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Drewes JL, Chen J, Markham NO, Knippel RJ, Domingue JC, Tam AJ, Chan JL, Kim L, McMann M, Stevens C, Dejea CM, Tomkovich S, Michel J, White JR, Mohammad F, Campodónico VL, Heiser CN, Wu X, Wu S, Ding H, Simner P, Carroll K, Shrubsole MJ, Anders RA, Walk ST, Jobin C, Wan F, Coffey RJ, Housseau F, Lau KS, Sears CL. Human Colon Cancer-Derived Clostridioides difficile Strains Drive Colonic Tumorigenesis in Mice. Cancer Discov 2022; 12:1873-1885. [PMID: 35678528 PMCID: PMC9357196 DOI: 10.1158/2159-8290.cd-21-1273] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 04/19/2022] [Accepted: 06/07/2022] [Indexed: 01/27/2023]
Abstract
Defining the complex role of the microbiome in colorectal cancer and the discovery of novel, protumorigenic microbes are areas of active investigation. In the present study, culturing and reassociation experiments revealed that toxigenic strains of Clostridioides difficile drove the tumorigenic phenotype of a subset of colorectal cancer patient-derived mucosal slurries in germ-free ApcMin/+ mice. Tumorigenesis was dependent on the C. difficile toxin TcdB and was associated with induction of Wnt signaling, reactive oxygen species, and protumorigenic mucosal immune responses marked by the infiltration of activated myeloid cells and IL17-producing lymphoid and innate lymphoid cell subsets. These findings suggest that chronic colonization with toxigenic C. difficile is a potential driver of colorectal cancer in patients. SIGNIFICANCE Colorectal cancer is a leading cause of cancer and cancer-related deaths worldwide, with a multifactorial etiology that likely includes procarcinogenic bacteria. Using human colon cancer specimens, culturing, and murine models, we demonstrate that chronic infection with the enteric pathogen C. difficile is a previously unrecognized contributor to colonic tumorigenesis. See related commentary by Jain and Dudeja, p. 1838. This article is highlighted in the In This Issue feature, p. 1825.
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Affiliation(s)
- Julia L. Drewes
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jie Chen
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Baltimore, Maryland
| | - Nicholas O. Markham
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Reece J. Knippel
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jada C. Domingue
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ada J. Tam
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - June L. Chan
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lana Kim
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Madison McMann
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Courtney Stevens
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christine M. Dejea
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sarah Tomkovich
- Department of Medicine, University of Florida, Gainesville, Florida
| | - John Michel
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Fuad Mohammad
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Victoria L. Campodónico
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Cody N. Heiser
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Cell and Developmental Biology and Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Xinqun Wu
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shaoguang Wu
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hua Ding
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Baltimore, Maryland
| | - Patricia Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Karen Carroll
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Martha J. Shrubsole
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Robert A. Anders
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Seth T. Walk
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, Florida
| | - Fengyi Wan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Robert J. Coffey
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee
| | - Franck Housseau
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ken S. Lau
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Cell and Developmental Biology and Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee
| | - Cynthia L. Sears
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Lapp Z, Sovacool KL, Lesniak N, King D, Barnier C, Flickinger M, Krüger J, Armour CR, Lapp MM, Tallant J, Diao R, Oneka M, Tomkovich S, Anderson JM, Lucas SK, Schloss PD. Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research. JOSE 2022; 5. [PMID: 35224460 PMCID: PMC8872090 DOI: 10.21105/jose.00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Inspired by well-established material and pedagogy provided by The Carpentries (Wilson, 2016), we developed a two-day workshop curriculum that teaches introductory R programming for managing, analyzing, plotting and reporting data using packages from the tidyverse (Wickham et al., 2019), the Unix shell, version control with git, and GitHub. While the official Software Carpentry curriculum is comprehensive, we found that it contains too much content for a two-day workshop. We also felt that the independent nature of the lessons left learners confused about how to integrate the newly acquired programming skills in their own work. Thus, we developed a new curriculum that aims to teach novices how to implement reproducible research principles in their own data analysis. The curriculum integrates live coding lessons with individual-level and group-based practice exercises, and also serves as a succinct resource that learners can reference both during and after the workshop. Moreover, it lowers the entry barrier for new instructors as they do not have to develop their own teaching materials or sift through extensive content. We developed this curriculum during a two-day sprint, successfully used it to host a two-day virtual workshop with almost 40 participants, and updated the material based on instructor and learner feedback. We hope that our new curriculum will prove useful to future instructors interested in teaching workshops with similar learning objectives.
