U.S. patent number RE46,816 [Application Number 14/228,173] was granted by the patent office on 2018-05-01 for composition and methods for the diagnosis of immune related diseases involving the pro52254 polypeptide.
This patent grant is currently assigned to Genentech, Inc.. The grantee listed for this patent is Genentech, Inc.. Invention is credited to Daryl T. Baldwin, Sarah C. Bodary-Winter, Andrew C. Chan, Hilary Clark, Janet K. Jackman, William I. Wood.
United States Patent |
RE46,816 |
Baldwin , et al. |
May 1, 2018 |
Composition and methods for the diagnosis of immune related
diseases involving the PRO52254 polypeptide
Abstract
The present invention relates to compositions containing a novel
protein and methods of using those compositions for the diagnosis
and treatment of immune related diseases involving detection of the
PRO52254 polypeptide.
Inventors: |
Baldwin; Daryl T. (Albany,
CA), Bodary-Winter; Sarah C. (Menlo Park, CA), Chan;
Andrew C. (Menlo Park, CA), Clark; Hilary (San
Francisco, CA), Jackman; Janet K. (Half Moon Bay, CA),
Wood; William I. (Cupertino, CA) |
Applicant: |
Name |
City |
State |
Country |
Type |
Genentech, Inc. |
South San Francisco |
CA |
US |
|
|
Assignee: |
Genentech, Inc. (South San
Francisco, CA)
|
Family
ID: |
1000003034915 |
Appl.
No.: |
14/228,173 |
Filed: |
March 27, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
Issue Date |
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14221160 |
Mar 20, 2014 |
|
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11537270 |
Sep 29, 2006 |
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10658482 |
Sep 9, 2003 |
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60410062 |
Sep 11, 2002 |
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Reissue of: |
12967886 |
Dec 14, 2010 |
8431350 |
Apr 30, 2013 |
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Reissue of: |
12967886 |
Dec 14, 2010 |
8431350 |
Apr 30, 2013 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07K
16/18 (20130101); C07K 14/47 (20130101); C12Q
1/6883 (20130101); A61K 2039/505 (20130101); G01N
2800/24 (20130101); G01N 2800/205 (20130101); G01N
2800/065 (20130101); C12Q 2600/158 (20130101); G01N
2500/10 (20130101); C12N 2799/026 (20130101) |
Current International
Class: |
G01N
33/53 (20060101); C07K 16/18 (20060101); C07K
14/47 (20060101); C12Q 1/68 (20180101); A61K
39/00 (20060101) |
Field of
Search: |
;435/7.1 |
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|
Primary Examiner: Ponnaluri; Shri
Attorney, Agent or Firm: Clark & Elbing LLP Elbing;
Karen L.
Parent Case Text
CROSS REFERENCE TO RELATED APPLICATIONS
.[.This application is a.]. .Iadd.More than one reissue application
has been filed for the reissue of U.S. Pat. No. 8,431,350, which
are U.S. application Ser. No. 14/221,160, filed Mar. 20, 2014; U.S.
application Ser. No. 14/228,172, filed Mar. 27, 2014; U.S.
application Ser. No. 14/228,173 (the present application), filed
Mar. 27, 2014; and U.S. application Ser. No. 14/699,845, filed Apr.
29, 2015. This application is a reissue application of U.S.
application Ser. No. 12/967,886, filed Dec. 14, 2010 (now U.S. Pat.
No. 8,431,350, issued Apr. 30, 2013), and a continuation reissue of
U.S. application Ser. No. 14/221,160, filed Mar. 20, 2014, which is
a reissue application of U.S. application Ser. No. 12/967,886,
filed Dec. 14, 2010 (now U.S. Pat. No. 8,431,350, issued Apr. 30,
2013), which is a .Iaddend.Continuation of U.S. application Ser.
No. 11/537,270, filed Sep. 29, 2006, .Iadd.now abandoned,
.Iaddend.which is a Continuation of U.S. application Ser. No.
10/658,482, filed Sep. 9, 2003 .[.both.]..Iadd., now abandoned, all
.Iaddend.of which claim the benefit of U.S. Provisional Application
No. 60/410,062, filed Sep. 11, 2002, the disclosures of which are
incorporated herein by reference in their entirety.
Claims
What is claimed:
.[.1. A method of diagnosing an immune related disease in a mammal,
wherein the immune related disease is psoriasis or inflammatory
bowel disease, said method comprising the steps of: (1) detecting
the level of expression of a gene encoding the polypeptide of SEQ
ID NO:2 in a test sample of tissue cells obtained from the mammal,
(2) detecting the level of expression of the gene encoding the
polypeptide of SEQ ID NO: 2 in a control sample of known normal
tissue cells of the same cell type, and (3) diagnosing the immune
related disease in the mammal when the level of expression of said
gene in the test sample is higher as compared to the level of
expression of said gene in the control sample..].
.[.2. The method of claim 1, wherein the immune related disease is
psoriasis..].
.[.3. The method of claim 1, wherein the immune related disease is
inflammatory bowel disease..].
.[.4. The method of claim 1, wherein the level of expression of the
gene encoding the polypeptide of SEQ ID NO:2 is detected with an
antibody that specifically binds to the polypeptide of SEQ ID NO:2,
or fragments thereof..].
.[.5. The method of claim 1, wherein the mammal is diagnosed of the
immune related disease when the level of expression of said gene is
at least 2 fold greater in the test sample as compared to the level
of expression of said gene in the control sample..].
.[.6. The method of claim 1, wherein the level of expression of the
gene encoding the polypeptide of SEQ ID NO:2 is detected by an
immunological method or a hybridization method..].
.[.7. The method of claim 6, wherein the immunological method is
immunohistochemical staining or ELISA..].
.[.8. The method of claim 7, wherein the immunological method is
ELISA..].
.[.9. The method of claim 6, wherein the hybridization method is
selected from the group consisting of Southern blotting, northern
blotting, dot blotting, polymerase chain reaction (PCR), microarray
analysis and in situ hybridization..].
.[.10. The method of claim 9, wherein the hybridization method is
microarray analysis..].
.[.11. The method of claim 1, wherein the inflammatory bowel
disease is ulcerative colitis..].
.[.12. A method of diagnosing an immune related disease in a
mammal, wherein the immune related disease is psoriasis or
inflammatory bowel disease, said method comprising the steps of:
(a) contacting an antibody that specifically binds to a polypeptide
comprising the amino acid sequence of SEQ ID NO:2, or fragments
thereof, with a test sample of tissue cells obtained from said
mammal, (b) contacting the antibody with a control sample of known
normal tissue cells of the same cell type, (c) detecting the
formation of a complex between the antibody and the polypeptide in
the test sample and in the control sample, and (d) diagnosing the
immune related disease in the mammal from which the test sample of
tissue cells were obtained when the quantity of complexes formed in
the test sample is larger as compared to the quantity of complexes
formed in the control sample..].
.[.13. The method of claim 12, wherein the immune related disease
is psoriasis..].
.[.14. The method of claim 12, wherein the immune related disease
is inflammatory bowel disease..].
.[.15. The method of claim 12, wherein the formation of a complex
between the antibody and the polypeptide is detected by
immunohistochemical staining or ELISA..].
.[.16. The method of claim 15, wherein the formation of a complex
between the antibody and the polypeptide is detected by
ELISA..].
.[.17. The method of claim 12, wherein the inflammatory bowel
disease is ulcerative colitis..].
.Iadd.18. A method of treating cancer in a human, the method
comprising administering to the human a therapeutically effective
amount of an antagonist of the polypeptide of SEQ ID NO: 2, wherein
the antagonist is an antibody, or antigen-binding fragment thereof,
that specifically binds SEQ ID NO: 2..Iaddend.
.Iadd.19. The method of claim 18, wherein the antibody, or
antigen-binding fragment thereof, is human..Iaddend.
.Iadd.20. The method of claim 18, wherein the antibody, or
antigen-binding fragment thereof, is humanized..Iaddend.
.Iadd.21. The method of claim 18, wherein the antibody, or
antigen-binding fragment thereof, is monoclonal, chimeric,
bispecific, monovalent, bivalent, or single chain..Iaddend.
.Iadd.22. The method of claim 18, wherein the antibody, of
antigen-binding fragment thereof, is in a heteroconjugate or an
immunoconjugate..Iaddend.
.Iadd.23. The method of claim 18, comprising administering the
antagonist of the polypeptide of SEQ ID NO: 2 in combination with
an anti-cancer therapeutic regimen..Iaddend.
.Iadd.24. The method of claim 23, wherein the anti-cancer
therapeutic regimen comprises administering an
antibody..Iaddend.
.Iadd.25. The method of claim 24, wherein the antibody binds to
CD20, CD11a, CD18, ErbB2, EGFR, ErbB3, ErbB4, or VEGF..Iaddend.
.Iadd.26. The method of claim 23, wherein the anti-cancer
therapeutic regimen comprises administering a growth regulating
agent, a cytotoxic agent, or a chemotherapeutic agent..Iaddend.
.Iadd.27. The method of claim 23, wherein the anti-cancer
therapeutic regimen comprises administering radiation
therapy..Iaddend.
Description
.Iadd.INCORPORATION BY REFERENCE OF SEQUENCE LISTING .Iaddend.
.Iadd.The content of the following submission on ASCII text file is
incorporated herein by reference in its entirety: a computer
readable form (CRF) of the Sequence Listing (file name:
146392021832_Sequence_Listing.txt, date recorded: Mar. 27, 2014,
size: 8,022 bytes.) .Iaddend.
FIELD OF THE INVENTION
The present invention relates to compositions and methods useful
for the diagnosis and treatment of immune related diseases.
BACKGROUND OF THE INVENTION
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.
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.
Many immune related diseases are known and have been extensively
studied. Such diseases include immune-mediated inflammatory
diseases, non-immune-mediated inflammatory diseases, infectious
diseases, immunodeficiency diseases, neoplasia, etc.
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.
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.
CD4+ T cells are known to be important regulators of inflammation.
