title: T cell receptor gene recombinations in human tumor specimen exome files: detection of T cell receptor-β VDJ recombinations associates with a favorable oncologic outcome for bladder cancer.
abstract: Understanding tumor-resident T cells is important for cancer prognosis and treatment options. Conventional, solid tumor specimen exome files can be searched directly for recombined T cell receptor (TcR)-α segments; RNASeq files can include TcR-β VDJ recombinations. To learn whether there are medically relevant uses of exome-based detection of TcR V(D)J recombinations in the tumor microenvironment, we searched cancer genome atlas and Moffitt Cancer Center, tumor specimen exome files for TcR-β, TcR-γ, and TcR-δ recombinations, for bladder and stomach cancer. We found that bladder cancer exomes with productive TcR-β recombinations had a significant association with No Subsequent Tumors and a positive response to drug treatments, with p < 0.004, p < 0.05, and p < 0.004, depending on the sample sets examined. We also discovered the opportunity to detect productive TcR-γ and TcR-δ recombinations in the tumor microenvironment, via the tumor specimen exome files.
authors.affiliation: Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd., Tampa, FL, 33612, USA.
authors.forename: Mohammad D
authors.initials: MD
authors.lastname: Samy
authors.affiliation: Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd., Tampa, FL, 33612, USA.
authors.forename: Wei Lue
authors.initials: WL
authors.lastname: Tong
authors.affiliation: Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd., Tampa, FL, 33612, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Yavorski
authors.affiliation: Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
authors.forename: Wade J
authors.initials: WJ
authors.lastname: Sexton
authors.affiliation: Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd., Tampa, FL, 33612, USA. gblanck@health.usf.edu.|Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA. gblanck@health.usf.edu.
authors.forename: George
authors.initials: G
authors.lastname: Blanck
mesh_terms: D059472:Exome; D019672:Genes, T-Cell Receptor; D019674:Genes, T-Cell Receptor beta; D006801:Humans; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics*; D016896:Treatment Outcome; D059016:Tumor Microenvironment; D001749:Urinary Bladder Neoplasms / Q000235:genetics*; D060152:V(D)J Recombination / Q000235:genetics*
chemical_list: D016693:Receptors, Antigen, T-Cell, alpha-beta
keywords: Bladder cancer; Exome; Stomach cancer; T cell receptor recombination; TCGA; Tumor microenvironment