibody of the present invention can adhere. Examples of solid
phases encompassed herein include those formed partially or
entirely of glass (e.g., controlled pore glass), polysaccharides
(e.g., agarose), polyacrylamides, polystyrene, polyvinyl alcohol
and silicones. In certain embodiments, depending on the context,
the solid phase can comprise the well of an assay plate; in others
it is a purification column (e.g., an affinity chromatography
column). This term also includes a discontinuous solid phase of
discrete particles, such as those described in U.S. Pat. No.
4,275,149.
[0173] A "liposome" is a small vesicle composed of various types of
lipids, phospholipids and/or surfactant which is useful for
delivery of a drug (such as a PRO polypeptide or antibody thereto)
to a mammal. The components of the liposome are commonly arranged
in a bilayer formation, similar to the lipid arrangement of
biological membranes.
[0174] A "small molecule" is defined herein to have a molecular
weight below about 500 Daltons.
[0175] The term "modulate" means to affect (e.g., either
upregulate, downregulate or otherwise control) the level of a
signaling pathway. Cellular processes under the control of signal
transduction include, but are not limited to, transcription of
specific genes, normal cellular functions, such as metabolism,
proliferation, differentiatiation, adhesion, apoptosis and
survival, as well as abnormal processes, such as transformation,
blocking of differentiation and metastasis.
[0176] "Active" or "activity" for the purposes herein refers to
form(s) of a PRO polypeptide which retain a biological and/or an
immunological activity of native or naturally-occurring PRO
polypeptides, wherein "biological" activity refers to a biological
function (either inhibitory or stimulatory) caused by a native or
naturally-occurring PRO polypeptide other than the ability to
induce the production of an antibody against an antigenic epitope
possessed by a native or naturally-occurring PRO polypeptide and an
"immunological" activity refers to the ability to induce the
production of an antibody against an antigenic epitope possessed by
a native or naturally-occurring PRO polypeptide. One preferred
biological activity includes inducing activation of NF-.kappa.B and
stimulation of the production of the proinflammatory chemokine
IL-8. Another preferred biological activity includes stimulation of
peripheral blood mononuclear cells or CD4.sup.+ cells. Another
preferred biological activity includes stimulation of the
proliferation of T-lymphocytes. Another preferred biological
activity includes, for example, the release of TNF-.alpha. from
THP1 cells. An alternative activity is the reduction in IL-1a
induced NO (nitric oxide) production from articular cartilage.
Another activity includes an enhancement of matrix synthesis in
articular cartilage. Alternatively, another activity includes
promoting breakdown of articular cartilage matrix as well as
inhibiting matrix synthesis. Another preferred biological activity
includes modulating the level of the interleukin-17 signalling
pathway during mild to severe stages of inflammatory bowel disease
or during stroke.
[0177] An "immunological" activity refers only to the ability to
induce the production of an antibody against an antigenic epitope
possessed by a native or naturally-occurring PRO polypeptide.
[0178] "Degenerative cartilagenous disorder" describes a host of
disorders that is characterized principally by the destruction of
the cartilage matrix. Additional pathologies includes nitric oxide
production, and elevated proteoglycan breakdown. Exemplary
disorders encompassed within this definition, include, for example,
arthritis (e.g., osteoarthritis, rheumatoid arthritis, psoriatic
arthritis).
[0179] The term "immune related disease" means a disease in which a
component of the immune system of a mammal causes, mediates or
otherwise contributes to a morbidity in the mammal. Also included
are diseases in which stimulation or intervention of the immune
response has an ameliorative effect on progression of the disease.
Included within this term are immune-mediated inflammatory
diseases, non-immune-mediated inflammatory diseases, infectious
diseases, immunodeficiency diseases, neoplasia, etc.
[0180] The term "T cell mediated disease" means a disease in which
T cells directly or indirectly mediate or otherwise contribute to a
morbidity in a mammal. The T cell mediated disease may be
associated with cell mediated effects, lymphokine mediated effects,
etc., and even effects associated with B cells if the B cells are
stimulated, for example, by the lymphokines secreted by T
cells.
[0181] Examples of immune-related and inflammatory diseases, some
of which are immune or T cell mediated, which can be treated
according to the invention include systemic lupus erythematosis,
rheumatoid arthritis, juvenile chronic arthritis,
spondyloarthropathies, systemic sclerosis (scleroderma), idiopathic
inflammatory myopathies (dermatomyositis, polymyositis), Sjogren's
syndrome, systemic vasculitis, sarcoidosis, autoimmune hemolytic
anemia (immune pancytopenia, paroxysmal nocturnal hemoglobinuria),
autoimmune thrombocytopenia (idiopathic thrombocytopenic purpura,
immune-mediated thrombocytopenia), thyroiditis (Grave's disease,
Hashimoto's thyroiditis, juvenile lymphocytic thyroiditis, atrophic
thyroiditis), diabetes mellitus, immune-mediated renal disease
(glomerulonephritis, tubulointerstitial nephritis), demyelinating
diseases of the central and peripheral nervous systems such as
multiple sclerosis, idiopathic demyelinating polyneuropathy or
Guillain-Barre syndrome, and chronic inflammatory demyelinating
polyneuropathy, hepatobiliary diseases such as infectious hepatitis
(hepatitis A, B, C, D, E and other non-hepatotropic viruses),
autoimmune chronic active hepatitis, primary biliary cirrhosis,
granulomatous hepatitis, and sclerosing cholangitis, inflammatory
bowel disease (ulcerative colitis: Crohn's disease),
gluten-sensitive enteropathy, and Whipple's disease, autoimmune or
immune-mediated skin diseases including bullous skin diseases,
erythema multiforme and contact dermatitis, psoriasis, allergic
diseases such as asthma, allergic rhinitis, atopic dermatitis, food
hypersensitivity and urticaria, immunologic diseases of the lung
such as eosinophilic pneumonias, idiopathic pulmonary fibrosis and
hypersensitivity pneumonitis, transplantation associated diseases
including graft rejection and graft-versus-host-disease. Infectious
diseases including viral diseases such as AIDS (HIV infection),
hepatitis A, B, C, D, and E, herpes, etc., bacterial infections,
fungal infections, protozoal infections and parasitic infections.
The term "effective amount" is a concentration or amount of a PRO
polypeptide and/or agonist/antagonist which results in achieving a
particular stated purpose. An "effective amount" of a PRO
polypeptide or agonist or antagonist thereof may be determined
empirically. Furthermore, a "therapeutically effective amount" is a
concentration or amount of a PRO polypeptide and/or
agonist/antagonist which is effective for achieving a stated
therapeutic effect. This amount may also be determined
empirically.
[0182] The term "cytotoxic agent" as used herein refers to a
substance that inhibits or prevents the function of cells and/or
causes destruction of cells. The term is intended to include
radioactive isotopes (e.g., I.sup.131, I.sup.125, Y.sup.90 and
Re.sup.186), chemotherapeutic agents, and toxins such as
enzymatically active toxins of bacterial, fungal, plant or animal
origin, or fragments thereof.
[0183] A "chemotherapeutic agent" is a chemical compound useful in
the treatment of cancer. Examples of chemotherapeutic agents
include adriamycin, doxorubicin, epirubicin, 5-fluorouracil,
cytosine arabinoside ("Ara-C"), cyclophosphamide, thiotepa,
busulfan, cytoxin, taxoids, e.g., paclitaxel (Taxol, Bristol-Myers
Squibb Oncology, Princeton, N.J.), and doxetaxel (Taxotere,
Rhone-Poulenc Rorer, Antony, France), toxotere, methotrexate,
cisplatin, melphalan, vinblastine, bleomycin, etoposide,
ifosfamide, mitomycin C, mitoxantrone, vincristine, vinorelbine,
carboplatin, teniposide, daunomycin, caminomycin, aminopterin,
dactinomycin, mitomycins, esperamicins (see U.S. Pat. No.
4,675,187), melphalan and other related nitrogen mustards. Also
included in this definition are hormonal agents that act to
regulate or inhibit hormone action on tumors such as tamoxifen and
onapristone.
[0184] A "growth inhibitory agent" when used herein refers to a
compound or composition which inhibits growth of a cell, especially
cancer cell overexpressing any of the genes identified herein,
either in vitro or in vivo. Thus, the growth inhibitory agent is
one which significantly reduces the percentage of cells
overexpressing such genes in S phase. Examples of growth inhibitory
agents include agents that block cell cycle progression (at a place
other than S phase), such as agents that induce G1 arrest and
M-phase arrest. Classical M-phase blockers include the vincas
(vincristine and vinblastine), taxol, and topo II inhibitors such
as doxorubicin, epirubicin, daunorubicin, etoposide, and bleomycin.
Those agents that arrest G1 also spill over into S-phase arrest,
for example, DNA alkylating agents such as tamoxifen, prednisone,
dacarbazine, mechlorethamine, cisplatin, methotrexate,
5-fluorouracil, and ara-C. Further information can be found in The
Molecular Basis of Cancer, Mendelsohn and Israel, eds., Chapter 1,
entitled "Cell cycle regulation, oncogens, and antineoplastic
drugs" by Murakami et al., (WB Saunders: Philadelphia, 1995),
especially p. 13.
[0185] The term "cytokine" is a generic term for proteins released
by one cell population which act on another cell as intercellular
mediators. Examples of such cytokines are lymphokines, monokines,
and traditional polypeptide hormones. Included among the cytokines
are growth hormone such as human growth hormone, N-methionyl human
growth hormone, and bovine growth hormone; parathyroid hormone;
thyroxine; insulin; proinsulin; relaxin; prorelaxin; glycoprotein
hormones such as follicle stimulating hormone (FSH), thyroid
stimulating hormone (TSH), and luteinizing hormone (LH); hepatic
growth factor; fibroblast growth factor; prolactin; placental
lactogen; tumor necrosis factor-.alpha. and -.beta.;
mullerian-inhibiting substance; mouse gonadotropin-associated
peptide; inhibin; activin; vascular endothelial growth factor;
integrin; thrombopoietin (TPO); nerve growth factors such as
NGF-.beta.; platelet-growth factor; transforming growth factors
(TGFs) such as TGF-.alpha. and TGF-.beta.; insulin-like growth
factor-I and -II; erythropoietin (EPO); osteoinductive factors;
interferons such as interferon-.alpha., -.beta., and -.gamma.;
colony stimulating factors (CSFs) such as macrophage-CSF (M-CSF);
granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-CSF);
interleukins (ILs) such as IL-1, IL-1a, IL-2, IL-3, IL4, IL-5,
IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, or IL-17; a tumor
necrosis factor such as TNF-.alpha. or TNF-.beta.; and other
polypeptide factors including LIF and kit ligand (KL). As used
herein, the term cytokine includes proteins from natural sources or
from recombinant cell culture and biologically active equivalents
of the native sequence cytokines.
TABLE-US-00001 TABLE 1 /* * * C-C increased from 12 to 15 * Z is
average of EQ * B is average of ND * match with stop is _M;
stop-stop = 0; J (joker) match = 0 */ #define _M -8 /* value of a
match with a stop */ int _day[26][26] = { /* A B C D E F G H I J K
L M N O P Q R S T U V W X Y Z */ /* A */ { 2, 0,-2, 0, 0,-4,
1,-1,-1, 0,-1,-2,-1, 0,_M, 1, 0,-2, 1, 1, 0, 0,-6, 0,-3, 0}, /* B
*/ { 0, 3,-4, 3, 2,-5, 0, 1,-2, 0, 0,-3,-2, 2,_M,-1, 1, 0, 0, 0,
0,-2,-5, 0,-3, 1}, /* C */ {-2,-4,15,-5,-5,-4,-3,-3,-2,
0,-5,-6,-5,-4,_M,-3,-5,-4, 0,-2, 0,-2,-8, 0, 0,-5}, /* D */ { 0,
3,-5, 4, 3,-6, 1, 1,-2, 0, 0,-4,-3, 2,_M,-1, 2,-1, 0, 0, 0,-2,-7,
0,-4, 2}, /* E */ { 0, 2,-5, 3, 4,-5, 0, 1,-2, 0, 0,-3,-2, 1,_M,-1,
2,-1, 0, 0, 0,-2,-7, 0,-4, 3}, /* F */ {-4,-5,-4,-6,-5, 9,-5,-2, 1,
0,-5, 2, 0,-4,_M,-5,-5,-4,-3,-3, 0,-1, 0, 0, 7,-5}, /* G */ { 1,
0,-3, 1, 0,-5, 5,-2,-3, 0,-2,-4,-3, 0,_M,-1,-1,-3, 1, 0, 0,-1,-7,
0,-5, 0}, /* H */ {-1, 1,-3, 1, 1,-2,-2, 6,-2, 0, 0,-2,-2, 2,_M, 0,
3, 2,-1,-1, 0,-2,-3, 0, 0, 2}, /* I */ {-1,-2,-2,-2,-2, 1,-3,-2, 5,
0,-2, 2, 2,-2,_M,-2,-2,-2,-1, 0, 0, 4,-5, 0,-1,-2}, /* J */ { 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,_M, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0}, /* K */ {-1, 0,-5, 0, 0,-5,-2, 0,-2, 0, 5,-3, 0, 1,_M,-1, 1,
3, 0, 0, 0,-2,-3, 0,-4, 0}, /* L */ {-2,-3,-6,-4,-3, 2,-4,-2, 2,
0,-3, 6, 4,-3,_M,-3,-2,-3,-3,-1, 0, 2,-2, 0,-1,-2}, /* M */
{-1,-2,-5,-3,-2, 0,-3,-2, 2, 0, 0, 4, 6,-2,_M,-2,-1, 0,-2,-1, 0,
2,-4, 0,-2,-1}, /* N */ { 0, 2,-4, 2, 1,-4, 0, 2,-2, 0, 1,-3,-2,
2,_M,-1, 1, 0, 1, 0, 0,-2,-4, 0,-2, 1}, /* O */
{_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,
0,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M}, /* P */ { 1,-1,-3,-1,-1,-5,-1,
0,-2, 0,-1,-3,-2,-1,_M, 6, 0, 0, 1, 0, 0,-1,-6, 0,-5, 0}, /* Q */ {
0, 1,-5, 2, 2,-5,-1, 3,-2, 0, 1,-2,-1, 1,_M, 0, 4, 1,-1,-1,
0,-2,-5, 0,-4, 3}, /* R */ {-2, 0,-4,-1,-1,-4,-3, 2,-2, 0, 3,-3, 0,
0,_M, 0, 1, 6, 0,-1, 0,-2, 2, 0,-4, 0}, /* S */ { 1, 0, 0, 0, 0,-3,
1,-1,-1, 0, 0,-3,-2, 1,_M, 1,-1, 0, 2, 1, 0,-1,-2, 0,-3, 0}, /* T
*/ { 1, 0,-2, 0, 0,-3, 0,-1, 0, 0, 0,-1,-1, 0,_M, 0,-1,-1, 1, 3, 0,
0,-5, 0,-3, 0}, /* U */ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0,_M, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, /* V */ {
0,-2,-2,-2,-2,-1,-1,-2, 4, 0,-2, 2, 2,-2,_M,-1,-2,-2,-1, 0, 0,
4,-6, 0,-2,-2}, /* W */ {-6,-5,-8,-7,-7, 0,-7,-3,-5,
0,-3,-2,-4,-4,_M,-6,-5, 2,-2,-5, 0,-6,17, 0, 0,-6}, /* X */ { 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,_M, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0}, /* Y */ {-3,-3, 0,-4,-4, 7,-5, 0,-1,
0,-4,-1,-2,-2,_M,-5,-4,-4,-3,-3, 0,-2, 0, 0,10,-4}, /* Z */ { 0,
1,-5, 2, 3,-5, 0, 2,-2, 0, 0,-2,-1, 1,_M, 0, 3, 0, 0, 0, 0,-2,-6,
0,-4, 4} }; /* */ #include <stdio.h> #include <ctype.h>
#define MAXJMP 16 /* max jumps in a diag */ #define MAXGAP 24 /*
don't continue to penalize gaps larger than this */ #define JMPS
1024 /* max jmps in an path */ #define MX 4 /* save if there's at
least MX-1 bases since last jmp */ #define DMAT 3 /* value of
matching bases */ #define DMIS 0 /* penalty for mismatched bases */
#define DINS0 8 /* penalty for a gap */ #define DINS1 1 /* penalty
per base */ #define PINS0 8 /* penalty for a gap */ #define PINS1 4
/* penalty per residue */ struct jmp { short n[MAXJMP]; /* size of
jmp (neg for dely) */ unsigned short x[MAXJMP]; /* base no. of jmp
in seq x */ }; /* limits seq to 2{circumflex over ( )}16 -1 */
struct diag { int score; /* score at last jmp */ long offset; /*
offset of prev block */ short ijmp; /* current jmp index */ struct
jmp jp; /* list of jmps */ }; struct path { int spc; /* number of
leading spaces */ short n[JMPS];/* size of jmp (gap) */ int
x[JMPS];/* loc of jmp (last elem before gap) */ }; char *ofile; /*
output file name */ char *namex[2]; /* seq names: getseqs( ) */
char *prog; /* prog name for err msgs */ char *seqx[2]; /* seqs:
getseqs( ) */ int dmax; /* best diag: nw( ) */ int dmax0; /* final
diag */ int dna; /* set if dna: main( ) */ int endgaps; /* set if
penalizing end gaps */ int gapx, gapy; /* total gaps in seqs */ int
len0, len1; /* seq lens */ int ngapx, ngapy; /* total size of gaps
*/ int smax; /* max score: nw( ) */ int *xbm; /* bitmap for
matching */ long offset; /* current offset in jmp file */ struct
diag *dx; /* holds diagonals */ struct path pp[2]; /* holds path
for seqs */ char *calloc( ), *malloc( ), *index( ), *strcpy( );
char *getseq( ), *g_calloc( ); /* Needleman-Wunsch alignment
program * * usage: progs file1 file2 * where file1 and file2 are
two dna or two protein sequences. * The sequences can be in upper-
or lower-case an may contain ambiguity * Any lines beginning with
`;`, `>` or `<` are ignored * Max file length is 65535
(limited by unsigned short x in the jmp struct) * A sequence with
1/3 or more of its elements ACGTU is assumed to be DNA * Output is
in the file "align.out" * * The program may create a tmp file in
/tmp to hold info about traceback. * Original version developed
under BSD 4.3 on a vax 8650 */ #include "nw.h" #include "day.h"
static _dbval[26] = {
1,14,2,13,0,0,4,11,0,0,12,0,3,15,0,0,0,5,6,8,8,7,9,0,10,0 }; static
_pbval[26] = { 1, 2|(1<<(`D`-`A`))|(1<<(`N`-`A`)), 4,
8, 16, 32, 64, 128, 256, 0xFFFFFFF, 1<<10, 1<<11,
1<<12, 1<<13, 1<<14, 1<<15, 1<<16,
1<<17, 1<<18, 1<<19, 1<<20, 1<<21,
1<<22, 1<<23, 1<<24,
1<<25|(1<<(`E`-`A`))|(1<<(`Q`-`A`)) }; main(ac,
av) main int ac; char *av[ ]; { prog = av[0]; if (ac != 3) {
fprintf(stderr,"usage: %s file1 file2\n", prog);
fprintf(stderr,"where file1 and file2 are two dna or two protein
sequences.\n"); fprintf(stderr,"The sequences can be in upper- or
lower-case\n"); fprintf(stderr,"Any lines beginning with `;` or
`<` are ignored\n"); fprintf(stderr,"Output is in the file
\"align.out\"\n"); exit(1); } namex[0] = av[1]; namex[1] = av[2];
seqx[0] = getseq(namex[0], &len0); seqx[1] = getseq(namex[1],
&len1); xbm = (dna)? _dbval : _pbval; endgaps = 0; /* 1 to
penalize endgaps */ ofile = "align.out"; /* output file */ nw( );
/* fill in the matrix, get the possible jmps */ readjmps( ); /* get
the actual jmps */ print( ); /* print stats, alignment */
cleanup(0); /* unlink any tmp files */ } /* do the alignment,
return best score: main( ) * dna: values in Fitch and Smith, PNAS,
80, 1382-1386, 1983 * pro: PAM 250 values * When scores are equal,
we prefer mismatches to any gap, prefer * a new gap to extending an
ongoing gap, and prefer a gap in seqx * to a gap in seq y. */ nw( )
nw { char *px, *py; /* seqs and ptrs */ int *ndely, *dely; /* keep
track of dely */ int ndelx, delx; /* keep track of delx */ int
*tmp; /* for swapping row0, row1 */ int mis; /* score for each type
*/ int ins0, ins1; /* insertion penalties */ register id; /*
diagonal index */ register ij; /* jmp index */ register *col0,
*col1; /* score for curr, last row */ register xx, yy; /* index
into seqs */ dx = (struct diag *)g_calloc("to get diags",
len0+len1+1, sizeof(struct diag)); ndely = (int *)g_calloc("to get
ndely", len1+1, sizeof(int)); dely = (int *)g_calloc("to get dely",
len1+1, sizeof(int)); col0 = (int *)g_calloc("to get col0", len1+1,
sizeof(int)); col1 = (int *)g_calloc("to get col1", len1+1,
sizeof(int)); ins0 = (dna)? DINS0 : PINS0; ins1 = (dna)? DINS1 :
PINS1; smax = -10000; if (endgaps) { for (col0[0] = dely[0] =
-ins0, yy = 1; yy <= len1; yy++) { col0[yy] = dely[yy] =
col0[yy-1] - ins1; ndely[yy] = yy; } col0[0] = 0; /* Waterman Bull
Math Biol 84 */ } else for (yy = 1; yy <= len1; yy++) dely[yy] =
-ins0; /* fill in match matrix */ for (px = seqx[0], xx = 1; xx
<= len0; px++, xx++) { /* initialize first entry in col */ if
(endgaps) { if (xx == 1) col1[0] = delx = -(ins0+ins1); else
col1[0] = delx = col0[0] - ins1; ndelx = xx; } else { col1[0] = 0;
delx = -ins0; ndelx = 0; } ...nw for (py = seqx[1], yy = 1; yy
<= len1; py++, yy++) { mis = col0[yy-1]; if (dna) mis +=
(xbm[*px-`A`]&xbm[*py-`A`])? DMAT : DMIS; else mis +=
_day[*px-`A`][*py-`A`]; /* update penalty for del in x seq; * favor
new del over ongong del * ignore MAXGAP if weighting endgaps */ if
(endgaps || ndely[yy] < MAXGAP) { if (col0[yy] - ins0 >=
dely[yy]) { dely[yy] = col0[yy] - (ins0+ins1); ndely[yy] = 1; }
else { dely[yy] -= ins1; ndely[yy]++; } } else { if (col0[yy] -
(ins0+ins1) >= dely[yy]) { dely[yy] = col0[yy] - (ins0+ins1);
ndely[yy] = 1; } else ndely[yy]++; } /* update penalty for del in y
seq;
* favor new del over ongong del */ if (endgaps || ndelx <
MAXGAP) { if (col1[yy-1] - ins0 >= delx) { delx = col1[yy-1] -
(ins0+ins1); ndelx = 1; } else { delx -= ins1; ndelx++; } } else {
if (col1[yy-1] - (ins0+ins1) >= delx) { delx = col1[yy-1] -
(ins0+ins1); ndelx = 1; } else ndelx++; } /* pick the maximum
score; we're favoring * mis over any del and delx over dely */
...nw id = xx - yy + len1 - 1; if (mis >= delx && mis
>= dely[yy]) col1[yy] = mis; else if (delx >= dely[yy]) {
col1[yy] = delx; ij = dx[id].ijmp; if (dx[id].jp.n[0] &&
(!dna || (ndelx >= MAXJMP && xx > dx[id].jp.x[ij]+MX)
|| mis > dx[id].score+DINS0)) { dx[id].ijmp++; if (++ij >=
MAXJMP) { writejmps(id); ij = dx[id].ijmp = 0; dx[id].offset =
offset; offset += sizeof(struct jmp) + sizeof(offset); } }
dx[id].jp.n[ij] = ndelx; dx[id].jp.x[ij] = xx; dx[id].score = delx;
} else { col1[yy] = dely[yy]; ij = dx[id].ijmp; if (dx[id].jp.n[0]
&& (!dna || (ndely[yy] >= MAXJMP && xx >
dx[id].jp.x[ij]+MX) || mis > dx[id].score+DINS0)) {
dx[id].ijmp++; if (++ij >= MAXJMP) { writejmps(id); ij =
dx[id].ijmp = 0; dx[id].offset = offset; offset += sizeof(struct
jmp) + sizeof(offset); } } dx[id].jp.n[ij] = -ndely[yy];
dx[id].jp.x[ij] = xx; dx[id].score = dely[yy]; } if (xx == len0
&& yy < len1) { /* last col */ if (endgaps) col1[yy] -=
ins0+ins1*(len1-yy); if (col1[yy] > smax) { smax = col1[yy];
dmax = id; } } } if (endgaps && xx < len0) col1[yy-1] -=
ins0+ins1*(len0-xx); if (col1[yy-1] > smax) { smax = col1[yy-1];
dmax = id; } tmp = col0; col0 = col1; col1 = tmp; } (void)
free((char *)ndely); (void) free((char *)dely); (void) free((char
*)col0); (void) free((char *)col1); } /* * * print( ) -- only
routine visible outside this module * * static: * getmat( ) --
trace back best path, count matches: print( ) * pr_align( ) --
print alignment of described in array p[ ]: print( ) * dumpblock( )
-- dump a block of lines with numbers, stars: pr_align( ) * nums( )
-- put out a number line: dumpblock( ) * putline( ) -- put out a
line (name, [num], seq, [num]): dumpblock( ) * stars( ) - -put a
line of stars: dumpblock( ) * stripname( ) -- strip any path and
prefix from a seqname */ #include "nw.h" #define SPC 3 #define
P_LINE 256 /* maximum output line */ #define P_SPC 3 /* space
between name or num and seq */ extern _day[26][26]; int olen; /*
set output line length */ FILE *fx; /* output file */ print( )
print { int lx, ly, firstgap, lastgap; /* overlap */ if ((fx =
fopen(ofile, "w")) == 0) { fprintf(stderr, "%s: can't write %s\n",
prog, ofile); cleanup(1); } fprintf(fx, "<first sequence: %s
(length = %d)\n", namex[0], len0); fprintf(fx, "<second
sequence: %s (length = %d)\n", namex[1], len1); olen = 60; lx =
len0; ly = len1; firstgap = lastgap = 0; if (dmax < len1 - 1) {
/* leading gap in x */ pp[0].spc = firstgap = len1 - dmax - 1; ly
-= pp[0].spc; } else if (dmax > len1 - 1) { /* leading gap in y
*/ pp[1].spc = firstgap = dmax - (len1 - 1); lx -= pp[1].spc; } if
(dmax0 < len0 - 1) { /* trailing gap in x */ lastgap = len0 -
dmax0 -1; lx -= lastgap; } else if (dmax0 > len0 - 1) { /*
trailing gap in y */ lastgap = dmax0 - (len0 - 1); ly -= lastgap; }
getmat(lx, ly, firstgap, lastgap); pr_align( ); } /* * trace back
the best path, count matches */ static getmat(lx, ly, firstgap,
lastgap) getmat int lx, ly; /* "core" (minus endgaps) */ int
firstgap, lastgap; /* leading trailing overlap */ { int nm, i0, i1,
siz0, siz1; char outx[32]; double pct; register n0, n1; register
char *p0, *p1; /* get total matches, score */ i0 = i1 = siz0 = siz1
= 0; p0 = seqx[0] + pp[1].spc; p1 = seqx[1] + pp[0].spc; n0 =
pp[1].spc + 1; n1 = pp[0].spc + 1; nm = 0; while ( *p0 &&
*p1 ) { if (siz0) { p1++; n1++; siz0--; } else if (siz1) { p0++;
n0++; siz1--; } else { if (xbm[*p0-`A`]&xbm[*p1-`A`]) nm++; if
(n0++ == pp[0].x[i0]) siz0 = pp[0].n[i0++]; if (n1++ ==
pp[1].x[i1]) siz1 = pp[1].n[i1++]; p0++; p1++; } } /* pct homology:
* if penalizing endgaps, base is the shorter seq * else, knock off
overhangs and take shorter core */ if (endgaps) lx = (len0 <
len1)? len0 : len1; else lx = (lx < ly)? lx : ly; pct =
100.*(double)nm/(double)lx; fprintf(fx, "\n"); fprintf(fx, "<%d
match%s in an overlap of %d: %.2f percent similarity\n", nm, (nm ==
1)? "" : "es", lx, pct); fprintf(fx, "<gaps in first sequence:
%d", gapx); ...getmat if (gapx) { (void) sprintf(outx, " (%d
%s%s)", ngapx, (dna)? "base":"residue", (ngapx == 1)? "":"s");
fprintf(fx,"%s", outx); fprintf(fx, ", gaps in second sequence:
%d", gapy); if (gapy) { (void) sprintf(outx, " (%d %s%s)", ngapy,
(dna)? "base":"residue", (ngapy == 1)? "":"s"); fprintf(fx,"%s",
outx); } if (dna) fprintf(fx, "\n<score: %d (match = %d,
mismatch = %d, gap penalty = %d + %d per base)\n", smax, DMAT,
DMIS, DINS0, DINS1); else fprintf(fx, "\n<score: %d (Dayhoff PAM
250 matrix, gap penalty = %d + %d per residue)\n", smax, PINS0,
PINS1); if (endgaps) fprintf(fx, "<endgaps penalized. left
endgap: %d %s%s, right endgap: %d %s%s\n", firstgap, (dna)? "base"
: "residue", (firstgap == 1)? "" : "s", lastgap, (dna)? "base" :
"residue", (lastgap == 1)? "" : "s"); else fprintf(fx, "<endgaps
not penalized\n"); } static nm; /* matches in core -- for checking
*/ static lmax; /* lengths of stripped file names */ static ij[2];
/* jmp index for a path */ static nc[2]; /* number at start of
current line */ static ni[2]; /* current elem number -- for gapping
*/ static siz[2]; static char *ps[2]; /* ptr to current element */
static char *po[2]; /* ptr to next output char slot */ static char
out[2][P_LINE]; /* output line */ static char star[P_LINE]; /* set
by stars( ) */ /* * print alignment of described in struct path pp[
] */ static pr_align( ) pr_align { int nn; /* char count */ int
more; register i; for (i = 0, lmax = 0; i < 2; i++) { nn =
stripname(namex[i]); if (nn > lmax) lmax = nn; nc[i] = 1; ni[i]
= 1; siz[i] = ij[i] = 0; ps[i] = seqx[i]; po[i] = out[i]; } for (nn
= nm = 0, more = 1; more; ) { ...pr_align for (i = more = 0; i <
2; i++) { /* * do we have more of this sequence? */
if (!*ps[i]) continue; more++; if (pp[i].spc) { /* leading space */
*po[i]++ = ` `; pp[i].spc--; } else if (siz[i]) { /* in a gap */
*po[i]++ = `-`; siz[i]--; } else { /* we're putting a seq element
*/ *po[i] = *ps[i]; if (islower(*ps[i])) *ps[i] = toupper(*ps[i]);
po[i]++; ps[i]++; /* * are we at next gap for this seq? */ if
(ni[i] == pp[i].x[ij[i]]) { /* * we need to merge all gaps * at
this location */ siz[i] = pp[i].n[ij[i]++]; while (ni[i] ==
pp[i].x[ij[i]]) siz[i] += pp[i].n[ij[i]++]; } ni[i]++; } } if (++nn
== olen || !more && nn) { dumpblock( ); for (i = 0; i <
2; i++) po[i] = out[i]; nn = 0; } } } /* * dump a block of lines,
including numbers, stars: pr_align( ) */ static dumpblock( )
dumpblock { register i; for (i = 0; i < 2; i++) *po[i]-- = `\0`;
...dumpblock (void) putc(`\n`, fx); for (i = 0; i < 2; i++) { if
(*out[i] && (*out[i] != ` ` || *(po[i]) != ` `)) { if (i ==
0) nums(i); if (i == 0 && *out[1]) stars( ); putline(i); if
(i == 0 && *out[1]) fprintf(fx, star); if (i == 1) nums(i);
} } } /* * put out a number line: dumpblock( ) */ static nums(ix)
nums int ix; /* index in out[ ] holding seq line */ { char
nline[P_LINE]; register i, j; register char *pn, *px, *py; for (pn
= nline, i = 0; i < lmax+P_SPC; i++, pn++) *pn = ` `; for (i =
nc[ix], py = out[ix]; *py; py++, pn++) { if (*py == ` ` || *py ==
`-`) *pn = ` `; else { if (i%10 == 0 || (i == 1 && nc[ix]
!= 1)) { j = (i < 0)? -i : i; for (px = pn; j; j /= 10, px--)
*px = j%10 + `0`; if (i < 0) *px = `-`; } else *pn = ` `; i++; }
} *pn = `\0`; nc[ix] = i; for (pn = nline; *pn; pn++) (void)
putc(*pn, fx); (void) putc(`\n`, fx); } /* * put out a line (name,
[num], seq, [num]): dumpblock( ) */ static putline(ix) putline int
ix; { ...putline int i; register char *px; for (px = namex[ix], i =
0; *px && *px != `:`; px++, i++) (void) putc(*px, fx); for
(; i < lmax+P_SPC; i++) (void) putc(` `, fx); /* these count
from 1: * ni[ ] is current element (from 1) * nc[ ] is number at
start of current line */ for (px = out[ix]; *px; px++) (void)
putc(*px&0x7F, fx); (void) putc(`\n`, fx); } /* * put a line of
stars (seqs always in out[0], out[1]): dumpblock( ) */ static
stars( ) stars { int i; register char *p0, *p1, cx, *px; if
(!*out[0] || (*out[0] == ` ` && *(po[0]) == ` `) ||
!*out[1] || (*out[1] == ` ` && *(po[1]) == ` `)) return; px
= star; for (i = lmax+P_SPC; i; i--) *px++ = ` `; for (p0 = out[0],
p1 = out[1]; *p0 && *p1; p0++, p1++) { if (isalpha(*p0)
&& isalpha(*p1)) { if (xbm[*p0-`A`]&xbm[*p1-`A`]) { cx
= `*`; nm++; } else if (!dna && _day[*p0-`A`][*p1-`A`] >
0) cx = `.`; else cx = ` `; } else cx = ` `; *px++ = cx; } *px++ =
`\n`; *px = `\0`; } /* * strip path or prefix from pn, return len:
pr_align( ) */ static stripname(pn) stripname char *pn; /* file
name (may be path) */ { register char *px, *py; py = 0; for (px =
pn; *px; px++) if (*px == `/`) py = px + 1; if (py) (void)
strcpy(pn, py); return(strlen(pn)); } /* * cleanup( ) -- cleanup
any tmp file * getseq( ) -- read in seq, set dna, len, maxlen *
g_calloc( ) -- calloc( ) with error checkin * readjmps( ) -- get
the good jmps, from tmp file if necessary * writejmps( ) -- write a
filled array of jmps to a tmp file: nw( ) */ #include "nw.h"
#include <sys/file.h> char *jname = "/tmp/homgXXXXXX"; /* tmp
file for jmps */ FILE *fj; int cleanup( ); /* cleanup tmp file */
long lseek( ); /* * remove any tmp file if we blow */ cleanup(i)
cleanup int i; { if (fj) (void) unlink(jname); exit(i); } /* *
read, return ptr to seq, set dna, len, maxlen * skip lines starting
with `;`, `<`, or `>` * seq in upper or lower case */ char *
getseq(file, len) getseq char *file; /* file name */ int *len; /*
seq len */ { char line[1024], *pseq; register char *px, *py; int
natgc, tlen; FILE *fp; if ((fp = fopen(file,"r")) == 0) {
fprintf(stderr,"%s: can't read %s\n", prog, file); exit(1); } tlen
= natgc = 0; while (fgets(line, 1024, fp)) { if (*line == `;` ||
*line == `<` || *line == `>`) continue; for (px = line; *px
!= `\n`; px++) if (isupper(*px) || islower(*px)) tlen++; } if
((pseq = malloc((unsigned)(tlen+6))) == 0) { fprintf(stderr,"%s:
malloc( ) failed to get %d bytes for %s\n", prog, tlen+6, file);
exit(1); } pseq[0] = pseq[1] = pseq[2] = pseq[3] = `\0`; ...getseq
py = pseq + 4; *len = tlen; rewind(fp); while (fgets(line, 1024,
fp)) { if (*line == `;` || *line == `<` || *line == `>`)
continue; for (px = line; *px != `\n`; px++) { if (isupper(*px))
*py++ = *px; else if (islower(*px)) *py++ = toupper(*px); if
(index("ATGCU",*(py-1))) natgc++; } } *py++ = `\0`; *py = `\0`;
(void) fclose(fp); dna = natgc > (tlen/3); return(pseq+4); }
char * g_calloc(msg, nx, sz) g_calloc char *msg; /* program,
calling routine */ int nx, sz; /* number and size of elements */
{
char *px, *calloc( ); if ((px = calloc((unsigned)nx, (unsigned)sz))
== 0) { if (*msg) { fprintf(stderr, "%s: g_calloc( ) failed %s
(n=%d, sz=%d)\n", prog, msg, nx, sz); exit(1); } } return(px); } /*
* get final jmps from dx[ ] or tmp file, set pp[ ], reset dmax:
main( ) */ readjmps( ) readjmps { int fd = -1; int siz, i0, i1;
register i, j, xx; if (fj) { (void) fclose(fj); if ((fd =
open(jname, O_RDONLY, 0)) < 0) { fprintf(stderr, "%s: can't
open( ) %s\n", prog, jname); cleanup(1); } } for (i = i0 = i1 = 0,
dmax0 = dmax, xx = len0; ; i++) { while (1) { for (j =
dx[dmax].ijmp; j >= 0 && dx[dmax].jp.x[j] >= xx; j--)
; ...readjmps if (j < 0 && dx[dmax].offset &&
fj) { (void) lseek(fd, dx[dmax].offset, 0); (void) read(fd, (char
*)&dx[dmax].jp, sizeof(struct jmp)); (void) read(fd, (char
*)&dx[dmax].offset, sizeof(dx[dmax].offset)); dx[dmax].ijmp =
MAXJMP-1; } else break; } if (i >= JMPS) { fprintf(stderr, "%s:
too many gaps in alignment\n", prog); cleanup(1); } if (j >= 0)
{ siz = dx[dmax].jp.n[j]; xx = dx[dmax].jp.x[j]; dmax += siz; if
(siz < 0) { /* gap in second seq */ pp[1].n[i1] = -siz; xx +=
siz; /* id = xx - yy + len1 - 1 */ pp[1].x[i1] = xx - dmax + len1 -
1; gapy++; ngapy -= siz; /* ignore MAXGAP when doing endgaps */ siz
= (-siz < MAXGAP || endgaps)? -siz : MAXGAP; i1++; } else if
(siz > 0) { /* gap in first seq */ pp[0].n[i0] = siz;
pp[0].x[i0] = xx; gapx++; ngapx += siz; /* ignore MAXGAP when doing
endgaps */ siz = (siz < MAXGAP || endgaps)? siz : MAXGAP; i0++;
} } else break; } /* reverse the order of jmps */ for (j = 0, i0--;
j < i0; j++, i0--) { i = pp[0].n[j]; pp[0].n[j] = pp[0].n[i0];
pp[0].n[i0] = i; i = pp[0].x[j]; pp[0].x[j] = pp[0].x[i0];
pp[0].x[i0] = i; } for (j = 0, i1--; j < i1; j++, i1--) { i =
pp[1].n[j]; pp[1].n[j] = pp[1].n[i1]; pp[1].n[i1] = i; i =
pp[1].x[j]; pp[1].x[j] = pp[1].x[i1]; pp[1].x[i1] = i; } if (fd
>= 0) (void) close(fd); if (fj) { (void) unlink(jname); fj = 0;
offset = 0; } } /* * write a filled jmp struct offset of the prev
one (if any): nw( ) */ writejmps(ix) writejmps int ix; { char
*mktemp( ); if (!fj) { if (mktemp(jname) < 0) { fprintf(stderr,
"%s: can't mktemp( ) %s\n", prog, jname); cleanup(1); } if ((fj =
fopen(jname, "w")) == 0) { fprintf(stderr, "%s: can't write %s\n",
prog, jname); exit(1); } } (void) fwrite((char *)&dx[ix].jp,
sizeof(struct jmp), 1, fj); (void) fwrite((char
*)&dx[ix].offset, sizeof(dx[ix].offset), 1, fj); }
TABLE-US-00002 TABLE 2 PRO XXXXXXXXXXXXXXX (Length = 15 amino
acids) Comparison XXXXXYYYYYYY (Length = 12 amino acids) Protein %
amino acid sequence identity = (the number of identically matching
amino acid residues between the two polypeptide sequences as
determined by ALIGN-2) divided by (the total number of amino acid
residues of the PRO polypeptide) = 5 divided by 15 = 33.3%
TABLE-US-00003 TABLE 3 PRO XXXXXXXXXX (Length = 10 amino acids)
Comparison XXXXXYYYYYYZZYZ (Length = 15 amino acids) Protein %
amino acid sequence identity = (the number of identically matching
amino acid residues between the two polypeptide sequences as
determined by ALIGN-2) divided by (the total number of amino acid
residues of the PRO polypeptide) = 5 divided by 10 = 50%
TABLE-US-00004 TABLE 4 PRO-DNA NNNNNNNNNNNNNN (Length = 14
nucleotides) Comparison NNNNNNLLLLLLLLLL (Length = 16 nucleotides)
DNA % nucleic acid sequence identity = (the number of identically
matching nucleotides between the two nucleic acid sequences as
determined by ALIGN-2) divided by (the total number of nucleotides
of the PRO-DNA nucleic acid sequence) = 6 divided by 14 = 42.9%
TABLE-US-00005 TABLE 5 PRO-DNA NNNNNNNNNNNN (Length = 12
nucleotides) Comparison DNA NNNNLLLVV (Length = 9 nucleotides) %
nucleic acid sequence identity = (the number of identically
matching nucleotides between the two nucleic acid sequences as
determined by ALIGN-2) divided by (the total number of nucleotides
of the PRO-DNA nucleic acid sequence) = 4 divided by 12 = 33.3%
II. Compositions and Methods of the Invention
[0186] A. Full-Length PRO Polypeptides
[0187] The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO polypeptides. In particular, cDNAs
encoding various PRO polypeptides have been identified and
isolated, as disclosed in further detail in the Examples below. It
is noted that proteins produced in separate expression rounds may
be given different PRO numbers but the UNQ number is unique for any
given DNA and the encoded protein, and will not be changed.
However, for sake of simplicity, in the present specification the
protein encoded by the full length native nucleic acid molecules
disclosed herein as well as all further native homologues and
variants included in the foregoing definition of PRO, will be
referred to as "PRO/number", regardless of their origin or mode of
preparation.
[0188] As disclosed in the Examples below, various cDNA clones have
been deposited with the ATCC. The actual nucleotide sequences of
those clones can readily be determined by the skilled artisan by
sequencing of the deposited clone using routine methods in the art.
The predicted amino acid sequence can be determined from the
nucleotide sequence using routine skill. For the PRO polypeptides
and encoding nucleic acids described herein, Applicants have
identified what is believed to be the reading frame best
identifiable with the sequence information available at the
time.
[0189] B. PRO Polypeptide Variants
[0190] In addition to the full-length native sequence PRO
polypeptides described herein, it is contemplated that PRO variants
can be prepared. PRO variants can be prepared by introducing
appropriate nucleotide changes into the PRO DNA, and/or by
synthesis of the desired PRO polypeptide. Those skilled in the art
will appreciate that amino acid changes may alter
post-translational processes of the PRO, such as changing the
number or position of glycosylation sites or altering the membrane
anchoring characteristics.
[0191] Variations in the native full-length sequence PRO or in
various domains of the PRO described herein, can be made, for
example, using any of the techniques and guidelines for
conservative and non-conservative mutations set forth, for
instance, in U.S. Pat. No. 5,364,934. Variations may be a
substitution, deletion or insertion of one or more codons encoding
the PRO that results in a change in the amino acid sequence of the
PRO as compared with the native sequence PRO. Optionally the
variation is by substitution of at least one amino acid with any
other amino acid in one or more of the domains of the PRO. Guidance
in determining which amino acid residue may be inserted,
substituted or deleted without adversely affecting the desired
activity may be found by comparing the sequence of the PRO with
that of homologous known protein molecules and minimizing the
number of amino acid sequence changes made in regions of high
homology. Amino acid substitutions can be the result of replacing
one amino acid with another amino acid having similar structural
and/or chemical properties, such as the replacement of a leucine
with a serine, i.e., conservative amino acid replacements.
Insertions or deletions may optionally be in the range of about 1
to 5 amino acids. The variation allowed may be determined by
systematically making insertions, deletions or substitutions of
amino acids in the sequence and testing the resulting variants for
activity exhibited by the full-length or mature native
sequence.
[0192] PRO polypeptide fragments are provided herein. Such
fragments may be truncated at the N-terminus or C-terminus, or may
lack internal residues, for example, when compared with a full
length native protein. Certain fragments lack amino acid residues
that are not essential for a desired biological activity of the PRO
polypeptide.
[0193] PRO fragments may be prepared by any of a number of
conventional techniques. Desired peptide fragments may be
chemically synthesized. An alternative approach involves generating
PRO fragments by enzymatic digestion, e.g., by treating the protein
with an enzyme known to cleave proteins at sites defined by
particular amino acid residues, or by digesting the DNA with
suitable restriction enzymes and isolating the desired fragment.
Yet another suitable technique involves isolating and amplifying a
DNA fragment encoding a desired polypeptide fragment, by polymerase
chain reaction (PCR). Oligonucleotides that define the desired
termini of the DNA fragment are employed at the 5' and 3' primers
in the PCR. Preferably, PRO polypeptide fragments share at least
one biological and/or immunological activity with the native PRO
polypeptide disclosed herein.
[0194] In particular embodiments, conservative substitutions of
interest are shown in Table 6 under the heading of preferred
substitutions. If such substitutions result in a change in
biological activity, then more substantial changes, denominated
exemplary substitutions in Table 6, or as further described below
in reference to amino acid classes, are introduced and the products
screened.
TABLE-US-00006 TABLE 6 Original Exemplary Preferred Residue
Substitutions Substitutions Ala (A) val; leu; ile val Arg (R) lys;
gln; asn lys Asn (N) gln; his; lys; arg gln Asp (D) glu glu Cys (C)
ser ser Gln (Q) asn asn Glu (E) asp asp Gly (G) pro; ala ala His
(H) asn; gln; lys; arg arg Ile (I) leu; val; met; ala; phe; leu
norleucine Leu (L) norleucine; ile; val; ile met; ala; phe Lys (K)
arg; gln; asn arg Met (M) leu; phe; ile leu Phe (F) leu; val; ile;
ala; tyr leu Pro (P) ala ala Ser (S) thr thr Thr (T) ser ser Trp
(W) tyr; phe tyr Tyr (Y) trp; phe; thr; ser phe Val (V) ile; leu;
met; phe; leu ala; norleucine
[0195] Substantial modifications in function or immunological
identity of the PRO polypeptide are accomplished by selecting
substitutions that differ significantly in their effect on
maintaining (a) the structure of the polypeptide backbone in the
area of the substitution, for example, as a sheet or helical
conformation, (b) the charge or hydrophobicity of the molecule at
the target site, or (c) the bulk of the side chain. Naturally
occurring residues are divided into groups based on common
side-chain properties:
(1) hydrophobic: norleucine, met, ala, val, leu, ile; (2) neutral
hydrophilic: cys, ser, thr; (3) acidic: asp, glu; (4) basic: asn,
gln, his, lys, arg; (5) residues that influence chain orientation:
gly, pro; and (6) aromatic: trp, tyr, phe.
[0196] Non-conservative substitutions will entail exchanging a
member of one of these classes for another class. Such substituted
residues also may be introduced into the conservative substitution
sites or, more preferably, into the remaining (non-conserved)
sites.
[0197] The variations can be made using methods known in the art
such as oligonucleotide-mediated (site-directed) mutagenesis,
alanine scanning, and PCR mutagenesis. Site-directed mutagenesis
[Carter et al., Nucl. Acids Res., 13:4331 (1986); Zoller et al.,
Nucl. Acids Res., 10:6487 (1987)], cassette mutagenesis (Wells et
al., Gene, 34:315 [1985]), restriction selection mutagenesis (Wells
et al., Philos. Trans. R. Soc. London SerA, 317:415 [1986]) or
other known techniques can be performed on the cloned DNA to
produce the PRO variant DNA.
[0198] Scanning amino acid analysis can also be employed to
identify one or more amino acids along a contiguous sequence. Among
the preferred scanning amino acids are relatively small, neutral
amino acids. Such amino acids include alanine, glycine, serine, and
cysteine. Alanine is typically a preferred scanning amino acid
among this group because it eliminates the side-chain beyond the
beta-carbon and is less likely to alter the main-chain conformation
of the variant (Cunningham and Wells, Science 244: 1081-1085
[1989]). Alanine is also typically preferred because it is the most
common amino acid. Further, it is frequently found in both buried
and exposed positions (Creighton, The Proteins, (W.H. Freeman &
Co., N.Y.); Chothia, J. Mol. Biol., 150:1 [1976]). If alanine
substitution does not yield adequate amounts of variant, an
isoteric amino acid can be used.
[0199] C. Modifications of PRO
[0200] Covalent modifications of PRO are included within the scope
of this invention. One type of covalent modification includes
reacting targeted amino acid residues of a PRO polypeptide with an
organic derivatizing agent that is capable of reacting with
selected side chains or the N- or C-terminal residues of the PRO.
Derivatization with bifunctional agents is useful, for instance,
for crosslinking PRO to a water-insoluble support matrix or surface
for use in the method for purifying anti-PRO antibodies, and
vice-versa. Commonly used crosslinking agents include, e.g.,
1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde,
N-hydroxysuccinimide esters, for example, esters with
4-azidosalicylic acid, homobifunctional imidoesters, including
disuccinimidyl esters such as
3,3'-dithiobis(succinimidylpropionate), bifunctional maleimides
such as bis-N-maleimido-1,8-octane and agents such as
methyl-3-[(p-azidophenyl)dithio]propioimidate.
[0201] Other modifications include deamidation of glutaminyl and
asparaginyl residues to the corresponding glutamyl and aspartyl
residues, respectively, hydroxylation of proline and lysine,
phosphorylation of hydroxyl groups of seryl or threonyl residues,
methylation of the .alpha.-amino groups of lysine, arginine, and
histidine side chains [T. E. Creighton, Proteins: Structure and
Molecular Properties, W.H. Freeman & Co., San Francisco, pp.
79-86 (1983)], acetylation of the N-terminal amine, and amidation
of any C-terminal carboxyl group.
[0202] Another type of covalent modification of the PRO polypeptide
included within the scope of this invention comprises altering the
native glycosylation pattern of the polypeptide. "Altering the
native glycosylation pattern" is intended for purposes herein to
mean deleting one or more carbohydrate moieties found in native
sequence PRO (either by removing the underlying glycosylation site
or by deleting the glycosylation by chemical and/or enzymatic
means), and/or adding one or more glycosylation sites that are not
present in the native sequence PRO. In addition, the phrase
includes qualitative changes in the glycosylation of the native
proteins, involving a change in the nature and proportions of the
various carbohydrate moieties present.
[0203] Addition of glycosylation sites to the PRO polypeptide may
be accomplished by altering the amino acid sequence. The alteration
may be made, for example, by the addition of, or substitution by,
one or more serine or threonine residues to the native sequence PRO
(for O-linked glycosylation sites). The PRO amino acid sequence may
optionally be altered through changes at the DNA level,
particularly by mutating the DNA encoding the PRO polypeptide at
preselected bases such that codons are generated that will
translate into the desired amino acids.
[0204] Another means of increasing the number of carbohydrate
moieties on the PRO polypeptide is by chemical or enzymatic
coupling of glycosides to the polypeptide. Such methods are
described in the art, e.g., in WO 87/05330 published 11 Sep. 1987,
and in Aplin and Wriston, CRC Crit. Rev. Biochem., pp. 259-306
(1981).
[0205] Removal of carbohydrate moieties present on the PRO
polypeptide may be accomplished chemically or enzymatically or by
mutational substitution of codons encoding for amino acid residues
that serve as targets for glycosylation. Chemical deglycosylation
techniques are known in the art and described, for instance, by
Hakimuddin, et al., Arch. Biochem. Biophys., 259:52 (1987) and by
Edge et al, Anal. Biochem., 118:131 (1981). Enzymatic cleavage of
carbohydrate moieties on polypeptides can be achieved by the use of
a variety of endo- and exo-glycosidases as described by Thotakura
et al., Meth. Enzymol., 138:350 (1987).
[0206] Another type of covalent modification of PRO comprises
linking the PRO polypeptide to one of a variety of nonproteinaceous
polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or
polyoxyalkylenes, in the manner set forth in U.S. Pat. Nos.
4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or
4,179,337.
[0207] The PRO of the present invention may also be modified in a
way to form a chimeric molecule comprising PRO fused to another,
heterologous polypeptide or amino acid sequence.
[0208] In one embodiment, such a chimeric molecule comprises a
fusion of the PRO with a tag polypeptide which provides an epitope
to which an anti-tag antibody can selectively bind. The epitope tag
is generally placed at the amino- or carboxyl-terminus of the PRO.
The presence of such epitope-tagged forms of the PRO can be
detected using an antibody against the tag polypeptide. Also,
provision of the epitope tag enables the PRO to be readily purified
by affinity purification using an anti-tag antibody or another type
of affinity matrix that binds to the epitope tag. Various tag
polypeptides and their respective antibodies are well known in the
art. Examples include poly-histidine (poly-his) or
poly-histidine-glycine (poly-his-gly) tags; the flu HA tag
polypeptide and its antibody 12CA5 [Field et al., Mol. Cell. Biol.,
8:2159-2165 (1988)]; the c-myc tag and the 8F9, 3C7, 6E10, G4, B7
and 9E10 antibodies thereto [Evan et al., Molecular and Cellular
Biology, 5:3610-3616 (1985)]; and the Herpes Simplex virus
glycoprotein D (gD) tag and its antibody [Paborsky et al., Protein
Engineering, 3(6):547-553 (1990)]. Other tag polypeptides include
the Flag-peptide [Hopp et al., BioTechnology, 6:1204-1210 (1988)];
the KT3 epitope peptide [Martin et al., Science, 255: 192-194
(1992)]; an .alpha.-tubulin epitope peptide [Skinner et al., J.
Biol. Chem., 266:15163-15166 (1991)]; and the T7 gene 10 protein
peptide tag [Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. USA,
87:6393-6397 (1990)].
[0209] In an alternative embodiment, the chimeric molecule may
comprise a fusion of the PRO with an immunoglobulin or a particular
region of an immunoglobulin. For a bivalent form of the chimeric
molecule (also referred to as an "immunoadhesin"), such a fusion
could be to the Fc region of an IgG molecule. The Ig fusions
preferably include the substitution of a soluble (transmembrane
domain deleted or inactivated) form of a PRO polypeptide in place
of at least one variable region within an Ig molecule. In a
particularly preferred embodiment, the immunoglobulin fusion
includes the hinge, CH2 and CH3, or the hinge, CH1, CH2 and CH3
regions of an IgG1 molecule. For the production of immunoglobulin
fusions see also U.S. Pat. No. 5,428,130 issued Jun. 27, 1995.
[0210] In yet a further embodiment, the PRO polypeptides of the
present invention may also be modified in a way to form a chimeric
molecule comprising a PRO polypeptide fused to a leucine zipper.
Various leucine zipper polypeptides have been described in the art.
See, e.g., Landschulz et al., Science. 240:1759 (1988); WO
94/10308; Hoppe et al., FEBS Letters, 344:1991 (1994); Maniatis et
al., Nature, 341:24 (1989). It is believed that use of a leucine
zipper fused to a PRO polypeptide may be desirable to assist in
dimerizing or trimerizing soluble PRO polypeptide in solution.
Those skilled in the art will appreciate that the leucine zipper
may be fused at either the N- or C-terminal end of the PRO
molecule.
[0211] D. Preparation of PRO
[0212] The description below relates primarily to production of PRO
by culturing cells transformed or transfected with a vector
containing PRO nucleic acid. It is, of course, contemplated that
alternative methods, which are well known in the art, may be
employed to prepare PRO. For instance, the PRO sequence, or
portions thereof, may be produced by direct peptide synthesis using
solid-phase techniques [see, e.g., Stewart et al., Solid-Phase
Peptide Synthesis, W.H. Freeman Co., San Francisco, Calif. (1969);
Merrifield, J. Am. Chem. Soc., 85:2149-2154 (1963)]. In vitro
protein synthesis may be performed using manual techniques or by
automation. Automated synthesis may be accomplished, for instance,
using an Applied Biosystems Peptide Synthesizer (Foster City,
Calif.) using manufacturer's instructions. Various portions of the
PRO may be chemically synthesized separately and combined using
chemical or enzymatic methods to produce the full-length PRO.
1. Isolation of DNA Encoding PRO
[0213] DNA encoding PRO may be obtained from a cDNA library
prepared from tissue believed to possess the PRO mRNA and to
express it at a detectable level. Accordingly, human PRO DNA can be
conveniently obtained from a cDNA library prepared from human
tissue, such as described in the Examples. The PRO-encoding gene
may also be obtained from a genomic library or by known synthetic
procedures (e.g., automated nucleic acid synthesis).
[0214] Libraries can be screened with probes (such as antibodies to
the PRO or oligonucleotides of at least about 20-80 bases) designed
to identify the gene of interest or the protein encoded by it.
Screening the cDNA or genomic library with the selected probe may
be conducted using standard procedures, such as described in
Sambrook et al., Molecular Cloning: A Laboratory Manual (New York:
Cold Spring Harbor Laboratory Press, 1989). An alternative means to
isolate the gene encoding PRO is to use PCR methodology [Sambrook
et al., supra; Dieffenbach et al., PCR Primer: A Laboratory Manual
(Cold Spring Harbor Laboratory Press, 1995)].
[0215] The Examples below describe techniques for screening a cDNA
library. The oligonucleotide sequences selected as probes should be
of sufficient length and sufficiently unambiguous that false
positives are minimized. The oligonucleotide is preferably labeled
such that it can be detected upon hybridization to DNA in the
library being screened. Methods of labeling are well known in the
art, and include the use of radiolabels like .sup.32P-labeled ATP,
biotinylation or enzyme labeling. Hybridization conditions,
including moderate stringency and high stringency, are provided in
Sambrook et al., supra.
[0216] Sequences identified in such library screening methods can
be compared and aligned to other known sequences deposited and
available in public databases such as GenBank or other private
sequence databases. Sequence identity (at either the amino acid or
nucleotide level) within defined regions of the molecule or across
the full-length sequence can be determined using methods known in
the art and as described herein.
[0217] Nucleic acid having protein coding sequence may be obtained
by screening selected cDNA or genomic libraries using the deduced
amino acid sequence disclosed herein for the first time, and, if
necessary, using conventional primer extension procedures as
described in Sambrook et al., supra, to detect precursors and
processing intermediates of mRNA that may not have been
reverse-transcribed into cDNA.
2. Selection and Transformation of Host Cells
[0218] Host cells are transfected or transformed with expression or
cloning vectors described herein for PRO production and cultured in
conventional nutrient media modified as appropriate for inducing
promoters, selecting transformants, or amplifying the genes
encoding the desired sequences. The culture conditions, such as
media, temperature, pH and the like, can be selected by the skilled
artisan without undue experimentation. In general, principles,
protocols, and practical techniques for maximizing the productivity
of cell cultures can be found in Mammalian Cell Biotechnology: a
Practical Approach, M. Butler, ed. (IRL Press, 1991) and Sambrook
et al., supra.
[0219] Methods of eukaryotic cell transfection and prokaryotic cell
transformation are known to the ordinarily skilled artisan, for
example, CaCl.sub.2, CaPO.sub.4, liposome-mediated and
electroporation. Depending on the host cell used, transformation is
performed using standard techniques appropriate to such cells. The
calcium treatment employing calcium chloride, as described in
Sambrook et al., supra, or electroporation is generally used for
prokaryotes. Infection with Agrobacterium tumefaciens is used for
transformation of certain plant cells, as described by Shaw et al.,
Gene, 23:315 (1983) and WO 89/05859 published 29 Jun. 1989. For
mammalian cells without such cell walls, the calcium phosphate
precipitation method of Graham and van der Eb, Virology, 52:456-457
(1978) can be employed. General aspects of mammalian cell host
system transfections have been described in U.S. Pat. No.
4,399,216. Transformations into yeast are typically carried out
according to the method of Van Solingen et al., J. Bact., 130:946
(1977) and Hsiao et al., Proc. Natl. Acad. Sci. (USA), 76:3829
(1979). However, other methods for introducing DNA into cells, such
as by nuclear microinjection, electroporation, bacterial protoplast
fusion with intact cells, or polycations, e.g., polybrene,
polyornithine, may also be used. For various techniques for
transforming mammalian cells, see Keown et al., Methods in
Enzymology, 185:527-537 (1990) and Mansour et al., Nature,
336:348-352 (1988).
[0220] Suitable host cells for cloning or expressing the DNA in the
vectors herein include prokaryote, yeast, or higher eukaryote
cells. Suitable prokaryotes include but are not limited to
eubacteria, such as Gram-negative or Gram-positive organisms, for
example, Enterobacteriaceae such as E. coli. Various E. coli
strains are publicly available, such as E. coli K12 strain MM294
(ATCC 31,446); E. coli X1776 (ATCC 31,537); E. coli strain W3110
(ATCC 27,325) and K5772 (ATCC 53,635). Other suitable prokaryotic
host cells include Enterobacteriaceae such as Escherichia, e.g., E.
coli, Enterobacter, Erwinia, Klebsiella, Proteus, Salmonella, e.g.,
Salmonella typhimurium, Serratia, e.g., Serratia marcescans, and
Shigella, as well as Bacilli such as B. subtilis and B.
licheniformis (e.g., B. licheniformis 41P disclosed in DD 266,710
published 12 Apr. 1989), Pseudomonas such as P. aeruginosa, and
Streptomyces. These examples are illustrative rather than limiting.
Strain W3110 is one particularly preferred host or parent host
because it is a common host strain for recombinant DNA product
fermentations. Preferably, the host cell secretes minimal amounts
of proteolytic enzymes. For example, strain W3110 may be modified
to effect a genetic mutation in the genes encoding proteins
endogenous to the host, with examples of such hosts including E.
coli W3110 strain 1A2, which has the complete genotype tonA ; E.
coli W3110 strain 9E4, which has the complete genotype tonA ptr3;
E. coli W3110 strain 27C7 (ATCC 55,244), which has the complete
genotype tonA ptr3 phoA E15 (argF-lac)I69 degP ompT kan.sup.r; E.
coli W3110 strain 37D6, which has the complete genotype tonA ptr3
phoA E15 (argF-lac)I69 degP ompT rbs7 ilvG kan.sup.r; E. coli W3110
strain 40B4, which is strain 37D6 with a non-kanamycin resistant
degP deletion mutation; and an E. coli strain having mutant
periplasmic protease disclosed in U.S. Pat. No. 4,946,783 issued 7
Aug. 1990. Alternatively, in vitro methods of cloning, e.g., PCR or
other nucleic acid polymerase reactions, are suitable.
[0221] In addition to prokaryotes, eukaryotic microbes such as
filamentous fungi or yeast are suitable cloning or expression hosts
for PRO-encoding vectors. Saccharomyces cerevisiae is a commonly
used lower eukaryotic host microorganism. Others include
Schizosaccharomyces pombe [Beach and Nurse, Nature, 290: 140
(1981); EP 139,383 published 2 May 1985]; Kluyveromyces hosts (U.S.
Pat. No. 4,943,529; Fleer et al., Bio/Technology, 9:968-975 [1991])
such as, e.g., K. lactis (MW98-8C, CBS683, CBS4574; Louvencourt et
al., J. Bacteriol., 154(2):737-742 [1983]), K. fragilis (ATCC
12,424), K. bulgaricus (ATCC 16,045), K. wickeramii (ATCC 24,178),
K. waltii (ATCC 56,500), K. drosophilarum (ATCC 36,906; Van den
Berg et al., Bio/Technology, 8:135 [1990]), K. thermotolerans, and
K. marxianus; yarrowia (EP 402,226); Pichia pastoris (EP 183,070;
Sreekrishna et al., J. Basic Microbiol., 28:265-278 [1988]);
Candida; Trichoderma reesia (EP 244,234); Neurospora crassa (Case
et al., Proc. Natl. Acad. Sci. USA, 76:5259-5263 [1979]);
Schwanniomyces such as Schwanniomyces occidentalis (EP 394,538
published 31 Oct. 1990); and filamentous fungi such as, e.g.,
Neurospora, Penicillium, Tolypocladium (WO 91/00357 published 10
Jan. 1991), and Aspergillus hosts such as A. nidulans (Ballance et
al., Biochem. Biophys. Res. Commun., 112:284-289 [1983]; Tilburn et
al., Gene, 26:205-221 [1983]; Yelton et al., Proc. Natl. Acad. Sci.
USA, 81:1470-1474 [1984]) and A. niger (Kelly and Hynes, EMBO J.
4:475-479 [1985]). Methylotropic yeasts are suitable herein and
include, but are not limited to, yeast capable of growth on
methanol selected from the genera consisting of Hansenula, Candida,
Kloeckera, Pichia, Saccharomyces, Torulopsis, and Rhodotorula. A
list of specific species that are exemplary of this class of yeasts
may be found in C. Anthony, The Biochemistry of Methylotrophs, 269
(1982).
[0222] Suitable host cells for the expression of glycosylated PRO
are derived from multicellular organisms. Examples of invertebrate
cells include insect cells such as Drosophila S2 and Spodoptera Sf9
or Spodoptera High 5 cells, as well as plant cells. Examples of
useful mammalian host cell lines include Chinese hamster ovary
(CHO) and COS cells. More specific examples include monkey kidney
CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human
embryonic kidney line (293 or 293 cells subcloned for growth in
suspension culture, Graham et al., J. Gen Virol., 36:59 (1977));
Chinese hamster ovary cells/-DHFR(CHO, Urlaub and Chasin, Proc.
Natl. Acad. Sci. USA, 77:4216 [1980]); mouse sertoli cells (TM4,
Mather, Biol. Reprod., 23:243-251 [1980]); human lung cells (W138,
ATCC CCL 75); human liver cells (Hep G2, HB 8065); and mouse
mammary tumor (MMT 060562, ATCC CCL51). The selection of the
appropriate host cell is deemed to be within the skill in the
art.
3. Selection and Use of a Replicable Vector
[0223] The nucleic acid (e.g., cDNA or genomic DNA) encoding PRO
may be inserted into a replicable vector for cloning (amplification
of the DNA) or for expression. Various vectors are publicly
available. The vector may, for example, be in the form of a
plasmid, cosmid, viral particle, or phage. The appropriate nucleic
acid sequence may be inserted into the vector by a variety of
procedures. In general, DNA is inserted into an appropriate
restriction endonuclease site(s) using techniques known in the art.
Vector components generally include, but are not limited to, one or
more of a signal sequence, an origin of replication, one or more
marker genes, an enhancer element, a promoter, and a transcription
termination sequence. Construction of suitable vectors containing
one or more of these components employs standard ligation
techniques which are known to the skilled artisan.
[0224] The PRO may be produced recombinantly not only directly, but
also as a fusion polypeptide with a heterologous polypeptide, which
may be a signal sequence or other polypeptide having a specific
cleavage site at the N-terminus of the mature protein or
polypeptide. In general, the signal sequence may be a component of
the vector, or it may be a part of the PRO-encoding DNA that is
inserted into the vector. The signal sequence may be a prokaryotic
signal sequence selected, for example, from the group of the
alkaline phosphatase, penicillinase, lpp, or heat-stable
enterotoxin II leaders. For yeast secretion the signal sequence may
be, e.g., the yeast invertase leader, alpha factor leader
(including Saccharomyces and Kluyveromyces .alpha.-factor leaders,
the latter described in U.S. Pat. No. 5,010,182), or acid
phosphatase leader, the C. albicans glucoamylase leader (EP 362,179
published 4 Apr. 1990), or the signal described in WO 90/13646
published 15 Nov. 1990. In mammalian cell expression, mammalian
signal sequences may be used to direct secretion of the protein,
such as signal sequences from secreted polypeptides of the same or
related species, as well as viral secretory leaders.
[0225] Both expression and cloning vectors contain a nucleic acid
sequence that enables the vector to replicate in one or more
selected host cells. Such sequences are well known for a variety of
bacteria, yeast, and viruses. The origin of replication from the
plasmid pBR322 is suitable for most Gram-negative bacteria, the
2.mu. plasmid origin is suitable for yeast, and various viral
origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for
cloning vectors in mammalian cells.
[0226] Expression and cloning vectors will typically contain a
selection gene, also termed a selectable marker. Typical selection
genes encode proteins that (a) confer resistance to antibiotics or
other toxins, e.g., ampicillin, neomycin, methotrexate, or
tetracycline, (b) complement auxotrophic deficiencies, or (c)
supply critical nutrients not available from complex media, e.g.,
the gene encoding D-alanine racemase for Bacilli.
[0227] An example of suitable selectable markers for mammalian
cells are those that enable the identification of cells competent
to take up the PRO-encoding nucleic acid, such as DHFR or thymidine
kinase. An appropriate host cell when wild-type DHFR is employed is
the CHO cell line deficient in DHFR activity, prepared and
propagated as described by Urlaub et al., Proc. Natl. Acad. Sci.
USA, 77:4216 (1980). A suitable selection gene for use in yeast is
the trp1 gene present in the yeast plasmid YRp7 [Stinchcomb et al.,
Nature, 282:39 (1979); Kingsman et al., Gene, 7:141 (1979);
Tschemper et al., Gene, 10:157 (1980)]. The trp1 gene provides a
selection marker for a mutant strain of yeast lacking the ability
to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1
[Jones, Genetics, 85:12 (1977)].
[0228] Expression and cloning vectors usually contain a promoter
operably linked to the PRO-encoding nucleic acid sequence to direct
mRNA synthesis. Promoters recognized by a variety of potential host
cells are well known. Promoters suitable for use with prokaryotic
hosts include the .beta.-lactamase and lactose promoter systems
[Chang et al., Nature, 275:615 (1978); Goeddel et al., Nature,
281:544 (1979)], alkaline phosphatase, a tryptophan (trp) promoter
system [Goeddel, Nucleic Acids Res., 8:4057 (1980); EP 36,776], and
hybrid promoters such as the tac promoter [deBoer et al., Proc.
Natl. Acad. Sci. USA, 80:21-25 (1983)]. Promoters for use in
bacterial systems also will contain a Shine-Dalgarno (S.D.)
sequence operably linked to the DNA encoding PRO.
[0229] Examples of suitable promoting sequences for use with yeast
hosts include the promoters for 3-phosphoglycerate kinase [Hitzeman
et al., J. Biol. Chem., 255:2073 (1980)] or other glycolytic
enzymes [Hess et al., J. Adv. Enzyme Reg., 7: 149 (1968); Holland,
Biochemistry, 17:4900 (1978)], such as enolase,
glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate
decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase,
3-phosphoglycerate mutase, pyruvate kinase, triosephosphate
isomerase, phosphoglucose isomerase, and glucokinase.
[0230] Other yeast promoters, which are inducible promoters having
the additional advantage of transcription controlled by growth
conditions, are the promoter regions for alcohol dehydrogenase 2,
isocytochrome C, acid phosphatase, degradative enzymes associated
with nitrogen metabolism, metallothionein,
glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible
for maltose and galactose utilization. Suitable vectors and
promoters for use in yeast expression are further described in EP
73,657.
[0231] PRO transcription from vectors in mammalian host cells is
controlled, for example, by promoters obtained from the genomes of
viruses such as polyoma virus, fowlpox virus (UK 2,211,504
published 5 Jul. 1989), adenovirus (such as Adenovirus 2), bovine
papilloma virus, avian sarcoma virus, cytomegalovirus, a
retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from
heterologous mammalian promoters, e.g., the actin promoter or an
immunoglobulin promoter, and from heat-shock promoters, provided
such promoters are compatible with the host cell systems.
[0232] Transcription of a DNA encoding the PRO by higher eukaryotes
may be increased by inserting an enhancer sequence into the vector.
Enhancers are cis-acting elements of DNA, usually about from 10 to
300 bp, that act on a promoter to increase its transcription. Many
enhancer sequences are now known from mammalian genes (globin,
elastase, albumin, .alpha.-fetoprotein, and insulin). Typically,
however, one will use an enhancer from a eukaryotic cell virus.
Examples include the SV40 enhancer on the late side of the
replication origin (bp 100-270), the cytomegalovirus early promoter
enhancer, the polyoma enhancer on the late side of the replication
origin, and adenovirus enhancers. The enhancer may be spliced into
the vector at a position 5' or 3' to the PRO coding sequence, but
is preferably located at a site 5' from the promoter.
[0233] Expression vectors used in eukaryotic host cells (yeast,
fungi, insect, plant, animal, human, or nucleated cells from other
multicellular organisms) will also contain sequences necessary for
the termination of transcription and for stabilizing the mRNA. Such
sequences are commonly available from the 5' and, occasionally 3',
untranslated regions of eukaryotic or viral DNAs or cDNAs. These
regions contain nucleotide segments transcribed as polyadenylated
fragments in the untranslated portion of the mRNA encoding PRO.
[0234] Still other methods, vectors, and host cells suitable for
adaptation to the synthesis of PRO in recombinant vertebrate cell
culture are described in Gething et al., Nature, 293:620-625
(1981); Mantei et al., Nature, 281:40-46 (1979); EP 117,060; and EP
117,058.
4. Detecting Gene Amplification/Expression
[0235] Gene amplification and/or expression may be measured in a
sample directly, for example, by conventional Southern blotting,
Northern blotting to quantitate the transcription of mRNA (Thomas,
Proc. Natl. Acad. Sci. USA, 77:5201-5205 [1980]), dot blotting (DNA
analysis), or in situ hybridization, using an appropriately labeled
probe, based on the sequences provided herein. Alternatively,
antibodies may be employed that can recognize specific duplexes,
including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes
or DNA-protein duplexes. The antibodies in turn may be labeled and
the assay may be carried out where the duplex is bound to a
surface, so that upon the formation of duplex on the surface, the
presence of antibody bound to the duplex can be detected.
[0236] Gene expression, alternatively, may be measured by
immunological methods, such as immunohistochemical staining of
cells or tissue sections and assay of cell culture or body fluids,
to quantitate directly the expression of gene product. Antibodies
useful for immunohistochemical staining and/or assay of sample
fluids may be either monoclonal or polyclonal, and may be prepared
in any mammal. Conveniently, the antibodies may be prepared against
a native sequence PRO polypeptide or against a synthetic peptide
based on the DNA sequences provided herein or against exogenous
sequence fused to PRO DNA and encoding a specific antibody
epitope.
5. Purification of Polypeptide
[0237] Forms of PRO may be recovered from culture medium or from
host cell lysates. If membrane-bound, it can be released from the
membrane using a suitable detergent solution (e.g., Triton-X 100)
or by enzymatic cleavage. Cells employed in expression of PRO can
be disrupted by various physical or chemical means, such as
freeze-thaw cycling, sonication, mechanical disruption, or cell
lysing agents.
[0238] It may be desired to purify PRO from recombinant cell
proteins or polypeptides. The following procedures are exemplary of
suitable purification procedures: by fractionation on an
ion-exchange column; ethanol precipitation; reverse phase HPLC;
chromatography on silica or on a cation-exchange resin such as
DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation;
gel filtration using, for example, Sephadex G-75; protein A
Sepharose columns to remove contaminants such as IgG; and metal
chelating columns to bind epitope-tagged forms of the PRO. Various
methods of protein purification may be employed and such methods
are known in the art and described for example in Deutscher,
Methods in Enzymology, 182 (1990); Scopes, Protein Purification:
Principles and Practice, Springer-Verlag, New York (1982). The
purification step(s) selected will depend, for example, on the
nature of the production process used and the particular PRO
produced.
[0239] E. Uses for PRO
[0240] Nucleotide sequences (or their complement) encoding PRO have
various applications in the art of molecular biology, including
uses as hybridization probes, in chromosome and gene mapping and in
the generation of anti-sense RNA and DNA. PRO nucleic acid will
also be useful for the preparation of PRO polypeptides by the
recombinant techniques described herein.
[0241] The full-length native sequence PRO gene, or portions
thereof, may be used as hybridization probes for a cDNA library to
isolate the full-length PRO cDNA or to isolate still other cDNAs
(for instance, those encoding naturally-occurring variants of PRO
or PRO from other species) which have a desired sequence identity
to the native PRO sequence disclosed herein. Optionally, the length
of the probes will be about 20 to about 50 bases. The hybridization
probes may be derived from at least partially novel regions of the
full length native nucleotide sequence wherein those regions may be
determined without undue experimentation or from genomic sequences
including promoters, enhancer elements and introns of native
sequence PRO. By way of example, a screening method will comprise
isolating the coding region of the PRO gene using the known DNA
sequence to synthesize a selected probe of about 40 bases.
Hybridization probes may be labeled by a variety of labels,
including radionucleotides such as .sup.32P or .sup.35S, or
enzymatic labels such as alkaline phosphatase coupled to the probe
via avidin/biotin coupling systems. Labeled probes having a
sequence complementary to that of the PRO gene of the present
invention can be used to screen libraries of human cDNA, genomic
DNA or mRNA to determine which members of such libraries the probe
hybridizes to. Hybridization techniques are described in further
detail in the Examples below.
[0242] Any EST sequences disclosed in the present application may
similarly be employed as probes, using the methods disclosed
herein.
[0243] Other useful fragments of the PRO nucleic acids include
antisense or sense oligonucleotides comprising a singe-stranded
nucleic acid sequence (either RNA or DNA) capable of binding to
target PRO mRNA (sense) or PRO DNA (antisense) sequences. Antisense
or sense oligonucleotides, according to the present invention,
comprise a fragment of the coding region of PRO DNA. Such a
fragment generally comprises at least about 14 nucleotides,
preferably from about 14 to 30 nucleotides. The ability to derive
an antisense or a sense oligonucleotide, based upon a cDNA sequence
encoding a given protein is described in, for example, Stein and
Cohen (Cancer Res. 48:2659, [1988]) and van der Krol et al.
(BioTechniques, 6:958, [1988]).
[0244] Binding of antisense or sense oligonucleotides to target
nucleic acid sequences results in the formation of duplexes that
block transcription or translation of the target sequence by one of
several means, including enhanced degradation of the duplexes,
premature termination of transcription or translation, or by other
means. The antisense oligonucleotides thus may be used to block
expression of PRO proteins. Antisense or sense oligonucleotides
further comprise oligonucleotides having modified
sugar-phosphodiester backbones (or other sugar linkages, such as
those described in WO 91/06629) and wherein such sugar linkages are
resistant to endogenous nucleases. Such oligonucleotides with
resistant sugar linkages are stable in vivo (i.e., capable of
resisting enzymatic degradation) but retain sequence specificity to
be able to bind to target nucleotide sequences.
[0245] Other examples of sense or antisense oligonucleotides
include those oligonucleotides which are covalently linked to
organic moieties, such as those described in WO 90/10048, and other
moieties that increases affinity of the oligonucleotide for a
target nucleic acid sequence, such as poly-(L-lysine). Further
still, intercalating agents, such as ellipticine, and alkylating
agents or metal complexes may be attached to sense or antisense
oligonucleotides to modify binding specificities of the antisense
or sense oligonucleotide for the target nucleotide sequence.
[0246] Antisense or sense oligonucleotides may be introduced into a
cell containing the target nucleic acid sequence by any gene
transfer method, including, for example, CaPO.sub.4-mediated DNA
transfection, electroporation, or by using gene transfer vectors
such as Epstein-Barr virus. In a preferred procedure, an antisense
or sense oligonucleotide is inserted into a suitable retroviral
vector. A cell containing the target nucleic acid sequence is
contacted with the recombinant retroviral vector, either in vivo or
ex vivo. Suitable retroviral vectors include, but are not limited
to, those derived from the murine retrovirus M-MuLV, N2 (a
retrovirus derived from M-MuLV), or the double copy vectors
designated DCT5A, DCT5B and DCT5C (see WO 90/13641).
[0247] Sense or antisense oligonucleotides also may be introduced
into a cell containing the target nucleotide sequence by formation
of a conjugate with a ligand binding molecule, as described in WO
91/04753. Suitable ligand binding molecules include, but are not
limited to, cell surface receptors, growth factors, other
cytokines, or other ligands that bind to cell surface receptors.
Preferably, conjugation of the ligand binding molecule does not
substantially interfere with the ability of the ligand binding
molecule to bind to its corresponding molecule or receptor, or
block entry of the sense or antisense oligonucleotide or its
conjugated version into the cell.
[0248] Alternatively, a sense or an antisense oligonucleotide may
be introduced into a cell containing the target nucleic acid
sequence by formation of an oligonucleotide-lipid complex, as
described in WO 90/10448. The sense or antisense
oligonucleotide-lipid complex is preferably dissociated within the
cell by an endogenous lipase.
[0249] Antisense or sense RNA or DNA molecules are generally at
least about 5 bases in length, about 10 bases in length, about 15
bases in length, about 20 bases in length, about 25 bases in
length, about 30 bases in length, about 35 bases in length, about
40 bases in length, about 45 bases in length, about 50 bases in
length, about 55 bases in length, about 60 bases in length, about
65 bases in length, about 70 bases in length, about 75 bases in
length, about 80 bases in length, about 85 bases in length, about
90 bases in length, about 95 bases in length, about 100 bases in
length, or more.
[0250] The probes may also be employed in PCR techniques to
generate a pool of sequences for identification of closely related
PRO coding sequences.
[0251] Nucleotide sequences encoding a PRO can also be used to
construct hybridization probes for mapping the gene which encodes
that PRO and for the genetic analysis of individuals with genetic
disorders. The nucleotide sequences provided herein may be mapped
to a chromosome and specific regions of a chromosome using known
techniques, such as in situ hybridization, linkage analysis against
known chromosomal markers, and hybridization screening with
libraries.
[0252] When the coding sequences for PRO encode a protein which
binds to another protein (example, where the PRO is a receptor),
the PRO can be used in assays to identify the other proteins or
molecules involved in the binding interaction. By such methods,
inhibitors of the receptor/ligand binding interaction can be
identified. Proteins involved in such binding interactions can also
be used to screen for peptide or small molecule inhibitors or
agonists of the binding interaction. Also, the receptor PRO can be
used to isolate correlative ligand(s). Screening assays can be
designed to find lead compounds that mimic the biological activity
of a native PRO or a receptor for PRO. Such screening assays will
include assays amenable to high-throughput screening of chemical
libraries, making them particularly suitable for identifying small
molecule drug candidates. Small molecules contemplated include
synthetic organic or inorganic compounds. The assays can be
performed in a variety of formats, including protein-protein
binding assays, biochemical screening assays, immunoassays and cell
based assays, which are well characterized in the art.
[0253] Nucleic acids which encode PRO or its modified forms can
also be used to generate either transgenic animals or "knock out"
animals which, in turn, are useful in the development and screening
of therapeutically useful reagents. A transgenic animal (e.g., a
mouse or rat) is an animal having cells that contain a transgene,
which transgene was introduced into the animal or an ancestor of
the animal at a prenatal, e.g., an embryonic stage. A transgene is
a DNA which is integrated into the genome of a cell from which a
transgenic animal develops. In one embodiment, cDNA encoding PRO
can be used to clone genomic DNA encoding PRO in accordance with
established techniques and the genomic sequences used to generate
transgenic animals that contain cells which express DNA encoding
PRO. Methods for generating transgenic animals, particularly
animals such as mice or rats, have become conventional in the art
and are described, for example, in U.S. Pat. Nos. 4,736,866 and
4,870,009. Typically, particular cells would be targeted for PRO
transgene incorporation with tissue-specific enhancers. Transgenic
animals that include a copy of a transgene encoding PRO introduced
into the germ line of the animal at an embryonic stage can be used
to examine the effect of increased expression of DNA encoding PRO.
Such animals can be used as tester animals for reagents thought to
confer protection from, for example, pathological conditions
associated with its overexpression. In accordance with this facet
of the invention, an animal is treated with the reagent and a
reduced incidence of the pathological condition, compared to
untreated animals bearing the transgene, would indicate a potential
therapeutic intervention for the pathological condition.
[0254] Alternatively, non-human homologues of PRO can be used to
construct a PRO "knock out" animal which has a defective or altered
gene encoding PRO as a result of homologous recombination between
the endogenous gene encoding PRO and altered genomic DNA encoding
PRO introduced into an embryonic stem cell of the animal. For
example, cDNA encoding PRO can be used to clone genomic DNA
encoding PRO in accordance with established techniques. A portion
of the genomic DNA encoding PRO can be deleted or replaced with
another gene, such as a gene encoding a selectable marker which can
be used to monitor integration. Typically, several kilobases of
unaltered flanking DNA (both at the 5' and 3' ends) are included in
the vector [see e.g., Thomas and Capecchi, Cell, 51:503 (1987) for
a description of homologous recombination vectors]. The vector is
introduced into an embryonic stem cell line (e.g., by
electroporation) and cells in which the introduced DNA has
homologously recombined with the endogenous DNA are selected [see,
e.g., Li et al., Cell, 69:915 (1992)]. The selected cells are then
injected into a blastocyst of an animal (e.g., a mouse or rat) to
form aggregation chimeras [see, e.g., Bradley, in Teratocarcinomas
and Embryonic Stem Cells: A Practical Approach, E. J. Robertson,
ed. (IRL, Oxford, 1987), pp. 113-152]. A chimeric embryo can then
be implanted into a suitable pseudopregnant female foster animal
and the embryo brought to term to create a "knock out" animal.
Progeny harboring the homologously recombined DNA in their germ
cells can be identified by standard techniques and used to breed
animals in which all cells of the animal contain the homologously
recombined DNA. Knockout animals can be characterized for instance,
for their ability to defend against certain pathological conditions
and for their development of pathological conditions due to absence
of the PRO polypeptide.
[0255] Nucleic acid encoding the PRO polypeptides may also be used
in gene therapy. In gene therapy applications, genes are introduced
into cells in order to achieve in vivo synthesis of a
therapeutically effective genetic product, for example for
replacement of a defective gene. "Gene therapy" includes both
conventional gene therapy where a lasting effect is achieved by a
single treatment, and the administration of gene therapeutic
agents, which involves the one time or repeated administration of a
therapeutically effective DNA or mRNA. Antisense RNAs and DNAs can
be used as therapeutic agents for blocking the expression of
certain genes in vivo. It has already been shown that short
antisense oligonucleotides can be imported into cells where they
act as inhibitors, despite their low intracellular concentrations
caused by their restricted uptake by the cell membrane. (Zamecnik
et al., Proc. Natl. Acad. Sci. USA, 83:4143-4146 [1986]). The
oligonucleotides can be modified to enhance their uptake, e.g., by
substituting their negatively charged phosphodiester groups by
uncharged groups.
[0256] There are a variety of techniques available for introducing
nucleic acids into viable cells. The techniques vary depending upon
whether the nucleic acid is transferred into cultured cells in
vitro, or in vivo in the cells of the intended host. Techniques
suitable for the transfer of nucleic acid into mammalian cells in
vitro include the use of liposomes, electroporation,
microinjection, cell fusion, DEAE-dextran, the calcium phosphate
precipitation method, etc. The currently preferred in vivo gene
transfer techniques include transfection with viral (typically
retroviral) vectors and viral coat protein-liposome mediated
transfection (Dzau et al., Trends in Biotechnology, 11: 205-210
[1993]). In some situations it is desirable to provide the nucleic
acid source with an agent that targets the target cells, such as an
antibody specific for a cell surface membrane protein or the target
cell, a ligand for a receptor on the target cell, etc. Where
liposomes are employed, proteins which bind to a cell surface
membrane protein associated with endocytosis may be used for
targeting and/or to facilitate uptake, e.g., capsid proteins or
fragments thereof tropic for a particular cell type, antibodies for
proteins which undergo internalization in cycling, proteins that
target intracellular localization and enhance intracellular
half-life. The technique of receptor-mediated endocytosis is
described, for example, by Wu et al., J. Biol. Chem., 262:
4429-4432 (1987); and Wagner et al., Proc. Natl. Acad. Sci. USA,
87: 3410-3414 (1990). For review of gene marking and gene therapy
protocols see Anderson et al., Science, 256: 808-813 (1992).
[0257] The PRO polypeptides described herein may also be employed
as molecular weight markers for protein electrophoresis purposes
and the isolated nucleic acid sequences may be used for
recombinantly expressing those markers.
[0258] The nucleic acid molecules encoding the PRO polypeptides or
fragments thereof described herein are useful for chromosome
identification. In this regard, there exists an ongoing need to
identify new chromosome markers, since relatively few chromosome
marking reagents, based upon actual sequence data are presently
available. Each PRO nucleic acid molecule of the present invention
can be used as a chromosome marker.
[0259] The PRO polypeptides and nucleic acid molecules of the
present invention may also be used diagnostically for tissue
typing, wherein the PRO polypeptides of the present invention may
be differentially expressed in one tissue as compared to another,
preferably in a diseased tissue as compared to a normal tissue of
the same tissue type. PRO nucleic acid molecules will find use for
generating probes for PCR, Northern analysis, Southern analysis and
Western analysis.
[0260] The PRO polypeptides described herein may also be employed
as therapeutic agents. The PRO polypeptides of the present
invention can be formulated according to known methods to prepare
pharmaceutically useful compositions, whereby the PRO product
hereof is combined in admixture with a pharmaceutically acceptable
carrier vehicle. Therapeutic formulations are prepared for storage
by mixing the active ingredient having the desired degree of purity
with optional physiologically acceptable carriers, excipients or
stabilizers (Remington's Pharmaceutical Sciences 16th edition,
Osol, A. Ed. (1980)), in the form of lyophilized formulations or
aqueous solutions. Acceptable carriers, excipients or stabilizers
are nontoxic to recipients at the dosages and concentrations
employed, and include buffers such as phosphate, citrate and other
organic acids; antioxidants including ascorbic acid; low molecular
weight (less than about 10 residues) polypeptides; proteins, such
as serum albumin, gelatin or immunoglobulins; hydrophilic polymers
such as polyvinylpyrrolidone, amino acids such as glycine,
glutamine, asparagine, arginine or lysine; monosaccharides,
disaccharides and other carbohydrates including glucose, mannose,
or dextrins; chelating agents such as EDTA; sugar alcohols such as
mannitol or sorbitol; salt-forming counterions such as sodium;
and/or nonionic surfactants such as TWEEN.TM., PLURONICS.TM. or
PEG.
