U.S. patent application number 13/689407 was filed with the patent office on 2013-06-06 for compositions and methods for prostate cancer analysis.
This patent application is currently assigned to GENENTECH, INC.. The applicant listed for this patent is Genentech, Inc.. Invention is credited to Siminder Atwal, Jo-Anne Hongo, Mark Lackner, Elizabeth Punnoose, Bonnee Rubinfeld, Rajesh Vij.
Application Number | 20130143237 13/689407 |
Document ID | / |
Family ID | 47324459 |
Filed Date | 2013-06-06 |
United States Patent
Application |
20130143237 |
Kind Code |
A1 |
Atwal; Siminder ; et
al. |
June 6, 2013 |
COMPOSITIONS AND METHODS FOR PROSTATE CANCER ANALYSIS
Abstract
The invention provides methods for diagnosing prostate cancer.
The invention also provides novel anti-STEAP-1 antibodies and uses
thereof.
Inventors: |
Atwal; Siminder; (South San
Francisco, CA) ; Hongo; Jo-Anne; (Redwood City,
CA) ; Lackner; Mark; (South San Francisco, CA)
; Punnoose; Elizabeth; (Hayward, CA) ; Rubinfeld;
Bonnee; (Danville, CA) ; Vij; Rajesh; (South
San Francisco, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Genentech, Inc.; |
South San Francisco |
CA |
US |
|
|
Assignee: |
GENENTECH, INC.
South San Francisco
CA
|
Family ID: |
47324459 |
Appl. No.: |
13/689407 |
Filed: |
November 29, 2012 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
61703099 |
Sep 19, 2012 |
|
|
|
61629886 |
Nov 29, 2011 |
|
|
|
Current U.S.
Class: |
435/7.23 ;
435/344.1; 435/419; 530/388.85; 530/389.7; 530/391.3;
536/23.53 |
Current CPC
Class: |
C12Y 116/01 20130101;
C07K 16/3069 20130101; G01N 33/57434 20130101; G01N 2333/90287
20130101; G01N 2333/916 20130101; C12N 5/0693 20130101; C12Y
301/03048 20130101; A61P 35/00 20180101; G01N 2800/52 20130101;
G01N 33/57492 20130101; G01N 2333/70596 20130101; G01N 2333/4742
20130101 |
Class at
Publication: |
435/7.23 ;
536/23.53; 435/344.1; 435/419; 530/389.7; 530/388.85;
530/391.3 |
International
Class: |
G01N 33/68 20060101
G01N033/68; C07K 16/30 20060101 C07K016/30 |
Claims
1. A method for diagnosing prostate cancer in a test subject,
comprising: a) contacting cancer cells of epithelial origin with an
antibody that specifically binds to a prostate-specific marker,
wherein the cancer cells are from a blood sample taken from the
test subject; and b) determining whether any of the cancer cells
express the prostate-specific marker, wherein the presence of
cancer cells that express the prostate-specific marker is
predictive of having prostate cancer in the test subject.
2. The method of claim 1, further comprising determining the amount
of the cancer cells that express the prostate-specific marker,
wherein such amount is predictive of the stage of prostate cancer
in the test subject.
3. The method of claim 1, further comprising determining the
expression level of the prostate-specific marker on the cancer
cells.
4. The method of claim 1, further comprising grading the cancer
cells based on their expression level of the prostate-specific
marker, and determining the percentage of the cancer cells in each
grade.
5. The method of claim 1, further comprising calculating a grade
score for each grade by multiplying the percentage of the cancer
cells in said grade with a unique grade number representative of
the expression level of the prostate-specific marker in said grade,
and summing up all the grade scores to obtain an H score, wherein
the H score is indicative of the stage of the prostate cancer in
the test subject.
6. The method of claim 1, wherein the cancer cells are identified
from the blood sample with a capturing composition comprising a
ligand that specifically binds to cancer cells of epithelial
origin.
7. The method of claim 6, wherein the ligand is an antibody that
specifically binds to an epithelial antigen preferentially
expressed on cancer cells.
8. The method of claim 7, wherein the epithelial antigen is
Epithelial Cell Adhesion Molecule (EpCAM).
9. The method of claim 6, wherein the identified cancer cells are
enriched in a cell fraction separated from the blood sample.
10. The method of claim 9, wherein the cell fraction is separated
under a magnetic field.
11. The method of claim 10, wherein the ligand in the capturing
composition is coupled to a magnetic particle.
12. The method of claim 11, wherein the ligand comprises an EpCAM
antibody.
13. The method of claim 1, wherein the prostate-specific marker is
selected from the group consisting of: a Six-Transmembrane
Epithelial Antigen of the Prostate (STEAP), Prostate-specific
membrane antigen (PSMA), Prostate carcinoma tumor antigen (PCTA-1),
and Prostate stem cell antigen (PSCA).
14. The method of claim 1, wherein the antibody that specifically
binds to a prostate-specific marker comprises an anti-STEAP-1
antibody.
15. The method of claim 14, wherein the anti-STEAP-1 antibody binds
to STEAP-1 with a K.sub.D of .ltoreq.1000 nM.
16. The method of claim 14, wherein the anti-STEAP-1 antibody is a
polyclonal antibody or a monoclonal antibody.
17. The method of claim 16, wherein the anti-STEAP-1 antibody is a
murine monoclonal antibody.
18. The method of claim 17, wherein the anti-STEAP-1 antibody is
15A5, produced by a hybridoma cell having a microorganism deposit
number of PTA-12259.
19. The method of claim 14, wherein the anti-STEAP-1 antibody is
conjugated with a first detectable label.
20. The method of claim 1, wherein the cancer cells are identified
with one or more reagents that allow detection of cancer cells of
epithelial origin.
21. The method of claim 20, wherein the reagents comprise a ligand
that specifically binds to a cytokeratin, and wherein the ligand is
optionally conjugated with a second detectable label.
22. The method of claim 21, wherein the reagents further comprise a
dye that differentiates cells from non-cell components.
23. The method of claim 22, wherein the dye is
4',6-diamidino-2-phenylindole (DAPI).
24. The method of claim 23, wherein the reagents further comprise a
ligand that specifically binds to a leukocyte marker, and wherein
the ligand is optionally conjugated with a third detectable
label.
25. The method of claim 24, wherein the ligand to a leukocyte
marker is a CD45 antibody.
26. The method of claim 1, wherein the determining is by a method
based on immunofluorescent microscopy, flow cytometry, fiber-optic
scanning cytometry, or laser scanning cytometry.
27. A method of predicting efficacy of prostate cancer therapy in a
test subject, comprising: a) contacting cancer cells of epithelial
origin with an antibody that specifically binds to a
prostate-specific marker, wherein the cancer cells are from a blood
sample taken from the test subject; and b) determining whether any
of the cancer cells express the prostate-specific marker, wherein
the presence of cancer cells that express the prostate-specific
marker is predictive of the efficacy of the prostate cancer therapy
in the test subject.
28. A method of monitoring response to a prostate cancer therapy in
a test subject, comprising: a) contacting a first group of cancer
cells of epithelial origin with an antibody that specifically binds
to a prostate-specific marker, wherein the first group of cancer
cells are from a first blood sample taken from the test subject; b)
determining the amount of the cancer cells in the first group that
express prostate-specific marker and/or the expression level of the
prostate-specific marker in the cancer cells; c) contacting a
second group of cancer cells of epithelial origin with the antibody
that specifically binds to a prostate-specific marker, wherein the
second group of cancer cells are from a second blood sample taken
from the test subject after a test period of prostate cancer
therapy; d) determining the amount of the cancer cells in the
second group that express prostate-specific marker and/or the
expression level of the prostate-specific marker in the cancer
cells; and e) comparing the amount of the cancer cells that express
the prostate-specific marker and/or the prostate-specific marker
expression level as determined in b) with that in d), wherein a
decrease in the amount of the cancer cells expressing the
prostate-specific marker and/or a decrease in the prostate-specific
marker expression level in the cancer cells indicates a response to
the prostate cancer therapy in the test subject.
29. The method of claim 27, wherein the prostate cancer therapy
comprises an antibody or antibody-drug conjugate (ADC) that binds
to the prostate-specific marker.
30. The method of claim 29, wherein the prostate-specific marker is
STEAP-1.
31. The method of claim 30, wherein the ADC comprises an
anti-STEAP-1 antibody covalently attached to a cytotoxic agent.
32. The method of claim 31, wherein the cytotoxic agent is selected
from a toxin, a chemotherapeutic agent, a drug moiety,
monomethylauristatin E (MMAE), an antibiotic, a radioactive
isotope, and a nucleolytic enzyme.
33. An antibody which binds to substantially the same epitope to
which antibody 15A5 binds, wherein antibody 15A5 is produced by a
hybridoma cell having a microorganism deposit number of:
PTA-12259.
34. The antibody of claim 33, which comprises at least one of the
CDR regions of the antibody 15A5.
35. The antibody of claim 34, which comprises the six CDR regions
of the antibody 15A5.
36. The antibody of claim 33, which comprises the heavy chain
variable region of the antibody 15A5.
37. The antibody of claim 33, which comprises the light chain
variable region of the antibody 15A5.
38. The antibody of claim 33, which is antibody 15A5 or an antigen
binding fragment thereof.
39. The antibody of claim 38, further conjugated to a detectable
label.
40. An isolated polynucleotide encoding the antibody of claim
35.
41. A host cell comprising the polynucleotide of claim 40.
42. A hybridoma cell line having a microorganism deposit number of
PTA-12259.
43. Use of the antibody of claim 33 or an antigen-binding fragment
thereof in the manufacture of a diagnostic agent for prostate
cancer.
44. A test kit for detecting presence of prostate cancer cells
expressing STEAP-1 in a blood sample, comprising an antibody that
specifically binds to STEAP-1.
45. The test kit of claim 44, wherein the antibody is conjugated
with a detectable label.
46. The test kit of claim 44, wherein the antibody is an antibody
of claim 33.
Description
RELATED APPLICATIONS
[0001] This application claims priority under 35 USC 119(e) to U.S.
provisional patent application No. 61/629,886 filed Nov. 29, 2011
and U.S. provisional patent application No. 61/703,099 filed Sep.
19, 2012, the contents of which are incorporated herein by
reference in their entirety.
FIELD OF THE INVENTION
[0002] The present invention relates to the field of oncology and
cancer diagnosis, and more specifically to compositions and methods
for prostate cancer screening, staging, and treatment
monitoring.
BACKGROUND
[0003] Prostate cancer is one of the most prevalent cancers in men.
