Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
02 08 2023
02 08 2023
Historique:
received:
27
09
2022
accepted:
19
06
2023
medline:
4
8
2023
pubmed:
3
8
2023
entrez:
2
8
2023
Statut:
epublish
Résumé
Systemic pan-tumor analyses may reveal the significance of common features implicated in cancer immunogenicity and patient survival. Here, we provide a comprehensive multi-omics data set for 32 patients across 25 tumor types for proteogenomic-based discovery of neoantigens. By using an optimized computational approach, we discover a large number of tumor-specific and tumor-associated antigens. To create a pipeline for the identification of neoantigens in our cohort, we combine DNA and RNA sequencing with MS-based immunopeptidomics of tumor specimens, followed by the assessment of their immunogenicity and an in-depth validation process. We detect a broad variety of non-canonical HLA-binding peptides in the majority of patients demonstrating partially immunogenicity. Our validation process allows for the selection of 32 potential neoantigen candidates. The majority of neoantigen candidates originates from variants identified in the RNA data set, illustrating the relevance of RNA as a still understudied source of cancer antigens. This study underlines the importance of RNA-centered variant detection for the identification of shared biomarkers and potentially relevant neoantigen candidates.
Identifiants
pubmed: 37532709
doi: 10.1038/s41467-023-39570-7
pii: 10.1038/s41467-023-39570-7
pmc: PMC10397250
doi:
Substances chimiques
Antigens, Neoplasm
0
Peptides
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4632Commentaires et corrections
Type : ErratumIn
Informations de copyright
© 2023. The Author(s).
Références
Nature. 2017 Jul 13;547(7662):222-226
pubmed: 28678784
Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8059-8064
pubmed: 28674023
N Engl J Med. 2016 Dec 8;375(23):2255-2262
pubmed: 27959684
Nat Genet. 2013 Jun;45(6):580-5
pubmed: 23715323
J Transl Med. 2019 Sep 23;17(1):319
pubmed: 31547885
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D655-8
pubmed: 16381952
Trends Pharmacol Sci. 2021 Apr;42(4):268-282
pubmed: 33711255
Sci Immunol. 2023 Feb 3;8(80):eabm6359
pubmed: 36735774
Nat Protoc. 2020 Feb;15(2):266-315
pubmed: 31907453
N Engl J Med. 2014 Dec 4;371(23):2189-2199
pubmed: 25409260
Front Oncol. 2020 Dec 10;10:593989
pubmed: 33363023
Cancer Cell. 2018 Apr 9;33(4):547-562
pubmed: 29634943
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
J Am Soc Mass Spectrom. 2016 Nov;27(11):1719-1727
pubmed: 27572102
Science. 2015 Apr 3;348(6230):124-8
pubmed: 25765070
Nature. 2021 Aug;596(7870):126-132
pubmed: 34290408
PeerJ. 2018 Jul 31;6:e5362
pubmed: 30083469
Nature. 2022 Jun;606(7912):172-179
pubmed: 35545680
Cancer Discov. 2021 Nov;11(11):2780-2795
pubmed: 34112699
Science. 2015 Dec 11;350(6266):1387-90
pubmed: 26516200
Mol Syst Biol. 2019 Feb 18;15(2):e8503
pubmed: 30777892
Nat Biotechnol. 2018 Oct 08;:
pubmed: 30295672
Nat Commun. 2018 Sep 25;9(1):3919
pubmed: 30254248
Cancer Sci. 2021 Jan;112(1):465-475
pubmed: 33155341
