U.S. patent application number 16/812845 was filed with the patent office on 2020-08-27 for t cell receptors recognizing mhc class ii-restricted mage-a3.
This patent application is currently assigned to The United States of America,as represented by the Secretary,Department of Health and Human Services. The applicant listed for this patent is The United States of America,as represented by the Secretary,Department of Health and Human Services, The United States of America,as represented by the Secretary,Department of Health and Human Services. Invention is credited to Paul F. Robbins, Steven A. Rosenberg, Xin Yao.
Application Number | 20200270329 16/812845 |
Document ID | / |
Family ID | 1000004824501 |
Filed Date | 2020-08-27 |
United States Patent
Application |
20200270329 |
Kind Code |
A1 |
Robbins; Paul F. ; et
al. |
August 27, 2020 |
T CELL RECEPTORS RECOGNIZING MHC CLASS II-RESTRICTED MAGE-A3
Abstract
The invention provides an isolated or purified T-cell receptor
(TCR) having antigenic specificity for MHC Class II-restricted
MAGE-A3. The invention further provides related polypeptides and
proteins, as well as related nucleic acids, recombinant expression
vectors, host cells, and populations of cells. Further provided by
the invention are antibodies, or an antigen binding portion
thereof, and pharmaceutical compositions relating to the TCRs of
the invention. Methods of detecting the presence of cancer in a
host and methods of treating or preventing cancer in a mammal are
further provided by the invention.
Inventors: |
Robbins; Paul F.; (Chevy
Chase, MD) ; Rosenberg; Steven A.; (Potomac, MD)
; Yao; Xin; (Rockville, MD) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The United States of America,as represented by the
Secretary,Department of Health and Human Services |
Bethesda |
MD |
US |
|
|
Assignee: |
The United States of America,as
represented by the Secretary,Department of Health and Human
Services
Bethesda
MD
|
Family ID: |
1000004824501 |
Appl. No.: |
16/812845 |
Filed: |
March 9, 2020 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15848344 |
Dec 20, 2017 |
10611815 |
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16812845 |
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14427671 |
Mar 12, 2015 |
9879065 |
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PCT/US2013/059608 |
Sep 13, 2013 |
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15848344 |
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61701056 |
Sep 14, 2012 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61K 38/1774 20130101;
G01N 33/57492 20130101; C07K 14/7051 20130101; G01N 2333/7051
20130101; C07K 14/70514 20130101; A61K 2039/585 20130101; A61K
39/0005 20130101; G01N 2333/47 20130101; C07K 16/00 20130101; C07K
2319/00 20130101; C07K 16/2809 20130101 |
International
Class: |
C07K 14/725 20060101
C07K014/725; A61K 38/17 20060101 A61K038/17; C07K 14/73 20060101
C07K014/73; A61K 39/00 20060101 A61K039/00; C07K 16/00 20060101
C07K016/00; C07K 16/28 20060101 C07K016/28; G01N 33/574 20060101
G01N033/574 |
Claims
1-2. (canceled)
3. The antibody, or antigen binding portion thereof, of claim 32,
wherein the TCR or functional variant comprises: (i) SEQ ID NO: 29,
wherein Xaa4 is Ser, Ala, Leu, Ile, Val, or Met; Xaa5 is Ser, Ala,
Leu, Ile, Val, or Met; Xaa6 is Gly, Ala, Leu, Ile, Val, or Met; and
Xaa7 is Thr, Ala, Leu, Ile, Val, or Met; and/or (ii) SEQ ID NO: 30,
wherein Xaa4 is Arg, Ala, Leu, Ile, Val, or Met; Xaa5 is Thr, Ala,
Leu, Ile, Val, or Met; Xaa6 is Gly, Ala, Leu, Ile, Val, or Met; and
Xaa7 is Pro, Ala, Leu, Ile, Val, or Met.
4. The antibody, or antigen binding portion thereof, of claim 3,
wherein the functional variant comprises: (a) SEQ ID NO: 29,
wherein Xaa4 is Ala, Xaa5 is Ser, Xaa6 is Gly, and Xaa7 is Thr, or
(b) SEQ ID NO: 29, wherein Xaa4 is Ser, Xaa5 is Ala, Xaa6 is Gly,
and Xaa7 is Thr.
5. The antibody, or antigen binding portion thereof, of claim 32,
wherein the TCR or functional variant comprises a murine constant
region.
6. The antibody, or antigen binding portion thereof, of claim 5,
wherein the TCR or functional variant comprises a murine constant
region comprising SEQ ID NO: 25 and/or SEQ ID NO: 26.
7. The antibody, or antigen binding portion thereof, of claim 32,
wherein the TCR or functional variant comprises: a first amino acid
sequence selected from the group consisting of (i) SEQ ID NO: 31,
wherein Xaa116 is Ser, Ala, Leu, Ile, Val, or Met; Xaa117 is Ser,
Ala, Leu, Ile, Val, or Met; Xaa118 is Gly, Ala, Leu, Ile, Val, or
Met; and Xaa119 is Thr, Ala, Leu, Ile, Val, or Met; and (ii) SEQ ID
NO: 9; and a second amino acid sequence selected from the group
consisting of (i) SEQ ID NO: 32, wherein Xaa115 is Arg, Ala, Leu,
Ile, Val, or Met; Xaa116 is Thr, Ala, Leu, Ile, Val, or Met; Xaa117
is Gly, Ala, Leu, Ile, Val, or Met; and Xaa118 is Pro, Ala, Leu,
Ile, Val, or Met; and (ii) SEQ ID NO: 10.
8. The antibody, or antigen binding portion thereof, of claim 7,
wherein the functional variant comprises: (a) SEQ ID NO: 31,
wherein Xaa116 is Ala, Xaa117 is Ser, Xaa118 is Gly, and Xaa119 is
Thr, or (b) SEQ ID NO: 31, wherein Xaa116 is Ser, Xaa117 is Ala,
Xaa118 is Gly, and Xaa119 is Thr.
9. The antibody, or antigen binding portion thereof, of claim 3,
wherein the TCR or functional variant comprises: a first amino acid
sequence selected from the group consisting of (i) SEQ ID NO: 33,
wherein Xaa116 is Ser, Ala, Leu, Ile, Val, or Met; Xaa117 is Ser,
Ala, Leu, Ile, Val, or Met; Xaa118 is Gly, Ala, Leu, Ile, Val, or
Met; and Xaa119 is Thr, Ala, Leu, Ile, Val, or Met; (ii) SEQ ID NO:
11; (iii) SEQ ID NO: 21; and (iv) SEQ ID NO: 27; and a second amino
acid sequence selected from the group consisting of (i) SEQ ID NO:
34, wherein Xaa115 is Arg, Ala, Leu, Ile, Val, or Met; Xaa116 is
Thr, Ala, Leu, Ile, Val, or Met; Xaa117 is Gly, Ala, Leu, Ile, Val,
or Met; and Xaa118 is Pro, Ala, Leu, Ile, Val, or Met; (ii) SEQ ID
NO: 12; (iii) SEQ ID NO: 22; and (iv) SEQ ID NO: 28.
10. The antibody, or antigen binding portion thereof, of claim 9,
wherein the functional variant comprises: (a) SEQ ID NO: 33,
wherein Xaa116 is Ala, Xaa117 is Ser, Xaa118 is Gly, and Xaa119 is
Thr, or (b) SEQ ID NO: 33, wherein Xaa116 is Ser, Xaa117 is Ala,
Xaa118 is Gly, and Xaa119 is Thr.
11-31. (canceled)
32. An antibody, or antigen binding portion thereof, which
specifically binds to a functional portion of a TCR or functional
variant of the TCR, wherein the TCR and functional variant have
antigenic specificity for MAGE-A3.sub.243-258 and MAGE-A6 and the
functional portion comprises (a) SEQ ID NOs: 3, 4, 6, 7, (i) SEQ ID
NO: 29, wherein Xaa4 is Ser, Ala, Leu, Ile, Val, or Met; Xaa5 is
Ser, Ala, Leu, Ile, Val, or Met; Xaa6 is Gly, Ala, Leu, Ile, Val,
or Met; and Xaa7 is Thr, Ala, Leu, Ile, Val, or Met; and (ii) SEQ
ID NO: 30, wherein Xaa4 is Arg, Ala, Leu, Ile, Val, or Met; Xaa5 is
Thr, Ala, Leu, Ile, Val, or Met; Xaa6 is Gly, Ala, Leu, Ile, Val,
or Met; and Xaa7 is Pro, Ala, Leu, Ile, Val, or Met; or (b) SEQ ID
NOs: 3-8.
33. A pharmaceutical composition comprising the antibody, or
antigen binding portion thereof, of claim 32, and a
pharmaceutically acceptable carrier.
34. A method of detecting the presence of cancer in a mammal,
comprising: (a) contacting a sample comprising one or more cells
from the mammal with the the antibody, or antigen binding portion
thereof, of claim 32, thereby forming a complex, and (b) detecting
the complex, wherein detection of the complex is indicative of the
presence of cancer in the mammal.
35. The method of claim 34, wherein the cancer is melanoma, breast
cancer, lung cancer, prostate cancer, synovial cell sarcoma, head
and neck cancer, esophageal cancer, or ovarian cancer.
36. A method of treating or preventing cancer in a mammal, the
method comprising administering to the mammal the antibody, or
antigen binding portion thereof, of claim 32, in an amount
effective to treat or prevent cancer in the mammal.
37. The method according to claim 36, wherein the cancer is
melanoma, breast cancer, lung cancer, prostate cancer, synovial
cell sarcoma, head and neck cancer, esophageal cancer, or ovarian
cancer.
Description
CROSS-REFERENCE TO RELATED APPLICATION
[0001] This application claims the benefit of U.S. Provisional
Application No. 61/701,056, filed on Sep. 14, 2012, the entire
contents of which are incorporated herein by reference.
INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED ELECTRONICALLY
[0002] Incorporated by reference in its entirety herein is a
computer-readable nucleotide/amino acid sequence listing submitted
concurrently herewith and identified as follows: One 63,888 Byte
ASCII (Text) file named "714146ST25.TXT," dated Aug. 20, 2013.
BACKGROUND OF THE INVENTION
[0003] Adoptive cell therapy (ACT) involves the transfer of
reactive T cells into patients, including the transfer of
tumor-reactive T cells into cancer patients. Adoptive cell therapy
using T-cells that target human leukocyte antigen (HLA)-A*02
restricted T-cell epitopes has been successful in causing the
regression of tumors in some patients. However, patients that lack
HLA-A*02 expression cannot be treated with T-cells that target
HLA-A*02 restricted T-cell epitopes. Such a limitation creates an
obstacle to the widespread application of adoptive cell therapy.
Accordingly, there exists a need for improved immunological
compositions and methods for treating cancer.
BRIEF SUMMARY OF THE INVENTION
[0004] An embodiment of the invention provides an isolated or
purified T-cell receptor (TCR), and functional portions and
functional variants thereof, having antigenic specificity for
MAGE-A3.sub.243-258 and MAGE-A6.
[0005] Another embodiment of the invention provides an isolated or
purified TCR comprising (a) SEQ ID NOs: 3-8 or (b) SEQ ID NOs:
21-22, or a functional variant of (a) or (b), wherein the
functional variant comprises (a) or (b) with at least one amino
acid substitution in any one or more of (a) or any one or more of
(b), and the functional variant has antigenic specificity for
MAGE-A3 in the context of HLA-DP.beta.1*04.
[0006] The invention further provides related polypeptides and
proteins, as well as related nucleic acids, recombinant expression
vectors, host cells, and populations of cells. Further provided by
the invention are antibodies, or antigen binding portions thereof,
and pharmaceutical compositions relating to the TCRs (including
functional portions and functional variants thereof) of the
invention.
[0007] Methods of detecting the presence of cancer in a mammal and
methods of treating or preventing cancer in a mammal are further
provided by the invention. The inventive method of detecting the
presence of cancer in a mammal comprises (i) contacting a sample
comprising cells of the cancer with any of the inventive TCRs
(including functional portions and functional variants thereof),
polypeptides, proteins, nucleic acids, recombinant expression
vectors, host cells, populations of host cells, or antibodies, or
antigen binding portions thereof, described herein, thereby forming
a complex, and (ii) detecting the complex, wherein detection of the
complex is indicative of the presence of cancer in the mammal.
[0008] The inventive method of treating or preventing cancer in a
mammal comprises administering to the mammal any of the TCRs
(including functional portions and functional variants thereof),
polypeptides, or proteins described herein, any nucleic acid or
recombinant expression vector comprising a nucleotide sequence
encoding any of the TCRs (including functional portions and
functional variants thereof), polypeptides, proteins described
herein, or any host cell or population of host cells comprising a
recombinant vector which encodes any of the TCRs (including
functional portions and functional variants thereof), polypeptides,
or proteins described herein, in an amount effective to treat or
prevent cancer in the mammal.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWING(S)
[0009] FIGS. 1A and 1B are bar graphs showing interferon
(IFN)-gamma secretion (pg/ml) by CD4+ T cells from first (1A) and
second (1B) donors in response to co-culture with 293-CIITA target
cells untransfected (292-CIITA) or transfected with full length
NY-ESO-1 (293-CIITA-NY-ESO-1) protein, MAGE-A1 protein
(293-CIITA-MAGE A1), MAGE-A3 protein (293-CIITA-MAGE-A3), MAGE-A6
protein (293-CIITA-MAGE-A6), or MAGE A12 protein
(293-CIITA-MAGE-A12). The T cells were untransduced (UT) or
transduced with F5 (anti-MART-1) TCR, R12C9 TCR, or 6F9 TCR.
[0010] FIG. 2A is a bar graph showing IFN-gamma secretion (pg/ml)
by T cells from a human donor that were untransduced or transduced
with 6F9 TCR or F5 TCR in response to co-culture with 526-CIITA
cells that were untreated or treated with anti-MAGE-A3 siRNA or
anti-MART-1 siRNA.
[0011] FIG. 2B is a bar graph showing IFN-gamma secretion (pg/ml)
by CD4+ T cells from a human donor that were untransduced or
transduced with 6F9 TCR in response to co-culture with H1299-CIITA
cells that were untreated or treated with anti-MAGE-A3 siRNA or
anti-MART-1 siRNA.
[0012] FIG. 3 is a bar graph showing IFN-gamma secretion (pg/ml) by
6F9-transduced PBL cultured alone (T cells only) or co-cultured
with 3071 cells, 3071-CIITA cells, 397 cells, 397-CIITA cells, 2630
cells, 2630-CIITA cells, 2984 cells, or 2984-CIITA cells.
[0013] FIG. 4 is a bar graph showing IFN-gamma secretion (pg/ml) by
CD4+ enriched PBL that were transduced with 6F9 TCR or untransduced
upon culture alone (T cell only) or in response to co-culture with
untreated H1299-CIITA cells, H1299-CIITA transfected with
anti-HLA-DP or anti-HLA-DR siRNA, untreated 526-CIITA cells, or
526-CIITA transfected with anti-HLA-DP or anti-HLA-DR siRNA.
[0014] FIG. 5 is a bar graph showing IFN-gamma (pg/ml) secretion by
PBL that were untransduced or transduced with wild-type (wt) 6F9
TCR or one of each of eight substituted TCRs: a1 (alpha chain
S116A), a2 (alpha chain S117A), a3 (alpha chain G118A), a4 (alpha
chain T119A), b1 (beta chain R115A), b2 (beta chain T116A), b3
(beta chain G117A), or b4 (beta chain P118A) upon culture alone (T
cell only; unshaded bars) or co-culture with 624-CIITA (checkered
bars), 526-CIITA (right crosshatched bars), 1359-CIITA (horizontal
striped bars), H1299-CIITA (left crosshatched bars), or 1764-CIITA
(vertical striped bars).
[0015] FIG. 6 is a bar graph showing IFN-gamma (pg/ml) secretion by
CD4+ enriched PBL that were untransduced or transduced with
wild-type (wt) 6F9 TCR or one of each of three substituted TCRs: a1
(alpha chain S116A), a2 (alpha chain S117A), or b2 (beta chain
T116A) upon culture alone (T cell only; unshaded bars) or
co-culture with 624-CIITA (checkered bars), 526-CIITA (right
crosshatched bars), 1359-CIITA (horizontal striped bars),
H1299-CIITA (left crosshatched bars), or 1764-CIITA (vertical
striped bars).
[0016] FIG. 7 is a bar graph showing IFN-gamma (pg/ml) secretion by
PBL that were untransduced or transduced with wild-type (wt) 6F9
TCR or one of each of ten substituted TCRs: a1 (alpha chain S116A),
a2 (alpha chain S117A), a1-1 (alpha chain S116L), a1-2 (alpha chain
S116I), a1-3 (alpha chain S116V), a1-4 (alpha chain S116M), a2-1
(alpha chain S117L), a2-2 (alpha chain S1170, a2-3 (alpha chain
S117V), or a2-4 (alpha chain S117M) upon culture alone or (T cell
only; unshaded bars) or co-culture with 624-CIITA (right
crosshatched bars), 526-CIITA (vertical striped bars), 1359-CIITA
(horizontal striped bars), H1299-CIITA (left crosshatched bars), or
1764-CIITA (black bars).
[0017] FIG. 8 is a bar graph showing IFN-gamma (pg/ml) secretion by
PBL that were untransduced (checkered bars) or transduced with
wild-type (wt) 6F9 TCR (horizontal striped bar) or 6F9mC TCR (SEQ
ID NOs: 27 and 28) (left crosshatched bars) upon culture alone (T
cells only) or co-culture with 624-CIITA, 1300-CIITA, 526-CIITA,
1359-CIITA, H1299-CIITA, 397-CIITA, 2630-CIITA, 2984-CIITA,
3071-CIITA, or 1764-CIITA cells.
[0018] FIGS. 9A and 9B are bar graphs showing IFN-gamma (pg/ml)
secretion by CD4+ (9A) or CD8+ (9B) enriched PBL that were
untransduced (checkered bars) or transduced with wild-type (wt) 6F9
TCR (horizontal striped bar) or 6F9mC TCR (SEQ ID NOs: 27 and 28)
(left crosshatched bars) upon culture alone (T cells only) or
co-culture with 624-CIITA, SK37-CIITA, 526-CIITA, 1359-CIITA,
H1299-CIITA, 397-CIITA, 2630-CIITA, 2984-CIITA, 3071-CIITA, or
1764-CIITA cells.
[0019] FIG. 10A is a bar graph showing IFN-gamma secretion by PBL
that were untransduced (UT; unshaded bars) or transduced with R12C9
TCR (grey bars) or 6F9 TCR (black bars) upon culture alone (none)
or co-culture with 293-CIITA transfectants that were transfected
with full length NY-ESO-1 protein, MAGE-A1 protein, MAGE-A3
protein, MAGE-A6 protein, MAGE-A12 protein, or 293-CIITA cells that
were pulsed with MAGE-A3243-258 peptide or MAGE-A3 protein.
[0020] FIG. 10B is a bar graph showing IFN-gamma secretion by PBL
that were untransduced (UT; black bars) or transduced with 6F9 TCR
(grey bars) upon culture alone (T cell alone) or co-culture with
non-small cell lung cancer (NSCLC) cell line H11299 or melanoma
cell line 526 mel, 624 mel, or 1359 mel.
DETAILED DESCRIPTION OF THE INVENTION
[0021] The invention provides an isolated or purified T cell
receptor (TCR), and functional portions and functional variants
thereof, having antigenic specificity for MAGE-A3, wherein the TCR
recognizes MAGE-A3 in the context of HLA-DP.beta.1*04. In an
embodiment of the invention, the isolated or purified TCR has
antigenic specificity for MAGE-A3243-258 and MAGE-A6.
[0022] MAGE-A3 and MAGE-A6 are members of the MAGE-A family of
twelve homologous proteins, also including MAGE-A1, MAGE-A2,
MAGE-A4, MAGE-A5, MAGE-A7, MAGE-A8, MAGE-A9, MAGE-A10, MAGE-A11,
and MAGE-A12. The MAGE-A proteins are cancer testis antigens (CTA),
which are expressed only in tumor cells and non-MHC expressing germ
cells of the testis and placenta. MAGE-A proteins are expressed in
a variety of human cancers including, but not limited to, melanoma,
breast cancer, leukemia, thyroid cancer, gastric cancer, pancreatic
cancer, liver cancer (e.g., hepatocellular carcinoma), lung cancer
(e.g., non-small cell lung carcinoma), ovarian cancer, multiple
myeloma, esophageal cancer, kidney cancer, head cancers (e.g.,
squamous cell carcinoma), neck cancers (e.g., squamous cell
carcinoma), prostate cancer, synovial cell sarcoma, and urothelial
cancer.
[0023] The TCRs (including functional portions and functional
variants thereof) of the invention provide many advantages,
including when used for adoptive cell transfer. For example, by
targeting MAGE-A3 that is presented in the context of
HLA-DP.beta.1*04, the inventive TCRs (including functional portions
and functional variants thereof) make it possible to treat patients
who are unable to be treated using TCRs that target MAGE antigens
that are presented in the context of other HLA molecules, e.g.,
HLA-A*02, HLA-A*01, or HLA-C*07. HLA-DP.beta.1*04 is a highly
prevalent allele that is expressed by from about 70% to about 80%
of the cancer patient population. Accordingly, the inventive TCRs
(including functional portions and functional variants thereof)
advantageously greatly expand the patient population that can be
treated. Additionally, without being bound by a particular theory,
it is believed that because MAGE-A3 and/or MAGE-A6 are expressed by
cells of multiple cancer types, the inventive TCRs (including
functional portions and functional variants thereof) advantageously
provide the ability to destroy cells of multiple types of cancer
and, accordingly, treat or prevent multiple types of cancer.
Additionally, without being bound to a particular theory, it is
believed that because the MAGE-A proteins are cancer testis
antigens that are expressed only in tumor cells and non-MHC
expressing germ cells of the testis and placenta, the inventive
TCRs (including functional portions and functional variants
thereof) advantageously target the destruction of cancer cells
while minimizing or eliminating the destruction of normal,
non-cancerous cells, thereby reducing, for example, by minimizing
or eliminating, toxicity.
[0024] The phrase "antigenic specificity" as used herein means that
the TCR can specifically bind to and immunologically recognize
MAGE-A3 and/or MAGE-A6 with high avidity. For example, a TCR may be
considered to have "antigenic specificity" for MAGE-A3 and/or
MAGE-A6 if T cells expressing the TCR secrete at least about 200
pg/ml or more (e.g., 200 pg/ml or more, 300 pg/ml or more, 400
pg/ml or more, 500 pg/ml or more, 600 pg/ml or more, 700 pg/ml or
more, 1000 pg/ml or more, 5,000 pg/ml or more, 7,000 pg/ml or more,
10,000 pg/ml or more, or 20,000 pg/ml or more) of IFN-.gamma. upon
co-culture with antigen-negative HLA-DP.beta.1*04+ target cells
pulsed with a low concentration of MAGE-A3 and/or MAGE-A6 peptide
(e.g., about 0.05 ng/ml to about 5 ng/ml, 0.05 ng/ml, 0.1 ng/ml,
0.5 ng/ml, 1 ng/ml, or 5 ng/ml). Alternatively or additionally, a
TCR may be considered to have "antigenic specificity" for MAGE-A3
and/or MAGE-A6 if T cells expressing the TCR secrete at least twice
as much IFN-.gamma. as the untransduced PBL background level of
IFN-.gamma. upon co-culture with antigen-negative HLA-
DP.beta.1*04+ target cells pulsed with a low concentration of
MAGE-A3 and/or MAGE-A6 peptide. The inventive TCRs (including
functional portions and functional variants thereof) may also
secrete IFN-.gamma. upon co-culture with antigen-negative HLA-
DP.beta.1*04+ target cells pulsed with higher concentrations of
MAGE-A3 and/or MAGE-A6 peptide.
[0025] An embodiment of the invention provides a TCR (including
functional portions and variants thereof) with antigenic
specificity for any MAGE-A3 protein, polypeptide or peptide. The
inventive TCR (including functional portions and functional
variants thereof) may have antigenic specificity for a MAGE-A3
protein comprising, consisting of, or consisting essentially of,
SEQ ID NO: 1. In a preferred embodiment of the invention, the TCR
(including functional portions and variants thereof) has antigenic
specificity for a MAGE-A3.sub.243-258 peptide comprising,
consisting of, or consisting essentially of, KKLLTQHFVQENYLEY (SEQ
ID NO: 2).