While most prostate cancers at early onset are symptom-free and
slow growing, certain prostate cancers are more aggressive, painful
and lead to fatality. At present, two major types of non-invasive
screening tests are available for detection of prostate cancer in
men. One is digital rectal exam (DRE), which allows a doctor to
detect prostate abnormalities by inserting a gloved finger into the
rectum and feeling the prostate gland, and the other is prostate
surface antigen test (PSA test), which measures the level of the
PSA antigen in a blood sample. Although FDA has approved use of PSA
test together with DRE to help detect prostate cancer in men, the
PSA test is controversial in screening as it is not clear whether
the test actually saves lives. In particular, the United States
Preventive Services Task Forces has recently recommended against
PSA screening in healthy men, based on findings that PSA screening
reduces no or little prostate cancer mortality while leading to
treatments or tests that cause unnecessary pain and side effects
(see, e.g., R. Chou et al, Ann. Intern. Med., Oct. 7, 2011 E-375;
Djulbegovic et al, BMJ 2010, 341: c4543). The most definitive
diagnosis of prostate cancer is biopsy, where a small piece of the
prostate from the suspected patient is removed for microscopic
examination for the presence of tumor cells. Obviously such
procedure is rather invasive and less desirable in early screening
and detection.
[0004] As in many other types of cancers, the main cause of death
in prostate cancer patients is not the primary tumor but rather the
metastasis. Some primary tumor cells can detach themselves from the
original tissue and enter into circulation. These cells are called
circulating tumor cells (CTCs). Once CTCs seed themselves to a
suitable site in the body, they may develop into metastatic
colonies that are difficult to detect yet can be life-threatening
as they progress into secondary tumors. Attempts have been made to
detect the CTCs. However, no methods have been developed that can
distinguish if the CTCs are originated from prostate and how the
prostate cancer has progressed. In view of the recent finding that
PSA screening fails in reducing mortality, there remain significant
needs for development of agents and methods that can provide
reliable results in the diagnosis and prognosis of prostate
cancer.
SUMMARY
[0005] In one aspect, the present disclosure provides methods for
diagnosing prostate cancer in a test subject, comprising: a)
contacting cancer cells of epithelial origin with an antibody that
specifically binds to a prostate-specific marker, wherein the
cancer cells are from a blood sample taken from the test subject;
and b) determining whether any of the cancer cells express the
prostate-specific marker, wherein the presence of cancer cells that
express the prostate-specific marker is predictive of having
prostate cancer in the test subject.
[0006] In certain embodiments, the method further comprises
determining the amount of the cancer cells that express the
prostate-specific marker, wherein such amount is predictive of the
stage of prostate cancer in the test subject.
[0007] In certain embodiments, the method further comprises
determining the expression level of the prostate-specific marker on
the cancer cells.
[0008] In certain embodiments, the method further comprises grading
the cancer cells based on their expression level of the
prostate-specific marker, and determining the percentage of the
cancer cells in each grade.
[0009] In certain embodiments, the method further comprises
calculating a grade score for each grade by multiplying the
percentage of the cancer cells in that grade with a unique grade
number assigned to that grade based on the expression level of the
prostate-specific marker, and summing up all the grade scores to
obtain an H score, wherein the H score is indicative of the stage
of the prostate cancer in the test subject.
[0010] In certain embodiments, the cancer cells are identified from
the blood sample with a capturing composition comprising a ligand
that specifically binds to cancer cells of epithelial origin. In
certain embodiments, the ligand is an antibody that specifically
binds to an epithelial antigen preferentially expressed on cancer
cells. In certain embodiments, the epithelial antigen is Epithelial
Cell Adhesion Molecule (EpCAM).
[0011] In certain embodiments, the identified cancer cells are
enriched in a cell fraction separated from the blood sample. In
certain embodiments, the cell fraction is separated under a
magnetic field. In certain embodiments, the ligand in the capturing
composition is coupled to a magnetic particle.
[0012] In certain embodiments, the antibody that specifically binds
to a prostate-specific marker comprises an anti-STEAP-1 antibody.
In certain embodiments, the anti-STEAP-1 antibody binds to STEAP-1
with a KD of .ltoreq.1000 nM. In certain embodiments, the
anti-STEAP-1 antibody is a murine monoclonal antibody. In certain
embodiments, the anti-STEAP-1 antibody is 15A5, produced by a
hybridoma cell having a microorganism deposit number PTA-12259.
[0013] In certain embodiments, the cancer cells are identified with
one or more reagents that allow detection of cancer cells of
epithelial origin. In certain embodiments, the reagents comprise a
ligand that specifically binds to a cytokeratin, and wherein the
ligand is optionally conjugated with a second detectable label. In
certain embodiments, the reagents further comprise a dye that
differentiates cells from non-cell components. In certain
embodiments, the reagents further comprise a ligand that
specifically binds to a leukocyte marker.
[0014] In certain embodiments, the cancer cells are detected by a
method based on immunofluorescent microscopy, flow cytometry,
fiber-optic scanning cytometry, or laser scanning cytometry.
[0015] In another aspect, the present disclosure provides methods
of predicting efficacy of prostate cancer therapy in a test
subject.
[0016] In another aspect, the present disclosure provides methods
of monitoring response to a prostate cancer therapy in a test
subject.
[0017] In another aspect, the present disclosure provides
antibodies which binds to substantially the same epitope to which
antibody 15A5 binds, wherein antibody 15A5 is produced by a
hybridoma cell having a microorganism deposit number of
PTA-12259.
[0018] In another aspect, the present disclosure provides a
hybridoma cell line having a microorganism deposit number of
PTA-12259.
[0019] In another aspect, the present disclosure provides test kits
for detecting presence of prostate cancer cells expressing STEAP-1
in a blood sample, comprising an antibody that specifically binds
to STEAP-1. In certain embodiments, the test kits further comprises
one or more compositions selected from the group consisting of:
magnetic particles coupled to a first ligand that specifically
binds to cancer cells of epithelial origin, a second ligand that
specifically binds to an epithelial marker, a third ligand that
specifically binds to a leukocyte marker, and a dye that
differentiates cells from non-cell components.
BRIEF DESCRIPTION OF THE FIGURES
[0020] FIG. 1 depicts the representative scoring criteria for CTCs
based on the level of staining by an anti-STEAP-1 antibody.
[0021] FIG. 2 depicts the STEAP-1 expression and H scores of
different cell lines as determined on CellSearch.RTM. system using
a sheep polyclonal anti-STEAP-1 antibody, a mouse monoclonal
anti-STEAP-1 antibody 37, and a rabbit polyclonal anti-STEAP-1
antibody: (a) expression on LB50 cells; (b) expression on PC3
cells; (c) H score of LB50 cells; and (d) H score of PC3 cells.
[0022] FIG. 3 depicts the STEAP-1 expression and H scores of
different spiked-in samples as determined on CellSearch.RTM. system
using a sheep polyclonal anti-STEAP-1 antibody: (a) expression, (b)
H scores.
[0023] FIG. 4 depicts the H scores of 11 patient blood samples as
determined on CellSearch.RTM. system using a sheep polyclonal
anti-STEAP-1 antibody.
[0024] FIGS. 5 depicts H scores of 10 patient blood samples as
determined on CellSearch.RTM. system using a sheep polyclonal
anti-STEAP-1 antibody (a), and the comparison with the IHC results
of the tumor tissue samples from the same patients (b-c).
[0025] FIG. 6 depicts the STEAP-1 expression and H scores of
different spiked-in samples as determined on CellSearch.RTM. system
using a sheep polyclonal anti-STEAP-1 antibody (a-b) and the mouse
monoclonal anti-STEAP-1 antibody 15A5 (c-d).
[0026] FIG. 7 depicts reproducibility of CTC enumeration in
duplicate patient samples as shown by CTC counts/patient (a) and
reproducibility of STEAP1 biomarker expression levels in CTCs from
duplicate patient samples as shown by H-score/patient (b).
[0027] FIG. 8 depicts strong correlation in CTC enumeration from
blood samples taken at baseline 1 and 2.
[0028] FIG. 9 depicts fold change in CTC counts of patients during
dose escalation treatment from Dose 1-7 post-dose -pre-dose.
[0029] FIG. 10 depicts CTC counts of patients during dose
escalation treatment from Dose 1-7 pre-dose and post-dose.
[0030] FIG. 11 depicts CTC counts of patients during dose
escalation treatment from Dose 1-7 pre-dose and post-dose.
DETAILED DESCRIPTION OF THE INVENTION
I. DEFINITIONS
[0031] The term "tumor" or "cancer", as used interchangeably
herein, refers to any medical condition characterized by neoplastic
or malignant cell growth, proliferation, or metastasis, and
includes both solid cancers and non-solid cancers such as
leukemia.
[0032] The term "prostate cancer" or "prostate tumor" as used
herein, refers to cancer or tumor that is originated from a
prostate tissue.
[0033] The term "stage" in the context of a disease (such as cancer
or tumor), refers to the progression status of the disease which is
indicative of the severity of the disease.
[0034] The term "staging" as used herein refers to identifying the
particular stage at which the disease has progressed.
[0035] The term "diagnosis" (along with grammatical variations
thereof such as "diagnosing" or "diagnostic") refers to the
identification of a molecular or pathological state, disease or
condition, such as the identification of cancer, or refers to the
identification of a cancer patient who may benefit from a
particular treatment regimen.
[0036] The term "prognosis" (and grammatical variations thereof
such as "prognosing" or "prognostic") refers to the prediction of
the likelihood of benefit from a treatment such as a cancer
therapy.
[0037] The term "prediction" or "predicting" is used herein to
refer to the likelihood that a patient will respond either
favorably or unfavorably to a particular anti-prostate cancer
therapy. In one embodiment, prediction or predicting relates to the
extent of those responses. In one embodiment, the prediction or
predicting relates to whether and/or the probability that a patient
will survive or improve following treatment, for example treatment
with a particular therapeutic agent, and for a certain period of
time without disease progression.
[0038] The term "benefit" is used in the broadest sense and refers
to any desirable effect and specifically includes clinical benefit
as defined herein.
[0039] An "individual" or "subject" is a mammal. Mammals include,
but are not limited to, domesticated animals (e.g., cows, sheep,
cats, dogs, and horses), primates (e.g., humans and non-human
primates such as monkeys), rabbits, and rodents (e.g., mice and
rats). In certain embodiments, the individual or subject is a
human.
[0040] The term Six-Transmembrane Epithelial Antigen of the
Prostate 1, also called STEAP-1, refers to a cell surface antigen
predominantly expressed in prostate tissue, and is found to be
upregulated in multiple cancer cell lines. Hubert et al. (1999),
Proc. Natl. Acad. Sci. USA, 96(25), 14523-8. An exemplary human
STEAP-1 has an amino acid sequence of SEQ ID NO:1 disclosed in US
2009/0280056 A1, filed 26 Oct. 2007, the entire disclosure of which
is expressly incorporated by reference herein.
[0041] The terms "anti-STEAP-1 antibody" and "an antibody that
binds to STEAP-1" refer to an antibody that is capable of binding
STEAP-1 with sufficient affinity such that the antibody is useful
as a diagnostic agent in targeting STEAP-1. In one embodiment, the
extent of binding of an anti-STEAP-1 antibody to an unrelated,
non-STEAP-1 protein is less than about 10% of the binding of the
antibody to STEAP-1 as measured, e.g., by a radioimmunoassay (RIA).
