U.S. patent application number 10/165044 was filed with the patent office on 2003-08-07 for serpentine transmembrane antigens expressed in human cancers and uses thereof.
Invention is credited to Afar, Daniel E. H., Faris, Mary, Hubert, Rene S., Jakobovits, Aya, Mitchell, Steven Chappell, Raitano, Arthur B., Saffran, Douglas.
Application Number | 20030149531 10/165044 |
Document ID | / |
Family ID | 27668165 |
Filed Date | 2003-08-07 |
United States Patent
Application |
20030149531 |
Kind Code |
A1 |
Hubert, Rene S. ; et
al. |
August 7, 2003 |
Serpentine transmembrane antigens expressed in human cancers and
uses thereof
Abstract
Described is a novel family of cell surface serpentine
transmembrane antigens. Two of the proteins in this family are
exclusively or predominantly expressed in the prostate, as well as
in prostate cancer, and thus members of this family have been
termed "STEAP" (Six Transmembrane Epithelial Antigen of the
Prostate). Four particular human STEAPs are described and
characterized herein. The human STEAPs exhibit a high degree of
structural conservation among them but show no significant
structural homology to any known human proteins. The prototype
member of the STEAP family, STEAP-1, appears to be a type IIIa
membrane protein expressed predominantly in prostate cells in
normal human tissues. Structurally, STEAP-1 is a 339 amino acid
protein characterized by a molecular topology of six transmembrane
domains and intracellular N- and C-termini, suggesting that it
folds in a "serpentine" manner into three extracellular and two
intracellular loops. STEAP-1 protein expression is maintained at
high levels across various stages of prostate cancer. Moreover,
STEAP-1 is highly over-expressed in certain other human
cancers.
Inventors: |
Hubert, Rene S.; (Los
Angeles, CA) ; Raitano, Arthur B.; (Los Angeles,
CA) ; Saffran, Douglas; (Encinitas, CA) ;
Afar, Daniel E. H.; (Brisbane, CA) ; Mitchell, Steven
Chappell; (Gurnee, IL) ; Faris, Mary; (Los
Angeles, CA) ; Jakobovits, Aya; (Beverly Hills,
CA) |
Correspondence
Address: |
Kate H. Murashige
Morrison & Foerster LLP
Suite 500
3811 Valley Centre Drive
San Diego
CA
92130
US
|
Family ID: |
27668165 |
Appl. No.: |
10/165044 |
Filed: |
June 6, 2002 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
60296656 |
Jun 6, 2001 |
|
|
|
Current U.S.
Class: |
702/1 ;
702/19 |
Current CPC
Class: |
C07K 2317/34 20130101;
C07K 16/3069 20130101; A61K 39/00 20130101; A61K 2039/505 20130101;
G01N 33/57407 20130101; G01N 33/57438 20130101; A61K 38/00
20130101; G01N 33/57449 20130101; C07K 14/705 20130101; C12Q 1/6886
20130101; G01N 33/57484 20130101; G01N 2333/705 20130101; C07K
2319/30 20130101; C07K 16/28 20130101; G01N 33/57419 20130101; C07K
14/4748 20130101; G01N 33/57423 20130101; A61K 51/1072 20130101;
C07K 2319/00 20130101; G01N 33/57492 20130101; G01N 33/57434
20130101; C12Q 2600/158 20130101 |
Class at
Publication: |
702/1 ;
702/19 |
International
Class: |
G06F 019/00; G01N
033/48; G01N 033/50 |
Foreign Application Data
Date |
Code |
Application Number |
Dec 6, 2000 |
PCT/US00/33040 |
Claims
1. A STEAP-2 protein having an amino acid sequence shown in FIG.
9A-D (SEQ ID NO: 8).
2. A STEAP-2 polypeptide that includes at least 10 contiguous amino
acids of an amino acid sequence selected from the group consisting
of amino acids 1-245, 2-204, 100-108, 121-454, 153-165, 182-454,
183-387, 227-235, 276-453, 306-314, 307-315, 345-358, 402-410, and
419-454 of the amino acid sequence shown in FIGS. 9A-D (SEQ ID NO:
8).
3. A polypeptide comprising an amino acid sequence which is at
least 90% identical to the amino acid sequence shown in FIGS. 9A-D
(SEQ ID NO: 8) over its entire length.
4. A polynucleotide selected from the group consisting of (a) a
polynucleotide having the sequence as shown in FIGS. 9A-D (SEQ ID
NO: 7), wherein T can also be U; (b) a polynucleotide encoding a
STEAP-2 polypeptide whose sequence is encoded by the cDNA contained
in plasmid 98P4B6-GTD3 as deposited with American Type Culture
Collection as Accession No. PTA-311; (c) a polynucleotide encoding
the STEAP-2 protein of claim 1; and (d) a polynucleotide which is
fully complementary to a polynucleotide of (a)-(c).
5. A polynucleotide that encodes the fragment of claim 2.
6. A recombinant expression vector which contains a polynucleotide
according to claim 4 or 5.
7. A host cell which contains an expression vector according to
claim 6.
8. A polynucleotide according to claim 4 or 5 which is labeled with
a detectable marker.
9. A process for producing a STEAP-2 protein comprising culturing a
host cell of claim 7 under conditions sufficient for the production
of the polypeptide and recovering the STEAP-2 protein from the
culture.
10. An antibody or fragment thereof which specifically binds to an
epitope within amino acids 1-245, 2-204, 100-108, 121-454, 153-165,
182-454, 183-387, 227-235, 276-453, 306-314, 307-315, 345-358,
402-410, or 419-454 of the STEAP-2 protein of claim 1.
11. The antibody or fragment thereof of claim 10 which is
monoclonal.
12. A recombinant protein comprising the antigen binding region of
a monoclonal antibody of claim 11.
13. The antibody or fragment thereof of claim 10 or 11, or the
recombinant protein of claim 12, which is labeled with a detectable
marker.
14. The antibody or fragment thereof or recombinant protein of
claim 13, wherein the detectable marker comprises a radioisotope,
metal chelator, enzyme or fluorescent, bioluminescent or
chemiluminescent compound.
15. The antibody fragment of claim 13, which is an Fab, F(ab')2, Fv
or Sfv fragment.
16. The antibody or fragment thereof of any one of claims 10, 11,
13 or 14, which is a human antibody.
17. The antibody of any one of claims 10, 11, 13 or 14, which
comprises murine antigen binding region residues and human antibody
residues.
18. A transgenic animal producing a monoclonal antibody of claim
11.
19. A hybridoma producing a monoclonal antibody of claim 11.
20. A single chain monoclonal antibody that comprises the variable
domains of the heavy and light chains of a monoclonal antibody of
claim 11.
21. A vector comprising a polynucleotide encoding a single chain
monoclonal antibody of claim 20.
22. The monoclonal antibody or fragment thereof of claim 11 which
is conjugated to a toxin, a radioisotope or a therapeutic
agent.
23. The monoclonal antibody or fragment thereof of claim 22,
wherein the toxin comprises ricin, ricin A-chain, doxorubicin,
daunorubicin, a maytansinoid, taxol, ethidium bromide, mitomycin,
etoposide, tenoposide, vincristine, vinblastine, colchicine,
dihydroxy anthracin dione, actinomycin, diphtheria toxin,
Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, modeccin A
chain, alpha-sarcin, gelonin, mitogellin, retstrictocin,
phenomycin, enomycin, curicin, crotin, calicheamicin, sapaonaria
officinalis inhibitor, or a glucocorticoid.
24. The monoclonal antibody or fragment thereof of claim 22,
wherein the radioisotope comprises .sup.212I, .sup.131I,
.sup.131In, .sup.90Y, or .sup.186Re.
25. An assay for detecting the presence of a STEAP-2 protein in a
biological sample comprising contacting the sample with an antibody
of claim 13, and detecting the binding of STEAP-2 protein in the
sample thereto.
26. An assay for detecting the presence of a STEAP-2 polynucleotide
in a biological sample, comprising: (a) contacting the sample with
a polynucleotide probe which specifically hybridizes to a
polynucleotide of claim 4; and (b) detecting the presence of a
hybridization complex formed by the hybridization of the probe with
STEAP-2 polynucleotide in the sample, wherein the presence of the
hybridization complex indicates the presence of STEAP-2
polynucleotide within the sample.
27. An assay for detecting the presence of STEAP-2 mRNA in a
biological sample comprising: (a) producing cDNA from the sample by
reverse transcription using at least one primer; (b) amplifying the
cDNA so produced using STEAP-2 polynucleotides as sense and
antisense primers to amplify STEAP-2 cDNAs therein; (c) detecting
the presence of the amplified STEAP-2 cDNA, wherein the STEAP-2
polynucleotides used as the sense and antisense primers are capable
of amplifying the polynucleotide shown in FIGS. 9A-D (SEQ ID NO:
7).
28. A pharmaceutical composition comprising an antibody or fragment
thereof according to claim 10, 11, 15, 16 or 17, a STEAP-2 protein
according to claim 1 or 2, or a STEAP-2 polynucleotide according to
claim 4 or 5, and a physiologically acceptable carrier.
29. A vaccine composition comprising a STEAP-2 protein according to
claim 1 or 2, or a STEAP-2 polynucleotide according to claim 4 or
5, and a physiologically acceptable carrier.
30. A method of inhibiting the development or progression of a
cancer expressing STEAP-2 in a patient, comprising administering to
the patient an effective amount of the vaccine composition of claim
29.
31. A method of inhibiting the growth of cells expressing STEAP-2
in a patient, comprising administering to the patient an effective
amount of the vaccine composition of claim 29.
32. A method of killing cells that express STEAP-2 in a patient,
comprising administering to the patient an effective amount of the
vaccine composition of claim 29.
33. A method of treating a patient with a cancer that expresses
STEAP-2, which comprises administering to said patient a vector
encoding a single chain monoclonal antibody that comprises the
variable domains of the heavy and light chains of a monoclonal
antibody that specifically binds to a STEAP-2 protein of claim 2,
such that the vector delivers the single chain monoclonal antibody
coding sequence to the cancer cells and the encoded single chain
antibody is expressed intracellularly therein.
34. A method of inhibiting growth of cells that express STEAP-2,
which comprises administering to said patient a vector encoding a
single chain monoclonal antibody that comprises the variable
domains of the heavy and light chains of a monoclonal antibody that
specifically binds to a STEAP-2 protein of claim 2, such that the
vector delivers the single chain monoclonal antibody coding
sequence to the cancer cells and the encoded single chain antibody
is expressed intracellularly therein.
35. A method of killing cells that express STEAP-2, which comprises
administering to said patient a vector encoding a single chain
monoclonal antibody that comprises the variable domains of the
heavy and light chains of a monoclonal antibody that specifically
binds to a STEAP-2 protein of claim 2, such that the vector
delivers the single chain monoclonal antibody coding sequence to
the cancer cells and the encoded single chain antibody is expressed
intracellularly therein.
36. A STEAP-3 protein having an amino acid sequence shown in FIGS.
10A-E (SEQ ID NO: 10).
37. A polypeptide of at least 10 contiguous amino acids of the
protein of claim 36.
38. A polypeptide comprising an amino acid sequence which is at
least 90% identical to the amino acid sequence shown in FIGS. 10A-E
(SEQ ID NO: 10) over its entire length.
39. A polynucleotide selected from the group consisting of (a) a
polynucleotide having the sequence as shown in FIGS. 10A-E (SEQ ID
NO: 9), wherein T can also be U; (b) a polynucleotide encoding the
STEAP-3 protein of claim 1; and (c) a polynucleotide which is fully
complementary to a polynucleotide of (a) or (b).
40. An antibody or fragment thereof which specifically binds to the
STEAP-3 protein of claim 36.
41. The antibody or fragment thereof of claim 40 which is
monoclonal.
42. A recombinant protein comprising the antigen binding region of
a monoclonal antibody of claim 41.
43. The antibody or fragment thereof of claim 40 or 41 which is
labeled with a detectable marker.
44. The antibody or fragment thereof or recombinant protein of
claim 43, wherein the detectable marker comprises a radioisotope,
metal chelator, enzyme or fluorescent, bioluminescent or
chemiluninescent compound.
45. The monoclonal antibody or fragment thereof of claim 41 which
is conjugated to a toxin, a radioisotope or a therapeutic
agent.
46. The monoclonal antibody or fragment thereof of claim 41,
wherein the toxin comprises ricin, ricin A-chain, doxorubicin,
daunorubicin, a maytansinoid, taxol, ethidium bromide, mitomycin,
etoposide, tenoposide, vincristine, vinblastine, colchicine,
dihydroxy anthracin dione, actinomycin, diphtheria toxin,
Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, modeccin A
chain, alpha-sarcin, gelonin, mitogellin, retstrictocin,
phenomycin, enomycin, curicin, crotin, calicheamicin, sapaonaria
officinalis inhibitor, or a glucocorticoid.
47. The monoclonal antibody or fragment thereof of claim 41,
wherein the radioisotope comprises .sup.212Bi, .sup.131I,
.sup.131In, .sup.90Y, or .sup.186Re.
48. The antibody fragment of claim 41, which is an Fab, F(ab')2, Fv
or Sfv fragment.
49. The antibody or fragment thereof of any one of claims 40, 41,
and 43-48, which is a human antibody.
50. The antibody or fragment thereof of any one of claims 40, 41,
and 43-48, which comprises murine antigen binding region residues
and human antibody residues.
51. A transgenic animal producing a monoclonal antibody of claim
41.
52. A hybridoma producing a monoclonal antibody of claim 41.
53. A single chain monoclonal antibody that comprises the variable
domains of the heavy and light chains of a monoclonal antibody of
claim 41.
54. A vector comprising a polynucleotide encoding a single chain
monoclonal antibody of claim 53.
55. An assay for detecting the presence of a STEAP-3 protein in a
biological sample comprising contacting the sample with an antibody
of claim 43 or 44, and detecting the binding of STEAP-3 protein in
the sample thereto.
56. An assay for detecting the presence of a STEAP-3 polynucleotide
in a biological sample, comprising (a) contacting the sample with a
polynucleotide probe which specifically hybridizes to a
polynucleotide of claim 39 or its complement; and (b) detecting the
presence of a hybridization complex formed by the hybridization of
the probe with STEAP-3 polynucleotidc in the sample, wherein the
presence of the hybridization complex indicates the presence of
STEAP-3 polynucleotide within the sample.
57. An assay for detecting the presence of STEAP-3 mRNA in a
biological sample comprising: (a) producing cDNA from the sample by
reverse transcription using at least one primer; (b) amplifying the
cDNA so produced using STEAP-3 polynucleotides as sense and
antisense primers to amplify STEAP-3 cDNAs therein; (c) detecting
the presence of the amplified STEAP-3 cDNA, wherein the STEAP-3
polynucleotides used as the sense and antisense primers are capable
of amplifying the polynucleotide of FIGS. 10A-E (SEQ ID NO: 9).
58. A pharmaceutical composition comprising an antibody or fragment
thereof or recombinant protein of any one of claims 40-50, a
STEAP-3 protein according to claim 36, or a STEAP-3 polynucleotide
according to claim 39, and a physiologically acceptable carrier.
Description
[0001] This application is related to U.S. patent application No.
60/087,520, filed Jun. 1, 1998, No. 60/091,183, filed Jun. 30,
1998, Ser. No. 09/323,873, filed Jun. 1, 1999, and Ser. No.
09/455,486, filed Dec. 6, 1999, and also to PCT/US99/12157 (WO
99/62941), filed Jun. 1, 1999, and PCT/US00/33040, filed Dec. 6,
2000, the entire contents of each of which is incorporated herein
by reference.
FIELD OF THE INVENTION
[0002] The invention described herein relates to a family of novel
genes and their encoded proteins and tumor antigens, termed STEAPs,
and to diagnostic and therapeutic methods and compositions useful
in the management of various cancers, particularly including
prostate cancer, colon cancer, bladder cancer, lung cancer, ovarian
cancer and pancreatic cancer.
BACKGROUND OF THE INVENTION
[0003] Cancer is the second leading cause of human death next to
coronary disease. Worldwide, millions of people die from cancer
every year. In the United States alone, cancer causes the death of
well over a half-million people annually, with some 1.4 million new
cases diagnosed per year. While deaths from heart disease have been
declining significantly, those resulting from cancer generally are
on the rise. In the early part of the next century, cancer is
predicted to become the leading cause of death.
[0004] Worldwide, several cancers stand out as the leading killers.
In particular, carcinomas of the lung, prostate, breast, colon,
pancreas, and ovary represent the primary causes of cancer death.
These and virtually all other carcinomas share a common lethal
feature. With very few exceptions, metastatic disease from a
carcinoma is fatal. Moreover, even for those cancer patients who
initially survive their primary cancers, common experience has
shown that their lives are dramatically altered. Many cancer
patients experience strong anxieties driven by the awareness of the
potential for recurrence or treatment failure. Many cancer patients
experience physical debilitations following treatment. Many cancer
patients experience a recurrence.
[0005] Worldwide, prostate cancer is the fourth most prevalent
cancer in men. In North America and Northern Europe, it is by far
the most common male cancer and is the second leading cause of
cancer death in men. In the United States alone, well over 40,000
men die annually of this disease--second only to lung cancer.
Despite the magnitude of these figures, there is still no effective
treatment for metastatic prostate cancer. Surgical prostatectomy,
radiation therapy, hormone ablation therapy, and chemotherapy
continue to be the main treatment modalities. Unfortunately, these
treatments are ineffective for many and are often associated with
undesirable consequences.
[0006] On the diagnostic front, the lack of a prostate tumor marker
that can accurately detect early-stage, localized tumors remains a
significant limitation in the management of this disease. Although
the serum PSA assay has been a very useful tool, its specificity
and general utility is widely regarded as lacking in several
important respects.
[0007] Progress in identifying additional specific markers for
prostate cancer has been improved by the generation of prostate
cancer xenografts that can recapitulate different stages of the
disease in mice. The LAPC (Los Angeles Prostate Cancer) xenografts
are prostate cancer xenografts that have survived passage in severe
combined immune deficient (SCID) mice and have exhibited the
capacity to mimic disease progression, including the transition
from androgen dependence to androgen independence and the
development of metastatic lesions (U.S. Pat. No. 6,107,540; Klein
et al., 1997, Nat. Med. 3:402). More recently identified prostate
cancer markers include PCTA-1 (Su et al., 1996, Proc. Natl. Acad.
Sci. USA 93: 7252), prostate stem cell antigen (PSCA) (Reiter et
al., 1998, Proc. Natl. Acad. Sci. USA 95: 1735), and STEAP (Hubert
et al., 1999, Proc. Natl. Acad. Sci. USA 96: 14523).
[0008] While previously identified markers such as PSA, PSM, PCTA
and PSCA have facilitated efforts to diagnose and treat prostate
cancer, there is need for the identification of additional markers
and therapeutic targets for prostate and related cancers in order
to further improve diagnosis and therapy.
SUMMARY OF THE INVENTION
[0009] The present invention relates to a novel family of cell
surface serpentine transmembrane antigens. Two of the proteins in
this family are exclusively or predominantly expressed in the
prostate, as well as in prostate cancer, and thus members of this
family have been termed "STEAP" (Six Transmembrane Epithelial
Antigen of the Prostate). Four particular human STEAPs are
described and characterized herein. The human STEAPs exhibit a high
degree of structural conservation among them but show no
significant structural homology to any known human proteins.
[0010] The prototype member of the STEAP family, STEAP-1, appears
to be a type IIIa membrane protein expressed predominantly in
prostate cells in normal human tissues. Structurally, STEAP-1 is a
339 amino acid protein characterized by a molecular topology of six
transmembrane domains and intracellular N- and C-termini suggesting
that it folds in a "serpentine" manner into three extracellular and
two intracellular loops. STEAP-1 protein expression is maintained
at high levels across various stages of prostate cancer. Moreover,
STEAP-1 is highly over-expressed in certain other human cancers. In
particular, cell surface expression of STEAP-1 has been
definitively confirmed in a variety of prostate and prostate cancer
cells, lung cancer, bladder cancer cells and colon cancer cells.
These characteristics indicate that STEAP-1 is a specific
cell-surface tumor antigen expressed at high levels in prostate,
bladder, colon, and other cancers.
[0011] A second member of the family, STEAP-2, is a 454 amino acid
protein with a predicted molecular topology similar to that of
STEAP-1. STEAP-2, like STEAP-1, is prostate-specific in normal
human tissues and is also expressed in prostate cancer. Alignment
of the STEAP-2 and STEAP-1 ORFs shows 54.9% identity over a 237
amino acid residue overlap, and the locations of the six putative
transmembrane domains in STEAP-2 coincide with the locations of the
transmembrane domains in STEAP-1 (FIGS. 11A-B).
[0012] STEAP-3 and STEAP-4 are also described herein. These are
also structurally related, and show unique expression profiles. In
particular, STEAP-3 and STEAP-4 appear to show a different tissue
restriction patterns. An amino acid sequence alignment of all four
STEAPs is shown in FIGS. 11A-B.
[0013] The invention provides polynucleotides corresponding or
complementary to all or part of the STEAP gene as described herein,
mRNAs, and/or coding sequences, preferably in isolated form,
including polynucleotides encoding STEAP proteins and fragments
thereof, DNA, RNA, DNA/RNA hybrid, and related molecules,
polynucleotides or oligonucleotides complementary to the STEAP gene
or mRNA sequences or parts thereof, and polynucleotides or
oligonucleotides which hybridize to the STEAP gene, mRNAs, or to
STEAP-encoding polynucleotides. Also provided are means for
isolating cDNAs and the genes encoding STEAP. Recombinant DNA
molecules containing STEAP polynucleotides, cells transformed or
transduced with such molecules, and host vector systems for the
expression of STEAP gene products are also provided.
[0014] The invention further provides STEAP proteins and
polypeptide fragments thereof. The invention further provides
antibodies that bind to STEAP proteins and polypeptide fragments
thereof, including polyclonal and monoclonal antibodies, murine and
other mammalian antibodies, chimeric antibodies, humanized and
fully human antibodies, and antibodies labeled with a detectable
marker, and antibodies conjugated to radionuclides/radioisotopes,
toxins or other therapeutic compositions. The invention further
provides methods for detecting the presence of STEAP
polynucleotides and proteins in various biological samples, as well
as methods for identifying cells that express a STEAP. The
invention further provides various therapeutic compositions and
strategies for treating prostate and other-cancers, including
particularly, antibody, vaccine and small molecule therapy.
[0015] The invention further provides methods for detecting the
presence of STEAP polynucleotides and proteins in various
biological samples, as well as methods for identifying cells that
express STEAP. The invention further provides various therapeutic
compositions and strategies, including particularly, antibody,
vaccine and small molecule therapy, for treating cancers of the
prostate. The extracellular nature of this protein presents a
number of therapeutic approaches using molecules that target STEAP
and its function, as well as molecules that target other proteins,
factors and ligands that interact with STEAP. These therapeutic
approaches include antibody therapy with anti-STEAP antibodies,
small molecule therapies, and vaccine therapies. In addition, given
its up-regulated expression in prostate cancer, STEAP is useful as
a diagnostic, staging and/or prognostic marker for prostate cancer
and, similarly, may be a marker for other cancers expressing this
protein. In particular, STEAP-1 provides an excellent marker for
identifying prostate cancer metastases.
BRIEF DESCRIPTION OF THE FIGURES
[0016] FIG. 1. STEAP-1 structure. 1A-B: Nucleotide and deduced
amino acid sequences of STEAP-1 (8P1B4) clone 10 cDNA (SEQ ID NOS.
1 and 2, respectively). The start methionine is indicated in bold
at amino acid residue position 1 and six putative transmembrane
domains are indicated in bold and are underlined. 1C: Schematic
representation of STEAP-1 transmembrane orientation; amino acid
residues bordering the predicted extracellular domains are
indicated and correspond to the numbering scheme of FIGS. 1A-B. 1D:
G/C rich 5' non-coding sequence of the STEAP-1 gene (SEQ ID NO: 3)
as determined by overlapping sequences of clone 10 and clone 3.
[0017] FIG. 2. Predominant expression of STEAP-1 in prostate
tissue. First strand cDNA was prepared from 16 normal tissues, the
LAPC xenografts (4AD, 4AI and 9AD) and HeLa cells. Normalization
was performed by PCR using primers to actin and GAPDH.
Semi-quantitative PCR, using primers derived from STEAP-1 (8P1D4)
cDNA (FIGS. 1A-B), shows predominant expression of STEAP-1 in
normal prostate and the LAPC xenografts. The following primers were
used to amplify STEAP-1:
1 8P1D4.1 5' ACTTTGTTGATGACCAGGATTGGA 3' (SEQ ID NO: 4) 8P1D4.2 5'
CAGAACTTGAGCACACACAGGAAC 3'. (SEQ ID NO: 5)
[0018] FIG. 2A. Lanes are as follows: 1 brain; 2 prostate; 3 LAPC-4
AD; 4 LAPC-4 Al; 5 LAPC-9 AD; 6 HeLa; 7 murine cDNA; 8 negative
control.
[0019] FIG. 2B. Lanes are as follows: 1 brain; 2 heart; 3 kidney; 4
liver; 5 lung; 6 pancreas; 7 placenta; 8 skeletal muscle.
[0020] FIG. 2C. Lanes are as follows: 1 colon; 2 ovary; 3
leukocytes; 4 prostate; 5 small intestine; 6 spleen; 7 testis; 8
thymus.
[0021] FIG. 3. Northern blot analyses of STEAP-1 expression in
various normal human tissues and prostate cancer xenografts,
showing predominant expression of STEAP-1 in prostate tissue.
[0022] FIG. 3A: Two multiple tissue northern blots (Clontech) were
probed with a full length STEAP cDNA clone 10 (FIGS. 1A-B). Size
standards in kilobases (kb) are indicated on the side. Each lane
contains 2 .mu.g of mRNA that was normalized by using a
.beta.-actin probe. A1 brain; A2 amygdala; A3 caudate nucleus; A4
cerebellum; A5 cerebral cortex; A6 frontal lobe; A7 hippocampus; A8
medulla oblongata; B1 occipital lobe; B2 putamen; B3 substantia
nigra; B4 temporal lobe; B5 thalamus; B6 sub-thalamic nucleus; B7
spinal cord; C1 heart; C2 aorta; C3 skeletal muscle; C4 colon; C5
bladder; C6 uterus; C7 prostate; C8 stomach; D1 testis; D2 ovary;
D3 pancreas; D4 pituitary gland; D5 adrenal gland; D6 thyroid
gland; D7 salivary gland; D8 mammary gland; E1 kidney; E2 liver; E3
small intestine; E4 spleen; E5 thymus ; E6 peripheral leukocytes;
E7 lymph node; E8 bone marrow; F1 appendix; F2 lung; F3 trachea; F4
placenta; G1 fetal brain; G2 fetal heart; G3 fetal kidney; G4 fetal
liver; G5 fetal spleen; G6 fetal thymus; G7 fetal lung.
[0023] FIG. 3B: Multiple tissue RNA dot blot (Clontech, Human
Master Blot cat#7770-1) probed with STEAP-1 cDNA clone 10 (FIGS.
1A-B), showing approximately five-fold greater expression in
prostate relative to other tissues with significant detectable
expression.
[0024] FIGS. 4A-B. Nucleotide sequence (SEQ ID NO: 6) of STEAP-1
GTH9 clone corresponding to the 4 kb message on northern blots
(FIG. 3A). The sequence contains an intron of 2399 base pairs
relative to the STEAP-1 clone 10 sequence of FIGS. 1A-B; coding
regions are nucleotides 96-857 and 3257-3510 (indicated in bold).
The start ATG is in bold and underlined, the STOP codon is in bold
and underlined, and the intron-exon boundaries are underlined.
[0025] FIG. 5. Expression of STEAP-1 in prostate and multiple
cancer cell lines and prostate cancer xenografts. Xenograft and
cell line filters were prepared with 10 .mu.g of total RNA per
lane. The blots were analyzed using the STEAP-1 clone 10 as probe.
All RNA samples were normalized by ethidium bromide staining and
subsequent analysis with a .beta.-actin probe. FIG. 5A: Expression
in various cancer cell lines and xenografts and prostate. Lanes as
follows: (1) PrEC cells, (2) normal prostate tissue, (3) LAPC-4 AD
xenograft, (4) LAPC-4 AI xenograft, (5) LAPC-9 AD xenograft, (6)
LAPC-9 AI xenograft, (7) LNCaP cells, (8) PC-3 cells, (9) DU145
cells, (10) PANC-1 cells, (11) BxPC-3 cells, (12) HPAC cells, (13)
Capan-1 cells, (14) CACO-2 cells, (15) LOVO cells, (16) T84 cells,
(17) COLO-205 cells, (18) KCL-22 cells (acute lymphocytic leukemia,
ALL), (19) HT1197 cells, (20) SCABER cells, (21) UM-UC-3 cells,
(22) TCCSUP cells, (23) J82 cells, (24) 5637 cells, (25) RD-ES
cells (Ewing sarcoma, EWS), (26) CAMA-1 cells, (27) DU4475 cells,
(28) MCF-7 cells, (29) MDA-MB-435s cells, (30) NTERA-2 cells, (31)
NCCIT cells, (32) TERA-1 cells, (33) TERA-2 cells, (34) A431 cells,
(35) HeLa cells, (36) OV-1063 cells, (37) PA-1 cells, (38) SW 626
cells, (39) CAOV-3 cells. FIG. 5B: The expression of STEAP-1 in
subcutaneously (sc) grown LAPC xenografts compared to the
expression in LAPC-4 and LAPC-9 xenografts grown in the tibia (it)
of mice.
[0026] FIGS. 6A-B. Western blot analysis of STEAP-1 protein
expression in tissues and multiple cell lines. Western blots of
cell lysates prepared from prostate cancer xenografts and cell
lines were probed with a polyclonal anti-STEAP-1 antibody
preparation. The samples contain 20 .mu.g of protein and were
normalized with anti-Grb-2 probing of the western blots.