Herein, CD4+ T cells were activated and the profile of genes
differentially expressed upon activation was analyzed. As such, the
activation specific genes may be potential therapeutic targets. In
vivo co-stimulation is necessary for a productive immune
proliferative response. The list of costimulatory molecules is
quite extensive and it is still unclear just which co-stimulatory
molecules play critical roles in different types and stages of
inflammation. In this application, the focus is on a gene
specifically upregulated by stimulation with anti-CD3/ICAM, or
anti-CD3/anti-CD28 and may be useful in targeting inflammatory
processes.
Several diseases of the skin are correlated with an aberrant immune
response and to autoimmunity. Diseases such as psoriasis are
hallmarked by skin blistering, skin flaking, edema and the presence
of autoantibodies that bind to skin proteins. In this application,
experiments determine that a gene is upregulated in psoriatic skin
vs. normal skin. Proteins or antagonists of the invention may be
useful in alleviating the symptoms of psoriasis.
The term inflammatory bowel disorder ("IBD") describes a group of
chronic inflammatory disorders of unknown causes in which the
intestine (bowel) becomes inflamed, often causing recurring cramps
or diarrhea. The prevalence of IBD in the US is estimated to be
about 200 per 100,000 population. Patients with IBD can be divided
into two major groups, those with ulcerative colitis ("UC") and
those with Crohn's disease ("CD").
In patients with UC, there is an inflammatory reaction primarily
involving the colonic mucosa. The inflammation is typically uniform
and continuous with no intervening areas of normal mucosa. Surface
mucosal cells as well as crypt epithelium and submucosa are
involved in an inflammatory reaction with neutrophil infiltration.
Ultimately, this situation typically progresses to epithelial
damage with loss of epithelial cells resulting in multiple
ulcerations, fibrosis, dysplasia and longitudinal retraction of the
colon.
CD differs from UC in that the inflammation extends through all
layers of the intestinal wall and involves mesentery as well as
lymph nodes. CD may affect any part of the alimentary canal from
mouth to anus. The disease is often discontinuous, i.e., severely
diseased segments of bowel are separated from apparently
disease-free areas. In CD, the bowel wall also thickens which can
lead to obstructions. In addition, fistulas and fissures are not
uncommon.
Clinically, IBD is characterized by diverse manifestations often
resulting in a chronic, unpredictable course. Bloody diarrhea and
abdominal pain are often accompanied by fever and weight loss.
Anemia is not uncommon, as is severe fatigue. Joint manifestations
ranging from arthralgia to acute arthritis as well as abnormalities
in liver function are commonly associated with IBD. Patients with
IBD also have an increased risk of colon carcinomas compared to the
general population. During acute "attacks" of IBD, work and other
normal activity are usually impossible, and often a patient is
hospitalized.
Although the cause of IBD remains unknown, several factors such as
genetic, infectious and immunologic susceptibility have been
implicated. IBD is much more common in Caucasians, especially those
of Jewish descent. The chronic inflammatory nature of the condition
has prompted an intense search for a possible infectious cause.
Although agents have been found which stimulate acute inflammation,
none has been found to cause the chronic inflammation associated
with IBD. The hypothesis that IBD is an autoimmune disease is
supported by the previously mentioned extraintestinal manifestation
of IBD as joint arthritis, and the known positive response to IBD
by treatment with therapeutic agents such as adrenal
glucocorticoids, cyclosporine and azathioprine, which are known to
suppress immune response. In addition, the GI tract, more than any
other organ of the body, is continuously exposed to potential
antigenic substances such as proteins from food, bacterial
byproducts (LPS), etc.
Further, the risk of colon cancer is highly elevated in patients
with severe ulcerative colitis, particularly if the disease has
existed for several years. About 20-25% of patients with IBD
eventually require surgery for removal of the colon because of
massive bleeding, chronic debilitating illness, performation of the
colon, or risk of cancer. Surgery is also sometimes performed when
other forms of medical treatment fail or when the side effects of
steroids or other medications threaten the patient's health. As
surgery is invasive and drastically life altering, it is not a
highly desirable treatment regimen, and is typically the treatment
of last resort. In order to better understand this disease and
possibly treat it, experiments determined that a gene was
upregulated both in CD and UC when compared to normal tissue. This
gene may prove useful in the treatment of forms of IBD.
Despite the above identified advances in immune disorder research,
there is a great need for additional diagnostic and therapeutic
agents capable of detecting the presence of a immune disorders in a
mammal and for effectively reducing these disorders. Accordingly,
it is an objective of the present invention to identify and
characterize a polypeptide that is overexpressed in various immune
disorders, and to use those polypeptides, and their encoding
nucleic acids, to produce compositions of matter useful in the
therapeutic treatment and diagnostic detection of immune disorders
in mammals.
SUMMARY OF THE INVENTION
A. Embodiments
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 are a result of stimulation of 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 PRO52254
polypeptides, 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 PRO52254 polypeptide, agonist or antagonist thereof
with a pharmaceutically acceptable carrier. Preferably, the
admixture is sterile.
In a further embodiment, the invention concerns a method of
identifying agonists or antagonists to a PRO52254 polypeptide which
comprises contacting the PRO52254 polypeptide with a candidate
molecule and monitoring a biological activity mediated by said
PRO52254 polypeptide. Preferably, the PRO52254 polypeptide is a
native sequence PRO52254 polypeptide. In a specific aspect, the
PRO52254 agonist or antagonist is an anti-PRO52254 antibody.
In another embodiment, the invention concerns a composition of
matter comprising a PRO52254 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) increasing
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.
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 an effective amount of a PRO52254
polypeptide, an agonist thereof, or an antagonist thereto. In a
preferred aspect, the immune related disorder is selected from 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.
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 PRO52254 polypeptide. In another aspect, the antibody
mimics the activity of a PRO52254 polypeptide (an agonist antibody)
or conversely the antibody inhibits or neutralizes the activity of
a PRO52254 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.
In yet another embodiment, the present invention provides a
composition comprising an anti-PRO52254 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.
In a further embodiment, the invention concerns an article of
manufacture, comprising: (a) a composition of matter comprising a
PRO52254 polypeptide or agonist or antagonist 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 PRO52254 polypeptide or agonist or
antagonist thereof in the treatment of an immune related disease.
The composition may comprise a therapeutically effective amount of
the PRO52254 polypeptide or the agonist or antagonist thereof.
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 PRO52254
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.
In another embodiment, the present invention concerns a method of
diagnosing an immune disease in a mammal, comprising (a) contacting
an anti-PRO52254 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 PRO52254 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.
In another embodiment, the invention provides a method for
determining the presence of a PRO52254 polypeptide in a sample
comprising exposing a test sample of cells suspected of containing
the PRO52254 polypeptide to an anti-PRO52254 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 PRO52254 polypeptide and the antibody binds to the
cell. The antibody is preferably detectably labeled and/or bound to
a solid support.
In another embodiment, the present invention concerns an
immune-related disease diagnostic kit, comprising an anti-PRO52254
antibody and a carrier in suitable packaging. The kit preferably
contains instructions for using the antibody to detect the presence
of the PRO52254 polypeptide. Preferably the carrier is
pharmaceutically acceptable.
In another embodiment, the present invention concerns a diagnostic
kit, containing an anti-PRO52254 antibody in suitable packaging.
The kit preferably contains instructions for using the antibody to
detect the PRO52254 polypeptide.
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 PRO52254 polypeptide in a
test sample of tissue cells obtained from said mammal, wherein the
presence or absence of the PRO52254 polypeptide in said test sample
is indicative of the presence of an immune-related disease in said
mammal.
In another embodiment, the present invention concerns a method for
identifying an agonist of a PRO52254 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 PRO52254 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.
In another embodiment, the invention concerns a method for
identifying a compound capable of inhibiting the activity of a
PRO52254 polypeptide comprising contacting a candidate compound
with a PRO52254 polypeptide under conditions and for a time
sufficient to allow these two components to interact and
determining whether the activity of the PRO52254 polypeptide is
inhibited. In a specific aspect, either the candidate compound or
the PRO52254 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 PRO52254 polypeptide under conditions suitable for
the induction of a cellular response normally induced by a PRO52254
polypeptide; and (b) determining the induction of said cellular
response to determine if the test compound is an effective
antagonist.
In another embodiment, the invention provides a method for
identifying a compound that inhibits the expression of a PRO52254
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 PRO52254 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 PRO52254
polypeptide; and
(b) determining the inhibition of expression of said
polypeptide.
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 PRO52254 polypeptide, (b) an
agonist of a PRO52254 polypeptide or (c) an antagonist of a
PRO52254 polypeptide, wherein said agonist or antagonist may be an
anti-PRO52254 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.
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 PRO52254 polypeptide, (b) an
agonist polypeptide of a PRO52254 polypeptide, or (c) an antagonist
polypeptide of a PRO52254 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 PRO52254
polypeptide.
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 PRO52254 polypeptide, (b) an agonist polypeptide of a
PRO52254 polypeptide or (c) an antagonist polypeptide of a PRO52254
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.
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 PRO52254 polypeptide, (b) an
agonist of a PRO52254 polypeptide, or (c) an antagonist of a
PRO52254 polypeptide, wherein the activity of T-lymphocytes in the
mammal is increased.
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 PRO52254 polypeptide, (b) an
agonist of a PRO52254 polypeptide, or (c) an antagonist of a
PRO52254 polypeptide, wherein the activity of T-lymphocytes in the
mammal is decreased.
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 PRO52254 polypeptide,
(b) an agonist of a PRO52254 polypeptide, or (c) an antagonist of a
PRO52254 polypeptide, wherein the proliferation of T-lymphocytes in
the mammal is increased.
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 PRO52254 polypeptide,
(b) an agonist of a PRO52254 polypeptide, or (c) an antagonist of a
PRO52254 polypeptide, wherein the proliferation of T-lymphocytes in
the mammal is decreased.
B. Additional Embodiments
In other 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, or yeast. 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.
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.
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 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.
In other embodiments, the invention provides an isolated nucleic
acid molecule comprising a nucleotide sequence that encodes a
PRO52254 polypeptide.
