CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No. 17/227,885, filed 12 Apr. 2021, which is a continuation of U.S. patent application Ser. No. 16/913,788, filed 26 Jun. 2020, now U.S. Pat. No. 11,001,616, issued 11 May 2021, which is a continuation of U.S. patent application Ser. No. 16/026,707, filed 3 Jul. 2018, now U.S. Pat. No. 10,800,823, issued 13 Oct. 2020, which claims priority to U.S. Provisional Application No. 62/529,758, filed 7 Jul. 2017, and German Patent Application No. 102017115301.2, filed 7 Jul. 2017, the content of each of these applications is herein incorporated by reference in their entirety.

This application is also related to PCT/EP2018/067979, filed 3 Jul. 2018, the content of which is incorporated herein by reference in its entirety.

REFERENCE TO SEQUENCE LISTING SUBMITTED AS A COMPLIANT ASCII TEXT FILE (.txt)

Pursuant to the EFS-Web legal framework and 37 CFR §§ 1.821-825 (see MPEP § 2442.03(a)), a Sequence Listing in the form of an ASCII-compliant text file (entitled “Sequence_Listing_2912919-089022_ST25.txt” created on 7 Jul. 2021, and 83,168 bytes in size) is submitted concurrently with the instant application, and the entire contents of the Sequence Listing are incorporated herein by reference.

BACKGROUND

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.

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.

DESCRIPTION OF RELATED ART

Lung cancer accounts for the most cancer-related deaths in both men and women. Worldwide, lung cancer is the most common canc er in terms of both incidence and mortality. In 2012, there were more than 1.8 million new cases (13% of total cancer incidence), and 1.6 million deaths (20% of total cancer mortality) due to lung cancer. Lung cancer is the leading cause of cancer death in men in 87 countries and in women in 26 countries. More than one third of all newly diagnosed cases occurred in China. The highest rates are in North America, Europe, and East Asia (World Cancer Report, 2014).

Since 1987, more women have died each year from lung cancer than from breast cancer. Death rates have continued to decline significantly in men from 1991-2003 by about 1.9% per year. Female lung cancer death rates are approaching a plateau after continuously increasing for several decades. These trends in lung cancer mortality reflect the decrease in smoking rates over the past 30 years.

An estimated 230,000 new cases of lung cancer and 160,000 deaths due to lung cancer are expected in 2013 in the USA according to the national cancer institute (NCI). Historically, small cell lung carcinoma (SCLC) has been distinguished from non-small cell lung carcinoma (NSCLC), which includes the histological types of adenocarcinoma, squamous cell carcinoma, and large cell carcinoma. However, in the past decade, the distinction between adenocarcinoma and squamous cell carcinoma has been increasingly recognized because of major differences in genetics and also in responses to specific therapies. Therefore, lung cancers are increasingly classified according to molecular subtypes, predicated on particular genetic alterations that drive and maintain lung tumorigenesis (Travis et al., 2013).

Prognosis is generally poor. Of all people with lung cancer, 10-15% survive for five years after diagnosis. Poor survival of lung cancer patients is due, at least in part, to 80% of patients being diagnosed with metastatic disease and more than half of patients having distant metastases (SEER Stat facts, 2014). At presentation, 30-40% of cases of NSCLC are stage IV, and 60% of SCLC are stage IV.

The 1-year relative survival for lung cancer has slightly increased from 35% in 1975-1979 to 44% in 2010, largely due to improvements in surgical techniques and combined therapies. However, the 5-year survival rate for all stages combined is only 17%. The survival rate is 54% for cases detected when the disease is still localized; however, only 16% of lung cancers are diagnosed at this early stage (SEER Stat facts, 2014).

Treatment options are determined by the type (small cell or non-small cell) and stage of cancer and include surgery, radiation therapy, chemotherapy, and targeted biological therapies such as bevacizumab (AVASTIN®) and erlotinib (TARCEVA®). For localized cancers, surgery is usually the treatment of choice. Recent studies indicate that survival with early-stage, non-small cell lung cancer is improved by chemotherapy following surgery. Because the disease has usually spread by the time it is discovered, radiation therapy and chemotherapy are often used, sometimes in combination with surgery. Chemotherapy alone or combined with radiation is the usual treatment of choice for small cell lung cancer; on this regimen, a large percentage of patients experience remission, which is long lasting in some cases surgery (S3-Leitlinie Lungenkarzinom, 2011).

Advanced lung cancer has also been resistant to traditional chemotherapy. However, recent advances have led to exciting progress in therapies that are dependent on histology and genetics. The level of scrutiny is exemplified by trials of adjuvant chemotherapy designed to differentiate not only between mutations in codons 12 and 13 of KRAS, but also between different amino acid substitutions as determined by particular mutations at codon 12 (Shepherd et al., 2013).

To expand the therapeutic options for NSCLC, different immunotherapeutic approaches have been studied or are still under investigation. While vaccination with L-BLP25 or MAGEA3 failed to demonstrate a vaccine-mediated survival advantage in NSCLC patients, an allogeneic cell line-derived vaccine showed promising results in clinical studies. Additionally, further vaccination trials targeting gangliosides, the epidermal growth factor receptor and several other antigens are currently ongoing. An alternative strategy to enhance the patient's anti-tumor T cell response consists of blocking inhibitory T cell receptors or their ligands with specific antibodies. The therapeutic potential of several of these antibodies, including ipilimumab, nivolumab, pembrolizumab, MPDL3280A and MEDI-4736, in NSCLC is currently evaluated in clinical trials (Reinmuth et al., 2015).

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 lung cancer (including NSCLC and SCLC) in particular. There is also a need to identify factors representing biomarkers for cancer in general and lung cancer (including NSCLC and SCLC), leading to better diagnosis of cancer, assessment of prognosis, and prediction of treatment success.

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.

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 β-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.

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.

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.

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. 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.

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).

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).

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.

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 (IFNγ) (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).

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).

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.

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.

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).

For proteins to be recognized by T-lymphocytes as tumor-specific or -associated antigens, and to be used in a therapy, 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.

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.

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”).

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

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: 489 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: 489, 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.

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: 489 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: 489, 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.

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. In Table 1, peptides with SEQ ID NO: 1 to SEQ ID NO: 83 bind to HLA-A*24, peptides with SEQ ID NO: 84 to SEQ ID NO: 133 bind to HLA-A*02, peptides with SEQ ID NO: 134 to SEQ ID NO: 201 bind to HLA-A*01, peptides with SEQ ID NO: 202 to SEQ ID NO: 219 bind to HLA-A*03, peptides with SEQ ID NO: 220 to SEQ ID NO: 295 bind to HLA-B*07, peptides with SEQ ID NO: 296 to SEQ ID NO: 318 bind to HLA-B*08, peptides with SEQ ID NO: 319 to SEQ ID NO: 374 bind to HLA-B*44. 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. In Table 2, peptides with SEQ ID NO: 375 to SEQ ID NO: 387 bind to HLA-A*24, peptides with SEQ ID NO: 388 to SEQ ID NO: 393 bind to HLA-A*02, peptides with SEQ ID NO: 394 to SEQ ID NO: 452 bind to HLA-A*01, peptides with SEQ ID NO: 453 to SEQ ID NO: 458 bind to HLA-A*03, peptides with SEQ ID NO: 459 to SEQ ID NO: 475 bind to HLA-B*07, peptides with SEQ ID NO: 476 to SEQ ID NO: 489 bind to HLA-B*44. The peptides in Table 3 are additional peptides that may be useful in combination with the other peptides of the invention. In Table 3, peptides with SEQ ID NO: 490 to SEQ ID NO: 508 bind to HLA-A*24, peptides with SEQ ID NO: 509 to SEQ ID NO: 528 bind to HLA-A*02, peptides with SEQ ID NO: 529 to SEQ ID NO: 530 bind to HLA-B*07, peptide with SEQ ID NO: 531 binds to HLA-B*44.

TABLE 1

Peptides according to the present invention.

Seq

ID

HLA

No
Sequence
Gene(s)
allotype

1
QYDPTPLTW
ADAMTS12
A*24

2
VWSNVTPLKF
MMP12
A*24

3
YLEKFYGL
MMP12
A*24

4
SYEKVINYL
MAGEA9, MAGEA9B
A*24

5
RYMKKDYLI
SLC35D3
A*24

6
KYKDYFPVI
MAGEC2, LOC392555
A*24

7
VQQWSVAVF
PTHLH
A*24/

B*15

8
PFLPPAACFF
ASCL1
A*24

9
RILRFPWQL
MMP11
A*24/

A*32

10
VWSDVTPLNF
MMP13
A*24

11
YYSKSVGFMQW
FAM111B
A*24

12
STIRGELFFF
MMP11
A*24/

B*57

13
HYTYILEVF
SLC7A11
A*24

14
SYSSCYSF
KRT13, KRT17
A*24

15
KYALLLQDL
PLEKHG4B
A*24

16
TYNPDFSSL
SP9
A*24

17
YYADKKTFIVL
SCN9A
A*24

18
DYIGSVEKW
HS6ST2
A*24

19
ILKEDPFLF
MACC1
A*24

20
EFTTVLYNF
TP63
A*24

21
SYEVRSTF
TAS2R38
A*24

22
TQPGDWTLF
POSTN
A*24/

B*15

23
KFIISDWRF
FAM83A
A*24

24
MYPDLSELLM
NUP155
A*24

25
SYNGYVFYL
ROS1
A*24

26
KTPTNYYLF
NMUR2
A*24/

B*35

27
NYTLYPITF
GXYLT1
A*24

28
YYSIISHTL
ROS1
A*24

29
VYPLLSRLYW
ROS1
A*24

30
QYLPGWTVLF
SLC22A31
A*24

31
QYQNVLTLW
DST
A*24

32
SLPDLTPTF
LAMB3
A*24

33
KSSVIASLLF
TMTC3
A*24/

B*57

34
MQPRMFFLF
FGD6
A*24

35
KYLEESVWL
GPR98
A*24

36
KQMEDGHTLF
UHRF1
A*24/

B*15

37
QWPWQASLQF
TMPRSS3
A*24

38
KYTNWKAFL
MBTD1
A*24

39
LIFMLANVF
GABRP
A*24/

A*32

40
QYEPPSAPSTTF
DROSHA
A*24

41
VIYFMGAIF
OR7E24
A*24/

B*15

42
TLPNTIYRF
ROS1
A*24

43
IQMDEPMAF
CDC7
A*24/

B*15

44
AYLSAVGTF
ABCC1
A*24

45
KYFVPPQLF
B3GNT6
A*24

46
AFPVTSIFHTF
KCNG1, KCNG2
A*24

47
KYADYFLEV
CCNJ
A*24

48
VFIDHPVHLKF
TENM4
A*24

49
LYISEVRNI
DST
A*24

50
SYPELVKMVW
C5orf34
A*24

51
KYALLLQEL
PLEKHG4
A*24

52
KYMKIFHKF
ZNF681
A*24

53
KYITNLEDL
TXNDC16
A*24

54
LLIKLLQTF
PRKDC
A*24/

B*15

55
RVVMDQRLVF
GABRP
A*24

56
VYMIEPLEL
ADAM23
A*24

57
YPSIIQEF
POLA1
A*24

58
QFAAPLRGIYF
C1QTNF6
A*24

59
KYSTTFFMV
XPR1
A*24

60
TYLSIFDQL
SF3A3
A*24

61
NYAENILTL
FIGNL1
A*24

62
LYQEILAQL
URB1
A*24

63
VMPSDSFFF
GAL3ST4
A*24

64
NYAIFDEGHML
SMARCAD1
A*24

65
VYPASKMFPFI
CKAP5
A*24

66
IYFRDSSFL
TEP1
A*24

67
RYPGKFYRV
ZAK
A*24

68
IYQQIIQTY
NCAPG2
A*24

69
IMPEKFEFW
CHD2
A*24

70
PYTNYTFDF
CNOT6, CNOT6L,
A*24

CNOT6LP1

71
SYMVLAPVF
SPIN1, SPNS1
A*24

72
RYEGILYTI
LSM14A, LSM14B
A*24

73
SYIGLPLTL
NPC1
A*24

74
VYDQYFITL
ATP8B2
A*24

75
NYIYSISVF
PLAA
A*24

76
WYGWHFPEL
NOP58
A*24

77
AYTLLGHEFV
CDC27
A*24

78
TWFPKTPMLF
KBTBD2
A*24

79
RYLADLPTL
CEP85
A*24

80
YYSPLRDLL
Rasa3
A*24

81
LYPEGLRLL
ATP6V0D2
A*24

82
RFLPSPVVI
CUL3
A*24

83
TYCQNIKEF
EIF3H
A*24

84
YVDINTFRL
MMP12
A*02

85
YIDEFQSLV
RTL1
A*02

86
FVIDGFDEL
NLRP2
A*02

87
TLYPYQISQL
KIF26B
A*02

88
VQMVITEAQKV
LAMC2
A*02

89
ILSTTMVTV
KIF26B
A*02

90
FLLMHPSI
NDST4
A*02

91
FALPGLLHA
LAMB3
A*02

92
NLRDLLSEV
KIF26B
A*02

93
TLQEKILQV
MYO3A
A*02

94
VLPDIETLIGV
TET1
A*02

95
ITIGVLARV
CEACAM6
A*02

96
HLVGGLHTV
DACH1, DACH2
A*02

97
VLALVNSTV
CBFA2T2
A*02

98
LQSSGLTLLL
MSLNL
A*02/

B*13

99
FLKEKVPGI
CDKAL1
A*02

100
RQYPTPFQL
ZNF280C
A*02/

B*48

101
FIISDWRFVL
FAM83A
A*02

102
SLLEQAIAL
ST18
A*02

103
FLYYPDPVL
PLXNA1
A*02

104
GMLDIFWGV
RASSF6
A*02

105
SLLTHIPTA
PLEKHG4
A*02

106
FIIDTTYPAYV
FAP
A*02

107
LLQGAIESV
PLEKHG4
A*02

108
MIIALSLYI
GPR33
A*02

109
LLLGSIGLLGV
OPN3
A*02

110
LLADFQALL
CCDC87
A*02

111
ALCLLLHLL
MRGPRE
A*02

112
SVSDGIHSV
CELSR1
A*02

113
AVLTGLVEV
LRBA
A*02

114
ILDERQVLL
ITGAE
A*02

115
MLLETQDALYV
ADORA2B
A*02

116
VLMEENSKL
HAP1
A*02

117
FLDPNARPLV
CAD
A*02

118
ALSSVLHSI
FGD6
A*02

119
RTADITVTV
ITGAE
A*02

120
ALLANLPAV
SLC26A9
A*02

121
ALVDTLTGI
IPO9
A*02

122
ALLEMFPEITV
TXNDC16
A*02

123
LMAFFLAVV
OR6C75
A*02

124
SVASVLLYL
PRKDC
A*02

125
VLQPFLPSI
IPO9
A*02

126
FLSTVTSV
SOGA2
A*02

127
GLDGSLVFL
MARCH6
A*02

128
FLGTTPTL
SF3B3
A*02

129
VLYDKDAVYV
BMS1
A*02

130
NLWGGQGLLGV
GORASP2
A*02

131
LLKEFVQRV
COL6A3
A*02

132
ALWLVDPLTV
SLC33A1
A*02

133
MTLPVDAVISV
UFSP2
A*02

134
AAEIGDKSWLY
PLA2G7
A*01

135
ASEDSVLLY
CHAF1B
A*01

136
ATDLVVLDRY
DICER1
A*01

137
ATSKFMEFY
EDNRA
A*01

138
DSDSCHFNY
DCBLD2
A*01

139
ECDMAFHIY
UHRF1, LOC728688
A*01

140
ESDREELNY
CBFA2T2
A*01

141
ESDVGVVVY
DDX60L
A*01

142
EVAEPSVLFDLY
C9orf114
A*01

143
Fl DYPKKEDY
PLAU
A*01

144
FLDSQNLSAY
BBS1, DPP3
A*01

145
FVDKPVAY
TAF1B
A*01

146
GLNTGSALSY
COL6A3
A*01/

B*15

147
GSSDSSTLPKL
TDRD5
A*01

148
GTEFTTI LY
TP73
A*01

149
GTEFTTVLY
TP63
A*01

150
GTELLSLVY
PRKDC
A*01

151
HSDLKVGEY
DICER1
A*01

152
HTDSLHLLI
ANKRD52, FLJ25613
A*01

153
KLDRSVFTAY
FAM111B
A*01

154
LLDISQKNLY
ZNF439
A*01

155
LLDPNPHMY
RGS17
A*01

156
LLDSLREQY
SESTD1
A*01

157
LMDRPIFY
GALNS
A*01

158
LSDLLKQGY
PKD2L1
A*01

159
LSDTSVIQFY
C16orf62
A*01

160
LTEAVLNRY
KIF26B
A*01

161
LVDDGTHGQY
TRPM2
A*01

162
LVDNSIRELQY
CARD8
A*01

163
NSDSSLTLREFY
FSTL4
A*01

164
NTDNNLAVY
CXorf61
A*01

165
NTDPTAPPY
CDH3
A*01

166
NTQITDIGRY
HMCN1
A*01

167
QSDPGTSVLGY
SEZ6
A*01

168
QTDHPQPI
LDRYITGAE
A*01

169
RLDTPLYFSY
LEPRE1
A*01

170
RSDDTAVYY
IGHA1, IGHA2, IGHD,
A*01

IGHG3, IGHV1-18,

IGHV1-2, IGHV4-31

171
RSDPVTLNVLY
CEACAM6, PSG1, PSG2,
A*01

PSG4, PSG5, PSG7, PSG8

172
RTDSCSSAQAQY
DCBLD2
A*01

173
RTEFNLNQY
COL12A1
A*01

174
SADDIRGIQSLY
MMP12
A*01

175
SDVTPLTF
MMP11
A*01

176
SRTINVSNLY
LAMA1
A*01

177
SSDEVNFLVY
TBL1XR1
A*01

178
SSDSSTLPKL
TDRD5
A*01/

C*12

179
STAKSATWTY
TP63, TP73
A*01

180
STDPWIQMAY
KDM1B
A*01

181
TADGKTYYY
TCERG1
A*01

182
TDYHVRVY
FNDC3B
A*01

183
TLEDIATSHLY
CBFA2T2
A*01

184
TSAHPEDSSFY
LOC731467, TRBV20-1
A*01

185
TSDSNLNKY
KCNH7
A*01

186
TTDIIEKY
DDX60L
A*01

187
VADLHLYLY
GARS
A*01

188
VSDAKLDKY
RCOR2, LOC441644
A*01

189
VSDSECLSRY
LAMA1
A*01

190
VTDGINPLIDRY
FREM2
A*01

191
VTDGSLYEGVAY
DSE
A*01

192
VTEESFDSKFY
CDKAL1
A*01

193
VTEFSLNTY
COL6A3
A*01

194
VVADTKMIEY
ADAMTS12
A*01

195
VVDSVGGYLY
ROS1
A*01

196
WMFFVINY
TMEM217
A*01

197
YADTVRPEFY
COL6A3
A*01

198
YLDPVQRDLY
ZNF655
A*01

199
YLPQHTIETY
TP63
A*01/

B*15

200
YSDEDVTKY
SDK2
A*01

201
YVGKEHMFY
MAGEA9, MAGEA9B
A*01

202
KLAELEGALQK
KRT81, KRT121P, KRT83,
A*03

KRT85, KRT86

203
KVKDTPGLGK
KIF26B
A*03

204
AVFDKFIRY
BTBD17
A*03

205
SLDGAARPK
SP6
A*03

206
KLIDLSQVMY
MACC1
A*03/

B*15

207
RSFNGLLTMY
LAMB3
A*03/

B*15

208
GLASRILDAK
LAMB3
A*03

209
RTQIPMSEK
RASSF6
A*03

210
ATSGVPVYK
SLC44A5
A*03

211
TVNPVAIHK
GLI2
A*03

212
KAYEQVMHY
FOXA2
A*03

213
LNINMTSPMGTK
PCSK2
A*03

214
RTMSEAALVRK
RASSF6
A*03

215
MMFSGPQILKL
ABCC1
A*03/

A*32

216
KLYAWELAF
ABCC1
A*03/

A*32

217
RILNQILYY
FGD6
A*03

218
KTLVAELLILK
POLQ
A*03

219
RLRSSLVFK
FAM83B
A*03

220
SPSVSQLSVL
PRAME
B*07

221
VPDVAQFVL
MMP1
B*07

222
NPFYPEVEL
MMP1
B*07

223
YPKDIYSSF
MMP1
B*07

224
GPQPWHAAL
MMP11
B*07

225
LPFDGPGGIL
MMP11
B*07

226
SPRMSGLLSQT
DLL3
B*07

227
YPRGNHWAVGH
GRP
B*07

228
YPRGNHWAVGHL
GRP
B*07

229
VPLPAGGGTV
GRP
B*07

230
VPLPAGGGTVL
GRP
B*07

231
RPRALRDLQL
NLRP7
B*07

232
RPRALRDLQLL
NLRP7
B*07

233
KPYQGNPTF
DNAH17
B*07

234
RAKNAGVTI
LAMC2
B*07

235
MPLKHYLLL
LRRC15
B*07

236
RVRGGEDGDRAL
INSM1
B*07

237
RPAATAVISL
SLC7A11
B*07

238
KPGPPWAAF
DCBLD2
B*07

239
YVPSASLFML
E2F7
B*07

240
SPREVTTVL
DCBLD2
B*07

241
SARLATDAL
FAM83A
B*07

242
SPRWLPVSL
BTBD17
B*07

243
RPIENRILIL
PSG1, PSG3, PSG4, PSG5,
B*07

PSG6, PSG7, PSG8, PSG9

244
FPYVRDFVM
COL6A3
B*07/

B*35

245
RIREHVPQL
COL6A3
B*07

246
TPLPAVIVL
SLC7A11
B*07

247
RALLARLLL
PLAU
B*07

248
IPNWARQDL
NLRP7
B*07

249
VPSSRILQL
THEG
B*07

250
SPRDFLSGL
ABCA2, TPH1
B*07

251
VPRSSGQTV
SP6
B*07

252
SPDIRNTTV
DCBLD2
B*07

253
RVIDAVRFTL
TP63
B*07

254
NPFPHLITL
ROS1
B*07

255
MPLLENLYL
MXRA5
B*07

256
SPRVPSIEL
COL7A1
B*07

257
LPRIPFADV
ROS1
B*07

258
LPRGPLASL
CDH3
B*07

259
RPPAAGLRGISL
SEZ6L
B*07

260
YPQHPGLNA
SOX2
B*07

261
APSARVGVC
KRT86
B*07

262
SAYPQRLEI
CYP24A1
B*07/

B*51

263
HPAPYGDLL
GLI2
B*07

264
RPILIIITL
TP73
B*07

265
SPRQPPRLV
CYP24A1
B*07

266
HAYPPGPGL
MMP10
B*07/

C*03

267
HPELVNHIVF
GALNT5
B*07/

B*35

268
YPLFRGINL
COL5A1
B*07

269
APRAPRLML
ITGA3
B*07

270
APGPRFLVT
CD109
B*07

271
MPLPWSLALP
EGFL6
B*07/

B*35

272
MPLPWSLALPL
EGFL6
B*07

273
MPLLWLRGF
INHBA
B*07/

B*35

274
TPYQEHVAL
ZNF618
B*07/

B*35

275
APHPPLSVV
IQGAP3
B*07

276
LPRAGGAFL
LAMB3
B*07

277
MPLFEPRVF
PTK7
B*07/

B*35

278
HPMIDINGIIVF
COL5A1
B*07/

B*35

279
SPARASPAL
TMPRSS13
B*07

280
VPISEEGTPVL
KIAA0754
B*07

281
RPRAPVTPA
HES6
B*07

282
MPQIETRVIL
ECT2
B*07

283
RPHSLSSEL
ITGAE
B*07

284
FPVTSIFHTF
KCNG1, KCNG2
B*07/

B*35

285
FPSFLTNSL
CEP192
B*07/

B*35

286
VPTLRSEL
DST, MACF1
B*07

287
APREEQQRSL
KIAA1211
B*07

288
FPQKFIDLL
SASS6
B*07

289
VPENHSVAL
FAM83B
B*07

290
APYRPPDISL
TANC2
B*07

291
SPQRLRGLL
CTHRC1
B*07

292
SPQRLRGLLL
CTHRC1
B*07

293
RPRSALPRLLLP
FZD2
B*07

294
GPTPNTGAAL
COL6A3
B*07

295
KPEGTRIAV
COL6A3
B*07

296
MPMQDIKM
PRAME
B*08

297
RAQLKLVAL
KLHDC7B
B*08

298
FNKRKPLSL
NLRP2
B*08

299
MAQFKEISL
NLRP2
B*08

300
VASPKHCVL
KIF26B
B*08

301
YMHKLLVL
PTH2
B*08/

B*35

302
HLLQKQTSI
TP63
B*08

303
LPFPKFTV
GALNT5
B*08

304
ELKKLYCQI
TP63
B*08

305
ALKLRVAVL
C16orf59
B*08

306
ILKVKVGL
POSTN
B*08

307
ILLPRTVSL
MXRA5
B*08

308
MLKQKVEEL
DST
B*08

309
DAIQRKYSC
DST
B*08

310
LPPKKFVL
NUP155
B*08

311
EIRIRVVQM
PRKDC
B*08

312
EAMLRNKEL
CENPF
B*08

313
ELKKKEYEEL
CENPF
B*08

314
AIISRLVAL
TANC2
B*08

315
DIYQRALNL
VPS13B
B*08

316
VIKEKALTL
USP9X, USP9Y
B*08

317
LVKVKVLL
ARID4A
B*08

318
EAAIRSVEL
DSCR3
B*08

319
AEMLERVIKNY
MAGEA4
B*44

320
MEVDPIGHVYIF
MAGEA3, MAGEA6
B*44

321
AEMLESVIKNY
MAGEA1, MAGEA8,
B*44

MAGEA9, MAGEA9B

322
KEVDPAGHSY
MAGEA8, MAGEA9,
B*44

MAGEA9B

323
SEFMQVIF
MAGEA9, MAGEA9B
B*44

324
TDSIHAWTF
SLC35D3
B*44/

B*18

325
QEQDVDLVQKY
MMP1
B*44

326
QEMQHFLGL
MMP12
B*44

327
YEIEARNQVF
MMP12
B*44/

B*18

328
FEYDFLLQRI
MMP12
B*44

329
NEHPSNNW
LAMC2
B*44

330
KEGDLGGKQW
ADAMTS12
B*44

331
EDAQGHIW
MMP11
B*44

332
MEVPVIKI
ECT2
B*44

333
AETLSTIQI
KIF26B
B*44

334
AEDEPAAAHL
KIF26B
B*44

335
KELEATKQY
KIF26B
B*44

336
ASSSGPMRWW
LAMB3
B*44/

B*57

337
TENRYCVQL
JUP, KRT13, KRT17
B*44

338
SEGSEPALLHSW
FAM83A
B*44

339
SEPALLHSW
FAM83A
B*44

340
TEFSLNTY
COL6A3
B*44

341
EEIEGKGSFTYF
POSTN
B*44

342
HEFSSPSHL
TP63
B*44

343
TEFTTVLY
TP63
B*44

344
EEATGQFHVY
CEACAM1, CEACAM3,
B*44

CEACAM6

345
IEFIHPQAF
MXRA5
B*44

346
VEAPGPVHVYW
PTK7
B*44

347
ALNPYQYQY
DLX5
B*44/

A*29

348
AEIQGNINHV
IQGAP3
B*44

349
AEQDMRELTY
DST
B*44

350
GECDVFKEIL
DCBLD2
B*44

351
EEVNYINTF
CCNE2
B*44

352
NEVLTYIKF
ABCC5
B*44

353
GEIIMQNNW
SERTAD4
B*44

354
TEDPTILRI
PLXNA1
B*44

355
SDMVRFHLF
SGK196
B*44

356
EEGRVYLF
ITGA2
B*44

357
RELENCFQIQ
DNAH14
B*44

358
KEADIHFLI
COL6A5
B*44

359
DELFSIALY
NUP155
B*44

360
AEVPTGVII
ITGA2
B*44

361
SENLFFASF
ITGA2
B*44

362
SEKGVIQVY
NUP155
B*44

363
AELDKLTSV
CENPF
B*44

364
AETPIQNVI
MET
B*44

365
SEMNVNMKY
MET
B*44

366
AENLFRAF
PRKDC
B*44

367
GEVHPSEMI
PRKDC
B*44

368
GEFPVRVQV
YEATS2
B*44

369
EEIERFFKL
NUP155
B*44

370
YEDLSQKY
CENPF
B*44

371
GELALKKKI
PRKDC
B*44

372
TEGIIMKDF
MET
B*44

373
MEMQKSPVF
FSTL4, GRM7,
B*44

LOC440173, LOC644919,

LOC728755, SLC44A5

374
DEVNFLVY
TBL1X, TBL1XR1, TBL1Y
B*44/

B*18

TABLE 2

Additional peptides according to the present

invention with no prior known cancer

association.

Seq ID

HLA

No
Sequence
Gene(s)
allotype

375
VYSDLHAFYY
MANEAL
A*24

376
KYVKDFHKF
ZNF724P
A*24

377
VYVGAVNRI
PLXNA1
A*24

378
KFLGPAEHLTF
PROM2
A*24

379
NYIVPDKQIF
POLA1
A*24

380
VFQEKHHVI
MOXD1
A*24

381
TYSKKHFRI
CHEK2
A*24

382
IYHSHHPTL
OPA1
A*24

383
RYKQDVERF
SMC5
A*24

384
KYVKVFDKF
ZNF107
A*24

385
MYINEVERL
PTPN14
A*24

386
VYNDHSIYVW
MAPKBP1
A*24

387
RWLPQKNAAQF
DOCK5,
A*24

PPP2R2A

388
FSIPEGALVAV
ABCC1
A*02

389
TLMEQPLTTL
TXNDC16
A*02

390
HIMPTVHTV
ADNP2
A*02

391
SLIDMRGIETV
SMC6
A*02

392
SLFKDQMEL
IPO8
A*02

393
ILLPYLQTL
TIPARP
A*02

394
ASEAEMRLFY
DHX37
A*01

395
ASEASRLAHY
HIST1H2BA,
A*01

HIST1H2BL,

HIST3H2BB

396
ASEFGNHYLY
SF3B3
A*01

397
ASEITSKGASLY
CLUAP1
A*01

398
ASEQQALHTVQY
NUP188
A*01

399
ATDIPCLLY
RINT1
A*01

400
ATDISRQNEY
PDE7A
A*01

401
DSDESYMEKSLY
CLSPN
A*01

402
DTDSQRLAY
E2F1
A*01

403
ELDSKVEVLTY
SNX7
A*01

404
ETARKFLYY
GPD2
A*01

405
ETEEGIYWRY
KREMEN2
A*01

406
ETEQTKFWDY
FUT11
A*01

407
FSDNDKLYLY
RFX5
A*01

408
FTEQVVTDGY
TLK2
A*01

409
FVDPLVTNY
TRIT1
A*01

410
GSDHQSPSSSSY
ZBTB43
A*01

411
GTVYEDLRY
UBE2C
A*01

412
ILDEVIMGY
KIF11
A*01

413
ISDRYYTALY
CEBPZ
A*01

414
KTDESLTKY
CHD8
A*01

415
LLDPRSYHTY
DOCK8
A*01

416
LLDTAQKNLY
ZNF614
A*01

417
LLEDKHFQSY
WDR6
A*01

418
LSDPSGPKSY
RPS6KC1
A*01

419
LSELKPMSY
TMTC3
A*01

420
LTEDKETLQY
TUBGCP2
A*01

421
LTELLERAAFY
SLC15A4
A*01

422
MIDVTKSYY
DCTN5
A*01

423
NLDAVHDITVAY
LCLAT1
A*01

424
NLDEEKQLLY
FRMD6
A*01

425
NLDIIQQEY
WDR75
A*01

426
NLDQATRVAY
SMC4
A*01

427
NSDEQKITEMVY
LRBA
A*01

428
NSELSCQLY
TYMS
A*01

429
NTEDSSMSGYLY
FGD6
A*01

430
NTEGLHHLY
SMEK2,
A*01

SMEK3P

431
NTSDMMGRMSY
ARID1A
A*01

432
NVDPVQHTY
AGRN
A*01

433
QIDTGENLY
ZNF267
A*01

434
QTDCAPNNGY
NOMO1,
A*01

NOMO2,

NOMO3

435
QTDDTWRTEY
ZMYM2
A*01

436
QTETGTPYMLY
RRM1
A*01

437
STDGKHWWVEY
CCNT1,
A*01

CCNT2

438
STDNFNCKY
FGD6
A*01

439
TLDAGKFQIY
DHX15
A*01

440
TLDENPGVRY
STXBP3
A*01

441
TLDSALNAASYY
TCTN3
A*01

442
TSDFSRFTNY
CCNE2
A*01

443
TTDFPSESSFEY
CXorf21
A*01

444
TTDTVIRSY
SETD4
A*01

445
VLDQGKITEY
ABCB10
A*01

446
VTAQVVGTERY
PLD2
A*01

447
VVDEDHELIY
CHST11
A*01

448
YLDIPNPRY
CIT
A*01

449
YLDRGTGNVSFY
TRIM4
A*01

450
YSDDGQKWTVY
DCBLD2
A*01

451
YSDSLVQKGY
MSH6
A*01

452
YVDAVLGKGHQY
NUP160
A*01

453
AINTSIKNK
TRPM8
A*03

454
KVYTPSISK
CDKAL1
A*03

455
RIADIFVKK
FGD6
A*03

456
SMFTAILKK
LRBA
A*03

457
SINKPTSER
NDC80
A*03

458
GIADFVLKY
RNFT2
A*03

459
RPMQQARAQL
KLHDC7B
B*07

460
MPMAGDMNGL
TP63
B*07

461
RPILIIVTL
TP63
B*07

462
RPFHTRATV
KIF26B
B*07

463
TPKAGPTL
KIF26B
B*07

464
YPRPGTPAA
CDKAL1
B*07

465
VPRPIFSQL
GREB1,
B*07

GREB1L

466
APYKSVTSL
FGD6
B*07

467
KPFSSFTSM
RASSF6
B*07

468
SPMYGQAGL
FOXA2
B*07

469
YPENGVVQM
UHRF1
B*07

470
SPNSYFRVL
PCDHB13,
B*07

PCDHB8

471
KPRPDVTNEL
CDCA7
B*07

472
NPRATDAQL
LRBA
B*07

473
LPRALLSSL
IL4I1
B*07

474
LPRLLPAL
HEATR2
B*07

475
RPHKPGLYL
MANEA
B*07

476
AEEEIMKKI
IGF2BP3
B*44

477
QENSYQSRL
LAMC2
B*44

478
SEIEQEIGSL
LAMC2
B*44

479
AEIQPQTQV
PTK7
B*44

480
GEVSGLTKDF
CDKAL1
B*44

481
RELQHEHSL
FAT1
B*44

482
TEREWADEW
CBFA2T2
B*44

483
EENDQSTHKW
YEATS2
B*44

484
AEVGFVRFF
MSH2
B*44

485
SEIEDSTKQVF
BRCA2
B*44

486
SEDDPILQI
NUP155
B*44

487
AEDQLHHSF
GXYLT1
B*44

488
TEFPIIKMY
TXNDC16
B*44

489
SEIGKAVGF
CLSPN
B*44

TABLE 3

Peptides according to the present invention useful

for e.g. personalized cancer therapies.

Seq ID

HLA

No
Sequence
Gene(s)
allotype

490
SYVKVLHHL
MAGEA12,
A*24

LOC101060230

491
KYLEKYYNL
MMP1
A*24

492
NYEDHFPLL
MAGEA10
A*24

493
TYKYVDINTF
MMP12
A*24

494
RYLEKFYGL
MMP12
A*24

495
SYNDALLTF
TRPM8
A*24

496
VFMKDGFFYF
MMP1
A*24

497
NYPKSIHSF
MMP12
A*24

498
EYIRALQQL
ASCL1
A*24

499
VYFVAPAKF
LAMC2
A*24

500
VWSDVTPLTF
MMP11
A*24

501
GYIDNVTLI
LAMC2
A*24

502
SVHKITSTF
LAMC2
A*24

503
VHFEDTGKTLLF
MMP13
A*24

504
VYEKNGYIYF
MMP13
A*24

505
AYISGLDVF
DNAH17
A*24

506
RYVFPLPYL
SOX14
A*24

507
VYIAELEKI
SMC1B
A*24

508
IYVTGGHLF
KLHDC7B
A*24

509
ALLEEEEGV
MAGEA4
A*02

510
KVLEHVVRV
MAGEA4, MAGEA8
A*02

511
KIWEELSVLEV
MAGEA3, MAGEA6
A*02

512
VLGEEQEGV
MAGEA9, MAGEA9B
A*02

513
KLVELEHTL
CXorf61
A*02

514
VQLDSIEDLEV
PRAME
A*02

515
KIFEMLEGV
CT45A1, CT45A2,
A*02

CT45A3, CT45A4,

CT45A5, CT45A6,

LOC101060208,

LOC101060210,

LOC101060211

516
YTFSGDVQL
MMP1
A*02

517
TLYNPERTITV
IGF2BP1, IGF2BP3
A*02

518
GLLEDERALQL
MEX3A
A*02

519
KIQEILTQV
IGF2BP3
A*02

520
KIQEMQHFL
MMP12
A*02

521
FVYGEPREL
MAGEC2, LOC392555
A*02

522
TLDEKVAEL
MAGEC2
A*02

523
HLIAEIHTA
PTHLH
A*02

524
KVWSDVTPL
MMP11, MMP13
A*02

525
RLDDLKMTV
LAMC2
A*02

526
VLSPFILTL
KLHDC7B
A*02

527
LLDSVSRL
LAMC2
A*02

528
RLLDSVSRL
LAMC2
A*02

529
HPSAHDVIL
LAMC2
B*07

530
APAAWLRSAA
MMP11
B*07

531
AEIEADRSY
LAMC2
B*44

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, acute myeloid leukemia, breast cancer, bile duct cancer, brain cancer, chronic lymphocytic leukemia, colorectal carcinoma, esophageal cancer, gallbladder cancer, gastric cancer, head and neck squamous cell carcinoma, hepatocellular cancer, melanoma, non-Hodgkin lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, renal cell cancer, urinary bladder cancer, uterine cancer.

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: 489. More preferred are the peptides—alone or in combination—selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 374 (see Table 1), and their uses in the immunotherapy of lung cancer (including NSCLC and SCLC), acute myeloid leukemia, breast cancer, bile duct cancer, brain cancer, chronic lymphocytic leukemia, colorectal carcinoma, esophageal cancer, gallbladder cancer, gastric cancer, head and neck squamous cell carcinoma, hepatocellular cancer, melanoma, non-Hodgkin lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, renal cell cancer, urinary bladder cancer, uterine cancer, and preferably lung cancer (including NSCLC and SCLC).

