Epstein-Barr Virus and Human Herpesvirus 6 Detection in a Non-Hodgkin's Diffuse Large B-Cell Lymphoma Cohort by Using RNA Sequencing

ABSTRACT Comprehensive virome analysis of RNA sequence (RNA-seq) data sets from 118 non-Hodgkin's B-cell lymphomas revealed a small subset that is positive for Epstein-Barr virus (EBV) or human herpesvirus 6B (HHV-6B), with one coinfection. EBV transcriptome analysis revealed expression of the latency genes RPMS1, LMP1, and LMP2, with one sample additionally showing a high level of early lytic expression and another sample showing a high level of EBNA2 expression. HHV-6B transcriptome analysis revealed that the majority of genes were transcribed.

[1]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[2]  L. Young,et al.  The role of the EBV-encoded latent membrane proteins LMP1 and LMP2 in the pathogenesis of nasopharyngeal carcinoma (NPC). , 2012, Seminars in cancer biology.

[3]  B. Thiers,et al.  Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma , 2009 .

[4]  Guorong Xu,et al.  SAMMate: a GUI tool for processing short read alignments in SAM/BAM format , 2011, Source Code for Biology and Medicine.

[5]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[6]  Joseph Coco,et al.  Detection of Murine Leukemia Virus in the Epstein-Barr Virus-Positive Human B-Cell Line JY, Using a Computational RNA-Seq-Based Exogenous Agent Detection Pipeline, PARSES , 2012, Journal of Virology.

[7]  Erika J. Thompson,et al.  Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq , 2013, Journal of Virology.

[8]  M. Gulley,et al.  An Epstein-Barr Virus (EBV) Mutant with Enhanced BZLF1 Expression Causes Lymphomas with Abortive Lytic EBV Infection in a Humanized Mouse Model , 2012, Journal of Virology.

[9]  Christopher M. Taylor,et al.  Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy , 2013, PLoS pathogens.

[10]  M. Gulley,et al.  Epstein-Barr Virus Lytic Infection Contributes to Lymphoproliferative Disease in a SCID Mouse Model , 2005, Journal of Virology.

[11]  G. Getz,et al.  PathSeq: software to identify or discover microbes by deep sequencing of human tissue , 2011, Nature Biotechnology.

[12]  W. Liang,et al.  9) TM4 Microarray Software Suite , 2006 .

[13]  P. Brennan,et al.  Epstein‐Barr virus infection and risk of lymphoma: Immunoblot analysis of antibody responses against EBV‐related proteins in a large series of lymphoma subjects and matched controls , 2007, International journal of cancer.

[14]  E. Robertson,et al.  Impact of EBV essential nuclear protein EBNA-3C on B-cell proliferation and apoptosis. , 2013, Future microbiology.

[15]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy , 2011, Nucleic Acids Res..

[16]  L. Frappier.  Role of EBNA1 in NPC tumourigenesis. , 2012, Seminars in cancer biology.

[17]  Richard A. Moore,et al.  Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. , 2012, Genome research.

[18]  M. Ogata.  Human herpesvirus 6 in hematological malignancies. , 2009, Journal of clinical and experimental hematopathology : JCEH.

[19]  Steven J. M. Jones,et al.  Frequent mutation of histone modifying genes in non-Hodgkin lymphoma , 2011, Nature.

[20]  A I Saeed,et al.  TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.

[21]  A. Mohar,et al.  Viruses other than HIV and non-Hodgkin's lymphoma. , 1992, Cancer research.

[22]  S. Schuster,et al.  Integrative analysis of environmental sequences using MEGAN4. , 2011, Genome research.

[23]  D. Hedges,et al.  Whole-Genome Sequencing of the Akata and Mutu Epstein-Barr Virus Strains , 2012, Journal of Virology.

[24]  David A. Nix,et al.  Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks , 2008, BMC Bioinformatics.

[25]  P. Dennis,et al.  The LMP2A signalosome--a therapeutic target for Epstein-Barr virus latency and associated disease. , 2002, Frontiers in bioscience : a journal and virtual library.

[26]  M. Eriksson,et al.  Concentrations of organohalogen compounds and titres of antibodies to Epstein-Barr virus antigens and the risk for non-Hodgkin lymphoma. , 2009, Oncology reports.

[27]  J. Kutok,et al.  Epstein-barr virus-associated diffuse large B-cell lymphoma in an immunocompetent woman. , 2010, Journal of Clinical Oncology.