Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence.
CD4+ lymphocytes
CD8+ lymphocytes
COVID-19
SARS-CoV-2
T cell
antigen (Ag)
artificial intelligence
vaccine
Journal
Frontiers in immunology
ISSN: 1664-3224
Titre abrégé: Front Immunol
Pays: Switzerland
ID NLM: 101560960
Informations de publication
Date de publication:
2023
2023
Historique:
received:
21
07
2023
accepted:
01
11
2023
medline:
5
12
2023
pubmed:
4
12
2023
entrez:
4
12
2023
Statut:
epublish
Résumé
During the COVID-19 pandemic we utilized an AI-driven T cell epitope prediction tool, the NEC Immune Profiler (NIP) to scrutinize and predict regions of T cell immunogenicity (hotspots) from the entire SARS-CoV-2 viral proteome. These immunogenic regions offer potential for the development of universally protective T cell vaccine candidates. Here, we validated and characterized T cell responses to a set of minimal epitopes from these AI-identified universal hotspots. Utilizing a flow cytometry-based T cell activation-induced marker (AIM) assay, we identified 59 validated screening hits, of which 56% (33 peptides) have not been previously reported. Notably, we found that most of these novel epitopes were derived from the non-spike regions of SARS-CoV-2 (Orf1ab, Orf3a, and E). In addition,
Identifiants
pubmed: 38045681
doi: 10.3389/fimmu.2023.1265044
pmc: PMC10691274
doi:
Substances chimiques
Epitopes, T-Lymphocyte
0
Viral Vaccines
0
Peptides
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1265044Informations de copyright
Copyright © 2023 Federico, Malone, Tennøe, Chaban, Osen, Gainullin, Smorodina, Kared, Akbar, Greiff, Stratford, Clancy and Munthe.
Déclaration de conflit d'intérêts
BM, ST, RS, and TC are employees of the commercial company NEC OncoImmunity. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
Front Immunol. 2023 Jul 07;14:1210899
pubmed: 37503339
J Exp Med. 1993 Jul 1;178(1):27-47
pubmed: 8315383
Immunome Res. 2008 Nov 26;4:6
pubmed: 19036163
Vaccines (Basel). 2018 Jul 31;6(3):
pubmed: 30065162
Immunity. 2022 Sep 13;55(9):1732-1746.e5
pubmed: 35961317
Nucleic Acids Res. 2019 Jan 8;47(D1):D339-D343
pubmed: 30357391
JCI Insight. 2023 Jun 22;8(12):
pubmed: 37159281
Int Immunol. 2000 Mar;12(3):375-83
pubmed: 10700472
Nucleic Acids Res. 2019 Jul 2;47(W1):W502-W506
pubmed: 31114900
Nat Biotechnol. 2022 Feb;40(2):175-188
pubmed: 34635837
Nat Biotechnol. 2019 Nov;37(11):1332-1343
pubmed: 31611695
Nat Med. 2021 Jul;27(7):1280-1289
pubmed: 34017137
Nat Rev Microbiol. 2021 Jul;19(7):409-424
pubmed: 34075212
Cell. 2020 Oct 1;183(1):158-168.e14
pubmed: 32979941
BMC Bioinformatics. 2017 Dec 28;18(1):585
pubmed: 29281985
Blood. 2013 Feb 14;121(7):1112-23
pubmed: 23255554
Immunity. 2019 Oct 15;51(4):766-779.e17
pubmed: 31495665
Future Virol. 2022 May;:
pubmed: 35747327
Nature. 1994 Mar 17;368(6468):215-21
pubmed: 8145819
Cell. 2020 Jun 25;181(7):1489-1501.e15
pubmed: 32473127
Front Immunol. 2018 Jul 25;9:1716
pubmed: 30090105
Sci Rep. 2020 Dec 23;10(1):22375
pubmed: 33361777
Cell Rep Med. 2021 Jul 20;2(7):100355
pubmed: 34230917
Nat Biotechnol. 2019 Nov;37(11):1283-1286
pubmed: 31611696
Sci Immunol. 2017 Aug 4;2(14):
pubmed: 28778905
Signal Transduct Target Ther. 2022 Jan 27;7(1):26
pubmed: 35087058
Annu Rev Immunol. 2020 Apr 26;38:123-145
pubmed: 32045313
BMC Bioinformatics. 2019 May 28;20(1):270
pubmed: 31138107
J Immunol. 1994 Aug 15;153(4):1665-73
pubmed: 7519208
Nat Immunol. 2022 Feb;23(2):186-193
pubmed: 35105982
Semin Immunol. 2023 Mar;66:101727
pubmed: 36764021
Front Immunol. 2022 Feb 09;13:801522
pubmed: 35222380
J Immunol. 2016 Aug 15;197(4):1517-24
pubmed: 27402703
Lancet Infect Dis. 2022 Sep;22(9):1293-1302
pubmed: 35753318
Bioinformatics. 2016 Feb 15;32(4):511-7
pubmed: 26515819
Nat Med. 2021 Nov;27(11):1990-2001
pubmed: 34522051
PLoS One. 2017 Oct 24;12(10):e0186998
pubmed: 29065175
Nat Struct Mol Biol. 2021 Jul;28(7):573-582
pubmed: 34158638
Vaccines (Basel). 2022 Jul 14;10(7):
pubmed: 35891287
Nat Biotechnol. 2020 Feb;38(2):199-209
pubmed: 31844290
Trends Immunol. 2006 Jan;27(1):11-6
pubmed: 16297661
mBio. 2018 May 22;9(3):
pubmed: 29789363
J Immunol Methods. 2023 Apr;515:113443
pubmed: 36842524
J Immunol. 2017 Nov 1;199(9):3360-3368
pubmed: 28978689
Nucleic Acids Res. 2020 Jan 8;48(D1):D783-D788
pubmed: 31722398
Bioinformatics. 2017 Sep 01;33(17):2658-2665
pubmed: 28444127
Lancet Rheumatol. 2022 Mar;4(3):e177-e187
pubmed: 34977602
Nat Immunol. 2020 Nov;21(11):1336-1345
pubmed: 32887977
Front Microbiol. 2022 Mar 09;13:854567
pubmed: 35356515
Front Microbiol. 2020 Oct 23;11:550674
pubmed: 33193132
Nature. 1995 Nov 30;378(6556):457-62
pubmed: 7477400
Biomed Pharmacother. 2023 Mar;159:114242
pubmed: 36652729
Sci Rep. 2016 Aug 25;6:32115
pubmed: 27558848