Thus, 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 lung cancer (including NSCLC and SCLC), acute myeloid leukemia, breast cancer, bile duct cancer, brain cancer, chronic lymphocytic leukemia, colorectal carcinoma, esophageal cancer, gallbladder cancer, gastric cancer, head and neck squamous cell carcinoma, hepatocellular cancer, melanoma, non-Hodgkin lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, renal cell cancer, urinary bladder cancer, uterine cancer.

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.

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: 489.

The present invention further relates to the peptides according to the present invention, wherein said peptide is modified and/or includes non-peptide bonds.

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 (li), or fused to (or into the sequence of) an antibody, such as, for example, an antibody that is specific for dendritic cells.

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.

The present invention further relates to an expression vector capable of expressing and/or expressing a nucleic acid according to the present invention.

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.

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.

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.

The antibodies and TCRs are additional embodiments of the immunotherapeutic use of the peptides according to the invention at hand.

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.

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.

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.

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.: 489, preferably containing SEQ ID No. 1 to SEQ ID No. 374, or a variant amino acid sequence.

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.

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.

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.

Preferably, said medicament is a cellular therapy, a vaccine or a protein based on a soluble TCR or antibody.

The present invention further relates to a use according to the present invention, wherein said cancer cells are lung cancer (including NSCLC and SCLC), acute myeloid leukemia, breast cancer, bile duct cancer, brain cancer, chronic lymphocytic leukemia, colorectal carcinoma, esophageal cancer, gallbladder cancer, gastric cancer, head and neck squamous cell carcinoma, hepatocellular cancer, melanoma, non-Hodgkin lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, renal cell cancer, urinary bladder cancer, uterine cancer, and preferably lung cancer (including NSCLC and SCLC) cells.

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 lung cancer (including NSCLC and SCLC). 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.

Optionally the antibody carries a further effector function such as an immune stimulating domain or toxin.

The present invention also relates to the use of these novel targets in the context of cancer treatment.

DETAILED DESCRIPTION OF A PREFERRED EMBODIMENT

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.

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, 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).

As used herein and except as noted otherwise all terms are defined as given below.

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.

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, or 12 or longer, and in case of MHC class II peptides (elongated variants of the peptides of the invention) they can be as long as 13, 14, 15, 16, 17, 18, 19 or 20 or more amino acids in length.

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.

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. 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.

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.

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.

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 4

Expression frequencies F of HLA-A*02, HLA-A*01, HLA-A*03,

HLA-A*24, HLA-B*07, HLA-B*08 and HLA-B*44 serotypes.

Haplotype frequencies Gf are derived from a study which used

HLA-typing data from a registry of more than 6.5 million volunteer

donors in the U.S. (Gragert et al., 2013). The haplotype frequency is

the frequency of a distinct allele on an individual chromosome. Due to

the diploid set of chromosomes within mammalian cells, the frequency

of genotypic occurrence of this allele is higher and can be calculated

employing the Hardy-Weinberg principle (F = 1 − (1 − Gf)²).

Calculated

phenotype

from allele

Allele
Population
frequency (F)

A*02
African (N = 28557)
32.3%

European Caucasian
49.3%

(N = 1242890)

Japanese (N = 24582)
42.7%

Hispanic, S + Cent Amer.
46.1%

(N = 146714)

Southeast Asian (N = 27978)
30.4%

A*01
African (N = 28557)
10.2%

European Caucasian
30.2%

(N = 1242890)

Japanese (N = 24582)
1.8%

Hispanic, S + Cent Amer.
14.0%

(N = 146714)

Southeast Asian (N = 27978)
21.0%

A*03
African (N = 28557)
14.8%

European Caucasian

(N = 1242890)
26.4%

Japanese (N = 24582)
1.8%

Hispanic, S + Cent Amer.
14.4%

(N = 146714)

Southeast Asian (N = 27978)
10.6%

A*24
African (N = 28557)
2.0%

European Caucasian
8.6%

(N = 1242890)

Japanese (N = 24582)
35.5%

Hispanic, S + Cent Amer.
13.6%

(N = 146714)

Southeast Asian (N = 27978)
16.9%

B*07
African (N = 28557)
14.7%

European Caucasian
25.0%

(N = 1242890)

Japanese (N = 24582)
11.4%

Hispanic, S + Cent Amer.
12.2%

(N = 146714)

Southeast Asian (N = 27978)
10.4%

B*08
African (N = 28557)
6.0%

European Caucasian
21.6%

(N = 1242890)

Japanese (N = 24582)
1.0%

Hispanic, S + Cent Amer.
7.6%

(N = 146714)

Southeast Asian (N = 27978)
6.2%

B*44
African (N = 28557)
10.6%

European Caucasian
26.9%

(N = 1242890)

Japanese (N = 24582)
13.0%

Hispanic, S + Cent Amer.
18.2%

(N = 146714)

Southeast Asian (N = 27978)
13.1%

The peptides of the invention, preferably when included into a vaccine of the invention as described herein bind to A*02, A*01, A*03, A*24, B*07, B*08 or B*44. 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-, A*01-, A*03-, A*24-, B*07-, B*08- or B*44-positive, whereas no selection for MHC class II allotypes is necessary due to the pan-binding nature of these peptides.

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).

TABLE 5

HLA alleles coverage in European Caucasian population

(calculated from (Gragert et al., 2013)).

coverage

combined

(at least
combined
combined
with

one A-
with
with
B*07

allele)
B*07
B*44
and B*44

A*02/A*01
70%
78%
78%
84%

A*02/A*03
68%
76%
76%
83%

A*02/A*24
61%
71%
71%
80%

A*′01/A*03
52%
64%
65%
75%

A*01/A*24
44%
58%
59%
71%

A*03/A*24
40%
55%
56%
69%

A*02/A*01/A*03
84%
88%
88%
91%

A*02/A*01/A*24
79%
84%
84%
89%

A*02/A*03/A*24
77%
82%
83%
88%

A*01/A*03/A*24
63%
72%
73%
81%

A*02/A*01/A*03/A*24
90%
92%
93%
95%

In a preferred embodiment, the term “nucleotide sequence” refers to a heteropolymer of deoxyribonucleotides.

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.

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.

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.

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.

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.

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).

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.

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.

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.

The term “promoter” means a region of DNA involved in binding of RNA polymerase to initiate transcription.

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.

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.

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.

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.

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.

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.

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: 489 or a variant thereof which is 88% homologous to SEQ ID NO: 1 to SEQ ID NO: 489, 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.

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.

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).

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: 489. 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.

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 489, 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.

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.”

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, IIe, Val, Cys); and Group 5-large, aromatic residues (Phe, Tyr, Trp).

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.

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.

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.

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.

The amino acid residues that do not substantially contribute to interactions with the T-cell receptor can be modified by replacement with other amino acid 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 6

Variants and motif of the peptides according

to SEQ ID NO: 4, 13, 90. 93, 138,

171, 202, 204, 224, 294, 306, 316, 322 and 327.

Position
1
2
3
4
5
6
7
8
9

SEQ ID No
S
Y
E
K
V
I
N
Y
L

4

Variant

I

F

F

I

F

F

F

SEQ ID No
H
Y
T
Y
I
L
E
V
F

13

Variant

I

L

F

I

F

L

F

Position
1
2
3
4
5
6
7
8

SEQ ID No
F
L
L
M
H
P
S
I

90

Variant

V

L

A

M

V

M

M

L

M

A

A

V

A

A

L

A

A

V

V

V

V

L

V

A

T

V

T

T

L

T

A

Q

V

Q

Q

L

Q

A

Position
1
2
3
4
5
6
7
8
9

SEQ ID No
T
L
Q
E
K
I
L
Q
V

93

Variant

I

L

A

M

M

I

M

L

M

A

A

A

I

A

L

A

A

V

V

I

V

L

V

A

T

T

I

T

L

T

A

Q

Q

I

Q

L

Q

A

SEQ ID No
D
S
D
S
C
H
F
N
Y

138

Variant

A

E

E

A

T

T

A

T
E

T
E

A

Position
1
2
3
4
5
6
7
8
9
10
11

SEQ ID No
R
S
D
P
V
T
L
N
V
L
Y

171

Variant

A

E

E

A

T

T

A

T
E

T
E

A

SEQ ID No
K
L
A
E
L
E
G
A
L
Q
K

202

Variant

Y

R

F

I

I

Y

I

R

I

F

M

M

Y

M

R

M

F

V

V

Y

V

R

V

F

T

T

Y

T

R

T

F

Position
1
2
3
4
5
6
7
8
9

SEQ ID No
A
V
F
D
K
F
I
R
Y

204

Variant

L

K

L

L

R

L

F

I

K

I

I

R

I

F

M

K

M

M

R

M

F

K

R

F

T

K

T

T

R

T

F

SEQ ID No
G
P
Q
P
W
H
A
A
L

224

Variant

F

V

M

A

I

Position
1
2
3
4
5
6
7
8
9
10

SEQ ID No
G
P
T
P
N
T
G
A
A
L

294

Variant

F

V

M

A

I

Position
1
2
3
4
5
6
7
8

SEQ ID No
I
L
K
V
K
V
G
L

306

Variant

V

I

M

F

R

R

V

R

I

R

M

R

F

H

H

V

H

I

H

M

H

F

R

R

V

R

I

R

M

R

F

R

R

R

R

V

R

R

I

R

R

M

R

R

F

R

H

R

H

V

R

H

I

R

H

M

R

H

F

L

L

V

L

I

L

M

L

F

L

R

L

R

V

L

R

I

L

R

M

L

R

F

L

H

L

H

V

L

H

I

L

H

M

L

H

F

Position
1
2
3
4
5
6
7
8
9

SEQ ID No
V
I
K
E
K
A
L
T
L

316

Variant

V

I

M

F

R

R

V

R

I

R

M

R

F

H

H

V

H

I

H

M

H

F

R

R

V

R

I

R

M

R

F

R

R

R

R

V

R

R

I

R

R

M

R

R

F

R

H

R

H

V

R

H

I

R

H

M

R

H

F

L

L

V

L

I

L

M

L

F

L

R

L

R

V

L

R

I

L

R

M

L

R

F

L

H

L

H

V

L

H

I

L

H

M

L

H

F

Position
1
2
3
4
5
6
7
8
9
10

SEQ ID No
K
E
V
D
P
A
G
H
S
Y

322

Variant

F

W

L

D

F

D

W

D

D

L

SEQ ID No
Y
E
I
E
A
R
N
Q
V
F

327

Variant

W

Y

L

D

D

W

D

Y

D

L

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.

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 7.

TABLE 7

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

1
0 or 1 or 2 or 3

0
0 or 1 or 2 or 3 or 4

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.

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.

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.

Accordingly, the present invention provides peptides and variants of MHC class I epitopes, wherein the peptide or variant has an overall length of from 8 and 100, from 9 and 100, from 10 and 100, from 11 and 100, from 12 and 100, preferably from 8 and 30, and from 9 and 30, from 10 and 30, from 11 and 30, from 12 and 30, most preferred from 8 and 14, from 9 and 14, from 10 and 14, from 11 and 14, from 12 and 14. The present invention further provides peptides and variants of MHC class I epitopes, wherein the peptide or variant has an overall length of namely 8, 9, 10, 11, 12, 13, or 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.

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.

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 μM, more preferably no more than about 1 nM, and still more preferably no more than about 100 μM, and most preferably no more than about 10 μM. 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.

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: 489.

“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 489 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.

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 “li”) 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.

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.

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.

A non-peptide bond is, for example, —CH₂—NH, —CH₂S—, —CH₂CH₂—, —CH═CH—, —COCH₂—, —CH(OH)CH₂—, and —CH₂SO—. U.S. Pat. No. 4,897,445 provides a method for the solid phase synthesis of non-peptide bonds (—CH₂—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 NaCNBH3.

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.

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.

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.

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 (www.sigma-aldrich.com) provide information on specific reagents.

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 α-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.

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.

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).

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.

A peptide or variant, wherein the peptide is modified or includes non-peptide bonds is a preferred embodiment of the invention.

Another embodiment of the present invention relates to a non-naturally occurring peptide wherein said peptide consists or consists essentially of an amino acid sequence according to SEQ ID NO: 1 to SEQ ID NO: 489 and has been synthetically produced (e.g. synthesized) as a pharmaceutically acceptable salt. Methods to synthetically produce peptides are well known in the art. The salts of the peptides according to the present invention differ substantially from the peptides in their state(s) in vivo, as the peptides as generated in vivo are no salts. The non-natural salt form of the peptide mediates the solubility of the peptide, in particular in the context of pharmaceutical compositions comprising the peptides, e.g. the peptide vaccines as disclosed herein. A sufficient and at least substantial solubility of the peptide(s) is required in order to efficiently provide the peptides to the subject to be treated. Preferably, the salts are pharmaceutically acceptable salts of the peptides. These salts according to the invention include alkaline and earth alkaline salts such as salts of the Hofmeister series comprising as anions PO₄³⁻, SO₄^2-, CH₃COO⁻, Cl⁻, Br⁻, NO₃—, ClO₄⁻, I⁻, SCN⁻ and as cations NH₄⁺, Rb⁺, K⁺, Na⁺, Cs⁺, Li⁺, Zn²⁺, Mg²⁺, Ca²⁺, Mn²⁺, Cu²⁺ and Ba²⁺. Particularly salts are selected from (NH₄)₃PO₄, (NH₄)₂HPO₄, (NH₄)H₂PO₄, (NH₄)₂SO₄, NH₄CH₃COO, NH₄Cl, NH₄Br, NH₄NO₃, NH₄ClO₄, NH₄I, NH₄SCN, Rb₃PO₄, Rb₂HPO₄, RbH₂PO₄, Rb₂SO₄, Rb₄CH₃COO, Rb₄Cl, Rb₄Br, Rb₄NO₃, Rb₄ClO₄, Rb₄I, Rb₄SCN, K₃PO₄, K₂HPO₄, KH₂PO₄, K₂SO₄, KCH₃COO, KCl, KBr, KNO₃, KClO₄, KI, KSCN, Na₃PO₄, Na₂HPO₄, NaH₂PO₄, Na₂SO₄, NaCH₃COO, NaCl, NaBr, NaNO₃, NaClO₄, NaI, NaSCN, ZnCl₂Cs₃PO₄, Cs₂HPO₄, CsH₂PO₄, Cs₂SO₄, CsCH₃COO, CsCl, CsBr, CsNO₃, CSClO₄, CsI, CsSCN, Li₃PO₄, Li₂HPO₄, LiH₂PO₄, Li₂SO₄, LiCH₃COO, LiCl, LiBr, LiNO₃, LiClO₄, LiI, LiSCN, Cu₂SO₄, Mg₃(PO₄)₂, Mg₂HPO₄, Mg(H₂PO₄)₂, Mg₂SO₄, Mg(CH₃COO)₂, MgCl₂, MgBr₂, Mg(NO₃)₂, Mg(ClO₄)₂, MgI₂, Mg(SCN)₂, MnCl₂, Ca₃(PO₄), Ca₂HPO₄, Ca(H₂PO₄)₂, CaSO₄, Ca(CH₃COO)₂, CaCl₂, CaBr₂, Ca(NO₃)₂, Ca(ClO₄)₂, Cal₂, Ca(SCN)₂, Ba₃(PO₄)₂, Ba₂HPO₄, Ba(H₂PO₄)₂, BaSO₄, Ba(CH₃COO)₂, BaCl₂, BaBr₂, Ba(NO₃)₂, Ba(ClO₄)₂, Bal₂, and Ba(SCN)₂. Particularly preferred are NH acetate, MgCl₂, KH₂PO₄, Na₂SO₄, KCl, NaCl, and CaCl₂, such as, for example, the chloride or acetate (trifluoroacetate) salts.

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).

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).

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.

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.

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) (cf. Example 1, FIGS. 1A through 1N).

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 lung cancer (including NSCLC and SCLC) samples (N=201 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 201 lung cancer (including NSCLC and SCLC) patients.

The discovery pipeline XPRESIDENT® 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.

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.

HLA-peptide complexes from lung cancer (including NSCLC and SCLC) tissue samples were purified and HLA-associated peptides were isolated and analyzed by LC-MS (see example 1). All TUMAPs contained in the present application were identified with this approach on lung cancer (including NSCLC and SCLC) samples confirming their presentation on lung cancer (including NSCLC and SCLC).

TUMAPs identified on multiple lung cancer (including NSCLC and SCLC) 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.

Besides over-presentation of the peptide, mRNA expression of the underlying gene was tested. mRNA data were obtained via RNASeq analyses of normal tissues and cancer tissues (cf. Example 2, FIGS. 2A through 2N). 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 whose coding mRNA is highly expressed in cancer tissue, but very low or absent in vital normal tissues, were preferably included in the present invention.

The present invention provides peptides that are useful in treating cancers/tumors, preferably lung cancer (including NSCLC and SCLC) 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 lung cancer (including NSCLC and SCLC) samples.

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 lung cells or other normal tissue cells, 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 lung cancer (including NSCLC and SCLC), but not on normal tissues (see Example 1).

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. lung cancer (including NSCLC and SCLC) cells presenting the derived peptides.

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 (see also below). 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.

The present description further relates to T-cell receptors (TCRs) comprising an alpha chain and a beta chain (“alpha/beta TCRs”). Also provided are peptides according to the invention capable of binding to TCRs and antibodies when presented by an MHC molecule.

The present description also relates to fragments of the TCRs according to the invention that are capable of binding to a peptide antigen according to the present invention when presented by an HLA molecule. The term particularly relates to soluble TCR fragments, for example TCRs missing the transmembrane parts and/or constant regions, single chain TCRs, and fusions thereof to, for example, with Ig.

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.

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.

In one embodiment the desembodiment, 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.

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.

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.

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.

TCRs of the present description preferably bind to a peptide-HLA molecule complex with a binding affinity (KD) of about 100 μM or less, about 50 μM or less, about 25 μM or less, or about 10 μM or less. More preferred are high affinity TCRs having binding affinities of about 1 μM 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.

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 a peptide-HLA molecule complex of 100 μM or less.

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.

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.

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.

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.

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 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. For TCRs specific for patogenes restricted to other alleles compared to tumor-associated self-antigens the KD values might be in a slightly different range, but there are no general differences between the different alleles with respect to the possibility of creating TCRs. 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 peptides can be enhanced by methods well known in the art.

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 healthy donors negative with respect to the allel at hand with the HLA/peptide monomers, incubating the PBMCs with tetramer-phycoerythrin (PE) and isolating the high avidity T-cells by fluorescence activated cell sorting (FACS)-Calibur analysis.

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 TCRαβ 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 a peptide, 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.

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.

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.

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), β-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.

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).

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.

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).

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 “op-timal” 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).

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).

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 CD3ζ (CD3ζ fusion) (Schmitt et al., 2009).

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.

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.

The pharmaceutical compositions comprise the peptides either in the free form or in the form of a pharmaceutically acceptable salt (see also above). In an aspect, a peptide described herein is in the form of a pharmaceutically acceptable salt. In another aspect, a peptide in the form of a pharmeutical salt is in crystalline form.

In an aspect, a pharmaceutically acceptable salt described herein refers to salts which possess toxicity profiles within a range that is acceptable for pharmaceutical applications.

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.

In an aspect, pharmaceutically acceptable salts may increase the solubility and/or stability of peptides of described herein. In another aspect, pharmacutical salts described herein may be prepared by conventional means from the corresponding carrier peptide or complex by reacting, for example, the appropriate acid or base with peptides or complexes as described herein. In another aspect, the pharmaceutically acceptable salts are in crystalline form or semi-crystalline form. In yet another aspect, pharmaceutically acceptable salts may include, for example, those described in Handbook of Pharmaceutical Salts: Properties, Selection, and Use By P. H. Stahl and C. G. Wermuth (Wiley-VCH 2002) and L. D. Bighley, S. M. Berge, D. C. Monkhouse, in “Encyclopedia of Pharmaceutical Technology”. Eds. J. Swarbrick and J. C. Boylan, Vol. 13, Marcel Dekker, Inc., New York, Basel, Hong Kong 1995, pp. 453-499, each of these references is herein incorporated by reference in their entirety.