[0027] FIGS. 7A-B. Cell surface biotinylation of STEAP-1. FIG. 7A:
Cell surface biotinylation of 293T cells transfected with vector
alone or with vector containing cDNA encoding 6His-tagged STEAP-1.
Cell lysates were immunoprecipitated with specific antibodies,
transferred to a membrane and probed with horseradish
peroxidase-conjugated streptavidin. Lanes 1-4 and 6 correspond to
immunoprecipitates from lysates prepared from STEAP-1 expressing
293T cells. Lanes 5 and 7 are immunoprecipitates from vector
transfected cells. The imImunoprecipitations were performed using
following antibodies: (1) sheep non-immune, (2) anti-Large T
antigen, (3) anti-CD71 (transferrin receptor), (4) anti-His, (5)
anti-His, (6) anti-STEAP-1, (7) anti-STEAP-1. FIG. 7B: Prostate
cancer (LNCaP, PC-3, DU145), bladder cancer (UM-U-3, TCCSUP) and
colon cancer (LOVO, COLO) cell lines were either biotinylated (+)
or not (-) prior to lysis. Western blots of streptavidin-gel
purified proteins were probed with anti-STEAP-1 antibodies.
Molecular weight markers are indicated in kilodaltons (kD).
[0028] FIG. 8. Immunohistochemical analysis of STEAP-1 expression
using anti-STEAP-1 polyclonal antibody. Tissues were fixed in 10%
formalin and embedded in paraffin. Tissue sections were stained
using anti-STEAP-1 polyclonal antibodies directed towards the
N-terminal peptide. FIG. 8A: LNCaP cells probed in the presence of
N-terminal STEAP-1 peptide 1, FIG. 8B: LNCaP plus non specific
peptide 2, FIG. 8C: normal prostate tissue, FIG. 8D: grade 3
prostate carcinoma, FIG. 8E: grade 2, Gleason 7 prostate carcinoma,
FIG. 8F: LAPC-9 AD xenograft, FIG. 8G: normal bladder, FIG. 8H:
normal colon. All images are at 400.times.magnification.
[0029] FIGS. 9A-D. Nucleotide (SEQ ID NO: 7) and deduced amino acid
(SEQ ID NO: 8) sequences of STEAP-2 (98P4B6) clone GTD3 cDNA. The
start methionine and Kozak sequence are indicated in bold, and the
putative transmembrane domains are underlined in bold. The 5' UTR
exhibits a high GC content of 72%.
[0030] FIGS. 10A-E. Nucleotide (SEQ ID NO: 9) and deduced amino
acid (SEQ ID NO: 10) sequences of STEAP-3. Kozak region is in
bold.
[0031] FIG. 10F. Nucleotide sequences (SEQ ID NOS: 11-14,
respectively) of dbEST database entries corresponding to additional
STEAP family members obtained by searching with the protein
sequence of STEAP-1.
[0032] FIG. 11. Primary structural comparisons of STEAP family
proteins:
[0033] FIGS. 11A-B. Amino acid sequence alignment of STEAPs 1-4
(SEQ ID NOS: 2, 8, 10 and 15, respectively) using PIMA program
(PIMA 1.4 program at Internet address:
<http:.backslash..backslash.dot.imgen.bcm.tmc.edu- :9331
.backslash.multi-align.backslash.multi-align.html>);
transmembrane domains identified by the SOSUI program (available at
Internet address
www.tuat.ac.jp.backslash..about.mitaku.backslash.adv_sos-
ui.backslash.submit.html) are in bold. PIMA maximal linkage
clustering results shown; identical residues shown in bold.
[0034] FIG. 11C. Amino acid sequence alignment of STEAP-1 (8P1D4
clone 10; SEQ ID NO: 2) and STEAP-2 (98P4B6 clone GTD3; SEQ ID NO:
8) sequences. The alignent was performed using the SIM alignment
program of the Baylor College of Medicine Search Launcher Web site.
Transmembrane domains are indicated in boldface. The results show a
54.9% identity in a 237 residues overlap (Score: 717.0; Gap
frequency: 0.0%).
[0035] FIG. 11D. Amino acid sequence alignment of STEAP-1 (SEQ ID
NO: 2) and STEAP-3 (98P4B6 clone GTD3; SEQ ID NO: 10) sequences.
Identical residues indicated with asterisks. SIM results: 40.9%
identity in 264 residues overlap; Score: 625.0; Gap frequency:
0.0%.
[0036] FIG. 11E. Amino acid sequence alignment of STEAP-2 (SEQ ID
NO: 8) and STEAP-3 (98P4B6 clone GTD3; SEQ ID NO: 10) sequences.
Identical residues indicated with asterisks. SIM results: 47.8%
identity in 416 residues overlap; Score: 1075.0; Gap frequency:
0.2%.
[0037] FIG. 12. Expression of STEAP-3 mRNA in normal tissues by
northern blot (FIGS. 12A-B) and RT-PCR (FIG. 12B). For RT-PCR
analysis, first strand cDNA was prepared from 16 normal tissues.
Normalization was performed by PCR using primers to actin and
GAPDH. Semi-quantitative PCR, using primers to AI139607, shows
predominant expression of AI139607 in placenta and prostate after
25 cycles of amplification. The following primers were used to
amplify AI139607:
2 AI139607.1 5' TTAGGACAACTTGATCACCAGCA 3' (SEQ ID NO: 16)
AI139607.2 5' TGTCCAGTCCAAACTGGGTTATTT 3'. (SEQ ID NO: 17)
[0038] FIG. 12A. Lanes are as follows (from left to tight): Panel
1: heart, brain, placenta, lung, liver, skeletal muscle, kidney and
pancreas; Panel 2: spleen, thymus, prostate, testis, ovary, small
intestine, colon and white blood cells.
[0039] FIG. 12B. Lanes are as follows: 1 brain; 2 heart; 3 kidney;
4 liver; 5 lung; 6 pancreas; 7 placenta; 8 skeletal muscle.
[0040] FIG. 12C. Lanes are as follows: 1 colon; 2 ovary; 3
leukocytes; 4 prostate; 5 small intestine; 6 spleen; 7 testis; 8
thymus.
[0041] FIG. 13. Predominant expression of STEAP-4/R80991 in liver.
First strand cDNA was prepared from 16 normal tissues.
Normalization was performed by PCR using primers to actin and
GAPDH. Semi-quantitative PCR, using primers to R80991, shows
predominant expression of R80991 in liver after 25 cycles of
amplification. The following primers were used to amplify
R80991:
3 R80991.1 5'AGGGAGTTCAGCTTCGTTCAGTC 3' (SEQ ID NO: 18) R80991.2
5'GGTAGAACTTGTAGCGGCTCTCCT 3'. (SEQ ID NO: 19)
[0042] FIG. 13A. Lanes are as follows: 1 brain; 2 heart; 3 kidney;
4 liver; 5 lung; 6 pancreas; 7 placenta; 8 skeletal muscle.
[0043] FIG. 13B. Lanes are as follows: 1 colon; 2 ovary; 3
leukocytes; 4 prostate; 5 small intestine; 6 spleen; 7 testis; 8
thymus.
[0044] FIG. 14. Predominant expression of STEAP-2 (98P4B6) in
prostate tissue. First strand cDNA was prepared from 8 normal
tissues, the LAPC xenografts (4AD, 4AI and 9AD) and HeLa cells.
Normalization was performed by PCR using primers to actin and
GAPDH. Semi-quantitative PCR, using primers to 98P4B6, shows
predominant expression of 98P4B6 in normal prostate and the LAPC
xenografts. The following primers were used to amplify STEAP
II:
4 98P4B6.1 5' GACTGAGCTGGAACTGGAATTTGT 3' (SEQ ID NO: 20) 98P4B6.2
5' TTTGAGGAGACTTCATCTCACTGG 3'. (SEQ ID NO: 21)
[0045] FIG. 14A. Lanes are as follows: 1 brain; 2 prostate; 3
LAPC-4 AD; 4 LAPC-4 Al; 5 LAPC-9 AD; 6 HeLa; 7 mutine cDNA; 8
negative control.
[0046] FIG. 14B. Lanes are as follows: 1 colon; 2 ovary; 3
leukocytes; 4 prostate; 5 small intestine; 6 spleen; 7 testis; 8
thymus.
[0047] FIG. 15. Expression of the prostate-specific STEAP-2/98P4B6
gene in normal tissues and in prostate cancer xenografts determined
by Northern blot analysis. Human normal tissue filters (A and B)
were obtained from CLONTECH and contain 2 .mu.g of mRNA per lane.
Xenograft filter (C) was prepared with 10 .mu.g of total RNA per
lane. The blots were analyzed using the SSH derived 98P4B6 clone as
probe. All RNA samples were normalized by ethidium bromide
staining.
[0048] FIG. 15A. Lanes are as follows: 1 heart; 2 brain; 3
placenta; 4 lung; 5 liver; 6 skeletal muscle; 7 kidney; 8
pancreas.
[0049] FIG. 15B. Lanes are as follows: 1 spleen; 2 thymus; 3
prostate; 4 testis; 5 ovary; 6 small intestine; 7 colon; 8
leukocytes.
[0050] FIG. 15C. Lanes are as follows: 1 prostate; 2 LAPC-4 AD; 3
LAPC-4 AI; 4 LAPC-9 AD; LAPC-9AI.
[0051] FIG. 16. Expression of STEAP-2 in prostate and select cancer
cell lines as determined by Northern blot analysis. Xenograft and
cell line filters were prepared with 10 .mu.g total RNA per lane.
The blots were analyzed using an SSH derived 98P4B6 clone as probe.
All RNA samples were normalized by ethidium bromide staining. Lanes
are as follows: 1 prostate; 2 LAPC-4 AD; 3 LAPC-4 AI; 4 LAPC-9 AD;
5 LAPC-9 AI; 6 TsuPr1; 7 DU145; 8 LNCaP; 9 PC-3; 10 LAPC-4 CL; 11
PrEC; 12 HT1197; 13 SCaBER; 14 UM-UC-3; 15 TCCSUP; 16 J82; 17 5637;
18 RD-ES; 19 293T; 20 PANC-1; 21 BxPC-3; 22 HPAC; 23 Capan-1; 24
LS180; 25 SK-CO-1; 26 CaCo-2; 27 LoVo; 28 T84; 29 Colo-205; 30
BT-20; 31 CAMA-1; 32 DU4475; 33 MCF-7; 34 MDA-MB-435s; 35 NTERA-2;
36 NCCIT; 37 TERA-1; 38 TERA-2; 39 A431; 40 HeLa; 41 OV-1063; 42
PA-1; 43 SW626; 44 CAOV-3.
[0052] FIG. 17. Chromosomal localization of STEAP family members.
The chromosomal localizations of the STEAP genes described herein
were determined using the GeneBridge4 radiation hybrid panel
(Research Genetics, Huntsville Ala.). The mapping for STEAP-2 and
AI139607 was performed using the Stanford G3 radiation hybrid panel
(Research Genetics, Huntsville Ala.).
[0053] FIG. 18. Schematic representation of Intron-Exon boundaries
within the ORF of human STEAP-1 gene. A total of 3 introns (i) and
4 exons (e) were identified.
[0054] FIG. 19. Zooblot southern analysis of STEAP-1 gene in
various species. Genomic DNA was prepared from several different
organisms including human, monkey, dog, mouse, chicken and
Drosophila. Ten micrograms of each DNA sample was digested with
EcoRI, blotted onto nitrocellulose and probed with a STEAP-1 probe.
Size standards are indicated on the side in kilobases (kb).
[0055] FIG. 20. Southern blot analysis of mouse BAC with a STEAP-1
probe. DNA was prepared from human cells to isolate genomic DNA and
from a mouse BAC clone (12P11) that contains the mouse STEAP gene.
Each DNA sample was digested with EcoRI, blotted onto
nitrocellulose and probed. Eight micrograms of genomic DNA was
compared to 250 ng of mouse BAC DNA. Lanes are as follows: (1) 1 kb
ladder; (2) human female genomic; (3) 12P11 BAC mus; (4) human
female genomic; (5) 12P11 BAC mus; (6) 3T3.
[0056] FIG. 21A. Immunohistochemical staining using a sheep
polyclonal antibody directed against STEAP-1 and showing
pericellular staining in a bladder cancer specimen.
[0057] FIG. 21B. Immunohistochemical staining using a sheep
polyclonal antibody directed against STEAP-1 and showing
pericellular staining in a second bladder cancer specimen.
[0058] FIG. 21C. Immunohistochemical staining using a sheep
polyclonal antibody directed against STEAP-1 and showing
pericellular staining in a lung cancer specimen.
[0059] FIG. 21D. Immunohistochemical staining using a sheep
polyclonal antibody directed against STEAP-1 and showing
pericellular staining in a second lung cancer specimen.
[0060] FIG. 22A. STEAP-2 expression in normal prostate shown by RNA
in situ hybridization with an antisense probe.
[0061] FIG. 22B. STEAP-2 expression in normal prostate by RNA in
situ hybridization using a sense probe as control.
[0062] FIG. 23A. STEAP-2 expression in prostate cancer shown by RNA
in situ hybridization with an antisense probe.
[0063] FIG. 23B. STEAP-2 expression in prostate cancer control for
RNA in situ hybridization using a sense probe.
[0064] FIG. 24. Expression of STEAP-2 in various cancer tissues as
examined using RT-PCR. Lane 1 represents a sample from an LAPC4 AD
xenograft; lane 2 is LAPC9 AD xenograft; lane 3 is LAPC9 AD.sup.2
xenograft (grown with human bone explant); lane 4 is LAPC9 AD IT
grown intratibially); lane 5 is pooled tissue from colon cancer
patients; lane 6 is pooled tissue from lung cancer patients; M
represents a marker lane; lane 7 is patient normal prostate tissue;
lane 8 is patient prostate cancer tissue; lane 9 is pooled tissue
from kidney cancer patients; lane 10 is pooled tissue from bladder
cancer patients; lane 11 is HeLa cells; and lane 12 is a water
blank.
[0065] FIG. 25. RNA dot blot analysis of STEAP-2 expression in 76
normal tissues, showing prostate-specific expression. RNA tissue
sources: A1 whole brain; A2 cerebellum, left; A3 substantia nigra;
A4 heart; A5 esophagus; A6 colon, transverse; A7 kidney; A8 lung;
A9 liver; A10 HL60, leukemia; Allfetal brain; B1 cerebral cortex;
B2 cerebellum, right; B3 accumbens nucleus; B4 aorta; B5 stomach;
B6 colon, descending; B7 skeletal muscle; B8 placenta; B9 pancreas;
B10 HeLa, S3; B11 fetal heart; C1 frontal lobe; C2 corpus callosum;
C3 thalamus; C4 atrium, left; C5 duodenum; C6 rectum; C7 spleen; C8
bladder; C9 adrenal gland; C10 K562, leukemia; C11 fetal kidney; D1
parietal lobe; D2 amygdala; D3 pituitary gland; D4 atrium, right;
D5 jejunum; D6 blank; D7 thymus; D8 uterus; D9 thyroid gland; D10
MOLT-4, leukemia; D11 fetal liver; E1 occipital lobe; E2 caudate
nucleus; E3 spinal cord; E4 ventricle, left; E5 ileum; E6 blank; E7
leukocytes; E8 prostate; E9 salivary gland; E10 RAJI, lymphoma; E11
fetal spleen; F1 temporal lobe; F2 hippocampus; F3 blank; F4
ventricle, right; F5 ileocecum; F6 blank; F7 lymph node; F8 testis;
F9 mammary gland; F10 DAUDI, lymphoma; F11 fetal thymus; G1
paracentral gyrus; G2 medulla oblongata; G3 blank; G4
interventricular septum; G5 appendix; G6 blank; G7 bone marrow; G8
ovary; G9 blank; G10 SW480, colon cancer; G11 fetal lung; HI pons;
H2 putamen; H3 blank; H4 apex of the heart; H5 colon, ascending; H6
blank; H7 trachea; H8 blank; H9 blank; H10 A549, lung cancer; H11
blank.
[0066] FIG. 26. Western blot with anti-phosphotyrosine (4G10 mAb)
showing that expression of STEAP-2 in PC3 cells is sufficient to
induce phosphorylation of various proteins on tyrosine residues,
including p150, p120 and p75. An overlay using anti-Gtb2 Ab shows
that the gel was equally loaded.
[0067] FIG. 27A. Western blot using anti-phospho-p38 showing that
expression of STEAP-1 or STEAP-2 in PC3 cells activates the p38
kinase, as compared to PC3-neo controls. TNF-NaSaI and NaSaI, known
p38 activators, served as positive controls.
[0068] FIG. 27B. Western blot, as in FIG. 27A, using anti-p38 to
demonstrate equal protein loading on the gels.
[0069] FIG. 28A. Western blot using anti-phospho-ERK to examine
activation of the ERK pathway in 1% FBS. PC3 cells expressing Ras
(positive control), STEAP-1, STEAP-2, or neo (negative control),
were grown in 1% FBS. The results show that, while expression of
the neo control gene has no effect on ERK phosphorylation,
expression of STEAP-1 and STEAP-2 induces ERK phosphorylation. An
anti-ERK antibody was used to confirm the presence of ERK in all
lanes.
[0070] FIG. 28B. Western blot using anti-phospho-ERK to examine
activation of the ERK pathway in 0.1% and 10% FBS. PC3 cells
expressing STEAP-1 or neo (negative control), were grown in either
0.1% or 10% FBS. The results confirm that expression of STEAP-1 is
sufficient to induce activation of the ERK signaling cascade.
[0071] FIG. 29. Signaling in PC3-STEAP-1 cells mediated by
odorants.
[0072] FIG. 29A. Anti-phosphotyrosine western blot of PC3 cells,
stably expressing neo, were grown overnight in 0.1% FBS to allow
for receptor occupancy, and then treated with citralva,
ethylvanillin or IBMP. Treatment with 10% FBS was used as a
control.
[0073] FIG. 29B. Anti-phosphotyrosine western blot of PC3 cells,
stably expressing STEAP-1, were treated as described for FIG. 29A.
The results show that citralva and ethylvanillin specifically
induce the phosphorylation of p136-140 in PC3-STEAP-1 cells. In
addition, citralva induces the de novo phosphorylation of a protein
at 160-200 kDa.
[0074] FIG. 30. Activation of the ERK cascade by odorants. Anti-ERK
western blot of PC3 cells, stably expressing either neo or STEAP-1,
were grown overnight in 0.1% FBS. Cells were then treated with
citralva for 5 min. Treatment with 10% FBS was used as a control.
Whole cell lysates were analyzed using anti-phospho-ERK. The
results show that citralva induces the phosphorylation of ERK, and
therefore activation of the ERK pathway, in a STEAP-1 specific
manner.
[0075] FIG. 31A. Anti-STEAP-1 immunohistochemistry analysis on the
LAPC-9 orthotopic prostate cancer tumor (magnification 200.times.).
Cells expressing STEAP-1 show perinuclear staining.
[0076] FIG. 31B. Anti-STEAP-1 immunohistochemistry analysis on the
LAPC-9 lymph node metastasis (magnification 400.times.). Cells
expressing STEAP-1 show perinuclear staining.
[0077] FIGS. 31C-D. Anti-STEAP-1 immunohistochemistry analysis on
the LAPC-9 lung metastasis (magnification 800.times.). Cells
expressing STEAP-1 show perinuclear staining.
[0078] FIGS. 31E-F. Anti-PSA immunohistochemistry analysis on a
LAPC-9 prostate cancer lung micrometastasis (magnification 800X).
Cells expressing PSA show perinuclear staining.
[0079] FIG. 32A. Immunohistochemical detection of STEAP-1 showing
intense pericellular staining in lymph node metastasis of a human
patient.
[0080] FIG. 32B. Immunohistochemical detection of STEAP-1 showing
intense pericellular staining in bone metastasis of a human
patient.
[0081] FIG. 33. Western blot showing that anti-STEAP-1 murine pAb
recognizes STEAP-1 protein in engineered cell lines and endogenous
STEAP-1 protein in LNCaP cells. Lysates of LNCaP cells and 293T
cells transfected with either pcDNA 3.1 MYC/HIS tagged STEAP-1 or
neo empty vector, and RAT1 cells engineered to express STEAP-1 or a
neo control gene, were separated by SDS-PAGE and transferred to
nitrocellulose. The blot was then subjected to anti-STEAP western
analysis using a 1:1000 dilution of serum from mice immunized with
a GST-STEAP-1 fusion protein.
DETAILED DESCRIPTION OF THE INVENTION
[0082] The present invention relates to a novel family of cell
surface serpentine transmembrane antigens. Two of the proteins in
this family are exclusively or predominantly expressed in the
prostate, as well as in prostate cancer, and thus members of this
family have been termed "STEAP" (Six Transmembrane Epithelial
Antigen of the Prostate). Four particular human STEAPs are
described and characterized herein. The human STEAPs exhibit a high
degree of structural conservation among them but show no
significant structural homology to any known human proteins. The
present invention relates to methods and compositions for the
diagnosis and therapy of prostate and other cancers, which methods
utilize isolated polynucleotides corresponding to human STEAP
genes, proteins encoded by the STEAP genes and fragments thereof,
and antibodies capable of specifically recognizing and binding to
STEAP proteins.
[0083] Unless otherwise defined, all terms of art, notations and
other scientific terminology used herein are intended to have the
meanings commonly understood by those of skill in the art to which
this invention pertains. In some cases, terms with commonly
understood meanings are defined herein for clarity and/or for ready
reference, and the inclusion of such definitions herein should not
necessarily be construed to represent a substantial difference over
what is generally understood in the art. The techniques and
procedures described or referenced herein are generally well
understood and commonly employed using conventional methodology by
those skilled in the art, such as, for example, the widely utilized
molecular cloning methodologies described in Sambrook et al.,
Molecular Cloning: A Laboratory Manual 2nd. edition (1989) Cold
Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. As
appropriate, procedures involving the use of commercially available
kits and reagents are generally carried out in accordance with
manufacturer defined protocols and/or parameters unless otherwise
noted.
[0084] As used herein, the terms "advanced prostate cancer",
"locally advanced prostate cancer", "advanced disease" and "locally
advanced disease" mean prostate cancers that have extended through
the prostate capsule, and are meant to include stage C disease
under the American Urological Association (AUA) system, stage C1-C2
disease under the Whitmore-Jewett system, and stage T3-T4 and N+
disease under the TNM (tumor, node, metastasis) system. In general,
surgery is not recommended for patients with locally advanced
disease, and these patients have substantially less favorable
outcomes compared to patients having clinically localized
(organ-confined) prostate cancer. Locally advanced disease is
clinically identified by palpable evidence of induration beyond the
lateral border of the prostate, or asymmetry or induration above
the prostate base. Locally advanced prostate cancer is presently
diagnosed pathologically following radical prostatectomy if the
tumor invades or penetrates the prostatic capsule, extends into the
surgical margin, or invades the seminal vesicles.
[0085] As used herein, the terms "metastatic prostate cancer" and
"metastatic disease" mean prostate cancers that have spread to
regional lymph nodes or to distant sites, and are meant to include
stage D disease under the AUA system and stage T.times.N.times.M+0
under the TNM system. As is the case with locally advanced prostate
cancer, surgery is generally not indicated for patients with
metastatic disease, and hormonal (androgen ablation) therapy is the
preferred treatment modality. Patients with metastatic prostate
cancer eventually develop an androgen-refractory state within 12 to
18 months of treatment initiation, and approximately half of these
patients die within 6 months thereafter. The most common site for
prostate cancer metastasis is bone. Prostate cancer bone metastases
are, on balance, characteristically osteoblastic rather than
osteolytic (i.e., resulting in net bone formation). Bone metastases
are found most frequently in the spine, followed by the femur,
pelvis, rib cage, skull and humerus. Other common sites for
metastasis include lymph nodes, lung, liver and brain. Metastatic
prostate cancer is typically diagnosed by open or laparoscopic
pelvic lymphadenectomy, whole body radionuclide scans, skeletal
radiography, and/or bone lesion biopsy.
[0086] As used herein, the term "polynucleotide" means a polymeric
form of nucleotides of at least 10 bases or base pairs in length,
either ribonucleotides or deoxynucleotides or a modified form of
either type of nucleotide, and is meant to include single and
double stranded forms of DNA.
[0087] As used herein, the term "polypeptide" means a polymer of at
least 10 amino acids. Throughout the specification, standard three
letter or single letter designations for amino acids are used.
[0088] As used herein, the terms "hybridize", "hybridizing",
"hybridizes" and the like, used in the context of polynucleotides,
are meant to refer to conventional hybridization conditions,
preferably such as hybridization in 50% formamide/6.times.SSC/0.1%
SDS/100 .mu.g/ml ssDNA, in which temperatures for hybridization are
above 37.degree. C. and temperatures for washing in
0.1.times.SSC/0.1% SDS are above 55.degree. C., and most preferably
to stringent hybridization conditions.
[0089] "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 that 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).
[0090] "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 x 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.
[0091] "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 than 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.
[0092] In the context of amino acid sequence comparisons, the term
"identity" is used to express the percentage of amino acid residues
at the same relative positions that are the same. Also in this
context, the term "homology" is used to express the percentage of
amino acid residues at the same relative positions that are either
identical or are similar, using the conserved amino acid criteria
of BLAST analysis, as is generally understood in the art. For
example, % identity values may be generated by WU-BLAST-2 (Altschul
et al., Methods in Enzymology, 266: 460-480 (1996):
http://blastwusd/edu/blast/README.html). Further details regarding
amino acid substitutions, which are considered conservative under
such criteria, are provided below.
[0093] Additional definitions are provided throughout the
subsections that follow.
[0094] Steap Polynucleotides
[0095] One aspect of the invention provides polynucleotides
corresponding or complementary to all or part of a STEAP gene,
mRNA, and/or coding sequence, preferably in isolated form,
including polynucleotides encoding a STEAP protein and fragments
thereof, DNA, RNA, DNA/RNA hybrid, and related molecules,
polynucleotides or oligonucleotides complementary to a STEAP gene
or mRNA sequence or a part thereof, and polynucleotides or
oligonucleotides that hybridize to a STEAP gene, mRNA, or to a
STEAP encoding polynucleotide (collectively, "STEAP
polynucleotides"). As used herein, STEAP genes and proteins are
meant to include the STEAP-1, STEAP-2 and STEAP-3 genes and
proteins, and the gene and protein corresponding to GenBank
Accession number R80991 (STEAP-4), and the genes and proteins
corresponding to other STEAP proteins and structurally similar
variants of the foregoing. Such other STEAP proteins and variants
will generally have coding sequences that are highly homologous to
the STEAP coding sequence, and preferably will share at least about
50% amino acid identity and at least about 60% amino acid homology
(using BLAST criteria), more preferably sharing 70% or greater
homology (using BLAST criteria).
[0096] The STEAP family member gene sequences described herein
encode STEAP proteins sharing unique highly conserved amino acid
sequence domains which distinguish them from other proteins.
Proteins which include one or more of these unique highly conserved
domains may be related to the STEAP family members or may represent
new STEAP proteins. Referring to FIGS. 11A-B, which is an amino
acid sequence alignment of the full STEAP-1, STEAP-2, and STEAP-3
protein sequences as well as the partial STEAP-4 sequence, it is
clear that the STEAPs are closely related at the structural level.
Referring to FIG. 11C, which is an amino acid sequence alignment of
the fill STEAP-1 and STEAP-2 protein sequences, close structural
conservation is apparent, particularly in the predicted
transmembrane domains. The STEAP-1 and STEAP-2 sequences share
54.9% identity over a 237 amino acid overlap. Additional amino acid
sequence alignments between the STEAPs are shown in FIGS. 11D and
11E. These alignments show that STEAP-1 and STEAP-3 are 40.9%
identical over a 264 amino acid region, while STEAP-2 and STEAP-3
are 47.8% identical over a 416 amino acid region.
[0097] A STEAP polynucleotide may comprise a polynucleotide having
the nucleotide sequence of human STEAP-1 as shown in FIGS. 1A-B,
the nucleotide sequence of human STEAP-2 as shown in FIGS. 9A-D,
the nucleotide sequence of human STEAP-3 as shown in FIGS. 10A-E,
or the nucleotide sequence of STEAP-4 as shown in FIG. 10F, or a
sequence complementary thereto, or a polynucleotide fragment of any
of the foregoing. Another embodiment comprises a polynucleotide
which encodes the human STEAP-1, STEAP-2, STEAP-3 or STEAP-4
protein amino acid sequences, a sequence complementary thereto, or
a polynucleotide fragment of any of the foregoing. Another
embodiment comprises a polynucleotide which is capable of
hybridizing under stringent hybridization conditions to the human
STEAP-1 cDNA shown in FIGS. 1A-B, the human STEAP-2 cDNA shown in
FIG. 9A-D, the human STEAP-3 cDNA shown in FIGS. 10A-E, or the
STEAP-4 as shown in FIG. 10F, or to a polynucleotide fragment
thereof Typical embodiments of the invention disclosed herein
include STEAP polynucleotides encoding specific portions of a STEAP
mRNA sequence such as those that encode the protein and fragments
thereof For example, representative embodiments of the invention
disclosed herein include: polynucleotides encoding about amino acid
1 to about amino acid 10 of a STEAP protein shown in FIGS. 11A-B,
polynucleotides encoding about amino acid 20 to about amino acid 30
of a STEAP protein shown in FIGS. 11A-B, polynucleotides encoding
about amino acid 30 to about amino acid 40 of a STEAP protein shown
in FIGS. 11A-B, polynucleotides encoding about amino acid 40 to
about amino acid 50 of a STEAP protein shown in FIGS. 11A-B,
polynucleotides encoding about amino acid 50 to about amino acid 60
of a STEAP protein shown in FIGS. 11A-B, polynucleotides encoding
about amino acid 60 to about amino acid 70 of a STEAP protein shown
in FIGS. 11A-B, polynucleotides encoding about amino acid 70 to
about amino acid 80 of a STEAP protein shown in FIGS. 11A-B,
polynucleotides encoding about amino acid 80 to about amino acid 90
of a STEAP protein shown in FIGS. 11A-B and polynucleotides
encoding about amino acid 90 to about amino acid 100 of a STEAP
protein shown in FIGS. 11A-B, etc. Following this scheme,
polynucleotides (of at least 10 amino acids) encoding further
portions of the amino acid sequence of a STEAP protein are typical
embodiments of the invention. Such portions of a STEAP protein
include amino acids 100-339 of a STEAP-1 protein shown in FIGS.
