Uncovering the Tumor Antigen Landscape: What to Know about the Discovery Process.

cancer immunotherapy epitope prediction immunopeptidome tumor antigens

Journal

Cancers
ISSN: 2072-6694
Titre abrégé: Cancers (Basel)
Pays: Switzerland
ID NLM: 101526829

Informations de publication

Date de publication:
23 Jun 2020
Historique:
received: 29 04 2020
revised: 11 06 2020
accepted: 20 06 2020
entrez: 27 6 2020
pubmed: 27 6 2020
medline: 27 6 2020
Statut: epublish

Résumé

According to the latest available data, cancer is the second leading cause of death, highlighting the need for novel cancer therapeutic approaches. In this context, immunotherapy is emerging as a reliable first-line treatment for many cancers, particularly metastatic melanoma. Indeed, cancer immunotherapy has attracted great interest following the recent clinical approval of antibodies targeting immune checkpoint molecules, such as PD-1, PD-L1, and CTLA-4, that release the brakes of the immune system, thus reviving a field otherwise poorly explored. Cancer immunotherapy mainly relies on the generation and stimulation of cytotoxic CD8 T lymphocytes (CTLs) within the tumor microenvironment (TME), priming T cells and establishing efficient and durable anti-tumor immunity. Therefore, there is a clear need to define and identify immunogenic T cell epitopes to use in therapeutic cancer vaccines. Naturally presented antigens in the human leucocyte antigen-1 (HLA-I) complex on the tumor surface are the main protagonists in evocating a specific anti-tumor CD8+ T cell response. However, the methodologies for their identification have been a major bottleneck for their reliable characterization. Consequently, the field of antigen discovery has yet to improve. The current review is intended to define what are today known as tumor antigens, with a main focus on CTL antigenic peptides. We also review the techniques developed and employed to date for antigen discovery, exploring both the direct elution of HLA-I peptides and the in silico prediction of epitopes. Finally, the last part of the review analyses the future challenges and direction of the antigen discovery field.

Identifiants

pubmed: 32585818
pii: cancers12061660
doi: 10.3390/cancers12061660
pmc: PMC7352969
pii:
doi:

Types de publication

Journal Article Review

Langues

eng

Subventions

Organisme : Horizon 2020 Framework Programme
ID : 681219
Organisme : Helsinki Institute of Life Science (HiLIFE)
ID : none
Organisme : Jane ja Aatos Erkon Säätiö
ID : 19072019
Organisme : Syöpäjärjestöt
ID : none

