Detection of Productively Rearranged TcR-α V–J Sequences in TCGA Exome Files: Implications for Tumor Immunoscoring and Recovery of Antitumor T-cells

• DOI: 10.4137/cin.s35784
• Publication Date: 2016-02-25T21:26:18Z
• Authors: Thomas R. Gill; Mohammad D. Samy; Shanitra N. Butler; James A. Mauro; Wade J. Sexton; George Blanck
• Keywords: Exome

Tumor immunoscoring is rapidly becoming a universal parameter of prognosis, and T-cells isolated from tumor masses are used for ex vivo amplification readministration to patients facilitate an antitumor immune response. We recently exploited the cancer genome atlas (TCGA) RNASeq data assess T-cell receptor (TcR) expression and, in particular, discovered strong correlations between major histocompatibility class II (MHCII) TcR-α constant region levels. In this article, we describe results searching TCGA exome files V-regions, followed by V-region datasets TcR-α-J regions. Both primary metastatic breast sample contained recombined V-J regions, ranging read counts 16-39, at higher level. Among four such rearrangements, three were productive rearrangements. Rearranged regions also detected TCGA-bladder cancer, -lung -ovarian datasets, as well representing bladder Moffitt Cancer Center patients. These suggest that direct search commonly available, conventional rearranged TcR segments could play role more sophisticated or identifying particular clones TcRs directed against antigens.