[0261] The formulations to be used for in vivo administration must
be sterile. This is readily accomplished by filtration through
sterile filtration membranes, prior to or following lyophilization
and reconstitution.
[0262] Therapeutic compositions herein generally are placed into a
container having a sterile access port, for example, an intravenous
solution bag or vial having a stopper pierceable by a hypodermic
injection needle.
[0263] The route of administration is in accord with known methods,
e.g., injection or infusion by intravenous, intraperitoneal,
intracerebral, intramuscular, intraocular, intraarterial or
intralesional routes, topical administration, or by sustained
release systems.
[0264] Dosages and desired drug concentrations of pharmaceutical
compositions of the present invention may vary depending on the
particular use envisioned. The determination of the appropriate
dosage or route of administration is well within the skill of an
ordinary physician. Animal experiments provide reliable guidance
for the determination of effective doses for human therapy.
Interspecies scaling of effective doses can be performed following
the principles laid down by Mordenti, J. and Chappell, W. "The use
of interspecies scaling in toxicokinetics" In Toxicokinetics and
New Drug Development, Yacobi et al., Eds., Pergamon Press, New York
1989, pp. 42-96.
[0265] When in vivo administration of a PRO polypeptide or agonist
or antagonist thereof is employed, normal dosage amounts may vary
from about 10 ng/kg to up to 100 mg/kg of mammal body weight or
more per day, preferably about 1 .mu.g/kg/day to 10 mg/kg/day,
depending upon the route of administration. Guidance as to
particular dosages and methods of delivery is provided in the
literature; see, for example, U.S. Pat. Nos. 4,657,760; 5,206,344;
or 5,225,212. It is anticipated that different formulations will be
effective for different treatment compounds and different
disorders, that administration targeting one organ or tissue, for
example, may necessitate delivery in a manner different from that
to another organ or tissue.
[0266] Where sustained-release administration of a PRO polypeptide
is desired in a formulation with release characteristics suitable
for the treatment of any disease or disorder requiring
administration of the PRO polypeptide, microencapsulation of the
PRO polypeptide is contemplated. Microencapsulation of recombinant
proteins for sustained release has been successfully performed with
human growth hormone (rhGH), interferon-(rhIFN-), interleukin-2,
and MN rgp120. Johnson et al., Nat. Med., 2:795-799 (1996); Yasuda,
Biomed. Ther., 27:1221-1223 (1993); Hora et al., Bio/Technology
8:755-758 (1990); Cleland, "Design and Production of Single
Immunization Vaccines Using Polylactide Polyglycolide Microsphere
Systems," in Vaccine Design: The Subunit and Adjuvant Approach,
Powell and Newman, eds, (Plenum Press: New York, 1995), pp.
439-462; WO 97/03692, WO 96/40072, WO 96/07399; and U.S. Pat. No.
5,654,010.
[0267] The sustained-release formulations of these proteins were
developed using poly-lactic-coglycolic acid (PLGA) polymer due to
its biocompatibility and wide range of biodegradable properties.
The degradation products of PLGA, lactic and glycolic acids, can be
cleared quickly within the human body. Moreover, the degradability
of this polymer can be adjusted from months to years depending on
its molecular weight and composition. Lewis, "Controlled release of
bioactive agents from lactide/glycolide polymer," in: M. Chasin and
R. Langer (Eds.), Biodegradable Polymers as Drug Delivery Systems
(Marcel Dekker: New York, 1990), pp. 141.
[0268] This invention encompasses methods of screening compounds to
identify those that mimic the PRO polypeptide (agonists) or prevent
the effect of the PRO polypeptide (antagonists). Screening assays
for antagonist drug candidates are designed to identify compounds
that bind or complex with the PRO polypeptides encoded by the genes
identified herein, or otherwise interfere with the interaction of
the encoded polypeptides with other cellular proteins. Such
screening assays will include assays amenable to high-throughput
screening of chemical libraries, making them particularly suitable
for identifying small molecule drug candidates.
[0269] The assays can be performed in a variety of formats,
including protein-protein binding assays, biochemical screening
assays, immunoassays, and cell-based assays, which are well
characterized in the art.
[0270] All assays for antagonists are common in that they call for
contacting the drug candidate with a PRO polypeptide encoded by a
nucleic acid identified herein under conditions and for a time
sufficient to allow these two components to interact.
[0271] In binding assays, the interaction is binding and the
complex formed can be isolated or detected in the reaction mixture.
In a particular embodiment, the PRO polypeptide encoded by the gene
identified herein or the drug candidate is immobilized on a solid
phase, e.g., on a microtiter plate, by covalent or non-covalent
attachments. Non-covalent attachment generally is accomplished by
coating the solid surface with a solution of the PRO polypeptide
and drying. Alternatively, an immobilized antibody, e.g., a
monoclonal antibody, specific for the PRO polypeptide to be
immobilized can be used to anchor it to a solid surface. The assay
is performed by adding the non-immobilized component, which may be
labeled by a detectable label, to the immobilized component, e.g.,
the coated surface containing the anchored component. When the
reaction is complete, the non-reacted components are removed, e.g.,
by washing, and complexes anchored on the solid surface are
detected. When the originally non-immobilized component carries a
detectable label, the detection of label immobilized on the surface
indicates that complexing occurred. Where the originally
non-immobilized component does not carry a label, complexing can be
detected, for example, by using a labeled antibody specifically
binding the immobilized complex.
[0272] If the candidate compound interacts with but does not bind
to a particular PRO polypeptide encoded by a gene identified
herein, its interaction with that polypeptide can be assayed by
methods well known for detecting protein-protein interactions. Such
assays include traditional approaches, such as, e.g.,
cross-linking, co-immunoprecipitation, and co-purification through
gradients or chromatographic columns. In addition, protein-protein
interactions can be monitored by using a yeast-based genetic system
described by Fields and co-workers (Fields and Song, Nature
(London), 340:245-246 [1989]); Chien et al., Proc. Natl. Acad. Sci.
USA, 88:9578-9582 [1991]) as disclosed by Chevray and Nathans,
Proc. Natl. Acad. Sci. USA, 89:5789-5793 (1991). Many
transcriptional activators, such as yeast GAL4, consist of two
physically discrete modular domains, one acting as the DNA-binding
domain, the other one functioning as the transcription-activation
domain. The yeast expression system described in the foregoing
publications (generally referred to as the "two-hybrid system")
takes advantage of this property, and employs two hybrid proteins,
one in which the target protein is fused to the DNA-binding domain
of GAL4, and another, in which candidate activating proteins are
fused to the activation domain. The expression of a GAL1-lacZ
reporter gene under control of a GAL4-activated promoter depends on
reconstitution of GAL4 activity via protein-protein interaction.
Colonies containing interacting polypeptides are detected with a
chromogenic substrate for .beta.-galactosidase. A complete kit
(MATCHMAKER.TM.) for identifying protein-protein interactions
between two specific proteins using the two-hybrid technique is
commercially available from Clontech. This system can also be
extended to map protein domains involved in specific protein
interactions as well as to pinpoint amino acid residues that are
crucial for these interactions.
[0273] Compounds that interfere with the interaction of a gene
encoding a PRO polypeptide identified herein and other intra- or
extracellular components can be tested as follows: usually a
reaction mixture is prepared containing the product of the gene and
the intra- or extracellular component under conditions and for a
time allowing for the interaction and binding of the two products.
To test the ability of a candidate compound to inhibit binding, the
reaction is run in the absence and in the presence of the test
compound. In addition, a placebo may be added to a third reaction
mixture, to serve as positive control. The binding (complex
formation) between the test compound and the intra- or
extracellular component present in the mixture is monitored as
described hereinabove. The formation of a complex in the control
reaction(s) but not in the reaction mixture containing the test
compound indicates that the test compound interferes with the
interaction of the test compound and its reaction partner.
[0274] To assay for antagonists, the PRO polypeptide may be added
to a cell along with the compound to be screened for a particular
activity and the ability of the compound to inhibit the activity of
interest in the presence of the PRO polypeptide indicates that the
compound is an antagonist to the PRO polypeptide. Alternatively,
antagonists may be detected by combining the PRO polypeptide and a
potential antagonist with membrane-bound PRO polypeptide receptors
or recombinant receptors under appropriate conditions for a
competitive inhibition assay. The PRO polypeptide can be labeled,
such as by radioactivity, such that the number of PRO polypeptide
molecules bound to the receptor can be used to determine the
effectiveness of the potential antagonist. The gene encoding the
receptor can be identified by numerous methods known to those of
skill in the art, for example, ligand panning and FACS sorting.
Coligan et al., Current Protocols in Immun., 1(2): Chapter 5
(1991). Preferably, expression cloning is employed wherein
polyadenylated RNA is prepared from a cell responsive to the PRO
polypeptide and a cDNA library created from this RNA is divided
into pools and used to transfect COS cells or other cells that are
not responsive to the PRO polypeptide. Transfected cells that are
grown on glass slides are exposed to labeled PRO polypeptide. The
PRO polypeptide can be labeled by a variety of means including
iodination or inclusion of a recognition site for a site-specific
protein kinase. Following fixation and incubation, the slides are
subjected to autoradiographic analysis. Positive pools are
identified and sub-pools are prepared and re-transfected using an
interactive sub-pooling and re-screening process, eventually
yielding a single clone that encodes the putative receptor.
[0275] As an alternative approach for receptor identification,
labeled PRO polypeptide can be photoaffinity-linked with cell
membrane or extract preparations that express the receptor
molecule. Cross-linked material is resolved by PAGE and exposed to
X-ray film. The labeled complex containing the receptor can be
excised, resolved into peptide fragments, and subjected to protein
micro-sequencing. The amino acid sequence obtained from
micro-sequencing would be used to design a set of degenerate
oligonucleotide probes to screen a cDNA library to identify the
gene encoding the putative receptor.
[0276] In another assay for antagonists, mammalian cells or a
membrane preparation expressing the receptor would be incubated
with labeled PRO polypeptide in the presence of the candidate
compound. The ability of the compound to enhance or block this
interaction could then be measured.
[0277] More specific examples of potential antagonists include an
oligonucleotide that binds to the fusions of immunoglobulin with
PRO polypeptide, and, in particular, antibodies including, without
limitation, poly- and monoclonal antibodies and antibody fragments,
single-chain antibodies, anti-idiotypic antibodies, and chimeric or
humanized versions of such antibodies or fragments, as well as
human antibodies and antibody fragments. Alternatively, a potential
antagonist may be a closely related protein, for example, a mutated
form of the PRO polypeptide that recognizes the receptor but
imparts no effect, thereby competitively inhibiting the action of
the PRO polypeptide.
[0278] Another potential PRO polypeptide antagonist is an antisense
RNA or DNA construct prepared using antisense technology, where,
e.g., an antisense RNA or DNA molecule acts to block directly the
translation of mRNA by hybridizing to targeted mRNA and preventing
protein translation. Antisense technology can be used to control
gene expression through triple-helix formation or antisense DNA or
RNA, both of which methods are based on binding of a polynucleotide
to DNA or RNA. For example, the 5' coding portion of the
polynucleotide sequence, which encodes the mature PRO polypeptides
herein, is used to design an antisense RNA oligonucleotide of from
about 10 to 40 base pairs in length. A DNA oligonucleotide is
designed to be complementary to a region of the gene involved in
transcription (triple helix--see Lee et al., Nucl. Acids Res.,
6:3073 (1979); Cooney et al., Science, 241:456 (1988); Dervan et
al., Science, 251:1360 (1991)), thereby preventing transcription
and the production of the PRO polypeptide. The antisense RNA
oligonucleotide hybridizes to the mRNA in vivo and blocks
translation of the mRNA molecule into the PRO polypeptide
(antisense-Okano, Neurochem., 56:560 (1991); Oligodeoxynucleotides
as Antisense Inhibitors of Gene Expression (CRC Press: Boca Raton,
Fla., 1988). The oligonucleotides described above can also be
delivered to cells such that the antisense RNA or DNA may be
expressed in vivo to inhibit production of the PRO polypeptide.
When antisense DNA is used, oligodeoxyribonucleotides derived from
the translation-initiation site, e.g., between about -10 and +10
positions of the target gene nucleotide sequence, are
preferred.
[0279] Potential antagonists include small molecules that bind to
the active site, the receptor binding site, or growth factor or
other relevant binding site of the PRO polypeptide, thereby
blocking the normal biological activity of the PRO polypeptide.
Examples of small molecules include, but are not limited to, small
peptides or peptide-like molecules, preferably soluble peptides,
and synthetic non-peptidyl organic or inorganic compounds.
[0280] Ribozymes are enzymatic RNA molecules capable of catalyzing
the specific cleavage of RNA. Ribozymes act by sequence-specific
hybridization to the complementary target RNA, followed by
endonucleolytic cleavage. Specific ribozyme cleavage sites within a
potential RNA target can be identified by known techniques. For
further details see, e.g., Rossi, Current Biology, 4:469-471
(1994), and PCT publication No. WO 97/33551 (published Sep. 18,
1997).
[0281] Nucleic acid molecules in triple-helix formation used to
inhibit transcription should be single-stranded and composed of
deoxynucleotides. The base composition of these oligonucleotides is
designed such that it promotes triple-helix formation via Hoogsteen
base-pairing rules, which generally require sizeable stretches of
purines or pyrimidines on one strand of a duplex. For further
details see, e.g., PCT publication No. WO 97/33551, supra.
[0282] These small molecules can be identified by any one or more
of the screening assays discussed hereinabove and/or by any other
screening techniques well known for those skilled in the art.
[0283] Diagnostic and therapeutic uses of the herein disclosed
molecules may also be based upon the positive functional assay hits
disclosed and described below
[0284] F. Tissue Distribution
[0285] The location of tissues expressing the PRO can be identified
by determining mRNA expression in various human tissues. The
location of such genes provides information about which tissues are
most likely to be affected by the stimulating and inhibiting
activities of the PRO polypeptides. The location of a gene in a
specific tissue also provides sample tissue for the activity
blocking assays discussed below.
[0286] As noted before, gene expression in various tissues may be
measured by conventional Southern blotting, Northern blotting to
quantitate the transcription of mRNA (Thomas, Proc. Natl. Acad.
Sci. USA, 77:5201-5205 [1980]), dot blotting (DNA analysis), or in
situ hybridization, using an appropriately labeled probe, based on
the sequences provided herein. Alternatively, antibodies may be
employed that can recognize specific duplexes, including DNA
duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein
duplexes.
[0287] Gene expression in various tissues, alternatively, may be
measured by immunological methods, such as immunohistochemical
staining of tissue sections and assay of cell culture or body
fluids, to quantitate directly the expression of gene product.
Antibodies useful for immunohistochemical staining and/or assay of
sample fluids may be either monoclonal or polyclonal, and may be
prepared in any mammal. Conveniently, the antibodies may be
prepared against a native sequence of a PRO polypeptide or against
a synthetic peptide based on the DNA sequences encoding the PRO
polypeptide or against an exogenous sequence fused to a DNA
encoding a PRO polypeptide and encoding a specific antibody
epitope. General techniques for generating antibodies, and special
protocols for Northern blotting and in situ hybridization are
provided below.
[0288] G. Antibody Binding Studies
[0289] The activity of the PRO polypeptides can be further verified
by antibody binding studies, in which the ability of anti-PRO
antibodies to inhibit the effect of the PRO polypeptides,
respectively, on tissue cells is tested. Exemplary antibodies
include polyclonal, monoclonal, humanized, bispecific, and
heteroconjugate antibodies, the preparation of which will be
described hereinbelow.
[0290] Antibody binding studies may be carried out in any known
assay method, such as competitive binding assays, direct and
indirect sandwich assays, and immunoprecipitation assays. Zola,
Monoclonal Antibodies: A Manual of Techniques, pp. 147-158 (CRC
Press, Inc., 1987).
[0291] Competitive binding assays rely on the ability of a labeled
standard to compete with the test sample analyte for binding with a
limited amount of antibody. The amount of target protein in the
test sample is inversely proportional to the amount of standard
that becomes bound to the antibodies. To facilitate determining the
amount of standard that becomes bound, the antibodies preferably
are insolubilized before or after the competition, so that the
standard and analyte that are bound to the antibodies may
conveniently be separated from the standard and analyte which
remain unbound.
[0292] Sandwich assays involve the use of two antibodies, each
capable of binding to a different immunogenic portion, or epitope,
of the protein to be detected. In a sandwich assay, the test sample
analyte is bound by a first antibody which is immobilized on a
solid support, and thereafter a second antibody binds to the
analyte, thus forming an insoluble three-part complex. See, e.g.,
U.S. Pat. No. 4,376,110. The second antibody may itself be labeled
with a detectable moiety (direct sandwich assays) or may be
measured using an anti-immunoglobulin antibody that is labeled with
a detectable moiety (indirect sandwich assay). For example, one
type of sandwich assay is an ELISA assay, in which case the
detectable moiety is an enzyme. For immunohistochemistry, the
tissue sample may be fresh or frozen or may be embedded in paraffin
and fixed with a preservative such as formalin, for example.
[0293] H. Cell-Based Assays
[0294] Cell-based assays and animal models for immune related
diseases can be used to further understand the relationship between
the genes and polypeptides identified herein and the development
and pathogenesis of immune related disease.
[0295] In a different approach, cells of a cell type known to be
involved in a particular immune related disease are transfected
with the cDNAs described herein, and the ability of these cDNAs to
stimulate or inhibit immune function is analyzed. Suitable cells
can be transfected with the desired gene, and monitored for immune
function activity. Such transfected cell lines can then be used to
test the ability of poly- or monoclonal antibodies or antibody
compositions to inhibit or stimulate immune function, for example
to modulate T-cell proliferation or inflammatory cell infiltration.
Cells transfected with the coding sequences of the genes identified
herein can further be used to identify drug candidates for the
treatment of immune related diseases.
[0296] In addition, primary cultures derived from transgenic
animals (as described below) can be used in the cell-based assays
herein, although stable cell lines are preferred. Techniques to
derive continuous cell lines from transgenic animals are well known
in the art (see, e.g., Small et al., Mol. Cell. Biol., 5: 642-648
[1985]).
[0297] One suitable cell based assay is the mixed lymphocyte
reaction (MLR). Current Protocols in Immunology, unit 3.12; edited
by J E Coligan, A M Kruisbeek, D H Marglies, E M Shevach, W
Strober, National Institutes of Health, Published by John Wiley
& Sons, Inc. In this assay, the ability of a test compound to
stimulate or inhibit the proliferation of activated T cells is
assayed. A suspension of responder T cells is cultured with
allogeneic stimulator cells and the proliferation of T cells is
measured by uptake of tritiated thymidine. This assay is a general
measure of T cell reactivity. Since the majority of T cells respond
to and produce IL-2 upon activation, differences in responsiveness
in this assay in part reflect differences in IL-2 production by the
responding cells. The MLR results can be verified by a standard
lymphokine (IL-2) detection assay. Current Protocols in Immunology,
above, 3.15, 6.3.
[0298] A proliferative T cell response in an MLR assay may be due
to direct mitogenic properties of an assayed molecule or to
external antigen induced activation. Additional verification of the
T cell stimulatory activity of the PRO polypeptides can be obtained
by a costimulation assay. T cell activation requires an antigen
specific signal mediated through the T-cell receptor (TCR) and a
costimulatory signal mediated through a second ligand binding
interaction, for example, the B7 (CD80, CD86)/CD28 binding
interaction. CD28 crosslinking increases lymphokine secretion by
activated T cells. T cell activation has both negative and positive
controls through the binding of ligands which have a negative or
positive effect. CD28 and CTLA-4 are related glycoproteins in the
Ig superfamily which bind to B7. CD28 binding to B7 has a positive
costimulation effect of T cell activation; conversely, CTLA-4
binding to B7 has a negative T cell deactivating effect. Chambers,
C. A. and Allison, J. P. Curr. Opin. Immunol., (1997) 9:396.
Schwartz, R. H., Cell (1992) 71:1065; Linsey, P. S. and Ledbetter,
J. A., Annu. Rev. Immunol. (1993) 11:191; June, C. H. et al.,
Immunol. Today (1994) 15:321; Jenkins, M. K., Immunity (1994)
1:405. In a costimulation assay, the PRO polypeptides are assayed
for T cell costimulatory or inhibitory activity.
[0299] PRO polypeptides, as well as other compounds of the
invention, which are stimulators (costimulators) of T cell
proliferation and agonists, e.g., agonist antibodies, thereto as
determined by MLR and costimulation assays, for example, are useful
in treating immune related diseases characterized by poor,
suboptimal or inadequate immune function. These diseases are
treated by stimulating the proliferation and activation of T cells
(and T cell mediated immunity) and enhancing the immune response in
a mammal through administration of a stimulatory compound, such as
the stimulating PRO polypeptides. The stimulating polypeptide may,
for example, be a PRO polypeptide or an agonist antibody
thereof.
[0300] Direct use of a stimulating compound as in the invention has
been validated in experiments with 4-1BB glycoprotein, a member of
the tumor necrosis factor receptor family, which binds to a ligand
(4-1BBL) expressed on primed T cells and signals T cell activation
and growth. Alderson, M. E. et al., J. Immunol., 24:2219
(1994).
[0301] The use of an agonist stimulating compound has also been
validated experimentally. Activation of 4-1BB by treatment with an
agonist anti-4-1BB antibody enhances eradication of tumors.
Hellstrom, I. and Hellstrom, K. E., Crit. Rev. Immunol., 18:1
(1998). Immunoadjuvant therapy for treatment of tumors, described
in more detail below, is another example of the use of the
stimulating compounds of the invention. An immune stimulating or
enhancing effect can also be achieved by antagonizing or blocking
the activity of a PRO which has been found to be inhibiting in the
MLR assay. Negating the inhibitory activity of the compound
produces a net stimulatory effect. Suitable antagonists/blocking
compounds are antibodies or fragments thereof which recognize and
bind to the inhibitory protein, thereby blocking the effective
interaction of the protein with its receptor and inhibiting
signaling through the receptor. This effect has been validated in
experiments using anti-CTLA-4 antibodies which enhance T cell
proliferation, presumably by removal of the inhibitory signal
caused by CTLA-4 binding. Walunas, T. L. et al., Immunity, 1:405
(1994).
[0302] Alternatively, an immune stimulating or enhancing effect can
also be achieved by administration of a PRO polypeptide which has
vascular permeability enhancing properties. Enhanced vacuolar
permeability would be beneficial to disorders which can be
attenuated by local infiltration of immune cells (e.g., monocytes,
eosinophils, PMNs) and inflammation.
[0303] On the other hand, PRO polypeptides, as well as other
compounds of the invention, which are direct inhibitors of T cell
proliferation/activation, lymphokine secretion, and/or vascular
permeability can be directly used to suppress the immune response.
These compounds are useful to reduce the degree of the immune
response and to treat immune related diseases characterized by a
hyperactive, superoptimal, or autoimmune response. This use of the
compounds of the invention has been validated by the experiments
described above in which CTLA-4 binding to receptor B7 deactivates
T cells. The direct inhibitory compounds of the invention function
in an analogous manner. The use of compound which suppress vascular
permeability would be expected to reduce inflammation. Such uses
would be beneficial in treating conditions associated with
excessive inflammation.
[0304] Alternatively, compounds, e.g., antibodies, which bind to
stimulating PRO polypeptides and block the stimulating effect of
these molecules produce a net inhibitory effect and can be used to
suppress the T cell mediated immune response by inhibiting T cell
proliferation/activation and/or lymphokine secretion. Blocking the
stimulating effect of the polypeptides suppresses the immune
response of the mammal. This use has been validated in experiments
using an anti-IL2 antibody. In these experiments, the antibody
binds to IL2 and blocks binding of IL2 to its receptor thereby
achieving a T cell inhibitory effect.
[0305] I. Animal Models
[0306] The results of the cell based in vitro assays can be further
verified using in vivo animal models and assays for T-cell
function. A variety of well known animal models can be used to
further understand the role of the genes identified herein in the
development and pathogenesis of immune related disease, and to test
the efficacy of candidate therapeutic agents, including antibodies,
and other antagonists of the native polypeptides, including small
molecule antagonists. The in vivo nature of such models makes them
predictive of responses in human patients. Animal models of immune
related diseases include both non-recombinant and recombinant
(transgenic) animals. Non-recombinant animal models include, for
example, rodent, e.g., murine models. Such models can be generated
by introducing cells into syngeneic mice using standard techniques,
e.g., subcutaneous injection, tail vein injection, spleen
implantation, intraperitoneal implantation, implantation under the
renal capsule, etc.
[0307] Graft-versus-host disease occurs when immunocompetent cells
are transplanted into immunosuppressed or tolerant patients. The
donor cells recognize and respond to host antigens. The response
can vary from life threatening severe inflammation to mild cases of
diarrhea and weight loss. Graft-versus-host disease models provide
a means of assessing T cell reactivity against MHC antigens and
minor transplant antigens. A suitable procedure is described in
detail in Current Protocols in Immunology, above, unit 4.3.
[0308] An animal model for skin allograft rejection is a means of
testing the ability of T cells to mediate in vivo tissue
destruction and a measure of their role in transplant rejection.
The most common and accepted models use murine tail-skin grafts.
Repeated experiments have shown that skin allograft rejection is
mediated by T cells, helper T cells and killer-effector T cells,
and not antibodies. Auchincloss, H. Jr. and Sachs, D. H.,
Fundamental Immunology, 2nd ed., W. E. Paul ed., Raven Press, NY,
889-992 (1989). A suitable procedure is described in detail in
Current Protocols in Immunology, above, unit 4.4. Other transplant
rejection models which can be used to test the compounds of the
invention are the allogeneic heart transplant models described by
Tanabe, M. et al., Transplantation, 58:23 (1994) and Tinubu, S. A.
et al., J. Immunol., 4330-4338 (1994).
[0309] Animal models for delayed type hypersensitivity provides an
assay of cell mediated immune function as well. Delayed type
hypersensitivity reactions are a T cell mediated in vivo immune
response characterized by inflammation which does not reach a peak
until after a period of time has elapsed after challenge with an
antigen. These reactions also occur in tissue specific autoimmune
diseases such as multiple sclerosis (MS) and experimental
autoimmune encephalomyelitis (EAE, a model for MS). A suitable
procedure is described in detail in Current Protocols in
Immunology, above, unit 4.5.
[0310] EAE is a T cell mediated autoimmune disease characterized by
T cell and mononuclear cell inflammation and subsequent
demyelination of axons in the central nervous system. EAE is
generally considered to be a relevant animal model for MS in
humans. Bolton, C., Multiple Sclerosis 1: 143 (1995). Both acute
and relapsing-remitting models have been developed. The compounds
of the invention can be tested for T cell stimulatory or inhibitory
activity against immune mediated demyelinating disease using the
protocol described in Current Protocols in Immunology, above, units
15.1 and 15.2. See also the models for myelin disease in which
oligodendrocytes or Schwann cells are grafted into the central
nervous system as described in Duncan, I. D. et al., Molec. Med.
Today, 554-561 (1997).
[0311] Contact hypersensitivity is a simple delayed type
hypersensitivity in vivo assay of cell mediated immune function. In
this procedure, cutaneous exposure to exogenous haptens which gives
rise to a delayed type hypersensitivity reaction which is measured
and quantitated. Contact sensitivity involves an initial
sensitizing phase followed by an elicitation phase. The elicitation
phase occurs when the T lymphocytes encounter an antigen to which
they have had previous contact. Swelling and inflammation occur,
making this an excellent model of human allergic contact
dermatitis. A suitable procedure is described in detail in Current
Protocols in Immunology, Eds. J. E. Cologan, A. M. Kruisbeek, D. H.
Margulies, E. M. Shevach and W. Strober, John Wiley & Sons,
Inc., unit 4.2 (1994). I also Grabbe, S, and Schwarz, T, Immun.
Today. 19 (1): 37-44 (1998).
[0312] An animal model for arthritis is collagen-induced arthritis.
This model shares clinical, histological and immunological
characteristics of human autoimmune rheumatoid arthritis and is an
acceptable model for human autoimmune arthritis. Mouse and rat
models are characterized by synovitis, erosion of cartilage and
subchondral bone. The compounds of the invention can be tested for
activity against autoimmune arthritis using the protocols described
in Current Protocols in Immunology, above, units 15.5. See also the
model using a monoclonal antibody to CD18 and VLA-4 integrins
described in Issekutz, A. C. et al., Immunology, 88:569 (1996).
[0313] A model of asthma has been described in which
antigen-induced airway hyper-reactivity, pulmonary eosinophilia and
inflammation are induced by sensitizing an animal with ovalbumin
and then challenging the animal with the same protein delivered by
aerosol. Several animal models (guinea pig, rat, non-human primate)
show symptoms similar to atopic asthma in humans upon challenge
with aerosol antigens. Murine models have many of the features of
human asthma. Suitable procedures to test the compounds of the
invention for activity and effectiveness in the treatment of asthma
are described by Wolyniec, W. W. et al., Am. J. Respir. Cell Mol.
Biol., 18:777 (1998) and the references cited therein.
[0314] Additionally, the compounds of the invention can be tested
on animal models for psoriasis like diseases. Evidence suggests a T
cell pathogenesis for psoriasis. The compounds of the invention can
be tested in the scid/scid mouse model described by Schon, M. P. et
al., Nat. Med., 3:183 (1997), in which the mice demonstrate
histopathologic skin lesions resembling psoriasis. Another suitable
model is the human skin/scid mouse chimera prepared as described by
Nickoloff, B. J. et al., Am. J. Path., 146:580 (1995).
[0315] Recombinant (transgenic) animal models can be engineered by
introducing the coding portion of the genes identified herein into
the genome of animals of interest, using standard techniques for
producing transgenic animals. Animals that can serve as a target
for transgenic manipulation include, without limitation, mice,
rats, rabbits, guinea pigs, sheep, goats, pigs, and non-human
primates, e.g., baboons, chimpanzees and monkeys. Techniques known
in the art to introduce a transgene into such animals include
pronucleic microinjection (Hoppe and Wanger, U.S. Pat. No.
4,873,191); retrovirus-mediated gene transfer into germ lines
(e.g., Van der Putten et al., Proc. Natl. Acad. Sci. USA , 82,
6148-615 [1985]); gene targeting in embryonic stem cells (Thompson
et al., Cell, 56, 313-321 [1989]); electroporation of embryos (Lo,
Mol. Cel. Biol., 3, 1803-1814 [1983]); sperm-mediated gene transfer
(Lavitrano et al., Cell, 57, 717-73 [1989]). For review, see, for
example, U.S. Pat. No. 4,736,866.
[0316] For the purpose of the present invention, transgenic animals
include those that carry the transgene only in part of their cells
("mosaic animals"). The transgene can be integrated either as a
single transgene, or in concatamers, e.g., head-to-head or
head-to-tail tandems. Selective introduction of a transgene into a
particular cell type is also possible by following, for example,
the technique of Lasko et al., Proc. Natl. Acad. Sci. USA. 89,
6232-636 (1992).
[0317] The expression of the transgene in transgenic animals can be
monitored by standard techniques. For example, Southern blot
analysis or PCR amplification can be used to verify the integration
of the transgene. The level of mRNA expression can then be analyzed
using techniques such as in situ hybridization, Northern blot
analysis, PCR, or immunocytochemistry.
[0318] The animals may be further examined for signs of immune
disease pathology, for example by histological examination to
determine infiltration of immune cells into specific tissues.
Blocking experiments can also be performed in which the transgenic
animals are treated with the compounds of the invention to
determine the extent of the T cell proliferation stimulation or
inhibition of the compounds. In these experiments, blocking
antibodies which bind to the PRO polypeptide, prepared as described
above, are administered to the animal and the effect on immune
function is determined.
[0319] Alternatively, "knock out" animals can be constructed which
have a defective or altered gene encoding a polypeptide identified
herein, as a result of homologous recombination between the
endogenous gene encoding the polypeptide and altered genomic DNA
encoding the same polypeptide introduced into an embryonic cell of
the animal. For example, cDNA encoding a particular polypeptide can
be used to clone genomic DNA encoding that polypeptide in
accordance with established techniques. A portion of the genomic
DNA encoding a particular polypeptide can be deleted or replaced
with another gene, such as a gene encoding a selectable marker
which can be used to monitor integration. Typically, several
kilobases of unaltered flanking DNA (both at the 5' and 3' ends)
are included in the vector [see e.g., Thomas and Capecchi, Cell,
51:503 (1987) for a description of homologous recombination
vectors]. The vector is introduced into an embryonic stem cell line
(e.g., by electroporation) and cells in which the introduced DNA
has homologously recombined with the endogenous DNA are selected
[see e.g., Li et al., Cell, 69:915 (1992)]. The selected cells are
then injected into a blastocyst of an animal (e.g., a mouse or rat)
to form aggregation chimeras [see e.g., Bradley, in
Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E.
J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-152]. A chimeric
embryo can then be implanted into a suitable pseudopregnant female
foster animal and the embryo brought to term to create a "knock
out" animal. Progeny harboring the homologously recombined DNA in
their germ cells can be identified by standard techniques and used
to breed animals in which all cells of the animal contain the
homologously recombined DNA. Knockout animals can be characterized
for instance, for their ability to defend against certain
pathological conditions and for their development of pathological
conditions due to absence of the polypeptide.
[0320] J. ImmunoAdjuvant Therapy
[0321] In one embodiment, the immunostimulating compounds of the
invention can be used in immunoadjuvant therapy for the treatment
of tumors (cancer). It is now well established that T cells
recognize human tumor specific antigens. One group of tumor
antigens, encoded by the MAGE, BAGE and GAGE families of genes, are
silent in all adult normal tissues , but are expressed in
significant amounts in tumors, such as melanomas, lung tumors, head
and neck tumors, and bladder carcinomas. DeSmet, C. et al., Proc.
Natl. Acad. Sci. USA, 93:7149 (1996). It has been shown that
costimulation of T cells induces tumor regression and an antitumor
response both in vitro and in vivo. Melero, I. et al., Nature
Medicine, 3:682 (1997); Kwon, E. D. et al., Proc. Natl. Acad. Sci.
USA. 94: 8099 (1997); Lynch, D. H. et al., Nature Medicine, 3:625
(1997); Finn, O. J. and Lotze, M. T., J. Immunol., 21:114 (1998).
The stimulatory compounds of the invention can be administered as
adjuvants, alone or together with a growth regulating agent,
cytotoxic agent or chemotherapeutic agent, to stimulate T cell
proliferation/activation and an antitumor response to tumor
antigens. The growth regulating, cytotoxic, or chemotherapeutic
agent may be administered in conventional amounts using known
administration regimes. Immunostimulating activity by the compounds
of the invention allows reduced amounts of the growth regulating,
cytotoxic, or chemotherapeutic agents thereby potentially lowering
the toxicity to the patient.
[0322] K. Screening Assays for Drug Candidates
[0323] Screening assays for drug candidates are designed to
identify compounds that bind to or complex with the polypeptides
encoded by the genes identified herein or a biologically active
fragment thereof, or otherwise interfere with the interaction of
the encoded polypeptides with other cellular proteins. Such
screening assays will include assays amenable to high-throughput
screening of chemical libraries, making them particularly suitable
for identifying small molecule drug candidates. Small molecules
contemplated include synthetic organic or inorganic compounds,
including peptides, preferably soluble peptides,
(poly)peptide-immunoglobulin fusions, and, in particular,
antibodies including, without limitation, poly- and monoclonal
antibodies and antibody fragments, single-chain antibodies,
anti-idiotypic antibodies, and chimeric or humanized versions of
such antibodies or fragments, as well as human antibodies and
antibody fragments. The assays can be performed in a variety of
formats, including protein-protein binding assays, biochemical
screening assays, immunoassays and cell based assays, which are
well characterized in the art. All assays are common in that they
call for contacting the drug candidate with a polypeptide encoded
by a nucleic acid identified herein under conditions and for a time
sufficient to allow these two components to interact.
[0324] In binding assays, the interaction is binding and the
complex formed can be isolated or detected in the reaction mixture.
In a particular embodiment, the polypeptide encoded by the gene
identified herein or the drug candidate is immobilized on a solid
phase, e.g., on a microtiter plate, by covalent or non-covalent
attachments. Non-covalent attachment generally is accomplished by
coating the solid surface with a solution of the polypeptide and
drying. Alternatively, an immobilized antibody, e.g., a monoclonal
antibody, specific for the polypeptide to be immobilized can be
used to anchor it to a solid surface. The assay is performed by
adding the non-immobilized component, which may be labeled by a
detectable label, to the immobilized component, e.g., the coated
surface containing the anchored component. When the reaction is
complete, the non-reacted components are removed, e.g., by washing,
and complexes anchored on the solid surface are detected. When the
originally non-immobilized component carries a detectable label,
the detection of label immobilized on the surface indicates that
complexing occurred. Where the originally non-immobilized component
does not carry a label, complexing can be detected, for example, by
using a labelled antibody specifically binding the immobilized
complex.
[0325] If the candidate compound interacts with but does not bind
to a particular protein encoded by a gene identified herein, its
interaction with that protein can be assayed by methods well known
for detecting protein-protein interactions. Such assays include
traditional approaches, such as, cross-linking,
co-immunoprecipitation, and co-purification through gradients or
chromatographic columns. In addition, protein-protein interactions
can be monitored by using a yeast-based genetic system described by
Fields and co-workers [Fields and Song, Nature (London), 340,
245-246 (1989); Chien et al., Proc. Natl. Acad. Sci. USA, 88,
9578-9582 (1991)] as disclosed by Chevray and Nathans, Proc. Natl.
Acad. Sci. USA, 89, 5789-5793 (1991). Many transcriptional
activators, such as yeast GAL4, consist of two physically discrete
modular domains, one acting as the DNA-binding domain, while the
other one functioning as the transcription activation domain. The
yeast expression system described in the foregoing publications
(generally referred to as the "two-hybrid system") takes advantage
of this property, and employs two hybrid proteins, one in which the
target protein is fused to the DNA-binding domain of GAL4, and
another, in which candidate activating proteins are fused to the
activation domain. The expression of a GAL1-lacZ reporter gene
under control of a GAL4-activated promoter depends on
reconstitution of GAL4 activity via protein-protein interaction.
Colonies containing interacting polypeptides are detected with a
chromogenic substrate for b-galactosidase. A complete kit
(MATCHMAKER.TM.) for identifying protein-protein interactions
between two specific proteins using the two-hybrid technique is
commercially available from Clontech. This system can also be
extended to map protein domains involved in specific protein
interactions as well as to pinpoint amino acid residues that are
crucial for these interactions.
[0326] In order to find compounds that interfere with the
interaction of a gene identified herein and other intra- or
extracellular components can be tested, a reaction mixture is
usually prepared containing the product of the gene and the intra-
or extracellular component under conditions and for a time allowing
for the interaction and binding of the two products. To test the
ability of a test compound to inhibit binding, the reaction is run
in the absence and in the presence of the test compound. In
addition, a placebo may be added to a third reaction mixture, to
serve as positive control. The binding (complex formation) between
the test compound and the intra- or extracellular component present
in the mixture is monitored as described above. The formation of a
complex in the control reaction(s) but not in the reaction mixture
containing the test compound indicates that the test compound
interferes with the interaction of the test compound and its
reaction partner.
[0327] L. Compositions and Methods for the Treatment of Immune
Related Diseases
[0328] The compositions useful in the treatment of immune related
diseases include, without limitation, proteins, antibodies, small
organic molecules, peptides, phosphopeptides, antisense and
ribozyme molecules, triple helix molecules, etc. that inhibit or
stimulate immune function, for example, T cell
proliferation/activation, lymphokine release, or immune cell
infiltration.
[0329] For example, antisense RNA and RNA molecules act to directly
block the translation of mRNA by hybridizing to targeted mRNA and
preventing protein translation. When antisense DNA is used,
oligodeoxyribonucleotides derived from the translation initiation
site, e.g., between about -10 and +10 positions of the target gene
nucleotide sequence, are preferred.
[0330] Ribozymes are enzymatic RNA molecules capable of catalyzing
the specific cleavage of RNA. Ribozymes act by sequence-specific
hybridization to the complementary target RNA, followed by
endonucleolytic cleavage. Specific ribozyme cleavage sites within a
potential RNA target can be identified by known techniques. For
further details see, e.g., Rossi, Current Biology, 4, 469-471
(1994), and PCT publication No. WO 97133551 (published Sep. 18,
1997).
[0331] Nucleic acid molecules in triple helix formation used to
inhibit transcription should be single-stranded and composed of
deoxynucleotides. The base composition of these oligonucleotides is
designed such that it promotes triple helix formation via Hoogsteen
base pairing rules, which generally require sizeable stretches of
purines or pyrimidines on one strand of a duplex. For further
details see, e.g., PCT publication No. WO 97/33551, supra.
[0332] These molecules can be identified by any or any combination
of the screening assays discussed above and/or by any other
screening techniques well known for those skilled in the art.
[0333] M. Anti-PRO Antibodies
[0334] The present invention further provides anti-PRO antibodies.
Exemplary antibodies include polyclonal, monoclonal, humanized,
bispecific, and heteroconjugate antibodies.
[0335] 1. Polyclonal Antibodies
[0336] The anti-PRO antibodies may comprise polyclonal antibodies.
Methods of preparing polyclonal antibodies are known to the skilled
artisan. Polyclonal antibodies can be raised in a mammal, for
example, by one or more injections of an immunizing agent and, if
desired, an adjuvant. Typically, the immunizing agent and/or
adjuvant will be injected in the mammal by multiple subcutaneous or
intraperitoneal injections. The immunizing agent may include the
PRO polypeptide or a fusion protein thereof. It may be useful to
conjugate the immunizing agent to a protein known to be immunogenic
in the mammal being immunized. Examples of such immunogenic
proteins include but are not limited to keyhole limpet hemocyanin,
serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor.
Examples of adjuvants which may be employed include Freund's
complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A,
synthetic trehalose dicorynomycolate). The immunization protocol
may be selected by one skilled in the art without undue
experimentation.
[0337] 2. Monoclonal Antibodies
[0338] The anti-PRO antibodies may, alternatively, be monoclonal
antibodies. Monoclonal antibodies may be prepared using hybridoma
methods, such as those described by Kohler and Milstein, Nature,
256:495 (1975). In a hybridoma method, a mouse, hamster, or other
appropriate host animal, is typically immunized with an immunizing
agent to elicit lymphocytes that produce or are capable of
producing antibodies that will specifically bind to the immunizing
agent. Alternatively, the lymphocytes may be immunized in
vitro.
[0339] The immunizing agent will typically include the PRO
polypeptide or a fusion protein thereof. Generally, either
peripheral blood lymphocytes ("PBLs") are used if cells of human
origin are desired, or spleen cells or lymph node cells are used if
non-human mammalian sources are desired. The lymphocytes are then
fused with an immortalized cell line using a suitable fusing agent,
such as polyethylene glycol, to form a hybridoma cell [Goding,
Monoclonal Antibodies: Principles and Practice, Academic Press,
(1986) pp. 59-103]. Immortalized cell lines are usually transformed
mammalian cells, particularly myeloma cells of rodent, bovine and
human origin. Usually, rat or mouse myeloma cell lines are
employed. The hybridoma cells may be cultured in a suitable culture
medium that preferably contains one or more substances that inhibit
the growth or survival of the unfused, immortalized cells. For
example, if the parental cells lack the enzyme hypoxanthine guanine
phosphoribosyl transferase (HGPRT or HPRT), the culture medium for
the hybridomas typically will include hypoxanthine, aminopterin,
and thymidine ("HAT medium"), which substances prevent the growth
of HGPRT-deficient cells.
[0340] Preferred immortalized cell lines are those that fuse
efficiently, support stable high level expression of antibody by
the selected antibody-producing cells, and are sensitive to a
medium such as HAT medium. More preferred immortalized cell lines
are murine myeloma lines, which can be obtained, for instance, from
the Salk Institute Cell Distribution Center, San Diego, Calif. and
the American Type Culture Collection, Manassas, Va. Human myeloma
and mouse-human heteromyeloma cell lines also have been described
for the production of human monoclonal antibodies [Kozbor, J.
Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody
Production Techniques and Applications, Marcel Dekker, Inc., New
York, (1987) pp. 51-63].
[0341] The culture medium in which the hybridoma cells are cultured
can then be assayed for the presence of monoclonal antibodies
directed against PRO. Preferably, the binding specificity of
monoclonal antibodies produced by the hybridoma cells is determined
by immunoprecipitation or by an in vitro binding assay, such as
radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay
(ELISA). Such techniques and assays are known in the art. The
binding affinity of the monoclonal antibody can, for example, be
determined by the Scatchard analysis of Munson and Pollard, Anal.
Biochem., 107:220 (1980).
[0342] After the desired hybridoma cells are identified, the clones
may be subcloned by limiting dilution procedures and grown by
standard methods [Goding, supra]. Suitable culture media for this
purpose include, for example, Dulbecco's Modified Eagle's Medium
and RPMI-1640 medium. Alternatively, the hybridoma cells may be
grown in vivo as ascites in a mammal.
[0343] The monoclonal antibodies secreted by the subclones may be
isolated or purified from the culture medium or ascites fluid by
conventional immunoglobulin purification procedures such as, for
example, protein A-Sepharose, hydroxylapatite chromatography, gel
electrophoresis, dialysis, or affinity chromatography.
[0344] The monoclonal antibodies may also be made by recombinant
DNA methods, such as those described in U.S. Pat. No. 4,816,567.
