Identification of pathogen signatures in prostate cancer using RNA-seq

PLoS ONE

Volumn 10, Issue 6, 2015, Pages

  Chen, Yunqin ^a   Wei, Jia ^a  

^a ASTRAZENECA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BACTERIAL INFECTION; BK VIRUS; CAUCASIAN; CHINESE; CONTROLLED STUDY; EPSTEIN BARR VIRUS; ETHNIC DIFFERENCE; GENE IDENTIFICATION; GENE MAPPING; GENE SEQUENCE; GENETIC TRANSCRIPTION; HEPATITIS B VIRUS; HUMAN; HUMAN CYTOMEGALOVIRUS; HUMAN TISSUE; JC VIRUS; MALE; MICROBIAL IDENTIFICATION; MICROORGANISM DETECTION; NEXT GENERATION SEQUENCING; NONHUMAN; PATHOGENESIS; PROPIONIBACTERIUM ACNES; PROSTATE CANCER; RNA SEQUENCE; SEQUENCE ALIGNMENT; SIMIAN VIRUS 40; VIRAL GENETICS; VIRUS INFECTION; WART VIRUS; XENOTROPIC MULV RELATED VIRUS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MICROBIOLOGY; PROCEDURES; PROSTATE TUMOR; SEQUENCE ANALYSIS; VIROLOGY; VIRUS;

BACTERIA (MICROORGANISMS); BK POLYOMAVIRUS; HEPATITIS B VIRUS; HERPESVIRIDAE; HUMAN HERPESVIRUS 4; HUMAN HERPESVIRUS 5; HUMAN PAPILLOMAVIRUS; PAPILLOMAVIRIDAE; POLYOMAVIRUS; PROPIONIBACTERIUM ACNES; XENOTROPIC MURINE LEUKEMIA VIRUS;

MESSENGER RNA;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENE EXPRESSION REGULATION, VIRAL; HUMANS; MALE; PROPIONIBACTERIUM ACNES; PROSTATIC NEOPLASMS; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; VIRUSES;

EID: 84936792200     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0128955     Document Type: Article

References (66)

