U.S. patent application number 16/901277 was filed with the patent office on 2021-05-27 for target peptides for colorectal cancer therapy and diagnostics.
This patent application is currently assigned to University of Virginia Patent Foundation. The applicant listed for this patent is The University of Birmingham, University of Virginia Patent Foundation. Invention is credited to Jennifer G. Abelin, Mark Cobbold, Donald F. Hunt, Sarah Penny, Jeffrey Shabanowitz.
Application Number | 20210154279 16/901277 |
Document ID | / |
Family ID | 1000005381225 |
Filed Date | 2021-05-27 |
![](/patent/app/20210154279/US20210154279A1-20210527-D00001.png)
![](/patent/app/20210154279/US20210154279A1-20210527-D00002.png)
![](/patent/app/20210154279/US20210154279A1-20210527-D00003.png)
![](/patent/app/20210154279/US20210154279A1-20210527-D00004.png)
![](/patent/app/20210154279/US20210154279A1-20210527-D00005.png)
![](/patent/app/20210154279/US20210154279A1-20210527-D00006.png)
![](/patent/app/20210154279/US20210154279A1-20210527-D00007.png)
![](/patent/app/20210154279/US20210154279A1-20210527-D00008.png)
United States Patent
Application |
20210154279 |
Kind Code |
A1 |
Hunt; Donald F. ; et
al. |
May 27, 2021 |
TARGET PEPTIDES FOR COLORECTAL CANCER THERAPY AND DIAGNOSTICS
Abstract
A set of target peptides are presented by HLA A*0201, B*0301,
B*0702 and B*2705 on the surface of disease cells. They are
envisioned to, among other things, stimulate an immune response to
the proliferative disease, e.g., colorectal cancer, to function as
immunotherapeutics in adoptive T cell therapy or as a vaccine,
facilitate antibody recognition of tumor boundaries in surgical
pathology samples, act as biomarkers for early detection and/or
diagnosis of the disease, and/or act as targets in the generation
antibody-like molecules which recognize the target-peptide/MHC
complex.
Inventors: |
Hunt; Donald F.;
(Charlottesville, VA) ; Shabanowitz; Jeffrey;
(Charlottesville, VA) ; Abelin; Jennifer G.;
(Sommers, CT) ; Cobbold; Mark; (Winchester,
MA) ; Penny; Sarah; (Birmingham, GB) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
University of Virginia Patent Foundation
The University of Birmingham |
Charlottesville
Birmingham |
VA |
US
GB |
|
|
Assignee: |
University of Virginia Patent
Foundation
Birmingham
GB
The University of Birmingham
|
Family ID: |
1000005381225 |
Appl. No.: |
16/901277 |
Filed: |
June 15, 2020 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
14425946 |
Mar 4, 2015 |
10682399 |
|
|
PCT/US2013/058255 |
Sep 5, 2013 |
|
|
|
16901277 |
|
|
|
|
61697274 |
Sep 5, 2012 |
|
|
|
61712807 |
Oct 12, 2012 |
|
|
|
61736466 |
Dec 12, 2012 |
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61K 39/001162 20180801;
A61K 2039/555 20130101; A61K 39/001132 20180801; A61K 39/001197
20180801; A61K 39/001151 20180801; A61K 39/001184 20180801; A61K
39/001194 20180801; A61K 39/001188 20180801; A61K 39/00119
20180801; A61K 39/001186 20180801; A61K 39/001164 20180801; A61K
39/0011 20130101; A61K 39/001156 20180801; A61K 39/001106 20180801;
A61K 39/001193 20180801; A61K 39/00111 20180801; A61K 39/001195
20180801; A61K 39/001189 20180801; G01N 33/57419 20130101; A61K
39/001157 20180801; A61K 39/001192 20180801; A61K 39/001181
20180801; A61K 39/001166 20180801; A61K 39/001182 20180801 |
International
Class: |
A61K 39/00 20060101
A61K039/00; G01N 33/574 20060101 G01N033/574 |
Goverment Interests
GRANT STATEMENT
[0002] This invention was made with government support under Grant
No. AI033993 awarded by the National Institutes of Health. The
government has certain rights in the invention.
Claims
1-41. (canceled)
42. A method of making a vaccine comprising synthesizing at least
one target peptide with an amino acid sequence selected from the
group consisting of: SEQ ID NO: 3, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 5, wherein the serine at the third
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 6, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 7, wherein the threonine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 12, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 13, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 14, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 15, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 20, wherein the threonine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 22, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 24, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 26, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 28, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 29, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 30, wherein the serine at the third
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 31, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 32, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 33, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 34, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 43, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 48, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 49, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 50, wherein the serine at the ninth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 52, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 54, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 56, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 61, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 63, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 67, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 68, wherein the serine at the ninth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 71, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 72, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 73, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 81, wherein the serine at the ninth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 85, wherein the serine at the seventh
position of is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 87, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 91, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 93, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 94, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 95, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine, the serine at the eighth position is phosphorylated
or replaced with a mimetic of phosphoserine, or any combination
thereof; SEQ ID NO: 96, wherein the threonine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 99, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 100, wherein the threonine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 101, wherein the threonine at the
sixth position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 103, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 104, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 105, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 106, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 108, wherein the serine at the seventh
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 109, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 110, wherein the threonine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 114, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 117, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 119, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine and the serine at the eighth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 123, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 126, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 128, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 129, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 131, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 132, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 135, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 140, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 141, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 143, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 144, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 146, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 147, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 148, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 149, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 150, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 154, wherein the serine at the third position is phosphorylated
or replaced with a mimetic of phosphoserine; SEQ ID NO: 155,
wherein the serine at the fourth position is phosphorylated or
replaced with a mimetic of phosphoserine; SEQ ID NO: 157, wherein
the serine at the fourth position of is phosphorylated or replaced
with a mimetic of phosphoserine; SEQ ID NO: 158, wherein the serine
at the sixth position is phosphorylated or replaced with a mimetic
of phosphoserine; SEQ ID NO: 159, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 160, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 161, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 162, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 164, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 165, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 167, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 170, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 172, wherein the threonine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 173, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 174, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 176, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; and SEQ ID NO: 177, wherein the threonine at the
sixth position is phosphorylated or replaced with a mimetic of
phosphothreonine.
43. A method of inducing a cellular immune response to a target
peptide in a subject, the method comprising administering to the
subject an effective amount of a target peptide selected from the
group consisting of: SEQ ID NO: 3, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 5, wherein the serine at the third
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 6, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 7, wherein the threonine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 12, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 13, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 14, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 15, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 20, wherein the threonine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 22, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 24, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 26, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 28, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 29, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 30, wherein the serine at the third
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 31, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 32, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 33, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 34, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 43, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 48, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 49, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 50, wherein the serine at the ninth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 52, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 54, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 56, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 61, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 63, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 67, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 68, wherein the serine at the ninth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 71, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 72, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 73, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 81, wherein the serine at the ninth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 85, wherein the serine at the seventh
position of is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 87, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 91, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 93, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 94, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 95, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine, the serine at the eighth position is phosphorylated
or replaced with a mimetic of phosphoserine, or any combination
thereof; SEQ ID NO: 96, wherein the threonine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 99, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 100, wherein the threonine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 101, wherein the threonine at the
sixth position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 103, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 104, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 105, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 106, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 108, wherein the serine at the seventh
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 109, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 110, wherein the threonine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 114, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 117, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 119, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine and the serine at the eighth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 123, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 126, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 128, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 129, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 131, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 132, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 135, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 140, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 141, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 143, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 144, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 146, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 147, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 148, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 149, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 150, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 154, wherein the serine at the third position is phosphorylated
or replaced with a mimetic of phosphoserine; SEQ ID NO: 155,
wherein the serine at the fourth position is phosphorylated or
replaced with a mimetic of phosphoserine; SEQ ID NO: 157, wherein
the serine at the fourth position of is phosphorylated or replaced
with a mimetic of phosphoserine; SEQ ID NO: 158, wherein the serine
at the sixth position is phosphorylated or replaced with a mimetic
of phosphoserine; SEQ ID NO: 159, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 160, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 161, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 162, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 164, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 165, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 167, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 170, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 172, wherein the threonine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 173, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 174, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 176, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; and SEQ ID NO: 177, wherein the threonine at the
sixth position is phosphorylated or replaced with a mimetic of
phosphothreonine.
44. A kit comprising a first container containing at least one
target peptide selected from group consisting of: SEQ ID NO: 3,
wherein the serine at the sixth position is phosphorylated or
replaced with a mimetic of phosphoserine; SEQ ID NO: 5, wherein the
serine at the third position is phosphorylated or replaced with a
mimetic of phosphoserine; SEQ ID NO: 6, wherein the serine at the
sixth position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 7, wherein the threonine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 12, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 13, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 14, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 15, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 20, wherein the threonine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 22, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 24, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 26, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 28, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 29, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 30, wherein the serine at the third
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 31, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 32, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 33, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 34, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 43, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 48, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 49, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 50, wherein the serine at the ninth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 52, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 54, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 56, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 61, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 63, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 67, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 68, wherein the serine at the ninth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 71, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 72, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 73, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 81, wherein the serine at the ninth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 85, wherein the serine at the seventh
position of is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 87, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 91, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 93, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 94, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 95, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine, the serine at the eighth position is phosphorylated
or replaced with a mimetic of phosphoserine, or any combination
thereof; SEQ ID NO: 96, wherein the threonine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 99, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 100, wherein the threonine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 101, wherein the threonine at the
sixth position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 103, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 104, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 105, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 106, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 108, wherein the serine at the seventh
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 109, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 110, wherein the threonine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 114, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 117, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 119, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine and the serine at the eighth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 123, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 126, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 128, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 129, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 131, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 132, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 135, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 140, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 141, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 143, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 144, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 146, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 147, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 148, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 149, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 150, wherein the serine at the fourth position is
phosphorylated or replaced with a mimetic of phosphoserine; SEQ ID
NO: 154, wherein the serine at the third position is phosphorylated
or replaced with a mimetic of phosphoserine; SEQ ID NO: 155,
wherein the serine at the fourth position is phosphorylated or
replaced with a mimetic of phosphoserine; SEQ ID NO: 157, wherein
the serine at the fourth position of is phosphorylated or replaced
with a mimetic of phosphoserine; SEQ ID NO: 158, wherein the serine
at the sixth position is phosphorylated or replaced with a mimetic
of phosphoserine; SEQ ID NO: 159, wherein the serine at the eighth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 160, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 161, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 162, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 164, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 165, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 167, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 170, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 172, wherein the threonine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphothreonine; SEQ ID NO: 173, wherein the serine at the fifth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 174, wherein the serine at the sixth
position is phosphorylated or replaced with a mimetic of
phosphoserine; SEQ ID NO: 176, wherein the serine at the fourth
position is phosphorylated or replaced with a mimetic of
phosphoserine; and SEQ ID NO: 177, wherein the threonine at the
sixth position is phosphorylated or replaced with a mimetic of
phosphothreonine; and a second container containing an adjuvant.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] The presently disclosed subject matter claims the benefit of
U.S. patent application Ser. No. 14/425,946, filed Mar. 4, 2015
(now pending); which is a U.S. National Stage Application of PCT
International Patent Application Serial No. PCT/US2013/058255,
filed Sep. 5, 2013; which itself claims the benefit of U.S. 10
Provisional Patent Application Ser. Nos. 61/697,274, filed Sep. 5,
2012; 61/712,807 filed Oct. 12, 2012; and 61/736,466, filed Dec.
12, 2012. The disclosure of each of these applications is
incorporated herein by reference in its entirety.
REFERENCE TO SEQUENCE LISTING
[0003] The Sequence Listing associated with the instant disclosure
has been electronically submitted to the United States Patent and
Trademark Office as a 106 kilobyte ASCII text file created on Jun.
15, 2020 and entitled "3062_4_2_PCT_US_CON_ST25.txt". The Sequence
Listing submitted via EFS-Web is hereby incorporated by reference
in its entirety.
TECHNICAL FIELD
[0004] The presently disclosed subject matter is related to the
area of diagnostics and therapeutics. In particular, it relates to
immunotherapies and diagnostics in the context of proliferative
diseases such as cancer.
BACKGROUND
[0005] The mammalian immune system has evolved a variety of
mechanisms to protect the host from cancerous cells. An important
component of this response is mediated by cells referred to as T
cells. Cytotoxic T lymphocytes (CTL) are specialized T cells that
primarily function by recognizing and killing cancerous cells or
infected cells, but they can also function by secreting soluble
molecules referred to as cytokines that can mediate a variety of
effects on the immune system. T helper cells primarily function by
recognizing antigen on specialized antigen presenting cells, and in
turn secreting cytokines that activate B cells, T cells, and
macrophages. A variety of evidence suggests that immunotherapy
designed to stimulate a tumor-specific CTL response would be
effective in controlling cancer. For example, it has been shown
that human CTL recognize sarcomas (Slovin et al., 1986), renal cell
carcinomas (Schendel et al., 1993), colorectal carcinomas (Jacob et
al., 1997), ovarian carcinomas (Peoples et al., 1993), pancreatic
carcinomas (Peiper et al., 1997), squamous tumors of the head and
neck (Yasumura et al., 1993), and squamous carcinomas of the lung
(Slingluff et al., 1994; Yoshino et al., 1994). The largest number
of reports of human tumor-reactive CTLs, however, has concerned
melanomas (Boon et al., 1994).
[0006] The ability of tumor-specific CTL to mediate tumor
regression, in both human (Parmiani et al., 2002; Weber, 2002) and
animal models, suggests that methods directed at increasing CTL
activity would likely have a beneficial effect with respect to
tumor treatment.
[0007] Colorectal cancer (CRC), commonly also known as colon cancer
or bowel cancer, is a cancer from uncontrolled cell growth in the
colon or rectum (parts of the large intestine), or in the appendix.
Symptoms typically include rectal bleeding and anemia which are
sometimes associated with weight loss and changes in bowel habits.
Most colorectal cancer occurs due to lifestyle and increasing age
with only a minority of cases associated with underlying genetic
disorders. It typically starts in the lining of the bowel and if
left untreated, can grow into the muscle layers underneath, and
then through the bowel wall. Screening is effective at decreasing
the chance of dying from colorectal cancer and is recommended
starting at the age of 50 and continuing until a person is 75 years
old. Localized bowel cancer is usually diagnosed through
sigmoidoscopy or colonoscopy. Cancers that are confined within the
wall of the colon are often curable with surgery while cancer that
has spread widely around the body is usually not curable and
management then focuses on extending the person's life via
chemotherapy and improving quality of life. Colorectal cancer is
the third most commonly diagnosed cancer in the world, but it is
more common in developed countries. Around 60% of cases were
diagnosed in the developed world. It is estimated that worldwide in
2008, 1.23 million new cases of colorectal cancer were clinically
diagnosed, and that it killed 608,000 people.
[0008] In Europe, the five year survival for colorectal cancer is
less than 60%. In the developed world, about a third of people who
get the disease die from it. Survival is directly related to
detection and the type of cancer involved, but overall is poor for
symptomatic cancers, as they are typically quite advanced. Survival
rates for early stage detection are about five times that of late
stage cancers. For example, patients with a tumor that has not
breached the muscularis mucosa (TNM stage Tis, N0, M0) have an
average 5-year survival of 100%, while those with an invasive
cancer, i.e. T1 (within the submucosal layer) or T2 (within the
muscular layer) cancer have an average 5-year survival of
approximately 90%. Those with a more invasive tumor, yet without
node involvement (T3-4, N0, M0) have an average 5-year survival of
approximately 70%. Patients with positive regional lymph nodes (any
T, N1-3, M0) have an average 5-year survival of approximately 40%,
while those with distant metastases (any T, any N, M1) have an
average 5-year survival of approximately 5%.
[0009] According to the American Cancer Society statistics in 2006,
over 20% of patients present with metastatic (Stage IV) colorectal
cancer at the time of diagnosis, and up to 25% of this group will
have isolated liver metastasis that is potentially resectable.
Lesions which undergo curative resection have demonstrated 5-year
survival outcomes now exceeding 50%. Nevertheless, additional
therapeutics that are safer and more effective than current
therapies are in high demand.
[0010] In order for CTL to kill or secrete cytokines in response to
a cancer cell, the CTL must first recognize the cancer cell
(Townsend & Bodmer, 1989). This process involves the
interaction of the T cell receptor, located on the surface of the
CTL, with what is generically referred to as an MHC-peptide complex
which is located on the surface of the cancerous cell. Major
histocompatibility complex (MHC)-encoded molecules have been
subdivided into two types, and are referred to as class I and class
II MHC-encoded molecules. In the human immune system, MHC molecules
are referred to as human leukocyte antigens (HLA). Within the MHC
complex, located on chromosome six, are three different loci that
encode for class I MHC molecules. MHC molecules encoded at these
loci are referred to as HLA-A, HLA-B, and HLA-C. The genes that can
be encoded at each of these loci are extremely polymorphic, and
thus, different individuals within the population express different
class I MHC molecules on the surface of their cells. HLA-A1,
HLA-A2, HLA-A3, HLA-B7, HLA-B14, HLA-B27, and HLA-B44 are examples
of different class I MHC molecules that can be expressed from these
loci.
[0011] The peptides which associate with the MHC molecules can
either be derived from proteins made within the cell, in which case
they typically associate with class I MHC molecules (Rock &
Goldberg, 1999); or they can be derived from proteins which are
acquired from outside of the cell, in which case they typically
associate with class II MHC molecules (Watts, 1997). The peptides
that evoke a cancer-specific CTL response most typically associate
with class I MHC molecules. The peptides themselves are typically
nine amino acids in length, but can vary from a minimum length of
eight amino acids to a maximum of fourteen amino acids in length.
Tumor antigens may also bind to class II MHC molecules on antigen
presenting cells and provoke a T helper cell response. The peptides
that bind to class II MHC molecules are generally twelve to
nineteen amino acids in length, but can be as short as ten amino
acids and as long as thirty amino acids.
[0012] The process by which intact proteins are degraded into
peptides is referred to as antigen processing. Two major pathways
of antigen processing occur within cells (Rock & Goldberg,
1999). One pathway, which is largely restricted to professional
antigen presenting cells such as dendritic cells, macrophages, and
B cells, degrades proteins that are typically phagocytosed or
endocytosed into the cell. Peptides derived from this pathway can
be presented on either class I or to class II MHC molecules. A
second pathway of antigen processing is present in essentially all
cells of the body. This second pathway primarily degrades proteins
that are made within the cells, and the peptides derived from this
pathway primarily bind to class I MHC molecules. Antigen processing
by this latter pathway involves polypeptide synthesis and
proteolysis in the cytoplasm, followed by transport of peptides to
the plasma membrane for presentation. These peptides, initially
being transported into the endoplasmic reticulum of the cell,
become associated with newly synthesized class I MHC molecules and
the resulting complexes are then transported to the cell surface.
Peptides derived from membrane and secreted proteins have also been
identified. In some cases these peptides correspond to the signal
sequence of the proteins which is cleaved from the protein by the
signal peptidase. In other cases, it is thought that some fraction
of the membrane and secreted proteins are transported from the
endoplasmic reticulum into the cytoplasm where processing
subsequently occurs. Once bound to the class I MHC molecule, the
peptides are recognized by antigen-specific receptors on CTL.
Several methods have been developed to identify the peptides
recognized by CTL, each method of which relies on the ability of a
CTL to recognize and kill only those cells expressing the
appropriate class I MHC molecule with the peptide bound to it. Mere
expression of the class I MHC molecule is insufficient to trigger
the CTL to kill the target cell if the antigenic peptide is not
bound to the class I MHC molecule. Such peptides can be derived
from a non-self source, such as a pathogen (for example, following
the infection of a cell by a bacterium or a virus) or from a
self-derived protein within a cell, such as a cancerous cell. The
tumor antigens from which the peptides are derived can broadly be
categorized as differentiation antigens, cancer/testis antigens,
mutated gene products, widely expressed proteins, viral antigens
and most recently, phosphopeptides derived from dysregulated signal
transduction pathways. (Zarling el al., 2006).
[0013] Immunization with cancer-derived, class I or class II
MHC-encoded molecule associated peptides, or with a precursor
polypeptide or protein that contains the peptide, or with a gene
that encodes a polypeptide or protein containing the peptide, are
forms of immunotherapy that can be employed in the treatment of
colorectal cancer. Identification of the immunogens is a necessary
first step in the formulation of the appropriate immunotherapeutic
agent or agents. Although a large number of tumor-associated
peptide antigens recognized by tumor reactive CTL have been
identified, there are few examples of antigens that are derived
from proteins that are selectively expressed on a broad array of
tumors, as well as associated with cellular proliferation and/or
transformation.
[0014] Attractive candidates for this type of antigen are peptides
derived from proteins that are differentially phosphorylated on
serine (Ser), threonine (Thr), and/or tyrosine (Tyr; Zarling et
al., 2000). Due to the increased and dysregulated phosphorylation
of cellular proteins in transformed cells as compared to normal
cells, tumors are likely to present a unique subset of
phosphorylated peptides on the cell surface that are available for
recognition by cytotoxic T-lymphocytes (CTL). Presently, there is
no way to predict which protein phosphorylation sites in a cell
will be unique to tumors, survive the antigen processing pathway,
and be presented to the immune system in the context of 8-14
residue phosphopeptides bound to class I MHC molecules.
[0015] Thirty-six phosphopeptides were disclosed as presented in
association with HLA-A*0201 on cancer cells (see Table 1 of Zarling
et al., 2006). Parent proteins for four of these peptides
(.beta.-catenin, insulin receptor substrate-2 (IRS-2), tensin-3,
and Jun-C/D) are associated with cytoplasmic signaling pathways and
cellular transformation.
[0016] Until the present disclosure, no studies have examined MHC
class-I-bound phosphopeptide displayed on primary human tumor
samples and, there is only limited evidence of a human immune
response against class-I-restricted phosphopeptides.
SUMMARY
[0017] This Summary lists several embodiments of the presently
disclosed subject matter, and in many cases lists variations and
permutations of these embodiments. This Summary is merely exemplary
of the numerous and varied embodiments. Mention of one or more
representative features of a given embodiment is likewise
exemplary. Such an embodiment can typically exist with or without
the feature(s) mentioned; likewise, those features can be applied
to other embodiments of the presently disclosed subject matter,
whether listed in this Summary or not. To avoid excessive
repetition, this Summary does not list or suggest all possible
combinations of such features.
[0018] In some embodiments, the presently disclosed subject matter
relates to compositions comprising at least or about 1, 2, 3, 4, 5,
6, 7, 8, 9, 10, or more synthetic target peptides, each of which
are about or at least 8, 9, 10, 11, 12, 13, 14, or 15 amino acids
long. In some embodiments, the target peptides comprise an amino
acid sequence as set forth in any of SEQ ID NOs: 1-177. In some
embodiments, the composition has the ability to stimulate a T
cell-mediated immune response to at least one of the synthetic
target peptides.
[0019] In some embodiments, at least one serine, tyrosine, and/or
threonine residue in any of the peptides is phosphorylated. In some
embodiments, at least one serine residue in any of the peptides is
replaced with a homoserine. In some embodiments, the composition
comprises a non-hydrolyzable phosphate. In some embodiments, at
least one phosphoserine residue in any of the peptides is replaced
by phosphohomoserine. In some embodiments, the composition is
immunologically suitable for at least 60 to 88% of colorectal
cancer patients. In some embodiments, the composition comprises at
least five different target peptides. In some embodiments, the
composition comprises at least ten different target peptides. In
some embodiments, the composition comprises at least fifteen
different target peptides.
[0020] In some embodiments, the composition comprises a target
peptide capable of binding to an MHC class I molecule. In some
embodiments, the target peptide is capable of binding to an MHC
class I molecule selected from the group consisting of HLA-A*0201,
HLA-A*0101, HLA-A*0301, HLA-B*4402, HLA-B*0702, HLA-B*-2705, and
HLA-B*1402. In some embodiments, the composition comprises a
peptide capable of binding to an MHC class I molecule selected from
the group consisting of HLA-A*0101, HLA-A*0301, HLA-B*4402,
HLA-B*0702, HLA-B*-2705, and HLA-B*1402. In some embodiments, the
composition comprises a peptide capable of binding to an MHC class
I molecule of the HLA-A*0201, HLA-A*0101, or HLA-B*0702
alleles.
[0021] In some embodiments, the composition is capable of
increasing the 5-year survival rate of colorectal cancer patients
treated with the composition by at least 5%, 10%, 15%, 20%, 25%,
30%, 40%, or 50% relative to average 5-year survival rates that
could have been expected without treatment with the composition. In
some embodiments, the composition is capable of increasing the
survival rate of colorectal cancer patients treated with the
composition by at least 5%, 10%, 15%, 20%, 25%, 30%, 40%, or 50%
relative to a survival rate that could have been expected without
treatment with the composition. In some embodiments, the
composition is capable of increasing the treatment response rate of
colorectal cancer patients treated with the composition by at least
5%, 10%, 15%, 20%, 25%, 30%, 40%, or 50% relative to a treatment
rate that could have been expected without treatment with the
composition. In some embodiments, the composition is capable of
increasing the overall median survival of patients of colorectal
cancer patients treated with the composition by at least two months
relative to an overall median survival that could have been
expected without treatment with the composition.
[0022] In some embodiments, the composition comprises at least one
peptide derived from MelanA (MART-I), gp100 (Pmel 17), tyrosinase,
TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, p15(58), CEA,
RAGE, NY-ESO (LAGE), SCP-1, Hom/Mel-40, PRAME, p53, H-Ras,
HER-2/neu, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, Epstein Barr
virus antigens, EBNA, human papillomavirus (HPV) antigens E6 and
E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, p185erbB2, p180erbB-3, c-met,
nm-23H1, PSA, TAG-72-4, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras,
.beta.-Catenin, CDK4, Mum-1, p16, TAGE, PSMA, PSCA, CT7,
telomerase, 43-9F, 5T4, 791Tgp72, .alpha.-fetoprotein, .beta.-HCG,
BCA225, BTAA, CA 125, CA 15-3 (CA 27.29\BCAA), CA 195, CA 242,
CA-50, CAM43, CD68\KP1, CO-029, FGF-5, G250, Ga733 (EpCAM),
HTgp-175, M344, MA-50, MG7-Ag, MOV18, NB/70K, NY-CO-1, RCAS1,
SDCCAG16, TA-90 (Mac-2 binding protein/cyclophilin C-associated
protein), TAAL6, TAG72, TLP and TPS.
[0023] In some embodiments, the composition comprises an adjuvant.
In some embodiments, the adjuvant is selected from the group
consisting of montanide ISA-51 (Seppic, Inc., Fairfield, N.J.,
United States of America), QS-21 (Aquila Biopharmaceuticals, Inc.,
Lexington, Mass., United States of America), tetanus helper
peptides, GM-CSF, cyclophosphamide, bacillus Calmette-Guerin (BCG),
Corynbacterium parvum, levamisole, azimezone, isoprinisone,
dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins (KLH),
Freunds adjuvant (complete and incomplete), mineral gels, aluminum
hydroxide (Alum), lysolecithin, pluronic polyols, polyanions,
peptides, oil emulsions, dinitrophenol, and diphtheria toxin
(DT).
[0024] In some embodiments, the presently disclosed subject matter
also relates to an in vitro population of dendritic cells
comprising a composition comprising at least one target peptide as
disclosed herein. In some embodiments, the at least one target
peptide selected from the group consisting of SEQ ID NOs:
1-177.
[0025] In some embodiments, the presently disclosed subject matter
also relates to an in vitro population of CD8.sup.+ T cells capable
of being activated upon being brought into contact with a
population of dendritic cells, wherein the dendritic cells comprise
a composition comprising at least one target peptide as disclosed
herein. In some embodiments, the at least one target peptide
selected from the group consisting of SEQ ID NOs: 1-177.
[0026] In some embodiments, the presently disclosed subject matter
also relates to an antibody or antibody-like molecule that
specifically binds to both a first complex of MHC class I molecule
and a target peptide. In some embodiments, the at least one target
peptide selected from the group consisting of SEQ ID NOs: 1-177. In
some embodiments, the antibody or antibody-like molecule is a
member of the immunoglobulin superfamily. In some embodiments, the
antibody or antibody-like molecule comprises a binding member
selected from the group consisting an Fab, Fab', F(ab').sub.2, Fv,
and a single-chain antibody. In some embodiments, the antibody or
antibody-like molecule comprises a therapeutic agent selected from
the group consisting of an alkylating agent, an antimetabolite, a
mitotic inhibitor, a taxoid, a vinca alkaloid, and an antibiotic.
In some embodiments, the antibody or antibody-like molecule is a T
cell receptor, which in some embodiments is optionally linked to a
CD3 agonist.
[0027] In some embodiments, the presently disclosed subject matter
also relates to an in vitro population of T cells transfected with
an mRNA encoding a target peptide-specific T cell receptor as
disclosed herein.
[0028] The presently disclosed subject matter also relates in some
embodiments to methods for treating and/or preventing cancer. In
some embodiments, the presently disclosed methods comprise
administering to a patient in need thereof one or more doses of a
composition comprising at least one target peptide as disclosed
herein. In some embodiments, the at least one target peptide
selected from the group consisting of SEQ ID NOs: 1-177.
[0029] In some embodiments, the presently disclosed subject matter
also relates to methods for treating and/or preventing colorectal
cancer. In some embodiments, the presently disclosed methods
comprise administering to a patient in need thereof one or more
doses of a composition comprising at least one target peptide as
disclosed herein, wherein the composition in some embodiments
comprises a pharmaceutically acceptable carrier, which in some
embodiments is pharmaceutically acceptable for use in a human. In
some embodiments, the at least one target peptide selected from the
group consisting of SEQ ID NOs: 1-177.
[0030] In some embodiments, the presently disclosed subject matter
also relates to methods for treating and/or preventing cancer
comprising administering to a patient in need thereof a dose of a
CD8.sup.+ T cell in combination with a pharmaceutically acceptable
carrier, optionally a carrier that is pharmaceutically acceptable
for use in a human. In some embodiments, the CD8.sup.+ T cell is
capable of being activated upon being brought into contact with a
population of dendritic cells, and further wherein the dendritic
cells comprise a composition comprising at least one target peptide
as disclosed herein.
[0031] In some embodiments, the presently disclosed subject matter
also relates to methods for treating and/or preventing cancer
comprising administering to a patient in need thereof the
population of dendritic cells comprising a composition comprising
at least one target peptide as disclosed herein. In some
embodiments, the dendritic cells are administered in combination
with a pharmaceutically acceptable carrier, optionally a carrier
that is pharmaceutically acceptable for use in a human.
[0032] The presently disclosed subject matter also relates in some
embodiments to methods for treating and/or preventing cancer
comprising administering to a patient in need thereof a population
T cells as disclosed herein in combination with a pharmaceutically
acceptable carrier, optionally a carrier that is pharmaceutically
acceptable for use in a human.
[0033] The presently disclosed subject matter also relates in some
embodiments to methods for making a cancer vaccine. In some
embodiments, the presently disclosed methods comprise combining a
composition as disclosed herein with an adjuvant and a
pharmaceutically acceptable carrier and placing the composition,
adjuvant, and pharmaceutical carrier into a syringe.
[0034] The presently disclosed subject matter also relates in some
embodiments to methods for screening a target peptide for inclusion
in an immunotherapy composition. In some embodiments, the presently
disclosed methods comprise administering the target peptide to a
human; determining whether the target peptide is capable of
inducing a target peptide-specific memory T cell response in the
human; and selecting the target peptide for inclusion in an
immunotherapy composition if the target peptide elicits a target
peptide-specific memory T cell response in the human.
[0035] In some embodiments, the presently disclosed subject matter
also relates to methods for determining a prognosis of a cancer
patient. In some embodiments, the presently disclosed methods
comprise administering a target peptide associated with the
patient's cancer to the patient; determining whether the target
peptide is capable of inducing a target peptide-specific memory T
cell response in the patient; and determining that the patient has
a better prognosis if the patient mounts a memory T cell response
to the target peptide than if the patient did not mount a memory T
cell response to the target peptide.
[0036] In some embodiments, the presently disclosed subject matter
also relates to kits comprising at least one target peptide
composition as disclosed herein, wherein the at least one target
peptide composition comprises at least one target peptide and a
cytokine and/or an adjuvant. In some embodiments, the kit comprises
at least 2, 3, 4, 5, or more target peptide compositions as
disclosed herein. In some embodiments, the cytokine is selected
from the group consisting of a transforming growth factor (TGF)
including but not limited to TGF-.alpha. and TGF-.beta.;
insulin-like growth factor (IGF)-I; IGF-II; erythropoietin (EPO);
an osteoinductive factor; an interferon (IFN) including but not
limited to IFN.alpha., IFN.beta., and IFN.gamma.; a colony
stimulating factor (CSF) including but not limited to
macrophage-CSF (M-CSF); granulocyte-macrophage-CSF (GM-CSF); and
granulocyte-CSF (G-CSF); an interleukin (IL) including but not
limited to IL-1, IL-1.alpha., IL-2, IL-3, IL-4, IL-5, IL-6, IL-7,
IL-8, IL-9, IL-10, IL-11, IL-12; IL-13, IL-14, IL-15, IL-16, IL-17,
IL-18; leukemia inhibitory factor (LIF); kit-ligand; FLT-3;
angiostatin; thrombospondin; endostatin; an tumor necrosis factor
(TNF) including but not limited to TNF.alpha. and TNF.beta.; and
lymphotoxin (LT). In some embodiments, the adjuvant selected from
the group consisting of montanide ISA-51 (Seppic, Inc., Fairfield,
N.J., United States of America), QS-21 (Aquila Biopharmaceuticals,
Inc., Lexington, Mass., United States of America), a tetanus helper
peptide, GM-CSF, cyclophosphamide, bacillus Calmette-Guerin (BCG),
Corynbacterium parvum, levamisole, azimezone, isoprinisone,
dinitrochlorobenezene (DNCB), keyhole limpet hemocyanin (KLH),
Freunds adjuvant (complete and incomplete), a mineral gel, aluminum
hydroxide (Alum), lysolecithin, a pluronic polyol, a polyanion, a
peptide, an oil emulsion, dinitrophenol, and diphtheria toxin
(DT).
[0037] In some embodiments, the kit comprises at least one
additional peptide. In some embodiments, the at least one
additional peptide is a peptide derived from MelanA (MART-I), gp100
(Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, MAGE-4,
MAGE-5, MAGE-6, BAGE, GAGE-1, GAGE-2, p15(58), CEA, RAGE, NY-ESO
(LAGE), SCP-1, Hom/Mel-40, PRAME, p53, H-Ras, HER-2/neu, BCR-ABL,
E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, an Epstein Barr virus antigen,
EBNA, human papillomavirus (HPV) antigen E6, HPV antigen E7,
TSP-180, p185erbB2, p180erbB-3, c-met, nm-23H1, PSA, TAG-72-4, CA
19-9, CA 72-4, CAM 17.1, NuMa, K-ras, .beta.-Catenin, CDK4, Mum-1,
p16, TAGE, PSMA, PSCA, CT7, telomerase, 43-9F, 5T4, 791Tgp72,
.alpha.-fetoprotein, .beta.-HCG, BCA225, BTAA, CA 125, CA 15-3 (CA
27.29/BCAA), CA 195, CA 242, CA-50, CAM43, CD68/KP1, CO-029, FGF-5,
G250, Ga733 (EpCAM), HTgp-175, M344, MA-50, MG7-Ag, MOV18, NB/70K,
NY-CO-1, RCAS1, SDCCAG16, TA-90 (Mac-2 binding protein/cyclophilin
C-associated protein), TAAL6, TAG72, TLP, and TPS.
[0038] In some embodiments, the kit comprises at least one target
peptide comprising an amino acid sequence as set forth in any of
SEQ ID NOs: 1-177.
[0039] In some embodiments, the presently disclosed subject matter
also provides methods for inducing a target peptide-specific memory
T cell response in a patient having a proliferative disorder. In
some embodiments, the presently disclosed methods comprise (a)
administering to a patient in need thereof a composition comprising
at least one target peptide and an adjuvant; and (b) inducing a
memory T cell response to the at least one target peptide. In some
embodiments, the memory T cell response is capable of treating the
proliferative disorder. In some embodiments, the at least one
target peptide is selected from SEQ ID NOs: 1-177. In some
embodiments, the proliferative disorder is cancer. In some
embodiments, the cancer is colorectal cancer. In some embodiments,
the adjuvant is a TLR agonist. In some embodiments, the adjuvant is
a Montanide ISA-51. In some embodiments, the adjuvant is a tetanus
helper peptide, a modified tetanus helper peptide (including but
not limited to a peptide that is at least 90% identical to a a
segment or fragment of a tetanus toxoid protein). In some
embodiments, the composition comprises at least one peptide derived
from MelanA (MART-I), gp100 (Pmel 17), tyrosinase, TRP-1, TRP-2,
MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, p15(58), CEA, RAGE, NY-ESO
(LAGE), SCP-1, Hom/Mel-40, PRAME, p53, H-Ras, HER-2/neu, BCR-ABL,
E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, an Epstein Barr virus antigen,
EBNA, a human papillomavirus (HPV) antigen E6 and/or E7, TSP-180,
MAGE-4, MAGE-5, MAGE-6, p185erbB2, p180erbB-3, c-met, nm-23H1, PSA,
TAG-72-4, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, .beta.-Catenin,
CDK4, Mum-1, p16, TAGE, PSMA, PSCA, CT7, telomerase, 43-9F, 5T4,
791Tgp72, .alpha.-fetoprotein, .beta.-HCG, BCA225, BTAA, CA 125, CA
15-3 (CA 27.29\BCAA), CA 195, CA 242, CA-50, CAM43, CD68KP1,
CO-029, FGF-5, G250, Ga733 (EpCAM), HTgp-175, M344, MA-50, MG7-Ag,
MOV18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90 (Mac-2 binding
protein/cyclophilin C-associated protein), TAAL6, TAG72, TLP, and
TPS. In some embodiments, the composition is immunologically
suitable for at least 60 to 88% of cancer patients. In some
embodiments, the composition comprises at least 1, 2, 3, 4, or 5
different target peptides. In some embodiments, the composition
comprises at least 10 different target peptides. In some
embodiments, the composition comprises at least 15 different target
peptides. In some embodiments, the composition comprises a peptide
capable of binding to an MHC class I molecule selected from the
group consisting of HLA-A*0201, HLA-A*0101, HLA-A*0301, HLA-B*4402,
HLA-B*0702, HLA-B*-2705 and HLA-B*1402. In some embodiments, the
composition comprises a peptide capable of binding to an MHC class
I molecule selected from the group consisting of HLA-A*0101,
HLA-A*0301, HLA-B*4402, HLA-B*0702, HLA-B*-2705, HLA-B*1402 and
combinations thereof. In some embodiments, the composition
comprises a peptide capable of binding to an MHC class I molecule
of the HLA-A*0201, HLA-A*0101 or HLA-B*0702 alleles. In some
embodiments, the composition comprises an agent selected from the
group consisting of a CTLA-4 antagonist, vermurafenib, ipilimumab,
dacarbazine, IL-2, temozolomide, imatinib, gefitinib, erlotinib,
sunitinib, tyrphostins, a PD-1 agonist, and telatinib.
