Method for treating non-small lung cancer with a population of activated cells
11576954 · 2023-02-14
Assignee
Inventors
- Andrea Mahr (Tuebingen, DE)
- Toni WEINSCHENK (Tuebingen, DE)
- Oliver Schoor (Tuebingen, DE)
- Jens Fritsche (Tuebingen, DE)
- Harpreet Singh (Tuebingen, DE)
Cpc classification
A61K39/00
HUMAN NECESSITIES
C07K16/3076
CHEMISTRY; METALLURGY
A61K9/0019
HUMAN NECESSITIES
C07K2319/40
CHEMISTRY; METALLURGY
C12Q2600/106
CHEMISTRY; METALLURGY
C07K14/4748
CHEMISTRY; METALLURGY
G01N33/57492
PHYSICS
C12Q1/6883
CHEMISTRY; METALLURGY
C12N15/115
CHEMISTRY; METALLURGY
A61P35/00
HUMAN NECESSITIES
International classification
A61K39/00
HUMAN NECESSITIES
C12N15/115
CHEMISTRY; METALLURGY
C07K16/28
CHEMISTRY; METALLURGY
A61P35/00
HUMAN NECESSITIES
Abstract
The present invention relates to peptides, proteins, nucleic acids and cells for use in immunotherapeutic methods. In particular, the present invention relates to the immunotherapy of cancer. The present invention furthermore relates to tumor-associated T-cell peptide epitopes, alone or in combination with other tumor-associated peptides that can for example serve as active pharmaceutical ingredients of vaccine compositions that stimulate anti-tumor immune responses, or to stimulate T cells ex vivo and transfer into patients. Peptides bound to molecules of the major histocompatibility complex (MHC), or peptides as such, can also be targets of antibodies, soluble T-cell receptors, and other binding molecules.
Claims
1. A method for treating a patient who has non-small cell lung cancer overexpressing DNAH11 polypeptide comprising the amino acid sequence of HYSTLVHMF (SEQ ID NO: 222), comprising administering to the patient a population of activated T cells that kill cancer cells, wherein the activated T cells are antigen-specific CD8.sup.+ cytotoxic T cells produced by contacting CD8.sup.+ T cells with an antigen presenting cell that presents a peptide consisting of the amino acid sequence of HYSTLVHMF (SEQ ID NO: 222) in a complex with an MHC class I molecule on the surface of the antigen presenting cell in vitro, for a period of time sufficient to activate said T cell.
2. The method of claim 1, wherein the T cells are autologous to the patient.
3. The method of claim 1, wherein the T cells are obtained from a healthy donor.
4. The method of claim 1, wherein the activated T cells are expanded in vitro.
5. The method of claim 4, wherein the expansion is in the presence of an anti-CD28 antibody and IL-12.
6. The method of claim 1, further comprising administering an adjuvant selected from the group consisting of anti-CD40 antibody, imiquimod, resiquimod, GM-CSF, cyclophosphamide, interferon-alpha, interferon-beta, CpG oligonucleotides and derivatives, poly-(I:C) and derivatives, RNA, sildenafil, particulate formulations with poly(lactide co-glycolide) (PLG), virosomes, interleukin (IL)-1, IL-2, IL-4, IL-7, IL-12, IL-13, IL-15, IL-21, and IL-23.
7. The method of claim 6, wherein the adjuvant is IL-2.
8. The method of claim 6, wherein the adjuvant is IL-7.
9. The method of claim 6, wherein the adjuvant is IL-15.
10. The method of claim 6, wherein the adjuvant is IL-21.
11. A method of eliciting an immune response in a patient who has non-small cell lung cancer overexpressing DNAH11 polypeptide comprising the amino acid sequence of HYSTLVHMF (SEQ ID NO: 222), comprising administering to the patient a population of activated T cells that selectively recognize cancer cells, wherein the activated T cells are antigen-specific CD8.sup.+ cytotoxic T cells produced by contacting CD8.sup.+ T cells with an antigen presenting cell that presents a peptide consisting of the amino acid sequence of HYSTLVHMF (SEQ ID NO: 222) in a complex with an MHC class I molecule on the surface of the antigen presenting cell in vitro, for a period of time sufficient to activate said T cell.
12. The method of claim 11, wherein the T cells are autologous to the patient.
13. The method of claim 11, wherein the T cells are obtained from a healthy donor.
14. The method of claim 11, wherein the activated T cells are expanded in vitro.
15. The method of claim 14, wherein the expansion is in the presence of an anti-CD28 antibody and IL-12.
16. The method of claim 11, further comprising administering an adjuvant selected from the group consisting of anti-CD40 antibody, imiquimod, resiquimod, GM-CSF, cyclophosphamide, interferon-alpha, interferon-beta, CpG oligonucleotides and derivatives, poly-(I:C) and derivatives, RNA, sildenafil, particulate formulations with poly(lactide co-glycolide) (PLG), virosomes, interleukin (IL)-1, IL-2, IL-4, IL-7, IL-12, IL-13, IL-15, IL-21, and IL-23.
17. The method of claim 16, wherein the adjuvant is IL-2.
18. The method of claim 16, wherein the adjuvant is IL-7.
19. The method of claim 16, wherein the adjuvant is IL-15.
20. The method of claim 16, wherein the adjuvant is IL-21.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
(1)
(2)
(3)
(4)
(5)
EXAMPLES
Example 1
(6) Identification and Quantitation of Tumor Associated Peptides Presented on the Cell Surface
(7) Tissue Samples
(8) Patients' tumor tissues were obtained under 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.
(9) Peptides were selected if two conditions were true: (1) Its underlying transcript(s) and/or exon(s) are expressed at very low levels, i.e. the median reads per kilobase per million reads (RPKM) was required to be less than two, and the 75% quartile was required to be less than 5 for the following organs: brain, blood vessel, heart, liver, lung, blood. In addition, the median RPKM was required to be less than 10 for the following organs: urinary bladder, salivary gland, stomach, adrenal gland, colon, small intestine, spleen, bone marrow, pancreas, muscle, adipose tissue, skin, esophagus, kidney, thyroid gland, pituitary gland, nerve. (2) The peptide was tumor-associated, i.e. found specifically or on tumors or over-expressed compared to a baseline of normal tissues (cf. Example 1).
(10) Sample numbers for HLA-A*02 TUMAP selection were: for pancreatic cancer N=16, for renal cancer N=20, for colorectal cancer N=28, for esophageal carcinoma including cancer of the gastric-esophageal junction N=15, for prostate tumors N=35, for hepatocellular carcinoma N=16, for non-small cell lung cancer N=88, for gastric cancer N=29, for breast cancer N=9, for melanoma N=3, for ovarian cancer N=20, for chronic lymphocytic leukemia N=13 (of 12 donors), for urinary bladder cancer N=5, for testis cancer N=1, for small-cell lung cancer N=18 (of 13 donors), for gallbladder cancer and cholangiocarcinoma N=3, for acute myeloid leukemia N=5 (of 4 donors), for glioblastoma N=40, and for uterine cancer N=5.
(11) Sample numbers for HLA-A*24 TUMAP selection were: for gastric cancer N=44, for prostate tumors N=37, for non-small cell lung cancer N=88, for hepatocellular carcinoma N=15, for renal cancer N=2, for colorectal cancer N=1, and for glioblastoma N=17.
(12) Isolation of HLA Peptides from Tissue Samples
(13) HLA peptide pools from shock-frozen tissue samples were obtained by immune precipitation from solid tissues according to published protocols (Falk et al., 1991; Seeger et al., 1999) with minor modifications using the HLA-A*02-specific antibody BB7.2, the HLA-A, -B, -C-specific antibody W6/32, the HLA class II-specific antibody L243, CNBr-activated sepharose, acid treatment, and ultrafiltration.
(14) Mass Spectrometry Analyses
(15) 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 and additional manual control. The identified peptide sequence was assured by comparison of the generated natural peptide fragmentation pattern with the fragmentation pattern of a synthetic sequence-identical reference peptide.
