U.S. patent application number 15/198608 was filed with the patent office on 2017-02-09 for novel peptides and combination of peptides for use in immunotherapy against ovarian cancer and other cancers.
The applicant listed for this patent is immatics biotechnologies GmbH. Invention is credited to Jens FRITSCHE, Helen HOERZER, Andrea MAHR, Oliver SCHOOR, Harpreet SINGH, Toni WEINSCHENK.
Application Number | 20170037111 15/198608 |
Document ID | / |
Family ID | 53872514 |
Filed Date | 2017-02-09 |
United States Patent
Application |
20170037111 |
Kind Code |
A1 |
MAHR; Andrea ; et
al. |
February 9, 2017 |
Novel peptides and combination of peptides for use in immunotherapy
against ovarian cancer and other cancers
Abstract
The present invention relates to peptides, proteins, nucleic
acids and cells for use in immunotherapeutic methods. In
particular, the present invention relates to the immunotherapy of
cancer. The present invention furthermore relates to
tumor-associated T-cell peptide epitopes, alone or in combination
with other tumor-associated peptides that can for example serve as
active pharmaceutical ingredients of vaccine compositions that
stimulate anti-tumor immune responses, or to stimulate T cells ex
vivo and transfer into patients. Peptides bound to molecules of the
major histocompatibility complex (MHC), or peptides as such, can
also be targets of antibodies, soluble T-cell receptors, and other
binding molecules.
Inventors: |
MAHR; Andrea; (Tuebingen,
DE) ; WEINSCHENK; Toni; (Aichwald, DE) ;
HOERZER; Helen; (Tuebingen, DE) ; SCHOOR; Oliver;
(Tuebingen, DE) ; FRITSCHE; Jens; (Dusslingen,
DE) ; SINGH; Harpreet; (Muenchen, DE) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
immatics biotechnologies GmbH |
Tuebingen |
|
DE |
|
|
Family ID: |
53872514 |
Appl. No.: |
15/198608 |
Filed: |
June 30, 2016 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
62187507 |
Jul 1, 2015 |
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12N 2310/16 20130101;
A61K 38/00 20130101; C07K 16/3046 20130101; C07K 7/06 20130101;
C07K 14/4705 20130101; C12N 15/115 20130101; C07K 14/705 20130101;
C07K 16/18 20130101; G01N 33/56977 20130101; G01N 33/57492
20130101; C07K 16/30 20130101; A61K 35/17 20130101; C07K 14/70539
20130101; C12N 5/0636 20130101; C07K 16/3038 20130101; C12Q 1/6886
20130101; G01N 2333/70539 20130101; C07K 2317/31 20130101; C07K
14/4748 20130101; C07K 16/3069 20130101; C07K 16/28 20130101; C07K
16/3015 20130101; C07K 16/303 20130101; C07K 2319/00 20130101; C07K
14/4738 20130101; C07K 14/82 20130101; C07K 16/32 20130101; C07K
7/08 20130101; C07K 2317/24 20130101; C12N 2501/998 20130101; C12Q
1/6881 20130101; C12P 21/02 20130101; C07K 2319/40 20130101; A61K
2035/124 20130101; A61P 37/04 20180101; C07K 2317/34 20130101; C12Q
2600/158 20130101; A61K 2039/5158 20130101; A61P 35/02 20180101;
G01N 33/57449 20130101; C07K 16/3053 20130101; C12N 2320/30
20130101; C07K 16/2833 20130101; A61K 39/0011 20130101; A61P 35/00
20180101; A61K 39/00 20130101; C07K 16/3023 20130101; C12N 2501/50
20130101 |
International
Class: |
C07K 14/82 20060101
C07K014/82; A61K 35/17 20060101 A61K035/17; C07K 16/32 20060101
C07K016/32; G01N 33/574 20060101 G01N033/574; C12N 15/115 20060101
C12N015/115; C12P 21/02 20060101 C12P021/02; C12N 5/0783 20060101
C12N005/0783; C12Q 1/68 20060101 C12Q001/68; C07K 7/06 20060101
C07K007/06; C07K 14/725 20060101 C07K014/725 |
Foreign Application Data
Date |
Code |
Application Number |
Jul 1, 2015 |
GB |
1511546.2 |
Claims
1. A peptide comprising an amino acid sequence comprising SEQ ID
No. 11, and variant sequences thereof which are at least 88%
homologous to SEQ ID No. 11, wherein said variant binds to
molecule(s) of the major histocompatibility complex (MHC) and/or
induces T cells cross-reacting with said variant peptide; and a
pharmaceutical acceptable salt thereof, wherein said peptide is not
a full-length polypeptide.
2. The peptide or variant according to claim 1, wherein said
peptide has the ability to bind to a MHC class-I or -II molecule,
and wherein said peptide, when bound to said MHC, is capable of
being recognized by CD4 and/or CD8 T cells.
3. The peptide or variant thereof according to claim 1, wherein the
amino acid sequence thereof comprises a continuous stretch of amino
acids according to the group of SEQ ID No. 11.
4. The peptide or variant thereof according to claim 1, wherein
said peptide or variant thereof has an overall length of from 8 to
100, optionally from 8 to 30, and optionally from 8 to 16 amino
acids, and optionally wherein the peptide consists or consists
essentially of an amino acid of SEQ ID No. 11.
5. The peptide or variant thereof according to claim 1, wherein
said peptide is part of a fusion protein, optionally comprising
N-terminal amino acids of the HLA-DR antigen-associated invariant
chain (Ii).
6. A nucleic acid, encoding a peptide or variant thereof according
to claim 1, optionally linked to a heterologous promoter
sequence.
7. An expression vector capable of expressing the nucleic acid
according to claim 6.
8. The peptide or variant thereof according to claim 1, a nucleic
acid encoding said peptide or variant or an expression vector
capable of expressing said nucleic acid, or a host cell comprising
said peptide or variant, capable of being used in medicine.
9. A method for producing the peptide or variant thereof according
to claim 1, the method comprising culturing a host cell that
presents the peptide or variant, or expresses a nucleic acid
encoding said peptide or variant or comprises an expression vector
capable of expressing said nucleic acid, and isolating the peptide
or variant thereof from the host cell or its culture medium.
10. An in vitro method for producing activated T lymphocytes, the
method comprising contacting in vitro T cells with antigen loaded
human class I or II MHC molecules expressed on the surface of a
suitable antigen-presenting cell or an artificial construct
mimicking an antigen-presenting cell for a period of time
sufficient to activate said T cells in an antigen specific manner,
wherein said antigen is a peptide according to claim 1.
11. An activated T cell, optionally an activated T lymphocyte,
produced by the method according to claim 10, that selectively
recognizes a cell which presents a polypeptide comprising an amino
acid sequence of SEQ ID No. 11, and variant sequences thereof which
are at least 88% homologous to SEQ ID No. 11.
12. A method for killing target cells in a patient which target
cells present a polypeptide comprising an amino acid sequence of
SEQ ID No. 11, and variant sequences thereof which are at least 88%
homologous to SEQ ID No. 11, the method comprising administering to
the patient an effective number of activated T cells as defined in
claim 11.
13. An antibody, optionally a soluble or membrane-bound antibody,
that specifically recognizes the peptide or variant thereof
according to claim 1, optionally the peptide or variant are bound
to an MHC molecule, and wherein said antibody optionally carries a
further effector function, optionally an immune stimulating domain
or toxin, wherein said antibody is optionally a polyclonal
antibody, monoclonal antibody, bi-specific antibody and/or a
chimeric antibody.
14. A method for the treatment of cancer and/or or in the
manufacture of a medicament against cancer, or in a diagnostic
method for detection of cancerous cells, said method comprising
utilizing a peptide or variant according to claim 1, a nucleic acid
encoding said peptide or variant or an expression vector capable of
expressing said nucleic acid, or a host cell comprising said
peptide or variant, an activated T lymphocyte that selectively
recognizes a cell which presents said peptide or variant or the
antibody optionally a soluble or membrane-bound antibody, that
specifically recognizes the peptide or variant.
15. The method of claim 14, wherein said cancer is selected from
the group consisting of ovarian cancer, non-small cell lung cancer,
small cell lung cancer, kidney cancer, brain cancer, colon or
rectum cancer, stomach cancer, liver cancer, pancreatic cancer,
prostate cancer, leukemia, breast cancer, Merkel cell carcinoma,
melanoma, esophageal cancer, urinary bladder cancer, uterine
cancer, gallbladder cancer, bile duct cancer and other tumors that
show an overexpression of a protein from which a peptide SEQ ID No.
11 is derived from.
16. A kit comprising: (a) a container comprising a pharmaceutical
composition containing the peptide(s) or the variant according to
claim 1, a nucleic acid encoding said peptide or variant or an
expression vector capable of expressing said nucleic acid, or a
host cell comprising said peptide or variant, an activated T
lymphocyte that selectively recognizes a cell which presents said
peptide or variant or the antibody optionally a soluble or
membrane-bound antibody, that specifically recognizes the peptide
or variant, in solution or in lyophilized form; (b) optionally, a
second container containing a diluent or reconstituting solution
for the lyophilized formulation; (c) optionally, at least one more
peptide of SEQ ID No. 11 or variant, and (d) optionally,
instructions for (i) use of the solution or (ii) reconstitution
and/or use of the lyophilized formulation.
17. A T-cell receptor, optionally soluble or membrane-bound, that
is reactive with an HLA ligand, wherein said ligand has at least
88% identity to an amino acid sequence of SEQ ID No. 11.
18. A pharmaceutical composition comprising at least one active
ingredient selected from the group consisting of a) a peptide of
SEQ ID No. 11 or variant thereof; b) a T-cell receptor reactive
with a peptide and/or the peptide-MHC complex according to a); c) a
fusion protein comprising a peptide according to a), and the
N-terminal amino acids 1 to 80 of the HLA-DR antigen-associated
invariant chain (Ii), d) a nucleic acid encoding for any of a) to
c) or an expression vector comprising said nucleic acid, e) a host
cell comprising the expression vector of d, f) an activated
T-lymphocyte, obtained by a method comprising contacting in vitro T
cells with a peptide according to a) expressed on the surface of a
suitable antigen presenting cell for a period of time sufficient to
activate said T cell in an antigen specific manner, as well as a
method to transfer these activated T cells into the autologous or
other patients; g) an antibody, or soluble T-cell receptor,
reactive to a peptide and/or the peptide--MHC complex according to
a) and/or a cell presenting a peptide according to a), and
potentially modified by fusion with for example immune-activating
domains or toxins, h) an aptamer recognizing a peptide of SEQ ID
11, and/or a complex of a peptide of SEQ ID No. 11 with a MHC
molecule, i) a conjugated or labelled peptide or scaffold according
to any of a) to h) and a pharmaceutically acceptable carrier, and
optionally, pharmaceutically acceptable excipients and/or
stabilizers.
19. An aptamer that specifically recognizes the peptide or variant
thereof according to claim 1, optionally the peptide or variant
thereof being bound to an MHC molecule.
20. A method of claim 15, wherein said cancer is ovarian cancer.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional
Application Ser. No. 62/187,507, filed 1 Jul. 2015, and Great
Britain Application No. 1511546.2, filed 1 Jul. 2015, the content
of each of these applications is herein incorporated by reference
in their entirety.
[0002] This application is also related to PCT/EP2016/065166 filed
29 Jun. 2016, the content of which in incorporated herein by
reference in its entirety.
REFERENCE TO SEQUENCE LISTING SUBMITTED AS A COMPLIANT ASCII TEXT
FILE (.TXT)
[0003] Pursuant to the EFS-Web legal framework and 37 CFR
.sctn..sctn.1.821-825 (see MPEP .sctn.2442.03(a)), a Sequence
Listing in the form of an ASCII-compliant text file (entitled
"2912919-050004_ST25" created on 28 Jun. 2016, and 105,449 bytes in
size) is submitted concurrently with the instant application, and
the entire contents of the Sequence Listing are incorporated herein
by reference.
FIELD
[0004] The present invention relates to peptides, proteins, nucleic
acids and cells for use in immunotherapeutic methods. In
particular, the present invention relates to the immunotherapy of
cancer. The present invention furthermore relates to
tumor-associated T-cell peptide epitopes, alone or in combination
with other tumor-associated peptides that can for example serve as
active pharmaceutical ingredients of vaccine compositions that
stimulate anti-tumor immune responses, or to stimulate T cells ex
vivo and transfer into patients. Peptides bound to molecules of the
major histocompatibility complex (MHC), or peptides as such, can
also be targets of antibodies, soluble T-cell receptors, and other
binding molecules.
[0005] The present invention relates to several novel peptide
sequences and their variants derived from HLA class I molecules of
human tumor cells that can be used in vaccine compositions for
eliciting anti-tumor immune responses, or as targets for the
development of pharmaceutically/immunologically active compounds
and cells.
BACKGROUND OF THE INVENTION
Ovarian Cancer
[0006] With an estimated 239 000 new cases in 2012, ovarian cancer
is the seventh most common cancer in women, representing 4% of all
cancers in women. The fatality rate of ovarian cancer tends to be
rather high relative to other cancers of the female reproductive
organs, and case fatality is higher in lower-resource settings. As
a consequence, ovarian cancer is the eighth most frequent cause of
cancer death among women, with 152 000 deaths. In 2012, almost 55%
of all new cases occurred in countries with high or very high
levels of human development; 37% of the new cases and 39% of the
deaths occurred in Europe and North America. Incidence rates are
highest in northern and eastern Europe, North America, and Oceania,
and tend to be relatively low in Africa and much of Asia. Incidence
rates have been declining in certain countries with very high
levels of human development, notably in Europe and North
America.
[0007] The most common ovarian cancers are ovarian carcinomas,
which are also the most lethal gynecological malignancies. Based on
histopathology and molecular genetics, ovarian carcinomas are
divided into five main types: high-grade serous (70%), endometrioid
(10%), clear cell (10%), mucinous (3%), and low-grade serous
carcinomas (<5%), which together account for more than 95% of
cases. Much less common are malignant germ cell tumours
(dysgerminomas, yolk sac tumours, and immature teratomas) (3% of
ovarian cancers) and potentially malignant sex cord stromal tumours
(1-2%), the most common of which are granulosa cell tumours.
[0008] Family history of ovarian cancer accounts for 10% of cases;
the risk is increased 3-fold when two or more first-degree
relatives have been affected. Women with germline mutations in
BRCA1 or BRCA2 have a 30-70% risk of developing ovarian cancer,
mainly high-grade serous carcinomas, by age 70 (Risch et al.,
2006).
[0009] Surgical resection is the primary therapy in early as well
as advanced stage ovarian carcinoma. Surgical removal is followed
by systemic chemotherapy with platinum analogs, except for very low
grade ovarian cancers (stage IA, grade 1), where post-operative
chemotherapy is not indicated. In advanced stage ovarian cancer,
the first line chemotherapy comprises a combination of carboplatin
with paclitaxel, which can be supplemented with bevacizumab. The
standard treatment for platinum-resistant ovarian cancers consists
of a monotherapy with one of the following chemotherapeutics:
pegylated liposomal doxorubicin, topotecane, gemcitabine or
paclitaxel (S3-Leitlinie maligne Ovarialtumore, 2013).
[0010] Immunotherapy appears to be a promising strategy to
ameliorate the treatment of ovarian cancer patients, as the
presence of pro-inflammatory tumor infiltrating lymphocytes,
especially CD8-positive T cells, correlates with good prognosis and
T cells specific for tumor-associated antigens can be isolated from
cancer tissue.
[0011] Therefore, a lot of scientific effort is put into the
investigation of different immunotherapies in ovarian cancer. A
considerable number of pre-clinical and clinical studies has
already been performed and further studies are currently ongoing.
Clinical data are available for cytokine therapy, vaccination,
monoclonal antibody treatment, adoptive cell transfer and
immunomodulation.
[0012] Cytokine therapy with interleukin-2, interferon-alpha,
interferon-gamma or granulocyte-macrophage colony stimulating
factor aims at boosting the patient's own anti-tumor immune
response and these treatments have already shown promising results
in small study cohorts.
[0013] Phase I and II vaccination studies, using single or multiple
peptides, derived from several tumor-associated proteins (Her2/neu,
NY-ESO-1, p53, Wilms tumor-1) or whole tumor antigens, derived from
autologous tumor cells revealed good safety and tolerability
profiles, but only low to moderate clinical effects.
[0014] Monoclonal antibodies that specifically recognize
tumor-associated proteins are thought to enhance immune
cell-mediated killing of tumor cells. The anti-CA-125 antibodies
oregovomab and abagovomab as well as the anti-EpCAM antibody
catumaxomab achieved promising results in phase II and III studies.
In contrast, the anti-MUC1 antibody HMFG1 failed to clearly enhance
survival in a phase III study.
[0015] An alternative approach uses monoclonal antibodies to target
and block growth factor and survival receptors on tumor cells.
While administration of trastuzumab (anti-HER2/neu antibody) and
MOv18 and MORAb-003 (anti-folate receptor alpha antibodies) only
conferred limited clinical benefit to ovarian cancer patients,
addition of bevacizumab (anti-VEGF antibody) to the standard
chemotherapy in advanced ovarian cancer appears to be
advantageous.
[0016] Adoptive transfer of immune cells achieved heterogeneous
results in clinical trials. Adoptive transfer of autologous, in
vitro expanded tumor infiltrating T cells was shown to be a
promising approach in a pilot trial. In contrast, transfer of T
cells harboring a chimeric antigen receptor specific for folate
receptor alpha did not induce a significant clinical response in a
phase I trial. Dendritic cells pulsed with tumor cell lysate or
tumor-associated proteins in vitro were shown to enhance the
anti-tumor T cell response upon transfer, but the extent of T cell
activation did not correlate with clinical effects. Transfer of
natural killer cells caused significant toxicities in a phase II
study.
[0017] Intrinsic anti-tumor immunity as well as immunotherapy are
hampered by an immunosuppressive tumor microenvironment. To
overcome this obstacle immunomodulatory drugs, like
cyclophosphamide, anti-CD25 antibodies and pegylated liposomal
doxorubicin are tested in combination with immunotherapy. Most
reliable data are currently available for ipilimumab, an anti-CTLA4
antibody, which enhances T cell activity. Ipilimumab was shown to
exert significant anti-tumor effects in ovarian cancer patients
(Mantia-Smaldone et al., 2012).
[0018] Considering the severe side-effects and expense associated
with treating cancer, there is a need to identify factors that can
be used in the treatment of cancer in general and ovarian cancer in
particular. There is also a need to identify factors representing
biomarkers for cancer in general and ovarian cancer in particular,
leading to better diagnosis of cancer, assessment of prognosis, and
prediction of treatment success.
[0019] Immunotherapy of cancer represents an option of specific
targeting of cancer cells while minimizing side effects. Cancer
immunotherapy makes use of the existence of tumor associated
antigens.
[0020] The current classification of tumor associated antigens
(TAAs) comprises the following major groups:
a) Cancer-testis antigens: The first TAAs ever identified that can
be recognized by T cells belong to this class, which was originally
called cancer-testis (CT) antigens because of the expression of its
members in histologically different human tumors and, among normal
tissues, only in spermatocytes/spermatogonia of testis and,
occasionally, in placenta. Since the cells of testis do not express
class I and II HLA molecules, these antigens cannot be recognized
by T cells in normal tissues and can therefore be considered as
immunologically tumor-specific. Well-known examples for CT antigens
are the MAGE family members and NY-ESO-1. b) Differentiation
antigens: These TAAs are shared between tumors and the normal
tissue from which the tumor arose. Most of the known
differentiation antigens are found in melanomas and normal
melanocytes. Many of these melanocyte lineage-related proteins are
involved in biosynthesis of melanin and are therefore not tumor
specific but nevertheless are widely used for cancer immunotherapy.
Examples include, but are not limited to, tyrosinase and
Melan-A/MART-1 for melanoma or PSA for prostate cancer. c)
Over-expressed TAAs: Genes encoding widely expressed TAAs have been
detected in histologically different types of tumors as well as in
many normal tissues, generally with lower expression levels. It is
possible that many of the epitopes processed and potentially
presented by normal tissues are below the threshold level for
T-cell recognition, while their over-expression in tumor cells can
trigger an anticancer response by breaking previously established
tolerance. Prominent examples for this class of TAAs are Her-2/neu,
survivin, telomerase, or WT1. d) Tumor-specific antigens: These
unique TAAs arise from mutations of normal genes (such as
.beta.-catenin, CDK4, etc.). Some of these molecular changes are
associated with neoplastic transformation and/or progression.
Tumor-specific antigens are generally able to induce strong immune
responses without bearing the risk for autoimmune reactions against
normal tissues. On the other hand, these TAAs are in most cases
only relevant to the exact tumor on which they were identified and
are usually not shared between many individual tumors.
Tumor-specificity (or -association) of a peptide may also arise if
the peptide originates from a tumor- (-associated) exon in case of
proteins with tumor-specific (-associated) isoforms. e) TAAs
arising from abnormal post-translational modifications: Such TAAs
may arise from proteins which are neither specific nor
overexpressed in tumors but nevertheless become tumor associated by
posttranslational processes primarily active in tumors. Examples
for this class arise from altered glycosylation patterns leading to
novel epitopes in tumors as for MUC1 or events like protein
splicing during degradation which may or may not be tumor specific.
f) Oncoviral proteins: These TAAs are viral proteins that may play
a critical role in the oncogenic process and, because they are
foreign (not of human origin), they can evoke a T-cell response.
Examples of such proteins are the human papilloma type 16 virus
proteins, E6 and E7, which are expressed in cervical carcinoma.
[0021] T-cell based immunotherapy targets peptide epitopes derived
from tumor-associated or tumor-specific proteins, which are
presented by molecules of the major histocompatibility complex
(MHC). The antigens that are recognized by the tumor specific T
lymphocytes, that is, the epitopes thereof, can be molecules
derived from all protein classes, such as enzymes, receptors,
transcription factors, etc. which are expressed and, as compared to
unaltered cells of the same origin, usually up-regulated in cells
of the respective tumor.
[0022] There are two classes of MHC-molecules, MHC class I and MHC
class II. MHC class I molecules are composed of an alpha heavy
chain and beta-2-microglobulin, MHC class II molecules of an alpha
and a beta chain. Their three-dimensional conformation results in a
binding groove, which is used for non-covalent interaction with
peptides.
[0023] MHC class I molecules can be found on most nucleated cells.
They present peptides that result from proteolytic cleavage of
predominantly endogenous proteins, defective ribosomal products
(DRIPs) and larger peptides. However, peptides derived from
endosomal compartments or exogenous sources are also frequently
found on MHC class I molecules. This non-classical way of class I
presentation is referred to as cross-presentation in the literature
(Brossart and Bevan, 1997; Rock et al., 1990). MHC class II
molecules can be found predominantly on professional antigen
presenting cells (APCs), and primarily present peptides of
exogenous or transmembrane proteins that are taken up by APCs e.g.
during endocytosis, and are subsequently processed.
[0024] Complexes of peptide and MHC class I are recognized by
CD8-positive T cells bearing the appropriate T-cell receptor (TCR),
whereas complexes of peptide and MHC class II molecules are
recognized by CD4-positive-helper-T cells bearing the appropriate
TCR. It is well known that the TCR, the peptide and the MHC are
thereby present in a stoichiometric amount of 1:1:1.
[0025] CD4-positive helper T cells play an important role in
inducing and sustaining effective responses by CD8-positive
cytotoxic T cells. The identification of CD4-positive T-cell
epitopes derived from tumor associated antigens (TAA) is of great
importance for the development of pharmaceutical products for
triggering anti-tumor immune responses (Gnjatic et al., 2003). At
the tumor site, T helper cells, support a cytotoxic T cell- (CTL-)
friendly cytokine milieu (Mortara et al., 2006) and attract
effector cells, e.g. CTLs, natural killer (NK) cells, macrophages,
and granulocytes (Hwang et al., 2007).
[0026] In the absence of inflammation, expression of MHC class II
molecules is mainly restricted to cells of the immune system,
especially professional antigen-presenting cells (APC), e.g.,
monocytes, monocyte-derived cells, macrophages, dendritic cells. In
cancer patients, cells of the tumor have been found to express MHC
class II molecules (Dengjel et al., 2006).
[0027] Elongated (longer) peptides of the invention can act as MHC
class II active epitopes. T-helper cells, activated by MHC class II
epitopes, play an important role in orchestrating the effector
function of CTLs in anti-tumor immunity. T-helper cell epitopes
that trigger a T-helper cell response of the TH1 type support
effector functions of CD8-positive killer T cells, which include
cytotoxic functions directed against tumor cells displaying
tumor-associated peptide/MHC complexes on their cell surfaces. In
this way tumor-associated T-helper cell peptide epitopes, alone or
in combination with other tumor-associated peptides, can serve as
active pharmaceutical ingredients of vaccine compositions that
stimulate anti-tumor immune responses.
[0028] It was shown in mammalian animal models, e.g., mice, that
even in the absence of CD8-positive T lymphocytes, CD4-positive T
cells are sufficient for inhibiting manifestation of tumors via
inhibition of angiogenesis by secretion of interferon-gamma
(IFN.gamma.) (Beatty and Paterson, 2001; Mumberg et al., 1999).
There is evidence for CD4 T cells as direct anti-tumor effectors
(Braumuller et al., 2013; Tran et al., 2014).
[0029] Since the constitutive expression of HLA class II molecules
is usually limited to immune cells, the possibility of isolating
class II peptides directly from primary tumors was previously not
considered possible. However, Dengjel et al. were successful in
identifying a number of MHC Class II epitopes directly from tumors
(WO 2007/028574, EP 1 760 088 B1).
[0030] Since both types of response, CD8 and CD4 dependent,
contribute jointly and synergistically to the anti-tumor effect,
the identification and characterization of tumor-associated
antigens recognized by either CD8+ T cells (ligand: MHC class I
molecule+peptide epitope) or by CD4-positive T-helper cells
(ligand: MHC class II molecule+peptide epitope) is important in the
development of tumor vaccines.
[0031] For an MHC class I peptide to trigger (elicit) a cellular
immune response, it also must bind to an MHC-molecule. This process
is dependent on the allele of the MHC-molecule and specific
polymorphisms of the amino acid sequence of the peptide.
MHC-class-I-binding peptides are usually 8-12 amino acid residues
in length and usually contain two conserved residues ("anchors") in
their sequence that interact with the corresponding binding groove
of the MHC-molecule. In this way each MHC allele has a "binding
motif" determining which peptides can bind specifically to the
binding groove.
[0032] In the MHC class I dependent immune reaction, peptides not
only have to be able to bind to certain MHC class I molecules
expressed by tumor cells, they subsequently also have to be
recognized by T cells bearing specific T cell receptors (TCR).
[0033] For proteins to be recognized by T-lymphocytes as
tumor-specific or -associated antigens, and to be used in a
therapy, particular prerequisites must be fulfilled. The antigen
should be expressed mainly by tumor cells and not, or in comparably
small amounts, by normal healthy tissues. In a preferred
embodiment, the peptide should be over-presented by tumor cells as
compared to normal healthy tissues. It is furthermore desirable
that the respective antigen is not only present in a type of tumor,
but also in high concentrations (i.e. copy numbers of the
respective peptide per cell). Tumor-specific and tumor-associated
antigens are often derived from proteins directly involved in
transformation of a normal cell to a tumor cell due to their
function, e.g. in cell cycle control or suppression of apoptosis.
Additionally, downstream targets of the proteins directly causative
for a transformation may be up-regulated und thus may be indirectly
tumor-associated. Such indirect tumor-associated antigens may also
be targets of a vaccination approach (Singh-Jasuja et al., 2004).
It is essential that epitopes are present in the amino acid
sequence of the antigen, in order to ensure that such a peptide
("immunogenic peptide"), being derived from a tumor associated
antigen, leads to an in vitro or in vivo T-cell-response.
[0034] Basically, any peptide able to bind an MHC molecule may
function as a T-cell epitope. A prerequisite for the induction of
an in vitro or in vivo T-cell-response is the presence of a T cell
having a corresponding TCR and the absence of immunological
tolerance for this particular epitope.
[0035] Therefore, TAAs are a starting point for the development of
a T cell based therapy including but not limited to tumor vaccines.
The methods for identifying and characterizing the TAAs are usually
based on the use of T-cells that can be isolated from patients or
healthy subjects, or they are based on the generation of
differential transcription profiles or differential peptide
expression patterns between tumors and normal tissues. However, the
identification of genes over-expressed in tumor tissues or human
tumor cell lines, or selectively expressed in such tissues or cell
lines, does not provide precise information as to the use of the
antigens being transcribed from these genes in an immune therapy.
This is because only an individual subpopulation of epitopes of
these antigens are suitable for such an application since a T cell
with a corresponding TCR has to be present and the immunological
tolerance for this particular epitope needs to be absent or
minimal. In a very preferred embodiment of the invention it is
therefore important to select only those over- or selectively
presented peptides against which a functional and/or a
proliferating T cell can be found. Such a functional T cell is
defined as a T cell, which upon stimulation with a specific antigen
can be clonally expanded and is able to execute effector functions
("effector T cell").
[0036] In case of targeting peptide-MHC by specific TCRs (e.g.
soluble TCRs) and antibodies or other binding molecules (scaffolds)
according to the invention, the immunogenicity of the underlying
peptides is secondary. In these cases, the presentation is the
determining factor.
SUMMARY OF THE INVENTION
[0037] In a first aspect of the present invention, the present
invention relates to a peptide comprising an amino acid sequence
selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO:
640 or a variant sequence thereof which is at least 77%, preferably
at least 88%, homologous (preferably at least 77% or at least 88%
identical) to SEQ ID NO: 1 to SEQ ID NO: 640, wherein said variant
binds to MHC and/or induces T cells cross-reacting with said
peptide, or a pharmaceutical acceptable salt thereof, wherein said
peptide is not the underlying full-length polypeptide.
[0038] The present invention further relates to a peptide of the
present invention comprising a sequence that is selected from the
group consisting of SEQ ID NO: 1 to SEQ ID NO: 640 or a variant
thereof, which is at least 77%, preferably at least 88%, homologous
(preferably at least 77% or at least 88% identical) to SEQ ID NO: 1
to SEQ ID NO: 640, wherein said peptide or variant thereof has an
overall length of between 8 and 100, preferably between 8 and 30,
and most preferred of between 8 and 14 amino acids.
[0039] The following tables show the peptides according to the
present invention, their respective SEQ ID NOs, and the prospective
source (underlying) genes for these peptides. All peptides in Table
1 and Table 2 bind to HLA-A*02. The peptides in Table 2 have been
disclosed before in large listings as results of high-throughput
screenings with high error rates or calculated using algorithms,
but have not been associated with cancer at all before. The
peptides in Table 3 are additional peptides that may be useful in
combination with the other peptides of the invention. The peptides
in Table 4 are furthermore useful in the diagnosis and/or treatment
of various other malignancies that involve an over-expression or
over-presentation of the respective underlying polypeptide.
TABLE-US-00001 TABLE 1 Peptides according to the present invention.
J = phospho-serine. SEQ ID Official NO. Sequence Gene ID(s) Gene
Symbol(s) 1 SLMEPPAVLLL 8900 CCNA1 2 SLLEADPFL 8900 CCNA1 3
SLASKLTTL 94025 MUC16 4 GIMEHITKI 94025 MUC16 5 HLTEVYPEL 94025
MUC16 6 VLVSDGVHSV 1952 CELSR2 7 SLVGLLLYL 100101267, 9883 POM121C,
POM121 8 FTLGNVVGMYL 100287425, 647087 C7orf73 9 GAAKDLPGV
100534599, 57461 ISY1-RAB43, ISY1 10 FLATFPLAAV 10076 PTPRU 11
KIFEMLEGV 101060208, 101060210, CT45A3, CT45A4, 101060211, 441519,
CT45A5, CT45A6, 441520, 441521, 541465, CT45A1, CT45A2
541466,728911 12 SLWPDPMEV 101060557,146177 VWA3A 13 YLMDESLNL
101060756,115948 CCDC151 14 AAYGGLNEKSFV 10140 TOB1 15 VLLTFKIFL
10149 GPR64 16 VLFQGQASL 10154 PLXNC1 17 GLLPGDRLVSV 10207 INADL 18
YLVAKLVEV 10277 UBE4B 19 FMVDNEAIYDI 10376, 112714, 113457, TUBA1B,
TUBA3E, 51807, 7277, 7278, 7846, TUBA3D, TUBA8, 84790 TUBA4A,
TUBA3C, TUBA1A, TUBA1C 20 RMIEYFIDV 10396, 153020 ATP8A1, RASGEF1B
21 VLDELDMEL 10437 IFI30 22 IMEENPGIFAV 10558 SPTLC1 23 VLLDDIFAQL
10565 ARFGEF1 24 SLSDGLEEV 10651 MTX2 25 FLPDEPYIKV 10686 CLDN16 26
ALLELAEEL 10694, 644131 CCT8, CCT8P1 27 ILADIVISA 10797 MTHFD2 28
QLLDETSAITL 10915 TCERG1 29 KMLGIPISNILMV 10964 IFI44L 30 LILDWVPYI
10975 UQCR11 31 YLAPELFVNV 11035 RIPK3 32 KLDDLTQDLTV 11116 FGFR1OP
33 VLLSLLEKV 1130 LYST 34 ILVEADSLWVV 11329 STK38 35 KINDTIYEV
113510 HELQ 36 YVLEDLEVTV 114960 ,22820, 26958 TSGA13, COPG1, COPG2
37 LLWDVVTGQSV 114987 WDR31 38 FLLEDDIHVS 116461 TSEN15 39
SVAPNLPAV 120114 FAT3 40 TLLVKVFSV 122402 TDRD9 41 SLMPHIPGL 122402
TDRD9 42 VLLQKIVSA 122402 TDRD9 43 VLSSLEINI 1233 CCR4 44
ILDPISSGFLL 127795 C1orf87 45 SLWQDIPDV 128272 ARHGEF19 46
ILTEENIHL 130540 ALS2CR12 47 ILLSVPLLVV 1314 COPA 48 ALAELYEDEV
137886 UBXN2B 49 YLPAVFEEV 9961 MVP 50 SLSELEALM 143686 SESN3 51
LLPDLEFYV 143888 KDELC2 52 FLLAHGLGFLL 144110 TMEM86A 53
KMIETDILQKV 146562 C16orf71 54 SLLEQGKEPWMV 147949, 163087, 342892,
ZNF583, ZNF383, 374899, 84503 ZNF850, ZNF829, ZNF527 55 SLLDLETLSL
148137 C19orf55 56 KLYEGIPVLL 152110 NEK10 57 TLAELQPPVQL 157922
CAMSAP1 58 FLDTLKDLI 162 AP1B1 59 IMEDIILTL 1656 DDX6 60 SLTIDGIYYV
1659 DHX8 61 FLQGYQLHL 19 ABCA1 62 VLLDVSAGQLLM 196463 PLBD2 63
YLLPSGGSVTL 196483, 286042, 348926, FAM86A, FAM86B3P, 55199, 692099
FAM86EP, FAM86C1, FAM86DP 64 YAAPGGLIGV 1968, 255308 EIF2S3 65
LKVNQGLESL 197358 NLRC3 66 FLDENIGGVAV 200424 TET3 67 TLLAEALVTV
200958 MUC20 68 SLMELPRGLFL 219527 LRRC55 69 FQLDPSSGVLVTV 2196
FAT2 70 GLLDYPVGV 219736 STOX1 71 GILARIASV 221322 C6orf170 72
SLLELDGINL 221806 VWDE 73 NIFDLQIYV 222256 CDHR3 74 ALLDPEVLSIFV
22898 DENND3 75 GLLEVMVNL 23001 WDFY3 76 ILIDSIYKV 23007 PLCH1 77
ILVEADGAWVV 23012 STK38L 78 SLFSSLEPQIQPV 23029 RBM34 79
SLFIGEKAVLL 23029 RBM34 80 FLYDNLVESL 23132 RAD54L2 81 FLFSQLQYL
23165 NUP205 82 FLSSVTYNL 23312 DMXL2 83 ILAPTVMMI 23312 DMXL2 84
VTFGEKLLGV 23428 SLC7A8 85 KMSELRVTL 23499 MACF1 86 NLIGKIENV 23639
LRRC6 87 ALPEAPAPLLPHIT 23786 BCL2L13 88 FLLVGDLMAV 23787 MTCH1 89
YILPTETIYV 254956 MORN5 90 TLLQIIETV 256309 CCDC110 91 IMQDFPAEIFL
25914 RTTN 92 YLIPFTGIVGL 26001 RNF167 93 LLQAIKLYL 260293 CYP4X1
94 YLIDIKTIAI 26160 IFT172 95 SVIPQIQKV 26272 FBXO4 96 YIFTDNPAAV
26301 GBGT1 97 SLINGSFLV 27 ABL2 98 LIIDQADIYL 27042 DIEXF 99
ALVSKGLATV 27044 SND1 100 YLLSTNAQL 27285 TEKT2 101 ILVGGGALATV
2820 GPD2 102 YLFESEGLVL 283431 GAS2L3 103 TLAEEVVAL 283755,
400322, 8924 HERC2P3, HERC2P2, HERC2 104 STMEQNFLL 284110 GSDMA 105
LLLEHSFEI 284361 EMC10 106 LLYDAVHIVSV 2899 GRIK3 107 FLQPVDDTQHL
2906 GRIN2D 108 ALFPGVALLLA 2923 PDIA3 109 IILSILEQA 2953, 653689
GSTT2, GSTT2B 110 FLSQVDFEL 2968 GTF2H4 111 YVWGFYPAEV 3109 HLA-DMB
112 FLITSNNQL 353497, 79441 POLN, HAUS3 113 GLLPTPLFGV 359710
BPIFB3 114 SLVGEPILQNV 359710 BPIFB3 115 AIAGAGILYGV 362 AQP5 116
YHIDEEVGF 3620 IDO1
117 ILPDGEDFLAV 3636 INPPL1 118 KLIDNNINV 3696 ITGB8 119 FLYIGDIVSL
3709 ITPR2 120 ALLGIPLTLV 3777, 60598 KCNK3, KCNK15 121 GVVDPRAISVL
387522, 7335 TMEM189-UBE2V1, UBE2V1 122 FLLAEDDIYL 389677 RBM12B
123 NLWDLTDASVV 3959 LGALS3BP 124 ALYETELADA 4001 LMNB1 125
VQIHQVAQV 4053 LTBP2 126 VLAYFLPEA 4171 MCM2 127 KIGDEPPKV 4291
MLF1 128 YLFDDPLSAV 4363 ABCC1 129 GLLDGGVDILL 4548 MTR 130
FLWNGEDSALL 4586, 727897 MUC5AC, MUC5B 131 FVPPVTVFPSL 4586, 727897
MUC5AC, MUC5B 132 LLVEQPPLAGV 4773 NFATC2 133 KVLSNIHTV 4867 NPHP1
134 YLQELIFSV 51000 SLC35B3 135 ALSEVDFQL 51059 FAM135B 136
YLADPSNLFVV 51072, 728556 MEMO1, MEMO1P1 137 TLVLTLPTV 51073 MRPL4
138 YQYPRAILSV 51105 PHF20L1 139 SVMEVNSGIYRV 51182 HSPA14 140
YMDAPKAAL 51246 SHISA5 141 YLDFSNNRL 51284 TLR7 142 FLFATPVFI 51296
SLC15A3 143 LLLDITPEI 51430 SUCO 144 YIMEPSIFNTL 51497 TH1L 145
FLATSGTLAGI 51522 TMEM14C 146 SLATAGDGLIEL 5245 PHB 147 SLLEAVSFL
5261 PHKG2 148 ALNPEIVSV 5277 PIGA 149 NLLELFVQL 5297 PI4KA 150
RLWEEGEELEL 5329 PLAUR 151 KILQQLVTL 541468 LURAP1 152 ILFEDIFDV
5437 POLR2H 153 FLIANVLYL 5476 CTSA 154 ALDDGTPAL 54798 DCHS2 155
RVANLHFPSV 54809 SAMD9 156 AISQGITLPSL 54856 GON4L 157 SLNDEVPEV
54919 HEATR2 158 KLFDVDEDGYI 54947 LPCAT2 159 GLVGNPLPSV 55127
HEATR1 160 FLFDEEIEQI 55132 LARP1B 161 ALLEGVNTV 55211 DPPA4 162
YQQAQVPSV 55217 TMLHE 163 ALDEMGDLLQL 55304 SPTLC3 164 ALLPQPKNLTV
5546 PRCC 165 SLLDEIRAV 55567 DNAH3 166 YLNHLEPPV 55666 NPLOC4 167
KVLEVTEEFGV 55705 IPO9 168 KILDADIQL 55779 WDR52 169 NLPEYLPFV
55832, 91689 CAND1, C22orf32 170 RLQETLSAA 5591 PRKDC 171 LLLPLQILL
5650 KLK7 172 VLYSYTI ITV 56941 C3orf37 173 LLDSASAGLYL 56992 KIF15
174 ALAQYLITA 57060 PCBP4 175 YLFENISQL 57115 PGLYRP4 176
YLMEGSYNKVFL 5714 PSMD8 177 YLLPEEYTSTL 57143 ADCK1 178 ALTEIAFVV
57148 RALGAPB 179 KVLNELYTV 57522 SRGAP1 180 FQIDPHSGLVTV 57526
PCDH19 181 LLWAGTAFQV 57535 KIAA1324 182 MLLEAPGIFL 57570 TRMT5 183
FGLDLVTEL 57674 RNF213 184 YLMDINGKMWL 57674 RNF213 185 FLIDDKGYTL
57685 CACHD1 186 TLFFQQNAL 5771 PTPN2 187 RQISIRGIVGV 5836 PYGL 188
GLFPVTPEAV 59352 LGR6 189 ALQRKLPYV 60598 KCNK15 190 FLSSLTETI 629
CFB 191 LLQEGQALEYV 629 CFB 192 KM LDGASFTL 63941 NECAB3 193
QLLDADGFLNV 63967 CLSPN 194 ALPLFVITV 64078 SLC28A3 195 GLFADLLPRL
642475 MROH6 196 YLYSVEIKL 642987 TMEM232 197 ALGPEGGRV 64321 SOX17
198 KTINKVPTV 6498 SKIL 199 ALQDVPLSSV 65003 MRPL11 200 LLFGSVQEV
65250 C5orf42 201 RLVDYLEGI 65260 SELRC1 202 ALLDQQGSRVVTL 6565
SLC15A2 203 VLLEDAHSHTL 6614 SIGLEC1 204 KIAENVEEV 6804 STX1A 205
SLYPGTETMGL 6840 SVIL 206 VLQEGKLQKLAQL 6891 TAP2 207 GLTSTNAEV
7029 TFDP2 208 KISPVTFSV 728661, 9906 SLC35E2B, SLC35E2 209
KLIESKHEV 7328 UBE2H 210 LLLNAVLTV 7374 UNG 211 LLWPGAALL 7462 LAT2
212 ALWDQDNLSV 7464 CORO2A 213 VTAAYMDTVSL 7498 XDH 214 FLLDLDPLLL
7915 ALDH5A1 215 QLINHLHAV 79365 BHLHE41 216 NLWEDPYYL 79659
DYNC2H1 217 ALIHPVSTV 79690 GAL3ST4 218 SALEELVNV 79707 NOL9 219
KLSDIGITV 79725 THAP9 220 LLQKFVPEI 79832 QSER1 221 ALYEEGLLL 80311
KLHL15 222 NLIENVQRL 8195 MKKS 223 ALLENIALYL 833 CARS 224
TLIDAQWVL 84000 TMPRSS13 225 SLLKVLPAL 84125 LRRIQ1 226 MLYVVPIYL
84187 TMEM164 227 ALMNTLLYL 84197 228 AMQEYIAVV 84320 ACBD6 229
RLPGPLGTV 84875 PARP10 230 ILVDWLVEV 85417, 890, 8900 CCNB3, CCNA2,
CCNA1 231 FLSPQQPPLLL 8621 CDK13 232 ALLEAQDVELYL 8701 DNAH11 233
VLSETLYEL 8914 TIMELESS 234 ALMEDTGRQML 89782 LMLN 235 YLNDLHEVLL
898 CCNE1 236 GLLEAKVSL 89845 ABCC10 237 ALLEASGTLLL 90580 C19orf52
238 YLISFQTHI 90592 ZNF700 239 AAFAGKLLSV 91543 RSAD2 240 ILLEQAFYL
92255 LMBRD2
241 SLVEVNPAYSV 92305 TMEM129 242 AIAYILQGV 92335 STRADA 243
LLLNELPSV 92345 NAF1 244 SLFGGTEITI 93035 PKHD1L1 245 SMIDDLLGV
93233 CCDC114 246 LLWEVVSQL 9462 RASAL2 247 VLLPNDLLEKV 9472 AKAP6
248 FLFPNQYVDV 9632 SEC24C 249 LLDGFLVNV 9632 SEC24C 250
ALSEEGLLVYL 9690 UBE3C 251 ALYTGFSILV 972 CD74 252 LLIGTDVSL 9730
VPRBP 253 GLDAATATV 9869 SETDB1 254 TLLAFIMEL 987 LRBA 255
VLASYNLTV 987 LRBA 256 FLPPEHTIVYI 9896 FIG4 257 SIFSAFLSV 9918
NCAPD2 258 ELAERVPAI 9918 NCAPD2 259 TLMRQLQQV 140680 C20orf96 260
TLLEGPDPAELLL 100101267, 9883 POM121C, POM121 261 YVLEFLEEI 10026
PIGK 262 LLWGDLIWL 101060729, 548593, SLX1A, SLX1B 79008 263
LLVSNLDFGV 10189 ALYREF 264 SLQEQLHSV 133584 EGFLAM 265 LLFGGTKTV
1572 CYP2F1 266 KITDTLIHL 2099 ESR1 267 ALQDFLLSV 2189 FANCG 268
IAGPGLPDL 220074 LRTOMT 269 RVLEVGALQAV 25885 POLR1A 270
LLLDEEGTFSL 27013 CNPPD1 271 LVYPLELYPA 29956 CERS2 272 ALGNTVPAV
352909 DNAAF3 273 NLFQSVREV 367 AR 274 SLLFSLFEA 3938 LCT 275
YLVYILNEL 51202 DDX47 276 ALFTFSPLTV 54665 RSBN1 277 LLPPLESLATV
5518 PPP2R1A 278 QLLDVVLTI 55295 KLHL26 279 ALWGGTQPLL 56063
TMEM234 280 VLPDPEVLEAV 57326 PBXIP1 281 ILRESTEEL 57639 CCDC146
282 LLADVVPTT 57661 PHRF1 283 ALYIGDGYVIHLA 5920 RARRES3 284
ILLSQTTGV 7175 TPR 285 QLLHVGVTV 79598 CEP97 286 YLFPGIPEL 80308
FLAD1 287 FLNEFFLNV 833 CARS 288 NLINEINGV 8672 EIF4G3 289
VLLEIEDLQV 8826 IQGAP1 290 GLLDLNNAILQL 2104 ESRRG 291 GLDSNLKYILV
23269 MGA 292 LLWEAGS EA 26167 PCDHB5 293 GLGELQELYL 2811 GP1BA 294
ILDPFQYQL 9420 CYP7B1 295 VLDRESPNV 1000 CDH2 296 FMEGAIIYV 10006
ABI1 297 VLADIELAQA 10039 PARP3 298 VMITKLVEV 10076 PTPRU 299
YLLETSGNL 10135 NAMPT 300 ALLGQTFSL 10147 SUGP2 301 FLVEDLVDSL
10313, 6253 RTN3, RTN2 302 ALLQEGEVYSA 10594 PRPF8 303 AILPQLFMV
10945 KDELR1 304 MTLGQIYYL 10959 TMED2 305 SIANFSEFYV 111, 112
ADCY5, ADCY6 306 ALVNVQIPL 11194 ABCB8 307 ALPVSLPQI 11218 DDX20
308 SQYSGQLHEV 114884 OSBPL10 309 GLFDGVPTTA 122618 PLD4 310
FLVDTPLARA 124975 GGT6 311 RLYTGMHTV 130367 SGPP2 312 IISDLTIAL
144110 TMEM86A 313 VLFDDELLMV 1687 DFNA5 314 ALIAEGIALV 1778
DYNC1H1 315 YLQDVVEQA 19 ABCA1 316 ILLERLWYV 215 ABCD1 317
SLAALVVHV 2196 FAT2 318 GLINTGVLSV 221656 KDM1B 319 SLEPQIQPV 23029
RBM34 320 KMFEFVEPLL 23092 ARHGAP26 321 GLFEDVTQPGILL 23140 ZZEF1
322 TLMTSLPAL 23154 NCDN 323 IQIGEETVITV 2316 FLNA 324 FLYDEIEAEV
23191, 26999 CYFIP1, CYFIP2 325 FIMPATVADATAV 23352 UBR4 326
FLPEALDFV 23511 NUP188 327 GLAPFTEGISFV 23780 APOL2 328 ALNDQVFEI
2475 MTOR 329 FLVTLNNVEV 25839 COG4 330 QLALKVEGV 25896 INTS7 331
KVDTVWVNV 25917 THUMPD3 332 YLISELEAA 25940 FAM98A 333 FLPDANSSV
25942 SIN3A 334 TLTKVLVAL 26292 MYCBP 335 YSLSSVVTV 28396, 3500,
3501, IGHV4-31, IGHG1, 3502, 3503,3507 IGHG2, IGHG3, IGHG4, IGHM
336 ILLTAIVQV 29100 TMEM208 337 HLLSELEAAPYL 2976 GTF3C2 338
SVLEDPVHAV 29927 SEC61A1 339 GLWEIENNPTVKA 3068 HDGF 340 ALLSMTFPL
3094 HINT1 341 SQIALNEKLVNL 339799, 8665 EIF3FP3, EIF3F 342
HIYDKVMTV 340706 VWA2 343 SLLEVNEESTV 3428 IF116 344 YLQDQHLLLTV
3636 INPPL1 345 VIWKALIHL 3689 ITGB2 346 LLDSKVPSV 3691 ITGB4 347
SLFKHDPAAWEA 3728 JUP 348 ILLDVKTRL 3728, 3861, 3868, 3872 JUP,
KRT14, KRT16, KRT17 349 SLTEYLQNV 3799 KIF5B 350 ALLDVTHSELTV 3911
LAMAS 351 SLIPNLRNV 3949 LDLR 352 SLLELLHIYV 401494 PTPLAD2 353
YLFEMDSSL 4074 M6PR 354 LILEGVDTV 4126 MANBA 355 SIQQSIERLLV 4809
NHP2L1 356 KLLGKLPEL 4929 NR4A2 357 SMHDLVLQV 51435 SCARA3 358
ALDEYTSEL 51477 ISYNA1 359 YLLPESVDL 51657 STYXL1 360 ALDJGASLLHL
54101 RIPK4 361 ALYELEGTTV 54625 PARP14 362 TLYGLSVLL 54896 PQLC2
363 KVLDVSDLESV 54961 SSH3 364 LLQNEQFEL 55329 MNS1
365 YVIDQGETDVYV 5573 PRKAR1A 366 RLLDMGETDLML 55898 UNC45A 367
SLQNHNHQL 56254, 9810 RNF20, RNF40 368 ILLEEVSPEL 5660 PSAP 369
GLFPEHLIDV 56997 ADCK3 370 SLLQDLVSV 57169 ZNFX1 371 FLQAHLHTA
57674 RNF213 372 TMLLNIPLV 57674 RNF213 373 SLLEDKGLAEV 59342
SCPEP1 374 FLLQQHLISA 5993 RFX5 375 SLTETIEGV 629 CFB 376
AMFESSQNVLL 64328 XPO4 377 FLLDSSASV 64856 VWA1 378 ALGYFVPYV 6567
SLC16A2 379 IMEGTLTRV 6654 SOS1 380 TLIEDEIATI 6788 STK3 381
FIDEAYVEV 6873 TAF2 382 ALQNYIKEA 7022 TFAP2C 383 ALLELENSVTL 715,
83481 C1R, EPPK1 384 ILFANPNIFV 728689, 8663 EIF3CL, EIF3C 385
SLLEQGLVEA 7468 WHSC1 386 ILFRYPLTI 767 CA8 387 ALFQATAEV 7840
ALMS1 388 SLTIDGIRYV 79665 DHX40 389 LLADVTHLL 79699 ZYG11B 390
ALFMKQIYL 79781 IQCA1 391 YVYPQRLNFV 81704 DOCK8 392 ALLHPQGFEV
8269 TMEM187 393 GLLDTQTSQVLTA 83481 EPPK1 394 LLAVIGGLVYL 84061
MAGT1 395 ALALGGIAVV 84159 ARID5B 396 ALLPDLPAL 84273 NOA1 397
YLFGERLLEC 84365 MKI67IP 398 KLLEEDGTIITL 84612 PARD6B 399
YLFEPLYHV 8534 CHST1 400 SLLTEQDLWTV 90806 ANGEL2 401 ILLDDTGLAYI
9125 RQCD1 402 VLFSGALLGL 968 CD68 403 KLYDRILRV 9746 CLSTN3 404
AIDIJGRDPAV 100288805, 54768 HYDIN2, HYDIN 405 ALYDVFLEV 1774
DNASE1L1 406 SVQGEDLYLV 2880 GPX5 407 YLMDLINFL 54536 EXOC6 408
VLDDSIYLV 57565 KLHL14 409 LLDAMNYHL 57565 KLHL14 410 VLSDVIPJI
139231 FAM199X 411 LLAHLSPEL 57194 ATP10A 412 YLDDLNEGVYI 9897
KIAA0196 413 TLLEKVEGC 149371 EXOC8 414 YVDDIFLRV 19 ABCA1 415
LLDKVYSSV 221960, 51622 CCZ1B, CCZ1 416 VLSDIIQNLSV 3071 NCKAP1L
417 NLQDTEYNL 472 ATM 418 ALAELENI EV 55561 CDC42BPG 419 GQYEGKVSSV
55705 IPO9 420 FMYDTPQEV 629 CFB 421 RLPETLPSL 6337 SCNN1A 422
FLPKLLLLA 6614 SIGLEC1 423 GLDGPPPTV 7127 TNFAIP2 424 TLLDALYEI
8690 JRKL 425 FLYEKSSQV 89876 MAATS1 426 RLADKSVLV 9918 NCAPD2
TABLE-US-00002 TABLE 2 Additional peptides according to the present
invention with no prior known cancer association. J =
phospho-serine. SEQ ID NO. Sequence Gene ID(s) Official Gene
Symbol(s) 427 ALLPLSPYL 79679 VTCN1 428 KLGHTDILVGV 23016 EXOSC7
429 GLVNDLARV 10075 HUWE1 430 HLYSSIEHLTT 10075 HUWE1 431 SLVNVVPKL
1020 CDK5 432 TLIEESAKV 10257 ABCC4 433 AMLNEPWAV 10379,55072 IRF9,
RNF31 434 KVSNSGITRV 10575 CCT4 435 WLMPVIPAL 10809, 134266,
STARD10, GRPEL2, FBXW8, 26259, 30820, KCNIP1, FAM208B, C8orf44,
54906, 56260, ISY1, SHROOM3, SLC25A14, 57461, 57619, L3MBTL4,
C12orf65 9016, 91133, 91574 436 HLAEVSAEV 11130 ZWINT 437
SMAPGLVIQAV 11160 ERLIN2 438 KLLPLAGLYL 113655 MFSD3 439 YLLQEIYGI
114804, 23295 RNF157, MGRN1 440 ALADGVTMQV 114960, 26958 TSGA13,
COPG2 441 ALLENPKMEL 140901, 149420 STK35, PDIK1L 442 GLLGGGGVLGV
149954 BPIFB4 443 GLWEIENNPTV 154150, 3068 HDGFL1, HDGF 444
GLLRDEALAEV 1663, 440081, DDX11, DDX12P 642846 445 GLYQDPVTL 201292
TRIM65 446 QLIPALAKV 2070, 2138, EYA4, EYA1, EYA2 2139 447
QLVPALAKV 2140 EYA3 448 NLLETKLQL 219988 PATL1 449 KLAEGLDIQL
221656 KDM1B 450 FMIDASVHPTL 221960, 51622 CCZ1B, CCZ1 451
LLLLDTVTMQV 22820 COPG1 452 ILLEHGADPNL 22852 ANKRD26 453 KLLEATSAV
100129478, C4orf46 201725 454 KLPPPPPQA 23028 KDM1A 455 SLLKEPQKVQL
23154 NCDN 456 LLIGHLERV 23165 NUP205 457 SLLPGNLVEKV 23341 DNAJC16
458 SLIDKLYNI 25885 POLR1A 459 ALITEVVRL 26005 C2CD3 460 AMLEKNYKL
26160 IFT172 461 VMFRTPLASV 26271 FBXO5 462 KLAKQPETV 27085 MTBP
463 SLVESHLSDQL 284361 EMC10 TL 464 ALNDCIYSV 3652 IPP 465
QLCDLNAEL 3833 KIFC1 466 VLIANLEKL 440590 ZYG11A 467 FLAKDFNFL 4600
MX2 468 YLRSVGDGET 4904, 8531 YBX1, CSDA V 469 YLASDEITTV 4976 OPA1
470 MLQDSIHVV 4999 ORC2 471 YLYNNMIAKI 51284 TLR7 472 KLLEVSDDPQV
51606 ATP6V1H 473 AMATESILHFA 5297 PI4KA 474 YLDPALELGPR 537
ATP6AP1 NV 475 LLLNEEALAQI 54497 HEATR5B 476 ALMERTGYSM 54502 RBM47
V 477 ALLPASGQIAL 54512 EXOSC4 478 YLLHEKLNL 55010 PARPBP 479
SLFGNSGILEN 55125 CEP192 V 480 ALLEDSCHYL 55161 TMEM33 481
GLIEDYEALL 55755 CDK5RAP2 482 SLAPAGIADA 55839 CENPN 483 ALTDIVSQV
56924 PAK6 484 SLIEKVTQL 56992 KIF15 485 NVPDSFNEV 57508 INT52 486
AVMESIQGV 57646 U5P28 487 LLINSVFHV 57655 GRAMD1A 488 FLAEDPKVTL
60489 APOBEC3G 489 KMWEELPEVV 622 BDH1 490 FLLQHVQEL 64127 NOD2 491
GLNDRSDAV 64151 NCAPG 492 SLFDGFADGL 64219, 9867 PJA1, PJA2 GV 493
GLLGEKTQDLI 6522 SLC4A2 GV 494 ALQPEPIKV 6653 SORL1 495 FIFSEKPVFV
6653 SORL1 496 FLVEKQPPQV 6778 STAT6 497 GLLEKLTAI 6875 TAF4B 498
KLWTGGLDNT 7088, 7090, 7091 TLE1, TLE3, TLE4 V 499 KIFDIDEAEEGV
728350, 8894 EIF252P4, EIF252 500 SLMEDQVLQL 7486 WRN 501
LLDPNVKSIFV 79033 ERI3 502 RLLAQVPGL 79096 C11orf49 503 SLNHFTHSV
79670 ZCCHC6 504 GLSDGNPSL 79684 MSANTD2 505 SLAPGDVVRQ 79729
5H3D21 V 506 KLLGKVETA 80185 TTI2 507 KLIDDQDISISL 80208 SPG11 508
ILAQEQLVVGV 80347 COASY 509 FLFDTKPLIV 821 CANX 510 KLYSVVSQL 8239,
8287 USP9X, USP9Y 511 FLDPYCSASV 85415 RHPN2 512 SLSEIVPCL 8900
CCNA1 513 SLWPSPEQL 90480 GADD45GIP1 514 ILVDWLVQV 9133 CCNB2 515
LLQELVLFL 93589 CACNA2D4 516 AVGPASILKEV 9406 ZRANB2 517
LLMPIPEGLTL 9540 TP53I3 518 KLNAEVACV 9569 GTF2IRD1 519 GLLHLTLLL
9603 NFE2L3 520 LAVHPSGVAL 9636 I5G15 521 MLLTKLPTI 9804 TOMM20 522
TLVVYRSPEV 983 CDK1 523 YQIPRTFTL 9846 GAB2 524 ALIENLTHQI
100508782, PPIP5K1 9677 525 VLLEAGEGLVT 10072, 582 DPP3, BBS1 I 526
RLAEVGQYEQ 23019 CNOT1 V 527 FLLEPGNLEV 23218 NBEAL2 528 SVAEGRALMS
51428 DDX41 V 529 LLADELITV 56904 SH3GLB2 530 VMYADIGGMDI 5704
PSMC4 531 YTLPIASSIRL 7249 TSC2 532 ALNNLLHSL 101060416, SMG1,
BOLA2, SMG1P1 101060589, 23049, 440345, 440354, 552900, 641298 533
RMVAEIQNV 11262 SP140 534 HLANIVERL 117854, 445372, TRIM6,
TRIM6-TRIM34, TRIM34 53840 535 KLIAQNLEL 3832 KIF11
536 YLVEGRFSV 55125 CEP192 537 TLAPGEVLRSV 3996 LLGL1 538 LLLAHIIAL
9415 FADS2 539 ALFDAQAQV 7297 TYK2 540 ALIPETTTLTV 100529251,
CKLF-CMTM1, CKLF 51192 541 SMLEPVPEL 10277 UBE4B 542 RVWDISTVSSV
11137 PWP1 543 GLLPTPITQQA 133619 PRRC1 SL 544 LLWDVPAPSL 1388,
7148 ATF6B, TNXB 545 LLADLLHNV 1677 DFFB 546 VMIAGKVAVV 191 AHOY
547 TLDITPHTV 2177 FANCD2 548 ALWENPESGE 22893 BAHD1 L 549
AMLENASDIKL 23 ABCF1 550 FLYDEIEAEVN 23191, 26999 CYFIP1, CYFIP2 L
551 KLYESLLPFA 23310 NCAPD3 552 GLLDLPFRVGV 23347 SMCHD1 553
SLLNQDLHWS 23355 VPS8 L 554 LLMPSSEDLLL 26046 LTN1 555 YVLEGLKSV
26098 C10orf137 556 FLTDLEDLTL 26151 NAT9 557 KLYDDMIRL 26160
IFT172 558 GLLENIPRV 2618 GART 559 VTVPPGPSL 266971, 5710 PIPSL,
PSMD4 560 ALWDIETGQQT 2782 GNB1 TT 561 YLQLTQSEL 283237 TTC9C 562
YLEELPEKLKL 2944, 2949 GSTM1, GSTM5 563 WLLPYNGVTV 2976 GTF3C2 564
TVTNAVVTV 3312 HSPA8 565 ALQETPTSV 3434 IFIT1 566 VIADGGIQNV 3615
IMPDH2 567 SLLPLDDIVRV 3708, 3709 ITPR1, ITPR2 568 TLYDIAHTPGV 4191
MDH2 569 KLVDRTWTL 441733, 5613, PRKXP1, PRKX, PRKY 5616 570
ALANQIPTV 4436 MSH2 571 LLLTTIPQI 4507 MTAP 572 ALADLIEKELSV 4850
CNOT4 573 ILVANAIVGV 488, 489 ATP2A2, ATP2A3 574 YLLQEPPRTV 5074
PAWR 575 YLISQVEGHQV 51002 TPRKB 576 ILLNNSGQIKL 51755 CDK12 577
VMFEDGVLMR 545 ATR L 578 FLDPGGPMMK 55627 SMPD4 L 579 NLMEMVAQL
55636 CHD7 580 LLMENAERV 55726 ASUN 581 RLWNETVEL 55789 DEPDC1B 582
TLCDVILMV 55975 KLHL7 583 ILANDGVLLAA 5685 PSMA4 584 ALAEVAAMEN
56987 BBX V 585 ALWDLAADKQ 5701 PSMC2 TL 586 KLKPGDLVGV 5702 PSMC3
587 VMNDRLYAI 57565 KLHL14 588 SLLPLSHLV 57674 RNF213 589
KLYPQLPAEI 57724 EPG5 590 SLIEKLWQT 5991 RFX3 591 SMAELDIKL 60561
RINT1 592 RLLJAAENFL 64092 SAMSN1 593 GLPRFGIEMV 64397 ZFP106 594
IMLKGDNITL 6635 SNRPE 595 VLLSIYPRV 6890 TAP1 596 ALLDQTKTLAE 7094
TLN1 SAL 597 KLLEGQVIQL 7629 ZNF76 598 FLFPHSVLV 79022 TMEM106C 599
YLLNDASLISV 79145 CHCHD7 600 ALAAPDIVPAL 79886 CAAP1 601 SAFPFPVTV
79939 SLC35E1 602 YLLEQIKLIEV 79956 ERMP1 603 FLIEPEHVNTV 80124
VCPIP1 604 SILDRDDIFV 8237 USP11 605 KLYEAVPQL 8317 CDC7 606
ALWETEVYI 8398 PLA2G6 607 RLYSGISGLEL 84172 POLR1B 608 SLLSVSHAL
84219 WDR24 609 ALWKQLLEL 85441 HELZ2 610 LLAPTPYIIGV 8567 MADD 611
YLLDDGTLVV 8872 CDC123 612 YLYNEGLSV 899 CCNF 613 RLLPPGAVVAV 90353
CTU1 614 LLLPDQPPYHL 9246 UBE2L6 615 VLPPDTDPA 93100 NAPRT1 616
VLIDEVESL 9319 TRIP13 617 ALMYESEKVG 9342 SNAP29 V 618 VLFDSESIGIYV
9555 H2AFY 619 ALQDRVPLA 9636 I5G15 620 KLLNKIYEA 9875 URB1 621
VLMDRLPSLL 9875 URB1 622 RLLGEEVVRVL 9894 TEL02 QA 623 YLVEDIQHI
9985 REC8 624 FLQEEPGQLL 101060729, SLX1A, SLX1B 548593, 79008 625
VVLEGASLETV 10436 EMG1 626 LLMATILHL 1315 COPB1 627 KLLETELLQEI
151636 DTX3L 628 KLWEFFQVDV 178 AGL 629 HLLNESPML 23165 NUP205 630
LLSHVIVAL 545 ATR 631 FLDVFLPRV 5591 PRKDC 632 YLIPDIDLKL 6599
SMARCC1 633 ALSRVSVNV 80746 TSEN2 634 VVAEFVPLI 8295 TRRAP 635
SLDSTLHAV 85444 LRRCC1 636 LLTEIRAVV 9263 STK17A 637 SIYGGFLLGV
9276 COPB2 638 KLIQESPTV 9702 CEP57 639 SLFQNCFEL 9716 AQR 640
YLFSEALNAA 987 LRBA
TABLE-US-00003 TABLE 3 Peptides useful for cancer therapy, e.g.
personalized cancer therapies SEQ ID Official NO. Sequence Gene
ID(s) Gene Symbol(s) 641 VLLPVEVATHYL 10568 SLC34A2 642 FLHDISDVQL
10715 CERS1 643 ALFPHLLQPV 1434 CSE1L 644 LTFGDVVAV 2173 FABP7 645
LLYDAVHIV 2899 GRIK3 646 ILSPTVVSI 3832 KIF11 647 SLGLFLAQV 51435
SCARA3 648 LLWGNAIFL 547 KIF1A 649 ALAFKLDEV 201780 SLC10A4 650
AIMGFIGFFV 23480 SEC61G 651 ILQDRLNQV 990 CDC6 652 TLWYRAPEV 1019,
1021 CDK4, CDK6 653 TLISRLPAV 1104 RCC1 654 KILEDVVGV 22974 TPX2
655 ALMDKEGLTAL 26115 TANC2 656 KLLEYIEEI 3161 HMMR 657 SLAERLFFQV
339983 NAT8L 658 LLQDRLVSV 57664 PLEKHA4 659 ILFPDIIARA 64110
MAGEF1 660 AILDTLYEV 84725 PLEKHA8 661 SLIDADPYL 890 CCNA2 662
KIQEILTQV 10643 IGF2BP3 663 KIQEMQHFL 4321 MMP12
[0040] The present invention furthermore generally relates to the
peptides according to the present invention for use in the
treatment of proliferative diseases, such as, for example non-small
cell lung cancer, small cell lung cancer, kidney cancer, brain
cancer, colon or rectum cancer, stomach cancer, liver cancer,
pancreatic cancer, prostate cancer, leukemia, breast cancer, Merkel
cell carcinoma, melanoma, esophageal cancer, urinary bladder
cancer, uterine cancer, gallbladder cancer, bile duct cancer.
[0041] Of particular interest and thus preferred is the peptide SEQ
ID NO. 466 (VLIANLEKL) and its uses in the immunotherapy of ovarian
cancer, non-small cell lung cancer, small cell lung cancer, kidney
cancer, brain cancer, colon or rectum cancer, stomach cancer, liver
cancer, pancreatic cancer, prostate cancer, leukemia, breast
cancer, Merkel cell carcinoma, melanoma, esophageal cancer, urinary
bladder cancer, uterine cancer, gallbladder cancer, bile duct
cancer, and preferably ovarian cancer.
[0042] Particularly preferred are the peptide--alone or in
combination--according to the present invention selected from the
group consisting of SEQ ID NO: 1, 11, 427, 408, 198, 512, 519, and
587 and their uses in the immunotherapy of ovarian cancer,
non-small cell lung cancer, small cell lung cancer, kidney cancer,
brain cancer, colon or rectum cancer, stomach cancer, liver cancer,
pancreatic cancer, prostate cancer, leukemia, breast cancer, Merkel
cell carcinoma, melanoma, esophageal cancer, urinary bladder
cancer, uterine cancer, gallbladder cancer, bile duct cancer, and
preferably ovarian cancer.
[0043] Particularly preferred are the peptide--alone or in
combination--according to the present invention selected from the
group consisting of SEQ ID NO: 3, 4, 5, 6, 8, 10, 12, 14, 15, 18,
20, 25, 29, 32, 37, 38, 39, 41, 44, 45, 52, 53, 54, 57, 64, 69, 72,
73, 77, 78, 83, 89, 90, 91, 93, 94, 96, 99, 100, 102, 104, 106,
107, 109, 113, 114, 117, 120, 123, 124, 136, 137, 138, 139, 141,
143, 148, 150, 151, 157, 158, 160, 163, 165, 166, 170, 171, 173,
175, 179, 180, 184, 185, 187, 189, 191, 192, 193, 194, 195, 196,
200, 202, 204, 206, 209, 211, 215, 216, 217, 250, 253, 258, 266,
267, 269, 301, 306, 347, 348, 350, 365, 367, 369, 378, 380, 426,
430, 432, 433, 438, 441, 442, 444, 449, 451, 455, 460, 461, 462,
463, 465, 467, 468, 470, 471, 478, 479, 481, 482, 484, 485, 489,
491, 494, 498, 505, 509, 511, 514, 515, 516, 518, 522, 532, 542,
547, 548, 552, 560, 578, and 620 and their uses in the
immunotherapy of ovarian cancer, non-small cell lung cancer, small
cell lung cancer, kidney cancer, brain cancer, colon or rectum
cancer, stomach cancer, liver cancer, pancreatic cancer, prostate
cancer, leukemia, breast cancer, Merkel cell carcinoma, melanoma,
esophageal cancer, urinary bladder cancer, uterine cancer,
gallbladder cancer, bile duct cancer, and preferably ovarian
cancer.
[0044] Particularly preferred are the peptides--alone or in
combination--according to the present invention selected from the
group consisting of SEQ ID NO: 1 to SEQ ID NO: 640. More preferred
are the peptides--alone or in combination--selected from the group
consisting of SEQ ID NO: 1 to SEQ ID NO: 259 (see Table 1), and
their uses in the immunotherapy of ovarian cancer, non-small cell
lung cancer, small cell lung cancer, kidney cancer, brain cancer,
colon or rectum cancer, stomach cancer, liver cancer, pancreatic
cancer, prostate cancer, leukemia, breast cancer, Merkel cell
carcinoma, melanoma, esophageal cancer, urinary bladder cancer,
uterine cancer, gallbladder cancer, bile duct cancer, and
preferably ovarian cancer.
[0045] As shown in the following Table 4A and B, many of the
peptides according to the present invention are also found on other
tumor types and can, thus, also be used in the immunotherapy of
other indications. Also refer to FIG. 1 and Example 1.
TABLE-US-00004 TABLE 4A Peptides according to the present invention
and their specific uses in other proliferative diseases, especially
in other cancerous diseases. The table shows for selected peptides
on which additional tumor types they were found and either
over-presented on more than 5% of the measured tumor samples, or
presented on more than 5% of the measured tumor samples with a
ratio of geometric means tumor vs normal tissues being larger than
3. Over-presentation is defined as higher presentation on the tumor
sample as compared to the normal sample with highest presentation.
