U.S. patent application number 13/717175 was filed with the patent office on 2013-09-05 for methods for diagnosis and treatment of proliferative disorders mediated by cd40 signaling.
This patent application is currently assigned to XOMA TECHNOLOGY LTD.. The applicant listed for this patent is NOVARTIS AG, XOMA TECHNOLOGY LTD.. Invention is credited to Sharon Lea Aukerman, Bahija Jallal, Mohammad Luqman.
Application Number | 20130230528 13/717175 |
Document ID | / |
Family ID | 37022828 |
Filed Date | 2013-09-05 |
United States Patent
Application |
20130230528 |
Kind Code |
A1 |
Aukerman; Sharon Lea ; et
al. |
September 5, 2013 |
METHODS FOR DIAGNOSIS AND TREATMENT OF PROLIFERATIVE DISORDERS
MEDIATED BY CD40 SIGNALING
Abstract
Methods for identifying subjects having a cancer or
pre-malignant condition that will benefit from anti-CD40
therapeutic agents that modulate CD40L-mediated CD40 signaling are
provided. The methods comprise the use of biomarkers of cellular
apoptosis, cell proliferation and survival, and CD40 signaling
pathways to monitor ex vivo response to one or more anti-CD40
therapeutic agents of interest that modulate CD40 signaling on
CD40-expressing neoplastic cells. The ex vivo prognostic assays can
be used alone or in conjunction with other prognostic assays to
identify candidate subjects who will benefit from treatment with
anti-CD40 therapeutic agents. Methods of the invention also
comprise the use of these biomarkers to monitor in vivo efficacy of
treatment with an anti-CD40 therapeutic agent.
Inventors: |
Aukerman; Sharon Lea;
(Moraga, CA) ; Jallal; Bahija; (Emeryville,
CA) ; Luqman; Mohammad; (Danville, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
NOVARTIS AG
XOMA TECHNOLOGY LTD. |
Basel
Berkeley |
CA |
CH
US |
|
|
Assignee: |
XOMA TECHNOLOGY LTD.
Berkeley
CA
NOVARTIS AG
Basel
|
Family ID: |
37022828 |
Appl. No.: |
13/717175 |
Filed: |
December 17, 2012 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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11914714 |
Jul 11, 2008 |
8337851 |
|
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PCT/US2006/019414 |
May 18, 2006 |
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13717175 |
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60682582 |
May 18, 2005 |
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60749285 |
Dec 9, 2005 |
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Current U.S.
Class: |
424/139.1 ;
435/6.11; 435/6.12; 435/6.13; 435/6.14; 435/7.24; 435/7.4 |
Current CPC
Class: |
C07K 16/2878 20130101;
G01N 33/5091 20130101; G01N 2333/70575 20130101; C07K 2317/73
20130101; A61K 2039/505 20130101; C07K 2317/21 20130101; A61P 35/02
20180101; A61P 35/00 20180101; A61P 31/00 20180101; C07K 2317/732
20130101; G01N 33/574 20130101; C12Q 1/6886 20130101; A61K 39/39558
20130101; G01N 33/6863 20130101; C07K 2317/76 20130101 |
Class at
Publication: |
424/139.1 ;
435/7.24; 435/6.14; 435/7.4; 435/6.12; 435/6.13; 435/6.11 |
International
Class: |
G01N 33/68 20060101
G01N033/68; C12Q 1/68 20060101 C12Q001/68; A61K 39/395 20060101
A61K039/395; G01N 33/50 20060101 G01N033/50 |
Claims
1. A method for identifying a subject having a cancer or
pre-malignant condition that is responsive to treatment with an
anti-CD40 therapeutic agent, said method comprising: a) providing a
test biological sample and a control biological sample from said
subject, wherein said test biological sample and said control
biological sample comprise CD40-expressing neoplastic cells that
have been stimulated with a CD40 ligand; b) contacting said test
biological sample with an effective amount of said anti-CD40
therapeutic agent; c) detecting the level of at least one biomarker
in said test biological sample, wherein said biomarker is selected
from the group consisting of a biomarker of cellular apoptosis, a
biomarker of a CD40L-mediated CD40 signaling pathway, and a
biomarker of cell survival; and d) comparing the level of said at
least one biomarker in said test biological sample to the level of
said at least one biomarker detected in said control biological
sample, wherein said control biological sample has not been
contacted with said anti-CD40 therapeutic agent.
2. The method of claim 1, wherein said CD40-expressing neoplastic
cells were stimulated ex vivo with a ligand of CD40 prior to said
contacting step.
3. The method of claim 2, wherein said ligand of CD40 is selected
from the group consisting of soluble CD40L and membrane-bound
CD40L.
4. The method of claim 1, wherein said anti-CD40 therapeutic agent
is an antagonist anti-CD40 monoclonal antibody that is capable of
specifically binding to a human CD40 antigen expressed on the
surface of a human B cell, said monoclonal antibody being free of
significant agonist activity when bound to the CD40 antigen
expressed on the surface of said B cell.
5. The method of claim 4, wherein said antagonist anti-CD40
monoclonal antibody is selected from the group consisting of: a)
the monoclonal antibody CHIR-5.9 or CHIR-12.12; b) the monoclonal
antibody produced by the hybridoma cell line 5.9 or 12.12; c) a
monoclonal antibody comprising an amino acid sequence selected from
the group consisting of the sequence shown in SEQ ID NO:6, the
sequence shown in SEQ ID NO:7, the sequence shown in SEQ ID NO:8,
both the sequence shown in SEQ ID NO:6 and SEQ ID NO:7, and both
the sequence shown in SEQ ID NO:6 and SEQ ID NO:8; d) a monoclonal
antibody comprising an amino acid sequence selected from the group
consisting of the sequence shown in SEQ ID NO:2, the sequence shown
in SEQ ID NO:4, the sequence shown in SEQ ID NO:5, both the
sequence shown in SEQ ID NO:2 and SEQ ID NO:4, and both the
sequence shown in SEQ ID NO:2 and SEQ ID NO:5; e) a monoclonal
antibody having an amino acid sequence encoded by a nucleic acid
molecule comprising a nucleotide sequence selected from the group
consisting of the sequence shown in SEQ ID NO:1, the sequence shown
in SEQ ID NO:3, and both the sequence shown in SEQ ID NO:1 and SEQ
ID NO:3; f) a monoclonal antibody that binds to an epitope capable
of binding the monoclonal antibody produced by the hybridoma cell
line 5.9 or 12.12; g) a monoclonal antibody that binds to an
epitope comprising residues 82-87 of the human CD40 sequence shown
in SEQ ID NO:10 or SEQ ID NO:12; h) a monoclonal antibody that
binds to an epitope comprising residues 82-89 of the human CD40
sequence shown in SEQ ID NO:10 or SEQ ID NO:12; i) a monoclonal
antibody that competes with the monoclonal antibody CHIR-5.9 or
CHIR-12.12 in a competitive binding assay; j) the monoclonal
antibody of preceding item a) or a monoclonal antibody of any one
of preceding items c)-i), wherein said antibody is recombinantly
produced; and k) a monoclonal antibody that is an antigen-binding
fragment of a monoclonal antibody of any one of preceding items
a)-j), wherein said fragment retains the capability of specifically
binding to said human CD40 antigen.
6. The method of claim 5, wherein said fragment is selected from
the group consisting of a Fab fragment, an F(ab').sub.2 fragment,
an Fv fragment, and a single-chain Fv fragment.
7. The method of claim 1, wherein said anti-CD40 therapeutic agent
is a CD40 ligand (CD40L) antagonist that inhibits CD40/CD40L
interaction or CD40L-mediated CD40 signaling.
8. The method of claim 7, wherein said CD40L antagonist is selected
from the group consisting of an anti-CD40L monoclonal antibody that
specifically binds to CD40L, a soluble form of CD40, a soluble form
of a fusion protein comprising CD40, and a pharmaceutical
agent.
9. The method of claim 1, wherein said biomarker of apoptosis is
selected from the group consisting of a cleaved Caspase protein,
cleaved poly ADP-ribose polymerase (PARP), cell surface expression
of phosphotidylserine (PS), genomic DNA fragmentation, and any
combinations thereof.
10. The method of claim 9, wherein said cleaved Caspase protein is
selected from the group consisting of cleaved Caspase-3, cleaved
Caspase-7, and cleaved Caspase-9.
11. The method of claim 9, wherein cell surface PS is detected by
annexin V staining and wherein genomic DNA fragmentation is
detected by TUNEL staining.
12. The method of claim 9, wherein an increase in the level of at
least one of said biomarkers of apoptosis within said test
biological sample relative to said control biological sample is
indicative of a subject who would benefit from treatment with said
anti-CD40 therapeutic agent.
13. The method of claim 1, wherein said CD40L-mediated CD40
signaling pathway is selected from the group consisting of the AKT
signaling pathway, the NF-.kappa.B signaling pathway, and a
mitogen-activated protein kinase (MAPK) signaling pathway.
14. The method of claim 13, wherein said MAPK signaling pathway is
selected from the group consisting of the MEK/ERK signaling pathway
and the MEK/p38 signaling pathway.
15. The method of claim 13, wherein said biomarker of said
CD40L-mediated CD40 signaling pathway is selected from the group
consisting of phospho-PI3K, phospho-PDK1, phospho-AKT, phospho-MEK,
phospho-ERK, phospho-p38, phospho-IKK.alpha./.beta.,
phospho-I.kappa.B protein, and activated NF-.kappa.B.
16. The method of claim 15, wherein a reduction in the level of at
least one of said biomarkers of at least one of said CD40L-mediated
CD40 signaling pathways within said test biological sample relative
to said control biological sample is indicative of a subject who
would benefit from treatment with said anti-CD40 therapeutic
agent.
17. The method of claim 1, wherein said biomarker of cell survival
is selected from the group consisting of an anti-apoptotic protein
that is a Bcl-2 family member, an IAP apoptosis inhibitor protein,
and TNF receptor-associated factor-1 (TRAF-1).
18. The method of claim 17, wherein said Bcl-2 family member is
selected from the group consisting of Bcl-xl and Mcl-1.
19. The method of claim 17, wherein said IAP apoptosis inhibitor
protein is selected from the group consisting of survivin, XIAP,
and cIAP1.
20. The method of claim 17, wherein a reduction in the level of at
least one of said biomarkers of cell survival in said test
biological sample relative to said control biological sample is
indicative of a subject who would benefit from treatment with said
anti-CD40 therapeutic agent.
21. The method of claim 1, further comprising detecting in said
test biological sample and said control biological sample the level
of at least one cytokine marker of CD40 signaling.
22. The method of claim 21, wherein said cytokine marker is
selected from the group consisting of vascular endothelial growth
factor (VEGF), interleukin (IL)-6, IL-8, IL-10, granulocyte
monocyte colony-stimulating factor (GM-CSF), tumor necrosis
factor-.alpha. (TNF-.alpha.), monocyte chemoattractant protein-1
(MCP-1), and macrophage inflammatory protein-1.beta.
(MIP-1.beta.).
23. The method of claim 21, wherein a reduction in the level of at
least one of said cytokine markers in said test biological sample
relative to said control biological sample is indicative of a
subject who would benefit from treatment with said anti-CD40
therapeutic agent.
24. The method of claim 1, wherein said anti-CD40 therapeutic agent
is an anti-CD40 monoclonal antibody that specifically binds to a
human CD40 antigen expressed on the surface of a CD40-expressing
cell, thereby modulating antibody-dependent cell-mediated
cytotoxity (ADCC) activity, and wherein said biomarker is a
biomarker of apoptosis.
25. The method of claim 24, wherein said anti-CD40 monoclonal
antibody is an antagonist anti-CD40 monoclonal antibody selected
from the group consisting of: a) the monoclonal antibody CHIR-5.9
or CHIR-12.12; b) the monoclonal antibody produced by the hybridoma
cell line 5.9 or 12.12; c) a monoclonal antibody comprising an
amino acid sequence selected from the group consisting of the
sequence shown in SEQ ID NO:6, the sequence shown in SEQ ID NO:7,
the sequence shown in SEQ ID NO:8, both the sequence shown in SEQ
ID NO:6 and SEQ ID NO:7, and both the sequence shown in SEQ ID NO:6
and SEQ ID NO:8; d) a monoclonal antibody comprising an amino acid
sequence selected from the group consisting of the sequence shown
in SEQ ID NO:2, the sequence shown in SEQ ID NO:4, the sequence
shown in SEQ ID NO:5, both the sequence shown in SEQ ID NO:2 and
SEQ ID NO:4, and both the sequence shown in SEQ ID NO:2 and SEQ ID
NO:5; e) a monoclonal antibody having an amino acid sequence
encoded by a nucleic acid molecule comprising a nucleotide sequence
selected from the group consisting of the sequence shown in SEQ ID
NO:1, the sequence shown in SEQ ID NO:3, and both the sequence
shown in SEQ ID NO:1 and SEQ ID NO:3; f) a monoclonal antibody that
binds to an epitope capable of binding the monoclonal antibody
produced by the hybridoma cell line 5.9 or 12.12; g) a monoclonal
antibody that binds to an epitope comprising residues 82-87 of the
human CD40 sequence shown in SEQ ID NO:10 or SEQ ID NO:12; h) a
monoclonal antibody that binds to an epitope comprising residues
82-89 of the human CD40 sequence shown in SEQ ID NO:10 or SEQ ID
NO:12; i) a monoclonal antibody that competes with the monoclonal
antibody CHIR-5.9 or CHIR-12.12 in a competitive binding assay; and
j) the monoclonal antibody of preceding item a) or a monoclonal
antibody of any one of preceding items c)-i), wherein said antibody
is recombinantly produced.
26. The method of claim 24, wherein said biomarker of apoptosis is
selected from the group consisting of a cleaved caspase protein,
cleaved poly ADP-ribose polymerase (PARP), cell surface expression
of phosphotidylserine (PS), genomic DNA fragmentation, and any
combinations thereof.
27. The method of claim 26, wherein said cleaved caspase protein is
selected from the group consisting of cleaved Caspase-3, cleaved
Caspase-7, and cleaved Caspase-9.
28. The method of claim 26, wherein cell surface PS is detected by
annexin V staining and wherein genomic DNA fragmentation is
detected by TUNEL staining.
29. The method of claim 24, wherein an increase in the level of at
least one of said biomarkers of apoptosis within said test
biological sample relative to said control biological sample is
indicative of a subject who would benefit from treatment with said
anti-CD40 antibody.
30. The method of claim 1, wherein said cancer is characterized by
neoplastic B cell growth.
31. The method of claim 30, wherein said cancer is selected from
the group consisting of non-Hodgkin's lymphoma, chronic lymphocytic
leukemia, multiple myeloma, B cell lymphoma, high-grade B cell
lymphoma, intermediate-grade B cell lymphoma, low-grade B cell
lymphoma, B cell acute lympohoblastic leukemia, Hodgkin's disease,
plasmacytoma, follicular lymphoma, follicular small cleaved
lymphoma, follicular large cell lymphoma, follicular mixed small
cleaved lymphoma, diffuse small cleaved cell lymphoma, diffuse
small lymphocytic lymphoma, prolymphocytic leukemia,
lymphoplasmacytic lymphoma, marginal zone lymphoma, mucosal
associated lymphoid tissue lymphoma, monocytoid B cell lymphoma,
splenic lymphoma, hairy cell leukemia, diffuse large cell lymphoma,
mediastinal large B cell lymphoma, lymphomatoid granulomatosis,
intravascular lymphomatosis, diffuse mixed cell lymphoma, diffuse
large cell lymphoma, immunoblastic lymphoma, Burkitt's lymphoma,
AIDS-related lymphoma, Waldenstrom's Macroglobulinemia, mantle cell
lymphoma, and heavy chain disease.
32. The method of claim 31, wherein said subject has chronic
lymphocytic leukemia.
33. The method of claim 32, further comprising assaying a
biological sample from said subject for at least one clinically
useful prognostic marker selected from the group consisting of
ZAP-70 expression level, CD38 expression level, .beta.2
microglobulin expression level, p53 mutational status, ATM
mutational status, chromosome 17p deletion, and chromosome 11q
deletion.
34. The method of claim 1, wherein said cancer is a non-B cell
hematological malignancy.
35. The method of claim 34, wherein said malignancy is selected
from the group consisting of acute leukemias, myeloblastic
leukemias, acute myelocytic leukemias, promyelocytic leukemia,
myelomonocytic leukemia, monocytic leukemia, erythroleukemia,
chronic myelocytic leukemia, and polycythemia vera.
36. The method of claim 1, wherein said cancer is a solid tumor
comprising neoplastic cells expressing CD40 antigen.
37. The method of claim 36, wherein said solid tumor is selected
from the group consisting of lung carcinoma, breast carcinoma,
ovarian carcinoma, skin carcinoma, colon carcinoma, urinary bladder
carcinoma, liver carcinoma, gastric carcinoma, prostate cancer,
renal cell carcinoma, nasopharyngeal carcinoma, squamous cell
carcinoma, thyroid papillary carcinoma, cervical carcinoma, and
sarcomas.
38. The method of claim 1, wherein said pre-malignant condition is
monoclonal gammopathy of undetermined significance (MGUS).
39. The method of claim 1, further comprising detecting in a
biological sample of said subject the level of expression of
cell-surface CD40, the level of expression of cell-surface CD40L,
or both, on CD40-expressing neoplastic cells within said biological
sample.
40. The method of claim 1, further comprising detecting the level
of circulating soluble CD40 or circulating soluble CD40L in a
biological sample collected from subject.
41. The method of claim 1, wherein detecting the level of said
biomarker comprises using an antibody to detect biomarker protein
expression.
42. The method of claim 1, wherein detecting the level of said
biomarker comprises nucleic acid hybridization.
43. The method of claim 1, wherein detecting the level of said
biomarker comprises performing quantitative RT-PCR.
44. A method of treating a subject with a cancer or pre-malignant
condition that is associated with CD40-expressing cells, said
method comprising screening said patient with a method according to
any one of claims 1 through 43, and then treating said subject with
said anti-CD40 therapeutic agent when said method according to any
one of claims 1 through 43 generates a result that is indicative of
a positive treatment outcome with said anti-CD40 therapeutic
agent.
45. A method for identifying a subject having a cancer or
pre-malignant condition that is responsive to treatment with an
anti-CD40 therapeutic agent, said method comprising: a) providing a
biological sample from said subject, wherein said biological sample
comprises CD40-expressing neoplastic cells; b) detecting the level
of at least one CD40-related factor in said biological sample,
wherein said CD40-related factor is selected from the group
consisting of cell-surface CD40 on said CD40-expressing neoplastic
cells and cell-surface CD40L on said CD40-expressing neoplastic
cells; and c) comparing the level of said at least one CD40-related
factor in said biological sample to the level of said at least one
CD40-related factor in a reference standard; wherein an increase in
the level of said at least one CD40-related factor in said
biological sample relative to the level of said at least one
CD40-related factor in said reference standard is indicative of a
positive treatment outcome with said anti-CD40 therapeutic
agent.
46. The method of claim 45, wherein said detecting comprises use of
flow cytometry, immunohistochemistry, Western Blot,
immunoprecipitation, magnetic bead selection, quantification of
neoplastic cells expressing cell-surface CD40, quantification of
neoplastic cells expressing cell-surface CD40L, or any combination
thereof.
47. A method for identifying a subject having a cancer or
pre-malignant condition that is responsive to treatment with an
anti-CD40 therapeutic agent, said method comprising: a) providing a
sample of blood or a blood component from said subject; b)
detecting the level of at least one CD40-related factor in said
sample, wherein said CD40-related factor is selected from the group
consisting of circulating level of CD40 and circulating level of
CD40L; and c) comparing the level of said at least one CD40-related
factor in said sample to the level of said at least one
CD40-related factor in a reference standard; wherein an increase in
the level of said at least one CD40-related factor in said sample
relative to the level of said at least one CD40-related factor in
said reference standard is indicative of a positive treatment
outcome with said anti-CD40 therapeutic agent.
48. The method of claim 47, wherein said detecting uses ELISA, RIA,
ECL, multiplexing technologies, or any combination thereof.
49. The method of claim 45, wherein said anti-CD40 therapeutic
agent is an antagonist anti-CD40 monoclonal antibody that is
capable of specifically binding to a human CD40 antigen expressed
on the surface of a human B cell, said monoclonal antibody being
free of significant agonist activity when bound to the CD40 antigen
expressed on the surface of said B cell.
50. The method of claim 49, wherein said antagonist anti-CD40
monoclonal antibody is selected from the group consisting of: a)
the monoclonal antibody CHIR-5.9 or CHIR-12.12; b) the monoclonal
antibody produced by the hybridoma cell line 5.9 or 12.12; c) a
monoclonal antibody comprising an amino acid sequence selected from
the group consisting of the sequence shown in SEQ ID NO:6, the
sequence shown in SEQ ID NO:7, the sequence shown in SEQ ID NO:8,
both the sequence shown in SEQ ID NO:6 and SEQ ID NO:7, and both
the sequence shown in SEQ ID NO:6 and SEQ ID NO:8; d) a monoclonal
antibody comprising an amino acid sequence selected from the group
consisting of the sequence shown in SEQ ID NO:2, the sequence shown
in SEQ ID NO:4, the sequence shown in SEQ ID NO:5, both the
sequence shown in SEQ ID NO:2 and SEQ ID NO:4, and both the
sequence shown in SEQ ID NO:2 and SEQ ID NO:5; e) a monoclonal
antibody having an amino acid sequence encoded by a nucleic acid
molecule comprising a nucleotide sequence selected from the group
consisting of the sequence shown in SEQ ID NO:1, the sequence shown
in SEQ ID NO:3, and both the sequence shown in SEQ ID NO:1 and SEQ
ID NO:3; f) a monoclonal antibody that binds to an epitope capable
of binding the monoclonal antibody produced by the hybridoma cell
line 5.9 or 12.12; g) a monoclonal antibody that binds to an
epitope comprising residues 82-87 of the human CD40 sequence shown
in SEQ ID NO:10 or SEQ ID NO:12; h) a monoclonal antibody that
binds to an epitope comprising residues 82-89 of the human CD40
sequence shown in SEQ ID NO:10 or SEQ ID NO:12; i) a monoclonal
antibody that competes with the monoclonal antibody CHIR-5.9 or
CHIR-12.12 in a competitive binding assay; j) the monoclonal
antibody of preceding item a) or a monoclonal antibody of any one
of preceding items c)-i), wherein said antibody is recombinantly
produced; and k) a monoclonal antibody that is an antigen-binding
fragment of a monoclonal antibody of any one of preceding items
a)-j), wherein said fragment retains the capability of specifically
binding to said human CD40 antigen.
51. The method of claim 50, wherein said fragment is selected from
the group consisting of a Fab fragment, an F(ab').sub.2 fragment,
an Fv fragment, and a single-chain Fv fragment.
52. The method of claim 45, wherein said anti-CD40 therapeutic
agent is a CD40 ligand (CD40L) antagonist that inhibits CD40/CD40L
interaction or CD40L-mediated CD40 signaling.
53. The method of claim 52, wherein said CD40L antagonist is
selected from the group consisting of an anti-CD40L monoclonal
antibody that specifically binds to CD40L, a soluble form of CD40,
a soluble form of a fusion protein comprising CD40, and a
pharmaceutical agent.
54. The method of claim 45, wherein said anti-CD40 therapeutic
agent is an anti-CD40 monoclonal antibody that specifically binds
to a human CD40 antigen expressed on the surface of a
CD40-expressing cell, thereby modulating ADCC activity.
55. The method of claim 54, wherein said anti-CD40 monoclonal
antibody is an antagonist anti-CD40 monoclonal antibody selected
from the group consisting of: a) the monoclonal antibody CHIR-5.9
or CHIR-12.12; b) the monoclonal antibody produced by the hybridoma
cell line 5.9 or 12.12; c) a monoclonal antibody comprising an
amino acid sequence selected from the group consisting of the
sequence shown in SEQ ID NO:6, the sequence shown in SEQ ID NO:7,
the sequence shown in SEQ ID NO:8, both the sequence shown in SEQ
ID NO:6 and SEQ ID NO:7, and both the sequence shown in SEQ ID NO:6
and SEQ ID NO:8; d) a monoclonal antibody comprising an amino acid
sequence selected from the group consisting of the sequence shown
in SEQ ID NO:2, the sequence shown in SEQ ID NO:4, the sequence
shown in SEQ ID NO:5, both the sequence shown in SEQ ID NO:2 and
SEQ ID NO:4, and both the sequence shown in SEQ ID NO:2 and SEQ ID
NO:5; e) a monoclonal antibody having an amino acid sequence
encoded by a nucleic acid molecule comprising a nucleotide sequence
selected from the group consisting of the sequence shown in SEQ ID
NO:1, the sequence shown in SEQ ID NO:3, and both the sequence
shown in SEQ ID NO:1 and SEQ ID NO:3; f) a monoclonal antibody that
binds to an epitope capable of binding the monoclonal antibody
produced by the hybridoma cell line 5.9 or 12.12; g) a monoclonal
antibody that binds to an epitope comprising residues 82-87 of the
human CD40 sequence shown in SEQ ID NO:10 or SEQ ID NO:12; h) a
monoclonal antibody that binds to an epitope comprising residues
82-89 of the human CD40 sequence shown in SEQ ID NO:10 or SEQ ID
NO:12; i) a monoclonal antibody that competes with the monoclonal
antibody CHIR-5.9 or CHIR-12.12 in a competitive binding assay; and
j) the monoclonal antibody of preceding item a) or a monoclonal
antibody of any one of preceding items c)-i), wherein said antibody
is recombinantly produced.
56. The method of claim 45, wherein said cancer is characterized by
neoplastic B cell growth.
57. The method of claim 56, wherein said cancer is selected from
the group consisting of non-Hodgkin's lymphoma, chronic lymphocytic
leukemia, multiple myeloma, B cell lymphoma, high-grade B cell
lymphoma, intermediate-grade B cell lymphoma, low-grade B cell
lymphoma, B cell acute lymphoblastic leukemia, Hodgkin's disease,
plasmacytoma, follicular lymphoma, follicular small cleaved
lymphoma, follicular large cell lymphoma, follicular mixed small
cleaved lymphoma, diffuse small cleaved cell lymphoma, diffuse
small lymphocytic lymphoma, prolymphocytic leukemia,
lymphoplasmacytic lymphoma, marginal zone lymphoma, mucosal
associated lymphoid tissue lymphoma, monocytoid B cell lymphoma,
splenic lymphoma, hairy cell leukemia, diffuse large cell lymphoma,
mediastinal large B cell lymphoma, lymphomatoid granulomatosis,
intravascular lymphomatosis, diffuse mixed cell lymphoma, diffuse
large cell lymphoma, immunoblastic lymphoma, Burkitt's lymphoma,
AIDS-related lymphoma, Waldenstrom's Macroglobulinemia, and mantle
cell lymphoma.
58. The method of claim 57, wherein said subject has chronic
lymphocytic leukemia.
59. The method of claim 58, further comprising assaying a
biological sample from said subject for at least one clinically
useful prognostic marker selected from the group consisting of
ZAP-70 expression level, CD38 expression level, .beta.2
microglobulin expression level, p53 mutational status, ATM
mutational status, chromosome 17p deletion, and chromosome 11q
deletion.
60. The method of claim 45, wherein said pre-malignant condition is
monoclonal gammopathy of undetermined significance (MGUS).
61. A method of treating a subject with a cancer or pre-malignant
condition that is associated with CD40-expressing cells, said
method comprising screening said patient with a method according to
any one of claims 45 through 60, and then treating said subject
with said anti-CD40 therapeutic agent when said method according to
any one of claims 46 through 62 generates a result that is
indicative of a positive treatment outcome with said anti-CD40
therapeutic agent.
62. A method for monitoring efficacy of an anti-CD40 therapeutic
agent in treatment of a subject for a cancer or pre-malignant
condition that is associated with CD40-expressing neoplastic cells,
said method comprising: a) obtaining a baseline biological sample
from said subject prior to administering a dose of said anti-CD40
therapeutic agent, wherein said baseline biological sample
comprises CD40-expressing neoplastic cells; b) detecting the level
of at least one biomarker in said baseline biological sample,
wherein said biomarker is selected from the group consisting of a
biomarker of cellular apoptosis, a biomarker of a CD40L-mediated
CD40 signaling pathway, and a biomarker of cell survival; c)
administering said anti-CD40 therapeutic agent to said subject; d)
obtaining from said subject at least one subsequent biological
sample; e) detecting the level of said at least one biomarker in
said at least one subsequent sample; and f) comparing the level of
said at least one biomarker in said at least one subsequent sample
with the level of said at least one biomarker in said baseline
biological sample, and correlating a change in the level of said at
least one biomarker with treatment efficacy.
63. The method of claim 62, wherein a single dose of said anti-CD40
therapeutic agent is administered to said subject.
64. The method of claim 62, wherein multiple doses of said
anti-CD40 therapeutic agent are administered to said subject.
65. The method of claim 62, wherein said anti-CD40 therapeutic
agent is an antagonist anti-CD40 monoclonal antibody that is
capable of specifically binding to a human CD40 antigen expressed
on the surface of a human B cell, said monoclonal antibody being
free of significant agonist activity when bound to the CD40 antigen
expressed on the surface of said B cell.
66. The method of claim 65, wherein said antagonist anti-CD40
monoclonal antibody is selected from the group consisting of: a)
the monoclonal antibody CHIR-5.9 or CHIR-12.12; b) the monoclonal
antibody produced by the hybridoma cell line 5.9 or 12.12; c) a
monoclonal antibody comprising an amino acid sequence selected from
the group consisting of the sequence shown in SEQ ID NO:6, the
sequence shown in SEQ ID NO:7, the sequence shown in SEQ ID NO:8,
both the sequence shown in SEQ ID NO:6 and SEQ ID NO:7, and both
the sequence shown in SEQ ID NO:6 and SEQ ID NO:8; d) a monoclonal
antibody comprising an amino acid sequence selected from the group
consisting of the sequence shown in SEQ ID NO:2, the sequence shown
in SEQ ID NO:4, the sequence shown in SEQ ID NO:5, both the
sequence shown in SEQ ID NO:2 and SEQ ID NO:4, and both the
sequence shown in SEQ ID NO:2 and SEQ ID NO:5; e) a monoclonal
antibody having an amino acid sequence encoded by a nucleic acid
molecule comprising a nucleotide sequence selected from the group
consisting of the sequence shown in SEQ ID NO:1, the sequence shown
in SEQ ID NO:3, and both the sequence shown in SEQ ID NO:1 and SEQ
ID NO:3; f) a monoclonal antibody that binds to an epitope capable
of binding the monoclonal antibody produced by the hybridoma cell
line 5.9 or 12.12; g) a monoclonal antibody that binds to an
epitope comprising residues 82-87 of the human CD40 sequence shown
in SEQ ID NO:10 or SEQ ID NO:12; h) a monoclonal antibody that
binds to an epitope comprising residues 82-89 of the human CD40
sequence shown in SEQ ID NO:10 or SEQ ID NO:12; i) a monoclonal
antibody that competes with the monoclonal antibody CHIR-5.9 or
CHIR-12.12 in a competitive binding assay; j) the monoclonal
antibody of preceding item a) or a monoclonal antibody of any one
of preceding items c)-i), wherein said antibody is recombinantly
produced; and k) a monoclonal antibody that is an antigen-binding
fragment of a monoclonal antibody of any one of preceding items
a)-j), wherein said fragment retains the capability of specifically
binding to said human CD40 antigen.
67. The method of claim 66, wherein said fragment is selected from
the group consisting of a Fab fragment, an F(ab').sub.2 fragment,
an Fv fragment, and a single-chain Fv fragment.
68. The method of claim 62, wherein said anti-CD40 therapeutic
agent is a CD40 ligand (CD40L) antagonist that inhibits CD40/CD40L
interaction or CD40L-mediated CD40 signaling.
69. The method of claim 68, wherein said CD40L antagonist is
selected from the group consisting of an anti-CD40L monoclonal
antibody that specifically binds to CD40L, a soluble form of CD40,
a soluble form of a fusion protein comprising CD40, and a
pharmaceutical agent.
70. The method of claim 62, wherein said biomarker of apoptosis is
selected from the group consisting of a cleaved Caspase protein,
cleaved poly ADP-ribose polymerase (PARP), cell surface expression
of phosphotidylserine (PS), genomic DNA fragmentation, and any
combinations thereof.
71. The method of claim 70, wherein said cleaved Caspase protein is
selected from the group consisting of cleaved Caspase-3, cleaved
Caspase-7, and cleaved Caspase-9.
72. The method of claim 70, wherein cell surface PS is detected by
annexin V staining and wherein genomic DNA fragmentation is
detected by TUNEL staining.
73. The method of claim 70, wherein an increase in the level of at
least one of said biomarkers of apoptosis within said subsequent
biological sample relative to said baseline biological sample is
indicative of efficacy of treatment with said anti-CD40 therapeutic
agent.
74. The method of claim 62, wherein said CD40L-mediated CD40
signaling pathway is selected from the group consisting of the AKT
signaling pathway, the NF-.kappa.B signaling pathway, and a
mitogen-activated protein kinase (MAPK) signaling pathway.
75. The method of claim 74, wherein said MAPK signaling pathway is
selected from the group consisting of the MEK/ERK signaling pathway
and the MEK/p38 signaling pathway.
76. The method of claim 74, wherein said biomarker of said
CD40L-mediated CD40 signaling pathway is selected from the group
consisting of phospho-PI3K, phospho-PDK1, phospho-AKT, phospho-MEK,
phospho-ERK, phospho-p38, phospho-IKK.alpha./.beta.,
phospho-I.kappa.B protein, and activated NF-.kappa.B.
77. The method of claim 76, wherein a reduction in the level of at
least one of said biomarkers of at least one of said CD40L-mediated
CD40 signaling pathways within said subsequent biological sample
relative to said baseline biological sample is indicative of
efficacy of treatment with said anti-CD40 therapeutic agent.
78. The method of claim 62, wherein said biomarker of cell survival
is selected from the group consisting of an anti-apoptotic protein
that is a Bcl-2 family member, an IAP apoptosis inhibitor protein,
and TNF receptor-associated factor-1 (TRAF-1).
79. The method of claim 78, wherein said Bcl-2 family member is
selected from the group consisting of Bcl-xl and Mcl-1.
80. The method of claim 78, wherein said IAP apoptosis inhibitor
protein is selected from the group consisting of survivin, XIAP,
and cIAP1.
81. The method of claim 78, wherein a reduction in the level of at
least one of said biomarkers of cell survival in said subsequent
biological sample relative to said baseline biological sample is
indicative of efficacy of treatment with said anti-CD40 therapeutic
agent.
82. The method of claim 62, further comprising detecting in said
subsequent biological sample and said baseline biological sample
the level of at least one cytokine marker of CD40 signaling.
83. The method of claim 82, wherein said cytokine marker is
selected from the group consisting of vascular endothelial growth
factor (VEGF), interleukin (IL)-6, IL-8, IL-10, granulocyte
monocyte colony-stimulating factor (GM-CSF), tumor necrosis
factor-.alpha. (TNF-.alpha.), monocyte chemoattractant protein-1
(MCP-1), and macrophage inflammatory protein-1.beta.
(MIP-1.beta.).
84. The method of claim 82, wherein a reduction in the level of at
least one of said cytokine markers in said subsequent biological
sample relative to said baseline biological sample is indicative of
efficacy of treatment with said anti-CD40 therapeutic agent.
85. The method of claim 62, wherein said anti-CD40 therapeutic
agent is an anti-CD40 monoclonal antibody that specifically binds
to a human CD40 antigen expressed on the surface of a
CD40-expressing cell, thereby modulating antibody-dependent
cell-mediated cytotoxity (ADCC), and wherein said biomarker is a
biomarker of apoptosis.
86. The method of claim 85, wherein said anti-CD40 monoclonal
antibody is an antagonist anti-CD40 monoclonal antibody selected
from the group consisting of: a) the monoclonal antibody CHIR-5.9
or CHIR-12.12; b) the monoclonal antibody produced by the hybridoma
cell line 5.9 or 12.12; c) a monoclonal antibody comprising an
amino acid sequence selected from the group consisting of the
sequence shown in SEQ ID NO:6, the sequence shown in SEQ ID NO:7,
the sequence shown in SEQ ID NO:8, both the sequence shown in SEQ
ID NO:6 and SEQ ID NO:7, and both the sequence shown in SEQ ID NO:6
and SEQ ID NO:8; d) a monoclonal antibody comprising an amino acid
sequence selected from the group consisting of the sequence shown
in SEQ ID NO:2, the sequence shown in SEQ ID NO:4, the sequence
shown in SEQ ID NO:5, both the sequence shown in SEQ ID NO:2 and
SEQ ID NO:4, and both the sequence shown in SEQ ID NO:2 and SEQ ID
NO:5; e) a monoclonal antibody having an amino acid sequence
encoded by a nucleic acid molecule comprising a nucleotide sequence
selected from the group consisting of the sequence shown in SEQ ID
NO:1, the sequence shown in SEQ ID NO:3, and both the sequence
shown in SEQ ID NO:1 and SEQ ID NO:3; f) a monoclonal antibody that
binds to an epitope capable of binding the monoclonal antibody
produced by the hybridoma cell line 5.9 or 12.12; g) a monoclonal
antibody that binds to an epitope comprising residues 82-87 of the
human CD40 sequence shown in SEQ ID NO:10 or SEQ ID NO:12; h) a
monoclonal antibody that binds to an epitope comprising residues
82-89 of the human CD40 sequence shown in SEQ ID NO:10 or SEQ ID
NO:12; i) a monoclonal antibody that competes with the monoclonal
antibody CHIR-5.9 or CHIR-12.12 in a competitive binding assay; and
j) the monoclonal antibody of preceding item a) or a monoclonal
antibody of any one of preceding items c)-i), wherein said antibody
is recombinantly produced.
87. The method of claim 85, wherein said biomarker of apoptosis is
selected from the group consisting of a cleaved caspase protein,
cleaved poly ADP-ribose polymerase (PARP), cell surface expression
of phosphotidylserine (PS), genomic DNA fragmentation, and any
combinations thereof.
88. The method of claim 87, wherein said cleaved caspase protein is
selected from the group consisting of cleaved Caspase-3, cleaved
Caspase-7, and cleaved Caspase-9.
89. The method of claim 87, wherein cell surface PS is detected by
annexin V staining and wherein genomic DNA fragmentation is
detected by TUNEL staining.
90. The method of claim 85, wherein an increase in the level of at
least one of said biomarkers of apoptosis within said subsequent
biological sample relative to said baseline biological sample is
indicative of efficacy of treatment with said anti-CD40 therapeutic
agent.
91. The method of claim 62, wherein said cancer is characterized by
neoplastic B cell growth.
92. The method of claim 91, wherein said cancer is selected from
the group consisting of non-Hodgkin's lymphoma, chronic lymphocytic
leukemia, multiple myeloma, B cell lymphoma, high-grade B cell
lymphoma, intermediate-grade B cell lymphoma, low-grade B cell
lymphoma, B cell acute lymphoblastic leukemia, Hodgkin's disease,
plasmacytoma, follicular lymphoma, follicular small cleaved
lymphoma, follicular large cell lymphoma, follicular mixed small
cleaved lymphoma, diffuse small cleaved cell lymphoma, diffuse
small lymphocytic lymphoma, prolymphocytic leukemia,
lymphoplasmacytic lymphoma, marginal zone lymphoma, mucosal
associated lymphoid tissue lymphoma, monocytoid B cell lymphoma,
splenic lymphoma, hairy cell leukemia, diffuse large cell lymphoma,
mediastinal large B cell lymphoma, lymphomatoid granulomatosis,
intravascular lymphomatosis, diffuse mixed cell lymphoma, diffuse
large cell lymphoma, immunoblastic lymphoma, Burkitt's lymphoma,
AIDS-related lymphoma, Waldenstrom's Macroglobulinemia, mantle cell
lymphoma, and heavy chain disease.
93. The method of claim 62, wherein said cancer is a non-B cell
hematological malignancy.
94. The method of claim 93, wherein said malignancy is selected
from the group consisting of acute leukemias, myeloblastic
leukemias, acute myelocytic leukemias, promyelocytic leukemia,
myelomonocytic leukemia, monocytic leukemia, erythroleukemia,
chronic myelocytic leukemia, and polycythemia vera.
95. The method of claim 62, wherein said cancer is a solid tumor
comprising neoplastic cells expressing CD40 antigen.
96. The method of claim 95, wherein said solid tumor is selected
from the group consisting of lung carcinoma, breast carcinoma,
ovarian carcinoma, skin carcinoma, colon carcinoma, urinary bladder
carcinoma, liver carcinoma, gastric carcinoma, prostate cancer,
renal cell carcinoma, nasopharyngeal carcinoma, squamous cell
carcinoma, thyroid papillary carcinoma, cervical carcinoma, and
sarcomas.
97. The method of claim 62, wherein said pre-malignant condition is
monoclonal gammopathy of undetermined significance (MGUS).
98. The method of claim 62, further comprising detecting in said
subsequent biological sample and said baseline biological sample
the level of expression of at least one CD40-related factor
selected from the group consisting of cell-surface CD40,
cell-surface CD40L, and both cell-surface CD40 and cell-surface
CD40L on CD40-expressing neoplastic cells within said subsequent
and baseline biological samples, wherein a reduction in the level
of expression of at least one of said CD40-related factors within
said subsequent biological sample relative to said baseline
biological sample is indicative of efficacy of treatment with said
anti-CD40 therapeutic agent.
99. The method of claim 62, further comprising collecting from said
subject a baseline sample of blood or a blood component and a
subsequent sample of blood or said blood component, and detecting
the level of circulating soluble CD40 or circulating soluble CD40L
in said baseline sample and said subsequent sample, wherein a
reduction in the level of expression of at least one of said
circulating soluble CD40 or circulating soluble CD40L within said
subsequent sample relative to said baseline sample is indicative of
efficacy of treatment with said anti-CD40 therapeutic agent.
100. A method for monitoring efficacy of an anti-CD40 therapeutic
agent in treatment of a subject for a cancer or pre-malignant
condition that is associated with CD40-expressing neoplastic cells,
said method comprising: a) obtaining a baseline biological sample
from said subject prior to administering a dose of said anti-CD40
therapeutic agent, wherein said baseline biological sample
comprises CD40-expressing neoplastic cells; b) detecting the level
of at least one CD40-related factor in said baseline biological
sample, wherein said CD40-related factor is selected from the group
consisting of cell-surface CD40 on said CD40-expressing neoplastic
cells and cell-surface CD40L on said CD40-expressing neoplastic
cells; c) administering said anti-CD40 therapeutic agent to said
subject; d) obtaining from said subject at least one subsequent
biological sample; e) detecting the level of said at least one
CD40-related factor in said at least one subsequent sample; and f)
comparing the level of said at least one CD40-related factor in
said at least one subsequent sample with the level of said at least
one CD40-related factor in said baseline biological sample, wherein
a reduction in the level of expression of at least one of said
CD40-related factors within said subsequent biological sample
relative to said baseline biological sample is indicative of
efficacy of treatment with said anti-CD40 therapeutic agent.
101. A method for monitoring efficacy of an anti-CD40 therapeutic
agent in treatment of a subject for a cancer or pre-malignant
condition that is associated with CD40-expressing neoplastic cells,
said method comprising: a) obtaining a baseline sample of blood or
a blood component from said subject prior to administering a dose
of said anti-CD40 therapeutic agent; b) detecting the level of at
least one CD40-related factor in said baseline sample, wherein said
CD40-related factor is selected from the group consisting of
circulating level of CD40 and circulating level of CD40L; c)
administering said anti-CD40 therapeutic agent to said subject; d)
obtaining from said subject at least one subsequent sample of blood
or said blood component; e) detecting the level of said at least
one CD40-related factor in said at least one subsequent sample; and
f) comparing the level of said at least one CD40-related factor in
said at least one subsequent sample with the level of said at least
one CD40-related factor in said baseline sample, wherein a
reduction in the level of expression of at least one of said
CD40-related factors within said subsequent sample relative to said
baseline sample is indicative of efficacy of treatment with said
anti-CD40 therapeutic agent.
102. The method of claim 100, wherein a single dose of said
anti-CD40 therapeutic agent is administered to said subject.
103. The method of claim 100, wherein multiple doses of said
anti-CD40 therapeutic agent are administered to said subject.
104. The method of claim 100, wherein said anti-CD40 therapeutic
agent is an antagonist anti-CD40 monoclonal antibody that is
capable of specifically binding to a human CD40 antigen expressed
on the surface of a human B cell, said monoclonal antibody being
free of significant agonist activity when bound to the CD40 antigen
expressed on the surface of said B cell.
105. The method of claim 104, wherein said antagonist anti-CD40
monoclonal antibody is selected from the group consisting of: a)
the monoclonal antibody CHIR-5.9 or CHIR-12.12; b) the monoclonal
antibody produced by the hybridoma cell line 5.9 or 12.12; c) a
monoclonal antibody comprising an amino acid sequence selected from
the group consisting of the sequence shown in SEQ ID NO:6, the
sequence shown in SEQ ID NO:7, the sequence shown in SEQ ID NO:8,
both the sequence shown in SEQ ID NO:6 and SEQ ID NO:7, and both
the sequence shown in SEQ ID NO:6 and SEQ ID NO:8; d) a monoclonal
antibody comprising an amino acid sequence selected from the group
consisting of the sequence shown in SEQ ID NO:2, the sequence shown
in SEQ ID NO:4, the sequence shown in SEQ ID NO:5, both the
sequence shown in SEQ ID NO:2 and SEQ ID NO:4, and both the
sequence shown in SEQ ID NO:2 and SEQ ID NO:5; e) a monoclonal
antibody having an amino acid sequence encoded by a nucleic acid
molecule comprising a nucleotide sequence selected from the group
consisting of the sequence shown in SEQ ID NO:1, the sequence shown
in SEQ ID NO:3, and both the sequence shown in SEQ ID NO:1 and SEQ
ID NO:3; f) a monoclonal antibody that binds to an epitope capable
of binding the monoclonal antibody produced by the hybridoma cell
line 5.9 or 12.12; g) a monoclonal antibody that binds to an
epitope comprising residues 82-87 of the human CD40 sequence shown
in SEQ ID NO:10 or SEQ ID NO:12; h) a monoclonal antibody that
binds to an epitope comprising residues 82-89 of the human CD40
sequence shown in SEQ ID NO:10 or SEQ ID NO:12; i) a monoclonal
antibody that competes with the monoclonal antibody CHIR-5.9 or
CHIR-12.12 in a competitive binding assay; j) the monoclonal
antibody of preceding item a) or a monoclonal antibody of any one
of preceding items c)-i), wherein said antibody is recombinantly
produced; and k) a monoclonal antibody that is an antigen-binding
fragment of a monoclonal antibody of any one of preceding items
a)-j), wherein said fragment retains the capability of specifically
binding to said human CD40 antigen.
106. The method of claim 105, wherein said fragment is selected
from the group consisting of a Fab fragment, an F(ab').sub.2
fragment, an Fv fragment, and a single-chain Fv fragment.
107. The method of claim 100, wherein said anti-CD40 therapeutic
agent is a CD40 ligand (CD40L) antagonist that inhibits CD40/CD40L
interaction or CD40L-mediated CD40 signaling.
108. The method of claim 107, wherein said CD40L antagonist is
selected from the group consisting of an anti-CD40L monoclonal
antibody that specifically binds to CD40L, a soluble form of CD40,
a soluble form of a fusion protein comprising CD40, and a
pharmaceutical agent.
109. The method of claim 100, wherein said anti-CD40 therapeutic
agent is an anti-CD40 monoclonal antibody that specifically binds
to a human CD40 antigen expressed on the surface of a
CD40-expressing cell, thereby modulating ADCC activity.
110. The method of claim 109, wherein said anti-CD40 monoclonal
antibody is an antagonist anti-CD40 monoclonal antibody selected
from the group consisting of: a) the monoclonal antibody CHIR-5.9
or CHIR-12.12; b) the monoclonal antibody produced by the hybridoma
cell line 5.9 or 12.12; c) a monoclonal antibody comprising an
amino acid sequence selected from the group consisting of the
sequence shown in SEQ ID NO:6, the sequence shown in SEQ ID NO:7,
the sequence shown in SEQ ID NO:8, both the sequence shown in SEQ
ID NO:6 and SEQ ID NO:7, and both the sequence shown in SEQ ID NO:6
and SEQ ID NO:8; d) a monoclonal antibody comprising an amino acid
sequence selected from the group consisting of the sequence shown
in SEQ ID NO:2, the sequence shown in SEQ ID NO:4, the sequence
shown in SEQ ID NO:5, both the sequence shown in SEQ ID NO:2 and
SEQ ID NO:4, and both the sequence shown in SEQ ID NO:2 and SEQ ID
NO:5; e) a monoclonal antibody having an amino acid sequence
encoded by a nucleic acid molecule comprising a nucleotide sequence
selected from the group consisting of the sequence shown in SEQ ID
NO:1, the sequence shown in SEQ ID NO:3, and both the sequence
shown in SEQ ID NO:1 and SEQ ID NO:3; f) a monoclonal antibody that
binds to an epitope capable of binding the monoclonal antibody
produced by the hybridoma cell line 5.9 or 12.12; g) a monoclonal
antibody that binds to an epitope comprising residues 82-87 of the
human CD40 sequence shown in SEQ ID NO:10 or SEQ ID NO:12; h) a
monoclonal antibody that binds to an epitope comprising residues
82-89 of the human CD40 sequence shown in SEQ ID NO:10 or SEQ ID
NO:12; i) a monoclonal antibody that competes with the monoclonal
antibody CHIR-5.9 or CHIR-12.12 in a competitive binding assay; and
j) the monoclonal antibody of preceding item a) or a monoclonal
antibody of any one of preceding items c)-i), wherein said antibody
is recombinantly produced.
111. The method of claim 100, wherein said cancer is characterized
by neoplastic B cell growth.
112. The method of claim 111, wherein said cancer is selected from
the group consisting of non-Hodgkin's lymphoma, chronic lymphocytic
leukemia, multiple myeloma, B cell lymphoma, high-grade B cell
lymphoma, intermediate-grade B cell lymphoma, low-grade B cell
lymphoma, B cell acute lymphoblastic leukemia, Hodgkin's disease,
plasmacytoma, follicular lymphoma, follicular small cleaved
lymphoma, follicular large cell lymphoma, follicular mixed small
cleaved lymphoma, diffuse small cleaved cell lymphoma, diffuse
small lymphocytic lymphoma, prolymphocytic leukemia,
lymphoplasmacytic lymphoma, marginal zone lymphoma, mucosal
associated lymphoid tissue lymphoma, monocytoid B cell lymphoma,
splenic lymphoma, hairy cell leukemia, diffuse large cell lymphoma,
mediastinal large B cell lymphoma, lymphomatoid granulomatosis,
intravascular lymphomatosis, diffuse mixed cell lymphoma, diffuse
large cell lymphoma, immunoblastic lymphoma, Burkitt's lymphoma,
AIDS-related lymphoma, Waldenstrom's Macroglobulinemia, mantle cell
lymphoma, and heavy chain disease.
113. The method of claim 100, wherein said pre-malignant condition
is monoclonal gammopathy of undetermined significance (MGUS).
114. A method of treating a subject for monoclonal gammopathy of
undetermined significance (MGUS) in order to block progression of
said MGUS to multiple myeloma in said subject, said method
comprising administering to said subject an antagonist anti-CD40
monoclonal antibody that is capable of specifically binding to a
human CD40 antigen expressed on the surface of a human B cell, said
monoclonal antibody being free of significant agonist activity when
bound to the CD40 antigen expressed on the surface of said B
cell.
115. The method of claim 114, wherein said antagonist anti-CD40
monoclonal antibody is selected from the group consisting of: a)
the monoclonal antibody CHIR-5.9 or CHIR-12.12; b) the monoclonal
antibody produced by the hybridoma cell line 5.9 or 12.12; c) a
monoclonal antibody comprising an amino acid sequence selected from
the group consisting of the sequence shown in SEQ ID NO:6, the
sequence shown in SEQ ID NO:7, the sequence shown in SEQ ID NO:8,
both the sequence shown in SEQ ID NO:6 and SEQ ID NO:7, and both
the sequence shown in SEQ ID NO:6 and SEQ ID NO:8; d) a monoclonal
antibody comprising an amino acid sequence selected from the group
consisting of the sequence shown in SEQ ID NO:2, the sequence shown
in SEQ ID NO:4, the sequence shown in SEQ ID NO:5, both the
sequence shown in SEQ ID NO:2 and SEQ ID NO:4, and both the
sequence shown in SEQ ID NO:2 and SEQ ID NO:5; e) a monoclonal
antibody having an amino acid sequence encoded by a nucleic acid
molecule comprising a nucleotide sequence selected from the group
consisting of the sequence shown in SEQ ID NO:1, the sequence shown
in SEQ ID NO:3, and both the sequence shown in SEQ ID NO:1 and SEQ
ID NO:3; f) a monoclonal antibody that binds to an epitope capable
of binding the monoclonal antibody produced by the hybridoma cell
line 5.9 or 12.12; g) a monoclonal antibody that binds to an
epitope comprising residues 82-87 of the human CD40 sequence shown
in SEQ ID NO:10 or SEQ ID NO:12; h) a monoclonal antibody that
binds to an epitope comprising residues 82-89 of the human CD40
sequence shown in SEQ ID NO:10 or SEQ ID NO:12; i) a monoclonal
antibody that competes with the monoclonal antibody CHIR-5.9 or
CHIR-12.12 in a competitive binding assay; j) the monoclonal
antibody of preceding item a) or a monoclonal antibody of any one
of preceding items c)-i), wherein said antibody is recombinantly
produced; and k) a monoclonal antibody that is an antigen-binding
fragment of a monoclonal antibody of any one of preceding items
a)-j), wherein said fragment retains the capability of specifically
binding to said human CD40 antigen.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 11/914,714, which is a national-stage filing under 35 U.S.C.