In certain embodiments, an antibody that binds to STEAP-1 has a
dissociation constant (Kd) of .ltoreq.1 .mu.M, .ltoreq.100 nM,
.ltoreq.10 nM, .ltoreq.1 nM, .ltoreq.0.1 nM, .ltoreq.0.01 nM, or
.ltoreq.0.001 nM (e.g. 10.sup.-8M or less, e.g. from 10.sup.-8M to
10.sup.-13M, e.g., from 10.sup.-9M to 10.sup.-13 M). In certain
embodiments, an anti-STEAP-1 antibody binds to an epitope of
STEAP-1 that is conserved among STEAP-1 from different species.
[0042] "Affinity" refers to the strength of the sum total of
noncovalent interactions between a single binding site of a
molecule (e.g., an antibody) and its binding partner (e.g., an
antigen). Unless indicated otherwise, as used herein, "binding
affinity" refers to intrinsic binding affinity which reflects a 1:1
interaction between members of a binding pair (e.g., antibody and
antigen). The affinity of a molecule X for its partner Y can
generally be represented by the dissociation constant (Kd).
Affinity can be measured by common methods known in the art,
including those described herein. Specific illustrative and
exemplary embodiments for measuring binding affinity are described
in the following.
[0043] The term "antibody" herein is used in the broadest sense and
encompasses various antibody structures, including but not limited
to monoclonal antibodies, polyclonal antibodies, multispecific
antibodies (e.g., bispecific antibodies), and antibody fragments so
long as they exhibit the desired antigen-binding activity.
[0044] An "antibody fragment" refers to a molecule other than an
intact antibody that comprises a portion of an intact antibody that
binds the antigen to which the intact antibody binds. Examples of
antibody fragments include but are not limited to Fv, Fab, Fab',
Fab'-SH, F(ab').sub.2; diabodies; linear antibodies; single-chain
antibody molecules (e.g. scFv); and multispecific antibodies formed
from antibody fragments.
[0045] An "antibody that binds to the same epitope" as a reference
antibody refers to an antibody that blocks binding of the reference
antibody to its antigen in a competition assay by 50% or more, and
conversely, the reference antibody blocks binding of the antibody
to its antigen in a competition assay by 50% or more. An exemplary
competition assay is provided herein.
[0046] The term "antibody 15A5" as used herein refers to a mouse
monoclonal anti-STEAP-1 antibody produced by a hybridoma cell line
having a microorganism deposit number of PTA-12259. The
microorganism deposit information of the hybridoma cell line is as
follows: ATCC Deposit No.: PTA-12259; Deposit Date: Nov. 17, 2011;
and Material Deposited: hybridoma 15A5.1.1.1 (also designated
7284), which produces antibody 15A5.
[0047] The "class" of an antibody refers to the type of constant
domain or constant region possessed by its heavy chain. There are
five major classes of antibodies: IgA, IgD, IgE, IgG, and IgM, and
several of these may be further divided into subclasses (isotypes),
e.g., IgG.sub.1, IgG.sub.2, IgG.sub.3, IgG.sub.4, IgA.sub.1, and
IgA.sub.2. The heavy chain constant domains that correspond to the
different classes of immunoglobulins are called .alpha., .delta.,
.epsilon., .gamma., and .mu., respectively.
[0048] The terms "full length antibody," "intact antibody," and
"whole antibody" are used herein interchangeably to refer to an
antibody having a structure substantially similar to a native
antibody structure or having heavy chains that contain an Fc region
as defined herein.
[0049] The term "monoclonal antibody" as used herein refers to an
antibody obtained from a population of substantially homogeneous
antibodies, i.e., the individual antibodies comprising the
population are identical and/or bind the same epitope, except for
possible variant antibodies, e.g., containing naturally occurring
mutations or arising during production of a monoclonal antibody
preparation, such variants generally being present in minor
amounts. In contrast to polyclonal antibody preparations, which
typically include different antibodies directed against different
determinants (epitopes), each monoclonal antibody of a monoclonal
antibody preparation is directed against a single determinant on an
antigen. Thus, the modifier "monoclonal" indicates the character of
the antibody as being obtained from a substantially homogeneous
population of antibodies, and is not to be construed as requiring
production of the antibody by any particular method. For example,
the monoclonal antibodies to be used in accordance with the present
invention may be made by a variety of techniques, including but not
limited to the hybridoma method, recombinant DNA methods,
phage-display methods, and methods utilizing transgenic animals
containing all or part of the human immunoglobulin loci, such
methods and other exemplary methods for making monoclonal
antibodies being described herein.
[0050] "Native antibodies" refer to naturally occurring
immunoglobulin molecules with varying structures. For example,
native IgG antibodies are heterotetrameric glycoproteins of about
150,000 daltons, composed of two identical light chains and two
identical heavy chains that are disulfide-bonded. From N- to
C-terminus, each heavy chain has a variable region (VH), also
called a variable heavy domain or a heavy chain variable domain,
followed by three constant domains (CH1, CH2, and CH3). Similarly,
from N- to C-terminus, each light chain has a variable region (VL),
also called a variable light domain or a light chain variable
domain, followed by a constant light (CL) domain. The light chain
of an antibody may be assigned to one of two types, called kappa
(.kappa.) and lambda (.lamda.), based on the amino acid sequence of
its constant domain.
[0051] The term "cytotoxic agent" as used herein refers to a
substance that inhibits or prevents a cellular function and/or
causes cell death or destruction. Cytotoxic agents include, but are
not limited to, radioactive isotopes (e.g., At.sup.211, I.sup.131,
I.sup.125, Y.sup.90, Re.sup.186, Re.sup.188, Sm.sup.153,
Bi.sup.212, P.sup.32, pb.sup.212 and radioactive isotopes of Lu);
chemotherapeutic agents or drugs (e.g., methotrexate, adriamicin,
vinca alkaloids (vincristine, vinblastine, etoposide), doxorubicin,
melphalan, mitomycin C, chlorambucil, daunorubicin or other
intercalating agents); growth inhibitory agents; enzymes and
fragments thereof such as nucleolytic enzymes; antibiotics; and
toxins such as small molecule toxins or enzymatically active toxins
of bacterial, fungal, plant or animal origin, including fragments
and/or variants thereof Non-limiting examples of cytotoxic agents
suitable for the present invention include those described in US
2009/0280056 A1, filed 26 Oct. 2007, the entire disclosure of which
is expressly incorporated by reference herein. For example, in
certain embodiments, a cytotoxic agent is monomethyl auristatin E
(MMAE).
[0052] An "isolated" antibody is one which has been separated from
a component of its natural environment. In some embodiments, an
antibody is purified to greater than 95% or 99% purity as
determined by, for example, electrophoretic (e.g., SDS-PAGE,
isoelectric focusing (IEF), capillary electrophoresis) or
chromatographic (e.g., ion exchange or reverse phase HPLC). For
review of methods for assessment of antibody purity, see, e.g.,
Flatman et al., J. Chromatogr. B 848:79-87 (2007).
[0053] An "isolated" nucleic acid refers to a nucleic acid molecule
that has been separated from a component of its natural
environment. An isolated nucleic acid includes a nucleic acid
molecule contained in cells that ordinarily contain the nucleic
acid molecule, but the nucleic acid molecule is present
extrachromosomally or at a chromosomal location that is different
from its natural chromosomal location.
[0054] "Isolated nucleic acid encoding an anti-STEAP-1 antibody"
refers to one or more nucleic acid molecules encoding antibody
heavy and light chains (or fragments thereof), including such
nucleic acid molecule(s) in a single vector or separate vectors,
and such nucleic acid molecule(s) present at one or more locations
in a host cell.
[0055] The term "vector," as used herein, refers to a nucleic acid
molecule capable of propagating another nucleic acid to which it is
linked. The term includes the vector as a self-replicating nucleic
acid structure as well as the vector incorporated into the genome
of a host cell into which it has been introduced. Certain vectors
are capable of directing the expression of nucleic acids to which
they are operatively linked. Such vectors are referred to herein as
"expression vectors."
[0056] The terms "host cell," "host cell line," and "host cell
culture" are used interchangeably and refer to cells into which
exogenous nucleic acid has been introduced, including the progeny
of such cells. Host cells include "transformants" and "transformed
cells," which include the primary transformed cell and progeny
derived therefrom without regard to the number of passages. Progeny
may not be completely identical in nucleic acid content to a parent
cell, but may contain mutations. Mutant progeny that have the same
function or biological activity as screened or selected for in the
originally transformed cell are included herein.
[0057] The term "package insert" is used to refer to instructions
customarily included in commercial packages of therapeutic
products, that contain information about the indications, usage,
dosage, administration, combination therapy, contraindications
and/or warnings concerning the use of such therapeutic
products.
II. METHODS
[0058] In one aspect, the present disclosure provides methods for
diagnosing or staging prostate cancer in a test subject using a
blood sample from the test subject. In particular, the present
disclosure provides method for diagnosing or staging prostate
cancer in a test subject by determining whether the circulating
tumor cells (CTCs) express one or more prostate-specific
markers.
[0059] In the methods provided herein, CTCs are analyzed for
expression of one or more prostate specific markers. The detection
of prostate specific markers on the CTCs provides further
information as to the diagnosis and staging of prostate cancer.
[0060] In certain embodiments, the present disclosure provides
methods for diagnosing or staging prostate cancer in a test
subject, comprising: a) contacting cancer cells of epithelial
origin with an antibody that specifically binds to a
prostate-specific marker, wherein the cancer cells are from a blood
sample taken from the test subject; and b) determining whether any
of the cancer cells express the prostate-specific marker, wherein
the presence of cancer cells that express the prostate-specific
marker is predictive of having prostate cancer in the test
subject.
[0061] The term "cancer cells of epithelial origin" refers to
cancer cells that express at least one epithelial marker. The term
"marker" as used herein refers to an antigen molecule that is
preferentially expressed on a particular type of cells and helps
distinguish those cells from other types of cells. For example, an
epithelial marker can be an antigen molecule universally expressed
on epithelial cells but not normally found on leukocytes. The
cancer cells of epithelial origin may also express a tumor marker,
for example, an antigen molecule preferentially found on tumor
cells but less frequently found on normal cells. In certain
embodiments, the cancer cells of epithelial origin comprise
CTCs.
[0062] In certain embodiments, the cancer cells of epithelial
origin express at least one epithelial marker which is also
preferentially found in cancer cells. Detection of such an
epithelial marker is indicative of a cancer cell of epithelial
origin. In certain embodiments, such an epithelial marker is
Epithelial Cell Adhesion Molecule (EpCAM).