Normal tissues against which over- presentation was tested were:
adipose tissue, adrenal gland, artery, bone marrow, brain, central
nerve, colon, duodenum, esophagus, gallbladder, heart, kidney,
liver, lung, lymph node, mononuclear white blood cells, pancreas,
peripheral nerve, peritoneum, pituitary, pleura, rectum, salivary
gland, skeletal muscle, skin, small intestine, spleen, stomach,
thymus, thyroid gland, trachea, ureter, urinary bladder, vein. J =
phospho-serine SEQ ID No Sequence Other relevant organs/cancerous
diseases 1 SLMEPPAVLLL NSCLC, SCLC, Esophageal Cancer 2 SLLEADPFL
Esophageal Cancer 6 VLVSDGVHSV SCLC, Brain Cancer, BrCa, MCC,
Esophageal Cancer 7 SLVGLLLYL RCC, PC, BrCa 9 GAAKDLPGV RCC, GC,
HCC, Urinary bladder Cancer 10 FLATFPLAAV Urinary bladder Cancer 11
KIFEMLEGV NSCLC 14 AAYGGLNEKSFV HCC, Urinary bladder Cancer 17
GLLPGDRLVSV NSCLC, SCLC, BrCa 19 FMVDNEAIYDI SCLC, CRC, HCC,
Leukemia, Melanoma, Esophageal Cancer, Urinary bladder Cancer 20
RMIEYFIDV SCLC, HCC, MCC 22 IMEENPGIFAV CRC, Leukemia, Melanoma 24
SLSDGLEEV CRC, PC, Urinary bladder Cancer 26 ALLELAEEL Leukemia,
Esophageal Cancer 27 ILADIVISA NSCLC, SCLC, PC, BrCa, Esophageal
Cancer 28 QLLDETSAITL SCLC, HCC, Leukemia, Urinary bladder Cancer
31 YLAPELFVNV SCLC, GC, Leukemia, Melanoma 32 KLDDLTQDLTV HCC, 33
VLLSLLEKV Leukemia 34 ILVEADSLWVV SCLC, PrC, Leukemia, Melanoma 36
YVLEDLEVTV SCLC, HCC, Leukemia 38 FLLEDDIHVS SCLC, Leukemia,
Melanoma 45 SLWQDIPDV NSCLC, SCLC 47 ILLSVPLLVV SCLC, Leukemia,
Gallbladder Cancer, Bile Duct Cancer 48 ALAELYEDEV SCLC, Brain
Cancer, HCC, Leukemia, Melanoma, Uterine Cancer 49 YLPAVFEEV
Leukemia 51 LLPDLEFYV SCLC, PrC, Gallbladder Cancer, Bile Duct
Cancer 54 SLLEQGKEPWMV SCLC, HCC, Gallbladder Cancer, Bile Duct
Cancer 55 SLLDLETLSL SCLC 56 KLYEGIPVLL BrCa 57 TLAELQPPVQL NSCLC,
SCLC, HCC, Leukemia, Melanoma, Esophageal Cancer 58 FLDTLKDLI
NSCLC, SCLC, GC, CRC, HCC, Leukemia, Melanoma, Esophageal Cancer,
Gallbladder Cancer, Bile Duct Cancer 59 IMEDIILTL SCLC, Leukemia,
BrCa 60 SLTIDGIYYV SCLC, Prostate, Leukemia 61 FLQGYQLHL NSCLC,
SCLC, BrCa, Melanoma, Esophageal Cancer 62 VLLDVSAGQLLM NSCLC,
Melanoma 63 YLLPSGGSVTL HCC, Melanoma, Esophageal Cancer 64
YAAPGGLIGV HCC, PC, Melanoma, Esophageal Cancer, Gallbladder
Cancer, Bile Duct Cancer 65 LKVNQGLESL NSCLC, SCLC, PC, Leukemia,
BrCa, Esophageal Cancer 66 FLDENIGGVAV SCLC, HCC 68 SLMELPRGLFL
Brain Cancer 69 FQLDPSSGVLVTV Esophageal Cancer 72 SLLELDGINL
NSCLC, SCLC, Prostate 74 ALLDPEVLSIFV NSCLC, Leukemia, Melanoma 75
GLLEVMVNL SCLC 76 ILIDSIYKV SCLC, CRC, BrCa 77 ILVEADGAWVV
Melanoma, Esophageal Cancer 79 SLFIGEKAVLL NSCLC, SCLC, CRC,
Leukemia, Esophageal Cancer, Urinary bladder Cancer 80 FLYDNLVESL
Leukemia 82 FLSSVTYNL SCLC, 84 VTFGEKLLGV NSCLC, CRC, PC, PrC,
Gallbladder Cancer, Bile Duct Cancer 85 KMSELRVTL SCLC, Esophageal
Cancer 86 NLIGKIENV Colon, Rectum 87 ALPEAPAPLLPHIT HCC, PC,
Urinary bladder Cancer, Gallbladder Cancer, Bile Duct Cancer 88
FLLVGDLMAV SCLC 91 IMQDFPAEIFL SCLC 92 YLIPFTGIVGL SCLC, HCC,
Leukemia, Melanoma 93 LLQAIKLYL BrCa 94 YLIDIKTIAI HCC 95 SVIPQIQKV
PC, Esophageal Cancer 97 SLINGSFLV NSCLC, RCC, CRC, HCC, PC,
Melanoma, Esophageal Cancer 98 LIIDQADIYL NSCLC, SCLC, RCC, CRC,
HCC, Leukemia, Melanoma, Esophageal Cancer 101 ILVGGGALATV
Melanoma, Urinary bladder Cancer 103 TLAEEVVAL SCLC, BrCa,
Esophageal Cancer 104 STMEQNFLL NSCLC, 105 LLLEHSFEI NSCLC,
Melanoma 106 LLYDAVHIVSV Brain Cancer 107 FLQPVDDTQHL Melanoma,
Esophageal Cancer 108 ALFPGVALLLA SCLC, HCC, Endometrium 110
FLSQVDFEL BrCa 117 ILPDGEDFLAV SCLC 118 KLIDNNINV Brain Cancer 119
FLYIGDIVSL Leukemia 121 GVVDPRAISVL Esophageal Cancer 123
NLWDLTDASVV SCLC, Prostate 125 VQIHQVAQV NSCLC, SCLC, HCC, PC,
Esophageal Cancer, Gallbladder Cancer, Bile Duct Cancer 126
VLAYFLPEA NSCLC, SCLC, CRC, PC, Leukemia, Esophageal Cancer,
Uterine Cancer 127 KIGDEPPKV NSCLC, SCLC, Brain Cancer, PC,
Esophageal Cancer, Uterine Cancer 128 YLFDDPLSAV Leukemia,
Esophageal Cancer 129 GLLDGGVDILL HCC, Leukemia, Esophageal Cancer,
Uterine Cancer 130 FLWNGEDSALL PC 131 FVPPVTVFPSL BrCa 132
LLVEQPPLAGV Leukemia 134 YLQELIFSV Endometrium 135 ALSEVDFQL SCLC,
Brain Cancer 137 TLVLTLPTV PC 139 SVMEVNSGIYRV HCC, MCC 141
YLDFSNNRL SCLC, BrCa 142 FLFATPVFI SCLC 143 LLLDITPEI NSCLC, Brain
Cancer, HCC, PC, BrCa, Melanoma, Esophageal Cancer 144 YIMEPSIFNTL
HCC, Leukemia, Melanoma, Urinary bladder Cancer 145 FLATSGTLAGI
Prostate 146 SLATAGDGLIEL Urinary bladder, Endometrium 148
ALNPEIVSV Esophageal Cancer, Urinary bladder Cancer 149 NLLELFVQL
SCLC, Leukemia, BrCa, Urinary bladder Cancer, Uterine Cancer 150
RLWEEGEELEL NSCLC, Melanoma, Esophageal Cancer 151 KILQQLVTL
Endometrium 152 ILFEDIFDV SCLC, Endometrium 153 FLIANVLYL SCLC,
Urinary bladder Cancer, Uterine Cancer 154 ALDDGTPAL HCC 155
RVANLHFPSV Melanoma, Esophageal Cancer 157 SLNDEVPEV NSCLC, Brain
Cancer, HCC, Esophageal Cancer, Uterine Cancer 159 GLVGNPLPSV HCC,
Leukemia 161 ALLEGVNTV NSCLC, Leukemia
163 ALDEMGDLLQL HCC 166 YLNHLEPPV SCLC, HCC, Leukemia, Esophageal
Cancer 167 KVLEVTEEFGV NSCLC, HCC, Melanoma 169 NLPEYLPFV SCLC,
BrCa, Urinary bladder Cancer 170 RLQETLSAA HCC, Esophageal Cancer
171 LLLPLQILL SCLC 174 ALAQYLITA Brain Cancer, HCC, PrC, Esophageal
Cancer, Urinary bladder Cancer 176 YLMEGSYNKVFL NSCLC, SCLC, CRC,
HCC, Melanoma 177 YLLPEEYTSTL Melanoma, Esophageal Cancer 178
ALTEIAFVV CRC, HCC, PrC 179 KVLNELYTV NSCLC 183 FGLDLVTEL NSCLC,
SCLC, RCC, GC, PC, Leukemia, BrCa, Melanoma 184 YLMDINGKMWL NSCLC,
SCLC, Melanoma 186 TLFFQQNAL Prostate, 188 GLFPVTPEAV Colon,
Rectum, HCC 190 FLSSLTETI Urinary bladder Cancer 195 GLFADLLPRL
NSCLC 197 ALGPEGGRV HCC 198 KTINKVPTV NSCLC, HCC 199 ALQDVPLSSV
Melanoma 200 LLFGSVQEV SCLC, PC, PrC, Esophageal Cancer,
Gallbladder Cancer, Bile Duct Cancer 201 RLVDYLEGI NSCLC, HCC,
Esophageal Cancer 204 KIAENVEEV NSCLC, HCC, PC, Leukemia, BrCa,
Esophageal Cancer 205 SLYPGTETMGL SCLC, Gallbladder, Bile duct 207
GLTSTNAEV HCC, PrC, Esophageal Cancer, Uterine Cancer 208 KISPVTFSV
HCC 209 KLIESKHEV Brain Cancer, HCC 210 LLLNAVLTV Urinary bladder
Cancer 212 ALWDQDNLSV HCC, PrC, BrCa, Urinary bladder Cancer 213
VTAAYMDTVSL NSCLC, SCLC, HCC, Melanoma, Esophageal Cancer,
Gallbladder Cancer, Bile Duct Cancer 214 FLLDLDPLLL SCLC, HCC,
Leukemia, Uterine Cancer 216 NLWEDPYYL SCLC, PrC, BrCa, Urinary
bladder Cancer 217 ALIHPVSTV NSCLC, RCC, HCC, Melanoma, Esophageal
Cancer 218 SALEELVNV RCC 222 NLIENVQRL NSCLC, RCC, CRC, HCC,
Melanoma, Esophageal Cancer, Urinary bladder Cancer 223 ALLENIALYL
Esophageal Cancer, Urinary bladder Cancer 226 MLYVVPIYL BrCa 228
AMQEYIAVV NSCLC, SCLC, Uterine Cancer, Gallbladder Cancer, Bile
Duct Cancer 229 RLPGPLGTV HCC, Esophageal Cancer, Endometrium 230
ILVDWLVEV Melanoma, Endometrium 233 VLSETLYEL SCLC, Endometrium 234
ALMEDTGRQML NSCLC, SCLC, HCC, Esophageal Cancer 235 YLNDLHEVLL
Esophageal Cancer, Uterine Cancer, Gallbladder Cancer, Bile Duct
Cancer 237 ALLEASGTLLL SCLC, HCC, PrC, Leukemia, Uterine Cancer,
Gallbladder Cancer, Bile Duct Cancer 240 ILLEQAFYL SCLC 241
SLVEVNPAYSV Prostate, Gallbladder, Bile duct 242 AIAYILQGV SCLC,
Leukemia, BrCa, Esophageal Cancer, Urinary bladder Cancer 243
LLLNELPSV Colon, Rectum, Esophageal Cancer 247 VLLPNDLLEKV Brain
Cancer 248 FLFPNQYVDV NSCLC, SCLC, HCC, Leukemia, Melanoma 249
LLDGFLVNV SCLC 251 ALYTGFSILV SCLC, Leukemia, Melanoma 252
LLIGTDVSL PrC, Leukemia, Esophageal Cancer, Urinary bladder Cancer
253 GLDAATATV Prostate, Leukemia 255 VLASYNLTV BrCa 256 FLPPEHTIVYI
SCLC, HCC, Leukemia, Melanoma 257 SIFSAFLSV Stomach, Urinary
bladder Cancer 258 ELAERVPAI Esophageal Cancer 262 LLWGDLIWL
Leukemia 263 LLVSNLDFGV NSCLC, SCLC, RCC, Leukemia 264 SLQEQLHSV
NSCLC, SCLC, PrC, BrCa, Melanoma, Esophageal Cancer 266 KITDTLIHL
BrCa 267 ALQDFLLSV HCC, Esophageal Cancer, Endometrium 268
IAGPGLPDL NSCLC, RCC, BrCa 269 RVLEVGALQAV HCC 270 LLLDEEGTFSL
Leukemia 271 LVYPLELYPA RCC, HCC, Leukemia, BrCa, Esophageal
Cancer, Urinary bladder Cancer 272 ALGNTVPAV PC, Leukemia,
Endometrium 273 NLFQSVREV HCC, BrCa 275 YLVYILNEL RCC, GC, HCC, PC,
Leukemia, Esophageal Cancer 276 ALFTFSPLTV Leukemia 277 LLPPLESLATV
SCLC, Leukemia, Melanoma 279 ALWGGTQPLL SCLC, Brain Cancer,
Esophageal Cancer 280 VLPDPEVLEAV Prostate, Leukemia 282 LLADVVPTT
Leukemia, Melanoma 283 ALYIGDGYVIHLA SCLC, BrCa, MCC, Melanoma 284
ILLSQTTGV Prostate, Leukemia 285 QLLHVGVTV NSCLC, RCC, CRC,
Leukemia, Esophageal Cancer 286 YLFPGIPEL SCLC, HCC 287 FLNEFFLNV
NSCLC, Leukemia, Melanoma, Esophageal Cancer 288 NLINEINGV SCLC,
PrC, Esophageal Cancer, Urinary bladder Cancer, Uterine Cancer 289
VLLEIEDLQV Leukemia, BrCa 290 GLLDLNNAILQL HCC 291 GLDSNLKYILV PC,
Melanoma 292 LLWEAGSEA Brain Cancer, PC 294 ILDPFQYQL HCC,
Esophageal Cancer 296 FMEGAIIYV SCLC, Leukemia 298 VMITKLVEV
Urinary bladder Cancer 299 YLLETSGNL Leukemia, Urinary bladder
Cancer 300 ALLGQTFSL SCLC, Brain Cancer, CRC 301 FLVEDLVDSL SCLC,
HCC, Leukemia 303 AILPQLFMV NSCLC, RCC, CRC, BrCa, Esophageal
Cancer, Urinary bladder Cancer 306 ALVNVQIPL HCC, Esophageal Cancer
308 SQYSGQLHEV Leukemia, Gallbladder, Bile duct 309 GLFDGVPTTA HCC,
Leukemia, BrCa, Melanoma 310 FLVDTPLARA Urinary bladder Cancer 311
RLYTGMHTV RCC, CRC, PC, Esophageal Cancer, Urinary bladder Cancer
312 IISDLTIAL SCLC, PC 313 VLFDDELLMV NSCLC, RCC, Brain Cancer,
HCC, Esophageal Cancer 314 ALIAEGIALV SCLC, Melanoma 315 YLQDVVEQA
SCLC, Endometrium 316 ILLERLWYV Melanoma 317 SLAALVVHV Esophageal
Cancer, Urinary bladder Cancer 318 GLINTGVLSV Colon, Rectum 319
SLEPQIQPV NSCLC, CRC, Leukemia, Esophageal Cancer 320 KMFEFVEPLL
Colon, Rectum 321 GLFEDVTQPGILL Leukemia, Melanoma 322 TLMTSLPAL
SCLC, 323 IQIGEETVITV NSCLC, SCLC, PrC, Leukemia, Melanoma,
Esophageal Cancer, Uterine Cancer, Gallbladder Cancer, Bile Duct
Cancer 324 FLYDEIEAEV Leukemia 325 FIMPATVADATAV Leukemia 327
GLAPFTEGISFV HCC 328 ALNDQVFEI SCLC, Brain Cancer, HCC, Esophageal
Cancer, Uterine Cancer 329 FLVTLNNVEV Melanoma 330 QLALKVEGV
Esophageal Cancer 331 KVDTVWVNV SCLC, Leukemia, BrCa, Melanoma,
Urinary bladder Cancer
332 YLISELEAA Brain Cancer, HCC, PC, PrC, Esophageal Cancer,
Uterine Cancer 333 FLPDANSSV NSCLC, Brain Cancer, PrC, Leukemia,
BrCa, Esophageal Cancer, Urinary bladder Cancer 334 TLTKVLVAL
Urinary bladder Cancer 335 YSLSSVVTV NSCLC, GC, PC, BrCa,
Gallbladder Cancer, Bile Duct Cancer 336 ILLTAIVQV BrCa, Esophageal
Cancer 338 SVLEDPVHAV NSCLC, SCLC, HCC, Melanoma 339 GLWEIENNPTVKA
HCC, Melanoma, Endometrium 340 ALLSMTFPL Brain Cancer, HCC, BrCa
341 SQIALNEKLVNL SCLC, HCC 342 HIYDKVMTV Colon, Rectum 343
SLLEVNEESTV NSCLC, Leukemia, Melanoma 344 YLQDQHLLLTV SCLC,
Melanoma 345 VIWKALIHL SCLC 346 LLDSKVPSV SCLC, HCC, PC, Esophageal
Cancer, Urinary bladder Cancer, Gallbladder Cancer, Bile Duct
Cancer 347 SLFKHDPAAWEA NSCLC, HCC, Esophageal Cancer, Urinary
bladder Cancer 348 ILLDVKTRL NSCLC, CRC, Esophageal Cancer, Urinary
bladder Cancer 349 SLTEYLQNV Colon, Rectum, HCC 351 SLIPNLRNV PC
354 LILEGVDTV Esophageal Cancer 355 SIQQSIERLLV NSCLC, CRC, HCC,
Leukemia, Melanoma, Esophageal Cancer 356 KLLGKLPEL NSCLC, CRC,
Esophageal Cancer 357 SMHDLVLQV Brain Cancer, PC, Endometrium 358
ALDEYTSEL Brain Cancer, PC, Leukemia, BrCa, Uterine Cancer 359
YLLPESVDL NSCLC, CRC, HCC, Esophageal Cancer 360 ALDJGASLLHL RCC,
HCC, Esophageal Cancer, Urinary bladder Cancer, Uterine Cancer 361
ALYELEGTTV Esophageal Cancer 362 TLYGLSVLL BrCa 363 KVLDVSDLESV
Urinary bladder, Endometrium 364 LLQNEQFEL RCC 365 YVIDQGETDVYV
Leukemia, Melanoma 366 RLLDMGETDLML SCLC, Leukemia, Melanoma 367
SLQNHNHQL HCC, Urinary bladder Cancer 369 GLFPEHLIDV HCC 370
SLLQDLVSV HCC 371 FLQAHLHTA BrCa 372 TMLLNIPLV SCLC, HCC, PC, PrC,
BrCa 373 SLLEDKGLAEV NSCLC, SCLC, Leukemia, BrCa, MCC, Melanoma 374
FLLQQHLISA Leukemia 375 SLTETIEGV BrCa, Esophageal Cancer 376
AMFESSQNVLL Colon, Rectum 378 ALGYFVPYV HCC 379 IMEGTLTRV Leukemia
381 FIDEAYVEV Leukemia 382 ALQNYIKEA Esophageal Cancer 383
ALLELENSVTL HCC 384 ILFANPNIFV CRC, Leukemia, Melanoma 385
SLLEQGLVEA NSCLC, SCLC, Brain Cancer, HCC, Esophageal Cancer,
Uterine Cancer, Gallbladder Cancer, Bile Duct Cancer 386 ILFRYPLTI
Urinary bladder Cancer 387 ALFQATAEV HCC, Esophageal Cancer 388
SLTIDGIRYV SCLC, Melanoma 389 LLADVTHLL Brain Cancer, Endometrium
390 ALFMKQIYL Urinary bladder Cancer 391 YVYPQRLNFV Leukemia,
Melanoma 393 GLLDTQTSQVLTA HCC, BrCa, Esophageal Cancer, Urinary
bladder Cancer 394 LLAVIGGLVYL NSCLC, SCLC, RCC, HCC, PrC,
Leukemia, Melanoma, Urinary bladder Cancer 395 ALALGGIAVV NSCLC,
CRC, HCC, PrC, Leukemia, BrCa, Melanoma, Esophageal Cancer, Urinary
bladder Cancer, Uterine Cancer 396 ALLPDLPAL HCC, BrCa 397
YLFGERLLEC Colon, Rectum, Leukemia 398 KLLEEDGTIITL Colon, Rectum,
PC 399 YLFEPLYHV SCLC 400 SLLTEQDLWTV Leukemia 401 ILLDDTGLAYI
SCLC, HCC, Leukemia, BrCa, Melanoma 403 KLYDRILRV NSCLC, RCC 404
AIDIJGRDPAV SCLC, Leukemia 405 ALYDVFLEV PC, Esophageal Cancer 406
SVQGEDLYLV HCC, Endometrium 407 YLMDLINFL PC, Prostate 408
VLDDSIYLV Leukemia 409 LLDAMNYHL HCC, Leukemia 410 VLSDVIPJI SCLC,
RCC, Brain Cancer, GC, HCC, PC, PrC, Leukemia, Melanoma, Esophageal
Cancer 411 LLAHLSPEL HCC 412 YLDDLNEGVYI Leukemia, Melanoma 415
LLDKVYSSV NSCLC, HCC, Leukemia, Esophageal Cancer 418 ALAELENIEV
SCLC, MCC 419 GQYEGKVSSV HCC 420 FMYDTPQEV SCLC, HCC, BrCa 421
RLPETLPSL NSCLC, SCLC, GC, CRC, PC 422 FLPKLLLLA BrCa 423 GLDGPPPTV
HCC, PC, BrCa, Urinary bladder Cancer, Uterine Cancer, Gallbladder
Cancer, Bile Duct Cancer 424 TLLDALYEI RCC, Esophageal Cancer,
Endometrium 425 FLYEKSSQV Brain Cancer, Endometrium 426 RLADKSVLV
Colon, Rectum 427 ALLPLSPYL NSCLC, SCLC, HCC, PC, BrCa, Uterine
Cancer 428 KLGHTDILVGV NSCLC, SCLC, CRC, HCC, Leukemia 429
GLVNDLARV NSCLC, HCC 430 HLYSSIEHLTT NSCLC, CRC, HCC, MCC,
Esophageal Cancer 431 SLVNVVPKL NSCLC, SCLC, RCC, Brain Cancer,
Melanoma, Esophageal Cancer 432 TLIEESAKV Prostate 433 AMLNEPWAV
SCLC 434 KVSNSGITRV NSCLC 435 WLMPVIPAL SCLC 437 SMAPGLVIQAV SCLC,
Prostate 439 YLLQEIYGI SCLC, BrCa 440 ALADGVTMQV Gallbladder, Bile
duct 441 ALLENPKMEL NSCLC, SCLC, CRC, HCC, MCC, Esophageal Cancer
443 GLWEIENNPTV NSCLC, SCLC, HCC, PC, PrC, Melanoma 444 GLLRDEALAEV
NSCLC, SCLC, CRC, Melanoma, Esophageal Cancer 446 QLIPALAKV NSCLC,
SCLC, PrC, BrCa, MCC, Uterine Cancer 447 QLVPALAKV NSCLC, SCLC,
HCC, PrC, Esophageal Cancer, Urinary bladder Cancer 448 NLLETKLQL
Colon, Rectum, Leukemia 449 KLAEGLDIQL SCLC, Colon, Rectum 450
FMIDASVHPTL NSCLC, SCLC, RCC, Brain Cancer, CRC, HCC, Leukemia,
Melanoma, Esophageal Cancer 451 LLLLDTVTMQV SCLC, HCC 452
ILLEHGADPNL HCC, Leukemia, Melanoma 454 KLPPPPPQA NSCLC, SCLC 455
SLLKEPQKVQL RCC 456 LLIGHLERV NSCLC, Brain Cancer, CRC, 457
SLLPGNLVEKV NSCLC, HCC, Leukemia, Melanoma 458 SLIDKLYNI NSCLC,
Colon, Rectum, 459 ALITEVVRL NSCLC, CRC, PC, Leukemia, BrCa,
Esophageal Cancer 461 VMFRTPLASV SCLC, Melanoma, Esophageal Cancer
463 SLVESHLSDQLTL NSCLC, SCLC, HCC, Melanoma 464 ALNDCIYSV Brain
Cancer, HCC, PC 465 QLCDLNAEL HCC, Esophageal Cancer 466 VLIANLEKL
BrCa, Esophageal Cancer 468 YLRSVGDGETV Leukemia, Melanoma 469
YLASDEITTV SCLC,
472 KLLEVSDDPQV HCC, MCC, Melanoma, Esophageal Cancer 473
AMATESILHFA SCLC, Brain Cancer, CRC, HCC, MCC, Gallbladder Cancer,
Bile Duct Cancer 474 YLDPALELGPRNV NSCLC, SCLC, Brain Cancer, HCC,
MCC, Melanoma 475 LLLNEEALAQI SCLC, Leukemia 476 ALMERTGYSMV HCC
477 ALLPASGQIAL NSCLC, HCC, Esophageal Cancer, Urinary bladder
Cancer 478 YLLHEKLNL Colon, Rectum, 479 SLFGNSGILENV NSCLC, SCLC,
HCC, MCC, Urinary bladder Cancer 480 ALLEDSCHYL NSCLC, CRC, HCC,
Leukemia, Esophageal Cancer 481 GLIEDYEALL SCLC 483 ALTDIVSQV
Urinary bladder Cancer 484 SLIEKVTQL HCC 485 NVPDSFNEV Stomach 486
AVMESIQGV NSCLC, HCC, PrC, Leukemia, Esophageal Cancer, Urinary
bladder Cancer, Uterine Cancer 487 LLINSVFHV Melanoma 488
FLAEDPKVTL Leukemia 489 KMWEELPEW NSCLC, HCC, Leukemia 490
FLLQHVQEL Leukemia 491 GLNDRSDAV Esophageal Cancer, Endometrium 492
SLFDGFADGLGV NSCLC, SCLC, Brain Cancer, HCC, PrC, Esophageal Cancer
493 GLLGEKTQDLIGV NSCLC, SCLC 494 ALQPEPIKV Urinary bladder,
Gallbladder, Bile duct 495 FIFSEKPVFV Urinary bladder Cancer 496
FLVEKQPPQV Leukemia, Melanoma 497 GLLEKLTAI NSCLC, RCC, Esophageal
Cancer, Uterine Cancer 498 KLWTGGLDNTV HCC, Esophageal Cancer 499
KIFDIDEAEEGV PC, Melanoma, Esophageal Cancer 500 SLMEDQVLQL SCLC,
Colon, Rectum 501 LLDPNVKSIFV NSCLC, SCLC, Brain Cancer, HCC, PrC,
MCC, Melanoma, Esophageal Cancer, Gallbladder Cancer, Bile Duct
Cancer 502 RLLAQVPGL RCC, Urinary bladder Cancer 503 SLNHFTHSV
NSCLC, Leukemia 504 GLSDGNPSL Leukemia, BrCa 505 SLAPGDVVRQV
Esophageal Cancer 506 KLLGKVETA NSCLC, Brain Cancer, Leukemia,
Esophageal Cancer 507 KLIDDQDISISL Leukemia 508 ILAQEQLVVGV
Leukemia, Esophageal Cancer 510 KLYSVVSQL Colon, Rectum, Leukemia
513 SLWPSPEQL HCC, Esophageal Cancer 514 ILVDWLVQV NSCLC, SCLC,
RCC, Brain Cancer, GC, CRC, HCC, Melanoma, Esophageal Cancer,
Urinary bladder Cancer, Uterine Cancer 517 LLMPIPEGLTL NSCLC, SCLC,
HCC, Melanoma 518 KLNAEVACV CRC, PrC, Esophageal Cancer 520
LAVHPSGVAL Leukemia 521 MLLTKLPTI NSCLC, SCLC, CRC, HCC, BrCa,
Melanoma, Urinary bladder Cancer 522 TLVVWYRSPEV SCLC 523 YQIPRTFTL
SCLC, Brain Cancer, HCC, Leukemia, Melanoma 525 VLLEAGEGLVTI
Melanoma 526 RLAEVGQYEQV NSCLC, HCC, MCC, Gallbladder Cancer, Bile
Duct Cancer 527 FLLEPGNLEV Urinary bladder Cancer 528 SVAEGRALMSV
Brain Cancer, CRC, HCC, Esophageal Cancer 529 LLADELITV Prostate,
Leukemia, Urinary bladder Cancer 530 VMYADIGGMDI SCLC, Melanoma 531
YTLPIASSIRL SCLC, CRC, HCC 533 RMVAEIQNV Leukemia, Esophageal
Cancer 535 KLIAQNLEL Colon, Rectum 536 YLVEGRFSV Leukemia 538
LLLAHIIAL NSCLC, Brain Cancer, HCC 539 ALFDAQAQV NSCLC, SCLC, Brain
Cancer, HCC, PC, PrC, BrCa, Esophageal Cancer, Urinary bladder
Cancer, Uterine Cancer, Gallbladder Cancer, Bile Duct Cancer 540
ALIPETTTLTV HCC, PC, Melanoma 541 SMLEPVPEL NSCLC, SCLC, Brain
Cancer, CRC, HCC, Esophageal Cancer 542 RVWDISTVSSV SCLC, Leukemia,
Melanoma, Esophageal Cancer 543 GLLPTPITQQASL Esophageal Cancer 544
LLWDVPAPSL Leukemia, Melanoma 545 LLADLLHNV NSCLC, SCLC, Colon,
Rectum 546 VMIAGKVAVV Colon, Rectum, HCC 549 AMLENASDIKL Melanoma
550 FLYDEIEAEVNL Leukemia, Melanoma 551 KLYESLLPFA SCLC, HCC, PrC,
Melanoma 552 GLLDLPFRVGV SCLC, Brain Cancer, Leukemia, Melanoma 554
LLMPSSEDLLL NSCLC, SCLC, CRC, HCC, PrC, BrCa, Esophageal Cancer,
Urinary bladder Cancer, Gallbladder Cancer, Bile Duct Cancer 555
YVLEGLKSV SCLC, Melanoma 556 FLTDLEDLTL SCLC, Leukemia 557
KLYDDMIRL Colon, Rectum, 558 GLLENIPRV NSCLC, SCLC, RCC, Brain
Cancer, HCC, Leukemia, Uterine Cancer, Gallbladder Cancer, Bile
Duct Cancer 559 VTVPPGPSL Leukemia 560 ALWDIETGQQTTT SCLC, HCC,
Melanoma, Esophageal Cancer 561 YLQLTQSEL SCLC, Leukemia,
Esophageal Cancer, Gallbladder Cancer, Bile Duct Cancer 563
WLLPYNGVTV SCLC, Melanoma 564 TVTNAVVTV RCC, GC, HCC, Melanoma 565
ALQETPTSV SCLC, Melanoma, Esophageal Cancer, Uterine Cancer 566
VIADGGIQNV Leukemia, Melanoma, Endometrium 567 SLLPLDDIVRV Leukemia
568 TLYDIAHTPGV NSCLC, SCLC, CRC, Melanoma, Esophageal Cancer 571
LLLTTIPQI Prostate, Leukemia 572 ALADLIEKELSV Leukemia 573
ILVANAIVGV NSCLC, HCC, Leukemia, Melanoma 574 YLLQEPPRTV SCLC 575
YLISQVEGHQV CRC, HCC, MCC, Melanoma, Esophageal Cancer 576
ILLNNSGQIKL NSCLC, CRC, HCC, Leukemia, BrCa, Melanoma, Esophageal
Cancer 577 VMFEDGVLMRL Colon, Rectum, Leukemia 578 FLDPGGPMMKL
NSCLC, CRC, MCC, Melanoma 579 NLMEMVAQL NSCLC, CRC, HCC, Leukemia
580 LLMENAERV CRC, Leukemia, BrCa, Melanoma 581 RLWNETVEL SCLC,
Colon, Rectum 583 ILANDGVLLAA HCC, Esophageal Cancer 584
ALAEVAAMENV Melanoma 585 ALWDLAADKQTL Urinary bladder Cancer 586
KLKPGDLVGV Brain Cancer, HCC 587 VMNDRLYAI Leukemia 588 SLLPLSHLV
Melanoma, Esophageal Cancer 589 KLYPQLPAEI NSCLC, SCLC, Brain
Cancer, HCC, Leukemia, MCC, Melanoma, Esophageal Cancer 590
SLIEKLWQT SCLC, Brain Cancer 591 SMAELDIKL Leukemia, Esophageal
Cancer, Endometrium 592 RLLJAAENFL SCLC, Brain Cancer, BrCa,
Esophageal Cancer 593 GLPRFGIEMV Brain Cancer 594 IMLKGDNITL
Esophageal Cancer 595 VLLSIYPRV NSCLC, SCLC, RCC, Leukemia, BrCa
596 ALLDQTKTLAESAL Leukemia, Melanoma 597 KLLEGQVIQL NSCLC, SCLC,
CRC, HCC, BrCa 599 YLLNDASLISV NSCLC, CRC, HCC, Melanoma, Uterine
Cancer 600 ALAAPDIVPAL Leukemia 601 SAFPFPVTV Stomach, Leukemia,
Esophageal Cancer 602 YLLEQIKLIEV NSCLC, SCLC 603 FLIEPEHVNTV HCC,
PC, Leukemia, Melanoma 604 SILDRDDIFV Leukemia 606 ALWETEVYI SCLC,
Brain Cancer, HCC, PrC 607 RLYSGISGLEL NSCLC
608 SLLSVSHAL RCC 609 ALWKQLLEL PC 610 LLAPTPYIIGV NSCLC, SCLC,
RCC, Brain Cancer, CRC, HCC, PrC, Leukemia, BrCa, MCC, Melanoma,
Esophageal Cancer, Urinary bladder Cancer, Gallbladder Cancer, Bile
Duct Cancer 611 YLLDDGTLVV HCC, Melanoma 613 RLLPPGAVVAV NSCLC,
SCLC, HCC 614 LLLPDQPPYHL Melanoma 616 VLIDEVESL NSCLC, SCLC, RCC,
GC, BrCa, Melanoma, Esophageal Cancer, Urinary bladder Cancer 617
ALMYESEKVGV HCC, Gallbladder, Bile duct 618 VLFDSESIGIYV SCLC,
Melanoma 619 ALQDRVPLA Brain Cancer, CRC, Esophageal Cancer,
Uterine Cancer 620 KLLNKIYEA Brain Cancer 621 VLMDRLPSLL Melanoma
622 RLLGEEVVRVLQA NSCLC, SCLC, CRC, Melanoma 624 FLQEEPGQLL
Leukemia, Melanoma, Esophageal Cancer 625 VVLEGASLETV SCLC,
Melanoma 626 LLMATILHL SCLC, Melanoma, Urinary bladder Cancer,
Gallbladder Cancer, Bile Duct Cancer 627 KLLETELLQEI NSCLC, SCLC,
CRC, HCC, MCC, Melanoma 628 KLWEFFQVDV SCLC, Brain Cancer, HCC 629
HLLNESPML SCLC, Esophageal Cancer 630 LLSHVIVAL PC, Leukemia 631
FLDVFLPRV PC, Leukemia, Melanoma, Esophageal Cancer 632 YLIPDIDLKL
NSCLC, SCLC, CRC, HCC, PC, Leukemia, Melanoma, Urinary bladder
Cancer, Uterine Cancer 633 ALSRVSVNV Melanoma, Esophageal Cancer
634 VVAEFVPLI Brain Cancer, Leukemia 635 SLDSTLHAV NSCLC, Brain
Cancer, CRC, HCC, BrCa, Esophageal Cancer 637 SIYGGFLLGV NSCLC,
SCLC, HCC, PrC, BrCa, Uterine Cancer 638 KLIQESPTV SCLC, HCC,
Prostate 639 SLFQNCFEL Leukemia SCLC, GC, CRC, HCC, PrC, BrCa, MCC,
Esophageal 640 YLFSEALNAA Cancer, Urinary bladder Cancer, Uterine
Cancer, Gallbladder Cancer, Bile Duct Cancer NSCLC = non-small cell
lung cancer, SCLC = small cell lung cancer, RCC = kidney cancer,
CRC = colorectal cancer, GC = gastric cancer, HCC = liver cancer,
PC = pancreatic cancer, PrC = prostate cancer, BrCa = breast
cancer, MCC = Merkel cell carcinoma
TABLE-US-00005 TABLE 5B Peptides according to the present invention
and their specific uses in other proliferative diseases, especially
in other cancerous diseases (amendment of Table 4). The table
shows, like Table 4A, for selected peptides on which additional
tumor types they were found showing over-presentation (including
specific presentation) on more than 5% of the measured tumor
samples, or presentation on more than 5% of the measured tumor
samples with a ratio of geometric means tumor vs normal tissues
being larger than 3. Over-presentation is defined as higher
presentation on the tumor sample as compared to the normal sample
with highest presentation. Normal tissues against which
over-presentation was tested were: adipose tissue, adrenal gland,
artery, bone marrow, brain, central nerve, colon, duodenum,
esophagus, eye, gallbladder, heart, kidney, liver, lung, lymph
node, mononuclear white blood cells, pancreas, parathyroid gland,
peripheral nerve, peritoneum, pituitary, pleura, rectum, salivary
gland, skeletal muscle, skin, small intestine, spleen, stomach,
thyroid gland, trachea, ureter, urinary bladder, vein. SEQ ID NO.
Sequence Additional organs/cancerous diseases 1 SLMEPPAVLLL BRCA,
Urinary Bladder Cancer, Uterine Cancer, AML, HNSCC 2 SLLEADPFL CLL,
Uterine Cancer, Gallbladder Cancer and Bile Duct Cancer 3 SLASKLTTL
Uterine Cancer 5 HLTEVYPEL Urinary Bladder Cancer, Uterine Cancer 6
VLVSDGVHSV Melanoma, Urinary Bladder Cancer, Uterine Cancer, HNSCC
7 SLVGLLLYL Gallbladder Cancer and Bile Duct Cancer, AML 8
FTLGNVVGMYL Melanoma, Urinary Bladder Cancer, Uterine Cancer 9
GAAKDLPGV Esophageal Cancer 11 KIFEMLEGV Gallbladder Cancer and
Bile Duct Cancer 13 YLMDESLNL NSCLC, Brain Cancer, BRCA, Melanoma
14 AAYGGLNEKSFV CLL, Esophageal Cancer 15 VLLTFKIFL Uterine Cancer,
NHL 16 VLFQGQASL Melanoma, Uterine Cancer, AML, NHL 18 YLVAKLVEV
NSCLC, BRCA, Urinary Bladder Cancer, HNSCC 21 VLDELDMEL Melanoma 22
IMEENPGIFAV CLL, Urinary Bladder Cancer, Gallbladder Cancer and
Bile Duct Cancer 23 VLLDDIFAQL CLL, Uterine Cancer, AML 24
SLSDGLEEV NSCLC, BRCA, Melanoma, Uterine Cancer, HNSCC 26 ALLELAEEL
BRCA, Melanoma, Urinary Bladder Cancer, Uterine Cancer, Gallbladder
Cancer and Bile Duct Cancer, AML, NHL, HNSCC 27 ILADIVISA Melanoma,
Uterine Cancer, Gallbladder Cancer and Bile Duct Cancer 28
QLLDETSAITL CLL 29 KMLGIPISNILMV Urinary Bladder Cancer,
Gallbladder Cancer and Bile Duct Cancer 30 LILDWVPYI Melanoma,
Uterine Cancer, HNSCC 31 YLAPELFVNV BRCA, Uterine Cancer 32
KLDDLTQDLTV SCLC, Esophageal Cancer, Urinary Bladder Cancer,
Gallbladder Cancer and Bile Duct Cancer, HNSCC 33 VLLSLLEKV CLL,
Melanoma 34 ILVEADSLWVV AML 36 YVLEDLEVTV NSCLC, CLL, BRCA,
Melanoma, Urinary Bladder Cancer, Uterine Cancer, Gallbladder
Cancer and Bile Duct Cancer, NHL, HNSCC 38 FLLEDDIHVS CLL, Urinary
Bladder Cancer, NHL 40 TLLVKVFSV Melanoma 42 VLLQKIVSA Esophageal
Cancer, AML 43 VLSSLEINI NHL 45 SLWQDIPDV BRCA, Urinary Bladder
Cancer, HNSCC 47 ILLSVPLLVV CLL, Uterine Cancer 49 YLPAVFEEV CLL 51
LLPDLEFYV Melanoma, Urinary Bladder Cancer 54 SLLEQGKEPWMV NSCLC,
CLL 57 TLAELQPPVQL CLL, Urinary Bladder Cancer, Uterine Cancer,
Gallbladder Cancer and Bile Duct Cancer, NHL, HNSCC 58 FLDTLKDLI
Urinary Bladder Cancer, Uterine Cancer, AML, NHL 60 SLTIDGIYYV
BRCA, Uterine Cancer 61 FLQGYQLHL Urinary Bladder Cancer, Uterine
Cancer, Gallbladder Cancer and Bile Duct Cancer, NHL, HNSCC 63
YLLPSGGSVTL Gallbladder Cancer and Bile Duct Cancer, HNSCC 64
YAAPGGLIGV NSCLC, SCLC, CLL, BRCA, Urinary Bladder Cancer, Uterine
Cancer, AML, NHL, HNSCC 65 LKVNQGLESL Melanoma, Gallbladder Cancer
and Bile Duct Cancer, AML, NHL 66 FLDENIGGVAV Melanoma, Urinary
Bladder Cancer, Uterine Cancer, Gallbladder Cancer and Bile Duct
Cancer, AML, NHL, HNSCC 67 TLLAEALVTV SCLC 69 FQLDPSSGVLVTV HNSCC
71 GILARIASV AML, NHL 72 SLLELDGINL BRCA, Uterine Cancer 73
NIFDLQIYV BRCA 75 GLLEVMVNL Gallbladder Cancer and Bile Duct Cancer
76 ILIDSIYKV Uterine Cancer 77 ILVEADGAWVV BRCA, Uterine Cancer,
AML, NHL 78 SLFSSLEPQIQPV CLL, Melanoma, Urinary Bladder Cancer,
AML, HNSCC 79 SLFIGEKAVLL CLL, BRCA, Melanoma, Gallbladder Cancer
and Bile Duct Cancer, AML, NHL, HNSCC 80 FLYDNLVESL CLL, NHL 81
FLFSQLQYL Gallbladder Cancer and Bile Duct Cancer, AML 82 FLSSVTYNL
Melanoma 83 ILAPTVMMI Melanoma 84 VTFGEKLLGV Melanoma 88 FLLVGDLMAV
Melanoma 91 IMQDFPAEIFL CLL, BRCA, Melanoma, Gallbladder Cancer and
Bile Duct Cancer, AML, NHL, HNSCC 92 YLIPFTGIVGL CLL, AML, NHL,
HNSCC 93 LLQAIKLYL Urinary Bladder Cancer, Gallbladder Cancer and
Bile Duct Cancer 94 YLIDIKTIAI SCLC, Melanoma, Urinary Bladder
Cancer 97 SLINGSFLV CLL, BRCA, Urinary Bladder Cancer, Uterine
Cancer, Gallbladder Cancer and Bile Duct Cancer 98 LIIDQADIYL CLL,
Urinary Bladder Cancer, Gallbladder Cancer and Bile Duct Cancer,
AML, NHL 100 YLLSTNAQL Urinary Bladder Cancer 102 YLFESEGLVL CLL,
Melanoma 103 TLAEEVVAL Melanoma, HNSCC 104 STMEQNFLL SCLC, BRCA,
Melanoma, Gallbladder Cancer and Bile Duct Cancer, HNSCC 105
LLLEHSFEI Urinary Bladder Cancer, Gallbladder Cancer and Bile Duct
Cancer, NHL, HNSCC 107 FLQPVDDTQHL Uterine Cancer, Gallbladder
Cancer and Bile Duct Cancer 108 ALFPGVALLLA Melanoma 111 YVWGFYPAEV
CLL, Uterine Cancer, NHL 117 ILPDGEDFLAV CLL, BRCA, Uterine Cancer,
NHL 119 FLYIGDIVSL CLL, Melanoma 120 ALLGIPLTLV Uterine Cancer 123
NLWDLTDASVV NSCLC, BRCA, Melanoma, Esophageal Cancer, Uterine
Cancer, Gallbladder Cancer and Bile Duct Cancer, HNSCC 124
ALYETELADA CLL, Uterine Cancer, AML, NHL 126 VLAYFLPEA CLL, BRCA,
Urinary Bladder Cancer, Gallbladder Cancer and Bile Duct Cancer,
AML, NHL, HNSCC 127 KIGDEPPKV BRCA, Melanoma, Urinary Bladder
Cancer, Gallbladder Cancer and Bile Duct Cancer, HNSCC 128
YLFDDPLSAV CLL BRCA, Uterine Cancer, Gallbladder Cancer and Bile
Duct Cancer, AML, NHL, HNSCC 129 GLLDGGVDILL HNSCC 131 FVPPVTVFPSL
Uterine Cancer 132 LLVEQPPLAGV CLL, Melanoma 134 YLQELIFSV CLL,
HNSCC 137 TLVLTLPTV SCLC, CLL, Urinary Bladder Cancer, Uterine
Cancer, Gallbladder Cancer and Bile Duct Cancer, AML, NHL, HNSCC
138 YQYPRAILSV NSCLC, AML
139 SVMEVNSGIYRV SCLC, CLL, Urinary Bladder Cancer, Uterine Cancer,
Gallbladder Cancer and Bile Duct Cancer, NHL, HNSCC 140 YMDAPKAAL
Melanoma, AML 141 YLDFSNNRL CLL 144 YIMEPSIFNTL CLL, BRCA 146
SLATAGDGLIEL BRCA 147 SLLEAVSFL Gallbladder Cancer and Bile Duct
Cancer, AML, HNSCC 148 ALNPEIVSV SCLC, CLL, Melanoma, NHL, HNSCC
150 RLWEEGEELEL Uterine Cancer, Gallbladder Cancer and Bile Duct
Cancer, HNSCC 151 KILQQLVTL BRCA, Melanoma, Gallbladder Cancer and
Bile Duct Cancer 152 ILFEDIFDV BRCA, Gallbladder Cancer and Bile
Duct Cancer 153 FLIANVLYL HNSCC 154 ALDDGTPAL Uterine Cancer 155
RVANLHFPSV CLL, HNSCC 157 SLNDEVPEV BRCA, Melanoma, Urinary Bladder
Cancer, Gallbladder Cancer and Bile Duct Cancer, NHL, HNSCC 159
GLVGNPLPSV BRCA 160 FLFDEEIEQI BRCA 161 ALLEGVNTV AML 163
ALDEMGDLLQL BRCA, Gallbladder Cancer and Bile Duct Cancer, HNSCC
164 ALLPQPKNLTV Melanoma 166 YLNHLEPPV Brain Cancer, CLL, BRCA,
AML, NHL 167 KVLEVTEEFGV BRCA, Urinary Bladder Cancer 170 RLQETLSAA
Urinary Bladder Cancer, AML 171 LLLPLQILL HNSCC 172 VLYSYTIITV
SCLC, CLL, Uterine Cancer, NHL 173 LLDSASAGLYL SCLC, Uterine
Cancer, AML, NHL 174 ALAQYLITA SCLC, BRCA, Melanoma, Gallbladder
Cancer and Bile Duct Cancer 175 YLFENISQL Esophageal Cancer,
Urinary Bladder Cancer, HNSCC 176 YLMEGSYNKVFL Urinary Bladder
Cancer, Gallbladder Cancer and Bile Duct Cancer 177 YLLPEEYTSTL
NHL, HNSCC 178 ALTEIAFVV SCLC, CLL, BRCA, Melanoma, Uterine Cancer
179 KVLNELYTV CRC, BRCA, Melanoma, Uterine Cancer 180 FQIDPHSGLVTV
SCLC 182 MLLEAPGIFL CLL 183 FGLDLVTEL CLL, Urinary Bladder Cancer,
Uterine Cancer, AML, NHL, HNSCC 184 YLMDINGKMWL CLL, Uterine
Cancer, Gallbladder Cancer and Bile Duct Cancer, NHL 185 FLIDDKGYTL
HNSCC 186 TLFFQQNAL PC, NHL, HNSCC 187 RQISIRGIVGV NSCLC, Urinary
Bladder Cancer, Uterine Cancer, AML, HNSCC 188 GLFPVTPEAV Uterine
Cancer 190 FLSSLTETI BRCA, Uterine Cancer, Gallbladder Cancer and
Bile Duct Cancer 191 LLQEGQALEYV Uterine Cancer, Gallbladder Cancer
and Bile Duct Cancer 192 KMLDGASFTL BRCA 193 QLLDADGFLNV SCLC, NHL
194 ALPLFVITV AML, HNSCC 195 GLFADLLPRL PC, Uterine Cancer, AML,
HNSCC 197 ALGPEGGRV Uterine Cancer 198 KTINKVPTV SCLC, Brain
Cancer, CRC, Urinary Bladder Cancer, Uterine Cancer, HNSCC 199
ALQDVPLSSV SCLC, Urinary Bladder Cancer 201 RLVDYLEGI SCLC, Uterine
Cancer, Gallbladder Cancer and Bile Duct Cancer, AML 205
SLYPGTETMGL AML 206 VLQEGKLQKLAQL NSCLC, SCLC, BRCA, Uterine
Cancer, HNSCC 207 GLTSTNAEV AML 209 KLIESKHEV Melanoma, Uterine
Cancer 210 LLLNAVLTV SCLC, AML, NHL 211 LLWPGAALL CLL, AML, NHL 214
FLLDLDPLLL Brain Cancer, CRC, CLL, Urinary Bladder Cancer 217
ALIHPVSTV BRCA, Urinary Bladder Cancer, Uterine Cancer, Gallbladder
Cancer and Bile Duct Cancer 218 SALEELVNV GC 224 TLIDAQWVL HNSCC
226 MLYVVPIYL SCLC, Melanoma, AML, NHL 227 ALMNTLLYL Uterine
Cancer, AML, HNSCC 228 AMQEYIAVV PC, Melanoma, HNSCC 229 RLPGPLGTV
BRCA, Melanoma, Gallbladder Cancer and Bile Duct Cancer 230
ILVDWLVEV Esophageal Cancer, Gallbladder Cancer and Bile Duct
Cancer, AML, NHL, HNSCC 233 VLSETLYEL BRCA, HNSCC 234 ALMEDTGRQML
Brain Cancer, Urinary Bladder Cancer, Gallbladder Cancer and Bile
Duct Cancer, HNSCC 235 YLNDLHEVLL NSCLC, Urinary Bladder Cancer 236
GLLEAKVSL Gallbladder Cancer and Bile Duct Cancer 237 ALLEASGTLLL
BRCA, AML 238 YLISFQTHI CLL 242 AIAYILQGV RCC, CRC, CLL, Melanoma,
Uterine Cancer, AML, NHL, HNSCC 243 LLLNELPSV SCLC, BRCA, Melanoma,
Urinary Bladder Cancer, Gallbladder Cancer and Bile Duct Cancer,
AML, HNSCC 244 SLFGGTEITI Uterine Cancer 246 LLWEVVSQL BRCA 247
VLLPNDLLEKV Melanoma 248 FLFPNQYVDV CLL, BRCA 249 LLDGFLVNV CLL,
Melanoma, NHL 250 ALSEEGLLVYL BRCA, Melanoma 252 LLIGTDVSL CLL, NHL
256 FLPPEHTIVYI CLL, Uterine Cancer 257 SIFSAFLSV Melanoma,
Gallbladder Cancer and Bile Duct Cancer, AML, NHL 258 ELAERVPAI
CLL, Urinary Bladder Cancer, Gallbladder Cancer and Bile Duct
Cancer, AML, NHL, HNSCC 259 TLMRQLQQV Uterine Cancer 260
TLLEGPDPAELLL AML 261 YVLEFLEEI RCC, CLL, BRCA 262 LLWGDLIWL CRC,
PrC, CLL, Melanoma, AML 263 LLVSNLDFGV CRC, CLL, Urinary Bladder
Cancer, AML, NHL 264 SLQEQLHSV Uterine Cancer 266 KITDTLIHL Uterine
Cancer 267 ALQDFLLSV NSCLC, SCLC, CRC, BRCA, Melanoma, Urinary
Bladder Cancer, AML, NHL, HNSCC 268 IAGPGLPDL HCC, Uterine Cancer,
NHL 269 RVLEVGALQAV CLL 270 LLLDEEGTFSL CLL, BRCA, Melanoma, NHL
271 LVYPLELYPA Gallbladder Cancer and Bile Duct Cancer 274
SLLFSLFEA Urinary Bladder Cancer, AML, NHL 275 YLVYILNEL CLL,
Melanoma, NHL 276 ALFTFSPLTV Uterine Cancer 277 LLPPLESLATV CLL,
BRCA, Urinary Bladder Cancer, HNSCC 278 QLLDVVLTI HNSCC 280
VLPDPEVLEAV Gallbladder Cancer and Bile Duct Cancer, NHL, SCLC 281
ILRESTEEL Melanoma 282 LLADVVPTT CLL, Uterine Cancer, AML, NHL,
HNSCC 283 ALYIGDGYVIHLA Esophageal Cancer, Urinary Bladder Cancer,
Uterine Cancer, NHL 284 ILLSQTTGV CLL, Urinary Bladder Cancer, AML,
HNSCC 285 QLLHVGVTV CLL, Melanoma, Urinary Bladder Cancer, AML, NHL
286 YLFPGIPEL NSCLC, CLL, Melanoma, AML, NHL, HNSCC 289 VLLEIEDLQV
CLL, NHL 290 GLLDLNNAILQL Uterine Cancer 292 LLWEAGSEA Melanoma 293
GLGELQELYL AML, NHL 294 ILDPFQYQL Melanoma, Gallbladder Cancer and
Bile Duct Cancer, NHL, HNSCC 297 VLADIELAQA CLL 298 VMITKLVEV
Gallbladder Cancer and Bile Duct Cancer
300 ALLGQTFSL AML, HNSCC 301 FLVEDLVDSL CLL, BRCA, Melanoma,
Uterine Cancer, AML 302 ALLQEGEVYSA Melanoma, Urinary Bladder
Cancer 303 AILPQLFMV Melanoma 304 MTLGQIYYL NSCLC, SCLC, CRC, HCC,
BRCA, Melanoma, Urinary Bladder Cancer, Uterine Cancer, Gallbladder
Cancer and Bile Duct Cancer, AML, HNSCC 306 ALVNVQIPL Melanoma,
Uterine Cancer 307 ALPVSLPQI CLL, BRCA, Melanoma, AML, NHL, HNSCC
308 SQYSGQLHEV CLL 309 GLFDGVPTTA SCLC, Urinary Bladder Cancer,
Gallbladder Cancer and Bile Duct Cancer, HNSCC 310 FLVDTPLARA
Gallbladder Cancer and Bile Duct Cancer, HNSCC 311 RLYTGMHTV SCLC,
BRCA, NHL, HNSCC 312 IISDLTIAL NSCLC, CRC, BRCA, Melanoma,
Esophageal Cancer, Uterine Cancer, Gallbladder Cancer and Bile Duct
Cancer, NHL, HNSCC 314 ALIAEGIALV Uterine Cancer 317 SLAALVVHV
NSCLC, Gallbladder Cancer and Bile Duct Cancer, HNSCC 318
GLINTGVLSV SCLC, CLL, NHL, HNSCC 319 SLEPQIQPV HCC, CLL, BRCA,
Melanoma, Gallbladder Cancer and Bile Duct Cancer, AML, HNSCC 320
KMFEFVEPLL SCLC, Brain Cancer, BRCA, Melanoma, Urinary Bladder
Cancer, Uterine Cancer, Gallbladder Cancer and Bile Duct Cancer,
AML, HNSCC 321 GLFEDVTQPGILL CLL 322 TLMTSLPAL CLL, BRCA, Melanoma,
Uterine Cancer, Gallbladder Cancer and Bile Duct Cancer, AML, NHL
323 IQIGEETVITV CRC, CLL, BRCA 324 FLYDEIEAEV CLL 325 FIMPATVADATAV
CLL, BRCA, Melanoma, Uterine Cancer, NHL 326 FLPEALDFV CLL, AML,
NHL 327 GLAPFTEGISFV NSCLC, Gallbladder Cancer and Bile Duct Cancer
328 ALNDQVFEI AML 330 QLALKVEGV CLL, Urinary Bladder Cancer, AML,
NHL, HNSCC 331 KVDTVWVNV CLL, Gallbladder Cancer and Bile Duct
Cancer, HNSCC 332 YLISELEAA RCC, GC, BRCA, Melanoma 333 FLPDANSSV
HCC, Melanoma 334 TLTKVLVAL CLL 335 YSLSSVVTV HNSCC 336 ILLTAIVQV
Melanoma 337 HLLSELEAAPYL CLL 338 SVLEDPVHAV BRCA, Esophageal
Cancer, Uterine Cancer, Gallbladder Cancer and Bile Duct Cancer,
NHL 339 GLWEIENNPTVKA Gallbladder Cancer and Bile Duct Cancer 340
ALLSMTFPL SCLC, AML 341 SQIALNEKLVNL Urinary Bladder Cancer 342
HIYDKVMTV Esophageal Cancer, Gallbladder Cancer and Bile Duct
Cancer 343 SLLEVNEESTV CLL 345 VIWKALIHL NSCLC, Melanoma, NHL 346
LLDSKVPSV HNSCC 347 SLFKHDPAAWEA Uterine Cancer, HNSCC 348
ILLDVKTRL Melanoma, Gallbladder Cancer and Bile Duct Cancer, HNSCC
350 ALLDVTHSELTV BRCA, HNSCC 351 SLIPNLRNV CRC, Esophageal Cancer
352 SLLELLHIYV CLL, AML 354 LILEGVDTV BRCA, Urinary Bladder Cancer,
Uterine Cancer, NHL 356 KLLGKLPEL Melanoma, Urinary Bladder Cancer
358 ALDEYTSEL Urinary Bladder Cancer 359 YLLPESVDL CLL, Uterine
Cancer, NHL, HNSCC 360 ALDJGASLLHL HNSCC 361 ALYELEGTTV NSCLC,
SCLC, CLL, BRCA, Urinary Bladder Cancer, Uterine Cancer,
Gallbladder Cancer and Bile Duct Cancer, HNSCC 362 TLYGLSVLL AML
363 KVLDVSDLESV NSCLC, Esophageal Cancer, Urinary Bladder Cancer,
Gallbladder Cancer and Bile Duct Cancer, HNSCC 364 LLQNEQFEL
Urinary Bladder Cancer, Uterine Cancer, Gallbladder Cancer and Bile
Duct Cancer 365 YVIDQGETDVYV CLL, Urinary Bladder Cancer, NHL 366
RLLDMGETDLML CLL, Urinary Bladder Cancer, AML, NHL 367 SLQNHNHQL
NSCLC, CRC, Melanoma, Esophageal Cancer, AML, NHL, HNSCC 370
SLLQDLVSV BRCA, Melanoma, Gallbladder Cancer and Bile Duct Cancer,
HNSCC 372 TMLLNIPLV CLL, Gallbladder Cancer and Bile Duct Cancer,
AML, NHL 374 FLLQQHLISA CLL 375 SLTETIEGV Gallbladder Cancer and
Bile Duct Cancer 376 AMFESSQNVLL CLL 379 IMEGTLTRV RCC, CLL,
Melanoma, Urinary Bladder Cancer, NHL 380 TLIEDEIATI SCLC,
Melanoma, Uterine Cancer, Gallbladder Cancer and Bile Duct Cancer,
AML, HNSCC 381 FIDEAYVEV GC, CLL, Melanoma, NHL 382 ALQNYIKEA BRCA
384 ILFANPNIFV CLL, Urinary Bladder Cancer, Uterine Cancer, NHL 385
SLLEQGLVEA BRCA, AML, HNSCC 386 ILFRYPLTI Melanoma, Uterine Cancer,
AML 387 ALFQATAEV SCLC, Melanoma, Urinary Bladder Cancer, Uterine
Cancer, Gallbladder Cancer and Bile Duct Cancer, AML, NHL, HNSCC
388 SLTIDGIRYV Brain Cancer 389 LLADVTHLL Melanoma, AML 393
GLLDTQTSQVLTA CRC, Gallbladder Cancer and Bile Duct Cancer, HNSCC
394 LLAVIGGLVYL BRCA 395 ALALGGIAVV CLL, NHL, HNSCC 396 ALLPDLPAL
SCLC, Gallbladder Cancer and Bile Duct Cancer, AML, NHL, HNSCC 397
YLFGERLLEC CLL, Uterine Cancer 398 KLLEEDGTIITL BRCA, Esophageal
Cancer, Gallbladder Cancer and Bile Duct Cancer 400 SLLTEQDLWTV CLL
401 ILLDDTGLAYI CLL, Urinary Bladder Cancer, Gallbladder Cancer and
Bile Duct Cancer, NHL 403 KLYDRILRV BRCA 407 YLMDLINFL AML 408
VLDDSIYLV CLL, Uterine Cancer, NHL 409 LLDAMNYHL CLL, NHL 411
LLAHLSPEL Melanoma 412 YLDDLNEGVYI BRCA 413 TLLEKVEGC Melanoma 414
YVDDIFLRV GC, Melanoma 415 LLDKVYSSV Brain Cancer, CLL, BRCA,
Urinary Bladder Cancer, Uterine Cancer, Gallbladder Cancer and Bile
Duct Cancer, AML, NHL, HNSCC 416 VLSDIIQNLSV CLL, NHL 417 NLQDTEYNL
CLL, AML, NHL 418 ALAELENIEV CLL, BRCA, Urinary Bladder Cancer,
Gallbladder Cancer and Bile Duct Cancer, HNSCC 419 GQYEGKVSSV BRCA
420 FMYDTPQEV Gallbladder Cancer and Bile Duct Cancer 422 FLPKLLLLA
Melanoma 423 GLDGPPPTV NHL 424 TLLDALYEI Melanoma, Gallbladder
Cancer and Bile Duct Cancer, AML, HNSCC 425 FLYEKSSQV SCLC 426
RLADKSVLV BRCA, AML 427 ALLPLSPYL Gallbladder Cancer and Bile Duct
Cancer 428 KLGHTDILVGV CLL, Uterine Cancer, HNSCC 429 GLVNDLARV
SCLC, BRCA, Melanoma, Gallbladder Cancer and Bile Duct Cancer, NHL
430 HLYSSIEHLTT SCLC, BRCA, Urinary Bladder Cancer, NHL 431
SLVNVVPKL CLL, BRCA, Urinary Bladder Cancer, Gallbladder Cancer and
Bile Duct Cancer, AML, NHL 433 AMLNEPWAV BRCA, Melanoma, Urinary
Bladder Cancer, HNSCC 434 KVSNSGITRV Esophageal Cancer, HNSCC
435 WLMPVIPAL Melanoma, Gallbladder Cancer and Bile Duct Cancer,
AML 436 HLAEVSAEV NSCLC, SCLC, CLL, BRCA, Melanoma, Urinary Bladder
Cancer, Gallbladder Cancer and Bile Duct Cancer, AML, NHL, HNSCC
438 KLLPLAGLYL CLL, BRCA, Melanoma, Uterine Cancer, Gallbladder
Cancer and Bile Duct Cancer, AML, HNSCC 439 YLLQEIYGI AML 440
ALADGVTMQV SCLC, BRCA, Melanoma, Uterine Cancer 441 ALLENPKMEL
Urinary Bladder Cancer 443 GLWEIENNPTV Gallbladder Cancer and Bile
Duct Cancer 444 GLLRDEALAEV CLL, BRCA, Urinary Bladder Cancer,
Uterine Cancer, AML, NHL, HNSCC 445 GLYQDPVTL Uterine Cancer, AML
446 QLIPALAKV Brain Cancer 447 QLVPALAKV BRCA, Melanoma, HNSCC 448
NLLETKLQL CLL, Melanoma, NHL, HNSCC 450 FMIDASVHPTL CLL, Urinary
Bladder Cancer, HNSCC 451 LLLLDTVTMQV Melanoma, HNSCC 452
ILLEHGADPNL CLL, Urinary Bladder Cancer, NHL 453 KLLEATSAV SCLC,
BRCA, Uterine Cancer, Gallbladder Cancer and Bile Duct Cancer, AML,
NHL, HNSCC 454 KLPPPPPQA BRCA, AML, HNSCC 455 SLLKEPQKVQL CLL,
Melanoma, HNSCC 456 LLIGHLERV BRCA, AML, NHL, HNSCC 458 SLIDKLYNI
SCLC, Brain Cancer, Melanoma, Urinary Bladder Cancer, AML, HNSCC
459 ALITEVVRL SCLC, CLL, AML, NHL 461 VMFRTPLASV BRCA, Urinary
Bladder Cancer, Uterine Cancer, NHL 462 KLAKQPETV NHL 463
SLVESHLSDQLTL CLL, BRCA, Urinary Bladder Cancer, Uterine Cancer,
Gallbladder Cancer and Bile Duct Cancer, NHL, HNSCC 464 ALNDCIYSV
HNSCC 465 QLCDLNAEL SCLC, Melanoma, AML, HNSCC 466 VLIANLEKL
Urinary Bladder Cancer, NHL 467 FLAKDFNFL NSCLC, Melanoma, Urinary
Bladder Cancer, Gallbladder Cancer and Bile Duct Cancer, NHL, HNSCC
468 YLRSVGDGETV Uterine Cancer 469 YLASDEITTV CLL 470 MLQDSIHVV
BRCA 472 KLLEVSDDPQV HNSCC 473 AMATESILHFA AML 474 YLDPALELGPRNV
BRCA 476 ALMERTGYSMV Uterine Cancer 477 ALLPASGQIAL CLL, BRCA,
Melanoma, Gallbladder Cancer and Bile Duct Cancer, HNSCC 478
YLLHEKLNL NHL 479 SLFGNSGILENV Melanoma, Uterine Cancer, AML, HNSCC
480 ALLEDSCHYL HNSCC 481 GLIEDYEALL Melanoma, AML 482 SLAPAGIADA
Melanoma, Uterine Cancer, HNSCC 483 ALTDIVSQV NSCLC, SCLC, BRCA,
Uterine Cancer, Gallbladder Cancer and Bile Duct Cancer, HNSCC 484
SLIEKVTQL SCLC, CRC, CLL, BRCA, Melanoma, Esophageal Cancer,
Urinary Bladder Cancer, Uterine Cancer, AML, NHL 486 AVMESIQGV CLL
487 LLINSVFHV Urinary Bladder Cancer, NHL 488 FLAEDPKVTL CLL, BRCA,
Melanoma, Urinary Bladder Cancer, NHL 489 KMWEELPEVV CLL,
Esophageal Cancer, Urinary Bladder Cancer, AML, NHL, HNSCC 490
FLLQHVQEL CLL, NHL 491 GLNDRSDAV BRCA, AML, HNSCC 492 SLFDGFADGLGV
BRCA 493 GLLGEKTQDLIGV CLL, Melanoma, Urinary Bladder Cancer,
Uterine Cancer, Gallbladder Cancer and Bile Duct Cancer, HNSCC 495
FIFSEKPVFV Melanoma, AML, NHL 496 FLVEKQPPQV CLL, NHL 497 GLLEKLTAI
SCLC, CLL, BRCA, Melanoma, Urinary Bladder Cancer, AML, NHL 498
KLWTGGLDNTV NSCLC Brain Cancer, CLL, Urinary Bladder Cancer,
Uterine Cancer, NHL 500 SLMEDQVLQL CLL, AML 501 LLDPNVKSIFV BRCA,
Urinary Bladder Cancer, HNSCC 502 RLLAQVPGL Melanoma, Uterine
Cancer, Gallbladder Cancer and Bile Duct Cancer, AML, NHL 503
SLNHFTHSV HCC, CLL, Urinary Bladder Cancer, AML, NHL, HNSCC 504
GLSDGNPSL CLL, Uterine Cancer 505 SLAPGDVVRQV BRCA, Urinary Bladder
Cancer, HNSCC 506 KLLGKVETA CLL, NHL 507 KLIDDQDISISL CLL, Urinary
Bladder Cancer, NHL 508 ILAQEQLVVGV SCLC, Gallbladder Cancer and
Bile Duct Cancer 509 FLFDTKPLIV CLL 510 KLYSVVSQL NHL 511
FLDPYCSASV SCLC, Uterine Cancer 512 SLSEIVPCL Uterine Cancer, AML,
HNSCC 513 SLWPSPEQL Melanoma, AML, NHL, HNSCC 514 ILVDWLVQV BRCA,
Gallbladder Cancer and Bile Duct Cancer, AML, NHL, HNSCC 517
LLMPIPEGLTL Urinary Bladder Cancer, Uterine Cancer, HNSCC 518
KLNAEVACV BRCA, Melanoma, Urinary Bladder Cancer, Uterine Cancer,
HNSCC 519 GLLHLTLLL SCLC, Gallbladder Cancer and Bile Duct Cancer,
AML, HNSCC 520 LAVHPSGVAL SCLC, CLL, BRCA, Gallbladder Cancer and
Bile Duct Cancer 521 MLLTKLPTI Brain Cancer, CLL, Uterine Cancer,
AML, NHL, HNSCC 522 TLWYRSPEV Melanoma 523 YQIPRTFTL CLL, AML 524
ALIENLTHQI CLL, Melanoma, NHL 525 VLLEAGEGLVTI NSCLC, SCLC, CLL,
Urinary Bladder Cancer, Uterine Cancer, NHL, HNSCC 526 RLAEVGQYEQV
Uterine Cancer, NHL 528 SVAEGRALMSV NSCLC, CLL, BRCA, Urinary
Bladder Cancer, Gallbladder Cancer and Bile Duct Cancer, HNSCC 529
LLADELITV SCLC, CLL, HNSCC 530 VMYADIGGMDI CLL, Urinary Bladder
Cancer, Uterine Cancer, Gallbladder Cancer and Bile Duct Cancer,
HNSCC 531 YTLPIASSIRL BRCA 532 ALNNLLHSL Melanoma, Esophageal
Cancer, Urinary Bladder Cancer, Uterine Cancer, Gallbladder Cancer
and Bile Duct Cancer, AML, NHL 533 RMVAEIQNV CLL, NHL 534 HLANIVERL
CLL 535 KLIAQNLEL AML, NHL, HNSCC 536 YLVEGRFSV CLL, Urinary
Bladder Cancer 538 LLLAHIIAL BRCA, Urinary Bladder Cancer, Uterine
Cancer 539 ALFDAQAQV Melanoma, AML 540 ALIPETTTLTV NHL 541
SMLEPVPEL Gallbladder Cancer and Bile Duct Cancer 542 RVWDISTVSSV
NSCLC, CLL, BRCA 543 GLLPTPITQQASL BRCA 544 LLWDVPAPSL CLL, Uterine
Cancer, HNSCC 545 LLADLLHNV BRCA 546 VMIAGKVAVV SCLC, Urinary
Bladder Cancer, HNSCC 547 TLDITPHTV Esophageal Cancer 548
ALWENPESGEL BRCA 549 AMLENASDIKL SCLC, CLL, Urinary Bladder Cancer
550 FLYDEIEAEVNL CLL 551 KLYESLLPFA CLL, BRCA, Urinary Bladder
Cancer, Gallbladder Cancer and Bile Duct Cancer, AML, NHL, HNSCC
552 GLLDLPFRVGV CLL, AML, NHL 553 SLLNQDLHWSL CLL 554 LLMPSSEDLLL
CLL, Melanoma, HNSCC 555 YVLEGLKSV CRC, CLL, Esophageal Cancer,
Urinary Bladder Cancer, Uterine Cancer, NHL, HNSCC
556 FLTDLEDLTL CLL, Uterine Cancer, NHL 557 KLYDDMIRL Brain Cancer,
NHL 558 GLLENIPRV CLL, BRCA, Melanoma, AML, NHL 559 VTVPPGPSL CLL,
AML 560 ALWDIETGQQTTT CLL, Urinary Bladder Cancer, Uterine Cancer,
Gallbladder Cancer and Bile Duct Cancer, NHL, HNSCC 561 YLQLTQSEL
CLL, NHL, HNSCC 563 WLLPYNGVTV CLL, Uterine Cancer, NHL 565
ALQETPTSV BRCA, Gallbladder Cancer and Bile Duct Cancer 566
VIADGGIQNV CRC, CLL, BRCA, Urinary Bladder Cancer, Gallbladder
Cancer and Bile Duct Cancer, NHL 567 SLLPLDDIVRV CLL, BRCA 568
TLYDIAHTPGV CLL, Urinary Bladder Cancer, NHL, HNSCC 570 ALANQIPTV
HCC 571 LLLTTIPQI Melanoma 572 ALADLIEKELSV CLL, NHL 573 ILVANAIVGV
CLL, SCLC, Urinary Bladder Cancer 575 YLISQVEGHQV NSCLC, SCLC,
BRCA, Urinary Bladder Cancer, HNSCC 577 VMFEDGVLMRL SCLC, CLL,
Urinary Bladder Cancer, AML, NHL, HNSCC 578 FLDPGGPMMKL SCLC, CLL,
BRCA, Urinary Bladder Cancer, HNSCC 579 NLMEMVAQL SCLC, CLL,
Melanoma, Urinary Bladder Cancer, NHL 580 LLMENAERV CLL, Esophageal
Cancer, Urinary Bladder Cancer, Uterine Cancer, NHL, HNSCC 581
RLWNETVEL AML, NHL 582 TLCDVILMV Melanoma 583 ILANDGVLLAA CLL,
BRCA, Urinary Bladder Cancer, Uterine Cancer, Gallbladder Cancer
and Bile Duct Cancer, NHL, HNSCC 585 ALWDLAADKQTL Melanoma 586
KLKPGDLVGV Uterine Cancer 587 VMNDRLYAI CLL, NHL 588 SLLPLSHLV CLL,
Gallbladder Cancer and Bile Duct Cancer, AML, NHL, HNSCC 589
KLYPQLPAEI CLL, BRCA, Urinary Bladder Cancer 590 SLIEKLWQT Uterine
Cancer, AML 591 SMAELDIKL AML, HNSCC 594 IMLKGDNITL Uterine Cancer
595 VLLSIYPRV CLL, Urinary Bladder Cancer, Gallbladder Cancer and
Bile Duct Cancer 596 ALLDQTKTLAESAL CLL, NHL 597 KLLEGQVIQL CLL,
Melanoma, Gallbladder Cancer and Bile Duct Cancer, AML 598
FLFPHSVLV CRC 599 YLLNDASLISV SCLC 600 ALAAPDIVPAL CLL, Uterine
Cancer, AML 601 SAFPFPVTV CLL, Gallbladder Cancer and Bile Duct
Cancer, AML 603 FLIEPEHVNTV CLL 604 SILDRDDIFV CLL, Melanoma, NHL
605 KLYEAVPQL Gallbladder Cancer and Bile Duct Cancer, HNSCC 607
RLYSGISGLEL CLL, Melanoma, AML, NHL 609 ALWKQLLEL CRC, Esophageal
Cancer, Uterine Cancer 611 YLLDDGTLVV Uterine Cancer 612 YLYNEGLSV
BRCA, Urinary Bladder Cancer, AML, NHL, HNSCC 613 RLLPPGAVVAV CLL,
BRCA, Urinary Bladder Cancer, Gallbladder Cancer and Bile Duct
Cancer, HNSCC 614 LLLPDQPPYHL CLL 615 VLPPDTDPA Melanoma,
Esophageal Cancer 616 VLIDEVESL CRC, Uterine Cancer, Gallbladder
Cancer and Bile Duct Cancer, AML, NHL, HNSCC 619 ALQDRVPLA BRCA,
Gallbladder Cancer and Bile Duct Cancer 620 KLLNKIYEA BRCA, AML 621
VLMDRLPSLL CLL 622 RLLGEEWRVLQA Urinary Bladder Cancer, AML, NHL
623 YLVEDIQHI NSCLC, PC 624 FLQEEPGQLL CLL, Urinary Bladder Cancer,
Uterine Cancer, Gallbladder Cancer and Bile Duct Cancer, NHL 625
VVLEGASLETV CLL, Urinary Bladder Cancer 626 LLMATILHL CLL, AML,
NHL, HNSCC 627 KLLETELLQEI CLL, Urinary Bladder Cancer 628
KLWEFFQVDV Melanoma 629 HLLNESPML RCC, PC, BRCA, Melanoma, Uterine
Cancer, Gallbladder Cancer and Bile Duct Cancer, AML 630 LLSHVIVAL
CLL, Gallbladder Cancer and Bile Duct Cancer, NHL 631 FLDVFLPRV
SCLC, CLL, NHL 632 YLIPDIDLKL CLL, AML, NHL, HNSCC 633 ALSRVSVNV
CLL 634 VVAEFVPLI CLL, AML, NHL 635 SLDSTLHAV SCLC, Melanoma,
Urinary Bladder Cancer, Uterine Cancer, Gallbladder Cancer and Bile
Duct Cancer 636 LLTEIRAVV CLL, NHL 637 SIYGGFLLGV Urinary Bladder
Cancer, Gallbladder Cancer and Bile Duct Cancer, HNSCC 638
KLIQESPTV Gallbladder Cancer and Bile Duct Cancer, AML 639
SLFQNCFEL CLL, Melanoma, Uterine Cancer, NHL, HNSCC NSCLC =
non-small cell lung cancer, SCLC = small cell lung cancer, RCC =
kidney cancer, CRC = colon or rectum cancer, GC = stomach cancer,
HCC = liver cancer, PC = pancreatic cancer, PrC = prostate cancer,
BRCA = breast cancer, NHL = non-Hodgkin lymphoma, AML = acute
myeloid leukemia, CLL = chronic lymphocytic leukemia, HNSCC = head
and neck squamous cell carcinoma.
[0046] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 1, 11, 17, 27, 45, 57, 58, 61,
62, 65, 72, 74, 79, 84, 97, 98, 104, 105, 125, 126, 143, 150, 157,
161, 167, 176, 179, 183, 184, 195, 198, 201, 204, 213, 217, 222,
228, 234, 248, 263, 264, 268, 285, 287, 303, 313, 319, 323, 333,
335, 338, 343, 347, 348, 355, 356, 359, 373, 385, 394, 395, 403,
415, 421, 427, 428, 429, 430, 431, 434, 441, 443, 444, 446, 447,
450, 454, 456, 457, 458, 459, 463, 474, 477, 479, 480, 486, 489,
492, 493, 497, 501, 503, 506, 514, 517, 521, 526, 538, 539, 540,
541, 545, 554, 558, 568, 573, 576, 578, 579, 589, 595, 597, 599,
602, 607, 610, 613, 616,
[0047] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No 1, 6, 17, 19, 20, 27, 28, 31, 34,
36, 38, 45, 47, 48, 51, 54, 55, 56, 57, 58, 59, 60, 61, 65, 66, 72,
75, 76, 79, 82, 85, 88, 91, 92, 98, 103, 108, 117, 123, 125, 126,
127, 135, 141, 142, 149, 152, 153, 166, 167, 169, 171, 176, 183,
184, 200, 205, 213, 214, 216, 228, 233, 234, 237, 240, 242, 248,
249, 251, 256, 263, 264, 277, 279, 283, 286, 288, 296, 300, 301,
312, 314, 315, 322, 323, 328, 331, 338, 341, 344, 345, 346, 366,
372, 373, 385, 388, 394, 399, 401, 404, 410, 418, 420, 421, 427,
428, 431, 433, 435, 437, 439, 441, 443, 444, 446, 449, 450, 451,
454, 461, 463, 469, 473, 474, 475, 479, 481, 492, 493, 500, 501,
514, 517, 521, 522, 523, 530, 531, 539, 541, 542, 545, 551, 552,
554, 555, 556, 558, 560, 561, 563, 565, 568, 574, 575, 581, 589,
590, 592, 595, 597, 602, 606, 610, 613, 616, 618, 622, 625, 626,
627, 628, 629, 632, 637, 638, and 640 for the--in one preferred
embodiment combined--treatment of SCLC.
[0048] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No 1, 2, 6, 19, 26, 27, 57, 58, 61,
63, 64, 65, 69, 77, 79, 85, 95, 97, 98, 103, 107, 121, 125, 126,
127, 128, 129, 143, 148, 150, 155, 157, 166, 170, 174, 177, 200,
201, 204, 207, 213, 217, 222, 223, 229, 234, 235, 242, 243, 252,
258, 264, 267, 271, 275, 279, 285, 287, 294, 303, 306, 311, 313,
317, 319, 323, 328, 330, 332, 333, 336, 346, 347, 348, 354, 355,
356, 359, 360, 361, 375, 382, 385, 387, 393, 395, 405, 410, 415,
424, 430, 431, 441, 444, 447, 450, 459, 461, 465, 466, 472, 477,
480, 486, 491, 492, 497, 498, 499, 501, 505, 506, 508, 513, 514,
518, 528, 533, 539, 541, 542, 543, 554, 560, 561, 565, 568, 575,
576, 583, 588, 589, 591, 592, 594, 601, 610, 616, 619, 624, 629,
631, 633, 635, and 640 for the--in one preferred embodiment
combined--treatment of esophageal cancer.
[0049] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 6, 48, 68, 106, 118, 127, 135,
143, 157, 174, 209, 247, 279, 292, 300, 313, 28, 332, 333, 340,
357, 538, 539, 541, 558, 586, 589, 590, 592, 593, 606, 610, 619,
620, 628, and 635 for the--in one preferred embodiment
combined--treatment of brain cancer.
[0050] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No 6, 7, 17, 27, 56, 59, 61, 65, 76,
93, 103, 110, 131, 141, 143, 149, 169, 204, 212, 216, 226, 228,
229, 230, 242, 255, 264, 266, 268, 271, 273, 283, 284, 285, 286,
287, 288, 289, 303, 309, 331, 333, 335, 336, 340, 358, 362, 371,
372, 373, 375, 393, 395, 396, 401, 420, 422, 423, 427, 439, 446,
459, 466, 504, 521, 539, 554, 576, 580, 592, 595, 597, 610, 616,
635, 637, and 640 for the--in one preferred embodiment
combined--treatment of breast cancer (BrCa).
[0051] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 6, 20, 139, 283, 373, 396, 418,
430, 441, 446, 472, 473, 474, 479, 501, 575, 578, 589, 627, and 640
for the--in one preferred embodiment combined--treatment of
MCC.
[0052] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 7, 9, 97, 98, 183, 217, 218,
222, 234, 235, 237, 240, 241, 242, 263, 268, 271, 275, 285, 303,
311, 313, 360, 364, 394, 403, 410, 424, 431, 450, 455, 497, 502,
514, 558, 564, 595, 608, 610, and 616 for the--in one preferred
embodiment combined--treatment of RCC.
[0053] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 7, 24, 27, 64, 65, 84, 87, 95,
97, 125, 126, 127, 130, 137, 143, 183, 200, 272, 275, 291, 292,
311, 312, 332, 335, 346, 351, 357, 358, 364, 372, 398, 405, 407,
410, 421, 423, 427, 443, 459, 464, 499, 539, 540, 603, 609, 630,
631, and 632 for the--in one preferred embodiment
combined--treatment of pancreatic cancer (PC).
[0054] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 9, 31, 58, 183, 275, 335, 410,
421, 499, 514, 564, 616, and 640 for the--in one preferred
embodiment combined--treatment of gastric cancer (GC).
[0055] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 9, 14, 19, 20, 28, 32, 36, 48,
54, 57, 58, 63, 64, 66, 87, 92, 94, 97, 98, 108, 125, 129, 139,
143, 144, 154, 157, 159, 163, 166, 167, 170, 174, 176, 178, 188,
197, 198, 201, 204, 207, 208, 209, 212, 213, 214, 217, 222, 229,
234, 237, 248, 256, 267, 269, 271, 273, 275, 286, 290, 294, 301,
306, 309, 313, 327, 328, 332, 338, 339, 340, 341, 346, 347, 349,
355, 359, 360, 367, 369, 370, 371, 372, 378, 383, 385, 387, 393,
394, 395, 396, 401, 406, 409, 410, 411, 415, 419, 420, 423, 427,
428, 429, 430, 432, 441, 443, 447, 450, 451, 452, 457, 463, 464,
465, 472, 473, 474, 476, 477, 479, 480, 484, 486, 489, 492, 498,
501, 513, 514, 517, 521, 523, 526, 528, 531, 538, 539, 540, 541,
546, 551, 554, 558, 560, 564, 573, 575, 576, 579, 583, 586, 589,
597, 599, 603, 606, 610, 611, 613, 617, 627, 628, 632, 635, 637,
638, and 640 for the--in one preferred embodiment
combined--treatment of hepatocellular carcinoma (HCC).
[0056] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 9, 10, 14, 19, 24, 28, 79, 87,
101, 144, 148, 149, 153, 169, 174, 190, 210, 212, 216, 222, 223,
242, 252, 257, 271, 288, 298, 299, 303, 310, 311, 317, 331, 333,
334, 346, 347, 348, 360, 367, 386, 390, 393, 394, 395, 423, 477,
479, 483, 486, 494, 495, 502, 514, 521, 527, 529, 539, 554, 585,
610, 616, 626, 632, and 640 for the--in one preferred embodiment
combined--treatment of urinary bladder cancer.
[0057] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 19, 22, 26, 28, 31, 33, 34, 36,
38, 47, 48, 49, 57, 58, 59, 60, 65, 74, 79, 80, 92, 98, 119, 126,
128, 129, 263, 270, 271, 272, 275, 276, 277, 280, 282, 284, 285,
287, 289, 296, 299, 301, 308, 309, 319, 321, 323, 324, 325, 331,
333, 343, 355, 358, 365, 366, 373, 374, 379, 381, 384, 391, 394,
395, 397, 400, 401, 404, 408, 409, 410, 412, 415, 428, 448, 450,
451, 452, 457, 459, 468, 475, 480, 486, 488, 489, 490, 496, 503,
504, 506, 507, 508, 510, 520, 523, 529, 533, 536, 542, 544, 550,
552, 556, 558, 559, 561, 566, 567, 571, 572, 573, 576, 577, 579,
580, 587, 589, 591, 595, 596, 600, 601, 603, 604, 610, 624, 630,
631, 632, 634, and 639 for the--in one preferred embodiment
combined--treatment of leukemia.
[0058] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 19, 22, 31, 34, 38, 48, 57, 58,
61, 62, 63, 64, 74, 77, 92, 97, 98, 101, 105, 107, 143, 144, 150,
155, 167, 176, 177, 183, 184, 199, 213, 217, 222, 230, 248, 251,
256, 264, 277, 282, 283, 287, 291, 309, 314, 316, 321, 323, 329,
331, 338, 339, 343, 344, 355, 365, 366, 373, 384, 388, 391, 394,
395, 401, 410, 412, 431, 443, 444, 450, 452, 457, 461, 463, 468,
472, 474, 487, 496, 499, 501, 514, 517, 521, 523, 525, 530, 540,
542, 544, 549, 550, 551, 552, 555, 560, 563, 564, 565, 566, 568,
572, 573, 575, 576, 578, 580, 584, 588, 589, 596, 599, 603, 611,
614, 616, 618, 621, 622, 624, 625, 626, 627, 631, 632, and 633 for
the--in one preferred embodiment combined--treatment of
melanoma.
[0059] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 19, 22, 24, 58, 76, 79, 84, 86,
97, 98, 126, 176, 178, 188, 222, 243, 285, 300, 301, 303, 311, 318,
319, 320, 342, 348, 349, 355, 356, 359, 376, 384, 395, 397, 398,
421, 426, 428, 430, 441, 444, 448, 449, 450, 456, 458, 459, 473,
478, 480, 510, 514, 518, 521, 528, 531, 535, 541, 545, 546, 554,
557, 568, 575, 576, 577, 578, 579, 580, 581, 597, 599, 610, 619,
622, 627, 632, 635, and 640 for the--in one preferred embodiment
combined--treatment of colorectal cancer (CRC).
[0060] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 34, 51, 84, 174, 178, 200, 207,
212, 216, 237, 252, 264, 288, 323, 332, 333, 372, 394, 395, 410,
443, 446, 447, 486, 492, 501, 518, 539, 551, 554, 606, 610, 637,
and 640 for the--in one preferred embodiment combined--treatment of
prostate cancer (PrC)
[0061] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 47, 51, 54, 58, 64, 84, 87, 125,
200, 213, 228, 235, 237, 323, 335, 346, 385, 423, 473, 501, 526,
539, 554, 558, 561, 610, 626, and 640 for the--in one preferred
embodiment combined--treatment of gallbladder cancer.
[0062] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 47, 51, 54, 58, 64, 84, 87, 125,
200, 213, 228, 235, 237, 323, 335, 346, 385, 423, 473, 501, 526,
539, 554, 558, 561, 610, 626, and 640 for the--in one preferred
embodiment combined--treatment of bile duct cancer.
[0063] Thus, another aspect of the present invention relates to the
use of at least one peptide according to the present invention
according to any one of SEQ ID No. 48, 126, 127, 129, 149, 153,
157, 207, 214, 228, 235, 237, 288, 323, 328, 332, 358, 360, 385,
395, 423, 427, 446, 497, 514, 539, 558, 565, 599, 619, 632, 637,
and 640 for the--in one preferred embodiment combined--treatment of
uterine cancer.
[0064] Then, another aspect of the present invention relates to the
use of the peptides according to the present invention for
the--preferably combined--treatment of a proliferative disease
selected from the group of ovarian cancer, non-small cell lung
cancer, small cell lung cancer, kidney cancer, brain cancer, colon
or rectum cancer, stomach cancer, liver cancer, pancreatic cancer,
prostate cancer, leukemia, breast cancer, Merkel cell carcinoma,
melanoma, esophageal cancer, urinary bladder cancer, uterine
cancer, gallbladder cancer, bile duct cancer.
[0065] The present invention furthermore relates to peptides
according to the present invention that have the ability to bind to
a molecule of the human major histocompatibility complex (MHC)
class-I or--in an elongated form, such as a length-variant--MHC
class-II.
[0066] The present invention further relates to the peptides
according to the present invention wherein said peptides (each)
consist or consist essentially of an amino acid sequence according
to SEQ ID NO: 1 to SEQ ID NO: 640.
[0067] The present invention further relates to the peptides
according to the present invention, wherein said peptide is
modified and/or includes non-peptide bonds.
[0068] The present invention further relates to the peptides
according to the present invention, wherein said peptide is part of
a fusion protein, in particular fused to the N-terminal amino acids
of the HLA-DR antigen-associated invariant chain (Ii), or fused to
(or into the sequence of) an antibody, such as, for example, an
antibody that is specific for dendritic cells.
[0069] The present invention further relates to a nucleic acid,
encoding the peptides according to the present invention. The
present invention further relates to the nucleic acid according to
the present invention that is DNA, cDNA, PNA, RNA or combinations
thereof.
[0070] The present invention further relates to an expression
vector capable of expressing and/or expressing a nucleic acid
according to the present invention.
[0071] The present invention further relates to a peptide according
to the present invention, a nucleic acid according to the present
invention or an expression vector according to the present
invention for use in the treatment of diseases and in medicine, in
particular in the treatment of cancer.
[0072] The present invention further relates to antibodies that are
specific against the peptides according to the present invention or
complexes of said peptides according to the present invention with
MHC, and methods of making these.
[0073] The present invention further relates to T-cell receptors
(TCRs), in particular soluble TCR (sTCRs) and cloned TCRs
engineered into autologous or allogeneic T cells, and methods of
making these, as well as NK cells or other cells bearing said TCR
or cross-reacting with said TCRs.
[0074] The antibodies and TCRs are additional embodiments of the
immunotherapeutic use of the peptides according to the invention at
hand.
[0075] The present invention further relates to a host cell
comprising a nucleic acid according to the present invention or an
expression vector as described before. The present invention
further relates to the host cell according to the present invention
that is an antigen presenting cell, and preferably is a dendritic
cell.
[0076] The present invention further relates to a method for
producing a peptide according to the present invention, said method
comprising culturing the host cell according to the present
invention, and isolating the peptide from said host cell or its
culture medium.
[0077] The present invention further relates to said method
according to the present invention, wherein the antigen is loaded
onto class I or II MHC molecules expressed on the surface of a
suitable antigen-presenting cell or artificial antigen-presenting
cell by contacting a sufficient amount of the antigen with an
antigen-presenting cell.
[0078] The present invention further relates to the method
according to the present invention, wherein the antigen-presenting
cell comprises an expression vector capable of expressing or
expressing said peptide containing SEQ ID No. 1 to SEQ ID No.: 640,
preferably containing SEQ ID No. 1 to SEQ ID No. 259, or a variant
amino acid sequence.
[0079] The present invention further relates to activated T cells,
produced by the method according to the present invention, wherein
said T cell selectively recognizes a cell which expresses a
polypeptide comprising an amino acid sequence according to the
present invention.
[0080] The present invention further relates to a method of killing
target cells in a patient which target cells aberrantly express a
polypeptide comprising any amino acid sequence according to the
present invention, the method comprising administering to the
patient an effective number of T cells as produced according to the
present invention.
[0081] The present invention further relates to the use of any
peptide as described, the nucleic acid according to the present
invention, the expression vector according to the present
invention, the cell according to the present invention, the
activated T lymphocyte, the T cell receptor or the antibody or
other peptide- and/or peptide-MHC-binding molecules according to
the present invention as a medicament or in the manufacture of a
medicament. Preferably, said medicament is active against
cancer.
[0082] Preferably, said medicament is a cellular therapy, a vaccine
or a protein based on a soluble TCR or antibody.
[0083] The present invention further relates to a use according to
the present invention, wherein said cancer cells are ovarian
cancer, non-small cell lung cancer, small cell lung cancer, kidney
cancer, brain cancer, colon or rectum cancer, stomach cancer, liver
cancer, pancreatic cancer, prostate cancer, leukemia, breast
cancer, Merkel cell carcinoma, melanoma, esophageal cancer, urinary
bladder cancer, uterine cancer, gallbladder cancer, bile duct
cancer, and preferably ovarian cancer cells.
[0084] The present invention further relates to biomarkers based on
the peptides according to the present invention, herein called
"targets", that can be used in the diagnosis of cancer, preferably
ovarian cancer. The marker can be over-presentation of the
peptide(s) themselves, or over-expression of the corresponding
gene(s). The markers may also be used to predict the probability of
success of a treatment, preferably an immunotherapy, and most
preferred an immunotherapy targeting the same target that is
identified by the biomarker. For example, an antibody or soluble
TCR can be used to stain sections of the tumor to detect the
presence of a peptide of interest in complex with MHC.
[0085] Optionally the antibody carries a further effector function
such as an immune stimulating domain or toxin.
[0086] The present invention also relates to the use of these novel
targets in the context of cancer treatment.
[0087] ABCA1 has been shown to be hyper-methylated in ovarian and
prostate cancer cell lines. ABCA1 methylation was linked with poor
prognosis in ovarian cancer patients (Lee et al., 2013a; Chou et
al., 2015). In colon cancer, over-expression of ABCA1 resulted in a
decrease of cellular cholesterol and inhibition of tumor growth.
This growth inhibition could be due to apoptosis since
over-expression of ABCA1 enhanced cytochrome c release from
mitochondria (Smith and Land, 2012).
[0088] ABCB8 is associated with drug resistance in human melanomas
(Chen et al., 2009b).
[0089] ABCC1 is up-regulated in primary breast cancer, lung and
esophageal cancers, leukemia and childhood neuroblastoma (Cole et
al., 1992; Burger et al., 1994; Norris et al., 1996; Nooter et al.,
1997). Scientists have identified ABCC1 as a direct transcriptional
target of Notch1 signaling in an etoposide-resistant variant of the
MCF7 breast cancer cell line (Cho et al., 2011). Several
publications have demonstrated that increased ABCC1 expression in
cancers was linked with loss of functional p53 (Fukushima et al.,
1999; Sullivan et al., 2000).
[0090] ABCC10 was shown to be associated with paclitaxel and
gemcitabine resistance in breast cancer, gemcitabine resistance in
the non-small cell lung cancer cell line A549 and vinorelbine
resistance in the non-small cell lung cancer cell lines SK-LC6 and
NCI-H23 (Ikeda et al., 2011; Bessho et al., 2009; Dorman et al.,
2015). ABCC10 was shown to be associated with breast cancer
pathogenesis (Domanitskaya et al., 2014). ABCC10 was shown to be
up-regulated in pancreatic ductal adenocarcinoma, hepatocellular
carcinoma, non-small cell lung cancer, chronic lymphocytic leukemia
and pediatric acute myeloid leukemia (Mohelnikova-Duchonova et al.,
2013b; Borel et al., 2012; Steinbach et al., 2006; Wang et al.,
2009c; Hoellein et al., 2010). ABCC10 expression was shown to be
correlated with tumor grade in colorectal cancer and pathological
grades and TNM stages in adenocarcinoma of the lung (Hlavata et
al., 2012; Wang et al., 2009c).
[0091] Elevated levels of ABCC4 were present in human NK/T-cell
lymphoma cells, lung cancer cells and gastric cancer cells.
Moreover, copy number variation in the ABCC4 gene has been
associated with the risk of esophageal squamous cell carcinoma (Sun
et al., 2014b; Zhao et al., 2014b; Zhang et al., 2015d; Zhang et
al., 2015n). Furthermore, silencing of ABCC4 expression in
drug-resistant gastric cancer cells resulted in an increase in
apoptosis and cell cycle arrest in the G1 phase. Another group has
shown that knockdown of ABCC4 inhibited gastric cancer cell growth
and blocked cell cycle progression (Chen et al., 2014d; Zhang et
al., 2015d).
[0092] Down-regulation of ABCD1 expression was observed in renal
cell carcinoma, colorectal cancers and melanoma tumorigenesis
(Heimerl et al., 2007; Galamb et al., 2009; Hour et al., 2009).
[0093] ABCF1 was up-regulated in post-treatment tumors compared
with non-neoplastic tissues (Hlavac et al., 2013). Moreover,
repressing ABCF1 expression by miR-23a over-expression or siABCF1
resulted in recovery of 5-fluorouracil sensitivity in
microsatellite unstable colorectal cancer cells (Li et al.,
2015c).
[0094] Several publications have shown elevated levels of ABM in
various types of cancer such as epithelial ovarian cancer,
colorectal carcinoma, breast cancer and hepatocellular carcinoma
(Wang et al., 2007a; Liu et al., 2009a; Steinestel et al., 2013;
Steinestel et al., 2014; Zhang et al., 2015f). In epithelial
ovarian cancer, over-expression of ABM was significantly associated
with advanced stage, high grade and elevated Ca-125 level (Zhang et
al., 2015f). Knockdown of ABM resulted in decreased invasiveness
and migration ability in breast cancer cell lines. Similarly,
silencing of ABM gene in leukemic cells led to impaired cell
migration and abnormal actin remodeling (Wang et al., 2007a; Yu et
al., 2008).
[0095] ABL2 was over-expressed in non-small cell lung cancers,
anaplastic thyroid cancers, melanoma, colorectal, pancreatic
cancers, hepatocellular carcinomas, ovarian serous
cystadenocarcinoma, lung adenocarcinoma and lung squamous cell
carcinoma (Gil-Henn et al., 2013; Greuber et al., 2013; Xing et
al., 2014). In highly invasive breast cancer cell lines, ABL2
regulates proliferation, survival, and invasion down-stream of
de-regulated EGFR, Her2, IGFR and Src kinases (Srinivasan and
Plattner, 2006; Srinivasan et al., 2008).
[0096] ADCK3 expression was shown to be altered in colorectal
cancer (Hennig et al., 2012).
[0097] ADCY5 encodes adenylate cyclase 5, a membrane-bound adenylyl
cyclase enzyme that mediates G protein-coupled receptor signaling
through the synthesis of the second messenger cAMP (RefSeq, 2002).
ADCY5 gene hyper-methylation and reduced mRNA expression occurs in
acute lymphoblastic leukemia, chronic lymphocytic leukemia and lung
adenocarcinoma (Kuang et al., 2008; Tong et al., 2010; Sato et al.,
2013).
[0098] The expression of ADCY6 was shown to be differentially
regulated in laryngeal squamous cell carcinoma (Colombo et al.,
2009).
[0099] AGL has been shown to be a tumor suppressor in bladder
cancer. Loss of AGL in cancer cells induces tumor growth both in
vitro and in vivo through increased glycine synthesis via induction
of the glycine synthesizing enzyme serine hydroxymethyltransferase
2 (Guin et al., 2014; Ritterson et al., 2015).
[0100] AHCY down-regulation contributes to tumorigenesis (Leal et
al., 2008). AHCY can promote apoptosis. It inhibits migration and
adhesion of esophageal squamous cell carcinoma cells suggesting a
role in carcinogenesis of the esophagus (Li et al., 2014c). AHCY
protein expression is up-regulated in colon cancer (Kim et al.,
2009a; Watanabe et al., 2008; Fan et al., 2011). AHCY might be a
potential biomarker in ovarian cancer (Peters et al., 2005).
[0101] Recent work has identified a mutation in the AKAP6 gene in
gastric cancer (Li et al., 2016).
[0102] ALDH5A1 has been reported to be over-expressed in breast
ductal carcinoma in situ. In addition, inhibitors of ALDH5A1 such
as disulfiram and valproic acid were able to inhibit net
proliferation of a breast ductal carcinoma models (Kaur et al.,
2012).