.sctn.371 of International Application No. PCT/US2006/019414, filed
May 18, 2006, which was published by the International Bureau in
English on Nov. 23, 2006, and which claims the benefit of U.S.
Provisional Application Ser. No. 60/749,285, filed Dec. 9, 2005,
and U.S. Provisional Application Ser. No. 60/682,582, filed May 18,
2005; the contents of each of which are herein incorporated by
reference in their entirety.
FIELD OF THE INVENTION
[0002] The invention relates to the field of diagnostic and
prognostic medicine, more particularly to methods for determining
efficacy of therapeutic agents in treatment of proliferative
disorders, including cancers and pre-malignant conditions,
associated with aberrant CD40 signaling.
BACKGROUND OF THE INVENTION
[0003] Many members of the tumor necrosis factor (TNF) family of
ligands and their corresponding receptors regulate growth of normal
cells by inducing apoptosis or enhancing cell survival and
proliferation. It is this balance between apoptotic signals and
survival and proliferation signals that maintains normal cellular
homeostasis. At least 26 TNF family receptors and 18 TNF family
ligands have been identified to date. The biologically active forms
of both the receptors and ligands are self-assembled protein
trimers. Transmembrane and soluble forms of both the receptors and
ligands have been identified. Though the intracellular domains of
the receptors share no sequence homology, their extracellular
domains comprise 40-amino-acid, cysteine-rich repeats. Their
cytoplasmic tails signal by interacting with two major groups of
intracellular proteins: TNF receptor-associated factors (TRAFs) and
death domain (DD)-containing proteins. Interaction between at least
six human TRAFs and TRAF-binding sites on the cytoplasmic tail of
some of these receptors initiates several signaling pathways,
including AKT (the serine/threonine kinase referred to as protein
kinase B or PKB), nuclear factor-.kappa.B (NF-.kappa.B), and
mitogen-activated protein kinases (MAPK). See, for example, the
review by Younes and Kadin (2003) J. Clin. Oncol. 18:3526-3534.
[0004] The TNF family receptor member CD40 is a 50-55 kDa
cell-surface antigen present on the surface of both normal and
neoplastic human B cells, dendritic cells, monocytes, macrophages,
CD8.sup.+ T cells, endothelial cells, monocytic and epithelial
cells, some epithelial carcinomas, and many solid tumors, including
lung, breast, ovary, urinary bladder, and colon cancers. Binding of
the CD40 ligand to the CD40 antigen on the B cell membrane provides
a positive costimulatory signal that stimulates B cell activation
and proliferation, resulting in B cell maturation into a plasma
cell that secretes high levels of soluble immunoglobulin. CD40
activates TRAF-1, TRAF-2, -3, -5, and -6, which upregulate diverse
signaling pathways following engagement of CD40 with CD40L (either
membrane-bound CD40L or soluble CD40L), including extracellular
signal-regulated kinase (ERK), c-jun amino terminal kinase (JNK),
p38 mitogen-activated protein kinase (MAPK), AKT, and NF-.kappa.B
(see, for example, Younes and Carbone (1999) Int. J. Biol. Markers
14:135-143; van Kooten and Banchereau (2000) J. Leukoc. Biol.
67:2-17).
[0005] Malignant B cells from tumor types of B-cell lineage express
CD40 and appear to depend on CD40 signaling for survival and
proliferation. Transformed cells from patients with low- and
high-grade B-cell lymphomas, B-cell acute lymphoblastic leukemia,
multiple myeloma, chronic lymphocytic leukemia, Walsdenstrom's
Macroglobulinemia, and Hodgkin's disease express CD40. CD40
expression is also detected in two-thirds of acute myeloblastic
leukemia cases and 50% of AIDS-related lymphomas.
[0006] A number of carcinomas and sarcomas also exhibit high levels
of CD40 expression, though the role of CD40 signaling in relation
to CD40 expression on these cancer cells is less well understood.
CD40-expressing carcinomas include urinary bladder carcinoma
(Paulie et al. (1989) J. Immunol. 142:590-595; Braesch-Andersen et
al. (1989) J. Immunol. 142:562-567), breast carcinoma (Hirano et
al. (1999) Blood 93:2999-3007; Wingett et al. (1998) Breast Cancer
Res. Treat. 50:27-36); prostate cancer (Rokhlin et al. (1997)
Cancer Res. 57:1758-1768), renal cell carcinoma (Kluth et al.
(1997) Cancer Res. 57:891-899), undifferentiated nasopharyngeal
carcinoma (UNPC) (Agathanggelou et al. (1995) Am. J. Pathol.
147:1152-1160), squamous cell carcinoma (SCC) (Amo et al. (2000)
Eur. J. Dermatol. 10:438-442; Posner et al. (1999) Clin. Cancer
Res. 5:2261-2270), thyroid papillary carcinoma (Smith et al. (1999)
Thyroid 9:749-755), cutaneous malignant melanoma (van den Oord et
al. (1996) Am. J. Pathol. 149:1953-1961), gastric carcinoma
(Yamaguchi et al. (2003) Int. J. Oncol. 23(6):1697-702), and liver
carcinoma (see, for example, Sugimoto et al. (1999) Hepatology
30(4):920-26, discussing human hepatocellular carcinoma). For
CD40-expressing sarcomas, see, for example, Lollini et al. (1998)
Clin. Cancer Res. 4(8):1843-849, discussing human osteosarcoma and
Ewing's sarcoma.
[0007] CD40 signaling protects immature B-cells and B-cell
lymphomas from apoptosis induced by IgM or Fas (see, for example,
Wang et al. (1995) J. Immunol. 155:3722-3725). Mantel cell lymphoma
cells express a high level of CD40, and the addition of exogenous
CD40 ligand was shown to enhance their survival and rescue them
from fludarabin-induced apoptosis (Clodi et al. (1998) Brit. J.
Haematol. 103:217-219).
[0008] The role of CD40 signaling in malignant B cell survival and
proliferation renders the CD40 antigen a potential target for
anti-cancer therapy. Indeed, antagonist anti-CD40 antibodies
inhibit proliferation and/or differentiation of malignant human B
cells in vitro (see, for example, U.S. Patent Application
Publication No. 20040109857). Further, murine models of aggressive
human lymphomas have demonstrated the in vivo efficacy of anti-CD40
antibodies in promoting animal survival. See, for example,
Funakoshi et al. (1994) Blood 83:2787-2794; Tutt et al. (1998) J.
Immunol. 161:3176-3185; and Szocinski et al. (2002) Blood 100:
217-223.
[0009] The CD40 ligand (CD40L), also known as CD154, is a 32-33 kDa
transmembrane protein that also exists in two smaller biologically
active soluble forms, 18 kDa and 31 kDa, respectively (Graf et al.
(1995) Eur. J. Immunol. 25:1749-1754; Mazzei et al. (1995) J. Biol.
Chem. 270:7025-7028; Pietravalle et al. (1996) J. Biol. Chem.
271:5965-5967). CD40L is expressed on activated, but not resting,
CD4.sup.+ T-helper cells (Lane et al. (1992) Eur. J. Immunol.
22:2573-2578; Spriggs et al. (1992) J. Exp. Med. 176:1543-1550; and
Roy et al. (1993) J. Immunol. 151:1-14). Both CD40 and CD40L have
been cloned and characterized (Stamenkovi et al. (1989) EMBO J.
8:1403-1410; Armitage et al. (1992) Nature 357:80-82; Lederman et
al. (1992) J. Exp. Med. 175:1091-1101; and Hollenbaugh et al.
(1992) EMBO J. 11:4313-4321). See also U.S. Pat. No. 5,945,513,
describing human CD40L. Cells transfected with the CD40L gene and
expressing the CD40L protein on their surface can trigger B-cell
proliferation, and together with other stimulatory signals, can
induce antibody production (Armitage et al. (1992) supra; and U.S.
Pat. No. 5,945,513). Patients with lymphoid malignancies,
autoimmune disease, cardiovascular disease, and essential
thrombocythemia have elevated serum levels of soluble CD40L
(sCD40L) that are not seen in healthy subjects. Constitutive
expression of CD40L has been observed in a subset of patients with
several B-cell lymphoid malignancies, including mantle-cell
lymphoma, follicular lymphoma, marginal zone lymphoma, chronic
lymphocytic leukemia (CLL), diffuse large B-cell lymphoma (DLBCL),
follicular lymphoma (FL), and HIV-infected B-cell lymphoma. See,
for example, Clodi et al. (1998) Br. J. Haematol. 103:270-275;
Schattner et al. (1998) Blood 91:2689-2697; Moses et al. (1997)
Nat. Med. 3:1242-1249; Trentin et al. (1997) Cancer Res.
57:4940-4947; and Pham et al. (2002) Immunity 16:37-50). CD40L may
play an important role in the cell contact-dependent interaction of
CD40-expressing tumor B-cells within the neoplastic follicles or
CD40-expressing Reed-Sternberg cells in Hodgkin's disease areas
(Carbone et al. (1995) Am. J. Pathol. 147:912-922). However, the
mechanism of CD40L-mediated CD40 signaling leading to survival
versus cell death responses of malignant B-cells is not completely
known. For example, in follicular lymphoma cells, down-regulation
of apoptosis-inducing TRAIL molecule (APO-2L) (Ribeiro et al.
(1998) British J. Haematol. 103:684-689) and overexpression of
Bcl-2, and in the case of B-CLL, down-regulation of CD95
(Fas/APO-1) (Laytragoon-Lewin et al. (1998) Eur. J. Haematol.
61:266-271) have been proposed as mechanisms of survival. In
contrast, evidence in follicular lymphoma indicates that CD40
activation leads to up-regulation of TNF (Worm et al. (1994)
International Immunol. 6:1883-1890) and CD95 molecules (Plumas et
al. (1998) Blood 91:2875-2885).
[0010] Given the important role of CD40 signaling in survival and
proliferation of neoplastic cells, methods for identifying
individuals who would be responsive to treatment regimens that
target CD40-expressing tumors and more specifically CD40 signaling
are needed.
BRIEF SUMMARY OF THE INVENTION
[0011] Methods for identifying subjects having a cancer or
pre-malignant condition that will benefit from anti-CD40
therapeutic agents including those that modulate CD40L-mediated
signaling and/or modulate antibody-dependent cellular cytotoxicity
(ADCC) are provided. Such anti-CD40 therapeutic agents include, but
are not limited to, antagonist anti-CD40 antibodies, antagonist
anti-CD40L antibodies, and pharmacologic agents that block or
interfere with CD40/CD40L interaction, particularly CD40L-mediated
CD40 signaling, as well as antagonist anti-CD40 antibodies that
additionally, or alternatively, have ADCC activity as a mode of
action. In some embodiments, the methods comprise the use of
biomarkers of cellular apoptosis, cell proliferation and survival,
and CD40 signaling pathways to monitor ex vivo cellular response to
one or more anti-CD40 therapeutic agents of interest. These ex vivo
prognostic assays comprise providing a test biological sample and a
control biological sample from a candidate subject, where these
biological samples comprise CD40-expressing neoplastic cells that
have been stimulated with a CD40 ligand, either in vivo or ex vivo;
contacting the test biological sample with the anti-CD40
therapeutic agent of interest; detecting the expression level of at
least one biomarker within the test biological sample; and
comparing the expression level of the biomarker(s) with the
corresponding expression level detected in the control biological
sample, which has not been contacted with the anti-CD40 therapeutic
agent of interest. Biomarkers for use in these ex vivo prognostic
assays include proteins and/or genes whose expression levels are
prognostic indicators of responsiveness to treatment intervention,
including biomarkers of cellular apoptosis, biomarkers of
CD40L-mediated CD40 signaling pathways, and biomarkers of cell
proliferation or survival, depending upon the mode of action of the
anti-CD40 therapeutic agent. Where the anti-CD40 therapeutic agent
has its mode of action via disruption of CD40L-mediated CD40
signaling, biomarkers of cellular apoptosis, CD40L-mediated CD40
signaling pathways, and cell proliferation or survival can be used
in these ex vivo prognostic assays. In some embodiments, additional
markers of CD40L-mediated CD40 signaling can be assayed, including,
but not limited to, cytokines that are upregulated via CD40L-CD40
interaction, for example, vascular endothelial growth factor
(VEGF), interleukin (IL)-6, IL-8, IL-10, granulocyte monocyte
colony-stimulating factor (GM-CSF), tumor necrosis factor-.alpha.
(TNF-.alpha.), monocyte chemoattractant protein-1 (MCP-1), and
macrophage inflammatory protein-1.beta. (MIP-1.beta.). Where the
anti-CD40 therapeutic agent has its mode of action via ADCC, for
example, an anti-CD40 antibody, biomarkers of cellular apoptosis
can be used in these ex vivo prognostic assays.
[0012] In other embodiments of the invention, candidate subjects
are screened for the expression level of one or more CD40-related
factors that are predictive of an individual, or a subpopulation of
individuals, who will benefit from intervention with anti-CD40
therapeutic agents. Thus, in one embodiment, biological samples
collected from candidate subjects, for example, subjects having a
cancer or pre-malignant condition of B-cell lineage, are screened
for one or more CD40-related factors selected from the group
consisting of expression level of cell-surface CD40 antigen on
neoplastic cells, expression level of cell-surface CD40L on
neoplastic cells, circulating level of soluble CD40 (sCD40), and
circulating level of soluble CD40L (sCD40L). These CD40-related
factors can be prognostic indicators of the disease, and can
further be used to identify subjects who would or would not respond
to therapeutic intervention with anti-CD40 therapeutic agents,
regardless of the mode of action of the anti-CD40 therapeutic
agent. An elevated level of expression of one or more of these
CD40-related factors within a biological sample when compared to a
control or reference standard would be indicative of an individual
who would benefit from therapeutic intervention with an anti-CD40
therapeutic agent that modulates CD40L-mediated CD40 signaling,
modulates ADCC, or both. Candidate subjects identified with this
screening process can be treated with an anti-CD40 therapeutic
agent of interest, or can be further screened for responsiveness to
anti-CD40 therapeutic agents using the ex vivo prognostic assays
described herein.
[0013] In yet other embodiments, candidate subjects are screened
for the presence or absence of one or more clinically useful
prognostic markers in order to define subpopulations of candidate
subjects who have a poor prognosis with other classes of cancer
therapeutics but who will benefit from intervention with anti-CD40
therapeutic agents. In this manner, biological samples collected
from candidate subjects are screened for one or more clinically
useful prognostic markers known to be indicators of poor prognosis
with current therapeutics whose mode of action is not via CD40
targeting or CD40L-mediated CD40 signaling. Any clinically useful
prognostic marker for a given cancer or pre-malignant condition can
be included in the screening process. In some embodiments, the
subpopulation of candidate subjects represents patients with
chronic lymphocytic leukemia (CLL) for whom current therapies of
treatment are not curative, and the clinically useful prognostic
markers included in the screening process are selected from the
group consisting of ZAP-70, CD38, 132 microglobulin, and
cytogenetic markers, for example, p53 mutational status, ATM
mutational status, and chromosome deletions, such as the chromosome
17p deletion and the chromosome 11q deletion. Candidate subjects
within a subpopulation identified with this screening process can
be further screened for responsiveness to anti-CD40 therapeutic
agents using the ex vivo prognostic assays described herein.
[0014] The present invention also provides methods for monitoring
efficacy of an anti-CD40 therapeutic agent in treatment of a
subject having a cancer comprising CD40-expressing neoplastic
cells, and in treatment of a subject having a pre-malignant
condition at risk of developing into a malignancy associated with
aberrant CD40 expression and/or signaling. In this manner, a
subject undergoing therapy with an anti-CD40 therapeutic agent, who
may or may not have been previously screened using an ex vivo
prognostic assay disclosed herein, is monitored for in vivo changes
in the expression of at least one biomarker of cellular apoptosis,
cell proliferation and survival, and/or one or more CD40L-mediated
CD40 signaling pathways following treatment with the anti-CD40
therapeutic agent. The particular biomarkers to be assayed can be
chosen based on mode of action of the therapeutic agent as noted
above. Alternatively, or additionally, the subject can be monitored
for in vivo changes in the expression level of one or more
CD40-related factors selected from the group consisting of
cell-surface CD40 antigen on neoplastic cells, cell-surface CD40L
on neoplastic cells, circulating level of sCD40, and circulating
level of sCD40L following treatment with the anti-CD40 therapeutic
agent. In this manner, a first biological sample is obtained from
the subject and assayed for the expression level of one or more of
these biomarkers and/or CD40-related factors to obtain a baseline
level of expression for each factor assayed, and then one or more
subsequent biological samples is obtained from the subject and
assayed for the same biomarker(s) and/or CD40-related factor(s),
where the subsequent biological sample is obtained following the
administration of at least one dose of the anti-CD40 therapeutic
agent of interest. Monitoring can occur at a single point in time,
or at multiple points in time, to ascertain efficacy of any given
treatment protocol wherein the anti-CD40 therapeutic agent is
administered to the subject. Depending upon the biomarker being
assayed, a decrease or increase in the expression level of the
biomarker between any two time points can be indicative of efficacy
of the anti-CD40 therapeutic agent in treatment of the cancer or
pre-malignant condition. Where monitoring reveals a decrease in the
expression level of one or more of the CD40-related factors, such a
result can be indicative of efficacy of the anti-CD40 therapeutic
agent in treatment of the cancer or pre-malignant condition.
[0015] Expression level of these various biomarkers and
CD40-related factors, and any clinically useful prognostic markers
in a biological sample can be detected at the protein or nucleic
acid level, using, for example, immunohistochemistry techniques or
nucleic acid-based techniques such as in situ hybridization and
RT-PCR. In some embodiments, an elevated level or an increase in
expression of at least one biomarker is indicative of a positive
therapeutic response to treatment with an anti-CD40 therapeutic
agent. In other embodiments, a diminished level or a decrease in
expression of at least one biomarker is indicative of a positive
therapeutic response to treatment with the anti-CD40 therapeutic
agent.
BRIEF DESCRIPTION OF THE DRAWINGS
[0016] FIG. 1 shows inhibition of CD40 ligand (CD40L)-mediated
survival by CHIR-12.12 in B-CLL cells obtained from B-CLL
patients.
[0017] FIG. 2 shows inhibition of CD40L-mediated survival by
CHIR-12.12 in B-CLL cells obtained from B-CLL patients.
[0018] FIG. 3 shows inhibition of CD40L-mediated survival by
CHIR-12.12 in B-CLL cells obtained from B-CLL patients.
[0019] FIG. 4 shows inhibition of CD40L-mediated signaling pathways
by CHIRb 12.12 in B-CLL cells obtained from B-CLL patients.
[0020] FIG. 5 shows inhibition of CD40L-mediated survival by
CHIR-12.12 in B-CLL cells obtained from B-CLL patients.
[0021] FIG. 6 shows inhibition of CD40L-mediated survival by
CHIR-12.12 in B-CLL cells obtained from B-CLL patients.
[0022] FIG. 7 demonstrates that CHIR-12.12 does not trigger
apoptosis without CD40L stimulation.
[0023] FIG. 8 shows the effect of inhibition of PI3K (LY294002) and
MEK (PD98595) on CD40L-mediated CD40 signaling pathways leading to
a reduction in p-ERK, p-Akt, and p-IKK .alpha./.beta..
[0024] FIG. 9 shows the effect of inhibition of PI3K (LY294002) and
MEK (PD98595) on survival mediated by CD40L interaction with
CD40.
[0025] FIG. 10 shows inhibition of CD40L-mediated survival (TUNEL)
by CHIR-12.12 in B-CLL cells obtained from B-CLL patients as
measured by flow cytometry.
[0026] FIG. 11 shows inhibition of CD40L-mediated survival (cleaved
PARP) by CHIR-12.12 in B-CLL cells obtained from B-CLL patients as
measured by flow cytometry.
[0027] FIG. 12 shows the effect of CHIR-12.12 on B-CLL cell markers
at the transcript level.
[0028] FIG. 13 shows the effect of CHIR-12.12 and the p38 MAPK
inhibitor SB203580 on CD40L-mediated CD40 signaling via the p38
pathway at 4 hr.
[0029] FIG. 14 shows the effect of CHIR-12.12 and the p38 MAPK
inhibitor SB203580 on CD40L-mediated CD40 signaling via the MEK/p38
pathway at 24 hr.
[0030] FIG. 15 shows p-p38 status in multiple B-CLL patients.
[0031] FIGS. 16A, B, and C show the CHIR-12.12-mediated
antibody-dependent cellular cytotoxicity (ADCC) against human
multiple myeloma cell lines KMS-12-BM (FIG. 16A), IM-9 (FIG. 16B),
or ARH-77 (FIG. 16C).
[0032] FIG. 17 shows the tumor volume in a multiple myeloma animal
model over time in animals administered with control IgG.sub.1 at
10 mg/kg, i.p. ( ), CHIR-12.12 anti-CD40 mAb at 1 mg/kg, i.p.
(.smallcircle.), CHIR-12.12 anti-CD40 mAb at 10 mg/kg, i.p. (*), or
bortezomib at 1 mg/kg, i.v. (.DELTA.). The upperward arrows
indicate bortezomib dosing, and the downward arrows indicate
CHIR-12.12 dosing.
[0033] FIG. 18 shows the tumor volume in a multiple myeloma animal
model over time in animals administered with control IgG.sub.1 at 1
mg/kg (.box-solid.), CHIR-12.12 anti-CD40 mAb at 1 mg/kg
(.tangle-solidup.), bortezomib at 1 mg/kg (.quadrature.), or
CHIR-12.12 anti-CD40 mAb at 1 mg/kg plus bortezomib at 1 mg/kg
(.smallcircle.). The larger arrows indicate antibody dosing, and
the smaller arrows indicate bortezomib dosing.
[0034] FIG. 19 shows the effect of CHIR-12.12 anti-CD40 mAb on
tumor cell proliferation in the human multiple myeloma xenograft
model IM-9, assayed by immunohistochemical staining for Ki67
expression, and induction of cell death as evidenced by an
increased level of the apoptotic biomarkers cleaved-Caspase 3 and
cleaved-PARP.
[0035] FIG. 20 shows the conditional survival rate over time in an
unstaged orthotopic IM-9 xenograft model in animals administered
with control IgG.sub.1 at 10 mg/kg ( ), anti-CD40 mAb CHIR-12.12 at
0.1 mg/kg (.diamond.), 1 mg/kg (.smallcircle.), 10 mg/kg (*), or
bortezomib at 0.5 mg/kg (-.tangle-solidup.-) or 1 mg/kg ( .cndot.
.cndot. .cndot. .tangle-solidup. .cndot. .cndot. .cndot. ). The
shaded arrows indicate bortezomib dosing, and the solid arrows
indicate antibody dosing.
[0036] FIG. 21 shows conditional survival rate over time in a
staged orthotopic IM-9 xenograft model in animals administered with
control IgG.sub.1 at 1 mg/kg, i.p. (.box-solid.), anti-CD40 mAb
CHIR-12.12 at 0.1 mg/kg, i.p ( ), 1 mg/kg, i.p. (-.diamond.-), or
10 mg/kg, i.p (.DELTA.), or bortezomib at 0.5 mg/kg, i.v.
(.quadrature.).
[0037] FIG. 22 shows the tumor volume in a human multiple myeloma
subcutaneous xenograft model over time in animals administered with
control IgG.sub.1 at 10 mg/kg, i.p. ( ), CHIR-12.12 anti-CD40 mAb
at 1 mg/kg, i.p. (.diamond.), CHIR-12.12 anti-CD40 mAb at 10 mg/kg,
i.p. (.diamond-solid.), or bortezomib at 1 mg/kg, i.v. ( .cndot.
.cndot. .cndot. .cndot. .cndot. .cndot. ). The larger arrows
indicate CHIR-12.12 dosing, and the smaller arrows indicate
bortezomib dosing.
[0038] FIG. 23 shows that signaling and survival of normal human B
Cells are induced by CD40L and blocked by CHIR-12.12.
[0039] FIG. 24 shows that CD40L rescues B-CLL cells from apoptosis
and CHIR-12.12 blocks this effect as determined by CellTiter-Glo
viability (A) and cPARP flow cytometry (B) assays.
[0040] FIG. 25 shows that CHIR-12.12 blocks the CD40L-mediated
decrease of cPARP and increase of Bcl-xl and Mcl-1expression in
B-CLL cells.
[0041] FIG. 26 shows that CHIR-12.12 inhibits the CD40L-induced
phosphorylation of Akt and p38 MAPK in B-CLL cells.
[0042] FIG. 27 shows that CHIR-12.12 inhibits the CD40L-induced
phosphorylation of IKK .alpha./.beta. and ERK 1/2 in B-CLL
cells.
DETAILED DESCRIPTION OF THE INVENTION
[0043] The present invention is directed to methods for identifying
subjects having a cancer or pre-malignant condition that would
benefit from treatment with anti-CD40 therapeutic agents that
target the CD40 receptor and which modulate ADCC, interfere with
CD40 signaling, particularly CD40 signaling pathways that are
mediated by interaction of CD40 with the CD40 ligand (CD40L), or
both. In one embodiment, the methods comprise the use of ex vivo
prognostic assays to monitor the effects of antagonist anti-CD40
therapeutic agents that block or interfere with CD40L-mediated CD40
signaling on the expression level of three classes of biomarkers
that are associated with CD40L-mediated CD40 signaling,
particularly biomarkers of cell proliferation or survival and cell
apopototic pathways and biomarkers of key CD40L-mediated CD40
signaling pathways, including the AKT, NF-.kappa.B, and
mitogen-activated protein kinase (MAPK) signaling pathways.
Additional markers that can serve to monitor effects of antagonist
anti-CD40 therapeutic agents that block or interfere with
CD40L-mediated CD40 signaling include cytokines that are
upregulated via CD40L-mediated CD40 signaling, as noted herein
below. Biomarkers for cell apoptotic pathways can also serve to
monitor effects of anti-CD40 therapeutic agents that modulate ADCC,
for example, anti-CD40 antibodies having ADCC as a mode of action.
Therapeutic agents that act as antagonists of CD40 signaling,
referred to herein as "CD40 antagonists," can interfere with one or
more of the signaling cues normally triggered by binding of CD40L
to the CD40 receptor. The ex vivo prognostic assays of the present
invention can be used to discriminate between subjects who would
benefit from intervention with CD40 antagonists and therapeutic
agents that target CD40 and modulate ADCC and those for whom
intervention with these types of therapeutic agents would not be
beneficial. Candidate subjects can additionally, or alternatively,
be screened for the presence or absence of, or elevated or
diminished levels of, one or more CD40-related factors and/or one
or more clinically useful prognostic markers to define individuals
or subpopulations of candidate subjects who would benefit from
therapeutic intervention with anti-CD40 therapeutic agents that
modulate CD40L-mediated CD40 signaling and/or ADCC. Subjects
identified in these screening methods can be further screened using
the ex vivo prognostic assays described herein. The biomarkers and
CD40-related factors described herein also find use in monitoring
efficacy of treatment with anti-CD40 therapeutic agents that
modulate CD40 signaling and/or ADCC, and in determining the basis
for drug responsiveness in individual cancer patients or
subpopulations of cancer patients.
[0044] "Tumor," as used herein, refers to all neoplastic cell
growth and proliferation, whether malignant or benign, and all
pre-cancerous and cancerous cells and tissues. "Neoplastic," as
used herein, refers to any form of dysregulated or unregulated cell
growth, whether malignant or benign, resulting in abnormal tissue
growth. Thus, "neoplastic cells" include malignant and benign cells
having dysregulated or unregulated cell growth.
[0045] The terms "cancer" and "cancerous" refer to or describe the
physiological condition in mammals that is typically characterized
by unregulated cell growth. Examples of cancer include, but are not
limited to, lymphoma and leukemia, and solid tumors. By "B
cell-related cancer" or "cancer of B-cell lineage" is intended any
type of cancer in which the dysregulated or unregulated cell growth
is associated with B cells.
[0046] By "refractory" in the context of a cancer is intended the
particular cancer is resistant to, or non-responsive to, therapy
with a particular therapeutic agent. A cancer can be refractory to
therapy with a particular therapeutic agent either from the onset
of treatment with the particular therapeutic agent (i.e.,
non-responsive to initial exposure to the therapeutic agent), or as
a result of developing resistance to the therapeutic agent, either
over the course of a first treatment period with the therapeutic
agent or during a subsequent treatment period with the therapeutic
agent.
[0047] By "CD40 antigen," "CD40 cell surface antigen," "CD40
receptor," or "CD40" is intended a transmembrane glycoprotein that
belongs to the tumor necrosis factor (TNF) receptor family (see,
for example, U.S. Pat. Nos. 5,674,492 and 4,708,871; Stamenkovic et
al. (1989) EMBO 8:1403; Clark (1990) Tissue Antigens 36:33; Barclay
et al. (1997) The Leucocyte Antigen Facts Book (2d ed.; Academic
Press, San Diego)). Two isoforms of human CD40, encoded by
alternatively spliced transcript variants of this gene, have been
identified. The first isoform (also known as the "long isoforms" or
"isoform 1") is expressed as a 277-amino-acid precursor polypeptide
(SEQ ID NO:12 (first reported as GenBank Accession No. CAA43045,
and identified as isoform 1 in GenBank Accession No.
NP.sub.--001241), encoded by SEQ ID NO:11 (see GenBank Accession
Nos. X60592 and NM.sub.--001250)), which has a signal sequence
represented by the first 19 residues. The second isoform (also
known as the "short isoforms" or "isoform 2") is expressed as a
203-amino-acid precursor polypeptide (SEQ ID NO:10 (GenBank
Accession No. NP.sub.--690593), encoded by SEQ ID NO:9 (GenBank
Accession No. NM.sub.--152854)), which also has a signal sequence
represented by the first 19 residues. The precursor polypeptides of
these two isoforms of human CD40 share in common their first 165
residues (i.e., residues 1-165 of SEQ ID NO:10 and SEQ ID NO:12).
The precursor polypeptide of the short isoform (shown in SEQ ID
NO:10) is encoded by a transcript variant (SEQ ID NO:9) that lacks
a coding segment, which leads to a translation frame shift; the
resulting CD40 isoform contains a shorter and distinct C-terminus
(residues 166-203 of SEQ ID NO:10) from that contained in the long
isoform of CD40 (C-terminus shown in residues 166-277 of SEQ ID
NO:12). For purposes of the present invention, the term "CD40
antigen," "CD40 cell surface antigen," "CD40 receptor," or "CD40"
encompasses both the short and long isoforms of CD40.
[0048] The CD40 antigen is displayed on the surface of a variety of
cell types, as described elsewhere herein. By "displayed on the
surface" and "expressed on the surface" is intended that all or a
portion of the CD40 antigen is exposed to the exterior of the cell.
The displayed or expressed CD40 antigen may be fully or partially
glycosylated.
[0049] By "agonist activity" is intended that a substance functions
as an agonist. An agonist combines with a receptor on a cell and
initiates a reaction or activity that is similar to or the same as
that initiated by the receptor's natural ligand. An agonist of CD40
induces any or all of, but not limited to, the following responses:
B cell proliferation and differentiation, antibody production,
intercellular adhesion, B cell memory generation, isotype
switching, up-regulation of cell-surface expression of MHC Class II
and CD80/86, and secretion of pro-inflammatory cytokines such as
VEGF, IL-8, IL-12, and TNF. By "antagonist activity" is intended
that the substance functions as an antagonist. An antagonist of
CD40 prevents or reduces induction of any of the responses induced
by binding of the CD40 receptor to an agonist ligand, particularly
CD40L. The antagonist may reduce induction of any one or more of
the responses to agonist binding by 5%, 10%, 15%, 20%, 25%, 30%,
35%, preferably 40%, 45%, 50%, 55%, 60%, more preferably 70%, 80%,
85%, and most preferably 90%, 95%, 99%, or 100%. Methods for
measuring CD40 ligand binding specificity and antagonist activity
of an anti-CD40 therapeutic agent, for example, an anti-CD40
antibody, are known in the art and include, but are not limited to,
standard competitive binding assays, assays for monitoring
immunoglobulin secretion by B cells, B cell proliferation assays,
Banchereau-Like-B cell proliferation assays, T cell helper assays
for antibody production, co-stimulation of B cell proliferation
assays, and assays for up-regulation of B cell activation markers.
See, for example, such assays disclosed in WO 00/75348 and U.S.
Pat. No. 6,087,329, herein incorporated by reference. Also see,
provisional applications entitled "Antagonist Anti-CD40 Monoclonal
Antibodies and Methods for Their Use," filed Nov. 4, 2003, Nov. 26,
2003, and Apr. 27, 2004, and assigned U.S. Patent Application Nos.
60/517,337 (Attorney Docket No. PP20107.001 (035784/258442)),
60/525,579 (Attorney Docket No. PP20107.002 (035784/271525)), and
60/565,710 (Attorney Docket No. PP20107.003 (035784/277214)),
respectively, and International Patent Application No.
PCT/US2004/037152 (Attorney Docket No. PP20107.004
(035784/282916)), also entitled "Antagonist Anti-CD40 Monoclonal
Antibodies and Methods for Their Use," filed Nov. 4, 2004, and
published as WO 2005/044854; the contents of each of which are
herein incorporated by reference in their entirety.
[0050] By "significant" agonist activity is intended an agonist
activity of at least 30%, 35%, 40%, 45%, 50%, 60%, 70%, 75%, 80%,
85%, 90%, 95%, or 100% greater than the agonist activity induced by
a neutral substance or negative control as measured in an assay of
a B cell response. Preferably, "significant" agonist activity is an
agonist activity that is at least 2-fold greater or at least 3-fold
greater than the agonist activity induced by a neutral substance or
negative control as measured in an assay of a B cell response.
Thus, for example, where the B cell response of interest is B cell
proliferation, "significant" agonist activity would be induction of
a level of B cell proliferation that is at least 2-fold greater or
at least 3-fold greater than the level of B cell proliferation
induced by a neutral substance or negative control. In one
embodiment, a non-specific immunoglobulin, for example IgG1, that
does not bind to CD40 serves as the negative control. A substance
"free of significant agonist activity" would exhibit an agonist
activity of not more than about 25% greater than the agonist
activity induced by a neutral substance or negative control,
preferably not more than about 20% greater, 15% greater, 10%
greater, 5% greater, 1% greater, 0.5% greater, or even not more
than about 0.1% greater than the agonist activity induced by a
neutral substance or negative control as measured in an assay of a
B cell response.
[0051] In some embodiments of the invention, the anti-CD40
therapeutic agent is an antagonist anti-CD40 antibody. Such
antibodies are free of significant agonist activity as noted above
when bound to a CD40 antigen on a human cell. In one embodiment of
the invention, the antagonist anti-CD40 antibody is free of
significant agonist activity in one cellular response. In another
embodiment of the invention, the antagonist anti-CD40 antibody is
free of significant agonist activity in assays of more than one
cellular response (e.g., proliferation and differentiation, or
proliferation, differentiation, and, for B cells, antibody
production). In some embodiments of the invention, the anti-CD40
therapeutic agent of interest is an antagonist anti-CD40 antibody,
for example, the fully human monoclonal antibody CHIR-12.12 or
CHIR-5.9, or antigen-binding fragment thereof, as noted herein
below.
[0052] Any of the assays known in the art can be used to determine
whether an anti-CD40 therapeutic agent acts as an antagonist of one
or more B cell responses. In some embodiments, the therapeutic
agent is an anti-CD40 antibody that acts as an antagonist of at
least one B cell response selected from the group consisting of B
cell proliferation, B cell differentiation, antibody production,
intercellular adhesion, B cell memory generation, isotype
switching, up-regulation of cell-surface expression of MHC Class II
and CD80/86, and secretion of pro-inflammatory cytokines such as
VEGF, IL-8, IL-12, and TNF. Of particular interest are antagonist
anti-CD40 antibodies that free of significant agonist activity with
respect to B cell proliferation when bound to the human CD40
antigen on the surface of a human B cell.
[0053] In one such embodiment, the anti-CD40 antibody is an
antagonist of B cell proliferation as measured in a B cell
proliferation assay such as that described in Example 6 herein
below, and the antagonist anti-CD40 antibody stimulates B cell
proliferation at a level that is not more than about 25% greater
than the B cell proliferation induced by a neutral substance or
negative control, preferably not more than about 20% greater, 15%
greater, 10% greater, 5% greater, 1% greater, 0.5% greater, or even
not more than about 0.1% greater than the B cell proliferation
induced by a neutral substance or negative control.
[0054] In other embodiments, the anti-CD40 antibody is an
antagonist of B cell proliferation that is induced by another
anti-CD40 antibody, for example, the S2C6 anti-CD40 antibody, as
measured in a B cell proliferation assay such as that described in
Example 6 herein below, and the level of B cell proliferation
stimulated by the other anti-CD40 antibody in the presence of the
antagonist anti-CD40 antibody is not more than about 25% of the B
cell proliferation induced by the other anti-CD40 antibody in the
absence of the antagonist anti-CD40 antibody (i.e., at least 75%
inhibition), preferably not more than about 20%, 15%, 10%, 5%, 1%,
0.5%, or even not more than about 0.1% of the B cell proliferation
induced by the other anti-CD40 antibody in the absence of the
antagonist anti-CD40 antibody.
[0055] In yet other embodiments, the anti-CD40 antibody is an
antagonist of B cell proliferation that is induced by the cell line
EL4B5 as measured in the B cell activation assay described in
Example 6 herein below, and the level of B cell proliferation
stimulated by the EL4B5 cell line in the presence of the antagonist
anti-CD40 antibody is not more than about 25% of the B cell
proliferation induced by this cell line in the absence of the
antagonist anti-CD40 antibody (i.e., at least 75% inhibition),
preferably not more than about 20%, 15%, 10%, 5%, 1%, 0.5%, or even
not more than about 0.1% of the B cell proliferation induced by
this cell line in the absence of the antagonist anti-CD40
antibody.
[0056] In still other embodiments, the anti-CD40 antibody is an
antagonist of human T-cell-induced antibody production by human B
cells as measured in the human T-cell helper assay for antibody
production by B cells described in Example 6 herein below. In this
manner, the level of IgG antibody production, IgM antibody
production, or both IgG and IgM antibody production by B cells
stimulated by T cells in the presence of the antagonist anti-CD40
antibody is not more than about 50% of the respective antibody
production by B cells stimulated by T cells in the absence of the
antagonist anti-CD40 antibody (i.e., at least 75% inhibition),
preferably not more than about 25%, 20%, 15%, 10%, 5%, 1%, 0.5%, or
even not more than about 0.1% of the respective antibody production
by B cells stimulated by T cells in the absence of the antagonist
anti-CD40 antibody.
[0057] By "CD40 ligand" is intended any peptide, polypeptide, or
protein that can bind to and activate one or more CD40 signaling
pathways. Thus, "CD40 ligands" include, but are not limited to,
full-length CD40 ligand proteins and variants and fragments thereof
that retain sufficient activity to carry out the function of
binding to and stimulating CD40 signaling on CD40-expressing cells.
Modifications to a native CD40 ligand, for example, human CD40
ligand (CD40L; also known as CD154), include, but are not limited
to, substitutions, deletions, truncations, extensions, fusion
proteins, fragments, peptidomimetics, and the like. In some
embodiments of the invention, the ex vivo prognostic assays include
the use of soluble CD40L, for example, soluble recombinant human
CD40L (Alexis Corporation, Bingham, Nottinghamshire, UK) to
stimulate CD40 signaling on CD40-expressing neoplastic cells of a
biological sample.
[0058] By "CD40L-mediated CD40 signaling" is intended any of the
biological activities that result from interaction of the
cell-surface receptor CD40 with a CD40 ligand. Examples of CD40
signaling are signals that lead to proliferation and survival of
CD40-expressing cells, and stimulation of one or more
CD40-signaling pathways within CD40-expressing cells. A CD40
"signaling pathway" or "signal transduction pathway" is intended to
mean at least one biochemical reaction, or a group of biochemical
reactions, that results from interaction of the CD40 receptor with
a CD40 ligand, for example, CD40L, and which generates a signal
that, when transmitted through the signal pathway, leads to
activation of one or more downstream molecules in the signaling
cascade. Signal transduction pathways involve a number of signal
transduction molecules that lead to transmission of a signal from
the cell-surface CD40 receptor across the plasma membrane of a
cell, and through one or more in a series of signal transduction
molecules, through the cytoplasm of the cell, and in some
instances, into the cell's nucleus. Of particular interest to the
present invention are CD40 signal transduction pathways, including
the AKT signaling pathway, which leads to activation of AKT, and
ultimately activation of NF-.kappa.B via the NF-.kappa.B signaling
pathway; and mitogen-activated protein kinase (MAPK) signaling
pathways, including the MEK/ERK signaling pathway and the MEK/p38
signaling pathway, which lead to activation of ERK and p38,
respectively. The balance between activation and blocking of these
signaling pathways favors either cell survival or apoptosis as
noted herein below.
[0059] The methods of the present invention are directed to ex vivo
prognostic assays, and prognostic assays that utilize antibodies,
either in a detection step, or as candidate anti-CD40 therapeutic
agents that are being tested in these ex vivo prognostic assays.
The following terms and definitions apply to such antibodies.
[0060] "Antibodies" and "immunoglobulins" (Igs) are glycoproteins
having the same structural characteristics. The terms are used
synonymously. In some instances the antigen specificity of the
immunoglobulin may be known.
[0061] The term "antibody" is used in the broadest sense and covers
fully assembled antibodies, antibody fragments that can bind
antigen (e.g., Fab, F(ab').sub.2, Fv, single chain antibodies,
diabodies, antibody chimeras, hybrid antibodies, bispecific
antibodies, humanized antibodies, and the like), and recombinant
peptides comprising the forgoing.
[0062] The terms "monoclonal antibody" and "mAb" as used herein
refer to an antibody obtained from a substantially homogeneous
population of antibodies, i.e., the individual antibodies
comprising the population are identical except for possible
naturally occurring mutations that may be present in minor
amounts.
[0063] "Native antibodies" and "native immunoglobulins" are usually
heterotetrameric glycoproteins of about 150,000 daltons, composed
of two identical light (L) chains and two identical heavy (H)
chains. Each light chain is linked to a heavy chain by one covalent
disulfide bond, while the number of disulfide linkages varies among
the heavy chains of different immunoglobulin isotypes. Each heavy
and light chain also has regularly spaced intrachain disulfide
bridges. Each heavy chain has at one end a variable domain
(V.sub.H) followed by a number of constant domains. Each light
chain has a variable domain at one end (V.sub.L) and a constant
domain at its other end; the constant domain of the light chain is
aligned with the first constant domain of the heavy chain, and the
light chain variable domain is aligned with the variable domain of
the heavy chain. Particular amino acid residues are believed to
form an interface between the light and heavy-chain variable
domains.
[0064] The term "variable" refers to the fact that certain portions
of the variable domains differ extensively in sequence among
antibodies. Variable regions confer antigen-binding specificity.
However, the variability is not evenly distributed throughout the
variable domains of antibodies. It is concentrated in three
segments called complementarity determining regions (CDRs) or
hypervariable regions, both in the light chain and the heavy-chain
variable domains. The more highly conserved portions of variable
domains are celled in the framework (FR) regions. The variable
domains of native heavy and light chains each comprise four FR
regions, largely adopting a .beta.-pleated-sheet configuration,
connected by three CDRs, which form loops connecting, and in some
cases forming part of, the .beta.-pleated-sheet structure. The CDRs
in each chain are held together in close proximity by the FR
regions and, with the CDRs from the other chain, contribute to the
formation of the antigen-binding site of antibodies (see, Kabat et
al. (1991) NIH Publ. No. 91-3242, Vol. I, pages 647-669). The
constant domains are not involved directly in binding an antibody
to an antigen, but exhibit various effector functions, such as Fc
receptor (FcR) binding, participation of the antibody in
antibody-dependent cellular toxicity, initiation of complement
dependent cytotoxicity, and mast cell degranulation.
[0065] The term "hypervariable region," when used herein, refers to
the amino acid residues of an antibody that are responsible for
antigen-binding. The hypervariable region comprises amino acid
residues from a "complementarily determining region" or "CDR"
(i.e., residues 24-34 (L1), 50-56 (L2), and 89-97 (L3) in the
light-chain variable domain and 31-35 (H1), 50-65 (H2), and 95-102
(H3) in the heavy-chain variable domain; Kabat et al. (1991)
Sequences of Proteins of Immunological Interest, 5th Ed. Public
Health Service, National Institute of Health, Bethesda, Md.) and/or
those residues from a "hypervariable loop" (i.e., residues 26-32
(L1), 50-52 (L2), and 91-96 (L3) in the light-chain variable domain
and (H1), 53-55 (H2), and 96-101 (H3) in the heavy chain variable
domain; Clothia and Lesk, (1987) J. Mol. Biol., 196:901-917).
"Framework" or "FR" residues are those variable domain residues
other than the hypervariable region residues, as herein deemed.
[0066] "Antibody fragments" comprise a portion of an intact
antibody, preferably the antigen-binding or variable region of the
intact antibody. Examples of antibody fragments include Fab, Fab,
F(ab')2, and Fv fragments; diabodies; linear antibodies (Zapata et
al. (1995) Protein Eng. 10:1057-1062); single-chain antibody
molecules; and multispecific antibodies formed from antibody
fragments. Papain digestion of antibodies produces two identical
antigen-binding fragments, called "Fab" fragments, each with a
single antigen-binding site, and a residual "Fc" fragment, whose
name reflects its ability to crystallize readily. Pepsin treatment
yields an F(ab')2 fragment that has two antigen-combining sites and
is still capable of cross-linking antigen.
[0067] "Fv" is the minimum antibody fragment that contains a
complete antigen recognition and binding site. This region consists
of a dimer of one heavy- and one light-chain variable domain in
tight, non-covalent association. It is in this configuration that
the three CDRs of each variable domain interact to define an
antigen-binding site on the surface of the V.sub.H-V.sub.L dimer.
Collectively, the six CDRs confer antigen-binding specificity to
the antibody. However, even a single variable domain (or half of an
Fv comprising only three CDRs specific for an antigen) has the
ability to recognize and bind antigen, although at a lower affinity
than the entire binding site.
[0068] The Fab fragment also contains the constant domain of the
light chain and the first constant domain (C.sub.H1) of the heavy
chain. Fab fragments differ from Fab' fragments by the addition of
a few residues at the carboxy terminus of the heavy chain C.sub.H1
domain including one or more cysteines from the antibody hinge
region. Fab'-SH is the designation herein for Fab' in which the
cysteine residue(s) of the constant domains bear a free thiol
group. Fab' fragments are produced by reducing the F(ab')2
fragment's heavy chain disulfide bridge. Other chemical couplings
of antibody fragments are also known.
[0069] The "light chains" of antibodies (immunoglobulins) from any
vertebrate species can be assigned to one of two clearly distinct
types, called kappa (.kappa.) and lambda (.lamda.), based on the
amino acid sequences of their constant domains.
[0070] Depending on the amino acid sequence of the constant domain
of their heavy chains, immunoglobulins can be assigned to different
classes. There are five major classes of human immunoglobulins:
IgA, IgD, IgE, IgG, and IgM, and several of these may be further
divided into subclasses (isotypes), e.g., IgG1, IgG2, IgG3, IgG4,
IgA1, and IgA2. The heavy-chain constant domains that correspond to
the different classes of immunoglobulins are called alpha, delta,
epsilon, gamma, and mu, respectively. The subunit structures and
three-dimensional configurations of different classes of
immunoglobulins are well known. Different isotypes have different
effector functions. For example, human IgG1 and IgG3 isotypes have
ADCC (antibody dependent cell-mediated cytotoxicity) activity.
[0071] The word "label" when used herein refers to a detectable
compound or composition that is conjugated directly or indirectly
to the antibody so as to generate a "labeled" antibody. The label
may be detectable by itself (e.g., radioisotope labels or
fluorescent labels) or, in the case of an enzymatic label, may
catalyze chemical alteration of a substrate compound or composition
that is detectable.
[0072] A "host cell," as used herein, refers to a microorganism or
a eukaryotic cell or cell line cultured as a unicellular entity
that can be, or has been, used as a recipient for a recombinant
vector or other transfer polynucleotides, and include the progeny
of the original cell that has been transfected. It is understood
that the progeny of a single cell may not necessarily be completely
identical in morphology or in genomic or total DNA complement as
the original parent, due to natural, accidental, or deliberate
mutation.
[0073] "Human effector cells" are leukocytes that express one or
more FcRs and perform effector functions. Preferably, the cells
express at least Fc.gamma.RIII and carry out antigen-dependent
cell-mediated cyotoxicity (ADCC) effector function. Examples of
human leukocytes that mediate ADCC include peripheral blood
mononuclear cells (PBMC), natural killer (NK) cells, monocytes,
macrophages, eosinophils, and neutrophils, with PBMCs and NK cells
being preferred. Antibodies that have ADCC activity are typically
of the IgG1 or IgG3 isotype. Note that in addition to isolating
IgG1 and IgG3 antibodies, such ADCC-mediating antibodies can be
made by engineering a variable region from a non-ADCC antibody or
variable region fragment to an IgG1 or IgG3 isotype constant
region.
[0074] The terms "Fc receptor" or "FcR" are used to describe a
receptor that binds to the Fc region of an antibody. The preferred
FcR is a native-sequence human FcR. Moreover, a preferred FcR is
one that binds an IgG antibody (a gamma receptor) and includes
receptors of the Fc.gamma.RI, Fc.gamma.RII, and Fc.gamma.RIII
subclasses, including allelic variants and alternatively spliced
forms of these receptors. Fc.gamma.RII receptors include
Fc.gamma.RIIA (an "activating receptor") and Fc.gamma.RIIB (an
"inhibiting receptor"), which have similar amino acid sequences
that differ primarily in the cytoplasmic domains thereof.
Activating receptor Fc.gamma.RIIA contains an immunoreceptor
tyrosine-based activation motif (ITAM) in its cytoplasmic domain
Inhibiting receptor Fc.gamma.RIIB contains an immunoreceptor
tyrosine-based inhibition motif (ITIM) in its cytoplasmic domain
(see Daeron (1997) Annu. Rev. Immunol. 15:203-234). FcRs are
reviewed in Ravetch and Kinet (1991) Annu. Rev. Immunol. 9:457-492;
Capel et al. (1994) Immunomethods 4:25-34; and de Haas et al.
(1995) J. Lab. Clin. Med. 126:330-341. Other FcRs, including those
to be identified in the future, are encompassed by the term "FcR"
herein. The term also includes the neonatal receptor, FcRn, which
is responsible for the transfer of maternal IgGs to the fetus
(Guyer et al. (1976) J. Immunol. 117:587 and Kim et al. (1994) J.
Immunol. 24:249).
[0075] There are a number of ways to make human antibodies. For
example, secreting cells can be immortalized by infection with the
Epstein-Barr virus (EBV). However, EBV-infected cells are difficult
to clone and usually produce only relatively low yields of
immunoglobulin (James and Bell (1987) J. Immunol. Methods
100:5-40). In the future, the immortalization of human B cells
might possibly be achieved by introducing a defined combination of
transforming genes. Such a possibility is highlighted by a recent
demonstration that the expression of the telomerase catalytic
subunit together with the SV40 large oncoprotein and an oncogenic
allele of H-ras resulted in the tumorigenic conversion of normal
human epithelial and fibroblast cells (Hahn et al. (1999) Nature
400:464-468). It is now possible to produce transgenic animals
(e.g., mice) that are capable, upon immunization, of producing a
repertoire of human antibodies in the absence of endogenous
immunoglobulin production (Jakobovits et al. (1993) Nature
362:255-258; Lonberg and Huszar (1995) Int. Rev. Immunol. 13:65-93;
Fishwild et al. (1996) Nat. Biotechnol. 14:845-851; Mendez et al.
(1997) Nat. Genet. 15:146-156; Green (1999) J. Immunol. Methods
231:11-23; Tomizuka et al. (2000) Proc. Natl. Acad. Sci. USA
97:722-727; reviewed in Little et al. (2000) Immunol. Today
21:364-370). For example, it has been described that the homozygous
deletion of the antibody heavy-chain joining region (J.sub.H) gene
in chimeric and germ-line mutant mice results in complete
inhibition of endogenous antibody production (Jakobovits et al.
