Abstract 3581: Characterization of T cell repertoire in transplanted patients with graft versus host disease using next generation DNA sequencer
Authors: Poh Yin Yew, Rui Yamaguchi, Michael Bishop, Amittha Wickrema, Andrew Artz, Satoru Miyano, Yusuke Nakamura
Journal: Cancer Research (2014)

Abstract Allogeneic hematopoietic stem cell transplantation (HSCT) is an effective therapy in treating patients for a range of high-risk hematologic malignancies. However, the success of allogeneic HSCT is limited due to graft versus host disease (GVHD). T cell receptor (TCR), a heterodimer of alpha and beta chains, is expressed on the surface of T cells, recognizes some antigens on the HLA molecule on host cells, enhances T cell proliferation, and release cytotoxic agents that cause the damage on host cells. The TCR in each T cell is unique due to the recombination of VJ (alpha) or VDJ (beta) segments that generates a diverse repertoire of T cells and enables T cells to recognize a vast number of different antigens. The development of next generation sequencing (NGS) has enabled us to obtain massive profiling of TCR to unravel the complexity of T cell diversity. In this study, we attempted to identify expanded T cell populations which are induced during the course of GVHD development after HSCT. To characterize millions of the TCR alpha and beta chains from a single individual, we performed very deep sequencing using cDNA derived from mRNA isolated from peripheral blood mononuclear cells of GVHD patients at different time-points (before and after HSCT) with Ion Personal Genome Machine (PGM™) Sequencer and a 400-bp reading kit. This sequencing technology has allowed us to obtain several million TCR sequences in a single experiment. A newly-developed algorithm was then applied for characterization of TCRs at each time-point. This approach has identified expansion of oligoclonal TCR alpha and beta chains, with unique V(D)J junction sequences around the rearranged regions, in T cells that are likely to be associated with development of GVHD. In the present study, a total of nine GVHD patients with different time-points (before and after HSCT) were examined. We obtained an average of 3,560,634 TCR alpha sequences with VJ combinations and 2,161,990 TCR beta sequences with VDJ combinations. Diversified TCR repertoire is observed in these samples. Further analysis of TCR alpha and beta chains for various time-points has suggested that a specific type(s) of T cells might be activated in the GVHD patients. Characterization of TCR may help delineate the molecular mechanisms of GVHD more precisely. Furthermore, it may aid in characterizing a personalized GVHD phenotype and predicting and/or monitoring the immunological responses after HSCT. Citation Format: Poh Yin Yew, Rui Yamaguchi, Michael Bishop, Amittha Wickrema, Andrew Artz, Satoru Miyano, Yusuke Nakamura. Characterization of T cell repertoire in transplanted patients with graft versus host disease using next generation DNA sequencer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3581. doi:10.1158/1538-7445.AM2014-3581