(16) 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 different cancer samples to a baseline of normal tissue samples. Presentation profiles of exemplary over-presented peptides are shown in
(17) Table 8 (A and B) and 9 (A and B) show 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. 1 for urinary bladder cancer, esophageal cancer, including cancer of the gastric-esophageal junction, hepatocellular carcinoma, non-small cell lung cancer, and pancreatic cancer, peptide SEQ ID No. 2 for renal cancer, esophageal cancer, including cancer of the gastric-esophageal, glioblastoma, . . . etc.).
(18) TABLE-US-00011 TABLE 8A Overview of presentation of selected HLA-A*02-binding tumor-associated peptides of the present invention across entities. GB = glioblastoma, BRCA = breast cancer, CRC = colorectal cancer, RCC = renal cell carcinoma, CLL = chronic lymphocytic leukemia, HCC = hepatocellular carcinoma, NSCLC = non-small cell lung cancer, SCLC = small cell lung cancer, NHL = non-Hodgkin lymphoma (8 samples), AML = acute myeloid leukemia, OC = ovarian cancer, PC = pancreatic cancer, cIPC = pancreatic cancer cell lines, PCA prostate cancer and benign prostate hyperplasia, OSCAR = esophageal cancer, including = cancer of the gastric-esophageal junction, GBC_CCC = gallbladder adenocarcinoma and cholangiocarcinoma, MEL = melanoma, GC = gastric cancer, TC = testis cancer, UBC = urinary bladder cancer, UEC = uterine cancer. SEQ ID No. Sequence Peptide Presentation on cancer entities 1 HLYNNEEQV UBC, OSCAR, HCC, NSCLC, cIPC 2 ALYGKLLKL RCC, OSCAR, GB, BRCA, CLL, UBC, HCC, SCLC, NSCLC, CRC, OC, GC, NHL 4 ELAEIVFKV CRC, CLL, NSCLC, GB 5 SLFGQEVYC HCC, GB, CRC 6 FLDPAQRDL UBC, NSCLC, GB, AML, cIPC 7 AAAAKVPEV NSCLC, GB, CRC 8 KLGPFLLNA GC, GB, cIPC, NSCLC 9 FLGDYVENL CLL, CRC, UBC 10 KTLDVFNIIL CLL, GC, GBC_CCC, OSCAR 11 GVLKVFLENV HCC, NSCLC, GC, OC, OSCAR 12 GLIYEETRGV GC, OSCAR, NSCLC, NHL 13 VLRDNIQGI NSCLC, GBC_CCC, OC, GC, BRCA, OSCAR, CRC, GB, UEC, CLL, RCC, UBC, HCC, MEL, SCLC, NHL 15 ALGDYVHAC HCC, GC 16 PLWGKVFYL GBC_CCC, NSCLC, GB, cIPC, CRC 17 ILHEHHIFL RCC, NSCLC 19 TLLPTVLTL RCC, UBC, SCLC 20 ALDGHLYAI RCC, UBC, GC 21 SLYHRVLLY RCC, OSCAR, NSCLC 22 MLSDLTLQL CRC, PCA, RCC, NSCLC, BRCA, GC, SCLC, PC, OSCAR 23 AQTVVVIKA GC 24 FLWNGEDSAL PC, CRC 25 IQADDFRTL GC 26 KVDGVVIQL OSCAR, GC 27 KVFGDLDQV OSCAR, GC 29 TLCNKTFTA PCA, GB 30 TVIDECTRI GC 31 ALSDETKNNWE AML, CLL V 32 ILADEAFFSV CLL, PC, GB, UBC, PCA, CRC, SCLC, HCC, RCC, OC, NSCLC, MEL, OSCAR, cIPC, GC, BRCA, NHL 34 LLPKKTESHHK CRC, HCC, NSCLC, GB T 35 YVLPKLYVKL CLL, CRC, NSCLC, GBC_CCC, UBC, OSCAR 36 KLYGIEIEV NSCLC, GB, RCC 37 ALINDILGELVKL cIPC, CRC, RCC, HCC 38 KMQEDLVTL NSCLC, RCC, OC, GC, GBC_CCC, OSCAR, cIPC, GB, BRCA, PCA, PC, UEC, HCC, CRC, SCLC, NHL 39 ALMAVVSGL OSCAR, GBC_CCC, CLL, BRCA, HCC, UBC, NSCLC, OC, GC, MEL 40 SLLALPQDLQA PCA, NSCLC, CRC, UBC, OC 41 FVLPLVVTL OC, OSCAR, CLL, PCA, SCLC, NSCLC, NHL 42 VLSPFILTL NSCLC, RCC, BRCA, UBC, OC, NHL 43 LLWAGPVTA CLL, HCC, CRC, NSCLC, RCC, UBC, NHL, TC 44 GLLWQIIKV CRC, NSCLC, GC 45 VLGPTPELV CRC, SCLC, GC, cIPC, PC 46 SLAKHGIVAL PC, NSCLC, CRC, RCC, OC, cIPC, PCA, NHL 47 GLYQAQVNL NSCLC, SCLC 48 TLDHKPVTV OC, PCA, NSCLC 49 LLDESKLTL UBC, OC, PCA, NSCLC, RCC 50 EYALLYHTL CRC, GC 51 LLLDGDFTL SCLC, HCC 52 ELLSSIFFL UBC, NSCLC, CRC, RCC 53 SLLSHVIVA cIPC, RCC, GBC_CCC, UBC, NSCLC 54 FINPKGNWLL UBC, NSCLC, cIPC 55 IASAIVNEL BRCA, GC 56 KILDLTRVL CRC, NSCLC 57 VLISSTVRL cIPC, RCC, CLL, NHL 58 ALDDSLTSL cIPC, PC, GB 59 ALTKILAEL UBC, NSCLC 60 FLIDTSASM UBC, SCLC, RCC 61 HLPDFVKQL BRCA, CLL, GBC_CCC 62 SLFNQEVQI CLL, NHL 63 TLSSERDFAL NSCLC, GC 66 FITDFYTTV GB 67 GVIETVTSL NSCLC, GC, CRC 68 ALYGFFFKI UBC 69 GIYDGILHSI UEC, GB 70 GLFSQHFNL HCC, NSCLC 71 GLITVDIAL SCLC, PCA 72 GMIGFQVLL UBC, OC, CLL, GB, GBC_CCC 74 ILDETLENV UBC, SCLC, NHL 76 ILLDESNFNHFL NSCLC 77 IVLSTIASV cIPC, CRC, PCA 81 VLFLGKLLV CRC, UBC 82 VLLRVLIL NSCLC, TC 83 ELLEYLPQL PC, GBC_CCC 84 FLEEEITRV CRC, GC 85 STLDGSLHAV OSCAR, PCA, GC 87 YLTEVFLHVV CLL, NHL 89 YLVAHNLLL RCC 90 GAVAEEVLSSI GB 92 LLRGPPVARA cIPC, PC, RCC, UBC, OSCAR 93 SLLTQPIFL RCC, HCC 321 SLWFKPEEL GC, BRCA, CLL, PC, GB, UBC, PCA, CRC, SCLC, HCC, MEL, OC, NSCLC, GBC_CCC, OSCAR, cIPC, NHL 322 ALVSGGVAQA GBC_CCC, OSCAR, BRCA, CLL, UBC, HCC, PC, SCLC, NSCLC, CRC, OC, NHL 323 ILSVVNSQL CRC, GC, BRCA, OC, CLL, NSCLC, NHL 324 AIFDFCPSV NSCLC, CRC, GC, MEL, GB, OSCAR, CLL 325 RLLPKVQEV OSCAR, NSCLC, CRC, SCLC, OC 326 SLLPLVWKI NSCLC, CRC, GB, RCC, MEL, CLL, TC 327 SIGDIFLKY GC, GB, CRC, RCC, NSCLC 328 SVDSAPAAV SCLC, OC, PC, OSCAR, RCC, NSCLC, UBC 329 FAWEPSFRDQV SCLC, HCC 330 FLWPKEVEL NSCLC, BRCA, SCLC, OC, CLL, NHL 331 AIWKELISL GB, CRC 332 AVTKYTSAK CLL, NSCLC, MEL, NHL 333 GTFLEGVAK RCC, CLL, HCC 334 GRADALRVL BRCA, SCLC, CLL 335 VLLAAGPSAA UBC, CLL, NSCLC, GC, cIPC 336 GLMDGSPHFL PC, NSCLC 337 KVLGKIEKV RCC, CRC 339 VLGPGPPPL NSCLC, cIPC, CLL, NHL 340 SVAKTILKR NSCLC, OSCAR
(19) Table 8B shows the presentation on additional 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.
(20) TABLE-US-00012 TABLE 8B Overview of presentation of selected HLA-A*02 peptides across entities. GB = glioblastoma, BRCA = breast cancer, CRC = colorectal cancer, RCC = renal cell carcinoma, CLL = chronic lymphocytic leukemia, HCC = hepatocellular carcinoma, NSCLC = non-small cell lung cancer, SCLC = small cell lung cancer, NHL = non-Hodgkin lymphoma, AML = acute myeloid leukemia, OC = ovarian cancer, PC = pancreatic cancer, BPH = prostate cancer and benign prostate hyperplasia, OSCAR = esophageal cancer, including cancer of the gastric- oesophageal junction, GBC_CCC = gallbladder adenocarcinoma and cholangiocarcinoma, MEL = melanoma, GC = gastric cancer, UBC = urinary bladder cancer, UTC = uterine cancer, HNSCC = head and neck squamous cell carcinoma. SEQ ID No. Sequence Peptide Presentation on cancer entities 1 HLYNNEEQV GBC_CCC 2 ALYGKLLKL cIPC, UTC, PCA, MEL, AML 3 TLLGKQVTL CLL, NSCLC, NHL, AML 5 SLFGQEVYC GBC_CCC, PCA 6 FLDPAQRDL MEL 7 AAAAKVPEV MEL, HNSCC, NHL 8 KLGPFLLNA UTC, HCC 9 FLGDYVENL UTC, AML, OC, cIPC 12 GLIYEETRGV AML, UTC, HNSCC 13 VLRDNIQGI AML, HNSCC 17 ILHEHHIFL UTC 18 YVLNEEDLQKV UTC, NSCLC 19 TLLPTVLTL GBC_CCC, BRCA, UTC 22 MLSDLTLQL MEL 24 FLWNGEDSAL NSCLC, GC, UTC 28 TLYSMDLMKV HNSCC, RCC 32 ILADEAFFSV HNSCC, UTC, AML, GBC_CCC 33 LLLPLLPPLSPSL MEL, NSCLC, GBC_CCC, GC, cIPC, SCLC, GB, PC, G MCC, CRC, HCC 34 LLPKKTESHHKT UTC 35 YVLPKLYVKL HNSCC, NHL, AML 36 KLYGIEIEV UTC 37 ALINDILGELVKL MEL, UTC 38 KMQEDLVTL MEL, AML 39 ALMAVVSGL HNSCC, NHL, UTC, AML 40 SLLALPQDLQA GBC_CCC, BRCA, UTC 41 FVLPLVVTL AML, CRC, BRCA, HNSCC, UTC 42 VLSPFILTL AML, CLL, UTC 43 LLWAGPVTA HNSCC 45 VLGPTPELV OSCAR, GBC_CCC, BRCA 46 SLAKHGIVAL UBC, HNSCC, GB, CLL, MEL, UTC, HCC 47 GLYQAQVNL OSCAR 50 EYALLYHTL GBC_CCC 51 LLLDGDFTL OSCAR 53 SLLSHVIVA HCC, AML, OC, OSCAR, HNSCC, MEL, CLL, NHL, BRCA 54 FINPKGNWLL UTC, HNSCC 55 IASAIVNEL HCC, GBC_CCC 56 KILDLTRVL GBC_CCC 57 VLISSTVRL MEL 59 ALTKILAEL HCC 60 FLIDTSASM AML, CLL, BRCA, HNSCC, UTC, NHL 61 HLPDFVKQL MEL, AML 64 GLSSSSYEL GBC_CCC, HCC 65 KLDGICWQV GBC_CCC, HCC 66 FITDFYTTV MEL, UBC, HCC, HNSCC, CRC 67 GVIETVTSL AML 70 GLFSQHFNL BRCA, UTC, HNSCC, UBC, AML, OSCAR, cIPC 71 GLITVDIAL AML, MEL, UTC 72 GMIGFQVLL HNSCC, AML 73 GVPDTIATL GC 74 ILDETLENV AML, BRCA 75 ILDNVKNLL AML 77 IVLSTIASV AML 78 LLWGHPRVA NSCLC 79 SLVPLQILL HCC 80 TLDEYLTYL HCC 81 VLFLGKLLV HNSCC 86 LLVTSLVVV HCC, GBC_CCC 88 ILLNTEDLASL RCC 91 SSLEPQIQPV MEL, CLL 93 SLLTQPIFL GBC_CCC 321 SLWFKPEEL UTC, HNSCC, AML 322 ALVSGGVAQA AML, GC, cIPC, UTC, MEL 323 ILSVVNSQL MEL, GBC_CCC, AML, OSCAR 324 AIFDFCPSV BRCA, NHL, UTC, AML, HNSCC 325 RLLPKVQEV AML, BRCA, UBC, GC 326 SLLPLVWKI AML 327 SIGDIFLKY MEL, AML 328 SVDSAPAAV NHL, BRCA, AML, UTC, CLL, HNSCC, MEL 329 FAWEPSFRDQV GBC_CCC 330 FLWPKEVEL AML 331 AIWKELISL MEL, CLL, NSCLC 333 GTFLEGVAK MEL, NSCLC 334 GRADALRVL MEL, GBC_CCC, AML 335 VLLAAGPSAA AML, CRC, UTC, NHL 336 GLMDGSPHFL MEL 338 LLYDGKLSSA CRC, UBC, OC 339 VLGPGPPPL MEL, GB, UTC, AML, HCC 340 SVAKTILKR NHL