[0103] It has been observed that a patient suffering from Alstrom
syndrome due to mutations in the ALMS1 gene developed also
papillary thyroid carcinoma. Another study identified ALMS1 as a
tumor neo-antigen in chronic lymphocytic leukemia (Rajasagi et al.,
2014; Papadakis et al., 2015).
[0104] ALS2CR12 was shown to be associated with cutaneous basal
cell carcinoma susceptibility (Stacey et al., 2015). An intronic
single nucleotide polymorphism in ALS2CR12 was shown to be
associated with breast cancer risk (Lin et al., 2015b).
[0105] In oral squamous cell carcinomas (OSCC) up-regulation of
ALYREF mRNA and protein level is linked to regional lymph node
metastasis caused by cellular invasiveness and migration (Saito et
al., 2013). ALYREF mRNA is over-expressed in a wide variety of
tumor tissues, whereas the protein level is poorly detected in
high-grade cancers (Dominguez-Sanchez et al., 2011). ALYREF is a
target of nuclear PI3K signaling, which regulates its sub-nuclear
residency, cell proliferation and mRNA export activities through
nuclear Akt phosphorylation and phosphoinositide association (Okada
et al., 2008).
[0106] ANKRD26 belongs to a gene family that was shown to be highly
expressed in cancer patients with poor outcome (Sahab et al.,
2010). ANKRD26 was shown to be associated with the putative tumor
suppressor RARRES1 (Sahab et al., 2010).
[0107] Homozygous deletion of the AP1B1 gene was found to be
inactive in sporadic meningioma. These findings imply that AP1B1
gene could play an important role in meningioma development
(Peyrard et al., 1994; Sayagues et al., 2007).
[0108] APOBEC3G is associated with liver metastasis of colorectal
cancer, hepatocellular carcinoma and lymphomas (Nowarski et al.,
2012; Chang et al., 2014b; Weidle et al., 2015). APOBEC3G is
associated with poor prognosis in colon carcinoma with hepatic
metastasis and with reduced overall survival in diffuse large
B-cell lymphoma (Lan et al., 2014; Jais et al., 2008).
[0109] APOL2 was shown to be over-expressed in ovarian/peritoneal
carcinoma (Davidson et al., 2011).
[0110] Over-expression of AQP5 has been linked to many kinds of
cancers such as colorectal, cervical, lung, breast and epithelial
ovarian cancer (Shan et al., 2014; Yan et al., 2014a). In non-small
cell lung cancer elevated AQP5 expression levels were associated
with lymph node metastasis. Furthermore, the expression levels of
AQP5 in stage III and IV tumors were significantly higher compared
with stage I and II tumors (Song et al., 2015a). Previous studies
have revealed that AQP5 can activate the RAS/ERK/RB pathway in
rectal cancer cells and enhance the incidence and progression of
cancer (Woo et al., 2008; Kang et al., 2008b).
[0111] AR has been implicated in the development of various cancers
such as prostate, castrate-resistant prostate, breast, glioblastoma
multiforme, colon and gastric (Wang et al., 2009d; Yu et al.,
2015b; Mehta et al., 2015; Wang et al., 2015a; Sukocheva et al.,
2015). In addition to promoting prostate cancer proliferation,
androgen signaling through AR leads to apoptosis via inducing the
expression of p21 (WAF1/CIP1), a cyclin-dependent kinase inhibitor
(Yeh et al., 2000).
[0112] A study has shown down-regulation of ARFGEF1 in breast
cancer cell lines. Another group reported ARFGEF1 to be a tumor
suppressor in breast cancer patients (Pongor et al., 2015; Kim et
al., 2011a). It is postulated that microRNA-27b mediated
up-regulation of ARFGEF1 promotes tumor growth by activating the
ARFGEF1/Akt pathway (Matsuyama et al., 2016).
[0113] ARHGAP26 was shown to be down-regulated in acute myeloid
leukemia and during the progression of CML (Qian et al., 2010; Aly
and Ghazy, 2014). ARHGAP26 is associated with metastatic brain
tumors from primary lung adenocarcinoma (Zohrabian et al., 2007).
ARHGAP26 is associated with risk and tumor size of uterine
leiomyoma, increased CML risk and is a favorable prognostic marker
for AML (Dzikiewicz-Krawczyk et al., 2014; Aissani et al.,
2015).
[0114] ARHGEF19 was shown to be associated with metastasis of
hepatocellular carcinoma (Zhou et al., 2014a). ARHGEF19 was
described as a part of the planar cell polarity/non-canonical Wnt
pathway, a pathway associated with cancer (Miller et al.,
2011).
[0115] ARID5B was shown to be dysregulated in prostate cancer
(Davalieva et al., 2015). ARID5B was shown to be associated with
susceptibility, relapse hazard and poorer treatment outcome in
childhood acute lymphoblastic leukemia (Xu et al., 2012; Evans et
al., 2014). ARID5B was shown to be a potential target regulated by
SALL4, a transcription factor which is associated with acute
myeloid leukemia (Milanovich et al., 2015). ARID5B was shown to be
a target of the oncogenic TEAD4 protein in gastric cancer (Lim et
al., 2014). ARID5B was shown to be frequently mutated in
endometrioid tumors (Kandoth et al., 2013). ARID5B might play a
role in cervical cancer development through its function as a human
papillomavirus 16 integration site (Matovina et al., 2009). ARID5B
was shown to be up-regulated in the highly metastatic adenoid
cystic carcinoma cell line ACC-M of human salivary glands, may be
involved in adenoid cystic carcinoma lung metastasis and might
serve as a diagnostic marker and therapeutic target (Sun et al.,
2004a).
[0116] ARL6IP1 is associated with cervical cancer cell growth and
invasion (Guo et al., 2010).
[0117] ASUN was shown to be up-regulated in testicular seminomas
and an ovarian carcinoma cell line (Bourdon et al., 2002). A study
has shown that ATF6B was essential for lysophosphatidic
acid-induced YAP dephosphorylation in human epithelial ovarian
cancer cell lines (Cai and Xu, 2013).
[0118] ATM is a tumor suppressor which is frequently mutated in a
broad range of human cancers including lung, colorectal, breast and
hematopoietic cancers (Weber and Ryan, 2014). Loss of ATM has been
associated with the increased risk of various cancers including,
breast, colorectal, prostate, lung and pancreatic ductal
adenocarcinoma (Swift et al., 1987; Geoffroy-Perez et al., 2001;
Angele et al., 2004; Roberts et al., 2012; Grant et al., 2013;
Russell et al., 2015). Studies have shown that IL-8 was able to
rescue cell migration and invasion defects in ATM-depleted cells
(Chen et al., 2015d). Low level of ATM protein was correlated with
poor metastasis-free survival in breast cancer patients. In
addition, miR-203 and miR-421 over-expression may be involved in
ATM deregulation in these patients (Bueno et al., 2014; Rondeau et
al., 2015).
[0119] ATP10A is associated with relapse and decrease of event-free
survival in B-cell precursor acute lymphatic leukemia (Olsson et
al., 2014).
[0120] ATP2A2 is associated with skin cancer, colon cancer and lung
cancer (Korosec et al., 2006; Hovnanian, 2007).
[0121] The expression of ATP2A3 is markedly decreased in colon,
stomach, lung and breast cancer and ATP2A3 expression is induced
when these cells undergo differentiation in vitro (Gelebart et al.,
2002; Arbabian et al., 2013; Papp et al., 2012). In colon cancer,
the expression of ATP2A3 has been shown to be negatively regulated
by the APC/beta-catenin/TCF4 oncogenic pathway (Brouland et al.,
2005). In addition, ATP2A3 expression was found to be negatively
related with lymphatic invasion (Gou et al., 2014).
[0122] Researchers have shown that patients with a variety of
malignancies such as melanoma, non-small cell lung carcinoma and
chronic myelogenous leukemia develop high-titer IgG antibodies
against ATP6AP1 following vaccination with irradiated, autologous
GM-CSF secreting tumor cells or allogeneic bone marrow
transplantation. Another report has detected elevated levels of
ATP6AP1 in invasive ductal and lobular carcinoma as well as breast
cancer. Furthermore, mutations in the ATP6AP1 gene were found in
follicular lymphoma (Hodi et al., 2002; Anderson et al., 2011;
Okosun et al., 2016).
[0123] ATP6V1H was shown to interact with the tumor associated gene
TM9SF4 in the colon cancer cell lines HCT116 and SW480 (Lozupone et
al., 2015). ATP6V1H, as part of the V-ATPase V1 sector, was shown
to be associated with invasive behavior of colon cancer cells and
tumor pH gradient (Lozupone et al., 2015).
[0124] Elevated levels of intracellular ATP8A1 protein diminished
the inhibitory role of miR-140-3p in the growth and mobility of
non-small-cell lung cancer cells (Dong et al., 2015).
[0125] ATR encodes ATR serine/threonine kinase, which belongs to
the PI3/P14-kinase family. This kinase has been shown to
phosphorylate checkpoint kinase CHK1, checkpoint proteins RAD17,
and RAD9, as well as tumor suppressor protein BRCA1 (RefSeq, 2002).
Copy number gain, amplification, or translocations of the ATR gene
were observed in oral squamous cell carcinoma cell lines (Parikh et
al., 2014). It has been demonstrated that truncating ATR mutations
in endometrial cancers are associated with reduced disease-free and
overall survival (Zighelboim et al., 2009). VE-822, an ATR
inhibitor was shown to radiosensitize and chemosensitize pancreatic
cancer cells in vitro and pancreatic tumor xenografts in vivo
(Fokas et al., 2012; Benada and Macurek, 2015).
[0126] AURKA is over-expressed in many tumors arising from breast,
colon, ovary, skin and other tissues, and it has been shown to
function as an oncogene when exogenously expressed in numerous cell
line models (Nikonova et al., 2013).
[0127] AURKB expression is up-regulated in different cancer types,
including lung, colorectal and breast cancer as well as leukemia
and thereby associated with poor prognosis. So development of AURKB
inhibitors for clinical therapy is an interesting field (Hayama et
al., 2007; Pohl et al., 2011; Hegyi et al., 2012; Goldenson and
Crispino, 2015). AURKB over-expression leads to phosphorylation of
histone H3 and to chromosome instability, a crucial factor for
carcinogenesis (Ota et al., 2002; Tatsuka et al., 1998). AURKB
activity augments the oncogenic Ras-mediated cell transformation
(Kanda et al., 2005).
[0128] Over-expression and gene amplification of AURKC was detected
in prostate and breast cancer cell lines as well as in colorectal
cancers, thyroid carcinoma and cervical cancer. Others have
observed an increase of AURKC protein in seminomas, implying that
it might play a role in the progression of testicular cancers. In
addition, AURKC has been shown to be oncogenic since its
over-expression transforms NIH 3T3 cells into tumors (Baldini et
al., 2010; Tsou et al., 2011; Khan et al., 2011; Zekri et al.,
2012). In colorectal cancer, the expression of AURKC was correlated
with the grade of disease and tumor size (Hosseini et al., 2015).
Furthermore, over-expression of AURKC induces an increase in the
proliferation, transformation and migration of cancer cells (Tsou
et al., 2011).
[0129] Heterozygous carriers of BBS1 gene seem to be at increased
risk of developing clear cell renal cell carcinoma (Beales et al.,
2000). Furthermore, BBS1 was recognized by serum antibodies of
melanoma patients but not by healthy controls (Hartmann et al.,
2005). It was reported that malignant pleural mesothelioma patients
with high BBS1 expression had an increased median overall survival
of 16.5 versus 8.7 months compared to those that showed low BBS1
expression (Vavougios et al., 2015).
[0130] BBX expression was shown to be associated with the
NF-kB/Snail/YY1/RKIP circuitry gene expression, which is associated
with metastatic prostate cancer and non-Hodgkin's lymphoma
(Zaravinos et al., 2014).
[0131] BCL2L13 was shown to be over-expressed in solid and blood
cancers, including glioblastoma and acute lymphoblastic leukemia
(Jensen et al., 2014; Yang et al., 2010). BCL2L13 is associated
with an unfavorable clinical outcome in childhood acute
lymphoblastic leukemia (Holleman et al., 2006).
[0132] Quantitative PCR and immunohistochemistry analysis revealed
that BDH1 was up-regulated in high-grade prostate cancer. Moreover,
the BDH1 gene was frequently amplified in metastatic conjunctival
melanomas (Lake et al., 2011; Saraon et al., 2013).
[0133] BHLHE41 is associated with breast cancer metastasis,
endometrial cancer metastasis, triple-negative breast cancer
metastasis, pancreatic cancer, human squamous carcinoma and lung
cancer (Sato et al., 2012a; Piccolo et al., 2013; Liao et al.,
2014a; Takeda et al., 2014; Falvella et al., 2008; Adam et al.,
2009). BHLHE41 is associated with CDDP resistance in human oral
cancer (Wu et al., 2012e).
[0134] BOLA2 was described as a novel candidate target gene of the
c-Myc oncogene which may be associated with malignant hepatocyte
transformation by altering cell cycle control (Hunecke et al.,
2012).
[0135] BOP1 is associated with ovarian cancer and colorectal cancer
(Wrzeszczynski et al., 2011; Killian et al., 2006). BOP1 was shown
to be a target gene of Wnt-catenin which induced EMT, cell
migration and experimental metastasis of colorectal cancer cells in
mice. Thus, BOP1 may serve as a therapeutic target in the treatment
of colorectal cancer metastasis (Qi et al., 2015). BOP1 is
associated with hepatocellular carcinoma invasiveness and
metastasis (Chung et al., 2011). BOP1 was described as a member of
a molecular pathway associated with cell cycle arrest in a gastric
cancer cell line upon treatment with mycophenolic acid, indicating
a potential association of BOP1 with the anticancer activity of the
drug (Dun et al., 2013a; Dun et al., 2013b). BOP1 may be a possible
marker for rectal cancer (Lips et al., 2008). BOP1 was described as
a potential oncogene in ovarian cancer (Wrzeszczynski et al.,
2011). BOP1 was shown to be up-regulated in hepatocellular
carcinoma (Chung et al., 2011). BOP1 was shown to be associated
with microvascular invasion, shorter disease-free survival and
metastasis in hepatocellular carcinoma (Chung et al., 2011). BOP1
was described as a subunit of the PeBoW complex, which is essential
for cell proliferation and maturation of the large ribosomal
subunit. Over-expression of BOP1 was shown to inhibit cell
proliferation (Rohrmoser et al., 2007). Expression of an
amino-terminally truncated form of BOP1 resulted in down-regulation
of G(1)-specific Cdk2 and Cdk4 kinase complexes, retinoblastoma and
cyclin A while Cdk inhibitors p21 and p27 were up-regulated. This
led to an arrest in the G(1) phase (Pestov et al., 2001).
[0136] BUB1B is a tumor inhibitory protein. BUB1B regulates the
spindle assembly checkpoint. BUB1B is inactivated or down-regulated
in tumors. Mutations in BUB1B are also linked to tumor development
(Aylon and Oren, 2011; Fagin, 2002; Malumbres and Barbacid, 2007;
Rao et al., 2009). BUB1B is associated with gastric carcinogenesis
through oncogenic activation (Resende et al., 2010). BUB1B mutation
is one of the causes for colorectal cancer (Karess et al., 2013;
Grady, 2004).
[0137] C10orf137 is associated with squamous cell lung cancer and
colorectal cancer (Gylfe et al., 2010; Zheng et al., 2013).
[0138] Over-expression of C1R has been found in the saliva of oral
squamous cell carcinoma patients. On the other hand, inactivation
of C1R was observed in paclitaxel-based treatment in hypopharynx
cancer patients (Xu et al., 2013a; Kawahara et al., 2016).
[0139] C2CD3 was shown to be associated with oropharyngeal squamous
cell carcinomas (Wang et al., 2013g).
[0140] C4orf46 was shown to be down-regulated in renal cell
carcinoma and C4orf46 expression was shown to be negatively
correlated with the Fuhrman grade in clear cell renal cell
carcinoma (Yu et al., 2014).
[0141] Increased expression of CA8 has previously been shown in
squamous cell carcinomas, adenocarcinomas, adenosquamous cell
carcinomas and colorectal carcinoma (Akisawa et al., 2003).
Over-expression of CA8 has been shown to induce apoptosis in lung
carcinoma A549 and human embryonic kidney HEK293 cells.
Furthermore, it inhibits cell proliferation in melanoma, prostate,
liver and bladder cancer cells (Liu et al., 2002a). siRNA-mediated
knockdown of CA8 revealed significant inhibition in cell
proliferation and colony formation of a colon cancer cell line
HCT116 (Nishikata et al., 2007).
[0142] CAAP1 was shown to be associated with drug resistance in
cancers (Wijdeven et al., 2015).
[0143] CAMSAP1 was shown to be associated with outcome in pediatric
acute lymphoblastic leukemia and prognosis of laryngeal squamous
cell carcinoma (Sun et al., 2014a; Wang et al., 2015c). CAMSAP1 was
shown to be up-regulated in laryngeal squamous cell carcinoma (Sun
et al., 2014a).
[0144] CAND1 is associated with prostate cancer and lung cancer
(Zhai et al., 2014; Salon et al., 2007).
[0145] Recent studies have shown that CANX was over-expressed in
lung cancer patients compared to healthy controls. These findings
imply that CANX could be used as a diagnostic marker for lung
cancer (Kobayashi et al., 2015b). CANX was down-regulated in HT-29
cells and MCF-7 human breast adenocarcinoma cells growing as
colonies compared to monolayers (Yeates and Powis, 1997).
[0146] Polymorphisms in the CARS gene have been linked to the
development of breast cancer in the Chinese population. Moreover,
CARS showed significantly higher association with different
molecular networks in glioblastoma multiforme (He et al., 2014; Kim
et al., 2012c).
[0147] CCAR1 is associated with medulloblastoma, small cell
prostate carcinoma, colon carcinoma and non-Hodgkin's Lymphoma
(Bish and Vogel, 2014; Levi et al., 2011; Scott et al., 2014; Ou et
al., 2009). CCAR1 was shown to be down-regulated in breast cancer
(Zhang et al., 2007).
[0148] CCDC110 was shown to interact with the high-risk human
papillomavirus 18 E6 oncogene in a yeast two-hybrid system and thus
may be a potential oncogenic target for cancer biotherapy (Li et
al., 2008b). CCDC110 was described as a cancer-testis antigen
associated with multiple myeloma which could potentially be used to
vaccinate patients (Condomines et al., 2007). CCDC110 was shown to
be a novel cancer-testis antigen which elicited humoral immune
responses in patients with various types of cancer. Thus, CCDC110
might be a target for cancer immunotherapy (Monji et al.,
2004).
[0149] CCNA1 encodes cyclin A1, which belongs to the highly
conserved cyclin family involved in the regulation of CDK kinases
(RefSeq, 2002). Elevated levels of CCNA1 were detected in
epithelial ovarian cancer, lymphoblastic leukemic cell lines as
well as in childhood acute lymphoblastic leukemia patients. Others
have observed over-expression of CCNA1 protein and mRNA in prostate
cancer and in tumor tissues of anaplastic thyroid carcinoma
patients (Holm et al., 2006; Wegiel et al., 2008; Marlow et al.,
2012; Arsenic et al., 2015). Recent studies have shown that
silencing of CCNA1 in highly cyclin A1 expressing ML1 leukemic
cells slowed S phase entry, decreased proliferation and inhibited
colony formation (Ji et al., 2005).
[0150] Over-expression of CCNA2 inhibits the proliferation of
hepatocellular carcinoma cells. Over-expression of CCNA2 in
endometrial adenocarcinoma cells decreases cell growth and
increases apoptosis. CCNA2 expression in melanoma cells reduces
tumor growth and metastasis and concomitantly increases apoptosis
in tumors (Lau, 2011). CCNA2 can promote cancer cell proliferation,
invasion, adhesion, differentiation, survival and metastasis. It
plays an important role in angiogenesis and extracellular matrix
production. CCNA2 promotes tumor growth and increases tumor
vascularization when over-expressed in gastric adenocarcinoma
cells. Silencing of CCNA2 expression decreases tumor growth in
pancreatic cancer cells. CCNA2 can promote the proliferation of
prostate cancer cells (Lau, 2011; Chen and Du, 2007). CCNA2
over-expression induces epithelial-mesenchymal transition, leading
to laryngeal tumor invasion and metastasis (Liu et al., 2015e).
CCNA2 is dysregulated in colorectal cancer (Chang et al., 2014a).
CCNA2 is over-expressed in prostate cancer, gliomas, pancreatic
cancer, and breast cancer. CCNA2 is associated with increased
aggressiveness, vascularization, and estrogen independence in
breast cancer, suggesting a major role of CCNA2 in breast cancer
progression (Zuo et al., 2010).
[0151] CCNB2 is up-regulated in colorectal adenocarcinoma (Park et
al., 2007). CCNB2 is over-expressed in various human tumors. Strong
CCNB2 expression in tumor cells is associated with a poor prognosis
in patients with adenocarcinoma of lung and invasive breast
carcinoma (Takashima et al., 2014; Albulescu, 2013).
[0152] A CCNB3-BCOR gene fusion was shown to be associated with the
cancer entity of undifferentiated small round cell sarcomas (Haidar
et al., 2015). CCNB3-BCOR (Ewing-like) sarcomas located in the
axial skeleton and soft tissues were shown to be associated with
shorter survival compared to Ewing sarcomas (Puls et al., 2014).
CCNB3 was shown to interact with cdk2, a protein involved in cell
cycle transition (Nguyen et al., 2002).
[0153] Over-expression and amplification of CCNE1 was observed in
various types of cancer, including breast, colon, gastric, lung,
endometrial intraepithelial carcinoma, uterine serous carcinoma and
high grade serous ovarian cancer (Donnellan and Chetty, 1999; Kuhn
et al., 2014; Noske et al., 2015). In addition, increased
expression of CCNE1 is a useful marker of poor prognosis in lung
cancer (Huang et al., 2012). A study has shown that CCNE1 is
down-regulated by both miR-497 and miR-34a, which synergistically
retard the growth of human lung cancer cells (Han et al.,
2015b).
[0154] Studies have shown that acute myeloid leukemia patients with
long-term in vitro proliferation of AML cells showed altered
expression in CCNF (Hatfield et al., 2014). Furthermore, low CCNF
expression was related to poor overall survival and recurrence-free
survival in hepatocellular carcinoma patients (Fu et al.,
2013a).
[0155] CCR4 has been described as a prognostic marker in various
tumors such as renal cell carcinoma, head and neck squamous cell
carcinoma, gastric cancer, breast cancer, colon cancer and Hodgkin
lymphoma (Ishida et al., 2006; Olkhanud et al., 2009; Yang et al.,
2011; Tsujikawa et al., 2013; Al-haidari et al., 2013; Liu et al.,
2014d). Studies have revealed that gastric cancer patients with
CCR4-positive tumors had significantly poorer prognosis compared to
those with CCR4-negative tumors (Lee et al., 2009).
[0156] CCT4 deregulation causes esophageal squamous cell carcinoma
and lung adenocarcinoma (Wang et al., 2015i; Tano et al., 2010).
CCT4 is upregulated in gastric cancers (Malta-Vacas et al.,
2009).
[0157] CCT5 is associated with breast cancer (Campone et al.,
2008). CCT5 was shown to be up-regulated in sinonasal
adenocarcinoma (Tripodi et al., 2009). CCT5 is associated with
overall survival in small cell lung cancer, drug resistance in
gastric carcinoma and breast cancer and lymph node metastasis in
esophageal squamous cell carcinoma (Niu et al., 2012; Ooe et al.,
2007; Uchikado et al., 2006; Ludwig et al., 2002).
[0158] CCT8 was shown to be up-regulated in hepatocellular
carcinoma (Huang et al., 2014b). CCT8 is associated with histologic
grades, tumor size and poor prognosis of hepatocellular carcinoma
(Huang et al., 2014b).
[0159] Strong CD68 expression was found in basal cell carcinoma,
fibrolamellar carcinomas, Hodgkin lymphoma, human glioma, squamous
cell carcinoma, adenocarcinoma, adenosquamous cell carcinoma, small
cell carcinoma, papillary adenocarcinoma, metastatic
adenocarcinoma, bronchioloalveolar carcinoma as well as in induced
rat tumors (Strojnik et al., 2006; Strojnik et al., 2009; Ross et
al., 2011; Glaser et al., 2011; Yoon et al., 2012; Banat et al.,
2015). In breast cancer, increased CD68 expression was correlated
with larger tumor size, higher TNM stages and Her-2 positivity.
Moreover, the number of CD68 cells was positively correlated with
the expression of Ras (Li et al., 2015b).
[0160] CD74 expression has been observed in various cancers,
including gastrointestinal, renal, non-small cell lung,
glioblastoma cell lines, thymic epithelial neoplasms and head and
neck squamous cell carcinomas (Ioachim et al., 1996; Datta et al.,
2000; Young et al., 2001; Ishigami et al., 2001; Kitange et al.,
2010; Gold et al., 2010; Kindt et al., 2014). Preclinical studies
in B-cell lymphoma and multiple myeloma revealed that CD74 could be
used as a therapeutic target for these disorders (Burton et al.,
2004).
[0161] Over-expression of CDC123 was observed in a choriocarcinoma
cell line. Other studies have detected CDC123 protein in basal
breast cancer (Adelaide et al., 2007; Kobayashi et al., 2013).
[0162] CDC6 expression is de-regulated in different cancer types
including gallbladder, cervical and prostate cancer (Wu et al.,
2009; Wang et al., 2009e; Robles et al., 2002; Shu et al., 2012).
CDC6 co-operates with c-Myc to promote genetic instability,
tumor-like transformation and apoptosis attenuation (Chen et al.,
2014a). Hypoxia-induced ATR promotes the degradation of CDC6.
Initiation of DNA replication is regulated by p53 through Cdc6
protein stability (Duursma and Agami, 2005; Martin et al.,
2012).
[0163] Several publications have reported over-expression of CDC7
in many human tumors, including ovarian cancer, colorectal cancer,
melanoma, diffuse large B-cell lymphoma, oral squamous cell
carcinoma and breast cancer (Clarke et al., 2009; Kulkarni et al.,
2009; Choschzick et al., 2010; Hou et al., 2012; Cheng et al.,
2013a; Chen et al., 2013b). Elevated levels of CDC7 protein
predicts disease-free survival in patients suffering from ovarian
cancer (Kulkarni et al., 2009).
[0164] Elevated levels of CDH2 have been reported in patients
suffering from gastric, breast, prostate, bladder, malignant bone
and soft tissue tumors (Rieger-Christ et al., 2001; Chan et al.,
2001; Jaggi et al., 2006; Nagi et al., 2005; Niimi et al., 2013).
In colorectal cancer, over-expression of CDH2 correlated with local
infiltration depth, tumor staging, vascular invasion and tumor
differentiation level (Ye et al., 2015).
[0165] CDK1 is over-expressed in different cancer types including
breast, gastric, liver and colorectal cancer and is associated with
tumor progression and poor prognosis (Kim et al., 1999; Sung et
al., 2014; Masuda et al., 2003; Kim, 2007; Ito et al., 2000; Chae
et al., 2011). CDK1 regulates via phosphorylation HIF-1alpha, Bcl-2
proteins, Sp1 and p53 and thereby influences tumor growth,
apoptosis and DNA damage response (Nantajit et al., 2010; Zhang et
al., 2011; Chuang et al., 2012; Sakurikar et al., 2012; Warfel et
al., 2013).
[0166] CDK12 mutations were identified in a variety of tumors,
including ovarian, breast, prostate, and intestinal tumors (Vrabel
et al., 2014).
[0167] CDK13 is associated with pancreatic cancer and skin cancer
(Ansari et al., 2015; Nelson et al., 1999; Chandramouli et al.,
2007). CDK13 is amplified in hepatocellular carcinoma (Kim et al.,
2012a).
[0168] Over-expression of CDK4 has been observed in many tumor
types, such as oral squamous cell carcinoma, pancreatic endocrine
tumors, lung cancer and nasopharyngeal carcinoma (Dobashi et al.,
2004; Wikman et al., 2005; Lindberg et al., 2007; Poomsawat et al.,
2010; Jiang et al., 2014c). Researchers have noted that patients
suffering from nasopharyngeal carcinoma with higher levels of CDK4
expression had poorer survival rates compared to those with lower
levels of CDK4 expression (Liu et al., 2014j).
[0169] CDK5 is over-expressed in many tumors including prostate
cancer, pancreatic cancer, lung cancer, glioblastoma and breast
cancer (Strock et al., 2006; Liu et al., 2008b; Feldmann et al.,
2010; Demelash et al., 2012; Liang et al., 2013). Inhibition of
CDK5 kinase activity using a CDK5 dominant-negative mutant or the
drug roscovitine significantly decreased the migration and invasion
of pancreatic cancer cells in vitro (Eggers et al., 2011; Pozo et
al., 2013).
[0170] CDK6 has been shown to regulate the activity of tumor
suppressor protein Rb. CDK6 can exert its tumor-promoting function
by enhancing proliferation and stimulating angiogenesis (Kollmann
et al., 2013). The pharmacological inhibition of CDK6 was shown to
inhibit the growth differentiation of abnormal leukemic cells
(Placke et al., 2014).
[0171] Over-expression of CELSR2 was found in head and neck
squamous cell carcinoma samples, whereas in breast cancer CELSR2
was down-regulated (Lin et al., 2004; Huang et al., 2005a).
[0172] CENPN may be a prognostic marker for early breast cancer (Li
et al., 2013d).
[0173] CEP55 is strongly up-regulated in human gastric cancer (Tao
et al., 2014b). Fibulin-5 increases the activity of CEP55 resulting
in a promotion of cell metastasis in nasopharyngeal carcinoma
(Hwang et al., 2013). CEP55 may regulate nasopharyngeal carcinoma
via the osteopontin/CD44 pathway (Chen et al., 2012a). CEP55 is
over-expressed in oropharyngeal squamous cell carcinoma (Janus et
al., 2011). CEP55 was identified as novel target in lung cancer
(Lai et al., 2010). CEP55 can be detected in colon cancer and
breast cancer (Colak et al., 2013; Inoda et al., 2009; Inoda et
al., 2011b; Inoda et al., 2011a; Castle et al., 2014).
Down-regulation of CEP55 inhibits cell motility and invasion in
ovarian cancer (Zhang et al., 2015m). CEP55 is significantly
up-regulated in ovarian cancer cell lines and lesions compared to
normal cells and adjacent non-cancerous ovarian tissue (Zhang et
al., 2015m). CEP55 is classified as an oncogene and its
dys-regulation affects the cell cycle pathway. This may play a role
in laryngeal squamous cell carcinoma progression (Hui et al.,
2015). CEP55 over-expression significantly correlates with tumor
stage, aggressiveness, metastasis and poor prognosis across
multiple tumor types (Jeffery et al., 2015b; Chen et al., 2009a;
Janus et al., 2011). The complex of CEP55 with Aurora-A may enhance
the progression and metastasis of head and neck cancer (Chen et
al., 2015a; Waseem et al., 2010). An extract of Graptopetalum
paraguayense can down-regulate the expression level of CEP55 in
hepatocellular carcinoma (Hsu et al., 2015). CEP55 is
over-expressed in bladder cancer and prostate cancer (Singh et al.,
2015; Shiraishi et al., 2011). CEP55 mRNA is significantly higher
expressed in muscle-invasive bladder cancer compared to
non-muscle-invasive bladder cancer. However, there is no difference
in protein expression (Singh et al., 2015).
[0174] It was reported that CEP57 is up-regulated in a subset of
primary prostate adenocarcinomas, whereas deletion in CEP57 gene
was detected in breast carcinoma (Gentile et al., 2001; Sinha et
al., 2011; Cuevas et al., 2013). Moreover, alterations of CEP57
were linked with poor prognosis in patients suffering from breast
cancer with early age of onset. On the other hand, in prostate
cancer elevated levels of CEP57 were not correlated with poor
patient survival but instead with a moderate yet significant
BCR-free survival advantage (Sinha et al., 2011; Mang et al.,
2015). It has been postulated that CEP57 may contribute to
apoptosis by modulating the activity or function of Bcl-2 in breast
cancer (Zhao et al., 2005).
[0175] CEP97 is associated with breast cancer (Rappa et al.,
2014).
[0176] CERS1 is down-regulated in nilotinib-resistant chronic
myeloid leukemia cells (Camgoz et al., 2013). CERS1 generated
C(18)-ceramide levels are significantly decreased in head and neck
squamous cell carcinoma (HNSCC) tumors. Decreased C(18)-ceramide
levels in HNSCC tumor tissues are significantly associated with the
higher incidences of lymphovascular invasion, and pathologic nodal
metastasis (Karahatay et al., 2007). CERS1 generated C(18)-ceramide
mediates cell death in cancer cells (Saddoughi and Ogretmen,
2013).
[0177] CERS2 was shown to be down-regulated in meningioma (Ke et
al., 2014b). CERS2 was shown to be up-regulated in colorectal
cancer, lung squamous cell carcinoma and breast cancer (Moriya et
al., 2012; Chen et al., 2015c; Schiffmann et al., 2009). CERS2 is
associated with metastasis and drug-resistance of breast cancer,
growth, invasion and metastasis of prostate cancer, diverse
proliferation, metastasis and invasion of bladder cancer and
hepatocellular carcinoma (Tang et al., 2010; Zhao et al., 2013a;
Perez et al., 2014; Xu et al., 2014a; Zi et al., 2015). CERS2 may
be a potential biomarker for colorectal cancer, meningioma and
bladder cancer (Zhao et al., 2013a; Ke et al., 2014b; Chen et al.,
2015c).
[0178] Studies have shown that the expression of CFB was reduced in
sera of patients suffering from nasopharyngeal carcinoma. On the
other hand, the expression of CFB was more than two times higher in
plasma samples from pancreatic ductal adenocarcinoma patients
compared with plasma from healthy individuals. Others have observed
an association of the CFB locus with melanoma (Budowle et al.,
1982; Seriramalu et al., 2010; Lee et al., 2014a).
[0179] CHCHD7 is associated with pleomorphic adenoma (Matsuyama et
al., 2011).
[0180] CHD7 is associated with cutaneous T-cell lymphoma, CpG
island methylator phenotype 1 colorectal carcinoma, gastric cancer
with microsatellite instability and small-cell lung cancer (Kim et
al., 2011b; Tahara et al., 2014; Litvinov et al., 2014b; Pleasance
et al., 2010). CHD7 was shown to be up-regulated in colon cancer
(Scanlan et al., 2002). CHD7 is associated with survival outcomes
of pancreatic cancer (Colbert et al., 2014).
[0181] A report has postulated that polymorphisms in the CHST1 gene
could account for 5-fluorouracil-induced toxicity in colorectal
cancer patients. Another study found that LN229 glioblastoma cells
express elevated levels of CHST1 (Hayatsu et al., 2008; Rumiato et
al., 2013; Arbitrio et al., 2016).
[0182] CKLF was shown to be up-regulated in high-grade glioma (Yang
et al., 2013).
[0183] CLDN16 was shown to be up-regulated in papillary thyroid
carcinomas and ovarian cancer (Rangel et al., 2003; Fluge et al.,
2006). CLDN16 expression was shown to be associated aggressiveness,
high mortality and poor prognosis in breast cancer (Martin et al.,
2008; Martin and Jiang, 2011). CLDN16 was shown to be associated
with kidney cancer (Men et al., 2015). CLDN16 was described as a
potential biomarker for breast cancer (Kuo et al., 2010).
[0184] CLSPN is up-regulated in non-small cell lung carcinoma
(NSCLC). Over-expression of CLSPN is associated with a bad
prognosis in NSCLC (Allera-Moreau et al., 2012).
[0185] Over-expression of CLSTN3 has been found in testicular
cancer as well as human embryonal carcinoma (Dormeyer et al.,
2008).
[0186] Single-nucleotide polymorphisms (SNPs) in the CNOT1 gene
were detected in osteosarcoma and acute lymphoblastic leukemia
(ALL) (Gutierrez-Camino et al., 2014; Bilbao-Aldaiturriaga et al.,
2015). CNOT1 depletion induces stabilization of mRNAs and
activation of ER stress-mediated apoptosis (Ito et al., 2011).
[0187] Single nucleotide polymorphism in the CNOT4 gene was
correlated with the risk of osteosarcoma (Bilbao-Aldaiturriaga et
al., 2015).
[0188] Changes in COPA gene expression and RNA editing were shown
to be associated with hepatocellular carcinoma and an experimental
study revealed anti-apoptotic effects of COPA in mesothelioma cells
(Qi et al., 2014; Sudo et al., 2010; Wong et al., 2003).
[0189] shRNA library screening identified COPB1 as determinants of
sensitivity to 2-deoxyglucose, a glycolytic inhibitor in cancer
cells. Moreover, silencing of COPB1 expression sensitized cells to
2-deoxyglucose toxicity (Kobayashi et al., 2015a).
[0190] COPB2 is expressed in various types of cancer such as
breast, colon, prostate, pancreas carcinomas, glioblastoma and lung
adenocarcinoma (Erdogan et al., 2009). Others have implicated COPB2
to be involved in anti-apoptotic function in mesothelioma (Sudo et
al., 2010).
[0191] COPG1 correlates with the age of the patients as well as a
higher grade of malignancy and the grade of gliosarcomas (Coppola
et al., 2014). COPG1 was found abundantly expressed in lung cancer
and lung cancer-related endothelial cells (Park et al., 2008).
[0192] Function-based genomic screening identified COPZ1 as an
essential gene for different tumor cells. Knock-down of COPZ1 was
shown to cause Golgi apparatus collapse, block autophagy, and
induce apoptosis in both proliferating and non-dividing tumor
cells. Thus, COPZ1 could be a novel therapeutic target, which
offers an opportunity for proliferation-independent selective
killing of tumor cells (Shtutman et al., 2011).
[0193] Over-expression of CORO2A has been found in breast cancer
and colon carcinoma (Bubnov et al., 2012; Rastetter et al., 2015).
Researchers have revealed that both MAPK14 and PRMT5 signaling
pathways play a crucial role in tumor progression (Rastetter et
al., 2015). Down-regulation of CORO2A in colorectal cancer cells
was correlated with reduced early apoptosis (Kim et al.,
2013a).
[0194] Single nucleotide polymorphisms as well as mutations in the
CSDA gene were associated with hepatocellular carcinoma. Another
group found higher mRNA expression levels of CSDA in hepatocellular
carcinoma compared to corresponding non-tumor tissues. In addition,
elevated levels of CSDA were observed in gastric cancer tissues and
cell lines compared to adjacent normal tissues (Hayashi et al.,
2002; Wang et al., 2009a; Yasen et al., 2012). Recent work has
shown a correlation between elevated levels of CSDA in
hepatocarcinomas and poorer prognosis (Yasen et al., 2005). In
chronic myeloid leukemia, both Akt and MEK/p90 ribosomal S6 kinase
can phosphorylate the serine 134 residue of CSDA (Sears et al.,
2010).
[0195] CSE1L was shown to be highly expressed in hepatocellular
carcinoma, bladder urothelial carcinoma, serous ovarian cancer,
breast cancer and metastatic cancer (Behrens et al., 2001; Tung et
al., 2009; Stawerski et al., 2010; Tai et al., 2012; Zang et al.,
2012). Researchers have demonstrated that CSE1L regulates
translocation and secretion of MMP-2 from colorectal cancer cells
(Liao et al., 2008; Tsao et al., 2009). Furthermore, inhibition of
MEK1 mediated phosphorylation resulted in enhanced paclitaxel
(Taxol) induced apoptosis in breast, ovarian, and lung tumor cell
lines. Since CSE1L is also activated by MEK1 altering the
activity/phosphorylation status of CSE1L via MEK1 inhibition may
present a potential strategy in experimental cancer therapy
(Behrens et al., 2003).
[0196] CT45 genes were shown to be potential prognostic biomarkers
and therapeutic targets in epithelial ovarian cancer (Zhang et al.,
20151). The CT45A1protein which is usually only expressed in
testicular germ cells was shown to be also expressed in lung
cancer, breast cancer and ovarian cancer (Chen et al., 2009d).
CT45A1 was also shown to be associated with poor prognosis and poor
outcomes in multiple myeloma (Andrade et al., 2009). CT45A1 was
described as gene up-regulating epithelial-mesenchymal transition
(EMT) and metastatic genes, promoting EMT and tumor dissemination.
Furthermore, CT45A1 was described as being implicated in the
initiation or maintenance of cancer stem-like cells, promoting
tumorigenesis and malignant progression (Yang et al., 2015a).
CT45A1 over-expression in a breast cancer model was shown to result
in the up-regulation of various oncogenic and metastatic genes,
constitutively activated ERK and CREB signaling pathways and
increased tumorigenesis, invasion and metastasis. Silencing of
CT45A1 was shown to reduce cancer cell migration and invasion.
Thus, CT45A1 may function as a novel proto-oncogene and may be a
target for anticancer drug discovery and therapy (Shang et al.,
2014).
[0197] CT45A2 was shown to be a novel spliced MLL fusion partner in
a pediatric patient with de novo bi-phenotypic acute leukemia and
thus might be relevant for leukemogenesis (Cerveira et al., 2010).
The cancer/testis antigen family 45 was shown to be frequently
expressed in both cancer cell lines and lung cancer specimens (Chen
et al., 2005). CT45 genes were shown to be potential prognostic
biomarkers and therapeutic targets in epithelial ovarian cancer
(Zhang et al., 20151).
[0198] The cancer/testis antigen family 45 was shown to be
frequently expressed in both cancer cell lines and lung cancer
specimens (Chen et al., 2005). CT45 genes were shown to be
potential prognostic biomarkers and therapeutic targets in
epithelial ovarian cancer (Zhang et al., 20151).
[0199] The cancer/testis antigen family 45 was shown to be
frequently expressed in both cancer cell lines and lung cancer
specimens (Chen et al., 2005). CT45 genes were shown to be
potential prognostic biomarkers and therapeutic targets in
epithelial ovarian cancer (Zhang et al., 20151).
[0200] The cancer/testis antigen family 45 was shown to be
frequently expressed in both cancer cell lines and lung cancer
specimens (Chen et al., 2005). CT45 genes were shown to be
potential prognostic biomarkers and therapeutic targets in
epithelial ovarian cancer (Zhang et al., 20151).
[0201] The cancer/testis antigen family 45 was shown to be
frequently expressed in both cancer cell lines and lung cancer
specimens (Chen et al., 2005). CT45 genes were shown to be
potential prognostic biomarkers and therapeutic targets in
epithelial ovarian cancer (Zhang et al., 20151).
[0202] Elevated levels of CTSA were found in squamous cell
carcinoma compared to normal mucosa. Others have detected higher
levels of CTSA activity in lysates of metastatic lesions of
malignant melanoma than in primary focus lysates. Another report
has demonstrated that the CTSA activity was twice as high in the
vitreous body of patients suffering from absolute glaucoma compared
to patients with intraocular tumors (Obuchowska et al., 1999;
Kozlowski et al., 2000; Marques Filho et al., 2006).
[0203] CYFIP1 was shown to be down-regulated during invasion of
epithelial tumors (Silva et al., 2009). CYFIP1 down-regulation is
associated with poor prognosis in epithelial tumors (Silva et al.,
2009).
[0204] CYFIP2 expression is increased in newly formed lymph nodes
in breast cancer (Gantsev et al., 2013). CYFIP2 expression is
reduced in human gastric tumor samples, compared with control
tissues (Cheng et al., 2013b). CYFIP2 is one of several
apoptosis-related genes methylated in chronic lymphocytic leukemia
(Halldorsdottir et al., 2012).
[0205] The expression of CYP2F1 was found in primary ovarian cancer
and non-cancerous nasopharynx tissues. However, it was absent in
breast tumors as well as in control tissues (Downie et al., 2005;
Iscan et al., 2001; Jiang et al., 2004). In colorectal cancer, the
expression of CYP2F1 in the lymph node metastasis strongly
correlated with its presence in corresponding primary tumors
(Kumarakulasingham et al., 2005).
[0206] CYP4X1 was shown to be present as an off-frame fusion
transcript with CYP4Z2P in breast cancer (Kim et al., 2015a).
CYP4X1 was shown to be associated with tumor grade in breast cancer
and may be a potential biomarker to aid decisions regarding optimal
adjuvant hormonal therapy (Murray et al., 2010). CYP4X1 was shown
to be a potential primary target of estrogen receptor beta (ERbeta)
in the ERbeta over-expressing HEK293 cell line (Zhao et al.,
2009).
[0207] A single polymorphism in the CYP7B1 gene has been associated
with the risk of prostate cancer. In addition, elevated levels of
CYP7B1 have been found in high-grade prostatic intraepithelial
neoplasia, adenocarcinomas and breast carcinoma (Jakobsson et al.,
2004; Olsson et al., 2007; Pu et al., 2015).
[0208] DCBLD2 is up-regulated in glioblastomas and head and neck
cancers (HNCs) and is required for EGFR-stimulated tumorigenesis
(Feng et al., 2014a). Furthermore, DCBLD2 is up-regulated in highly
metastatic lung cancer sublines and tissue samples (Koshikawa et
al., 2002). In contrast, the expression of DCBLD2 is silenced by
hypermethylation of its promoter in gastric cancer (Kim et al.,
2008b).
[0209] DCHS2 is associated with gastric cancers and colorectal
cancers with high microsatellite instability (An et al., 2015).
[0210] DDX11, belonging to the DEAH family of DNA helicases, is
highly expressed in advanced melanoma and is essential for the
survival of melanoma cells (Bhattacharya et al., 2012).
[0211] DDX20 was shown to be down-regulated in hepatocellular
carcinoma (Takata et al., 2013a). DDX20 is associated with
increased risk of colorectal cancer and bladder cancer as well as
reduced overall survival in breast cancer and increased metastatic
potential (Yang et al., 2008a; Zhao et al., 2015b; Shin et al.,
2014). DDX20 may be a prognostic biomarker for breast cancer (Shin
et al., 2014).
[0212] DDX41 is associated with acute myeloid leukemia
(Antony-Debre and Steidl, 2015).
[0213] DDX47 may be a potential marker to discriminate different
disease phases of chronic myeloid leukemia (Oehler et al.,
2009).
[0214] DDX6 was found to be over-expressed in colorectal
adenocarcinomas, gastric cancer, hepatocellular carcinoma, nodal
marginal zone lymphoma, neuroblastoma, rhabdomyosarcoma and lung
cancer cell lines (Akao et al., 1995; Nakagawa et al., 1999; Miyaji
et al., 2003; Lin et al., 2008a; Stary et al., 2013; Iio et al.,
2013). In nodal marginal zone lymphoma, DDX6 seems to interfere
with the expression of BCL6 and BCL2 in an NF-I.degree.B
independent manner (Stary et al., 2013). Recent studies have shown
that DDX6 post-transcriptionally down-regulated miR-143/145
expression by prompting the degradation of its host gene product,
NCR143/145 RNA (Iio et al., 2013).
[0215] DEPDC1B was shown to be up-regulated in oral cancer and
non-small cell lung cancer (Yang et al., 2014e; Su et al., 2014).
DEPDC1B expression is associated with patient survival, migration
and metastasis of non-small cell lung cancer and radiation
sensitivity of lymphoblastoid tumor cell lines (Niu et al., 2010;
Yang et al., 2014e).
[0216] High levels of the DFFB gene were detected in cisplatin
resistance in bladder cancer, whereas the levels of DFFB were
decreased in oligodendrogliomas with 1p-allelic loss. Another group
found no mutation in the DFFB gene in neuroblastomas (Judson et
al., 2000; McDonald et al., 2005; Kim et al., 2016).
Over-expression of DFFB resulted in a decrease in the viability of
breast cancer cells incubated with acetazolamide and
sulfabenzamide. In addition, there was enhanced apoptosis in these
groups, especially with acetazolamide. Similarly, DFFB fused with
GM-CSF was found to facilitate targeted killing of acute myeloid
leukemia cells by inducing apoptosis (Mathew et al., 2013; Bagheri
et al., 2014).
[0217] DFNA5 expression was found to be lower in hepatocellular
carcinoma cells, estrogen receptor (ER)-positive breast carcinoma
and gastric cancer cell lines (Thompson and Weigel, 1998; Akino et
al., 2007; Wang et al., 2013c). Moreover, etoposide resistance in
melanoma cells was linked to reduced DFNA5 expression (Lage et al.,
2001). DFNA5 knock-down resulted in an increase in cell invasion,
colony numbers, colony size and cell growth in colorectal carcinoma
cell lines (Kim et al., 2008c).
[0218] DHX40 is associated with epithelial ovarian cancer (Zheng et
al., 2004).
[0219] PrognoScan database revealed that DHX8 is expressed in
bladder cancer, blood cancer, brain cancer, breast cancer,
colorectal cancer, eye cancer, head and neck cancer, lung cancer,
ovarian cancer, skin cancer and soft tissue cancer tissues (Wang et
al., 2014f). Researchers have observed that DHX8 was present both
in the normal adrenal cortex as well as in the malignant
adrenocortical cancer (Szabo et al., 2009).
[0220] DEF was shown to mediate the non-proteasomal degradation of
the tumor-suppressor p53 (Tao et al., 2013).
[0221] Studies have revealed that DLG5 is down-regulated in
prostate cancer as well as bladder cancer. On the other hand,
over-expression of DLG5 was observed in pancreatic ductal
adenocarcinoma. Moreover, single nucleotide polymorphisms in the
DLG5 gene were not correlated with risk of colorectal cancer
(Taniuchi et al., 2005; Suchy et al., 2008; Tomiyama et al., 2015;
Zhou et al., 2015b). Knockdown of endogenous DLG5 resulted in an
increase in prostate cancer cell migration and invasion, while it
suppressed the growth of pancreatic ductal adenocarcinoma (Taniuchi
et al., 2005; Tomiyama et al., 2015).
[0222] DMXL2 was shown to be up-regulated in ER-alpha positive
breast cancer (Faronato et al., 2015). DMXL2 is a functional
biomarker for ER-alpha positive breast cancer (Faronato et al.,
2015).
[0223] DNAH3 is associated with colon cancer (Tanaka et al.,
2008a).
[0224] Studies have detected DNASE1L1 in patients suffering from
oral squamous cell carcinoma. Furthermore, DNASE1L1 expression was
linked with poor disease-free survival rate in these patients
(Grimm et al., 2013).
[0225] DOCK8 was shown to be down-regulated in squamous cell
carcinoma of the lung (Kang et al., 2010). DOCK8 was shown to be
associated with neuroblastomas, pediatric pilocytic astrocytomas,
hepatocellular carcinomas, gliomas and lung cancer (Schramm et al.,
2015; Saelee et al., 2009; Takahashi et al., 2006; Zhao et al.,
2014a; ldbaih et al., 2008). DOCK8 was shown to be associated with
radiosensitivity in the esophageal cancer cell line TE-11 (Ogawa et
al., 2008).
[0226] A report has revealed over-expression of DPP3 in
glioblastoma cells as well as in squamous cell lung carcinoma.
Similarly, higher DPP3 activity was observed in endometrial and
ovarian malignant tumors compared to the activity in normal tissues
(Simaga et al., 1998; Simaga et al., 2003; Hast et al., 2013; Singh
et al., 2014).
[0227] DPPA4 was shown to be up-regulated in colon cancer (Zhang et
al., 2015j). DPPA4 is associated with bladder cancer, prostate
cancer, embryonal carcinomas, pluripotent germ cell tumors and
sarcoma (Tung et al., 2013; Amini et al., 2014). DPPA4 is
associated with stage, invasion depth, distant metastasis and
differentiation of colon cancer (Zhang et al., 2015j). DPPA4 is an
independent prognostic indicator of disease-free survival and
overall survival of colon cancer (Zhang et al., 2015j).
[0228] DTX3L was shown to be up-regulated in melanomas, squamous
cell carcinomas of the cervix and diffuse large B-cell lymphomas
with a prominent inflammatory infiltrate (Thang et al., 2015;
Wilting et al., 2008; Juszczynski et al., 2006). DTX3L was shown to
mediate regulation of invasion and metastasis in melanoma through
FAK/PI3K/AKT signaling. Thus, DTX3L may serve as a potential
therapeutic target as well as a potential biomarker for melanomas
(Thang et al., 2015). DTX3L was described as a chemotherapy
resistance factor which is up-regulated in EZH2 gain-of-function
mutant diffuse large B-cell lymphomas (Johnson et al., 2015). DTX3L
was shown to be a novel oncogenic factor in metastatic prostate
cancer cells which mediates proliferation, chemo-resistance and
survival of metastatic prostate cancer in interaction with
oncogenic proteins ARTD8 and ARTD9 (Bachmann et al., 2014). DTX3L
was shown to be associated with transcription factors STAT1 and
STAT3 as well as the tumor suppressor IRF1 in metastatic prostate
cancer cells (Bachmann et al., 2014). DTX3L was described as a bona
fide member of a DNA damage response pathway, which is directly
associated with PARP1 activation and recruitment of the tumor
suppressor BRCA1 (Yan et al., 2013b).
[0229] A whole exome sequencing study uncovered somatic mutations
within the DYNC1H1 gene in patients with intra-ductal papillary
mucinous neoplasm of the pancreas (Furukawa et al., 2011).
[0230] DYNC2H1 was shown to be up-regulated in glioblastoma
multiforme (Yokota et al., 2006).
[0231] EGFLAM promoter CGI methylation ratio was decreased in
epithelial ovarian cancer compared to benign ovarian diseases (Gu
et al., 2009). The promoter CGI of EGFLAM may be a novel candidate
for ovarian cancer-specific hypo-methylated tumor markers (Gu et
al., 2009).
[0232] EIF2S2 has been shown to be amplified in patients suffering
from highly proliferative luminal breast tumors (Gatza et al.,
2014).
[0233] EIF2S3 is one of 5 molecular markers that were
differentially expressed between peripheral blood samples of
colorectal cancer patients and healthy controls (Chang et al.,
2014c). EIF2S3 interacts with N-myc down-stream regulated gene 1
(NDRG1), which plays a role in cell differentiation and inhibition
of prostate cancer metastasis (Tu et al., 2007).
[0234] EIF3C is highly expressed in colon cancer (Song et al.,
2013c). EIF3C mRNA is over-expressed in testicular seminomas (Rothe
et al., 2000).
[0235] Down-regulation of EIF3F expression was reported in
pancreatic cancer and in melanoma. Furthermore, loss of EIF3F and a
statistically significant reduced gene copy number was demonstrated
in both melanoma and pancreatic tumors as compared to normal
tissues (Shi et al., 2006; Doldan et al., 2008a; Doldan et al.,
2008b). Recent work showed that decreased expression of EIF3F could
be used as a prognostic marker for poor outcome in patients
affected by gastric cancer (Cheng et al., 2015a). High levels of
EIF3F inhibited cell proliferation and induced apoptosis in
melanoma and pancreatic cancer cells (Shi et al., 2006; Doldan et
al., 2008a).
[0236] EIF4G3 is up-regulated in diffuse large B-cell lymphoma.
Moreover, down-regulation of EIF4G3 by siRNA resulted in a
reduction of translation, cell proliferation and the ability to
form colonies as well as induction of cellular senescence
(Mazan-Mamczarz et al., 2014).
[0237] EMC10 up-regulation was shown to be associated with
high-grade gliomas and modulation of signaling pathways involved in
tumorigenesis (Junes-Gill et al., 2011; Junes-Gill et al., 2014).
EMC10 was shown to inhibit glioma-induced cell cycle progression,
cell migration, invasion and angiogenesis and thus may be a
potential therapeutic for malignant glioblastoma (Junes-Gill et
al., 2014).
[0238] Down-regulation of EMG1 was noted in hepatocellular
carcinoma cell lines after treatment with platycodin D (Lu et al.,
2015).
[0239] EPG5 is associated with breast cancer (Halama et al.,
2007).
[0240] EPPK1 was shown to be associated with intrahepatic
cholangiocarcinoma and cervical squamous cell carcinoma (Zou et
al., 2014b; Guo et al., 2015).
[0241] ERLIN2 is associated with breast cancer and hepatocellular
carcinoma (Wang et al., 2012a).
[0242] ERMP1 was shown to be associated with breast cancer (Wu et
al., 2012c).
[0243] Mutations and single nucleotide polymorphisms of ESR1 are
associated with risk for different cancer types including liver,
prostate, gallbladder and breast cancer. The up-regulation of ESR1
expression is connected with cell proliferation and tumor growth
but the overall survival of patients with ESR1 positive tumors is
better due to the successfully therapy with selective estrogen
receptor modulators (Sun et al., 2015c; Hayashi et al., 2003;
Bogush et al., 2009; Miyoshi et al., 2010; Xu et al., 2011;
Yakimchuk et al., 2013; Fuqua et al., 2014). ESR1 signaling
interferes with different pathways responsible for cell
transformation, growth and survival like the EGFR/IGFR,
PI3K/Akt/mTOR, p53, HER2, NFkappaB and TGF-beta pathways (Frasor et
al., 2015; Band and Laiho, 2011; Berger et al., 2013; Skandalis et
al., 2014; Mehta and Tripathy, 2014; Ciruelos Gil, 2014).
[0244] ESRRG signaling has been correlated with reduced distant
metastasis-free survival in ER+ breast cancer treated with
tamoxifen (Madhavan et al., 2015). Recent work demonstrated that
ESRRG mediated the effects of estrogen on the proliferation of
endometrial cancer cells via the activation of AKT and ERK1/2
signaling pathways (Sun et al., 2014c). High levels of ESRRG
induced proliferation in ER+ breast cancer cells in the presence or
absence of estrogen. In contrast, silencing of ESRRG inhibited
hepatocellular carcinoma cell lines growth and induced cell
apoptosis (Ijichi et al., 2011; Yuan et al., 2015).
[0245] EXOC8 was shown to interact with the cancer-associated
Ras-like small GTPase RalA in the brain (Das et al., 2014). EXOC8
interaction with RalA was described as necessary for migration and
invasion of prostate cancer tumor cells (Hazelett and Yeaman,
2012). EXOC8 was shown to be involved in the tumor-promoting
function of dermal fibroblasts, which is executed by RalA. The RalA
signaling cascade in dermal fibroblasts involves EXOC8 and was
described as a potential anti-cancer target upon progression of
squamous cell carcinoma of the skin (Sowalsky et al., 2011). EXOC8
was described as a protein fostering oncogenic ras-mediated
tumorigenesis (Issaq et al., 2010).
[0246] EXOSC4 promotor activity is increased in hepatocellular
carcinoma, due to DNA hypomethylation. EXOSC4 effectively and
specifically inhibits cancer cell growth and cell invasive
capacities (Stefanska et al., 2014; Drazkowska et al., 2013).
[0247] EXOSC7 is associated with cervical cancer (Choi et al.,
2007).
[0248] In gastric tumor tissues, the expression of EYA1 is
significantly decreased compared with adjacent normal tissues.
Moreover, EYA1 was significantly over-expressed in Wilms tumors (Li
et al., 2002; Nikpour et al., 2014). It is reported that genetic
silencing of EYA1 significantly sensitizes breast cancer cells to
pharmacological inhibition of PI3K/Akt signaling. These findings
imply that they may function together to regulate cancer cell
behavior (Sun et al., 2015g).
[0249] EYA2 over-expression has been observed in several tumor
types, such as epithelial ovarian tumor, prostate, breast cancer,
urinary tract cancers, glioblastoma, lung adenocarcinoma, cervical
cancer, colon and hematopoietic cancers (Bierkens et al., 2013;
Zhang et al., 2005a; Guo et al., 2009; Patrick et al., 2013; Kohrt
et al., 2014). Studies have revealed that EYA2 influences
transcription of TGF beta pathway members as well as
phosphorylation of TGFBR2, implying a dual role of EYA2 in the
pancreas (Vincent et al., 2014).
[0250] EYA3 is highly expressed in Ewing sarcoma tumor samples and
cell lines compared with mesenchymal stem cells. On the other hand,
deletion of the EYA3 gene has been linked to certain pancreatic
ductal adenocarcinomas (Gutierrez et al., 2011; Robin et al.,
2012). Recent work has shown that over-expression of EYA3 results
in increased proliferation, migration, invasion and transformation
of breast cancer cells (Pandey et al., 2010).
[0251] It has been reported that EYA4 is frequently and
concomitantly deleted, hyper-methylated and under-expressed in
non-small-cell lung cancer subtypes as well as in the earliest
stages of lung cancer and in adenocarcinoma in situ, colorectal
cancer and hepatocellular carcinoma (Selamat et al., 2011; Wilson
et al., 2014; Hou et al., 2014; Kim et al., 2015c). In colorectal
cancer, EYA4 is a tumor suppressor gene that acts by inducing
up-regulation of DKK1 and inhibiting the Wnt signaling pathway (Kim
et al., 2015c).
[0252] Expression analyses have shown FABP7 transcripts in tumors
or urine of patients with renal cell carcinoma, as well as in
tissues of glioblastoma and melanoma (Liang et al., 2005; Seliger
et al., 2005; Goto et al., 2010; Takaoka et al., 2011). In
addition, FABP7 over-expression in glioblastoma and melanoma
correlates with shorter survival (Liang et al., 2006; Slipicevic et
al., 2008). In glioma cell lines, NFI de-phosphorylation is
correlated with FABP7 expression (Bisgrove et al., 2000).
[0253] FADS2 is up-regulated in hepatocellular carcinoma (Muir et
al., 2013). FADS2 activity is increased in breast cancer tissue
(Pender-Cudlip et al., 2013). FADS2 expression is associated with
aggressiveness of breast cancer (Lane et al., 2003). FADS2
inhibition impedes intestinal tumorigenesis (Hansen-Petrik et al.,
2002).
[0254] FAM135B is associated with esophageal squamous cell
carcinoma (Song et al., 2014b).
[0255] FAM86A was shown to interact with the tumor-associated
eukaryotic elongation factor 2 (Davydova et al., 2014).
[0256] Down-regulation or dysfunction of FANCD2 due to genetic
mutations has been reported in different cancer types including
breast cancer, acute lymphatic leukemia and testicular seminomas
and is associated with cancer development. Otherwise also
re-expression and up-regulation of FANCD2 was shown to be
associated with tumor progression and metastasis in gliomas and
colorectal cancer (Patil et al., 2014; Shen et al., 2015a; Shen et
al., 2015b; Ozawa et al., 2010; Rudland et al., 2010; Zhang et al.,
2010a; Smetsers et al., 2012). PI3K/mTOR/Akt pathway promotes
FANCD2 inducing the ATM/Chk2 checkpoint as DNA damage response and
mono-ubiquitinilated FANCD2 activates the transcription of the
tumor suppressor TAp63 (Shen et al., 2013; Park et al., 2013).
[0257] The expression level of FANCG mRNA in newly diagnosed acute
myeloid leukemia patients is significantly lower than that in
control and acute myeloid leukemia complete remission groups.
Moreover, germline mutations of FANCG might contribute to the
progression of pancreatic cancer. In contrast, mutations in FANCG
could not be detected in bladder carcinoma cell lines (Couch et
al., 2005; Neveling et al., 2007; Duan et al., 2013). Endogenous
disruption of FANCG in a human adenocarcinoma cell line resulted in
increased clastogenic damage, G2/M arrest and decreased
proliferation (Gallmeier et al., 2006).
[0258] Mutations in the FAT2 gene have been found in esophageal
squamous cell carcinoma as well as head and neck squamous cell
carcinoma. In addition, FAT2 mRNA was expressed in gastric cancer,
pancreatic cancer and ovarian cancer (Katoh and Katoh, 2006; Lin et
al., 2014; Gao et al., 2014).
[0259] FAT3 was shown to be down-regulated in taxol resistant
ovarian carcinoma cell lines upon silencing of androgen receptor,
resulting in increased sensitization to taxol in these cell lines.
Thus, FAT3 may be a candidate gene associated with taxol resistance
(Sun et al., 2015e). FAT3 was shown to be mutated in esophageal
squamous cell carcinoma, resulting in dysregulation of the Hippo
signaling pathway (Gao et al., 2014). FAT3 was shown to be mutated
recurrently in early T-cell precursor acute lymphoblastic leukemia
(Neumann et al., 2013). FAT3 was described as a gene with
signatures specific for meningothelial meningiomas, therefore being
associated with tumorigenesis in this subtype of benign meningiomas
(Fevre-Montange et al., 2009). FAT3 was described as a tumor
suppressor which is repressed upon lung cancer development from
dysplastic cells (Rohrbeck and Borlak, 2009).
[0260] FBXO4 was shown to be down-regulated in hepatocellular
carcinoma (Chu et al., 2014). FBXO4 is associated with esophageal
squamous cell carcinoma, melanoma, lymphomas and histiocytic
sarcomas (Vaites et al., 2011; Lee et al., 2013b; Lian et al.,
2015).
[0261] FBXO5 was shown to be up-regulated in breast cancer and
hepatocellular carcinoma (Zhao et al., 2013c; Liu et al., 2014h).
FBXO5 was shown to be down-regulated in primary gastric cancer
(Zhang et al., 2014e). FBXO5 is associated with invasion and
metastatic potential in breast cancer, tumor size, infiltration,
clinical grade and prognosis in gastric cancer, histologic grade in
breast cancer, histologic grade and poor overall survival in
ovarian clear cell carcinoma, stage and prognosis in hepatocellular
carcinoma and poor prognosis in esophageal squamous cell carcinoma
(Kogo et al., 2011; Zhao et al., 2013c; Min et al., 2013; Liu et
al., 2013d; Zhang et al., 2014e; Liu et al., 2014h). FBXO5 is
associated with breast cancer, ovarian cancer, hepatocellular
cancer, prostate cancer and mantle cell lymphoma (Johansson et al.,
2014; Schraders et al., 2008). FBXO5 is a prognostic predictor of
breast cancer and esophageal squamous cell carcinoma (Kogo et al.,
2011; Liu et al., 2014h).
[0262] FBXW8 was shown to be up-regulated in choriocarcinoma (Shi
et al., 2014a). FBXW8 is associated with pancreatic cancer and
choriocarcinoma (Wang et al., 2014b; Lin et al., 2011).
[0263] FGFR1OP is associated with chronic myelomonocytic leukemia,
acute myeloid leukemia and myeloproliferative neoplasms (Hu et al.,
2011; Bossi et al., 2014). FGFR1OP was shown to be up-regulated in
lung cancer (Mano et al., 2007). FGFR1OP expression is associated
with shorter tumor-specific survival times (Mano et al., 2007).
FGFR1OP is a prognostic biomarker for lung cancer (Mano et al.,
2007).
[0264] Over-expression of FIG. 4 was found in the triple negative
breast cancer compared to non-tumorigenic cells (Ikonomov et al.,
2013).
[0265] FLAD1 was shown to be associated with non-small cell lung
cancer (Mitra et al., 2011).
[0266] Depending on its subcellular localization, filamin A plays a
dual role in cancer: In the cytoplasm, filamin A functions in
various growth signaling pathways, in addition to being involved in
cell migration and adhesion pathways. Thus, its over-expression has
a tumor-promoting effect. In contrast to full-length filamin A, the
C-terminal fragment, which is released upon proteolysis of the
protein, localizes to the nucleus, where it interacts with
transcription factors and thereby suppresses tumor growth and
metastasis (Savoy and Ghosh, 2013).
[0267] Over-expression of FOXM1 has been found in a variety of
aggressive human carcinomas including lung cancer, glioblastomas,
prostate cancer, basal cell carcinomas, hepatocellular carcinoma,
primary breast cancer and pancreatic cancer (Teh et al., 2002;
Kalinichenko et al., 2004; Kalin et al., 2006; Kim et al., 2006;
Liu et al., 2006; Wang et al., 2007b). Recent study suggest that
the FOXM1 gene is up-regulated in pancreatic cancer due to
transcriptional regulation by the Sonic Hedgehog pathway (Katoh and
Katoh, 2004).
[0268] Several lines of evidence have implicated GAB2 in cancer,
for instance elevated levels of GAB2 were found in breast cancer,
ovarian cancer as well as some metastatic melanomas. Others have
revealed that GAB2 is required for BCR/ABL-mediated transformation
in chronic myeloid leukemia (Sattler et al., 2002; Daly et al.,
2002; Horst et al., 2009; Wang et al., 2012c). In ovarian cancer,
over-expression of GAB2 resulted in the activation of the
phosphatidylinositol 3-kinase pathway (Dunn et al., 2014).
[0269] GADD45GIP1 was shown to interact with leukemia-associated
Lck (Vahedi et al., 2015). GADD45GIP1 was shown to be
down-regulated in acute myeloid leukemia (Ran et al., 2014).
GADD45GIP1 was shown to have a tumor suppressor effect in the
cervical and ovarian cancer cell lines HeLa and SKOV3 (Nakayama et
al., 2007). GADD45GIP1 was shown to interact with the tumor
suppressor STAT3 in prostate cancer and with CDK2 as a
cyclin-dependent kinase inhibitor (Ran et al., 2014; Tan et al.,
2014). GADD45GIP1 was shown to be negatively regulated by NAC1,
which is considered to have adverse effects on prognosis in ovarian
and cervical carcinomas (Nishi et al., 2012). GADD45GIP1 was shown
to be associated with paclitaxel resistance in ovarian cancer
(Jinawath et al., 2009). GADD45GIP1 may play an important role in
the regulation of androgen receptor (AR)-positive growth of
prostate cancer through its function as an AR corepressor (Suh et
al., 2008). GADD45GIP1 was shown to be up-regulated in lymph node
(+) breast carcinomas (Abba et al., 2007).
[0270] The expression of GART is significantly up-regulated in
human glioma and hepatocellular carcinoma. Single nucleotide
polymorphisms in GART are significantly associated with
hepatocellular carcinoma risk in the Chinese population (Liu et
al., 2014g; Cong et al., 2014; Zhang et al., 2015e). In
hepatocellular carcinoma, over-expression of GART correlated
positively with the histologic grade, tumor size, number of
tumorous nodes and intrahepatic metastases (Cong et al., 2014).
GART is able to act as a regulator of tumor progression and
survival in renal cell carcinoma by targeting tumor associated
macrophages (Ohba et al., 2005).
[0271] GAS2L3 was shown to be down-regulated in the gastric cancer
cell line HSC45-M2 upon incubation in lethal doses of
(213)Bi-d9Mab. Thus, GAS2L3 might be a new target for selective
elimination of tumor cells (Seidl et al., 2010).
[0272] GBGT1 is associated with ovarian cancer and oral squamous
cell carcinoma (Viswanathan et al., 2003; Jacob et al., 2014).
[0273] GGT6 was shown to be amplified in a patient with choroid
plexus papilloma (de Leon et al., 2015).
[0274] Researchers have observed higher mRNA transcript levels of
GNB1 in breast cancer specimens compared to normal glandular
tissue. In endometrial cancer, the expression of GNB1 was
significantly changed in comparison to the control group (Orchel et
al., 2012; Wazir et al., 2013). Furthermore, the mRNA expression of
GNB1 increased with TNM stage, tumor grade and was linked with
adverse patient outcomes (Wazir et al., 2013).
[0275] GON4L is associated with hepatocellular carcinoma and
salivary gland cancer (Simons et al., 2013; Kim et al., 2009b).
[0276] The variable number of tandem repeats polymorphism of the
GP1BA gene has been associated with the risk of oral and breast
cancer. On the contrary, others did not detect any association
between the variable number of tandem repeats polymorphism of the
GP1BA gene and breast cancer aggressiveness (Oleksowicz et al.,
1998; Ayala et al., 2003; Vairaktaris et al., 2007). In breast
cancer, GP1BA expression correlated significantly with tumor stage,
tumor size and estrogen receptor negativity (Oleksowicz et al.,
1998).
[0277] GPD2 abundance and activity is significantly up-regulated in
prostate cancer cells and is associated with the high reactive
oxygen species (ROS) production in cancer cells (Chowdhury et al.,
2005; Chowdhury et al., 2007).
[0278] In breast cancer cell lines, knockdown of GPR64 resulted in
a strong reduction in cell adhesion as well as in cell migration
(Peeters et al., 2015).
[0279] GPX5 rs451774 was found to be associated with overall
survival in patients suffering from non-small cell lung cancer
receiving platinum plus gemcitabine treatment (Li et al.,
2011c).
[0280] GRAMD1A was shown to be expressed in cancer cell lines (Song
et al., 2014a).
[0281] GRHL2 was shown to be up-regulated in colorectal cancer and
oral squamous cell carcinoma (Quan et al., 2015b; Kang et al.,
2009). GRHL2 was shown to be down-regulated in cervical cancer and
diverse breast cancer subclasses (Cieply et al., 2012; Torres-Reyes
et al., 2014). GRHL2 was shown to be associated with poor prognosis
in colorectal cancer, lower disease-free survival in clear cell
renal cell carcinoma and poor relapse free survival in breast
cancer (Butz et al., 2014; Quan et al., 2015b; Xiang et al., 2012).
GRHL2 was shown to be associated with metastasis in breast cancer
and hepatocellular carcinoma (Tanaka et al., 2008b; Werner et al.,
2013). GRHL2 may be a prognostic biomarker for colorectal cancer,
clear cell renal cell carcinoma and hepatocellular carcinoma (Butz
et al., 2014; Quan et al., 2015b; Tanaka et al., 2008b).
[0282] GRIK3 is associated with lung adenocarcinoma (methylation,
functional modifications), pediatric central nervous system tumors,
lymphocytic leukemia, and neuroblastoma (Pradhan et al., 2013).
GRIK3 is differentially expressed in several pediatric tumors of
the central nervous system (Brocke et al., 2010).
[0283] Over-expression or somatic mutations of GRIN2D was found in
pediatric central nervous system tumors, human breast cancers as
well as prostate cancer cell lines. In addition, knockdown of
GRIN2D did not influence cancer phenotype in TE671 and RPMI8226
cancer cell lines (Brocke et al., 2010; Pissimissis et al., 2009;
Luksch et al., 2011; Jiao et al., 2012).
[0284] GSDMA was described as frequently silenced in gastric cancer
cell lines and to be associated with apoptosis (Lin et al., 2015a).
GSDMA was shown to be mutated in the 3'-UTR in different cancers,
resulting in the creation or disruption of putative microRNA target
sites, thus, potentially resulting in dysregulation of gene
expression (Ziebarth et al., 2012). Expression analysis of GSDMA in
esophageal and gastric cancer suggests that GSDMA is a tumor
suppressor (Saeki et al., 2009).
[0285] Breast cancer patients exhibited higher frequency of
homozygous deletion of the GSTM1 gene compared with the control
group. Genetic polymorphism of the GSTM1 gene has been also
associated with bladder cancer susceptibility in the Iranian
population, lung cancer risk in the Chinese population, prostate,
esophageal and cervical cancer in the Indian population (Mittal et
al., 2004; Singh et al., 2008; Safarinejad et al., 2013; Sharma et
al., 2013; Possuelo et al., 2013; Chen et al., 2014g).
[0286] Studies have shown frequent down-regulation and promoter DNA
hyper-methylation of GSTM5 in Barrett's adenocarcinoma compared to
normal samples. On the other hand, GSTM5 transcript was not
detected in acute lymphoblastic leukemia patients (Kearns et al.,
2003; Peng et al., 2009). Researchers have observed that
single-nucleotide polymorphisms in GSTM5 gene may affect overall
survival in stages I to II or low-stage non-small cell lung cancer
(Pankratz et al., 2011).
[0287] GSTT2 promoter polymorphisms and their haplotypes are
associated with colorectal cancer risk in the Korean population.
Others have reported that deletion in the GSTT2 gene may have a
protective effect on the initiation and development of esophageal
squamous cell carcinoma in the Mixed Ancestry South African
population. In addition, low frequency of DNA methylation of GSTT2
gene was found in Barrett's adenocarcinoma (Peng et al., 2009; Jang
et al., 2007; Matejcic et al., 2011).
[0288] GSTT2B was shown to be associated with esophageal squamous
cell carcinoma since a GSTT2B deletion had a potential protective
effect on the risk of esophageal squamous cell carcinoma in the
Mixed Ancestry South African population (Matejcic et al.,
2011).
[0289] Single nucleotide polymorphisms in the GTF2H4 gene were
reported to increase the risk to develop smoking-related lung
cancer and papilloma virus-induced cervical cancer (Buch et al.,
2012; Mydlikova et al., 2010; Wang et al., 2010).
[0290] Researchers have observed GTF2IRD1-ALK fusion in thyroid
cancer (Stransky et al., 2014).
[0291] Researchers have identified GTF3C2 as a novel ALK fusion in
a cohort of Spitz tumors (Yeh et al., 2015).
[0292] Several publications have reported down-regulation of H2AFY
in variety of human cancers including colorectal, lung, testicular,
bladder, cervical, breast, colon, ovarian and endometrial (Novikov
et al., 2011; Sporn and Jung, 2012). Additionally, knockdown of
H2AFY in melanoma cells resulted in significantly increased
proliferation and migration in vitro and growth and metastasis in
vivo (Kapoor et al., 2010). In bladder cancer, depletion of H2AFY
expression was significantly associated with elevated levels of
Lin28B expression (Park et al., 2016).
[0293] HAUS3 is associated with breast cancer (Shah et al.,
2009).
[0294] High level of HDGF expression has been linked with poor
prognosis in breast cancer and pancreatic ductal carcinoma (Uyama
et al., 2006; Chen et al., 2012b). Studies have revealed that HDGF
plays an important role in inducing cancer cell proliferation,
angiogenesis, invasion and migration in various malignancies such
as oral squamous cell carcinoma, gastric, colonic, lung and
esophageal cancers (Yamamoto et al., 2007; Mao et al., 2008; Liao
et al., 2010; Meng et al., 2010; Lin et al., 2012; Tao et al.,
2014a).
[0295] HEATR1 was shown to be up-regulated in glioblastoma (Wu et
al., 2014c).
[0296] HELQ was described to interact with the RAD51 paralog
complex BCDX2. Different components of this complex are associated
with increased risk of ovarian cancer and breast cancer,
respectively (Pelttari et al., 2015). HELQ was shown to be a
candidate ovarian cancer gene due to its association with RAD51
paralogs (Takata et al., 2013b). HELQ, as part of the polymerase
pathway, was shown to be associated with oral cavity/pharynx
cancers due to a missense mutation in the second exon (Babron et
al., 2014). HELQ was shown to play a role in DNA repair and tumor
suppression (Adelman et al., 2013). HELQ was shown to be associated
with esophageal squamous cell carcinoma using a genome-wide
association study in a Han Chinese population (Li et al.,
2013b).
[0297] HELZ2 was shown to be one biomarker in gene panel allowing
earlier diagnosis of epithelial ovarian cancer (Pils et al.,
2013).
[0298] The HERC2/OCA2 region on chromosome 15q13.1 is one of
several loci that predispose to cutaneous melanoma (Amos et al.,
2011; Xiao et al., 2014). HERC2 regulates the stability of
different DNA repair factors including CHK1, p53 and BRCA1
(Bekker-Jensen et al., 2010; Cubillos-Rojas et al., 2014; Zhu et
al., 2014a; Peng et al., 2015c).
[0299] HINT1 is transcriptionally silenced or down-regulated in
various cancers including hepatocellular carcinoma, some human
non-small cell lung cancer cell lines and gastric cancer. In
contrast, HINT1 is over-expressed in prostate cancer (Zhang et al.,
2009; Huang et al., 2011; Symes et al., 2013). It has been observed
that in a hepatoma cell line, HINT1 inhibits activity of
Wnt/beta-catenin signaling and gene transcription via TCF4 (Wang et
al., 2009b).
[0300] It has been demonstrated that variants in the HLA-DMB gene
could be associated with the risk of HIV-related Kaposi's sarcoma.
In addition, deregulation of HLA-DMB gene was noted in ERG-positive
and ETV1-positive prostate carcinomas (Paulo et al., 2012; Aissani
et al., 2014). Furthermore, elevated levels of HLA-DMB expression
in the tumor epithelium was correlated with improved survival in
advanced serous ovarian cancer (Callahan et al., 2008).
[0301] HLTF is a member of the SWI/SNF family of transcriptional
regulators with helicase and E3 ubiquitin ligase activity and was
found to be inactivated by hyper-methylation in colon, gastric,
uterine, bladder and lung tumors (Castro et al., 2010; Debauve et
al., 2008; Garcia-Baquero et al., 2014).
[0302] HMMR expression is up-regulated in different cancer entities
including breast, colon, gastric, pancreatic and prostate cancer
and correlates with cell motility, invasion and metastasis (Yamada
et al., 1999; Wang et al., 1998; Abetamann et al., 1996; Gust et
al., 2009; Ishigami et al., 2011; Sankaran et al., 2012). HMMR
interacts with BRCA1 leading to tumor progression by promoting
genomic instability. Furthermore, HMMR associates with Src, which
elevates cell motility and HMMR-CD44 partnering stimulates ERK
signaling resulting in tumor promotion. Additionally, HMMR is a
target of several tumor associated proteins including E2F1, p53 and
Ras (Blanco et al., 2015; Hall et al., 1995; Hall and Turley, 1995;
Maxwell et al., 2008; Sohr and Engeland, 2008; Meier et al.,
2014).
[0303] HSPA14 was shown to be up-regulated in hepatocellular
carcinoma (Yang et al., 2015c). HSPA14 is associated with non-small
cell lung cancer (Wu et al., 2011a).
[0304] HSPA8 was shown to be over-expressed in esophageal squamous
cell carcinoma and high expression levels of HSPA8 in esophageal
cancer cells in vitro counter-acted oxidative stress-induced
apoptosis of these cells. Furthermore, HSPA8 is over-expressed in
multiple myeloma and colonic carcinoma and BCR-ABL1-induced
expression of HSPA8 promotes cell survival in chronic myeloid
leukemia (Chatterjee et al., 2013; Dadkhah et al., 2013;
Jose-Eneriz et al., 2008; Kubota et al., 2010; Wang et al.,
2013b).
[0305] Over-expression of HUWE1 has been found in various types of
tumors such as lung carcinoma, breast carcinoma, prostate
carcinoma, glioblastoma and colon carcinoma. Another report has
revealed that HUWE1 is implicated in the pathogenesis of
hepatocellular carcinoma (Yoon et al., 2005; Adhikary et al., 2005;
Liu et al., 2012). In addition, depletion of HUWE1 prevented the
proliferation of a subset of human tumor cells while elevated
levels of HUWE1 correlated with detectable p53 (Adhikary et al.,
2005; Confalonieri et al., 2009).
[0306] IDO1 was found to be expressed in a variety of tumors, such
as colorectal cancer, melanoma, serous ovarian cancer and papillary
thyroid micro-carcinoma (Brandacher et al., 2006; Takao et al.,
2007; Brody et al., 2009; Ryu et al., 2014). Over-expression of
IDO1 in endometrial cancer tissues as well as in childhood acute
myeloid leukemia positively correlated with disease progression and
impaired patient survival (Ino et al., 2008; Folgiero et al.,
2014).
[0307] IFI16 protein was relatively low or was not detectable in
certain human prostate and breast cancer cell lines (Xin et al.,
2003; Alimirah et al., 2007). Researchers have noted that IFI16 is
expressed in the human-papillomavirus-positive head and neck
squamous cell carcinomas and correlates with a better prognosis
(Azzimonti et al., 2004). Furthermore, treatment of breast cancer
cell lines with 5-aza-dC resulted in up-regulation of IFI16
expression (Fujiuchi et al., 2004).
[0308] IFI30 expression was shown to be associated with diminished
cellular activation, including decrease of phosphorylated ERK1/2,
decreased cellular proliferation and cancer patient survival
(Rausch and Hastings, 2015). IFI30 was shown to be down-regulated
in primary and metastatic breast cancer (Xiang et al., 2014).
Reduced IFI30 expression in breast cancer was shown to be
associated with poorer disease-free survival while absence of IFI30
was positively correlated with adverse characteristics of breast
cancers such as tumor size and lymph node status (Xiang et al.,
2014). Thus, IFI30 may act as a potential tumor suppressor and
novel independent prognostic factor in breast cancer (Xiang et al.,
2014). Reduced IFI30 expression in diffuse large B-cell lymphoma
was shown to be associated with poor overall survival (Phipps-Yonas
et al., 2013). A single nucleotide polymorphism in IFI30 was shown
to be a significant predictor for disease progression in advanced
prostate cancer patients treated with androgen-deprivation therapy
(Bao et al., 2011). IFI30 was shown to be one of several genes
up-regulated in squamous cell carcinoma and basal cell carcinoma of
the skin (Wenzel et al., 2008). IFI30 was shown to be associated
with disparities in the profile of antigenic epitopes displayed by
melanomas and bystander antigen-presenting cells, and thus may
contribute to tumor cell survival in the face of immunological
defenses (Hague et al., 2002).
[0309] IFI44L was shown to be associated with CDKN2A, a gene
associated with cutaneous melanoma and non-melanoma skin cancer and
miR-9, which is associated with nasopharyngeal carcinoma (Gao et
al., 2013; Puig-Butille et al., 2014).
[0310] The IFIT1 gene is down-regulated in MCF7 breast cancer
cells. Others reported that the IFIT1 gene was inactivated in
hypopharynx cancer (Xu et al., 2013a; Motaghed et al., 2014).
Furthermore, miR-9 can modulate the expression of IFIT1 gene in
human cancer cells (Gao et al., 2013).
[0311] IFT172 is associated with chemoresistance in gastric cancer
(Huang et al., 2014a).
[0312] IGHG1 was over-expressed in human pancreatic cancer tissues
compared to adjacent non-cancerous tissues. On the contrary, the
IGHG1 protein was down-regulated in infiltrating ductal carcinomas
tissues (Kabbage et al., 2008; Li et al., 2011b). siRNA targeted
silencing of IGHG1 was able to inhibit cell viability and promote
apoptosis (Pan et al., 2013).
[0313] Researchers have observed expression of IGHG3 in Saudi
females affected by breast cancer. Similarly, gains in copy number
as well as elevated levels of IGHG3 were detected in African
American men suffering from prostate cancer. Another report showed
that IGHG3 expression is found in squamous non-small cell lung
cancers, malignant mesothelioma as well as on tumor cells that are
sporadically seen in MALT lymphomas and that show a propensity for
differentiation into plasma cells (Remmelink et al., 2005; Bin Amer
et al., 2008; Ledet et al., 2013; Zhang et al., 2013c; Sugimoto et
al., 2014).
[0314] Recent work has detected rearrangements involving IGHG4 in
primary testicular diffuse large B cell lymphoma (Twa et al.,
2015).
[0315] Studies have observed down-regulation of IGHM in Chinese
patients affected by rhabdomyosarcoma. Others have detected
expression of IGHM in diffuse large B-cell lymphoma. Another group
has found that in diffuse large B-cell lymphoma the IGHM gene is
conserved only on the productive IGH allele in most IgM+ tumors. In
addition, epithelioid angiomyolipoma samples did not show any
reactivity for transcription factor binding to IGHM enhancer 3 or
transcription factor EB (Kato et al., 2009; Blenk et al., 2007;
Ruminy et al., 2011; Liu et al., 2014a).
[0316] IMPDH2 over-expression was found in osteosarcoma and human
prostate cancer tissues as well as in leukemic cells (Nagai et al.,
1991; Zhou et al., 2014b). Inhibitors of IMPDH2 such as tiazofurin
and benzamide riboside exhibited a good clinical response in
patients with acute myeloid leukemia and chronic myeloid leukemia
in blast crisis (Wright et al., 1996; Jayaram et al., 1999).