[0063] The cancer cells of epithelial origin are from a blood
sample obtained from the test subject. The blood samples can be any
sample that is derived from human blood, for example, a plasma
sample, a serum sample, whole blood, or blood that has been treated
with certain agents such as an anti-coagulant. Blood samples can be
obtained directly from the test subjects, or can be obtained from
organizations that collect the samples from the test subjects.
[0064] In certain embodiments, the cancer cells are identified from
the blood sample with a capturing composition. In certain
embodiments, the capturing composition comprises a ligand that
specifically binds to cancer cells of epithelial origin. In certain
embodiments, the ligand is an antibody that specifically binds to
an epithelial antigen preferentially expressed on cancer cells. In
certain embodiments, the epithelial antigen is EpCAM.
[0065] The term "identify" or "identification" as used herein,
refers to substantially differentiating the cancer cells of
epithelial origin from the rest of the components in the blood
sample. For example, the cancer cells of epithelial origin can be
bound or captured by the capturing composition, while the rest of
the components are not bound or captured.
[0066] The identified cancer cells may or may not be separated from
the rest of the components in the blood sample. In certain
embodiments, the identified cancer cells are not separated or
enriched from the other components in the sample. For example, a
blood sample, e.g. a serum sample, may be loaded to a slide,
identified with a capturing composition, and without any separation
or enrichment operations, the sample may be further contacted with
other reagents.
[0067] In certain embodiments, the identified cancer cells are
enriched in a cell fraction separated from the blood sample. The
term "enriched" as used herein refers to the density of the
identified cancer cells in the cell fraction is higher than in the
blood sample. Any suitable techniques may be used to separate the
cell fraction. Techniques commonly employed in the art include,
without limitation, gravitational separation, magnetic separation
or affinity separation, for example, after the cancer cells form a
complex with the capturing composition which allows separation of
the cancer cells. For gravitational separation, the capturing
composition may be coupled to particles or beads that can be spin
down to allow enrichment of the identified cancer cells. For
magnetic separation, the capturing composition may be coupled to
magnetic particles that can be separated in suitable magnetic
fields. For affinity separation, the capturing composition may be
immobilized on a device, such as a slide, and allows capture of the
identified cells.
[0068] In certain embodiments, the cell fraction is separated under
a magnetic field. In certain embodiments, the ligand in the
capturing composition is coupled to a magnetic particle.
[0069] Magnetic particles suitable for the methods disclosed herein
can be prepared using methods known in the art, see for example,
U.S. Pat. Nos. 5,597,531, 5,698,271, and 6,365,362, and also
procedures described in Liberti et al, In Fine Particles Science
and Technology, 777-90, E. Pelizzetti (ed.) (1996). Briefly, the
magnetic particles comprise a magnetic core (e.g. iron oxides)
which is coated with polymers or proteins (e.g., bovine serum
albumin and casein). The magnetic mass and size of the magnetic
particles can be controlled such that the magnetic particles are
magnetically responsive yet are substantially invisible to cell
analytical techniques such as immunofluorescence detection. The
suitable size of the magnetic particles may be less than 200 nm,
preferably with a suitable size distribution range, for example,
within 90-150 nm The magnetic mass of the particles may be between
70-90%.
[0070] In certain embodiments, the magnetic particle is colloidal.
Such colloidal magnetic particles are substantially stable in
solution over an extended period of time, and do not tend to
aggregate under gravitational force or in the absence of an applied
magnetic field. In certain embodiments, the magnetic particle is
colloidal nanoparticles.
[0071] The ligand in the capturing composition can be coupled to
the magnetic particles using any suitable methods known in the art.
For example, the capturing composition may be direct coupled to a
magnetic particle using heterobifunctional linkers, such as
succinimidylpropiono-dithiopyridine (SPDP), and
sulfosuccinimidil-4-[maleimidomethyl]cyclohexane-1-carboxylate(SMCC)).
For another example, the capturing composition comprising a
biotinylated antibody may be coupled to a magnetic particle
conjugated with streptavidin. The capturing composition and the
magnetic particles may also be introduced with other conjugating
pairs that can bring about the coupling, for example,
avidin-biotin, protein A-Antibody Fc, receptor-ligand, and
lectin-carbohydrate.
[0072] In certain embodiments, the capturing composition comprises
an EpCAM antibody coupled to magnetic colloidal nanoparticles. In
certain embodiments, the CellSearch.RTM. System (Veridex, N.J.) may
be used to separate the cell fraction enriched with the identified
cells.
[0073] The cancer cells of epithelial origin are contacted with an
antibody that specifically binds to a prostate-specific marker. The
term "prostate-specific" as used herein indicates that, the marker
is preferentially found in prostate tissues, and substantially
distinguishes prostate tissues or cells from other tissues or
cells. In certain embodiments, the prostate-specific marker is a
surface or membrane marker of prostate cells. In certain
embodiments, the prostate-specific marker is selected from the
group consisting of: Six-transmembrane epithelial antigen of the
prostate (STEAP-1) (see, e.g. Hubert et al., (1999) Proc. Natl.
Acad. Sci. USA, 96, 14523-14528), Prostate-specific membrane
antigen (PSM) (see, e.g., Israeli, R. S. et al., (1993) Cancer Res.
53, 227-230), Prostate carcinoma tumor antigen (PCTA-1) (see, e.g.,
Su, Z. Z. et al., (1996) Proc. Natl. Acad. Sci. USA 93, 7252-7257),
and Prostate stem cell antigen (PSCA) (see, e.g., Reiter, R. E. et
al. (1998) Proc. Natl. Acad. Sci USA 95, 1735-1740). An exemplary
human STEAP-1 has an amino acid sequence of SEQ ID NO:1 disclosed
in US 2009/0280056 A1, filed 26 Oct. 2007, the entire disclosure of
which is expressly incorporated by reference herein.
[0074] In certain embodiments, the antibody that specifically binds
to a prostate-specific marker comprises an anti-STEAP-1 antibody.
In certain embodiments, the anti-STEAP-1 antibody binds to STEAP-1
with a K.sub.D of .ltoreq.1000 nM. The anti-STEAP-1 antibody can be
a polyclonal antibody or a monoclonal antibody, and can be of any
suitable species, such as for example, a sheep antibody, a rabbit
antibody, or a murine antibody.
[0075] In certain embodiments, the anti-STEAP-1 antibody is a
murine monoclonal antibody. In certain embodiments, the
anti-STEAP-1 antibody is 15A5, produced by a hybridoma cell having
a microorganism deposit number of PTA-12259. In certain
embodiments, the anti-STEAP-1 antibody is an antibody which bind to
substantially the same epitope to which antibody 15A5 binds.
[0076] In certain embodiments, the anti-STEAP-1 antibody is
conjugated with a first detectable label. Any suitable detectable
labels may be used. In certain embodiments, the detectable label is
a fluorescent label, such as for example, fluorophore AF-488,
derivatives of cyanine dyes, fluorescein, rhodamine, Texas red,
aminomethylcoumarin (AMCA), phycoerythrin, fluorescein
isothiocyanante (FITC), among others. Methods of conjugating an
antibody with a detectable label are well known in the art, see for
example, Hermanson, G. T., Bioconjugate techniques, Academic Press,
2008.
[0077] In certain embodiments, the anti-STEAP-1 antibody is not
conjugated. The un-conjugated anti-STEAP-1 antibody can be detected
with a secondary antibody conjugated with a detectable label (e.g.
the first detectable label). Such secondary antibody can be any
antibody raised in a different species than the anti-STEAP-1
antibody and recognizes the constant region of the anti-STEAP-1
antibody, as is commonly employed in the art.
[0078] In certain embodiments, the cancer cells are identified with
one or more reagents that allow detection of cancer cells of
epithelial origin.
[0079] In certain embodiments, the reagents comprise a ligand that
specifically binds to an epithelial marker. In certain embodiments,
the epithelial marker is not EpCAM. In certain embodiments, the
epithelial marker is a cytokeratin. Cytokeratins are a group of
proteins typically expressed in epithelial cells, and form
keratin-containing filaments in the cytoskeleton of epithelial
tissue.
[0080] In certain embodiments, the ligand that specifically binds
to an epithelial marker is an anti-cytokeratin antibody, optionally
conjugated with a second detectable label. Any suitable detectable
label may be used, for example, a fluorescent label such as
phycoerythrin.
[0081] In certain embodiments, the reagents further comprise a
cell-specific dye that differentiates cells from non-cell
components. For example, dyes that stain cell nucleus may be used.
In certain embodiments, the dye is 4',6-diamidino-2-phenylindole
(DAPI).
[0082] In certain embodiments, the reagents further comprise a
ligand that specifically binds to a leukocyte marker. The leukocyte
marker may be selected as universally expressed on leukocytes but
not typically on non-leukocytes, for example, CD45 may be a
suitable leukocyte marker. In certain embodiments, the ligand that
specifically binds to a leukocyte marker is conjugated with a third
detectable label. For example, the ligand can be an anti-CD45
antibody conjugated with allophycocyanin. The staining of the
identified cells by an anti-CD45 antibody can be helpful to exclude
the leukocytes from the CTCs of epithelial origin.
[0083] In case more than one detectable label (including a dye) is
used in one testing, it is preferred that the detectable labels are
selected such that each label can be independently detected without
substantial interference to any other detectable signals present in
the sample. For example, the detectable labels (including a dye)
may be different fluorescent molecules showing different colors
under the detection condition.
[0084] The detection can be carried out by any suitable method, for
example, those based on immunofluorescent microscopy, flow
cytometry, fiber-optic scanning cytometry, or laser scanning
cytometry.
[0085] In certain embodiments, the cancer cells are visualized
under fluorescent microscopy after stained with cell-specific dye
and differently labeled antibodies or ligands for epithelial
marker, prostate-specific marker and leukocyte marker. The cells
positive for cell-specific dye, epithelial marker and
prostate-specific marker, but negative for leukocyte marker are
classified as cancer cells of epithelial origin that express the
prostate-specific marker. Such cells may also be analyzed using
flow cytometry, see, for example, Cruz, I., et al., Am J Clin
Pathol, Vol. 123: 66-74 (2005).
[0086] Alternatively, the cancer cells may also be deposited on a
surface of a glass slide, and scanned for cells positive for
cell-specific dye, epithelial marker and prostate-specific marker,
but negative for leukocyte marker (see, for example, Marrinucci, D.
et al., Human Pathology, Vol. 38, No. 3, 514-519 (2007)).
Similarly, the identified cells deposited on a glass slide may also
be analyzed using laser-scanning technology (see, for example,
Pachmann, K. et al., Breast Cancer Research, Vol. 7, No. 6,
R975-R979 (2005)).
[0087] In certain embodiments, the methods further comprise
determining the amount of the cancer cells that express the
prostate-specific marker, wherein such amount is predictive of the
stage of prostate cancer in the test subject. Assumptions have been
made to correlate the size and/or aggressiveness of a tumor with
the number of tumor cells in peripheral blood. For example, it is
reported that a patient with a 1-mm diameter tumor may have a
frequency of tumor cells in peripheral blood of about 6 tumor cells
per 100 ml blood (see, for example, U.S. Pat. No. 6,365,362).