(1993) Proc. Natl. Acad. Sci. USA 90:2551-2555). Transfer of the
human germ-line immunoglobulin gene array in such germ-line mutant
mice results in the production of human antibodies upon antigen
challenge (Jakobovits et al. (1993) Nature 362:255-258). Mendez et
al. (1997) (Nature Genetics 15:146-156) have generated a line of
transgenic mice that, when challenged with an antigen, generates
high affinity fully human antibodies. This was achieved by
germ-line integration of megabase human heavy-chain and light-chain
loci into mice with deletion into endogenous J.sub.H segment as
described above. These mice (XenoMouse.RTM. II technology (Abgenix;
Fremont, Calif.)) harbor 1,020 kb of human heavy-chain locus
containing approximately 66 V.sub.H genes, complete D.sub.H and
J.sub.H regions, and three different constant regions, and also
harbors 800 kb of human .kappa. locus containing 32 V.kappa. genes,
J.kappa. segments, and C.kappa. genes. The antibodies produced in
these mice closely resemble that seen in humans in all respects,
including gene rearrangement, assembly, and repertoire. The human
antibodies are preferentially expressed over endogenous antibodies
due to deletion in endogenous segment that prevents gene
rearrangement in the murine locus. Such mice may be immunized with
an antigen of particular interest.
[0076] Sera from such immunized animals may be screened for
antibody reactivity against the initial antigen. Lymphocytes may be
isolated from lymph nodes or spleen cells and may further be
selected for B cells by selecting for CD138-negative and
CD19-positive cells. In one aspect, such B cell cultures (BCCs) may
be fused to myeloma cells to generate hybridomas as detailed
above.
[0077] In another aspect, such B cell cultures may be screened
further for reactivity against the initial antigen, preferably.
Such screening includes enzyme-linked immunosorbent assay (ELISA)
with the target/antigen protein, a competition assay with known
antibodies that bind the antigen of interest, and in vitro binding
to transiently transfected CHO or other cells that express the
target antigen.
Biomarkers, Cytokine Markers, CD40-Related Factors, and Clinically
Useful Prognostic Markers for Use in the Prognostic Assays of the
Invention
[0078] In some embodiments, the methods of the present invention
comprise the use of ex vivo prognostic assays to monitor changes in
the expression level of one or more biomarkers of cell survival,
proliferation, apoptosis, and CD40 signaling pathways. The ex vivo
prognostic assays can be used alone, or in combination with other
prognostic assays, for example, prognostic assays that identify
candidate subjects having a cancer or pre-malignant condition that
would be responsive to treatment with anti-CD40 therapeutic agents
based on expression of other CD40-related factors and/or based on
the presence or absence of, or elevated or diminished expression
of, other clinically useful prognostic markers that are indicative
of poor prognosis with treatment intervention with standard
therapeutic agents having a different mode of action from that
exerted by anti-CD40 therapeutic agents. By "responsive to
treatment with an anti-CD40 therapeutic agent" is intended the
candidate subject (i.e., an individual with a cancer or
pre-malignant condition as noted herein below), when treated with
the anti-CD40 therapeutic agent, would have a positive therapeutic
response with respect to the cancer or pre-malignant condition for
which treatment is sought.
Biomarkers for Use in Ex Vivo Prognostic Assays.
[0079] Signaling pathways are characterized by protein families
that facilitate signal transduction. The term "family" when
referring to protein and nucleic acid molecules is intended to mean
two or more proteins or nucleic acid molecules having a common
structural domain or motif and having sufficient amino acid or
nucleotide sequence homology as defined herein. Such family members
can be naturally or non-naturally occurring and can be from either
the same or different species. For example, a family can contain a
first protein of human origin, as well as other, distinct proteins
of human origin or alternatively, can contain homologues of
non-human origin. Members of a family may also have common
functional characteristics.
[0080] The AKT (sometimes referred to as PKB, for protein kinase B)
family of serine/threonine kinases, is integrally involved in cell
growth, survival, and metabolism. PKB was originally identified as
a retroviral oncogene. Currently, three variants of the AKT family,
the 480-residue AKT-1, the 481-residue AKT-2, and the 479-residue
AKT-3, have been characterized. The role of the Akt genes in
malignancy is exemplified by their amplification and/or the
overexpression of the AKT proteins in a number of cancers. See, for
example, Nicholson and Anderson (2002) Cell Signal 14:381-398; Sun
et al. (2001) Cancer Res. 61:5985-5991; Cheng et al. (1997)
Oncogene 14:2793-2801; Ruggeri et al. (1998) Mol. Carcinog.
21:81-86; Liu et al. (1998) Cancer Res. 58:2973-2977; Lin et al.
(2001) Langenbecks Arch. Surg. 386:293-301). For purposes of the
present invention, members of the AKT family of proteins will be
referred to generally as AKT proteins, though it is recognized that
the methods of the present invention apply to all three forms of
AKT, i.e., AKT-1, AKT-2, and AKT-3, and variants thereof.
[0081] AKT is a growth factor-regulated serine/threonine kinase
that contains a PH (pleckstrin homology) domain. This PH domain
interacts with lipid products of phosphatidylinositol 3-kinase
(PI3K), phosphatidylinositol-3,4-biphosphate, and
phosphatidylinositol-3,4,5-triphosphate, which results in
translocation of AKT from a cell's cytosol to its plasma membrane.
This translocation is required in order to present AKT to an
upstream activation kinase, PDK1 (phosphoinositide-dependent kinase
1). A variety of survival and growth factors such as PDGF, EGF,
insulin, thrombin, and NGF are known to activate the translocation
of AKT. The activated (i.e., phosphorylated) form of AKT/PKB
protein phosphorylates numerous substrates, including GSK-3
(glycogen synthase kinase 3), eNOS (endothelial nitric oxide
synthase), FKHR 1 (forkhead transcription factor family member 1),
Bad (Bcl-2 pro-apoptotic family member), and p21 CIP (inhibitor of
cell cycle progression). These actions can result in diverse
biological effects such as suppression of apoptosis, control of
glucose metabolism, cell proliferation, transcription, translation,
cell migration, and angiogenesis. The AKT proteins have
anti-apoptotic activity that correlates with their activation when
cells become cancerous. It is believed that the phosphorylation of
AKT triggers nucleo-cytoplasmic localization of substrates involved
in cell cycle and apoptosis. This leads to a host of events
culminating in malignancy, including acquired growth signal
autonomy, insensitivity to apoptotic signals, unlimited
replication, sustained angiogenesis, tissue invasion, and
metastasis.
[0082] Activated AKT (i.e., p-AKT) promotes cell survival through
several distinct pathways that involve phosphorylation of
downstream effector molecules. First, p-AKT inhibits apoptosis by
phosphorylating the Bad component of the Bad/Bcl-xl complex.
Phosphorylated Bad binds to 14-3-3 causing dissociation of the
Bad/Bcl-xl complex and thereby freeing Bcl-xl to allow for cell
survival. Second, NF-.kappa.B, which is kept inactive in the
cytoplasm through association with inhibitory proteins of the I
kappa-B (I.kappa.-B) family, can be activated by interaction with
NF-.kappa.B inducing kinase (NIK) or it can be activated by the AKT
signaling pathway. In this manner, activated AKT (i.e., p-AKT)
activates an NF-.kappa.B inhibitory molecule of the I.kappa.-B
family (for example, I.kappa.-B.alpha.), via intermediate
phosphorylation of the I.kappa.-B kinase multiprotein complex
(IKK-.alpha./.beta.); activation of an I.kappa.-B leads to its
degradation and release of previously bound NF-.kappa.B, which
leads to activation of this transcription factor. The active form
of NF-.kappa..beta. can then translocate into the nucleus and
regulate the expression of hundreds of genes to oppose apoptosis.
Another means by which AKT promotes cell survival and opposes
apoptosis is by phosphorylation of the protease Caspase 9 or
forkhead transcription factors such as FKHRL1.
[0083] In some embodiments, the methods of the present invention to
identify subjects having a cancer or pre-malignant condition that
would benefit from treatment with an anti-CD40 therapeutic agent
that blocks or interferes with CD40L-mediated CD40 signaling
comprise the use of an ex vivo prognostic assay to monitor the
effects of anti-CD40 therapeutic agents on CD40 signaling through
the AKT and NF-.kappa.B signaling pathways. In this manner, a test
biological sample collected from a candidate subject is contacted
with the anti-CD40 therapeutic agent of interest for sufficient
time to allow for modulation of CD40L-mediated CD40 signaling as
noted herein below, and that sample is then assayed for changes in
the expression level of at least one CD40 signaling biomarker
selected from the group consisting of phosphorylated AKT (p-AKT),
phosphorylated PI3K (p-PI3K), phosphorylated PDK1 (p-PDK1),
phosphorylated IKK-.alpha./.beta. (p-IKK-.alpha./.beta.),
phosphorylated I.kappa.-B (p-I.kappa.-B; for example,
p-I.kappa.-B.alpha.), and activated NF-.kappa.B. Detection of
decreased expression levels of these phosphorylated biomarkers in a
test biological sample comprising CD40L-stimulated CD40-expressing
neoplastic cells in response to incubation with an anti-CD40
therapeutic agent relative to that observed for a control
biological sample is indicative of downregulation of CD40L-mediated
CD40 signaling, and therefore indicative of a positive treatment
outcome with that anti-CD40 therapeutic agent. In some embodiments,
the level of expression of any given biomarker of CD40 signaling
through the AKT and NF-.kappa.B signaling pathways is reduced by at
least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%,
60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to that
detected in the control biological sample.
[0084] CD40/CD40L interaction also leads to activation of the MAPK
signaling cascades including the MEK/ERK signaling pathway, the
MEK/p38 signaling pathway, and the MEKK/JNKK/JNK signaling pathway.
All MAPK pathways operate through sequential phosphorylation events
to phosphorylate transcription factors and regulate gene
expression. They can also phosphorylate cytosolic targets to
regulate intracellular events. These cascades are implicated in the
regulation of cellular proliferation, differentiaion, development,
cell cycle, and transmission of oncogenic signals. Of particular
interest to the methods of the present invention are activation of
the MEK/ERK and MEK/p38 signaling pathways.
[0085] The MAP kinases (also referred to as extracellular
signal-regulated protein kinases, or ERKs) are the terminal enzymes
in a three-kinase cascade, where each enzyme phosphorylates and
thereby activates the next member in the sequence. Each MAPK module
consists of three protein kinases: a MAPK kinase kinase (or MEKK)
that activates a MAPK kinase (or MEK), which in turn activates a
MAPK/ERK enzyme. The MEKKs are serine/threonine-specific protein
kinases that dually phosphorylate, and thereby activate, one or
more of the MEK enzymes on Ser or Thr residues (Ser-X-X-X-Ser/Thr)
within the catalytic core. The MEKs are
Serine/Threonine/Tyrosine-specific protein kinases that activate
MAPKs by phosphorylating both Thr and Tyr within the TXY consensus
sequence of the MAPKs. This dual phosphorylation is required for
activation. ERK1 (p44), ERK2 (p42), p38/HOG, and JNK/SAPK represent
related yet distinct terminal MAPKs in parallel pathways.
[0086] In some embodiments, the methods of the invention to
identify subjects having a cancer or pre-malignant condition that
would benefit from treatment with an anti-CD40 therapeutic agent
comprise the use of an ex vivo prognostic assay to monitor the
effects of anti-CD40 therapeutic agents on CD40 signaling through
the MEK/ERK and MEK/p38 pathways. In this manner, a test biological
sample collected from a candidate subject is contacted with the
therapeutic agent of interest for sufficient time to allow for
modulation of CD40L-mediated CD40 signaling as noted herein below,
and that sample is then assayed for changes in the expression level
of at least one CD40 signaling biomarker selected from the group
consisting of phosphorylated MEK (p-MEK), for example, p-MEK1,
p-MEK2, p-MEK3, and p-MEK6, phosphorylated ERK (p-ERK), for
example, p-ERK1 or p-ERK2, and phosphorylated p38 (p-p38).
Detection of decreased expression levels of these phosphorylated
biomarkers in a biological sample comprising CD40L-stimulated
CD40-expressing neoplastic cells in response to incubation with an
anti-CD40 therapeutic agent relative to that observed for a control
biological sample is indicative of downregulation of CD40L-mediated
CD40 signaling, and therefore indicative of a positive treatment
outcome with that anti-CD40 therapeutic agent. In some embodiments,
the level of expression of any given biomarker of CD40 signaling
through the MEK/ERK and MEK/p38 pathways is reduced by at least
about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%,
65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to that
detected in the control biological sample.
[0087] Responsiveness of a candidate subject to therapy with an
anti-CD40 therapeutic agent that blocks or interferes with
CD40L-mediated CD40 signaling can also be assessed by monitoring ex
vivo effects of the therapeutic agent on expression level of any of
the cytokine markers of CD40L-mediated CD40 signaling. Engagement
of CD40 by its natural ligand in vivo results in upregulation of a
number of proinflammatory cytokines depending upon the type of
CD40-expressing cell. Ex vivo CD40L stimulation of normal B cells
results in upregulation of production of several cytokines,
including, but not limited to, vascular endothelial growth factor
(VEGF), interleukin (IL)-6, IL-8, IL-10, tumor necrosis
factor-.alpha. (TNF-.alpha.), monocyte chemoattractant protein-1
(MCP-1), and macrophage inflammatory protein-1.beta. (MIP-1.beta.),
while ex vivo CD40L stimulation of neoplastic B-cells, for example
chronic lyphocytic leukemia cells, results in upregulation of
production of VEGF, IL-8, IL-10, granulocyte monocyte
colony-stimulating factor (GM-CSF), TNF-.alpha., and MCP-1, as
noted herein below.
[0088] In accordance with the screening methods of the present
invention, a test biological sample collected from a candidate
subject is contacted with the anti-CD40 therapeutic agent of
interest for sufficient time to allow for modulation of
CD40L-mediated CD40 signaling as noted herein below, and that
sample is then assayed for changes in the expression level of at
least one cytokine marker selected from the group consisting of
VEGF, IL-6, IL-8, IL-10, GM-CSF, TNF-.alpha., MCP-1, and
MIP-1.beta.. Level of expression of cytokines can be accomplished
using any detection method known in the art as noted herein below.
Detection of decreased expression levels of these cytokine markers
in a test biological sample comprising CD40L-stimulated
CD40-expressing neoplastic cells in response to incubation with an
anti-CD40 therapeutic agent relative to that observed for a control
biological sample is indicative of downregulation of CD40L-mediated
CD40 signaling, and therefore indicative of a positive treatment
outcome with that anti-CD40 therapeutic agent. In some embodiments,
the level of expression of any given cytokine is reduced by at
least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%,
60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to that
detected in the control biological sample.
[0089] The AKT, NF-.kappa.B, and MAPK signaling pathways are all
involved in cell proliferation and survival. In the immune system,
apoptosis plays an important role in selection of T cell
repertoire, deletion of self-reactive T and B lymphocytes, removal
of peripheral effector T cells following termination of an immune
response, regulation of immunological memory, and in the
cytotoxicity of target cells by CTL and NK cells. For malignancies
of B-cell lineage, aberrant regulation of the balance between B
cell proliferation and apoptosis results in uncontrolled
proliferation of neoplastic B cells. Therapeutic agents that can
block CD40 survival signaling on neoplastic B cells and promote
cellular apoptotic processes would be beneficial in treating
pre-malignant conditions and malignancies of B-cell lineage.
[0090] Thus, in addition to monitoring CD40 signaling on neoplastic
cells, the methods of the present invention to identify subjects
having a cancer or pre-malignant condition that would benefit from
treatment with an anti-CD40 therapeutic agent comprise the use of
ex vivo prognostic assays that monitor the effects of anti-CD40
therapeutic agents on expression of one or more biomarkers of
apoptosis, particularly cellular pro-apoptotic proteins, including,
but not limited to, cleaved caspase proteins and cleaved poly
ADP-ribose polymerase (PARP). Additional biomarkers of apoptosis
that can be assayed include, but are not limited to, alterations in
the plasma membrane at the cell surface, for example, presence of
cell surface phosphotidylserine (PS), and cleavage or fragmentation
of genomic DNA. PS normally is located exclusively at the inner
side of the plasma membrance, but is translocated to the external
surface of the cell during the early phases of apoptotic cell death
during which the cell membrane remains intact. Presence of cell
surface PS and genomic DNA fragmentation can be detected, for
example, by annexin V staining and TUNEL staining, respectively, as
noted herein below. Detection of increased expression levels of one
or more of these biomarkers of apoptosis in a test biological
sample comprising CD40L-stimulated CD40-expressing neoplastic cells
in response to incubation with an anti-CD40 therapeutic agent
relative to that observed in a control biological sample is
indicative of a positive treatment outcome with that anti-CD40
therapeutic agent. In some embodiments, the level of expression of
any given biomarker of apoptosis is increased by at least about 5%,
10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%,
75%, 80%, 85%, 90%, 95%, 100%, 125%, 150%, 200%, 250%, 300%, or
higher relative to that detected in the control biological
sample.
[0091] Alternatively, or in combination with the ex vivo assays
described above, the methods of the present invention comprise the
use of ex vivo prognostic assays that monitor the effects of
anti-CD40 therapeutic agents on expression of one or more proteins
that are biomarkers of cell proliferation and/or cell survival,
including, but not limited to, an anti-apoptotic protein that is a
member of the Bcl-2 family, an IAP apoptosis inhibitor protein, and
TNF receptor-associated factor-1 (TRAF-1). Detection of decreased
expression levels of these biomarkers of cell proliferation and/or
cell survival in a test biological sample comprising
CD40-expressing neoplastic cells in response to incubation with an
anti-CD40 therapeutic agent relative to that observed in a control
biological sample is indicative of a positive treatment outcome
with that anti-CD40 therapeutic agent. In some embodiments, the
level of expression of any given biomarker of cell proliferation
and/or cell survival is reduced by at least about 5%, 10%, 15%,
20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%,
85%, 90%, 95%, or 100% relative to that detected in the control
biological sample.
[0092] Members of the caspase family of proteins are major
effectors of cellular apoptosis. The caspases are cysteine
proteases that exist within the cell as inactive pro-forms or
so-called "zymogens." The zymogens are cleaved to form active
enzymes following the induction of apoptosis either via the death
receptor-mediated pathway or the mitochondrial pathway of
apoptosis. See, for example, Gupta et al. (2003) Intl. J. Oncol.
22:15-20; herein incorporated by reference in its entirety.
Depending upon the apoptotic pathway, different caspases initiate
the apoptotic process, with Caspase-8 and -10 initiating the death
receptor pathway, and Caspase-9 initiating the mitochondrial
pathway. Active initiator caspases then activate (i.e., cleave)
effector caspases, for example, Caspase-3, -6, and -7, to induce
apopotosis. These effector caspases cleave key cellular proteins
that lead to the typical morphological changes observed in cells
undergoing apoptosis.
[0093] Thus, in some embodiments, the methods of the present
invention to identify subjects having a cancer or pre-malignant
condition that would benefit from treatment with an anti-CD40
therapeutic agent comprise the use of ex vivo prognostic assays to
monitor the proteolysis of specific cellular proteins associated
with apoptosis. For example, poly(ADP-ribose) polymerase (PARP-1)
is specifically cleaved during apoptosis. PARP-1 is a DNA-binding
protein that catalyzes the addition of poly(ADP-ribose) chains to
some nuclear proteins and is thought to play a critical role in DNA
damage repair. PARP-1 is rapidly activated during cellular
stresses, such as heat shock, ionizing radiation, exposure to
carcinogens, and treatment with chemotherapy agents (Scovassi and
Poirier (1999) Mol. Cell. Biochem. 199:125-137; Wyllie (1997) Eur.
J. Cell Biol. 73:189-197). During apoptosis, activated (i.e.,
cleaved) caspase-3 in turn cleaves PARP-1; in fact, the resolution
of the 89 kDa and 24 kDa proteolytic fragments is accepted as a
hallmarks of apoptosis (Scovassi and Poirier (1999) supra; Wyllie
et al. (1997) supra. The ex vivo prognostic assays described herein
monitor changes in the level of one or more cleaved Caspase
proteins, for example, cleaved Caspase-3, cleaved Caspase-7, and
cleaved Caspase-9, and optionally, the level of cleaved PARP-1,
cell surface PS, and/or genomic DNA fragmentation, in a test
biological sample obtained from a candidate subject in response to
anti-CD40 therapeutic agents that modulate CD40L-mediated CD40
signaling and/or modulate ADCC. Elevated levels of apoptotic
biomarkers within a biological sample can be detected using any
method known to those of skill in the art, including those
described herein below.
[0094] Biomarkers of cell survival and proliferation include, but
are not limited to, anti-apoptotic proteins that are members of the
Bcl-2 family of proteins. The Bcl-2 family of proteins, which
comprises at least 16 members, participates in the regulation of
cellular apoptosis. Some of the family members are anti-apoptotic,
for example, Bcl-2, Bcl-xl, Mcl-1, Bcl-w, and Al, and thus
biomarkers of cell survival, and others are pro-apoptotic (for
example, Bid, Bim, Bik, Bmf, Bad, Hrk, BNIP3, Bax, Bak, and Bok),
and thus biomarkers of apoptotic activity. Bcl-2 family members
have been suggested to act through many different mechanisms,
including pore formation in the outer mitochondrial membrane,
through which cytochrome c (Cyt c) and other intermembrane proteins
can escape; and heterodimerization between pro- and anti-apoptotic
family members.
[0095] Effects of anti-CD40 therapeutic agents on CD40 signaling
and modulation of apoptosis can be assessed with the ex vivo
prognostic assays described herein to monitor one or more of these
biomarkers of cell survival/apoptosis. Biomarkers of cell survival
that are of particular interest include, but are not limited to,
the anti-apoptotic proteins Bcl-xl and Mcl-1.
[0096] The bcl-2 gene, which encodes the mitochondrial membrane
protein Bcl-2, was first identified in B-cell lymphomas (Tsujimoto
et al. (1984) Science 226:1097) where the causal genetic lesion has
been characterised as a chromosomal translocation (t(14:18)) that
places the bcl-2 gene under the control of the immunoglobulin
promoter. The resulting overexpression of Bcl-2 retards the normal
course of apoptotic cell death that otherwise maintains B-cell
homeostasis, resulting in B-cell accumulation and follicular
lymphoma (Adams and Cory, 1998; Cory (1994) Philos. Trans. R. Soc.
Lond. B. Biol. Sci. 345:289). This observation showed that cancers
do not strictly arise from unrestrained cell proliferation, but
could also be due to insufficient apoptotic turnover. In addition
to follicular lymphomas, Bcl-2 levels are elevated in a broad range
of other human cancers, indicating that this molecule may have a
role in raising the apoptotic threshold in a broad spectrum of
cancerous disorders. Bcl-2 can exist as a homodimer or can form a
heterodimer with bax. As a homodimer, bax functions to induce
apoptosis. However, the formation of a bax-Bcl-2 complex blocks
apoptosis. Bcl-2 expression may also play a role in the development
of drug resistance. The expression of Bcl-2 is negatively regulated
by p53. Overexpression of Bcl-2 is not present in preneoplastic
lesions suggesting that changes in Bcl-2 occur relatively late in
tumor progression.
[0097] Several genes with homology to the bcl-2 gene have
subsequently been characterized, including the following: al, which
encodes the 80-amino acid Al protein that is rapidly induced in
macrophages in response to GM-CSF or LPS (Lin et al. (1993) J.
Immunol. 151: 1979-1988); mcl-1, an early response gene in myeloid
cell lines that undergo macrophage differentiation (Kozopas et al.
(1993) Proc. Natl. Acad. Sci. USA 90:3516-3520); and bak, a bcl-2
homologue that may enhance apoptosis (Chittenden et al. (1995)
Nature 374:733; Kiefer et al. (1995) Nature 374:736). Other
proteins which interact with and/or are structurally related to the
bcl-2 gene product have also been identified, such as for example,
Bcl-xl, and Bcl-xs (Boise et al. (1993) Cell 74:597); Ced-9 (Vaux
et al. (1992) Science 258:1955).
[0098] The bcl-x gene product, Bcl-x, which is closely related to
the Bcl-2 protein, also protects cells from apoptosis. Alternative
splicing of human Bcl-x may result in at least two distinct Bcl-x
mRNA species, Bcl-xl and Bcl-xs. The predominant protein product
(233 amino acids) of the larger bcl-x mRNA, Bcl-xl, inhibits cell
death upon growth factor withdrawal (Boise et al. (1993) Cell
74:597-608) and its transgenic expression alters thymocyte
maturation leading to increased numbers of mature thymocytes (Chao
et al. (1995) J. Exp. Med. 182:821-828; Grillot et al. (1995) J.
Exp. Med. 182:1973-1983).
[0099] The myeloid cell leukemia associated gene mcl-1 encodes a
protein, Mcl-1, that is expressed early during the programming of
differentiation in myeloid cell leukemia (see, for example, U.S.
Patent Application Publication No. 20020086321). The carboxyl
portion of Mcl-1 shares homology to Bcl-2. Like other members of
the Bcl-2 family, Mcl-1 is characterized by an association with the
programming of transitions in cell fate, such as from viability to
death or from proliferation to differentiation. High expression of
the mcl-1 gene reportedly is associated with poor outcome in
non-Hodgkin's lymphoma (Kuramoto et al. (2002) Br. J. Haematol.
116:158-161). Further, a relatively high level of mcl-1 gene
expression reportedly correlates with high-grade morphology, a high
proliferative state, and p53 overexpression in mantle cell lymphoma
(MCL) (Khoury et al. (2003) J. Pathol. 199:90-97).
[0100] In addition to members of the Bcl-2 family, cell survival
biomarkers for use in the methods of the present invention include
members of the gene family of inhibitors of apoptosis related to
the baculovirus IAP gene (Bimbaum et al. (1994) J. Virol.
68:2521-2528; Clem et al. (1994) Mol. Cell. Biol. 14:5212-5222;
Duckett et al. (1996) EMBO J. (1996) 15:2685-2694; Hay et al.
(1995) Cell 83:1253-1262; Liston et al. (1996) Nature 379:349-353;
Rothe et al. (1995) Cell 83:1243-1252; Roy et al. (1995) Cell
80:167-178). At least eight human IAPs have been identified
(Salvesen and Duckett (2002) Nat. Rev. Mol. Cell. Biol.
3:401-410).
[0101] The IAPs are highly conserved evolutionarily; they share a
similar architecture organized in one to three approximately 70
amino acid amino terminus Cys/His baculovirus IAP repeats (BIR) and
by a carboxy terminus zinc-binding domain, designated RING finger.
The IAP family proteins are recognized as having potentially
important roles in the regulation of apoptosis and tumorigenesis
(Deveraux and Reed (1999) Genes Dev. 13:239-252; Tamm et al. (2000)
Clin. Cancer Res. 6:1796-1803). The expression of survivin, one of
the IAP family proteins, is significantly increased in several
human cancers (Hoffman et al. (2002) J. Biol. Chem. 277:3247-3257).
Also, c-IAP2 has been suggested as a causative gene of
mucosa-associated lymphoid tissue lymphoma and to have a role in
carcinogenesis and tumor progression (Dierlamm et al. (1999) Blood
93:3601-3609).
[0102] The IAPs suppress cell death by inhibiting upstream and
terminal caspases (see, for example, Thompson (1995) Science
267:1456). The active (i.e., cleaved) forms of Caspase-3 and -7 are
directly inhibited by XIAP, c-IAP1, and c-IAP2 (see, for example,
Roy et al. (1997), supra), which can also prevent the proteolytic
processing of pro-Caspase-3, -6, and -7 by blocking the cytochrome
c-induced activation of pro-Caspase-9 (Deveraux et al. (1998) EMBO
J. 17:2215-2223). Therapeutic and diagnostic uses of nucleic acids
that encode various inhibitors of apoptosis relating to a member of
the IAP family have been described in the patent literature. See,
for example, International Patent Applications No. WO 97/06255, WO
97/26331, and WO 97/32601. Examples of IAP proteins that can be
used as biomarkers of cell survival include, but are not limited
to, XIAP, cIAP1, cIAP2, and survivin.
[0103] XIAP is the most widely expressed and most potent inhibitor
of caspases (see, for example, Takahasi et al. (1998) J. Biol.
Chem. 273:7787; Reed (1994) J. Cell Biol.
[0104] 124:1). Expression of this IAP is reportedly elevated in
certain cancers and cancer cell lines (Kornblau et al. (1999) Clin
Cancer Res. 5:1758; Kitada et al. (1998) Blood 91:3379; Tamm et al.
(2000) Clin. Cancer Res. 6:1796-1803). Downregulation of XIAP has
been shown to induce apoptosis in chemoresistant human ovarian
cancer cells (Altman et al. (1994) J. Natl. Cancer Inst.
86:829).
[0105] Survivin is an approximately 16.5 kDa cytoplasmic protein
(see, for example, U.S. Patent Application Publication No.
20030100525) containing a single BIR, and a highly charged
carboxyl-terminus coiled-coil region instead of a RING finger,
which inhibits apoptosis induced by growth factor (IL-3) withdrawal
when transferred in B cell precursors (Ambrosini et al. (1997)
Nature Med. 3:917-921). At variance with Bcl-2 or other IAP
proteins, survivin is undetectable in adult tissues, but becomes
prominently expressed in all the most common human cancers of lung,
colon, breast, pancreas, and prostate, and in about 50% of
high-grade non-Hodgkin's lymphomas, in vivo. Survivin reportedly is
negatively regulated by wild-type p53. Overexpression of exogenous
survivin protein rescues cells from p53-induced apoptosis in a
dose-dependent manner, suggesting that loss of survivin mediates,
at least, in part the p53-dependent apoptotic pathway (Mirza et al.
(2002) Oncogene 21:2613-2622).
[0106] Another representative biomarker of cell survival for use in
the methods of the invention is TRAF-1. The TRAF family members
bind to the cytoplasmic domain of CD40 and mediate activation of
multiple signaling pathways that regulate B-cell survival,
proliferation, differentiation, isotype switching, development of
the germinal center, and the humoral memory response (see, for
example, Pullen et al. (1999) J. Biol. Chem. 274:14246-14254). It
has been reported that activation of the CD40 receptor can result
in transcription of the TRAF-1 gene (Schwenzer et al. (1999) J.
Biol. Chem. 274(27):19368-19374). The increase in TRAF-1 gene
expression as a consequence of CD40 receptor activation may be
differentially regulated in normal B cells and chronic lymphocytic
leukemia (CLL) cells (Gricks et al. (2004) Blood
104(13):4002-4009). Thus while effects on TRAF-1 gene expression
may or may not be indicative of CD40 activity in normal B cells,
changes in TRAF-1 gene expression in response to CD40 receptor
activation in neoplastic hematological cells may be predictive of
drug efficacy, thereby providing a suitable biomarker for assessing
and/or monitoring the effects of anti-CD40 therapeutics on
CD40L-mediated CD40 signaling and modulation of cell
survival/apoptosis. Changes in TRAF-1 expression can be easily
detected at either the mRNA level by techniques such as Northern
blot or quantitative RT-PCR or the protein level, for example, by
Western blot, as noted herein below.
[0107] The foregoing biomarkers of cell survival can be monitored
in the ex vivo prognostic assays described herein in any
combination, including one or all of these biomarkers, as well as
in combination with other biomarkers of cellular proliferation.
Thus in one embodiment, the ex vivo prognostic assays described
herein are also used to monitor in a test biological sample from a
candidate subject the expression of the cell proliferation
biomarker Ki67.
[0108] Ki67 is a cell cycle related nuclear protein that is present
in the nuclei of cells in the G1, S, M and G2 phases of dividing
cells, but not in the G0 phase of quiescent cells (Gerdes et al.
(1984) J. Immunol. 133, 1710-1715). For these reason, it is used as
a cell proliferation marker. It has also been used to stratify good
and poor prognostic categories in invasive breast cancer (Tan et
al. (2005) Mod. Pathol.
[0109] 18:374-81) and pulmonary adenocarcinoma (Haga et al. (2003)
Ann. Thorac. Surg. 75:1727-32). High expression of Ki67 is also
associated with poor prognosis in ovarian cancer (Henriksen et al.
(1994) Gynecol. Oncol. 53:301-6; Henzen-Logmans et al. (1994) Int.
J. Cancer 57:468-72; Wong and Tattersall (1989) Br. J. Obstet.
Gynaecol. 96:720-4). Additionally, antisense suppression of Ki67
protein expression has been shown to prevent cell proliferation
(Schluter et al. (1993) J. Cell Biol. 123:513-522).
[0110] Thus the biomarkers that are to be monitored in the ex vivo
prognostic assays of the present invention include the cell
survival and apoptotic proteins described above, and proteins
involved in the CD40 signaling pathways as noted herein above.
Monitoring can be at the protein or nucleic acid level. Thus, the
biomarkers include these proteins and the genes encoding these
proteins. Where detection is at the protein level, the biomarker
protein comprises the full-length polypeptide or any detectable
fragment thereof, and can include variants of these protein
sequences. Similarly, where detection is at the nucleotide level,
the biomarker nucleic acid includes DNA comprising the full-length
coding sequence, a fragment of the full-length coding sequence,
variants of these sequences, for example naturally occurring
variants or splice-variants, or the complement of such a sequence.
Biomarker nucleic acids also include RNA, for example, mRNA,
comprising the full-length sequence encoding the biomarker protein
of interest, a fragment of the full-length RNA sequence of
interest, or variants of these sequences. Biomarker proteins and
biomarker nucleic acids also include variants of these sequences.
By "fragment" is intended a portion of the polynucleotide or a
portion of the amino acid sequence and hence protein encoded
thereby. Polynucleotides that are fragments of a biomarker
nucleotide sequence generally comprise at least 10, 15, 20, 50, 75,
100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700,
800, 900, 1,000, 1,100, 1,200, 1,300, or 1,400 contiguous
nucleotides, or up to the number of nucleotides present in a
full-length biomarker polynucleotide disclosed herein. A fragment
of a biomarker polynucleotide will generally encode at least 15,
25, 30, 50, 100, 150, 200, or 250 contiguous amino acids, or up to
the total number of amino acids present in a full-length biomarker
protein of the invention. "Variant" is intended to mean
substantially similar sequences. Generally, variants of a
particular biomarker of the invention will have at least about 40%,
45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,
94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that
biomarker as determined by sequence alignment programs known in the
art. The protein and corresponding coding sequence for each of
these markers is known in the art. See Table 6 in Example 5 herein
below.
CD40-Related Factors and Clinically Useful Prognostic Markers for
Use in Other Prognostic Assays.
[0111] In accordance with the methods of the present invention,
individuals or subpopulations of patients having a cancer or
pre-malignant condition that would benefit from treatment with
anti-CD40 therapeutic agents can also be identified using
prognostic assays that look for the presence or absence of, or
elevated or diminished levels of, one or more CD40-related factors.
Subjects identified as being responsive to treatment with an
anti-CD40 therapeutic agent on the basis of these CD40-related
factors can be treated with the anti-CD40 therapeutic agent.
Alternatively, they can be further screened for potential benefit
from treatment with anti-CD40 therapeutic agents using the ex vivo
prognostic assays described herein, for example, to identify
whether the cancer or pre-malignant condition would be more
responsive to treatment with an anti-CD40 therapeutic agent that
blocks CD40L-mediated CD40 signaling or which modulates ADCC
activity, or which has both of these modes of action.
[0112] CD40-related factors of interest include, but are not
limited to, expression level of cell surface CD40 antigen,
expression level of cell surface CD40L, circulating levels of
soluble CD40 (sCD40), and circulating levels of soluble CD40L
(sCD40L). In this manner, a biological sample collected from a
candidate subject is analyzed for expression level of at least one
of these CD40-related factors. The expression level of these
CD40-related factors may be used as prognostic markers for CLL and
other cancers of B-cell lineage. They may be useful as diagnostics
of subjects who would or would not respond to anti-CD40 therapeutic
agents.
[0113] Any method known in the art can be used for analysis of
these markers. Circulating levels of ssCD40 or sCD40L, for example,
in a blood sample obtained from a candidate subject, can be
measured, for example, by ELISA, radioimmunoassay (RIA),
electrochemiluminescence (ECL), Western blot, multiplexing
technologies, or other similar methods. Cell surface expression of
CD40 or CD40L can be measured, for example, by flow cytometry,
immunohistochemistry, Western Blot, immunoprecipitation, magnetic
bead selection, and quantification of cells expressing either of
these cell surface markers. CD40 and CD40L RNA expression levels
could be measured by RT-PCR, Qt-PCR, microarray, Northern blot, or
other similar technologies. The sequences for the CD40 antigen,
CD40L, and soluble CD40L are known in the art. See, for example,
Table 7 in Example 5 herein below. In some embodiments, the sCD40
is isolated and sequenced to ascertain a distinction between sCD40
that is secreted by the CD40-expressing neoplastic cells versus
sCD40 that is proteolytically cleaved from the surface of these
cells. Expression level of secreted sCD40 and/or proteolytically
cleaved sCD40 can be correlated to disease state and/or to
responsiveness of the disease to treatment with an anti-CD40
therapeutic agent of interest.
[0114] In other embodiments of the invention, subpopulations of
patients having a cancer or pre-malignant condition that would
benefit from treatment with an anti-CD40 therapeutic agent are
identified by screening candidate subjects for one or more
clinically useful prognostic markers known in the art. Any
clinically useful prognostic marker known to those of skill in the
art can be used. In some embodiments, the subpopulation includes
patients having chronic lymphocytic leukemia (CLL), and the
clinically useful prognostic markers of particular interest
include, but are not limited to, ZAP-70, CD38, .beta.2
microglobulin, and cytogenetic markers, for example, p53 mutational
status, ATM mutational status, chromosome deletions, such as the
chromosome 17p deletion and the chromosome 11q deletion, all of
which are clinically useful prognostic markers for this disease.
Thus, in one embodiment, the subpopulation of candidate subjects
represents patients with CLL for whom current therapies of
treatment are not curative, but for whom therapy with an anti-CD40
therapeutic agent would be beneficial.
[0115] ZAP-70 is a tyrosine kinase that associates with the zeta
subunit of the T cell antigen receptor (TCR) and plays a pivotal
role in T cell activation and development (Chan et al. (1992) Cell
71:649-662). ZAP-70 undergoes tyrosine phosphorylation and is
essential in mediating signal transduction following TCR
stimulation.
[0116] Overexpression or constitutive activation of tyrosine
kinases has been demonstrated to be involved in a number of
malignancies including leukemias and several types of solid tumors.
For example, increased ZAP-70 RNA expression levels are a
prognostic marker of chronic lymphocytic leukemia (CLL) (Rosenwald
et al. (2001) J. Exp. Med. 194:1639-1647). ZAP-70 is expressed in
T-cells and natural killer cells, but is not known to be expressed
in normal B-cells. However, ZAP-70 is expressed at high levels in
the B-cells of chronic lymphocytic leukemia/small lymphocytic
lymphoma (CLL/SLL) patients, and more particularly in the subset of
CLL patients who tend to have the more aggressive clinical course
that is found in CLL/SLL patients with unmutated Ig genes (Wiestner
et al. (2003) Blood 101: 4944-4951; U.S. Patent Application
Publication No. 20030203416). Because of the correlation between
ZAP-70 expression levels and Ig gene mutation status, ZAP-70 can be
used as a prognostic indicator to identify those patients likely to
have severe disease (high ZAP-70, unmutated Ig genes), and who are
therefore candidates for aggressive therapy.
[0117] CD38 is a signal transduction molecule as well as an
ectoenzyme catalyzing the synthesis and degradation of cyclic ADP
ribose (cADPR). CD38 expression is present at high levels in bone
marrow precursor B cells, is down-regulated in resting normal B
cells, and then is re-expressed in terminally differentiated plasma
cells (Campana et al. (2000) Chem. Immunol. 75:169-188). CD38 is a
reliable prognostic indicator in B-CLL, with the expression of CD38
generally indicating a less favorable outcome (D'Arena et al.
(2001) Leuk. Lymphoma 42:109; Del Poeta et al. (2001) Blood
98:2633; Dung et al. (2002) Leukemia 16:30; Ibrahim et al. (2001)
Blood 98:181; Deaglio et al. (2003) Blood 102:2146-2155). The
unfavorable clinical indications that CD38 expression has been
associated with include an advanced stage of disease, poor
responsiveness to chemotherapy, a shorter time before initial
treatment is required, and a shorter survival time (Deaglio et al.
(2003) Blood 102:2146-2155). Initially, a strong correlation
between CD38 expression and IgV gene mutation was observed, with
patients having unmutated V genes displaying higher percentages of
CD38.sup.+ B-CLL cells than those with mutated V genes (Damle et
al. (1999) Blood 94:1840-1847). However, subsequent studies have
indicated that CD38 expression does not always correlate with the
rearrangement of the IgV genes (Hamblin et al. (2002) Blood
99:1023; Thunberg et al. (2001) Blood 97:1892).
[0118] p53 is a nuclear phosphoprotein that acts as a tumor
suppressor. Wild-type p53 is involved in regulating cell growth and
division. p53 binds to DNA, stimulating the production of a protein
(p21) that interacts with a cell division-stimulating protein
(cdk2). When p21 is bound to cdk2, the cell is blocked from
entering the next stage of cell division. Mutant p53 is incapable
of binding DNA effectively, thus preventing p21 from acting as the
stop signal for cell division, resulting in uncontrolled cell
division, and tumor formation. p53 also regulates the induction of
programmed cell death (apoptosis) in response to DNA damage, cell
stress or the aberrant expression of some oncogenes. Expression of
wild type p53 in some cancer cell lines has been shown to restore
growth suppression control (Casey et al. (1991) Oncogene
6:1791-1797; Takahashi et al. (1992) Cancer Res. 52:734-736).
Mutations in p53 are found in most tumor types, including tumors of
the colon, breast, lung, ovary, bladder, and many other organs. p53
mutations have been found to be associated with Burkitt's lymphoma,
L3-type B-cell acute lymphoblastic leukemia, B-cell chronic
lymphocytic leukemia (Gaidano et al. (1991) Proc. Natl. Acad. Sci.
U.S.A. 88:5413-5417). p53 abnormalities have also been found
associated with B-cell prolymphocytic leukemia (Lens et al. (1997)
Blood 89:2015-2023). The gene for p53 is located on the short arm
of chromosome 17 at 17p13.105-p12.
[0119] .beta.2-microglobulin is an extracellular protein that is
noncovalently associated with the .alpha. chain of the class I
major histocompatibility complex (MHC). It is detectable in the
serum, and is an adverse prognostic indicator in CLL (Keating et
al. (1998) Blood 86:606a) and Hodgkin's lymphoma (Chronowski et al.
(2002) Cancer 95:2534-2538). It is clinically used for
lymphoproliferative diseases including leukemia, lymphoma, and
multiple myeloma, where serum .beta.2-microglobulin levels are
related to tumor cell load, prognosis, and disease activity
(Bataille et al. (1983) Br. J. Haematol. 55:439-447; Aviles et al.
(1992) Rev. Invest. Clin. 44:215-220). .beta.2 microglobulin is
also useful in staging myeloma patients (Pasqualetti et al. (1991)
Eur. J. Cancer 27:1123-1126).
[0120] Cytogenetic aberrations may also be used as markers to
predict poor response to current cancer therapies. Chromosome
abnormalities are found in a large percentage of CLL patients and
are helpful in predicting the course of CLL. For example, a 17p
deletion is indicative of aggressive disease progression. In
addition, CLL patients with a chromosome 17p deletion or mutation
in p53, or both, are known to respond poorly to chemotherapeutics
and rituximab. Allelic loss on chromosome 17p may be also be a
useful prognostic marker in colorectal cancer, where patients with
a 17p deletion are associated with an increased tendency of disease
dissemination in colorectal cancer (Khine et al. (1994) Cancer
73:28-35).
[0121] Deletions of the long arm of chromosome 11 (11q) are one of
the most frequent structural chromosome aberrations in various
types of lymphoproliferative disorders. CLL patients with
chromosome 11q deletion and possibly ATM mutations have a poor
survival compared to patients without either this defect or the 17p
deletion. Furthermore, an 11q deletion is often accompanied by
extensive lymph node involvement (Dohner et al. (1997) Blood
89:2516-2522). This deletion also identifies patients who are at
high risk for disease persistence after high-dose therapy and
autologous transplantation.
[0122] The ataxia telangiectasia mutated (ATM) gene is a tumor
suppressor gene that is involved in cell cycle arrest, apoptosis,
and repair of DNA double-strand breaks. It is found on chromosome
11. ATM mutations are associated with increased risk for breast
cancer among women with a family history of breast cancer
(Chenevix-Trench et al. (2002) J. Natl. Cancer Inst. 94:205-215;
Thorstenson et al. (2003) Cancer Res. 63:3325-3333) and/or
early-onset breast cancers (Izatt et al. (1999) Genes Chromosomes
Cancer 26:286-294; Teraoka et al. (2001) Cancer 92:479-487). There
is also a high frequency of association of rhabdomyosarcoma with
ATM gene mutation/deletion (Zhang et al. (2003) Cancer Biol. Ther.
1:87-91).
[0123] Methods for detecting chromosomal abnormalities in a patient
are well know in the art (see, for example, Cuneo et al. (1999)
Blood 93:1372-1380; Dohner et al. (1997) Blood 89:2516-2522).
Methods to measure mutated proteins, such as ATM, are well known in
the art (see, for example, Butch et al. (2004) Clin. Chem. 50:
2302-2308).
[0124] Thus, subpopulations of cancer patients that are less
responsive to existing therapeutics can be readily identified by
currently used assay methods, including prognostic assays disclosed
herein that utilize one or more of these clinically useful
prognostic markers. Having identified a subject that falls within
one of these subpopulations based on these clinically useful
prognostic markers, the subject can be further screened using one
or more of the ex vivo prognostic assays identified herein above to
assess the benefit of treating this subject with an anti-CD40
therapeutic that modulates CD40L-mediated CD40 signaling and/or
ADCC activity.
Prognostic Assays
[0125] In some embodiments of the present invention, potential
therapeutic benefit with an anti-CD40 therapeutic agent that
modulates CD40L-mediated CD40 signaling, modulates ADCC, or both is
assessed using ex vivo prognostic assays that monitor changes in
the expression level of one or more of the aforementioned
biomarkers of cell proliferation and survival, cellular apoptosis,
and CD40 signaling pathways in a biological sample that is
collected from a candidate subject that is in need of therapeutic
intervention for a cancer or pre-malignant condition that is
mediated by stimulation of CD40 signaling on CD40-expressing cells.
By "CD40-expressing cell" is intended normal, pre-malignant, and
malignant cells expressing CD40 antigen. In some embodiments, the
CD40-expressing cell is a malignant B cell. By "malignant" B cell
is intended any neoplastic B cell, including but not limited to B
cells derived from lymphomas including low-, intermediate-, and
high-grade B cell lymphomas, immunoblastic lymphomas, non-Hodgkin's
lymphomas, Hodgkin's disease, Epstein-Barr Virus (EBV) induced
lymphomas, and AIDS-related lymphomas, as well as B cell acute
lymphoblastic leukemias, myelomas, chronic lymphocytic leukemias,
and the like. In other embodiments, the CD40-expressing cell is a
carcinoma or sarcoma cell. By "CD40-expressing carcinoma cell" or
CD40-expressing sarcoma cell" is intended any malignant (i.e.,
neoplastic) or pre-malignant carcinoma or sarcoma cell of a solid
tumor that expresses the CD40 cell-surface antigen. For purposes of
the present invention, cancerous and pre-cancerous or pre-malignant
cells that express the CD40 antigen are referred to as
"CD40-expressing neoplastic cells." Methods for detecting CD40
expression in cells are well known in the art and include, but are
not limited to, PCR techniques, immunohistochemistry, flow
cytometry, Western blot, ELISA, and the like. Where the ex vivo
assays generate a favorable change in the expression level of one
or more biomarkers of interest within the biological sample,
treatment intervention with the anti-CD40 therapeutic agent is
warranted. Furthermore, biomarkers, cytokine markers, and
CD40-related factors discussed herein can be used to monitor
treatment efficacy of an anti-CD40 therapeutic agent in a subject,
who may or may not have been screened using the ex vivo prognostic
assays disclosed herein, and thus determine whether further
treatment with the same anti-CD40 therapeutic agent is warranted,
or whether alternative treatment protocols are necessary or
desirable. Where treatment with an anti-CD40 therapeutic agent is
warranted as determined by the methods of the present invention,
the therapeutic agent can be administered by any suitable route of
administration.
[0126] The candidate subject who is being considered for treatment
intervention with an anti-CD40 therapeutic agent that modulates
CD40L-mediated CD40 signaling, modulates ADCC, or both can be
afflicted with, or at risk of developing or relapsing with, any
cancer or pre-malignant condition that is mediated by CD40
signaling on CD40-expressing neoplastic cells. Examples of such
cancers and pre-malignant conditions include, but are not limited
to, any of the cancers of B-cell lineage, non-B cell hematological
malignancies, and solid tumors that are known to be mediated via
CD40 signaling on CD40-expressing neoplastic cells.
[0127] Examples of cancers of B-cell lineage that comprise
CD40-expressing neoplastic cells are acute lymphoblastic leukemia
(ALL), chronic lymphocytic leukemia (CLL), prolymphocytic leukemia
(PLL), hairy cell leukemia, Hodgkin's disease, multiple myeloma,
Waldenstrom's macroglobulinemia, heavy chain disease, and the
lymphomas, including, but not limited to, diffuse small lymphocytic
lymphoma, follicular, DLBCL, mucosal associated lymphoid tissue
lymphoma, monocytoid B cell lymphoma, splenic lymphoma,
lymphomatoid granulomatosis, intravascular lymphomatosis,
immunoblastic lymphoma, AIDS-related lymphoma, and the like.
[0128] Thus, the methods of the invention find use in the
identification and treatment of subjects having non-Hodgkin's
lymphomas related to abnormal, uncontrollable B cell proliferation
or accumulation. For purposes of the present invention, such
lymphomas will be referred to according to the Working Formulation
classification scheme, that is those B cell lymphomas categorized
as low grade, intermediate grade, and high grade (see "The
Non-Hodgkin's Lymphoma Pathologic Classification Project," Cancer
49 (1982):2112-2135). Thus, low-grade B cell lymphomas include
small lymphocytic, follicular small-cleaved cell, and follicular
mixed small-cleaved and large cell lymphomas; intermediate-grade
lymphomas include follicular large cell, diffuse small cleaved
cell, diffuse mixed small and large cell, and diffuse large cell
lymphomas; and high-grade lymphomas include large cell
immunoblastic, lymphoblastic, and small non-cleaved cell lymphomas
of the Burkitt's and non-Burkitt's type.
[0129] It is recognized that the methods of the invention are
useful in identification and the therapeutic treatment of B cell
lymphomas that are classified according to the Revised European and
American Lymphoma Classification (REAL) system. Such B cell
lymphomas include, but are not limited to, lymphomas classified as
precursor B cell neoplasms, such as B lymphoblastic
leukemia/lymphoma; peripheral B cell neoplasms, including B cell
chronic lymphocytic leukemia/small lymphocytic lymphoma,
lymphoplasmacytoid lymphoma/immunocytoma, mantle cell lymphoma
(MCL), follicle center lymphoma (follicular) (including diffuse
small cell, diffuse mixed small and large cell, and diffuse large
cell lymphomas), marginal zone B cell lymphoma (including
extranodal, nodal, and splenic types), plasmacytoma/myeloma,
diffuse large cell B cell lymphoma of the subtype primary
mediastinal (thymic), Burkitt's lymphoma, and Burkitt's like
high-grade B cell lymphoma; and unclassifiable low-grade or
high-grade B cell lymphomas.
[0130] These assays can also be used to identify subjects having
the pre-malignant condition known as MGUS (monoclonal gammopathy of
undetermined significance) who would benefit from treatment with a
modulator of CD40L-mediated CD40 signaling. Approximately 25% of
patients with MGUS eventually develop multiple myeloma (MM) or a
related plasma cell disorder (Kyle (1993) Mayo Clinic. Proc.
68:26-36). Proliferation of malignant plasma cells in the bone
marrow, detection of a serum or urine monoclonal protein (M
protein), anemia, hypercalcemia, renal insufficiency, and lytic
bone lesions are clinical manifestations of MM, while MGUS is
clinically recognized as the presence of M protein in the serum or
urine without other clinical features of MM (see, for example, Kyle
and Lust (1989) Semin. Hematol. 26:176-200; Greipp and Lust Stem
Cells (1995) 13:10-21). MGUS patients are asymptomatic and have
stable measurements of M protein (Kyle (1993) Mayo Clinic. Proc.
68:26-36). Once MGUS is identified in a subject, maintenance
therapy with an appropriate anti-CD40 therapeutic agent, for
example, an antagonist anti-CD40 antibody disclosed herein, may
block the development of multiple myeloma in these subjects. Thus,
the ex vivo prognostic assays disclosed herein can be used to
identify subjects with MGUS who would benefit from treatment with
an anti-CD40 therapeutic agent. Alternatively, or in addition, the
biomarkers, cytokine markers, and CD40-related factors described
herein can be used to monitor efficacy of treatment with an
anti-CD40 therapeutic agent as noted elsewhere herein.
[0131] In particular, the methods of the invention are useful for
identifying and treating B cell lymphomas, including those listed
above, that are refractory to (i.e., resistant to, or have become
resistant to) first-line oncotherapeutic treatments. The term
"oncotherapeutic" is intended to mean a treatment for cancer such
as chemotherapy, surgery, radiation therapy, single anti-cancer
antibody therapy, and combinations thereof. The ex vivo prognostic
assays can be used to identify subpopulations of patients for whom
treatment intervention with one or more anti-CD40 therapeutic
agents that modulates CD40L-mediated CD40 signaling, modulates
ADCC, or both is desirable.
