Epstein-Barr virus and human herpesvirus 6 detection in a Non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing

Journal of Virology

Volumn 87, Issue 23, 2013, Pages 13059-13062

  Strong, Michael J ^a,b   O'Grady, Tina ^a,b   Lin, Zhen ^a,b   Xu, Guorong ^c   Baddoo, Melody ^a,b   Parsons, Chris ^d   Zhang, Kun ^e   Taylor, Christopher M ^d,f   Flemington, Erik K ^a,b  

^a TULANE UNIVERSITY   (United States)

^b TULANE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c BAYLOR INSTITUTE FOR IMMUNOLOGY RESEARCH   (United States)

^d LOUISIANA STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e XAVIER UNIVERSITY OF LOUISIANA   (United States)

^f CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; EBNA2 GENE; EPSTEIN BARR VIRUS; EPSTEIN BARR VIRUS INFECTION; FOLLICULAR LYMPHOMA; HERPES SIMPLEX; HUMAN; HUMAN HERPESVIRUS 6; LARGE CELL LYMPHOMA; LMP1 GENE; LMP2 GENE; MAJOR CLINICAL STUDY; MIXED INFECTION; PRIORITY JOURNAL; RNA SEQUENCE; RPMS1 GENE; TRANSCRIPTOMICS; VIRUS DETECTION; VIRUS GENE;

COHORT STUDIES; EPSTEIN-BARR VIRUS INFECTIONS; GENE EXPRESSION REGULATION, VIRAL; HERPESVIRUS 4, HUMAN; HERPESVIRUS 6, HUMAN; HUMANS; LYMPHOMA, LARGE B-CELL, DIFFUSE; ROSEOLOVIRUS INFECTIONS; SEQUENCE ANALYSIS, RNA; VIRAL PROTEINS;

EID: 84887193368     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.02380-13     Document Type: Article

References (26)

1. Ogata M. 2009. Human herpesvirus 6 in hematological malignancies. J. Clin. Exp. Hematopathol. 49:57-67.
2. Feng H, Shuda M, Chang Y, Moore PS. 2008. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319:1096-1100.
3. Castellarin M, Warren R, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA. 2012. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res. 22:299-306.
4. Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RGW, Getz G, Meyerson M. 2011. PathSeq:software to identify or discover microbes by deep sequencing of human tissue. Nat. Biotechnol. 29:393-396.
5. Strong MJ, Xu G, Coco J, Baribault C, Vinay DS, Lacey MR, Strong AL, Lehman TA, Seddon MB, Lin Z, Concha M, Baddoo M, Ferris M, Swan KF, Sullivan DE, Burow ME, Taylor CM, Flemington EK. 2013. Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity:implications for possible immune adjuvant therapy. PLoS Pathog. 9:e1003341. doi:10.1371/journal.ppat.1003341.
6. Lin Z, Puetter A, Coco J, Xu G, Strong MJ, Wang X, Fewell C, Baddoo M, Taylor C, Flemington EK. 2012. 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. J. Virol. 86:2970-2977.
7. Khoury JD, Tannir NM, Williams MD, Chen Y, Yao H, Zhang J, Thompson EJ, Network T, Meric-Bernstam F, Medeiros LJ, Weinstein JN, Su X. 2013. Landscape of DNA virus associations across human malignant cancers:analysis of 3,775 cases using RNA-seq. J. Virol. 87: 8916-8926.
8. de Sanjosé S, Bosch R, Schouten T, Verkuijlen S, Nieters A, Foretova L, Maynadié M, Cocco PL, Staines A, Becker N, Brennan P, Benavente Y, Boffetta P, Meijer CJ, Middeldorp JM. 2007. 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. Int. J. Cancer 121:1806-1812.
9. Hardell K, Carlberg M, Hardell L, Björnfoth H, Ericson Jogsten I, Eriksson M, Van Bavel B, Lindström G. 2009. Concentrations of organohalogen compounds and titres of antibodies to Epstein-Barr virus antigens and the risk for non-Hodgkin lymphoma. Oncol. Rep. 21:1567-1576.
10. Mueller NE, Mohar A, Evans A. 1992. Viruses other than HIV and non-Hodgkin's lymphoma. Cancer Res. 52:5479s-5481s.
11. Pozdnyakova O, Spieler PJ, Abraham J, Freedman AS, Kutok JL. 2010. Epstein-Barr virus-associated diffuse large B-cell lymphoma in an immunocompetent woman. J. Clin. Oncol. 28:e75-e78.
12. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S. 2011. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 476:298-303.
13. Nix D, Courdy S, Boucher K. 2008. Empirical methods for controlling false positives and estimating confidence in ChIP-seq peaks. BMC Bioinformatics 9:523. doi:10.1186/1471-2105-9-523.
14. Pruitt KD, Tatusova T, Brown GR, Maglott DR. 2012. NCBI reference sequences (RefSeq):current status, new features and genome annotation policy. Nucleic Acids Res. 40:D130-D135.
15. Huson DH, Mitra S, Ruscheweyh H-J, Weber N, Schuster SC. 2011. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 21:1552-1560.
16. Lin Z, Wang X, Strong MJ, Concha M, Baddoo M, Xu G, Baribault C, Fewell C, Hulme W, Hedges D, Taylor CM, Flemington EK. 2013. Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains. J. Virol. 87:1172-1182.
17. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. 2013. STAR:ultrafast universal RNA-seq aligner. Bioinformatics 29:15-21.
18. Xu G, Deng N, Zhao Z, Judeh T, Flemington E, Zhu D. 2011. SAMMate: a GUI tool for processing short read alignments in SAM/BAM format. Source Code Biol. Med. 6:2. doi:10.1186/1751-0473-6-2.
19. Saeed A, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J. 2003. TM4:a free, open-source system for microarray data management and analysis. Biotechniques 34:374-378.
20. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. 2011. Integrative genomics viewer. Nat. Biotech. 29:24-26.
21. Hong GK, Gulley ML, Feng W-H, Delecluse H-J, Holley-Guthrie E, Kenney SC. 2005. Epstein-Barr virus lytic infection contributes to lymphoproliferative disease in a SCID mouse model. J. Virol. 79:13993-14003.
22. Ma S, Yu X, Mertz JE, Gumperz JE, Reinheim E, Zhou Y, Tang W, Burlingham WJ, Gulley ML, Kenney SC. 2012. An Epstein-Barr virus (EBV) mutant with enhanced BZLF1 expression causes lymphomas with abortive lytic EBV infection in a humanized mouse model. J. Virol. 86: 7976-7987.
23. Dawson CW, Port RJ, Young LS. 2012. The role of the EBV-encoded latent membrane proteins LMP1 and LMP2 in the pathogenesis of nasopharyngeal carcinoma (NPC). Semin. Cancer Biol. 22:144-153.
24. Frappier L. 2012. Role of EBNA1 in NPC tumourigenesis. Semin. Cancer Biol. 22:154-161.
25. Portis T, Cooper L, Dennis P, Longnecker R. 2002. The LMP2A signalosome-a therapeutic target for Epstein-Barr virus latency and associated disease. Front. Biosci. 1:d414-d426.
26. Saha A, Robertson ES. 2013. Impact of EBV essential nuclear protein EBNA-3C on B-cell proliferation and apoptosis. Future Microbiol. 8:323-352.