(21) TABLE-US-00013 TABLE 9A Overview of presentation of selected HLA-A*24-binding tumor-associated peptides of the present invention across entities. GB = glioblastoma, HCC = hepatocellular carcinoma, NSCLC = non-small cell lung cancer, PCA = prostate cancer, GC = gastric cancer, CRC = colorectal cancer, RCC = renal cell carcinoma. SEQ ID NO. Sequence ENTITIES 96 LYSPVPFTL HCC, NSCLC, GC, GB 97 TYTFLKETF PCA, HCC, NSCLC, GB 98 VFPRLHNVLF HCC, NSCLC, GC 99 QYILAVPVL NSCLC, GC, GB, PCA 100 VYIESRIGTSTSF GB, HCC, NSCLC, GC 101 IYIPVLPPHL HCC, NSCLC 102 VYPFENFEF GC, NSCLC 103 NYIPVKNGKQF PCA, HCC, NSCLC, GB 104 SYLTWHQQI PCA, HCC, NSCLC 105 IYNETITDLL GC, GB, HCC, NSCLC 106 IYNETVRDLL GC, GB, NSCLC 107 KYFPYLVVI HCC, NSCLC, GC 109 LFITGGQFF HCC, NSCLC, GC 110 SYPKIIEEF GB, HCC, NSCLC, GC 111 VYVQILQKL GC, HCC, NSCLC 112 IYNFVESKL NSCLC, GC 113 IYSFHTLSF NSCLC, GC, GB 114 QYLDGTWSL NSCLC, GC, GB 115 RYLNKSFVL NSCLC, GC, GB, PCA, HCC 116 AYVIAVHLF GB, PCA, HCC, NSCLC 117 IYLSDLTYI HCC, NSCLC, GC, PCA 118 KYLNSVQYI HCC, NSCLC, GC, GB, PCA 119 VYRVYVTTF NSCLC, GC 120 GYIEHFSLW HCC, NSCLC, GC 121 RYGLPAAWSTF HCC, NSCLC, GC 122 EYQARIPEF NSCLC, GC, GB, PCA, HCC 123 VYTPVLEHL NSCLC, GC, GB, HCC 124 TYKDYVDLF GC, RCC, GB, PCA, HCC, NSCLC 125 VFSRDFGLLVF GC, HCC, NSCLC 126 PYDPALGSPSRLF NSCLC, GC, PCA, HCC 127 QYFTGNPLF NSCLC, GC, GB, RCC, PCA 128 VYPFDWQYI GB, PCA, HCC, NSCLC, GC 129 KYIDYLMTW NSCLC, GC, GB, PCA, HCC 130 VYAHIYHQHF NSCLC, GC, PCA, HCC 131 EYLDRIGQLFF NSCLC, GC, RCC, GB, PCA, HCC 132 RYPALFPVL HCC, NSCLC, GC, GB, PCA 133 KYLEDMKTYF HCC, NSCLC, GC, GB 134 AYIPTPIYF PCA, NSCLC, GB 135 VYEAMVPLF GC, NSCLC 136 IYPEWPVVFF GC 137 EYLHNCSYF GC, PCA, HCC, NSCLC 138 VYNAVSTSF NSCLC, GC 139 IFGIFPNQF PCA, NSCLC 142 VYVDDIYVI NSCLC, GC 143 KYIFQLNEI GB, NSCLC 144 VFASLPGFLF NSCLC, GC 145 VYALKVRTI NSCLC 147 LYLAFPLAF NSCLC, GC, PCA, HCC 148 SYGTVSQIF PCA, HCC, NSCLC, GC, GB 149 SYGTVSQI HCC, NSCLC, GB 150 IYITRQFVQF PCA, HCC, NSCLC, GB 151 AYISGLDVF HCC, NSCLC, PCA 153 VYVPFGGKSMITF NSCLC 154 VYGVPTPHF GB, NSCLC 155 IYKWITDNF HCC, NSCLC, GC, GB 156 YYMELTKLLL NSCLC, GC, HCC 157 DYIPASGFALF NSCLC, GB 158 IYEETRGVLKVF HCC, NSCLC, GC 159 IYEETRGVL HCC, NSCLC 160 RYGDGGSSF PCA, NSCLC, GC 161 KYPDIVQQF PCA, HCC, NSCLC, GC 162 KYTSYILAF NSCLC, GC, PCA, HCC 163 RYLTISNLQF NSCLC 165 EYFTPLLSGQF NSCLC 166 FYTLPFHLI HCC, NSCLC 168 RYLEAALRL NSCLC, GC, GB, PCA, HCC 169 NYITGKGDVF NSCLC, PCA 170 QYPFHVPLL GC, PCA, HCC, NSCLC 174 VYEKNGYIYF NSCLC, GB 175 YYTQYSQTI GB, NSCLC 176 FYINGQYQF GB, PCA, HCC, NSCLC, GC 177 VYFKAGLDVF PCA, NSCLC 178 NYSSAVQKF PCA, HCC, NSCLC, GB 179 TYIPVGLGRLL NSCLC, GC 180 KYLQVVGMF NSCLC, GB 182 AYAQLGYLLF NSCLC 183 PYLQDVPRI NSCLC, GB 186 VFTTSSNIF NSCLC, GB 187 AYAANVHYL NSCLC 188 GYKTFFNEF NSCLC 192 RYSTFSEIF HCC, NSCLC, GC 194 VYQSLSNSL NSCLC 195 AYIKGGWIL RCC, HCC, NSCLC, GC 196 GYIRGSWQF NSCLC, GC 197 IFTDIFHYL HCC, NSCLC, GC, GB 199 SYLNHLNNL NSCLC 201 GYNPNRVFF GB, NSCLC 202 RYVEGIVSL NSCLC 204 EYLSTCSKL NSCLC, HCC 206 NYLDVATFL NSCLC, GC, GB, PCA, HCC 207 LYSDAFKFIVF NSCLC 209 AFIETPIPLF NSCLC 210 IYAGVGEFSF NSCLC, GC 215 SYVASFFLL GC, NSCLC 217 IYISNSIYF NSCLC, GC 221 KYIGNLDLL NSCLC, GB 223 TFITQSPLL NSCLC 225 TYTNTLERL NSCLC 226 MYLKLVQLF HCC, GC 228 IYQYVADNF NSCLC 229 IYQFVADSF NSCLC 232 YYLSDSPLL NSCLC, GC 234 SYLPAIWLL GC 235 VYKDSIYYI GB, PCA, HCC, NSCLC, GC 236 VYLPKIPSW HCC, NSCLC 238 SYLEKVRQL NSCLC 240 YYFFVQEKI HCC, NSCLC 243 SYLELANTL PCA, NSCLC 248 AFPTFSVQL NSCLC 249 RYHPTTCTI NSCLC 250 KYPDIASPTF HCC 251 VYTKALSSL NSCLC, HCC 252 AFGQETNVPLNNF HCC 253 IYGFFNENF HCC 254 KYLESSATF NSCLC 255 VYQKIILKF HCC 257 IFIDNSTQPLHF HCC 259 YFIKSPPSQLF NSCLC, GC 260 VYMNVMTRL NSCLC 261 GYIKLINFI GC 262 VYSSQFETI GB 264 LYTETRLQF NSCLC 265 SYLNEAFSF PCA 266 KYTDVVTEFL HCC, NSCLC, GC, GB, PCA 268 IFITKALQI GC 269 QYPYLQAFF NSCLC 271 RFLMKSYSF HCC 274 KQLDIANYELF NSCLC, GB, HCC 275 KYGTLDVTF NSCLC 276 QYLDVLHAL GC, RCC 277 FYTFPFQQL GC, RCC, PCA, HCC, NSCLC 280 TYNPNLQDKL HCC 281 NYSPGLVSLIL NSCLC 284 DYLKDPVTI NSCLC 285 VYVGDALLHAI PCA 286 SYGTILSHI NSCLC 288 VYPDTVALTF NSCLC, GC 289 FFHEGQYVF GC 290 KYGDFKLLEF PCA, GB 295 SYLVIHERI NSCLC, GC 296 SYQVIFQHF NSCLC, GC 297 TYIDTRTVF PCA, HCC, NSCLC, GC 298 AYKSEVVYF NSCLC, GB 299 KYQYVLNEF NSCLC, GC, GB 300 TYPSQLPSL CRC, GC 301 KFDDVTMLF NSCLC, GC, HCC 303 LYSVIKEDF GB, PCA, HCC, NSCLC, GC 304 EYNEVANLF HCC, NSCLC, GC, RCC, GB, PCA 305 NYENKQYLF NSCLC, GB, HCC 306 VYPAEQPQI NSCLC 307 GYAFTLPLF NSCLC, GC 308 TFDGHGVFF NSCLC, GC 309 KYYRQTLLF PCA, HCC, NSCLC, GC, GB 310 IYAPTLLVF GC, GB, RCC, HCC, NSCLC 311 EYLQNLNHI PCA 312 SYTSVLSRL PCA, HCC, NSCLC 313 KYTHFIQSF NSCLC, GC, RCC, GB, PCA, HCC 314 RYFKGDYSI GB, HCC 315 FYIPHVPVSF HCC, NSCLC 316 VYFEGSDFKF GB, PCA, HCC, NSCLC 317 VFDTSIAQLF GB, RCC, HCC, NSCLC, GC 318 TYSNSAFQYF GC, RCC, PCA, HCC, NSCLC 319 KYSDVKNLI PCA, HCC, NSCLC, GB 320 KFILALKVLF HCC, NSCLC 341 SYLTQHQRI PCA, NSCLC 343 NYLGGTSTI PCA, HCC, GB 344 EYNSDLHQF GB, RCC, HCC, NSCLC, GC 345 EYNSDLHQFF GB, NSCLC 346 IYVIPQPHF NSCLC, GC, GB, HCC 347 VYAEVNSL GB, NSCLC, GC 348 IYLEHTESI GC, HCC, NSCLC 349 QYSIISNVF GC, HCC, NSCLC 350 KYGNFIDKL NSCLC, GC, HCC 351 IFHEVPLKF HCC, NSCLC 352 QYGGDLTNTF NSCLC, GB 353 TYGKIDLGF HCC, NSCLC, GC, GB 354 VYNEQIRDLL NSCLC, GC, GB 355 IYVTGGHLF HCC, NSCLC, GC, RCC, GB, PCA 356 NYMPGQLTI RCC, NSCLC, GC 357 QFITSTNTF NSCLC 358 YYSEVPVKL NSCLC, GB 359 NYGVLHVTF RCC, HCC, NSCLC 360 VFSPDGHLF GB, PCA, HCC, NSCLC 361 TYADIGGLDNQI PCA, NSCLC, GC, GB, RCC 362 VYNYAEQTL GC, GB, NSCLC 363 SYAELGTTI GB, NSCLC, GC 365 VFIDHPVHL NSCLC, GB 366 QYLELAHSL HCC, NSCLC, GC 367 LYQDHMQYI HCC, NSCLC, GC, GB, PCA 368 KYQNVKHNL NSCLC, HCC 369 VYTHEVVTL NSCLC 370 RFIGIPNQF PCA 371 AYSHLRYVF GB, PCA, HCC, NSCLC 373 GYISNGELF PCA, HCC 375 KYTDYILKI NSCLC 376 VYTPVASRQSL HCC, NSCLC, GC, GB, PCA 377 QYTPHSHQF HCC, NSCLC 378 VYIAELEKI HCC, NSCLC 380 VYTGIDHHW NSCLC, GC, RCC, GB, PCA, HCC 382 AYLPPLQQVF PCA, HCC, NSCLC, GC, RCC, GB 383 RYKPGEPITF GB, PCA, HCC, NSCLC 384 RYFDVGLHNF GC, GB, PCA, HCC, NSCLC 385 QYIEELQKF NSCLC, HCC 386 TFSDVEAHF HCC, NSCLC, GC, GB 387 KYTEKLEEI HCC, NSCLC, GB, PCA 388 IYGEKTYAF HCC, NSCLC, GC, RCC, GB, PCA 389 EYLPEFLHTF NSCLC 390 RYLWATVTI GC, HCC, NSCLC 391 LYQILQGIVF NSCLC, GC, GB, RCC, HCC 392 RYLDSLKAIVF NSCLC, GC, RCC, HCC 393 KYIEAIQWI HCC, NSCLC 394 FYQPKIQQF GB, PCA, HCC, NSCLC, GC 395 LYINKANIW NSCLC, GC, HCC 396 YYHFIFTTL GB 397 IYNGKLFDL GB, NSCLC, GC 398 IYNGKLFDLL CRC, GC, RCC, GB, PCA, HCC, NSCLC 399 SYIDVLPEF HCC, NSCLC, GC, RCC, GB, PCA 400 KYLEKYYNL NSCLC 401 VFMKDGFFYF NSCLC, GC, PCA 402 VWSDVTPLTF NSCLC, CRC, GC, RCC, GB, PCA, HCC 403 TYKYVDINTF NSCLC, GC 404 RYLEKFYGL NSCLC, GC, HCC 405 NYPKSIHSF NSCLC 406 TYSEKTTLF NSCLC, GC 407 VYGIRLEHF HCC, NSCLC, GC, GB 408 QYASRFVQL GC, GB, HCC, NSCLC 409 YFISHVLAF GC, NSCLC 410 RFLSGIINF NSCLC, GC, GB, HCC 411 VYIGHTSTI NSCLC 412 SYNPLWLRI GB, RCC, HCC, NSCLC, GC 413 NYLLYVSNF HCC, NSCLC, GC 414 MYPYIYHVL HCC, NSCLC, GC, GB, PCA 415 SYQKVIELF PCA, HCC, NSCLC, CRC, GC, RCC, GB 416 AYSDGHFLF NSCLC, GC, RCC, GB, PCA, HCC 417 VYKVVGNLL GB, RCC, HCC, NSCLC, GC
(22) Table 9B show the presentation on additional 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.