[0317] INADL is down-regulated in non-small cell lung cancer in
response to cisplatin-gemcitabine combination chemotherapy (Ma et
al., 2015).
[0318] Over-expression of INPPL1 has been observed in breast
cancer, non-small cell lung cancer, hepatocellular carcinoma and
laryngeal squamous cell carcinoma (Prasad et al., 2008b; Zhou et
al., 2011; Fu et al., 2013b; Fu et al., 2013c). It has been
reported that INPPL1 silencing in breast cancer cells reduces cell
proliferation in vitro and cancer growth in vivo and inhibits tumor
metastases (Prasad et al., 2008a).
[0319] The expression of IPP was elevated in human breast tumor
samples compared to non-cancer tissues (Govindaraj et al.,
2012).
[0320] Several lines of evidence have shown that IQGAP1 is
over-expressed in various tumor types, including colorectal
carcinoma, gastric cancer, hepatocellular carcinoma, pancreatic
cancer, ovarian cancer and esophageal squamous cell carcinoma
(Takemoto et al., 2001; Dong et al., 2006; Hayashi et al., 2010;
White et al., 2010; Wang et al., 2013i; Wang et al., 2014i). In
addition, high levels of IQGAP1 were correlated with poor prognosis
in ovarian carcinomas and colorectal carcinoma (Dong et al., 2006;
Hayashi et al., 2010).
[0321] A recent study suggested a genetic association of IRAK2
rs35060588 with colorectal cancer survival. On the other hand, no
mutations were found in IRAK2 in patients suffering from chronic
lymphocytic leukemia (Martinez-Trillos et al., 2014; Wang et al.,
2014c). Researchers have observed that over-expression of IRAK2
correlated with decreased disease-free survival of patients with
non-adenocarcinoma (Seol et al., 2014).
[0322] IL6 up-regulates IRF9 in prostate cancer cell lines both at
the mRNA and protein levels (Erb et al., 2013). Another study has
shown that that up-regulated IRF9 confers resistance to the
anti-microtubule agent paclitaxel in drug-resistant breast cancer
cells (Luker et al., 2001).
[0323] Many studies have reported over-expression of ISG15 in
several tumors, such as bladder cancer, breast cancer, oral
squamous cell carcinoma, cervical cancer and prostate cancer
(Andersen et al., 2006; Chi et al., 2009; Kiessling et al., 2009;
Rajkumar et al., 2011; Wood et al., 2012; Vincent-Chong et al.,
2012). In breast cancer, high ISG15 expression was associated with
an unfavorable prognosis (Wood et al., 2012).
[0324] ISYNA1 is associated with chemotherapy response in cutaneous
malignant melanoma (Azimi et al., 2014). ISYNA1 was shown to be
up-regulated in the human liver carcinoma cell line HepG2 under
various conditions (Guan et al., 2003). ISYNA1 inhibition is
associated with decreased proliferation in the SK-N-SH
neuroblastoma cell line (Ye and Greenberg, 2015).
[0325] ITGB2 gene polymorphisms have been associated with
colorectal neoplasia and sporadic infiltrative duct breast
carcinoma. Moreover, over-expression of ITGB2 was observed in
peripheral blood neutrophils in patients with advanced epithelial
ovarian cancer as well as in leukemia. On the contrary, ITGB2 was
absent or only dimly expressed in promyelocytic leukemia
(Phongpradist et al., 2010; Fu et al., 2011; Zhou et al., 2012b;
Chang et al., 2013; Bednarska et al., 2016). cIBR-coupled PLGA
nanoparticles targeting ITGB2 hold promise as a selective drug
delivery system for leukemia treatment (Chittasupho et al.,
2010).
[0326] ITGB4 is associated with prostate cancer, gastric cancer,
breast cancer, oral squamous cell carcinoma and ovarian cancer and
was shown to be up-regulated in pancreatic ductal adenocarcinoma
(Chen et al., 2014e; Xin et al., 2014; Zubor et al., 2015; Masugi
et al., 2015; Gao et al., 2015; Kawakami et al., 2015). ITGB4 (also
called CD104) tends to associate with the alpha 6 subunit and is
likely to play a pivotal role in the biology of several invasive
carcinomas such as esophageal squamous cell carcinoma, bladder and
ovarian carcinoma (Kwon et al., 2013; Pereira et al., 2014; Chen et
al., 2014e). A single nucleotide polymorphism in ITGB4 seems to
influence tumor aggressiveness and survival and may have prognostic
value for breast cancer patients (Brendle et al., 2008).
[0327] Over-expression of ITGB8 has been observed in several
cancers including hepatocellular carcinoma, head and neck cancer,
some ovarian cancer and melanoma cell lines as well as primary
non-small lung cancer samples and brain metastases from several
epithelial cancers (Liu et al., 2002b; Goodman et al., 2012;
Vogetseder et al., 2013). Furthermore, silencing of ITGB8 caused
Snail and NF-I.degree.B transcriptional activation and MEK and Akt
phosphorylation level changes in lung cancer cell lines (Xu and Wu,
2012). Knockdown of ITGB8 in PC-3 and 22Rv1 prostate cancer cells
in vitro resulted in significant reduction of cell migration and
invasion (Mertens-Walker et al., 2015). Researchers have found that
over-expression of ITGB8 could be an inducer of gefitinib
resistance of hepatic cancer. ITGB8 might interact with TGF-beta
pathway to achieve its anti-gefitinib effects (Wang et al.,
2015f).
[0328] It has been reported that the expression of ITPR1 is altered
in tamoxifen resistance breast cancer cell lines (Elias et al.,
2015). Researchers have postulated a role for the HIF2alpha/ITPR1
axis in regulating clear cell renal cell carcinomas cell survival.
In addition, ITPR1 was significantly correlated with overall
survival in breast cancer (Messai et al., 2014; Gu et al.,
2016).
[0329] Single nucleotide polymorphism in the ITPR2 gene was
correlated with risk of renal cell carcinoma in a Chinese
population. Likewise, two common variants in linkage
disequilibrium, rs718314 and rs1049380 in the ITPR2 gene were
identified as novel susceptibility loci for renal cell carcinoma.
Moreover, over-expression of ITPR2 was observed in normal acute
myeloid leukemia patients compared to healthy persons (Wu et al.,
2012d; Shi et al., 2015; Zhang et al., 2016a). In normal acute
myeloid leukemia, elevated levels of ITPR2 expression were
associated with shorter overall survival and event-free survival
(Shi et al., 2015).
[0330] Studies have detected expression of JUP in colorectal cancer
and lung adenocarcinoma, while a high ITGB4/JUP ratio was found in
oral squamous cell carcinoma (Wang and Zheng, 2014; Yang et al.,
2012a; Schuetz et al., 2012; Sheng and Zhu, 2014; Nagata et al.,
2013).
[0331] Over-expression of KARS was found in gastric carcinoma as
well as tumor-associated inflammatory cells. Moreover, mutations in
the KARS gene were identified in patients suffering from colorectal
cancer. Others have observed that whole-arm loss of chromosome 16q
in breast cancer was related with decreased expression of KARS (Yen
et al., 2009; Hungermann et al., 2011; Kim et al., 2014a). It is
reported that KARS is involved in cell-cell and cell-ECM adhesion
during KARS-mediated metastasis (Nam et al., 2015).
[0332] KCNK15 gene hyper-methylation was found in several cell
lines, including colon cancer, leukemia, and bladder cancer (Shu et
al., 2006).
[0333] KDELR1 has a role in tumorigenesis (Yi et al., 2009).
Decreased KDELR1 levels are found in hepatoma cells (Hou et al.,
2015). Down-regulation of KDELR1 is seen in acute myeloid leukemia
(Caldarelli et al., 2013).
[0334] Over-expression of KDM1A promotes tumor cell proliferation,
migration and invasion and was associated with poor prognosis in
NSCLC and HCC (Lv et al., 2012; Zhao et al., 2013d). Elevated
expression of KDM1A correlates with prostate cancer recurrence and
with increased VEGF-A expression (Kashyap et al., 2013). Inhibition
of KDM1A with a combination of trichostatin A (TSA) and
5-aza-2'-deoxycytidine (decitabine) suppresses the tumorigenicity
of the ovarian cancer ascites cell line SKOV3 (Meng et al.,
2013).
[0335] KDM1B was shown to inhibit cell growth in the lung cancer
cell line A549 due to its E3 ubiquitin ligase activity (Yang et
al., 2015b). KDM1B was shown to be involved in the regulation of
the presumed tumor suppressor tissue factor pathway inhibitor-2
(Mino et al., 2014). KDM1B was shown to be up-regulated in breast
cancer and amplified and up-regulated in high grade urothelial
carcinomas (Heidenblad et al., 2008; Katz et al., 2014). KDM1B was
shown to play a role in DNA methylation and gene silencing in
breast cancer. Inhibition of both KDM1B and DNA methyltransferase
was described as a novel approach for epigenetic therapy of breast
cancer (Katz et al., 2014). KDM1B was shown to be associated with
the acquisition of cancer stem cell properties, including
self-renewal, clonal formation, and chemotherapy resistance in
hyaluronan-CD44v3 activated head and neck cancer (Bourguignon et
al., 2012).
[0336] Over-expression of KIAA0196 was observed in clinical
prostate carcinomas and was also amplified in 30-40% of xenografts
and hormone-refractory tumors (Porkka et al., 2004). Amplification
of KIAA0196 gene was correlated with worse prognosis in high-grade
estrogen receptor-negative breast cancer (Chin et al., 2007). In
prostate cancer, KIAA0196 did not seem to have any significant role
in growth, anchorage-independent growth or invasion in vitro
(Jalava et al., 2009).
[0337] KIAA1324 is over-expressed in different cancer types
including breast, lung, pancreatic and ovarian cancer (Schlumbrecht
et al., 2011; Estrella et al., 2014; Bauer et al., 2004). KIAA1324
shows a tumor suppressor behavior in gastric cancer where KIAA1324
is down-regulated and this is associated with poor prognosis (Kang
et al., 2015b).
[0338] Inhibition of KIF11 was shown to stop growth of the more
treatment-resistant glioblastoma tumor-initiating cells (TICs) as
well as non-TICs and impeded tumor initiation and self-renewal of
the TIC population (Venere et al., 2015). Targeting KIF11 was also
shown to reduce glioma cell invasion and to prolong survival of
mice bearing ortho-topic glioblastoma (Venere et al., 2015). Thus,
KIF11 plays a role as a driver of invasion, proliferation, and
self-renewal in glioblastoma (Venere et al., 2015). Higher
expression of mitosis-associated genes such as KIF11 was shown to
be associated with complete response of hepatocellular carcinomas
to trans-arterial chemoembolization treatment (Gaba et al., 2015).
Interfering with KIF11 function was described to cause potent
inhibition of tumor angiogenesis in experimental tumor models
(Exertier et al., 2013). KIF11 was shown to be down-regulated in
bone marrow samples from patients with multiple myeloma and acute
myeloid leukemia (Cohen et al., 2014). Nuclear KIF11 expression was
described as a potential predictive biomarker for docetaxel
response in metastatic castrate-resistant aggressive prostate
cancer and as a prognostic biomarker for prostate cancer
aggressiveness (Wissing et al., 2014). KIF11 was shown to be
essential for tumor cell survival in non-small cell lung cancer and
head and neck squamous cell carcinoma and thus may be a potential
anti-cancer target (Martens-de Kemp et al., 2013). Up-regulation of
KIF11 was shown to be associated with ependymoma recurrence in
children (Peyre et al., 2010).
[0339] In breast cancer, KIF15 was shown to be over-expressed and
to be immunogenic, as anti-KIF15 antibodies could be isolated from
breast cancer patients (Scanlan et al., 2001). Furthermore, KIF15
appears to be implicated in lung adenocarcinoma (Bidkhori et al.,
2013).
[0340] Methylation of KIF1A is known to be frequent and higher
levels were shown in thyroid cancer, breast cancer, head and neck
squamous cell carcinoma (Aviles et al., 1991; Hoque et al., 2008;
Demokan et al., 2010; Guerrero-Preston et al., 2014). Moreover,
KIF1A was found in plasma and saliva of lung cancer and head and
neck squamous cell carcinoma patients compared to controls. These
findings suggest that it could be used as a biomarker for early
detection in these disorders (Ostrow et al., 2010). In breast
cancer, over-expression of KIF1A was found to correlate with
chemotherapy resistance in cell lines (De et al., 2009).
[0341] Over-expression of KIF20A was detected in pancreatic ductal
adenocarcinoma, melanoma, bladder cancer, non-small cell lung
cancer and cholangiocellular carcinoma (Imai et al., 2011;
Yamashita et al., 2012; Stangel et al., 2015). Recently, it was
reported that patients with pancreatic ductal adenocarcinoma
vaccinated with a KIF20A-derived peptide exhibited better prognosis
compared to the control group (Asahara et al., 2013). In addition,
silencing of KIF20A resulted in an inhibition of proliferation,
motility, and invasion of pancreatic cancer cell lines (Stangel et
al., 2015).
[0342] Fusions of the KIF5B gene and the ret proto-oncogene (RET)
have been observed in patients suffering from lung cancers,
adenocarcinoma and non-small cell lung cancer (Kohno et al., 2012;
Cai et al., 2013b; Qian et al., 2014). KIF5B-RET expression in
Ba/F3 cells resulted in oncogenic transformation as determined by
interleukin-3 (IL-3)-independent growth (Lipson et al., 2012).
[0343] KIFC1 plays a crucial role by the cell division of meiotic
cells by focusing acentrisomal microtubule organizing centers into
two spindle poles. In cancer cells, KIFC1 was shown to be essential
for proper spindle assembly, stable pole-focusing and survival of
cancer cells independently from number of formed centrosomes
(normal or supernumerary centrisomes). A constitutive activation of
the DNA damage response in cancer was shown partially to mediate
acentrisomal spindle formation. The dependency of acentrisomal
spindle formation from KIFC1 makes KIFC1 to the attractive target
for cancer therapy. A number of potential KIFC1 inhibitors are
under current investigation (Li et al., 2015e; Kleylein-Sohn et
al., 2012; Wu et al., 2013a; Watts et al., 2013; Zhang et al.,
2016b). Furthermore, KIFC1 shows centrosome clustering-independent
pro-proliferative effects which is based on the protection of
survivin from proteasome-mediated degradation (Pannu et al., 2015).
KIFC1 expression was shown to be up-regulated in breast cancer,
particularly in estrogen receptor negative, progesterone receptor
negative and triple negative breast cancer, and 8 human breast
cancer cell lines. In estrogen receptor-positive breast cancer
cells, KIFC1 was one of 19 other kinesins whose expression was
strongly induced by estrogen. In breast cancer, the overexpression
of KIFC1 and its nuclear accumulation was shown to correlate with
histological grade and predict poor progression-free and overall
survival. In breast cancer cell lines, the overexpression of KIFC1
was shown to mediate the resistance to docetaxel. The KIFC1
silencing negatively affected the breast cancer cell viability (Zou
et al., 2014a; Pannu et al., 2015; De et al., 2009; Li et al.,
2015e). KIFC1 was shown to be overexpressed in ovarian cancer which
was associated with tumor aggressiveness, advanced tumor grade and
stage. Thus, KIFC1 may serve as a potential biomarker that predicts
worse prognosis, poor overall survival and onset of metastatic
dissemination (Pawar et al., 2014). KIFC1 was identified as one of
three genes, whose higher expression in primary NSCLC tumors
indicated the higher risk for development of brain metastasis
(Grinberg-Rashi et al., 2009).
[0344] KLHL14 is associated with primary central nervous system
lymphoma (Vater et al., 2015).
[0345] KLHL15 was shown to interact as an E3 ubiquitin ligase
adaptor with the protein phosphatase 2A, a tumor suppressor that
was shown to be genetically altered or functionally inactivated in
many solid cancers (Oberg et al., 2012; Perrotti and Neviani,
2013).
[0346] KLHL7 was shown to be up-regulated in thyroid tumors
(Jacques et al., 2005). KLHL7 is associated with lymphocyte-rich
classical Hodgkin's lymphoma, follicular lymphoma and diffuse large
B-cell lymphoma (Weigert et al., 2012; Trifonov et al., 2013;
Nam-Cha et al., 2009).
[0347] Several publications have detected over-expression of KLK7
mRNA and protein in early-stage ovarian tumors, colon cancer,
cervical cancer and breast cancer. Others have observed low levels
of KLK7 expression in prostate cancer (Talieri et al., 2004; Walker
et al., 2014; Li et al., 2014e; Zhang et al., 2015c; Tamir et al.,
2014). In addition, KLK7 expression was correlated with poor
outcome of patients suffering from unresectable pancreatic ductal
adenocarcinomas and breast cancer (Talieri et al., 2004; Iakovlev
et al., 2012). It seems that KLK7 induces cancer cell migration,
invasiveness and induces epithelial-mesenchymal transition-like
changes in prostate tumor cells (Mo et al., 2010).
[0348] KRT14 is highly expressed in various squamous cell
carcinomas such as esophageal, lung, larynx, uterine cervical as
well as in adenomatoid odontogenic tumor. However, it was absent in
small cell carcinoma of the urinary bladder and weak in lung
adenocarcinoma, gastric adenocarcinoma, colorectal adenocarcinoma,
hepatocellular carcinoma, pancreatic ductal adenocarcinoma, breast
infiltrating ductal adenocarcinoma, thyroid papillary carcinoma and
uterine endometrioid adenocarcinoma (Xue et al., 2010; Terada,
2012; Vasca et al., 2014; Hammam et al., 2014; Shruthi et al.,
2014). In bladder cancer, KRT14 expression was strongly associated
with poor survival (Volkmer et al., 2012).
[0349] Over-expression of KRT16 was found in basal-like breast
cancer cell lines as well as in carcinoma in situ. Others did not
find significant difference in immunohistochemical expression of
KRT16 between non-recurrent ameloblastomas and recurrent
ameloblastomas (Joosse et al., 2012; Ida-Yonemochi et al., 2012;
Safadi et al., 2016). In addition, in silico analyses showed
correlation between KRT16 expression and shorter relapse-free
survival in metastatic breast cancer (Joosse et al., 2012).
[0350] Over-expression of KRT17 was found in various cancers such
as carcinoma in situ, squamous cell carcinoma, Ewing sarcoma and
epithelial ovarian cancer (Mikami et al., 2011; Wang et al., 2013j;
Sankar et al., 2013). Furthermore, high levels of KRT17 expression
were significantly associated with poor survival of squamous cell
carcinoma, epithelial ovarian cancer, breast cancer and pancreatic
cancer (van de Rijn et al., 2002; Sarbia et al., 2007; Wang et al.,
2013j; Escobar-Hoyos et al., 2014). Researchers have demonstrated
that KRT17 expression promotes squamous cell carcinoma cell growth
and cell size but does not affect cell migration (Mikami et al.,
2015).
[0351] L3MBTL4 was shown to be targeted by deletion, breakage and
mutations in breast cancer. It was also shown to be down-regulated
in breast cancer and thus may be a potential tumor suppressor gene
(Addou-Klouche et al., 2010). L3MBTL4 resides in a chromosome
region that was shown to be frequently deleted in a rare subtype
with poor prognosis of acute myeloid leukemia (Veigaard et al.,
2011).
[0352] Studies have shown that the level of LAMA5 was elevated in
basal cell carcinoma, cervical cancer and breast carcinoma
(Simonova et al., 2015; Scotto et al., 2008; Mostafa et al., 2010;
Georgiou et al., 2013).
[0353] LAT2 expression is able to separate T lineage leukemias into
two subgroups, while others have reported that LAT2 acts as a tumor
suppressor able to enhance the proximal signaling of leukemic
blasts (Svojgr et al., 2009; Svojgr et al., 2012). In addition,
loss of LAT2 suppressed AKT activation, decreased cell
proliferation and increased cell sensitivity to drugs such as ODPC,
perifosine and arsenic trioxide (Thome et al., 2012).
[0354] The C/C(-13910) genotype of the LCT gene is significantly
associated with increased risk of colorectal cancer in the Finnish
population but not in the British or Spanish subjects (Fairfield et
al., 2004; Rasinpera et al., 2005; Travis et al., 2013). A
decreased survival rate was observed in patients suffering from
colorectal cancer with LCT C/C(-13910) genotype (Bacsi et al.,
2008).
[0355] Several studies have observed high levels or ineffectively
regulated LDLR expression in various types of cancer, for instance
over-expression of LDLR was reported in lung adenocarcinoma cell
line, prostate cancer cells as well as human colorectal cancer
biopsies. In contrast, decreased feedback regulation of LDLR has
been reported in leukemic cells from acute myelogenous patients
(Gueddari et al., 1993; Tatidis et al., 1997; Lum et al., 1999;
Chen and Hughes-Fulford, 2001).
[0356] Studies have detected up-regulation of mRNA and protein
level of LGALS3BP in colorectal carcinoma tissues as well as in
lung cancer (Ozaki et al., 2004; lacovazzi et al., 2010; Wu et al.,
2008). Elevated levels of LGALS3BP were correlated with poor
prognosis in diffuse large B-cell lymphomas (Kim et al., 2008d).
Moreover, in lung cancer LGALS3BP is involved in cancer metastasis
by increasing adhesiveness of cancer cells (Ozaki et al.,
2004).
[0357] LGR6 is associated with triple-negative breast cancer,
gastric cancer and colon cancer (Gong et al., 2012; Rocken, 2013;
Purrington et al., 2014). LGR6 was shown to be up-regulated in
gastric cancer (Steffen et al., 2012). LGR6 is associated with
local tumor growth and patient survival in gastric cancer (Steffen
et al., 2012).
[0358] LLGL1 expression is reduced or absent in breast cancers,
lung cancers, prostate cancers, ovarian cancers, colorectal
cancers, melanomas, endometrial cancers and hepatocellular
carcinomas (Schimanski et al., 2005; Kuphal et al., 2006; Tsuruga
et al., 2007; Lu et al., 2009; Song et al., 2013b). It seems that
LLGL1 inhibits proliferation and promotes apoptosis in the
esophageal carcinoma cell line through a mitochondria-related
pathway. Furthermore, reduced LLGL1 transcription has been linked
with lymph node metastases, whereas over-expression of LLGL1
resulted in increased cell adhesion and decreased cell migration
(Schimanski et al., 2005; Kuphal et al., 2006; Tsuruga et al.,
2007; Song et al., 2013b).
[0359] Expression of LMNB1 is reduced in colon cancer and gastric
cancer, whereas it is over-expressed in prostate cancer,
hepatocellular carcinoma and pancreatic cancer (Moss et al., 1999;
Lim et al., 2002; Coradeghini et al., 2006; Li et al., 2013a). In
hepatocellular carcinoma, the expression level of LMNB1 correlated
positively with tumor stage, tumor sizes and number of nodules.
These findings suggest that LMNB1 could be used to detect early
stages of hepatocellular carcinoma (Sun et al., 2010).
[0360] The cancer/testis antigen family 45 was shown to be
frequently expressed in both cancer cell lines and lung cancer
specimens (Chen et al., 2005). CT45 genes were shown to be
potential prognostic biomarkers and therapeutic targets in
epithelial ovarian cancer (Zhang et al., 20151).
[0361] LPCAT2 is associated with prostate cancer (Williams et al.,
2014). LPCAT2 was shown to be up-regulated in breast cancer,
cervical cancer and colorectal cancer (Agarwal and Garg, 2010).
LPCAT2 expression is associated with patient outcome in prostate
cancer (Williams et al., 2014).
[0362] Inhibition of LRBA expression by RNA interference, or by a
dominant-negative mutant, resulted in the growth inhibition of
cancer cells. These findings imply that deregulated expression of
LRBA contributes to the altered growth properties of a cancer cell
(Wang et al., 2004).
[0363] LTBP2 has been shown to be up-regulated in hepatocellular
carcinoma, pancreatic ductal adenocarcinoma, whereas in esophageal
squamous cell carcinoma cell lines and tumor tissues the expression
of LTBP2 was down-regulated (Chan et al., 2011; Turtoi et al.,
2011; Cho et al., 2016). In hepatocellular carcinoma, high levels
of LTBP2 were significantly correlated with shorter time to tumor
recurrence. Similarly, elevated levels of LTBP2 were associated
with poor outcome for ER(-)/PR(-) breast cancer patients (Naba et
al., 2014; Cho et al., 2016).
[0364] LTN1, also known as ZNF294, encodes the listerin E3
ubiquitin protein ligase 1 and is located on chromosome 21q22.11
(RefSeq, 2002). LTN1 is associated with high level microsatellite
instability in colorectal cancer (Reuschenbach et al., 2010).
[0365] LURAP1 was shown to be a NF-kB activator which may be a
candidate gene for regulating the function of dendritic cells to
resist tumor-associated factor-mediated dysfunction (Jing et al.,
2010).
[0366] It has been reported that the LYST gene is localized within
the copy number aberration regions in multiple myeloma (Ivyna Bong
et al., 2014).
[0367] Researchers have reported expression of M6PR in colon
carcinoma cell lines as well as in choriocarcinoma cells (Braulke
et al., 1992; O'Gorman et al., 2002). In breast cancer, low-level
expression of M6PR was associated with poor patient prognosis
(Esseghir et al., 2006). Furthermore, over-expression of M6PR
resulted in a decreased cellular growth rate in vitro and decreased
tumor growth in nude mice (O'Gorman et al., 2002).
[0368] MACF1 is associated with colorectal cancer, renal cell
carcinoma and lung adenocarcinoma (Bidkhori et al., 2013; Arai et
al., 2014; Kim et al., 2015b). MACF1 was shown to be associated
with neuroblastoma in the CLB-Bar cell line (Schleiermacher et al.,
2005).
[0369] Over-expression of MADD has been found in many types of
human tumors, including non-small cell lung cancer, lung
adenocarcinoma, squamous cell carcinoma, thyroid cancer, breast
cancer and ovarian cancer (Subramanian et al., 2009; Li et al.,
2011a; Wei et al., 2012; Bi et al., 2013; Turner et al., 2013).
Researchers have demonstrated that elevated levels of MADD in the
A549 cells inhibited apoptosis and increased survival, while
knock-down of MADD promoted apoptosis and reduced cell
proliferation (Wei et al., 2012; Bi et al., 2013). Additionally,
MADD function is regulated by PTEN-PI3K-Akt signaling pathway
(Jayarama et al., 2014).
[0370] MAGEA4 was described as a cancer testis antigen which was
found to be expressed in a small fraction of classic seminomas but
not in non-seminomatous testicular germ cell tumors, in breast
carcinoma, Epstein-Barr Virus-negative cases of Hodgkin's lymphoma,
esophageal carcinoma, lung carcinoma, bladder carcinoma, head and
neck carcinoma, and colorectal cancer, oral squamous cell
carcinoma, and hepatocellular carcinoma (Ries et al., 2005; Bode et
al., 2014; Li et al., 2005; Ottaviani et al., 2006; Hennard et al.,
2006; Chen et al., 2003). MAGEA4 was shown to be frequently
expressed in primary mucosal melanomas of the head and neck and
thus may be a potential target for cancer testis antigen-based
immunotherapy (Prasad et al., 2004). MAGEA4 was shown to be
preferentially expressed in cancer stem-like cells derived from
LHK2 lung adenocarcinoma cells, SW480 colon adenocarcinoma cells
and MCF7 breast adenocarcinoma cells (Yamada et al., 2013).
Over-expression of MAGEA4 in spontaneously transformed normal oral
keratinocytes was shown to promote growth by preventing cell cycle
arrest and by inhibiting apoptosis mediated by the p53
transcriptional targets BAX and CDKN1A (Bhan et al., 2012). MAGEA4
was shown to be more frequently expressed in hepatitis C
virus-infected patients with cirrhosis and late-stage
hepatocellular carcinoma compared to patients with early stage
hepatocellular carcinoma, thus making the detection of MAGEA4
transcripts potentially helpful to predict prognosis (Hussein et
al., 2012). MAGEA4 was shown to be one of several cancer/testis
antigens that are expressed in lung cancer and which may function
as potential candidates in lung cancer patients for polyvalent
immunotherapy (Kim et al., 2012b). MAGEA4 was described as being
up-regulated in esophageal carcinoma and hepatocellular carcinoma
(Zhao et al., 2002; Wu et al., 2011c). A MAGEA4-derived native
peptide analogue called p286-1Y2L9L was described as a novel
candidate epitope suitable to develop peptide vaccines against
esophageal cancer (Wu et al., 2011c). Several members of the MAGE
gene family, including MAGEA4, were shown to be frequently mutated
in melanoma (Caballero et al., 2010).
[0371] The expression of MAGEA8 was detected in various tumors such
as hepatocellular carcinoma, colorectal carcinoma and ovarian
cancer (Hasegawa et al., 1998; Tahara et al., 1999; Eng et al.,
2015). Furthermore, over-expression of MAGEA8 was associated with
poor progression free survival in patients with high CD3 tumors
(Eng et al., 2015).
[0372] MAGEC3 was described as being expressed only in testis and
in tumors of different histological origins. Thus, MAGEC3 could be
a target for cancer immunotherapy (Lucas et al., 2000).
[0373] Flavopiridol induces an inhibition of human tumor cell
proliferation and the down-regulation of MAGEF1 in different human
tumor cell lines (Lu et al., 2004). MAGEF1 is significantly
over-expressed in colorectal cancer tissues (Chung et al.,
2010).
[0374] MAGT1 was shown to be associated with a predisposition to
lymphoma (Chaigne-Delalande et al., 2013).
[0375] A polymorphism in the MANBA gene was associated with the
risk of colorectal cancer in the Swedish population, but not in the
Chinese population. Others have observed elevated levels of MANBA
in esophageal cancer (Sud et al., 2004; Gao et al., 2008).
[0376] MCM10 was show to be up-regulated in esophageal squamous
cell carcinoma and cervical cancer (Das et al., 2013a; Lu et al.,
2014b). MCM10 expression is associated with tumor grade in glioma
and cervical cancer (Das et al., 2013a; Hua et al., 2014). MCM10 is
associated with early gastric cancer, breast cancer and lung cancer
(Wu et al., 2012a; Kang et al., 2013). MCM10 may be used as a
biomarker for esophageal squamous cell carcinoma (Lu et al.,
2014b).
[0377] MCM2 has been shown to be the most sensitive marker of
proliferation and prognosis in early breast cancer, renal cell
carcinomas, esophageal and laryngeal squamous cell carcinoma and
oligodendroglioma of the brain (Wharton et al., 2001; Going et al.,
2002; Rodins et al., 2002; Gonzalez et al., 2003; Cai et al., 2012;
Joshi et al., 2015).
[0378] Researchers have observed lower levels of MDH2 expression in
paragangliomas. On the other hand, others reported over-expression
of MDH2 in gastric cancer as well as in prostate cancer cell lines
and in patient specimens (Liu et al., 2013b; Yao et al., 2015;
Cascon et al., 2015). In gastric cancer, elevated levels of MDH2
were associated with depth of invasion, lymph node metastasis,
distant metastasis and TNM staging (Yao et al., 2015). MDH2 has
been shown to be involved in the development of
doxorubicin-resistant uterine cancer, while others have revealed
that MDH2 induces prostate cancer resistance to
docetaxel-chemotherapy via JNK pathway (Liu et al., 2013b; Lo et
al., 2015).
[0379] MEMO1 is associated with buccal mucosa squamous cell
carcinoma (Shah et al., 2013). MEMO1 is associated with migration,
invasion and lung metastasis of breast cancer (MacDonald et al.,
2014). MEMO1 was shown to be up-regulated in the pancreatic cancer
cell line PaCa (Kalinina et al., 2010). MEMO1 is a prognostic
factor of early distant metastasis of primary breast cancer
(MacDonald et al., 2014).
[0380] Over-expression of MFGE8 has been found in various tumors
including breast cancer, malignant melanoma, bladder tumors,
ovarian cancer and squamous cell carcinoma (Jinushi et al., 2008;
Sugano et al., 2011; Carrascosa et al., 2012; Tibaldi et al., 2013;
Yamazaki et al., 2014). It seems that MFGE8 is able to enhance
tumorigenicity and metastatic capacity via Akt-dependent and
Twist-dependent pathways (Jinushi et al., 2008).
[0381] MGA was shown to be mutated in lung adenocarcinoma (2014).
MGA was shown to be inactivated in non-small cell lung cancer,
small cell lung cancer and chronic lymphocytic leukemia (De et al.,
2013; Romero et al., 2014).
[0382] MGRN1 is associated with osteosarcoma (Man et al.,
2004).
[0383] MKI67IP was shown to be trans-activated by c-Myc and
silencing of MKI67IP resulted in inhibition of cell proliferation.
Thus, MKI67IP may play a role in cancer (Pan et al., 2015).
[0384] A study has shown that MKKS is up-regulated in tumors with
synchronous adenoma (Kim et al., 2008a).
[0385] Methylation and over-expression of MLF1 has been linked with
lung squamous cell carcinoma, myeloid leukemia and gastric cancer.
Genomic profiling studies have identified MLF1 gene in human
esophageal cancer (Shi et al., 2012; Matsumoto et al., 2000; Sun et
al., 2004b; Chen et al., 2008). In gastric cancer, methylation of
MLF1 gene was positively associated with the number of lymph node
metastasis. However, it did not have any prognostic value for
gastric cancer patients (Shi et al., 2012). It is reported that
MLF1 promotes prostate cancer cell proliferation, colony formation
and significantly inhibits apoptosis (Zhang et al., 2015h).
[0386] MMP7 is frequently over-expressed in human cancer tissue,
including colorectal cancer, metastatic lung carcinoma and gastric
cancer and is associated with cancer progression and metastasis
formation (Ii et al., 2006; Sun et al., 2015b; Han et al., 2015a;
Long et al., 2014). MMP7 has been shown to play important tumor
promoting roles, like degradation of extracellular matrix proteins,
activation of tumor cell proliferation by increasing the
bioavailability of insulin-like growth factor and heparin-binding
epidermal growth factor and induction of apoptosis in
tumor-adjacent cells by cleaving membrane bound Fas ligand (Ii et
al., 2006).
[0387] MRPL11 was shown to be differently expressed in squamous
cell carcinoma compared to normal tissue (Sugimoto et al., 2009).
MRPL11 expression is associated with progression free survival and
metastatic phenotypes of cervical cancer (Lyng et al., 2006).
[0388] Several studies have reported associations between MSH2 gene
methylation and various malignancies such as hepatocellular
carcinoma, acute lymphoblastic leukemia, clear cell renal cell
carcinoma and esophageal squamous cell carcinoma. On the contrary,
promoter hyper-methylation of MSH2 in sporadic colorectal cancer
was a rare event (Vlaykova et al., 2011; Ling et al., 2012;
Hinrichsen et al., 2014; Wang et al., 2014a; Yoo et al., 2014).
Recent work has demonstrated that cisplatin could up-regulate the
expression of MSH2 by down-regulating miR-21 to inhibit A549 cell
proliferation (Zhang et al., 2013e).
[0389] In mesothelioma, it has been shown that MSLN induces tumor
cell invasion by increasing MMP-9 secretion (Servais et al., 2012).
Several publications have shown over-expression of MSLN in various
types of cancer such as mesothelioma, triple negative breast
carcinomas, pancreatic, ovarian and lung adenocarcinomas (Chang and
Pastan, 1996; Argani et al., 2001; Ho et al., 2007; Tozbikian et
al., 2014).
[0390] Loss of MTAP activity was observed in many tumors such as
breast cancer, leukemia, glioblastoma, non-small cell lung cancer
and bladder cancer. In addition, promoter hyper-methylation is
thought to be the preponderant inactivating mechanism in
MTAP-deficient hepatocellular carcinomas (Nobori et al., 1991;
Smaaland et al., 1987; Kamatani and Carson, 1980; Stadler et al.,
1994; Nobori et al., 1993; Hellerbrand et al., 2006). MTAP
re-expression in MTAP-deficient myxofibrosarcoma cell lines
inhibited cell migration, invasion, proliferation,
anchorage-independent colony formation and down-regulated cyclin D1
(Li et al., 2014a).
[0391] MTBP was shown to be down-regulated in hepatocellular
carcinoma (Bi et al., 2015). MTBP was shown to be up-regulated in
breast cancer and lymphomas (Grieb et al., 2014; Odvody et al.,
2010). MTBP was shown to be negatively correlated with
capsular/vascular invasion and lymph node metastasis in
hepatocellular carcinoma (Bi et al., 2015). MTBP is associated with
patient survival in breast cancer and head and neck squamous cell
carcinoma (Iwakuma and Agarwal, 2012; Grieb et al., 2014). MTBP may
be a potential biomarker for cancer progression in osteosarcoma
(Agarwal et al., 2013).
[0392] MTCH1 is associated with 5-fluorouracil resistance in
ContinB and ContinD colon cancer cell lines (De Angelis et al.,
2006).
[0393] MTHFD2 was shown to be up-regulated in Burkitt's lymphoma,
diffuse large cell lymphoma, breast cancer and in the saPC-3
prostate cancer cell line (Liu et al., 2014b; Patrikainen et al.,
2007; Tedeschi et al., 2015). MTHFD2 expression is correlated with
tumor size, histological grade, lymph node metastasis and distant
metastases in breast cancer (Liu et al., 2014b). MTHFD2 is
associated with poor survival in breast cancer and greater cancer
susceptibility and survival in bladder cancer (Nilsson et al.,
2014; Andrew et al., 2009). MTHFD2 is a prognostic factor in breast
cancer (Liu et al., 2014b).
[0394] Over-expression of MTOR signaling has been linked with poor
clinical outcome in various types of cancers such as renal, lung,
breast, laryngeal squamous cell carcinoma, neuroendocrine tumors,
biliary tract adenocarcinoma, colorectal, cervical, ovarian,
esophageal cancers, malignant melanoma and head and neck squamous
cell carcinoma (Faried et al., 2006; Hou et al., 2007; Liu et al.,
2007; Molinolo et al., 2007; Karbowniczek et al., 2008; Faried et
al., 2008; Shao et al., 2014). Researchers have revealed that MTOR
gene knockdown via lentivirus mediated MTOR specific shRNA resulted
in a significant decrease in the viability and growth of prostate
cancer cells (Du et al., 2014b).
[0395] Researchers found a significant association of polymorphisms
in the MTR gene with breast cancer, multiple myeloma and squamous
cell carcinoma of the head and neck (Zhang et al., 2005b; Kim et
al., 2007; Cui et al., 2012; Lopez-Cortes et al., 2013; Hosseini,
2013; Yang et al., 2014a).
[0396] MTX2 is associated with discrimination of patient prognosis
among acute myelogenous leukemia subgroups (Vey et al., 2004).
[0397] MUC1 was up-regulated in several tumors such as colorectal
cancer, breast cancer, lung cancer and esophageal adenocarcinoma
(Khodarev et al., 2009; Gronnier et al., 2014; Kesari et al.,
2015). In pancreatic cancer, MUC1 affects cell proliferation,
migration and invasion by targeting certain signaling pathways such
as p42-44 MAPK, Akt, Bcl-2 and MMP13. Others have observed that
elevated levels of MUC1 in B16 and B16BL6 murine melanoma cells
mediates up-regulation of Akt phosphorylation (Trehoux et al.,
2015; Wang et al., 2015h). Over-expression of MUC1 has been shown
to decrease translocation of I.sup.2-catenin into the nucleus,
reduce the activity of T cell factor and inhibit the expression of
cyclin D1 and c-Myc (Wang et al., 2013e).
[0398] MUC16 was initially recognized to be over-expressed in
ovarian cancer. It can be detected in the serum of ovarian cancer
patients and is an established biomarker for this cancer type.
Furthermore, MUC16 over-expression has been reported in pancreatic
and breast cancer. Cancer patients carrying elevated levels of
MUC16 exhibit higher likelihood of tumor recurrence (Haridas et
al., 2014).
[0399] MUC20 was described as a prognostic molecular biomarker
which is up-regulated in some epithelial tumors (Wang et al.,
2015b). MUC20 expression in combination with MUC13 expression was
shown to be a potential prognostic marker for patients with
esophageal squamous cell carcinoma, who received neoadjuvant
chemotherapy followed by surgery (Wang et al., 2015b). MUC20 was
shown to be up-regulated in colorectal cancer and endometrial
cancer (Chen et al., 2013a; Xiao et al., 2013). MUC20 expression
was shown to be associated with recurrence and poor outcome in
colorectal cancer. Disease-free survival and overall survival were
significantly worse upon up-regulation of MUC20 (Xiao et al.,
2013). MUC20 was shown to be a prognostic factor for poor survival
which is also associated with cell growth, migration, and invasion
in endometrial cancer (Chen et al., 2013a). MUC20 might play a role
in tumorigenesis of carcinosarcomas (Vekony et al., 2009).
[0400] MUC5AC is de-regulated in a variety of cancer types
including colorectal, gastric, lung and pancreatic cancer.
Depletion or low expression in colorectal and gastric tumors is
associated with a more aggressive behavior and poor prognosis.
Over-expression in lung cancer results in an increased likelihood
of recurrence and metastases (Yonezawa et al., 1999; Kocer et al.,
2002; Kim et al., 2014b; Yu et al., 1996). MUC5AC expression is
regulated by different pathways and transcription factors including
Sp1, PKC/ERK/AP-1, PKC/JNK/AP-1, CREB, NF-kappaB and
II-1beta/EGFR/Akt/GK-3beta/beta-catenin (Kato et al., 2006; Raja et
al., 2012; Chen et al., 2014h).
[0401] MUC5B is over-expressed in different cancer entities
including colorectal, lung and breast cancer and is associated with
tumor progression (Sonora et al., 2006; Valque et al., 2012; Walsh
et al., 2013; Nagashio et al., 2015). MUC5B can be repressed under
the influence of methylation and can be up-regulated by ATF-1,
c-Myc, NFkappaB, Sp1, CREB, TTF-11 and GCR (Perrais et al., 2001;
Van, I et al., 2000).
[0402] MVP is highly expressed in several central nervous system
tumors (Yang et al., 2012b). MVP is highly expressed in cancer, and
in several chemoresistant cancer cell lines (Szaflarski et al.,
2011; Mossink et al., 2003). MVP expression level increases with
age and facilitates apoptosis resistance (Ryu and Park, 2009).
[0403] Allelic gene expression of MX2 following lipopolysaccharide
stimulation has been shown in hepatocellular carcinoma cells.
Furthermore, single nucleotide polymorphism in the MX2 gene was
significantly associated with multiple primary melanoma (Park et
al., 2014; Gibbs et al., 2015).
[0404] MYCBP was shown to be up-regulated in colon carcinoma cells
and the oral cancer cell lines Hep-2, SSC-9 and Tu-177 (Rey et al.,
1999; Jung and Kim, 2005). MYCBP is associated with
chemosensitivity in oligodendroglial tumors (Shaw et al., 2011).
MYCBP was shown to be associated with cancer cell survival during
limited glucose and oxygen availability in the breast cancer cell
line MCF-7 (Sedoris et al., 2010). MYCBP was shown to be
differentially expressed in chronic myeloid leukemia (Pizzatti et
al., 2006).
[0405] MYO1G was shown to be important for cell survival and
lysosomal stability in the breast cancer cell line MCF7
(Groth-Pedersen et al., 2012).
[0406] NAF1 was shown to interact with GRIM-1, a potential co-tumor
suppressor in the prostate (Nallar et al., 2011).
[0407] Polymorphisms of NAMPT gene were linked with the risk of
developing esophageal squamous cell carcinoma as well as bladder
cancer. Moreover, elevated levels of NAMPT were reported in
colorectal, breast, prostatic, gastric, thyroid, ovarian and
pancreatic cancers (Shackelford et al., 2010; Dalamaga, 2012; Zhang
et al., 2014c; Zhang et al., 2015b; Sawicka-Gutaj et al., 2015).
Furthermore, single nucleotide polymorphisms of NAMPT gene were
significantly correlated with recurrence-free survival for total
bladder cancer patients and non-muscle-invasive bladder cancer
patients (Zhang et al., 2014c).
[0408] NAPRT1 was shown to be associated with cancer. It was also
shown that mutations that decrease NAPRT1 expression can predict
usefulness of nicotinic acid in tumor treatments with NAMPT
inhibitors (Duarte-Pereira et al., 2014). NAPRT1 expression was
shown to be lost in many cancer types due to promoter
hyper-methylation, resulting in inactivation of one of two NAD
salvage pathways. Co-administration of a NAMPT inhibitor blocking
the second NAD salvage pathway resulted in synthetic lethality.
Thus, NAPRT1 provides a novel predictive biomarker for NAMPT
inhibitors (Shames et al., 2013). NAPRT1 was described to be lost
in a high frequency of glioblastomas, neuroblastomas, and sarcomas
and may be associated with tumor apoptosis (Cerna et al., 2012).
NARPT1 was shown to be down-regulated in Hodgkin's lymphoma (Olesen
et al., 2011).
[0409] NAT8L expression is elevated in approximately 40% of
adenocarcinoma and squamous cell carcinoma cases. The
over-expression leads to elevated N-acetylaspartate levels in the
blood of NSCLC patients presenting a potential biomarker for early
lung-cancer detection (Lou et al., 2016).
[0410] NBEAL2 deficiency is associated with protection against
cancer metastasis in mice (Guerrero et al., 2014). NBEAL2 is part
of a set of biomarkers for stage discrimination in ovarian cancer
(Kashuba et al., 2012).
[0411] NCAPD2 over-expression was found in the development of
ovarian cancer together with its amplification and mutation during
tumor progression (Emmanuel et al., 2011).
[0412] NCAPD3 is a potential biomarker for subtype-1 prostate
cancer and for postoperative biochemical recurrence in prostate
cancer (Jung et al., 2014; Lapointe et al., 2008).
[0413] NCAPG is down-regulated in patients with multiple myeloma,
acute myeloid leukemia, and leukemic cells from blood or myeloma
cells (Cohen et al., 2014). NCAPG may be a multi-drug resistant
gene in colorectal cancer (Li et al., 2012a). NCAPG is highly
up-regulated in the chromophobe subtype of human cell carcinoma but
not in conventional human renal cell carcinoma (Kim et al., 2010).
Up-regulation of NCAPG is associated with melanoma progression (Ryu
et al., 2007). NCAPG is associated with uveal melanoma (Van Ginkel
et al., 1998). NCAPG shows variable expression in different tumor
cells (Jager et al., 2000).
[0414] NCKAP1L over-expression was linked with poor outcome in
chronic lymphocytic leukemia. On the other hand, down-regulation of
NCKAP1L in patient chronic lymphocytic leukemia cells resulted in a
significant increase in their susceptibility to
fludarabine-mediated killing (Joshi et al., 2007).
[0415] The non-synonymous single-nucleotide polymorphism
NEK10-L513S at 3p24 was shown to be associated with breast cancer
risk (Milne et al., 2014). Single-nucleotide polymorphisms in
SLC4A7/NEK10 in BRCA2 carriers were shown to be associated with
ER-positive breast cancer (Mulligan et al., 2011). NEK10 was
described as being implicated in DNA damage response (Fry et al.,
2012). NEK10 was described as a mediator of G2/M cell cycle arrest
which is associated with the MAPK/ERK signaling pathway members
ERK1/2, Raf-1 and MEK1 (Moniz and Stambolic, 2011).
[0416] NFATC2 has been shown to be expressed in human cancers, such
as breast cancer and lung cancer. In addition, chromosomal
translocation of NFATC2 and in-frame fusion with the EWSR1 oncogene
have been found in Ewing sarcomas. Moreover, the NFATC2 gene was
highly amplified in pancreatic cancer (Holzmann et al., 2004; Yiu
and Toker, 2006; Szuhai et al., 2009; Liu et al., 2013a). In breast
cancer, NFATC2 is able to induce invasion through the induction of
COX-2. Others have reported that NFATC2 increases invasion of
breast cancer cells via a LCN2/TWEAKR/TWEAK axis (Yiu and Toker,
2006; Gaudineau et al., 2012).
[0417] Loss of NFE2L3 predisposes mice to lymphoma development.
Others have observed high levels of NFE2L3 in colorectal cancer
cells, whereas aberrant expression of NFE2L3 was found in Hodgkin
lymphoma. Furthermore, NFE2L3 exhibited hyper-methylation in ER
positive tumors (Kuppers et al., 2003; Chevillard et al., 2011;
Palma et al., 2012; Rauscher et al., 2015).
[0418] Elevated levels of NHP2L1 were found in lung tumors
containing neuroendocrine elements as well as in small cell lung
cancer (Jensen et al., 1994; Harken et al., 1999).
[0419] NLRC3 was shown to be down-regulated in colorectal cancer,
and down-regulation was correlated with cancer progression (Liu et
al., 2015d). NLRC3 was described as a potential negative regulator
of inflammatory responses which interacts with different
inflammasome components, such as caspases 1 and 5 (Gultekin et al.,
2015).
[0420] NOA1 over-expression was shown to induce apoptosis in the
human mammary adenocarcinoma cell line MCF-7 by increasing
mitochondrial protein tyrosine nitration and cytochrome c release
(Parihar et al., 2008a). NOA1 was shown to regulate apoptosis of
human neuroblastoma cells (Parihar et al., 2008b).
[0421] NOD2 is associated with colorectal cancer, risk of gastric
cancer, MALT lymphoma, breast cancer, lung cancer, laryngeal cancer
and prostate cancer (Kang et al., 2012; Liu et al., 2014c;
Castano-Rodriguez et al., 2014; Ahangari et al., 2014). NOD2 is
associated with lymph node metastasis in urothelial bladder cancer
(Guirado et al., 2012). NOD2 gene polymorphisms may be associated
with altered risk of testicular, liver, gallbladder, biliary tract,
pancreatic, small bowel, kidney and skin cancer, non-thyroid
endocrine tumors, lymphoma and leukemia (Kutikhin, 2011).
[0422] NPLOC4 was shown to be associated with p97 and Ufd1 in a
complex mediating the alternative NF-kB pathway, which has been
implicated in cancer (Zhang et al., 2015o).
[0423] NR4A2 is highly expressed in several cancers such as
bladder, colorectal cancer and gastric cancer. In contrast,
down-regulation of NR4A2 expression was observed in breast cancer
compared to normal breast tissues (Holla et al., 2006; Inamoto et
al., 2008; Llopis et al., 2013; Han et al., 2013). In
nasopharyngeal carcinoma, high cytoplasmic expression of NR4A2 was
significantly correlated with tumor size, lymph node metastasis and
clinical stage. In addition, patients with higher cytoplasmic NR4A2
expression exhibited a significantly lower survival rate compared
to those with lower cytoplasmic NR4A2 expression (Wang et al.,
2013f).
[0424] siRNAs targeting MAPK inhibit cervical cancer cell line
growth and lead to a down-regulation of NUP188 (Huang et al., 2008;
Yuan et al., 2010). NUP188 seems to be a target of the tumor
suppressor gene BRCA1 in breast cancer (Bennett et al., 2008).
NUP188 is required for the chromosome alignment in mitosis through
K-fiber formation and recruitment of NUMA to the spindle poles
(Itoh et al., 2013).
[0425] NUP205 is stabilized by TMEM209. This interaction is a
critical driver for lung cancer proliferation (Fujitomo et al.,
2012).
[0426] NUP62 is associated with drug resistance in cultured
high-grade ovarian carcinoma cells (Kinoshita et al., 2012).
[0427] Over-expression of OPA1 was detected in oncocytic thyroid
tumors as well as lung adenocarcinoma (Fang et al., 2012;
Ferreira-da-Silva et al., 2015). Others reported that
hepatocellular carcinoma cells can be sensitized to
sorafenib-induced apoptosis by OPA1 siRNA knockdown. Furthermore,
silencing of OPA1 expression resulted in reduced cisplatin
resistance, increased release of cytochrome c and activation of
caspase-dependent apoptotic pathway (Fang et al., 2012; Zhao et
al., 2013b).
[0428] Elevated levels of ORC2 have been observed in metastatic
clear-cell renal-cell carcinoma specimens (Tan et al., 2008).
Researchers have demonstrated that pancreatic cancer cells
expressing the Plk1 non-phosphorylatable mutant of ORC2 are more
sensitive to gemcitabine treatment (Song et al., 2013a).
[0429] OSBPL10 was shown to be an oncogene mutated in breast cancer
(Pongor et al., 2015). OSBPL10 was shown to be a target of aberrant
somatic hyper-mutation associated with primary central nervous
system lymphoma (Vater et al., 2015).
[0430] PAK6 was shown to be up-regulated in colon cancer tissues
and cell lines and hepatocellular carcinoma (Chen et al., 2014b;
Tian et al., 2015). PAK6 was shown to be down-regulated in clear
cell renal cell carcinoma (Liu et al., 2014e). PAK6 was shown to
promote chemoresistance and progression in colon cancer and
motility and invasion of prostate cancer cells in the cell line
LNCap (Liu et al., 2013c; Chen et al., 2015b). PAK6 is associated
with prostate cancer (Zapatero et al., 2014). PAK6 is associated
with unfavorable overall survival and recurrence-free survival in
clear cell renal cell carcinoma, poor prognosis in hepatocellular
carcinoma and drug (gefitinib) resistance in head and neck cancer
cell lines (Chen et al., 2014b; Liu et al., 2014e; Hickinson et
al., 2009). PAK6 is a prognostic biomarker for adjuvant 5-FU
chemotherapy in stage II and III colon cancer, overall and
disease-free survival in colon cancer and overall survival as well
as recurrence-free survival in clear cell renal cell carcinoma
after nephrectomy (Liu et al., 2014e; Chen et al., 2015b). PAK6 may
be a useful marker to distinguish uterine cervical adenocarcinoma
from uterine cervical squamous cell carcinoma (Lee et al.,
2010).
[0431] PARD6B was shown to be a novel candidate target gene of p53
(Garritano et al., 2013). PARD6B was shown to be up-regulated in
breast cancer cell lines (Cunliffe et al., 2012). PARD6B was shown
to play a role in morphogenesis of the human epithelial colorectal
adenocarcinoma cell line Caco-2 (Durgan et al., 2011). PARD6B was
shown to be regulated by the oncogene steroid receptor
coactivator-3 in the breast cancer cell line MCF-7 (Labhart et al.,
2005).
[0432] PARP10 was shown to be associated with apoptosis, NF-kB
signaling, and DNA damage repair and might have a function in
cancer biology (Kaufmann et al., 2015). PARP10 was shown to be a
regulator of NF-kB signaling (Verheugd et al., 2013). PARP10 was
shown to interact with the proto-oncogene c-Myc (Yu et al.,
2005).
[0433] PARP14 is one factor that mediates proliferation,
chemo-resistance and survival of metastatic prostate cancer cells
(Bachmann et al., 2014). PARP14 is highly expressed in myeloma
plasma cells and associated with disease progression and poor
survival. PARP14 is critically involved in JNK2-dependent survival.
PARP14 was found to promote the survival of myeloma cells by
binding and inhibiting JNK1 (Barbarulo et al., 2013).
[0434] Researchers have detected elevated levels of mRNA and
protein of PARP3 in primary glioblastoma tissues. Another group
found down-regulation of PARP3 in breast cancer as well as in
non-small cell lung cancer (Frias et al., 2008; Bieche et al.,
2013; Quan et al., 2015a). Silencing of PARP3 gene resulted in
decreased cell proliferation and inhibition of tumor growth in vivo
in a glioblastoma xenograft mouse model. In lung cancer cell lines,
miR-630 reduced apoptosis by downregulating several apoptotic
modulators such as PARP3 (Cao et al., 2014; Quan et al.,
2015a).
[0435] PARPBP was shown to be up-regulated in pancreatic cancer
(O'Connor et al., 2013). PARPBP was shown to be potentially
associated with cervical cancer in the HeLa cell line (van et al.,
2012).
[0436] PAWR has been shown to be down-regulated in many cancers
including, breast cancer, lymphoma and renal cell carcinoma (Cook
et al., 1999; Boehrer et al., 2001; Nagai et al., 2010). In
addition, reduced expression of PAWR was correlated with poor
prognosis in breast cancer patients (Nagai et al., 2010; Alvarez et
al., 2013). Phosphorylation of PAWR by Akt results in its binding
and sequestration in the cytoplasm hence preventing apoptosis in
prostate cancer cells (Goswami et al., 2005).
[0437] PBXIP1 was shown to be up-regulated in colorectal cancer,
oral squamous cell carcinoma, high-grade glioma, ependymoma and
liver cancer (Xu et al., 2013b; van Vuurden et al., 2014; Okada et
al., 2015; Feng et al., 2015b). PBXIP1 is associated with breast
cancer and hepatocellular carcinoma (Okada et al., 2015; Bugide et
al., 2015; Wang et al., 2008). PBXIP1 promotes cell migration and
invasion in colorectal cancer (Feng et al., 2015b). PBXIP1 is
associated with poor clinical outcome in colorectal cancer and
overall survival in leiomyosarcoma (Silveira et al., 2013; Feng et
al., 2015b).
[0438] PCBP4 was shown to be down-regulated in lung cancer (Pio et
al., 2004).
[0439] PDIA3 may be used as a biomarker and in the diagnosis of
tumors (Shishkin et al., 2013). PDIA3 is differentially expressed
in gliomas (Deighton et al., 2010). PDIA3 is implicated in human
pathology including cancer and Alzheimer's disease (Coe and
Michalak, 2010). PDIA3 is an auxiliary factor of TAP which loads
viral and self-peptides on MHC class I (Coe and Michalak, 2010;
Abele and Tampe, 2011).
[0440] PHB activates the Raf/MEK/ERK pathway which is involved in
cell growth and malignant transformation (Rajalingam and Rudel,
2005). PHB is a potential biomarker in nasopharyngeal carcinoma
that predicts the treatment response to radiotherapy (Chen et al.,
2015e). PHB was identified in the proteomic analysis of
drug-resistant cancer cells, drug action, and disease state tissues
(Guo et al., 2013). PHB is over-expressed in many cancer entities
(Zhou and Qin, 2013). The core protein of hepatitis C virus, which
is a major risk factor for hepatocellular carcinoma, induces
over-production of oxidative stress by impairing prohibitin (Theiss
and Sitaraman, 2011; Schrier and Falk, 2011; Koike, 2014). PHB is
differentially expressed in gliomas (Deighton et al., 2010).
[0441] PHF20L1 was shown to be associated with breast cancer in the
cell line ZR-75-30 (Schulte et al., 2012). PHF20L1 is associated
with ovarian cancer (Wrzeszczynski et al., 2011).
[0442] PHKG2 is frequently methylated in papillary thyroid cancer
(Kikuchi et al., 2013). PHKG2 is de-regulated in endometrial
carcinomas and may function as a molecular biomarker (Colas et al.,
2011).
[0443] PHRF1 is associated with acute promyelocytic leukemia
(Prunier et al., 2015). PHRF1 was shown to be deleted or silenced
in breast cancer (Ettahar et al., 2013).
[0444] Elevated levels of PI4KA were observed in hepatocellular
carcinoma versus normal liver tissue. In addition, the PI4KA gene
was detected in pancreatic cancer cell line (Ishikawa et al., 2003;
Ilboudo et al., 2014). Patients suffering from hepatocellular
carcinoma with higher PI4KA mRNA concentrations had a higher risk
of tumor recurrence as well as shorter disease-specific survival
(Ilboudo et al., 2014). Recently, PI4KA has been identified to be
involved in cell proliferation and resistance to cisplatin
treatment in a medulloblastoma cell line. Others have revealed that
PI4KA plays a crucial role in invasion and metastasis in pancreatic
cancer (Ishikawa et al., 2003; Guerreiro et al., 2011).
[0445] Researchers have demonstrated the use of loss of
GPI-anchored protein expression resulting from PIGA mutation as a
new technique for finding mutator (Mut) phenotypes in cancer (Chen
et al., 2001). Recent work has revealed that PIGA causes apoptosis
in rat C6 glioma cells. In addition, cytosolic accumulation of
cytochrome c, caspase-3 activation and DNA fragmentation were
observed in PIGA-treated cells. Others have reported that leukemic
cells with PIGA mutations were less susceptible than their control
counterparts to be killed by natural killer cells in vitro
(Nagakura et al., 2002; Chelli et al., 2005).
[0446] Single nucleotide polymorphism in the PIGK gene was detected
in patients affected by colorectal cancer. Another report observed
down-regulation of PIGK mRNA level in bladder carcinoma,
hepatocellular carcinoma and colon carcinoma (Nagpal et al., 2008;
Dasgupta et al., 2012).
[0447] PJA1 was shown to be up-regulated in gastric cancer (Mishra
et al., 2005a).
[0448] Over-expression of PJA2 was found in lysates from papillary
thyroid cancer and glioblastoma samples compared to anaplastic
thyroid cancers (Cantara et al., 2012; Lignitto et al., 2013). In
addition, PJA2-FER tyrosine kinase mRNA chimeras were found to be
associated with poor postoperative prognosis in non-small cell lung
cancer (Kawakami et al., 2013). Recent work has demonstrated that
PJA2 is a key element in controlling cAMP dependent PKA activity
and pro-survival signaling (Hedrick et al., 2013).
[0449] PKHD1L1 was shown to be expressed as a fusion transcript in
T-cell large granular lymphocyte leukemia (Izykowska et al.,
2014).
[0450] In gastric cancer, elevated levels of PLA2G6 were correlated
to tumor size, tumor differentiation, TNM stage and it was an
independent predictor of survival for patients with gastric cancer
(Wang et al., 2013h). Over-expression of PLA2G6 was detected in a
variety of human cancers, including cholangiocarcinomas, gastric
cancer, colorectal cancer, lung cancer, pancreatic cancer, bladder
cancer and Barrett's adenocarcinoma (Wu et al., 2002;
[0451] Lagorce-Pages et al., 2004; Cai et al., 2013a; Wang et al.,
2013h). Bromoenol lactone, an inhibitor of PLA2G6 caused an
increase in apoptosis in ovarian cancer cells as well as inducing
cell cycle arrest in S- and G2/M-phases (Song et al., 2007).
[0452] Several publications have shown up-regulation of PLAUR in
various tumors such as urothelial neoplasia of the bladder,
colorectal cancer and breast cancer (Bianchi et al., 1994; Illemann
et al., 2014; Dohn et al., 2015). Over-expression of PLAUR was
correlated with overall survival of colorectal and gastric cancer
patients (Yang et al., 2000; Seetoo et al., 2003; Alpizar-Alpizar
et al., 2012).
[0453] PLCH1 is associated with squamous cell carcinoma of the
lungs (Zhang et al., 2013d).
[0454] PLEKHA8 was shown to be associated with colorectal cancer
(Eldai et al., 2013). PLEKHA8 was shown to be associated with
responsiveness to 5-fluorouracil in primary breast cancer culture
cells (Tsao et al., 2010).
[0455] Recent work identified somatic missense mutations of PLXNC1
and copy number loss in pancreatic ductal adenocarcinomas and
melanoma. Another group showed a significant loss of PLXNC1 in
metastatic melanoma compared with primary melanoma. Others have
reported down-regulation of PLXNC1 in acute myeloid leukemia
(Stirewalt et al., 2008; Lazova et al., 2009; Balakrishnan et al.,
2009). It appears that PLXNC1 significantly inhibits migration and
proliferation in melanoma (Chen et al., 2013c).
[0456] POLN was shown to be borderline significant in lung cancer
in a gene-based association analysis (Kazma et al., 2012). POLN was
shown to be associated with increased melanoma risk in melanoma
families with and without CDKN2A mutations (Liang et al., 2012b).
POLN was shown to be involved in DNA repair and is associated with
homologous recombination and cross-link repair (Moldovan et al.,
2010). POLN was shown to be disrupted by translocation breakpoints
in neuroblastoma and therefore might play a role in neuroblastoma
development (Schleiermacher et al., 2005).
[0457] RNA polymerase I (Pol I) activity is commonly deregulated in
human cancers. POLR1A functions as the Pol I large catalytic
subunit protein and may therefore represent a therapeutic target in
cancer (Colis et al., 2014). Furthermore, drug induced POLR1A
destruction was shown to be associated with cancer cell killing
across NCI60 cancer cell lines (Peltonen et al., 2014).
Interference of POLR1A was shown to inhibit rRNA synthesis and to
hinder cell cycle progression in cells with inactivated p53. Thus,
POLR1A may be a novel selective target to hinder proliferation of
p53-deficient cancer cells (Donati et al., 2011).
[0458] POLR1B was shown to be regulated by the proto-oncogene c-Myc
(Poortinga et al., 2011). POLR1B was shown to be associated with
the pathogenesis of therapy-related acute myeloid leukemia (Cahan
and Graubert, 2010).
[0459] A recent study has identified POM121 as a PAX5 fusion
protein in leukemia and childhood acute lymphoblastic leukemia
(Nebral et al., 2009; Fortschegger et al., 2014).
[0460] Low levels of PPIP5K1 were found in the MCF7DAP3kd and
MDA-MB-231DAP1kd breast cancer cell lines (Wazir et al., 2015a;
Wazir et al., 2015b). High levels of PPIP5K1 have been shown to
promote the induction of the pro-apoptotic gene TRAIL, whereas
anti-apoptotic genes like BCL2, BIRC3 and PRKCE were suppressed.
Moreover, PPIP5K1 is able to induce caspase activation. A recent
work has revealed that PPIP5K1 induces cancer cell migration,
invasion and tumor metastasis via LKB1 inactivation (Rao et al.,
2015; Kumar et al., 2015).
[0461] Mutations in the PPP2R1A gene have been attributed to
various cancers such as breast cancer, prostate cancer and uterine
serous carcinomas. Others observed that mutations in PPP2R1A were
infrequent in ovarian carcinoma, endometrioid cancer and absent in
clear cell and carcinosarcoma subtypes (Calin et al., 2000; Shih et
al., 2011; Cheng et al., 2011; Nagendra et al., 2012; Rahman et
al., 2013). Researchers have demonstrated that the
[0462] PRAME was shown to be up-regulated in multiple myeloma,
clear cell renal cell carcinoma, breast cancer, acute myeloid
leukemia, melanoma, chronic myeloid leukemia, head and neck
squamous cell carcinoma and osteosarcoma cell lines (Dannenmann et
al., 2013; Yao et al., 2014a; Zou et al., 2012; Szczepanski and
Whiteside, 2013; Zhang et al., 2013b; Beard et al., 2013;
Abdelmalak et al., 2014; Qin et al., 2014). PRAME is associated
with myxoid and round-cell liposarcoma (Hemminger et al., 2014).
PRAME is associated with shorter progression-free survival and
chemotherapeutic response in diffuse large B-cell lymphoma treated
with R-CHOP, markers of poor prognosis in head and neck squamous
cell carcinoma, poor response to chemotherapy in urothelial
carcinoma and poor prognosis and lung metastasis in osteosarcoma
(Tan et al., 2012; Dyrskjot et al., 2012; Szczepanski et al., 2013;
Mitsuhashi et al., 2014). PRAME is associated with lower relapse,
lower mortality and overall survival in acute lymphoblastic
leukemia (Abdelmalak et al., 2014). PRAME may be a prognostic
marker for diffuse large B-cell lymphoma treated with R-CHOP
therapy (Mitsuhashi et al., 2014).
[0463] Several publications have shown that translocation found in
papillary renal cell carcinoma leads to the fusion of a PRCC gene
to the TFE3 transcription factor (Sidhar et al., 1996; Weterman et
al., 1996; Weterman et al., 2001).
[0464] Some researchers have observed a significant increase in
PRKAR1A expression in undifferentiated thyroid carcinomas compared
to normal thyroid tissue and differentiated thyroid tumors. On the
contrary, down-regulation of PRKAR1A expression was reported in a
subset of odontogenic tumors. Another group revealed that PRKAR1A
could be involved in the pathogenesis of odontogenic myxomas as
well as in sporadic adrenocortical adenomas (Bertherat et al.,
2003; Perdigao et al., 2005; Ferrero et al., 2015; Sousa et al.,
2015).
[0465] PRKDC is a frequently mutated gene in
endometriosis-associated ovarian cancer and breast cancer (Er et
al., 2016; Wheler et al., 2015). PRKDC is up-regulated in cancerous
tissues compared with normal tissues in colorectal carcinoma.
Patients with high PRKDC expression show poorer overall survival
(Sun et al., 2016).
[0466] Over-expression of PRKX was detected in keratocystic
odontogenic tumor of the jaw bones (Kong et al., 2015). It was
reported that down-regulation of PRKX sensitized kidney carcinoma
and melanoma-cell lines against Sunitinib. Similarly, decreased
levels of PRKX were detected in the three FOLR1 siRNA-treated
taxol-resistant nasopharyngeal carcinoma cells (Bender and Ullrich,
2012; Song et al., 2015b).
[0467] Studies have detected expression of PRKY in prostate cancer
tissues, whereas in gonadoblastoma PRKY expression was undetectable
(Dasari et al., 2001; Lau and Zhang, 2000; Su et al., 2006).
[0468] PRPF8 is associated with poor prognosis in acute myeloid
leukemia and drug resistance in Mcl1-dependent neuroblastoma
(Laetsch et al., 2014; Kurtovic-Kozaric et al., 2015).
[0469] PRRC1 was shown to be fused with MLL in secondary acute
lymphoblastic leukemia (Douet-Guilbert et al., 2014).
[0470] It has been reported that PSAP is amplified and
over-expressed in a number of androgen independent human prostate
cancer cell lines, breast cancer cell lines and esophageal squamous
cell carcinoma (Koochekpour et al., 2005b; Pawar et al., 2011; Wu
et al., 2012f). Furthermore, high mRNA levels of PSAP were
significantly linked with shorter progression-free survival in
patients suffering from breast cancer with recurrent disease
treated with first-line tamoxifen therapy (Meijer et al., 2009).
Recent studies showed that PSAP induces cell proliferation,
migration and invasion in prostate cancer cell lines (Lee et al.,
2004; Koochekpour et al., 2005a).
[0471] Single nucleotide polymorphisms in the PSMA4 gene have been
associated with the risk of lung cancer in Chinese Han population.
Others reported that single nucleotide polymorphisms in the PSMA4
gene are no major contributors to non-small cell lung cancer
susceptibility. In addition, over-expression of PSMA4 was observed
in lung tumors compared to normal lung tissues (Liu et al., 2008a;
Liu et al., 2009b; Yongjun Zhang et al., 2013; Wang et al.,
2015e).
[0472] Up-regulation of PSMC2 has been reported in tumors of
transgenic mice as well as in human hepatocellular carcinoma (Cui
et al., 2006). It has been postulated that PSMC2 could play an
important role in the apoptosis and partial differentiation of
acute promyelocytic leukemia cell line (Wang et al., 2003).
[0473] PSMC3 was identified as human gastric carcinoma-associated
antigen. In addition, PSMC3 was able to react with sera from
patients suffering from hepatocellular carcinoma (Zeng et al.,
2007; Uemura et al., 2003).
[0474] PSMC4 is significantly and coherently up-regulated in
prostate carcinoma cells compared with the corresponding adjacent
normal prostate tissue (Hellwinkel et al., 2011).
[0475] Increased PSMD4 levels were detected in colon cancer,
myeloma and hepatocellular carcinoma (Arlt et al., 2009; Midorikawa
et al., 2002; Shaughnessy, Jr. et al., 2011).
[0476] Increased expression of PSMD8 in the peripheral lung may be
potentially informative as to what critical cell populations are
involved in the development of invasive cancers (Zhou et al.,
1996).
[0477] PTPLAD2 was shown to be down-regulated in esophageal
squamous cell carcinoma, which is correlated with poor prognosis
(Zhu et al., 2014b). PTPLAD2 was shown to interact with STAT3 and
to inhibit tumor proliferation upon up-regulation. Thus, PTPLAD2 is
a potential tumor suppressor and prognostic indicator as well as a
possible target for esophageal squamous cell carcinoma treatment
(Zhu et al., 2014b). PTPLAD2 was described as a novel candidate
tumor suppressor gene encompassed within homozygously deleted loci
in glioblastoma (Nord et al., 2009).
[0478] Down-regulation of PTPN2 protein levels were observed in a
subset of human breast cancer cell lines. In addition, PTPN2 was
deleted in all human T-cell acute lymphoblastic leukemias.
Furthermore, a bi-allelic inactivation of the PTPN2 gene was
identified in the Hodgkin's lymphoma cell line SUP-HD1 (Kleppe et
al., 2010; Kleppe et al., 2011a; Kleppe et al., 2011b; Shields et
al., 2013). Recent work has revealed that PTPN2 gene loss and lower
mRNA levels were correlated with poor prognosis in breast cancer
(Karlsson et al., 2015). It seems that PTPN2 acts as classical
tumor suppressor via inhibition of JAK/STAT signaling pathways
(Kleppe et al., 2011b).
[0479] Elevated levels of PTPRU expression were found in gastric
cancer tissues as well as in glioma. Others have reported PTPRU to
act as a tumor suppressor in colon cancer (Yan et al., 2006; Zhu et
al., 2014c; Liu et al., 2014i). Furthermore, knockdown of PTPRU
repressed growth and motility in gastric cancer, whereas in glioma
it suppressed proliferation, survival, invasion, migration and
adhesion. In breast cancer, PTPRU prevents tumor growth and the
formation of metastases (Zhu et al., 2014c; Liu et al., 2014i; Liu
et al., 2015f).
[0480] PWP1 was shown to be up-regulated in pancreatic cancer
(Honore et al., 2002).
[0481] Over-expression of PYGL was observed in a
multidrug-resistant cancer cell line. In addition, polymorphisms in
the PYGL gene were correlated with higher risk of relapse in
childhood acute lymphoblastic leukemia (Heim and Lage, 2005; Yang
et al., 2012c).
[0482] RAD54L2 is associated with shorter overall survival in
gastrointestinal stromal tumors (Schoppmann et al., 2013).
[0483] RALGAPB depletion was shown to cause chromosome misalignment
and decrease of mitotic cyclin B1, whereas over-expression
interfered with cell division. Deregulation of RALGAPB might cause
genomic instability, leading to carcinogenesis (Personnic et al.,
2014). Suppression of the Ral GTPase activating protein was shown
to cause mTORC1-dependent pancreatic tumor cell invasion,
indicating a crosstalk between the Ral and mTOR signaling networks.
MTOR signaling is associated with cancer (Martin et al., 2014).
[0484] Several publications have observed diminished RARRES3
expression in basal cell carcinomas and in advanced squamous cell
carcinomas (DiSepio et al., 1998; Duvic et al., 2000; Duvic et al.,
2003). In addition, RARRES3 was shown to inhibit RAS signaling
pathways in cervical cancer cells (Tsai et al., 2006). In skin
cancer, RARRES3 has been shown to induce pericentrosomal organelle
accumulation, which in turn resulted in reduced cyclin D1, cyclin E
and cyclin A levels and increased p21 level. Moreover, in
testicular cancer cells RARRES3 significantly inhibited cell
migration and invasion (Scharadin et al., 2011; Wu et al.,
2012b).
[0485] RASAL2 is a RAS-GTPase-activating protein with tumor
suppressor functions in estrogen receptor-positive breast cancer,
ovarian cancer and lung cancer (Huang et al., 2014d; Li and Li,
2014). In contrast, RASAL2 is oncogenic in triple-negative breast
cancer and drives mesenchymal invasion and metastasis (Feng et al.,
2014b).
[0486] RASGEF1B was described as a promoter of Ras activation which
is regulated by the cell cycle-associated transcription factor E2F1
(Korotayev et al., 2008).
[0487] RBM47 is associated with breast cancer progression and
metastasis (Vanharanta et al., 2014).
[0488] Recent work revealed down-regulation of RCC1 in poorly
differentiated gastric cell lines and gastric carcinoma tissues.
Others have reported elevated levels of RCC1 in response to PTEN
expression in a PTEN-null T-cell leukemia line (Huang et al.,
2005b; Lin et al., 2015c). In gastric cancer, loss of RCC1
expression was associated with tumor differentiation and depth of
invasion (Lin et al., 2015c).
[0489] REC8 encodes REC8 meiotic recombination protein a member of
the kleisin family of structural maintenance of chromosome protein
partners (RefSeq, 2002). A recent study has revealed that the REC8
gene is heterogeneously expressed in patients with cutaneous T-cell
lymphoma as well as in patient-derived cell lines. Others have
shown that REC8 was hypermethylated in melanoma. In addition, REC8
was constitutively expressed in endopolyploid tumor cells (Litvinov
et al., 2014a; Furuta et al., 2006; Erenpreisa et al., 2009).
Hyper-methylation of REC8 has been correlated with poor
clinicopathological outcomes of patients affected by thyroid
cancer, including advanced tumor, disease stages and patient
mortality (Liu et al., 2015a).
[0490] Genomic rearrangement or over-expression of RFX3 has been
detected in papillary tumors of the pineal region and primary
testicular diffuse large B cell lymphoma. Others have reported low
levels of RFX3 expression in gastric cancer cells (Twa et al.,
2015; Fevre-Montange et al., 2006; Seidl et al., 2010).
[0491] Mutations in the RFX5 gene have been found in microsatellite
instability colorectal cancer lesions. These findings suggest that
mutations of the RFX5 gene represent a new mechanism of loss of HLA
class II antigen expression in tumor cells. Recent work has shown
that RFX5 is related to gastrointestinal cancer (Satoh et al.,
2004; Michel et al., 2010; Surmann et al., 2015).
[0492] RHPN2 was shown to be associated with colorectal cancer (He
et al., 2015). A RHPN2 polymorphism may be a prognostic biomarker
for patients with surgically resected colorectal cancer (He et al.,
2015). RHPN2 was shown to be associated with survival outcome,
worse prognosis for disease-free survival and overall survival in
colorectal cancer and decreased survival of patients with
glioblastoma (Danussi et al., 2013; Kang et al., 2015a). RHPN2 was
shown to play a role in the formation of human pituitary
nonfunctional adenoma (Zhan and Desiderio, 2006).
[0493] RINT1 is described as an oncogene in glioblastoma multiforme
and as a moderately penetrant cancer susceptibility gene seen in
breast cancer as well as in Lynch syndrome-related cancers (Ngeow
and Eng, 2014; Quayle et al., 2012).
[0494] RIPK3 was shown to be down-regulated in colorectal cancer,
breast cancer and serous ovarian cancer (McCabe et al., 2014; Koo
et al., 2015a; Feng et al., 2015a). RIPK3 expression is associated
with the clinical outcome of PolyIC-based immunotherapeutic
approaches in cervical cancer and better survival in the
osteosarcoma cell line U2OS after 5-aminolevulic acid-mediated
photodynamic therapy (Coupienne et al., 2011; Schmidt et al.,
2015). RIPK3 is associated with non-Hodgkin lymphoma and lung
cancer (Yang et al., 2005; Fukasawa et al., 2006; Cerhan et al.,
2007). RIPK3 is an independent prognostic factor for overall
survival and disease-free survival in colorectal cancer (Feng et
al., 2015a). RIPK3 is a potential marker for predicting cisplatin
sensitivity in apoptosis-resistant and advanced esophageal cancer
(Xu et al., 2014b).
[0495] RIPK4 was shown to be down-regulated in squamous cell
carcinoma of the skin (Poligone et al., 2015). RIPK4 is associated
with migration and invasion in the tongue squamous cell carcinoma
cell line Tca-8113, survival of diffuse large B-cell lymphoma and
overall as well as disease-free survival, progression and poor
prognosis in cervical squamous cell carcinoma (Wang et al., 2014h;
Liu et al., 2015b; Kim et al., 2008e). RIPK4 is associated with
familial pancreatic cancer (Lucito et al., 2007). RIPK4 may be a
potential diagnostic and independent prognostic biomarker for
cervical squamous cell carcinoma and a biomarker for tongue cancer
prognosis and treatment (Wang et al., 2014h; Liu et al.,
2015b).
[0496] Point mutations of the RING domain of RNF167 have been
identified in human tumor samples, which abrogate ubiquitin ligase
activity and function (van Dijk et al., 2014). RNF167 functions in
concert with UbcH6 as an ubiquitin ligase for the putative tumor
suppressor TSSC5, a gene found to be mutated in certain tumors.
Together with UbcH6, RNF167 may define a novel ubiquitin-proteasome
pathway that targets TSSC5 (Yamada and Gorbsky, 2006).
[0497] RNF20 was shown to be down-regulated in testicular seminoma
and metastatic prostate cancer (Jaaskelainen et al., 2012;
Chernikova et al., 2012).
[0498] RNF213 is associated with chronic myeloid leukemia (Zhou et
al., 2013b). RNF213 is associated with poor prognosis in anaplastic
lymphoma kinase positive anaplastic large cell lymphoma (Moritake
et al., 2011).
[0499] RNF31 was shown to be up-regulated in breast cancer and in
lung metastasis of the osteosarcoma LM8 cell line (Tomonaga et al.,
2012; Zhu et al., 2015). RNF31 is associated with the activated B
cell-like subtype of diffuse large B-cell lymphoma (Yang et al.,
2014f; Grumati and Dikic, 2014). RNF31 is associated with
cisplatin-resistance in ovarian cancer (Mackay et al., 2014).
[0500] Down-regulation of RNF40 has been reported in testicular
germ cell cancer seminoma compared to normal testis. Others have
also observed low levels of RNF40 in colorectal cancer (Chernikova
et al., 2012; Tarcic et al., 2016). Moreover, loss of RNF40
strongly retarded the growth of prostate cancer cells (Jaaskelainen
et al., 2012).
[0501] Recently, a mutation in the RQCD1 gene was identified in
melanoma. In addition, over-expression of RQCD1 was found in breast
cancer specimens as well as breast cancer cell lines (Ajiro et al.,
2009; Wong et al., 2015). In breast cancer cell lines, RQCD1
protein was shown to interact with GIGYF1 and GIGYF2 proteins,
which are involved in regulation of Akt activation. Furthermore,
knockdown of RQCD1 resulted in a reduction in the Akt
phosphorylation level that was induced by epidermal growth factor
stimulation (Ajiro et al., 2009; Ajiro et al., 2010).
[0502] Recent work has demonstrated that over-expression of RTN2
induces anti-estrogen resistance in human breast cancer cell lines
(Near et al., 2007; Makkinje et al., 2009).
[0503] Over-expression of RTN3 was detected in the saliva of
patients suffering from oral squamous cell cancer. Similarly,
elevated levels of RTN3 were detected in the sera of epithelial
ovarian carcinoma patients in all stages, but in particular it was
highest in stage III. Others have observed high levels RTN3 in
leukemia and urogenital cancer (Mitchell et al., 1988; Dunzendorfer
et al., 1980; Chen et al., 2009c; Jessie et al., 2013).
Furthermore, it was shown that circulating RTN3 was significantly
associated with the stage of tumor and survival of epithelial
ovarian carcinoma patients (Zhao et al., 2007).
[0504] SAMD9 was shown to be down-regulated in breast cancer, colon
cancer, non-small cell lung cancer and fibromatosis (Ma et al.,
2014; Li et al., 2007). SAMD9 is associated with invasion,
migration and proliferation in the non-small cell lung cancer cell
line H1299, lymphatic invasion and metastasis in esophageal
squamous cell carcinoma and myeloid leukemias (Nagamachi et al.,
2013; Tang et al., 2014b; Ma et al., 2014).
[0505] SAMSN1 was shown to be up-regulated in glioblastoma
multiforme (Yan et al., 2013c). SAMSN1 was shown to be
down-regulated in hepatocellular carcinoma, multiple myeloma and in
the large cell lung carcinoma cell line Calu-6 (Noll et al., 2014;
Sueoka et al., 2015; Yamada et al., 2008). SAMSN1 is associated
with ulcerative colitis-associated cancer and acute myeloid
leukemias (Watanabe et al., 2011; Claudio et al., 2001). SAMSN1 is
associated with shorter overall and recurrence-free survival in
hepatocellular carcinoma and poor overall survival of glioblastoma
multiforme (Yan et al., 2013c; Sueoka et al., 2015). SAMSN1 is an
independent prognostic factor of hepatocellular carcinoma
progression and a potential prognostic marker of multiple myeloma
(Ni et al., 2012; Sueoka et al., 2015).
[0506] SCARA3 was shown to be up-regulated in ovarian/primary
peritoneal carcinoma (Bock et al., 2012). SCARA3 is a predictor of
multiple myeloma progression and therapeutic response (Brown et
al., 2013).
[0507] Methylation of SCNN1A was detected in breast cancer cell
lines as well as in neuroblastoma. A recent study suggested that
SCNN1A could be implicated in the aetiology of testicular germ cell
tumors, since retinoic acid suppresses the tumorigenicity of
embryonal carcinoma cells (Giuliano et al., 2005; Roll et al.,
2008; Caren et al., 2011). Researchers have used a cox proportional
hazards model and showed that SCNN1A could predict patients'
prognosis in adenocarcinoma (Endoh et al., 2004).
[0508] SEC61A1 is associated with prostate cancer (Bull et al.,
2001).
[0509] SEC61G was shown to be up-regulated in gastric cancer
(Tsukamoto et al., 2008). SEC61G is associated with gliomas
(Neidert et al., 2013).
[0510] SESN3 was described as a unique cellular inhibitor of mTOR
complex 1 (Vakana et al., 2013). SESN3 was described to be induced
through the tumor suppressor FOXO3 in the context of reactive
oxygen species detoxification (Hagenbuchner and Ausserlechner,
2013). SESN3 repression was shown to be induced through oncogenic
Ras in the context of regulation of reactive oxygen species upon
cell proliferation (Zamkova et al., 2013). SESN3 was shown to be
regulated by the tumor suppressor p53 upon nerve growth
factor-mediated differentiation of the PC12 cell line (Brynczka et
al., 2007). SESN3 5' CpG island methylation was shown to be a novel
endometrial cancer-specific marker (Zighelboim et al., 2007).
[0511] Researchers have identified SETDB1 as a novel oncogene in a
zebrafish melanoma model as well as in human lung cancers.
Furthermore, over-expression of SETDB1 has been found in non-small
cell lung cancer, prostate cancer and glioma (Ceol et al., 2011;
Rodriguez-Paredes et al., 2014; Spyropoulou et al., 2014; Sun et
al., 2014d; Sun et al., 2015f). It appears that SETDB1 is able to
positively stimulate the activity of the WNT-beta-catenin pathway
(Sun et al., 2015f). In addition, knockdown of SETDB1 by siRNA
inhibited prostate cancer cell growth, invasion, migration, reduced
colony formation and induced cell cycle arrest (Sun et al.,
2014d).
[0512] SGPP2 was shown to be down-regulated in
sphingosine-1-phosphate enriched glioblastomas (Abuhusain et al.,
2013). SGPP2 was shown to be a NF-kB dependent gene which thus
might be a potential novel player in pro-inflammatory signaling
(Mechtcheriakova et al., 2007).
[0513] SH3GLB2 was shown to be up-regulated in prostate cancer
metastasis (Fasso et al., 2008).
[0514] SHISA5 is associated with squamous cell carcinoma of the
head and neck (Ghosh et al., 2008).
[0515] Increased SIGLEC1 expression has been observed in splenic
marginal cell lymphoma as well as in AIDS-related Kaposi's sarcoma.
Others have found mutations in the SIGLEC1 gene to be linked to the
development of pancreatic ductal adenocarcinoma (Zhou et al.,
2012a; Cornelissen et al., 2003; Marmey et al., 2006). Elevated
levels of SIGLEC1 expression correlated with a better prognosis in
patients suffering from colorectal carcinoma and malignant melanoma
(Ohnishi et al., 2013; Saito et al., 2015).
