An international report on bacterial communities in esophageal squamous cell carcinoma
Year: 2021
Type: article
Study design: Observational Study
Abstract: NOTE: Full authorship list and affiliations are listed at the end of this description. This repository contains the R analysis code and GATK-PathSeq output data necessary to reproduce the analysis and findings of the manuscript "An international report on bacterial communities in esophageal squamous cell carcinoma". ABSTRACT: The incidence of esophageal squamous cell carcinoma (ESCC) is disproportionately high in the eastern corridor of Africa and parts of Asia. Emerging research has identified a potential association between poor oral health and ESCC. One proposed biological pathway linking poor oral health and ESCC involves the alteration of the microbiome. Thus, we performed an integrated analysis of four independent sequencing efforts of ESCC tumors from patients from high- and low- incidence regions of the world. Using whole genome sequencing (WGS) and RNA sequencing (RNAseq) of ESCC tumors and WGS of synchronous collections of saliva specimens from 61 patients in Tanzania, we identified a community of bacteria, including members of the genera Fusobacterium, Selenomonas, Prevotella, Streptococcus, Porphyromonas, Veillonella, and Campylobacter, present at high abundance in ESCC tumors. We then characterized the microbiome of 238 ESCC tumor specimens collected in two additional independent sequencing efforts consisting of patients from other high-ESCC incidence regions (Tanzania, Malawi, Kenya, Iran, China). This analysis revealed a similar tumor enrichment of the ESCC-associated bacterial community in these cancers. Because these genera are traditionally considered members of the oral microbiota, we explored if there is a relationship between the synchronous saliva and tumor microbiomes of ESCC patients in Tanzania. Comparative analyses revealed that paired saliva and tumor microbiomes are significantly similar with a specific enrichment of Fusobacterium and Prevotella in the tumor microbiome. Together, these data indicate that cancer-associated oral bacteria are associated with ESCC tumors at the time of diagnosis and support a model in which oral bacteria are present in high abundance in both saliva and tumors of ESCC patients. Longitudinal studies of the pre-diagnostic oral microbiome are needed to investigate whether these cross-sectional similarities reflect temporal associations. FULL AUTHOR LIST: Jason Nomburg1,2,3, Susan Bullman4, Dariush Nasrollahzadeh5,6, Eric A. Collisson7,8, Behnoush Abedi-Ardekani6, Larry O. Akoko9, Joshua R. Atkins6, Geoffrey C. Buckle7,8, Satish Gopal10, Nan Hu11, Bongani Kaimila12, Masoud Khoshnia5, Reza Malekzadeh5, Diana Menya13, Blandina T. Mmbaga14,15, Sarah Moody16, Gift Mulima17, Beatrice P. Mushi9, Julius Mwaiselage18, Ally Mwanga9, Yulia Newton19, Dianna L. Ng7,20, Amie Radenbaugh19, Deogratias S. Rwakatema14,15, Msiba Selekwa9, Joachim Schüz21, Philip R. Taylor11, Charles Vaske19, Alisa Goldstein11, Michael R. Stratton16, Valerie McCormack21, Paul Brennan6, James A. DeCaprio1,3,22, Matthew Meyerson1,2,22,23*, Elia J. Mmbaga9*, Katherine Van Loon7,8* 1 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 2 Broad Institute of MIT and Harvard, Cambridge, MA 3 Harvard Program in Virology, Harvard Medical School, Boston, MA 4 Fred Hutchinson Cancer Research Center, Seattle, Washington, USA 5 Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Shariati Hospital. Tehran Iran. 6 International Agency for Research on Cancer (IARC/WHO), Genomic Epidemiology Branch, Lyon, France 7 University of California, San Francisco (UCSF) Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA 8 Division of Hematology/Oncology, Department of Medicine, UCSF, San Francisco, California, USA 9 Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania 10 University of North Carolina, Chapel Hill, North Carolina, USA 11 Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA 12 UNC Project - Lilongwe, Malawi 13 School of Public Health, Moi University, Eldoret, Kenya 14 Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania 15 Kilimanjaro Christian Medical University College, Moshi, Tanzania 16 Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK 17 Kamuzu Central Hospital, Lilongwe, Malawi 18 Ocean Road Cancer Institute, Dar es Salaam, Tanzania 19 NantOmics/NantHealth, Inc., El Segundo, California, USA 20 Department of Pathology, UCSF, San Francisco, CA, USA 21 International Agency for Research on Cancer (IARC/WHO), Environment and Lifestyle Epidemiology Branch, Lyon, France 22 Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 23 Department of Genetics, Harvard Medical School, Boston, MA
Authors: Nomburg, Jason, Meyerson, Matthew, Mmbaga, Elia J., Van Loon, Katherine
Language: English
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W6893682157