(23) TABLE-US-00014 TABLE 9B Overview of presentation of selected HLA-A*24 peptides across cancer entities. GB = glioblastoma, CRC = colorectal cancer, RCC = renal cell carcinoma, HCC = hepatocellular carcinoma, NSCLC = non-small cell lung cancer, PCA = prostate cancer and benign prostate hyperplasia, GC = gastric cancer. SEQ ID No. Sequence Peptide Presentation on cancer entities 50 EYALLYHTL PCA, HCC, NSCLC, CRC, GC, RCC 104 SYLTWHQQI GB 108 PYLVVIHTL NSCLC 110 SYPKIIEEF PCA 132 RYPALFPVL RCC 135 VYEAMVPLF HCC 140 RYLINSYDF NSCLC 141 SYNGHLTIWF GB 146 NYYERIHAL NSCLC 148 SYGTVSQIF CRC 152 KFFDDLGDELLF NSCLC 155 IYKWITDNF PCA 164 HYVPATKVF NSCLC 167 RYGFYYVEF GB 171 NYEDHFPLL NSCLC 172 VFIFKGNEF NSCLC 173 QYLEKYYNL NSCLC 181 VYPPYLNYL PCA 184 IYSVGAFENF NSCLC 185 QYLVHVNDL GB 189 AYFKQSSVF NSCLC 190 LYSELTETL NSCLC 191 TYPDGTYTGRIF NSCLC 193 LYLENNAQTQF NSCLC 198 DYVGFTLKI NSCLC 200 VFIHHLPQF HCC 203 VYNVEVKNAEF NSCLC 204 EYLSTCSKL PCA 205 VYPVVLNQI NSCLC 208 TYLEKIDGF NSCLC 211 VFKSEGAYF NSCLC 212 SYAPPSEDLF NSCLC 213 SYAPPSEDLFL NSCLC 214 KYLMELTLI NSCLC 216 FYVNVKEQF NSCLC 218 LYSELNKWSF NSCLC 219 SYLKAVFNL NSCLC 220 SYSEIKDFL NSCLC 222 HYSTLVHMF NSCLC 224 PYFFANQEF HCC 227 IYRFITERF NSCLC 230 TYGMVMVTF NSCLC 231 AFADVSVKF NSCLC 233 QYLTAAALHNL NSCLC 237 KYVGQLAVL HCC 239 VYAIFRILL GC 241 SYVKVLHHL HCC 242 VYGEPRELL HCC 244 VHFEDTGKTLLF NSCLC 245 LYPQLFVVL GC 246 KYLSVQLTL NSCLC 247 SFTKTSPNF HCC 256 VFGKSAYLF NSCLC 258 AYAQLGYLL NSCLC 263 RYILENHDF HCC 267 SFLNIEKTEILF HCC 270 YYSQESKVLYL HCC 272 RYVFPLPYL NSCLC 273 IYGEKLQFIF NSCLC 278 KYVNLVMYF NSCLC 279 VWLPASVLF NSCLC 282 NYLVDPVTI NSCLC 283 EYQEIFQQL NSCLC 287 IYNPNLLTASKF NSCLC 291 YYLGSGRETF NSCLC, GB, PCA, HCC 292 FYPQIINTF NSCLC 293 VYPHFSTTNLI HCC 294 RFPVQGTVTF PCA 302 LYLPVHYGF NSCLC 342 NYAFLHRTL NSCLC 344 EYNSDLHQF PCA 348 IYLEHTESI GB 350 KYGNFIDKL PCA 364 KYLNENQLSQL NSCLC 372 VYVIEPHSMEF NSCLC 374 VFLPRVTEL NSCLC 379 VFIAQGYTL NSCLC 381 KYPASSSVF RCC, NSCLC
Example 2
(24) Expression Profiling of Genes Encoding the Peptides of the Invention
(25) 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, and a high tumor-to-normal ratio of gene expression indicates a therapeutic window. Moreover, over-expression of source genes in tumor entities that were not yet analyzed for peptide presentation indicates that a certain peptide may be of importance in the respective entity.
(26) For HLA class I-binding peptides of this invention, normal tissue expression of all source genes was shown to be minimal based on a database of RNASeq data covering around 3000 normal tissue samples (Lonsdale, 2013). In addition, gene expression data from tumors vs normal tissues were analyzed to assess target coverage in various tumor entities.
(27) RNA Sources and Preparation
(28) 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.
(29) Total RNA from healthy human tissues for RNASeq experiments was obtained from: Asterand (Detroit, Mich., USA and Royston, Herts, UK); Bio-Options Inc. (Brea, Calif., USA); ProteoGenex Inc. (Culver City, Calif., USA); Geneticist Inc. (Glendale, Calif., USA); Istituto Nazionale Tumori “Pascale” (Naples, Italy); University Hospital of Heidelberg (Heidelberg, Germany); BioCat GmbH (Heidelberg, Germany), BioServe (Beltsville, Md., USA), Capital BioScience Inc. (Rockville, Md., USA).
(30) Total RNA from tumor tissues for RNASeq experiments was obtained from: Asterand (Detroit, Mich., USA & Royston, Herts, UK), Bio-Options Inc. (Brea, Calif., USA), BioServe (Beltsville, Md., USA), Geneticist Inc. (Glendale, Calif., USA), ProteoGenex Inc. (Culver City, Calif., USA), Tissue Solutions Ltd (Glasgow, UK), University Hospital Bonn (Bonn, Germany), University Hospital Heidelberg (Heidelberg, Germany), University Hospital Tübingen (Tübingen, Germany)
(31) 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).
(32) RNAseq Experiments
(33) Gene expression analysis of tumor and normal tissue RNA samples was performed by next generation sequencing (RNAseq) by CeGaT (Tübingen, 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.
(34) Exemplary expression profiles of source genes of the present invention that are highly over-expressed or exclusively expressed in different cancers are shown in
(35) TABLE-US-00015 TABLE 10A Target coverage within various tumor entities, for expression of source genes of selected peptides. Over-expression was defined as more than 1.5-fold higher expression on a tumor compared to the relevant normal tissue that showed highest expression of the gene. <19% over-expression = I, 20-49% = II, 50-69% = III, >70% = IV. If a peptide could be derived from several source genes, the gene with minimal coverage was decisive. The baseline included the following relevant normal tissues: adipose tissue, adrenal gland, artery, bone marrow, brain, cartilage, colon, esophagus, gallbladder, heart, kidney, liver, lung, lymph node, pancreas, pituitary, rectum, skeletal muscle, skin, small intestine, spleen, stomach, thymus, thyroid gland, trachea, urinary bladder and vein. 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. SEQ ID AML BRCA CLL CRC GB HCC pNSCLC OC OSCAR PC RCC SCLC NO Sequence (N = 7) (N = 10) (N = 10) (N = 20) (N = 24) (N = 15) (N = 11) (N = 12) (N = 11) (N = 26) (N = 10) (N = 10) 2 ALYGKLLKL I II I I I I I I I I I I 3 TLLGKQVTL I II I I I I I I I I I I 5 SLFGQEVYC I I I I I II I I I I I I 9 FLGDYVENL I I IV I III I I I I I I II 10 KTLDVFNIIL I I IV I III I I I I I I II 11 GVLKVFLENV I II I I I I I II I I I I 12 GLIYEETRGV I II I I I I I II I I I I 13 VLRDNIQGI I II I I I I I II I I I I 14 LLDHLSFINKI I I III I I I I I I I I III 16 HLYNNEEQV I I I I I IV I I II I II I 17 ILHEHHIFL I I I II I II II II I II IV I 18 YVLNEEDLQKV I I I II I II II II I II IV I 19 TLLPTVLTL I I I I I I I I I I IV I 20 ALDGHLYAI I I I I I I I I I I IV I 27 KVFGDLDQV I I I I I I I I I I II I 28 TLYSMDLMKV I I I I I I I I I I II I 31 ALSDETKNNWEV I III I II III I III III II I I IV 32 ILADEAFFSV I III I II III I III III II I I IV 33 LLLPLLPPLSPSLG I I I I I I I I I I I II 36 KLYGIEIEV I I I I II I I I I I I I 39 ALMAVVSGL I I IV I I I I I I I I I 42 VLSPFILTL I I I I I I I I II I I I 44 GLLWQIIKV I I I III I I I I I I I I 45 VLGPTPELV I I I I I I I I I II I I 46 SLAKHGIVAL I II I I I I I I I I I I 47 GLYQAQVNL I I I II II II III I IV II I II 49 LLDESKLTL I I I I I I I I I I III I 50 EYALLYHTL I I I II I I I I I I II I 51 LLLDGDFTL I I I I I III I I I I I I 52 ELLSSIFFL I I I I I I II I II I II II 53 SLLSHVIVA I II I II I I II II II I I II 54 FINPKGNWLL I I I I I I II I I II I I 55 IASAIVNEL I II II I II I II II I I I II 59 ALTKILAEL I I I I I I I I I I I II 63 TLSSERDFAL I I I I I III I I I I II I 64 GLSSSSYEL I I I I I III I I I I I I 65 KLDGICWQV I I I I I II I I I I I I 67 GVIETVTSL IV I I I I I I I I I I I 69 GIYDGILHSI I I I II II II II II II I I II 70 GLFSQHFNL III I I I I I I I II I I I 73 GVPDTIATL I I I II I I I I I I I I 75 ILDNVKNLL IV I I I I I I I I I I I 78 LLWGHPRVA I IV I II I I III III IV III I I 79 SLVPLQILL I I I I I II I I I I I I 80 TLDEYLTYL I I I I I II I II I I I I 81 VLFLGKLLV I I II II III II I II II II II IV 84 FLEEEITRV I I I I I I I I I I I II 86 LLVTSLVW I I I I I III I I I I I I 88 ILLNTEDLASL I I I I I I I I I I II II 91 SSLEPQIQPV I II II I II I I II III I II I 322 ALVSGGVAQA I III I I I I I III III II I I 323 ILSVVNSQL I I IV II I I I I I I I I 324 AIFDFCPSV I I IV I I I I I I I I I 325 RLLPKVQEV I I I I II I I I I I I I 327 SIGDIFLKY I II I III II I IV III III II I IV 328 SVDSAPAAV I I I I I I I I I I I II 329 FAWEPSFRDQV I I I I I III I I I I I I 331 AIWKELISL I I I I II I I I I I I III 332 AVTKYTSAK I II I I I II I I I I I II 334 GRADALRVL I I IV I I I I I I I I I 335 VLLAAGPSAA I I II I I I I I I I I II 336 GLMDGSPHFL I II I I I I I I I I I I 337 KVLGKIEKV I II I I I I I I I I I II 338 LLYDGKLSSA I II I I I I I I I I I II 96 YYTQYSQTI I IV I II I I III III IV III I I 98 VFPRLHNVLF I I I I I I I I I I I II 100 VYIESRIGTSTSF I II I I I I I II II I I II 101 IYIPVLPPHL I IV I I I I IV III III I I I 103 NYIPVKNGKQF I I III I I I I I I I I I 106 IYNETVRDLL I I I I I I I II I I I I 107 KYFPYLWI I II I I I I I II III I II I 108 PYLWIHTL I II I I I I I II III I II I 110 SYPKIIEEF I I III I I I I I I I I I 113 IYSFHTLSF I I I I II I I I I I I III 114 QYLDGTWSL I IV I II II I IV II IV III I II 115 RYLNKSFVL I II I II I I I III I I I II 117 IYLSDLTYI I I IV I I I I I I I I I 118 KYLNSVQYI I I IV I I I I I I I I I 119 VYRVYVTTF I I I I I I II I II I I I 121 RYGLPAAWSTF I I IV I I I I I I I I I 123 VYTPVLEHL I III I II III I III III II I I IV 124 TYKDYVDLF I III I II III I III III II I I IV 125 VFSRDFGLLVF I III I II III I III III II I I IV 126 PYDPALGSPSRLF I I I II I III I II I I I I 127 QYFTGNPLF I I I I I I I I I I I II 132 RYPALFPVL I I I I I I I II I I I I 135 VYEAMVPLF I I I I I I I I I I I II 138 VYNAVSTSF I I I I I I I I I I I II 139 IFGIFPNQF IV I I I I I I I I I II I 140 RYLINSYDF I I I I I I II I I I I II 141 SYNGHLTIWF I I I I III I I I I I I I 146 NYYERIHAL III I IV I II I II II I I I I 147 LYLAFPLAF I II I I I I I I I I I I 151 AYISGLDVF I I I I I I II I IV I I II 152 KFFDDLGDELLF I I I I I I II I IV I I II 156 YYMELTKLLL I I I I I I I I III I I IV 157 DYIPASGFALF I I I I II I I I I I I I 158 IYEETRGVLKVF I II I I I I I II I I I I 159 IYEETRGVL I II I I I I I II I I I I 162 KYTSYILAF I I I I I I I II I I II I 164 HYVPATKVF I II I I I I IV IV III I II