In silico veritas? Potential limitations for SARS-CoV-2 vaccine development based on T-cell epitope prediction

English version

Autoři: Sandra Silva-Arrieta ^aff001; Philip J. R. Goulder ^aff002; Christian Brander ^aff001
Působiště autorů: IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain ^aff001; Department of Paediatrics, University of Oxford, Oxford, United Kingdom ^aff002; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa ^aff003; Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America ^aff004; University of Vic–Central University of Catalonia, Catalonia, Vic, Spain ^aff005; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain ^aff006
Vyšlo v časopise: In silico veritas? Potential limitations for SARS-CoV-2 vaccine development based on T-cell epitope prediction. PLoS Pathog 16(6): e32767. doi:10.1371/journal.ppat.1008607
Kategorie: Opinion
doi: https://doi.org/10.1371/journal.ppat.1008607

Zdroje

1. Falk K, Rötzschke O, Stevanovic S, Jung G, Rammensee HG. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature. 1991;351(6324):290–6.

2. Gotch F, Rothbard J, Howland K, Townsend A, McMichael A. Cytotoxic T lymphocytes recognize a fragment of influenza virus matrix protein in association with HLA-A2. Nature. 1987;326(6116):881–2.

3. Nixon DF, Townsend AR, Elvin JG, Rizza CR, Gallwey J, McMichael AJ. HIV-1 gag-specific cytotoxic T lymphocytes defined with recombinant vaccinia virus and synthetic peptides Nature. 1988;336(6198):484–7.

4. Brander C, Walker BD. The HLA-class I restricted CTL response in HIV-1 infection: Identification of optimal epitopes. In: Korber B, Brander C, Walker BD, Koup R, Moore J, Haynes B, Myers G, editors. HIV Molecular Immunology Database 1995. Los Alamos, NM: Los Alamos National Laboratory: Theoretical Biology and Biophysics; 1995. p. 1–9.

5. Llano A, Cedeño S, Silva-Arrieta S, Brander C. The 2019 Optimal HIV CTL epitopes update: Growing diversity in epitope length and HLA restriction. In: Yusim K, Korber BTM, Brander C, Barouch D, de Boer R, Haynes BF, Koup R, Moore JP, Walker BD, Watkins DI, editors. HIV Molecular Immunology 2018. Los Alamos, NM: Los Alamos National Laboratory, Theoretical Biology and Biophysics; 2019. p. 3–27.

6. Burrows SR, Rossjohn J, McCluskey J. Have we cut ourselves too short in mapping CTL epitopes? Trends Immunol. 2006;27 : 11–6.

7. Yaciuk JC, Skaley M, Bardet W, Schafer F, Mojsilovic D, Cate S, et al. Direct interrogation of viral peptides presented by the class I HLA of HIV-infected T cells. J Virol. 2014;88(22):12992–3004. doi: 10.1128/JVI.01914-14 25165114

8. Goulder PJ, Tang Y, Pelton SI, Walker BD. HLA-B57-restricted cytotoxic T-lymphocyte activity in a single infected subject toward two optimal epitopes, one of which is entirely contained within the other. J Virol. 2000;74(11):5291–9.

9. de Campos-Lima PO, Gavioli R, Zhang QJ, Wallace LE, Dolcetti R, Rowe M, et al. HLA-A11 epitope loss isolates of Epstein-Barr virus from a highly A111 population. Science. 1993;260 : 98–100.

10. Gutiérrez MI, Spangler G, Kingma D, Raffeld M, Guerrero I, Misad O, et al. Epstein-Barr virus in nasal lymphomas contains multiple ongoing mutations in the EBNA-1 gene. Blood. 1998;92(2):600–6.

11. Sidney J, Peters B, Frahm N, Brander C, Sette A. HLA class I supertypes: a revised and updated classification. BMC Immunol. 2008;9 : 1. doi: 10.1186/1471-2172-9-1 18211710

12. Frahm N, Yusim K, Suscovich TJ, Adams S, Sidney J, Hraber P, et al. Extensive HLA class I allele promiscuity among viral CTL epitopes. Eur J Immunol. 2007;37(9):2419–33

13. Walters LC, Harlos K, Brackenridge S, Rozbesky D, Barrett JR, Jain V, et al. Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding. Nat Commun. 2018;9(1):3137. doi: 10.1038/s41467-018-05459-z 30087334

14. Chen G, Wu D, Guo W, Cao Y, Huang D, Wang H, et al. Clinical and immunologic features in severe and moderate Coronavirus Disease 2019. J Clin Invest. 2020;130(5)2620–2629. doi: 10.1172/JCI137244 Epub 2020 Mar 27. 32217835

15. Friberg H, Beaumier CM, Park S, Pazoles P, Endy TP, Mathew A, et al. Protective versus pathologic pre-exposure cytokine profiles in dengue virus infection. PLoS Negl Trop Dis. 2018;12(12):e0006975. doi: 10.1371/journal.pntd.0006975 eCollection 2018 Dec. 30557313

16. Ruiz-Riol M, Llano A, Ibarrondo J, Zamarreño J, Yusim K, Bach V, et al. Alternative effector-function profiling identifies broad HIV-specific T-cell responses in highly HIV-exposed individuals who remain uninfected. J Infect Dis. 2015;211(6):936–46. doi: 10.1093/infdis/jiu534 Epub 2014 Sep 23. 25249264

Článek Various miRNAs compensate the role of miR-122 on HCV replication

Článek Novel partiti-like viruses are conditional mutualistic symbionts in their normal lepidopteran host, African armyworm, but parasitic in a novel host, Fall armyworm

Článek Microbiome factors in HPV-driven carcinogenesis and cancers

Článek Head-to-head comparisons of Toxoplasma gondii and its near relative Hammondia hammondi reveal dramatic differences in the host response and effectors with species-specific functions

Článek Rapid in vitro generation of bona fide exhausted CD8+ T cells is accompanied by Tcf7 promotor methylation

Článek Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis

Článek Different roles of integrin-β1 and integrin-αv for type IV secretion of CagA versus cell elongation phenotype and cell lifting by Helicobacter pylori

Článek Potentiation of rifampin activity in a mouse model of tuberculosis by activation of host transcription factor EB

Článek Cellular plasticity of pathogenic fungi during infection

Článek Bacterial killing by complement requires direct anchoring of membrane attack complex precursor C5b-7

Článek Transmission modes affect the population structure of potato virus Y in potato

Článek A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization