Molecular constraints on CDR3 for thymic selection of MHC-restricted TCRs from a random pre-selection repertoire View Full Text


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Article Info

DATE

2019-12

AUTHORS

Jinghua Lu, François Van Laethem, Abhisek Bhattacharya, Marco Craveiro, Ingrid Saba, Jonathan Chu, Nicholas C. Love, Anastasia Tikhonova, Sergei Radaev, Xiaoping Sun, Annette Ko, Tomer Arnon, Eric Shifrut, Nir Friedman, Nan-Ping Weng, Alfred Singer, Peter D. Sun

ABSTRACT

The αβ T cell receptor (TCR) repertoire on mature T cells is selected in the thymus, but the basis for thymic selection of MHC-restricted TCRs from a randomly generated pre-selection repertoire is not known. Here we perform comparative repertoire sequence analyses of pre-selection and post-selection TCR from multiple MHC-sufficient and MHC-deficient mouse strains, and find that MHC-restricted and MHC-independent TCRs are primarily distinguished by features in their non-germline CDR3 regions, with many pre-selection CDR3 sequences not compatible with MHC-binding. Thymic selection of MHC-independent TCR is largely unconstrained, but the selection of MHC-specific TCR is restricted by both CDR3 length and specific amino acid usage. MHC-restriction disfavors TCR with CDR3 longer than 13 amino acids, limits positively charged and hydrophobic amino acids in CDR3β, and clonally deletes TCRs with cysteines in their CDR3 peptide-binding regions. Together, these MHC-imposed structural constraints form the basis to shape VDJ recombination sequences into MHC-restricted repertoires. More... »

PAGES

1019

References to SciGraph publications

  • 2009-04. Germline-encoded amino acids in the αβ T-cell receptor control thymic selection in NATURE
  • 2016-08. Hydrophobic CDR3 residues promote the development of self-reactive T cells in NATURE IMMUNOLOGY
  • 1949-01. National Museums and Galleries in Britain in NATURE
  • 2015-12. Thymoproteasomes produce unique peptide motifs for positive selection of CD8+ T cells in NATURE COMMUNICATIONS
  • 2009-02. The molecular basis of TCR germline bias for MHC is surprisingly simple in NATURE IMMUNOLOGY
  • 2014-12. Comparative analysis of human and mouse immunoglobulin variable heavy regions from IMGT/LIGM-DB with IMGT/HighV-QUEST in THEORETICAL BIOLOGY AND MEDICAL MODELLING
  • 2009-12. Naive T cell homeostasis: from awareness of space to a sense of place in NATURE REVIEWS IMMUNOLOGY
  • 1984-08. Genomic organization and sequence of T-cell receptor β-chain constant- and joining-region genes in NATURE
  • 2015-11. T cell receptor reversed polarity recognition of a self-antigen major histocompatibility complex in NATURE IMMUNOLOGY
  • 2012-06. Clonal deletion and the fate of autoreactive thymocytes that survive negative selection in NATURE IMMUNOLOGY
  • 2014-06. Towards error-free profiling of immune repertoires in NATURE METHODS
  • 2016-12. αβ T cell receptor germline CDR regions moderate contact with MHC ligands and regulate peptide cross-reactivity in SCIENTIFIC REPORTS
  • 2013-02. IL-7 signaling must be intermittent, not continuous, during CD8+ T cell homeostasis to promote cell survival instead of cell death in NATURE IMMUNOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41467-019-08906-7

    DOI

    http://dx.doi.org/10.1038/s41467-019-08906-7

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1112507554

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30833553


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    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-08906-7'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-08906-7'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-08906-7'

    RDF/XML is a standard XML format for linked data.

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