Assuming an increase in tumor size may be proportional to this
frequency, criteria may be established to indicate the stage of the
cancer in the test subject. In certain embodiments, clinical blood
samples from patients diagnosed of early stage or metastatic
prostate cancer may be used to determine a statistical level of
cancer cells in the peripheral blood for those patients, and
thereby provides for criteria for future detection and
analysis.
[0088] In certain embodiments, the methods further comprise
determining the expression level of the prostate-specific marker on
the cancer cells. Some prostate-specific markers are antigens whose
expression level may be up-regulated as a result of tumor growth,
metastasis and/or an advanced stage of the cancer. Such
prostate-specific markers may include, without limitation, STEAP-1,
PSMA, PCTA-1, and PSCA. The expression levels of the
prostate-specific markers on the cancer cells may be determined by
any suitable methods, for example, by determining the intensity of
the fluorescence signal corresponding to the prostate-specific
marker.
[0089] In certain embodiments, the methods further comprise grading
the cancer cells based on their expression level of the
prostate-specific marker, and determining the percentage of the
cancer cells in each grade. In certain embodiments, cancer cells
expressing high level, medium level and low level of the
prostate-specific marker are respectively graded. The criteria for
"high level", "medium level", and "low level" can be determined,
for example, using established cell lines having known expression
levels of the marker. For example, the LB50 cell line is known to
express a high level of STEAP-1, the LnCAPner cell line is known to
express a medium level of STEAP-1, and the PC3 cell line is known
to express a low level of STEAP-1. Therefore, cancer cells as
detected to have a STEAP-1 expression level comparable to or higher
than the LB 50 cell line may be graded as "high level". Similarly,
"medium level" may be assigned to cancer cells whose STEAP-1
expression level is comparable to or higher than that of LnCAPner
cell line but is lower than that of LB 50 cell line. Those having
an STEAP-1 expression level comparable to or lower than that of PC3
cell line may be graded as or "low level."
[0090] The number of the cancer cells in each grade may be further
determined In certain embodiments, the percentage of the cancer
cells in each grade may be calculated. A higher percentage of
cancer cells in the high level grade can be indicative of a more
advanced stage of the prostate cancer. Similarly, prostate cancer
at an early stage may show lower percentage of cancer cells in the
high level grade, and/or higher percentage of cancer cells in low
level grade.
[0091] In certain embodiments, the methods further comprise
calculating a grade score for each grade by multiplying the
percentage of the cancer cells in that grade with a unique grade
number assigned to that grade based on the expression level of the
prostate-specific marker, and summing up all the grade scores to
obtain an H score, wherein the H score is indicative of the stage
of the prostate cancer in the test subject. For example, a grade
number of 3 may be assigned to the high level grade, 2 to the
medium level grade, and 1 to the low level grade, which defines the
range of the H score within 0 to 300. A higher H score is
indicative of more cells in the high level grade, i.e. a more
advanced stage of the prostate cancer, and a lower H score
indicates more cells in the low level grade, i.e. a relatively
early stage of the prostate cancer.
[0092] In some embodiments, the methods further comprise
determining the presence of a marker and/or frequency of presence
of a marker. In some embodiments, the presence of a marker is
determined by immunohistochemical ("IHC"), Western blot analysis,
immunoprecipitation, molecular binding assays, ELISA, ELIFA,
fluorescence activated cell sorting ("FACS"), MassARRAY,
proteomics, quantitative blood based assays (as for example Serum
ELISA), biochemical enzymatic activity assays, in situ
hybridization, Northern analysis, polymerase chain reaction ("PCR")
including quantitative real time PCR ("qRT-PCR") and other
amplification type detection methods, such as, for example,
branched DNA, SISBA, TMA and the like), RNA-Seq, FISH, microarray
analysis, gene expression profiling, and/or serial analysis of gene
expression ("SAGE"), as well as any one of the wide variety of
assays that can be performed by protein, gene, and/or tissue array
analysis. In some embodiments, the presence of a marker is
determined by fluorescent in situ hybridization (FISH). In some
embodiments, the marker is PTEN. In some embodiments, the CTC is
triploid. In some embodiments, the CTC is triploid with PTEN loss.
In some embodiments, the CTC is determined to be triploid by CEP10
FISH. In some embodiments, the CTC is determined comprise PTEN loss
by PTEN FISH.
[0093] In another aspect, the present disclosure also provides
methods of predicting efficacy of prostate cancer therapy in a test
subject, comprising: a) contacting cancer cells of epithelial
origin with an antibody that specifically binds to a
prostate-specific marker, wherein the cancer cells are from a blood
sample taken from the test subject; and b) determining whether any
of the cancer cells express the prostate-specific marker, wherein
the presence of cancer cells that express the prostate-specific
marker is predictive of the efficacy of the prostate cancer therapy
in the test subject.
[0094] Certain prostate-specific markers may also be therapeutic
targets for prostate cancer treatment. Therefore, the expression
level of such marker on the CTCs and changes in such level can be
predicative of the efficacy of therapies that target such
marker.
[0095] In certain embodiments, the methods further comprise
determining the amount of the cancer cells that express the
prostate-specific marker, and/or determining the expression level
of a prostate-specific marker on the cancer cells. For example, the
expression level of a prostate-specific marker (e.g. STEAP-1) on
the cancer cells from the baseline pre-treated sample in early
phase clinical trials can be correlated with clinical endpoints
such as progression free survival, PSA changes, patient-reported
bone pain, overall survival, or others, in order to determine
whether expression of the prostate-specific marker above a certain
threshold is predictive of clinical activity of the prostate cancer
therapy (e.g. STEAP-1 Antibody-Drug Conjugate (ADC) based therapy).
Dynamic changes in expression level of the prostate-specific marker
(e.g. STEAP-1) in the cancer cells (i.e. down-regulation in
post-treatment samples) can also be correlated to clinical outcome
measures to determine if such changes are predictive of therapeutic
activity. Such methods can be used as a first step in qualifying
the assay as a candidate predictive biomarker that could be used to
select patients for a prostate cancer therapy (e.g. STEAP-1
ADC-based therapy), followed by prospective validation in a
confirmatory phase III study.
[0096] In another aspect, the present disclosure also provides
methods of monitoring response to a prostate cancer therapy in a
test subject, comprising: a) contacting a first group of cancer
cells of epithelial origin with an antibody that specifically binds
to a prostate-specific marker, wherein the first group of cancer
cells are from a first blood sample taken from the test subject; b)
determining the amount of the cancer cells in the first group that
express prostate-specific marker and/or the expression level of the
prostate-specific marker in the cancer cells; c) contacting a
second group of cancer cells of epithelial origin with the antibody
that specifically binds to a prostate-specific marker, wherein the
second group of cancer cells are from a second blood sample taken
from the test subject after a test period of prostate cancer
therapy; d) determining the amount of the cancer cells in the
second group that express prostate-specific marker and/or the
expression level of the prostate-specific marker in the cancer
cells; and e) comparing the amount of the cancer cells that express
the prostate-specific marker and/or the prostate-specific marker
expression level as determined in b) with that in step d), wherein
the change in the amount of the cancer cells expressing the
prostate-specific marker and/or an increase in the
prostate-specific marker expression level in the cancer cells is
predicative of the response to the prostate cancer therapy in the
test subject. In certain embodiments, the prostate-specific marker
is STEAP-1.
III. Antibodies
[0097] In another aspect, the present disclosure provides
antibodies which bind to substantially the same epitope to which
antibody 15A5 binds, wherein antibody 15A5 is produced by a
hybridoma cell having a microorganism deposit number of
PTA-12259.
[0098] In certain embodiments, the antibodies provided herein
compete with 15A5 antibody for binding to STEAP-1. Competition
assays may be used to identify an antibody that competes with the
anti-STEAP-1 antibody 15A5 for binding to STEAP-1.
[0099] In an exemplary competition assay, immobilized STEAP-1 is
incubated in a solution comprising a first labeled antibody that
binds to STEAP-1 (e.g., 15A5) and a second unlabeled antibody that
is being tested for its ability to compete with the first antibody
for binding to STEAP-1. The second antibody may be present in a
hybridoma supernatant. As a control, immobilized STEAP-1 is
incubated in a solution comprising the first labeled antibody but
not the second unlabeled antibody. After incubation under
conditions permissive for binding of the first antibody to STEAP-1,
excess unbound antibody is removed, and the amount of label
associated with immobilized STEAP-1 is measured. If the amount of
label associated with immobilized STEAP-1 is substantially reduced
in the test sample relative to the control sample, then that
indicates that the second antibody is competing with the first
antibody for binding to STEAP-1. See Harlow and Lane (1988)
Antibodies: A Laboratory Manual ch.14 (Cold Spring Harbor
Laboratory, Cold Spring Harbor, N.Y.).
[0100] In certain embodiments, the antibodies provided herein has a
dissociation constant (Kd) to STEAP-1 of .ltoreq.1000 nM,
.ltoreq.100 nM, .ltoreq.10 nM, .ltoreq.1 nM, .ltoreq.0.1 nM,
.ltoreq.0.01 nM, or .ltoreq.0.001 nM (e.g. 10.sup.-8 M or less,
e.g. from 10.sup.-8M to 10.sup.-13M, e.g., from 10.sup.-9M to
10.sup.-13 M).
[0101] In one embodiment, Kd is measured by a radiolabeled antigen
binding assay (RIA) performed with the Fab version of an antibody
of interest and its antigen as described by the following assay.
Solution binding affinity of Fabs for antigen is measured by
equilibrating Fab with a minimal concentration of
(.sup.125I)-labeled antigen in the presence of a titration series
of unlabeled antigen, then capturing bound antigen with an anti-Fab
antibody-coated plate (see, e.g., Chen et al., J. Mol. Biol.
293:865-881(1999)). To establish conditions for the assay,
MICROTITER.RTM. multi-well plates (Thermo Scientific) are coated
overnight with 5 .mu.g/ml of a capturing anti-Fab antibody (Cappel
Labs) in 50 mM sodium carbonate (pH 9.6), and subsequently blocked
with 2% (w/v) bovine serum albumin in PBS for two to five hours at
room temperature (approximately 23.degree. C.). In a non-adsorbent
plate (Nunc #269620), 100 pM or 26 pM [.sup.125I]-antigen are mixed
with serial dilutions of a Fab of interest (e.g., consistent with
assessment of the anti-VEGF antibody, Fab-12, in Presta et al.,
Cancer Res. 57:4593-4599 (1997)). The Fab of interest is then
incubated overnight; however, the incubation may continue for a
longer period (e.g., about 65 hours) to ensure that equilibrium is
reached. Thereafter, the mixtures are transferred to the capture
plate for incubation at room temperature (e.g., for one hour). The
solution is then removed and the plate washed eight times with 0.1%
polysorbate 20 (TWEEN-20.RTM.) in PBS. When the plates have dried,
150 .mu.l/well of scintillant (MICROSCINT-20.TM.; Packard) is
added, and the plates are counted on a TOPCOUNT.TM. gamma counter
(Packard) for ten minutes. Concentrations of each Fab that give
less than or equal to 20% of maximal binding are chosen for use in
competitive binding assays.