1. Siegel R, Naishadham D, Jemal A. Cancer statistics, 2013. CA: a cancer journal for clinicians. 2013; 63(1):11-30. doi: 10.3322/caac.21166 PMID: 23335087.
2. Nelson WG, De Marzo AM, Isaacs WB. Prostate cancer. The New England journal of medicine. 2003; 349(4):366-81. doi: 10.1056/NEJMra021562 PMID: 12878745.
3. Sfanos KS, De Marzo AM. Prostate cancer and inflammation: the evidence. Histopathology. 2012; 60(1):199-215. doi: 10.1111/j.1365-2559.2011.04033.x PMID: 22212087
4. McDowell A, Patrick S, Eishi Y, Lambert P, Eady A. Propionibacterium acnes in human health and disease. BioMed research international. 2013; 2013:493564. doi: 10.1155/2013/493564 PMID: 24455697; PubMed Central PMCID: PMC3884696.
5. Bojar RA, Holland KT. Acne and Propionibacterium acnes. Clinics in dermatology. 2004; 22(5):375-9. doi: 10.1016/j.clindermatol.2004.03.005 PMID: 15556721.
6. Perry A, Lambert P. Propionibacterium acnes: infection beyond the skin. Expert review of anti-infective therapy. 2011; 9(12):1149-56. doi: 10.1586/eri.11.137 PMID: 22114965.
7. Palapattu GS, Sutcliffe S, Bastian PJ, Platz EA, De Marzo AM, Isaacs WB, et al. Prostate carcinogenesis and inflammation: emerging insights. Carcinogenesis. 2005; 26(7):1170-81. doi: 10.1093/carcin/bgh317 PMID: 15498784.
8. Cohen RJ, Shannon BA, McNeal JE, Shannon T, Garrett KL. Propionibacterium acnes associated with inflammation in radical prostatectomy specimens: a possible link to cancer evolution? The Journal of urology. 2005; 173(6):1969-74. doi: 10.1097/01.ju.0000158161.15277.78 PMID: 15879794.
9. Fassi Fehri L, Mak TN, Laube B, Brinkmann V, Ogilvie LA, Mollenkopf H, et al. Prevalence of Propionibacterium acnes in diseased prostates and its inflammatory and transforming activity on prostate epithelial cells. International journal of medical microbiology: IJMM. 2011; 301(1):69-78. doi: 10.1016/j.ijmm.2010.08.014 PMID: 20943438.
10. Shannon BA, Garrett KL, Cohen RJ. Links between Propionibacterium acnes and prostate cancer. Future oncology. 2006; 2(2):225-32. doi: 10.2217/14796694.2.2.225 PMID: 16563091.
11. Ayub A, Ashfaq UA, Haque A. HBV induced HCC: major risk factors from genetic to molecular level. BioMed research international. 2013; 2013:810461. doi: 10.1155/2013/810461 PMID: 23991421; PubMed Central PMCID: PMC3749539.
12. Sung WK, Zheng H, Li S, Chen R, Liu X, Li Y, et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nature genetics. 2012; 44(7):765-9. doi: 10.1038/ng.2295 PMID: 22634754.
13. Saha A, Kaul R, Murakami M, Robertson ES. Tumor viruses and cancer biology: Modulating signaling pathways for therapeutic intervention. Cancer biology & therapy. 2010; 10(10):961-78. PMID: 21084867.
14. Nelson WG, De Marzo AM, DeWeese TL, Isaacs WB. The role of inflammation in the pathogenesis of prostate cancer. The Journal of urology. 2004; 172(5 Pt 2):S6-11; discussion S-2. PMID: 15535435.
15. Klein EA, Silverman R. Inflammation, infection, and prostate cancer. Current opinion in urology. 2008; 18(3):315-9. doi: 10.1097/MOU.0b013e3282f9b3b7 PMID: 18382242.
16. Pang KR, Wu JJ, Huang DB, Tyring SK, Baron S. Biological and clinical basis for molecular studies of interferons. Methods in molecular medicine. 2005; 116:1-23. doi: 10.1385/1-59259-939-7:1 PMID: 16007741.
17. Das D, Wojno K, Imperiale MJ. BK virus as a cofactor in the etiology of prostate cancer in its early stages. Journal of virology. 2008; 82(6):2705-14. doi: 10.1128/JVI.02461-07 PMID: 18160432
18. Ahsan N, Shah KV. Polyomaviruses and human diseases. Advances in experimental medicine and biology. 2006; 577:1-18. doi: 10.1007/0-387-32957-9-1 PMID: 16626024.
19. Samanta M, Harkins L, Klemm K, Britt WJ, Cobbs CS. High prevalence of human cytomegalovirus in prostatic intraepithelial neoplasia and prostatic carcinoma. The Journal of urology. 2003; 170(3):998-1002. doi: 10.1097/01.ju.0000080263.46164.97 PMID: 12913758.