[0132] The methods of the present invention are also useful for
identifying and treating non-B cell related hematological
malignancies. Such malignances include, but are not limited to,
acute leukemias; myeloblastic leukemias; acute myelocytic
leukemias; promyelocytic leukemia; myelomonocytic leukemia;
monocytic leukemia; erythroleukemia; granulocytic leukemia (chronic
myelocytic leukemia); polycythemia vera; and the like.
[0133] Solid tumors that comprise CD40-expressing neoplastic cells
include, but are not limited to, ovarian, lung (for example,
non-small cell lung cancer of the squamous cell carcinoma,
adenocarcinoma, and large cell carcinoma types, and small cell lung
cancer), breast, colon, kidney (including, for example, renal cell
carcinomas), bladder, liver (including, for example, hepatocellular
carcinomas), gastric, cervical, prostate, nasopharyngeal, thyroid
(for example, thyroid papillary carcinoma), skin cancers such as
melanoma, and sarcomas, including, for example, osteosarcomas and
Ewing's sarcomas.
[0134] The term "prognosis" is recognized in the art and
encompasses predictions about the likely course of response to
therapeutic intervention, and the likely course of disease or
disease progression, particularly with respect to likelihood of
disease remission, disease relapse, tumor recurrence, metastasis,
and death. The ex vivo prognostic assays of the present invention
can be used to predict the response of a candidate subject to a
particular anti-CD40 therapeutic agent, or class of anti-CD40
therapeutic agents, that modulates CD40L-mediated CD40 signaling,
modulates ADCC, or both. By "predicting the response of a candidate
subject" is intended assessing the likelihood that a subject in
question will experience a positive or negative outcome with a
particular anti-CD40 therapeutic agent. For purposes of the present
invention, "indicative of a positive treatment outcome" in the
context of the ex vivo prognostic assays of the present invention
is intended to mean an increased likelihood that the candidate
subject will experience beneficial results in response to treatment
with the anti-CD40 therapeutic agent under consideration, and thus
treatment intervention with that anti-CD40 therapeutic agent would
be warranted. In contrast, "indicative of a negative treatment
outcome" is intended to mean an increased likelihood that the
patient will not benefit from treatment intervention with the
anti-CD40 therapeutic agent under consideration, and thus treatment
intervention with that anti-CD400 therapeutic agent would not be
warranted.
[0135] Beneficial results that can be achieved with treatment
intervention with anti-CD40 therapeutic agents that modulate
CD40L-mediated CD40 signaling include any positive therapeutic
response. By "positive therapeutic response" with respect to cancer
treatment is intended an improvement in the disease in association
with the anti-tumor activity of the anti-CD40 therapeutic agent
and/or an improvement in the symptoms associated with the disease
of interest. That is, an anti-proliferative effect, the prevention
of further tumor outgrowths, a reduction in tumor size, a reduction
in the number of cancer cells, and/or a decrease in one or more
symptoms mediated by stimulation of CD40-expressing cells can be
observed. Thus, for example, a positive therapeutic response would
refer to one or more of the following improvements in the disease:
(1) a reduction in tumor size; (2) a reduction in the number of
cancer (i.e., neoplastic) cells; (3) an increase in neoplastic cell
death; (4) inhibition of neoplastic cell survival; (4) inhibition
(i.e., slowing to some extent, preferably halting) of tumor growth;
(5) inhibition (i.e., slowing to some extent, preferably halting)
of cancer cell infiltration into peripheral organs; (6) inhibition
(i.e., slowing to some extent, preferably halting) of tumor
metastasis; (7) the prevention of further tumor outgrowths; (8) an
increased patient survival rate; and (9) some extent of relief from
one or more symptoms associated with the cancer. Positive
therapeutic responses in any given malignancy can be determined by
standardized response criteria specific to that malignancy.
[0136] Tumor response can be assessed for changes in tumor
morphology (i.e., overall tumor burden, tumor size, and the like)
using screening techniques such as magnetic resonance imaging (MRI)
scan, x-radiographic imaging, computed tomographic (CT) scan, bone
scan imaging, endoscopy, and tumor biopsy sampling including bone
marrow aspiration (BMA) and counting of tumor cells in the
circulation. In addition to these positive therapeutic responses,
the subject undergoing therapy with the anti-CD40 therapeutic agent
may experience the beneficial effect of an improvement in the
symptoms associated with the disease. Thus for B cell tumors, the
subject may experience a decrease in the so-called B symptoms,
i.e., night sweats, fever, weight loss, and/or urticaria. For
pre-malignant conditions, therapy with an anti-CD40 therapeutic
agent may block and/or prolong the time before development of a
related malignant condition, for example, development of multiple
myeloma in subjects suffering from monoclonal gammopathy of
undertermined significance (MGUS).
[0137] In some embodiments, the ex vivo prognostic assays for use
in the methods of the present invention comprise providing a test
biological sample and a control biological sample from a candidate
subject in need of prognosis for treatment intervention with an
anti-CD40 therapeutic agent as noted herein, where the test and
control biological samples comprise CD40-expressing neoplastic
cells that have been stimulated with a CD40 ligand, either in vivo
or ex vivo; contacting the test biological sample with an effective
amount of the anti-CD40 therapeutic agent of interest; detecting
the level of at least one biomarker in this test biological sample,
where the biomarker is selected from the group consisting of a
biomarker of cellular apoptosis, a biomarker of a CD40L-mediated
CD40 signaling pathway, and a biomarker of cell survival, depending
upon the mode of action of the anti-CD40 therapeutic agent of
interest; and comparing the level of the biomarker(s) in the test
biological sample to the level of the biomarker(s) in the control
biological sample, which has not been contacted with the anti-CD40
therapeutic agent. Where the anti-CD40 therapeutic agent is an
antagonist that blocks or interferes with CD40L-mediated CD40
signaling, or blocks or interferes with this signaling and also
modulates ADCC, the ex vivo prognostic assays disclosed herein for
any or all of these biomarkers of cell proliferation and survival,
apoptosis, and CD40L-mediated CD40 signaling, can be used to assess
the potential beneficial effect of the therapeutic agent, alone or
in combination with assays for cytokine markers that are
upregulated by CD40L-mediated CD40 signaling, and/or assays for one
or more of the CD40-related factors described herein, in order to
identify a subject having a cancer or pre-malignant condition that
would be responsive to treatment with that anti-CD40 therapeutic
agent. Where the anti-CD40 therapeutic agent has its mode of action
via modulating ADCC activity, for example, an anti-CD40 antibody,
the ex vivo prognostic assay for one or more markers of apoptosis
can be used to assess the potential beneficial effect of the
therapeutic agent, alone or in combination with assays for one or
more of the CD40-related factors described herein, in order to
identify a subject having a cancer or pre-malignant condition that
would be responsive to treatment with that anti-CD40 therapeutic
agent.
[0138] In accordance with the ex vivo prognostic assays of the
invention, expression level of one or more biomarkers, and
optionally one or more cytokine markers, in a test biological
sample that is contacted with the anti-CD40 therapeutic agent of
interest is compared to expression level for the biomarker(s), and
optionally cytokine marker(s) in a control biological sample. By
"test biological sample" is intended a biological sample comprising
CD40-expressing neoplastic cells obtained from the candidate
subject, and which will be contacted with the anti-CD40 therapeutic
agent under consideration for treatment of the candidate subject.
By "control biological sample" is intended a biological sample that
is comparable to the test biological sample in that it also
comprises approximately the same number and kind of CD40-expressing
neoplastic cells and has been obtained from the candidate subject
in the same timeframe and in a manner equivalent to that used to
obtain the test biological sample, and which will be subjected to
the same experimental conditions as the test sample, but which will
not be contacted with the anti-CD40 therapeutic agent of interest.
The test biological sample and control biological sample can be
provided from a single biological sample that has been obtained
from the subject and divided into subsamples, one of which is
designated the test biological sample and another of which is
designated the control biological sample. Alternatively, the test
biological sample and control biological sample can be provided
from two or more biological samples, which can be pooled and then
subdivided into subsamples as above, or which can individually
represent the test and control biological samples.
[0139] While it is recognized that the CD40-expressing neoplastic
cells obtained from the candidate subject may have been
constitutively stimulated by CD40L in vivo prior to the collection
of a biological sample, it is preferable to stimulate the
CD40-expressing neoplastic cells of the test and control biological
samples ex vivo so that antagonistic effects of an anti-CD40
therapeutic agent on CD40-related activities, for example,
stimulation of cell proliferation and CD40 signaling, can
effectively be assessed.
[0140] In this manner, prior to contacting the test biological
sample of CD40-expressing neoplastic cells with the anti-CD40
therapeutic agent of interest, the CD40-expressing neoplastic cells
within any given biological sample collected from the candidate
subject can be stimulated, for example, with CD40L, to ensure
upregulation of CD40 signaling on the CD40-expressing neoplastic
cells of the test and control biological samples to be used in the
ex vivo prognostic assay. Any source of CD40L can be used,
including, but not limited to, soluble CD40L. Other suitable
CD40-stimulatory molecules can include, for example, agonist
antibodies that bind specifically to the extracellular domain of
CD40. Thus, in some embodiments, suitable CD40-stimulatory
molecules include, but are not limited to, membrane-bound CD40L
(for example, CD40L bound to the plasma membrane of a cell, for
example, formaldehyde-fixed CHO cells transfectant-expressing
CD40L; or CD40L incorporated into a synthetic lipid-based substrate
such as a liposome or micelle), soluble CD40L, an agonist anti-CD40
antibody, for example, the anti-human CD40 antibody G28-5
(Bristol-Myers Squibb, Seattle, Wash.), and mixtures thereof. An
effective amount of a stimulatory molecule to be contacted with
cells of a collected biological sample or subsample thereof in
order to stimulate one or more CD40 signaling pathways will depend
upon factors such as the type of ligand used (e.g., monomeric or
multimeric; solubility and permeability, and the like) and the
abundance of the CD40 receptor on the CD40-expressing neoplastic
cells. Preferably, between about 1.0 nM and about 1 mM of CD40L or
soluble CD40L is used to stimulate CD40 signaling.
[0141] In some embodiments, CD40-expressing neoplastic cells within
the biological sample or subsample thereof are stimulated with
soluble recombinant human CD40L (Alexis Corporation, Bingham,
Nottinghamshire, UK) prior to the contacting step by incubating the
biological sample or subsample thereof with soluble CD40L for a
time sufficient to stimulate CD40 signaling. In some embodiments,
the incubation time is about 10 minutes to about 4 hours. The
amount of soluble CD40L present during the incubation period is
readily determined by titration. In one such embodiment, the amount
of soluble CD40L is about 1 mg/ml. Any acceptable protocol to
contact the test biological sample with an anti-CD40 therapeutic
agent of interest can be used in the ex vivo prognostic assays of
the invention. Factors to be considered include, but are not
limited to, the number of cells to be contacted within a container
comprising the test biological sample; the concentration of the
anti-CD40 therapeutic agent to be contacted with the test
biological sample; the incubation time of the anti-CD40 therapeutic
agent with the cells in the test biological sample; where
applicable, the concentration of a stimulatory molecule, for
example, CD40L, soluble CD40L, or stimulatory fragment or variant
thereof, to be contacted with the test biological sample; and,
where applicable, the incubation time of the stimulatory molecule
with the cells in the test biological sample. Determination of such
factors can be accomplished by those skilled in the art based on
variables such as the type of biological sample being tested, size
of the holding container, the volume of liquid in the container,
and the chemical composition of the anti-CD40 therapeutic agent
(i.e., size, charge, and the like) being tested.
[0142] In one embodiment, a test biological sample or subsample
thereof comprising a suitable number of CD40-expressing neoplastic
cells is added to a 96-well tissue culture dish. The suitable
number of cells is a number of cells that enables one to detect a
change in one or more of the CD40-mediated activities (i.e., cell
proliferation and cell survival, level of apoptosis, CD40 signaling
pathways) using one or more of the detection methods described
elsewhere herein. In some embodiments, the suitable number of cells
is between about 1 and about 1.times.10.sup.6 cells per well of a
96-well tissue culture dish. Following addition of the cells to the
tissue culture dish, the cells can be preincubated between about 0
to about 96 hours before contacting the cells with the anti-CD40
therapeutic agent. In some embodiments, the cells are preincubated
with a CD40-stimulatory molecule as noted herein above.
[0143] An effective amount of an anti-CD40 therapeutic agent is
added to the cells of the test biological sample to provide for
regulation of a CD40-mediated activity of interest (i.e.,
CD40L-mediated CD40 signaling, ADCC activity of an agent that binds
to CD40, or both) such that the regulation is detectable using one
or more detection methods disclosed elsewhere herein. The effective
amount will of course be dependent upon the anti-CD40 therapeutic
agent being tested. Generally, an effective amount of an anti-CD40
therapeutic agent is between about 1 nM to about 10 mM of the agent
per well of a 96-well plate. In one embodiment, the anti-CD40
therapeutic agent is an antagonist anti-CD40 antibody, for example,
the CHIR-12.12 or CHIR-5.9 fully human monoclonal antibody, or
antigen-binding fragment thereof, and the effective amount is about
0.01 .mu.g/ml to about 30 .mu.g/ml, including about 0.01 .mu.g/ml,
0.1 .mu.g/ml, 0.5 .mu.g/ml, 1 .mu.g/ml, 5 .mu.g/ml, 10 .mu./ml, 20
.mu.g/ml, and 30 .mu.g/ml, and other such values between about 0.01
.mu.g/ml and about 30 .mu.g/ml. The cells within the test
biological sample or subsample thereof are allowed to incubate for
a suitable length of time to allow the anti-CD40 therapeutic agent
to interact with the cells and generate one or more biological
responses. In some embodiments, the preferred incubation time
between the anti-CD40 therapeutic agent and the cells of the test
biological sample or subsample thereof is between about 1 minute to
about 48 hours. In other embodiments, the incubation time is about
20 minutes, about 30 minutes, about 1 hour, about 4 hours, about 12
hours, about 22 hours, or about 24 hours.
[0144] The biological sample(s) that serve(s) as the test and
control biological samples can be provided from any collection of
cells, tissue, or bodily fluid that comprises neoplastic cells
expressing the CD40 antigen. Examples of such biological samples
include, but are not limited to, blood, lymph, biopsies, smears,
and the like. Biological samples can be collected from a candidate
subject using any acceptable procedure in the art, for example, by
needle aspiration of bodily fluids, removal of a tissue sample
(i.e., biopsy, for example, fine needle aspiration biopsy, core
needle biopsy, or excisional biopsy), and the like. Where a
biological sample must be stored prior to assay, the biological
sample can be transferred to a glass slide prior to assay or may be
frozen for later preparation or immediately placed in a fixative
solution.
[0145] As previously noted, detection of the biomarker of interest
at the protein or nucleotide level can be accomplished using any
detection method known to those of skill in the art. By "detecting
expression" or "detecting the level of" is intended determining the
quantity or presence of a biomarker protein or gene in the
biological sample. Thus, "detecting expression" encompasses
instances where a biomarker is determined not to be expressed, not
to be detectably expressed, expressed at a low level, expressed at
a normal level, or overexpressed. In order to determine the effect
of an anti-CD40 therapeutic agent on CD40L-mediated CD40 signaling,
a test biological sample comprising CD40-expressing neoplastic
cells that have been stimulated with a CD40 ligand (either in vivo
or ex vivo) is contacted with the anti-CD40 therapeutic agent for a
sufficient time to allow the therapeutic agent to exert a cellular
response, and then expression level of one or more biomarkers of
interest in that test biological sample is compared to the
expression level in the control biological sample that has not been
contacted with the anti-CD40 therapeutic agent. In some
embodiments, the control biological sample of neoplastic cells is
contacted with a neutral substance or negative control that does
not interfere with CD40L-mediated CD40 signaling. For example, in
one embodiment, a non-specific immunoglobulin, for example IgG1,
that does not bind to CD40 serves as the negative control.
Detection can occur over a time course to allow for monitoring of
changes in biomarkers over time. Detection can also occur with
exposure to different concentrations of the anti-CD40 therapeutic
agent to generate a "dose-response" curve for any given biomarker
of interest.
[0146] Methods for detecting expression of the biomarkers of the
invention, and optionally cytokine markers, within the test and
control biological samples comprise any methods that determine the
quantity or the presence of these markers either at the nucleic
acid or protein level. Such methods are well known in the art and
include but are not limited to western blots, northern blots,
ELISA, immunoprecipitation, immunofluorescence, flow cytometry,
immunohistochemistry, nucleic acid hybridization techniques,
nucleic acid reverse transcription methods, and nucleic acid
amplification methods. In particular embodiments, expression of a
biomarker is detected on a protein level using, for example,
antibodies that are directed against specific biomarker proteins.
These antibodies can be used in various methods such as Western
blot, ELISA, multiplexing technologies, immunoprecipitation, or
immunohistochemistry techniques. In some embodiments, detection of
cytokine markers is accomplished by electrochemiluminescence (ECL).
Any of these detection methods for biomarkers and optionally
cytokine markers can be combined with assessment of clinical
information, conventional prognostic methods, expression of other
CD40-related factors, particularly expression of cell-surface CD40
and/or CD40L and circulating levels of soluble CD40 and/or CD40L,
and expression of, or presence of, clinically useful prognostic
markers known in the art, including, but not limited to, those
noted herein above for CLL patients (e.g., ZAP-70, CD38, .beta.2
microglobulin, soluble CD52, and cytogenetic markers, for example,
p53 mutational status, ATM mutational status, and chromosome
deletions, such as the chromosome 17p deletion and the chromosome
11q deletion. In this manner, the disclosed methods may permit the
more accurate determination of candidate subjects whose cancer or
pre-malignant condition would benefit from therapeutic intervention
with an anti-CD40 therapeutic agent described herein.
[0147] Thus, in some embodiments, a candidate subject having a
cancer or pre-malignant condition that is associated with
CD40-expressing neoplastic cells is tested for responsiveness to an
anti-CD40 therapeutic agent of interest using the ex vivo
prognostic assays described herein, wherein effects of the
therapeutic agent on one or more CD40-mediated activities is
assessed. Where further refinement of the ex vivo prognostic assay
is desirable, the candidate subject can be examined for the level
of expression of, or absence of expression of, one or more
CD40-related factors identified herein above, one or more
clinically useful prognostic markers, including those identified
herein above for CLL patients, or both. In this manner, a
biological sample comprising CD40-expressing neoplastic cells can
be collected from a candidate subject and assessed for the level of
expression of, or absence of expression of, the CD40-related
factor(s) and/or clinically useful prognostic marker(s) of
interest. Any biological sample comprising CD40-expressing
neoplastic cells as noted herein above can be collected for these
prognostic assays. Further, any detection method known to those of
skill in the art can be used to detect the level of expression, or
absence of expression, of the CD40-related factor(s) and/or
clinically useful prognostic marker(s) of interest, as noted
elsewhere herein.
[0148] Where the expression level of one or more CD40-related
factors is to be assessed in order to identify a subject having a
cancer or pre-malignant condition that will be responsive to
treatment with an anti-CD40 therapeutic agent, a biological sample
is collected from the subject, and the level of expression in that
sample is compared to the level of expression of that factor (or
factors) in a control or reference standard. For expression level
of cell-surface CD40 and/or cell-surface CD40L, any biological
sample comprising CD40-expressing and/or CD40L-expressing
neoplastic cells can be used as noted herein above. For circulating
levels of sCD40 and/or sCD40L, a blood sample or sample comprising
a blood component such as plasma or serum can be obtained from the
candidate subject. By "control" or "reference standard" is intended
a standard that is of the same biological source (i.e., tissue or
bodily fluid) and which distinguishes subjects having the cancer or
pre-malignant condition from healthy subjects that are not
afflicted with the disease. A skilled artisan can provide a
reference standard by taking a measurement of expression levels of
these CD40-related factors (i.e., cell-surface CD40, cell-surface
CD40L, sCD40, sCD40L) in healthy subjects that do not have the
disease and subjects that do have the disease, controlling for age,
sex, race, and the like, and comparing the expression levels to
determine the standard level of expression to be expected in a
healthy subject. In some embodiments, the expression level in the
candidate subject having the cancer or pre-malignant condition is
at least 20%, 30%, 40%, 50%, 60%, 70%, 80%, 100%, 150%, 200%, 250%,
300% greater than the expression level in the reference standard.
It is recognized that the applicability of treatment with an
anti-CD40 therapeutic agent can be assessed by detecting the level
of expression of one or more of these CD40-related factors, wherein
an increased level of expression in a biological sample relative to
the reference standard is sufficient to establish that the subject
has a cancer or pre-malignant condition that will be responsive to
treatment with the anti-CD40 therapeutic agent of interest without
having to do additional screening for ex vivo effects of the
anti-CD40 therapeutic agent on CD40-mediated activities such as
cell survival and proliferation, and/or ADCC activity.
[0149] The present invention also encompasses kits for carrying out
the ex vivo prognostic assays of the present invention. For
example, the kit can comprise a labeled compound or agent capable
of detecting a biomarker described herein, e.g., a biomarker of
apoptosis, cellular proliferation or survival, or a CD40L-mediated
CD40 signaling pathway, either at the protein or nucleic acid
level, in a biological sample and means for determining the amount
of the biomarker in the sample (for example, an antibody or an
oligonucleotide probe that binds to RNA encoding a biomarker of
interest) following incubation of the sample with an anti-CD40
therapeutic agent of interest. Kits can be packaged to allow for
detection of multiple biomarkers of interest by including
individual labeled compounds or agents capable of detecting each
individual biomarker of interest and means for determining the
amount of each biomarker in the sample. Kits can also include
instructions for treating a subject when the ex vivo prognostic
assay generates a result that is indicative of a positive treatment
outcome with the anti-CD40 therapeutic agent.
[0150] For antibody-based kits, the kit can comprise, for example:
(1) a first antibody (e.g., attached to a solid support) that binds
to a biomarker of interest; and, optionally, (2) a second,
different antibody that binds to the biomarker or the first
antibody and is conjugated to a detectable agent. For
oligonucleotide-based kits, the kit can comprise, for example: (1)
an oligonucleotide, e.g., a detectably labeled oligonucleotide,
that hybridizes to a nucleic acid sequence encoding the biomarker
or (2) a pair of primers useful for amplifying a nucleic acid
molecule encoding the biomarker of interest. The kit can also
comprise, e.g., a buffering agent, a preservative, or a protein
stabilizing agent. The kit can also comprise components necessary
for detecting the detectable agent (e.g., an enzyme or a
substrate). The kit can also contain a control sample or a series
of control samples that can be assayed and compared to the test
sample contained. Each component of the kit is usually enclosed
within an individual container, and all of the various containers
are within a single package along with instructions for observing
whether the tested subject is a candidate for treatment with the
anti-CD40 therapeutic agent.
Detection Methods
[0151] Any means for specifically identifying and quantifying a
biomarker, cytokine marker, or CD40-related factor protein of
interest (for example, a biomarker of cell survival or
proliferation, a biomarker of apoptosis, a biomarker of a
CD40L-mediated CD40 signaling pathway, circulating soluble CD40 or
CD40L, cell-surface CD40 or CD40L, or a clinically useful
prognostic marker, for example, ZAP-70, CD38, and .beta.2
microglobulin for a CLL patient) in the biological sample of a
candidate subject is contemplated. Thus, in some embodiments,
expression level of a biomarker protein of interest in a biological
sample is detected by means of a binding protein capable of
interacting specifically with that biomarker protein or a
biologically active variant thereof. Preferably, labeled
antibodies, binding portions thereof, or other binding partners may
be used. The word "label" when used herein refers to a detectable
compound or composition that is conjugated directly or indirectly
to the antibody so as to generate a "labeled" antibody. The label
may be detectable by itself (e.g., radioisotope labels or
fluorescent labels) or, in the case of an enzymatic label, may
catalyze chemical alteration of a substrate compound or composition
that is detectable.
[0152] The antibodies for detection of a biomarker protein may be
monoclonal or polyclonal in origin, or may be synthetically or
recombinantly produced. The amount of complexed protein, for
example, the amount of biomarker protein associated with the
binding protein, for example, an antibody that specifically binds
to the biomarker protein, is determined using standard protein
detection methodologies known to those of skill in the art. A
detailed review of immunological assay design, theory and protocols
can be found in numerous texts in the art (see, for example,
Ausubel et al., eds. (1995) Current Protocols in Molecular Biology)
(Greene Publishing and Wiley-Interscience, NY)); Coligan et al.,
eds. (1994) Current Protocols in Immunology (John Wiley & Sons,
Inc., New York, N.Y.).
[0153] A variety of assays are available for detecting proteins
with labeled antibodies. In a one-step assay, the target protein of
interest to be detected, if it is present, is immobilized and
incubated with a labeled antibody. The labeled antibody binds to
the immobilized target protein molecule. After washing to remove
unbound molecules, the sample is assayed for the presence of the
label. In a standard format, a single protein is assayed per
sample. Using newer multiplex technologies, multiple proteins can
be assayed in a single sample by using different labels for each
detecting antibody.
[0154] In a two-step assay, the immobilized target protein molecule
of interest is incubated with an unlabeled antibody. The target
protein-unlabeled antibody complex, if present, is then bound to a
second, labeled antibody that is specific for the unlabeled
antibody. The sample is washed and assayed for the presence of the
label.
[0155] The choice of marker used to label the antibodies will vary
depending upon the application. However, the choice of the marker
is readily determinable to one skilled in the art. These labeled
antibodies may be used in immunoassays as well as in histological
applications to detect the presence of any biomarker or protein of
interest. The labeled antibodies may be polyclonal or monoclonal.
Further, the antibodies for use in detecting a protein of interest
may be labeled with a radioactive atom, an enzyme, a chromophoric
or fluorescent moiety, or a colorimetric tag as described elsewhere
herein. The choice of tagging label also will depend on the
detection limitations desired. Enzyme assays (ELISAs) typically
allow detection of a colored product formed by interaction of the
enzyme-tagged complex with an enzyme substrate. Radionuclides that
can serve as detectable labels include, for example, I-131, I-123,
I-125, Y-90, Re-188, Re-186, At-211, Cu-67, Bi-212, and Pd-109.
Examples of enzymes that can serve as detectable labels include,
but are not limited to, horseradish peroxidase, alkaline
phosphatase, beta-galactosidase, and glucose-6-phosphate
dehydrogenase. Chromophoric moieties include, but are not limited
to, fluorescein and rhodamine. The antibodies may be conjugated to
these labels by methods known in the art. For example, enzymes and
chromophoric molecules may be conjugated to the antibodies by means
of coupling agents, such as dialdehydes, carbodiimides,
dimaleimides, and the like. Alternatively, conjugation may occur
through a ligand-receptor pair. Examples of suitable
ligand-receptor pairs are biotin-avidin or biotin-streptavidin, and
antibody-antigen.
[0156] In some embodiments, the present invention contemplates the
use of a sandwich technique for detecting one or more biomarkers,
or other proteins of interest as noted herein above, in serum and
other biological fluids. As described in International Publication
No. WO 93/09437, such a technique uses two antibodies capable of
binding the protein of interest: e.g., one of which is free in
solution but labeled with a detectable chemical compound, the other
of which is immobilized onto a solid support. Examples of chemical
labels that may be used for the second antibody include but are not
limited to radioisotopes, fluorescent compounds, and enzymes or
other molecules that generate colored or electrochemically active
products when exposed to a reactant or enzyme substrate. When
samples containing the biomarker or other protein of interest are
placed in this system, the biomarker or other protein of interest
binds to both the immobilized antibody and the labeled antibody.
The result is a "sandwich" immune complex on the support's surface.
The complexed protein is detected by washing away nonbound sample
components and excess labeled antibody, and measuring the amount of
labeled antibody complexed to protein on the support's surface. The
sandwich immunoassay is highly specific and very sensitive,
provided that labels with good limits of detection are used.
[0157] Biological samples can be screened individually;
alternatively, numerous samples of biological fluids can be
screened at the same time, for example, using the conventional
96-well microtiter format, which is widely used and easily
automatable. There are also several commercially available
spectrometers ("plate readers") for calorimetrically analyzing
96-well plates. Further, biological samples can be screened for one
biomarker, or multiple markers, for example, a panel of biomarkers,
using methods well known in the art.
[0158] In preferred embodiments, expression of one or more
biomarkers or other proteins of interest within a biological
sample, for example, a sample of bodily fluid, is detected by
radioimmunoassays or enzyme-linked immunoassays (ELISAs),
competitive binding enzyme-linked immunoassays, dot blot (see, for
example, Promega Protocols and Applications Guide (2.sup.nd ed.;
Promega Corporation (1991), Western blot (see, for example,
Sambrook et al. (1989) Molecular Cloning, A Laboratory Manual, Vol.
3, Chapter 18 (Cold Spring Harbor Laboratory Press, Plainview,
N.Y.), chromatography, preferably high performance liquid
chromatography (HPLC), or other assays known in the art. Thus, the
detection assays can involve steps such as, but not limited to,
immunoblotting, immunodiffusion, immunoelectrophoresis, or
immunoprecipitation.
[0159] For any given protein detection assay, the biological
sample, or a subsample thereof comprising CD40-expressing
neoplastic cells, is contacted with the binding partner, for
example, the antibody, or detectably labeled antibody, for the
biomarker or other protein of interest, for a time sufficient to
permit the formation of antibody-antigen complexes, and then
antibody binding is detected, for example, by any means noted
herein above. Antibodies and detectably labeled antibodies to the
biomarkers, CD40-related factors, and clinically useful prognostic
markers described herein are well known in the art and commercially
available. See, for example, antibodies specific to biomarkers of
apoptosis, cell survival, and CD40 signaling pathways, as well as
clinically useful prognostic markers such as ZAP-70 and p53
available, for example, from Cell Signaling Technology, Beverly,
Mass.; DAKO, Copenhagen, Denmark; and the like. Alternatively,
antibodies, or detectably labeled forms of these antibodies, can be
generated using antibody production methods well known in the art,
and further described herein below.
[0160] A number of assay kits for biomarkers of caspases are
commercially available. For example, the Homogeneous Caspases Assay
(Roche Applied Sciences, Indianapolis, Ind.), is a fluorimetric
assay for the quantitative in vitro determination of caspase
activity in microplates. The assay is particularly useful for
high-throughput screening, allowing, for example, for 100 tests on
96-well plates, and 400 tests on 384-well plates (Cat. No. 3 005
372). This assay allows for detection of several caspases,
including Caspase-2, Caspase-3, Caspase-7, and to a lesser extent,
Caspase-6, Caspase-8, Caspase-9, and Caspase-10, in biological
samples, including, for example, serum or plasma. The Cell Death
Detection ELISA.sup.PLUS assay (Cat. No. 1 774 425; Roche Applied
Sciences, Indianapolis, Ind.) is based on a quantitative
sandwich-enzyme-immunoassay principle, using mouse monoclonal
antibodies directed against DNA and histones, respectively. This
assay allows the specific detection and quantitation of mono- and
oligonucleosomes that are released into the cytoplasm of cells that
die from apoptosis. It can be used for a variety of samples,
including cell lysates, serum, culture supernatant, and the
like.
[0161] Cell surface PS can be detected using any of the
commercially available Annexin V staining reagents, which are based
on the high affinity of annexin V for PS. See, for example, the
Annexin V staining reagents commercially available from Roche
Applied Science. By conjugating FITC to Annexin V it is possible to
identify and quantitate apoptotic cells on a single-cell basis by
flow cytometry. Staining cells simultaneously with FITC-Annexin V
(green fluorescence) and the non-vital dye propidium iodide (red
fluorescence) can provide for the discrimination of intact cells
(FITC-PI-), early apoptotic (FITC+PI-), and late apoptotic or
necrotic cells (FITC+PI+).
[0162] Further, elevated apoptosis within a biological sample can
be confirmed with nucleic acid-based methods that detect the DNA
fragmentation that is characteristic of apoptosis. When resolved
using electrophoresis on agarose gels, apoptotic DNA initially has
a characteristic "ladder" pattern, as opposed to a smear of nucleic
acids that is observed, for example, in necrosis or other
non-specific DNA degradation. A common histochemical technique to
detect DNA fragmentation uses end-labeled DNA. Kits for such are
commercially available, such as the APOLERT DNA fragmentation kit
(Clontech Laboratories, Inc., Palo Alto, Calif.). This assay is
based on terminal deoxynucleotidyltransferase (Tdt)-mediated dUTP
nick-end labeling (TUNEL), where Tdt catalyzes the incorporation of
fluorescein-dUTP at the free 3'-hydroxyl ends of fragmented DNA in
cells undergoing apoptosis.
[0163] Any method known in the art can be used to detect production
of cytokine markers. Standard assays comprise an ELISA format,
where one cytokine is measured per sample. Alternatively, a more
sensitive technology is electrochemiluminescence (ECL). In one
embodiment, cytokine production is assayed using ECL, for example,
using a multi-array system such as the commercially available Meso
Scale Discovery.RTM. system for high performance cytokine assays
(Meso Scale Discovery, Gaithersburg, Md.). Other formats that allow
for measuring multiple cytokines (or other analytes) at once within
a sample include the multiplex technologies. One such product is
the Luminex.RTM. bead technology (Luminex Corporation, Austin,
Tex.), in which up to 100 color-coded microspheres coated with
reagents specific to a particular bioassay (such as an antibody to
a cytokine) can be mixed together and analyzed using lasar
technology.
[0164] The presence of one or more of the biomarkers, cytokines,
CD40-related factors, and clinically useful prognostic markers
described herein within a biological sample obtained from a
candidate subject may also be determined at the nucleic acid level.
Nucleic acid-based techniques for assessing expression are well
known in the art and include, for example, determining the level of
biomarker mRNA in a biological sample. Many expression detection
methods use isolated RNA. Any RNA isolation technique that does not
select against the isolation of mRNA can be utilized for the
purification of RNA (see, e.g., Ausubel et al., ed. (1987-1999)
Current Protocols in Molecular Biology (John Wiley & Sons, New
York). Additionally, large numbers of tissue samples can readily be
processed using techniques well known to those of skill in the art,
such as, for example, the single-step RNA isolation process
disclosed in U.S. Pat. No. 4,843,155.
[0165] Thus, in some embodiments, the detection of a biomarker or
other protein of interest is assayed at the nucleic acid level
using nucleic acid probes. The term "nucleic acid probe" refers to
any molecule that is capable of selectively binding to a
specifically intended target nucleic acid molecule, for example, a
nucleotide transcript. Probes can be synthesized by one of skill in
the art, or derived from appropriate biological preparations.
Probes may be specifically designed to be labeled, for example,
with a radioactive label, a fluorescent label, an enzyme, a
chemiluminescent tag, a colorimetric tag, or other labels or tags
that are discussed above or that are known in the art. Examples of
molecules that can be utilized as probes include, but are not
limited to, RNA and DNA.
[0166] For example, isolated mRNA can be used in hybridization or
amplification assays that include, but are not limited to, Southern
or Northern analyses, polymerase chain reaction analyses and probe
arrays. One method for the detection of mRNA levels involves
contacting the isolated mRNA with a nucleic acid molecule (probe)
that can hybridize to the mRNA encoded by the gene being detected.
The nucleic acid probe can be, for example, a full-length cDNA, or
a portion thereof, such as an oligonucleotide of at least 7, 15,
30, 50, 100, 250 or 500 nucleotides in length and sufficient to
specifically hybridize under stringent conditions to an mRNA or
genomic DNA encoding a biomarker, CD40-related factor, or
clinically useful prognostic marker described herein above.
Hybridization of an mRNA with the probe indicates that the
biomarker or other target protein of interest is being
expressed.
[0167] In one embodiment, the mRNA is immobilized on a solid
surface and contacted with a probe, for example by running the
isolated mRNA on an agarose gel and transferring the mRNA from the
gel to a membrane, such as nitrocellulose. In an alternative
embodiment, the probe(s) are immobilized on a solid surface and the
mRNA is contacted with the probe(s), for example, in a gene chip
array. A skilled artisan can readily adapt known mRNA detection
methods for use in detecting the level of mRNA encoding the
biomarkers or other proteins of interest.
[0168] An alternative method for determining the level of a mRNA of
interest in a sample involves the process of nucleic acid
amplification, e.g., by RT-PCR (see, for example, U.S. Pat. No.
4,683,202), ligase chain reaction (Barany (1991) Proc. Natl. Acad.
Sci. USA 88:189-193), self-sustained sequence replication (Guatelli
et al. (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878),
transcriptional amplification system (Kwoh et al. (1989) Proc.
Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi et
al. (1988) Bio/Technology 6:1197), rolling circle replication (U.S.
Pat. No. 5,854,033) or any other nucleic acid amplification method,
followed by the detection of the amplified molecules using
techniques well known to those of skill in the art. These detection
schemes are especially useful for the detection of nucleic acid
molecules if such molecules are present in very low numbers. In
particular aspects of the invention, biomarker expression, or
expression of a CD40-related factor or other clinically useful
prognostic marker, is assessed by quantitative fluorogenic RT-PCR
(i.e., the TaqMan.RTM. System).
[0169] Expression levels of an RNA of interest may be monitored
using a membrane blot (such as used in hybridization analysis such
as Northern, dot, and the like), or microwells, sample tubes, gels,
beads or fibers (or any solid support comprising bound nucleic
acids). See U.S. Pat. Nos. 5,770,722, 5,874,219, 5,744,305,
5,677,195 and 5,445,934, which are incorporated herein by
reference. The detection of expression may also comprise using
nucleic acid probes in solution.
[0170] In one embodiment of the invention, microarrays are used to
detect expression of one or more biomarkers, CD40-related factors,
and/or clinically useful prognostic markers. Microarrays are
particularly well suited for this purpose because of the
reproducibility between different experiments. DNA microarrays
provide one method for the simultaneous measurement of the
expression levels of large numbers of genes. Each array consists of
a reproducible pattern of capture probes attached to a solid
support. Labeled RNA or DNA is hybridized to complementary probes
on the array and then detected by laser scanning Hybridization
intensities for each probe on the array are determined and
converted to a quantitative value representing relative gene
expression levels. See, U.S. Pat. Nos. 6,040,138, 5,800,992 and
6,020,135, 6,033,860, and 6,344,316, which are incorporated herein
by reference. High-density oligonucleotide arrays are particularly
useful for determining the gene expression profile for a large
number of RNA's in a sample.
[0171] Techniques for the synthesis of these arrays using
mechanical synthesis methods are described in, e.g., U.S. Pat. No.
5,384,261, incorporated herein by reference in its entirety.
Although a planar array surface is preferred, the array may be
fabricated on a surface of virtually any shape or even a
multiplicity of surfaces. Arrays may be peptides or nucleic acids
on beads, gels, polymeric surfaces, fibers such as fiber optics,
glass or any other appropriate substrate, see U.S. Pat. Nos.
5,770,358, 5,789,162, 5,708,153, 6,040,193 and 5,800,992, each of
which is hereby incorporated in its entirety for all purposes.
Arrays may be packaged in such a manner as to allow for diagnostics
or other manipulation of an all-inclusive device. See, for example,
U.S. Pat. Nos. 5,856,174 and 5,922,591, herein incorporated by
reference.
[0172] In one approach, total mRNA isolated from the sample is
converted to labeled cRNA and then hybridized to an oligonucleotide
array. Each sample is hybridized to a separate array. Relative
transcript levels may be calculated by reference to appropriate
controls present on the array and in the sample.
Anti-CD40 Therapeutic Agents
[0173] The ex vivo prognostic assays described herein can be used
to identify subjects having a cancer or pre-malignant condition
associated with CD40-expressing neoplastic cells who would benefit
from treatment with any anti-CD40 therapeutic agent of interest. Of
particular interest are anti-CD40 therapeutic agents that modulate
CD40L-mediated CD40 signaling and/or modulate ADCC. Such anti-CD40
therapeutic agents include, but are not limited to, antagonist
anti-CD40 antibodies that block or interfere with CD40L-mediated
signaling and/or modulate ADCC activity when bound to CD40, CD40L
antagonists, including anti-CD40L antibodies, mutated forms of
CD40L that can bind to CD40 but which do not trigger CD40
signaling, soluble CD40, soluble forms of fusion proteins
comprising CD40, and pharmacologic agents that disrupt or interfere
with CD40L-CD40 interaction and/or interfere with CD40 signaling,
for example, the CD40:CD40L binding interruptor compounds disclosed
in U.S. Patent Application Publication No. 20040067982, herein
incorporated by reference in its entirety. Of particular interest
are antagonist anti-CD40 therapeutic agents, for example,
antagonist anti-CD40 antibodies and antagonist anti-CD40L
antibodies, or antigen-binding fragments thereof that serve to
block CD40L-mediated CD40 signaling, and anti-CD40 therapeutic
agents that modulate ADCC, for example, anti-CD40 antibodies and
antigen-binding fragments thereof.
Anti-CD40 Antibodies.
[0174] Monoclonal antibodies to CD40 are known in the art. See, for
example, the sections dedicated to B-cell antigen in McMichael, ed.
(1987; 1989) Leukocyte Typing III and IV (Oxford University Press,
New York); U.S. Pat. Nos. 5,674,492; 5,874,082; 5,677,165;
6,056,959; WO 00/63395; International Publication Nos. WO 02/28905
and WO 02/28904; Gordon et al. (1988) J. Immunol. 140:1425; Valle
et al. (1989) Eur. J. Immunol. 19:1463; Clark et al. (1986) PNAS
83:4494; Paulie et al. (1989) J. Immunol. 142:590; Gordon et al.
(1987) Eur. J. Immunol. 17:1535; Jabara et al. (1990) J. Exp. Med.
172:1861; Zhang et al. (1991) J. Immunol. 146:1836; Gascan et al.
(1991) J. Immunol. 147:8; Banchereau et al. (1991) Clin. Immunol.
Spectrum 3:8; and Banchereau et al. (1991) Science 251:70; all of
which are herein incorporated by reference. Other anti-CD40
monoclonal antibodies include, but are not limited to, humanized
anti-CD40 antibodies, such as SGN-40 (Tai et al. (2004) Cancer Res.
64:2846-52; U.S. Pat. No. 6,838,261), which is the humanized form
of the murine anti-CD40 antibody SGN-14 (Francisco et al. (2000)
Cancer Res. 60:3225-31), and the agonist and antagonist antibodies
disclosed in U.S. Patent Application Publication No. 2004/0120948;
herein incorporated by reference in their entirety.
[0175] In one embodiment, the ex vivo prognostic assays are used to
examine suitability or efficacy of treatment with antagonist
anti-CD40 antibodies. Antagonist anti-CD40 antibodies for use in
the methods of the invention include monoclonal antibodies or
antigen-binding fragments thereof that are capable of specifically
binding to human CD40 antigen expressed on the surface of a human
cell. In some embodiments, antagonist anti-CD40 antibodies for use
in the methods of the present invention exhibit a strong
single-site binding affinity for the CD40 cell-surface antigen.
Such monoclonal antibodies exhibit a dissociation equilibrium
constant (K.sub.D) for CD40 of at least 10.sup.-5 M, at least
3.times.10.sup.-5 M, preferably at least 10.sup.-6 M to 10.sup.-7
M, more preferably at least 10.sup.-8M to about 10.sup.-12 M,
measured using a standard assay such as Biacore.TM.. Biacore
analysis is known in the art and details are provided in the
"BIAapplications handbook." Methods described in WO 01/27160 can be
used to modulate the binding affinity.
[0176] Of particular interest are antagonist anti-CD40 antibodies
that are free of significant agonist activity as defined herein
above but exhibit antagonist activity when bound to CD40 antigen on
human cells, particularly when bound to CD40 antigen on neoplastic
human B cells. In one embodiment of the invention, the antagonist
anti-CD40 antibody is free of significant agonist activity in one B
cell response. In another embodiment of the invention, the
antagonist anti-CD40 antibody is free of significant agonist
activity in assays of more than one B cell response (e.g.,
proliferation and differentiation, or proliferation,
differentiation, and antibody production). Suitable monoclonal
anti-CD40 antibodies have human constant regions; preferably they
also have wholly or partially humanized framework regions; and most
preferably are fully human antibodies or antigen-binding fragments
thereof. Examples of such monoclonal antibodies are the antibodies
designated herein as CHIR-5.9 and CHIR-12.12.
[0177] The monoclonal antibodies CHIR-5.9 and CHIR-12.12 represent
antagonist anti-CD40 antibodies for use in the methods of the
present invention. The CHIR-5.9 and CHIR-12.12 antibodies are fully
human anti-CD40 monoclonal antibodies of the IgG.sub.1 isotype
produced from the hybridoma cell lines 131.2F8.5.9 (referred to
herein as the cell line 5.9) and 153.8E2.D10.D6.12.12 (referred to
herein as the cell line 12.12). These cell lines were created using
splenocytes from immunized xenotypic mice containing the human
IgG.sub.1 heavy chain locus and the human .kappa. chain locus
(XenoMouse.RTM. technology; Abgenix; Fremont, Calif.). The spleen
cells were fused with the mouse myeloma SP2/0 cells (Sierra
BioSource). The resulting hybridomas were sub-cloned several times
to create the stable monoclonal cell lines 5.9 and 12.12. Other
antibodies of the invention may be prepared similarly using mice
transgenic for human immunoglobulin loci or by other methods known
in the art and/or described herein.
[0178] The nucleotide and amino acid sequences of the variable
regions of the CHIR-12.12 antibody, and the amino acid sequences of
the variable regions of the CHIR-5.9 antibody, are disclosed. More
particularly, the amino acid sequences for the leader, variable,
and constant regions for the light chain and heavy chain for mAb
CHIR-12.12 are set forth in SEQ ID NO:2 (complete sequence for the
light chain of mAb CHIR-12.12), SEQ ID NO:4 (complete sequence for
the heavy chain for mAb CHIR-12.12), and SEQ ID NO:5 (complete
sequence for a variant of the heavy chain for mAb CHIR-12.12 set
forth in SEQ ID NO:4, where the variant comprises a serine
substitution for the alanine residue at position 153 of SEQ ID
NO:4). The nucleotide sequences encoding the light chain and heavy
chain for mAb CHIR-12.12 are set forth in SEQ ID NO:1 (coding
sequence for the light chain for mAb CHIR-12.12) and SEQ ID NO:3
(coding sequence for the heavy chain for mAb CHIR-12.12). The amino
acid sequences for the leader, variable, and constant regions for
the light chain and heavy chain of the CHIR-5.9 mAb are set forth
in SEQ ID NO:6 (complete sequence for the light chain of mAb
CHIR-5.9), SEQ ID NO:7 (complete sequence for the heavy chain of
mAb CHIR-5.9), and SEQ ID NO:8 (complete sequence for a variant of
the heavy chain of mAb CHIR-5.9 set forth in SEQ ID NO:7, where the
variant comprises a serine substitution for the alanine residue at
position 158 of SEQ ID NO:7). Further, hybridomas expressing
CHIR-5.9 and CHIR-12.12 antibodies have been deposited with the
ATCC with a patent deposit designation of PTA-5542 and PTA-5543,
respectively.
[0179] In addition to antagonist activity, anti-CD40 antibodies for
use in the methods of the present invention can have another
mechanism of action against a tumor cell. For example, native
CHIR-5.9 and CHIR-12.12 antibodies have ADCC activity.
Alternatively, the variable regions of the CHIR-5.9 and CHIR-12.12
antibodies can be expressed on another antibody isotype that has
ADCC activity. It is also possible to conjugate native forms,
recombinant forms, or antigen-binding fragments of CHIR-5.9 or
CHIR-12.12 to a cytotoxin, a therapeutic agent, or a radioactive
metal ion or radioisotope, as noted herein below.
[0180] The CHIR-5.9 and CHIR-12.12 monoclonal antibodies bind
soluble CD40 in ELISA-type assays, prevent the binding of
CD40-ligand to cell-surface CD40, and displace the pre-bound
CD40-ligand, as determined by flow cytometric assays. Antibodies
CHIR-5.9 and CHIR-12.12 compete with each other for binding to CD40
but not with 15B8, the anti-CD40 monoclonal antibody described in
U.S. Provisional Application Ser. No. 60/237,556, titled "Human
Anti-CD40 Antibodies," filed Oct. 2, 2000, and PCT International
Application No. PCT/US01/30857, also titled "Human Anti-CD40
Antibodies," filed Oct. 2, 2001 (Attorney Docket No. PP16092.003),
both of which are herein incorporated by reference in their
entirety. When tested in vitro for effects on proliferation of B
cells from normal human subjects, CHIR-5.9 and CHIR-12.12 act as
antagonist anti-CD40 antibodies. Furthermore, CHIR-5.9 and
CHIR-12.12 do not induce strong proliferation of human lymphocytes
from normal subjects. These antibodies are able to kill
CD40-expressing target cells by antibody dependent cellular
cytotoxicity (ADCC). The binding affinity of CHIR-5.9 for human
CD40 is 1.2.times.10.sup.-8 M and the binding affinity of
CHIR-12.12 is 5.times.10.sup.-10 M, as determined by the
Biacore.TM. assay.
[0181] Other antagonist anti-CD40 antibodies that share the binding
characteristics of the monoclonal antibodies CHIR-5.9 and
CHIR-12.12 described above include, but are not limited to the
following: (1) the monoclonal antibodies produced by the hybridoma
cell lines designated 131.2F8.5.9 (referred to herein as the cell
line 5.9) and 153.8E2.D10.D6.12.12 (referred to herein as the cell
line 12.12), deposited with the ATCC as Patent Deposit No. PTA-5542
and Patent Deposit No. PTA-5543, respectively; (2) a monoclonal
antibody comprising an amino acid sequence selected from the group
consisting of the sequence shown in SEQ ID NO:2, the sequence shown
in SEQ ID NO:4, the sequence shown in SEQ ID NO:5, both the
sequences shown in SEQ ID NO:2 and SEQ ID NO:4, and both the
sequences shown in SEQ ID NO:2 and SEQ ID NO:5; (3) a monoclonal
antibody comprising an amino acid sequence selected from the group
consisting of the sequence shown in SEQ ID NO:6, the sequence shown
in SEQ ID NO:7, the sequence shown in SEQ ID NO:8, both the
sequences shown in SEQ ID NO:6 and SEQ ID NO:7, and both the
sequences shown in SEQ ID NO:6 and SEQ ID NO:8; (4) a monoclonal
antibody having an amino acid sequence encoded by a nucleic acid
molecule comprising a nucleotide sequence selected from the group
consisting of the nucleotide sequence shown in SEQ ID NO:1, the
nucleotide sequence shown in SEQ ID NO:3, and both the sequences
shown in SEQ ID NO:1 and SEQ ID NO:3; (5) a monoclonal antibody
that binds to an epitope capable of binding the monoclonal antibody
produced by the hybridoma cell line 5.9 or the hybridoma cell line
12.12; (6) a monoclonal antibody that binds to an epitope
comprising residues 82-87 of the amino acid sequence shown in SEQ
ID NO:10 or SEQ ID NO:12; (7) a monoclonal antibody that competes
with the monoclonal antibody CHIR-5.9 or CHIR-12.12 in a
competitive binding assay; and (8) a monoclonal antibody that is an
antigen-binding fragment of the CHIR-12.12 or CHIR-5.9 monoclonal
antibody or the foregoing monoclonal antibodies in preceding items
(1)-(7), where the fragment retains the capability of specifically
binding to the human CD40 antigen.
[0182] Those skilled in the art recognize that the antibodies and
antigen-binding fragments of these antibodies described herein
include antibodies and antigen-binding fragments thereof that are
produced recombinantly using methods well known in the art and
described herein below, and include, for example, monoclonal
antibodies CHIR-5.9 and CHIR-12.12 that have been recombinantly
produced.
[0183] Additional antagonist anti-CD40 antibodies include the
monoclonal antibodies referred to as 5D12, 3A8 and 3C6, which are
secreted by a hybridoma having ATCC accession numbers HB 11339, HB
12024 and HB 11340, respectively. See, for example, U.S. Pat. No.
6,315,998, herein incorporated by reference in its entirety.
[0184] Other antagonist anti-CD40 antibodies are known in the art.
See, for example, the human anti-CD40 antibody produced by the
hybridoma designated F4-465 disclosed in U.S. Patent Application
Publication Nos. 20020142358 and 20030059427; herein incorporated
by reference in their entirety. F4-465 was obtained from the HAC
mouse (Kuroiwa et al. (2000) Nature Biotech. 10:1086 (2000)) and
therefore expresses the human lambda light chain.
Antagonist Anti-CD40L Antibodies.
[0185] Antibodies that bind to CD40L and thereby interfere with
CD40/CD40L interaction or CD40L-mediated CD40 signaling are known
in the art. Examples include, but are not limited to, those
disclosed in International Patent Publication WO 95/06666, the
content of which is herein by reference in its entirety. Specific
examples include, but are not limited to antagonist anti-CD40L
antibodies designated 89-76 and 24-31, which are produced by the
89-76 and 24-31 hybridomas, respectively, deposited with the
American Type Culture Collection (ATCC), 10801 University Blvd.,
Manassas, Virgina 20110-2209, and assigned ATCC Accession Number
HB11713 and HB11712, respectively.