[0102] According to another embodiment, Kd is measured using
surface plasmon resonance assays using a BIACORE.RTM.-2000 or a
BIACORE.RTM.-3000 (BIAcore, Inc., Piscataway, N.J.) at 25.degree.
C. with immobilized antigen CMS chips at .about.10 response units
(RU). Briefly, carboxymethylated dextran biosensor chips (CMS,
BIAcore, Inc.) are activated with
N-ethyl-N'-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC)
and N-hydroxysuccinimide (NHS) according to the supplier's
instructions. Antigen is diluted with 10 mM sodium acetate, pH 4.8,
to 5 .mu.g/ml (-0.2 .mu.M) before injection at a flow rate of 5
.mu.l/minute to achieve approximately 10 response units (RU) of
coupled protein. Following the injection of antigen, 1 M
ethanolamine is injected to block unreacted groups. For kinetics
measurements, two-fold serial dilutions of Fab (0.78 nM to 500 nM)
are injected in PBS with 0.05% polysorbate 20 (TWEEN-20.TM.)
surfactant (PBST) at 25.degree. C. at a flow rate of approximately
25 .mu.l/min. Association rates (k.sub.on) and dissociation rates
(k.sub.off) are calculated using a simple one-to-one Langmuir
binding model (BIACORE.RTM. Evaluation Software version 3.2) by
simultaneously fitting the association and dissociation
sensorgrams. The equilibrium dissociation constant (Kd) is
calculated as the ratio k.sub.off/k.sub.on. See, e.g., Chen et al.,
J. Mol. Biol. 293:865-881 (1999). If the on-rate exceeds 10.sup.6
M.sup.-1 s.sup.-1 by the surface plasmon resonance assay above,
then the on-rate can be determined by using a fluorescent quenching
technique that measures the increase or decrease in fluorescence
emission intensity (excitation=295 nm; emission=340 nm, 16 nm
band-pass) at 25.degree. C. of a 20 nM anti-antigen antibody (Fab
form) in PBS, pH 7.2, in the presence of increasing concentrations
of antigen as measured in a spectrometer, such as a stop-flow
equipped spectrophometer (Aviv Instruments) or a 8000-series
SLM-AMINCO.TM. spectrophotometer (ThermoSpectronic) with a stirred
cuvette.
[0103] Kinetic binding measurements can also be performed on an
Octet Red instrument (ForteBio, Menlo Park, Calif., USA). For
example, all washes, dilutions and measurements are performed in
Octet buffer (0.2% dodecylmaltoside, or DDM, -PBS) with the plate
shaking at 1000 rpm. Streptavidin biosensors are equilibrated in
Octet buffer for 10 min and then loaded with biotinylated STEAP-1
(from viral lysate in 1% DDM, diluted 1:8 in Octet Buffer) for 5
min and washed for 10 min. For the association phase, the
ligand-coated streptavidin tips are immersed in anti-STEAP-1
antibody fragments for 10 min (eight serial two-fold dilutions,
starting at 500 or 50 nM). Dissociation of the Ab-STEAP-1 complex
can be measured in wells containing Octet buffer alone for 600 s.
KD, Ka and Kd are determined with Octet evaluation software v6.3
using a 1:1 binding model with global fitting.
[0104] In certain embodiments, the antibodies provided herein
include, without limitation, murine antibodies, sheep antibodies
and rabbit antibodies. In certain embodiments, the antibodies are
murine monoclonal antibody.
[0105] in certain embodiments, the antibodies provided herein
comprise at least one of the CDR regions of the antibody 15A5. The
CDR regions of an antibody can be determined using methods known in
the art. Exemplary CDRs (CDR-L1, CDR-L2, CDR-L3, CDR-H1, CDR-H2,
and CDR-H3) occur at amino acid residues 24-34 of L1, 50-56 of L2,
89-97 of L3, 31-35B of H1, 50-65 of H2, and 95-102 of H3. (Kabat et
al., Sequences of Proteins of Immunological Interest, 5th Ed.
Public Health Service, National Institutes of Health, Bethesda, Md.
(1991).) With the exception of CDR1 in heavy chain variable
regions, CDRs generally comprise the amino acid residues that form
the hypervariable loops. CDRs also comprise "specificity
determining residues," or "SDRs," which are residues that contact
antigen. SDRs are contained within regions of the CDRs called
abbreviated-CDRs, or a-CDRs. Exemplary a-CDRs (a-CDR-L1, a-CDR-L2,
a-CDR-L3, a-CDR-H1, a-CDR-H2, and a-CDR-H3) occur at amino acid
residues 31-34 of L1, 50-55 of L2, 89-96 of L3, 31-35B of H1, 50-58
of H2, and 95-102 of H3. (See Almagro and Fransson, Front. Biosci.
13:1619-1633 (2008).) Unless otherwise indicated, CDR residues and
other residues in the variable domain (e.g., FR residues) are
numbered herein according to Kabat et al., supra.
[0106] In certain embodiments, the antibodies provided herein
comprise at least one of the heavy chain variable regions of the
antibody 15A5, or at least one of the light chain variable regions
of the antibody 15A5.
[0107] The term "variable region" or "variable domain" refers to
the domain of an antibody heavy or light chain that is involved in
binding the antibody to antigen. The variable domains of the heavy
chain and light chain (VH and VL, respectively) of a native
antibody generally have similar structures, with each domain
comprising four conserved framework regions (FRs) and three
hypervariable regions (HVRs). (See, e.g., Kindt et al. Kuby
Immunology, 6.sup.th ed., W. H. Freeman and Co., page 91 (2007).) A
single VH or VL domain may be sufficient to confer antigen-binding
specificity. Furthermore, antibodies that bind a particular antigen
may be isolated using a VH or VL domain from an antibody that binds
the antigen to screen a library of complementary VL or VH domains,
respectively. See, e.g., Portolano et al., J. Immunol. 150:880-887
(1993); Clarkson et al., Nature 352:624-628 (1991).
[0108] Antibody fragments of the antibodies provided herein are
also encompassed by the present disclosure. In certain embodiments,
an antibody provided herein is an antibody fragment. Antibody
fragments include, but are not limited to, Fab, Fab', Fab'-SH,
F(ab').sub.2, Fv, and scFv fragments, and other fragments described
below. For a review of certain antibody fragments, see Hudson et
al. Nat. Med. 9:129-134 (2003). For a review of scFv fragments,
see, e.g., Pluckthun, in The Pharmacology of Monoclonal Antibodies,
vol. 113, Rosenburg and Moore eds., (Springer-Verlag, New York),
pp. 269-315 (1994); see also WO 93/16185; and U.S. Pat. Nos.
5,571,894 and 5,587,458. For discussion of Fab and F(ab').sub.2
fragments comprising salvage receptor binding epitope residues and
having increased in vivo half-life, see U.S. Pat. No.
5,869,046.
[0109] Diabodies are antibody fragments with two antigen-binding
sites that may be bivalent or bispecific. See, for example, EP
404,097; WO 1993/01161; Hudson et al., Nat. Med. 9:129-134 (2003);
and Hollinger et al., Proc. Natl. Acad. Sci. USA 90: 6444-6448
(1993). Triabodies and tetrabodies are also described in Hudson et
al., Nat. Med. 9:129-134 (2003).
[0110] Single-domain antibodies are antibody fragments comprising
all or a portion of the heavy chain variable domain or all or a
portion of the light chain variable domain of an antibody. In
certain embodiments, a single-domain antibody is a human
single-domain antibody (Domantis, Inc., Waltham, Mass.; see, e.g.,
U.S. Pat. No. 6,248,516 B1).
[0111] Antibody fragments can be made by various techniques,
including but not limited to proteolytic digestion of an intact
antibody as well as production by recombinant host cells (e.g. E.
coli or phage), as described herein.
[0112] In certain embodiments, the antibodies provided herein is
antibody 15A5 or its antigen binding fragment.
[0113] In certain embodiments, the antibodies provided herein are
further conjugated with a detectable label. Suitable labels
include, but are not limited to, labels or moieties that are
detected directly (such as fluorescent, chromophoric,
electron-dense, chemiluminescent, and radioactive labels), as well
as moieties, such as enzymes or ligands, that are detected
indirectly, e.g., through an enzymatic reaction or molecular
interaction. Exemplary labels include, but are not limited to, the
radioisotopes .sup.32P, .sup.14C, .sup.125I, .sup.3H, and
.sup.131I, fluorophores such as rare earth chelates or fluorescein
and its derivatives, rhodamine and its derivatives, dansyl,
umbelliferone, luceriferases, e.g., firefly luciferase and
bacterial luciferase (U.S. Pat. No. 4,737,456), luciferin,
2,3-dihydrophthalazinediones, horseradish peroxidase (HRP),
alkaline phosphatase, .beta.-galactosidase, glucoamylase, lysozyme,
saccharide oxidases, e.g., glucose oxidase, galactose oxidase, and
glucose-6-phosphate dehydrogenase, heterocyclic oxidases such as
uricase and xanthine oxidase, coupled with an enzyme that employs
hydrogen peroxide to oxidize a dye precursor such as HRP,
lactoperoxidase, or microperoxidase, biotin/avidin, spin labels,
bacteriophage labels, stable free radicals, and the like.
IV. Nucleic Acids and Host Cells
[0114] Antibodies may be produced using recombinant methods and
compositions, e.g., as described in U.S. Pat. No. 4,816,567. In one
embodiment, isolated nucleic acid encoding an anti-STEAP-1 antibody
described herein is provided. Such nucleic acid may encode an amino
acid sequence comprising the VL and/or an amino acid sequence
comprising the VH of the antibody (e.g., the light and/or heavy
chains of the antibody). In a further embodiment, one or more
vectors (e.g., expression vectors) comprising such nucleic acid are
provided. In a further embodiment, a host cell comprising such
nucleic acid is provided. In one such embodiment, a host cell
comprises (e.g., has been transformed with): (1) a vector
comprising a nucleic acid that encodes an amino acid sequence
comprising the VL of the antibody and an amino acid sequence
comprising the VH of the antibody, or (2) a first vector comprising
a nucleic acid that encodes an amino acid sequence comprising the
VL of the antibody and a second vector comprising a nucleic acid
that encodes an amino acid sequence comprising the VH of the
antibody. In one embodiment, the host cell is eukaryotic, e.g. a
Chinese Hamster Ovary (CHO) cell or lymphoid cell (e.g., Y0, NS0,
Sp20 cell). In one embodiment, a method of making an anti-STEAP-1
antibody is provided, wherein the method comprises culturing a host
cell comprising a nucleic acid encoding the antibody, as provided
above, under conditions suitable for expression of the antibody,
and optionally recovering the antibody from the host cell (or host
cell culture medium).