[0026] The inventive TCRs (including functional portions and
functional variants thereof) are able to recognize MAGE-A3 in a
human leukocyte antigen (HLA)-DP.beta.1*04-dependent manner.
"HLA-DP.beta.1*04-dependent manner," as used herein, means that the
TCR elicits an immune response upon binding to a MAGE-A3 protein,
polypeptide or peptide within the context of an HLA-DP.beta.1*04
molecule. The inventive TCRs (including functional portions and
functional variants thereof) are able to recognize MAGE-A3 that is
presented by an HLA-DP.beta.1*04 molecule and may bind to the
HLA-DP.beta.1*04 molecule in addition to MAGE-A3. Exemplary
HLA-DP.beta.1*04 molecules, in the context of which the inventive
TCRs (including functional portions and functional variants
thereof) recognize MAGE-A3, include those encoded by the
HLA-DP.beta.1*0401 and/or HLA-DP.beta.1*0402 alleles.
[0027] An embodiment of the invention provides a TCR (including
functional portions and variants thereof) with antigenic
specificity for any MAGE-A6 protein, polypeptide or peptide. The
inventive TCR (including functional portions and functional
variants thereof) may have antigenic specificity for a MAGE-A6
protein comprising, consisting of, or consisting essentially of,
SEQ ID NO: 45. In a preferred embodiment of the invention, the TCR
(including functional portions and functional variants thereof) has
antigenic specificity for a MAGE-A6.sub.243-258 peptide comprising,
consisting of, or consisting essentially of, KKLLTQYFVQENYLEY (SEQ
ID NO: 46).
[0028] The invention provides a TCR comprising two polypeptides
(i.e., polypeptide chains), such as an alpha (.alpha.) chain of a
TCR, a beta (.beta.) chain of a TCR, a gamma (.gamma.) chain of a
TCR, a delta (.delta.) chain of a TCR, or a combination thereof.
The polypeptides of the inventive TCR can comprise any amino acid
sequence, provided that the TCR has antigenic specificity for
MAGE-A3 in the context of HLA-DP.beta.1*04.
[0029] In an embodiment of the invention, the TCR comprises two
polypeptide chains, each of which comprises a variable region
comprising a complementarity determining region (CDR)1, a CDR2, and
a CDR3 of a TCR. In an embodiment of the invention, the TCR
comprises a first polypeptide chain comprising a CDR1 comprising
the amino acid sequence of SEQ ID NO: 3 or 13 (CDR1 of .alpha.
chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 4
or 14 (CDR2 of .alpha. chain), and a CDR3 comprising the amino acid
sequence of SEQ ID NO: 5 or 15 (CDR3 of .alpha. chain), and a
second polypeptide chain comprising a CDR1 comprising the amino
acid sequence of SEQ ID NO: 6 or 16 (CDR1 of .beta. chain), a CDR2
comprising the amino acid sequence of SEQ ID NO: 7 or 17 (CDR2 of
.beta. chain), and a CDR3 comprising the amino acid sequence of SEQ
ID NO: 8 or 18 (CDR3 of .beta. chain). In this regard, the
inventive TCR can comprise any one or more of the amino acid
sequences selected from the group consisting of any one or more of
SEQ ID NOs: 3-5, 6-8, 13-15, and 16-18. Preferably the TCR
comprises the amino acid sequences of SEQ ID NOs: 3-8 or 13-18.
More preferably the TCR comprises the amino acid sequences of SEQ
ID NOs: 3-8.
[0030] Alternatively or additionally, the TCR can comprise an amino
acid sequence of a variable region of a TCR comprising the CDRs set
forth above. In this regard, the TCR can comprise the amino acid
sequence of SEQ ID NO: 9 or 19 (the variable region of an .alpha.
chain) or 10 or 20 (the variable region of a .beta. chain), both
SEQ ID NOs: 9 and 10 or both SEQ ID NOs: 19 and 20. Preferably, the
inventive TCR comprises the amino acid sequences of both SEQ ID
NOs: 9 and 10.
[0031] Alternatively or additionally, the TCR can comprise an
.alpha. chain of a TCR and a .beta. chain of a TCR. Each of the
.alpha. chain and .beta. chain of the inventive TCR can
independently comprise any amino acid sequence. Preferably, the
.alpha. chain comprises the variable region of an .alpha. chain as
set forth above. In this regard, the inventive TCR can comprise the
amino acid sequence of SEQ ID NO: 11 or 21. An .alpha. chain of
this type can be paired with any .beta. chain of a TCR. Preferably,
the .beta. chain of the inventive TCR comprises the variable region
of a .beta. chain as set forth above. In this regard, the inventive
TCR can comprise the amino acid sequence of SEQ ID NO: 12 or 22.
The inventive TCR, therefore, can comprise the amino acid sequence
of SEQ ID NO: 11, 12, 21, or 22, both SEQ ID NOs: 11 and 12 or both
SEQ ID NOs: 21 and 22. Preferably, the inventive TCR comprises the
amino acid sequences of both SEQ ID NOs: 11 and 12.
[0032] Included in the scope of the invention are functional
variants of the inventive TCRs described herein. The term
"functional variant" as used herein refers to a TCR, polypeptide,
or protein having substantial or significant sequence identity or
similarity to a parent TCR, polypeptide, or protein, which
functional variant retains the biological activity of the TCR,
polypeptide, or protein of which it is a variant. Functional
variants encompass, for example, those variants of the TCR,
polypeptide, or protein described herein (the parent TCR,
polypeptide, or protein) that retain the ability to specifically
bind to MAGE-A3 and/or MAGE-A6 for which the parent TCR has
antigenic specificity or to which the parent polypeptide or protein
specifically binds, to a similar extent, the same extent, or to a
higher extent, as the parent TCR, polypeptide, or protein. In
reference to the parent TCR, polypeptide, or protein, the
functional variant can, for instance, be at least about 30%, 50%,
75%, 80%, 90%, 95%, 96%, 97%, 98%, 99% or more identical in amino
acid sequence to the parent TCR, polypeptide, or protein.
[0033] The functional variant can, for example, comprise the amino
acid sequence of the parent TCR, polypeptide, or protein with at
least one conservative amino acid substitution. Conservative amino
acid substitutions are known in the art, and include amino acid
substitutions in which one amino acid having certain physical
and/or chemical properties is exchanged for another amino acid that
has the same chemical or physical properties. For instance, the
conservative amino acid substitution can be an acidic amino acid
substituted for another acidic amino acid (e.g., Asp or Glu), an
amino acid with a nonpolar side chain substituted for another amino
acid with a nonpolar side chain (e.g., Ala, Gly, Val, Ile, Leu,
Met, Phe, Pro, Trp, Val, etc.), a basic amino acid substituted for
another basic amino acid (Lys, Arg, etc.), an amino acid with a
polar side chain substituted for another amino acid with a polar
side chain (Asn, Cys, Gln, Ser, Thr, Tyr, etc.), etc.
[0034] Alternatively or additionally, the functional variants can
comprise the amino acid sequence of the parent TCR, polypeptide, or
protein with at least one non-conservative amino acid substitution.
In this case, it is preferable for the non-conservative amino acid
substitution to not interfere with or inhibit the biological
activity of the functional variant. Preferably, the
non-conservative amino acid substitution enhances the biological
activity of the functional variant, such that the biological
activity of the functional variant is increased as compared to the
parent TCR, polypeptide, or protein.
[0035] In this regard, an embodiment of the invention provides an
isolated or purified TCR comprising (a) SEQ ID NOs: 3-8, (b) SEQ ID
NOs: 21-22, or a functional variant of (a) or (b), wherein the
functional variant comprises (a) or (b) with at least one amino
acid substitution in any one or more of (a) or any one or more of
(b), and the functional variant has antigenic specificity for
MAGE-A3 in the context of HLA-DP.beta.1*04. Preferably, the amino
acid substitution is located in a CDR3 region of the alpha or beta
chain, preferably in the CDR3 region of the alpha chain. In some
embodiments, the functional variant (or functional portions
thereof) provide an increased reactivity against MAGE-A3 as
compared to the parent TCR amino acid sequence. In general, the
substituted .alpha. chain amino acid sequences SEQ ID NOs: 29, 31,
and 33 correspond with all or portions of the native, unsubstituted
SEQ ID NO: 11 (TCR .alpha. chain), with SEQ ID NOs: 29, 31, and 33
having at least one substitution when compared to SEQ ID NO: 11.
Preferably, one or more of the native Ser116, Ser117, Glyl18, and
Thr119 is substituted. Likewise, the substituted .beta. chain amino
acid sequences SEQ ID NOs: 30, 32, and 34 correspond with all or
portions of the native, unsubstituted SEQ ID NO: 12 (TCR .beta.
chain), with SEQ ID NOs: 30, 32, and 34 having at least one
substitution when compared to SEQ ID NO: 12. Preferably, one or
more of the native Arg115, Thr116, Glyl17, and Pro118 is
substituted.
[0036] In particular, the invention provides a functional variant
of a TCR comprising (i) SEQ ID NO: 29, wherein Xaa4 is Ser, Ala,
Leu, Ile, Val, or Met; Xaa5 is Ser, Ala, Leu, Ile, Val, or Met;
Xaa6 is Gly, Ala, Leu, Ile, Val, or Met; and Xaa7 is Thr, Ala, Leu,
Ile, Val, or Met and/or (ii) SEQ ID NO: 30, wherein Xaa4 is Arg,
Ala, Leu, Ile, Val, or Met; Xaa5 is Thr, Ala, Leu, Ile, Val, or
Met; Xaa6 is Gly, Ala, Leu, Ile, Val, or Met; and Xaa7 is Pro, Ala,
Leu, Ile, Val, or Met. SEQ ID NO: 29 generally corresponds to
positions 113-123 of the native, unsubstituted SEQ ID NO: 11 with
the exception that in SEQ ID NO: 29, one or more of Ser4, Ser5,
Gly6, and Thr7 is substituted. Preferably, the functional variant
comprises (a) SEQ ID NO: 29, wherein Xaa4 is Ala, Xaa5 is Ser, Xaa6
is Gly, and Xaa7 is Thr, or (b) SEQ ID NO: 29, wherein Xaa4 is Ser,
Xaa5 is Ala, Xaa6 is Gly, and Xaa7 is Thr. Although in some
embodiments, SEQ ID NO: 29 may comprise wild-type CDR3.alpha. SEQ
ID NO: 5, preferably, SEQ ID NO: 29 does not comprise SEQ ID NO: 5.
SEQ ID NO: 30 generally corresponds to positions 112-126 of the
native, unsubstituted SEQ ID NO: 12 with the exception that in SEQ
ID NO: 30, one or more of Arg4, Thr5, Gly6, and Pro7 is
substituted. Although in some embodiments, SEQ ID NO: 30 may
comprise wild-type CDR3.beta. SEQ ID NO: 8, preferably, SEQ ID NO:
30 does not comprise SEQ ID NO: 8.
[0037] The invention also provides a functional variant of a TCR
comprising (i) SEQ ID NO: 31, wherein Xaa116 is Ser, Ala, Leu, Ile,
Val, or Met; Xaa117 is Ser, Ala, Leu, Ile, Val, or Met; Xaa1118 is
Gly, Ala, Leu, Ile, Val, or Met; and Xaa119 is Thr, Ala, Leu, Ile,
Val, or Met; and/or (ii) SEQ ID NO: 32, wherein Xaa115 is Arg, Ala,
Leu, Ile, Val, or Met; Xaa116 is Thr, Ala, Leu, Ile, Val, or Met;
Xaa117 is Gly, Ala, Leu, Ile, Val, or Met; and Xaa118 is Pro, Ala,
Leu, Ile, Val, or Met. SEQ ID NO: 31 generally corresponds to
positions 1-134 of the native, unsubstituted SEQ ID NO: 11 with the
exception that in SEQ ID NO: 31, one or more of one or more of
Ser116, Ser117, Glyl18, and Thr119 is substituted. Preferably, the
functional variant comprises (a) SEQ ID NO: 31, wherein Xaa116 is
Ala, Xaa117 is Ser, Xaa118 is Gly, and Xaa119 is Thr, or (b) SEQ ID
NO: 31, wherein Xaa116 is Ser, Xaa117 is Ala, Xaa118 is Gly, and
Xaa119 is Thr. Although in some embodiments, SEQ ID NO: 31 may
comprise wild-type CDR3a SEQ ID NO: 5, preferably, SEQ ID NO: 31
does not comprise SEQ ID NO: 5. SEQ ID NO: 32 generally corresponds
to positions 1-137 of the native, unsubstituted SEQ ID NO: 12 with
the exception that in SEQ ID NO: 32, one or more of one or more of
Arg115, Thr116, Glyl17, and Pro118 is substituted. Although in some
embodiments, SEQ ID NO: 32 may comprise wild-type CDR3.beta. SEQ ID
NO: 8, preferably, SEQ ID NO: 32 does not comprise SEQ ID NO:
8.
[0038] Also provided by the invention is functional variant of a
TCR comprising (i) SEQ ID NO: 33, wherein Xaa116 is Ser, Ala, Leu,
Ile, Val, or Met; Xaa117 is Ser, Ala, Leu, Ile, Val, or Met; Xaa118
is Gly, Ala, Leu, Ile, Val, or Met; and Xaa119 is Thr, Ala, Leu,
Ile, Val, or Met; and/or (ii) SEQ ID NO: 34, wherein Xaa115 is Arg,
Ala, Leu, Ile, Val, or Met; Xaa116 is Thr, Ala, Leu, Ile, Val, or
Met; Xaa117 is Gly, Ala, Leu, Ile, Val, or Met; and Xaa118 is Pro,
Ala, Leu, Ile, Val, or Met. SEQ ID NO: 33 generally corresponds to
positions 1-275 of the native, unsubstituted SEQ ID NO: 11 with the
exception that in SEQ ID NO: 33, one or more of one or more of
Ser116, Ser117, Glyl18, and Thr119 is substituted. Preferably, the
functional variant comprises (a) SEQ ID NO: 33, wherein Xaa116 is
Ala, Xaa117 is Ser, Xaa118 is Gly, and Xaa119 is Thr, or (b) SEQ ID
NO: 33, wherein Xaa116 is Ser, Xaa117 is Ala, Xaa118 is Gly, and
Xaa119 is Thr. Although in some embodiments, SEQ ID NO: 33 may
comprise wild-type CDR3.alpha. SEQ ID NO: 5, preferably, SEQ ID NO:
33 does not comprise SEQ ID NO: 5. SEQ ID NO: 34 generally
corresponds to positions 1-313 of the native, unsubstituted SEQ ID
NO: 12 with the exception that in SEQ ID NO: 34, one or more of one
or more of Arg115, Thr116, Glyl17, and Pro118 is substituted.
Although in some embodiments, SEQ ID NO: 34 may comprise wild-type
CDR3.beta. SEQ ID NO: 8, preferably, SEQ ID NO: 34 does not
comprise SEQ ID NO: 8.
[0039] Like the TCRs of the invention, the functional variants
described herein comprise two polypeptide chains, each of which
comprises a variable region comprising a CDR1, a CDR2, and a CDR3
of a TCR. Preferably, the first polypeptide chain comprises a CDR1
comprising the amino acid sequence of SEQ ID NO: 3 (CDR1 of .alpha.
chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 4
(CDR2 of .alpha. chain), and a substituted CDR3 comprising the
amino acid sequence of SEQ ID NO: 29 (substituted CDR3 of .alpha.
chain), and the second polypeptide chain comprises a CDR1
comprising the amino acid sequence of SEQ ID NO: 6 (CDR1 of .beta.
chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 7
(CDR2 of .beta. chain), and a CDR3 comprising the amino acid
sequence of SEQ ID NO: 8 (CDR3 of .beta. chain). In another
embodiment, the first polypeptide chain comprises a CDR1 comprising
the amino acid sequence of SEQ ID NO: 3 (CDR1 of .alpha. chain), a
CDR2 comprising the amino acid sequence of SEQ ID NO: 4 (CDR2 of
.alpha. chain), and a CDR3 comprising the amino acid sequence of
SEQ ID NO: 5 (CDR3 of .alpha. chain), and the second polypeptide
chain comprises a CDR1 comprising the amino acid sequence of SEQ ID
NO: 6 (CDR1 of .beta. chain), a CDR2 comprising the amino acid
sequence of SEQ ID NO: 7 (CDR2 of .beta. chain), and a substituted
CDR3 comprising the amino acid sequence of SEQ ID NO: 30
(substituted CDR3 of .beta. chain). In this regard, the inventive
functional variant of a TCR can comprise the amino acid sequences
selected from the group consisting of SEQ ID NOs: 3-5; SEQ ID NOs:
3-4 and 29; SEQ ID NOs: 6-8; and SEQ ID NOs: 6-7 and 30. Preferably
the functional variant of a TCR comprises the amino acid sequences
of SEQ ID NOs: 3-4, 29, and 6-8; SEQ ID NOs: 3-7 and 30; or SEQ ID
NOs: 3-4, 29, 6-7, and 30. More preferably, the functional variant
of a TCR comprises the amino acid sequences of SEQ ID NOs: 3-4, 29,
and 6-8.
[0040] Alternatively or additionally, the functional variant of a
TCR can comprise a substituted amino acid sequence of a variable
region of a TCR comprising the CDRs set forth above. In this
regard, the TCR can comprise the substituted amino acid sequence of
SEQ ID NO: 31 (the substituted variable region of an .alpha.
chain), 10 (the variable region of a .beta. chain), both SEQ ID
NOs: 31 and 10, the substituted amino acid sequence of SEQ ID NO:
32 (the substituted variable region of an .beta. chain), 9 (the
variable region of an .alpha. chain), both SEQ ID NOs: 9 and 32, or
both SEQ ID NOs: 31 and 32. Preferably, the inventive functional
variant of a TCR comprises the amino acid sequences of SEQ ID NOs:
31 and 10 or SEQ ID NOs: 32 and 9. More preferably, the inventive
functional variant of a TCR comprises the amino acid sequences of
SEQ ID NOs: 31 and 10.
[0041] Alternatively or additionally, the functional variant of a
TCR can comprise a substituted .alpha. chain of a TCR and a .beta.
chain of a TCR. Each of the .alpha. chain and .beta. chain of the
inventive TCR can independently comprise any amino acid sequence.
Preferably, the substituted .alpha. chain comprises a substituted
variable region of an .alpha. chain as set forth above. In this
regard, the inventive substituted .alpha. chain of the TCR can
comprise the amino acid sequence of SEQ ID NO: 33. An inventive
substituted .alpha. chain of this type can be paired with any
.beta. chain of a TCR. Preferably, the .beta. chain of the
inventive TCR comprises the variable region of a .beta. chain as
set forth above. In this regard, the inventive TCR can comprise the
amino acid sequence of SEQ ID NO: 12 or the substituted amino acid
sequence SEQ ID NO: 34. An inventive substituted .beta. chain of
this type can be paired with any .alpha. chain of a TCR. In this
regard, the inventive TCR can comprise the amino acid sequence of
SEQ ID NO: 11 or 33. The inventive functional variant of a TCR,
therefore, can comprise the amino acid sequence of SEQ ID NO: 11,
12, 33, 34, both SEQ ID NOs: 33 and 34; both SEQ ID NOs: 11 and 34;
or both SEQ ID NOs: 12 and 33. Preferably, the inventive functional
variant of a TCR comprises the amino acid sequences of SEQ ID NOs:
11 and 34 or SEQ ID NOs: 12 and 33. More preferably, the functional
variant of a TCR comprises the amino acid sequences of SEQ ID NOs:
12 and 33.
[0042] In an embodiment of the invention, the TCR (or functional
variant thereof) may comprise a human constant region. In this
regard, the TCR (or functional variant thereof) can comprise a
human constant region comprising SEQ ID NO: 23 or 35 (human
constant region of an .alpha. chain), SEQ ID NO: 24 or 36 (human
constant region of .beta. chain), both SEQ ID NOs: 23 and 24, or
both SEQ ID NOs: 35 and 36. Preferably, the TCR (or functional
variant thereof) comprises both SEQ ID NOs: 23 and 24.
[0043] In another embodiment of the invention, the TCR (or
functional variant thereof) can comprise a human/mouse chimeric TCR
(or functional variant thereof). In this regard, the TCR (or
functional variant thereof) can comprise a mouse constant region
comprising SEQ ID NO: 25 (mouse constant region of an .alpha.
chain), SEQ ID NO: 26 (mouse constant region of .beta. chain), or
both SEQ ID NOs: 25 and 26. Preferably, the TCR (or functional
variant thereof) comprises both SEQ ID NOs: 25 and 26.
[0044] The inventive human/mouse chimeric TCR (or functional
variant or functional portion thereof) can comprise any of the CDRs
set forth above. In this regard, the inventive human/mouse chimeric
TCR (or functional variant or functional portion thereof) can
comprise the amino acid sequences selected from the group
consisting of SEQ ID NOs: 3-5; SEQ ID NOs: 13-15; SEQ ID NOs:
16-18; SEQ ID NOs: 3-4 and 29; SEQ ID NOs: 6-8; and SEQ ID NOs: 6-7
and 30. Preferably the human/mouse chimeric TCR (or functional
variant or functional portion thereof) comprises the amino acid
sequences of SEQ ID NOs: 3-8; SEQ ID NOs: 13-18; SEQ ID NOs: 3-4,
29, and 6-8; SEQ ID NOs: 3-7 and 30; or SEQ ID NOs: 3-4, 29, 6-7,
and 30. More preferably, the human/mouse chimeric TCR (or
functional variant or functional portion thereof) comprises the
amino acid sequences of SEQ ID NOs: 3-4, 29, and 6-8 or SEQ ID NOs:
3-8.
[0045] Alternatively or additionally, the human/mouse chimeric TCR
(or functional variant or functional portion thereof) can comprise
any of the variable regions set forth above. In this regard, the
inventive human/mouse chimeric TCR (or functional variant or
functional portion thereof) can comprise the substituted amino acid
sequence of SEQ ID NO: 31 (the substituted variable region of an
.alpha. chain), SEQ ID NO: 10 or 20 (the variable region of a
.beta. chain), the substituted amino acid sequence of SEQ ID NO: 32
(the substituted variable region of an .beta. chain), SEQ ID NO: 9
or 19 (the variable region of an .alpha. chain), both SEQ ID NOs: 9
and 32, both SEQ ID NOs: 31 and 32, both SEQ ID NOs: 31 and 10,
both SEQ ID NOs: 9 and 10, or both SEQ ID NOs: 19 and 20.
Preferably, the inventive human/mouse chimeric TCR (or functional
variant or functional portion thereof) comprises the amino acid
sequences of SEQ ID NOs: 31 and 10, SEQ ID NOs: 9 and 10, or SEQ ID
NOs: 32 and 9. More preferably, the inventive functional variant or
functional portion of a TCR comprises the amino acid sequences of
SEQ ID NOs: 31 and 10 or SEQ ID NOs: 9 and 10.
[0046] Alternatively or additionally, the human/mouse chimeric TCR
(or functional variant or functional portion thereof) can comprise
an .alpha. chain of a TCR (or functional variant or functional
portion thereof) and a .beta. chain of a TCR (or functional variant
or functional portion thereof). Each of the .alpha. chain and
.beta. chain of the inventive human/mouse chimeric TCR (or
functional variant or functional portion thereof) can independently
comprise any amino acid sequence. Preferably, the .alpha. chain
comprises the variable region of an .alpha. chain as set forth
above. In this regard, the inventive human/mouse chimeric TCR (or
functional variant or functional portion thereof) can comprise the
amino acid sequence of SEQ ID NO: 27. An inventive human/mouse
chimeric TCR (or functional variant or functional portion thereof)
of this type can be paired with any .beta. chain of a TCR (or
functional variant or functional portion thereof). Preferably, the
.beta. chain of the inventive human/mouse chimeric TCR (or
functional variant or functional portion thereof) comprises the
variable region of a .beta. chain as set forth above. In this
regard, the inventive human/mouse chimeric TCR (or functional
variant or functional portion thereof) can comprise the amino acid
sequence of SEQ ID NO: 28. The inventive human/mouse chimeric TCR
(or functional variant or functional portion thereof), therefore,
can comprise the amino acid sequence of SEQ ID NO: 27 or 28, or
both SEQ ID NOs: 27 and 28. Preferably, the inventive TCR comprises
the amino acid sequences of SEQ ID NOs: 27 and 28.