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Affiliation(s)
- Zena Lapp
- Department of Computational Medicine & Bioinformatics, University of Michigan
| | - Kelly L Sovacool
- Department of Computational Medicine & Bioinformatics, University of Michigan
| | - Nick Lesniak
- Department of Microbiology & Immunology, University of Michigan
| | - Dana King
- BRCF Bioinformatics Core, University of Michigan
| | - Catherine Barnier
- Department of Computational Medicine & Bioinformatics, University of Michigan
| | | | - Jule Krüger
- Center for Political Studies, Institute for Social Research, University of Michigan
| | | | | | | | - Rucheng Diao
- Department of Computational Medicine & Bioinformatics, University of Michigan
| | - Morgan Oneka
- Department of Computational Medicine & Bioinformatics, University of Michigan
| | - Sarah Tomkovich
- Department of Microbiology & Immunology, University of Michigan
| | | | - Sarah K Lucas
- Department of Microbiology & Immunology, University of Michigan
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3
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Hagan AK, Lesniak NA, Balunas MJ, Bishop L, Close WL, Doherty MD, Elmore AG, Flynn KJ, Hannigan GD, Koumpouras CC, Jenior ML, Kozik AJ, McBride K, Rifkin SB, Stough JMA, Sovacool KL, Sze MA, Tomkovich S, Topcuoglu BD, Schloss PD. Ten simple rules to increase computational skills among biologists with Code Clubs. PLoS Comput Biol 2020; 16:e1008119. [PMID: 32853198 PMCID: PMC7451508 DOI: 10.1371/journal.pcbi.1008119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Ada K. Hagan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nicholas A. Lesniak
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Marcy J. Balunas
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Lucas Bishop
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - William L. Close
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Matthew D. Doherty
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Amanda G. Elmore
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kaitlin J. Flynn
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Geoffrey D. Hannigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Charlie C. Koumpouras
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Matthew L. Jenior
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ariangela J. Kozik
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kathryn McBride
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Samara B. Rifkin
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Joshua M. A. Stough
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kelly L. Sovacool
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Marc A. Sze
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sarah Tomkovich
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Begum D. Topcuoglu
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Patrick D. Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
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4
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Tomkovich S, Gharaibeh RZ, Dejea CM, Pope JL, Jiang J, Winglee K, Gauthier J, Newsome RC, Yang Y, Fodor AA, Schmittgen TD, Sears CL, Jobin C. Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer. mSystems 2020; 5:e00451-19. [PMID: 31937674 PMCID: PMC6967385 DOI: 10.1128/msystems.00451-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/21/2019] [Indexed: 01/09/2023] Open
Abstract
Disrupted interactions between host and intestinal bacteria are implicated in colorectal cancer (CRC) development. However, activities derived from these bacteria and their interplay with the host are unclear. Here, we examine this interplay by performing mouse and microbiota RNA sequencing on colon tissues and 16S and small RNA sequencing on stools from germfree (GF) and gnotobiotic ApcMin Δ 850/+ ;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BF+T) and biofilm-negative healthy (BF-bx) tissues. The bacteria in BF+T mice differentially expressed (DE) >2,900 genes, including genes related to bacterial secretion, virulence, and biofilms but affected only 62 host genes. Small RNA sequencing of stools from these cohorts revealed eight significant DE host microRNAs (miRNAs) based on biofilm status and several miRNAs that correlated with bacterial taxon abundances. Additionally, computational predictions suggest that some miRNAs preferentially target bacterial genes while others primarily target mouse genes. 16S rRNA sequencing of mice that were reassociated with mucosa-associated communities from the initial association revealed a set of 13 bacterial genera associated with cancer that were maintained regardless of whether the reassociation inoculums were initially obtained from murine proximal or distal colon tissues. Our findings suggest that complex interactions within bacterial communities affect host-derived miRNA, bacterial composition, and CRC development.IMPORTANCE Bacteria and bacterial biofilms have been implicated in colorectal cancer (CRC), but it is still unclear what genes these microbial communities express and how they influence the host. MicroRNAs regulate host gene expression and have been explored as potential biomarkers for CRC. An emerging area of research is the ability of microRNAs to impact growth and gene expression of members of the intestinal microbiota. This study examined the bacteria and bacterial transcriptome associated with microbes derived from biofilm-positive human cancers that promoted tumorigenesis in a murine model of CRC. The murine response to different microbial communities (derived from CRC patients or healthy people) was evaluated through RNA and microRNA sequencing. We identified a complex interplay between biofilm-associated bacteria and the host during CRC in mice. These findings may lead to the development of new biomarkers and therapeutics for identifying and treating biofilm-associated CRCs.