[0516] SIN3A was shown to be associated with invasion in the lung
adenocarcinoma cell line A549 (Das et al., 2013b). SIN3A is
associated with breast cancer (Ellison-Zelski and Alarid, 2010).
SIN3A was shown to be down-regulated in non-small cell lung cancer
(Suzuki et al., 2008).
[0517] Over-expression of SKIL has been observed in human breast
cancer cell lines, lung adenocarcinoma cell lines, melanoma and
osteosarcoma. Others reported that SKIL was amplified in primary
esophageal squamous cell carcinomas (Imoto et al., 2001; Zhang et
al., 2003; Zhu et al., 2007). In breast cancer, reduced expression
of SKIL was associated with longer distant disease-free survival in
estrogen receptor-positive patients (Zhang et al., 2003).
[0518] A study has revealed that the highest SLC15A2 mRNA levels
were found on prostate cancer cell line LNCaP compared to PC-3 and
DU145 cells. Others reported that genomic variants in the SLC15A2
gene could be associated with sorafenib response in patients
suffering from hepatocellular carcinoma (Tai et al., 2013; Lee et
al., 2015).
[0519] SLC15A3 is associated with colorectal cancer (Zhou et al.,
2013a). SLC15A3 was shown to be associated with prostate cancer in
the prostate cancer cell lines LNCaP, DU-145, PC-3 and MDA2b
(Ibragimova et al., 2010).
[0520] Down-regulation of SLC16A2 was reported in medullary thyroid
carcinomas compared to non-tumor thyroid tissue (Hudson et al.,
2013).
[0521] A report has shown that the expression of SLC25A14 was
significantly and negatively associated with postmenopausal human
breast tumors with a low ERalpha/ERbeta ratio. Others have observed
elevated levels of SLC25A14 in breast cancer cell lines with low
ERalpha/ERbeta ratio. In addition, high levels of SLC25A14 were
found in colonic cancer cells, which were correlated with
mitochondrial dysfunction (Santandreu et al., 2009; Nadal-Serrano
et al., 2012; Sastre-Serra et al., 2013).
[0522] SLC28A3 was shown to be down-regulated in pancreatic ductal
adenocarcinoma (Mohelnikova-Duchonova et al., 2013a). SLC28A3 is
associated with clinical outcome in metastatic breast cancer
treated with paclitaxel and gemcitabine chemotherapy, overall
survival in gemcitabine treated non-small cell lung cancer and
overall survival in gemcitabine-based chemoradiation treated
pancreatic adenocarcinoma (Li et al., 2012c; Lee et al., 2014b;
Marechal et al., 2009). SLC28A3 is associated with fludarabine
resistance in chronic lymphocytic leukemia and drug resistance in
T-cell leukemia (Karim et al., 2011; Fernandez-Calotti et al.,
2012).
[0523] SLC29A3 is associated with overall survival in non-small
cell lung cancer patients treated with gemcitabine-based
chemotherapy and overall survival in pancreatic cancer patients
treated with nucleoside analogs (Mohelnikova-Duchonova et al.,
2013a; Chen et al., 2014f). SLC29A3 is a potential prognostic
biomarker for patients with advanced non-small cell lung cancer who
receive gemcitabine (Chen et al., 2014f).
[0524] The expression of SLC34A2 was significantly different
between surgical samples of non-small cell lung cancer and normal
tissues. Furthermore, low levels of SLC34A2 expression were found
in lung adenocarcinoma cell lines. Others have demonstrated that
SLC34A2 could be the target of MX35, an antibody developed to treat
ovarian cancer (Yin et al., 2008; Yang et al., 2014c; Wang et al.,
2015k). Moreover, up-regulation of SLC34A2 in lung adenocarcinoma
cell lines was able to significantly inhibit cell viability and
invasion in vitro (Wang et al., 2015k). On the other hand,
decreased SLC34A2 expression sensitized breast cancer stem cells to
doxorubicin via SLC34A2-Bmi1-ABCC5 signaling (Ge et al., 2015).
[0525] SLC35B3 is associated with colorectal carcinoma (Kamiyama et
al., 2011). SLC35B3 was shown to be associated with chemotherapy
resistance in ovarian cancer (Cheng et al., 2010).
[0526] SLC35E1 was shown to be associated with rectal carcinoma
response to neoadjuvant radiochemotherapy (Rimkus et al.,
2008).
[0527] Down-regulation of SLC35E2 has been reported in
neuroblastoma (Thorell et al., 2009).
[0528] The SLC35E2B transcripts showed significantly lower
expression in unfavorable neuroblastoma tumors (Thorell et al.,
2009).
[0529] Over-expression of SLC4A2 has been observed in colon cancer
and hepatocellular carcinoma. On the other hand, SLC4A2 expression
was down-regulated in gastric cancer (Wu et al., 2006; Yang et al.,
2008b; Song et al., 2012). In colon cancer, elevated levels of
SLC4A2 were correlated with poor prognosis (Song et al., 2012). In
addition, inhibition of SLC4A2 expression reduced cell viability,
arrested cell cycle at sub-G1 phase, and induced cell apoptosis in
poorly differentiated hepatocellular carcinoma cells (Hwang et al.,
2009).
[0530] SLC7A8 is associated with leiomyoma (Xia et al., 2010; Luo
et al., 2009). SLC7A8 was shown to be associated with drug
resistance in ovarian cancer cell line W1 variants (Januchowski et
al., 2013). SLC7A8 was shown to be up-regulated in the estrogen
receptor alpha positive breast cancer cell line T-47D (Thakkar et
al., 2010).
[0531] Several publications have reported increased expression of
SMARCC1 mRNA and protein in prostate cancer, colorectal cancer and
cervical intraepithelial neoplasia. In contrast, SMARCC1 protein
expression was not detected in ovarian cancer cell lines (Shadeo et
al., 2008; Heeboll et al., 2008; Andersen et al., 2009; DelBove et
al., 2011). Furthermore, over-expression of SMARCC1 was associated
with poor prognosis and recurrence in colorectal cancer (Andersen
et al., 2009). Researchers have shown that methylation of SMARCC1
at arginine residue R1064 affects the colony-formation capacity of
MCF7 breast cancer cells. Moreover, it seems that this modification
is entirely dependent on CARM1 (Wang et al., 2014e).
[0532] SMCHD1 is associated with hematopoietic cancers (Leong et
al., 2013).
[0533] SMG1 was shown to be up-regulated in pancreatic cancer (Wang
et al., 2015d). SMG1 was shown to be down-regulated in
hepatocellular carcinoma (Han et al., 2014). SMG1 was shown to be
associated with gemcitabine and cisplatin chemosensitivity in
pancreatic cancer cell lines and in the lung cancer cell line H1299
and sorafenib resistance in hepatocellular carcinoma cell lines
(Xia et al., 2011; Nam et al., 2014; Wang et al., 2015d). SMG1 is
associated with acute myeloid leukemia (Du et al., 2014a). SMG1 is
associated with poor overall survival in hepatocellular carcinoma
(Han et al., 2014).
[0534] SMPD4 was shown to be associated with cellular stress
response, DNA damage and p53 activation and expression was shown to
be deregulated in several types of primary tumors (Corcoran et al.,
2008).
[0535] SND1 was shown to be up-regulated in non-small cell lung
cancer, breast cancer, colon cancer, hepatocellular carcinoma,
glioma and prostate cancer (Cappellari et al., 2014; Emdad et al.,
2015; Yu et al., 2015a; Zagryazhskaya et al., 2015). SND1 is
associated with chemoresistance in non-small cell lung cancer
(Zagryazhskaya et al., 2015). SND1 is associated with prostate
cancer, primary cutaneous malignant melanoma and cutaneous
malignant melanoma metastases (Sowalsky et al., 2015; Sand et al.,
2012). SND1 is associated with migration and invasion in
hepatocellular carcinoma (Santhekadur et al., 2014). SND1 is
associated with shorter overall survival and poor prognosis in
colon cancer (Wang et al., 2012b). SND1 is a promising prostate
cancer biomarker (Kuruma et al., 2009).
[0536] SNRPE was over-expressed in hepatocellular carcinoma as well
as in high-grade prostate cancer (Jia et al., 2011; Anchi et al.,
2012; Xu et al., 2015c). Furthermore, elevated levels of SNRPE were
correlated with worse prognosis in patients with lung cancer
(Valles et al., 2012). siRNA-mediated depletion of SNRPE resulted
in reduction of cell viability in breast, lung and melanoma cancer
cell lines (Quidville et al., 2013).
[0537] Studies have detected high levels of serum SORL1 in
follicular lymphoma, diffuse large B-cell lymphoma and peripheral
T-cell lymphoma patients compared to healthy controls. Another
report also observed elevated levels of SORL1 in acute leukemia
patients, whereas patients with acute myeloid leukemia and acute
lymphoblastic leukemia in remission exhibited significantly
decreased SORL1 levels. Additionally, down-regulation of SORL1 was
also seen in high-grade astrocytomas (MacDonald et al., 2007; Sakai
et al., 2012; Bujo, 2012; Fujimura et al., 2014).
[0538] Over-expression of SOS1 was found in Egyptian patients
suffering from bladder cancer as well as prostate cancer epithelial
cells. Another report has identified missense SOS1 mutations in a
single pancreatic tumor, one lung adenocarcinoma and a T-cell acute
lymphoblastic leukemia cell line (Zekri et al., 2015; Swanson et
al., 2008; Timofeeva et al., 2009). In prostate cancer cells,
depletion of SOS1 resulted in decreased cell proliferation,
migration and invasion (Timofeeva et al., 2009).
[0539] SOX17 was shown to be down-regulated in breast cancer,
penile carcinoma, hepatocellular carcinoma, acute myeloid leukemia
and esophageal squamous cell carcinoma (Kuo et al., 2014; Tang et
al., 2014a; Yang et al., 2014b; Kuasne et al., 2015; Fu et al.,
2015). SOX17 is associated with ovarian cancer, oligodendroglioma,
melanoma, papillary thyroid carcinoma and gastric cancer (Oishi et
al., 2012; Li et al., 2012b; Lu et al., 2014a; Li et al., 2014b; Du
et al., 2015b). SOX17 is associated with poor disease-free survival
and overall survival in breast cancer, progression and unfavorable
survival of melanoma patients, shorter overall survival in acute
myeloid leukemia and overall survival in gastric cancer
(Balgkouranidou et al., 2013; Tang et al., 2014a; Lu et al., 2014a;
Fu et al., 2015). SOX17 is a useful prognostic biomarker for breast
cancer, melanoma, germ cell cancer and esophageal squamous cell
carcinoma (Kuo et al., 2014; van der Zwan et al., 2015; Lu et al.,
2014a; Fu et al., 2015).
[0540] SP140 was shown to be up-regulated in laryngeal squamous
cell carcinoma (Zhou et al., 2007). SP140 is associated with
chronic lymphocytic leukemia, multiple myeloma and acute
promyelocytic leukemia (Bloch et al., 1996; Lan et al., 2010;
Kortum et al., 2015).
[0541] SPG11 was shown to be down-regulated in the gastric cancer
cell line HSC45-M2 in response to treatment with alpha-emitter
(213)Bi conjugated antibodies and may be a potential new target for
selective elimination of tumor cells (Seidl et al., 2010).
[0542] Elevated expression and activity of SPLTC1 was detected in
malignant tissues and in endometrial cancer tissue (Carton et al.,
2003; Knapp et al., 2010). Moreover, SPTLC1 could be used as a
potential therapeutic target to alleviate imatinib resistance in
BCR-ABL-positive leukemia cells (Taouji et al., 2013).
[0543] SPTLC3 is associated with invasive micropapillary carcinoma
of the breast (Gruel et al., 2014).
[0544] SRGAP1 was shown to be associated with glioblastoma
multiforme in the cell lines U87-IM3 and U251-IM3, familial forms
of non-medullary thyroid carcinoma, papillary thyroid carcinoma and
epithelial ovarian cancer (He et al., 2013; Chen et al., 2014c;
Pereira et al., 2015; Koo et al., 2015b).
[0545] STARD10 was shown to be up-regulated in breast cancer
(Olayioye et al., 2005). STARD10 is associated with poor prognosis
in breast cancer (Murphy et al., 2010).
[0546] Researchers have identified single nucleotide polymorphisms
as well as mutations in the STAT6 gene to be involved in the
development of cervical cancer and follicular lymphoma. Moreover,
over-expression of STAT6 was noted in solitary fibrous tumor,
prostate and colon cancer (Ni et al., 2002; Li et al., 2008a;
Yoshida et al., 2014; Zhang et al., 2014g; Yildiz et al., 2015).
Others have reported that STAT6 knockdown induces the inhibition of
cell proliferation, G1/S phase arrest and apoptosis in HT-29 colon
cancer cells. On the contrary, un-phosphorylated STAT6 increases
the expression of COX-2, thereby protecting non-small cell lung
cancer against apoptosis (Zhang et al., 2006; Cui et al.,
2007).
[0547] De-regulated expression of STK17A is associated with
different cancer types. Decreased expression in cervical and
colorectal cancer is related to the pro-apoptotic character of
STK17A connected with tumor progression. STK17A in glioblastoma and
head and neck cancer is over-expressed in a grade-dependent manner,
maybe caused through the influence on other tumor relevant pathways
like TGF-beta (Mao et al., 2013a; Thomas et al., 2013; Park et al.,
2015; Bandres et al., 2004). STK17A is a direct target of the tumor
suppressor gene p53 and a modulator of reactive oxygen species
(ROS) (Kerley-Hamilton et al., 2005; Mao et al., 2011).
[0548] Hypermethylation of STK3 was found in soft tissue sarcoma,
whereas in squamous cell carcinomas of head and neck it was less
frequent. Others reported that loss of STK3 resulted in the
development of hepatocellular carcinoma (Seidel et al., 2007; Zhou
et al., 2009; Steinmann et al., 2009).
[0549] STK35 was shown to regulate CDKN2A and to inhibit G1- to
S-phase transition in endothelial cells, thus, playing a role in
the linkage of the cell cycle and migration of endothelial cells
(Goyal et al., 2011).
[0550] STK38 is associated with B-cell lymphoma (Bisikirska et al.,
2013). STK38 was shown to be associated with radiosensitivity in
the cervical cancer cell line HeLa (Enomoto et al., 2013). STK38
was shown to be down-regulated in gastric cancer (Cui et al.,
2005).
[0551] STK38L was shown to be down-regulated in human skin tumors
(Hummerich et al., 2006). STK38L is associated with glioma (Deng et
al., 2005).
[0552] STRADA is a regulatory partner of the tumor suppressor LKB1
(Sun et al., 2015a). STRADA was shown to play a role in cell
proliferation and viability of the prostate cancer cell line LNCaP
and thus may be a novel prostate cancer drug target (Dahlman et
al., 2012). STRADA was shown to be involved in cell proliferation
and cisplatin resistance in medulloblastoma cell lines (Guerreiro
et al., 2011). STRADA was shown to be up-regulated in
medulloblastoma (Guerreiro et al., 2011). STRADA was shown to be a
breast cancer antigen (Scanlan et al., 2001).
[0553] Over-expression of STX1A was found in breast cancer as well
as in small cell lung carcinoma. Recent work has identified STX1A
as a target for the treatment of metastatic osteosarcoma (Graff et
al., 2001; Diao et al., 2014; Fernandez-Nogueira et al., 2016).
Studies have revealed that the expression of STX1A was
significantly associated with a shorter overall survival and
distant metastasis-free survival in breast cancer subtypes
(Fernandez-Nogueira et al., 2016). Inhibition of STX1A reduced the
proliferation and migratory capacity of glioblastoma cells (Ulloa
et al., 2015).
[0554] STYXL1 is associated with Ewing's sarcoma family tumors
(Siligan et al., 2005).
[0555] SVIL is significantly down-regulated in prostate cancer
tissue mainly through promoter methylation (Vanaja et al., 2006).
SVIL regulates cell survival through control of p53 levels. SVIL
expression is necessary for the cross-talk between survival
signaling and cell motility pathways (Fang and Luna, 2013).
[0556] Researchers have observed amplifications, copy number gains
and mRNA over-expression of TAF2 in high-grade serous ovarian
cancers (Ribeiro et al., 2014).
[0557] Amplifications, copy number gains, or mRNA up-regulation of
TAF4B has been reported in high-grade serous ovarian cancers
(Ribeiro et al., 2014). In addition, TAF4B is able together with
AP-1 to regulate the target gene integrin alpha 6 involved in
epithelial-to-mesenchymal transition, hence changing the cancer
related migration properties (Kalogeropoulou et al., 2010).
[0558] TANC2 was shown to be up-regulated in breast cancer (Mahmood
et al., 2014).
[0559] Single nucleotide polymorphisms as well as loss of the TAP1
gene seem to be implicated in certain cancer types such as
melanoma, cervical carcinoma, colorectal cancer and head and neck
squamous cell carcinoma. On the other hand, up-regulation of TAP1
has been observed in lung cancer and ovarian serous carcinoma (Yang
et al., 2003; Meissner et al., 2005; Vermeulen et al., 2007;
Yamauchi et al., 2014; Zhang et al., 2015g; Nymoen et al., 2015).
In addition, expression of TAP1 was significantly associated with
tumor grade, clinical stage, overall survival and progression-free
survival in patients affected by prostate cancer (Tahara et al.,
2015). In lung cancer, loss of TAP1 inhibited cell proliferation
and caused cell cycle arrest in a p53-independent manner (Zhang et
al., 2015g).
[0560] Some studies did not find an association between TAP2 gene
polymorphism with renal cell carcinoma and cervical cancer. In
contrast, others observed a correlation between the TAP2 gene
polymorphism and susceptibility to chronic lymphoid leukemia. In
addition, the expression of TAP2 was reduced in breast carcinoma,
gastric cancer, small cell lung carcinoma and head and neck
squamous cell carcinoma (Restifo et al., 1993; Vitale et al., 1998;
Kang et al., 2000; Hodson et al., 2003; Kordi Tamandani et al.,
2009; Bandoh et al., 2010; Ozbas-Gerceker et al., 2013).
[0561] TCERG1 was shown to function as a transcriptional
co-regulator of DACH1, a transcription factor which was shown to be
associated with various types of cancer (Zhou et al., 2010).
[0562] TELO2 is de-regulated in different cancer types including
leukemias, breast cancer and nasopharyngeal carcinoma (He et al.,
2007; Sang et al., 2015; Kawagoe et al., 2004). Over-expression of
TELO2 decreases cell cycle length, hyper-sensitizes the cell to
apoptosis and increases telomere length. Inhibition of TELO2
expression arrests the cell cycle reversibly (Jiang et al., 2003).
Activated TELO2 is essential for the stability of PIKK family
proteins like mTOR, ATM, ATR and SMG-1. TELO2 plays an important
role in the regulation of translation, cell growth and DNA damage
signaling (Kaizuka et al., 2010; Horejsi et al., 2010).
[0563] TET3 was shown to be down-regulated in hepatocellular
carcinoma, colorectal cancer and gastric cancer
(Rawluszko-Wieczorek et al., 2015; Sajadian et al., 2015; Du et
al., 2015a). TET3 was shown to be up-regulated in diffuse intrinsic
pontine glioma (Ahsan et al., 2014). TET3 was shown to be
associated with tumor hypoxia, tumor malignancy, and poor prognosis
in breast cancer (Wu et al., 2015). TET3 was shown to be associated
with TNFalpha-p38-MAPK signaling (Wu et al., 2015). TET3 was
described as a regulator of 5-hydroxymethylation, an epigenetic
modification associated with malignant tumors. In leiomyoma,
epigenetic imbalance in the 5-hydroxymethylation content was
described as a result of TET3 up-regulation which might lead to the
discovery of new therapeutic targets in leiomyoma (Navarro et al.,
2014). TET3 was shown to be recurrently mutated in colon cancer and
may provide a potential therapeutic intervention opportunity
(Seshagiri et al., 2012). TET3 was described as a potential
regulator of histone modification and WNT pathways in
myelodysplastic syndromes and acute myeloid leukemia (Gelsi-Boyer
et al., 2009).
[0564] Over-expression of TFAP2C has been found in breast
carcinomas as well as in germ cell tumors (Turner et al., 1998;
Hoei-Hansen et al., 2004). It is reported that TFAP2C induces p21
expression, arrests cell cycle and suppresses the tumor growth of
breast carcinoma cells (Li et al., 2006).
[0565] Down-regulation of TFDP2 was observed in human papillary
carcinoma tissues, while others reported over-expression of TFDP2
in hepatocellular carcinoma compared to normal liver tissues. In
addition, TFDP2 variants have been linked to ovarian cancer (Liu et
al., 2003; Lapouge et al., 2005; Cunningham et al., 2009).
[0566] TH1L might play an important role in regulation of
proliferation and invasion in human breast cancer, and could be a
potential target for human breast cancer treatment (Zou et al.,
2010).
[0567] Some researchers have reported over-expression of TIMELESS
protein and mRNA in hepatocellular carcinoma as well as in
colorectal cancer, cervical cancer, lung cancer and prostate
cancer. On the other hand, another study reported down-regulation
of TIMELESS in hepatocellular carcinomas. In addition, single
nucleotide polymorphism in the TIMELESS gene were not associated
with risk of prostate cancer but correlated with breast cancer risk
(Lin et al., 2008b; Fu et al., 2012; Mazzoccoli et al., 2011;
Yoshida et al., 2013; Mao et al., 2013b; Markt et al., 2015;
Elgohary et al., 2015). In lung cancer, elevated levels of TIMELESS
were associated with poor overall survival (Yoshida et al.,
2013).
[0568] Over-expression and epigenetic inactivation of TLE1 have
been found in various cancers including lung tumors, synovial
sarcoma, malignant mesothelioma, leukemia and lymphoma (Allen et
al., 2006; Fraga et al., 2008; Matsuyama et al., 2010; Seo et al.,
2011; Rekhi et al., 2012). Additionally, TLE1 suppresses apoptosis
induced by doxorubicin in synovial sarcoma cells. In lung cancer
cell lines TLE1 was able to potentiate epithelial-to-mesenchymal
transition by suppressing the tumor suppressor gene E-cadherin (Seo
et al., 2011; Yao et al., 2014b). Furthermore, it was observed that
trichostatin A significantly inhibited lung tumorigenesis in TLE1
transgenic mice (Liu et al., 2015c).
[0569] Over-expression of TLE3 has been observed in some malignant
meningiomas compared to benign and atypical meningiomas. Others
have reported elevated levels of spliced isoform of TLE3 in
prostate tumors as well as in prostate tumor cell lines (Cuevas et
al., 2005; Nakaya et al., 2007). Studies have revealed that TLE3
mRNA levels were predictive for progression-free survival in breast
cancer patients receiving tamoxifen. In contrast, others reported
that TLE3 expression does not represent a viable biomarker for
taxane benefit in breast cancer. Another report demonstrated that
TLE3 expression predicts a favorable response to taxane containing
chemotherapy regimens in ovarian carcinoma (van et al., 2009;
Samimi et al., 2012; Bartlett et al., 2015).
[0570] Recent work has identified a missense mutation in the TLE4
gene in acute myeloid leukemia. Other studies have shown
over-expression of TLE4 in colorectal cancer as well as in adenomas
(Greif et al., 2011; Ruebel et al., 2006; Wang et al., 2016a). In
colorectal cancer, elevated levels of TLE4 were correlated with
advanced Dukes stage, lymph node metastasis and poor prognosis of
colorectal cancer (Wang et al., 2016a). It seems that
over-expression of miR-93 negatively regulates mRNA and protein
expression of TLE4 (Yu et al., 2011).
[0571] Previous studies have found over-expression of TLN1 in
several tumors, including prostate cancer, oral squamous cell
carcinoma, ovarian serous carcinoma and nasopharyngeal carcinoma
(Sakamoto et al., 2010; Lai et al., 2011; Tang et al., 2013; Xu et
al., 2015d). Over-expression of TLN1 was associated with reduced
overall survival in patients suffering from oral squamous cell
carcinoma (Lai et al., 2011). It appears that TLN1 S425
phosphorylation plays a crucial role in beta1 integrin activation,
cell adhesion, migration, invasion and metastasis of prostate
cancer cells. In addition, elevated levels of TLN1 are correlated
with reduced invasion, migration as well as decreased malignancy in
hepatocellular carcinoma cell lines (Fang et al., 2014; Jin et al.,
2015).
[0572] TLR7 was shown to be up-regulated in pancreatic cancer, oral
squamous cell carcinoma and hepatocellular carcinoma (Mohamed et
al., 2015; Ni et al., 2015; Grimmig et al., 2015). TLR7 is
associated with tumor cell proliferation and chemoresistance in
pancreatic cancer (Grimmig et al., 2015). TLR7 over-expression is
associated with poor clinical outcome and chemotherapy resistance
in lung cancer and poor prognosis in oral squamous cell carcinoma
(Ni et al., 2015; Dajon et al., 2015). TLR7 is associated with
bladder cancer (Cheng et al., 2014).
[0573] TMEM14C is associated with breast cancer survival (Burleigh
et al., 2015). TMEM14C is associated with tamoxifen resistance in
the breast cancer cell line ZR-75-1 (Zarubin et al., 2005).
[0574] TMEM189-UBE2V1 isoform 2 (Uev1B) was shown to be associated
with ubiquitin and Hrs and over-expression of the protein abrogated
the ability of Hrs to colocalize with the cancer-associated protein
EGFR (Duex et al., 2010).
[0575] TMPRSS13 encodes a member of the type II transmembrane
serine protease family, which is known to function in development,
homeostasis, infection, and tumorigenesis (RefSeq, 2002). TMPRSS13
was shown to function as a hepatocyte growth factor
(HGF)-converting protease, converting pro-HGF to biologically
active HGF. HGF was shown to interact with the oncogene c-Met and
is associated with a variety of cancers (Hashimoto et al.,
2010).
[0576] TNFAIP2 encodes TNF alpha induced protein 2 and it has been
suggested to be a retinoic acid target gene in acute promyelocytic
leukemia (RefSeq, 2002). TNFAIP2 rs8126 polymorphism has been
significantly associated with susceptibility of head and neck
squamous cell carcinoma, gastric cancer and esophageal squamous
cell carcinoma. Moreover, the TNFAIP2 mRNA and protein were found
to be elevated in nasopharyngeal carcinoma tumor cells compared
with adjacent normal tissues. Others have observed over-expression
of TNFAIP2 in glioma samples (Chen et al., 2011; Liu et al., 2011;
Xu et al., 2013c; Zhang et al., 2014b; Cheng et al., 2015b).
Furthermore, over-expression of TNFAIP2 was correlated with shorter
distant metastasis-free survival in nasopharyngeal carcinoma
patients (Chen et al., 2011).
[0577] Up-regulation of TNXB has been observed in ovarian cancer
and malignant mesothelioma, whereas in peripheral nerve sheath
tumors TNXB was significantly down-regulated. Recent work has
identified TNXB in glioblastoma multiforme cell lines (Levy et al.,
2007; Yuan et al., 2009; Polisetty et al., 2011; Kramer et al.,
2015). Studies have shown that deficiency in TNXB led to tumor
invasion and metastasis through the activation of the MMP2 and MMP9
genes (Matsumoto et al., 2001).
[0578] Low levels of TOB1 have been observed in gastric, lung and
breast cancers. Others have shown that mice lacking TOB1 are
predisposed to spontaneous formation of tumors in various tissues
(Yoshida et al., 2003; Iwanaga et al., 2003; O'Malley et al., 2009;
Zhang et al., 2015k). In gastric cancer, cytoplasmic expression
levels of TOB1 were correlated with the depth of invasion,
differentiation grade and tumor-node-metastasis stage (Zhang et
al., 2015k). Down-regulation of TOB1 increased the metastasis,
invasion and proliferation of gastric cancer cells (Li et al.,
2015a).
[0579] Some reports have shown high staining of TOMM20 in papillary
thyroid cancer compared to noncancerous thyroid tissue. Others have
observed that epithelial cancer cells exhibited high levels of the
mitochondrial membrane marker TOMM20. On the contrary, no
significant difference in the mRNA expression of the TOMM20 gene
was found in prostate cancer tissue (Whitaker-Menezes et al., 2011;
Asmarinah et al., 2014; Curry et al., 2015). In gastric cancer,
over-expression of TOMM20 was correlated with reduced overall
survival and disease-free survival (Zhao et al., 2014c).
[0580] Over-expression of TP53I3 was found in papillary thyroid
carcinoma, gemcitabine resistant non-small cell lung cancer,
whereas it was down-regulated in esophageal squamous cell carcinoma
and diffuse large B cell lymphoma. In addition, variant genotypes
of (TGYCC)n repeats in the TP53I3 promoter were correlated with
risk of squamous cell carcinoma of the head and neck. Others have
reported an association of TP53I3 promoter VNTRs with generation of
invasive bladder cancer (Dadkhah et al., 2013; Ito et al., 2006;
Guan et al., 2013; Zhu et al., 2013a; Zhang et al., 2013a; Xu et
al., 2015b). Researchers have observed that TP53I3 silencing in
papillary thyroid carcinoma cell lines resulted in a reduction in
the activity of the PI3K/AKT/PTEN pathway (Xu et al., 2015b).
[0581] The TPR-MET rearrangement has been detected in several cell
lines derived from human tumors of non-hematopoietic origin as well
as in gastric carcinoma. One study has detected a TPR-NTRK1 fusion
in colorectal cancer, while TPR-ALK fusion has been seen in lung
adenocarcinoma. In addition, loss or deletion of TPR gene has been
reported in gastric cancer (Soman et al., 1991; Soman et al., 1990;
Cunningham et al., 1997; Yu et al., 2000; Choi et al., 2014;
Creancier et al., 2015). Recent work has revealed that TPR
depletion leads to G0/G1 phase arrest, which in turn induces a
senescent-like phenotype in tumor cell lines (David-Watine,
2011).
[0582] TPX2 was shown to be up-regulated in hepatocellular
carcinoma, pancreatic cancer, cervical cancer, medullary thyroid
cancer, colon cancer and prostate cancer (Vainio et al., 2012; Wei
et al., 2013; Yang et al., 2014d; Jiang et al., 2014b; Miwa et al.,
2015; Liang et al., 2015b). TPX2 is associated with poor prognosis
in hepatocellular carcinoma, poor overall survival and lower
disease free survival in high-grade serous epithelial ovarian
cancer, patient outcome and poor prognosis of esophageal squamous
cell carcinoma, development and progression of bladder carcinoma
and poor 5-year survival in lung adenocarcinoma (Li et al., 2013c;
Yan et al., 2013a; Hsu et al., 2014; Caceres-Gorriti et al., 2014;
Liang et al., 2015b). TPX2 is associated with colorectal cancer,
non-small cell lung cancer, head and neck squamous cell carcinoma,
metastasis of ER positive breast cancer, metastasis of
hepatocellular carcinoma, metastasis and disease stage of medullary
thyroid cancer and metastasis of colon cancer (Martens-de Kemp et
al., 2013; Wei et al., 2013; Yang et al., 2014d; Huang et al.,
2014c; Geiger et al., 2014; Takahashi et al., 2015). TPX2 is a
potential biomarker for early diagnosis and prognosis of
hepatocellular carcinoma and for prognosis of high-grade serous
epithelial ovarian cancer and colon cancer (Wei et al., 2013;
Caceres-Gorriti et al., 2014; Liang et al., 2015a).
[0583] TRIM6 was shown to regulate the transcriptional activity of
the proto-oncogene Myc (Sato et al., 2012b).
[0584] TRIP13 was shown to promote Mad2 localization to unattached
kinetochores in the spindle checkpoint response (Nelson et al.,
2015). TRIP13 over-expression was described as a hallmark of cancer
cells showing chromosomal instability (Wang et al., 2014d).
Premature mitotic checkpoint silencing triggered by TRIP13
over-expression was suggested to promote cancer development (Wang
et al., 2014d). TRIP13 was shown to be involved in modulating tumor
cell motility in breast cancer (Maurizio et al., 2016). High
expression of TRIP13 in squamous cell carcinoma of the head and
neck was shown to lead to aggressive, treatment-resistant tumors
and enhanced repair of DNA damage and promoted error-prone
non-homologous end joining (Banerjee et al., 2014). TRIP13 was
described as a putative marker of prostate cancer progression which
can be used to predict recurrence in prostate cancer when combined
with pre-operative PSA level and Gleason score (Larkin et al.,
2012). TRIP13 was described as one of several genes evidencing high
genomic copy number changes in early-stage non-small cell lung
cancer (Kang et al., 2008a).
[0585] Recent studies have implicated TRPS1 in several human
cancers such as breast cancer, colon cancer, osteosarcoma,
leukemia, endometrial cancer and prostate cancer (Chang et al.,
2004; Asou et al., 2007; Chen et al., 2010; Liang et al., 2012a;
Hong et al., 2013; Li et al., 2015f). In addition, TRPS1 expression
was correlated significantly with improved survival in patients
with breast cancer (Chen et al., 2010). Furthermore,
over-expression of TRPS1 induced angiogenesis by affecting the
expression of vascular endothelial growth factor in breast cancer
(Hu et al., 2014).
[0586] Mutations in the TRRAP gene were found in colorectal cancer
and in melanoma, whereas in thyroid and ovarian cancers mutations
in the TRRAP gene were absent (Wei et al., 2011; Murugan et al.,
2013; Mouradov et al., 2014; Zou et al., 2015). Furthermore,
knockdown of TRRAP resulted in a decreased self-renewal of cultured
brain tumor-initiating cells and sensitized the cells to
temozolomide-induced apoptosis (Wurdak et al., 2010).
[0587] A single nucleotide polymorphism of the TSC2 gene was
significantly associated with colon cancer. Furthermore,
down-regulation of TSC2 was observed in patients suffering from
hepatocellular carcinoma and acute myeloid leukemia. In one case, a
mutation in the TSC2 gene seemed to be responsible for pancreatic
neuroendocrine tumors. Others have noted elevated levels of
phosphorylated TSC2 in non-small cell lung carcinoma (Xu et al.,
2009; Yoshizawa et al., 2010; Slattery et al., 2010; Bombardieri et
al., 2013; Huynh et al., 2015). Recent work has demonstrated that
expression of TSC2 in ERC-18 cells increases susceptibility to
apoptosis induced by OKA and the phosphatidylinositol-3' kinase
inhibitor LY294002 (Kolb et al., 2005).
[0588] TSEN15 is a target of miRNA-449a, which functions as a tumor
suppressor in neuroblastoma. TSEN15 plays an important role in
mediating the differentiation-inducing function of miRNA-449a (Zhao
et al., 2015c). TSEN15 is associated with cell differentiation
potential in human fetal femur-derived cells (Mirmalek-Sani et al.,
2009).
[0589] TSGA13 was shown to be down-regulated in most types of human
carcinoma tissues compared to adjacent normal tissues except
glioblastoma and lung cancer. Hence, an association between TSGA13
and tumor malignancy is likely (Zhao et al., 2015a).
[0590] De-regulated expression of TUBA1A and some other genes,
caused by chromosomal rearrangements in radiation-transformed and
tumorigenic breast cell lines, might reflect early molecular events
in breast carcinogenesis (Unger et al., 2010). Using comparative
proteomic analysis of advanced serous epithelial ovarian carcinoma,
TUBA1A was identified as one potential predictor for
chemoresistance (Kim et al., 2011c).
[0591] The differential expression of TUBA1B in combination with
the expression of some other genes was associated with prognosis in
mantle cell lymphoma, prediction of relapse among patients with
stage II colorectal cancer and differentiation between uveal
melanomas that subsequently metastasized and those that did not
(Blenk et al., 2008; Agesen et al., 2012; Linge et al., 2012).
TUBA1B expression was up-regulated in hepatocellular cancer tissues
and proliferating hepatocellular cancer cells. An increased TUBA1B
expression was associated with poor overall survival and resistance
to paclitaxel of hepatocellular cancer patients (Lu et al., 2013).
In ovarian cancer cells, the reduced expression of TUBA1B was
associated with oxaliplatin resistance (Tummala et al., 2009).
[0592] The expression of TUBA1C was shown to be up-regulated in
osteosarcoma and HCV-associated hepatocellular cancer and may be a
potential biomarker for osteosarcoma tumorigenesis or
well-differentiated HCV-associated hepatocellular cancer (Li et
al., 2010; Kuramitsu et al., 2011).
[0593] The comparative proteomic analysis of esophageal squamous
cell carcinoma (ESCC) showed an increased expression of TUBA4A (Qi
et al., 2005).
[0594] In mouse liver, TUBA8 was induced after treatment with
phenobarbital, a non-genotoxic carcinogen. In hepatocellular
carcinoma cell lines, the over-expression of TUBA8 was shown to
affect cell growth, proliferation and migration (Kamino et al.,
2011).
[0595] Several publications have observed over-expression of TYK2
in human breast cancer cell lines, as well as in prostate cancers
and squamous cervical carcinomas. In contrast, lack of TYK2 in mice
has been linked to the development of Abelson-induced B lymphoid
leukemia and lymphoma. In addition, single nucleotide polymorphism
in the TYK2 gene has been associated with rectal cancer (Stoiber et
al., 2004; Ide et al., 2008; Song et al., 2008; Zhu et al., 2009;
Slattery et al., 2013). In prostate cancer cell lines, suppression
of Tyk2 with siRNA inhibited the ability of these cells to migrate
(Ide et al., 2008).
[0596] Recent work has identified a gain in copy number of the
UBE2H gene in hepatocellular carcinoma. Others have observed an
increase in the levels of UBE2H in breast cancer, whereas this was
not the case in colon cancer (Chen and Madura, 2005; Keng et al.,
2009).
[0597] Down-regulation of UBE2L6 has been observed in
nasopharyngeal carcinoma, whereas in esophageal squamous cell
carcinoma UBE2L6 was over-expressed (Dadkhah et al., 2013; Zhou et
al., 2015a). In addition, low levels of UBE2L6 have been linked
with poor outcome in patients suffering from nasopharyngeal
carcinoma (Zhou et al., 2015a). Moreover, UBE2L6 has been shown to
disrupt F-actin architecture and formation of focal adhesions in
breast cancer cell lines as well as promoting cell migration.
Furthermore, restored expression of UBE2L6 suppressed proliferation
and colony formation in nasopharyngeal carcinoma cells, while at
the same time inducing apoptosis (Desai et al., 2012; Zhou et al.,
2015a). Researchers have postulated that UBE2L6 could be used as a
biomarker of treatment response to bortezomib in patients with
acute promyelocytic leukemia (Takenokuchi et al., 2015).
[0598] Elevated levels of UBE2V1 expression were detected in breast
cancer samples as well as in cultured tumor cell lines. Moreover,
UBE2V1 gene has been identified to be associated with the
development of prostate cancer (Stubbs et al., 1999; Xiao et al.,
1998; Tanner et al., 1995). Researchers have shown that UBE2V1
induced cell migration and invasion in breast cancer. Similarly,
high levels of UBE2V1 promoted tumor growth and metastasis in a
xenograft mouse model. NSC697923, an inhibitor of UBE2V1 was able
to inhibit proliferation and survival of diffuse large B-cell
lymphoma cells (Pulvino et al., 2012; Wu et al., 2014b).
[0599] Some researchers have observed over-expression of UBE3C in
clear-cell renal cell carcinoma tissues compared with adjacent
normal tissues. Others have also found elevated levels of UBE3C in
hepatocellular carcinoma. In addition, up-regulation of UBE3C gene
was reported in myeloma side-population cells (Jiang et al., 2014a;
Tagawa, 2014; Wen et al., 2015). Furthermore, over-expression of
UBE3C in hepatocellular carcinoma tissues was associated with
decreased survival and early tumor recurrence in post-operative
hepatocellular carcinoma patients (Jiang et al., 2014a).
[0600] Researchers have identified a mutation in the UBE4B gene in
a patient suffering from neuroblastoma. Genome-wide association
study revealed that the UBE4B gene might be involved in hepatitis B
virus-related hepatocellular carcinoma. Others reported
over-expression of UBE4B in breast cancer and in brain tumors
(Krona et al., 2003; Zhang et al., 2010b; Wu et al., 2011b; Zhang
et al., 2014f). Moreover, down-regulation of UBE4B was correlated
with poor outcome in patients with neuroblastoma (Zage et al.,
2013).
[0601] UBR4 was shown to be associated with invasive micropapillary
carcinoma of the breast (Gruel et al., 2014).
[0602] UNC45A was shown to be up-regulated in breast carcinoma and
ovarian carcinoma (Guo et al., 2011; Bazzaro et al., 2007). UNC45A
is associated with metastasis in breast cancer (Guo et al., 2011).
UNC45A is associated with drug resistance in neuroblastoma (Epping
et al., 2009).
[0603] Novel germline sequence variations in UNG were detected in
patients affected by colorectal cancer with familial aggregation,
emphasizing that these variants could be involved in disease
susceptibility. In addition, UNG activity in colorectal tissue
appeared to be higher in tumor tissue compared to normal bowel
(Dusseau et al., 2001; Broderick et al., 2006; Marian et al., 2011;
Yin et al., 2014). Furthermore, knockdown of UNG induced apoptosis
in prostate cancer cell lines, reduced cell proliferation and
increased cellular sensitivity to genotoxic stress. Others have
observed that colon cancer cells lacking UNG are hypersensitive to
pemetrexed-induced uracil accumulation, which leads to cell cycle
arrest, DNA double strand break formation and apoptosis (Pulukuri
et al., 2009; Weeks et al., 2013).
[0604] UQCR11 is associated with renal cell carcinoma (Sarto et
al., 1997).
[0605] USP11 plays a major role in promyelocytic leukemia and
pancreatic cancer (Burkhart et al., 2013; Wu et al., 2014a).
[0606] USP28 was shown to be up-regulated in intestinal cancer,
bladder cancer, colon carcinoma and breast carcinoma (Guo et al.,
2014; Diefenbacher et al., 2014; Popov et al., 2007). USP28 is
associated with colorectal cancer and breast cancer (Wu et al.,
2013b; Diefenbacher et al., 2014). USP28 over-expression is
associated with low survival and poor prognosis in non-small cell
lung cancer patients (Zhang et al., 2015i). USP28 is a potential
prognostic marker for bladder cancer (Guo et al., 2014).
[0607] Several publications have found an association between USP9X
and various types of cancer including, breast cancer, lung cancer,
colon cancer, non-small cell lung cancer and low grade serous
ovarian tumors (Deng et al., 2007; Peddaboina et al., 2012; Peng et
al., 2015b; Hunter et al., 2015). Furthermore, elevated levels of
USP9X were correlated with positive lymph node metastasis, clinical
stage and a reduced overall survival rate in patients affected by
non-small cell lung cancer (Wang et al., 2015j). Silencing of USP9X
expression by siRNA resulted in cell apoptosis, inhibited cell
growth and cell migration in hepatocellular carcinoma cell lines
(Hu et al., 2015).
[0608] Over-expression of USP9Y has been observed in breast cancer
and prostate cancer. Recently, a USP9Y-TTTY15 fusion was identified
in a Chinese population suffering from prostate cancer. However,
others have demonstrated that the USP9Y-TTTY15 fusion is not
specific to prostate cancer, but it was also found in non-malignant
prostate tissues as well as non-malignant tissue from other organs
(Deng et al., 2007; Dasari et al., 2001; Ren et al., 2012; Ren et
al., 2014).
[0609] VCPIP1 was shown to be associated with breast cancer
(Kuznetsova et al., 2007). VCPIP1 is down-regulated in breast
cancer (Kuznetsova et al., 2007). VCPIP1 is one of the
de-ubiquitinating enzymes, being part of the ovarian tumor family
(OTU) (Enesa and Evans, 2014).
[0610] In lung adenocarcinoma patients, VPRBP was correlated with
poor prognosis (Wang et al., 2013a). Others have revealed that
down-regulation of VPRBP-mediated phosphorylation of Histone 2A
(H2AT120p) impeded cancer cell proliferation and xenograft tumor
progression (Kim et al., 2013b).
[0611] VPS13D was shown to be a phosphopeptide relevant for the
oncogenic phosphatidylinositol 3-kinase (PI3K) pathway which can be
regulated by PI3K pathway inhibiting drugs (Andersen et al.,
2010).
[0612] VTCN1 was shown to be up-regulated in lung cancer,
colorectal cancer, hepatocellular carcinoma, osteosarcoma, breast
cancer, cervical cancer, urothelial cell carcinoma, gastric cancer,
endometrial cancer, thyroid cancer and laryngeal carcinoma (Klatka
et al., 2013; Zhu et al., 2013b; Vanderstraeten et al., 2014; Shi
et al., 2014b; Fan et al., 2014; Wang et al., 2014g; Leong et al.,
2015; Dong and Ma, 2015; Zhang et al., 2015a; Peng et al., 2015a;
Xu et al., 2015a). VTCN1 is associated with poor overall survival
and higher recurrence probability in hepatocellular carcinoma and
poor overall survival in osteosarcoma, urothelial cell carcinoma,
pancreatic cancer, gastric cancer, cervical cancer, melanoma and
thyroid cancer (Zhu et al., 2013b; Seliger, 2014; Liu et al.,
2014f; Chen et al., 2014i; Fan et al., 2014; Dong and Ma, 2015;
Zhang et al., 2015a). VTCN1 is associated with clear cell renal
cell carcinoma (Xu et al., 2014c). VTCN1 expression levels were
shown to be inversely correlated with patient survival in ovarian
cancer (Smith et al., 2014). VTCN1 may be a potential prognostic
indicator of urothelial cell carcinoma and gastric cancer (Shi et
al., 2014b; Fan et al., 2014).
[0613] VWA1 is associated with clear-cell ovarian cancer (Cicek et
al., 2013).
[0614] VWA2 was shown to be associated with colorectal cancer (Hoff
et al., 2015). VWA2 was shown to be highly induced in stage II, III
and IV colon cancers, colon adenomas and colon cancer cell lines.
Thus, VWA2 is a novel candidate for development as a diagnostic
serum marker of early stage colon cancer (Xin et al., 2005).
[0615] VWA3A was shown to be associated with survival in ovarian
cancer (Madden et al., 2014).
[0616] VWDE is mutated and shows an oncogenic character in breast
cancer patients (Pongor et al., 2015).
[0617] WDFY3 was shown to be down-regulated in colorectal cancer
(Piepoli et al., 2012).
[0618] Recent studies have observed elevated levels of WHSC1
protein in several types of human cancers such as carcinomas of the
gastrointestinal tract (esophagus, stomach, colon, anal canal),
small cell lung carcinoma, prostate cancer and tumors of the
urinary bladder, female genitals and skin. Others have reported
that WHSC1 over-expression resulting from chromosomal translocation
significantly affected the tumorigenicity of multiple myeloma cells
in a xenograft model (Lauring et al., 2008; Hudlebusch et al.,
2011; Yang et al., 2012d). Knock-down of WHSC1 in prostate cancer
cell lines resulted in a reduction of cell proliferation, colony
formation in soft agar as well as decreased cell migration and
invasion. Similarly, in squamous cell carcinoma of the head and
neck cell knock-down of WHSC1 resulted in significant growth
suppression, induction of apoptosis, and delay of the cell-cycle
progression. Furthermore, WHSC1 expression has been shown to induce
cellular adhesion, clonogenic growth and tumorigenicity in multiple
myeloma (Kassambara et al., 2009; Ezponda et al., 2013; Saloura et
al., 2015).
[0619] Single nucleotide polymorphisms of the WRN gene have been
associated with the risk of breast cancer both in a German and
Australian population. Others have found a correlation between
single nucleotide polymorphisms of the WRN gene and susceptibility
for colorectal, prostate and esophageal cancers. In addition,
aberrant methylation of WRN was observed in specimens of cervical
cancer (Wirtenberger et al., 2006; Wang et al., 2011; Li et al.,
2012d; Masuda et al., 2012; Sun et al., 2015d; Zins et al., 2015).
Furthermore, siRNA-mediated silencing of WRN gene suppressed
carcinoma cell growth in vitro (Arai et al., 2011).
[0620] Accumulating evidence reveals that the WT1 gene is highly
expressed in different forms of tumors including acute myeloid
leukemias, acute lymphoid leukemias, hepatocellular carcinoma and
squamous cell carcinoma of the head and neck (Miwa et al., 1992;
Perugorria et al., 2009; Li et al., 2015d). Additionally,
over-expression of WT1 is a significant positive prognostic factor
in primary high-grade serous ovarian carcinoma regarding overall
survival and progression free survival. Similarly, overall survival
and disease-free survival was significantly lower in acute
myeloblastic leukemia patients with WT1 gene mutation. Others have
also reported a correlation between the WT1 variant rs2234593 and
relapse as well as overall survival in acute myeloid leukemia
(Niavarani et al., 2015; Taube et al., 2016; Toogeh et al.,
2016).
[0621] Some researchers have observed low XDH expression in
hepatocellular carcinomas, serous ovarian cancer and breast cancer.
However, others reported a significant increase in XDH activity in
bilharzial bladder cancer and non-bilharzial bladder cancer, brain
tumors and small-cell and non-small cell lung cancer (Kokoglu et
al., 1990; Stirpe et al., 2002; Linder et al., 2005; Kaynar et al.,
2005; Metwally et al., 2011; Linder et al., 2012). Moreover,
down-regulation of XDH was reported to be associated with poorer
prognosis in patients with serous ovarian cancer and breast cancer
(Linder et al., 2005; Linder et al., 2012).
[0622] XPO4 expression is down-regulated by promoter methylation in
hepatocellular cancer and associated with tumor size,
histopathological classification and a significantly poor prognosis
of patient's survival (Liang et al., 2011; Zhang et al., 2014a).
Mutation of the catalytic subunit of the PI3K leads to a highly
activated Akt/mTOR pathway and down-regulation of the tumor
suppressor genes Pten, Xpo4 and Dlc1 (Kudo et al., 2011).
[0623] YBX1 has been shown to be up-regulated in various types of
cancer, including colorectal, gastric, multiple myeloma and breast
cancer (Bargou et al., 1997; Chatterjee et al., 2008; Wu et al.,
2012g; Yan et al., 2014b). In breast cancer, over-expression of
YBX1 was neither associated with lymph node status nor high
histological grade, but with ER negativity, HER2 positivity and it
had an adverse impact on 5-year overall survival (Wang et al.,
2015g). Researchers have shown that YBX1 may promote the
proliferation, apoptosis resistance, invasion and migration of
colorectal cancer cells by regulating epithelial-mesenchymal
transition (Yan et al., 2014c).
[0624] The TUTase ZCCHC6 was shown to be recruited by the
tumorigenesis associated RNA-binding protein Lin28 to block let-7
biogenesis. Restoring let-7 expression in cancer through TUTase
inhibitors could be exploited in future drug discovery (Lin and
Gregory, 2015).
[0625] ZNF583 was described as a potential biomarker for colorectal
cancer (Mori et al., 2011).
[0626] ZNF700 was shown to be a capture antigen for the detection
of autoantibodies in colorectal cancer. In a panel with other zinc
finger proteins, ZNF-specific autoantibody detection allowed the
detection of colorectal cancer (O'Reilly et al., 2015).
[0627] ZNFX1 could function as a novel prostate cancer antigen
(Dunphy and McNeel, 2005).
[0628] ZRANB2 has been shown to be over-expressed in grade III
ovarian serous papillary carcinoma (Schaner et al., 2003; Mangs and
Morris, 2008).
[0629] ZWINT was shown to be associated with the arrest of prostate
cancer cell cycle progression upon inhibition of COX-2 (Bieniek et
al., 2014). ZWINT expression in chronic lymphocytic leukemia cells
in lymph nodes was shown to be correlated with clinical outcome
(Gilling et al., 2012). ZWINT was described as an androgen receptor
target gene which was shown to be up-regulated in
castration-resistant prostate cancer (Urbanucci et al., 2012).
ZWINT was described as a gene of particular predictive value in a
prognostic model of pulmonary adenocarcinoma (Endoh et al.,
2004).
[0630] ZYG11A serves as an oncogene in non-small cell lung cancer
and influences CCNE1 expression (Wang et al., 2016b).
[0631] ZZEF1 was described to be potentially linked to cancer and
is located in a chromosome region associated with medulloblastomas
(Cvekl, Jr. et al., 2004).
DETAILED DESCRIPTION OF THE INVENTION
[0632] Stimulation of an immune response is dependent upon the
presence of antigens recognized as foreign by the host immune
system. The discovery of the existence of tumor associated antigens
has raised the possibility of using a host's immune system to
intervene in tumor growth. Various mechanisms of harnessing both
the humoral and cellular arms of the immune system are currently
being explored for cancer immunotherapy.
[0633] Specific elements of the cellular immune response are
capable of specifically recognizing and destroying tumor cells. The
isolation of T-cells from tumor-infiltrating cell populations or
from peripheral blood suggests that such cells play an important
role in natural immune defense against cancer. CD8-positive T-cells
in particular, which recognize class I molecules of the major
histocompatibility complex (MHC)-bearing peptides of usually 8 to
10 amino acid residues derived from proteins or defect ribosomal
products (DRIPS) located in the cytosol, play an important role in
this response. The MHC-molecules of the human are also designated
as human leukocyte-antigens (HLA).
[0634] As used herein and except as noted otherwise all terms are
defined as given below.
[0635] The term "T-cell response" means the specific proliferation
and activation of effector functions induced by a peptide in vitro
or in vivo. For MHC class I restricted cytotoxic T cells, effector
functions may be lysis of peptide-pulsed, peptide-precursor pulsed
or naturally peptide-presenting target cells, secretion of
cytokines, preferably Interferon-gamma, TNF-alpha, or IL-2 induced
by peptide, secretion of effector molecules, preferably granzymes
or perforins induced by peptide, or degranulation.
[0636] The term "peptide" is used herein to designate a series of
amino acid residues, connected one to the other typically by
peptide bonds between the alpha-amino and carbonyl groups of the
adjacent amino acids. The peptides are preferably 9 amino acids in
length, but can be as short as 8 amino acids in length, and as long
as 10, 11, 12, 13, or 14 or longer, and in case of MHC class II
peptides (elongated variants of the peptides of the invention) they
can be as long as 15, 16, 17, 18, 19 or 20 or more amino acids in
length.
[0637] Furthermore, the term "peptide" shall include salts of a
series of amino acid residues, connected one to the other typically
by peptide bonds between the alpha-amino and carbonyl groups of the
adjacent amino acids. Preferably, the salts are pharmaceutical
acceptable salts of the peptides, such as, for example, the
chloride or acetate (trifluoroacetate) salts. It has to be noted
that the salts of the peptides according to the present invention
differ substantially from the peptides in their state(s) in vivo,
as the peptides are not salts in vivo.
[0638] The term "peptide" shall also include "oligopeptide". The
term "oligopeptide" is used herein to designate a series of amino
acid residues, connected one to the other typically by peptide
bonds between the alpha-amino and carbonyl groups of the adjacent
amino acids. The length of the oligopeptide is not critical to the
invention, as long as the correct epitope or epitopes are
maintained therein. The oligopeptides are typically less than about
30 amino acid residues in length, and greater than about 15 amino
acids in length.
[0639] The term "polypeptide" designates a series of amino acid
residues, connected one to the other typically by peptide bonds
between the alpha-amino and carbonyl groups of the adjacent amino
acids. The length of the polypeptide is not critical to the
invention as long as the correct epitopes are maintained. In
contrast to the terms peptide or oligopeptide, the term polypeptide
is meant to refer to molecules containing more than about 30 amino
acid residues.
[0640] A peptide, oligopeptide, protein or polynucleotide coding
for such a molecule is "immunogenic" (and thus is an "immunogen"
within the present invention), if it is capable of inducing an
immune response. In the case of the present invention,
immunogenicity is more specifically defined as the ability to
induce a T-cell response. Thus, an "immunogen" would be a molecule
that is capable of inducing an immune response, and in the case of
the present invention, a molecule capable of inducing a T-cell
response. In another aspect, the immunogen can be the peptide, the
complex of the peptide with MHC, oligopeptide, and/or protein that
is used to raise specific antibodies or TCRs against it.
[0641] A class I T cell "epitope" requires a short peptide that is
bound to a class I MHC receptor, forming a ternary complex (MHC
class I alpha chain, beta-2-microglobulin, and peptide) that can be
recognized by a T cell bearing a matching T-cell receptor binding
to the MHC/peptide complex with appropriate affinity. Peptides
binding to MHC class I molecules are typically 8-14 amino acids in
length, and most typically 9 amino acids in length.
[0642] In humans there are three different genetic loci that encode
MHC class I molecules (the MHC-molecules of the human are also
designated human leukocyte antigens (HLA)): HLA-A, HLA-B, and
HLA-C. HLA-A*01, HLA-A*02, and HLA-B*07 are examples of different
MHC class I alleles that can be expressed from these loci.
TABLE-US-00006 TABLE 6 Expression frequencies F of HLA-A*02 and
HLA-A*24 and the most frequent HLA-DR serotypes. Frequencies are
deduced from haplotype frequencies Gf within the American
population adapted from Mori et al. (Mori et al., 1997) employing
the Hardy-Weinberg formula F = 1 - (1 - Gf).sup.2. Combinations of
A*02 or A*24 with certain HLA-DR alleles might be enriched or less
frequent than expected from their single frequencies due to linkage
disequilibrium. For details refer to Chanock et al. (Chanock et
al., 2004). Calculated phenotype Allele Population from allele
frequency A*02 Caucasian (North America) 49.1% A*02 African
American (North America) 34.1% A*02 Asian American (North America)
43.2% A*02 Latin American (North American) 48.3% DR1 Caucasian
(North America) 19.4% DR2 Caucasian (North America) 28.2% DR3
Caucasian (North America) 20.6% DR4 Caucasian (North America) 30.7%
DR5 Caucasian (North America) 23.3% DR6 Caucasian (North America)
26.7% DR7 Caucasian (North America) 24.8% DR8 Caucasian (North
America) 5.7% DR9 Caucasian (North America) 2.1% DR1 African
(North) American 13.20% DR2 African (North) American 29.80% DR3
African (North) American 24.80% DR4 African (North) American 11.10%
DR5 African (North) American 31.10% DR6 African (North) American
33.70% DR7 African (North) American 19.20% DR8 African (North)
American 12.10% DR9 African (North) American 5.80% DR1 Asian
(North) American 6.80% DR2 Asian (North) American 33.80% DR3 Asian
(North) American 9.20% DR4 Asian (North) American 28.60% DR5 Asian
(North) American 30.00% DR6 Asian (North) American 25.10% DR7 Asian
(North) American 13.40% DR8 Asian (North) American 12.70% DR9 Asian
(North) American 18.60% DR1 Latin (North) American 15.30% DR2 Latin
(North) American 21.20% DR3 Latin (North) American 15.20% DR4 Latin
(North) American 36.80% DR5 Latin (North) American 20.00% DR6 Latin
(North) American 31.10% DR7 Latin (North) American 20.20% DR8 Latin
(North) American 18.60% DR9 Latin (North) American 2.10% A*24
Philippines 65% A*24 Russia Nenets 61% A*24:02 Japan 59% A*24
Malaysia 58% A*24:02 Philippines 54% A*24 India 47% A*24 South
Korea 40% A*24 Sri Lanka 37% A*24 China 32% A*24:02 India 29% A*24
Australia West 22% A*24 USA 22% A*24 Russia Samara 20% A*24 South
America 20% A*24 Europe 18%
[0643] The peptides of the invention, preferably when included into
a vaccine of the invention as described herein bind to A*02. A
vaccine may also include pan-binding MHC class II peptides.
Therefore, the vaccine of the invention can be used to treat cancer
in patients that are A*02 positive, whereas no selection for MHC
class II allotypes is necessary due to the pan-binding nature of
these peptides.
[0644] If A*02 peptides of the invention are combined with peptides
binding to another allele, for example A*24, a higher percentage of
any patient population can be treated compared with addressing
either MHC class I allele alone. While in most populations less
than 50% of patients could be addressed by either allele alone, a
vaccine comprising HLA-A*24 and HLA-A*02 epitopes can treat at
least 60% of patients in any relevant population. Specifically, the
following percentages of patients will be positive for at least one
of these alleles in various regions: USA 61%, Western Europe 62%,
China 75%, South Korea 77%, Japan 86% (calculated from
www.allelefrequencies.net).
[0645] In a preferred embodiment, the term "nucleotide sequence"
refers to a heteropolymer of deoxyribonucleotides.
[0646] The nucleotide sequence coding for a particular peptide,
oligopeptide, or polypeptide may be naturally occurring or they may
be synthetically constructed. Generally, DNA segments encoding the
peptides, polypeptides, and proteins of this invention are
assembled from cDNA fragments and short oligonucleotide linkers, or
from a series of oligonucleotides, to provide a synthetic gene that
is capable of being expressed in a recombinant transcriptional unit
comprising regulatory elements derived from a microbial or viral
operon.
[0647] As used herein the term "a nucleotide coding for (or
encoding) a peptide" refers to a nucleotide sequence coding for the
peptide including artificial (man-made) start and stop codons
compatible for the biological system the sequence is to be
expressed by, for example, a dendritic cell or another cell system
useful for the production of TCRs.
[0648] As used herein, reference to a nucleic acid sequence
includes both single stranded and double stranded nucleic acid.
Thus, for example for DNA, the specific sequence, unless the
context indicates otherwise, refers to the single strand DNA of
such sequence, the duplex of such sequence with its complement
(double stranded DNA) and the complement of such sequence.
[0649] The term "coding region" refers to that portion of a gene
which either naturally or normally codes for the expression product
of that gene in its natural genomic environment, i.e., the region
coding in vivo for the native expression product of the gene.
[0650] The coding region can be derived from a non-mutated
("normal"), mutated or altered gene, or can even be derived from a
DNA sequence, or gene, wholly synthesized in the laboratory using
methods well known to those of skill in the art of DNA
synthesis.
[0651] The term "expression product" means the polypeptide or
protein that is the natural translation product of the gene and any
nucleic acid sequence coding equivalents resulting from genetic
code degeneracy and thus coding for the same amino acid(s).
[0652] The term "fragment", when referring to a coding sequence,
means a portion of DNA comprising less than the complete coding
region, whose expression product retains essentially the same
biological function or activity as the expression product of the
complete coding region.
[0653] The term "DNA segment" refers to a DNA polymer, in the form
of a separate fragment or as a component of a larger DNA construct,
which has been derived from DNA isolated at least once in
substantially pure form, i.e., free of contaminating endogenous
materials and in a quantity or concentration enabling
identification, manipulation, and recovery of the segment and its
component nucleotide sequences by standard biochemical methods, for
example, by using a cloning vector. Such segments are provided in
the form of an open reading frame uninterrupted by internal
non-translated sequences, or introns, which are typically present
in eukaryotic genes. Sequences of non-translated DNA may be present
downstream from the open reading frame, where the same do not
interfere with manipulation or expression of the coding
regions.
[0654] The term "primer" means a short nucleic acid sequence that
can be paired with one strand of DNA and provides a free 3'-OH end
at which a DNA polymerase starts synthesis of a deoxyribonucleotide
chain.
[0655] The term "promoter" means a region of DNA involved in
binding of RNA polymerase to initiate transcription.
[0656] The term "isolated" means that the material is removed from
its original environment (e.g., the natural environment, if it is
naturally occurring). For example, a naturally-occurring
polynucleotide or polypeptide present in a living animal is not
isolated, but the same polynucleotide or polypeptide, separated
from some or all of the coexisting materials in the natural system,
is isolated. Such polynucleotides could be part of a vector and/or
such polynucleotides or polypeptides could be part of a
composition, and still be isolated in that such vector or
composition is not part of its natural environment.
[0657] The polynucleotides, and recombinant or immunogenic
polypeptides, disclosed in accordance with the present invention
may also be in "purified" form. The term "purified" does not
require absolute purity; rather, it is intended as a relative
definition, and can include preparations that are highly purified
or preparations that are only partially purified, as those terms
are understood by those of skill in the relevant art. For example,
individual clones isolated from a cDNA library have been
conventionally purified to electrophoretic homogeneity.
Purification of starting material or natural material to at least
one order of magnitude, preferably two or three orders, and more
preferably four or five orders of magnitude is expressly
contemplated. Furthermore, a claimed polypeptide which has a purity
of preferably 99.999%, or at least 99.99% or 99.9%; and even
desirably 99% by weight or greater is expressly encompassed.
[0658] The nucleic acids and polypeptide expression products
disclosed according to the present invention, as well as expression
vectors containing such nucleic acids and/or such polypeptides, may
be in "enriched form". As used herein, the term "enriched" means
that the concentration of the material is at least about 2, 5, 10,
100, or 1000 times its natural concentration (for example),
advantageously 0.01%, by weight, preferably at least about 0.1% by
weight. Enriched preparations of about 0.5%, 1%, 5%, 10%, and 20%
by weight are also contemplated. The sequences, constructs,
vectors, clones, and other materials comprising the present
invention can advantageously be in enriched or isolated form. The
term "active fragment" means a fragment, usually of a peptide,
polypeptide or nucleic acid sequence, that generates an immune
response (i.e., has immunogenic activity) when administered, alone
or optionally with a suitable adjuvant or in a vector, to an
animal, such as a mammal, for example, a rabbit or a mouse, and
also including a human, such immune response taking the form of
stimulating a T-cell response within the recipient animal, such as
a human. Alternatively, the "active fragment" may also be used to
induce a T-cell response in vitro.
[0659] As used herein, the terms "portion", "segment" and
"fragment", when used in relation to polypeptides, refer to a
continuous sequence of residues, such as amino acid residues, which
sequence forms a subset of a larger sequence. For example, if a
polypeptide were subjected to treatment with any of the common
endopeptidases, such as trypsin or chymotrypsin, the oligopeptides
resulting from such treatment would represent portions, segments or
fragments of the starting polypeptide. When used in relation to
polynucleotides, these terms refer to the products produced by
treatment of said polynucleotides with any of the
endonucleases.
[0660] In accordance with the present invention, the term "percent
identity" or "percent identical", when referring to a sequence,
means that a sequence is compared to a claimed or described
sequence after alignment of the sequence to be compared (the
"Compared Sequence") with the described or claimed sequence (the
"Reference Sequence"). The percent identity is then determined
according to the following formula:
percent identity=100[1-(C/R)]
wherein C is the number of differences between the Reference
Sequence and the Compared Sequence over the length of alignment
between the Reference Sequence and the Compared Sequence, wherein
(i) each base or amino acid in the Reference Sequence that does not
have a corresponding aligned base or amino acid in the Compared
Sequence and (ii) each gap in the Reference Sequence and (iii) each
aligned base or amino acid in the Reference Sequence that is
different from an aligned base or amino acid in the Compared
Sequence, constitutes a difference and (iiii) the alignment has to
start at position 1 of the aligned sequences; and R is the number
of bases or amino acids in the Reference Sequence over the length
of the alignment with the Compared Sequence with any gap created in
the Reference Sequence also being counted as a base or amino
acid.
[0661] If an alignment exists between the Compared Sequence and the
Reference Sequence for which the percent identity as calculated
above is about equal to or greater than a specified minimum Percent
Identity, then the Compared Sequence has the specified minimum
percent identity to the Reference Sequence even though alignments
may exist in which the herein above calculated percent identity is
less than the specified percent identity.
[0662] As mentioned above, the present invention thus provides a
peptide comprising a sequence that is selected from the group of
consisting of SEQ ID NO: 1 to SEQ ID NO: 640 or a variant thereof
which is 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 640, or a
variant thereof that will induce T cells cross-reacting with said
peptide. The peptides of the invention have the ability to bind to
a molecule of the human major histocompatibility complex (MHC)
class-I or elongated versions of said peptides to class II.
[0663] In the present invention, the term "homologous" refers to
the degree of identity (see percent identity above) between
sequences of two amino acid sequences, i.e. peptide or polypeptide
sequences. The aforementioned "homology" is determined by comparing
two sequences aligned under optimal conditions over the sequences
to be compared. Such a sequence homology can be calculated by
creating an alignment using, for example, the ClustalW algorithm.
Commonly available sequence analysis software, more specifically,
Vector NTI, GENETYX or other tools are provided by public
databases.
[0664] A person skilled in the art will be able to assess, whether
T cells induced by a variant of a specific peptide will be able to
cross-react with the peptide itself (Appay et al., 2006; Colombetti
et al., 2006; Fong et al., 2001; Zaremba et al., 1997).
[0665] By a "variant" of the given amino acid sequence the
inventors mean that the side chains of, for example, one or two of
the amino acid residues are altered (for example by replacing them
with the side chain of another naturally occurring amino acid
residue or some other side chain) such that the peptide is still
able to bind to an HLA molecule in substantially the same way as a
peptide consisting of the given amino acid sequence in consisting
of SEQ ID NO: 1 to SEQ ID NO: 640. For example, a peptide may be
modified so that it at least maintains, if not improves, the
ability to interact with and bind to the binding groove of a
suitable MHC molecule, such as HLA-A*02 or -DR, and in that way it
at least maintains, if not improves, the ability to bind to the TCR
of activated T cells.
[0666] These T cells can subsequently cross-react with cells and
kill cells that express a polypeptide that contains the natural
amino acid sequence of the cognate peptide as defined in the
aspects of the invention. As can be derived from the scientific
literature and databases (Rammensee et al., 1999; Godkin et al.,
1997), certain positions of HLA binding peptides are typically
anchor residues forming a core sequence fitting to the binding
motif of the HLA receptor, which is defined by polar,
electrophysical, hydrophobic and spatial properties of the
polypeptide chains constituting the binding groove. Thus, one
skilled in the art would be able to modify the amino acid sequences
set forth in SEQ ID NO: 1 to SEQ ID NO 640, by maintaining the
known anchor residues, and would be able to determine whether such
variants maintain the ability to bind MHC class I or II molecules.
The variants of the present invention retain the ability to bind to
the TCR of activated T cells, which can subsequently cross-react
with and kill cells that express a polypeptide containing the
natural amino acid sequence of the cognate peptide as defined in
the aspects of the invention.
[0667] The original (unmodified) peptides as disclosed herein can
be modified by the substitution of one or more residues at
different, possibly selective, sites within the peptide chain, if
not otherwise stated. Preferably those substitutions are located at
the end of the amino acid chain. Such substitutions may be of a
conservative nature, for example, where one amino acid is replaced
by an amino acid of similar structure and characteristics, such as
where a hydrophobic amino acid is replaced by another hydrophobic
amino acid. Even more conservative would be replacement of amino
acids of the same or similar size and chemical nature, such as
where leucine is replaced by isoleucine. In studies of sequence
variations in families of naturally occurring homologous proteins,
certain amino acid substitutions are more often tolerated than
others, and these are often show correlation with similarities in
size, charge, polarity, and hydrophobicity between the original
amino acid and its replacement, and such is the basis for defining
"conservative substitutions."
[0668] Conservative substitutions are herein defined as exchanges
within one of the following five groups: Group 1-small aliphatic,
nonpolar or slightly polar residues (Ala, Ser, Thr, Pro, Gly);
Group 2-polar, negatively charged residues and their amides (Asp,
Asn, Glu, Gln); Group 3-polar, positively charged residues (His,
Arg, Lys); Group 4-large, aliphatic, nonpolar residues (Met, Leu,
Ile, Val, Cys); and Group 5-large, aromatic residues (Phe, Tyr,
Trp).
[0669] Less conservative substitutions might involve the
replacement of one amino acid by another that has similar
characteristics but is somewhat different in size, such as
replacement of an alanine by an isoleucine residue. Highly
non-conservative replacements might involve substituting an acidic
amino acid for one that is polar, or even for one that is basic in
character. Such "radical" substitutions cannot, however, be
dismissed as potentially ineffective since chemical effects are not
totally predictable and radical substitutions might well give rise
to serendipitous effects not otherwise predictable from simple
chemical principles.
[0670] Of course, such substitutions may involve structures other
than the common L-amino acids. Thus, D-amino acids might be
substituted for the L-amino acids commonly found in the antigenic
peptides of the invention and yet still be encompassed by the
disclosure herein. In addition, non-standard amino acids (i.e.,
other than the common naturally occurring proteinogenic amino
acids) may also be used for substitution purposes to produce
immunogens and immunogenic polypeptides according to the present
invention.
[0671] If substitutions at more than one position are found to
result in a peptide with substantially equivalent or greater
antigenic activity as defined below, then combinations of those
substitutions will be tested to determine if the combined
substitutions result in additive or synergistic effects on the
antigenicity of the peptide. At most, no more than 4 positions
within the peptide would be simultaneously substituted.
[0672] A peptide consisting essentially of the amino acid sequence
as indicated herein can have one or two non-anchor amino acids (see
below regarding the anchor motif) exchanged without that the
ability to bind to a molecule of the human major histocompatibility
complex (MHC) class-I or -II is substantially changed or is
negatively affected, when compared to the non-modified peptide. In
another embodiment, in a peptide consisting essentially of the
amino acid sequence as indicated herein, one or two amino acids can
be exchanged with their conservative exchange partners (see herein
below) without that the ability to bind to a molecule of the human
major histocompatibility complex (MHC) class-I or -II is
substantially changed, or is negatively affected, when compared to
the non-modified peptide.
[0673] The amino acid residues that do not substantially contribute
to interactions with the T-cell receptor can be modified by
replacement with other amino acids whose incorporation does not
substantially affect T-cell reactivity and does not eliminate
binding to the relevant MHC. Thus, apart from the proviso given,
the peptide of the invention may be any peptide (by which term the
inventors include oligopeptide or polypeptide), which includes the
amino acid sequences or a portion or variant thereof as given.
TABLE-US-00007 TABLE 7 Variants and motif of the peptides according
to SEQ ID NO: 20, 40, and 217 Position 1 2 3 4 5 6 7 8 9 SEQ ID NO.
20 R M I E Y F I D V Variants I L A L I L L L L A A I A L A A A V I
V L V V A T I T L T T A Q I Q L Q Q A SEQ ID NO. 40 T L L V K V F S
V Variants I L I I I I A M L M I M M A A L A I A A A V L V I V V A
T L T I T T A Q L Q I Q Q A SEQ ID NO. 217 A L I H P V S T V
Variants L I A M L M I M M A A L A I A A A V L V I V V A T L T I T
T A Q L Q I Q Q A
[0674] Longer (elongated) peptides may also be suitable. It is
possible that MHC class I epitopes, although usually between 8 and
11 amino acids long, are generated by peptide processing from
longer peptides or proteins that include the actual epitope. It is
preferred that the residues that flank the actual epitope are
residues that do not substantially affect proteolytic cleavage
necessary to expose the actual epitope during processing.
[0675] The peptides of the invention can be elongated by up to four
amino acids, that is 1, 2, 3 or 4 amino acids can be added to
either end in any combination between 4:0 and 0:4. Combinations of
the elongations according to the invention can be found in Table
8.
TABLE-US-00008 TABLE 8 Combinations of the elongations of peptides
of the invention C-terminus N-terminus 4 0 3 0 or 1 2 0 or 1 or 2 1
0 or 1 or 2 or 3 0 0 or 1 or 2 or 3 or 4 N-terminus C-terminus 4 0
3 0 or 1 2 0 or 1 or 2 C-terminus N-terminus 1 0 or 1 or 2 or 3 0 0
or 1 or 2 or 3 or 4
[0676] The amino acids for the elongation/extension can be the
peptides of the original sequence of the protein or any other amino
acid(s). The elongation can be used to enhance the stability or
solubility of the peptides.
[0677] Thus, the epitopes of the present invention may be identical
to naturally occurring tumor-associated or tumor-specific epitopes
or may include epitopes that differ by no more than four residues
from the reference peptide, as long as they have substantially
identical antigenic activity.
[0678] In an alternative embodiment, the peptide is elongated on
either or both sides by more than 4 amino acids, preferably to a
total length of up to 30 amino acids. This may lead to MHC class II
binding peptides. Binding to MHC class II can be tested by methods
known in the art.
[0679] Accordingly, the present invention provides peptides and
variants of MHC class I epitopes, wherein the peptide or variant
has an overall length of between 8 and 100, preferably between 8
and 30, and most preferred between 8 and 14, namely 8, 9, 10, 11,
12, 13, 14 amino acids, in case of the elongated class II binding
peptides the length can also be 15, 16, 17, 18, 19, 20, 21 or 22
amino acids.
[0680] Of course, the peptide or variant according to the present
invention will have the ability to bind to a molecule of the human
major histocompatibility complex (MHC) class I or II. Binding of a
peptide or a variant to a MHC complex may be tested by methods
known in the art.
[0681] Preferably, when the T cells specific for a peptide
according to the present invention are tested against the
substituted peptides, the peptide concentration at which the
substituted peptides achieve half the maximal increase in lysis
relative to background is no more than about 1 mM, preferably no
more than about 1 .mu.M, more preferably no more than about 1 nM,
and still more preferably no more than about 100 pM, and most
preferably no more than about 10 pM. It is also preferred that the
substituted peptide be recognized by T cells from more than one
individual, at least two, and more preferably three
individuals.
[0682] In a particularly preferred embodiment of the invention the
peptide consists or consists essentially of an amino acid sequence
according to SEQ ID NO: 1 to SEQ ID NO: 640.
[0683] "Consisting essentially of" shall mean that a peptide
according to the present invention, in addition to the sequence
according to any of SEQ ID NO: 1 to SEQ ID NO 640 or a variant
thereof contains additional N- and/or C-terminally located
stretches of amino acids that are not necessarily forming part of
the peptide that functions as an epitope for MHC molecules
epitope.
[0684] Nevertheless, these stretches can be important to provide an
efficient introduction of the peptide according to the present
invention into the cells. In one embodiment of the present
invention, the peptide is part of a fusion protein which comprises,
for example, the 80 N-terminal amino acids of the HLA-DR
antigen-associated invariant chain (p33, in the following "Ii") as
derived from the NCBI, GenBank Accession number X00497. In other
fusions, the peptides of the present invention can be fused to an
antibody as described herein, or a functional part thereof, in
particular into a sequence of an antibody, so as to be specifically
targeted by said antibody, or, for example, to or into an antibody
that is specific for dendritic cells as described herein.
[0685] In addition, the peptide or variant may be modified further
to improve stability and/or binding to MHC molecules in order to
elicit a stronger immune response. Methods for such an optimization
of a peptide sequence are well known in the art and include, for
example, the introduction of reverse peptide bonds or non-peptide
bonds.
[0686] In a reverse peptide bond amino acid residues are not joined
by peptide (--CO--NH--) linkages but the peptide bond is reversed.
Such retro-inverso peptidomimetics may be made using methods known
in the art, for example such as those described in Meziere et al
(1997) (Meziere et al., 1997), incorporated herein by reference.
This approach involves making pseudopeptides containing changes
involving the backbone, and not the orientation of side chains.
Meziere et al. (Meziere et al., 1997) show that for MHC binding and
T helper cell responses, these pseudopeptides are useful.
Retro-inverse peptides, which contain NH--CO bonds instead of
CO--NH peptide bonds, are much more resistant to proteolysis.
[0687] A non-peptide bond is, for example, --CH.sub.2--NH,
--CH.sub.2S--, --CH.sub.2CH.sub.2--, --CH.dbd.CH--, --COCH.sub.2--,
--CH(OH)CH.sub.2--, and --CH.sub.2SO--. U.S. Pat. No. 4,897,445
provides a method for the solid phase synthesis of non-peptide
bonds (--CH.sub.2--NH) in polypeptide chains which involves
polypeptides synthesized by standard procedures and the non-peptide
bond synthesized by reacting an amino aldehyde and an amino acid in
the presence of NaCNBH.sub.3.
[0688] Peptides comprising the sequences described above may be
synthesized with additional chemical groups present at their amino
and/or carboxy termini, to enhance the stability, bioavailability,
and/or affinity of the peptides. For example, hydrophobic groups
such as carbobenzoxyl, dansyl, or t-butyloxycarbonyl groups may be
added to the peptides' amino termini. Likewise, an acetyl group or
a 9-fluorenylmethoxy-carbonyl group may be placed at the peptides'
amino termini. Additionally, the hydrophobic group,
t-butyloxycarbonyl, or an amido group may be added to the peptides'
carboxy termini.
[0689] Further, the peptides of the invention may be synthesized to
alter their steric configuration. For example, the D-isomer of one
or more of the amino acid residues of the peptide may be used,
rather than the usual L-isomer. Still further, at least one of the
amino acid residues of the peptides of the invention may be
substituted by one of the well-known non-naturally occurring amino
acid residues. Alterations such as these may serve to increase the
stability, bioavailability and/or binding action of the peptides of
the invention.
[0690] Similarly, a peptide or variant of the invention may be
modified chemically by reacting specific amino acids either before
or after synthesis of the peptide. Examples for such modifications
are well known in the art and are summarized e.g. in R. Lundblad,
Chemical Reagents for Protein Modification, 3rd ed. CRC Press, 2004
(Lundblad, 2004), which is incorporated herein by reference.
Chemical modification of amino acids includes but is not limited
to, modification by acylation, amidination, pyridoxylation of
lysine, reductive alkylation, trinitrobenzylation of amino groups
with 2,4,6-trinitrobenzene sulphonic acid (TNBS), amide
modification of carboxyl groups and sulphydryl modification by
performic acid oxidation of cysteine to cysteic acid, formation of
mercurial derivatives, formation of mixed disulphides with other
thiol compounds, reaction with maleimide, carboxymethylation with
iodoacetic acid or iodoacetamide and carbamoylation with cyanate at
alkaline pH, although without limitation thereto. In this regard,
the skilled person is referred to Chapter 15 of Current Protocols
In Protein Science, Eds. Coligan et al. (John Wiley and Sons NY
1995-2000) (Coligan et al., 1995) for more extensive methodology
relating to chemical modification of proteins.
[0691] Briefly, modification of e.g. arginyl residues in proteins
is often based on the reaction of vicinal dicarbonyl compounds such
as phenylglyoxal, 2,3-butanedione, and 1,2-cyclohexanedione to form
an adduct. Another example is the reaction of methylglyoxal with
arginine residues. Cysteine can be modified without concomitant
modification of other nucleophilic sites such as lysine and
histidine. As a result, a large number of reagents are available
for the modification of cysteine. The websites of companies such as
Sigma-Aldrich (http://www.sigma-aldrich.com) provide information on
specific reagents.
[0692] Selective reduction of disulfide bonds in proteins is also
common. Disulfide bonds can be formed and oxidized during the heat
treatment of biopharmaceuticals. Woodward's Reagent K may be used
to modify specific glutamic acid residues.
N-(3-(dimethylamino)propyl)-N'-ethylcarbodiimide can be used to
form intra-molecular crosslinks between a lysine residue and a
glutamic acid residue. For example, diethylpyrocarbonate is a
reagent for the modification of histidyl residues in proteins.
Histidine can also be modified using 4-hydroxy-2-nonenal. The
reaction of lysine residues and other .alpha.-amino groups is, for
example, useful in binding of peptides to surfaces or the
cross-linking of proteins/peptides. Lysine is the site of
attachment of poly(ethylene)glycol and the major site of
modification in the glycosylation of proteins. Methionine residues
in proteins can be modified with e.g. iodoacetamide,
bromoethylamine, and chloramine T.
[0693] Tetranitromethane and N-acetylimidazole can be used for the
modification of tyrosyl residues. Cross-linking via the formation
of dityrosine can be accomplished with hydrogen peroxide/copper
ions.
[0694] Recent studies on the modification of tryptophan have used
N-bromosuccinimide, 2-hydroxy-5-nitrobenzyl bromide or
3-bromo-3-methyl-2-(2-nitrophenylmercapto)-3H-indole
(BPNS-skatole).
[0695] Successful modification of therapeutic proteins and peptides
with PEG is often associated with an extension of circulatory
half-life while cross-linking of proteins with glutaraldehyde,
polyethylene glycol diacrylate and formaldehyde is used for the
preparation of hydrogels. Chemical modification of allergens for
immunotherapy is often achieved by carbamylation with potassium
cyanate.
[0696] A peptide or variant, wherein the peptide is modified or
includes non-peptide bonds is a preferred embodiment of the
invention. Generally, peptides and variants (at least those
containing peptide linkages between amino acid residues) may be
synthesized by the Fmoc-polyamide mode of solid-phase peptide
synthesis as disclosed by Lukas et al. (Lukas et al., 1981) and by
references as cited therein. Temporary N-amino group protection is
afforded by the 9-fluorenylmethyloxycarbonyl (Fmoc) group.
Repetitive cleavage of this highly base-labile protecting group is
done using 20% piperidine in N, N-dimethylformamide. Side-chain
functionalities may be protected as their butyl ethers (in the case
of serine, threonine, and tyrosine), butyl esters (in the case of
glutamic acid and aspartic acid), butyloxycarbonyl derivative (in
the case of lysine and histidine), trityl derivative (in the case
of cysteine) and 4-methoxy-2,3,6-trimethylbenzenesulphonyl
derivative (in the case of arginine). Where glutamine or asparagine
are C-terminal residues, use is made of the
4,4'-dimethoxybenzhydryl group for protection of the side chain
amido functionalities. The solid-phase support is based on a
polydimethyl-acrylamide polymer constituted from the three monomers
dimethylacrylamide (backbone-monomer), bisacryloylethylene diamine
(cross linker) and acryloylsarcosine methyl ester (functionalizing
agent). The peptide-to-resin cleavable linked agent used is the
acid-labile 4-hydroxymethyl-phenoxyacetic acid derivative. All
amino acid derivatives are added as their preformed symmetrical
anhydride derivatives with the exception of asparagine and
glutamine, which are added using a reversed N,
N-dicyclohexyl-carbodiimide/1 hydroxybenzotriazole mediated
coupling procedure. All coupling and deprotection reactions are
monitored using ninhydrin, trinitrobenzene sulphonic acid or isotin
test procedures. Upon completion of synthesis, peptides are cleaved
from the resin support with concomitant removal of side-chain
protecting groups by treatment with 95% trifluoroacetic acid
containing a 50% scavenger mix. Scavengers commonly used include
ethanedithiol, phenol, anisole and water, the exact choice
depending on the constituent amino acids of the peptide being
synthesized. Also a combination of solid phase and solution phase
methodologies for the synthesis of peptides is possible (see, for
example, (Bruckdorfer et al., 2004), and the references as cited
therein).
[0697] Trifluoroacetic acid is removed by evaporation in vacuo,
with subsequent trituration with diethyl ether affording the crude
peptide. Any scavengers present are removed by a simple extraction
procedure which on lyophilization of the aqueous phase affords the
crude peptide free of scavengers. Reagents for peptide synthesis
are generally available from e.g. Calbiochem-Novabiochem
(Nottingham, UK).
[0698] Purification may be performed by any one, or a combination
of, techniques such as re-crystallization, size exclusion
chromatography, ion-exchange chromatography, hydrophobic
interaction chromatography and (usually) reverse-phase high
performance liquid chromatography using e.g. acetonitrile/water
gradient separation.
[0699] Analysis of peptides may be carried out using thin layer
chromatography, electrophoresis, in particular capillary
electrophoresis, solid phase extraction (CSPE), reverse-phase high
performance liquid chromatography, amino-acid analysis after acid
hydrolysis and by fast atom bombardment (FAB) mass spectrometric
analysis, as well as MALDI and ESI-Q-TOF mass spectrometric
analysis.
[0700] In order to select over-presented peptides, a presentation
profile is calculated showing the median sample presentation as
well as replicate variation. The profile juxtaposes samples of the
tumor entity of interest to a baseline of normal tissue samples.
