[HTML][HTML] Identification of antigen-specific TCR sequences based on biological and statistical enrichment in unselected individuals

NP Smith, B Ruiter, YV Virkud, AA Tu, B Monian… - JCI insight, 2021 - ncbi.nlm.nih.gov
NP Smith, B Ruiter, YV Virkud, AA Tu, B Monian, JJ Moon, JC Love, WG Shreffler
JCI insight, 2021ncbi.nlm.nih.gov
Recent advances in high-throughput T cell receptor (TCR) sequencing have allowed for new
insights into the human TCR repertoire. However, methods for capturing antigen-specific
repertoires remain an area of development. Here, we describe a potentially novel approach
that utilizes both a biological and statistical enrichment to define putatively antigen-specific
complementarity-determining region 3 (CDR3) repertoires in unselected individuals. The
biological enrichment entailed FACS of in vitro antigen-activated memory CD4+ T cells …
Abstract
Recent advances in high-throughput T cell receptor (TCR) sequencing have allowed for new insights into the human TCR repertoire. However, methods for capturing antigen-specific repertoires remain an area of development. Here, we describe a potentially novel approach that utilizes both a biological and statistical enrichment to define putatively antigen-specific complementarity-determining region 3 (CDR3) repertoires in unselected individuals. The biological enrichment entailed FACS of in vitro antigen-activated memory CD4+ T cells, followed by TCRβ sequencing. The resulting TCRβ sequences were then filtered by selecting those that are statistically enriched when compared with their frequency in the autologous resting T cell compartment. Applying this method to define putatively peanut protein–specific repertoires in 27 peanut-allergic individuals resulted in a library of 7345 unique CDR3β amino acid sequences that had similar characteristics to other validated antigen-specific repertoires in terms of homology and diversity. In-depth analysis of these CDR3βs revealed 36 public sequences that demonstrated high levels of convergent recombination. In a network analysis, the public CDR3βs were shown to be core sequences with more edges than their private counterparts. This method has the potential to be applied to a wide range of T cell–mediated disorders and to yield new biomarkers and biological insights.
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