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 PRO52254 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).
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 PRO52254 polypeptide cDNA as disclosed herein, the
coding sequence of a PRO52254 polypeptide lacking the signal
peptide as disclosed herein, the coding sequence of an
extracellular domain of a transmembrane PRO52254 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).
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).
Another aspect the invention provides an isolated nucleic acid
molecule comprising a nucleotide sequence encoding a PRO52254
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 PRO52254 polypeptides
are contemplated.
Another embodiment is directed to fragments of a PRO52254
polypeptide coding sequence, or the complement thereof, that may
find use as, for example, hybridization probes, for encoding
fragments of a PRO52254 polypeptide that may optionally encode a
polypeptide comprising a binding site for an anti-PRO52254 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 PRO52254 polypeptide-encoding
nucleotide sequence may be determined in a routine manner by
aligning the PRO52254 polypeptide-encoding nucleotide sequence with
other known nucleotide sequences using any of a number of well
known sequence alignment programs and determining which PRO52254
polypeptide-encoding nucleotide sequence fragment(s) are novel. All
of such PRO52254 polypeptide-encoding nucleotide sequences are
contemplated herein. Also contemplated are the PRO52254 polypeptide
fragments encoded by these nucleotide molecule fragments,
preferably those PRO52254 polypeptide fragments that comprise a
binding site for an anti-PRO52254 antibody.
In another embodiment, the invention provides isolated PRO52254
polypeptide encoded by any of the isolated nucleic acid sequences
herein above identified.
In a certain aspect, the invention concerns an isolated PRO52254
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 PRO52254 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.
In a further aspect, the invention concerns an isolated PRO52254
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.
In a specific aspect, the invention provides an isolated PRO52254
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 herein before 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 PRO52254
polypeptide and recovering the PRO52254 polypeptide from the cell
culture.
Another aspect the invention provides an isolated PRO52254
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 PRO52254 polypeptide and recovering
the PRO52254 polypeptide from the cell culture.
In yet another embodiment, the invention concerns agonists and
antagonists of a native PRO52254 polypeptide as defined herein. In
a particular embodiment, the agonist or antagonist is an
anti-PRO52254 antibody or a small molecule.
In a further embodiment, the invention concerns a method of
identifying agonists or antagonists to a PRO52254 polypeptide which
comprise contacting the PRO52254 polypeptide with a candidate
molecule and monitoring a biological activity mediated by said
PRO52254 polypeptide. Preferably, the PRO52254 polypeptide is a
native PRO52254 polypeptide.
In a still further embodiment, the invention concerns a composition
of matter comprising a PRO52254 polypeptide, or an agonist or
antagonist of a PRO52254 polypeptide as herein described, or an
anti-PRO52254 antibody, in combination with a carrier. Optionally,
the carrier is a pharmaceutically acceptable carrier.
Another embodiment of the present invention is directed to the use
of a PRO52254 polypeptide, or an agonist or antagonist thereof as
herein before described, or an anti-PRO52254 antibody, for the
preparation of a medicament useful in the treatment of a condition
which is responsive to the PRO52254 polypeptide, an agonist or
antagonist thereof or an anti-PRO52254 antibody.
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows a nucleotide sequence (SEQ ID NO:1) of a native
sequence PRO52254 cDNA, wherein SEQ ID NO:1 is a clone designated
herein as "DNA327145".
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.
FIG. 3 shows a nucleotide sequence (SEQ ID NO:3) of a native MURINE
sequence PRO71302 cDNA, wherein SEQ ID NO:3 is a clone designated
herein as "DNA327512".
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.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
I. Definitions
The terms "PRO52254 polypeptide" and "PRO52254" as used herein and
when immediately followed by a numerical designation refer to
various polypeptides, wherein the complete designation (i.e.,
PRO52254/number) refers to specific polypeptide sequences as
described herein. The terms "PRO52254/number polypeptide" and
"PRO52254/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 PRO52254 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 "PRO52254 polypeptide" refers to each individual
PRO52254/number polypeptide disclosed herein. All disclosures in
this specification which refer to the "PRO52254 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 "PRO52254 polypeptide" also includes
variants of the PRO52254/number polypeptides disclosed herein.
A "native sequence PRO52254 polypeptide" comprises a polypeptide
having the same amino acid sequence as the corresponding PRO52254
polypeptide derived from nature. Such native sequence PRO52254
polypeptides can be isolated from nature or can be produced by
recombinant or synthetic means. The term "native sequence PRO52254
polypeptide" specifically encompasses naturally-occurring truncated
or secreted forms of the specific PRO52254 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 PRO52254 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 PRO52254
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 PRO52254 polypeptides.
The PRO52254 polypeptide "extracellular domain" or "ECD" refers to
a form of the PRO52254 polypeptide which is essentially free of the
transmembrane and cytoplasmic domains. Ordinarily, a PRO52254
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 PRO52254 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 PRO52254 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
contemplated by the present invention.
The approximate location of the "signal peptides" of the various
PRO52254 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.
"PRO52254 polypeptide variant" means an active PRO52254 polypeptide
as defined above or below having at least about 80% amino acid
sequence identity with a full-length native sequence PRO52254
polypeptide sequence as disclosed herein, a PRO52254 polypeptide
sequence lacking the signal peptide as disclosed herein, an
extracellular domain of a PRO52254 polypeptide, with or without the
signal peptide, as disclosed herein or any other fragment of a
full-length PRO52254 polypeptide sequence as disclosed herein. Such
PRO52254 polypeptide variants include, for instance, PRO52254
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 PRO52254 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 PRO52254 polypeptide sequence as disclosed herein,
a PRO52254 polypeptide sequence lacking the signal peptide as
disclosed herein, an extracellular domain of a PRO52254
polypeptide, with or without the signal peptide, as disclosed
herein or any other specifically defined fragment of a full-length
PRO52254 polypeptide sequence as disclosed herein. Ordinarily,
PRO52254 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.
"Percent (%) amino acid sequence identity" with respect to the
PRO52254 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 PRO52254
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.
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 "PRO52254", wherein "PRO52254" represents the
amino acid sequence of a hypothetical PRO52254 polypeptide of
interest, "Comparison Protein" represents the amino acid sequence
of a polypeptide against which the "PRO52254" polypeptide of
interest is being compared, and "X, "Y" and "Z" each represent
different hypothetical amino acid residues.
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 PRO52254
polypeptide of interest having a sequence derived from the native
PRO52254 polypeptide and the comparison amino acid sequence of
interest (i.e., the sequence against which the PRO52254 polypeptide
of interest is being compared which may be a PRO52254 variant
polypeptide) as determined by WU-BLAST-2 by (b) the total number of
amino acid residues of the PRO52254 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
PRO52254 polypeptide of interest.
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.
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.
"PRO52254 variant polynucleotide" or "PRO52254 variant nucleic acid
sequence" means a nucleic acid molecule which encodes an active
PRO52254 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 PRO52254 polypeptide
sequence as disclosed herein, a full-length native sequence
PRO52254 polypeptide sequence lacking the signal peptide as
disclosed herein, an extracellular domain of a PRO52254
polypeptide, with or without the signal peptide, as disclosed
herein or any other fragment of a full-length PRO52254 polypeptide
sequence as disclosed herein. Ordinarily, a PRO52254 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 PRO52254 polypeptide sequence as disclosed herein, a
full-length native sequence PRO52254 polypeptide sequence lacking
the signal peptide as disclosed herein, an extracellular domain of
a PRO52254 polypeptide, with or without the signal sequence, as
disclosed herein or any other fragment of a full-length PRO52254
polypeptide sequence as disclosed herein. Variants do not encompass
the native nucleotide sequence.
Ordinarily, PRO52254 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.
"Percent (%) nucleic acid sequence identity" with respect to
PRO52254-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 PRO52254 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.
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 "PRO52254-DNA", wherein "PRO52254-DNA"
represents a hypothetical PRO52254-encoding nucleic acid sequence
of interest, "Comparison DNA" represents the nucleotide sequence of
a nucleic acid molecule against which the "PRO52254-DNA" nucleic
acid molecule of interest is being compared, and "N", "L" and "V"
each represent different hypothetical nucleotides.
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 PRO52254 polypeptide-encoding nucleic acid molecule of interest
having a sequence derived from the native sequence PRO52254
polypeptide-encoding nucleic acid and the comparison nucleic acid
molecule of interest (i.e., the sequence against which the PRO52254
polypeptide-encoding nucleic acid molecule of interest is being
compared which may be a variant PRO52254 polynucleotide) as
determined by WU-BLAST-2 by (b) the total number of nucleotides of
the PRO52254 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 PRO52254 polypeptide-encoding nucleic
acid molecule of interest.
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.
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.
In other embodiments, PRO52254 variant polynucleotides are nucleic
acid molecules that encode an active PRO52254 polypeptide and which
are capable of hybridizing, preferably under stringent
hybridization and wash conditions, to nucleotide sequences encoding
a full-length PRO52254 polypeptide as disclosed herein. PRO52254
variant polypeptides may be those that are encoded by a PRO52254
variant polynucleotide.
"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 PRO52254 polypeptide natural
environment will not be present. Ordinarily, however, isolated
polypeptide will be prepared by at least one purification step.
An "isolated" PRO52254 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.
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.
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.
The term "antibody" is used in the broadest sense and specifically
covers, for example, single anti-PRO52254 monoclonal antibodies
(including agonist, antagonist, and neutralizing antibodies),
anti-PRO52254 antibody compositions with polyepitopic specificity,
single chain anti-PRO52254 antibodies, and fragments of
anti-PRO52254 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.
"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).
"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.
"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.
The term "epitope tagged" when used herein refers to a chimeric
polypeptide comprising a PRO52254 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).
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.
"Active" or "activity" for the purposes herein refers to form(s) of
a PRO52254 polypeptide which retain a biological and/or an
immunological activity of native or naturally-occurring PRO52254,
wherein "biological" activity refers to a biological function
(either inhibitory or stimulatory) caused by a native or
naturally-occurring PRO52254 other than the ability to induce the
production of an antibody against an antigenic epitope possessed by
a native or naturally-occurring PRO52254 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 PRO52254.
