351
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Jin Y, Liu Y, Zhao L, Zhao F, Feng J, Li S, Chen H, Sun J, Zhu B, Geng R, Wei Y. Gut microbiota in patients after surgical treatment for colorectal cancer. Environ Microbiol 2018; 21:772-783. [PMID: 30548192 PMCID: PMC7379540 DOI: 10.1111/1462-2920.14498] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 11/30/2018] [Indexed: 01/05/2023]
Abstract
Colorectal cancer (CRC) is a common disease worldwide that is strongly associated with the gut microbiota. However, little is known regarding the gut microbiota after surgical treatment. 16S rRNA gene sequencing was used to evaluate differences in gut microbiota among colorectal adenoma patients, CRC patients, CRC postoperative patients and healthy controls by comparing gut microbiota diversity, overall composition and taxonomic signature abundance. The gut microbiota of CRC patients, adenoma patients and healthy controls developed in accordance with the adenoma‐carcinoma sequence, with impressive shifts in the gut microbiota before or during the development of CRC. The gut microbiota of postoperative patients and CRC patients differed significantly. Subdividing CRC postoperative patients according to the presence or absence of newly developed adenoma which based on the colonoscopy findings revealed that the gut microbiota of newly developed adenoma patients differed significantly from that of clean intestine patients and was more similar to the gut microbiota of carcinoma patients than to the gut microbiota of healthy controls. The alterations of the gut microbiota between the two groups of postoperative patients corresponded to CRC prognosis. More importantly, we used the different gut microbiota as biomarkers to distinguish postoperative patients with or without newly developed adenoma, achieving an AUC value of 0.72. These insights on the changes in the gut microbiota of CRC patients after surgical treatment may allow the use of the microbiota as non‐invasive biomarkers for the diagnosis of newly developed adenomas and to help prevent cancer recurrence in postoperative patients.
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Affiliation(s)
- Ye Jin
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Yang Liu
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Lei Zhao
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Fuya Zhao
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Jing Feng
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Shengda Li
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Huinan Chen
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Jiayu Sun
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Biqiang Zhu
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Rui Geng
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
| | - Yunwei Wei
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China 150001
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352
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Shao L, Ling Z, Chen D, Liu Y, Yang F, Li L. Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study. Front Microbiol 2018; 9:3166. [PMID: 30631318 PMCID: PMC6315199 DOI: 10.3389/fmicb.2018.03166] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/07/2018] [Indexed: 12/14/2022] Open
Abstract
Early detection and effective interventions for liver cirrhosis (LC) remain an urgent unmet clinical need. Inspired from intestinal disorders in LC patients, we investigated the associations between gut microbiome and disease progression based on a raw metagenomic dataset of 47 healthy controls, 49 compensated, and 46 decompensated LC patients from our previous study, and a metabolomic dataset of urine samples from the same controls/patients using ultra-performance liquid chromatography/mass spectrophotometry system. It was found that the combination and relative abundance of gut microbiome, the inter-microbiome regulatory networks, and the microbiome-host correlation patterns varied during disease progression. The significant reduction of bacteria involved in fermentation of plant cell wall polysaccharides and resistant starch (such as Alistipes sp. HG5, Clostridium thermocellum) contributed to the reduced supply of energy sources, the disorganized self-feeding and cross-feeding networks and the thriving of some opportunistic pathogens in genus Veillonella. The marked decrease of butyrate-producing bacteria and increase of Ruminococcus gnavus implicated in degradation of elements from the mucus layer provided an explanation for the impaired intestinal barrier function and systematic inflammation in LC patients. Our results pave the way for further developments in early detection and intervention of LC targeting on gut microbiome.
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Affiliation(s)
- Li Shao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zongxin Ling
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Deying Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yufeng Liu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Fengling Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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353
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Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer. PLoS One 2018; 13:e0207002. [PMID: 30412600 PMCID: PMC6226189 DOI: 10.1371/journal.pone.0207002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/23/2018] [Indexed: 12/15/2022] Open
Abstract
Microbes colonizing colorectal cancer (CRC) tumors have the potential to affect disease, and vice-versa. The manner in which they differ from microbes in physically adjacent tissue or stool within the case in terms of both, taxonomy and biological activity remains unclear. In this study, we systematically analyzed previously published 16S rRNA sequence data from CRC patients with matched tumor:tumor-adjacent biopsies (n = 294 pairs, n = 588 biospecimens) and matched tumor biopsy:fecal pairs (n = 42 pairs, n = 84 biospecimens). Procrustes analyses, random effects regression, random forest (RF) modeling, and inferred functional pathway analyses were conducted to assess community similarity and microbial diversity across heterogeneous patient groups and studies. Our results corroborate previously reported association of increased Fusobacterium with tumor biopsies. Parvimonas and Streptococcus abundances were also elevated while Faecalibacterium and Ruminococcaceae abundances decreased in tumors relative to tumor-adjacent biopsies and stool samples from the same case. With the exception of these limited taxa, the majority of findings from individual studies were not confirmed by other 16S rRNA gene-based datasets. RF models comparing tumor and tumor-adjacent specimens yielded an area under curve (AUC) of 64.3%, and models of tumor biopsies versus fecal specimens exhibited an AUC of 82.5%. Although some taxa were shared between fecal and tumor samples, their relative abundances varied substantially. Inferred functional analysis identified potential differences in branched amino acid and lipid metabolism. Microbial markers that reliably occur in tumor tissue can have implications for microbiome based and microbiome targeting therapeutics for CRC.
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354
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Nowak A, Paliwoda A, Błasiak J. Anti-proliferative, pro-apoptotic and anti-oxidative activity of Lactobacillus and Bifidobacterium strains: A review of mechanisms and therapeutic perspectives. Crit Rev Food Sci Nutr 2018; 59:3456-3467. [PMID: 30010390 DOI: 10.1080/10408398.2018.1494539] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Lactobacillus and Bifidobacterium strains, their isolated constituents and substances that they secrete exert various anti-cancer actions, resulting from their anti-proliferative, pro-apoptotic and anti-oxidant properties. They can express and secrete anti-oxidant enzymes, bind reactive oxygen species, release small molecular weight anti-oxidants and chelate transition metals, preventing detrimental actions of many carcinogens. Lactobacillus and Bifidobacterium can interact with proteins regulating the cell cycle inhibiting proliferation of cancer cells, which often are intrinsically resistant to apoptosis. Lactobacilli and bifidobacteria can break this resistance through activation of pro-caspases and downregulation of the anti-apoptotic Bcl-2 and upregulation of pro-apoptotic Bax proteins. Anti-cancer effects of these bacteria can be also associated with their multi-pathways action in the microbiota. However, exact mechanism of their anti-cancer action is poorly known and needs further studies, which are justified by the important role of these bacteria in cancer biology as well as their potential preventive and therapeutic use.
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Affiliation(s)
- Adriana Nowak
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, Lodz, Poland
| | - Anna Paliwoda
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, Lodz, Poland
| | - Janusz Błasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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355
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Al Bakir I, Curtius K, Graham TA. From Colitis to Cancer: An Evolutionary Trajectory That Merges Maths and Biology. Front Immunol 2018; 9:2368. [PMID: 30386335 PMCID: PMC6198656 DOI: 10.3389/fimmu.2018.02368] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/24/2018] [Indexed: 12/25/2022] Open
Abstract
Patients with inflammatory bowel disease have an increased risk of developing colorectal cancer, and this risk is related to disease duration, extent, and cumulative inflammation burden. Carcinogenesis follows the principles of Darwinian evolution, whereby somatic cells acquire genomic alterations that provide them with a survival and/or growth advantage. Colitis represents a unique situation whereby routine surveillance endoscopy provides a serendipitous opportunity to observe somatic evolution over space and time in vivo in a human organ. Moreover, somatic evolution in colitis is evolution in the ‘fast lane': the repeated rounds of inflammation and mucosal healing that are characteristic of the disease accelerate the evolutionary process and likely provide a strong selective pressure for inflammation-adapted phenotypic traits. In this review, we discuss the evolutionary dynamics of pre-neoplastic clones in colitis with a focus on how measuring their evolutionary trajectories could deliver a powerful way to predict future cancer occurrence. Measurements of somatic evolution require an interdisciplinary approach that combines quantitative measurement of the genotype, phenotype and the microenvironment of somatic cells–paying particular attention to spatial heterogeneity across the colon–together with mathematical modeling to interpret these data within an evolutionary framework. Here we take a practical approach in discussing how and why the different “evolutionary ingredients” can and should be measured, together with our viewpoint on subsequent translation into clinical practice. We highlight the open questions in the evolution of colitis-associated cancer as a stimulus for future work.
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Affiliation(s)
- Ibrahim Al Bakir
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, London, United Kingdom.,Inflammatory Bowel Disease Unit, St Mark's Hospital, Harrow, United Kingdom
| | - Kit Curtius
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, London, United Kingdom
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, London, United Kingdom
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356
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Abstract
Purpose of Review The trillions of microbes collectively referred to as the human microbiota, inhabit the human body and establish a beneficial relationship with the host. It is clear however that dysbiosis impacting microbial diversity in the gut, may lead to development of inflammatory and malignant gastrointestinal diseases including colorectal cancer (CRC). We provide a literature review of the recent influx of information related to the alterations in gut microbiota composition that influences CRC incidence and progression. Recent Findings A growing body of evidence implicates altered gut microbiota in the development of CRC. Profiles of CRC associated microbiota have been shown to differ from those in healthy subjects and bacterial phylotypes vary depending on the primary tumor location. The compositional variation in the microbial profile is not restricted to cancerous tissue however and is different between cancers of the proximal and distal colons, respectively. More recently, studies have shed light on the "driver-passenger" model for CRC wherein, driver bacteria cause inflammation, increased cell proliferation and production of genotoxic substances to contribute towards mutational acquisition associated with adenoma-carcinoma sequence. These changes facilitate gradual replacement of driver bacteria by passengers that either promote or suppress tumor progression. Significant advances have also been made in associating individual bacterial species to consensus molecular subtypes (CMS) of CRC and this remarkable development is expected to galvanize scientific community into advancing therapeutic strategies for CRC. Summary Increasing evidence suggests a link between the intestinal microbiota and CRC development although the mechanisms through which the bacterial constituents of the microbiome contribute towards CRC are complex and yet to be fully fathomed. Thus, more exhaustive and mechanistic studies are needed to identify key interactions amongst diet, microbial community and metabolites that help facilitate the adenoma-carcinoma sequence evolution in CRC. It is expected that development of therapeutics based on microbial association with CMS will likely facilitate the translation of molecular subtypes into the clinic for CRCs and potentially other malignancies.
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357
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Kamath SD, Kalyan A, Benson AB. Pembrolizumab for the treatment of gastric cancer. Expert Rev Anticancer Ther 2018; 18:1177-1187. [PMID: 30280940 DOI: 10.1080/14737140.2018.1526084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Gastric cancer is one of a few gastrointestinal malignancies in which immunotherapy has shown meaningful activity. Pembrolizumab is the first and only immune checkpoint inhibitor to be FDA-approved in gastric cancer. Areas Covered: This review summarizes the current and emerging clinical evidence for immune checkpoint inhibitors in advanced and metastatic gastric cancer, with a focus on pembrolizumab. Expert Commentary: Pembrolizumab has shown impressive activity in the third-line treatment of locally advanced and metastatic gastric cancer. It is currently being studied as upfront therapy in combination with chemotherapy. The emerging understanding of the molecular alterations and tumor immune microenvironment as predictors of immunotherapy response in gastric cancer are discussed. The impact of gastric mucosal dysbiosis on gastric carcinogenesis and the modulation of immunotherapy response by the gut microbiome are also reviewed.