Références

Nucleic Acids Res. 2017 Jul 3;45(W1):W458-W463
pubmed: 28407089
J Biomed Inform. 2015 Feb;53:405-14
pubmed: 25464113
Cancer Immunol Immunother. 2010 Jun;59(6):943-53
pubmed: 20140431
Transplantation. 1988 Mar;45(3):610-3
pubmed: 3347938
Clin Dev Immunol. 2010;2010:150591
pubmed: 20981248
Lancet Glob Health. 2016 Sep;4(9):e609-16
pubmed: 27470177
Blood. 2001 Nov 15;98(10):2887-93
pubmed: 11698267
Nat Rev Immunol. 2016 Apr;16(4):207-19
pubmed: 27026073
Methods Mol Biol. 2019;2024:269-285
pubmed: 31364056
Curr Oncol Rep. 2014 Sep;16(9):400
pubmed: 25030654
Curr Opin Immunol. 1997 Oct;9(5):684-93
pubmed: 9368778
J Immunol. 2003 Aug 15;171(4):1741-9
pubmed: 12902473
Int J Cancer. 2005 Nov 1;117(2):256-64
pubmed: 15900605
Nat Rev Cancer. 2011 Oct 24;11(11):805-12
pubmed: 22020206
Proc Natl Acad Sci U S A. 1994 Apr 26;91(9):3515-9
pubmed: 8170938
Sci Rep. 2017 Sep 11;7(1):11137
pubmed: 28894200
Proc Natl Acad Sci U S A. 2004 Jul 20;101(29):10697-702
pubmed: 15252201
Nat Rev Cancer. 2005 Aug;5(8):615-25
pubmed: 16034368
Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):540-5
pubmed: 19122146
Int J Cancer. 2000 May 15;86(4):538-47
pubmed: 10797269
Proc Natl Acad Sci U S A. 1994 Jul 5;91(14):6458-62
pubmed: 8022805
Cell Res. 2017 Jan;27(1):59-73
pubmed: 28008927
AIDS. 2012 Jul 17;26(11):F21-9
pubmed: 22617051
Bioinformatics. 2019 Jul 15;35(14):i278-i283
pubmed: 31510651
Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7976-80
pubmed: 7644523
Bioinformatics. 2013 Jan 1;29(1):8-14
pubmed: 23097419
Immunogenetics. 2005 Apr;57(1-2):33-41
pubmed: 15744535
J Exp Med. 1997 Aug 29;186(5):785-93
pubmed: 9271594
Br J Cancer. 2007 Feb 12;96(3):485-91
pubmed: 17245339
Cell Mol Life Sci. 2011 May;68(9):1503-20
pubmed: 21387143
Pathol Int. 2019 Sep;69(9):511-518
pubmed: 31397525
Nucleic Acids Res. 2020 Jan 8;48(D1):D948-D955
pubmed: 31667505
Mol Cell Proteomics. 2018 Mar;17(3):533-548
pubmed: 29242379
Science. 1995 Sep 1;269(5228):1281-4
pubmed: 7652577
J Clin Invest. 2015 Sep;125(9):3413-21
pubmed: 26258412
Mol Ther. 2011 Mar;19(3):620-6
pubmed: 21157437
Annu Rev Immunol. 2019 Apr 26;37:173-200
pubmed: 30550719
Front Immunol. 2018 Jul 25;9:1716
pubmed: 30090105
J Exp Med. 1995 Feb 1;181(2):799-804
pubmed: 7836932
EMBO J. 1987 Mar;6(3):605-10
pubmed: 3034598
Nature. 2017 Jul 13;547(7662):217-221
pubmed: 28678778
J Immunol. 1993 Oct 1;151(7):3719-27
pubmed: 7690811
BMC Bioinformatics. 2011 Nov 15;12:446
pubmed: 22085524
Proteomics. 2004 Jan;4(1):59-77
pubmed: 14730672
PLoS One. 2007 Aug 29;2(8):e796
pubmed: 17726526
Cell. 2015 Jan 15;160(1-2):48-61
pubmed: 25594174
Nucleic Acids Res. 2018 Jan 4;46(D1):D406-D412
pubmed: 29087479
Tissue Antigens. 2004 Jun;63(6):509-17
pubmed: 15140026
Clin Cancer Res. 2019 Jul 15;25(14):4248-4254
pubmed: 31036542
Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14704-7
pubmed: 8962118
Nat Protoc. 2019 Jun;14(6):1687-1707
pubmed: 31092913
Immunogenetics. 1994;40(5):360-9
pubmed: 7927540
Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18769-76
pubmed: 20974924
Bioinformatics. 2018 Feb 1;34(3):469-476
pubmed: 28968726
J Clin Invest. 2013 May;123(5):1976-87
pubmed: 23543059
Cancer Immunol Immunother. 2017 May;66(5):657-666
pubmed: 28314956
J Immunol. 2016 Sep 15;197(6):2492-9
pubmed: 27511729
EMBO J. 1992 Nov;11(11):3887-95
pubmed: 1396582
Nat Methods. 2014 Nov;11(11):1114-25
pubmed: 25357241
J Exp Med. 1996 Mar 1;183(3):1185-92
pubmed: 8642260
Blood. 2011 Mar 24;117(12):3353-62
pubmed: 21278353
Mol Oncol. 2011 Apr;5(2):164-82
pubmed: 21376678
Nature. 2017 Jul 13;547(7662):222-226
pubmed: 28678784
Blood. 2015 Jun 25;125(26):4017-23
pubmed: 25999455
J Immunol Methods. 2013 Jan 31;387(1-2):293-302
pubmed: 23058674
Hum Immunol. 2001 Nov;62(11):1200-16
pubmed: 11704282
Biomed Res Int. 2015;2015:948501
pubmed: 26161423
Nucleic Acids Res. 2020 Jan 8;48(D1):D1057-D1062
pubmed: 31588507
Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14889-94
pubmed: 17001009
Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6671-5
pubmed: 8341685
J Exp Med. 1998 Apr 20;187(8):1163-7
pubmed: 9547328
J Immunol. 2016 Aug 15;197(4):1517-24
pubmed: 27402703
Clin Epigenetics. 2018 Sep 5;10(1):115
pubmed: 30185218
Genome Med. 2015 Nov 20;7:119
pubmed: 26589500
Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):E166-75
pubmed: 25548167
J Exp Med. 2001 Jan 1;193(1):73-88
pubmed: 11136822
Cancer Res. 1996 Oct 15;56(20):4766-72
pubmed: 8840996
J Clin Invest. 2008 Mar;118(3):1099-109
pubmed: 18292810
Nucleic Acids Res. 2018 Jan 4;46(D1):D419-D427
pubmed: 28977646
J Immunol. 1999 Dec 1;163(11):5851-9
pubmed: 10570269
J Exp Med. 2000 Dec 4;192(11):1637-44
pubmed: 11104805
J Exp Med. 1993 Aug 1;178(2):489-95
pubmed: 8340755
Am J Reprod Immunol. 1998 Sep;40(3):172-6
pubmed: 9764361
Cancer Immunol Res. 2017 May;5(5):376-384
pubmed: 28314751
J Proteomics. 2014 Sep 23;109:240-4
pubmed: 25050860
Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1914-8
pubmed: 9050879
Front Immunol. 2019 Nov 01;10:2559
pubmed: 31736974
J Immunol. 2016 Feb 15;196(4):1480-7
pubmed: 26783342
Curr Opin Immunol. 2016 Aug;41:9-17
pubmed: 27155075
Bioinformatics. 2016 Feb 15;32(4):511-7
pubmed: 26515819
Sci Rep. 2018 Mar 12;8(1):4327
pubmed: 29531253
Cell. 2015 Apr 9;161(2):205-14
pubmed: 25860605
Gigascience. 2017 May 1;6(5):1-11
pubmed: 28327987
J Exp Med. 1999 Sep 6;190(5):705-15
pubmed: 10477554
Proc Natl Acad Sci U S A. 1977 Jan;74(1):272-5
pubmed: 264681
Science. 1992 Mar 6;255(5049):1261-3
pubmed: 1546328
J Virol. 2014 Nov;88(22):12992-3004
pubmed: 25165114
Cell. 1989 Jul 28;58(2):293-303
pubmed: 2568889
Front Immunol. 2018 May 01;9:947
pubmed: 29770138
J Exp Med. 1995 Jun 1;181(6):2109-17
pubmed: 7539040
J Immunother Emphasis Tumor Immunol. 1993 Aug;14(2):94-103
pubmed: 7506576
Protein Eng. 2002 Apr;15(4):287-96
pubmed: 11983929
Mol Cell Proteomics. 2018 Dec;17(12):2347-2357
pubmed: 30171158
Oncologist. 2008 May;13(5):577-85
pubmed: 18515742
Eur J Immunol. 1991 Nov;21(11):2891-4
pubmed: 1718764
Sci Rep. 2015 Dec 17;5:18413
pubmed: 26674250
Immunity. 1997 Feb;6(2):199-208
pubmed: 9047241
J Exp Med. 1995 Aug 1;182(2):459-65
pubmed: 7543139
Science. 1991 Dec 13;254(5038):1643-7
pubmed: 1840703
Eur J Immunol. 2008 Jun;38(6):1503-10
pubmed: 18446792
Mol Ther. 2013 Apr;21(4):904-12
pubmed: 23423337
Proteins. 2017 May;85(5):908-916
pubmed: 28160322
Methods Mol Biol. 2018;1719:209-221
pubmed: 29476514
Nature. 2017 Mar 30;543(7647):723-727
pubmed: 28329770
Molecules. 2019 Mar 02;24(5):
pubmed: 30832312
Cancer Res. 2008 Feb 1;68(3):889-92
pubmed: 18245491
Clin Lung Cancer. 2009 Sep;10(5):371-4
pubmed: 19808198
N Engl J Med. 2007 Jul 5;357(1):39-51
pubmed: 17611206
Bioinformatics. 2019 Dec 1;35(23):4946-4954
pubmed: 31120490
Proc Natl Acad Sci U S A. 1986 Jul;83(14):5252-6
pubmed: 2425364
Clin Cancer Res. 2009 Apr 15;15(8):2895-904
pubmed: 19351776
Trends Immunol. 2017 Dec;38(12):904-915
pubmed: 28830734
J Immunother. 2013 Jan;36(1):66-76
pubmed: 23211628
J Natl Cancer Inst. 1997 Feb 19;89(4):293-300
pubmed: 9048833
Proc Natl Acad Sci U S A. 1997 Sep 30;94(20):10850-5
pubmed: 9380723
Proc Natl Acad Sci U S A. 1982 Aug;79(15):4718-22
pubmed: 6981814
Cancer Res. 2018 Aug 15;78(16):4627-4641
pubmed: 29789417
Mol Cell Proteomics. 2019 Dec;18(12):2459-2477
pubmed: 31578220
Oncotarget. 2016 Feb 2;7(5):5110-7
pubmed: 26819371
Nucleic Acids Res. 2019 Jan 8;47(D1):D339-D343
pubmed: 30357391
Blood. 2012 Mar 22;119(12):2709-20
pubmed: 22160384
Methods Mol Biol. 2013;960:145-157
pubmed: 23329485
Mol Cell Proteomics. 2020 Jan;19(1):31-49
pubmed: 31744855
Front Immunol. 2019 Feb 08;10:168
pubmed: 30800125
Immunogenetics. 2014 Aug;66(7-8):449-56
pubmed: 24863339
Immunity. 1997 Mar;6(3):273-81
pubmed: 9075928
Nature. 1991 May 23;351(6324):290-6
pubmed: 1709722
J Immunol. 2018 Oct 1;201(7):1875-1888
pubmed: 30135181
Curr Opin Cell Biol. 2015 Dec;37:1-8
pubmed: 26342994
Cancer Res. 2008 Oct 1;68(19):7693-706
pubmed: 18829521
