title: Identification of immunoglobulin V(D)J recombinations in solid tumor specimen exome files: Evidence for high level B-cell infiltrates in breast cancer.
abstract: It has recently become apparent that it is possible to characterize productively recombined, T-cell receptor (TcR) gene segments in tumor exome files, which presumably include representations of the DNA of other cells in the microenvironment. Similar characterizations have been done for TcR recombinations in tumor specimen RNASeq files. While exome files have been used to characterize immunoglobulin gene segment recombinations for tumors closely related to B-cells, immunoglobulin recombinations have yet to be characterized for putative microenvironment cells for solid tumors. Here we report a novel scripted algorithm that detects productive and unproductive immunoglobulin recombinations in both B-cell related tumor exome files and in solid tumor exome files, with the most important result being the relatively high level B-cell infiltrate in breast cancer. This analysis has the potential of streamlining and dramatically augmenting the knowledge base regarding B-cell infiltrates into solid tumors; and leading to antibody reagents directed against tumor antigens and tissue resident, infectious pathogens.
authors.affiliation: a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL , USA.
authors.forename: Wei Lue
authors.initials: WL
authors.lastname: Tong
authors.affiliation: a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL , USA.
authors.forename: Yaping N
authors.initials: YN
authors.lastname: Tu
authors.affiliation: a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL , USA.
authors.forename: Mohammad D
authors.initials: MD
authors.lastname: Samy
authors.affiliation: b 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: a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL , USA.|c Immunology Program , H. Lee Moffitt Cancer Center and Research Institute , Tampa , FL , USA.
authors.forename: George
authors.initials: G
authors.lastname: Blanck
mesh_terms: D000951:Antigens, Neoplasm / Q000276:immunology*; D001402:B-Lymphocytes / Q000276:immunology*; D001943:Breast Neoplasms / Q000276:immunology*; D059472:Exome; D005260:Female; D006801:Humans; D007136:Immunoglobulins / Q000235:genetics*; D060152:V(D)J Recombination
chemical_list: D000951:Antigens, Neoplasm; D007136:Immunoglobulins
keywords: breast cancer; cancer immunology; genomics-based immunoscoring; recombined V(D)J regions; the cancer genome atlas; tumor exome files; tumor infiltrating B-cells