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Affiliation(s)
- Suneel D Kamath
- a Division of Hematology/Oncology , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
| | - Aparna Kalyan
- a Division of Hematology/Oncology , Northwestern University Feinberg School of Medicine , Chicago , IL , USA.,b Northwestern Medicine Developmental Therapeutics Institute , Robert H. Lurie Comprehensive Cancer of Northwestern University , Chicago , IL , USA
| | - Al B Benson
- a Division of Hematology/Oncology , Northwestern University Feinberg School of Medicine , Chicago , IL , USA.,c Northwestern Medicine, Feinberg School of Medicine , Robert H. Lurie Comprehensive Cancer Center of Northwestern University , Chicago , IL , USA
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358
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Liu L, Tabung FK, Zhang X, Nowak JA, Qian ZR, Hamada T, Nevo D, Bullman S, Mima K, Kosumi K, da Silva A, Song M, Cao Y, Twombly TS, Shi Y, Liu H, Gu M, Koh H, Li W, Du C, Chen Y, Li C, Li W, Mehta RS, Wu K, Wang M, Kostic AD, Giannakis M, Garrett WS, Hutthenhower C, Chan AT, Fuchs CS, Nishihara R, Ogino S, Giovannucci EL. Diets That Promote Colon Inflammation Associate With Risk of Colorectal Carcinomas That Contain Fusobacterium nucleatum. Clin Gastroenterol Hepatol 2018; 16:1622-1631.e3. [PMID: 29702299 PMCID: PMC6151288 DOI: 10.1016/j.cgh.2018.04.030] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/28/2018] [Accepted: 04/15/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Specific nutritional components are likely to induce intestinal inflammation, which is characterized by increased levels of interleukin 6 (IL6), C-reactive protein (CRP), and tumor necrosis factor-receptor superfamily member 1B (TNFRSF1B) in the circulation and promotes colorectal carcinogenesis. The inflammatory effects of a diet can be estimated based on an empiric dietary inflammatory pattern (EDIP) score, calculated based on intake of 18 foods associated with plasma levels of IL6, CRP, and TNFRSF1B. An inflammatory environment in the colon (based on increased levels of IL6, CRP, and TNFRSF1B in peripheral blood) contributes to impairment of the mucosal barrier and altered immune cell responses, affecting the composition of the intestinal microbiota. Colonization by Fusobacterium nucleatum has been associated with the presence and features of colorectal adenocarcinoma. We investigated the association between diets that promote inflammation (based on EDIP score) and colorectal cancer subtypes classified by level of F nucleatum in the tumor microenvironment. METHODS We calculated EDIP scores based on answers to food frequency questionnaires collected from participants in the Nurses' Health Study (through June 1, 2012) and the Health Professionals Follow-up Study (through January 31, 2012). Participants in both cohorts reported diagnoses of rectal or colon cancer in biennial questionnaires; deaths from unreported colorectal cancer cases were identified through the National Death Index and next of kin. Colorectal tumor tissues were collected from hospitals where the patients underwent tumor resection and F nucleatum DNA was quantified by a polymerase chain reaction assay. We used multivariable duplication-method Cox proportional hazard regression to assess the associations of EDIP scores with risks of colorectal cancer subclassified by F nucleatum status. RESULTS During 28 years of follow-up evaluation of 124,433 participants, we documented 951 incident cases of colorectal carcinoma with tissue F nucleatum data. Higher EDIP scores were associated with increased risk of F nucleatum-positive colorectal tumors (Ptrend = .03); for subjects in the highest vs lowest EDIP score tertiles, the hazard ratio for F nucleatum-positive colorectal tumors was 1.63 (95% CI, 1.03-2.58). EDIP scores did not associate with F nucleatum-negative tumors (Ptrend = .44). High EDIP scores associated with proximal F nucleatum-positive colorectal tumors but not with proximal F nucleatum-negative colorectal tumors (Pheterogeneity = .003). CONCLUSIONS Diets that may promote intestinal inflammation, based on EDIP score, are associated with increased risk of F nucleatum-positive colorectal carcinomas, but not carcinomas that do not contain these bacteria. These findings indicate that diet-induced intestinal inflammation alters the gut microbiome to contribute to colorectal carcinogenesis; nutritional interventions might be used in precision medicine and cancer prevention.
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Affiliation(s)
- Li Liu
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Fred K. Tabung
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xuehong Zhang
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan A. Nowak
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhi Rong Qian
- The 7th Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, P.R. China
| | - Tsuyoshi Hamada
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Daniel Nevo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Kosuke Mima
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Keisuke Kosumi
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Annacarolina da Silva
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Mingyang Song
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yin Cao
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Tyler S. Twombly
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Yan Shi
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA,Medical Oncology Department 2, Chinese PLA General Hospital, Beijing, P.R. China
| | - Hongli Liu
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA,Cancer Center, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Mancang Gu
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA,College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, P.R. China
| | - Hideo Koh
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Wanwan Li
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Chunxia Du
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Yang Chen
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Chenxi Li
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA,Oncology Department, The First Affiliated Hospital of Chinese PLA General Hospital, Beijing, P.R. China
| | - Wenbin Li
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Raaj S. Mehta
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kana Wu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Molin Wang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Aleksander D. Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA,Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA,Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Wendy S. Garrett
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Curtis Hutthenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Andrew T. Chan
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Charles S. Fuchs
- Yale Cancer Center, New Haven, CT, USA,Department of Medicine, Yale School of Medicine, New Haven, CT, USA,Smilow Cancer Hospital, New Haven, CT, USA
| | - Reiko Nishihara
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA,Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA,Correspondence to: Shuji Ogino, MD, PhD, MS, Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, 450 Brookline Ave., Room SM1036, Boston, MA 02215 USA, Tel: +1-617-632-1972; Fax: +1-617-582-8558, , Edward L Giovannucci, MD, ScD, Department of Nutrition, Harvard T.H. Chan School of Public Health, 665 Huntington Ave., Bldg. 2, Room 371, Boston, MA 02115 USA, Tel: +1-617-432-4648; Fax: +1-617-432-2435,
| | - Shuji Ogino
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Broad Institute of Massachusetts Institute of Technology, Harvard, Cambridge, Massachusetts; Program in MPE Molecular Pathological Epidemiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Edward L. Giovannucci
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA,Correspondence to: Shuji Ogino, MD, PhD, MS, Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, 450 Brookline Ave., Room SM1036, Boston, MA 02215 USA, Tel: +1-617-632-1972; Fax: +1-617-582-8558, , Edward L Giovannucci, MD, ScD, Department of Nutrition, Harvard T.H. Chan School of Public Health, 665 Huntington Ave., Bldg. 2, Room 371, Boston, MA 02115 USA, Tel: +1-617-432-4648; Fax: +1-617-432-2435,
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Farhana L, Antaki F, Murshed F, Mahmud H, Judd SL, Nangia-Makker P, Levi E, Yu Y, Majumdar APN. Gut microbiome profiling and colorectal cancer in African Americans and Caucasian Americans. World J Gastrointest Pathophysiol 2018; 9:47-58. [PMID: 30283710 PMCID: PMC6163128 DOI: 10.4291/wjgp.v9.i2.47] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/08/2018] [Accepted: 08/26/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To determine whether and to what extent the gut microbiome is involved in regulating racial disparity in colorectal cancer (CRC).
METHODS All patients were recruited and experiments were performed in accordance with the relevant guidelines and regulations by the Institutional Review Boards (IRB), committees of the John D. Dingell VAMC and Wayne State University guidelines. African American (AA) and Caucasian American (CA) patients were scheduled for an outpatient screening for colonoscopy, and no active malignancy volunteer patients were doubly consented, initially by the gastroenterologist and later by the study coordinator, for participation in the study. The gut microbial communities in colonic effluents from AAs and CAs were examined using 16sRNA profiling, and bacterial identifications were validated by performing SYBR-based Real Time PCR. For metagenomic analysis to characterize the microbial communities, multiple software/tools were used, including Metastats and R statistical software.
RESULTS It is generally accepted that the incidence and mortality of CRC is higher in AAs than in CAs. However, the reason for this disparity is not well understood. We hypothesize that the gut microbiome plays a role in regulating this disparity. Indeed, we found significant differences in species richness and diversity between AAs and CAs. Bacteroidetes was more abundant in AAs than in CAs. In particular, the pro-inflammatory bacteria Fusobacterium nucleatum and Enterobacter species were significantly higher in AAs, whereas probiotic Akkermansia muciniphila and Bifidobacterium were higher in CAs. The polyphyletic Clostridia class showed a divergent pattern, with Clostridium XI elevated in AAs, and Clostridium IV, known for its beneficial function, higher in CAs. Lastly, the AA group had decreased microbial diversity overall in comparison to the CA group. In summary, there were significant differences in pro-inflammatory bacteria and microbial diversity between AA and CA, which may help explain the CRC disparity between groups.
CONCLUSION Our current investigation, for the first time, demonstrates microbial dysbiosis between AAs and CAs, which could contribute to the racial disparity of CRC.
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Affiliation(s)
- Lulu Farhana
- Department of Internal Medicine, John D Dingell Veterans Affairs Medical Center, Detroit, MI 48201, United States
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Fadi Antaki
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, United States
- Division of Gastroenterology, John D Dingell VA Medical Center, Detroit, MI 48201, United States
| | - Farhan Murshed
- Department of Internal Medicine, John D Dingell Veterans Affairs Medical Center, Detroit, MI 48201, United States
| | - Hamidah Mahmud
- Department of Internal Medicine, John D Dingell Veterans Affairs Medical Center, Detroit, MI 48201, United States
| | - Stephanie L Judd
- Division of Gastroenterology, John D Dingell VA Medical Center, Detroit, MI 48201, United States
| | - Pratima Nangia-Makker
- Department of Internal Medicine, John D Dingell Veterans Affairs Medical Center, Detroit, MI 48201, United States
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, United States
- Department of Medicine, Karmanos Cancer Institute, Detroit, MI 48201, United States
| | - Edi Levi
- Department of Pathology Service, John D Dingell VA Medical Center, Detroit, MI 48201, United States
| | - Yingjie Yu
- Department of Internal Medicine, John D Dingell Veterans Affairs Medical Center, Detroit, MI 48201, United States
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Adhip PN Majumdar
- Department of Internal Medicine, John D Dingell Veterans Affairs Medical Center, Detroit, MI 48201, United States
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI 48201, United States
- Department of Medicine, Karmanos Cancer Institute, Detroit, MI 48201, United States
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Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Nat Genet 2018; 50:1524-1532. [PMID: 30250126 PMCID: PMC6241851 DOI: 10.1038/s41588-018-0224-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 08/02/2018] [Indexed: 02/05/2023]
Abstract
Despite a growing body of evidence, the role of the gut microbiome in cardiovascular diseases (CVDs) is still unclear. Here we present a systems-genome-wide and metagenome-wide association study on plasma concentrations of 92 CVD-related proteins in the population cohort Lifelines-DEEP. We identified genetic components for 73 proteins and microbial associations for 41 proteins, of which 31 were associated to both. The genetic and microbial factors identified mostly exert additive effects and collectively explain up to 76.6% of inter-individual variation (17.5% on average). Genetics contributes most to concentrations of immune-related proteins, while the gut microbiome contributes most to proteins involved in metabolism and intestinal health. We found several host-microbe interactions that impact proteins involved in epithelial function, lipid metabolism and central nervous system function. This study reveals important evidence for a joint genetic and microbial effect in cardiovascular disease and provides directions for future applications in personalized medicine.
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361
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Mendonça LABM, Dos Santos Ferreira R, de Cássia Avellaneda Guimarães R, de Castro AP, Franco OL, Matias R, Carvalho CME. The Complex Puzzle of Interactions Among Functional Food, Gut Microbiota, and Colorectal Cancer. Front Oncol 2018; 8:325. [PMID: 30234008 PMCID: PMC6133950 DOI: 10.3389/fonc.2018.00325] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 07/30/2018] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer exerts a strong influence on the epidemiological panorama worldwide, and it is directly correlated to etiologic factors that are substantiated by genetic and environmental elements. This complex mixture of factors also has a relationship involving the structural dependence and composition of the gut microbiome, leading to a dysbacteriosis process that may evolve to serious modifications in the intestinal lining, eventually causing the development of a neoplasm. The gastrointestinal tract presents defense strategies and immunological properties that interfere in intestinal permeability, inhibiting the bacterial translocation, thus maintaining the integrity of intestinal homeostasis. The modulation of the intestinal microbiome and the extinction of risk factors associated with intestinal balance losses, especially of environmental factors, make cell and defense alterations impossible. This modulation may be conducted by means of functional foods in the diet, especially soluble fibers, polyunsaturated fatty acids, antioxidants and prebiotics that signal immunomodulatory effects in the intestinal microbiota, with preventive and therapeutic action for colorectal cancer. In summary, this review focuses on the importance of dietary modulation of the intestinal microbiota as an instrument for dysbacteriosis and, consequently, for the prevention of colorectal cancer, suggesting anticarcinogenic, and antiangiogenic properties. Among the intestinal modulating agents considered here are functional foods, especially flaxseed, oat and soy, composing a Bioactive Food Compound.
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Affiliation(s)
- Lígia A B M Mendonça
- S-Inova Biotech Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Brazil
| | - Rosângela Dos Santos Ferreira
- Post Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Rita de Cássia Avellaneda Guimarães
- Post Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Alinne P de Castro
- S-Inova Biotech Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Brazil
| | - Octávio L Franco
- S-Inova Biotech Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Brazil.,Center of Proteomic and Biochemical Analysis, Post Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasilia, Brasilia, Brazil
| | - Rosemary Matias
- Post Graduate Program in Environmental Sciences and Agricultural Sustainability, Catholic University Dom Bosco, Campo Grande, Brazil.,Post Graduate Program in Environment and Regional Development, University Anhanguera Uniderp, Campo Grande, Brazil
| | - Cristiano M E Carvalho
- S-Inova Biotech Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Brazil.,Post Graduate Program in Environment and Regional Development, University Anhanguera Uniderp, Campo Grande, Brazil
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362
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Alexander JL, Scott AJ, Pouncey AL, Marchesi J, Kinross J, Teare J. Colorectal carcinogenesis: an archetype of gut microbiota-host interaction. Ecancermedicalscience 2018; 12:865. [PMID: 30263056 PMCID: PMC6145524 DOI: 10.3332/ecancer.2018.865] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Indexed: 12/14/2022] Open
Abstract
Sporadic colorectal cancer (CRC) remains a major cause of worldwide mortality. Epidemiological evidence of markedly increased risk in populations that migrate to Western countries, or adopt their lifestyle, suggests that CRC is a disease whose aetiology is defined primarily by interactions between the host and his environment. The gut microbiome sits directly at this interface and is now increasingly recognised as a modulator of colorectal carcinogenesis. Bacteria such as Fusobacterium nucleatum and Escherichia coli (E. Coli) are found in abundance in patients with CRC and have been shown in experimental studies to promote neoplasia. A whole armamentarium of bacteria-derived oncogenic mechanisms has been defined, including the subversion of apoptosis and the production of genotoxins and pro-inflammatory factors. But the microbiota may also be protective: for example, they are implicated in the metabolism of dietary fibre to produce butyrate, a short chain fatty acid, which is anti-inflammatory and anti-carcinogenic. Indeed, although our understanding of this immensely complex, highly individualised and multi-faceted relationship is expanding rapidly, many questions remain: Can we define friends and foes, and drivers and passengers? What are the critical functions of the microbiota in the context of colorectal neoplasia?