Future Oncol. 2016 Jun;12(11):1321-9
pubmed: 27044454
PLoS One. 2015 May 28;10(5):e0128194
pubmed: 26020952
Nucleic Acids Res. 2009 Jan;37(Database issue):D816-9
pubmed: 18838390
AIDS Res Hum Retroviruses. 2006 Jan;22(1):52-6
pubmed: 16438646
NPJ Vaccines. 2019 Feb 8;4:7
pubmed: 30774998
Mol Immunol. 2012 Jun;51(2):136-42
pubmed: 22424782
Bioinformatics. 2017 Sep 15;33(18):2924-2929
pubmed: 28481982
Cell. 2017 Sep 7;170(6):1109-1119.e10
pubmed: 28886381
J Exp Med. 1996 Feb 1;183(2):527-34
pubmed: 8627164
Methods Mol Biol. 2020;2120:173-181
pubmed: 32124319
Cancers (Basel). 2019 Jul 15;11(7):
pubmed: 31311081
J Immunol. 2017 Nov 1;199(9):3360-3368
pubmed: 28978689
Science. 2015 Apr 3;348(6230):69-74
pubmed: 25838375
In Silico Biol. 1999;1(2):109-21
pubmed: 11471244
Cell Syst. 2019 Aug 28;9(2):159-166.e3
pubmed: 31176619
J Exp Med. 1992 Nov 1;176(5):1453-7
pubmed: 1402688
J Hematol Oncol. 2019 Sep 14;12(1):99
pubmed: 31521180
Ann Oncol. 2018 Nov 1;29(11):2183-2191
pubmed: 30239576
Semin Cancer Biol. 1999 Apr;9(2):67-81
pubmed: 10202129
Clin Cancer Res. 2009 Jan 1;15(1):169-80
pubmed: 19118044
J Exp Med. 1994 Mar 1;179(3):921-30
pubmed: 8113684
Nat Rev Cancer. 2012 Mar 22;12(4):252-64
pubmed: 22437870
J Immunol. 2013 Oct 1;191(7):3955-67
pubmed: 24018273
Nature. 1990 Nov 15;348(6298):213-6
pubmed: 1700303
Nat Commun. 2016 Nov 21;7:13404
pubmed: 27869121
Curr Opin Immunol. 1999 Apr;11(2):203-8
pubmed: 10322157
Front Immunol. 2019 Nov 29;10:2820
pubmed: 31849987
Proteomics. 2019 Feb;19(4):e1800357
pubmed: 30578603
Hum Immunol. 1994 Jul;40(3):228-34
pubmed: 7960967
Front Immunol. 2019 Apr 16;10:827
pubmed: 31057550
Immunogenetics. 1996;44(5):323-30
pubmed: 8781117
Immunity. 1995 Feb;2(2):167-75
pubmed: 7895173
Cell Syst. 2018 Jul 25;7(1):129-132.e4
pubmed: 29960884
J Immunol. 2000 Jun 15;164(12):6120-9
pubmed: 10843661
Nucleic Acids Res. 2015 Jul 1;43(W1):W349-55
pubmed: 26007650
Clin Cancer Res. 2014 Oct 1;20(19):5009-22
pubmed: 25124688
Bioinformatics. 2007 Apr 15;23(8):942-9
pubmed: 17384427
J Immunother. 2013 Feb;36(2):133-51
pubmed: 23377668
J Exp Med. 1995 Sep 1;182(3):689-98
pubmed: 7544395
Blood. 2010 Nov 18;116(20):4099-102
pubmed: 20668228
Cancer Res. 2001 Jul 15;61(14):5544-51
pubmed: 11454705
J Immunol. 2015 Dec 1;195(11):5117-22
pubmed: 26589749
J Exp Med. 1996 Dec 1;184(6):2207-16
pubmed: 8976176
Curr Opin Immunol. 2020 Jan 11;64:9-14
pubmed: 31935516
Immunogenetics. 2015 Feb;67(2):85-93
pubmed: 25475908
Nucleic Acids Res. 2008 Jan;36(Database issue):D202-5
pubmed: 17998252
Immunity. 2017 Aug 15;47(2):203-208
pubmed: 28813649
Eur J Immunol. 2005 Aug;35(8):2295-303
pubmed: 15997466
Immunol Med. 2019 Jun;42(2):65-70
pubmed: 31318319
Front Microbiol. 2018 Feb 13;9:178
pubmed: 29487579
J Exp Med. 2000 Dec 18;192(12):1755-62
pubmed: 11120772
Eur J Immunol. 2002 Jan;32(1):213-22
pubmed: 11782012
Blood. 2003 Jul 15;102(2):571-6
pubmed: 12576330
Science. 2015 Apr 3;348(6230):62-8
pubmed: 25838374
BMC Immunol. 2008 Jan 22;9:1
pubmed: 18211710
PLoS Comput Biol. 2013 Oct;9(10):e1003266
pubmed: 24204222
Proteomics. 2018 Jun;18(12):e1700259
pubmed: 29314742
Curr Opin Immunol. 2017 Aug;47:103-109
pubmed: 28806603
J Exp Clin Cancer Res. 2019 Jun 13;38(1):255
pubmed: 31196207
Cancer Res. 2016 Apr 15;76(8):2177-85
pubmed: 26862115
Front Genet. 2019 Nov 28;10:1191
pubmed: 31850062
Immunogenetics. 2010 Jun;62(6):357-68
pubmed: 20379710
J Exp Med. 1995 Jan 1;181(1):363-8
pubmed: 7807017
Cancer Res. 2002 Oct 1;62(19):5510-6
pubmed: 12359761
Science. 1994 Apr 29;264(5159):716-9
pubmed: 7513441
Science. 2015 Apr 3;348(6230):56-61
pubmed: 25838373
Immunogenetics. 2012 Mar;64(3):177-86
pubmed: 22009319
Cancer Res. 1998 Nov 1;58(21):4895-901
pubmed: 9809996
Immunology. 2014 Jan;141(1):18-26
pubmed: 23927693
Nat Commun. 2020 Mar 10;11(1):1293
pubmed: 32157095
J Biol Chem. 1979 Sep 25;254(18):8709-12
pubmed: 479147
Sci Rep. 2019 Oct 10;9(1):14530
pubmed: 31601838
Nature. 1967 Nov 18;216(5116):659-63
pubmed: 6082462