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Affiliation(s)
- Sarah Tomkovich
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Raad Z Gharaibeh
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Christine M Dejea
- Bloomberg-Kimmel Institute of Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- Department of Oncology and Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jillian L Pope
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jinmai Jiang
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Kathryn Winglee
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Josee Gauthier
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Rachel C Newsome
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Ye Yang
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Anthony A Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Thomas D Schmittgen
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Cynthia L Sears
- Bloomberg-Kimmel Institute of Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- Department of Oncology and Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida, USA
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, Florida, USA
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5
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Tomkovich S, Dejea CM, Winglee K, Drewes JL, Chung L, Housseau F, Pope JL, Gauthier J, Sun X, Mühlbauer M, Liu X, Fathi P, Anders RA, Besharati S, Perez-Chanona E, Yang Y, Ding H, Wu X, Wu S, White JR, Gharaibeh RZ, Fodor AA, Wang H, Pardoll DM, Jobin C, Sears CL. Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic. J Clin Invest 2019; 129:1699-1712. [PMID: 30855275 DOI: 10.1172/jci124196] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/01/2019] [Indexed: 12/13/2022] Open
Abstract
Mucus-invasive bacterial biofilms are identified on the colon mucosa of approximately 50% of colorectal cancer (CRC) patients and approximately 13% of healthy subjects. Here, we test the hypothesis that human colon biofilms comprise microbial communities that are carcinogenic in CRC mouse models. Homogenates of human biofilm-positive colon mucosa were prepared from tumor patients (tumor and paired normal tissues from surgical resections) or biofilm-positive biopsies from healthy individuals undergoing screening colonoscopy; homogenates of biofilm-negative colon biopsies from healthy individuals undergoing screening colonoscopy served as controls. After 12 weeks, biofilm-positive, but not biofilm-negative, human colon mucosal homogenates induced colon tumor formation in 3 mouse colon tumor models (germ-free ApcMinΔ850/+;Il10-/- or ApcMinΔ850/+ and specific pathogen-free ApcMinΔ716/+ mice). Remarkably, biofilm-positive communities from healthy colonoscopy biopsies induced colon inflammation and tumors similarly to biofilm-positive tumor tissues. By 1 week, biofilm-positive human tumor homogenates, but not healthy biopsies, displayed consistent bacterial mucus invasion and biofilm formation in mouse colons. 16S rRNA gene sequencing and RNA-Seq analyses identified compositional and functional microbiota differences between mice colonized with biofilm-positive and biofilm-negative communities. These results suggest human colon mucosal biofilms, whether from tumor hosts or healthy individuals undergoing screening colonoscopy, are carcinogenic in murine models of CRC.