11A-B, or amino acids 100-454 of a STEAP-2 protein shown in FIGS.
11A-B, or Amino acids 100-459 of a STEAP-3 protein shown in FIGS.
11A-B, and amino acids 100-133 of a STEAP-4 protein shown in FIGS.
11A-B. Polynucleotides encoding larger portions of the STEAP
protein are also contemplated. For example polynucleotides encoding
from about amino acid 1 (or 20 or 30 or 40 etc.) to about amino
acid 20, (or 30, or 40 or 50 etc.) of a STEAP protein shown in
FIGS. 11A-B may be generated by a variety of techniques well known
in the art.
[0098] Additional illustrative embodiments of the invention
disclosed herein include STEAP polynucleotide fragments encoding
one or more of the biological motifs contained within the STEAP
protein sequence. In one embodiment, typical polynucleotide
fragments of the invention can encode one or more of the regions of
STEAP that exhibit homology to other STEAP family members, such as
one or more of the transmembrane domains. In another embodiment of
the invention, typical polynucleotide fragments can encode
sequences that are unique to one or more STEAP alternative splicing
variants. In yet another embodiment, typical polynucleotide
fragments can encode an immunogenic portion of a STEAP protein. One
example of an immunogenic portion of a STEAP protein is amino acid
residues 14 through 28 of the STEAP-1 amino acid sequence as shown
in FIG. 1A-B (WKMKPRRNLEEDDYL; SEQ ID NO: 22).
[0099] The polynucleotides of the preceding paragraphs have a
number of different specific uses. As STEAPs are differentially
expressed in prostate and other cancers, these polynucleotides may
be used in methods assessing the status of STEAP gene products in
normal versus cancerous tissues. Typically, polynucleotides
encoding specific regions of a STEAP protein may be used to assess
the presence of perturbations (such as deletions, insertions, point
mutations etc.) in specific regions of the STEAP gene products.
Exemplary assays include both RT-PCR assays as well as
single-strand conformation polymorphism (SSCP) analysis (see e.g.
Marrogi et al., J. Cutan. Pathol. 26(8): 369-378 (1999), both of
which utilize polynucleotides encoding specific regions of a
protein to examine these regions within the protein. Assays and
methods for analyzing sequences to detect single nucleotide
polymorphisms are also available (Irizarry, et al., 2000, Nature
Genetics 26(2):223-236.
[0100] Other specifically contemplated embodiments of the invention
disclosed herein are genomic DNA, cDNAs, ribozymes, and antisense
molecules, including morpholino anti-sense molecules, as well as
nucleic acid molecules based on an alternative backbone or
including alternative bases, whether derived from natural sources
or synthesized. For example, antisense molecules can be RNAs or
other molecules, including peptide nucleic acids (PNAs) or
non-nucleic acid molecules such as phosphorothioate derivatives,
that specifically bind DNA or RNA in a base pair-dependent manner.
A skilled artisan can readily obtain these classes of nucleic acid
molecules using the STEAP polynucleotides and polynucleotide
sequences disclosed herein.
[0101] Antisense technology entails the administration of exogenous
oligonucleotides that bind to a target polynucleotide located
within the cells. The term "antisense" refers to the fact that such
oligonucleotides are complementary to their intracellular targets,
e.g., STEAP. See for example, Jack Cohen, OLIGODEOXYNUCLEOTIDES,
Antisense Inhibitors of Gene Expression, CRC Press, 1989; and
Synthesis 1:1-5 (1988). The STEAP antisense oligonucleotides of the
present invention include derivatives such as S-oligonucleotides
(phosphorothioate derivatives or S-oligos, see, Jack Cohen, supta),
which exhibit enhanced cancer cell growth inhibitory action.
S-oligos (nucleoside phosphorothioates) are isoelectronic analogs
of an oligonucleotide (O-oligo) in which a nonbridging oxygen atom
of the phosphate group is replaced by a sulfur atom. The S-oligos
of the present invention may be prepared by treatment of the
corresponding O-oligos with 3H-1,2-benzodithiol-3-one-1,1-dioxide,
which is a sulfur transfer reagent. See Iyer, R. P. et al, J. Org.
Chem. 55:4693-4698 (1990); and Iyer, R. P. et al., J. Am. Chem.
Soc. 112:1253-1254 (1990), the disclosures of which are fully
incorporated by reference herein. Additional STEAP antisense
oligonucleotides of the present invention include morpholino
antisense oligonucleotides known in the art (see e.g. Partridge et
al., 1996, Antisense & Nucleic Acid Drug Development 6:
169-175).
[0102] The STEAP antisense oligonucleotides of the present
invention typically may be RNA or DNA that is complementary to and
stably hybridizes with the first 100 N-terminal codons or last 100
C-terminal codons, or overlapping with the ATG start site, of the
STEAP genome or the corresponding mRNA. While absolute
complementarity is not required, high degrees of complementarity
are preferred. Use of an oligonucleotide complementary to this
region allows for the selective hybridization to STEAP mRNA and not
to mRNA specifying other regulatory subunits of protein kinase.
Preferably, the STEAP antisense oligonucleotides of the present
invention are a 15 to 30-mer fragment of the antisense DNA molecule
having a sequence that hybridizes to STEAP mRNA. Optionally, STEAP
antisense oligonucleotide is a 30-mer oligonucleotide that is
complementary to a region in the first 10 N-terminal codons and
last 10 C-terminal codons of STEAP. Alternatively, the antisense
molecules are modified to employ ribozymes in the inhibition of
STEAP expression. L. A. Couture & D. T. Stinchcomb; Trends
Genet 12: 510-515 (1996).
[0103] Further specific embodiments of this aspect of the invention
include primers and primer pairs, which allow the specific
amplification of the polynucleotides of the invention or of any
specific parts thereof, and probes that selectively or specifically
hybridize to nucleic acid molecules of the invention or to any part
thereof Probes may be labeled with a detectable marker, such as,
for example, a radioisotope, fluorescent compound, bioluminescent
compound, a chemiluminescent compound, metal chelator or enzyme.
Such probes and primers can be used to detect the presence of a
STEAP polynucleotide in a sample and as a means for detecting a
cell expressing a STEAP protein. Examples of such probes include
polypeptides comprising all or part of a human STEAP cDNA sequence
shown in FIGS. 1A-B (SEQ ID NO: 1), FIGS. 9A-D (SEQ ID NO: 7) or
FIGS. 10A-E (SEQ ID NO: 9). Examples of primer pairs capable of
specifically amplifying STEAP mRNAs are also described in the
Examples that follow. As will be understood by the skilled artisan,
a great many different primers and probes may be prepared based on
the sequences provided in herein and used effectively to amplify
and/or detect a STEAP mRNA.
[0104] As used herein, a polynucleotide is said to be "isolated"
when it is substantially separated from contaminant polynucleotides
that correspond or are complementary to genes other than the STEAP
gene or that encode polypeptides other than STEAP gene product or
fragments thereof. A skilled artisan can readily employ nucleic
acid isolation procedures to obtain an isolated STEAP
polynucleotide.
[0105] The STEAP polynucleotides of the invention are useful for a
variety of purposes, including but not limited to their use as
probes and primers for the amplification and/or detection of the
STEAP gene(s), mRNA(s), or fragments thereof; as reagents for the
diagnosis and/or prognosis of prostate cancer and other cancers; as
tools for identifying molecules that inhibit calcium entry
specifically into prostate cells; as coding sequences capable of
directing the expression of STEAP polypeptides; as tools for
modulating or inhibiting the expression of the STEAP gene(s) and/or
translation of the STEAP transcript(s); and as therapeutic
agents.
[0106] Molecular and Biochemical Features of the STEAPs
[0107] The invention relates to a novel family of proteins, termed
STEAPs. Four STEAPs are specifically described herein by way of
structural, molecular and biochemical features. As is further
described in the Examples which follow, the STEAPs have been
characterized in a variety of ways. For example, analyses of
nucleotide coding and amino acid sequences were conducted in order
to identify conserved structural elements within the STEAP family.
Extensive RT-PCR and Northern blot analyses of STEAP mRNA
expression were conducted in order to establish the range of normal
and cancerous tissues expressing the various STEAP messages.
Western blot, immunohistochemical and flow cytometric analyses of
STEAP protein expression were conducted to determine protein
expression profiles, cell surface localization and gross molecular
topology of STEAP.
[0108] The prototype member of the STEAP family, STEAP-1, is a
six-transmembrane cell surface protein of 339 amino acids with no
identifiable homology to any known human protein. The cDNA
nucleotide and deduced amino acid sequences of human STEAP-1 are
shown in FIGS. 1A-B. A gross topological schematic of the STEAP-1
protein integrated within the cell membrane is shown in FIG. 1B.
STEAP-1 expression is predominantly prostate-specific in normal
tissues. Specifically, extensive analysis of STEAP-1 nRNA and
protein expression in normal human tissues shows that STEAP-1
protein is predominantly expressed in prostate and, to a far
smaller degree, in bladder. STEAP-1 mRNA is also relatively
prostate specific, with only very low level expression detected in
a few other normal tissues. In cancer, STEAP-1 mRNA and protein is
consistently expressed at high levels in prostate cancer (including
androgen-dependent and androgen-independent tumors) and during all
stages of the disease. STEAP-1 is also expressed in other cancers.
Specifically, STEAP-1 mRNA is expressed at very high levels in
bladder, colon, pancreatic, and ovarian cancer (as well as other
cancers). In addition, cell surface expression of STEAP-1 protein
has been established in prostate, bladder, lung and colon cancers.
Therefore, STEAP-1 has all of the hallmark characteristics of an
excellent diagnostic and therapeutic target for the treatment of
certain cancers, including particularly prostate, colon and bladder
carcinomas.
[0109] A second member of the family, STEAP-2, is a 454 amino acid
protein encoded by a distinct gene and having a predicted molecular
topology similar to that of STEAP-1. The cDNA nucleotide and
deduced amino acid sequences of STEAP-2 are shown in FIG. 9A-D.
Amino acid alignment of the STEAP-1 and STEAP-2 sequences show a
high degree of structural conservation (54.9% identity over a 237
amino acid residue overlap, and the locations of the six putative
transmembrane domains in STEAP-1 and STEAP-2 coincide (FIGS. 11A-B,
11C). Structural homology between these STEAP-1 and STEAP-2 is
highest in the regions spanned by the first putative extracellular
loop to the fifth transmembrane domain. However, some significant
structural differences between STEAP-1 and STEAP-2 are apparent.
For example, STEAP-2 exhibits a 205 a.a. long intracellular
N-terminus (compared to 69 a.a. in STEAP-1) and a short 4 a.a.
intracellular C-terminus (compared to 26 a.a. in STEAP-1). In
addition, both the STEAP-1 and STEAP-2 genes are located on
chromosome 7, but on different arms. These differences could imply
significant differences in function and/or interaction with
intracellular signaling pathways.
[0110] STEAP-2 is expressed only in normal prostate among human
tissues tested (FIGS. 14 and 15) and is also expressed in prostate
cancer (FIG. 15), and thus shows some similarity in expression
profile to STEAP-1. However, STEAP-2 exhibits a different mRNA
expression profile relative to STEAP-1 in prostate cancer samples
(compare FIGS. 3 and 15) and in other non-prostate cancers tested
(compare FIGS. 5 and 16). These differences in the expression
profiles of STEAP-1 and STEAP-2 suggest that they are
differentially regulated.
[0111] STEAP-3 and STEAP-4 appear to be closely related to both
STEAP-1 and STEAP-2 on a structural level, and both appear to be
transmembrane proteins as well. STEAP-3 is more related to STEAP-2
(47.8% identity) than to STEAP-1 (40.9% identity). STEAP-3 and
STEAP-4 show unique expression profiles. STEAP-3, for example,
appears to have an expression pattern which is predominantly
restricted to placenta and, to a smaller degree, expression is seen
in prostate but not in other normal tissues tested. STEAP-4 seems
to be expressed predominantly in liver by RT-PCR analysis. Neither
STEAP-3 nor STEAP-4 appear to be expressed in prostate cancer
xenografts which exhibit high level STEAP-1 and STEAP-2
expression.
[0112] The STEAP proteins exhibit characteristics of proteins
involved in cell signaling pathways. Specifically, STEAP-1 and
STEAP-2, when expressed in PC3 cells, activate phosphorylation of
p38, a protein involved in the MAPK signaling cascade. In addition,
STEAP-2 expression induces tyrosine phosphorylation, and STEAP-1
mediates activation of tyrosine kinase in odorant-treated cells.
These findings support the use of STEAP-related molecules and cells
modified to express STEAP in high throughput assays to identify
molecules capable of altering cellular signaling pathways, leading
to the identification of novel therapeutic agents. In one
embodiment, the assay identifies molecules capable of inhibiting
STEAP function, which molecules are thereby capable of modulating
the progression of cancer or other disease associated with
dysregulated cell growth.
[0113] Three of the four STEAPs described herein map to human
chromosome 7 (STEAP-1, -2 and 3). Interestingly, STEAP-1 maps
within 7p22 (7p22.3), a large region of allelic gain reported for
both primary and recurrent prostate cancers (Visakorpi et al., 1995
Cancer Res. 55: 342, Nupponen et al., 1998 American J. Pathol. 153:
141), suggesting that up-regulation of STEAP-1 in cancer might
include genomic mechanisms. In addition, both STEAP-2 and STEAP-3
locate to chromosome 7q21, suggesting that these two genes arose by
gene duplication.
[0114] Other cell surface molecules that contain six transmembrane
domains include ion channels Dolly and Parcej, 1996 J Bioenerg
Biomembr 28:231) and water channels or aquaporins (Reizer et al.,
1993 Crit Rev Biochem Mol Biol 28:235). Structural studies show
that both types of molecules assemble into tetrameric complexes to
form functional channels (Christie, 1995, Clin Exp Pharmacol
Physiol 22:944, Walz et al., 1997 Nature 387:624, Cheng et al.,
1997 Nature 387:627). Immunohistochemical staining of STEAP-1 in
the prostate gland seems to be concentrated at the cell-cell
boundaries, with less staining detected at the lumenal side. This
may suggest a role for STEAP-1 in tight-junctions, gap-junctions,
cell communication, adhesion or as a transporter protein.
[0115] To test these possibilities, xenopus oocytes (or other
cells) expressing STEAP may be analyzed using voltage-clamp and
patch-clamp experiments to determine if STEAP functions as an
ion-channel. Oocyte cell volume may also be measured to determine
if STEAP exhibits water channel properties. If STEAPs function as
channel or gap-junction proteins, they may serve as excellent
targets for inhibition using, for example, antibodies, small
molecules, and polynucleotides capable of inhibiting expression or
function. The restricted expression pattern in normal tissue, and
the high levels of expression in cancer tissue suggest that
interfering with STEAP function may selectively kill cancer
cells.
[0116] Since the STEAP gene family is predominantly expressed in
epithelial tissue, it seems possible that the STEAP proteins
function as ion channels, transport proteins or gap-junction
proteins in epithelial cell function. Ion channels have been
implicated in proliferation and invasiveness of prostate cancer
cells (Lalani et al., 1997, Cancer Metastasis Rev 16:29). Both rat
and human prostate cancer cells contain sub-population of cells
with higher and lower expression levels of sodium channels. Higher
levels of sodium channel expression correlate with more aggressive
invasiveness in vitro (Smith et al., 1998, FEBS Lett. 423:19).
Similarly, it has been shown that a specific blockade of sodium
channels inhibits the invasiveness of PC-3 cells in vitro (Laniado
et al., 1997, Am. J. Pathol. 150:1213), while specific inhibition
of potassium channels in LNCaP cells inhibited cell proliferation
(Skryma et al., 1997, Prostate 33:112). These reports suggest a
role for ion channels in prostate cancer and also demonstrate that
small molecules that inhibit ion channel function may interfere
with prostate cancer proliferation.
[0117] Isolation of STEAP-Encoding Nucleic Acid Molecules
[0118] The STEAP cDNA sequences described herein enable the
isolation of other polynucleotides encoding STEAP gene product(s),
as well as the isolation of polynucleotides encoding STEAP gene
product homologues, alternatively spliced isoforms, allelic
variants, and mutant forms of the STEAP gene product. Various
molecular cloning methods that can be employed to isolate full
length cDNAs encoding a STEAP gene are well known (See, for
example, Sambrook, J. et al. Molecular Cloning: A Laboratory
Manual, 2d edition., Cold Spring Harbor Press, New York, 1989;
Current Protocols in Molecular Biology. Ausubel et al., Eds., Wiley
and Sons, 995). For example, lambda phage cloning methodologies may
be conveniently employed, using commercially available cloning
systems (e.g., Lambda ZAP Express, Stratagene). Phage clones
containing STEAP gene cDNAs may be identified by probing with
labeled STEAP cDNA or a fragment thereof. For example, in one
embodiment, a STEAP cDNA or a portion thereof can be synthesized
and used as a probe to retrieve overlapping and full length cDNAs
corresponding to a STEAP gene. The STEAP gene itself may be
isolated by screening genomic DNA libraries, bacterial artificial
chromosome libraries (BACs), yeast artificial chromosome libraries
(YACs), and the like, with STEAP DNA probes or primers.
[0119] Recombinant DNA Molecules and Host-Vector Systems
[0120] The invention also provides recombinant DNA or RNA molecules
containing a STEAP polynucleotide, including but not limited to
phages, plasmids, phagemids, cosmids, YACs, BACs, as well as
various viral and non-viral vectors well known in the art, and
cells transformed or transfected with such recombinant DNA or RNA
molecules. As used herein, a recombinant DNA or RNA molecule is a
DNA or RNA molecule that has been subjected to molecular
manipulation in vitro. Methods for generating such molecules are
well known (see, for example, Sambrook et al, 1989, supra).
[0121] The invention further provides a host-vector system
comprising a recombinant DNA molecule containing a STEAP
polynucleotide within a suitable prokaryotic or eukaryotic host
cell. Examples of suitable eukaryotic host cells include a yeast
cell, a plant cell, or an animal cell, such as a mammalian cell or
an insect cell (e.g., a baculovirus-infectible cell such as an Sf9
cell). Examples of suitable mammalian cells include various
prostate cancer cell lines such LNCaP, PC-3, DU145, LAPC-4, TsuPr1,
other transfectable or transducible prostate cancer cell lines, as
well as a number of mammalian cells routinely used for the
expression of recombinant proteins (e.g., COS, CHO, 293, 293T
cells). More particularly, a polynucleotide comprising the coding
sequence of a STEAP may be used to generate STEAP proteins or
fragments thereof using any number of host vector systems routinely
used and widely known in the art.
[0122] A wide range of host vector systems suitable for the
expression of STEAP proteins or fragments thereof are available,
see for example, Sambrook et al., 1989, supra; Current Protocols in
Molecular Biology, 1995, supra). Preferred vectors for mammalian
expression include but are not limited to pcDNA 3.1 myc-His-tag
(Invitrogen) and the retroviral vector pSR.alpha.tkneo (Muller et
al., 1991, MCB 11:1785). Using these expression vectors, STEAP may
be preferably expressed in several prostate cancer and non-prostate
cell lines, including for example 293, 293T, rat-1, 3T3, PC-3,
LNCaP and TsuPr1. The host vector systems of the invention are
useful for the production of a STEAP protein or fragment thereof.
Such host-vector systems may be employed to study the functional
properties of STEAP and STEAP mutations.
[0123] Proteins encoded by the STEAP genes, or by fragments
thereof, will have a variety of uses, including but not limited to
generating antibodies and in methods for identifying ligands and
other agents and cellular constituents that bind to a STEAP gene
product. Antibodies raised against a STEAP protein or fragment
thereof may be useful in diagnostic and prognostic assays, imaging
methodologies (including, particularly, cancer imaging), and
therapeutic methods in the management of human cancers
characterized by expression of a STEAP protein, including but not
limited to cancer of the prostate. Various immunological assays
useful for the detection of STEAP proteins are contemplated,
including but not limited to various types of radioimmunoassays,
enzyme-linked immunosorbent assays (ELISA), enzyme-linked
immunofluorescent assays (ELIFA), immunocytochemical methods, and
the like. Such antibodies may be labeled and used as immunological
imaging reagents capable of detecting prostate cells (e.g., in
radioscintigraphic imaging methods). STEAP proteins may also be
particularly useful in generating cancer vaccines, as further
described below.
[0124] STEAP Proteins
[0125] Another aspect of the present invention provides various
STEAP proteins and polypeptide fragments thereof. As used herein, a
STEAP protein refers to a protein that has or includes the amino
acid sequence of human STEAP-1 as provided in FIG. 1A-B, human
STEAP-2 as provided in FIGS. 9A-D, human STEAP-3 as provided in
FIGS. 10A-E, the amino acid sequence of other mammalian STEAP
homologs (e.g., STEAP-4) and variants, as well as allelic variants
and conservative substitution mutants of these proteins that have
STEAP biological activity, to the extent that such variants and
homologs can be isolated/generated and characterized without undue
experimentation following the methods outlined below. Fusion
proteins that combine parts of different STEAP proteins or
fragments thereof, as well as fusion proteins of a STEAP protein
and a heterologous polypeptide, are also included. Such STEAP
proteins will be collectively referred to as the STEAP proteins,
the proteins of the invention, or STEAP. As used herein, the term
"STEAP polypeptide" refers to a polypeptide fragment or a STEAP
protein of at least 10 amino acids, preferably at least 15 amino
acids.
[0126] A specific embodiment of a STEAP protein comprises a
polypeptide having the amino acid sequence of human STEAP-1 as
shown in FIG. 1A-B. Another embodiment of a STEAP protein comprises
a polypeptide containing the STEAP-2 amino acid sequence as shown
in FIGS. 9A-D. Another embodiment comprises a polypeptide
containing the STEAP-3 amino acid sequence of shown in FIGS. 10A-E.
Yet another embodiment comprises a polypeptide containing the
partial STEAP-4 amino acid sequence of shown in FIGS. 11A-B.
[0127] In general, naturally occurring allelic variants of human
STEAP will share a high degree of structural identity and homology
(e.g., 90% or more identity). Typically, allelic variants of the
STEAP proteins will contain conservative amino acid substitutions
within the STEAP sequences described herein or will contain a
substitution of an amino acid from a corresponding position in a
STEAP homologue. One class of STEAP allelic variants will be
proteins that share a high degree of homology with at least a small
region of a particular STEAP amino acid sequence, but will further
contain a radical departure from the sequence, such as a
non-conservative substitution, truncation insertion or frame
shift.
[0128] Conservative amino acid substitutions can frequently be made
in a protein without altering either the conformation or the
function of the protein. Such changes include substituting any of
isoleucine (I), valine (V), and leucine (L) for any other of these
hydrophobic amino acids; aspartic acid (D) for glutamic acid (E)
and vice versa; glutamine (Q) for asparagine (N) and vice versa;
and serine (S) for threonine (t) and vice versa. Other
substitutions can also be considered conservative, depending on the
environment of the particular amino acid and its role in the
three-dimensional structure of the protein. For example, glycine
(G) and alanine (A) can frequently b interchangeable, as can
alanine (A) and valine (V). Methionine (M), which is relatively
hydrophobic, can frequently be interchanged with leucine and
isoleucine, and sometimes with valine. Lysine (K) and arginine (R)
are frequently interchangeable in locations in which the
significant feature of the amino acid residue is its charge and the
differing pK's of these two amino acid residues are not
significant. Still other changes can be considered "conservative"
in particular environments.
[0129] STEAP proteins, including variants, comprise at least one
epitope in common with a STEAP protein having an amino acid
sequence shown in FIGS. 11A-B, such that an antibody that
specifically binds to a STEAP protein or variant will also
specifically bind to the STEAP protein having an amino acid
sequence shown in FIGS. 11A-B. One class of STEAP protein variants
shares 90% or more identity with an amino acid sequence of FIGS.
11A-B. A more specific class of STEAP protein variants comprises an
extracellular protein SCP motif as described above. Preferred STEAP
protein variants are capable of exhibiting one or more of the
defensin functions described herein, including, for example, the
ability to induce tumor death or to chemoattract and/or induce
migration of cells.
[0130] STEAP proteins may be embodied in many forms, preferably in
isolated form. As used herein, a protein is said to be "isolated"
when physical, mechanical or chemical methods are employed to
remove the STEAP protein from cellular constituents that are
normally associated with the protein. A skilled artisan can readily
employ standard purification methods to obtain an isolated STEAP
protein. A purified STEAP protein molecule will be substantially
free of other proteins or molecules that impair the binding of
STEAP to antibody or other ligand. The nature and degree of
isolation and purification will depend on the intended use.
Embodiments of a STEAP protein include a purified STEAP protein and
a functional, soluble STEAP protein. In one form, such functional,
soluble STEAP proteins or fragments thereof retain the ability to
bind antibody or other ligand.
[0131] The invention also provides STEAP polypeptides comprising
biologically active fragments of the STEAP amino acid sequence,
such as a polypeptide corresponding to part of the amino acid
sequences for STEAP-1 as shown in FIGS. 1A-B, STEAP-2 as shown in
FIGS. 9A-D, STEAP-3 as shown in FIGS. 10A-E, or STEAP-4 as shown in
FIGS. 41A-B. Such polypeptides of the invention exhibit properties
of a STEAP protein, such as the ability to elicit the generation of
antibodies which specifically bind an epitope associated with a
STEAP protein. Polypeptides comprising amino acid sequences which
are unique to a particular STEAP protein (relative to other STEAP
proteins) may be used to generate antibodies which will
specifically react with that particular STEAP protein. For example,
referring to the amino acid alignment of the STEAP structures shown
in FIGS. 11A-E, the skilled artisan will readily appreciate that
each molecule contains stretches of sequence unique to its
structure. These unique stretches can be used to generate
antibodies specific to a particular STEAP. Similarly, regions of
conserved sequence may be used to generate antibodies that may bind
to multiple STEAPs.
[0132] Embodiments of the invention disclosed herein include a wide
variety of art accepted variants of STEAP proteins such as
polypeptides having amino acid insertions, deletions and
substitutions. STEAP variants can be made using methods known in
the art such as 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 STEAP
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. 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
isosteric amino acid can be used.
[0133] As discussed above, embodiments of the claimed invention
include polypeptides containing less than the full amino acid
sequence of a STEAP protein shown in FIGS. 1A-B. For example,
representative embodiments of the invention disclosed herein
include polypeptides consisting of about amino acid 1 to about
amino acid 10 of a STEAP protein shown in FIGS. 11A-B, polypeptides
consisting of about amino acid 20 to about amino acid 30 of a STEAP
protein shown in FIGS. 11A-B, polypeptides consisting of about
amino acid 30 to about amino acid 40 of a STEAP protein shown in
FIGS. 11A-B, polypeptides consisting of about amino acid 40 to
about amino acid 50 of a STEAP protein shown in FIGS. 11A-B,
polypeptides consisting of about amino acid 50 to about amino acid
60 of a STEAP protein shown in FIGS. 11A-B, polypeptides consisting
of about amino acid 60 to about amino acid 70 of a STEAP protein
shown in FIGS. 11A-B, polypeptides consisting of about amino acid
70 to about amino acid 80 of a STEAP protein shown in FIGS. 11A-B,
polypeptides consisting of about amino acid 80 to about amino acid
90 of a STEAP protein shown in FIGS. 11A-B and polypeptides
consisting of about amino acid 90 to about amino acid 100 of a
STEAP protein shown in FIGS. 11A-B, etc. Following this scheme,
polypeptides consisting of portions of the amino acid sequence of
amino acids 100-339 of a STEAP-1 protein shown in FIGS. 11A-B, or
amino acids 100-454 of a STEAP-2 protein shown in FIGS. 11A-B, or
amino acids 100-459 of a STEAP-3 protein shown in FIGS. 11A-B, or
amino acids 100-133 of a STEAP-4 protein shown in FIGS. 11A-B, are
typical embodiments of the invention. Polypeptides consisting of
larger portions of the STEAP protein are also contemplated. For
example polypeptides consisting of about amino acid 1 (or 20 or 30
or 40 etc.) to about amino acid 20, (or 30, or 40 or 50 etc.) of a
STEAP protein shown in FIGS. 11A-B may be generated by a variety of
techniques well known in the art.
[0134] Additional illustrative embodiments of the invention
disclosed herein include STEAP polypeptides containing the amino
acid residues of one or more of the biological motifs contained
within a STEAP polypeptide sequence as shown in FIGS. 11A-B. STEAP
polypeptides containing one or more of these motifs or other select
regions of interest described herein will typically include an
additional 5 to 25 or more amino acid residues of adjacent STEAP
protein sequence on one or both sides of the selected motif(s). In
one embodiment, typical polypeptides of the invention can contain
one or more of the regions of STEAP that exhibit homology to one or
more other STEAP proteins. In another embodiment, typical
polypeptides of the invention can contain one or more immunogenic
portions of a STEAP protein. One example of an immunogenic portion
of a STEAP protein is amino acid residues 14 through 28 of the
STEAP-1 amino acid sequence as shown in FIGS. 1A-B
(WKMKPRRNLEEDDYL; SEQ ID NO: 22). In another embodiment, typical
polypeptides of the invention can contain one or more predicted
HLA-A2 binding peptides such as amino acids 165-173 of STEAP-1,
amino acids 86-94 of STEAP-1, amino acids 262-270 of STEAP-1, amino
acids 302-310 of STEAP-1, amino acids 158-166 of STEAP-1, amino
acids 227-235 of STEAP-2, amino acids 402-410 of STEAP-2, amino
acids 307-315 of STEAP-2, amino acids 306-314 of STEAP-2,-and amino
acids 100-108 of STEAP-2. In another embodiment, typical
polypeptides of the invention consist of all or part of a fragment
of STEAP-2, such as amino acids 1-245, 2-204, 121-454, 153-165,
182-454, 183-387, 276-453, 345-358, or 419-454 of the STEAP-2
protein shown in FIG. 8. Related embodiments of these inventions
include polypeptides containing combinations of the different
motifs discussed above with preferable embodiments being those that
contain no insertions, deletions or substitutions either within the
motifs or the intervening sequences of these polypeptides.
