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Transcriptional Profiles of Mart-1(27-35) Epitope Specific TCReng Human CD8+ and CD4+ T Cells upon Epitope Encounter as Elucidated by RNASeq

Prashant Singh, Nitya G Chakraborty, Sidharth S Jha, Umar Farooq, Mei Xiao, Veneta Qendro, Arvind Chhabra, Richard Everson, David I Dorsky, Upendra P Hegde and Bijay Mukherji

Adoptive cell therapy (ACT) with in vitro expanded populations of T cells engineered to express tumor epitope specific T cell receptors (TCR) is now undergoing clinical trials for various malignancies. In this context, ACT with the melanoma epitope, Mart-1(27-35), specific TCR engineered T cells has shown encouraging results in metastatic melanoma. A number of biological processes regulating T cell functions have, however, turned out to be impediments in this form of cancer therapy. As such, efforts are underway to gain a fuller understanding of the biology (functionality and constraints) of TCR-engineered (TCReng) T cells so as to extract more robust therapeutic effects from ACT. Traditional T cell-based assays are, however, somewhat inadequate for the purpose. Using Next Generation RNASeq (NGS) and qRT-PCR assays, we examined the transcriptome of melanoma epitope, Mart-1(27-35), specific TCReng human T cells. We found that the transcriptional profiles of the Mart-1(27-35), specific TCReng T cell (both CD8+ and CD4+) is remarkably similar when exposed to the cognate peptide. The genes responsible for T-cell activation, apoptosis, cellular proliferation, cytolytic response, and T-cell differentiation showed similar patterns of expression. Further, our analysis also revealed a number of alternate splice variants and novel isoforms related to immune response previously not associated with T cell activation, as well as expression of a number of recently discovered long non-coding RNAs (lncRNA).