II 167 RYGFYYVEF I I I I IV I III II II I I I 171 NYEDHFPLL I I I I I I I II II I I II 172 VFIFKGNEF I I I I I I II I II I I I 173 QYLEKYYNL I I I I I I II I II I I I 174 VYEKNGYIYF I II I I I I II I III I I I 175 LYSPVPFTL I I I I I I I I II I I I 176 FYINGQYQF III I III I II I II I II I I II 177 VYFKAGLDVF I II I II I I I II I I I I 178 NYSSAVQKF I I I I III I I I I I I I 179 TYIPVGLGRLL I I I I I I I III II I I II 181 VYPPYLNYL I II I I I I I I I I I I 182 AYAQLGYLLF I I I I I I I I I I I II 184 IYSVGAFENF I II I I I I I I I I I II 185 QYLVHVNDL I I I I II I I I I I II II 189 AYFKQSSVF II I II I I I I I I I I I 190 LYSELTETL IV III IV I II I IV I I II I IV 191 TYPDGTYTGRIF I I II I I I I I I I I I 193 LYLENNAQTQF I I I I I I II I IV I I I 195 AYIKGGWIL I I I I I II I I I I I I 198 DYVGFTLKI I I I I III I II I I I I I 203 VYNVEVKNAEF I I I I I I I I I I I II 204 EYLSTCSKL II II I I I I I II I I I III 205 VYPWLNQI I I I I I I I I I I I II 206 NYLDVATFL I I I I II I II I I I I II 208 TYLEKIDGF I I I I I I I I II I I I 210 IYAGVGEFSF I I I I I I I I I I I II 211 VFKSEGAYF I I I I I I I I I I I II 212 SYAPPSEDLF I II I I I I I I I I I I 213 SYAPPSEDLFL I II I I I I I I I I I I 214 KYLMELTLI I I I I I I I I I I I II 216 FYVNVKEQF I I I I I I I I I I I II 218 LYSELNKWSF I I I I I I II I I I I I 219 SYLKAVFNL I III I I I I I I I I I I 220 SYSEIKDFL I I IV I I I I I I I I I 221 KYIGNLDLL I I I I I I I I I I II I 222 HYSTLVHMF I I I I I I I I I I II I 224 PYFFANQEF II I I I I I I I I I I I 226 MYLKLVQLF I I I I I I I I I I I II 227 IYRFITERF I I I I I I I I I I I II 230 TYGMVMVTF I I I I II I I I I I I I 231 AFADVSVKF I I I I II I I I I I I I 233 QYLTAAALHNL I I I I I I I I I I I I 235 VYKDSIYYI II I IV I I I I I I I I I 236 VYLPKIPSW I I I I I II I I I I I I 237 KYVGQLAVL I I I I I I I I I I I II 239 VYAIFRILL I II I I I I I I I I I II 240 YYFFVQEKI I I I I II I I I I I I I 241 SYVKVLHHL I I I I I I I I I I I II 242 VYGEPRELL I II I I I II I I I I I II 243 SYLELANTL I I I I I I I I II I I I 244 VHFEDTGKTLLF I II I I I I II I III I I I 245 LYPQLFWL I I I I I I I II I I I I 246 KYLSVQLTL I I I I I I I I I I I II 247 SFTKTSPNF I I I II I I I I I I I I 251 VYTKALSSL I I I I I I I I I I I III 256 VFGKSAYLF II I I I I I I I I I I I 258 AYAQLGYLL I I I I I I I I I I I II 263 RYILENHDF I I I I I II I I I I I I 267 SFLNIEKTEILF I I I I I III I I I I I I 270 YYSQESKVLYL I II II I II I I III II I I II 272 RYVFPLPYL I I I II I II I I I I I I 273 IYGEKLQFIF I I I I I I I I I I I II 274 KQLDIANYELF I III I I II I I II I I I II 276 QYLDVLHAL I II I I I I I II II I II II 277 FYTFPFQQL I I I I I I I I I I I II 278 KYVNLVMYF I I I I I I I II I I I I 279 VWLPASVLF I I I I I I I I I I I II 282 NYLVDPVTI I II I I I I I III I I I I 283 EYQEIFQQL I II I I I I I III I I I I 287 IYNPNLLTASKF I III I I I I I III III I I I 291 YYLGSGRETF I I I I II I II II III I I II 292 FYPQIINTF I I I I II I I I I I I I 293 VYPHFSTTNLI I I I I II I I I I I I I 294 RFPVQGTVTF I IV I I I I I II I I I I 295 SYLVIHERI I I II I II I I III I I I II 300 TYPSQLPSL I I I II I I I I I I I I 302 LYLPVHYGF I I I II I I I I I I I II 304 EYNEVANLF I I I I II I I I I I I I 307 GYAFTLPLF I II I II II I I II I I II II 308 TFDGHGVFF I I I II I I I I II I I I 309 KYYRQTLLF I I I I I I I III IV I II II 310 IYAPTLLVF I II II I I I I I I I I I 314 RYFKGDYSI I I I I II I I I I I I I 315 FYIPHVPVSF I I I I I III I I I I I I 320 KFILALKVLF I I I I I I I I I I I II 342 NYAFLHRTL II I I I I I I II III I I I 343 NYLGGTSTI I II I I I II I I I I I II 344 EYNSDLHQF I I I I I I I I I I I II 345 EYNSDLHQFF I I I I I I I I I I I II 348 IYLEHTESI I I II I I I I I I I I I 350 KYGNFIDKL I I I I I I I II I I I I 351 IFHEVPLKF I I I I I I I I I I I II 352 QYGGDLTNTF I I I I I I II I I II I I 353 TYGKIDLGF I I I I I I I I I I I II 354 VYNEQIRDLL I I I I I I I I I I I II 355 IYVTGGHLF I I I I I I I I II I I I 356 NYMPGQLTI I I I II I I II II I II II I 358 YYSEVPVKL I IV I II I I III III IV III I I 359 NYGVLHVTF II I II II II III I I I I II II 360 VFSPDGHLF I II I I I I I I I I I I 361 TYADIGGLDNQI II I I I I I I I I I I I 363 SYAELGTTI I I I I II I I I II I I I 364 KYLNENQLSQL I I I I I I I I I I I III 365 VFIDHPVHL I I I I II I I I I I I II 366 QYLELAHSL I I I I I I I II I I I II 367 LYQDHMQYI I I I I I I I I II I I I 368 KYQNVKHNL I I I I I I I I I I I II 371 AYSHLRYVF I I I IV III I IV II IV III III II 372 VYVIEPHSMEF I I II I I I I I I I I II 374 VFLPRVTEL I III I II III I III III II I I IV 376 VYTPVASRQSL I I I I II I I I I I I II 377 QYTPHSHQF I I I I II I II I I I I III 378 VYIAELEKI I II I I I I I I I I I II 379 VFIAQGYTL I I I I I I II I II I II II 380 VYTGIDHHW I II I II I I II III IV I I III 381 KYPASSSVF I I I I I I I II I I III I 382 AYLPPLQQVF I I I I I I I I I I I II 383 RYKPGEPITF II IV I II I I IV II II I I II 385 QYIEELQKF I I IV I I I I I I I I I 386 TFSDVEAHF I I I I I I I I I I I II 387 KYTEKLEEI I I I I IV I I II I I I III
(36) TABLE-US-00016 TABLE 10B Target coverage for source genes of selected peptides. Over-expression was defined as more than 1.5-fold higher expression on a tumor compared to the relevant normal tissue that showed highest expression of the gene. <19% over-expression = I, 20-49% = II, 50-69% = III, >70% = IV. If a peptide could be derived from several source genes, the gene with minimal coverage was decisive. The baseline included the following relevant normal tissues: adipose tissue, adrenal gland, artery, bone marrow, brain, cartilage, colon, esophagus, gallbladder, heart, kidney, liver, lung, lymph node, pancreas, pituitary, rectum, skeletal muscle, skin, small intestine, spleen, stomach, thymus, thyroid gland, trachea, urinary bladder and vein. 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. NHL = non-Hodgkin lymphoma, PCA = prostate cancer and benign prostate hyperplasia, GC = gastric cancer, GBC_CCC = gallbladder adenocarcinoma and cholangiocarcinoma, MEL = melanoma, UBC = urinary bladder cancer, UTC = uterine cancer, HNSCC = head and neck small cell carcinoma. SEQ GBC_ ID NHL OCA GC CCC MEL UBC UTC HNSCC NO. Sequence (N = 10) (N = 10) (N = 11) (N = 10) (N = 10) (N = 10) (N = 10) (N = 10) 2 ALYGKLLKL I I I I I I I I 3 TLLGKQVTL I I I I I I I I 4 ELAEIVFKV I I I I I I I II 9 FLGDYVENL I I I I I I I I 12 GLIYEETRGV II II I I II I I I 13 VLRDNIQGI II II I I II I I I 19 TLLPTVLTL I I I I I III I I 32 ILADEAFFSV II I I I II I I I 34 LLPKKTESHHKT II I I I I I I I 35 YVLPKLYVKL I I I I I I I I 37 ALINDILGELVKL I I I I I I I I 39 ALMAVVSGL II I I I I I I I 41 FVLPLVVTL I I I I I I I I 42 VLSPFILTL I I I II I II I II 45 VLGPTPELV I I II II I I I I 46 SLAKHGIVAL I I I I I I II I 47 GLYQAQVNL I I I II IV II I III 51 LLLDGDFTL I I I I I I I I 53 SLLSHVIVA III I I II I I II I 55 IASAIVNEL II I I II I I I I 60 FLIDTSASM I I I I I I I I 61 HLPDFVKQL I I I I I I I I 70 GLFSQHFNL I I I II I II III II 96 YYTQYSQTI I I I II I I I II 98 VFPRLHNVLF I I I I I I I I 99 QYILAVPVL I I I I I I I I 100 VYIESRIGTSTSF I I I I II I I I 101 IYIPVLPPHL III III I III I II III III 103 NYIPVKNGKQF I I I I I I I I 104 SYLTWHQQI I I I I I I I I 105 IYNETITDLL I I I I I I I I 110 SYPKIIEEF II I I I I I I I 113 IYSFHTLSF I I I I I I I II 114 QYLDGTWSL II I II IV IV III IV III 116 AYVIAVHLF I I I I I I I I 117 IYLSDLTYI II I I I I I I I 118 KYLNSVQYI II I I I I I I I 119 VYRVYVTTF I I I I I I II I 121 RYGLPAAWSTF I I I I I I I I 123 VYTPVLEHL II I I I II I I I 124 TYKDYVDLF II I I I II I I I 126 PYDPALGSPSRLF I II II II I I III I 127 QYFTGNPLF I I I I I I I I 128 VYPFDWQYI I I I I I I I I 132 RYPALFPVL I I I I I I I I 135 VYEAMVPLF I I I I I I I I 144 VFASLPGFLF III I I I I I I I 145 VYALKVRTI II I I II II II I II 147 LYLAFPLAF I I I I I I I I 150 IYITRQFVQF I I I I II I I I 151 AYISGLDVF I I I I I I I III 155 IYKWITDNF I I I I I I II I 156 YYMELTKLLL II I I II I I I I 158 IYEETRGVLKVF II II I I II I I I 161 KYPDIVQQF II I I I I I I I 162 KYTSYILAF II I I II I I I I 163 RYLTISNLQF I I I I I I I I 165 EYFTPLLSGQF I I I I I I I I 166 FYTLPFHLI I I I I I I I I 168 RYLEAALRL I I I I II I I I 170 QYPFHVPLL III I I I I I I I 171 NYEDHFPLL I I II I IV II I II 172 VFIFKGNEF I I I I I I I I 175 LYSPVPFTL I I I II I I I II 176 FYINGQYQF I II I I I I I II 177 VYFKAGLDVF I III I II I II II I 178 NYSSAVQKF I III I I II I I I 179 TYIPVGLGRLL I I I I I I III II 180 KYLQVVGMF I I I I I I I I 191 TYPDGTYTGRIF II I I I I I I I 195 AYIKGGWIL I I I I I I I I 197 IFTDIFHYL I I I I I I I I 204 EYLSTCSKL II II I I I I IV II 206 NYLDVATFL I I I I I I II I 235 VYKDSIYYI IV I I I I I I I 277 FYTFPFQQL I I I I I I I II 291 YYLGSGRETF I I I II II II III III 296 SYQVIFQHF I I I I I I I II 297 TYIDTRTVF I I I I I I III I 304 EYNEVANLF I III I I I I I I 307 GYAFTLPLF I II I I I I II I 309 KYYRQTLLF I I I I I I II I 312 SYTSVLSRL II I I I II I I I 316 VYFEGSDFKF II I I I I I I I 317 VFDTSIAQLF I I I I I I I I 318 TYSNSAFQYF I I I I I I I I 319 KYSDVKNLI I I I I I I I I 326 SLLPLVWKI I I I I I I I I 327 SIGDIFLKY I I II III I I III II 328 SVDSAPAAV II I I I I I I I 330 FLWPKEVEL II I I I I I I I 331 AIWKELISL I I I I I I I II 332 AVTKYTSAK I I I I I I I I 333 GTFLEGVAK I I I I I I I I 334 GRADALRVL I I I I I I I I 335 VLLAAGPSAA III I I I I I I I 342 NYAFLHRTL I I I I I II I I 343 NYLGGTSTI I IV I I I I II I 344 EYNSDLHQF II I I I I I I I 345 EYNSDLHQFF II I I I I I I I 347 VYAEVNSL I I I I I I I I 348 IYLEHTESI I I I I I I I I 350 KYGNFIDKL I I I I I I I I 352 QYGGDLTNTF I I I II I II I I 353 TYGKIDLGF II I I I I I I I 354 VYNEQIRDLL I I I I I I I I 355 IYVTGGHLF I I I II I II I II 356 NYMPGQLTI I I II II I I I I 359 NYGVLHVTF IV I I I II I I I 360 VFSPDGHLF II I I I I I I I 361 TYADIGGLDNQI I I I I I I I I 362 VYNYAEQTL I I I I I I I I 363 SYAELGTTI I I I I I I I I 365 VFIDHPVHL I I I I I I I I 366 QYLELAHSL I I I I I I I I 367 LYQDHMQYI I I I I I I I I 371 AYSHLRYVF I I III II I IV I II 376 VYTPVASRQSL II I I II I II I II 380 VYTGIDHHW II I I II I I I II 383 RYKPGEPITF II III I III I II III II 386 TFSDVEAHF II I I I I I I I 387 KYTEKLEEI I I I I I I I I