[0135] STEAP polypeptides can be generated using standard peptide
synthesis technology or using chemical cleavage methods well known
in the art based on the amino acid sequences of the human STEAP
proteins disclosed herein. Alternatively, recombinant methods can
be used to generate nucleic acid molecules that encode a
polypeptide fragment of a STEAP protein. In this regard, the
STEAP-encoding nucleic acid molecules described herein provide
means for generating defined fragments of STEAP proteins. STEAP
polypeptides are particularly useful in generating and
characterizing domain specific antibodies (e.g., antibodies
recognizing an extracellular or intracellular epitope of a STEAP
protein), in identifying agents or cellular factors that bind to
STEAP or a particular structural domain thereof, and in various
therapeutic contexts, including but not limited to cancer vaccines.
STEAP polypeptides containing particularly interesting structures
can be predicted and/or identified using various analytical
techniques well known in the art, including, for example, the
methods of Chou-Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg,
Karplus-Schultz or Jameson-Wolf analysis, or on the basis of
immunogenicity. Fragments containing such structures are
particularly useful in generating subunit specific anti-STEAP
antibodies or in identifying cellular factors that bind to
STEAP.
[0136] In a specific embodiment described in the examples that
follow, a secreted form of STEAP may be conveniently expressed in
293T cells transfected with a CMV-driven expression vector encoding
STEAP with a C-terminal 6.times.His and MYC tag (pcDNA3.1/mycHIS,
Invitrogen). The secreted HIS-tagged STEAP in the culture media may
be purified using a nickel column and standard techniques.
Alternatively, an AP-tag system may be used. Various constructs for
expression of STEAP are described in the examples below.
[0137] Modifications of STEAP such as covalent modifications are
included within the scope of this invention. One type of covalent
modification includes reacting targeted amino acid residues of an
STEAP polypeptide with an organic derivatizing agent that is
capable of reacting with selected side chains or the N- or
C-terminal residues of the STEAP. Another type of covalent
modification of the STEAP 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 STEAP (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 STEAP. 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. Another type of covalent modification of STEAP
comprises linking the STEAP 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.
[0138] The STEAP of the present invention may also be modified in a
way to form a chimeric molecule comprising STEAP fused to another,
heterologous polypeptide or amino acid sequence. In one embodiment,
such a chimeric molecule comprises a fusion of the STEAP with a
polyhistidine epitope tag, which provides an epitope to which
immobilized nickel can selectively bind. The epitope tag is
generally placed at the amino- or carboxyl-terminus of the STEAP.
In an alternative embodiment, the chimeric molecule may comprise a
fusion of the STEAP 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 an STEAP 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.
[0139] STEAP Antibodies
[0140] Another aspect of the invention provides antibodies that
bind to STEAP proteins and polypeptides. The most preferred
antibodies will selectively bind to a STEAP protein and will not
bind (or will bind weakly) to non-STEAP proteins and polypeptides.
Anti-STEAP antibodies that are particularly contemplated include
monoclonal and polyclonal antibodies as well as fragments
containing the antigen-binding domain and/or one or more
complementarity determining regions of these antibodies. As used
herein, an antibody fragment is defined as at least a portion of
the variable region of the immunoglobulin molecule that binds to
its target, i.e., the antigen binding region.
[0141] For some applications, it may be desirable to generate
antibodies which specifically react with a particular STEAP protein
and/or an epitope within a particular structural domain. For
example, preferred antibodies useful for cancer therapy and
diagnostic imaging purposes are those which react with an epitope
in an extracellular region of the STEAP protein as expressed in
cancer cells. Such antibodies may be generated by using the STEAP
proteins described herein, or using peptides derived from predicted
extracellular domains thereof, as an immunogen. In this regard,
with reference to the STEAP-1 protein topological schematic shown
in FIG. 1B, regions in the extracellular loops between the
indicated transmembrane domains may be selected as used to design
appropriate immunogens for raising extracellular-specific
antibodies.
[0142] STEAP antibodies of the invention may be particularly useful
in prostate cancer therapeutic strategies, diagnostic and
prognostic assays, and imaging methodologies. Similarly, such
antibodies may be useful in the treatment, diagnosis, and/or
prognosis of other cancers, to the extent STEAP is also expressed
or overexpressed in other types of cancer. The invention provides
various immunological assays useful for the detection and
quantification of STEAP and mutant STEAP proteins and polypeptides.
Such assays generally comprise one or more STEAP antibodies capable
of recognizing and binding a STEAP or mutant STEAP protein, as
appropriate, and may be performed within various immunological
assay formats well known in the art, including but not limited to
various types of radioimmunoassays, enzyme-linked immunosorbent
assays (ELI SA), enzyme-linked immunofluorescent assays (ELIFA),
and the like. In addition, immunological imaging methods capable of
detecting prostate cancer are also provided by the invention,
including but limited to radioscintigraphic imaging methods using
labeled STEAP antibodies. Such assays may be used clinically in the
detection, monitoring, and prognosis of prostate cancer,
particularly advanced prostate cancer.
[0143] STEAP antibodies may also be used in methods for purifying
STEAP and mutant STEAP proteins and polypeptides and for isolating
STEAP homologues and related molecules. For example, in one
embodiment, the method of purifying a STEAP protein comprises
incubating a STEAP antibody, which has been coupled to a solid
matrix, with a lysate or other solution containing STEAP under
conditions which permit the STEAP antibody to bind to STEAP;
washing the solid matrix to eliminate impurities; and eluting the
STEAP from the coupled antibody. Other uses of the STEAP antibodies
of the invention include generating anti-diotypic antibodies that
mimic the STEAP protein.
[0144] STEAP antibodies may also be used therapeutically by, for
example, modulating or inhibiting the biological activity of a
STEAP protein or targeting and destroying cancer cells expressing a
STEAP protein. Antibody therapy of prostate and other cancers is
mote specifically described in a separate subsection below.
[0145] Various methods for the preparation of antibodies are well
known in the art. For example, antibodies may be prepared by
immunizing a suitable mammalian host using a STEAP protein,
peptide, or fragment, in isolated or immunoconjugated form
(Antibodies: A Laboratory Manual, CSH Press, Eds., Harlow, and Lane
(1988); Harlow, Antibodies, Cold Spring Harbor Press, NY (1989)).
Examples of protein immunogens include recombinant STEAP (expressed
in a baculovirus system, mammalian system, etc.), STEAP
extracellular domain or extracellular loops of STEAP protein
conjugated to one or more antibody constant regions, AP-tagged
STEAP, etc. In addition, fusion proteins of STEAP may also be used,
such as a fusion of STEAP with GST, maltose-binding protein (MBP),
green fluorescent protein (GFP), HisMax-TOPO or MycHis (see
Examples below).
[0146] In a particular embodiment, a GST fusion protein comprising
all or most of an open reading frame amino acid sequence as shown
in FIGS. 11A-B may be produced and used as an immunogen to generate
appropriate antibodies. Cells expressing or overexpressing STEAP
may also be used for immunizations. Similarly, any cell engineered
to express STEAP may be used. Such strategies may result in the
production of monoclonal antibodies with enhanced capacities for
recognizing endogenous STEAP. Another useful immunogen comprises
STEAP peptides linked to the plasma membrane of sheep red blood
cells.
[0147] The amino acid sequences of STEAP proteins as shown in FIGS.
11A-B may be used to select specific regions of a STEAP protein for
generating antibodies. For example, hydrophobicity and
hydrophilicity analyses of the STEAP amino acid sequence may be
used to identify hydrophilic regions in the STEAP structure.
Regions of the STEAP protein that show immunogenic structure, as
well as other regions and domains, can readily be identified using
various other methods known in the art, such as Chou-Fasman,
Garnier Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or
Jameson-Wolf analysis. Peptides of STEAP predicted to bind HLA-A2
may be selected for the generation of antibodies or used to
generate a CTL response. Such predicted HLA-A2 binding peptides
include, but are not limited to, amino acids 165-173 of STEAP-1,
amino acids 86-94 of STEAP-1, amino acids 262-270 of STEAP-1, amino
acids 302-310 of STEAP-1, amino acids 158-166 of STEAP-1, amino
acids 227-235 of STEAP-2, amino acids 402-410 of STEAP-2, amino
acids 307-315 of STEAP-2, amino acids 306-314 of STEAP-2, and amino
acids 100-108 of STEAP-2. As discussed in the examples below,
immunogenicity has been demonstrated with STEAP, which was used to
generate polyclonal and monoclonal antibodies using rabbits and
mice, respectively. This B cell response (antibody production) is
the result of an initial T cell response elicited by the
immunogenic portions of STEAP.
[0148] Methods for preparing a protein or polypeptide for use as an
immunogen and for preparing immunogenic conjugates of a protein
with a carrier such as BSA, KLH, or other carrier proteins are well
known in the art. In some circumstances, direct conjugation using,
for example, carbodiimide reagents may be used; in other instances
linking reagents such as those supplied by Pierce Chemical Co.,
Rockford, Ill., may be effective. Administration of a STEAP
immunogen is conducted generally by injection over a suitable
period and with use of a suitable adjuvant, as is generally
understood in the art. During the immunization schedule, titers of
antibodies can be taken to determine adequacy of antibody
formation.
[0149] STEAP monoclonal antibodies are preferred and may be
produced by various means well known in the art. For example,
immortalized cell lines which secrete a desired monoclonal antibody
may be prepared using the standard hybridoma technology of Kohler
and Milstein or modifications which immortalize producing B cells,
a is generally known. The immortalized cell lines secreting the
desired antibodies are screened by immunoassay in which the antigen
is the STEAP protein or STEAP fragment. When the appropriate
immortalized cell culture secreting the desired antibody is
identified, the cells may be expanded and antibodies produced
either from in vitro cultures or from ascites fluid.
[0150] The antibodies or fragments may also be produced, using
current technology, by recombinant means. Regions that bind
specifically to the desired regions of the STEAP protein can also
be produced in the context of chimeric or CDR grafted antibodies of
multiple species origin. Humanized or human STEAP antibodies may
also be produced and are preferred for use in therapeutic contexts.
Methods for humanizing murine and other non-human antibodies by
substituting one or more of the non-human antibody CDRs for
corresponding human antibody sequences are well known (see for
example, Jones et al., 1986, Nature 321: 522-525; Riechmann et al.,
1988, Nature 332: 323-327; Verhoeyen et al., 1988, Science
239:1534-1536). See also, Carter et al., 1993, Proc. Nat'l Acad.
Sci. USA 89: 4285 and Sims et al., 1993, J. Immunol. 151: 2296.
Methods for producing fully human monoclonal antibodies include
phage display and transgenic animal technologies (for review, see
Vaughan et al., 1998, Nature Biotechnology 16: 535-539).
[0151] Fully human STEAP monoclonal antibodies may be generated
using cloning technologies employing large human Ig gene
combinatorial libraries (i.e., phage display) (Griffiths and
Hoogenboom, Building an in vitro immune system: human antibodies
from phage display libraries. In: Protein Engineering of Antibody
Molecules for Prophylactic and Therapeutic Applications in Man.
Clark, M. (Ed.), Nottingham Academic, pp 45-64 (1993); Burton and
Barbas, Human Antibodies from combinatorial libraries. Id., pp
65-82). Fully human STEAP monoclonal antibodies may also be
produced using transgenic mice engineered to contain human
immunoglobulin gene loci as described in U.S. Pat. No. 6,150,584
and in PCT Patent Application WO98/24893, published Dec. 3, 1997
(see also, Jakobovits, 1998, Exp. Opin. Invest. Drugs 7(4):
607-614). This method avoids the in vitro manipulation required
with phage display technology and efficiently produces high
affinity authentic human antibodies.
[0152] Reactivity of STEAP antibodies with a STEAP protein may be
established by a number of well known means, including western
blot, immunoprecipitation, ELISA, and FACS analyses using, as
appropriate, STEAP proteins, peptides, STEAP expressing cells or
extracts thereof.
[0153] A STEAP antibody or fragment thereof of the invention may be
labeled with a detectable marker or conjugated to a second
molecule, such as a cytotoxin or other therapeutic agent, and used
for targeting the second molecule to a STEAP positive cell
(Vitetta, E. S. et al., 1993, Immunotoxin therapy, in DeVita, Jr.,
V. T. et al., eds., Cancer: Principles and Practice of Oncology,
4th ed., J. B. Lippincott Co., Philadelphia, 2624-2636). Examples
of cytotoxic agents include, but are not limited to ricin, ricin
A-chain, doxorubicin, maytansinoids, daunorubicin, taxol, ethidium
bromide, mitomycin, etoposide, tenoposide, vincristine,
vinblastine, colchicine, dihydroxy anthracin dione, actinomycin,
diphtheria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A
chain, modeccin A chain, alpha-sarcin, gelonin, mitogellin,
retstrictocin, phenomycin, enomycin, curicin, crotin,
calicheamicin, sapaonaria officinalis inhibitor, and glucocorticoid
and other chemotherapeutic agents, as well as radioisotopes such as
.sup.212Bi, .sup.131I, .sup.131In, .sup.90Y, and .sup.186Re.
Suitable detectable markers include, but are not limited to, a
radioisotope, a fluorescent compound, a bioluminescent compound,
chemiluminescent compound, a metal chelator or an enzyme.
Antibodies may also be conjugated to an anti-cancer pro-drug
activating enzyme capable of converting the pro-drug to its active
form. See, for example, U.S. Pat. No. 4,975,287.
[0154] Further, bi-specific antibodies specific for two or more
STEAP epitopes may be generated using methods generally known in
the art. Further, antibody effector functions may be modified to
enhance the therapeutic effect of STEAP antibodies on cancer cells.
For example, cysteine residues may be engineered into the Fc
region, permitting the formation of interchain disulfide bonds and
the generation of homodimers which may have enhanced capacities for
internalization, ADCC and/or complement mediated cell killing (see,
for example, Caron et al., 1992, J. Exp. Med. 176: 1191-1195;
Shopes, 1992, J. Immunol. 148: 2918-2922). Homodimeric antibodies
may also be generated by cross-linking techniques known in the art
(e.g., Wolff et al., Cancer Res. 53: 2560-2565).
[0155] STEAP Transgenic Animals
[0156] Nucleic acids that encode STEAP or its modified forms can
also be used to generate either transgenic animals or "knock out"
animals which, in turn, are useful in the development and screening
of therapeutically useful reagents. A transgenic animal (e.g., a
mouse or rat) is an animal having cells that contain a transgene,
which transgene was introduced into the animal or an ancestor of
the animal at a prenatal, e.g., an embryonic stage. A transgene is
a DNA that is integrated into the genome of a cell from which a
transgenic animal develops. In one embodiment, cDNA encoding STEAP
can be used to clone genomic DNA encoding STEAP in accordance with
established techniques and the genomic sequences used to generate
transgenic animals that contain cells that express DNA encoding
STEAP.
[0157] Methods for generating transgenic animals, particularly
animals such as mice or rats, have become conventional in the art
and are described, for example, in U.S. Pat. Nos. 4,736,866 and
4,870,009. Typically, particular cells would be targeted for STEAP
transgene incorporation with tissue-specific enhancers. Transgenic
animals that include a copy of a transgene encoding STEAP
introduced into the germ line of the animal at an embryonic stage
can be used to examine the effect of increased expression of DNA
encoding STEAP. Such animals can be used as tester animals for
reagents thought to confer protection from, for example,
pathological conditions associated with its overexpression. In
accordance with this facet of the invention, an animal is treated
with the reagent and a reduced incidence of the pathological
condition, compared to untreated animals beating the transgene,
would indicate a potential therapeutic intervention for the
pathological condition.
[0158] Alternatively, non-human homologues of STEAP can be used to
construct a STEAP "knock out" animal that has a defective or
altered gene encoding STEAP as a result of homologous recombination
between the endogenous gene encoding STEAP and altered genomic DNA
encoding STEAP introduced into an embryonic cell of the animal. For
example, cDNA encoding STEAP can be used to clone genomic DNA
encoding STEAP in accordance with established techniques. A portion
of the genomic DNA encoding STEAP can be deleted or replaced with
another gene, such as a gene encoding a selectable marker that can
be used to monitor integration.
[0159] 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, 1987, Cell 51:503 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., 1992, Cell 69:915). 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).
[0160] 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 STEAP
polypeptide.
[0161] Monitoring the Status of STEAP and its Products
[0162] Assays that evaluate the status of a STEAP gene and STEAP
gene products in an individual may provide information on the
growth or oncogenic potential of a biological sample from this
individual. For example, because STEAP mRNA is so highly expressed
in prostate, and not in most normal tissue, and because its
expression is associated with certain cancers, assays that evaluate
the relative levels of STEAP mRNA transcripts or proteins in a
biological sample may be used to diagnose a disease associated with
STEAP dysregulation, such as cancer or benign prostatic hyperplasia
(BPH), and may provide prognostic information useful in defining
appropriate therapeutic options. Similarly, assays that evaluate
the integrity STEAP nucleotide and amino acid sequences in a
biological sample, may also be used in this context.
[0163] The finding that STEAP mRNA is expressed in prostate and
other cancers, and not in most normal tissue, provides evidence
that this gene is associated with dysregulated cell growth and
therefore identifies this gene and its products as targets that the
skilled artisan can use to evaluate biological samples from
individuals suspected of having a disease associated with STEAP
dysregulation. In another example, because the expression of STEAP
is normally restricted to prostate, one can also evaluate
biological samples taken from other tissues to detect STEAP
expression as an indication of metastasis. For example, as shown in
FIGS. 31A-F, antibodies directed to STEAP-1 provide a superior
marker for detection of metastases, as compared to the conventional
prostate cancer marker, PSA. Such a marker can be useful both in
evaluation tissue biopsies and as part of in vivo imaging
strategies. In this context, the evaluation of the expression
status of STEAP gene and its products can be used to gain
information on the disease potential of a tissue sample. The terms
"expression status" in this context is used to broadly refer to the
variety of factors involved in the expression, function and
regulation of a gene and its products such as the level of mRNA
expression, the integrity of the expressed gene products (such as
the nucleic and amino acid sequences) and transcriptional and
translational modifications to these molecules.
[0164] The expression status of STEAP may provide information
useful for predicting susceptibility to particular disease stages,
progression, and/or tumor aggressiveness. The invention provides
methods and assays for determining STEAP expression status and
diagnosing cancers that express STEAP, such as cancers of the
prostate. STEAP expression status in patient samples may be
analyzed by a number of means well known in the art, including
without limitation, immunohistochemical analysis, in situ
hybridization, RT-PCR analysis on laser capture micro-dissected
samples, western blot analysis of clinical samples and cell lines,
and tissue array analysis. Typical protocols for evaluating the
expression status of the STEAP gene and gene products can be found,
for example in Current Protocols In Molecular Biology, Units 2
[Northern Blotting], 4 [Southern Blotting], 15 [Immunoblotting] and
18 [PCR Analysis], Frederick M. Ausubul et al. eds., 1995.
[0165] In one aspect, the invention provides methods for monitoring
ST AP gene products by determining the status of STEAP gene
products expressed by cells in a test tissue sample from an
individual suspected of having a disease associated with
dysregulated cell growth (such as hyperplasia or cancer) and then
comparing the status so determined to the status of STEAP gene
products in a corresponding normal sample, the presence of aberrant
or altered status of STEAP gene products in the test sample
relative to the normal sample providing an indication of the
presence of dysregulated cell growth within the cells of the
individual.
[0166] The invention additionally provides methods of examining a
biological sample for evidence of dysregulated cellular growth. In
one embodiment, the method comprises comparing the status of STEAP
in the biological sample to the status of STEAP in a corresponding
normal sample, wherein alterations in the status of STEAP in the
biological sample are associated with dysregulated cellular growth.
The status of STEAP in the biological sample can be evaluated by,
for example, examining levels of STEAP mRNA expression or levels of
STEAP protein expression. In one embodiment, an alteration in the
status of STEAP is identified by the presence of STEAP expressing
cells in a biological sample from a tissue in which STEAP
expressing cells are normally absent.
[0167] In another aspect, the invention provides assays useful in
determining the presence of cancer in an individual, comprising
detecting a significant increase in STEAP MRNA or protein
expression in a test cell or tissue sample relative to expression
levels in the corresponding normal cell or tissue. The presence of
STEAP mRNA may, for example, be evaluated in tissue samples
including but not limited to colon, lung, prostate, pancreas,
bladder, breast, ovary, cervix, testis, head and neck, brain,
stomach, bone, etc. The presence of significant STEAP expression in
any of these tissues may be useful to indicate the emergence,
presence and/or severity of these cancers or a metastasis of cancer
originating in another tissue, since the corresponding normal
tissues do not express STEAP mRNA or express it at lower
levels.
[0168] In a related embodiment, STEAP expression status may be
determined at the protein level rather than at the nucleic acid
level. For example, such a method or assay would comprise
determining the level of STEAP protein expressed by cells in a test
tissue sample and comparing the level so determined to the level of
STEAP expressed in a corresponding normal sample. In one
embodiment, the presence of STEAP protein is evaluated, for
example, using immunohistochemical methods. STEAP antibodies or
binding partners capable of detecting STEAP protein expression may
be used in a variety of assay formats well known in the art for
this purpose. As shown in the accompanying examples, STEAP
immunoreactivity is associated with prostate, bladder and lung
cancer, as well as BPH and prostate cancer metastases.
[0169] In other related embodiments, one can evaluate the integrity
STEAP nucleotide and amino acid sequences in a biological sample in
order to identify perturbations in the structure of these molecules
such as insertions, deletions, substitutions and the like. Such
embodiments are useful because perturbations in the nucleotide and
amino acid sequences are observed in a large number of proteins
associated with a growth dysregulated phenotype (see e.g. Marrogi
et al., J. Cutan. Pathol. 26(8): 369-378 (1999)). In this context,
a wide variety of assays for observing perturbations in nucleotide
and amino acid sequences are well known in the art. For example,
the size and structure of nucleic acid or amino acid sequences of
STEAP gene products may be observed by the northern, Southern,
western, PCR and DNA sequencing protocols discussed herein. In
addition, other methods for observing perturbations in nucleotide
and amino acid sequences such as single strand conformation
polymorphism analysis are well known in the art (see e.g. U.S. Pat.
Nos. 5,382,510 and 5,952,170).
[0170] In another embodiment, one can examine the methylation
status of the STEAP gene in a biological sample. Aberrant
demethylation and/or hypermethylation of CpG islands in gene 5'
regulatory regions frequently occurs in immortalized and
transformed cells and can result in altered expression of various
genes. For example, promoter hypermethylation of the pi-class
glutathione S-transferase (a protein expressed in normal prostate
but not expressed in >90% of prostate carcinomas) appears to
permanently silence transcription of this gene and is the most
frequently detected genomic alteration in prostate carcinomas (De
Marzo et al., 1999, Am. J. Pathol. 155(6): 1985-1992). In addition,
this alteration is present in at least 70% of cases of high-grade
prostatic intraepithelial neoplasia (PIN) (Brooks et al., 1998,
Cancer Epidemiol. Biomarkers Prev., 7:531-536).
[0171] In another example, expression of the LAGE-I tumor specific
gene (which is not expressed in normal prostate but is expressed in
25-50% of prostate cancers) is induced by deoxy-azacytidine in
lymphoblastoid cells, suggesting that tumoral expression is due to
demethylation (Lethe et al., 1998, Int. J. Cancer 76(6): 903-908).
In this context, a variety of assays for examining methylation
status of a gene are well known in the art For example, one can
utilize in Southern hybridization approaches methylation-sensitive
restriction enzymes which can not cleave sequences that contain
methylated CpG sites in order to assess the overall methylation
status of CpG islands.
[0172] In addition, MSP (methylation specific PCR) can rapidly
profile the methylation status of all the CpG sites present in a
CpG island of a given gene. This procedure involves initial
modification of DNA by sodium bisulfite (which will convert all
unmethylated cytosines to uracil) followed by amplification using
primers specific for methylated versus unmethylated DNA. Protocols
involving methylation interference can also be found for example in
Current Protocols In Molecular Biology, Units 12, Frederick M.
Ausubel et al. eds., 1995.
[0173] In another related embodiment, the invention provides assays
useful in determining the presence of cancer in an individual,
comprising detecting a significant change in the STEAP alternative
splice variants expressed in a test cell or tissue sample relative
to expression levels in the corresponding normal cell or tissue.
The monitoring of alternative splice variants of STEAP is useful
because changes in the alternative splicing of proteins is
suggested as one of the steps in a series of events that lead to
the progression of cancers (see e.g. Carstens et al., Oncogene
15(250: 3059-3065 (1997)).
[0174] Gene amplification provides an additional method of
assessing the status of STEAP. Gene amplification 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.
[0175] In addition to the tissues discussed above, peripheral blood
may be conveniently assayed for the presence of cancer cells,
including but not limited to prostate cancers, using RT-PCR to
detect STEAP expression. The presence of RT-PCR amplifiable STEAP
mRNA provides an indication of the presence of the cancer. RT-PCR
detection assays for tumor cells in peripheral blood are currently
being evaluated for use in the diagnosis and management of a number
of human solid tumors. In the prostate cancer field, these include
RT-PCR assays for the detection of cells expressing PSA and PSM
(Verkaik et al., 1997, Urol. Res. 25: 373-384; Ghossein et al.,
1995, J. Clin. Oncol. 13: 1195-2000; Heston et al., 1995, Clin.
Chem. 41: 1687-1688). RT-PCR assays are well known in the art.
[0176] A related aspect of the invention is directed to predicting
susceptibility to developing cancer in an individual. In one
embodiment, a method for predicting susceptibility to cancer
comprises detecting STEAP mRNA or STEAP protein in a tissue sample,
its presence indicating susceptibility to cancer, wherein the
degree of STEAP mRNA expression present is proportional to the
degree of susceptibility. In a specific embodiment, the presence of
STEAP in prostate tissue is examined, with the presence of STEAP in
the sample providing an indication of prostate cancer
susceptibility (or the emergence or existence of a prostate tumor).
In a closely related embodiment, one can evaluate the integrity
STEAP nucleotide and amino acid sequences in a biological sample in
order to identify perturbations in the structure of these molecules
such as insertions, deletions, substitutions and the like, with the
presence of one or more perturbations in STEAP gene products in the
sample providing an indication of cancer susceptibility (or the
emergence or existence of a tumor).
[0177] Yet another related aspect of the invention is directed to
methods for gauging tumor aggressiveness. In one embodiment, a
method for gauging aggressiveness of a tumor comprises determining
the level of STEAP mRNA or STEAP protein expressed by cells in a
sample of the tumor, comparing the level so determined to the level
of STEAP mRNA or STEAP protein expressed in a corresponding normal
tissue taken from the same individual or a normal tissue reference
sample, wherein the degree of STEAP mRNA or STEAP protein
expression in the tumor sample relative to the normal sample
indicates the degree of aggressiveness. In a specific embodiment,
aggressiveness of prostate tumors is evaluated by determining the
extent to which STEAP is expressed in the tumor cells, with higher
expression levels indicating more aggressive tumors. In a closely
related embodiment, one can evaluate the integrity STEAP nucleotide
and amino acid sequences in a biological sample in order to
identify perturbations in the structure of these molecules such as
insertions, deletions, substitutions and the like, with the
presence of one or more perturbations indicating more aggressive
tumors.
[0178] Yet another related aspect of the invention is directed to
methods for observing the progression of a malignancy in an
individual over time. In one embodiment, methods for observing the
progression of a malignancy in an individual over time comprise
determining the level of STEAP mRNA or STEAP protein expressed by
cells in a sample of the tumor, comparing the level so determined
to the level of STEAP mRNA or STEAP protein expressed in an
equivalent tissue sample taken from the same individual at a
different time, wherein the degree of STEAP mRNA or STEAP protein
expression in the tumor sample over time provides information on
the progression of the cancer. In a specific embodiment, the
progression of a cancer is evaluated by determining the extent to
which STEAP expression in the tumor cells alters over time, with
higher expression levels indicating a progression of the cancer. In
a closely related embodiment, one can evaluate the integrity STEAP
nucleotide and amino acid sequences in a biological sample in order
to identify perturbations in the structure of these molecules such
as insertions, deletions, substitutions and the like, with the
presence of one or more perturbations indicating a progression of
the cancer.
[0179] The above diagnostic approaches may be combined with any one
of a wide variety of prognostic and diagnostic protocols known in
the art. For example, another embodiment of the invention disclosed
herein is directed to methods for observing a coincidence between
the expression of STEAP gene and STEAP gene products (or
perturbations in STEAP gene and STEAP gene products) and a factor
that is associated with malignancy as a means of diagnosing and
prognosticating the status of a tissue sample. In this context, a
wide variety of factors associated with malignancy may be utilized
such as the expression of genes otherwise associated with
malignancy (including PSA, PSCA and PSM expression) as well as
gross cytological observations (see e.g. Bocking et al., 1984,
Anal. Quant. Cytol. 6(2):74-88; Epstein, 1995, Hum. Pathol. 1995
February; 26(2):223-9; Thorson et al., 1998, Mod. Pathol.
11(6):543-51; Baisden et al., 1999, Am. J. Surg. Pathol.