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Affiliation(s)
- Sarah Tomkovich
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Christine M Dejea
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Kathryn Winglee
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Julia L Drewes
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Liam Chung
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Franck Housseau
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Jillian L Pope
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Josee Gauthier
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Xiaolun Sun
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Marcus Mühlbauer
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Xiuli Liu
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Payam Fathi
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Robert A Anders
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sepideh Besharati
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Ye Yang
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Hua Ding
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Xinqun Wu
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Shaoguang Wu
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | | | - Raad Z Gharaibeh
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Anthony A Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Hao Wang
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Drew M Pardoll
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida, USA.,Department of Infectious Diseases and Immunology, University of Florida, Gainesville, Florida, USA
| | - Cynthia L Sears
- Bloomberg-Kimmel Institute for Immunotherapy, Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
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6
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He Z, Gharaibeh RZ, Newsome RC, Pope JL, Dougherty MW, Tomkovich S, Pons B, Mirey G, Vignard J, Hendrixson DR, Jobin C. Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin. Gut 2019; 68:289-300. [PMID: 30377189 PMCID: PMC6352414 DOI: 10.1136/gutjnl-2018-317200] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/12/2018] [Accepted: 10/04/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Campylobacter jejuni produces a genotoxin, cytolethal distending toxin (CDT), which has DNAse activity and causes DNA double-strand breaks. Although C. jejuni infection has been shown to promote intestinal inflammation, the impact of this bacterium on carcinogenesis has never been examined. DESIGN Germ-free (GF) ApcMin/+ mice, fed with 1% dextran sulfate sodium, were used to test tumorigenesis potential of CDT-producing C. jejuni. Cells and enteroids were exposed to bacterial lysates to determine DNA damage capacity via γH2AX immunofluorescence, comet assay and cell cycle assay. To examine the interplay of CDT-producing C. jejuni, gut microbiome and host in tumorigenesis, colonic RNA-sequencing and faecal 16S rDNA sequencing were performed. Rapamycin was administrated to investigate the prevention of CDT-producing C. jejuni-induced tumorigenesis. RESULTS GF ApcMin/+ mice colonised with human clinical isolate C. jejuni81-176 developed significantly more and larger tumours when compared with uninfected mice. C. jejuni with a mutated cdtB subunit, mutcdtB, attenuated C. jejuni-induced tumorigenesis in vivo and decreased DNA damage response in cells and enteroids. C. jejuni infection induced expression of hundreds of colonic genes, with 22 genes dependent on the presence of cdtB. The C. jejuni-infected group had a significantly different microbial gene expression profile compared with the mutcdtB group as shown by metatranscriptomic data, and different microbial communities as measured by 16S rDNA sequencing. Finally, rapamycin could diminish the tumorigenic capability of C. jejuni. CONCLUSION Human clinical isolate C. jejuni 81-176 promotes colorectal cancer and induces changes in microbial composition and transcriptomic responses, a process dependent on CDT production.
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Affiliation(s)
- Zhen He
- Department of Medicine, University of Florida, Gainesville, Florida, USA,Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Raad Z Gharaibeh
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Rachel C Newsome
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jllian L Pope
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | | | - Sarah Tomkovich
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Benoit Pons
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP- Purpan, UPS, Toulouse, France
| | - Gladys Mirey
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP- Purpan, UPS, Toulouse, France
| | - Julien Vignard
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP- Purpan, UPS, Toulouse, France
| | - David R Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida, USA,Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida, USA,Department of Infectious Diseases and Immunology, University of Florida, Gainesville, Florida, USA
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7
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Tomkovich S, Yang Y, Winglee K, Gauthier J, Mühlbauer M, Sun X, Mohamadzadeh M, Liu X, Martin P, Wang GP, Oswald E, Fodor AA, Jobin C. Locoregional Effects of Microbiota in a Preclinical Model of Colon Carcinogenesis. Cancer Res 2017; 77:2620-2632. [PMID: 28416491 DOI: 10.1158/0008-5472.can-16-3472] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/31/2017] [Accepted: 03/15/2017] [Indexed: 02/07/2023]
Abstract
Inflammation and microbiota are critical components of intestinal tumorigenesis. To dissect how the microbiota contributes to tumor distribution, we generated germ-free (GF) ApcMin/+ and ApcMin/+ ;Il10-/- mice and exposed them to specific-pathogen-free (SPF) or colorectal cancer-associated bacteria. We found that colon tumorigenesis significantly correlated with inflammation in SPF-housed ApcMin/+ ;Il10-/- , but not in ApcMin/+ mice. In contrast, small intestinal neoplasia development significantly correlated with age in both ApcMin/+ ;Il10-/- and ApcMin/+ mice. GF ApcMin/+ ;Il10-/- mice conventionalized by an SPF microbiota had significantly more colon tumors compared with GF mice. Gnotobiotic studies revealed that while Fusobacterium nucleatum clinical isolates with FadA and Fap2 adhesins failed to induce inflammation and tumorigenesis, pks+Escherichia coli promoted tumorigenesis in the ApcMin/+ ;Il10-/- model in a colibactin-dependent manner, suggesting colibactin is a driver of carcinogenesis. Our results suggest a distinct etiology of cancers in different locations of the gut, where colon cancer is primarily driven by inflammation and the microbiome, while age is a driving force for small intestine cancer. Cancer Res; 77(10); 2620-32. ©2017 AACR.