[0040] In some embodiments, the presently disclosed methods
increase the 5-year survival rate of the patients treated with the
composition by at least 20 percent relative to average 5-year
survival rates that could have been expected without treatment with
the composition. In some embodiments, the presently disclosed
methods are capable of increasing the overall median survival of
patients treated with the composition by at least two months
relative to an overall median survival that could have been
expected without treatment with the composition.
[0041] In some embodiments, the presently disclosed methods further
comprise administering to the patient darcarbazine, carmustine,
tamoxifen, or a combination thereof including but not limited to
administering darcarbazine, carmustine, and tamoxifen.
[0042] In some embodiments, the presently disclosed methods further
comprise administering to the patient an adjuvant selected from the
group consisting of montanide ISA-51 (Seppic, Inc.), QS-21 (Aquila
Pharmaceuticals, Inc.), a tetanus helper peptide, GM-CSF,
cyclophosphamide, bacillus Calmette-Guerin (BCG), Corynbacterium
parvum, levamisole, azimezone, isoprinisone, dinitrochlorobenezene
(DNCB), keyhole limpet hemocyanins (KLH), Freunds adjuvant
(complete and incomplete), mineral gels, aluminum hydroxide (Alum),
lysolecithin, pluronic polyols, polyanions, peptides, oil
emulsions, dinitrophenol, diphtheria toxin (DT).
[0043] In some embodiments, the presently disclosed methods further
comprise determining that the T cell memory response is a T cell
central memory response (T.sub.CM).
[0044] These and other aspects and embodiments that will be
apparent to those of skill in the art upon reading the
specification provide the art with immunological tools and agents
useful for diagnosing, prognosing, monitoring, and/or treating
cancers including but not limited to human cancers.
BRIEF DESCRIPTION OF THE FIGURES
[0045] A more complete understanding of the presently disclosed
subject matter can be obtained by reference to the accompanying
Figures, when considered in conjunction with the subsequent
Detailed Description. The embodiments illustrated in the Figures
are intended to be exemplary only, and should not be construed as
limiting the presently disclosed subject matter.
[0046] FIGS. 1A-1C illustrate various T cell responses to tumor
specific phosphopeptides of the presently disclosed subject matter.
FIG. 1A depicts the results of multiplexed intracellular cytokine
staining for IL-2, IFN.gamma., and TNF.alpha.. FIG. 1B is a graph
showing that multifunctional TILs responded to the phosphopeptides
identified producing IL-2, IFN.gamma., and TNF.alpha.. In FIG. 1B,
responses to IL-2/IFN.gamma./TNF.alpha., TNF.alpha. alone,
IFN.gamma. and TNF.alpha., IFN.gamma. alone, IL-2 and IFN.gamma.,
IL-2 alone, and TNF.alpha. and IL-2 are depicted. The responses are
also summarized in FIG. 1C. In FIG. 1C, white boxes indicate less
than 0.5%, hatched boxes indicate 0.5-1.0%, light gray boxes
indicate 1.0-2.00%, and dark gray boxes indicate greater than
2.0%.
[0047] FIG. 2 illustrates T cell responses in 13 healthy donors to
a variety of CRC-associated phosphopeptides. In FIG. 2, a box with
a diagonal line indicates that the corresponding phosphopeptide was
not detected, a white box indicates that 5-24 spots were detected
by ELISpot, a light gray box indicates that 25-99 spots were
detected, and a dark gray box indicates that 100 or more spots were
detected.
[0048] FIG. 3 is a series of graphs illustrating that T cells lines
established against phosphopeptide targets IRS2 (HLA-A2; bottom
panel) and ZPF36L2 (HLA-B7; top panel) were able to specifically
kill the CRC cell line SW620 (ATCC.RTM. CCL-227.TM.: American Type
Culture Collection, Manassas, Va., United States of America).
[0049] FIG. 4 is a Table summarizing the results of a Day 7 ELISpot
experiment that demonstrated that healthy humans have an
immunological recall response to certain colorectal class I
phosphopeptides. Importantly, this response comes from central
memory T cells and is comparable to the recall response that the
same individuals have to viral peptides presented as a result of
flu, EBV, etc. The left column lists various synthetic samples of
CRC phosphopeptides. They were tested on 8 healthy B7/A3 donors and
memory T cell responses were observed for several of the peptides.
"KPE" is KPEsRRSSLL (SEQ ID NO: 54); "AVR" is AVRPTRLsL (SEQ ID NO:
93); "RPD" is RPDsAHKML (SEQ ID NO: 67); "SPR" is SPRsPDRTL (SEQ ID
NO: 87); "RPT" is RPTKIGRRsL (SEQ ID NO: 81); "QPQ" is QPQRRsLRL
(SEQ ID NO: 63); "RPG" is RPGsRQAGL (SEQ ID NO: 71); "SPF" is
SPFKRQLsL (SEQ ID NO: 84); "APD": is APDsPRAFL (SEQ ID NO: 49);
"LPI" is LPIFSRLsI (SEQ ID NO: 60); "RPR" is RPRARsVDAL (SEQ ID NO:
75); "RLS" is RLSsPISKR (SEQ ID NO: 39); "SVR" is SVRRsVLMK (SEQ ID
NO: 45); "RTM" is RTMsEAALVRK (SEQ ID NO: 40); "RPF" is RPFHGISTVsL
(SEQ ID NO: 69); "RQAv" is RQAsIELPSMAV (SEQ ID NO: 18); "RRG" is
RRGsFEVTL (SEQ ID NO: 132); "RTH" is RTHsLLLLL (SEQ ID NO: 176);
"NLV"and" TPR" are cytomegalovirus (CMV) peptides, "GLC" and "RPP"
are Epstein-Barr Virus (EBV) peptides; "FLU" and "ADENO" are
influenza and adenoviral peptides respectively. Phosphopeptide
sequences; pSer, pThr, and pTyr are specified by lowercase s, t,
and y, respectively.
[0050] FIG. 5 is a schematic diagram of the isolating and
characterization of phosphopeptides present in CRC tumor
samples.
[0051] FIG. 6 is two graphs showing TIL responses to
phosphopeptides derived from IRS2 (left panel) and ZFP36L2 (SEQ ID
NO: 60; right panel).
BRIEF DESCRIPTION OF TABLES 3-9
[0052] Tables 3-5 provide a listing of exemplary peptides including
phosphopeptides of the presently disclosed subject matter.
[0053] Tables 3 and 4 are Table showing a list of selected
CRC-associated phosphopeptides, predicted HLA type, presence in the
liver in the form of a metastasis, and notes on the pathway with
which the protein from which the phosphopeptide is derived is
associated.
[0054] Table 5 is a Table listing various phosphopeptides
associated with CRC.
[0055] Tables 6-8 list characteristics of HLA-DR-associated
phosphopeptides selectively expressed by melanoma cells. Table 6 is
a table derived from PCT International Patent Application
Publication No. WO 2010/129537 that lists characteristics of
HLA-DR-associated phosphopeptides selectively expressed by melanoma
cells. Tables 7 and 8 are derived from Depontieu et al., 2009,
including Depontieu et al. Supplemental Information, 10.1073 Proc
Natl Acad Sci USA 0903852106. Table 7 lists characteristics of
HLA-DR-associated phosphopeptides selectively expressed by
EBV-transformed B Cells. Table 8 lists characteristics of
HLA-DR-associated phosphopeptides commonly expressed by melanoma
and EBV-transformed B Cells.
[0056] Table 9 lists characteristics of source proteins generating
HLA-DR-restricted phosphopeptides.
DETAILED DESCRIPTION
[0057] While the following terms are believed to be well understood
by one of ordinary skill in the art, the following definitions are
set forth to facilitate explanation of the presently disclosed
subject matter.
[0058] All technical and scientific terms used herein, unless
otherwise defined below, are intended to have the same meaning as
commonly understood by one of ordinary skill in the art. Mention of
techniques employed herein are intended to refer to the techniques
as commonly understood in the art, including variations on those
techniques or substitutions of equivalent techniques that would be
apparent to one of skill in the art. While the following terms are
believed to be well understood by one of ordinary skill in the art,
the following definitions are set forth to facilitate explanation
of the presently disclosed subject matter.
[0059] Following long-standing patent law convention, the terms
"a", "an", and "the" refer to "one or more" when used in this
application, including the claims. Thus, in some embodiments the
phrase "a peptide" refers to one or more peptides.
[0060] The term "about", as used herein to refer to a measurable
value such as an amount of weight, time, dose (e.g., therapeutic
dose), etc., is meant to encompass in some embodiments variations
of +20%, in some embodiments .+-.10%, in some embodiments .+-.5%,
in some embodiments .+-.1%, in some embodiments .+-.0.1%, in some
embodiments 0.5%, and in some embodiments .+-.0.01% from the
specified amount, as such variations are appropriate to perform the
disclosed methods.
[0061] As used herein, the term "and/or" when used in the context
of a list of entities, refers to the entities being present singly
or in any possible combination or subcombination. Thus, for
example, the phrase "A, B, C, and/or D" includes A, B, C, and D
individually, but also includes any and all combinations and
subcombinations of A, B, C, and D.
I. Target Peptides
[0062] The presently disclosed subject matter relates in some
embodiments to post-translationally modified immunogenic
therapeutic target peptides, e.g., phosphopeptides and optionally
phosphopeptides comprising modified amino acids including, but not
limited to phosphohomoserine, for use in immunotherapy and
diagnostic methods of using the target peptides, as well as methods
of selecting the same to make compositions for immunotherapy, e.g.,
in vaccines and/or in compositions useful in adaptive cell
transfer.
[0063] In some embodiments, the target peptides of the presently
disclosed subject matter are post-translationally modified by being
provided with a phosphate group, (i.e., "phosphopeptides"
including, but not limited to peptides comprising phosphoserine,
phosphothreonine, phosphotyrosine, and derivatives thereof
including but not limited to phosphohomoserine).
[0064] The target peptides of the presently disclosed subject
matter are in some embodiments not the entire proteins from which
they are derived (i.e., are fragments and/or subsequences of larger
polypeptides). They are in some embodiments from 8 to 50 contiguous
amino acid residues of the native human protein. In some
embodiments, they can contain exactly, about, or at least 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,
45, 46, 47, 48, 49, or 50 amino acids. The peptides of the
presently disclosed subject matter can in some embodiments also
have a length that falls in the ranges of 8-10, 9-12, 10-13, 11-14,
12-15, 15-20, 20-25, 25-30, 30-35, 35-40, and 45-50 amino acids. In
some embodiments, exactly, about, or at least 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17 or more of the amino acid
residues within a recited sequence of a target peptide is
phosphorylated and/or contains a modified phosphoamino acid
including, but not limited to phosphohomoserine.
[0065] Target peptides can be modified and analogs (using for
example, .beta.-amino acids, L-amino acids, N-methylated amino
acids, amidated amino acids, non-natural amino acids, retro inverse
peptides, peptoids, PNA, halogenated amino acids) can be
synthesized that retain their ability to stimulate a particular
immune response but which also gain one or more beneficial
features, such as those described herein below. Thus, a particular
target peptide can, for example, have use for treating and
vaccinating against multiple cancer types.
[0066] Substitutions can be made in the target peptides at residues
known to interact with the MHC molecule. Such substitutions can
have the effect of increasing the binding affinity of the target
peptides for the MHC molecule and can also increase the half-life
of the target peptide-MHC complex, the consequence of which is that
the substituted target peptide is a more potent stimulator of an
immune response than is the original target peptide.
[0067] Additionally, in some embodiments the substitutions have no
effect on the immunogenicity of the target peptide per se, but
rather prolong its biological half-life and/or prevent it from
undergoing spontaneous alterations which might otherwise negatively
impact on the immunogenicity of the peptide.
[0068] The target peptides disclosed herein can have differing
levels of immunogenicity, MHC binding, and ability to elicit CTL
responses against cells displaying a native target peptide (e.g.,
on the surface of a tumor cell).
[0069] A phosphopeptide as disclosed herein is in some embodiments
modified such that its immunogenicity and/or its binding is
enhanced. In some embodiments, the modified target peptide binds to
an MHC class I molecule about or at least 10, 20, 30, 40, 50, 60,
70, 80, 90, 95, 100, 110, 125, 150, 175, 200, 225, 250, 275, 300,
350, 375, 400, 450, 500, 600, 700, 800, 1000% or more tightly than
its native counterpart.
[0070] However, given the exquisite sensitivity of the T cell
receptor, it cannot be foreseen whether such enhanced binding
and/or immunogenicity will render a modified target peptide still
capable of inducing an activated CTL that will cross react with the
native target peptide being displayed on the surface of a tumor.
Indeed, it is disclosed herein that the binding affinity of a
target peptide does not predict its functional ability to elicit a
T cell response.
[0071] Target peptides of the presently disclosed subject matter
can in some embodiments be mixed together to form a cocktail. The
target peptides can be in an admixture, or they can be linked
together in a concatamer and/or in other arrangement as a single
molecule. Linkers between individual target peptides can be used;
these can, for example, be formed in some embodiments by any 10 to
20 amino acid residues. The linkers can be random sequences, or
they can be optimized for degradation by dendritic cells.
[0072] In certain specified positions, a native amino acid residue
in a native human protein can be altered to enhance its binding to
an MHC class I molecule. These occur in "anchor" positions of the
target peptides, often in positions 1, 2, 3, 9, or 10. Valine,
alanine, lysine, leucine tyrosine, arginine, phenylalanine,
proline, glutamic acid, 5 threonine, serine, aspartic acid,
tryptophan, and methionine can also be used as improved anchoring
residues. Anchor residues for different HLA molecules are listed
below in Table 1.
TABLE-US-00001 TABLE 1 Anchor Residues for HLA Molecules HLA Type
Residue Position Anchor Residue(s) HLA A*0201 2 L, M 9 or Last V
HLA A*0301 2 L, M 9 or Last K HLA A*0101 2 T, S 3 D, E 9 or Last Y
HLA B*2705 1 R 2 R 9 or Last L, F, K, R, M HLA B*0702 2 P 9 or Last
L, M, V, F HLA B*4402 2 E 9 or Last F, Y, W
[0073] In some embodiments, the immunogenicity of a target peptide
is measured using transgenic mice expressing human MHC class I
genes. For example, "ADD Tg mice" express an interspecies hybrid
class I MHC gene, AAD, which contains the .alpha.-1 and .alpha.-2
domains of the human HLA-A2.1 gene and the .alpha.-3 transmembrane
and cytoplasmic domains of the mouse H-2Dd gene, under the
transcriptional control of the human HLA-A2.1 promoter.
Immunodetection of the HLA-A2.1 recombinant transgene established
that expression was at equivalent levels to endogenous mouse class
I molecules. The mouse .alpha.-3 domain expression enhances the
immune response in this system. Compared to unmodified HLA-A2.1,
the chimeric HLA-A2.1/H2-Dd MHC Class I molecule mediates efficient
positive selection of mouse T cells to provide a more complete T
cell repertoire capable of recognizing peptides presented by
HLA-A2.1 Class I molecules.
[0074] The peptide epitopes presented and recognized by mouse T
cells in the context of the HLA-A2.1/H2-Dd class I molecule are the
same as those presented in HLA-A2.1.sup.+ humans. This transgenic
strain enables the modeling of human T cell immune responses to
HLA-A2 presented antigens, and identification of those antigens.
This transgenic strain is a preclinical model for design and
testing of vaccines for infectious diseases or cancer therapy
involving optimal stimulation of CD8.sup.+ cytolytic T cells.
[0075] In some embodiments, the immunogenicity of a modified
phosphopeptide is determined by the degree of Interferon gamma
(IFN.gamma.) and/or tumor necrosis factor-alpha (TNF-.alpha.)
production of T cells from ADD Tg mice immunized with the target
peptide, e.g., by immunization with target peptide pulsed bone
marrow derived dendritic cells.
[0076] In some embodiments, the modified target peptides are about
or at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 95, 100, 110, 125,
150, 175, 200, 225, 250, 275, 300, 350, 375, 400, 450, 500, 600,
700, 800, 1000, 1500, 2000, 2500, 3000, 4000, 5000% or more
immunogenic, e.g., in terms of numbers of IFN.gamma.- and/or
TNF-.alpha.-positive (i.e., "activated") T cells relative to
numbers elicited by native target peptides in ADD Tg mice immunized
with phosphopeptide-pulsed bone marrow derived dendritic cells
(BMDCs). In some embodiments, the target peptides are modified
target peptides. In some embodiments, the modified target peptides
are able to elicit CD8.sup.+ T cells that are cross-reactive with
the modified and the native target peptide in general and when such
modified and native target peptides are complexed with MHC class I
molecules in particular. In some embodiments, the CD8 T cells that
are cross-reactive with the modified and the native target peptides
are able to reduce tumor size by about or at least 10%, 20%, 30%,
40%, 50%, 60%, 70%, 80%, 90%, 95%, 97% or 99% in a
NOD/SCID/IL-2R.gamma.c.sup.-/- knock out mouse relative to IL-2
treatment without such cross-reactive CD8.sup.+ T cells.
[0077] The phrase "capable of inducing a target peptide-specific
memory T cell response in a patient" as used herein relates to
eliciting a response from memory T cells (also referred to as
"antigen-experienced T cell"), which are a subset of infection- and
cancer-fighting T cells that have previously encountered and
responded to their cognate antigen. Such T cells can recognize
foreign invaders, such as bacteria or viruses, as well as cancer
cells. Memory T cells have become "experienced" by having
encountered antigen during a prior infection, having encountered
cancer, or via previous vaccination. At a second encounter with the
cognate antigen (e.g., by way of an initial inoculation with a
target peptide of the presently disclosed subject matter), memory T
cells can reproduce to mount a faster and stronger immune response
than the first time the immune system responded to the invader
(e.g., through the body's own consciously unperceived recognition
of a target peptide being associated with diseased tissue). This
behavior can be assayed in T lymphocyte proliferation assays, which
can reveal exposure to specific antigens.
[0078] Memory T cells comprise two subtypes: central memory T cells
(T.sub.CM cells) and effector memory T cells (T.sub.EM cells).
Memory cells can be either CD4.sup.+ or CD8.sup.+. Memory T cells
typically express the cell surface protein CD45RO. Central memory
(T.sub.CM) cells generally express L-selectin and CCR7, and they
secrete IL-2 but not IFN.gamma. or IL-4. Effector memory (T.sub.EM)
cells, however, generally do not express L-selectin or CCR7 but
produce effector cytokines like IFN.gamma. and IL-4.
[0079] A memory T cell response generally results in the
proliferation of memory T cells and/or the upregulation or
increased secretion of factors such as CD45RO, L-selectin, CCR7,
IL-2, IFN.gamma., CD45RA, CD27, and/or IL-4. In some embodiments,
the target peptides of the presently disclosed subject matter are
capable of inducing a T.sub.CM cell response associated with
L-selectin, CCR7, IL-2 but not IFN.gamma. or IL-4 expression and/or
secretion. See e.g., Hamann et al., 1997. In some embodiments, a
T.sub.CM cell response is associated with an at least or an about
1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 45%, 50%, 55%, 60%, 65%, 70%,
75%, 80%, 90%, 95%, 97%, 98.degree., 99%, 100%, 125%, 150%, 175%,
200%, 250%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, 1000%, 1500%,
2000% or more increase in T cell CD45RO/RA, L-selectin, CCR7, or
IL-2 expression and/secretion.
[0080] In some embodiments, the target peptides of the presently
disclosed subject matter are capable of inducing a CD8.sup.+
T.sub.CM cell response in a patient the first time that patient is
provided the composition including the selected target peptides. As
such, the target peptides of the presently disclosed subject matter
can in some embodiments be referred to as "neo-antigens." Although
target peptides might be considered "self" for being derived from
self-tissue, they generally are only found on the surface of cells
with a dysregulated metabolism (e.g., aberrant phosphorylation),
and they are likely never presented to immature T cells in the
thymus. As such, these "self" antigens act are neo-antigens because
they are nevertheless capable of eliciting an immune response.
[0081] In some embodiments, about or at least 1%, 5%, 10%, 15%,
20%, 25%, 30%, 35%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 90%,
95%, 97%, 98%, or 99% of T cells activated by particular target
peptide in a particular patient sample are T.sub.CM cells.
[0082] In some embodiments, a patient sample is isolated exactly,
about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or
more days after an initial exposure to a particular target peptide
and then assayed for target peptide-specific activated T cells and
the proportion of T.sub.CM cells thereof.
[0083] In some embodiments, the compositions of the presently
disclosed subject matter are able to elicit a CD8.sup.+ T.sub.CM
cell response in at least or about 1%, 5%, 10%, 15%, 200%, 25%,
30%, 35%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 90%, 95%, 97%,
98%, or 99% of patients and/or healthy volunteers.
[0084] In some embodiments, the compositions of the presently
disclosed subject matter are able to elicit a CD8.sup.+ T.sub.CM
cell response in about or at least 1%, 5%, 10%, 15%, 200%, 25%,
30%, 35%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 90%, 95%, 97%,
98%, 99% of patients and/or healthy volunteers specific, and in
some embodiments the CD8.sup.+ T.sub.CM cell response elicited is
directed against all or at least or about 1, 2, 3, 4, 5, 6, 7, 8,
9, 10, or more target peptides that are present in the composition.
In some embodiments, the aforementioned T cell activation tests are
done by ELISpot assay.
II. Phosphopeptides
[0085] The term "phosphopeptides" includes MHC class I- and MHC
class II-specific phosphopeptides. Exemplary MHC class I
phosphopeptides are set forth in Table 5, for example.
[0086] In some embodiments, the phosphopeptides contain the
sequences of at least one of the MHC class I-binding peptides
listed in SEQ ID NO. 1-177. Moreover, in some embodiments about or
at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more
of the serine, homoserine, threonine, or tyrosine residues within
the recited sequence is phosphorylated. The phosphorylation can be
with a natural phosphorylation (--CH.sub.2--O--PO.sub.3H) or with
an enzyme non-degradable, modified phosphorylation, such as but not
limited to --CH.sub.2--CF.sub.2--PO.sub.3H or
--CH.sub.2--CH.sub.2--PO.sub.3H. Some phosphopeptides can contain
more than one of the peptides listed in SEQ ID NO: 1-177, for
example, if they are overlapping, adjacent, or nearby within the
native protein from which they are derived.
[0087] The chemical structure of a phosphopeptide mimetic
appropriate for use in the presently disclosed subject matter can
in some embodiments closely approximate the natural phosphorylated
residue which is mimicked, and also be chemically stable (e.g.,
resistant to dephosphorylation by phosphatase enzymes). This can be
achieved with a synthetic molecule in which the phosphorous atom is
linked to the amino acid residue, not through oxygen, but through
carbon. In some embodiments, a CF.sub.2 group links the amino acid
to the phosphorous atom. Mimetics of several amino acids which are
phosphorylated in nature can be generated by this approach.
Mimetics of phosphoserine, phosphothreonine, and phosphotyrosine
can be generated by placing a CF.sub.2 linkage from the appropriate
carbon to the phosphate moiety. The mimetic molecule L-2-amino-4
(diethylphosphono)-4, 4-difluorobutanoic acid (F2Pab) can
substitute for phosphoserine (Otaka et al., 1995).
L-2-amino-4-phosphono-4, 4-difluoro-3-methylbutanoic acid (F2Pmb)
can substitute for phosphothreonine, and L-2-amino-4-phosphono
(difluoromethyl) phenylalanine (F2Pmp) can substitute for
phosphotyrosine (Smyth et al., 1992; Akamatsu et al., 1997).
Alternatively, the oxygen bridge of the natural amino acid can be
replaced with a methylene group. In some embodiments, serine and
threonine residues are substituted with homoserine and
homothreonine residues, respectively. A phosphomimetic may also
include vanadate, pyrophosphate or fluorophosphates.
[0088] IRS-2 over-expression either at the gene or protein level,
is evident in many different cancer types, and has been
demonstrated to cause mammary tumorigenesis and enhanced metastasis
in vivo. IRS proteins are adapter proteins that link signaling from
upstream activators to multiple downstream effectors to modulate
normal growth, metabolism, survival and differentiation. It is
disclosed herein that phosphorylated IRS-2 is broadly displayed on
multiple cancer types and the resulting phosphopeptide is
endogenously processed and presented at levels that allow strong
immune responses to be generated against it.
Phosphopeptide-specific CD8+ T cells can be generated from HLA-A2
transgenic mice upon immunization with the pIRS2 phosphopeptide and
these T cells are capable of recognizing and killing human melanoma
and breast tumors in vitro and controlled tumor growth in a
xenograft tumor model system.
[0089] Tensin 3 (TNS3) plays a role in actin remodeling. It is
involved in the dissociation of the integrin-tensin-actin complex.
EGF activates TNS4 and down-regulates TNS3 which results in capping
the tail of ITGB1. TN3 also seems to be involved in mammary cell
migration and may be involved in cell migration and bone
development. The Tensin 3 phosphopeptide (VMIGsPKKV, SEQ ID NO: 27)
of the presently disclosed subject matter has been surprisingly
discovered to be capable of inducing a strong
phosphopeptide-specific memory T cell response in a patient. This
further supports the position that peptide/MHC binding affinity
does not correlate with the ability of a phosphopeptide to induce a
phosphopeptide specific immune response.
III. Immunosuitablity
[0090] In some embodiments, the target peptides are combined into
compositions that can be used in vaccine compositions for eliciting
anti-tumor immune responses and/or in adoptive T cell therapy of
colorectal cancer patients. Table 5 provides phosphopeptides
presented on the surface of cancer cells.
[0091] Although individuals in the human population display
hundreds of different HLA alleles, some are more prevalent than
others. For example, 88% of colorectal cancer patients carry at
least one of the six HLA alleles: HLA-A*0201 (51%), HLA-A*0101
(29%), HLA-A*0301 (21%), HLA-B*4402 (27%), HLA-B*0702 (30%), and
HLA-B*-2705 (7%).
[0092] The presently disclosed subject matter provides in some
embodiments target peptides which are immunologically suitable for
each of the foregoing HLA alleles. "Immunologically suitable" means
that a target peptide will bind at least one allele of an MHC class
I molecule in a given patient. Compositions of the presently
disclosed subject matter are in some embodiments immunologically
suitable for a patient when at least one target peptide of the
composition will bind at least one allele of an MHC class I
molecule in a given patient. Compositions of multiple target
peptides presented by each of the most prevalent alleles used in a
cocktail ensures coverage of the human population and to minimize
the possibility that the tumor will be able to escape immune
surveillance by down-regulating expression of any one class I
target peptide.
[0093] The compositions of the presently disclosed subject matter
can in some embodiments comprise at least one target peptide
specific for one or more of the following alleles: HLA-A*0201,
HLA-A*0101, HLA-A*0301, HLA-B*4402, HLA-B*0702, HLA-B*-2705, and
HLA-B*1402. The compositions of the presently disclosed subject
matter can in some embodiments have at least one target peptide
specific for one or more of the following alleles HLA-A*0201,
HLA-A*0101, HLA-A*0301, HLA-B*4402, and HLA-B*0702. Alternatively,
the compositions of the presently disclosed subject matter can in
some embodiments have at least one target peptide specific for
HLA-A*0201, HLA-A*0101, HLA-A*0301, HLA-B*4402, HLA-B*0702,
HLA-B*-2705, HLA-B*1402, or any combination thereof. The
compositions may have at least one phosphopeptide specific for
about or at least 1, 2, 3, 4, 5, or all 6 of the aforementioned
alleles.
[0094] As such, the compositions of the presently disclosed subject
matter containing various combinations of target peptides are in
some embodiments immunologically suitable for between or about
3-88%, 80-89%, 70-79%, 60-69%, 57-59%, 55-57%, 53-55% or 51-53% or
5-90%, 10-80%, 15-75%, 20-70%, 25-65%, 30-60%, 35-55% or 40-50% of
the population of a particular cancer including, but not limited to
colorectal cancer. In some embodiments, the compositions of the
presently disclosed subject matter are able to act as vaccine
compositions for eliciting anti-tumor immune responses and/or in
adoptive T cell therapy of colorectal cancer patients wherein the
compositions are immunologically suitable for about or at least 88,
87, 86, 85, 84, 83, 82, 81, 80, 79, 78, 77, 76, 75, 74, 73, 72, 71,
70, 69, 68, 67, 66, 65, 64, 63, 62, 61, 60, 59, 58, 57, 56, 55, 54,
53, 52, 51, 50, 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37,
36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 20, 19,
18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, or 3 percent
of cancer such as, but not limited to colorectal cancer
patients.
IV. Compositions
[0095] The phrase "target peptide compositions" as used herein
refers to at least one target peptide formulated, for example, as a
vaccine; or as a preparation for pulsing cells in a manner such
that the pulsed cells, e.g., dendritic cells, will display the at
least one target peptide in the composition on their surface, e.g.,
to T cells in the context of adoptive T cell therapy.
[0096] The compositions of the presently disclosed subject matter
can in some embodiments include about or at least 1, 2, 3, 4, 5, 6,
7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,
41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 50-55, 55-65, 65-80,
80-120, 90-150, 100-175, or 175-250 different target peptides.
[0097] The compositions of the presently disclosed subject matter
in some embodiments generally include MHC class I specific target
peptide(s) but can also include one or more target peptides
specific for MHC class 11, such as but not limited to the peptides
set forth in Tables 6-9, or other peptides associated with tumors
(e.g., tumor associated antigen ("TAA")).
[0098] Compositions comprising the target peptide are typically
substantially free of other human proteins or peptides. They can be
made synthetically or by purification from a biological source.
They can be made recombinantly. Desirably they are in some
embodiments at least 90% pure, in some embodiments at least 92%
pure, in some embodiments at least 93% pure, in some embodiments at
least 94% pure, in some embodiments at least 95% pure, in some
embodiments at least 96% pure, in some embodiments at least 97%
pure, in some embodiments at least 98% pure, and in some
embodiments at least 99% pure. For administration to a human, they
generally do not contain other components that might be harmful to
a human recipient (referred to herein as "pharmaceutically
acceptable for use in a human"). The compositions are typically
devoid of cells, both human and recombinant producing cells.
However, as noted below, in some cases, it can be desirable to load
dendritic cells with a target peptide and use those loaded
dendritic cells as either an immunotherapy agent themselves or as a
reagent to stimulate a patient's T cells ex vivo. The stimulated T
cells can be used as an immunotherapy agent.
[0099] In some cases, it can be desirable to form a complex between
a target peptide and an HLA molecule of the appropriate type. Such
complexes can be formed in vitro or in vivo. Such complexes are in
some embodiments tetrameric with respect to an HLA-target peptide
complex.
[0100] In some embodiments, the target peptide of the presently
disclosed subject matter comprises an amino acid sequence that has
at least 50, 60, 70, 80, 90, 95, 98, 99 or 100 percent sequence
homology to an amino acid sequence as set forth in any of SEQ ID
NOs: 1-177. As used herein, the phrase "sequence homology" refers
to the presence of homology between two amino acid sequences. The
"percentage of sequence homology" can be determined by comparing
two optimally aligned sequences over a comparison window (e.g.,
about 5-25 contiguous amino acids or more), wherein the portion of
the amino acid sequence in the comparison window can include
additions or deletions (i.e., gaps) as compared to a reference
sequence for optimal alignment of the two sequences. Optimal
alignment of sequences for comparison can be conducted by
computerized implementations of known algorithms, or by visual
inspection. Readily available sequence comparison and multiple
sequence alignment algorithms are, respectively, the Basic Local
Alignment Search Tool (BLAST; Altschul et al., 1990; Altschul et
al., 1997) and ClustalX (Chenna et al., 2003) programs, both
available on the Internet. Other suitable programs include, but are
not limited to, GAP, BestFit, PlotSimilarity, and FASTA, which are
part of the Accelrys GCG Package available from Accelrys Software,
Inc. of San Diego, Calif., United States of America.
[0101] Under certain circumstances it can be desirable to add
additional proteins or peptides, for example, to make a cocktail
having the ability to stimulate an immune response in a number of
different HLA type hosts. Alternatively, additional proteins and/or
peptides can provide an interacting function within a single host,
such as but not limited to an adjuvant function or a stabilizing
function. As a non-limiting example, other tumor antigens can be
used in admixture with the target peptides such that multiple
different immune responses are induced in a single patient.
[0102] Administration of target peptides to a mammalian recipient
can be accomplished using long target peptides (e.g., longer than
15 residues), and/or using target peptide-loaded dendritic cells.
See Melief, 2009. In some embodiments, an immediate goal of the
administration of target peptides is to induce activation of
CD8.sup.+ T cells in a subject. Additional components that can be
administered to the same subject, either at the same time and/or
close in time (such as but not limited to within 3, 5, 7, 10, 14,
17, or 21 days of each other, or even longer) include TLR-ligand
oligonucleotide CpG and related target peptides that have
overlapping sequences of at least six amino acid residues. To
ensure efficacy, mammalian recipients should express the
appropriate human HLA molecules to bind to the target peptides.
Transgenic mammals can be used as recipients, for example, if they
express appropriate human HLA molecules. If a mammal's own immune
system recognizes a similar target peptide then it can be used as
model system directly without introducing a transgene. Useful
models and recipients can be at increased risk of developing
metastatic cancer, such as metastatic colorectal cancer. Other
useful models and recipients can be predisposed, e.g., genetically
and/or environmentally, to develop colorectal cancer or other
cancer.
[0103] IV.A. Selection of Target Peptides
[0104] Disclosed herein is the finding that immune responses can be
generated against phosphorylated peptides tested in healthy and
diseased individuals. The T cells associated with these immune
responses, when expanded in vitro, are able to recognize and kill
malignant tissue (both established cells lines and primary tumor
samples). Cold-target inhibition studies reveal that these target
peptide-specific T cell lines kill primary tumor tissue in a target
peptide-specific manner.
[0105] When selecting target peptides of the presently disclosed
subject matter for inclusion in immunotherapy, e.g., in adaptive
cell therapy or in the context of a vaccine, one can in some
embodiments pick target peptides using one or more of the following
criteria: 1) peptides associated with a particular cancer/tumor
cell type; 2) a peptide derived from a gene and/or a protein
associated with cell proliferation, transformation, and/or
malignancy; 3) a peptide that is specific for an HLA allele carried
the group of patients to be treated; and/or 4) a peptide that is
capable of inducing a target peptide-specific memory T cell
response in the patients to be treated upon a first exposure to a
composition including the selected target peptides.
[0106] IV.B. Target Peptide Vaccines
[0107] The antigen target peptides can also be employed in a
composition designed to vaccinate an individual. The antigen target
peptides can in some embodiments be injected alone and can in some
embodiments be administered in combination with an adjuvant and/or
a pharmaceutically acceptable carrier. Vaccines are envisioned to
prevent and/or treat certain diseases in general, and cancers in
particular.
[0108] The target peptide-containing compositions of the presently
disclosed subject matter can in some embodiments be used as a
vaccine for cancer, and more specifically for melanoma, leukemia,
ovarian, breast, colorectal, or lung squamous cancer, sarcoma,
renal cell carcinoma, pancreatic carcinomas, squamous tumors of the
head and neck, brain cancer, liver cancer, prostate cancer, ovarian
cancer, and cervical cancer. The compositions can include target
peptides. The vaccine compositions can in some embodiments include
only the target peptides, or peptides disclosed herein, or they can
include other cancer antigens that have been identified.
[0109] The vaccine compositions of the presently disclosed subject
matter can be used prophylactically for the purposes of preventing,
reducing the risk of, and/or delaying initiation of a cancer in an
individual that does not currently have cancer. Alternatively, they
can be used to treat an individual that already has cancer, so that
recurrence or metastasis is delayed and/or prevented. Prevention
relates to a process of prophylaxis in which the individual is
immunized prior to the induction or onset of cancer. For example,
in some embodiments individuals with a history of poor life style
choices and at risk for developing colorectal cancer, might be
immunized prior to the onset of the disease.
[0110] Alternatively, individuals that already have cancer can be
immunized with the target peptide-containing compositions of the
presently disclosed subject matter so as to stimulate an immune
response that would be reactive against the cancer. A clinically
relevant immune response would be one in which the cancer partially
or completely regresses and is eliminated from the patient, and it
would also include those responses in which the progression of the
cancer is blocked without being eliminated. Similarly, prevention
need not be total, but may result in a reduced risk, delayed onset,
or delayed progression or metastasis.
[0111] The target peptide vaccines of the presently disclosed
subject matter can be given to patients in some embodiments before,
in some embodiments after, and/or in some embodiments during any
stage of colorectal cancer. In some embodiments, they are given to
patients with malignant colorectal cancer.
[0112] In some embodiments, the 5-year survival rate of patients
treated with the vaccines of the presently disclosed subject matter
is increased by a statistically significant amount that is, in some
embodiments, by about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,
45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,
62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
96, 97, 98, 99, 100 or more percent, relative to the average 5-year
survival rates described above.
