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Liu Z, Zhang Q, Zhang H, Yi Z, Ma H, Wang X, Wang J, Liu Y, Zheng Y, Fang W, Huang P, Liu X. Colorectal cancer microbiome programs DNA methylation of host cells by affecting methyl donor metabolism. Genome Med 2024; 16:77. [PMID: 38840170 PMCID: PMC11151592 DOI: 10.1186/s13073-024-01344-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 05/09/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) arises from complex interactions between host and environment, which include the gut and tissue microbiome. It is hypothesized that epigenetic regulation by gut microbiota is a fundamental interface by which commensal microbes dynamically influence intestinal biology. The aim of this study is to explore the interplay between gut and tissue microbiota and host DNA methylation in CRC. METHODS Metagenomic sequencing of fecal samples was performed on matched CRC patients (n = 18) and healthy controls (n = 18). Additionally, tissue microbiome was profiled with 16S rRNA gene sequencing on tumor (n = 24) and tumor-adjacent normal (n = 24) tissues of CRC patients, while host DNA methylation was assessed through whole-genome bisulfite sequencing (WGBS) in a subset of 13 individuals. RESULTS Our analysis revealed substantial alterations in the DNA methylome of CRC tissues compared to adjacent normal tissues. An extensive meta-analysis, incorporating publicly available and in-house data, identified significant shifts in microbial-derived methyl donor-related pathways between tumor and adjacent normal tissues. Of note, we observed a pronounced enrichment of microbial-associated CpGs within the promoter regions of genes in adjacent normal tissues, a phenomenon notably absent in tumor tissues. Furthermore, we established consistent and recurring associations between methylation patterns of tumor-related genes and specific bacterial taxa. CONCLUSIONS This study emphasizes the pivotal role of the gut microbiota and pathogenic bacteria in dynamically shaping DNA methylation patterns, impacting physiological homeostasis, and contributing to CRC tumorigenesis. These findings provide valuable insights into the intricate host-environment interactions in CRC development and offer potential avenues for therapeutic interventions in this disease.
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Affiliation(s)
- Zhi Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Qingqing Zhang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Hong Zhang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Zhongyuan Yi
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Huihui Ma
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xiaoyi Wang
- Core Facility Center, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, China
| | - Jingjing Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215008, China
| | - Yang Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yi Zheng
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weijia Fang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Ping Huang
- Department of Surgery, The Third Affiliated Hospital, Nanjing Medical University, Nanjing, 211166, China.
| | - Xingyin Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China.
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215008, China.
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Cai L, Zhu H, Mou Q, Wong PY, Lan L, Ng CWK, Lei P, Cheung MK, Wang D, Wong EWY, Lau EHL, Yeung ZWC, Lai R, Meehan K, Fung S, Chan KCA, Lui VWY, Cheng ASL, Yu J, Chan PKS, Chan JYK, Chen Z. Integrative analysis reveals associations between oral microbiota dysbiosis and host genetic and epigenetic aberrations in oral cavity squamous cell carcinoma. NPJ Biofilms Microbiomes 2024; 10:39. [PMID: 38589501 PMCID: PMC11001959 DOI: 10.1038/s41522-024-00511-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
Dysbiosis of the human oral microbiota has been reported to be associated with oral cavity squamous cell carcinoma (OSCC) while the host-microbiota interactions with respect to the potential impact of pathogenic bacteria on host genomic and epigenomic abnormalities remain poorly studied. In this study, the mucosal bacterial community, host genome-wide transcriptome and DNA CpG methylation were simultaneously profiled in tumors and their adjacent normal tissues of OSCC patients. Significant enrichment in the relative abundance of seven bacteria species (Fusobacterium nucleatum, Treponema medium, Peptostreptococcus stomatis, Gemella morbillorum, Catonella morbi, Peptoanaerobacter yurli and Peptococcus simiae) were observed in OSCC tumor microenvironment. These tumor-enriched bacteria formed 254 positive correlations with 206 up-regulated host genes, mainly involving signaling pathways related to cell adhesion, migration and proliferation. Integrative analysis of bacteria-transcriptome and bacteria-methylation correlations identified at least 20 dysregulated host genes with inverted CpG methylation in their promoter regions associated with enrichment of bacterial pathogens, implying a potential of pathogenic bacteria to regulate gene expression, in part, through epigenetic alterations. An in vitro model further confirmed that Fusobacterium nucleatum might contribute to cellular invasion via crosstalk with E-cadherin/β-catenin signaling, TNFα/NF-κB pathway and extracellular matrix remodeling by up-regulating SNAI2 gene, a key transcription factor of epithelial-mesenchymal transition (EMT). Our work using multi-omics approaches explored complex host-microbiota interactions and provided important insights into genetic and functional basis in OSCC tumorigenesis, which may serve as a precursor for hypothesis-driven study to better understand the causational relationship of pathogenic bacteria in this deadly cancer.
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Affiliation(s)
- Liuyang Cai
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hengyan Zhu
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qianqian Mou
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Po Yee Wong
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Linlin Lan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Cherrie W K Ng
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pu Lei
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Man Kit Cheung
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Daijuanru Wang
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Eddy W Y Wong
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Eric H L Lau
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zenon W C Yeung
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ronald Lai
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Katie Meehan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sherwood Fung
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwan Chee A Chan
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Vivian W Y Lui
- Georgia Cancer Center, Augusta, GA, 30912, USA
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Alfred S L Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jun Yu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Paul K S Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jason Y K Chan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China.