(37) TABLE-US-00017 TABLE 8 Target coverage within various tumor entities, for expression of source genes of selected peptides. A gene was considered over-expressed if its expression level in a tumor sample was more than 2-fold above the highest 75% percentile of expression levels determined from samples of the following normal organs (adjacent to tumors): rectum (n = 10), esophagus (n = 11), bladder (n = 19), kidney (n = 129), stomach (n = 35), colon (n = 41), head and neck (n = 43), liver (n = 50), lung (n = 51), thyroid (n = 59), lung (n = 59). Over-expression categories are indicated as “A” (>=50% of tumors above the cutoff), “B” (>=20% of tumors above the cutoff, but <50%), and “C” (>=5% of tumors above the cutoff, but <20%). SEQ ID ACC(N = BLCA(N = CESC(N = CHOL(N = DLBC(N = HNSC(N = KICH(N = KIRP(N = LGG(N = MESO(N = PCPG(N = NO. 79) 408) 307) 36) 48) 521) 66) 291) 534) 87) 184) 16 C C C C C 2 3 4 B C B B 5 6 8 C C 9 10 11 C B B B A C C C C B 12 C B B B A C C C C B 13 C B B B A C C C C B 1 C B B C 17 B A C 18 B A C 21 C 22 C 24 C 27 28 29 30 31 C C B 32 C C B 34 C C B 35 36 C C B C C 37 38 C 39 C B 40 C C A C C C 42 A A B B B C C 45 47 C C C C B C 48 C 49 51 C 52 C 53 54 C C C C 55 56 58 C 60 C C B C C 61 62 B 63 64 C 65 66 C B A 67 B 68 C 69 70 B B C B B 72 C C B C 74 A 75 76 C 78 C C C B 79 80 81 C C C C C C C 84 A 86 87 C 88 C A 90 C C 91 C C 92 B C C C 321 B B C C B B C A B B 323 B 325 C B C B A 326 327 B A C A C 328 C B C C 329 330 C C C A C C A 331 332 C B A B B B C B 334 A 335 B A C A C C 336 340 B B 175 C C B 97 98 C C 100 C B A C B B 101 103 104 105 B A B B 106 B A A B 107 C B 108 C B 110 B A A C C 111 C A B B 112 C A B B 113 114 C B C C C C 115 116 B B A 117 C B 118 C B 119 C 121 A 122 123 C C B 124 C C B 125 C C B 126 C C C 127 128 C 129 B B 130 B B 131 B 132 133 C 134 B C 135 C C 136 137 138 B A C B B C 139 B 140 141 142 C B B B C 144 C 145 C C 146 B 147 148 C 149 C 150 151 C A B 152 C A B 153 155 C 156 C C A A B 157 B B C 158 C B B B A C C C C B 159 C B B B A C C C C B 161 C 162 C B A C C 164 B B C A B B B 165 166 167 C 168 C C 169 170 C C A C C 171 B C C 172 C B A 173 C B A 174 B B C A C 96 C C C B 176 177 178 A 180 C A C B A C 181 C B 182 C 183 184 185 C C C 186 187 C C C A 188 C B B B B 189 190 191 A 192 B 193 C B 194 B A C A B C B 195 196 197 198 C 199 C B B 200 202 C 203 C C A C C C C C 204 205 C 206 C 207 C C C C 208 C C 209 210 B A B B C C 211 B B A B C C C 212 213 214 B A B B C 216 C B A B B C 217 218 C C 219 C C 220 221 B 222 B 223 224 225 C C 226 C B A C A B 227 C 228 A 229 C 230 B B C 231 B B C 232 C B A C A B C C 233 B C B 234 C C 235 A 236 237 C A A C A A C B 238 C C B C 240 C C 241 C B C C 242 C C C C 243 C 244 B B C A C 247 C C C A 249 C 250 C A C C 251 C B A C A B C C 253 C B B 255 256 C 258 C 259 C C 262 C B 263 264 C A C 265 266 C B 267 C 268 269 C A A C B C 270 271 272 273 C C B A C C 274 C C 276 277 C C 278 B 279 C 282 283 284 285 286 287 288 C C B B C C 289 291 C C 292 C C 293 C C 294 C 295 296 C C C C 297 C C C 298 300 A A 301 C 302 B 304 305 C B C A 306 C C C B B 307 C 309 B 312 313 C 314 B 315 C 316 317 319 B 320 C B B B B 341 B 342 C C C C 343 C 344 B B A B C 345 B B A B C 346 C B B B C 347 348 B A A C C 349 350 351 352 C C C C 353 C B A C A A C B 354 C B A C B B B 355 A A B B B C C 356 C B 357 C B C C C B 358 C C C B 359 C B 360 C C B C 361 C C C C 363 C C C C B 364 B A C C B 365 C 366 C B A C B B 367 368 369 C B A B B 371 C B 372 B A C A C C 373 C 374 C C B 375 B 376 C C C C C 377 C 378 C A C 379 C 380 C C C 382 383 385 C B 386 C C C 387 B B 388 C 389 C B B 390 C B A C B B A 391 C B A B B 392 B B A C B B C 393 394 B A C A B C C 395 396 A B 397 A A C A A C C 398 A A C A A C C 399 B A C 400 B B B A C 401 B B B A C 402 C A A A C A C A A C 403 C B B B 404 C B B B 405 C B B B 406 C B C C C B 407 C A A C A B C C 408 B A B B 409 B A B B 410 C A A C A B C C 412 C B A C B B A 413 414 A 415 C C B C C C 416 C 417 C B A B B C SEQ ID PRAD(N = SARC(N = SKCM(N = STAD(N = TGCT(N = THCA(N = THYM(N = UCEC(N = UCS(N = UVM NO. 498) 263) 473) 415) 156) 513) 120) 546) 57) (N = 80) 16 2 3 4 C C A C C 5 6 8 C 9 10 11 A C B B B C A A B C 12 A C B B B C A A B C 13 A C B B B C A A B C 1 C C B A B C B 17 C C A B 18 C C A B 21 B 22 B 24 C C 27 C 28 C 29 C 30 C 31 C C B B B C 32 C C B B B C 34 C B B B C 35 B 36 C 37 38 39 C 40 C A A C B A 42 C C C C A C 45 B 47 C B C C C 48 C C 49 51 C C 52 53 54 C C C 55 C 56 C 58 B C 60 C C 61 62 C C C C 63 64 65 66 C C C C C 67 C B 68 69 C 70 C C C A B A A 72 B C C B C C C 74 A A 75 B 76 78 B B C C C 79 C 80 81 C C C 84 86 87 C 88 B 90 B A C A 91 C C 92 C C C 321 C B B C B B B B 323 325 C B C B C 326 A C C C 327 B C A A B B 328 C B A C C B 329 330 C C A A C C 331 B 332 A B B B A C B A B B 334 C C C C 335 C C B B C A B C 336 340 C 175 C C 97 C B 98 B C B 100 B B B A B B A 101 103 104 105 B C A B B C B 106 B B C A A B A 107 108 110 C B C A B B B 111 C C C A B C 112 C C C A B C 113 B 114 B B B C C C C C 115 C 116 B C B A B C C 117 C 118 C 119 121 C C C C 122 123 C C B B B C 124 C C B B B C 125 C C B B B C 126 B C B B B 127 C 128 B C 129 C 130 C 131 132 C C 133 134 B C C B A C B B 135 C C 136 C 137 138 C C A A B C B 139 C B 140 141 142 B C A A C C 144 C 145 C C B 146 C 147 C 148 149 150 C A 151 152 153 155 B C 156 C C C B B C C 157 C 158 A C B B B C A A B C 159 A C B B B C A A B C 161 B 162 C B C B C C 164 B B B A C C A B 165 C 166 C 167 C B 168 B C C C A 169 170 C C C B B 171 B C C C C 172 C C C 173 C C C 174 B B C C C C C 96 B B C C C 176 177 B 178 C C 180 C C C C C C 181 C A C 182 183 C C 184 185 C C 186 C C C 187 C C C C C C C 188 B B 189 190 191 C C C 192 C B C A C B C 193 194 B B A A B B 195 196 197 C 198 199 C C 200 A 202 203 B C A C C B 204 205 C 206 C 207 208 B C A C 209 B C 210 B B B A B B B 211 A B B A B B A 212 C C 213 C C 214 B C B A A C B 216 B B C B B C B 217 C 218 219 C C 220 C B 221 C C 222 C C 223 C 224 B 225 C C C 226 B B A A C B B 227 C C 228 229 A 230 C 231 C 232 B A B A A B A 233 234 C C C 235 C 236 237 B A A A A B A 238 C B 240 C B 241 C A B C C C 242 C B C B C 243 C 244 B B C C C C C 247 249 B 250 B B C C B 251 A B B A A B A 253 C C C C C 255 C B 256 B C 258 259 C B B 262 C B 263 B 264 C C B C 265 C 266 267 C C 268 269 B B C B C C 270 C C 271 C A 272 B C C C 273 C C B A A C B 274 C 276 A C C A 277 C C 278 C C C 279 282 C C C 283 C C C 284 C 285 C 286 B C C B 287 288 B C B A A C B 289 C C 291 C C C B 292 C B 293 C B 294 C C 295 B C 296 297 B C C C 298 C 300 B A B 301 C 302 304 305 B C 306 C C C B C C 307 C C C C C 309 C C C 312 C 313 C 314 315 316 C 317 B C 319 320 B B B A C C A 341 C C 342 C 343 B 344 B B A A B B A 345 B B A A B B A 346 B C A A C C 347 C 348 C B C A B B B 349 C B 350 C C 351 352 C C C 353 B B A A B B A 354 B B A A B B A 355 C C C C A C 356 C 357 C A C 358 B B C C C 359 C C 360 C C B 361 C B C B C 363 C 364 B C A A C B C 365 366 C B A A C B A C 367 368 C 369 B C B C B B B 371 C C 372 C C B B C A B C 373 374 C C B B B C 375 C 376 C B C B 377 C 378 C C C C C 379 380 C C C B C B C 382 C 383 385 C 386 C B B C C 387 C C C 388 389 C C 390 B B A A B C B 391 B C B C B B B 392 A B B B A B C B 393 C A 394 B B B A A B B 395 C C B 396 C C C 397 B B B A A B A 398 B B B A A B A 399 C C A B 400 C C A C C 401 C C A C C 402 C A B A B B B A A 403 B B 404 B B 405 B B 406 C A C 407 B B B A A B A 408 B C B A B B B 409 C C B B B C 410 B B B A A B A 412 B B A A B C B 413 C 414 C C 415 C B B C C C C 416 417 B B A A B B ACC = Adrenocortical carcinoma (N = 79), BLCA = Bladder urothelial carcinoma (N = 408), LGG = Lower grade glioma (N = 534), CESC = Cervical squamous cell carcinoma and endocervical adenocarcinoma (N = 307), STAD = Stomach adenocarcinoma (N = 415), CHOL = Cholangiocarcinoma (N = 36), MESO = Mesothelioma (N = 87), KICH = Kidney chromophobe (N = 66), PRAD = Prostate adenocarcinoma (N = 498), DLBC = Lymphoid neoplasm diffuse large B-cell lymphoma (N = 48), PCPG = Pheochromocytoma and paraganglioma (N = 184), KIRP = Kidney renal papillary cell carcinoma (N = 291), SKCM = Skin cutaneous melanoma (N = 473), SARC = Sarcoma (N = 263), THCA = Thyroid carcinoma (N = 513), THYM = Thymoma (N = 120), UCS = Uterine carcinosarcoma (N = 57), UCEC = Uterine corpus endometrial carcinoma (N = 546), UVM = Uveal melanoma (N = 80), TGCT = Testicular germ cell tumors (N = 156), HNSC = Head and neck squamous cell carcinoma (N = 521)
Example 3
In Vitro Immunogenicity for MHC Class I Presented Peptides
(38) 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.sup.+ T cells with artificial antigen presenting cells (aAPCs) loaded with peptide/WIC complexes and anti-CD28 antibody. This way the inventors could show immunogenicity for HLA-A*02:01 restricted TUMAPs of the invention, demonstrating that these peptides are T-cell epitopes against which CD8.sup.+ precursor T cells exist in humans (Table 9).