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Affiliation(s)
- James L Alexander
- Centre for Digestive and Gut Health, Department of Surgery and Cancer, Imperial College London, 10th Floor QEQM Building, St Mary's Hospital, South Wharf Road, London W2 1NY, UK
| | - Alasdair J Scott
- Centre for Digestive and Gut Health, Department of Surgery and Cancer, Imperial College London, 10th Floor QEQM Building, St Mary's Hospital, South Wharf Road, London W2 1NY, UK
| | - Anna L Pouncey
- Centre for Digestive and Gut Health, Department of Surgery and Cancer, Imperial College London, 10th Floor QEQM Building, St Mary's Hospital, South Wharf Road, London W2 1NY, UK
| | - Julian Marchesi
- Centre for Digestive and Gut Health, Department of Surgery and Cancer, Imperial College London, 10th Floor QEQM Building, St Mary's Hospital, South Wharf Road, London W2 1NY, UK
| | - James Kinross
- Centre for Digestive and Gut Health, Department of Surgery and Cancer, Imperial College London, 10th Floor QEQM Building, St Mary's Hospital, South Wharf Road, London W2 1NY, UK
| | - Julian Teare
- Centre for Digestive and Gut Health, Department of Surgery and Cancer, Imperial College London, 10th Floor QEQM Building, St Mary's Hospital, South Wharf Road, London W2 1NY, UK
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363
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Mullish BH, Osborne LS, Marchesi JR, McDonald JA. The implementation of omics technologies in cancer microbiome research. Ecancermedicalscience 2018; 12:864. [PMID: 30263055 PMCID: PMC6145519 DOI: 10.3332/ecancer.2018.864] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Indexed: 12/21/2022] Open
Abstract
Whilst the interplay between host genetics and the environment plays a pivotal role in the aetiopathogenesis of cancer, there are other key contributors of importance as well. One such factor of central and growing interest is the contribution of the microbiota to cancer. Even though the field is only a few years old, investigation of the 'cancer microbiome' has already led to major advances in knowledge of the basic biology of cancer risk and progression, opened novel avenues for biomarkers and diagnostics, and given a better understanding of mechanisms underlying response to therapy. Recent developments in microbial DNA sequencing techniques (and the bioinformatics required for analysis of these datasets) have allowed much more in-depth profiling of the structure of microbial communities than was previously possible. However, for more complete assessment of the functional implications of microbial changes, there is a growing recognition of the importance of the integration of microbial profiling with other omics modalities, with metabonomics (metabolite profiling) and proteomics (protein profiling) both gaining particular recent attention. In this review, we give an overview of some of the key scientific techniques being used to unravel the role of the cancer microbiome. We have aimed to highlight practical aspects related to sample collection and preparation, choice of the modality of analysis, and examples of where different omics technologies have been complementary to each other to highlight the significance of the cancer microbiome.
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Affiliation(s)
- Benjamin H Mullish
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Laura S Osborne
- Microbiomes, Microbes and Informatics Research Department, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Julian R Marchesi
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.,Microbiomes, Microbes and Informatics Research Department, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Julie Ak McDonald
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
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364
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Shanahan ER, Shah A, Koloski N, Walker MM, Talley NJ, Morrison M, Holtmann GJ. Influence of cigarette smoking on the human duodenal mucosa-associated microbiota. MICROBIOME 2018; 6:150. [PMID: 30157953 PMCID: PMC6116507 DOI: 10.1186/s40168-018-0531-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/12/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cigarette smoking is a known risk factor in a number of gastrointestinal (GI) diseases in which the microbiota is implicated, including duodenal ulcer and Crohn's disease. Smoking has the potential to alter the microbiota; however, to date, the impact of smoking on the mucosa-associated microbiota (MAM), and particularly that of the upper GI tract, remains very poorly characterised. Thus, we investigated the impact of smoking on the upper small intestinal MAM. A total of 102 patients undergoing upper GI endoscopy for the assessment of GI symptoms, iron deficiency, or Crohn's disease, but without identifiable lesions in the duodenum, were recruited. Smoking status was determined during clinical assessment and patients classified as current (n = 21), previous smokers (n = 40), or having never smoked (n = 41). The duodenal (D2) MAM was profiled via 16S rRNA gene amplicon sequencing. RESULTS Smoking, both current and previous, is associated with significantly reduced bacterial diversity in the upper small intestinal mucosa, as compared to patients who had never smoked. This was accompanied by higher relative abundance of Firmicutes, specifically Streptococcus and Veillonella spp. The relative abundance of the genus Rothia was also observed to be greater in current smokers; while in contrast, levels of Prevotella and Neisseria were lower. The MAM profiles and diversity of previous smokers were observed to be intermediate between current and never smokers. Smoking did not impact the total density of bacteria present on the mucosa. CONCLUSIONS These data indicate the duodenal MAM of current smokers is characterised by reduced bacterial diversity, which is partially but not completely restored in previous smokers. While the precise mechanisms remain to be elucidated, these microbiota changes may in some part explain the adverse effects of smoking on mucosa-associated diseases of the GI tract. Smoking status requires consideration when interpreting MAM data.
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Affiliation(s)
- Erin R. Shanahan
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, and Faculty of Medicine, The University of Queensland, 199 Ipswich Road, Woolloongabba, Brisbane, Queensland 4102 Australia
- Translational Research Institute, Woolloongabba, Queensland Australia
- Faculty of Medicine, The University of Queensland Diamantina Institute, The University of Queensland, Saint Lucia, Queensland 4072 Australia
- Present address: School of Life and Environmental Sciences, Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales Australia
| | - Ayesha Shah
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, and Faculty of Medicine, The University of Queensland, 199 Ipswich Road, Woolloongabba, Brisbane, Queensland 4102 Australia
- Translational Research Institute, Woolloongabba, Queensland Australia
| | - Natasha Koloski
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, and Faculty of Medicine, The University of Queensland, 199 Ipswich Road, Woolloongabba, Brisbane, Queensland 4102 Australia
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales Australia
| | - Marjorie M. Walker
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales Australia
| | - Nicholas J. Talley
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales Australia
| | - Mark Morrison
- Translational Research Institute, Woolloongabba, Queensland Australia
- Faculty of Medicine, The University of Queensland Diamantina Institute, The University of Queensland, Saint Lucia, Queensland 4072 Australia
| | - Gerald J. Holtmann
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, and Faculty of Medicine, The University of Queensland, 199 Ipswich Road, Woolloongabba, Brisbane, Queensland 4102 Australia
- Translational Research Institute, Woolloongabba, Queensland Australia
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Zhang Y, Yu X, Yu E, Wang N, Cai Q, Shuai Q, Yan F, Jiang L, Wang H, Liu J, Chen Y, Li Z, Jiang Q. Changes in gut microbiota and plasma inflammatory factors across the stages of colorectal tumorigenesis: a case-control study. BMC Microbiol 2018; 18:92. [PMID: 30157754 PMCID: PMC6114884 DOI: 10.1186/s12866-018-1232-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 08/15/2018] [Indexed: 02/07/2023] Open
Abstract
Background Colorectal cancer (CRC) is a common malignant gastrointestinal tumor. In China, CRC is the 5th most commonly diagnosed cancer. The vast majority of CRC cases are sporadic and evolve with the adenoma-carcinoma sequence. There is mounting evidence indicating that gut microbiota and inflammation play important roles in the development of CRC although study results are not entirely consistent. In the current study, we investigated the changes in the CRC-associated bacteria and plasma inflammatory factors and their relationships based on data from a case-control study of Han Chinese. We included 130 initially diagnosed CRC patients, 88 advanced colorectal adenoma patients (A-CRA), 62 patients with benign intestinal polyps and 130 controls. Results Fecal microbiota composition was obtained using 16S ribosomal DNA (16S rDNA) sequencing. PCOA analysis showed structural differences in microbiota among the four study groups (P = 0.001, Unweighted Unifrac). Twenty-four CRC-associated bacteria were selected by a two-step statistical method and significant correlations were observed within these microbes. CRC-associated bacteria were found to change with the degree of malignancy. Plasma C-reactive protein (CRP) and soluble tumor necrosis factor II (sTNFR-II) displayed significant differences among the four study groups and increased with adenoma-carcinoma sequence. The correlations of CRP and sTNFR-II with several CRC-associated microbes were also explored. Conclusions CRC-associated species and plasma inflammatory factors tended to change along the adenoma-carcinoma sequence. Several CRC-associated bacteria were correlated with CRP and sTNFR-II. It is likely that gut microbiome and inflammation gradually form a microenvironment that is associated with CRC development. Electronic supplementary material The online version of this article (10.1186/s12866-018-1232-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yongzhen Zhang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China.,The 92914th Military Hospital of PLA, Shanghai, China
| | - Xin Yu
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, 130 Dong'an Road, Shanghai, 200032, China
| | - Enda Yu
- Department of General Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200032, China
| | - Na Wang
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, 130 Dong'an Road, Shanghai, 200032, China
| | - Quancai Cai
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China.
| | - Qun Shuai
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Feihu Yan
- Department of General Surgery, Changhai Hospital, Naval Medical University, Shanghai, 200032, China
| | - Lufang Jiang
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, 130 Dong'an Road, Shanghai, 200032, China
| | - Hexing Wang
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, 130 Dong'an Road, Shanghai, 200032, China
| | - Jianxiang Liu
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, 130 Dong'an Road, Shanghai, 200032, China
| | - Yue Chen
- School of Epidemiology and Public Health, University of Ottawa Faculty of Medicine, Ottawa, Canada
| | - Zhaoshen Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China.
| | - Qingwu Jiang
- Key Laboratory of Public Health Safety of Ministry of Education, School of Public Health, Fudan University, 130 Dong'an Road, Shanghai, 200032, China.
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Wang Z, Zolnik CP, Qiu Y, Usyk M, Wang T, Strickler HD, Isasi CR, Kaplan RC, Kurland IJ, Qi Q, Burk RD. Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies. Front Cell Infect Microbiol 2018; 8:301. [PMID: 30234027 PMCID: PMC6127643 DOI: 10.3389/fcimb.2018.00301] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/07/2018] [Indexed: 12/24/2022] Open
Abstract
Background: Integrated microbiome and metabolomics analyses hold the potential to reveal interactions between host and microbiota in relation to disease risks. However, there are few studies evaluating how field methods influence fecal microbiome characterization and metabolomics profiling. Methods: Five fecal collection methods [immediate freezing at -20°C without preservative, OMNIgene GUT, 95% ethanol, RNAlater, and Flinders Technology Associates (FTA) cards] were used to collect 40 fecal samples from eight healthy volunteers. We performed gut microbiota 16S rRNA sequencing, untargeted metabolomics profiling, and targeted metabolomics focusing on short chained fatty acids (SCFAs). Metrics included α-diversity and β-diversity as well as distributions of predominant phyla. To evaluate the concordance with the "gold standard" immediate freezing, the intraclass correlation coefficients (ICCs) for alternate fecal collection systems were calculated. Correlations between SCFAs and gut microbiota were also examined. Results: The FTA cards had the highest ICCs compared to the immediate freezing method for α-diversity indices (ICCs = 0.96, 0.96, 0.76 for Shannon index, Simpson's Index, Chao-1 Index, respectively), followed by OMNIgene GUT, RNAlater, and 95% ethanol. High ICCs (all >0.88) were observed for all methods for the β-diversity metric. For untargeted metabolomics, in comparison to immediate freezing which detected 621 metabolites at ≥75% detectability level, 95% ethanol showed the largest overlapping set of metabolites (n = 430; 69.2%), followed by FTA cards (n = 330; 53.1%) and OMNIgene GUT (n = 213; 34.3%). Both OMNIgene GUT (ICCs = 0.82, 0.93, 0.64) and FTA cards (ICCs = 0.87, 0.85, 0.54) had acceptable ICCs for the top three predominant SCFAs (butyric acid, propionic acid and acetic acid). Nominally significant correlations between bacterial genera and SCFAs (P < 0.05) were observed in fecal samples collected by different methods. Of note, a high correlation between the genus Blautia (known butyrate producer) and butyric acid was observed for both immediate freezing (r = 0.83) and FTA cards (r = 0.74). Conclusions: Four alternative fecal collection methods are generally comparable with immediate freezing, but there are differences in certain measures of the gut microbiome and fecal metabolome across methods. Choice of method depends on the research interests, simplicity of fecal collection procedures and ease of transportation to the lab, especially for large epidemiological studies.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Christine P. Zolnik
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Biology, Long Island University, Brooklyn, NY, United States
| | - Yunping Qiu
- Department of Medicine, Stable Isotope and Metabolomics Core Facility, Diabetes Center, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Mykhaylo Usyk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Howard D. Strickler
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Carmen R. Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Irwin J. Kurland
- Department of Medicine, Stable Isotope and Metabolomics Core Facility, Diabetes Center, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Robert D. Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
- Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Obstetrics, Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, United States
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367
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Wang G, Liu Q, Guo L, Zeng H, Ding C, Zhang W, Xu D, Wang X, Qiu J, Dong Q, Fan Z, Zhang Q, Pan J. Gut Microbiota and Relevant Metabolites Analysis in Alcohol Dependent Mice. Front Microbiol 2018; 9:1874. [PMID: 30158912 PMCID: PMC6104187 DOI: 10.3389/fmicb.2018.01874] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/25/2018] [Indexed: 12/21/2022] Open
Abstract
Alcohol abuse is a major public health crisis. Relative evidences supported that the gut microbiota (GM) played an important role in central nervous system (CNS) function, and the composition of them had changed after alcohol drinking. We sought to explore the changes of GM in alcohol dependence. In our study, the GM of mice with alcohol administration was detected through analyzed 16S rRNA gene sequencing and the fecal metabolites were analyzed by LC-MS. The microbial diversity was significantly higher in the alcohol administration group, the abundance of phylum Firmicutes and its class Clostridiales were elevated, meanwhile the abundance of Lachnospiraceae, Alistipes, and Odoribacter showed significant differences among the three groups. Based on LC-MS results, bile acid, secondary bile acid, serotonin and taurine level had varying degrees of changes in alcohol model. From paraffin sections, tissue damage was observed in liver and colon. These findings provide direct evidence that alcohol intake affects the composition of GM, enable a better understanding of the function of GM in the microbiota-gut-brain (MGB) axis, and give a new thought for alcohol addiction treatment.