[0113] In some embodiments, the target peptide vaccine composition
will increase survival rates in patients with metastatic colorectal
cancer by a statistically significant amount of time that is, in
some embodiments, by about or at least, 0.25, 0.5, 0.75, 1.0, 1.25,
1.5, 1.75, 2.0, 2.25, 2.5, 2.75, 3.0, 3.25, 3.5, 4.0, 4.25, 4.5,
4.75, 5.0, 5.25, 5.5, 5.75, 6.0, 6.25, 6.5, 6.75, 7.0, 7.25, 7.5,
7.75, 8.0, 8.25, 8.5, 8.75, 9.0, 9.25, 9.50, 9.75, 10.0, 10.25,
10.5, 10.75, 11.0, 11.25, 11.5, 11.75 or 12 months or more compared
to what could have been expected without vaccine treatment.
[0114] In some embodiments, the survival rate (e.g., the 1, 2, 3,
4, or 5-year survival rate) of patients treated with the vaccines
of the presently disclosed subject matter are increased by a
statistically significant amount that is, in some embodiments, by
about, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,
49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65,
66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82,
83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99,
or 100 percent, or even greater than 100 percent, relative to the
average 5-year survival rates described above.
[0115] The target peptide vaccines of the presently disclosed
subject matter are in some embodiments envisioned to illicit a T
cell-associated immune response such as, but not limited to
generating activated CD8 T cells specific for native target
peptide/MHC class I expressing cells. In some embodiments, the
CD8.sup.+ T cells specific for native target peptide/MHC class I
expressing cells are specific for at least or about 1, 2, 3, 4, 5,
6, 7, 8, 9, 10, or more of the target peptides in the vaccine in a
patient for about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,
29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,
46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62,
63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79,
80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96,
97, 98, 99, or 100 or more days after providing the vaccine to the
patient.
[0116] In some embodiments, the treatment response rates of
patients treated with the target peptide vaccines of the presently
disclosed subject matter are increased by a statistically
significant amount that is, in some embodiments by about or at
least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,
35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,
69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85,
86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 150,
200, 250, 300, 350, 400, 450, or 500 or more percent, relative to
treatment without the vaccine.
[0117] In some embodiments, overall median survival of patients
treated with the target peptide vaccines of the presently disclosed
subject matter are increased by a statistically significant amount
that is, in some embodiments, by about or at least 1, 2, 3, 4, 5,
6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,
41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,
58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91,
92, 93, 94, 95, 96, 97, 98, 99, 100, 150, 200, 250, 300, 350, 400,
450, or 500 or more percent, relative to treatment without the
vaccine. Preferably, the overall median survival of colorectal
cancer patients treated the target peptide vaccines is envisioned
to be about or at least 10.0, 10.25, 10.5, 10.75, 11.0, 11.25,
11.5, 11.75, 12, 12.25, 12.5, 12.75, 13, 13.25, 13.5, 13.75, 14,
14.25, 14.5, 14.75, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
27, 28, 29, 30, 31, 32, 33, 34, 35, 36 or more months.
[0118] In some embodiments, tumor size of patients treated with the
target peptide vaccines of the presently disclosed subject matter
is decreased by a statistically significant amount that is, in some
embodiments, by about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,
45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,
62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
96, 97, 98, 99, 100, 150, 200, 250, 300, 350, 400, 450, or 500 or
more percent, relative to treatment without the vaccine.
[0119] In some embodiments, the compositions of the presently
disclosed subject matter provide an clinical tumor regression by a
statistically significant amount such as, but not limited to about
or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,
51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84,
85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100,
150, 200, 250, 300, 350, 400, 450, or 500 or more percent, relative
to treatment without the vaccine.
[0120] In some embodiments, the compositions of the presently
disclosed subject matter provide a CTL response specific for the
cancer being treated (e.g., colorectal cancer) by a statistically
significant amount such as, but not limited to about or at least 1,
2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88,
89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 percent of patients
treated with the composition.
[0121] In some embodiments, the compositions of the presently
disclosed subject matter provide an increase in progression free
survival in the cancer being treated, such as but not limited to
colorectal cancer, of about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,
44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60,
61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77,
78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,
95, 96, 97, 98, 99, 100, 110, 120, 130, 140, 150, 160, 170, 180,
190, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475,
500 or more weeks or months compared to the progression free
survival or patients not treated with the composition.
[0122] In some embodiments, one or more of progression free
survival, CTL response rates, clinical tumor regression rates,
tumor size, survival rates (such as but not limited to overall
survival rates), and/or response rates are determined, assessed,
calculated, and/or estimated weekly, monthly, bi-monthly,
quarterly, semi-annually, annually, and/or bi-annually over a
period of about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15 or more years or about or at least 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,
42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58,
59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75,
76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, 99, 100, 110, 120, 130, 140, 150, 160, 170,
180, 190, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450,
475, 500 or more weeks.
[0123] IV.C. Compositions for Priming T Cells
[0124] Adoptive cell transfer (ACT) is the passive transfer of
cells, in some embodiments immune-derived cells, into a recipient
host with the goal of transferring the immunologic functionality
and characteristics into the host. Clinically, this approach has
been exploited to transfer either immune-promoting or tolerogenic
cells (often lymphocytes) to patients to enhance immunity against
cancer. The adoptive transfer of autologous tumor infiltrating
lymphocytes (TIL) or genetically redirected peripheral blood
mononuclear cells has been used to successfully treat patients with
advanced solid tumors, including melanoma and colorectal carcinoma,
as well as patients with CD19-expressing hematologic malignancies.
In some embodiments, ACT therapies achieve T cell stimulation ex
vivo by activating and expanding autologous tumor-reactive T cell
populations to large numbers of cells that are then transferred
back to the patient. See Gattinoni et al., 2006.
[0125] The target peptides of the presently disclosed subject
matter can in some embodiments take the form of antigenic peptides
formulated in a composition added to autologous dendritic cells and
used to stimulate a T helper cell or CTL response in vitro. The in
vitro generated T helper cells or CTL can then be infused into a
patient with cancer (Yee et al., 2002), and specifically a patient
with a form of cancer that expresses one or more of antigenic
target peptides.
[0126] Alternatively, the target peptides can be added to dendritic
cells (DCs) in vitro to produce loaded DCs, with the loaded DCs
being subsequently transferred into an individual with cancer in
order to stimulate an immune response. Alternatively, the loaded
DCs can be used to stimulate CD8.sup.+ T cells ex vivo with
subsequent reintroduction of the stimulated T cells to the patient.
Although a particular target peptide might be identified on one
particular cancer cell type, it might also be found on other cancer
cell types.
[0127] The presently disclosed subject matter envisions treating
cancer by providing a patient with cells pulsed with a composition
of target peptides. The use of DCs pulsed with target peptides
peptide antigens enables manipulation of the immunogen in two ways:
varying the number of cells injected and varying the density of
antigen presented on each cell. Exemplary non-limiting methods for
DC-based based treatments can be found, for example in Mackensen et
at, 2000.
[0128] IV.D. Additional Peptides Present in Target Peptide
Compositions
[0129] The target peptide compositions (or target peptide
composition kits comprising the same) of the presently disclosed
subject matter can in some embodiments also include at least one
additional peptide derived from one or more tumor-associated
antigens (TAAs). Examples of TAAs include MelanA (MART-I), gp100
(Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1,
GAGE-2, p15(58), CEA, RAGE, NY-ESO (LAGE), SCP-1, Hom/Mel-40,
PRAME, p53, H-Ras, HER-2/neu, BCR-ABL, E2A-PRL, 4-RET, IGH-IGK,
MYL-RAR, Epstein Barr virus antigens, EBNA, human papillomavirus
(HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6,
p185erbB2, p180erbB-3, c-met, nm-23H1, PSA, TAG-724, CA 19-9, CA
72-4, CAM 17.1, NuMa, K-ras, .beta.-Catenin, CDK4, Mum-1, p16,
TAGE, PSMA, PSCA, CT7, telomerase, 43-9F, 5T4, 791Tgp72,
.alpha.-fetoprotein, .beta.-HCG, BCA225, BTAA, CA 125, CA 15-3
(CA27.29\BCAA), CA 195, CA 242, CA-50, CAM43, CD68\KP1, CO-029,
FGF-5, G250, Ga733 (EpCAM), HTgp-275, M344, MA-50, MG7-Ag, MOV18,
NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90 (Mac-2 binding
protein/cyclophilin C-associated protein), TAAL6, TAG72, TLP, TPS,
prostatic acid phosphatase, and the like. Exemplary, non-limiting
peptides derived from TAAs that can be incorporated into target
peptide compositions (or target peptide composition kits comprising
the same) of the presently disclosed subject matter are presented
in Table 2.
TABLE-US-00002 TABLE 2 Tumor-associated Antigen.sup.1 Peptide
Sequence.sup.2 gp100.sub.280-288 YLEPGPVTA (SEQ ID NO: 178)
Tyr.sub.369-377 DYMDGTMSQV (SEQ ID NO: 179) gp100.sub.l7-25
ALLAVGATK (SEQ ID NO: 180) Tyr.sub.243-251 KCDICTDEY (SEQ ID NO:
181) TAG-1, 2 RLSNRLLLR (SEQ ID NO: 182) -- SQNFPGSQK (SEQ ID NO:
183) gp100.sub.l54-162 KTWGQYWQV (SEQ ID NO: 184) gp100.sub.209-217
I(T/M)DQVPFSV (SEQ ID NO: 185) gp100.sub.476-485 VLYRYGSFSV (SEQ ID
NO: 186) MART-1/MelanA.sub.27-35 AAGIGDLTV (SEQ ID NO: 187) gp100
ALNFPGSQK (SEQ ID NO: 188) gp100.sub.614-622 LIYRRRLMK (SEQ ID NO:
189) NY-ESO-1 AAQERRVPR (SEQ ID NO: 190) NY-ESO-1.sub.53-62
ASGPGGGAPR (SEQ ID NO: 191) NY-ESO-1 LLGPGRPYR (SEQ ID NO: 192)
Tyr.sub.240-251 SDAEKSDICTDEY (SEQ ID NO: 193) Tyr.sub.146-156
SSDYVIPIGTY (SEQ ID NO: 194) MAGE-A1.sub.161-169 EADPTGHSY (SEQ ID
NO: 195) MAGE-A3.sub.168-176 EVDPIGHLY (SEQ ID NO: 196)
gp100.sub.209-217 IMDQVPFSV (SEQ ID NO: 197) MAGE-A10.sub.254-262
GLYDGMEHL (SEQ ID NO: 198) Tyr.sub.56-70 AQNILLSNAPLGPQFP (SEQ ID
NO: 199) Tyr.sub.388-406 FLLHHAFVDSI FEQWLQRHRP (SEQ ID NO: 200)
Melan-A/MART-1.sub.51-73 RNGYRALMDKSL HVGTQCALTRR (SEQ ID NO: 201)
MAGE-A3.sub.281-295 TSYVKVLHHMVKISG (SEQ ID NO: 202) MAGE-A1, 2, 3,
6.sub.121-134 LLKYRAREPVTKAE (SEQ ID NO: 203) Gp100.sub.44-59
WNRQLYPEWTEAQRLD (SEQ ID NO: 204) p2.sub.830-844 AQYIKANSKFIGITEL
(SEQ ID NO: 205) Her2/neu.sub.369-377 KIFGSLAFL (SEQ ID NO: 206)
CEA.sub.571-579 YLSGADLNL (SEQ ID NO: 207) Her2/neu.sub.754-762
VLRENTSPK (SEQ ID NO: 208) FBP.sub.191-199 EIWTHSYKV (SEQ ID NO:
209) MAGE-A1.sub.96-104 SLFRAVITK (SEQ ID NO: 210) CEA.sub.27-35
HLFGYSWYK (SEQ ID NO: 211) MART-1.sub.97-116 APPAYEKLS (SEQ ID NO:
212) MART-1.sub.98-109 PPAYEKLSA (SEQ ID NO: 213) MART-1.sub.99-110
PAYEKLSAE (SEQ ID NO: 214) MART-1.sub.97-116 VPNAPPAYEK LsAEQSPPPY
(SEQ ID NO: 215) MART-1.sub.98-109 PNAPPAYEKLsA (SEQ ID NO: 216)
MART-1.sub.99-110 NAPPAYEKLsAE (SEQ ID NO: 217) MART-1.sub.100-111
APPAYEKLsAEQ (SEQ ID NO: 218) MART-1.sub.100-114 APPAYEKLsAEQSPP
(SEQ ID NO: 219) MART-1.sub.100-115 APPAYEKLsAEQSPPP (SEQ ID NO:
220) MART-1.sub.101-112 PPAYEKLsAEQS (SEQ ID NO: 221)
MART-1.sub.102-113 PAYEKLsAEQSP (SEQ ID NO: 222) MART-1.sub.103-114
AYEKLsAEQSPP (SEQ ID NO: 223) MART-1.sub.104-115 YEKLSAEQSPPP (SEQ
ID NO: 224) MART-1.sub.100-115 APPAYEKLSAEQSPPP (SEQ ID NO: 225)
MART-1.sub.100-116 APPAYEKLsAEQSPPPY (SEQ ID NO: 226) .sup.1the
numbers listed in subscript denote the amino acid positions of the
peptide sequences for each TAA. .sup.2lowercase letters (s, t, or
y) indicate positions of phosphorylation.
[0130] Such tumor-specific peptides (including the MHC class II
phosphopeptides 5 disclosed in Tables 6-9) can be added to the
target peptide compositions in a manner, number, and in an amount
as if they were an additional target peptide added to the target
peptide compositions as described herein.
[0131] IV.E. Combination Therapies
[0132] In some embodiments, the target peptide compositions (or
target peptide composition kits) of the presently disclosed subject
matter are administered as a vaccine or in the form of pulsed cells
as first, second, third, or fourth line treatment for the cancer.
In some embodiments, the compositions of the presently disclosed
subject matter are administered to a patient in combination with
one or more therapeutic agents. Exemplary, non-limiting therapeutic
agents include anti-Programed Death-1 (PD1) or PD1-antagonists such
as the anti-PD1 antibody BMS-936558 (Bristol-Myers Squibb Co., New
York, N.Y., United States of America); anti-CTLA-4 or CTLA-4
antagonists; vermurafenib; ipilimumab; Dacarbazine; IL-2;
Temozolomide; receptor tyrosine kinase inhibitors, including but
not limited to imatinib, gefitinib, erlotinib, sunitinib,
tyrphostins, telatinib; sipileucel-T; a platinum-based agent; a
taxane; an alkylating agent; an antimetabolite and/or a vinca
alkaloid; and combinations thereof.
[0133] In some embodiments, the cancer is sensitive to and/or
refractory, relapsed, and/or resistant to one or more
chemotherapeutic agents such as, but not limited to a
platinum-based agent, a taxane, an alkylating agent, an
anthracycline (e.g., doxorubicin including but not limited to
liposomal doxorubicin), an antimetabolite, and/or a vinca alkaloid.
In some embodiments, the cancer is an ovarian cancer, and the
ovarian cancer is refractory, relapsed, or resistant to a
platinum-based agent (e.g., carboplatin, cisplatin, oxaliplatin), a
taxane (e.g., paclitaxel, docetaxel, larotaxel, cabazitaxel),
and/or an anthracycline (e.g., doxorubicin including but not
limited to liposomal doxorubicin). In some embodiments, the cancer
is colorectal cancer, and the cancer is refractory, relapsed, or
resistant to an antimetabolite (e.g., an antifolate (e.g.,
pemetrexed, floxuridine, raltitrexed) a pyrimidine analogue (e.g.,
capecitabine, cytrarabine, gemcitabine, 5FU)), and/or a
platinum-based agent (e.g., carboplatin, cisplatin, irinoptecan,
oxaliplatin). In some embodiments, the cancer is lung cancer, and
the cancer is refractory, relapsed, or resistant to a taxane (e.g.,
paclitaxel, docetaxel, larotaxel, cabazitaxel), a platinum-based
agent (e.g., carboplatin, cisplatin, oxaliplatin), a vinca alkaloid
(e.g., vinblastine, vincristine, vindesine, vinorelbine), a
vascular endothelial growth factor (VEGF) pathway inhibitor, an
epidermal growth factor (EGF) pathway inhibitor) and/or an
antimetabolite (e.g., an antifolate including but not limited to
pemetrexed, floxuridine, or raltitrexed), and a pyrimidine analogue
(e.g., capecitabine, cytrarabine, gemcitabine, 5FU). In some
embodiments, the cancer is breast cancer, and the cancer is
refractory, relapsed, or resistant to a taxane (e.g., paclitaxel,
docetaxel, larotaxel, cabazitaxel), a VEGF pathway inhibitor, an
anthracycline (e.g., daunorubicin, doxorubicin including but not
limited to liposomal doxorubicin, epirubicin, valrubicin,
idarubicin), a platinum-based agent (e.g., carboplatin, cisplatin,
oxaliplatin), and/or an antimetabolite (e.g., an antifolate
including but not limited to pemetrexed, floxuridine, or
raltitrexed), and a pyrimidine analogue (e.g., capecitabine,
cytrarabine, gemcitabine, 5FU). In some embodiments, the cancer is
gastric cancer, and the cancer is refractory, relapsed, or
resistant to an antimetabolite (e.g., an antifolate including but
not limited to pemetrexed, floxuridine, raltitrexed) and a
pyrimidine analogue (e.g., capecitabine, cytrarabine, gemcitabine,
5FU) and/or a platinum-based agent (e.g., carboplatin, cisplatin,
oxaliplatin).
[0134] In some embodiments, the cancer is colorectal cancer. In
some embodiments, chemotherapy for colorectal cancer comprises
treatment with 5FU, capecitabine, irinoptecan, and/or oxaliplatin.
In some embodiments, a combination of chemotherapeutics is
employed. Exemplary, non-limiting chemotherapeutics that can be
employed combination therapies include FOLFOX (5FU, leucovorin, and
oxaliplatin); FOLFIRI (5FU, leucovorin, and irinotecan); FOLFOXIRI
(leucovorin, 5FU, oxaliplatin, and irinotecan); CapeOx
(capecitabine and oxaliplatin); 5FU and leucovorin; and/or
capecitabine.
[0135] In some embodiments, the target peptide compositions (or
target peptide composition kits comprising the same) of the
presently disclosed subject matter are associated with agents that
inhibit T cell apoptosis or anergy thus potentiating a T cell
response (referred to herein as a "T cell potentiator"). Such
agents include B7RP1 agonists, B7-H3 antagonists, B7-H4
antagonists, HVEM antagonists, HVEM antagonists, GAL9 antagonists
or alternatively CD27 agonists, OX40 agonists, CD137 agonists, BTLA
agonists, ICOS agonists, CD28 agonists, or soluble versions of
PDL1, PDL2, CD80, CD96, B7RP1, CD137L, OX40 or CD70. See Pardoll,
2012.
[0136] In some embodiments, the T cell potentiator is a PD1
antagonist. Programmed death 1 (PD1) is a key immune checkpoint
receptor expressed by activated T cells, and it mediates
immunosuppression. PD1 functions primarily in peripheral tissues,
where T cells can encounter the immunosuppressive PD1 ligands PD-L1
(B7-H1) and PD-L2 (B7-DC), which are expressed by tumor cells,
stromal cells, or both. In some embodiments, the anti-PD1
monoclonal antibody BMS-936558 (also known as MDX-1106 and
ONO-4538; Bristol-Myers Squibb) is used. In some embodiments, the T
cell potentiator (e.g., PD1 antagonist) is administered as an
intravenous infusion at least or about every 1, 1.5, 2, 2.5, 3,
3.5, or 4 weeks of each 4, 5, 6, 7, 8, 9, or 10-week treatment
cycle of about for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, or more cycles. Exemplary,
non-limiting doses of the PD1 antagonists are in some embodiments
exactly, about, or at least 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8,
0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, or more mg/kg. See Brahmer et al., 2012.
[0137] The exemplary therapeutic agents listed herein above are
envisioned to be administered at a concentration of in some
embodiments about 1 to 100 mg/m.sup.2, in some embodiments about 10
to 80 mg/m.sup.2, and in some embodiments about 40 to 60
mg/m.sup.2. Further exemplary dosages include, but are not limited
to about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,
35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,
69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85,
86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, or
more mg/m.sup.2. Alternatively, an exemplary dosage range can be in
some embodiments about or at least 0.001 to 100 mg/kg, in some
embodiments about or at least 0.1 to 1 mg/kg, and in some
embodiments about or at least 0.01 to 10 mg/kg.
[0138] The target peptide compositions (or target peptide
composition kits) of the presently disclosed subject matter can in
some embodiments be co-administered with cytokines such as
lymphokines, monokines, growth factors, and traditional polypeptide
hormones. Exemplary cytokines are growth hormones including but not
limited to human growth hormone, N-methionyl human growth hormone,
and bovine growth hormone; parathyroid hormone; thyroxine; insulin;
proinsulin; relaxin; prorelaxin; glycoprotein hormones including
but not limited to follicle stimulating hormone (FSH), thyroid
stimulating hormone (TSH), and luteinizing hormone (LH); hepatic
growth factor; prostaglandin, fibroblast growth factor; prolactin;
placental lactogen, OB protein; TNF-.alpha. and TNF-.beta.;
mullerian-inhibiting substance; mouse gonadotropin-associated
peptide; inhibin; activin; VEGF; integrin; thrombopoietin (TPO);
nerve growth factors including but not limited to NGF-.beta.;
platelet-growth factor; transforming growth factors (TGFs)
including but not limited to TGF-.alpha. and TGF-.beta.;
insulin-like growth factor (IGF)-I and IGF-II; erythropoietin
(EPO); osteoinductive factors; interferons (IFN) including but not
limited to IFN.alpha., IFN.beta., and IFN.gamma.; colony
stimulating factors (CSFs) including but not limited to
macrophage-CSF (M-CSF), granulocyte-macrophage-CSF (GM-CSF), and
granulocyte-CSF (G-CSF); interleukins (ILs) including but not
limited to IL-1, IL-1.alpha., IL-2, IL-3, IL-4, IL-5, IL-6, IL-7,
IL-8, I-9, IL-10, IL-11, IL-12; IL-13, IL-14, IL-15, IL-16, IL-17,
and IL-18 leukemia inhibitory factor (LIF), kit-ligand; FLT-3;
angiostatin; thrombospondin; endostatin; and lymphotoxin (LT). As
used herein, the term cytokine includes proteins from natural
sources and/or from recombinant cell culture and biologically
active equivalents thereof.
[0139] The target peptide compositions of the presently disclosed
subject matter can in some embodiments be provided with
administration of cytokines around the time of (including but not
limited to about or at least 1, 2, 3, or 4 weeks or days before
and/or after) the initial dose of a target peptide composition.
[0140] Exemplary non-limiting doses of the cytokine are in some
embodiments about or at least 1-100, 10-80, 20-70, 30-60, 40-50, or
1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 Mu/m.sup.2/day over about or at
least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,
35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,
69, or 70 days. The cytokine can in some embodiments be delivered
at least or about once every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 hours. Cytokine
treatment can be provided in at least or about 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
25, 26, 27, 28, 29, or 30 cycles of at least or about 1, 2, 3, 4,
5, 6, 7, 8, 9, 10, or more weeks, wherein each cycle has at least
or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more
cytokine doses. Cytokine treatment can in some embodiments be on
the same schedule as administration of the target peptide
compositions or in some embodiments on a different schedule, which
differing schedule can in some embodiments be an overlapping
schedule.
[0141] In some embodiments, the cytokine is IL-2 and is dosed in an
amount about or at least 100,000 to 1,000,000; 200,000-900,000;
300,000-800,000; 450,000-750,000; 600,000-800,000; or
700,000-800,000 (in some embodiments, 720,000) units (IU)/kg
administered, e.g., as a bolus, every 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 hours for 1, 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or more days, in a cycle, for
example.
V. Types of Proliferative Diseases
[0142] In some embodiments, the compositions of the presently
disclosed subject matter are envisioned to be useful in the
treatment of benign and/or malignant proliferative diseases.
Excessive proliferation of cells and turnover of cellular matrix
contribute significantly to the pathogenesis of several diseases
including but not limited to cancer, atherosclerosis, rheumatoid
arthritis, psoriasis, idiopathic pulmonary fibrosis, scleroderma
and cirrhosis of the liver, ductal hyperplasia, lobular
hyperplasia, papillomas, and others.
[0143] In some embodiments, the proliferative disease is cancer,
including but not limited to breast cancer, colorectal cancer,
squamous carcinoma of the lung, sarcoma, renal cell carcinoma,
pancreatic carcinomas, squamous tumors of the head and neck,
leukemia, brain cancer, liver cancer, prostate cancer, ovarian
cancer, and cervical cancer. In some embodiments, the presently
disclosed compositions and methods are used to treat colorectal
cancer, acute myelogenous leukemia (AML), acute lyphocytic leukemia
(ALL), chronic lymphocytic lymphoma (CLL), chronic myelogenous
leukemia (CML), breast cancer, renal cancer, pancreatic cancer,
and/or ovarian cancer.
[0144] In some embodiments, the target peptide compositions of the
presently disclosed subject matter can be used to treat colorectal
cancer. Colorectal cancer is typically staged in five stages: Stage
0-IV, with several substages. When metastatic (i.e., Stage IV), the
colorectal cancer has in some embodiments spread to the lung, bone,
liver, and/or brain.
[0145] In some embodiments, the cancer is a cancer described
herein. For example, the cancer can be a cancer of the bladder
(including but not limited to accelerated and metastatic bladder
cancer), breast (including but not limited to estrogen receptor
positive breast cancer, estrogen receptor negative breast cancer,
HER-2 positive breast cancer, HER-2 negative breast cancer, triple
negative breast cancer, and inflammatory breast cancer), colon
(including but not limited to colorectal cancer), kidney (including
but not limited to renal cell carcinoma), liver, lung (including
but not limited to small cell lung cancer and non-small cell lung
cancer such as but not limited to adenocarcinoma, squamous cell
carcinoma, bronchoalveolar carcinoma and large cell carcinoma),
genitourinary tract cancer, including but not limited to ovary
(such as but not limited to fallopian, endometrial, and peritoneal
cancers), cervix, prostate, and testes, lymphatic system, rectum,
larynx, pancreas (including but not limited to exocrine pancreatic
carcinoma), stomach (including but not limited to gastroesophageal,
upper gastric, and lower gastric cancers), gastrointestinal cancer
(including but not limited to anal cancer), gall bladder, thyroid,
lymphoma (including but not limited to Burkitt's, Hodgkin's, and
non-Hodgkin's lymphoma), leukemia (including but not limited to
acute myeloid leukemia), Ewing's sarcoma, nasoesophageal cancer,
nasopharyngeal cancer, neural and glial cell cancers (including but
not limited to glioblastoma multiforme), and head and neck cancers.
Exemplary non-limiting cancers also include melanoma, breast cancer
(including but not limited to metastatic or locally advanced breast
cancer), prostate cancer (including but not limited to hormone
refractory prostate cancer), renal cell carcinoma, lung cancer
(including but not limited to small cell lung cancer and non-small
cell lung cancer (including adenocarcinoma, squamous cell
carcinoma, bronchoalveolar carcinoma, and large cell carcinoma),
pancreatic cancer, gastric cancer (including but not limited to
gastroesophageal, upper gastric, and/or lower gastric cancer),
colorectal cancer, squamous cell cancer of the head and neck,
ovarian cancer (including but not limited to advanced ovarian
cancer, platinum-based agent-resistant, and/or relapsed ovarian
cancer), lymphoma (including but not limited to Burkitt's,
Hodgkin's, or non-Hodgkin's lymphoma), leukemia (including but not
limited to acute myeloid leukemia), and gastrointestinal
cancer.
VI. Administration of Vaccine Compositions
[0146] VI.A. Routes of Administration
[0147] The target peptide compositions of the presently disclosed
subject matter can be administered parenterally, systemically,
topically, or any combination thereof. By way of example and not
limitation, composition injections can be performed by intravenous
(i.v.) injection, subcutaneous (s.c.) injection, intradermal (i.d.)
injection, intraperitoneal (i.p.) injection, and/or intramuscular
(i.m.) injection. One or more such routes can be employed.
Parenteral administration can be, for example, by bolus injection
or by gradual perfusion over time. Alternatively or in addition,
administration can be by the oral route.
[0148] In some embodiments, an injection is an intradermal (i.d.)
injection. The target peptide compositions are in some embodiments
suitable for administration of the peptides by any acceptable route
such as but not limited to oral (enteral), nasal, ophthal, and
transdermal. In some embodiments, the administration is
subcutaneous, and in some embodiments the subcutaneous
administration is by an infusion pump.
[0149] VI.B. Formulations
[0150] Pharmaceutical carriers, diluents, and excipients are
generally added to the target peptide compositions or (target
peptide compositions kits) that are compatible with the active
ingredients and acceptable for pharmaceutical use. Examples of such
carriers include but are not limited to water, saline solutions,
dextrose, and/or glycerol. Combinations of carriers can also be
used.
[0151] The vaccine compositions of the presently disclosed subject
matter can further incorporate additional substances to stabilize
pH and/or to function as adjuvants, wetting agents, and/or
emulsifying agents, which can serve to improve the effectiveness of
the vaccine.
[0152] The target peptide compositions can in some embodiments
include one or more adjuvants such as for example: montanide ISA-51
(Seppic Inc., Fairfield, N.J., United States of America); QS-21
(Aquila Biopharmaceuticals, Inc., Framingham, Mass., United States
of America); Arlacel A; oeleic acid; tetanus helper peptides (such
as but not limited to QYIKANSKFIGITEL (SEQ ID NO: 368) or
AQYIKANSKFIGITEL (SEQ ID NO: 205)); GM-CSF; cyclophosamide;
bacillus Calmette-Guerin (BCG); Corynbacterium parvum; levamisole,
azimezone; isoprinisone; dinitrochlorobenezene (DNCB); keyhole
limpet hemocyanin (KLH); Freunds adjuvant (complete and
incomplete); mineral gels; aluminum hydroxide (Alum); lysolecithin;
pluronic polyols; polyanions; peptides; oil emulsions; nucleic
acids (such as but not limited to double-stranded RNAs; dsRNA)
dinitrophenol; diphtheria toxin (DT); toll-like receptor (TLR; such
as but not limited to TLR3, TLR4, TLR7, TLR8, and/or TLR9) agonists
(including but not limited to endotoxins such as lipopolysaccharide
(LPS); monophosphoryl lipid A (MPL); and/or
polyinosinic-polycytidylic acid (poly-ICLC/HILTONOL.RTM.; Oncovir,
Inc., Washington, D.C., United States of America); IMO-2055;
glucopyranosyl lipid A (GLA); QS-21 (a saponin extracted from the
bark of the Quillaja saponaria tree, also known as the soap bark
tree or Soapbark); resiquimod (a TLR7/8 agonist); CDX-1401 (a
fusion protein consisting of a fully human monoclonal antibody with
specificity for the dendritic cell receptor DEC-205 linked to the
NY-ESO-1 tumor antigen); Juvaris' Cationic Lipid-DNA Complex;
Vaxfectin; and combinations thereof.
[0153] In some embodiments, the tetanus peptide can be about or at
least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
25, (in some embodiments 10-25) natural or non-natural amino acids
in length. In some embodiments, the tetanus peptide is a segment or
fragment of a tetanus toxoid protein. In some embodiments the
tetanus toxoid peptide used herein is at least or about 70%, 75%,
80%, 85%, 90%, 95%, 98%, 99%, or 100% identical to a 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 amino acids
segment of the wild type tetanus toxoid protein. In some
embodiments the tetanus toxoid peptide used herein is at least or
about 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% identical to
SEQ ID NOs: 205 or 368. In some embodiments, the tetanus peptide
binds to one or more MHC Class II molecules. In some embodiments,
the tetanus peptide is modified so as to prevent formation of
tetanus peptide secondary structures. In some embodiments, a
nucleic acid (e.g., DNA or RNA) is provided that encodes a tetanus
peptide. In some embodiments, the tetanus peptide belongs to the
830 to 844 amino acid sequence of the tetanus toxin Tc (see Demotz
el al., 1989; El Kasmi et al., 2000).
[0154] Polyinosinic-Polycytidylic acid (Poly IC) is a
double-stranded RNA (dsRNA) that acts as a TLR3 agonist. To
increase half-life, it has been stabilized with polylysine and
carboxymethylcellulose as poly-ICLC. It has been used to induce
interferon in cancer patients, with intravenous doses up to 300
.mu.g/kg. Like poly-IC, poly-ICLC is a TLR3 agonist. TLR3 is
expressed in the early endosome of myeloid DC; thus poly-ICLC
preferentially activates myeloid dendritic cells, thus favoring a
Th1 cytotoxic T cell response. Poly-ICLC activates natural killer
(NK) cells, induces cytolytic potential, and induces IFN.gamma.
from myeloid DC.
[0155] In some embodiments, an adjuvant is provided at about or at
least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140,
150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270,
280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400,
410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530,
540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660,
670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790,
800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920,
930, 940, 950, 960, 970, 980, 990, or 1000 .mu.g per dose or per kg
in each dose. In some embodiments, the adjuvant is provided in a
dosage of at least or about 0.1, 0.2, 0.3, 0.40, 0.50, 0.60, 0.70,
0.80, 0.90, 0.100, 1.10, 1.20, 1.30, 1.40, 1.50, 1.60, 1.70, 1.80,
1.90, 2.00, 2.10, 2.20, 2.30, 2.40, 2.50, 2.60, 2.70, 2.80, 2.90,
3.00, 3.10, 3.20, 3.30, 3.40, 3.50, 3.60, 3.70, 3.80, 3.90, 4.00,
4.10, 4.20, 4.30, 4.40, 4.50, 4.60, 4.70, 4.80, 4.90, 5.00, 5.10,
5.20, 5.30, 5.40, 5.50, 5.60, 5.70, 5.80, 5.90, 6.00, 6.10, 6.20,
6.30, 6.40, 6.50, 6.60, 6.70, 6.80, 6.90, 7.00, 7.10, 7.20, 7.30,
7.40, 7.50, 7.60, 7.70, 7.80, 7.90, 8.00, 8.10, 8.20, 8.30, 8.40,
8.50, 8.60, 8.70, 8.80, 8.90, 9.00, 9.10, 9.20, 9.30, 9.40, 9.50,
9.60, 9.70, 9.80, 9.90, or 10.00 grams per dose or per kg in each
dose. In some embodiments, the adjuvant is given at about or at
least 10, 15, 20, 25, 50, 75, 100, 125, 150, 175, 150, 175, 200,
225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 500, 525, 550,
575, 600, 625, 675, 700, 725, 750, 775, 800, 900, 1000, 1100, 1200,
1300, 1400, 1500, 1600, 1700, 1800, 1900 or 2000 endotoxin units
("EU") per dose.
[0156] The target peptide compositions of the presently disclosed
subject matter can in some embodiments be provided with an
administration of cyclophosamide around the time (such as but not
limited to about or at least 1, 2, 3, or 4 weeks or days before or
after) of the initial dose of a target peptide composition.
Exemplary non-limiting dose of cyclophosamide are in some
embodiments about or at least 100, 200, 300, 400, 500, 600, 700,
800, 900 or 1000 Mg/m.sup.2/day over about or at least 1, 2, 3, 4,
5, 6, 7, 8, 9 or 10 days.
[0157] The compositions may comprise the target peptides in the
free form and/or in the form of a pharmaceutically acceptable salt.
As used herein, "a pharmaceutically acceptable salt" refers to a
derivative of a disclosed target peptide wherein the target peptide
is modified by making acid or base salts of the agent. For example,
acid salts are prepared from the free base (typically wherein the
neutral form of the drug has a neutral --NH.sub.2 group) involving
reaction with a suitable acid. Suitable acids for preparing acid
salts include both organic acids such as but not limited to acetic
acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid,
malic acid, malonic acid, succinic acid, maleic acid, fumaric acid,
tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic
acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic
acid, salicylic acid, and the like, as well as inorganic acids such
as but not limited to hydrochloric acid, hydrobromic acid, sulfuric
acid, nitric acid phosphoric acid, and the like. Conversely, basic
salts of acid moieties that can be present on a target peptide are
in some embodiments prepared using a pharmaceutically acceptable
base such as but not limited to sodium hydroxide, potassium
hydroxide, ammonium hydroxide, calcium hydroxide, trimmethylamine,
and the like. By way of example and not limitation, the
compositions can comprise target peptides as salts of acetic acid
(acetates), ammonium, or hydrochloric acid (chlorides).
[0158] In some embodiments, a composition can include one or more
sugars, sugar alcohols, amino acids such but not limited to
glycine, arginine, glutamic acid, and/or others as framework
formers. The sugars can be mono-, di-, or trisaccharides. These
sugars can be used alone and/or in combination with sugar alcohols.
Exemplary sugars include glucose, mannose, galactose, fructose, or
sorbose as monosaccharides; sucrose, lactose, maltose, and
trehalose as disaccharides; and raffinose as a trisaccharide. A
sugar alcohol can be, for example, mannitose. In some embodiments,
the composition comprises sucrose, lactose, maltose, trehalose,
mannitol, and/or sorbitol. In some embodiments, the composition
comprises mannitol.
[0159] Furthermore, in some embodiments compositions can include
physiological well-tolerated excipients (see Handbook of
Pharmaceutical Excipients. 5.sup.th ed., edited by Raymond Rowe,
Paul Sheskey and Sian Owen, Pharmaceutical Press (2006)) such as
antioxidants like ascorbic acid or glutathione; preserving agents
such as phenol, m-cresol, methyl- or propylparabene, chlorobutanol,
thiomersal/thimerosal, and/or benzalkoniumchloride; stabilizers,
framework formers such as sucrose, lactose, maltose, trehalose,
mannitose, mannitol, and/or sorbitol; mannitol and/or lactose and
solubilizers such as polyethylene glycols (PEG; e.g., PEG 3000,
3350, 4000, or 6000), cyclodextrins (e.g.,
hydroxypropyl-.beta.-cyclodextrin,
sulfobutylethyl-.beta.-cyclodextrin, or .gamma.-cyclodextrin),
dextrans, or poloxamers (e.g., poloxamer 407 or poloxamer 188); or
TWEEN.RTM. 20 or TWEEN.RTM. 80. In some embodiments, one or more
well-tolerated excipients can be included, optionally selected from
the group consisting of antioxidants, framework formers, and
stabilizers.