Each of these profiles can then be consolidated into an
over-presentation score by calculating the p-value of a Linear
Mixed-Effects Model (Pinheiro et al., 2015) adjusting for multiple
testing by False Discovery Rate (Benjamini and Hochberg, 1995).
[0701] For the identification and relative quantitation of HLA
ligands by mass spectrometry, HLA molecules from shock-frozen
tissue samples were purified and HLA-associated peptides were
isolated. The isolated peptides were separated and sequences were
identified by online nano-electrospray-ionization (nanoESI) liquid
chromatography-mass spectrometry (LC-MS) experiments. The resulting
peptide sequences were verified by comparison of the fragmentation
pattern of natural tumor-associated peptides (TUMAPs) recorded from
ovarian cancer samples (N=20 A*02-positive samples) with the
fragmentation patterns of corresponding synthetic reference
peptides of identical sequences. Since the peptides were directly
identified as ligands of HLA molecules of primary tumors, these
results provide direct evidence for the natural processing and
presentation of the identified peptides on primary cancer tissue
obtained from 20 ovarian cancer patients.
[0702] The discovery pipeline XPRESIDENT.RTM. v2.1 (see, for
example, US 2013-0096016, which is hereby incorporated by reference
in its entirety) allows the identification and selection of
relevant over-presented peptide vaccine candidates based on direct
relative quantitation of HLA-restricted peptide levels on cancer
tissues in comparison to several different non-cancerous tissues
and organs. This was achieved by the development of label-free
differential quantitation using the acquired LC-MS data processed
by a proprietary data analysis pipeline, combining algorithms for
sequence identification, spectral clustering, ion counting,
retention time alignment, charge state deconvolution and
normalization.
[0703] Presentation levels including error estimates for each
peptide and sample were established. Peptides exclusively presented
on tumor tissue and peptides over-presented in tumor versus
non-cancerous tissues and organs have been identified.
[0704] HLA-peptide complexes from ovarian cancer tissue samples
were purified and HLA-associated peptides were isolated and
analyzed by LC-MS (see examples). All TUMAPs contained in the
present application were identified with this approach on primary
ovarian cancer samples confirming their presentation on primary
ovarian cancer.
[0705] TUMAPs identified on multiple ovarian cancer and normal
tissues were quantified using ion-counting of label-free LC-MS
data. The method assumes that LC-MS signal areas of a peptide
correlate with its abundance in the sample. All quantitative
signals of a peptide in various LC-MS experiments were normalized
based on central tendency, averaged per sample and merged into a
bar plot, called presentation profile. The presentation profile
consolidates different analysis methods like protein database
search, spectral clustering, charge state deconvolution
(decharging) and retention time alignment and normalization.
[0706] Furthermore, the discovery pipeline XPRESIDENT.RTM. v2.x
allows the direct absolute quantitation of MHC-, preferably
HLA-restricted, peptide levels on cancer or other infected tissues.
Briefly, the total cell count was calculated from the total DNA
content of the analyzed tissue sample. The total peptide amount for
a TUMAP in a tissue sample was measured by nanoLC-MS/MS as the
ratio of the natural TUMAP and a known amount of an
isotope-labelled version of the TUMAP, the so-called internal
standard. The efficiency of TUMAP isolation was determined by
spiking peptide:MHC complexes of all selected TUMAPs into the
tissue lysate at the earliest possible point of the TUMAP isolation
procedure and their detection by nanoLC-MS/MS following completion
of the peptide isolation procedure. The total cell count and the
amount of total peptide were calculated from triplicate
measurements per tissue sample. The peptide-specific isolation
efficiencies were calculated as an average from 10 spike
experiments each measured as a triplicate (see Example 6 and Table
12).
[0707] In addition to an over-presentation of the peptide, the mRNA
expression of the underlying gene was analyzed as well. mRNA data
were obtained via RNASeq analyses of normal tissues and cancer
tissues (see Example 2). An additional source of normal tissue data
was a database of publicly available RNA expression data from
around 3000 normal tissue samples (Lonsdale, 2013). Peptides which
are derived from proteins that show a highly expressed coding mRNA
in cancer tissue, but a very low or absent one in vital healthy
(normal) tissues, were included as preferred into the present
invention.
[0708] The present invention provides peptides that are useful in
treating cancers/tumors, preferably ovarian cancer that over- or
exclusively present the peptides of the invention. These peptides
were shown by mass spectrometry to be naturally presented by HLA
molecules on primary human ovarian cancer samples.
[0709] Many of the source gene/proteins (also designated
"full-length proteins" or "underlying proteins") from which the
peptides are derived were shown to be highly over-expressed in
cancer compared with normal tissues--"normal tissues" in relation
to this invention shall mean either healthy ovaries or other normal
tissues, demonstrating a high degree of tumor association of the
source genes (see Example 2). Moreover, the peptides themselves are
strongly over-presented on tumor tissue--"tumor tissue" in relation
to this invention shall mean a sample from a patient suffering from
ovarian cancer, but not on normal tissues (see Example 1).
[0710] HLA-bound peptides can be recognized by the immune system,
specifically T lymphocytes. T cells can destroy the cells
presenting the recognized HLA/peptide complex, e.g. ovarian cancer
cells presenting the derived peptides.
[0711] The peptides of the present invention have been shown to be
capable of stimulating T cell responses and/or are over-presented
and thus can be used for the production of antibodies and/or TCRs,
such as soluble TCRs, according to the present invention (see
Example 3, Example 4). Furthermore, the peptides when complexed
with the respective MHC can be used for the production of
antibodies and/or TCRs, in particular sTCRs, according to the
present invention, as well. Respective methods are well known to
the person of skill, and can be found in the respective literature
as well. Thus, the peptides of the present invention are useful for
generating an immune response in a patient by which tumor cells can
be destroyed. An immune response in a patient can be induced by
direct administration of the described peptides or suitable
precursor substances (e.g. elongated peptides, proteins, or nucleic
acids encoding these peptides) to the patient, ideally in
combination with an agent enhancing the immunogenicity (i.e. an
adjuvant). The immune response originating from such a therapeutic
vaccination can be expected to be highly specific against tumor
cells because the target peptides of the present invention are not
presented on normal tissues in comparable copy numbers, preventing
the risk of undesired autoimmune reactions against normal cells in
the patient.
[0712] The present description further relates to T-cell receptors
(TCRs) comprising an alpha chain and a beta chain ("alpha/beta
TCRs"). Also provided are HAVCR1-001 peptides capable of binding to
TCRs and antibodies when presented by an MHC molecule. The present
description also relates to nucleic acids, vectors and host cells
for expressing TCRs and peptides of the present description; and
methods of using the same.
[0713] The term "T-cell receptor" (abbreviated TCR) refers to a
heterodimeric molecule comprising an alpha polypeptide chain (alpha
chain) and a beta polypeptide chain (beta chain), wherein the
heterodimeric receptor is capable of binding to a peptide antigen
presented by an HLA molecule. The term also includes so-called
gamma/delta TCRs.
[0714] In one embodiment the description provides a method of
producing a TCR as described herein, the method comprising
culturing a host cell capable of expressing the TCR under
conditions suitable to promote expression of the TCR.
[0715] The description in another aspect relates to methods
according to the description, wherein the antigen is loaded onto
class I or II MHC molecules expressed on the surface of a suitable
antigen-presenting cell or artificial antigen-presenting cell by
contacting a sufficient amount of the antigen with an
antigen-presenting cell or the antigen is loaded onto class I or II
MHC tetramers by tetramerizing the antigen/class I or II MHC
complex monomers.
[0716] The alpha and beta chains of alpha/beta TCR's, and the gamma
and delta chains of gamma/delta TCRs, are generally regarded as
each having two "domains", namely variable and constant domains.
The variable domain consists of a concatenation of variable region
(V), and joining region (J). The variable domain may also include a
leader region (L). Beta and delta chains may also include a
diversity region (D). The alpha and beta constant domains may also
include C-terminal transmembrane (TM) domains that anchor the alpha
and beta chains to the cell membrane.
[0717] With respect to gamma/delta TCRs, the term "TCR gamma
variable domain" as used herein refers to the concatenation of the
TCR gamma V (TRGV) region without leader region (L), and the TCR
gamma J (TRGJ) region, and the term TCR gamma constant domain
refers to the extracellular TRGC region, or to a C-terminal
truncated TRGC sequence. Likewise the term "TCR delta variable
domain" refers to the concatenation of the TCR delta V (TRDV)
region without leader region (L) and the TCR delta D/J (TRDD/TRDJ)
region, and the term "TCR delta constant domain" refers to the
extracellular TRDC region, or to a C-terminal truncated TRDC
sequence.
[0718] TCRs of the present description preferably bind to an
HAVCR1-001 peptide-HLA molecule complex with a binding affinity
(KD) of about 100 .mu.M or less, about 50 .mu.M or less, about 25
.mu.M or less, or about 10 .mu.M or less. More preferred are high
affinity TCRs having binding affinities of about 1 .mu.M or less,
about 100 nM or less, about 50 nM or less, about 25 nM or less.
Non-limiting examples of preferred binding affinity ranges for TCRs
of the present invention include about 1 nM to about 10 nM; about
10 nM to about 20 nM; about 20 nM to about 30 nM; about 30 nM to
about 40 nM; about 40 nM to about 50 nM; about 50 nM to about 60
nM; about 60 nM to about 70 nM; about 70 nM to about 80 nM; about
80 nM to about 90 nM; and about 90 nM to about 100 nM.
[0719] As used herein in connect with TCRs of the present
description, "specific binding" and grammatical variants thereof
are used to mean a TCR having a binding affinity (KD) for an
HAVCR1-001 peptide-HLA molecule complex of 100 .mu.M or less.
[0720] Alpha/beta heterodimeric TCRs of the present description may
have an introduced disulfide bond between their constant domains.
Preferred TCRs of this type include those which have a TRAC
constant domain sequence and a TRBC1 or TRBC2 constant domain
sequence except that Thr 48 of TRAC and Ser 57 of TRBC1 or TRBC2
are replaced by cysteine residues, the said cysteines forming a
disulfide bond between the TRAC constant domain sequence and the
TRBC1 or TRBC2 constant domain sequence of the TCR.
[0721] With or without the introduced inter-chain bond mentioned
above, alpha/beta heterodimeric TCRs of the present description may
have a TRAC constant domain sequence and a TRBC1 or TRBC2 constant
domain sequence, and the TRAC constant domain sequence and the
TRBC1 or TRBC2 constant domain sequence of the TCR may be linked by
the native disulfide bond between Cys4 of exon 2 of TRAC and Cys2
of exon 2 of TRBC1 or TRBC2.
[0722] TCRs of the present description may comprise a detectable
label selected from the group consisting of a radionuclide, a
fluorophore and biotin. TCRs of the present description may be
conjugated to a therapeutically active agent, such as a
radionuclide, a chemotherapeutic agent, or a toxin.
[0723] In an embodiment, a TCR of the present description having at
least one mutation in the alpha chain and/or having at least one
mutation in the beta chain has modified glycosylation compared to
the unmutated TCR.
[0724] In an embodiment, a TCR comprising at least one mutation in
the TCR alpha chain and/or TCR beta chain has a binding affinity
for, and/or a binding half-life for, a HAVCR1-001 peptide-HLA
molecule complex, which is at least double that of a TCR comprising
the unmutated TCR alpha chain and/or unmutated TCR beta chain.
Affinity-enhancement of tumor-specific TCRs, and its exploitation,
relies on the existence of a window for optimal TCR affinities. The
existence of such a window is based on observations that TCRs
specific for HLA-A2-restricted pathogens have KD values that are
generally about 10-fold lower when compared to TCRs specific for
HLA-A2-restricted tumor-associated self-antigens. It is now known,
although tumor antigens have the potential to be immunogenic,
because tumors arise from the individual's own cells only mutated
proteins or proteins with altered translational processing will be
seen as foreign by the immune system. Antigens that are upregulated
or overexpressed (so called self-antigens) will not necessarily
induce a functional immune response against the tumor: T-cells
expressing TCRs that are highly reactive to these antigens will
have been negatively selected within the thymus in a process known
as central tolerance, meaning that only T-cells with low-affinity
TCRs for self-antigens remain. Therefore, affinity of TCRs or
variants of the present description to HAVCR1-001 can be enhanced
by methods well known in the art.
[0725] The present description further relates to a method of
identifying and isolating a TCR according to the present
description, said method comprising incubating PBMCs from
HLA-A*02-negative healthy donors with A2/HAVCR1-001 monomers,
incubating the PBMCs with tetramer-phycoerythrin (PE) and isolating
the high avidity T-cells by fluorescence activated cell sorting
(FACS)-Calibur analysis.
[0726] The present description further relates to a method of
identifying and isolating a TCR according to the present
description, said method comprising obtaining a transgenic mouse
with the entire human TCR.alpha..beta. gene loci (1.1 and 0.7 Mb),
whose T-cells express a diverse human TCR repertoire that
compensates for mouse TCR deficiency, immunizing the mouse with
HAVCR1-001, incubating PBMCs obtained from the transgenic mice with
tetramer-phycoerythrin (PE), and isolating the high avidity T-cells
by fluorescence activated cell sorting (FACS)-Calibur analysis.
[0727] In one aspect, to obtain T-cells expressing TCRs of the
present description, nucleic acids encoding TCR-alpha and/or
TCR-beta chains of the present description are cloned into
expression vectors, such as gamma retrovirus or lentivirus. The
recombinant viruses are generated and then tested for
functionality, such as antigen specificity and functional avidity.
An aliquot of the final product is then used to transduce the
target T-cell population (generally purified from patient PBMCs),
which is expanded before infusion into the patient.
[0728] In another aspect, to obtain T-cells expressing TCRs of the
present description, TCR RNAs are synthesized by techniques known
in the art, e.g., in vitro transcription systems. The in
vitro-synthesized TCR RNAs are then introduced into primary CD8+
T-cells obtained from healthy donors by electroporation to
re-express tumor specific TCR-alpha and/or TCR-beta chains.
[0729] To increase the expression, nucleic acids encoding TCRs of
the present description may be operably linked to strong promoters,
such as retroviral long terminal repeats (LTRs), cytomegalovirus
(CMV), murine stem cell virus (MSCV) U3, phosphoglycerate kinase
(PGK), .beta.-actin, ubiquitin, and a simian virus 40 (SV40)/CD43
composite promoter, elongation factor (EF)-1a and the spleen
focus-forming virus (SFFV) promoter. In a preferred embodiment, the
promoter is heterologous to the nucleic acid being expressed.
[0730] In addition to strong promoters, TCR expression cassettes of
the present description may contain additional elements that can
enhance transgene expression, including a central polypurine tract
(cPPT), which promotes the nuclear translocation of lentiviral
constructs (Follenzi et al., 2000), and the woodchuck hepatitis
virus posttranscriptional regulatory element (wPRE), which
increases the level of transgene expression by increasing RNA
stability (Zufferey et al., 1999).
[0731] The alpha and beta chains of a TCR of the present invention
may be encoded by nucleic acids located in separate vectors, or may
be encoded by polynucleotides located in the same vector.
[0732] Achieving high-level TCR surface expression requires that
both the TCR-alpha and TCR-beta chains of the introduced TCR be
transcribed at high levels. To do so, the TCR-alpha and TCR-beta
chains of the present description may be cloned into bi-cistronic
constructs in a single vector, which has been shown to be capable
of over-coming this obstacle. The use of a viral intraribosomal
entry site (IRES) between the TCR-alpha and TCR-beta chains results
in the coordinated expression of both chains, because the TCR-alpha
and TCR-beta chains are generated from a single transcript that is
broken into two proteins during translation, ensuring that an equal
molar ratio of TCR-alpha and TCR-beta chains are produced. (Schmitt
et al. 2009).
[0733] Nucleic acids encoding TCRs of the present description may
be codon optimized to increase expression from a host cell.
Redundancy in the genetic code allows some amino acids to be
encoded by more than one codon, but certain codons are less
"optimal" than others because of the relative availability of
matching tRNAs as well as other factors (Gustafsson et al., 2004).
Modifying the TCR-alpha and TCR-beta gene sequences such that each
amino acid is encoded by the optimal codon for mammalian gene
expression, as well as eliminating mRNA instability motifs or
cryptic splice sites, has been shown to significantly enhance
TCR-alpha and TCR-beta gene expression (Scholten et al., 2006).
[0734] Furthermore, mispairing between the introduced and
endogenous TCR chains may result in the acquisition of
specificities that pose a significant risk for autoimmunity. For
example, the formation of mixed TCR dimers may reduce the number of
CD3 molecules available to form properly paired TCR complexes, and
therefore can significantly decrease the functional avidity of the
cells expressing the introduced TCR (Kuball et al., 2007).
[0735] To reduce mispairing, the C-terminus domain of the
introduced TCR chains of the present description may be modified in
order to promote interchain affinity, while de-creasing the ability
of the introduced chains to pair with the endogenous TCR. These
strategies may include replacing the human TCR-alpha and TCR-beta
C-terminus domains with their murine counterparts (murinized
C-terminus domain); generating a second interchain disulfide bond
in the C-terminus domain by introducing a second cysteine residue
into both the TCR-alpha and TCR-beta chains of the introduced TCR
(cysteine modification); swapping interacting residues in the
TCR-alpha and TCR-beta chain C-terminus domains ("knob-in-hole");
and fusing the variable domains of the TCR-alpha and TCR-beta
chains directly to CD3 (CD3 fusion). (Schmitt et al. 2009).
[0736] In an embodiment, a host cell is engineered to express a TCR
of the present description. In preferred embodiments, the host cell
is a human T-cell or T-cell progenitor. In some embodiments the
T-cell or T-cell progenitor is obtained from a cancer patient. In
other embodiments the T-cell or T-cell progenitor is obtained from
a healthy donor. Host cells of the present description can be
allogeneic or autologous with respect to a patient to be treated.
In one embodiment, the host is a gamma/delta T-cell transformed to
express an alpha/beta TCR.
[0737] A "pharmaceutical composition" is a composition suitable for
administration to a human being in a medical setting. Preferably, a
pharmaceutical composition is sterile and produced according to GMP
guidelines.
[0738] The pharmaceutical compositions comprise the peptides either
in the free form or in the form of a pharmaceutically acceptable
salt (see also above). As used herein, "a pharmaceutically
acceptable salt" refers to a derivative of the disclosed peptides
wherein the 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 --NH2
group) involving reaction with a suitable acid. Suitable acids for
preparing acid salts include both organic acids, e.g., 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, methane sulfonic acid, ethane sulfonic acid,
p-toluenesulfonic acid, salicylic acid, and the like, as well as
inorganic acids, e.g., hydrochloric acid, hydrobromic acid,
sulfuric acid, nitric acid phosphoric acid and the like.
Conversely, preparation of basic salts of acid moieties which may
be present on a peptide are prepared using a pharmaceutically
acceptable base such as sodium hydroxide, potassium hydroxide,
ammonium hydroxide, calcium hydroxide, trimethylamine or the
like.
[0739] In an especially preferred embodiment, the pharmaceutical
compositions comprise the peptides as salts of acetic acid
(acetates), trifluoro acetates or hydrochloric acid
(chlorides).
[0740] Preferably, the medicament of the present invention is an
immunotherapeutics such as a vaccine. It may be administered
directly into the patient, into the affected organ or systemically
i.d., i.m., s.c., i.p. and i.v., or applied ex vivo to cells
derived from the patient or a human cell line which are
subsequently administered to the patient, or used in vitro to
select a subpopulation of immune cells derived from the patient,
which are then re-administered to the patient. If the nucleic acid
is administered to cells in vitro, it may be useful for the cells
to be transfected so as to co-express immune-stimulating cytokines,
such as interleukin-2. The peptide may be substantially pure, or
combined with an immune-stimulating adjuvant (see below) or used in
combination with immune-stimulatory cytokines, or be administered
with a suitable delivery system, for example liposomes. The peptide
may also be conjugated to a suitable carrier such as keyhole limpet
haemocyanin (KLH) or mannan (see WO 95/18145 and (Longenecker et
al., 1993)). The peptide may also be tagged, may be a fusion
protein, or may be a hybrid molecule. The peptides whose sequence
is given in the present invention are expected to stimulate CD4 or
CD8 T cells. However, stimulation of CD8 T cells is more efficient
in the presence of help provided by CD4 T-helper cells. Thus, for
MHC Class I epitopes that stimulate CD8 T cells the fusion partner
or sections of a hybrid molecule suitably provide epitopes which
stimulate CD4-positive T cells. CD4- and CD8-stimulating epitopes
are well known in the art and include those identified in the
present invention.
[0741] In one aspect, the vaccine comprises at least one peptide
having the amino acid sequence set forth SEQ ID No. 1 to SEQ ID No.
640, and at least one additional peptide, preferably two to 50,
more preferably two to 25, even more preferably two to 20 and most
preferably two, three, four, five, six, seven, eight, nine, ten,
eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen or
eighteen peptides. The peptide(s) may be derived from one or more
specific TAAs and may bind to MHC class I molecules.
[0742] A further aspect of the invention provides a nucleic acid
(for example a polynucleotide) encoding a peptide or peptide
variant of the invention. The polynucleotide may be, for example,
DNA, cDNA, PNA, RNA or combinations thereof, either single- and/or
double-stranded, or native or stabilized forms of polynucleotides,
such as, for example, polynucleotides with a phosphorothioate
backbone and it may or may not contain introns so long as it codes
for the peptide. Of course, only peptides that contain naturally
occurring amino acid residues joined by naturally occurring peptide
bonds are encodable by a polynucleotide. A still further aspect of
the invention provides an expression vector capable of expressing a
polypeptide according to the invention.
[0743] A variety of methods have been developed to link
polynucleotides, especially DNA, to vectors for example via
complementary cohesive termini. For instance, complementary
homopolymer tracts can be added to the DNA segment to be inserted
to the vector DNA. The vector and DNA segment are then joined by
hydrogen bonding between the complementary homopolymeric tails to
form recombinant DNA molecules.
[0744] Synthetic linkers containing one or more restriction sites
provide an alternative method of joining the DNA segment to
vectors. Synthetic linkers containing a variety of restriction
endonuclease sites are commercially available from a number of
sources including International Biotechnologies Inc. New Haven,
Conn., USA.
[0745] A desirable method of modifying the DNA encoding the
polypeptide of the invention employs the polymerase chain reaction
as disclosed by Saiki R K, et al. (Saiki et al., 1988). This method
may be used for introducing the DNA into a suitable vector, for
example by engineering in suitable restriction sites, or it may be
used to modify the DNA in other useful ways as is known in the art.
If viral vectors are used, pox- or adenovirus vectors are
preferred.
[0746] The DNA (or in the case of retroviral vectors, RNA) may then
be expressed in a suitable host to produce a polypeptide comprising
the peptide or variant of the invention. Thus, the DNA encoding the
peptide or variant of the invention may be used in accordance with
known techniques, appropriately modified in view of the teachings
contained herein, to construct an expression vector, which is then
used to transform an appropriate host cell for the expression and
production of the polypeptide of the invention. Such techniques
include those disclosed, for example, in U.S. Pat. Nos. 4,440,859,
4,530,901, 4,582,800, 4,677,063, 4,678,751, 4,704,362, 4,710,463,
4,757,006, 4,766,075, and 4,810,648.
[0747] The DNA (or in the case of retroviral vectors, RNA) encoding
the polypeptide constituting the compound of the invention may be
joined to a wide variety of other DNA sequences for introduction
into an appropriate host. The companion DNA will depend upon the
nature of the host, the manner of the introduction of the DNA into
the host, and whether episomal maintenance or integration is
desired.
[0748] Generally, the DNA is inserted into an expression vector,
such as a plasmid, in proper orientation and correct reading frame
for expression. If necessary, the DNA may be linked to the
appropriate transcriptional and translational regulatory control
nucleotide sequences recognized by the desired host, although such
controls are generally available in the expression vector. The
vector is then introduced into the host through standard
techniques. Generally, not all of the hosts will be transformed by
the vector. Therefore, it will be necessary to select for
transformed host cells. One selection technique involves
incorporating into the expression vector a DNA sequence, with any
necessary control elements, that codes for a selectable trait in
the transformed cell, such as antibiotic resistance.
[0749] Alternatively, the gene for such selectable trait can be on
another vector, which is used to co-transform the desired host
cell.
[0750] Host cells that have been transformed by the recombinant DNA
of the invention are then cultured for a sufficient time and under
appropriate conditions known to those skilled in the art in view of
the teachings disclosed herein to permit the expression of the
polypeptide, which can then be recovered.
[0751] Many expression systems are known, including bacteria (for
example E. coli and Bacillus subtilis), yeasts (for example
Saccharomyces cerevisiae), filamentous fungi (for example
Aspergillus spec.), plant cells, animal cells and insect cells.
Preferably, the system can be mammalian cells such as CHO cells
available from the ATCC Cell Biology Collection.
[0752] A typical mammalian cell vector plasmid for constitutive
expression comprises the CMV or SV40 promoter with a suitable poly
A tail and a resistance marker, such as neomycin. One example is
pSVL available from Pharmacia, Piscataway, N.J., USA. An example of
an inducible mammalian expression vector is pMSG, also available
from Pharmacia. Useful yeast plasmid vectors are pRS403-406 and
pRS413-416 and are generally available from Stratagene Cloning
Systems, La Jolla, Calif. 92037, USA. Plasmids pRS403, pRS404,
pRS405 and pRS406 are Yeast Integrating plasmids (YIps) and
incorporate the yeast selectable markers HIS3, TRP1, LEU2 and URA3.
Plasmids pRS413-416 are Yeast Centromere plasmids (Ycps). CMV
promoter-based vectors (for example from Sigma-Aldrich) provide
transient or stable expression, cytoplasmic expression or
secretion, and N-terminal or C-terminal tagging in various
combinations of FLAG, 3.times.FLAG, c-myc or MAT. These fusion
proteins allow for detection, purification and analysis of
recombinant protein. Dual-tagged fusions provide flexibility in
detection.
[0753] The strong human cytomegalovirus (CMV) promoter regulatory
region drives constitutive protein expression levels as high as 1
mg/L in COS cells. For less potent cell lines, protein levels are
typically .about.0.1 mg/L. The presence of the SV40 replication
origin will result in high levels of DNA replication in SV40
replication permissive COS cells. CMV vectors, for example, can
contain the pMB1 (derivative of pBR322) origin for replication in
bacterial cells, the b-lactamase gene for ampicillin resistance
selection in bacteria, hGH polyA, and the f1 origin. Vectors
containing the pre-pro-trypsin leader (PPT) sequence can direct the
secretion of FLAG fusion proteins into the culture medium for
purification using ANTI-FLAG antibodies, resins, and plates. Other
vectors and expression systems are well known in the art for use
with a variety of host cells.
[0754] In another embodiment two or more peptides or peptide
variants of the invention are encoded and thus expressed in a
successive order (similar to "beads on a string" constructs). In
doing so, the peptides or peptide variants may be linked or fused
together by stretches of linker amino acids, such as for example
LLLLLL, or may be linked without any additional peptide(s) between
them. These constructs can also be used for cancer therapy, and may
induce immune responses both involving MHC I and MHC II.
[0755] The present invention also relates to a host cell
transformed with a polynucleotide vector construct of the present
invention. The host cell can be either prokaryotic or eukaryotic.
Bacterial cells may be preferred prokaryotic host cells in some
circumstances and typically are a strain of E. coli such as, for
example, the E. coli strains DH5 available from Bethesda Research
Laboratories Inc., Bethesda, Md., USA, and RR1 available from the
American Type Culture Collection (ATCC) of Rockville, Md., USA (No
ATCC 31343). Preferred eukaryotic host cells include yeast, insect
and mammalian cells, preferably vertebrate cells such as those from
a mouse, rat, monkey or human fibroblastic and colon cell lines.
Yeast host cells include YPH499, YPH500 and YPH501, which are
generally available from Stratagene Cloning Systems, La Jolla,
Calif. 92037, USA. Preferred mammalian host cells include Chinese
hamster ovary (CHO) cells available from the ATCC as CCL61, NIH
Swiss mouse embryo cells NIH/3T3 available from the ATCC as CRL
1658, monkey kidney-derived COS-1 cells available from the ATCC as
CRL 1650 and 293 cells which are human embryonic kidney cells.
Preferred insect cells are Sf9 cells which can be transfected with
baculovirus expression vectors. An overview regarding the choice of
suitable host cells for expression can be found in, for example,
the textbook of Paulina Balbas and Argelia Lorence "Methods in
Molecular Biology Recombinant Gene Expression, Reviews and
Protocols," Part One, Second Edition, ISBN 978-1-58829-262-9, and
other literature known to the person of skill.
[0756] Transformation of appropriate cell hosts with a DNA
construct of the present invention is accomplished by well-known
methods that typically depend on the type of vector used. With
regard to transformation of prokaryotic host cells, see, for
example, Cohen et al. (Cohen et al., 1972) and (Green and Sambrook,
2012). Transformation of yeast cells is described in Sherman et al.
(Sherman et al., 1986). The method of Beggs (Beggs, 1978) is also
useful. With regard to vertebrate cells, reagents useful in
transfecting such cells, for example calcium phosphate and
DEAE-dextran or liposome formulations, are available from
Stratagene Cloning Systems, or Life Technologies Inc.,
Gaithersburg, Md. 20877, USA. Electroporation is also useful for
transforming and/or transfecting cells and is well known in the art
for transforming yeast cell, bacterial cells, insect cells and
vertebrate cells.
[0757] Successfully transformed cells, i.e. cells that contain a
DNA construct of the present invention, can be identified by
well-known techniques such as PCR. Alternatively, the presence of
the protein in the supernatant can be detected using
antibodies.
[0758] It will be appreciated that certain host cells of the
invention are useful in the preparation of the peptides of the
invention, for example bacterial, yeast and insect cells. However,
other host cells may be useful in certain therapeutic methods. For
example, antigen-presenting cells, such as dendritic cells, may
usefully be used to express the peptides of the invention such that
they may be loaded into appropriate MHC molecules. Thus, the
current invention provides a host cell comprising a nucleic acid or
an expression vector according to the invention.
[0759] In a preferred embodiment the host cell is an antigen
presenting cell, in particular a dendritic cell or antigen
presenting cell. APCs loaded with a recombinant fusion protein
containing prostatic acid phosphatase (PAP) were approved by the
U.S. Food and Drug Administration (FDA) on Apr. 29, 2010, to treat
asymptomatic or minimally symptomatic metastatic HRPC
(Sipuleucel-T) (Rini et al., 2006; Small et al., 2006).
[0760] A further aspect of the invention provides a method of
producing a peptide or its variant, the method comprising culturing
a host cell and isolating the peptide from the host cell or its
culture medium.
[0761] In another embodiment the peptide, the nucleic acid or the
expression vector of the invention are used in medicine. For
example, the peptide or its variant may be prepared for intravenous
(i.v.) injection, sub-cutaneous (s.c.) injection, intradermal
(i.d.) injection, intraperitoneal (i.p.) injection, intramuscular
(i.m.) injection. Preferred methods of peptide injection include
s.c., i.d., i.p., i.m., and i.v. Preferred methods of DNA injection
include i.d., i.m., s.c., i.p. and i.v. Doses of e.g. between 50
.mu.g and 1.5 mg, preferably 125 .mu.g to 500 .mu.g, of peptide or
DNA may be given and will depend on the respective peptide or DNA.
Dosages of this range were successfully used in previous trials
(Walter et al., 2012).
[0762] The polynucleotide used for active vaccination may be
substantially pure, or contained in a suitable vector or delivery
system. The nucleic acid may be DNA, cDNA, PNA, RNA or a
combination thereof. Methods for designing and introducing such a
nucleic acid are well known in the art. An overview is provided by
e.g. Teufel et al. (Teufel et al., 2005). Polynucleotide vaccines
are easy to prepare, but the mode of action of these vectors in
inducing an immune response is not fully understood. Suitable
vectors and delivery systems include viral DNA and/or RNA, such as
systems based on adenovirus, vaccinia virus, retroviruses, herpes
virus, adeno-associated virus or hybrids containing elements of
more than one virus. Non-viral delivery systems include cationic
lipids and cationic polymers and are well known in the art of DNA
delivery. Physical delivery, such as via a "gene-gun" may also be
used. The peptide or peptides encoded by the nucleic acid may be a
fusion protein, for example with an epitope that stimulates T cells
for the respective opposite CDR as noted above.
[0763] The medicament of the invention may also include one or more
adjuvants. Adjuvants are substances that non-specifically enhance
or potentiate the immune response (e.g., immune responses mediated
by CD8-positive T cells and helper-T (TH) cells to an antigen, and
would thus be considered useful in the medicament of the present
invention. Suitable adjuvants include, but are not limited to, 1018
ISS, aluminum salts, AMPLIVAX.RTM., AS15, BCG, CP-870,893, CpG7909,
CyaA, dSLIM, flagellin or TLR5 ligands derived from flagellin, FLT3
ligand, GM-CSF, IC30, IC31, Imiquimod (ALDARA.RTM.), resiquimod,
ImuFact IMP321, Interleukins as IL-2, IL-13, IL-21,
Interferon-alpha or -beta, or pegylated derivatives thereof, IS
Patch, ISS, ISCOMATRIX, ISCOMs, JuvImmune.RTM., LipoVac, MALP2,
MF59, monophosphoryl lipid A, Montanide IMS 1312, Montanide ISA
206, Montanide ISA 50V, Montanide ISA-51, water-in-oil and
oil-in-water emulsions, OK-432, OM-174, OM-197-MP-EC, ONTAK, OspA,
PepTel.RTM. vector system, poly(lactid co-glycolid) [PLG]-based and
dextran microparticles, talactoferrin SRL172, Virosomes and other
Virus-like particles, YF-17D, VEGF trap, R848, beta-glucan,
Pam3Cys, Aquila's QS21 stimulon, which is derived from saponin,
mycobacterial extracts and synthetic bacterial cell wall mimics,
and other proprietary adjuvants such as Ribi's Detox, Quil, or
Superfos. Adjuvants such as Freund's or GM-CSF are preferred.
Several immunological adjuvants (e.g., MF59) specific for dendritic
cells and their preparation have been described previously (Allison
and Krummel, 1995). Also cytokines may be used. Several cytokines
have been directly linked to influencing dendritic cell migration
to lymphoid tissues (e.g., TNF-), accelerating the maturation of
dendritic cells into efficient antigen-presenting cells for
T-lymphocytes (e.g., GM-CSF, IL-1 and IL-4) (U.S. Pat. No.
5,849,589, specifically incorporated herein by reference in its
entirety) and acting as immunoadjuvants (e.g., IL-12, IL-15, IL-23,
IL-7, IFN-alpha. IFN-beta) (Gabrilovich et al., 1996).
[0764] CpG immunostimulatory oligonucleotides have also been
reported to enhance the effects of adjuvants in a vaccine setting.
Without being bound by theory, CpG oligonucleotides act by
activating the innate (non-adaptive) immune system via Toll-like
receptors (TLR), mainly TLR9. CpG triggered TLR9 activation
enhances antigen-specific humoral and cellular responses to a wide
variety of antigens, including peptide or protein antigens, live or
killed viruses, dendritic cell vaccines, autologous cellular
vaccines and polysaccharide conjugates in both prophylactic and
therapeutic vaccines. More importantly it enhances dendritic cell
maturation and differentiation, resulting in enhanced activation of
TH1 cells and strong cytotoxic T-lymphocyte (CTL) generation, even
in the absence of CD4 T cell help. The TH1 bias induced by TLR9
stimulation is maintained even in the presence of vaccine adjuvants
such as alum or incomplete Freund's adjuvant (IFA) that normally
promote a TH2 bias. CpG oligonucleotides show even greater adjuvant
activity when formulated or co-administered with other adjuvants or
in formulations such as microparticles, nanoparticles, lipid
emulsions or similar formulations, which are especially necessary
for inducing a strong response when the antigen is relatively weak.
They also accelerate the immune response and enable the antigen
doses to be reduced by approximately two orders of magnitude, with
comparable antibody responses to the full-dose vaccine without CpG
in some experiments (Krieg, 2006). U.S. Pat. No. 6,406,705 B1
describes the combined use of CpG oligonucleotides, non-nucleic
acid adjuvants and an antigen to induce an antigen-specific immune
response. A CpG TLR9 antagonist is dSLIM (double Stem Loop
Immunomodulator) by Mologen (Berlin, Germany) which is a preferred
component of the pharmaceutical composition of the present
invention. Other TLR binding molecules such as RNA binding TLR 7,
TLR 8 and/or TLR 9 may also be used.
[0765] Other examples for useful adjuvants include, but are not
limited to chemically modified CpGs (e.g. CpR, Idera), dsRNA
analogues such as Poly(I:C) and derivates thereof (e.g.
AmpliGen.RTM., Hiltonol.RTM., poly-(ICLC), poly(IC-R),
poly(I:C12U), non-CpG bacterial DNA or RNA as well as immunoactive
small molecules and antibodies such as cyclophosphamide, sunitinib,
Bevacizumab.RTM., celebrex, NCX-4016, sildenafil, tadalafil,
vardenafil, sorafenib, temozolomide, temsirolimus, XL-999,
CP-547632, pazopanib, VEGF Trap, ZD2171, AZD2171, anti-CTLA4, other
antibodies targeting key structures of the immune system (e.g.
anti-CD40, anti-TGFbeta, anti-TNFalpha receptor) and SC58175, which
may act therapeutically and/or as an adjuvant. The amounts and
concentrations of adjuvants and additives useful in the context of
the present invention can readily be determined by the skilled
artisan without undue experimentation.
[0766] Preferred adjuvants are anti-CD40, imiquimod, resiquimod,
GM-CSF, cyclophosphamide, sunitinib, bevacizumab, interferon-alpha,
CpG oligonucleotides and derivates, poly-(I:C) and derivates, RNA,
sildenafil, and particulate formulations with PLG or virosomes.
[0767] In a preferred embodiment, the pharmaceutical composition
according to the invention the adjuvant is selected from the group
consisting of colony-stimulating factors, such as Granulocyte
Macrophage Colony Stimulating Factor (GM-CSF, sargramostim),
cyclophosphamide, imiquimod, resiquimod, and interferon-alpha.
[0768] In a preferred embodiment, the pharmaceutical composition
according to the invention the adjuvant is selected from the group
consisting of colony-stimulating factors, such as Granulocyte
Macrophage Colony Stimulating Factor (GM-CSF, sargramostim),
cyclophosphamide, imiquimod and resiquimod. In a preferred
embodiment of the pharmaceutical composition according to the
invention, the adjuvant is cyclophosphamide, imiquimod or
resiquimod. Even more preferred adjuvants are Montanide IMS 1312,
Montanide ISA 206, Montanide ISA 50V, Montanide ISA-51, poly-ICLC
(Hiltonol.RTM.) and anti-CD40 mAB, or combinations thereof.
[0769] This composition is used for parenteral administration, such
as subcutaneous, intradermal, intramuscular or oral administration.
For this, the peptides and optionally other molecules are dissolved
or suspended in a pharmaceutically acceptable, preferably aqueous
carrier. In addition, the composition can contain excipients, such
as buffers, binding agents, blasting agents, diluents, flavors,
lubricants, etc. The peptides can also be administered together
with immune stimulating substances, such as cytokines. An extensive
listing of excipients that can be used in such a composition, can
be, for example, taken from A. Kibbe, Handbook of Pharmaceutical
Excipients (Kibbe, 2000). The composition can be used for a
prevention, prophylaxis and/or therapy of adenomatous or cancerous
diseases. Exemplary formulations can be found in, for example,
EP2112253.
[0770] It is important to realize that the immune response
triggered by the vaccine according to the invention attacks the
cancer in different cell-stages and different stages of
development. Furthermore, different cancer associated signaling
pathways are attacked. This is an advantage over vaccines that
address only one or few targets, which may cause the tumor to
easily adapt to the attack (tumor escape). Furthermore, not all
individual tumors express the same pattern of antigens. Therefore,
a combination of several tumor-associated peptides ensures that
every single tumor bears at least some of the targets. The
composition is designed in such a way that each tumor is expected
to express several of the antigens and cover several independent
pathways necessary for tumor growth and maintenance. Thus, the
vaccine can easily be used "off-the-shelf" for a larger patient
population. This means that a pre-selection of patients to be
treated with the vaccine can be restricted to HLA typing, does not
require any additional biomarker assessments for antigen
expression, but it is still ensured that several targets are
simultaneously attacked by the induced immune response, which is
important for efficacy (Banchereau et al., 2001; Walter et al.,
2012).
[0771] As used herein, the term "scaffold" refers to a molecule
that specifically binds to an (e.g. antigenic) determinant. In one
embodiment, a scaffold is able to direct the entity to which it is
attached (e.g. a (second) antigen binding moiety) to a target site,
for example to a specific type of tumor cell or tumor stroma
bearing the antigenic determinant (e.g. the complex of a peptide
with MHC, according to the application at hand). In another
embodiment a scaffold is able to activate signaling through its
target antigen, for example a T cell receptor complex antigen.
Scaffolds include but are not limited to antibodies and fragments
thereof, antigen binding domains of an antibody, comprising an
antibody heavy chain variable region and an antibody light chain
variable region, binding proteins comprising at least one Ankyrin
repeat motif and single domain antigen binding (SDAB) molecules,
aptamers, (soluble) TCRs and (modified) cells such as allogenic or
autologous T cells. To assess whether a molecule is a scaffold
binding to a target, binding assays can be performed.
[0772] "Specific" binding means that the scaffold binds the
peptide-MHC-complex of interest better than other naturally
occurring peptide-MHC-complexes, to an extent that a scaffold armed
with an active molecule that is able to kill a cell bearing the
specific target is not able to kill another cell without the
specific target but presenting other peptide-MHC complex(es).
Binding to other peptide-MHC complexes is irrelevant if the peptide
of the cross-reactive peptide-MHC is not naturally occurring, i.e.
not derived from the human HLA-peptidome. Tests to assess target
cell killing are well known in the art. They should be performed
using target cells (primary cells or cell lines) with unaltered
peptide-MHC presentation, or cells loaded with peptides such that
naturally occurring peptide-MHC levels are reached.
[0773] Each scaffold can comprise a labelling which provides that
the bound scaffold can be detected by determining the presence or
absence of a signal provided by the label. For example, the
scaffold can be labelled with a fluorescent dye or any other
applicable cellular marker molecule. Such marker molecules are well
known in the art. For example, a fluorescence-labelling, for
example provided by a fluorescence dye, can provide a visualization
of the bound aptamer by fluorescence or laser scanning microscopy
or flow cytometry.
[0774] Each scaffold can be conjugated with a second active
molecule such as for example IL-21, anti-CD3, anti-CD28.
[0775] For further information on polypeptide scaffolds see for
example the background section of WO 2014/071978A1 and the
references cited therein.
[0776] The present invention further relates to aptamers. Aptamers
(see for example WO 2014/191359 and the literature as cited
therein) are short single-stranded nucleic acid molecules, which
can fold into defined three-dimensional structures and recognize
specific target structures. They have appeared to be suitable
alternatives for developing targeted therapies. Aptamers have been
shown to selectively bind to a variety of complex targets with high
affinity and specificity.
[0777] Aptamers recognizing cell surface located molecules have
been identified within the past decade and provide means for
developing diagnostic and therapeutic approaches. Since aptamers
have been shown to possess almost no toxicity and immunogenicity
they are promising candidates for biomedical applications. Indeed,
aptamers, for example prostate-specific membrane-antigen
recognizing aptamers, have been successfully employed for targeted
therapies and shown to be functional in xenograft in vivo models.
Furthermore, aptamers recognizing specific tumor cell lines have
been identified.
[0778] DNA aptamers can be selected to reveal broad-spectrum
recognition properties for various cancer cells, and particularly
those derived from solid tumors, while non-tumorigenic and primary
healthy cells are not recognized. If the identified aptamers
recognize not only a specific tumor sub-type but rather interact
with a series of tumors, this renders the aptamers applicable as
so-called broad-spectrum diagnostics and therapeutics.
[0779] Further, investigation of cell-binding behavior with flow
cytometry showed that the aptamers revealed very good apparent
affinities that are within the nanomolar range.
[0780] Aptamers are useful for diagnostic and therapeutic purposes.
Further, it could be shown that some of the aptamers are taken up
by tumor cells and thus can function as molecular vehicles for the
targeted delivery of anti-cancer agents such as siRNA into tumor
cells.
[0781] Aptamers can be selected against complex targets such as
cells and tissues and complexes of the peptides comprising,
preferably consisting of, a sequence according to any of SEQ ID NO
1 to SEQ ID NO 640, according to the invention at hand with the MHC
molecule, using the cell-SELEX (Systematic Evolution of Ligands by
Exponential enrichment) technique.
[0782] The peptides of the present invention can be used to
generate and develop specific antibodies against MHC/peptide
complexes. These can be used for therapy, targeting toxins or
radioactive substances to the diseased tissue. Another use of these
antibodies can be targeting radionuclides to the diseased tissue
for imaging purposes such as PET. This use can help to detect small
metastases or to determine the size and precise localization of
diseased tissues.
[0783] Therefore, it is a further aspect of the invention to
provide a method for producing a recombinant antibody specifically
binding to a human major histocompatibility complex (MHC) class I
or II being complexed with a HLA-restricted antigen, the method
comprising: immunizing a genetically engineered non-human mammal
comprising cells expressing said human major histocompatibility
complex (MHC) class I or II with a soluble form of a MHC class I or
II molecule being complexed with said HLA-restricted antigen;
isolating mRNA molecules from antibody producing cells of said
non-human mammal; producing a phage display library displaying
protein molecules encoded by said mRNA molecules; and isolating at
least one phage from said phage display library, said at least one
phage displaying said antibody specifically binding to said human
major histocompatibility complex (MHC) class I or II being
complexed with said HLA-restricted antigen.
[0784] It is a further aspect of the invention to provide an
antibody that specifically binds to a human major
histocompatibility complex (MHC) class I or II being complexed with
a HLA-restricted antigen, wherein the antibody preferably is a
polyclonal antibody, monoclonal antibody, bi-specific antibody
and/or a chimeric antibody.
[0785] Respective methods for producing such antibodies and single
chain class I major histocompatibility complexes, as well as other
tools for the production of these antibodies are disclosed in WO
03/068201, WO 2004/084798, WO 01/72768, WO 03/070752, and in
publications (Cohen et al., 2003a; Cohen et al., 2003b; Denkberg et
al., 2003), which for the purposes of the present invention are all
explicitly incorporated by reference in their entireties.
[0786] Preferably, the antibody is binding with a binding affinity
of below 20 nanomolar, preferably of below 10 nanomolar, to the
complex, which is also regarded as "specific" in the context of the
present invention.
[0787] The present invention relates to a peptide comprising a
sequence that is selected from the group consisting of SEQ ID NO: 1
to SEQ ID NO: 640, or a variant thereof which is at least 88%
homologous (preferably identical) to SEQ ID NO: 1 to SEQ ID NO: 640
or a variant thereof that induces T cells cross-reacting with said
peptide, wherein said peptide is not the underlying full-length
polypeptide.
[0788] The present invention further relates to a peptide
comprising a sequence that is selected from the group consisting of
SEQ ID NO: 1 to SEQ ID NO: 640 or a variant thereof which is at
least 88% homologous (preferably identical) to SEQ ID NO: 1 to SEQ
ID NO: 640, wherein said peptide or variant has an overall length
of between 8 and 100, preferably between 8 and 30, and most
preferred between 8 and 14 amino acids.
[0789] The present invention further relates to the peptides
according to the invention that have the ability to bind to a
molecule of the human major histocompatibility complex (MHC)
class-I or -II.
[0790] The present invention further relates to the peptides
according to the invention wherein the peptide consists or consists
essentially of an amino acid sequence according to SEQ ID NO: 1 to
SEQ ID NO: 640.
[0791] The present invention further relates to the peptides
according to the invention, wherein the peptide is (chemically)
modified and/or includes non-peptide bonds.
[0792] The present invention further relates to the peptides
according to the invention, wherein the peptide is part of a fusion
protein, in particular comprising N-terminal amino acids of the
HLA-DR antigen-associated invariant chain (Ii), or wherein the
peptide is fused to (or into) an antibody, such as, for example, an
antibody that is specific for dendritic cells.
[0793] The present invention further relates to a nucleic acid,
encoding the peptides according to the invention, provided that the
peptide is not the complete (full) human protein.
[0794] The present invention further relates to the nucleic acid
according to the invention that is DNA, cDNA, PNA, RNA or
combinations thereof.
[0795] The present invention further relates to an expression
vector capable of expressing a nucleic acid according to the
present invention.
[0796] The present invention further relates to a peptide according
to the present invention, a nucleic acid according to the present
invention or an expression vector according to the present
invention for use in medicine, in particular in the treatment of
ovarian cancer.
[0797] The present invention further relates to a host cell
comprising a nucleic acid according to the invention or an
expression vector according to the invention.
[0798] The present invention further relates to the host cell
according to the present invention that is an antigen presenting
cell, and preferably a dendritic cell.
[0799] The present invention further relates to a method of
producing a peptide according to the present invention, said method
comprising culturing the host cell according to the present
invention, and isolating the peptide from said host cell or its
culture medium.
[0800] The present invention further relates to the method
according to the present invention, where-in the antigen is loaded
onto class I or II MHC molecules expressed on the surface of a
suitable antigen-presenting cell by contacting a sufficient amount
of the antigen with an antigen-presenting cell.
[0801] The present invention further relates to the method
according to the invention, wherein the antigen-presenting cell
comprises an expression vector capable of expressing said peptide
containing SEQ ID NO: 1 to SEQ ID NO: 640 or said variant amino
acid sequence.
[0802] The present invention further relates to activated T cells,
produced by the method according to the present invention, wherein
said T cells selectively recognizes a cell which aberrantly
expresses a polypeptide comprising an amino acid sequence according
to the present invention.
[0803] The present invention further relates to a method of killing
target cells in a patient which target cells aberrantly express a
polypeptide comprising any amino acid sequence according to the
present invention, the method comprising administering to the
patient an effective number of T cells as according to the present
invention.
[0804] The present invention further relates to the use of any
peptide described, a nucleic acid according to the present
invention, an expression vector according to the present invention,
a cell according to the present invention, or an activated
cytotoxic T lymphocyte according to the present invention as a
medicament or in the manufacture of a medicament. The present
invention further relates to a use according to the present
invention, wherein the medicament is active against cancer.
[0805] The present invention further relates to a use according to
the invention, wherein the medicament is a vaccine. The present
invention further relates to a use according to the invention,
wherein the medicament is active against cancer.
[0806] The present invention further relates to a use according to
the invention, wherein said cancer cells are ovarian cancer cells
or other solid or hematological tumor cells such as non-small cell
lung cancer, small cell lung cancer, kidney cancer, brain cancer,
colon or rectum cancer, stomach cancer, liver cancer, pancreatic
cancer, prostate cancer, leukemia, breast cancer, Merkel cell
carcinoma, melanoma, esophageal cancer, urinary bladder cancer,
uterine cancer, gallbladder cancer, bile duct cancer.
[0807] The present invention further relates to particular marker
proteins and biomarkers based on the peptides according to the
present invention, herein called "targets" that can be used in the
diagnosis and/or prognosis of ovarian cancer. The present invention
also relates to the use of these novel targets for cancer
treatment.
[0808] The term "antibody" or "antibodies" is used herein in a
broad sense and includes both polyclonal and monoclonal antibodies.
In addition to intact or "full" immunoglobulin molecules, also
included in the term "antibodies" are fragments (e.g. CDRs, Fv, Fab
and Fc fragments) or polymers of those immunoglobulin molecules and
humanized versions of immunoglobulin molecules, as long as they
exhibit any of the desired properties (e.g., specific binding of a
ovarian cancer marker (poly)peptide, delivery of a toxin to a
ovarian cancer cell expressing a cancer marker gene at an increased
level, and/or inhibiting the activity of a ovarian cancer marker
polypeptide) according to the invention.
[0809] Whenever possible, the antibodies of the invention may be
purchased from commercial sources. The antibodies of the invention
may also be generated using well-known methods. The skilled artisan
will understand that either full length ovarian cancer marker
polypeptides or fragments thereof may be used to generate the
antibodies of the invention. A polypeptide to be used for
generating an antibody of the invention may be partially or fully
purified from a natural source, or may be produced using
recombinant DNA techniques.
[0810] For example, a cDNA encoding a peptide according to the
present invention, such as a peptide according to SEQ ID NO: 1 to
SEQ ID NO: 640 polypeptide, or a variant or fragment thereof, can
be expressed in prokaryotic cells (e.g., bacteria) or eukaryotic
cells (e.g., yeast, insect, or mammalian cells), after which the
recombinant protein can be purified and used to generate a
monoclonal or polyclonal antibody preparation that specifically
bind the ovarian cancer marker polypeptide used to generate the
antibody according to the invention.
[0811] One of skill in the art will realize that the generation of
two or more different sets of monoclonal or polyclonal antibodies
maximizes the likelihood of obtaining an antibody with the
specificity and affinity required for its intended use (e.g.,
ELISA, immunohistochemistry, in vivo imaging, immunotoxin therapy).
The antibodies are tested for their desired activity by known
methods, in accordance with the purpose for which the antibodies
are to be used (e.g., ELISA, immunohistochemistry, immunotherapy,
etc.; for further guidance on the generation and testing of
antibodies, see, e.g., Greenfield, 2014 (Greenfield, 2014)). For
example, the antibodies may be tested in ELISA assays or, Western
blots, immunohistochemical staining of formalin-fixed cancers or
frozen tissue sections. After their initial in vitro
characterization, antibodies intended for therapeutic or in vivo
diagnostic use are tested according to known clinical testing
methods.
[0812] The term "monoclonal antibody" as used herein refers to an
antibody obtained from a substantially homogeneous population of
antibodies, i.e.; the individual antibodies comprising the
population are identical except for possible naturally occurring
mutations that may be present in minor amounts. The monoclonal
antibodies herein specifically include "chimeric" antibodies in
which a portion of the heavy and/or light chain is identical with
or homologous to corresponding sequences in antibodies derived from
a particular species or belonging to a particular antibody class or
subclass, while the remainder of the chain(s) is identical with or
homologous to corresponding sequences in antibodies derived from
another species or belonging to another antibody class or subclass,
as well as fragments of such antibodies, so long as they exhibit
the desired antagonistic activity (U.S. Pat. No. 4,816,567, which
is hereby incorporated in its entirety).
[0813] Monoclonal antibodies of the invention may be prepared using
hybridoma methods. In a hybridoma method, a mouse or other
appropriate host animal is typically immunized with an immunizing
agent to elicit lymphocytes that produce or are capable of
producing antibodies that will specifically bind to the immunizing
agent. Alternatively, the lymphocytes may be immunized in
vitro.
[0814] The monoclonal antibodies may also be made by recombinant
DNA methods, such as those described in U.S. Pat. No. 4,816,567.
DNA encoding the monoclonal antibodies of the invention can be
readily isolated and sequenced using conventional procedures (e.g.,
by using oligonucleotide probes that are capable of binding
specifically to genes encoding the heavy and light chains of murine
antibodies).
[0815] In vitro methods are also suitable for preparing monovalent
antibodies. Digestion of antibodies to produce fragments thereof,
particularly Fab fragments, can be accomplished using routine
techniques known in the art. For instance, digestion can be
performed using papain. Examples of papain digestion are described
in WO 94/29348 and U.S. Pat. No. 4,342,566. Papain digestion of
antibodies typically produces two identical antigen binding
fragments, called Fab fragments, each with a single antigen binding
site, and a residual Fc fragment. Pepsin treatment yields a F(ab')2
fragment and a pFc' fragment.
[0816] The antibody fragments, whether attached to other sequences
or not, can also include insertions, deletions, substitutions, or
other selected modifications of particular regions or specific
amino acids residues, provided the activity of the fragment is not
significantly altered or impaired compared to the non-modified
antibody or antibody fragment. These modifications can provide for
some additional property, such as to remove/add amino acids capable
of disulfide bonding, to increase its bio-longevity, to alter its
secretory characteristics, etc. In any case, the antibody fragment
must possess a bioactive property, such as binding activity,
regulation of binding at the binding domain, etc. Functional or
active regions of the antibody may be identified by mutagenesis of
a specific region of the protein, followed by expression and
testing of the expressed polypeptide. Such methods are readily
apparent to a skilled practitioner in the art and can include
site-specific mutagenesis of the nucleic acid encoding the antibody
fragment.
[0817] The antibodies of the invention may further comprise
humanized antibodies or human antibodies. Humanized forms of
non-human (e.g., murine) antibodies are chimeric immunoglobulins,
immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab'
or other antigen-binding subsequences of antibodies) which contain
minimal sequence derived from non-human immunoglobulin. Humanized
antibodies include human immunoglobulins (recipient antibody) in
which residues from a complementary determining region (CDR) of the
recipient are replaced by residues from a CDR of a non-human
species (donor antibody) such as mouse, rat or rabbit having the
desired specificity, affinity and capacity. In some instances, Fv
framework (FR) residues of the human immunoglobulin are replaced by
corresponding non-human residues. Humanized antibodies may also
comprise residues which are found neither in the recipient antibody
nor in the imported CDR or framework sequences. In general, the
humanized antibody will comprise substantially all of at least one,
and typically two, variable domains, in which all or substantially
all of the CDR regions correspond to those of a non-human
immunoglobulin and all or substantially all of the FR regions are
those of a human immunoglobulin consensus sequence. The humanized
antibody optimally also will comprise at least a portion of an
immunoglobulin constant region (Fc), typically that of a human
immunoglobulin.
[0818] Methods for humanizing non-human antibodies are well known
in the art. Generally, a humanized antibody has one or more amino
acid residues introduced into it from a source which is non-human.
These non-human amino acid residues are often referred to as
"import" residues, which are typically taken from an "import"
variable domain. Humanization can be essentially performed by
substituting rodent CDRs or CDR sequences for the corresponding
sequences of a human antibody. Accordingly, such "humanized"
antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567),
wherein substantially less than an intact human variable domain has
been substituted by the corresponding sequence from a non-human
species. In practice, humanized antibodies are typically human
antibodies in which some CDR residues and possibly some FR residues
are substituted by residues from analogous sites in rodent
antibodies.
[0819] Transgenic animals (e.g., mice) that are capable, upon
immunization, of producing a full repertoire of human antibodies in
the absence of endogenous immunoglobulin production can be
employed. For example, it has been described that the homozygous
deletion of the antibody heavy chain joining region gene in
chimeric and germ-line mutant mice results in complete inhibition
of endogenous antibody production. Transfer of the human germ-line
immunoglobulin gene array in such germ-line mutant mice will result
in the production of human antibodies upon antigen challenge. Human
antibodies can also be produced in phage display libraries.
[0820] Antibodies of the invention are preferably administered to a
subject in a pharmaceutically acceptable carrier. Typically, an
appropriate amount of a pharmaceutically-acceptable salt is used in
the formulation to render the formulation isotonic. Examples of the
pharmaceutically-acceptable carrier include saline, Ringer's
solution and dextrose solution. The pH of the solution is
preferably from about 5 to about 8, and more preferably from about
7 to about 7.5. Further carriers include sustained release
preparations such as semipermeable matrices of solid hydrophobic
polymers containing the antibody, which matrices are in the form of
shaped articles, e.g., films, liposomes or microparticles. It will
be apparent to those persons skilled in the art that certain
carriers may be more preferable depending upon, for instance, the
route of administration and concentration of antibody being
administered.
[0821] The antibodies can be administered to the subject, patient,
or cell by injection (e.g., intravenous, intraperitoneal,
subcutaneous, intramuscular), or by other methods such as infusion
that ensure its delivery to the bloodstream in an effective form.
The antibodies may also be administered by intratumoral or
peritumoral routes, to exert local as well as systemic therapeutic
effects. Local or intravenous injection is preferred.
[0822] Effective dosages and schedules for administering the
antibodies may be determined empirically, and making such
determinations is within the skill in the art. Those skilled in the
art will understand that the dosage of antibodies that must be
administered will vary depending on, for example, the subject that
will receive the antibody, the route of administration, the
particular type of antibody used and other drugs being
administered. A typical daily dosage of the antibody used alone
might range from about 1 (.mu.g/kg to up to 100 mg/kg of body
weight or more per day, depending on the factors mentioned above.
Following administration of an antibody, preferably for treating
ovarian cancer, the efficacy of the therapeutic antibody can be
assessed in various ways well known to the skilled practitioner.
For instance, the size, number, and/or distribution of cancer in a
subject receiving treatment may be monitored using standard tumor
imaging techniques. A therapeutically-administered antibody that
arrests tumor growth, results in tumor shrinkage, and/or prevents
the development of new tumors, compared to the disease course that
would occur in the absence of antibody administration, is an
efficacious antibody for treatment of cancer.
[0823] It is a further aspect of the invention to provide a method
for producing a soluble T-cell receptor (sTCR) recognizing a
specific peptide-MHC complex. Such soluble T-cell receptors can be
generated from specific T-cell clones, and their affinity can be
increased by mutagenesis targeting the complementarity-determining
regions. For the purpose of T-cell receptor selection, phage
display can be used (US 2010/0113300, (Liddy et al., 2012)). For
the purpose of stabilization of T-cell receptors during phage
display and in case of practical use as drug, alpha and beta chain
can be linked e.g. by non-native disulfide bonds, other covalent
bonds (single-chain T-cell receptor), or by dimerization domains
(Boulter et al., 2003; Card et al., 2004; Willcox et al., 1999).
The T-cell receptor can be linked to toxins, drugs, cytokines (see,
for example, US 2013/0115191), domains recruiting effector cells
such as an anti-CD3 domain, etc., in order to execute particular
functions on target cells. Moreover, it could be expressed in T
cells used for adoptive transfer. Further information can be found
in WO 2004/033685A1 and WO 2004/074322A1. A combination of sTCRs is
described in WO 2012/056407A1. Further methods for the production
are disclosed in WO 2013/057586A1.
[0824] In addition, the peptides and/or the TCRs or antibodies or
other binding molecules of the present invention can be used to
verify a pathologist's diagnosis of a cancer based on a biopsied
sample.
[0825] The antibodies or TCRs may also be used for in vivo
diagnostic assays. Generally, the antibody is labeled with a
radionucleotide (such as .sup.111In, .sup.99TC, .sup.14C,
.sup.131I, .sup.3H, .sup.32P or .sup.35S) so that the tumor can be
localized using immunoscintiography. In one embodiment, antibodies
or fragments thereof bind to the extracellular domains of two or
more targets of a protein selected from the group consisting of the
above-mentioned proteins, and the affinity value (Kd) is less than
1.times.10 .mu.M.
[0826] Antibodies for diagnostic use may be labeled with probes
suitable for detection by various imaging methods. Methods for
detection of probes include, but are not limited to, fluorescence,
light, confocal and electron microscopy; magnetic resonance imaging
and spectroscopy; fluoroscopy, computed tomography and positron
emission tomography. Suitable probes include, but are not limited
to, fluorescein, rhodamine, eosin and other fluorophores,
radioisotopes, gold, gadolinium and other lanthanides, paramagnetic
iron, fluorine-18 and other positron-emitting radionuclides.
Additionally, probes may be bi- or multi-functional and be
detectable by more than one of the methods listed. These antibodies
may be directly or indirectly labeled with said probes. Attachment
of probes to the antibodies includes covalent attachment of the
probe, incorporation of the probe into the antibody, and the
covalent attachment of a chelating compound for binding of probe,
amongst others well recognized in the art. For
immunohistochemistry, the disease tissue sample may be fresh or
frozen or may be embedded in paraffin and fixed with a preservative
such as formalin. The fixed or embedded section contains the sample
are contacted with a labeled primary antibody and secondary
antibody, wherein the antibody is used to detect the expression of
the proteins in situ.
[0827] Another aspect of the present invention includes an in vitro
method for producing activated T cells, the method comprising
contacting in vitro T cells with antigen loaded human MHC molecules
expressed on the surface of a suitable antigen-presenting cell for
a period of time sufficient to activate the T cell in an antigen
specific manner, wherein the antigen is a peptide according to the
invention. Preferably a sufficient amount of the antigen is used
with an antigen-presenting cell.
[0828] Preferably the mammalian cell lacks or has a reduced level
or function of the TAP peptide transporter. Suitable cells that
lack the TAP peptide transporter include T2, RMA-S and Drosophila
cells. TAP is the transporter associated with antigen
processing.
[0829] The human peptide loading deficient cell line T2 is
available from the American Type Culture Collection, 12301 Parklawn
Drive, Rockville, Md. 20852, USA under Catalogue No CRL 1992; the
Drosophila cell line Schneider line 2 is available from the ATCC
under Catalogue No CRL 19863; the mouse RMA-S cell line is
described in Ljunggren et al. (Ljunggren and Karre, 1985).
[0830] Preferably, before transfection the host cell expresses
substantially no MHC class I molecules. It is also preferred that
the stimulator cell expresses a molecule important for providing a
co-stimulatory signal for T-cells such as any of B7.1, B7.2, ICAM-1
and LFA 3. The nucleic acid sequences of numerous MHC class I
molecules and of the co-stimulator molecules are publicly available
from the GenBank and EMBL databases.
[0831] In case of a MHC class I epitope being used as an antigen,
the T cells are CD8-positive T cells.
[0832] If an antigen-presenting cell is transfected to express such
an epitope, preferably the cell comprises an expression vector
capable of expressing a peptide containing SEQ ID NO: 1 to SEQ ID
NO: 640, or a variant amino acid sequence thereof.
[0833] A number of other methods may be used for generating T cells
in vitro. For example, autologous tumor-infiltrating lymphocytes
can be used in the generation of CTL. Plebanski et al. (Plebanski
et al., 1995) made use of autologous peripheral blood lymphocytes
(PLBs) in the preparation of T cells. Furthermore, the production
of autologous T cells by pulsing dendritic cells with peptide or
polypeptide, or via infection with recombinant virus is possible.
Also, B cells can be used in the production of autologous T cells.
In addition, macrophages pulsed with peptide or polypeptide, or
infected with recombinant virus, may be used in the preparation of
autologous T cells. S. Walter et al. (Walter et al., 2003) describe
the in vitro priming of T cells by using artificial antigen
presenting cells (aAPCs), which is also a suitable way for
generating T cells against the peptide of choice. In the present
invention, aAPCs were generated by the coupling of preformed
MHC:peptide complexes to the surface of polystyrene particles
(microbeads) by biotin:streptavidin biochemistry. This system
permits the exact control of the MHC density on aAPCs, which allows
to selectively elicit high- or low-avidity antigen-specific T cell
responses with high efficiency from blood samples. Apart from
MHC:peptide complexes, aAPCs should carry other proteins with
co-stimulatory activity like anti-CD28 antibodies coupled to their
surface. Furthermore, such aAPC-based systems often require the
addition of appropriate soluble factors, e.g. cytokines, like
interleukin-12.
[0834] Allogeneic cells may also be used in the preparation of T
cells and a method is described in detail in WO 97/26328,
incorporated herein by reference. For example, in addition to
Drosophila cells and T2 cells, other cells may be used to present
antigens such as CHO cells, baculovirus-infected insect cells,
bacteria, yeast, vaccinia-infected target cells. In addition, plant
viruses may be used (see, for example, Porta et al. (Porta et al.,
1994) which describes the development of cowpea mosaic virus as a
high-yielding system for the presentation of foreign peptides.
[0835] The activated T cells that are directed against the peptides
of the invention are useful in therapy. Thus, a further aspect of
the invention provides activated T cells obtainable by the
foregoing methods of the invention.
[0836] Activated T cells, which are produced by the above method,
will selectively recognize a cell that aberrantly expresses a
polypeptide that comprises an amino acid sequence of SEQ ID NO: 1
to SEQ ID NO 640.
[0837] Preferably, the T cell recognizes the cell by interacting
through its TCR with the HLA/peptide-complex (for example,
binding). The T cells are useful in a method of killing target
cells in a patient whose target cells aberrantly express a
polypeptide comprising an amino acid sequence of the invention
wherein the patient is administered an effective number of the
activated T cells. The T cells that are administered to the patient
may be derived from the patient and activated as described above
(i.e. they are autologous T cells). Alternatively, the T cells are
not from the patient but are from another individual. Of course, it
is preferred if the individual is a healthy individual. By "healthy
individual" the inventors mean that the individual is generally in
good health, preferably has a competent immune system and, more
preferably, is not suffering from any disease that can be readily
tested for, and detected.
[0838] In vivo, the target cells for the CD8-positive T cells
according to the present invention can be cells of the tumor (which
sometimes express MHC class II) and/or stromal cells surrounding
the tumor (tumor cells) (which sometimes also express MHC class II;
(Dengjel et al., 2006)).
[0839] The T cells of the present invention may be used as active
ingredients of a therapeutic composition. Thus, the invention also
provides a method of killing target cells in a patient whose target
cells aberrantly express a polypeptide comprising an amino acid
sequence of the invention, the method comprising administering to
the patient an effective number of T cells as defined above.
[0840] By "aberrantly expressed" the inventors also mean that the
polypeptide is over-expressed compared to normal levels of
expression or that the gene is silent in normal (healthy) tissues.
By "over-expressed" the inventors mean that the polypeptide is
present at a level at least 1.2-fold of that present in normal
tissue; preferably at least 2-fold, and more preferably at least
5-fold or 10-fold the level present in normal tissue.
[0841] T cells may be obtained by methods known in the art, e.g.
those described above.
[0842] Protocols for this so-called adoptive transfer of T cells
are well known in the art. Reviews can be found in: Gattioni et al.
and Morgan et al. (Gattinoni et al., 2006; Morgan et al.,
2006).
[0843] Another aspect of the present invention includes the use of
the peptides complexed with MHC to generate a T-cell receptor whose
nucleic acid is cloned and is introduced into a host cell,
preferably a T cell. This engineered T cell can then be transferred
to a patient for therapy of cancer.
[0844] Any molecule of the invention, i.e. the peptide, nucleic
acid, antibody, expression vector, cell, activated T cell, T-cell
receptor or the nucleic acid encoding it, is useful for the
treatment of disorders, characterized by cells escaping an immune
response. Therefore, any molecule of the present invention may be
used as medicament or in the manufacture of a medicament. The
molecule may be used by itself or combined with other molecule(s)
of the invention or (a) known molecule(s).
[0845] The present invention further provides a medicament that is
useful in treating cancer, in particular ovarian cancer and other
malignancies.
[0846] The present invention is further directed at a kit
comprising:
(a) a container containing a pharmaceutical composition as
described above, 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.
[0847] 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. The
container is preferably a bottle, a vial, a syringe or test tube;
and it may be a multi-use container. The pharmaceutical composition
is preferably lyophilized.
[0848] Kits of the present invention preferably comprise a
lyophilized formulation of the present invention 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 may be formed from a variety of materials such
as glass or plastic. Preferably the kit and/or container contain/s
instructions on or associated with the container that indicates
directions for reconstitution and/or use. For example, the label
may indicate that the lyophilized formulation is to be
reconstituted to peptide concentrations as described above. The
label may further indicate that the formulation is useful or
intended for subcutaneous administration.
[0849] The container holding the formulation may be a multi-use
vial, which allows for repeat administrations (e.g., from 2-6
administrations) of the reconstituted formulation. The kit may
further comprise a second container comprising a suitable diluent
(e.g., sodium bicarbonate solution).
[0850] Upon mixing of the diluent and the lyophilized formulation,
the final peptide concentration in the reconstituted formulation is
preferably at least 0.15 mg/mL/peptide (=75 .mu.g) and preferably
not more than 3 mg/mL/peptide (=1500 .mu.g). The kit may further
include other materials desirable from a commercial and user
standpoint, including other buffers, diluents, filters, needles,
syringes, and package inserts with instructions for use.
[0851] Kits of the present invention may have a single container
that contains the formulation of the pharmaceutical compositions
according to the present invention with or without other components
(e.g., other compounds or pharmaceutical compositions of these
other compounds) or may have distinct container for each
component.
[0852] Preferably, kits of the invention include a formulation of
the invention packaged for use in combination with the
co-administration of a second compound (such as adjuvants (e.g.
GM-CSF), 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 pharmaceutical
composition thereof. The components of the kit may be pre-complexed
or each component may be in a separate distinct container prior to
administration to a patient. The components of the kit may be
provided in one or more liquid solutions, preferably, an aqueous
solution, more preferably, a sterile aqueous solution. The
components of the kit may also be provided as solids, which may be
converted into liquids by addition of suitable solvents, which are
preferably provided in another distinct container.
[0853] The container of a therapeutic kit may be a vial, test tube,
flask, bottle, syringe, or any other means of enclosing a solid or
liquid. Usually, when there is more than one component, the kit
will contain a second vial or other container, which allows for
separate dosing. The kit may also contain another container for a
pharmaceutically acceptable liquid. Preferably, a therapeutic kit
will contain an apparatus (e.g., one or more needles, syringes, eye
droppers, pipette, etc.), which enables administration of the
agents of the invention that are components of the present kit.
[0854] The present formulation is one that is suitable for
administration of the peptides by any acceptable route such as oral
(enteral), nasal, ophthal, subcutaneous, intradermal,
intramuscular, intravenous or transdermal. Preferably, the
administration is s.c., and most preferably i.d. administration may
be by infusion pump.
[0855] Since the peptides of the invention were isolated from
ovarian cancer, the medicament of the invention is preferably used
to treat ovarian cancer.
[0856] The present invention further relates to a method for
producing a personalized pharmaceutical for an individual patient
comprising manufacturing a pharmaceutical composition comprising at
least one peptide selected from a warehouse of pre-screened TUMAPs,
wherein the at least one peptide used in the pharmaceutical
composition is selected for suitability in the individual patient.
In one embodiment, the pharmaceutical composition is a vaccine. The
method could also be adapted to produce T cell clones for
down-stream applications, such as TCR isolations, or soluble
antibodies, and other treatment options.
[0857] A "personalized pharmaceutical" shall mean specifically
tailored therapies for one individual patient that will only be
used for therapy in such individual patient, including actively
personalized cancer vaccines and adoptive cellular therapies using
autologous patient tissue.
[0858] As used herein, the term "warehouse" shall refer to a group
or set of peptides that have been pre-screened for immunogenicity
and/or over-presentation in a particular tumor type. The term
"warehouse" is not intended to imply that the particular peptides
included in the vaccine have been pre-manufactured and stored in a
physical facility, although that possibility is contemplated. It is
expressly contemplated that the peptides may be manufactured de
novo for each individualized vaccine produced, or may be
pre-manufactured and stored. The warehouse (e.g. in the form of a
database) is composed of tumor-associated peptides which were
highly overexpressed in the tumor tissue of ovarian cancer patients
with various HLA-A HLA-B and HLA-C alleles. It may contain MHC
class I and MHC class II peptides or elongated MHC class I
peptides. In addition to the tumor associated peptides collected
from several ovarian cancer tissues, the warehouse may contain
HLA-A*02 and HLA-A*24 marker peptides. These peptides allow
comparison of the magnitude of T-cell immunity induced by TUMAPS in
a quantitative manner and hence allow important conclusion to be
drawn on the capacity of the vaccine to elicit anti-tumor
responses. Secondly, they function as important positive control
peptides derived from a "non-self" antigen in the case that any
vaccine-induced T-cell responses to TUMAPs derived from "self"
antigens in a patient are not observed. And thirdly, it may allow
conclusions to be drawn, regarding the status of immunocompetence
of the patient.
[0859] TUMAPs for the warehouse are identified by using an
integrated functional genomics approach combining gene expression
analysis, mass spectrometry, and T-cell immunology
(XPresident.RTM.)). The approach assures that only TUMAPs truly
present on a high percentage of tumors but not or only minimally
expressed on normal tissue, are chosen for further analysis. For
initial peptide selection, ovarian cancer samples from patients and
blood from healthy donors were analyzed in a stepwise approach:
1. HLA ligands from the malignant material were identified by mass
spectrometry 2. Genome-wide messenger ribonucleic acid (mRNA)
expression analysis was used to identify genes over-expressed in
the malignant tissue (ovarian cancer) compared with a range of
normal organs and tissues 3. Identified HLA ligands were compared
to gene expression data. Peptides over-presented or selectively
presented on tumor tissue, preferably encoded by selectively
expressed or over-expressed genes as detected in step 2 were
considered suitable TUMAP candidates for a multi-peptide vaccine.
4. Literature research was performed in order to identify
additional evidence supporting the relevance of the identified
peptides as TUMAPs 5. The relevance of over-expression at the mRNA
level was confirmed by redetection of selected TUMAPs from step 3
on tumor tissue and lack of (or infrequent) detection on healthy
tissues. 6. In order to assess, whether an induction of in vivo
T-cell responses by the selected peptides may be feasible, in vitro
immunogenicity assays were performed using human T cells from
healthy donors as well as from ovarian cancer patients.
[0860] In an aspect, the peptides are pre-screened for
immunogenicity before being included in the warehouse. By way of
example, and not limitation, the immunogenicity of the peptides
included in the warehouse is determined by a method comprising in
vitro T-cell priming through repeated stimulations of CD8+ T cells
from healthy donors with artificial antigen presenting cells loaded
with peptide/MHC complexes and anti-CD28 antibody.
[0861] This method is preferred for rare cancers and patients with
a rare expression profile. In contrast to multi-peptide cocktails
with a fixed composition as currently developed, the warehouse
allows a significantly higher matching of the actual expression of
antigens in the tumor with the vaccine. Selected single or
combinations of several "off-the-shelf" peptides will be used for
each patient in a multitarget approach. In theory an approach based
on selection of e.g. 5 different antigenic peptides from a library
of 50 would already lead to approximately 17 million possible drug
product (DP) compositions.
[0862] In an aspect, the peptides are selected for inclusion in the
vaccine based on their suitability for the individual patient based
on the method according to the present invention as described
herein, or as below.
[0863] The HLA phenotype, transcriptomic and peptidomic data is
gathered from the patient's tumor material, and blood samples to
identify the most suitable peptides for each patient containing
"warehouse" and patient-unique (i.e. mutated) TUMAPs. Those
peptides will be chosen, which are selectively or over-expressed in
the patients' tumor and, where possible, show strong in vitro
immunogenicity if tested with the patients' individual PBMCs.
[0864] Preferably, the peptides included in the vaccine are
identified by a method comprising: (a) identifying tumor-associated
peptides (TUMAPs) presented by a tumor sample from the individual
patient; (b) comparing the peptides identified in (a) with a
warehouse (database) of peptides as described above; and (c)
selecting at least one peptide from the warehouse (database) that
correlates with a tumor-associated peptide identified in the
patient. For example, the TUMAPs presented by the tumor sample are
identified by: (al) comparing expression data from the tumor sample
to expression data from a sample of normal tissue corresponding to
the tissue type of the tumor sample to identify proteins that are
over-expressed or aberrantly expressed in the tumor sample; and
(a2) correlating the expression data with sequences of MHC ligands
bound to MHC class I and/or class II molecules in the tumor sample
to identify MHC ligands derived from proteins over-expressed or
aberrantly expressed by the tumor. Preferably, the sequences of MHC
ligands are identified by eluting bound peptides from MHC molecules
isolated from the tumor sample, and sequencing the eluted ligands.
Preferably, the tumor sample and the normal tissue are obtained
from the same patient.
[0865] In addition to, or as an alternative to, selecting peptides
using a warehousing (database) model, TUMAPs may be identified in
the patient de novo, and then included in the vaccine. As one
example, candidate TUMAPs may be identified in the patient by (al)
comparing expression data from the tumor sample to expression data
from a sample of normal tissue corresponding to the tissue type of
the tumor sample to identify proteins that are over-expressed or
aberrantly expressed in the tumor sample; and (a2) correlating the
expression data with sequences of MHC ligands bound to MHC class I
and/or class II molecules in the tumor sample to identify MHC
ligands derived from proteins over-expressed or aberrantly
expressed by the tumor. As another example, proteins may be
identified containing mutations that are unique to the tumor sample
relative to normal corresponding tissue from the individual
patient, and TUMAPs can be identified that specifically target the
mutation. For example, the genome of the tumor and of corresponding
normal tissue can be sequenced by whole genome sequencing: For
discovery of non-synonymous mutations in the protein-coding regions
of genes, genomic DNA and RNA are extracted from tumor tissues and
normal non-mutated genomic germline DNA is extracted from
peripheral blood mononuclear cells (PBMCs). The applied NGS
approach is confined to the re-sequencing of protein coding regions
(exome re-sequencing). For this purpose, exonic DNA from human
samples is captured using vendor-supplied target enrichment kits,
followed by sequencing with e.g. a HiSeq2000 (Illumina).
Additionally, tumor mRNA is sequenced for direct quantification of
gene expression and validation that mutated genes are expressed in
the patients' tumors. The resultant millions of sequence reads are
processed through software algorithms. The output list contains
mutations and gene expression. Tumor-specific somatic mutations are
determined by comparison with the PBMC-derived germline variations
and prioritized. The de novo identified peptides can then be tested
for immunogenicity as described above for the warehouse, and
candidate TUMAPs possessing suitable immunogenicity are selected
for inclusion in the vaccine.
[0866] In one exemplary embodiment, the peptides included in the
vaccine are identified by: (a) identifying tumor-associated
peptides (TUMAPs) presented by a tumor sample from the individual
patient by the method as described above; (b) comparing the
peptides identified in a) with a warehouse of peptides that have
been prescreened for immunogenicity and overpresentation in tumors
as compared to corresponding normal tissue; (c) selecting at least
one peptide from the warehouse that correlates with a
tumor-associated peptide identified in the patient; and (d)
optionally, selecting at least one peptide identified de novo in
(a) confirming its immunogenicity.
[0867] In one exemplary embodiment, the peptides included in the
vaccine are identified by: (a) identifying tumor-associated
peptides (TUMAPs) presented by a tumor sample from the individual
patient; and (b) selecting at least one peptide identified de novo
in (a) and confirming its immunogenicity.
[0868] Once the peptides for a personalized peptide based vaccine
are selected, the vaccine is produced. The vaccine preferably is a
liquid formulation consisting of the individual peptides dissolved
in between 20-40% DMSO, preferably about 30-35% DMSO, such as about
33% DMSO.
[0869] Each peptide to be included into a product is dissolved in
DMSO. The concentration of the single peptide solutions has to be
chosen depending on the number of peptides to be included into the
product. The single peptide-DMSO solutions are mixed in equal parts
to achieve a solution containing all peptides to be included in the
product with a concentration of .about.2.5 mg/ml per peptide. The
mixed solution is then diluted 1:3 with water for injection to
achieve a concentration of 0.826 mg/ml per peptide in 33% DMSO. The
diluted solution is filtered through a 0.22 .mu.m sterile filter.
The final bulk solution is obtained.
[0870] Final bulk solution is filled into vials and stored at
-20.degree. C. until use. One vial contains 700 .mu.L solution,
containing 0.578 mg of each peptide. Of this, 500 .mu.L (approx.
400 .mu.g per peptide) will be applied for intradermal
injection.
[0871] In addition to being useful for treating cancer, the
peptides of the present invention are also useful as diagnostics.
Since the peptides were generated from ovarian cancer samples and
since it was determined that these peptides are not or at lower
levels present in normal tissues, these peptides can be used to
diagnose the presence of a cancer.
[0872] The presence of claimed peptides on tissue biopsies in blood
samples can assist a pathologist in diagnosis of cancer. Detection
of certain peptides by means of antibodies, mass spectrometry or
other methods known in the art can tell the pathologist that the
tissue sample is malignant or inflamed or generally diseased, or
can be used as a biomarker for ovarian cancer. Presence of groups
of peptides can enable classification or sub-classification of
diseased tissues.
[0873] The detection of peptides on diseased tissue specimen can
enable the decision about the benefit of therapies involving the
immune system, especially if T-lymphocytes are known or expected to
be involved in the mechanism of action. Loss of MHC expression is a
well described mechanism by which infected of malignant cells
escape immuno-surveillance. Thus, presence of peptides shows that
this mechanism is not exploited by the analyzed cells.
[0874] The peptides of the present invention might be used to
analyze lymphocyte responses against those peptides such as T cell
responses or antibody responses against the peptide or the peptide
complexed to MHC molecules. These lymphocyte responses can be used
as prognostic markers for decision on further therapy steps. These
responses can also be used as surrogate response markers in
immunotherapy approaches aiming to induce lymphocyte responses by
different means, e.g. vaccination of protein, nucleic acids,
autologous materials, adoptive transfer of lymphocytes. In gene
therapy settings, lymphocyte responses against peptides can be
considered in the assessment of side effects. Monitoring of
lymphocyte responses might also be a valuable tool for follow-up
examinations of transplantation therapies, e.g. for the detection
of graft versus host and host versus graft diseases.
[0875] The present invention will now be described in the following
examples which describe preferred embodiments thereof, and with
reference to the accompanying figures, nevertheless, without being
limited thereto. For the purposes of the present invention, all
references as cited herein are incorporated by reference in their
entireties.
BRIEF DESCRIPTION OF THE DRAWINGS
[0876] The patent or application file contains at least one drawing
executed in color. Copies of this patent or patent application
publication with color drawing(s) will be provided by the Office
upon request and payment of the necessary fee.
[0877] FIGS. 1A to 1AE show the over-presentation of various
peptides in normal tissues (white bars) and ovarian cancer (black
bars). FIG. 1A) Gene symbol: CLSR2, Peptide: VLVSDGVHSV (SEQ ID
NO.: 6); Tissues from left to right: 1 adipose tissues, 3 adrenal
glands, 6 arteries, 5 bone marrows, 7 brains, 3 breasts, 1 central
nerve, 13 colons, 1 duodenum, 8 esophagi, 2 gallbladders, 5 hearts,
16 kidneys, 2 lymph nodes, 21 livers, 46 lungs, 1 lymph node
metastasis, 4 leukocyte samples, 7 pancreas, 4 peripheral nerves, 1
peritoneum, 3 pituitary glands, 2 placentas, 3 pleuras, 3
prostates, 6 recti, 7 salivary glands, 3 skeletal muscles, 5 skins,
2 small intestines, 4 spleens, 7 stomachs, 4 testis, 3 thymi, 4
thyroid glands, 7 tracheas, 3 ureters, 6 urinary bladders, 2 uteri,
2 veins, 3 ovaries, 20 OC. The peptide has additionally been
detected on 1/6 breast cancers, 1/2 Merkel cell carcinomas, 3/17
esophageal cancers, 3/91 lung cancers, 10/29 brain cancers, 1/22
renal cancers and 1/15 small cell lung cancers (not shown). FIG.