In an especially preferred embodiment, the pharmaceutical compositions comprise the peptides as salts of acetic acid (acetates), trifluoro acetates or hydrochloric acid (chlorides).

Preferably, the medicament of the present invention is an immunotherapeutic 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.

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. 489, 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.

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.

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.

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.

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.

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.

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.

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.

Alternatively, the gene for such selectable trait can be on another vector, which is used to co-transform the desired host cell.

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.

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.

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 (Ylps) 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×FLAG, c-myc or MAT. These fusion proteins allow for detection, purification and analysis of recombinant protein. Dual-tagged fusions provide flexibility in detection.

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 ˜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.

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.

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 Balbes 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.

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.

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.

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.

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).

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.

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 μg and 1.5 mg, preferably 125 μg to 500 μg, 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).

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.

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®, AS15, BCG, CP-870,893, CpG7909, CyaA, dSLIM, flagellin or TLR5 ligands derived from flagellin, FLT3 ligand, GM-CSF, IC30, IC31, Imiquimod (ALDARA®), 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®, 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® 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).

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.

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®, Hiltonol®, 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®, 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.

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.

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®) and anti-CD40 mAB, or combinations thereof.

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.

In an aspect, peptides or other molecules described herein may be combined with an aqeuous carrier. In an aspect, the aqeuous carrier is selected from ion exchangers, alumina, aluminum stearate, magnesium stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, dicalcium phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, polyvinylpyrrolidone-vinyl acetate, cellulose-based substances (e.g., microcrystalline cellulose, hydroxypropyl methylcellulose, hydroxypropyl methylcellulose acetate succinate, hydroxypropyl methylcellulose Phthalate), starch, lactose monohydrate, mannitol, trehalose sodium lauryl sulfate, and crosscarmellose sodium, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, polymethacrylate, waxes, polyethylene-polyoxypropylene-block polymers, polyethylene glycol and wool fat.

In an aspect, the aquous carrier contains multiple components, such as water together with a non-water carrier component, such as those components described herein. In another aspect, the aquous carrier is capable of imparting improved properties when combined with a peptide or other molecule described herein, for example, improved solubility, efficiacy, and/or improved immunotherapy. In addition, the composition can contain excipients, such as buffers, binding agents, blasting agents, diluents, flavors, lubricants, etc. A “pharmaceutically acceptable diluent,” for example, may include solvents, bulking agents, stabilizing agents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like which are physiologically compatible. Examples of pharmaceutically acceptable diluents include one or more of saline, phosphate buffered saline, dextrose, glycerol, ethanol, and the like as well as combinations thereof. In many cases it will be preferable to include one or more isotonic agents, for example, sugars such as trehalose and sucrose, polyalcohols such as mannitol, sorbitol, or sodium chloride in the composition. Pharmaceutically acceptable substances such as wetting or minor amounts of auxiliary substances such as wetting or emulsifying agents, preservatives or buffers, are also within the scope of the present invention.in addition, the composition can contain excipients, such as buffers, binding agents, blasting agents, diluents, flavors, and lubricants.

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).

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.

“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.

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.

Each scaffold can be conjugated with a second active molecule such as for example IL-21, anti-CD3, and anti-CD28.

For further information on polypeptide scaffolds see for example the background section of WO 2014/071978A1 and the references cited therein.

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.

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. 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.

Further, investigation of cell-binding behavior with flow cytometry showed that the aptamers revealed very good apparent affinities that are within the nanomolar range.

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.

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 489, according to the present invention with the MHC molecule, using the cell-SELEX (Systematic Evolution of Ligands by Exponential enrichment) technique.

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.

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 (preferably a peptide according to the present invention), 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.

It is thus 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.

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.

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.

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: 489, or a variant thereof which is at least 88% homologous (preferably identical) to SEQ ID NO: 1 to SEQ ID NO: 489 or a variant thereof that induces T cells cross-reacting with said peptide, wherein said peptide is not the underlying full-length polypeptide.

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: 489 or a variant thereof which is at least 88% homologous (preferably identical) to SEQ ID NO: 1 to SEQ ID NO: 489, 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.

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.

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: 489.

The present invention further relates to the peptides according to the invention, wherein the peptide is (chemically) modified and/or includes non-peptide bonds.

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 (li), or wherein the peptide is fused to (or into) an antibody, such as, for example, an antibody that is specific for dendritic cells.

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.

The present invention further relates to the nucleic acid according to the invention that is DNA, cDNA, PNA, RNA or combinations thereof.

The present invention further relates to an expression vector capable of expressing a nucleic acid according to the present invention.

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 lung cancer (including NSCLC and SCLC).

The present invention further relates to a host cell comprising a nucleic acid according to the present invention or an expression vector according to the present invention.

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.

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.

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.

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: 489 or said variant amino acid sequence.

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.

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.

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.

The present invention further relates to a use according to the invention, wherein said cancer cells are lung cancer (including NSCLC and SCLC) cells or other solid or hematological tumor cells such as acute myeloid leukemia, breast cancer, bile duct cancer, brain cancer, chronic lymphocytic leukemia, colorectal carcinoma, esophageal cancer, gallbladder cancer, gastric cancer, head and neck squamous cell carcinoma, hepatocellular cancer, melanoma, non-Hodgkin lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, renal cell cancer, urinary bladder cancer, uterine cancer.

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 lung cancer (including NSCLC and SCLC). The present invention also relates to the use of these novel targets for cancer treatment.

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 lung cancer (including NSCLC and SCLC) marker (poly)peptide, delivery of a toxin to a lung cancer (including NSCLC and SCLC) cell expressing a cancer marker gene at an increased level, and/or inhibiting the activity of a lung cancer (including NSCLC and SCLC) marker polypeptide) according to the invention.

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 lung cancer (including NSCLC and SCLC) 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.

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: 489 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 lung cancer (including NSCLC and SCLC) marker polypeptide used to generate the antibody according to the invention.

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.

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).

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.

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).

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.

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.

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.

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.

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.

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.

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.

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 (μg/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 lung cancer (including NSCLC and SCLC), 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 occurs in the absence of antibody administration, is an efficacious antibody for treatment of cancer.

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), and 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.

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.

The antibodies or TCRs may also be used for in vivo diagnostic assays. Generally, the antibody is labeled with a radionucleotide (such as ¹¹¹In, ⁹⁹Tc, ¹⁴C, ¹³¹I, ³H, ³²P or 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 1×10 μM.

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.

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.

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.

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).

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.

In case of a MHC class I epitope being used as an antigen, the T cells are CD8-positive T cells.

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: 489, or a variant amino acid sequence thereof.

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.

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, and 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.

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.

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 489.

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.

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)).

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.

By “aberrantly expressed” the inventors also mean that the polypeptide is over-expressed compared to levels of expression in normal tissues or that the gene is silent in the tissue from which the tumor is derived but in the tumor it is expressed. 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 4-fold or 6-fold the level present in normal tissue.

T cells may be obtained by methods known in the art, e.g. those described above.

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).

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.

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).

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.

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.

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.

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).

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 μg) and preferably not more than 3 mg/mL/peptide (=1500 μg). 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.

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.

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.

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.

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.

Since the peptides of the invention were isolated from lung cancer (including NSCLC and SCLC), the medicament of the invention is preferably used to treat lung cancer (including NSCLC and SCLC).

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.

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.

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 lung cancer (including NSCLC and SCLC) 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 lung cancers (including NSCLC and SCLC) tissues, the warehouse may contain HLA-A*02, HLA-A*01, HLA-A*03, HLA-A*24, HLA-B*07, HLA-B*08 and HLA-B*44 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.

TUMAPs for the warehouse are identified by using an integrated functional genomics approach combining gene expression analysis, mass spectrometry, and T-cell immunology (XPresident®). 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, lung cancer (including NSCLC and SCLC) 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 (lung cancer (including NSCLC and SCLC)) 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 lung cancer (including NSCLC and SCLC) patients.

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.

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.

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.

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.

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: (a1) 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.

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 (a1) 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.

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.

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.

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 ˜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 μm sterile filter. The final bulk solution is obtained.

Final bulk solution is filled into vials and stored at −20° C. until use. One vial contains 700 μL solution, containing 0.578 mg of each peptide. Of this, 500 μL (approx. 400 μg per peptide) will be applied for intradermal injection.

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 lung cancer (including NSCLC and SCLC) cells 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.

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 lung cancer (including NSCLC and SCLC). Presence of groups of peptides can enable classification or sub-classification of diseased tissues.

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.

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.

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.

FIGURES

FIGS. 1A through 1N show the over-presentation of various peptides in different cancer tissues (black dots). Upper part: Median MS signal intensities from technical replicate measurements are plotted as dots for single positive normal (grey dots) and tumor samples (black dots) on which the peptide was detected. Tumor and normal samples are grouped according to organ of origin, and box-and-whisker plots represent median, 25th and 75th percentile (box), and minimum and maximum (whiskers) of normalized signal intensities over multiple samples. Normal organs are ordered according to risk categories (blood cells, blood vessels, brain, liver, lung: high risk, grey dots; reproductive organs, breast, prostate: low risk, grey dots; all other organs: medium risk; grey dots). Lower part: The relative peptide detection frequency in every organ is shown as spine plot. Numbers below the panel indicate number of samples on which the peptide was detected out of the total number of samples analyzed for each organ. If the peptide has been detected on a sample but could not be quantified for technical reasons, the sample is included in this representation of detection frequency, but no dot is shown in the upper part of the figure. FIGS. 1A to 1B show the over-presentation of various peptides in HLA-A*24 cancer tissues compared to a panel of HLA-A*24 normal samples (N=19 for normal samples, N=94 for tumor samples). Tissues (from left to right): Normal samples: bloodvess (blood vessels); brain; heart; liver; lung; kidney; pituit (pituitary). Tumor samples: GBM: glioblastoma; GC: gastric cancer; HCC: hepatocellular carcinoma; NSCLCadeno (non-small cell lung cancer adenocarcinoma); NSCLCother (non-small cell lung cancer); NSCLCsquam (non-small cell lung cancer squamous cell); SCLC: small cell lung cancer. FIG. 1A) Gene symbol: URB1, Peptide: LYQEILAQL (SEQ ID NO.: 62), FIG. 1B) Gene symbol: CKAP5, Peptide: VYPASKMFPFI (SEQ ID NO.: 65). FIGS. 1C to 1D show the over-presentation of various peptides in HLA-A*02 cancer tissues compared to a panel of HLA-A*02 normal samples (N=469 for normal samples, N=528 for tumor samples). Tissues (from left to right): Normal samples: blood cells; bloodvess (blood vessels); brain; heart; liver; lung; adipose (adipose tissue); adren.gl. (adrenal gland); bile duct; bladder; BM (bone marrow); esoph (esophagus); eye; gallb (gallbladder); head&neck; kidney; large_int (large intestine); LN (lymph node); nerve; pancreas; parathyr (parathyroid gland); perit (peritoneum); pituit (pituitary); pleura; skel.mus (skeletal muscle); skin; small_int (small intestine); spleen; stomach; thyroid; trachea; ureter; breast; ovary; placenta; prostate; testis; thymus; uterus. Tumor samples: AML: acute myeloid leukemia; BRCA: breast cancer; CCC: cholangiocellular carcinoma; CLL: chronic lymphocytic leukemia; CRC: colorectal cancer; GBC: gallbladder cancer; GBM: glioblastoma; GC: gastric cancer; GEJC: stomach cardia esophagus, cancer; HCC: hepatocellular carcinoma; HNSCC: head-and-neck cancer; MEL: melanoma; NHL: non-hodgkin lymphoma; NSCLCadeno (non-small cell lung cancer adenocarcinoma); NSCLCother (non-small cell lung cancer); NSCLCsquam (non-small cell lung cancer squamous cell); OC: ovarian cancer; OSCAR: esophageal cancer; PACA: pancreatic cancer; PRCA: prostate cancer; RCC: renal cell carcinoma; SCLC: small cell lung cancer; UBC: urinary bladder carcinoma; UEC: uterine and endometrial cancer. FIG. 1C) Gene symbol: BMS1, Peptide: VLYDKDAVYV (SEQ ID NO.: 129), FIG. 1D) Gene symbol: GORASP2, Peptide: NLWGGQGLLGV (SEQ ID NO.: 130). FIGS. 1E to 1F show the over-presentation of various peptides in HLA-A*01 cancer tissues compared to a panel of HLA-A*01 normal samples (N=13 for normal samples, N=40 for tumor samples). Tissues (from left to right): Normal samples: blood cells; brain; heart; liver; lung. Tumor samples: GBM: glioblastoma; HCC: hepatocellular carcinoma; NSCLCadeno (non-small cell lung cancer adenocarcinoma); NSCLCother (non-small cell lung cancer); NSCLCsquam (non-small cell lung cancer squamous cell); SCLC: small cell lung cancer. FIG. 1E) Gene symbol: ZNF439, Peptide: LLDISQKNLY (SEQ ID NO.: 154), FIG. 1F) Gene symbol: MMP12, Peptide: SADDIRGIQSLY (SEQ ID NO.: 174). FIGS. 1G to 1H show the over-presentation of various peptides in HLA-A*03 cancer tissues compared to a panel of HLA-A*03 normal samples (N=12 for normal samples, N=28 for tumor samples). Tissues (from left to right): Normal samples: blood cells; bloodvess (blood vessels); brain; heart; liver; lung. Tumor samples: GBM: glioblastoma; GC: gastric cancer; NHL: non-hodgkin lymphoma; NSCLCadeno (non-small cell lung cancer adenocarcinoma); NSCLCother (non-small cell lung cancer); NSCLCsquam (non-small cell lung cancer squamous cell); SCLC: small cell lung cancer. FIG. 1G) Gene symbols: KRT81, KRT121P, KRT83, KRT85, KRT86, Peptide: KLAELEGALQK (SEQ ID NO.: 202), FIG. 1H) Gene symbol: NDC80, Peptide: SINKPTSER (SEQ ID NO.: 457). FIGS. 1I to 1J show the over-presentation of various peptides in HLA-B*07 cancer tissues compared to a panel of HLA-B*07 normal samples (N=13 for normal samples, N=36 for tumor samples). Tissues (from left to right): Normal samples: blood cells; bloodvess (blood vessels); brain; heart; liver; lung. Tumor samples: GBM: glioblastoma; NSCLCadeno (non-small cell lung cancer adenocarcinoma); NSCLCother (non-small cell lung cancer); NSCLCsquam (non-small cell lung cancer squamous cell); OC: ovarian cancer; SCLC: small cell lung cancer. FIG. 1I) Gene symbol: CTHRC1, Peptide: SPQRLRGLL (SEQ ID NO.: 291), FIG. 1J) Gene symbol: MANEA, Peptide: RPHKPGLYL (SEQ ID NO.: 475). FIGS. 1K to 1L show the over-presentation of various peptides in HLA-B*08 cancer tissues compared to a panel of HLA-B*08 normal samples (N=1 for normal samples, N=22 for tumor samples). Tissues (from left to right): Normal samples: lung. Tumor samples: GBM: glioblastoma; NSCLCadeno (non-small cell lung cancer adenocarcinoma); NSCLCother (non-small cell lung cancer); NSCLCsquam (non-small cell lung cancer squamous cell); SCLC: small cell lung cancer. FIG. 1K) Gene symbol: VPS13B, Peptide: DIYQRALNL (SEQ ID NO.: 315), FIG. 1L) Gene symbol: ARID4A, Peptide: LVKVKVLL (SEQ ID NO.: 317). FIGS. 1M to 1N show the over-presentation of various peptides in HLA-B*44 cancer tissues compared to a panel of HLA-B*44 normal samples (N=15 for normal samples, N=25 for tumor samples). Tissues (from left to right): Normal samples: brain; heart; liver; lung. Tumor samples: GBM: glioblastoma; NSCLCadeno (non-small cell lung cancer adenocarcinoma); NSCLCother (non-small cell lung cancer); NSCLCsquam (non-small cell lung cancer squamous cell); SCLC: small cell lung cancer. FIG. 1M) Gene symbol: NUP155, Peptide: SEKGVIQVY (SEQ ID NO.: 362), FIG. 1N) Gene symbol: CLSPN, Peptide: SEIGKAVGF (SEQ ID NO.: 489).

FIGS. 2A through 2N show exemplary exon expression profile of source genes of the present invention that are over-expressed in different cancer samples. Tumor (black dots) and normal (grey dots) samples are grouped according to organ of origin, and box-and-whisker plots represent median, 25th and 75th percentile (box), and minimum and maximum (whiskers) RPKM values. Normal organs are ordered according to risk categories. FPKM=fragments per kilobase per million mapped reads. Normal samples: blood cells; bloodvess: blood vessel; brain; heart; liver; lung; adipose: adipose tissue; adren.gl.: adrenal gland; bile duct; bladder; BM: bone marrow; cartilage; esoph: esophagus; eye; gallb: gallbladder; head and neck; kidney; large_int: large intestine; LN: lymph node; nerve; pancreas; parathyr: parathyroid; perit: peritoneum; pituit: pituitary; pleura; skel.mus: skeletal muscle; skin; small_int: small intestine; spleen; stomach; thyroid; trachea; ureter; breast; ovary; placenta; prostate; testis; thymus; uterus. Tumor samples: AML: acute myeloid leukemia; BRCA: breast cancer; CCC: cholangiocellular carcinoma; CLL: chronic Iymphocytic leukemia; CRC: colorectal cancer; GBC: gallbladder cancer; GBM: glioblastoma; GC: gastric cancer; HCC: hepatocellular carcinoma; HNSCC: head-and-neck cancer; MEL: melanoma; NHL: non-hodgkin lymphoma; NSCLCadeno: non-small cell lung cancer adenocarcinoma; NSCLCother: non-small cell lung cancer; NSCLCsquam: non-small cell lung cancer squamous cell; OC: ovarian cancer; OSCAR: esophageal cancer; PACA: pancreatic cancer; PRCA: prostate cancer; RCC: renal cell carcinoma; SCLC: small cell lung cancer; UBC: urinary bladder carcinoma; UEC: uterine and endometrial cancer. FIG. 2A) Gene symbol: ADAMTS12, Peptide: QYDPTPLTW (SEQ ID No.: 1), FIG. 2B) Gene symbol: MMP12, Peptide: VWSNVTPLKF (SEQ ID No.: 2), FIG. 2C) Gene symbol: MMP12, Peptide: YVDINTFRL (SEQ ID No.: 84), FIG. 2D) Gene symbol: KIF26B, Peptide: TLYPYQISQL (SEQ ID No.: 87), FIG. 2E) Gene symbol: CT83, Peptide: NTDNNLAVY (SEQ ID No.: 164), FIG. 2F) Gene symbol: LAMA1, Peptide: VSDSECLSRY (SEQ ID No.: 189), FIG. 2G) Gene symbol: KIF26B, Peptide: KVKDTPGLGK (SEQ ID No.: 203), FIG. 2H) Gene symbol: SP6, Peptide: SLDGAARPK (SEQ ID No.: 205), FIG. 2I) Gene symbol: PRAME, Peptide: SPSVSQLSVL (SEQ ID No.: 220), FIG. 2J) Gene symbol: MMP1, Peptide: NPFYPEVEL (SEQ ID No.: 222), FIG. 2K) Gene symbol: NLRP2, Peptide: FNKRKPLSL (SEQ ID No.: 298), FIG. 2L) Gene symbol: KIF26B, Peptide: VASPKHCVL (SEQ ID No.: 300), FIG. 2M) Gene symbols: MAGEA3, MAGEA6, Peptide: MEVDPIGHVYIF (SEQ ID No.: 320), FIG. 2N) Gene symbol: MMP12, Peptide: QEMQHFLGL (SEQ ID No.: 326).