[0115] For recombinant production of an anti-STEAP-1 antibody,
nucleic acid encoding an antibody, e.g., as described above, is
isolated and inserted into one or more vectors for further cloning
and/or expression in a host cell. Such nucleic acid may be readily
isolated and sequenced using conventional procedures (e.g., by
using oligonucleotide probes that are capable of binding
specifically to genes encoding the heavy and light chains of the
antibody).
[0116] Suitable host cells for cloning or expression of
antibody-encoding vectors include prokaryotic or eukaryotic cells
described herein. For example, antibodies may be produced in
bacteria, in particular when glycosylation and Fc effector function
are not needed. For expression of antibody fragments and
polypeptides in bacteria, see, e.g., U.S. Pat. Nos. 5,648,237,
5,789,199, and 5,840,523. (See also Charlton, Methods in Molecular
Biology, Vol. 248 (B.K.C. Lo, ed., Humana Press, Totowa, N.J.,
2003), pp. 245-254, describing expression of antibody fragments in
E. coli.) After expression, the antibody may be isolated from the
bacterial cell paste in a soluble fraction and can be further
purified.
[0117] In addition to prokaryotes, eukaryotic microbes such as
filamentous fungi or yeast are suitable cloning or expression hosts
for antibody-encoding vectors, including fungi and yeast strains
whose glycosylation pathways have been "humanized," resulting in
the production of an antibody with a partially or fully human
glycosylation pattern. See Gerngross, Nat. Biotech. 22:1409-1414
(2004), and Li et al., Nat. Biotech. 24:210-215 (2006).
[0118] Suitable host cells for the expression of glycosylated
antibody are also derived from multicellular organisms
(invertebrates and vertebrates). Examples of invertebrate cells
include plant and insect cells. Numerous baculoviral strains have
been identified which may be used in conjunction with insect cells,
particularly for transfection of Spodoptera frugiperda cells.
[0119] Plant cell cultures can also be utilized as hosts. See,
e.g., U.S. Pat. Nos. 5,959,177, 6,040,498, 6,420,548, 7,125,978,
and 6,417,429 (describing PLANTIBODIES.TM. technology for producing
antibodies in transgenic plants).
[0120] Vertebrate cells may also be used as hosts. For example,
mammalian cell lines that are adapted to grow in suspension may be
useful. Other examples of useful mammalian host cell lines are
monkey kidney CV1 line transformed by SV40 (COS-7); human embryonic
kidney line (293 or 293 cells as described, e.g., in Graham et al.,
J. Gen Virol. 36:59 (1977)); baby hamster kidney cells (BHK); mouse
sertoli cells (TM4 cells as described, e.g., in Mather, Biol.
Reprod. 23:243-251 (1980)); monkey kidney cells (CV1); African
green monkey kidney cells (VERO-76); human cervical carcinoma cells
(HELA); canine kidney cells (MDCK; buffalo rat liver cells (BRL
3A); human lung cells (W138); human liver cells (Hep G2); mouse
mammary tumor (MMT 060562); TRI cells, as described, e.g., in
Mather et al., Annals N.Y. Acad. Sci. 383:44-68 (1982); MRC 5
cells; and FS4 cells. Other useful mammalian host cell lines
include Chinese hamster ovary (CHO) cells, including DHFR.sup.- CHO
cells (Urlaub et al., Proc. Natl. Acad. Sci. USA 77:4216 (1980));
and myeloma cell lines such as Y0, NS0 and Sp2/0. For a review of
certain mammalian host cell lines suitable for antibody production,
see, e.g., Yazaki and Wu, Methods in Molecular Biology, Vol. 248
(B.K.C. Lo, ed., Humana Press, Totowa, N.J.), pp. 255-268
(2003).
[0121] A hybridoma cell line is also provided herein, having a
microorganism deposit number of PTA-12259. The hybridoma cell line
produces the antibody 15A5.
V. Use of the Antibodies
[0122] The antibodies provided herein can be used in the
manufacture of a diagnostic reagent for prostate cancer. The
antibodies may be further conjugated with a detectable label
suitable for the diagnostic purpose, and may be presented in a
suitable form, such as in lyophilized powers or in suitable
solution form.
VI. Test Kits
[0123] In another aspect of the present disclosure, test kits
containing compositions useful for the diagnosis or prognosis of
prostate cancer is provided.
[0124] The present disclosure further provides test kits for
detecting presence of prostate cancer cells expressing STEAP-1 in a
blood sample, comprising an antibody that specifically binds to
STEAP-1.
[0125] In certain embodiments, the antibody is conjugated with a
first detectable label. Any suitable detectable label may be used,
such as fluorescent label.
[0126] In certain embodiments, the antibody is an anti-STEAP-1
antibody provided herein. In certain embodiments, the antibody is
antibody 15A5.
[0127] In certain embodiments, the test kits further comprise one
or more compositions selected from the group consisting of:
magnetic particles coupled to a first ligand that specifically
binds to cancer cells of epithelial origin, a second ligand that
specifically binds to an epithelial marker; a third ligand
specifically binds to a leukocyte marker, and a dye that
differentiates cells from non-cell components.
[0128] In certain embodiments, the second ligand is conjugated to a
second detectable label, and/or the third ligand is conjugated to a
third detectable label. In certain embodiments, when the test kits
comprises more than one detectable label (including a dye), it is
preferred that the detectable labels (including a dye) are selected
such that each label can be independently detected without
substantial interference to any other detectable signals present in
the sample.
[0129] In certain embodiments, the first ligand, the second ligand
and/or the third ligand comprises an antibody. In certain
embodiments, the first ligand comprises an anti-EpCAM antibody. In
certain embodiments, the second ligand comprises an anti-keratin
antibody. In certain embodiments, the third ligand comprises an
anti-CD45 antibody.
[0130] The test kits can further comprise a container and a label
or package insert on or associated with the container. Suitable
containers include, for example, bottles, vials, syringes, IV
solution bags, etc. The containers may be formed from a variety of
materials such as glass or plastic. The container holds a
composition which is by itself or combined with another composition
effective for diagnosing the condition. At least one reagent in the
composition is an antibody of the invention. The label or package
insert indicates that the composition is used for in vitro
diagnosis of the condition of choice.
VII. EXAMPLES
[0131] The following are examples of methods and compositions of
the invention. It is understood that various other embodiments may
be practiced, given the general description provided above.
Example 1
Detection of STEAP-1 on Different Cell Lines
[0132] Three anti-STEAP-1 antibodies were used to detect STEAP-1
expression on three prostate cancer cell lines using an
immunohistochemistry (IHC) assay. 293 LB50 was used as a high
STEAP-1 expressing cell line; LnCAPner was used as a medium STEAP-1
expressing cell line; and PC3 was used as a low to negative STEAP-1
expressing cell line. The tested anti-STEAP-1 antibodies were:
antibody-37, which is a mouse monoclonal anti-STEAP-1 antibody; a
sheep polyclonal anti-STEAP-1 antibody, and sc-25514, which is a
rabbit polyclonal anti-STEAP-1 antibody. The three antibodies were
conjugated with the fluorophore AF-488.
[0133] The antibodies were incubated respectively with the three
cell lines. Antibody-antigen bindings were visualized under
fluorescent microscopy for AF-488 signal. Results showed that all
three antibodies gave expected signal intensities relative to the
expression levels of the three cell lines, i.e., the antibodies
showed strongest staining on 293 LB50 cells, medium staining on
LnCAPner cells, and low to negative staining on PC3 cells.
Example 2
Detection of STEAP-1 Expression in Prostate Cancer Cells Using
Anti-STEAP-1 Antibodies on the CellSearch.RTM. System
[0134] The three antibodies (mouse antibody-37, Sheep polyclonal
antibody, and rabbit sc-25514) were tested on the CellSearch.RTM.
system for their ability to detect the STEAP-1 expression on LB50
cells and PC3 cells, respectively.
[0135] The spike-in assay was performed as follows. The LB50 cells
and PC3 cells were grown in T75 flasks. When cells reached 80%
confluence, cells were washed with 10 ml PBS and then treated with
3 ml trypsin. 7 ml of media was added to the detached cells, and
the whole suspension was transferred into a falcon tube followed by
centrifugation for 5 minutes at 13000 rpm. Supernatant was removed
and the pellet was re-suspended in 10 ml of PBS. 0.5 ml of each
cell suspension was transfer into vicell tubes and counted using
the Beckman Coulter counter. The cell suspension was diluted to
5000 cells/ml solution in 10 ml of media. A suitable amount of
cells were spiked into 10 ml blood, in which 7.5 ml of blood was to
be used in the CellSearch method. For 100 cell spike in, 26.6 uls
of the cell suspension was added to 10 ml of blood. The blood with
cells spiked-in was rotated for 20 minutes.
[0136] To ensure there were approximately 100 cells spiked into
blood, 5u1 of each cell suspension was added onto poly L lysine
gridded slides (electron microscopy science) repetitively for 5
times. 5 ul cell suspension approximately equaled to 25 cells. The
cells on each slide were counted, and the cell number was used to
calculate the recovery of the cells by counting the number of
"CTCs" (i.e., spiked-in cells) captured on CellSearch/the actual
number of cells counted on slide.
[0137] When the blood with cells spiked-in has been thoroughly
mixed, the blood samples were run on CellSearch with the three
anti-STEAP-1 antibodies, respectively, following the CellSearch CTC
protocol. Briefly, each testing sample was mixed with anti-EpCAM
antibody conjugated with magnetic colloid nanoparticles, and then
was subject to a magnetic field to allow separation of a cell
fraction enriched with EpCAM positive epithelial cells in the
sample. The cell fraction was then mixed with
phycoerythrin-conjugated anti-cytokeratin antibodies,
allophycocyanin-conjugated anti-CD45 antibodies, DAPI, and one of
the three anti-STEAP-1 antibodies conjugated with AF-488, which was
used in the 4.sup.th filter. The conjugated anti-STEAP-1 antibodies
were diluted to 1:50 in PBS. The samples were run on CellSearch and
the CTCs were scored on the CellTracks analyzer. Cells stained
positive for cytokeratin and DAPI, but negative for CD45 were
determined as CTCs. CTCs on the CellSearch autoprep systems that
showed STEAP-1 staining were selected, and were further quantified
for fluorescence intensities of the anti-STEAP-1 antibody that
indicated the STEAP-1 expression level.