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Affiliation(s)
- Guanhao Wang
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Qing Liu
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Liang Guo
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Haijuan Zeng
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Chengchao Ding
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Wentong Zhang
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Dongpo Xu
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xiang Wang
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Jingxuan Qiu
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Qingli Dong
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Ziquan Fan
- Thermo Fisher Scientific, Shanghai, China
| | - Qi Zhang
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Jing Pan
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
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368
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Ding C, Tang W, Fan X, Wu G. Intestinal microbiota: a novel perspective in colorectal cancer biotherapeutics. Onco Targets Ther 2018; 11:4797-4810. [PMID: 30147331 PMCID: PMC6097518 DOI: 10.2147/ott.s170626] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
It is believed that genetic factors, immune system dysfunction, chronic inflammation, and intestinal microbiota (IM) dysbiosis contribute to the pathogenesis of colorectal cancer (CRC). The beneficial role played by the direct regulation of IM in inflammatory bowel disease treatment is identified by the decreased growth of harmful bacteria and the increased production of anti-inflammatory factors. Interestingly, gut microbiota has been proven to inhibit tumor formation and progression in inflammation/carcinogen-induced CRC mouse models. Recently, evidence has indicated that IM is involved in the negative regulation of tumor immune response in tumor microenvironment, which then abolishes or accelerates anticancer immunotherapy in several tumor animals. In clinical trials, a benefit of IM-based CRC therapies in improving the intestinal immunity balance, epithelial barrier function, and quality of life has been reported. Meanwhile, specific microbiota signature can modulate host's sensitivity to chemo-/radiotherapy and the prognosis of CRC patients. In this review, we aim to 1) summarize the potential methods of IM-based therapeutics according to the recent results; 2) explore its roles and underlying mechanisms in combination with other therapies, especially in biotherapeutics; 3) discuss its safety, deficiency, and future perspectives.
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Affiliation(s)
- Chenbo Ding
- Medical School of Southeast University, Nanjing, Jiangsu Province, People's Republic of China,
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu Province, People's Republic of China,
| | - Wendong Tang
- Medical School of Southeast University, Nanjing, Jiangsu Province, People's Republic of China,
| | - Xiaobo Fan
- Medical School of Southeast University, Nanjing, Jiangsu Province, People's Republic of China,
| | - Guoqiu Wu
- Medical School of Southeast University, Nanjing, Jiangsu Province, People's Republic of China,
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu Province, People's Republic of China,
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369
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Flemer B, Warren RD, Barrett MP, Cisek K, Das A, Jeffery IB, Hurley E, O‘Riordain M, Shanahan F, O‘Toole PW. The oral microbiota in colorectal cancer is distinctive and predictive. Gut 2018; 67:1454-1463. [PMID: 28988196 PMCID: PMC6204958 DOI: 10.1136/gutjnl-2017-314814] [Citation(s) in RCA: 371] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Microbiota alterations are linked with colorectal cancer (CRC) and notably higher abundance of putative oral bacteria on colonic tumours. However, it is not known if colonic mucosa-associated taxa are indeed orally derived, if such cases are a distinct subset of patients or if the oral microbiome is generally suitable for screening for CRC. METHODS We profiled the microbiota in oral swabs, colonic mucosae and stool from individuals with CRC (99 subjects), colorectal polyps (32) or controls (103). RESULTS Several oral taxa were differentially abundant in CRC compared with controls, for example, Streptococcus and Prevotellas pp. A classification model of oral swab microbiota distinguished individuals with CRC or polyps from controls (sensitivity: 53% (CRC)/67% (polyps); specificity: 96%). Combining the data from faecal microbiota and oral swab microbiota increased the sensitivity of this model to 76% (CRC)/88% (polyps). We detected similar bacterial networks in colonic microbiota and oral microbiota datasets comprising putative oral biofilm forming bacteria. While these taxa were more abundant in CRC, core networks between pathogenic, CRC-associated oral bacteria such as Peptostreptococcus, Parvimonas and Fusobacterium were also detected in healthy controls. High abundance of Lachnospiraceae was negatively associated with the colonisation of colonic tissue with oral-like bacterial networks suggesting a protective role for certain microbiota types against CRC, possibly by conferring colonisation resistance to CRC-associated oral taxa and possibly mediated through habitual diet. CONCLUSION The heterogeneity of CRC may relate to microbiota types that either predispose or provide resistance to the disease, and profiling the oral microbiome may offer an alternative screen for detecting CRC.
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Affiliation(s)
- Burkhardt Flemer
- APC Microbiome Institue, University College Cork, National University of Ireland, Cork, Ireland,Schools of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Ryan D Warren
- APC Microbiome Institue, University College Cork, National University of Ireland, Cork, Ireland
| | - Maurice P Barrett
- APC Microbiome Institue, University College Cork, National University of Ireland, Cork, Ireland,Schools of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | | | | | - Ian B Jeffery
- APC Microbiome Institue, University College Cork, National University of Ireland, Cork, Ireland,Schools of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Eimear Hurley
- Schools of Microbiology, University College Cork, National University of Ireland, Cork, Ireland,Department of Dentistry, University College Cork, National University of Ireland, Cork, Ireland
| | - Micheal O‘Riordain
- Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
| | - Fergus Shanahan
- APC Microbiome Institue, University College Cork, National University of Ireland, Cork, Ireland,Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
| | - Paul W O‘Toole
- APC Microbiome Institue, University College Cork, National University of Ireland, Cork, Ireland,Schools of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
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370
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Kwong TNY, Wang X, Nakatsu G, Chow TC, Tipoe T, Dai RZW, Tsoi KKK, Wong MCS, Tse G, Chan MTV, Chan FKL, Ng SC, Wu JCY, Wu WKK, Yu J, Sung JJY, Wong SH. Association Between Bacteremia From Specific Microbes and Subsequent Diagnosis of Colorectal Cancer. Gastroenterology 2018; 155:383-390.e8. [PMID: 29729257 DOI: 10.1053/j.gastro.2018.04.028] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 04/09/2018] [Accepted: 04/24/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Colorectal cancer (CRC) development has been associated with increased proportions of Bacteroides fragilis and certain Streptococcus, Fusobacterium, and Peptostreptococcus species in the intestinal microbiota. We investigated associations between bacteremia from specific intestinal microbes and occurrence of CRC. METHODS We performed a retrospective study after collecting data on 13,096 adult patients (exposed group) in Hong Kong hospitalized with bacteremia (identified by blood culture test) without a previous diagnosis of cancer from January 1, 2006 through December 31, 2015. We collected data on intestinal microbes previously associated with CRC (genera Bacteroides, Clostridium, Filifactor, Fusobacterium, Gemella, Granulicatella, Parvimonas, Peptostreptococcus, Prevotella, Solobacterium, and Streptococcus). Clinical information, including patient demographics, comorbid medical conditions, date of bacteremia, and bacterial species identified, were collected. The incidence of biopsy-proved CRC was compared between the exposed and unexposed (patients without bacteremia matched for age, sex, and comorbidities) groups. RESULTS The risk of CRC was increased in patients with bacteremia from B fragilis (hazard ratio [HR] = 3.85, 95% CI = 2.62-5.64, P = 5.5 × 10-12) or Streptococcus gallolyticus (HR = 5.73, 95% CI = 2.18-15.1, P = 4.1 × 10-4) compared with the unexposed group. In addition, the risk of CRC was increased in patients with bacteremia from Fusobacterium nucleatum (HR = 6.89, 95% CI = 1.70-27.9, P = .007), Peptostreptococcus species (HR = 3.06, 95% CI = 1.47-6.35, P = .003), Clostridium septicum (HR = 17.1, 95% CI = 1.82-160, P = .013), Clostridium perfringens (HR = 2.29, 95% CI = 1.16-4.52, P = .017), or Gemella morbillorum (HR = 15.2, 95% CI = 1.54-150, P = .020). We observed no increased risk in patients with bacteremia caused by microbes not previously associated with colorectal neoplasms. CONCLUSIONS In a retrospective analysis of patients hospitalized for bacteremia, we associated later diagnosis of CRC with B fragilis and S gallolyticus and other intestinal microbes. These bacteria might have entered the bloodstream from intestinal dysbiosis and perturbed barrier function. These findings support a model in which specific members of the intestinal microbiota promote colorectal carcinogenesis. Clinicians should evaluate patients with bacteremia from these species for neoplastic lesions in the colorectum.
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Affiliation(s)
- Thomas N Y Kwong
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Xiansong Wang
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong; Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong
| | - Geicho Nakatsu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Tai Cheong Chow
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Timothy Tipoe
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong
| | - Rudin Z W Dai
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Kelvin K K Tsoi
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong; Stanley Ho Big Data Decision Analytics Research Centre, The Chinese University of Hong Kong, Hong Kong
| | - Martin C S Wong
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong
| | - Gary Tse
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Matthew T V Chan
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong
| | - Francis K L Chan
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Siew C Ng
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Justin C Y Wu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - William K K Wu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong
| | - Jun Yu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Joseph J Y Sung
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Sunny H Wong
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, and CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong.
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371
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Shifts of Faecal Microbiota During Sporadic Colorectal Carcinogenesis. Sci Rep 2018; 8:10329. [PMID: 29985435 PMCID: PMC6037773 DOI: 10.1038/s41598-018-28671-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 06/27/2018] [Indexed: 12/18/2022] Open
Abstract
Gut microbiota has been implicated in the etiopathogenesis of colorectal cancer. The development of colorectal cancer is a multistep process by which healthy epithelium slowly develops into preneoplastic lesions, which in turn progress into malignant carcinomas over time. In particular, sporadic colorectal cancers can arise from adenomas (about 85% of cases) or serrated polyps through the "adenoma-carcinoma" or the "serrated polyp-carcinoma" sequences, respectively. In this study, we performed 16 S rRNA gene sequencing of bacterial DNA extracted from faecal samples to compare the microbiota of healthy subjects and patients with different preneoplastic and neoplastic lesions. We identified putative microbial biomarkers associated with stage-specific progression of colorectal cancer. In particular, bacteria belonging to the Firmicutes and Actinobacteria phyla, as well as members of the Lachnospiraceae family, proved to be specific of the faecal microbiota of patients with preneoplastic lesions, including adenomas and hyperplastic polyps. On the other hand, two families of the Proteobacteria phylum, Alcaligeneaceae and Enterobacteriaceae, with Sutterella and Escherichia/Shigella being the most representative genera, appeared to be associated with malignancy. These findings, once confirmed on larger cohorts of patients, can represent an important step towards the development of more effective diagnostic strategies.
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372
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Zhang H, Sun L. When human cells meet bacteria: precision medicine for cancers using the microbiota. Am J Cancer Res 2018; 8:1157-1175. [PMID: 30094091 PMCID: PMC6079160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 06/14/2018] [Indexed: 06/08/2023] Open
Abstract
The human microbiota interacts with the host immune system in multiple ways to influence the development of diseases, including cancers; however, a detailed understanding of their relationship is unavailable. Accumulating evidence has only revealed an association rather than a causal link between microbial alterations and carcinogenesis. The regulatory loops among the microbiome, human cells and the immune system are far more complicated and require further studies to be revealed. In this review, we discuss the impact of the microbiota on cancer initiation, development and progression in different types of human cells, mainly focusing on the clinical translation from microbiome research to an accurate diagnosis, subtype classification and precision medicine.