FIG. 3A and FIG. 3B show exemplary results of peptide-specific in vitro CD8+ T cell responses of a healthy HLA-A*02+ donor. CD8+ T cells were primed using artificial APCs coated with anti-CD28 mAb and HLA-A*02 in complex with SeqID No 520 peptide (KIQEMQHFL, Seq ID NO: 520) (FIG. 3A, left panel). After three cycles of stimulation, the detection of peptide-reactive cells was performed by 2D multimer staining with A*02/SeqID 520 (FIG. 3A). Right panel (FIG. 3B) 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.

FIG. 4A and FIG. 4B show exemplary results of peptide-specific in vitro CD8+ T cell responses of a healthy HLA-A*24+ donor. CD8+ T cells were primed using artificial APCs coated with anti-CD28 mAb and HLA-A*24 in complex with SeqID No 504 peptide (FIG. 4A, left panel). After three cycles of stimulation, the detection of peptide-reactive cells was performed by 2D multimer staining with A*24/SeqID No 504 (VYEKNGYIYF, Seq ID NO: 504) (FIG. 4A). Right panel (FIG. 4B) shows control staining of cells stimulated with irrelevant A*24/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.

FIG. 5A and FIG. 5B show exemplary results of peptide-specific in vitro CD8+ T cell responses of a healthy HLA-A*01+ donor. CD8+ T cells were primed using artificial APCs coated with anti-CD28 mAb and HLA-A*01 in complex with SeqID No 153 peptide (KLDRSVFTAY, Seq ID NO: 153) (FIG. 5A, left panel) and SeqID No 173 peptide (RTEFNLNQY, Seq ID NO: 173) (FIG. 5B, left panel), respectively. After three cycles of stimulation, the detection of peptide-reactive cells was performed by 2D multimer staining with A*01/SeqID No 153 (FIG. 5A) or A*01/SeqID No 173. Right panels (FIGS. 5A and 5B) show control staining of cells stimulated with irrelevant A*01/peptide complexes. Viable single 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.

FIG. 6A and FIG. 6B show exemplary results of peptide-specific in vitro CD8+ T cell responses of a healthy HLA-A*02+ donor. CD8+ T cells were primed using artificial APCs coated with anti-CD28 mAb and HLA-A*02 in complex with SeqID No 89 peptide (ILSTTMVTV, Seq ID NO: 89) (FIG. 6A, left panel) and SeqID No 88 peptide (VQMVITEAQKV, Seq ID NO: 88) (FIG. 6B, 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 89 (FIG. 6A) or A*02/SeqID No 88 (FIG. 6B). Right panels (FIGS. 6A and 6B) show control staining of cells stimulated with irrelevant A*02/peptide complexes. Viable single 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.

FIG. 7A and FIG. 7B show exemplary results of peptide-specific in vitro CD8+ T cell responses of a healthy HLA-A*03+ donor. CD8+ T cells were primed using artificial APCs coated with anti-CD28 mAb and HLA-A*03 in complex with SeqID No 208 peptide (GLASRILDAK, Seq ID NO: 208) (FIG. 7A, left panel) and SeqID No 210 peptide (ATSGVPVYK, Seq ID NO: 210) (FIG. 7B, left panel), respectively. After three cycles of stimulation, the detection of peptide-reactive cells was performed by 2D multimer staining with A*03/SeqID No 208 (FIG. 7A) or A*03/SeqID No 210 (FIG. 7B). Right panels (FIGS. 7A and 7B) show control staining of cells stimulated with irrelevant A*03/peptide complexes. Viable single 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.

FIG. 8A and FIG. 8B show exemplary results of peptide-specific in vitro CD8+ T cell responses of a healthy HLA-A*24+ donor. CD8+ T cells were primed using artificial APCs coated with anti-CD28 mAb and HLA-A*24 in complex with SeqID No 15 peptide (KYALLLQDL, Seq ID NO: 15) (FIG. 8A, left panel) and SeqID No 11 peptide (YYSKSVGFMQW, Seq ID NO: 11) (FIG. 8B, left panel), respectively. After three cycles of stimulation, the detection of peptide-reactive cells was performed by 2D multimer staining with A*24/SeqID No 15 (FIG. 8A) or A*24/SeqID No 11 (FIG. 8B). Right panels (FIGS. 8A and 8B) show control staining of cells stimulated with irrelevant A*24/peptide complexes. Viable single 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.

FIG. 9A and FIG. 9B show exemplary results of peptide-specific in vitro CD8+ T cell responses of a healthy HLA-B*07+ donor. CD8+ T cells were primed using artificial APCs coated with anti-CD28 mAb and HLA-B*07 in complex with SeqID No 225 peptide (LPFDGPGGIL, Seq ID NO: 225) (FIG. 9A, left panel) and SeqID No 248 peptide (IPNWARQDL, Seq ID NO: 248) (FIG. 9B, left panel), respectively. After three cycles of stimulation, the detection of peptide-reactive cells was performed by 2D multimer staining with B*07/SeqID No 225 (FIG. 9A) or B*07/SeqID No 248 (FIG. 9B). Right panels (FIGS. 9A and 9B) show control staining of cells stimulated with irrelevant B*07/peptide complexes. Viable single 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.

FIG. 10A and FIG. 10B show exemplary results of peptide-specific in vitro CD8+ T cell responses of a healthy HLA-B*08+ donor. CD8+ T cells were primed using artificial APCs coated with anti-CD28 mAb and HLA-B*08 in complex with SeqID No 299 peptide (MAQFKEISL, Seq ID NO: 299) (FIG. 10A, left panel) and SeqID No 297 peptide (RAQLKLVAL, Seq ID NO: 297) (FIG. 10B, left panel), respectively. After three cycles of stimulation, the detection of peptide-reactive cells was performed by 2D multimer staining with B*08/SeqID No 299 (FIG. 10A) or B*08/SeqID No 297 (FIG. 10B). Right panels (FIGS. 10A and 10B) show control staining of cells stimulated with irrelevant B*08/peptide complexes. Viable single 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.

FIG. 11A and FIG. 11B show exemplary results of peptide-specific in vitro CD8+ T cell responses of a healthy HLA-B*44+ donor. CD8+ T cells were primed using artificial APCs coated with anti-CD28 mAb and HLA-B*44 in complex with SeqID No 325 peptide (QEQDVDLVQKY, Seq ID NO: 325) (FIG. 11A, left panel) and SeqID No 331 peptide (EDAQGHIW, Seq ID NO: 331) (FIG. 11B, left panel), respectively. After three cycles of stimulation, the detection of peptide-reactive cells was performed by 2D multimer staining single cells were gated for CD8+ lymphocytes with B*44/SeqID No 325 (FIG. 11A) or B*44/SeqID No 331 (FIG. 11B). Right panels (FIGS. 11A and 11B) show control staining of cells stimulated with irrelevant B*44/peptide complexes. Viable single 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

Patients' tumor tissues were obtained from: Asterand (Detroit, Mich., USA & Royston, Herts, UK); Bio-Options Inc. (Brea, Calif., USA); Geneticist Inc. (Glendale, Calif., USA); University Hospital Heidelberg (Heidelberg, Germany); ProteoGenex Inc. (Culver City, Calif., USA); Tissue Solutions Ltd (Glasgow, UK); University Hospital Munich (Munich, Germany). Normal tissues were obtained from Asterand (Detroit, Mich., USA & Royston, Herts, UK); Bio-Options Inc. (Brea, Calif., USA); BioServe (Beltsville, Md., USA); Capital BioScience Inc. (Rockville, Md., USA); Centre for Clinical Transfusion Medicine Tuebingen (Tubingen, Germany); Geneticist Inc. (Glendale, Calif., USA); Kyoto Prefectural University of Medicine (KPUM) (Kyoto, Japan); Osaka City University (OCU) (Osaka, Japan); ProteoGenex Inc. (Culver City, Calif., USA); Tissue Solutions Ltd (Glasgow, UK); University Hospital Geneva (Geneva, Switzerland); University Hospital Heidelberg (Heidelberg, Germany); University Hospital Tubingen (Tubingen, Germany); University Hospital Munich (Munich, Germany). 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° C. or below.

Isolation of HLA Peptides from Tissue Samples

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, the HLA-DR specific antibody L243 and the HLA DP specific antibody B7/21, CNBr-activated sepharose, acid treatment, and ultrafiltration.

Mass Spectrometry Analyses

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 μm i.d.×250 mm) packed with 1.7 μm 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 at a fixed false discovery rate (q≤0.05) and additional manual control. In cases where the identified peptide sequence was uncertain it was additionally validated by comparison of the generated natural peptide fragmentation pattern with the fragmentation pattern of a synthetic sequence-identical reference peptide.

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 cancer samples to a baseline of normal tissue samples. Presentation profiles of peptides exemplary over-presented or exclusively presented on tumors are shown in FIGS. 1A through 1N.

Table 8 shows the presentation on various cancer entities for selected peptides, and thus the particular relevance of the peptides as mentioned for the diagnosis and/or treatment of the cancers as indicated (e.g. peptide SEQ ID No. 3 for hepatocellular carcinoma, peptide SEQ ID No. 11 for melanoma, ovarian cancer and uterine cancer).

TABLE 8

Overview of presentation of selected tumor-associated peptides

of the present invention across entities.