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Affiliation(s)
- Sarah Tomkovich
- Department of Medicine, University of Florida, Gainesville, Florida.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ye Yang
- Department of Medicine, University of Florida, Gainesville, Florida
| | - Kathryn Winglee
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina
| | - Josee Gauthier
- Department of Medicine, University of Florida, Gainesville, Florida
| | - Marcus Mühlbauer
- Department of Medicine, University of Florida, Gainesville, Florida
| | - Xiaolun Sun
- Department of Medicine, University of Florida, Gainesville, Florida
| | - Mansour Mohamadzadeh
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida
| | - Xiuli Liu
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida
| | - Patricia Martin
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France.,CHU Toulouse, Service de Bactériologie-Hygiène, Toulouse, France
| | - Gary P Wang
- Department of Medicine, Division of Infectious Diseases and Global Medicine, University of Florida, Gainesville, Florida
| | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France.,CHU Toulouse, Service de Bactériologie-Hygiène, Toulouse, France
| | - Anthony A Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida. .,Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida
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8
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Pope JL, Tomkovich S, Yang Y, Jobin C. Microbiota as a mediator of cancer progression and therapy. Transl Res 2017; 179:139-154. [PMID: 27554797 PMCID: PMC5674984 DOI: 10.1016/j.trsl.2016.07.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/18/2016] [Accepted: 07/20/2016] [Indexed: 12/19/2022]
Abstract
Complex and intricate circuitries regulate cellular proliferation, survival, and growth, and alterations of this network through genetic and epigenetic events result in aberrant cellular behaviors, often leading to carcinogenesis. Although specific germline mutations have been recognized as cancer inducers, the vast majority of neoplastic changes in humans occur through environmental exposure, lifestyle, and diet. An emerging concept in cancer biology implicates the microbiota as a powerful environmental factor modulating the carcinogenic process. For example, the intestinal microbiota influences cancer development or therapeutic responses through specific activities (immune responses, metabolites, microbial structures, and toxins). The numerous effects of microbiota on carcinogenesis, ranging from promoting, preventing, or even influencing therapeutic outcomes, highlight the complex relationship between the biota and the host. In this review, we discuss the latest findings on this complex microbial interaction with the host and highlight potential mechanisms by which the microbiota mediates such a wide impact on carcinogenesis.
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Affiliation(s)
- Jillian L Pope
- Department of Medicine, University of Florida, Gainesville, Fla
| | - Sarah Tomkovich
- Department of Medicine, University of Florida, Gainesville, Fla; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ye Yang
- Department of Medicine, University of Florida, Gainesville, Fla
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Fla; Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Fla.
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9
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Abstract
This chapter describes a method to assay compounds modulating NSAID-induced intestinal injury in zebrafish larvae. The assay employs the NSAID glafenine, which causes intestinal epithelial cell damage and death by inducing organelle stress responses (endoplasmic reticulum and mitochondrial) and blocking the unfolded protein response pathway. This epithelial damage includes sloughing of intestinal cells into the lumen and out the cloaca of the zebrafish larvae. Exposing larvae to acridine orange highlights this injury when visualized under fluorescence microscope; injured fish develop intensely red-staining intestines, as well as a "tube" or cord of red color extending through the intestine and out the cloaca. Using this rapid visually screenable method, various candidate compounds were successfully tested for their ability to prevent glafenine-induced intestinal injury. Because this assay involves examination of larval zebrafish intestinal pathology, we have also included our protocol for preparation and analysis of zebrafish histology. The protocol includes numerous steps to generate high-quality zebrafish histology slides, as well as protocols to establish accurate anatomic localization of any given tissue cross-section-processes that are made technically difficult by the small size of zebrafish larvae.