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Affiliation(s)
- Han Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeKunming 650031, Yunnan, China
| | - Litao Sun
- The Scripps Laboratories for tRNA Synthetase Research, The Scripps Research InstituteLa Jolla, CA 92037, USA
- Department of Molecular Medicine, The Skaggs Institute for Chemical Biology, The Scripps Research InstituteLa Jolla, CA 92037, USA
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373
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Huang Q, Peng Y, Xie F. Fecal fusobacterium nucleatum for detecting colorectal cancer: a systematic review and meta-analysis. Int J Biol Markers 2018; 33:1724600818781301. [PMID: 29968498 DOI: 10.1177/1724600818781301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE The purpose of this systematic review and meta-analysis was to evaluate the efficacy of fecal Fusobacterium nucleatum ( Fn) for detecting colorectal cancer. It is the first systematic review and meta-analysis to focus exclusively on fecal Fn for colorectal cancer. MATERIALS AND METHODS Comprehensive searches of several databases before January 2018 were conducted. Fecal Fn for detecting colorectal cancer was evaluated via pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the curve. Heterogeneity was explored using meta-regression and subgroup analyses. The publication bias and the overall quality of evidence were also analyzed. RESULTS Our analysis included six papers containing seven case-control studies in the systematic review and meta-analysis. Overall sensitivity and specificity were 0.68 (95% confidence interval (CI) 0.64, 0.72) and 0.78 (95% CI 0.75, 0.81), respectively. The positive likelihood ratio and negative likelihood ratio in detecting colorectal cancer were 2.87 (95% CI 1.62, 5.10) and 0.40 (95% CI 0.30, 0.54) respectively. The diagnostic odds ratio (OR) was 8.75 (95% CI 4.86, 15.78) and the area under the curve was 0.80. A subgroup analysis showed that in Asia, the colorectal cancer sample size ⩾50 had higher specificity (specificity 0.85, 95% CI 0.80, 0.88). No publication bias existed. The GRADEpro showed a moderate level of the available evidence. CONCLUSIONS Compared to other examinations, the fecal Fn test seems a good choice for detecting colorectal cancer. It also has better diagnostic performance in Asians. However, more clinical trials with large sample sizes and strict randomization are needed to further verify the evidence.
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Affiliation(s)
- Qian Huang
- 1 Department of Oncology, the 476 Hospital of PLA, Fuzhou, Fujian, P.R. China
| | - Yonghai Peng
- 2 Department of Oncology, Fuzhou General Hospital, Fujian, P.R. China
| | - Fangwei Xie
- 2 Department of Oncology, Fuzhou General Hospital, Fujian, P.R. China
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374
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Abstract
You are what you eat. This adage has been confirmed by many studies demonstrating the high impact of nutrition on risk of cardiovascular diseases, many malignancies and other diseases. Dietary factors are of major relevance in the evolution of colorectal carcinoma. Various aspects are involved in colorectal carcinoma pathogenesis including genetics, lifestyle, age, chronic inflammation and others. It has only recently been recognized that the gut microbiota might reflect an important missing link in the interaction between diet and subsequent colorectal carcinoma development. Dietary factors are a major confounding factor affecting the composition of the intestinal microbiota. Several preclinical and clinical studies have recently suggested a role for the intestinal microbiota in potentially initiating and driving colorectal carcinoma. Therefore it is increasingly acknowledged that dietary factors might favor carcinogenesis via manipulation of the gut microbiota via potential outgrowth of certain bacterial populations, such as Fusobacterium nucleatum, Escherichia coli or Bacteroides fragilis. Excitingly, recent large clinical studies also highlighted a role for the gut microbiota and in particular Akkermansia muciniphila in tumor response toward chemotherapeutic agents and immune checkpoint inhibitors. This review will concentrate on the role of dietary factors in affecting the microbiota and implications in colorectal carcinoma.
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375
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Burns MB, Montassier E, Abrahante J, Priya S, Niccum DE, Khoruts A, Starr TK, Knights D, Blekhman R. Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment. PLoS Genet 2018; 14:e1007376. [PMID: 29924794 PMCID: PMC6028121 DOI: 10.1371/journal.pgen.1007376] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/02/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023] Open
Abstract
Variation in the gut microbiome has been linked to colorectal cancer (CRC), as well as to host genetic variation. However, we do not know whether, in addition to baseline host genetics, somatic mutational profiles in CRC tumors interact with the surrounding tumor microbiome, and if so, whether these changes can be used to understand microbe-host interactions with potential functional biological relevance. Here, we characterized the association between CRC microbial communities and tumor mutations using microbiome profiling and whole-exome sequencing in 44 pairs of tumors and matched normal tissues. We found statistically significant associations between loss-of-function mutations in tumor genes and shifts in the abundances of specific sets of bacterial taxa, suggestive of potential functional interaction. This correlation allows us to statistically predict interactions between loss-of-function tumor mutations in cancer-related genes and pathways, including MAPK and Wnt signaling, solely based on the composition of the microbiome. In conclusion, our study shows that CRC microbiomes are correlated with tumor mutational profiles, pointing towards possible mechanisms of molecular interaction.
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Affiliation(s)
- Michael B. Burns
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
- * E-mail: (MBB); (RB)
| | - Emmanuel Montassier
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- MiHAR lab, Université de Nantes, 44000 Nantes, France
| | - Juan Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - David E. Niccum
- Department of Medicine, Division of Gastroenterology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Alexander Khoruts
- Department of Medicine, Division of Gastroenterology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Timothy K. Starr
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- * E-mail: (MBB); (RB)
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376
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Villéger R, Lopès A, Veziant J, Gagnière J, Barnich N, Billard E, Boucher D, Bonnet M. Microbial markers in colorectal cancer detection and/or prognosis. World J Gastroenterol 2018; 24:2327-2347. [PMID: 29904241 PMCID: PMC6000297 DOI: 10.3748/wjg.v24.i22.2327] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/03/2018] [Accepted: 05/18/2018] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer worldwide. CRC is still associated with a poor prognosis among patients with advanced disease. On the contrary, due to its slow progression from detectable precancerous lesions, the prognosis for patients with early stages of CRC is encouraging. While most robust methods are invasive and costly, actual patient-friendly screening methods for CRC suffer of lack of sensitivity and specificity. Therefore, the development of sensitive, non-invasive and cost-effective methods for CRC detection and prognosis are necessary for increasing the chances of a cure. Beyond its beneficial functions for the host, increasing evidence suggests that the intestinal microbiota is a key factor associated with carcinogenesis. Many clinical studies have reported a disruption in the gut microbiota balance and an alteration in the faecal metabolome of CRC patients, suggesting the potential use of a microbial-based test as a non-invasive diagnostic and/or prognostic tool for CRC screening. This review aims to discuss the microbial signatures associated with CRC known to date, including dysbiosis and faecal metabolome alterations, and the potential use of microbial variation markers for non-invasive early diagnosis and/or prognostic assessment of CRC and advanced adenomas. We will finally discuss the possible use of these markers as predicators for treatment response and their limitations.
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Affiliation(s)
- Romain Villéger
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
| | - Amélie Lopès
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Research Biologics, Sanofi R&D, Vitry-Sur-Seine 94400, France
| | - Julie Veziant
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Chirurgie digestive, Centre Hospitalier Universitaire, Clermont-Ferrand 63000, France
| | - Johan Gagnière
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Chirurgie digestive, Centre Hospitalier Universitaire, Clermont-Ferrand 63000, France
| | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - Elisabeth Billard
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - Delphine Boucher
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - Mathilde Bonnet
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, Clermont-Ferrand 63000, France
- Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand 63000, France
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377
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Tilg H, Adolph TE, Gerner RR, Moschen AR. The Intestinal Microbiota in Colorectal Cancer. Cancer Cell 2018; 33:954-964. [PMID: 29657127 DOI: 10.1016/j.ccell.2018.03.004] [Citation(s) in RCA: 479] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/08/2018] [Accepted: 03/01/2018] [Indexed: 02/07/2023]
Abstract
Experimental evidence from the past years highlights a key role for the intestinal microbiota in inflammatory and malignant gastrointestinal diseases. Diet exhibits a strong impact on microbial composition and provides risk for developing colorectal carcinoma (CRC). Large metagenomic studies in human CRC associated microbiome signatures with the colorectal adenoma-carcinoma sequence, suggesting a fundamental role of the intestinal microbiota in the evolution of gastrointestinal malignancy. Basic science established a critical function for the intestinal microbiota in promoting tumorigenesis. Further studies are needed to decipher the mechanisms of tumor promotion and microbial co-evolution in CRC, which may be exploited therapeutically in the future.
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Affiliation(s)
- Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology & Endocrinology, Medical University Innsbruck, Innsbruck, Austria.
| | - Timon E Adolph
- Department of Internal Medicine I, Gastroenterology, Hepatology & Endocrinology, Medical University Innsbruck, Innsbruck, Austria
| | - Romana R Gerner
- Department of Internal Medicine I, Gastroenterology, Hepatology & Endocrinology, Medical University Innsbruck, Innsbruck, Austria; Christian Doppler Laboratory of Mucosal Immunology, Medical University Innsbruck, Innsbruck, Austria
| | - Alexander R Moschen
- Department of Internal Medicine I, Gastroenterology, Hepatology & Endocrinology, Medical University Innsbruck, Innsbruck, Austria; Christian Doppler Laboratory of Mucosal Immunology, Medical University Innsbruck, Innsbruck, Austria
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378
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Ogino S, Nowak JA, Hamada T, Phipps AI, Peters U, Milner DA, Giovannucci EL, Nishihara R, Giannakis M, Garrett WS, Song M. Integrative analysis of exogenous, endogenous, tumour and immune factors for precision medicine. Gut 2018; 67:1168-1180. [PMID: 29437869 PMCID: PMC5943183 DOI: 10.1136/gutjnl-2017-315537] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/02/2018] [Accepted: 01/05/2018] [Indexed: 12/14/2022]
Abstract
Immunotherapy strategies targeting immune checkpoints such as the CTLA4 and CD274 (programmed cell death 1 ligand 1, PD-L1)/PDCD1 (programmed cell death 1, PD-1) T-cell coreceptor pathways are revolutionising oncology. The approval of pembrolizumab use for solid tumours with high-level microsatellite instability or mismatch repair deficiency by the US Food and Drug Administration highlights promise of precision immuno-oncology. However, despite evidence indicating influences of exogenous and endogenous factors such as diet, nutrients, alcohol, smoking, obesity, lifestyle, environmental exposures and microbiome on tumour-immune interactions, integrative analyses of those factors and immunity lag behind. Immune cell analyses in the tumour microenvironment have not adequately been integrated into large-scale studies. Addressing this gap, the transdisciplinary field of molecular pathological epidemiology (MPE) offers research frameworks to integrate tumour immunology into population health sciences, and link the exposures and germline genetics (eg, HLA genotypes) to tumour and immune characteristics. Multilevel research using bioinformatics, in vivo pathology and omics (genomics, epigenomics, transcriptomics, proteomics and metabolomics) technologies is possible with use of tissue, peripheral blood circulating cells, cell-free plasma, stool, sputum, urine and other body fluids. This immunology-MPE model can synergise with experimental immunology, microbiology and systems biology. GI neoplasms represent exemplary diseases for the immunology-MPE model, given rich microbiota and immune tissues of intestines, and the well-established carcinogenic role of intestinal inflammation. Proof-of-principle studies on colorectal cancer provided insights into immunomodulating effects of aspirin, vitamin D, inflammatory diets and omega-3 polyunsaturated fatty acids. The integrated immunology-MPE model can contribute to better understanding of environment-tumour-immune interactions, and effective immunoprevention and immunotherapy strategies for precision medicine.