23(8):918-24). Methods for observing a coincidence between the
expression of STEAP gene and STEAP gene products (or perturbations
in STEAP gene and STEAP gene products) and an additional factor
that is associated with malignancy are useful, for example, because
the presence of a set or constellation of specific factors that
coincide provides information crucial for diagnosing and
prognosticating the status of a tissue sample.
[0180] In a typical embodiment, methods for observing a coincidence
between the expression of STEAP gene and STEAP gene products (or
perturbations in STEAP gene and STEAP gene products) and a factor
that is associated with malignancy entails detecting the
overexpression of STEAP mRNA or protein in a tissue sample,
detecting the overexpression of PSA mRNA or protein in a tissue
sample, and observing a coincidence of STEAP mRNA or protein and
PSA mRNA or protein overexpression. In a specific embodiment, the
expression of STEAP and PSA mRNA in prostate tissue is examined. In
a preferred embodiment, the coincidence of STEAP and PSA mRNA
overexpression in the sample provides an indication of prostate
cancer, prostate cancer susceptibility or the emergence or
existence of a prostate tumor.
[0181] Methods for detecting and quantifying the expression of
STEAP mRNA or protein are described herein and use standard nucleic
acid and protein detection and quantification technologies well
known in the art. Standard methods for the detection and
quantification of STEAP mRNA include in situ hybridization using
labeled STEAP riboptobes, northern blot and related techniques
using STEAP polynucleotide probes, RT-PCR analysis using primers
specific for STEAP, and other amplification type detection methods,
such as, for example, branched DNA, SISBA, TMA and the like. In a
specific embodiment, semi-quantitative RT-PCR may be used to detect
and quantity STEAP mRNA expression as described in the Examples
that follow. Any number of primers capable of amplifying STEAP may
be used for this purpose, including but not limited to the various
primer sets specifically described herein. Standard methods for the
detection and quantification of protein may be used for this
purpose. In a specific embodiment, polyclonal or monoclonal
antibodies specifically reactive with the wild-type STEAP protein
may be used in an immunohistochemical assay of biopsied tissue.
Antibodies directed against STEAP protein can also be used to
detect STEAP in a patient specimen (e.g., blood, urine, semen or
other sample) using conventional techniques such as
fluorescence-activated cell sorting (FACS) and/or ELISA.
[0182] Identifying Molecules that Interact with STEAP
[0183] The STEAP protein sequences disclosed herein allow the
skilled artisan to identify proteins, small molecules and other
agents that interact with STEAP and pathways activated by STEAP via
any one of a variety of art accepted protocols. For example one can
utilize one of the variety of so-called interaction trap systems
(also referred to as the "two-hybrid assay"). In such systems,
molecules that interact reconstitute a transcription factor and
direct expression of a reporter gene, the expression of which is
then assayed. Typical systems identify protein-protein interactions
in vivo through reconstitution of a eukaryotic transcriptional
activator and are disclosed for example in U.S. Pat. Nos.
5,955,280, 5,925,523, 5,846,722 and 6,004,746.
[0184] Alternatively one can identify molecules that interact with
STEAP protein sequences by screening peptide libraries. In such
methods, peptides that bind to selected receptor molecules such as
STEAP are identified by screening libraries that encode a random or
controlled collection of amino acids. Peptides encoded by the
libraries are expressed as fusion proteins of bacteriophage coat
proteins, and bacteriophage particles are then screened against the
receptors of interest. Peptides having a wide variety of uses, such
as therapeutic or diagnostic reagents, may thus be identified
without any prior information on the structure of the expected
ligand or receptor molecule. Typical peptide libraries and
screening methods that can be used to identify molecules that
interact with STEAP protein sequences are disclosed for example in
U.S. Pat. Nos. 5,723,286 and 5,733,731.
[0185] Alternatively, cell lines expressing STEAP can be used to
identify protein-protein interactions mediated by STEAP. This
possibility can be examined using immunoprecipitation techniques as
shown by others (Hamilton B J, et al. Biochem. Biophys. Res.
Commun. 1999, 261:646-51). Typically STEAP protein can be
immunoprecipitated from STEAP expressing prostate cancer cell lines
using anti-STEAP antibodies. Alternatively, antibodies against
His-tag can be used in a cell line engineered to express STEAP
(vectors mentioned above). The immunoprecipitated complex can be
examined for protein association by procedures such as western
blotting, .sup.35S-methionine labeling of proteins, protein
microsequencing, silver staining and two dimensional gel
electrophoresis.
[0186] Small molecules that interact with STEAP can be identified
through related embodiments of such screening assays. For example,
small molecules can be identified that interfere with STEAP
function, including molecules that interfere with STEAP's ability
to bind to cells and/or to modulate tumor formation, progression,
migration and/or apoptosis. Typical methods are discussed for
example in U.S. Pat. No. 5,928,868 and include methods for forming
hybrid ligands in which at least one ligand is a small molecule. In
an illustrative embodiment, the hybrid ligand is introduced into
cells that in turn contain a first and a second expression vector.
Each expression vector includes DNA for expressing a hybrid protein
that encodes a target protein linked to a coding sequence for a
transcriptional module. The cells further contains a reporter gene,
the expression of which is conditioned on the proximity of the
first and second hybrid proteins to each other, an event that
occurs only if the hybrid ligand binds to target sites on both
hybrid proteins. Those cells that express the reporter gene are
selected and the unknown small molecule or the unknown hybrid
protein is identified.
[0187] A typical embodiment of this invention consists of a method
of screening for a molecule that interacts with a STEAP amino acid
sequence shown in FIGS. 11A-B, comprising the steps of contacting a
population of molecules with the STEAP amino acid sequence,
allowing the population of molecules and the STEAP amino acid
sequence to interact under conditions that facilitate an
interaction, determining the presence of a molecule that interacts
with the STEAP amino acid sequence and then separating molecules
that do not interact with the STEAP amino acid sequence from
molecules that do interact with the STEAP amino acid sequence. In a
specific embodiment, the method further includes purifying a
molecule that interacts with the STEAP amino acid sequence. In a
preferred embodiment, the STEAP amino acid sequence is contacted
with a library of peptides. Additional assays for identifying
molecules that modulate STEAP function are described in the
Examples that follow.
[0188] The invention additionally provides a method of screening
for a molecule that modulates the activity of STEAP or a
STEAP-related pathway. The method comprises contacting a molecule
with a cell that expresses a STEAP protein and determining the
activity of STEAP or a STEAP-related pathway. The determining can
be via use of one of the phosphorylation assays described in the
examples that follow, such as western blotting with an antibody
directed to a phosphorylated signaling molecule. Alterations in the
phosphorylation of the signaling molecule indicate a candidate
molecule that modulates the activity of STEAP or a STEAP-related
pathway.
[0189] Therapeutic Methods and Compositions
[0190] The identification of STEAP as a prostate cancer protein
opens a number of therapeutic approaches to the treatment of
prostate and other STEAP-associated cancers. As discussed above,
STEAP is a transmembrane protein, and its interaction with other
cells and molecules likely plays a role in the regulation of the
prostate environment and the initiation, development and/or
progression of cancer. STEAP can be targeted for therapy via
approaches aimed at inhibiting activity of the STEAP protein,
inhibiting the binding or association of STEAP protein with other
cells and molecules, inhibiting transcription or translation of
STEAP, and/or via the use of cancer vaccines based on STEAP. The
therapeutic strategy can thus be designed to inhibit a function of
the molecule or to target the STEAP molecule itself.
[0191] The expression profile of STEAP is reminiscent of the MAGEs,
PSA and PMSA, which are tissue-specific genes that are up-regulated
in melanomas and other cancers (Van den Eynde and Boon, Int J Clin
Lab Res. 27:81-86, 1997). Due to their tissue-specific expression
and high expression levels in cancer, these molecules are currently
being investigated as targets for cancer vaccines (Durrant,
Anticancer Drugs 8:727-733, 1997; Reynolds et al., Int J Cancer
72:972-976, 1997). The expression pattern of STEAP provides
evidence that it is likewise an ideal target for a cancer vaccine
approach to prostate cancer, as its expression is not detected in
most normal tissues.
[0192] Accordingly, therapeutic approaches targeting particular
motifs of STEAP, or aimed at inhibiting the activity of the STEAP
protein, are expected to be useful for patients suffering from
prostate cancer and other cancers expressing STEAP. The therapeutic
approaches aimed at inhibiting the activity of the STEAP protein
generally fall into two classes. One class comprises various
methods for inhibiting the binding or association of the STEAP
protein with its binding partner or with other proteins. Another
class comprises a variety of methods for inhibiting the
transcription of the STEAP gene or translation of STEAP mRNA.
[0193] STEAP as a Target for Antibody-Based Therapy
[0194] The cell surface nature and expression profiles of the
STEAPs in cancers including prostate cancer indicate that they are
promising targets for antibody therapy of prostate and other
cancers expressing STEAPs. The experimental results described in
the Examples herein provide compelling evidence that STEAP-1 and
STEAP-2 are strongly expressed uniformly over the surface of
glandular epithelial cells within prostate and prostate cancer
cells. In particular, immunohistochemical analysis results show
that the surface of human prostate epithelial cells (normal and
cancer) appear to be uniformly coated with STEAP-1. Biochemical
analysis confirms the cell surface localization of STEAP-1
initially suggested by its putative 6-transmembrane primary
structural elements and by the pericellular staining plainly
evident by immunohistochemical staining.
[0195] STEAP-1 and STEAP-2 are uniformly expressed at high levels
over the surface of prostate glandular epithelia, an ideal
situation for immunotherapeutic intervention strategies that target
extracellular STEAP epitopes. Systemic administration of
STEAP-immunoreactive compositions would be expected to result in
extensive contact of the composition with prostate epithelial cells
via binding to STEAP extracellular epitopes. Moreover, given the
near absence of STEAP-1 protein expression in normal human tissues,
there is ample reason to expect exquisite sensitivity without
toxic, non-specific and/or non-target effects caused by the binding
of the immunotherapeutic composition to STEAP-1 on non-target
organs and tissues.
[0196] In addition to the high level expression of STEAP-1 in
prostate and prostate cancer cells, STEAP-1 appears to be
substantially over-expressed in a variety of other human cancers,
including bladder, lung, colon, pancreatic and ovarian cancers. In
particular, high level STEAP-1 mRNA expression is detected in all
tested prostate cancer tissues and cell lines, and in most of the
pancreatic, colon, and bladder cancer cell lines tested. High level
expression of STEAP-1 is also observed in some ovarian cancer cell
lines. Lower level expression is observed in some breast,
testicular, and cervical cancer cell lines. Very high level
expression is also detected in a Ewing sarcoma cell line.
Applicants have shown that cell surface STEAP-1 protein is
expressed in bladder, lung and colon cancers, while there is no
detectable cell surface (or intracellular) STEAP-1 protein in
normal colon and low expression in normal bladder. Antibodies
specifically reactive with extracellular domains of STEAP-1 may be
useful to treat these cancers systemically, either as toxin or
therapeutic agent conjugates or as naked antibodies capable of
inhibiting cell proliferation or function.
[0197] STEAP-2 protein is also expressed in prostate cancer, and in
other cancers as well, including colon and lung cancers. STEAP-2
mRNA analysis by RT-PCR and northern blot show that expression is
restricted to prostate in normal tissues, is also expressed in some
prostate, pancreatic, colon, testicular, ovarian and other cancers.
Therefore, antibodies reactive with STEAP-2 may be useful in the
treatment of prostate and other cancers. Similarly, the expression
of STEAP-3 and STEAP-4 (as well as other STEAPs) may be associated
with some cancers. Thus antibodies reactive with these STEAP family
member proteins may also be useful therapeutically.
[0198] STEAP antibodies may be introduced into a patient such that
the antibody binds to STEAP on the cancer cells and mediates the
destruction of the cells and the tumor, inhibits the growth of the
cells or the tumor, and/or eliminates STEAP function in the primary
tumor, in circulating micrometastases, and/or in established
metastases. The degree of tumor vascularization may provide
guidance on which delivery approach is recommended. Similarly, the
grade and/or stage of disease would be expected to provide useful
information in this regard. For example, a higher grade, more
advanced tumor may be more likely to seed metastases, suggesting
systemic administration in order to treat or prevent the emergence
of metastases. Mechanisms by which such antibodies exert a
therapeutic effect may include complement-mediated cytolysis,
antibody-dependent cellular cytotoxicity, modulating the
physiologic function of STEAP, inhibiting ligand binding or signal
transduction pathways, modulating tumor cell differentiation,
altering tumor angiogenesis factor profiles, and/or by inducing
apoptosis. STEAP antibodies conjugated to toxic or therapeutic
agents may also be used therapeutically to deliver the toxic or
therapeutic agent directly to STEAP-beating tumor cells.
[0199] Cancer immunotherapy using anti-STEAP antibodies may follow
the teachings generated from various approaches that have been
successfully employed in the treatment of other types of cancer,
including but not limited to colon cancer (Arlen et al., 1998,
Crit. Rev. Immunol. 18:133-138), multiple myeloma (Ozaki et al.,
1997, Blood 90:3179-3186; Tsunenari et al., 1997, Blood
90:2437-2444), gastric cancer (Kasprzyk et al., 1992, Cancer Res.
52:2771-2776), B-cell lymphoma (Funakoshi et al., 1996, J.
Immunother. Emphasis Tumor Immunol. 19:93-101), leukemia (Zhong et
al., 1996, Leuk. Res. 20:581-589), colorectal cancer (Moun et al.,
1994, Cancer Res. 54:6160-6166); Velders et al., 1995, Cancer Res.
55:4398-4403), and breast cancer (Shepard et al., 1991, J. Clin.
Immunol. 11:117-127). Some therapeutic approaches involve
conjugation of naked antibody to a toxin, such as the conjugation
of 131I to anti-CD20 antibodies (e.g., Bexxar, Coulter
Pharmaceutical), while others involve co-administration of
antibodies and other therapeutic agents, such as Herceptin.TM.
(trastuzumab) with paclitaxel (Genentech, Inc.). For treatment of
prostate cancer, for example, STEAP antibodies can be administered
in conjunction with radiation, chemotherapy or hormone
ablation.
[0200] Although STEAP antibody therapy may be useful for all stages
of cancer, antibody therapy may be particularly appropriate in
advanced or metastatic cancers. Treatment with the antibody therapy
of the invention may be indicated for patients who have received
previously one or more chemotherapy, while combining the antibody
therapy of the invention with a chemotherapeutic or radiation
regimen may be preferred for patients who have not received
chemotherapeutic treatment. Additionally, antibody therapy may
enable the use of reduced dosages of concomitant chemotherapy,
particularly for patients who do not tolerate the toxicity of the
chemotherapeutic agent very well.
[0201] It may be desirable for some cancer patients to be evaluated
for the presence and level of STEAP expression, preferably using
immunohistochemical assessments of tumor tissue, quantitative STEAP
imaging, or other techniques capable of reliably indicating the
presence and degree of STEAP expression. Immunohistochemical
analysis of tumor biopsies or surgical specimens may be preferred
for this purpose. Methods for immunohistochemical analysis of tumor
tissues are well known in the art.
[0202] Anti-STEAP monoclonal antibodies useful in treating prostate
and other cancers include those that are capable of initiating a
potent immune response against the tumor and those that are capable
of direct cytotoxicity. In this regard, anti-STEAP monoclonal
antibodies (mAbs) may elicit tumor cell lysis by either
complement-mediated or antibody-dependent cell cytotoxicity (ADCC)
mechanisms, both of which require an intact Fc portion of the
immunoglobulin molecule for interaction with effector cell Fc
receptor sites or complement proteins. In addition, anti-STEAP mAbs
that exert a direct biological effect on tumor growth are useful in
the practice of the invention. Potential mechanisms by which such
directly cytotoxic mAbs may act include inhibition of cell growth,
modulation of cellular differentiation, modulation of tumor
angiogenesis factor profiles, and the induction of apoptosis. The
mechanism by which a particular anti-STEAP mAb exerts an anti-tumor
effect may be evaluated using any number of in vitro assays
designed to determine ADCC, ADMMC, complement-mediated cell lysis,
and so forth, as is generally known in the art.
[0203] The anti-tumor activity of a particular anti-STEAP mAb, or
combination of anti-STEAP mAbs, may be evaluated in vivo using a
suitable animal model. For example, xenogenic prostate cancer
models wherein human prostate cancer explants or passaged xenograft
tissues are introduced into immune compromised animals, such as
nude or SCID mice, are appropriate in relation to prostate cancer
and have been described (U.S. Pat. No. 6,107,540; Klein et al.,
1997, Nature Medicine 3: 402-408). For Example, PCT Patent
Application WO98/16628, Sawyers et al., published Apr. 23, 1998,
describes various xenograft models of human prostate cancer capable
of recapitulating the development of primary tumors,
micrometastasis, and the formation of osteoblastic metastases
characteristic of late stage disease. Efficacy may be predicted
using assays which measure inhibition of tumor formation, tumor
regression or metastasis, and the like.
[0204] The use of murine or other non-human monoclonal antibodies,
or human/mouse chimeric mAbs may induce moderate to strong immune
responses in some patients. In some cases, this will result in
clearance of the antibody from circulation and reduced efficacy. In
the most severe cases, such an immune response may lead to the
extensive formation of immune complexes that, potentially, can
cause renal failure. Accordingly, preferred monoclonal antibodies
used in the practice of the therapeutic methods of the invention
are those that are either fully human or humanized and that bind
specifically to the target STEAP antigen with high affinity but
exhibit low or no antigenicity in the patient.
[0205] Therapeutic methods of the invention contemplate the
administration of single anti-STEAP mAbs as well as combinations,
or cocktails, of different mAbs. Such mAb cocktails may have
certain advantages inasmuch as they contain mAbs that target
different epitopes, exploit different effector mechanisms or
combine directly cytotoxic mAbs with mAbs that rely on immune
effector functionality. Such mAbs in combination may exhibit
synergistic therapeutic effects. In addition, the administration of
anti-STEAP mAbs may be combined with other therapeutic agents,
including but not limited to various chemotherapeutic agents,
androgen-blockers, and immune modulators (e.g., IL-2, GM-CSF). The
anti-STEAP mAbs may be administered in their "naked" or
unconjugated form, or may have therapeutic agents conjugated to
them.
[0206] The anti-STEAP monoclonal antibodies used in the practice of
the method of the invention may be formulated into pharmaceutical
compositions comprising a carrier suitable for the desired delivery
method. Suitable carriers include any material which when combined
with the anti-STEAP mAbs retains the anti-tumor function of the
antibody and is non-reactive with the subject's immune systems.
Examples include, but are not limited to, any of a number of
standard pharmaceutical carriers such as sterile phosphate buffered
saline solutions, bacteriostatic water, and the like.
[0207] The anti-STEAP antibody formulations may be administered via
any route capable of delivering the antibodies to the tumor site.
Potentially effective routes of administration include, but are not
limited to, intravenous, intraperitoneal, intramuscular,
intratumor, intradermal, and the like. The preferred route of
administration is by intravenous injection. A preferred formulation
for intravenous injection comprises the anti-STEAP mAbs in a
solution of preserved bacteriostatic water, sterile unpreserved
water, and/or diluted in polyvinylchloride or polyethylene bags
containing 0.9% sterile Sodium Chloride for Injection, USP. The
anti-STEAP mAb preparation may be lyophilized and stored as a
sterile powder, preferably under vacuum, and then reconstituted in
bacteriostatic water containing, for example, benzyl alcohol
preservative, or in sterile water prior to injection.
[0208] Treatment will generally involve the repeated administration
of the anti-STEAP antibody preparation via an acceptable route of
administration such as intravenous injection (IV), typically at a
dose in the range of about 0.1 to about 10 mg/kg body weight. Doses
in the range of 10-500 mg mAb per week may be effective and well
tolerated. Based on clinical experience with the Herceptin mAb in
the treatment of metastatic breast cancer, an initial loading dose
of approximately 4 mg/kg patient body weight IV followed by weekly
doses of about 2 mg/kg IV of the anti-STEAP mAb preparation may
represent an acceptable dosing regimen. Preferably, the initial
loading dose is administered as a 90 minute or longer infusion. The
periodic maintenance dose may be administered as a 30 minute or
longer infusion, provided the initial dose was well tolerated.
However, as one of skill in the art will understand, various
factors will influence the ideal dose regimen in a particular case.
Such factors may include, for example, the binding affinity and
half life of the mAb or mAbs used, the degree of STEAP
overexpression in the patient, the extent of circulating shed STEAP
antigen, the desired steady-state antibody concentration level,
frequency of treatment, and the influence of chemotherapeutic
agents used in combination with the treatment method of the
invention.
[0209] Optimally, patients should be evaluated for the level of
circulating shed STEAP antigen in serum in order to assist in the
determination of the most effective dosing regimen and related
factors. Such evaluations may also be used for monitoring purposes
throughout therapy, and may be useful to gauge therapeutic success
in combination with evaluating other parameters (such as serum PSA
levels in prostate cancer therapy).
[0210] Inhibition of STEAP Protein Function
[0211] The invention includes various methods and compositions for
inhibiting the binding of STEAP to its binding partner or ligand,
or its association with other protein(s) as well as methods for
inhibiting STEAP function.
[0212] Inhibition of STEAP With Recombinant Proteins
[0213] In one approach, recombinant molecules that are capable of
binding to STEAP thereby preventing STEAP from accessing/binding to
its binding partner(s) or associating with other protein(s) are
used to inhibit STEAP function. Such recombinant molecules may, for
example, contain the reactive part(s) of a STEAP specific antibody
molecule. In a particular embodiment, the STEAP binding domain of a
STEAP binding partner may be engineered into a dimeric fusion
protein comprising two STEAP ligand binding domains linked to the
Fc portion of a human IgG, such as human IgG1. Such IgG portion may
contain, for example, the C.sub.H2 and C.sub.H3 domains and the
hinge region, but not the C.sub.H1 domain. Such dimeric fusion
proteins may be administered in soluble form to patients suffering
from a cancer associated with the expression of STEAP, including
but not limited to prostate cancer, where the dimeric fusion
protein specifically binds to STEAP thereby blocking STEAP
interaction with a binding partner and/or modulating STEAP
function. Such dimeric fusion proteins may be further combined into
multimeric proteins using known antibody linking technologies.
[0214] Inhibition of STEAP With Intracellular Antibodies
[0215] In another approach, recombinant vectors encoding single
chain antibodies that specifically bind to STEAP may be introduced
into STEAP expressing cells via gene transfer technologies, wherein
the encoded single chain anti-STEAP antibody is expressed
intracellularly, binds to STEAP protein, and thereby inhibits its
function. Methods for engineering such intracellular single chain
antibodies are well known. Such intracellular antibodies, also
known as "intrabodies", may be specifically targeted to a
particular compartment within the cell, providing control over
where the inhibitory activity of the treatment will be focused.
This technology has been successfully applied in the art (for
review, see Richardson and Marasco, 1995, TIBTECH vol. 13).
Intrabodies have been shown to virtually eliminate the expression
of otherwise abundant cell surface receptors. See, for example,
Richardson et al., 1995, Proc. Nati. Acad. Sci. USA 92: 3137-3141;
Beerli et al., 1994, J. Biol. Chem. 289: 23931-23936; Deshane et
al., 1994, Gene Ther. 1: 332-337.
[0216] Single chain antibodies comprise the variable domains of the
heavy and light chain joined by a flexible linker polypeptide, and
are expressed as a single polypeptide. Optionally, single chain
antibodies may be expressed as a single chain variable region
fragment joined to the light chain constant region. Well known
intracellular trafficking signals may be engineered into
recombinant polynucleotide vectors encoding such single chain
antibodies in order to precisely target the expressed intrabody to
the desired intracellular compartment. For example, intrabodies
targeted to the endoplasmic reticulum (ER) may be engineered to
incorporate a leader peptide and, optionally, a C-terminal ER
retention signal, such as the KDEL amino acid motif. Intrabodies
intended to exert activity in the nucleus may be engineered to
include a nuclear localization signal. Lipid moieties may be joined
to intrabodies in order to tether the intrabody to the cytosolic
side of the plasma membrane. Intrabodies may also be targeted to
exert function in the cytosol. For example, cytosolic intrabodies
may be used to sequester factors within the cytosol, thereby
preventing them from being transported to their natural cellular
destination.
[0217] In one embodiment, STEAP intrabodies are designed to bind
specifically to a particular STEAP domain. For example, cytosolic
intrabodies that specifically bind to the STEAP protein may be used
to prevent STEAP related molecules from gaining access to the
nucleus, thereby preventing it from exerting any biological
activity within the nucleus.
[0218] In order to direct the expression of such intrabodies
specifically to particular tumor cells, the transcription of the
intrabody may be placed under the regulatory control of an
appropriate tumor-specific promoter and/or enhancer. In order to
target intrabody expression specifically to prostate, for example,
the PSA promoter and/or promoter/enhancer may be utilized (See, for
example, U.S. Pat. No. 5,919,652).
[0219] Inhibition of STEAP Transcription or Translation
[0220] Within another class of therapeutic approaches, the
invention provides various methods and compositions for inhibiting
the transcription of the STEAP gene. Similarly, the invention also
provides methods and compositions for inhibiting the translation of
STEAP MRNA into protein.
[0221] In one approach, a method of inhibiting the transcription of
the STEAP gene comprises contacting the STEAP gene with a STEAP
antisense polynucleotide. In another approach, a method of
inhibiting STEAP mRNA translation comprises contacting the STEAP
mRNA with an antisense polynucleotide. In another approach, a STEAP
specific ribozyme may be used to cleave the STEAP message, thereby
inhibiting translation. Such antisense and ribozyme based methods
may also be directed to the regulatory regions of the STEAP gene,
such as the STEAP promoter and/or enhancer elements. Similarly,
proteins capable of inhibiting a STEAP gene transcription factor
may be used to inhibit STEAP mRNA transcription. The various
polynucleotides and compositions useful in the aforementioned
methods have been described above. The use of antisense and
ribozyme molecules to inhibit transcription and translation is well
known in the art.
[0222] Other factors that inhibit the transcription of STEAP
through interfering with STEAP transcriptional activation may also
be useful for the treatment of cancers expressing STEAP. Similarly,
factors that are capable of interfering with STEAP processing may
be useful for the treatment of cancers expressing STEAP. Cancer
treatment methods utilizing such factors are also within the scope
of the invention.
[0223] General Considerations for Therapeutic Strategies
[0224] Gene transfer and gene therapy technologies may be used for
delivering therapeutic polynucleotide molecules to tumor cells
synthesizing STEAP (i.e., antisense, ribozyme, polynucleotides
encoding intrabodies and other STEAP inhibitory molecules). A
number of gene therapy approaches are known in the art. Recombinant
vectors encoding STEAP antisense polynucleotides, ribozymes,
factors capable of interfering with STEAP transcription, and so
forth, may be delivered to target tumor cells using such gene
therapy approaches.
[0225] The above therapeutic approaches may be combined with any
one of a wide variety of chemotherapy or radiation therapy
regimens. These therapeutic approaches may also enable the use of
reduced dosages of chemotherapy and/or less frequent
administration, particularly in patients that do not tolerate the
toxicity of the chemotherapeutic agent well.
[0226] The anti-tumor activity of a particular composition (e.g.,
antisense, ribozyme, intrabody), or a combination of such
compositions, may be evaluated using various in vitro and in vivo
assay systems. In vitro assays for evaluating therapeutic potential
include cell growth assays, soft agar assays and other assays
indicative of tumor promoting activity, binding assays capable of
determining the extent to which a therapeutic composition will
inhibit the binding of STEAP to a binding partner, etc.
[0227] In vivo, the effect of a STEAP therapeutic composition may
be evaluated in a suitable animal model. For example, xenogeneic
prostate cancer models wherein human prostate cancer explants or
passaged xenograft tissues are introduced into immune compromised
animals, such as nude or SCID mice, are appropriate in relation to
prostate cancer and have been described (Klein et al., 1997, Nature
Medicine 3: 402-408). For example, PCT Patent Application
WO98/16628, Sawyers et al., published Apr. 23, 1998, describes
various xenograft models of human prostate cancer capable of
recapitulating the development of primary tumors, micrometastasis,
and the formation of osteoblastic metastases characteristic of late
stage disease. Efficacy may be predicted using assays that measure
inhibition of tumor formation, tumor regression or metastasis, and
the like. See, also, the Examples below.
[0228] In vivo assays that qualify the promotion of apoptosis may
also be useful in evaluating potential therapeutic compositions. In
one embodiment, xenografts from bearing mice treated with the
therapeutic composition may be examined for the presence of
apoptotic foci and compared to untreated control xenograft-bearing
mice. The extent to which apoptotic foci are found in the tumors of
the treated mice provides an indication of the therapeutic efficacy
of the composition.
[0229] The therapeutic compositions used in the practice of the
foregoing methods may be formulated into pharmaceutical
compositions, including vaccine compositions, comprising a carrier
suitable for the desired delivery method. Suitable carriers include
any material that when combined with the therapeutic composition
retains the anti-tumor function of the therapeutic composition and
is non-reactive with the patient's immune system. Examples include,
but are not limited to, any of a number of standard pharmaceutical
carriers such as sterile phosphate buffered saline solutions,
bacteriostatic water, and the like (see, generally, Remington's
Pharmaceutical Sciences 16.sup.th Edition, A. Osal., Ed.,
1980).
[0230] Therapeutic formulations may be solubilized and administered
via any route capable of delivering the therapeutic composition to
the tumor site. Potentially effective routes of administration
include, but are not limited to, intravenous, parenteral,
intraperitoneal, intramuscular, intratumor, intradermal,
intraorgan, orthotopic, and the like. A preferred formulation for
intravenous injection comprises the therapeutic composition in a
solution of preserved bacteriostatic water, sterile unpreserved
water, and/or diluted in polyvinylchloride or polyethylene bags
containing 0.9% sterile Sodium Chloride for Injection, USP.