Production of Antibodies
[0186] The antibodies for use in the methods of the present
invention, for example, the antagonist anti-CD40 antibodies
disclosed herein and any antibody that specifically binds to a
biomarker or other clinically useful prognostic marker of interest,
can be produced using any antibody production method known to those
of skill in the art. Thus, polyclonal sera may be prepared by
conventional methods. In general, a solution containing the antigen
of interest, for example, the CD40 antigen or CD40L antigen, is
first used to immunize a suitable animal, preferably a mouse, rat,
rabbit, or goat. Rabbits or goats are preferred for the preparation
of polyclonal sera due to the volume of serum obtainable, and the
availability of labeled anti-rabbit and anti-goat antibodies.
[0187] Polyclonal sera can be prepared in a transgenic animal,
preferably a mouse bearing human immunoglobulin loci. In a
preferred embodiment, Sf9 cells expressing the protein of interest,
for example, CD40 or CD40L, are used as the immunogen. Immunization
can also be performed by mixing or emulsifying the
antigen-containing solution in saline, preferably in an adjuvant
such as Freund's complete adjuvant, and injecting the mixture or
emulsion parenterally (generally subcutaneously or
intramuscularly). A dose of 50-200 .mu.g/injection is typically
sufficient Immunization is generally boosted 2-6 weeks later with
one or more injections of the protein in saline, preferably using
Freund's incomplete adjuvant. One may alternatively generate
antibodies by in vitro immunization using methods known in the art,
which for the purposes of this invention is considered equivalent
to in vivo immunization. Polyclonal antisera are obtained by
bleeding the immunized animal into a glass or plastic container,
incubating the blood at 25.degree. C. for one hour, followed by
incubating at 4.degree. C. for 2-18 hours. The serum is recovered
by centrifugation (e.g., 1,000.times.g for 10 minutes). About 20-50
ml per bleed may be obtained from rabbits.
[0188] Production of the Sf 9 (Spodoptera frugiperda) cells is
disclosed in U.S. Pat. No. 6,004,552, incorporated herein by
reference. In the case of CD40, briefly, sequences encoding human
CD40 were recombined into a baculovirus using transfer vectors. The
plasmids were co-transfected with wild-type baculovirus DNA into Sf
9 cells. Recombinant baculovirus-infected Sf 9 cells were
identified and clonally purified.
[0189] Preferably the antibody is monoclonal in nature. By
"monoclonal antibody" is intended an antibody obtained from a
population of substantially homogeneous antibodies, i.e., the
individual antibodies comprising the population are identical
except for possible naturally occurring mutations that may be
present in minor amounts. The term is not limited regarding the
species or source of the antibody. The term encompasses whole
immunoglobulins as well as fragments such as Fab, F(ab')2, Fv, and
others which retain the antigen binding function of the antibody.
Monoclonal antibodies are highly specific, being directed against a
single antigenic site; for example, in the case of anti-CD40
antibodies or anti-CD40L antibodies, the CD40 cell surface antigen
or CD40L cell surface antigen, respectively. Furthermore, in
contrast to conventional (polyclonal) antibody preparations that
typically include different antibodies directed against different
determinants (epitopes), each monoclonal antibody is directed
against a single determinant on the antigen. 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 the
hybridoma method first described by Kohler et al. (1975) Nature
256:495, or may be made by recombinant DNA methods (see, e.g., U.S.
Pat. No. 4,816,567). The "monoclonal antibodies" may also be
isolated from phage antibody libraries using the techniques
described in, for example, Clackson et al. (1991) Nature
352:624-628; Marks et al. (1991) J. Mol. Biol. 222:581-597; and
U.S. Pat. No. 5,514,548.
[0190] By "epitope" is intended the part of an antigenic molecule
to which an antibody is produced and to which the antibody will
bind. Epitopes can comprise linear amino acid residues (i.e.,
residues within the epitope are arranged sequentially one after
another in a linear fashion), nonlinear amino acid residues
(referred to herein as "nonlinear epitopes"; these epitopes are not
arranged sequentially), or both linear and nonlinear amino acid
residues.
[0191] Monoclonal antibodies can be prepared using the method of
Kohler et al. (1975) Nature 256:495-496, or a modification thereof.
Typically, a mouse is immunized with a solution containing an
antigen Immunization can be performed by mixing or emulsifying the
antigen-containing solution in saline, preferably in an adjuvant
such as Freund's complete adjuvant, and injecting the mixture or
emulsion parenterally. Any method of immunization known in the art
may be used to obtain the monoclonal antibodies of the invention.
After immunization of the animal, the spleen (and optionally,
several large lymph nodes) are removed and dissociated into single
cells. The spleen cells may be screened by applying a cell
suspension to a plate or well coated with the antigen of interest.
The B cells expressing membrane bound immunoglobulin specific for
the antigen bind to the plate and are not rinsed away. Resulting B
cells, or all dissociated spleen cells, are then induced to fuse
with myeloma cells to form hybridomas, and are cultured in a
selective medium. The resulting cells are plated by serial dilution
and are assayed for the production of antibodies that specifically
bind the antigen of interest (and that do not bind to unrelated
antigens). The selected monoclonal antibody (mAb)-secreting
hybridomas are then cultured either in vitro (e.g., in tissue
culture bottles or hollow fiber reactors), or in vivo (as ascites
in mice).
[0192] Where antibodies for use in the methods of the invention,
for example, antagonist anti-CD40 antibodies or antagonist
anti-CD40L antibodies, are to be prepared using recombinant DNA
methods, the DNA encoding the monoclonal antibodies is readily
isolated and sequenced using conventional procedures (e.g., by
using oligonucleotide probes that are capable of binding
specifically to genes encoding the heavy and light chains of murine
antibodies). The hybridoma cells described herein serve as a
preferred source of such DNA. Once isolated, the DNA may be placed
into expression vectors, which are then transfected into host cells
such as E. coli cells, simian COS cells, Chinese Hamster Ovary
(CHO) cells, or myeloma cells that do not otherwise produce
immunoglobulin protein, to obtain the synthesis of monoclonal
antibodies in the recombinant host cells. Review articles on
recombinant expression in bacteria of DNA encoding the antibody
include Skerra et al. (1993) Curr. Opinion in Immunol. 5:256 and
Phickthun (1992) Immunol. Revs. 130:151. Alternatively, antibody
can be produced in a cell line such as a CHO cell line, as
disclosed in U.S. Pat. Nos. 5,545,403; 5,545,405; and 5,998,144;
incorporated herein by reference. Briefly the cell line is
transfected with vectors capable of expressing a light chain and a
heavy chain, respectively. By transfecting the two proteins on
separate vectors, chimeric antibodies can be produced. Another
advantage is the correct glycosylation of the antibody.
[0193] In some embodiments, the antagonist anti-CD40 antibody, for
example, the CHIR-12.12 or CHIR-5.9 antibody, or antigen-binding
fragment thereof is produced in CHO cells using the GS gene
expression system (Lonza Biologics, Portsmouth, N.H.), which uses
glutamine synthetase as a marker. See, also U.S. Pat. Nos.
5,122,464; 5,591,639; 5,658,759; 5,770,359; 5,827,739; 5,879,936;
5,891,693; and 5,981,216; the contents of which are herein
incorporated by reference in their entirety.
[0194] Additionally, antibodies for use in the methods of the
invention can be chimeric antibodies that have the desired binding
characteristics. Thus, for example, chimeric anti-CD40 antibodies
for use in the methods of the invention could have the binding
characteristics of the CHIR-5.9 and CHIR-12.12 monoclonal
antibodies described herein. By "chimeric" antibodies is intended
antibodies that are most preferably derived using recombinant
deoxyribonucleic acid techniques and which comprise both human
(including immunologically "related" species, e.g., chimpanzee) and
non-human components. Thus, the constant region of the chimeric
antibody is most preferably substantially identical to the constant
region of a natural human antibody; the variable region of the
chimeric antibody is most preferably derived from a non-human
source and has the desired antigenic specificity to the antigen of
interest, for example, CD40 or CD40L antigen. The non-human source
can be any vertebrate source that can be used to generate
antibodies to a human antigen or material comprising a human CD40
antigen. Such non-human sources include, but are not limited to,
rodents (e.g., rabbit, rat, mouse, etc.; see, for example, U.S.
Pat. No. 4,816,567, herein incorporated by reference) and non-human
primates (e.g., Old World Monkey, Ape, etc.; see, for example, U.S.
Pat. Nos. 5,750,105 and 5,756,096; herein incorporated by
reference). As used herein, the phrase "immunologically active"
when used in reference, for example, to chimeric anti-CD40
antibodies or chimeric anti-CD40L antibodies, means a chimeric
antibody that binds human CD40 or human CD40L, respectively.
[0195] By "humanized" is intended forms of antibodies that contain
minimal sequence derived from non-human immunoglobulin sequences.
For the most part, humanized antibodies are human immunoglobulins
(recipient antibody) in which residues from a hypervariable region
(also known as complementarity determining region or CDR) of the
recipient are replaced by residues from a hypervariable region of a
non-human species (donor antibody) such as mouse, rat, rabbit, or
nonhuman primate having the desired specificity, affinity, and
capacity. The phrase "complementarity determining region" refers to
amino acid sequences which together define the binding affinity and
specificity of the natural Fv region of a native immunoglobulin
binding site. See, e.g., Chothia et al (1987) J. Mol. Biol.
196:901-917; Kabat et al (1991) U.S. Dept. of Health and Human
Services, NIH Publication No. 91-3242). The phrase "constant
region" refers to the portion of the antibody molecule that confers
effector functions. In previous work directed towards producing
non-immunogenic antibodies for use in therapy of human disease,
mouse constant regions were substituted by human constant regions.
The constant regions of the subject humanized antibodies were
derived from human immunoglobulins. However, these humanized
antibodies still elicited an unwanted and potentially dangerous
immune response in humans and there was a loss of affinity.
Humanized antibodies, for example, humanized anti-CD40 antibodies,
for use in the methods of the present invention have binding
characteristics similar to those exhibited by the parent antibody
of interest, for example, the CHIR-5.9 and CHIR-12.12 monoclonal
antibodies described herein.
[0196] Humanization can be essentially performed following the
method of Winter and co-workers (Jones et al. (1986) Nature
321:522-525; Riechmann et al. (1988) Nature 332:323-327; Verhoeyen
et al. (1988) Science 239:1534-1536), by substituting rodent or
mutant rodent CDRs or CDR sequences for the corresponding sequences
of a human antibody. See also U.S. Pat. Nos. 5,225,539; 5,585,089;
5,693,761; 5,693,762; 5,859,205; herein incorporated by reference.
In some instances, residues within the framework regions of one or
more variable regions of the human immunoglobulin are replaced by
corresponding non-human residues (see, for example, U.S. Pat. Nos.
5,585,089; 5,693,761; 5,693,762; and 6,180,370). Furthermore,
humanized antibodies may comprise residues that are not found in
the recipient antibody or in the donor antibody. These
modifications are made to further refine antibody performance
(e.g., to obtain desired affinity). In general, the humanized
antibody will comprise substantially all of at least one, and
typically two, variable domains, in which all or substantially all
of the hypervariable regions correspond to those of a non-human
immunoglobulin and all or substantially all of the framework
regions are those of a human immunoglobulin sequence. The humanized
antibody optionally also will comprise at least a portion of an
immunoglobulin constant region (Fc), typically that of a human
immunoglobulin. For further details see Jones et al. (1986) Nature
331:522-525; Riechmann et al. (1988) Nature 332:323-329; and Presta
(1992) Curr. Op. Struct. Biol. 2:593-596; herein incorporated by
reference. Accordingly, such "humanized" antibodies may include
antibodies wherein substantially less than an intact human variable
domain has been substituted by the corresponding sequence from a
non-human species. In practice, humanized antibodies are typically
human antibodies in which some CDR residues and possibly some
framework residues are substituted by residues from analogous sites
in rodent antibodies. See, for example, U.S. Pat. Nos. 5,225,539;
5,585,089; 5,693,761; 5,693,762; 5,859,205. See also U.S. Pat. No.
6,180,370, and International Publication No. WO 01/27160, where
humanized antibodies and techniques for producing humanized
antibodies having improved affinity for a predetermined antigen are
disclosed.
[0197] The present invention can also be practiced using xenogeneic
or modified antibodies produced in a non-human mammalian host, more
particularly a transgenic mouse, characterized by inactivated
endogenous immunoglobulin (Ig) loci. In such transgenic animals,
competent endogenous genes for the expression of light and heavy
subunits of host immunoglobulins are rendered non-functional and
substituted with the analogous human immunoglobulin loci. These
transgenic animals produce human antibodies in the substantial
absence of light or heavy host immunoglobulin subunits. See, for
example, U.S. Pat. Nos. 5,877,397 and 5,939,598, herein
incorporated by reference.
[0198] In some embodiments, fully human antibodies to CD40, for
example, are obtained by immunizing transgenic mice. One such mouse
is obtained using XenoMouse.RTM. technology (Abgenix; Fremont,
Calif.), and is disclosed in U.S. Pat. Nos. 6,075,181, 6,091,001,
and 6,114,598, all of which are incorporated herein by reference.
To produce the antibodies disclosed herein, mice transgenic for the
human Ig G.sub.1 heavy chain locus and the human K light chain
locus were immunized with Sf 9 cells expressing human CD40. Mice
can also be transgenic for other isotypes. Fully human anti-CD40
antibodies useful in the methods of the present invention are
characterized by binding properties similar to those exhibited by
the CHIR-5.9 and CHIR-12.12 monoclonal antibodies disclosed
herein.
[0199] Fragments of a particular antibody of interest, for example,
an anti-CD40 antibody or anti-CD40L antibody, are suitable for use
in the methods of the invention so long as they retain the desired
affinity of the full-length antibody. Thus, for example, a fragment
of an anti-CD40 antibody will retain the ability to bind to the
CD40 B cell surface antigen. Such fragments are characterized by
properties similar to the corresponding full-length antibody. Thus,
for example, a fragment of a full-length antagonist anti-CD40
antibody will specifically bind a human CD40 antigen expressed on
the surface of a human cell, and is free of significant agonist
activity but exhibits antagonist activity when bound to a CD40
antigen on a human CD40-expressing cell. Such fragments are
referred to herein as "antigen-binding" fragments.
[0200] Suitable antigen-binding fragments of an antibody comprise a
portion of a full-length antibody, generally the antigen-binding or
variable region thereof. Examples of antibody fragments include,
but are not limited to, Fab, F(ab').sub.2, and Fv fragments and
single-chain antibody molecules. By "Fab" is intended a monovalent
antigen-binding fragment of an immunoglobulin that is composed of
the light chain and part of the heavy chain. By F(ab').sub.2 is
intended a bivalent antigen-binding fragment of an immunoglobulin
that contains both light chains and part of both heavy chains. By
"single-chain Fv" or "sFv" antibody fragments is intended fragments
comprising the V.sub.H and V.sub.L domains of an antibody, wherein
these domains are present in a single polypeptide chain. See, for
example, U.S. Pat. Nos. 4,946,778, 5,260,203, 5,455,030, and
5,856,456, herein incorporated by reference. Generally, the Fv
polypeptide further comprises a polypeptide linker between the
V.sub.H and V.sub.L domains that enables the sFv to form the
desired structure for antigen binding. For a review of sFv see
Pluckthun (1994) in The Pharmacology of Monoclonal Antibodies, Vol.
113, ed. Rosenburg and Moore (Springer-Verlag, New York), pp.
269-315. Antigen-binding fragments of the antagonist anti-CD40
antibodies disclosed herein can also be conjugated to a cytotoxin
to effect killing of the target cancer cells, as described herein
below.
[0201] Antibodies or antibody fragments can be isolated from
antibody phage libraries generated using the techniques described
in, for example, McCafferty et al. (1990) Nature 348:552-554 (1990)
and U.S. Pat. No. 5,514,548. Clackson et al. (1991) Nature
352:624-628 and Marks et al. (1991) J. Mol. Biol. 222:581-597
describe the isolation of murine and human antibodies,
respectively, using phage libraries. Subsequent publications
describe the production of high affinity (nM range) human
antibodies by chain shuffling (Marks et al. (1992) Bio/Technology
10:779-783), as well as combinatorial infection and in vivo
recombination as a strategy for constructing very large phage
libraries (Waterhouse et al. (1993) Nucleic. Acids Res.
21:2265-2266). Thus, these techniques are viable alternatives to
traditional monoclonal antibody hybridoma techniques for isolation
of monoclonal antibodies.
[0202] Various techniques have been developed for the production of
antibody fragments. Traditionally, these fragments were derived via
proteolytic digestion of intact antibodies (see, e.g., Morimoto et
al. (1992) Journal of Biochemical and Biophysical Methods
24:107-117 (1992) and Brennan et al. (1985) Science 229:81).
However, these fragments can now be produced directly by
recombinant host cells. For example, the antibody fragments can be
isolated from the antibody phage libraries discussed above.
Alternatively, Fab'-SH fragments can be directly recovered from E.
coli and chemically coupled to form F(ab').sub.2 fragments (Carter
et al. (1992) Bio/Technology 10:163-167). According to another
approach, F(ab').sub.2 fragments can be isolated directly from
recombinant host cell culture. Other techniques for the production
of antibody fragments will be apparent to the skilled
practitioner.
[0203] Antagonist anti-CD40 antibodies for use in the methods of
the present invention include the CHIR-5.9 and CHIR-12.12
monoclonal antibodies disclosed herein as well as antibodies
differing from this antibody but retaining the CDRs; and antibodies
with one or more amino acid addition(s), deletion(s), or
substitution(s), wherein the antagonist activity is measured by
inhibition of B-cell proliferation and/or differentiation. The
invention also encompasses de-immunized antibodies, particularly
de-immunized antagonist anti-CD40 antibodies, which can be produced
as described in, for example, International Publication Nos. WO
98/52976 and WO 0034317; herein incorporated by reference. In this
manner, residues within the antagonist anti-CD40 antibodies of the
invention are modified so as to render the antibodies non- or less
immunogenic to humans while retaining their antagonist activity
toward human CD40-expressing cells, wherein such activity is
measured by assays noted elsewhere herein. Also included within the
scope of the present invention are fusion proteins comprising an
antibody of interest, for example, an antagonist anti-CD40 antibody
or an antagonist anti-CD40L antibody, or a fragment thereof, which
fusion proteins can be synthesized or expressed from corresponding
polynucleotide vectors, as is known in the art. Such fusion
proteins are described with reference to conjugation of antibodies
as noted elsewhere herein.
[0204] Any known antibody having the binding specificity of
interest can have sequence variations produced using methods
described in, for example, Patent Publication Nos. EP 0 983 303 A1,
WO 00/34317, and WO 98/52976, incorporated herein by reference. For
example, it has been shown that sequences within the CDR can cause
an antibody to bind to MHC Class II and trigger an unwanted helper
T-cell response. A conservative substitution can allow the antibody
to retain binding activity yet lose its ability to trigger an
unwanted T-cell response. Any such conservative or non-conservative
substitutions can be made using art-recognized methods, such as
those noted elsewhere herein, and the resulting antibodies can also
be used in the methods of the present invention. The variant
antibodies can be routinely tested for the particular activity, for
example, antagonist activity, affinity, and specificity using
methods described herein.
[0205] Where the anti-CD40 therapeutic agent is an antagonist
anti-CD40 antibody, the antagonist anti-CD40 antibody produced by
any of the methods described above, or any other method not
disclosed herein, can be used in a manner similar to the CHIR-12.12
or CHIR-5.9 antibody where it possesses at least one of the
following biological activities: inhibition of immunoglobulin
secretion by normal human peripheral B cells stimulated by T cells;
inhibition of survival and/or proliferation of normal human
peripheral B cells stimulated by Jurkat T cells; inhibition of
survival and/or proliferation of normal human peripheral B cells
stimulated by CD40L-expressing cells or soluble CD40 ligand
(sCD40L); inhibition of "survival" anti-apoptotic intracellular
signals in any cell stimulated by sCD40L or solid-phase CD40L;
inhibition of CD40 signal transduction in any cell upon ligation
with sCD40L or solid-phase CD40L; and inhibition of proliferation
of human malignant B cells as noted below. Assays for such
biological activities can be performed as described herein and in
provisional applications entitled "Antagonist Anti-CD40 Monoclonal
Antibodies and Methods for Their Use," filed Nov. 4, 2003, Nov. 26,
2003, and Apr. 27, 2004, and assigned U.S. Patent Application Nos.
60/517,337 (Attorney Docket No. PP20107.001 (035784/258442)),
60/525,579 (Attorney Docket No. PP20107.002 (035784/271525)), and
60/565,710 (Attorney Docket No. PP20107.003 (035784/277214)),
respectively; and International Patent Application No.
PCT/US2004/037152 (Attorney Docket No. PP20107.004
(035784/282916)), also entitled "Antagonist Anti-CD40 Monoclonal
Antibodies and Methods for Their Use," filed Nov. 4, 2004; the
contents of each of which are herein incorporated by reference in
their entirety. See also the assays described in Schultze et al.
(1998) Proc. Natl. Acad. Sci. USA 92:8200-8204; Denton et al.
(1998) Pediatr. Transplant. 2:6-15; Evans et al. (2000) J. Immunol.
164:688-697; Noelle (1998) Agents Actions Suppl. 49:17-22; Lederman
et al. (1996) Curr. Opin. Hematol. 3:77-86; Coligan et al. (1991)
Current Protocols in Immunology 13:12; Kwekkeboom et al. (1993)
Immunology 79:439-444; and U.S. Pat. Nos. 5,674,492 and 5,847,082;
herein incorporated by reference.
[0206] A representative assay to detect antagonist anti-CD40
antibodies specific to the CD40-antigen epitopes identified herein
is a "competitive binding assay." Competitive binding assays are
serological assays in which unknowns are detected and quantitated
by their ability to inhibit the binding of a labeled known ligand
to its specific antibody. This is also referred to as a competitive
inhibition assay. In a representative competitive binding assay,
labeled CD40 polypeptide is precipitated by candidate antibodies in
a sample, for example, in combination with monoclonal antibodies
raised against one or more epitopes of the monoclonal antibodies of
the invention. Anti-CD40 antibodies that specifically react with an
epitope of interest can be identified by screening a series of
antibodies prepared against a CD40 protein or fragment of the
protein comprising the particular epitope of the CD40 protein of
interest. For example, for human CD40, epitopes of interest include
epitopes comprising linear and/or nonlinear amino acid residues of
the short isoform of human CD40 (see GenBank Accession No.
NP.sub.--690593) set forth in SEQ ID NO:10, encoded by the sequence
set forth SEQ ID NO:9; see also GenBank Accession No.
NM.sub.--152854), or of the long isoform of human CD40 (see GenBank
Accession Nos. CAA43045 and NP.sub.--001241, set forth in SEQ ID
NO:12, encoded by the sequence set forth in SEQ ID NO:11; see
GenBank Accession Nos. X60592 and NM.sub.--001250). Alternatively,
competitive binding assays with previously identified suitable
antagonist anti-CD40 antibodies could be used to select monoclonal
antibodies comparable to the previously identified antibodies.
[0207] Antibodies employed in such immunoassays may be labeled or
unlabeled. Unlabeled antibodies may be employed in agglutination;
labeled antibodies may be employed in a wide variety of assays,
employing a wide variety of labels. Detection of the formation of
an antibody-antigen complex between an anti-CD40 antibody and an
epitope of interest can be facilitated by attaching a detectable
substance to the antibody. Suitable detection means include the use
of labels such as radionuclides, enzymes, coenzymes, fluorescers,
chemiluminescers, chromogens, enzyme substrates or co-factors,
enzyme inhibitors, prosthetic group complexes, free radicals,
particles, dyes, and the like. Examples of suitable enzymes include
horseradish peroxidase, alkaline phosphatase, .beta.-galactosidase,
or acetylcholinesterase; examples of suitable prosthetic group
complexes include streptavidin/biotin and avidin/biotin; examples
of suitable fluorescent materials include umbelliferone,
fluorescein, fluorescein isothiocyanate, rhodamine,
dichlorotriazinylamine fluorescein, dansyl chloride or
phycoerythrin; an example of a luminescent material is luminol;
examples of bioluminescent materials include luciferase, luciferin,
and aequorin; and examples of suitable radioactive material include
.sup.125I, .sup.131I, .sup.35S, or .sup.3H. Such labeled reagents
may be used in a variety of well-known assays, such as
radioimmunoassays, enzyme immunoassays, e.g., ELISA, fluorescent
immunoassays, and the like. See for example, U.S. Pat. Nos.
3,766,162; 3,791,932; 3,817,837; and 4,233,402.
[0208] Any of the previously described antibodies, for example,
antagonist anti-CD40 antibodies or antibody fragments thereof, may
be conjugated prior to use in the methods of the present invention.
Methods for producing conjugated antibodies are known in the art.
Thus, the antibody may be labeled using an indirect labeling or
indirect labeling approach. By "indirect labeling" or "indirect
labeling approach" is intended that a chelating agent is covalently
attached to an antibody and at least one radionuclide is inserted
into the chelating agent. See, for example, the chelating agents
and radionuclides described in Srivagtava and Mease (1991) Nucl.
Med. Bio. 18:589-603, herein incorporated by reference. Suitable
labels include fluorophores, chromophores, radioactive atoms
(particularly .sup.32P and .sup.1251), electron-dense reagents,
enzymes, and ligands having specific binding partners. Enzymes are
typically detected by their activity. For example, horseradish
peroxidase is usually detected by its ability to convert
3,3',5,5'-tetramethylbenzidine (TMB) to a blue pigment,
quantifiable with a spectrophotometer. "Specific binding partner"
refers to a protein capable of binding a ligand molecule with high
specificity, as for example in the case of an antigen and a
monoclonal antibody specific therefore. Other specific binding
partners include biotin and avidin or streptavidin, Ig G and
protein A, and the numerous receptor-ligand couples known in the
art. It should be understood that the above description is not
meant to categorize the various labels into distinct classes, as
.sup.125I may the same label may serve in several different modes.
For example, serve as a radioactive label or as an electron-dense
reagent. HRP may serve as enzyme or as antigen for a mAb. Further,
one may combine various labels for desired effect. For example,
mAbs and avidin also require labels in the practice of this
invention: thus, one might label a mAb with biotin, and detect its
presence with avidin labeled with .sup.125I, or with an anti-biotin
mAb labeled with HRP. Other permutations and possibilities will be
readily apparent to those of ordinary skill in the art, and are
considered as equivalents within the scope of the instant
invention.
[0209] Alternatively, an antibody of interest, for example, an
anti-CD40 antibody, may be labeled using "direct labeling" or a
"direct labeling approach," where a radionuclide is covalently
attached directly to an antibody (typically via an amino acid
residue). Preferred radionuclides are provided in Srivagtava and
Mease (1991) supra. The indirect labeling approach is particularly
preferred. See also, for example, International Publication Nos. WO
00/52031 and WO 00/52473, where a linker is used to attach a
radioactive label to antibodies; and the labeled forms of anti-CD40
antibodies described in U.S. Pat. No. 6,015,542; herein
incorporated by reference.
Variants of Antibodies
[0210] The methods of the present invention can be carried out
using variants of an antibody known in the art. Such variants will
retain the desired binding properties of the parent antibody. Thus,
for example, where the anti-CD40 therapeutic agent to be tested is
an antagonist anti-CD40 antibody, the variant antibody will retain
the binding properties of the parent antagonist anti-CD40 antibody,
for example, the CHIR-12.12 or CHIR-5.9 antibody. Methods for
making antibody variants are generally available in the art. Though
the following discussion refers to variants of an antagonist
anti-CD40 antibody, the methods are generally applicable to any
antibody of interest, for example, an antibody that specifically
binds to a biomarker or clinically useful prognostic marker
disclosed herein.
[0211] For example, amino acid sequence variants of an antagonist
anti-CD40 antibody, for example, the CHIR-5.9 or CHIR-12.12
monoclonal antibody described herein, can be prepared by mutations
in the cloned DNA sequence encoding the antibody of interest.
Methods for mutagenesis and nucleotide sequence alterations are
well known in the art. See, for example, Walker and Gaastra, eds.
(1983) Techniques in Molecular Biology (MacMillan Publishing
Company, New York); Kunkel (1985) Proc. Natl. Acad. Sci. USA
82:488-492; Kunkel et al. (1987) Methods Enzymol. 154:367-382;
Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (Cold
Spring Harbor, N.Y.); U.S. Pat. No. 4,873,192; and the references
cited therein; herein incorporated by reference. Guidance as to
appropriate amino acid substitutions that do not affect biological
activity of the polypeptide of interest may be found in the model
of Dayhoff et al. (1978) in Atlas of Protein Sequence and Structure
(Natl. Biomed. Res. Found., Washington, D.C.), herein incorporated
by reference. Conservative substitutions, such as exchanging one
amino acid with another having similar properties, may be
preferred. Examples of conservative substitutions include, but are
not limited to, GlyAla, ValIleLeu, AspGlu, LysArg, AsnGln, and
PheTrpTyr.
[0212] In constructing variants of an antibody of interest, for
example, an antagonist anti-CD40 antibody polypeptide of interest,
modifications are made such that variants continue to possess the
desired activity, i.e., similar binding affinity and, in the case
of antagonist anti-CD40 antibodies, are capable of specifically
binding to a human CD40 antigen expressed on the surface of a human
cell, and being free of significant agonist activity but exhibiting
antagonist activity when bound to a CD40 antigen on a human
CD40-expressing cell. Obviously, any mutations made in the DNA
encoding the variant polypeptide must not place the sequence out of
reading frame and preferably will not create complementary regions
that could produce secondary mRNA structure. See EP Patent
Application Publication No. 75,444.
[0213] In addition, the constant region of an antibody, for
example, an antagonist anti-CD40 antibody, can be mutated to alter
effector function in a number of ways. For example, see U.S. Pat.
No. 6,737,056B1 and U.S. Patent Application Publication No.
2004/0132101A1, which disclose Fc mutations that optimize antibody
binding to Fc receptors.
[0214] Preferably, variants of a reference antibody, for example,
an antagonist anti-CD40 antibody, have amino acid sequences that
have at least 70% or 75% sequence identity, preferably at least 80%
or 85% sequence identity, more preferably at least 90%, 91%, 92%,
93%, 94% or 95% sequence identity to the amino acid sequence for
the reference antibody, for example, an antagonist anti-CD40
antibody molecule, for example, the CHIR-5.9 or CHIR-12.12
monoclonal antibody described herein, or to a shorter portion of
the reference antibody molecule. More preferably, the molecules
share at least 96%, 97%, 98% or 99% sequence identity. For purposes
of the present invention, percent sequence identity is determined
using the Smith-Waterman homology search algorithm using an affine
gap search with a gap open penalty of 12 and a gap extension
penalty of 2, BLOSUM matrix of 62. The Smith-Waterman homology
search algorithm is taught in Smith and Waterman (1981) Adv. Appl.
Math. 2:482-489. A variant may, for example, differ from the
reference antibody, for example, an antagonist anti-CD40 antibody,
by as few as 1 to 15 amino acid residues, as few as 1 to 10 amino
acid residues, such as 6-10, as few as 5, as few as 4, 3, 2, or
even 1 amino acid residue.
[0215] With respect to optimal alignment of two amino acid
sequences, the contiguous segment of the variant amino acid
sequence may have additional amino acid residues or deleted amino
acid residues with respect to the reference amino acid sequence.
The contiguous segment used for comparison to the reference amino
acid sequence will include at least 20 contiguous amino acid
residues, and may be 30, 40, 50, or more amino acid residues.
Corrections for sequence identity associated with conservative
residue substitutions or gaps can be made (see Smith-Waterman
homology search algorithm).
Methods of Therapy
[0216] The ex vivo prognostic assays described herein can also be
used in methods of therapy for a subject in need of treatment for a
cancer or pre-malignant condition associated with CD40-expressing
neoplastic cells. Thus, in some embodiments, the ex vivo prognostic
assay is carried out on a candidate subject, and, where results of
the assay predict a favorable response with treatment with the
anti-CD40 therapeutic agent, the subject is then treated with that
anti-CD40 therapeutic agent. As noted herein above, the information
obtained from the ex vivo prognostic assay can be used alone to
render a decision with regard to benefit of treatment with the
anti-CD40 therapeutic agent. Alternatively, the ex vivo prognostic
assay can be used in combination with prognostic assays that screen
for level of expression, or presence or absence of expression, of
one or more of the CD40-related factors identified herein;
prognostic assays that screen for level of expression, or presence
or absence of expression, of one or more clinically useful
prognostic markers for the particular cancer or pre-malignant
condition, for example, for a subject with CLL, a clinically useful
prognostic marker such as ZAP-70 expression level, CD38 expression
level, .beta.2 microglobulin expression level, p53 mutational
status, ATM mutational status, chromosome 17p deletion, and
chromosome 11q deletion identified herein above; or both.
[0217] In this manner, a subject identified using the ex vivo
prognostic assays of the present invention, alone or in combination
with other prognostic assays described herein, can be further
treated with one or more therapeutically effective doses of the
anti-CD40 therapeutic agent that has been identified in the
screening process as being beneficial for treatment of the disease
in the candidate subject. "Treatment" is herein defined as the
application or administration of an anti-CD40 therapeutic agent to
a patient, or application or administration of an anti-CD40
therapeutic agent to an isolated tissue or cell line from a
patient, where the patient has a disease, a symptom of a disease,
or a predisposition toward a disease, where the purpose is to cure,
heal, alleviate, relieve, alter, remedy, ameliorate, improve, or
affect the disease, the symptoms of the disease, or the
predisposition toward the disease. By "treatment" is also intended
the application or administration of a pharmaceutical composition
comprising the anti-CD40 therpaeutic agent to a patient, or
application or administration of a pharmaceutical composition
comprising the anti-CD40 therapeutic agent, to an isolated tissue
or cell line from a patient, who has a disease, a symptom of a
disease, or a predisposition toward a disease, where the purpose is
to cure, heal, alleviate, relieve, alter, remedy, ameliorate,
improve, or affect the disease, the symptoms of the disease, or the
predisposition toward the disease.
[0218] By "anti-tumor activity" is intended a reduction in the rate
of malignant CD40-expressing cell proliferation or accumulation,
and hence a decline in growth rate of an existing tumor or in a
tumor that arises during therapy, and/or destruction of existing
neoplastic (tumor) cells or newly formed neoplastic cells, and
hence a decrease in the overall size of a tumor during therapy.
Therapy with at least one anti-CD40 therapeutic agent identified
using the ex vivo prognostic assays described herein causes a
physiological response that is beneficial with respect to treatment
of cancers and pre-malignant conditions associated with stimulation
of CD40 signaling on CD40-expressing cells in a human.
[0219] By "therapeutically effective dose or amount" or "effective
amount" is intended an amount of the anti-CD40 therapeutic agent
that, when administered brings about a positive therapeutic
response with respect to treatment of a patient with a disease
comprising CD40-expressing neoplastic cells. In some embodiments of
the invention, the anti-CD40 therapeutic agent is an antagonist
anti-CD40 antibody, an antagonist anti-CD40L antibody, or
antigen-binding fragment thereof, and the therapeutically effective
dose of the anti-CD40 antibody, anti-CD40L antibody, or fragment
thereof, is in the range from about 0.01 mg/kg to about 40 mg/kg,
from about 0.01 mg/kg to about 30 mg/kg, from about 0.1 mg/kg to
about 30 mg/kg, from about 1 mg/kg to about 30 mg/kg, from about 3
mg/kg to about 30 mg/kg, from about 3 mg/kg to about 25 mg/kg, from
about 3 mg/kg to about 20 mg/kg, from about 5 mg/kg to about 15
mg/kg, or from about 7 mg/kg to about 12 mg/kg. It is recognized
that the method of treatment may comprise a single administration
of a therapeutically effective dose or multiple administrations of
a therapeutically effective dose of the anti-CD40 therapeutic
agent, for example, an antagonist anti-CD40 antibody, antagonist
anti-CD40L antibody, or antigen-binding fragment thereof.
[0220] In some embodiments, the ex vivo prognostic assays of the
invention can be used to ascertain the physiological basis for
responsiveness, or lack of responsiveness, to treatment with a
particular anti-CD40 therapeutic agent. Thus, where a cancer or
pre-malignant condition in a subject is initially responsive to
therapy with an anti-CD40 therapeutic agent, and CD40-expressing
neoplastic cells of the cancer or pre-malignant condition develop
resistance to this line of therapy, the ex vivo prognostic assays
can be used to define which CD40L-CD40 interaction(s) contribute to
the refractory nature of these CD40-expressing neoplastic
cells.
[0221] The biomarkers of CD40L-mediated CD40 signaling, i.e.,
biomarkers of apoptosis, cell proliferation and survival, cytokine
markers of CD40L-mediated CD40 signaling, and CD40-related factors
described herein can also be used, alone or in any combination
thereof, to monitor efficacy of treatment with an anti-CD40
therapeutic agent. In this manner, a subject who is undergoing
treatment with an anti-CD40 therapeutic agent, who may or may not
have been previously screened for suitability of treatment with the
anti-CD40 therapeutic agent using a prognostic assay described
above, is monitored for in vivo changes in the expression of at
least one biomarker of cellular apoptosis, cell proliferation and
survival, and/or one or more CD40 signaling pathways, wherein
cytokine production is optionally monitored (depending upon the
mode of action of the anti-CD40 therapeutic agent) following
treatment with the anti-CD40 therapeutic agent. Alternatively, or
additionally, the subject can be monitored for in vivo changes in
the expression level of one or more CD40-related factors selected
from the group consisting of cell-surface CD40 antigen on
neoplastic cells, cell-surface CD40L on neoplastic cells,
circulating level of sCD40, and circulating level of sCD40L
following treatment with the anti-CD40 therapeutic agent.
[0222] In this manner, a first biological sample is obtained from
the subject prior to treatment with the anti-CD40 therapeutic agent
of interest and assayed for the expression level of one or more of
these biomarkers and/or CD40-related factors to obtain a baseline
level of expression for each factor assayed. This first biological
sample is referred to as the "baseline biological sample." One or
more subsequent biological samples, of the same tissue type or
bodily fluid, is obtained from the subject and assayed for the same
biomarker(s) and/or CD40-related factor(s), where the subsequent
biological sample is obtained following the administration of at
least one dose of the anti-CD40 therapeutic agent of interest.
Monitoring can occur at a single point in time, or at multiple
points in time to ascertain efficacy of any given treatment
protocol wherein the anti-CD40 therapeutic agent is administered to
the subject. Depending upon the biomarker being assayed, a decrease
or increase in the level of the biomarker between any two time
points is indicative of efficacy of the anti-CD40 therapeutic agent
in treatment of the cancer or pre-malignant condition. Where
monitoring reveals a decrease in the expression level of one or
more of the CD40-related factors, such a result is indicative of
efficacy of the anti-CD40 therapeutic agent in treatment of the
cancer or pre-malignant condition.
[0223] Thus, in some embodiments, efficacy of treatment of a
subject with an anti-CD40 therapeutic agent that blocks or
interferes with CD40L-mediated CD40 signaling is monitored by
obtaining a baseline biological sample from the subject and
detecting the level of expression of one or more biomarkers of cell
survival and/or a CD40L-mediated CD40 signaling pathway described
herein above; administering at least one dose of the therapeutic
agent, for example, an antagonist anti-CD40 antibody such as
CHIR-12.12 or CHIR-5.9 or antigen-binding fragment thereof, to the
subject; obtaining a subsequent biological sample from the subject,
for example, within about 30 minutes to about 24 hours, including
about 30 minutes to about 12 hours, about 30 minutes to about 6
hours, about 30 minutes to about 4 hours, and about 1 hour to about
4 hours; and detecting the level of expression of the biomarker(s)
of cell survival and/or CD40L-mediated CD40 signaling pathway in
the subsequent biological sample; wherein a reduction in the level
of expression in the subsequent biological sample compared to the
level of expression in the baseline biological sample is indicative
of efficacy of treatment with the anti-CD40 therapeutic agent.
Detection can be accomplished using any method known in the art
including those methods disclosed elsewhere herein. In some
embodiments, the level of expression is reduced by at least about
5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,
70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to that detected in
the baseline biological sample. A percent change from baseline of
at least 25% (i.e., at least a 25% reduction relative to the
baseline biological sample) is indicative of efficacy of the
anti-CD40 therapeutic agent, with intermediate responsiveness
indicated by a percent change of at least 30% or at least 40%.
Preferably, the percent change from baseline is at least 50% (i.e.,
at least a 50% reduction relative to the baseline biological
sample) or higher.
[0224] In some embodiments, efficacy of treatment of a subject with
an anti-CD40 therapeutic agent that blocks or interferes with
CD40L-mediated CD40 signaling is monitored by obtaining a baseline
biological sample from the subject and detecting the level of
expression of cytokine markers of CD40L-mediated CD40 signaling
described herein above; administering at least one dose of the
therapeutic agent, for example, an antagonist anti-CD40 antibody
such as CHIR-12.12 or CHIR-5.9 or antigen-binding fragment thereof,
to the subject; obtaining a subsequent biological sample from the
subject, for example, within about 24 hours to about 3 weeks,
including about 48 hours, about 72 hours, about 1 week, or about 2
weeks, after dosing; and detecting the level of expression of the
biomarker(s) of cell survival and/or CD40L-mediated CD40 signaling
pathway in the subsequent biological sample; wherein a reduction in
the level of expression in the subsequent biological sample
compared to the level of expression in the baseline biological
sample is indicative of efficacy of treatment with the anti-CD40
therapeutic agent. Detection can be accomplished using any method
known in the art including those methods disclosed elsewhere
herein. Further, cytokines that are not affected by CD40L-mediated
CD40 signaling (for example, IL-1b and IL-12; see the Experimental
section herein below) can be used as a control to normalize data.
In some embodiments, the level of expression is reduced by at least
about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%,
65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to that
detected in the baseline biological sample. A percent change from
baseline of at least 20% (i.e., at least a 20% reduction relative
to the baseline biological sample) or higher is indicative of
efficacy of the anti-CD40 therapeutic agent. In some embodiments,
baseline biological samples comprising serum or serum extract are
frozen for subsequent analysis of cytokine markers.
[0225] In other embodiments, efficacy of treatment of a subject
with an anti-CD40 therapeutic agent that blocks or interferes with
CD40L-mediated CD40 signaling, or which has ADCC as its mode of
action, is monitored by obtaining a baseline biological sample from
the subject and detecting the level of expression of one or more
biomarkers of apoptosis described herein above; administering at
least one dose of the therapeutic agent, for example, an antagonist
anti-CD40 antibody such as CHIR-12.12 or CHIR-5.9 or
antigen-binding fragment thereof, to the subject; obtaining a
subsequent biological sample from the subject, for example, within
about 8 hours, 12 hours, 24 hours, 36 hours, 48 hours, or 72 hours
after dosing, and optionally again about 1 week, about 2 weeks, or
about 3 weeks after dosing; and detecting the level of expression
of the biomarker(s) of apoptosis in the subsequent biological
sample(s); wherein an increase in the level of expression in the
subsequent biological sample(s) compared to the level of expression
in the baseline biological sample is indicative of efficacy of
treatment with the anti-CD40 therapeutic agent. Detection can be
accomplished using any method known in the art including those
methods disclosed elsewhere herein. In some embodiments, the level
of expression is increased by at least about 5%, 10%, 15%, 20%,
25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%,
90%, 95%, 100%, 125%, 150%, 200%, 250%, 300%, or higher relative to
that detected in the baseline biological sample. A percent change
from baseline of at least 20% (i.e., at least a 20% increase
relative to the baseline biological sample) or higher is indicative
of efficacy of the anti-therapeutic agent.
[0226] In yet other embodiments, efficacy of treatment of a subject
with an anti-CD40 therapeutic agent that blocks or interferes with
CD40L-mediated CD40 signaling, modulates ADCC, or both, is
monitored by obtaining a baseline biological sample from the
subject and detecting the level of expression of one or more
CD40-related factors described herein above (i.e., cell-surface
CD40 and/or CD40L on neoplastic cells, and/or circulating levels of
sCD40 and/or sCD40L); administering at least one dose of the
therapeutic agent, for example, an antagonist anti-CD40 antibody
such as CHIR-12.12 or CHIR-5.9 or antigen-binding fragment thereof,
to the subject; obtaining a subsequent biological sample from the
subject, for example, within about 1 day (i.e., 24 hours), 2 days,
3 days, 4 days, or 1 week; and detecting the level of expression of
the CD40-related factor; wherein a reduction in the level of
expression in the subsequent biological sample compared to the
level of expression in the baseline biological sample is indicative
of efficacy of treatment with the anti-CD40 therapeutic agent. In
some embodiments, the level of expression is reduced by at least
about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%,
65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to that
detected in the baseline biological sample.
[0227] It is recognized that any one or a combination of these
assays can be carried out to monitor efficacy of treatment of a
subject with a cancer or pre-malignant condition with an anti-CD40
therapeutic agent of interest, depending upon its mode of action.
Where efficacy is demonstrated, subsequent doses of the anti-CD40
therapeutic agent can be administered according to the recommended
dosing regimen, for example, daily, every other day, thrice weekly,
twice weekly, once a week, bi-weekly, monthly, and the like.
Alternatively, the in vivo level of expression of the marker(s) of
interest (i.e., biomarker(s) of cell proliferation and survival,
biomarker(s) of CD40L-mediated CD40 signaling pathways, cytokine
marker(s), CD40-related factor(s), and any combination thereof can
serve as a guide to dosing frequency, and can also serve as an
indication as to therapeutically effective dose to be administered.
In this manner, where subsequent biological samples continue to
show an acceptable reduction or increase in the expression level of
the respective marker(s) of interest, further dosing with the
anti-CD40 therapeutic agent can be delayed until such time as the
expression level of the respective marker(s) approaches that
observed in the baseline biological sample. As some biomarkers may
fluctuate independently of the effects of the therapeutic agent,
which also will vary in half-life and residence times, preferably
at least two consecutive measurements (for example, within a 24-48
hour period) are taken into consideration when using the expression
level of the marker (i.e, biomarker of apoptosis, cell survival,
CD40-signaling pathway, cytokine marker, and/or CD40-related
factor) as a guide to dosing frequency.
[0228] Where results of these assays continue to show desired
downregulation of CD40L-mediated CD40 signaling with respect to a
decline in expression of one or more of the biomarkers of cell
survival, one or more of the biomarkers of a CD40 signaling
pathway, and/or one or more of the CD40-related factors, and an
increase in expression of one or more of the markers of cell
apoptosis, further treatment with the anti-CD40 therapeutic agent
is warranted. Biological samples can be collected at various time
intervals over the course of a treatment period as noted herein
above to allow for monitoring of treatment efficacy over time, and
to determine whether treatment should be continued or
withdrawn.
[0229] The following examples are offered by way of illustration
and not by way of limitation.
EXPERIMENTAL
Introduction
[0230] The antagonist anti-CD40 antibodies used in the examples
below are CHIR-5.9 and CHIR-12.12. The CHIR-5.9 and CHIR-12.12
anti-CD40 antibodies are human IgG.sub.1 subtype anti-human CD40
monoclonal antibodies (mAbs) generated by immunization of
transgenic mice bearing the human IgG.sub.1 heavy chain locus and
the human .kappa. light chain locus (XenoMouse.RTM. technology
(Abgenix; Fremont, Calif.)). SF9 insect cells expressing CD40
extracellular domain were used as immunogen.
[0231] Briefly, splenocytes from immunized mice were fused with SP
2/0 or P 3.times.63Ag8.653 murine myeloma cells at a ratio of 10:1
using 50% polyethylene glycol as previously described by de Boer et
al. (1988) J. Immunol. Meth. 113:143. The fused cells were
resuspended in complete IMDM medium supplemented with hypoxanthine
(0.1 mM), aminopterin (0.01 mM), thymidine (0.016 mM), and 0.5
ng/ml hIL-6 (Genzyme, Cambridge, Mass.). The fused cells were then
distributed between the wells of 96-well tissue culture plates, so
that each well contained 1 growing hybridoma on average.
[0232] After 10-14 days, the supernatants of the hybridoma
populations were screened for specific antibody production. For the
screening of specific antibody production by the hybridoma clones,
the supernatants from each well were pooled and tested for
anti-CD40 activity specificity by ELISA first. The positives were
then used for fluorescent cell staining of EBV-transformed B cells
using a standard FACS assay. Positive hybridoma cells were cloned
twice by limiting dilution in IMDM/FBS containing 0.5 ng/ml
hIL-6
[0233] A total of 31 mice spleens were fused with the mouse myeloma
SP2/0 cells to generate 895 antibodies that recognize recombinant
CD40 in ELISA. On average approximately 10% of hybridomas produced
using Abgenix XenoMouse.RTM. technology (Abgenix; Fremont, Calif.)
may contain mouse lambda light chain instead of human kappa chain.
The antibodies containing mouse light lambda chain were selected
out. A subset of 260 antibodies that also showed binding to
cell-surface CD40 were selected for further analysis. Stable
hybridomas selected during a series of subcloning procedures were
used for further characterization in binding and functional assays.
For further details of the selection process, see copending
provisional applications entitled "Antagonist Anti-CD40 Monoclonal
Antibodies and Methods for Their Use," filed Nov. 4, 2003, Nov. 26,
2003, and Apr. 27, 2004, and assigned U.S. Patent Application Nos.
60/517,337 (Attorney Docket No. PP20107.001 (035784/258442)),
60/525,579 (Attorney Docket No. PP20107.002 (035784/271525)), and
60/565,710 (Attorney Docket No. PP20107.003 (035784/277214)),
respectively, and International Patent Application No.
PCT/US2004/037152 (Attorney Docket No. PP20107.004
(035784/282916)), also entitled "Antagonist Anti-CD40 Monoclonal
Antibodies and Methods for Their Use," filed Nov. 4, 2004, and
published as WO 2005/044854; the contents of each of which are
herein incorporated by reference in their entirety.
[0234] Clones from 7 other hybridomas were identified as having
antagonistic activity. Based on their relative antagonistic potency
and ADCC activities, two hybridoma clones were selected for further
evaluation (Table 1 below). They are named 131.2F8.5.9 (5.9) and
153.8E2.D10.D6.12.12 (12.12).
TABLE-US-00001 TABLE 1 Summary of initial set of data with
anti-CD40 IgG1 antibodies CHIR-5.9 and CHIR-12.12. Mother Hybridoma
Cell surface V-region Hybridoma clones binding Antagonist ADCC CDC
CMCC# DNA sequence 131.2F5 131.2F5.8.5.9 +++ +++ ++ - 12047 Yes
153.8E2 153.8E2D10D6.12.12 +++ +++ ++++ - 12056 Yes
[0235] Mouse hybridoma line 131.2F8.5.9 (CMCC#12047) and hybridoma
line 153.8E2.D10.D6.12.12 (CMCC#12056) have been deposited with the
American Type Culture Collection (ATCC; 10801 University Blvd.,
Manassas, Va. 20110-2209 (USA)) under Patent Deposit Number
PTA-5542 and PTA-5543, respectively.
[0236] The cDNAs encoding the variable regions of the candidate
antibodies were amplified by PCR, cloned, and sequenced. The amino
acid sequences for the light chain and heavy chain of the
CHIR-12.12 antibody are set forth in SEQ ID NO:2 (light chain for
mAb CHIR-12.12) and SEQ ID NO:4 (heavy chain for mAb CHIR-12.12). A
variant of the heavy chain for mAb CHIR-12.12 is shown in SEQ ID
NO:5, which differs from SEQ ID NO:4 in having a serine residue
substituted for the alanine residue at position 153 of SEQ ID NO:4.
The nucleotide sequences encoding the light chain and heavy chain
of the CHIR-12.12 antibody are set forth in SEQ ID NO:1 (coding
sequence for light chain for mAb CHIR-12.12) and SEQ ID NO:3
(coding sequence for heavy chain for mAb CHIR-12.12). The amino
acid sequences for the light chain and heavy chain of the CHIR-5.9
antibody are set forth in SEQ ID NO:6 (light chain for mAb
CHIR-5.9) and SEQ ID NO:7 (heavy chain for mAb CHIR-5.9). A variant
of the heavy chain for mAb CHIR-5.9 is shown in SEQ ID NO:8, which
differs from SEQ ID NO:7 in having a serine residue substituted for
the alanine residue at position 158 of SEQ ID NO:7.
[0237] As expected for antibodies derived from independent
hybridomas, there is substantial variation in the nucleotide
sequences in the complementarity determining regions (CDRs). The
diversity in the CDR3 region of V.sub.H is believed to most
significantly determine antibody specificity.
[0238] As shown by FACS analysis, CHIR-5.9 and CHIR-12.12 bind
specifically to human CD40 and can prevent CD40-ligand binding.
Both mAbs can compete off CD40-ligand pre-bound to cell surface
CD40. The binding affinity of CHIR-5.9 to human CD40 is
1.2.times.10.sup.-8 M and the binding affinity of CHIR-12.12 to
human CD40 is 5.times.10.sup.-10 M. The CHIR-12.12 and CHIR-5.9
monoclonal antibodies are strong antagonists and inhibit in vitro
CD40 ligand-mediated proliferation of normal B cells, as well as
inhibiting in vitro CD40 ligand-mediated proliferation of cancer
cells from NHL and CLL patients. The CHIR-12.12 monoclonal antibody
directly inhibits survival and signaling pathways mediated by CD40
ligand (CD40L) in normal human B-lymphocytes. In vitro, both
antibodies kill primary cancer cells from NHL patients by ADCC.
