Using DNA sequencing data to quantify T cell fraction and therapy response

Article

关键词: TUMOR-INFILTRATING LYMPHOCYTES;    COPY NUMBER;    GENOMIC CHARACTERIZATION;    MUTATIONAL LANDSCAPE;    BRANCHED EVOLUTION;    CTLA-4 BLOCKADE;    PD-1 BLOCKADE;    HETEROGENEITY;    ARCHITECTURE;    IPILIMUMAB;   

DOI  :  10.1038/s41586-021-03894-5

来源: SCIE

【 摘 要 】

The immune microenvironment influences tumour evolution and can be both prognostic and predict response to immunotherapy(1,2). However, measurements of tumour infiltrating lymphocytes (TI Ls) are limited by a shortage of appropriate data. Whole-exome sequencing (WES) of DNA is frequently performed to calculate tumour mutational burden and identify actionable mutations. Here we develop T cell exome TREC tool (T cell ExTRECT), a method for estimation ofT cell fraction from WES samples using a signal from T cell receptor excision circle (TREC) loss during V(D)J recombination of the T cell receptor-alpha gene (TCRA (also known as TRA)). TCRA T cell fraction correlates with orthogonal TIL estimates and is agnosticto sample type. Blood TCRA T cell fraction is higher in females than in males and correlates with both tumour immune infiltrate and presence of bacterial sequencing reads. Tumour TCRA T cell fraction is prognostic in lung adenocarcinoma. Using a meta-analysis of tumour streated with immunotherapy, we show that tumour TCRA T cell fraction predicts immunotherapy response, providing value beyond measuring tumour mutational burden. Applying T cell ExTRECT to a multi-sample pan-cancer cohort reveals a high diversity of the degree of immune infiltration within tumours. Subclonal loss of 12q24.31-32, encompassing SPPL3, is associated with reduced TCRA T cell fraction. T cell ExTRECT provides a cost-effective technique to characterize immune infiltrate alongside somatic changes.

【 授权许可】

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