[0160] In some embodiments, the pH for intravenous and/or
intramuscular administration is selected from pH 2 to pH 12. In
some embodiments, the pH for subcutaneous administration is
selected from pH 2.7 to pH 9.0 as the rate of in vivo dilution is
reduced resulting in more potential for irradiation at the
injection site (Strickley, 2004).
[0161] VI.C. Dosage
[0162] It is understood that a suitable dosage of a target peptide
composition vaccine immunogen cam depend upon the age, sex, health,
and/or weight of the recipient, the kind of concurrent treatment,
if any, the frequency of treatment, and the nature of the effect
desired. However, it is understood that dosages can be tailored to
the individual subject, as determined by the researcher or
clinician. The total dose required for any given treatment will in
some embodiments be determined with respect to a standard reference
dose based on the experience of the researcher or clinician, such
dose being administered either in a single treatment or in a series
of doses, the success of which will depend on the production of a
desired immunological result (such as but not limited to successful
production of a T helper cell and/or CTL-mediated response to the
target peptide immunogen composition, which response gives rise to
the prevention and/or treatment desired).
[0163] Thus, in some embodiments the overall administration
schedule is considered in determining the success of a course of
treatment and not whether a single dose, given in isolation, would
or would not produce the desired immunologically therapeutic result
or effect.
[0164] Thus, the therapeutically effective amount (i.e., in some
embodiments that amount that produces a desired T helper cell
and/or CTL-mediated response) can depend on the antigenic
composition of the vaccine used, the nature of the disease
condition, the severity of the disease condition, the extent of any
need to prevent such a condition where it has not already been
detected, the manner of administration dictated by the situation
requiring such administration, the weight and state of health of
the individual receiving such administration, and/or the sound
judgment of the clinician or researcher. In some embodiments, the
efficacy of administering additional doses and/or of increasing or
decreasing the interval can be continually re-evaluated in view of
the recipient's immunocompetence (including but not limited to the
level of T helper cell and/or CTL activity with respect to
tumor-associated or tumor-specific antigens).
[0165] The concentration of the T helper or CTL stimulatory target
peptides of the presently disclosed subject matter in
pharmaceutical formulations can be subject to wide variation,
including anywhere from less than 0.01% by weight to as much as 50%
or more. Factors such as volume and viscosity of the resulting
composition can in some embodiments also be considered. The
solvents or diluents used for such compositions can include water,
phosphate buffered saline (PBS), and/or saline, or any other
possible carriers or excipients.
[0166] The immunogens of the presently disclosed subject matter can
in some embodiments also be contained in artificially created
structures such as liposomes, which structures in some embodiments
can contain additional molecules such as but not limited to
proteins or polysaccharides, inserted in the outer membranes of
said structures and having the effect of targeting the liposomes to
particular areas of the body and/or to particular cells within a
given organ or tissue. Such targeting molecules can in some
embodiments comprise an immunoglobulin. Antibodies can work
particularly well for targeting of liposomes and/or other scaffolds
to tumor cells.
[0167] Single i.d., i.m., s.c., i.p., and/or i.v. doses of in some
embodiments about 1 to 50 .mu.g, in some embodiments about 1 to 100
.mu.g, in some embodiments about 1 to 500 .mu.g, in some
embodiments about 1 to 1000 .mu.g, in some embodiments about 1 to
50 mg, in some embodiments about 1 to 100 mg, in some embodiments
about 1 to 500 mg, or in some embodiments about 1 to 1000 mg of
target peptide composition can be given and can depend from the
respective compositions of target peptides with respect to total
amount for all target peptides in the composition or alternatively
for each individual target peptide in the composition. A single
dose of a target peptide vaccine composition of the presently
disclosed subject matter can in some embodiments have a target
peptide amount (e.g., total amount for all target peptides in the
composition or alternatively for each individual target peptide in
the composition) of about or at least 1, 5, 10, 15, 20, 25, 30, 35,
40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175,
200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500,
525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775, 800, 825,
850, 875, 900, or 950 .mu.g. In some embodiments, a single dose of
a target peptide composition of the presently disclosed subject
matter can have a total target peptide amount (e.g., total amount
for all target peptides in the composition or alternatively for
each individual target peptide in the composition) of about or at
least 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,
80, 85, 90, 95, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325,
350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650,
675, 700, 725, 750, 775, 800, 825, 850, 875, 900, or 950 mg. In
some embodiments, the target peptides of a composition of the
presently disclosed subject matter are present in equal amounts of
about 100 micrograms per dose in combination with an adjuvant
peptide present in an amount of about 200 micrograms per dose.
[0168] In a single dose of the target peptide composition of the
presently disclosed subject matter, the amount of each target
peptide in the composition is in some embodiments equal or
substantially equal. Alternatively, a ratio of the target peptides
present in the least amount relative to the target peptide present
in the greatest amount is about or at least 1:1.25, 1:1.5, 1:1.75,
1:2.0, 1:2.25, 1:2.5, 1:2.75, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9,
1:10, 1:20, 1:30; 1:40, 1:50, 1:100, 1:200, 1:500, 1:1000, 1:5000;
1:10,000; or 1:100,000. Alternatively, a ratio of the target
peptides present in the least amount relative to the target peptide
present in the greatest amount is about or at least 1 or 2 to 25; 1
or 2 to 20; 1 or 2 to 15; 1 or 2 to 10; 1 to 3; 1 to 4; 1 to 5; 1
to 6; 1 to 7; 1 to 10; 2 to 3; 2 to 4; 2 to 5; 2 to 6; 2 to 7; 2 to
10; 3 to 4; 3 to 5; 3 to 6; 3 to 7; 3 to 10; 5 to 10; 10 to 15; 15
to 20:20 to 25; 1 to 40; 1 to 30; 1 to 20; 1 to 15; 10 to 40; 10 to
30; 10 to 20; 10 to 15; 20 to 40; 20 to 30; or 20 to 25; 1 to 100;
25 to 100; 50 to 100; 75 to 100; 25 to 75, 25 to 50, or 50 to 75;
25 to 40; 25 to 50; 30 to 50; 30 to 40; or 30 to 75.
[0169] Single dosages can be given to a patient about or at least
1, 2, 3, 4, or 5 times per day. Single dosages can be given to a
patient about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 36, 48, 60, or 72 hours
subsequent to a previous dose.
[0170] Single dosages can be given to a patient about or at least
1, 2, 3, 4, 5, 6, or 7 times per week, or every other, third,
fourth, or fifth day. Single doses can also be given every week,
every other week, or only during 1, 2, or 3 weeks per month. A
course of treatment can in some embodiments last about or at least
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months.
[0171] In some embodiments, the single dosages of the compositions
of the presently disclosed subject matter can be provided to a
patient in at least two phases: e.g., during an initial phase and
then during a subsequent phase. An initial phase can be about or at
least 1, 2, 3, 4, 5, or 6 weeks in length. The subsequent phase can
last at least or about 1, 2, 3, 4, 5, 6, 7, or 8 times as long as
the initial phase. The initial phase can be separated from the
subsequent phase by about or at least 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, or 12 weeks or months.
[0172] The target peptide composition dosage during the subsequent
phase can be at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30,
40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800,
900, or 1000 times greater than during the initial phase.
[0173] The target peptide composition dosage during the subsequent
phase can be at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30,
40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800,
900, or 1000 times less than during the initial phase.
[0174] In some embodiments, the initial phase is about three weeks
and the second phase is about 9 weeks. The target peptide
compositions can be administered to the patient on or about days 1,
8, 15, 36, 57, and 78.
[0175] VI.D. Kits and Storage
[0176] In some embodiments, a kit is disclosed comprising (a) a
container that contains at least one target peptide composition as
described herein, in solution or in lyophilized form; (b)
optionally, a second container containing a diluent or
reconstituting solution for the lyophilized formulation; and (c)
optionally, instructions for (i) use of the solution or (ii)
reconstitution and/or use of the lyophilized formulation. The kit
may further comprise one or more of (iii) a buffer, (iv) a diluent,
(v) a filter, (vi) a needle, or (v) a syringe. In some embodiments,
the container is selected from the group consisting of: a bottle, a
vial, a syringe, a test tube, or a multi-use container. In some
embodiments, the target peptide composition is lyophilized.
[0177] The kits can contain exactly, about, or at least 1, 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,
40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, or more target
peptide-containing compositions. Each composition in the kit can be
administered at the same time and/or at different times.
[0178] In some embodiments, the kits can comprise a lyophilized
formulation of the presently disclosed compositions and/or vaccines
in a suitable container and instructions for its reconstitution
and/or use. Suitable containers include, for example, bottles,
vials (e.g., dual chamber vials), syringes (such as dual chamber
syringes), and test tubes. The container can be formed from a
variety of materials such as glass or plastic. In some embodiments,
the kit and/or the container contain(s) instructions on or
associated therewith that indicate(s) directions for reconstitution
and/or use of a lyophilized formulation. For example, the label can
indicate that the lyophilized formulation is to be reconstituted to
target peptide concentrations as described herein. The label can
further indicate that the formulation is useful or intended for
subcutaneous administration. Lyophilized and liquid formulations
are typically stored at -20.degree. C. to -80.degree. C.
[0179] The container holding the target peptide composition(s) can
be a multi-use vial, which in some embodiments allows for repeat
administrations (e.g., from 2-6 or more administrations) of the
reconstituted formulation. The kit can further comprise a second
container comprising a suitable diluent (e.g., sodium bicarbonate
solution).
[0180] In some embodiments, upon mixing of the diluent and the
lyophilized formulation, the final peptide concentration in the
reconstituted formulation is at least or about 0.15, 0.20, 0.25,
0.5, 0.75, 1.0, 1.25, 1.5, 1.75, 2.0, 2.25, 2.5, 2.75, 3.0, 3.25,
3.50, 3.75, 4.0, 4.25, 4.5, 4.75, 5.0, 6.0, 7.0, 8.0, 9.0, or 10
mg/mL/target peptide. In some embodiments, upon mixing of the
diluent and the lyophilized formulation, the final peptide
concentration in the reconstituted formulation is at least or about
0.15, 0.20, 0.25, 0.5, 0.75, 1.0, 1.25, 1.5, 1.75, 2.0, 2.25, 2.5,
2.75, 3.0, 3.25, 3.50, 3.75, 4.0, 4.25, 4.5, 4.75, 5.0, 6.0, 7.0,
8.0, 9.0, or 10 .mu.g/mL/target peptide.
[0181] The kit can further include other materials desirable from a
commercial and/or user standpoint, including other buffers,
diluents, filters, needles, syringes, and package inserts with or
without instructions for use.
[0182] The kits can have a single container that contains the
formulation of the target peptide compositions with or without
other components (e.g., other compounds or compositions of these
other compounds) or can have a distinct container for each
component.
[0183] Additionally, the kits can include a formulation of the
presently disclosed target peptide compositions and/or vaccines
packaged for use in combination with the co-administration of a
second compound such as an adjuvant including but not limited to
imiquimod, a chemotherapeutic agent, a natural product, a hormone
or antagonist, an anti-angiogenesis agent or inhibitor, an
apoptosis-inducing agent or a chelator) or a composition thereof.
One or more of the components of the kit can be pre-complexed or
one or more components can be in a separate distinct container
prior to administration to a patient. One or more of the components
of the kit can be provided in one or more liquid solutions. In some
embodiments, the liquid solution is an aqueous solution. In some
embodiments, the liquid solution is a sterile aqueous solution. One
or more of the components of the kit can also be provided as
solids, which in some embodiments can be converted into liquids by
addition of suitable solvents, which in some embodiments can be
provided in another distinct container.
[0184] The container of a therapeutic kit can be a vial, a test
tube, a flask, a bottle, a syringe, or any other structure suitable
for enclosing a solid or liquid. Typically, when there is more than
one component, the kit contains a second vial or other container
that allows for separate dosing. The kit can also contain another
container for a pharmaceutically acceptable liquid. In some
embodiments, a therapeutic kit contains an apparatus (e.g., one or
more needles, syringes, eye droppers, pipette, etc.), which enables
administration of the agents of the disclosure that are components
of the kit.
[0185] VI.E. Markers for Efficacy
[0186] When administered to a patient, the vaccine compositions of
the presently disclosed subject matter are in some embodiments
envisioned to have certain physiological effects including but not
limited to the induction of a T cell mediated immune response.
[0187] VI.E.1. Immunohistochemistry, Immunofluorescence. Western
Blots, and Flow Cytometry
[0188] Validation and testing of antibodies for characterization of
cellular and molecular features of lymphoid neogenesis has been
performed. Commercially available antibodies for use in
immunohistochemistry (IHC), immunofluorescence (IF), flow cytometry
(FC), and/or western blotting (WB) can be used. In some
embodiments, such techniques can be employed to assay patient
samples including but not limited to formalin-fixed,
paraffin-embedded tissue samples for the presence or absence of
and/or for a level of expression of one or more of CD1a, S100,
CD83, DC-LAMP, CD3, CD4, CD8, CD20, CD45, CD79a, PNAd, TNF.alpha.,
LIGHT, CCL19, CCL21, CXCL12, TLR4, TLR7, FoxP3, PD-1, and Ki67 gene
products. In some embodiments, flow cytometry is used to determine
an expression level for one or more of CD3, CD4, CD8, CD13, CD14,
CD16, CD19, CD45RA, CD45RO, CD56, CD62L, CD27, CD28, CCR7, FoxP3
(intracellular), and MHC-peptide tetramers for class I MHC
associated (phospho)-peptides. In some embodiments, a positive
control is employed, which in some embodiments can comprise a
tissue sample comprising normal human peripheral blood lymphocytes
(PBL), PBL activated with CD3/CD28 beads (activated PBL), human
lymph node tissue from non-colorectal cancer patients (LN), and/or
inflamed human tissue from a surgical specimen of Crohn's disease
(Crohn's), although any other positive control cell and/or tissue
can be employed.
[0189] VI.E.2. ELISpot Assay
[0190] In some embodiments, vaccination site infiltrating
lymphocytes and lymphocytes from the sentinel immunized node (SIN)
and vaccine site can be evaluated by ELISpot. ELISpot permits the
direct counting of T cells reacting to antigen by production of
IFN.gamma.. Peripheral blood lymphocytes can be evaluated by
ELISpot assay for the number of peptide-reactive T cells. Vaccine
site infiltrating lymphocytes and SIN lymphocytes can be compared
to those in peripheral blood. It is envisioned that positive
results of the ELISpot assay correlates with increased patient
progression free survival. Progression free survival is defined as
the time from start of treatment until death from any cause or date
of last follow up.
[0191] VI.E.3. Tetramer Assay
[0192] Peripheral blood lymphocytes and lymphocytes from the SIN
and vaccine site can be evaluated by flow cytometry after
incubation with MHC-peptide tetramers for the number of
peptide-reactive T cells.
[0193] VI.E.4. Proliferation Assay and Cytokine Analysis
[0194] Peripheral blood mononuclear cells (PBMC), vaccine-site
inflammatory cells, and/or lymphocytes from the SIN isolated from
subjects can be evaluated for CD4.sup.+ T cell reactivity to, e.g.,
tetanus helper peptide mixture, using a .sup.3H-thymidine uptake
assay. Additionally, Th1 (IL-2, IFN.gamma., TNF.alpha.), Th2 (IL-4,
IL-5, IL-10), Th17 (IL-17, and IL23), and T-reg (TGF-.beta.)
cytokines in media from 48 hours in that proliferation assay can be
used to determine if the microenvironment supports generation of
Th1, Th2, Th17, and/or T-reg responses. In some embodiments, one or
both of the following peptides are used as negative controls: a
tetanus peptide and the PADRE peptide (AK(X)VAAWTLKAA; SEQ ID NO:
367.
[0195] VI.E.5. Evaluation of Tumors
[0196] In some embodiments, tumor tissue collected prior to
treatment or at the time of progression can be evaluated by routine
histology and immunohistochemistry. Alternatively or in addition,
in vitro evaluations of tumor tissue and tumor infiltrating
lymphocytes can be performed.
[0197] VI.E.6. Studies of Homing Receptor Expression
[0198] Patient samples can be studied for T cell homing receptors
induced by vaccination with the compositions of the presently
disclosed subject matter. These include but are not limited to
integrins (including but not limited to .alpha.E.beta.7,
.alpha.1.beta.1, .alpha.4.beta.1), chemokine receptors (including
but not limited to CXCR3), and selectin ligands (including but not
limited to CLA and PSL) on lymphocytes, and their ligands in the
vaccine sites and SIN. In some embodiments, these can be assayed by
immunohistochemistry, flow cytometry, and/or any other appropriate
technique(s).
[0199] VI.E.7. Studies of Gene and Protein Expression
[0200] Differences in gene expression and/or differences in protein
expression profiles can be determined by high-throughput screening
assays (e.g., nucleic acid chips, protein arrays, etc.) of samples
isolated from vaccine sites and/or SIN.
VII. Antibodies and Antibody-Like Molecules
[0201] Antibodies and antibody-like molecules (including but not
limited to T cell receptors) specific for target peptides and/or
target peptide/MHC complexes are in some embodiments useful for
analyzing biological samples. In some embodiments, an analysis can
comprise determining the pathological nature of tumor margins.
[0202] Antibodies and antibody-like molecules can also be used as
therapeutics. In some embodiments, such molecules can be used as
therapeutics that target cells, including but not limited to tumor
cells, which display target peptides on their surfaces. In some
embodiments, antibodies and antibody-like molecules bind to
phosphorylated target peptides and/or target peptide-MHC complex
specifically and do not substantially cross react with the
corresponding non-phosphorylated native peptides.
[0203] As used herein, the terms "antibody", "antibody peptide(s)",
and "antibody-like molecule(s)" refer to an intact antibody, a
binding fragment thereof (i.e., a fragment of an antibody that
comprises a paratope), or a polypeptide that can specifically
recognize an antigen or epitope and bind to the same in a fashion
that mimics antibody binding. In some embodiments, antibodies,
antibody peptides, and antibody-like molecules compete with intact
antibodies for specific binding to an antigen or epitope.
[0204] In some embodiments, antibody fragments can be produced by
recombinant DNA techniques and/or by enzymatic and/or chemical
cleavage of intact antibodies. Antibody fragments thus include but
are not limited to Fab fragments, Fab' fragments, F(ab').sub.2
fragments, Fv, and single-chain antibodies including but not
limited to single-chain fragment variable (scFv) antibodies. An
antibody is said to be "monospecific" if each of its paratopes is
identical and/or binds to the same epitope. Similarly, "bispecific"
or "bifunctional" antibodies comprise paratopes that bind to
different antigens and/or epitopes. In some embodiments, an
antibody substantially inhibits adhesion of a receptor to a
counterreceptor when an excess of antibody reduces the quantity of
receptor bound to counterreceptor by at least about 20%, 40%, 60%,
80%, 85%, 90%, 95%, or more as measured by, for example, an in
vitro competitive binding assay.
[0205] The term "MHC" as used herein refers to the Major
Histocompability Complex, which is defined as a set of gene loci
specifying major histocompatibility antigens. The term "HLA" as
used herein will be understood to refer to Human Leukocyte
Antigens, which is defined as the histocompatibility antigens found
in humans. As used herein, "HLA" is the human form of "MHC". IN
murine species, the MHC is referred to as the "H-2" complex.
[0206] The terms "MHC light chain" and "MHC heavy chain" as used
herein refer to particular portions of a MHC molecule.
Structurally, class I molecules are heterodimers comprised of two
noncovalently bound polypeptide chains, a larger "heavy" chain
(.alpha.) and a smaller "light" chain (.beta.2-microglobulin or
.beta.2m). The polymorphic, polygenic heavy chain (45 kDa), encoded
within the MHC on chromosome human 6 is subdivided into three
extracellular domains (designated 1, 2, and 3), one intracellular
domain, and one transmembrane domain. The two outermost
extracellular domains, 1 and 2, together form the groove that binds
to antigenic peptides and/or other epitopes. Thus, interaction with
the TCR occurs at this region of the protein. Domain 3 of the
molecule contains the recognition site for the CD8 protein on the
CTL. This interaction serves to stabilize the contact between the T
cell and an antigen-presenting cell (APC). The invariant light
chain (12 kDa), encoded on human chromosome 15, consists of a
single, extracellular polypeptide. The terms "MHC light chain",
".beta.2-microglobulin", and ".beta.2m" are used interchangeably
herein.
[0207] The term "epitope" includes any protein determinant capable
of specific binding to an antibody, antibody peptide, and/or
antibody-like molecule (including but not limited to a T cell
receptor) as defined herein. Epitopic determinants typically
consist of chemically active surface groups of molecules such as
amino acids or sugar side chains and generally have specific three
dimensional structural characteristics as well as specific charge
characteristics. An antibody or antibody-like molecule is said to
"specifically" bind an antigen when the dissociation constant
(K.sub.d) is in some embodiments less than about 1 .mu.M, in some
embodiments less that about 100 nM, and in some embodiments less
than about 10 nM. Interactions between antibodies and antibody-like
molecules and an epitope can also be characterized by an affinity
constant (K.sub.a). In some embodiments, a K.sub.a of less than
about 10.sup.7/M is considered "high affinity".
[0208] The term "antibody" is used in the broadest sense, and
covers monoclonal antibodies (including full length monoclonal
antibodies), polyclonal antibodies, multispecific antibodies (e.g.,
bispecific and/or trispecific antibodies), and antibody fragments
(including but not limited to Fab, F(ab').sub.2 and Fv fragments)
as well as antibody-like molecules provided that they exhibit the
desired biological activity (e.g., antigen binding). Antibodies
(Abs) and immunoglobulins (Igs) are glycoproteins that in some
embodiments have the same structural characteristics. The term is
also meant to encompass "antibody like molecules" and other members
of the immunoglobulin superfamily including, but not limited to T
cell receptors, MHC molecules, and other polypeptides that contain
one or more antigen-binding regions and/or variable regions
including, but not limited to complementary determining regions
(CDRs) that specifically bind the target peptides disclosed
herein.
[0209] In some embodiments, antibodies and antibody-like molecules
bind to the target peptides disclosed herein but do not
substantially and/or specifically crossreact with the same peptide
in a modified form. See e.g., U.S. Patent Application Publication
No. 2009/0226474, which is incorporated by reference.
[0210] The presently disclosed subject matter includes in some
embodiments antibodies that recognize target peptides associated
with a tumorigenic or disease state, wherein the peptides are
displayed in the context of HLA molecules. These antibodies can
mimic the specificity of a T cell receptor (TCR) but can have
higher binding affinities such that the molecules can be employed
as therapeutic, diagnostic, and/or research reagents. Methods of
producing a T cell receptor mimic of the presently disclosed
subject matter in some embodiments comprise identifying a target
peptide of interest, generating and isolating CD8.sup.+ T cells
specific for the target peptide, and cloning gene sequences that
encode the target peptide-specific TCR.
[0211] In some embodiments an immunogen comprising at least one
target peptide/MHC complex is formed. An effective amount of the
immunogen is in some embodiments administered to a host to elicit
an immune response in the host, and serum collected from the host
can assayed to determine if antibodies that recognize a
three-dimensional presentation of the target peptide in the binding
groove of the MHC molecule have been produced. The desired
antibodies can in some embodiments differentiate the target
peptide/MHC complex from the MHC molecule alone, the target peptide
alone, and/or a complex of MHC and an irrelevant peptide (in some
embodiments, a peptide having the same amino acid composition as a
target peptide but wherein the amino acids are in a different order
that in the target peptide). Finally, in some embodiments the
desired antibodies can be isolated.
[0212] The term "antibody" also encompasses soluble T cell receptor
(TCR) cytoplasmic domains that are stable at low concentrations and
which can recognize MHC-peptide complexes. See e.g., U.S. Patent
Application Publication No. 2002/0119149, which is incorporated by
reference. Such soluble TCRs can in some embodiments be conjugated
to immunostimulatory peptides and/or proteins, and/or moieties such
as but not limited to CD3 agonists (e.g., anti-CD3 antibodies). The
CD3 antigen is present on mature human T cells, thymocytes, and a
subset of natural killer cells. It is associated with the TCR and
is involved in signal transduction of the TCR. Antibodies specific
for the human CD3 antigen are well known. One such antibody is the
murine monoclonal antibody OKT3 which was the first monoclonal
antibody approved by the FDA. OKT3 is reported to be a potent T
cell mitogen (Van Wauve, 1980; U.S. Pat. No. 4,361,539) and a
potent T cell killer (Wong, 1990). Other antibodies specific for
the CD3 antigen have also been reported (see PCT International
Patent Application Publication No. WO 2004/106380; U.S. Patent
Application Publication No. 2004/0202657; U.S. Pat. Nos. 6,750,325;
6,706,265; United Kingdom Patent GB 2249310A; Clark et al., 1989;
U.S. Pat. No. 5,968,509; and U.S. Patent Application Publication
No. 2009/0117102). Immune mobilizing mTCR Against Cancer (ImmTAC;
Immunocore Limited, Milton Park, Abington, Oxon, United Kingdom)
are bifunctional proteins that combine high-affinity monoclonal T
cell receptor (mTCR) targeting with a therapeutic mechanism of
action (i.e., an anti-CD3 scFv).
[0213] Native antibodies and immunoglobulins are generally
heterotetrameric glycoproteins of about 150,000 daltons (Da)
composed of two identical light (L) chains and two identical heavy
(H) chains. Each light chain is linked to a heavy chain by a
covalent disulfide bond. Disulfide bonds also link the heavy chains
of intact antibodies, although the number of disulfide bonds
between the heavy chains of different immunoglobulin isotypes can
vary. Each heavy and light chain also has regularly spaced
intrachain disulfide bridges. Each heavy chain has at one end a
variable domain (V.sub.H) followed by a number of constant domains.
Each light chain has a variable domain at one end (V.sub.L) and a
constant domain at its other end. The constant domain of the light
chain is aligned with the first constant domain of the heavy chain,
and the light chain variable domain is aligned with the variable
domain of the heavy chain. Particular amino acid residues are
believed to form an interface between the light and heavy chain
variable domains (Clothia et al., 1985; Novotny & Haber,
1985).
[0214] An "isolated" antibody is one which has been identified
and/or separated and/or recovered from a component of the
environment in which it was produced or otherwise present.
Contaminant components of its production environment are materials
that in some embodiments interfere with diagnostic and/or
therapeutic uses for the antibody, and in some embodiments can
include enzymes, hormones, and other proteinaceous or
nonproteinaceous solutes. In some embodiments, an antibody can be
purified as measurable by one or more of the following methods: 1)
to greater than 50%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%
by weight of antibody as determined by the Lowry method; 2) to a
degree sufficient to obtain at least 10 or 15 residues of
N-terminal or internal amino acid sequence by use of a spinning cup
sequenator; or 3) to homogeneity by SDS-PAGE under reducing or
non-reducing conditions using Coomassie blue or, in some
embodiments, silver stain. Isolated antibodies include an antibody
in situ within recombinant cells since at least one component of
the antibody's natural environment will not be present. Ordinarily,
however, isolated antibodies will be prepared by a method that
comprises at least one purification step.
[0215] The terms "antibody mutant" and "antibody variant" refer to
antibodies that relative to a reference antibody comprise one or
more amino acid sequence differences, wherein one or more of the
amino acid residues have been modified such as but not limited to
substitution and/or deletion. Such mutants and/or variants comprise
in some embodiments less than 100%, 99%, 98%, 97%, 96%, 95%, 90%,
85%, 80%, or 75% sequence identity and/or similarity to the amino
acid sequence of either the heavy or light chain variable domain
amino acid sequence of the reference antibody.
[0216] The term "variable" in the context of variable domain of
antibodies, refers to the fact that certain portions of the
variable domains differ extensively in sequence among antibodies
and are used in the binding and specificity of each particular
antibody for its particular antigen. However, sequence variability
is generally not evenly distributed throughout the variable domains
of antibodies. Typically, sequence variability is concentrated in
three segments called complementarity determining regions (CDRs;
also known as hypervariable regions) both in the light chain and
heavy chain variable domains.
[0217] There are at least two techniques for determining CDRs: (1)
an approach based on cross-species sequence variability (i.e.,
Kabat et al., 1991); and (2) an approach based on crystallographic
studies of antigen-antibody complexes (Chothia et al., 1989). The
more highly conserved portions of variable domains are called the
framework (FR). The variable domains of native heavy and light
chains each comprise four FR regions, largely adopting a
.beta.-sheet configuration, connected by three CDRs, which form
loops connecting, and in some cases forming part of, the
.beta.-sheet structure. The CDRs in each chain are held together in
close proximity by the FR regions and, with the CDRs from the other
chain, contribute to the formation of the antigen binding site of
antibodies (see Kabat et al., 1991) The constant domains are
generally not involved directly in binding between antibody and
antigen, but exhibit various effector functions such as but not
limited to participation of the antibody in antibody-dependent
cellular toxicity.
[0218] The term "antibody fragment" refers to a portion of a
full-length antibody, generally the antigen binding or variable
region. Examples of antibody fragments include Fab, Fab',
F(ab').sub.2, and Fv fragments. Papain digestion of antibodies
produces two identical antigen binding fragments, called the Fab
fragment, each with a single antigen binding site, and a residual
"Fc" fragment, so-called for its ability to crystallize readily.
Pepsin treatment yields an F(ab').sub.2 fragment that has two
antigen binding fragments which are capable of cross-linking
antigen, and a residual other fragment (which is termed pFc'). As
used herein, the phrase "functional fragment" with respect to
antibodies refers in some embodiments to a fragment that contains
at least one antigen-binding domain (referred to as a "paratope"),
and thus includes, but is not limited to Fv, F(ab) and F(ab').sub.2
fragments.
[0219] An "Fv" fragment is the minimum antibody fragment which
contains a complete antigen recognition and binding site. This
region consists of a heterodimer of one heavy and one light chain
variable domain in a tight, non-covalent or covalent association
(V.sub.H-V.sub.L dimer). It is in this configuration that the three
CDRs of each variable domain interact to define an antigen binding
site (paratope) on the surface of the V.sub.H-V.sub.L dimer.
Collectively, the six CDRs confer antigen binding specificity to
the antibody. However, in some embodiments even a single variable
domain (or half of an Fv comprising only three CDRs specific for an
antigen) has the ability to recognize and bind antigen, although at
a lower affinity than the entire binding site.
[0220] The Fab or F(ab) fragment also contains the constant domain
of the light chain and the first constant domain (CH1) of the heavy
chain. Fab' fragments differ from Fab fragments by the addition of
a few residues at the carboxyl terminus of the heavy chain CH1
domain including one or more cysteines from the antibody hinge
region. Fab'-SH is the designation herein for Fab' in which the
cysteine residue(s) of the constant domains have a free thiol
group. F(ab') fragments are produced by cleavage of the disulfide
bond at the hinge cysteines of the F(ab').sub.2 pepsin digestion
product. Additional chemical couplings of antibody fragments are
known to those of ordinary skill in the art.
[0221] The light chains of antibodies (immunoglobulin) from any
vertebrate species can be assigned to one of two clearly distinct
types, called kappa (.kappa.) and lambda (.lamda.), based on the
amino sequences of the corresponding constant domain.
[0222] Depending on the amino acid sequences of the constant domain
of their heavy chains, immunoglobulins can be assigned to different
classes. There are at least five (5) major classes of
immunoglobulins: IgA, IgD, IgE, IgG and IgM, and several of these
may be further divided into subclasses or isotypes (e.g.,
IgG.sub.1, IgG.sub.2, IgG.sub.3, IgG.sub.4, IgA.sub.1, IgA.sub.2,
etc.). The heavy chains constant domains that correspond to the
different classes of immunoglobulins are called alpha (.alpha.),
delta (.DELTA.), epsilon (.epsilon.), gamma (.gamma.), and mu
(.mu.), respectively. The subunit structures and three-dimensional
configurations of different classes of immunoglobulins are well
known.
[0223] The term "monoclonal antibody" as used herein refers to an
antibody obtained from a population of substantially homogeneous
antibodies, i.e., the individual antibodies comprising the
population are identical except for possible naturally occurring
mutations that can be present in minor amounts. Monoclonal
antibodies are highly specific, being directed against a single
antigenic site. Furthermore, in contrast to conventional
(polyclonal) antibody preparations, which typically include
different antibodies directed against different determinants
(epitopes), each monoclonal antibody is directed against a single
determinant on the antigen. In additional to their specificity,
monoclonal antibodies can be advantageous in that they are
typically synthesized from hybridomas and thus can be isolated in a
form that is uncontaminated by other immunoglobulins. Methods for
generating hybridomas are known in the art. The modifier
"monoclonal" indicates the character of the antibody as being
obtained from a substantially homogeneous population of antibodies,
and is not to be construed as requiring production of the antibody
by any particular method. By way of example and not limitation,
monoclonal antibodies to be used in accordance with the presently
disclosed subject matter can be made by the hybridoma method first
described by Kohler & Milstein, 1975, or can be made by
recombinant methods (see e.g., U.S. Pat. No. 4,816,567; Harlow
& Lane, 1988). In some embodiments, the monoclonal antibodies
for use with the presently disclosed subject matter can be isolated
from phage antibody libraries using the techniques described in
Clackson et al., 1991 and/or Marks et al., 1991.
[0224] Utilization of the monoclonal antibodies of the presently
disclosed subject matter can in some embodiments comprise
administering one or more monoclonal antibodies to a subject, such
as but not limited to a human subject. However, when the monoclonal
antibodies are produced in a non-human animal, such as a rodent,
administration of such antibodies to a human patient can elicit an
immune response, wherein the immune response is directed towards
the administered antibodies themselves. Such reactions can limit
the duration and effectiveness of such a therapy. In order to
overcome such a problem, the monoclonal antibodies of the presently
disclosed subject matter can in some embodiments be "humanized",
that is, the antibodies are engineered such that antigenic portions
thereof are removed and like portions of a human antibody are
substituted therefor, while the antibodies' affinity for specific
peptide/MHC complexes is retained. This engineering can involve a
few amino acids, or can include the entire framework regions of the
antibody, leaving only the complementarity determining regions of
the parent antibody intact. Several methods of humanizing
antibodies are known in the art and are disclosed in U.S. Pat. Nos.
6,180,370; 6,054,927; 5,869,619; 5,861,155; 5,712,120; and
4,816,567, the entire disclosure of each of which is hereby
expressly incorporated herein by reference in its entirety.
[0225] Humanized forms of antibodies are thus chimeric
immunoglobulins, immunoglobulin chains, or fragments thereof (such
as Fv, Fab, Fab', F(ab').sub.2 or other antigen-binding
subsequences of antibodies) that are principally comprised of the
sequence of a human immunoglobulin, but that contain at least some
subsequences derived from a non-human immunoglobulin. Humanization
can be performed following the method of Winter and co-workers by
substituting rodent CDRs or CDR sequences for the corresponding
sequences of a human antibody (Jones et al., 1986; Riechmann et
al., 1988; Verhoeyen et al., 1988; see also U.S. Pat. No.
5,225,539). In some embodiments, F.sub.v framework residues of a
human immunoglobulin are replaced with corresponding non-human
residues from an antibody of interest. Humanized antibodies can
also comprise residues which are found neither in the recipient
antibody nor in the imported CDR or framework sequences. In
general, the humanized antibody comprises substantially all of at
least one, and typically two, variable domains, in which all or
substantially all of the CDR regions correspond to those of a
non-human immunoglobulin and all or substantially all of the
framework regions are those of a human immunoglobulin consensus
sequence. The humanized antibody optimally can also comprise at
least a portion of an immunoglobulin constant region (Fc),
typically that of a human immunoglobulin (Jones et al., 1986;
Riechmann et al., 1988; and Presta, 1992).
[0226] Exemplary publications relating to the generation and/or use
of humanized antibodies include Sandborn et al., 2001; Mihara et
al., 2001; Yenari et al., 2001; Morales et al., 2000; Richards et
al., 1999; Yenari et al., 1998; and Shinkura et al., 1998; each of
which is expressly incorporated by reference herein in its
entirety. For example, a treatment protocol that can be utilized in
such a method includes a single dose, generally administered
intravenously, of 10-20 mg of humanized mAb per kg (see e.g.,
Sandborn et al., 2001). In some cases, alternative dosing patterns
can be appropriate, such as the use of three infusions,
administered once every two weeks, of 800-1600 mg or even higher
amounts of humanized mAb (see e.g., Richards et al., 1999).
However, it is to be understood that the presently disclosed
subject matter is not limited to the treatment protocols described
herein, and further that other treatment protocols that are known
to one of ordinary skill in the art can be employed in the methods
of the presently disclosed subject matter.
[0227] In some embodiments, the presently disclosed subject matter
further relates to fully human monoclonal antibodies against
specific target peptide/MHC complexes. Fully human antibodies
essentially relate to antibody molecules in which the entire
sequence of both the light chain and the heavy chain, including the
CDRs, arise from human genes. Such antibodies are referred to
herein as "human antibodies" or "fully human antibodies".
[0228] Human monoclonal antibodies can be prepared by the trioma
technique (see U.S. Pat. No. 4,714,681; PCT International Patent
Application Publication No. WO 1999/047929); the human B-cell
hybridoma technique (see Kozbor et al., 1983), and/or the EBV
hybridoma technique (see Cole et al., 1985). In some embodiments,
human monoclonal antibodies can be utilized in the practice of the
presently disclosed subject matter and can be produced by using
human hybridomas (see Cote et al., 1983) or by transforming human
B-cells with Epstein Barr Virus in vitro (see Cole et al., 1985).