Dose-dependent anti-tumor activity was seen in a xenograft human
lymphoma model. For a more detailed description of these results,
and the assays used to obtain them, see provisional applications
entitled "Antagonist Anti-CD40 Monoclonal Antibodies and Methods
for Their Use," filed Nov. 4, 2003, Nov. 26, 2003, and Apr. 27,
2004, and assigned U.S. Patent Application Nos. 60/517,337
(Attorney Docket No. PP20107.001 (035784/258442)), 60/525,579
(Attorney Docket No. PP20107.002 (035784/271525)), and 60/565,710
(Attorney Docket No. PP20107.003 (035784/277214)), respectively,
and International Patent Application No. PCT/US2004/037152
(Attorney Docket No. PP20107.004 (035784/282916)), also entitled
"Antagonist Anti-CD40 Monoclonal Antibodies and Methods for Their
Use," filed Nov. 4, 2004; the contents of each of which are herein
incorporated by reference in their entirety.
Example 1
CHIR-12.12 Blocks CD40L-Mediated CD40 Survival and Signaling
Pathways in Human B-CLL Cells
[0239] The studies described below demonstrate that CHIR-12.12 also
directly inhibits survival and signaling pathways mediated by CD40
ligand (CD40L) in B-CLL. CD40L activates B-lymphocytes and induces
various functional responses, including enhancement of survival,
and activation of NFkB, ERK/MAPK, and PI3K/Akt signaling pathways.
In addition, CD40L stimulation provides survival signals
demonstrated by reduction of cleaved PARP and induction of the
antiapoptotic proteins, Bcl-xl, XIAP, and cIAP. In contrast,
treatment of CD40L stimulated B-CLL with CHIR-12.12 resulted in
induction of cleaved caspase-3 and cleaved PARP as well as
reduction of Bcl-xl, XIAP, and cIAP in a time- and dose-dependent
manner. CHIR-12.12 alone did not trigger apoptosis without CD40L
stimulation. We examined signal transduction events induced by CD40
activation with its ligand. The engagement of CD40 with CD40 ligand
led to activation of multiple signaling pathways including NFkB,
ERK/MAPK, p38, and PI3K/Akt signaling pathways. CHIR-12.12
treatment inhibited phosphorylation of IkB kinase (IKK) alpha and
beta (NFkB pathway), ERK, and Akt mediated by CD40L. Using
pharmacological inhibitors of PI3K (LY294002) and MEK (PD98595), we
showed that CLL cell survival is at least in part dependent on the
PI3K/Akt pathway. CHIR-12.12 treatment of CD40L stimulated CLL
cells also inhibited cyclin D1. These results demonstrate that
CHIR-12.12 blocked survival and multiple signaling pathways
including NFkB, ERK, and PI3K/Akt that are mediated by CD40L in
B-CLL.
[0240] The fully human antagonist anti-CD40 monoclonal antibody
CHIR-12.12 was generated in XenoMouse.TM. mice (Abgenix, Inc.) as
noted above. B-CLL cells were purchased (Cureline, Inc.; South San
Francisco, Calif.), and in vitro experiments were carried out to
evaluate the effect of the anti-CD40 antibody CHIR-12.12 on
survival and signaling pathways mediated by CD40 ligand.
NF.kappa.B, ERK, and Akt pathways were studied in these
experiments.
CHIR-12.12 Treatment Inhibits Survival Mediated by CD40 Ligand in
B-CLL Cells.
[0241] In these experiments, 1.0.times.10.sup.6 B-CLL cells from
patients were stimulated with 1 .mu.g/ml sCD40L (Alexis
Corporation, Bingham, Nottinghamshire, UK). CHIR-12.12 (10
.mu.g/ml) and control IgG were then added. Cells were collected at
24 hours post CHIR-12.12 treatment. Cleaved PARP, which is a
biomarker of apoptosis, and Bcl-xl, Bcl-2, and cIAP1, which are
biomarkers of survival, were detected in cell lysates by Western
blot analysis using commercially available antibodies specific for
these biomarkers.
[0242] As shown in FIG. 1, treatment with CHIR-12.12 resulted in
the induction of cleaved PARP and reduction of Bcl-xl, XIAP and
cIAP1 in B-CLL cell samples from two patients (#4 and #21). There
were no changes of Bcl-2 and TRAIL level between control and
CHIR-12.12 treated cells.
[0243] Western blot analysis with B-CLL cells from patient #30 is
shown in FIG. 2. CHIR-12.12 treatment induced the expression of
cleaved PARP and reduced the expression of XIAP and Bcl-2 compared
to the control IgG treated group.
[0244] Western blot analysis with B-CLL cells from patient #31 is
shown in FIG. 3. CHIR-12.12 treatment induced the expression of
cleaved PARP and reduced the expression of cyclin D1 and Bcl-xl
compared to the control IgG treated group.
CHIR-12.12 Treatment Inhibits NF.kappa.B, ERK, PI3K/Akt, and p38
MAPK Signaling Pathways Mediated by CD40 Ligand in B-CLL.
[0245] In these experiments, 1.0.times.10.sup.6 B-CLL cells from
patients were stimulated with 1 .mu.g/ml sCD40L (Alexis
Corporation, Bingham, Nottinghamshire, UK). CHIR-12.12 (10
.mu.g/ml) and control IgG were then added. Cells were collected at
0 and 20 minutes. Phosphorylated IKKa (Ser180) and IKK .beta. (Ser
181) (p-IKK .alpha./.beta.; NFkB pathway), phosphorylated ERK
(p-ERK), phosphorylated Akt (p-Akt), and phosphorylated p38 MAPK
(p-p38) were detected in cell lysates by Western blot.
[0246] As shown in FIG. 4, sCD40L stimulated phosphorylation of IKK
.alpha./.beta., ERK, and Akt in control IgG treated B-CLL cells
within 20 minutes, and there was a significant inhibition of
phosphorylation of IKK .alpha./.beta., ERK, and Akt in CHIR-12.12
treated B-CLL cells. Interestingly, in these B-CLL patient samples,
there was a constitutively activated p38 MAPK, and CHIR-12.12 did
not significantly inhibit p38 MAPK activation.
Dose-Dependent Effect of CHIR 12.12 on Survival Mediated by CD40
Ligand in B-CLL Cells.
[0247] In these experiments, 1.0.times.10.sup.6 B-CLL cells from
patients were stimulated with 1 .mu.g/ml sCD40L (Alexis Corp.,
Bingham, Nottinghamshire, UK). CHIR-12.12 (0, 0.01 0, 1, 1.0, 10,
and 20 .mu.g/ml) and control IgG were then added. Cells were
collected at 22-24 hours. Western blot analysis with antibodies to
cleaved PARP, caspase-3, and Bcl-xl were conducted on cell lysates.
Antibody against .beta.-actin was used for detecting equal loading
and transfer efficiency.
[0248] As shown in FIGS. 5 and 6, treatment of sCD40L stimulated
B-CLL cells with CHIR-12.12 resulted in induction of cleaved PARP
and caspase-3 as well as reduction of Bcl-xl in a dose-dependent
manner at doses as low as 0.01 .mu.g/ml.
Effect of CHIR-12.12 on Apoptosis does not Occur without CD40L
Stimulation in B-CLL Cells.
[0249] In this experiment, 1.0.times.10.sup.6 B-CLL cells from
patients, not stimulated with CD40L, were treated with CHIR-12.12
(10 .mu.g/ml) or control IgG. Cells were collected at 1, 4, and 24
hours. Western blot analysis with antibodies to cleaved PARP
(apoptotic protein) and XIAP (anti-apoptotic protein) was conducted
on cell lysates.
[0250] The results shown in FIG. 7 indicate that CD40 ligand
stimulation is necessary for survival of B-CLL cells, and
CHIR-12.12 alone did not trigger additional apoptosis of B-CLL
cells.
Signaling Pathways Required for CLL Cell Survival.
[0251] A PI3K inhibitor (LY294002; Sigma, St. Louis, Mo.) and MEK
inhibitor (PD98595; Cell Signaling Technology, Beverly, Mass.) were
used to dissect the pathways required for CLL cell survival. In
these experiments, 1.0.times.10.sup.6 B-CLL cells from patients
were serum starved in 1% FBS containing media for 4 hours.
Serum-starved cells were then pretreated with LY294002 (PI3K
inhibitor, 30 .mu.M) or PD98595 (MEK inhibitor, 10 .mu.M). Cell
lysates were then collected before and 20 minutes after CD40L
stimulation. Western blot analysis with antibodies to p-IKK
.alpha./.beta., p-ERK, p-Akt was conducted, and equal loading was
evaluated by probing antibodies to total ERK and .beta.-actin.
[0252] As shown in FIG. 8 and as expected, PD98595 inhibited
activation of ERK and LY294002 inhibited activation of Akt that
were induced by CD40L treatment. There was no change of IKK/NFkB
activation by either inhibitor.
[0253] However, only B-CLL cells treated with PI3K inhibitor,
LY294002, showed induction of cleaved PARP and caspase-3 as well as
reduction of Bcl-xl, an anti-apoptotic protein (FIG. 9). There was
no change of survival mediated by CD40L with MEK inhibitor,
PD98595. This supports the finding that B-CLL cell survival is
mediated through the PI3K/Akt signaling pathway.
CHIR-12.12 Treatment Inhibits Survival Mediated by CD40 Ligand in
B-CLL Patient Cells Using Flow Cytometry Analysis.
[0254] In this experiment, 0.4.times.10.sup.6B-CLL cells from
patients were stimulated with 1 mg/ml sCD40L (Alexis Corp.,
Bingham, Nottinghamshire, UK). CHIR12.12 (10 .mu.g/ml) or control
IgG was then added. Cells were collected at 24 hours post-treatment
with CHIR-12.12. After fixation and permeablization, the cells were
stained for cleaved PARP and TUNEL methods.
[0255] Flow cytometry analysis on cells treated with CHIR12.12 is
shown in FIGS. 10 and 11. Cleaved PARP and TUNEL methods were used
to assess apoptosis. After culturing cells for 24 hrs in the
absence of sCD40L, the cells began to show signs of apoptosis,
resulting in cells staining positive for cleaved PARP and TUNEL.
The addition of sCD40L induced a decrease in the percentage of
cells that stained positive for these two markers. When CHIR-12.12
was added in conjunction with sCD40L, the percentage of positive
cells for cleaved PARP or TUNEL returned to the levels seen without
sCD40L stimulation. This indicates that the survival induced by
sCD40L is inhibited by the addition of CHIR-12.12.
Effect of CHIR 12.12 Treatment on CD40 Ligand-Mediated Signaling
Events in B-CLL Cells at the Transcript Level.
[0256] CHIR-12.12 was used in a timecourse to determine how it
mediates transcriptional regulation in B-CLL cells. In this
experiment, 1.0.times.10.sup.6 B-CLL cells from patients were
simultaneously treated with IgG1 (10 .mu.g/mL) or CHIR-12.12 (10
.mu.g/mL) and sCD40L. Cell pellets were collected at 0 hr (no
CD40L), 1, 4 and 24 hr and lysed simultaneously at the end. RNA was
isolated using the RNeasy kit, and cDNA was prepared using the ABI
RT kit. Two-step RT-PCR was done with the genes shown in two
separate reactions, based on T.sub.M of each set of oligos.
[0257] Various genes showed CHIR-12.12-mediated transcriptional
changes at certain timepoints when compared to the IgGI control
samples (FIG. 12). CD40, CD40L, VEGF, TRAF2, and TRAF3 all showed
inhibition of RNA expression, with TRAF6 and Mcl-1 showing minor
down-regulation. IL-6 showed no transcriptional changes.
CHIR-12.12 Treatment Inhibits CD40 Ligand-Mediated p38 MAPK
Signaling in B-CLL Cells.
[0258] A p38 MAPK inhibitor (SB203580) and CHIR-12.12 were used at
two different timepoints, 4 hours and 24 hours, to dissect the role
of the p38 MAPK pathway in CD40 signaling. In the four-hour
experiment, approximately 0.8.times.10.sup.6 B-CLL cells per well
were serum starved in 1% FBS-containing media for 4 hours. Cells
were pretreated with SB203580 (30 and 60 .mu.M) and CHIR-12.12 (10
.mu.g/mL). Cell lysates were collected before and 20 minutes after
CD40L stimulation. Western blot analysis with antibodies against
specific proteins shown were conducted, and equal loading was
evaluated by probing with antibodies to total p38 (t-p38) and
.beta.-actin.
[0259] In the 24-hour experiment, approximately 0.8.times.10.sup.6
B-CLL cells per well were placed in full serum (10% FBS)-containing
media for 24 hours. Cells were simultaneously pretreated with
either SB203580 (30 and 60 .mu.M) or CHIR-12.12 (10 .mu.g/mL) for
24 hours and stimulated with CD40L. Western blot analysis with
antibodies against specific proteins shown was conducted, and equal
loading was evaluated by probing with antibodies against
.beta.-actin.
[0260] FIG. 13 shows that p38 was not constitutively phosphorylated
in this patient, however, the constitutive activity has been
variable between patients. Its activation by CD40L was slightly
inhibited by SB203580 inhibitor and fully inhibited by CHIR-12.12
at 4 hours. Phospho-IKK.alpha./.beta. activation by CD40L was also
inhibited by CHIR12.12.
[0261] As shown in FIG. 14, cleaved-PARP was significantly induced
by both SB203580 and CHIR.12.12, thereby inhibiting CD40L-mediated
stimulation, while cleaved Caspase-3 was induced to a lesser
extent. Bcl-xl expression was also blocked, especially at the 60
.mu.M concentration of SB203580 and 10 .mu.g/ml of CHIR-12.12; p38
phosphorylation was similarly blocked as was seen in the 4 hour
experiment. CD40 expression also was inhibited by CHIR-12.12.
[0262] FIG. 15 shows that p38 basal phosphorylation status varies
among the CLL patient samples that have been tested. Patients with
low basal p-p38 activity have a higher induction of phosphorylation
by CD40L stimulation than patients with a higher basal expression.
CHIR-12.12 lowered p-p38 levels back to basal phosphorylation
regardless of whether that basal level was high or low.
Example 2
Ability of Anti-CD40 mAb CHIR-12.12 to Lyse Multiple Myeloma (MM)
Cell Lines by Antibody-Dependent Cellular Cytotoxicity (ADCC)
[0263] Human MM cell lines, KMS-12-BM, IM-9, and ARH-77, were
washed 3 times using R2 medium (Pheno red-free RPMI with 2% FBS)
and re-suspended in R10 medium (Pheno red-free RPMI with 10% FBS)
at the density of 1.times.10.sup.6/mL. Cells were labeled by adding
Calcein AM (final concentration 5 mM) and incubating for 30 minutes
at 37.degree. C. in a humidified atmosphere with 5% CO2. Purified
human NK cells and Calcein-labeled target cells were mixed in R10
medium at the ratio of 10 to 1 (5.times.10.sup.4 NK cells and
5.times.10.sup.3 target cells in 200 mL) and added in U-bottom 96
well plate (Packard's Instrument, Meriden, Conn.). CHIR-12.12 was
serial diluted at desired concentration and added in triplicates
into the wells containing NK/target cell mixture. 1% NP-40 was
added in 3 wells for the maximum cell lysis. Cells were incubated
for 4 hours without disturbance at 37.degree. C. in a humidified
atmosphere with 5% CO2. The plate was then centrifuged at 300 rpm
without brake for 5 minutes. 100 mL supernatant was transferred
into a new 96 well plate. The released Calcein in the supernatant
was measured in arbitrary fluorescent unit (AFU) at 485 nm
excitation and 535 nm emission using Tecan SpectraFluor Plus (Tecan
U.S., Inc., Research Triangle, NC). The percent of specific lysis
was calculated as: 100.times.(AFU test-AFU spontaneous
release)/(AFU maximal release-AFU spontaneous release).
[0264] The ED.sub.50 was determined for each cell line by plotting
the log of antibody concentration versus the percent specific lysis
(see FIG. 16). The ED.sub.50 of CHIR-12.12 for KMS-12-BM cells was
17.9 mM; the ED.sub.50 of CHIR-12.12 for IM-9 cells was 5.9 .mu.M,
and the ED.sub.50 of CHIR-12.12 for ARH-77 cells was 23.9
.mu.M.
Example 3
CHIR-12.12 Anti-Tumor Activity in Multiple Myeloma Animal
Models
[0265] When administered intraperitoneally (i.p.) once a week for a
total of 3 doses, CHIR-12.12 significantly inhibited the growth of
multiple myeloma tumors in several tumor models in a dose-dependent
manner. When CHIR-12.12 was combined with bortezomib (VELCADE.RTM.)
the efficacy observed was additive.
IM-9 Multiple Myeloma Xenograft Model
[0266] SCID mice were inoculated subcutaneously with 1M-9 tumor
cells (a human multiple myeloma cell line expressing both CD40 and
CD20) in 50% MATRIGEL.TM. at 5.times.10.sup.6 cells per mouse. In
the first study, tumor-bearing mice were injected intraperitoneally
with control IgG.sub.1 at 10 mg/kg, CHIR-12.12 anti-CD40 mAb at 1
mg/kg, or CHIR-12.12 anti-CD40 mAb at 10 mg/kg on days 5, 12, and
18 after tumor implantation. Alternatively, bortezomib dosing at 1
mg/kg intravenously occurred on days 5, 8, 12, and 15 after tumor
implantation. In the second study, tumor-bearing mice were injected
with control IgG.sub.1 at 1 mg/kg intraperitoneally, CHIR-12.12
anti-CD40 mAb at 1 mg/kg intraperitoneally, or bortezomib at 1
mg/kg intravenously. Antibody dosing occurred on days 8, 14, and 21
post tumor implantation, while bortezomib dosing occurred on days
8, 11, 14 and 18 post tumor implantation. Alternatively,
tumor-bearing mice were injected with CHIR-12.12 anti-CD40 mAb at 1
mg/kg intraperitoneally on days 8, 14, and 21 post tumor
implantation plus bortezomib at 1 mg/kg intravenously on days 8,
11, 14, and 18 post tumor implantation. Data were analyzed using
the log-rank test.
[0267] Administration of CHIR-12.12 at 1 and 10 mg/kg inhibited
tumor growth at 15, 18, and 21 days post tumor implantation (see
FIG. 17). Bortezomib, when administered at 1 mg/kg on days 5, 8,
12, and 15, after tumor implantation also inhibited tumor growth at
15, 18, and 21 days post tumor implantation (see FIG. 17). In the
second study, 1 mg/kg bortezomib did not display stastistically
significant growth inhibition. When CHIR-12.12 was administered (1
mg/kg) in combination with the maximally tolerated dose of
bortezomib, a tumor volume reduction was observed on days 13, 16,
20, 23, and 26 (see FIG. 18).
[0268] In summary, anti-CD40 mAb CHIR-12.12 administration
inhibited tumor growth in experimental multiple myeloma models at 1
mg/kg and 10 mg/kg administered weekly. Bortezomib at 1 mg/kg twice
a week demonstrated borderline activity as the tumor growth
inhibition in one experiment was statistically significant (FIG.
17) and in the second study it was not (FIG. 18). Further,
combining CHIR-12.12 with bortezomib treatment enhanced the
inhibition of tumor growth. These data suggest that the anti-CD40
mAb CHIR-12.12 has potent anti-tumor activity and could be
clinically effective for the treatment of multiple myeloma, either
alone or in combination with other chemotherapeutic agents.
CHIR-12.12 Reduces Proliferation Rate and Increases Cell Death in
IM-9 Xenografts.
[0269] When CHIR-12.12 was tested in the subcutaneous IM-9
xenograft model, histology was performed 5 days after a single dose
of CHIR-12.12. CHIR-12.12 treatment significantly reduced the
number of Ki67.sup.+proliferating cells and increased the level of
cleaved caspase 3 and cleaved PARP, two apoptosis markers,
demonstrating the inhibition of cell proliferation and induction of
cell death resulted from CHIR-12.12 treatment.
CHIR-12.12 Prolongs Survival in the Unstaged or Staged Orthotopic
(i.v.) IM-9 Xenograft Model.
[0270] SCID mice were inoculated subcutaneously with 1M-9 tumor
cells (a human multiple myeloma cell line expressing both CD40 and
CD20) in 50% MATRIGEL.TM. at 5.times.10.sup.6 cells per mouse. In
unstaged models, treatment was initiated one day after tumor
implantation. Tumor-bearing mice were injected with control
IgG.sub.1 at 10 mg/kg or anti-CD40 mAb CHIR-12.12 at 0.1 mg/kg, 1
mg/kg or 10 mg/kg intraperitoneally once a week. Alternatively,
tumor-bearing mice were injected with bortezomib at 0.5 mg/kg or 1
mg/kg intravenously once a week. Data were analyzed using the
log-rank test.
[0271] In an unstaged conditional survival model, CHIR-12.12
prolonged the survival of tumor-bearing mice (FIG. 20). In staged
models, treatment was initiated 7 days after tumor cell
implantation. Tumor-bearing mice were injected with control
IgG.sub.1 at 1 mg/kg or anti-CD40 mAb CHIR-12.12 at 0.1 mg/kg, 1
mg/kg, or 10 mg/kg intraperitoneally once a week. Alternatively,
tumor-bearing mice were injected with bortezomib at 0.5 mg/kg
intravenously. Data were analyzed using the log-rank test. In this
staged orthotopic model, CHIR-12.12 also prolonged survival of
tumor-bearing mice (FIG. 21).
CHIR-12.12 Inhibits Growth of Human KMS-12-BM Subcutaneous
Xenograft Model.
[0272] Female SCID mice were treated with 3Gy irradiation one day
prior to implantation of tumor cells. On the day of implantation,
cells were prepared at a concentration of 5.times.10.sup.7 cells/ml
in 50% matrigel. Cells were implanted subcutaneously over the right
flank at 5.times.10.sup.6 cells/100 ml/mouse. When tumor volume
reached 100.about.200 mm.sup.3, mice were randomized and treated
with either IgG.sub.1 isotype control antibody at 10 mg/kg,
anti-CD40 antibody CHIR-12.12 at 1 mg/kg or 10 mg/kg, or bortezomib
at 1 mg/kg. Antibodies were administered intraperitoneally once a
week for 4 weeks. Bortezomib was administered intravenously twice a
week for two weeks.
[0273] Primary tumor growth was dose-dependently inhibited by
administration of CHIR-12.12 at 42 days post cell implantation. The
KMS-12-BM tumor volume was reduced 32% (P>0.05, Anova followed
by Tukey multi-comparison test) and 35% (P<0.05) in 1 mg/kg and
in 10 mg/kg groups, respectively. Bortezomib only showed a trend
toward inhibition, with tumor volume reduction of 22% (P>0.05)
at the maximal tolerated dose of 1 mg/kg.
Example 4
Evaluation of CD40 Ligand-Induced Cytokine Secretion in CD40+
Cells
[0274] CD40 is highly expressed in B cell malignancies. Stimulation
of CD40 by its ligand provides survival and proliferative signals
for normal and malignant B cells. The antagonist anti-CD40 antibody
CHIR-12.12 does not induce the proliferation of human peripheral
blood lymphocytes but inhibits CD40L-induced lymphocyte
proliferation. CD40 signaling also induces cells to produce a
variety of cytokines. In this example, the ability of CHIR-12.12 to
modulate cytokine production by normal B cells and primary patient
CLL cells was investigated.
[0275] Cells (1.times.10.sup.5 cells per well) were cultured in a
96-well plate in the presence or absence of CD40L (CD40
transfected, formaldehyde fixed CHO cells, 2.times.10.sup.5 per
well). Cells were incubated with huIgG1 (control) or CHIR-12.12 at
10 .mu.g/ml at 37 C for 24 hours, and supernatants were harvested.
Production of hIL-6, hIL-8, hIL-10, hTNF-.alpha., hGM-CSF, hIL-1b,
hIL-12p70, MCP-1, and MIP-1.beta. was measured by Meso Scale
Discovery.RTM. multi-array system (Meso Scale Discovery,
Gaithersburg, Md.).
[0276] Cells cultured with CHIR-12.12 alone in the absence of CD40L
did not produce any of the cytokines above background levels
suggesting that CHIR-12.12 does not have an agonistic activity for
cytokine production. In contrast CD40L-induced production of
hIL-10, hTNF-.alpha., hIL-8, hIL-6, MCP-1, and MIP-1.beta. in
normal B cells (n=3) (Table 2). Addition of CHIR-12.12 to these
cultures inhibited production of all cytokines (see Table 3).
TABLE-US-00002 TABLE 2 CD40L-induced cytokine secretions from
normal B cells (values are folds of induction over background).
Cytokine Donor 1 Donor 2 Donor 3 hIL-1b no induction no induction
no induction hIL-12p70 no induction ND no induction hIL-10 3.6 ND
3.6 hGM-CSF no induction ND no induction hTNF-.alpha. 3.7 4.8 22.8
hIL-8 7.7 14.7 49.3 hIL-6 5.7 3.8 20.5 MCP-1 5.5 not tested 1.7
MIP-1.beta. 2.2 2.6 17.8
TABLE-US-00003 TABLE 3 CHIR-12.12 inhibits secretion from normal B
cells of all cytokines induced by CD40L (values are % inhibition).
Cytokine Donor 1 Donor 2 Donor 3 hIL-1b no induction no induction
no induction hIL-12p70 no induction ND no induction hIL-10 90.5 ND
94.4 hGM-CSF no induction ND no induction hTNF-.alpha. 92.8 97.4
98.5 hIL-8 98.2 84.7 99.5 hIL-6 92.2 99.9 99.3 MCP-1 55.3 not
tested 25.7 MIP-1.beta. 54.4 92 92.5
[0277] In preliminary experiments with CLL patient cells,
CHIR-12.12 inhibited CD40L-induced production of hIL-10, hGM-CSF,
hTNF-.alpha., hIL-8 and MCP-1 (n=1) (Table 4 versus Table 5).
TABLE-US-00004 TABLE 4 CD40L-induced cytokine secretions by CLL
cells (values are folds of induction over background). Cytokine CLL
#1 hIL-1b no induction hIL-12p70 ND hIL-10 9.2 hGM-CSF 7.6
hTNF-.alpha. 3.3 hIL-8 4.0 hIL-6 no induction MCP-1 5.5 MIP-1.beta.
no induction
TABLE-US-00005 TABLE 5 CHIR-12.2 inhibits secretion by CLL cells of
all cytokines induced by CD40-ligand (values are % inhibition).
Cytokine CLL #1 hIL-1b no induction hIL-12p70 ND hIL-10 99.6
hGM-CSF 86.5 hTNF-.alpha. 89.6 hIL-8 91.0 hIL-6 no induction MCP-1
34.8 MIP-1.beta. no induction
[0278] Together, these data show that CHIR-12.12 is a potent
antagonist for CD40-ligand mediated survival, proliferation, and
cytokine production.
[0279] CD40 ligation can also induce the expression of VEGF in
normal (Melter et al. (2000) Blood 96(12):3801-3808) and neoplastic
cells (Farahani et al. (2005) Leukemia 19(4):524-530; Tai et al.
(2005) Cancer Res. 65(13):5898-5906). VEGF has been shown to
promote cell growth and migration in multiple myeloma cells (Podar
et al. (2001) Blood 98(2):428-435) and to promote cell survival in
CLL cells (Farahani et al. (2005), supra). As such, changes in VEGF
levels may provide a useful cytokine marker of CD40L-mediated CD40
signaling. Because VEGF is a secreted protein, changes in VEGF
protein expression can be easily detected in cell culture
supernatants or in plasma obtained from patient blood samples using
techniques such as Western blot or ELISA. Alternatively it can be
detected from the mRNA obtained from tumor cells, using any of a
number of techniques such as Northern blot or
quantitative-RT-PCR.
[0280] In another experiment, CD40L-induced production of VEGF in
normal B cells and CLL cells obtained from patients with CLL is
examined in a manner similar to that described above. Addition of
CHIR-12.12 to these cell cultures is found to inhibit CD40L-induced
production of VEGF.
Example 5
Biomarkers and Prognostic Indicators
[0281] The ex vivo prognostic assays and additional prognostic
assays to be used in the methods of the present invention require
screening biological samples for the level of expression of
biomarkers whose mature protein sequences and nucleotide sequences
are known in the art. See for example, the information shown in
Table 3 below. It is recognized that probes for detecting these
biomarkers, either at the protein (for example, antibody probes) or
nucleic acid level (for example, PCR probes), can be designed based
on this sequence information, and that probes can be designed to
detect variants of the sequences disclosed herein.
TABLE-US-00006 TABLE 6 Amino Acid and Nucleotide Sequences for
Biomarkers and Prognostic Markers. Biomarker Name Accession No.
Accession No. AKT-1 NM_005163 NP_005154 AKT-2 NM_001626 NP_001617
AKT-3 AF135794 AAD24196 PI3K Y13892 CAA74194 PDK1 BC006339 AAH06339
IKK.alpha. AF012890 AAC51662 IKK.beta. AF031416 AAC64675 I.kappa.B
BT006743 Q15653 NF-.kappa.B NM_003998 NP_003989 MEK1 L11284
NM_002755 NP_002746 MEK2 L11285 NM_030662 NP_109587 MEK3 NM_002746
NP_002737 MEK6 U49732 AAB05035 ERK1 NM_002746 NP_002737 ERK2
NM_002745 NP_002736 p38 L35253 AAA74301 Caspase 3 NM_004346
NP_004337 Caspase 7 BT006683 AAP35329 Caspase 9 BT006911 AAP35557
PARP NM_001618 NP_001609 Bcl-2 M14745 AAA35591 Bcl-xl Z23115
CAA80661 Mcl-1 AF118124 AAD13299 XIAP U45880 AAC50373 cIAP1 U45879
AAC50372 survivin U75285 AAC51660 TRAF-1 NM_005658 NP_005649 Ki67
X65550 CAA46519 ZAP70 BC039039 AAH39039 CD38 D84284 BAA18966
.beta.2-microglobulin CR457066 CAG33347 CD52 NM_001803 NP_001794
p53 NM_000546 NP_000537
TABLE-US-00007 TABLE 7 Amino Acid and Nucleotide Sequences for CD40
and CD40L. Nucleotide Sequence Amino Acid Sequence Accession
Sequence Accession Sequence Name No. Identifier No. Identifier CD40
NM_152854 SEQ ID NP_690593 SEQ ID short NO: 9 NO: 10 isoform CD40
X60592 SEQ ID CAA43045 SEQ ID long NO: 11 NO: 12 isoform CD40L
NM_000074 SEQ ID NP_000065 SEQ ID NO: 13 NO: 14 Soluble NM_000074
SEQ ID NP_000065 SEQ ID CD40L NO: 15 NO: 16 (nucleotides (residues
139-786 of 47-261 of SEQ ID SEQ ID NO: 13) NO: 14)
Example 6
Assays for Antagonist Activity of Anti-CD40 Therapeutic Agents
[0282] The following assays can be used to assess the antagonist
activity of an anti-CD40 antibody. Human B cells for these assays
can be obtained, for example, by isolation from tonsils obtained
from individuals undergoing tonsillectomies, essentially as
described in De Groot et al. (1990) Lymphokine Research (1990)
9:321. Briefly, the tissue is dispersed with scalpel blades,
phagocytic and NK cells are depleted by treatment with 5 mM
L-leucine methyl ester and T cells are removed by one cycle of
rosetting with sheep erythrocytes (SRBC) treated with 2-aminoethyl
isothiouronium bromide. The purity of the resulting B lymphocyte
preparations can be checked by indirect immunofluorescent labelling
with anti-(CD20) mAb B1 (Coulter Clone, Hialeah, FA) or anti-(CD3)
mAb OKT3 (Ortho, Raritan, N.J.) and a FITC-conjugated F(ab').sub.2
fragment of rabbit anti-(mouse Ig) (Zymed, San Francisco, Calif.),
and FACS analysis.
B-Cell Proliferation Assay.
[0283] B cells (4.times.10.sup.4 per well) are cultured in 200
.mu.l IMDM supplemented with 10% fetal calf serum in flat bottom
96-well microtiter plates. B cells are stimulated by addition of
immobilized anti-(IgM) antibodies (Immunobeads; 5 .mu.g/ml; BioRad,
Richmond, Calif.). Where desired, 100 U/ml recombinant IL-2 is
added. Varying concentrations of test monoclonal antibodies (mAbs)
are added at the onset of the microcultures and proliferation is
assessed at day 3 by measurement of the incorporation of
(.sup.3H)-thymidine after 18 hour pulsing.
[0284] An antagonist anti-CD40 antibody does not significantly
costimulate human B-cell proliferation in the presence of
immobilized anti-IgM or in the presence of immobilized anti-IgM and
IL-2.
Banchereau-Like B-Cell Proliferation Assay.
[0285] For testing the ability of anti-CD40 monoclonal antibodies
to stimulate B-cell proliferation in a culture system analogous to
that described by Banchereau et al. (1991) Science (1991) 251:70,
mouse 3T6 transfectant cells expressing the HR allellic form of
human Fc.gamma.RII are used. B cells (2.times.10.sup.4 per well)
are cultured in flat-bottom microwells in the presence of
1.times.10.sup.4 transfectant cells (irradiated with 5000 Rad) in
200 .mu.l IMDM supplemented with 10% fetal calf serum and 100 U/ml
recombinant IL-4. Before addition of the B cells, the 3T6 cells are
allowed to adhere to the culture plastic for at least 5 hours.
Anti-CD40 mAbs are added at concentrations varying from 15 ng/ml to
2000 ng/ml and proliferation of B cells is assessed by measurement
of thymidine incorporation at day 7, upon 18 hour pulsing with
[.sup.3H]thymidine.
Inhibition of 52C6-Stimulated B-Cell Proliferation Using Antagonist
Anti-CD40 mAbs.
[0286] Antagonist anti-CD40 monoclonal antibodies (mAbs) can also
be characterized by their ability to inhibit stimulation of B-cell
proliferation by an anti-CD40 antibody such as S2C6 (also known as
SGN-14, which is reportedly an agonist of CD40 stimulation of
proliferation of normal B cells; Francisco et al. (2000) Cancer
Res. 60:3225-3231) using the B-cell Proliferation Assay described
above. Human tonsillar B cells (4.times.10.sup.4 per well) are
cultured in 200 .mu.l in microwells in the presence of anti-IgM
coupled to Sepharose beads (5 .mu.g/ml) and anti-CD40 mAb S2C6
(1.25 .mu.g/ml). Varying concentrations of an anti-CD40 mAb of
interest are added and [.sup.3H]-thymidine incorporation is
assessed after 3 days. As a control anti-(glucocerebrosidase) mAb
8E4 can be added in similar concentrations. Barneveld et al. (1983)
Eur. J. Biochem. 134:585. An antagonist anti-CD40 antibody can
inhibit the costimulation of anti-IgM induced human B-cell
proliferation by mAb S2C6, for example, by at least 75% or more
(i.e., S2C6-stimulated proliferation in the presence of an
antagonist anti-CD40 antibody is no more than 25% of that observed
in the absence of the antagonist anti-CD40 antibody). In contrast,
no significant inhibition would be seen with equivalent amounts of
non-relevant mAb 8E4, directed to .beta.-glucocerebrosidase.
Barneveld et al., supra. Such a result would indicate that the
anti-CD40 mAbs does not deliver stimulatory signals for the
proliferation of human B cells, but, conversely, can inhibit
stimulatory signals exerted by triggering CD40 with another
mAb.
B-Cell Activation Assay with EL4B5 Cells.
[0287] Zubler et al. (1985) J. Immunol. (1985) 134:3662 observed
that a mutant subclone of the mouse thymoma EL-4 line, known as
EL4B5, could strongly stimulate B cells of both murine and human
origin to proliferate and differentiate into
immunoglobulin-secreting plasma cells in vitro. This activation was
found to be antigen-independent and not MHC restricted. For optimal
stimulation of human B cells, the presence of supernatant from
activated human T cells was needed but a B-cell response also
occurred when EL4B5 cells were preactivated with
phorbol-12-myristate 13-acetate (PMA) or IL-1. Zubler et al. (1987)
Immunological Reviews 99:281; and Zhang et al. (1990) J. Immunol.
144:2955. B-cell activation in this culture system is
efficient--limiting dilution experiments have shown that the
majority of human B cells can be activated to proliferate and
differentiate into antibody-secreting cells. Wen et al. (1987) Eur.
J. Immunol. 17:887.
[0288] B cells (1000 per well) are cultured together with
irradiated (5000 Rad) EL4B5 cells (5.times.10.sup.4 per well) in
flat bottom microtiter plates in 200 .mu.l IMDM supplemented with
10% heat-inactivated fetal calf serum, 5 ng/ml phorbol-12-myristate
13-acetate (Sigma) and 5% human T-cell supernatant. mAbs are added
at varying concentrations at the onset of the cultures and
thymidine incorporation is assessed at day 6 after 18 hour pulsing
with [.sup.3H]-thymidine. For the preparation of T-cell
supernatant, purified T cells are cultured at a density of
10.sup.6/ml for 36 hours in the presence of 1 .mu.g/ml PHA and 10
ng/ml PMA. Wen et al. (1987) Eur. J. Immunol. (1987) 17:887. T-cell
supernatant is obtained by centrifugation of the cells and stored
at -20.degree. C. The effectiveness of T-cell supernatants in
enhancing proliferation of human B cells in EL4B5-B cell cultures
is tested and the most effective supernatants are pooled for use in
experiments. When assessing the effect of an anti-CD40 antibody on
EL4B5-induced human B-cell proliferation, a monoclonal antibody
such as MOPC-141 (IgG2b) can be added as a control.
[0289] An antagonist anti-CD40 antibody can inhibit B-cell
proliferation stimulated by the EL4B5 cell line, for example, by at
least 75% or more (i.e., EL4B5-induced B cell proliferation in the
presence of an antagonist anti-CD40 antibody is no more than 25% of
that observed in the absence of the antagonist anti-CD40 antibody).
In contrast, a control antibody such as MOPC-141 would have no
significant effect on EL4B5-induced B cell proliferation.
Human T Cell Helper Assay for Antibody Production by B Cells.
[0290] An antagonist anti-CD40 antibody can function as an
antagonist of immunoglobulin production by B cells. An anti-CD40
antibody can be tested for this type of antagonist activity by
assessing the antibody's ability to inhibit immunoglobulin
production by B cells that have been stimulated in a
contact-dependent manner with activated T cells in a T cell helper
assay. In this manner, 96-well tissue culture plates are coated
with a 1:500 dilution of ascites fluid of anti-CD3 mAb CLB-T3/3
(CLB, Amsterdam, The Netherlands). As indicated costimulatory mAbs
are added: anti CD2 mAbs CLB-T11.1/1 and CLB-T11.2/1 (CLB,
Amsterdam, The Netherlands), both ascites 1:1000 and anti-CD28 mAb
CLB-28/1 (CLB, Amsterdam, The Netherlands). Subsequently, tonsillar
T cells (irradiated, 3000 Rad; 10.sup.5 per well), tonsillar B
cells (10.sup.4 per well), and rIL-2 (20 U/ml) are added. The final
volume of each cell culture is 200 .mu.l. After 8 days, cells are
spun down, and cell-free supernatant is harvested. The
concentrations of human IgM and IgG in (diluted) samples is
estimated by ELISA as described below.
[0291] In one embodiment, human tonsillar B cells (10.sup.4/well)
are cultured together with irradiated purified T cells (3000 rad,
10.sup.5/well) in 96-well plates, coated with anti-CD3 mAb and with
or without different mAbs to costimulate the T cells. After 8 days
of culture the supernatants are harvested for the determination of
immunoglobulin production by the B cells Immunoglobulin production
by the B cells is assessed by the ELISA assay described below. The
anti-CD40 antibody of interest is added in varying concentrations
from the onset of the cultures. As a control, mAb MOPC-141 can be
added.
[0292] An antagonist anti-CD40 antibody can inhibit IgG and IgM
antibody production of B cells stimulated by human T cells by at
least 50% or more (i.e., T cell-induced antibody production by B
cells in the presence of an antagonist anti-CD40 antibody is no
more than 50% of that observed in the absence of the antagonist
anti-CD40 antibody). In contrast, a control antibody such as
MOPC-141 would have no significant effect on T cell-induced
antibody production by B cells.
ELISA Assay for Immunoglobulin Quantification.
[0293] The concentrations of human IgM and IgG are estimated by
ELISA. 96-well ELISA plates are coated with 4 .mu.g/ml mouse
anti-human IgG mAb MH 16-01 (CLB, Amsterdam, The Netherlands) or
with 1.2 .mu.g/ml mouse anti-human IgM mAb 4102 (Tago, Burlingame,
Calif.) in 0.05 M carbonate buffer (pH=9.6), by incubation for 16 h
at 4.degree. C. Plates are washed 3 times with PBS-0.05% Tween-20
(PBS-Tween) and saturated with BSA for 1 hour. After 2 washes the
plates are incubated for 1 h at 37.degree. C. with different
dilutions of the test samples. After 3 washes, bound Ig is detected
by incubation for 1 h at 37.degree. C. with 1 .mu.g/ml
peroxidase-labeled mouse anti-human IgG mAb MH 16-01 (CLB) or mouse
anti-human IgM mAb MH 15-01 (CLB). Plates are washed 4 times and
bound peroxidase activity is revealed by the addition of
O-phenylenediamine as a substrate. Human standard serum (H00, CLB)
is used to establish a standard curve for each assay.
Example 7
Comparisons of Effects of CHIR-12.12 on CD40 Ligand-Mediated CD40
Signaling in Normal B Cells and B-Chronic Lymphocytic Leukemia
Cells
[0294] The activation of CD40 by CD40 ligand (CD40L) can regulate
the survival, proliferation, and differentiation of normal B
lymphocytes. In B cells, ligation of CD40 leads to its binding with
tumor necrosis factor receptor-associated factors (TRAFs) and the
subsequent activation of multiple downstream signaling pathways
involved in cellular proliferation and survival. The activation of
this pathway can be demonstrated ex vivo, where addition of CD40L
to cultured normal B cells promotes their survival and
proliferation. Similar to its activity in normal B cells in
culture, CD40L promotes the survival and proliferation of B-chronic
lymphocytic leukemia (CLL) cells obtained from patient samples, and
this pathway is sensitive to pharmacological intervention.
[0295] The additional studies described below were undertaken to
further characterize the effects of the CHIR-12.12 monoclonal
antibody on CD40L-mediated CD40 survival and signaling pathways in
normal human B cells and human B-CLL cells. These studies confirmed
the observations outlined above. Thus, CHIR-12.12 treatment blocked
CD40L binding to CD40 and inhibited CD40L-induced
proliferation/survival of normal human B cells and primary B-CLL
cells. CD40L-mediated survival was associated with a reduction in
the levels of the apoptotic marker cPARP and induction of
anti-apoptotic proteins Mcl-1 and Bcl-xl. Additionally,
CD40L-induced survival was associated with the phosphorylation of
Akt, p38 MAPK, ERK, and I.kappa.B kinases (IKK) .alpha. and .beta..
In contrast, CHIR-12.12 treatment of CD40L-stimulated primary B-CLL
cells ex vivo inhibited the expression of these anti-apoptotic
proteins and the phosphorylation of the downstream signaling
proteins, ultimately leading to B-CLL cell apoptosis. The majority
of CLL samples analyzed in this study appeared to be responsive to
CD40L stimulation and antibody inhibition. The few CLL samples that
were insensitive are under investigation to identify the pathways
in these samples that may account for their insensitivity.
CHIR-12.12 Treatment Blocks CD40 Ligand-Mediated CD40 Survival and
Signaling Pathways in Normal Human B Cells.
[0296] Normal human B cells were purified from peripheral blood by
negative selection using the MACS B cell isolation kit II (Miltenyi
Biotech INC, Auburn, Calif.) and cultured for 24 hr with or without
2 .mu.g/ml of recombinant human soluble CD40L (rhsCD40L) in the
presence of 10 .mu.g/ml of CHIR-12.12 or isotype control hIgG1.
Cells were lysed and whole cell lysates resolved by SDS-PAGE and
Western blotting using antibodies specific to human cPARP, Mcl-1,
Bcl-xl, p-Akt, and p-p38 MAPK. All membranes were stripped and
re-probed for either .beta.-actin or AKT or p38 MAPK total protein,
as appropriate. Results are shown in FIG. 23.
[0297] CD40L stimulation of normal B cells decreased levels of the
apoptotic marker (cPARP), increased expression of anti-apoptotic
markers (Mcl-1, Bcl-xl), and activated phosphorylation of signaling
markers (p-Akt, p-p38). CHIR-12.12 treatment blocked these
CD40L-mediated effects on normal B cells, leading to apoptosis of
these cells.
Effects of CHIR-12.12 Treatment on CD40 Ligand-Mediated Survival
and Signaling Pathways in B-CLL Cells.
[0298] In order to further assess the effects of CHIR-12.12 on
survival and signaling pathways in B-CLL cells, PBMCs were isolated
from peripheral blood of CLL patients using Vacutainer.RTM. CPT.TM.
Cell Preparation Tubes with sodium citrate (BD Biosciences, San
Jose, Calif.), stained for CD5, CD19, and CD40 (mouse anti-human
CD5-PerCP Cy5.5 (BD Biosciences, San Jose, Calif.), mouse
anti-human CD19-PE (Ancell, Bayport, Minn.), and FITC-labeled mouse
anti-human CD40 antibody (FITC-CHIR-12.12, Chiron Corporation,
Emeryville, Calif.)), fixed, and analyzed by flow cytometry.
Patient and PBMC expression characteristics are summarized in Table
8.
TABLE-US-00008 TABLE 8 Patient and PBMC Characteristics of CLL
Samples. % Total PBMC % Total PBMC Patient ID Age Gender
CD5.sup.+CD19.sup.+ CD40.sup.+ M1 70 M n/a 74 M2 74 M 97 97 M3 59 F
92 93 M4 64 F 91 96 M5 68 M 97 98 M6 67 F 92 92 M7 40 F 85 81
[0299] CHIR-12.12 Treatment Blocks CD40 Ligand-Mediated Survival
Pathway in B-CLL Cells.
[0300] PBMCs (50,000/well in duplicate wells) were seeded in
96-well tissue culture plates (Corning Costar, Corning, N.Y.) in
RPMI+10% FCS and pen/strep alone or in the presence of 2
.mu.g/rnlrhsCD40L+4 .mu.g/ml CD40L enhancer with either 10 .mu.g/ml
CHIR-12.12 or control human IgG1. Cell viability was determined
after 72 hours using the CellTiter-Glo.RTM. Luminescent Cell
Viability Kit (Promega, Madison, Wis.), which measures cellular
ATP, and expressed as Relative Luminescence Units (RLU). Percent
blockade was calculated as follows:
% blockade = { 1 - [ ( 12.12 + L ) - ( cells alone ) ] [ ( IgG 1 +
L ) - ( cells alone ) ] } .times. 100. ##EQU00001##
[0301] cPARP analysis by flow cytometry was performed after 24
hours in culture. Cells were treated with FACSLysis buffer (BD
Biosciences) and frozen. After fixation in 1% formaldehyde for 45
min, cells were washed and incubated with PE-conjugated mouse
anti-human CD19 for 30 min at room temperature (RT). Cells were
then permeabilized using 70% ethanol on ice for 30 min and stained
for 30 min at RT with rabbit anti-human cPARP antibody or isotype
control rabbit IgG along with PerCP-Cy5.5-labeled mouse anti-human
CD5. This was followed by incubation with goat anti-rabbit
IgG-AlexaFluor 647 for 30 min at RT before fixing with 1%
formaldehyde and analyzing by flow cytometry. Percent blockade was
calculated as follows:
% blockade = { 1 - [ ( cells alone ) - ( 12.12 + L ) ] [ ( cells
alone ) - ( IgG 1 + L ) ] } .times. 100. ##EQU00002##
[0302] Stimulation with CD40L could promote survival/prevent
apoptosis in cultured B-CLL cells, and these effects could be
blocked by CHIR-12.12 (FIG. 24). In 7/7 samples in the
CellTiter-Glo assay and 6/7 samples in the cPARP flow cytometry
assay, CD40L promoted survival of B-CLL cells and in each case,
these effects were blocked by CHIR-12.12 (Table 9).
TABLE-US-00009 TABLE 9 Effects of CHIR-12.12 treatment on
CD40L-mediated B-CLL cell survival as measured by CellTiter-Glo
assay and cPARP flow cytometry. CellTiter-Glo Assay cPARP Flow
Cytometry % Block of % cPARP.sup.+ % Block of Non-treated Fold
rhsCD40L Cells In Fold rhsCD40L Subject Control Induction by CHIR-
Non-treated Inhibition by CHIR- ID (RLU .times. 10.sup.3) by
rhsCD40L 12.12 Control by rhsCD40L 12.12 Normal B 100 3.0 99 19 3
83 M1 200 3.1 94 14 5.8 77 M2 290 2.9 95 14 2.6 70 M3 270 1.9 92 14
2.1 48 M4 240 2.3 87 22 3.2 71 M5 110 3.5 71 5 2.3 48 M6 230 2.6 72
7 0.9 109 M7 75 3.8 96 50 5.2 80
[0303] Effects of CHIR-12.12 Treatment on Expression of
Anti-Apoptotic Proteins.
[0304] Following PBMC isolation, 2.times.10.sup.6 cells/ml were
cultured as described above for data shown in FIG. 24. Whole cell
lysates were prepared in RIPA lysis buffer (1% Nonidet P-40, 0.5%
sodium deoxycholate, 0.1% Sodium dodecylsulfate in 1.times.
phosphate buffered saline, pH 7.2). 10-20 .mu.g of protein per
sample were resolved on a 10% Tris-Glycine gel and transferred to
nitrocellulose membranes, and membranes were probed using mAbs
specific to human cPARP, Mcl-1, or Bcl-xl. The membranes were
stripped and re-probed for .beta.-actin and developed using ECL.
Results are shown in FIG. 25. CHIR-12.12 treatment blocked the
CD40L-mediated decrease of cPARP levels and CD40L-mediated increase
of Mcl-1 and Bcl-xl expression in primary B-CLL cells.
[0305] Effects of CHIR-12.12 Treatment on CD40 Ligand-Mediated
Signaling Pathways in B-CLL Cells.
[0306] The effects of CHIR-12.12 on CD40 ligand-mediated signaling
in the AKT and p38 MAPK signaling pathways were assessed for B-CLL
cells. To evaluate phosphorylated Akt (p-Akt), PBMC were cultured
as described above for data shown in FIG. 24. To detect p38 MAPK,
cells were cultured for 3 hr using the previously described
conditions, with rhsCD40L being added in the last 20 min of
incubation. Cells were processed as described above for data shown
in FIG. 25. mAbs specific to human p-Akt and p-p38 MAPK were used
to probe the resultant membranes, which were re-probed for AKT and
p38 total protein, respectively. Results are shown in FIG. 26.
While in some samples CD40L did not appear to stimulate
phosphorylation of AKT, in a number of samples, CD40L activated the
AKT pathway and CHIR-12.12 blocked this effect. While the levels of
p38 MAPK phosphorylation in untreated cells varied, treatment with
rhsCD40L enhanced the phosphorylation of p38 MAPK and CHIR-12.12
blocked this effect.
[0307] To evaluate the effects of rhsCD40L and CHIR-12.12 on IKK
.alpha./.beta. and ERK 1/2, PBMCs were cultured and processed as
described for detection of p38 in FIG. 26. Resultant membranes were
probed using mAbs specific to human p-IKK .alpha./.beta. and p-ERK.
Results are shown in FIG. 27. CHIR-12.12 treatment inhibited the
CD40L-induced phosphorylation of IKK .alpha./.beta. and ERK 1/2 in
B-CLL cells.
Summary
[0308] When placed in culture, normal B lymphocytes undergo
spontaneous apoptosis, and this can be reversed by addition of
CD40L to the cultures. In the studies described herein, addition of
CD40L to normal B lymphocytes resulted in upregulation of survival
proteins such as Mcl-1 and Bcl-xl and activated the AKT and p38
pathways. B-CLL cells obtained from chronic lymphocytic leukemia
patient samples were similarly responsive to CD40L in the described
assays. In addition CD40L stimulated phosphorylation of IKK .alpha.
and .beta. and ERK 1/2 in B-CLL cells. These pathways were
evaluated in B-CLL cells as they have been shown to be important in
B cell survival and may contribute to the disregulated survival of
B-CLL cells. In both normal B cells and the B-CLL cell samples
responsive to CD40L stimulation, each of the described effects
could be blocked by the antagonistic anti-CD40 antibody,
CHIR-12.12.
[0309] Many modifications and other embodiments of the inventions
set forth herein will come to mind to one skilled in the art to
which these inventions pertain having the benefit of the teachings
presented in the foregoing descriptions and the associated
drawings. Therefore, it is to be understood that the inventions are
not to be limited to the specific embodiments disclosed and that
modifications and other embodiments are intended to be included
within the scope of the appended claims. Although specific terms
are employed herein, they are used in a generic and descriptive
sense only and not for purposes of limitation.
[0310] All publications and patent applications mentioned in the
specification are indicative of the level of those skilled in the
art to which this invention pertains. All publications and patent
applications are herein incorporated by reference to the same
extent as if each individual publication or patent application was
specifically and individually indicated to be incorporated by
reference.