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 PRO52254 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 PRO52254 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 PRO52254
polypeptides, peptides, antisense oligonucleotides, small organic
molecules, etc. Methods for identifying agonists or antagonists of
a PRO52254 polypeptide may comprise contacting a PRO52254
polypeptide with a candidate agonist or antagonist molecule and
measuring a detectable change in one or more biological activities
normally associated with the PRO52254 polypeptide.
"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.
"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.
"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.
Administration "in combination with" one or more further
therapeutic agents includes simultaneous (concurrent) and
consecutive administration in any order.
"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..
"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.
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.
"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.
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.
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.
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.
"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).
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).
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.
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.
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.
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.
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 PRO52254 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.
A "small molecule" is defined herein to have a molecular weight
below about 500 Daltons.
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.
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.
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
PRO52254 polypeptide and/or agonist/antagonist which results in
achieving a particular stated purpose. An "effective amount" of a
PRO52254 polypeptide or agonist or antagonist thereof may be
determined empirically. Furthermore, a "therapeutically effective
amount" is a concentration or amount of a PRO52254 polypeptide
and/or agonist/antagonist which is effective for achieving a stated
therapeutic effect. This amount may also be determined
empirically.
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.
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.
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.
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-1.alpha., IL-2, IL-3, IL-4,
IL-5, IL-6, IL-7, IL-8, IL-9, IL-11, IL-12; 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.
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.
As used herein, the term "inflammatory cells" designates cells that
enhance the inflammatory response such as mono-nuclear cells,
eosinophils, macrophages, and polymorphonuclear neutrophils
(PMN).
TABLE-US-00001 TABLE 2 PRO52254 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 PRO52254 polypeptide) = 5 divided by 15 = 33.3%
TABLE-US-00002 TABLE 3 PRO52254 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 PRO52254 polypeptide) = 5 divided by 10 =
50%
TABLE-US-00003 TABLE 4 PRO52254- NNNNNNNNNNNNNN (Length = 14
nucleotides) DNA 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 PRO52254-DNA nucleic acid sequence) = 6 divided
by 14 = 42.9%
TABLE-US-00004 TABLE 5 PRO52254-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 PRO52254-DNA nucleic acid sequence) = 4 divided by 12 =
33.3%
II. Compositions and Methods of the Invention
A. Full-Length PRO52254 Polypeptides
The present invention provides newly identified and isolated
nucleotide sequences encoding polypeptides referred to in the
present application as PRO52254 polypeptides. In particular, cDNAs
encoding various PRO52254 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 PRO52254 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 PRO52254, will be
referred to as "PRO52254/number", regardless of their origin or
mode of preparation.
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 PRO52254
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.
B. PRO52254 Polypeptide Variants
In addition to the full-length native sequence PRO52254
polypeptides described herein, it is contemplated that PRO52254
variants can be prepared. PRO52254 variants can be prepared by
introducing appropriate nucleotide changes into the PRO52254 DNA,
and/or by synthesis of the desired PRO52254 polypeptide. Those
skilled in the art will appreciate that amino acid changes may
alter post-translational processes of the PRO52254, such as
changing the number or position of glycosylation sites or altering
the membrane anchoring characteristics.
Variations in the native full-length sequence PRO52254 or in
various domains of the PRO52254 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 PRO52254 that results in a change in the amino acid sequence of
the PRO52254 as compared with the native sequence PRO52254.
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
PRO52254. 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
PRO52254 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.
PRO52254 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 PRO52254
polypeptide.
PRO52254 fragments may be prepared by any of a number of
conventional techniques. Desired peptide fragments may be
chemically synthesized. An alternative approach involves generating
PRO52254 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, PRO52254 polypeptide fragments share at
least one biological and/or immunological activity with the native
PRO52254 polypeptide disclosed herein.
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-00005 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
Substantial modifications in function or immunological identity of
the PRO52254 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.
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.
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
PRO52254 variant DNA.
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.
C. Modifications of PRO52254
Covalent modifications of PRO52254 are included within the scope of
this invention. One type of covalent modification includes reacting
targeted amino acid residues of a PRO52254 polypeptide with an
organic derivatizing agent that is capable of reacting with
selected side chains or the N- or C-terminal residues of the
PRO52254. Derivatization with bifunctional agents is useful, for
instance, for crosslinking PRO52254 to a water-insoluble support
matrix or surface for use in the method for purifying anti-PRO52254
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.
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.
Another type of covalent modification of the PRO52254 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 PRO52254 (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 PRO52254. 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.
Addition of glycosylation sites to the PRO52254 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
PRO52254 (for O-linked glycosylation sites). The PRO52254 amino
acid sequence may optionally be altered through changes at the DNA
level, particularly by mutating the DNA encoding the PRO52254
polypeptide at preselected bases such that codons are generated
that will translate into the desired amino acids.
Another means of increasing the number of carbohydrate moieties on
the PRO52254 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).
Removal of carbohydrate moieties present on the PRO52254
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).
Another type of covalent modification of PRO52254 comprises linking
the PRO52254 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.
The PRO52254 of the present invention may also be modified in a way
to form a chimeric molecule comprising PRO52254 fused to another,
heterologous polypeptide or amino acid sequence.
In one embodiment, such a chimeric molecule comprises a fusion of
the PRO52254 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
PRO52254. The presence of such epitope-tagged forms of the PRO52254
can be detected using an antibody against the tag polypeptide.
Also, provision of the epitope tag enables the PRO52254 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)].
In an alternative embodiment, the chimeric molecule may comprise a
fusion of the PRO52254 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 PRO52254 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.
D. Preparation of PRO52254
The description below relates primarily to production of PRO52254
by culturing cells transformed or transfected with a vector
containing PRO52254 nucleic acid. It is, of course, contemplated
that alternative methods, which are well known in the art, may be
employed to prepare PRO52254. For instance, the PRO52254 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 PRO52254 may be chemically synthesized separately and
combined using chemical or enzymatic methods to produce the
full-length PRO52254.
1. Isolation of DNA Encoding PRO52254
DNA encoding PRO52254 may be obtained from a cDNA library prepared
from tissue believed to possess the PRO52254 mRNA and to express it
at a detectable level. Accordingly, human PRO52254 DNA can be
conveniently obtained from a cDNA library prepared from human
tissue, such as described in the Examples. The PRO52254-encoding
gene may also be obtained from a genomic library or by known
synthetic procedures (e.g., automated nucleic acid synthesis).
Libraries can be screened with probes (such as antibodies to the
PRO52254 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 PRO52254 is to use PCR methodology
[Sambrook et al., supra; Dieffenbach et al., PCR Primer: A
Laboratory Manual (Cold Spring Harbor Laboratory Press, 1995)].
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.
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.
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
Host cells are transfected or transformed with expression or
cloning vectors described herein for PRO52254 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.
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).
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 K5 772 (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) 169 degP ompT kan.sup.r; E.
coli W3110 strain 37D6, which has the complete genotype tonA ptr3
phoA E15 (argF-lac) 169 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.
In addition to prokaryotes, eukaryotic microbes such as filamentous
fungi or yeast are suitable cloning or expression hosts for
PRO52254-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).
Suitable host cells for the expression of glycosylated PRO52254 are
derived from multicellular organisms. Examples of invertebrate
cells include insect cells such as Drosophila S2 and Spodoptera
Sf9, 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
The nucleic acid (e.g., cDNA or genomic DNA) encoding PRO52254 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.
The PRO52254 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 PRO52254-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, 1pp, 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.
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.
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.
An example of suitable selectable markers for mammalian cells are
those that enable the identification of cells competent to take up
the PRO52254-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)].
Expression and cloning vectors usually contain a promoter operably
linked to the PRO52254-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 PRO52254.
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.
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.
PRO52254 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.
Transcription of a DNA encoding the PRO52254 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 PRO52254 coding sequence,
but is preferably located at a site 5' from the promoter.
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
PRO52254.
Still other methods, vectors, and host cells suitable for
adaptation to the synthesis of PRO52254 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
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.
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 PRO52254 polypeptide or against a synthetic peptide based
on the DNA sequences provided herein or against exogenous sequence
fused to PRO52254 DNA and encoding a specific antibody epitope.
5. Purification of Polypeptide
Forms of PRO52254 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 PRO52254 can
be disrupted by various physical or chemical means, such as
freeze-thaw cycling, sonication, mechanical disruption, or cell
lysing agents.
It may be desired to purify PRO52254 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 PRO52254. 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 PRO52254
produced.
E. Tissue Distribution
The location of tissues expressing the PRO52254 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 PRO52254 polypeptides. The location of a gene in
a specific tissue also provides sample tissue for the activity
blocking assays discussed below.
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.
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 PRO52254 polypeptide or against a synthetic
peptide based on the DNA sequences encoding the PRO52254
polypeptide or against an exogenous sequence fused to a DNA
encoding a PRO52254 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.
F. Antibody Binding Studies
The activity of the PRO52254 polypeptides can be further verified
by antibody binding studies, in which the ability of anti-PRO52254
antibodies to inhibit the effect of the PRO52254 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.
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).
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.
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.
G. Cell-Based Assays
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.
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.
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]).
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.
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 PRO52254 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 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 PRO52254 polypeptides are assayed for T cell
costimulatory or inhibitory activity.
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. (1994) 24:2219.
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. (1998) 18:1.
Immunoadjuvant therapy for treatment of tumors, described in more
detail below, is another example of the use of the stimulating
compounds of the invention.
Alternatively, an immune stimulating or enhancing effect can also
be achieved by administration of a PRO52254 which has vascular
permeability enhancing properties. Enhanced vascular permeability
would be beneficial to disorders which can be attenuated by local
infiltration of immune cells (e.g., monocytes, eosinophils, PMNs)
and inflammation.
On the other hand, PRO52254 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.
Alternatively, compounds, e.g., antibodies, which bind to
stimulating PRO52254 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.
H. Animal Models
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.
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.
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, 1989, 889-992. 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 (1994) 58:23 and Tinubu, S. A. et al, J. Immunol.
