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Article

The Intersection between Oral Microbiota, Host Gene Methylation and Patient Outcomes in Head and Neck Squamous Cell Carcinoma

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Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
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Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
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Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
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Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
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State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
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Institute of Digestive Disease, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
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CUHK Shenzhen Research Institute, Shenzhen, China
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Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong SAR, China
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Department of Otolaryngology, Head and Neck Surgery, Oregon Health and Science University, Portland, OR 97239, USA
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School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
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Department of Anatomical and Cellular Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
*
Authors to whom correspondence should be addressed.
Cancers 2020, 12(11), 3425; https://doi.org/10.3390/cancers12113425
Received: 14 October 2020 / Revised: 8 November 2020 / Accepted: 16 November 2020 / Published: 18 November 2020
Recently, there has been increased recognition of an association between the bacterial microbiome and cancer. In this study, we characterized the non-HPV head and neck squamous cell carcinoma (HNSCC) microbiome. We found a significant enrichment of Fusobacterium, depletion of Streptococcus, and the microbial signatures of twelve bacterial genera distinguishing HNSCC. With increased Fusobacterium—in particular, F. nucleatum—in our HNSCC cohort and its known association with prognosis in colorectal cancers (CRC), we sought to further characterize the association between clinical outcomes and F. nucleatum, and the host interaction with F. nucleatum. We identified a higher abundance of F. nucleatum in non-smokers and an improved survival, in contrast to CRC. An integrative analysis also identified that the enrichment of F. nucleatum was associated with host gene promoter methylation, suggesting that the bacterial mircobiome status may have a potential role as a prognostic biomarker and be involved in the pathogenesis of HNSCC.
The role of oral microbiota in head and neck squamous cell carcinoma (HNSCC) is poorly understood. Here we sought to evaluate the association of the bacterial microbiome with host gene methylation and patient outcomes, and to explore its potential as a biomarker for early detection or intervention. Here we performed 16S rRNA gene amplicon sequencing in sixty-eight HNSCC patients across both tissue and oral rinse samples to identify oral bacteria with differential abundance between HNSCC and controls. A subset of thirty-one pairs of HNSCC tumor tissues and the adjacent normal tissues were characterized for host gene methylation profile using bisulfite capture sequencing. We observed significant enrichments of Fusobacterium and Peptostreptococcus in HNSCC tumor tissues when compared to the adjacent normal tissues, and in HNSCC oral rinses when compared to healthy subjects, while ten other bacterial genera were largely depleted. These HNSCC-related bacteria were discriminative for HNSCC and controls with area under the receiver operating curves (AUCs) of 0.84 and 0.86 in tissue and oral rinse samples, respectively. Moreover, Fusobacterium nucleatum abundance in HNSCC cases was strongly associated with non-smokers, lower tumor stage, lower rate of recurrence, and improved disease-specific survival. An integrative analysis identified that enrichment of F. nucleatum was associated with host gene promoter methylation, including hypermethylation of tumor suppressor genes LXN and SMARCA2, for which gene expressions were downregulated in the HNSCC cohort from The Cancer Genome Atlas. In conclusion, we identified a taxonomically defined microbial consortium associated with HNSCC that may have clinical potential regarding biomarkers for early detection or intervention. Host–microbe interactions between F. nucleatum enrichment and clinical outcomes or host gene methylation imply a potential role of F. nucleatum as a pro-inflammatory driver in initiating HNSCC without traditional risk factors, which warrants further investigation for the underlying mechanisms. View Full-Text
Keywords: HNSCC; microbiome; Fusobacterium; methylation; host-microbiome interaction HNSCC; microbiome; Fusobacterium; methylation; host-microbiome interaction
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MDPI and ACS Style

Chen, Z.; Wong, P.Y.; Ng, C.W.K.; Lan, L.; Fung, S.; Li, J.W.; Cai, L.; Lei, P.; Mou, Q.; Wong, S.H.; Wu, W.K.K.; Li, R.J.; Meehan, K.; Lui, V.W.Y.; Chow, C.; Lo, K.W.; Chan, A.B.W.; Boon, S.S.; Lau, E.H.L.; Yeung, Z.; Chan, K.C.A.; Wong, E.W.Y.; Cheng, A.S.L.; Yu, J.; Chan, P.K.S.; Chan, J.Y.K. The Intersection between Oral Microbiota, Host Gene Methylation and Patient Outcomes in Head and Neck Squamous Cell Carcinoma. Cancers 2020, 12, 3425. https://doi.org/10.3390/cancers12113425

AMA Style

Chen Z, Wong PY, Ng CWK, Lan L, Fung S, Li JW, Cai L, Lei P, Mou Q, Wong SH, Wu WKK, Li RJ, Meehan K, Lui VWY, Chow C, Lo KW, Chan ABW, Boon SS, Lau EHL, Yeung Z, Chan KCA, Wong EWY, Cheng ASL, Yu J, Chan PKS, Chan JYK. The Intersection between Oral Microbiota, Host Gene Methylation and Patient Outcomes in Head and Neck Squamous Cell Carcinoma. Cancers. 2020; 12(11):3425. https://doi.org/10.3390/cancers12113425

Chicago/Turabian Style

Chen, Zigui, Po Y. Wong, Cherrie W.K. Ng, Linlin Lan, Sherwood Fung, Jing W. Li, Liuyang Cai, Pu Lei, Qianqian Mou, Sunny H. Wong, William K.K. Wu, Ryan J. Li, Katie Meehan, Vivian W.Y. Lui, Chit Chow, Kwok W. Lo, Amy B.W. Chan, Siaw S. Boon, Eric H.L. Lau, Zenon Yeung, Kwan C.A. Chan, Eddy W.Y. Wong, Alfred S.L. Cheng, Jun Yu, Paul K.S. Chan, and Jason Y.K. Chan 2020. "The Intersection between Oral Microbiota, Host Gene Methylation and Patient Outcomes in Head and Neck Squamous Cell Carcinoma" Cancers 12, no. 11: 3425. https://doi.org/10.3390/cancers12113425

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