1B) Gene symbol: CCNA1, Peptide: SLMEPPAVLLL (SEQ ID NO.: 1);
Tissues from left to right: 1 adipose tissues, 3 adrenal glands, 6
arteries, 5 bone marrows, 7 brains, 3 breasts, 1 central nerve, 13
colons, 1 duodenum, 8 esophagi, 2 gallbladders, 5 hearts, 16
kidneys, 2 lymph nodes, 21 livers, 46 lungs, 1 lymph node
metastasis, 4 leukocyte samples, 7 pancreas, 4 peripheral nerves, 1
peritoneum, 3 pituitary glands, 2 placentas, 3 pleuras, 3
prostates, 6 recti, 7 salivary glands, 3 skeletal muscles, 5 skins,
2 small intestines, 4 spleens, 7 stomachs, 4 testis, 3 thymi, 4
thyroid glands, 7 tracheas, 3 ureters, 6 urinary bladders, 2 uteri,
2 veins, 3 ovaries, 20 OC. The peptide has additionally been
detected on 1/2 AMLs, 1/28 colorectal cancers, 2/17 esophageal
cancers, 7/91 lung cancers, 1/29 brain cancers, 1/22 renal cancers
and 2/15 small cell lung cancers (not shown). FIG. 1C) Gene symbol:
VTCN1, Peptide: ALLPLSPYL (SEQ ID NO.: 427); Tissues from left to
right: 1 adipose tissues, 3 adrenal glands, 6 arteries, 5 bone
marrows, 7 brains, 3 breasts, 1 central nerve, 13 colons, 1
duodenum, 8 esophagi, 2 gallbladders, 5 hearts, 16 kidneys, 2 lymph
nodes, 21 livers, 46 lungs, 1 lymph node metastasis, 4 leukocyte
samples, 7 pancreas, 4 peripheral nerves, 1 peritoneum, 3 pituitary
glands, 2 placentas, 3 pleuras, 3 prostates, 6 recti, 7 salivary
glands, 3 skeletal muscles, 5 skins, 2 small intestines, 4 spleens,
7 stomachs, 4 testis, 3 thymi, 4 thyroid glands, 7 tracheas, 3
ureters, 6 urinary bladders, 2 uteri, 2 veins, 3 ovaries, 20 OC.
The peptide has additionally been detected on 4/43 prostate
cancers, 3/6 breast cancers, 4/16 liver cancers, 1/17 esophageal
cancers, 4/19 pancreatic cancers, 19/91 lung cancers, 1/15 small
cell lung cancers, 1/4 urinary bladder cancers and 3/4 uterine
cancers (not shown). FIG. 1D) Gene symbol: AP1B1, Peptide:
FLDTLKDLI SEQ ID NO.: 514); Tissues from left to right: 6 cell
lines (1 lyphocytic, 1 kidney, 1 pancreatic, 2 PBMCs, K562-A2), 4
normal tissues (2 bone marrows, 2 spleens), 49 cancer tissues (1
breast cancer, 3 colon cancers, 2 esophageal cancers, 1 gallbladder
cancer, 2 leukemias, 3 liver cancers, 21 lung cancers, 7 ovarian
cancers, 23 rectum cancers, 1 skin cancer, 4 stomach cancers, 1
testis cancer, 1 urinary bladder cancer). The normal tissue panel
and the cancer cell lines and xenografts tested were the same as in
FIG. 1A-C, consisting of 1 adipose tissue, 3 adrenal glands, 6
arteries, 5 bone marrows, 7 brains, 3 breasts, 1 central nerve, 13
colons, 1 duodenum, 8 esophagi, 2 gallbladders, 5 hearts, 16
kidneys, 2 lymph nodes, 21 livers, 46 lungs, 1 lymph node
metastasis, 4 leukocyte samples, 7 pancreas, 4 peripheral nerves, 1
peritoneum, 3 pituitary glands, 2 placentas, 3 pleuras, 3
prostates, 6 recti, 7 salivary glands, 3 skeletal muscles, 5 skins,
2 small intestines, 4 spleens, 7 stomachs, 4 testes, 3 thymi, 4
thyroid glands, 7 tracheas, 3 ureters, 6 urinary bladders, 2 uteri,
2 veins, 3 ovaries, 20 OC. The peptide has additionally been
detected on 2/12 chronic lymphocytic leukemias, 5/28 colorectal
cancers, 2/16 liver cancers, 1/2 melanomas, 2/17 esophageal
cancers, 17/91 lung cancers, 4/46 stomach cancers, 4/15 small cell
lung cancers and 1/4 urinary bladder cancers. Discrepancies
regarding the list of tumor types between FIG. 1D and table 4 might
be due to the more stringent selection criteria applied in table 4
(for details please refer to table 4). FIG. 1D shows all samples
with detectable presentation of the peptide Y, regardless of
over-presentation parameters and technical sample quality check.
FIG. 1E) Gene symbol(s): CELSR2, Peptide: VLVSDGVHSV (SEQ ID NO.:
6). Tissues from left to right: 6 adipose tissues, 8 adrenal
glands, 24 blood cells, 15 blood vessels, 10 bone marrows, 13
brains, 7 breasts, 9 esophagi, 2 eyes, 3 gallbladders, 16 hearts,
17 kidneys, 25 large intestines, 24 livers, 49 lungs, 7 lymph
nodes, 12 nerves, 3 ovaries, 13 pancreases, 6 parathyroid glands, 1
peritoneum, 6 pituitary glands, 7 placentas, 1 pleura, 4 prostates,
7 salivary glands, 9 skeletal muscles, 11 skins, 9 small
intestines, 12 spleens, 8 stomachs, 5 testes, 3 thymi, 5 thyroid
glands, 16 tracheas, 7 ureters, 8 urinary bladders, 6 uteri, 20
ovarian cancer samples. The peptide has additionally been found on
15/34 brain cancers, 3/18 breast cancers, 3/18 esophageal cancers,
4/12 head and neck cancers, 1/23 kidney cancers, 6/107 lung
cancers, 5/18 skin cancers, 5/15 urinary bladder cancers, 3/16
uterus cancers. FIG. 1F) Gene symbol(s): SUCO, Peptide: LLLDITPEI
(SEQ ID NO.: 143). Tissues from left to right: 6 adipose tissues, 8
adrenal glands, 24 blood cells, 15 blood vessels, 10 bone marrows,
13 brains, 7 breasts, 9 esophagi, 2 eyes, 3 gallbladders, 16
hearts, 17 kidneys, 25 large intestines, 24 livers, 49 lungs, 7
lymph nodes, 12 nerves, 3 ovaries, 13 pancreases, 6 parathyroid
glands, 1 peritoneum, 6 pituitary glands, 7 placentas, 1 pleura, 4
prostates, 7 salivary glands, 9 skeletal muscles, 11 skins, 9 small
intestines, 12 spleens, 8 stomachs, 5 testes, 3 thymi, 5 thyroid
glands, 16 tracheas, 7 ureters, 8 urinary bladders, 6 uteri, 20
ovarian cancer samples. The peptide has additionally been found on
2/34 brain cancers, 4/18 breast cancers, 2/18 esophageal cancers,
1/12 head and neck cancers, 2/21 liver cancers, 6/107 lung cancers,
2/18 skin cancers, 1/45 stomach cancers, 2/15 urinary bladder
cancers. FIG. 1G) Gene symbol(s): PLAUR, Peptide: RLWEEGEELEL (SEQ
ID NO.: 150). Tissues from left to right: 6 adipose tissues, 8
adrenal glands, 24 blood cells, 15 blood vessels, 10 bone marrows,
13 brains, 7 breasts, 9 esophagi, 2 eyes, 3 gallbladders, 16
hearts, 17 kidneys, 25 large intestines, 24 livers, 49 lungs, 7
lymph nodes, 12 nerves, 3 ovaries, 13 pancreases, 6 parathyroid
glands, 1 peritoneum, 6 pituitary glands, 7 placentas, 1 pleura, 4
prostates, 7 salivary glands, 9 skeletal muscles, 11 skins, 9 small
intestines, 12 spleens, 8 stomachs, 5 testes, 3 thymi, 5 thyroid
glands, 16 tracheas, 7 ureters, 8 urinary bladders, 6 uteri, 20
ovarian cancer samples. The peptide has additionally been found on
4/17 gallbladder and bile duct cancers, 1/18 breast cancers, 1/29
colon cancers, 2/18 esophageal cancers, 1/12 head and neck cancers,
10/107 lung cancers, 2/18 skin cancers, 1/16 uterus cancers. FIG.
1H) Gene symbol(s): HEATR2, Peptide: SLNDEVPEV (SEQ ID NO.: 157).
Tissues from left to right: 6 adipose tissues, 8 adrenal glands, 24
blood cells, 15 blood vessels, 10 bone marrows, 13 brains, 7
breasts, 9 esophagi, 2 eyes, 3 gallbladders, 16 hearts, 17 kidneys,
25 large intestines, 24 livers, 49 lungs, 7 lymph nodes, 12 nerves,
3 ovaries, 13 pancreases, 6 parathyroid glands, 1 peritoneum, 6
pituitary glands, 7 placentas, 1 pleura, 4 prostates, 7 salivary
glands, 9 skeletal muscles, 11 skins, 9 small intestines, 12
spleens, 8 stomachs, 5 testes, 3 thymi, 5 thyroid glands, 16
tracheas, 7 ureters, 8 urinary bladders, 6 uteri, 20 ovarian cancer
samples. The peptide has additionally been found on 1/17 bile duct
cancers, 5/34 brain cancers, 1/18 breast cancers, 1/29 colon
cancers, 2/18 esophageal cancers, 1/12 head and neck cancers, 2/23
kidney cancers, 1/21 liver cancers, 4/107 lung cancers, 2/20 lymph
node cancers, 1/18 skin cancers, 1/15 urinary bladder cancers, 1/16
uterus cancers. FIG. 1I) Gene symbol(s): VTCN1, Peptide: ALLPLSPYL
(SEQ ID NO.: 427). Tissues from left to right: 6 adipose tissues, 8
adrenal glands, 24 blood cells, 15 blood vessels, 10 bone marrows,
13 brains, 7 breasts, 9 esophagi, 2 eyes, 3 gallbladders, 16
hearts, 17 kidneys, 25 large intestines, 24 livers, 49 lungs, 7
lymph nodes, 12 nerves, 3 ovaries, 13 pancreases, 6 parathyroid
glands, 1 peritoneum, 6 pituitary glands, 7 placentas, 1 pleura, 4
prostates, 7 salivary glands, 9 skeletal muscles, 11 skins, 9 small
intestines, 12 spleens, 8 stomachs, 5 testes, 3 thymi, 5 thyroid
glands, 16 tracheas, 7 ureters, 8 urinary bladders, 6 uteri, 20
ovarian cancer samples. The peptide has additionally been found on
7/17 gallbladder and bile duct cancers, 9/18 breast cancers, 2/18
esophageal cancers, 1/12 head and neck cancers, 7/21 liver cancers,
22/107 lung cancers, 4/19 pancreas cancers, 4/87 prostate cancers,
2/15 urinary bladder cancers, 11/16 uterus cancers. FIG. 1J) Gene
symbol(s): DDX11, DDX12P, LOC642846, Peptide: GLLRDEALAEV (SEQ ID
NO.: 444). Tissues from left to right: 6 adipose tissues, 8 adrenal
glands, 24 blood cells, 15 blood vessels, 10 bone marrows, 13
brains, 7 breasts, 9 esophagi, 2 eyes, 3 gallbladders, 16 hearts,
17 kidneys, 25 large intestines, 24 livers, 49 lungs, 7 lymph
nodes, 12 nerves, 3 ovaries, 13 pancreases, 6 parathyroid glands, 1
peritoneum, 6 pituitary glands, 7 placentas, 1 pleura, 4 prostates,
7 salivary glands, 9 skeletal muscles, 11 skins, 9 small
intestines, 12 spleens, 8 stomachs, 5 testes, 3 thymi, 5 thyroid
glands, 16 tracheas, 7 ureters, 8 urinary bladders, 6 uteri, 20
ovarian cancer samples. The peptide has additionally been found on
2/18 breast cancers, 3/29 colon or rectum cancers, 1/18 esophageal
cancers, 1/12 head and neck cancers, 1/23 kidney cancers, 2/17
leukocytic leukemia cancers, 9/107 lung cancers, 6/20 lymph node
cancers, 1/18 myeloid cells cancer, 2/18 skin cancers, 2/15 urinary
bladder cancers, 1/16 uterus cancers. FIG. 1K) Gene symbol(s):
KDM1B, Peptide: KLAEGLDIQL (SEQ ID NO.: 449). Tissues from left to
right: 6 adipose tissues, 8 adrenal glands, 24 blood cells, 15
blood vessels, 10 bone marrows, 13 brains, 7 breasts, 9 esophagi, 2
eyes, 3 gallbladders, 16 hearts, 17 kidneys, 25 large intestines,
24 livers, 49 lungs, 7 lymph nodes, 12 nerves, 3 ovaries, 13
pancreases, 6 parathyroid glands, 1 peritoneum, 6 pituitary glands,
7 placentas, 1 pleura, 4 prostates, 7 salivary glands, 9 skeletal
muscles, 11 skins, 9 small intestines, 12 spleens, 8 stomachs, 5
testes, 3 thymi, 5 thyroid glands, 16 tracheas, 7 ureters, 8
urinary bladders, 6 uteri, 20 ovarian cancer samples. The peptide
has additionally been found on 3/29 colon or rectum cancers, 6/107
lung cancers, 1/20 lymph node cancers. FIG. 1L) Gene symbol(s):
CCNA1, Peptide: SLMEPPAVLLL (SEQ ID NO.: 1). Tissues from left to
right: 1 cancer cell line, 1 normal tissue (1 lymph node), 45
cancer tissues (3 bone marrow cancers, 1 brain cancer, 1 breast
cancer, 2 esophageal cancers, 1 head and neck cancer, 1 kidney
cancer, 3 leukocytic leukemia cancers, 12 lung cancers, 1 myeloid
cell cancer, 11 ovarian cancers, 2 urinary bladder cancers, 7
uterus cancers. The normal tissue panel tested was the same as in
FIG. 1E-K. FIG. 1M) Gene symbol(s): CT45A5, LOC101060208, CT45A3,
CT45A1, LOC101060211, CT45A6, CT45A4, LOC101060210, CT45A2,
Peptide: KIFEMLEGV (SEQ ID NO.: 11). Tissues from left to right: 3
normal tissues (1 brain, 1 lung, 1 ureter), 21 cancer tissues (1
bile duct cancer, 1 esophageal cancer, 1 liver cancer, 10 lung
cancers, 1 lymph node cancer, 5 ovarian cancers, 2 uterus cancers).
The normal tissue panel tested was the same as in FIG. 1E-K. FIG.
1N) Gene symbol(s): FGFR1OP, Peptide: KLDDLTQDLTV (SEQ ID NO.: 32).
Tissues from left to right: 1 cell line, 1 normal tissue (1 liver),
29 cancer tissues (2 bile duct cancers, 1 esophageal cancer, 2 head
and neck cancers, 4 liver cancers, 4 lung cancers, 3 lymph node
cancers, 8 ovarian cancers, 1 prostate cancer, 1 rectum cancer, 2
urinary bladder cancers, 1 uterus cancer). The normal tissue panel
tested was the same as in FIG. 1E-K. FIG. 1O) Gene symbol(s):
TSEN15, Peptide: FLLEDDIHVS (SEQ ID NO.: 38). Tissues from left to
right: 1 primary culture, 1 normal tissue (1 trachea), 28 cancer
tissues (2 breast cancers, 1 head and neck cancer, 4 leukocytic
leukemia cancers, 5 lung cancers, 6 lymph node cancers, 1 myeloid
cell cancer, 2 ovarian cancers, 1 rectum cancer, 3 skin cancers, 2
urinary bladder cancers, 1 uterus cancer). The normal tissue panel
tested was the same as in FIG. 1E-K. FIG. 1P) Gene symbol(s):
ZNF527, ZNF829, ZNF383, ZNF850, ZNF583, Peptide: SLLEQGKEPWMV (SEQ
ID NO.: 54). Tissues from left to right: 1 cell line, 18 cancer
tissues (2 brain cancers, 1 breast cancer, 1 gallbladder cancer, 1
leukocytic leukemia cancer, 2 liver cancers, 7 lung cancers, 1
lymph node cancer, 2 ovarian cancers, 1 urinary bladder cancer).
The normal tissue panel tested was the same as in FIG. 1E-K. FIG.
1Q) Gene symbol(s): CAMSAP1, Peptide: TLAELQPPVQL (SEQ ID NO.: 57).
Tissues from left to right: 4 cell lines and primary cultures, 32
cancer tissues (1 bile duct cancer, 1 brain cancer, 2 esophageal
cancers, 3 head and neck cancers, 2 leukocytic leukemia cancers, 1
liver cancer, 9 lung cancers, 4 lymph node cancers, 5 ovarian
cancers, 2 skin cancers, 1 urinary bladder cancer, 1 uterus
cancer). The normal tissue panel tested was the same as in FIG.
1E-K. FIG. 1R) Gene symbol(s): STK38L, Peptide: ILVEADGAWVV (SEQ ID
NO.: 77). Tissues from left to right: 4 cell lines, 19 cancer
tissues (1 brain cancer, 2 breast cancers, 1 colon cancer, 1
leukocytic leukemia cancer, 4 lung cancers, 3 lymph node cancers, 3
ovarian cancers, 1 prostate cancer, 1 skin cancer, 1 urinary
bladder cancer, 1 uterus cancer). The normal tissue panel tested
was the same as in FIG. 1E-K. FIG. 1S) Gene symbol(s): PIGA,
Peptide: ALNPEIVSV (SEQ ID NO.: 148). Tissues from left to right: 3
cell lines, 20 cancer tissues (1 esophageal cancer, 2 head and neck
cancers, 1 leukocytic leukemia cancer, 5 lung cancers, 3 lymph node
cancers, 2 ovarian cancers, 2 skin cancers, 4 urinary bladder
cancers). The normal tissue panel tested was the same as in FIG.
1E-K. FIG. 1T) Gene symbol(s): NPLOC4, Peptide: YLNHLEPPV (SEQ ID
NO.: 166). Tissues from left to right: 2 cell lines, 20 cancer
tissues (3 brain cancers, 1 breast cancer, 1 esophageal cancer, 3
leukocytic leukemia cancers, 2 liver cancers, 4 lung cancers, 2
lymph node cancers, 1 myeloid cells cancer, 3 ovarian cancers). The
normal tissue panel tested was the same as in FIG. 1E-K. FIG. 1U)
Gene symbol(s): RNF213, Peptide: YLMDINGKMWL (SEQ ID NO.: 184).
Tissues from left to right: 1 cell line, 19 cancer tissues (1
breast cancer, 1 gallbladder cancer, 1 leukocytic leukemia cancer,
6 lung cancers, 2 lymph node cancers, 5 ovarian cancers, 2 skin
cancers, 1 uterus cancer). The normal tissue panel tested was the
same as in
FIG. 1E-K. FIG. 1V) Gene symbol(s): SKIL, Peptide: KTINKVPTV (SEQ
ID NO.: 198). Tissues from left to right: 2 cell lines and primary
cultures, 1 normal tissue (1 lung), 36 cancer tissues (3 brain
cancers, 2 breast cancers, 2 colon cancers, 1 head and neck cancer,
1 liver cancer, 14 lung cancers, 1 lymph node cancer, 8 ovarian
cancers, 1 rectum cancer, 2 urinary bladder cancers, 1 uterus
cancer). The normal tissue panel tested was the same as in FIG.
1E-K. FIG. 1W) Gene symbol(s): SEC24C, Peptide: FLFPNQYVDV (SEQ ID
NO.: 248). Tissues from left to right: 3 cell lines and primary
cultures, 1 normal tissue (1 spleen), 24 cancer tissues (1 bile
duct cancer, 2 breast cancers, 2 leukocytic leukemia cancers, 1
liver cancer, 9 lung cancers, 2 lymph node cancers, 3 ovarian
cancers, 1 prostate cancer, 2 skin cancers, 1 uterus cancer). The
normal tissue panel tested was the same as in FIG. 1E-K. FIG. 1X)
Gene symbol(s): PDIK1L, STK35, Peptide: ALLENPKMEL (SEQ ID NO.:
441). Tissues from left to right: 5 cell lines and primary
cultures, 1 normal tissue (1 adrenal gland), 26 cancer tissues (1
breast cancer, 1 colon cancer, 1 esophageal cancer, 1 head and neck
cancer, 2 liver cancers, 10 lung cancers, 5 ovarian cancers, 1
prostate cancer, 1 rectum cancer, 2 urinary bladder cancers, 1
uterus cancer). The normal tissue panel tested was the same as in
FIG. 1E-K. FIG. 1Y) Gene symbol(s): EMC10, Peptide: SLVESHLSDQLTL
(SEQ ID NO.: 463). Tissues from left to right: 1 primary culture,
32 cancer tissues (1 bile duct cancer, 2 brain cancers, 2 breast
cancers, 2 head and neck cancers, 3 leukocytic leukemia cancers, 1
liver cancer, 8 lung cancers, 3 lymph node cancers, 5 ovarian
cancers, 2 skin cancers, 2 urinary bladder cancers, 1 uterus
cancer). The normal tissue panel tested was the same as in FIG.
1E-K. FIG. 1Z) Gene symbol(s): ZYG11A, Peptide: VLIANLEKL (SEQ ID
NO.: 466). Tissues from left to right: 5 cell lines, 17 cancer
tissues (3 breast cancers, 2 esophageal cancers, 1 liver cancer, 2
lung cancers, 5 lymph node cancers, 3 ovarian cancers, 1 urinary
bladder cancer). The normal tissue panel tested was the same as in
FIG. 1E-K. FIG. 1AA) Gene symbol(s): CEP192, Peptide: SLFGNSGILENV
(SEQ ID NO.: 479). Tissues from left to right: 7 cell lines, 1
normal tissue (1 spleen), 33 cancer tissues (1 breast cancer, 1
colon cancer, 1 esophageal cancer, 1 head and neck cancer, 1
leukocytic leukemia cancer, 3 liver cancers, 10 lung cancers, 1
lymph node cancer, 1 myeloid cell cancer, 7 ovarian cancers, 2 skin
cancers, 3 urinary bladder cancers, 1 uterus cancer). The normal
tissue panel tested was the same as in FIG. 1E-K. FIG. 1AB) Gene
symbol(s): CCNA1, Peptide: SLSEIVPCL (SEQ ID NO.: 512). Tissues
from left to right: 9 cancer tissues (1 head and neck cancer, 2
lung cancers, 1 myeloid cell cancer, 3 ovarian cancers, 2 uterus
cancers). The normal tissue panel tested was the same as in FIG.
1E-K. FIG. 1AC) Gene symbol(s): GNB1, Peptide: ALWDIETGQQTTT (SEQ
ID NO.: 560), Tissues from left to right: 5 cell lines and primary
cultures, 26 cancer tissues (1 brain cancer, 1 esophageal cancer, 1
esophageal and stomach cancer, 1 gallbladder cancer, 2 head and
neck cancers, 1 leukocytic leukemia cancer, 1 liver cancer, 5 lung
cancers, 6 lymph node cancers, 3 ovarian cancers, 1 prostate
cancer, 1 skin cancer, 1 urinary bladder cancer, 1 uterus cancer).
The normal tissue panel tested was the same as in FIG. 1E-K. FIG.
1AD) Gene symbol(s): KLHL14, Peptide: VMNDRLYAI (SEQ ID NO.: 587),
Tissues from left to right: 5 normal tissues (1 pancreas, 3
spleens, 1 thyroid gland), 38 cancer tissues (14 leukocytic
leukemia cancers, 10 lymph node cancers, 9 ovarian cancers, 1
prostate cancer, 4 uterus cancers). The normal tissue panel tested
was the same as in FIG. 1E-K. FIG. 1AE) Gene symbol(s): URB1,
Peptide: KLLNKIYEA (SEQ ID NO.: 620), Tissues from left to right: 3
cell lines and primary cultures, 2 normal tissues (1 lung, 1
uterus), 27 cancer tissues (5 brain cancers, 2 breast cancers, 2
esophageal cancers, 5 lung cancers, 1 lymph node cancer, 1 myeloid
cell cancer, 5 ovarian cancers, 3 prostate cancers, 1 rectum
cancer, 1 urinary bladder cancer, 1 uterus cancer). The normal
tissue panel tested was the same as in FIG. 1E-K.
[0878] FIGS. 2A to 2D show exemplary expression profiles of source
genes of the present invention that are highly over-expressed or
exclusively expressed in ovarian cancer in a panel of normal
tissues (white bars) and 20 ovarian cancer samples (black bars).
Tissues from left to right: 7 arteries, 1 brain, 1 heart, 2 livers,
2 lungs, 2 veins, 1 adipose tissue, 1 adrenal gland, 4 bone
marrows, 1 colon, 2 esophagi, 2 gallbladders, 1 kidney, 6 lymph
nodes, 1 pancreas, 1 pituitary gland, 1 rectum, 1 skeletal muscle,
1 skin, 1 small intestine, 1 spleen, 1 stomach, 1 thymus, 1 thyroid
gland, 5 tracheae, 1 urinary bladder, 1 breast, 3 ovaries, 3
placentae, 1 prostate, 1 testis, 1 uterus. FIG. 2A) CT45A1, CT45A3,
CT45A5, CT45A6, CT45A2, RP11-342L5.1, FIG. 2B) CLDN16; FIG. 2C)
ESR1; FIG. 2D) IDO1.
[0879] FIGS. 3A to 3F show exemplary immunogenicity data: flow
cytometry results after peptide-specific multimer staining. CD8+ T
cells were primed using artificial APCs coated with anti-CD28 mAb
and HLA-A*02 in complex with SeqID No 662 (A, left panel), SeqID No
663 (B, left panel), SeqID No 11 peptide (C, left panel), SeqID No
198 peptide (D, left panel), SeqID No 587 peptide (E, left panel)
and SeqID No 427 peptide (F, left panel), respectively. After three
cycles of stimulation, the detection of peptide-reactive cells was
performed by 2D multimer staining with A*02/SeqID No 662 (A),
A*02/SeqID No 663 (B), A*02/SeqID No 11 (C), A*02/SeqID No 198 (D),
A*02/SeqID No 587 (E) or A*02/SeqID No 427 (F). Right panels (A, B,
C, D, E, and F) show control staining of cells stimulated with
irrelevant A*02/peptide complexes. Viable singlet cells were gated
for CD8+ lymphocytes. Boolean gates helped excluding false-positive
events detected with multimers specific for different peptides.
Frequencies of specific multimer+ cells among CD8+ lymphocytes are
indicated.
EXAMPLES
Example 1
Identification and Quantitation of Tumor Associated Peptides
Presented on the Cell Surface
Tissue Samples
[0880] Patients' tumor tissues were obtained from Asterand
(Detroit, USA and Royston, Herts, UK); Val d'Hebron University
Hospital (Barcelona); ProteoGenex Inc., (Culver City, Calif., USA);
Stanford Cancer Center (Stanford, Calif., USA); University Hospital
of Tubingen. Normal (healthy) tissues were obtained from Asterand
(Detroit, USA and Royston, Herts, UK); Bio-Options Inc., CA, USA;
BioServe, Beltsville, Md., USA; Capital BioScience Inc., Rockville,
Md., USA; Geneticist Inc., Glendale, Calif., USA; University
Hospital of Geneva; University Hospital of Heidelberg; University
Hospital Munich; ProteoGenex Inc., Culver City, Calif., USA;
University Hospital of Tubingen, Kyoto Precatural University if
Medicine (KPUM). Written informed consents of all patients had been
given before surgery or autopsy. Tissues were shock-frozen
immediately after excision and stored until isolation of TUMAPs at
-70.degree. C. or below.
Isolation of HLA Peptides from Tissue Samples
[0881] HLA peptide pools from shock-frozen tissue samples were
obtained by immune precipitation from solid tissues according to a
slightly modified protocol (Falk et al., 1991; Seeger et al., 1999)
using the HLA-A*02-specific antibody BB7.2, the HLA-A, --B,
--C-specific antibody W6/32, CNBr-activated sepharose, acid
treatment, and ultrafiltration.
Mass Spectrometry Analyses
[0882] The HLA peptide pools as obtained were separated according
to their hydrophobicity by reversed-phase chromatography
(nanoAcquity UPLC system, Waters) and the eluting peptides were
analyzed in LTQ-velos and fusion hybrid mass spectrometers
(ThermoElectron) equipped with an ESI source. Peptide pools were
loaded directly onto the analytical fused-silica micro-capillary
column (75 .mu.m i.d..times.250 mm) packed with 1.7 .mu.m C18
reversed-phase material (Waters) applying a flow rate of 400 nL per
minute. Subsequently, the peptides were separated using a two-step
180 minute-binary gradient from 10% to 33% B at a flow rate of 300
nL per minute. The gradient was composed of Solvent A (0.1% formic
acid in water) and solvent B (0.1% formic acid in acetonitrile). A
gold coated glass capillary (PicoTip, New Objective) was used for
introduction into the nanoESI source. The LTQ-Orbitrap mass
spectrometers were operated in the data-dependent mode using a TOP5
strategy. In brief, a scan cycle was initiated with a full scan of
high mass accuracy in the Orbitrap (R=30 000), which was followed
by MS/MS scans also in the Orbitrap (R=7500) on the 5 most abundant
precursor ions with dynamic exclusion of previously selected ions.
Tandem mass spectra were interpreted by SEQUEST and additional
manual control. The identified peptide sequence was assured by
comparison of the generated natural peptide fragmentation pattern
with the fragmentation pattern of a synthetic sequence-identical
reference peptide.
[0883] Label-free relative LC-MS quantitation was performed by ion
counting i.e. by extraction and analysis of LC-MS features (Mueller
et al., 2007). The method assumes that the peptide's LC-MS signal
area correlates with its abundance in the sample. Extracted
features were further processed by charge state deconvolution and
retention time alignment (Mueller et al., 2008; Sturm et al.,
2008). Finally, all LC-MS features were cross-referenced with the
sequence identification results to combine quantitative data of
different samples and tissues to peptide presentation profiles. The
quantitative data were normalized in a two-tier fashion according
to central tendency to account for variation within technical and
biological replicates. Thus each identified peptide can be
associated with quantitative data allowing relative quantification
between samples and tissues. In addition, all quantitative data
acquired for peptide candidates was inspected manually to assure
data consistency and to verify the accuracy of the automated
analysis. For each peptide a presentation profile was calculated
showing the mean sample presentation as well as replicate
variations. The profiles juxtapose ovarian cancer samples to a
baseline of normal tissue samples. Presentation profiles of
exemplary over-presented peptides are shown in FIG. 1. Presentation
scores for exemplary peptides are shown in Table 9.
TABLE-US-00009 TABLE 9 Presentation scores. The table lists
peptides that are very highly over-presented on tumors compared to
a panel of normal tissues (+++), highly over-presented on tumors
compared to a panel of normal tissues (++) or over-presented on
tumors compared to a panel of normal tissues (+). The panel of
normal tissues consisted of: adipose tissue, adrenal gland, artery,
vein, bone marrow, brain, central and peripheral nerve, colon,
rectum, small intestine incl. duodenum, esophagus, gallbladder,
heart, kidney, liver, lung, lymph node, mononuclear white blood
cells, pancreas, peritoneum, pituitary, pleura, salivary gland,
skeletal muscle, skin, spleen, stomach, thymus, thyroid gland,
trachea, ureter, urinary bladder. SEQ Peptide ID No. Sequence
Presentation 1 SLMEPPAVLLL +++ 2 SLLEADPFL +++ 3 SLASKLTTL +++ 4
GIMEHITKI +++ 5 HLTEVYPEL +++ 6 VLVSDGVHSV +++ 7 SLVGLLLYL +++ 8
FTLGNVVGMYL +++ 9 GAAKDLPGV ++ 10 FLATFPLAAV +++ 11 KIFEMLEGV +++
12 SLWPDPMEV +++ 13 YLMDESLNL +++ 14 AAYGGLNEKSFV +++ 15 VLLTFKIFL
+++ 16 VLFQGQASL ++ 17 GLLPGDRLVSV +++ 18 YLVAKLVEV +++ 20
RMIEYFIDV +++ 21 VLDELDMEL +++ 23 VLLDDIFAQL +++ 24 SLSDGLEEV ++ 25
FLPDEPYIKV +++ 26 ALLELAEEL +++ 27 ILADIVISA + 28 QLLDETSAITL +++
29 KMLGIPISNILMV ++ 30 LILDWVPYI ++ 31 YLAPELFVNV +++ 32
KLDDLTQDLTV +++ 33 VLLSLLEKV ++ 34 ILVEADSLWVV +++ 35 KINDTIYEV +++
36 YVLEDLEVTV +++ 37 LLWDVVTGQSV +++ 38 FLLEDDIHVS +++ 39 SVAPNLPAV
+++ 40 TLLVKVFSV +++ 41 SLMPHIPGL +++ 42 VLLQKIVSA +++ 43 VLSSLEINI
+ 44 ILDPISSGFLL +++ 45 SLWQDIPDV +++ 46 ILTEENIHL +++ 47
ILLSVPLLVV +++ 48 ALAELYEDEV +++ 50 SLSELEALM +++ 51 LLPDLEFYV +++
52 FLLAHGLGFLL +++ 53 KMIETDILQKV +++ 54 SLLEQGKEPWMV +++ 55
SLLDLETLSL +++ 56 KLYEGIPVLL +++ 57 TLAELQPPVQL +++ 58 FLDTLKDLI ++
59 IMEDIILTL +++ 60 SLTIDGIYYV +++ 61 FLQGYQLHL +++ 62 VLLDVSAGQLLM
+++ 63 YLLPSGGSVTL +++ 64 YAAPGGLIGV + 65 LKVNQGLESL +++ 67
TLLAEALVTV +++ 68 SLMELPRGLFL +++ 69 FQLDPSSGVLVTV +++ 70 GLLDYPVGV
+++ 71 GILARIASV +++ 72 SLLELDGINL +++ 73 NIFDLQIYV +++ 74
ALLDPEVLSIFV +++ 75 GLLEVMVNL +++ 76 ILIDSIYKV +++ 77 ILVEADGAWVV
+++ 78 SLFSSLEPQIQPV +++ 79 SLFIGEKAVLL ++ 81 FLFSQLQYL +++ 82
FLSSVTYNL +++ 83 ILAPTVMMI +++ 84 VTFGEKLLGV +++ 86 NLIGKIENV + 87
ALPEAPAPLLPHIT +++ 88 FLLVGDLMAV +++ 89 YILPTETIYV +++ 90 TLLQIIETV
+++ 91 IMQDFPAEIFL +++ 92 YLIPFTGIVGL +++ 93 LLQAIKLYL +++ 94
YLIDIKTIAI +++ 96 YIFTDNPAAV +++ 97 SLINGSFLV +++ 98 LIIDQADIYL +++
99 ALVSKGLATV +++ 100 YLLSTNAQL +++ 101 ILVGGGALATV +++ 102
YLFESEGLVL +++ 103 TLAEEVVAL +++ 105 LLLEHSFEI ++ 106 LLYDAVHIVSV
+++ 107 FLQPVDDTQHL +++ 108 ALFPGVALLLA +++ 109 IILSILEQA +++ 110
FLSQVDFEL +++ 111 YVWGFYPAEV +++ 112 FLITSNNQL +++ 113 GLLPTPLFGV
+++ 114 SLVGEPILQNV +++ 116 YHIDEEVGF +++ 117 ILPDGEDFLAV +++ 118
KLIDNNINV +++ 119 FLYIGDIVSL ++ 120 ALLGIPLTLV +++ 122 FLLAEDDIYL
+++ 123 NLWDLTDASVV +++ 124 ALYETELADA +++ 125 VQIHQVAQV +++
126 VLAYFLPEA + 127 KIGDEPPKV ++ 129 GLLDGGVDILL ++ 130 FLWNGEDSALL
+++ 131 FVPPVTVFPSL +++ 132 LLVEQPPLAGV +++ 134 YLQELIFSV +++ 135
ALSEVDFQL +++ 136 YLADPSNLFVV +++ 137 TLVLTLPTV +++ 138 YQYPRAILSV
+++ 139 SVMEVNSGIYRV +++ 141 YLDFSNNRL +++ 142 FLFATPVFI +++ 143
LLLDITPEI +++ 144 YIMEPSIFNTL ++ 145 FLATSGTLAGI +++ 146
SLATAGDGLIEL +++ 147 SLLEAVSFL + 148 ALNPEIVSV +++ 149 NLLELFVQL
+++ 150 RLWEEGEELEL +++ 151 KILQQLVTL +++ 152 ILFEDIFDV +++ 153
FLIANVLYL +++ 155 RVANLHFPSV + 156 AISQGITLPSL +++ 157 SLNDEVPEV
+++ 158 KLFDVDEDGYI +++ 159 GLVGNPLPSV +++ 160 FLFDEEIEQI ++ 161
ALLEGVNTV +++ 162 YQQAQVPSV +++ 163 ALDEMGDLLQL +++ 164 ALLPQPKNLTV
+++ 165 SLLDEIRAV +++ 166 YLNHLEPPV +++ 167 KVLEVTEEFGV ++ 168
KILDADIQL +++ 169 NLPEYLPFV +++ 170 RLQETLSAA +++ 171 LLLPLQILL +++
172 VLYSYTIITV +++ 173 LLDSASAGLYL +++ 174 ALAQYLITA ++ 175
YLFENISQL +++ 176 YLMEGSYNKVFL +++ 177 YLLPEEYTSTL +++ 178
ALTEIAFVV + 179 KVLNELYTV +++ 180 FQIDPHSGLVTV +++ 181 LLWAGTAFQV
+++ 182 MLLEAPGIFL +++ 183 FGLDLVTEL ++ 184 YLMDINGKMWL +++ 185
FLIDDKGYTL +++ 186 TLFFQQNAL + 187 RQISIRGIVGV +++ 188 GLFPVTPEAV +
189 ALQRKLPYV +++ 190 FLSSLTETI +++ 191 LLQEGQALEYV +++ 192
KMLDGASFTL +++ 193 QLLDADGFLNV +++ 194 ALPLFVITV +++ 196 YLYSVEIKL
+++ 197 ALGPEGGRV ++ 198 KTINKVPTV +++ 199 ALQDVPLSSV +++ 200
LLFGSVQEV +++ 201 RLVDYLEGI +++ 202 ALLDQQGSRWTL +++ 203
VLLEDAHSHTL +++ 204 KIAENVEEV +++ 205 SLYPGTETMGL +++ 206
VLQEGKLQKLAQL +++ 208 KISPVTFSV +++ 209 KLIESKHEV +++ 210 LLLNAVLTV
++ 211 LLWPGAALL +++ 212 ALWDQDNLSV +++ 213 VTAAYMDTVSL ++ 215
QLINHLHAV +++ 216 NLWEDPYYL +++ 217 ALIHPVSTV +++ 218 SALEELVNV +++
219 KLSDIGITV +++ 220 LLQKFVPEI +++ 221 ALYEEGLLL +++ 222 NLIENVQRL
++ 223 ALLENIALYL +++ 224 TLIDAQWVL +++ 225 SLLKVLPAL +++ 226
MLYVVPIYL +++ 227 ALMNTLLYL +++ 228 AMQEYIAVV + 229 RLPGPLGTV ++
230 ILVDWLVEV +++ 231 FLSPQQPPLLL +++ 232 ALLEAQDVELYL +++ 233
VLSETLYEL ++ 234 ALMEDTGRQML +++ 235 YLNDLHEVLL +++ 236 GLLEAKVSL
+++ 237 ALLEASGTLLL +++ 238 YLISFQTHI +++ 239 AAFAGKLLSV +++ 240
ILLEQAFYL +++ 241 SLVEVNPAYSV +++ 242 AIAYILQGV +++ 243 LLLNELPSV
++ 244 SLFGGTEITI +++ 245 SMIDDLLGV +++ 246 LLWEVVSQL +++ 247
VLLPNDLLEKV +++ 248 FLFPNQYVDV + 249 LLDGFLVNV +++ 251 ALYTGFSILV
+++ 252 LLIGTDVSL +++ 253 GLDAATATV +++ 254 TLLAFIMEL +++ 255
VLASYNLTV +++ 256 FLPPEHTIVYI +++ 257 SIFSAFLSV +++ 259 TLMRQLQQV
++
261 YVLEFLEEI + 263 LLVSNLDFGV +++ 267 ALQDFLLSV +++ 271 LVYPLELYPA
++ 274 SLLFSLFEA + 275 YLVYILNEL + 277 LLPPLESLATV + 278 QLLDVVLTI
+ 279 ALWGGTQPLL ++ 280 VLPDPEVLEAV + 281 ILRESTEEL + 282 LLADVVPTT
+ 285 QLLHVGVTV + 288 NLINEINGV +++ 289 VLLEIEDLQV + 292 LLWEAGSEA
+ 296 FMEGAIIYV ++ 298 VMITKLVEV ++ 303 AILPQLFMV + 307 ALPVSLPQI +
308 SQYSGQLHEV + 311 RLYTGMHTV + 315 YLQDVVEQA ++ 318 GLINTGVLSV +
319 SLEPQIQPV + 320 KMFEFVEPLL + 321 GLFEDVTQPGILL ++ 322 TLMTSLPAL
++ 323 IQIGEETVITV + 325 FIMPATVADATAV +++ 327 GLAPFTEGISFV ++ 328
ALNDQVFEI + 331 KVDTVWVNV + 332 YLISELEAA + 333 FLPDANSSV ++ 334
TLTKVLVAL + 338 SVLEDPVHAV + 341 SQIALNEKLVNL + 342 HIYDKVMTV + 343
SLLEVNEESTV + 345 VIWKALIHL ++ 346 LLDSKVPSV ++ 348 ILLDVKTRL +++
351 SLIPNLRNV +++ 352 SLLELLHIYV + 356 KLLGKLPEL ++ 357 SMHDLVLQV
++ 358 ALDEYTSEL + 359 YLLPESVDL + 360 ALDJGASLLHL + 363
KVLDVSDLESV ++ 368 ILLEEVSPEL + 370 SLLQDLVSV + 372 TMLLNIPLV +++
373 SLLEDKGLAEV + 375 SLTETIEGV +++ 379 IMEGTLTRV + 382 ALQNYIKEA +
384 ILFANPNIFV + 385 SLLEQGLVEA + 386 ILFRYPLTI ++ 390 ALFMKQIYL ++
394 LLAVIGGLVYL + 395 ALALGGIAVV ++ 396 ALLPDLPAL ++ 397 YLFGERLLEC
+ 398 KLLEEDGTIITL + 399 YLFEPLYHV +++ 401 ILLDDTGLAYI + 403
KLYDRILRV ++ 404 AIDIJGRDPAV + 406 SVQGEDLYLV ++ 410 VLSDVIPJI ++
411 LLAHLSPEL + 413 TLLEKVEGC ++ 414 YVDDIFLRV + 415 LLDKVYSSV +
418 ALAELENIEV + 419 GQYEGKVSSV + 420 FMYDTPQEV ++ 421 RLPETLPSL ++
423 GLDGPPPTV +++ 424 TLLDALYEI + 425 FLYEKSSQV + 427 ALLPLSPYL +++
428 KLGHTDILVGV ++ 429 GLVNDLARV + 430 HLYSSIEHLTT + 431 SLVNVVPKL
+ 432 TLIEESAKV +++ 433 AMLNEPWAV +++ 434 KVSNSGITRV +++ 435
WLMPVIPAL +++ 436 HLAEVSAEV +++ 437 SMAPGLVIQAV +++ 438 KLLPLAGLYL
+++ 439 YLLQEIYGI +++ 440 ALADGVTMQV +++ 441 ALLENPKMEL +++ 442
GLLGGGGVLGV +++ 443 GLWEIENNPTV ++ 444 GLLRDEALAEV +++ 446
QLIPALAKV +++ 447 QLVPALAKV +++ 448 NLLETKLQL ++ 450 FMIDASVHPTL
+++ 451 LLLLDTVTMQV +++ 454 KLPPPPPQA +++ 455 SLLKEPQKVQL + 456
LLIGHLERV ++ 457 SLLPGNLVEKV +++ 458 SLIDKLYNI +++ 459 ALITEVVRL
+++ 460 AMLEKNYKL +++ 461 VMFRTPLASV +++ 462 KLAKQPETV +++ 463
SLVESHLSDQLTL +++ 464 ALNDCIYSV +++ 465 QLCDLNAEL +++ 466 VLIANLEKL
+++ 468 YLRSVGDGETV + 470 MLQDSIHVV +++ 471 YLYNNMIAKI +++ 472
KLLEVSDDPQV ++ 473 AMATESILHFA +++ 474 YLDPALELGPRNV +
475 LLLNEEALAQI +++ 476 ALMERTGYSMV +++ 477 ALLPASGQIAL +++ 478
YLLHEKLNL +++ 479 SLFGNSGILENV + 480 ALLEDSCHYL + 481 GLIEDYEALL
+++ 482 SLAPAGIADA +++ 483 ALTDIVSQV + 486 AVMESIQGV ++ 487
LLINSVFHV + 488 FLAEDPKVTL + 489 KMWEELPEVV +++ 490 FLLQHVQEL +++
491 GLNDRSDAV +++ 492 SLFDGFADGLGV +++ 494 ALQPEPIKV +++ 495
FIFSEKPVFV + 496 FLVEKQPPQV +++ 497 GLLEKLTAI + 498 KLVVTGGLDNTV +
499 KIFDIDEAEEGV +++ 500 SLMEDQVLQL + 501 LLDPNVKSIFV ++ 502
RLLAQVPGL +++ 503 SLNHFTHSV + 504 GLSDGNPSL +++ 505 SLAPGDVVRQV +++
506 KLLGKVETA +++ 507 KLIDDQDISISL + 508 ILAQEQLVVGV +++ 509
FLFDTKPLIV +++ 510 KLYSVVSQL +++ 511 FLDPYCSASV +++ 512 SLSEIVPCL
+++ 513 SLWPSPEQL +++ 514 ILVDWLVQV +++ 515 LLQELVLFL +++ 516
AVGPASILKEV +++ 517 LLMPIPEGLTL + 518 KLNAEVACV +++ 519 GLLHLTLLL
+++ 520 LAVHPSGVAL ++ 521 MLLTKLPTI ++ 522 TLVVYRSPEV +++ 523
YQIPRTFTL + 525 VLLEAGEGLVTI + 526 RLAEVGQYEQV + 527 FLLEPGNLEV +++
528 SVAEGRALMSV + 529 LLADELITV ++ 530 VMYADIGGMDI + 531
YTLPIASSIRL + 538 LLLAHIIAL ++ 539 ALFDAQAQV ++ 540 ALIPETTTLTV ++
541 SMLEPVPEL + 543 GLLPTPITQQASL + 545 LLADLLHNV + 546 VMIAGKVAVV
+ 550 FLYDEIEAEVNL + 551 KLYESLLPFA ++ 554 LLMPSSEDLLL ++ 557
KLYDDMIRL + 558 GLLENIPRV ++ 560 ALWDIETGQQTTT + 561 YLQLTQSEL +++
563 WLLPYNGVTV + 564 TVTNAVVTV ++ 565 ALQETPTSV ++ 566 VIADGGIQNV
++ 568 TLYDIAHTPGV ++ 570 ALANQIPTV + 574 YLLQEPPRTV + 575
YLISQVEGHQV + 576 ILLNNSGQIKL ++ 579 NLMEMVAQL ++ 586 KLKPGDLVGV +
588 SLLPLSHLV + 589 KLYPQLPAEI + 590 SLIEKLWQT + 591 SMAELDIKL ++
593 GLPRFGIEMV + 595 VLLSIYPRV + 597 KLLEGQVIQL + 599 YLLNDASLISV
++ 601 SAFPFPVTV + 603 FLIEPEHVNTV + 606 ALWETEVYI ++ 610
LLAPTPYIIGV + 613 RLLPPGAVVAV ++ 618 VLFDSESIGIYV + 619 ALQDRVPLA +
625 VVLEGASLETV + 626 LLMATILHL ++ 627 KLLETELLQEI + 629 HLLNESPML
++ 630 LLSHVIVAL + 631 FLDVFLPRV + 632 YLIPDIDLKL ++ 634 VVAEFVPLI
+ 637 SIYGGFLLGV ++ 638 KLIQESPTV + 639 SLFQNCFEL + 640 YLFSEALNAA
+
Example 2
Expression Profiling of Genes Encoding the Peptides of the
Invention
[0884] Over-presentation or specific presentation of a peptide on
tumor cells compared to normal cells is sufficient for its
usefulness in immunotherapy, and some peptides are tumor-specific
despite their source protein occurring also in normal tissues.
Still, mRNA expression profiling adds an additional level of safety
in selection of peptide targets for immunotherapies. Especially for
therapeutic options with high safety risks, such as
affinity-matured TCRs, the ideal target peptide will be derived
from a protein that is unique to the tumor and not found on normal
tissues.
RNA Sources and Preparation
[0885] Surgically removed tissue specimens were provided as
indicated above (see Example 1) after written informed consent had
been obtained from each patient. Tumor tissue specimens were
snap-frozen immediately after surgery and later homogenized with
mortar and pestle under liquid nitrogen. Total RNA was prepared
from these samples using TRI Reagent (Ambion, Darmstadt, Germany)
followed by a cleanup with RNeasy (QIAGEN, Hilden, Germany); both
methods were performed according to the manufacturer's
protocol.
[0886] Total RNA from healthy human tissues for RNASeq experiments
was obtained from: Asterand, Detroit, USA and Royston, Herts, UK;
ProteoGenex Inc. Culver City, Calif., USA, Geneticist Inc.,
Glendale, Calif., USA, Istituto Nazionale Tumori "Pascale",
Molecular Biology and Viral Oncology Unit (IRCCS), Naples, Italy,
University Hospital of Heidelberg, Germany, BioCat GmbH,
Heidelberg, Germany.
[0887] Quality and quantity of all RNA samples were assessed on an
Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) using the
RNA 6000 Pico LabChip Kit (Agilent).
RNAseq Experiments
[0888] Gene expression analysis of--tumor and normal tissue RNA
samples was performed by next generation sequencing (RNAseq) by
CeGaT (Tubingen, Germany). Briefly, sequencing libraries are
prepared using the Illumina HiSeq v4 reagent kit according to the
provider's protocol (Illumina Inc., San Diego, Calif., USA), which
includes RNA fragmentation, cDNA conversion and addition of
sequencing adaptors. Libraries derived from multiple samples are
mixed equimolar and sequenced on the Illumina HiSeq 2500 sequencer
according to the manufacturer's instructions, generating 50 bp
single end reads. Processed reads are mapped to the human genome
(GRCh38) using the STAR software. Expression data are provided on
transcript level as RPKM (Reads Per Kilobase per Million mapped
reads, generated by the software Cufflinks) and on exon level
(total reads, generated by the software Bedtools), based on
annotations of the ensembl sequence database (Ensembl77). Exon
reads are normalized for exon length and alignment size to obtain
RPKM values.
[0889] Exemplary expression profiles of source genes of the present
invention that are highly over-expressed or exclusively expressed
in ovarian cancer are shown in FIGS. 2A to 2D. Expression scores
for further exemplary genes are shown in Table 10.
TABLE-US-00010 TABLE 10 Expression scores. The table lists peptides
from genes that are very highly over-expressed in tumors compared
to a panel of normal tissues (+++), highly over-expressed in tumors
compared to a panel of normal tissues (++) or over- expressed in
tumors compared to a panel of normal tissues (+). The baseline for
this score was calculated from measurements of the following normal
tissues: adipose tissue, adrenal gland, artery, bone marrow, brain,
colon, esophagus, gallbladders, heart, kidney, liver, lung, lymph
node, pancreas, pituitary, rectum, skeletal muscle, skin, small
intestine, spleen, stomach, thymus, thyroid gland, trachea, urinary
bladder, vein. SEQ ID Gene No. Gene Name Sequence Expression 1
CCNA1 SLMEPPAVLLL +++ 2 CCNA1 SLLEADPFL +++ 3 MUC16 SLASKLTTL +++ 4
MUC16 GIMEHITKI +++ 5 MUC16 HLTEVYPEL +++ 11 CT45A1, CT45A3,
KIFEMLEGV +++ CT45A5, CT45A6, CT45A2, RP11- 342L5.1 15 GPR64
VLLTFKIFL +++ 21 IFI30 VLDELDMEL + 25 CLDN16 FLPDEPYIKV +++ 41
TDRD9 SLMPHIPGL + 42 TDRD9 VLLQKIVSA + 45 ARHGEF19 SLWQDIPDV ++ 67
MUC20 TLLAEALVTV + 69 FAT2 FQLDPSSGVLVTV +++ 72 VWDE SLLELDGINL +++
81 NUP205 FLFSQLQYL + 101 GPD2 ILVGGGALATV + 102 GAS2L3 YLFESEGLVL
++ 113 BPIFB3 GLLPTPLFGV +++ 114 BPIFB3 SLVGEPILQNV +++ 115 AQP5
AIAGAGILYGV ++ 116 IDO1 YHIDEEVGF +++ 118 ITGB8 KLIDNNINV ++ 126
MCM2 VLAYFLPEA + 171 KLK7 LLLPLQILL +++ 173 KIF15 LLDSASAGLYL +++
181 KIAA1324 LLWAGTAFQV + 183 RNF213 FGLDLVTEL ++ 184 RNF213
YLMDINGKMWL ++ 193 CLSPN QLLDADGFLNV +++ 194 SLC28A3 ALPLFVITV ++
195 MROH6 GLFADLLPRL + 197 SOX17 ALGPEGGRV ++ 210 UNG LLLNAVLTV +
215 BHLHE41 QLINHLHAV ++ 230 CCNA2, CCNA1, ILVDWLVEV +++ CCNB3 233
TIMELESS VLSETLYEL ++ 235 CCNE1 YLNDLHEVLL ++ 239 RSAD2 AAFAGKLLSV
+ 244 PKHD1L1 SLFGGTEITI +++ 258 NCAPD2 ELAERVPAI ++ 259 C20orf96
TLMRQLQQV + 266 ESR1 KITDTLIHL +++ 310 GGT6 FLVDTPLARA + 311 SGPP2
RLYTGMHTV + 317 FAT2 SLAALVVHV ++ 327 APOL2 GLAPFTEGISFV ++ 335
IGHG1, IGHG4, YSLSSVVTV +++ IGHG3, IGHG2 339 HDGF GLWEIENNPTVKA +
342 VWA2 HIYDKVMTV ++ 350 LAMA5 ALLDVTHSELTV ++ 371 RNF213
FLQAHLHTA ++ 372 RNF213 TMLLNIPLV ++ 387 ALMS1 ALFQATAEV + 393
EPPK1 GLLDTQTSQVLTA ++ 395 ARID5B ALALGGIAVV + 408 KLHL14 VLDDSIYLV
+++ 409 KLHL14 LLDAMNYHL +++ 421 SCNN1A RLPETLPSL +++ 423 TNFAIP2
GLDGPPPTV ++ 426 NCAPD2 RLADKSVLV + 427 VTCN1 ALLPLSPYL +++ 432
ABCC4 TLIEESAKV + 442 BPIFB4 GLLGGGGVLGV ++ 443 HDGF, HDGFL1
GLWEIENNPTV + 446 EYA4, EYA1, QLIPALAKV +++ EYA2 456 NUP205
LLIGHLERV + 465 KIFC1 QLCDLNAEL ++ 466 ZYG11A VLIANLEKL ++ 467 MX2
FLAKDFNFL ++ 484 KIF15 SLIEKVTQL +++ 494 SORL1 ALQPEPIKV ++ 495
SORL1 FIFSEKPVFV + 509 CANX FLFDTKPLIV + 512 CCNA1 SLSEIVPCL +++
519 NFE2L3 GLLHLTLLL +++ 523 GAB2 YQIPRTFTL +++ 551 NCAPD3
KLYESLLPFA + 579 CHD7 NLMEMVAQL ++ 580 ASUN LLMENAERV + 587 KLHL14
VMNDRLYAI +++ 588 RNF213 SLLPLSHLV + 595 TAP1 VLLSIYPRV ++ 602
ERMP1 YLLEQIKLIEV ++ 609 HELZ2 ALWKQLLEL + 614 UBE2L6 LLLPDQPPYHL
++ 616 TRIP13 VLIDEVESL ++ 629 NUP205 HLLNESPML + 631 PRKDC
FLDVFLPRV + 632 SMARCC1 YLIPDIDLKL +
Example 3
In Vitro Immunogenicity for MHC Class I Presented Peptides
[0890] In order to obtain information regarding the immunogenicity
of the TUMAPs of the present invention, the inventors performed
investigations using an in vitro T-cell priming assay based on
repeated stimulations of CD8+ T cells with artificial antigen
presenting cells (aAPCs) loaded with peptide/MHC complexes and
anti-CD28 antibody. This way the inventors could show
immunogenicity for 22 HLA-A*0201 restricted TUMAPs of the invention
so far, demonstrating that these peptides are T-cell epitopes
against which CD8+ precursor T cells exist in humans (Table
11).
In Vitro Priming of CD8+ T Cells
[0891] In order to perform in vitro stimulations by artificial
antigen presenting cells loaded with peptide-MHC complex (pMHC) and
anti-CD28 antibody, the inventors first isolated CD8+ T cells from
fresh HLA-A*02 leukapheresis products via positive selection using
CD8 microbeads (Miltenyi Biotec, Bergisch-Gladbach, Germany) of
healthy donors obtained from the University clinics Mannheim,
Germany, after informed consent.
[0892] PBMCs and isolated CD8+ lymphocytes were incubated in T-cell
medium (TCM) until use consisting of RPMI-Glutamax (Invitrogen,
Karlsruhe, Germany) supplemented with 10% heat inactivated human AB
serum (PAN-Biotech, Aidenbach, Germany), 100 U/ml Penicillin/100
.mu.g/ml Streptomycin (Cambrex, Cologne, Germany), 1 mM sodium
pyruvate (CC Pro, Oberdorla, Germany), 20 .mu.g/ml Gentamycin
(Cambrex). 2.5 ng/ml IL-7 (PromoCell, Heidelberg, Germany) and 10
U/ml IL-2 (Novartis Pharma, Nurnberg, Germany) were also added to
the TCM at this step.
[0893] Generation of pMHC/anti-CD28 coated beads, T-cell
stimulations and readout was performed in a highly defined in vitro
system using four different pMHC molecules per stimulation
condition and 8 different pMHC molecules per readout condition.
[0894] The purified co-stimulatory mouse IgG2a anti human CD28 Ab
9.3 (Jung et al., 1987) was chemically biotinylated using
Sulfo-N-hydroxysuccinimidobiotin as recommended by the manufacturer
(Perbio, Bonn, Germany). Beads used were 5.6 .mu.m diameter
streptavidin coated polystyrene particles (Bangs Laboratories,
Illinois, USA).
[0895] pMHC used for positive and negative control stimulations
were A*0201/MLA-001 (peptide ELAGIGILTV (SEQ ID NO. 664) from
modified Melan-A/MART-1) and A*0201/DDX5-001 (YLLPAIVHI from DDX5,
SEQ ID NO. 665), respectively.
[0896] 800.000 beads/200 .mu.l were coated in 96-well plates in the
presence of 4.times.12.5 ng different biotin-pMHC, washed and 600
ng biotin anti-CD28 were added subsequently in a volume of 200
.mu.l. Stimulations were initiated in 96-well plates by
co-incubating 1.times.10.sup.6 CD8+ T cells with 2.times.10.sup.5
washed coated beads in 200 .mu.l TCM supplemented with 5 ng/ml
IL-12 (PromoCell) for 3 days at 37.degree. C. Half of the medium
was then exchanged by fresh TCM supplemented with 80 U/ml IL-2 and
incubating was continued for 4 days at 37.degree. C. This
stimulation cycle was performed for a total of three times. For the
pMHC multimer readout using 8 different pMHC molecules per
condition, a two-dimensional combinatorial coding approach was used
as previously described (Andersen et al., 2012) with minor
modifications encompassing coupling to 5 different fluorochromes.
Finally, multimeric analyses were performed by staining the cells
with Live/dead near IR dye (Invitrogen, Karlsruhe, Germany),
CD8-FITC antibody clone SK1 (BD, Heidelberg, Germany) and
fluorescent pMHC multimers. For analysis, a BD LSRII SORP cytometer
equipped with appropriate lasers and filters was used. Peptide
specific cells were calculated as percentage of total CD8+ cells.
Evaluation of multimeric analysis was done using the FlowJo
software (Tree Star, Oregon, USA). In vitro priming of specific
multimer+CD8+ lymphocytes was detected by comparing to negative
control stimulations. Immunogenicity for a given antigen was
detected if at least one evaluable in vitro stimulated well of one
healthy donor was found to contain a specific CD8+ T-cell line
after in vitro stimulation (i.e. this well contained at least 1% of
specific multimer+ among CD8+ T-cells and the percentage of
specific multimer+ cells was at least 10.times. the median of the
negative control stimulations).
In Vitro Immunogenicity for Ovarian Cancer Peptides
[0897] For tested HLA class I peptides, in vitro immunogenicity
could be demonstrated by generation of peptide specific T-cell
lines. Exemplary flow cytometry results after TUMAP-specific
multimer staining for two peptides of the invention are shown in
FIG. 3 together with corresponding negative controls. Results for
six peptides from the invention are summarized in Table 11A and
B.
TABLE-US-00011 TABLE 11A in vitro immunogenicity of HLA class I
peptides of the invention. Exemplary results of in vitro
immunogenicity experiments conducted by the applicant for the
peptides of the invention. <20% = +; 20%-49% = ++; 50%-69% =
+++; > = 70% = ++++ SEQ ID NO: Sequence wells donors 283
ALYIGDGYVIHLA + +++ 648 LLWGNAIFL ++ +++ 652 TLWYRAPEV +++ ++++ 659
ILFPDIIARA + +++ 662 KIQEILTQV + +++ 663 KIQEMQHFL + +++
TABLE-US-00012 TABLE 12B in vitro immunogenicity of additional HLA
class I peptides of the invention. Exemplary results of in vitro
immunogenicity experiments conducted by the applicant for HLA-A*02
restricted peptides of the invention. Results of in vitro
immunogenicity experiments are indicated. Percentage of positive
wells and donors (among evaluable) are summarized as indicated
<20% = +; 20%-49% = ++; 50%-69% = +++; > = 70% = ++++ SEQ ID
NO: Sequence Wells positive [%] 2 SLLEADPFL ''+'' 3 SLASKLTTL ''+''
5 HLTEVYPEL ''+++'' 7 SLVGLLLYL ''++'' 8 FTLGNVVGMYL ''+'' 11
KIFEMLEGV ''+'' 17 GLLPGDRLVSV ''++'' 19 FMVDNEAIYDI ''++'' 36
YVLEDLEVTV ''+'' 38 FLLEDDIHVS ''+'' 40 TLLVKVFSV ''++'' 48
ALAELYEDEV ''+'' 49 YLPAVFEEV ''++'' 56 KLYEGIPVLL ''+'' 60
SLTIDGIYYV ''++++'' 61 FLQGYQLHL ''++'' 79 SLFIGEKAVLL ''+'' 108
ALFPGVALLLA ''++'' 113 GLLPTPLFGV ''+'' 118 KLIDNNINV ''+'' 141
YLDFSNNRL ''+'' 143 LLLDITPEI ''+'' 150 RLWEEGEELEL ''+'' 152
ILFEDIFDV ''++'' 157 SLNDEVPEV ''+++'' 166 YLNHLEPPV ''++++'' 191
LLQEGQALEYV ''+++'' 198 KTINKVPTV ''++'' 199 ALQDVPLSSV ''+'' 215
QLINHLHAV ''++'' 242 AIAYILQGV ''+++'' 247 VLLPNDLLEKV ''+'' 319
SLEPQIQPV ''+'' 384 ILFANPNIFV ''+'' 395 ALALGGIAVV ''+++'' 443
GLWEIENNPTV ''+'' 446 QLIPALAKV ''++'' 454 KLPPPPPQA ''++'' 460
AMLEKNYKL ''+'' 463 SLVESHLSDQLTL ''++'' 489 KMWEELPEVV ''+'' 499
KIFDIDEAEEGV ''+'' 511 FLDPYCSASV ''+'' 518 KLNAEVACV ''++'' 603
FLIEPEHVNTV ''+''
Example 4
Synthesis of Peptides
[0898] All peptides were synthesized using standard and
well-established solid phase peptide synthesis using the
Fmoc-strategy. Identity and purity of each individual peptide have
been determined by mass spectrometry and analytical RP-HPLC. The
peptides were obtained as white to off-white lyophilizates
(trifluoro acetate salt) in purities of >50%. All TUMAPs are
preferably administered as trifluoro-acetate salts or acetate
salts, other salt-forms are also possible.
Example 5
MHC Binding Assays
[0899] Candidate peptides for T cell based therapies according to
the present invention were further tested for their MHC binding
capacity (affinity). The individual peptide-MHC complexes were
produced by UV-ligand exchange, where a UV-sensitive peptide is
cleaved upon UV-irradiation, and exchanged with the peptide of
interest as analyzed. Only peptide candidates that can effectively
bind and stabilize the peptide-receptive MHC molecules prevent
dissociation of the MHC complexes. To determine the yield of the
exchange reaction, an ELISA was performed based on the detection of
the light chain (.beta.2m) of stabilized MHC complexes. The assay
was performed as generally described in Rodenko et al. (Rodenko et
al., 2006).
[0900] 96 well MAXISorp plates (NUNC) were coated over night with 2
ug/ml streptavidin in PBS at room temperature, washed 4.times. and
blocked for 1h at 37.degree. C. in 2% BSA containing blocking
buffer. Refolded HLA-A*02:01/MLA-001 monomers served as standards,
covering the range of 15-500 ng/ml. Peptide-MHC monomers of the
UV-exchange reaction were diluted 100 fold in blocking buffer.
Samples were incubated for 1h at 37.degree. C., washed four times,
incubated with 2 ug/ml HRP conjugated anti-.beta.2m for 1h at
37.degree. C., washed again and detected with TMB solution that is
stopped with NH2SO4. Absorption was measured at 450 nm. Candidate
peptides that show a high exchange yield (preferably higher than
50%, most preferred higher than 75%) are generally preferred for a
generation and production of antibodies or fragments thereof,
and/or T cell receptors or fragments thereof, as they show
sufficient avidity to the MHC molecules and prevent dissociation of
the MHC complexes.
TABLE-US-00013 TABLE 11 MHC class I binding scores. Binding of
HLA-class I restricted peptides to HLA-A*02:01 was ranged by
peptide exchange yield: .gtoreq.10% = +; .gtoreq.20% = ++;
.gtoreq.50% = +++; .gtoreq.75% = ++++ SEQID Sequence Peptide
exchange 1 SLMEPPAVLLL ''+++'' 2 SLLEADPFL ''+++'' 3 SLASKLTTL
''++++'' 4 GIMEHITKI ''++++'' 5 HLTEVYPEL ''+++'' 6 VLVSDGVHSV
''+++'' 7 SLVGLLLYL ''++++'' 8 FTLGNVVGMYL ''++++'' 9 GAAKDLPGV
''++'' 10 FLATFPLAAV ''++++'' 11 KIFEMLEGV ''+++'' 12 SLWPDPMEV
''+++'' 13 YLMDESLNL ''+++'' 14 AAYGGLNEKSFV ''+++'' 15 VLLTFKIFL
''++'' 16 VLFQGQASL ''+++'' 17 GLLPGDRLVSV ''+++'' 18 YLVAKLVEV
''++'' 19 FMVDNEAIYDI ''++++'' 20 RMIEYFIDV ''+++'' 21 VLDELDMEL
''++'' 22 IMEENPGIFAV ''+++'' 23 VLLDDIFAQL ''+++'' 24 SLSDGLEEV
''++'' 25 FLPDEPYIKV ''+++'' 26 ALLELAEEL ''+++'' 27 ILADIVISA
''+++'' 28 QLLDETSAITL ''+++'' 29 KMLGIPISNILMV ''+++'' 30
LILDWVPYI ''+++'' 31 YLAPELFVNV ''++'' 32 KLDDLTQDLTV ''++'' 33
VLLSLLEKV ''++'' 34 ILVEADSLWVV ''+++'' 35 KINDTIYEV ''+++'' 36
YVLEDLEVTV ''++'' 38 FLLEDDIHVS ''+++'' 39 SVAPNLPAV ''+++'' 40
TLLVKVFSV ''+++'' 41 SLMPHIPGL ''+++'' 42 VLLQKIVSA ''+++'' 43
VLSSLEINI ''++'' 44 ILDPISSGFLL ''++'' 45 SLWQDIPDV ''+++'' 46
ILTEENIHL ''+++'' 47 ILLSVPLLVV ''++'' 48 ALAELYEDEV ''+++'' 49
YLPAVFEEV ''+++'' 50 SLSELEALM ''+++'' 51 LLPDLEFYV ''++++'' 52
FLLAHGLGFLL ''++++'' 53 KMIETDILQKV ''++++'' 54 SLLEQGKEPWMV
''+++'' 55 SLLDLETLSL ''++++'' 56 KLYEGIPVLL ''++++'' 57
TLAELQPPVQL ''+++'' 58 FLDTLKDLI ''+++'' 59 IMEDIILTL ''+++'' 60
SLTIDGIYYV ''++++'' 61 FLQGYQLHL ''++++'' 62 VLLDVSAGQLLM ''++++''
63 YLLPSGGSVTL ''++'' 64 YAAPGGLIGV ''++'' 66 FLDENIGGVAV ''+++''
67 TLLAEALVTV ''+++'' 68 SLMELPRGLFL ''++++'' 69 FQLDPSSGVLVTV
''+++'' 70 GLLDYPVGV ''+++'' 71 GILARIASV ''+++'' 72 SLLELDGINL
''+++'' 73 NIFDLQIYV ''+++'' 74 ALLDPEVLSIFV ''+++'' 75 GLLEVMVNL
''+++'' 76 ILIDSIYKV ''+++'' 77 ILVEADGAWVV ''++++'' 78
SLFSSLEPQIQPV ''+++'' 79 SLFIGEKAVLL ''+++'' 80 FLYDNLVESL ''++''
81 FLFSQLQYL ''++'' 82 FLSSVTYNL ''+++'' 83 ILAPTVMMI ''+++'' 84
VTFGEKLLGV ''++'' 85 KMSELRVTL ''+++'' 86 NLIGKIENV ''+++'' 87
ALPEAPAPLLPHIT ''++'' 88 FLLVGDLMAV ''+++'' 89 YILPTETIYV ''++++''
90 TLLQIIETV ''+++'' 91 IMQDFPAEIFL ''++++'' 92 YLIPFTGIVGL ''++''
93 LLQAIKLYL ''++'' 94 YLIDIKTIAI ''++'' 95 SVIPQIQKV ''+++'' 96
YIFTDNPAAV ''+++'' 97 SLINGSFLV ''+++'' 98 LIIDQADIYL ''+++'' 99
ALVSKGLATV ''++'' 100 YLLSTNAQL ''++++'' 101 ILVGGGALATV ''+++''
102 YLFESEGLVL ''+++'' 103 TLAEEVVAL ''+++'' 104 STMEQNFLL ''++++''
106 LLYDAVHIVSV ''+++'' 107 FLQPVDDTQHL ''+++'' 108 ALFPGVALLLA
''++++'' 109 IILSILEQA ''++++'' 110 FLSQVDFEL ''+++'' 111
YVWGFYPAEV ''+++'' 113 GLLPTPLFGV ''+++'' 114 SLVGEPILQNV ''++''
115 AIAGAGILYGV ''++'' 116 YHIDEEVGF ''+'' 117 ILPDGEDFLAV ''+++''
118 KLIDNNINV ''+++'' 119 FLYIGDIVSL ''++++'' 120 ALLGIPLTLV
''+++'' 121 GVVDPRAISVL ''++'' 122 FLLAEDDIYL ''+++'' 123
NLWDLTDASVV ''+++'' 124 ALYETELADA ''++'' 125 VQIHQVAQV ''+++''
126 VLAYFLPEA ''++++'' 127 KIGDEPPKV ''++'' 128 YLFDDPLSAV ''++''
129 GLLDGGVDILL ''+++'' 130 FLWNGEDSALL ''+++'' 131 FVPPVTVFPSL
''++'' 132 LLVEQPPLAGV ''+++'' 133 KVLSNIHTV ''++'' 134 YLQELIFSV
''+++'' 135 ALSEVDFQL ''+++'' 136 YLADPSNLFVV ''+++'' 137 TLVLTLPTV
''++++'' 138 YQYPRAILSV ''+++'' 139 SVMEVNSGIYRV ''+++'' 140
YMDAPKAAL ''++'' 141 YLDFSNNRL ''++'' 142 FLFATPVFI ''+++'' 143
LLLDITPEI ''++++'' 144 YIMEPSIFNTL ''+++'' 145 FLATSGTLAGI ''++''
146 SLATAGDGLIEL ''++'' 147 SLLEAVSFL ''+++'' 148 ALNPEIVSV ''++''
149 NLLELFVQL ''+++'' 150 RLWEEGEELEL ''+++'' 151 KILQQLVTL ''+++''
152 ILFEDIFDV ''+++'' 153 FLIANVLYL ''+'' 154 ALDDGTPAL ''++'' 155
RVANLHFPSV ''+++'' 157 SLNDEVPEV ''++'' 158 KLFDVDEDGYI ''+++'' 159
GLVGNPLPSV ''++++'' 160 FLFDEEIEQI ''+++'' 161 ALLEGVNTV ''+++''
162 YQQAQVPSV ''+++'' 163 ALDEMGDLLQL ''+++'' 164 ALLPQPKNLTV
''+++'' 165 SLLDEIRAV ''+++'' 166 YLNHLEPPV ''+++'' 167 KVLEVTEEFGV
''+++'' 168 KILDADIQL ''++++'' 169 NLPEYLPFV ''+++'' 170 RLQETLSAA
''+++'' 171 LLLPLQILL ''+++'' 172 VLYSYTIITV ''++'' 173 LLDSASAGLYL
''+++'' 174 ALAQYLITA ''+++'' 175 YLFENISQL ''+++'' 176
YLMEGSYNKVFL ''++'' 177 YLLPEEYTSTL ''++++'' 178 ALTEIAFVV ''++++''
179 KVLNELYTV ''+++'' 180 FQIDPHSGLVTV ''++'' 181 LLWAGTAFQV
''+++'' 182 MLLEAPGIFL ''+++'' 183 FGLDLVTEL ''+++'' 184
YLMDINGKMWL ''+++'' 185 FLIDDKGYTL ''++'' 186 TLFFQQNAL ''++'' 187
RQISIRGIVGV ''+++'' 188 GLFPVTPEAV ''+++'' 189 ALQRKLPYV ''+++''
190 FLSSLTETI ''+++'' 191 LLQEGQALEYV ''++'' 192 KMLDGASFTL ''+++''
193 QLLDADGFLNV ''+++'' 194 ALPLFVITV ''+++'' 195 GLFADLLPRL
''+++'' 196 YLYSVEIKL ''++++'' 197 ALGPEGGRV ''++'' 198 KTINKVPTV
''+++'' 199 ALQDVPLSSV ''+++'' 200 LLFGSVQEV ''+++'' 201 RLVDYLEGI
''+++'' 202 ALLDQQGSRVVTL ''+++'' 204 KIAENVEEV ''++'' 205
SLYPGTETMGL ''+++'' 206 VLQEGKLQKLAQL ''+++'' 207 GLTSTNAEV ''++''
208 KISPVTFSV ''+++'' 209 KLIESKHEV ''++'' 210 LLLNAVLTV ''++'' 211
LLWPGAALL ''++'' 212 ALWDQDNLSV ''++'' 214 FLLDLDPLLL ''+++'' 215
QLINHLHAV ''+++'' 216 NLWEDPYYL ''+++'' 217 ALIHPVSTV ''++'' 218
SALEELVNV ''++'' 219 KLSDIGITV ''+++'' 220 LLQKFVPEI ''++'' 221
ALYEEGLLL ''++'' 222 NLIENVQRL ''++'' 223 ALLENIALYL ''+++'' 224
TLIDAQVVVL ''+++'' 225 SLLKVLPAL ''+++'' 226 MLYVVPIYL ''++'' 227
ALMNTLLYL ''++'' 228 AMQEYIAVV ''++'' 229 RLPGPLGTV ''++'' 230
ILVDWLVEV ''+'' 231 FLSPQQPPLLL ''++'' 232 ALLEAQDVELYL ''++'' 233
VLSETLYEL ''++'' 234 ALMEDTGRQML ''++'' 235 YLNDLHEVLL ''++++'' 236
GLLEAKVSL ''+++'' 237 ALLEASGTLLL ''++++'' 238 YLISFQTHI ''+++''
239 AAFAGKLLSV ''+++'' 240 ILLEQAFYL ''+++'' 241 SLVEVNPAYSV
''+++'' 242 AIAYILQGV ''++'' 243 LLLNELPSV ''+++'' 244 SLFGGTEITI
''+++'' 245 SMIDDLLGV ''+++'' 246 LLWEVVSQL ''+++'' 247 VLLPNDLLEKV
''+++'' 248 FLFPNQYVDV ''+++'' 249 LLDGFLVNV ''+++'' 250
ALSEEGLLVYL ''+++'' 251 ALYTGFSILV ''++'' 252 LLIGTDVSL ''+++'' 253
GLDAATATV ''++'' 254 TLLAFIMEL ''+++''
255 VLASYNLTV ''+++'' 256 FLPPEHTIVYI ''+++'' 257 SIFSAFLSV ''+++''
258 ELAERVPAI ''++'' 261 YVLEFLEEI ''++'' 262 LLWGDLIWL ''+++'' 263
LLVSNLDFGV ''+++'' 264 SLQEQLHSV ''+++'' 265 LLFGGTKTV ''++'' 266
KITDTLIHL ''+++'' 267 ALQDFLLSV ''+++'' 269 RVLEVGALQAV ''++'' 270
LLLDEEGTFSL ''++'' 271 LVYPLELYPA ''+++'' 272 ALGNTVPAV ''+++'' 273
NLFQSVREV ''++'' 274 SLLFSLFEA ''++'' 275 YLVYILNEL ''++'' 276
ALFTFSPLTV ''+++'' 277 LLPPLESLATV ''++'' 278 QLLDVVLTI ''++'' 279
ALWGGTQPLL ''++'' 280 VLPDPEVLEAV ''+++'' 281 ILRESTEEL ''+++'' 282
LLADVVPTT ''+++'' 283 ALYIGDGYVIHLA ''+++'' 284 ILLSQTTGV ''+++''
285 QLLHVGVTV ''+++'' 286 YLFPGIPEL ''+++'' 287 FLNEFFLNV ''+++''
288 NLINEINGV ''+++'' 289 VLLEIEDLQV ''++++'' 295 VLDRESPNV ''+++''
296 FMEGAIIYV ''+++'' 297 VLADIELAQA ''+++'' 298 VMITKLVEV ''+++''
299 YLLETSGNL ''+++'' 300 ALLGQTFSL ''+++'' 301 FLVEDLVDSL ''+++''
302 ALLQEGEVYSA ''+++'' 303 AILPQLFMV ''++++'' 304 MTLGQIYYL
''+++'' 305 SIANFSEFYV ''++++'' 306 ALVNVQIPL ''+++'' 307 ALPVSLPQI
''+++'' 308 SQYSGQLHEV ''+++'' 309 GLFDGVPTTA ''+++'' 310
FLVDTPLARA ''++++'' 311 RLYTGMHTV ''+++'' 312 IISDLTIAL ''+++'' 313
VLFDDELLMV ''+++'' 314 ALIAEGIALV ''+++'' 315 YLQDVVEQA ''+++'' 316
ILLERLWYV ''+++'' 317 SLAALVVHV ''+++'' 318 GLINTGVLSV ''++'' 319
SLEPQIQPV ''++'' 320 KMFEFVEPLL ''++++'' 321 GLFEDVTQPGILL ''++++''
322 TLMTSLPAL ''+++'' 324 FLYDEIEAEV ''+++'' 325 FIMPATVADATAV
''+++'' 326 FLPEALDFV ''+++'' 327 GLAPFTEGISFV ''+++'' 328
ALNDQVFEI ''+++'' 329 FLVTLNNVEV ''++++'' 330 QLALKVEGV ''+++'' 331
KVDTVWVNV ''+++'' 332 YLISELEAA ''+++'' 333 FLPDANSSV ''++'' 334
TLTKVLVAL ''+++'' 335 YSLSSVVTV ''+++'' 336 ILLTAIVQV ''+++'' 337
HLLSELEAAPYL ''++++'' 339 GLWEIENNPTVKA ''++++'' 340 ALLSMTFPL
''++++'' 341 SQIALNEKLVNL ''+++'' 342 HIYDKVMTV ''+++'' 343
SLLEVNEESTV ''+++'' 344 YLQDQHLLLTV ''+++'' 345 VIWKALIHL ''+++''
346 LLDSKVPSV ''+++'' 347 SLFKHDPAAWEA ''++++'' 348 ILLDVKTRL
''++++'' 349 SLTEYLQNV ''++++'' 350 ALLDVTHSELTV ''+++'' 351
SLIPNLRNV ''+++'' 352 SLLELLHIYV ''+++'' 353 YLFEMDSSL ''++'' 354
LILEGVDTV ''++'' 355 SIQQSIERLLV ''++'' 356 KLLGKLPEL ''+++'' 357
SMHDLVLQV ''+++'' 358 ALDEYTSEL ''++++'' 359 YLLPESVDL ''+++'' 361
ALYELEGTTV ''+++'' 362 TLYGLSVLL ''+++'' 363 KVLDVSDLESV ''++'' 364
LLQNEQFEL ''+++'' 365 YVIDQGETDVYV ''+++'' 366 RLLDMGETDLML ''+++''
367 SLQNHNHQL ''+++'' 369 GLFPEHLIDV ''+++'' 370 SLLQDLVSV ''+++''
371 FLQAHLHTA ''++++'' 372 TMLLNIPLV ''++'' 373 SLLEDKGLAEV ''++''
374 FLLQQHLISA ''++'' 375 SLTETIEGV ''++'' 376 AMFESSQNVLL ''++''
377 FLLDSSASV ''++'' 378 ALGYFVPYV ''+++'' 379 IMEGTLTRV ''++'' 380
TLIEDEIATI ''++'' 381 FIDEAYVEV ''++'' 382 ALQNYIKEA ''++'' 383
ALLELENSVTL ''+++'' 384 ILFANPNIFV ''+++'' 385 SLLEQGLVEA ''++''
386 ILFRYPLTI ''+++'' 387 ALFQATAEV ''++++'' 388 SLTIDGIRYV ''+++''
389 LLADVTHLL ''++'' 390 ALFMKQIYL ''+++'' 391 YVYPQRLNFV
''+++''
392 ALLHPQGFEV ''++'' 393 GLLDTQTSQVLTA ''++'' 394 LLAVIGGLVYL
''+++'' 395 ALALGGIAVV ''++++'' 396 ALLPDLPAL ''+++'' 397
YLFGERLLEC ''+++'' 398 KLLEEDGTIITL ''++'' 399 YLFEPLYHV ''+++''
400 SLLTEQDLWTV ''++'' 401 ILLDDTGLAYI ''+++'' 402 VLFSGALLGL
''++'' 403 KLYDRILRV ''++'' 405 ALYDVFLEV ''++'' 407 YLMDLINFL
''+++'' 408 VLDDSIYLV ''++'' 409 LLDAMNYHL ''++'' 412 YLDDLNEGVYI
''++'' 426 RLADKSVLV ''+++'' 427 ALLPLSPYL ''+++'' 428 KLGHTDILVGV
''++'' 429 GLVNDLARV ''++'' 430 HLYSSIEHLTT ''+++'' 431 SLVNVVPKL
''++'' 432 TLIEESAKV ''++'' 433 AMLNEPWAV ''+++'' 434 KVSNSGITRV
''++'' 436 HLAEVSAEV ''+++'' 437 SMAPGLVIQAV ''+++'' 438 KLLPLAGLYL
''++++'' 439 YLLQEIYGI ''+++'' 440 ALADGVTMQV ''++'' 441 ALLENPKMEL
''+++'' 442 GLLGGGGVLGV ''+++'' 443 GLWEIENNPTV ''+++'' 444
GLLRDEALAEV ''+++'' 446 QLIPALAKV ''+++'' 447 QLVPALAKV ''++'' 448
NLLETKLQL ''+++'' 449 KLAEGLDIQL ''+++'' 450 FMIDASVHPTL ''+++''
451 LLLLDTVTMQV ''++'' 452 ILLEHGADPNL ''+++'' 453 KLLEATSAV ''++''
454 KLPPPPPQA ''+++'' 455 SLLKEPQKVQL ''++'' 456 LLIGHLERV ''+++''
457 SLLPGNLVEKV ''+++'' 458 SLIDKLYNI ''++'' 459 ALITEVVRL ''++''
460 AMLEKNYKL ''++++'' 461 VMFRTPLASV ''++'' 462 KLAKQPETV ''+++''
463 SLVESHLSDQLTL ''+++'' 464 ALNDCIYSV ''+++'' 465 QLCDLNAEL
''+++'' 466 VLIANLEKL ''++++'' 467 FLAKDFNFL ''+++'' 468
YLRSVGDGETV ''+++'' 469 YLASDEITTV ''+++'' 471 YLYNNMIAKI ''+++''
472 KLLEVSDDPQV ''+++'' 473 AMATESILHFA ''+++'' 474 YLDPALELGPRNV
''+++'' 475 LLLNEEALAQI ''+++'' 476 ALMERTGYSMV ''+++'' 477
ALLPASGQIAL ''+++'' 478 YLLHEKLNL ''+++'' 479 SLFGNSGILENV ''+++''
480 ALLEDSCHYL ''+++'' 481 GLIEDYEALL ''+++'' 484 SLIEKVTQL ''+++''
485 NVPDSFNEV ''+++'' 486 AVMESIQGV ''+++'' 487 LLINSVFHV ''+++''
488 FLAEDPKVTL ''+++'' 489 KMWEELPEVV ''+++'' 490 FLLQHVQEL ''+++''
491 GLNDRSDAV ''++'' 492 SLFDGFADGLGV ''+++'' 493 GLLGEKTQDLIGV
''+++'' 494 ALQPEPIKV ''++'' 495 FIFSEKPVFV ''+++'' 496 FLVEKQPPQV
''+++'' 497 GLLEKLTAI ''+++'' 498 KLWTGGLDNTV ''+++'' 499
KIFDIDEAEEGV ''++'' 500 SLMEDQVLQL ''+++'' 501 LLDPNVKSIFV ''+++''
502 RLLAQVPGL ''+++'' 503 SLNHFTHSV ''+++'' 504 GLSDGNPSL ''++''
505 SLAPGDVVRQV ''++'' 506 KLLGKVETA ''+++'' 507 KLIDDQDISISL
''+++'' 508 ILAQEQLVVGV ''+++'' 509 FLFDTKPLIV ''+++'' 510
KLYSVVSQL ''++'' 511 FLDPYCSASV ''++'' 512 SLSEIVPCL ''+++'' 513
SLWPSPEQL ''++'' 514 ILVDWLVQV ''+++'' 515 LLQELVLFL ''+++'' 516
AVGPASILKEV ''++'' 517 LLMPIPEGLTL ''+++'' 518 KLNAEVACV ''+++''
519 GLLHLTLLL ''+++'' 520 LAVHPSGVAL ''+'' 521 MLLTKLPTI ''+++''
522 TLWYRSPEV ''++'' 523 YQIPRTFTL ''++'' 524 ALIENLTHQI ''++'' 525
VLLEAGEGLVTI ''+++'' 526 RLAEVGQYEQV ''++'' 527 FLLEPGNLEV ''++++''
528 SVAEGRALMSV ''+++'' 529 LLADELITV ''+++'' 530 VMYADIGGMDI
''+++'' 531 YTLPIASSIRL ''+++'' 537 TLAPGEVLRSV ''+++'' 538
LLLAHIIAL ''++'' 539 ALFDAQAQV ''+++'' 541 SMLEPVPEL ''+++'' 542
RVWDISTVSSV ''+++'' 543 GLLPTPITQQASL ''+++'' 544 LLWDVPAPSL
''+++'' 545 LLADLLHNV ''+++''
546 VMIAGKVAVV ''+++'' 547 TLDITPHTV ''+++'' 548 ALWENPESGEL ''++''
549 AMLENASDIKL ''+++'' 550 FLYDEIEAEVNL ''+++'' 551 KLYESLLPFA
''+++'' 552 GLLDLPFRVGV ''++++'' 553 SLLNQDLHWSL ''++++'' 554
LLMPSSEDLLL ''+++'' 555 YVLEGLKSV ''+++'' 556 FLTDLEDLTL ''+++''
557 KLYDDMIRL ''+++'' 558 GLLENIPRV ''+++'' 559 VTVPPGPSL ''++''
560 ALWDIETGQQTTT ''+++'' 561 YLQLTQSEL ''+++'' 562 YLEELPEKLKL
''+++'' 563 WLLPYNGVTV ''+++'' 564 TVTNAVVTV ''+++'' 565 ALQETPTSV
''++'' 566 VIADGGIQNV ''++'' 567 SLLPLDDIVRV ''+++'' 568
TLYDIAHTPGV ''++++'' 569 KLVDRTWTL ''+++'' 570 ALANQIPTV ''++'' 571
LLLTTIPQI ''+++'' 572 ALADLIEKELSV ''+++'' 573 ILVANAIVGV ''+++''
574 YLLQEPPRTV ''++'' 575 YLISQVEGHQV ''+++'' 576 ILLNNSGQIKL
''++++'' 577 VMFEDGVLMRL ''+++'' 578 FLDPGGPMMKL ''+++'' 579
NLMEMVAQL ''++'' 580 LLMENAERV ''++'' 582 TLCDVILMV ''+++'' 583
ILANDGVLLAA ''+++'' 584 ALAEVAAMENV ''+++'' 585 ALWDLAADKQTL
''++++'' 586 KLKPGDLVGV ''+++'' 587 VMNDRLYAI ''+++'' 588 SLLPLSHLV
''+++'' 589 KLYPQLPAEI ''+++'' 590 SLIEKLWQT ''++'' 591 SMAELDIKL
''+++'' 592 RLLJAAENFL ''+++'' 593 GLPRFGIEMV ''+++'' 594
IMLKGDNITL ''+++'' 595 VLLSIYPRV ''+++'' 596 ALLDQTKTLAESAL ''+++''
597 KLLEGQVIQL ''+++'' 598 FLFPHSVLV ''+++'' 599 YLLNDASLISV
''+++'' 600 ALAAPDIVPAL ''+++'' 601 SAFPFPVTV ''+++'' 602
YLLEQIKLIEV ''++++'' 603 FLIEPEHVNTV ''++'' 604 SILDRDDIFV ''+++''
605 KLYEAVPQL ''+++'' 606 ALWETEVYI ''+++'' 607 RLYSGISGLEL ''+++''
608 SLLSVSHAL ''+++'' 609 ALWKQLLEL ''+++'' 610 LLAPTPYIIGV ''+++''
611 YLLDDGTLVV ''++++'' 612 YLYNEGLSV ''+++'' 613 RLLPPGAVVAV
''+++'' 614 LLLPDQPPYHL ''+++'' 615 VLPPDTDPA ''++'' 616 VLIDEVESL
''+++'' 617 ALMYESEKVGV ''+++'' 618 VLFDSESIGIYV ''+++'' 619
ALQDRVPLA ''+++'' 620 KLLNKIYEA ''++++'' 621 VLMDRLPSLL ''++++''
622 RLLGEEVVRVLQA ''+++'' 623 YLVEDIQHI ''+++'' 635 SLDSTLHAV
''+++''
Example 6
Absolute Quantitation of Tumor Associated Peptides Presented on the
Cell Surface
[0901] The generation of binders, such as antibodies and/or TCRs,
is a laborious process, which may be conducted only for a number of
selected targets. In the case of tumor-associated and -specific
peptides, selection criteria include but are not restricted to
exclusiveness of presentation and the density of peptide presented
on the cell surface. In addition to the isolation and relative
quantitation of peptides as described in EXAMPLE 1, the inventors
did analyze absolute peptide copies per cell as described in patent
application PCT/EP2015/79873. The quantitation of TUMAP copies per
cell in solid tumor samples requires the absolute quantitation of
the isolated TUMAP, the efficiency of TUMAP isolation, and the cell
count of the tissue sample analyzed. Experimental steps are
described below.