DNA encoding the monoclonal antibodies of the invention can be
readily isolated and sequenced using conventional procedures (e.g.,
by using oligonucleotide probes that are capable of binding
specifically to genes encoding the heavy and light chains of murine
antibodies). The hybridoma cells of the invention serve as a
preferred source of such DNA. Once isolated, the DNA may be placed
into expression vectors, which are then transfected into host cells
such as simian COS cells, Chinese hamster ovary (CHO) cells, or
myeloma cells that do not otherwise produce immunoglobulin protein,
to obtain the synthesis of monoclonal antibodies in the recombinant
host cells. The DNA also may be modified, for example, by
substituting the coding sequence for human heavy and light chain
constant domains in place of the homologous murine sequences [U.S.
Pat. No. 4,816,567; Morrison et al., supra] or by covalently
joining to the immunoglobulin coding sequence all or part of the
coding sequence for a non-immunoglobulin polypeptide. Such a
non-immunoglobulin polypeptide can be substituted for the constant
domains of an antibody of the invention, or can be substituted for
the variable domains of one antigen-combining site of an antibody
of the invention to create a chimeric bivalent antibody.
[0345] The antibodies may be monovalent antibodies. Methods for
preparing monovalent antibodies are well known in the art. For
example, one method involves recombinant expression of
immunoglobulin light chain and modified heavy chain. The heavy
chain is truncated generally at any point in the Fc region so as to
prevent heavy chain crosslinking. Alternatively, the relevant
cysteine residues are substituted with another amino acid residue
or are deleted so as to prevent crosslinking.
[0346] In vitro methods are also suitable for preparing monovalent
antibodies. Digestion of antibodies to produce fragments thereof,
particularly, Fab fragments, can be accomplished using routine
techniques known in the art.
[0347] 3. Human and Humanized Antibodies
[0348] The anti-PRO antibodies of the invention may further
comprise humanized antibodies or human antibodies. Humanized forms
of non-human (e.g., murine) antibodies are chimeric
immunoglobulins, immunoglobulin chains or fragments thereof (such
as Fv, Fab, Fab', F(ab')2 or other antigen-binding subsequences of
antibodies) which contain minimal sequence derived from non-human
immunoglobulin. Humanized antibodies include human immunoglobulins
(recipient antibody) in which residues from a complementary
determining region (CDR) of the recipient are replaced by residues
from a CDR of a non-human species (donor antibody) such as mouse,
rat or rabbit having the desired specificity, affinity and
capacity. In some instances, Fv framework residues of the human
immunoglobulin are replaced by corresponding non-human residues.
Humanized antibodies may also comprise residues which are found
neither in the recipient antibody nor in the imported CDR or
framework sequences. In general, the humanized antibody will
comprise substantially all of at least one, and typically two,
variable domains, in which all or substantially all of the CDR
regions correspond to those of a non-human immunoglobulin and all
or substantially all of the FR regions are those of a human
immunoglobulin consensus sequence. The humanized antibody optimally
also will comprise at least a portion of an immunoglobulin constant
region (Fc), typically that of a human immunoglobulin [Jones et
al., Nature, 321:522-525 (1986); Riechmann et al., Nature,
332:323-329 (1988); and Presta, Curr. Op. Struct. Biol., 2:593-596
(1992)].
[0349] Methods for humanizing non-human antibodies are well known
in the art. Generally, a humanized antibody has one or more amino
acid residues introduced into it from a source which is non-human.
These non-human amino acid residues are often referred to as
"import" residues, which are typically taken from an "import"
variable domain. Humanization can be essentially performed
following the method of Winter and co-workers [Jones et al.,
Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-327
(1988); Verhoeyen et al., Science 239:1534-1536 (1988)], by
substituting rodent CDRs or CDR sequences for the corresponding
sequences of a human antibody. Accordingly, such "humanized"
antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567),
wherein substantially less than an intact human variable domain has
been substituted by the corresponding sequence from a non-human
species. In practice, humanized antibodies are typically human
antibodies in which some CDR residues and possibly some FR residues
are substituted by residues from analogous sites in rodent
antibodies.
[0350] Human antibodies can also be produced using various
techniques known in the art, including phage display libraries
[Hoogenboom and Winter, J. Mol. Biol., 227:381 (1991); Marks et
al., J. Mol. Biol., 222:581 (1991)]. The techniques of Cole et al.,
and Boerner et al., are also available for the preparation of human
monoclonal antibodies (Cole et al., Monoclonal Antibodies and
Cancer Therapy, Alan R. Liss, p. 77 (1985) and Boerner et al., J.
Immunol., 147(1):86-95 (1991)]. Similarly, human antibodies can be
made by introducing of human immunoglobulin loci into transgenic
animals, e.g., mice in which the endogenous immunoglobulin genes
have been partially or completely inactivated. Upon challenge,
human antibody production is observed, which closely resembles that
seen in humans in all respects, including gene rearrangement,
assembly, and antibody repertoire. This approach is described, for
example, in U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825;
5,625,126; 5,633,425; 5,661,016, and in the following scientific
publications: Marks et al., Bio/Technology., 10, 779-783 (1992);
Lonberg et al., Nature, 368: 856-859 (1994); Morrison, Nature, 368:
812-13 (1994); Fishwild et al., Nature Biotechnology, 14: 845-51
(1996); Neuberger, Nature Biotechnology, 14: 826 (1996); Lonberg
and Huszar, Intern. Rev. Immunol., 13: 65-93 (1995).
[0351] The antibodies may also be affinity matured using known
selection and/or mutagenesis methods as described above. Preferred
affinity matured antibodies have an affinity which is five times,
more preferably 10 times, even more preferably 20 or 30 times
greater than the starting antibody (generally murine, humanized or
human) from which the matured antibody is prepared.
[0352] 4. Bispecific Antibodies
[0353] Bispecific antibodies are monoclonal, preferably human or
humanized, antibodies that have binding specificities for at least
two different antigens. In the present case, one of the binding
specificities is for the PRO, the other one is for any other
antigen, and preferably for a cell-surface protein or receptor or
receptor subunit.
[0354] Methods for making bispecific antibodies are known in the
art. Traditionally, the recombinant production of bispecific
antibodies is based on the co-expression of two immunoglobulin
heavy-chain/light-chain pairs, where the two heavy chains have
different specificities [Milstein and Cuello, Nature, 305:537-539
(1983)]. Because of the random assortment of immunoglobulin heavy
and light chains, these hybridomas (quadromas) produce a potential
mixture of ten different antibody molecules, of which only one has
the correct bispecific structure. The purification of the correct
molecule is usually accomplished by affinity chromatography steps.
Similar procedures are disclosed in WO 93/08829, published 13 May
1993, and in Traunecker et al., EMBO J., 10:3655-3659 (1991).
[0355] Antibody variable domains with the desired binding
specificities (antibody-antigen combining sites) can be fused to
immunoglobulin constant domain sequences. The fusion preferably is
with an immunoglobulin heavy-chain constant domain, comprising at
least part of the hinge, CH2, and CH3 regions. It is preferred to
have the first heavy-chain constant region (CH1) containing the
site necessary for light-chain binding present in at least one of
the fusions. DNAs encoding the immunoglobulin heavy-chain fusions
and, if desired, the immunoglobulin light chain, are inserted into
separate expression vectors, and are co-transfected into a suitable
host organism. For further details of generating bispecific
antibodies see, for example, Suresh et al., Methods in Enzymology,
121:210 (1986).
[0356] According to another approach described in WO 96/27011, the
interface between a pair of antibody molecules can be engineered to
maximize the percentage of heterodimers which are recovered from
recombinant cell culture. The preferred interface comprises at
least a part of the CH3 region of an antibody constant domain. In
this method, one or more small amino acid side chains from the
interface of the first antibody molecule are replaced with larger
side chains (e.g., tyrosine or tryptophan). Compensatory "cavities"
of identical or similar size to the large side chain(s) are created
on the interface of the second antibody molecule by replacing large
amino acid side chains with smaller ones (e.g., alanine or
threonine). This provides a mechanism for increasing the yield of
the heterodimer over other unwanted end-products such as
homodimers.
[0357] Bispecific antibodies can be prepared as full length
antibodies or antibody fragments (e.g., F(ab')2 bispecific
antibodies). Techniques for generating bispecific antibodies from
antibody fragments have been described in the literature. For
example, bispecific antibodies can be prepared can be prepared
using chemical linkage. Brennan et al., Science. 229:81 (1985)
describe a procedure wherein intact antibodies are proteolytically
cleaved to generate F(ab')2 fragments. These fragments are reduced
in the presence of the dithiol complexing agent sodium arsenite to
stabilize vicinal dithiols and prevent intermolecular disulfide
formation. The Fab' fragments generated are then converted to
thionitrobenzoate (TNB) derivatives. One of the Fab'-TNB
derivatives is then reconverted to the Fab'-thiol by reduction with
mercaptoethylamine and is mixed with an equimolar amount of the
other Fab'-TNB derivative to form the bispecific antibody. The
bispecific antibodies produced can be used as agents for the
selective immobilization of enzymes.
[0358] Fab' fragments may be directly recovered from E. coli and
chemically coupled to form bispecific antibodies. Shalaby et al.,
J. Exp. Med., 175:217-225 (1992) describe the production of a fully
humanized bispecific antibody F(ab')2 molecule. Each Fab' fragment
was separately secreted from E. coli and subjected to directed
chemical coupling in vitro to form the bispecific antibody. The
bispecific antibody thus formed was able to bind to cells
overexpressing the ErbB2 receptor and normal human T cells, as well
as trigger the lytic activity of human cytotoxic lymphocytes
against human breast tumor targets.
[0359] Various technique for making and isolating bispecific
antibody fragments directly from recombinant cell culture have also
been described. For example, bispecific antibodies have been
produced using leucine zippers. Kostelny et al., J. Immunol.
148(5): 1547-1553 (1992). The leucine zipper peptides from the Fos
and Jun proteins were linked to the Fab' portions of two different
antibodies by gene fusion. The antibody homodimers were reduced at
the hinge region to form monomers and then re-oxidized to form the
antibody heterodimers. This method can also be utilized for the
production of antibody homodimers. The "diabody" technology
described by Hollinger et al., Proc. Natl. Acad. Sci. USA,
90:6444-6448 (1993) has provided an alternative mechanism for
making bispecific antibody fragments. The fragments comprise a
heavy-chain variable domain (VH) connected to a light-chain
variable domain (VL) by a linker which is too short to allow
pairing between the two domains on the same chain. Accordingly, the
VH and VL domains of one fragment are forced to pair with the
complementary VL and VH domains of another fragment, thereby
forming two antigen-binding sites. Another strategy for making
bispecific antibody fragments by the use of single-chain Fv (sFv)
dimers has also been reported. See, Gruber et al., J. Immunol.,
152:5368 (1994).
[0360] Antibodies with more than two valencies are contemplated.
For example, trispecific antibodies can be prepared. Tutt et al.,
J. Immunol., 147:60 (1991).
[0361] Exemplary bispecific antibodies may bind to two different
epitopes on a given PRO polypeptide herein. Alternatively, an
anti-PRO polypeptide arm may be combined with an arm which binds to
a triggering molecule on a leukocyte such as a T-cell receptor
molecule (e.g., CD2, CD3, CD28, or B7), or Fc receptors for IgG
(FcgR), such as FcgRI (CD64), FcgRII (CD32) and FcgRIII (CD16) so
as to focus cellular defense mechanisms to the cell expressing the
particular PRO polypeptide. Bispecific antibodies may also be used
to localize cytotoxic agents to cells which express a particular
PRO polypeptide. These antibodies possess a PRO-binding arm and an
arm which binds a cytotoxic agent or a radionuclide chelator, such
as EOTUBE, DPTA, DOTA, or TETA. Another bispecific antibody of
interest binds the PRO polypeptide and further binds tissue factor
(TF).
[0362] 5. Heteroconjugate Antibodies
[0363] Heteroconjugate antibodies are also within the scope of the
present invention. Heteroconjugate antibodies are composed of two
covalently joined antibodies. Such antibodies have, for example,
been proposed to target immune system cells to unwanted cells [U.S.
Pat. No. 4,676,980], and for treatment of HIV infection [WO
91/00360; WO 92/200373; EP 03089]. It is contemplated that the
antibodies may be prepared in vitro using known methods in
synthetic protein chemistry, including those involving crosslinking
agents. For example, immunotoxins may be constructed using a
disulfide exchange reaction or by forming a thioether bond.
Examples of suitable reagents for this purpose include
iminothiolate and methyl-4-mercaptobutyrimidate and those
disclosed, for example, in U.S. Pat. No. 4,676,980.
[0364] 6. Effector Function Engineering
[0365] It may be desirable to modify the antibody of the invention
with respect to effector function, so as to enhance, e.g., the
effectiveness of the antibody in treating cancer. For example,
cysteine residue(s) may be introduced into the Fc region, thereby
allowing interchain disulfide bond formation in this region. The
homodimeric antibody thus generated may have improved
internalization capability and/or increased complement-mediated
cell killing and antibody-dependent cellular cytotoxicity (ADCC).
See Caron et al., J. Exp Med., 176: 1191-1195 (1992) and Shopes, J.
Immunol., 148: 2918-2922 (1992). Homodimeric antibodies with
enhanced anti-tumor activity may also be prepared using
heterobifunctional cross-linkers as described in Wolff et al.,
Cancer Research, 53: 2560-2565 (1993). Alternatively, an antibody
can be engineered that has dual Fc regions and may thereby have
enhanced complement lysis and ADCC capabilities. See Stevenson et
al., Anti-Cancer Drug Design, 3: 219-230 (1989).
[0366] 7. Immunoconjugates
[0367] The invention also pertains to immunoconjugates comprising
an antibody conjugated to a cytotoxic agent such as a
chemotherapeutic agent, toxin (e.g., an enzymatically active toxin
of bacterial, fungal, plant, or animal origin, or fragments
thereof), or a radioactive isotope (i.e., a radioconjugate).
[0368] Chemotherapeutic agents useful in the generation of such
immunoconjugates have been described above. Enzymatically active
toxins and fragments thereof that can be used include diphtheria A
chain, nonbinding active fragments of diphtheria toxin, exotoxin A
chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain,
modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin
proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S),
momordica charantia inhibitor, curcin, crotin, sapaonaria
officinalis inhibitor, gelonin, mitogellin, restrictocin,
phenomycin, enomycin, and the tricothecenes. A variety of
radionuclides are available for the production of radioconjugated
antibodies. Examples include .sup.212Bi, .sup.131I, .sup.131In,
.sup.90Y, and .sup.186Re.
[0369] Conjugates of the antibody and cytotoxic agent are made
using a variety of bifunctional protein-coupling agents such as
N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP),
iminothiolane (IT), bifunctional derivatives of imidoesters (such
as dimethyl adipimidate HCl), active esters (such as disuccinimidyl
suberate), aldehydes (such as glutareldehyde), bis-azido compounds
(such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium
derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine),
diisocyanates (such as tolyene 2,6-diisocyanate), and bis-active
fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene). For
example, a ricin immunotoxin can be prepared as described in
Vitetta et al., Science, 23:1098 (1987). Carbon-14-labeled
1-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid
(MX-DTPA) is an exemplary chelating agent for conjugation of
radionucleotide to the antibody. See WO94/11026.
[0370] In another embodiment, the antibody may be conjugated to a
"receptor" (such streptavidin) for utilization in tumor
pretargeting wherein the antibody-receptor conjugate is
administered to the patient, followed by removal of unbound
conjugate from the circulation using a clearing agent and then
administration of a "ligand" (e.g., avidin) that is conjugated to a
cytotoxic agent (e.g., a radionucleotide).
[0371] 8. Immunoliposomes
[0372] The antibodies disclosed herein may also be formulated as
immunoliposomes. Liposomes containing the antibody are prepared by
methods known in the art, such as described in Epstein et al.,
Proc. Natl. Acad. Sci. USA, 82:3688 (1985); Hwang et al., Proc.
Natl. Acad. Sci. USA, 77:4030 (1980); and U.S. Pat. Nos. 4,485,045
and 4,544,545. Liposomes with enhanced circulation time are
disclosed in U.S. Pat. No. 5,013,556.
[0373] Particularly useful liposomes can be generated by the
reverse-phase evaporation method with a lipid composition
comprising phosphatidylcholine, cholesterol, and PEG-derivatized
phosphatidylethanolamine (PEG-PE). Liposomes are extruded through
filters of defined pore size to yield liposomes with the desired
diameter. Fab' fragments of the antibody of the present invention
can be conjugated to the liposomes as described in Martin et al.,
J. Biol. Chem., 257: 286-288 (1982) via a disulfide-interchange
reaction. A chemotherapeutic agent (such as Doxorubicin) is
optionally contained within the liposome. See Gabizon et al., J.
National Cancer Inst., 81(19):1484 (1989).
[0374] 9. Uses for Anti-PRO Antibodies
[0375] The anti-PRO antibodies of the invention have various
utilities. For example, anti-PRO antibodies may be used in
diagnostic assays for PRO, e.g., detecting its expression (and in
some cases, differential expression) in specific cells, tissues, or
serum. Various diagnostic assay techniques known in the art may be
used, such as competitive binding assays, direct or indirect
sandwich assays and immunoprecipitation assays conducted in either
heterogeneous or homogeneous phases [Zola, Monoclonal Antibodies: A
Manual of Techniques, CRC Press, Inc. (1987) pp. 147-158]. The
antibodies used in the diagnostic assays can be labeled with a
detectable moiety. The detectable moiety should be capable of
producing, either directly or indirectly, a detectable signal. For
example, the detectable moiety may be a radioisotope, such as
.sup.3H, .sup.14C, .sup.32P, .sup.35S, or .sup.125I, a fluorescent
or chemiluminescent compound, such as fluorescein isothiocyanate,
rhodamine, or luciferin, or an enzyme, such as alkaline
phosphatase, beta-galactosidase or horseradish peroxidase. Any
method known in the art for conjugating the antibody to the
detectable moiety may be employed, including those methods
described by Hunter et al., Nature, 144:945 (1962); David et al.,
Biochemistry, 13:1014 (1974); Pain et al., J. Immunol. Meth.,
40:219 (1981); and Nygren, J. Histochem. and Cytochem., 30:407
(1982).
[0376] Anti-PRO antibodies also are useful for the affinity
purification of PRO from recombinant cell culture or natural
sources. In this process, the antibodies against PRO are
immobilized on a suitable support, such a Sephadex resin or filter
paper, using methods well known in the art. The immobilized
antibody then is contacted with a sample containing the PRO to be
purified, and thereafter the support is washed with a suitable
solvent that will remove substantially all the material in the
sample except the PRO, which is bound to the immobilized antibody.
Finally, the support is washed with another suitable solvent that
will release the PRO from the antibody.
[0377] The following examples are offered for illustrative purposes
only, and are not intended to limit the scope of the present
invention in any way.
[0378] All patent and literature references cited in the present
specification are hereby incorporated by reference in their
entirety.
[0379] N. Pharmaceutical Compositions
[0380] The active PRO molecules of the invention (e.g., PRO
polypeptides, anti-PRO antibodies, and/or variants of each) as well
as other molecules identified by the screening assays disclosed
above, can be administered for the treatment of immune related
diseases, in the form of pharmaceutical compositions. Therapeutic
formulations of the active PRO molecule, preferably a polypeptide
or antibody of the invention, are prepared for storage by mixing
the active molecule having the desired degree of purity with
optional pharmaceutically acceptable carriers, excipients or
stabilizers (Remington's Pharmaceutical Sciences 16th edition,
Osol, A. Ed. [1980]), in the form of lyophilized formulations or
aqueous solutions. Acceptable carriers, excipients, or stabilizers
are nontoxic to recipients at the dosages and concentrations
employed, and include buffers such as phosphate, citrate, and other
organic acids; antioxidants including ascorbic acid and methionine;
preservatives (such as octadecyldimethylbenzyl ammonium chloride;
hexamethonium chloride; benzalkonium chloride, benzethonium
chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as
methyl or propyl paraben; catechol; resorcinol; cyclohexanol;
3-pentanol; and m-cresol); low molecular weight (less than about 10
residues) polypeptides; proteins, such as serum albumin, gelatin,
or immunoglobulins; hydrophilic polymers such as
polyvinylpyrrolidone; amino acids such as glycine, glutamine,
asparagine, histidine, arginine, or lysine; monosaccharides,
disaccharides, and other carbohydrates including glucose, mannose,
or dextrins; chelating agents such as EDTA; sugars such as sucrose,
mannitol, trehalose or sorbitol; salt-forming counter-ions such as
sodium; metal complexes (e.g., Zn-protein complexes); and/or
non-ionic surfactants such as TWEEN.TM., PLURONICS.TM. or
polyethylene glycol (PEG).
[0381] Compounds identified by the screening assays disclosed
herein can be formulated in an analogous manner, using standard
techniques well known in the art.
[0382] Lipofections or liposomes can also be used to deliver the
PRO molecule into cells. Where antibody fragments are used, the
smallest inhibitory fragment which specifically binds to the
binding domain of the target protein is preferred. For example,
based upon the variable region sequences of an antibody, peptide
molecules can be designed which retain the ability to bind the
target protein sequence. Such peptides can be synthesized
chemically and/or produced by recombinant DNA technology (see,
e.g., Marasco et al., Proc. Natl. Acad. Sci. USA. 90:7889-7893
[1993]).
[0383] The formulation herein may also contain more than one active
compound as necessary for the particular indication being treated,
preferably those with complementary activities that do not
adversely affect each other. Alternatively, or in addition, the
composition may comprise a cytotoxic agent, cytokine or growth
inhibitory agent. Such molecules are suitably present in
combination in amounts that are effective for the purpose
intended.
[0384] The active PRO molecules may also be entrapped in
microcapsules prepared, for example, by coacervation techniques or
by interfacial polymerization, for example, hydroxymethylcellulose
or gelatin-microcapsules and poly-(methylmethacylate)
microcapsules, respectively, in colloidal drug delivery systems
(for example, liposomes, albumin microspheres, microemulsions,
nano-particles and nanocapsules) or in macroemulsions. Such
techniques are disclosed in Remington's Pharmaceutical Sciences
16th edition, Osol, A. Ed. (1980).
[0385] The formulations to be used for in vivo administration must
be sterile. This is readily accomplished by filtration through
sterile filtration membranes.
[0386] Sustained-release preparations or the PRO molecules may be
prepared. Suitable examples of sustained-release preparations
include semipermeable matrices of solid hydrophobic polymers
containing the antibody, which matrices are in the form of shaped
articles, e.g., films, or microcapsules. Examples of
sustained-release matrices include polyesters, hydrogels (for
example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)),
polylactides (U.S. Pat. No. 3,773,919), copolymers of L-glutamic
acid and .gamma.-ethyl-L-glutamate, non-degradable ethylene-vinyl
acetate, degradable lactic acid-glycolic acid copolymers such as
the LUPRON DEPOT.TM. (injectable microspheres composed of lactic
acid-glycolic acid copolymer and leuprolide acetate), and
poly-D-(-)-3-hydroxybutyric acid. While polymers such as
ethylene-vinyl acetate and lactic acid-glycolic acid enable release
of molecules for over 100 days, certain hydrogels release proteins
for shorter time periods. When encapsulated antibodies remain in
the body for a long time, they may denature or aggregate as a
result of exposure to moisture at 37.degree. C., resulting in a
loss of biological activity and possible changes in immunogenicity.
Rational strategies can be devised for stabilization depending on
the mechanism involved. For example, if the aggregation mechanism
is discovered to be intermolecular S--S bond formation through
thio-disulfide interchange, stabilization may be achieved by
modifying sulfhydryl residues, lyophilizing from acidic solutions,
controlling moisture content, using appropriate additives, and
developing specific polymer matrix compositions.
[0387] O. Methods of Treatment
[0388] It is contemplated that the polypeptides, antibodies and
other active compounds of the present invention may be used to
treat various immune related diseases and conditions, such as T
cell mediated diseases, including those characterized by
infiltration of inflammatory cells into a tissue, stimulation of
T-cell proliferation, inhibition of T-cell proliferation, increased
or decreased vascular permeability or the inhibition thereof.
[0389] Exemplary conditions or disorders to be treated with the
polypeptides, antibodies and other compounds of the invention,
include, but are not limited to systemic lupus erythematosis,
rheumatoid arthritis, juvenile chronic arthritis, osteoarthritis,
spondyloarthropathies, systemic sclerosis (scleroderma), idiopathic
inflammatory myopathies (dermatomyositis, polymyositis), Sjogren's
syndrome, systemic vasculitis, sarcoidosis, autoimmune hemolytic
anemia (immune pancytopenia, paroxysmal nocturnal hemoglobinuria),
autoimmune thrombocytopenia (idiopathic thrombocytopenic purpura,
immune-mediated thrombocytopenia), thyroiditis (Grave's disease,
Hashimoto's thyroiditis, juvenile lymphocytic thyroiditis, atrophic
thyroiditis), diabetes mellitus, immune-mediated renal disease
(glomerulonephritis, tubulointerstitial nephritis), demyelinating
diseases of the central and peripheral nervous systems such as
multiple sclerosis, idiopathic demyelinating polyneuropathy or
Guillain-Barre syndrome, and chronic inflammatory demyelinating
polyneuropathy, hepatobiliary diseases such as infectious hepatitis
(hepatitis A, B, C, D, E and other non-hepatotropic viruses),
autoimmune chronic active hepatitis, primary biliary cirrhosis,
granulomatous hepatitis, and sclerosing cholangitis, inflammatory
bowel disease (ulcerative colitis: Crohn's disease),
gluten-sensitive enteropathy, and Whipple's disease, autoimmune or
immune-mediated skin diseases including bullous skin diseases,
erythema multiforme and contact dermatitis, psoriasis, allergic
diseases such as asthma, allergic rhinitis, atopic dermatitis, food
hypersensitivity and urticaria, immunologic diseases of the lung
such as eosinophilic pneumonias, idiopathic pulmonary fibrosis and
hypersensitivity pneumonitis, transplantation associated diseases
including graft rejection and graft-versus-host-disease.
[0390] In systemic lupus erythematosus, the central mediator of
disease is the production of auto-reactive antibodies to self
proteins/tissues and the subsequent generation of immune-mediated
inflammation. Antibodies either directly or indirectly mediate
tissue injury. Though T lymphocytes have not been shown to be
directly involved in tissue damage, T lymphocytes are required for
the development of auto-reactive antibodies. The genesis of the
disease is thus T lymphocyte dependent. Multiple organs and systems
are affected clinically including kidney, lung, musculoskeletal
system, mucocutaneous, eye, central nervous system, cardiovascular
system, gastrointestinal tract, bone marrow and blood.
[0391] Rheumatoid arthritis (RA) is a chronic systemic autoimmune
inflammatory disease that mainly involves the synovial membrane of
multiple joints with resultant injury to the articular cartilage.
The pathogenesis is T lymphocyte dependent and is associated with
the production of rheumatoid factors, auto-antibodies directed
against self IgG, with the resultant formation of immune complexes
that attain high levels in joint fluid and blood. These complexes
in the joint may induce the marked infiltrate of lymphocytes and
monocytes into the synovium and subsequent marked synovial changes;
the joint space/fluid if infiltrated by similar cells with the
addition of numerous neutrophils. Tissues affected are primarily
the joints, often in symmetrical pattern. However, extra-articular
disease also occurs in two major forms. One form is the development
of extra-articular lesions with ongoing progressive joint disease
and typical lesions of pulmonary fibrosis, vasculitis, and
cutaneous ulcers. The second form of extra-articular disease is the
so called Felty's syndrome which occurs late in the RA disease
course, sometimes after joint disease has become quiescent, and
involves the presence of neutropenia, thrombocytopenia and
splenomegaly. This can be accompanied by vasculitis in multiple
organs with formations of infarcts, skin ulcers and gangrene.
Patients often also develop rheumatoid nodules in the subcutis
tissue overlying affected joints; the nodules late stage have
necrotic centers surrounded by a mixed inflammatory cell
infiltrate. Other manifestations which can occur in RA include:
pericarditis, pleuritis, coronary arteritis, intestitial
pneumonitis with pulmonary fibrosis, keratoconjunctivitis sicca,
and rheumatoid nodules.
[0392] Juvenile chronic arthritis is a chronic idiopathic
inflammatory disease which begins often at less than 16 years of
age. Its phenotype has some similarities to RA; some patients which
are rheumatoid factor positive are classified as juvenile
rheumatoid arthritis. The disease is sub-classified into three
major categories: pauciarticular, polyarticular, and systemic. The
arthritis can be severe and is typically destructive and leads to
joint ankylosis and retarded growth. Other manifestations can
include chronic anterior uveitis and systemic amyloidosis.
[0393] Spondyloarthropathies are a group of disorders with some
common clinical features and the common association with the
expression of HLA-B27 gene product. The disorders include:
ankylosing sponylitis, Reiter's syndrome (reactive arthritis),
arthritis associated with inflammatory bowel disease, spondylitis
associated with psoriasis, juvenile onset spondyloarthropathy and
undifferentiated spondyloarthropathy. Distinguishing features
include sacroileitis with or without spondylitis; inflammatory
asymmetric arthritis; association with HLA-B27 (a serologically
defined allele of the HLA-B locus of class I MHC); ocular
inflammation, and absence of autoantibodies associated with other
rheumatoid disease. The cell most implicated as key to induction of
the disease is the CD8.sup.+ T lymphocyte, a cell which targets
antigen presented by class I MHC molecules. CD8.sup.+ T cells may
react against the class I MHC allele HLA-B27 as if it were a
foreign peptide expressed by MHC class I molecules. It has been
hypothesized that an epitope of HLA-B27 may mimic a bacterial or
other microbial antigenic epitope and thus induce a CD8.sup.+ T
cells response.
[0394] Systemic sclerosis (scleroderma) has an unknown etiology. A
hallmark of the disease is induration of the skin; likely this is
induced by an active inflammatory process. Scleroderma can be
localized or systemic; vascular lesions are common and endothelial
cell injury in the microvasculature is an early and important event
in the development of systemic sclerosis; the vascular injury may
be immune mediated. An immunologic basis is implied by the presence
of mononuclear cell infiltrates in the cutaneous lesions and the
presence of anti-nuclear antibodies in many patients. ICAM-1 is
often upregulated on the cell surface of fibroblasts in skin
lesions suggesting that T cell interaction with these cells may
have a role in the pathogenesis of the disease. Other organs
involved include: the gastrointestinal tract: smooth muscle atrophy
and fibrosis resulting in abnormal peristalsis/motility; kidney:
concentric subendothelial intimal proliferation affecting small
arcuate and interlobular arteries with resultant reduced renal
cortical blood flow, results in proteinuria, azotemia and
hypertension; skeletal muscle: atrophy, interstitial fibrosis;
inflammation; lung: interstitial pneumonitis and interstitial
fibrosis; and heart: contraction band necrosis,
scarring/fibrosis.
[0395] Idiopathic inflammatory myopathies including
dermatomyositis, polymyositis and others are disorders of chronic
muscle inflammation of unknown etiology resulting in muscle
weakness. Muscle injury/inflammation is often symmetric and
progressive. Autoantibodies are associated with most forms. These
myositis-specific autoantibodies are directed against and inhibit
the function of components, proteins and RNA's, involved in protein
synthesis.
[0396] Sjogren's syndrome is due to immune-mediated inflammation
and subsequent functional destruction of the tear glands and
salivary glands. The disease can be associated with or accompanied
by inflammatory connective tissue diseases. The disease is
associated with autoantibody production against Ro and La antigens,
both of which are small RNA-protein complexes. Lesions result in
keratoconjunctivitis sicca, xerostomia, with other manifestations
or associations including bilary cirrhosis, peripheral or sensory
neuropathy, and palpable purpura.
[0397] Systemic vasculitis are diseases in which the primary lesion
is inflammation and subsequent damage to blood vessels which
results in ischemia/necrosis/degeneration to tissues supplied by
the affected vessels and eventual end-organ dysfunction in some
cases. Vasculitides can also occur as a secondary lesion or
sequelae to other immune-inflammatory mediated diseases such as
rheumatoid arthritis, systemic sclerosis, etc., particularly in
diseases also associated with the formation of immune complexes.
Diseases in the primary systemic vasculitis group include: systemic
necrotizing vasculitis: polyarteritis nodosa, allergic angiitis and
granulomatosis, polyangiitis; Wegener's granulomatosis;
lymphomatoid granulomatosis; and giant cell arteritis.
Miscellaneous vasculitides include: mucocutaneous lymph node
syndrome (MLNS or Kawasaki's disease), isolated CNS vasculitis,
Behet's disease, thromboangiitis obliterans (Buerger's disease) and
cutaneous necrotizing venulitis. The pathogenic mechanism of most
of the types of vasculitis listed is believed to be primarily due
to the deposition of immunoglobulin complexes in the vessel wall
and subsequent induction of an inflammatory response either via
ADCC, complement activation, or both.
[0398] Sarcoidosis is a condition of unknown etiology which is
characterized by the presence of epithelioid granulomas in nearly
any tissue in the body; involvement of the lung is most common. The
pathogenesis involves the persistence of activated macrophages and
lymphoid cells at sites of the disease with subsequent chronic
sequelae resultant from the release of locally and systemically
active products released by these cell types.
[0399] Autoimmune hemolytic anemia including autoimmune hemolytic
anemia, immune pancytopenia, and paroxysmal noctural hemoglobinuria
is a result of production of antibodies that react with antigens
expressed on the surface of red blood cells (and in some cases
other blood cells including platelets as well) and is a reflection
of the removal of those antibody coated cells via complement
mediated lysis and/or ADCC/Fc-receptor-mediated mechanisms.
[0400] In autoimmune thrombocytopenia including thrombocytopenic
purpura, and immune-mediated thrombocytopenia in other clinical
settings, platelet destruction/removal occurs as a result of either
antibody or complement attaching to platelets and subsequent
removal by complement lysis, ADCC or FC-receptor mediated
mechanisms.
[0401] Thyroiditis including Grave's disease, Hashimoto's
thyroiditis, juvenile lymphocytic thyroiditis, and atrophic
thyroiditis, are the result of an autoimmune response against
thyroid antigens with production of antibodies that react with
proteins present in and often specific for the thyroid gland.
Experimental models exist including spontaneous models: rats (BUF
and BB rats) and chickens (obese chicken strain); inducible models:
immunization of animals with either thyroglobulin, thyroid
microsomal antigen (thyroid peroxidase).
[0402] Type I diabetes mellitus or insulin-dependent diabetes is
the autoimmune destruction of pancreatic islet cells; this
destruction is mediated by auto-antibodies and auto-reactive T
cells. Antibodies to insulin or the insulin receptor can also
produce the phenotype of insulin-non-responsiveness.
[0403] Immune mediated renal diseases, including glomerulonephritis
and tubulointerstitial nephritis, are the result of antibody or T
lymphocyte mediated injury to renal tissue either directly as a
result of the production of autoreactive antibodies or T cells
against renal antigens or indirectly as a result of the deposition
of antibodies and/or immune complexes in the kidney that are
reactive against other, non-renal antigens. Thus other
immune-mediated diseases that result in the formation of
immune-complexes can also induce immune mediated renal disease as
an indirect sequelae. Both direct and indirect immune mechanisms
result in inflammatory response that produces/induces lesion
development in renal tissues with resultant organ function
impairment and in some cases progression to renal failure. Both
humoral and cellular immune mechanisms can be involved in the
pathogenesis of lesions.
[0404] Demyelinating diseases of the central and peripheral nervous
systems, including Multiple Sclerosis; idiopathic demyelinating
polyneuropathy or Guillain-Barre syndrome; and Chronic Inflammatory
Demyelinating Polyneuropathy, are believed to have an autoimmune
basis and result in nerve demyelination as a result of damage
caused to oligodendrocytes or to myelin directly. In MS there is
evidence to suggest that disease induction and progression is
dependent on T lymphocytes. Multiple Sclerosis is a demyelinating
disease that is T lymphocyte-dependent and has either a
relapsing-remitting course or a chronic progressive course. The
etiology is unknown; however, viral infections, genetic
predisposition, environment, and autoimmunity all contribute.
Lesions contain infiltrates of predominantly T lymphocyte mediated,
microglial cells and infiltrating macrophages; CD4.sup.+T
lymphocytes are the predominant cell type at lesions. The mechanism
of oligodendrocyte cell death and subsequent demyelination is not
known but is likely T lymphocyte driven.
[0405] Inflammatory and Fibrotic Lung Disease, including
Eosinophilic Pneumonias; Idiopathic Pulmonary Fibrosis, and
Hypersensitivity Pneumonitis may involve a disregulated
immune-inflammatory response. Inhibition of that response would be
of therapeutic benefit.
[0406] Autoimmune or Immune-mediated Skin Disease including Bullous
Skin Diseases, Erythema Multiforme, and Contact Dermatitis are
mediated by auto-antibodies, the genesis of which is T
lymphocyte-dependent.
[0407] Psoriasis is a T lymphocyte-mediated inflammatory disease.
Lesions contain infiltrates of T lymphocytes, macrophages and
antigen processing cells, and some neutrophils.
[0408] Allergic diseases, including asthma; allergic rhinitis;
atopic dermatitis; food hypersensitivity; and urticaria are T
lymphocyte dependent. These diseases are predominantly mediated by
T lymphocyte induced inflammation, IgE mediated-inflammation or a
combination of both.
[0409] Transplantation associated diseases, including Graft
rejection and Graft-Versus-Host-Disease (GVHD) are T
lymphocyte-dependent; inhibition of T lymphocyte function is
ameliorative.
[0410] Other diseases in which intervention of the immune and/or
inflammatory response have benefit are infectious disease including
but not limited to viral infection (including but not limited to
AIDS, hepatitis A, B, C, D, E and herpes) bacterial infection,
fungal infections, and protozoal and parasitic infections
(molecules (or derivatives/agonists) which stimulate the MLR can be
utilized therapeutically to enhance the immune response to
infectious agents), diseases of immunodeficiency
(molecules/derivatives/agonists) which stimulate the MLR can be
utilized therapeutically to enhance the immune response for
conditions of inherited, acquired, infectious induced (as in HIV
infection), or iatrogenic (i.e., as from chemotherapy)
immunodeficiency, and neoplasia.
[0411] It has been demonstrated that some human cancer patients
develop an antibody and/or T lymphocyte response to antigens on
neoplastic cells. It has also been shown in animal models of
neoplasia that enhancement of the immune response can result in
rejection or regression of that particular neoplasm. Molecules that
enhance the T lymphocyte response in the MLR have utility in vivo
in enhancing the immune response against neoplasia. Molecules which
enhance the T lymphocyte proliferative response in the MLR (or
small molecule agonists or antibodies that affected the same
receptor in an agonistic fashion) can be used therapeutically to
treat cancer. Molecules that inhibit the lymphocyte response in the
MLR also function in vivo during neoplasia to suppress the immune
response to a neoplasm; such molecules can either be expressed by
the neoplastic cells themselves or their expression can be induced
by the neoplasm in other cells. Antagonism of such inhibitory
molecules (either with antibody, small molecule antagonists or
other means) enhances immune-mediated tumor rejection.
[0412] Additionally, inhibition of molecules with proinflammatory
properties may have therapeutic benefit in reperfusion injury;
stroke; myocardial infarction; atherosclerosis; acute lung injury;
hemorrhagic shock; burn; sepsis/septic shock; acute tubular
necrosis; endometriosis; degenerative joint disease and pancreatis.
The compounds of the present invention, e.g., polypeptides or
antibodies, are administered to a mammal, preferably a human, in
accord with known methods, such as intravenous administration as a
bolus or by continuous infusion over a period of time, by
intramuscular, intraperitoneal, intracerobrospinal, subcutaneous,
intra-articular, intrasynovial, intrathecal, oral, topical, or
inhalation (intranasal, intrapulmonary) routes. Intravenous or
inhaled administration of polypeptides and antibodies is preferred.
In immunoadjuvant therapy, other therapeutic regimens, such
administration of an anti-cancer agent, may be combined with the
administration of the proteins, antibodies or compounds of the
instant invention. For example, the patient to be treated with a
the immunoadjuvant of the invention may also receive an anti-cancer
agent (chemotherapeutic agent) or radiation therapy. Preparation
and dosing schedules for such chemotherapeutic agents may be used
according to manufacturers' instructions or as determined
empirically by the skilled practitioner. Preparation and dosing
schedules for such chemotherapy are also described in Chemotherapy
Service, Ed., M. C. Perry, Williams & Wilkins, Baltimore, Md.
(1992). The chemotherapeutic agent may precede, or follow
administration of the immunoadjuvant or may be given simultaneously
therewith. Additionally, an anti-oestrogen compound such as
tamoxifen or an anti-progesterone such as onapristone (see, EP
616812) may be given in dosages known for such molecules. It may be
desirable to also administer antibodies against other immune
disease associated or tumor associated antigens, such as antibodies
which bind to CD20, CD11a, CD18, ErbB2, EGFR, ErbB3, ErbB4, or
vascular endothelial factor (VEGF). Alternatively, or in addition,
two or more antibodies binding the same or two or more different
antigens disclosed herein may be coadministered to the patient.
Sometimes, it may be beneficial to also administer one or more
cytokines to the patient. In one embodiment, the PRO polypeptides
are coadministered with a growth inhibitory agent. For example, the
growth inhibitory agent may be administered first, followed by a
PRO polypeptide. However, simultaneous administration or
administration first is also contemplated. Suitable dosages for the
growth inhibitory agent are those presently used and may be lowered
due to the combined action (synergy) of the growth inhibitory agent
and the PRO polypeptide. For the treatment or reduction in the
severity of immune related disease, the appropriate dosage of an a
compound of the invention will depend on the type of disease to be
treated, as defined above, the severity and course of the disease,
whether the agent is administered for preventive or therapeutic
purposes, previous therapy, the patient's clinical history and
response to the compound, and the discretion of the attending
physician. The compound is suitably administered to the patient at
one time or over a series of treatments.
[0413] For example, depending on the type and severity of the
disease, about 1 mg/kg to 15 mg/kg (e.g., 0.1-20 mg/kg) of
polypeptide or antibody is an initial candidate dosage for
administration to the patient, whether, for example, by one or more
separate administrations, or by continuous infusion. A typical
daily dosage might range from about 1 mg/kg to 100 mg/kg or more,
depending on the factors mentioned above. For repeated
administrations over several days or longer, depending on the
condition, the treatment is sustained until a desired suppression
of disease symptoms occurs. However, other dosage regimens may be
useful. The progress of this therapy is easily monitored by
conventional techniques and assays.
[0414] P. Articles of Manufacture
[0415] In another embodiment of the invention, an article of
manufacture containing materials (e.g., comprising a PRO molecule)
useful for the diagnosis or treatment of the disorders described
above is provided. The article of manufacture comprises a container
and an instruction. Suitable containers include, for example,
bottles, vials, syringes, and test tubes. The containers may be
formed from a variety of materials such as glass or plastic. The
container holds a composition which is effective for diagnosing or
treating the condition and may have a sterile access port (for
example the container may be an intravenous solution bag or a vial
having a stopper pierceable by a hypodermic injection needle). The
active agent in the composition is usually a polypeptide or an
antibody of the invention. An instruction or label on, or
associated with, the container indicates that the composition is
used for diagnosing or treating the condition of choice. The
article of manufacture may further comprise a second container
comprising a pharmaceutically-acceptable buffer, such as
phosphate-buffered saline, Ringer's solution and dextrose solution.
It may further include other materials desirable from a commercial
and user standpoint, including other buffers, diluents, filters,
needles, syringes, and package inserts with instructions for
use.
[0416] Q. Diagnosis and Prognosis of Immune Related Disease
[0417] Cell surface proteins, such as proteins which are
overexpressed in certain immune related diseases, are excellent
targets for drug candidates or disease treatment. The same proteins
along with secreted proteins encoded by the genes amplified in
immune related disease states find additional use in the diagnosis
and prognosis of these diseases. For example, antibodies directed
against the protein products of genes amplified in multiple
sclerosis, rheumatoid arthritis, inflammatory bowel disorder, or
another immune related disease, can be used as diagnostics or
prognostics.
[0418] For example, antibodies, including antibody fragments, can
be used to qualitatively or quantitatively detect the expression of
proteins encoded by amplified or overexpressed genes ("marker gene
products"). The antibody preferably is equipped with a detectable,
e.g., fluorescent label, and binding can be monitored by light
microscopy, flow cytometry, fluorimetry, or other techniques known
in the art. These techniques are particularly suitable, if the
overexpressed gene encodes a cell surface protein Such binding
assays are performed essentially as described above.
[0419] In situ detection of antibody binding to the marker gene
products can be performed, for example, by immunofluorescence or
immunoelectron microscopy. For this purpose, a histological
specimen is removed from the patient, and a labeled antibody is
applied to it, preferably by overlaying the antibody on a
biological sample. This procedure also allows for determining the
distribution of the marker gene product in the tissue examined. It
will be apparent for those skilled in the art that a wide variety
of histological methods are readily available for in situ
detection.
[0420] The following examples are offered for illustrative purposes
only, and are not intended to limit the scope of the present
invention in any way.
[0421] All patent and literature references cited in the present
specification are hereby incorporated by reference in their
entirety.
EXAMPLES
[0422] Commercially available reagents referred to in the examples
were used according to manufacturer's instructions unless otherwise
indicated. The source of those cells identified in the following
examples, and throughout the specification, by ATCC accession
numbers is the American Type Culture Collection, Manassas, Va.
