Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas

Genome Medicine

Volumn 9, Issue 1, 2017, Pages

  Wang, Hannah ^a,b   Funchain, Pauline ^a,c   Bebek, Gurkan ^e,f   Altemus, Jessica ^a   Zhang, Huan ^a,b   Niazi, Farshad ^a   Peterson, Charissa ^a   Lee, Walter T ^d   Burkey, Brian B ^a   Eng, Charis ^a,b,c,e,f  

^a LERNER RESEARCH INSTITUTE   (United States)

^b CLEVELAND CLINIC LERNER COLLEGE OF MEDICINE   (United States)

^c TAUSSIG CANCER INSTITUTE   (United States)

^d DUKE UNIVERSITY MEDICAL CENTER   (United States)

^e CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f Center for Proteomics and Bioinformatics ^*  (United States)

Author keywords

Bacteria; Head and neck squamous cell carcinoma (HNSCC); Microbiome

Indexed keywords

DNA 16S;

ACTINOMYCES; ADULT; ARTICLE; BACTERIAL MICROBIOME; CANCER TISSUE; CLINICAL FEATURE; CONTROLLED STUDY; DNA EXTRACTION; DNA SEQUENCE; FEMALE; HEAD AND NECK SQUAMOUS CELL CARCINOMA; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; MALE; MOUTH FLORA; PARVIMONAS; TUMOR MICROENVIRONMENT; AGED; BACTERIUM; HEAD AND NECK TUMOR; INTESTINE FLORA; ISOLATION AND PURIFICATION; MICROBIOLOGY; MIDDLE AGED; MOUTH; SQUAMOUS CELL CARCINOMA;

AGED; BACTERIA; CARCINOMA, SQUAMOUS CELL; FEMALE; GASTROINTESTINAL MICROBIOME; HEAD AND NECK NEOPLASMS; HUMANS; MALE; MIDDLE AGED; MOUTH;

EID: 85011860340     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-017-0405-5     Document Type: Article

References (55)