20. Zambrano A, Kalantari M, Simoneau A, Jensen JL, Villarreal LP. Detection of human polyomaviruses and papillomaviruses in prostatic tissue reveals the prostate as a habitat for multiple viral infections. Prostate. 2002; 53(4):263-76. doi: 10.1002/pros.10157 PMID: 12430138.
21. Whitaker NJ, Glenn WK, Sahrudin A, Orde MM, Delprado W, Lawson JS. Human papillomavirus and Epstein Barr virus in prostate cancer: Koilocytes indicate potential oncogenic influences of human papillomavirus in prostate cancer. The Prostate. 2013; 73(3):236-41. doi: 10.1002/pros.22562 PMID: 22851253
22. Walboomers JM, Jacobs MV, Manos MM, Bosch FX, Kummer JA, Shah KV, et al. Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. The Journal of pathology. 1999; 189(1):12-9. doi: 10.1002/(SICI)1096-9896(199909)189:1<12::AID-PATH431>3.0.CO;2-F PMID: 10451482
23. Lin Y, Mao Q, Zheng X, Yang K, Chen H, Zhou C, et al. Human papillomavirus 16 or 18 infection and prostate cancer risk: a meta-analysis. Irish journal of medical science. 2011; 180(2):497-503. doi: 10.1007/s11845-011-0692-6 PMID: 21400096
24. Blaheta RA, Weich E, Marian D, Bereiter-Hahn J, Jones J, Jonas D, et al. Human cytomegalovirus infection alters PC3 prostate carcinoma cell adhesion to endothelial cells and extracellular matrix. Neoplasia. 2006; 8(10):807-16. doi: 10.1593/neo.06379 PMID: 17032497; PubMed Central PMCID: PMC1715925.
25. Maeda E, Akahane M, Kiryu S, Kato N, Yoshikawa T, Hayashi N, et al. Spectrum of Epstein-Barr virus-related diseases: a pictorial review. Japanese journal of radiology. 2009; 27(1):4-19. doi: 10.1007/s11604-008-0291-2 PMID: 19373526.
26. Urisman A, Molinaro RJ, Fischer N, Plummer SJ, Casey G, Klein EA, et al. Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. PLoS pathogens. 2006; 2(3):e25-e. doi: 10.1371/journal.ppat.0020025 PMID: 16609730
27. Lombardi VC, Ruscetti FW, Das Gupta J, Pfost MA, Hagen KS, Peterson DL, et al. Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome. Science. 2009; 326(5952):585-9. doi: 10.1126/science.1179052 PMID: 19815723.
28. Cingöz O, Paprotka T, Delviks-Frankenberry KA, Wildt S, Hu W-S, Pathak VK, et al. Characterization, mapping, and distribution of the two XMRV parental proviruses. Journal of virology. 2012; 86(1):328-38. doi: 10.1128/JVI.06022-11 PMID: 22031947
29. Silverman RH, Nguyen C, Weight CJ, Klein EA. The human retrovirus XMRV in prostate cancer and chronic fatigue syndrome. Nature reviews Urology. 2010; 7(7):392-402. doi: 10.1038/nrurol.2010.77 PMID: 20517289
30. Arnold RS, Makarova NV, Osunkoya AO, Suppiah S, Scott TA, Johnson NA, et al. XMRV infection in patients with prostate cancer: novel serologic assay and correlation with PCR and FISH. Urology. 2010; 75(4):755-61. doi: 10.1016/j.urology.2010.01.038 PMID: 20371060
31. Fischer N, Hellwinkel O, Schulz C, Chun FKH, Huland H, Aepfelbacher M, et al. Prevalence of human gammaretrovirus XMRV in sporadic prostate cancer. Journal of Clinical Virology. 2008; 43(3):277-83. doi: 10.1016/j.jcv.2008.04.016 PMID: 18823818
32. Aloia AL, Sfanos KS, Isaacs WB, Zheng Q, Maldarelli F, De Marzo AM, et al. XMRV: a new virus in prostate cancer? Cancer research. 2010; 70(24):10028-33. doi: 10.1158/0008-5472.CAN-10-2837 PMID: 20966126; PubMed Central PMCID: PMC3005136.
33. Knox K, Carrigan D, Simmons G, Teque F, Zhou Y, Hackett J Jr, et al. No evidence of murine-like gammaretroviruses in CFS patients previously identified as XMRV-infected. Science. 2011; 333(6038):94-7. doi: 10.1126/science.1204963 PMID: 21628393.
34. Katzourakis A, Hué S, Kellam P, Towers GJ. Phylogenetic analysis of murine leukemia virus sequences from longitudinally sampled chronic fatigue syndrome patients suggests PCR contamination rather than viral evolution. Journal of virology. 2011; 85(20):10909-13. doi: 10.1128/JVI.00827-11 PMID: 21849443