In addition, human antibodies can also be produced using additional
techniques, such as but not limited to phage display libraries
(Hoogenboom et al., 1991; Marks et al., 1991). Similarly, human
antibodies can be made by introducing human immunoglobulin loci
into transgenic animals, e.g., mice in which the endogenous
immunoglobulin genes have been partially or completely inactivated.
Upon challenge, human antibody production is observed, which
closely resembles that seen in humans in all respects, including
gene rearrangement, assembly, and antibody repertoire. This
approach is described, for example, in U.S. Pat. Nos. 5,545,807;
5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016, and in Marks
et al., 1992; Lonberg et al., 1994; Fishwild et al., 1996;
Neuberger, 1996; and Lonberg & Huszar, 1995.
[0229] Human antibodies can additionally be produced using
transgenic non-human animals that have been modified to produce
fully human antibodies in addition to or rather than the non-human
animal's endogenous antibodies in response to challenge by an
antigen. See PCT International Patent Application Publication No.
WO 1994/02602. In some embodiments, endogenous genes encoding the
heavy and light immunoglobulin chains present in the non-human
animal have been deleted or otherwise inactivated, and nucleic
acids encoding human heavy and light chain immunoglobulins have
been inserted into the host's genome. The human genes are
incorporated, for example, using yeast artificial chromosomes
containing the requisite human DNA segments. An animal that
provides all the desired modifications is then obtained as progeny
by crossbreeding intermediate transgenic animals containing fewer
than the full complement of the modifications.
[0230] One embodiment of such a non-human animal is a mouse termed
the XENOMOUSE.TM., which is described in PCT International Patent
Application Publication Nos. WO 1996/33735 and WO 1996/34096. The
XENOMOUSE.TM. produces B cells that secrete fully human
immunoglobulins. The antibodies can be obtained directly from the
animal after immunization with an immunogen of interest, as, for
example, a preparation of polyclonal antibodies, or alternatively
from immortalized B cells derived from an immunized animal, such as
hybridomas producing monoclonal antibodies. Additionally, the genes
encoding the immunoglobulins with human variable regions can be
recovered and expressed to obtain the antibodies directly and/or
can be further modified to obtain analogs of antibodies such as,
for example, single chain Fv molecules.
[0231] An example of a method for producing a non-human animal such
as but not limited to a mouse that lacks expression of an
endogenous immunoglobulin heavy chain is disclosed in U.S. Pat. No.
5,939,598, incorporated herein by reference. Such a non-human
animal can be obtained by a method that comprises deleting the J
segment genes from at least one endogenous heavy chain locus in an
embryonic stem cell, thereby preventing rearrangement of the locus
and formation of an RNA encoding a rearranged immunoglobulin heavy
chain locus. In some embodiments, the deletion can be effected by a
targeting vector that contains a selectable marker, Thereafter, a
transgenic animal (e.g., a mouse) having somatic and germ cells
containing the gene encoding the selectable marker can be produced
from the embryonic stem cell. The transgenic animal would be
expected to be unable to rearrange its endogenous immunoglobulin
heavy chain locus, and thus would be expected to be unable to
produce endogenous immunoglobulins.
[0232] A method for producing an antibody of interest, such as a
human antibody, is also disclosed in U.S. Pat. No. 5,916,771,
incorporated herein by reference. It includes introducing a first
expression vector that contains a nucleotide sequence encoding a
heavy chain into one mammalian host cell in culture, introducing a
second expression vector containing a nucleotide sequence encoding
a light chain into another mammalian host cell, and fusing the two
cells to form a hybrid cell. The hybrid cell can express thus an
antibody made up of a heavy chain and a light chain encoded by the
first and second expression vectors.
[0233] Target peptides disclosed herein are in some embodiments
expressed on a variety of cancer cell types. Thus, in some
embodiments antibodies and antibody-like molecules can be used in
treating, diagnosing, vaccinating, preventing, retarding, and
attenuating a cancer such as but not limited to melanoma, ovarian
cancer, breast cancer, colorectal cancer, squamous carcinoma of the
lung, sarcoma, renal cell carcinoma, pancreatic carcinomas,
squamous tumors of the head and neck, leukemia, brain cancer, liver
cancer, prostate cancer, ovarian cancer, and cervical cancer.
[0234] Antibodies generated with specificity for a target peptide
as disclosed herein can be used to detect the corresponding target
peptides in a biological sample. The biological sample is in some
embodiments isolated from an individual who is suspected of having
cancer, and thus detection could serve to diagnose the cancer.
Alternatively, the biological sample could be isolated from an
individual known to have cancer, and detection of a target peptide
therein can serve as an indicator of disease prognosis, cancer
characterization, treatment efficacy, disease progression, or any
combination thereof. Immunoassays that can be employed for these
purposes are known in the art and include, but are not limited to,
immunohistochemistry, flow cytometry, radioimmunoassay, western
blotting, and ELISA. Biological samples suitable for such testing
include, but are not limited to, cells, tissue biopsy specimens,
whole blood, plasma, serum, sputum, cerebrospinal fluid, pleural
fluid, and urine.
[0235] Antigens recognized by T cells, whether helper T lymphocytes
or CTL, are not recognized as intact proteins, but rather as small
peptides that associate with class I or class II MHC proteins on
the surface of cells. During the course of a naturally occurring
immune response, antigens that are recognized in association with
class II MHC molecules on antigen presenting cells (APCs) are
acquired from outside the cell, internalized, and processed into
small peptides that associate with the class II MHC molecules.
[0236] Antigens that give rise to proteins that are recognized in
association with class I MHC molecules are generally proteins that
are produced within the cells, and these antigens are processed and
associate with class I MHC molecules. It is now understood that the
peptides that associate with given class I or class II MHC
molecules are characterized as having a common binding motif, and
the binding motifs for a large number of different class I and II
MHC molecules have been determined. Synthetic peptides can also be
synthesized that correspond to the amino acid sequence of a given
antigen and that contain a binding motif for a given class I or II
MHC molecule. These peptides can then be added to appropriate APCs,
and the APCs can be used to stimulate a T helper cell or CTL
response either in vitro or in vivo. The binding motifs, methods
for synthesizing the peptides, and methods for stimulating a T
helper cell or CTL response are all known and readily available to
one of ordinary skill in the art.
[0237] Kits can be prepared to assist in diagnosis, monitoring,
and/or prognosis of diseases. In some embodiments, the kits
facilitate the detection and/or measurement of cancer-specific
phosphopeptides and/or phosphoproteins. Such kits can contain, in a
single or divided container, a molecule comprising an
antigen-binding region. In some embodiments, such molecules are
antibodies or antibody-like molecules. Additional components that
can be included in the kit include one or more of solid supports,
detection reagents, secondary antibodies, instructions for use,
vessels for running assays, gels, control samples, and the like. In
some embodiments, an antibody or antibody-like molecules can
optionally be directly or indirectly labeled.
[0238] Alternatively, the antibody or antibody-like molecules
specific for phosphopeptides and/or phosphopeptide/MHC complexes
can be conjugated to therapeutic agents. Exemplary therapeutic
agents include, but are not limited to the following:
[0239] Alkylating Agents. Alkylating agents are drugs that directly
interact with genomic DNA to prevent cells from proliferating. This
category of chemotherapeutic drugs represents agents that affect
all phases of the cell cycle (i.e., they are not cell cycle
phase-specific). Alkylating agents include, but are not limited to
nitrogen mustards, ethylenimenes, methylmelamines, alkyl
sulfonates, nitrosoureas, and triazines. Particularly exemplary
alkylating agents include but are not limited to busulfan,
chlorambucil, cisplatin, cyclophosphamide (cytoxan), dacarbazine,
ifosfamide, mechlorethamine (mustargen), and melphalan.
[0240] Antimetabolites. Antimetabolites disrupt DNA and RNA
synthesis. Unlike alkylating agents, they specifically influence
the cell cycle during S phase. Antimetabolites can be
differentiated into various categories, such as folic acid analogs,
pyrimidine analogs, purine analogs, and related inhibitory
compounds. Antimetabolites include but are not limited to
5-fluorouracil (5-FU), cytarabine (Ara-C), fludarabine,
gemcitabine, and methotrexate.
[0241] Natural Products. Natural products generally refer to
compounds originally isolated from a natural source and identified
as having a desirable pharmacological activity. Such compounds,
including analogs and derivatives thereof, can be isolated from a
natural source, chemically synthesized, and/or recombinantly
produced by any technique known to those of skill in the art.
Natural products include such categories as mitotic inhibitors,
antitumor antibiotics, enzymes, and biological response
modifiers.
[0242] Mitotic inhibitors include plant alkaloids and other natural
agents that can in some embodiments inhibit protein synthesis
required for cell division and in some embodiments inhibit mitosis.
They typically operate during a specific phase of the cell cycle.
Mitotic inhibitors include, for example, docetaxel, etoposide
(VP16), teniposide, paclitaxel, taxol, vinblastine, vincristine,
and vinorelbine, among others.
[0243] Taxoids are a class of related compounds isolated from the
bark of the ash tree, Taxus brevifolia. Taxoids include but are not
limited to compounds such as docetaxel and paclitaxel. Paclitaxel
binds to tubulin (at a site distinct from that used by the vinca
alkaloids) and promotes the assembly of microtubules.
[0244] Vinca alkaloids are a type of plant alkaloid identified to
have pharmaceutical activity. Exemplary vinca alkaloids include
vinblastine (VLB) and vincristine.
[0245] Antibiotics. Certain antibiotics have both antimicrobial
and/or cytotoxic activity. These drugs also interfere with DNA by
chemically inhibiting enzymes and mitosis or altering cellular
membranes. These agents are typically not cell cycle
phase-specific. Examples of cytotoxic antibiotics include but are
not limited to bleomycin, dactinomycin, daunorubicin, doxorubicin
(Adriamycin), plicamycin (mithramycin), and idarubicin.
[0246] Miscellaneous Agents. Miscellaneous cytotoxic agents that do
not fall into the previous categories include but are not limited
to platinum coordination complexes, anthracenediones, substituted
ureas, methyl hydrazine derivatives, amsacrine, L-asparaginase, and
tretinoin. Platinum coordination complexes include such compounds
as carboplatin and cisplatin (cis-DDP). An exemplary
anthracenedione is mitoxantrone. An exemplary substituted urea is
hydroxyurea. An exemplary methyl hydrazine derivative is
procarbazine (N-methylhydrazine, MIH). These examples are
non-limiting and it is contemplated that any known cytotoxic,
cytostatic, and/or cytocidal agent can be attached to a targeting
peptide of the presently disclosed subject matter and administered
to a targeted organ, tissue, and/or cell type.
[0247] Chemotherapeutic (cytotoxic) agents including, but are not
limited to, 5-fluorouracil, bleomycin, busulfan, camptothecin,
carboplatin, chlorambucil, cisplatin (CDDP), cyclophosphamide,
dactinomycin, daunorubicin, doxorubicin, estrogen receptor binding
agents, etoposide (VP16), farnesyl-protein transferase inhibitors,
gemcitabine, ifosfamide, mechlorethamine, melphalan, mitomycin,
navelbine, nitrosurea, plicomycin, procarbazine, raioxifene,
tamoxifen, taxol, temazolomide (an aqueous form of DTIC),
transplatinum, vinblastine, methotrexate, vincristine, and any
analogs and/or derivatives or variants of the foregoing. Most
chemotherapeutic agents fall into the categories of alkylating
agents, antimetabolites, antitumor antibiotics, corticosteroid
hormones, mitotic inhibitors, and nitrosoureas, hormone agents,
miscellaneous agents, and any analog, derivative, or variant
thereof.
[0248] The peptides identified and tested thus far in peptide-based
vaccine approaches have generally fallen into one of three
categories: 1) mutated on individual tumors, and thus not displayed
on a broad cross-section of tumors from different patients; 2)
derived from unmutated tissue-specific proteins, and thus
compromised by mechanisms of self-tolerance; and 3) expressed in
subsets of cancer cells and normal testes.
[0249] Antigens linked to transformation or oncogenic processes are
of primary interest for immunotherapeutic development based on the
hypothesis that tumor escape through mutation of these proteins
could be more difficult without compromising tumor growth or
metastatic potential
[0250] The target peptides of the presently disclosed subject
matter are in some embodiments unique in that the identified target
peptides are modified by intracellular modification. This
modification is of particular relevance because it is associated
with a variety of cellular control processes, some of which are
dysregulated in cancer cells. For example, the source proteins for
class I MHC-associated phosphopeptides are often known
phosphoproteins, supporting the idea that the phosphopeptides are
processed from folded proteins participating in signaling
pathways.
[0251] Although not wishing to be bound by any particular theory,
it is envisioned that in some embodiments the target peptides of
the presently disclosed subject matter are unexpectedly superior
than known tumor-associated antigen-derived peptides for use in
immunotherapy because: 1) they only displayed on the surface of
cells in which intracellular phosphorylation is dysregulated (i.e.,
cancer cells) and not normal thymus cells, and thus they are not
compromised by self-tolerance (as opposed to TAAs generally, which
are associated with overexpression or otherwise expressed on
non-mutated cells); and/or 2) they identify a cell displaying them
on their surface as having dysregulated phosphorylation. Thus,
post-translationally modified phosphopeptides that are
differentially displayed on cancer cells and derived from source
proteins objectively linked to cellular transformation and
metastasis allow for more extensive anti-tumor responses to be
elicited following vaccination. Target peptides are, therefore,
better immunogens in peptide-based vaccines, as target peptides are
derived from proteins involved with cellular growth control,
survival, and/or metastasis, and alterations in these proteins as a
mechanism of immune escape might interfere with the malignant
phenotype of tumors.
[0252] As such, the presently disclosed subject matter also
includes in some embodiments methods of identifying target peptides
for use in immunotherapy which are displayed on transformed cells
but are not substantially expressed on normal tissue in general or
in the thymus in particular. In some embodiments, such target
peptides bind the MHC class I molecule more tightly than their
non-phosphorylated native counterparts. Moreover, such target
peptides might have additional binding strength by having amino
acid substitutions at certain anchor positions. In some
embodiments, such modified target peptides will remain
cross-reactive with TCRs specific for native target peptide MHC
complexes.
[0253] Additionally, it is envisioned that the target peptides
associated with proteins involved in intracellular signaling
cascades or cycle regulation are of particular interest for use in
immunotherapy. In some cases, the TCR might specifically react with
the phosphate groups on the target peptide being displayed on an
MHC class I molecule.
[0254] In some embodiments, a method for screening target peptides
for use in immunotherapy (e.g., in adaptive cell therapy or in a
vaccine) involves determining whether the candidate target peptides
are capable of inducing a memory T cell response. The contemplated
screening methods can include providing target peptides (including
but not limited to those disclosed herein or those to be identified
in the future) to a healthy volunteer and determining the extent to
which a target peptide-specific T cell response is observed. In
some embodiments, the extent to which the T cell response is a
memory T cell response is also determined. In some embodiments, the
extent to which a T.sub.CM response is elicited, such as but not
limited to the extent to which a T.sub.CM response is elicited
relative to other T cell types, is determined. In some embodiments,
those target peptides that are capable of inducing a memory T cell
response in healthy and/or diseased patients are selected for
inclusion in the therapeutic compositions of the presently
disclosed subject matter.
[0255] In some embodiments, the presently disclosed subject matter
also provides methods for inducing a target peptide-specific memory
T cell (e.g., T.sub.CM) response in a patient by providing the
patient with a composition comprising the target peptides disclosed
herein. In some embodiments, the compositions are provided in a
dosing regimen as disclosed herein.
[0256] In some embodiments, the presently disclosed subject matter
also relates to methods for determining a cancer disease prognosis.
These methods can involve providing a patient with target peptide
compositions and determining the extent to which the patient is
able to mount a target peptide-specific T cell response. In some
embodiments, the target peptide composition comprises target
peptides selected in substantially the same manner that one would
select target peptides for inclusion in a therapeutic composition.
If a patient is able to mount a significant target peptide specific
T cell response, then the patient is likely to have a better
prognosis than a patient with the similar disease and therapeutic
regimen who is not able to mount a target peptide specific T cell
response. In some embodiments, the methods involve determining
whether the target peptide specific T cell response is a T.sub.CM
response. In some embodiments, the presence of a target
peptide-specific T cell response as a result of the contemplated
diagnostic method correlates with an at least or about 5, 10, 15,
20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95,
100, 125, 150, 175, 200, 250, 300, 400, 500 or more percent
increase in progression free survival over standard of care.
[0257] The above disclosure generally describes the presently
disclosed subject matter. A more complete understanding can be
obtained by reference to the following specific examples which are
provided herein for purposes of illustration only, and are not
intended to limit the scope of the presently disclosed subject
matter.
EXAMPLES
[0258] The following Examples provide further illustrative
embodiments. In light of the present disclosure and the general
level of skill in the art, those of skill will appreciate that the
following EXAMPLES are intended to be exemplary only and that
numerous changes, modifications, and alterations can be employed
without departing from the scope of the presently disclosed subject
matter.
Example 1
MHC Class-I-Associated Phosphopeptides Associated with CRC
[0259] Disclosed herein are MHC class-I-associated phosphopeptides
associated with colorectal cancer (CRC). CRC tumors and matched
normal tissues were lysed, the MHC class-I complexes
affinity-purified, and bound peptides eluted. Phosphopeptides were
enriched using immobilized metal affinity chromatography and
characterized using mass spectrometry. Phosphopeptides were
considered tumor specific if their levels in tumor were at least
double that of the matched normal tissue.
[0260] 21 tumor-specific CRC-associated MHC class I phosphopeptides
were identified from a liver metastasis. A selection of these
phosphopeptides was also found on primary tumors and CRC cell
lines. These phosphopeptides derive from proteins that contribute
to key CRC-associated oncogenic pathways, including the MAP kinase,
interleukin, and p53 signaling pathways.
[0261] Tumor infiltrating lymphocytes ("TILs") from the same
tumors, were extracted and expanded, and their responses to the
phosphopeptides assessed using multiplexed intracellular cytokine
staining for IL-2, IFN.gamma., and TNF.alpha. as depicted in FIG.
1A. Multifunctional TILs were found that responded to the
phosphopeptides identified producing IL-2, IFN.gamma., and
TNF.alpha. (see FIG. 1B). These responses are summarized in FIG.
1C.
[0262] The TILs from the tumor from which the phosphopeptides were
identified responded to many more of the phosphopeptides than TILs
from other tumors. In particular, there was a significant response
(.about.2% of TILs, equivalent to the EBV peptide response) to the
HLA-B7-associated phosphopeptide from LISCH7, which was also the
most abundant phosphopeptide found on the tumor. There were,
however, TIL responses from other tumors to some of the
tumor-specific phosphopeptides, particularly those MHC
class-I-associated phosphopeptides whose HLA specificity is
unknown. These phosphopeptides have been found on many tumors from
patients of differing HLA-types. Additionally, responses were seen
to the phosphopeptide from RASSF6, a key oncoprotein involved in
MAPK signaling, suggesting that these oncogenic proteins may be
good targets for tumor immunotherapeutics.
Example 2
Healthy Donor PBMC Responses to Exemplary CRC Tumor-Specific
Phosphopeptides Assessed by ELISpot
[0263] Healthy donor PBMC responses to the CRC tumor-specific
phosphopeptides were assessed using a cultured IFN.gamma. ELISpot
on day 7. Heterogeneous responses were seen to many of the
phosphopeptides from different HLA-matched healthy donors (see FIG.
2). This indicates that these phosphopeptides are good vaccine
candidates. In particular, many responses were seen to the RNASE4
phosphopeptide, of unknown HLA-specificity, the HLA-B7
phosphopeptide from ZPF36L2 and strong responses were often seen to
the two IRS2 phosphopeptides.
Example 3
Establishment of Phosphopeptide-Specific T Cell Lines and Assays
for Ability to Kill CRC Cell Line SW620
[0264] T cells lines were established against some of these key
phosphopeptide targets. Both the IRS2 (A2) and ZPF36L2 (B7)
phosphopeptide-specific cell lines were shown to specifically kill
the CRC cell line SW620 (see FIG. 3).
[0265] The phosphopeptides disclosed herein are involved in key CRC
oncogenic pathways. TILs from the same tumor as that which the
phosphopeptides were identified in, respond to a subset of the
phosphopeptides. TILs from other tumors also respond to some of
these phosphopeptides. The phosphopeptides are also immunogenic in
healthy donors, producing heterogeneous responses and are thus good
vaccine candidates. Phosphopeptide-specific T cell lines from
healthy donors can kill a CRC cell line.
Example 4
T Cell Recognition and Memory Response Assays
[0266] Generally, quantification of T cell IFN.gamma. production in
response to peptides was performed by ELISpot as per manufacturer's
instructions. In brief, ELISpotPRO wells, pre-coated with
IFN.gamma. monoclonal antibody mAb 1-D1K (MabTech, product code:
3420-2APW-2), were washed four times with sterile PBS and blocked
for 30 minutes with 200 .mu.l 10% RPMI 1640 after which the
blocking medium was removed.
[0267] For ELISpot analysis, PBMCs and CD8+ T cells were isolated
fresh from healthy donors and patients. 1.times.10.sup.6 PBMCs were
isolated from both disease patients and healthy donors and
re-suspended in AIM-V media (10% human AB serum) in a 96 well
plate. Peptide or phosphopeptides were added individually at 10
.mu.g/ml and placed at 37.degree. C. in CO.sub.2 incubator for 7
days. Cells were then harvested, washed four times, and
re-challenged with either phosphopeptides, peptides, anti CD3
(OKT3, 100 ng/ml, Mabtech) as per manufacturer's instructions.
Individual cytokine-producing cells were identified as dark spots
after a 15 minute reaction with 5-bromo-4-chloro-3-indolyl
phosphate and NBT by means of an alkaline phosphatase conjugate
substrate (Mabtech). Spots were counted using an automated reader,
(AID-Diagnostika), and results displayed as number of spot-forming
cells (SFC) per 10.sup.6 PBMCs (see FIGS. 2 and 4).
[0268] It is envisioned that the T cell activated by the peptides
disclosed herein express increased levels of CD45RA and/or CD27 in
accordance with the target peptides' ability to stimulate central
memory (T.sub.CM) T cells.
Example 5
TIL Responses to Tumor-Specific, MHC Class-I Associated
Phosphopeptide Discovered in Patient Samples
[0269] An exemplary scheme for isolating and characterizing
phosphopeptides from CRC tumor samples is depicted in FIG. 5.
Summarily, tumor and normal tissue were taken from the same patient
at resection. These were each lysed and the MHC Class I complexes
affinity purified using pan Class I antibody, W6/32. The MHC Class
I-associated peptides were eluted in acid and phosphopeptides
enriched using immobilized metal affinity chromatography (IMAC).
These phosphopeptides were characterized using CAD and ETD LC-MS/MS
and the sequences manually assigned. The phosphopeptides were then
synthesized and verified.
[0270] Tumor infiltrating lymphocytes (TILs) were also taken from
the patient tumors at resection and expanded, using high-dose IL-2
(6000 IU/ml). TIL responses to the phosphopeptides were then tested
using ICS. TILs were stimulated with phosphopeptide and cultured
for 7 days before being re-stimulated in an intracellular cytokine
staining assay assessing production of tumor necrosis factor alpha
(TNF.alpha.), interferon gamma (IFN.gamma.) and interleukin-2
(IL-2). The results are depicted in FIG. 6.
REFERENCES
[0271] All references listed in the instant disclosure, including
but not limited to all patents, patent applications and
publications thereof, scientific journal articles, and database
entries (including but not limited to Uniprot and GENBANK.RTM.
database entries and including all annotations available therein)
are incorporated herein by reference in their entireties to the
extent that they supplement, explain, provide a background for,
and/or teach methodology, techniques, and/or compositions employed
herein. The discussion of the references is intended merely to
summarize the assertions made by their authors. No admission is
made that any reference (or a portion of any reference) is relevant
prior art. Applicants reserve the right to challenge the accuracy
and pertinence of any cited reference. [0272] Akamatsu et al.
(1997) Bioorg Aed Chem 5:157-163. [0273] Altman et al. (1996)
Phenotypic analysis of antigen-specific T lymphocytes. Science
274:94-96 [published erratum appears in Science 1998 Jun. 19;
280(5371):1821]. [0274] Altschul et al. (1990) Basic local
alignment search tool. J Mol Biol 215:403-10. [0275] Altschul et
al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein
database search programs. Nucleic Acids Res 25:3389-3402. [0276]
Arentz-Hansen et al. (2000) The intestinal T cell response to
alpha-gliadin in adult celiac disease is focused on a single
deamidated glutamine targeted by tissue transglutaminase. J Exp Med
191:603-612. [0277] Arozarena et al. (2011) In melanoma,
beta-catenin is a suppressor of invasion. Oncogene
30(45):4531-4543. [0278] Bachmann et al. (2005) Importance of
P-cadherin, beta-catenin, and Wnt5a/frizzled for progression of
melanocytic tumors and prognosis in cutaneous melanoma. Clin Cancer
Res 11:8606-8614. [0279] Baron et al. (2005) Graft-versus-tumor
effects after allogeneic hematopoietic cell transplantation with
nonmyeloablative conditioning. J Clin Oncol 23:1993-2003. [0280]
Bertoletti et al. (1994) Natural variants of cytotoxic epitopes are
T cell receptor antagonists for antiviral cytotoxic T cells. Nature
369:407-410. [0281] Berzofsky et al. (1988) Antigen processing for
presentation to T lymphocytes: function, mechanisms, and
implications for the T cell repertoire. Immunol Rev 106:5-31.
[0282] Boon et al. (1994) Anms Rev Immunol 12:337-365. [0283]
Bullock et al. (2000) The density of peptides displayed by
dendritic cells affects immune responses to human tyrosinase and
gp100 in HLA-A2 transgenic mice. J Immunol 164:2354-2361. [0284]
Chenna et al. (2003) Multiple sequence alignment with the Clustal
series of programs. Nucleic Acids Res 31:3497-3500. [0285] Chi
(2011) Cancer research: Promise of protection. Nature 471:537-538.
[0286] Chien et al. (2009) Activated Wnt/beta-catenin signaling in
melanoma is associated with decreased proliferation in patient
tumors and a murine melanoma model. Proc Natl Acad Sci USA
106:1193-1198. [0287] Chothia et al. (1989) Nature 342:877-883.
[0288] Clackson et al. (1991) Nature 352: 624-628. [0289] Clark et
al. (1989) Eur J Immunol 19:381-388. [0290] Clothia et al. (1985) J
Mol Biol 186:651-666. [0291] Cobbold et al. (2005) Adoptive
transfer of cytomegalovirus-specific CTL to stem cell transplant
patients after selection by HLA-peptide tetramers. J Exp Med
202:379-386. [0292] Cole et al. (1985) Proc Natl Acad Sci USA
82:859. [0293] Cote et al. (1983) Proc Natl Acad Sci USA 80:2026.
[0294] Crawford et al. (1999) The metalloproteinase matrilysin is a
target of beta-catenin transactivation in intestinal tumors.
Oncogene 18:2883-2891. [0295] Demotz et al. (1989) Delineation of
several DR-restricted tetanus toxin T cell epitopes. J Immunol
142:394-402. [0296] Demunter et al. (2002) Loss of membranous
expression of beta-catenin is associated with tumor progression in
cutaneous melanoma and rarely caused by exon 3 mutations. Modern
Pathol 15:454-461. [0297] Dephoure et al. (2008) A quantitative
atlas of mitotic phosphorylation. Proc Natl Acad Sci USA
105:10762-10767. [0298] Depontieu et al. (2009) Identification of
tumor-associated, MHC class II-restricted phosphopeptides as
targets for immunotherapy. Proc Natl Acad Sci USA 106:12073-12078.
[0299] Depontieu et al. Supplemental Information, 10.1073 Proc Natl
Acad Sci USA 0903852106. [0300] Dudley et al. (2008) Adoptive cell
therapy for patients with metastatic melanoma: evaluation of
intensive myeloablative chemoradiation preparative regimens. J Clin
Oncol 26:5233-5239. [0301] DuPage et al. (2012) Expression of
tumour-specific antigens underlies cancer immunoediting. Nature
482:405-409. [0302] El Kasmi et al. (2000) Neutralization of
measles virus wild-type isolates after immunization with a
synthetic peptide vaccine which is not recognized by neutralizing
passive antibodies. J Gen Virol 81:729. [0303] Finn (2003)
Premalignant lesions as targets for cancer vaccines. J Exp Med
198:1623-1626. [0304] Fiol et al. (1988) Phosphoserine as a
recognition determinant for glycogen synthase kinase-3:
phosphorylation of a synthetic peptide based on the G-component of
protein phosphatase-1. Arch Biochem Biophys 267:797-802. [0305]
Fiol et al. (1990) Ordered multisite protein phosphorylation.
Analysis of glycogen synthase kinase 3 action using model peptide
substrates. J Biol Chem 265:6061-6065. [0306] Fischbein et al.
(2000) CD40 signaling replaces CD4.sup.+ lymphocytes and its
blocking prevents chronic rejection of heart transplants. J Immunol
165:7316-7322. [0307] Fishwild et al. (1996) Nature Biotechnol
14:845. [0308] Gale et al. (1994) Identical-twin bone marrow
transplants for leukemia. Ann Intern Med 120:646-652. [0309]
Gattinoni et al. (2006) Nat Rev Immunol 6: 383-93. [0310] Gerdes et
al. (1999) Analysis of beta-catenin gene mutations in pancreatic
tumors. Digestion 60:544-548. [0311] Girbal-Neuhauser et al. (1999)
The epitopes targeted by the rheumatoid arthritis-associated
antifilaggrin autoantibodies are posttranslationally generated on
various sites of (pro)filaggrin by deimination of arginine
residues. J Immunol 162:585-594. [0312] Goldman & DeFrancesco
(2009) The cancer vaccine roller coaster, Nat Biotech 27:129-139
(Corrected online: 7 Jun. 2010 doi:10.1038/nbt0209-129). [0313]
Hall et al. (2010) Comprehensive analysis of phosphorylation sites
in TensinI reveals regulation by p38MAPK. Mol Cellul Proteom
9:2853-2863. [0314] Haluska et al. (2006) Genetic alterations in
signaling pathways in melanoma. Clin Cancer Res 12:2301s-2307s.
[0315] Hamann et al. (1997) Phenotypic and functional separation of
memory and effector human CD8+ T cells. J Exp Med 186:1407-1418.
[0316] He et al. (1998) Identification of c-MYC as a target of the
APC pathway. Science 281:1509-1512. [0317] Hirohashi et al. (2009)
The functioning antigens: beyond just as the immunological targets.
Cancer Sci 100:798-806. [0318] Ho et al. (2006) In vitro methods
for generating CD8.sup.+ T cell clones for immunotherapy from the
naive repertoire. J Immunol Meth 310:40-52. [0319] Hoek et al.
(2006) Metastatic potential of melanomas defined by specific gene
expression profiles with no BRAF signature. Pigment Cell Res
19:290-302. [0320] Hogan et al. (1998) The peptide recognized by
HLA-A68.2-restricted, squamous cell carcinoma of the lung-specific
cytotoxic T lymphocytes is derived from a mutated elongation factor
2 gene. Cancer Res 58:5144-5150. [0321] Homfray et al. (1998)
Defects in mismatch repair occur after APC mutations in the
pathogenesis of sporadic colorectal tumours. Human Mutation
11:114-120. [0322] Hoogenboom et al. (1991) Nucleic Acids Res
19:4133. [0323] Horowitz et al. (1990) Graft-versus-leukemia
reactions after bone marrow transplantation. Blood 75:555-562.
[0324] Hulsken et al. (1994) E-cadherin and APC compete for the
interaction with beta-catenin and the cytoskeleton. J Cell Biol
127:2061-2069. [0325] Ilyas et al. (1997) Beta-catenin mutations in
cell lines established from human colorectal cancers. Proc Natl
Acad Sci USA 94:10330-10334. [0326] Isakoff et al. (2005) Breast
cancer-associated PIK3CA mutations are oncogenic in mammary
epithelial cells. Cancer Res 65:10992-11000. [0327] Jacob et al.
(1997) Int J Cancer 71:325-332. [0328] Jimbow et al. (1975) Mitotic
activity in non-neoplastic melanocytes in vivo as determined by
histochemical, autoradiographic, and electron microscope studies. J
Cell Biol 66:663-670. [0329] Jones et al. (1986) Nature
321:522-525. [0330] Jones et al. (2008) Core signaling pathways in
human pancreatic cancers revealed by global genomic analyses.
Science 321:1801-1806. [0331] Kabat et al., (1991) Sequences of
Proteins of Immunological Interest, Fifth Edition, NIH Publication
No. 91-3242, National Institute of Health, Bethesda, Md., United
States of America. [0332] Kageshita et al. (2001) Loss of
beta-catenin expression associated with disease progression in
malignant melanoma. Br J Dermatol 145:210-216. [0333] Kantoff et
al. (2010) Sipuleucel-T immunotherapy for castration-resistant
prostate cancer. N Ergl J Med 363:411-422. [0334] Kielhorn et al.
(2003) Tissue microarray-based analysis shows phospho-beta-catenin
expression in malignant melanoma is associated with poor outcome.
Int J Cancer 103:652-656. [0335] Kim et al. (2000) beta-catenin
expression and mutational analysis in renal cell carcinomas. Pathol
Intl 50:725-730. [0336] Kimelman & Xu (2006) beta-catenin
destruction complex: insights and questions from a structural
perspective. Oncogene 25:7482-7491. [0337] Klenerman et al. (1994)
Cytotoxic T cell activity antagonized by naturally occurring HIV-1
Gag variants. Nature 369:403-407. [0338] Kohler & Milstein
(1975) Nature 256:495. [0339] Kolb (2008) Graft-versus-leukemia
effects of transplantation and donor lymphocytes. Blood
112:4371-4383. [0340] Kolb et al. (1990) Donor leukocyte
transfusions for treatment of recurrent chronic myelogenous
leukemia in marrow transplant patients. Blood 76:2462-2465. [0341]
Kozbor et al. (1983) Hybridoma 2:7. [0342] Krengel et al. (2004)
Cadherin expression pattern in melanocytic tumors more likely
depends on the melanocyte environment than on tumor cell
progression. J Cutaneous Pathol 31:1-7. [0343] Kroger et al. (2005)
Stem cell transplantation from identical twins in patients with
myelodysplastic syndromes. Bone Marrow Transplant 35:37-43. [0344]
Ley et al. (2008) DNA sequencing of a cytogenetically normal acute
myeloid leukaemia genome. Nature 456:66-72. [0345] Liu et al.
(2002) Control of beta-catenin phosphorylation/degradation by a
dual-kinase mechanism. Cell 108:837-847. [0346] Lonberg &
Huszar (1995) Int Rev Immunol 13:65. [0347] Lonberg et al. (1994)
Nature 368:856. [0348] Lucas & Coulie (2008) About human tumor
antigens to be used in immunotherapy. Seminars Immunol 20:301-307.
[0349] Mackensen et al. (2000) Int J Cancer 86, 385-392. [0350]
Maelandsmo et al. (2003) Reduced beta-catenin expression in the
cytoplasm of advanced-stage superficial spreading malignant
melanoma. Clin Cancer Res 9:3383-3388. [0351] Mamula et al. (1999)
Isoaspartyl post-translational modification triggers autoimmune
responses to self-proteins. J Biol Chem 274:22321-22327. [0352]
Marafioti et al. (2004) Leukocyte-specific phosphoprotein-1 and
PU.1: two useful markers for distinguishing T cell-rich B-cell
lymphoma from lymphocyte-predominant Hodgkin's disease.
Haematologica 89:957-964. [0353] Marks et al. (1991) J Mol Biol
222:581-597. [0354] Marks et al. (1992) J Biol Chem 267:16007.
[0355] Matsushita et al. (2012) Cancer exome analysis reveals a T
cell-dependent mechanism of cancer immunoediting. Nature
482:400-404. [0356] Meyer et al. (2009) Identification of natural
MHC class II presented phosphopeptides and tumor-derived MHC class
I phospholigands. J Proteome Res 8:3666-3674. [0357] Mihara et al.
(2001) Clin Immunol 98:319. [0358] Miyake et al. (2001) Absence of
mutations in the beta-catenin and adenomatous polyposis coli genes
in papillary and follicular thyroid carcinomas. Pathol Intl
51:680-685. [0359] Mohammed et al. (2008) Phosphorylation-dependent
interaction between antigenic peptides and MHC class I: a molecular
basis for the presentation of transformed self. Nat Immunol
9:1236-1243. [0360] Molina et al. (2007) Global proteomic profiling
of phosphopeptides using electron transfer dissociation tandem mass
spectrometry. Proc Natl Acad Sci USA 104:2199-2204. [0361] Morales
et al. (2000) Nucl Med Biol 27:199. [0362] Morin et al. (1997)
Activation of beta-catenin-Tcf signaling in colon cancer by
mutations in beta-catenin or APC. Science 275:1787-1790. [0363]
Neuberger (1996) Nat Biotechnol 14:826. [0364] Newberg et al.
(1992) Species specificity in the interaction of CD8 with the
.alpha.3 domain of MHC class I molecules. J Immunol 149:136-142.
[0365] Niedermann et al. (1995) Contribution of proteasome-mediated
proteolysis to the hierarchy of epitopes presented by major
histocompatibility complex class I molecules. Immunity 2:289-299.
[0366] Novotny & Haber (1985) Proc Natl Acad Sci USA
82:4592-4596. [0367] Nunes et al. (2011) A novel tumor antigen
derived from enhanced degradation of bax protein in human cancers.
Cancer Res 71:5435-5444. [0368] Offringa (2009) Antigen choice in
adoptive T cell therapy of cancer. Curr Opin Immunol 21:190-199.
[0369] Ogasawara et al. (2006) Mutations and nuclear accumulation
of beta-catenin correlate with intestinal phenotypic expression in
human gastric cancer. Histopathology 49:612-621. [0370] Ohgaki et
al. (2004) APC mutations are infrequent but present in human lung
cancer. Cancer Lett 207:197-203. [0371] Oliva et al. (2006) High
frequency of beta-catenin mutations in borderline endometrioid
tumours of the ovary. J Pathol 208:708-713. [0372] Olmeda et al.
