Immune responses play a critical role in various disease conditions including cancer and autoimmune diseases. However, to date, there has not been a rapid, sensitive, comprehensive, and quantitative analysis method to examine T-cell or B-cell immune responses. Here, we report a new approach to characterize T cell receptor (TCR) repertoire by sequencing millions of cDNA of TCR α and β chains in combination with a newly-developed algorithm. Using samples from lung cancer patients treated with cancer peptide vaccines as a model, we demonstrate that detailed information of the V-(D)-J combination along with complementary determining region 3 (CDR3) sequences can be determined. We identified extensive abnormal splicing of TCR transcripts in lung cancer samples, indicating the dysfunctional splicing machinery in T lymphocytes by prior chemotherapy. In addition, we found three potentially novel TCR exons that have not been described previously in the reference genome. This newly developed TCR NGS platform can be applied to better understand immune responses in many disease areas including immune disorders, allergies, and organ transplantations.
Keywords: APC, antigen presenting cell; CDCA1, cell division cycle-associated protein 1; CDR3, complementary determining region 3; CTL, cytotoxic T lymphocytes; CTLA-4, cytotoxic T-lymphocyte antigen-4; ELISPOT, enzyme-linked immunospot; FDA, Food and Drug Administration; IFA, incomplete Freund's adjuvant; IFNγ, γ-interferon; IRB, institutional review board; KIF20A, kinesin family member 20A; LY6K, lymphocyte antigen 6 complex locus K; MHC, major histocompatibility complex; NGS, Next Generation Sequencing; NSCLC, non-small cell lung cancer; ORF, Open reading frames; OS, overall survival; PBL, peripheral blood lymphocyte; PGM, Personal Genome Machine; RACE, rapid amplification of cDNA end; T cell repertoire; TCR, T cell receptor; cancer peptide vaccines; complementary determining region 3; immune responses; next-generation sequencing.