In Vitro Priming of CD8.SUP.+ T Cells
(39) In order to perform in vitro stimulations by artificial antigen presenting cells loaded with peptide-WIC complex (pMEIC) and anti-CD28 antibody, the inventors first isolated CD8.sup.+ T cells from fresh HLA-A*02 leukapheresis products via positive selection using CD8 microbeads (Miltenyi Biotec, Bergisch-Gladbach, Germany) of healthy donors obtained from the University clinics Mannheim, Germany, after informed consent.
(40) PBMCs and isolated CD8.sup.+ lymphocytes were incubated in T-cell medium (TCM) until use consisting of RPMI-Glutamax (lnvitrogen, 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, Nürnberg, Germany) were also added to the TCM at this step.
(41) 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.
(42) 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).
(43) pMHC used for positive and negative control stimulations were A*0201/MLA-001 (peptide ELAGIGILTV (SEQ ID NO. 418) from modified Melan-A/MART-1) and A*0201/DDX5-001 (YLLPAIVHI from DDX5, SEQ ID NO. 419), 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 pl. Stimulations were initiated in 96-well plates by co-incubating 1×10.sup.6 CD8.sup.+ T cells with 2×10.sup.5 washed 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 (lnvitrogen, 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.sup.+ cells. Evaluation of multimeric analysis was done using the FlowJo software (Tree Star, Oreg., USA). In vitro priming of specific multimer+CD8.sup.+ 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.sup.+ T-cell line after in vitro stimulation (i.e. this well contained at least 1% of specific multimer+ among CD8.sup.+ T-cells and the percentage of specific multimer+ cells was at least 10x the median of the negative control stimulations).
(44) In Vitro Immunogenicity for Different Cancer Peptides
(45) 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 2 peptides of the invention are shown in
(46) TABLE-US-00018 TABLE 9A in vitro immunogenicity of HLA class I peptides of the invention Exemplary results of in vitro immunogenicity experiments conducted by the applicant for the peptides of the invention. <20% = +; 20%-49% = ++; 50%-69% = +++; > = 70% = ++++ Seq ID Sequence wells 393 KYIEAIQWI ++ 399 SYIDVLPEF ++ 400 KYLEKYYNL ++ 407 VYGIRLEHF +++ 414 MYPYIYHVL ++
(47) TABLE-US-00019 TABLE 12B in vitro immunogenicity of HLA class I peptides of the invention Exemplary results of in vitro immunogenicity experiments conducted by the applicant for the peptides of the invention. <20% = +; 20%-49% = ++; 50%-69% = +++; > = 70% = ++++ Seq ID Sequence Wells positive [%] 2 ALYGKLLKL ++++ 7 AAAAKVPEV + 8 KLGPFLLNA +++ 9 FLGDYVENL + 17 ILHEHHIFL + 43 LLWAGPVTA ++++ 322 ALVSGGVAQA + 331 AIWKELISL ++ 96 YYTQYSQTI + 98 VFPRLHNVLF + 99 QYILAVPVL +++ 102 VYPFENFEF +++ 103 NYIPVKNGKQF + 104 SYLTWHQQI + 105 IYNETITDLL + 106 IYNETVRDLL + 107 KYFPYLVVI ++ 109 LFITGGQFF ++ 110 SYPKIIEEF ++ 111 VYVQILQKL + 112 IYNFVESKL +++ 114 QYLDGTWSL +++ 115 RYLNKSFVL + 119 VYRVYVTTF +++ 120 GYIEHFSLW ++ 122 EYQARIPEF ++ 132 RYPALFPVL + 137 EYLHNCSYF + 139 IFGIFPNQF ++ 140 RYLINSYDF +++ 142 VYVDDIYVI ++++ 144 VFASLPGFLF ++ 155 IYKWITDNF ++ 156 YYMELTKLLL + 157 DYIPASGFALF + 158 IYEETRGVLKVF + 160 RYGDGGSSF + 161 KYPDIVQQF + 162 KYTSYILAF + 163 RYLTISNLQF + 164 HYVPATKVF + 166 FYTLPFHLI ++++ 167 RYGFYYVEF ++++ 168 RYLEAALRL +++ 170 QYPFHVPLL +++ 171 NYEDHFPLL ++ 172 VFIFKGNEF + 174 VYEKNGYIYF ++++ 175 LYSPVPFTL + 177 VYFKAGLDVF + 179 TYIPVGLGRLL +++ 180 KYLQVVGMF + 181 VYPPYLNYL ++++ 182 AYAQLGYLLF +++ 186 VFTTSSNIF + 190 LYSELTETL ++++ 277 FYTFPFQQL +++ 344 EYNSDLHQF + 345 EYNSDLHQFF ++ 349 QYSIISNVF ++ 350 KYGNFIDKL +++ 351 IFHEVPLKF ++ 353 TYGKIDLGF + 354 VYNEQIRDLL + 356 NYMPGQLTI + 358 YYSEVPVKL ++++ 359 NYGVLHVTF + 360 VFSPDGHLF ++ 363 SYAELGTTI + 365 VFIDHPVHL + 366 QYLELAHSL ++ 367 LYQDHMQYI ++ 371 AYSHLRYVF ++ 380 VYTGIDHHW +
Example 4
(48) Synthesis of Peptides
(49) All peptides were synthesized using standard and well-established solid phase peptide synthesis using the Fmoc-strategy. Identity and purity of each individual peptide have been determined by mass spectrometry and analytical RP-HPLC. The peptides were obtained as white to off-white lyophilizates (trifluoro acetate salt) in purities of >50%. All TUMAPs are preferably administered as trifluoro-acetate salts or acetate salts, other salt-forms are also possible.
Example 5
(50) MHC Binding Assays
(51) 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).
(52) 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 1 h at 37° C., washed again and detected with TMB solution that is stopped with NH.sub.2SO.sub.4. 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.
(53) TABLE-US-00020 TABLE 13 MHC class I binding scores. Binding of HLA-class I restricted peptides to HLA-A*02 was ranged by peptide exchange yield: <20% = +; 20%-49% = ++; 50%-75% = +++; > = 75% = ++++ Seq ID Sequence Peptide exchange 1 PLWGKVFYL ++ 2 ALYGKLLKL +++ 3 TLLGKQVTL +++ 4 ELAEIVFKV +++ 5 SLFGQEVYC +++ 6 FLDPAQRDL +++ 7 AAAAKVPEV +++ 8 KLGPFLLNA +++ 9 FLGDYVENL ++ 10 KTLDVFNIIL ++ 11 GVLKVFLENV ++ 12 GLIYEETRGV ++ 13 VLRDNIQGI +++ 14 LLDHLSFINKI ++ 16 HLYNNEEQV ++ 17 ILHEHHIFL +++ 18 YVLNEEDLQKV +++ 19 TLLPTVLTL +++ 20 ALDGHLYAI +++ 21 SLYHRVLLY ++++ 22 MLSDLTLQL ++++ 23 AQTVVVIKA + 24 FLWNGEDSAL +++ 25 IQADDFRTL ++ 26 KVDGVVIQL +++ 27 KVFGDLDQV +++ 28 TLYSMDLMKV +++ 29 TLCNKTFTA +++ 31 ALSDETKNNWEV ++++ 32 ILADEAFFSV +++ 33 LLLPLLPPLSPSLG +++ 35 YVLPKLYVKL ++ 36 KLYGIEIEV ++++ 37 ALINDILGELVKL +++ 38 KMQEDLVTL +++ 39 ALMAVVSGL +++ 40 SLLALPQDLQA +++ 41 FVLPLVVTL +++ 42 VLSPFILTL +++ 43 LLWAGPVTA +++ 44 GLLWQIIKV ++ 45 VLGPTPELV +++ 46 SLAKHGIVAL +++ 47 GLYQAQVNL +++ 48 TLDHKPVTV ++ 49 LLDESKLTL +++ 50 EYALLYHTL ++ 51 LLLDGDFTL +++ 52 ELLSSIFFL +++ 53 SLLSHVIVA +++ 54 FINPKGNWLL +++ 55 IASAIVNEL ++ 56 KILDLTRVL ++ 57 VLISSTVRL ++ 58 ALDDSLTSL ++ 59 ALTKILAEL +++ 60 FLIDTSASM ++ 61 HLPDFVKQL ++ 62 SLFNQEVQI +++ 63 TLSSERDFAL + 64 GLSSSSYEL ++ 65 KLDGICWQV +++ 66 FITDFYTTV +++ 67 GVIETVTSL ++ 69 GIYDGILHSI +++ 70 GLFSQHFNL +++ 71 GLITVDIAL +++ 72 GMIGFQVLL +++ 74 ILDETLENV ++ 75 ILDNVKNLL +++ 76 ILLDESNFNHFL +++ 77 IVLSTIASV +++ 78 LLWGHPRVA +++ 79 SLVPLQILL ++++ 80 TLDEYLTYL +++ 81 VLFLGKLLV ++ 82 VLLRVLIL ++ 83 ELLEYLPQL +++ 84 FLEEEITRV +++ 85 STLDGSLHAV +++ 87 YLTEVFLHVV +++ 88 ILLNTEDLASL +++ 89 YLVAHNLLL +++ 90 GAVAEEVLSSI + 91 SSLEPQIQPV + 92 LLRGPPVARA ++ 93 SLLTQPIFL +++ 321 SLWFKPEEL +++ 322 ALVSGGVAQA +++ 323 ILSVVNSQL +++ 324 AIFDFCPSV ++++ 325 RLLPKVQEV ++ 326 SLLPLVWKI +++ 327 SIGDIFLKY +++ 328 SVDSAPAAV ++ 329 FAWEPSFRDQV ++ 330 FLWPKEVEL +++ 331 AIWKELISL +++ 333 GTFLEGVAK +++ 334 GRADALRVL +++ 335 VLLAAGPSAA ++ 336 GLMDGSPHFL ++ 337 KVLGKIEKV +++ 338 LLYDGKLSSA ++ 339 VLGPGPPPL ++ 340 SVAKTILKR ++
(54) TABLE-US-00021 TABLE 14 MHC class I binding scores. Binding of HLA-class I restricted peptides to HLA-A*24 was ranged by peptide exchange yield: <20% = +; 20%-49% = ++; 50%-75% = +++; > = 75% = ++++ Seq ID Sequence Peptide exchange 96 YYTQYSQTI ++++ 97 TYTFLKETF ++++ 98 VFPRLHNVLF +++ 99 QYILAVPVL ++++ 100 VYIESRIGTSTSF +++ 102 VYPFENFEF +++ 103 NYIPVKNGKQF +++ 104 SYLTWHQQI ++++ 105 IYNETITDLL +++ 106 IYNETVRDLL +++ 107 KYFPYLVVI +++ 108 PYLVVIHTL +++ 109 LFITGGQFF ++++ 110 SYPKIIEEF +++ 111 VYVQILQKL +++ 112 IYNFVESKL +++ 113 IYSFHTLSF +++ 114 QYLDGTWSL ++++ 115 RYLNKSFVL +++ 116 AYVIAVHLF ++++ 117 IYLSDLTYI +++ 118 KYLNSVQYI +++ 119 VYRVYVTTF +++ 120 GYIEHFSLW ++++ 121 RYGLPAAWSTF +++ 122 EYQARIPEF +++ 123 VYTPVLEHL ++ 124 TYKDYVDLF + 125 VFSRDFGLLVF +++ 127 QYFTGNPLF +++ 128 VYPFDWQYI ++++ 129 KYIDYLMTW ++++ 131 EYLDRIGQLFF +++ 132 RYPALFPVL ++++ 133 KYLEDMKTYF +++ 134 AYIPTPIYF +++ 135 VYEAMVPLF ++++ 136 IYPEWPVVFF +++ 137 EYLHNCSYF ++++ 138 VYNAVSTSF ++ 139 IFGIFPNQF +++ 140 RYLINSYDF ++++ 141 SYNGHLTIWF +++ 142 VYVDDIYVI +++ 143 KYIFQLNEI +++ 144 VFASLPGFLF ++++ 145 VYALKVRTI +++ 146 NYYERIHAL +++ 147 LYLAFPLAF +++ 148 SYGTVSQIF ++++ 149 SYGTVSQI ++++ 152 KFFDDLGDELLF ++ 153 VYVPFGGKSMITF ++++ 154 VYGVPTPHF ++++ 155 IYKWITDNF ++++ 156 YYMELTKLLL ++++ 157 DYIPASGFALF +++ 158 IYEETRGVLKVF +++ 159 IYEETRGVL +++ 160 RYGDGGSSF +++ 161 KYPDIVQQF +++ 162 KYTSYILAF ++ 163 RYLTISNLQF ++++ 164 HYVPATKVF +++ 165 EYFTPLLSGQF +++ 166 FYTLPFHLI ++++ 167 RYGFYYVEF +++ 168 RYLEAALRL +++ 169 NYITGKGDVF +++ 170 QYPFHVPLL ++++ 171 NYEDHFPLL +++ 172 VFIFKGNEF ++++ 173 QYLEKYYNL ++++ 174 VYEKNGYIYF +++ 175 LYSPVPFTL +++ 176 FYINGQYQF +++ 177 VYFKAGLDVF +++ 178 NYSSAVQKF +++ 179 TYIPVGLGRLL +++ 180 KYLQVVGMF +++ 181 VYPPYLNYL +++ 182 AYAQLGYLLF ++++ 183 PYLQDVPRI +++ 184 IYSVGAFENF ++++ 185 QYLVHVNDL ++++ 186 VFTTSSNIF ++++ 187 AYAANVHYL ++++ 188 GYKTFFNEF +++ 190 LYSELTETL +++ 191 TYPDGTYTGRIF +++ 192 RYSTFSEIF +++ 193 LYLENNAQTQF +++ 194 VYQSLSNSL +++ 195 AYIKGGWIL +++ 196 GYIRGSWQF ++++ 197 IFTDIFHYL ++++ 198 DYVGFTLKI ++ 199 SYLNHLNNL +++ 200 VFIHHLPQF +++ 201 GYNPNRVFF +++ 202 RYVEGIVSL +++ 204 EYLSTCSKL +++ 205 VYPVVLNQI +++ 206 NYLDVATFL ++++ 207 LYSDAFKFIVF +++ 208 TYLEKIDGF ++++ 209 AFIETPIPLF ++++ 210 IYAGVGEFSF ++++ 211 VFKSEGAYF ++++ 212 SYAPPSEDLF ++ 213 SYAPPSEDLFL ++ 214 KYLMELTLI +++ 215 SYVASFFLL ++ 216 FYVNVKEQF +++ 217 IYISNSIYF ++++ 218 LYSELNKWSF +++ 219 SYLKAVFNL +++ 220 SYSEIKDFL ++++ 221 KYIGNLDLL ++++ 223 TFITQSPLL ++++ 224 PYFFANQEF +++ 225 TYTNTLERL +++ 226 MYLKLVQLF ++ 227 IYRFITERF +++ 228 IYQYVADNF +++ 229 IYQFVADSF +++ 230 TYGMVMVTF +++ 231 AFADVSVKF ++++ 232 YYLSDSPLL +++ 233 QYLTAAALHNL +++ 234 SYLPAIWLL +++ 235 VYKDSIYYI +++ 236 VYLPKIPSW +++ 237 KYVGQLAVL +++ 239 VYAIFRILL +++ 240 YYFFVQEKI +++ 241 SYVKVLHHL +++ 242 VYGEPRELL +++ 243 SYLELANTL +++ 244 VHFEDTGKTLLF +++ 245 LYPQLFVVL +++ 246 KYLSVQLTL ++ 247 SFTKTSPNF +++ 248 AFPTFSVQL ++++ 249 RYHPTTCTI ++++ 250 KYPDIASPTF ++ 251 VYTKALSSL +++ 252 AFGQETNVPLNNF ++++ 253 IYGFFNENF +++ 254 KYLESSATF +++ 255 VYQKIILKF +++ 256 VFGKSAYLF +++ 257 IFIDNSTQPLHF +++ 258 AYAQLGYLL +++ 259 YFIKSPPSQLF ++ 260 VYMNVMTRL ++++ 261 GYIKLINFI ++++ 262 VYSSQFETI ++++ 263 RYILENHDF +++ 264 LYTETRLQF ++++ 265 SYLNEAFSF ++++ 266 KYTDVVTEFL +++ 267 SFLNIEKTEILF ++ 268 IFITKALQI ++ 269 QYPYLQAFF +++ 270 YYSQESKVLYL +++ 271 RFLMKSYSF ++++ 272 RYVFPLPYL ++++ 273 IYGEKLQFIF +++ 274 KQLDIANYELF ++++ 275 KYGTLDVTF ++++ 276 QYLDVLHAL ++++ 277 FYTFPFQQL +++ 279 VWLPASVLF +++ 280 TYNPNLQDKL ++++ 281 NYSPGLVSLIL +++ 282 NYLVDPVTI +++ 283 EYQEIFQQL +++ 284 DYLKDPVTI +++ 285 VYVGDALLHAI +++ 286 SYGTILSHI ++++ 287 IYNPNLLTASKF +++ 288 VYPDTVALTF ++ 289 FFHEGQYVF ++++ 290 KYGDFKLLEF ++++ 291 YYLGSGRETF +++ 292 FYPQIINTF ++++ 293 VYPHFSTTNLI ++++ 294 RFPVQGTVTF +++ 295 SYLVIHERI +++ 296 SYQVIFQHF ++++ 297 TYIDTRTVF ++++ 298 AYKSEVVYF ++++ 299 KYQYVLNEF +++ 300 TYPSQLPSL +++ 301 KFDDVTMLF ++++ 302 LYLPVHYGF +++ 303 LYSVIKEDF +++ 304 EYNEVANLF +++ 305 NYENKQYLF ++++ 306 VYPAEQPQI +++ 307 GYAFTLPLF +++ 308 TFDGHGVFF +++ 309 KYYRQTLLF ++ 310 IYAPTLLVF +++ 311 EYLQNLNHI ++++ 312 SYTSVLSRL +++ 313 KYTHFIQSF ++++ 314 RYFKGDYSI +++ 315 FYIPHVPVSF +++ 316 VYFEGSDFKF +++ 317 VFDTSIAQLF +++ 318 TYSNSAFQYF +++ 319 KYSDVKNLI ++++ 341 SYLTQHQRI +++ 342 NYAFLHRTL +++ 343 NYLGGTSTI +++ 344 EYNSDLHQF +++ 345 EYNSDLHQFF +++ 347 VYAEVNSL +++ 348 IYLEHTESI +++ 349 QYSIISNVF +++ 350 KYGNFIDKL +++ 351 IFHEVPLKF +++ 352 QYGGDLTNTF +++ 353 TYGKIDLGF +++ 354 VYNEQIRDLL +++ 355 IYVTGGHLF +++ 356 NYMPGQLTI ++++ 357 QFITSTNTF ++++ 358 YYSEVPVKL +++ 359 NYGVLHVTF ++++ 360 VFSPDGHLF +++ 361 TYADIGGLDNQI +++ 362 VYNYAEQTL ++ 363 SYAELGTTI ++ 364 KYLNENQLSQL +++ 365 VFIDHPVHL ++++ 366 QYLELAHSL +++ 367 LYQDHMQYI ++ 368 KYQNVKHNL +++ 369 VYTHEVVTL +++ 370 RFIGIPNQF +++ 371 AYSHLRYVF ++ 372 VYVIEPHSMEF +++ 373 GYISNGELF +++ 374 VFLPRVTEL ++ 375 KYTDYILKI +++ 376 VYTPVASRQSL +++ 377 QYTPHSHQF +++ 378 VYIAELEKI +++ 379 VFIAQGYTL ++++ 380 VYTGIDHHW ++++ 381 KYPASSSVF +++ 382 AYLPPLQQVF +++ 383 RYKPGEPITF +++ 384 RYFDVGLHNF +++ 385 QYIEELQKF +++ 386 TFSDVEAHF +++ 387 KYTEKLEEI +++ 388 IYGEKTYAF +++
Example 6
(55) Absolute Quantitation of Tumor Associated Peptides Presented on the Cell Surface
(56) The generation of binders, such as antibodies and/or TCRs, is a laborious process, which may be conducted only for a number of selected targets. In the case of tumor-associated and—specific peptides, selection criteria include but are not restricted to exclusiveness of presentation and the density of peptide presented on the cell surface. In addition to the isolation and relative quantitation of peptides as described in Example 1, the inventors did analyze absolute peptide copies per cell as described. The quantitation of TUMAP copies per cell in solid tumor samples requires the absolute quantitation of the isolated TUMAP, the efficiency of TUMAP isolation, and the cell count of the tissue sample analyzed.
(57) Peptide Quantitation by nanoLC-MS/MS
(58) For an accurate quantitation of peptides by mass spectrometry, a calibration curve was generated for each peptide using the internal standard method. The internal standard is a double-isotope-labeled variant of each peptide, i.e. two isotope-labeled amino acids were included in TUMAP synthesis. It differs from the tumor-associated peptide only in its mass but shows no difference in other physicochemical properties (Anderson et al., 2012). The internal standard was spiked to each MS sample and all MS signals were normalized to the MS signal of the internal standard to level out potential technical variances between MS experiments.
(59) The calibration curves were prepared in at least three different matrices, i.e. HLA peptide eluates from natural samples similar to the routine MS samples, and each preparation was measured in duplicate MS runs. For evaluation, MS signals were normalized to the signal of the internal standard and a calibration curve was calculated by logistic regression.
(60) For the quantitation of tumor-associated peptides from tissue samples, the respective samples were also spiked with the internal standard, the MS signals were normalized to the internal standard and quantified using the peptide calibration curve.
(61) Efficiency of Peptide/MHC Isolation
(62) As for any protein purification process, the isolation of proteins from tissue samples is associated with a certain loss of the protein of interest. To determine the efficiency of TUMAP isolation, peptide/MHC complexes were generated for all TUMAPs selected for absolute quantitation. To be able to discriminate the spiked from the natural peptide/MHC complexes, single-isotope-labeled versions of the TUMAPs were used, i.e. one isotope-labeled amino acid was included in TUMAP synthesis. These complexes were spiked into the freshly prepared tissue lysates, i.e. at the earliest possible point of the TUMAP isolation procedure, and then captured like the natural peptide/MHC complexes in the following affinity purification. Measuring the recovery of the single-labeled TUMAPs therefore allows conclusions regarding the efficiency of isolation of individual natural TUMAPs.
(63) The efficiency of isolation was analyzed in a low number of samples and was comparable among these tissue samples. In contrast, the isolation efficiency differs between individual peptides. This suggests that the isolation efficiency, although determined in only a limited number of tissue samples, may be extrapolated to any other tissue preparation. However, it is necessary to analyze each TUMAP individually as the isolation efficiency may not be extrapolated from one peptide to others.
(64) Determination of the Cell Count in Solid, Frozen Tissue
(65) In order to determine the cell count of the tissue samples subjected to absolute peptide quantitation, the inventors applied DNA content analysis. This method is applicable to a wide range of samples of different origin and, most importantly, frozen samples (Alcoser et al., 2011; Forsey and Chaudhuri, 2009; Silva et al., 2013). During the peptide isolation protocol, a tissue sample is processed to a homogenous lysate, from which a small lysate aliquot is taken. The aliquot is divided in three parts, from which DNA is isolated (QiaAmp DNA Mini Kit, Qiagen, Hilden, Germany). The total DNA content from each DNA isolation is quantified using a fluorescence-based DNA quantitation assay (Qubit dsDNA HS Assay Kit, Life Technologies, Darmstadt, Germany) in at least two replicates.
(66) In order to calculate the cell number, a DNA standard curve from aliquots of single healthy blood cells, with a range of defined cell numbers, has been generated. The standard curve is used to calculate the total cell content from the total DNA content from each DNA isolation. The mean total cell count of the tissue sample used for peptide isolation is extrapolated considering the known volume of the lysate aliquots and the total lysate volume.
(67) Peptide Copies Per Cell
(68) With data of the aforementioned experiments, the inventors calculated the number of TUMAP copies per cell by dividing the total peptide amount by the total cell count of the sample, followed by division through isolation efficiency. Copy cell number for selected peptides is shown in Table 15.
(69) TABLE-US-00022 TABLE 15 Absolute copy numbers. The table lists the results of absolute peptide quantitation in tumor samples. The median number of copies per cell are indicated for each peptide: <100 = +; >=100 = ++; >=1,000 +++; >=10,000 = +++. The number of samples, in which evaluable, high quality MS data are available is indicated. Copies Number SEQ ID per cell of No. Peptide Code (median) samples 70 DNMT3B-001 ++ 16 323 KIAA0226L-002 ++ 19 325 ZNF-003 ++ 14
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