SEQ ID

No.
Sequence
Peptide Presentation on cancer entities

3
YLEKFYGL
HCC

6
KYKDYFPVI
HCC

9
RILRFPWQL
MEL

11
YYSKSVGFMQW
MEL, OC, UEC

13
HYTYILEVF
GC, UEC

14
SYSSCYSF
GC

18
DYIGSVEKW
PRCA

19
ILKEDPFLF
OC, RCC

21
SYEVRSTF
CCC, OC, PRCA

22
TQPGDWTLF
MEL

23
KFIISDWRF
MEL

24
MYPDLSELLM
AML, GBM, OC, UEC

26
KTPTNYYLF
GC

28
YYSIISHTL
HCC

31
QYQNVLTLW
GBM, GC, HCC, MEL, NHL, PRCA, RCC, UEC

32
SLPDLTPTF
PRCA

33
KSSVIASLLF
GBM

34
MQPRMFFLF
AML, GBM, HCC, MEL, UEC

36
KQMEDGHTLF
AML, OC

37
QWPWQASLQF
GC

38
KYTNWKAFL
AML, HCC

41
VIYFMGAIF
HCC, PRCA, UEC

43
IQMDEPMAF
AML, MEL, OC

44
AYLSAVGTF
AML, GC, MEL

45
KYFVPPQLF
GC

47
KYADYFLEV
GBM, OC, UEC

48
VFIDHPVHLKF
UEC

50
SYPELVKMVW
AML, GC, HCC

51
KYALLLQEL
AML, CLL, GBM, GC, HCC, MEL, OC, PRCA,

RCC, UEC

52
KYMKIFHKF
OC, UEC

53
KYITNLEDL
PRCA

54
LLIKLLQTF
AML, GBM, MEL, OC, PRCA, RCC

55
RWMDQRLVF
GC, HCC, MEL, UEC

56
VYMIEPLEL
GBM, NHL

57
YPSIIQEF
GBM, RCC

58
QFAAPLRGIYF
GBM, HCC

59
KYSTTFFMV
GBM

60
TYLSIFDQL
AML, GC, HCC, OC

61
NYAENILTL
AML, GBM, GC, MEL

62
LYQEILAQL
AML, GBM, GC, HCC, MEL, PRCA, RCC

63
VMPSDSFFF
MEL, NHL, OC, UEC

64
NYAIFDEGHML
GBM, GC

65
VYPASKMFPFI
GBM, GC, HCC, MEL, NHL, OC, UEC

66
IYFRDSSFL
AML, GC, MEL

67
RYPGKFYRV
OC

68
IYQQIIQTY
GC, MEL, UEC

69
IMPEKFEFW
AML, GC, MEL, NHL, UEC

70
PYTNYTFDF
GC, MEL

71
SYMVLAPVF
MEL

72
RYEGILYTI
GC, HCC, NHL, PRCA

73
SYIGLPLTL
GC, HCC, RCC

74
VYDQYFITL
AML, PRCA

76
VVYGWHFPEL
AML, GC, HCC, RCC, UEC

77
AYTLLGHEFV
GC, MEL, OC

78
TWFPKTPMLF
AML, GBM, GC, HCC, MEL, UEC

79
RYLADLPTL
GC, HCC, OC, UEC

80
YYSPLRDLL
MEL

82
RFLPSPVVI
AML, GC, HCC, MEL, PRCA, UEC

83
TYCQNIKEF
AML, OC, PRCA, UEC

84
YVDINTFRL
HCC

86
FVIDGFDEL
CRC, GC, NHL, OSCAR

87
TLYPYQISQL
HCC, OSCAR

90
FLLMHPSI
CLL, HCC, RCC

91
FALPGLLHA
GC, HCC, NHL, OSCAR, RCC

92
NLRDLLSEV
HCC

93
TLQEKILQV
CLL, GBM, NHL

95
ITIGVLARV
CRC, PACA

96
HLVGGLHTV
AML, BRCA, CRC, GC, MEL, OC, PRCA

97
VLALVNSTV
CLL

98
LQSSGLTLLL
GBM, OC, PRCA

99
FLKEKVPGI
CLL, GC, MEL, NHL

100
RQYPTPFQL
AML, CLL, CRC, GBM, NHL, OC, RCC

101
FIISDWRFVL
HNSCC

102
SLLEQAIAL
GC, HCC, NHL, OC, UEC

103
FLYYPDPVL
GBC, HCC, MEL, NHL

105
SLLTHIPTA
AML, CRC, HNSCC, MEL, OC, OSCAR, RCC,

UBC, UEC

106
FIIDTTYPAYV
CRC, OC, OSCAR

107
LLQGAIESV
BRCA, CLL, CRC, HNSCC, MEL, NHL, UBC,

UEC

108
MIIALSLYI
AML, BRCA

110
LLADFQALL
RCC

111
ALCLLLHLL
AML, GBC, HCC, HNSCC, RCC

113
AVLTGLVEV
BRCA, CLL, CRC, GC, HCC, NHL, OSCAR,

RCC, UEC

114
ILDERQVLL
AML, BRCA, CRC, GBC, GC, HCC, HNSCC,

MEL, NHL, OC, OSCAR, PACA, UBC, UEC

115
MLLETQDALYV
HNSCC

116
VLMEENSKL
GBM

117
FLDPNARPLV
NHL, OC

118
ALSSVLHSI
AML, BRCA, CRC, GBC, HCC, HNSCC, MEL,

NHL, OC, OSCAR, PACA, RCC, UBC

119
RTADITVTV
AML, CRC, UBC

120
ALLANLPAV
GBC, GC, OC, PACA

121
ALVDTLTGI
HNSCC, NHL, UEC

122
ALLEMFPEITV
BRCA, OC, PRCA

123
LMAFFLAVV
CCC, HCC, NHL, OSCAR, RCC

124
SVASVLLYL
AML, BRCA, CLL, HCC, HNSCC, NHL, OC

125
VLQPFLPSI
AML, BRCA, CCC, CLL, CRC, HCC, HNSCC,

MEL, NHL, OC, RCC

126
FLSTVTSV
CCC, GBM, HCC, HNSCC, MEL, NHL, OSCAR,

PACA, RCC, UBC, UEC

127
GLDGSLVFL
AML, CLL, CRC, GBM, HCC, HNSCC, MEL,

NHL, OC, OSCAR, UBC

128
FLGTTPTL
AML, CLL, GBM, HNSCC, NHL, OC, UBC, UEC

129
VLYDKDAVYV
AML, CLL, CRC, HNSCC, NHL, OC, UBC, UEC

130
NLWGGQGLLGV
BRCA, GBC, GBM, GC, HCC, OC, PRCA, UEC

131
LLKEFVQRV
BRCA, CRC, HCC, HNSCC, OC, OSCAR

132
ALWLVDPLTV
CLL, CRC, GBM, HCC

133
MTLPVDAVISV
CLL, CRC, HCC, HNSCC, NHL, PRCA, UEC

134
AAEIGDKSWLY
GC, MEL, NHL, UEC

135
ASEDSVLLY
GBM, GC, MEL, NHL, OSCAR, PRCA,

136
ATDLVVLDRY
GBM, GC, HCC, MEL, NHL, OSCAR, PRCA,

UEC

137
ATSKFMEFY
GBM, MEL, OC, PRCA, UEC

139
ECDMAFHIY
MEL, OC

140
ESDREELNY
GC, PRCA

141
ESDVGVVVY
GBM, GC

142
EVAEPSVLFDLY
GC, MEL, NHL, OC, UEC

144
FLDSQNLSAY
GC

145
FVDKPVAY
GBM, GC, MEL

146
GLNTGSALSY
GC, OC

148
GTEFTTILY
GC, NHL, OSCAR, PRCA

149
GTEFTTVLY
GC, HNSCC, MEL, OSCAR, PRCA

150
GTELLSLVY
GC, MEL, NHL, OC, PRCA, UEC

152
HTDSLHLLI
GC, MEL, OC

154
LLDISQKNLY
GBM, NHL, PRCA

155
LLDPNPHMY
PRCA

156
LLDSLREQY
GC, NHL, OSCAR

157
LMDRPIFY
GBM, GC, MEL, NHL

159
LSDTSVIQFY
GBM, GC, HCC, MEL, NHL, PRCA

160
LTEAVLNRY
OC

161
LVDDGTHGQY
GBM, GC, MEL

162
LVDNSIRELQY
GC, HCC, MEL, NHL, OC, UEC

163
NSDSSLTLREFY
HCC, PRCA

166
NTQITDIGRY
MEL

167
QSDPGTSVLGY
GBM

169
RLDTPLYFSY
MEL, OC

170
RSDDTAVYY
CLL, GC, HCC, NHL, PRCA, UEC

172
RTDSCSSAQAQY
MEL

173
RTEFNLNQY
GBC, GC, MEL, UEC

177
SSDEVNFLVY
GC, MEL, OC, UEC

178
SSDSSTLPKL
GC, OC, PRCA

179
STAKSATWTY
PRCA

180
STDPWIQMAY
GBM, GC, MEL

181
TADGKTYYY
GBM, HCC, MEL, PRCA

182
TDYHVRVY
GBM, PRCA

184
TSAHPEDSSFY
GC, NHL, PRCA

186
TTDIIEKY
GC, MEL,

187
VADLHLYLY
GC, MEL, OC, PRCA, RCC

190
VTDGINPLIDRY
MEL

191
VTDGSLYEGVAY
GC, MEL, UEC

192
VTEESFDSKFY
GC

193
VTEFSLNTY
GBC, GC, MEL, OC, OSCAR, UEC

196
WMFFVINY
UEC

197
YADTVRPEFY
OC

198
YLDPVQRDLY
GBM, GC, HCC, MEL, NHL, OC, UEC

202
KLAELEGALQK
MEL, OC, UEC

204
AVFDKFIRY
GBM

207
RSFNGLLTMY
MEL, OC

210
ATSGVPVYK
UEC

211
TVNPVAIHK
GBM, NHL, OC, PRCA, UEC

212
KAYEQVMHY
UEC

213
LNINMTSPMGTK
GBM, GC, MEL, NHL, PACA

214
RTMSEAALVRK
GC, NHL, OC, PRCA, UEC

215
MMFSGPQILKL
MEL

216
KLYAWELAF
AML, GBM, MEL, OC, PRCA

217
RILNQILYY
AML, GBM, GC, HCC, MEL, NHL, PRCA, UEC

218
KTLVAELLILK
AML, NHL, UEC

219
RLRSSLVFK
UEC

220
SPSVSQLSVL
UEC

235
MPLKHYLLL
MEL, NHL, OC, UEC

237
RPAATAVISL
GBM, NHL, OC

244
FPYVRDFVM
GBC, MEL, NHL, OC, UEC

247
RALLARLLL
NHL

251
VPRSSGQTV
BRCA, GBM, UEC

255
MPLLENLYL
OC, UEC

256
SPRVPSIEL
NHL

259
RPPAAGLRGISL
GBM

260
YPQHPGLNA
BRCA, GBM, GC, NHL

262
SAYPQRLEI
GC

263
HPAPYGDLL
UEC

271
MPLPWSLALP
MEL

273
MPLLWLRGF
UEC

274
TPYQEHVAL
OC

275
APHPPLSVV
AML, BRCA, MEL

276
LPRAGGAFL
NHL, OC, RCC, UEC

277
MPLFEPRVF
OC, UEC

278
HPMIDINGIIVF
UEC

280
VPISEEGTPVL
MEL, OC, PRCA, UEC

281
RPRAPVTPA
GBM

282
MPQIETRVIL
UEC

283
RPHSLSSEL
AML, NHL

284
FPVTSIFHTF
MEL, OC, UEC

285
FPSFLTNSL
AML

286
VPTLRSEL
OC

288
FPQKFIDLL
UEC

289
VPENHSVAL
UEC

290
APYRPPDISL
BRCA

292
SPQRLRGLLL
NHL

293
RPRSALPRLLLP
NHL, UEC

295
KPEGTRIAV
NHL, UEC

296
MPMQDIKM
UEC

300
VASPKHCVL
OC

301
YMHKLLVL
AML, NHL, OC, PRCA, UEC

305
ALKLRVAVL
NHL

306
ILKVKVGL
MEL, OC

308
MLKQKVEEL
OSCAR

311
EIRIRVVQM
MEL, NHL, OC, PRCA

313
ELKKKEYEEL
NHL

314
AIISRLVAL
NHL, OSCAR, UBC

316
VIKEKALTL
NHL, OC, PRCA, RCC

318
EAAIRSVEL
GBM, MEL, NHL, OC

321
AEMLESVIKNY
NHL

322
KEVDPAGHSY
NHL

323
SEFMQVIF
NHL

328
FEYDFLLQRI
UEC

330
KEGDLGGKQW
NHL

335
KELEATKQY
MEL, NHL

337
TENRYCVQL
HCC

342
HEFSSPSHL
NHL

343
TEFTTVLY
GBM, NHL, PRCA

345
IEFIHPQAF
GBM, GC, NHL, PRCA

347
ALNPYQYQY
UEC

348
AEIQGNINHV
UEC

351
EEVNYINTF
AML, MEL, NHL, OC

354
TEDPTILRI
GC, HCC, OC, PRCA, UEC

356
EEGRVYLF
GBM, PRCA

357
RELENCFQIQ
UEC

359
DELFSIALY
NHL

363
AELDKLTSV
GBM, UEC

366
AENLFRAF
GBM, NHL, OC

367
GEVHPSEMI
UEC

368
GEFPVRVQV
AML, GC, OC, UEC

370
YEDLSQKY
GBM, NHL, OC

371
GELALKKKI
UEC

372
TEGIIMKDF
OC, PRCA, RCC, UEC

373
MEMQKSPVF
NHL, OC

374
DEVNFLVY
CCC, GBC, GBM, NHL, OC, PRCA

375
VYSDLHAFYY
GBM, GC, HCC, MEL, PRCA

376
KYVKDFHKF
AML, OC, PRCA, UEC

377
VYVGAVNRI
GC, HCC, PRCA

378
KFLGPAEHLTF
OC

379
NYIVPDKQIF
GBM, GC, HCC, MEL, OC, PRCA

380
VFQEKHHVI
PRCA

381
TYSKKHFRI
MEL, OC

382
IYHSHHPTL
AML, MEL, NHL, OC, UEC

383
RYKQDVERF
AML, MEL, OC, PRCA, UEC

384
KYVKVFDKF
AML, UEC

385
MYINEVERL
GBM, MEL, OC, PRCA, UEC

386
VYNDHSIYVW
AML, GBM, HCC, MEL, NHL, PRCA, UEC

387
RWLPQKNAAQF
AML, GC, HCC, MEL, OC, RCC, UEC

388
FSIPEGALVAV
AML, CCC, CLL, CRC, GBC, GC, HCC,

HNSCC, MEL, NHL, OC, OSCAR, PRCA, RCC,

UBC, UEC

389
TLMEQPLTTL
AML, BRCA, CRC, HCC, HNSCC, NHL, OC,

PRCA, UEC

390
HIMPTVHTV
BRCA, CLL, GBM, HCC, HNSCC, MEL, NHL,

OC, OSCAR, UBC, UEC

391
SLIDMRGIETV
BRCA, CLL, GBM, HCC, HNSCC, OC, UBC

392
SLFKDQMEL
AML, BRCA, CLL, CRC, GBM, HCC, MEL, NHL,

OC, PRCA, RCC, UBC, UEC

393
ILLPYLQTL
AML, BRCA, CLL, CRC, GBM, HCC, HNSCC,

NHL, OC

394
ASEAEMRLFY
GBM, GC, MEL, NHL

395
ASEASRLAHY
GBM, GC, NHL, PRCA, UEC

396
ASEFGNHYLY
GBM, GC, MEL, UEC

397
ASEITSKGASLY
GBM, GC, HCC, MEL, OC, PRCA

398
ASEQQALHTVQY
GBM, GC, MEL, NHL, PRCA, UEC

399
ATDIPCLLY
MEL

400
ATDISRQNEY
GBM, GC, NHL, OC

401
DSDESYMEKSLY
GC

402
DTDSQRLAY
GBM, GC, MEL

403
ELDSKVEVLTY
GBM, GC, MEL, OC, PRCA

404
ETARKFLYY
GBM

405
ETEEGIYWRY
GC

406
ETEQTKFWDY
GBM, GC, MEL, OC, RCC, UEC

407
FSDNDKLYLY
GBM, GC, MEL, NHL, PRCA, UEC

408
FTEQWTDGY
GBM, GC, OC, OSCAR, PRCA,

409
FVDPLVTNY
GBM, GC, HCC, MEL, NHL, OC, OSCAR,

PRCA, RCC

410
GSDHQSPSSSSY
GBM, GC, MEL, OC, PRCA,

411
GTVYEDLRY
GBM, GC, HCC, MEL, NHL, OC, OSCAR

412
ILDEVIMGY
GBM, GC, MEL, NHL, OC, OSCAR

413
ISDRYYTALY
GBM, GC, PRCA, UEC

414
KTDESLTKY
GC, NHL, PRCA

415
LLDPRSYHTY
GC, NHL

416
LLDTAQKNLY
GBM, NHL, PRCA

417
LLEDKHFQSY
GBM, GC, HCC, MEL, NHL, OC, PRCA, UEC

418
LSDPSGPKSY
GBM, HCC, PRCA

419
LSELKPMSY
GBM, GC, HCC, MEL, OSCAR, PRCA, RCC,

UEC

420
LTEDKETLQY
GC, HCC, MEL, NHL, PRCA

421
LTELLERAAFY
GC, MEL, NHL, UEC

422
MIDVTKSYY
GBM, GC, MEL, NHL, OC, OSCAR, PRCA,

UEC

423
NLDAVHDITVAY
GC, MEL, PRCA, UEC

424
NLDEEKQLLY
MEL, PRCA

425
NLDIIQQEY
GBM, GC, HCC, MEL, NHL, OC, OSCAR,

PRCA, UEC

426
NLDQATRVAY
NHL

427
NSDEQKITEMVY
GC

428
NSELSCQLY
GBM, GC, MEL, RCC

429
NTEDSSMSGYLY
GC, MEL,

430
NTEGLHHLY
GBM, HCC, MEL, PRCA

431
NTSDMMGRMSY
GC, MEL, NHL, OC,

432
NVDPVQHTY
GBM, GC, HCC, HNSCC, MEL, NHL, OC,

OSCAR, PRCA, RCC, UEC

433
QIDTGENLY
GC, MEL

434
QTDCAPNNGY
GBM, GC, MEL, PRCA

435
QTDDTWRTEY
GBM, GC, MEL, NHL, PRCA

436
QTETGTPYMLY
GBM, GC, MEL, NHL, OC, OSCAR, PRCA,

UEC

437
STDGKHWWEY
GC, MEL, NHL, PRCA

438
STDNFNCKY
GC, HCC, MEL

439
TLDAGKFQIY
GC, HCC, MEL, NHL, PRCA, UEC

440
TLDENPGVRY
GBM, GC, HCC, MEL, NHL, PRCA, UEC

441
TLDSALNAASYY
GBM, GC, MEL, NHL, PRCA, RCC

442
TSDFSRFTNY
GBM

443
TTDFPSESSFEY
GC, MEL, NHL, OC, PRCA, UEC

444
TTDTVIRSY
GC, MEL, UEC

445
VLDQGKITEY
GBM, HCC

446
VTAQVVGTERY
GC, MEL

447
VVDEDHELIY
GBM

448
YLDIPNPRY
GBM, MEL, RCC

449
YLDRGTGNVSFY
GBM, GC, HCC, MEL, PRCA, RCC

450
YSDDGQKWTVY
MEL

451
YSDSLVQKGY
GBM, GC, HCC, OC, PRCA, UEC

452
YVDAVLGKGHQY
GBM, GC, MEL, NHL, OC, PRCA, UEC

453
AINTSIKNK
PRCA

454
KVYTPSISK
GBM, HCC, MEL, UEC

455
RIADIFVKK
GC, MEL, NHL, OC, UEC

456
SMFTAILKK
AML, MEL, NHL, OC, UEC

457
SINKPTSER
GBM

458
GIADFVLKY
AML, BRCA, GBM, MEL, NHL, UEC

461
RPILIIVTL
NHL

464
YPRPGTPAA
AML, GC, MEL, NHL, OC, RCC

465
VPRPIFSQL
NHL

468
SPMYGQAGL
RCC

469
YPENGVVQM
AML, OC

470
SPNSYFRVL
RCC

471
KPRPDVTNEL
NHL

472
NPRATDAQL
AML

473
LPRALLSSL
NHL, OC

474
LPRLLPAL
AML, NHL

476
AEEEIMKKI
NHL

477
QENSYQSRL
OC

479
AEIQPQTQV
UEC

480
GEVSGLTKDF
MEL, NHL, OC

481
RELQHEHSL
OC

482
TEREWADEW
AML, MEL, NHL, OC, RCC

483
EENDQSTHKW
MEL, NHL, OC, RCC, UEC

484
AEVGFVRFF
AML, MEL, NHL, OC

485
SEIEDSTKQVF
MEL, NHL, OC

486
SEDDPILQI
NHL, OC, UEC

487
AEDQLHHSF
AML, NHL

488
TEFPIIKMY
AML, MEL, NHL, OC, PRCA

AML = acute myeloid leukemia, BRCA = breast cancer, CCC = bile duct cancer, GBM = brain cancer, CLL = chronic lymphocytic leukemia, CRC = colorectal carcinoma, OSCAR = esophageal cancer, GBC = gallbladder adenocarcinoma, GC = gastric cancer, HNSCC = head and neck squamous cell carcinoma, HCC = hepatocellular carcinoma, MEL = melanoma, NHL = non-Hodgkin lymphoma, OC = ovarian cancer, PACA = pancreatic cancer, PRCA = prostate cancer and benign prostate hyperplasia, RCC = renal cell carcinoma, UBC = urinary bladder cancer, UEC = uterine cancer.

Example 2

Expression Profiling of Genes Encoding the Peptides of the Invention

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

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.

Total RNA from healthy human tissues for RNASeq experiments was obtained from: Asterand (Detroit, Mich., USA & Royston, Herts, UK); Bio-Options Inc. (Brea, Calif., USA); BioCat GmbH (Heidelberg, Germany); BioServe (Beltsville, Md., USA); Capital BioScience Inc. (Rockville, Md., USA); Geneticist Inc. (Glendale, Calif., USA); Heidelberg University Hospital (Thoraxklinik, Heidelberg, Germany); Istituto Nazionale Tumori “Pascale” (Naples, Italy); ProteoGenex Inc. (Culver City, Calif., USA).

Total RNA from tumor tissues for RNASeq experiments was obtained from: Asterand (Detroit, Mich., USA & Royston, Herts, UK); Geneticist Inc. (Glendale, Calif., USA); ProteoGenex Inc. (Culver City, Calif., USA); Tissue Solutions Ltd (Glasgow, UK); University Hospital Bonn (Bonn, Germany); University Hospital Tubingen (Tubingen, Germany).

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

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.

Exemplary expression profiles of source genes of the present invention that are highly over-expressed or exclusively expressed in lung cancer (including NSCLC and SCLC) are shown in FIGS. 2A through 2N. Expression scores for further exemplary genes are shown in Table 9.

TABLE 9

Expression scores.