[0138] CTCs with STEAP-1 expression were scored based on the
staining intensity, i.e. the level of expression of STEAP-1. CTCs
with high STEAP-1 expression, which was demonstrated by strong
staining intensity and minimal to no background was given a score
of 3, medium staining intensity with some background was given a
score as 2 and low staining intensity with relatively high
background was given a score of 1. A representative example is
shown in FIG. 1.
[0139] As shown in FIG. 2 (a), all three tested antibodies detected
the STEAP-1 high expresser LB50 cells spiked in to the blood,
although the dynamic range was different. As shown in FIG. 2 (b),
the sheep polyclonal antibody and the rabbit sc-25514 also detected
STEAP-1 low expresser PC3 cells spiked in to the blood.
[0140] H score was calculated for the CTCs with STEAP-1 expression,
from the sum of (1 x the percentage of cells staining weakly
positive)+(2.times.the percentage of cells staining moderately
positive)+(3.times.the percentage of cells staining strongly
positive) with a maximum score of 300 (McCall et al. (2008) British
Journal of Cancer 98(6):1094-1101).
[0141] As shown in FIGS. 2 (c)-(d), sheep polyclonal antibody
demonstrated the best dynamic range, and therefore sheep polyclonal
antibody was chosen for further testing with clinical samples.
Example 3
Analysis of STEAP-1-Expressing Cells in Spiked-in Samples Using
Sheep Polyclonal Antibody on the CellSearch.RTM. System
[0142] The anti-STEAP-1 sheep polyclonal antibody was used to
determine STEAP-1 expression on cells spiked-in to blood samples.
The spike-in assay was performed in a similar procedure as
described in Example 2. The three cell lines, 293 LB50, LnCAPner
and PC3 were spiked in to respective blood samples and mixed
thoroughly. The sheep polyclonal antibody was diluted to 1:50 in
PBS and added to the blood sample in the 4.sup.th filter on
CellSearch. The samples were run on CellSearch and the CTCs were
scored on the CellTracks analyzer. Cells stained positive for
cytokeratin and DAPI, but negative for CD45 were determined as
CTCs. CTCs on the CellSearch autoprep systems that showed STEAP-1
staining were selected, and were further quantified for
fluorescence intensities of the anti-STEAP-1 antibody that
indicated the STEAP-1 expression level. H scores were also
calculated according the same method as described in Example 2.
[0143] As shown in FIGS. 3 (a)-(b), the sheep polyclonal antibody
detected STEAP-1 expression on all of the three cell lines tested
and with good dynamic range. As detected by the sheep polyclonal
antibody, the sample spiked in with 293 LB50 cells had the more
than 60% CTCs with a high intensity level, and the H score was
determined above 200; the sample spiked in with LnCAPner cells had
an H score of about 100; and the sample spiked in with PC3 cells
had an H score of below 100.
Example 4
Detection of STEAP-1 Expression in CTCs of Prostate Cancer Patients
Using Anti-STEAP-1 Antibody on the CellSearch.RTM. System
[0144] Blood samples from 11 prostate cancer patients were obtained
from a clinic. The blood samples were analyzed on the
CellSearch.RTM. system using the anti-STEAP-1 sheep polyclonal
antibody. The sheep polyclonal antibody was diluted to 1:50 in PBS
and added to the blood sample in the 4.sup.th filter on CellSearch.
The samples were run on CellSearch and the CTCs were scored on the
CellTracks analyzer. Cells stained positive for cytokeratin and
DAPI, but negative for CD45 were determined as CTCs. CTCs on the
CellSearch autoprep systems that showed STEAP-1 staining were
selected, and were further quantified for fluorescence intensities
of the anti-STEAP-1 antibody that indicated the STEAP-1 expression
level. The number of CTCs were counted for each sample, and H
scores were also calculated as described in Example 2. Results are
shown in FIG. 4.
Example 5
Correlation of CTC Assay With Immunohistochemistry (IHC) Assay
[0145] Blood samples and tumor tissue samples were collected from
10 prostate cancer patients in a phase I clinical trial.
[0146] The blood samples were analyzed on the CellSearch.RTM.
system using the anti-STEAP-1 sheep polyclonal antibody. The number
of CTCs was counted for each sample, and H scores were also
calculated as described in Example 2. Results are shown in FIG. 5
(a).
[0147] The tumor tissue samples were tested using conventional IHC
methods, and the expression level of STEAP-1 in the tissue were
shown in overall scores: 1+, 2+and 3+. The larger number indicated
the higher expression level of STEAP-1.
[0148] The CellSearch.RTM. results and the IHC results are shown
and compared in FIG. 5 (b)-(c). The CellSearch.RTM. results showed
good correlation with the IHC results, indicating that the
CellSearch.RTM. method using the sheep polyclonal antibody was
effective in detecting the STEAP-1-expressing CTCs in blood
sample.
Example 6
Comparison of the Sheep Polyclonal Antibody With the Mouse
Monoclonal Antibody 15A5
[0149] The mouse monoclonal antibody 15A5 was tested using the
spike-in assay on the CellSearch.RTM. system and compared with the
sheep polycoloncal antibody. 293 LB50 cells (high-expresser),
LnCAPner cells (medium-expresser), and PC3 cells (low-expresser)
were spiked into respective blood samples as described in Example
2. The blood samples were analyzed on the CellSearch.RTM. system,
using the sheep polyclonal antibody and the mouse monoclonal
antibody 15A5, respectively. H scores were also calculated. The
procedure and methods were similar to those described in Example
2.
[0150] As shown in FIG. 6 (a)-(d), both antibodies showed
comparable results for each sample in intensity level and in H
score. The mouse monoclonal antibody 15A5 also showed good dynamic
range in the assay.
[0151] There are advantages to using monoclonal antibody 15A5 over
a polyclonal antibody. For example, the monoclonal antibody will
show less batch-to-batch variability, less background, and greater
reproducibility among experiments, as compared to a polyclonal
antibody.
Example 7
Analysis of STEAP-1-Expressing Cells in Patient Samples Using the
Mouse Monoclonal Antibody 15A5 on the CellSearch.RTM. System
[0152] Blood samples from prostate cancer patients are collected
and analyzed on the CellSearch.RTM. system using the anti-STEAP-1
monoclonal antibody 15A5. The antibody 15A5 is diluted to, for
example, 1:50 in PBS and added to the blood sample. The samples are
run on CellSearch and the CTCs scored on the CellTracks analyzer.
Cells stained positive for cytokeratin and DAPI, but negative for
CD45 are determined as CTCs. CTCs on the CellSearch autoprep
systems that show STEAP-1 staining are selected and further
quantified for fluorescence intensities of the anti-STEAP-1
antibody that represent the STEAP-1 expression level. The number of
CTCs are counted for each sample, and H scores are also calculated
as described in Example 2.
[0153] Furthermore, the expression level of STEAP-1 on CTCs in
blood samples collected from "baseline" (i.e., pre-treated)
patients in clinical trials are correlated with clinical endpoints
such as progression free survival, PSA changes, patient-reported
bone pain, overall survival, or others, in order to determine
whether expression of the prostate-specific marker above a certain
threshold is predictive of clinical activity of the prostate cancer
therapy (e.g., an anti-STEAP-1 Antibody-Drug Conjugate (ADC) based
therapy). Dynamic changes in expression level of the
prostate-specific marker (e.g. STEAP-1) in the cancer cells (i.e.,
down-regulation in post-treatment samples) is correlated to
clinical outcome measures to determine if such changes are
predictive of therapeutic activity. Such methods can be used as a
first step in qualifying the assay as a candidate predictive
biomarker that could be used to select patients for a prostate
cancer therapy (e.g. anti-STEAP-1 ADC-based therapy), followed by
prospective validation in a confirmatory phase III study.
Example 8
CTC Enumeration in Patient Samples
[0154] Blood samples from prostate cancer patients were drawn in
duplicate before initiation of therapy (Baseline samples). Samples
were analyzed on the CellSearch.RTM. system and CTC enumeration was
scored on the CellTracks analyzer as described above. Briefly,
cells stained positive for cytokeratin and DAPI, but negative for
CD45 were scored as CTCs. Mean CTC counts and STDEV were computed
for each duplicate pair, and errors (+-SDEV) were plotted in a
histogram. As shown in FIG. 7A, there was a large dynamic range for
mean CTC enumeration in these patients, with tight counts between
duplicate samples (small error bars), demonstrating high
reproducibility in CTC enumeration using this system.
[0155] Blood samples from prostate cancer patients were drawn in
duplicate before initiation of therapy (Baseline samples). Samples
were analyzed on the CellSearch.RTM. system using the anti-STEAP-1
monoclonal antibody 15A5 at 20 ug/ml in the A488 channel. CTC
enumeration and STEAP1 expression were scored on the CellTracks
analyzer, as described in Example 2. Briefly, CTCs on the
CellSearch autoprep systems that showed STEAP-1 staining were
selected, and were further quantified for fluorescence intensities
of the anti-STEAP-1 antibody using a weighted intensity scoring
system (H-score, see Example 2). Mean H-scores and STDEV were
computed for each duplicate pair, and errors (+-SDEV) were plotted.
As shown in FIG. 7B, there was a large dynamic range for STEAP-1
expression levels in the patient population, and further indicates
tight H-scores between duplicate samples, demonstrating high
reproducibility in the quantification of target expression level
using the CellSearch system.
[0156] Blood samples from prostate cancer patients were drawn at 2
different time-points before initiation of therapy, Baseline 1 and
Baseline 2, about 2-4 weeks apart. Blood samples were analyzed on
the CellSearch.RTM. system and CTC enumeration were scored on the
CellTracks analyzer, as described above. To evaluate biological
variability in CTC enumeration, CTC counts were compared between
the 2 baseline samples for each patient.
[0157] In FIG. 8, each dot represents a patient, with the CTCs
counted at baseline 1 on the X -axis, and the CTCs counted at
baseline 2 on the Y-axis. The plot includes data from 14 patients,
and shows a strong correlation between CTC enumeration taken at
different time point, suggesting low biological variability in CTC
enumeration before initiation of the treatment. These data was used
to calculate the normal variability in CTC counts, computed as the
95% Confidence Interval for the distribution of CTC counts
pre-treatment.
[0158] The Confidence Interval was used to determine the
significance of CTC changes observed during treatment. A decrease
in CTC counts above the calculated Confidence Interval was used to
assess dose effects and evidence of drug activity. Blood samples
from prostate cancer patients were drawn at 2 different time-points
before pre-dosage of anti-STEAP1 ADC therapy and post-dosage of
anti-STEAP1 ADC therapy. Samples were analyzed on the
CellSearch.RTM. system, and CTC enumeration and STEAP1 expression
were scored on the CellTracks analyzer as described above. As shown
in FIGS. 9-11, a significant decrease in CTC counts was observed at
higher dosages based on fold changes in CTC post-dosage and
pre-dosage as well a favorable CTC prognostic conversion. Further,
higher STEAP1 target expression was observed in patients with
significant CTC decrease upon treatment (data not shown).
* * * * *