(1994) 4330-4338.
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.
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 (1995) 1:143. 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 (1997)
554-561.
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., 1994,
unit 4.2. See also Grabbe, S, and Schwarz, T, Immun. Today 19 (1):
37-44 (1998).
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 (1996) 88:569.
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.
(1998) 18:777 and the references cited therein.
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. (1997) 3:183, 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. (1995) 146:580.
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.
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).
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.
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 PRO52254 polypeptide, prepared as described above, are
administered to the animal and the effect on immune function is
determined.
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.
I. ImmunoAdjuvant Therapy
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., (1996) Proc. Natl. Acad. Sci. USA,
93:7149. 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 (1997) 3:682; Kwon, E. D.
et al., Proc. Natl. Acad. Sci. USA (1997) 94: 8099; Lynch, D. H. et
al, Nature Medicine (1997) 3:625; Finn, O. J. and Lotze, M. T., J.
Immunol. (1998) 21:114. 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.
J. Screening Assays for Drug Candidates
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.
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.
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 .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.
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.
K. Compositions and Methods for the Treatment of Immune Related
Diseases
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.
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.
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).
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.
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.
L. Anti-PRO52254 Antibodies
The present invention further provides anti-PRO52254 antibodies.
Exemplary antibodies include polyclonal, monoclonal, humanized,
bispecific, and heteroconjugate antibodies.
1. Polyclonal Antibodies
The anti-PRO52254 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
PRO52254 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.
2. Monoclonal Antibodies
The anti-PRO52254 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.
The immunizing agent will typically include the PRO52254
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 [coding,
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.
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].
The culture medium in which the hybridoma cells are cultured can
then be assayed for the presence of monoclonal antibodies directed
against PRO52254. 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).
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.
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.
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.
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.
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.
3. Human and Humanized Antibodies
The anti-PRO52254 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').sub.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)].
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.
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).
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.
4. Bispecific Antibodies
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 PRO52254, the other one is for any other
antigen, and preferably for a cell-surface protein or receptor or
receptor subunit.
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).
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).
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.
Bispecific antibodies can be prepared as full length antibodies or
antibody fragments (e.g. F(ab').sub.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').sub.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.
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').sub.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.
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 (V.sub.H) connected to a light-chain
variable domain (V.sub.L) by a linker which is too short to allow
pairing between the two domains on the same chain. Accordingly, the
V.sub.H and V.sub.L domains of one fragment are forced to pair with
the complementary V.sub.L and V.sub.H 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). Antibodies with more than two valencies
are contemplated. For example, trispecific antibodies can be
prepared. Tutt et al., J. Immunol. 147:60 (1991).
Exemplary bispecific antibodies may bind to two different epitopes
on a given PRO52254 polypeptide herein. Alternatively, an
anti-PRO52254 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 (Fc.gamma.R), such as Fc.gamma.RI (CD64), Fc.gamma.RII (CD32)
and Fc.gamma.RIII (CD16) so as to focus cellular defense mechanisms
to the cell expressing the particular PRO52254 polypeptide.
Bispecific antibodies may also be used to localize cytotoxic agents
to cells which express a particular PRO52254 polypeptide. These
antibodies possess a PRO52254-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
PRO52254 polypeptide and further binds tissue factor (TF).
5. Heteroconjugate Antibodies
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.
6. Effector Function Engineering
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 crosslinkers 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).
7. Immunoconjugates
The invention also pertains to immunoconjugates comprising an
antibody conjugated to a cytotoxic agent such as a chemotherapeutic
agent, toxin (e.g., an enzymatically active toxin of bacterial,
fungal, plant, or animal origin, or fragments thereof), or a
radioactive isotope (i.e., a radioconjugate).
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.
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, 238: 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.
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).
8. Immunoliposomes
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.
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).
M. Pharmaceutical Compositions
The active PRO52254 molecules of the invention (e.g., PRO52254
polypeptides, anti-PRO52254 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 PRO52254 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).
Compounds identified by the screening assays disclosed herein can
be formulated in an analogous manner, using standard techniques
well known in the art.
Lipofections or liposomes can also be used to deliver the PRO52254
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]).
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.
The active PRO52254 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).
The formulations to be used for in vivo administration must be
sterile. This is readily accomplished by filtration through sterile
filtration membranes.
Sustained-release preparations or the PRO52254 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 -hydroxyethylmethacrylate), 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.
N. Methods of Treatment
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.
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.
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.
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, interstitial
pneumonitis with pulmonary fibrosis, keratoconjunctivitis sicca,
and rhematoid nodules.
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
rhematoid 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.
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
spondylitis, 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+ T lymphocyte, a cell which targets antigen
presented by class I MHC molecules. CD8+ 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+ T cells response.
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 antinuclear 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.
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.
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.
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.
Sarcoidosis is a condition of unknown etiology which is
characterized by the presence of epitheloid 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.
Autoimmune hemolytic anemia including autoimmune hemolytic anemia,
immune pancytopenia, and paroxysmal nocturnal 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.
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.
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).
Type I diabetes mellitus or insulin-dependent diabetes is the
autoimmune destruction of pancreatic islet .beta. 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.
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.
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+ 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.
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.
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.
Psoriasis is a T lymphocyte-mediated inflammatory disease. Lesions
contain infiltrates of T lymphocytes, macrophages and antigen
processing cells, and some neutrophils.
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.
Transplantation associated diseases, including Graft rejection and
Graft-Versus-Host-Disease (GVHD) are T lymphocyte-dependent;
inhibition of T lymphocyte function is ameliorative. 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.
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.
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-estrogen 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 PRO52254
polypeptides are coadministered with a growth inhibitory agent. For
example, the growth inhibitory agent may be administered first,
followed by a PRO52254 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 PRO52254
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.
For example, depending on the type and severity of the disease,
about 1 .mu.g/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 .mu.g/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.
O. Articles of Manufacture
In another embodiment of the invention, an article of manufacture
containing materials (e.g., comprising a PRO52254 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.
P. Diagnosis and Prognosis of Immune Related Disease
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, or another immune related disease, can be
used as diagnostics or prognostics.
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.
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.
The following examples are offered for illustrative purposes only,
and are not intended to limit the scope of the present invention in
any way.
All patent and literature references cited in the present
specification are hereby incorporated by reference in their
entirety.
EXAMPLES
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
Cloning of PRO52254
An expressed sequence tag (EST) DNA database (Merck/Washington
University) was searched and an EST was identified which contained
domains of interest, specifically Immunoglobulin (Ig) domain(s) and
Immuno Tyrosine Inhibition Motif(s) (ITIM). The search was
performed using the computer program BLAST or BLAST2 [Altschul et
al., Methods in Enzymology, 266:460-480 (1996)] using as a
comparison the domains of interest to a 6 frame translation of the
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 if necessary, assembled into consensus DNA
sequences with the program "phrap" (Phil Green, University of
Washington, Seattle, Wash.).
Based on the sequence as described above, 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 PRO52254. 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.
The oligonucleotide probes employed were as follows:
TABLE-US-00006 (forward primer) (SEQ ID NO: 5) 5'
CGTCCTATCTGCAGTCGGCTACTTTCA 3' (reverse primer) (SEQ ID NO: 6) 5'
CCAGAAGATGCCTCTGGTTGCTAACCA 3'
A pool of 50 different human cDNA libraries from various tissues
was used in cloning. 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.
The entire nucleotide sequence of the clone, designated herein as
DNA327145, is shown in FIG. 1 (SEQ ID NO: 1). The DNA327145 clone
contains a single open reading frame with an apparent translational
initiation site at nucleotide positions 77-79 and a stop signal at
nucleotide positions 809-811 (FIG. 1, SEQ ID NO:1). The predicted
polypeptide precursor is 244 amino acids long, has a calculated
molecular weight of approximately 26318.98 daltons and an estimated
pI of approximately 5.71. Analysis of the full-length PRO52254
sequence shown in FIG. 2 (SEQ ID NO:2) evidences the presence of a
variety of important polypeptide domains as shown in FIG. 2,
wherein the locations given for those polypeptide domains are
approximate as described.
An analysis of the current protein database, using the ALIGN-2
sequence alignment analysis of the full-length sequence shown in
FIG. 2 (SEQ ID NO:2), evidenced sequence identity between the
PRO52254 amino acid sequence and no known protein sequences.
Using the human PRO52254 sequence a murine database was searched
for homolgous sequences. Oligonucleotides were designed against
these putative homologues and murine cDNA libraries were probed via
PCR. A positive library was then used to isolate clones encoding
the gene of interest using the probe oligonucleotide and one of the
primer pairs.
The oligonucleotide probes employed were as follows:
TABLE-US-00007 (forward primer) (SEQ ID NO: 7) 5'
CAGGACCAGCTTCTGGCCATTTATAGTGT 3' (reverse primer) (SEQ ID NO: 8) 5'
CTGCTTCCAGTCGACTTGGGTCACTT 3' (probe) (SEQ ID NO: 9) 5'
CCTGGTGGGATTTACAAGGGGAGAATATTCCT GAAGGTCCAAGAAA 3'
The full length MURINE homologue of PRO52254 was cloned and this
clone was given the designation PRO71302 for the polypeptide
sequence and DNA327512 for the nucleotide sequence. The entire
nucleotide sequence of the clone, designated herein as DNA327512,
is shown in FIG. 3 (SEQ ID NO: 3). The DNA clone contains a single
open reading frame with an apparent translational initiation site
at nucleotide positions 60-62 and a stop signal at nucleotide
positions 783-785 (FIG. 3, SEQ ID NO:3). The predicted polypeptide
precursor is 241 amino acids long, has a calculated molecular
weight of approximately 26088.51 daltons and an estimated pI of
approximately 5.12. Analysis of the full-length PRO sequence shown
in FIG. 4 (SEQ ID NO:4) evidences the presence of a variety of
important polypeptide domains as shown in FIG. 4, wherein the
locations given for those important polypeptide domains are
approximate as described.