35. Sfanos KS, Aloia AL, De Marzo AM, Rein A. XMRV and prostate cancer - a 'final' perspective. Nature reviews Urology. 2012; 9(2):111-8. doi: 10.1038/nrurol.2011.225 PMID: 22231291
36. Menendez-Arias L. Evidence and controversies on the role of XMRV in prostate cancer and chronic fatigue syndrome. Reviews in medical virology. 2011; 21(1):3-17. doi: 10.1002/rmv.673 PMID: 21294212.
37. Selth LA, Roberts MJ, Chow CW, Marshall VR, Doi SA, Vincent AD, et al. Human seminal fluid as a source of prostate cancer-specific microRNA biomarkers. Endocrine-related cancer. 2014; 21(4):L17-21. doi: 10.1530/ERC-14-0234 PMID: 24859988.
38. Kannan K, Wang L, Wang J, Ittmann MM, Li W, Yen L. Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing. Proceedings of the National Academy of Sciences of the United States of America. 2011; 108(22):9172-7. doi: 10.1073/pnas.1100489108 PMID: 21571633; PubMed Central PMCID: PMC3107329.
39. Ren S, Peng Z, Mao J-H, Yu Y, Yin C, Gao X, et al. RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings. Cell research. 2012; 22(5):806-21. doi: 10.1038/cr.2012.30 PMID: 22349460
40. Patel RK, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PloS one. 2012; 7(2):e30619-e. doi: 10.1371/journal.pone.0030619 PMID: 22312429
41. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biology. 2009; 10(3):R25-R. doi: 10.1186/gb-2009-10-3-r25 PMID: 19261174
42. Kent WJ. BLAT - the BLAST-like alignment tool. Genome research. 2002; 12(4):656-64. doi: 10.1101/gr.229202. Article published online before March 2002. PMID: 11932250
43. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature biotechnology. 2010; 28(5):511-5. doi: 10.1038/nbt.1621 PMID: 20436464; PubMed Central PMCID: PMC3146043.
44. Brooks MJ, Rajasimha HK, Roger JE, Swaroop A. Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes. Molecular vision. 2011; 17:3034-54. PMID: 22162623; PubMed Central PMCID: PMC3233386.
45. Holland C, Mak TN, Zimny-Arndt U, Schmid M, Meyer TF, Jungblut PR, et al. Proteomic identification of secreted proteins of Propionibacterium acnes. BMC microbiology. 2010; 10:230. doi: 10.1186/1471-2180-10-230 PMID: 20799957; PubMed Central PMCID: PMC3224659.
46. Davidson AL, Dassa E, Orelle C, Chen J. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiology and molecular biology reviews: MMBR. 2008; 72(2):317-64, table of contents. doi: 10.1128/MMBR.00031-07 PMID: 18535149; PubMed Central PMCID: PMC2415747.
47. Rui S, Tse-Dinh YC. Topoisomerase function during bacterial responses to environmental challenge. Frontiers in bioscience: a journal and virtual library. 2003; 8:d256-63. PMID: 12456368.
48. Fitz-Gibbon S, Tomida S, Chiu BH, Nguyen L, Du C, Liu M, et al. Propionibacterium acnes strain populations in the human skin microbiome associated with acne. The Journal of investigative dermatology. 2013; 133(9):2152-60. doi: 10.1038/jid.2013.21 PMID: 23337890; PubMed Central PMCID: PMC3745799.
49. Mak TN, Sfanos KS, Bruggemann H. Draft Genome Sequences of Two Strains of Propionibacterium acnes Isolated from Radical Prostatectomy Specimens. Genome announcements. 2013; 1(6). doi: 10.1128/genomeA.01071-13 PMID: 24356837; PubMed Central PMCID: PMC3868861.
50. McDowell A, Perry AL, Lambert PA, Patrick S. A new phylogenetic group of Propionibacterium acnes. Journal of medical microbiology. 2008; 57(Pt 2):218-24. doi: 10.1099/jmm.0.47489-0 PMID: 18201989.
51. McDowell A, Valanne S, Ramage G, Tunney MM, Glenn JV, McLorinan GC, et al. Propionibacterium acnes types I and II represent phylogenetically distinct groups. Journal of clinical microbiology. 2005; 43(1):326-34. doi: 10.1128/JCM.43.1.326-334.2005 PMID: 15634990; PubMed Central PMCID: PMC540145.