Sequence CWU 1 SEQUENCE LISTING <160> NUMBER OF SEQ ID
NOS: 16 <210> SEQ ID NO 1 <211> LENGTH: 720 <212>
TYPE: DNA <213> ORGANISM: Artificial Sequence <220>
FEATURE: <223> OTHER INFORMATION: Coding sequence for light
chain of 12.12 human anti-CD40 antibody <221> NAME/KEY: CDS
<222> LOCATION: (1)...(720) <400> SEQUENCE: 1 atg gcg
ctc cct gct cag ctc ctg ggg ctg cta atg ctc tgg gtc tct 48 Met Ala
Leu Pro Ala Gln Leu Leu Gly Leu Leu Met Leu Trp Val Ser 1 5 10 15
gga tcc agt ggg gat att gtg atg act cag tct cca ctc tcc ctg acc 96
Gly Ser Ser Gly Asp Ile Val Met Thr Gln Ser Pro Leu Ser Leu Thr 20
25 30 gtc acc cct gga gag ccg gcc tcc atc tcc tgc agg tcc agt cag
agc 144 Val Thr Pro Gly Glu Pro Ala Ser Ile Ser Cys Arg Ser Ser Gln
Ser 35 40 45 ctc ctg tat agt aat gga tac aac tat ttg gat tgg tac
ctg cag aag 192 Leu Leu Tyr Ser Asn Gly Tyr Asn Tyr Leu Asp Trp Tyr
Leu Gln Lys 50 55 60 cca ggg cag tct cca cag gtc ctg atc tct ttg
ggt tct aat cgg gcc 240 Pro Gly Gln Ser Pro Gln Val Leu Ile Ser Leu
Gly Ser Asn Arg Ala 65 70 75 80 tcc ggg gtc cct gac agg ttc agt ggc
agt gga tca ggc aca gat ttt 288 Ser Gly Val Pro Asp Arg Phe Ser Gly
Ser Gly Ser Gly Thr Asp Phe 85 90 95 aca ctg aaa atc agc aga gtg
gag gct gag gat gtt ggg gtt tat tac 336 Thr Leu Lys Ile Ser Arg Val
Glu Ala Glu Asp Val Gly Val Tyr Tyr 100 105 110 tgc atg caa gct cga
caa act cca ttc act ttc ggc cct ggg acc aaa 384 Cys Met Gln Ala Arg
Gln Thr Pro Phe Thr Phe Gly Pro Gly Thr Lys 115 120 125 gtg gat atc
aga cga act gtg gct gca cca tct gtc ttc atc ttc ccg 432 Val Asp Ile
Arg Arg Thr Val Ala Ala Pro Ser Val Phe Ile Phe Pro 130 135 140 cca
tct gat gag cag ttg aaa tct gga act gcc tct gtt gtg tgc ctg 480 Pro
Ser Asp Glu Gln Leu Lys Ser Gly Thr Ala Ser Val Val Cys Leu 145 150
155 160 ctg aat aac ttc tat ccc aga gag gcc aaa gta cag tgg aag gtg
gat 528 Leu Asn Asn Phe Tyr Pro Arg Glu Ala Lys Val Gln Trp Lys Val
Asp 165 170 175 aac gcc ctc caa tcg ggt aac tcc cag gag agt gtc aca
gag cag gac 576 Asn Ala Leu Gln Ser Gly Asn Ser Gln Glu Ser Val Thr
Glu Gln Asp 180 185 190 agc aag gac agc acc tac agc ctc agc agc acc
ctg acg ctg agc aaa 624 Ser Lys Asp Ser Thr Tyr Ser Leu Ser Ser Thr
Leu Thr Leu Ser Lys 195 200 205 gca gac tac gag aaa cac aaa gtc tac
gcc tgc gaa gtc acc cat cag 672 Ala Asp Tyr Glu Lys His Lys Val Tyr
Ala Cys Glu Val Thr His Gln 210 215 220 ggc ctg agc tcg ccc gtc aca
aag agc ttc aac agg gga gag tgt tag 720 Gly Leu Ser Ser Pro Val Thr
Lys Ser Phe Asn Arg Gly Glu Cys * 225 230 235 <210> SEQ ID NO
2 <211> LENGTH: 239 <212> TYPE: PRT <213>
ORGANISM: Artificial Sequence <220> FEATURE: <223>
OTHER INFORMATION: Coding sequence for light chain of 12.12 human
anti-CD40 antibody <400> SEQUENCE: 2 Met Ala Leu Pro Ala Gln
Leu Leu Gly Leu Leu Met Leu Trp Val Ser 1 5 10 15 Gly Ser Ser Gly
Asp Ile Val Met Thr Gln Ser Pro Leu Ser Leu Thr 20 25 30 Val Thr
Pro Gly Glu Pro Ala Ser Ile Ser Cys Arg Ser Ser Gln Ser 35 40 45
Leu Leu Tyr Ser Asn Gly Tyr Asn Tyr Leu Asp Trp Tyr Leu Gln Lys 50
55 60 Pro Gly Gln Ser Pro Gln Val Leu Ile Ser Leu Gly Ser Asn Arg
Ala 65 70 75 80 Ser Gly Val Pro Asp Arg Phe Ser Gly Ser Gly Ser Gly
Thr Asp Phe 85 90 95 Thr Leu Lys Ile Ser Arg Val Glu Ala Glu Asp
Val Gly Val Tyr Tyr 100 105 110 Cys Met Gln Ala Arg Gln Thr Pro Phe
Thr Phe Gly Pro Gly Thr Lys 115 120 125 Val Asp Ile Arg Arg Thr Val
Ala Ala Pro Ser Val Phe Ile Phe Pro 130 135 140 Pro Ser Asp Glu Gln
Leu Lys Ser Gly Thr Ala Ser Val Val Cys Leu 145 150 155 160 Leu Asn
Asn Phe Tyr Pro Arg Glu Ala Lys Val Gln Trp Lys Val Asp 165 170 175
Asn Ala Leu Gln Ser Gly Asn Ser Gln Glu Ser Val Thr Glu Gln Asp 180
185 190 Ser Lys Asp Ser Thr Tyr Ser Leu Ser Ser Thr Leu Thr Leu Ser
Lys 195 200 205 Ala Asp Tyr Glu Lys His Lys Val Tyr Ala Cys Glu Val
Thr His Gln 210 215 220 Gly Leu Ser Ser Pro Val Thr Lys Ser Phe Asn
Arg Gly Glu Cys 225 230 235 <210> SEQ ID NO 3 <211>
LENGTH: 2016 <212> TYPE: DNA <213> ORGANISM: Artificial
Sequence <220> FEATURE: <223> OTHER INFORMATION: Coding
sequence for heavy chain of 12.12 human anti-CD40 antibody (with
introns) <400> SEQUENCE: 3 atggagtttg ggctgagctg ggttttcctt
gttgctattt taagaggtgt ccagtgtcag 60 gtgcagttgg tggagtctgg
gggaggcgtg gtccagcctg ggaggtccct gagactctcc 120 tgtgcagcct
ctggattcac cttcagtagc tatggcatgc actgggtccg ccaggctcca 180
ggcaaggggc tggagtgggt ggcagttata tcatatgagg aaagtaatag ataccatgca
240 gactccgtga agggccgatt caccatctcc agagacaatt ccaagatcac
gctgtatctg 300 caaatgaaca gcctcagaac tgaggacacg gctgtgtatt
actgtgcgag agatgggggt 360 atagcagcac ctgggcctga ctactggggc
cagggaaccc tggtcaccgt ctcctcagca 420 agtaccaagg gcccatccgt
cttccccctg gcgcccgcta gcaagagcac ctctgggggc 480 acagcggccc
tgggctgcct ggtcaaggac tacttccccg aaccggtgac ggtgtcgtgg 540
aactcaggcg ccctgaccag cggcgtgcac accttcccgg ctgtcctaca gtcctcagga
600 ctctactccc tcagcagcgt ggtgaccgtg ccctccagca gcttgggcac
ccagacctac 660 atctgcaacg tgaatcacaa gcccagcaac accaaggtgg
acaagagagt tggtgagagg 720 ccagcacagg gagggagggt gtctgctgga
agccaggctc agcgctcctg cctggacgca 780 tcccggctat gcagtcccag
tccagggcag caaggcaggc cccgtctgcc tcttcacccg 840 gaggcctctg
cccgccccac tcatgctcag ggagagggtc ttctggcttt ttccccaggc 900
tctgggcagg cacaggctag gtgcccctaa cccaggccct gcacacaaag gggcaggtgc
960 tgggctcaga cctgccaaga gccatatccg ggaggaccct gcccctgacc
taagcccacc 1020 ccaaaggcca aactctccac tccctcagct cggacacctt
ctctcctccc agattccagt 1080 aactcccaat cttctctctg cagagcccaa
atcttgtgac aaaactcaca catgcccacc 1140 gtgcccaggt aagccagccc
aggcctcgcc ctccagctca aggcgggaca ggtgccctag 1200 agtagcctgc
atccagggac aggccccagc cgggtgctga cacgtccacc tccatctctt 1260
cctcagcacc tgaactcctg gggggaccgt cagtcttcct cttcccccca aaacccaagg
1320 acaccctcat gatctcccgg acccctgagg tcacatgcgt ggtggtggac
gtgagccacg 1380 aagaccctga ggtcaagttc aactggtacg tggacggcgt
ggaggtgcat aatgccaaga 1440 caaagccgcg ggaggagcag tacaacagca
cgtaccgtgt ggtcagcgtc ctcaccgtcc 1500 tgcaccagga ctggctgaat
ggcaaggagt acaagtgcaa ggtctccaac aaagccctcc 1560 cagcccccat
cgagaaaacc atctccaaag ccaaaggtgg gacccgtggg gtgcgagggc 1620
cacatggaca gaggccggct cggcccaccc tctgccctga gagtgaccgc tgtaccaacc
1680 tctgtcccta cagggcagcc ccgagaacca caggtgtaca ccctgccccc
atcccgggag 1740 gagatgacca agaaccaggt cagcctgacc tgcctggtca
aaggcttcta tcccagcgac 1800 atcgccgtgg agtgggagag caatgggcag
ccggagaaca actacaagac cacgcctccc 1860 gtgctggact ccgacggctc
cttcttcctc tatagcaagc tcaccgtgga caagagcagg 1920 tggcagcagg
ggaacgtctt ctcatgctcc gtgatgcatg aggctctgca caaccactac 1980
acgcagaaga gcctctccct gtctccgggt aaatga 2016 <210> SEQ ID NO
4 <211> LENGTH: 469 <212> TYPE: PRT <213>
ORGANISM: Artificial Sequence <220> FEATURE: <223>
OTHER INFORMATION: Heavy chain of 12.12 human anti-CD40 antibody
<400> SEQUENCE: 4 Met Glu Phe Gly Leu Ser Trp Val Phe Leu Val
Ala Ile Leu Arg Gly 1 5 10 15 Val Gln Cys Gln Val Gln Leu Val Glu
Ser Gly Gly Gly Val Val Gln 20 25 30 Pro Gly Arg Ser Leu Arg Leu
Ser Cys Ala Ala Ser Gly Phe Thr Phe 35 40 45 Ser Ser Tyr Gly Met
His Trp Val Arg Gln Ala Pro Gly Lys Gly Leu 50 55 60 Glu Trp Val
Ala Val Ile Ser Tyr Glu Glu Ser Asn Arg Tyr His Ala 65 70 75 80 Asp
Ser Val Lys Gly Arg Phe Thr Ile Ser Arg Asp Asn Ser Lys Ile 85 90
95 Thr Leu Tyr Leu Gln Met Asn Ser Leu Arg Thr Glu Asp Thr Ala Val
100 105 110 Tyr Tyr Cys Ala Arg Asp Gly Gly Ile Ala Ala Pro Gly Pro
Asp Tyr 115 120 125 Trp Gly Gln Gly Thr Leu Val Thr Val Ser Ser Ala
Ser Thr Lys Gly 130 135 140 Pro Ser Val Phe Pro Leu Ala Pro Ala Ser
Lys Ser Thr Ser Gly Gly 145 150 155 160 Thr Ala Ala Leu Gly Cys Leu
Val Lys Asp Tyr Phe Pro Glu Pro Val 165 170 175 Thr Val Ser Trp Asn
Ser Gly Ala Leu Thr Ser Gly Val His Thr Phe 180 185 190 Pro Ala Val
Leu Gln Ser Ser Gly Leu Tyr Ser Leu Ser Ser Val Val 195 200 205 Thr
Val Pro Ser Ser Ser Leu Gly Thr Gln Thr Tyr Ile Cys Asn Val 210 215
220 Asn His Lys Pro Ser Asn Thr Lys Val Asp Lys Arg Val Glu Pro Lys
225 230 235 240 Ser Cys Asp Lys Thr His Thr Cys Pro Pro Cys Pro Ala
Pro Glu Leu 245 250 255 Leu Gly Gly Pro Ser Val Phe Leu Phe Pro Pro
Lys Pro Lys Asp Thr 260 265 270 Leu Met Ile Ser Arg Thr Pro Glu Val
Thr Cys Val Val Val Asp Val 275 280 285 Ser His Glu Asp Pro Glu Val
Lys Phe Asn Trp Tyr Val Asp Gly Val 290 295 300 Glu Val His Asn Ala
Lys Thr Lys Pro Arg Glu Glu Gln Tyr Asn Ser 305 310 315 320 Thr Tyr
Arg Val Val Ser Val Leu Thr Val Leu His Gln Asp Trp Leu 325 330 335
Asn Gly Lys Glu Tyr Lys Cys Lys Val Ser Asn Lys Ala Leu Pro Ala 340
345 350 Pro Ile Glu Lys Thr Ile Ser Lys Ala Lys Gly Gln Pro Arg Glu
Pro 355 360 365 Gln Val Tyr Thr Leu Pro Pro Ser Arg Glu Glu Met Thr
Lys Asn Gln 370 375 380 Val Ser Leu Thr Cys Leu Val Lys Gly Phe Tyr
Pro Ser Asp Ile Ala 385 390 395 400 Val Glu Trp Glu Ser Asn Gly Gln
Pro Glu Asn Asn Tyr Lys Thr Thr 405 410 415 Pro Pro Val Leu Asp Ser
Asp Gly Ser Phe Phe Leu Tyr Ser Lys Leu 420 425 430 Thr Val Asp Lys
Ser Arg Trp Gln Gln Gly Asn Val Phe Ser Cys Ser 435 440 445 Val Met
His Glu Ala Leu His Asn His Tyr Thr Gln Lys Ser Leu Ser 450 455 460
Leu Ser Pro Gly Lys 465 <210> SEQ ID NO 5 <211> LENGTH:
469 <212> TYPE: PRT <213> ORGANISM: Artificial Sequence
<220> FEATURE: <223> OTHER INFORMATION: Heavy chain of
variant of 12.12 human anti-CD40 antibody <400> SEQUENCE: 5
Met Glu Phe Gly Leu Ser Trp Val Phe Leu Val Ala Ile Leu Arg Gly 1 5
10 15 Val Gln Cys Gln Val Gln Leu Val Glu Ser Gly Gly Gly Val Val
Gln 20 25 30 Pro Gly Arg Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly
Phe Thr Phe 35 40 45 Ser Ser Tyr Gly Met His Trp Val Arg Gln Ala
Pro Gly Lys Gly Leu 50 55 60 Glu Trp Val Ala Val Ile Ser Tyr Glu
Glu Ser Asn Arg Tyr His Ala 65 70 75 80 Asp Ser Val Lys Gly Arg Phe
Thr Ile Ser Arg Asp Asn Ser Lys Ile 85 90 95 Thr Leu Tyr Leu Gln
Met Asn Ser Leu Arg Thr Glu Asp Thr Ala Val 100 105 110 Tyr Tyr Cys
Ala Arg Asp Gly Gly Ile Ala Ala Pro Gly Pro Asp Tyr 115 120 125 Trp
Gly Gln Gly Thr Leu Val Thr Val Ser Ser Ala Ser Thr Lys Gly 130 135
140 Pro Ser Val Phe Pro Leu Ala Pro Ser Ser Lys Ser Thr Ser Gly Gly
145 150 155 160 Thr Ala Ala Leu Gly Cys Leu Val Lys Asp Tyr Phe Pro
Glu Pro Val 165 170 175 Thr Val Ser Trp Asn Ser Gly Ala Leu Thr Ser
Gly Val His Thr Phe 180 185 190 Pro Ala Val Leu Gln Ser Ser Gly Leu
Tyr Ser Leu Ser Ser Val Val 195 200 205 Thr Val Pro Ser Ser Ser Leu
Gly Thr Gln Thr Tyr Ile Cys Asn Val 210 215 220 Asn His Lys Pro Ser
Asn Thr Lys Val Asp Lys Arg Val Glu Pro Lys 225 230 235 240 Ser Cys
Asp Lys Thr His Thr Cys Pro Pro Cys Pro Ala Pro Glu Leu 245 250 255
Leu Gly Gly Pro Ser Val Phe Leu Phe Pro Pro Lys Pro Lys Asp Thr 260
265 270 Leu Met Ile Ser Arg Thr Pro Glu Val Thr Cys Val Val Val Asp
Val 275 280 285 Ser His Glu Asp Pro Glu Val Lys Phe Asn Trp Tyr Val
Asp Gly Val 290 295 300 Glu Val His Asn Ala Lys Thr Lys Pro Arg Glu
Glu Gln Tyr Asn Ser 305 310 315 320 Thr Tyr Arg Val Val Ser Val Leu
Thr Val Leu His Gln Asp Trp Leu 325 330 335 Asn Gly Lys Glu Tyr Lys
Cys Lys Val Ser Asn Lys Ala Leu Pro Ala 340 345 350 Pro Ile Glu Lys
Thr Ile Ser Lys Ala Lys Gly Gln Pro Arg Glu Pro 355 360 365 Gln Val
Tyr Thr Leu Pro Pro Ser Arg Glu Glu Met Thr Lys Asn Gln 370 375 380
Val Ser Leu Thr Cys Leu Val Lys Gly Phe Tyr Pro Ser Asp Ile Ala 385
390 395 400 Val Glu Trp Glu Ser Asn Gly Gln Pro Glu Asn Asn Tyr Lys
Thr Thr 405 410 415 Pro Pro Val Leu Asp Ser Asp Gly Ser Phe Phe Leu
Tyr Ser Lys Leu 420 425 430 Thr Val Asp Lys Ser Arg Trp Gln Gln Gly
Asn Val Phe Ser Cys Ser 435 440 445 Val Met His Glu Ala Leu His Asn
His Tyr Thr Gln Lys Ser Leu Ser 450 455 460 Leu Ser Pro Gly Lys 465
<210> SEQ ID NO 6 <211> LENGTH: 239 <212> TYPE:
PRT <213> ORGANISM: Artificial Sequence <220> FEATURE:
<223> OTHER INFORMATION: Light chain of 5.9 human anti-CD40
antibody <400> SEQUENCE: 6 Met Ala Leu Leu Ala Gln Leu Leu
Gly Leu Leu Met Leu Trp Val Pro 1 5 10 15 Gly Ser Ser Gly Ala Ile
Val Met Thr Gln Pro Pro Leu Ser Ser Pro 20 25 30 Val Thr Leu Gly
Gln Pro Ala Ser Ile Ser Cys Arg Ser Ser Gln Ser 35 40 45 Leu Val
His Ser Asp Gly Asn Thr Tyr Leu Asn Trp Leu Gln Gln Arg 50 55 60
Pro Gly Gln Pro Pro Arg Leu Leu Ile Tyr Lys Phe Phe Arg Arg Leu 65
70 75 80 Ser Gly Val Pro Asp Arg Phe Ser Gly Ser Gly Ala Gly Thr
Asp Phe 85 90 95 Thr Leu Lys Ile Ser Arg Val Glu Ala Glu Asp Val
Gly Val Tyr Tyr 100 105 110 Cys Met Gln Val Thr Gln Phe Pro His Thr
Phe Gly Gln Gly Thr Arg 115 120 125 Leu Glu Ile Lys Arg Thr Val Ala
Ala Pro Ser Val Phe Ile Phe Pro 130 135 140 Pro Ser Asp Glu Gln Leu
Lys Ser Gly Thr Ala Ser Val Val Cys Leu 145 150 155 160 Leu Asn Asn
Phe Tyr Pro Arg Glu Ala Lys Val Gln Trp Lys Val Asp 165 170 175 Asn
Ala Leu Gln Ser Gly Asn Ser Gln Glu Ser Val Thr Glu Gln Asp 180 185
190 Ser Lys Asp Ser Thr Tyr Ser Leu Ser Ser Thr Leu Thr Leu Ser Lys
195 200 205 Ala Asp Tyr Glu Lys His Lys Val Tyr Ala Cys Glu Val Thr
His Gln 210 215 220 Gly Leu Ser Ser Pro Val Thr Lys Ser Phe Asn Arg
Gly Glu Cys 225 230 235 <210> SEQ ID NO 7 <211> LENGTH:
474 <212> TYPE: PRT <213> ORGANISM: Artificial Sequence
<220> FEATURE: <223> OTHER INFORMATION: Heavy chain of
5.9 human anti-CD40 antibody <400> SEQUENCE: 7 Met Gly Ser
Thr Ala Ile Leu Ala Leu Leu Leu Ala Val Leu Gln Gly 1 5 10 15 Val
Cys Ala Glu Val Gln Leu Val Gln Ser Gly Ala Glu Val Lys Lys 20 25
30 Pro Gly Glu Ser Leu Lys Ile Ser Cys Lys Gly Ser Gly Tyr Ser Phe
35 40 45 Thr Ser Tyr Trp Ile Gly Trp Val Arg Gln Met Pro Gly Lys
Gly Leu 50 55 60 Glu Trp Met Gly Ile Ile Tyr Pro Gly Asp Ser Asp
Thr Arg Tyr Ser 65 70 75 80 Pro Ser Phe Gln Gly Gln Val Thr Ile Ser
Ala Asp Lys Ser Ile Ser 85 90 95 Thr Ala Tyr Leu Gln Trp Ser Ser
Leu Lys Ala Ser Asp Thr Ala Met 100 105 110 Tyr Tyr Cys Ala Arg Gly
Thr Ala Ala Gly Arg Asp Tyr Tyr Tyr Tyr 115 120 125 Tyr Gly Met Asp
Val Trp Gly Gln Gly Thr Thr Val Thr Val Ser Ser 130 135 140 Ala Ser
Thr Lys Gly Pro Ser Val Phe Pro Leu Ala Pro Ala Ser Lys 145 150 155
160 Ser Thr Ser Gly Gly Thr Ala Ala Leu Gly Cys Leu Val Lys Asp Tyr
165 170 175 Phe Pro Glu Pro Val Thr Val Ser Trp Asn Ser Gly Ala Leu
Thr Ser 180 185 190 Gly Val His Thr Phe Pro Ala Val Leu Gln Ser Ser
Gly Leu Tyr Ser 195 200 205 Leu Ser Ser Val Val Thr Val Pro Ser Ser
Ser Leu Gly Thr Gln Thr 210 215 220 Tyr Ile Cys Asn Val Asn His Lys
Pro Ser Asn Thr Lys Val Asp Lys 225 230 235 240 Arg Val Glu Pro Lys
Ser Cys Asp Lys Thr His Thr Cys Pro Pro Cys 245 250 255 Pro Ala Pro
Glu Leu Leu Gly Gly Pro Ser Val Phe Leu Phe Pro Pro 260 265 270 Lys
Pro Lys Asp Thr Leu Met Ile Ser Arg Thr Pro Glu Val Thr Cys 275 280
285 Val Val Val Asp Val Ser His Glu Asp Pro Glu Val Lys Phe Asn Trp
290 295 300 Tyr Val Asp Gly Val Glu Val His Asn Ala Lys Thr Lys Pro
Arg Glu 305 310 315 320 Glu Gln Tyr Asn Ser Thr Tyr Arg Val Val Ser
Val Leu Thr Val Leu 325 330 335 His Gln Asp Trp Leu Asn Gly Lys Glu
Tyr Lys Cys Lys Val Ser Asn 340 345 350 Lys Ala Leu Pro Ala Pro Ile
Glu Lys Thr Ile Ser Lys Ala Lys Gly 355 360 365 Gln Pro Arg Glu Pro
Gln Val Tyr Thr Leu Pro Pro Ser Arg Glu Glu 370 375 380 Met Thr Lys
Asn Gln Val Ser Leu Thr Cys Leu Val Lys Gly Phe Tyr 385 390 395 400
Pro Ser Asp Ile Ala Val Glu Trp Glu Ser Asn Gly Gln Pro Glu Asn 405
410 415 Asn Tyr Lys Thr Thr Pro Pro Val Leu Asp Ser Asp Gly Ser Phe
Phe 420 425 430 Leu Tyr Ser Lys Leu Thr Val Asp Lys Ser Arg Trp Gln
Gln Gly Asn 435 440 445 Val Phe Ser Cys Ser Val Met His Glu Ala Leu
His Asn His Tyr Thr 450 455 460 Gln Lys Ser Leu Ser Leu Ser Pro Gly
Lys 465 470 <210> SEQ ID NO 8 <211> LENGTH: 474
<212> TYPE: PRT <213> ORGANISM: Artificial Sequence
<220> FEATURE: <223> OTHER INFORMATION: Heavy chain of
variant of 5.9 human anti-CD40 antibody <400> SEQUENCE: 8 Met
Gly Ser Thr Ala Ile Leu Ala Leu Leu Leu Ala Val Leu Gln Gly 1 5 10
15 Val Cys Ala Glu Val Gln Leu Val Gln Ser Gly Ala Glu Val Lys Lys
20 25 30 Pro Gly Glu Ser Leu Lys Ile Ser Cys Lys Gly Ser Gly Tyr
Ser Phe 35 40 45 Thr Ser Tyr Trp Ile Gly Trp Val Arg Gln Met Pro
Gly Lys Gly Leu 50 55 60 Glu Trp Met Gly Ile Ile Tyr Pro Gly Asp
Ser Asp Thr Arg Tyr Ser 65 70 75 80 Pro Ser Phe Gln Gly Gln Val Thr
Ile Ser Ala Asp Lys Ser Ile Ser 85 90 95 Thr Ala Tyr Leu Gln Trp
Ser Ser Leu Lys Ala Ser Asp Thr Ala Met 100 105 110 Tyr Tyr Cys Ala
Arg Gly Thr Ala Ala Gly Arg Asp Tyr Tyr Tyr Tyr 115 120 125 Tyr Gly
Met Asp Val Trp Gly Gln Gly Thr Thr Val Thr Val Ser Ser 130 135 140
Ala Ser Thr Lys Gly Pro Ser Val Phe Pro Leu Ala Pro Ser Ser Lys 145
150 155 160 Ser Thr Ser Gly Gly Thr Ala Ala Leu Gly Cys Leu Val Lys
Asp Tyr 165 170 175 Phe Pro Glu Pro Val Thr Val Ser Trp Asn Ser Gly
Ala Leu Thr Ser 180 185 190 Gly Val His Thr Phe Pro Ala Val Leu Gln
Ser Ser Gly Leu Tyr Ser 195 200 205 Leu Ser Ser Val Val Thr Val Pro
Ser Ser Ser Leu Gly Thr Gln Thr 210 215 220 Tyr Ile Cys Asn Val Asn
His Lys Pro Ser Asn Thr Lys Val Asp Lys 225 230 235 240 Arg Val Glu
Pro Lys Ser Cys Asp Lys Thr His Thr Cys Pro Pro Cys 245 250 255 Pro
Ala Pro Glu Leu Leu Gly Gly Pro Ser Val Phe Leu Phe Pro Pro 260 265
270 Lys Pro Lys Asp Thr Leu Met Ile Ser Arg Thr Pro Glu Val Thr Cys
275 280 285 Val Val Val Asp Val Ser His Glu Asp Pro Glu Val Lys Phe
Asn Trp 290 295 300 Tyr Val Asp Gly Val Glu Val His Asn Ala Lys Thr
Lys Pro Arg Glu 305 310 315 320 Glu Gln Tyr Asn Ser Thr Tyr Arg Val
Val Ser Val Leu Thr Val Leu 325 330 335 His Gln Asp Trp Leu Asn Gly
Lys Glu Tyr Lys Cys Lys Val Ser Asn 340 345 350 Lys Ala Leu Pro Ala
Pro Ile Glu Lys Thr Ile Ser Lys Ala Lys Gly 355 360 365 Gln Pro Arg
Glu Pro Gln Val Tyr Thr Leu Pro Pro Ser Arg Glu Glu 370 375 380 Met
Thr Lys Asn Gln Val Ser Leu Thr Cys Leu Val Lys Gly Phe Tyr 385 390
395 400 Pro Ser Asp Ile Ala Val Glu Trp Glu Ser Asn Gly Gln Pro Glu
Asn 405 410 415 Asn Tyr Lys Thr Thr Pro Pro Val Leu Asp Ser Asp Gly
Ser Phe Phe 420 425 430 Leu Tyr Ser Lys Leu Thr Val Asp Lys Ser Arg
Trp Gln Gln Gly Asn 435 440 445 Val Phe Ser Cys Ser Val Met His Glu
Ala Leu His Asn His Tyr Thr 450 455 460 Gln Lys Ser Leu Ser Leu Ser
Pro Gly Lys 465 470 <210> SEQ ID NO 9 <211> LENGTH: 612
<212> TYPE: DNA <213> ORGANISM: Homo sapiens
<220> FEATURE: <221> NAME/KEY: CDS <222>
LOCATION: (1)...(612) <221> NAME/KEY: misc_feature
<222> LOCATION: (0)...(0) <223> OTHER INFORMATION:
Coding sequence for short isoform of human CD40 <400>
SEQUENCE: 9 atg gtt cgt ctg cct ctg cag tgc gtc ctc tgg ggc tgc ttg
ctg acc 48 Met Val Arg Leu Pro Leu Gln Cys Val Leu Trp Gly Cys Leu
Leu Thr 1 5 10 15 gct gtc cat cca gaa cca ccc act gca tgc aga gaa
aaa cag tac cta 96 Ala Val His Pro Glu Pro Pro Thr Ala Cys Arg Glu
Lys Gln Tyr Leu 20 25 30 ata aac agt cag tgc tgt tct ttg tgc cag
cca gga cag aaa ctg gtg 144 Ile Asn Ser Gln Cys Cys Ser Leu Cys Gln
Pro Gly Gln Lys Leu Val 35 40 45 agt gac tgc aca gag ttc act gaa
acg gaa tgc ctt cct tgc ggt gaa 192 Ser Asp Cys Thr Glu Phe Thr Glu
Thr Glu Cys Leu Pro Cys Gly Glu 50 55 60 agc gaa ttc cta gac acc
tgg aac aga gag aca cac tgc cac cag cac 240 Ser Glu Phe Leu Asp Thr
Trp Asn Arg Glu Thr His Cys His Gln His 65 70 75 80 aaa tac tgc gac
ccc aac cta ggg ctt cgg gtc cag cag aag ggc acc 288 Lys Tyr Cys Asp
Pro Asn Leu Gly Leu Arg Val Gln Gln Lys Gly Thr 85 90 95 tca gaa
aca gac acc atc tgc acc tgt gaa gaa ggc tgg cac tgt acg 336 Ser Glu
Thr Asp Thr Ile Cys Thr Cys Glu Glu Gly Trp His Cys Thr 100 105 110
agt gag gcc tgt gag agc tgt gtc ctg cac cgc tca tgc tcg ccc ggc 384
Ser Glu Ala Cys Glu Ser Cys Val Leu His Arg Ser Cys Ser Pro Gly 115
120 125 ttt ggg gtc aag cag att gct aca ggg gtt tct gat acc atc tgc
gag 432 Phe Gly Val Lys Gln Ile Ala Thr Gly Val Ser Asp Thr Ile Cys
Glu 130 135 140 ccc tgc cca gtc ggc ttc ttc tcc aat gtg tca tct gct
ttc gaa aaa 480 Pro Cys Pro Val Gly Phe Phe Ser Asn Val Ser Ser Ala
Phe Glu Lys 145 150 155 160 tgt cac cct tgg aca agg tcc cca gga tcg
gct gag agc cct ggt ggt 528 Cys His Pro Trp Thr Arg Ser Pro Gly Ser
Ala Glu Ser Pro Gly Gly 165 170 175 gat ccc cat cat ctt cgg gat cct
gtt tgc cat cct ctt ggt gct ggt 576 Asp Pro His His Leu Arg Asp Pro
Val Cys His Pro Leu Gly Ala Gly 180 185 190 ctt tat caa aaa ggt ggc
caa gaa gcc aac caa taa 612 Leu Tyr Gln Lys Gly Gly Gln Glu Ala Asn
Gln * 195 200 <210> SEQ ID NO 10 <211> LENGTH: 203
<212> TYPE: PRT <213> ORGANISM: Homo sapiens
<400> SEQUENCE: 10 Met Val Arg Leu Pro Leu Gln Cys Val Leu
Trp Gly Cys Leu Leu Thr 1 5 10 15 Ala Val His Pro Glu Pro Pro Thr
Ala Cys Arg Glu Lys Gln Tyr Leu 20 25 30 Ile Asn Ser Gln Cys Cys
Ser Leu Cys Gln Pro Gly Gln Lys Leu Val 35 40 45 Ser Asp Cys Thr
Glu Phe Thr Glu Thr Glu Cys Leu Pro Cys Gly Glu 50 55 60 Ser Glu
Phe Leu Asp Thr Trp Asn Arg Glu Thr His Cys His Gln His 65 70 75 80
Lys Tyr Cys Asp Pro Asn Leu Gly Leu Arg Val Gln Gln Lys Gly Thr 85
90 95 Ser Glu Thr Asp Thr Ile Cys Thr Cys Glu Glu Gly Trp His Cys
Thr 100 105 110 Ser Glu Ala Cys Glu Ser Cys Val Leu His Arg Ser Cys
Ser Pro Gly 115 120 125 Phe Gly Val Lys Gln Ile Ala Thr Gly Val Ser
Asp Thr Ile Cys Glu 130 135 140 Pro Cys Pro Val Gly Phe Phe Ser Asn
Val Ser Ser Ala Phe Glu Lys 145 150 155 160 Cys His Pro Trp Thr Arg
Ser Pro Gly Ser Ala Glu Ser Pro Gly Gly 165 170 175 Asp Pro His His
Leu Arg Asp Pro Val Cys His Pro Leu Gly Ala Gly 180 185 190 Leu Tyr
Gln Lys Gly Gly Gln Glu Ala Asn Gln 195 200 <210> SEQ ID NO
11 <211> LENGTH: 834 <212> TYPE: DNA <213>
ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY:
CDS <222> LOCATION: (1)...(834) <221> NAME/KEY:
misc_feature <222> LOCATION: (0)...(0) <223> OTHER
INFORMATION: Coding sequence for long isoform of human CD40
<400> SEQUENCE: 11 atg gtt cgt ctg cct ctg cag tgc gtc ctc
tgg ggc tgc ttg ctg acc 48 Met Val Arg Leu Pro Leu Gln Cys Val Leu
Trp Gly Cys Leu Leu Thr 1 5 10 15 gct gtc cat cca gaa cca ccc act
gca tgc aga gaa aaa cag tac cta 96 Ala Val His Pro Glu Pro Pro Thr
Ala Cys Arg Glu Lys Gln Tyr Leu 20 25 30 ata aac agt cag tgc tgt
tct ttg tgc cag cca gga cag aaa ctg gtg 144 Ile Asn Ser Gln Cys Cys
Ser Leu Cys Gln Pro Gly Gln Lys Leu Val 35 40 45 agt gac tgc aca
gag ttc act gaa acg gaa tgc ctt cct tgc ggt gaa 192 Ser Asp Cys Thr
Glu Phe Thr Glu Thr Glu Cys Leu Pro Cys Gly Glu 50 55 60 agc gaa
ttc cta gac acc tgg aac aga gag aca cac tgc cac cag cac 240 Ser Glu
Phe Leu Asp Thr Trp Asn Arg Glu Thr His Cys His Gln His 65 70 75 80
aaa tac tgc gac ccc aac cta ggg ctt cgg gtc cag cag aag ggc acc 288
Lys Tyr Cys Asp Pro Asn Leu Gly Leu Arg Val Gln Gln Lys Gly Thr 85
90 95 tca gaa aca gac acc atc tgc acc tgt gaa gaa ggc tgg cac tgt
acg 336 Ser Glu Thr Asp Thr Ile Cys Thr Cys Glu Glu Gly Trp His Cys
Thr 100 105 110 agt gag gcc tgt gag agc tgt gtc ctg cac cgc tca tgc
tcg ccc ggc 384 Ser Glu Ala Cys Glu Ser Cys Val Leu His Arg Ser Cys
Ser Pro Gly 115 120 125 ttt ggg gtc aag cag att gct aca ggg gtt tct
gat acc atc tgc gag 432 Phe Gly Val Lys Gln Ile Ala Thr Gly Val Ser
Asp Thr Ile Cys Glu 130 135 140 ccc tgc cca gtc ggc ttc ttc tcc aat
gtg tca tct gct ttc gaa aaa 480 Pro Cys Pro Val Gly Phe Phe Ser Asn
Val Ser Ser Ala Phe Glu Lys 145 150 155 160 tgt cac cct tgg aca agc
tgt gag acc aaa gac ctg gtt gtg caa cag 528 Cys His Pro Trp Thr Ser
Cys Glu Thr Lys Asp Leu Val Val Gln Gln 165 170 175 gca ggc aca aac
aag act gat gtt gtc tgt ggt ccc cag gat cgg ctg 576 Ala Gly Thr Asn
Lys Thr Asp Val Val Cys Gly Pro Gln Asp Arg Leu 180 185 190 aga gcc
ctg gtg gtg atc ccc atc atc ttc ggg atc ctg ttt gcc atc 624 Arg Ala
Leu Val Val Ile Pro Ile Ile Phe Gly Ile Leu Phe Ala Ile 195 200 205
ctc ttg gtg ctg gtc ttt atc aaa aag gtg gcc aag aag cca acc aat 672
Leu Leu Val Leu Val Phe Ile Lys Lys Val Ala Lys Lys Pro Thr Asn 210
215 220 aag gcc ccc cac ccc aag cag gaa ccc cag gag atc aat ttt ccc
gac 720 Lys Ala Pro His Pro Lys Gln Glu Pro Gln Glu Ile Asn Phe Pro
Asp 225 230 235 240 gat ctt cct ggc tcc aac act gct gct cca gtg cag
gag act tta cat 768 Asp Leu Pro Gly Ser Asn Thr Ala Ala Pro Val Gln
Glu Thr Leu His 245 250 255 gga tgc caa ccg gtc acc cag gag gat ggc
aaa gag agt cgc atc tca 816 Gly Cys Gln Pro Val Thr Gln Glu Asp Gly
Lys Glu Ser Arg Ile Ser 260 265 270 gtg cag gag aga cag tga 834 Val
Gln Glu Arg Gln * 275 <210> SEQ ID NO 12 <211> LENGTH:
277 <212> TYPE: PRT <213> ORGANISM: Homo sapiens
<400> SEQUENCE: 12 Met Val Arg Leu Pro Leu Gln Cys Val Leu
Trp Gly Cys Leu Leu Thr 1 5 10 15 Ala Val His Pro Glu Pro Pro Thr
Ala Cys Arg Glu Lys Gln Tyr Leu 20 25 30 Ile Asn Ser Gln Cys Cys
Ser Leu Cys Gln Pro Gly Gln Lys Leu Val 35 40 45 Ser Asp Cys Thr
Glu Phe Thr Glu Thr Glu Cys Leu Pro Cys Gly Glu 50 55 60 Ser Glu
Phe Leu Asp Thr Trp Asn Arg Glu Thr His Cys His Gln His 65 70 75 80
Lys Tyr Cys Asp Pro Asn Leu Gly Leu Arg Val Gln Gln Lys Gly Thr 85
90 95 Ser Glu Thr Asp Thr Ile Cys Thr Cys Glu Glu Gly Trp His Cys
Thr 100 105 110 Ser Glu Ala Cys Glu Ser Cys Val Leu His Arg Ser Cys
Ser Pro Gly 115 120 125 Phe Gly Val Lys Gln Ile Ala Thr Gly Val Ser
Asp Thr Ile Cys Glu 130 135 140 Pro Cys Pro Val Gly Phe Phe Ser Asn
Val Ser Ser Ala Phe Glu Lys 145 150 155 160 Cys His Pro Trp Thr Ser
Cys Glu Thr Lys Asp Leu Val Val Gln Gln 165 170 175 Ala Gly Thr Asn
Lys Thr Asp Val Val Cys Gly Pro Gln Asp Arg Leu 180 185 190 Arg Ala
Leu Val Val Ile Pro Ile Ile Phe Gly Ile Leu Phe Ala Ile 195 200 205
Leu Leu Val Leu Val Phe Ile Lys Lys Val Ala Lys Lys Pro Thr Asn 210
215 220 Lys Ala Pro His Pro Lys Gln Glu Pro Gln Glu Ile Asn Phe Pro
Asp 225 230 235 240 Asp Leu Pro Gly Ser Asn Thr Ala Ala Pro Val Gln
Glu Thr Leu His 245 250 255 Gly Cys Gln Pro Val Thr Gln Glu Asp Gly
Lys Glu Ser Arg Ile Ser 260 265 270 Val Gln Glu Arg Gln 275
<210> SEQ ID NO 13 <211> LENGTH: 786 <212> TYPE:
DNA <213> ORGANISM: Homo sapiens <220> FEATURE:
<221> NAME/KEY: CDS <222> LOCATION: (1)...(786)
<221> NAME/KEY: misc_feature <222> LOCATION: (0)...(0)
<223> OTHER INFORMATION: CD40L <400> SEQUENCE: 13 atg
atc gaa aca tac aac caa act tct ccc cga tct gcg gcc act gga 48 Met
Ile Glu Thr Tyr Asn Gln Thr Ser Pro Arg Ser Ala Ala Thr Gly 1 5 10
15 ctg ccc atc agc atg aaa att ttt atg tat tta ctt act gtt ttt ctt
96 Leu Pro Ile Ser Met Lys Ile Phe Met Tyr Leu Leu Thr Val Phe Leu
20 25 30 atc acc cag atg att ggg tca gca ctt ttt gct gtg tat ctt
cat aga 144 Ile Thr Gln Met Ile Gly Ser Ala Leu Phe Ala Val Tyr Leu
His Arg 35 40 45 agg ttg gac aag ata gaa gat gaa agg aat ctt cat
gaa gat ttt gta 192 Arg Leu Asp Lys Ile Glu Asp Glu Arg Asn Leu His
Glu Asp Phe Val 50 55 60 ttc atg aaa acg ata cag aga tgc aac aca
gga gaa aga tcc tta tcc 240 Phe Met Lys Thr Ile Gln Arg Cys Asn Thr
Gly Glu Arg Ser Leu Ser 65 70 75 80 tta ctg aac tgt gag gag att aaa
agc cag ttt gaa ggc ttt gtg aag 288 Leu Leu Asn Cys Glu Glu Ile Lys
Ser Gln Phe Glu Gly Phe Val Lys 85 90 95 gat ata atg tta aac aaa
gag gag acg aag aaa gaa aac agc ttt gaa 336 Asp Ile Met Leu Asn Lys
Glu Glu Thr Lys Lys Glu Asn Ser Phe Glu 100 105 110 atg caa aaa ggt
gat cag aat cct caa att gcg gca cat gtc ata agt 384 Met Gln Lys Gly
Asp Gln Asn Pro Gln Ile Ala Ala His Val Ile Ser 115 120 125 gag gcc
agc agt aaa aca aca tct gtg tta cag tgg gct gaa aaa gga 432 Glu Ala
Ser Ser Lys Thr Thr Ser Val Leu Gln Trp Ala Glu Lys Gly 130 135 140
tac tac acc atg agc aac aac ttg gta acc ctg gaa aat ggg aaa cag 480
Tyr Tyr Thr Met Ser Asn Asn Leu Val Thr Leu Glu Asn Gly Lys Gln 145
150 155 160 ctg acc gtt aaa aga caa gga ctc tat tat atc tat gcc caa
gtc acc 528 Leu Thr Val Lys Arg Gln Gly Leu Tyr Tyr Ile Tyr Ala Gln
Val Thr 165 170 175 ttc tgt tcc aat cgg gaa gct tcg agt caa gct cca
ttt ata gcc agc 576 Phe Cys Ser Asn Arg Glu Ala Ser Ser Gln Ala Pro
Phe Ile Ala Ser 180 185 190 ctc tgc cta aag tcc ccc ggt aga ttc gag
aga atc tta ctc aga gct 624 Leu Cys Leu Lys Ser Pro Gly Arg Phe Glu
Arg Ile Leu Leu Arg Ala 195 200 205 gca aat acc cac agt tcc gcc aaa
cct tgc ggg caa caa tcc att cac 672 Ala Asn Thr His Ser Ser Ala Lys
Pro Cys Gly Gln Gln Ser Ile His 210 215 220 ttg gga gga gta ttt gaa
ttg caa cca ggt gct tcg gtg ttt gtc aat 720 Leu Gly Gly Val Phe Glu
Leu Gln Pro Gly Ala Ser Val Phe Val Asn 225 230 235 240 gtg act gat
cca agc caa gtg agc cat ggc act ggc ttc acg tcc ttt 768 Val Thr Asp
Pro Ser Gln Val Ser His Gly Thr Gly Phe Thr Ser Phe 245 250 255 ggc
tta ctc aaa ctc tga 786 Gly Leu Leu Lys Leu * 260 <210> SEQ
ID NO 14 <211> LENGTH: 261 <212> TYPE: PRT <213>
ORGANISM: Homo sapiens <400> SEQUENCE: 14 Met Ile Glu Thr Tyr
Asn Gln Thr Ser Pro Arg Ser Ala Ala Thr Gly 1 5 10 15 Leu Pro Ile
Ser Met Lys Ile Phe Met Tyr Leu Leu Thr Val Phe Leu 20 25 30 Ile
Thr Gln Met Ile Gly Ser Ala Leu Phe Ala Val Tyr Leu His Arg 35 40
45 Arg Leu Asp Lys Ile Glu Asp Glu Arg Asn Leu His Glu Asp Phe Val
50 55 60 Phe Met Lys Thr Ile Gln Arg Cys Asn Thr Gly Glu Arg Ser
Leu Ser 65 70 75 80 Leu Leu Asn Cys Glu Glu Ile Lys Ser Gln Phe Glu
Gly Phe Val Lys 85 90 95 Asp Ile Met Leu Asn Lys Glu Glu Thr Lys
Lys Glu Asn Ser Phe Glu 100 105 110 Met Gln Lys Gly Asp Gln Asn Pro
Gln Ile Ala Ala His Val Ile Ser 115 120 125 Glu Ala Ser Ser Lys Thr
Thr Ser Val Leu Gln Trp Ala Glu Lys Gly 130 135 140 Tyr Tyr Thr Met
Ser Asn Asn Leu Val Thr Leu Glu Asn Gly Lys Gln 145 150 155 160 Leu
Thr Val Lys Arg Gln Gly Leu Tyr Tyr Ile Tyr Ala Gln Val Thr 165 170
175 Phe Cys Ser Asn Arg Glu Ala Ser Ser Gln Ala Pro Phe Ile Ala Ser
180 185 190 Leu Cys Leu Lys Ser Pro Gly Arg Phe Glu Arg Ile Leu Leu
Arg Ala 195 200 205 Ala Asn Thr His Ser Ser Ala Lys Pro Cys Gly Gln
Gln Ser Ile His 210 215 220 Leu Gly Gly Val Phe Glu Leu Gln Pro Gly
Ala Ser Val Phe Val Asn 225 230 235 240 Val Thr Asp Pro Ser Gln Val
Ser His Gly Thr Gly Phe Thr Ser Phe 245 250 255 Gly Leu Leu Lys Leu
260 <210> SEQ ID NO 15 <211> LENGTH: 648 <212>
TYPE: DNA <213> ORGANISM: Homo sapiens <220> FEATURE:
<221> NAME/KEY: CDS <222> LOCATION: (1)...(648)
<221> NAME/KEY: misc_feature <222> LOCATION: (0)...(0)
<223> OTHER INFORMATION: Soluble CD40L <400> SEQUENCE:
15 cat aga agg ttg gac aag ata gaa gat gaa agg aat ctt cat gaa gat
48 His Arg Arg Leu Asp Lys Ile Glu Asp Glu Arg Asn Leu His Glu Asp
1 5 10 15 ttt gta ttc atg aaa acg ata cag aga tgc aac aca gga gaa
aga tcc 96 Phe Val Phe Met Lys Thr Ile Gln Arg Cys Asn Thr Gly Glu
Arg Ser 20 25 30 tta tcc tta ctg aac tgt gag gag att aaa agc cag
ttt gaa ggc ttt 144 Leu Ser Leu Leu Asn Cys Glu Glu Ile Lys Ser Gln
Phe Glu Gly Phe 35 40 45 gtg aag gat ata atg tta aac aaa gag gag
acg aag aaa gaa aac agc 192 Val Lys Asp Ile Met Leu Asn Lys Glu Glu
Thr Lys Lys Glu Asn Ser 50 55 60 ttt gaa atg caa aaa ggt gat cag
aat cct caa att gcg gca cat gtc 240 Phe Glu Met Gln Lys Gly Asp Gln
Asn Pro Gln Ile Ala Ala His Val 65 70 75 80 ata agt gag gcc agc agt
aaa aca aca tct gtg tta cag tgg gct gaa 288 Ile Ser Glu Ala Ser Ser
Lys Thr Thr Ser Val Leu Gln Trp Ala Glu 85 90 95 aaa gga tac tac
acc atg agc aac aac ttg gta acc ctg gaa aat ggg 336 Lys Gly Tyr Tyr
Thr Met Ser Asn Asn Leu Val Thr Leu Glu Asn Gly 100 105 110 aaa cag
ctg acc gtt aaa aga caa gga ctc tat tat atc tat gcc caa 384 Lys Gln
Leu Thr Val Lys Arg Gln Gly Leu Tyr Tyr Ile Tyr Ala Gln 115 120 125
gtc acc ttc tgt tcc aat cgg gaa gct tcg agt caa gct cca ttt ata 432
Val Thr Phe Cys Ser Asn Arg Glu Ala Ser Ser Gln Ala Pro Phe Ile 130
135 140 gcc agc ctc tgc cta aag tcc ccc ggt aga ttc gag aga atc tta
ctc 480 Ala Ser Leu Cys Leu Lys Ser Pro Gly Arg Phe Glu Arg Ile Leu
Leu 145 150 155 160 aga gct gca aat acc cac agt tcc gcc aaa cct tgc
ggg caa caa tcc 528 Arg Ala Ala Asn Thr His Ser Ser Ala Lys Pro Cys
Gly Gln Gln Ser 165 170 175 att cac ttg gga gga gta ttt gaa ttg caa
cca ggt gct tcg gtg ttt 576 Ile His Leu Gly Gly Val Phe Glu Leu Gln
Pro Gly Ala Ser Val Phe 180 185 190 gtc aat gtg act gat cca agc caa
gtg agc cat ggc act ggc ttc acg 624 Val Asn Val Thr Asp Pro Ser Gln
Val Ser His Gly Thr Gly Phe Thr 195 200 205 tcc ttt ggc tta ctc aaa
ctc tga 648 Ser Phe Gly Leu Leu Lys Leu * 210 215 <210> SEQ
ID NO 16 <211> LENGTH: 215 <212> TYPE: PRT <213>
ORGANISM: Homo sapiens <400> SEQUENCE: 16 His Arg Arg Leu Asp
Lys Ile Glu Asp Glu Arg Asn Leu His Glu Asp 1 5 10 15 Phe Val Phe
Met Lys Thr Ile Gln Arg Cys Asn Thr Gly Glu Arg Ser 20 25 30 Leu
Ser Leu Leu Asn Cys Glu Glu Ile Lys Ser Gln Phe Glu Gly Phe 35 40
45 Val Lys Asp Ile Met Leu Asn Lys Glu Glu Thr Lys Lys Glu Asn Ser
50 55 60 Phe Glu Met Gln Lys Gly Asp Gln Asn Pro Gln Ile Ala Ala
His Val 65 70 75 80 Ile Ser Glu Ala Ser Ser Lys Thr Thr Ser Val Leu
Gln Trp Ala Glu 85 90 95 Lys Gly Tyr Tyr Thr Met Ser Asn Asn Leu
Val Thr Leu Glu Asn Gly 100 105 110 Lys Gln Leu Thr Val Lys Arg Gln
Gly Leu Tyr Tyr Ile Tyr Ala Gln 115 120 125 Val Thr Phe Cys Ser Asn
Arg Glu Ala Ser Ser Gln Ala Pro Phe Ile 130 135 140 Ala Ser Leu Cys
Leu Lys Ser Pro Gly Arg Phe Glu Arg Ile Leu Leu 145 150 155 160 Arg
Ala Ala Asn Thr His Ser Ser Ala Lys Pro Cys Gly Gln Gln Ser 165 170
175 Ile His Leu Gly Gly Val Phe Glu Leu Gln Pro Gly Ala Ser Val Phe
180 185 190 Val Asn Val Thr Asp Pro Ser Gln Val Ser His Gly Thr Gly
Phe Thr 195 200 205 Ser Phe Gly Leu Leu Lys Leu 210 215