Example 1
Isolation of cDNA Clones Encoding Human PRO1031
[0423] The extracellular domain (ECD) sequences (including the
secretion signal, if any) of from about 950 known secreted proteins
from the Swiss-Prot public protein database were used to search
expressed sequence tag (EST) databases. The EST databases included
public EST databases (e.g., GenBank, Merck/Wash U.) and a
proprietary EST DNA database (LIFESEQ.RTM., Incyte Pharmaceuticals,
Palo Alto, Calif.). The search was performed using the computer
program BLAST or BLAST2 (Altshul et al., Methods in Enzymology,
266:460-480 (1996)) as a comparison of the ECD protein sequences to
a 6 frame translation of the EST sequence. Those comparisons
resulting in a BLAST score of 70 (or in some cases, 90) or greater
that did not encode known proteins were clustered and assembled
into consensus DNA sequences with the program "phrap" (Phil Green,
University of Washington, Seattle, Wash.).
[0424] An initial virtual sequence fragment (consensus assembly)
was assembled relative to other EST sequences using phrap. The
initial consensus DNA sequence was extended using repeated cycles
of BLAST and phrap to extend the consensus sequence as far as
possible using the sources of EST sequences discussed above. The
results of this consensus assembly is referred to as DNA47332.
[0425] One sequence comprising the consensus assembly, W74558
(clone 344649) was further examined. The sequence was obtained from
the IMAGE consortium and analyzed. Lennon et al., Genomics, 33: 151
(1996). DNA sequencing gave the full-length DNA sequence for
PRO1031 [herein designated as DNA59294-1381] (SEQ ID NO:1) and the
derived PRO1031 protein sequence (UNQ516) (SEQ ID NO: 2).
[0426] The entire nucleotide sequence of DNA59294-1381 is shown in
FIG. 1 (SEQ ID NO:1). Clone DNA59294-1381 contains a single open
reading frame with an apparent translational initiation site at
nucleotide positions 42-44 and ending at the stop codon at
nucleotide positions 582-584 (FIG. 1; SEQ ID NO:1). The predicted
polypeptide precursor is 180 amino acids long (FIG. 2; SEQ ID
NO:2). The full-length PRO1031 (UNQ516) protein shown in FIG. 2
(SEQ ID NO:2) has an estimated molecular weight of about 20,437
daltons and a pI of about 9.58. Clone DNA59294-1381 has been
deposited with the ATCC, and has been assigned deposit number
209866. In the event of any sequencing irregularities or errors
with the sequences provided herein, it is understood that the
deposited clone contains the correct sequence for DNA59624-1381
(SEQ ID NO:1). Furthermore, the sequences provided herein are the
result of known sequencing techniques.
[0427] Analysis of the amino acid sequence of the full-length
PRO1031 polypeptide (UNQ516) (SEQ ID NO:2) suggests that it is a
novel interleukin-17 homolog, herein designated as IL-17B.
[0428] Further analysis of the amino acid sequence of SEQ ID NO:2
reveals that the putative signal peptide is at about amino acids
1-20 of SEQ ID NO:2. An N-glycosylation site is at about amino
acids 75-78 of SEQ ID NO:2. A region having sequence identity with
IL-17 is at about amino acids 96-180. The corresponding nucleotides
can be routinely determined given the sequences provided
herein.
Example 2
Isolation of cDNA clones Encoding Human PRO1122
[0429] An expressed sequence tag (EST) DNA database (LIFESEQ.RTM.,
Incyte Pharmaceuticals, Palo Alto, Calif.) was searched and an EST
was identified. The EST was Incyte 1347523 also called DNA49665.
Based on DNA49665, oligonucleotides were synthesized: 1) to
identify by PCR a cDNA library that contained the sequence of
interest, and 2) for use as probes to isolated a clone of the
full-length coding sequence for the PRO1122. [e.g., Sambrook et
al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring
Harbor Laboratory Press, 1989); Dieffenbach et al., PCR Primer: A
Laboratory Manual (Cold Spring Harbor Laboratory Press, 1995)].
[0430] Forward and reverse PCR primers generally range from 20 to
30 nucleotides and are often designed to give a PCR product of
about 100-1000 bp in length. The probes sequences are typically
40-55 bp in length. In some cases, additional oligonucleotides are
synthesized when the consensus sequence is greater than about 1-1.5
kpb. In order to screen several libraries for a full-length clone,
DNA from the libraries was screened by PCR amplification, as per
Ausuble et al., Current Protocols in Molecular Biology, with the
PCR primer pair. A positive library was then used to isolate clones
encoding the gene of interest using the probe oligonucleotide and
one of the primer pairs.
[0431] PCR primers (forward, reverse and hybridization) were
synthesized:
TABLE-US-00007 forward PCR primer: (SEQ ID NO:19)
5'-ATCCACAGAAGCTGGCCTTCGCCG-3' reverse PCR primer: (SEQ ID NO:20)
5'-GGGACGTGGATGAACTCGGTGTGG-3' hybridization probe: (SEQ ID NO:21)
5'-TATCCACAGAAGCTGGCCTTCGCCGAGTGCCTGTGCAGAG-3'.
[0432] In order to screen several libraries for a source of a
full-length clone, DNA from the libraries was screened by PCR
amplification with the PCR primer pair identified above. A positive
library was then used to isolate clones encoding the PRO1122 gene
using the probe oligonucleotide and one of the PCR primers.
[0433] RNA for construction of the cDNA libraries was isolated from
human fetal kidney tissue. The cDNA libraries used to isolate the
cDNA clones were constructed using standard methods using
commercially available reagents such as those from Invitrogen, San
Diego, Calif. The cDNA was primed with oligo dT containing a NotI
site, linked with blunt to SalI hemikinased adaptors, cleaved with
NotI, sized appropriately by gel electrophoresis, and cloned in a
defined orientation into a suitable cloning vector (such as pRKB or
pRKD; pRK5B is a precursor of pRK5D that does not contain the SfiI
site; see, Holmes et al., Science, 235: 1278-1280 (1991)) in the
unique XhoI and NotI sites.
[0434] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for PRO1122 [herein designated as
DNA62377-1381-1](SEQ ID NO:3) and the derived protein PRO1122
sequence (UNQ561) (SEQ ID NO:4).
[0435] The entire nucleotide sequence of DNA62377-1381-1 (SEQ ID
NO:3) is shown in FIG. 3 (SEQ ID NO:3). Clone DNA62377-1381-1 (SEQ
ID NO:3) contains a single open reading frame with an apparent
translational initiation site at nucleotide positions 50-52 and
ending at the stop codon at nucleotide positions 641-643 of SEQ ID
NO:3 (FIG. 3). The predicted polypeptide precursor is 197 amino
acids long (FIG. 4; SEQ ID NO:4). The full-length PRO1122 protein
shown in FIG. 4 (UNQ561) (SEQ ID NO:4) has an estimated molecular
weight of about 21765 daltons and a pI of about 8.53. Clone
DNA62377-1381-1 has been deposited with the ATCC on Dec. 22, 1998
and has been assigned deposit number 203552. It is understood that
in the event or a sequencing irregularity or error in the sequences
provided herein, the correct sequence is the sequence deposited.
Furthermore, all sequences provided herein are the result of known
sequencing techniques.
[0436] Analysis of the amino acid sequence of the isolated
full-length PRO1122 (UNQ561) suggests that it possesses similarity
with IL-17, thereby indicating that PRO1122 (UNQ561) may be a novel
cytokine and is herein designated IL-17C. FIG. 4 (SEQ ID NO:4) also
shows the approximate locations of the signal peptide, leucine
zipper pattern, and a region having sequence identity with
IL-17.
Example 3
Isolation of cDNA Clones Encoding Human PRO10272
[0437] The extracellular domain (ECD) sequences (including the
secretion signal sequence, if any) from about 950 known secreted
proteins from the Swiss-Prot public database were used to search
genomic DNA sequences from GenBank. The search was performed using
the computer program BLAST or BLAST2 [Altschul et al., Methods in
Enzymology, 266:460-480 (1996)] as a comparison of the ECD protein
sequences to a 6 frame translation of the EST sequences. Those
comparisons resulting in a BLAST score of 70 (or in some cases, 90)
or greater that did not encode known proteins were clustered and
assembled into consensus DNA sequences with the program "phrap"
(Phil Green, University of Washington, Seattle, Wash.).
[0438] A consensus DNA sequence was assembled relative to other EST
sequences using phrap as described above. This consensus sequence
is herein designated DNA146646. In some cases, the consensus
sequence derives from an intermediate consensus DNA sequence which
was extended using repeated cycles of BLAST and phrap to extend
that intermediate consensus sequence as far as possible using the
sources of EST sequences discussed above.
[0439] Based on the DNA146646 consensus sequence, oligonucleotides
were synthesized: 1) to identify by PCR a cDNA library that
contained the sequence of interest, and 2) for use as probes to
isolate a clone of the full-length coding sequence for PRO10272.
Forward and reverse PCR primers generally range from 20 to 30
nucleotides and are often designed to give a PCR product of about
100-1000 bp in length. The probe sequences are typically 40-55 bp
in length. In some cases, additional oligonucleotides are
synthesized when the consensus sequence is greater than about 1-1.5
kbp. In order to screen several libraries for a full-length clone,
DNA from the libraries was screened by PCR amplification, as per
Ausubel et al., Current Protocols in Molecular Biology, supra, with
the PCR primer pair. A positive library was then used to isolate
clones encoding the gene of interest using the probe
oligonucleotide and one of the primer pairs. PCR primers (forward
and reverse) were synthesized:
TABLE-US-00008 forward PCR primer:
5'-GTTGCATTCTTTGGCAATGGTCATGGGA-3' (SEQ ID NO:22) reverse PCR
primer: 5'-GGTCCATGTGGGAGCCTGTCTGTA-3' (SEQ ID NO:23)
Additionally, a synthetic oligonucleotide hybridization probe was
constructed from the consensus DNA146646 sequence which had the
following nucleotide sequence:
TABLE-US-00009 hybridization probe (SEQ ID NO:24)
5'-CAGCAGCTCCTCAGAGGTGTCCTGCCCTTTGCTGGGGCAGCAGC T-3'
[0440] RNA for construction of the cDNA libraries was isolated from
human testis tissue. The cDNA libraries used to isolate the cDNA
clones were constructed by standard methods using commercially
available reagents such as those from Invitrogen, San Diego, Calif.
The cDNA was primed with oligo dT containing a NotI site, linked
with blunt to SalI hemikinased adaptors, cleaved with NotI, sized
appropriately by gel electrophoresis, and cloned in a defined
orientation into a suitable cloning vector (such as pRKB or pRKD;
pRK5B is a precursor of pRK5D that does not contain the SfiI site;
see, Holmes et al., Science, 253:1278-1280 (1991)) in the unique
XhoI and NotI sites.
[0441] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for a full-length PRO10272
polypeptide (designated herein as DNA 147531-2821 [FIG. 5, SEQ ID
NO: 5]) and the derived protein sequence for that PRO10272
polypeptide.
[0442] The full length clone identified above contained a single
open reading frame with an apparent translational initiation site
at nucleotide positions 259-261 and a stop signal at nucleotide
positions 790-792 (FIG. 5, SEQ ID NO:5). The predicted polypeptide
precursor is 177 amino acids long, has a calculated molecular
weight of approximately 20,330 daltons and an estimated pI of
approximately 8.78. Analysis of the full-length PRO10272 sequence
shown in FIG. 6 (SEQ ID NO:6) evidences the presence of a variety
of important polypeptide domains as shown in FIG. 6, wherein the
locations given for those important polypeptide domains are
approximate as described above. Clone DNA147531-2821 has been
deposited with ATCC on Jan. 11, 2000 and is assigned ATCC deposit
no. PTA-1185.
[0443] Analysis of the amino acid sequence of the isolated
full-length PRO10272 suggests that it possesses similarity with
IL-17 and various homologs of it, thereby indicating that PRO10272
may be a novel cytokine and is herein designated IL-17E.
Specifically, an analysis of the Dayhoff database (version 35.45
SwissProt 35), using the ALIGN-2 sequence alignment analysis of the
full-length sequence shown in FIG. 6 (SEQ ID NO:6), evidenced
sequence identity between the PRO10272 amino acid sequence and the
following Dayhoff sequences: P_Y22197, P_W85620, AF18469.sub.--1,
P_Y41762, P_Y28235, P_W97350, P_Y22198, P_Y28236, P_W28514,
P_W13651.
Example 4
Isolation of cDNA Clones Encoding a Human PRO21175
[0444] An expressed sequence tag (EST) DNA database from
Merck/Washington University was searched and an EST was identified
which showed homology to Interleukin-17.
[0445] A pool of 50 different human cDNA libraries from various
tissues was used in cloning. The cDNA libraries used to isolate the
cDNA clones encoding human PRO21175 were constructed by standard
methods using commercially available reagents such as those from
Invitrogen, San Diego, Calif. The cDNA was primed with oligo dT
containing a NotI site, linked with blunt to SalI hemikinased
adaptors, cleaved with NotI, sized appropriately by gel
electrophoresis, and cloned in a defined orientation into a
suitable cloning vector (such as pRKB or pRKD; pRK5B is a precursor
of pRK5D that does not contain the SfiI site; see, Holmes et al.,
Science, 253:1278-1280 (1991)) in the unique XhoI and NotI.
[0446] Oligonucleotides probes based upon the above described EST
sequence were then synthesized: 1) to identify by PCR a cDNA
library that contained the sequence of interest, and 2) for use as
probes to isolate a clone of the full-length coding sequence for
PRO21175. Forward and reverse PCR primers generally range from 20
to 30 nucleotides and are often designed to give a PCR product of
about 100-1000 bp in length. The probe sequences are typically
40-55 bp in length. In order to screen several libraries for a
full-length clone, DNA from the libraries was screened by PCR
amplification, as per Ausubel et al., Current Protocols in
Molecular Biology, supra, with the PCR primer pair. A positive
library was then used to isolate clones encoding the gene of
interest using the probe oligonucleotide and one of the primer
pairs.
[0447] The oligonucleotide probes employed were as follows:
TABLE-US-00010 forward PCR primer (SEQ ID NO:25)
5'-GCTCAGTGCCTTCCACCACACGC-3' reverse PCR primer (SEQ ID NO:26)
5'-CTGCGTCCTTCTCCGGCTCGG-3' hybridization probe (SEQ ID NO:27) 5'
CGTTCCGTCTACACCGAGGCCTACGTCACCATCCCCGTGGGCTG C-3'
[0448] A full length clone was identified that contained a single
open reading frame with an apparent translational initiation site
at nucleotide positions 1-3 and a stop signal at nucleotide
positions 607-609 (FIG. 7, SEQ ID NO:7). The predicted polypeptide
precursor is 202 amino acids long, has a calculated molecular
weight of approximately 21,879 daltons and an estimated pI of
approximately 9.3. Analysis of the full-length PRO21175 sequence
shown in FIG. 8 (SEQ ID NO:8) evidences the presence of a variety
of important polypeptide domains as shown in FIG. 8, wherein the
locations given for those important polypeptide domains are
approximate as described above. Chromosome mapping evidences that
the PRO21175-encoding nucleic acid maps to 13q11 in humans. Clone
DNA173894-2947 has been deposited with ATCC on Jun. 20, 2000 and is
assigned ATCC deposit no. PTA-2108.
[0449] Analysis of the amino acid sequence of the isolated
full-length PRO21175 suggests that it possesses similarity with
IL-17, thereby indicating that PRO21175 may be a novel cytokine and
is herein designated IL-17D. Specifically, an analysis of the
protein database (version 35.45 SwissProt 35), using the ALIGN-2
sequence alignment analysis of the full-length sequence shown in
FIG. 8 (SEQ ID NO:8), evidenced sequence identity between the
PRO21175 amino acid sequence and the following sequence:
AF152099.sub.--1.
Example 5
Isolation of cDNA Clones Encoding a Human PRO5801
[0450] The extracellular domain (ECD) sequences (including the
secretion signal sequence, if any) from about 950 known secreted
proteins from the Swiss-Prot public database were used to search
EST databases. The EST databases included (1) public EST databases
(e.g., GenBank) and (2) a proprietary EST database (LIFESEQ.RTM.,
Incyte Pharmaceuticals, Palo Alto, Calif.). The search was
performed using the computer program BLAST or BLAST2 [Altschul et
al., Methods in Enzymology, 266:460-480 (1996)] as a comparison of
the ECD protein sequences to a 6 frame translation of the EST
sequences. Those comparisons resulting in a BLAST score of 70 (or
in some cases, 90) or greater that did not encode known proteins
were clustered and assembled into consensus DNA sequences with the
program "phrap" (Phil Green, University of Washington, Seattle,
Wash.).
[0451] A consensus DNA sequence was assembled relative to other EST
sequences using phrap as described above. This consensus sequence
is herein designated DNA105850. In some cases, the consensus
sequence derives from an intermediate consensus DNA sequence which
was extended using repeated cycles of BLAST and phrap to extend
that intermediate consensus sequence as far as possible using the
sources of EST sequences discussed above.
[0452] Based on the DNA105850 consensus sequence, oligonucleotides
were synthesized: 1) to identify by PCR a cDNA library that
contained the sequence of interest, and 2) for use as probes to
isolate a clone of the full-length coding sequence for PRO5801.
Forward and reverse PCR primers generally range from 20 to 30
nucleotides and are often designed to give a PCR product of about
100-1000 bp in length. The probe sequences are typically 40-55 bp
in length. In some cases, additional oligonucleotides are
synthesized when the consensus sequence is greater than about 1-1.5
kbp. In order to screen several libraries for a full-length clone,
DNA from the libraries was screened by PCR amplification, as per
Ausubel et al., Current Protocols in Molecular Biology, supra, with
the PCR primer pair. A positive library was then used to isolate
clones encoding the gene of interest using the probe
oligonucleotide and one of the primer pairs.
[0453] PCR primers (forward and reverse) were synthesized:
TABLE-US-00011 forward PCR primer 1 5'-ACTCCATATTTTCCTACTTGTGGCA-3'
(SEQ ID NO:28) forward PCR primer 2 5'-CCCAAAGTGACCTAAGAAC-3' (SEQ
ID NO:29) reverse PCR primer 5'-TCACTGAATTTCTTCAAAACCATTGCA-3' (SEQ
ID NO:30)
Additionally, a synthetic oligonucleotide hybridization probe was
constructed from the consensus DNA105850 sequence which had the
following nucleotide sequence
TABLE-US-00012 hybridization probe (SEQ ID NO:31)
5'-TGTGGCAGCGACTGCATCCGACATAAAGGAACAGTTGTGCTCTGC CCACA-3'
[0454] RNA for construction of the cDNA libraries was isolated from
human fetal liver tissue. The cDNA libraries used to isolate the
cDNA clones were constructed by standard methods using commercially
available reagents such as those from Invitrogen, San Diego, Calif.
The cDNA was primed with oligo dT containing a NotI site, linked
with blunt to SalI hemikinased adaptors, cleaved with NotI, sized
appropriately by gel electrophoresis, and cloned in a defined
orientation into a suitable cloning vector (such as pRKB or pRKD;
pRK5B is a precursor of pRK5D that does not contain the SfiI site;
see, Holmes et al., Science, 253:1278-1280 (1991)) in the unique
XhoI and NotI sites.
[0455] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for a full-length PRO5801
polypeptide (designated herein as DNA115291-2681 [FIG. 11, SEQ ID
NO: 11]) and the derived protein sequence for that PRO5801
polypeptide.
[0456] The full length clone identified above contained a single
open reading frame with an apparent translational initiation site
at nucleotide positions 7-9 and a stop signal at nucleotide
positions 1513-1515 (FIG. 12, SEQ ID NO:12). The predicted
polypeptide precursor is 502 amino acids long, has a calculated
molecular weight of approximately 55,884 daltons and an estimated
pI of approximately 8.52. Analysis of the full-length PRO5801
sequence shown in FIG. 12 (SEQ ID NO:12) evidences the presence of
a variety of important polypeptide domains as shown in FIG. 12,
wherein the locations given for those important polypeptide domains
are approximate as described above. Clone DNA115291-2681 has been
deposited with ATCC on Jun. 8, 1999 and is assigned ATCC deposit
no. PTA-202.
[0457] An analysis of the Dayhoff database shows that PRO5801 has
sequence similarity to an IL-17 receptor protein and PRO5801 is
also designated herein as IL-17RH1 as described in Example 22 of
the present application. Specifically, an analysis of the Dayhoff
database (version 35.45 SwissProt 35), using the ALIGN-2 sequence
alignment analysis of the fall-length sequence shown in FIG. 12
(SEQ ID NO:12), evidenced sequence identity between the PRO5801
amino acid sequence and the following Dayhoff sequences:
HSU58917.sub.--1, P_W92409, P_W61272, P_WO4185, P_W61271, P_WO4184,
P_W92408, GEN13979, MMU31993.sub.--1 and YSO2_CAEEL.
Example 6
Isolation of cDNA Clones Encoding a Human PRO20040
[0458] An expressed sequence tag (EST) DNA database
(Merck/Washington University) was searched and an EST was
identified which showed homology to Interleukin 17 receptor.
[0459] RNA for construction of cDNA libraries was then isolated
from a pool of 50 different human cDNA libraries. The cDNA
libraries used to isolate the cDNA clones encoding human PRO20040
were constructed by standard methods using commercially available
reagents such as those from Invitrogen, San Diego, Calif. The cDNA
was primed with oligo dT containing a NotI site, linked with blunt
to SalI hemikinased adaptors, cleaved with NotI, sized
appropriately by gel electrophoresis, and cloned in a defined
orientation into a suitable cloning vector (such as pRKB or pRKD;
pRK5B is a precursor of pRK5D that does not contain the SfiI site;
see, Holmes et al., Science, 253:1278-1280 (1991)) in the unique
XhoI and NotI.
[0460] Oligonucleotides probes based upon the above described EST
sequence were then synthesized: 1) to identify by PCR a cDNA
library that contained the sequence of interest, and 2) for use as
probes to isolate a clone of the full-length coding sequence for
PRO20040. Forward and reverse PCR primers generally range from 20
to 30 nucleotides and are often designed to give a PCR product of
about 100-1000 bp in length. The probe sequences are typically
40-55 bp in length. In order to screen several libraries for a
full-length clone, DNA from the libraries was screened by PCR
amplification, as per Ausubel et al., Current Protocols in
Molecular Biology, supra, with the PCR primer pair. A positive
library was then used to isolate clones encoding the gene of
interest using the probe oligonucleotide and one of the primer
pairs.
[0461] The oligonucleotide probes employed were as follows:
TABLE-US-00013 forward PCR primer (SEQ ID NO:32)
5'-CCGACTTCTTGCAGGGCCGG-3' reverse PCR primer (SEQ ID NO:33)
5'-GCAGCACGCAGCTGAGCGAG-3' hybridization probe (SEQ ID NO:34)
5'-AGCGAGTGGCTACAGGATGGGGTGTCCGGGCCC-3'
[0462] A full length clone was identified that contained a single
open reading frame with an apparent translational initiation site
at nucleotide positions 233-235 and a stop signal at nucleotide
positions 2348-2350 (FIG. 13, SEQ ID NO:13). The predicted
polypeptide precursor is 705 amino acids long, has a calculated
molecular weight of approximately 76,898 daltons and an estimated
pI of approximately 6.08 Analysis of the full-length PRO20040
sequence shown in FIG. 14 (SEQ ID NO:14) evidences the presence of
a variety of important polypeptide domains as shown in FIG. 14,
wherein the locations given for those important polypeptide domains
are approximate as described above. Clone DNA164625-2890 has been
deposited with ATCC on Mar. 21, 2000 and is assigned ATCC deposit
no. PTA-1535.
[0463] An analysis of the Dayhoff database shows that PRO20040 has
sequence similarity to an IL-17 receptor protein and PRO20040 is
also designated herein as IL-17RH2 as described in Example 20 of
the present application. Specifically, an analysis of the Dayhoff
database (version 35.45 SwissProt 35), using the ALIGN-2 sequence
alignment analysis of the full-length sequence shown in FIG. 14
(SEQ ID NO:14), evidenced sequence identity between the PRO20040
amino acid sequence and the following Dayhoff sequences:
HSU58917.sub.--1.
Example 7
Isolation of cDNA Clones Encoding a Human PRO9877
[0464] DNA119502-2789 was identified by applying a proprietary
signal sequence finding algorithm developed by Genentech, Inc.
(South San Francisco, Calif.) upon ESTs as well as clustered and
assembled EST fragments from public (e.g., GenBank) and/or private
(LIFESEQ.RTM., Incyte Pharmaceuticals, Inc., Palo Alto, Calif.)
databases. The signal sequence algorithm computes a secretion
signal score based on the character of the DNA nucleotides
surrounding the first and optionally the second methionine codon(s)
(ATG) at the 5'-end of the sequence or sequence fragment under
consideration. The nucleotides following the first ATG must code
for at least 35 unambiguous amino acids without any stop codons. If
the first ATG has the required amino acids, the second is not
examined. If neither meets the requirement, the candidate sequence
is not scored. In order to determine whether the EST sequence
contains an authentic signal sequence, the DNA and corresponding
amino acid sequences surrounding the ATG codon are scored using a
set of seven sensors (evaluation parameters) known to be associated
with secretion signals.
[0465] Use of the above described signal sequence algorithm allowed
identification of an EST cluster sequence from the LIFESEQ.RTM.
database, designated herein as CLU42993. This EST cluster sequence
was then compared to a variety of expressed sequence tag (EST)
databases which included public EST databases (e.g., GenBank) and a
proprietary EST DNA database (LIFESEQ.RTM. Incyte Pharmaceuticals,
Palo Alto, Calif.) to identify existing homologies. The homology
search was performed using the computer program BLAST or BLAST2
(Altshul et al., Methods in Enzymology, 266:460-480 (1996)). Those
comparisons resulting in a BLAST score of 70 (or in some cases, 90)
or greater that did not encode known proteins were clustered and
assembled into a consensus DNA sequence with the program "phrap"
(Phil Green, University of Washington, Seattle, Wash.). The
consensus sequence obtained therefrom is herein designated
DNAFROM.
[0466] In light of an observed sequence homology between the
DNAFROM sequence and an EST sequence encompassed within clone no.
700536 from the LIFESEQ.RTM. database, clone no. 700536 was
purchased and the cDNA insert was obtained and sequenced. It was
found herein that that cDNA insert encoded a full-length protein.
The sequence of this cDNA insert is shown in FIG. 15 and is herein
designated as DNA119502-2789.
[0467] Clone DNA119502-2789 contains a single open reading frame
with an apparent translational initiation site at nucleotide
positions 106-108 and ending at the stop codon at nucleotide
positions 2107-2109 (FIG. 15; SEQ ID NO:15). The predicted
polypeptide precursor is 667 amino acids long (FIG. 16). The
full-length PRO9877 protein shown in FIG. 16 has an estimated
molecular weight of about 74,810 daltons and a pI of about 9.55.
Analysis of the full-length PRO9877 sequence shown in FIG. 16 (SEQ
ID NO:16) evidences the presence of a variety of important
polypeptide domains as shown in FIG. 16, wherein the locations
given for those important polypeptide domains are approximate as
described above. Clone DNA119502-2789 has been deposited with ATCC
on Dec. 22, 1999 and is assigned ATCC deposit no. PTA-1082.
[0468] An analysis of the Dayhoff database shows that PRO9877 has
sequence similarity to an IL-17 receptor protein and PRO9877 is
also designated herein as IL-17RH3. Specifically, an analysis of
the Dayhoff database (version 35.45 SwissProt 35), using the
ALIGN-2 sequence alignment analysis of the full-length sequence
shown in FIG. 16 (SEQ ID NO:16), evidenced sequence identity
between the PRO9877 amino acid sequence and the following Dayhoff
sequences: P_W61272, HSU58917.sub.--1, P_WO4185, P_W92409,
GEN13979, P_WO4184, P_W92408, MMU31993.sub.--1, P_W61271, and
AF090114.sub.--1.
Example 8
Isolation of cDNA Clones Encoding a Human PRO20026
[0469] The extracellular domain (ECD) sequences (including the
secretion signal sequence, if any) from about 950 known secreted
proteins from the Swiss-Prot public database were used to search
EST databases. The EST databases included a proprietary EST
database (LIFESEQ.RTM., Incyte Pharmaceuticals, Palo Alto, Calif.).
The search was performed using the computer program BLAST or BLAST2
[Altschul et al., Methods in Enzymology, 266:460-480 (1996)] as a
comparison of the ECD protein sequences to a 6 frame translation of
the EST sequences. Those comparisons resulting in a BLAST score of
70 (or in some cases, 90) or greater that did not encode known
proteins were clustered and assembled into consensus DNA sequences
with the program "phrap" (Phil Green, University of Washington,
Seattle, Wash.).
[0470] A consensus DNA sequence was assembled relative to other EST
sequences using phrap as described above. This consensus sequence
is herein designated DNA149870. In some cases, the DNA149870
consensus sequence derives from an intermediate consensus DNA
sequence which was extended using repeated cycles of BLAST and
phrap to extend that intermediate consensus sequence as far as
possible using the sources of EST sequences discussed above.
[0471] Based on the DNA149870 consensus sequence, flip cloning was
performed. Oligonucleotides were synthesized: 1) to identify by PCR
a cDNA library that contained the sequence of interest, and 2) for
use as probes to isolate a clone of the full-length coding sequence
for PRO20026. Forward and reverse PCR primers generally range from
20 to 30 nucleotides and are often designed to give a PCR product
of about 100-1000 bp in length. The probe sequences are typically
40-55 bp in length. In some cases, additional oligonucleotides are
synthesized when the consensus sequence is greater than about 1-1.5
kbp. In order to screen several libraries for a full-length clone,
DNA from the libraries was screened by Flip PCR amplification, as
per Schanke et al., BioTechniques, 16:414-416 (1994), with the PCR
primer pair. A positive library was then used to isolate clones
encoding the gene of interest using the probe oligonucleotide and
one of the primer pairs.
[0472] PCR primers (forward and reverse) were synthesized:
TABLE-US-00014 forward PCR primer: 5'-CGTTGTTTGTCAGTGGAGAGCAGGG-3'
(SEQ ID NO:35) reverse PCR primer 5'-CAGGAACACCTGAGGCAGAAGCG-3'
(SEQ ID NO: 36)
Additionally, a synthetic oligonucleotide hybridization probe was
constructed from the consensus DNA149870 sequence which had the
following nucleotide sequence
TABLE-US-00015 hybridization probe (SEQ ID NO: 37)
5'-CTATCTCCCTGCCAGGAGGCCGGAGTGGGGGAGGTCAGAC-3'
[0473] RNA for construction of the cDNA libraries was isolated from
human tissue. The cDNA libraries used to isolate the cDNA clones
were constructed by standard methods using commercially available
reagents such as those from Invitrogen, San Diego, Calif. The cDNA
was primed with oligo dT containing a NotI site, linked with blunt
to SalI hemikinased adaptors, cleaved with NotI, sized
appropriately by gel electrophoresis, and cloned in a defined
orientation into a suitable cloning vector (such as pRKB or pRKD;
pRK5B is a precursor of pRK5D that does not contain the SfiI site;
see, Holmes et al., Science, 253:1278-1280 (1991)) in the unique
XhoI and NotI sites.
[0474] DNA sequencing of the clones isolated as described above
gave the full-length DNA sequence for a full-length PRO20026
polypeptide (designated herein as DNA154095-2998 [FIG. 17, SEQ ID
NO: 17]) and the derived protein sequence for that PRO20026
polypeptide.
[0475] The full length clone identified above contained a single
open reading frame with an apparent translational initiation site
at nucleotide positions 70-72 and a stop signal at nucleotide
positions 2254-2256 (FIG. 17, SEQ ID NO: 17). The predicted
polypeptide precursor is 728 amino acids long, has a calculated
molecular weight of approximately 81,310 daltons and an estimated
pI of approximately 6.84. Analysis of the full-length PRO20026
sequence shown in FIG. 18 (SEQ ID NO: 18) evidences the presence of
a variety of important polypeptide domains as shown in FIG. 18,
wherein the locations given for those important polypeptide domains
are approximate as described above. Clone DNA154095-2998 has been
deposited with ATCC on Oct. 10, 2000 and is assigned ATCC Deposit
No. PTA-2591.
[0476] An analysis of the Dayhoff database shows that PRO20026 has
sequence similarity to an IL-17 receptor protein and PRO2006 is
also designated herein as IL-17RH4. Specifically, an analysis of
the Dayhoff database (version 35.45 SwissProt 35), using the
ALIGN-2 sequence alignment analysis of the full-length sequence
shown in FIG. 18 (SEQ ID NO: 18), evidenced sequence identity
between the PRO20026 amino acid sequence and the following Dayhoff
sequences: T42695, P_WO4185, P_W92409, P_W61272,
NM.sub.--014339.sub.--1, HSU58917.sub.--1, MMU31993.sub.--1,
GEN13979, P_WO4184, P_W61271.
Example 9
Use of PRO as a Hybridization Probe
[0477] The following method describes use of a nucleotide sequence
encoding PRO as a hybridization probe.
[0478] DNA comprising the coding sequence of full-length or mature
PRO as disclosed herein is employed as a probe to screen for
homologous DNAs (such as those encoding naturally-occurring
variants of PRO) in human tissue cDNA libraries or human tissue
genomic libraries.
[0479] Hybridization and washing of filters containing either
library DNAs is performed under the following high stringency
conditions. Hybridization of radiolabeled PRO-derived probe to the
filters is performed in a solution of 50% formamide, 5.times.SSC,
0.1% SDS, 0.1% sodium pyrophosphate, 50 mM sodium phosphate, pH
6.8, 2.times.Denhardt's solution, and 10% dextran sulfate at
42.degree. C. for 20 hours. Washing of the filters is performed in
an aqueous solution of 0.1.times.SSC and 0.1% SDS at 42.degree.
C.
[0480] DNAs having a desired sequence identity with the DNA
encoding full-length native sequence PRO can then be identified
using standard techniques known in the art.
Example 10
In Situ Hybridization
[0481] In situ hybridization is a powerful and versatile technique
for the detection and localization of nucleic acid sequences within
cell or tissue preparations. It may be useful, for example, to
identify sites of gene expression, analyze the tissue distribution
of transcription, identify and localize viral infection, follow
changes in specific mRNA synthesis and aid in chromosome
mapping.
[0482] In situ hybridization was performed following an optimized
version of the protocol by Lu and Gillett, Cell Vision, 1:169-176
(1994), using PCR-generated .sup.33P-labeled riboprobes. Briefly,
formalin-fixed, paraffin-embedded human tissues were sectioned,
deparaffinized, deproteinated in proteinase K (20 g/ml) for 15
minutes at 37.degree. C., and further processed for in situ
hybridization as described by Lu and Gillett, supra. A [.sup.33-P]
UTP-labeled antisense riboprobe was generated from a PCR product
and hybridized at 55.degree. C. overnight. The slides were dipped
in Kodak NTB2 nuclear track emulsion and exposed for 4 weeks.
.sup.33P-Riboprobe Synthesis
[0483] 6.0 .mu.l (125 mCi) of .sup.33P-UTP (Amersham BF 1002,
SA<2000 Ci/mmol) were speed vac dried. To each tube containing
dried .sup.33P-UTP, the following ingredients were added:
[0484] 2.0 .mu.l 5.times. transcription buffer
[0485] 1.0 .mu.l DTT (100 mM)
[0486] 2.0 .mu.l NTP mix (2.5 mM: 10 .mu.l; each of 10 mM GTP, CTP
& ATP+10 .mu.l H.sub.2O)
[0487] 1.0 .mu.l UTP (50 .mu.M)
[0488] 1.0 .mu.l Rnasin
[0489] 1.0 .mu.l DNA template (1 .mu.g)
[0490] 1.0 .mu.l H.sub.2O
[0491] 1.0 .mu.l RNA polymerase (for PCR products T3=AS, T7=S,
usually)
[0492] The tubes were incubated at 37.degree. C. for one hour. 1.0
.mu.l RQ1 DNase were added, followed by incubation at 37.degree. C.
for 15 minutes. 90 .mu.l TE (10 mM Tris pH 7.6/1 mM EDTA pH 8.0)
were added, and the mixture was pipetted onto DE81 paper. The
remaining solution was loaded in a Microcon-50 ultrafiltration
unit, and spun using program 10 (6 minutes). The filtration unit
was inverted over a second tube and spun using program 2 (3
minutes). After the final recovery spin, 100 .mu.l TE were added. 1
.mu.l of the final product was pipetted on DE81 paper and counted
in 6 ml of Biofluor II.
[0493] The probe was run on a TBE/urea gel. 1-3 .mu.L of the probe
or 5 .mu.l of RNA Mrk III were added to 3 .mu.l of loading buffer.
After heating on a 95.degree. C. heat block for three minutes, the
gel was immediately placed on ice. The wells of gel were flushed,
the sample loaded, and run at 180-250 volts for 45 minutes. The gel
was wrapped in saran wrap and exposed to XAR film with an
intensifying screen in -70.degree. C. freezer one hour to
overnight.
.sup.33P-Hybridization
[0494] A. Pretreatment of Frozen Sections
[0495] The slides were removed from the freezer, placed on
aluminium trays and thawed at room temperature for 5 minutes. The
trays were placed in 55.degree. C. incubator for five minutes to
reduce condensation. The slides were fixed for 10 minutes in 4%
paraformaldehyde on ice in the fume hood, and washed in
0.5.times.SSC for 5 minutes, at room temperature (25 ml
20.times.SSC+975 ml SQ H.sub.2O). After deproteination in 0.5
.mu.g/ml proteinase K for 10 minutes at 37.degree. C. (12.5 .mu.l
of 10 mg/ml stock in 250 ml prewarmed RNase-free RNAse buffer), the
sections were washed in 0.5.times.SSC for 10 minutes at room
temperature. The sections were dehydrated in 70%, 95%, 100%
ethanol, 2 minutes each.
[0496] B. Pretreatment of Paraffin-Embedded Sections
[0497] The slides were deparaffinized, placed in SQ H.sub.2O, and
rinsed twice in 2.times.SSC at room temperature, for 5 minutes each
time. The sections were deproteinated in 20 .mu.g/ml proteinase K
(500 .mu.l of 10 mg/ml in 250 ml RNase-free RNase buffer;
37.degree. C., 15 minutes)--human embryo, or 8.times. proteinase K
(100 .mu.l in 250 ml Rnase buffer, 37.degree. C., 30
minutes)--formalin tissues. Subsequent rinsing in 0.5.times.SSC and
dehydration were performed as described above.
[0498] C. Prehybridization
[0499] The slides were laid out in a plastic box lined with Box
buffer (4.times.SSC, 50% formamide)-saturated filter paper. The
tissue was covered with 50 .mu.l of hybridization buffer (3.75 g
Dextran Sulfate+6 ml SQ H.sub.2O), vortexed and heated in the
microwave for 2 minutes with the cap loosened. After cooling on
ice, 18.75 ml formamide, 3.75 ml 20.times.SSC and 9 ml SQ H.sub.2O
were added, the tissue was vortexed well, and incubated at
42.degree. C. for 1-4 hours.
[0500] D. Hybridization
[0501] 1.0.times.10.sup.6 cpm probe and 1.0 .mu.l tRNA (50 mg/ml
stock) per slide were heated at 95.degree. C. for 3 minutes. The
slides were cooled on ice, and 48 .mu.l hybridization buffer were
added per slide. After vortexing, 50 .mu.L .sup.33P mix were added
to 50 .mu.l prehybridization on slide. The slides were incubated
overnight at 55.degree. C.
[0502] E. Washes
[0503] Washing was done 2.times.10 minutes with 2.times.SSC, EDTA
at room temperature (400 ml 20.times.SSC+16 ml 0.25M EDTA,
V.sub.f=4L), followed by RNaseA treatment at 37.degree. C. for 30
minutes (500 .mu.l of 10 mg/ml in 250 ml Rnase buffer=20 .mu.g/ml),
The slides were washed 2.times.10 minutes with 2.times.SSC, EDTA at
room temperature. The stringency wash conditions were as follows: 2
hours at 55.degree. C., 0.1.times.SSC, EDTA (20 ml 20.times.SSC+16
ml EDTA, V.sub.f=4L).
[0504] F. Oligonucleotides
[0505] In situ analysis was performed on DNA59294-1381 disclosed
herein. The oligonucleotides employed for this analysis were
derived from the nucleotide sequences disclosed herein and
generally range from about 40 to 55 nucleotides in length.
[0506] G. Results
[0507] In situ analysis was performed on DNA59294-1381 as disclosed
herein. The results from this analysis is as follows.
DNA59294-1381 (PRO1031)
[0508] The expression of this IL17 homologue was evaluated in a
panel consisting of normal adult and fetal tissues and tissues with
inflammation, predominantly chronic lymphocytic inflammation. This
panel is designed to specifically evaluate the expression pattern
in immune mediated inflammatory disease of novel proteins that
modulate T lymphocyte function (stimulatory or inhibitory). This
protein when expressed as an Ig-fusion protein was
immunostimulatory in a dose dependent fashion in the human mixed
lymphocyte reaction (MLR); it caused a 285% and 147% increase above
the baseline stimulation index when utilized at two different
concentrations (1.0% and 0.1% of a 560 nM stock) [see EXAMPLE 25
below]. Summary: expression was restricted to muscle, certain types
of smooth muscle in the adult and in skeletal and smooth muscle in
the human fetus. Expression in adult human was in smooth muscle of
tubular organs evaluated including colon and gall bladder. There
was no expression in the smooth muscle of vessels or bronchi. No
adult human skeletal muscle was evaluated. In fetal tissues there
was moderate to high diffuse expression in skeletal muscle, in the
axial skeleton and limbs. There was weak expression in the smooth
muscle of the intestinal wall but no expression in cardiac muscle.
Adult human tissues with expression include: Colon: there was low
level diffuse expression in the smooth muscle (tunica muscularis)
in 5 specimens with chronic inflammatory bowel disease; Gall
bladder: there was weak to low level expression in the smooth
muscle of the gall bladder; Fetal human tissues with expression:
there was moderate diffuse expression in skeletal muscle and weak
tolow expression in smooth muscle, there was no expression in fetal
heart or any other fetal organ including liver, spleen, CNS,
kidney, gut, lung; Human tissues with no expression: lung with
chronic granulomatous inflammation and chronic bronchitis (5
patients), peripheral nerve, prostate, heart, placenta, liver
(disease multiblock), brain (cerbrum and cerebellum), tonsil
(reactive hyperplasia), peripheral lymph node, thymus.
Example 11
Expression of PRO in E. coli
[0509] This example illustrates preparation of an unglycosylated
form of PRO polypeptides by recombinant expression in E. coli.
[0510] The DNA sequence encoding a PRO polypeptide is initially
amplified using selected PCR primers. The primers should contain
restriction enzyme sites which correspond to the restriction enzyme
sites on the selected expression vector. A variety of expression
vectors may be employed. An example of a suitable vector is pBR322
(derived from E. coli; see Bolivar et al., Gene, 2:95 (1977)) which
contains genes for ampicillin and tetracycline resistance. The
vector is digested with restriction enzyme and dephosphorylated.
The PCR amplified sequences are then ligated into the vector. The
vector will preferably include sequences which encode for an
antibiotic resistance gene, a trp promoter, a polyHis leader
(including the first six STII codons, polyHis sequence, and
enterokinase cleavage site), the PRO polypeptide coding region,
lambda transcriptional terminator, and an argU gene.
[0511] The ligation mixture is then used to transform a selected E.
coli strain using the methods described in Sambrook et al., supra.
Transformants are identified by their ability to grow on LB plates
and antibiotic resistant colonies are then selected. Plasmid DNA
can be isolated and confirmed by restriction analysis and DNA
sequencing.
[0512] Selected clones can be grown overnight in liquid culture
medium such as LB broth supplemented with antibiotics. The
overnight culture may subsequently be used to inoculate a larger
scale culture. The cells are then grown to a desired optical
density, during which the expression promoter is turned on.
[0513] After culturing the cells for several more hours, the cells
can be harvested by centrifugation. The cell pellet obtained by the
centrifugation can be solubilized using various agents known in the
art, and the solubilized PRO protein can then be purified using a
metal chelating column under conditions that allow tight binding of
the protein.
[0514] PRO polypeptides may be expressed in E. coli in a poly-His
tagged form, using the following procedure. The DNA encoding a PRO
polypeptide is initially amplified using selected PCR primers. The
primers will contain restriction enzyme sites which correspond to
the restriction enzyme sites on the selected expression vector, and
other useful sequences providing for efficient and reliable
translation initiation, rapid purification on a metal chelation
column, and proteolytic removal with enterokinase. The
PCR-amplified, poly-His tagged sequences are then ligated into an
expression vector, which is used to transform an E. coli host based
on strain 52 (W3110 fuhA(tonA) ion galE rpoHts(htpRts) clpP(lacIq).
Transformants are first grown in LB containing 50 mg/ml
carbenicillin at 30.degree. C. with shaking until an O.D.600 of 3-5
is reached. Cultures are then diluted 50-100 fold into CRAP media
(prepared by mixing 3.57 g (NH.sub.4).sub.2SO.sub.4, 0.71 g sodium
citrate.2H2O, 1.07 g KCl, 5.36 g Difco yeast extract, 5.36 g
Sheffield hycase SF in 500 mL water, as well as 110 mM MPOS, pH
7.3, 0.55% (w/v) glucose and 7 mM MgSO.sub.4) and grown for
approximately 20-30 hours at 30.degree. C. with shaking. Samples
are removed to verify expression by SDS-PAGE analysis, and the bulk
culture is centrifuged to pellet the cells. Cell pellets are frozen
until purification and refolding.