[0047] Also provided by the invention is a polypeptide comprising a
functional portion of any of the TCRs or functional variants
described herein. The term "polypeptide" as used herein includes
oligopeptides and refers to a single chain of amino acids connected
by one or more peptide bonds.
[0048] With respect to the inventive polypeptides, the functional
portion can be any portion comprising contiguous amino acids of the
TCR (or functional variant thereof) of which it is a part, provided
that the functional portion specifically binds to MAGE-A3 and/or
MAGE-A6. The term "functional portion" when used in reference to a
TCR (or functional variant thereof) refers to any part or fragment
of the TCR (or functional variant thereof) of the invention, which
part or fragment retains the biological activity of the TCR (or
functional variant thereof) of which it is a part (the parent TCR
or parent functional variant thereof). Functional portions
encompass, for example, those parts of a TCR (or functional variant
thereof) that retain the ability to specifically bind to MAGE-A3
(e.g., in an HLA-DP.beta.1*04-dependent manner) or MAGE-A6, or
detect, treat, or prevent cancer, to a similar extent, the same
extent, or to a higher extent, as the parent TCR (or functional
variant thereof). In reference to the parent TCR (or functional
variant thereof), the functional portion can comprise, for
instance, about 10%, 25%, 30%, 50%, 68%, 80%, 90%, 95%, or more, of
the parent TCR (or functional variant thereof).
[0049] The functional portion can comprise additional amino acids
at the amino or carboxy terminus of the portion, or at both
termini, which additional amino acids are not found in the amino
acid sequence of the parent TCR or functional variant thereof.
Desirably, the additional amino acids do not interfere with the
biological function of the functional portion, e.g., specifically
binding to MAGE-A3 and/or MAGE-A6; and/or having the ability to
detect cancer, treat or prevent cancer, etc. More desirably, the
additional amino acids enhance the biological activity, as compared
to the biological activity of the parent TCR or functional variant
thereof
[0050] The polypeptide can comprise a functional portion of either
or both of the .alpha. and .beta. chains of the TCRs or functional
variant thereof of the invention, such as a functional portion
comprising one of more of CDR1, CDR2, and CDR3 of the variable
region(s) of the .alpha. chain and/or .beta. chain of a TCR or
functional variant thereof of the invention. In this regard, the
polypeptide can comprise a functional portion comprising the amino
acid sequence of SEQ ID NO: 3 or 13 (CDR1 of .alpha. chain), 4 or
14 (CDR2 of .alpha. chain), 5, 15, or 29 (CDR3 of .alpha. chain), 6
or 16 (CDR1 of .beta. chain), 7 or 17 (CDR2 of .beta. chain), 8,
18, or 30 (CDR3 of .beta. chain), or a combination thereof.
Preferably, the inventive polypeptide comprises a functional
portion comprising SEQ ID NOs: 3-5; 3-4 and 29; 6-8; 6-7 and 30;
13-15; 16-18; all of SEQ ID NOs: 3-8; all of SEQ ID NOs: 13-18; all
of SEQ ID NOs: 3-4, 29, and 6-8; all of SEQ ID NOs: 3-7 and 30; or
all of SEQ ID NOs: 3-4, 29, 6-7, and 30. More preferably, the
polypeptide comprises a functional portion comprising the amino
acid sequences of all of SEQ ID NOs: 3-8 or all of SEQ ID NOs: 3-4,
29, and 6-8.
[0051] Alternatively or additionally, the inventive polypeptide can
comprise, for instance, the variable region of the inventive TCR or
functional variant thereof comprising a combination of the CDR
regions set forth above. In this regard, the polypeptide can
comprise the amino acid sequence of SEQ ID NO: 9, 19, or 31 (the
variable region of an .alpha. chain), SEQ ID NO: 10, 20, or 32 (the
variable region of a .beta. chain), both SEQ ID NOs: 9 and 10, both
SEQ ID NOs: 19 and 20; both SEQ ID NOs: 31 and 32; both SEQ ID NOs:
9 and 32; or both SEQ ID NOs: 10 and 31. Preferably, the
polypeptide comprises the amino acid sequences of both SEQ ID NOs:
9 and 10 or both SEQ ID NOs: 10 and 31.
[0052] Alternatively or additionally, the inventive polypeptide can
comprise the entire length of an a or 13 chain of one of the TCRs
or functional variant thereof described herein. In this regard, the
inventive polypeptide can comprise an amino acid sequence of SEQ ID
NOs: 11, 12, 21, 22, 27, 28, 33, or 34. Alternatively, the
polypeptide of the invention can comprise .alpha. and .beta. chains
of the TCRs or functional variants thereof described herein. For
example, the inventive polypeptide can comprise the amino acid
sequences of both SEQ ID NOs: 11 and 12, both SEQ ID NOs: 21 and
22, both SEQ ID NOs: 33 and 34, both SEQ ID NOs: 11 and 34, both
SEQ ID NOs: 12 and 33, or both SEQ ID NOs: 27 and 28. Preferably,
the polypeptide comprises the amino acid sequences of both SEQ ID
NOs: 11 and 12, both SEQ ID NOs: 33 and 12, or both SEQ ID NOs: 27
and 28.
[0053] The invention further provides a protein comprising at least
one of the polypeptides described herein. By "protein" is meant a
molecule comprising one or more polypeptide chains.
[0054] In an embodiment, the protein of the invention can comprise
a first polypeptide chain comprising the amino acid sequences of
SEQ ID NOs: 3-5, SEQ ID NOs: 13-15, or SEQ ID NOs: 3-4 and 29 and a
second polypeptide chain comprising the amino acid sequence of SEQ
ID NOs: 6-8, SEQ ID NOs: 16-18, or SEQ ID NOs: 6-7 and 30.
Alternatively or additionally, the protein of the invention can
comprise a first polypeptide chain comprising the amino acid
sequence of SEQ ID NO: 9, 19, or 31 and a second polypeptide chain
comprising the amino acid sequence of SEQ ID NO: 10, 20, or 32. The
protein of the invention can, for example, comprise a first
polypeptide chain comprising the amino acid sequence of SEQ ID NO:
11, 21, 27, or 33 and a second polypeptide chain comprising the
amino acid sequence of SEQ ID NO: 12, 22, 28, or 34. In this
instance, the protein of the invention can be a TCR. Alternatively,
if, for example, the protein comprises a single polypeptide chain
comprising SEQ ID NO: 11, 21, 27, or 33 and SEQ ID NO: 12, 22, 28,
or 34, or if the first and/or second polypeptide chain(s) of the
protein further comprise(s) other amino acid sequences, e.g., an
amino acid sequence encoding an immunoglobulin or a portion
thereof, then the inventive protein can be a fusion protein. In
this regard, the invention also provides a fusion protein
comprising at least one of the inventive polypeptides described
herein along with at least one other polypeptide. The other
polypeptide can exist as a separate polypeptide of the fusion
protein, or can exist as a polypeptide, which is expressed in frame
(in tandem) with one of the inventive polypeptides described
herein. The other polypeptide can encode any peptidic or
proteinaceous molecule, or a portion thereof, including, but not
limited to an immunoglobulin, CD3, CD4, CD8, an MHC molecule, a CD1
molecule, e.g., CD1a, CD1b, CD1c, CD1d, etc.
[0055] The fusion protein can comprise one or more copies of the
inventive polypeptide and/or one or more copies of the other
polypeptide. For instance, the fusion protein can comprise 1, 2, 3,
4, 5, or more, copies of the inventive polypeptide and/or of the
other polypeptide. Suitable methods of making fusion proteins are
known in the art, and include, for example, recombinant methods.
See, for instance, Choi et al., Mol. Biotechnol. 31: 193-202
(2005).
[0056] In some embodiments of the invention, the TCRs (and
functional portions and functional variants thereof), polypeptides,
and proteins of the invention may be expressed as a single protein
comprising a linker peptide linking the .alpha. chain and the
.beta. chain. In this regard, the TCRs (and functional variants and
functional portions thereof), polypeptides, and proteins of the
invention comprising SEQ ID NO: 11, 21, 27, or 33 and SEQ ID NO:
12, 22, 28, or 34 may further comprise a linker peptide. The linker
peptide may advantageously facilitate the expression of a
recombinant TCR (including functional portions and functional
variants thereof), polypeptide, and/or protein in a host cell. Upon
expression of the construct including the linker peptide by a host
cell, the linker peptide may be cleaved, resulting in separated
.alpha. and .beta. chains.
[0057] The protein of the invention can be a recombinant antibody
comprising at least one of the inventive polypeptides described
herein. As used herein, "recombinant antibody" refers to a
recombinant (e.g., genetically engineered) protein comprising at
least one of the polypeptides of the invention and a polypeptide
chain of an antibody, or a portion thereof. The polypeptide of an
antibody, or portion thereof, can be a heavy chain, a light chain,
a variable or constant region of a heavy or light chain, a single
chain variable fragment (scFv), or an Fc, Fab, or F(ab)2' fragment
of an antibody, etc. The polypeptide chain of an antibody, or
portion thereof, can exist as a separate polypeptide of the
recombinant antibody. Alternatively, the polypeptide chain of an
antibody, or portion thereof, can exist as a polypeptide, which is
expressed in frame (in tandem) with the polypeptide of the
invention. The polypeptide of an antibody, or portion thereof, can
be a polypeptide of any antibody or any antibody fragment,
including any of the antibodies and antibody fragments described
herein.
[0058] The TCR (or functional variant thereof), polypeptide, or
protein can consist essentially of the specified amino acid
sequence or sequences described herein, such that other components
of the TCR (or functional variant thereof), polypeptide, or
protein, e.g., other amino acids, do not materially change the
biological activity of the TCR (or functional variant thereof),
polypeptide, or protein. In this regard, the inventive TCR (or
functional variant thereof), polypeptide, or protein can, for
example, consist essentially of the amino acid sequence of SEQ ID
NO: 11, 12, 21, 22, 27, 28, 33, and 34, both SEQ ID NOs: 11 and 12,
both SEQ ID NOs: 21 and 22, both SEQ ID NOs: 27 and 28, both SEQ ID
NOs: 33 and 34, both SEQ ID NOs: 11 and 34, or both SEQ ID NOs: 12
and 33. Also, for instance, the inventive TCRs (including
functional variants thereof), polypeptides, or proteins can consist
essentially of the amino acid sequence(s) of SEQ ID NO: 9, 10, 19,
20, 31, 32, both SEQ ID NOs: 9 and 10, both SEQ ID NOs: 19 and 20,
both SEQ ID NOs: 31 and 32, both SEQ ID NOs: 9 and 32, both SEQ ID
NOs: 10 and 31. Furthermore, the inventive TCRs (including
functional variants thereof), polypeptides, or proteins can consist
essentially of the amino acid sequence of SEQ ID NO: 3 or 13 (CDR1
of .alpha. chain), SEQ ID NO: 4 or 14 (CDR2 of .alpha. chain), SEQ
ID NO: 5, 15, or 29 (CDR3 of .alpha. chain), SEQ ID NO: 6 or 16
(CDR1 of .beta. chain), SEQ ID NO: 7 or 17 (CDR2 of .beta. chain),
SEQ ID NO: 8, 18, or 30 (CDR3 of .beta. chain), or any combination
thereof, e.g., SEQ ID NOs: 3-5; 6-8; 3-8; 13-15; 16-18; 13-18; 3-4
and 29; 6-7 and 30; 3-4, 29, and 6-8; 3-7 and 30; or 3-4, 29, 6-7,
and 30.
[0059] The TCRs, polypeptides, and proteins of the invention
(including functional variants thereof) can be of any length, i.e.,
can comprise any number of amino acids, provided that the TCRs,
polypeptides, or proteins (or functional variants thereof) retain
their biological activity, e.g., the ability to specifically bind
to MAGE-A3 and/or MAGE-A6; detect cancer in a mammal; or treat or
prevent cancer in a mammal, etc. For example, the polypeptide can
be in the range of from about 50 to about 5000 amino acids long,
such as 50, 70, 75, 100, 125, 150, 175, 200, 300, 400, 500, 600,
700, 800, 900, 1000 or more amino acids in length. In this regard,
the polypeptides of the invention also include oligopeptides.
[0060] The TCRs, polypeptides, and proteins of the invention
(including functional variants thereof) of the invention can
comprise synthetic amino acids in place of one or more
naturally-occurring amino acids. Such synthetic amino acids are
known in the art, and include, for example, aminocyclohexane
carboxylic acid, norleucine, .alpha.-amino n-decanoic acid,
homoserine, S-acetylaminomethyl-cysteine, trans-3- and
trans-4-hydroxyproline, 4-aminophenylalanine, 4-nitrophenylalanine,
4-chlorophenylalanine, 4-carboxyphenylalanine, .beta.-phenylserine
.beta.-hydroxyphenylalanine, phenylglycine,
.alpha.-naphthylalanine, cyclohexylalanine, cyclohexylglycine,
indoline-2-carboxylic acid,
1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid, aminomalonic
acid, aminomalonic acid monoamide, N'-benzyl-N'-methyl-lysine,
N',N'-dibenzyl-lysine, 6-hydroxylysine, ornithine,
.alpha.-aminocyclopentane carboxylic acid, .alpha.-aminocyclohexane
carboxylic acid, .alpha.-aminocycloheptane carboxylic acid,
.alpha.-(2-amino-2-norbornane)-carboxylic acid,
.alpha.,.gamma.-diaminobutyric acid,
.alpha.,.beta.-diaminopropionic acid, homophenylalanine, and
.alpha.-tert-butylglycine.
[0061] The TCRs, polypeptides, and proteins of the invention
(including functional variants thereof) can be glycosylated,
amidated, carboxylated, phosphorylated, esterified, N-acylated,
cyclized via, e.g., a disulfide bridge, or converted into an acid
addition salt and/or optionally dimerized or polymerized, or
conjugated.
[0062] The TCR, polypeptide, and/or protein of the invention
(including functional variants thereof) can be obtained by methods
known in the art. Suitable methods of de novo synthesizing
polypeptides and proteins are described in references, such as Chan
et al., Fmoc Solid Phase Peptide Synthesis, Oxford University
Press, Oxford, United Kingdom, 2005; Peptide and Protein Drug
Analysis, ed. Reid, R., Marcel Dekker, Inc., 2000; Epitope Mapping,
ed. Westwood et al., Oxford University Press, Oxford, United
Kingdom, 2000; and U.S. Pat. No. 5,449,752. Also, polypeptides and
proteins can be recombinantly produced using the nucleic acids
described herein using standard recombinant methods. See, for
instance, Sambrook et al., Molecular Cloning: A Laboratory Manual,
3.sup.rd ed., Cold Spring Harbor Press, Cold Spring Harbor, N.Y.
2001; and Ausubel et al., Current Protocols in Molecular Biology,
Greene Publishing Associates and John Wiley & Sons, NY, 1994.
Further, some of the TCRs, polypeptides, and proteins of the
invention (including functional variants thereof) can be isolated
and/or purified from a source, such as a plant, a bacterium, an
insect, a mammal, e.g., a rat, a human, etc. Methods of isolation
and purification are well-known in the art. Alternatively, the
TCRs, polypeptides, and/or proteins described herein (including
functional variants thereof) can be commercially synthesized by
companies, such as Synpep (Dublin, Calif.), Peptide Technologies
Corp. (Gaithersburg, Md.), and Multiple Peptide Systems (San Diego,
Calif.). In this respect, the inventive TCRs (including functional
variants thereof), polypeptides, and proteins can be synthetic,
recombinant, isolated, and/or purified.
[0063] Included in the scope of the invention are conjugates, e.g.,
bioconjugates, comprising any of the inventive TCRs, polypeptides,
or proteins (including any of the functional variants thereof),
nucleic acids, recombinant expression vectors, host cells,
populations of host cells, or antibodies, or antigen binding
portions thereof. Conjugates, as well as methods of synthesizing
conjugates in general, are known in the art (See, for instance,
Hudecz, F., Methods Mol. Biol. 298: 209-223 (2005) and Kirin et
al., Inorg Chem. 44(15): 5405-5415 (2005)).
[0064] By "nucleic acid" as used herein includes "polynucleotide,"
"oligonucleotide," and "nucleic acid molecule," and generally means
a polymer of DNA or RNA, which can be single-stranded or
double-stranded, synthesized or obtained (e.g., isolated and/or
purified) from natural sources, which can contain natural,
non-natural or altered nucleotides, and which can contain a
natural, non-natural or altered internucleotide linkage, such as a
phosphoroamidate linkage or a phosphorothioate linkage, instead of
the phosphodiester found between the nucleotides of an unmodified
oligonucleotide. It is generally preferred that the nucleic acid
does not comprise any insertions, deletions, inversions, and/or
substitutions. However, it may be suitable in some instances, as
discussed herein, for the nucleic acid to comprise one or more
insertions, deletions, inversions, and/or substitutions.
[0065] Preferably, the nucleic acids of the invention are
recombinant. As used herein, the term "recombinant" refers to (i)
molecules that are constructed outside living cells by joining
natural or synthetic nucleic acid segments to nucleic acid
molecules that can replicate in a living cell, or (ii) molecules
that result from the replication of those described in (i) above.
For purposes herein, the replication can be in vitro replication or
in vivo replication.
[0066] The nucleic acids can be constructed based on chemical
synthesis and/or enzymatic ligation reactions using procedures
known in the art. See, for example, Sambrook et al., supra, and
Ausubel et al., supra. For example, a nucleic acid can be
chemically synthesized using naturally occurring nucleotides or
variously modified nucleotides designed to increase the biological
stability of the molecules or to increase the physical stability of
the duplex formed upon hybridization (e.g., phosphorothioate
derivatives and acridine substituted nucleotides). Examples of
modified nucleotides that can be used to generate the nucleic acids
include, but are not limited to, 5-fluorouracil, 5-bromouracil,
5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine,
4-acetylcytosine, 5-(carboxyhydroxymethyl) uracil,
5-carboxymethylaminomethyl-2-thiouridine,
5-carboxymethylaminomethyluracil, dihydrouracil,
beta-D-galactosylqueosine, inosine, N.sup.6-isopentenyladenine,
1-methylguanine, 1-methylinosine, 2,2-dimethylguanine,
2-methyladenine, 2-methylguanine, 3-methylcytosine,
5-methylcytosine, N.sup.6-substituted adenine, 7-methylguanine,
5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil,
beta-D-mannosylqueosine, 5'-methoxycarboxymethyluracil,
5-methoxyuracil, 2-methylthio-N.sup.6-isopentenyladenine,
uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine,
2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil,
5-methyluracil, uracil-5-oxyacetic acid methylester,
3-(3-amino-3-N-2-carboxypropyl) uracil, and 2,6-diaminopurine.
Alternatively, one or more of the nucleic acids of the invention
can be purchased from companies, such as Macromolecular Resources
(Fort Collins, Colo.) and Synthegen (Houston, Tex.).
[0067] The nucleic acid can comprise any nucleotide sequence which
encodes any of the TCRs, polypeptides, proteins, or functional
functional variants thereof described herein. For example, the
nucleic acid can comprise, consist, or consist essentially of any
one or more of the nucleotide sequence SEQ ID NOs: 37-44.
[0068] The invention also provides a nucleic acid comprising a
nucleotide sequence which is complementary to the nucleotide
sequence of any of the nucleic acids described herein or a
nucleotide sequence which hybridizes under stringent conditions to
the nucleotide sequence of any of the nucleic acids described
herein.
[0069] The nucleotide sequence which hybridizes under stringent
conditions preferably hybridizes under high stringency conditions.
By "high stringency conditions" is meant that the nucleotide
sequence specifically hybridizes to a target sequence (the
nucleotide sequence of any of the nucleic acids described herein)
in an amount that is detectably stronger than non-specific
hybridization. High stringency conditions include conditions which
would distinguish a polynucleotide with an exact complementary
sequence, or one containing only a few scattered mismatches from a
random sequence that happened to have a few small regions (e.g.,
3-10 bases) that matched the nucleotide sequence. Such small
regions of complementarity are more easily melted than a
full-length complement of 14-17 or more bases, and high stringency
hybridization makes them easily distinguishable. Relatively high
stringency conditions would include, for example, low salt and/or
high temperature conditions, such as provided by about 0.02-0.1 M
NaCl or the equivalent, at temperatures of about 50-70.degree. C.
Such high stringency conditions tolerate little, if any, mismatch
between the nucleotide sequence and the template or target strand,
and are particularly suitable for detecting expression of any of
the inventive TCRs (including functional portions and functional
variants thereof). It is generally appreciated that conditions can
be rendered more stringent by the addition of increasing amounts of
formamide.
[0070] The invention also provides a nucleic acid comprising a
nucleotide sequence that is at least about 70% or more, e.g., about
80%, about 90%, about 91%, about 92%, about 93%, about 94%, about
95%, about 96%, about 97%, about 98%, or about 99% identical to any
of the nucleic acids described herein.
[0071] The nucleic acids of the invention can be incorporated into
a recombinant expression vector. In this regard, the invention
provides recombinant expression vectors comprising any of the
nucleic acids of the invention. For purposes herein, the term
"recombinant expression vector" means a genetically-modified
oligonucleotide or polynucleotide construct that permits the
expression of an mRNA, protein, polypeptide, or peptide by a host
cell, when the construct comprises a nucleotide sequence encoding
the mRNA, protein, polypeptide, or peptide, and the vector is
contacted with the cell under conditions sufficient to have the
mRNA, protein, polypeptide, or peptide expressed within the cell.
The vectors of the invention are not naturally-occurring as a
whole. However, parts of the vectors can be naturally-occurring.
The inventive recombinant expression vectors can comprise any type
of nucleotides, including, but not limited to DNA and RNA, which
can be single-stranded or double-stranded, synthesized or obtained
in part from natural sources, and which can contain natural,
non-natural or altered nucleotides. The recombinant expression
vectors can comprise naturally-occurring, non-naturally-occurring
intemucleotide linkages, or both types of linkages. Preferably, the
non-naturally occurring or altered nucleotides or intemucleotide
linkages does not hinder the transcription or replication of the
vector.
[0072] The recombinant expression vector of the invention can be
any suitable recombinant expression vector, and can be used to
transform or transfect any suitable host cell. Suitable vectors
include those designed for propagation and expansion or for
expression or both, such as plasmids and viruses. The vector can be
selected from the group consisting of the pUC series (Fermentas
Life Sciences), the pBluescript series (Stratagene, LaJolla,
Calif.), the pET series (Novagen, Madison, Wis.), the pGEX series
(Pharmacia Biotech, Uppsala, Sweden), and the pEX series (Clontech,
Palo Alto, Calif.). Bacteriophage vectors, such as .lamda.GT10,
.lamda.GT11, .lamda.ZapII (Stratagene), .lamda.EMBL4, and
.lamda.NM1149, also can be used. Examples of plant expression
vectors include pBI01, pBI101.2, pBI101.3, pBI121 and pBIN19
(Clontech). Examples of animal expression vectors include pEUK-Cl,
pMAM and pMAMneo (Clontech). Preferably, the recombinant expression
vector is a viral vector, e.g., a retroviral vector.
[0073] The recombinant expression vectors of the invention can be
prepared using standard recombinant DNA techniques described in,
for example, Sambrook et al., supra, and Ausubel et al., supra.
Constructs of expression vectors, which are circular or linear, can
be prepared to contain a replication system functional in a
prokaryotic or eukaryotic host cell. Replication systems can be
derived, e.g., from ColEl, 2.mu. plasmid, .lamda., SV40, bovine
papilloma virus, and the like.
[0074] Desirably, the recombinant expression vector comprises
regulatory sequences, such as transcription and translation
initiation and termination codons, which are specific to the type
of host cell (e.g., bacterium, fungus, plant, or animal) into which
the vector is to be introduced, as appropriate and taking into
consideration whether the vector is DNA- or RNA-based.
[0075] The recombinant expression vector can include one or more
marker genes, which allow for selection of transformed or
transfected host cells. Marker genes include biocide resistance,
e.g., resistance to antibiotics, heavy metals, etc.,
complementation in an auxotrophic host cell to provide prototrophy,
and the like. Suitable marker genes for the inventive expression
vectors include, for instance, neomycin/G418 resistance genes,
hygromycin resistance genes, histidinol resistance genes,
tetracycline resistance genes, and ampicillin resistance genes.
[0076] The recombinant expression vector can comprise a native or
nonnative promoter operably linked to the nucleotide sequence
encoding the TCR, polypeptide, or protein (including functional
variants thereof), or to the nucleotide sequence which is
complementary to or which hybridizes to the nucleotide sequence
encoding the TCR, polypeptide, or protein (including functional
variants thereof). The selection of promoters, e.g., strong, weak,
inducible, tissue-specific and developmental-specific, is within
the ordinary skill of the artisan. Similarly, the combining of a
nucleotide sequence with a promoter is also within the skill of the
artisan. The promoter can be a non-viral promoter or a viral
promoter, e.g., a cytomegalovirus (CMV) promoter, an SV40 promoter,
an RSV promoter, and a promoter found in the long-terminal repeat
of the murine stem cell virus.
[0077] The inventive recombinant expression vectors can be designed
for either transient expression, for stable expression, or for
both. Also, the recombinant expression vectors can be made for
constitutive expression or for inducible expression. Further, the
recombinant expression vectors can be made to include a suicide
gene.
[0078] As used herein, the term "suicide gene" refers to a gene
that causes the cell expressing the suicide gene to die. The
suicide gene can be a gene that confers sensitivity to an agent,
e.g., a drug, upon the cell in which the gene is expressed, and
causes the cell to die when the cell is contacted with or exposed
to the agent. Suicide genes are known in the art (see, for example,
Suicide Gene Therapy: Methods and Reviews, Springer, Caroline J.
(Cancer Research UK Centre for Cancer Therapeutics at the Institute
of Cancer Research, Sutton, Surrey, UK), Humana Press, 2004) and
include, for example, the Herpes Simplex Virus (HSV) thymidine
kinase (TK) gene, cytosine daminase, purine nucleoside
phosphorylase, and nitroreductase.
[0079] Another embodiment of the invention further provides a host
cell comprising any of the recombinant expression vectors described
herein. As used herein, the term "host cell" refers to any type of
cell that can contain the inventive recombinant expression vector.
The host cell can be a eukaryotic cell, e.g., plant, animal, fungi,
or algae, or can be a prokaryotic cell, e.g., bacteria or protozoa.
The host cell can be a cultured cell or a primary cell, i.e.,
isolated directly from an organism, e.g., a human. The host cell
can be an adherent cell or a suspended cell, i.e., a cell that
grows in suspension. Suitable host cells are known in the art and
include, for instance, DH5.alpha. E. coli cells, Chinese hamster
ovarian cells, monkey VERO cells, COS cells, HEK293 cells, and the
like. For purposes of amplifying or replicating the recombinant
expression vector, the host cell is preferably a prokaryotic cell,
e.g., a DH5.alpha. cell. For purposes of producing a recombinant
TCR, polypeptide, or protein, the host cell is preferably a
mammalian cell. Most preferably, the host cell is a human cell.
While the host cell can be of any cell type, can originate from any
type of tissue, and can be of any developmental stage, the host
cell preferably is a peripheral blood lymphocyte (PBL) or a
peripheral blood mononuclear cell (PBMC). More preferably, the host
cell is a T cell.
[0080] For purposes herein, the T cell can be any T cell, such as a
cultured T cell, e.g., a primary T cell, or a T cell from a
cultured T cell line, e.g., Jurkat, SupT1, etc., or a T cell
obtained from a mammal. If obtained from a mammal, the T cell can
be obtained from numerous sources, including but not limited to
blood, bone marrow, lymph node, the thymus, or other tissues or
fluids. T cells can also be enriched for or purified. Preferably,
the T cell is a human T cell. More preferably, the T cell is a T
cell isolated from a human. The T cell can be any type of T cell
and can be of any developmental stage, including but not limited
to, CD4.sup.+/CD8.sup.+ double positive T cells, CD.sup.4+ helper T
cells, e.g., Th.sub.1 and Th.sub.2 cells, CD4+ T cells, CD8.sup.+ T
cells (e.g., cytotoxic T cells), tumor infiltrating lymphocytes
(TILs), memory T cells (e.g., central memory T cells and effector
memory T cells), naive T cells, and the like.
[0081] Also provided by the invention is a population of cells
comprising at least one host cell described herein. The population
of cells can be a heterogeneous population comprising the host cell
comprising any of the recombinant expression vectors described, in
addition to at least one other cell, e.g., a host cell (e.g., a T
cell), which does not comprise any of the recombinant expression
vectors, or a cell other than a T cell, e.g., a B cell, a
macrophage, a neutrophil, an erythrocyte, a hepatocyte, an
endothelial cell, an epithelial cells, a muscle cell, a brain cell,
etc. Alternatively, the population of cells can be a substantially
homogeneous population, in which the population comprises mainly of
host cells (e.g., consisting essentially of) comprising the
recombinant expression vector. The population also can be a clonal
population of cells, in which all cells of the population are
clones of a single host cell comprising a recombinant expression
vector, such that all cells of the population comprise the
recombinant expression vector. In one embodiment of the invention,
the population of cells is a clonal population comprising host
cells comprising a recombinant expression vector as described
herein.
[0082] The invention further provides an antibody, or antigen
binding portion thereof, which specifically binds to a functional
portion of any of the TCRs (or functional variant thereof)
described herein. Preferably, the functional portion specifically
binds to the cancer antigen, e.g., the functional portion
comprising the amino acid sequence SEQ ID NO: 3 or 13 (CDR1 of
.alpha. chain), 4 or 14 (CDR2 of .alpha. chain), 5, 15, or 29 (CDR3
of .alpha. chain), 6 or 16 (CDR1 of .beta. chain), 7 or 17 (CDR2 of
.beta. chain), 8, 18, or 30 (CDR3 of .beta. chain), SEQ ID NO: 9,
19, or 31 (variable region of .alpha. chain), SEQ ID NO: 10, 20, or
32 (variable region of .beta. chain), or a combination thereof,
e.g., 3-5; 6-8; 3-8; 13-15; 16-18; 13-18; 3-4 and 29; 6-7 and 30;
3-4, 29, and 6-8; or 3-7 and 30; 3-4, 29, 6-7, and 30. More
preferably, the functional portion comprises the amino acid
sequences of SEQ ID NOs: 3-8 or SEQ ID NOs: 3-4, 29, and 6-8. In a
preferred embodiment, the antibody, or antigen binding portion
thereof, binds to an epitope which is formed by all 6 CDRs (CDR1-3
of the alpha chain and CDR1-3 of the beta chain). The antibody can
be any type of immunoglobulin that is known in the art. For
instance, the antibody can be of any isotype, e.g., IgA, IgD, IgE,
IgG, IgM, etc. The antibody can be monoclonal or polyclonal. The
antibody can be a naturally-occurring antibody, e.g., an antibody
isolated and/or purified from a mammal, e.g., mouse, rabbit, goat,
horse, chicken, hamster, human, etc. Alternatively, the antibody
can be a genetically-engineered antibody, e.g., a humanized
antibody or a chimeric antibody. The antibody can be in monomeric
or polymeric form. Also, the antibody can have any level of
affinity or avidity for the functional portion of the inventive TCR
(or functional variant thereof). Desirably, the antibody is
specific for the functional portion of the inventive TCR (or
functional variants thereof), such that there is minimal
cross-reaction with other peptides or proteins.
[0083] Methods of testing antibodies for the ability to bind to any
functional portion or functional variant of the inventive TCR are
known in the art and include any antibody-antigen binding assay,
such as, for example, radioimmunoassay (RIA), ELISA, Western blot,
immunoprecipitation, and competitive inhibition assays (see, e.g.,
Janeway et al., infra, and U.S. Patent Application Publication No.
2002/0197266 A1).
[0084] Suitable methods of making antibodies are known in the art.
For instance, standard hybridoma methods are described in, e.g.,
Kohler and Milstein, Eur. I Immunol., 5, 511-519 (1976), Harlow and
Lane (eds.), Antibodies: A Laboratory Manual, CSH Press (1988), and
C. A. Janeway et al. (eds.), Immunobiology, 5.sup.th Ed., Garland
Publishing, New York, N.Y. (2001)). Alternatively, other methods,
such as EBV-hybridoma methods (Haskard and Archer, J. Immunol.
Methods, 74(2), 361-67 (1984), and Roder et al., Methods Enzymol.,
121, 140-67 (1986)), and bacteriophage vector expression systems
(see, e.g., Huse et al., Science, 246, 1275-81 (1989)) are known in
the art. Further, methods of producing antibodies in non-human
animals are described in, e.g., U.S. Pat. Nos. 5,545,806,
5,569,825, and 5,714,352, and U.S. Patent Application Publication
No. 2002/0197266 A1.
[0085] Phage display furthermore can be used to generate the
antibody of the invention. In this regard, phage libraries encoding
antigen-binding variable (V) domains of antibodies can be generated
using standard molecular biology and recombinant DNA techniques
(see, e.g., Sambrook et al. (eds.), Molecular Cloning, A Laboratory
Manual, 3.sup.rd Edition, Cold Spring Harbor Laboratory Press, New
York (2001)). Phage encoding a variable region with the desired
specificity are selected for specific binding to the desired
antigen, and a complete or partial antibody is reconstituted
comprising the selected variable domain. Nucleic acid sequences
encoding the reconstituted antibody are introduced into a suitable
cell line, such as a myeloma cell used for hybridoma production,
such that antibodies having the characteristics of monoclonal
antibodies are secreted by the cell (see, e.g., Janeway et al.,
supra, Huse et al., supra, and U.S. Pat. No. 6,265,150).
[0086] Antibodies can be produced by transgenic mice that are
transgenic for specific heavy and light chain immunoglobulin genes.
Such methods are known in the art and described in, for example
U.S. Pat. Nos. 5,545,806 and 5,569,825, and Janeway et al.,
supra.
[0087] Methods for generating humanized antibodies are well known
in the art and are described in detail in, for example, Janeway et
al., supra, U.S. Pat. Nos. 5,225,539, 5,585,089 and 5,693,761,
European Patent No. 0239400 B1, and United Kingdom Patent No.
2188638. Humanized antibodies can also be generated using the
antibody resurfacing technology described in, for example, U.S.
Pat. No. 5,639,641 and Pedersen et al., J. Mol. Biol., 235, 959-973
(1994).
[0088] The invention also provides antigen binding portions of any
of the antibodies described herein. The antigen binding portion can
be any portion that has at least one antigen binding site, such as
Fab, F(ab')2, dsFv, sFv, diabodies, and triabodies.
[0089] A single-chain variable region fragment (sFv) antibody
fragment, which consists of a truncated Fab fragment comprising the
variable (V) domain of an antibody heavy chain linked to a V domain
of a light antibody chain via a synthetic peptide, can be generated
using routine recombinant DNA technology techniques (see, e.g.,
Janeway et al., supra). Similarly, disulfide-stabilized variable
region fragments (dsFv) can be prepared by recombinant DNA
technology (see, e.g., Reiter et al., Protein Engineering, 7,
697-704 (1994)). Antibody fragments of the invention, however, are
not limited to these exemplary types of antibody fragments.
[0090] Also, the antibody, or antigen binding portion thereof, can
be modified to comprise a detectable label, such as, for instance,
a radioisotope, a fluorophore (e.g., fluorescein isothiocyanate
(FITC), phycoerythrin (PE)), an enzyme (e.g., alkaline phosphatase,
horseradish peroxidase), and element particles (e.g., gold
particles).
[0091] The inventive TCRs, polypeptides, proteins, (including
functional variants thereof), nucleic acids, recombinant expression
vectors, host cells (including populations thereof), and antibodies
(including antigen binding portions thereof), can be isolated
and/or purified. The term "isolated" as used herein means having
been removed from its natural environment. The term "purified" as
used herein means having been increased in purity, wherein "purity"
is a relative term, and not to be necessarily construed as absolute
purity. For example, the purity can be at least about 50%, can be
greater than 60%, 70%, 80%, 90%, 95%, or can be 100%.
[0092] The inventive TCRs, polypeptides, proteins (including
functional variants thereof), nucleic acids, recombinant expression
vectors, host cells (including populations thereof), and antibodies
(including antigen binding portions thereof), all of which are
collectively referred to as "inventive TCR materials" hereinafter,
can be formulated into a composition, such as a pharmaceutical
composition. In this regard, the invention provides a
pharmaceutical composition comprising any of the TCRs,
polypeptides, proteins, functional portions, functional variants,
nucleic acids, expression vectors, host cells (including
populations thereof), and antibodies (including antigen binding
portions thereof), and a pharmaceutically acceptable carrier. The
inventive pharmaceutical compositions containing any of the
inventive TCR materials can comprise more than one inventive TCR
material, e.g., a polypeptide and a nucleic acid, or two or more
different TCRs (including functional portions and functional
variants thereof). Alternatively, the pharmaceutical composition
can comprise an inventive TCR material in combination with another
pharmaceutically active agents or drugs, such as a chemotherapeutic
agents, e.g., asparaginase, busulfan, carboplatin, cisplatin,
daunorubicin, doxorubicin, fluorouracil, gemcitabine, hydroxyurea,
methotrexate, paclitaxel, rituximab, vinblastine, vincristine,
etc.
[0093] Preferably, the carrier is a pharmaceutically acceptable
carrier. With respect to pharmaceutical compositions, the carrier
can be any of those conventionally used for the particular
inventive TCR material under consideration. Such pharmaceutically
acceptable carriers are well-known to those skilled in the art and
are readily available to the public. It is preferred that the
pharmaceutically acceptable carrier be one which has no detrimental
side effects or toxicity under the conditions of use.
[0094] The choice of carrier will be determined in part by the
particular inventive TCR material, as well as by the particular
method used to administer the inventive TCR material. Accordingly,
there are a variety of suitable formulations of the pharmaceutical
composition of the invention. Suitable formulations may include any
of those for oral, aerosol, parenteral, subcutaneous, intravenous,
intramuscular, intraarterial, intrathecal, or interperitoneal
administration. More than one route can be used to administer the
inventive TCR materials, and in certain instances, a particular
route can provide a more immediate and more effective response than
another route.
[0095] Preferably, the inventive TCR material is administered by
injection, e.g., intravenously. When the inventive TCR material is
a host cell expressing the inventive TCR (or functional variant
thereof), the pharmaceutically acceptable carrier for the cells for
injection may include any isotonic carrier such as, for example,
normal saline (about 0.90% w/v of NaCl in water, about 300 mOsm/L
NaCl in water, or about 9.0 g NaCl per liter of water), NORMOSOL R
electrolyte solution (Abbott, Chicago, IL), PLASMA-LYTE A (Baxter,
Deerfield, Ill.), about 5% dextrose in water, or Ringer's lactate.
In an embodiment, the pharmaceutically acceptable carrier is
supplemented with human serum albumen.
[0096] In an embodiment of the invention, the pharmaceutical
composition may further comprise MHC Class I restricted TCRs, or
polypeptides, proteins, nucleic acids, or recombinant expression
vectors encoding MHC Class I restricted TCRs, or host cells or
populations of cells expressing MHC Class I restricted TCRs.
Without being bound to a particular theory, it is believed that MHC
Class I restricted CD8+ T cells augment the reactivity of MHC Class
II restricted CD4+ T cells and enhance the ability of the MHC Class
II restricted CD4+ T cells to treat or prevent cancer.
[0097] For purposes of the invention, the amount or dose (e.g.,
numbers of cells when the inventive TCR material is one or more
cells) of the inventive TCR material administered should be
sufficient to effect, e.g., a therapeutic or prophylactic response,
in the subject or animal over a reasonable time frame. For example,
the dose of the inventive TCR material should be sufficient to bind
to a cancer antigen, or detect, treat or prevent cancer in a period
of from about 2 hours or longer, e.g., 12 to 24 or more hours, from
the time of administration. In certain embodiments, the time period
could be even longer. The dose will be determined by the efficacy
of the particular inventive TCR material and the condition of the
animal (e.g., human), as well as the body weight of the animal
(e.g., human) to be treated.
[0098] Many assays for determining an administered dose are known
in the art. For purposes of the invention, an assay, which
comprises comparing the extent to which target cells are lysed or
IFN-.gamma. is secreted by T cells expressing the inventive TCR (or
functional variant or functional portion thereof), polypeptide, or
protein upon administration of a given dose of such T cells to a
mammal among a set of mammals of which is each given a different
dose of the T cells, could be used to determine a starting dose to
be administered to a mammal. The extent to which target cells are
lysed or IFN-.gamma. is secreted upon administration of a certain
dose can be assayed by methods known in the art.
[0099] The dose of the inventive TCR material also will be
determined by the existence, nature and extent of any adverse side
effects that might accompany the administration of a particular
inventive TCR material. Typically, the attending physician will
decide the dosage of the inventive TCR material with which to treat
each individual patient, taking into consideration a variety of
factors, such as age, body weight, general health, diet, sex,
inventive TCR material to be administered, route of administration,
and the severity of the condition being treated. In an embodiment
in which the inventive TCR material is a population of cells, the
number of cells administered per infusion may vary, e.g., from
about 1.times.10.sup.6 to about 1.times.10.sup.11 cells or
more.
[0100] One of ordinary skill in the art will readily appreciate
that the inventive TCR materials of the invention can be modified
in any number of ways, such that the therapeutic or prophylactic
efficacy of the inventive TCR materials is increased through the
modification. For instance, the inventive TCR materials can be
conjugated either directly or indirectly through a bridge to a
targeting moiety. The practice of conjugating compounds, e.g.,
inventive TCR materials, to targeting moieties is known in the art.
See, for instance, Wadwa et al., J. Drug Targeting 3: 111 (1995)
and U.S. Pat. No. 5,087,616. The term "targeting moiety" as used
herein, refers to any molecule or agent that specifically
recognizes and binds to a cell-surface receptor, such that the
targeting moiety directs the delivery of the inventive TCR
materials to a population of cells on which surface the receptor is
expressed. Targeting moieties include, but are not limited to,
antibodies, or fragments thereof, peptides, hormones, growth
factors, cytokines, and any other natural or non-natural ligands,
which bind to cell surface receptors (e.g., Epithelial Growth
Factor Receptor (EGFR), T-cell receptor (TCR), B-cell receptor
(BCR), CD28, Platelet-derived Growth Factor Receptor (PDGF),
nicotinic acetylcholine receptor (nAChR), etc.). The term "bridge"
as used herein, refers to any agent or molecule that links the
inventive TCR materials to the targeting moiety. One of ordinary
skill in the art recognizes that sites on the inventive TCR
materials, which are not necessary for the function of the
inventive TCR materials, are ideal sites for attaching a bridge
and/or a targeting moiety, provided that the bridge and/or
targeting moiety, once attached to the inventive TCR materials,
do(es) not interfere with the function of the inventive TCR
materials, i.e., the ability to bind to MAGE-A3 or MAGE-A6; or to
detect, treat, or prevent cancer.
[0101] It is contemplated that the inventive pharmaceutical
compositions, TCRs (including functional variants thereof),
polypeptides, proteins, nucleic acids, recombinant expression
vectors, host cells, or populations of cells can be used in methods
of treating or preventing cancer. Without being bound to a
particular theory, the inventive TCRs (and functional variants
thereof) are believed to bind specifically to MAGE-A3 and/or
MAGE-A6, such that the TCR (or related inventive polypeptide or
protein and functional variants thereof) when expressed by a cell
is able to mediate an immune response against a target cell
expressing MAGE-A3 or MAGE-A6. In this regard, the invention
provides a method of treating or preventing cancer in a mammal,
comprising administering to the mammal any of the pharmaceutical
compositions, TCRs (and functional variants thereof), polypeptides,
or proteins described herein, any nucleic acid or recombinant
expression vector comprising a nucleotide sequence encoding any of
the TCRs (and functional variants thereof), polypeptides, proteins
described herein, or any host cell or population of cells
comprising a recombinant vector which encodes any of the TCRs (and
functional variants thereof), polypeptides, or proteins described
herein, in an amount effective to treat or prevent cancer in the
mammal.
[0102] In an embodiment of the invention, the inventive methods of
treating or preventing cancer may further comprise co-administering
MHC Class I restricted TCRs, or polypeptides, proteins, nucleic
acids, or recombinant expression vectors encoding MHC Class I
restricted TCRs, or host cells or populations of cells expressing
MHC Class I restricted TCRs, to the mammal.
[0103] The terms "treat," and "prevent" as well as words stemming
therefrom, as used herein, do not necessarily imply 100% or
complete treatment or prevention. Rather, there are varying degrees
of treatment or prevention of which one of ordinary skill in the
art recognizes as having a potential benefit or therapeutic effect.
In this respect, the inventive methods can provide any amount of
any level of treatment or prevention of cancer in a mammal.
Furthermore, the treatment or prevention provided by the inventive
method can include treatment or prevention of one or more
conditions or symptoms of the disease, e.g., cancer, being treated
or prevented. Also, for purposes herein, "prevention" can encompass
delaying the onset of the disease, or a symptom or condition
thereof
[0104] Also provided is a method of detecting the presence of
cancer in a mammal. The method comprises (i) contacting a sample
comprising cells of the cancer with any of the inventive TCRs (and
functional variants thereof), polypeptides, proteins, nucleic
acids, recombinant expression vectors, host cells, populations of
cells, or antibodies, or antigen binding portions thereof,
described herein, thereby forming a complex, and detecting the
complex, wherein detection of the complex is indicative of the
presence of cancer in the mammal.
[0105] With respect to the inventive method of detecting cancer in
a mammal, the sample of cells of the cancer can be a sample
comprising whole cells, lysates thereof, or a fraction of the whole
cell lysates, e.g., a nuclear or cytoplasmic fraction, a whole
protein fraction, or a nucleic acid fraction.
[0106] For purposes of the inventive detecting method, the
contacting can take place in vitro or in vivo with respect to the
mammal. Preferably, the contacting is in vitro.
[0107] Also, detection of the complex can occur through any number
of ways known in the art. For instance, the inventive TCRs (and
functional variants thereof), polypeptides, proteins, nucleic
acids, recombinant expression vectors, host cells, populations of
cells, or antibodies, or antigen binding portions thereof,
described herein, can be labeled with a detectable label such as,
for instance, a radioisotope, a fluorophore (e.g., fluorescein
isothiocyanate (FITC), phycoerythrin (PE)), an enzyme (e.g.,
alkaline phosphatase, horseradish peroxidase), and element
particles (e.g., gold particles).
[0108] For purposes of the inventive methods, wherein host cells or
populations of cells are administered, the cells can be cells that
are allogeneic or autologous to the mammal. Preferably, the cells
are autologous to the mammal.
[0109] With respect to the inventive methods, the cancer can be any
cancer, including any of sarcomas (e.g., synovial sarcoma,
osteogenic sarcoma, leiomyosarcoma uteri, and alveolar
rhabdomyosarcoma), lymphomas (e.g., Hodgkin lymphoma and
non-Hodgkin lymphoma), hepatocellular carcinoma, glioma, head
cancers (e.g., squamous cell carcinoma), neck cancers (e.g.,
squamous cell carcinoma), acute lymphocytic cancer, leukemias
(e.g., acute myeloid leukemia and chronic lymphocytic leukemia),
bone cancer, brain cancer, breast cancer, cancer of the anus, anal
canal, or anorectum, cancer of the eye, cancer of the intrahepatic
bile duct, cancer of the joints, cancer of the neck, gallbladder,
or pleura, cancer of the nose, nasal cavity, or middle ear, cancer
of the oral cavity, cancer of the vulva, chronic myeloid cancer,
colon cancers (e.g., colon carcinoma), esophageal cancer, cervical
cancer, gastric cancer, gastrointestinal carcinoid tumor,
hypopharynx cancer, larynx cancer, liver cancers (e.g.,
hepatocellular carcinoma), lung cancers (e.g., non-small cell lung
carcinoma), malignant mesothelioma, melanoma, multiple myeloma,
nasopharynx cancer, ovarian cancer, pancreatic cancer, peritoneum,
omentum, and mesentery cancer, pharynx cancer, prostate cancer,
rectal cancer, kidney cancers (e.g., renal cell carcinoma), small
intestine cancer, soft tissue cancer, stomach cancer, testicular
cancer, thyroid cancer, and urothelial cancers (e.g., ureter cancer
and urinary bladder cancer). Preferably, the cancer is melanoma,
breast cancer, lung cancer, prostate cancer, synovial cell sarcoma,
head and neck cancer, esophageal cancer, or ovarian cancer.