52. Bergh Drott J. The role of microorganisms in prostate cancer development. Umeå Universitet; 2012.
53. Thompson MP, Kurzrock R. Epstein-Barr virus and cancer. Clinical cancer research: an official journal of the American Association for Cancer Research. 2004; 10(3):803-21. PMID: 14871955.
54. Alexeyev OA, Marklund I, Shannon B, Golovleva I, Olsson J, Andersson C, et al. Direct visualization of Propionibacterium acnes in prostate tissue by multicolor fluorescent in situ hybridization assay. Journal of clinical microbiology. 2007; 45(11):3721-8. doi: 10.1128/JCM.01543-07 PMID: 17881550; PubMed Central PMCID: PMC2168516.
55. Webster GF, Leyden JJ. Characterization of serum-independent polymorphonuclear leukocyte chemotactic factors produced by Propionibacterium acnes. Inflammation. 1980; 4(3):261-9. PMID: 7429606.
56. Fischer N, Mak TN, Shinohara DB, Sfanos KS, Meyer TF, Bruggemann H. Deciphering the intracellular fate of Propionibacterium acnes in macrophages. BioMed research international. 2013; 2013:603046. doi: 10.1155/2013/603046 PMID: 23862148; PubMed Central PMCID: PMC3687600.
57. Kim J, Ochoa MT, Krutzik SR, Takeuchi O, Uematsu S, Legaspi AJ, et al. Activation of toll-like receptor 2 in acne triggers inflammatory cytokine responses. Journal of immunology. 2002; 169(3):1535-41. PMID: 12133981.
58. Graham GM, Farrar MD, Cruse-Sawyer JE, Holland KT, Ingham E. Proinflammatory cytokine production by human keratinocytes stimulated with Propionibacterium acnes and P. acnes GroEL. The British journal of dermatology. 2004; 150(3):421-8. doi: 10.1046/j.1365-2133.2004.05762.x PMID: 15030323.
59. Nagy I, Pivarcsi A, Koreck A, Szell M, Urban E, Kemeny L. Distinct strains of Propionibacterium acnes induce selective human beta-defensin-2 and interleukin-8 expression in human keratinocytes through toll-like receptors. The Journal of investigative dermatology. 2005; 124(5):931-8. doi: 10.1111/j.0022-202X.2005.23705.x PMID: 15854033.
60. Chandran UR, Dhir R, Ma C, Michalopoulos G, Becich M, Gilbertson J. Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors. BMC cancer. 2005; 5:45. doi: 10.1186/1471-2407-5-45 PMID: 15892885; PubMed Central PMCID: PMC1173092.
61. Khoury JD, Tannir NM, Williams MD, Chen Y, Yao H, Zhang J, et al. Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq. J Virol. 2013; 87(16): 8916-26. doi: 10.1128/JVI.00340-13 PMID: 23740984; PubMed Central PMCID: PMC3754044.
62. Tang KW, Alaei-Mahabadi B, Samuelsson T, Lindh M, Larsson E. The landscape of viral expression and host gene fusion and adaptation in human cancer. Nature communications. 2013; 4:2513. doi: 10.1038/ncomms3513 PMID: 24085110; PubMed Central PMCID: PMC3806554.
63. Zambrano A, Kalantari M, Simoneau A, Jensen JL, Villarreal LP. Detection of human polyomaviruses and papillomaviruses in prostatic tissue reveals the prostate as a habitat for multiple viral infections. The Prostate. 2002; 53(4):263-76. doi: 10.1002/pros.10157 PMID: 12430138
64. Simmons G, Glynn SA, Komaroff AL, Mikovits JA, Tobler LH, Hackett J Jr, et al. Failure to confirm XMRV/MLVs in the blood of patients with chronic fatigue syndrome: a multi-laboratory study. Science. 2011; 334(6057):814-7. doi: 10.1126/science.1213841 PMID: 21940862; PubMed Central PMCID: PMC3299483.
65. Mendoza R, Silverman RH, Klein EA, Miller AD. No biological evidence of XMRV in blood or prostatic fluid from prostate cancer patients. PloS ONE. 2012; 7(5):e36073. doi: 10.1371/journal.pone.0036073 PMID: 22615749
66. Groom HC, Warren AY, Neal DE, Bishop KN. No evidence for infection of UK prostate cancer patients with XMRV, BK virus, Trichomonas vaginalis or human papilloma viruses. PloS one. 2012; 7(3):e34221. doi: 10.1371/journal.pone.0034221 PMID: 22470540