title: Quantitative T cell repertoire analysis by deep cDNA sequencing of T cell receptor α and β chains using next-generation sequencing (NGS).
abstract: 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.
authors.affiliation: Committee on Clinical Pharmacology and Pharmacogenomics; The University of Chicago ; Chicago, IL USA ; Section of Hematology/Oncology; Department of Medicine; The University of Chicago ; Chicago, IL USA.
authors.forename: Hua
authors.initials: H
authors.lastname: Fang
authors.affiliation: Human Genome Center; Institute of Medical Science; The University of Tokyo ; Tokyo, Japan.
authors.forename: Rui
authors.initials: R
authors.lastname: Yamaguchi
authors.affiliation: Section of Hematology/Oncology; Department of Medicine; The University of Chicago ; Chicago, IL USA.
authors.forename: Xiao
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Medical Oncology; Shiga University of Medical Science Hospital ; Shiga, Japan.
authors.forename: Yataro
authors.initials: Y
authors.lastname: Daigo
authors.affiliation: Section of Hematology/Oncology; Department of Medicine; The University of Chicago ; Chicago, IL USA.
authors.forename: Poh Yin
authors.initials: PY
authors.lastname: Yew
authors.affiliation: Human Genome Center; Institute of Medical Science; The University of Tokyo ; Tokyo, Japan.
authors.forename: Chizu
authors.initials: C
authors.lastname: Tanikawa
authors.affiliation: Human Genome Center; Institute of Medical Science; The University of Tokyo ; Tokyo, Japan.
authors.forename: Koichi
authors.initials: K
authors.lastname: Matsuda
authors.affiliation: Human Genome Center; Institute of Medical Science; The University of Tokyo ; Tokyo, Japan.
authors.forename: Seiya
authors.initials: S
authors.lastname: Imoto
authors.affiliation: Human Genome Center; Institute of Medical Science; The University of Tokyo ; Tokyo, Japan.
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
authors.affiliation: Committee on Clinical Pharmacology and Pharmacogenomics; The University of Chicago ; Chicago, IL USA ; Section of Hematology/Oncology; Department of Medicine; The University of Chicago ; Chicago, IL USA ; Department of Surgery; The University of Chicago ; Chicago, IL USA ; Center for Personalized Therapeutics; The University of Chicago ; Chicago, IL, USA.
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Nakamura
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