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Pogorelyy MV, Fedorova AD, McLaren JE, Ladell K, Bagaev DV, Eliseev AV, Mikelov AI, Koneva AE, Zvyagin IV, Price DA, Chudakov DM, Shugay M. Exploring the pre-immune landscape of antigen-specific T cells. Genome Med 2018; 10:68. [PMID: 30144804 PMCID: PMC6109350 DOI: 10.1186/s13073-018-0577-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/06/2018] [Indexed: 12/26/2022] Open
Abstract
Background Adaptive immune responses to newly encountered pathogens depend on the mobilization of antigen-specific clonotypes from a vastly diverse pool of naive T cells. Using recent advances in immune repertoire sequencing technologies, models of the immune receptor rearrangement process, and a database of annotated T cell receptor (TCR) sequences with known specificities, we explored the baseline frequencies of T cells specific for defined human leukocyte antigen (HLA) class I-restricted epitopes in healthy individuals. Methods We used a database of TCR sequences with known antigen specificities and a probabilistic TCR rearrangement model to estimate the baseline frequencies of TCRs specific to distinct antigens epitopespecificT-cells. We verified our estimates using a publicly available collection of TCR repertoires from healthy individuals. We also interrogated a database of immunogenic and non-immunogenic peptides is used to link baseline T-cell frequencies with epitope immunogenicity. Results Our findings revealed a high degree of variability in the prevalence of T cells specific for different antigens that could be explained by the physicochemical properties of the corresponding HLA class I-bound peptides. The occurrence of certain rearrangements was influenced by ancestry and HLA class I restriction, and umbilical cord blood samples contained higher frequencies of common pathogen-specific TCRs. We also identified a quantitative link between specific T cell frequencies and the immunogenicity of cognate epitopes presented by defined HLA class I molecules. Conclusions Our results suggest that the population frequencies of specific T cells are strikingly non-uniform across epitopes that are known to elicit immune responses. This inference leads to a new definition of epitope immunogenicity based on specific TCR frequencies, which can be estimated with a high degree of accuracy in silico, thereby providing a novel framework to integrate computational and experimental genomics with basic and translational research efforts in the field of T cell immunology. Electronic supplementary material The online version of this article (10.1186/s13073-018-0577-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Alla D Fedorova
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Dmitri V Bagaev
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia
| | - Alexey V Eliseev
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Artem I Mikelov
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skoltech, Moscow, Russia
| | - Anna E Koneva
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia
| | - Ivan V Zvyagin
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
| | - Dmitry M Chudakov
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skoltech, Moscow, Russia.,Central European Institute of Technology, CEITEC, Brno, Czech Republic
| | - Mikhail Shugay
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia. .,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia. .,Center for Data-Intensive Biomedicine and Biotechnology, Skoltech, Moscow, Russia.
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