(2003) Beta-catenin regulation during the cell cycle: implications
in G2/M and apoptosis. Mol Biol Cell 14:2844-2860. [0373] Omholt et
al. (2001) Cytoplasmic and nuclear accumulation of beta-catenin is
rarely caused by CTNNB1 exon 3 mutations in cutaneous malignant
melanoma. Intl J Cancer 92:839-842. [0374] Otaka et al. (1995)
Tetrahedron Lett 36:927-930. [0375] Pardoll (2012) The blockade of
immune checkpoints in cancer immunotherapy. Nature Reviews Cancer
12:252-264. [0376] Parmiani et al. (2002) J Natl Cancer Inst
94:805-818. [0377] Parsons et al. (2011) The Genetic Landscape of
the Childhood Cancer Medulloblastoma. Science 331:435-439. [0378]
Pavletic et al. (2007) Genetically identical twin transplantation
for chronic lymphocytic leukemia. Leukemia 21:2452-2455. [0379] PCT
International Patent Application Publication Nos. WO 1994/02602; WO
1996/033735; WO 1996/034096; WO 2004/106380; WO 2004/106380;
2010/129537; WO 2011/149909. [0380] Pecina-Slaus et al. (2007)
E-cadherin and beta-catenin expression patterns in malignant
melanoma assessed by image analysis. J Cutaneous Pathol 34:239-246.
[0381] Peiper et al. (1997) Eur J Immunol 27:1115-1123. [0382]
Peoples et al. (1993) Surgery 114:227-234. [0383] Petersen et al.
(2009) Phosphorylated self-peptides alter human leukocyte antigen
class I-restricted antigen presentation and generate tumor-specific
epitopes.
Proc Natl Acad Sci USA 106:2776-2781. [0384] Pollock & Hayward
(2002) Mutations in exon 3 of the beta-catenin gene are rare in
melanoma cell lines. Melanoma Res 12:183-186. [0385] Presta (1992)
Proc Natl Acad Sci USA 89:4285-4289. [0386] Preudhomme et al.
(2010) Imatinib plus peginterferon alfa-2a in chronic myeloid
leukemia. N Engl J Med 363:2511-2521 [0387] Rappsilber et al.
(2007) Protocol for micro-purification, enrichment,
pre-fractionation and storage of peptides for proteomics using
StageTips. Nat Protocols 2:1896-1906. [0388] Restifo et al. (1993)
Identification of human cancers deficient in antigen processing. J
Exper Med 177:265-272. [0389] Richards et al. (1999) Cancer Res
59:2096. [0390] Riechmann et al. (1988) Nature 332:323-327. [0391]
Rimm et al. (1999) Frequent nuclear/cytoplasmic localization of
beta-catenin without exon 3 mutations in malignant melanoma. Am J
Pathol 154:325-329. [0392] Robila et al. (2008) MHC class II
presentation of gp100 epitopes in melanoma cells requires the
function of conventional endosomes and is influenced by
melanosomes. J Immunol 181:7843-7852. [0393] Rock & Goldberg
(1999) Annu Rev Immunol 17:739-779. [0394] Rosenberg & Dudley
(2009) Adoptive cell therapy for the treatment of patients with
metastatic melanoma. Curr Opin Immunol 21:233-240. [0395] Rosenberg
et al. (1986) A new approach to the adoptive immunotherapy of
cancer with tumor-infiltrating lymphocytes. Science 233:1318-1321.
[0396] Rosenberg et al. (2004) Cancer immunotherapy: moving beyond
current vaccines. Nat Med 10:909-915. [0397] Ruppert et al. (1993)
Prominent role of secondary anchor residues in peptide binding to
A2.1 molecules. Cell 74:929-937. [0398] Sadot et al. (2002)
Regulation of S33/S37 phosphorylated beta-catenin in normal and
transformed cells. J Cell Sci 115:2771-2780. [0399] Sandborn et al.
(2001) Gastroenterology, 120:1330-1338. [0400] Sanders et al.
(1999) Alterations in cadherin and catenin expression during the
biological progression of melanocytic tumours. Mol Pathol
52:151-157. [0401] Schendel et al. (1993) J Immunol 151:4209-4220.
[0402] Schreiber et al. (2011) Cancer immunoediting: integrating
immunity's roles in cancer suppression and promotion. Science
331:1565-1570. [0403] Seidensticker & Behrens (2000)
Biochemical interactions in the wnt pathway. Biochim Biophys Acta
1495:168-182. [0404] Sette et al. (1994) The relationship between
class I binding affinity and immunogenicity of potential cytotoxic
T cell epitopes. J Immunol 153:5586-5592. [0405] Shinkura et al.
(1998) Anticancer Res 18:1217. [0406] Slawson et al. (2005)
Perturbations in O-linked .beta.-N-acetylglucosamine proteim
modification cause severe defects in mitotic progression and
cytokinesis. J Biol Chem, 280:32944-32956. [0407] Slawson et al.
(2008) A mitotic GlcN Acylation/phosphorylation signaling complex
alters the posttranslational state of the cytoskeletal proteim
vimentin. Mol Biol Cell 19:4130-4140. [0408] Slingluff et al.
(1994) Cancer Res 54:2731-2737. [0409] Slingluff et al. (2000)
Melanomas with concordant loss of multiple melanocytic
differentiation proteins: immune escape that may be overcome by
targeting unique or undefined antigens. Cancer Immunol Immunother
48:661-672. [0410] Slovin et al. (1986) J Immunol 137:3042-3048.
[0411] Smyth et al. (1992) Tetrahedron Lett 33:4137-4140. [0412]
Strickley (2004) Solubilizing excipients in oral and injectable
formulations. Pharm Res 21:201-230. [0413] Sun et al. (2005)
Infrequent mutation of APC, AXIN1, and GSK3B in human pituitary
adenomas with abnormal accumulation of CTNNB1. J Neuro-Oncol
73:131-134. [0414] Takahashi et al. (2002) Identification of
membrane-type matrix metalloproteinase-1 as a target of the
beta-catenin/Tcf4 complex in human colorectal cancers. Oncogene
21:5861-5867. [0415] Takemaru et al. (2008) An oncogenic hub:
.beta.-catenin as a molecular target for cancer therapeutics. Handb
Exp Pharmacol 186:261-284. [0416] Talpaz et al. (1986) Hematologic
remission and cytogenetic improvement induced by recombinant human
interferon alpha A in chronic myelogenous leukemia. N Engl J Med
314:1065-1069. [0417] Tetsu & McCormick (1999) Beta-catenin
regulates expression of cyclin D1 in colon carcinoma cells. Nature
398:422-426. [0418] Townsend & Bodmer (1989) Ann Rev Immunol
7:601-624. [0419] United Kingdom Patent GB 2249310A. [0420] United
States Patent Application Publication Nos. 2002/0119149;
2004/0202657 2005/0277161; 2009/0117102; 2009/0226474. [0421] U.S.
Pat. Nos. 4,361,539; 4,816,567; 5,225,539; 5,545,806; 5,545,807;
5,569,825; 5,625,126; 5,633,425; 5,661,016; 5,712,120; 5,861,155;
5,869,619; 5,916,771; 5,939,598; 5,968,509; 6,054,927; 6,180,370;
6,706,265; 6,750,325. [0422] U.S, Provisional Patent Application
Ser. Nos. 61/695,776. [0423] Utz et al. (1997) Proteins
phosphorylated during stress-induced apoptosis are common targets
for autoantibody production in patients with systemic lupus
erythematosus. J Exp Aed 185:843-854. [0424] van Doom et al. (2005)
Epigenetic profiling of cutaneous T cell lymphoma: promoter
hypermethylation of multiple tumor suppressor genes including
BCL7a, PTPRG, and p73. J Clin Oncol 23:3886-3896. [0425] van Wauve
(1980) J Immunol 124:2708-18. [0426] Verhoeyen et al. (1988)
Science 239:1534-1536. [0427] Wang et al. (2007) Dynamic interplay
between O-linked N-acetylglucosaminylation and glyocen synthase
kinase-3-dependent phosphorylation. Mol Cell Proteomics
6:1365-1379. [0428] Wang et al. (2010) Extensive Crosstalk Between
O-GlcNAcylation and Phosphorylation Regulates Cytokinesis, Sci
Signal 3(104):ra2, including Supplemental Materials. [0429] Watts
(1997) Am Rev Immunol 15:821-850. [0430] Waun Ki Hong et al.
Holland-Frei Cancer Medicine 10 A. D. McGraw-Hill Medical. Ref
Type: Edited Book [0431] Weber (2002) Cancer Invest 20:208-221.
[0432] Wong (1990) Transplantation 50:683-689. [0433] Worm et al.
(2004) Genetic and epigenetic alterations of the APC gene in
malignant melanoma. Oncogene 23:5215-5226. [0434] Wuttge et al.
(1999) T cell recognition of lipid peroxidation products breaks
tolerance to self proteins. Immunol 98:273-279. [0435] Yasumura et
al. (1993) Cancer Res 53:1461-1468. [0436] Yee et al. (2002) Proc
Natl Acad Sci USA 99:16168-16173. [0437] Yenari et al. (1998) Exp
Neurol 153:223. [0438] Yenari et al. (2001) Neurol Res 23:72.
[0439] Yewdell (2002) To DRiP or not to DRiP: generating peptide
ligands for MHC class I molecules from biosynthesized proteins. Mol
Immunol 39:139-146. [0440] Yoshino et al. (1994) Cancer Res
54:3387-3390. [0441] Yost et al. (1996) The axis-inducing activity,
stability, and subcellular distribution of beta-catenin is
regulated in Xenopus embryos by glycogen synthase kinase 3. Genes
Dev 10:1443-1454. [0442] Zarling et al. (2000) Phosphorylated
peptides are naturally processed and presented by MHC class I
molecules in vivo. J Exp Med 192:1755-1762. [0443] Zarling et al.
(2006) Identification of class I MHC associated phosphopeptides as
targets for cancer immunotherapy. Proc Natl Acad Sci USA
103:14889-14894.
[0444] It will be understood that various details of the presently
disclosed subject matter may be changed without departing from the
scope of the presently disclosed subject matter. Furthermore, the
foregoing description is for the purpose of illustration only, and
not for the purpose of limitation.
TABLE-US-00003 TABLE 3 Annotation for Protein Sources of Class I
MHC Phosphopeptides Presented on Colorectal Cancer Expression
Levels Source Predicted Liver Cell Protein HLA Type Metastasis
Primary Line CRC Pathway RASSF6 A2 + MPAK signaling DENND4C B7 ++
IRS2 A2 Insulin signaling LSP1 A2 BARD1 A3 ++ DNA damage signaling
PDCL A3 + Rab11FIP1 B7 ++ IRS2 A2 +++ Insulin signaling PALLD B7 ++
MUC12 B7 +++ TGF.beta. signaling AHCYL2 B7 ++ Methionine metabolism
TPX2 B7 ++ p53 signaling PDLIM2 B7 ++ IL-12 signaling NUMBL B7 +++
++ Notch signaling Unidentified B7 ++ ZFP36L2 B7 ++ ++ LISCH7 B7
++++ YT521 Unknown ++ RNASE4 Unknown +++ ++ FILIP1L Unknown +++ ++
SELH Unknown +++ ++
TABLE-US-00004 TABLE 4 Exemplary MHC Class Cancer I Phosphopeptides
Associated with Colorectal Cancer MHC SEQ Source Class I Peptide ID
Protein Subtype Sequence NO. RASSF6 A*0301 RTMsEAALVRK 40 DENND4C
B*0702 RPFHGISTVsL 69 IRS2 A*0201 RVAsPTSGV 23 LSP1 A*0201
RQAsIELPSMAV 18 BARD1 A*0301 RLSsPISKR 39 PDCL A*0301 SVRRsVLMK 45
Rab11-FIP1 B*0702 KPEsRRSSLL 54 IRS2 A*0201 AVRPTRLsL 93 PALLD
B*0702 RPDsAHKML 67 MUC12 B*0702 SPRsPDRTL 87 AHCYL2 B*0702
RPTKIGRRsL 81 TPX2 B*0702 QPQRRsLRL 63 PDZ-LIM2 B*0702 RPGsRQAGL 71
NUMB B*0702 SPFKRQLsL 84 ZFP36L2 B*0702 LPIFSRLsI 60 LISCH7 B*0702
RPRARsVDAL 75 TTC22 B*0702 APRDRRAVsF 50 SELH B*2705 RRGsFEVTL 132
RNASE4 unknown RTHsLLLLL 176 FILIP1L B*2705 RRIsDPQVF 135 YT521
unknown RARGIsPIVF 64
TABLE-US-00005 TABLE 5 Exemplary Phosphopeptides Associated with
Colorectal Cancer (CRC) SEQ ID Amino NO Sequence Accession.sup.a
Acids.sup.b Source Protein 1 ISSsMHSLY P50616 222-230 Protein Tob1
2 ITQGtPLKY Q9Y618 1459-1467 Nuclear receptor corepressor 2 3
LTDPSsP Q8IX90 341-352 Spindle and kinetochore-associated protein 3
TISSY 4 TMAsPGKDNY O60684 3-12 Importin subunit alpha-7 5 AIsDLQQL
O15302 152-159 CaM kinase II isoform 6 DLKRRsMSI Q96N67 175-183
Dedicator of cytokinesis protein 7 7 FLDtPIAKV Q969G9 320-238
Protein naked cuticle homolog 1 8 KAFsPVRSV Q02363 2-10 DNA-binding
protein inhibitor ID-2 9 KLAsPELERL P05412 70-79 Transcription
factor AP-1 10 KLFPDtPLAL Q12906 587-596 Interleukin
enhancer-binding factor 3 11 KLIDRTEsL P33241 197-205
Lymphocyte-specific protein 1 12 KLIDVsSQKV O14757 461-471 Serine;
threonine-protein kinase Chk1 13 KVQsLRRAL Q969G5 185-193 PRKCDBP;
Protein kinase C delta-binding protein 14 LLLsEEVEL Q8IY92 489-497
Structure-specific endonuclease subunit SLX4 15 RLAsYLDRV P05783
90-98 Keratin, type I, cytoskeletal 18 16 RLSsPLHFV Q8NC44 400-408
Protein FAM134A 17 RQAsIELPSM P33241 249-258 Lymphocyte-specific
protein 1 18 RQAsEEL P33241 249-260 Lymphocyte-specific protein 1
PSMAV 19 RQDsTPGKVFL P13056 61-71 Nuclear receptor subfamily 2
group C member 1 20 RQDStPGKVFL P13056 61-71 Nuclear receptor
subfamily 2 group C member 1 21 RQIsQDVKL Q01433 165-173 AMP
deaminase 2 22 RTLsPEIITV Q9H4A3 1802-1812 Serine;
threonine-protein kinase WNK1 23 RVAsPTSGV Q9Y4H2 1097-1105 Insulin
receptor substrate 2; IRS2 24 RVLHsPPAV Q9Y4B5 1510-1518 SOGA2;
coiled-coil domain-containing protein 165 25 SMTRsPPRV Q9BRL6
248-256 Serine; arginine-rich splicing factor 8 26 SVKPRRTsL P15822
766-774 Zinc finger protein 40 27 VMIGsPKKV Q68CZ2 1437-1445
Tensin-3 28 RADsPVHM O95402 444-451 Mediator of RNA polymerase II
transcription subunit 26 29 RAHSsPASL P46937 124-132 Yorkie
homolog; 65 kDa Yes-associated protein; YAP65 30 RIsHELDS P10451
301-308 Osteopontin 31 RSHSsPASL Q9GZV5 86-94 WW domain-containing
transcription regulator protein 1 32 YAVPRRGsL O95425 993-1001
Supervillin 33 GIMsPLAKK Q03989 253-262 AT-rich interactive
domain-containing protein 5A 34 KLPsPAPARK Q8IY33 140-149 MICALL2;
MICAL-Iike protein 2 35 RAKsPISLK Q9BXL7 509-517 Caspase
recruitment domain-containing protein 11; CARD-containing MAGUK
protein 1; CARMA1 36 RILsGVVTK P62280 71-79 40S ribosomal protein
S11 37 RIYQyIQSR Q9Y463 269-277 Dual specificity
tyrosine-phosphorylation- regulated kinase 1B 38 RIYQyIQSRF Q9Y463
269-278 Dual specificity tyrosine-phosphorylation- regulated kinase
1B 39 RLSsPISKR Q99728 327-335 BARD1; BRCA1-associated RING domain
protein 1 40 RTMsEAALVRK Q6ZTQ3 184-194 RASSF6; RASF6; Ras
association domain- containing protein 6 41 RTRsLSSLREK O94915
1975-1985 FRYU; FRYL; Protein furry homolog-like 42 RVAsPTSGVK
Q9Y4H2 1097-1106 Insulin receptor substrate 2; IRS2 43 RVLsPLIIK
Q8NCN4 400-408 E3 Ubiquitin-protein ligase RNF169 44 RVYsPYNHR
Q9NS56 582-590 E3 Ubiquitin-protein ligase Topers 45 SVRRsVLMK
Q9H2J4 223-231 PDCL3; Phosducin-like protein 3 46 KRAsVFVKL P50502
153-161 Hsc70-interacting protein 47 SVKsPVTVK Q9HCS4 329-337
Transcription factor 7-like 1 48 INKERRSsL Q5JTZ5 81-89
Uncharacterized protein C9orf152 49 APDsPRAFL -- -- No data base
hit 50 APRDRRAVsF Q5TAA0 560-569 TTC22; Tetratricopeptide repeat
protein 22 51 APRRYsSSL Q68EM7 697-705 ARHGAP17; RGH17; Rho
GTPase-activating protein 17 52 GPRsPKAPP Q6PJ34 313-321 ARHGAP4
protein 53 KPAsPKFIVTL Q6PJT7 512-522 Zinc finger CCCH
domain-containing protein 14 54 KPEsRRSSLL Q6WKZ4 428-437
RAB11-FIP1; Rab 11 family-interacting protein 1 55 KPRPPPLsP
Q15642; 328-336 Cdc42-interacting protein 4; CIP4 XP_ 005259738 56
KPRsPFSKI Q9BXF6 185-193 RAB11-FIP5; RFIP5; Rab11 family-
interacting protein 5 57 KPRsPPRAL Q86TG8; 249-257
Retrotransposon-derived protein P07288; PEG10 isoform 2 NP_
001035242 58 KPRsPVVEL P25098 667-675 Beta-Adrenergic receptor
kinase 1 59 LPAsPRARL Q3KQU3 443-451 Map 7 domain-containing
protein 1 60 LPIFSRLsI P47974 483-491 ZFP36L2; Zinc finger protein
36, C3H1 type-like 2 61 LPVsPRLQL P40199 185-193 Carcinoembryonic
antigen-related cell adhesion molecule 6 62 MPRQPsATRL Q6P582
134-143 Mitotic-spindle organizing protein 2A 63 QPQRRsLRL Q9ULW0
116-124 TPX2; Targeting protein for Xklp2 64 RARGIsPIVF Q96MU7
303-312 YTHDC1; YTDC1; YTH domain-containing protein 1; YT521 65
RPAsAGAML Q14814 198-206 Monocyte-specific enhancer factor 20 66
RPAsPQRAQL -- -- No data base hit 67 RPDsAHKML B7ZMM5 969-977
PALLD; Palladin protein 68 RPDVAKRLsL O75815 282-291 BCAR3; Breast
cancer anti-estrogen resistance protein 3 69 RPFHGISTVsL Q5VZ89
1417-1427 DENND4C; DENN domain-containing protein 4C 70 RPFsPREAL
Q86V48 742-750 Leucine zipper protein 1 71 RPGsRQAGL Q96JY6 175-183
PDZ-LIM2; PDZ and LIM domain protein 2 72 RPKsPLSKM Q9HCD6
1576-1584 TANC2; Tetratricopeptide repeat 73 RPKsVDFDSL Q9Y5K6
455-464 CD2AP; CD2-associated protein 74 RPQRATsNVF P19105 13-22
Myosin regulatory light chain 12A 75 RPRARsVDAL Q9BT33; 426-435 LSR
Protein; Lipolysis-stimulated Q86X29 lipoprotein receptor; LISCH7
76 RPRGsQSLL P21860 1040-1047 Receptor tyrosine-protein kinase
erbB-3 77 RPRPVsPSSL P57059 430-439 Serine/threonine-protein kinase
SIK1 78 RPRsAVLL Q12802 1873-1880 A-kinase anchor protein 13;
AKAP-13 79 RPRsPNMQDL Q6T310 214-223 RASL-11A; Ras-like protein
family member 11A 80 RPRsPRQNSI Q99700 689-698 Ataxin-2 81
RPTKIGRRsL Q96HN2 135-144 AHCYL2; SAHH3; Putative
adenosylhomocysteinase 3 82 RPTsRLNRL Q15788 860-868 NCoA1; Nuclear
receptor coactivator 1 83 RPVtPVSDL Q13118 63-71 KLF10;
Krueppel-like factor 10 84 SPFKRQLsL P49757 288-296 NUMB; Numb
protein homolog 85 SPRAPVsPLKF Q9UBS0 417-427 RPS6KB2; Ribosomal
protein S6 kinase beta-2 86 SPRRsRSISL Q16629 159-168
Serine/arginine-rich splicing factor 7 87 SPRsPDRTL Q9UKN1 286-294
MUC12; Mucin-12 88 SPRSPsTTYL Q13111 772-781 Chromatin assembly
factor 1 subunit A 89 SPRsPSTTYL Q13111 772-781 Chromatin assembly
factor 1 subunit A 90 TPRsPPLGL Q16584 755-763 Mitogen-activated
protein kinase kinase kinase 11 91 VPRPERRsSL Q6UWJ1 668-677 TMCO3;
Transmembrane and coiled-coil domain- containing protein 3 92
APRKGsFSAL Q13619 5-14 Cullin-4A 93 AVRPTRLsL Q9Y4H2 887-895
Insulin receptor substrate 2; IRS2 94 KPRPLsMDL Q9BY89 279-287
Uncharacterized protein KIAA1671 95 KPRRFsRsL Q7L4I2 209-217
Arginine/serine-rich coiled-coil protein 2 96 LPRtPRPEL Q8N1W2
174-182 Zinc finger protein 710 97 RPAsPAAKL Q9P2N6 512-520
KIAA1310; KAT8 regulatory NSL complex subunit 3 98 RPDsPTRPTL
Q7RTP6 1646-1655 Protein-methionine sulfoxide oxidase MICAL3 99
RPIsPRIGAL Q9Y6I3; 93-102 Epsin-1 NP_ 001123543 100 RPRAAtW P10644
333-340 cAMP-dependent protein kinase type 1- alpha regulatory
subunit 101 RPRAAtWA P10644 333-341 cAMP-dependent protein kinase
type 1- alpha regulatory subunit 102 RPRANsGGVDL Q92766 1162-1172
Ras-responsive element-binding protein 1 103 RPRsAVEQL Q9HAU0
882-890 Pleckstrin homology domain- containing family A member
5
104 RPRsMTVSA O43312 457-465 Metastasis suppressor protein 1 105
RPRsPPGGP Q86UZ6 573-581 Zinc finger and BTB domain-containing
protein 46 106 RPRsPT Q9HAU0 882-890 Pleckstrin homology domain-
GPSNSF containing family A member 5 107 SPKsPGLKA B7ZKW8; 75-83
CapZ-interacting protein isoform XI XP_ 005245662 108 YPGGRRsSL
P22897 1037-1045 Macrophage mannose receptor 1 109 KYIsGPHEL P49454
1270-1279 Centromere protein F 110 RYQtQPVTL O95425 849-857
Supervillin 111 FRRsPTKSSL Q96PK6 624-633 RNA-binding protein 14
112 FRRsPTK Q96PK6 624-635 RNA-binding protein 14 SSLDY 113
GRKsPPPSF B4DLE8; 713-721 Beta/gamma crystallin domain-containing
NP_705833 protein 3 114 GRLsPAYSL Q86UU1 536-544 Pleckstrin
homology-like domain family B member 1 115 GRLsPVPVPR Q9UKM9
132-141 RNA-binding protein Raly 116 HRLsPVKGEF Q9Y2L9 367-376
Leucine-rich repeat and calponin homology domain-containing protein
1 117 HRNsMKVFL Q9NPR2 735-743 Semaphorin-4B 118 KRFsFKKSF P29966
156-164 Myristoylated alanine-rich C-kinase substrate 119 KRFsFKKsF
P29966 156-164 Myristoylated alanine-rich C-kinase substrate 120
KRFsGTVRL P62906 47-55 RPL10N 60S ribosomal protein L10a; NEDD-6
121 KRLsPAPQL Q9UH99 51-59 SUN domain-containing protein 2 122
KRLsVERIY P11388 26-34 DNA Topoisomerase 2-alpha; TOP2A 123
KRMsPKPEL P41208 17-25 Centrin-2 124 KRYsGNMEY O95835 275-283
Serine/threonine-protein kinase LATS1 125 RRAsLSEIGF Q00537 177-186
Cyclin-dependent kinase 17 126 RRAsQEANL Q6PJG2 458-466
Uncharacterized protein C14orf43; LM2 and SANT domain-containing
protein 1 127 RRDsIVAEL O14579 96-104 Coatomer subunit epsilon 128
RRDsLQKPGL Q9NRM7 376-386 Serine/threonine-protein kinase LATS2 129
RRFsGTAVY Q6AHZ1 652-660 ZNF518N Zinc linger protein 518A 130
RRFsPPRRM Q15287 248-256 RNA-binding protein with serine-rich
domain 1 131 RRFsRLENRY O43293 411-420 Death-associated protein
kinase 3 132 RRGsFEVTL Q8IZQ5; 75-83 Protein C11orf31;
selenoprotein H; SELH NP_734467 133 RRIDlsPSTF Q9Y2W1 677-686
Thyroid hormone receptor-associated protein 3 134 RMDIsPSTLR Q9NYF8
653-663 Bcl-2-associated transcription factor 1 135 RRIsDPQVF
Q4L180 788-796 FILIP1L; Filamin A-interacting protein 1-like 136
RRIsGVDRY O15239 52-60 NADH dehydrogenase [ubiquinone] 1 alpha
subcomplex subunit 1 137 RRIsGVDRYY O15239 52-61 NADH dehydrogenase
[ubiquinone)1 alpha subcomplex subunit 1 138 RRKsQVAEL Q9BYG3
244-252 MKI67 FHA domain-interacting nucleolar phosphoprotein 139
RRLsADIRL O60307 744-752 Microtubule-associated
serine/threonine-protein kinase 3 140 RRLsDSPW P47974 435-443 Zinc
finger protein 36, C3H1 type-like 2 141 RJlLsESSAL Q96S55 72-80
ATPase WRNIP1 142 RRLsGPLHTL Q86Y91 610-619 Kinesin-like protein
KIF18B 143 RRLsLFLNV Q99836 31-39 Myeloid differentiation primary
response protein My088 144 RRMsFQKP Q8N573 88-95 Oxidation
resistance protein 1 145 RRMsLLSVV Q9ULI2 314-322
Beta-citryl-glutamate synthase B 146 RRNsAPVSV Q2M1Z3 1175-1183 Rho
GTPase-activating protein 31 147 RRNsINRNF O00160 731-739
Unconventional myosin-1f 148 RRPsLLSEF O75376 67-75 Nuclear
receptor corepressor 1 149 RRQsKVEAL Q03169 120-128 TNFAIP2; tumor
necrosis factor alpha-induced protein 2 150 RRLsELLRY P08238
449-457 Heat shock Protein HSP 90-beta 151 RRLsFLVSY P47897 67-75
Giutamine-tRNA ligase 152 RRSsFLQVF Q15436 585-593 Protein
transport protein Sec23A 153 RRSsIQSTF Q92542 232-240 Nicastrin 154
RRsSIQSTF Q92542 232-240 Nicastrin 155 RRSsSVAQV O15205 107-115
Ubiquitin D 156 RRYsPPIQ AAP97290; 592-599 Ser/Arg repetitive
nuclear matrix protein 1 AF419855 157 VRAsKDLAQ 60563 164-172
CCNT1; Cyclin-T1 158 KRLEKsPSF Q92625 656-664 Ankyrin repeat and
SAM domain-containing protein 1A 159 KRLEKSPsF Q92625 656-664
Ankyrin repeat and SAM domain-containing protein 1A 160 KRWQsPVTK
XP_ 518-526 Serine/arginine repetitive matrix protein 1 isoform X6
005245779 161 RRFsIATLR Q16696 128-136 Cytochrome P450 2A13 162
RRFsLTTLR P10632 124-132 Cytochrome P450 2C8 163 RRFsRsPIR P18583
2026-2034 Protein SON isoform B 164 RRFsVSTLR P10635 132-140
Cytochrome P450 2D6 165 RRFsVTTMR P20813 125-133 Cytochrome P450
2B6 166 RRVVQRSsL Q04637 1098-1105 Eukaryotic translation
initiation factor 4 gamma 1 isoform 2 167 RRYsPPIER Q8IYB3 594-602
Serine/arginine repetitive matrix protein 1 168 RRYsPPIQR Q8IYB3
594-602 Serine/arginine repetitive matrix protein 1 169 AENsPTRQQF
Q86XP3 93-102 ATP-dependent RNA helicase DDX42 170 EELsPTKAF Q99612
117-125 Krueppel-like factor 6 171 KEMsPTRQL Q4G0N7 36-44 UPF0731
protein C6orf225; protein FAM229B 172 RFKtQPVTF Q7Z7L8 365-373
Uncharacterized protein C11orf96 173 EERRsPPAP P15408 196-204
Fos-related antigen 2 174 FEDDDsNEKL O43719 697-706 HIV
Tat-specific factor 1 175 KsLVRLLLL P07998 5-13 Ribonuclease
pancreatic 176 RTHsLLLLL P34096 5-13 RNASE4; Ribonuclease 4 177
RTSSFtFQN P27540 440-448 Aryl hydrocarbon receptor nuclear
translocator; ARNT .sup.aRefers to the Uniprot and/or GENBANK.RTM.
biosequence database accession number(s). .sup.bRefers to the amino
acid positions for the peptide in the corresponding Uniprot and/or
GENBANK.COPYRGT. biosequence database accession(s).
TABLE-US-00006 TABLE 6 Characteristics of HLA-DR-associated
Phosphopeptides Selectively Expressed by Melanoma Cells SEQ ID
Source Protein Phosphopeptide NO 1363-mel and
.sub.100APPAYEKLsAEQ.sub.111 218 2048-mel
.sub.100APPAYEKLsAEQSPP.sub.114 219 Melanoma
.sub.100APPAYEKLsAEQSPPP.sub.115 220 antigen
.sub.100APPAYEKLsAEQSPPPY.sub.116 226 recognized by T cells-
1/MART-1 Tensin-3 .sub.1434VSKVMIGsPKKV.sub.1445 227
.sub.1437VMIGsPKKV.sub.1445 228 1363-mel alone
.sub.142KYsPGKLRGN.sub.151 229 Matrix- remodeling- Associated
Protein 7 2048-mel .sub.176SKEDKNGHDGDTHQ 230 alone Amino-
EDDGEKsD.sub.197 terminal enhancer of split Ankyrin
.sub.43GSALGGGGAGLSGRASGG 231 repeat AQsPLRYLHV.sub.71 domain-
.sub.46LGGGGAGLSGRASGG 232 containing AQsPLRYLHV.sub.71 protein-54
.sub.58SGGAQsPLRYLHVL.sub.72 233 Anoctamin-8
.sub.638EEGsPTMVEKGLEPGVFTL.sub.656 234
.sub.639EGsPTMVEKGLEPGVFEU.sub.656 235
.sub.640GsPTMVEKGLEPGVFTL.sub.656 236 AP-3 complex
.sub.779EEMPENALPsDEDD 237 subunit-.DELTA.-1 KDPNDPYRAL.sub.802
Casein .sub.202QAASNFKsPVKTIR.sub.215 238 kinase II
.sub.203AASNFKsPVKTIR.sub.215 239 subunit-.beta.