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Affiliation(s)
- Jason R Goldsmith
- Department of Internal Medicine, University of Michigan, 1500 E Medical Center Drive, Ann Arbor, 48109, MI, USA
| | - Sarah Tomkovich
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27713, USA.,Division of Gastroenterology, Department of Medicine, College of Medicine, University of Florida, CGRC, 2033 Mowry Rd, Office 461, P.O. Box 103633, 32610, Gainesville, FL, 32611-0882, USA
| | - Christian Jobin
- Division of Gastroenterology, Department of Medicine, College of Medicine, University of Florida, CGRC, 2033 Mowry Rd, Office 461, P.O. Box 103633, 32610, Gainesville, FL, 32611-0882, USA.
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10
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Tomkovich S, Jobin C. Microbiota and host immune responses: a love-hate relationship. Immunology 2015; 147:1-10. [PMID: 26439191 DOI: 10.1111/imm.12538] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/09/2015] [Accepted: 09/18/2015] [Indexed: 12/13/2022] Open
Abstract
A complex relationship between the microbiota and the host emerges early at birth and continues throughout life. The microbiota includes the prokaryotes, viruses and eukaryotes living among us, all of which interact to different extents with various organs and tissues in the body, including the immune system. Although the microbiota is most dense in the lower intestine, its influence on host immunity extends beyond the gastrointestinal tract. These interactions with the immune system operate through the actions of various microbial structures and metabolites, with outcomes ranging from beneficial to deleterious for the host. These differential outcomes are dictated by host factors, environment, and the type of microbes or products present in a specific ecosystem. It is also becoming clear that the microbes are in turn affected and respond to the host immune system. Disruption of this complex dialogue between host and microbiota can lead to immune pathologies such as inflammatory bowel diseases, diabetes and obesity. This review will discuss recent advances regarding the ways in which the host immune system and microbiota interact and communicate with one another.
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Affiliation(s)
- Sarah Tomkovich
- Department of Medicine, University of Florida, Gainesville, FL, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL, USA.,Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL, USA
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11
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Abstract
Understanding a complex pathology such as inflammatory bowel disease, where host genetics (innate and adaptive immunity, barrier function) and environmental factors (microbes, diet, and stress) interact together to influence disease onset and severity, requires multipronged approaches to model these numerous variables. Researchers have typically relied on preclinical models of mouse and rat origin to push the boundary of knowledge further. However, incorporation of novel vertebrate models may contribute to new knowledge on specific aspects of intestinal homeostasis. An emerging literature has seen the use of zebrafish as a novel animal system to study key aspects of host-microbe interactions in the intestine. In this review, we briefly introduce components of host-microbiota interplay in the developing zebrafish intestine and summarize key lessons learned from this animal system; review important chemically induced and genetically engineered zebrafish models of intestinal immune disorders; and discuss perspectives and limitations of the zebrafish model system.
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Affiliation(s)
- Ye Yang
- Department of Medicine, University of Florida, Gainesville, Florida
| | - Sarah Tomkovich
- Department of Medicine, University of Florida, Gainesville, Florida,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida,Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida
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12
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Kanther M, Tomkovich S, Xiaolun S, Grosser MR, Koo J, Flynn EJ, Jobin C, Rawls JF. Commensal microbiota stimulate systemic neutrophil migration through induction of serum amyloid A. Cell Microbiol 2014; 16:1053-67. [PMID: 24373309 DOI: 10.1111/cmi.12257] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 12/18/2022]
Abstract
Neutrophils serve critical roles in inflammatory responses to infection and injury, and mechanisms governing their activity represent attractive targets for controlling inflammation. The commensal microbiota is known to regulate the activity of neutrophils and other leucocytes in the intestine, but the systemic impact of the microbiota on neutrophils remains unknown. Here we utilized in vivo imaging in gnotobiotic zebrafish to reveal diverse effects of microbiota colonization on systemic neutrophil development and function. The presence of a microbiota resulted in increased neutrophil number and myeloperoxidase expression, and altered neutrophil localization and migratory behaviours. These effects of the microbiota on neutrophil homeostasis were accompanied by an increased recruitment of neutrophils to injury. Genetic analysis identified the microbiota-induced acute phase protein serum amyloid A (Saa) as a host factor mediating microbial stimulation of tissue-specific neutrophil migratory behaviours. In vitro studies revealed that zebrafish cells respond to Saa exposure by activating NF-κB, and that Saa-dependent neutrophil migration requires NF-κB-dependent gene expression. These results implicate the commensal microbiota as an important environmental factor regulating diverse aspects of systemic neutrophil development and function, and reveal a critical role for a Saa-NF-κB signalling axis in mediating neutrophil migratory responses.