An analysis of the current protein database, using the ALIGN-2
sequence alignment analysis of the full-length sequence shown in
FIG. 2 (SEQ ID NO:2), evidenced sequence identity between the
PRO71302 amino acid sequence and no known protein sequences.
Example 2
Microarray Analysis of Stimulated T-Cells
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 (in this instance, activated CD4+ T cells) sample is greater
than hybridization signal of a probe from a control (in this
instance, non-stimulated CD4+ T cells) sample, the gene or genes
overexpressed in the test tissue are identified. The implication of
this result is that an overexpressed protein in a test 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.
The methodology of hybridization of nucleic acids and microarray
technology is well known in the art. In one example, the specific
preparation of nucleic acids for hybridization and probes, slides,
and hybridization conditions are all detailed in PCT Patent
Application Serial No. PCT/US01/10482, filed on Mar. 30, 2001 and
which is herein incorporated by reference.
In this experiment, CD4+ T cells were purified from a single donor
using the RossetteSep.TM. protocol from (Stem Cell Technologies,
Vancouver BC) which contains anti-CD8, anti-CD16, anti-CD19,
anti-CD36 and anti-CD56 antibodies used to produce a population of
isolated CD4+ T cells. Isolated CD4+ T cells were activated with an
anti-CD3 antibody (used at a concentration that does not stimulate
proliferation) together with either ICAM-1 or anti-CD28 antibody.
At 24 or 72 hours cells were harvested, RNA extracted and analysis
run on Affimax.TM. (Affymetrix Inc. Santa Clara, Calif.)
microarrays. Non-stimulated (resting) cells were harvested
immediately after purification, and subjected to the same analysis.
Genes were compared whose expression was upregulated at either of
the two timepoints in activated vs. resting cells.
The result of these experiments, is that PRO52254 polypeptides of
the present invention are significantly over-expressed in isolated
CD4+ T cells activated by anti-CD3/ICAM-1 and anti-CD3/anti-CD28 as
compared to isolated resting CD4+ T cells. As described above,
these data demonstrate that the PRO52254 polypeptides of the
present invention are useful not only as diagnostic markers for the
presence of one or more immune disorders, but also serve as
therapeutic targets for the treatment of those immune
disorders.
Example 3
Microarray Analysis of PRO52254 in Psoriasis
Skin biopsies from psoriatic patients and from healthy donors were
obtained. For each psoriatic patient, skin samples were taken from
lesional and non-lesional sites. All of the psoriatic skin samples
were analyzed for Keratin16 staining via immunohistochemistry and
epidermal thickness. All samples were stored at -70.degree. C.
until ready for RNA isolation. The skin biopsies were homogenized
in 600 .mu.l of RLT buffer (+BME) and RNA was isolated using
Qiagen.TM. Rneasy Mini columns (Qiagen) with on-column DNase
treatment following the manufacturers guidelines. Following RNA
isolation, RNA was quantitated using RiboGreen.TM. (Molecular
Probes) following the manufacturer's guidelines and checked on
agarose gels for integrity. The RNA yields ranged from 19 to 54
.mu.g for psoriatic lesional skin, 7.7 to 24 .mu.g for non-lesional
matched control skin and 5.4 to 10 .mu.g for normal skin. 4 .mu.g
of RNA was labeled for microarray analysis.
Biopsies were obtained from lesional and non-lesional skin from 11
psoriatic patients in order to identify disease-specific genes
which are differentially expressed in psoriatic tissue. Normal skin
from 6 non-psoriatic donors were also obtained for comparison
purposes. To evaluate gene expression profiles in peripheral blood
mononuclear cells (PBMC) from the same psoriatic patients, blood
was obtained and PBMCs were isolated. PBMCs from 16 non-psoriatic
donors were also obtained for comparison purposes RNA isolated from
the skin and PBMCs were hybridized to Affymetrix Microarrays
(representing approximately 33,000 genes) as well as Genentech
proprietary microarray. Statistically significant alterations in
gene expression (greater than 2-fold) in lesional vs non-lesional
and normal skin samples and in PBMCs from normal and
psoriasis-affected patients were identified. The result of this
experiment is PRO52254 is expressed higher in psoriatic blood than
in normal blood. The identification of genes differentially
expressed in lesional and non-lesional skin and PBMCs of psoriatics
may aid in our understanding of the pathogenesis of this disease at
the molecular level and lead to the discovery of new therapeutic
for psoriasis and other autoimmune disease targets. Therefore,
antagonists of PRO52254 would be useful in the alleviation of
psoriasis.
Example 4
PRO52254 in Inflammatory Bowel Disease
In this experiment, a microarray assay was used to find genes that
are overexpressed in IBD as compared to normal bowel tissue.
Biopsies from patients with IBD were obtained. For each IBD
patient, samples were taken from disease (either UC or Crohn's)
tissue and from healthy bowel, so that expression patterns could be
better compared. All samples were stored at -70.degree. C. until
ready for RNA isolation. The biopsies were homogenized in 600 ul of
RLT buffer (+BME) and RNA was isolated using Qiagen.TM. Rneasy Mini
columns (Qiagen) with on-column DNase treatment following the
manufacturer's guidelines. Following RNA isolation, RNA was
quantitated using RiboGreen.TM. (Molecular Probes) following the
manufacturer's guidelines and checked on agarose gels for
integrity. Appropriate amounts of RNA were labeled for microarray
analysis and samples were run on proprietary Genentech microarray
and Affymetrics.TM. microarrays. Genes were compared whose
expression was upregulated in IBD tissue vs normal bowel, matching
biopsies from normal bowel and IBD tissue from the same patient.
The results of this experiment showed that PRO52254 has been
identified as being significantly overexpressed in IBD samples as
compared to normal bowel tissue.
Example 5
Expression of PRO52254 in NK Cells
Natural killer (NK) cells are an important effector cell of the
innate immune system. They are specialized to effect killing
against host cells that have either been infected by viruses,
parasites or that have become cancerous. Phenotypically, NK cells
are large granular lymphocytes that constitute .about.2% of the
circulating lymphocyte population. They are commonly identified by
cell surface expression of CD56 and CD16 They mature in the bone
marrow from a CD34+ precursor cell that they share with T cells.
The mature NK cell, shares expression of CD8, cytolytic machinery,
and some KIRs, with T cells, but remains distinct from T cells by
the lack of CD3 and the T cell receptors. Like cytotoxic T cells,
they contain granules filled with pore forming protein, cytotoxins,
serine esterases and proteoglycans that mediate lysis of target
cells. Both cytotoxic T cells and NK cells kill on contact by
binding to their targets and delivering their lethal burst of
chemicals that produces holes in the target cell's membrane. Unlike
cytotoxic T cells, NK cells do not need to recognize a specific
antigen before initiating lysis. Rather, NK cell activation can be
mediated by growth factors and cytokines (in particular, IL-2,
IL-12 and IL-15 have been shown to mediate proliferative and
cytotoxic activities or by a delicate balance between two classes
of NK cell receptors, one that activates the cells, and another
that inhibits. Killer Ig-like receptors (KIRs) are NK cell
receptors that transmit an inhibitory signal if they encounter
class I MHC molecules on a cell surface. This is important for
killing of both cancerous cells and virally infected cells. Because
viruses often suppress class I MHC expression in cells they infect,
the virus-infected cell becomes susceptible to killing by NK cells.
Likewise, cancer cells have reduced or no class I MHC expression
and they, too, become susceptible to killing by NK cells. Natural
cytotoxicity receptors (NCRs) constitute a family of activating
receptors on NK cells. In some effector-target systems, the surface
density of NCRs correlates with the cytolytic activity of the NK
cells, while in other systems killing requires cooperation between
NCR, another activating receptor NKG2D and its adaptor polypeptide
DAP10. Additionally, the strength of the signals can be influenced
by engagement of coreceptors such as 2B4 and NTB-A. The ligands for
NCRs and NKG2D, hemoglutanins and MICA, MICB respectively are not
expressed by most normal cells, but are induced in most tumor cell
lines. Expression of the ligands by tumor cells triggers a dramatic
immune response resulting in tumor cell rejection. Activation of NK
cells with IL-15 or IL-12 have been shown to induce both cytotoxic
and proliferative effects. Junctinal adhesion molecule 2 (JAM2) has
been shown to bind to NK cells and has been hypothesized to play a
role in lymphocyte extravasation to sites of inflammation.
Therefore, a DNA microarray experiment comparing differential
expression of genes from these three modes of activation versus
resting NK cells has the potential to reveal novel genes or novel
gene associations with NK cell activity. Therapeutic antibodies,
peptides or small molecules could be developed to target specific
genes revealed by these microarrays for the treatment of immune
mediated inflammatory diseases and malignancies. Peripheral blood
NK cells were isolated from leukopacks by negative selection using
the NK cell isolation kit with the MACS.TM. magnetic cell sorting
system (Miltenyi Biotec). Cell purity was confirmed by staining
with PE anti-CD56 for FACS analysis. Purity of cell preps ranged
from 89% to 96%. Cell culture: Set up in-vitro cultures in 6 well
plates 5 ml cultures/well. Media: RPMI 1640, 10% heat inactivated
FBS, 100 units/mL of Penicillin, 100 mg/mL of streptomycin, 2 mM
L-glutamine, and 5.5.times.10-5 Beta-mercaptoethanol. Experimental
treatments: Time 0 hrs, Untreated CD56(+) cells. Time 16 hrs.
Untreated, IL2 (10 nM), IL15 (10 nM), JAM-IT (10 nM) stimulated.
Activation of NK cells was monitored by FACS for cell surface
expression of CD56 and CD69. In this series of experiments it was
determined that PRO52254 is expressed on both on resting and
activated NK cells, but expression does not significantly increase
upon the above described stimulation.