Therapeutic protein preparations may be lyophilized and stored as
sterile powders, preferably under vacuum, and then reconstituted in
bacteriostatic water containing, for example, benzyl alcohol
preservative, or in sterile water prior to injection.
[0231] Dosages and administration protocols for the treatment of
cancers using the foregoing methods will vary with the method and
the target cancer and will generally depend on a number of other
factors appreciated in the art.
[0232] Cancer Vaccines
[0233] The invention further provides cancer vaccines comprising a
STEAP protein or fragment thereof, as well as DNA based vaccines.
In view of the prostate- and tumor-restricted expression of STEAP,
STEAP cancer vaccines are expected to be effective at specifically
preventing and/or treating STEAP expressing cancers without
creating non-specific effects on non-target tissues. The use of a
tumor antigen in a vaccine for generating humoral and cell-mediated
immunity for use in anti-cancer therapy is well known in the art
and has been employed in prostate cancer using human PSMA and
rodent PAP immunogens (Hodge et al., 1995, Int. J. Cancer 63:
231-237; Fong et al., 1997, J. Immunol. 159: 3113-3117). Such
methods can be readily practiced by employing a STEAP protein, or
fragment thereof, or a STEAP-encoding nucleic acid molecule and
recombinant vectors capable of expressing and appropriately
presenting the STEAP immunogen.
[0234] For example, viral gene delivery systems may be used to
deliver a STEAP-encoding nucleic acid molecule. Various viral gene
delivery systems that can be used in the practice of this aspect of
the invention include, but are not limited to, vaccinia, fowlpox,
canarypox, adenovitus, influenza, poliovirus, adeno-associated
virus, lentivirus, and sindbus virus (Restifo, 1996, Curr. Opin.
Immunol. 8: 658-663). Non-viral delivery systems may also be
employed by using naked DNA encoding a STEAP protein or fragment
thereof introduced into the patient (e.g., intramuscularly) to
induce an anti-tumor response. In one embodiment, the full-length
human STEAP cDNA may be employed.
[0235] In one embodiment, a STEAP cancer vaccine is based on the
identification of immunogenic peptides within a STEAP amino acid
sequence shown in FIGS. 11A-B. As discussed further in the examples
below, STEAPs have been shown to induce T and B cell responses.
STEAP-1 and STEAP-2 polypeptides have been used to generate an
immune response in mice and rabbits for the production of
monoclonal and polyclonal antibodies. Thus, specific portions of
STEAP, and polynucleotides encoding these portions, may be selected
for the production of a cancer vaccine. One example of such a
portion of a STEAP protein is amino acid residues 14 through 28 of
the STEAP-1 amino acid sequence as shown in FIGS. 1A-B
(WKMKPRRNLEEDDYL; SEQ ID NO: 22).
[0236] In another embodiment, STEAP nucleic acid molecules encoding
specific cytotoxic T lymphocyte (CTL) epitopes may be employed. CTL
epitopes can be determined using specific algorithms (e.g., Epimer,
Brown University) to identify peptides within a STEAP protein that
are capable of optimally binding to specified HLA alleles. One
suitable algorithm is the HLA Peptide Motif Search algorithm
available at the Bioinformatics and Molecular Analysis Section
(BIMAS) web site (http://bimas.dcrt.nih.go- v/). This algorithm is
based on binding of specific peptide sequences in the groove of HLA
Class I molecules and specifically HLA-A2 (Falk et al., 1991,
Nature 351:290-6; Hunt et al., 1992, Science 255:1261-3; Parker et
al., 1992, J. ImmunoL 149:3580-7; Parker et al., 1994, J. Immunol.
152:163-75). The HLA Peptide Motif Search algorithm allows location
and ranking of 8-mer, 9-mer, and 10-mer peptides from a complete
protein sequence for predicted binding to HLA-A2 as well as other
Class I molecules. Most HLA-A2 binding peptides are 9-mers,
favorably containing a leucine at position 2 and a valine or
leucine at position 9 (Parker et al., 1992, J. Immunol.
149:3580-7). Actual binding of peptides to HLA-A2 can be evaluated
by stabilization of HILA-A2 expression on the antigen processing
defective cell line T2 (Xue et al., 1997, Prostate 30:73-8; Peshwa
et al., 1998, Prostate 36:129-38). Immunogenicity of specific
peptides can be evaluated in vivo by stimulation of CD8+ CTL in the
presence of dendritic cells (Xue et al.; Peshwa et al., supra).
[0237] Specific STEAP peptides predicted to bind HLA-A2 and
preferred for use in cancer vaccines include peptides corresponding
to amino acids 165-173 of STEAP-1, amino acids 86-94 of STEAP-1,
amino acids 262-270 of STEAP-1, amino acids 302-310 of STEAP-1,
amino acids 158-166 of STEAP-1, amino acids 227-235 of STEAP-2,
amino acids 402-410 of STEAP-2, amino acids 307-315 of STEAP-2,
amino acids 306-314 of STEAP-2, and amino acids 100-108 of
STEAP-2.
[0238] Various ex vivo strategies may also be employed. One
approach involves the use of dendritic cells to present STEAP
antigen to a patient's immune system. Dendritic cells express MHC
class I and II, B7 co-stimulator, and IL-12, and are thus highly
specialized antigen presenting cells. In prostate cancer,
autologous dendritic cells pulsed with peptides of the
prostate-specific membrane antigen (PSMA) are being used in a Phase
I clinical trial to stimulate prostate cancer patients' immune
systems (Tjoa et al., 1996, Prostate 28: 65-69; Murphy et al.,
1996, Prostate 29: 371-380). Dendritic cells can be used to present
STEAP peptides to T cells in the context of MHC class I and II
molecules. In one embodiment, autologous dendritic cells are pulsed
with STEAP peptides capable of binding to MHC molecules. In another
embodiment, dendritic cells are pulsed with the complete STEAP
protein. Yet another embodiment involves engineering the
overexpression of the STEAP gene in dendritic cells using various
implementing vectors known in the art, such as adenovirus (Arthur
et al., 1997, Cancer Gene Ther. 4: 17-25), retrovirus (Henderson et
al., 1996, Cancer Res. 56: 3763-3770), lentivirus, adeno-associated
virus, DNA transfection (Ribas et al., 1997, Cancer Res. 57:
2865-2869), and tumor-derived RNA transfection (Ashley et al.,
1997, J. Exp. Med. 186: 1177-1182). Cells expressing STEAP may also
be engineered to express immune modulators, such as GM-CSF, and
used as immunizing agents.
[0239] Anti-idiotypic anti-STEAP antibodies can also be used in
anti-cancer therapy as a vaccine for inducing an immune response to
cells expressing a STEAP protein. Specifically, the generation of
anti-idiotypic antibodies is well known in the art and can readily
be adapted to generate anti-idiotypic anti-STEAP antibodies that
mimic an epitope on a STEAP protein (see, for example, Wagner et
aL, 1997, Hybridoma 16: 33-40; Foon et al., 1995, J Clin Invest 96:
334-342; Herlyn et al., 1996, Cancer Immunol Immunother 43: 65-76).
Such an anti-idiotypic antibody can be used in cancer vaccine
strategies.
[0240] Genetic immunization methods may be employed to generate
prophylactic or therapeutic humoral and cellular immune responses
directed against cancer cells expressing STEAP. Constructs
comprising DNA encoding a STEAP protein/immunogen and appropriate
regulatory sequences may be injected directly into muscle or skin
of an individual such that the cells of the muscle or skin take up
the construct and express the encoded STEAP protein/immunogen.
Expression of the STEAP protein immunogen results in the generation
of prophylactic or therapeutic humoral and cellular immunity
against prostate and other STEAP-expressing cancers. Various
prophylactic and therapeutic genetic immunization techniques known
in the art may be used (for review, see information and references
published at Internet address www.genweb.com).
[0241] Diagnostic Compositions and Kits
[0242] For use in the diagnostic and therapeutic applications
described or suggested above, kits are also provided by the
invention. Such kits may comprise a carrier means being
compartmentalized to receive in close confinement one or more
container means such as vials, tubes, and the like, each of the
container means comprising one of the separate elements to be used
in the method. For example, one of the container means may comprise
a probe that is or can be detectably labeled. Such probe may be an
antibody or polynucleotide specific for a STEAP protein or a STEAP
gene or message, respectively. Where the kit utilizes nucleic acid
hybridization to detect the target nucleic acid, the kit may also
have containers containing nucleotide(s) for amplification of the
target nucleic acid sequence and/or a container comprising a
reporter-means, such as a biotin-binding protein, such as avidin or
streptavidin, bound to a reporter molecule, such as an enzymatic,
florescent, or radioisotope label.
[0243] The kit of the invention will typically comprise the
container described above and one or more other containers
comprising materials desirable from a commercial and user
standpoint, including buffers, diluents, filters, needles,
syringes, and package inserts with instructions for use. A label
may be present on the on the container to indicate that the
composition is used for a specific therapy or non-therapeutic
application, and may also indicate directions for either in vivo or
in firm use, such as those described above.
[0244] Accordingly, the invention also provides diagnostic
compositions comprising STEAP-related molecules. Such molecules
include the various STEAP polynudeotides, primers, probes,
proteins, fragments, antibodies described herein. The molecules
included in the diagnostic composition may optionally be labeled
with a detectable market. STEAP diagnostic compositions may further
comprise appropriate buffers, diluents, and other ingredients as
desired.
EXAMPLES
[0245] Various aspects of the invention are further described and
illustrated by way of the several examples that follow, none of
which are intended to limit the scope of the invention.
Example 1
SSH-Generated Isolation of cDNA Fragment of the STEAP Gene
[0246] Materials and Methods
[0247] LAPC Xenografts:
[0248] LAPC xenografts were obtained from Dr. Charles Sawyers
(UCLA) and generated as described (Klein et al, 1997, Nature Med.
3: 402-408; Craft et al., 1999, Cancer Res. 59: 5030-5036).
Androgen dependent and independent LAPC-4 xenografts (LAPC-4 AD and
Al, respectively) and LAPC-9 xenografts (LAPC-9 AD and AI,
respectively) were grown in intact male SCID mice or in castrated
males, respectively, and were passaged as small tissue chunks in
recipient males. LAPC-4 AI xenografts were derived from LAPC-4 AD
tumors and LAPC-9 AI xenografts were derived from LAPC-9 AD tumors.
To generate the AI xenografts, male mice bearing LAPC AD tumors
were castrated and maintained for 2-3 months. After the LAPC tumors
re-grew, the tumors were harvested and passaged in castrated males
or in female SCID mice.
[0249] LAPC-4 AD xenografts were grown intratibially as follows.
LAPC-4 AD xenograft tumor tissue grown subcutaneously was minced
into 1-2 mm.sup.3 sections while the tissue was bathed in
1.times.Iscoves medium, minced tissue was then centrifuged at 1.3K
rpm for 4 minutes, the supernatant was resuspended in 10 ml ice
cold 1.times.Iscoves medium and centrifuged at 1.3K rpm for 4
minutes. The pellet was then resuspended in 1.times.Iscoves with 1%
pronase E and incubated for 20 minutes at room temperature with
mild rocking agitation followed by incubation on ice for 2-4
minutes. Filtrate was centrifuged at 1.3K rmp for 4 minutes, and
the pronase was removed from the aspirated pellet by resuspending
in 10 ml Iscoves and re-centrifuging. Clumps of cells were then
plated in PrEGM medium and grown overnight. The cells were then
harvested, filtered, washed 2.times.RPMI, and counted.
Approximately 50,000 cells were mixed with and equal volume of
ice-cold Matrigel on ice, and surgically injected into the proximal
tibial metaphyses of SCID mice via-a 27 gauge needle. After 10-12
weeks, LAPC-4 tumors growing in bone marrow were recovered.
[0250] Cell Lines and Tissues:
[0251] Human cell lines (e.g., HeLa) were obtained from the ATCC
and were maintained in DMEM with 5% fetal calf serum. Human tissues
for RNA and protein analyses were obtained from the Human Tissue
Resource Center (HTRC) at the UCLA (Los Angeles, Calif.) and from
QualTek, Inc. (Santa Barbara, Calif.).
[0252] RNA Isolation:
[0253] Tumor tissue and cell lines were homogenized in Trizol
reagent (Life Technologies, Gibco BRL) using 10 ml/g tissue or 10
ml/10.sup.8 cells to isolate total RNA. Poly A RNA was purified
from total RNA using Qiagen's Oligotex mRNA Mini and Midi kits.
Total and MRNA were quantified by spectrophotometric analysis (O.D.
260/280 nm) and analyzed by gel electrophoresis.
[0254] Oligonucleotides:
[0255] The following HPLC purified oligonucleotides were used.
5 DPNCDN (cDNA synthesis primer): (SEQ ID NO: 23)
5'TTTTGATCAAGCTT.sub.303' Adaptor 1: (SEQ ID NO: 24,25)
5'CTAATACGACTCACTATAGGGCTCGAGCGGCCGCCCGGGCAG3' 3'GGCCCGTCCTAG5'
Adaptor 2: (SEQ ID NO: 26,27)
5'GTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAG3' 3'CGGCTCCTAG5' PCR
primer 1: (SEQ ID NO: 28) 5'CTAATACGACTCACTATAGGGC3' Nested primer
(NP)1: (SEQ ID NO: 29) 5'CGAGCGGCCGCCCGGGCAGGA3' Nested primer
(NP)2: (SEQ ID NO: 30) 5'AGCGTGGTCGCGGCCGAGGA3'
[0256] Suppression Subtractive Hybridization:
[0257] Suppression Subtractive Hybridization (SSH) was used to
identify cDNAs corresponding to genes which may be up-regulated in
androgen dependent prostate cancer compared to benign prostatic
hyperplasia (BPH).
[0258] Double stranded cDNAs corresponding to the LAPC-4 AD
xenograft (tester) and the BPH tissue (driver) were synthesized
from 2 .mu.g of poly(A)+ RNA isolated from xenograft and BPH
tissue, as described above, using CLONTECH's PCR-Select cDNA
Subtraction Kit and 1 ng of oligonucleotide RSACDN as primer.
First- and second-strand synthesis were carried out as described in
the Kit's user manual protocol (CLONTECH Protocol No. PT1117-1,
Catalog No. K1804-1). The resulting cDNA was digested with Rsa I
for 3 hrs. at 37.degree. C. Digested cDNA was extracted with
phenol/chloroform (1:1) and ethanol precipitated.
[0259] Driver cDNA (BPH) was generated by combining in a 4 to 1
ratio Rsa I digested BPH cDNA with digested cDNA from mouse liver,
in order to ensure that murine genes were subtracted from the
tester cDNA (LAPC-4 AD).
[0260] Tester cDNA (LAPC-4 AD) was generated by diluting 1 .mu.l of
Rsa I digested LAPC-4 AD cDNA (400 ng) in 5 .mu.l of water. The
diluted cDNA (2 al, 160 ng) was then ligated to 2 .mu.l of adaptor
1 and adaptor 2 (10 .mu.M), in separate ligation reactions, in a
total volume of 10 .mu.l at 16.degree. C. overnight, using 400 u of
T4 DNA ligase (CLONTECH). Ligation was terminated with 1 .mu.l of
0.2 M EDTA and heating at 72.degree. C. for 5 min.
[0261] The first hybridization was performed by adding 1.5 .mu.l
(600 ng) of driver cDNA to each of two tubes containing 1.5 .mu.l
(20 ng) adaptor 1- and adaptor 2-ligated tester cDNA. In a final
volume of 4 .mu.l, the samples were overlayed with mineral oil,
denatured in an MJ Research thermal cycler at 98.degree. C. for 1.5
minutes, and then were allowed to hybridize for 8 hrs at 68.degree.
C. The two hybridizations were then mixed together with an
additional 1 .mu.l of fresh denatured driver cDNA and were allowed
to hybridize overnight at 68.degree. C. The second hybridization
was then diluted in 200 .mu.l of 20 mM Hepes, pH 8.3, 50 mM NaCl,
0.2 mM EDTA, heated at 70.degree. C. for 7 min. and stored at
-20.degree. C.
[0262] PCR Amplification, Cloning and Sequencing of Gene Fragments
Generated from SSH:
[0263] To amplify gene fragments resulting from SSH reactions, two
PCR amplifications were performed. In the primary PCR reaction 1
.mu.l of the diluted final hybridization mix was added to 1 .mu.l
of PCR primer 1 (10 .mu.M), 0.5 .mu.l dNTP mix (10 .mu.M), 2.5
.mu.l 10.times.reaction buffer (CLONTECH) and 0.5 .mu.l
50.times.Advantage cDNA polymerase Mix (CLONTECH) in a final volume
of 25 .mu.l. PCR 1 was conducted using the following conditions:
75.degree. C. for 5 min., 94.degree. C. for 25 sec., then 27 cycles
of 94.degree. C. for 10 sec, 66.degree. C. for 30 sec, 72.degree.
C. for 1.5 min. Five separate primary PCR reactions were performed
for each experiment. The products were pooled and diluted 1:10 with
water. For the secondary PCR reaction, 1 .mu.l from the pooled and
diluted primary PCR reaction was added to the same reaction mix as
used for PCR 1, except that primers NP1 and NP2 (10 .mu.M were used
instead of PCR primer 1. PCR 2 was performed using 10-12 cycles of
94.degree. C. for 10 sec, 68.degree. C. for 30 sec, 72.degree. C.
for 1.5 minutes. The PCR products were analyzed using 2% agarose
gel electrophoresis.
[0264] The PCR products were inserted into pCR2.1 using the T/A
vector cloning kit (Invitrogen). Transformed E. coli were subjected
to blue/white and ampicillin selection. White colonies were picked
and arrayed into 96 well plates and were grown in liquid culture
overnight. To identify inserts, PCR amplification was performed on
1 ml of bacterial culture using the conditions of PCR1 and NP1 and
NP2 as primers. PCR products were analyzed using 2% agarose gel
electrophoresis.
[0265] Bacterial clones were stored in 20% glycerol in a 96 well
format. Plasmid DNA was prepared, sequenced, and subjected to
nucleic acid homology searches of the GenBank, dbEST, and NCI-CGAP
databases.
[0266] RT-PCR Expression Analysis:
[0267] First strand cDNAs were generated from 1 .mu.g of mRNA with
oligo (dT)12-18 priming using the Gibco-BRL Superscript
Preamplification system. The manufacturers protocol was used and
included an incubation for 50 min at 42.degree. C. with reverse
transcriptase followed by RNase H treatment at 37.degree. C. for 20
min. After completing the reaction, the volume was increased to 200
.mu.l with water prior to normalization. First strand cDNAs from 16
different normal human tissues were obtained from Clontech.
[0268] Normalization of the first strand cDNAs from multiple
tissues was performed by using the primers
5'atatcgccgcgctcgtcgtcgacaa3' (SEQ ID NO: 31) and
5'agccacacgcagctcattgtagaagg 3' (SEQ ID NO: 32) to amplify
.beta.-actin. First strand cDNA (5 .mu.l) was amplified in a total
volume of 50 .mu.l containing 0.4 .mu.M primers, 0.2 .mu.M each
dNTPs, 1.times.PCR buffer (Clontech, 10 mM Tris-HCL, 1.5 mM
MgCl.sub.2, 50 mM KCl, pH 8.3) and 1.times.Klentaq DNA polymerase
(Clontech). Five .mu.l of the PCR reaction was removed at 18, 20,
and 22 cycles and used for agarose gel electrophoresis. PCR was
performed using an MJ Research thermal cycler under the following
conditions: initial denaturation was at 94.degree. C. for 15 sec,
followed by a 18, 20, and 22 cycles of 94.degree. C. for 15,
65.degree. C. for 2 min, 72.degree. C. for 5 sec. A final extension
at 72.degree. C. was carried out for 2 min. After agarose gel
electrophoresis, the band intensities of the 283 bp .beta.-actin
bands from multiple tissues were compared by visual inspection.
Dilution factors for the first strand cDNAs were calculated to
result in equal .beta.-actin band intensities in all tissues after
22 cycles of PCR. Three rounds of normalization were required to
achieve equal band intensities in all tissues after 22 cycles of
PCR.
[0269] To determine expression levels of the 8P1D4 gene, 5 .mu.l of
normalized first strand cDNA was analyzed by PCR using 25, 30, and
35 cycles of amplification using the following primer pairs:
6 (SEQ ID NO: 4) 5' ACT TTG TTG ATG ACC AGG ATT GGA 3' (SEQ ID NO:
5) 5' CAG AAC TTC AGC ACA CAC AGG AAC 3'
[0270] Semi quantitative expression analysis was achieved by
comparing the PCR products at cycle numbers that give light band
intensities.
[0271] Results
[0272] Several SSH experiments were conduced as described in the
Materials and Methods, supra, and led to the isolation of numerous
candidate gene fragment clones. All candidate clones were sequenced
and subjected to homology analysis against all sequences in the
major public gene and EST databases in order to provide information
on the identity of the corresponding gene and to help guide the
decision to analyze a particular gene for differential expression.
In general, gene fragments which had no homology to any known
sequence in any of the searched databases, and thus considered to
represent novel genes, as well as gene fragments showing homology
to previously sequenced expressed sequence tags (ESTs), were
subjected to differential expression analysis by RT-PCR and/or
Northern analysis.
[0273] One of the cDNA clones, designated 8P1D4, was 436 bp in
length and showed homology to an EST sequence in the NCI-CGAP tumor
gene database. The full length cDNA encoding the 8P1D4 gene was
subsequently isolated using this cDNA and re-named STEAP-1. The
8P1D4 cDNA nucleotide sequence corresponds to nucleotide residues
150 through 585 in the STEAP-1 cDNA sequence as shown in FIGS.
1A-B. Another clone, designated 28P3E1, 561 bp in length showed
homology to a number of EST sequences in the NCI-CGAP tumor gene
database or in other databases. Part of the 28P3E1 sequence (356
bp) is identical to an EST derived from human fetal tissue. After
the full length STEAP-1 cDNA was obtained and sequenced, it became
apparent that this clone also corresponds to STEAP-1 (more
specifically, to residues 622 through the 3' end of the STEAP-1
nucleotide sequence as shown in FIGS. 1A-B).
[0274] Differential expression analysis by RT-PCR using primers
derived from the 8P1D4 cDNA clone showed that the 8P1D4 (STEAP-1)
gene is expressed at approximately equal levels in normal prostate
and the LAPC-4 and LAPC-9 xenografts (FIG. 2, panel A). Further
RT-PCR expression analysis of first strand cDNAs from 16 normal
tissues showed greatest levels of 8P1D4 expression in prostate.
Substantially lower level expression in several other normal
tissues (i.e., colon, ovary, small intestine, spleen and testis)
was detectable only at 30 cycles of amplification in brain,
pancreas, colon and small intestine (FIG. 2, panels B and C).
Example 2
Isolation of Full Length STEAP-1 Encoding cDNA
[0275] The 436 bp 8P1D4 gene fragment (Example 1) was used to
isolate additional cDNAs encoding the 8PlD4/STEAP-1 gene. Briefly,
a normal human prostate cDNA library (Clontech) was screened with a
labeled probe generated from the 436 bp 8P1D4 cDNA. One of the
positive clones, clone 10, is 1195 bp in length and encodes a 339
amino acid protein having nucleotide and encoded amino acid
sequences bearing no significant homology to any known human genes
or proteins (homology to a rat Kidney Injury Protein recently
described in International Application WO98/53071). The encoded
protein contains at least 6 predicted transmembrane motifs implying
a cell surface orientation (see FIGS. 1A-B, predicted transmembrane
motifs underlined). These structural features led to the
designation "STEAP", for "Six Transmembrane Epithelial Antigen of
the Prostate".
[0276] Subsequent identification of additional STEAP proteins led
to the re-designation of the 8P1D4 gene product as "STEAP-1". The
STEAP-1 cDNA and encoded amino acid sequences are shown in FIG.
1A-B and correspond to SEQ ID NOS: 1 and 2, respectively. STEAP-1
cDNA clone 10 was deposited with the American Type Culture
Collection ("ATCC") (10801 University Blvd., Manassas, Va.
20110-2209 USA) as plasmid 8P1D4 clone 10.1 on Aug. 26, 1998 as
ATCC Accession Number 98849. The STEAP-1 cDNA clone can be excised
therefrom using EcoRI/XbaI double digest (EcoRI at the 5' end, XbaI
at the 3' end).
Example 3
STEAP-1 Gene and Protein Expression Analysis
[0277] In order to begin to characterize the biological
characteristics of STEAP-1, an extensive evaluation of STEAP-1 mRNA
and STEAP-1 protein expression across a variety of human tissue
specimens was undertaken. This evaluation included Northern blot,
Western blot and immunohistochemical analysis of STEAP-1 expression
in a large number of normal human tissues, human prostate cancer
xenografts and cell lines, and various other human cancer cell
lines.
Example 3A
Northern Blot Analysis of STEAP-1 mRNA Expression in Normal Human
Tissues
[0278] Initial analysis of STEAP-1 mRNA expression in normal human
tissues was conducted by northern blotting two multiple tissue
blots obtained from Clontech (Palo Alto, Calif.), comprising a
total of 16 different normal human tissues, using labeled STEAP-1
clone 10 as a probe. RNA samples were quantitatively normalized
with a actin probe. The results are shown in FIG. 3A. The highest
expression level was detected in normal prostate, with an
approximately 5-10 fold lower level of expression detected in colon
and liver. These northern blots showed two transcripts of
approximately 1.4 kb and 4.0 kb, the former of which corresponds to
the full length STEAP-1 clone 10 cDNA, which encodes the entire
STEAP-1 open reading frame. The larger transcript was separately
cloned as a 3627 bp cDNA from a normal prostate library, the
sequence of which contains a 2399 bp intron (FIG. 4).
[0279] This initial analysis was extended by using the STEAP-1
clone 10 probe to analyze an RNA dot blot matrix of 37 normal human
tissues (Clontech, Palo Alto, Calif.; Human Master Blot.TM.). The
results are shown in FIG. 3B and show strong STEAP-1 expression
only in prostate. Very low level STEAP-1 RNA expression was
detected in liver, lung, trachea and fetal liver tissue, at perhaps
a 5-fold lower level compared to prostate. No expression was
detected in any of the remaining tissues. Based on these analyses,
significant STEAP-1 expression appears to be prostate specific in
normal tissues.
Example 3B
Northern Blot Analysis of STEAP-1 mRNA Expression in Prostate
Cancer Xenografts and Cell Lines
[0280] To analyze STEAP-1 expression in human cancer tissues and
cell lines, RNAs derived from human prostate cancer xenografts and
an extensive panel of prostate and non-prostate cancer cell lines
were analyzed by Northern blot using STEAP-1 cDNA clone 10 as
probe. All RNA samples were quantitatively normalized by ethidium
bromide staining and subsequent analysis with a labeled
.beta.-actin probe.
[0281] The results, presented in FIG. 5, show high level STEAP-1
expression in all the LAPC xenografts and all of the prostate
cancer cell lines. Expression in the LAPC-9 xenografts was higher
compared to the LAPC-4 xenografts, with no significant difference
observed between androgen-dependent and androgen-independent
sublines (FIG. 5A). Expression in the LAPC-4 xenografts was
comparable to expression in normal prostate. Lower levels of
expression were detected in PrEC cells (Clonetics), which represent
the basal cell compartment of the prostate. Analysis of prostate
cancer cell lines showed highest expression levels in LNCaP, an
androgen dependent prostate carcinoma cell line. Significant
expression was also detected in the androgen-independent cell lines
PC-3 and DU145. High levels of STEAP expression were also detected
in LAPC-4 and LAPC-9 tumors that were grown within the tibia of
mice as a model of prostate cancer bone metastasis (FIG. 5B).
[0282] Significantly, very strong STEAP-1 expression was also
detected in many of the non-prostate human cancer cell lines
analyzed (FIG. 5A). Particularly high level expression was observed
in RD-ES cells, an Ewing sarcoma (EWS) derived cell line.
Additionally, very high level expression was also detected in
several of the colon cancer cell lines (e.g., CaCo-2, LoVo, T84 and
Colo-205), bladder carcinoma cell lines (e.g., SCABER, UM-UC-3,
TCCSUP and 5637), ovarian cancer cell lines (e.g., OV-1063 and SW
626) and pancreatic cancer cell lines (e.g., HPAC, Capan-1, PANC-1
and BxPC-3). These results, combined with the absence of strong
expression in the corresponding normal tissues (FIG. 3), indicate
that STEAP-1 may be generally up-regulated in these types (as well
as other types) of human cancers.
Example 3C
Western Blot Analysis of STEAP-1 Protein Expression in Prostate and
Other Cancers
[0283] A 15 mer peptide corresponding to amino acid residues 14
through 28 of the STEAP-1 amino acid sequence as shown in FIGS.
1A-B (WKMKPRRNLEEDDYL; SEQ ID NO: 22) was synthesized and used to
immunize sheep for the generation of sheep polyclonal antibodies
towards the amino-terminus of the protein (anti-STEAP-1) as
follows. The peptide was conjugated to KLH (keyhole limpet
hemocyanin). The sheep was initially immunized with 400 .mu.g of
peptide in complete Freund's adjuvant. The animal was subsequently
boosted every two weeks with 200 .mu.g of peptide in incomplete
Freund's adjuvant. Anti-STEAP antibody was affinity-purified from
sheep serum using STEAP peptide coupled to affigel 10 (Bio Rad).
Purified antibody is stored in phosphate-buffered saline with 0.1%
sodium azide.
[0284] To test antibody specificity, the cDNA of STEAP-1 was cloned
into a retrovital expression vector (pSR.alpha.tkneo, Muller et
al., 1991, MCB 11:1785). NIH 3T3 cells were infected with
retroviruses encoding STEAP-1 and were selected in G418 for 2
weeks. Western blot analysis of protein extracts of infected and
uninfected NIH 3T3 cells showed expression of a protein with an
apparent molecular weight of 36 kD only in the infected cells (FIG.
6, lanes marked "3T3 STEAP" AND "3T3").