[0110] The mammal referred to in the inventive methods can be any
mammal. As used herein, the term "mammal" refers to any mammal,
including, but not limited to, mammals of the order Rodentia, such
as mice and hamsters, and mammals of the order Logomorpha, such as
rabbits. It is preferred that the mammals are from the order
Carnivora, including Felines (cats) and Canines (dogs). It is more
preferred that the mammals are from the order Artiodactyla,
including Bovines (cows) and Swines (pigs) or of the order
Perssodactyla, including Equines (horses). It is most preferred
that the mammals are of the order Primates, Ceboids, or Simoids
(monkeys) or of the order Anthropoids (humans and apes). An
especially preferred mammal is the human.
[0111] The following examples further illustrate the invention but,
of course, should not be construed as in any way limiting its
scope.
EXAMPLE 1A
[0112] This example demonstrates the isolation of TCRs from T cell
clones.
[0113] Anti-MAGE-A3.sub.243-258 CD4+ effector clone R12C9 and
anti-MAGE-A3.sub.243-258 Treg clone 6F9 was cultured with peptide
(MAGE-A3.sub.243-258)-pulsed EBV B cells. Cytokine secretion,
percentage of indicator cells suppressed, percentage of FOXP3+ Treg
cells, and percentage of unmethylated FOXP3 sequences were
measured. Unmethylated FOXP3 intron 1 sequences are considered to
be a marker for a stable Treg phenotype. The results for the 6F9
and R12C9 clones are shown in Tables 1A and 1B.
TABLE-US-00001 TABLE 1A % Indicator Cells % Unmethylated Clone
Suppressed % FOXP3+ FOXP3 sequences 6F9 57 95 72 R12C9 0 8 2
TABLE-US-00002 TABLE 1B Cytokine Secretion (pg/25,000 cells) Clone
IFN-.gamma. IL-2 IL-10 IL-4 IL-5 TNF-.alpha. 6F9 0 0 0 0 0 12 R12C9
922 46 479 8 28 422
[0114] Treg clones can inhibit the proliferation of indicator cells
after stimulation by an appropriate peptide. As shown in Table 1A,
clone 6F9 is a Treg clone.
[0115] A TCR comprising SEQ ID NOs: 21 and 22 was cloned from the
anti-MAGE-A3.sub.243-258 CD4+ effector clone R12C9 ("R12C9 TCR"). A
TCR comprising SEQ ID NOs: 11 and 12 was cloned from the
anti-MAGE-A3.sub.243-258 Treg clone 6F9 ("6F9 TCR").
EXAMPLE 1B
[0116] This example demonstrates the transduction efficiency of
PBMC transduced with a nucleotide sequence encoding the 6F9 TCR or
R12C9 TCR of Example 1.
[0117] Transcripts encoding the TCR alpha and beta chains of R12C9
and 6F9 were linked with sequences encoding a P2A self-cleaving
peptide and cloned into an MSGV1 retroviral vector. PBMC from three
patients were stimulated with OKT3, transduced with transient
retroviral supernatants on day two, and enriched for CD4+ T cells
on day seven. The levels of TCR expression were evaluated by
staining transduced cells with anti-V.beta.22 or V.beta.6.7, which
detect the 6F9 or R12C9 TCR, respectively. Analysis of PBMC from
patient 1 indicated that between 25 and 35% of the T cells were
transduced with the individual TCRs and similar transduction levels
were obtained with PBMC from patients 2 and 3.
EXAMPLE 2
[0118] This example demonstrates that T cells transduced with
nucleotide sequences encoding the anti-MAGE-A3.sub.243-258 TCRs of
Example 1 recognize 293-class II, major histocompatibility complex,
transactivator (CIITA) transfectants of MAGE-A3 and peptide-pulsed
targets. This example also demonstrates that the 6F9 TCR recognizes
293-CIITA transfectants of MAGE-A3 and MAGE-A6.
[0119] CD4+ enriched peripheral blood lymphocytes (PBL) from two
human donors were untransduced (UT) or transduced with F5
(anti-MART-1) TCR, R12C9 TCR, or 6F9 TCR. The cells were cultured
with 293-CIITA-transfected target cells pulsed with
MAGE-A3.sub.243-258 (SEQ ID NO: 2) peptide. The 293-CIITA cells are
293 cells transduced with CIITA, which is a human gene which
encodes the class II, major histocompatibility complex
transactivator protein. The results obtained with 6F9 and R12C9
TCR-transduced cells are shown in Table 2 and FIG. 10A. PBL
transduced by R12C9 TCR or 6F9 TCR recognized MAGE-A3.sub.243-258
peptide-pulsed HLA-DP*0401+ target cells. Titration of the
MAGE-A3.sub.243-258 peptide indicated that CD4.sup.+ T cells
transduced with the 6F9 or R12C9 TCRs released comparable levels of
IFN-.gamma. in response to targets pulsed with a minimum of between
0.001 and 0.01 mg/ml of the MAGE-A3:.sub.243-258 peptide. The
experiments were repeated using PBL from a third human donor and
similar results were obtained.
TABLE-US-00003 TABLE 2 IFN-gamma (pg/ml) Peptide Untransduced 6F9
TCR DP4+ (.mu.g/ml) (UT) transduced Donor 1 293-CIITA + z 0.0001 2
328 MAGE-A3.sub.243-258 0.001 17 596 0.01 4 1609 0.1 2 7440 1 4
34800 10 0 52100 Donor 2 293-CIITA + 0.0001 28 110
MAGE-A3.sub.243-258 0.001 30 323 0.01 37 1830 0.1 40 9760 1 44
55000 10 0 59050
[0120] 293-CIITA target cells were transfected with DNA constructs
(pCDNA3 vector) encoding full-length MAGE-A3 protein or MAGE-A6
protein, which differ at only a single position (249), or
full-length MAGE-A1 protein or MAGE-A12 protein. Untransduced and
transduced PBL were co-cultured with the transfected 293-CIITA
cells and interferon (IFN) gamma secretion was measured. The
results are shown in FIGS. 1A, 1B, and 10A.
[0121] As shown in FIGS. 1A, 1B, and 10A, although T cells
transduced with R12C9 TCR or 6F9 TCR recognized peptide-pulsed
targets, PBL transduced with the 6F9 TCR were the most highly
reactive to each of MAGE-A3 and MAGE-A6 293-CIITA transfectants.
CD4.sup.+ T cells transduced with the 6F9 but not the R12C9 TCR
recognized HLA DP*0401+293-CIITA cells transfected with genes
encoding MAGE-A3 or MAGE-A6, but not MAGE-A1 or A12. Comparison of
amino acid sequences of the corresponding regions of the MAGE
family members indicated that MAGE-A3 and MAGE-A6 only differed at
one position (residue 249), whereas the other MAGE family members
differed from MAGE-A3 at two (MAGE-A12.sub.243-258 (SEQ ID NO: 70))
or three (MAGE-A1.sub.243-258 (SEQ ID NO: 71)) positions. In
addition, CD4.sup.+ T cells transduced with the 6F9 TCR but not the
R12C9 TCR recognized the MAGE-A3.sup.+/HLA-DP*0401.sup.+ melanoma
cell line 1359 mel-CIITA but failed to recognize the
MAGE-A3.sup.+/HLA-DP*0401.sup.- melanoma cell line 624 mel-CIITA.
CD4.sup.+ T cells transduced with the R12C9 TCR failed to recognize
either of the tested melanoma cell lines. Cells transduced with the
MART-1 reactive TCR DMFS failed to recognize the transfected
293-CIITA cells or MAGE-A3:.sub.243-258 pulsed target cells, but
recognized the HLA-A*0201+ and MART-1+ cell line 624 mel-CIITA. The
experiments were repeated using PBL from a third human donor and
similar results were obtained. Because the 6F9 TCR was obtained
from a Treg clone, which are involved in the suppression of immune
activity, the reactivity of the 6F9 TCR was surprising and
unexpected. These results indicated that while CD4+ T cells
transduced with 6F9 or R12C9 recognized peptide pulsed target
cells, only cells transduced with the 6F9 TCR recognized
transfected target cells as well as MAGE-A3.sup.+ and HLA-DP*04+
tumor cells.
EXAMPLE 3
[0122] This example demonstrates that 6F9-transduced PBLs show high
reactivity to MAGE-A3 full-length protein processed and presented
by HLA-DP4+ B cells.
[0123] PBL from two human donors was untransduced or transduced
with a nucleotide sequence encoding the 6F9 TCR. The cells were
co-cultured with HLA-DP4+ B cells that had processed and presented
full-length MAGE-A3 protein (SEQ ID NO: 1). The results are shown
in Table 3 and FIG. 10A. As shown in Table 3 and FIG. 10A, the
6F9-transduced PBLs were highly reactive to MAGE-A3 full-length
protein processed and presented by HLA-DP4+ B cells.
TABLE-US-00004 TABLE 3 IFN-.gamma. (pg/ml) MAGE-A3 Untransduced 6F9
TCR DP4 (.mu.g/ml) (UT) transduced Donor 1 B cells + MAGE-A3 + 10
360 23640 full length + 1 420 12440 + 0.1 358 2360 + 0.01 362 580 +
0.001 343 427 + 0.0001 349 387 + 0 343 405 B cells + NY-ESO-1 + 10
313 363 full length Donor 2 B cells + MAGE-A3 + 10 2080 63100 full
length + 1 1810 21270 + 0.1 1382 3590 + 0.01 1519 685 + 0.001 1297
470 + 0.0001 1568 542 + 0 1351 404 B cells + NY-ESO-1 + 10 1549 530
full length
EXAMPLE 4
[0124] This example demonstrates that 6F9 TCR-transduced PBLs are
reactive to tumor lines with endogenous class II presentation of
MAGE-A3 protein.
[0125] PBL from two human donors were untransduced or transduced
with a nucleotide sequence encoding the 6F9 TCR or F5 TCR. The
cells were cultured alone (T cell only) or co-cultured with
624-CIITA cells, 526-CIITA cells, or H1299-CIITA cells (tumor cell
lines transfected with CIITA). The results are shown in Table 4. As
shown in Table 4, 6F9 TCR-transduced PBLs were reactive to tumor
lines with endogenous class II presentation of MAGE-A3 protein.
TABLE-US-00005 TABLE 4 IFN-gamma (pg/ml) F5 6F9 MAGE Untrans-
trans- trans- DP4 A3 duced duced duced Donor 1 624-CIITA - + 223
1483 238 526-CIITA + + 636 2360 1314 (DP4 0401) H1299-CIITA + + 284
243 4330 (DP4 0401) T-cell only 131 45 112 Donor 2 624-CIITA - +
819 1435 153 526-CIITA + + 117 2530 1339 H1299-CIITA + + 147 172
3630 T-cell only 65 27 88
EXAMPLE 5
[0126] This example demonstrates that the 6F9 TCR is MAGE-A3
specific.
[0127] PBL from a human donor were CD4+ enriched and the number of
cells was rapidly expanded on day 27. Cells were untransduced or
transduced with F5 TCR or 6F9 TCR and co-cultured with 526-CIITA
cells or H1299-CIITA cells alone or with anti-MAGE-A3 siRNA or
anti-MART-1 siRNA. IFN-gamma secretion was measured. The results
are shown in FIGS. 2A and 2B.
[0128] As shown in FIGS. 2A and 2B, the anti-MAGE-A3 siRNA reduced
the reactivity of the 6F9-TCR transduced cells. Accordingly, the
siRNA knockdown assay confirmed that the 6F9 TCR is MAGE-A3
specific.
EXAMPLE 6
[0129] This example demonstrates that 6F9 TCR recognizes MAGE-A3 in
an HLA-DP restricted manner.
[0130] 624, 526, 1359, H1299, 1300, 1764, 3071, 397, 2630, and 2984
tumor cell lines were transduced with CIITA (624-CIITA, 526-CIITA,
1359-CIITA, H1299-CIITA, 1300-CIITA, 1764-CIITA, 3071-CIITA,
397-CIITA, 2630-CIITA, and 2984-CIITA) and HLA-DP expression was
measured by flow cytometry. DP4 and MAGE-A3 expression is shown in
Table 5A.
TABLE-US-00006 TABLE 5A Transduced Tumor Cell Line DP4 MAGE-A3
624-CIITA -- + 1300-CIITA -- + 3071-CIITA 0402 + Whitington-CIITA
0401 - 526-CIITA 0401 + 1359-CIITA 0401 + H1299-CIITA 0401 +
397-CIITA 0401 + 2630-CIITA 0401 + 2984-CIITA 0401 +
[0131] 6F9-transduced PBL were cultured alone (T cells only) or
co-cultured with 3071 cells, 3071-CIITA cells, 397 cells, 397-CIITA
cells, 2630 cells, 2630-CIITA cells, 2984 cells, and 2984-CIITA
cells. IFN-gamma secretion was measured. The results are shown in
FIG. 3. As shown in FIG. 3, 6F9-transduced PBL were reactive with
CIITA-expressing tumor cell lines.
[0132] The 6F9 TCR was further evaluated by determining the
reactivity of CD4.sup.+ and CD8.sup.+ T cells separated from two
patient PBMCs against a panel of tumor cell lines including
624-CIITA, 526-CIITA, 1359-CIITA, H1299-CIITA, SK37-CIITA,
1764-CIITA, 3071-CIITA, 397-CIITA, 2630-CIITA, and 2984-CIITA. Five
melanoma cell lines that expressed MAGE-A3 and HLA-DP*0401
(2630-CIITA, 397-CIITA, 2984-CIITA, 526-CIITA, and 1359-CIITA), as
well as the non-small cell lung carcinoma cell line H1299
NSCLC-CIITA were recognized by transduced CD4.sup.+ and CD8.sup.+ T
cells, although CD4.sup.+ T cells secreted higher amounts of
cytokine in response to tumor targets than transduced CD8.sup.+ T
cells.
[0133] H1299-CIITA and 526-CIITA cells were transfected with
anti-HLA-DP or anti-HLA-DR siRNA to knock down HLA-DP or HLA-DR
expression. 3071-CIITA and 526-CIITA cells were transfected with
anti-HLA-DQ siRNA to knock down HLA-DQ expression. HLA-DP, HLA-DR,
or HLA-DQ knockout was confirmed by flow cytometry.
[0134] PBL from a human donor were enriched for CD4+ and the number
of cells was rapidly expanded on day 30. The cells were transduced
with 6F9 TCR or untransduced. The cells were cultured alone (T cell
only) or co-cultured with untreated H1299-CIITA cells, H1299-CIITA
transfected with anti-HLA-DP or anti-HLA-DR siRNA, untreated
526-CIITA cells, or 526-CIITA transfected with anti-HLA-DP or
anti-HLA-DR siRNA. IFN-gamma secretion was measured. The results
are shown in FIG. 4. As shown in FIG. 4, the anti-HLA-DP siRNA
reduced the reactivity of the 6F9-TCR transduced cells.
[0135] Further studies employing antibodies confirmed that the 6F9
TCR recognizes MAGE-A3 in an HLA-class II restricted manner. PBL
transduced with 6F9 TCR were co-cultured with the cells set forth
in Table 5B and blocked with the antibodies set forth in Table 5B.
IFN-gamma was measured, and the results are set forth in Table
5B.
TABLE-US-00007 TABLE 5B 6F9 TCR-transduced PBL IFN-gamma
co-cultured with: Blocked with antibody: (pg/ml) 293-CIITA (DP4+)
W6/32 (.alpha.-HLA class I) >10,000 transfected with HB22
(.alpha.-HLA class DR) >10,000 MAGE-A3 gene IVA12 (.alpha.-HLA
class II) 902 Allen B cells (A2+ DP4+) W6/32 (.alpha.-HLA class I)
15038 Incubated with HB22 (.alpha.-HLA class DR) 16599 MAGE-A3
protein IVA12 (.alpha.-HLA class II) 129 SK37 CIITA W6/32
(.alpha.-HLA class I) 1965 (A2+ DP4+ MAGE-A3+) HB22 (.alpha.-HLA
class DR) 6248 IVA12 (.alpha.-HLA class II) 674 Hl299 CIITA W6/32
(.alpha.-HLA class I) 2684 (A2- DP4+ MAGE-A3+) HB22 (.alpha.-HLA
class DR) 7888 IVA12 (.alpha.-HLA class II) 0 1764 RCC CIITA W6/32
(.alpha.-HLA class I) 0 (A2-DP4+ MAGE-A3-) HB22 (.alpha.-HLA class
DR) 0 IVA12 (.alpha.-HLA class II) 0
[0136] As shown in Table 5B, the antibody blocking studies showed
that the 6F9 TCR recognizes MAGE-A3 in an HLA Class II-restricted
manner, but not in an HLA-DR-restricted manner or in an HLA Class
I-restricted manner.
EXAMPLE 7
[0137] This example demonstrates that an alanine substitution at
position 116 or 117 of the alpha chain of the 6F9 TCR increases the
reactivity of the 6F9 TCR.
[0138] Eight different substituted TCRs, each having one alanine
substitution at a different location in the CDR3 region of the 6F9
TCR, were prepared as set forth in Table 6.
TABLE-US-00008 TABLE 6 Name Description SEQ ID NO: a1 Alanine SEQ
ID NO: 12 (wild-type (wt) beta chain) substitution SEQ ID NO: 33
(substituted alpha chain), at position wherein Xaa at 116 is Ala,
Xaa at 117 is 116 of alpha Ser, Xaa at 118 is Gly, and Xaa at 119
chain (S116A) is Thr a2 Alanine SEQ ID NO: 12 (wild-type (wt) beta
chain) substitution SEQ ID NO: 33 (substituted alpha chain), at
position wherein Xaa at 116 is Ser, Xaa at 117 of alpha 117 is Ala,
Xaa at 118 is Gly, and Xaa at chain (S117A) 119 is Thr a3 Alanine
SEQ ID NO: 12 (wild-type (wt) beta chain) substitution SEQ ID NO:
33 (substituted alpha chain), at position wherein Xaa at 116 is
Ser, Xaa at 118 of alpha 117 is Ser, Xaa at 118 is Ala, and Xaa at
chain (G118A) 119 is Thr a4 Alanine SEQ ID NO: 12 (wild-type (wt)
beta chain) substitution SEQ ID NO: 33 (substituted alpha chain),
at position wherein Xaa at 116 is Ser, Xaa at 119 of alpha 117 is
Ser, Xaa at 118 is Gly, and Xaa at chain (T119A) 119 is Ala b1
Alanine SEQ ID NO: 11 (wild-type (wt) alpha chain) substitution and
SEQ ID NO: 34, wherein Xaa at 115 is at position Ala, Xaa at 116 is
Thr, Xaa at 117 is Gly, 115 of beta c and Xaa at 118 is Pro hain
(R115A) b2 Alanine SEQ ID NO: 11 (wild-type (wt) alpha chain)
substitution and SEQ ID NO: 34, wherein Xaa at 115 is at position
Arg, Xaa at 116 is Ala, Xaa at 117 is Gly, 116 of beta and Xaa at
118 is Pro chain (T116A) b3 Alanine SEQ ID NO: 11 (wild-type (wt)
alpha chain) substitution and SEQ ID NO: 34, wherein Xaa at 115 is
Arg, at position Xaa at 116 is Thr, Xaa at 117 is Ala, and 117 of
beta Xaa at 118 is Pro chain (G117A) b4 Alanine SEQ ID NO: 11
(wild-type (wt) alpha chain) substitution and SEQ ID NO: 34,
wherein Xaa at 115 is Arg, at position Xaa at 116 is Thr, Xaa at
117 is Gly, and 118 of beta Xaa at 118 is Ala chain (P118A)
[0139] PBL from a human donor were untransduced or transduced with
wild-type (wt) 6F9 TCR or one of each of the eight substituted TCRs
in Table 6. The cells were cultured alone (T cell only) or
co-cultured with 624-CIITA, 526-CIITA, 1359-CIITA, H1299-CIITA, or
1764-CIITA. IFN-gamma secretion was measured. The results are set
forth in FIG. 5. As shown in FIG. 5, the a1 and a2 substituted TCRs
demonstrated increased reactivity as compared to wt 6F9 TCR.
[0140] A separate experiment with transduced, CD4+ enriched PBL
also confirmed the superior reactivity of the a1 and a2 substituted
TCRs (FIG. 6). As shown in FIG. 6, the a1 and a2 substituted TCRs
showed an approximately 2-fold increase in anti-tumor activity as
compared to wt 6F9 TCR. The a1 and a2 substituted TCRs also showed
better tetramer (SEQ ID NO: 2) binding as compared to the wt 6F9
TCR, as measured by flow cytometry.
EXAMPLE 8
[0141] This example demonstrates the reactivity of substituted 6F9
TCRs.
[0142] Eight different substituted TCRs, each having one amino acid
substitution at a different location in the CDR3 region of the
alpha chain of the 6F9 TCR, were prepared as set forth in Table
7.
TABLE-US-00009 TABLE 7 Name Description SEQ ID NO: a1-1 Leucine SEQ
ID NO: 12 (wild-type (wt) beta chain) substitution SEQ ID NO: 33
(substituted alpha chain), at position wherein Xaa at 116 is Leu,
Xaa at 117 is 116 of alpha Ser, Xaa at 118 is Gly, and Xaa at 119
chain (S116L) is Thr a1-2 Isoleucine SEQ ID NO: 12 (wild-type (wt)
beta chain) substitution SEQ ID NO: 33 (substituted alpha chain),
at position wherein Xaa at 116 is Ile, Xaa at 117 is 116 of alpha
Ser, Xaa at 118 is Gly, and Xaa at 119 is chain (S116I) Thr a1-3
Valine SEQ ID NO: 12 (wild-type (wt) beta chain) substitution SEQ
ID NO: 33 (substituted alpha chain), at position wherein Xaa at 116
is Val, Xaa at 117 is 116 of alpha Ser, Xaa at 118 is Gly, and Xaa
at 119 is chain (S116V) Thr a1-4 Methionine SEQ ID NO: 12
(wild-type (wt) beta chain) substitution SEQ ID NO: 33 (substituted
alpha chain), at position wherein Xaa at 116 is Met, Xaa at 117 116
of alpha is Ser, Xaa at 118 is Gly, and Xaa at chain (S116M) 119 is
Thr a2-1 Leucine SEQ ID NO: 12 (wild-type (wt) beta chain)
substitution SEQ ID NO: 33 (substituted alpha chain), at position
wherein Xaa at 116 is Ser, Xaa at 117 117 of beta is Leu, Xaa at
118 is Gly, and Xaa at chain (S117L) 119 is Thr a2-2 Isoleucine SEQ
ID NO: 12 (wild-type (wt) beta chain) substitution SEQ ID NO: 33
(substituted alpha chain), at position wherein Xaa at 116 is Ser,
Xaa at 117 117 of beta is Ile, Xaa at 118 is Gly, and Xaa at chain
(S117I) 119 is Thr a2-3 Valine SEQ ID NO: 12 (wild-type (wt) beta
chain) substitution SEQ ID NO: 33 (substituted alpha chain),
atposition wherein Xaa at 116 is Ser, Xaa at 117 117 of beta is
Val, Xaa at 118 is Gly, and Xaa at 119 chain (S117V) is Thr a2-4
Methionine SEQ ID NO: 12 (wild-type (wt) beta chain) substitution
SEQ ID NO: 33 (substituted alpha chain), at position wherein Xaa at
116 is Ser, Xaa at 117 117 of beta is Met, Xaa at 118 is Gly, and
Xaa at 119 chain (S117M) is Thr
[0143] PBL from a human donor were untransduced or transduced with
wild-type (wt) 6F9 TCR or one of each of the eight substituted
TCRs. The cells were cultured alone (T cell only) or co-cultured
with 624-CIITA, 526-CIITA, 1359-CIITA, H1299-CIITA, or 1764-CIITA.
IFN-gamma secretion was measured. The results are set forth in FIG.
7. As shown in FIG. 7, the a1, a2, and a1-3 substituted TCRs
demonstrated reactivity against CIITA-tumor cell lines.
EXAMPLE 9
[0144] This example demonstrates that substitution of the native
constant region of the 6F9 TCR with a murine constant region
increases the reactivity of the 6F9 TCR.
[0145] A TCR was prepared comprising the variable regions of the
.alpha. and .beta. chains of the wt 6F9 TCR and a murine constant
region (6F9mC TCR) (SEQ ID NOs: 27 and 28).
[0146] The 6F9mC TCR demonstrated better MAGE-A3 tetramer and
V.beta. staining as compared to wt 6F9 TCR, as measured by flow
cytometry. Without being bound to a particular theory, it is
believed that the 6F9mC TCR provides improved pairing of the TCR
.alpha. and .beta. chains.