1. Parsonnet J, Friedman GD, Vandersteen DP, Chang Y, Vogelman JH, Orentreich N, et al. Helicobacter pylori infection and the risk of gastric carcinoma. N Engl J Med. 1991;325:1127-31.
2. Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res. 2012;22:299-306.
3. Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 2012;22:292-8.
4. Rubinstein MR, Wang X, Liu W, Hao Y, Cai G, Han YW. Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-Cadherin/??-Catenin signaling via its FadA adhesin. Cell Host Microbe. 2013;14:195-206.
5. Kostic AD, Chun E, Robertson L, Glickman JN, Gallini CA, Michaud M, et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe. 2013;14:207-15.
6. Consortium THMP. Structure, function and diversity of the healthy human microbiome. Nature. 2013;486:207-14.
7. Fujimura KE, Slusher NA, Cabana MD, Lynch SV. Role of the gut microbiota in defining human health. Expert Rev Anti Infect Ther. 2010;8:435-54.
8. Ma B, Forney LJ, Ravel J. Vaginal microbiome: rethinking health and disease. Annu Rev Microbiol. 2012;66:371-89.
9. Peterson SN, Snesrud E, Liu J, Ong AC, Kilian M, Schork NJ, Bretz W. The dental plaque microbiome in health and disease. PLoS One. 2013;8:e58487.
10. Struzycka I. The oral microbiome in dental caries. Pol J Microbiol. 2014;63:127-35.
11. Chaturvedi AK, Anderson WF, Lortet-Tieulent J, Paula Curado M, Ferlay J, Franceschi S, et al. Worldwide trends in incidence rates for oral cavity and oropharyngeal cancers. J Clin Oncol. 2013;31:4550-9.
12. Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D. Global cancer statistics. CA Cancer J Clin. 2011;61:69-90.
13. Sturgis EM, Wei Q, Spitz MR. Descriptive epidemiology and risk factors for head and neck cancer. Semin Oncol. 2004;31:726-33.
14. Sturgis EM, Ang KK. The epidemic of HPV-associated oropharyngeal cancer is here: is it time to change our treatment paradigms? J Natl Compr Canc Netw. 2011;9:665-73.
15. Wu J, Peters BA, Dominianni C, Zhang Y, Pei Z, Yang L, et al. Cigarette smoking and the oral microbiome in a large study of American adults. ISME J. 2016;10:2435-46.
16. Leclercq S, Matamoros S, Cani PD, Neyrinck AM, Jamar F, Stärkel P, et al. Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity. Proc Natl Acad Sci U S A. 2014;111:E4485-93.
17. Bebek G, Bennett KL, Funchain P, Campbell R, Seth R, Scharpf J, et al. Microbiomic subprofiles and MDR1 promoter methylation in head and neck squamous cell carcinoma. Hum Mol Genet. 2012;21:1557-65.
18. Schmidt BL, Kuczynski J, Bhattacharya A, Huey B, Corby PM, Queiroz ELS, et al. Changes in abundance of oral microbiota associated with oral cancer. PLoS One. 2014;9:e98741.
19. Gong H, Shi Y, Zhou X, Wu C, Cao P, Xu C, et al. Microbiota in the throat and risk factors for laryngeal carcinoma. Appl Environ Microbiol. 2014;80:7356-63.
20. Hooper SJ, Crean SJ, Fardy MJ, Lewis MA, Spratt DA, Wade WG, et al. A molecular analysis of the bacteria present within oral squamous cell carcinoma. J Med Microbiol. 2007;56:1651-9.
21. Hooper SJ, Crean SJ, Lewis MAO, Spratt DA, Wade WG, Wilson MJ. Viable bacteria present within oral squamous cell carcinoma tissue. J Clin Microbiol. 2006;44:1719-25.
22. Gong H-L, Shi Y, Zhou L, Wu C-P, Cao P-Y, Tao L, et al. The composition of microbiome in larynx and the throat biodiversity between laryngeal squamous cell carcinoma patients and control population. PLoS One. 2013;8:e66476.
23. Edge SB, Compton CC. The American Joint Committee on Cancer: the 7th edition of the AJCC cancer staging manual and the future of TNM. Ann Surg Oncol. 2010;17:1471-4.
24. Dauphin LA, Stephens KW, Eufinger SC, Bowen MD. Comparison of five commercial DNA extraction kits for the recovery of Yersinia pestis DNA from bacterial suspensions and spiked environmental samples. J Appl Microbiol. 2010;108:163-72.
25. Tamariz J, Voynarovska K, Prinz M, Caragine T. The application of ultraviolet irradiation to exogenous sources of DNA in plasticware and water for the amplification of low copy number DNA. J Forensic Sci. 2006;51:790-4.
26. Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, et al. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ. 2014;2:e545.
27. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72:5069-72.
28. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610-8.
29. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460-1.
30. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics. 2010;26:266-7.
31. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490.
32. Hill TCJ, Walsh KA, Harris JA, Moffett BF. Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol. 2003;43:1-11.
33. Barker GM. Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation. Biol J Linn Soc. 2008;76:165-94.
34. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005;71:8228-35.
35. Lozupone CA, Hamady M, Kelley ST, Knight R. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol. 2007;73:1576-85.
36. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335-6.
37. Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26:32-46.
38. Sarkar D. SpringerLink (Online service). Lattice multivariate data visualization with R. Use R! J Stat Software. 2008;25(ii):1-265. http://dsarkar.fhcrc.org/lattice/.
39. Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ. 2015;3:e1029.
40. Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010;Chapter 19:Unit 19.10.1-21
41. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner ACR, Yu WH, et al. The human oral microbiome. J Bacteriol. 2010;192:5002-17.
42. Ahn J, Yang L, Paster BJ, Ganly I, Morris L, Pei Z, et al. Oral microbiome profiles: 16 s rRNA pyrosequencing and microarray assay comparison. PLoS One. 2011;6:e22788.
43. Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, et al. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol. 2012;13:R42.
44. Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, et al. Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J. 2010;4:962-74.
45. Pushalkar S, Ji X, Li Y, Estilo C, Yegnanarayana R, Singh B, et al. Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma. BMC Microbiol. 2012;12:144.
46. Takeshita T, Kageyama S, Furuta M, Tsuboi H, Takeuchi K, Shibata Y, et al. Bacterial diversity in saliva and oral health-related conditions: the Hisayama Study. Sci Rep. 2016;6:22164.
47. Slaughter DP, Southwick HW, Smejkal W. Field cancerization in oral stratified squamous epithelium; clinical implications of multicentric origin. Cancer. 1953;6:963-8.
48. Wong VK, Turmezei TD. Actinomycosis. Britiish Med J. 2011;343:1-7.
49. Hozumi M, Ogawa M, Sugimura T, Takeuchi T, Umezawa H. Inhibition of tumorigenesis in mouse skin by leupeptin, a protease inhibitor from actinomycetes. Cancer Res. 1972;32:1725-28.
50. Schulze A, Harris AL. How cancer metabolism is tuned for proliferation and vulnerable to disruption. Nature. 2012;491:364-73.
51. Hamady M, Knight R. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res. 2009;19:1141-52.
52. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol. 2008;6:776-88.
53. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science. 2008;320:1647-51.
54. McKenna P, Hoffmann C, Minkah N, Aye PP, Lackner A, Liu Z, et al. The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog. 2008;4:e20.
55. Smith BC, McAndrew T, Chen Z, Harari A, Barris DM, Viswanathan S, et al. The cervical microbiome over 7 years and a comparison of methodologies for its characterization. PLoS One. 2012;7:e40425.