[0515] E. coli paste from 0.5 to 1 L fermentations (6-10 g pellets)
is resuspended in 10 volumes (w/v) in 7 M guanidine, 20 mM Tris, pH
8 buffer. Solid sodium sulfite and sodium tetrathionate is added to
make final concentrations of 0.1M and 0.02 M, respectively, and the
solution is stirred overnight at 4.degree. C. This step results in
a denatured protein with all cysteine residues blocked by
sulfitolization. The solution is centrifuged at 40,000 rpm in a
Beckman Ultracentifuge for 30 min. The supernatant is diluted with
3-5 volumes of metal chelate column buffer (6 M guanidine, 20 mM
Tris, pH 7.4) and filtered through 0.22 micron filters to clarify.
The clarified extract is loaded onto a 5 ml Qiagen Ni-NTA metal
chelate column equilibrated in the metal chelate column buffer. The
column is washed with additional buffer containing 50 mM imidazole
(Calbiochem, Utrol grade), pH 7.4. The protein is eluted with
buffer containing 250 mM imidazole. Fractions containing the
desired protein are pooled and stored at 4.degree. C. Protein
concentration is estimated by its absorbance at 280 nm using the
calculated extinction coefficient based on its amino acid
sequence.
[0516] The proteins are refolded by diluting the sample slowly into
freshly prepared refolding buffer consisting of: 20 mM Tris, pH
8.6, 0.3 M NaCl, 2.5 M urea, 5 mM cysteine, 20 mM glycine and 1 mM
EDTA. Refolding volumes are chosen so that the final protein
concentration is between 50 to 100 micrograms/ml. The refolding
solution is stirred gently at 4.degree. C. for 12-36 hours. The
refolding reaction is quenched by the addition of TFA to a final
concentration of 0.4% (pH of approximately 3). Before further
purification of the protein, the solution is filtered through a
0.22 micron filter and acetonitrile is added to 2-10% final
concentration. The refolded protein is chromatographed on a Poros
R1/H reversed phase column using a mobile buffer of 0.1% TFA with
elution with a gradient of acetonitrile from 10 to 80%. Aliquots of
fractions with A280 absorbance are analyzed on SDS polyacrylamide
gels and fractions containing homogeneous refolded protein are
pooled. Generally, the properly refolded species of most proteins
are eluted at the lowest concentrations of acetonitrile since those
species are the most compact with their hydrophobic interiors
shielded from interaction with the reversed phase resin. Aggregated
species are usually eluted at higher acetonitrile concentrations .
In addition to resolving misfolded forms of proteins from the
desired form, the reversed phase step also removes endotoxin from
the samples.
[0517] Fractions containing the desired folded PRO polypeptide are
pooled and the acetonitrile removed using a gentle stream of
nitrogen directed at the solution. Proteins are formulated into 20
mM Hepes, pH 6.8 with 0.14 M sodium chloride and 4% mannitol by
dialysis or by gel filtration using G25 Superfine (Pharmacia)
resins equilibrated in the formulation buffer and sterile
filtered.
[0518] Many of the PRO polypeptides disclosed herein were
successfully expressed as described above.
Example 12
Expression of PRO in Mammalian Cells
[0519] This example illustrates preparation of a potentially
glycosylated form of PRO polypeptides by recombinant expression in
mammalian cells.
[0520] The vector, pRK5 (see EP 307,247, published Mar. 15, 1989),
is employed as the expression vector. Optionally, the PRO DNA is
ligated into pRK5 with selected restriction enzymes to allow
insertion of the PRO DNA using ligation methods such as described
in Sambrook et al., supra. The resulting vector is called
pRK5-PRO.
[0521] In one embodiment, the selected host cells may be 293 cells.
Human 293 cells (ATCC CCL 1573) are grown to confluence in tissue
culture plates in medium such as DMEM supplemented with fetal calf
serum and optionally, nutrient components and/or antibiotics. About
10 .mu.g pRK5-PRO DNA is mixed with about 1 .mu.g DNA encoding the
VA RNA gene [Thimmappaya et al., Cell, 31:543 (1982)] and dissolved
in 500 .mu.l of 1 mM Tris-HCl, 0.1 mM EDTA, 0.227 M CaCl.sub.2. To
this mixture is added, dropwise, 500 .mu.l of 50 mM HEPES (pH
7.35), 280 mM NaCl, 1.5 mM NAPO.sub.4, and a precipitate is allowed
to form for 10 minutes at 25.degree. C. The precipitate is
suspended and added to the 293 cells and allowed to settle for
about four hours at 37.degree. C. The culture medium is aspirated
off and 2 ml of 20% glycerol in PBS is added for 30 seconds. The
293 cells are then washed with serum free medium, fresh medium is
added and the cells are incubated for about 5 days.
[0522] Approximately 24 hours after the transfections, the culture
medium is removed and replaced with culture medium (alone) or
culture medium containing 200 .mu.Ci/ml .sup.35S-cysteine and 200
.mu.Ci/ml .sup.35S-methionine. After a 12 hour incubation, the
conditioned medium is collected, concentrated on a spin filter, and
loaded onto a 15% SDS gel. The processed gel may be dried and
exposed to film for a selected period of time to reveal the
presence of the PRO polypeptide. The cultures containing
transfected cells may undergo further incubation (in serum free
medium) and the medium is tested in selected bioassays.
[0523] In an alternative technique, PRO may be introduced into 293
cells transiently using the dextran sulfate method described by
Somparyrac et al., Proc. Natl. Acad. Sci., 12:7575 (1981). 293
cells are grown to maximal density in a spinner flask and 700 .mu.g
pRK5-PRO DNA is added. The cells are first concentrated from the
spinner flask by centrifugation and washed with PBS. The
DNA-dextran precipitate is incubated on the cell pellet for four
hours. The cells are treated with 20% glycerol for 90 seconds,
washed with tissue culture medium, and re-introduced into the
spinner flask containing tissue culture medium, 5 .mu.g/ml bovine
insulin and 0.1 .mu.g/ml bovine transferrin. After about four days,
the conditioned media is centrifuged and filtered to remove cells
and debris. The sample containing the expressed PRO polypeptide can
then be concentrated and purified by any selected method, such as
dialysis and/or column chromatography.
[0524] In another embodiment, PRO polypeptides can be expressed in
CHO cells. The pRK5-PRO can be transfected into CHO cells using
known reagents such as CaPO.sub.4 or DEAE-dextran. As described
above, the cell cultures can be incubated, and the medium replaced
with culture medium (alone) or medium containing a radiolabel such
as .sup.35S-methionine. After determining the presence of the PRO
polypeptide, the culture medium may be replaced with serum free
medium. Preferably, the cultures are incubated for about 6 days,
and then the conditioned medium is harvested. The medium containing
the expressed PRO polypeptide can then be concentrated and purified
by any selected method.
[0525] Epitope-tagged PRO may also be expressed in host CHO cells.
The PRO may be subcloned out of the pRK5 vector. The subclone
insert can undergo PCR to fuse in frame with a selected epitope tag
such as a poly-His tag into a Baculovirus expression vector. The
poly-His tagged PRO insert can then be subcloned into a SV40 driven
vector containing a selection marker such as DHFR for selection of
stable clones. Finally, the CHO cells can be transfected (as
described above) with the SV40 driven vector. Labeling may be
performed, as described above, to verify expression. The culture
medium containing the expressed poly-His tagged PRO can then be
concentrated and purified by any selected method, such as by
Ni.sup.2+-chelate affinity chromatography.
[0526] PRO polypeptides may also be expressed in CHO and/or COS
cells by a transient expression procedure or in CHO cells by
another stable expression procedure.
[0527] Stable expression in CHO cells is performed using the
following procedure. The proteins are expressed as an IgG construct
(immunoadhesin), in which the coding sequences for the soluble
forms (e.g., extracellular domains) of the respective proteins are
fused to an IgG/l constant region sequence containing the hinge,
CH2 and CH2 domains, and/or as a poly-His tagged form.
[0528] Following PCR amplification, the respective DNAs are
subcloned in a CHO expression vector using standard techniques as
described in Ausubel et al., Current Protocols of Molecular
Biology, Unit 3.16, John Wiley and Sons (1997). CHO expression
vectors are constructed to have compatible restriction sites 5' and
3' of the DNA of interest to allow the convenient shuttling of
cDNA's. The vector used in expression in CHO cells is as described
in Lucas et al., Nucl. Acids Res., 24:9 (1774-1779 (1996), and uses
the SV40 early promoter/enhancer to drive expression of the cDNA of
interest and dihydrofolate reductase (DHFR). DHFR expression
permits selection for stable maintenance of the plasmid following
transfection.
[0529] Twelve micrograms of the desired plasmid DNA is introduced
into approximately 10 million CHO cells using commercially
available transfection reagents Superfect.RTM. (Qiagen),
Dosper.RTM. or Fugene.RTM. (Boehringer Mannheim). The cells are
grown as described in Lucas et al., supra. Approximately
3.times.10.sup.7 cells are frozen in an ampule for further growth
and production as described below.
[0530] The ampules containing the plasmid DNA are thawed by
placement into water bath and mixed by vortexing. The contents are
pipetted into a centrifuge tube containing 10 mL of media and
centrifuged at 1000 rpm for 5 minutes. The supernatant is aspirated
and the cells are resuspended in 10 mL of selective media (0.2
.mu.m filtered PS20 with 5% 0.2 .mu.m diafiltered fetal bovine
serum). The cells are then aliquoted into a 100 mL spinner
containing 90 mL of selective media. After 1-2 days, the cells are
transferred into a 250 mL spinner filled with 150 mL selective
growth medium and incubated at 37.degree. C. After another 2-3
days, 250 mL, 500 mL and 2000 mL spinners are seeded with
3.times.10.sup.5 cells/mL. The cell media is exchanged with fresh
media by centrifugation and resuspension in production medium.
Although any suitable CHO media may be employed, a production
medium described in U.S. Pat. No. 5,122,469, issued Jun. 16, 1992
may actually be used. A 3 L production spinner is seeded at
1.2.times.10.sup.6 cells/mL. On day 0, the cell number pH ie
determined. On day 1, the spinner is sampled and sparging with
filtered air is commenced. On day 2, the spinner is sampled, the
temperature shifted to 33.degree. C., and 30 mL of 500 g/L glucose
and 0.6 mL of 10% antifoam (e.g., 35% polydimethylsiloxane
emulsion, Dow Corning 365 Medical Grade Emulsion) taken. Throughout
the production, the pH is adjusted as necessary to keep it at
around 7.2. After 10 days, or until the viability dropped below
70%, the cell culture is harvested by centrifugation and filtering
through a 0.22 .mu.m filter. The filtrate was either stored at
4.degree. C. or immediately loaded onto columns for
purification.
[0531] For the poly-His tagged constructs, the proteins are
purified using a Ni-NTA column (Qiagen). Before purification,
imidazole is added to the conditioned media to a concentration of 5
mM. The conditioned media is pumped onto a 6 ml Ni-NTA column
equilibrated in 20 mM Hepes, pH 7.4, buffer containing 0.3 M NaCl
and 5 mM imidazole at a flow rate of 4-5 ml/min. at 4.degree. C.
After loading, the column is washed with additional equilibration
buffer and the protein eluted with equilibration buffer containing
0.25 M imidazole. The highly purified protein is subsequently
desalted into a storage buffer containing 10 mM Hepes, 0.14 M NaCl
and 4% mannitol, pH 6.8, with a 25 ml G25 Superfine (Pharmacia)
column and stored at -80.degree. C.
[0532] Immunoadhesin (Fc-containing) constructs are purified from
the conditioned media as follows. The conditioned medium is pumped
onto a 5 ml Protein A column (Pharmacia) which had been
equilibrated in 20 mM Na phosphate buffer, pH 6.8. After loading,
the column is washed extensively with equilibration buffer before
elution with 100 mM citric acid, pH 3.5. The eluted protein is
immediately neutralized by collecting 1 ml fractions into tubes
containing 275 .mu.l of 1 M Tris buffer, pH 9. The highly purified
protein is subsequently desalted into storage buffer as described
above for the poly-His tagged proteins. The homogeneity is assessed
by SDS polyacrylamide gels and by N-terminal amino acid sequencing
by Edman degradation.
[0533] Many of the PRO polypeptides disclosed herein were
successfully expressed as described above.
Example 13
Expression of PRO in Yeast
[0534] The following method describes recombinant expression of PRO
polypeptides in yeast.
[0535] First, yeast expression vectors are constructed for
intracellular production or secretion of PRO from the ADH2/GAPDH
promoter. DNA encoding the PRO polypeptide and the promoter is
inserted into suitable restriction enzyme sites in the selected
plasmid to direct intracellular expression of the PRO polypeptide.
For secretion, DNA encoding PRO can be cloned into the selected
plasmid, together with DNA encoding the ADH2/GAPDH promoter, a
native PRO signal peptide or other mammalian signal peptide, or,
for example, a yeast alpha-factor or invertase secretory
signal/leader sequence, and linker sequences (if needed) for
expression of PRO.
[0536] Yeast cells, such as yeast strain AB110, can then be
transformed with the expression plasmids described above and
cultured in selected fermentation media. The transformed yeast
supernatants can be analyzed by precipitation with 10%
trichloroacetic acid and separation by SDS-PAGE, followed by
staining of the gels with Coomassie Blue stain.
[0537] Recombinant PRO polypeptides can subsequently be isolated
and purified by removing the yeast cells from the fermentation
medium by centrifugation and then concentrating the medium using
selected cartridge filters. The concentrate containing the PRO
polypeptide may further be purified using selected column
chromatography resins.
[0538] Many of the PRO polypeptides disclosed herein were
successfully expressed as described above.
Example 14
Expression of PRO in Baculovirus-Infected Insect Cells
[0539] The following method describes recombinant expression of PRO
polypeptides in Baculovirus-infected insect cells.
[0540] The sequence coding for PRO is fused upstream of an epitope
tag contained within a baculovirus expression vector. Such epitope
tags include poly-His tags and immunoglobulin tags (like Fc regions
of IgG). A variety of plasmids may be employed, including plasmids
derived from commercially available plasmids such as pVL1393
(Novagen). Briefly, the sequence encoding PRO or the desired
portion of the coding sequence of PRO such as the sequence encoding
the extracellular domain of a transmembrane protein or the sequence
encoding the mature protein if the protein is extracellular is
amplified by PCR with primers complementary to the 5' and 3'
regions. The 5' primer may incorporate flanking (selected)
restriction enzyme sites. The product is then digested with those
selected restriction enzymes and subcloned into the expression
vector.
[0541] Recombinant baculovirus is generated by co-transfecting the
above plasmid and BaculoGold.TM. virus DNA (Pharmingen) into
Spodoptera frugiperda ("Sf9") cells (ATCC CRL 1711) using
lipofectin (commercially available from GIBCO-BRL). After 4-5 days
of incubation at 28.degree. C., the released viruses are harvested
and used for further amplifications. Viral infection and protein
expression are performed as described by O'Reilley et al.,
Baculovirus expression vectors: A Laboratory Manual, Oxford: Oxford
University Press (1994).
[0542] Expressed poly-His tagged PRO can then be purified, for
example, by Ni.sup.2+-chelate affinity chromatography as follows.
Extracts are prepared from recombinant virus-infected Sf9 cells as
described by Rupert et al., Nature, 362:175-179 (1993). Briefly,
Sf9 cells are washed, resuspended in sonication buffer (25 mL
Hepes, pH 7.9; 12.5 mM MgCl.sub.2; 0.1 mM EDTA; 10% glycerol; 0.1%
NP-40; 0.4 M KCl), and sonicated twice for 20 seconds on ice. The
sonicates are cleared by centrifugation, and the supernatant is
diluted 50-fold in loading buffer (50 mM phosphate, 300 mM NaCl,
10% glycerol, pH 7.8) and filtered through a 0.45 .mu.m filter. A
Ni.sup.2+-NTA agarose column (commercially available from Qiagen)
is prepared with a bed volume of 5 mL, washed with 25 mL of water
and equilibrated with 25 mL of loading buffer. The filtered cell
extract is loaded onto the column at 0.5 mL per minute. The column
is washed to baseline A.sub.280 with loading buffer, at which point
fraction collection is started. Next, the column is washed with a
secondary wash buffer (50 mM phosphate; 300 mM NaCl, 10% glycerol,
pH 6.0), which elutes nonspecifically bound protein. After reaching
A.sub.280 baseline again, the column is developed with a 0 to 500
mM Imidazole gradient in the secondary wash buffer. One mL
fractions are collected and analyzed by SDS-PAGE and silver
staining or Western blot with Ni.sup.2+-NTA-conjugated to alkaline
phosphatase (Qiagen). Fractions containing the eluted
His.sub.10-tagged PRO are pooled and dialyzed against loading
buffer.
[0543] Alternatively, purification of the IgG tagged (or Fc tagged)
PRO can be performed using known chromatography techniques,
including for instance, Protein A or protein G column
chromatography.
[0544] Many of the PRO polypeptides disclosed herein were
successfully expressed as described above.
Example 15
Preparation of Antibodies that Bind PRO
[0545] This example illustrates preparation of monoclonal
antibodies which can specifically bind PRO.
[0546] Techniques for producing the monoclonal antibodies are known
in the art and are described, for instance, in Goding, supra.
Immunogens that may be employed include purified PRO polypeptides,
fusion proteins containing PRO polypeptides, and cells expressing
recombinant PRO polypeptides on the cell surface. Selection of the
immunogen can be made by the skilled artisan without undue
experimentation.
[0547] Mice, such as Balb/c, are immunized with the PRO immunogen
emulsified in complete Freund's adjuvant and injected
subcutaneously or intraperitoneally in an amount from 1-100
micrograms. Alternatively, the immunogen is emulsified in MPL-TDM
adjuvant (Ribi Immunochemical Research, Hamilton, Mont.) and
injected into the animal's hind foot pads. The immunized mice are
then boosted 10 to 12 days later with additional immunogen
emulsified in the selected adjuvant. Thereafter, for several weeks,
the mice may also be boosted with additional immunization
injections. Serum samples may be periodically obtained from the
mice by retro-orbital bleeding for testing in ELISA assays to
detect anti-PRO antibodies.
[0548] After a suitable antibody titer has been detected, the
animals "positive" for antibodies can be injected with a final
intravenous injection of PRO. Three to four days later, the mice
are sacrificed and the spleen cells are harvested. The spleen cells
are then fused (using 35% polyethylene glycol) to a selected murine
myeloma cell line such as P3X63AgU.1, available from ATCC, No. CRL
1597. The fusions generate hybridoma cells which can then be plated
in 96 well tissue culture plates containing HAT (hypoxanthine,
aminopterin, and thymidine) medium to inhibit proliferation of
non-fused cells, myeloma hybrids, and spleen cell hybrids.
[0549] The hybridoma cells will be screened in an ELISA for
reactivity against PRO. Determination of "positive" hybridoma cells
secreting the desired monoclonal antibodies against PRO is within
the skill in the art.
[0550] The positive hybridoma cells can be injected
intraperitoneally into syngeneic Balb/c mice to produce ascites
containing the anti-PRO monoclonal antibodies. Alternatively, the
hybridoma cells can be grown in tissue culture flasks or roller
bottles. Purification of the monoclonal antibodies produced in the
ascites can be accomplished using ammonium sulfate precipitation,
followed by gel exclusion chromatography. Alternatively, affinity
chromatography based upon binding of antibody to protein A or
protein G can be employed.
Example 16
Purification of PRO Polypeptides Using Specific Antibodies
[0551] Native or recombinant PRO polypeptides may be purified by a
variety of standard techniques in the art of protein purification.
For example, pro-PRO polypeptide, mature PRO polypeptide, or
pre-PRO polypeptide is purified by immunoaffinity chromatography
using antibodies specific for the PRO polypeptide of interest. In
general, an immunoaffinity column is constructed by covalently
coupling the anti-PRO polypeptide antibody to an activated
chromatographic resin.
[0552] Polyclonal immunoglobulins are prepared from immune sera
either by precipitation with ammonium sulfate or by purification on
immobilized Protein A (Pharmacia LKB Biotechnology, Piscataway,
N.J.). Likewise, monoclonal antibodies are prepared from mouse
ascites fluid by ammonium sulfate precipitation or chromatography
on immobilized Protein A. Partially purified immunoglobulin is
covalently attached to a chromatographic resin such as
CnBr-activated SEPHAROSE.TM. (Pharmacia LKB Biotechnology). The
antibody is coupled to the resin, the resin is blocked, and the
derivative resin is washed according to the manufacturer's
instructions.
[0553] Such an immunoaffinity column is utilized in the
purification of PRO polypeptide by preparing a fraction from cells
containing PRO polypeptide in a soluble form. This preparation is
derived by solubilization of the whole cell or of a subcellular
fraction obtained via differential centrifugation by the addition
of detergent or by other methods well known in the art.
Alternatively, soluble PRO polypeptide containing a signal sequence
may be secreted in useful quantity into the medium in which the
cells are grown.
[0554] A soluble PRO polypeptide-containing preparation is passed
over the immunoaffinity column, and the column is washed under
conditions that allow the preferential absorbance of PRO
polypeptide (e.g., high ionic strength buffers in the presence of
detergent). Then, the column is eluted under conditions that
disrupt antibody/PRO polypeptide binding (e.g., a low pH buffer
such as approximately pH 2-3, or a high concentration of a
chaotrope such as urea or thiocyanate ion), and PRO polypeptide is
collected.
Example 17
Drug Screening
[0555] This invention is particularly useful for
screening-compounds by using PRO polypeptides or binding fragment
thereof in any of a variety of drug screening techniques. The PRO
polypeptide or fragment employed in such a test may either be free
in solution, affixed to a solid support, borne on a cell surface,
or located intracellularly. One method of drug screening utilizes
eukaryotic or prokaryotic host cells which are stably transformed
with recombinant nucleic acids expressing the PRO polypeptide or
fragment. Drugs are screened against such transformed cells in
competitive binding assays. Such cells, either in viable or fixed
form, can be used for standard binding assays. One may measure, for
example, the formation of complexes between PRO polypeptide or a
fragment and the agent being tested. Alternatively, one can examine
the diminution in complex formation between the PRO polypeptide and
its target cell or target receptors caused by the agent being
tested.
[0556] Thus, the present invention provides methods of screening
for drugs or any other agents which can affect a PRO
polypeptide-associated disease or disorder. These methods comprise
contacting such an agent with an PRO polypeptide or fragment
thereof and assaying (i) for the presence of a complex between the
agent and the PRO polypeptide or fragment, or (ii) for the presence
of a complex between the PRO polypeptide or fragment and the cell,
by methods well known in the art. In such competitive binding
assays, the PRO polypeptide or fragment is typically labeled. After
suitable incubation, free PRO polypeptide or fragment is separated
from that present in bound form, and the amount of free or
uncomplexed label is a measure of the ability of the particular
agent to bind to PRO polypeptide or to interfere with the PRO
polypeptide/cell complex.
[0557] Another technique for drug screening provides high
throughput screening for compounds having suitable binding affinity
to a polypeptide and is described in detail in WO 84/03564,
published on Sep. 13, 1984. Briefly stated, large numbers of
different small peptide test compounds are synthesized on a solid
substrate, such as plastic pins or some other surface. As applied
to a PRO polypeptide, the peptide test compounds are reacted with
PRO polypeptide and washed. Bound PRO polypeptide is detected by
methods well known in the art. Purified PRO polypeptide can also be
coated directly onto plates for use in the aforementioned drug
screening techniques. In addition, non-neutralizing antibodies can
be used to capture the peptide and immobilize it on the solid
support.
[0558] This invention also contemplates the use of competitive drug
screening assays in which neutralizing antibodies capable of
binding PRO polypeptide specifically compete with a test compound
for binding to PRO polypeptide or fragments thereof. In this
manner, the antibodies can be used to detect the presence of any
peptide which shares one or more antigenic determinants with PRO
polypeptide.
Example 18
Rational Drug Design
[0559] The goal of rational drug design is to produce structural
analogs of biologically active polypeptide of interest (i.e., a PRO
polypeptide) or of small molecules with which they interact, e.g.,
agonists, antagonists, or inhibitors. Any of these examples can be
used to fashion drugs which are more active or stable forms of the
PRO polypeptide or which enhance or interfere with the function of
the PRO polypeptide in vivo (c.f., Hodgson, Bio/Technology, 9:
19-21 (1991)).
[0560] In one approach, the three-dimensional structure of the PRO
polypeptide, or of an PRO polypeptide-inhibitor complex, is
determined by x-ray crystallography, by computer modeling or, most
typically, by a combination of the two approaches. Both the shape
and charges of the PRO polypeptide must be ascertained to elucidate
the structure and to determine active site(s) of the molecule. Less
often, useful information regarding the structure of the PRO
polypeptide may be gained by modeling based on the structure of
homologous proteins. In both cases, relevant structural information
is used to design analogous PRO polypeptide-like molecules or to
identify efficient inhibitors. Useful examples of rational drug
design may include molecules which have improved activity or
stability as shown by Braxton and Wells, Biochemistry, 31:7796-7801
(1992) or which act as inhibitors, agonists, or antagonists of
native peptides as shown by Athauda et al., J. Biochem. 113:742-746
(1993).
[0561] It is also possible to isolate a target-specific antibody,
selected by functional assay, as described above, and then to solve
its crystal structure. This approach, in principle, yields a
pharmacore upon which subsequent drug design can be based. It is
possible to bypass protein crystallography altogether by generating
anti-idiotypic antibodies (anti-ids) to a functional,
pharmacologically active antibody. As a mirror image of a mirror
image, the binding site of the anti-ids would be expected to be an
analog of the original receptor. The anti-id could then be used to
identify and isolate peptides from banks of chemically or
biologically produced peptides. The isolated peptides would then
act as the pharmacore.
[0562] By virtue of the present invention, sufficient amounts of
the PRO polypeptide may be made available to perform such
analytical studies as X-ray crystallography. In addition, knowledge
of the PRO polypeptide amino acid sequence provided herein will
provide guidance to those employing computer modeling techniques in
place of or in addition to x-ray crystallography.
Example 19
Differential Tissue Expression Distribution
[0563] Oligonucleotide probes were constructed from the PRO1031,
PRO1122, PRO21175, PRO10272, PRO20110, PRO5801, PRO20040, PRO9877,
and PRO20026 polypeptide-encoding nucleotide sequences shown in the
accompanying figures for use in quantitative PCR amplification
reactions. The oligonucleotide probes were chosen so as to give an
approximately 200-600 base pair amplified fragment from the 3' end
of its associated template in a standard PCR reaction. The
oligonucleotide probes were employed in standard quantitative PCR
amplification reactions with cDNA libraries isolated from different
human adult and/or fetal tissue sources and analyzed by agarose gel
electrophoresis so as to obtain a quantitative determination of the
level of expression of the polypeptide-encoding nucleic acids in
the various tissues tested. Knowledge of the expression pattern or
the differential expression of the polypeptide-encoding nucleic
acid in various different human tissue types provides a diagnostic
marker useful for tissue typing, with or without other
tissue-specific markers, for determining the primary tissue source
of a metastatic tumor, and the like. These assays provided the
following results:
TABLE-US-00016 DNA Molecule Tissues w/ Significant Expression
Tissues w/o Significant Expression DNA59294-1381 highly expressed
in mammary gland, weakly expressed in intestine, bone trachea,
testis and spine marrow, lung, kidney and thymus; no expression in
pancreas, liver, brain or spleen DNA62377-1381-1 strongly expressed
in testis, spleen, weakly expressed in intestine, fetal thymus, and
trachea brain, mammary, uterus, colon, lung, placenta and stomach;
no expression in muscle, pancreas, liver, spine, brain and fetal
liver DNA173894-2974 highly expressed in muscle, spine not
expressed in intestine, mammary and brain gland, marrow, uterus,
trachea, colon, salivary gland, lung, pancreas, liver, prostate,
adrenal, kidney, thymus, placenta, heart, stomach and spleen
DNA147531-2821 expressed at low levels in brain, no expression in
heart, liver, colon, kidney, lung, prostate, testis, spinal marrow,
intestine, spleen, muscle, chord, adrenal gland and trachea
stomach, uterus, placenta, thymus, muscle, uterus, placenta,
pancreas, salivary gland, and mammary gland DNA166819 highly
expressed in testis, kidney not expressed in intestine, mammary
thymus, and stomach gland, marrow, uterus, trachea, colon, salivary
gland, lung, muscle, pancreas, liver, prostate, adrenal gland,
placenta Heart, spine, brain, and spleen DNA115291-2681 highly
expressed in the kidney; not expressed in heart, bone marrow,
significant expression in liver and spleen and placenta peripheral
organs such as colon, small intestine, prostate, testis, pancreas
and uterus DNA164625-2890 highly expressed in prostate; expressed
in weakly expressed in heart, cartilage, kidney, spine, placenta,
liver, lung, colon, colon tumor, substantia nigra and spleen,
uterus, dendrocyte and and macrophage; it is not expressed in
hippocampus, intestine, mammary gland, lymphoblasts bone marrow,
testis, muscle, stomach and thymus DNA119502-2789 strongly
expressed in mammary not expressed in muscle, liver, and gland,
placenta and prostate; expressed heart; weakly expressed in marrow,
in intestine, colon, lung, kidney, thymus, uterus, testis and brain
stomach, spine and spleen DNA154095-2998 strongly expressed in
fetal brain; negligible expression in mammary significant
expression in uterus and gland, bone marrow, trachea, colon,
testis; expressed in prostate, esophagus lung, muscle, pancreas,
liver, and esophagial tumors, normal adrenal gland, thymus,
placenta, stomach and stomach tumor, kidney but heart, brain and
spleen, rectum; not expressed higher in kidney tumor, lung
expressed in liver tumor tumor, and rectal tumor
Example 20
Identification of Receptor/Ligand Interactions--Overview of
Screening Assay of PRO Polypeptides for Identification of
Receptor/Ligand Interactions
[0564] In this assay, various PRO polypeptides are tested for
ability to bind to a panel of potential receptor or ligand
molecules for the purpose of identifying receptor/ligand
interactions. The identification of a ligand for a known receptor,
a receptor for a known ligand or a novel receptor/ligand pair is
useful for a variety of indications including, for example,
targeting bioactive molecules (linked to the ligand or receptor) to
a cell known to express the receptor or ligand, use of the receptor
or ligand as a reagent to detect the presence of the ligand or
receptor in a composition suspected of containing the same, wherein
the composition may comprise cells suspected of expressing the
ligand or receptor, modulating the growth of or another biological
or immunological activity of a cell known to express or respond to
the receptor or ligand, modulating the immune response of cells or
toward cells that express the receptor or ligand, allowing the
preparation of agonists, antagonists and/or antibodies directed
against the receptor or ligand which will modulate the growth of or
a biological or immunological activity of a cell expressing the
receptor or ligand, and various other indications which will be
readily apparent to the ordinarily skilled artisan.
[0565] In general, the assay is performed as follows. A PRO
polypeptide of the present invention suspected of being a ligand
for a receptor is expressed as a fusion protein containing the Fc
domain of human IgG (an immunoadhesin). Receptor-ligand binding is
detected by allowing interaction of the immunoadhesin polypeptide
with cells (e.g. Cos cells) expressing candidate PRO polypeptide
receptors and visualization of bound immunoadhesin with fluorescent
reagents directed toward the Fc fusion domain and examination by
microscope. Cells expressing candidate receptors are produced by
transient transfection, in parallel, of defined subsets of a
library of cDNA expression vectors encoding PRO polypeptides that
may function as receptor molecules. Cells are then incubated for 1
hour in the presence of the PRO polypeptide immunoadhesin being
tested for possible receptor binding. The cells are then washed and
fixed with paraformaldehyde. The cells are then incubated with
fluorescent conjugated antibody directed against the Fc portion of
the PRO polypeptide immunoadhesin (e.g. FITC conjugated goat
anti-human-Fc antibody). The cells are then washed again and
examined by microscope. A positive interaction is judged by the
presence of fluorescent labeling of cells transfected with cDNA
encoding a particular PRO polypeptide receptor or pool of receptors
and an absence of similar fluorescent labeling of similarly
prepared cells that have been transfected with other cDNA or pools
of cDNA. If a defined pool of cDNA expression vectors is judged to
be positive for interaction with a PRO polypeptide immunoadhesin,
the individual cDNA species that comprise the pool are tested
individually (the pool is "broken down") to determine the specific
cDNA that encodes a receptor able to interact with the PRO
polypeptide immunoadhesin.
[0566] In another embodiment of this assay, an epitope-tagged
potential ligand PRO polypeptide (e.g., 8 histidine "His" tag) is
allowed to interact with a panel of potential receptor PRO
polypeptide molecules that have been expressed as fusions with the
Fc domain of human IgG (immunoadhesins). Following a 1 hour
co-incubation with the epitope tagged PRO polypeptide, the
candidate receptors are each immunoprecipitated with protein A
beads and the beads are washed. Potential ligand interaction is
determined by Western blot analysis of the immunoprecipitated
complexes with antibody directed towards the epitope tag. An
interaction is judged to occur if a band of the anticipated
molecular weight of the epitope tagged protein is observed in the
Western blot analysis with a candidate receptor, but is not
observed to occur with the other members of the panel of potential
receptors.
[0567] Using the above described assays, the following
receptor/ligand interactions have been herein identified:
(1) PRO1031 (designated herein as human IL-17B ligand) binds to
PRO5801 (designated herein as human IL-17RH1 receptor). (2)
PRO10272 (designated herein as human IL-17E ligand) binds to
PRO5801 (designated herein as human IL-17RH1 receptor). (3)
PRO20110 (designated herein as human IL-17F ligand) binds to the
human IL-17 receptor (IL-17R) [(Yao et al., Cytokine, 9(11):794-800
(1997); also herein designated as PRO1] and to PRO20040 (designated
herein as human IL-17RH2 receptor). (4) PRO1031 (IL-17B ligand) and
PRO1122 (IL-17C ligand) do not bind to the human IL-17 receptor (Li
et al., Proc. Natl. Acad. Sci. (USA), 97(2):773-778 (2000)).
Example 21
Human IL-17 Receptor (IL-17R: Designated PRO1) Binding with Novel
Ligands IL-17B (Designated PRO1031) and IL-17C (Designated
PRO1122)
A. Cloning of the ECD of Human IL-17 Receptor (Designated IL-17R;
Designated Herein as PRO1):
[0568] The ECD of human IL-17 receptor (IL-117R) [Yao et al.,
Cytokine 9(11):794-800 (1997)] was cloned in order to study the
ligand/receptor interactions of the novel IL-17 homolog
polypeptides IL-17B and IL-17C. Two oligonucleotide primers were
designed at the 5' and 3' ends of the human IL-17R ECD based on the
published sequence. [Yao et al., Cytokine, 9:794 (1997)]. The two
probes had the following sequences:
TABLE-US-00017 (SEQ ID NO:38) primer 1: 5'-CTG TAC CTC GAG GGT GCA
GAG-3' (SEQ ID NO:39) primer 2: 5'-CCC AAG CTT GGG TCA ATG ATG ATG
ATG ATG ATG ATG ATG CCA CAG GGG CAT GTA GTC C-3'
[0569] The above primers were used in PCR reactions to amplify the
full-length cDNA from a human testis cDNA library with Pfu Turbo
DNA polymerase (Promega). A C-terminal His tag was introduced by
PCR through the addition of nucleotides encoding eight histidines
to the 3' end primer. The PCR product was then subcloned into an
expression plasmid vector pRK5B. Sequence analysis confirmed that
the insert contains a DNA fragment encoding the extracellular
domain (1-320 amino acids) of the published hIL-17 receptor.
B. Immunoprecipitation of the IL-17R ECD:
[0570] The differential activity of IL-17 when compared to IL-17B
(PRO1031; SEQ ID NO:2) and IL-17C (PRO1122; SEQ ID NO:4) (see
Examples 28 through 30 of the present application) suggested that
they might bind and activate different cell surface receptors. In
order to test whether IL-17B (PRO1031) or IL-17C (PRO1122) directly
bind to the receptor, an expression plasmid containing the IL-17R
(PRO1)(C-terminal His-tagged) was transfected into 293 cells using
SuperFect transfection reagent (Qiagen). Metabolic labeling of 293
cells was performed 16 hours after transfection using 50 mCi/ml
[.sup.3S]-Cys/Met mixture for 6 hours. Conditioned medium was
collected and concentrated (Centricon-10, Amicon). To examine the
expression of the IL-17R ECD, Ni-NTA beads (Qiagen) were used to
affinity precipitate the His-tagged IL-17R ECD from the conditioned
medium.
[0571] The conditioned medium was diluted in RIPA buffer (1% NP40,
0.5% sodium deoxycholate, 0.1% SDS in PBS) and was incubated with
IL-17 and the Fc fusion proteins overnight at 4.degree. C. Protein
A-agarose beads (Pierce) were added to precipitate the Fc fusion
proteins. The precipitates were washed three times to precipitate
the Fc fusion proteins. The precipitates were washed three times in
RIPA buffer, denatured in SDS sample buffer, and electrophoresed on
NuPAGE 4-12% Bis-Tris gels (Novex). For IL-17 immunoprecipitation,
anti-IL-17 antibody (R&D Systems) was added. In a competitive
binding experiment, immunoprecipitation of IL-17R ECD by IL-17 is
performed in the presence of a 5-fold molar excess of IL-17B.His,
IL-17C.His and control his tagged protein.
[0572] The IL-17R ECD migrated as a 60 kDa band when purified via
its histidine tag (FIG. 29A.), lane 1). Furthermore, the IL-17R ECD
also precipitated in combination with IL-17 (lane 3). However, both
IL-17B and IL-17C failed to compete for the binding of IL-17 for
the labeled IL-17 receptor ECD (FIG. 29B.), lane 15 and 16).
Example 22
Novel Human IL-17 Receptor (IL-17RH1) (Designated PRO5801) Binding
with Human IL-17 and Novel Ligands IL-17B (Designated PRO1031),
IL-17C (Designated PRO1122, and IL-17E (Designated PRO10272);
Induction of NF-.kappa.B Activity and IL-8 Production by IL-17E
A. Isolation of IL-17E (PRO10272) and Construction of Expression
Vectors:
[0573] IL-17E (DNA147531-2821; SEQ ID NO:5) and IL-17RH1
(DNA115291-2681; SEQ ID NO:11) cDNA clones were isolated from a
human cDNA library and sequenced in their entirety as described in
EXAMPLE 3 and EXAMPLE 5, respectively. Fc fusion proteins
(immunoadhesions) were prepared by fusion of the entire open
reading frames of IL-17, IL-17B (PRO1031), IL-17C (PRO1122), and
IL-17E (PRO10272) in frame with the Fc region of human IgG1 in the
eukaryotic expression vector pRK5tkNEO and the baculovirus vector
pHIF, a derivative of pVL1393 purchased from Pharmingen. Fusion
proteins were transiently expressed in human 293 cells or Sf9
insect cells and purified over a Protein A column. The
extracellular domain of the IL-17RH1 receptor (PRO5801) was also
expressed as a C-terminal 8.times.His-tag fusion in baculovirus and
purified by nickel affinity column. IL-17E (PRO10272) was also
expressed as a 8.times.His-tag fusion in E. coli and was purified
and refolded. The identities of the purified proteins were verified
by N-terminal sequence analysis.
B. Western Blot, Northern Blot and Taqman Analysis:
[0574] Western blot analysis of binding of IL-17E (PRO10272) to
IL-17RH1 (PRO5801) was performed essentially as described by Xie et
al., Cytokine, 11(10):729-735 (1999) and Xie et al., J. Biol.
Chem., 275(40): 31335-31339 (2000). For Northern blot analysis,
multiple tissue Northern blots (Clontech) were probed with a
.sup.32P-labeled probe of random primed IL-17RH1 cDNA according to
manufacturer's recommendations and exposed to X-omat (Kodak) for 72
hours. For quantitative PCR analysis (Taqman.TM.), total mRNA from
human tissues (50 ng) was analyzed as recommended (Perkin Elmer)
with primers based on the coding sequence of IL-17RH1.
C. FACS Analysis:
[0575] Human 293 cells were transiently co-transfected with
expression vectors for green fluorescent protein (GFP), and
IL-17RH1 (PRO5801) or IL-17R (designated PRO1) as indicated. After
24 hours, cells were incubated with Fc tagged ligand as indicated
and binding was revealed with PE conjugated anti-human Fc antibody.
FACS curves show PE staining within the co-transfected GFP positive
cell population. (FIG. 32A)
D. NF-.kappa.B, and IL-8 Assays and Western Blot Analysis:
[0576] Luciferase reporter assays were conducted essentially as
described by Gurney et al., Curr Biol., 94):215-218 (1999).
Briefly, 293 or TK-10 cells (2.times.10.sup.5) were transfected by
Effectine (Qiagen) transfection with 0.5 .mu.g of the firefly
luciferase reporter plasmid pGL3-ELAM.tk and 0.05 .mu.g of the
Renilla luciferase reporter plasmid as internal transfection
control as well as IL-17E expression plasmid (0.1 .mu.g) and
carrier plasmid pRK5D to maintain constant DNA between
transfections. After 24 hours cells were harvested and luciferase
activity assayed as recommended (Pharmacia). IL-8 ELISA were
performed according to manufacturer's instructions R&D)
Systems). (FIG. 33)
E. Results and Discussion:
[0577] As described supra, novel members of IL-17 family have been
identified and characterized, designated herein as IL-17B
(PRO1031), IL-17C (PRO1122), IL-17D (PRO21175), and IL-17E
(PRO10272). Four members of the IL-17 family: IL-17, IL-17B, IL-17C
and IL-17E share greatest similarity in the C-terminal portion of
the molecule with 20-30% amino acid sequence identity and strict
conservation of four cysteines. Additional cysteines that may be
functionally conserved are present with differences in position. In
contrast, there is little conservation apparent in the N-terminal
80 residues. The alignment of the IL-17 family members [IL-17 (SEQ
ID NO:40); IL-17B (PRO1031; SEQ ID NO:2); IL-17C (PRO1122, SEQ ID
NO:4); and IL-17E (PRO10272, SEQ ID NO:6)] is demonstrated in FIG.
30. The predicted signal sequences are underlined. Conserved
cysteines are indicated by bullet, and potential N-linked
glycosylation sites are boxed.
[0578] IL-17E mRNA was not detected by Northern blot analysis.
However, IL-17E was detected at very low levels in several tissues
including brain, kidney, lung, prostate, testis, spinal chord,
adrenal gland and trachea by RT-PCR using primers designed to
distinguish spliced mRNA from genomic DNA. The results of RT-PCR
analysis of IL-17E (PRO10272) expression is shown in FIG. 23. As
described above, RNA from the indicated tissues was subjected to
RT-PCR with primers that were designed to amplify the entire coding
sequence of IL-17E. The PCR product was resolved by agarose gel
electrophoresis, transferred to nylon membrane and probed with a
.sup.32P labeled IL-17E cDNA probe.
[0579] Applicants have demonstrated that IL-17B (PRO1031) and
IL-17C (PRO1122) do not bind to the human IL-17 receptor
(designated herein PRO1)(see EXAMPLE 21). A novel IL-17 receptor
(designated herein as IL-17RH1; PRO5801) has been herein identified
and characterized. IL-17RH1 (DNA115291-2681; SEQ ID NO:11) cDNA
clones were isolated from a human cDNA library and sequenced in
their entirety as described in EXAMPLE 5. IL-17RH1 mRNA expression
was examined by Northern blot analysis as shown in FIG. 31A and
quantitative PCR as shown in FIG. 31B. Highest levels of expression
of IL-17RH1 (PRO5801) were observed in kidney, with significant
expression also observed in liver, and other peripheral organs such
as colon, small intestine, prostate, testis, pancreas and
uterus.
[0580] Binding studies were conducted to determine whether this new
molecule (designated IL-17RH1; PRO5801) serves as a receptor for
other members of IL-17 family. Human 293 kidney cells transfected
with an expression vector for IL-17RH1 were shown to bind to
IL-17E-Fc fusion protein (immunoadhesin), but do not show
significant binding of human IL-17 (as shown in FIG. 32A). IL-17E
immunoadhesin binding to IL-17RH1 expressing cells could be
completely inhibited by competition with His epitope tagged IL-17E.
In comparison, cells transfected with expression vector for IL-17R
bind IL-17 immunoadhesin but not IL-17E. To examine whether there
was direct interaction with members of the IL-17 family, ligand
binding studies were conducted with epitope tagged extracellular
domain of the IL-17RH1 receptor. As shown in FIG. 32B, this novel
receptor exhibits strong binding of IL-17E-Fc, and weak binding to
IL-17.beta.-Fc but does not bind IL-17-Fc or IL-17C-Fc.
[0581] IL-17 has been observed to induce NF-.kappa.B activity
(Jovanovic et al., supra). A study was done to determine whether
IL-17E (PRO10272) would also induce activation of a NF-.kappa.B
responsive luciferase reporter gene in two human renal cell
carcinoma cell lines, 293 and TK-10 cells (both of these cell lines
were found to express endogenous IL-17RH1 mRNA). The results of
these studies are shown in FIG. 33A. Transfection of expression
vector for IL-17E markedly induced luciferase activity. The
luciferase activity was induced in a dose dependent manner, and was
of similar magnitude to that observed by the overexpression of the
TNF receptor superfamily member GITR (see FIG. 33B), previously
shown to be a potent inducer of NF-.kappa.B activity (Gurney et
al., supra). NF-.kappa.B is thought to mediate a proinflammatory
signal, suggesting that IL-17E may have proinflammatory action. To
examine this possibility, the production of IL-8, a proinflammatory
chemokine induced by IL-17, was examined. As shown in FIG. 34,
IL-17E (PRO10272) induced activation of IL-8 in TK-10 cells.