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Affiliation(s)
- Shuji Ogino
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Jonathan A Nowak
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tsuyoshi Hamada
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Danny A Milner
- American Society for Clinical Pathology, Chicago, Illinois, USA
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Reiko Nishihara
- Program in MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Marios Giannakis
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Wendy S Garrett
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mingyang Song
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Massachusetts, USA,Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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379
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Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WKK, Wong SH, Chen Z, Sung JJY, Yu J. Mucosal microbiome dysbiosis in gastric carcinogenesis. Gut 2018; 67:1024-1032. [PMID: 28765474 PMCID: PMC5969346 DOI: 10.1136/gutjnl-2017-314281] [Citation(s) in RCA: 396] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/23/2017] [Accepted: 06/09/2017] [Indexed: 12/12/2022]
Abstract
OBJECTIVES We aimed to characterise the microbial changes associated with histological stages of gastric tumourigenesis. DESIGN We performed 16S rRNA gene analysis of gastric mucosal samples from 81 cases including superficial gastritis (SG), atrophic gastritis (AG), intestinal metaplasia (IM) and gastric cancer (GC) from Xi'an, China, to determine mucosal microbiome dysbiosis across stages of GC. We validated the results in mucosal samples of 126 cases from Inner Mongolia, China. RESULTS We observed significant mucosa microbial dysbiosis in IM and GC subjects, with significant enrichment of 21 and depletion of 10 bacterial taxa in GC compared with SG (q<0.05). Microbial network analysis showed increasing correlation strengths among them with disease progression (p<0.001). Five GC-enriched bacterial taxa whose species identifications correspond to Peptostreptococcus stomatis, Streptococcus anginosus, Parvimonas micra, Slackia exigua and Dialister pneumosintes had significant centralities in the GC ecological network (p<0.05) and classified GC from SG with an area under the receiver-operating curve (AUC) of 0.82. Moreover, stronger interactions among gastric microbes were observed in Helicobacter pylori-negative samples compared with H. pylori-positive samples in SG and IM. The fold changes of selected bacteria, and strengths of their interactions were successfully validated in the Inner Mongolian cohort, in which the five bacterial markers distinguished GC from SG with an AUC of 0.81. CONCLUSIONS In addition to microbial compositional changes, we identified differences in bacterial interactions across stages of gastric carcinogenesis. The significant enrichments and network centralities suggest potentially important roles of P. stomatis, D. pneumosintes, S. exigua, P. micra and S. anginosus in GC progression.
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Affiliation(s)
- Olabisi Oluwabukola Coker
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhenwei Dai
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, Xijing Hospital, Fourth Military Medical University, Xian, China
| | - Guijun Zhao
- Department of Gastroenterology and Hepatology, Inner Mongolia People’s Hospital, Hohhot, China
| | - Lei Cao
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Geicho Nakatsu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - William KK Wu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny Hei Wong
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph J Y Sung
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
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380
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Chen EB, Cason C, Gilbert JA, Ho KJ. Current State of Knowledge on Implications of Gut Microbiome for Surgical Conditions. J Gastrointest Surg 2018; 22:1112-1123. [PMID: 29623674 PMCID: PMC5966332 DOI: 10.1007/s11605-018-3755-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/20/2018] [Indexed: 02/06/2023]
Abstract
The role of the microbiome in human health has become a central tenant of current medical research, infiltrating a diverse disciplinary base whereby microbiology, computer science, ecology, gastroenterology, immunology, neurophysiology and psychology, metabolism, and cardiovascular medicine all intersect. Traditionally, commensal gut microbiota have been assumed to play a significant role only in the metabolic processing of dietary nutrients and host metabolites, the fortification of gut epithelial barrier function, and the development of mucosal immunity. However, over the last 20 years, new technologies and renewed interest have uncovered a considerably broader influence of the microbiota on health maintenance and disease development, many of which are of particular relevance for surgeons. This article provides a broad overview of the current state of knowledge and a review of the technology that helped in their formation.
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Affiliation(s)
- Edmund B Chen
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cori Cason
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jack A Gilbert
- Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Karen J Ho
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Division of Vascular Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 650, Chicago, IL, 60611, USA.
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381
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Gamage S, Dissabandara L, Lam AKY, Gopalan V. The role of heme iron molecules derived from red and processed meat in the pathogenesis of colorectal carcinoma. Crit Rev Oncol Hematol 2018; 126:121-128. [DOI: 10.1016/j.critrevonc.2018.03.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 02/05/2018] [Accepted: 03/28/2018] [Indexed: 12/31/2022] Open
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382
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Herstad KMV, Moen AEF, Gaby JC, Moe L, Skancke E. Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors. PLoS One 2018; 13:e0198342. [PMID: 29852000 PMCID: PMC5979030 DOI: 10.1371/journal.pone.0198342] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 05/17/2018] [Indexed: 12/17/2022] Open
Abstract
Colorectal epithelial tumors occur spontaneously in dogs, and the pathogenesis seems to parallel that of humans. The development of human colorectal tumorigenesis has been linked to alterations in the composition of the intestinal microbiota. This study characterized the fecal- and mucosa-associated microbiota in dogs with colorectal epithelial tumors (n = 10). The fecal microbiota was characterized by 16S rDNA analysis and compared with that of control dogs (n = 13). We also determined the mucosa-associated microbiota composition in colonic tumor tissue (n = 8) and in adjacent non-tumor tissue (n = 5) by 16S rDNA- and rRNA profiling. The fecal microbial community structure in dogs with tumors was different from that of control samples and was distinguished by oligotypes affiliated with Enterobacteriaceae, Bacteroides, Helicobacter, Porphyromonas, Peptostreptococcus and Streptococcus, and lower abundance of Ruminococcaceae, Slackia, Clostridium XI and Faecalibacterium. The overall community structure and populations of mucosal bacteria were not different based on either the 16S rDNA or the 16S rRNA profile in tumor tissue vs. adjacent non-tumor tissue. However, the proportion of live, potentially active bacteria appeared to be higher in non-tumor tissue compared with tumor tissue and included Slackia, Roseburia, unclass. Ruminococcaeceae, unclass. Lachnospiraceae and Oscillibacter. Colorectal tumors are rarely diagnosed in dogs, but despite this limitation, we were able to show that dogs with colorectal tumors have distinct fecal microbiota profiles. These initial results support the need for future case-control studies that are adequately powered, as well as age-matched and breed-matched, in order to evaluate the influence of bacteria on colorectal cancer etiopathogenesis and to determine whether the bacteria may have potential as biomarkers in clinical settings.
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Affiliation(s)
- Kristin Marie Valand Herstad
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
- * E-mail:
| | - Aina Elisabeth Fossum Moen
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog and University of Oslo, Oslo, Norway
| | - John Christian Gaby
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Lars Moe
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Ellen Skancke
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
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383
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Xun Z, Zhang Q, Xu T, Chen N, Chen F. Dysbiosis and Ecotypes of the Salivary Microbiome Associated With Inflammatory Bowel Diseases and the Assistance in Diagnosis of Diseases Using Oral Bacterial Profiles. Front Microbiol 2018; 9:1136. [PMID: 29899737 PMCID: PMC5988890 DOI: 10.3389/fmicb.2018.01136] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 05/14/2018] [Indexed: 12/16/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are chronic, idiopathic, relapsing disorders of unclear etiology affecting millions of people worldwide. Aberrant interactions between the human microbiota and immune system in genetically susceptible populations underlie IBD pathogenesis. Despite extensive studies examining the involvement of the gut microbiota in IBD using culture-independent techniques, information is lacking regarding other human microbiome components relevant to IBD. Since accumulated knowledge has underscored the role of the oral microbiota in various systemic diseases, we hypothesized that dissonant oral microbial structure, composition, and function, and different community ecotypes are associated with IBD; and we explored potentially available oral indicators for predicting diseases. We examined the 16S rRNA V3–V4 region of salivary bacterial DNA from 54 ulcerative colitis (UC), 13 Crohn’s disease (CD), and 25 healthy individuals using Illumina sequencing. Distinctive sample clusters were driven by disease or health based on principal coordinate analysis (PCoA) of both the Operational Taxonomic Unit profile and Kyoto Encyclopedia of Genes and Genomes pathways. Comparisons of taxa abundances revealed enrichment of Streptococcaceae (Streptococcus) and Enterobacteriaceae in UC and Veillonellaceae (Veillonella) in CD, accompanied by depletion of Lachnospiraceae and [Prevotella] in UC and Neisseriaceae (Neisseria) and Haemophilus in CD, most of which have been demonstrated to exhibit the same variation tendencies in the gut of IBD patients. IBD-related oral microorganisms were associated with white blood cells, reduced basic metabolic processes, and increased biosynthesis and transport of substances facilitating oxidative stress and virulence. Furthermore, UC and CD communities showed robust sub-ecotypes that were not demographic or severity-specific, suggesting their value for future applications in precision medicine. Additionally, indicator species analysis revealed several genera indicative of UC and CD, which were confirmed in a longitudinal cohort. Collectively, this study demonstrates evident salivary dysbiosis and different ecotypes in IBD communities and provides an option for identifying at-risk populations, not only enhancing our understanding of the IBD microbiome apart from the gut but also offering a clinically useful strategy to track IBD as saliva can be sampled conveniently and non-invasively.
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Affiliation(s)
- Zhe Xun
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Qian Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China.,National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing, China
| | - Tao Xu
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Ning Chen
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China
| | - Feng Chen
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China.,National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing, China
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384
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Wong SH, Kwong TNY, Wu CY, Yu J. Clinical applications of gut microbiota in cancer biology. Semin Cancer Biol 2018; 55:28-36. [PMID: 29782923 DOI: 10.1016/j.semcancer.2018.05.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/23/2018] [Accepted: 05/14/2018] [Indexed: 12/17/2022]
Abstract
The involvement of microorganisms in cancer has been increasing recognized. Collectively, microorganisms have been estimated to account for ∼20% of all cancers worldwide. Recent advances in metagenomics and bioinformatics have provided new insights on the microbial ecology in different tumors, pinpointing the roles of microorganisms in cancer formation, development and response to treatments. Furthermore, studies have emphasized the importance of host-microbial and inter-microbial interactions in the cancer microbiota. These studies have not only revolutionized our understanding of cancer biology, but also opened up new opportunities for cancer prevention, diagnosis, prognostication and treatment. This review article aims to summarize the microbiota in various cancers and their treatments, and explore clinical applications for such relevance.
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Affiliation(s)
- Sunny H Wong
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region; CUHK Shenzhen Research Institute, Shenzhen, People's Republic of China
| | - Thomas N Y Kwong
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Chun-Ying Wu
- Division of Translational Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei, 11217, Taiwan; School of Medicine, National Yang-Ming University, Taipei, Taiwan; College of Public Health and Graduate Institute of Clinical Medicine, China Medical University, Taichung, Taiwan.
| | - Jun Yu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region; CUHK Shenzhen Research Institute, Shenzhen, People's Republic of China.
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385
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Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer. mSystems 2018; 3:mSystems00205-17. [PMID: 29795787 PMCID: PMC5954203 DOI: 10.1128/msystems.00205-17] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/23/2018] [Indexed: 12/13/2022] Open
Abstract
Recent studies have found an association between colorectal cancer (CRC) and the gut microbiota. One potential mechanism by which the microbiota can influence host physiology is through affecting gene expression in host cells. MicroRNAs (miRNAs) are small noncoding RNA molecules that can regulate gene expression and have important roles in cancer development. Here, we investigated the link between the gut microbiota and the expression of miRNA in CRC. We found that dozens of miRNAs are differentially regulated in CRC tumors and adjacent normal colon and that these miRNAs are correlated with the abundance of microbes in the tumor microenvironment. Moreover, we found that microbes that have been previously associated with CRC are correlated with miRNAs that regulate genes related to interactions with microbes. Notably, these miRNAs likely regulate glycan production, which is important for the recruitment of pathogenic microbial taxa to the tumor. This work provides a first systems-level map of the association between microbes and host miRNAs in the context of CRC and provides targets for further experimental validation and potential interventions. Although variation in gut microbiome composition has been linked with colorectal cancer (CRC), the factors that mediate the interactions between CRC tumors and the microbiome are poorly understood. MicroRNAs (miRNAs) are known to regulate CRC progression and are associated with patient survival outcomes. In addition, recent studies suggested that host miRNAs can also regulate bacterial growth and influence the composition of the gut microbiome. Here, we investigated the association between miRNA expression and microbiome composition in human CRC tumor and normal tissues. We identified 76 miRNAs as differentially expressed (DE) in tissue from CRC tumors and normal tissue, including the known oncogenic miRNAs miR-182, miR-503, and mir-17~92 cluster. These DE miRNAs were correlated with the relative abundances of several bacterial taxa, including Firmicutes, Bacteroidetes, and Proteobacteria. Bacteria correlated with DE miRNAs were enriched with distinct predicted metabolic categories. Additionally, we found that miRNAs that correlated with CRC-associated bacteria are predicted to regulate targets that are relevant for host-microbiome interactions and highlight a possible role for miRNA-driven glycan production in the recruitment of pathogenic microbial taxa. Our work characterized a global relationship between microbial community composition and miRNA expression in human CRC tissues. IMPORTANCE Recent studies have found an association between colorectal cancer (CRC) and the gut microbiota. One potential mechanism by which the microbiota can influence host physiology is through affecting gene expression in host cells. MicroRNAs (miRNAs) are small noncoding RNA molecules that can regulate gene expression and have important roles in cancer development. Here, we investigated the link between the gut microbiota and the expression of miRNA in CRC. We found that dozens of miRNAs are differentially regulated in CRC tumors and adjacent normal colon and that these miRNAs are correlated with the abundance of microbes in the tumor microenvironment. Moreover, we found that microbes that have been previously associated with CRC are correlated with miRNAs that regulate genes related to interactions with microbes. Notably, these miRNAs likely regulate glycan production, which is important for the recruitment of pathogenic microbial taxa to the tumor. This work provides a first systems-level map of the association between microbes and host miRNAs in the context of CRC and provides targets for further experimental validation and potential interventions.