[0147] PBL from a human donor were untransduced or transduced with
wt 6F9 TCR or 6F9mC TCR and cultured alone (T-cell only) or
co-cultured with 624-CIITA, 1300-CIITA, 526-CIITA, 1359-CIITA,
H1299-CIITA, 397-CIITA, 2630-CIITA, 2984-CIITA, 3071-CIITA, or
1764-CIITA cells. IFN-gamma secretion was measured. The results are
shown in FIG. 8. As shown in FIG. 8, the 6F9mC-transduced cells
showed a 2-5 fold increase in anti-tumor activity as compared to wt
6F9 TCR-transduced cells.
[0148] Untransduced cells, 6F9 TCR-transduced cells, or 6F9mC
TCR-transduced cells were enriched for CD8 or CD4 and cultured
alone (T-cell only) or co-cultured with 624-CIITA, SK37-CIITA,
526-CIITA, 1359-CIITA, H1299-CIITA, 397-CIITA, 2630-CIITA,
2984-CIITA, 3071-CIITA, or 1764-CIITA cells. Interferon-gamma
secretion was measured. The results are shown in FIGS. 9A and 9B.
As shown in FIGS. 9A and 9B, the CD8 and CD4 enriched
6F9mC-transduced cells maintained higher anti-tumor activity as
compared to 6F9 TCR transduced cells for several cell lines,
indicating high affinity of the 6F9mC TCR independent of
co-receptors. The experiments were repeated using PBL from a second
human donor and similar results were obtained. Comparisons of
responses of CD4+ T cells transduced with the wild-type (Wt) 6F9
TCR with those of the cells transduced with the 6F9mc TCR indicated
that the murine constant regions resulted in between two and
five-fold enhancement in the response of transduced T cells against
the seven MAGE-A3.sup.+ and HLA-DP*0401.sup.+ targets that were
evaluated. In addition, the response of CD8.sup.+ T cells
transduced with the 6F9mc were enhanced by between two and ten-fold
above those seen in cells transduced with the wt 6F9 TCR. The
responses of CD8.sup.+ T cells transduced with the 6F9mc were
generally lower than CD4.sup.+ T cells transduced with this TCR,
although comparable cytokine responses were observed in responses
to some tumor targets.
EXAMPLE 10
[0149] This example demonstrates that upon tumor stimulation, 6F9mC
TCR-transduced cells produce high levels of IFN-gamma and TNF-alpha
and show a highly activated phenotype (as measured by increased
4-1BB, CD25, and CD69 expression).
[0150] Cells were CD4 or CD8 enriched and transduced with 6F9mC
TCR. Transduced cells were co-cultured with tumor lines 624-CIITA,
2630-CIITA, 2984-CIITA, or Whitington-CIITA for 6 hours and then
stained for intracellular IFN-gamma, interleukin (IL)-2, or tumor
necrosis factor (TNF)-.alpha.. The 6F9mC TCR transduced cells
showed specific intracellular IFN-gamma production upon tumor
stimulation. The 6F9mC TCR transduced cells showed detectable IL-2
production and specific high TNF-.alpha. production upon tumor
stimulation in the CD4-enriched fraction.
[0151] Cells were CD4 enriched and transduced with 6F9mC TCR.
Transduced cells were co-cultured with tumor lines 624-CIITA,
2630-CIITA, 2984-CIITA, or Whitington-CIITA overnight and then
stained for 4-1BB, CD25, and CD69. After overnight tumor
stimulation, the majority of 6F9mC TCR-transduced cells expressed
high levels of 4-1BB (indicative of antigen-specific activation),
CD25, and CD69.
EXAMPLE 11
[0152] This example demonstrates that the 6F9 TCR mediates tumor
cell recognition.
[0153] PBL were untransduced or transduced with wild-type 6F9 TCR
and cultured alone or co-cultured with non-small cell lung cancer
(NSCLC) cell line H11299 or melanoma cell line 526 mel, 624 mel, or
1359 mel. MAGE-A3 and DP*04 expression is shown in Table 8.
TABLE-US-00010 TABLE 8 Cell line MAGE-A3 DP*04 H1299 NSCLC + + 526
mel + + 624 mel + - 1359 mel + -
[0154] IFN-gamma expression was measured. The results are shown in
FIG. 10B. As shown in FIG. 10B, the 6F9 TCR mediates tumor cell
recognition.
EXAMPLE 12
[0155] This example demonstrates that the 6F9 and 6F9mc TCR possess
a high degree of specificity for the MAGE-A3:.sub.248-258
peptide.
[0156] In order to evaluate the fine specificity of antigen
recognition mediated by cells transduced with the 6F9 and 6F9mc
TCR, HLA-DP*0401.sup.+ target cells were pulsed with truncations of
the MAGE-A3:.sub.243-258 peptide or related peptides from MAGE
family members. CD4+ T cells isolated from two patients' PBMC
(PBMC-1 or PBMC-2) by negative selection were transduced with
either the 6F9 TCR, the 6F9mc TCR, or were un-transduced and
assayed 10 days following OKT3 stimulation for their response to
293-CIITA cells that were pulsed with 10 mg/ml of the peptides
indicated in Table 9.
[0157] Analysis of the response to truncated MAGE-A3 peptides from
two cultures of transduced CD4.sup.+ PBMC indicated that the 11-mer
peptide QHFVQENYLEY (SEQ ID NO: 54) corresponding to amino acids
248-258 of the MAGE-A3 protein represented the minimal peptide that
elicited a response comparable to that elicited by the
MAGE-A3:.sub.243-258 peptide (Table 9). The MAGE-A3:.sub.243-258
peptide was predicted using an epitope prediction algorithm to
possess a high affinity for HLA-DP*0401, and in addition,
recognition of the truncated MAGE-A3 peptides appeared to correlate
with T cell recognition (Table 9). Significant recognition was
observed for the MAGE-A6:.sub.248-258 peptide that contained a
single substitution of tyrosine for histidine at position 249, but
minimal reactivity was observed against additional members of the
MAGE family of gene products that possessed between two and five
differences from the MAGE-A3:.sub.248-258 peptide. A BLAST search
of the NCBI database revealed that the most closely related peptide
was derived from the protein necdin. This peptide, which possessed
five differences from the MAGE-A3:.sub.248-258 peptide, was also
not recognized by T cells transduced with the 6F9 or 6F9mc TCR.
These findings indicate that the 6F9 TCR possesses a high degree of
specificity for the MAGE-A3:.sub.248-258 peptide, and suggest that
T cells transduced with this TCR may possess little or no
cross-reactivity with peptides derived from additional human
proteins.
TABLE-US-00011 TABLE 9 PBMC-1 transduced PBMC-2 transduced SEQ
with: with: Predicted ID Amino Acid None 6F9 affinity Gene
(position) NO: Sequence 6F9 6F9mc IFN-g (pg/ml) 6F9mc None (nM)
MAGE-A3: 243-258 2 KKLLTQHFVQENYLEY 10,220 15,210 33 10,350 17,520
45 3 MAGE-A3: 243-256 47 KKLLTQHFVQENYL 1,018 1,815 72 1,670 2,490
78 323 MAGE-A3: 243-255 48 KKLLTQHFVQENY 76 137 29 111 117 71 378
MAGE-A3: 243-254 49 KKLLTQHFVQEN 28 0 67 30 39 78 466 MAGE-A3:
243-253 50 KKLLTQHFVQE 0 40 38 30 45 90 2444 MAGE-A3: 245-258 51
LLTQHFVQENYLEY 9,290 14,970 84 8,920 17,820 74 3 MAGE-A3: 246-258
52 LTQHFVQENYLEY 7,140 12,700 56 9,200 16,170 76 3 MAGE-A3: 247-258
53 TQHFVQENYLEY 6,710 10,600 30 6,810 13,280 41 3 MAGE-A3: 248-258
54 QHFVQENYLEY 6,220 9,000 52 7,400 8,700 56 4 MAGE-A3: 249-258 55
HFVQENYLEY 669 1,643 57 922 2,034 66 5 MAGE-A6: 248-258 56
QYFVQENYLEY 6,440 11,800 54 13,200 8,370 127 3 MAGE-A2/A12: 248-258
57 QDLVQENYLEY 33 66 49 37 56 65 59 MAGE-A4/A9: 249-259 58
QDWVQENYLEY 0 23 32 22 26 62 92 MAGE-A8: 251-261 59 QEWVQENYLEY 43
58 79 39 41 55 87 MAGE-A1/B4: 241-251 60 QDLVQEKYLEY 129 126 55 108
84 53 16 MAGE-B2: 250-260 61 KDLVQEKYLEY 0 0 43 7 20 38 16
MAGE-B10: 250-260 62 KDLVKENYLEY 22 18 69 28 34 66 105 MAGE-B16:
252-262 63 KDFVKEKYLEY 0 27 16 11 28 42 3 MAGE-C1: 113-123 64
KVWVQEHYLEY 9 0 30 25 27 30 35 MAGE-D4: 300-315 65 RKLITDDFVKQKYLEY
193 234 81 194 268 80 6 MAGE-D2: 413-428 66 KKLITDEFVKQKYLDY 82 43
56 226 223 71 8 MAGE-L2: 582-597 67 KKLITEVFVRQKYLEY 45 56 58 78
107 114 6 MAGE-G1: 220-235 68 KKLITEDFVRQRYLEY 0 29 68 25 33 62 3
Necdin: 237-247 69 EEFVQMNYLKY 0 22 59 21 32 83 13 No peptide 0 5
58 15 25 59
[0158] All references, including publications, patent applications,
and patents, cited herein are hereby incorporated by reference to
the same extent as if each reference were individually and
specifically indicated to be incorporated by reference and were set
forth in its entirety herein.
[0159] The use of the terms "a" and "an" and "the" and "at least
one" and similar referents in the context of describing the
invention (especially in the context of the following claims) are
to be construed to cover both the singular and the plural, unless
otherwise indicated herein or clearly contradicted by context. The
use of the term "at least one" followed by a list of one or more
items (for example, "at least one of A and B") is to be construed
to mean one item selected from the listed items (A or B) or any
combination of two or more of the listed items (A and B), unless
otherwise indicated herein or clearly contradicted by context. The
terms "comprising," "having," "including," and "containing" are to
be construed as open-ended terms (i.e., meaning "including, but not
limited to,") unless otherwise noted. Recitation of ranges of
values herein are merely intended to serve as a shorthand method of
referring individually to each separate value falling within the
range, unless otherwise indicated herein, and each separate value
is incorporated into the specification as if it were individually
recited herein. All methods described herein can be performed in
any suitable order unless otherwise indicated herein or otherwise
clearly contradicted by context. The use of any and all examples,
or exemplary language (e.g., "such as") provided herein, is
intended merely to better illuminate the invention and does not
pose a limitation on the scope of the invention unless otherwise
claimed. No language in the specification should be construed as
indicating any non-claimed element as essential to the practice of
the invention.
[0160] Preferred embodiments of this invention are described
herein, including the best mode known to the inventors for carrying
out the invention. Variations of those preferred embodiments may
become apparent to those of ordinary skill in the art upon reading
the foregoing description. The inventors expect skilled artisans to
employ such variations as appropriate, and the inventors intend for
the invention to be practiced otherwise than as specifically
described herein. Accordingly, this invention includes all
modifications and equivalents of the subject matter recited in the
claims appended hereto as permitted by applicable law. Moreover,
any combination of the above-described elements in all possible
variations thereof is encompassed by the invention unless otherwise
indicated herein or otherwise clearly contradicted by context.
Sequence CWU 1
1
711314PRTHomo sapiens 1Met Pro Leu Glu Gln Arg Ser Gln His Cys Lys
Pro Glu Glu Gly Leu1 5 10 15Glu Ala Arg Gly Glu Ala Leu Gly Leu Val
Gly Ala Gln Ala Pro Ala 20 25 30Thr Glu Glu Gln Glu Ala Ala Ser Ser
Ser Ser Thr Leu Val Glu Val 35 40 45Thr Leu Gly Glu Val Pro Ala Ala
Glu Ser Pro Asp Pro Pro Gln Ser 50 55 60Pro Gln Gly Ala Ser Ser Leu
Pro Thr Thr Met Asn Tyr Pro Leu Trp65 70 75 80Ser Gln Ser Tyr Glu
Asp Ser Ser Asn Gln Glu Glu Glu Gly Pro Ser 85 90 95Thr Phe Pro Asp
Leu Glu Ser Glu Phe Gln Ala Ala Leu Ser Arg Lys 100 105 110Val Ala
Glu Leu Val His Phe Leu Leu Leu Lys Tyr Arg Ala Arg Glu 115 120
125Pro Val Thr Lys Ala Glu Met Leu Gly Ser Val Val Gly Asn Trp Gln
130 135 140Tyr Phe Phe Pro Val Ile Phe Ser Lys Ala Ser Ser Ser Leu
Gln Leu145 150 155 160Val Phe Gly Ile Glu Leu Met Glu Val Asp Pro
Ile Gly His Leu Tyr 165 170 175Ile Phe Ala Thr Cys Leu Gly Leu Ser
Tyr Asp Gly Leu Leu Gly Asp 180 185 190Asn Gln Ile Met Pro Lys Ala
Gly Leu Leu Ile Ile Val Leu Ala Ile 195 200 205Ile Ala Arg Glu Gly
Asp Cys Ala Pro Glu Glu Lys Ile Trp Glu Glu 210 215 220Leu Ser Val
Leu Glu Val Phe Glu Gly Arg Glu Asp Ser Ile Leu Gly225 230 235
240Asp Pro Lys Lys Leu Leu Thr Gln His Phe Val Gln Glu Asn Tyr Leu
245 250 255Glu Tyr Arg Gln Val Pro Gly Ser Asp Pro Ala Cys Tyr Glu
Phe Leu 260 265 270Trp Gly Pro Arg Ala Leu Val Glu Thr Ser Tyr Val
Lys Val Leu His 275 280 285His Met Val Lys Ile Ser Gly Gly Pro His
Ile Ser Tyr Pro Pro Leu 290 295 300His Glu Trp Val Leu Arg Glu Gly
Glu Glu305 310216PRTHomo sapiens 2Lys Lys Leu Leu Thr Gln His Phe
Val Gln Glu Asn Tyr Leu Glu Tyr1 5 10 1537PRTHomo sapiens 3Thr Ser
Glu Ser Asp Tyr Tyr1 547PRTHomo sapiens 4Gln Glu Ala Tyr Lys Gln
Gln1 5511PRTHomo sapiens 5Ala Leu Arg Ser Ser Gly Thr Tyr Lys Tyr
Ile1 5 1065PRTHomo sapiens 6Ser Gly His Thr Ala1 576PRTHomo sapiens
7Phe Gln Gly Asn Ser Ala1 5815PRTHomo sapiens 8Ala Ser Ile Arg Thr
Gly Pro Phe Phe Ser Gly Asn Thr Ile Tyr1 5 10 159134PRTHomo sapiens
9Met Ala Cys Pro Gly Phe Leu Trp Ala Leu Val Ile Ser Thr Cys Leu1 5
10 15Glu Phe Ser Met Ala Gln Thr Val Thr Gln Ser Gln Pro Glu Met
Ser 20 25 30Val Gln Glu Ala Glu Thr Val Thr Leu Ser Cys Thr Tyr Asp
Thr Ser 35 40 45Glu Ser Asp Tyr Tyr Leu Phe Trp Tyr Lys Gln Pro Pro
Ser Arg Gln 50 55 60Met Ile Leu Val Ile Arg Gln Glu Ala Tyr Lys Gln
Gln Asn Ala Thr65 70 75 80Glu Asn Arg Phe Ser Val Asn Phe Gln Lys
Ala Ala Lys Ser Phe Ser 85 90 95Leu Lys Ile Ser Asp Ser Gln Leu Gly
Asp Ala Ala Met Tyr Phe Cys 100 105 110Ala Leu Arg Ser Ser Gly Thr
Tyr Lys Tyr Ile Phe Gly Thr Gly Thr 115 120 125Arg Leu Lys Val Leu
Ala 13010137PRTHomo sapiens 10Met Gly Thr Arg Leu Leu Phe Trp Val
Ala Phe Cys Leu Leu Gly Ala1 5 10 15Asp His Thr Gly Ala Gly Val Ser
Gln Ser Pro Ser Asn Lys Val Thr 20 25 30Glu Lys Gly Lys Asp Val Glu
Leu Arg Cys Asp Pro Ile Ser Gly His 35 40 45Thr Ala Leu Tyr Trp Tyr
Arg Gln Ser Leu Gly Gln Gly Leu Glu Phe 50 55 60Leu Ile Tyr Phe Gln
Gly Asn Ser Ala Pro Asp Lys Ser Gly Leu Pro65 70 75 80Ser Asp Arg
Phe Ser Ala Glu Arg Thr Gly Gly Ser Val Ser Thr Leu 85 90 95Thr Ile
Gln Arg Thr Gln Gln Glu Asp Ser Ala Val Tyr Leu Cys Ala 100 105
110Ser Ile Arg Thr Gly Pro Phe Phe Ser Gly Asn Thr Ile Tyr Phe Gly
115 120 125Glu Gly Ser Trp Leu Thr Val Val Glu 130 13511275PRTHomo
sapiens 11Met Ala Cys Pro Gly Phe Leu Trp Ala Leu Val Ile Ser Thr
Cys Leu1 5 10 15Glu Phe Ser Met Ala Gln Thr Val Thr Gln Ser Gln Pro
Glu Met Ser 20 25 30Val Gln Glu Ala Glu Thr Val Thr Leu Ser Cys Thr
Tyr Asp Thr Ser 35 40 45Glu Ser Asp Tyr Tyr Leu Phe Trp Tyr Lys Gln
Pro Pro Ser Arg Gln 50 55 60Met Ile Leu Val Ile Arg Gln Glu Ala Tyr
Lys Gln Gln Asn Ala Thr65 70 75 80Glu Asn Arg Phe Ser Val Asn Phe
Gln Lys Ala Ala Lys Ser Phe Ser 85 90 95Leu Lys Ile Ser Asp Ser Gln
Leu Gly Asp Ala Ala Met Tyr Phe Cys 100 105 110Ala Leu Arg Ser Ser
Gly Thr Tyr Lys Tyr Ile Phe Gly Thr Gly Thr 115 120 125Arg Leu Lys
Val Leu Ala Asn Ile Gln Asn Pro Asp Pro Ala Val Tyr 130 135 140Gln
Leu Arg Asp Ser Lys Ser Ser Asp Lys Ser Val Cys Leu Phe Thr145 150
155 160Asp Phe Asp Ser Gln Thr Asn Val Ser Gln Ser Lys Asp Ser Asp
Val 165 170 175Tyr Ile Thr Asp Lys Thr Val Leu Asp Met Arg Ser Met
Asp Phe Lys 180 185 190Ser Asn Ser Ala Val Ala Trp Ser Asn Lys Ser
Asp Phe Ala Cys Ala 195 200 205Asn Ala Phe Asn Asn Ser Ile Ile Pro
Glu Asp Thr Phe Phe Pro Ser 210 215 220Pro Glu Ser Ser Cys Asp Val
Lys Leu Val Glu Lys Ser Phe Glu Thr225 230 235 240Asp Thr Asn Leu
Asn Phe Gln Asn Leu Ser Val Ile Gly Phe Arg Ile 245 250 255Leu Leu
Leu Lys Val Ala Gly Phe Asn Leu Leu Met Thr Leu Arg Leu 260 265
270Trp Ser Ser 27512313PRTHomo sapiens 12Met Gly Thr Arg Leu Leu
Phe Trp Val Ala Phe Cys Leu Leu Gly Ala1 5 10 15Asp His Thr Gly Ala
Gly Val Ser Gln Ser Pro Ser Asn Lys Val Thr 20 25 30Glu Lys Gly Lys
Asp Val Glu Leu Arg Cys Asp Pro Ile Ser Gly His 35 40 45Thr Ala Leu
Tyr Trp Tyr Arg Gln Ser Leu Gly Gln Gly Leu Glu Phe 50 55 60Leu Ile
Tyr Phe Gln Gly Asn Ser Ala Pro Asp Lys Ser Gly Leu Pro65 70 75
80Ser Asp Arg Phe Ser Ala Glu Arg Thr Gly Gly Ser Val Ser Thr Leu
85 90 95Thr Ile Gln Arg Thr Gln Gln Glu Asp Ser Ala Val Tyr Leu Cys
Ala 100 105 110Ser Ile Arg Thr Gly Pro Phe Phe Ser Gly Asn Thr Ile
Tyr Phe Gly 115 120 125Glu Gly Ser Trp Leu Thr Val Val Glu Asp Leu
Asn Lys Val Phe Pro 130 135 140Pro Glu Val Ala Val Phe Glu Pro Ser
