A new high-throughput sequencing method for determining diversity and similarity of T cell receptor TCR α and β repertoires and identifying potential new invariant TCR α chainsReportar como inadecuado




A new high-throughput sequencing method for determining diversity and similarity of T cell receptor TCR α and β repertoires and identifying potential new invariant TCR α chains - Descarga este documento en PDF. Documentación en PDF para descargar gratis. Disponible también para leer online.

BMC Immunology

, 17:38

Immunogenetics

Abstract

BackgroundHigh-throughput sequencing of T cell receptor TCR genes is a powerful tool for analyses of antigen specificity, clonality and diversity of T lymphocytes. Here, we developed a new TCR repertoire analysis method using 454 DNA sequencing technology in combination with an adaptor-ligation mediated polymerase chain reaction PCR. This method allows the amplification of all TCR genes without PCR bias. To compare gene usage, diversity and similarity of expressed TCR repertoires among individuals, we conducted next-generation sequencing NGS of TRA and TRB genes in peripheral blood mononuclear cells from 20 healthy human individuals.

ResultsFrom a total of 267,037 sequence reads from 20 individuals, 149,216 unique sequence reads were identified. Preferential usage of several V and J genes were observed while some recombinations of TRAV with TRAJ appeared to be restricted. The extent of TCR diversity was not significantly different between TRA and TRB, while TRA repertoires were more similar between individuals than TRB repertoires were. The interindividual similarity of TRA depended largely on the frequent presence of shared TCRs among two or more individuals. A publicly available TRA had a near-germline TCR with a shorter CDR3. Notably, shared TRA sequences, especially those shared among a large number of individuals’, often contained TCRα related with invariant TCRα derived from invariant natural killer T cells and mucosal-associated invariant T cells.

ConclusionThese results suggest that retrieval of shared TCRs by NGS would be useful for the identification of potential new invariant TCRα chains. This NGS method will enable the comprehensive quantitative analysis of TCR repertoires at a clonal level.

KeywordsT cell receptor Repertoire Next generation sequencing Immune profiling Invariant TCRα AbbreviationsCDRComplementarity determining region

TRAT cell receptor alpha

TRAJT cell receptor alpha joining

TRAVT cell receptor alpha variable

TRBT cell receptor beta

TRBJT cell receptor alpha joining

TRBVT cell receptor beta variable

Electronic supplementary materialThe online version of this article doi:10.1186-s12865-016-0177-5 contains supplementary material, which is available to authorized users.

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Autor: Kazutaka Kitaura - Tadasu Shini - Takaji Matsutani - Ryuji Suzuki

Fuente: https://link.springer.com/







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