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386
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Osman MA, Neoh HM, Ab Mutalib NS, Chin SF, Jamal R. 16S rRNA Gene Sequencing for Deciphering the Colorectal Cancer Gut Microbiome: Current Protocols and Workflows. Front Microbiol 2018; 9:767. [PMID: 29755427 PMCID: PMC5934490 DOI: 10.3389/fmicb.2018.00767] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/04/2018] [Indexed: 12/15/2022] Open
Abstract
The human gut holds the densest microbiome ecosystem essential in maintaining a healthy host physiology, whereby disruption of this ecosystem has been linked to the development of colorectal cancer (CRC). The advent of next-generation sequencing technologies such as the 16S rRNA gene sequencing has enabled characterization of the CRC gut microbiome architecture in an affordable and culture-free approach. Nevertheless, the lack of standardization in handling and storage of biospecimens, nucleic acid extraction, 16S rRNA gene primer selection, length, and depth of sequencing and bioinformatics analyses have contributed to discrepancies found in various published studies of this field. Accurate characterization of the CRC microbiome found in different stages of CRC has the potential to be developed into a screening tool in the clinical setting. This mini review aims to concisely compile all available CRC microbiome studies performed till end of 2016 and to suggest standardized protocols that are crucial in developing a gut microbiome screening panel for CRC.
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Affiliation(s)
- Muhammad-Afiq Osman
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | | | - Siok-Fong Chin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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387
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Weinroth MD, Carlson CR, Martin JN, Metcalf JL, Morley PS, Belk KE. Rapid Communication: 16S ribosomal ribonucleic acid characterization of liver abscesses in feedlot cattle from three states in the United States. J Anim Sci 2018; 95:4520-4525. [PMID: 29108068 DOI: 10.2527/jas2017.1743] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Liver abscesses are a major economic burden to beef producers. Although a few causative organisms have been cultured from purulent material, the full polymicrobial diversity of liver abscesses has not been reported. The objective of this study was to characterize purulent material collected from liver abscess in beef cattle produced in different production systems in 3 cattle producing states in the United States using 16S rRNA gene sequencing. Differences between purulent material microbial communities among geographic region of feeding and application of a common antimicrobial were also investigated. Cattle included in the study were fed in California (dairy type) and Colorado and Texas (both beef type). Liver abscesses from a cross section of feedlots, geographic areas, and tylosin phosphate-administered groups were collected at harvest; DNA from 34 liver abscess samples was extracted; and the V4 region of the 16S rRNA gene was amplified and sequenced. Sequences were classified into 5 phyla, 13 classes, and 17 orders in the domain Bacteria. The phyla identified included Bacteroidetes (35.2% of reads), Proteobacteria (28.6%), Fusobacteria (18.2%), Firmicutes (12.4%), and Actinobacteria (5.5%). Sequences matching the genera and , which have previously been identified as causative agents in liver abscesses, were both present in the abscess bacterial communities at a relative abundance of 15.1 and 3.2%, respectively, of the overall relative abundance. Furthermore, 3 of the most common phyla were Gram-negative bacteria. An analysis-of-similarities test was conducted on Euclidean distances to assess differences between cattle treated and not treated with tylosin as well as to assess differences between geographic regions. Geographical region and treatment with tylosin did affect the microbiome ( = 0.002 and = 0.026 respectively); however, a more robust sample scheme is needed to explore these differences. To our knowledge, this is the first publication describing the complex community of liver purulent material using next generation sequencing in cattle. These data provide a framework for research on a more targeted approach to liver abscess prevention and treatment.
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388
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Klimesova K, Jiraskova Zakostelska Z, Tlaskalova-Hogenova H. Oral Bacterial and Fungal Microbiome Impacts Colorectal Carcinogenesis. Front Microbiol 2018; 9:774. [PMID: 29731748 PMCID: PMC5920026 DOI: 10.3389/fmicb.2018.00774] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 04/05/2018] [Indexed: 12/31/2022] Open
Abstract
Host's physiology is significantly influenced by microbiota colonizing the epithelial surfaces. Complex microbial communities contribute to proper mucosal barrier function, immune response, and prevention of pathogen invasion and have many other crucial functions. The oral cavity and large intestine are distant parts of the digestive tract, both heavily colonized by commensal microbiota. Nevertheless, they feature different proportions of major bacterial and fungal phyla, mostly due to distinct epithelial layers organization and different oxygen levels. A few obligate anaerobic strains inhabiting the oral cavity are involved in the pathogenesis of oral diseases. Interestingly, these microbiota components are also enriched in gut inflammatory and tumor tissue. An altered microbiota composition - dysbiosis - and formation of polymicrobial biofilms seem to play important roles in the development of oral diseases and colorectal cancer. In this review, we describe the differences in composition of commensal microbiota in the oral cavity and large intestine and the mechanisms by which microbiota affect the inflammatory and carcinogenic response of the host.
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Affiliation(s)
- Klara Klimesova
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the CAS, Prague, Czechia
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389
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Lyu M, Chen J, Jiang Y, Dong W, Fang Z, Li S. KDiamend: a package for detecting key drivers in a molecular ecological network of disease. BMC SYSTEMS BIOLOGY 2018; 12:5. [PMID: 29671403 PMCID: PMC5907152 DOI: 10.1186/s12918-018-0531-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Background Microbial abundance profiles are applied widely to understand diseases from the aspect of microbial communities. By investigating the abundance associations of species or genes, we can construct molecular ecological networks (MENs). The MENs are often constructed by calculating the Pearson correlation coefficient (PCC) between genes. In this work, we also applied multimodal mutual information (MMI) to construct MENs. The members which drive the concerned MENs are referred to as key drivers. Results We proposed a novel method to detect the key drivers. First, we partitioned the MEN into subnetworks. Then we identified the most pertinent subnetworks to the disease by measuring the correlation between the abundance pattern and the delegated phenotype—the variable representing the disease phenotypes. Last, for each identified subnetwork, we detected the key driver by PageRank. We developed a package named KDiamend and applied it to the gut and oral microbial data to detect key drivers for Type 2 diabetes (T2D) and Rheumatoid Arthritis (RA). We detected six T2D-relevant subnetworks and three key drivers of them are related to the carbohydrate metabolic process. In addition, we detected nine subnetworks related to RA, a disease caused by compromised immune systems. The extracted subnetworks include InterPro matches (IPRs) concerned with immunoglobulin, Sporulation, biofilm, Flaviviruses, bacteriophage, etc., while the development of biofilms is regarded as one of the drivers of persistent infections. Conclusion KDiamend is feasible to detect key drivers and offers insights to uncover the development of diseases. The package is freely available at http://www.deepomics.org/pipelines/3DCD6955FEF2E64A/.
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Affiliation(s)
- Mengxuan Lyu
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Hong Kong, China
| | - Jiaxing Chen
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Hong Kong, China
| | - Yiqi Jiang
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Hong Kong, China
| | - Wei Dong
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Hong Kong, China
| | - Zhou Fang
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Hong Kong, China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Hong Kong, China.
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390
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A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks. EBioMedicine 2018; 31:79-91. [PMID: 29669699 PMCID: PMC6013753 DOI: 10.1016/j.ebiom.2018.04.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/14/2018] [Accepted: 04/03/2018] [Indexed: 12/22/2022] Open
Abstract
The International Classification of Diseases (ICD) relies on clinical features and lags behind the current understanding of the molecular specificity of disease pathobiology, necessitating approaches that incorporate growing biomedical data for classifying diseases to meet the needs of precision medicine. Our analysis revealed that the heterogeneous molecular diversity of disease chapters and the blurred boundary between disease categories in ICD should be further investigated. Here, we propose a new classification of diseases (NCD) by developing an algorithm that predicts the additional categories of a disease by integrating multiple networks consisting of disease phenotypes and their molecular profiles. With statistical validations from phenotype-genotype associations and interactome networks, we demonstrate that NCD improves disease specificity owing to its overlapping categories and polyhierarchical structure. Furthermore, NCD captures the molecular diversity of diseases and defines clearer boundaries in terms of both phenotypic similarity and molecular associations, establishing a rational strategy to reform disease taxonomy. The International Classification of Diseases (ICD) lags behind the current molecular characteristics of disease. We quantified the limitations (specificity and blurred boundary) of ICD with integrated phenotypic and molecular profiles. An integrative disease network integrating phenotypic and genotypic profiles proposes a refined disease category framework.
Disease taxonomy is one of the foundations of medical science and healthcare solutions. The most widely used disease taxonomy in clinical settings is the International Classification of Diseases (ICD), a system established >100 years ago and maintained by the World Health Organization to track disease incidence. It is well recognized that ICD, which is based on clinical observations, largely lags behind the molecular achievements of this medical big data era. We quantified the limitations of ICD using integrated phenotypic and molecular profiles and proposed a refined disease taxonomy with possible applications for precision medicine.
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391
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Cao Y, Wu K, Mehta R, Drew DA, Song M, Lochhead P, Nguyen LH, Izard J, Fuchs CS, Garrett WS, Huttenhower C, Ogino S, Giovannucci EL, Chan AT. Long-term use of antibiotics and risk of colorectal adenoma. Gut 2018; 67:672-678. [PMID: 28377387 PMCID: PMC5628103 DOI: 10.1136/gutjnl-2016-313413] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/07/2017] [Accepted: 02/09/2017] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Recent evidence suggests that antibiotic use, which alters the gut microbiome, is associated with an increased risk of colorectal cancer. However, the association between antibiotic use and risk of colorectal adenoma, the precursor for the majority of colorectal cancers, has not been investigated. DESIGN We prospectively evaluated the association between antibiotic use at age 20-39 and 40-59 (assessed in 2004) and recent antibiotic use (assessed in 2008) with risk of subsequent colorectal adenoma among 16 642 women aged ≥60 enrolled in the Nurses' Health Study who underwent at least one colonoscopy through 2010. We used multivariate logistic regression to calculate ORs and 95% CIs. RESULTS We documented 1195 cases of adenoma. Increasing duration of antibiotic use at age 20-39 (ptrend=0.002) and 40-59 (ptrend=0.001) was significantly associated with an increased risk of colorectal adenoma. Compared with non-users, women who used antibiotics for ≥2 months between age 20 and 39 had a multivariable OR of 1.36 (95% CI 1.03 to 1.79). Women who used ≥2 months of antibiotics between age 40 and 59 had a multivariable OR of 1.69 (95% CI 1.24 to 2.31). The associations were similar for low-risk versus high-risk adenomas (size ≥1 cm, or with tubulovillous/villous histology, or ≥3 detected lesions), but appeared modestly stronger for proximal compared with distal adenomas. In contrast, recent antibiotic use within the past four years was not associated with risk of adenoma (ptrend=0.44). CONCLUSIONS Long-term antibiotic use in early-to-middle adulthood was associated with increased risk of colorectal adenoma.
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Affiliation(s)
- Yin Cao
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Kana Wu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Raaj Mehta
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - David A. Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Paul Lochhead
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Long H. Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Jacques Izard
- Food Science and Technology Department, University of Nebraska, Lincoln, NE
| | - Charles S. Fuchs
- Yale Cancer Center, New Haven, CT
- Department of Medicine, Yale School of Medicine, New Haven, CT
- Smilow Cancer Hospital, New Haven, CT
| | - Wendy S. Garrett
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Shuji Ogino
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
- Division of MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Edward L. Giovannucci
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
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392
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Zhou Y, He H, Xu H, Li Y, Li Z, Du Y, He J, Zhou Y, Wang H, Nie Y. Association of oncogenic bacteria with colorectal cancer in South China. Oncotarget 2018; 7:80794-80802. [PMID: 27821805 PMCID: PMC5348355 DOI: 10.18632/oncotarget.13094] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/28/2016] [Indexed: 12/15/2022] Open
Abstract
To quantify Fusobacterium spp., Enterococcus faecalis (E.faecalis), Enterotoxigenic Bacteroides fragilis (ETBF), and Enteropathogenic Escherichia coli in colorectal cancer (CRC) patients and their possible association with CRC clinicopathogical features, we collected the resected tumors and adjacent normal tissues (N) from 97 CRC patients. 48 age- and sex-matched healthy controls (HC) were also recruited. Real-time PCR was used for bacterial quantification. The median abundance ofFusobacterium spp.(p < 0.001, vs. N; p < 0.01,vs. HC), E.faecalis (p < 0.05, vs. N; p < 0.01, vs. HC) and ETBF (p < 0.001, vs. N; p < 0.05,vs. HC) in tumor tissues was significantly higher than that detected in normal tissue and HC. E.faecalis was detected in 95.88% of tumors and 93.81% of adjacent tissues. Fusobacterium spp. was detected in 72.16% of tumors and 67.01% of adjacent tissues. The combined E.faecalis and Fusobacterium spp. were detected in 70.10% of tumors and 36.08% of adjacent normal tissues. All four bacteria were detected in 33.72% and 22.09% of paired tumor and adjacent normal tissues, respectively. E.faecalis and Fusobacterium spp. are enriched in both tumor and adjacent tissue of CRC patients when compared to HC, suggesting that it is possible to be previously undetected changes in the pathohistologically normal colon tissue in the proximity of the tumor.