Glu Ala Glu Ile Ser His Thr145 150 155 160Gln Lys Ala Thr Leu Val
Cys Leu Ala Thr Gly Phe Phe Pro Asp His 165 170 175Val Glu Leu Ser
Trp Trp Val Asn Gly Lys Glu Val His Ser Gly Val 180 185 190Ser Thr
Asp Pro Gln Pro Leu Lys Glu Gln Pro Ala Leu Asn Asp Ser 195 200
205Arg Tyr Cys Leu Ser Ser Arg Leu Arg Val Ser Ala Thr Phe Trp Gln
210 215 220Asn Pro Arg Asn His Phe Arg Cys Gln Val Gln Phe Tyr Gly
Leu Ser225 230 235 240Glu Asn Asp Glu Trp Thr Gln Asp Arg Ala Lys
Pro Val Thr Gln Ile 245 250 255Val Ser Ala Glu Ala Trp Gly Arg Ala
Asp Cys Gly Phe Thr Ser Val 260 265 270Ser Tyr Gln Gln Gly Val Leu
Ser Ala Thr Ile Leu Tyr Glu Ile Leu 275 280 285Leu Gly Lys Ala Thr
Leu Tyr Ala Val Leu Val Ser Ala Leu Val Leu 290 295 300Met Ala Met
Val Lys Arg Lys Asp Phe305 310137PRTHomo sapiens 13Thr Ser Glu Ser
Asp Tyr Tyr1 5147PRTHomo sapiens 14Gln Glu Ala Tyr Lys Gln Gln1
51517PRTHomo sapiens 15Ala Tyr Thr Val Pro Ser Asn Ala Gly Gly Thr
Ser Tyr Gly Lys Leu1 5 10 15Thr165PRTHomo sapiens 16Ser Asn His Leu
Tyr1 5176PRTHomo sapiens 17Phe Tyr Asn Asn Glu Ile1 51812PRTHomo
sapiens 18Ala Ser Ser Glu Arg Gly Gln Gly Tyr Gly Tyr Thr1 5
1019140PRTHomo sapiens 19Met Ala Cys Pro Gly Phe Leu Trp Ala Leu
Val Ile Ser Thr Cys Leu1 5 10 15Glu Phe Ser Met Ala Gln Thr Val Thr
Gln Ser Gln Pro Glu Met Ser 20 25 30Val Gln Glu Ala Glu Thr Val Thr
Leu Ser Cys Thr Tyr Asp Thr Ser 35 40 45Glu Ser Asp Tyr Tyr Leu Phe
Trp Tyr Lys Gln Pro Pro Ser Arg Gln 50 55 60Met Ile Leu Val Ile Arg
Gln Glu Ala Tyr Lys Gln Gln Asn Ala Thr65 70 75 80Glu Asn Arg Phe
Ser Val Asn Phe Gln Lys Ala Ala Lys Ser Phe Ser 85 90 95Leu Lys Ile
Ser Asp Ser Gln Leu Gly Asp Ala Ala Met Tyr Phe Cys 100 105 110Ala
Tyr Thr Val Pro Ser Asn Ala Gly Gly Thr Ser Tyr Gly Lys Leu 115 120
125Thr Phe Gly Gln Gly Thr Ile Leu Thr Val His Pro 130 135
14020134PRTHomo sapiens 20Met Asp Thr Trp Leu Val Cys Trp Ala Ile
Phe Ser Leu Leu Lys Ala1 5 10 15Gly Leu Thr Glu Pro Glu Val Thr Gln
Thr Pro Ser His Gln Val Thr 20 25 30Gln Met Gly Gln Glu Val Ile Leu
Arg Cys Val Pro Ile Ser Asn His 35 40 45Leu Tyr Phe Tyr Trp Tyr Arg
Gln Ile Leu Gly Gln Lys Val Glu Phe 50 55 60Leu Val Ser Phe Tyr Asn
Asn Glu Ile Ser Glu Lys Ser Glu Ile Phe65 70 75 80Asp Asp Gln Phe
Ser Val Glu Arg Pro Asp Gly Ser Asn Phe Thr Leu 85 90 95Lys Ile Arg
Ser Thr Lys Leu Glu Asp Ser Ala Met Tyr Phe Cys Ala 100 105 110Ser
Ser Glu Arg Gly Gln Gly Tyr Gly Tyr Thr Phe Gly Ser Gly Thr 115 120
125Arg Leu Thr Val Val Glu 13021281PRTHomo sapiens 21Met Ala Cys
Pro Gly Phe Leu Trp Ala Leu Val Ile Ser Thr Cys Leu1 5 10 15Glu Phe
Ser Met Ala Gln Thr Val Thr Gln Ser Gln Pro Glu Met Ser 20 25 30Val
Gln Glu Ala Glu Thr Val Thr Leu Ser Cys Thr Tyr Asp Thr Ser 35 40
45Glu Ser Asp Tyr Tyr Leu Phe Trp Tyr Lys Gln Pro Pro Ser Arg Gln
50 55 60Met Ile Leu Val Ile Arg Gln Glu Ala Tyr Lys Gln Gln Asn Ala
Thr65 70 75 80Glu Asn Arg Phe Ser Val Asn Phe Gln Lys Ala Ala Lys
Ser Phe Ser 85 90 95Leu Lys Ile Ser Asp Ser Gln Leu Gly Asp Ala Ala
Met Tyr Phe Cys 100 105 110Ala Tyr Thr Val Pro Ser Asn Ala Gly Gly
Thr Ser Tyr Gly Lys Leu 115 120 125Thr Phe Gly Gln Gly Thr Ile Leu
Thr Val His Pro Asn Ile Gln Asn 130 135 140Pro Asp Pro Ala Val Tyr
Gln Leu Arg Asp Ser Lys Ser Ser Asp Lys145 150 155 160Ser Val Cys
Leu Phe Thr Asp Phe Asp Ser Gln Thr Asn Val Ser Gln 165 170 175Ser
Lys Asp Ser Asp Val Tyr Ile Thr Asp Lys Thr Val Leu Asp Met 180 185
190Arg Ser Met Asp Phe Lys Ser Asn Ser Ala Val Ala Trp Ser Asn Lys
195 200 205Ser Asp Phe Ala Cys Ala Asn Ala Phe Asn Asn Ser Ile Ile
Pro Glu 210 215 220Asp Thr Phe Phe Pro Ser Pro Glu Ser Ser Cys Asp
Val Lys Leu Val225 230 235 240Glu Lys Ser Phe Glu Thr Asp Thr Asn
Leu Asn Phe Gln Asn Leu Ser 245 250 255Val Ile Gly Phe Arg Ile Leu
Leu Leu Lys Val Ala Gly Phe Asn Leu 260 265 270Leu Met Thr Leu Arg
Leu Trp Ser Ser 275 28022310PRTHomo sapiens 22Met Asp Thr Trp Leu
Val Cys Trp Ala Ile Phe Ser Leu Leu Lys Ala1 5 10 15Gly Leu Thr Glu
Pro Glu Val Thr Gln Thr Pro Ser His Gln Val Thr 20 25 30Gln Met Gly
Gln Glu Val Ile Leu Arg Cys Val Pro Ile Ser Asn His 35 40 45Leu Tyr
Phe Tyr Trp Tyr Arg Gln Ile Leu Gly Gln Lys Val Glu Phe 50 55 60Leu
Val Ser Phe Tyr Asn Asn Glu Ile Ser Glu Lys Ser Glu Ile Phe65 70 75
80Asp Asp Gln Phe Ser Val Glu Arg Pro Asp Gly Ser Asn Phe Thr Leu
85 90 95Lys Ile Arg Ser Thr Lys Leu Glu Asp Ser Ala Met Tyr Phe Cys
Ala 100 105 110Ser Ser Glu Arg Gly Gln Gly Tyr Gly Tyr Thr Phe Gly
Ser Gly Thr 115 120 125Arg Leu Thr Val Val Glu Asp Leu Asn Lys Val
Phe Pro Pro Glu Val 130 135 140Ala Val Phe Glu Pro Ser Glu Ala Glu
Ile Ser His Thr Gln Lys Ala145 150 155 160Thr Leu Val Cys Leu Ala
Thr Gly Phe Phe Pro Asp His Val Glu Leu 165 170 175Ser Trp Trp Val
Asn Gly Lys Glu Val His Ser Gly Val Ser Thr Asp 180 185 190Pro Gln
Pro Leu Lys Glu Gln Pro Ala Leu Asn Asp Ser Arg Tyr Cys 195 200
205Leu Ser Ser Arg Leu Arg Val Ser Ala Thr Phe Trp Gln Asn Pro Arg
210 215 220Asn His Phe Arg Cys Gln Val Gln Phe Tyr Gly Leu Ser Glu
Asn Asp225 230 235 240Glu Trp Thr Gln Asp Arg Ala Lys Pro Val Thr
Gln Ile Val Ser Ala 245 250 255Glu Ala Trp Gly Arg Ala Asp Cys Gly
Phe Thr Ser Val Ser Tyr Gln 260 265 270Gln Gly Val Leu Ser Ala Thr
Ile Leu Tyr Glu Ile Leu Leu Gly Lys 275 280 285Ala Thr Leu Tyr Ala
Val Leu Val Ser Ala Leu Val Leu Met Ala Met 290 295 300Val Lys Arg
Lys Asp Phe305 31023141PRTHomo sapiens 23Asn Ile Gln Asn Pro Asp
Pro Ala Val Tyr Gln Leu Arg Asp Ser Lys1 5 10 15Ser Ser Asp Lys Ser
Val Cys Leu Phe Thr Asp Phe Asp Ser Gln Thr 20 25 30Asn Val Ser Gln
Ser Lys Asp Ser Asp Val Tyr Ile Thr Asp Lys Thr 35 40 45Val Leu Asp
Met Arg Ser Met Asp Phe Lys Ser Asn Ser Ala Val Ala 50 55 60Trp Ser
Asn Lys Ser Asp Phe Ala Cys Ala Asn Ala Phe Asn Asn Ser65 70 75
80Ile Ile Pro Glu Asp Thr Phe Phe Pro Ser Pro Glu Ser Ser Cys Asp
85 90 95Val Lys Leu Val Glu Lys Ser Phe Glu Thr Asp Thr Asn Leu Asn
Phe 100 105 110Gln Asn Leu Ser Val Ile Gly Phe Arg Ile Leu Leu Leu
Lys Val Ala 115 120 125Gly Phe Asn Leu Leu Met Thr Leu Arg Leu Trp
Ser Ser 130 135 14024176PRTHomo sapiens 24Asp Leu Asn Lys Val Phe
Pro Pro Glu Val Ala Val Phe Glu Pro Ser1 5 10 15Glu Ala Glu Ile Ser
His Thr Gln Lys Ala Thr Leu Val Cys Leu Ala 20 25 30Thr Gly Phe Phe
Pro Asp His Val Glu Leu Ser Trp Trp Val Asn Gly 35 40 45Lys Glu Val
His Ser Gly Val Ser Thr Asp Pro Gln Pro Leu Lys Glu 50 55 60Gln Pro
Ala Leu Asn Asp Ser Arg Tyr Cys Leu Ser Ser Arg Leu Arg65 70 75
80Val Ser Ala Thr Phe Trp Gln Asn Pro Arg Asn His Phe Arg Cys Gln
85 90 95Val Gln Phe Tyr Gly Leu Ser Glu Asn Asp Glu Trp Thr Gln Asp
Arg 100 105 110Ala Lys Pro Val Thr Gln Ile Val Ser Ala Glu Ala Trp
Gly Arg Ala
115 120 125Asp Cys Gly Phe Thr Ser Val Ser Tyr Gln Gln Gly Val Leu
Ser Ala 130 135 140Thr Ile Leu Tyr Glu Ile Leu Leu Gly Lys Ala Thr
Leu Tyr Ala Val145 150 155 160Leu Val Ser Ala Leu Val Leu Met Ala
Met Val Lys Arg Lys Asp Phe 165 170 17525137PRTMus musculus 25Asn
Ile Gln Asn Pro Glu Pro Ala Val Tyr Gln Leu Lys Asp Pro Arg1 5 10
15Ser Gln Asp Ser Thr Leu Cys Leu Phe Thr Asp Phe Asp Ser Gln Ile
20 25 30Asn Val Pro Lys Thr Met Glu Ser Gly Thr Phe Ile Thr Asp Lys
Thr 35 40 45Val Leu Asp Met Lys Ala Met Asp Ser Lys Ser Asn Gly Ala
Ile Ala 50 55 60Trp Ser Asn Gln Thr Ser Phe Thr Cys Gln Asp Ile Phe
Lys Glu Thr65 70 75 80Asn Ala Thr Tyr Pro Ser Ser Asp Val Pro Cys
Asp Ala Thr Leu Thr 85 90 95Glu Lys Ser Phe Glu Thr Asp Met Asn Leu
Asn Phe Gln Asn Leu Ser 100 105 110Val Met Gly Leu Arg Ile Leu Leu
Leu Lys Val Ala Gly Phe Asn Leu 115 120 125Leu Met Thr Leu Arg Leu
Trp Ser Ser 130 13526172PRTMus musculus 26Asp Leu Arg Asn Val Thr
Pro Pro Lys Val Ser Leu Phe Glu Pro Ser1 5 10 15Lys Ala Glu Ile Ala
Asn Lys Gln Lys Ala Thr Leu Val Cys Leu Ala 20 25 30Arg Gly Phe Phe
Pro Asp His Val Glu Leu Ser Trp Trp Val Asn Gly 35 40 45Lys Glu Val
His Ser Gly Val Ser Thr Asp Pro Gln Ala Tyr Lys Glu 50 55 60Ser Asn
Tyr Ser Tyr Cys Leu Ser Ser Arg Leu Arg Val Ser Ala Thr65 70 75
80Phe Trp His Asn Pro Arg Asn His Phe Arg Cys Gln Val Gln Phe His
85 90 95Gly Leu Ser Glu Glu Asp Lys Trp Pro Glu Gly Ser Pro Lys Pro
Val 100 105 110Thr Gln Asn Ile Ser Ala Glu Ala Trp Gly Arg Ala Asp
Cys Gly Ile 115 120 125Thr Ser Ala Ser Tyr His Gln Gly Val Leu Ser
Ala Thr Ile Leu Tyr 130 135 140Glu Ile Leu Leu Gly Lys Ala Thr Leu
Tyr Ala Val Leu Val Ser Gly145 150 155 160Leu Val Leu Met Ala Met
Val Lys Arg Lys Asn Ser 165 17027271PRTArtificial SequenceSynthetic
27Met Ala Cys Pro Gly Phe Leu Trp Ala Leu Val Ile Ser Thr Cys Leu1
5 10 15Glu Phe Ser Met Ala Gln Thr Val Thr Gln Ser Gln Pro Glu Met
Ser 20 25 30Val Gln Glu Ala Glu Thr Val Thr Leu Ser Cys Thr Tyr Asp
Thr Ser 35 40 45Glu Ser Asp Tyr Tyr Leu Phe Trp Tyr Lys Gln Pro Pro
Ser Arg Gln 50 55 60Met Ile Leu Val Ile Arg Gln Glu Ala Tyr Lys Gln
Gln Asn Ala Thr65 70 75 80Glu Asn Arg Phe Ser Val Asn Phe Gln Lys
Ala Ala Lys Ser Phe Ser 85 90 95Leu Lys Ile Ser Asp Ser Gln Leu Gly
Asp Ala Ala Met Tyr Phe Cys 100 105 110Ala Leu Arg Ser Ser Gly Thr
Tyr Lys Tyr Ile Phe Gly Thr Gly Thr 115 120 125Arg Leu Lys Val Leu
Ala Asn Ile Gln Asn Pro Glu Pro Ala Val Tyr 130 135 140Gln Leu Lys
Asp Pro Arg Ser Gln Asp Ser Thr Leu Cys Leu Phe Thr145 150 155
160Asp Phe Asp Ser Gln Ile Asn Val Pro Lys Thr Met Glu Ser Gly Thr
165 170 175Phe Ile Thr Asp Lys Thr Val Leu Asp Met Lys Ala Met Asp
Ser Lys 180 185 190Ser Asn Gly Ala Ile Ala Trp Ser Asn Gln Thr Ser
Phe Thr Cys Gln 195 200 205Asp Ile Phe Lys Glu Thr Asn Ala Thr Tyr
Pro Ser Ser Asp Val Pro 210 215 220Cys Asp Ala Thr Leu Thr Glu Lys
Ser Phe Glu Thr Asp Met Asn Leu225 230 235 240Asn Phe Gln Asn Leu
Ser Val Met Gly Leu Arg Ile Leu Leu Leu Lys 245 250 255Val Ala Gly
Phe Asn Leu Leu Met Thr Leu Arg Leu Trp Ser Ser 260 265
27028309PRTArtificial SequenceSynthetic 28Met Gly Thr Arg Leu Leu
Phe Trp Val Ala Phe Cys Leu Leu Gly Ala1 5 10 15Asp His Thr Gly Ala
Gly Val Ser Gln Ser Pro Ser Asn Lys Val Thr 20 25 30Glu Lys Gly Lys
Asp Val Glu Leu Arg Cys Asp Pro Ile Ser Gly His 35 40 45Thr Ala Leu
Tyr Trp Tyr Arg Gln Ser Leu Gly Gln Gly Leu Glu Phe 50 55 60Leu Ile
Tyr Phe Gln Gly Asn Ser Ala Pro Asp Lys Ser Gly Leu Pro65 70 75
80Ser Asp Arg Phe Ser Ala Glu Arg Thr Gly Gly Ser Val Ser Thr Leu
85 90 95Thr Ile Gln Arg Thr Gln Gln Glu Asp Ser Ala Val Tyr Leu Cys
Ala 100 105 110Ser Ile Arg Thr Gly Pro Phe Phe Ser Gly Asn Thr Ile
Tyr Phe Gly 115 120 125Glu Gly Ser Trp Leu Thr Val Val Glu Asp Leu
Arg Asn Val Thr Pro 130 135 140Pro Lys Val Ser Leu Phe Glu Pro Ser
Lys Ala Glu Ile Ala Asn Lys145 150 155 160Gln Lys Ala Thr Leu Val
Cys Leu Ala Arg Gly Phe Phe Pro Asp His 165 170 175Val Glu Leu Ser
Trp Trp Val Asn Gly Lys Glu Val His Ser Gly Val 180 185 190Ser Thr
Asp Pro Gln Ala Tyr Lys Glu Ser Asn Tyr Ser Tyr Cys Leu 195 200
205Ser Ser Arg Leu Arg Val Ser Ala Thr Phe Trp His Asn Pro Arg Asn
210 215 220His Phe Arg Cys Gln Val Gln Phe His Gly Leu Ser Glu Glu
Asp Lys225 230 235 240Trp Pro Glu Gly Ser Pro Lys Pro Val Thr Gln
Asn Ile Ser Ala Glu 245 250 255Ala Trp Gly Arg Ala Asp Cys Gly Ile
Thr Ser Ala Ser Tyr His Gln 260 265 270Gly Val Leu Ser Ala Thr Ile
Leu Tyr Glu Ile Leu Leu Gly Lys Ala 275 280 285Thr Leu Tyr Ala Val
Leu Val Ser Gly Leu Val Leu Met Ala Met Val 290 295 300Lys Arg Lys
Asn Ser3052911PRTArtificial SequenceSyntheticMISC_FEATURE(4)..(5)X
at 4 and 5 is Ser, Ala, Leu, Ile, Val, or MetMISC_FEATURE(6)..(6)X
at 6 is Gly, Ala, Leu, Ile, Val, or MetMISC_FEATURE(7)..(7)X at 7
is Thr, Ala, Leu, Ile, Val, or MetMISC_FEATURE(7)..(7)X at 7 is
Thr, Ala, Leu, Ile, Val, or Met 29Ala Leu Arg Xaa Xaa Xaa Xaa Tyr
Lys Tyr Ile1 5 103015PRTArtificial
SequenceSyntheticMISC_FEATURE(4)..(4)X at 4 is Arg, Ala, Leu, Ile,
Val, or MetMISC_FEATURE(5)..(5)X at 5 is Thr, Ala, Leu, Ile, Val,
or MetMISC_FEATURE(6)..(6)X at 6 is Gly, Ala, Leu, Ile, Val, or
MetMISC_FEATURE(7)..(7)X at 7 is Pro, Ala, Leu, Ile, Val, or Met
30Ala Ser Ile Xaa Xaa Xaa Xaa Phe Phe Ser Gly Asn Thr Ile Tyr1 5 10
1531134PRTArtificial
SequenceSyntheticMISC_FEATURE(116)..(117)MISC_FEATURE(116)..(117)MISC_FEA-
TURE(118)..(118)MISC_FEATURE(119)..(119) 31Met Ala Cys Pro Gly Phe
Leu Trp Ala Leu Val Ile Ser Thr Cys Leu1 5 10 15Glu Phe Ser Met Ala
Gln Thr Val Thr Gln Ser Gln Pro Glu Met Ser 20 25 30Val Gln Glu Ala
Glu Thr Val Thr Leu Ser Cys Thr Tyr Asp Thr Ser 35 40 45Glu Ser Asp
Tyr Tyr Leu Phe Trp Tyr Lys Gln Pro Pro Ser Arg Gln 50 55 60Met Ile
Leu Val Ile Arg Gln Glu Ala Tyr Lys Gln Gln Asn Ala Thr65 70 75
80Glu Asn Arg Phe Ser Val Asn Phe Gln Lys Ala Ala Lys Ser Phe Ser
85 90 95Leu Lys Ile Ser Asp Ser Gln Leu Gly Asp Ala Ala Met Tyr Phe
Cys 100 105 110Ala Leu Arg Xaa Xaa Xaa Xaa Tyr Lys Tyr Ile Phe Gly
Thr Gly Thr 115 120 125Arg Leu Lys Val Leu Ala
13032137PRTArtificial SequenceSyntheticmisc_feature(115)..(115)X at
115 is Arg, Ala, Leu, Ile, Val, or Metmisc_feature(116)..(116)X at
116 is Thr, Ala, Leu, Ile, Val, or Metmisc_feature(117)..(117)X at
117 is Gly, Ala, Leu, Ile, Val, or Metmisc_feature(118)..(118)X at
118 is Pro, Ala, Leu, Ile, Val, or Met 32Met Gly Thr Arg Leu Leu
Phe Trp Val Ala Phe Cys Leu Leu Gly Ala1 5 10 15Asp His Thr Gly Ala
Gly Val Ser Gln Ser Pro Ser Asn Lys Val Thr 20 25 30Glu Lys Gly Lys
Asp Val Glu Leu Arg Cys Asp Pro Ile Ser Gly His 35 40 45Thr Ala Leu
Tyr Trp Tyr Arg Gln Ser Leu Gly Gln Gly Leu Glu Phe 50 55 60Leu Ile
Tyr Phe Gln Gly Asn Ser Ala Pro Asp Lys Ser Gly Leu Pro65 70 75
80Ser Asp Arg Phe Ser Ala Glu Arg Thr Gly Gly Ser Val Ser Thr Leu
85 90 95Thr Ile Gln Arg Thr Gln Gln Glu Asp Ser Ala Val Tyr Leu Cys
Ala 100 105 110Ser Ile Xaa Xaa Xaa Xaa Phe Phe Ser Gly Asn Thr Ile
Tyr Phe Gly 115 120 125Glu Gly Ser Trp Leu Thr Val Val Glu 130
13533275PRTArtificial SequenceSyntheticMISC_FEATURE(116)..(117)X at
116 and 117 is Ser, Ala, Leu, Ile, Val, or
MetMISC_FEATURE(118)..(118)X at 118 is Gly, Ala, Leu, Ile, Val, or
MetMISC_FEATURE(119)..(119)X at 119 is Thr, Ala, Leu, Ile, Val, or
Met 33Met Ala Cys Pro Gly Phe Leu Trp Ala Leu Val Ile Ser Thr Cys
Leu1 5 10 15Glu Phe Ser Met Ala Gln Thr Val Thr Gln Ser Gln Pro Glu
Met Ser 20 25 30Val Gln Glu Ala Glu Thr Val Thr Leu Ser Cys Thr Tyr
Asp Thr Ser 35 40 45Glu Ser Asp Tyr Tyr Leu Phe Trp Tyr Lys Gln Pro
Pro Ser Arg Gln 50 55 60Met Ile Leu Val Ile Arg Gln Glu Ala Tyr Lys
Gln Gln Asn Ala Thr65 70 75 80Glu Asn Arg Phe Ser Val Asn Phe Gln
Lys Ala Ala Lys Ser Phe Ser 85 90 95Leu Lys Ile Ser Asp Ser Gln Leu
Gly Asp Ala Ala Met Tyr Phe Cys 100 105 110Ala Leu Arg Xaa Xaa Xaa
Xaa Tyr Lys Tyr Ile Phe Gly Thr Gly Thr 115 120 125Arg Leu Lys Val
Leu Ala Asn Ile Gln Asn Pro Asp Pro Ala Val Tyr 130 135 140Gln Leu
Arg Asp Ser Lys Ser Ser Asp Lys Ser Val Cys Leu Phe Thr145 150 155
160Asp Phe Asp Ser Gln Thr Asn Val Ser Gln Ser Lys Asp Ser Asp Val
165 170 175Tyr Ile Thr Asp Lys Thr Val Leu Asp Met Arg Ser Met Asp
Phe Lys 180 185 190Ser Asn Ser Ala Val Ala Trp Ser Asn Lys Ser Asp
Phe Ala Cys Ala 195 200 205Asn Ala Phe Asn Asn Ser Ile Ile Pro Glu
Asp Thr Phe Phe Pro Ser 210 215 220Pro Glu Ser Ser Cys Asp Val Lys
Leu Val Glu Lys Ser Phe Glu Thr225 230 235 240Asp Thr Asn Leu Asn
Phe Gln Asn Leu Ser Val Ile Gly Phe Arg Ile 245 250 255Leu Leu Leu
Lys Val Ala Gly Phe Asn Leu Leu Met Thr Leu Arg Leu 260 265 270Trp
Ser Ser 27534313PRTArtificial
SequenceSyntheticMISC_FEATURE(115)..(115)X at 115 is Arg, Ala, Leu,
Ile, Val, or MetMISC_FEATURE(116)..(116)X at 116 is Thr, Ala, Leu,
Ile, Val, or MetMISC_FEATURE(117)..(117)X at 117 is Gly, Ala, Leu,
Ile, Val, or MetMISC_FEATURE(118)..(118)X at 118 is Pro, Ala, Leu,
Ile, Val, or Met 34Met Gly Thr Arg Leu Leu Phe Trp Val Ala Phe Cys
Leu Leu Gly Ala1 5 10 15Asp His Thr Gly Ala Gly Val Ser Gln Ser Pro
Ser Asn Lys Val Thr 20 25 30Glu Lys Gly Lys Asp Val Glu Leu Arg Cys
Asp Pro Ile Ser Gly His 35 40 45Thr Ala Leu Tyr Trp Tyr Arg Gln Ser
Leu Gly Gln Gly Leu Glu Phe 50 55 60Leu Ile Tyr Phe Gln Gly Asn Ser
Ala Pro Asp Lys Ser Gly Leu Pro65 70 75 80Ser Asp Arg Phe Ser Ala
Glu Arg Thr Gly Gly Ser Val Ser Thr Leu 85 90 95Thr Ile Gln Arg Thr
Gln Gln Glu Asp Ser Ala Val Tyr Leu Cys Ala 100 105 110Ser Ile Xaa