Cell. 2021 Feb 4;184(3):596-614.e14
pubmed: 33508232
Blood. 2011 Aug 25;118(8):2128-37
pubmed: 21715316
Cancer Cell. 2015 Oct 12;28(4):515-528
pubmed: 26439496
Brief Bioinform. 2022 Mar 10;23(2):
pubmed: 35279714
Nat Commun. 2021 Jun 7;12(1):3346
pubmed: 34099720
Genomics Inform. 2019 Sep;17(3):e23
pubmed: 31610619
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Genome Biol. 2014;15(12):550
pubmed: 25516281
Cell. 2015 Jan 15;160(1-2):48-61
pubmed: 25594174
Bioinformatics. 2011 Jun 15;27(12):1739-40
pubmed: 21546393
Nature. 2020 May;581(7809):434-443
pubmed: 32461654
Bioinformatics. 2019 Jun 1;35(12):2084-2092
pubmed: 30395178
Genome Res. 2015 Jun;25(6):918-25
pubmed: 25883319
Cancer Cell. 2018 May 14;33(5):817-828.e7
pubmed: 29706454
Front Immunol. 2022 Jan 26;13:835454
pubmed: 35154160
Nat Methods. 2019 Nov;16(11):1131-1138
pubmed: 31636457
Cancer Discov. 2019 Nov;9(11):1493-1510
pubmed: 31611195
Cell Rep. 2018 Apr 3;23(1):50-57
pubmed: 29617672
Bioinformatics. 2016 Feb 15;32(4):511-7
pubmed: 26515819
BMC Bioinformatics. 2009 Oct 03;10:317
pubmed: 19799796
Cell Syst. 2015 Dec 23;1(6):417-425
pubmed: 26771021
Mol Cell Proteomics. 2015 Dec;14(12):3105-17
pubmed: 26628741
Science. 2017 Aug 18;357(6352):
pubmed: 28818916
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
pubmed: 16199517
Nature. 2017 Oct 11;550(7675):249-254
pubmed: 29022589
Nat Commun. 2023 Aug 2;14(1):4632
pubmed: 37532709
Genome Res. 2014 Mar;24(3):365-76
pubmed: 24347612
Curr Protoc Bioinformatics. 2015 Sep 03;51:11.14.1-11.14.19
pubmed: 26334920
Nucleic Acids Res. 2019 Jan 8;47(D1):D339-D343
pubmed: 30357391
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Genome Res. 2002 Apr;12(4):656-64
pubmed: 11932250
Science. 2022 Feb 25;375(6583):877-884
pubmed: 35113651
Nat Biotechnol. 2018 Dec;36(11):1056-1058
pubmed: 30114007
Mol Cell Proteomics. 2021;20:100076
pubmed: 33823297
Nature. 2016 Aug 4;536(7614):91-5
pubmed: 27350335
Nat Methods. 2019 Jun;16(6):509-518
pubmed: 31133760
Genome Res. 2017 Nov;27(11):1843-1858
pubmed: 29021288
Mol Cell Proteomics. 2014 Aug;13(8):2056-71
pubmed: 24623587
Nat Med. 2021 Mar;27(3):515-525
pubmed: 33479501
Nat Methods. 2018 Aug;15(8):591-594
pubmed: 30013048
Nat Commun. 2016 Nov 21;7:13404
pubmed: 27869121
Nature. 2013 Aug 22;500(7463):415-21
pubmed: 23945592
Sci Transl Med. 2018 Dec 5;10(470):
pubmed: 30518613
Genome Res. 1999 Aug;9(8):677-9
pubmed: 10447503
Cancer Discov. 2021 Aug;11(8):1938-1951
pubmed: 33811047
J Proteome Res. 2018 Aug 3;17(8):2908-2914
pubmed: 29978702
Exp Mol Med. 2020 Apr;52(4):582-593
pubmed: 32346127
Cell Syst. 2018 Jul 25;7(1):129-132.e4
pubmed: 29960884
Clin Cancer Res. 2014 Jan 1;20(1):44-55
pubmed: 24045181
Nucleic Acids Res. 2022 Jan 7;50(D1):D543-D552
pubmed: 34723319
Science. 2017 Jul 28;357(6349):409-413
pubmed: 28596308
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Nat Genet. 2019 Feb;51(2):202-206
pubmed: 30643254
Nat Commun. 2021 Nov 18;12(1):6689
pubmed: 34795224
Bioinformatics. 2014 Dec 1;30(23):3310-6
pubmed: 25143287
Nat Commun. 2020 Mar 10;11(1):1293
pubmed: 32157095