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Affiliation(s)
- Michelle Kanther
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, 27599, USA
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13
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Arthur JC, Gharaibeh RZ, Uronis JM, Perez-Chanona E, Sha W, Tomkovich S, Mühlbauer M, Fodor AA, Jobin C. VSL#3 probiotic modifies mucosal microbial composition but does not reduce colitis-associated colorectal cancer. Sci Rep 2013; 3:2868. [PMID: 24100376 PMCID: PMC3792409 DOI: 10.1038/srep02868] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/18/2013] [Indexed: 02/07/2023] Open
Abstract
Although probiotics have shown success in preventing the development of experimental colitis-associated colorectal cancer (CRC), beneficial effects of interventional treatment are relatively unknown. Here we show that interventional treatment with VSL#3 probiotic alters the luminal and mucosally-adherent microbiota, but does not protect against inflammation or tumorigenesis in the azoxymethane (AOM)/Il10⁻/⁻ mouse model of colitis-associated CRC. VSL#3 (10⁹ CFU/animal/day) significantly enhanced tumor penetrance, multiplicity, histologic dysplasia scores, and adenocarcinoma invasion relative to VSL#3-untreated mice. Illumina 16S sequencing demonstrated that VSL#3 significantly decreased (16-fold) the abundance of a bacterial taxon assigned to genus Clostridium in the mucosally-adherent microbiota. Mediation analysis by linear models suggested that this taxon was a contributing factor to increased tumorigenesis in VSL#3-fed mice. We conclude that VSL#3 interventional therapy can alter microbial community composition and enhance tumorigenesis in the AOM/Il10⁻/⁻ model.
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Affiliation(s)
| | - Raad Z. Gharaibeh
- Bioinformatics Services Division, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Kannapolis, NC 28081, USA
| | | | | | - Wei Sha
- Bioinformatics Services Division, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Kannapolis, NC 28081, USA
| | - Sarah Tomkovich
- Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Anthony A. Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Christian Jobin
- Department of Medicine, Chapel Hill, NC 27599, USA
- Pharmacology, Chapel Hill, NC 27599, USA
- Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Medicine, University of Florida at Gainesville, Gainesville, FL32611, USA
- Department of Infectious Diseases and Pathology, University of Florida at Gainesville, Gainesville, FL32611, USA
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14
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Arthur JC, Perez-Chanona E, Mühlbauer M, Tomkovich S, Uronis JM, Fan TJ, Campbell BJ, Abujamel T, Dogan B, Rogers AB, Rhodes JM, Stintzi A, Simpson KW, Hansen JJ, Keku TO, Fodor AA, Jobin C. Intestinal inflammation targets cancer-inducing activity of the microbiota. Science 2012; 338:120-3. [PMID: 22903521 DOI: 10.1126/science.1224820] [Citation(s) in RCA: 1489] [Impact Index Per Article: 124.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Inflammation alters host physiology to promote cancer, as seen in colitis-associated colorectal cancer (CRC). Here, we identify the intestinal microbiota as a target of inflammation that affects the progression of CRC. High-throughput sequencing revealed that inflammation modifies gut microbial composition in colitis-susceptible interleukin-10-deficient (Il10(-/-)) mice. Monocolonization with the commensal Escherichia coli NC101 promoted invasive carcinoma in azoxymethane (AOM)-treated Il10(-/-) mice. Deletion of the polyketide synthase (pks) genotoxic island from E. coli NC101 decreased tumor multiplicity and invasion in AOM/Il10(-/-) mice, without altering intestinal inflammation. Mucosa-associated pks(+) E. coli were found in a significantly high percentage of inflammatory bowel disease and CRC patients. This suggests that in mice, colitis can promote tumorigenesis by altering microbial composition and inducing the expansion of microorganisms with genotoxic capabilities.
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Affiliation(s)
- Janelle C Arthur
- Department of Medicine, Pharmacology and Immunology-Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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