Auteurs

Sara Feola (S)

Drug Research Program (DRP) ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Viikinkaari 5E, University of Helsinki, 00790 Helsinki, Finland.
Helsinki Institute of Life Science (HiLIFE), Fabianinkatu 33, University of Helsinki, 00710 Helsinki, Finland.
Translational Immunology Program (TRIMM), Faculty of Medicine, Haartmaninkatu 8, University of Helsinki, 00290 Helsinki, Finland.
Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, FI-00014 Helsinki, Finland.

Jacopo Chiaro (J)

Drug Research Program (DRP) ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Viikinkaari 5E, University of Helsinki, 00790 Helsinki, Finland.
Helsinki Institute of Life Science (HiLIFE), Fabianinkatu 33, University of Helsinki, 00710 Helsinki, Finland.
Translational Immunology Program (TRIMM), Faculty of Medicine, Haartmaninkatu 8, University of Helsinki, 00290 Helsinki, Finland.
Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, FI-00014 Helsinki, Finland.

Beatriz Martins (B)

Drug Research Program (DRP) ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Viikinkaari 5E, University of Helsinki, 00790 Helsinki, Finland.
Helsinki Institute of Life Science (HiLIFE), Fabianinkatu 33, University of Helsinki, 00710 Helsinki, Finland.
Translational Immunology Program (TRIMM), Faculty of Medicine, Haartmaninkatu 8, University of Helsinki, 00290 Helsinki, Finland.
Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, FI-00014 Helsinki, Finland.

Vincenzo Cerullo (V)

Drug Research Program (DRP) ImmunoViroTherapy Lab (IVT), Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Viikinkaari 5E, University of Helsinki, 00790 Helsinki, Finland.
Helsinki Institute of Life Science (HiLIFE), Fabianinkatu 33, University of Helsinki, 00710 Helsinki, Finland.
Translational Immunology Program (TRIMM), Faculty of Medicine, Haartmaninkatu 8, University of Helsinki, 00290 Helsinki, Finland.
Digital Precision Cancer Medicine Flagship (iCAN), University of Helsinki, FI-00014 Helsinki, Finland.

Classifications MeSH