[0582] In summary, IL-17RH1 (PRO5801) is the second receptor
identified which binds to members of the IL-17 family. The IL-17
receptor family is quite unrelated to other proteins. However,
comparison of the two receptors does reveal conservation of many
cysteines within the extracellular domain, suggesting they share
similar structure. There are conserved elements within the
intracellular domain as well, suggesting that these receptors
likely engage similar intracellular machinery. This is supported by
the observation that like IL-17, IL-17E signals activation of
NK-.kappa.B. The regions of conservation within the intracellular
domain do not bear obvious similarity to other receptor families
known to activate NF-.kappa.B, the IL1/Toll and TNF receptor
families.
[0583] IL-17E induces production of IL-8, a proinflammatory
molecule that has also been observed to be induced by IL-17,
suggesting the biological activities of these two cytokines may be
similar. The IL-17 receptor has a very broad expression pattern, in
contrast to the somewhat more restricted mRNA expression pattern of
IL-17RH1 (PRO5801) (see FIG. 31). If these molecules mediate
generally analolous proinflammatory responses, a key consideration
in understanding the function of the different members of the
expanding IL17 cytokine family will be the expression patterns and
regulation of the cognate receptors.
[0584] FIGS. 25 through 28 show the relative tissue expression
distribution for the novel IL-17 receptor homologs identified
herein as IL-17RH1 (PRO5801; SEQ ID NO:12), IL-17RH2 (PRO20040; SEQ
ID NO:14), IL-17RH3 (PRO9877; SEQ ID NO:16) and IL-17RH4 (PRO20026;
SEQ ID NO:18), respectively.
[0585] In summary, FIG. 35 depicts the IL-17 family of cytokines
complex pattern of overlapping receptor-ligand specificities. As
shown, ligands IL-17C and IL-17D appear to have specificity for a
different interleukin-17 receptor other than IL-17R, IL-17RH1 or
IL-17RH2. In addition, FIGS. 20 through 28 and FIG. 31 demonstrate
the relative tissue expression distribution for the novel IL-17
homologues and IL-17 receptors identified herein.
Example 23
Induction of c-fos in Endothelial Cells (ASSAY #34)
[0586] This assay is designed to determine whether PRO polypeptides
show the ability to induce c-fos in endothelial cells. PRO
polypeptides testing positive in this assay would be expected to be
useful for the therapeutic treatment of conditions or disorders
where angiogenesis would be beneficial including, for example,
wound healing, and the like (as would agonists of these PRO
polypeptides). Antagonists of the PRO polypeptides testing positive
in this assay would be expected to be useful for the therapeutic
treatment of cancerous tumors.
[0587] Human venous umbilical vein endothelial cells (HUVEC, Cell
Systems) in growth media (50% Ham's F12 w/o GHT: low glucose, and
50% DMEM without glycine: with NaHCO.sub.3, 1% glutamine, 10 mM
HEPES, 10% FBS, 10 ng/ml bFGF) are plated on 96-well microtiter
plates at a cell density of 1.times.10.sup.4 cells/well. The day
after plating, the cells are starved by removing the growth media
and treating the cells with 100 .mu.l/well test samples and
controls (positive control: growth media; negative control: 10 mM
HEPES, 140 mM NaCl, 4% (w/v) mannitol, pH 6.8). The cells are
incubated for 30 minutes at 37.degree. C., in 5% CO.sub.2. The
samples are removed, and the first part of the bDNA kit protocol
(Chiron Diagnostics, cat. #6005-037) is followed, where each
capitalized reagent/buffer listed below is available from the
kit.
[0588] Briefly, the amounts of the TM Lysis Buffer and Probes
needed for the tests are calculated based on information provided
by the manufacturer. The appropriate amounts of thawed Probes are
added to the TM Lysis Buffer. The Capture Hybridization Buffer is
warmed to room temperature. The bDNA strips are set up in the metal
strip holders, and 100 .mu.l of Capture Hybridization Buffer are
added to each b-DNA well needed, followed by incubation for at
least 30 minutes. The test plates with the cells are removed from
the incubator, and the media are gently removed using the vacuum
manifold. 100 .mu.l of Lysis Hybridization Buffer with Probes are
quickly pipetted into each well of the microtiter plates. The
plates are then incubated at 55.degree. C. for 15 minutes. Upon
removal from the incubator, the plates are placed on the vortex
mixer with the microtiter adapter head and vortex on the #2 setting
for one minute. 80 .mu.l of the lysate are removed and added to the
bDNA wells containing the Capture Hybridization Buffer, and
pipetted up and down to mix. The plates are incubated at 53.degree.
C. for at least 16 hours.
[0589] On the next day, the second part of the bDNA kit protocol is
followed. Specifically, the plates are removed from the incubator
and placed on the bench to cool for 10 minutes. The volumes of
additions needed are calculated based upon information provided by
the manufacturer. An Amplifier Working Solution is prepared by
making a 1:100 dilution of the Amplifier Concentrate (20 fm/.mu.l)
in AL Hybridization Buffer. The hybridization mixture is removed
from the plates and washed twice with Wash A. 50 .mu.l of Amplifier
Working Solution are added to each well and the wells are incubated
at 53.degree. C. for 30 minutes. The plates are then removed from
the incubator and allowed to cool for 10 minutes. The Label Probe
Working Solution is prepared by making a 1:100 dilution of Label
Concentrate (40 pmoles/.mu.l) in AL Hybridization Buffer. After the
10-minute cool-down period, the amplifier hybridization mixture is
removed and the plates are washed twice with Wash A. 50 .mu.l of
Label Probe Working Solution are added to each well and the wells
are incubated at 53.degree. C. for 15 minutes. After cooling for 10
minutes, the Substrate is warmed to room temperature. Upon addition
of 3 .mu.l of Substrate Enhancer to each ml of Substrate needed for
the assay, the plates are allowed to cool for 10 minutes, the label
hybridization mixture is removed, and the plates are washed twice
with Wash A and three times with Wash D. 50 .mu.l of the Substrate
Solution with Enhancer are added to each well. The plates are
incubated for 30 minutes at 37.degree. C. and RLU is read in an
appropriate luminometer.
[0590] The replicates are averaged and the coefficient of variation
is determined. The measure of activity of the fold increase over
the negative control (HEPES buffer described above) value is
indicated by chemiluminescence units (RLU). Samples that show an at
least two-fold value over the negative control value are considered
positive.
[0591] PRO1031 assayed "positive" as shown below:
TABLE-US-00018 ASSAY #1 Negative control = 1.0 RLU Positive control
= 10.96 RLU PRO1031 at 0.056 nM = 2.22 RLU ASSAY #2 Negative
control = 1.0 RLU Positive control = 10.96 RLU PRO1031 at 0.56 nM =
2.01 RLU
Example 24
Skin Vascular Permeability Assay (ASSAY #64)
[0592] This assay shows that certain PRO polypeptides stimulate an
immune response and induce inflammation by inducing mononuclear
cell, eosinophil and PMN infiltration at the site of injection of
the animal. This skin vascular permeability assay is conducted as
follows. Hairless guinea pigs weighing 350 grams or more are
anesthetized with ketamine (75-80 mg/Kg) and 5 mg/Kg Xylazine
intramuscularly (IM). A sample of purified PRO polypeptide or a
conditioned media test sample is injected intradermally onto the
backs of the test animals with 100 .mu.L per injection site. It is
possible to have about 10-30, preferably about 16-24, injection
sites per animal. One mL of Evans blue dye (1% in physiologic
buffered saline) is injected intracardially. Blemishes at the
injection sites are then measured (mm diameter) at 1 hr, 6 hrs and
24 hrs post injection. Animals were sacrificed at 6 hrs after
injection. Each skin injection site is biopsied and fixed in
paraformaldehyde. The skins are then prepared for histopathalogic
evaluation. Each site is evaluated for inflammatory cell
infiltration into the skin. Sites with visible inflammatory cell
inflammation are scored as positive. Inflammatory cells may be
neutrophilic, eosinophilic, monocytic or lymphocytic.
[0593] At least a minimal perivascular infiltrate at the injection
site is scored as positive, no infiltrate at the site of injection
is scored as negative. PRO1031 gave positive results at time
interval 24 hours in this assay.
Example 25
Stimulatory Activity in Mixed Lymphocyte Reaction (MLR) (ASSAY
#24)
[0594] This example shows that the polypeptides of the invention
are active as stimulators of the proliferation of T-lymphocytes.
Compounds which stimulate proliferation of lymphocytes are useful
therapeutically where enhancement of an immune response is
beneficial. A therapeutic agent may also take the form of
antagonists of the PRO polypeptides of the invention, for example,
murine-human chimeric, humanized or human antibodies against the
polypeptide, which would be expected to inhibit T-lymphocyte
proliferation.
[0595] The basic protocol for this assay is described in Current
Protocols in Immunology, unit 3.12; edited by J. E. Coligan, A. M.
Kruisbeek, D. H. Marglies, E. M. Shevach, W. Strober, National
Institutes of Health, Published by John Wiley & Sons, Inc.
[0596] More specifically, in one assay variant, peripheral blood
mononuclear cells (PBMC) are isolated from mammalian individuals,
for example a human volunteer, by leukopheresis (one donor will
supply stimulator PBMCs, the other donor will supply responder
PBMCs). If desired, the cells are frozen in fetal bovine serum and
DMSO after isolation. Frozen cells may be thawed overnight in assay
media (37.degree. C., 5% CO.sub.2) and then washed and resuspended
to 3.times.10.sup.6 cells/ml of assay media (RPMI; 10% fetal bovine
serum, 1% penicillin/streptomycin, 1% glutamine, 1% HEPES, 1%
non-essential amino acids, 1% pyruvate). The stimulator PBMCs are
prepared by irradiating the cells (about 3000 Rads). The assay is
prepared by plating in triplicate wells a mixture of: 100:1 of test
sample diluted to 1% or to 0.1%; 50 :1 of irradiated stimulator
cells and 50 :1 of responder PBMC cells. 100 microliters of cell
culture media or 100 microliter of CD4-IgG is used as the control.
The wells are then incubated at 37.degree. C., 5% CO.sub.2 for 4
days. On day 5 and each well is pulsed with tritiated thymidine
(1.0 mCi/well; Amersham). After 6 hours the cells are washed 3
times and then the uptake of the label is evaluated.
[0597] In another variant of this assay, PBMCs are isolated from
the spleens of Balb/c mice and C57B6 mice. The cells are teased
from freshly harvested spleens in assay media (RPMI; 10% fetal
bovine serum, 1% penicillin/streptomycin, 1% glutamine, 1% HEPES,
1% non-essential amino acids, 1% pyruvate) and the PBMCs are
isolated by overlaying these cells over Lymphocyte M (Organon
Teknika), centrifuging at 2000 rpm for 20 minutes, collecting and
washing the mononuclear cell layer in assay media and resuspending
the cells to 1.times.10.sup.7 cells/ml of assay media. The assay is
then conducted as described above. Positive increases over control
are considered positive with increases of greater than or equal to
180% being preferred. However, any value greater than control
indicates a stimulatory effect for the test protein. The results of
this assay for compounds of the invention are shown below:
TABLE-US-00019 PRO PRO Concentration Percent Increase Over Control
PRO10272 0.84 nM 201.5
Example 26
Stimulation of Peripheral Blood Mononuclear Cells (PBMCs) or
CD4.sup.+ Cells with Anti CD3 and PRO Protein (ASSAY #99)
[0598] This assay shows that one or more of the PRO polypeptides
are active as enhancers of the stimulation of PBMCs or CD4.sup.+
cells. CD4.sup.+ cells are enriched by negative selection using
MACs beads after LSM separation. The ability of the PRO polypeptide
to replace anti-CD28 is examined to determine the stimulatory
effect.
[0599] Anti-CD3 and anti-CD28 are known to stimulate PBMCs. The
basic protocol for the isolation of PBMCs used in this assay is
described in Current Protocols in Immunology, unit 3.12; edited by
J. E. Coligan, A. M. Kruisbeek, D. H. Marglies, E. M. Shevach, W.
Strober, National Institutes of Health, Published by John Wiley
& Sons, Inc.
[0600] More specifically, in one assay variant, peripheral blood
mononuclear cells (PBMC) are isolated from mammalian individuals,
for example a human volunteer, by leukopheresis. If desired, the
cells are enriched for CD4.sup.+ cells, then frozen in 90% fetal
bovine serum and 10% DMSO after isolation. Frozen cells may be
thawed overnight in assay media (37.degree. C., 5% CO.sub.2) and
then washed and resuspended to 0.5.times.10.sup.6 cells/ml of assay
media (RPMI; 10% fetal bovine serum, 1% penicillin/streptomycin, 1%
glutamine, 1% HEPES, 1% non-essential amino acids, 1%
pyruvate).
[0601] The assay is prepared by plating in triplicate wells a
mixture of: 200 .mu.l of cells after the overnight coat of anti-CD3
and PRO protein.
[0602] 50 .mu.l of anti-CD3 (50 ng/ml, Amac 0178) and 50 .mu.l of
1% of the PRO protein are coated on a 96 well plate in PBS
4.degree. C. overnight. 50 .mu.l Hu-IgG is used as the control in
place of the PRO protein. The wells are then incubated at
37.degree. C., 5% CO.sub.2 for about 3 days. On day 4, each well is
pulsed with tritiated thymidine (1.0 mC/well; Amersham). After 6
hours the cells are harvested and then the uptake of the label is
evaluated.
[0603] A result which indicates a stimulatory effect (i.e.,
.sup.3[H]-thymidine incorporation) greater than 200% of the control
is considered to be positive stimulatory result.
[0604] In another variant of this assay, PBMCs or CD4.sup.+
splenocytes are isolated from the spleens of Balb/c mice. The cells
are teased from freshly harvested spleens in assay media (RPMI; 10%
fetal bovine serum, 1% penicillin/streptomycin, 1% glutamine, 1%
HEPES, 1% non-essential amino acids, 1% pyruvate) and the PBMCs are
isolated by overlaying these cells over Lympholyte M (Organon
Teknika), centrifuging at 2000 rpm for 20 minutes, collecting and
washing the mononuclear cell layer in assay media. CD4.sup.+ cells
are enriched by negative selection using beads, washed in media and
resuspended the cells to 1.times.10.sup.7 cells/ml of assay media.
The assay is then conducted as described above. Results are shown
below:
TABLE-US-00020 PRO concentration stimulation (+)/inhibition (-)
PRO1031 5.6 nM (+) 285% above baseline stimulation index PRO1031
0.56 nM (+) 147% above baseline stimulation index
Example 27
Generating IL-17B and IL-17C Fc/His Fusion Proteins
[0605] The coding sequences of IL17B and IL17C were amplified by
PCR and subcloned into the EcoRI and SmaI sites of pBPH.His.c to
generate a C-terminal GHHHHHHHH tag or the EcoRI and Stu sites of
pBPH.IgG to generate a C-terminal fusion with the Fc region of
human IgG1. Vectors pBPH.His.c and pBPH.IgG are derivatives of the
baculovirus expression vector pVL1393 (Pharmingen). A control Fc or
His-tagged protein was constructed in a similar way be C-terminally
linking pancreatitis-associated protein (175 amino acid) to the Fc
portion of the human IgG1 or a his-8 tag.
[0606] The fusion proteins were expressed in High 5 cells using the
manufacturer's recommended procedure (Invitrogen). In brief, the
DNA constructs were co-transfected with BaculoGold Baculovirus DNA
(Pharmingen) in a 7:1 ratio into adherent Sf9 cells. Cells were
incubated at 28.degree. C. for 4 days and the supernatent was
harvested. The transfection supernatant was amplified and was
subject to affinity purification by either protein A-sepharose
beads (Pharmacia) for Fc fusion proteins or Ni-NTA agarose beads
(QIAGEN) for His-tagged proteins.
[0607] To examine the protein expression, SDS-PAGE analysis was
performed on the affinity purified recombinant proteins under
non-reducing and reducing conditions, followed by silver
staining.
Example 28
Induction of IL-6 and TNF-.alpha. Release by IL-17B (PRO1031) and
IL-17C (PRO1122)
[0608] Using the procedure outlined in Yao et al., J. Immunol.,
155: 5483 (1995) for IL-6 release, human foreskin fibroblast cells
(ATCC CRL-2091) were cultured in MEM media (10% FBS) with the test
cytokine. After incubation for 18 hours at 37.degree. C. and 5%
CO.sub.2, conditioned media were assayed for IL-6 using an ELISA
kit (R&D Systems). For TNF-.alpha. secretion, human leukemia
monocytic THP-1 cells were cultured in RPMI media (10% FBS) with
test cytokine. After incubation for 18 hour at 37.degree. C. and 5%
CO.sub.2, conditioned media were quantitated for TNF-.alpha. using
and ELISA assay kit (R&D Systems).
[0609] Human foreskin fibroblast cells (ATCC) were separately
cultured in MEM media (10% FBS) in the presence of IL-17B (PRO1031)
and IL-17C (PRO1122). After incubation for 18 hours at 37.degree.
C. and 5% CO.sub.2, conditioned media were assayed for IL-6 using
an ELISA kit (R&D Systems). In contrast to the high level of
IL-6 induced by IL-17, both IL-17B (PRO1031) and IL17C (PRO1122)
failed to stimulate IL-6 secretion in fibroblast cells (as shown in
FIG. 36A).
[0610] Using the procedure outlined in Yao et al., Cytokine, 9: 794
(1997), a human leukemic monocytic cell line, THP-1, was used to
assay for the stimulation of TNF-.alpha. release by IL-17, IL17B
(PRO1031) and IL-17C (PRO1031) by culturing in RPMI media (10%
FBS). After incubation for 18 hour at 37.degree. C. and 5%
CO.sub.2, conditioned media were quantitated for TNF-.alpha. using
an ELISA assay kit (R&D Systems). While IL-17 induced only a
low level of TNF-.alpha. in THP-1 cells, both IL-17B and IL-17C (as
Fc fusion proteins) stimulated TNF-.alpha. production in THP-1
cells (as shown in FIG. 36B). A control Fc fusion protein had no
effect.
[0611] In order to further characterize the stimulation of
TNF-.alpha. release by IL-17B and IL-17C, the time course and
concentration dependence of the response were assayed in THP-1
cells. FIG. 37 illustrates that IL-17B and IL-17C stimulate the
release of TNF-.alpha. in a time- and concentration-dependent
manner. The EC50 for IL-17B stimulation is 2.4 nM, while the EC50
for IL-17C is 25 nM.
[0612] While the IL-17B and IL-17C preparations used in these
experiments contained undetectable level of endotoxin (less than 1
EU/ml), additional control experiments were performed to confirm
that the TNF-.alpha. release from THP-1 cells was real and not
artifactual. The IL-17B and IL-17C activities were unaffected by
polymyxin B treatment and were abolished by heat treatment, further
supporting the notion that the proteins themselves were responsible
for the activities and not any contaminating endotoxin.
Example 29
Fluorescence-Activated Cell Sorter (FACS) Analysis of Binding to
THP-1 Cells by IL-17, IL-17B and IL-17C Fusion Proteins
[0613] THP-1 cells (5.times.10.sup.5) were pre-incubated in PBS
containing 5% horse serum at 4.degree. C. for 30 minutes to block
non-specific binding. IL-17, IL-17B.Fc, IL-17C.Fc, or control Fc (1
mg each) were added and incubated with the THP-1 cells in a volume
of 0.25 ml on ice for 1 hour. For the IL-17 binding experiment,
primary anti hIL-17 antibody (1:100 dilution) and secondary goat
anti-mouse antibody conjugated to FITC (Jackson Immunology Lab,
1:100 dilution) were added sequentially with 30-60 minutes
incubation and extensive washes before each addition. For the Fc
fusion proteins, the cells were stained with FITC conjugated goat
anti-human IgG (Fc specific, Jackson Immunology Lab, 1:100
dilution). After thorough washes, a minimum of 5,000 cells were
analyzed using a FACScan (Becton Dickinson).
[0614] The resulting of the above procedure was that both IL-17B
and IL-17C Fc fusion proteins displayed binding to THP-1 cells
compared with a control Fc fusion protein (as shown in FIG.
38).
Example 30
Articular Cartilage Explant Assay For IL-17 and IL-17C
A. Introduction:
[0615] As mentioned previously, IL-17 is likely to play a role in
the initiation or maintenance of the proinflammatory response.
IL-17 is a cytokine expressed by CD4.sup.+ Th cells and induces the
secretion of proinflammatory and hematopoietic cytokines (e.g.,
IL-1b, TNF-.alpha., IL-6, IL-8, GM-CSF) in a number of cell types
including synoviocytes and macrophages [Aarvak et al., J. Immunol.,
162:1246-1251 (1999); Fossiez et al., J. Exp. Med. 183:2593-2603
(1996); Jovanovic et al., J. Immunol., 160:3513-3521 (1998)]. In
the presence of IL-17, fibroblasts sustain the proliferation of
CD34.sup.+ hematopoietic progenitors and induce their preferential
maturation into neutrophils. As a result, IL-17 may constitute an
early initiator of the T cell-dependent inflammatory reaction and
be part of the cytokine network which bridges the immune system to
hematopoiesis.
[0616] Expression of IL-17 has been found in the synovium of
patients with rheumatoid arthritis, psoriatic arthritis, or
osteoarthritis, but not in normal joint tissues. IL-17 can
synergize with the monocyte-derived, proinflammatory cytokines
IL-1b or TNF-.alpha. to induce IL-6 and GM-CSF. By acting directly
on synoviocytes, IL-17 could enhance secretion of proinflammatory
cytokines in vivo and thus exacerbate joint inflammation and
destruction.
[0617] To further understand the possible role of IL-17, Applicants
have tested the effects of IL-17 on cartilage matrix metabolism. In
light of the known catabolic effects of nitric oxide (NO) on
cartilage, and the existence of high levels of NO in arthritic
joints, NO production was also measured.
B. Methods:
[0618] Articular cartilage explants: The metacarpophalangeal joint
of a 4-6 month old female pigs was aseptically dissected, and
articular cartilage is removed by free-hand slicing in a careful
manner so as to avoid the underlying bone. The cartilage was minced
and cultured in bulk for at least 24 hours in a humidified
atmosphere of 95% air 5% CO.sub.2 in serum free (SF) media
(DME/F121:1) with 0.1% BSA and antibiotics. After washing three
times, approximately 80 mg of articular cartilage was aliquoted
into micronics tubes and incubated for at least 24 hours in the
above SF media. Test proteins were then added at 1% either alone or
in combination with IL-1a (10 ng/ml). Media was harvested and
changed at various timepoints (0, 24, 48, 72 hours) and assayed for
proteoglycan content using the 1,9-dimethyl-methylene blue (DMB)
colorimetric assay described in Farndale and Buttle, Biochem.
Biophys. Acta, 883:173-177 (1985). After labeling (overnight) with
.sup.35S-sulfur, the tubes were weighed to determine the amount of
tissue. Following an overnight digestion, the amount of
proteoglycan remaining in the tissue as well as proteoglycan
synthesis (.sup.35S-incorporation) is determined.
[0619] Measurement of NO production: The assay is based on the
principle that 2,3-diaminonapthalene (DAN) reacts with nitrite
under acidic conditions to form 1-(H)-naphthotriazole, a
fluorescent product. As NO is quickly metabolized into nitrite
(NO2-1) and nitrate (NO3-1), detection of nitrite, is one means of
detecting (albeit undercounting) the actual NO produced. 10 mL of
DAN (0.05 mg/mL in 0.62 M HCl) is added to 100 mL of sample (cell
culture supernatant), mixed, and incubated at room temperature for
10-20 minutes. Reaction is terminated with 5 mL of 2.8N NaOH.
Formation of 2,3-diaminonaphthotriazole was measured using a
Cytoflor fluorescent plate reader with excitation at 360 nm and
emission read at 450 nm. For optimal measurement of fluorescent
intensity, black plates with clear bottoms were used.
C. Results and Discussion:
[0620] IL-17 was observed to both increase the release of and
decrease the synthesis of proteoglycans (as shown in FIG. 39).
Moreover, this effect was additive to the effect observed from
IL-1a. The effects of IL-17 are not mediated by the production of
nitric oxide, nor does inhibition of nitric oxide release augment
matrix breakdown (see FIGS. 40 to 42). IL-17C (PRO1122) increases
matrix breakdown and inhibits matrix synthesis (FIG. 43). Thus,
expression of PRO1122 is likely to be associated with degenerative
cartilagenous disorders.
[0621] In conclusion, IL-17 likely contributes to loss of articular
cartilage in arthritic joints, and thus inhibition of its activity
might limit inflammation and cartilage destruction. IL-1a and IL-17
have similar yet distinct activities, due to their use of different
receptors and overlapping downstream signaling mechanisms. Given
the findings of the potent catabolic effects of IL-17 on articular
cartilage explants and the homology of IL-17B (PRO1031) and IL-17C
(PRO1122) to IL-17, antagonists to any or all of these proteins may
be useful for the treatment of inflammatory conditions and
cartilage defects such as arthritis.
[0622] Finally, it is well known that growth factors can have
biphasic effects and that diseased tissue can respond differently
than normal tissue to a given factor in vivo. For these reasons,
antagonists or agonists (e.g., the proteins themselves) of IL-17B
(PRO1031), IL-17C (PRO1122), or IL-17, may be useful for the
treatment of inflammatory conditions and joint disorders such as
arthritis.
Example 31
Inflammatory Bowel Disease (IBD): Expression of IL-17 Family in
Mouse Model of IBD
[0623] Mice deficient in the cytokine receptor CRF2-4/IL-10Rb
develop spontaneous and progressive colitis that resembles the
human condition of inflammatory bowel disease (IBD). This phenotype
has been previously reported (Spencer et al., J. Exp. Med.,
187:571-578 [1998]). To examine the role of expression of IL-17
family members in this model of IBD, colons were harvested from
normal (wild type "WT") mice and from CRF2-4 deficient mice. Colons
from CRF2-4 deficient mice were sub-categorized into specimens
exhibiting mild IBD and specimens exhibiting more advanced severe
IBD. RNA was isolated from the colon samples and the relative
expression of IL-17 family members was determined by quantitative
PCR (Taqman.TM.). FIG. 44 demonstrates the relative expression of
IL-17, IL-17E (DNA147531-2821), IL-17B (DNA59294-1381-1), and
IL-17D (DNA173894-2947) represented by -delta CT relative to GAPDH.
The expression of IL-17E markedly decreases in more advanced severe
IBD compared to expression levels in normal (wild type "WT") mice.
In contrast, increased expression values of IL-17 were observed in
mild to severe IBD. Thus, IL-17E may serve as a marker for this
inflammatory condition.
Example 32
IL-17D Expression in Mouse Model of Stroke
[0624] IL-17D (DNA173894-2947) expression was examined in a murine
experimental model of stroke. The right common carotid artery
(RCCA) of C57B1/6 male mice was isolated via a midline incision. A
loose tie was placed around the vessel. The middle cerebral artery
(MCA) was visualized by forming a cranial window in the skull at
the level of the rhinal fissure. At the appointed time, the MCA and
the RCCA were occluded for a 45 minute ischemic period with 11-0
suture and 6-0 suture, respectively. Following this ischemic
insult, the RCCA and MCA sutures were untied to allow reperfusion
of the MCA territory. The relative expression of IL-17D was
determined by quantitative PCR (Taqman.TM.) using RNA isolated from
ischemic cortex at five time points following reperfusion (3, 6,
12, 24 and 72 hours) and compared with the expression of IL-17D
observed in RNA isolated from control non-ischemic tissue. FIG. 45
depicts the results of this study. As shown, IL-17D expression
decreases rapidly following stroke when examined over the five
illustrated time points.
Example 33
Microarray Analysis to Detect Overexpression of PRO Polypeptides in
Cancerous Tumors
[0625] Nucleic acid microarrays, often containing thousands of gene
sequences, are useful for identifying differentially expressed
genes in diseased tissues as compared to their normal counterparts.
Using nucleic acid microarrays, test and control mRNA samples from
test and control tissue samples are reverse transcribed and labeled
to generate cDNA probes. The cDNA probes are then hybridized to an
array of nucleic acids immobilized on a solid support. The array is
configured such that the sequence and position of each member of
the array is known. For example, a selection of genes known to be
expressed in certain disease states may be arrayed on a solid
support. Hybridization of a labeled probe with a particular array
member indicates that the sample from which the probe was derived
expresses that gene. If the hybridization signal of a probe from a
test (disease tissue) sample is greater than hybridization signal
of a probe from a control (normal tissue) sample, the gene or genes
overexpressed in the disease tissue are identified. The implication
of this result is that an overexpressed protein in a diseased
tissue is useful not only as a diagnostic marker for the presence
of the disease condition, but also as a therapeutic target for
treatment of the disease condition.
[0626] The methodology of hybridization of nucleic acids and
microarray technology is well known in the art. In the present
example, the specific preparation of nucleic acids for
hybridization and probes, slides, and hybridization conditions are
all detailed in U.S. Provisional Patent Application Ser. No.
60/193,767, filed on Mar. 31, 2000 and which is herein incorporated
by reference.
[0627] In the present example, cancerous tumors derived from
various human tissues were studied for PRO polypeptide-encoding
gene expression relative to non-cancerous human tissue in an
attempt to identify those PRO polypeptides which are overexpressed
in cancerous tumors. Two sets of experimental data were generated.
In one set, cancerous human colon tumor tissue and matched
non-cancerous human colon tumor tissue from the same patient
("matched colon control") were obtained and analyzed for PRO
polypeptide expression using the above described microarray
technology. In the second set of data, cancerous human tumor tissue
from any of a variety of different human tumors was obtained and
compared to a "universal" epithelial control sample which was
prepared by pooling non-cancerous human tissues of epithelial
origin, including liver, kidney, and lung. mRNA isolated from the
pooled tissues represents a mixture of expressed gene products from
these different tissues. Microarray hybridization experiments using
the pooled control samples generated a linear plot in a 2-color
analysis. The slope of the line generated in a 2-color analysis was
then used to normalize the ratios of (test:control detection)
within each experiment. The normalized ratios from various
experiments were then compared and used to identify clustering of
gene expression. Thus, the pooled "universal control" sample not
only allowed effective relative gene expression determinations in a
simple 2-sample comparison, it also allowed multi-sample
comparisons across several experiments.
[0628] In the present experiments, nucleic acid probes derived from
the herein described PRO polypeptide-encoding nucleic acid
sequences were used in the creation of the microarray and RNA from
the tumor tissues listed above were used for the hybridization
thereto. A value based upon the normalized ratio:experimental ratio
was designated as a "cutoff ratio". Only values that were above
this cutoff ratio were determined to be significant. Table 7 below
shows the results of these experiments, demonstrating that various
PRO polypeptides of the present invention are significantly
overexpressed in various human tumor tissues as compared to a
non-cancerous human tissue control. As described above, these data
demonstrate that the PRO polypeptides of the present invention are
useful not only as diagnostic markers for the presence of one or
more cancerous tumors, but also serve as therapeutic targets for
the treatment of those tumors.
TABLE-US-00021 TABLE 7 Molecule is overexpressed in: as compared
to: PRO1031 lung tumor universal normal control PRO1122 breast
tumor universal normal control PRO1122 lung tumor universal normal
control PRO5801 colon tumor universal normal control PRO21175
breast tumor universal normal control PRO21175 colon tumor
universal normal control PRO21175 lung tumor universal normal
control
Deposit of Material
[0629] The following materials have been deposited with the
American Type Culture Collection, 10801 University Blvd., Manassas,
Va. 20110-2209, USA (ATCC):
TABLE-US-00022 Material ATCC Dep. No. Deposit Date DNA59294-1381
209866 May 14, 1998 DNA62377-1381-1 203552 Dec. 22, 1998
DNA147531-2821 PTA-1185 Jan. 11, 2000 DNA173894-2947 PTA-2108 Jun.
20, 2000 DNA115291-2681 PTA-202 Jun. 8, 1999 DNA164625-2890
PTA-1535 Mar. 21, 2000 DNA119502-2789 PTA-1082 Dec. 22, 1999
DNA154095-2998 PTA-2591 Oct. 10, 2000
[0630] These deposits were made under the provisions of the
Budapest Treaty on the International Recognition of the Deposit of
Microorganisms for the Purpose of Patent Procedure and the
Regulations thereunder (Budapest Treaty). This assures maintenance
of a viable culture of the deposit for 30 years from the date of
deposit. The deposits win be made available by ATCC under the terms
of the Budapest Treaty, and subject to an agreement between
Genentech, Inc. and ATCC, which assures permanent and unrestricted
availability of the progeny of the culture of the deposit to the
public upon issuance of the pertinent U.S. patent or upon laying
open to the public of any U.S. or foreign patent application,
whichever comes first, and assures availability of the progeny to
one determined by the U.S. Commissioner of Patents and Trademarks
to be entitled thereto according to 35 USC .sctn. 122 and the
Commissioner's rules pursuant thereto (including 37 CFR .sctn. 1.14
with particular reference to 886 OG 638).
[0631] The assignee of the present application has agreed that if a
culture of the materials on deposit should die or be lost or
destroyed when cultivated under suitable conditions, the materials
will be promptly replaced on notification with another of the same.
Availability of the deposited material is not to be construed as a
license to practice the invention in contravention of the rights
granted under the authority of any government in accordance with
its patent laws.
[0632] The foregoing written specification is considered to be
sufficient to enable one skilled in the art to practice the
invention. The present invention is not to be limited in scope by
the construct deposited, since the deposited embodiment is intended
as a single illustration of certain aspects of the invention and
any constructs that are functionally equivalent are within the
scope of this invention. The deposit of material herein does not
constitute an admission that the written description herein
contained is inadequate to enable the practice of any aspect of the
invention, including the best mode thereof, nor is it to be
construed as limiting the scope of the claims to the specific
illustrations that it represents. Indeed, various modifications of
the invention in addition to those shown and described herein will
become apparent to those skilled in the art from the foregoing
description and fall within the scope of the appended claims.