Example 6
Expression of PRO52254 on CD45RO+ Memory T Cells
T cells play a central role in host defense. T cells are able to
modulate the immune response of other cell lineages through the
production of a variety of cytokines and immune modulatory
molecules. In addition they are responsible for surveying cells
throughout the organism for the presence of non-self. This highly
sophisticated process utilizes the T cell receptor (TCR), which is
able to recognize and discriminate between self and non-self
peptides displayed by the MHC complex on other cells. This process
also integrates co-stimulatory signals that provide additional
information to the T cell about the nature of the potential
non-self threat. These two signals, the TCR signal and the
co-stimulatory signal can be experimentally triggered by use of
agonist antibodies such as certain antibodies to the T cell
receptor component CD3, and the co-stimulatory receptor CD28. While
T cells are essential components of normal immune function, it is
believed that inappropriate T cell function underlies many very
serious medical conditions including autoimmune disease. Diseases
that are impacted by pathologic T cell function are thought to
include asthma, arthritis, psoriasis, multiple sclerosis,
inflammatory bowel disease, diabetes, graft versus host disease and
many others. In these diseases the portion of the T cell repertoire
that has a "memory" phenotype is thought to contribute to the
disease pathology. It is therefore of great importance to
understand the molecular events that occur upon activation of
memory T cells. In humans, memory T cells can be identified through
the use of the antigen CD45RO which is expressed on memory T cells
but not on resting naive T cells. The use of DNA microarrays
provides a powerful experimental approach to identify molecular
changes that occur upon activation of this critical cell
population. Understanding the identity of molecules whose
expression is altered upon memory T cell activation can enable
therapeutic strategies that target the pathways impacted by these
alterations in gene expression. Such therapeutic strategies can
include the use of recombinant proteins, soluble receptors,
antibodies, peptides, or small molecule drugs.
100 ml of fresh blood was obtained from donors. PBMC were isolated
with LSM (ficol) (ICN Biomedicals) by step gradient separation.
Monocytes were depleted by adherence to culture flask. CD45 RA and
CD45 RO high cells were sorted by FACS with additional gating on
lymphocytes by forward and side scatter. Cells of intermediate
expression of either CD45RA or CD45 RO were not collected. Sorting
was verified by re-FACS of samples of the sorted population and
found to be approximately 99% correctly sorted. Cells were cultured
for 16 hours in RPMI 1640, 10% heat inactivated FBS, 100 units/mL
of Penicillin, 100 mg/mL of streptomycin, 2 mM L-glutamine and IL-2
(100 U/ml) and in the presence or absence of plate bound anti-CD3
(10 ug/ml) and soluble anti-CD28 (10 ug/ml). The activation status
of the cells was monitored by FACS for cell surface expression of
CD69 and CD25. At 24 or 72 hours cells were harvested, RNA
extracted by Qiagen.TM. miniprep and analysis run on (Affymetrix
Inc. Santa Clara, Calif.) microarrays and proprietary Genentech
microarrays. Non-stimulated (resting) cells were harvested
immediately after purification, and subjected to the same analysis.
Genes were compared whose expression was upregulated at either of
the two timepoints in activated vs. resting cells, and it was found
that PRO52254 is expressed in CD45RO+ memory T cells in both the
resting and activated state, and expression of PRO52254 does not
increase upon the above described stimulation.
Example 7
Use of PRO52254 as a Hybridization Probe
The following method describes use of a nucleotide sequence
encoding PRO52254 as a hybridization probe.
DNA comprising the coding sequence of full-length or mature
PRO52254 as disclosed herein is employed as a probe to screen for
homologous DNAs (such as those encoding naturally-occurring
variants of PRO52254) in human tissue cDNA libraries or human
tissue genomic libraries.
Hybridization and washing of filters containing either library DNAs
is performed under the following high stringency conditions.
Hybridization of radiolabeled PRO52254-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.
DNAs having a desired sequence identity with the DNA encoding
full-length native sequence PRO52254 can then be identified using
standard techniques known in the art.
Example 8
Expression of PRO52254 in E. coli
This example illustrates preparation of an unglycosylated form of
PRO52254 by recombinant expression in E. coli.
The DNA sequence encoding PRO52254 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 PRO52254 coding region, lambda transcriptional
terminator, and an argU gene.
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.
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.
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 PRO52254 protein can then be purified
using a metal chelating column under conditions that allow tight
binding of the protein.
PRO52254 may be expressed in E. coli in a poly-His tagged form,
using the following procedure. The DNA encoding PRO52254 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) lon 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 MgSO4) 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.
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 0.1 M 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.
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.
Fractions containing the desired folded PRO52254 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.
The PRO52254 polypeptides disclosed herein were successfully
expressed as described above.
Example 9
Expression of PRO52254 in Mammalian Cells
This example illustrates preparation of a potentially glycosylated
form of PRO52254 by recombinant expression in mammalian cells.
The vector, pRK5 (see EP 307,247, published Mar. 15, 1989), is
employed as the expression vector. Optionally, the PRO52254 DNA is
ligated into pRK5 with selected restriction enzymes to allow
insertion of the PRO52254 DNA using ligation methods such as
described in Sambrook et al., supra. The resulting vector is called
pRK5-PRO52254.
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-PRO52254 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.
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 PRO52254
polypeptide. The cultures containing transfected cells may undergo
further incubation (in serum free medium) and the medium is tested
in selected bioassays.
In an alternative technique, PRO52254 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-PRO52254 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 expressed PRO52254 can then be
concentrated and purified by any selected method, such as dialysis
and/or column chromatography.
In another embodiment, PRO52254 can be expressed in CHO cells. The
pRK5-PRO52254 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 PRO52254
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 PRO52254 can then be concentrated and purified by any
selected method.
Epitope-tagged PRO52254 may also be expressed in host CHO cells.
The PRO52254 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 PRO52254 insert can then be subcloned into a SV40
promoter/enhancer containing 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
promoter/enhancer containing vector. Labeling may be performed, as
described above, to verify expression. The culture medium
containing the expressed poly-His tagged PRO52254 can then be
concentrated and purified by any selected method, such as by
Ni.sup.2+-chelate affinity chromatography.
PRO52254 may also be expressed in CHO and/or COS cells by a
transient expression procedure or in CHO cells by another stable
expression procedure.
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 IgG1 constant region sequence containing the hinge, CH2
and CH2 domains and/or is a poly-His tagged form.
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 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.
Twelve micrograms of the desired plasmid DNA is introduced into
approximately 10 million CHO cells using commercially available
transfection reagents Superfect.RTM. (Quiagen), 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.
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 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, pH is 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.
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.
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.
Many of the PRO52254 polypeptides disclosed herein were
successfully expressed as described above.
Example 10
Expression of PRO52254 in Yeast
The following method describes recombinant expression of PRO52254
in yeast. First, yeast expression vectors are constructed for
intracellular production or secretion of PRO52254 from the
ADH2/GAPDH promoter. DNA encoding PRO52254 and the promoter is
inserted into suitable restriction enzyme sites in the selected
plasmid to direct intracellular expression of PRO52254. For
secretion, DNA encoding PRO52254 can be cloned into the selected
plasmid, together with DNA encoding the ADH2/GAPDH promoter, a
native PRO52254 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 PRO52254.
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.
Recombinant PRO52254 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 PRO52254 may further
be purified using selected column chromatography resins.
Many of the PRO52254 polypeptides disclosed herein were
successfully expressed as described above.
Example 11
Expression of PRO52254 in Baculovirus-Infected Insect Cells
The following method describes recombinant expression of PRO52254
in Baculovirus-infected insect cells.
The sequence coding for PRO52254 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 PRO52254 or the desired
portion of the coding sequence of PRO52254 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.
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).
Expressed poly-his tagged PRO52254 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 PRO52254 are pooled and dialyzed against loading
buffer.
Alternatively, purification of the IgG tagged (or Fc tagged)
PRO52254 can be performed using known chromatography techniques,
including for instance, Protein A or protein G column
chromatography.
Many of the PRO52254 polypeptides disclosed herein were
successfully expressed as described above.
Example 12
Preparation of Antibodies that Bind PRO52254
This example illustrates preparation of monoclonal antibodies which
can specifically bind PRO52254.
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 PRO52254, fusion proteins
containing PRO52254, and cells expressing recombinant PRO52254 on
the cell surface. Selection of the immunogen can be made by the
skilled artisan without undue experimentation.
Mice, such as Balb/c, are immunized with the PRO52254 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-PRO52254 antibodies.
After a suitable antibody titer has been detected, the animals
"positive" for antibodies can be injected with a final intravenous
injection of PRO52254. 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.
The hybridoma cells will be screened in an ELISA for reactivity
against PRO52254. Determination of "positive" hybridoma cells
secreting the desired monoclonal antibodies against PRO52254 is
within the skill in the art.
The positive hybridoma cells can be injected intraperitoneally into
syngeneic Balb/c mice to produce ascites containing the
anti-PRO52254 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 13
Purification of PRO52254 Polypeptides Using Specific Antibodies
Native or recombinant PRO52254 polypeptides may be purified by a
variety of standard techniques in the art of protein purification.
For example, pro-PRO52254 polypeptide, mature PRO52254 polypeptide,
or pre-PRO52254 polypeptide is purified by immunoaffinity
chromatography using antibodies specific for the PRO52254
polypeptide of interest. In general, an immunoaffinity column is
constructed by covalently coupling the anti-PRO52254 polypeptide
antibody to an activated chromatographic resin.
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.
Such an immunoaffinity column is utilized in the purification of
PRO52254 polypeptide by preparing a fraction from cells containing
PRO52254 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 PRO52254 polypeptide containing a signal sequence may be
secreted in useful quantity into the medium in which the cells are
grown.
A soluble PRO52254 polypeptide-containing preparation is passed
over the immunoaffinity column, and the column is washed under
conditions that allow the preferential absorbance of PRO52254
polypeptide (e.g., high ionic strength buffers in the presence of
detergent). Then, the column is eluted under conditions that
disrupt antibody/PRO52254 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 PRO52254
polypeptide is collected.
Example 14
Drug Screening
This invention is particularly useful for screening compounds by
using PRO52254 polypeptides or binding fragment thereof in any of a
variety of drug screening techniques. The PRO52254 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 PRO52254 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 PRO52254 polypeptide or
a fragment and the agent being tested. Alternatively, one can
examine the diminution in complex formation between the PRO52254
polypeptide and its target cell or target receptors caused by the
agent being tested.