Xaa Xaa Xaa Phe Phe Ser Gly Asn Thr Ile Tyr Phe Gly 115 120 125Glu
Gly Ser Trp Leu Thr Val Val Glu Asp Leu Asn Lys Val Phe Pro 130 135
140Pro Glu Val Ala Val Phe Glu Pro Ser Glu Ala Glu Ile Ser His
Thr145 150 155 160Gln Lys Ala Thr Leu Val Cys Leu Ala Thr Gly Phe
Phe Pro Asp His 165 170 175Val Glu Leu Ser Trp Trp Val Asn Gly Lys
Glu Val His Ser Gly Val 180 185 190Ser Thr Asp Pro Gln Pro Leu Lys
Glu Gln Pro Ala Leu Asn Asp Ser 195 200 205Arg Tyr Cys Leu Ser Ser
Arg Leu Arg Val Ser Ala Thr Phe Trp Gln 210 215 220Asn Pro Arg Asn
His Phe Arg Cys Gln Val Gln Phe Tyr Gly Leu Ser225 230 235 240Glu
Asn Asp Glu Trp Thr Gln Asp Arg Ala Lys Pro Val Thr Gln Ile 245 250
255Val Ser Ala Glu Ala Trp Gly Arg Ala Asp Cys Gly Phe Thr Ser Val
260 265 270Ser Tyr Gln Gln Gly Val Leu Ser Ala Thr Ile Leu Tyr Glu
Ile Leu 275 280 285Leu Gly Lys Ala Thr Leu Tyr Ala Val Leu Val Ser
Ala Leu Val Leu 290 295 300Met Ala Met Val Lys Arg Lys Asp Phe305
31035141PRTHomo sapiens 35Asn Ile Gln Asn Pro Asp Pro Ala Val Tyr
Gln Leu Arg Asp Ser Lys1 5 10 15Ser Ser Asp Lys Ser Val Cys Leu Phe
Thr Asp Phe Asp Ser Gln Thr 20 25 30Asn Val Ser Gln Ser Lys Asp Ser
Asp Val Tyr Ile Thr Asp Lys Thr 35 40 45Val Leu Asp Met Arg Ser Met
Asp Phe Lys Ser Asn Ser Ala Val Ala 50 55 60Trp Ser Asn Lys Ser Asp
Phe Ala Cys Ala Asn Ala Phe Asn Asn Ser65 70 75 80Ile Ile Pro Glu
Asp Thr Phe Phe Pro Ser Pro Glu Ser Ser Cys Asp 85 90 95Val Lys Leu
Val Glu Lys Ser Phe Glu Thr Asp Thr Asn Leu Asn Phe 100 105 110Gln
Asn Leu Ser Val Ile Gly Phe Arg Ile Leu Leu Leu Lys Val Ala 115 120
125Gly Phe Asn Leu Leu Met Thr Leu Arg Leu Trp Ser Ser 130 135
14036176PRTHomo sapiens 36Asp Leu Asn Lys Val Phe Pro Pro Glu Val
Ala Val Phe Glu Pro Ser1 5 10 15Glu Ala Glu Ile Ser His Thr Gln Lys
Ala Thr Leu Val Cys Leu Ala 20 25 30Thr Gly Phe Phe Pro Asp His Val
Glu Leu Ser Trp Trp Val Asn Gly 35 40 45Lys Glu Val His Ser Gly Val
Ser Thr Asp Pro Gln Pro Leu Lys Glu 50 55 60Gln Pro Ala Leu Asn Asp
Ser Arg Tyr Cys Leu Ser Ser Arg Leu Arg65 70 75 80Val Ser Ala Thr
Phe Trp Gln Asn Pro Arg Asn His Phe Arg Cys Gln 85 90 95Val Gln Phe
Tyr Gly Leu Ser Glu Asn Asp Glu Trp Thr Gln Asp Arg 100 105 110Ala
Lys Pro Val Thr Gln Ile Val Ser Ala Glu Ala Trp Gly Arg Ala 115 120
125Asp Cys Gly Phe Thr Ser Val Ser Tyr Gln Gln Gly Val Leu Ser Ala
130 135 140Thr Ile Leu Tyr Glu Ile Leu Leu Gly Lys Ala Thr Leu Tyr
Ala Val145 150 155 160Leu Val Ser Ala Leu Val Leu Met Ala Met Val
Lys Arg Lys Asp Phe 165 170 17537828DNAHomo sapiens 37atggcatgcc
ctggcttcct gtgggcactt gtgatctcca cctgtcttga atttagcatg 60gctcagacag
tcactcagtc tcaaccagag atgtctgtgc aggaggcaga gaccgtgacc
120ctgagctgca catatgacac cagtgagagt gattattatt tattctggta
caagcagcct 180cccagcaggc agatgattct cgttattcgc caagaagctt
ataagcaaca gaatgcaaca 240gagaatcgtt tctctgtgaa cttccagaaa
gcagccaaat ccttcagtct caagatctca 300gactcacagc tgggggatgc
cgcgatgtat ttctgtgctc tccggagctc aggaacctac 360aaatacatct
ttggaacagg caccaggctg aaggttttag caaatatcca gaaccctgac
420cctgccgtgt accagctgag agactctaaa tccagtgaca agtctgtctg
cctattcacc 480gattttgatt ctcaaacaaa tgtgtcacaa agtaaggatt
ctgatgtgta tatcacagac 540aaaactgtgc tagacatgag gtctatggac
ttcaagagca acagtgctgt ggcctggagc 600aacaaatctg actttgcatg
tgcaaacgcc ttcaacaaca gcattattcc agaagacacc 660ttcttcccca
gcccagaaag ttcctgtgat gtcaagctgg tcgagaaaag ctttgaaaca
720gatacgaacc taaactttca aaacctgtca gtgattgggt tccgaatcct
cctcctgaaa 780gtggccgggt ttaatctgct catgacgctg cggctgtggt ccagctga
82838942DNAHomo sapiens 38atgggcacca ggctcctctt ctgggtggcc
ttctgtctcc tgggggcaga tcacacagga 60gctggagtct cccagtcccc cagtaacaag
gtcacagaga agggaaagga tgtagagctc 120aggtgtgatc caatttcagg
tcatactgcc ctttactggt accgacagag cctggggcag 180ggcctggagt
ttttaattta cttccaaggc aacagtgcac cagacaaatc agggctgccc
240agtgatcgct tctctgcaga gaggactggg ggatccgtct ccactctgac
gatccagcgc 300acacagcagg aggactcggc cgtgtatctc tgtgccagca
tccggacagg gccttttttc 360tctggaaaca ccatatattt tggagaggga
agttggctca ctgttgtaga ggacctgaac 420aaggtgttcc cacccgaggt
cgctgtgttt gagccatcag aagcagagat ctcccacacc 480caaaaggcca
cactggtgtg cctggccaca ggcttcttcc ctgaccacgt ggagctgagc
540tggtgggtga atgggaagga ggtgcacagt ggggtcagca cggacccgca
gcccctcaag 600gagcagcccg ccctcaatga ctccagatac tgcctgagca
gccgcctgag ggtctcggcc 660accttctggc agaacccccg caaccacttc
cgctgtcaag tccagttcta cgggctctcg 720gagaatgacg agtggaccca
ggatagggcc aaacccgtca cccagatcgt cagcgccgag 780gcctggggta
gagcagactg tggctttacc tcggtgtcct accagcaagg ggtcctgtct
840gccaccatcc tctatgagat cctgctaggg aaggccaccc tgtatgctgt
gctggtcagc 900gcccttgtgt tgatggccat ggtcaagaga aaggatttct ga
94239846DNAHomo sapiens 39atggcatgcc ctggcttcct gtgggcactt
gtgatctcca cctgtcttga atttagcatg 60gctcagacag tcactcagtc tcaaccagag
atgtctgtgc aggaggcaga gaccgtgacc 120ctgagctgca catatgacac
cagtgagagt gattattatt tattctggta caagcagcct 180cccagcaggc
agatgattct cgttattcgc caagaagctt ataagcaaca gaatgcaaca
240gagaatcgtt tctctgtgaa cttccagaaa gcagccaaat ccttcagtct
caagatctca 300gactcacagc tgggggatgc cgcgatgtat ttctgtgctt
acacggttcc ctctaatgct 360ggtggtacta gctatggaaa gctgacattt
ggacaaggga ccatcttgac tgtccatcca 420aatatccaga accctgaccc
tgccgtgtac cagctgagag actctaaatc cagtgacaag 480tctgtctgcc
tattcaccga ttttgattct caaacaaatg tgtcacaaag taaggattct
540gatgtgtata tcacagacaa aactgtgcta gacatgaggt ctatggactt
caagagcaac 600agtgctgtgg cctggagcaa caaatctgac tttgcatgtg
caaacgcctt caacaacagc 660attattccag aagacacctt cttccccagc
ccagaaagtt cctgtgatgt caagctggtc 720gagaaaagct ttgaaacaga
tacgaaccta aactttcaaa acctgtcagt gattgggttc 780cgaatcctcc
tcctgaaagt ggccgggttt aatctgctca tgacgctgcg gctgtggtcc 840agctga
84640933DNAHomo sapiens 40atggatacct ggctcgtatg ctgggcaatt
tttagtctct tgaaagcagg actcacagaa 60cctgaagtca cccagactcc cagccatcag
gtcacacaga tgggacagga agtgatcttg 120cgctgtgtcc ccatctctaa
tcacttatac ttctattggt acagacaaat cttggggcag 180aaagtcgagt
ttctggtttc cttttataat aatgaaatct cagagaagtc tgaaatattc
240gatgatcaat tctcagttga aaggcctgat ggatcaaatt tcactctgaa
gatccggtcc 300acaaagctgg aggactcagc catgtacttc tgtgccagca
gtgaaagggg acagggttat 360ggctacacct tcggttcggg gaccaggtta
accgttgtag aggacctgaa caaggtgttc 420ccacccgagg tcgctgtgtt
tgagccatca gaagcagaga tctcccacac ccaaaaggcc 480acactggtgt
gcctggccac aggcttcttc cccgaccacg tggagctgag ctggtgggtg
540aatgggaagg aggtgcacag tggggtcagc acagacccgc agcccctcaa
ggagcagccc 600gccctcaatg actccagata ctgcctgagc agccgcctga
gggtctcggc caccttctgg 660cagaaccccc gcaaccactt ccgctgtcaa
gtccagttct acgggctctc ggagaatgac 720gagtggaccc aggatagggc
caaacccgtc acccagatcg tcagcgccga ggcctggggt 780agagcagact
gtggctttac ctcggtgtcc taccagcaag gggtcctgtc tgccaccatc
840ctctatgaga tcctgctagg gaaggccacc ctgtatgctg tgctggtcag
cgcccttgtg 900ttgatggcca tggtcaagag aaaggatttc tga
93341816DNAArtificial SequenceSynthetic 41atggcatgcc ctggcttcct
gtgggcactt gtgatctcca cctgtcttga atttagcatg 60gctcagacag tcactcagtc
tcaaccagag atgtctgtgc aggaggcaga gaccgtgacc 120ctgagctgca
catatgacac cagtgagagt gattattatt tattctggta caagcagcct
180cccagcaggc agatgattct cgttattcgc caagaagctt ataagcaaca
gaatgcaaca 240gagaatcgtt tctctgtgaa cttccagaaa gcagccaaat
ccttcagtct caagatctca 300gactcacagc tgggggatgc cgcgatgtat
ttctgtgctc tccggagctc aggaacctac 360aaatacatct ttggaacagg
caccaggctg aaggttttag caaatatcca gaaccctgaa 420cctgctgtgt
accagttaaa agatcctcgg tctcaggaca gcaccctctg cctgttcacc
480gactttgact cccaaatcaa tgtgccgaaa accatggaat ctggaacgtt
catcactgac 540aaaactgtgc tggacatgaa agctatggat tccaagagca
atggggccat tgcctggagc 600aaccagacaa gcttcacctg ccaagatatc
ttcaaagaga ccaacgccac ctaccccagt 660tcagacgttc cctgtgatgc
cacgttgact gagaaaagct ttgaaacaga tatgaaccta 720aactttcaaa
acctgtcagt tatgggactc cgaatcctcc tgctgaaagt agccggattt
780aacctgctca tgacgctgag gctgtggtcc agttga 81642930DNAArtificial
SequenceSynthetic 42atgggcacca ggctcctctt ctgggtggcc ttctgtctcc
tgggggcaga tcacacagga 60gctggagtct cccagtcccc cagtaacaag gtcacagaga
agggaaagga tgtagagctc 120aggtgtgatc caatttcagg tcatactgcc
ctttactggt accgacagag cctggggcag 180ggcctggagt ttttaattta
cttccaaggc aacagtgcac cagacaaatc agggctgccc 240agtgatcgct
tctctgcaga gaggactggg ggatccgtct ccactctgac gatccagcgc
300acacagcagg aggactcggc cgtgtatctc tgtgccagca tccggacagg
gccttttttc 360tctggaaaca ccatatattt tggagaggga agttggctca
ctgttgtaga ggacctgaga 420aacgtgaccc cacccaaggt ctccttgttt
gagccatcaa aagcagagat tgcaaacaaa 480caaaaggcta ccctcgtgtg
cttggccagg ggcttcttcc ctgaccacgt ggagctgagc 540tggtgggtga
atggcaagga ggtccacagt ggggtcagca cggaccctca ggcctacaag
600gagagcaatt atagctactg cctgagcagc cgcctgaggg tctctgctac
cttctggcac 660aatcctcgaa accacttccg ctgccaagtg cagttccatg
ggctttcaga ggaggacaag 720tggccagagg gctcacccaa acctgtcaca
cagaacatca gtgcagaggc ctggggccga 780gcagactgtg gaatcacttc
agcatcctat catcaggggg ttctgtctgc aaccatcctc 840tatgagatcc
tactggggaa ggccacccta tatgctgtgc tggtcagtgg cctggtgctg
900atggctatgg tcaaaagaaa gaactcatga 93043828DNAArtificial
SequenceSyntheticmisc_feature(346)..(348)nnn at 346-348 is AGC,
GCC, or any codon that encodes Ser, Ala, Leu, Ile, Val, or
Metmisc_feature(349)..(351)nnn at 349-351 is TCA, GCC, or any codon
that encodes Ser, Ala, Leu, Ile, Val, or
Metmisc_feature(352)..(354)352-354 is GGA, GCC, or any codon that
encodes Gly, Ala, Leu, Ile, Val, or Metmisc_feature(355)..(357)nnn
at misc feature nnn at 355-357 is ACC, GCC, or any codon that
encodes Thr, Ala, Leu, Ile, Val, or Met 43atggcatgcc ctggcttcct
gtgggcactt gtgatctcca cctgtcttga atttagcatg 60gctcagacag tcactcagtc
tcaaccagag atgtctgtgc aggaggcaga gaccgtgacc 120ctgagctgca
catatgacac cagtgagagt gattattatt tattctggta caagcagcct
180cccagcaggc agatgattct cgttattcgc caagaagctt ataagcaaca
gaatgcaaca 240gagaatcgtt tctctgtgaa cttccagaaa gcagccaaat
ccttcagtct caagatctca 300gactcacagc tgggggatgc cgcgatgtat
ttctgtgctc tccggnnnnn nnnnnnntac 360aaatacatct ttggaacagg
caccaggctg aaggttttag caaatatcca gaaccctgac 420cctgccgtgt
accagctgag agactctaaa tccagtgaca agtctgtctg cctattcacc
480gattttgatt ctcaaacaaa tgtgtcacaa agtaaggatt ctgatgtgta
tatcacagac 540aaaactgtgc tagacatgag gtctatggac ttcaagagca
acagtgctgt ggcctggagc 600aacaaatctg actttgcatg tgcaaacgcc
ttcaacaaca gcattattcc agaagacacc 660ttcttcccca gcccagaaag
ttcctgtgat gtcaagctgg tcgagaaaag ctttgaaaca 720gatacgaacc
taaactttca aaacctgtca gtgattgggt tccgaatcct cctcctgaaa
780gtggccgggt ttaatctgct catgacgctg cggctgtggt ccagctga
82844942DNAArtificial SequenceSyntheticmisc_feature(343)..(345)NNN
at 343-345 is CGG, GCC, or any codon that encodes Arg, Ala, Leu,
Ile, Val, or Metmisc_feature(346)..(348)NNN at 346-348 is ACA, GCC,
or any codon that encodes Thr, Ala, Leu, Ile, Val, or
Metmisc_feature(349)..(351)NNN at 349-351 is GGG, GCC, or any codon
that encodes Gly, Ala, Leu, Ile, Val, or
Metmisc_feature(352)..(354)NNN at 352-354 is CCT, GCC, or any codon
that encodes Pro, Ala, Leu, Ile, Val, or Met 44atgggcacca
ggctcctctt ctgggtggcc ttctgtctcc tgggggcaga tcacacagga 60gctggagtct
cccagtcccc cagtaacaag gtcacagaga agggaaagga tgtagagctc
120aggtgtgatc caatttcagg tcatactgcc ctttactggt accgacagag
cctggggcag 180ggcctggagt ttttaattta cttccaaggc aacagtgcac
cagacaaatc agggctgccc 240agtgatcgct tctctgcaga gaggactggg
ggatccgtct ccactctgac gatccagcgc 300acacagcagg aggactcggc
cgtgtatctc tgtgccagca tcnnnnnnnn nnnntttttc 360tctggaaaca
ccatatattt tggagaggga agttggctca ctgttgtaga ggacctgaac
420aaggtgttcc cacccgaggt cgctgtgttt gagccatcag aagcagagat
ctcccacacc 480caaaaggcca cactggtgtg cctggccaca ggcttcttcc
ctgaccacgt ggagctgagc 540tggtgggtga atgggaagga ggtgcacagt
ggggtcagca cggacccgca gcccctcaag 600gagcagcccg ccctcaatga
ctccagatac tgcctgagca gccgcctgag ggtctcggcc 660accttctggc
agaacccccg caaccacttc cgctgtcaag tccagttcta cgggctctcg
720gagaatgacg agtggaccca ggatagggcc aaacccgtca cccagatcgt
cagcgccgag 780gcctggggta gagcagactg tggctttacc tcggtgtcct
accagcaagg ggtcctgtct 840gccaccatcc tctatgagat cctgctaggg
aaggccaccc tgtatgctgt gctggtcagc 900gcccttgtgt tgatggccat
ggtcaagaga aaggatttct ga 94245314PRTHomo sapiens 45Met Pro Leu Glu
Gln Arg Ser Gln His Cys Lys Pro Glu Glu Gly Leu1 5 10 15Glu Ala Arg
Gly Glu Ala Leu Gly Leu Val Gly Ala Gln Ala Pro Ala 20 25 30Thr Glu
Glu Gln Glu Ala Ala Ser Ser Ser Ser Thr Leu Val Glu Val 35 40 45Thr
Leu Gly Glu Val Pro Ala Ala Glu Ser Pro Asp Pro Pro Gln Ser 50 55
60Pro Gln Gly Ala Ser Ser Leu Pro Thr Thr Met Asn Tyr Pro Leu Trp65
70 75 80Ser Gln Ser Tyr Glu Asp Ser Ser Asn Gln Glu Glu Glu Gly Pro
Ser 85 90 95Thr Phe Pro Asp Leu Glu Ser Glu Phe Gln Ala Ala Leu Ser
Arg Lys 100 105 110Val Ala Lys Leu Val His Phe Leu Leu Leu Lys Tyr
Arg Ala Arg Glu 115 120 125Pro Val Thr Lys Ala Glu Met Leu Gly Ser
Val Val Gly Asn Trp Gln 130 135 140Tyr Phe Phe Pro Val Ile Phe Ser
Lys Ala Ser Asp Ser Leu Gln Leu145 150 155 160Val Phe Gly Ile Glu
Leu Met Glu Val Asp Pro Ile Gly His Val Tyr 165 170 175Ile Phe Ala
Thr Cys Leu Gly Leu Ser Tyr Asp Gly Leu Leu Gly Asp 180 185 190Asn
Gln Ile Met Pro Lys Thr Gly Phe Leu Ile Ile Ile Leu Ala Ile 195 200
205Ile Ala Lys Glu Gly Asp Cys Ala Pro Glu Glu Lys Ile Trp Glu Glu
210 215 220Leu Ser Val Leu Glu Val Phe Glu Gly Arg Glu Asp Ser Ile
Phe Gly225 230 235 240Asp Pro Lys Lys Leu Leu Thr Gln Tyr Phe Val
Gln Glu Asn Tyr Leu 245 250 255Glu Tyr Arg Gln Val Pro Gly Ser Asp
Pro Ala Cys Tyr Glu Phe Leu 260 265 270Trp Gly Pro Arg Ala Leu Ile
Glu Thr Ser Tyr Val Lys Val Leu His 275 280 285His Met Val Lys Ile
Ser Gly Gly Pro Arg Ile Ser Tyr Pro Leu Leu 290 295 300His Glu Trp
Ala Leu Arg Glu Gly Glu Glu305 3104616PRTHomo sapiens 46Lys Lys Leu
Leu Thr Gln Tyr Phe Val Gln Glu Asn Tyr Leu Glu Tyr1 5 10
154714PRTArtificial SequenceSynthetic 47Lys Lys Leu Leu Thr Gln His
Phe Val Gln Glu Asn Tyr Leu1 5 104813PRTArtificial
SequenceSynthetic 48Lys Lys Leu Leu Thr Gln His Phe Val Gln Glu Asn
Tyr1 5 104912PRTArtificial SequenceSynthetic 49Lys Lys Leu Leu Thr
Gln His Phe Val Gln Glu Asn1 5 105011PRTArtificial
SequenceSynthetic 50Lys Lys Leu Leu Thr Gln His Phe Val Gln Glu1 5
105114PRTArtificial SequenceSynthetic 51Leu Leu Thr Gln His Phe Val
Gln Glu Asn Tyr Leu Glu Tyr1 5 105213PRTArtificial
SequenceSynthetic 52Leu Thr Gln His Phe Val Gln Glu Asn Tyr Leu Glu
Tyr1 5 105312PRTArtificial SequenceSynthetic 53Thr Gln His Phe Val
Gln Glu Asn Tyr Leu Glu Tyr1 5 105411PRTArtificial
SequenceSynthetic 54Gln His Phe Val Gln Glu Asn Tyr Leu Glu Tyr1 5
105510PRTArtificial SequenceSynthetic 55His Phe Val Gln Glu Asn Tyr
Leu Glu Tyr1 5 105611PRTArtificial SequenceSynthetic 56Gln Tyr Phe
Val Gln Glu Asn Tyr Leu Glu Tyr1 5 105711PRTArtificial
SequenceSynthetic 57Gln Asp Leu Val Gln Glu Asn Tyr Leu Glu Tyr1 5
105811PRTArtificial SequenceSynthetic 58Gln Asp Trp Val Gln Glu Asn
Tyr Leu Glu Tyr1 5 105911PRTArtificial SequenceSynthetic 59Gln Glu
Trp Val Gln Glu Asn Tyr Leu Glu Tyr1 5 106011PRTArtificial
SequenceSynthetic 60Gln Asp Leu Val Gln Glu Lys Tyr Leu Glu Tyr1 5
106111PRTArtificial SequenceSynthetic 61Lys Asp Leu Val Gln Glu Lys
Tyr Leu Glu Tyr1 5 106211PRTArtificial SequenceSynthetic 62Lys Asp
Leu Val Lys Glu Asn Tyr Leu Glu Tyr1 5 106311PRTArtificial
SequenceSynthetic 63Lys Asp Phe Val Lys Glu Lys Tyr Leu Glu Tyr1 5
106411PRTArtificial SequenceSynthetic 64Lys Val Trp Val Gln Glu His
Tyr Leu Glu Tyr1 5 106516PRTArtificial SequenceSynthetic 65Arg Lys
Leu Ile Thr Asp Asp Phe Val Lys Gln Lys Tyr Leu Glu Tyr1 5 10
156616PRTArtificial SequenceSynthetic 66Lys Lys Leu Ile Thr Asp Glu
Phe Val Lys Gln Lys Tyr Leu Asp Tyr1 5 10 156716PRTArtificial
SequenceSynthetic 67Lys Lys Leu Ile Thr Glu Val Phe Val Arg Gln Lys
Tyr Leu Glu Tyr1 5 10 156816PRTArtificial SequenceSynthetic 68Lys
Lys Leu Ile Thr Glu Asp Phe Val Arg Gln Arg Tyr Leu Glu Tyr1 5 10
156911PRTArtificial SequenceSynthetic 69Glu Glu Phe Val Gln Met Asn
Tyr Leu Lys Tyr1 5 107016PRTArtificial SequenceSynthetic 70Lys Lys
Leu Leu Thr Gln Asp Leu Val Gln Glu Asn Tyr Leu Glu Tyr1 5 10
157116PRTArtificial SequenceSynthetic 71Lys Lys Leu Leu Thr Gln Asp
Leu Val Gln Glu Lys Tyr Leu Glu Tyr1 5 10 15
* * * * *