.sub.205SNFKsPVKTIR.sub.215 240 .sub.206NFKsPVKTK.sub.215 241
.sub.207FKsPVKTIR.sub.215 242 Claudin-11
.sub.191YYTAGSSsPTHAKSAHV.sub.207 243 .sub.196SSsPTHAKSAHV.sub.207
244 Emerin .sub.117VRQsVTSFPDADAFHHQ.sub.133 245 FLJ20689
.sub.471FKMPQEKsPGYS.sub.482 246 Insulin
.sub.1097RVAsPTSGVKR.sub.1107 247 receptor Substrate 2 Interleukin
1 .sub.543QVAMPVKKSPRRSSS 248 receptor DEQGLSYSSLKNV.sub.570
accessory .sub.544VAMPVKKSPRRSSSDE 249 protein QGLSYSSLKNV.sub.570
LUC7-like .sub.353SSNGKMASRRsEEKEAG.sub.369 250 isoform b
.sub.353SSNGKMASRRSEEKEAGEI.sub.371 251 Membrane-
.sub.172KEGEEPTVYsDEE 252 associated EPKDESARKND.sub.195
progesterone .sub.173EGEEPTVYsDEEE 253 receptor PKDESARKND.sub.195
component 1 NF-.kappa.B inhibitor- .sub.165ASKMTQPQSKSAFPLS 254
Interacting RKNKGsGsLDG.sub.191 Ras-like protein 2 Probable
.sub.348APPPLVPAPRPSsPP 255 fibrosin-1 RGPGPARADR.sub.372 long
transcript protein isoform 2 Small acidic
.sub.2SAARESHPHGVKRSAsPDDDLG.sub.23 256 protein
.sub.2(AcS)AARESHPHGVKRS 257 AsPDDDLG.sub.23 Synaptojanin-170
.sub.1561ASKAsPTLDFTER.sub.1573 258 Tetraspanin-10
.sub.4GERsPLLSQETAGQKP.sub.19 259 .sub.4GERsPLLSQETAGQKPL.sub.20
260 .sub.5ERsPLLSQETAGQKP.sub.19 261 .sub.5ERsPLLSQETAGQKPL.sub.20
262 Transmembrane .sub.424TIGEKKEPsDKSVDS.sub.438 263 protein
184
TABLE-US-00007 TABLE 7 Characteristics of HLA-DR-associated
Phosphopeptides Selectively Expressed by EBV-transformed B Cells
SEQ ID Source Protein Phosphopeptide NO. B lymphocyte
.sub.25SGPKPLFRRMsSLVGPTQ.sub.42 264 antigen CD20
.sub.26GPKPLFRRMsS.sub.36 265 .sub.26GPKPLFRRMsSL.sub.37 266
.sub.26GPKPLFRRMsSLV.sub.38 267 .sub.26GPKPLFRRMsSLVG.sub.39 268
.sub.26GPKPLFRRMsSLVGP.sub.40 269 .sub.26GPKPLFRRMsSLVGPT.sub.41
270 .sub.26GPKPLFRRMsSLVGPTQ.sub.42 271
.sub.26GPKPLFRRMsSLVGPTQS.sub.43 272 Lymphoid-restricted
.sub.130AsPTIEAQGTSPAHDN.sub.145 273 membrane protein
.sub.130AsPTIEAQGTSPAHDNI.sub.146 274
.sub.130AsPTIEAQGTSPAHDNIA.sub.147 275
.sub.402SSsWRILGSKQSEHRP.sub.417 276 1363-EBV alone ADAM 8
.sub.758SPPFPVPVYTRQAPKQVIK.sub.776 277 B lymphocyte
.sub.328DPTRRFFKVtPPPGSGPQ.sub.345 278 antigen CD19 Germinal center
B .sub.142/76RSPEDEYEL 279 cell-Expressed LMPHRISSH.sub.159/93
transcript 2 .sub.143/77SPEDEYELLMPH 280 protein RISSH.sub.159/93
.sub.143/77SPEDEYELLMPH 281 RIsSH.sub.159/93
.sub.149/83ELLMPHRIsSHF.sub.160/94 282
.sub.149/83ELLMPHRIsSHFL.sub.161/95 283 Interleukin-2
.sub.282TPDPSKFFSQLsSEHGGDV.sub.300 284 receptor subunit-.sup.5
.sub.282TPDPSKFFSQLsSEHGGDVQ.sub.301 285 Optineurin
.sub.473sDFHAERAAREK.sub.484 286 Phosphoglycerate
.sub.203SPERPFLAILGGAKVADK.sub.220 287 kinase 1
.sub.203SPERPFLAILGGAKVADKIQ.sub.222 288 Solute carrier
.sub.1050TKDKYMASRGQKAKsMEG.sub.1067 289 family 12, member 6,
isoform a TNFAIP3-interacting .sub.559VPHHGFEDWsQIR.sub.571 290
protein 1 Tumor necrosis factor .sub.513/50KIEKIyIMK 291
ADTVIVG.sub.528/65 receptor superfamily
.sub.514/51IEKIyIMKADTVIVG.sub.528/65 292 member 8 UPF0501 protein
.sub.136EESsDDGKKY.sub.145 293 KIAA1430 Xenotropic and
.sub.657KNRsWKYN.sub.664 294 polytropic .sub.657KNRsWKYNQ.sub.665
295 retrovirus .sub.657KNRsWKYNQSISLR.sub.670 296 receptor 1
.sub.657KNRsWKYNQSISLRRP.sub.672 297 .sub.658NRsWKYNQSISLR.sub.670
298 .sub.658NRsWKYNQSISLRRP.sub.672 299
.sub.659RsWKYNQSISLRRP.sub.672 300 2048-EBV alone BCL2-associated
.sub.653RRIDIsPSTLR.sub.663 134 transcription factor 1 Caspase
recruitment .sub.653RRIDIsPSTLRK.sub.664 301 domain-containing
.sub.509RAKsPISLK.sub.517 35 protein 11 Chromatin-modifying
.sub.49/177ESsVRSQEDQLSR.sub.61/189 302 protein 1a
.sub.49/177ESsVRSQEDQLSRR.sub.62/190 303 Interleukin-10
.sub.293DKLSVIAEDSESGKQ.sub.307 304 receptor-5 chain
.sub.293DKLsVIAEDSESGKQN.sub.308 305
.sub.293DKLsVIAEDSESGKQNP.sub.309 306
.sub.293DKLSVIAEDSESGKQNPG.sub.310 307
.sub.293DKLsVIAEDSESGKQNPGDS.sub.312 308
.sub.294KLsVIAEDSESGKQN.sub.308 309
.sub.294KLsVIAEDSESGKQNP.sub.309 310
.sub.294KLsVIAEDSESGKQNPG.sub.310 311 NADH-ubiquinone
.sub.88NLELSKFRMPQPSSGREsPRH.sub.108 312 oxidoreductase
.sub.91LSKFRMPQPSSGREsPRH.sub.108 313 flavoprotein 3 Protein FAM40A
.sub.318PPLPEDSIKVIRN 314 MRAAsPPA.sub.338 Ras association
.sub.184/152/140RTMsEAA 40 domain LVRK.sub.194/162/150 containing
protein 6 SH2 domain .sub.80MPRPsIKKAQNSQAARQ.sub.96 315 containing
3C isoform 1 Taxi-binding .sub.106THKGEIRGASTPFQFRAssP.sub.125 316
protein 1, .sub.107HKGEIRGASTPFQFRAssP.sub.125 317 isoform 1 or 2
UPF0492 protein .sub.391STIQNSPTKK.sub.400 318 C20orf94
TABLE-US-00008 TABLE 8 Characteristics of FILA-DR-associated
Phosphopeptides Commonly Expressed by Melanoma and EBV-B Cells SEQ
ID Source Protein Phosphopeptide NO Elongin A
.sub.122RSYsPDHRQK.sub.131 319 Ferritin
.sub.171FDKHTLGDsDNES.sub.183 320 heavy chain 321 Frizzled-6
.sub.617EPAsPAAsISRLSGEQVDGKG.sub.637
.sub.620SPAASISRLsGEQVDGKG.sub.637 322
.sub.623ASISRLsGEQVDGKG.sub.637 323 .sub.623AsISRLsGEQVDGKG.sub.637
324 .sub.623AsISRLSGEQVDGKG.sub.637 325 Insulin like
.sub.2392TTKsVKALSSLHG.sub.2104 326 growth
.sub.2392TTKsVKALSSLHGDD.sub.2406 327 factor 2
.sub.2392TTKsVKALSSLHGDDQ.sub.2407 328 receptor
.sub.2392TTKsVKALSSLHGDDQD.sub.2408 329
.sub.2392TTKsVKALSSLHGDDQDS.sub.2409 330
.sub.2393TKsVKALSSLHGDD.sub.2406 331
.sub.2393TKsVKALSSLHGDDQ.sub.2407 332
.sub.2393TKsVKALSSLHGDDQD.sub.2408 333
.sub.2394KsVKALSSLHGDDQ.sub.2407 334
.sub.2394KsVKALSSLHGDDQD.sub.2408 335
.sub.2392TTKSVKALSSLHGDDQDsED.sub.2411 336
.sub.2392TTKSVKALSSLHGDDQDsEDE.sub.2412 337
.sub.2394KSVKALSSLHGDDQDsEDE.sub.2412 338
.sub.2476KLVSFHDDSDEDL.sub.2488 339 Lipolysis-
.sub.324/287/305APSTYAHLs 340 stimulated PAK.sub.335/398/316
lipoprotein .sub.324/287/305APSTYAHLsPAKTP 341 receptor
PPP.sub.340/303/321 Plakophilin-4 .sub.206NRAMRRVsSVPSR.sub.215 342
.sub.206NRAMRRVsSVPSRAQ.sub.220 343
.sub.278RPAsPtAIRRIGSVTSRQT.sub.296 344 Sequestosome-1
.sub.332SGGDDDWTHLSSKEVDPST.sub.350 345
.sub.332SGGDDDWTHLSSKEVDPSTG.sub.351 346
.sub.332SGGDDDWTHLSSKEVDPSTGE.sub.352 347
.sub.332sGGDDDWTHLSSKEVDPSTGEL.sub.353 348
.sub.332sGGDDDWTHLSSKEVDPSTGELQ.sub.354 349
.sub.333GGDDDWTHLsSKEVDPS.sub.349 350
.sub.333GGDDDWTHLsSKEYDPSTG.sub.351 351
.sub.334GDDDWTHLsSKEVD.sub.347 352 .sub.334GDDDWTHLSSKEVDP.sub.318
353 .sub.334GDDDWTHLSSKEVDPS.sub.349 354
.sub.334GDDDWTULSSKEVDPSTG.sub.331 355
.sub.335DDDWTHLSSKEVDPS.sub.349 356
.sub.335DDDWTHLSSKEVDPSTG.sub.351 357
.sub.336DDWTHLsSKEVDPS.sub.349 358 .sub.337DWTHLSSKEVDPS.sub.349
359 .sub.337DWTHLsSKEVDPSTG.sub.351 360
.sub.338WTHLsSKEVDPS.sub.349 361 .sub.338WTHLsSKEVDPSTG.sub.351 362
Sorting nexin-17 .sub.402GtLRRSDSQQAVK.sub.414 363
.sub.403GtLRRSDSQQAVKS.sub.415 364 .sub.402GtLRRSDSQQAVKSPP.sub.417
365 UPF0555 protein .sub.783VLKSRKSSVTEE.sub.94 366 KIAA0776
TABLE-US-00009 TABLE 9 Characteristics of Source Proteins
Generating HLA-DR-restricted Phosphopeptides GENBANK .RTM. Known
Source protein Accession No. Phosphoprotein? Function Other Names
ADAM 8 P78325 N Cellular trafficking A disintegrin and
metalloproteinase domain 8, Cell surface antigen MS2, CD 156a
Amino-terminal enhancer Q08117 N Transcriptional GRG protein,
Protein ESP1, Gp130-associated protein of split regulation GAM
Ankyrin repeat domain- Q6NXT1 Y Unknown N/A containing protein 54
Anoctamin-8 Q9HCE9 N Ion transport Transmembrane protein 16H AP-3
complex subunit- O14617 Y Trafficking Adapter-related protein
complex 3 subunit-A-1, AP-3 A-1 complex subunit-.DELTA.,
.DELTA.-adaptin BCL2-associated A2RU75 N Transcription factor N/A
transcription factor 1 B lymphocyte antigen P15391 Y
Receptor/signal Differentiation antigen CD19, B lymphocyte surface
CD19 transduction antigen B4, Leu-12 B lymphocyte antigen P11836 Y
Receptor/signal Membrane-spanning 4-domains subfamily A member CD20
transduction 1, B lymphocyte surface antigen 81, Leu-16, Bp35
Casein kinase II subunit- P67870 Y Signal transduction Phosvitin,
G5a ll Caspase recruitment Q9BXL7 N Signal transduction
CARD-containing MAGUK protein 3, Carma 1 domain-containing protein
11 Chromatin-modifying Q9HD42 N Cell cycle/protein
Chromatin-modifying protein 1a, Vacuolar protein protein 1a
trafficking sorting-associated protein 46-1 Claudin-11 O75508 N
Cell adhesion Oligodendrocyte-specific protein Elongin A Q14241 Y
Transcriptional Transcription elongation factor B polypeptide 3,
RNA regulation polymerase II transcription factor Sill subunit A 1,
SIII p110, Elongin 110-kDa subunit Emerin P50402 Y Protein binding
N/A Ferritin heavy chain P02794 Y Ion storage Cell
proliferation-inducing gene 15 protein FU20689 Q9H3M3 N Unknown N/A
Frizzled-6 O60353 Y Receptor/Signal N/A transduction Germinal
center B-cell- Q8N6F7 Y Signal transduction.cndot. Germinal
center-associated lymphoma protein expressed transcript 2 protein
Insulin-like growth factor P11717 Y Metabolism Cation-independent
mannose-6-phosphate receptor, 2 receptor M6P/IGF2 receptor, 300 kDa
mannose 6- phosphate receptor, CD222 Insulin receptor substrate 2
Q9Y4H2 Y Receptor/signal N/A transduction lnterleukin 1 receptor
Q9NPH3 N Receptor/signal N/A accessory protein transduction
lnterleukin-2 receptor P14784 Y Receptor/signal High-affinity ll-2
receptor subunit-.beta., P70-75, CD122 subunit-ll transduction
lnterleukin-10 receptor-.beta. Q08334 N Receptor/signal ll-10R2,
Cytokine receptor family 2 member 4, chain transduction CDw210b
Lipolysis-stimulated Q86X29 Y Receptor/metabolism N/A lipoprotein
receptor LUC7-Iike isoform b Q53G47 Y Unknown N/A
Lymphoid-restricted Q12912 N Metabolism Protein Jaw1 membrane
protein Matrix-remodeling- P84157 N Unknown Transmembrane anchor
protein 1 associated protein 7 Melanoma antigen Q16655 N Unknown
MART-1, Melan-A, Antigen SK29-AA, Antigen recognized by T cells 1
LB39-AA Membrane-associated O00264 Y Receptor N/A progesterone
receptor component 1 NADH-ubiquinone P56181 N Metabolism
NADH-ubiquinone oxidoreductase 9-kDa subunit, oxidoreductase
Complex 1-9 kD, Renal carcinoma antigen NY- flavoprotein 3 REN-4
Nf-KB inhibitor- Q9NYR9 N Signal regulation I.kappa.B-interacting
Ras-like protein 2 interacting Ras-like protein 2 Optineurin Q96CV9
Y Signal transduction/ Optic neuropathy-inducing protein, E3-14.7K-
protein trafficking interacting protein, FIP-2,
Huntingtin-interacting protein L, Huntingtin yeast partner L, NEMO-
related protein, Transcription factor IIIA- interacting protein
Phosphoglycerate kinase 1 P005658 Y Metabolism Primer recognition
protein 2, Cell migration-inducing gene 10 protein Plakophilin-4
Q99569 Y Cell adhesion p0071 Probable fibrosin-1 long- Q9HAH7 Y
Unknown N/A transcript protein isoform 2 Protein FAM40A QSVSL9 Y
Unknown N/A Ras association domain- Q6ZTQ3 N Signal transduction
N/A containing protein 6 Sequestosome-1 Q13501 Y Signal
transduction Phosphotyrosine-independent ligand for the Lck SH2
domain of 62 kDa, Ubiquitin-binding protein p62, EBI3-associated
protein of 60 kDa SH2 domain containing QBN5H7 Y Signal
transduction Novel SH2-containing protein 3 3C isoform 1 Small
acidic protein O00193 Y Unknown N/A Solute carrier family 12,
Q9UHW9 Y Ion transport Electroneutral potassium chloride
cotransporter 3, KCI member 6, isoform a cotransporter 3 Sorting
nexin-17 Q15036 Y Trafficking* N/A Synaptojanin-170 O43426 Y
Metabolism Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1
Tax1-binding protein 1, Q86VP1 N Signal transduction TRAF6-binding
protein isoform 1 or 2 Tensin-3 Q68CZ2 Y Cellular structure Tumor
endothelial marker 6, Tensin-like SH2 domain- containing protein 1
Tetrasporin-10 Q9H1Z9 N Unknown Oculospanin TNFAIP3 interacting
Q15025 Y Signal transduction Nef-associated factor 1, HIV-1
Net-interacting protein, protein 1 Virion-associated nuclear
shuttling protein, Nip40-1 Transmembrane protein Q9NVA4 N Unknown
Transmembrane protein 34 184C Tumor necrosis factor P28908 N
Receptor/signal CD30L receptor, Lymphocyte activation antigen
receptor superfamily transduction CD30, Kl-1 antigen, CD30 member 8
UPF0492 protein Q5VYV7 N Unknown N/A C20orf94 UPF0501 protein
Q9P2B7 Y Unknown N/A KIAA1430 UPF0555 protein O94874 Y Unknown N/A
KIAA0776 Xenotropic and Q9UBH6 Y Receptor/signal Protein SYG 1
homolog, Xenotropic and polytropic polytropic retrovirus
transduction murine leukemia virus receptor X3 receptor 1
Sequence CWU 1
1
36819PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 1Ile Ser Ser Ser Met His Ser
Leu Tyr1 529PRTHomo sapiensMISC_FEATURE(5)..(5)The amino acid at
the noted position is optionally phosphorylated 2Ile Thr Gln Gly
Thr Pro Leu Lys Tyr1 5312PRTHomo sapiensMISC_FEATURE(6)..(6)The
amino acid at the noted position is optionally phosphorylated 3Leu
Thr Asp Pro Ser Ser Pro Thr Ile Ser Ser Tyr1 5 10410PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 4Thr Met Ala Ser Pro Gly Lys Asp Asn Tyr1
5 1058PRTHomo sapiensMISC_FEATURE(3)..(3)The amino acid at the
noted position is optionally phosphorylated 5Ala Ile Ser Asp Leu
Gln Gln Leu1 569PRTHomo sapiensMISC_FEATURE(6)..(6)The amino acid
at the noted position is optionally phosphorylated 6Asp Leu Lys Arg
Arg Ser Met Ser Ile1 579PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated 7Phe
Leu Asp Thr Pro Ile Ala Lys Val1 589PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 8Lys Ala Phe Ser Pro Val Arg Ser Val1
5910PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 9Lys Leu Ala Ser Pro Glu Leu
Glu Arg Leu1 5 101010PRTHomo sapiensMISC_FEATURE(6)..(6)The amino
acid at the noted position is optionally phosphorylated 10Lys Leu
Phe Pro Asp Thr Pro Leu Ala Leu1 5 10119PRTHomo
sapiensMISC_FEATURE(8)..(8)The amino acid at the noted position is
optionally phosphorylated 11Lys Leu Ile Asp Arg Thr Glu Ser Leu1
51210PRTHomo sapiensMISC_FEATURE(6)..(6)The amino acid at the noted
position is optionally phosphorylated 12Lys Leu Ile Asp Val Ser Ser
Gln Lys Val1 5 10139PRTHomo sapiensMISC_FEATURE(4)..(4)The amino
acid at the noted position is optionally phosphorylated 13Lys Val
Gln Ser Leu Arg Arg Ala Leu1 5149PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 14Leu Leu Leu Ser Glu Glu Val Glu Leu1
5159PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 15Arg Leu Ala Ser Tyr Leu Asp
Arg Val1 5169PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 16Arg Leu Ser Ser
Pro Leu His Phe Val1 51710PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated 17Arg
Gln Ala Ser Ile Glu Leu Pro Ser Met1 5 101812PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 18Arg Gln Ala Ser Ile Glu Leu Pro Ser Met
Ala Val1 5 101911PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 19Arg Gln Asp
Ser Thr Pro Gly Lys Val Phe Leu1 5 102011PRTHomo
sapiensMISC_FEATURE(5)..(5)The amino acid at the noted position is
optionally phosphorylated 20Arg Gln Asp Ser Thr Pro Gly Lys Val Phe
Leu1 5 10219PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 21Arg Gln Ile Ser
Gln Asp Val Lys Leu1 52210PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated 22Arg
Thr Leu Ser Pro Glu Ile Ile Thr Val1 5 10239PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 23Arg Val Ala Ser Pro Thr Ser Gly Val1
5249PRTHomo sapiensMISC_FEATURE(5)..(5)The amino acid at the noted
position is optionally phosphorylated 24Arg Val Leu His Ser Pro Pro
Ala Val1 5259PRTHomo sapiensMISC_FEATURE(5)..(5)The amino acid at
the noted position is optionally phosphorylated 25Ser Met Thr Arg
Ser Pro Pro Arg Val1 5269PRTHomo sapiensMISC_FEATURE(8)..(8)The
amino acid at the noted position is optionally phosphorylated 26Ser
Val Lys Pro Arg Arg Thr Ser Leu1 5279PRTHomo
sapiensMISC_FEATURE(5)..(5)The amino acid at the noted position is
optionally phosphorylated 27Val Met Ile Gly Ser Pro Lys Lys Val1
5288PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 28Arg Ala Asp Ser Pro Val His
Met1 5299PRTHomo sapiensMISC_FEATURE(5)..(5)The amino acid at the
noted position is optionally phosphorylated 29Arg Ala His Ser Ser
Pro Ala Ser Leu1 5308PRTHomo sapiensMISC_FEATURE(3)..(3)The amino
acid at the noted position is optionally phosphorylated 30Arg Ile
Ser His Glu Leu Asp Ser1 5319PRTHomo sapiensMISC_FEATURE(5)..(5)The
amino acid at the noted position is optionally phosphorylated 31Arg
Ser His Ser Ser Pro Ala Ser Leu1 5329PRTHomo
sapiensMISC_FEATURE(8)..(8)The amino acid at the noted position is
optionally phosphorylated 32Tyr Ala Val Pro Arg Arg Gly Ser Leu1
5339PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 33Gly Ile Met Ser Pro Leu Ala
Lys Lys1 53410PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 34Lys Leu Pro Ser
Pro Ala Pro Ala Arg Lys1 5 10359PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 35Arg Ala Lys Ser Pro Ile Ser Leu Lys1
5369PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 36Arg Ile Leu Ser Gly Val Val
Thr Lys1 5379PRTHomo sapiensMISC_FEATURE(5)..(5)The amino acid at
the noted position is optionally phosphorylated 37Arg Ile Tyr Gln
Tyr Ile Gln Ser Arg1 53810PRTHomo sapiensMISC_FEATURE(5)..(5)The
amino acid at the noted position is optionally phosphorylated 38Arg
Ile Tyr Gln Tyr Ile Gln Ser Arg Phe1 5 10399PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 39Arg Leu Ser Ser Pro Ile Ser Lys Arg1
54011PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 40Arg Thr Met Ser Glu Ala Ala
Leu Val Arg Lys1 5 104111PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated 41Arg
Thr Arg Ser Leu Ser Ser Leu Arg Glu Lys1 5 104210PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 42Arg Val Ala Ser Pro Thr Ser Gly Val
Lys1 5 10439PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 43Arg Val Leu Ser
Pro Leu Ile Ile Lys1 5449PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated 44Arg
Val Tyr Ser Pro Tyr Asn His Arg1 5459PRTHomo
sapiensMISC_FEATURE(5)..(5)The amino acid at the noted position is
optionally phosphorylated 45Ser Val Arg Arg Ser Val Leu Met Lys1
5469PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 46Lys Arg Ala Ser Val Phe Val
Lys Leu1 5479PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 47Ser Val Lys Ser
Pro Val Thr Val Lys1 5489PRTHomo sapiensMISC_FEATURE(8)..(8)The
amino acid at the noted position is optionally phosphorylated 48Ile
Asn Lys Glu Arg Arg Ser Ser Leu1 5499PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 49Ala Pro Asp Ser Pro Arg Ala Phe Leu1
55010PRTHomo sapiensMISC_FEATURE(9)..(9)The amino acid at the noted
position is optionally phosphorylated 50Ala Pro Arg Asp Arg Arg Ala
Val Ser Phe1 5 10519PRTHomo sapiensMISC_FEATURE(6)..(6)The amino
acid at the noted position is optionally phosphorylated 51Ala Pro
Arg Arg Tyr Ser Ser Ser Leu1 5529PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 52Gly Pro Arg Ser Pro Lys Ala Pro Pro1
55311PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 53Lys Pro Ala Ser Pro Lys Phe
Ile Val Thr Leu1 5 105410PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated 54Lys
Pro Glu Ser Arg Arg Ser Ser Leu Leu1 5 10559PRTHomo
sapiensMISC_FEATURE(8)..(8)The amino acid at the noted position is
optionally phosphorylated 55Lys Pro Arg Pro Pro Pro Leu Ser Pro1
5569PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 56Lys Pro Arg Ser Pro Phe Ser
Lys Ile1 5579PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 57Lys Pro Arg Ser
Pro Pro Arg Ala Leu1 5589PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated 58Lys
Pro Arg Ser Pro Val Val Glu Leu1 5599PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 59Leu Pro Ala Ser Pro Arg Ala Arg Leu1
5609PRTHomo sapiensMISC_FEATURE(8)..(8)The amino acid at the noted
position is optionally phosphorylated 60Leu Pro Ile Phe Ser Arg Leu
Ser Ile1 5619PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 61Leu Pro Val Ser
Pro Arg Leu Gln Leu1 56210PRTHomo sapiensMISC_FEATURE(6)..(6)The
amino acid at the noted position is optionally phosphorylated 62Met
Pro Arg Gln Pro Ser Ala Thr Arg Leu1 5 10639PRTHomo
sapiensMISC_FEATURE(6)..(6)The amino acid at the noted position is
optionally phosphorylated 63Gln Pro Gln Arg Arg Ser Leu Arg Leu1
56410PRTHomo sapiensMISC_FEATURE(6)..(6)The amino acid at the noted
position is optionally phosphorylated 64Arg Ala Arg Gly Ile Ser Pro
Ile Val Phe1 5 10659PRTHomo sapiensMISC_FEATURE(4)..(4)The amino
acid at the noted position is optionally phosphorylated 65Arg Pro
Ala Ser Ala Gly Ala Met Leu1 56610PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 66Arg Pro Ala Ser Pro Gln Arg Ala Gln
Leu1 5 10679PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 67Arg Pro Asp Ser
Ala His Lys Met Leu1 56810PRTHomo sapiensMISC_FEATURE(9)..(9)The
amino acid at the noted position is optionally phosphorylated 68Arg
Pro Asp Val Ala Lys Arg Leu Ser Leu1 5 106911PRTHomo
sapiensMISC_FEATURE(10)..(10)The amino acid at the noted position
is optionally phosphorylated 69Arg Pro Phe His Gly Ile Ser Thr Val
Ser Leu1 5 10709PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 70Arg Pro Phe
Ser Pro Arg Glu Ala Leu1 5719PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated 71Arg
Pro Gly Ser Arg Gln Ala Gly Leu1 5729PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 72Arg Pro Lys Ser Pro Leu Ser Lys Met1
57310PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 73Arg Pro Lys Ser Val Asp Phe
Asp Ser Leu1 5 107410PRTHomo sapiensMISC_FEATURE(7)..(7)The amino
acid at the noted position is optionally phosphorylated 74Arg Pro
Gln Arg Ala Thr Ser Asn Val Phe1 5 107510PRTHomo
sapiensMISC_FEATURE(6)..(6)The amino acid at the noted position is
optionally phosphorylated 75Arg Pro Arg Ala Arg Ser Val Asp Ala
Leu1 5 10769PRTHomo sapiensMISC_FEATURE(5)..(5)The amino acid at
the noted position is optionally phosphorylated 76Arg Pro Arg Gly
Ser Gln Ser Leu Leu1 57710PRTHomo sapiensMISC_FEATURE(6)..(6)The
amino acid at the noted position is optionally phosphorylated 77Arg
Pro Arg Pro Val Ser Pro Ser Ser Leu1 5 10788PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 78Arg Pro Arg Ser Ala Val Leu Leu1
57910PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 79Arg Pro Arg Ser Pro Asn Met
Gln Asp Leu1 5 108010PRTHomo sapiensMISC_FEATURE(4)..(4)The amino
acid at the noted position is optionally phosphorylated 80Arg Pro
Arg Ser Pro Arg Gln Asn Ser Ile1 5 108110PRTHomo
sapiensMISC_FEATURE(9)..(9)The amino acid at the noted position is
optionally phosphorylated 81Arg Pro Thr Lys Ile Gly Arg Arg Ser
Leu1 5 10829PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 82Arg Pro Thr Ser
Arg Leu Asn Arg Leu1 5839PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated 83Arg
Pro Val Thr Pro Val Ser Asp Leu1 5849PRTHomo
sapiensMISC_FEATURE(8)..(8)The amino acid at the noted position is
optionally phosphorylated 84Ser Pro Phe Lys Arg Gln Leu Ser Leu1
58511PRTHomo sapiensMISC_FEATURE(7)..(7)The amino acid at the noted
position is optionally phosphorylated 85Ser Pro Arg Ala Pro Val Ser
Pro Leu Lys Phe1 5 108610PRTHomo sapiensMISC_FEATURE(5)..(5)The
amino acid at the noted position is optionally phosphorylated 86Ser
Pro Arg Arg Ser Arg Ser Ile Ser Leu1 5 10879PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 87Ser Pro Arg Ser Pro Asp Arg Thr Leu1
58810PRTHomo sapiensMISC_FEATURE(6)..(6)The amino acid at the noted
position is optionally phosphorylated 88Ser Pro Arg Ser Pro Ser Thr
Thr Tyr Leu1 5 108910PRTHomo sapiensMISC_FEATURE(4)..(4)The amino
acid at the noted position is optionally phosphorylated 89Ser Pro
Arg Ser Pro Ser Thr Thr Tyr Leu1 5 10909PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 90Thr Pro Arg Ser Pro Pro Leu Gly Leu1
59110PRTHomo sapiensMISC_FEATURE(8)..(8)The amino acid at the noted
position is optionally phosphorylated 91Val Pro Arg Pro Glu Arg Arg
Ser Ser Leu1 5 109210PRTHomo sapiensMISC_FEATURE(6)..(6)The amino
acid at the noted position is optionally phosphorylated 92Ala Pro
Arg Lys Gly Ser Phe Ser Ala Leu1 5 10939PRTHomo
sapiensMISC_FEATURE(8)..(8)The amino acid at the noted position is
optionally phosphorylated 93Ala Val Arg Pro Thr Arg Leu Ser Leu1
5949PRTHomo sapiensMISC_FEATURE(6)..(6)The amino acid at the noted
position is optionally phosphorylated 94Lys Pro Arg Pro Leu Ser Met
Asp Leu1 5959PRTHomo sapiensMISC_FEATURE(6)..(6)The amino acid at
the noted position is optionally phosphorylated 95Lys Pro Arg Arg
Phe Ser Arg Ser Leu1 5969PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated 96Leu
Pro Arg Thr Pro Arg Pro Glu Leu1 5979PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 97Arg Pro Ala Ser Pro Ala Ala Lys Leu1
59810PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 98Arg Pro Asp Ser Pro Thr Arg
Pro Thr Leu1 5 109910PRTHomo sapiensMISC_FEATURE(4)..(4)The amino
acid at the noted position is optionally phosphorylated 99Arg Pro
Ile Ser Pro Arg Ile Gly Ala Leu1 5 101008PRTHomo
sapiensMISC_FEATURE(6)..(6)The amino acid at the noted position is
optionally phosphorylated 100Arg Pro Arg Ala Ala Thr Val Val1
51019PRTHomo sapiensMISC_FEATURE(6)..(6)The amino acid at the noted
position is optionally phosphorylated 101Arg Pro Arg Ala Ala Thr
Val Val Ala1 510211PRTHomo sapiensMISC_FEATURE(6)..(6)The amino
acid at the noted position is optionally phosphorylated 102Arg Pro
Arg Ala Asn Ser Gly Gly Val Asp Leu1 5 101039PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 103Arg Pro Arg Ser Ala Val Glu Gln Leu1
51049PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 104Arg Pro Arg Ser Met Thr
Val Ser Ala1 51059PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 105Arg Pro Arg
Ser Pro Pro Gly Gly Pro1 510612PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 106Arg Pro Arg Ser Pro Thr Gly Pro Ser
Asn Ser Phe1 5 101079PRTHomo sapiensMISC_FEATURE(4)..(4)The amino
acid at the noted position is optionally phosphorylated 107Ser Pro
Lys Ser Pro Gly Leu Lys Ala1 51089PRTHomo
sapiensMISC_FEATURE(7)..(7)The amino acid at the noted position is
optionally phosphorylated 108Tyr Pro Gly Gly Arg Arg Ser Ser Leu1
51099PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 109Lys Tyr Ile Ser Gly Pro
His Glu Leu1 51109PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 110Arg Tyr Gln
Thr Gln Pro Val Thr Leu1 511110PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 111Phe Arg Arg Ser Pro Thr Lys Ser Ser
Leu1 5 1011212PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 112Phe Arg Arg Ser
Pro Thr Lys Ser Ser Leu Asp Tyr1 5 101139PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 113Gly Arg Lys Ser Pro Pro Pro Ser Phe1
51149PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 114Gly Arg Leu Ser Pro Ala
Tyr Ser Leu1 511510PRTHomo sapiensMISC_FEATURE(4)..(4)The amino
acid at the noted position is optionally phosphorylated 115Gly Arg
Leu Ser Pro Val Pro Val Pro Arg1 5 1011610PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 116His Arg Leu Ser Pro Val Lys Gly Glu
Phe1 5 101179PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 117His Arg Asn Ser
Met Lys Val Phe Leu1 51189PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated
118Lys Arg Phe Ser Phe Lys Lys Ser Phe1 51199PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 119Lys Arg Phe Ser Phe Lys Lys Ser Phe1
51209PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 120Lys Arg Phe Ser Gly Thr
Val Arg Leu1 51219PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 121Lys Arg Leu
Ser Pro Ala Pro Gln Leu1 51229PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 122Lys Arg Leu Ser Val Glu Arg Ile Tyr1
51239PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 123Lys Arg Met Ser Pro Lys
Pro Glu Leu1 51249PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 124Lys Arg Tyr
Ser Gly Asn Met Glu Tyr1 512510PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 125Arg Arg Ala Ser Leu Ser Glu Ile Gly
Phe1 5 101269PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 126Arg Arg Ala Ser
Gln Glu Ala Asn Leu1 51279PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated
127Arg Arg Asp Ser Ile Val Ala Glu Leu1 512810PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 128Arg Arg Asp Ser Leu Gln Lys Pro Gly
Leu1 5 101299PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 129Arg Arg Phe Ser
Gly Thr Ala Val Tyr1 51309PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated
130Arg Arg Phe Ser Pro Pro Arg Arg Met1 513110PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 131Arg Arg Phe Ser Arg Leu Glu Asn Arg
Tyr1 5 101329PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 132Arg Arg Gly Ser
Phe Glu Val Thr Leu1 513310PRTHomo sapiensMISC_FEATURE(6)..(6)The
amino acid at the noted position is optionally phosphorylated
133Arg Arg Ile Asp Ile Ser Pro Ser Thr Phe1 5 1013411PRTHomo
sapiensMISC_FEATURE(6)..(6)The amino acid at the noted position is
optionally phosphorylated 134Arg Arg Ile Asp Ile Ser Pro Ser Thr
Leu Arg1 5 101359PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 135Arg Arg Ile
Ser Asp Pro Gln Val Phe1 51369PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 136Arg Arg Ile Ser Gly Val Asp Arg Tyr1
513710PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the
noted position is optionally phosphorylated 137Arg Arg Ile Ser Gly
Val Asp Arg Tyr Tyr1 5 101389PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated
138Arg Arg Lys Ser Gln Val Ala Glu Leu1 51399PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 139Arg Arg Leu Ser Ala Asp Ile Arg Leu1
51409PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 140Arg Arg Leu Ser Asp Ser
Pro Val Phe1 51419PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 141Arg Arg Leu
Ser Glu Ser Ser Ala Leu1 514210PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 142Arg Arg Leu Ser Gly Pro Leu His Thr
Leu1 5 101439PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 143Arg Arg Leu Ser
Leu Phe Leu Asn Val1 51448PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated
144Arg Arg Met Ser Phe Gln Lys Pro1 51459PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 145Arg Arg Met Ser Leu Leu Ser Val Val1
51469PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 146Arg Arg Asn Ser Ala Pro
Val Ser Val1 51479PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 147Arg Arg Asn
Ser Ile Asn Arg Asn Phe1 51489PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 148Arg Arg Pro Ser Leu Leu Ser Glu Phe1
51499PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 149Arg Arg Gln Ser Lys Val
Glu Ala Leu1 51509PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 150Arg Arg Leu
Ser Glu Leu Leu Arg Tyr1 51519PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 151Arg Arg Leu Ser Phe Leu Val Ser Tyr1
51529PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 152Arg Arg Ser Ser Phe Leu
Gln Val Phe1 51539PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 153Arg Arg Ser
Ser Ile Gln Ser Thr Phe1 51549PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 154Arg Arg Ser Ser Ile Gln Ser Thr Phe1
51559PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 155Arg Arg Ser Ser Ser Val
Ala Gln Val1 51568PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 156Arg Arg Tyr
Ser Pro Pro Ile Gln1 51579PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated
157Val Arg Ala Ser Lys Asp Leu Ala Gln1 51589PRTHomo
sapiensMISC_FEATURE(6)..(6)The amino acid at the noted position is
optionally phosphorylated 158Lys Arg Leu Glu Lys Ser Pro Ser Phe1
51599PRTHomo sapiensMISC_FEATURE(8)..(8)The amino acid at the noted
position is optionally phosphorylated 159Lys Arg Leu Glu Lys Ser
Pro Ser Phe1 51609PRTHomo sapiensMISC_FEATURE(5)..(5)The amino acid
at the noted position is optionally phosphorylated 160Lys Arg Trp
Gln Ser Pro Val Thr Lys1 51619PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 161Arg Arg Phe Ser Ile Ala Thr Leu Arg1
51629PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 162Arg Arg Phe Ser Leu Thr
Thr Leu Arg1 51639PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 163Arg Arg Phe