Sequence CWU 1
1
391687DNAHomo Sapien 1aggcgggcag cagctgcagg ctgaccttgc agcttggcgg
aatggactgg 50cctcacaacc tgctgtttct tcttaccatt tccatcttcc tggggctggg
100ccagcccagg agccccaaaa gcaagaggaa ggggcaaggg cggcctgggc
150ccctggcccc tggccctcac caggtgccac tggacctggt gtcacggatg
200aaaccgtatg cccgcatgga ggagtatgag aggaacatcg aggagatggt
250ggcccagctg aggaacagct cagagctggc ccagagaaag tgtgaggtca
300acttgcagct gtggatgtcc aacaagagga gcctgtctcc ctggggctac
350agcatcaacc acgaccccag ccgtatcccc gtggacctgc cggaggcacg
400gtgcctgtgt ctgggctgtg tgaacccctt caccatgcag gaggaccgca
450gcatggtgag cgtgccggtg ttcagccagg ttcctgtgcg ccgccgcctc
500tgcccgccac cgccccgcac agggccttgc cgccagcgcg cagtcatgga
550gaccatcgct gtgggctgca cctgcatctt ctgaatcacc tggcccagaa
600gccaggccag cagcccgaga ccatcctcct tgcacctttg tgccaagaaa
650ggcctatgaa aagtaaacac tgacttttga aagcaag 6872180PRTHomo Sapien
2Met Asp Trp Pro His Asn Leu Leu Phe Leu Leu Thr Ile Ser Ile 1 5 10
15Phe Leu Gly Leu Gly Gln Pro Arg Ser Pro Lys Ser Lys Arg Lys 20 25
30Gly Gln Gly Arg Pro Gly Pro Leu Ala Pro Gly Pro His Gln Val 35 40
45Pro Leu Asp Leu Val Ser Arg Met Lys Pro Tyr Ala Arg Met Glu 50 55
60Glu Tyr Glu Arg Asn Ile Glu Glu Met Val Ala Gln Leu Arg Asn 65 70
75Ser Ser Glu Leu Ala Gln Arg Lys Cys Glu Val Asn Leu Gln Leu 80 85
90Trp Met Ser Asn Lys Arg Ser Leu Ser Pro Trp Gly Tyr Ser Ile 95
100 105Asn His Asp Pro Ser Arg Ile Pro Val Asp Leu Pro Glu Ala Arg
110 115 120Cys Leu Cys Leu Gly Cys Val Asn Pro Phe Thr Met Gln Glu
Asp 125 130 135Arg Ser Met Val Ser Val Pro Val Phe Ser Gln Val Pro
Val Arg 140 145 150Arg Arg Leu Cys Pro Pro Pro Pro Arg Thr Gly Pro
Cys Arg Gln 155 160 165Arg Ala Val Met Glu Thr Ile Ala Val Gly Cys
Thr Cys Ile Phe 170 175 18031047DNAHomo Sapien 3gccaggtgtg
caggccgctc caagcccagc ctgccccgct gccgccacca 50tgacgctcct ccccggcctc
ctgtttctga cctggctgca cacatgcctg 100gcccaccatg acccctccct
cagggggcac ccccacagtc acggtacccc 150acactgctac tcggctgagg
aactgcccct cggccaggcc cccccacacc 200tgctggctcg aggtgccaag
tgggggcagg ctttgcctgt agccctggtg 250tccagcctgg aggcagcaag
ccacaggggg aggcacgaga ggccctcagc 300tacgacccag tgcccggtgc
tgcggccgga ggaggtgttg gaggcagaca 350cccaccagcg ctccatctca
ccctggagat accgtgtgga cacggatgag 400gaccgctatc cacagaagct
ggccttcgcc gagtgcctgt gcagaggctg 450tatcgatgca cggacgggcc
gcgagacagc tgcgctcaac tccgtgcggc 500tgctccagag cctgctggtg
ctgcgccgcc ggccctgctc ccgcgacggc 550tcggggctcc ccacacctgg
ggcctttgcc ttccacaccg agttcatcca 600cgtccccgtc ggctgcacct
gcgtgctgcc ccgttcagtg tgaccgccga 650ggccgtgggg cccctagact
ggacacgtgt gctccccaga gggcaccccc 700tatttatgtg tatttattgt
tatttatatg cctcccccaa cactaccctt 750ggggtctggg cattccccgt
gtctggagga cagcccccca ctgttctcct 800catctccagc ctcagtagtt
gggggtagaa ggagctcagc acctcttcca 850gcccttaaag ctgcagaaaa
ggtgtcacac ggctgcctgt accttggctc 900cctgtcctgc tcccggcttc
ccttacccta tcactggcct caggccccgc 950aggctgcctc ttcccaacct
ccttggaagt acccctgttt cttaaacaat 1000tatttaagtg tacgtgtatt
attaaactga tgaacacatc cccaaaa 10474197PRTHomo Sapien 4Met Thr Leu
Leu Pro Gly Leu Leu Phe Leu Thr Trp Leu His Thr 1 5 10 15Cys Leu
Ala His His Asp Pro Ser Leu Arg Gly His Pro His Ser 20 25 30His Gly
Thr Pro His Cys Tyr Ser Ala Glu Glu Leu Pro Leu Gly 35 40 45Gln Ala
Pro Pro His Leu Leu Ala Arg Gly Ala Lys Trp Gly Gln 50 55 60Ala Leu
Pro Val Ala Leu Val Ser Ser Leu Glu Ala Ala Ser His 65 70 75Arg Gly
Arg His Glu Arg Pro Ser Ala Thr Thr Gln Cys Pro Val 80 85 90Leu Arg
Pro Glu Glu Val Leu Glu Ala Asp Thr His Gln Arg Ser 95 100 105Ile
Ser Pro Trp Arg Tyr Arg Val Asp Thr Asp Glu Asp Arg Tyr 110 115
120Pro Gln Lys Leu Ala Phe Ala Glu Cys Leu Cys Arg Gly Cys Ile 125
130 135Asp Ala Arg Thr Gly Arg Glu Thr Ala Ala Leu Asn Ser Val Arg
140 145 150Leu Leu Gln Ser Leu Leu Val Leu Arg Arg Arg Pro Cys Ser
Arg 155 160 165Asp Gly Ser Gly Leu Pro Thr Pro Gly Ala Phe Ala Phe
His Thr 170 175 180Glu Phe Ile His Val Pro Val Gly Cys Thr Cys Val
Leu Pro Arg 185 190 195Ser Val51320DNAHomo Sapien 5ggcttgctga
aaataaaatc aggactccta acctgctcca gtcagcctgc 50ttccacgagg cctgtcagtc
agtgcccgac ttgtgactga gtgtgcagtg 100cccagcatgt accaggtcag
tgcagagggc tgcctgaggg ctgtgctgag 150agggagagga gcagagatgc
tgctgagggt ggagggaggc caagctgcca 200ggtttggggc tgggggccaa
gtggagtgag aaactgggat cccaggggga 250gggtgcagat gagggagcga
cccagattag gtgaggacag ttctctcatt 300agccttttcc tacaggtggt
tgcattcttg gcaatggtca tgggaaccca 350cacctacagc cactggccca
gctgctgccc cagcaaaggg caggacacct 400ctgaggagct gctgaggtgg
agcactgtgc ctgtgcctcc cctagagcct 450gctaggccca accgccaccc
agagtcctgt agggccagtg aagatggacc 500cctcaacagc agggccatct
ccccctggag atatgagttg gacagagact 550tgaaccggct cccccaggac
ctgtaccacg cccgttgcct gtgcccgcac 600tgcgtcagcc tacagacagg
ctcccacatg gacccccggg gcaactcgga 650gctgctctac cacaaccaga
ctgtcttcta caggcggcca tgccatggcg 700agaagggcac ccacaagggc
tactgcctgg agcgcaggct gtaccgtgtt 750tccttagctt gtgtgtgtgt
gcggccccgt gtgatgggct agccggacct 800gctggaggct ggtccctttt
tgggaaacct ggagccaggt gtacaaccac 850ttgccatgaa gggccaggat
gcccagatgc ttggcccctg tgaagtgctg 900tctggagcag caggatcccg
ggacaggatg gggggctttg gggaaaacct 950gcacttctgc acattttgaa
aagagcagct gctgcttagg gccgccggaa 1000gctggtgtcc tgtcattttc
tctcaggaaa ggttttcaaa gttctgccca 1050tttctggagg ccaccactcc
tgtctcttcc tcttttccca tcccctgcta 1100ccctggccca gcacaggcac
tttctagata tttccccctt gctggagaag 1150aaagagcccc tggttttatt
tgtttgttta ctcatcactc agtgagcatc 1200tactttgggt gcattctagt
gtagttacta gtcttttgac atggatgatt 1250ctgaggagga agctgttatt
gaatgtatag agatttatcc aaataaatat 1300ctttatttaa aaatgaaaaa
13206177PRTHomo Sapien 6Met Arg Glu Arg Pro Arg Leu Gly Glu Asp Ser
Ser Leu Ile Ser 1 5 10 15Leu Phe Leu Gln Val Val Ala Phe Leu Ala
Met Val Met Gly Thr 20 25 30His Thr Tyr Ser His Trp Pro Ser Cys Cys
Pro Ser Lys Gly Gln 35 40 45Asp Thr Ser Glu Glu Leu Leu Arg Trp Ser
Thr Val Pro Val Pro 50 55 60Pro Leu Glu Pro Ala Arg Pro Asn Arg His
Pro Glu Ser Cys Arg 65 70 75Ala Ser Glu Asp Gly Pro Leu Asn Ser Arg
Ala Ile Ser Pro Trp 80 85 90Arg Tyr Glu Leu Asp Arg Asp Leu Asn Arg
Leu Pro Gln Asp Leu 95 100 105Tyr His Ala Arg Cys Leu Cys Pro His
Cys Val Ser Leu Gln Thr 110 115 120Gly Ser His Met Asp Pro Arg Gly
Asn Ser Glu Leu Leu Tyr His 125 130 135Asn Gln Thr Val Phe Tyr Arg
Arg Pro Cys His Gly Glu Lys Gly 140 145 150Thr His Lys Gly Tyr Cys
Leu Glu Arg Arg Leu Tyr Arg Val Ser 155 160 165Leu Ala Cys Val Cys
Val Arg Pro Arg Val Met Gly 170 17571754DNAHomo Sapien 7atgctggtag
ccggcttcct gctggcgctg ccgccgagct gggccgcggg 50cgcccccagg gcgggcaggc
gccccgcgcg gccgcggggc tgcgcggacc 100ggccggagga gctactggag
cagctgtacg ggcgcctggc ggccggcgtg 150ctcagtgcct tccaccacac
gctgcagctg gggccgcgtg agcaggcgcg 200caacgcgagc tgcccggcag
ggggcaggcc cggcgaccgc cgcttccggc 250cgcccaccaa cctgcgcagc
gtgtcgccct gggcctacag aatctcctac 300gacccggcga ggtaccccag
gtacctgcct gaagcctact gcctgtgccg 350gggctgcctg accgggctgt
tcggcgagga ggacgtgcgc ttccgcagcg 400cccctgtcta catgcccacc
gtcgtcctgc gccgcacccc cgcctgcgcc 450ggcggccgtt ccgtctacac
cgaggcctac gtcaccatcc ccgtgggctg 500cacctgcgtc cccgagccgg
agaaggacgc agacagcatc aactccagca 550tcgacaaaca gggcgccaag
ctcctgctgg gccccaacga cgcgcccgct 600ggcccctgag gccggtcctg
ccccgggagg tctccccggc ccgcatcccg 650aggcgcccaa gctggagccg
cctggagggc tcggtcggcg acctctgaag 700agagtgcacc gagcaaacca
agtgccggag caccagcgcc gcctttccat 750ggagactcgt aagcagcttc
atctgacacg ggcatccctg gcttgctttt 800agctacaagc aagcagcgtg
gctggaagct gatgggaaac gacccggcac 850gggcatcctg tgtgcggccc
gcatggaggg tttggaaaag ttcacggagg 900ctccctgagg agcctctcag
atcggctgct gcgggtgcag ggcgtgactc 950accgctgggt gcttgccaaa
gagataggga cgcatatgct ttttaaagca 1000atctaaaaat aataataagt
atagcgacta tatacctact tttaaaatca 1050actgttttga atagaggcag
agctatttta tattatcaaa tgagagctac 1100tctgttacat ttcttaacat
ataaacatcg ttttttactt cttctggtag 1150aattttttaa agcataattg
gaatccttgg ataaattttg tagctggtac 1200actctggcct gggtctctga
attcagcctg tcaccgatgg ctgactgatg 1250aaatggacac gtctcatctg
acccactctt ccttccactg aaggtcttca 1300cgggcctcca ggtggaccaa
agggatgcac aggcggctcg catgccccag 1350ggccagctaa gagttccaaa
gatctcagat ttggttttag tcatgaatac 1400ataaacagtc tcaaactcgc
acaatttttt cccccttttg aaagccactg 1450gggccaattt gtggttaaga
ggtggtgaga taagaagtgg aacgtgacat 1500ctttgccagt tgtcagaaga
atccaagcag gtattggctt agttgtaagg 1550gctttaggat caggctgaat
atgaggacaa agtgggccac gttagcatct 1600gcagagatca atctggaggc
ttctgtttct gcattctgcc acgagagcta 1650ggtccttgat cttttcttta
gattgaaagt ctgtctctga acacaattat 1700ttgtaaaagt tagtagttct
tttttaaatc attaaaagag gcttgctgaa 1750ggat 17548202PRTHomo Sapien
8Met Leu Val Ala Gly Phe Leu Leu Ala Leu Pro Pro Ser Trp Ala 1 5 10
15Ala Gly Ala Pro Arg Ala Gly Arg Arg Pro Ala Arg Pro Arg Gly 20 25
30Cys Ala Asp Arg Pro Glu Glu Leu Leu Glu Gln Leu Tyr Gly Arg 35 40
45Leu Ala Ala Gly Val Leu Ser Ala Phe His His Thr Leu Gln Leu 50 55
60Gly Pro Arg Glu Gln Ala Arg Asn Ala Ser Cys Pro Ala Gly Gly 65 70
75Arg Pro Gly Asp Arg Arg Phe Arg Pro Pro Thr Asn Leu Arg Ser 80 85
90Val Ser Pro Trp Ala Tyr Arg Ile Ser Tyr Asp Pro Ala Arg Tyr 95
100 105Pro Arg Tyr Leu Pro Glu Ala Tyr Cys Leu Cys Arg Gly Cys Leu
110 115 120Thr Gly Leu Phe Gly Glu Glu Asp Val Arg Phe Arg Ser Ala
Pro 125 130 135Val Tyr Met Pro Thr Val Val Leu Arg Arg Thr Pro Ala
Cys Ala 140 145 150Gly Gly Arg Ser Val Tyr Thr Glu Ala Tyr Val Thr
Ile Pro Val 155 160 165Gly Cys Thr Cys Val Pro Glu Pro Glu Lys Asp
Ala Asp Ser Ile 170 175 180Asn Ser Ser Ile Asp Lys Gln Gly Ala Lys
Leu Leu Leu Gly Pro 185 190 195Asn Asp Ala Pro Ala Gly Pro
2009559DNAHomo Sapien 9caactgcacc tcggttctat cgatagccac cagcgcaaca
tgacagtgaa 50gaccctgcat ggcccagcca tggtcaagta cttgctgctg tcgatattgg
100ggcttgcctt tctgagtgag gcggcagctc ggaaaatccc caaagtagga
150catacttttt tccaaaagcc tgagagttgc ccgcctgtgc caggaggtag
200tatgaagctt gacattggca tcatcaatga aaaccagcgc gtttccatgt
250cacgtaacat cgagagccgc tccacctccc cctggaatta cactgtcact
300tgggacccca accggtaccc ctcggaagtt gtacaggccc agtgtaggaa
350cttgggctgc atcaatgctc aaggaaagga agacatctcc atgaattccg
400ttcccatcca gcaagagacc ctggtcgtcc ggaggaagca ccaaggctgc
450tctgtttctt tccagttgga gaaggtgctg gtgactgttg gctgcacctg
500cgtcacccct gtcatccacc atgtgcagta agaggtgcat atccactcag
550ctgaagaag 55910163PRTHomo Sapien 10Met Thr Val Lys Thr Leu His
Gly Pro Ala Met Val Lys Tyr Leu 1 5 10 15Leu Leu Ser Ile Leu Gly
Leu Ala Phe Leu Ser Glu Ala Ala Ala 20 25 30Arg Lys Ile Pro Lys Val
Gly His Thr Phe Phe Gln Lys Pro Glu 35 40 45Ser Cys Pro Pro Val Pro
Gly Gly Ser Met Lys Leu Asp Ile Gly 50 55 60Ile Ile Asn Glu Asn Gln
Arg Val Ser Met Ser Arg Asn Ile Glu 65 70 75Ser Arg Ser Thr Ser Pro
Trp Asn Tyr Thr Val Thr Trp Asp Pro 80 85 90Asn Arg Tyr Pro Ser Glu
Val Val Gln Ala Gln Cys Arg Asn Leu 95 100 105Gly Cys Ile Asn Ala
Gln Gly Lys Glu Asp Ile Ser Met Asn Ser 110 115 120Val Pro Ile Gln
Gln Glu Thr Leu Val Val Arg Arg Lys His Gln 125 130 135Gly Cys Ser
Val Ser Phe Gln Leu Glu Lys Val Leu Val Thr Val 140 145 150Gly Cys
Thr Cys Val Thr Pro Val Ile His His Val Gln 155 160111515DNAHomo
Sapien 11ccggcgatgt cgctcgtgct gctaagcctg gccgcgctgt gcaggagcgc
50cgtaccccga gagccgaccg ttcaatgtgg ctctgaaact gggccatctc
100cagagtggat gctacaacat gatctaatcc ccggagactt gagggacctc
150cgagtagaac ctgttacaac tagtgttgca acaggggact attcaatttt
200gatgaatgta agctgggtac tccgggcaga tgccagcatc cgcttgttga
250aggccaccaa gatttgtgtg acgggcaaaa gcaacttcca gtcctacagc
300tgtgtgaggt gcaattacac agaggccttc cagactcaga ccagaccctc
350tggtggtaaa tggacatttt cctacatcgg cttccctgta gagctgaaca
400cagtctattt cattggggcc cataatattc ctaatgcaaa tatgaatgaa
450gatggccctt ccatgtctgt gaatttcacc tcaccaggct gcctagacca
500cataatgaaa tataaaaaaa agtgtgtcaa ggccggaagc ctgtgggatc
550cgaacatcac tgcttgtaag aagaatgagg agacagtaga agtgaacttc
600acaaccactc ccctgggaaa cagatacatg gctcttatcc aacacagcac
650tatcatcggg ttttctcagg tgtttgagcc acaccagaag aaacaaacgc
700gagcttcagt ggtgattcca gtgactgggg atagtgaagg tgctacggtg
750cagctgactc catattttcc tacttgtggc agcgactgca tccgacataa
800aggaacagtt gtgctctgcc cacaaacagg cgtccctttc cctctggata
850acaacaaaag caagccggga ggctggctgc ctctcctcct gctgtctctg
900ctggtggcca catgggtgct ggtggcaggg atctatctaa tgtggaggca
950cgaaaggatc aagaagactt ccttttctac caccacacta ctgcccccca
1000ttaaggttct tgtggtttac ccatctgaaa tatgtttcca tcacacaatt
1050tgttacttca ctgaatttct tcaaaaccat tgcagaagtg aggtcatcct
1100tgaaaagtgg cagaaaaaga aaatagcaga gatgggtcca gtgcagtggc
1150ttgccactca aaagaaggca gcagacaaag tcgtcttcct tctttccaat
1200gacgtcaaca gtgtgtgcga tggtacctgt ggcaagagcg agggcagtcc
1250cagtgagaac tctcaagacc tcttccccct tgcctttaac cttttctgca
1300gtgatctaag aagccagatt catctgcaca aatacgtggt ggtctacttt
1350agagagattg atacaaaaga cgattacaat gctctcagtg tctgccccaa
1400gtaccacctc atgaaggatg ccactgcttt ctgtgcagaa cttctccatg
1450tcaagcagca ggtgtcagca ggaaaaagat cacaagcctg ccacgatggc
1500tgctgctcct tgtag 151512502PRTHomo Sapien 12Met Ser Leu Val Leu
Leu Ser Leu Ala Ala Leu Cys Arg Ser Ala 1 5 10 15Val Pro Arg Glu
Pro Thr Val Gln Cys Gly Ser Glu Thr Gly Pro 20 25 30Ser Pro Glu Trp
Met Leu Gln His Asp Leu Ile Pro Gly Asp Leu 35 40 45Arg Asp Leu Arg
Val Glu Pro Val Thr Thr Ser Val Ala Thr Gly 50 55 60Asp Tyr Ser Ile
Leu Met Asn Val Ser Trp Val Leu Arg Ala Asp 65
70 75Ala Ser Ile Arg Leu Leu Lys Ala Thr Lys Ile Cys Val Thr Gly 80
85 90Lys Ser Asn Phe Gln Ser Tyr Ser Cys Val Arg Cys Asn Tyr Thr 95
100 105Glu Ala Phe Gln Thr Gln Thr Arg Pro Ser Gly Gly Lys Trp Thr
110 115 120Phe Ser Tyr Ile Gly Phe Pro Val Glu Leu Asn Thr Val Tyr
Phe 125 130 135Ile Gly Ala His Asn Ile Pro Asn Ala Asn Met Asn Glu
Asp Gly 140 145 150Pro Ser Met Ser Val Asn Phe Thr Ser Pro Gly Cys
Leu Asp His 155 160 165Ile Met Lys Tyr Lys Lys Lys Cys Val Lys Ala
Gly Ser Leu Trp 170 175 180Asp Pro Asn Ile Thr Ala Cys Lys Lys Asn
Glu Glu Thr Val Glu 185 190 195Val Asn Phe Thr Thr Thr Pro Leu Gly
Asn Arg Tyr Met Ala Leu 200 205 210Ile Gln His Ser Thr Ile Ile Gly
Phe Ser Gln Val Phe Glu Pro 215 220 225His Gln Lys Lys Gln Thr Arg
Ala Ser Val Val Ile Pro Val Thr 230 235 240Gly Asp Ser Glu Gly Ala
Thr Val Gln Leu Thr Pro Tyr Phe Pro 245 250 255Thr Cys Gly Ser Asp
Cys Ile Arg His Lys Gly Thr Val Val Leu 260 265 270Cys Pro Gln Thr
Gly Val Pro Phe Pro Leu Asp Asn Asn Lys Ser 275 280 285Lys Pro Gly
Gly Trp Leu Pro Leu Leu Leu Leu Ser Leu Leu Val 290 295 300Ala Thr
Trp Val Leu Val Ala Gly Ile Tyr Leu Met Trp Arg His 305 310 315Glu
Arg Ile Lys Lys Thr Ser Phe Ser Thr Thr Thr Leu Leu Pro 320 325
330Pro Ile Lys Val Leu Val Val Tyr Pro Ser Glu Ile Cys Phe His 335
340 345His Thr Ile Cys Tyr Phe Thr Glu Phe Leu Gln Asn His Cys Arg
350 355 360Ser Glu Val Ile Leu Glu Lys Trp Gln Lys Lys Lys Ile Ala
Glu 365 370 375Met Gly Pro Val Gln Trp Leu Ala Thr Gln Lys Lys Ala
Ala Asp 380 385 390Lys Val Val Phe Leu Leu Ser Asn Asp Val Asn Ser
Val Cys Asp 395 400 405Gly Thr Cys Gly Lys Ser Glu Gly Ser Pro Ser
Glu Asn Ser Gln 410 415 420Asp Leu Phe Pro Leu Ala Phe Asn Leu Phe
Cys Ser Asp Leu Arg 425 430 435Ser Gln Ile His Leu His Lys Tyr Val
Val Val Tyr Phe Arg Glu 440 445 450Ile Asp Thr Lys Asp Asp Tyr Asn
Ala Leu Ser Val Cys Pro Lys 455 460 465Tyr His Leu Met Lys Asp Ala
Thr Ala Phe Cys Ala Glu Leu Leu 470 475 480His Val Lys Gln Gln Val
Ser Ala Gly Lys Arg Ser Gln Ala Cys 485 490 495His Asp Gly Cys Cys
Ser Leu 500132380DNAHomo Sapien 13acactggcca aacaaaaacg aaagcactcc
gtgctggaag taggaggaga 50gtcaggactc ccaggacaga gagtgcacaa actacccagc
acagccccct 100ccgccccctc tggaggctga agagggattc cagcccctgc
cacccacaga 150cacgggctga ctggggtgtc tgcccccctt gggggggggc
agcacagggc 200ctcaggcctg ggtgccacct ggcacctaga agatgcctgt
gccctggttc 250ttgctgtcct tggcactggg ccgaagccca gtggtccttt
ctctggagag 300gcttgtgggg cctcaggacg ctacccactg ctctccgggc
ctctcctgcc 350gcctctggga cagtgacata ctctgcctgc ctggggacat
cgtgcctgct 400ccgggccccg tgctggcgcc tacgcacctg cagacagagc
tggtgctgag 450gtgccagaag gagaccgact gtgacctctg tctgcgtgtg
gctgtccact 500tggccgtgca tgggcactgg gaagagcctg aagatgagga
aaagtttgga 550ggagcagctg actcaggggt ggaggagcct aggaatgcct
ctctccaggc 600ccaagtcgtg ctctccttcc aggcctaccc tactgcccgc
tgcgtcctgc 650tggaggtgca agtgcctgct gcccttgtgc agtttggtca
gtctgtgggc 700tctgtggtat atgactgctt cgaggctgcc ctagggagtg
aggtacgaat 750ctggtcctat actcagccca ggtacgagaa ggaactcaac
cacacacagc 800agctgcctgc cctgccctgg ctcaacgtgt cagcagatgg
tgacaacgtg 850catctggttc tgaatgtctc tgaggagcag cacttcggcc
tctccctgta 900ctggaatcag gtccagggcc ccccaaaacc ccggtggcac
aaaaacctga 950ctggaccgca gatcattacc ttgaaccaca cagacctggt
tccctgcctc 1000tgtattcagg tgtggcctct ggaacctgac tccgttagga
cgaacatctg 1050ccccttcagg gaggaccccc gcgcacacca gaacctctgg
caagccgccc 1100gactgcgact gctgaccctg cagagctggc tgctggacgc
accgtgctcg 1150ctgcccgcag aagcggcact gtgctggcgg gctccgggtg
gggacccctg 1200ccagccactg gtcccaccgc tttcctggga gaacgtcact
gtggacaagg 1250ttctcgagtt cccattgctg aaaggccacc ctaacctctg
tgttcaggtg 1300aacagctcgg agaagctgca gctgcaggag tgcttgtggg
ctgactccct 1350ggggcctctc aaagacgatg tgctactgtt ggagacacga
ggcccccagg 1400acaacagatc cctctgtgcc ttggaaccca gtggctgtac
ttcactaccc 1450agcaaagcct ccacgagggc agctcgcctt ggagagtact
tactacaaga 1500cctgcagtca ggccagtgtc tgcagctatg ggacgatgac
ttgggagcgc 1550tatgggcctg ccccatggac aaatacatcc acaagcgctg
ggccctcgtg 1600tggctggcct gcctactctt tgccgctgcg ctttccctca
tcctccttct 1650caaaaaggat cacgcgaaag ggtggctgag gctcttgaaa
caggacgtcc 1700gctcgggggc ggccgccagg ggccgcgcgg ctctgctcct
ctactcagcc 1750gatgactcgg gtttcgagcg cctggtgggc gccctggcgt
cggccctgtg 1800ccagctgccg ctgcgcgtgg ccgtagacct gtggagccgt
cgtgaactga 1850gcgcgcaggg gcccgtggct tggtttcacg cgcagcggcg
ccagaccctg 1900caggagggcg gcgtggtggt cttgctcttc tctcccggtg
cggtggcgct 1950gtgcagcgag tggctacagg atggggtgtc cgggcccggg
gcgcacggcc 2000cgcacgacgc cttccgcgcc tcgctcagct gcgtgctgcc
cgacttcttg 2050cagggccggg cgcccggcag ctacgtgggg gcctgcttcg
acaggctgct 2100ccacccggac gccgtacccg cccttttccg caccgtgccc
gtcttcacac 2150tgccctccca actgccagac ttcctggggg ccctgcagca
gcctcgcgcc 2200ccgcgttccg ggcggctcca agagagagcg gagcaagtgt
cccgggccct 2250tcagccagcc ctggatagct acttccatcc cccggggact
cccgcgccgg 2300gacgcggggt gggaccaggg gcgggacctg gggcggggga
cgggacttaa 2350ataaaggcag acgctgtttt tctaaaaaaa 238014705PRTHomo
Sapien 14Met Pro Val Pro Trp Phe Leu Leu Ser Leu Ala Leu Gly Arg
Ser 1 5 10 15Pro Val Val Leu Ser Leu Glu Arg Leu Val Gly Pro Gln
Asp Ala 20 25 30Thr His Cys Ser Pro Gly Leu Ser Cys Arg Leu Trp Asp
Ser Asp 35 40 45Ile Leu Cys Leu Pro Gly Asp Ile Val Pro Ala Pro Gly
Pro Val 50 55 60Leu Ala Pro Thr His Leu Gln Thr Glu Leu Val Leu Arg
Cys Gln 65 70 75Lys Glu Thr Asp Cys Asp Leu Cys Leu Arg Val Ala Val
His Leu 80 85 90Ala Val His Gly His Trp Glu Glu Pro Glu Asp Glu Glu
Lys Phe 95 100 105Gly Gly Ala Ala Asp Ser Gly Val Glu Glu Pro Arg
Asn Ala Ser 110 115 120Leu Gln Ala Gln Val Val Leu Ser Phe Gln Ala
Tyr Pro Thr Ala 125 130 135Arg Cys Val Leu Leu Glu Val Gln Val Pro
Ala Ala Leu Val Gln 140 145 150Phe Gly Gln Ser Val Gly Ser Val Val
Tyr Asp Cys Phe Glu Ala 155 160 165Ala Leu Gly Ser Glu Val Arg Ile
Trp Ser Tyr Thr Gln Pro Arg 170 175 180Tyr Glu Lys Glu Leu Asn His
Thr Gln Gln Leu Pro Ala Leu Pro 185 190 195Trp Leu Asn Val Ser Ala
Asp Gly Asp Asn Val His Leu Val Leu 200 205 210Asn Val Ser Glu Glu
Gln His Phe Gly Leu Ser Leu Tyr Trp Asn 215 220 225Gln Val Gln Gly
Pro Pro Lys Pro Arg Trp His Lys Asn Leu Thr 230 235 240Gly Pro Gln
Ile Ile Thr Leu Asn His Thr Asp Leu Val Pro Cys 245 250 255Leu Cys
Ile Gln Val Trp Pro Leu Glu Pro Asp Ser Val Arg Thr 260 265 270Asn
Ile Cys Pro Phe Arg Glu Asp Pro Arg Ala His Gln Asn Leu 275 280
285Trp Gln Ala Ala Arg Leu Arg Leu Leu Thr Leu Gln Ser Trp Leu 290
295 300Leu Asp Ala Pro Cys Ser Leu Pro Ala Glu Ala Ala Leu Cys Trp
305 310 315Arg Ala Pro Gly Gly Asp Pro Cys Gln Pro Leu Val Pro Pro
Leu 320 325 330Ser Trp Glu Asn Val Thr Val Asp Lys Val Leu Glu Phe
Pro Leu 335 340 345Leu Lys Gly His Pro Asn Leu Cys Val Gln Val Asn
Ser Ser Glu 350 355 360Lys Leu Gln Leu Gln Glu Cys Leu Trp Ala Asp
Ser Leu Gly Pro 365 370 375Leu Lys Asp Asp Val Leu Leu Leu Glu Thr
Arg Gly Pro Gln Asp 380 385 390Asn Arg Ser Leu Cys Ala Leu Glu Pro
Ser Gly Cys Thr Ser Leu 395 400 405Pro Ser Lys Ala Ser Thr Arg Ala
Ala Arg Leu Gly Glu Tyr Leu 410 415 420Leu Gln Asp Leu Gln Ser Gly
Gln Cys Leu Gln Leu Trp Asp Asp 425 430 435Asp Leu Gly Ala Leu Trp
Ala Cys Pro Met Asp Lys Tyr Ile His 440 445 450Lys Arg Trp Ala Leu
Val Trp Leu Ala Cys Leu Leu Phe Ala Ala 455 460 465Ala Leu Ser Leu
Ile Leu Leu Leu Lys Lys Asp His Ala Lys Gly 470 475 480Trp Leu Arg
Leu Leu Lys Gln Asp Val Arg Ser Gly Ala Ala Ala 485 490 495Arg Gly
Arg Ala Ala Leu Leu Leu Tyr Ser Ala Asp Asp Ser Gly 500 505 510Phe
Glu Arg Leu Val Gly Ala Leu Ala Ser Ala Leu Cys Gln Leu 515 520
525Pro Leu Arg Val Ala Val Asp Leu Trp Ser Arg Arg Glu Leu Ser 530
535 540Ala Gln Gly Pro Val Ala Trp Phe His Ala Gln Arg Arg Gln Thr
545 550 555Leu Gln Glu Gly Gly Val Val Val Leu Leu Phe Ser Pro Gly
Ala 560 565 570Val Ala Leu Cys Ser Glu Trp Leu Gln Asp Gly Val Ser
Gly Pro 575 580 585Gly Ala His Gly Pro His Asp Ala Phe Arg Ala Ser
Leu Ser Cys 590 595 600Val Leu Pro Asp Phe Leu Gln Gly Arg Ala Pro
Gly Ser Tyr Val 605 610 615Gly Ala Cys Phe Asp Arg Leu Leu His Pro
Asp Ala Val Pro Ala 620 625 630Leu Phe Arg Thr Val Pro Val Phe Thr
Leu Pro Ser Gln Leu Pro 635 640 645Asp Phe Leu Gly Ala Leu Gln Gln
Pro Arg Ala Pro Arg Ser Gly 650 655 660Arg Leu Gln Glu Arg Ala Glu
Gln Val Ser Arg Ala Leu Gln Pro 665 670 675Ala Leu Asp Ser Tyr Phe
His Pro Pro Gly Thr Pro Ala Pro Gly 680 685 690Arg Gly Val Gly Pro
Gly Ala Gly Pro Gly Ala Gly Asp Gly Thr 695 700 705152138DNAHomo
Sapien 15cgagggctcc tgctggtact gtgttcgctg ctgcacagca aggccctgcc
50acccaccttc aggccatgca gccatgttcc gggagcccta attgcacaga
100agcccatggg gagctccaga ctggcagccc tgctcctgcc tctcctcctc
150atagtcatcg acctctctga ctctgctggg attggctttc gccacctgcc
200ccactggaac acccgctgtc ctctggcctc ccacacggat gacagtttca
250ctggaagttc tgcctatatc ccttgccgca cctggtgggc cctcttctcc
300acaaagcctt ggtgtgtgcg agtctggcac tgttcccgct gtttgtgcca
350gcatctgctg tcaggtggct caggtcttca acggggcctc ttccacctcc
400tggtgcagaa atccaaaaag tcttccacat tcaagttcta taggagacac
450aagatgccag cacctgctca gaggaagctg ctgcctcgtc gtcacctgtc
500tgagaagagc catcacattt ccatcccctc cccagacatc tcccacaagg
550gacttcgctc taaaaggacc caaccttcgg atccagagac atgggaaagt
600cttcccagat tggactcaca aaggcatgga ggacccgagt tctcctttga
650tttgctgcct gaggcccggg ctattcgggt gaccatatct tcaggccctg
700aggtcagcgt gcgtctttgt caccagtggg cactggagtg tgaagagctg
750agcagtccct atgatgtcca gaaaattgtg tctgggggcc acactgtaga
800gctgccttat gaattccttc tgccctgtct gtgcatagag gcatcctacc
850tgcaagagga cactgtgagg cgcaaaaaat gtcccttcca gagctggcca
900gaagcctatg gctcggactt ctggaagtca gtgcacttca ctgactacag
950ccagcacact cagatggtca tggccctgac actccgctgc ccactgaagc
1000tggaagctgc cctctgccag aggcacgact ggcataccct ttgcaaagac
1050ctcccgaatg ccacggctcg agagtcagat gggtggtatg ttttggagaa
1100ggtggacctg cacccccagc tctgcttcaa gttctctttt ggaaacagca
1150gccatgttga atgcccccac cagactgggt ctctcacatc ctggaatgta
1200agcatggata cccaagccca gcagctgatt cttcacttct cctcaagaat
1250gcatgccacc ttcagtgctg cctggagcct cccaggcttg gggcaggaca
1300ctttggtgcc ccccgtgtac actgtcagcc aggcccgggg ctcaagccca
1350gtgtcactag acctcatcat tcccttcctg aggccagggt gctgtgtcct
1400ggtgtggcgg tcagatgtcc agtttgcctg gaagcacctc ttgtgtccag
1450atgtctctta cagacacctg gggctcttga tcctggcact gctggccctc
1500ctcaccctac tgggtgttgt tctggccctc acctgccggc gcccacagtc
1550aggcccgggc ccagcgcggc cagtgctcct cctgcacgcg gcggactcgg
1600aggcgcagcg gcgcctggtg ggagcgctgg ctgaactgct acgggcagcg
1650ctgggcggcg ggcgcgacgt gatcgtggac ctgtgggagg ggaggcacgt
1700ggcgcgcgtg ggcccgctgc cgtggctctg ggcggcgcgg acgcgcgtag
1750cgcgggagca gggcactgtg ctgctgctgt ggagcggcgc cgaccttcgc
1800ccggtcagcg gccccgaccc ccgcgccgcg cccctgctcg ccctgctcca
1850cgctgccccg cgcccgctgc tgctgctcgc ttacttcagt cgcctctgcg
1900ccaagggcga catccccccg ccgctgcgcg ccctgccgcg ctaccgcctg
1950ctgcgcgacc tgccgcgtct gctgcgggcg ctggacgcgc ggcctttcgc
2000agaggccacc agctggggcc gccttggggc gcggcagcgc aggcagagcc
2050gcctagagct gtgcagccgg cttgaacgag aggccgcccg acttgcagac
2100ctaggttgag cagagctcca ccgcagtccc gggtgtct 213816667PRTHomo
Sapien 16Met Gly Ser Ser Arg Leu Ala Ala Leu Leu Leu Pro Leu Leu
Leu 1 5 10 15Ile Val Ile Asp Leu Ser Asp Ser Ala Gly Ile Gly Phe
Arg His 20 25 30Leu Pro His Trp Asn Thr Arg Cys Pro Leu Ala Ser His
Thr Asp 35 40 45Asp Ser Phe Thr Gly Ser Ser Ala Tyr Ile Pro Cys Arg
Thr Trp 50 55 60Trp Ala Leu Phe Ser Thr Lys Pro Trp Cys Val Arg Val
Trp His 65 70 75Cys Ser Arg Cys Leu Cys Gln His Leu Leu Ser Gly Gly
Ser Gly 80 85 90Leu Gln Arg Gly Leu Phe His Leu Leu Val Gln Lys Ser
Lys Lys 95 100 105Ser Ser Thr Phe Lys Phe Tyr Arg Arg His Lys Met
Pro Ala Pro 110 115 120Ala Gln Arg Lys Leu Leu Pro Arg Arg His Leu
Ser Glu Lys Ser 125 130 135His His Ile Ser Ile Pro Ser Pro Asp Ile
Ser His Lys Gly Leu 140 145 150Arg Ser Lys Arg Thr Gln Pro Ser Asp
Pro Glu Thr Trp Glu Ser 155 160 165Leu Pro Arg Leu Asp Ser Gln Arg
His Gly Gly Pro Glu Phe Ser 170 175 180Phe Asp Leu Leu Pro Glu Ala
Arg Ala Ile Arg Val Thr Ile Ser 185 190 195Ser Gly Pro Glu Val Ser
Val Arg Leu Cys His Gln Trp Ala Leu 200 205 210Glu Cys Glu Glu Leu
Ser Ser Pro Tyr Asp Val Gln Lys Ile Val 215 220 225Ser Gly Gly His
Thr Val Glu Leu Pro Tyr Glu Phe Leu Leu Pro 230 235 240Cys Leu Cys
Ile Glu Ala Ser Tyr Leu Gln Glu Asp Thr Val Arg 245 250 255Arg Lys
Lys Cys Pro Phe Gln Ser Trp Pro Glu Ala Tyr Gly Ser 260 265 270Asp
Phe Trp Lys Ser Val His Phe Thr Asp Tyr Ser Gln His Thr 275 280
285Gln Met Val Met Ala Leu Thr Leu Arg Cys Pro Leu Lys Leu Glu 290
295 300Ala Ala Leu Cys Gln Arg His Asp Trp His Thr Leu Cys Lys Asp
305 310 315Leu Pro Asn Ala Thr Ala Arg Glu Ser Asp Gly Trp Tyr Val
Leu 320 325 330Glu Lys Val
Asp Leu His Pro Gln Leu Cys Phe Lys Phe Ser Phe 335 340 345Gly Asn
Ser Ser His Val Glu Cys Pro His Gln Thr Gly Ser Leu 350 355 360Thr
Ser Trp Asn Val Ser Met Asp Thr Gln Ala Gln Gln Leu Ile 365 370
375Leu His Phe Ser Ser Arg Met His Ala Thr Phe Ser Ala Ala Trp 380
385 390Ser Leu Pro Gly Leu Gly Gln Asp Thr Leu Val Pro Pro Val Tyr
395 400 405Thr Val Ser Gln Ala Arg Gly Ser Ser Pro Val Ser Leu Asp
Leu 410 415 420Ile Ile Pro Phe Leu Arg Pro Gly Cys Cys Val Leu Val
Trp Arg 425 430 435Ser Asp Val Gln Phe Ala Trp Lys His Leu Leu Cys
Pro Asp Val 440 445 450Ser Tyr Arg His Leu Gly Leu Leu Ile Leu Ala
Leu Leu Ala Leu 455 460 465Leu Thr Leu Leu Gly Val Val Leu Ala Leu
Thr Cys Arg Arg Pro 470 475 480Gln Ser Gly Pro Gly Pro Ala Arg Pro
Val Leu Leu Leu His Ala 485 490 495Ala Asp Ser Glu Ala Gln Arg Arg
Leu Val Gly Ala Leu Ala Glu 500 505 510Leu Leu Arg Ala Ala Leu Gly
Gly Gly Arg Asp Val Ile Val Asp 515 520 525Leu Trp Glu Gly Arg His
Val Ala Arg Val Gly Pro Leu Pro Trp 530 535 540Leu Trp Ala Ala Arg
Thr Arg Val Ala Arg Glu Gln Gly Thr Val 545 550 555Leu Leu Leu Trp
Ser Gly Ala Asp Leu Arg Pro Val Ser Gly Pro 560 565 570Asp Pro Arg
Ala Ala Pro Leu Leu Ala Leu Leu His Ala Ala Pro 575 580 585Arg Pro
Leu Leu Leu Leu Ala Tyr Phe Ser Arg Leu Cys Ala Lys 590 595 600Gly
Asp Ile Pro Pro Pro Leu Arg Ala Leu Pro Arg Tyr Arg Leu 605 610
615Leu Arg Asp Leu Pro Arg Leu Leu Arg Ala Leu Asp Ala Arg Pro 620
625 630Phe Ala Glu Ala Thr Ser Trp Gly Arg Leu Gly Ala Arg Gln Arg
635 640 645Arg Gln Ser Arg Leu Glu Leu Cys Ser Arg Leu Glu Arg Glu
Ala 650 655 660Ala Arg Leu Ala Asp Leu Gly 665172319DNAHomo Sapien
17gccaggccct atctccctgc caggaggccg gagtggggga ggtcagacgg
50ggcggttgga gggggaggga tgccacgcgc ttctgcctca ggtgttcctg
100cgttgtttgt cagtggagag cagggagtgg ggccagccag cagaaacagt
150gggctgtaca acatcacctt caaatatgac aattgtacca cctacttgaa
200tccagtgggg aagcatgtga ttgctgacgc ccagaatatc accatcagcc
250agtatgcttg ccatgaccaa gtggcagtca ccattctttg gtccccaggg
300gccctcggca tcgaattcct gaaaggattt cgggtaatac tggaggagct
350gaagtcggag ggaagacagt gccaacaact gattctaaag gatccgaagc
400agctcaacag tagcttcaaa agaactggaa tggaatctca acctttcctg
450aatatgaaat ttgaaacgga ttatttcgta aaggttgtcc cttttccttc
500cattaaaaac gaaagcaatt accacccttt cttctttaga acccgagcct
550gtgacctgtt gttacagccg gacaatctag cttgtaaacc cttctggaag
600cctcggaacc tgaacatcag ccagcatggc tcggacatgc aggtgtcctt
650cgaccacgca ccgcatggct cggacatgca ggtgtccttc gaccacgcac
700cgcacaactt cggcttccgt ttcttctatc ttcactacaa gctcaagcac
750gaaggacctt tcaagcgaaa gacctgtaag caggagcaaa ctacagagat
800gaccagctgc ctccttcaaa atgtttctcc aggggattat ataattgagc
850tggtggatga cactaacaca acaagaaaag tgatgcatta tgccttaaag
900ccagtgcact ccccgtgggc cgggcccatc agagccgtgg ccatcacagt
950gccactggta gtcatatcgg cattcgcgac gctcttcact gtgatgtgcc
1000gcaagaagca acaagaaaat atatattcac atttagatga agagagctct
1050gagtcttcca catacactgc agcactccca agagagaggc tccggccgcg
1100gccgaaggtc tttctctgct attccagtaa agatggccag aatcacatga
1150atgtcgtcca gtgtttcgcc tacttcctcc aggacttctg tggctgtgag
1200gtggctctgg acctgtggga agacttcagc ctctgtagag aagggcagag
1250agaatgggtc atccagaaga tccacgagtc ccagttcatc attgtggttt
1300gttccaaagg tatgaagtac tttgtggaca agaagaacta caaacacaaa
1350ggaggtggcc gaggctcggg gaaaggagag ctcttcctgg tggcggtgtc
1400agccattgcc gaaaagctcc gccaggccaa gcagagttcg tccgcggcgc
1450tcagcaagtt tatcgccgtc tactttgatt attcctgcga gggagacgtc
1500cccggtatcc tagacctgag taccaagtac agactcatgg acaatcttcc
1550tcagctctgt tcccacctgc actcccgaga ccacggcctc caggagccgg
1600ggcagcacac gcgacagggc agcagaagga actacttccg gagcaagtca
1650ggccggtccc tatacgtcgc catttgcaac atgcaccagt ttattgacga
1700ggagcccgac tggttcgaaa agcagttcgt tcccttccat cctcctccac
1750tgcgctaccg ggagccagtc ttggagaaat ttgattcggg cttggtttta
1800aatgatgtca tgtgcaaacc agggcctgag agtgacttct gcctaaaggt
1850agaggcggct gttcttgggg caaccggacc agccgactcc cagcacgaga
1900gtcagcatgg gggcctggac caagacgggg aggcccggcc tgcccttgac
1950ggtagcgccg ccctgcaacc cctgctgcac acggtgaaag ccggcagccc
2000ctcggacatg ccgcgggact caggcatcta tgactcgtct gtgccctcat
2050ccgagctgtc tctgccactg atggaaggac tctcgacgga ccagacagaa
2100acgtcttccc tgacggagag cgtgtcctcc tcttcaggcc tgggtgagga
2150ggaacctcct gcccttcctt ccaagctcct ctcttctggg tcatgcaaag
2200cagatcttgg ttgccgcagc tacactgatg aactccacgc ggtcgcccct
2250ttgtaacaaa acgaaagagt ctaagcattg ccactttaaa aaaaaaaaaa
2300aaaaaaaaaa aaaaaaaaa 231918728PRTHomo Sapien 18Met Pro Arg Ala
Ser Ala Ser Gly Val Pro Ala Leu Phe Val Ser 1 5 10 15Gly Glu Gln
Gly Val Gly Pro Ala Ser Arg Asn Ser Gly Leu Tyr 20 25 30Asn Ile Thr
Phe Lys Tyr Asp Asn Cys Thr Thr Tyr Leu Asn Pro 35 40 45Val Gly Lys
His Val Ile Ala Asp Ala Gln Asn Ile Thr Ile Ser 50 55 60Gln Tyr Ala
Cys His Asp Gln Val Ala Val Thr Ile Leu Trp Ser 65 70 75Pro Gly Ala
Leu Gly Ile Glu Phe Leu Lys Gly Phe Arg Val Ile 80 85 90Leu Glu Glu
Leu Lys Ser Glu Gly Arg Gln Cys Gln Gln Leu Ile 95 100 105Leu Lys
Asp Pro Lys Gln Leu Asn Ser Ser Phe Lys Arg Thr Gly 110 115 120Met
Glu Ser Gln Pro Phe Leu Asn Met Lys Phe Glu Thr Asp Tyr 125 130
135Phe Val Lys Val Val Pro Phe Pro Ser Ile Lys Asn Glu Ser Asn 140
145 150Tyr His Pro Phe Phe Phe Arg Thr Arg Ala Cys Asp Leu Leu Leu
155 160 165Gln Pro Asp Asn Leu Ala Cys Lys Pro Phe Trp Lys Pro Arg
Asn 170 175 180Leu Asn Ile Ser Gln His Gly Ser Asp Met Gln Val Ser
Phe Asp 185 190 195His Ala Pro His Gly Ser Asp Met Gln Val Ser Phe
Asp His Ala 200 205 210Pro His Asn Phe Gly Phe Arg Phe Phe Tyr Leu
His Tyr Lys Leu 215 220 225Lys His Glu Gly Pro Phe Lys Arg Lys Thr
Cys Lys Gln Glu Gln 230 235 240Thr Thr Glu Met Thr Ser Cys Leu Leu
Gln Asn Val Ser Pro Gly 245 250 255Asp Tyr Ile Ile Glu Leu Val Asp
Asp Thr Asn Thr Thr Arg Lys 260 265 270Val Met His Tyr Ala Leu Lys
Pro Val His Ser Pro Trp Ala Gly 275 280 285Pro Ile Arg Ala Val Ala
Ile Thr Val Pro Leu Val Val Ile Ser 290 295 300Ala Phe Ala Thr Leu
Phe Thr Val Met Cys Arg Lys Lys Gln Gln 305 310 315Glu Asn Ile Tyr
Ser His Leu Asp Glu Glu Ser Ser Glu Ser Ser 320 325 330Thr Tyr Thr
Ala Ala Leu Pro Arg Glu Arg Leu Arg Pro Arg Pro 335 340 345Lys Val
Phe Leu Cys Tyr Ser Ser Lys Asp Gly Gln Asn His Met 350 355 360Asn
Val Val Gln Cys Phe Ala Tyr Phe Leu Gln Asp Phe Cys Gly 365 370
375Cys Glu Val Ala Leu Asp Leu Trp Glu Asp Phe Ser Leu Cys Arg 380
385 390Glu Gly Gln Arg Glu Trp Val Ile Gln Lys Ile His Glu Ser Gln
395 400 405Phe Ile Ile Val Val Cys Ser Lys Gly Met Lys Tyr Phe Val
Asp 410 415 420Lys Lys Asn Tyr Lys His Lys Gly Gly Gly Arg Gly Ser
Gly Lys 425 430 435Gly Glu Leu Phe Leu Val Ala Val Ser Ala Ile Ala
Glu Lys Leu 440 445 450Arg Gln Ala Lys Gln Ser Ser Ser Ala Ala Leu
Ser Lys Phe Ile 455 460 465Ala Val Tyr Phe Asp Tyr Ser Cys Glu Gly
Asp Val Pro Gly Ile 470 475 480Leu Asp Leu Ser Thr Lys Tyr Arg Leu
Met Asp Asn Leu Pro Gln 485 490 495Leu Cys Ser His Leu His Ser Arg
Asp His Gly Leu Gln Glu Pro 500 505 510Gly Gln His Thr Arg Gln Gly
Ser Arg Arg Asn Tyr Phe Arg Ser 515 520 525Lys Ser Gly Arg Ser Leu
Tyr Val Ala Ile Cys Asn Met His Gln 530 535 540Phe Ile Asp Glu Glu
Pro Asp Trp Phe Glu Lys Gln Phe Val Pro 545 550 555Phe His Pro Pro
Pro Leu Arg Tyr Arg Glu Pro Val Leu Glu Lys 560 565 570Phe Asp Ser
Gly Leu Val Leu Asn Asp Val Met Cys Lys Pro Gly 575 580 585Pro Glu
Ser Asp Phe Cys Leu Lys Val Glu Ala Ala Val Leu Gly 590 595 600Ala
Thr Gly Pro Ala Asp Ser Gln His Glu Ser Gln His Gly Gly 605 610
615Leu Asp Gln Asp Gly Glu Ala Arg Pro Ala Leu Asp Gly Ser Ala 620
625 630Ala Leu Gln Pro Leu Leu His Thr Val Lys Ala Gly Ser Pro Ser
635 640 645Asp Met Pro Arg Asp Ser Gly Ile Tyr Asp Ser Ser Val Pro
Ser 650 655 660Ser Glu Leu Ser Leu Pro Leu Met Glu Gly Leu Ser Thr
Asp Gln 665 670 675Thr Glu Thr Ser Ser Leu Thr Glu Ser Val Ser Ser
Ser Ser Gly 680 685 690Leu Gly Glu Glu Glu Pro Pro Ala Leu Pro Ser
Lys Leu Leu Ser 695 700 705Ser Gly Ser Cys Lys Ala Asp Leu Gly Cys
Arg Ser Tyr Thr Asp 710 715 720Glu Leu His Ala Val Ala Pro Leu
7251924DNAArtificial SequenceSynthetic Oligonucleotide Probe
19atccacagaa gctggccttc gccg 242024DNAArtificial SequenceSynthetic
Oligonucleotide Probe 20gggacgtgga tgaactcggt gtgg
242140DNAArtificial SequenceSynthetic Oligonucleotide Probe
21tatccacaga agctggcctt cgccgagtgc ctgtgcagag 402227DNAArtificial
SequenceSynthetic Oligonucleotide Probe 22gttgcattct tggcaatggt
catggga 272324DNAArtificial SequenceSynthetic Oligonucleotide Probe
23ggtccatgtg ggagcctgtc tgta 242445DNAArtificial SequenceSynthetic
Oligonucleotide Probe 24cagcagctcc tcagaggtgt cctgcccttt gctggggcag
cagct 452523DNAArtificial SequenceSynthetic Oligonucleotide Probe
25gctcagtgcc ttccaccaca cgc 232621DNAArtificial SequenceSynthetic
Oligonucleotide Probe 26ctgcgtcctt ctccggctcg g 212745DNAArtificial
SequenceSynthetic Oligonucleotide Probe 27cgttccgtct acaccgaggc
ctacgtcacc atccccgtgg gctgc 452825DNAArtificial SequenceSynthetic
Oligonucleotide Probe 28actccatatt ttcctacttg tggca
252919DNAArtificial SequenceSynthetic Oligonucleotide Probe
29cccaaagtga cctaagaac 193027DNAArtificial SequenceSynthetic
Oligonucleotide Probe 30tcactgaatt tcttcaaaac cattgca
273150DNAArtificial SequenceSynthetic Oligonucleotide Probe
31tgtggcagcg actgcatccg acataaagga acagttgtgc tctgcccaca
503220DNAArtificial SequenceSynthetic Oligonucleotide Probe
32ccgacttctt gcagggccgg 203320DNAArtificial SequenceSynthetic
Oligonucleotide Probe 33gcagcacgca gctgagcgag 203433DNAArtificial
SequenceSynthetic Oligonucleotide Probe 34agcgagtggc tacaggatgg
ggtgtccggg ccc 333525DNAArtificial SequenceSynthetic
Oligonucleotide Probe 35cgttgtttgt cagtggagag caggg
253623DNAArtificial SequenceSynthetic Oligonucleotide Probe
36caggaacacc tgaggcagaa gcg 233740DNAArtificial SequenceSynthetic
Oligonucleotide Probe 37ctatctccct gccaggaggc cggagtgggg gaggtcagac
403821DNAArtificial SequenceSynthetic Oligonucleotide Probe
38ctgtacctcg agggtgcaga g 213958DNAArtificial SequenceSynthetic
Oligonucleotide Probe 39cccaagcttg ggtcaatgat gatgatgatg atgatgatgc
cacaggggca 50tgtagtcc 58
* * * * *
References