SEQ

ID

Gene Expression

No

Sequence
NSCLCadeno
NSCLCsquam
NSCLCother
SCLC

1

QYDPTPLTW
+++
+++
+
+

2

VWSNVTPLKF
+++
+++
+
+++

3

YLEKFYGL
+++
+++

+++

4

SYEKVINYL

+++

+++

5

RYMKKDYLI

+++

6

KYKDYFPVI
+
+++

++

7

VQQWSVAVF

+++

8

PFLPPAACFF

+++

9

RILRFPWQL
+++
++

10

VWSDVTPLNF
++
+++

11

YYSKSVGFM

++

QW

12

STIRGELFFF
++
++

13

HYTYILEVF
++
++

14

SYSSCYSF

++

15

KYALLLQDL

+

++

16

TYNPDFSSL

++

17

YYADKKTFI
+
++
+

VL

18

DYIGSVEKW
+
+

19

ILKEDPFLF
+

20

EFTTVLYNF

+

21

SYEVRSTF
+
+

+

22

TQPGDWTLF
+

23

KFIISDWRF
+

24

MYPDLSELLM

+
+

25

SYNGYVFYL
+

+

26

KTPTNYYLF

+

27

NYTLYPITF

+

28

YYSIISHTL
+

+

29

VYPLLSRLYW
+

+

30

QYLPGWTVLF
+

31

QYQNVLTLW

+

32

SLPDLTPTF
+
+

33

KSSVIASLLF

+

34

MQPRMFFLF
+
+

35

KYLEESVWL

+

36

KQMEDGHTLF

+

37

QWPWQASLQF

+

38

KYTNWKAFL

+

39

LIFMLANVF

+

40

QYEPPSAPST

+

TF

41

VIYFMGAIF

+

42

TLPNTIYRF
+

+

43

IQMDEPMAF

+

44

AYLSAVGTF

+

45

KYFVPPQLF
+

46

AFPVTSIFH

+

+

TF

47

KYADYFLEV

+

48

VFIDHPVHL

+

KF

49

LYISEVRNI

+

50

SYPELVKMVW

+

51

KYALLLQEL

+

52

KYMKIFHKF

+

53

KYITNLEDL

+

54

LLIKLLQTF

+

55

RWMDQRLVF

+

56

VYMIEPLEL

+

57

YPSIIQEF

+

84

YVDINTFRL
+++
+++
+
+++

85

YIDEFQSLV

++

86

FVIDGFDEL
++
++

++

87

TLYPYQISQL
++
++
+
++

88

VQMVITEAQ
++
++

KV

89

ILSTTMVTV
++
++
+
+

90

FLLMHPSI

++

91

FALPGLLHA
++
++

92

NLRDLLSEV
++
++
+
+

93

TLQEKILQV

++

94

VLPDIETLI

++

++

GV

95

ITIGVLARV
++

96

HLVGGLHTV

+

97

VLALVNSTV

+

98

LQSSGLTLLL
+
+

+

99

FLKEKVPGI

+

100

RQYPTPFQL

+

+

101

FIISDWRFVL
+

102

SLLEQAIAL

+

103

FLYYPDPVL

+

104

GMLDIFWGV

+

105

SLLTHIPTA

+

106

FIIDTTYPA
+

YV

107

LLQGAIESV

+

108

MIIALSLYI
+
+

109

LLLGSIGLL
+

GV

110

LLADFQALL

+

111

ALCLLLHLL

+

112

SVSDGIHSV

+

113

AVLTGLVEV

+

114

ILDERQVLL

+
+

115

MLLETQDAL
+
+

YV

116

VLMEENSKL

+

117

FLDPNARPLV

+

118

ALSSVLHSI
+

119

RTADITVTV

+
+

120

ALLANLPAV
+

+

121

ALVDTLTGI

+

122

ALLEMFPEI

+

TV

123

LMAFFLAVV

+

124

SVASVLLYL

+

138

DSDSCHFNY
++

139

ECDMAFHIY

+

140

ESDREELNY

+

143

FIDYPKKEDY
++
+

146

GLNTGSALSY
++
+

147

GSSDSSTLP

+

KL

148

GTEFTTILY

+

149

GTEFTTVLY

+

150

GTELLSLVY

+

153

KLDRSVFTAY

++

155

LLDPNPHMY
+

++

158

LSDLLKQGY

++
+

160

LTEAVLNRY
++
++
+
++

163

NSDSSLTLRE
+

+

FY

164

NTDNNLAVY
+++
+++

+

165

NTDPTAPPY
+
+

166

NTQITDIGRY
+
+

167

QSDPGTSVL

+

GY

168

QTDHPQPIL

+
++

DRY

171

RSDPVTLNV
++

LY

172

RTDSCSSAQ
+

AQY

174

SADDIRGIQ
+++
+++
+
+++

SLY

175

SDVTPLTF
+++
++

176

SRTINVSNLY

+

+

177

SSDEVNFLVY

+
+

178

SSDSSTLPKL

+

179

STAKSATWTY

++

183

TLEDIATSH

+

LY

185

TSDSNLNKY

++

188

VSDAKLDKY

+

189

VSDSECLSRY

+++

+++

190

VTDGINPLI

++

DRY

192

VTEESFDSK

+

FY

193

VTEFSLNTY
++
+

194

VVADTKMIEY
++
+

195

VVDSVGGYLY
+

++

199

YLPQHTIETY

+

200

YSDEDVTKY

+

++

201

YVGKEHMFY

+++

+++

202

KLAELEGAL
+++
+

QK

203

KVKDTPGLGK
++
++
+
+

204

AVFDKFIRY

++

205

SLDGAARPK
+
+

++

206

KLIDLSQVMY
+

207

RSFNGLLTMY
+
+

208

GLASRILDAK
+
+

209

RTQIPMSEK

+

210

ATSGVPVYK
+

+

211

TVNPVAIHK

+

212

KAYEQVMHY

+

213

LNINMTSPM

+

GTK

214

RTMSEAALV

+

RK

215

MMFSGPQIL

+

KL

216

KLYAWELAF

+

217

RILNQILYY
+

218

KTLVAELLI

+

+

LK

219

RLRSSLVFK

+

220

SPSVSQLSVL
++
+++

+++

221

VPDVAQFVL
+++
+++

222

NPFYPEVEL
+++
+++

223

YPKDIYSSF
++
+++

224

GPQPWHAAL
+++
++

+

225

LPFDGPGGIL
+++
++

226

SPRMSGLLS

+++

QT

227

YPRGNHWAV

+++

GH

228

YPRGNHWAV

+++

GHL

229

VPLPAGGGTV

+++

230

VPLPAGGGT

+++

VL

231

RPRALRDLQL
+
++

+

232

RPRALRDLQ
+
++

+

LL

233

KPYQGNPTF

++

234

RAKNAGVTI
++
++

235

MPLKHYLLL
++

236

RVRGGEDGD

++

RAL

237

RPAATAVISL
++
++

238

KPGPPWAAF
++

239

YVPSASLFML

+

++

240

SPREVTTVL
++

241

SARLATDAL
++

242

SPRWLPVSL

++

243

RPIENRILIL
+
++

244

FPYVRDFVM
++
+

245

RIREHVPQL
++
+

246

TPLPAVIVL
+
++

247

RALLARLLL
++
+

248

IPNWARQDL

++
+

249

VPSSRILQL

++

+

250

SPRDFLSGL

++

251

VPRSSGQTV
+
+

++

252

SPDIRNTTV
++

253

RVIDAVRFTL

++

254

NPFPHLITL
+
+
+

255

MPLLENLYL
+
+

256

SPRVPSIEL

+

257

LPRIPFADV
+
+
++

258

LPRGPLASL
+
+

259

RPPAAGLRG

+

ISL

260

YPQHPGLNA

+

+

261

APSARVGVC
+
+
+

262

SAYPQRLEI
+

263

HPAPYGDLL

+

+

264

RPILIIITL

+

265

SPRQPPRLV
+

266

HAYPPGPGL

+

267

HPELVNHIVF
+

268

YPLFRGINL
+
+

269

APRAPRLML
+

270

APGPRFLVT
+
+

271

MPLPWSLALP

+

272

MPLPWSLAL

+

PL

273

MPLLWLRGF
+
+
+

274

TPYQEHVAL

+

275

APHPPLSVV

+

276

LPRAGGAFL
+
+

277

MPLFEPRVF
+
+

+

278

HPMIDINGI
+
+

IVF

279

SPARASPAL
+

280

VPISEEGTP

+

VL

281

RPRAPVTPA

+

282

MPQIETRVIL

+

+

283

RPHSLSSEL

+
+

284

FPVTSIFHTF

+

+

285

FPSFLTNSL

+

286

VPTLRSEL

+

287

APREEQQRSL

+

288

FPQKFIDLL

+

289

VPENHSVAL

+

290

APYRPPDISL
+

296

MPMQDIKM
+++
+++

+++

297

RAQLKLVAL

+++

298

FNKRKPLSL
+
++

+

299

MAQFKEISL
+
++

+

300

VASPKHCVL
++
++
+
+

301

YMHKLLVL

++

302

HLLQKQTSI

++

303

LPFPKFTV
++

304

ELKKLYCQI

+

305

ALKLRVAVL

+

306

ILKVKVGL
+

307

ILLPRTVSL
+
+

308

MLKQKVEEL

+

309

DAIQRKYSC

+

310

LPPKKFVL

+

311

EIRIRVVQM

+

312

EAMLRNKEL

+

313

ELKKKEYEEL

+

314

AIISRLVAL
+

319

AEMLERVIK
++
+++

+++

NY

320

MEVDPIGHV
+++
+++

+++

YIF

321

AEMLESVIK
+
+++

+++

NY

322

KEVDPAGHSY

+++

+++

323

SEFMQVIF

+++

+++

324

TDSIHAWTF

+++

325

QEQDVDLVQKY
+++
+++

326

QEMQHFLGL
+++
+++

+++

327

YEIEARNQVF
+++
+++

+++

328

FEYDFLLQRI
++
+++

+++

329

NEHPSNNW
++
+++

330

KEGDLGGKQW
++
++
+
+

331

EDAQGHIW
++
++

332

MEVPVIKI
+
++
+
++

333

AETLSTIQI
++
++

+

334

AEDEPAAAHL
++
++
+
+

335

KELEATKQY
++
++

+

336

ASSSGPMRWW
++
++

337

TENRYCVQL

++

338

SEGSEPALLHSW
++

339

SEPALLHSW
++

340

TEFSLNTY
++
+

341

EEIEGKGSFTYF
++

342

HEFSSPSHL

++

343

TEFTTVLY

+

344

EEATGQFHVY
+

345

IEFIHPQAF
+
+

346

VEAPGPVHVYW
+
+

+

347

ALNPYQYQY

+

348

AEIQGNINHV

+

349

AEQDMRELTY

+

350

GECDVFKEIL
+

351

EEVNYINTF

+

352

NEVLTYIKF

+

353

GEIIMQNNW

+

354

TEDPTILRI

+

355

SDMVRFHLF

+
+
+

356

EEGRVYLF
+
+

357

RELENCFQIQ

+

358

KEADIHFLI
+
+
+

359

DELFSIALY

+

360

AEVPTGVII
+

361

SENLFFASF
+

362

SEKGVIQVY

+

363

AELDKLTSV

+

364

AETPIQNVI
+

365

SEMNVNMKY
+

366

AENLFRAF

+

+

367

GEVHPSEMI

+

+

368

GEFPVRVQV

+

369

EEIERFFKL

+

370

YEDLSQKY

+

371

GELALKKKI

+

372

TEGIIMKDF
+

373

MEMQKSPVF

+

374

DEVNFLVY

+
+

375

VYSDLHAFYY

++

376

KYVKDFHKF

+

377

VYVGAVNRI

+

378

KFLGPAEHL
+

TF

388

FSIPEGALV

+

AV

389

TLMEQPLTTL

+

401

DSDESYMEK

+

SLY

402

DTDSQRLAY

+

405

ETEEGIYWRY

++

409

FVDPLVTNY

+

419

LSELKPMSY

+

427

NSDEQKITE

+

MVY

429

NTEDSSMSG
+

YLY

432

NVDPVQHTY
+

438

STDNFNCKY
+
+

442

TSDFSRFTNY

+

450

YSDDGQKW
++

TVY

454

KVYTPSISK

+

455

RIADIFVKK
+
+

456

SMFTAILKK

+

457

SINKPTSER

+

458

GIADFVLKY

+

459

RPMQQARAQL

+++

460

MPMAGDMNGL

++

461

RPILIIVTL

+

462

RPFHTRATV
++
++
+
+

463

TPKAGPTL
++
++
+
+

464

YPRPGTPAA

+

465

VPRPIFSQL

+

466

APYKSVTSL
+
+

467

KPFSSFTSM

+

468

SPMYGQAGL

+

469

YPENGVVQM

+

470

SPNSYFRVL

+

471

KPRPDVTNEL

+

472

NPRATDAQL

+

476

AEEEIMKKI
+++
+++
+
+++

477

QENSYQSRL
++
+++

478

SEIEQEIGSL
++
++

479

AEIQPQTQV
+
+

+

480

GEVSGLTKDF

+

481

RELQHEHSL
+
+

482

TEREWADEW

+

483

EENDQSTHKW

+

484

AEVGFVRFF

+

485

SEIEDSTK

+

QVF

486

SEDDPILQI

+

487

AEDQLHHSF

+

488

TEFPIIKMY

+

489

SEIGKAVGF

+

The table lists peptides from genes that are very highly over-expressed in lung cancer tissues (NSCLCadeno = non-small cell lung carcinoma adenocarcinoma; NSCLCsquam = non-small cell lung carcinoma squamous cell; NSCLCother = non-small cell lung carcinoma, other subtypes; SCLC = small cell lung carcinoma) 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 relevant normal tissues: adipose tissue, adrenal gland, bile duct, blood cells, blood vessels, bone marrow, brain, cartilage, esophagus, eye, gallbladder, heart, head&neck, kidney, large intestine, liver, lung, lymph node, nerve, parathyroid, pancreas, pituitary, pleura, skeletal muscle, skin, small intestine, spleen, stomach, thyroid gland, trachea, urinary bladder, ureter. In case expression data for several samples of the same tissue type were available, the arithmetic mean of all respective samples was used for the calculation.

Example 3

In Vitro Immunogenicity for MHC Class I Presented Peptides

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 for HLA-A*02:01, HLA-A*24:02, HLA-A*01:01, HLA-A*03:01, HLA-B*07:02, HLA-B*08:01 and HLA-B*44:02 restricted TUMAPs of the invention, demonstrating that these peptides are T-cell epitopes against which CD8+ precursor T cells exist in humans (Table 10a and Table 10b).

In Vitro Priming of CD8+ T Cells

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, HLA-A*24, HLA-A*01, HLA-A*03, HLA-B*07, HLA-B*08 or HLA-B*44 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.

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 μg/ml Streptomycin (Cambrex, Cologne, Germany), 1 mM sodium pyruvate (CC Pro, Oberdorla, Germany), 20 μg/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.

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.

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 μm diameter streptavidin coated polystyrene particles (Bangs Laboratories, Illinois, USA).

pMHC used for positive and negative control stimulations were A*02:01/MLA-001 (peptide ELAGIGILTV (SEQ ID NO. 532) from modified Melan-A/MART-1) and A*02:01/DDX5-001 (YLLPAIVHI from DDX5, SEQ ID NO. 533), respectively.

800.000 beads/200 μl were coated in 96-well plates in the presence of 4×12.5 ng different biotin-pMHC, washed and 600 ng biotin anti-CD28 were added subsequently in a volume of 200 μl. Stimulations were initiated in 96-well plates by co-incubating 1×10⁶CD8+ T cells with 2×10⁵washed coated beads in 200 μl TCM supplemented with 5 ng/ml IL-12 (PromoCell) for 3 days at 37° 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° 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, Oreg., 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× the median of the negative control stimulations).

In Vitro Immunogenicity for Lung Cancer (Including NSCLC and SCLC) Peptides

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 16 peptides of the invention are shown in FIGS. 3A through 11B together with corresponding negative controls. Results for 152 peptides from the invention are summarized in Table 10a and Table 10b.

TABLE 10a

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

Wells

ID

positive

No
Sequence
[%]

491
KYLEKYYNL
++

492
NYEDHFPLL
++

493
TYKYVDINTF
+

494
RYLEKFYGL
+

495
SYNDALLTF
+++

496
VFMKDGFFYF
+

498
EYIRALQQL
+

500
VWSDVTPLTF
+

504
VYEKNGYIYF
++++

510
KVLEHVVRV
+

513
KLVELEHTL
+

515
KIFEMLEGV
+

516
YTFSGDVQL
+

519
KIQEILTQV
+

520
KIQEMQHFL
+

525
RLDDLKMTV
+

528
RLLDSVSRL
+

TABLE 10b

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

Wells

ID

positive

No
Sequence
[%]
HLA

136
ATDLVVLDRY
“+”
A*01

143
FIDYPKKEDY
“+”
A*01

153
KLDRSVFTAY
“++++”
A*01

160
LTEAVLNRY
“++”
A*01

164
NTDNNLAVY
“+”
A*01

173
RTEFNLNQY
“++++”
A*01

174
SADDIRGIQSLY
“+”
A*01

185
TSDSNLNKY
“+”
A*01

187
VADLHLYLY
“+++”
A*01

189
VSDSECLSRY
“++”
A*01

193
VTEFSLNTY
“+”
A*01

201
YVGKEHMFY
“+”
A*01

395
ASEASRLAHY
“++”
A*01

398
ASEQQALHTVQY
“+”
A*01

405
ETEEGIYWRY
“+”
A*01

430
NTEGLHHLY
“+”
A*01

436
QTETGTPYMLY
“+”
A*01

451
YSDSLVQKGY
“+”
A*01

452
YVDAVLGKGHQY
“+”
A*01

84
YVDINTFRL
“+”
A*02

85
YIDEFQSLV
“++”
A*02

87
TLYPYQISQL
“++”
A*02

88
VQMVITEAQKV
“++”
A*02

89
ILSTTMVTV
“+++”
A*02

93
TLQEKILQV
“+”
A*02

94
VLPDIETLIGV
“+++”
A*02

95
ITIGVLARV
“++++”
A*02

96
HLVGGLHTV
“+++”
A*02

97
VLALVNSTV
“+++”
A*02

101
FIISDWRFVL
“+”
A*02

125
VLQPFLPSI
“++++”
A*02

127
GLDGSLVFL
“++”
A*02

128
FLGTTPTL
“+”
A*02

129
VLYDKDAVYV
“++”
A*02

130
NLWGGQGLLGV
“+”
A*02

131
LLKEFVQRV
“++++”
A*02

132
ALWLVDPLTV
“+++”
A*02

133
MTLPVDAVISV
“+”
A*02

392
SLFKDQMEL
“+”
A*02

393
ILLPYLQTL
“+”
A*02

205
SLDGAARPK
“++”
A*03

208
GLASRILDAK
“+”
A*03

209
RTQIPMSEK
“+”
A*03

210
ATSGVPVYK
“++++”
A*03

214
RTMSEAALVRK
“+”
A*03

218
KTLVAELLILK
“+”
A*03

1
QYDPTPLTW
“+”
A*24

2
VWSNVTPLKF
“+”
A*24

4
SYEKVINYL
“+”
A*24

6
KYKDYFPVI
“+”
A*24

8
PFLPPAACFF
“+”
A*24

10
VWSDVTPLNF
“+”
A*24

11
YYSKSVGFMQW
“++”
A*24

13
HYTYILEVF
“+++”
A*24

15
KYALLLQDL
“+++”
A*24

16
TYNPDFSSL
“+”
A*24

59
KYSTTFFMV
“++”
A*24

60
TYLSIFDQL
“+”
A*24

61
NYAENILTL
“++”
A*24

62
LYQEILAQL
“+”
A*24

65
VYPASKMFPFI
“+”
A*24

66
IYFRDSSFL
“++”
A*24

72
RYEGILYTI
“+”
A*24

76
WYGWHFPEL
“+”
A*24

79
RYLADLPTL
“+”
A*24

83
TYCQNIKEF
“+”
A*24

375
VYSDLHAFYY
“+”
A*24

379
NYIVPDKQIF
“+”
A*24

380
VFQEKHHVI
“+”
A*24

383
RYKQDVERF
“+++”
A*24

384
KYVKVFDKF
“+++”
A*24

386
VYNDHSIYVW
“++”
A*24

220
SPSVSQLSVL
“++++”
B*07

221
VPDVAQFVL
“++”
B*07

222
NPFYPEVEL
“+”
B*07

223
YPKDIYSSF
“++”
B*07

224
GPQPWHAAL
“++”
B*07

225
LPFDGPGGIL
“++++”
B*07

226
SPRMSGLLSQT
“+++”
B*07

228
YPRGNHWAVGHL
“++”
B*07

231
RPRALRDLQL
“++”
B*07

232
RPRALRDLQLL
“+++”
B*07

233
KPYQGNPTF
“+”
B*07

237
RPAATAVISL
“+”
B*07

241
SARLATDAL
“+++”
B*07

242
SPRWLPVSL
“++++”
B*07

244
FPYVRDFVM
“+”
B*07

245
RIREHVPQL
“++”
B*07

248
IPNWARQDL
“++++”
B*07

249
VPSSRILQL
“+++”
B*07

250
SPRDFLSGL
“+”
B*07

252
SPDIRNTTV
“+”
B*07

274
TPYQEHVAL
“+”
B*07

285
FPSFLTNSL
“++++”
B*07

292
SPQRLRGLLL
“+++”
B*07

293
RPRSALPRLLLP
“++”
B*07

294
GPTPNTGAAL
“+++”
B*07

460
MPMAGDMNGL
“++”
B*07

462
RPFHTRATV
“++”
B*07

463
TPKAGPTL
“+”
B*07

473
LPRALLSSL
“++”
B*07

474
LPRLLPAL
“+++”
B*07

320
MEVDPIGHVYIF
“+”
B*44

322
KEVDPAGHSY
“++”
B*44

323
SEFMQVIF
“+”
B*44

325
QEQDVDLVQKY
“+”
B*44

326
QEMQHFLGL
“+”
B*44

328
FEYDFLLQRI
“+”
B*44

329
NEHPSNNW
“+”
B*44

330
KEGDLGGKQW
“+”
B*44

331
EDAQGHIW
“++”
B*44

333
AETLSTIQI
“+”
B*44

334
AEDEPAAAHL
“+”
B*44

337
TENRYCVQL
“++”
B*44

338
SEGSEPALLHSW
“+”
B*44

339
SEPALLHSW
“++”
B*44

342
HEFSSPSHL
“+”
B*44

476
AEEEIMKKI
“+”
B*44

477
QENSYQSRL
“+”
B*44

297
RAQLKLVAL
“+”
B*08

298
FNKRKPLSL
“+”
B*08

299
MAQFKEISL
“++++”
B*08

300
VASPKHCVL
“+”
B*08

303
LPFPKFTV
“++”
B*08

305
ALKLRVAVL
“+”
B*08

306
ILKVKVGL
“+”
B*08

307
ILLPRTVSL
“+”
B*08

308
MLKQKVEEL
“+”
B*08

311
EIRIRVVQM
“+”
B*08

312
EAMLRNKEL
“+”
B*08

313
ELKKKEYEEL
“+”
B*08

314
AIISRLVAL
“++”
B*08

315
DIYQRALNL
“+”
B*08

316
VIKEKALTL
“+”
B*08

318
EAAIRSVEL
“++”
B*08

Example 4

Synthesis of Peptides

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 lyophilizes (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

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 (β2m) of stabilized MHC complexes. The assay was performed as generally described in Rodenko et al. (Rodenko et al., 2006).