Ser Arg Ser Pro Ile Arg1 51649PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 164Arg Arg Phe Ser Val Ser Thr Leu Arg1
51659PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 165Arg Arg Phe Ser Val Thr
Thr Met Arg1 51669PRTHomo sapiensMISC_FEATURE(8)..(8)The amino acid
at the noted position is optionally phosphorylated 166Arg Arg Val
Val Gln Arg Ser Ser Leu1 51679PRTArtificial SequenceArtificially
synthesized peptideMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 167Arg Arg Tyr Ser Pro Pro
Ile Glu Arg1 51689PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid
at the noted position is optionally phosphorylated 168Arg Arg Tyr
Ser Pro Pro Ile Gln Arg1 516910PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 169Ala Glu Asn Ser Pro Thr Arg Gln Gln
Phe1 5 101709PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 170Glu Glu Leu Ser
Pro Thr Lys Ala Phe1 51719PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated
171Lys Glu Met Ser Pro Thr Arg Gln Leu1 51729PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 172Arg Phe Lys Thr Gln Pro Val Thr Phe1
51739PRTHomo sapiensMISC_FEATURE(5)..(5)The amino acid at the noted
position is optionally phosphorylated 173Glu Glu Arg Arg Ser Pro
Pro Ala Pro1 517410PRTHomo sapiensMISC_FEATURE(6)..(6)The amino
acid at the noted position is optionally phosphorylated 174Phe Glu
Asp Asp Asp Ser Asn Glu Lys Leu1 5 101759PRTHomo
sapiensMISC_FEATURE(2)..(2)The amino acid at the noted position is
optionally phosphorylated 175Lys Ser Leu Val Arg Leu Leu Leu Leu1
51769PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the noted
position is optionally phosphorylated 176Arg Thr His Ser Leu Leu
Leu Leu Leu1 51779PRTHomo sapiensMISC_FEATURE(6)..(6)The amino acid
at the noted position is optionally phosphorylated 177Arg Thr Ser
Ser Phe Thr Phe Gln Asn1 51789PRTHomo sapiens 178Tyr Leu Glu Pro
Gly Pro Val Thr Ala1 517910PRTHomo sapiens 179Asp Tyr Met Asp Gly
Thr Met Ser Gln Val1 5 101809PRTHomo sapiens 180Ala Leu Leu Ala Val
Gly Ala Thr Lys1 51819PRTHomo sapiens 181Lys Cys Asp Ile Cys Thr
Asp Glu Tyr1 51829PRTHomo sapiens 182Arg Leu Ser Asn Arg Leu Leu
Leu Arg1 51839PRTHomo sapiens 183Ser Gln Asn Phe Pro Gly Ser Gln
Lys1 51849PRTHomo sapiens 184Lys Thr Trp Gly Gln Tyr Trp Gln Val1
51859PRTHomo sapiensMISC_FEATURE(2)..(2)Xaa can be Thr or Met
185Ile Xaa Asp Gln Val Pro Phe Ser Val1 518610PRTHomo sapiens
186Val Leu Tyr Arg Tyr Gly Ser Phe Ser Val1 5 101879PRTHomo sapiens
187Ala Ala Gly Ile Gly Ile Leu Thr Val1 51889PRTHomo sapiens 188Ala
Leu Asn Phe Pro Gly Ser Gln Lys1 51899PRTHomo sapiens 189Leu Ile
Tyr Arg Arg Arg Leu Met Lys1 51909PRTHomo sapiens 190Ala Ala Gln
Glu Arg Arg Val Pro Arg1 519110PRTHomo sapiens 191Ala Ser Gly Pro
Gly Gly Gly Ala Pro Arg1 5 101929PRTHomo sapiens 192Leu Leu Gly Pro
Gly Arg Pro Tyr Arg1 519313PRTHomo sapiens 193Ser Asp Ala Glu Lys
Ser Asp Ile Cys Thr Asp Glu Tyr1 5 1019411PRTHomo sapiens 194Ser
Ser Asp Tyr Val Ile Pro Ile Gly Thr Tyr1 5 101959PRTHomo sapiens
195Glu Ala Asp Pro Thr Gly His Ser Tyr1 51969PRTHomo sapiens 196Glu
Val Asp Pro Ile Gly His Leu Tyr1 51979PRTHomo sapiens 197Ile Met
Asp Gln Val Pro Phe Ser Val1 51989PRTHomo sapiens 198Gly Leu Tyr
Asp Gly Met Glu His Leu1 519916PRTHomo sapiens 199Ala Gln Asn Ile
Leu Leu Ser Asn Ala Pro Leu Gly Pro Gln Phe Pro1 5 10
1520021PRTHomo sapiens 200Phe Leu Leu His His Ala Phe Val Asp Ser
Ile Phe Glu Gln Trp Leu1 5 10 15Gln Arg His Arg Pro 2020123PRTHomo
sapiens 201Arg Asn Gly Tyr Arg Ala Leu Met Asp Lys Ser Leu His Val
Gly Thr1 5 10 15Gln Cys Ala Leu Thr Arg Arg 2020215PRTHomo sapiens
202Thr Ser Tyr Val Lys Val Leu His His Met Val Lys Ile Ser Gly1 5
10 1520314PRTHomo sapiens 203Leu Leu Lys Tyr Arg Ala Arg Glu Pro
Val Thr Lys Ala Glu1 5 1020416PRTHomo sapiens 204Trp Asn Arg Gln
Leu Tyr Pro Glu Trp Thr Glu Ala Gln Arg Leu Asp1 5 10
1520516PRTArtificial SequenceArtificially synthesized tetanus
peptide 205Ala Gln Tyr Ile Lys Ala Asn Ser Lys Phe Ile Gly Ile Thr
Glu Leu1 5 10 152069PRTHomo sapiens 206Lys Ile Phe Gly Ser Leu Ala
Phe Leu1 52079PRTHomo sapiens 207Tyr Leu Ser Gly Ala Asp Leu Asn
Leu1 52089PRTHomo sapiens 208Val Leu Arg Glu Asn Thr Ser Pro Lys1
52099PRTHomo sapiens 209Glu Ile Trp Thr His Ser Tyr Lys Val1
52109PRTHomo sapiens 210Ser Leu Phe Arg Ala Val Ile Thr Lys1
52119PRTHomo sapiens 211His Leu Phe Gly Tyr Ser Trp Tyr Lys1
52129PRTHomo sapiens 212Ala Pro Pro Ala Tyr Glu Lys Leu Ser1
52139PRTHomo sapiens 213Pro Pro Ala Tyr Glu Lys Leu Ser Ala1
52149PRTHomo sapiens 214Pro Ala Tyr Glu Lys Leu Ser Ala Glu1
521520PRTHomo sapiensMISC_FEATURE(12)..(12)The amino acid at the
noted position is optionally phosphorylated 215Val Pro Asn Ala Pro
Pro Ala Tyr Glu Lys Leu Ser Ala Glu Gln Ser1 5 10 15Pro Pro Pro Tyr
2021612PRTHomo sapiensMISC_FEATURE(11)..(11)The amino acid at the
noted position is optionally phosphorylated 216Pro Asn Ala Pro Pro
Ala Tyr Glu Lys Leu Ser Ala1 5 1021712PRTHomo
sapiensMISC_FEATURE(10)..(10)The amino acid at the noted position
is optionally phosphorylated 217Asn Ala Pro Pro Ala Tyr Glu Lys Leu
Ser Ala Glu1 5 1021812PRTHomo sapiensMISC_FEATURE(9)..(9)The amino
acid at the noted position is optionally phosphorylated 218Ala Pro
Pro Ala Tyr Glu Lys Leu Ser Ala Glu Gln1 5 1021915PRTHomo
sapiensMISC_FEATURE(9)..(9)The amino acid at the noted position is
optionally phosphorylated 219Ala Pro Pro Ala Tyr Glu Lys Leu Ser
Ala Glu Gln Ser Pro Pro1 5 10 1522016PRTHomo
sapiensMISC_FEATURE(9)..(9)The amino acid at the noted position is
optionally phosphorylated 220Ala Pro Pro Ala Tyr Glu Lys Leu Ser
Ala Glu Gln Ser Pro Pro Pro1 5 10
1522112PRTHomo sapiensMISC_FEATURE(8)..(8)The amino acid at the
noted position is optionally phosphorylated 221Pro Pro Ala Tyr Glu
Lys Leu Ser Ala Glu Gln Ser1 5 1022212PRTHomo
sapiensMISC_FEATURE(7)..(7)The amino acid at the noted position is
optionally phosphorylated 222Pro Ala Tyr Glu Lys Leu Ser Ala Glu
Gln Ser Pro1 5 1022312PRTHomo sapiensMISC_FEATURE(6)..(6)The amino
acid at the noted position is optionally phosphorylated 223Ala Tyr
Glu Lys Leu Ser Ala Glu Gln Ser Pro Pro1 5 1022412PRTHomo sapiens
224Tyr Glu Lys Leu Ser Ala Glu Gln Ser Pro Pro Pro1 5
1022516PRTHomo sapiens 225Ala Pro Pro Ala Tyr Glu Lys Leu Ser Ala
Glu Gln Ser Pro Pro Pro1 5 10 1522617PRTHomo
sapiensMISC_FEATURE(9)..(9)The amino acid at the noted position is
optionally phosphorylated 226Ala Pro Pro Ala Tyr Glu Lys Leu Ser
Ala Glu Gln Ser Pro Pro Pro1 5 10 15Tyr22712PRTHomo
sapiensMISC_FEATURE(8)..(8)The amino acid at the noted position is
optionally phosphorylated 227Val Ser Lys Val Met Ile Gly Ser Pro
Lys Lys Val1 5 102289PRTHomo sapiensMISC_FEATURE(5)..(5)The amino
acid at the noted position is optionally phosphorylated 228Val Met
Ile Gly Ser Pro Lys Lys Val1 522910PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 229Lys Tyr Ser Pro Gly Lys Leu Arg Gly
Asn1 5 1023022PRTHomo sapiensMISC_FEATURE(21)..(21)The amino acid
at the noted position is optionally phosphorylated 230Ser Lys Glu
Asp Lys Asn Gly His Asp Gly Asp Thr His Gln Glu Asp1 5 10 15Asp Gly
Glu Lys Ser Asp 2023128PRTHomo sapiensMISC_FEATURE(21)..(21)The
amino acid at the noted position is optionally phosphorylated
231Gly Ser Ala Leu Gly Gly Gly Gly Ala Gly Leu Ser Gly Arg Ala Ser1
5 10 15Gly Gly Ala Gln Ser Pro Leu Arg Tyr Leu His Val 20
2523225PRTHomo sapiensMISC_FEATURE(18)..(18)The amino acid at the
noted position is optionally phosphorylated 232Leu Gly Gly Gly Gly
Ala Gly Leu Ser Gly Arg Ala Ser Gly Gly Ala1 5 10 15Gln Ser Pro Leu
Arg Tyr Leu His Val 20 2523314PRTHomo
sapiensMISC_FEATURE(6)..(6)The amino acid at the noted position is
optionally phosphorylated 233Ser Gly Gly Ala Gln Ser Pro Leu Arg
Tyr Leu His Val Leu1 5 1023419PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 234Glu Glu Gly Ser Pro Thr Met Val Glu
Lys Gly Leu Glu Pro Gly Val1 5 10 15Phe Thr Leu23518PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 235Glu Gly Ser Pro Thr Met Val Glu Lys
Gly Leu Glu Pro Gly Val Phe1 5 10 15Thr Leu23617PRTHomo
sapiensMISC_FEATURE(2)..(2)The amino acid at the noted position is
optionally phosphorylated 236Gly Ser Pro Thr Met Val Glu Lys Gly
Leu Glu Pro Gly Val Phe Thr1 5 10 15Leu23724PRTHomo
sapiensMISC_FEATURE(10)..(10)The amino acid at the noted position
is optionally phosphorylated 237Glu Glu Met Pro Glu Asn Ala Leu Pro
Ser Asp Glu Asp Asp Lys Asp1 5 10 15Pro Asn Asp Pro Tyr Arg Ala Leu
2023814PRTHomo sapiensMISC_FEATURE(8)..(8)The amino acid at the
noted position is optionally phosphorylated 238Gln Ala Ala Ser Asn
Phe Lys Ser Pro Val Lys Thr Ile Arg1 5 1023913PRTHomo
sapiensMISC_FEATURE(7)..(7)The amino acid at the noted position is
optionally phosphorylated 239Ala Ala Ser Asn Phe Lys Ser Pro Val
Lys Thr Ile Arg1 5 1024011PRTHomo sapiensMISC_FEATURE(5)..(5)The
amino acid at the noted position is optionally phosphorylated
240Ser Asn Phe Lys Ser Pro Val Lys Thr Ile Arg1 5 1024110PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 241Asn Phe Lys Ser Pro Val Lys Thr Ile
Arg1 5 102429PRTHomo sapiensMISC_FEATURE(3)..(3)The amino acid at
the noted position is optionally phosphorylated 242Phe Lys Ser Pro
Val Lys Thr Ile Arg1 524317PRTHomo sapiensMISC_FEATURE(8)..(8)The
amino acid at the noted position is optionally phosphorylated
243Tyr Tyr Thr Ala Gly Ser Ser Ser Pro Thr His Ala Lys Ser Ala His1
5 10 15Val24412PRTHomo sapiensMISC_FEATURE(3)..(3)The amino acid at
the noted position is optionally phosphorylated 244Ser Ser Ser Pro
Thr His Ala Lys Ser Ala His Val1 5 1024517PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 245Val Arg Gln Ser Val Thr Ser Phe Pro
Asp Ala Asp Ala Phe His His1 5 10 15Gln24612PRTHomo
sapiensMISC_FEATURE(8)..(8)The amino acid at the noted position is
optionally phosphorylated 246Phe Lys Met Pro Gln Glu Lys Ser Pro
Gly Tyr Ser1 5 1024711PRTHomo sapiensMISC_FEATURE(4)..(4)The amino
acid at the noted position is optionally phosphorylated 247Arg Val
Ala Ser Pro Thr Ser Gly Val Lys Arg1 5 1024828PRTHomo
sapiensMISC_FEATURE(14)..(14)The amino acid at the noted position
is optionally phosphorylated 248Gln Val Ala Met Pro Val Lys Lys Ser
Pro Arg Arg Ser Ser Ser Asp1 5 10 15Glu Gln Gly Leu Ser Tyr Ser Ser
Leu Lys Asn Val 20 2524927PRTHomo sapiensMISC_FEATURE(13)..(13)The
amino acid at the noted position is optionally phosphorylated
249Val Ala Met Pro Val Lys Lys Ser Pro Arg Arg Ser Ser Ser Asp Glu1
5 10 15Gln Gly Leu Ser Tyr Ser Ser Leu Lys Asn Val 20
2525017PRTHomo sapiensMISC_FEATURE(11)..(11)The amino acid at the
noted position is optionally phosphorylated 250Ser Ser Asn Gly Lys
Met Ala Ser Arg Arg Ser Glu Glu Lys Glu Ala1 5 10 15Gly25119PRTHomo
sapiensMISC_FEATURE(11)..(11)The amino acid at the noted position
is optionally phosphorylated 251Ser Ser Asn Gly Lys Met Ala Ser Arg
Arg Ser Glu Glu Lys Glu Ala1 5 10 15Gly Glu Ile25224PRTHomo
sapiensMISC_FEATURE(10)..(10)The amino acid at the noted position
is optionally phosphorylated 252Lys Glu Gly Glu Glu Pro Thr Val Tyr
Ser Asp Glu Glu Glu Pro Lys1 5 10 15Asp Glu Ser Ala Arg Lys Asn Asp
2025323PRTHomo sapiensMISC_FEATURE(9)..(9)The amino acid at the
noted position is optionally phosphorylated 253Glu Gly Glu Glu Pro
Thr Val Tyr Ser Asp Glu Glu Glu Pro Lys Asp1 5 10 15Glu Ser Ala Arg
Lys Asn Asp 2025427PRTHomo sapiensMISC_FEATURE(22)..(22)The amino
acid at the noted position is optionally
phosphorylatedMISC_FEATURE(24)..(24)The amino acid at the noted
position is optionally phosphorylated 254Ala Ser Lys Met Thr Gln
Pro Gln Ser Lys Ser Ala Phe Pro Leu Ser1 5 10 15Arg Lys Asn Lys Gly
Ser Gly Ser Leu Asp Gly 20 2525525PRTHomo
sapiensMISC_FEATURE(13)..(13)The amino acid at the noted position
is optionally phosphorylated 255Ala Pro Pro Pro Leu Val Pro Ala Pro
Arg Pro Ser Ser Pro Pro Arg1 5 10 15Gly Pro Gly Pro Ala Arg Ala Asp
Arg 20 2525622PRTHomo sapiensMISC_FEATURE(16)..(16)The amino acid
at the noted position is optionally phosphorylated 256Ser Ala Ala
Arg Glu Ser His Pro His Gly Val Lys Arg Ser Ala Ser1 5 10 15Pro Asp
Asp Asp Leu Gly 2025722PRTHomo sapiensMISC_FEATURE(1)..(1)Ser-1 can
be acetylated (Acetyl-Ser)MISC_FEATURE(16)..(16)The amino acid at
the noted position is optionally phosphorylated 257Ser Ala Ala Arg
Glu Ser His Pro His Gly Val Lys Arg Ser Ala Ser1 5 10 15Pro Asp Asp
Asp Leu Gly 2025813PRTHomo sapiensMISC_FEATURE(5)..(5)The amino
acid at the noted position is optionally phosphorylated 258Ala Ser
Lys Ala Ser Pro Thr Leu Asp Phe Thr Glu Arg1 5 1025916PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 259Gly Glu Arg Ser Pro Leu Leu Ser Gln
Glu Thr Ala Gly Gln Lys Pro1 5 10 1526017PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 260Gly Glu Arg Ser Pro Leu Leu Ser Gln
Glu Thr Ala Gly Gln Lys Pro1 5 10 15Leu26115PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 261Glu Arg Ser Pro Leu Leu Ser Gln Glu
Thr Ala Gly Gln Lys Pro1 5 10 1526216PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 262Glu Arg Ser Pro Leu Leu Ser Gln Glu
Thr Ala Gly Gln Lys Pro Leu1 5 10 1526315PRTHomo
sapiensMISC_FEATURE(9)..(9)The amino acid at the noted position is
optionally phosphorylated 263Thr Ile Gly Glu Lys Lys Glu Pro Ser
Asp Lys Ser Val Asp Ser1 5 10 1526418PRTHomo
sapiensMISC_FEATURE(11)..(11)The amino acid at the noted position
is optionally phosphorylated 264Ser Gly Pro Lys Pro Leu Phe Arg Arg
Met Ser Ser Leu Val Gly Pro1 5 10 15Thr Gln26511PRTHomo
sapiensMISC_FEATURE(10)..(10)The amino acid at the noted position
is optionally phosphorylated 265Gly Pro Lys Pro Leu Phe Arg Arg Met
Ser Ser1 5 1026612PRTHomo sapiensMISC_FEATURE(10)..(10)The amino
acid at the noted position is optionally phosphorylated 266Gly Pro
Lys Pro Leu Phe Arg Arg Met Ser Ser Leu1 5 1026713PRTHomo
sapiensMISC_FEATURE(10)..(10)The amino acid at the noted position
is optionally phosphorylated 267Gly Pro Lys Pro Leu Phe Arg Arg Met
Ser Ser Leu Val1 5 1026814PRTHomo sapiensMISC_FEATURE(10)..(10)The
amino acid at the noted position is optionally phosphorylated
268Gly Pro Lys Pro Leu Phe Arg Arg Met Ser Ser Leu Val Gly1 5
1026915PRTHomo sapiensMISC_FEATURE(10)..(10)The amino acid at the
noted position is optionally phosphorylated 269Gly Pro Lys Pro Leu
Phe Arg Arg Met Ser Ser Leu Val Gly Pro1 5 10 1527016PRTHomo
sapiensMISC_FEATURE(10)..(10)The amino acid at the noted position
is optionally phosphorylated 270Gly Pro Lys Pro Leu Phe Arg Arg Met
Ser Ser Leu Val Gly Pro Thr1 5 10 1527117PRTHomo
sapiensMISC_FEATURE(10)..(10)The amino acid at the noted position
is optionally phosphorylated 271Gly Pro Lys Pro Leu Phe Arg Arg Met
Ser Ser Leu Val Gly Pro Thr1 5 10 15Gln27218PRTHomo
sapiensMISC_FEATURE(10)..(10)The amino acid at the noted position
is optionally phosphorylated 272Gly Pro Lys Pro Leu Phe Arg Arg Met
Ser Ser Leu Val Gly Pro Thr1 5 10 15Gln Ser27316PRTHomo
sapiensMISC_FEATURE(2)..(2)The amino acid at the noted position is
optionally phosphorylated 273Ala Ser Pro Thr Ile Glu Ala Gln Gly
Thr Ser Pro Ala His Asp Asn1 5 10 1527417PRTHomo
sapiensMISC_FEATURE(2)..(2)The amino acid at the noted position is
optionally phosphorylated 274Ala Ser Pro Thr Ile Glu Ala Gln Gly
Thr Ser Pro Ala His Asp Asn1 5 10 15Ile27518PRTHomo
sapiensMISC_FEATURE(2)..(2)The amino acid at the noted position is
optionally phosphorylated 275Ala Ser Pro Thr Ile Glu Ala Gln Gly
Thr Ser Pro Ala His Asp Asn1 5 10 15Ile Ala27616PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 276Ser Ser Ser Trp Arg Ile Leu Gly Ser
Lys Gln Ser Glu His Arg Pro1 5 10 1527719PRTHomo
sapiensMISC_FEATURE(1)..(1)The amino acid at the noted position is
optionally phosphorylated 277Ser Pro Pro Phe Pro Val Pro Val Tyr
Thr Arg Gln Ala Pro Lys Gln1 5 10 15Val Ile Lys27818PRTHomo
sapiensMISC_FEATURE(10)..(10)The amino acid at the noted position
is optionally phosphorylated 278Asp Pro Thr Arg Arg Phe Phe Lys Val
Thr Pro Pro Pro Gly Ser Gly1 5 10 15Pro Gln27918PRTHomo
sapiensMISC_FEATURE(2)..(2)The amino acid at the noted position is
optionally phosphorylated 279Arg Ser Pro Glu Asp Glu Tyr Glu Leu
Leu Met Pro His Arg Ile Ser1 5 10 15Ser His28017PRTHomo
sapiensMISC_FEATURE(1)..(1)The amino acid at the noted position is
optionally phosphorylated 280Ser Pro Glu Asp Glu Tyr Glu Leu Leu
Met Pro His Arg Ile Ser Ser1 5 10 15His28117PRTHomo
sapiensMISC_FEATURE(15)..(15)The amino acid at the noted position
is optionally phosphorylated 281Ser Pro Glu Asp Glu Tyr Glu Leu Leu
Met Pro His Arg Ile Ser Ser1 5 10 15His28212PRTHomo
sapiensMISC_FEATURE(9)..(9)The amino acid at the noted position is
optionally phosphorylated 282Glu Leu Leu Met Pro His Arg Ile Ser
Ser His Phe1 5 1028313PRTHomo sapiensMISC_FEATURE(9)..(9)The amino
acid at the noted position is optionally phosphorylated 283Glu Leu
Leu Met Pro His Arg Ile Ser Ser His Phe Leu1 5 1028419PRTHomo
sapiensMISC_FEATURE(12)..(12)The amino acid at the noted position
is optionally phosphorylated 284Thr Pro Asp Pro Ser Lys Phe Phe Ser
Gln Leu Ser Ser Glu His Gly1 5 10 15Gly Asp Val28520PRTHomo
sapiensMISC_FEATURE(1)..(1)The amino acid at the noted position is
optionally phosphorylated 285Thr Pro Asp Pro Ser Lys Phe Phe Ser
Gln Leu Ser Ser Glu His Gly1 5 10 15Gly Asp Val Gln 2028612PRTHomo
sapiensMISC_FEATURE(1)..(1)The amino acid at the noted position is
optionally phosphorylated 286Ser Asp Phe His Ala Glu Arg Ala Ala
Arg Glu Lys1 5 1028718PRTHomo sapiensMISC_FEATURE(1)..(1)The amino
acid at the noted position is optionally phosphorylated 287Ser Pro
Glu Arg Pro Phe Leu Ala Ile Leu Gly Gly Ala Lys Val Ala1 5 10 15Asp
Lys28820PRTHomo sapiensMISC_FEATURE(1)..(1)The amino acid at the
noted position is optionally phosphorylated 288Ser Pro Glu Arg Pro
Phe Leu Ala Ile Leu Gly Gly Ala Lys Val Ala1 5 10 15Asp Lys Ile Gln
2028918PRTHomo sapiensMISC_FEATURE(15)..(15)The amino acid at the
noted position is optionally phosphorylated 289Thr Lys Asp Lys Tyr
Met Ala Ser Arg Gly Gln Lys Ala Lys Ser Met1 5 10 15Glu
Gly29013PRTHomo sapiensMISC_FEATURE(10)..(10)The amino acid at the
noted position is optionally phosphorylated 290Val Pro His His Gly
Phe Glu Asp Trp Ser Gln Ile Arg1 5 1029116PRTHomo
sapiensMISC_FEATURE(6)..(6)The amino acid at the noted position is
optionally phosphorylated 291Lys Ile Glu Lys Ile Tyr Ile Met Lys
Ala Asp Thr Val Ile Val Gly1 5 10 1529215PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 292Ile Glu Lys Ile Tyr Ile Met Lys Ala
Asp Thr Val Ile Val Gly1 5 10 1529310PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 293Glu Glu Ser Ser Asp Asp Gly Lys Lys
Tyr1 5 102948PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at
the noted position is optionally phosphorylated 294Lys Asn Arg Ser
Trp Lys Tyr Asn1 52959PRTHomo sapiensMISC_FEATURE(4)..(4)The amino
acid at the noted position is optionally phosphorylated 295Lys Asn
Arg Ser Trp Lys Tyr Asn Gln1 529614PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 296Lys Asn Arg Ser Trp Lys Tyr Asn Gln
Ser Ile Ser Leu Arg1 5 1029716PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 297Lys Asn Arg Ser Trp Lys Tyr Asn Gln
Ser Ile Ser Leu Arg Arg Pro1 5 10 1529813PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 298Asn Arg Ser Trp Lys Tyr Asn Gln
Ser Ile Ser Leu Arg1 5 1029915PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 299Asn Arg Ser Trp Lys Tyr Asn Gln Ser
Ile Ser Leu Arg Arg Pro1 5 10 1530014PRTHomo
sapiensMISC_FEATURE(2)..(2)The amino acid at the noted position is
optionally phosphorylated 300Arg Ser Trp Lys Tyr Asn Gln Ser Ile
Ser Leu Arg Arg Pro1 5 103019PRTHomo sapiensMISC_FEATURE(6)..(6)The
amino acid at the noted position is optionally phosphorylated
301Arg Ala Lys Ser Pro Ile Ser Leu Lys1 530213PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 302Glu Ser Ser Val Arg Ser Gln Glu Asp
Gln Leu Ser Arg1 5 1030314PRTHomo sapiensMISC_FEATURE(3)..(3)The
amino acid at the noted position is optionally phosphorylated
303Glu Ser Ser Val Arg Ser Gln Glu Asp Gln Leu Ser Arg Arg1 5
1030415PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the
noted position is optionally phosphorylated 304Asp Lys Leu Ser Val
Ile Ala Glu Asp Ser Glu Ser Gly Lys Gln1 5 10 1530516PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 305Asp Lys Leu Ser Val Ile Ala Glu Asp
Ser Glu Ser Gly Lys Gln Asn1 5 10 1530617PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 306Asp Lys Leu Ser Val Ile Ala Glu Asp
Ser Glu Ser Gly Lys Gln Asn1 5 10 15Pro30718PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 307Asp Lys Leu Ser Val Ile Ala Glu Asp
Ser Glu Ser Gly Lys Gln Asn1 5 10 15Pro Gly30820PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 308Asp Lys Leu Ser Val Ile Ala Glu Asp
Ser Glu Ser Gly Lys Gln Asn1 5 10 15Pro Gly Asp Ser 2030915PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 309Lys Leu Ser Val Ile Ala Glu Asp Ser
Glu Ser Gly Lys Gln Asn1 5 10 1531016PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 310Lys Leu Ser Val Ile Ala Glu Asp Ser
Glu Ser Gly Lys Gln Asn Pro1 5 10 1531117PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 311Lys Leu Ser Val Ile Ala Glu Asp Ser
Glu Ser Gly Lys Gln Asn Pro1 5 10 15Gly31221PRTHomo
sapiensMISC_FEATURE(18)..(18)The amino acid at the noted position
is optionally phosphorylated 312Asn Leu Glu Leu Ser Lys Phe Arg Met
Pro Gln Pro Ser Ser Gly Arg1 5 10 15Glu Ser Pro Arg His
2031318PRTHomo sapiensMISC_FEATURE(15)..(15)The amino acid at the
noted position is optionally phosphorylated 313Leu Ser Lys Phe Arg
Met Pro Gln Pro Ser Ser Gly Arg Glu Ser Pro1 5 10 15Arg
His31421PRTHomo sapiensMISC_FEATURE(18)..(18)The amino acid at the
noted position is optionally phosphorylated 314Pro Pro Leu Pro Glu
Asp Ser Ile Lys Val Ile Arg Asn Met Arg Ala1 5 10 15Ala Ser Pro Pro
Ala 2031517PRTHomo sapiensMISC_FEATURE(5)..(5)The amino acid at the
noted position is optionally phosphorylated 315Met Pro Arg Pro Ser
Ile Lys Lys Ala Gln Asn Ser Gln Ala Ala Arg1 5 10 15Gln31620PRTHomo
sapiensMISC_FEATURE(18)..(18)The amino acid at the noted position
is optionally phosphorylatedMISC_FEATURE(19)..(19)The amino acid at
the noted position is optionally phosphorylated 316Thr His Lys Gly
Glu Ile Arg Gly Ala Ser Thr Pro Phe Gln Phe Arg1 5 10 15Ala Ser Ser
Pro 2031719PRTHomo sapiensMISC_FEATURE(17)..(17)The amino acid at
the noted position is optionally
phosphorylatedMISC_FEATURE(18)..(18)The amino acid at the noted
position is optionally phosphorylated 317His Lys Gly Glu Ile Arg
Gly Ala Ser Thr Pro Phe Gln Phe Arg Ala1 5 10 15Ser Ser
Pro31810PRTHomo sapiensMISC_FEATURE(6)..(6)The amino acid at the
noted position is optionally phosphorylated 318Ser Thr Ile Gln Asn
Ser Pro Thr Lys Lys1 5 1031910PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 319Arg Ser Tyr Ser Pro Asp His Arg Gln
Lys1 5 1032013PRTHomo sapiensMISC_FEATURE(9)..(9)The amino acid at
the noted position is optionally phosphorylated 320Phe Asp Lys His
Thr Leu Gly Asp Ser Asp Asn Glu Ser1 5 1032121PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylatedMISC_FEATURE(8)..(8)The amino acid at the
noted position is optionally phosphorylated 321Glu Pro Ala Ser Pro
Ala Ala Ser Ile Ser Arg Leu Ser Gly Glu Gln1 5 10 15Val Asp Gly Lys
Gly 2032218PRTHomo sapiensMISC_FEATURE(10)..(10)The amino acid at
the noted position is optionally phosphorylated 322Ser Pro Ala Ala
Ser Ile Ser Arg Leu Ser Gly Glu Gln Val Asp Gly1 5 10 15Lys
Gly32315PRTHomo sapiensMISC_FEATURE(7)..(7)The amino acid at the
noted position is optionally phosphorylated 323Ala Ser Ile Ser Arg
Leu Ser Gly Glu Gln Val Asp Gly Lys Gly1 5 10 1532415PRTHomo
sapiensMISC_FEATURE(2)..(2)The amino acid at the noted position is
optionally phosphorylatedMISC_FEATURE(7)..(7)The amino acid at the
noted position is optionally phosphorylated 324Ala Ser Ile Ser Arg
Leu Ser Gly Glu Gln Val Asp Gly Lys Gly1 5 10 1532515PRTHomo
sapiensMISC_FEATURE(2)..(2)The amino acid at the noted position is
optionally phosphorylated 325Ala Ser Ile Ser Arg Leu Ser Gly Glu
Gln Val Asp Gly Lys Gly1 5 10 1532613PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 326Thr Thr Lys Ser Val Lys Ala Leu Ser
Ser Leu His Gly1 5 1032715PRTHomo sapiensMISC_FEATURE(4)..(4)The
amino acid at the noted position is optionally phosphorylated
327Thr Thr Lys Ser Val Lys Ala Leu Ser Ser Leu His Gly Asp Asp1 5
10 1532816PRTHomo sapiensMISC_FEATURE(4)..(4)The amino acid at the
noted position is optionally phosphorylated 328Thr Thr Lys Ser Val
Lys Ala Leu Ser Ser Leu His Gly Asp Asp Gln1 5 10 1532917PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 329Thr Thr Lys Ser Val Lys Ala Leu Ser
Ser Leu His Gly Asp Asp Gln1 5 10 15Asp33018PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylated 330Thr Thr Lys Ser Val Lys Ala Leu Ser
Ser Leu His Gly Asp Asp Gln1 5 10 15Asp Ser33114PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 331Thr Lys Ser Val Lys Ala Leu Ser Ser
Leu His Gly Asp Asp1 5 1033215PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 332Thr Lys Ser Val Lys Ala Leu Ser Ser
Leu His Gly Asp Asp Gln1 5 10 1533316PRTHomo
sapiensMISC_FEATURE(3)..(3)The amino acid at the noted position is
optionally phosphorylated 333Thr Lys Ser Val Lys Ala Leu Ser Ser
Leu His Gly Asp Asp Gln Asp1 5 10 1533414PRTHomo
sapiensMISC_FEATURE(2)..(2)The amino acid at the noted position is
optionally phosphorylated 334Lys Ser Val Lys Ala Leu Ser Ser Leu
His Gly Asp Asp Gln1 5 1033515PRTHomo
sapiensMISC_FEATURE(2)..(2)The amino acid at the noted position is
optionally phosphorylated 335Lys Ser Val Lys Ala Leu Ser Ser Leu
His Gly Asp Asp Gln Asp1 5 10 1533620PRTHomo
sapiensMISC_FEATURE(18)..(18)The amino acid at the noted position
is optionally phosphorylated 336Thr Thr Lys Ser Val Lys Ala Leu Ser
Ser Leu His Gly Asp Asp Gln1 5 10 15Asp Ser Glu Asp 2033721PRTHomo
sapiensMISC_FEATURE(18)..(18)The amino acid at the noted position
is optionally phosphorylated 337Thr Thr Lys Ser Val Lys Ala Leu Ser
Ser Leu His Gly Asp Asp Gln1 5 10 15Asp Ser Glu Asp Glu
2033819PRTHomo sapiensMISC_FEATURE(16)..(16)The amino acid at the
noted position is optionally phosphorylated 338Lys Ser Val Lys Ala
Leu Ser Ser Leu His Gly Asp Asp Gln Asp Ser1 5 10 15Glu Asp
Glu33913PRTHomo sapiensMISC_FEATURE(9)..(9)The amino acid at the
noted position is optionally phosphorylated 339Lys Leu Val Ser Phe
His Asp Asp Ser Asp Glu Asp Leu1 5 1034012PRTHomo
sapiensMISC_FEATURE(10)..(10)The amino acid at the noted position
is optionally phosphorylated 340Ala Pro Ser Thr Tyr Ala His Leu Ser
Pro Ala Lys1 5 1034117PRTHomo sapiensMISC_FEATURE(9)..(9)The amino
acid at the noted position is optionally phosphorylated 341Ala Pro
Ser Thr Tyr Ala His Leu Ser Pro Ala Lys Thr Pro Pro Pro1 5 10
15Pro34213PRTHomo sapiensMISC_FEATURE(8)..(8)The amino acid at the
noted position is optionally phosphorylated 342Asn Arg Ala Met Arg
Arg Val Ser Ser Val Pro Ser Arg1 5 1034315PRTHomo
sapiensMISC_FEATURE(8)..(8)The amino acid at the noted position is
optionally phosphorylated 343Asn Arg Ala Met Arg Arg Val Ser Ser
Val Pro Ser Arg Ala Gln1 5 10 1534419PRTHomo
sapiensMISC_FEATURE(4)..(4)The amino acid at the noted position is
optionally phosphorylatedMISC_FEATURE(6)..(6)The amino acid at the
noted position is optionally phosphorylated 344Arg Pro Ala Ser Pro
Thr Ala Ile Arg Arg Ile Gly Ser Val Thr Ser1 5 10 15Arg Gln
Thr34519PRTHomo sapiensMISC_FEATURE(1)..(1)The amino acid at the
noted position is optionally phosphorylated 345Ser Gly Gly Asp Asp
Asp Trp Thr His Leu Ser Ser Lys Glu Val Asp1 5 10 15Pro Ser
Thr34620PRTHomo sapiensMISC_FEATURE(1)..(1)The amino acid at the
noted position is optionally phosphorylated 346Ser Gly Gly Asp Asp
Asp Trp Thr His Leu Ser Ser Lys Glu Val Asp1 5 10 15Pro Ser Thr Gly
2034721PRTHomo sapiensMISC_FEATURE(1)..(1)The amino acid at the
noted position is optionally phosphorylated 347Ser Gly Gly Asp Asp
Asp Trp Thr His Leu Ser Ser Lys Glu Val Asp1 5 10 15Pro Ser Thr Gly
Glu 2034822PRTHomo sapiensMISC_FEATURE(1)..(1)The amino acid at the
noted position is optionally phosphorylated 348Ser Gly Gly Asp Asp
Asp Trp Thr His Leu Ser Ser Lys Glu Val Asp1 5 10 15Pro Ser Thr Gly
Glu Leu 2034923PRTHomo sapiensMISC_FEATURE(1)..(1)The amino acid at
the noted position is optionally phosphorylated 349Ser Gly Gly Asp
Asp Asp Trp Thr His Leu Ser Ser Lys Glu Val Asp1 5 10 15Pro Ser Thr
Gly Glu Leu Gln 2035017PRTHomo sapiensMISC_FEATURE(10)..(10)The
amino acid at the noted position is optionally phosphorylated
350Gly Gly Asp Asp Asp Trp Thr His Leu Ser Ser Lys Glu Val Asp Pro1
5 10 15Ser35119PRTHomo sapiensMISC_FEATURE(10)..(10)The amino acid
at the noted position is optionally phosphorylated 351Gly Gly Asp
Asp Asp Trp Thr His Leu Ser Ser Lys Glu Val Asp Pro1 5 10 15Ser Thr
Gly35214PRTHomo sapiensMISC_FEATURE(9)..(9)The amino acid at the
noted position is optionally phosphorylated 352Gly Asp Asp Asp Trp
Thr His Leu Ser Ser Lys Glu Val Asp1 5 1035315PRTHomo
sapiensMISC_FEATURE(9)..(9)The amino acid at the noted position is
optionally phosphorylated 353Gly Asp Asp Asp Trp Thr His Leu Ser
Ser Lys Glu Val Asp Pro1 5 10 1535416PRTHomo
sapiensMISC_FEATURE(9)..(9)The amino acid at the noted position is
optionally phosphorylated 354Gly Asp Asp Asp Trp Thr His Leu Ser
Ser Lys Glu Val Asp Pro Ser1 5 10 1535518PRTHomo
sapiensMISC_FEATURE(9)..(9)The amino acid at the noted position is
optionally phosphorylated 355Gly Asp Asp Asp Trp Thr His Leu Ser
Ser Lys Glu Val Asp Pro Ser1 5 10 15Thr Gly35615PRTHomo
sapiensMISC_FEATURE(8)..(8)The amino acid at the noted position is
optionally phosphorylated 356Asp Asp Asp Trp Thr His Leu Ser Ser
Lys Glu Val Asp Pro Ser1 5 10 1535717PRTHomo
sapiensMISC_FEATURE(8)..(8)The amino acid at the noted position is
optionally phosphorylated 357Asp Asp Asp Trp Thr His Leu Ser Ser
Lys Glu Val Asp Pro Ser Thr1 5 10 15Gly35814PRTHomo
sapiensMISC_FEATURE(7)..(7)The amino acid at the noted position is
optionally phosphorylated 358Asp Asp Trp Thr His Leu Ser Ser Lys
Glu Val Asp Pro Ser1 5 1035913PRTHomo
sapiensMISC_FEATURE(6)..(6)The amino acid at the noted position is
optionally phosphorylated 359Asp Trp Thr His Leu Ser Ser Lys Glu
Val Asp Pro Ser1 5 1036015PRTHomo sapiensMISC_FEATURE(6)..(6)The
amino acid at the noted position is optionally phosphorylated
360Asp Trp Thr His Leu Ser Ser Lys Glu Val Asp Pro Ser Thr Gly1 5
10 1536112PRTHomo sapiensMISC_FEATURE(5)..(5)The amino acid at the
noted position is optionally phosphorylated 361Trp Thr His Leu Ser
Ser Lys Glu Val Asp Pro Ser1 5 1036214PRTHomo
sapiensMISC_FEATURE(5)..(5)The amino acid at the noted position is
optionally phosphorylated 362Trp Thr His Leu Ser Ser Lys Glu Val
Asp Pro Ser Thr Gly1 5 1036313PRTHomo
sapiensMISC_FEATURE(2)..(2)The amino acid at the noted position is
optionally phosphorylated 363Gly Thr Leu Arg Arg Ser Asp Ser Gln
Gln Ala Val Lys1 5 1036414PRTHomo sapiensMISC_FEATURE(2)..(2)The
amino acid at the noted position is optionally phosphorylated
364Gly Thr Leu Arg Arg Ser Asp Ser Gln Gln Ala Val Lys Ser1 5
1036516PRTHomo sapiensMISC_FEATURE(2)..(2)The amino acid at the
noted position is optionally phosphorylated 365Gly Thr Leu Arg Arg
Ser Asp Ser Gln Gln Ala Val Lys Ser Pro Pro1 5 10 1536612PRTHomo
sapiensMISC_FEATURE(7)..(7)The amino acid at the noted position is
optionally phosphorylatedMISC_FEATURE(8)..(8)The amino acid at the
noted position is optionally phosphorylated 366Val Leu Lys Ser Arg
Lys Ser Ser Val Thr Glu Glu1 5 1036712PRTArtificial
SequenceArtificially synthesized peptideMISC_FEATURE(3)..(3)Xaa can
be any naturally occurring amino acid 367Ala Lys Xaa Val Ala Ala
Trp Thr Leu Lys Ala Ala1 5 1036815PRTClostridium tetani 368Gln Tyr
Ile Lys Ala Asn Ser Lys Phe Ile Gly Ile Thr Glu Leu1 5 10 15
* * * * *