[0285] The anti-STEAP-1 polyclonal antibody was used to probe
western blots of cell lysates prepared from a variety of prostate
cancer xenograft tissues, prostate cancer cell lines and other
non-prostate cancer cell lines. Protein samples (20 .mu.g each)
were quantitatively normalized by probing the blots with an
anti-Grb-2 antibody.
[0286] The results are shown in FIG. 6. STEAP-1 protein was
detected in all of the LAPC prostate cancer xenografts, all of the
prostate cancer cell lines, a primary prostate cancer specimen and
its matched normal prostate control. Highest STEAP-1 protein
expression was detected in the LAPC-9 xenograft and in LNCaP cells,
in agreement with the northern blot analysis described immediately
above. High level expression was also observed in the bladder
carcinoma cell line UM-UC-3. Expression in other cancer cell lines
was also detectable (FIG. 6).
Example 3D
Immunohistochemical Analysis of STEAP-1 Protein Expression in
Prostate Tumor Biopsy and Surgical Specimens
[0287] To determine the extent of STEAP-1 protein expression in
clinical materials, tissue sections were prepared from a variety of
prostate cancer biopsies and surgical samples for
immunohistochemical analysis. Tissues were fixed in 10% formalin,
embedded in paraffin, and sectioned according to standard protocol.
Formalin-fixed, paraffin-embedded sections of LNCaP cells were used
as a positive control. Sections were stained with a sheep
anti-STEAP-1 polyclonal antibody directed against a STEAP-1
N-terminal epitope (as described immediately above). LNCaP sections
were stained in the presence of an excess amount of the STEAP-1
N-terminal peptide immunogen used to generate the polyclonal
antibody (peptide 1) or a non-specific peptide derived from a
distinct region of the STEAP-1 protein (peptide 2; YQQVQQNKEDAWIEH;
SEQ ID NO: 33).
[0288] The results are shown in FIG. 8. LNCaP cells showed
uniformly strong pericellular staining in all cells RIG. 8B).
Excess STEAP N-terminal peptide (peptide 1) was able to
competitively inhibit antibody staining (FIG. 8A), while peptide 2
had no effect (FIG. 8B). Similarly, uniformly strong pericellular
staining was seen in the LAPC-9 (FIG. 8F) and LAPC-4 prostate
cancer xenografts. These results are clear and suggest that the
staining is STEAP specific. Moreover, these results show
localization of STEAP to the plasma membrane, corroborating the
biochemical findings presented in Example 4 below.
[0289] The results obtained with the various clinical specimens are
show in FIG. 8C (normal prostate tissue), FIG. 8D (grade 3
prostatic carcinoma), and FIG. 8E (grade 4 prostatic carcinoma),
and are also included in the summarized results shown in Table 1.
Light to strong staining was observed in the glandular epithelia of
all prostate cancer samples tested as well as in all samples
derived from normal prostate or benign disease (e.g., BPH). The
signal appears to be strongest at the cell membrane of the
epithelial cells, especially at the cell-cell junctions (FIGS.
8C-E) and is also inhibited with excess STEAP N-terminal peptide 1.
Some basal cell staining is also seen in normal prostate (FIG. 8C),
which is more apparent when examining atrophic glands. STEAP-1
seems to be expressed at all stages of prostate cancer since lower
grades (FIG. 8D), higher grades (FIG. 8E) and metastatic prostate
cancer (represented by LAPC-9; FIG. 8F; See also human patient
metastases shown in FIGS. 32A-B) all exhibit strong staining.
[0290] Immunohistochemical staining of a large panel of normal
non-prostate tissues showed no detectable STEAP-1 expression in
most of these normal tissues (Table 1). Normal bladder exhibited
low levels of cell surface staining in the transitional epithelium
(FIG. 8G). Pancreas, stomach, uterus, fallopian tubes and pituitary
showed low levels of cytoplasmic staining (Table 1). It is unclear
whether the observed cytoplasmic staining is specific or is due to
non-specific binding of the antibody, since northern blotting
showed little to no STEAP-1 expression in pancreas (FIG. 3). These
results indicate that cell surface expression of STEAP-1 in normal
tissues appears to be restricted to prostate and bladder.
7TABLE 1 Immunohistochemical Staining of Human Tissues With
Anti-STEAP-1 Sheep Polyclonal Antibody Staining Intensity Tissues*
None Cerebellum, cerebral cortex, spinal cord, heart, skeletal
muscle (2), artery, thymus, spleen (4), bone marrow, lymph node
(3), lung (8), liver (4), ileum, kidney (2), testis (2), ovary,
placenta, breast, adrenal gland (2), thyroid gland (2), skin (2)
Light Ureter, bladder cancer (2/5), colon (4/7), colon cancer
(4/7), Cytoplasmic fallopian tubes (2), pituitary gland, pancreas,
stomach (1/2), uterus (1/2) Light Prostate cancer bone marrow
metastasis (1/6), prostate Membrane cancer lymph node metastasis
(1/5), lung cancer (1/6) Moderate Prostate (7/7), BPH (5/5),
prostate cancer (20/20)**, to prostate cancer lymph node metastasis
(4/5), prostate cancer Strong bone marrow metastasis (5/6), bladder
(2/5), bladder cancer Membrane (3/5), lung cancer (3/6) *In cases
where more than one sample was analyzed per tissue, the number in
parenthesis indicates how many samples showed positive
staining/total analyzed. **Prostate cancer grades varied from 3 to
5 and Gleason scores of 7 to 10.
Example 3E
Immunohistochemical Analysis of STEAP-1 Protein Expression in
Bladder and Lung Cancer
[0291] To determine the extent of STEAP-1 protein expression in
other cancers, tissue from bladder and lung cancer clinical
specimens were subjected to immunohistochemical analysis using the
polyclonal antibody and methods as described in Example 3D. The
results, shown in FIGS. 21A-D, reveal a pericellular staining
pattern similar to that observed with prostate cancer tissue.
Example 4
Biochemical Characterization of STEAP-1 Protein
[0292] To initially characterize the STEAP-1 protein, cDNA clone 10
was cloned into the pcDNA 3.1 Myc-His plasmid (Invitrogen), which
encodes a 6His tag at the carboxyl-terminus, transfected into 293T
cells, and analyzed by flow cytometry using anti-His monoclonal
antibody (His-probe, Santa Cruz) as well as the anti-STEAP-1
polyclonal antibody described above. Staining of cells was
performed on intact cells as well as permeabilized cells. The
results indicated that only permeabilized cells stained with both
antibodies, suggesting that both termini of the STEAP-1 protein are
localized intracellularly. It is therefore possible that one or
more of the STEAP-1 protein termini are associated with
intracellular organelles rather than the plasma membrane.
[0293] To determine whether STEAP-1 protein is expressed at the
cell surface, intact STEAP-1-transfected 293T cells were labeled
with a biotinylation reagent that does not enter live cells.
STEAP-1 was then immunoprecipitated from cell extracts using the
anti-His and anti-STEAP antibodies. SV40 large T antigen, an
intracellular protein that is expressed at high levels in 293T
cells, and the endogenous cell surface transferrin receptor were
immunoprecipitated as negative and positive controls, respectively.
After immunoprecipitation, the proteins were transferred to a
membrane and visualized with horseradish peroxidase-conjugated
streptavidin. The results of this analysis are shown in FIG. 7.
Only the transferrin receptor (positive control) and STEAP-1 were
labeled with biotin, while the SV40 large T antigen (negative
control) was not detectably labeled (FIG. 7A). Since only cell
surface proteins are labeled with this technique, it is clear from
these results that STEAP-1 is a cell surface protein. Combined with
the results obtained from the flow cytometric analysis, it is clear
that STEAP-1 is a cell surface protein with intracellular amino-
and carboxyl- termini.
[0294] Furthermore, the above results together with the STEAP-1
secondary structural predictions, shows that STEAP-1 is a type IIIa
membrane protein with a molecular topology of six potential
transmembrane domains, 3 extracellular loops, 2 intracellular loops
and two intracellular termini. A schematic representation of
STEAP-1 protein topology relative to the cell membrane is shown in
FIG. 1B.
[0295] In addition, prostate, bladder and colon cancer cells were
directly analyzed for cell surface expression of STEAP-1 by
biotinylation studies. Briefly, biotinylated cell surface proteins
were affinity purified with streptavidin-gel and probed with the
anti-STEAP-1 polyclonal antibody described above. Western blotting
of the streptavidin purified proteins clearly show cell surface
biotinylation of endogenous STEAP-1 in all prostate (LNCaP, PC-3,
DU145), bladder (UM-UC-3, TCCSUP) and colon cancer (LoVo, Colo)
cells tested, as well as in NIH 3T3 cells infected with a STEAP-1
encoding retrovirus, but not in non-expressing NIH 3T3 cells used
as a negative control (FIG. 7B). In a further negative control,
STEAP-1 protein was not detected in streptavidin precipitates from
non-biotinylated STEAP expressing cells (FIG. 7B).
Example 5
Constructs for Recombinant Expression of STEAP-1
[0296] pGEX Constructs
[0297] To express STEAP-1 in bacterial cells, portions of STEAP-1
were fused to the Glutathione S-transferase (GST) gene by cloning
into pGEX-6P-1 (Amersham Pharmacia Biotech, NJ). All constructs
were made to generate recombinant STEAP-1 protein sequences with
GST fused at the N-terminus and a six histidine epitope at the
C-terminus. The six histidine epitope tag was generated by adding
the histidine codons to the cloning primer at the 3' end of the
ORF. A PreScission.TM. recognition site permits cleavage of the GST
tag from STEAP-1. The ampicillin resistance gene and pBR322 origin
permits selection and maintenance of the plasmid in E. coli. The
following fragments of STEAP-1 were cloned into pGEX-6P-1:
[0298] Amino acids 148 to 251; amino acids 144 to 339; amino acids
39 to 253; amino acids 70 to 136; amino acids 254 to 313.
[0299] And into pGEX-4T: Amino acids 2 to 247; amino acids 135-318;
and amino acids 144-339.
[0300] Exemplary additional constructs that can be made in
pGEX-6P-1 spanning the following regions of the STEAP-1 protein
include:
[0301] Amino acids 1 to 339; amino acids 1 to 144.
[0302] pcDNA3.1/MycHis Construct
[0303] To express STEAP-1 in mammalian cells, the 1,017 bp STEAP-1
ORF (with translational start Kozak consensus) was cloned into
pcDNA3.1/MycHis_Version B (Invitrogen, Carlsbad, Calif.). Protein
expression is driven from the cytomegalovirus (CMV) promoter. The
recombinant protein has the myc and six histidines fused to the
C-terminus. The pcDNA3.1/MycHis vector also contains the bovine
growth hormone (BGH) polyadenylation signal and transcription
termination sequence to enhance mRNA stability along with the SV40
origin for episomal replication and simple vector rescue in cell
lines expressing the large T antigen. The Neomycin resistance gene
allows for selection of mammalian cells expressing the protein and
the ampicillin resistance gene and ColE1 origin permits selection
and maintenance of the plasmid in E. coli.
[0304] pSRa Constructs
[0305] To generate mammalian cell lines expressing STEAP-1
constitutively, the 1,017 bp ORF (with translational start Kozak
consensus) was cloned into pSRa constructs. Amphotropic and
ecotropic retroviruses are generated by transfection of pSRa
constructs into the 293T-10A1 packaging line or co-transfection of
pSRa and a helper plasmid (.psi.-) in 293 cells, respectively. The
retrovirus can be used to infect a variety of mammalian cell lines,
resulting in the integration of the cloned gene, STEAP-1, into the
host cell lines. Protein expression is driven from a long terminal
repeat (LTR). The Neomycin resistance gene allows for selection of
mammalian cells expressing the protein and the ampicillin
resistance gene and ColE1 origin permits selection and maintenance
of the plasmid in E. coli. Additional pSRa constructs were made
that fused the FLAG tag to the C and N-terminus to allow detection
using anti-FLAG antibodies. The FLAG sequence 5' gat tac aag gat
gac gac gat aag 3' (SEQ ID NO: 34) were added to cloning primer at
the 3' end of the ORF. Another pSRa construct was made that
contained amino acids 182 to 454. This truncated form of the
STEAP-1 protein will help determine the function of the long
extracellular N-Terminal region.
[0306] An Additional pSRa construct is being made to produce a
myc/6 HIS fusion protein of the fill length STEAP-1 protein.
Example 6
Identification and Structural Analysis of Other Human STEAPs
[0307] STEAP-1 has no homology to any known human genes. In an
attempt to identify additional genes that are homologous to
STEAP-1, the protein sequence of STEAP-1 was used as an electronic
probe to identify family members in the public EST (expression
sequence tag) database (dbEST). Using the "tblastn" function in
NCBI (National Center for Biotechnology Information), the dbEST
database was queried with the STEAP-1 protein sequence. This
analysis revealed additional putative STEAP-1 homologues or STEAP
family members, as further described below.
[0308] In addition, SSH cloning experiments also identified a
STEAP-1 related cDNA fragment, clone 98P4B6. This clone was
isolated from SSH cloning using normal prostate cDNA as tester and
LAPC-4 AD cDNA as driver. A larger partial sequence of the 98P4B6
clone was subsequently isolated from a normal prostate library;
this clone encodes an ORF of 173 amino acids with close homology to
the primary structure of STEAP-1, and thus was designated STEAP-2.
A full length STEAP-2 cDNA of 2454 bp was isolated from a prostate
library. The STEAP-2 nucleotide and encoded ORF amino acid
sequences are shown in FIG. 9A-D. An amino acid alignment of the
STEAP-1 and partial STEAP-2 primary structures is shown in FIGS.
11A-B and 11C. STEAP-1 and -2 share 61% identity over their 171
amino acid residue overlap (FIG. 11C). The STEAP-2 cDNA has been
deposited with the American Type Culture Collection ("ATCC"; 10801
University Blvd., Manassas, Va. 20110-2209 USA) as plasmid
98P4B6-GTD3 on Jul. 2, 1999 as ATCC Accession Number PTA-311.
[0309] The STEAP-2 cDNA (98P4B6-GTD3) contains a 355 bp 5' UTR
(untranslated region) that is 72% GC rich, suggesting that it
contains translational regulatory elements. The cDNA encodes an
open reading frame (ORF) of 454 amino acids (a.a.) with six
potential transmembrane domains. This is in contrast to STEAP-1,
which is 339 a.a. in length. Alignment with STEAP-1 demonstrates
54.9% identity over a 237 amino acid overlap. Interestingly, the
locations of the six putative transmembrane domains in STEAP-2
coincide with the locations of the transmembrane domains in STEAP-1
(see alignment). The homology of STEAP-2 with STEAP-1 is highest in
the regions spanned by the first putative extracellular loop to the
fifth transmembrane domain. This analysis and the sequence of
STEAP-2 suggest some significant differences between STEAP-1 and
STEAP-2: STEAP-2 exhibits a 205 a.a. long intracellular N-terminus
(compared to 69 a.a. in STEAP-1) and a short 4 a.a. intracellular
C-terminus (compared to 26 a.a. in STEAP-1). These differences
could imply significant differences in function and/or interaction
with intracellular signaling pathways. To identify a unique mouse
EST corresponding to STEAP-2, the unique N-terminus of STEAP-2 was
used to query the dbEST database. One mouse EST was isolated
(AI747886, mouse kidney) that may be used in the identification of
mouse STEAP-2 and in expression analysis of STEAP-2 in mouse.
[0310] Two ESTs encoding ORFs bearing close homology to the STEAP-1
and STEAP-2 sequences were also identified by electronic probing
with the STEAP-1 protein sequence. These ESTs (AI139607 and R80991)
were provisionally designated STEAP-3 and STEAP4. A fUil length
cDNA encoding STEAP-3 was subsequently cloned, and its nucleotide
and deduced amino acid sequences are shown in FIGS. 10A-E. The
STEAP-3 cDNA has been deposited with the American Type Culture
Collection ("ATCC"; 10801 University Blvd., Manassas, Va.
20110-2209 USA) on Dec. 8, 1999 as plasmid pSTEAP-3 EBB4 as ATCC
Accession Number PTA-1033. The nucleotide sequences of the ESTs
corresponding to the STEAPs are reproduced in FIG. 10F.
[0311] An amino acid alignment of the structures of STEAP-1,
STEAP-2, STEAP-3 and the partial sequence of the putative STEAP-4
is shown in FIGS. 11A-B. This alignment shows a close structural
similarity between all four STEAP family proteins, particularly in
the predicted transmembrane domains. As indicated above, STEAP-1
and STEAP-2 demonstrate 54.9% identity over a 237 amino acid
overlap. STEAP-1 and STEAP-3 are 40.9% identical over a 264 amino
acid region, while STEAP-2 and STEAP-3 are 47.8% identical over a
416 amino acid region.
Example 7
Constructs for Recombinant Expression of STEAP-2
[0312] pGEX Constructs
[0313] To express STEAP-2 in bacterial cells, portions of STEAP-2
were fused to the Glutathione S-transferase (GST) gene by cloning
into pGEX-6P-1 (Amersham Pharmacia Biotech, NJ). All constructs
were made to generate recombinant STEAP-2 protein sequences with
GST fused at the N-terminus and a six histidine epitope at the
C-terminus. The six histidine epitope tag was generated by adding
the histidine codons to the cloning primer at the 3' end of the
ORF. A PreScission.TM. recognition site permits cleavage of the GST
tag from STEAP-2. The ampicillin resistance gene and pBR322 origin
permits selection and maintenance of the plasmid in E. coli. The
following fragments of STEAP-2 were cloned into pGEX-6P-1:
[0314] Amino acids 287 to 390; amino acids 285 to 454; amino acids
193 to 454.
[0315] Additional exemplary constructs that can be made in
pGEX-6P-1 spanning the following regions of the STEAP-2 protein
include:
[0316] Amino acids 1 to 193; amino acids 1 to 454.
[0317] And in pGEX-4T: Amino acids 2-204; 183-387; and 276-453.
[0318] pCRII Construct
[0319] To generate sense and anti-sense riboprobes for RNA in situ
investigations, a pCRII construct was generated using bp 367 to 877
of the GTD3 STEAP-2 cDNA. The pCRII vector has Sp6 and T7 promoters
flanking the insert to drive the production of STEAP-2 RNA
riboprobes which were used in RNA in situ hybridization
experiments.
[0320] pcDNA4/HisMax-TOPO Construct
[0321] To express STEAP-2 in mammalian cells, the 1,362 bp STEAP-2
ORF was cloned into pcDNA4/HisMax-TOPO Version A (cat# K864-20,
Invitrogen, Carlsbad, Calif.). Protein expression is driven from
the cytomegalovirus (CMV) promoter and the SP163 translational
enhancer. The recombinant protein has Xpress.TM. and six histidine
epitopes fused to the N-terminus. In addition to this construct
containing only the 1,362 bp ORF an additional construct was made
with the C-terminus of the recombinant protein containing a 28
amino acid fusion resulting from vector sequences prior to the
termination codon. The pcDNA4/HisMax-TOPO vector also contains the
bovine growth hormone (BGH) polyadenylation signal and
transcription termination sequence to enhance mRNA stability along
with the SV40 origin for episomal replication and simple vector
rescue in cell lines expressing the large T antigen. The Zeocin
resistance gene allows for selection of mammalian cells expressing
the protein and the ampicillin resistance gene and ColE1 origin
permits selection and maintenance of the plasmid in E. coli.
[0322] pcDNA3.1/MycHis Construct
[0323] To express STEAP-2 in mammalian cells, the 1,362 bp STEAP-2
ORF (with start Kozak consensus) was cloned into
pcDNA3.1/MycHis_Version A (Invitrogen, Carlsbad, Calif.). Protein
expression is driven from the cytomegalovirus (CMV) promoter. The
recombinant protein has the myc and six histidines fused to the
C-terminus. The pcDNA3.1/MycHis vector also contains the bovine
growth hormone (BGH) polyadenylation signal and transcription
termination sequence to enhance mRNA stability along with the SV40
origin for episomal replication and simple vector rescue in cell
lines expressing the large T antigen. The neomycin resistance gene
allows for selection of mammalian cells expressing the protein and
the ampicillin resistance gene and ColE1 origin permits selection
and maintenance of the plasmid in E. coli. Additional
pcDNA3.1/MycHis constructs were generated using STEAP-2 amino acids
6 to 454, 121-454 and 182-454.
[0324] pBlueBacHIS2a
[0325] To express STEAP-1 in SF9 insect cells, the STEAP-1 ORF was
cloned into pBlueBacHIS2A (nvitrogen, California). Protein
expression is driven under the polyhedrin promoter. N-terminus poly
HIS and Xpress tags allow for detection and purification of the
recombinant STEAP-1 protein. A C-terminus enterokinase recognition
site allows for cleavage of these tags. The ampicillin resistance
gene and ColE1 origin permits selection and maintenance of the
plasmid in E. coli. Following cotransfection with AcMNPV DNA, a
homologous recombination event occurs between these sequences
resulting in a recombinant virus carrying the gene of interest and
the polyhedrin. A variety of restriction enzyme sites for
simplified subcloning are present. In addition, a reporter gene
(b-galactosidase) conveniently identifies recombinant plaques, to
eliminate tedious plaque screening.
[0326] pcDNA3.1CT-GFP-TOPO Construct
[0327] To express STEAP-2 in mammalian cells and to allow detection
of the recombinant protein using fluorescence, the 1,362 bp ORF
(with start Kozak consensus) was cloned into pcDNA3.1CT-GFP-TOPO
(Invitrogen, CA). Protein expression is driven from the
cytomegalovirus (CMV) promoter. The recombinant protein has the
Green Fluorescent Protein (GFP) fused to the C-terminus
facilitating non-invasive, in vivo detection and cell biology
studies. The pcDNA3.1/MycHis vector also contains the bovine growth
hormone (BGH) polyadenylation signal and transcription termination
sequence to enhance mRNA stability along with the SV40 origin for
episomal replication and simple vector rescue in cell lines
expressing the large T antigen. The neomycin resistance gene allows
for selection of mammalian cells expressing the protein and the
ampicillin resistance gene and ColE1 origin permits selection and
maintenance of the plasmid in E. coli.
[0328] An additional construct with a N-terminal GFP fusion is
being made in pcDNA3.1NT-GFP-TOPO spanning the entire length of the
STEAP-2 protein. pSRa Constructs To generate mammalian cell lines
expressing STEAP-2 constitutively, the 1362 bp ORF was cloned into
pSRa constructs. Amphotropic and ecotropic retroviruses are
generated by transfection of pSRa constructs into the 293T-10AI
packaging line or co-transfection of pSRa and a helper plasmid
(.psi.-) in 293 cells, respectively. The retrovirus can be used to
infect a variety of mammalian cell lines, resulting in the
integration of the cloned gene, STEAP-2, into the host cell-lines.
Protein expression is driven from a long terminal repeat (LTR). The
neomycin resistance gene allows for selection of mammalian cells
expressing the protein and the ampicillin resistance gene and ColE1
origin permits selection and maintenance of the plasmid in E. coli.
Additional pSRa constructs were made that fused the FLAG tag to the
C and N-terminus to allow detection using anti-FLAG antibodies. The
FLAG sequence 5' gat tac aag gat gac gac gat aag 3' (SEQ ID NO: 34)
was added to cloning primer at the 3' end of the ORF. Another pSRa
construct was made that contained amino acids 182 to 454. This
truncated form of the STEAP-2 protein will help determine the
function of the long extracellular N-Terminal region.
[0329] In addition, a pSRa construct can be made to produce a myc/6
HIS fusion protein of the full length STEAP protein.
Example 8
Expression Analysis of STEAP-2 and Other Human STEAP Family
Members
Example 8A
Tissue Specific Expression of STEAP Family Members in Normal Human
Tissues
[0330] RT-PCR analysis of STEAP-2 shows expression in all the LAPC
prostate cancer xenografts and in normal prostate (FIG. 14, panel
A). Analysis of 8 normal human tissues shows prostate-specific
expression after 25 cycles of amplification (FIG. 14, panel B).
Lower level expression in other tissues was detected only after 30
cycles of amplification. Northern blotting for STEAP-2 shows a
pattern of 2 transcripts (approximately 3 and 8 kb in size)
expressed only in prostate (and at significantly lower levels in
the LAPC xenografts), with no detectable expression in any of the
15 other normal human tissues analyzed (FIG. 15, panel C). Thus,
STEAP-2 expression in normal human tissues appears to be highly
prostate-specific.
[0331] Expression analysis of STEAP family members in normal
tissues was performed by Northern blot and/or RT-PCR. All STEAP
family members appeared to exhibit tissue restricted expression
patterns. STEAP-3/AI139607 expression is shown in FIG. 12A
(Northern) and FIG. 12B (RT-PCR). STEAP-4/R80991 expression is
shown in FIG. 13.
Example 8B
Expression of STEAP-2 in Various Cancer Cell Lines
[0332] The RT-PCR results above suggested that the different STEAP
family members exhibit different tissue expression patterns.
Interestingly, STFAP-2, which appears very prostate-specific, seems
to be expressed at lower levels in the LAPC xenografts. This is in
contrast to STEAP-1, which is highly expressed in both normal and
malignant prostate tissue.
[0333] To better characterize this suggested difference in the
STEAP-2 prostate cancer expression profile (relative to STEAP-1),
Northern blotting was performed on RNA derived from the LAPC
xenografts, as well as several prostate and other cancer cell
lines, using a STEAP-2 specific probe labeled cDNA clone 98P4B6).
The results are shown in FIG. 16 and can be summarized as follows.
STEAP-2 is highly expressed in normal prostate and in some of the
prostate cancer xenografts and cell lines. More particularly, very
strong expression was observed in the LAPC-9 AD xenograft and the
LNCaP cells. Significantly attenuated or no expression was observed
in the other prostate cancer xenografts and cell lines. Very strong
expression was also evident in the Ewing Sarcoma cell line RD-ES.
Unlike STEAP-1, which is highly expressed in cancer cell lines
derived from bladder, colon, pancreatic and ovarian tumors, STEAP-2
showed low to non-detectable expression in these same cell lines
(compare with FIG. 5). Interestingly, STEAP-2 was also
non-detectable in PrEC cells, which are representative of the
normal basal cell compartment of the prostate. These results
suggests that expression of STEAP-1 and STEAP-2 are differentially
regulated. While STEAP-1 may be a gene that is generally
up-regulated in cancer, STEAP-2 may be a gene that is more
restricted to normal prostate and prostate cancer.
Example 8C
Analysis of in Situ Expression of STEAP-2 RNA in Normal Prostate
and Prostate Cancer
[0334] The expression of STEAP-2 RNA was evaluated using in situ
hybridization with a labeled antisense probe and using a labeled
sense probe as control. All four of four normal prostate tissue
specimens examined were positive for STEAP (FIGS. 22A-B). Likewise,
five of five prostate cancer tissue specimens were positive using
STEAP RNA in Jiu hybridization (FIGS. 23A-B). A PIN specimen and a
sample of LNCaP cells that were examined were positive as well.
Example 8D
Analysis of STEAP-2 Expression in Cancer Tissues
[0335] The expression of STEAP-2 in various cancer tissues was
examined using RT-PCR. The results are shown in FIG. 24, in which
lane 1 represents a sample from an LAPC4 AD xenograft; lane 2 is
LAPC9 AD xenograft; lane 3 is LAPC9 AD.sup.2 xenograft (grown with
human bone explant); lane 4 is LAPC9 AD IT (grown intratibially);
lane 5 is pooled tissue from colon cancer patients; lane 6 is
pooled tissue from lung cancer patients; M represents a marker
lane; lane 7 is patient normal prostate tissue; lane 8 is patient
prostate cancer tissue; lane 9 is pooled tissue from kidney cancer
patients; lane 10 is pooled tissue from bladder cancer patients;
lane 11 is HeLa cells; and lane 12 is a water blank. The highest
expression is found in the three LAPC9 AD xenografts. High
expression is observed in the LAPC4 AD xenograft as well, and in
normal prostate and lung cancer. Significant expression was
detected also in colon and bladder cancer. Lower expression was
detected in prostate and kidney cancer patient samples.
Example 8E
Analysis of STEAP-2 Expression in Normal Tissues
[0336] The expression of STEAP-2 in 76 normal human tissues was
examined using a dot blot analysis of RNA samples. As shown in FIG.
25, STEAP-2 is expressed at very high levels only in normal
prostate.
Example 9
Chromosomal Localization of STEAP Genes
[0337] The chromosomal localization of STEAP-1 was determined using
the GeneBridge 4 Human/Hamster radiation hybrid (RH) panel (Walter
et al., 1994, Nat. Genetics 7:22) (Research Genetics, Huntsville
Ala.), while STEAP-2 and the STEAP homologues were mapped using the
Stanford G3 radiation hybrid panel (Stewart et al., 1997, Genome
Res. 7:422).
[0338] The following PCR primers were used for STEAP-1:
8 8P1D4.1 5' ACTTTGTTGATGACCAGGATTGGA 3' (SEQ ID NO: 4) 8P1D4.2 5'
CAGAACTTCAGCACACACAGGAAC 3' (SEQ ID NO: 5)
[0339] The resulting STEAP-1 mapping vector for the 93 radiation
hybrid panel DNAs
(2100000201101010001000000101110101221000111001110110101000100-
010001010010 21000001111001010000), and the mapping program
available at the internet address
<http://www-genome.wi.mit.edu/cgi-bin/contig/rhma- pper.pl>,
localized the STEAP-1 gene to chromosome 7p22.3, telomeric to
D7S531.
[0340] The following PCR primers were used for 98P4B6/STEAP-2:
9 98P4B6.1 5' GACTGAGCTGGAACTGGAATTTGT 3' (SEQ ID NO: 20) 98P4B6.2
5' TTTGAGGAGACTTCATCTCACTGG 3' (SEQ ID NO: 21)
[0341] The resulting vector
(000001001000000000000000000000001001000000000- 0100
0100000000000001000010101010010011), and the mapping program
available at the internet address
<http://www-shgc.stanford.edu/RH/ths- erverformew.html> maps
the 98P4B6 (STEAP-2) gene to chromosome 7q21.
[0342] The following PCR primers were used for AI139607:
10 AI139607.1 5' TTAGGACAACTTGATCACCAGCA 3' (SEQ ID NO: 16)
AI139607.2 5' TGTCCAGTCCAAACTGGGTTATTT 3' (SEQ ID NO: 17)
[0343] The resulting vector
(000000001000000000000000000010001000002000000- 0100
0100000001000000100010001010000010), and the mapping program
available at the internet address
<http://www-shgc.stanford.edu/RH/rhs- erverfortnnew.html>,
maps AI139607 to chromosome 7q21.
[0344] The following PCR primers were used for R80991:
11 R80991.3 5' ACAAGAGCCACCTCTGGGTGAA 3' (SEQ ID NO: 35) R80991.4
5' AGTTGAGCGAGTTTGCAATGGAC 3' (SEQ ID NO: 36)
[0345] The resulting vector (0000000000020000102000000001
000000000000000000 0010000000001000011100000001001000001), and the
mapping program available at the internet address
<http://www-shgc.sta- nford.edu/RH/rhserverformew.html> maps
R80991 to chromosome 2q14-q21, near D2S2591.
[0346] In summary, the above results show that three of the
putative human STEAP family members localize to chromosome 7, as is
schematically depicted in FIG. 17. In particular, the STEAP-1 gene
localizes to the far telomeric region of the short arm of
chromosome 7, at 7p22.3, while STEAP-2 and AI139607 localize to the
long arm of chromosome 7, at 7q21 (FIG. 17). R80991 maps to
chromosome 2q14-q.sup.21.
Example 10
Identification of Intron-Exon Boundaries of STEAP-1
[0347] Genomic clones for STEAP-1 were identified by searching
GenBank for BAC clones containing STEAP-1 sequences, resulting in
the identification of accession numbers AC004969 (PAC DJ1121E10)
and AC005053 (BAC RG141D11). Using the sequences derived from the
PAC and BAC clones for STEAP the intron-exon boundaries were
defined (FIG. 18). A total of 4 exons and 3 introns were identified
within the coding region of the STEAP gene. Knowledge of the exact
exon-intron structure of the STEAP-1 gene may be used for designing
primers within intronic sequences which in turn may be used for
genomic amplification of exons. Such amplification permits
single-stranded confotmational polymorphism (SSCP) analysis to
search for polymorphisms associated with cancer. Mutant or
polymorphic exons may be sequenced and compared to wild type STEAP.
Such analysis may be useful to identify patients who are more
susceptible to aggressive prostate cancer, as well as other types
of cancer, particularly colon, bladder, pancreatic, ovarian,
cervical and testicular cancers.
[0348] Southern blot analysis shows that the STEAP-1 gene exists in
several species including mouse (FIG. 19). Therefore, a mouse BAC
library (Mouse ES 129-V release I, Genome Systems, FRAC-4431) was
screened with the human cDNA for STEAP-1 (clone 10, Example 2). One
positive clone, 12P11, was identified and confirmed by southern
blotting (FIG. 20). The intron-exon boundary information for human
STEAP may be used to identify the mouse STEAP-1 coding
sequences.
[0349] The mouse STEAP-1 genomic clone may be used to study the
biological role of STEAP-1 during development and tumorigenesis.
Specifically, the mouse genomic STEAP-1 clone may be inserted into
a gene knock-out (K/O) vector for targeted disruption of the gene
in mice, using methods generally known in the art. In addition, the
role of STEAP in metabolic processes and epithelial cell function
may be elucidated. Such K/O mice may be crossed with other prostate
cancer mouse models, such as the TRAMP model (Greenberg et al.,
1995, PNAS 92:3439), to determine whether STEAP influences the
development and progression of more or less aggressive and
metastatic prostate cancers.
Example 11
Predicted HLA-A2 Binding Peptides of STEAP-1 and STEAP-2
[0350] The complete amino acid sequences of the STEAP-1 and STEAP-2
proteins were entered into the HLA Peptide Motif Search algorithm
found in the Bioinformatics and Molecular Analysis Section (BIMAS)
Web site (http://bimas.dcrt.nih.gov/). The HLA Peptide Motif Search
algorithm was developed by Dr. Ken Parker based on binding of
specific peptide sequences in the groove of HLA Class I molecules
and specifically HLA-A2 (Falk et al., 1991, Nature 351: 290-6; Hunt
et al., 1992, Science 255:1261-3; Parker et al., 1992, J. Immunol.
149:3580-7; Parker et al., 1994, J. Immunol. 152:163-75). This
algorithm allows location and ranking of 8-mer, 9-mer, and 10-mer
peptides from a complete protein sequence for predicted binding to
HLA-A2 as well as other HLA Class I molecules. Most HLA-A2 binding
peptides are 9-mers favorably containing a leucine (L) at position
2 and a valine (V) or leucine (L) at position 9.
[0351] The results of STEAP-1 and STEAP-2 predicted binding
peptides ate shown in Table 2 below. For both proteins the top 5
ranking candidates are shown along with their location, the amino
acid sequence of each specific peptide, and an estimated binding
score. The binding score corresponds to the estimated half-time of
dissociation of complexes containing the peptide at 37.degree. C.
at pH 6.5. Peptides with the highest binding score (i.e. 10776.470
for STEAP-1 peptide 165; 1789.612 for STEAP-2 peptide 227) are
predicted to be the most tightly bound to HLA Class I on the cell
surface and thus represent the best immunogenic targets for T-cell
recognition. Actual binding of peptides to HLA-A2 can be evaluated
by stabilization of HLA-A2 expression on the antigen-processing
defective cell line T2 (Refs. 5,6). Immunogenicity of specific
peptides can be evaluated in vitro by stimulation of CD8+ cytotoxic
T lymphocytes (CTL) in the presence of dendritic cells (Xue et al.,
1997, Prostate 30:73-8; Peshwa et al., 1998, Prostate
36:129-38).
12TABLE 2 Predicted Binding of STEAP-1 and STEAP-2 Peptide
Sequences With Highest Affinity for HLA-A2 Start Subsequence Score
(Estimate of Half Rank Position Residue Listing Time of
Disassociation) STEAP-1 1 165 GLLSFFFAV 10776.470 2 86 FLYTLLREV
470.951 3 262 LLLGTIHAL 309.050 4 302 LIFKSILFL 233.719 5 158
MLTRKQFGL 210.633 STEAP-2 1 227 FLYSFVRDV 1789.612 2 402 ALLISTFHV
1492.586 3 307 LLSFFFAMV 853.681 4 306 GLLSFFFAM 769.748 5 100
SLWDLRHLL 726.962
Example 12
STEAP-2 Induction of Tyrosine Phosphorylation of Cellular
Proteins
[0352] Multi-transmembrane proteins have the ability to transmit
signal from the membrane and initiate signaling cascades that
regulate a variety of downstream events, including gene expression,
cellular differentiation, migration and proliferation (Biochim.
Biophys. Acta 1997; 1348:56-62, J. Virol. 1995; 69:675-83). In
order to determine the involvement of STEAP-1 and STEAP-2 in
downstream signaling events, the effect of STEAP-1 and STEAP-2 on
tyrosine phosphorylation of PC3 cells was investigated (FIG. 26).
PC3 cells, stably expressing neo, STEAP-1, or STEAP-2 were grown
overnight in 1% fetal bovine serum (FBS) to reduce receptor
occupancy and background activity. The cells were then incubated
for 5 minutes in the presence of either 1% or 10% FBS, lysed and
analyzed by western blotting with anti-phosphotyrosine (4G10 mAb).
An overlay using anti-Grb2 Ab was used to show that the gel was
equally loaded.
[0353] The results (FIG. 26) show that expression of STEAP-2 in PC3
cells induces the phosphorylation of several proteins on tyrosine
residues, including p150, p120 and p75. In contrast, expression of
STEAP-1 induced the de-phosphorylation of p150. Several of the
phosphorylated proteins correspond to known signaling proteins,
indicating that STEAP-1 and STEAP-2 may be controlling the
activation of specific signaling cascades.
Example 13
STEAP-1- and STEAP-2-Mediated Activation of MAPK Cascades
[0354] Several multi-transmembrane proteins induce specific
biological responses by activating protein kinase cascades,
including the MAPK pathways (Curr. Med. Chem. 2000; 7:911-43, Life
Sci. 2000; 67:335-6, Biol. Chem. 2000; 275:4660-9). In order to
determine whether expression of STEAP-1 and STEAP-2 is sufficient
to regulate specific signaling pathways not otherwise active in
resting PC3 cells, the effect of these genes on the activation of
the p.sup.38 MAPK cascade was investigated in the prostate cancer
cell line PC3 (FIGS. 27A-B). Activation of the p38 kinase is
dependent on its phosphorylation on tyrosine and serine residues.
Phosphorylated p.sup.38 can be distinguished from the
non-phosphorylated state by a Phospho-p38 mAb. This
phospho-specific Ab was used to study the phosphorylation state of
p38 in engineered PC3 cell lines.
[0355] PC3 cells stably expressing STEAP-1, STEAP-2 or neo were
grown overnight in either 1% or 10% FBS. Whole cell lysates were
analyzed by western blotting. PC3 cells treated with the known p38
activators, NaSaI or TNF, were used as a positive control. The
results show that while expression of the control neo gene has no
effect on p38 phosphorylation, expression of STEAP-1 and STEAP-2 in
PC3 cells is sufficient to induce the activation of the p38 pathway
(FIG. 27A). The results were verified using western blotting with
an anti-p38 Ab, which shows equal protein loading on the gels (FIG.
27B).
[0356] In another set of experiments, the sufficiency of expression
of STEAP-1 or STEAP-2 in the prostate cancer cell line PC3 to
activate the mitogenic MAPK pathway, namely the ERK cascade, was
examined (FIGS. 28A-B). Activation of ERK is dependent on its
phosphorylation on tyrosine and serine residues. Phosphorylated ERK
can be distinguished from the non-phosphorylated state by a
Phospho-ERK mAb. This phospho-specific Ab was used to study the
phosphorylation state of ERK in engineered PC3 cell lines. PC3
cells, expressing an activated form of Ras, were used as a positive
control.
[0357] The results show that while expression of the control neo
gene has no effect on ERK phosphorylation, expression of STEAP-2 in
PC3 cells is sufficient to induce at least a 3-fold increase in ERK
phosphorylation (FIG. 28A). Expression of STEAP-1 also induced some
ERK phosphorylation in PC3 cells grown in 1% FBS. These results
were verified using anti-ERK western blotting (FIG. 28A) and
confirm the activation of the ERK pathway by STEAP-1 and
STEAP-2.
[0358] Since FBS contains several components that may contribute to
receptor-mediated ERK activation, we examined the effect of STEAP-1
in low and optimal levels of FBS. PC3 cells expressing neo or
STEAP-1 were grown in either 0.1% or 10% FBS overnight. The cells
were analyzed by anti-Phospho-ERK western blotting. This experiment
shows that STEAP-1 induces the phosphorylation of ERK in 0.1% FBS,
and confirms that expression of STEAP-1 is sufficient to induce
activation of the ERK signaling cascade in the absence of
additional stimuli.
Example 14
Ligand-Mediated Activation of STEAP-1
[0359] Several factors have been shown to activate
multi-transmembrane proteins and mediate downstream signaling
events, including ions, leukotrienes, lipophosphatidic acid, etc.
(Cell Biochem. Biophys. 1999; 30:213-42). One group of compounds
known to activate multi-transmembrane proteins are odorants (Neuron
2000; 25:503-4). In this example, 3 classes of odorants were
screened for their ability to induce the activation of tyrosine
kinase-mediated signaling in PC3 cells (FIG. 29).
[0360] PC3 cells, stably expressing neo or STEAP-1 were grown
overnight in 0.10% FBS to allow for receptor occupancy. The cells
were then treated for 5 min with the indicated concentrations
(0.1-10 .mu.M) of citralva, ethylvanilin or IBMP. Treatment with
10% FBS was used as a control. Whole cell lysates (20 .mu.g)
generated from the different treatment conditions were separated by
SDS-PAGE and analyzed by anti-phosphotyrosine western blotting.
[0361] This experiment shows that, while all 3 classes of odorant
induce some tyrosine phosphorylation in PC3-STEAP-1 cells, only
IBMP had a measurable effect on the phosphorylation of PC3-neo
cells that do not express the STEAP-1 gene. Moreover both citralva
and ethylvanillin induced an increase in the phosphorylation of
p136-140 and p200-210 in PC3-STEAP-1 cells in a STEAP-1 specific
manner. In addition, citralva induced the de novo phosphorylation
of a protein at 160-200 kDa. The results demonstrate that STEAP-1
is mediating the activation of tyrosine kinase pathways in odorant
treated cells.
[0362] The finding that citralva induced the tyrosine
phosphorylation of proteins in a STEAP-1 mediated manner suggests
that STEAP-1 may initiate the activation of one or more signaling
cascades. In order to identify potential signaling cascade
associated with odorant activation of STEAP-1, the effect of
odorants on the activation of the MAPK cascade was studied in PC3
cells (FIG. 30). PC3 cells, stably expressing either neo or
STEAP-1, were grown overnight in 0.1% FBS. Cells were then treated
with citralva for 5 min. Treatment with 10% FBS was used as a
control. As observed using phospho-specific mAb (anti-phospho-ERK),
citralva activated the ERK pathway in a STEAP-2 specific manner.
These results also confirm the findings described in FIGS. 27-28,
that expression of STEAP-1 alone is sufficient to induce the
activation of the ERK pathway.
Example 15
Identification of Potential Signal Transduction Pathways
[0363] To confirm that STEAP directly or indirectly activates known
signal transduction pathways in cells and to delineate
STEAP-mediated downstream events, luciferase (luc) based
transcriptional reporter assays are carried out in cells expressing
STEAP. These transcriptional reporters contain consensus binding
sites for known transcription factors which lie downstream of well
characterized signal transduction pathways. The reporters and
examples of their associated transcription factors, signal
transduction pathways, and activation stimuli are listed below.
[0364] 1. NFkB-luc, NFkB/Rel; Ik-kinase/SAPK;
growth/apoptosis/stress
[0365] 2. SRE-luc, SRF/TCF/ELK1; MAPK/SAPK;
growth/differentiation
[0366] 3. AP-1-luc, FOS/JUN; MAPK/SAPK/PKC;
growth/apoptosis/stress
[0367] 4. ARE-luc, androgen receptor; steroids/MAPK;
growth/differentiation/apoptosis
[0368] 5. p53-luc, p53; SAPK; growth/differentiation/apoptosis
[0369] 6. CRE-luc, CREB/ATF2; PKA/p38; growth/apoptosis/stress
[0370] STEAP-mediated effects may be assayed in cells showing mRNA
expression. Luciferase reporter plasmids may be introduced by lipid
mediated transfection (TFX-50, Promega). Luciferase activity, an
indicator of relative transcriptional activity, is measured by
incubation of cells extracts with luciferin substrate and
luminescence of the reaction is monitored in a luminometer.
Example 16
In vitro Assays of STEAP Function
[0371] The expression profile of STEAP in prostate cancer suggests
a functional role in tumor initiation, progression and/or
maintenance. STEAP function can be assessed in mammalian cells
using in vitro approaches. For mammalian expression, STEAP can be
cloned into a number of appropriate vectors, including pcDNA 3.1
myc-His-tag and the retroviral vector pSR.alpha.tkneo (Muller et
al., 1991, MCB 11:1785). Using such expression vectors, STEAP can
be expressed in several cancer cell lines, including for example
PC-3, NIH 3T3, LNCaP and 293T. Expression of STEAP can be monitored
using anti-STEAP antibodies.
[0372] Mammalian cell lines expressing STEAP can be tested in
several in vitro and in vivo assays, including cell proliferation
in tissue culture, activation of apoptotic signals, primary and
metastatic tumor formation in SCID mice, and in vitro invasion
using a membrane invasion culture system (MICS) (Welch et al., Int.
J. Cancer 43: 449-457). STEAP cell phenotype is compared to the
phenotype of cells that lack expression of STEAP. In addition,
cells treated with and without exogenously added STEAP protein may
be analyzed for altered growth parameters.
[0373] Cell lines expressing STEAP can also be assayed for
alteration of invasive and migratory properties by measuring
passage of cells through a matrigel coated porous membrane chamber
(Becton Dickinson). Passage of cells through the membrane to the
opposite side is monitored using a fluorescent assay (Becton
Dickinson Technical Bulletin #428) using calcein-Am (Molecular
Probes) loaded indicator cells. Cell lines analyzed include
parental and STEAP overexpressing PC3, 3T3 and LNCaP cells. To
assay whether STEAP has chemoattractant properties, parental
indicator cells are monitored for passage through the porous
membrane toward a gradient of STEAP conditioned media compared to
control media. This assay may also be used to qualify and quantify
specific neutralization of the STEAP induced effect by candidate
cancer therapeutic compositions.
[0374] In order to establish whether STEAP binds to cellular
proteins expressed in prostate cancer cells and other cancer cells
or normal cells, two approaches may be taken. In the first
approach, in vitro assay for recombinant HIS-tagged STEAP binding
to various cell lines are used. In another approach, a recombinant
alkaline phosphatase-STEAP fusion protein is generated using the
AP-TAG system from GenHunter Corporation (Nashville, Tenn., cat#
Q202), and the AP-TAG fusion used to test STEAP binding to a
variety of prostate cancer cell lines as described (Cheng and
Flanagan, 1994, Cell 79:157-168). After washing the cells and
adding the AP substrate BCIP, which forms an insoluble blue
precipitate upon dephosphorylation, STEAP binding is determined by
identifying cells staining blue under the light microscope.
[0375] Various cancer cell lines can be examined, including without
limitation, various prostate cancer cell lines (e.g., LNCaP, PC-3,
DU145, TSUPR, LAPC4). Other cell lines such as PREC prostate cell
line, 293T, PIN cells, and NIH 3T3, etc. may also be examined.
Additionally, the LAPC and other prostate cancer xenografts may be
tested. Equilibrium dissociation rate constants may be calculated
to evaluate the strength of the binding interaction. In addition,
the number of cell surface receptors per cell can be determined.
Cell lines or tissues with the highest binding capacity for STEAP
would be preferred for cloning a STEAP binding partner.
[0376] In another functional assay, NIH-3T3 cells stably expressing
STEAP can be analyzed for their ability to form colonies in soft
agar. In these experiments, cells used in such procedures (e.g.
NIH-3T3 cells), can be transfected to stably express STEAP or neo
or activated-Ras (as the test gene, the negative and the positive
controls, respectively) in order to assess the transforming
capabilities of STEAP. Typically experiments are performed in
duplicate and the assays are evaluated approximately 4 weeks after
cell plating. Where experimental observations demonstrate that
STEAP induces an increase in colony formation relative to a
negative control (e.g. neo) such results indicate that STEAP has
significant transforming capabilities.
Example 17
In Vivo Assay for STEAP Tumor Growth Promotion
[0377] The effect of the STEAP protein on tumor cell growth may be
evaluated in vivo by gene overexpression in tumor-bearing mice. For
example, SCID mice can be injected subcutaneously on each flank
with 1.times.10.sup.6 of a prostate cell line containing tkNeo
empty vector or STEAP. At least two strategies may be used: (1)
Constitutive STEAP expression under regulation of an LTR promoter,
and (2) Regulated expression under control of an inducible vector
system, such as ecdysone, tet, etc. Tumor volume is then monitored
at the appearance of palpable tumors and followed over time to
determine if STEAP expressing cells grow at a faster rate.
Additionally, mice may be implanted with 1.times.10.sup.5 of the
same cells orthotopically to determine if STEAP has an effect on
local growth in the target tissue (i.e., prostate) or on the
ability of the cells to metastasize, specifically to lungs, lymph
nodes, liver, bone marrow, etc. The effect of STEAP on bone tumor
formation and growth may be assessed by injecting prostate tumor
cells intratibially, as described in Example 1.
[0378] These assays are also useful to determine the STEAP
inhibitory effect of candidate therapeutic compositions, such as
for example, STEAP antibodies, STEAP antisense molecules and
ribozymes.
Example 18
Detection of Prostate Cancer Metastases in Mice and Humans Using
Anti-STEAP-1 Polyclonal Antibodies
[0379] Mice
[0380] STEAP-1 immunohistochemical analysis was performed on 4
.mu.m formalin-fixed tissues derived from mice bearing orthotopic
LAPC-9 prostate cancer tumors and their derived lung and lymph node
metastases. Serial lung sections were tested using anti-STEAP-1
sheep polyclonal antibody and anti-PSA rabbit polyclonal antibody
(pAb). Microscopic examination of stained tissue was used to detect
LAPC-9 prostate cancer cells, and the results are shown in FIGS.
31A-F.
[0381] The anti-STEAP-1 sheep pAb readily detected human prostate
cancer cells in the mouse prostate (FIG. 31A), as well as in
metastases to lymph nodes (FIG. 31B) and lung (FIGS. 31C-D). Both
small (FIG. 31C) and large (FIG. 31D) micrometastases to the lung
were readily detected using the anti-STEAP-1 pAb. To confirm that
the lung metastases were of prostate cancer origin,
immunohistochemistry on serial lung sections was performed using
the anti-PSA pAb (FIGS. 31E-F). The strong cell surface staining
observed with the anti-STEAP-1 pAb allows for easier detection of
micrometastases as compared to the use of the anti-PSA polyclonal
antibody.
[0382] Humans
[0383] The STEAP-1 polyclonal Ab was used in a similar
immunohistochemical assay of metastatic prostate cancer specimens
from human patients. High expression of STEAP-1 was detected in
both the lymph node and bone metastases studied. As shown in FIGS.
32A (lymph node metastasis) and 32B (bone metastasis), intense
pericellular staining is observed in these human patient samples,
confirming that STEAP-1 is an excellent marker for the detection of
metastatic prostate cancer.
Example 19
STEAP-1, STEAP-2 and STEAP-3 Extracellular Loop-Fc Fusion
Constructs
[0384] To express and secrete the extracellular loops of STEAP-1,
STEAP-2, and STEAP-3 into conditioned media of mammalian cell
lines, fragments of these genes can be cloned into the pFc vector
to generate C-terminal fusions of the human IgG1 Fc region. The pFc
vector was generated by cloning human immunoglobulin G1, Fc (bases
74-768 of GenBank accession X70421) proceeded by the IgA protease
cleavage site (Roche, Cat 1461265) coded by 5'
cctcgacctccaacaccgggg 3' (SEQ ID NO: 47) into pTag-5 (GenHunter
Corp. Nashville, Tenn.) using XhoI and ApaI. This construct
generates an IgG1 Fc fusion at the C-terminus of STEAP-1, STEAP-2
and STEAP-3 extracellular regions while fusing the IgGK signal
sequence to N-terminus.
[0385] The resulting recombinant proteins are optimized for
secretion into the media of transfected mammalian cells and can be
used to identify proteins such as ligands or receptors that
interact with the STEAP-1, STEAP-2, and STEAP-3 protein. These
protein fusions can also be used as immunogen to generate
antibodies. Protein expression is driven from the CMV promoter. The
Zeosin resistance gene allows for selection of mammalian cells
expressing the protein and the ampicillin resistance gene permits
selection of the plasmid in E. coli.
[0386] The following extracellular loops of the STEAP-1, STEAP-2,
and STEAP-3 proteins are suitable for cloning into pFc:
13 STEAP-1 revihplatshqqyfykipilv (SEQ ID NO: 37)
rrsyrykllnwayqqvqqnkedawiehdvwrmei (SEQ ID NO: 38) widikqfvwytpptf
(SEQ ID NO: 39) STEAP-2 ysfvrdvihpyarnqqsdfykipiei (SEQ ID NO: 40)
rrserylflnmayqqvhanienswneeevwrie (SEQ ID NO: 41) krafeeeyyrfy (SEQ
ID NO: 42) STEAP-3 ypyvyekkdntfrmaisipnrifp (SEQ ID NO: 43)
yyvrwrlgnltvtqailkkenpfstssawlsdsy (SEQ ID NO: 44)
Example 20
Generation of Polyclonal Antibodies to STEAP-2
[0387] Three immunogens were used to generate antibodies specific
to STEAP-2. Two immunogens were peptides encoding amino acids
153-165 (ALQLGPIDASRQV; SEQ ID NO: 45) and amino acids 345-358
(IENSWNEEEVWRIE; SEQ ID NO: 46) of the STEAP-2 protein sequence.
The first peptide resides in the N-terminus of STEAP-2, which is
intracellular using the membrane topology prediction program SOSUI.
The latter peptide resides in the region between transmembrane
domains 3 and 4, and this region is predicted to encode the second
of 3 extracellular loops. A third immunogen was a
glutathione-S-transferase (GSI) fusion protein encompassing amino
acids 2-204 of the STEAP-2 protein sequence. The recombinant
GST-STEAP-2 fusion protein was purified from induced bacteria by
glutathione-sepharose affinity chromatography.
[0388] In addition to the above antigens, peptides encoding other
regions of the STEAP-2 protein, or bacterial and baculovirus virus
produced proteins encoding either full length or partial sequences
of the STEAP-2 protein, are use to generate a variety of STEAP-2
specific antibodies. These antibodies are directed to regions that
may modulate STEAP-2 function.
[0389] Generation of Polyclonal Antibodies (pAbs)
[0390] To generate pAbs to STEAP-2, the purified GST-fusion protein
and the peptides coupled to Keyhole limpet hemacyanin (KLH) were
used to immunize individual rabbits as follows. The rabbits were
immunized with 200 .mu.g of fusion protein or KLH-peptide antigen
mixed in complete Freund's adjuvant. The rabbits were then injected
every two weeks with 200 .mu.g of immunogen in incomplete Freund's
adjuvant. Test bleeds were taken approximately 7-10 days following
each immunization. The titer of peptide 153-165 antiserum was at
least 25,000 and of peptide 345-358 antiserum at least 10,000 as
determined by ELISA to the respective immunogens. The titer of the
GST-fusion serum was at least 300,000. Peptide antiserum is
affinity purified by passage-of the serum over an affinity column
composed of the respective peptide covalently coupled to Affigel
matrix (BioRad). Serum raised to the GST-fusion is semi-purified
first by removal of GST-reactive antibodies by passage over a GST
affinity column. STEAP-2 specific antibody is then isolated by
passage over a GST-STEAP-2 affinity column. Alternatively, STEAP-2
specific antisera is isolated by affinity chromatography using a
maltose binding protein (MBP)-STEAP-2 fusion protein encoding the
same amino acids
Example 21
Generation of Monoclonal Antibodies to STEAP Proteins
[0391] To generate mabs to STEAP-1, STEAP-2, STEAP-3, or STEAP-4
proteins, Balb C mice are immunized intraperitoneally with 20-50
.mu.g of KLH-coupled peptide or with bacterial recombinant
polypeptides, such as GST-fusion proteins, encoding regions of the
respective STEAP member protein sequence mixed in complete Freund's
adjuvant. Mice are then subsequently immunized every 2-4 weeks with
20-50 .mu.g of immunogen mixed in Freund's incomplete adjuvant.
Alternatively, Ribi adjuvant is used for initial immunizations.
Test bleeds are taken 7-10 days following immunization to monitor
titer and specificity of the immune response.
[0392] Serum from mice immunized with a GST-fusion protein
encompassing amino acids 148-251 of STEAP-1 attained a titer of at
least 8.times.10.sup.6 as determined by ELISA and specifically
recognized STEAP-1 protein by western blot (FIG. 33). Once
appropriate reactivity and specificity are obtained as determined
by ELISA, western blotting, and flow cytometry analyses, fusion and
hybridoma generation is then carried out using established
procedures well known in the art (Harlow and Lane, 1988).
[0393] FIG. 33 is a western blot showing that anti-STEAP-1 murine
pAb recognizes STEAP-1 protein in engineered cell lines and
endogenous STEAP-1 protein in LNCaP cells. Lysates of LNCaP cells
and 293T cells transfected with either pcDNA 3.1 MYC/HIS tagged
STEAP-1 or neo empty vector, and RAT1 cells engineered to express
STEAP-1 or a neo control gene, were separated by SDS-PAGE and
transferred to nitrocellulose. The blot was then subjected to
anti-STEAP western analysis using a 1:1000 dilution of serum from
mice immunized with a GST-STEAP-1 fusion protein.
[0394] Alternative antigens and immunization strategies are also
used to generate mAbs with specific reactivity and specificity to
various regions of the STEAP proteins. Such antigens may include
baculovirus produced recombinant proteins or mammalian expressed
and secreted human IgG FC-fusion proteins encoding various regions
of each STEAP family member protein sequence, such as predicted
extracellular domains. A cell based immunization strategy is also
used in which the cDNA of a STEAP family member is overexpressed in
cells such as NIH3T3 mouse fibroblasts or 300.19 murine pre-B cells
and whole cells or membrane preparations from these cells are used
as immunogen. In addition, a DNA-based immunization protocol in
which a mammalian expression vector encoding the STEAP-1 or STEAP-2
cDNA such as pcDNA 3.1 is used to immunize mice by direct injection
of the plasmid DNA. This protocol is used either alone or in
combination with protein and/or cell-based immunization
strategies.
[0395] Throughout this application, various publications are
referenced. The disclosures of these publications are hereby
incorporated by reference herein in their entireties.
[0396] The present invention is not to be limited in scope by the
embodiments disclosed herein, which are intended as single
illustrations of individual aspects of the invention, and any that
are functionally equivalent are within the scope of the invention.
Various modifications to the models and methods of the invention,
in addition to those described herein, will become apparent to
those skilled in the art from the foregoing description and
teachings, and are similarly intended to fall within the scope of
the invention. Such modifications or other embodiments can be
practiced without departing from the true scope and spirit of the
invention.
* * * * *
References