1 SEQUENCE LISTING <160> NUMBER OF SEQ ID NOS: 16 <210>
SEQ ID NO 1 <211> LENGTH: 720 <212> TYPE: DNA
<213> ORGANISM: Artificial Sequence <220> FEATURE:
<223> OTHER INFORMATION: Coding sequence for light chain of
12.12 human anti-CD40 antibody <221> NAME/KEY: CDS
<222> LOCATION: (1)...(720) <400> SEQUENCE: 1 atg gcg
ctc cct gct cag ctc ctg ggg ctg cta atg ctc tgg gtc tct 48 Met Ala
Leu Pro Ala Gln Leu Leu Gly Leu Leu Met Leu Trp Val Ser 1 5 10 15
gga tcc agt ggg gat att gtg atg act cag tct cca ctc tcc ctg acc 96
Gly Ser Ser Gly Asp Ile Val Met Thr Gln Ser Pro Leu Ser Leu Thr 20
25 30 gtc acc cct gga gag ccg gcc tcc atc tcc tgc agg tcc agt cag
agc 144 Val Thr Pro Gly Glu Pro Ala Ser Ile Ser Cys Arg Ser Ser Gln
Ser 35 40 45 ctc ctg tat agt aat gga tac aac tat ttg gat tgg tac
ctg cag aag 192 Leu Leu Tyr Ser Asn Gly Tyr Asn Tyr Leu Asp Trp Tyr
Leu Gln Lys 50 55 60 cca ggg cag tct cca cag gtc ctg atc tct ttg
ggt tct aat cgg gcc 240 Pro Gly Gln Ser Pro Gln Val Leu Ile Ser Leu
Gly Ser Asn Arg Ala 65 70 75 80 tcc ggg gtc cct gac agg ttc agt ggc
agt gga tca ggc aca gat ttt 288 Ser Gly Val Pro Asp Arg Phe Ser Gly
Ser Gly Ser Gly Thr Asp Phe 85 90 95 aca ctg aaa atc agc aga gtg
gag gct gag gat gtt ggg gtt tat tac 336 Thr Leu Lys Ile Ser Arg Val
Glu Ala Glu Asp Val Gly Val Tyr Tyr 100 105 110 tgc atg caa gct cga
caa act cca ttc act ttc ggc cct ggg acc aaa 384 Cys Met Gln Ala Arg
Gln Thr Pro Phe Thr Phe Gly Pro Gly Thr Lys 115 120 125 gtg gat atc
aga cga act gtg gct gca cca tct gtc ttc atc ttc ccg 432 Val Asp Ile
Arg Arg Thr Val Ala Ala Pro Ser Val Phe Ile Phe Pro 130 135 140 cca
tct gat gag cag ttg aaa tct gga act gcc tct gtt gtg tgc ctg 480 Pro
Ser Asp Glu Gln Leu Lys Ser Gly Thr Ala Ser Val Val Cys Leu 145 150
155 160 ctg aat aac ttc tat ccc aga gag gcc aaa gta cag tgg aag gtg
gat 528 Leu Asn Asn Phe Tyr Pro Arg Glu Ala Lys Val Gln Trp Lys Val
Asp 165 170 175 aac gcc ctc caa tcg ggt aac tcc cag gag agt gtc aca
gag cag gac 576 Asn Ala Leu Gln Ser Gly Asn Ser Gln Glu Ser Val Thr
Glu Gln Asp 180 185 190 agc aag gac agc acc tac agc ctc agc agc acc
ctg acg ctg agc aaa 624 Ser Lys Asp Ser Thr Tyr Ser Leu Ser Ser Thr
Leu Thr Leu Ser Lys 195 200 205 gca gac tac gag aaa cac aaa gtc tac
gcc tgc gaa gtc acc cat cag 672 Ala Asp Tyr Glu Lys His Lys Val Tyr
Ala Cys Glu Val Thr His Gln 210 215 220 ggc ctg agc tcg ccc gtc aca
aag agc ttc aac agg gga gag tgt tag 720 Gly Leu Ser Ser Pro Val Thr
Lys Ser Phe Asn Arg Gly Glu Cys * 225 230 235 <210> SEQ ID NO
2 <211> LENGTH: 239 <212> TYPE: PRT <213>
ORGANISM: Artificial Sequence <220> FEATURE: <223>
OTHER INFORMATION: Coding sequence for light chain of 12.12 human
anti-CD40 antibody <400> SEQUENCE: 2 Met Ala Leu Pro Ala Gln
Leu Leu Gly Leu Leu Met Leu Trp Val Ser 1 5 10 15 Gly Ser Ser Gly
Asp Ile Val Met Thr Gln Ser Pro Leu Ser Leu Thr 20 25 30 Val Thr
Pro Gly Glu Pro Ala Ser Ile Ser Cys Arg Ser Ser Gln Ser 35 40 45
Leu Leu Tyr Ser Asn Gly Tyr Asn Tyr Leu Asp Trp Tyr Leu Gln Lys 50
55 60 Pro Gly Gln Ser Pro Gln Val Leu Ile Ser Leu Gly Ser Asn Arg
Ala 65 70 75 80 Ser Gly Val Pro Asp Arg Phe Ser Gly Ser Gly Ser Gly
Thr Asp Phe 85 90 95 Thr Leu Lys Ile Ser Arg Val Glu Ala Glu Asp
Val Gly Val Tyr Tyr 100 105 110 Cys Met Gln Ala Arg Gln Thr Pro Phe
Thr Phe Gly Pro Gly Thr Lys 115 120 125 Val Asp Ile Arg Arg Thr Val
Ala Ala Pro Ser Val Phe Ile Phe Pro 130 135 140 Pro Ser Asp Glu Gln
Leu Lys Ser Gly Thr Ala Ser Val Val Cys Leu 145 150 155 160 Leu Asn
Asn Phe Tyr Pro Arg Glu Ala Lys Val Gln Trp Lys Val Asp 165 170 175
Asn Ala Leu Gln Ser Gly Asn Ser Gln Glu Ser Val Thr Glu Gln Asp 180
185 190 Ser Lys Asp Ser Thr Tyr Ser Leu Ser Ser Thr Leu Thr Leu Ser
Lys 195 200 205 Ala Asp Tyr Glu Lys His Lys Val Tyr Ala Cys Glu Val
Thr His Gln 210 215 220 Gly Leu Ser Ser Pro Val Thr Lys Ser Phe Asn
Arg Gly Glu Cys 225 230 235 <210> SEQ ID NO 3 <211>
LENGTH: 2016 <212> TYPE: DNA <213> ORGANISM: Artificial
Sequence <220> FEATURE: <223> OTHER INFORMATION: Coding
sequence for heavy chain of 12.12 human anti-CD40 antibody (with
introns) <400> SEQUENCE: 3 atggagtttg ggctgagctg ggttttcctt
gttgctattt taagaggtgt ccagtgtcag 60 gtgcagttgg tggagtctgg
gggaggcgtg gtccagcctg ggaggtccct gagactctcc 120 tgtgcagcct
ctggattcac cttcagtagc tatggcatgc actgggtccg ccaggctcca 180
ggcaaggggc tggagtgggt ggcagttata tcatatgagg aaagtaatag ataccatgca
240 gactccgtga agggccgatt caccatctcc agagacaatt ccaagatcac
gctgtatctg 300 caaatgaaca gcctcagaac tgaggacacg gctgtgtatt
actgtgcgag agatgggggt 360 atagcagcac ctgggcctga ctactggggc
cagggaaccc tggtcaccgt ctcctcagca 420 agtaccaagg gcccatccgt
cttccccctg gcgcccgcta gcaagagcac ctctgggggc 480 acagcggccc
tgggctgcct ggtcaaggac tacttccccg aaccggtgac ggtgtcgtgg 540
aactcaggcg ccctgaccag cggcgtgcac accttcccgg ctgtcctaca gtcctcagga
600 ctctactccc tcagcagcgt ggtgaccgtg ccctccagca gcttgggcac
ccagacctac 660 atctgcaacg tgaatcacaa gcccagcaac accaaggtgg
acaagagagt tggtgagagg 720 ccagcacagg gagggagggt gtctgctgga
agccaggctc agcgctcctg cctggacgca 780 tcccggctat gcagtcccag
tccagggcag caaggcaggc cccgtctgcc tcttcacccg 840 gaggcctctg
cccgccccac tcatgctcag ggagagggtc ttctggcttt ttccccaggc 900
tctgggcagg cacaggctag gtgcccctaa cccaggccct gcacacaaag gggcaggtgc
960 tgggctcaga cctgccaaga gccatatccg ggaggaccct gcccctgacc
taagcccacc 1020 ccaaaggcca aactctccac tccctcagct cggacacctt
ctctcctccc agattccagt 1080 aactcccaat cttctctctg cagagcccaa
atcttgtgac aaaactcaca catgcccacc 1140 gtgcccaggt aagccagccc
aggcctcgcc ctccagctca aggcgggaca ggtgccctag 1200 agtagcctgc
atccagggac aggccccagc cgggtgctga cacgtccacc tccatctctt 1260
cctcagcacc tgaactcctg gggggaccgt cagtcttcct cttcccccca aaacccaagg
1320 acaccctcat gatctcccgg acccctgagg tcacatgcgt ggtggtggac
gtgagccacg 1380 aagaccctga ggtcaagttc aactggtacg tggacggcgt
ggaggtgcat aatgccaaga 1440 caaagccgcg ggaggagcag tacaacagca
cgtaccgtgt ggtcagcgtc ctcaccgtcc 1500 tgcaccagga ctggctgaat
ggcaaggagt acaagtgcaa ggtctccaac aaagccctcc 1560 cagcccccat
cgagaaaacc atctccaaag ccaaaggtgg gacccgtggg gtgcgagggc 1620
cacatggaca gaggccggct cggcccaccc tctgccctga gagtgaccgc tgtaccaacc
1680 tctgtcccta cagggcagcc ccgagaacca caggtgtaca ccctgccccc
atcccgggag 1740 gagatgacca agaaccaggt cagcctgacc tgcctggtca
aaggcttcta tcccagcgac 1800 atcgccgtgg agtgggagag caatgggcag
ccggagaaca actacaagac cacgcctccc 1860 gtgctggact ccgacggctc
cttcttcctc tatagcaagc tcaccgtgga caagagcagg 1920 tggcagcagg
ggaacgtctt ctcatgctcc gtgatgcatg aggctctgca caaccactac 1980
acgcagaaga gcctctccct gtctccgggt aaatga 2016 <210> SEQ ID NO
4 <211> LENGTH: 469 <212> TYPE: PRT <213>
ORGANISM: Artificial Sequence <220> FEATURE: <223>
OTHER INFORMATION: Heavy chain of 12.12 human anti-CD40 antibody
<400> SEQUENCE: 4 Met Glu Phe Gly Leu Ser Trp Val Phe Leu Val
Ala Ile Leu Arg Gly 1 5 10 15 Val Gln Cys Gln Val Gln Leu Val Glu
Ser Gly Gly Gly Val Val Gln 20 25 30 Pro Gly Arg Ser Leu Arg Leu
Ser Cys Ala Ala Ser Gly Phe Thr Phe 35 40 45 Ser Ser Tyr Gly Met
His Trp Val Arg Gln Ala Pro Gly Lys Gly Leu 50 55 60 Glu Trp Val
Ala Val Ile Ser Tyr Glu Glu Ser Asn Arg Tyr His Ala 65 70 75 80 Asp
Ser Val Lys Gly Arg Phe Thr Ile Ser Arg Asp Asn Ser Lys Ile 85 90
95 Thr Leu Tyr Leu Gln Met Asn Ser Leu Arg Thr Glu Asp Thr Ala Val
100 105 110 Tyr Tyr Cys Ala Arg Asp Gly Gly Ile Ala Ala Pro Gly Pro
Asp Tyr 115 120 125
Trp Gly Gln Gly Thr Leu Val Thr Val Ser Ser Ala Ser Thr Lys Gly 130
135 140 Pro Ser Val Phe Pro Leu Ala Pro Ala Ser Lys Ser Thr Ser Gly
Gly 145 150 155 160 Thr Ala Ala Leu Gly Cys Leu Val Lys Asp Tyr Phe
Pro Glu Pro Val 165 170 175 Thr Val Ser Trp Asn Ser Gly Ala Leu Thr
Ser Gly Val His Thr Phe 180 185 190 Pro Ala Val Leu Gln Ser Ser Gly
Leu Tyr Ser Leu Ser Ser Val Val 195 200 205 Thr Val Pro Ser Ser Ser
Leu Gly Thr Gln Thr Tyr Ile Cys Asn Val 210 215 220 Asn His Lys Pro
Ser Asn Thr Lys Val Asp Lys Arg Val Glu Pro Lys 225 230 235 240 Ser
Cys Asp Lys Thr His Thr Cys Pro Pro Cys Pro Ala Pro Glu Leu 245 250
255 Leu Gly Gly Pro Ser Val Phe Leu Phe Pro Pro Lys Pro Lys Asp Thr
260 265 270 Leu Met Ile Ser Arg Thr Pro Glu Val Thr Cys Val Val Val
Asp Val 275 280 285 Ser His Glu Asp Pro Glu Val Lys Phe Asn Trp Tyr
Val Asp Gly Val 290 295 300 Glu Val His Asn Ala Lys Thr Lys Pro Arg
Glu Glu Gln Tyr Asn Ser 305 310 315 320 Thr Tyr Arg Val Val Ser Val
Leu Thr Val Leu His Gln Asp Trp Leu 325 330 335 Asn Gly Lys Glu Tyr
Lys Cys Lys Val Ser Asn Lys Ala Leu Pro Ala 340 345 350 Pro Ile Glu
Lys Thr Ile Ser Lys Ala Lys Gly Gln Pro Arg Glu Pro 355 360 365 Gln
Val Tyr Thr Leu Pro Pro Ser Arg Glu Glu Met Thr Lys Asn Gln 370 375
380 Val Ser Leu Thr Cys Leu Val Lys Gly Phe Tyr Pro Ser Asp Ile Ala
385 390 395 400 Val Glu Trp Glu Ser Asn Gly Gln Pro Glu Asn Asn Tyr
Lys Thr Thr 405 410 415 Pro Pro Val Leu Asp Ser Asp Gly Ser Phe Phe
Leu Tyr Ser Lys Leu 420 425 430 Thr Val Asp Lys Ser Arg Trp Gln Gln
Gly Asn Val Phe Ser Cys Ser 435 440 445 Val Met His Glu Ala Leu His
Asn His Tyr Thr Gln Lys Ser Leu Ser 450 455 460 Leu Ser Pro Gly Lys
465 <210> SEQ ID NO 5 <211> LENGTH: 469 <212>
TYPE: PRT <213> ORGANISM: Artificial Sequence <220>
FEATURE: <223> OTHER INFORMATION: Heavy chain of variant of
12.12 human anti-CD40 antibody <400> SEQUENCE: 5 Met Glu Phe
Gly Leu Ser Trp Val Phe Leu Val Ala Ile Leu Arg Gly 1 5 10 15 Val
Gln Cys Gln Val Gln Leu Val Glu Ser Gly Gly Gly Val Val Gln 20 25
30 Pro Gly Arg Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly Phe Thr Phe
35 40 45 Ser Ser Tyr Gly Met His Trp Val Arg Gln Ala Pro Gly Lys
Gly Leu 50 55 60 Glu Trp Val Ala Val Ile Ser Tyr Glu Glu Ser Asn
Arg Tyr His Ala 65 70 75 80 Asp Ser Val Lys Gly Arg Phe Thr Ile Ser
Arg Asp Asn Ser Lys Ile 85 90 95 Thr Leu Tyr Leu Gln Met Asn Ser
Leu Arg Thr Glu Asp Thr Ala Val 100 105 110 Tyr Tyr Cys Ala Arg Asp
Gly Gly Ile Ala Ala Pro Gly Pro Asp Tyr 115 120 125 Trp Gly Gln Gly
Thr Leu Val Thr Val Ser Ser Ala Ser Thr Lys Gly 130 135 140 Pro Ser
Val Phe Pro Leu Ala Pro Ser Ser Lys Ser Thr Ser Gly Gly 145 150 155
160 Thr Ala Ala Leu Gly Cys Leu Val Lys Asp Tyr Phe Pro Glu Pro Val
165 170 175 Thr Val Ser Trp Asn Ser Gly Ala Leu Thr Ser Gly Val His
Thr Phe 180 185 190 Pro Ala Val Leu Gln Ser Ser Gly Leu Tyr Ser Leu
Ser Ser Val Val 195 200 205 Thr Val Pro Ser Ser Ser Leu Gly Thr Gln
Thr Tyr Ile Cys Asn Val 210 215 220 Asn His Lys Pro Ser Asn Thr Lys
Val Asp Lys Arg Val Glu Pro Lys 225 230 235 240 Ser Cys Asp Lys Thr
His Thr Cys Pro Pro Cys Pro Ala Pro Glu Leu 245 250 255 Leu Gly Gly
Pro Ser Val Phe Leu Phe Pro Pro Lys Pro Lys Asp Thr 260 265 270 Leu
Met Ile Ser Arg Thr Pro Glu Val Thr Cys Val Val Val Asp Val 275 280
285 Ser His Glu Asp Pro Glu Val Lys Phe Asn Trp Tyr Val Asp Gly Val
290 295 300 Glu Val His Asn Ala Lys Thr Lys Pro Arg Glu Glu Gln Tyr
Asn Ser 305 310 315 320 Thr Tyr Arg Val Val Ser Val Leu Thr Val Leu
His Gln Asp Trp Leu 325 330 335 Asn Gly Lys Glu Tyr Lys Cys Lys Val
Ser Asn Lys Ala Leu Pro Ala 340 345 350 Pro Ile Glu Lys Thr Ile Ser
Lys Ala Lys Gly Gln Pro Arg Glu Pro 355 360 365 Gln Val Tyr Thr Leu
Pro Pro Ser Arg Glu Glu Met Thr Lys Asn Gln 370 375 380 Val Ser Leu
Thr Cys Leu Val Lys Gly Phe Tyr Pro Ser Asp Ile Ala 385 390 395 400
Val Glu Trp Glu Ser Asn Gly Gln Pro Glu Asn Asn Tyr Lys Thr Thr 405
410 415 Pro Pro Val Leu Asp Ser Asp Gly Ser Phe Phe Leu Tyr Ser Lys
Leu 420 425 430 Thr Val Asp Lys Ser Arg Trp Gln Gln Gly Asn Val Phe
Ser Cys Ser 435 440 445 Val Met His Glu Ala Leu His Asn His Tyr Thr
Gln Lys Ser Leu Ser 450 455 460 Leu Ser Pro Gly Lys 465 <210>
SEQ ID NO 6 <211> LENGTH: 239 <212> TYPE: PRT
<213> ORGANISM: Artificial Sequence <220> FEATURE:
<223> OTHER INFORMATION: Light chain of 5.9 human anti-CD40
antibody <400> SEQUENCE: 6 Met Ala Leu Leu Ala Gln Leu Leu
Gly Leu Leu Met Leu Trp Val Pro 1 5 10 15 Gly Ser Ser Gly Ala Ile
Val Met Thr Gln Pro Pro Leu Ser Ser Pro 20 25 30 Val Thr Leu Gly
Gln Pro Ala Ser Ile Ser Cys Arg Ser Ser Gln Ser 35 40 45 Leu Val
His Ser Asp Gly Asn Thr Tyr Leu Asn Trp Leu Gln Gln Arg 50 55 60
Pro Gly Gln Pro Pro Arg Leu Leu Ile Tyr Lys Phe Phe Arg Arg Leu 65
70 75 80 Ser Gly Val Pro Asp Arg Phe Ser Gly Ser Gly Ala Gly Thr
Asp Phe 85 90 95 Thr Leu Lys Ile Ser Arg Val Glu Ala Glu Asp Val
Gly Val Tyr Tyr 100 105 110 Cys Met Gln Val Thr Gln Phe Pro His Thr
Phe Gly Gln Gly Thr Arg 115 120 125 Leu Glu Ile Lys Arg Thr Val Ala
Ala Pro Ser Val Phe Ile Phe Pro 130 135 140 Pro Ser Asp Glu Gln Leu
Lys Ser Gly Thr Ala Ser Val Val Cys Leu 145 150 155 160 Leu Asn Asn
Phe Tyr Pro Arg Glu Ala Lys Val Gln Trp Lys Val Asp 165 170 175 Asn
Ala Leu Gln Ser Gly Asn Ser Gln Glu Ser Val Thr Glu Gln Asp 180 185
190 Ser Lys Asp Ser Thr Tyr Ser Leu Ser Ser Thr Leu Thr Leu Ser Lys
195 200 205 Ala Asp Tyr Glu Lys His Lys Val Tyr Ala Cys Glu Val Thr
His Gln 210 215 220 Gly Leu Ser Ser Pro Val Thr Lys Ser Phe Asn Arg
Gly Glu Cys 225 230 235 <210> SEQ ID NO 7 <211> LENGTH:
474 <212> TYPE: PRT <213> ORGANISM: Artificial Sequence
<220> FEATURE: <223> OTHER INFORMATION: Heavy chain of
5.9 human anti-CD40 antibody <400> SEQUENCE: 7 Met Gly Ser
Thr Ala Ile Leu Ala Leu Leu Leu Ala Val Leu Gln Gly 1 5 10 15 Val
Cys Ala Glu Val Gln Leu Val Gln Ser Gly Ala Glu Val Lys Lys 20 25
30 Pro Gly Glu Ser Leu Lys Ile Ser Cys Lys Gly Ser Gly Tyr Ser Phe
35 40 45 Thr Ser Tyr Trp Ile Gly Trp Val Arg Gln Met Pro Gly Lys
Gly Leu 50 55 60 Glu Trp Met Gly Ile Ile Tyr Pro Gly Asp Ser Asp
Thr Arg Tyr Ser 65 70 75 80
Pro Ser Phe Gln Gly Gln Val Thr Ile Ser Ala Asp Lys Ser Ile Ser 85
90 95 Thr Ala Tyr Leu Gln Trp Ser Ser Leu Lys Ala Ser Asp Thr Ala
Met 100 105 110 Tyr Tyr Cys Ala Arg Gly Thr Ala Ala Gly Arg Asp Tyr
Tyr Tyr Tyr 115 120 125 Tyr Gly Met Asp Val Trp Gly Gln Gly Thr Thr
Val Thr Val Ser Ser 130 135 140 Ala Ser Thr Lys Gly Pro Ser Val Phe
Pro Leu Ala Pro Ala Ser Lys 145 150 155 160 Ser Thr Ser Gly Gly Thr
Ala Ala Leu Gly Cys Leu Val Lys Asp Tyr 165 170 175 Phe Pro Glu Pro
Val Thr Val Ser Trp Asn Ser Gly Ala Leu Thr Ser 180 185 190 Gly Val
His Thr Phe Pro Ala Val Leu Gln Ser Ser Gly Leu Tyr Ser 195 200 205
Leu Ser Ser Val Val Thr Val Pro Ser Ser Ser Leu Gly Thr Gln Thr 210
215 220 Tyr Ile Cys Asn Val Asn His Lys Pro Ser Asn Thr Lys Val Asp
Lys 225 230 235 240 Arg Val Glu Pro Lys Ser Cys Asp Lys Thr His Thr
Cys Pro Pro Cys 245 250 255 Pro Ala Pro Glu Leu Leu Gly Gly Pro Ser
Val Phe Leu Phe Pro Pro 260 265 270 Lys Pro Lys Asp Thr Leu Met Ile
Ser Arg Thr Pro Glu Val Thr Cys 275 280 285 Val Val Val Asp Val Ser
His Glu Asp Pro Glu Val Lys Phe Asn Trp 290 295 300 Tyr Val Asp Gly
Val Glu Val His Asn Ala Lys Thr Lys Pro Arg Glu 305 310 315 320 Glu
Gln Tyr Asn Ser Thr Tyr Arg Val Val Ser Val Leu Thr Val Leu 325 330
335 His Gln Asp Trp Leu Asn Gly Lys Glu Tyr Lys Cys Lys Val Ser Asn
340 345 350 Lys Ala Leu Pro Ala Pro Ile Glu Lys Thr Ile Ser Lys Ala
Lys Gly 355 360 365 Gln Pro Arg Glu Pro Gln Val Tyr Thr Leu Pro Pro
Ser Arg Glu Glu 370 375 380 Met Thr Lys Asn Gln Val Ser Leu Thr Cys
Leu Val Lys Gly Phe Tyr 385 390 395 400 Pro Ser Asp Ile Ala Val Glu
Trp Glu Ser Asn Gly Gln Pro Glu Asn 405 410 415 Asn Tyr Lys Thr Thr
Pro Pro Val Leu Asp Ser Asp Gly Ser Phe Phe 420 425 430 Leu Tyr Ser
Lys Leu Thr Val Asp Lys Ser Arg Trp Gln Gln Gly Asn 435 440 445 Val
Phe Ser Cys Ser Val Met His Glu Ala Leu His Asn His Tyr Thr 450 455
460 Gln Lys Ser Leu Ser Leu Ser Pro Gly Lys 465 470 <210> SEQ
ID NO 8 <211> LENGTH: 474 <212> TYPE: PRT <213>
ORGANISM: Artificial Sequence <220> FEATURE: <223>
OTHER INFORMATION: Heavy chain of variant of 5.9 human anti-CD40
antibody <400> SEQUENCE: 8 Met Gly Ser Thr Ala Ile Leu Ala
Leu Leu Leu Ala Val Leu Gln Gly 1 5 10 15 Val Cys Ala Glu Val Gln
Leu Val Gln Ser Gly Ala Glu Val Lys Lys 20 25 30 Pro Gly Glu Ser
Leu Lys Ile Ser Cys Lys Gly Ser Gly Tyr Ser Phe 35 40 45 Thr Ser
Tyr Trp Ile Gly Trp Val Arg Gln Met Pro Gly Lys Gly Leu 50 55 60
Glu Trp Met Gly Ile Ile Tyr Pro Gly Asp Ser Asp Thr Arg Tyr Ser 65
70 75 80 Pro Ser Phe Gln Gly Gln Val Thr Ile Ser Ala Asp Lys Ser
Ile Ser 85 90 95 Thr Ala Tyr Leu Gln Trp Ser Ser Leu Lys Ala Ser
Asp Thr Ala Met 100 105 110 Tyr Tyr Cys Ala Arg Gly Thr Ala Ala Gly
Arg Asp Tyr Tyr Tyr Tyr 115 120 125 Tyr Gly Met Asp Val Trp Gly Gln
Gly Thr Thr Val Thr Val Ser Ser 130 135 140 Ala Ser Thr Lys Gly Pro
Ser Val Phe Pro Leu Ala Pro Ser Ser Lys 145 150 155 160 Ser Thr Ser
Gly Gly Thr Ala Ala Leu Gly Cys Leu Val Lys Asp Tyr 165 170 175 Phe
Pro Glu Pro Val Thr Val Ser Trp Asn Ser Gly Ala Leu Thr Ser 180 185
190 Gly Val His Thr Phe Pro Ala Val Leu Gln Ser Ser Gly Leu Tyr Ser
195 200 205 Leu Ser Ser Val Val Thr Val Pro Ser Ser Ser Leu Gly Thr
Gln Thr 210 215 220 Tyr Ile Cys Asn Val Asn His Lys Pro Ser Asn Thr
Lys Val Asp Lys 225 230 235 240 Arg Val Glu Pro Lys Ser Cys Asp Lys
Thr His Thr Cys Pro Pro Cys 245 250 255 Pro Ala Pro Glu Leu Leu Gly
Gly Pro Ser Val Phe Leu Phe Pro Pro 260 265 270 Lys Pro Lys Asp Thr
Leu Met Ile Ser Arg Thr Pro Glu Val Thr Cys 275 280 285 Val Val Val
Asp Val Ser His Glu Asp Pro Glu Val Lys Phe Asn Trp 290 295 300 Tyr
Val Asp Gly Val Glu Val His Asn Ala Lys Thr Lys Pro Arg Glu 305 310
315 320 Glu Gln Tyr Asn Ser Thr Tyr Arg Val Val Ser Val Leu Thr Val
Leu 325 330 335 His Gln Asp Trp Leu Asn Gly Lys Glu Tyr Lys Cys Lys
Val Ser Asn 340 345 350 Lys Ala Leu Pro Ala Pro Ile Glu Lys Thr Ile
Ser Lys Ala Lys Gly 355 360 365 Gln Pro Arg Glu Pro Gln Val Tyr Thr
Leu Pro Pro Ser Arg Glu Glu 370 375 380 Met Thr Lys Asn Gln Val Ser
Leu Thr Cys Leu Val Lys Gly Phe Tyr 385 390 395 400 Pro Ser Asp Ile
Ala Val Glu Trp Glu Ser Asn Gly Gln Pro Glu Asn 405 410 415 Asn Tyr
Lys Thr Thr Pro Pro Val Leu Asp Ser Asp Gly Ser Phe Phe 420 425 430
Leu Tyr Ser Lys Leu Thr Val Asp Lys Ser Arg Trp Gln Gln Gly Asn 435
440 445 Val Phe Ser Cys Ser Val Met His Glu Ala Leu His Asn His Tyr
Thr 450 455 460 Gln Lys Ser Leu Ser Leu Ser Pro Gly Lys 465 470
<210> SEQ ID NO 9 <211> LENGTH: 612 <212> TYPE:
DNA <213> ORGANISM: Homo sapiens <220> FEATURE:
<221> NAME/KEY: CDS <222> LOCATION: (1)...(612)
<221> NAME/KEY: misc_feature <222> LOCATION: (0)...(0)
<223> OTHER INFORMATION: Coding sequence for short isoform of
human CD40 <400> SEQUENCE: 9 atg gtt cgt ctg cct ctg cag tgc
gtc ctc tgg ggc tgc ttg ctg acc 48 Met Val Arg Leu Pro Leu Gln Cys
Val Leu Trp Gly Cys Leu Leu Thr 1 5 10 15 gct gtc cat cca gaa cca
ccc act gca tgc aga gaa aaa cag tac cta 96 Ala Val His Pro Glu Pro
Pro Thr Ala Cys Arg Glu Lys Gln Tyr Leu 20 25 30 ata aac agt cag
tgc tgt tct ttg tgc cag cca gga cag aaa ctg gtg 144 Ile Asn Ser Gln
Cys Cys Ser Leu Cys Gln Pro Gly Gln Lys Leu Val 35 40 45 agt gac
tgc aca gag ttc act gaa acg gaa tgc ctt cct tgc ggt gaa 192 Ser Asp
Cys Thr Glu Phe Thr Glu Thr Glu Cys Leu Pro Cys Gly Glu 50 55 60
agc gaa ttc cta gac acc tgg aac aga gag aca cac tgc cac cag cac 240
Ser Glu Phe Leu Asp Thr Trp Asn Arg Glu Thr His Cys His Gln His 65
70 75 80 aaa tac tgc gac ccc aac cta ggg ctt cgg gtc cag cag aag
ggc acc 288 Lys Tyr Cys Asp Pro Asn Leu Gly Leu Arg Val Gln Gln Lys
Gly Thr 85 90 95 tca gaa aca gac acc atc tgc acc tgt gaa gaa ggc
tgg cac tgt acg 336 Ser Glu Thr Asp Thr Ile Cys Thr Cys Glu Glu Gly
Trp His Cys Thr 100 105 110 agt gag gcc tgt gag agc tgt gtc ctg cac
cgc tca tgc tcg ccc ggc 384 Ser Glu Ala Cys Glu Ser Cys Val Leu His
Arg Ser Cys Ser Pro Gly 115 120 125 ttt ggg gtc aag cag att gct aca
ggg gtt tct gat acc atc tgc gag 432 Phe Gly Val Lys Gln Ile Ala Thr
Gly Val Ser Asp Thr Ile Cys Glu 130 135 140 ccc tgc cca gtc ggc ttc
ttc tcc aat gtg tca tct gct ttc gaa aaa 480 Pro Cys Pro Val Gly Phe
Phe Ser Asn Val Ser Ser Ala Phe Glu Lys 145 150 155 160 tgt cac cct
tgg aca agg tcc cca gga tcg gct gag agc cct ggt ggt 528 Cys His Pro
Trp Thr Arg Ser Pro Gly Ser Ala Glu Ser Pro Gly Gly 165 170 175 gat
ccc cat cat ctt cgg gat cct gtt tgc cat cct ctt ggt gct ggt 576 Asp
Pro His His Leu Arg Asp Pro Val Cys His Pro Leu Gly Ala Gly 180 185
190 ctt tat caa aaa ggt ggc caa gaa gcc aac caa taa 612 Leu Tyr Gln
Lys Gly Gly Gln Glu Ala Asn Gln * 195 200 <210> SEQ ID NO 10
<211> LENGTH: 203 <212> TYPE: PRT <213> ORGANISM:
Homo sapiens <400> SEQUENCE: 10
Met Val Arg Leu Pro Leu Gln Cys Val Leu Trp Gly Cys Leu Leu Thr 1 5
10 15 Ala Val His Pro Glu Pro Pro Thr Ala Cys Arg Glu Lys Gln Tyr
Leu 20 25 30 Ile Asn Ser Gln Cys Cys Ser Leu Cys Gln Pro Gly Gln
Lys Leu Val 35 40 45 Ser Asp Cys Thr Glu Phe Thr Glu Thr Glu Cys
Leu Pro Cys Gly Glu 50 55 60 Ser Glu Phe Leu Asp Thr Trp Asn Arg
Glu Thr His Cys His Gln His 65 70 75 80 Lys Tyr Cys Asp Pro Asn Leu
Gly Leu Arg Val Gln Gln Lys Gly Thr 85 90 95 Ser Glu Thr Asp Thr
Ile Cys Thr Cys Glu Glu Gly Trp His Cys Thr 100 105 110 Ser Glu Ala
Cys Glu Ser Cys Val Leu His Arg Ser Cys Ser Pro Gly 115 120 125 Phe
Gly Val Lys Gln Ile Ala Thr Gly Val Ser Asp Thr Ile Cys Glu 130 135
140 Pro Cys Pro Val Gly Phe Phe Ser Asn Val Ser Ser Ala Phe Glu Lys
145 150 155 160 Cys His Pro Trp Thr Arg Ser Pro Gly Ser Ala Glu Ser
Pro Gly Gly 165 170 175 Asp Pro His His Leu Arg Asp Pro Val Cys His
Pro Leu Gly Ala Gly 180 185 190 Leu Tyr Gln Lys Gly Gly Gln Glu Ala
Asn Gln 195 200 <210> SEQ ID NO 11 <211> LENGTH: 834
<212> TYPE: DNA <213> ORGANISM: Homo sapiens
<220> FEATURE: <221> NAME/KEY: CDS <222>
LOCATION: (1)...(834) <221> NAME/KEY: misc_feature
<222> LOCATION: (0)...(0) <223> OTHER INFORMATION:
Coding sequence for long isoform of human CD40 <400>
SEQUENCE: 11 atg gtt cgt ctg cct ctg cag tgc gtc ctc tgg ggc tgc
ttg ctg acc 48 Met Val Arg Leu Pro Leu Gln Cys Val Leu Trp Gly Cys
Leu Leu Thr 1 5 10 15 gct gtc cat cca gaa cca ccc act gca tgc aga
gaa aaa cag tac cta 96 Ala Val His Pro Glu Pro Pro Thr Ala Cys Arg
Glu Lys Gln Tyr Leu 20 25 30 ata aac agt cag tgc tgt tct ttg tgc
cag cca gga cag aaa ctg gtg 144 Ile Asn Ser Gln Cys Cys Ser Leu Cys
Gln Pro Gly Gln Lys Leu Val 35 40 45 agt gac tgc aca gag ttc act
gaa acg gaa tgc ctt cct tgc ggt gaa 192 Ser Asp Cys Thr Glu Phe Thr
Glu Thr Glu Cys Leu Pro Cys Gly Glu 50 55 60 agc gaa ttc cta gac
acc tgg aac aga gag aca cac tgc cac cag cac 240 Ser Glu Phe Leu Asp
Thr Trp Asn Arg Glu Thr His Cys His Gln His 65 70 75 80 aaa tac tgc
gac ccc aac cta ggg ctt cgg gtc cag cag aag ggc acc 288 Lys Tyr Cys
Asp Pro Asn Leu Gly Leu Arg Val Gln Gln Lys Gly Thr 85 90 95 tca
gaa aca gac acc atc tgc acc tgt gaa gaa ggc tgg cac tgt acg 336 Ser
Glu Thr Asp Thr Ile Cys Thr Cys Glu Glu Gly Trp His Cys Thr 100 105
110 agt gag gcc tgt gag agc tgt gtc ctg cac cgc tca tgc tcg ccc ggc
384 Ser Glu Ala Cys Glu Ser Cys Val Leu His Arg Ser Cys Ser Pro Gly
115 120 125 ttt ggg gtc aag cag att gct aca ggg gtt tct gat acc atc
tgc gag 432 Phe Gly Val Lys Gln Ile Ala Thr Gly Val Ser Asp Thr Ile
Cys Glu 130 135 140 ccc tgc cca gtc ggc ttc ttc tcc aat gtg tca tct
gct ttc gaa aaa 480 Pro Cys Pro Val Gly Phe Phe Ser Asn Val Ser Ser
Ala Phe Glu Lys 145 150 155 160 tgt cac cct tgg aca agc tgt gag acc
aaa gac ctg gtt gtg caa cag 528 Cys His Pro Trp Thr Ser Cys Glu Thr
Lys Asp Leu Val Val Gln Gln 165 170 175 gca ggc aca aac aag act gat
gtt gtc tgt ggt ccc cag gat cgg ctg 576 Ala Gly Thr Asn Lys Thr Asp
Val Val Cys Gly Pro Gln Asp Arg Leu 180 185 190 aga gcc ctg gtg gtg
atc ccc atc atc ttc ggg atc ctg ttt gcc atc 624 Arg Ala Leu Val Val
Ile Pro Ile Ile Phe Gly Ile Leu Phe Ala Ile 195 200 205 ctc ttg gtg
ctg gtc ttt atc aaa aag gtg gcc aag aag cca acc aat 672 Leu Leu Val
Leu Val Phe Ile Lys Lys Val Ala Lys Lys Pro Thr Asn 210 215 220 aag
gcc ccc cac ccc aag cag gaa ccc cag gag atc aat ttt ccc gac 720 Lys
Ala Pro His Pro Lys Gln Glu Pro Gln Glu Ile Asn Phe Pro Asp 225 230
235 240 gat ctt cct ggc tcc aac act gct gct cca gtg cag gag act tta
cat 768 Asp Leu Pro Gly Ser Asn Thr Ala Ala Pro Val Gln Glu Thr Leu
His 245 250 255 gga tgc caa ccg gtc acc cag gag gat ggc aaa gag agt
cgc atc tca 816 Gly Cys Gln Pro Val Thr Gln Glu Asp Gly Lys Glu Ser
Arg Ile Ser 260 265 270 gtg cag gag aga cag tga 834 Val Gln Glu Arg
Gln * 275 <210> SEQ ID NO 12 <211> LENGTH: 277
<212> TYPE: PRT <213> ORGANISM: Homo sapiens
<400> SEQUENCE: 12 Met Val Arg Leu Pro Leu Gln Cys Val Leu
Trp Gly Cys Leu Leu Thr 1 5 10 15 Ala Val His Pro Glu Pro Pro Thr
Ala Cys Arg Glu Lys Gln Tyr Leu 20 25 30 Ile Asn Ser Gln Cys Cys
Ser Leu Cys Gln Pro Gly Gln Lys Leu Val 35 40 45 Ser Asp Cys Thr
Glu Phe Thr Glu Thr Glu Cys Leu Pro Cys Gly Glu 50 55 60 Ser Glu
Phe Leu Asp Thr Trp Asn Arg Glu Thr His Cys His Gln His 65 70 75 80
Lys Tyr Cys Asp Pro Asn Leu Gly Leu Arg Val Gln Gln Lys Gly Thr 85
90 95 Ser Glu Thr Asp Thr Ile Cys Thr Cys Glu Glu Gly Trp His Cys
Thr 100 105 110 Ser Glu Ala Cys Glu Ser Cys Val Leu His Arg Ser Cys
Ser Pro Gly 115 120 125 Phe Gly Val Lys Gln Ile Ala Thr Gly Val Ser
Asp Thr Ile Cys Glu 130 135 140 Pro Cys Pro Val Gly Phe Phe Ser Asn
Val Ser Ser Ala Phe Glu Lys 145 150 155 160 Cys His Pro Trp Thr Ser
Cys Glu Thr Lys Asp Leu Val Val Gln Gln 165 170 175 Ala Gly Thr Asn
Lys Thr Asp Val Val Cys Gly Pro Gln Asp Arg Leu 180 185 190 Arg Ala
Leu Val Val Ile Pro Ile Ile Phe Gly Ile Leu Phe Ala Ile 195 200 205
Leu Leu Val Leu Val Phe Ile Lys Lys Val Ala Lys Lys Pro Thr Asn 210
215 220 Lys Ala Pro His Pro Lys Gln Glu Pro Gln Glu Ile Asn Phe Pro
Asp 225 230 235 240 Asp Leu Pro Gly Ser Asn Thr Ala Ala Pro Val Gln
Glu Thr Leu His 245 250 255 Gly Cys Gln Pro Val Thr Gln Glu Asp Gly
Lys Glu Ser Arg Ile Ser 260 265 270 Val Gln Glu Arg Gln 275
<210> SEQ ID NO 13 <211> LENGTH: 786 <212> TYPE:
DNA <213> ORGANISM: Homo sapiens <220> FEATURE:
<221> NAME/KEY: CDS <222> LOCATION: (1)...(786)
<221> NAME/KEY: misc_feature <222> LOCATION: (0)...(0)
<223> OTHER INFORMATION: CD40L <400> SEQUENCE: 13 atg
atc gaa aca tac aac caa act tct ccc cga tct gcg gcc act gga 48 Met
Ile Glu Thr Tyr Asn Gln Thr Ser Pro Arg Ser Ala Ala Thr Gly 1 5 10
15 ctg ccc atc agc atg aaa att ttt atg tat tta ctt act gtt ttt ctt
96 Leu Pro Ile Ser Met Lys Ile Phe Met Tyr Leu Leu Thr Val Phe Leu
20 25 30 atc acc cag atg att ggg tca gca ctt ttt gct gtg tat ctt
cat aga 144 Ile Thr Gln Met Ile Gly Ser Ala Leu Phe Ala Val Tyr Leu
His Arg 35 40 45 agg ttg gac aag ata gaa gat gaa agg aat ctt cat
gaa gat ttt gta 192 Arg Leu Asp Lys Ile Glu Asp Glu Arg Asn Leu His
Glu Asp Phe Val 50 55 60 ttc atg aaa acg ata cag aga tgc aac aca
gga gaa aga tcc tta tcc 240 Phe Met Lys Thr Ile Gln Arg Cys Asn Thr
Gly Glu Arg Ser Leu Ser 65 70 75 80 tta ctg aac tgt gag gag att aaa
agc cag ttt gaa ggc ttt gtg aag 288 Leu Leu Asn Cys Glu Glu Ile Lys
Ser Gln Phe Glu Gly Phe Val Lys 85 90 95 gat ata atg tta aac aaa
gag gag acg aag aaa gaa aac agc ttt gaa 336 Asp Ile Met Leu Asn Lys
Glu Glu Thr Lys Lys Glu Asn Ser Phe Glu 100 105 110 atg caa aaa ggt
gat cag aat cct caa att gcg gca cat gtc ata agt 384 Met Gln Lys Gly
Asp Gln Asn Pro Gln Ile Ala Ala His Val Ile Ser 115 120 125 gag gcc
agc agt aaa aca aca tct gtg tta cag tgg gct gaa aaa gga 432 Glu Ala
Ser Ser Lys Thr Thr Ser Val Leu Gln Trp Ala Glu Lys Gly 130 135 140
tac tac acc atg agc aac aac ttg gta acc ctg gaa aat ggg aaa cag 480
Tyr Tyr Thr Met Ser Asn Asn Leu Val Thr Leu Glu Asn Gly Lys Gln 145
150 155 160 ctg acc gtt aaa aga caa gga ctc tat tat atc tat gcc caa
gtc acc 528 Leu Thr Val Lys Arg Gln Gly Leu Tyr Tyr Ile Tyr Ala Gln
Val Thr 165 170 175 ttc tgt tcc aat cgg gaa gct tcg agt caa gct cca
ttt ata gcc agc 576 Phe Cys Ser Asn Arg Glu Ala Ser Ser Gln Ala Pro
Phe Ile Ala Ser 180 185 190 ctc tgc cta aag tcc ccc ggt aga ttc gag
aga atc tta ctc aga gct 624
Leu Cys Leu Lys Ser Pro Gly Arg Phe Glu Arg Ile Leu Leu Arg Ala 195
200 205 gca aat acc cac agt tcc gcc aaa cct tgc ggg caa caa tcc att
cac 672 Ala Asn Thr His Ser Ser Ala Lys Pro Cys Gly Gln Gln Ser Ile
His 210 215 220 ttg gga gga gta ttt gaa ttg caa cca ggt gct tcg gtg
ttt gtc aat 720 Leu Gly Gly Val Phe Glu Leu Gln Pro Gly Ala Ser Val
Phe Val Asn 225 230 235 240 gtg act gat cca agc caa gtg agc cat ggc
act ggc ttc acg tcc ttt 768 Val Thr Asp Pro Ser Gln Val Ser His Gly
Thr Gly Phe Thr Ser Phe 245 250 255 ggc tta ctc aaa ctc tga 786 Gly
Leu Leu Lys Leu * 260 <210> SEQ ID NO 14 <211> LENGTH:
261 <212> TYPE: PRT <213> ORGANISM: Homo sapiens
<400> SEQUENCE: 14 Met Ile Glu Thr Tyr Asn Gln Thr Ser Pro
Arg Ser Ala Ala Thr Gly 1 5 10 15 Leu Pro Ile Ser Met Lys Ile Phe
Met Tyr Leu Leu Thr Val Phe Leu 20 25 30 Ile Thr Gln Met Ile Gly
Ser Ala Leu Phe Ala Val Tyr Leu His Arg 35 40 45 Arg Leu Asp Lys
Ile Glu Asp Glu Arg Asn Leu His Glu Asp Phe Val 50 55 60 Phe Met
Lys Thr Ile Gln Arg Cys Asn Thr Gly Glu Arg Ser Leu Ser 65 70 75 80
Leu Leu Asn Cys Glu Glu Ile Lys Ser Gln Phe Glu Gly Phe Val Lys 85
90 95 Asp Ile Met Leu Asn Lys Glu Glu Thr Lys Lys Glu Asn Ser Phe
Glu 100 105 110 Met Gln Lys Gly Asp Gln Asn Pro Gln Ile Ala Ala His
Val Ile Ser 115 120 125 Glu Ala Ser Ser Lys Thr Thr Ser Val Leu Gln
Trp Ala Glu Lys Gly 130 135 140 Tyr Tyr Thr Met Ser Asn Asn Leu Val
Thr Leu Glu Asn Gly Lys Gln 145 150 155 160 Leu Thr Val Lys Arg Gln
Gly Leu Tyr Tyr Ile Tyr Ala Gln Val Thr 165 170 175 Phe Cys Ser Asn
Arg Glu Ala Ser Ser Gln Ala Pro Phe Ile Ala Ser 180 185 190 Leu Cys
Leu Lys Ser Pro Gly Arg Phe Glu Arg Ile Leu Leu Arg Ala 195 200 205
Ala Asn Thr His Ser Ser Ala Lys Pro Cys Gly Gln Gln Ser Ile His 210
215 220 Leu Gly Gly Val Phe Glu Leu Gln Pro Gly Ala Ser Val Phe Val
Asn 225 230 235 240 Val Thr Asp Pro Ser Gln Val Ser His Gly Thr Gly
Phe Thr Ser Phe 245 250 255 Gly Leu Leu Lys Leu 260 <210> SEQ
ID NO 15 <211> LENGTH: 648 <212> TYPE: DNA <213>
ORGANISM: Homo sapiens <220> FEATURE: <221> NAME/KEY:
CDS <222> LOCATION: (1)...(648) <221> NAME/KEY:
misc_feature <222> LOCATION: (0)...(0) <223> OTHER
INFORMATION: Soluble CD40L <400> SEQUENCE: 15 cat aga agg ttg
gac aag ata gaa gat gaa agg aat ctt cat gaa gat 48 His Arg Arg Leu
Asp Lys Ile Glu Asp Glu Arg Asn Leu His Glu Asp 1 5 10 15 ttt gta
ttc atg aaa acg ata cag aga tgc aac aca gga gaa aga tcc 96 Phe Val
Phe Met Lys Thr Ile Gln Arg Cys Asn Thr Gly Glu Arg Ser 20 25 30
tta tcc tta ctg aac tgt gag gag att aaa agc cag ttt gaa ggc ttt 144
Leu Ser Leu Leu Asn Cys Glu Glu Ile Lys Ser Gln Phe Glu Gly Phe 35
40 45 gtg aag gat ata atg tta aac aaa gag gag acg aag aaa gaa aac
agc 192 Val Lys Asp Ile Met Leu Asn Lys Glu Glu Thr Lys Lys Glu Asn
Ser 50 55 60 ttt gaa atg caa aaa ggt gat cag aat cct caa att gcg
gca cat gtc 240 Phe Glu Met Gln Lys Gly Asp Gln Asn Pro Gln Ile Ala
Ala His Val 65 70 75 80 ata agt gag gcc agc agt aaa aca aca tct gtg
tta cag tgg gct gaa 288 Ile Ser Glu Ala Ser Ser Lys Thr Thr Ser Val
Leu Gln Trp Ala Glu 85 90 95 aaa gga tac tac acc atg agc aac aac
ttg gta acc ctg gaa aat ggg 336 Lys Gly Tyr Tyr Thr Met Ser Asn Asn
Leu Val Thr Leu Glu Asn Gly 100 105 110 aaa cag ctg acc gtt aaa aga
caa gga ctc tat tat atc tat gcc caa 384 Lys Gln Leu Thr Val Lys Arg
Gln Gly Leu Tyr Tyr Ile Tyr Ala Gln 115 120 125 gtc acc ttc tgt tcc
aat cgg gaa gct tcg agt caa gct cca ttt ata 432 Val Thr Phe Cys Ser
Asn Arg Glu Ala Ser Ser Gln Ala Pro Phe Ile 130 135 140 gcc agc ctc
tgc cta aag tcc ccc ggt aga ttc gag aga atc tta ctc 480 Ala Ser Leu
Cys Leu Lys Ser Pro Gly Arg Phe Glu Arg Ile Leu Leu 145 150 155 160
aga gct gca aat acc cac agt tcc gcc aaa cct tgc ggg caa caa tcc 528
Arg Ala Ala Asn Thr His Ser Ser Ala Lys Pro Cys Gly Gln Gln Ser 165
170 175 att cac ttg gga gga gta ttt gaa ttg caa cca ggt gct tcg gtg
ttt 576 Ile His Leu Gly Gly Val Phe Glu Leu Gln Pro Gly Ala Ser Val
Phe 180 185 190 gtc aat gtg act gat cca agc caa gtg agc cat ggc act
ggc ttc acg 624 Val Asn Val Thr Asp Pro Ser Gln Val Ser His Gly Thr
Gly Phe Thr 195 200 205 tcc ttt ggc tta ctc aaa ctc tga 648 Ser Phe
Gly Leu Leu Lys Leu * 210 215 <210> SEQ ID NO 16 <211>
LENGTH: 215 <212> TYPE: PRT <213> ORGANISM: Homo
sapiens <400> SEQUENCE: 16 His Arg Arg Leu Asp Lys Ile Glu
Asp Glu Arg Asn Leu His Glu Asp 1 5 10 15 Phe Val Phe Met Lys Thr
Ile Gln Arg Cys Asn Thr Gly Glu Arg Ser 20 25 30 Leu Ser Leu Leu
Asn Cys Glu Glu Ile Lys Ser Gln Phe Glu Gly Phe 35 40 45 Val Lys
Asp Ile Met Leu Asn Lys Glu Glu Thr Lys Lys Glu Asn Ser 50 55 60
Phe Glu Met Gln Lys Gly Asp Gln Asn Pro Gln Ile Ala Ala His Val 65
70 75 80 Ile Ser Glu Ala Ser Ser Lys Thr Thr Ser Val Leu Gln Trp
Ala Glu 85 90 95 Lys Gly Tyr Tyr Thr Met Ser Asn Asn Leu Val Thr
Leu Glu Asn Gly 100 105 110 Lys Gln Leu Thr Val Lys Arg Gln Gly Leu
Tyr Tyr Ile Tyr Ala Gln 115 120 125 Val Thr Phe Cys Ser Asn Arg Glu
Ala Ser Ser Gln Ala Pro Phe Ile 130 135 140 Ala Ser Leu Cys Leu Lys
Ser Pro Gly Arg Phe Glu Arg Ile Leu Leu 145 150 155 160 Arg Ala Ala
Asn Thr His Ser Ser Ala Lys Pro Cys Gly Gln Gln Ser 165 170 175 Ile
His Leu Gly Gly Val Phe Glu Leu Gln Pro Gly Ala Ser Val Phe 180 185
190 Val Asn Val Thr Asp Pro Ser Gln Val Ser His Gly Thr Gly Phe Thr
195 200 205 Ser Phe Gly Leu Leu Lys Leu 210 215
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