T-cell receptor repertoire analysis based on RNA sequencing data from tumor cells and tumor-infiltrating lymphocytes.

Abstract

3058 Background: T-cell receptor (TCR) repertoire has been thought to be indicative in cancer progression and treatment response. Previous methods mainly focused on peripheral blood or fresh tumor tissue, which were sometimes logistically limited in clinical settings. Tumor-infiltrating lymphocytes (TILs), which harbored TCR characteristics, were also mingled with tumor cells (TCs), which brought hurdles in extracting TCR signals from bulk RNA sequencing data. Here we employed a set of RNA sequencing data from paired FFPE tumor samples and their micro-dissected TILs, to analyze and compare the TCR features in tumor cells and TILs. Methods: RNA sequencing data of 14 tumor cell samples and matched TILs were downloaded from NCBI-SRA (accession: PRJEB36554). Raw data were cleaned up by Trim Galore (v0.6.2). TCR clonotypes were assembled and quantified from clean fastq files by MiXCR (v3.0.4). Diversity and clonality metrics were analyzed using VDJtools (v1.2.1) and in-house Pearl scripts. Results: The median mapping rates of sequencing reads to TCR regions were 0.29% and 1.80% for TCs and TILs respectively (p = 0.00051). TCR diversity of TCs and TILs was characterized by Shannon and Simpson index respectively. The median Shannon index was 1.889 and 2.694 in TCs and TILs (p = 0.00034, unpaired Wilcoxon rank-sum test); the median Simpson index was 0.8724 and 0.9420 in TCs and TILs (p = 0.0058). Conclusions: RNA isolated from clinical FFPE samples could be used for TCR analysis. Micro-dissection of TILs could enhance TCR signals of unprocessed tumor tissues.