Thus, the present invention provides methods of screening for drugs
or any other agents which can affect a PRO52254
polypeptide-associated disease or disorder. These methods comprise
contacting such an agent with an PRO52254 polypeptide or fragment
thereof and assaying (I) for the presence of a complex between the
agent and the PRO52254 polypeptide or fragment, or (ii) for the
presence of a complex between the PRO52254 polypeptide or fragment
and the cell, by methods well known in the art. In such competitive
binding assays, the PRO52254 polypeptide or fragment is typically
labeled. After suitable incubation, free PRO52254 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 PRO52254 polypeptide or to
interfere with the PRO52254 polypeptide/cell complex.
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 PRO52254
polypeptide, the peptide test compounds are reacted with PRO52254
polypeptide and washed. Bound PRO52254 polypeptide is detected by
methods well known in the art. Purified PRO52254 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.
This invention also contemplates the use of competitive drug
screening assays in which neutralizing antibodies capable of
binding PRO52254 polypeptide specifically compete with a test
compound for binding to PRO52254 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
PRO52254 polypeptide.
Example 15
Rational Drug Design
The goal of rational drug design is to produce structural analogs
of biologically active polypeptide of interest (i.e., a PRO52254
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
PRO52254 polypeptide or which enhance or interfere with the
function of the PRO52254 polypeptide in vivo (c.f., Hodgson,
Bio/Technology, 9: 19-21 (1991)).
In one approach, the three-dimensional structure of the PRO52254
polypeptide, or of a PRO52254 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 PRO52254 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 PRO52254 polypeptide may be gained by modeling based on the
structure of homologous proteins. In both cases, relevant
structural information is used to design analogous PRO52254
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).
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.
By virtue of the present invention, sufficient amounts of the
PRO52254 polypeptide may be made available to perform such
analytical studies as X-ray crystallography. In addition, knowledge
of the PRO52254 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.
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 LISTINGS
1
91831DNAHomo sapiens 1cgtcctatct gcagtcggct actttcagtg gcagaagagg
ccacatctgc 50ttcctgtagg ccctctgggc agaagcatgc gctggtgtct cctcctgatc
100tgggcccagg ggctgaggca ggctcccctc gcctcaggaa tgatgacagg
150cacaatagaa acaacgggga acatttctgc agagaaaggt ggctctatca
200tcttacaatg tcacctctcc tccaccacgg cacaagtgac ccaggtcaac
250tgggagcagc aggaccagct tctggccatt tgtaatgctg acttggggtg
300gcacatctcc ccatccttca aggatcgagt ggccccaggt cccggcctgg
350gcctcaccct ccagtcgctg accgtgaacg atacagggga gtacttctgc
400atctatcaca cctaccctga tgggacgtac actgggagaa tcttcctgga
450ggtcctagaa agctcagtgg ctgagcacgg tgccaggttc cagattccat
500tgcttggagc catggccgcg acgctggtgg tcatctgcac agcagtcatc
550gtggtggtcg cgttgactag aaagaagaaa gccctcagaa tccattctgt
600ggaaggtgac ctcaggagaa aatcagctgg acaggaggaa tggagcccca
650gtgctccctc acccccagga agctgtgtcc aggcagaagc tgcacctgct
700gggctctgtg gagagcagcg gggagaggac tgtgccgagc tgcatgacta
750cttcaatgtc ctgagttaca gaagcctggg taactgcagc ttcttcacag
800agactggtta gcaaccagag gcatcttctg g 8312244PRTHomo sapiens 2Met
Arg Trp Cys Leu Leu Leu Ile Trp Ala Gln Gly Leu Arg Gln 1 5 10
15Ala Pro Leu Ala Ser Gly Met Met Thr Gly Thr Ile Glu Thr Thr 20 25
30Gly Asn Ile Ser Ala Glu Lys Gly Gly Ser Ile Ile Leu Gln Cys 35 40
45His Leu Ser Ser Thr Thr Ala Gln Val Thr Gln Val Asn Trp Glu 50 55
60Gln Gln Asp Gln Leu Leu Ala Ile Cys Asn Ala Asp Leu Gly Trp 65 70
75His Ile Ser Pro Ser Phe Lys Asp Arg Val Ala Pro Gly Pro Gly 80 85
90Leu Gly Leu Thr Leu Gln Ser Leu Thr Val Asn Asp Thr Gly Glu 95
100 105Tyr Phe Cys Ile Tyr His Thr Tyr Pro Asp Gly Thr Tyr Thr Gly
110 115 120Arg Ile Phe Leu Glu Val Leu Glu Ser Ser Val Ala Glu His
Gly 125 130 135Ala Arg Phe Gln Ile Pro Leu Leu Gly Ala Met Ala Ala
Thr Leu 140 145 150Val Val Ile Cys Thr Ala Val Ile Val Val Val Ala
Leu Thr Arg 155 160 165Lys Lys Lys Ala Leu Arg Ile His Ser Val Glu
Gly Asp Leu Arg 170 175 180Arg Lys Ser Ala Gly Gln Glu Glu Trp Ser
Pro Ser Ala Pro Ser 185 190 195Pro Pro Gly Ser Cys Val Gln Ala Glu
Ala Ala Pro Ala Gly Leu 200 205 210Cys Gly Glu Gln Arg Gly Glu Asp
Cys Ala Glu Leu His Asp Tyr 215 220 225Phe Asn Val Leu Ser Tyr Arg
Ser Leu Gly Asn Cys Ser Phe Phe 230 235 240Thr Glu Thr
Gly31006DNAHomo sapiens 3gccagtttca gttggaggag aggccacatc
cactttgctg taggcctctg 50gttagaagca tgcatggctg gctgctcctg gtctgggtcc
aggggctgat 100acaggctgcc ttcctcgcta caggagccac agcaggcacg
atagatacaa 150agaggaacat ctctgcagag gaaggtggct ctgtcatctt
acagtgtcac 200ttctcctctg acacagctga agtgacccaa gtcgactgga
agcagcagga 250ccagcttctg gccatttata gtgttgacct ggggtggcat
gtcgcttcag 300tcttcagtga tcgggtggtc ccaggcccca gcctaggcct
caccttccag 350tctctgacaa tgaatgacac gggagagtac ttctgtacct
atcatacgta 400tcctggtggg atttacaagg ggagaatatt cctgaaggtc
caagaaagct 450cagtggctca gttccagact gccccgcttg gaggaaccat
ggctgctgtg 500ctgggactca tttgcttaat ggtcacagga gtgactgtac
tggctagaaa 550gaagtctatt agaatgcatt ctatagaaag tggccttggg
agaacagaag 600cggagccaca ggaatggaac ctgaggagtc tctcatcccc
tggaagccct 650gtccagacac aaactgcccc tgctggtccc tgtggagagc
aggcagaaga 700tgactatgct gacccacagg aatactttaa tgtcctgagc
tacagaagcc 750tagagagctt cattgctgta tcgaagactg gctaacgaca
gctctctatc 800cctctcccta tgtctctctc tctgtctctc tctgtctctc
tctgtctctg 850tctctgtctc tgtctctctc tctctctctc tctctctctc
tgtgtgtgtg 900tgtgtgtatg tgtgtataca tcattaatgt tcattaacac
taactgcata 950tggtggagga ccaggaaata aaagtttgtg ttgctaataa
aattaagtgc 1000taactt 10064241PRTHomo sapiens 4Met His Gly Trp Leu
Leu Leu Val Trp Val Gln Gly Leu Ile Gln 1 5 10 15Ala Ala Phe Leu
Ala Thr Gly Ala Thr Ala Gly Thr Ile Asp Thr 20 25 30Lys Arg Asn Ile
Ser Ala Glu Glu Gly Gly Ser Val Ile Leu Gln 35 40 45Cys His Phe Ser
Ser Asp Thr Ala Glu Val Thr Gln Val Asp Trp 50 55 60Lys Gln Gln Asp
Gln Leu Leu Ala Ile Tyr Ser Val Asp Leu Gly 65 70 75Trp His Val Ala
Ser Val Phe Ser Asp Arg Val Val Pro Gly Pro 80 85 90Ser Leu Gly Leu
Thr Phe Gln Ser Leu Thr Met Asn Asp Thr Gly 95 100 105Glu Tyr Phe
Cys Thr Tyr His Thr Tyr Pro Gly Gly Ile Tyr Lys 110 115 120Gly Arg
Ile Phe Leu Lys Val Gln Glu Ser Ser Val Ala Gln Phe 125 130 135Gln
Thr Ala Pro Leu Gly Gly Thr Met Ala Ala Val Leu Gly Leu 140 145
150Ile Cys Leu Met Val Thr Gly Val Thr Val Leu Ala Arg Lys Lys 155
160 165Ser Ile Arg Met His Ser Ile Glu Ser Gly Leu Gly Arg Thr Glu
170 175 180Ala Glu Pro Gln Glu Trp Asn Leu Arg Ser Leu Ser Ser Pro
Gly 185 190 195Ser Pro Val Gln Thr Gln Thr Ala Pro Ala Gly Pro Cys
Gly Glu 200 205 210Gln Ala Glu Asp Asp Tyr Ala Asp Pro Gln Glu Tyr
Phe Asn Val 215 220 225Leu Ser Tyr Arg Ser Leu Glu Ser Phe Ile Ala
Val Ser Lys Thr 230 235 240Gly527DNAArtificial
sequenceoligonucleotide probe - forward primer 5cgtcctatct
gcagtcggct actttca 27627DNAArtificial sequenceoligonucleotide probe
- reverse primer 6ccagaagatg cctctggttg ctaacca 27729DNAArtificial
sequenceoligonucleotide probe - forward primer 7caggaccagc
ttctggccat ttatagtgt 29826DNAArtificial sequenceoligonucleotide
probe - reverse primer 8ctgcttccag tcgacttggg tcactt
26946DNAArtificial sequenceoligonucleotide probe 9cctggtggga
tttacaaggg gagaatattc ctgaaggtcc aagaaa 46
* * * * *
References