Peptide Quantitation by nanoLC-MS/MS
[0902] For an accurate quantitation of peptides by mass
spectrometry, a calibration curve was generated for each peptide
using the internal standard method. The internal standard is a
double-isotope-labelled variant of each peptide, i.e. two
isotope-labelled amino acids were included in TUMAP synthesis. It
differs from the tumor-associated peptide only in its mass but
shows no difference in other physicochemical properties (Anderson
et al., 2012). The internal standard was spiked to each MS sample
and all MS signals were normalized to the MS signal of the internal
standard to level out potential technical variances between MS
experiments.
[0903] The calibration curves were prepared in at least three
different matrices, i.e. HLA peptide eluates from natural samples
similar to the routine MS samples, and each preparation was
measured in duplicate MS runs. For evaluation, MS signals were
normalized to the signal of the internal standard and a calibration
curve was calculated by logistic regression.
[0904] For the quantitation of tumor-associated peptides from
tissue samples, the respective samples were also spiked with the
internal standard; the MS signals were normalized to the internal
standard and quantified using the peptide calibration curve.
Efficiency of Peptide/MHC Isolation
[0905] As for any protein purification process, the isolation of
proteins from tissue samples is associated with a certain loss of
the protein of interest. To determine the efficiency of TUMAP
isolation, peptide/MHC complexes were generated for all TUMAPs
selected for absolute quantitation. To be able to discriminate the
spiked from the natural peptide/MHC complexes,
single-isotope-labelled versions of the TUMAPs were used, i.e. one
isotope-labelled amino acid was included in TUMAP synthesis. These
complexes were spiked into the freshly prepared tissue lysates,
i.e. at the earliest possible point of the TUMAP isolation
procedure, and then captured like the natural peptide/MHC complexes
in the following affinity purification. Measuring the recovery of
the single-labelled TUMAPs therefore allows conclusions regarding
the efficiency of isolation of individual natural TUMAPs.
[0906] The efficiency of isolation was analyzed in a low number of
samples and was comparable among these tissue samples. In contrast,
the isolation efficiency differs between individual peptides. This
suggests that the isolation efficiency, although determined in only
a limited number of tissue samples, may be extrapolated to any
other tissue preparation. However, it is necessary to analyze each
TUMAP individually as the isolation efficiency may not be
extrapolated from one peptide to others.
Determination of the Cell Count in Solid, Frozen Tissue
[0907] In order to determine the cell count of the tissue samples
subjected to absolute peptide quantitation, the inventors applied
DNA content analysis. This method is applicable to a wide range of
samples of different origin and, most importantly, frozen samples
(Alcoser et al., 2011; Forsey and Chaudhuri, 2009; Silva et al.,
2013). During the peptide isolation protocol, a tissue sample is
processed to a homogenous lysate, from which a small lysate aliquot
is taken. The aliquot is divided in three parts, from which DNA is
isolated (QiaAmp DNA Mini Kit, Qiagen, Hilden, Germany). The total
DNA content from each DNA isolation is quantified using a
fluorescence-based DNA quantitation assay (Qubit dsDNA HS Assay
Kit, Life Technologies, Darmstadt, Germany) in at least two
replicates.
[0908] In order to calculate the cell number, a DNA standard curve
from aliquots of single healthy blood cells, with a range of
defined cell numbers, has been generated. The standard curve is
used to calculate the total cell content from the total DNA content
from each DNA isolation. The mean total cell count of the tissue
sample used for peptide isolation is extrapolated considering the
known volume of the lysate aliquots and the total lysate
volume.
Peptide Copies Per Cell
[0909] With data of the aforementioned experiments, the inventors
calculated the number of TUMAP copies per cell by dividing the
total peptide amount by the total cell count of the sample,
followed by division through isolation efficiency. Copy cell number
for selected peptides are shown in Table 12
TABLE-US-00014 TABLE 12 Absolute copy numbers. The table lists the
results of absolute peptide quantitation in NSCLC tumor samples.
The median number of copies per cell are indicated for each
peptide: <100 = +; > = 100 = ++; > = 1,000 +++; > =
10,000 = ++++. The number of samples, in which evaluable, high
quality MS data are available, is indicated. Number of Copy Number
quantifiable Seq ID Sequence Category samples 11 KIFEMLEGV ++ 32
198 KTINKVPTV ++ 14 408 VLDDSIYLV ++ 17 427 ALLPLSPYL +++ 13 587
VMNDRLYAI ++ 18
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Sequence CWU 1
1
665111PRTHomo sapiens 1Ser Leu Met Glu Pro Pro Ala Val Leu Leu Leu
1 5 10 29PRTHomo sapiens 2Ser Leu Leu Glu Ala Asp Pro Phe Leu 1 5
39PRTHomo sapiens 3Ser Leu Ala Ser Lys Leu Thr Thr Leu 1 5
49PRTHomo sapiens 4Gly Ile Met Glu His Ile Thr Lys Ile 1 5
59PRTHomo sapiens 5His Leu Thr Glu Val Tyr Pro Glu Leu 1 5
610PRTHomo sapiens 6Val Leu Val Ser Asp Gly Val His Ser Val 1 5 10
79PRTHomo sapiens 7Ser Leu Val Gly Leu Leu Leu Tyr Leu 1 5
811PRTHomo sapiens 8Phe Thr Leu Gly Asn Val Val Gly Met Tyr Leu 1 5
10 99PRTHomo sapiens 9Gly Ala Ala Lys Asp Leu Pro Gly Val 1 5
1010PRTHomo sapiens 10Phe Leu Ala Thr Phe Pro Leu Ala Ala Val 1 5
10 119PRTHomo sapiens 11Lys Ile Phe Glu Met Leu Glu Gly Val 1 5
129PRTHomo sapiens 12Ser Leu Trp Pro Asp Pro Met Glu Val 1 5
139PRTHomo sapiens 13Tyr Leu Met Asp Glu Ser Leu Asn Leu 1 5
1412PRTHomo sapiens 14Ala Ala Tyr Gly Gly Leu Asn Glu Lys Ser Phe
Val 1 5 10 159PRTHomo sapiens 15Val Leu Leu Thr Phe Lys Ile Phe Leu
1 5 169PRTHomo sapiens 16Val Leu Phe Gln Gly Gln Ala Ser Leu 1 5
1711PRTHomo sapiens 17Gly Leu Leu Pro Gly Asp Arg Leu Val Ser Val 1
5 10 189PRTHomo sapiens 18Tyr Leu Val Ala Lys Leu Val Glu Val 1 5
1911PRTHomo sapiens 19Phe Met Val Asp Asn Glu Ala Ile Tyr Asp Ile 1
5 10 209PRTHomo sapiens 20Arg Met Ile Glu Tyr Phe Ile Asp Val 1 5
219PRTHomo sapiens 21Val Leu Asp Glu Leu Asp Met Glu Leu 1 5
2211PRTHomo sapiens 22Ile Met Glu Glu Asn Pro Gly Ile Phe Ala Val 1
5 10 2310PRTHomo sapiens 23Val Leu Leu Asp Asp Ile Phe Ala Gln Leu
1 5 10 249PRTHomo sapiens 24Ser Leu Ser Asp Gly Leu Glu Glu Val 1 5
2510PRTHomo sapiens 25Phe Leu Pro Asp Glu Pro Tyr Ile Lys Val 1 5
10 269PRTHomo sapiens 26Ala Leu Leu Glu Leu Ala Glu Glu Leu 1 5
279PRTHomo sapiens 27Ile Leu Ala Asp Ile Val Ile Ser Ala 1 5
2811PRTHomo sapiens 28Gln Leu Leu Asp Glu Thr Ser Ala Ile Thr Leu 1
5 10 2913PRTHomo sapiens 29Lys Met Leu Gly Ile Pro Ile Ser Asn Ile
Leu Met Val 1 5 10 309PRTHomo sapiens 30Leu Ile Leu Asp Trp Val Pro
Tyr Ile 1 5 3110PRTHomo sapiens 31Tyr Leu Ala Pro Glu Leu Phe Val
Asn Val 1 5 10 3211PRTHomo sapiens 32Lys Leu Asp Asp Leu Thr Gln
Asp Leu Thr Val 1 5 10 339PRTHomo sapiens 33Val Leu Leu Ser Leu Leu
Glu Lys Val 1 5 3411PRTHomo sapiens 34Ile Leu Val Glu Ala Asp Ser
Leu Trp Val Val 1 5 10 359PRTHomo sapiens 35Lys Ile Asn Asp Thr Ile
Tyr Glu Val 1 5 3610PRTHomo sapiens 36Tyr Val Leu Glu Asp Leu Glu
Val Thr Val 1 5 10 3711PRTHomo sapiens 37Leu Leu Trp Asp Val Val
Thr Gly Gln Ser Val 1 5 10 3810PRTHomo sapiens 38Phe Leu Leu Glu
Asp Asp Ile His Val Ser 1 5 10 399PRTHomo sapiens 39Ser Val Ala Pro
Asn Leu Pro Ala Val 1 5 409PRTHomo sapiens 40Thr Leu Leu Val Lys
Val Phe Ser Val 1 5 419PRTHomo sapiens 41Ser Leu Met Pro His Ile
Pro Gly Leu 1 5 429PRTHomo sapiens 42Val Leu Leu Gln Lys Ile Val
Ser Ala 1 5 439PRTHomo sapiens 43Val Leu Ser Ser Leu Glu Ile Asn
Ile 1 5 4411PRTHomo sapiens 44Ile Leu Asp Pro Ile Ser Ser Gly Phe
Leu Leu 1 5 10 459PRTHomo sapiens 45Ser Leu Trp Gln Asp Ile Pro Asp
Val 1 5 469PRTHomo sapiens 46Ile Leu Thr Glu Glu Asn Ile His Leu 1
5 4710PRTHomo sapiens 47Ile Leu Leu Ser Val Pro Leu Leu Val Val 1 5
10 4810PRTHomo sapiens 48Ala Leu Ala Glu Leu Tyr Glu Asp Glu Val 1
5 10 499PRTHomo sapiens 49Tyr Leu Pro Ala Val Phe Glu Glu Val 1 5
509PRTHomo sapiens 50Ser Leu Ser Glu Leu Glu Ala Leu Met 1 5
519PRTHomo sapiens 51Leu Leu Pro Asp Leu Glu Phe Tyr Val 1 5
5211PRTHomo sapiens 52Phe Leu Leu Ala His Gly Leu Gly Phe Leu Leu 1
5 10 5311PRTHomo sapiens 53Lys Met Ile Glu Thr Asp Ile Leu Gln Lys
Val 1 5 10 5412PRTHomo sapiens 54Ser Leu Leu Glu Gln Gly Lys Glu
Pro Trp Met Val 1 5 10 5510PRTHomo sapiens 55Ser Leu Leu Asp Leu
Glu Thr Leu Ser Leu 1 5 10 5610PRTHomo sapiens 56Lys Leu Tyr Glu
Gly Ile Pro Val Leu Leu 1 5 10 5711PRTHomo sapiens 57Thr Leu Ala
Glu Leu Gln Pro Pro Val Gln Leu 1 5 10 589PRTHomo sapiens 58Phe Leu
Asp Thr Leu Lys Asp Leu Ile 1 5 599PRTHomo sapiens 59Ile Met Glu
Asp Ile Ile Leu Thr Leu 1 5 6010PRTHomo sapiens 60Ser Leu Thr Ile
Asp Gly Ile Tyr Tyr Val 1 5 10 619PRTHomo sapiens 61Phe Leu Gln Gly
Tyr Gln Leu His Leu 1 5 6212PRTHomo sapiens 62Val Leu Leu Asp Val
Ser Ala Gly Gln Leu Leu Met 1 5 10 6311PRTHomo sapiens 63Tyr Leu
Leu Pro Ser Gly Gly Ser Val Thr Leu 1 5 10 6410PRTHomo sapiens
64Tyr Ala Ala Pro Gly Gly Leu Ile Gly Val 1 5 10 6510PRTHomo
sapiens 65Leu Lys Val Asn Gln Gly Leu Glu Ser Leu 1 5 10
6611PRTHomo sapiens 66Phe Leu Asp Glu Asn Ile Gly Gly Val Ala Val 1
5 10 6710PRTHomo sapiens 67Thr Leu Leu Ala Glu Ala Leu Val Thr Val
1 5 10 6811PRTHomo sapiens 68Ser Leu Met Glu Leu Pro Arg Gly Leu
Phe Leu 1 5 10 6913PRTHomo sapiens 69Phe Gln Leu Asp Pro Ser Ser
Gly Val Leu Val Thr Val 1 5 10 709PRTHomo sapiens 70Gly Leu Leu Asp
Tyr Pro Val Gly Val 1 5 719PRTHomo sapiens 71Gly Ile Leu Ala Arg
Ile Ala Ser Val 1 5 7210PRTHomo sapiens 72Ser Leu Leu Glu Leu Asp
Gly Ile Asn Leu 1 5 10 739PRTHomo sapiens 73Asn Ile Phe Asp Leu Gln
Ile Tyr Val 1 5 7412PRTHomo sapiens 74Ala Leu Leu Asp Pro Glu Val
Leu Ser Ile Phe Val 1 5 10 759PRTHomo sapiens 75Gly Leu Leu Glu Val
Met Val Asn Leu 1 5 769PRTHomo sapiens 76Ile Leu Ile Asp Ser Ile
Tyr Lys Val 1 5 7711PRTHomo sapiens 77Ile Leu Val Glu Ala Asp Gly
Ala Trp Val Val 1 5 10 7813PRTHomo sapiens 78Ser Leu Phe Ser Ser
Leu Glu Pro Gln Ile Gln Pro Val 1 5 10 7911PRTHomo sapiens 79Ser
Leu Phe Ile Gly Glu Lys Ala Val Leu Leu 1 5 10 8010PRTHomo sapiens
80Phe Leu Tyr Asp Asn Leu Val Glu Ser Leu 1 5 10 819PRTHomo sapiens
81Phe Leu Phe Ser Gln Leu Gln Tyr Leu 1 5 829PRTHomo sapiens 82Phe
Leu Ser Ser Val Thr Tyr Asn Leu 1 5 839PRTHomo sapiens 83Ile Leu
Ala Pro Thr Val Met Met Ile 1 5 8410PRTHomo sapiens 84Val Thr Phe
Gly Glu Lys Leu Leu Gly Val 1 5 10 859PRTHomo sapiens 85Lys Met Ser
Glu Leu Arg Val Thr Leu 1 5 869PRTHomo sapiens 86Asn Leu Ile Gly
Lys Ile Glu Asn Val 1 5 8714PRTHomo sapiens 87Ala Leu Pro Glu Ala
Pro Ala Pro Leu Leu Pro His Ile Thr 1 5 10 8810PRTHomo sapiens
88Phe Leu Leu Val Gly Asp Leu Met Ala Val 1 5 10 8910PRTHomo
sapiens 89Tyr Ile Leu Pro Thr Glu Thr Ile Tyr Val 1 5 10 909PRTHomo
sapiens 90Thr Leu Leu Gln Ile Ile Glu Thr Val 1 5 9111PRTHomo
sapiens 91Ile Met Gln Asp Phe Pro Ala Glu Ile Phe Leu 1 5 10
9211PRTHomo sapiens 92Tyr Leu Ile Pro Phe Thr Gly Ile Val Gly Leu 1
5 10 939PRTHomo sapiens 93Leu Leu Gln Ala Ile Lys Leu Tyr Leu 1 5
9410PRTHomo sapiens 94Tyr Leu Ile Asp Ile Lys Thr Ile Ala Ile 1 5
10 959PRTHomo sapiens 95Ser Val Ile Pro Gln Ile Gln Lys Val 1 5
9610PRTHomo sapiens 96Tyr Ile Phe Thr Asp Asn Pro Ala Ala Val 1 5
10 979PRTHomo sapiens 97Ser Leu Ile Asn Gly Ser Phe Leu Val 1 5
9810PRTHomo sapiens 98Leu Ile Ile Asp Gln Ala Asp Ile Tyr Leu 1 5
10 9910PRTHomo sapiens 99Ala Leu Val Ser Lys Gly Leu Ala Thr Val 1
5 10 1009PRTHomo sapiens 100Tyr Leu Leu Ser Thr Asn Ala Gln Leu 1 5
10111PRTHomo sapiens 101Ile Leu Val Gly Gly Gly Ala Leu Ala Thr Val
1 5 10 10210PRTHomo sapiens 102Tyr Leu Phe Glu Ser Glu Gly Leu Val
Leu 1 5 10 1039PRTHomo sapiens 103Thr Leu Ala Glu Glu Val Val Ala
Leu 1 5 1049PRTHomo sapiens 104Ser Thr Met Glu Gln Asn Phe Leu Leu
1 5 1059PRTHomo sapiens 105Leu Leu Leu Glu His Ser Phe Glu Ile 1 5
10611PRTHomo sapiens 106Leu Leu Tyr Asp Ala Val His Ile Val Ser Val
1 5 10 10711PRTHomo sapiens 107Phe Leu Gln Pro Val Asp Asp Thr Gln
His Leu 1 5 10 10811PRTHomo sapiens 108Ala Leu Phe Pro Gly Val Ala
Leu Leu Leu Ala 1 5 10 1099PRTHomo sapiens 109Ile Ile Leu Ser Ile
Leu Glu Gln Ala 1 5 1109PRTHomo sapiens 110Phe Leu Ser Gln Val Asp
Phe Glu Leu 1 5 11110PRTHomo sapiens 111Tyr Val Trp Gly Phe Tyr Pro
Ala Glu Val 1 5 10 1129PRTHomo sapiens 112Phe Leu Ile Thr Ser Asn
Asn Gln Leu 1 5 11310PRTHomo sapiens 113Gly Leu Leu Pro Thr Pro Leu
Phe Gly Val 1 5 10 11411PRTHomo sapiens 114Ser Leu Val Gly Glu Pro
Ile Leu Gln Asn Val 1 5 10 11511PRTHomo sapiens 115Ala Ile Ala Gly
Ala Gly Ile Leu Tyr Gly Val 1 5 10 1169PRTHomo sapiens 116Tyr His
Ile Asp Glu Glu Val Gly Phe 1 5 11711PRTHomo sapiens 117Ile Leu Pro
Asp Gly Glu Asp Phe Leu Ala Val 1 5 10 1189PRTHomo sapiens 118Lys
Leu Ile Asp Asn Asn Ile Asn Val 1 5 11910PRTHomo sapiens 119Phe Leu
Tyr Ile Gly Asp Ile Val Ser Leu 1 5 10 12010PRTHomo sapiens 120Ala
Leu Leu Gly Ile Pro Leu Thr Leu Val 1 5 10 12111PRTHomo sapiens
121Gly Val Val Asp Pro Arg Ala Ile Ser Val Leu 1 5 10 12210PRTHomo
sapiens 122Phe Leu Leu Ala Glu Asp Asp Ile Tyr Leu 1 5 10
12311PRTHomo sapiens 123Asn Leu Trp Asp Leu Thr Asp Ala Ser Val Val
1 5 10 12410PRTHomo sapiens 124Ala Leu Tyr Glu Thr Glu Leu Ala Asp
Ala 1 5 10 1259PRTHomo sapiens 125Val Gln Ile His Gln Val Ala Gln
Val 1 5 1269PRTHomo sapiens 126Val Leu Ala Tyr Phe Leu Pro Glu Ala
1 5 1279PRTHomo sapiens 127Lys Ile Gly Asp Glu Pro Pro Lys Val 1 5
12810PRTHomo sapiens 128Tyr Leu Phe Asp Asp Pro Leu Ser Ala Val 1 5
10 12911PRTHomo sapiens 129Gly Leu Leu Asp Gly Gly Val Asp Ile Leu
Leu 1 5 10 13011PRTHomo sapiens 130Phe Leu Trp Asn Gly Glu Asp Ser
Ala Leu Leu 1 5 10 13111PRTHomo sapiens 131Phe Val Pro Pro Val Thr
Val Phe Pro Ser Leu 1 5 10 13211PRTHomo sapiens 132Leu Leu Val Glu
Gln Pro Pro Leu Ala Gly Val 1 5 10 1339PRTHomo sapiens 133Lys Val
Leu Ser Asn Ile His Thr Val 1 5 1349PRTHomo sapiens 134Tyr Leu Gln
Glu Leu Ile Phe Ser Val 1 5 1359PRTHomo sapiens 135Ala Leu Ser Glu
Val Asp Phe Gln Leu 1 5 13611PRTHomo sapiens 136Tyr Leu Ala Asp Pro
Ser Asn Leu Phe Val Val 1 5 10 1379PRTHomo sapiens 137Thr Leu Val
Leu Thr Leu Pro Thr Val 1 5 13810PRTHomo sapiens 138Tyr Gln Tyr Pro
Arg Ala Ile Leu Ser Val 1 5 10 13912PRTHomo sapiens 139Ser Val Met
Glu Val Asn Ser Gly Ile Tyr Arg Val 1 5 10 1409PRTHomo sapiens
140Tyr Met Asp Ala Pro Lys Ala Ala Leu 1 5 1419PRTHomo sapiens
141Tyr Leu Asp Phe Ser Asn Asn Arg Leu 1 5 1429PRTHomo sapiens
142Phe Leu Phe Ala Thr Pro Val Phe Ile 1 5 1439PRTHomo sapiens
143Leu Leu Leu Asp Ile Thr Pro Glu Ile 1 5 14411PRTHomo sapiens
144Tyr Ile Met Glu Pro Ser Ile Phe Asn Thr Leu 1 5 10 14511PRTHomo
sapiens 145Phe Leu Ala Thr Ser Gly Thr Leu Ala Gly Ile 1 5 10
14612PRTHomo sapiens 146Ser Leu Ala Thr Ala Gly Asp Gly Leu Ile Glu
Leu 1 5 10 1479PRTHomo sapiens 147Ser Leu Leu Glu Ala Val Ser Phe
Leu 1 5 1489PRTHomo sapiens 148Ala Leu Asn Pro Glu Ile Val Ser Val
1 5 1499PRTHomo sapiens 149Asn Leu Leu Glu Leu Phe Val Gln Leu 1 5
15011PRTHomo sapiens 150Arg Leu Trp Glu Glu Gly Glu Glu Leu Glu Leu
1 5 10 1519PRTHomo sapiens 151Lys Ile Leu Gln Gln Leu Val Thr Leu 1
5 1529PRTHomo sapiens 152Ile Leu Phe Glu Asp Ile Phe Asp Val 1 5
1539PRTHomo sapiens 153Phe Leu Ile Ala Asn Val Leu Tyr Leu 1 5
1549PRTHomo sapiens 154Ala Leu Asp Asp Gly Thr Pro Ala Leu 1 5
15510PRTHomo sapiens 155Arg Val Ala Asn Leu His Phe Pro Ser Val 1 5
10 15611PRTHomo sapiens 156Ala Ile Ser Gln Gly Ile Thr Leu Pro Ser
Leu 1 5 10 1579PRTHomo sapiens 157Ser Leu Asn Asp Glu Val Pro Glu
Val 1 5 15811PRTHomo sapiens 158Lys Leu Phe Asp Val Asp Glu Asp Gly
Tyr Ile 1 5 10 15910PRTHomo sapiens 159Gly Leu Val Gly Asn Pro Leu
Pro Ser Val 1 5 10 16010PRTHomo sapiens 160Phe Leu Phe Asp Glu Glu
Ile Glu Gln Ile 1 5 10 1619PRTHomo sapiens 161Ala Leu Leu Glu Gly
Val Asn Thr Val 1 5 1629PRTHomo sapiens 162Tyr Gln Gln Ala Gln Val
Pro Ser Val 1 5 16311PRTHomo sapiens 163Ala Leu Asp Glu Met Gly Asp
Leu Leu Gln Leu 1 5 10 16411PRTHomo sapiens 164Ala Leu Leu Pro Gln
Pro Lys Asn Leu Thr Val 1 5 10 1659PRTHomo sapiens 165Ser Leu Leu
Asp Glu Ile Arg Ala Val 1 5 1669PRTHomo sapiens 166Tyr Leu Asn His
Leu Glu Pro Pro Val 1 5 16711PRTHomo sapiens 167Lys Val Leu Glu Val
Thr Glu Glu Phe Gly Val 1 5 10 1689PRTHomo sapiens 168Lys Ile Leu
Asp Ala Asp Ile Gln Leu 1 5 1699PRTHomo sapiens 169Asn Leu Pro Glu
Tyr Leu Pro Phe Val 1 5 1709PRTHomo sapiens 170Arg Leu Gln Glu Thr
Leu Ser Ala Ala 1 5 1719PRTHomo sapiens 171Leu Leu Leu Pro Leu Gln
Ile Leu Leu 1 5 17210PRTHomo sapiens 172Val Leu Tyr Ser Tyr Thr Ile
Ile Thr Val 1 5 10 17311PRTHomo sapiens 173Leu Leu Asp Ser Ala Ser
Ala Gly Leu Tyr Leu 1 5 10 1749PRTHomo sapiens 174Ala Leu Ala Gln
Tyr Leu Ile Thr Ala 1 5 1759PRTHomo sapiens 175Tyr Leu Phe Glu Asn
Ile Ser Gln Leu 1 5 17612PRTHomo sapiens 176Tyr Leu Met Glu Gly Ser
Tyr Asn Lys Val Phe Leu 1 5 10 17711PRTHomo sapiens 177Tyr Leu Leu
Pro Glu Glu Tyr Thr Ser Thr Leu 1 5 10 1789PRTHomo sapiens 178Ala
Leu Thr Glu Ile Ala Phe Val Val 1 5 1799PRTHomo sapiens 179Lys Val
Leu Asn Glu Leu Tyr Thr Val 1
5 18012PRTHomo sapiens 180Phe Gln Ile Asp Pro His Ser Gly Leu Val
Thr Val 1 5 10 18110PRTHomo sapiens 181Leu Leu Trp Ala Gly Thr Ala
Phe Gln Val 1 5 10 18210PRTHomo sapiens 182Met Leu Leu Glu Ala Pro
Gly Ile Phe Leu 1 5 10 1839PRTHomo sapiens 183Phe Gly Leu Asp Leu
Val Thr Glu Leu 1 5 18411PRTHomo sapiens 184Tyr Leu Met Asp Ile Asn
Gly Lys Met Trp Leu 1 5 10 18510PRTHomo sapiens 185Phe Leu Ile Asp
Asp Lys Gly Tyr Thr Leu 1 5 10 1869PRTHomo sapiens 186Thr Leu Phe
Phe Gln Gln Asn Ala Leu 1 5 18711PRTHomo sapiens 187Arg Gln Ile Ser
Ile Arg Gly Ile Val Gly Val 1 5 10 18810PRTHomo sapiens 188Gly Leu
Phe Pro Val Thr Pro Glu Ala Val 1 5 10 1899PRTHomo sapiens 189Ala
Leu Gln Arg Lys Leu Pro Tyr Val 1 5 1909PRTHomo sapiens 190Phe Leu
Ser Ser Leu Thr Glu Thr Ile 1 5 19111PRTHomo sapiens 191Leu Leu Gln
Glu Gly Gln Ala Leu Glu Tyr Val 1 5 10 19210PRTHomo sapiens 192Lys
Met Leu Asp Gly Ala Ser Phe Thr Leu 1 5 10 19311PRTHomo sapiens
193Gln Leu Leu Asp Ala Asp Gly Phe Leu Asn Val 1 5 10 1949PRTHomo
sapiens 194Ala Leu Pro Leu Phe Val Ile Thr Val 1 5 19510PRTHomo
sapiens 195Gly Leu Phe Ala Asp Leu Leu Pro Arg Leu 1 5 10
1969PRTHomo sapiens 196Tyr Leu Tyr Ser Val Glu Ile Lys Leu 1 5
1979PRTHomo sapiens 197Ala Leu Gly Pro Glu Gly Gly Arg Val 1 5
1989PRTHomo sapiens 198Lys Thr Ile Asn Lys Val Pro Thr Val 1 5
19910PRTHomo sapiens 199Ala Leu Gln Asp Val Pro Leu Ser Ser Val 1 5
10 2009PRTHomo sapiens 200Leu Leu Phe Gly Ser Val Gln Glu Val 1 5
2019PRTHomo sapiens 201Arg Leu Val Asp Tyr Leu Glu Gly Ile 1 5
20212PRTHomo sapiens 202Ala Leu Leu Asp Gln Gln Gly Ser Arg Trp Thr
Leu 1 5 10 20311PRTHomo sapiens 203Val Leu Leu Glu Asp Ala His Ser
His Thr Leu 1 5 10 2049PRTHomo sapiens 204Lys Ile Ala Glu Asn Val
Glu Glu Val 1 5 20511PRTHomo sapiens 205Ser Leu Tyr Pro Gly Thr Glu
Thr Met Gly Leu 1 5 10 20613PRTHomo sapiens 206Val Leu Gln Glu Gly
Lys Leu Gln Lys Leu Ala Gln Leu 1 5 10 2079PRTHomo sapiens 207Gly
Leu Thr Ser Thr Asn Ala Glu Val 1 5 2089PRTHomo sapiens 208Lys Ile
Ser Pro Val Thr Phe Ser Val 1 5 2099PRTHomo sapiens 209Lys Leu Ile
Glu Ser Lys His Glu Val 1 5 2109PRTHomo sapiens 210Leu Leu Leu Asn
Ala Val Leu Thr Val 1 5 2119PRTHomo sapiens 211Leu Leu Trp Pro Gly
Ala Ala Leu Leu 1 5 21210PRTHomo sapiens 212Ala Leu Trp Asp Gln Asp
Asn Leu Ser Val 1 5 10 21311PRTHomo sapiens 213Val Thr Ala Ala Tyr
Met Asp Thr Val Ser Leu 1 5 10 21410PRTHomo sapiens 214Phe Leu Leu
Asp Leu Asp Pro Leu Leu Leu 1 5 10 2159PRTHomo sapiens 215Gln Leu
Ile Asn His Leu His Ala Val 1 5 2169PRTHomo sapiens 216Asn Leu Trp
Glu Asp Pro Tyr Tyr Leu 1 5 2179PRTHomo sapiens 217Ala Leu Ile His
Pro Val Ser Thr Val 1 5 2189PRTHomo sapiens 218Ser Ala Leu Glu Glu
Leu Val Asn Val 1 5 2199PRTHomo sapiens 219Lys Leu Ser Asp Ile Gly
Ile Thr Val 1 5 2209PRTHomo sapiens 220Leu Leu Gln Lys Phe Val Pro
Glu Ile 1 5 2219PRTHomo sapiens 221Ala Leu Tyr Glu Glu Gly Leu Leu
Leu 1 5 2229PRTHomo sapiens 222Asn Leu Ile Glu Asn Val Gln Arg Leu
1 5 22310PRTHomo sapiens 223Ala Leu Leu Glu Asn Ile Ala Leu Tyr Leu
1 5 10 2249PRTHomo sapiens 224Thr Leu Ile Asp Ala Gln Trp Val Leu 1
5 2259PRTHomo sapiens 225Ser Leu Leu Lys Val Leu Pro Ala Leu 1 5
2269PRTHomo sapiens 226Met Leu Tyr Val Val Pro Ile Tyr Leu 1 5
2279PRTHomo sapiens 227Ala Leu Met Asn Thr Leu Leu Tyr Leu 1 5
2289PRTHomo sapiens 228Ala Met Gln Glu Tyr Ile Ala Val Val 1 5
2299PRTHomo sapiens 229Arg Leu Pro Gly Pro Leu Gly Thr Val 1 5
2309PRTHomo sapiens 230Ile Leu Val Asp Trp Leu Val Glu Val 1 5
23111PRTHomo sapiens 231Phe Leu Ser Pro Gln Gln Pro Pro Leu Leu Leu
1 5 10 23212PRTHomo sapiens 232Ala Leu Leu Glu Ala Gln Asp Val Glu
Leu Tyr Leu 1 5 10 2339PRTHomo sapiens 233Val Leu Ser Glu Thr Leu
Tyr Glu Leu 1 5 23411PRTHomo sapiens 234Ala Leu Met Glu Asp Thr Gly
Arg Gln Met Leu 1 5 10 23510PRTHomo sapiens 235Tyr Leu Asn Asp Leu
His Glu Val Leu Leu 1 5 10 2369PRTHomo sapiens 236Gly Leu Leu Glu
Ala Lys Val Ser Leu 1 5 23711PRTHomo sapiens 237Ala Leu Leu Glu Ala
Ser Gly Thr Leu Leu Leu 1 5 10 2389PRTHomo sapiens 238Tyr Leu Ile
Ser Phe Gln Thr His Ile 1 5 23910PRTHomo sapiens 239Ala Ala Phe Ala
Gly Lys Leu Leu Ser Val 1 5 10 2409PRTHomo sapiens 240Ile Leu Leu
Glu Gln Ala Phe Tyr Leu 1 5 24111PRTHomo sapiens 241Ser Leu Val Glu
Val Asn Pro Ala Tyr Ser Val 1 5 10 2429PRTHomo sapiens 242Ala Ile
Ala Tyr Ile Leu Gln Gly Val 1 5 2439PRTHomo sapiens 243Leu Leu Leu
Asn Glu Leu Pro Ser Val 1 5 24410PRTHomo sapiens 244Ser Leu Phe Gly
Gly Thr Glu Ile Thr Ile 1 5 10 2459PRTHomo sapiens 245Ser Met Ile
Asp Asp Leu Leu Gly Val 1 5 2469PRTHomo sapiens 246Leu Leu Trp Glu
Val Val Ser Gln Leu 1 5 24711PRTHomo sapiens 247Val Leu Leu Pro Asn
Asp Leu Leu Glu Lys Val 1 5 10 24810PRTHomo sapiens 248Phe Leu Phe
Pro Asn Gln Tyr Val Asp Val 1 5 10 2499PRTHomo sapiens 249Leu Leu
Asp Gly Phe Leu Val Asn Val 1 5 25011PRTHomo sapiens 250Ala Leu Ser
Glu Glu Gly Leu Leu Val Tyr Leu 1 5 10 25110PRTHomo sapiens 251Ala
Leu Tyr Thr Gly Phe Ser Ile Leu Val 1 5 10 2529PRTHomo sapiens
252Leu Leu Ile Gly Thr Asp Val Ser Leu 1 5 2539PRTHomo sapiens
253Gly Leu Asp Ala Ala Thr Ala Thr Val 1 5 2549PRTHomo sapiens
254Thr Leu Leu Ala Phe Ile Met Glu Leu 1 5 2559PRTHomo sapiens
255Val Leu Ala Ser Tyr Asn Leu Thr Val 1 5 25611PRTHomo sapiens
256Phe Leu Pro Pro Glu His Thr Ile Val Tyr Ile 1 5 10 2579PRTHomo
sapiens 257Ser Ile Phe Ser Ala Phe Leu Ser Val 1 5 2589PRTHomo
sapiens 258Glu Leu Ala Glu Arg Val Pro Ala Ile 1 5 2599PRTHomo
sapiens 259Thr Leu Met Arg Gln Leu Gln Gln Val 1 5 26013PRTHomo
sapiens 260Thr Leu Leu Glu Gly Pro Asp Pro Ala Glu Leu Leu Leu 1 5
10 2619PRTHomo sapiens 261Tyr Val Leu Glu Phe Leu Glu Glu Ile 1 5
2629PRTHomo sapiens 262Leu Leu Trp Gly Asp Leu Ile Trp Leu 1 5
26310PRTHomo sapiens 263Leu Leu Val Ser Asn Leu Asp Phe Gly Val 1 5
10 2649PRTHomo sapiens 264Ser Leu Gln Glu Gln Leu His Ser Val 1 5
2659PRTHomo sapiens 265Leu Leu Phe Gly Gly Thr Lys Thr Val 1 5
2669PRTHomo sapiens 266Lys Ile Thr Asp Thr Leu Ile His Leu 1 5
2679PRTHomo sapiens 267Ala Leu Gln Asp Phe Leu Leu Ser Val 1 5
2689PRTHomo sapiens 268Ile Ala Gly Pro Gly Leu Pro Asp Leu 1 5
26911PRTHomo sapiens 269Arg Val Leu Glu Val Gly Ala Leu Gln Ala Val
1 5 10 27011PRTHomo sapiens 270Leu Leu Leu Asp Glu Glu Gly Thr Phe
Ser Leu 1 5 10 27110PRTHomo sapiens 271Leu Val Tyr Pro Leu Glu Leu
Tyr Pro Ala 1 5 10 2729PRTHomo sapiens 272Ala Leu Gly Asn Thr Val
Pro Ala Val 1 5 2739PRTHomo sapiens 273Asn Leu Phe Gln Ser Val Arg
Glu Val 1 5 2749PRTHomo sapiens 274Ser Leu Leu Phe Ser Leu Phe Glu
Ala 1 5 2759PRTHomo sapiens 275Tyr Leu Val Tyr Ile Leu Asn Glu Leu
1 5 27610PRTHomo sapiens 276Ala Leu Phe Thr Phe Ser Pro Leu Thr Val
1 5 10 27711PRTHomo sapiens 277Leu Leu Pro Pro Leu Glu Ser Leu Ala
Thr Val 1 5 10 2789PRTHomo sapiens 278Gln Leu Leu Asp Val Val Leu
Thr Ile 1 5 27910PRTHomo sapiens 279Ala Leu Trp Gly Gly Thr Gln Pro
Leu Leu 1 5 10 28011PRTHomo sapiens 280Val Leu Pro Asp Pro Glu Val
Leu Glu Ala Val 1 5 10 2819PRTHomo sapiens 281Ile Leu Arg Glu Ser
Thr Glu Glu Leu 1 5 2829PRTHomo sapiens 282Leu Leu Ala Asp Val Val
Pro Thr Thr 1 5 28313PRTHomo sapiens 283Ala Leu Tyr Ile Gly Asp Gly
Tyr Val Ile His Leu Ala 1 5 10 2849PRTHomo sapiens 284Ile Leu Leu
Ser Gln Thr Thr Gly Val 1 5 2859PRTHomo sapiens 285Gln Leu Leu His
Val Gly Val Thr Val 1 5 2869PRTHomo sapiens 286Tyr Leu Phe Pro Gly
Ile Pro Glu Leu 1 5 2879PRTHomo sapiens 287Phe Leu Asn Glu Phe Phe
Leu Asn Val 1 5 2889PRTHomo sapiens 288Asn Leu Ile Asn Glu Ile Asn
Gly Val 1 5 28910PRTHomo sapiens 289Val Leu Leu Glu Ile Glu Asp Leu
Gln Val 1 5 10 29012PRTHomo sapiens 290Gly Leu Leu Asp Leu Asn Asn
Ala Ile Leu Gln Leu 1 5 10 29111PRTHomo sapiens 291Gly Leu Asp Ser
Asn Leu Lys Tyr Ile Leu Val 1 5 10 2929PRTHomo sapiens 292Leu Leu
Trp Glu Ala Gly Ser Glu Ala 1 5 29310PRTHomo sapiens 293Gly Leu Gly
Glu Leu Gln Glu Leu Tyr Leu 1 5 10 2949PRTHomo sapiens 294Ile Leu
Asp Pro Phe Gln Tyr Gln Leu 1 5 2959PRTHomo sapiens 295Val Leu Asp
Arg Glu Ser Pro Asn Val 1 5 2969PRTHomo sapiens 296Phe Met Glu Gly
Ala Ile Ile Tyr Val 1 5 29710PRTHomo sapiens 297Val Leu Ala Asp Ile
Glu Leu Ala Gln Ala 1 5 10 2989PRTHomo sapiens 298Val Met Ile Thr
Lys Leu Val Glu Val 1 5 2999PRTHomo sapiens 299Tyr Leu Leu Glu Thr
Ser Gly Asn Leu 1 5 3009PRTHomo sapiens 300Ala Leu Leu Gly Gln Thr
Phe Ser Leu 1 5 30110PRTHomo sapiens 301Phe Leu Val Glu Asp Leu Val
Asp Ser Leu 1 5 10 30211PRTHomo sapiens 302Ala Leu Leu Gln Glu Gly
Glu Val Tyr Ser Ala 1 5 10 3039PRTHomo sapiens 303Ala Ile Leu Pro
Gln Leu Phe Met Val 1 5 3049PRTHomo sapiens 304Met Thr Leu Gly Gln
Ile Tyr Tyr Leu 1 5 30510PRTHomo sapiens 305Ser Ile Ala Asn Phe Ser
Glu Phe Tyr Val 1 5 10 3069PRTHomo sapiens 306Ala Leu Val Asn Val
Gln Ile Pro Leu 1 5 3079PRTHomo sapiens 307Ala Leu Pro Val Ser Leu
Pro Gln Ile 1 5 30810PRTHomo sapiens 308Ser Gln Tyr Ser Gly Gln Leu
His Glu Val 1 5 10 30910PRTHomo sapiens 309Gly Leu Phe Asp Gly Val
Pro Thr Thr Ala 1 5 10 31010PRTHomo sapiens 310Phe Leu Val Asp Thr
Pro Leu Ala Arg Ala 1 5 10 3119PRTHomo sapiens 311Arg Leu Tyr Thr
Gly Met His Thr Val 1 5 3129PRTHomo sapiens 312Ile Ile Ser Asp Leu
Thr Ile Ala Leu 1 5 31310PRTHomo sapiens 313Val Leu Phe Asp Asp Glu
Leu Leu Met Val 1 5 10 31410PRTHomo sapiens 314Ala Leu Ile Ala Glu
Gly Ile Ala Leu Val 1 5 10 3159PRTHomo sapiens 315Tyr Leu Gln Asp
Val Val Glu Gln Ala 1 5 3169PRTHomo sapiens 316Ile Leu Leu Glu Arg
Leu Trp Tyr Val 1 5 3179PRTHomo sapiens 317Ser Leu Ala Ala Leu Val
Val His Val 1 5 31810PRTHomo sapiens 318Gly Leu Ile Asn Thr Gly Val
Leu Ser Val 1 5 10 3199PRTHomo sapiens 319Ser Leu Glu Pro Gln Ile
Gln Pro Val 1 5 32010PRTHomo sapiens 320Lys Met Phe Glu Phe Val Glu
Pro Leu Leu 1 5 10 32113PRTHomo sapiens 321Gly Leu Phe Glu Asp Val
Thr Gln Pro Gly Ile Leu Leu 1 5 10 3229PRTHomo sapiens 322Thr Leu
Met Thr Ser Leu Pro Ala Leu 1 5 32311PRTHomo sapiens 323Ile Gln Ile
Gly Glu Glu Thr Val Ile Thr Val 1 5 10 32410PRTHomo sapiens 324Phe
Leu Tyr Asp Glu Ile Glu Ala Glu Val 1 5 10 32513PRTHomo sapiens
325Phe Ile Met Pro Ala Thr Val Ala Asp Ala Thr Ala Val 1 5 10
3269PRTHomo sapiens 326Phe Leu Pro Glu Ala Leu Asp Phe Val 1 5
32712PRTHomo sapiens 327Gly Leu Ala Pro Phe Thr Glu Gly Ile Ser Phe
Val 1 5 10 3289PRTHomo sapiens 328Ala Leu Asn Asp Gln Val Phe Glu
Ile 1 5 32910PRTHomo sapiens 329Phe Leu Val Thr Leu Asn Asn Val Glu
Val 1 5 10 3309PRTHomo sapiens 330Gln Leu Ala Leu Lys Val Glu Gly
Val 1 5 3319PRTHomo sapiens 331Lys Val Asp Thr Val Trp Val Asn Val
1 5 3329PRTHomo sapiens 332Tyr Leu Ile Ser Glu Leu Glu Ala Ala 1 5
3339PRTHomo sapiens 333Phe Leu Pro Asp Ala Asn Ser Ser Val 1 5
3349PRTHomo sapiens 334Thr Leu Thr Lys Val Leu Val Ala Leu 1 5
3359PRTHomo sapiens 335Tyr Ser Leu Ser Ser Val Val Thr Val 1 5
3369PRTHomo sapiens 336Ile Leu Leu Thr Ala Ile Val Gln Val 1 5
33712PRTHomo sapiens 337His Leu Leu Ser Glu Leu Glu Ala Ala Pro Tyr
Leu 1 5 10 33810PRTHomo sapiens 338Ser Val Leu Glu Asp Pro Val His
Ala Val 1 5 10 33913PRTHomo sapiens 339Gly Leu Trp Glu Ile Glu Asn
Asn Pro Thr Val Lys Ala 1 5 10 3409PRTHomo sapiens 340Ala Leu Leu
Ser Met Thr Phe Pro Leu 1 5 34112PRTHomo sapiens 341Ser Gln Ile Ala
Leu Asn Glu Lys Leu Val Asn Leu 1 5 10 3429PRTHomo sapiens 342His
Ile Tyr Asp Lys Val Met Thr Val 1 5 34311PRTHomo sapiens 343Ser Leu
Leu Glu Val Asn Glu Glu Ser Thr Val 1 5 10 34411PRTHomo sapiens
344Tyr Leu Gln Asp Gln His Leu Leu Leu Thr Val 1 5 10 3459PRTHomo
sapiens 345Val Ile Trp Lys Ala Leu Ile His Leu 1 5 3469PRTHomo
sapiens 346Leu Leu Asp Ser Lys Val Pro Ser Val 1 5 34712PRTHomo
sapiens 347Ser Leu Phe Lys His Asp Pro Ala Ala Trp Glu Ala 1 5 10
3489PRTHomo sapiens 348Ile Leu Leu Asp Val Lys Thr Arg Leu 1 5
3499PRTHomo sapiens 349Ser Leu Thr Glu Tyr Leu Gln Asn Val 1 5
35012PRTHomo sapiens 350Ala Leu Leu Asp Val Thr His Ser Glu Leu Thr
Val 1 5 10 3519PRTHomo sapiens 351Ser Leu Ile Pro Asn Leu Arg Asn
Val 1 5 35210PRTHomo sapiens 352Ser Leu Leu Glu Leu Leu His Ile Tyr
Val 1 5 10 3539PRTHomo sapiens 353Tyr Leu Phe Glu Met Asp Ser Ser
Leu 1 5 3549PRTHomo sapiens 354Leu Ile Leu Glu Gly Val Asp Thr Val
1 5 35511PRTHomo sapiens 355Ser Ile Gln Gln Ser Ile Glu Arg Leu Leu
Val 1 5 10 3569PRTHomo sapiens 356Lys Leu Leu Gly Lys Leu Pro Glu
Leu 1 5 3579PRTHomo sapiens 357Ser Met His Asp Leu Val Leu Gln Val
1 5 3589PRTHomo sapiens 358Ala Leu Asp Glu Tyr Thr Ser Glu Leu 1
5
3599PRTHomo sapiens 359Tyr Leu Leu Pro Glu Ser Val Asp Leu 1 5
36011PRTHomo sapiens 360Ala Leu Asp Ser Gly Ala Ser Leu Leu His Leu
1 5 10 36110PRTHomo sapiens 361Ala Leu Tyr Glu Leu Glu Gly Thr Thr
Val 1 5 10 3629PRTHomo sapiens 362Thr Leu Tyr Gly Leu Ser Val Leu
Leu 1 5 36311PRTHomo sapiens 363Lys Val Leu Asp Val Ser Asp Leu Glu
Ser Val 1 5 10 3649PRTHomo sapiens 364Leu Leu Gln Asn Glu Gln Phe
Glu Leu 1 5 36512PRTHomo sapiens 365Tyr Val Ile Asp Gln Gly Glu Thr
Asp Val Tyr Val 1 5 10 36612PRTHomo sapiens 366Arg Leu Leu Asp Met
Gly Glu Thr Asp Leu Met Leu 1 5 10 3679PRTHomo sapiens 367Ser Leu
Gln Asn His Asn His Gln Leu 1 5 36810PRTHomo sapiens 368Ile Leu Leu
Glu Glu Val Ser Pro Glu Leu 1 5 10 36910PRTHomo sapiens 369Gly Leu
Phe Pro Glu His Leu Ile Asp Val 1 5 10 3709PRTHomo sapiens 370Ser
Leu Leu Gln Asp Leu Val Ser Val 1 5 3719PRTHomo sapiens 371Phe Leu
Gln Ala His Leu His Thr Ala 1 5 3729PRTHomo sapiens 372Thr Met Leu
Leu Asn Ile Pro Leu Val 1 5 37311PRTHomo sapiens 373Ser Leu Leu Glu
Asp Lys Gly Leu Ala Glu Val 1 5 10 37410PRTHomo sapiens 374Phe Leu
Leu Gln Gln His Leu Ile Ser Ala 1 5 10 3759PRTHomo sapiens 375Ser
Leu Thr Glu Thr Ile Glu Gly Val 1 5 37611PRTHomo sapiens 376Ala Met
Phe Glu Ser Ser Gln Asn Val Leu Leu 1 5 10 3779PRTHomo sapiens
377Phe Leu Leu Asp Ser Ser Ala Ser Val 1 5 3789PRTHomo sapiens
378Ala Leu Gly Tyr Phe Val Pro Tyr Val 1 5 3799PRTHomo sapiens
379Ile Met Glu Gly Thr Leu Thr Arg Val 1 5 38010PRTHomo sapiens
380Thr Leu Ile Glu Asp Glu Ile Ala Thr Ile 1 5 10 3819PRTHomo
sapiens 381Phe Ile Asp Glu Ala Tyr Val Glu Val 1 5 3829PRTHomo
sapiens 382Ala Leu Gln Asn Tyr Ile Lys Glu Ala 1 5 38311PRTHomo
sapiens 383Ala Leu Leu Glu Leu Glu Asn Ser Val Thr Leu 1 5 10
38410PRTHomo sapiens 384Ile Leu Phe Ala Asn Pro Asn Ile Phe Val 1 5
10 38510PRTHomo sapiens 385Ser Leu Leu Glu Gln Gly Leu Val Glu Ala
1 5 10 3869PRTHomo sapiens 386Ile Leu Phe Arg Tyr Pro Leu Thr Ile 1
5 3879PRTHomo sapiens 387Ala Leu Phe Gln Ala Thr Ala Glu Val 1 5
38810PRTHomo sapiens 388Ser Leu Thr Ile Asp Gly Ile Arg Tyr Val 1 5
10 3899PRTHomo sapiens 389Leu Leu Ala Asp Val Thr His Leu Leu 1 5
3909PRTHomo sapiens 390Ala Leu Phe Met Lys Gln Ile Tyr Leu 1 5
39110PRTHomo sapiens 391Tyr Val Tyr Pro Gln Arg Leu Asn Phe Val 1 5
10 39210PRTHomo sapiens 392Ala Leu Leu His Pro Gln Gly Phe Glu Val
1 5 10 39313PRTHomo sapiens 393Gly Leu Leu Asp Thr Gln Thr Ser Gln
Val Leu Thr Ala 1 5 10 39411PRTHomo sapiens 394Leu Leu Ala Val Ile
Gly Gly Leu Val Tyr Leu 1 5 10 39510PRTHomo sapiens 395Ala Leu Ala
Leu Gly Gly Ile Ala Val Val 1 5 10 3969PRTHomo sapiens 396Ala Leu
Leu Pro Asp Leu Pro Ala Leu 1 5 39710PRTHomo sapiens 397Tyr Leu Phe
Gly Glu Arg Leu Leu Glu Cys 1 5 10 39812PRTHomo sapiens 398Lys Leu
Leu Glu Glu Asp Gly Thr Ile Ile Thr Leu 1 5 10 3999PRTHomo sapiens
399Tyr Leu Phe Glu Pro Leu Tyr His Val 1 5 40011PRTHomo sapiens
400Ser Leu Leu Thr Glu Gln Asp Leu Trp Thr Val 1 5 10 40111PRTHomo
sapiens 401Ile Leu Leu Asp Asp Thr Gly Leu Ala Tyr Ile 1 5 10
40210PRTHomo sapiens 402Val Leu Phe Ser Gly Ala Leu Leu Gly Leu 1 5
10 4039PRTHomo sapiens 403Lys Leu Tyr Asp Arg Ile Leu Arg Val 1 5
40411PRTHomo sapiens 404Ala Ile Asp Ile Ser Gly Arg Asp Pro Ala Val
1 5 10 4059PRTHomo sapiens 405Ala Leu Tyr Asp Val Phe Leu Glu Val 1
5 40610PRTHomo sapiens 406Ser Val Gln Gly Glu Asp Leu Tyr Leu Val 1
5 10 4079PRTHomo sapiens 407Tyr Leu Met Asp Leu Ile Asn Phe Leu 1 5
4089PRTHomo sapiens 408Val Leu Asp Asp Ser Ile Tyr Leu Val 1 5
4099PRTHomo sapiens 409Leu Leu Asp Ala Met Asn Tyr His Leu 1 5
4109PRTHomo sapiens 410Val Leu Ser Asp Val Ile Pro Ser Ile 1 5
4119PRTHomo sapiens 411Leu Leu Ala His Leu Ser Pro Glu Leu 1 5
41211PRTHomo sapiens 412Tyr Leu Asp Asp Leu Asn Glu Gly Val Tyr Ile
1 5 10 4139PRTHomo sapiens 413Thr Leu Leu Glu Lys Val Glu Gly Cys 1
5 4149PRTHomo sapiens 414Tyr Val Asp Asp Ile Phe Leu Arg Val 1 5
4159PRTHomo sapiens 415Leu Leu Asp Lys Val Tyr Ser Ser Val 1 5
41611PRTHomo sapiens 416Val Leu Ser Asp Ile Ile Gln Asn Leu Ser Val
1 5 10 4179PRTHomo sapiens 417Asn Leu Gln Asp Thr Glu Tyr Asn Leu 1
5 41810PRTHomo sapiens 418Ala Leu Ala Glu Leu Glu Asn Ile Glu Val 1
5 10 41910PRTHomo sapiens 419Gly Gln Tyr Glu Gly Lys Val Ser Ser
Val 1 5 10 4209PRTHomo sapiens 420Phe Met Tyr Asp Thr Pro Gln Glu
Val 1 5 4219PRTHomo sapiens 421Arg Leu Pro Glu Thr Leu Pro Ser Leu
1 5 4229PRTHomo sapiens 422Phe Leu Pro Lys Leu Leu Leu Leu Ala 1 5
4239PRTHomo sapiens 423Gly Leu Asp Gly Pro Pro Pro Thr Val 1 5
4249PRTHomo sapiens 424Thr Leu Leu Asp Ala Leu Tyr Glu Ile 1 5
4259PRTHomo sapiens 425Phe Leu Tyr Glu Lys Ser Ser Gln Val 1 5
4269PRTHomo sapiens 426Arg Leu Ala Asp Lys Ser Val Leu Val 1 5
4279PRTHomo sapiens 427Ala Leu Leu Pro Leu Ser Pro Tyr Leu 1 5
42811PRTHomo sapiens 428Lys Leu Gly His Thr Asp Ile Leu Val Gly Val
1 5 10 4299PRTHomo sapiens 429Gly Leu Val Asn Asp Leu Ala Arg Val 1
5 43011PRTHomo sapiens 430His Leu Tyr Ser Ser Ile Glu His Leu Thr
Thr 1 5 10 4319PRTHomo sapiens 431Ser Leu Val Asn Val Val Pro Lys
Leu 1 5 4329PRTHomo sapiens 432Thr Leu Ile Glu Glu Ser Ala Lys Val
1 5 4339PRTHomo sapiens 433Ala Met Leu Asn Glu Pro Trp Ala Val 1 5
43410PRTHomo sapiens 434Lys Val Ser Asn Ser Gly Ile Thr Arg Val 1 5
10 4359PRTHomo sapiens 435Trp Leu Met Pro Val Ile Pro Ala Leu 1 5
4369PRTHomo sapiens 436His Leu Ala Glu Val Ser Ala Glu Val 1 5
43711PRTHomo sapiens 437Ser Met Ala Pro Gly Leu Val Ile Gln Ala Val
1 5 10 43810PRTHomo sapiens 438Lys Leu Leu Pro Leu Ala Gly Leu Tyr
Leu 1 5 10 4399PRTHomo sapiens 439Tyr Leu Leu Gln Glu Ile Tyr Gly
Ile 1 5 44010PRTHomo sapiens 440Ala Leu Ala Asp Gly Val Thr Met Gln
Val 1 5 10 44110PRTHomo sapiens 441Ala Leu Leu Glu Asn Pro Lys Met
Glu Leu 1 5 10 44211PRTHomo sapiens 442Gly Leu Leu Gly Gly Gly Gly
Val Leu Gly Val 1 5 10 44311PRTHomo sapiens 443Gly Leu Trp Glu Ile
Glu Asn Asn Pro Thr Val 1 5 10 44411PRTHomo sapiens 444Gly Leu Leu
Arg Asp Glu Ala Leu Ala Glu Val 1 5 10 4459PRTHomo sapiens 445Gly
Leu Tyr Gln Asp Pro Val Thr Leu 1 5 4469PRTHomo sapiens 446Gln Leu
Ile Pro Ala Leu Ala Lys Val 1 5 4479PRTHomo sapiens 447Gln Leu Val
Pro Ala Leu Ala Lys Val 1 5 4489PRTHomo sapiens 448Asn Leu Leu Glu
Thr Lys Leu Gln Leu 1 5 44910PRTHomo sapiens 449Lys Leu Ala Glu Gly
Leu Asp Ile Gln Leu 1 5 10 45011PRTHomo sapiens 450Phe Met Ile Asp
Ala Ser Val His Pro Thr Leu 1 5 10 45111PRTHomo sapiens 451Leu Leu
Leu Leu Asp Thr Val Thr Met Gln Val 1 5 10 45211PRTHomo sapiens
452Ile Leu Leu Glu His Gly Ala Asp Pro Asn Leu 1 5 10 4539PRTHomo
sapiens 453Lys Leu Leu Glu Ala Thr Ser Ala Val 1 5 4549PRTHomo
sapiens 454Lys Leu Pro Pro Pro Pro Pro Gln Ala 1 5 45511PRTHomo
sapiens 455Ser Leu Leu Lys Glu Pro Gln Lys Val Gln Leu 1 5 10
4569PRTHomo sapiens 456Leu Leu Ile Gly His Leu Glu Arg Val 1 5
45711PRTHomo sapiens 457Ser Leu Leu Pro Gly Asn Leu Val Glu Lys Val
1 5 10 4589PRTHomo sapiens 458Ser Leu Ile Asp Lys Leu Tyr Asn Ile 1
5 4599PRTHomo sapiens 459Ala Leu Ile Thr Glu Val Val Arg Leu 1 5
4609PRTHomo sapiens 460Ala Met Leu Glu Lys Asn Tyr Lys Leu 1 5
46110PRTHomo sapiens 461Val Met Phe Arg Thr Pro Leu Ala Ser Val 1 5
10 4629PRTHomo sapiens 462Lys Leu Ala Lys Gln Pro Glu Thr Val 1 5
46313PRTHomo sapiens 463Ser Leu Val Glu Ser His Leu Ser Asp Gln Leu
Thr Leu 1 5 10 4649PRTHomo sapiens 464Ala Leu Asn Asp Cys Ile Tyr
Ser Val 1 5 4659PRTHomo sapiens 465Gln Leu Cys Asp Leu Asn Ala Glu
Leu 1 5 4669PRTHomo sapiens 466Val Leu Ile Ala Asn Leu Glu Lys Leu
1 5 4679PRTHomo sapiens 467Phe Leu Ala Lys Asp Phe Asn Phe Leu 1 5
46811PRTHomo sapiens 468Tyr Leu Arg Ser Val Gly Asp Gly Glu Thr Val
1 5 10 46910PRTHomo sapiens 469Tyr Leu Ala Ser Asp Glu Ile Thr Thr
Val 1 5 10 4709PRTHomo sapiens 470Met Leu Gln Asp Ser Ile His Val
Val 1 5 47110PRTHomo sapiens 471Tyr Leu Tyr Asn Asn Met Ile Ala Lys
Ile 1 5 10 47211PRTHomo sapiens 472Lys Leu Leu Glu Val Ser Asp Asp
Pro Gln Val 1 5 10 47311PRTHomo sapiens 473Ala Met Ala Thr Glu Ser
Ile Leu His Phe Ala 1 5 10 47413PRTHomo sapiens 474Tyr Leu Asp Pro
Ala Leu Glu Leu Gly Pro Arg Asn Val 1 5 10 47511PRTHomo sapiens
475Leu Leu Leu Asn Glu Glu Ala Leu Ala Gln Ile 1 5 10 47611PRTHomo
sapiens 476Ala Leu Met Glu Arg Thr Gly Tyr Ser Met Val 1 5 10
47711PRTHomo sapiens 477Ala Leu Leu Pro Ala Ser Gly Gln Ile Ala Leu
1 5 10 4789PRTHomo sapiens 478Tyr Leu Leu His Glu Lys Leu Asn Leu 1
5 47912PRTHomo sapiens 479Ser Leu Phe Gly Asn Ser Gly Ile Leu Glu
Asn Val 1 5 10 48010PRTHomo sapiens 480Ala Leu Leu Glu Asp Ser Cys
His Tyr Leu 1 5 10 48110PRTHomo sapiens 481Gly Leu Ile Glu Asp Tyr
Glu Ala Leu Leu 1 5 10 48210PRTHomo sapiens 482Ser Leu Ala Pro Ala
Gly Ile Ala Asp Ala 1 5 10 4839PRTHomo sapiens 483Ala Leu Thr Asp
Ile Val Ser Gln Val 1 5 4849PRTHomo sapiens 484Ser Leu Ile Glu Lys
Val Thr Gln Leu 1 5 4859PRTHomo sapiens 485Asn Val Pro Asp Ser Phe
Asn Glu Val 1 5 4869PRTHomo sapiens 486Ala Val Met Glu Ser Ile Gln
Gly Val 1 5 4879PRTHomo sapiens 487Leu Leu Ile Asn Ser Val Phe His
Val 1 5 48810PRTHomo sapiens 488Phe Leu Ala Glu Asp Pro Lys Val Thr
Leu 1 5 10 48910PRTHomo sapiens 489Lys Met Trp Glu Glu Leu Pro Glu
Val Val 1 5 10 4909PRTHomo sapiens 490Phe Leu Leu Gln His Val Gln
Glu Leu 1 5 4919PRTHomo sapiens 491Gly Leu Asn Asp Arg Ser Asp Ala
Val 1 5 49212PRTHomo sapiens 492Ser Leu Phe Asp Gly Phe Ala Asp Gly
Leu Gly Val 1 5 10 49313PRTHomo sapiens 493Gly Leu Leu Gly Glu Lys
Thr Gln Asp Leu Ile Gly Val 1 5 10 4949PRTHomo sapiens 494Ala Leu
Gln Pro Glu Pro Ile Lys Val 1 5 49510PRTHomo sapiens 495Phe Ile Phe
Ser Glu Lys Pro Val Phe Val 1 5 10 49610PRTHomo sapiens 496Phe Leu
Val Glu Lys Gln Pro Pro Gln Val 1 5 10 4979PRTHomo sapiens 497Gly
Leu Leu Glu Lys Leu Thr Ala Ile 1 5 49811PRTHomo sapiens 498Lys Leu
Trp Thr Gly Gly Leu Asp Asn Thr Val 1 5 10 49912PRTHomo sapiens
499Lys Ile Phe Asp Ile Asp Glu Ala Glu Glu Gly Val 1 5 10
50010PRTHomo sapiens 500Ser Leu Met Glu Asp Gln Val Leu Gln Leu 1 5
10 50111PRTHomo sapiens 501Leu Leu Asp Pro Asn Val Lys Ser Ile Phe
Val 1 5 10 5029PRTHomo sapiens 502Arg Leu Leu Ala Gln Val Pro Gly
Leu 1 5 5039PRTHomo sapiens 503Ser Leu Asn His Phe Thr His Ser Val
1 5 5049PRTHomo sapiens 504Gly Leu Ser Asp Gly Asn Pro Ser Leu 1 5
50511PRTHomo sapiens 505Ser Leu Ala Pro Gly Asp Val Val Arg Gln Val
1 5 10 5069PRTHomo sapiens 506Lys Leu Leu Gly Lys Val Glu Thr Ala 1
5 50712PRTHomo sapiens 507Lys Leu Ile Asp Asp Gln Asp Ile Ser Ile
Ser Leu 1 5 10 50811PRTHomo sapiens 508Ile Leu Ala Gln Glu Gln Leu
Val Val Gly Val 1 5 10 50910PRTHomo sapiens 509Phe Leu Phe Asp Thr
Lys Pro Leu Ile Val 1 5 10 5109PRTHomo sapiens 510Lys Leu Tyr Ser
Val Val Ser Gln Leu 1 5 51110PRTHomo sapiens 511Phe Leu Asp Pro Tyr
Cys Ser Ala Ser Val 1 5 10 5129PRTHomo sapiens 512Ser Leu Ser Glu
Ile Val Pro Cys Leu 1 5 5139PRTHomo sapiens 513Ser Leu Trp Pro Ser
Pro Glu Gln Leu 1 5 5149PRTHomo sapiens 514Ile Leu Val Asp Trp Leu
Val Gln Val 1 5 5159PRTHomo sapiens 515Leu Leu Gln Glu Leu Val Leu
Phe Leu 1 5 51611PRTHomo sapiens 516Ala Val Gly Pro Ala Ser Ile Leu
Lys Glu Val 1 5 10 51711PRTHomo sapiens 517Leu Leu Met Pro Ile Pro
Glu Gly Leu Thr Leu 1 5 10 5189PRTHomo sapiens 518Lys Leu Asn Ala
Glu Val Ala Cys Val 1 5 5199PRTHomo sapiens 519Gly Leu Leu His Leu
Thr Leu Leu Leu 1 5 52010PRTHomo sapiens 520Leu Ala Val His Pro Ser
Gly Val Ala Leu 1 5 10 5219PRTHomo sapiens 521Met Leu Leu Thr Lys
Leu Pro Thr Ile 1 5 5229PRTHomo sapiens 522Thr Leu Trp Tyr Arg Ser
Pro Glu Val 1 5 5239PRTHomo sapiens 523Tyr Gln Ile Pro Arg Thr Phe
Thr Leu 1 5 52410PRTHomo sapiens 524Ala Leu Ile Glu Asn Leu Thr His
Gln Ile 1 5 10 52512PRTHomo sapiens 525Val Leu Leu Glu Ala Gly Glu
Gly Leu Val Thr Ile 1 5 10 52611PRTHomo sapiens 526Arg Leu Ala Glu
Val Gly Gln Tyr Glu Gln Val 1 5 10 52710PRTHomo sapiens 527Phe Leu
Leu Glu Pro Gly Asn Leu Glu Val 1 5 10 52811PRTHomo sapiens 528Ser
Val Ala Glu Gly Arg Ala Leu Met Ser Val 1 5 10 5299PRTHomo sapiens
529Leu Leu Ala Asp Glu Leu Ile Thr Val 1 5 53011PRTHomo sapiens
530Val Met Tyr Ala Asp Ile Gly Gly Met Asp Ile 1 5 10 53111PRTHomo
sapiens 531Tyr Thr Leu Pro Ile Ala Ser Ser Ile Arg Leu 1 5 10
5329PRTHomo sapiens 532Ala Leu Asn Asn Leu Leu His Ser Leu 1 5
5339PRTHomo sapiens 533Arg Met Val Ala Glu Ile Gln Asn Val 1 5
5349PRTHomo sapiens 534His Leu Ala Asn Ile Val Glu Arg Leu 1 5
5359PRTHomo sapiens 535Lys Leu Ile Ala Gln Asn Leu Glu Leu 1 5
5369PRTHomo sapiens 536Tyr Leu Val Glu Gly Arg Phe
Ser Val 1 5 53711PRTHomo sapiens 537Thr Leu Ala Pro Gly Glu Val Leu
Arg Ser Val 1 5 10 5389PRTHomo sapiens 538Leu Leu Leu Ala His Ile
Ile Ala Leu 1 5 5399PRTHomo sapiens 539Ala Leu Phe Asp Ala Gln Ala
Gln Val 1 5 54011PRTHomo sapiens 540Ala Leu Ile Pro Glu Thr Thr Thr
Leu Thr Val 1 5 10 5419PRTHomo sapiens 541Ser Met Leu Glu Pro Val
Pro Glu Leu 1 5 54211PRTHomo sapiens 542Arg Val Trp Asp Ile Ser Thr
Val Ser Ser Val 1 5 10 54313PRTHomo sapiens 543Gly Leu Leu Pro Thr
Pro Ile Thr Gln Gln Ala Ser Leu 1 5 10 54410PRTHomo sapiens 544Leu
Leu Trp Asp Val Pro Ala Pro Ser Leu 1 5 10 5459PRTHomo sapiens
545Leu Leu Ala Asp Leu Leu His Asn Val 1 5 54610PRTHomo sapiens
546Val Met Ile Ala Gly Lys Val Ala Val Val 1 5 10 5479PRTHomo
sapiens 547Thr Leu Asp Ile Thr Pro His Thr Val 1 5 54811PRTHomo
sapiens 548Ala Leu Trp Glu Asn Pro Glu Ser Gly Glu Leu 1 5 10
54911PRTHomo sapiens 549Ala Met Leu Glu Asn Ala Ser Asp Ile Lys Leu
1 5 10 55012PRTHomo sapiens 550Phe Leu Tyr Asp Glu Ile Glu Ala Glu
Val Asn Leu 1 5 10 55110PRTHomo sapiens 551Lys Leu Tyr Glu Ser Leu
Leu Pro Phe Ala 1 5 10 55211PRTHomo sapiens 552Gly Leu Leu Asp Leu
Pro Phe Arg Val Gly Val 1 5 10 55311PRTHomo sapiens 553Ser Leu Leu
Asn Gln Asp Leu His Trp Ser Leu 1 5 10 55411PRTHomo sapiens 554Leu
Leu Met Pro Ser Ser Glu Asp Leu Leu Leu 1 5 10 5559PRTHomo sapiens
555Tyr Val Leu Glu Gly Leu Lys Ser Val 1 5 55610PRTHomo sapiens
556Phe Leu Thr Asp Leu Glu Asp Leu Thr Leu 1 5 10 5579PRTHomo
sapiens 557Lys Leu Tyr Asp Asp Met Ile Arg Leu 1 5 5589PRTHomo
sapiens 558Gly Leu Leu Glu Asn Ile Pro Arg Val 1 5 5599PRTHomo
sapiens 559Val Thr Val Pro Pro Gly Pro Ser Leu 1 5 56013PRTHomo
sapiens 560Ala Leu Trp Asp Ile Glu Thr Gly Gln Gln Thr Thr Thr 1 5
10 5619PRTHomo sapiens 561Tyr Leu Gln Leu Thr Gln Ser Glu Leu 1 5
56211PRTHomo sapiens 562Tyr Leu Glu Glu Leu Pro Glu Lys Leu Lys Leu
1 5 10 56310PRTHomo sapiens 563Trp Leu Leu Pro Tyr Asn Gly Val Thr
Val 1 5 10 5649PRTHomo sapiens 564Thr Val Thr Asn Ala Val Val Thr
Val 1 5 5659PRTHomo sapiens 565Ala Leu Gln Glu Thr Pro Thr Ser Val
1 5 56610PRTHomo sapiens 566Val Ile Ala Asp Gly Gly Ile Gln Asn Val
1 5 10 56711PRTHomo sapiens 567Ser Leu Leu Pro Leu Asp Asp Ile Val
Arg Val 1 5 10 56811PRTHomo sapiens 568Thr Leu Tyr Asp Ile Ala His
Thr Pro Gly Val 1 5 10 5699PRTHomo sapiens 569Lys Leu Val Asp Arg
Thr Trp Thr Leu 1 5 5709PRTHomo sapiens 570Ala Leu Ala Asn Gln Ile
Pro Thr Val 1 5 5719PRTHomo sapiens 571Leu Leu Leu Thr Thr Ile Pro
Gln Ile 1 5 57212PRTHomo sapiens 572Ala Leu Ala Asp Leu Ile Glu Lys
Glu Leu Ser Val 1 5 10 57310PRTHomo sapiens 573Ile Leu Val Ala Asn
Ala Ile Val Gly Val 1 5 10 57410PRTHomo sapiens 574Tyr Leu Leu Gln
Glu Pro Pro Arg Thr Val 1 5 10 57511PRTHomo sapiens 575Tyr Leu Ile
Ser Gln Val Glu Gly His Gln Val 1 5 10 57611PRTHomo sapiens 576Ile
Leu Leu Asn Asn Ser Gly Gln Ile Lys Leu 1 5 10 57711PRTHomo sapiens
577Val Met Phe Glu Asp Gly Val Leu Met Arg Leu 1 5 10 57811PRTHomo
sapiens 578Phe Leu Asp Pro Gly Gly Pro Met Met Lys Leu 1 5 10
5799PRTHomo sapiens 579Asn Leu Met Glu Met Val Ala Gln Leu 1 5
5809PRTHomo sapiens 580Leu Leu Met Glu Asn Ala Glu Arg Val 1 5
5819PRTHomo sapiens 581Arg Leu Trp Asn Glu Thr Val Glu Leu 1 5
5829PRTHomo sapiens 582Thr Leu Cys Asp Val Ile Leu Met Val 1 5
58311PRTHomo sapiens 583Ile Leu Ala Asn Asp Gly Val Leu Leu Ala Ala
1 5 10 58411PRTHomo sapiens 584Ala Leu Ala Glu Val Ala Ala Met Glu
Asn Val 1 5 10 58512PRTHomo sapiens 585Ala Leu Trp Asp Leu Ala Ala
Asp Lys Gln Thr Leu 1 5 10 58610PRTHomo sapiens 586Lys Leu Lys Pro
Gly Asp Leu Val Gly Val 1 5 10 5879PRTHomo sapiens 587Val Met Asn
Asp Arg Leu Tyr Ala Ile 1 5 5889PRTHomo sapiens 588Ser Leu Leu Pro
Leu Ser His Leu Val 1 5 58910PRTHomo sapiens 589Lys Leu Tyr Pro Gln
Leu Pro Ala Glu Ile 1 5 10 5909PRTHomo sapiens 590Ser Leu Ile Glu
Lys Leu Trp Gln Thr 1 5 5919PRTHomo sapiens 591Ser Met Ala Glu Leu
Asp Ile Lys Leu 1 5 59210PRTHomo sapiens 592Arg Leu Leu Ser Ala Ala
Glu Asn Phe Leu 1 5 10 59310PRTHomo sapiens 593Gly Leu Pro Arg Phe
Gly Ile Glu Met Val 1 5 10 59410PRTHomo sapiens 594Ile Met Leu Lys
Gly Asp Asn Ile Thr Leu 1 5 10 5959PRTHomo sapiens 595Val Leu Leu
Ser Ile Tyr Pro Arg Val 1 5 59614PRTHomo sapiens 596Ala Leu Leu Asp
Gln Thr Lys Thr Leu Ala Glu Ser Ala Leu 1 5 10 59710PRTHomo sapiens
597Lys Leu Leu Glu Gly Gln Val Ile Gln Leu 1 5 10 5989PRTHomo
sapiens 598Phe Leu Phe Pro His Ser Val Leu Val 1 5 59911PRTHomo
sapiens 599Tyr Leu Leu Asn Asp Ala Ser Leu Ile Ser Val 1 5 10
60011PRTHomo sapiens 600Ala Leu Ala Ala Pro Asp Ile Val Pro Ala Leu
1 5 10 6019PRTHomo sapiens 601Ser Ala Phe Pro Phe Pro Val Thr Val 1
5 60211PRTHomo sapiens 602Tyr Leu Leu Glu Gln Ile Lys Leu Ile Glu
Val 1 5 10 60311PRTHomo sapiens 603Phe Leu Ile Glu Pro Glu His Val
Asn Thr Val 1 5 10 60410PRTHomo sapiens 604Ser Ile Leu Asp Arg Asp
Asp Ile Phe Val 1 5 10 6059PRTHomo sapiens 605Lys Leu Tyr Glu Ala
Val Pro Gln Leu 1 5 6069PRTHomo sapiens 606Ala Leu Trp Glu Thr Glu
Val Tyr Ile 1 5 60711PRTHomo sapiens 607Arg Leu Tyr Ser Gly Ile Ser
Gly Leu Glu Leu 1 5 10 6089PRTHomo sapiens 608Ser Leu Leu Ser Val
Ser His Ala Leu 1 5 6099PRTHomo sapiens 609Ala Leu Trp Lys Gln Leu
Leu Glu Leu 1 5 61011PRTHomo sapiens 610Leu Leu Ala Pro Thr Pro Tyr
Ile Ile Gly Val 1 5 10 61110PRTHomo sapiens 611Tyr Leu Leu Asp Asp
Gly Thr Leu Val Val 1 5 10 6129PRTHomo sapiens 612Tyr Leu Tyr Asn
Glu Gly Leu Ser Val 1 5 61311PRTHomo sapiens 613Arg Leu Leu Pro Pro
Gly Ala Val Val Ala Val 1 5 10 61411PRTHomo sapiens 614Leu Leu Leu
Pro Asp Gln Pro Pro Tyr His Leu 1 5 10 6159PRTHomo sapiens 615Val
Leu Pro Pro Asp Thr Asp Pro Ala 1 5 6169PRTHomo sapiens 616Val Leu
Ile Asp Glu Val Glu Ser Leu 1 5 61711PRTHomo sapiens 617Ala Leu Met
Tyr Glu Ser Glu Lys Val Gly Val 1 5 10 61812PRTHomo sapiens 618Val
Leu Phe Asp Ser Glu Ser Ile Gly Ile Tyr Val 1 5 10 6199PRTHomo
sapiens 619Ala Leu Gln Asp Arg Val Pro Leu Ala 1 5 6209PRTHomo
sapiens 620Lys Leu Leu Asn Lys Ile Tyr Glu Ala 1 5 62110PRTHomo
sapiens 621Val Leu Met Asp Arg Leu Pro Ser Leu Leu 1 5 10
62213PRTHomo sapiens 622Arg Leu Leu Gly Glu Glu Val Val Arg Val Leu
Gln Ala 1 5 10 6239PRTHomo sapiens 623Tyr Leu Val Glu Asp Ile Gln
His Ile 1 5 62410PRTHomo sapiens 624Phe Leu Gln Glu Glu Pro Gly Gln
Leu Leu 1 5 10 62511PRTHomo sapiens 625Val Val Leu Glu Gly Ala Ser
Leu Glu Thr Val 1 5 10 6269PRTHomo sapiens 626Leu Leu Met Ala Thr
Ile Leu His Leu 1 5 62711PRTHomo sapiens 627Lys Leu Leu Glu Thr Glu
Leu Leu Gln Glu Ile 1 5 10 62810PRTHomo sapiens 628Lys Leu Trp Glu
Phe Phe Gln Val Asp Val 1 5 10 6299PRTHomo sapiens 629His Leu Leu
Asn Glu Ser Pro Met Leu 1 5 6309PRTHomo sapiens 630Leu Leu Ser His
Val Ile Val Ala Leu 1 5 6319PRTHomo sapiens 631Phe Leu Asp Val Phe
Leu Pro Arg Val 1 5 63210PRTHomo sapiens 632Tyr Leu Ile Pro Asp Ile
Asp Leu Lys Leu 1 5 10 6339PRTHomo sapiens 633Ala Leu Ser Arg Val
Ser Val Asn Val 1 5 6349PRTHomo sapiens 634Val Val Ala Glu Phe Val
Pro Leu Ile 1 5 6359PRTHomo sapiens 635Ser Leu Asp Ser Thr Leu His
Ala Val 1 5 6369PRTHomo sapiens 636Leu Leu Thr Glu Ile Arg Ala Val
Val 1 5 63710PRTHomo sapiens 637Ser Ile Tyr Gly Gly Phe Leu Leu Gly
Val 1 5 10 6389PRTHomo sapiens 638Lys Leu Ile Gln Glu Ser Pro Thr
Val 1 5 6399PRTHomo sapiens 639Ser Leu Phe Gln Asn Cys Phe Glu Leu
1 5 64010PRTHomo sapiens 640Tyr Leu Phe Ser Glu Ala Leu Asn Ala Ala
1 5 10 64112PRTHomo sapiens 641Val Leu Leu Pro Val Glu Val Ala Thr
His Tyr Leu 1 5 10 64210PRTHomo sapiens 642Phe Leu His Asp Ile Ser
Asp Val Gln Leu 1 5 10 64310PRTHomo sapiens 643Ala Leu Phe Pro His
Leu Leu Gln Pro Val 1 5 10 6449PRTHomo sapiens 644Leu Thr Phe Gly
Asp Val Val Ala Val 1 5 6459PRTHomo sapiens 645Leu Leu Tyr Asp Ala
Val His Ile Val 1 5 6469PRTHomo sapiens 646Ile Leu Ser Pro Thr Val
Val Ser Ile 1 5 6479PRTHomo sapiens 647Ser Leu Gly Leu Phe Leu Ala
Gln Val 1 5 6489PRTHomo sapiens 648Leu Leu Trp Gly Asn Ala Ile Phe
Leu 1 5 6499PRTHomo sapiens 649Ala Leu Ala Phe Lys Leu Asp Glu Val
1 5 65010PRTHomo sapiens 650Ala Ile Met Gly Phe Ile Gly Phe Phe Val
1 5 10 6519PRTHomo sapiens 651Ile Leu Gln Asp Arg Leu Asn Gln Val 1
5 6529PRTHomo sapiens 652Thr Leu Trp Tyr Arg Ala Pro Glu Val 1 5
6539PRTHomo sapiens 653Thr Leu Ile Ser Arg Leu Pro Ala Val 1 5
6549PRTHomo sapiens 654Lys Ile Leu Glu Asp Val Val Gly Val 1 5
65511PRTHomo sapiens 655Ala Leu Met Asp Lys Glu Gly Leu Thr Ala Leu
1 5 10 6569PRTHomo sapiens 656Lys Leu Leu Glu Tyr Ile Glu Glu Ile 1
5 65710PRTHomo sapiens 657Ser Leu Ala Glu Arg Leu Phe Phe Gln Val 1
5 10 6589PRTHomo sapiens 658Leu Leu Gln Asp Arg Leu Val Ser Val 1 5
65910PRTHomo sapiens 659Ile Leu Phe Pro Asp Ile Ile Ala Arg Ala 1 5
10 6609PRTHomo sapiens 660Ala Ile Leu Asp Thr Leu Tyr Glu Val 1 5
6619PRTHomo sapiens 661Ser Leu Ile Asp Ala Asp Pro Tyr Leu 1 5
6629PRTHomo sapiens 662Lys Ile Gln Glu Ile Leu Thr Gln Val 1 5
6639PRTHomo sapiens 663Lys Ile Gln Glu Met Gln His Phe Leu 1 5
66410PRTHomo sapiens 664Glu Leu Ala Gly Ile Gly Ile Leu Thr Val 1 5
10 6659PRTHomo sapiens 665Tyr Leu Leu Pro Ala Ile Val His Ile 1
5
* * * * *
References