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Affiliation(s)
- Youlian Zhou
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Hanchang He
- The First People's Foshan Hospital, Chancheng District, Foshan, 528000, Guangdong, China
| | - Haoming Xu
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Yingfei Li
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Zhiming Li
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Yanlei Du
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Jie He
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Yongjian Zhou
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Hong Wang
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
| | - Yuqiang Nie
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, China
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393
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Yang SY, Cho MS, Kim NK. Difference between right-sided and left-sided colorectal cancers: from embryology to molecular subtype. Expert Rev Anticancer Ther 2018; 18:351-358. [PMID: 29458272 DOI: 10.1080/14737140.2018.1442217] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Colorectal cancer is one of the most common malignancies in the world, and it exhibits differences in incidence, pathogenesis, molecular pathways, and outcome depending on the location of the tumor. Differences in the microbiome, clinical characteristics, and chromosomal and molecular characteristics have been reported between the right and left side of the colon. Areas covered: This review focuses on the latest developments in epidemiological and chromosomal and molecular studies, which have enhanced our understanding on the underlying genetic and immunological differences between the right-sided colon and the left-sided colorectum in metastatic colorectal cancer. Expert commentary: The numerous findings regarding differences between right- and left-sided colon cancers should have an impact on colorectal cancer screening and therapy. The location of the colorectal cancer should be considered before group stratification into genetic, clinical, and especially chemotherapy trials. A more tailored approach to colon cancer treatment would be highly desirable if future trials further support the hypothesis of two distinct tumor entities.
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Affiliation(s)
- Seung Yoon Yang
- a Department of Surgery, Severance Hospital , Yonsei University College of Medicine , Seoul , South Korea
| | - Min Soo Cho
- a Department of Surgery, Severance Hospital , Yonsei University College of Medicine , Seoul , South Korea
| | - Nam Kyu Kim
- a Department of Surgery, Severance Hospital , Yonsei University College of Medicine , Seoul , South Korea
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394
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Coleman OI, Haller D. Bacterial Signaling at the Intestinal Epithelial Interface in Inflammation and Cancer. Front Immunol 2018; 8:1927. [PMID: 29354132 PMCID: PMC5760496 DOI: 10.3389/fimmu.2017.01927] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/15/2017] [Indexed: 12/11/2022] Open
Abstract
The gastrointestinal (GI) tract provides a compartmentalized interface with an enormous repertoire of immune and metabolic activities, where the multicellular structure of the mucosa has acquired mechanisms to sense luminal factors, such as nutrients, microbes, and a variety of host-derived and microbial metabolites. The GI tract is colonized by a complex ecosystem of microorganisms, which have developed a highly coevolved relationship with the host’s cellular and immune system. Intestinal epithelial pattern recognition receptors (PRRs) substantially contribute to tissue homeostasis and immune surveillance. The role of bacteria-derived signals in intestinal epithelial homeostasis and repair has been addressed in mouse models deficient in PRRs and signaling adaptors. While critical for host physiology and the fortification of barrier function, the intestinal microbiota poses a considerable health challenge. Accumulating evidence indicates that dysbiosis is associated with the pathogenesis of numerous GI tract diseases, including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). Aberrant signal integration at the epithelial cell level contributes to such diseases. An increased understanding of bacterial-specific structure recognition and signaling mechanisms at the intestinal epithelial interface is of great importance in the translation to future treatment strategies. In this review, we summarize the growing understanding of the regulation and function of the intestinal epithelial barrier, and discuss microbial signaling in the dynamic host–microbe mutualism in both health and disease.
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Affiliation(s)
| | - Dirk Haller
- Technical University of Munich, Munich, Germany.,ZIEL-Institute for Food & Health, Technical University of Munich, Munich, Germany
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395
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Pan P, Oshima K, Huang YW, Yearsley M, Zhang J, Arnold M, Yu J, Wang LS. Gut bacteria are required for the benefits of black raspberries in Apc Min/+ mice. JOURNAL OF BERRY RESEARCH 2018; 8:239-249. [PMID: 30636993 PMCID: PMC6326590 DOI: 10.3233/jbr-180337] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
BACKGROUND The gut microbiota plays a pivotal role in the development of inflammatory bowel disease and colorectal cancer. OBJECTIVE To determine whether the gut microbiota is required for the chemoprotective effects of black raspberries (BRBs) in Apc Min/+ mice. METHODS Apc Min/+ mice were given (a) a control diet for 8 weeks, or (b) the control diet for 4 weeks and then a 5% BRB diet for additional 4 weeks, or (c) the control diet and antibiotics for 4 weeks followed by the 5% BRB diet and antibiotics for the next 4 weeks. At the end of the study, all the mice were euthanized, and colonic and intestinal polyps were counted. mRNA expression levels of TLR4, NF-κB1, and COX2 were determined in colon and small intestine of these Apc Min/+ mice by quantitative real-time PCR. RESULTS 5% BRBs significantly suppressed intestinal and colonic polyp development in the Apc Min/+ mice, whereas antibiotics significantly abolished BRBs' chemoprotective effects. BRBs decreased mRNA levels of TLR4, NF-κB1, and COX2 in colon, whereas significantly enhanced mRNA levels of TLR4 and NF-κB1 were observed in small intestine of BRB-treated Apc Min/+ mice fed antibiotics. CONCLUSIONS The gut microbiota is required for BRBs' chemoprotection against polyp development in Apc Min/+ mice.
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Affiliation(s)
- Pan Pan
- Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kiyoko Oshima
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Martha Yearsley
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Jianying Zhang
- Department of Science of Informatics, Division of Biostatistics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Mark Arnold
- Department of Surgery, The Ohio State University, OH, USA
| | - Jianhua Yu
- Hematologic Malignancies and Stem Cell Transplantation Institute, Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Li-Shu Wang
- Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
- Corresponding author: Li-Shu Wang, Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, RM C4930, 8701 Watertown Plank Rd, Milwaukee, WI, 53226, USA. Tel.: +1 414 955 2827; Fax: +1 414 955 6059; .
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396
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Hussan H, Clinton SK, Roberts K, Bailey MT. Fusobacterium's link to colorectal neoplasia sequenced: A systematic review and future insights. World J Gastroenterol 2017; 23:8626-8650. [PMID: 29358871 PMCID: PMC5752723 DOI: 10.3748/wjg.v23.i48.8626] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/09/2017] [Accepted: 11/08/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To critically evaluate previous scientific evidence on Fusobacterium's role in colorectal neoplasia development. METHODS Two independent investigators systematically reviewed all original scientific articles published between January, 2000, and July, 2017, using PubMed, EMBASE, and MEDLINE. A total of 355 articles were screened at the abstract level. Of these, only original scientific human, animal, and in vitro studies investigating Fusobacterium and its relationship with colorectal cancer (CRC) were included in the analysis. Abstracts, review articles, studies investigating other colonic diseases, and studies written in other languages than English were excluded from our analysis. Ninety articles were included after removing duplicates, resolving disagreements between the two reviewers, and applying the above criteria. RESULTS Studies have consistently identified positive associations between Fusobacterium, especially Fusobacterium nucleatum (F. nucleatum), and CRC. Stronger associations were seen in CRCs proximal to the splenic flexure and CpG island methylator phenotype (CIMP)-high CRCs. There was evidence of temporality and a biological gradient, with increased F. nucleatum DNA detection and quantity along the traditional adenoma-carcinoma sequence and in CIMP-high CRC precursors. Diet may have a differential impact on colonic F. nucleatum enrichment; evidence suggests that high fiber diet may reduce the risk of a subset of CRCs that are F. nucleatum DNA-positive. Data also suggest shorter CRC and disease-specific survival with increased amount of F. nucleatum DNA in CRC tissue. The pathophysiology of enrichment of F. nucleatum and other Fusobacterium species in colonic tissue is unclear; however, the virulence factors and changes to the local colonic environment with disruption of the protective mucus layer may contribute. The presence of a host lectin (Gal-GalNAc) in the colonic epithelium may also mediate F. nucleatum attachment to CRC and precursors through interaction with an F. nucleatum protein, fibroblast activation protein 2 (FAP2). The clinical significance of detection or enrichment of Fusobacterium in colorectal neoplasia is ambiguous, but data suggest a procarcinogenic effect of F. nucleatum, likely due to activation of oncogenic and inflammatory pathways and modulation of the tumor immune environment. This is hypothesized to be mediated by certain F. nucleatum strains carrying invasive properties and virulence factors such as FadA and FAP. CONCLUSION Evidence suggests a potential active role of Fusobacterium, specifically F. nucleatum, in CRC. Future prospective and experimental human studies would fill an important gap in this literature.
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Affiliation(s)
- Hisham Hussan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Steven K Clinton
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Kristen Roberts
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Michael T Bailey
- Department of Pediatrics, OSU College of Medicine And Center for Microbial Pathogenesis, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, United States
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397
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Gut microbiome: a new player in gastrointestinal disease. Virchows Arch 2017; 472:159-172. [PMID: 29243124 PMCID: PMC5849673 DOI: 10.1007/s00428-017-2277-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 02/07/2023]
Abstract
The gastrointestinal (GI) tract harbors a diverse and host-specific gut microbial community. Whereas host-microbe interactions are based on homeostasis and mutualism, the microbiome also contributes to disease development. In this review, we summarize recent findings connecting the GI microbiome with GI disease. Starting with a description of biochemical factors shaping microbial compositions in each gut segment along the longitudinal axis, improved histological techniques enabling high resolution visualization of the spatial microbiome structure are highlighted. Subsequently, inflammatory and neoplastic diseases of the esophagus, stomach, and small and large intestines are discussed and the respective changes in microbiome compositions summarized. Finally, approaches aiming to restore disturbed microbiome compositions thereby promoting health are discussed.
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398
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Bruneau A, Baylatry MT, Joly AC, Sokol H. [Gut microbiota: What impact on colorectal carcinogenesis and treatment?]. Bull Cancer 2017; 105:70-80. [PMID: 29217301 DOI: 10.1016/j.bulcan.2017.10.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023]
Abstract
The gut microbiota, composed of 1014 microorganisms, is now considered as a "hidden organ", regarding to its digestive, metabolic and immune functions, which are helpful to its host. For the last 15 years, advances in molecular biology have highlighted the association of gut microbiota dysbiosis with several diseases, including colorectal cancer. An increased abundance of some bacteria (including Fusobacterium nucleatum, Bacteroides fragilis, Escherichia coli) is associated with cancer, whereas others seem to be protective (Faecalibacterium prausnitzii). Several mechanisms, which are species-specific, are involved in colorectal carcinogenesis. Most of the time, bacterial toxins are involved in pro-inflammatory processes and in activation of angiogenesis and cellular proliferation pathways. The identification of these bacteria leads to envisage the gut microbiota as potential screening tool for colorectal cancer. Recent studies showed a relation between the gut microbiota and the efficacy and toxicity of chemotherapies (oxaliplatin, irinotecan) and immunotherapies (including ipilimumab). Therapeutic approaches targeting the gut microbiota are now available (probiotics, fecal microbiota transplantation…). New therapeutic strategy combining both chemotherapy and/or immunotherapy with an adjuvant treatment targeting the gut microbiota can now be developed in order to improve treatment response and tolerance.
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Affiliation(s)
- Antoine Bruneau
- AP-HP, hôpital Saint-Antoine, pharmacie hospitaliere, 184, rue du faubourg Saint-Antoine, 75012 Paris, France
| | - Minh-Tam Baylatry
- AP-HP, hôpital Saint-Antoine, pharmacie hospitaliere, 184, rue du faubourg Saint-Antoine, 75012 Paris, France
| | - Anne Christine Joly
- AP-HP, hôpital Saint-Antoine, pharmacie hospitaliere, 184, rue du faubourg Saint-Antoine, 75012 Paris, France
| | - Harry Sokol
- AP-HP, hôpital Saint-Antoine, service de gastro-entérologie et nutrition, 184, rue du faubourg Saint-Antoine, 75571 Paris, France.
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399
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Lam SY, Yu J, Wong SH, Peppelenbosch MP, Fuhler GM. The gastrointestinal microbiota and its role in oncogenesis. Best Pract Res Clin Gastroenterol 2017; 31:607-618. [PMID: 29566903 DOI: 10.1016/j.bpg.2017.09.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 09/03/2017] [Indexed: 02/07/2023]
Abstract
Advances in research techniques have made it possible to map the microbial communities in the gastrointestinal (GI) tract, where the majority of bacteria in the human body reside. Disturbances in these communities are referred to as dysbiosis and have been associated with GI cancers. Although dysbiosis is observed in several GI malignancies, the specific role of these changes has not been understood to the extent of Helicobacter pylori (HP) in gastric cancer (GC). This review will address the bacterial communities along the GI tract, from the oral cavity to the anal canal, particularly focusing on bacterial dysbiosis and carcinogenesis. Just as non-HP bacteria in the stomach may interact with HP in gastric carcinogenesis, the same may hold true for other GI tract malignancies, where an interplay between microbes in carcinogenesis seems conceivable, especially in colorectal cancer (CRC). In the last part of this review we will discuss the potential mechanisms of bacterial dysbiosis in GI carcinogenesis.
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Affiliation(s)
- S Y Lam
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - J Yu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences and CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong.
| | - S H Wong
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences and CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong.
| | - M P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - G M Fuhler
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
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400
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Affiliation(s)
- Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida; Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida; Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida.
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