96 well MAXISorp plates (NUNC) were coated over night with 2 ug/ml streptavidin in PBS at room temperature, washed 4× and blocked for 1 h at 37° 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 1 h at 37° C., washed four times, incubated with 2 ug/ml HRP conjugated anti-β2m for 1h at 37° 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 11

MHC class I binding scores. Binding of

HLA-class I restricted peptides to

HLA-A*01 was ranged by peptide exchange

yield: >10% = +; >20% = ++; >50 = +++;

>75% = ++++

Seq

ID

Peptide

No
Sequence
exchange

134
AAEIGDKSWLY
“++++”

135
ASEDSVLLY
“++++”

136
ATDLVVLDRY
“++++”

137
ATSKFMEFY
“++++”

138
DSDSCHFNY
“++++”

139
ECDMAFHIY
“++++”

140
ESDREELNY
“+++”

141
ESDVGVVVY
“+++”

142
EVAEPSVLFDLY
“+++”

143
FIDYPKKEDY
“+++”

144
FLDSQNLSAY
“+++”

145
FVDKPVAY
“+++”

146
GLNTGSALSY
“++”

147
GSSDSSTLPKL
“++”

148
GTEFTTILY
“++++”

149
GTEFTTVLY
“++++”

150
GTELLSLVY
“++++”

151
HSDLKVGEY
“+++”

152
HTDSLHLLI
“+++”

153
KLDRSVFTAY
“+++”

154
LLDISQKNLY
“+++”

155
LLDPNPHMY
“++++”

156
LLDSLREQY
“+++”

157
LMDRPIFY
“++++”

158
LSDLLKQGY
“++++”

159
LSDTSVIQFY
“++++”

160
LTEAVLNRY
“+++”

161
LVDDGTHGQY
“+++”

162
LVDNSIRELQY
“+++”

163
NSDSSLTLREFY
“+++”

164
NTDNNLAVY
“++++”

165
NTDPTAPPY
“+++”

166
NTQITDIGRY
“+++”

167
QSDPGTSVLGY
“+++”

168
QTDHPQPILDRY
“++++”

169
RLDTPLYFSY
“++++”

170
RSDDTAVYY
“++++”

171
RSDPVTLNVLY
“++++”

172
RTDSCSSAQAQY
“+++”

173
RTEFNLNQY
“++++”

174
SADDIRGIQSLY
“++++”

176
SRTINVSNLY
“+++”

177
SSDEVNFLVY
“++++”

178
SSDSSTLPKL
“++”

179
STAKSATWTY
“++++”

180
STDPWIQMAY
“++++”

181
TADGKTYYY
“+++”

182
TDYHVRVY
“+++”

183
TLEDIATSHLY
“++++”

184
TSAHPEDSSFY
“+++”

185
TSDSNLNKY
“++++”

186
TTDIIEKY
“+++”

187
VADLHLYLY
“+++”

188
VSDAKLDKY
“+++”

189
VSDSECLSRY
“++++”

190
VTDGINPLIDRY
“+++”

191
VTDGSLYEGVAY
“++++”

192
VTEESFDSKFY
“++++”

193
VTEFSLNTY
“++++”

194
VVADTKMIEY
“+”

195
VVDSVGGYLY
“++++”

196
WMFFVINY
“+”

197
YADTVRPEFY
“+++”

198
YLDPVQRDLY
“++++”

199
YLPQHTIETY
“++”

200
YSDEDVTKY
“++++”

201
YVGKEHMFY
“++++”

394
ASEAEMRLFY
“++++”

395
ASEASRLAHY
“++++”

396
ASEFGNHYLY
“++++”

397
ASEITSKGASLY
“++++”

398
ASEQQALHTVQY
“++++”

399
ATDIPCLLY
“++++”

400
ATDISRQNEY
“+++”

401
DSDESYMEKSLY
“++++”

402
DTDSQRLAY
“+++”

403
ELDSKVEVLTY
“+++”

404
ETARKFLYY
“++++”

405
ETEEGIYWRY
“++++”

406
ETEQTKFWDY
“++++”

407
FSDNDKLYLY
“++++”

408
FTEQWTDGY
“+++”

409
FVDPLVTNY
“++++”

410
GSDHQSPSSSSY
“++++”

411
GTVYEDLRY
“++++”

412
ILDEVIMGY
“++++”

413
ISDRYYTALY
“++++”

414
KTDESLTKY
“+++”

415
LLDPRSYHTY
“+++”

416
LLDTAQKNLY
“++++”

417
LLEDKHFQSY
“++++”

418
LSDPSGPKSY
“+++”

419
LSELKPMSY
“++++”

420
LTEDKETLQY
“++++”

421
LTELLERAAFY
“++++”

422
MIDVTKSYY
“++++”

423
NLDAVHDITVAY
“++++”

424
NLDEEKQLLY
“+++”

425
NLDIIQQEY
“++++”

426
NLDQATRVAY
“+++”

427
NSDEQKITEMVY
“++++”

428
NSELSCQLY
“++++”

429
NTEDSSMSGYLY
“++++”

430
NTEGLHHLY
“++++”

431
NTSDMMGRMSY
“++++”

432
NVDPVQHTY
“+++”

433
QIDTGENLY
“++++”

434
QTDCAPNNGY
“++++”

435
QTDDTWRTEY
“++++”

436
QTETGTPYMLY
“++++”

437
STDGKHWWEY
“++++”

438
STDNFNCKY
“+++”

439
TLDAGKFQIY
“+++”

440
TLDENPGVRY
“+++”

441
TLDSALNAASYY
“++++”

442
TSDFSRFTNY
“++++”

443
TTDFPSESSFEY
“++++”

444
TTDTVIRSY
“+++”

445
VLDQGKITEY
“+++”

446
VTAQVVGTERY
“++++”

447
VVDEDHELIY
“+++”

448
YLDIPNPRY
“+++”

449
YLDRGTGNVSFY
“++++”

450
YSDDGQKWTVY
“++++”

451
YSDSLVQKGY
“++++”

452
YVDAVLGKGHQY
“++++”

TABLE 12

MHC class I binding scores. Binding of

HLA-class I restricted peptides to

HLA-A*02 was ranged by peptide exchange

yield: >10% = +; >20% = ++; >50 = +++;

>75% = ++++

Seq

ID

Peptide

No
Sequence
exchange

84
YVDINTFRL
“++++”

85
YIDEFQSLV
“++++”

86
FVIDGFDEL
“++++”

87
TLYPYQISQL
“++++”

88
VQMVITEAQKV
“++++”

89
ILSTTMVTV
“++++”

91
FALPGLLHA
“+++”

92
NLRDLLSEV
“+++”

93
TLQEKILQV
“++++”

94
VLPDIETLIGV
“++++”

95
ITIGVLARV
“++++”

96
HLVGGLHTV
“++++”

97
VLALVNSTV
“++++”

98
LQSSGLTLLL
“++++”

99
FLKEKVPGI
“++++”

100
RQYPTPFQL
“++++”

101
FIISDWRFVL
“+++”

102
SLLEQAIAL
“++++”

103
FLYYPDPVL
“++++”

104
GMLDIFWGV
“++++”

105
SLLTHIPTA
“++++”

106
FIIDTTYPAYV
“++++”

107
LLQGAIESV
“++++”

109
LLLGSIGLLGV
“++++”

110
LLADFQALL
“++++”

111
ALCLLLHLL
“+”

112
SVSDGIHSV
“++++”

113
AVLTGLVEV
“++++”

114
ILDERQVLL
“++++”

115
MLLETQDALYV
“++++”

116
VLMEENSKL
“++++”

117
FLDPNARPLV
“++++”

118
ALSSVLHSI
“++++”

119
RTADITVTV
“++++”

120
ALLANLPAV
“++++”

121
ALVDTLTGI
“++++”

122
ALLEMFPEITV
“++++”

123
LMAFFLAVV
“++”

124
SVASVLLYL
“++++”

125
VLQPFLPSI
“++++”

126
FLSTVTSV
“++++”

127
GLDGSLVFL
“++++”

128
FLGTTPTL
“++++”

129
VLYDKDAVYV
“++++”

130
NLWGGQGLLGV
“++++”

131
LLKEFVQRV
“++++”

132
ALWLVDPLTV
“++++”

133
MTLPVDAVISV
“++++”

388
FSIPEGALVAV
“++++”

389
TLMEQPLTTL
“++++”

390
HIMPTVHTV
“++++”

391
SLIDMRGIETV
“++++”

392
SLFKDQMEL
“++++”

393
ILLPYLQTL
“++++”

TABLE 13

MHC class I binding scores. Binding

of HLA-class I restricted peptides to

HLA-A*03 was ranged by peptide

exchange yield: >10% = +; >20% = ++;

>50 = +++; >75% = ++++

Seq

ID

Peptide

No
Sequence
exchange

202
KLAELEGALQK
“++++”

203
KVKDTPGLGK
“++++”

204
AVFDKFIRY
“++++”

205
SLDGAARPK
“++++”

206
KLIDLSQVMY
“++++”

207
RSFNGLLTMY
“++++”

208
GLASRILDAK
“++++”

209
RTQIPMSEK
“++++”

210
ATSGVPVYK
“++++”

211
TVNPVAIHK
“++++”

212
KAYEQVMHY
“++++”

214
RTMSEAALVRK
“++++”

215
MMFSGPQILKL
“++++”

216
KLYAWELAF
“+++”

217
RILNQILYY
“++++”

218
KTLVAELLILK
“+++”

219
RLRSSLVFK
“++++”

453
AINTSIKNK
“++++”

454
KVYTPSISK
“++++”

455
RIADIFVKK
“++++”

456
SMFTAILKK
“++++”

457
SINKPTSER
“++++”

458
GIADFVLKY
“++++”

TABLE 14

MHC class I binding scores. Binding

of HLA-class I restricted peptides to

HLA-A*24 was ranged by peptide exchange

yield: >10% = +; >20% = ++;

>50 = +++; >75% = ++++

Seq

ID

Peptide

No
Sequence
exchange

1
QYDPTPLTW
“++++”

2
VWSNVTPLKF
“++++”

3
YLEKFYGL
“++”

4
SYEKVINYL
“++++”

5
RYMKKDYLI
“++++”

6
KYKDYFPVI
“++++”

7
VQQWSVAVF
“+++”

8
PFLPPAACFF
“++++”

10
VWSDVTPLNF
“++++”

11
YYSKSVGFMQW
“++++”

12
STIRGELFFF
“+”

13
HYTYILEVF
“++++”

14
SYSSCYSF
“+++”

15
KYALLLQDL
“++++”

16
TYNPDFSSL
“+++”

17
YYADKKTFIVL
“+++”

18
DYIGSVEKW
“++++”

19
ILKEDPFLF
“+”

20
EFTTVLYNF
“++++”

21
SYEVRSTF
“+++”

22
TQPGDWVTLF
“++++”

23
KFIISDWRF
“++++”

24
MYPDLSELLM
“++++”

25
SYNGYVFYL
“++++”

26
KTPTNYYLF
“++++”

27
NYTLYPITF
“++++”

28
YYSIISHTL
“++++”

29
VYPLLSRLYW
“++++”

30
QYLPGWTVLF
“++++”

31
QYQNVLTLW
“++++”

32
SLPDLTPTF
“++++”

33
KSSVIASLLF
“+++”

34
MQPRMFFLF
“++++”

35
KYLEESVWL
“++++”

36
KQMEDGHTLF
“++”

37
QWPWQASLQF
“++++”

38
KYTNWKAFL
“++++”

39
LIFMLANVF
“+”

40
QYEPPSAPSTTF
“+++”

42
TLPNTIYRF
“++++”

43
IQMDEPMAF
“+”

44
AYLSAVGTF
“++++”

45
KYFVPPQLF
“++++”

46
AFPVTSIFHTF
“++++”

47
KYADYFLEV
“++++”

48
VFIDHPVHLKF
“++++”

49
LYISEVRNI
“++++”

50
SYPELVKMVW
“++++”

51
KYALLLQEL
“++++”

52
KYMKIFHKF
“++++”

53
KYITNLEDL
“++++”

54
LLIKLLQTF
“+++”

55
RWMDQRLVF
“++++”

56
VYMIEPLEL
“++++”

57
YPSIIQEF
“++++”

58
QFAAPLRGIYF
“++++”

59
KYSTTFFMV
“++”

60
TYLSIFDQL
“+++”

61
NYAENILTL
“+++”

62
LYQEILAQL
“++++”

63
VMPSDSFFF
“++++”

64
NYAIFDEGHML
“++++”

65
VYPASKMFPFI
“++++”

66
IYFRDSSFL
“++++”

67
RYPGKFYRV
“++++”

68
IYQQIIQTY
“++++”

69
IMPEKFEFW
“++++”

70
PYTNYTFDF
“++++”

71
SYMVLAPVF
“++++”

72
RYEGILYTI
“++++”

73
SYIGLPLTL
“+++”

74
VYDQYFITL
“++++”

75
NYIYSISVF
“++++”

76
WYGWHFPEL
“+++”

77
AYTLLGHEFV
“+”

78
TWFPKTPMLF
“++++”

79
RYLADLPTL
“++++”

80
YYSPLRDLL
“++++”

81
LYPEGLRLL
“++++”

82
RFLPSPVVI
“++++”

83
TYCQNIKEF
“++++”

375
VYSDLHAFYY
“++++”

376
KYVKDFHKF
“++++”

377
VYVGAVNRI
“++++”

378
KFLGPAEHLTF
“++++”

379
NYIVPDKQIF
“+++”

380
VFQEKHHVI
“+++”

381
TYSKKHFRI
“++++”

382
IYHSHHPTL
“+++”

383
RYKQDVERF
“+++”

384
KYVKVFDKF
“++++”

385
MYINEVERL
“++++”

386
VYNDHSIYVW
“++++”

387
RWLPQKNAAQF
“+++”

TABLE 15

MHC class I binding scores.

Binding of HLA-class I restricted

peptides to HLA-B*07 was ranged by

peptide exchange yield: >10% = +;

>20% = ++; >50 = +++; >75% = ++++

Seq

ID

Peptide

No
Sequence
exchange

220
SPSVSQLSVL
“++++”

221
VPDVAQFVL
“++++”

222
NPFYPEVEL
“+++”

223
YPKDIYSSF
“++++”

224
GPQPWHAAL
“++++”

225
LPFDGPGGIL
“++++”

226
SPRMSGLLSQT
“++++”

227
YPRGNHWAVGH
“++++”

228
YPRGNHWAVGHL
“++++”

229
VPLPAGGGTV
“+++”

230
VPLPAGGGTVL
“+++”

231
RPRALRDLQL
“++++”

232
RPRALRDLQLL
“++++”

233
KPYQGNPTF
“++++”

234
RAKNAGVTI
“++++”

235
MPLKHYLLL
“++++”

236
RVRGGEDGDRAL
“++++”

237
RPAATAVISL
“+++”

238
KPGPPWAAF
“++++”

239
YVPSASLFML
“++++”

240
SPREVTTVL
“++++”

241
SARLATDAL
“++++”

242
SPRWLPVSL
“++++”

243
RPIENRILIL
“++++”

244
FPYVRDFVM
“++++”

245
RIREHVPQL
“+++”

246
TPLPAVIVL
“++++”

247
RALLARLLL
“+++”

248
IPNWARQDL
“++++”

249
VPSSRILQL
“++++”

250
SPRDFLSGL
“++++”

251
VPRSSGQTV
“++++”

252
SPDIRNTTV
“++++”

253
RVIDAVRFTL
“+++”

254
NPFPHLITL
“++++”

255
MPLLENLYL
“++++”

256
SPRVPSIEL
“++++”

257
LPRIPFADV
“++++”

258
LPRGPLASL
“++++”

259
RPPAAGLRGISL
“++++”

260
YPQHPGLNA
“+++”

261
APSARVGVC
“+++”

262
SAYPQRLEI
“+”

263
HPAPYGDLL
“++++”

265
SPRQPPRLV
“++++”

267
HPELVNHIVF
“++”

268
YPLFRGINL
“++++”

269
APRAPRLML
“++++”

270
APGPRFLVT
“++++”

271
MPLPWSLALP
“+++”

272
MPLPWSLALPL
“++++”

273
MPLLWLRGF
“++”

274
TPYQEHVAL
“+++”

275
APHPPLSVV
“+++”

276
LPRAGGAFL
“+++”

278
HPMIDINGIIVF
“++”

279
SPARASPAL
“+++”

280
VPISEEGTPVL
“+++”

281
RPRAPVTPA
“++++”

282
MPQIETRVIL
“+++”

283
RPHSLSSEL
“++++”

284
FPVTSIFHTF
“++”

285
FPSFLTNSL
“++++”

286
VPTLRSEL
“++++”

287
APREEQQRSL
“+++”

288
FPQKFIDLL
“++”

289
VPENHSVAL
“++++”

290
APYRPPDISL
“++++”

291
SPQRLRGLL
“++++”

292
SPQRLRGLLL
“+++”

293
RPRSALPRLLLP
“++++”

294
GPTPNTGAAL
“++++”

295
KPEGTRIAV
“++++”

459
RPMQQARAQL
“+++”

460
MPMAGDMNGL
“++++”

462
RPFHTRATV
“++++”

463
TPKAGPTL
“++++”

464
YPRPGTPAA
“++++”

465
VPRPIFSQL
“++++”

466
APYKSVTSL
“++++”

467
KPFSSFTSM
“++++”

468
SPMYGQAGL
“++++”

469
YPENGVVQM
“++”

470
SPNSYFRVL
“++++”

471
KPRPDVTNEL
“++++”

472
NPRATDAQL
“++++”

473
LPRALLSSL
“++++”

474
LPRLLPAL
“++++”

475
RPHKPGLYL
“++++”

TABLE 16

MHC class I binding scores. Binding of

HLA-class I restricted peptides to

HLA-B*08 was ranged by peptide exchange

yield: >10% = +; >20% = ++; >50 = +++;

>75% = ++++

Seq

ID
Sequence

No
Peptide
exchange

296
MPMQDIKM
“++++”

297
RAQLKLVAL
“++++”

298
FNKRKPLSL
“+++”

299
MAQFKEISL
“++++”

300
VASPKHCVL
“+++”

301
YMHKLLVL
“++++”

302
HLLQKQTSI
“+++”

303
LPFPKFTV
“++++”

304
ELKKLYCQI
“++++”

305
ALKLRVAVL
“++++”

306
ILKVKVGL
“++++”

307
ILLPRTVSL
“++++”

308
MLKQKVEEL
“++++”

309
DAIQRKYSC
“+++”

310
LPPKKFVL
“++++”

311
EIRIRVVQM
“++++”

312
EAMLRNKEL
“++++”

313
ELKKKEYEEL
“++++”

314
AIISRLVAL
“++++”

315
DIYQRALNL
“++++”

316
VIKEKALTL
“+++”

317
LVKVKVLL
“++++”

318
EAAIRSVEL
“++++”

TABLE 17

MHC class I binding scores.

Binding of HLA-class I restricted

peptides to HLA-B*44 was ranged

by peptide exchange yield:

>10% = +; >20% = ++; >50 =+++;

>75% = ++++

Seq

ID

Peptide

No
Sequence
exchange

319
AEMLERVIKNY
“++++”

320
MEVDPIGHVYIF
“++++”

321
AEMLESVIKNY
“+++”

322
KEVDPAGHSY
“++”

323
SEFMQVIF
“+++”

324
TDSIHAWTF
“+++”

325
QEQDVDLVQKY
“++”

326
QEMQHFLGL
“+++”

327
YEIEARNQVF
“+++”

328
FEYDFLLQRI
“++++”

329
NEHPSNNW
“+++”

330
KEGDLGGKQW
“+++”

331
EDAQGHIW
“+++”

332
MEVPVIKI
“++”

333
AETLSTIQI
“+++”

334
AEDEPAAAHL
“++”

335
KELEATKQY
“++”

336
ASSSGPMRWW
“++”

337
TENRYCVQL
“++++”

338
SEGSEPALLHSW
“+++”

339
SEPALLHSW
“+++”

340
TEFSLNTY
—

341
EEIEGKGSFTYF
“+++”

342
HEFSSPSHL
“+++”

343
TEFTTVLY
“++”

344
EEATGQFHVY
“+++”

345
IEFIHPQAF
“++++”

346
VEAPGPVHVYW
“++++”

347
ALNPYQYQY
“+++”

348
AEIQGNINHV
“+++”

349
AEQDMRELTY
“+++”

350
GECDVFKEIL
“+++”

351
EEVNYINTF
“+++”

352
NEVLTYIKF
“++++”

353
GEIIMQNNW
“++++”

354
TEDPTILRI
“+++”

355
SDMVRFHLF
“++”

356
EEGRVYLF
“+++”

357
RELENCFQIQ
“+++”

358
KEADIHFLI
“++++”

359
DELFSIALY
“+++”

360
AEVPTGVII
“++++”

361
SENLFFASF
“++++”

362
SEKGVIQVY
“+++”

363
AELDKLTSV
“+++”

364
AETPIQNVI
“+++”

365
SEMNVNMKY
“++++”

366
AENLFRAF
“++”

367
GEVHPSEMI
“+++”

368
GEFPVRVQV
“++”

369
EEIERFFKL
“+++”

370
YEDLSQKY
“+”

371
GELALKKKI
“++”

372
TEGIIMKDF
“++”

373
MEMQKSPVF
“+++”

374
DEVNFLVY
“+”

476
AEEEIMKKI
“++”

477
QENSYQSRL
“+++”

478
SEIEQEIGSL
“+++”

479
AEIQPQTQV
“+++”

480
GEVSGLTKDF
“++”

481
RELQHEHSL
“+++”

482
TEREWADEW
“+++”

483
EENDQSTHKW
“+++”

484
AEVGFVRFF
“++++”

485
SEIEDSTKQVF
“+++”

486
SEDDPILQI
“+++”

487
AEDQLHHSF
“+++”

488
TEFPIIKMY
“++”

489
SEIGKAVGF
“++++”

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