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3
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Simon DA, Kellermayer R. INVITED COMMENTARY on Andersen S, et al. Developmental Windows of Environmental Vulnerability for Inflammatory Bowel Disease. JOURNAL OF PEDIATRICS. CLINICAL PRACTICE 2024; 11:200104. [PMID: 38827481 PMCID: PMC11138252 DOI: 10.1016/j.jpedcp.2024.200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 06/04/2024]
Affiliation(s)
- David A. Simon
- Division of Pediatric Gastroenterology, Texas Children’s Hospital Baylor College of Medicine, Houston, TX
| | - Richard Kellermayer
- Division of Pediatric Gastroenterology, Texas Children’s Hospital Baylor College of Medicine, Houston, TX
- USDA/ARS Children’s Nutrition Research Center, Houston, TX
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4
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de Ponthaud C, Abdalla S, Belot MP, Shao X, Penna C, Brouquet A, Bougnères P. Increased CpG methylation at the CDH1 locus in inflamed ileal mucosa of patients with Crohn disease. Clin Epigenetics 2024; 16:28. [PMID: 38355645 PMCID: PMC10865720 DOI: 10.1186/s13148-024-01631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND E-cadherin, a major actor of cell adhesion in the intestinal barrier, is encoded by the CDH1 gene associated with susceptibility to Crohn Disease (CD) and colorectal cancer. Since epigenetic mechanisms are suspected to contribute to the multifactorial pathogenesis of CD, we studied CpG methylation at the CDH1 locus. The methylation of the CpG island (CGI) and of the 1st enhancer, two critical regulatory positions, was quantified in surgical specimens of inflamed ileal mucosa and in peripheral blood mononuclear cells (PBMC) of 21 CD patients. Sixteen patients operated on for a non-inflammatory bowel disease, although not normal controls, provided a macroscopically normal ileal mucosa and PBMC for comparison. RESULTS In ileal mucosa, 19/21 (90%) CD patients vs 8/16 control patients (50%) (p < 0.01) had a methylated CDH1 promoter CGI. In PBMC, CD patients with methylated CGI were 11/21 (52%) vs 7/16 controls (44%), respectively. Methylation in the 1st enhancer of CDH1 was also higher in the CD group for each of the studied CpGs and for their average value (45 ± 17% in CD patients vs 36 ± 17% in controls; p < 0.001). Again, methylation was comparable in PBMC. Methylation of CGI and 1st enhancer were not correlated in mucosa or PBMC. CONCLUSIONS Methylation of several CpGs at the CDH1 locus was increased in the inflamed ileal mucosa, not in the PBMC, of CD patients, suggesting the association of CDH1 methylation with ileal inflammation. Longitudinal studies will explore if this increased methylation is a risk marker for colorectal cancer.
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Affiliation(s)
- Charles de Ponthaud
- Department of Visceral and Digestive Surgery, Hôpital Bicêtre AP-HP, Paris Saclay University, 94276, Le Kremlin-Bicêtre Cedex, France
- UMR INSERM 1169 and Université Paris Saclay, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Solafah Abdalla
- Department of Visceral and Digestive Surgery, Hôpital Bicêtre AP-HP, Paris Saclay University, 94276, Le Kremlin-Bicêtre Cedex, France
- UMR INSERM 1169 and Université Paris Saclay, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Marie-Pierre Belot
- Groupe d'Études sur le Diabète, l'Obésité, la Croissance, GETDOC, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Xiaojian Shao
- Digital Technologies Research Center, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada
| | - Christophe Penna
- Department of Visceral and Digestive Surgery, Hôpital Bicêtre AP-HP, Paris Saclay University, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Antoine Brouquet
- Department of Visceral and Digestive Surgery, Hôpital Bicêtre AP-HP, Paris Saclay University, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Pierre Bougnères
- UMR INSERM 1169 and Université Paris Saclay, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France.
- Groupe d'Études sur le Diabète, l'Obésité, la Croissance, GETDOC, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France.
- MIRCEN Institute, CEA Paris-Saclay/site de Fontenay-aux-Roses, Bâtiment 56 PC 103, 18 route du Panorama, BP6 92265, Fontenay-aux-Roses Cedex, France.
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5
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Schirmer M, Stražar M, Avila-Pacheco J, Rojas-Tapias DF, Brown EM, Temple E, Deik A, Bullock K, Jeanfavre S, Pierce K, Jin S, Invernizzi R, Pust MM, Costliow Z, Mack DR, Griffiths AM, Walters T, Boyle BM, Kugathasan S, Vlamakis H, Hyams J, Denson L, Clish CB, Xavier RJ. Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. Cell Host Microbe 2024; 32:209-226.e7. [PMID: 38215740 PMCID: PMC10923022 DOI: 10.1016/j.chom.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/14/2024]
Abstract
Understanding the role of the microbiome in inflammatory diseases requires the identification of microbial effector molecules. We established an approach to link disease-associated microbes to microbial metabolites by integrating paired metagenomics, stool and plasma metabolomics, and culturomics. We identified host-microbial interactions correlated with disease activity, inflammation, and the clinical course of ulcerative colitis (UC) in the Predicting Response to Standardized Colitis Therapy (PROTECT) pediatric inception cohort. In severe disease, metabolite changes included increased dipeptides and tauro-conjugated bile acids (BAs) and decreased amino-acid-conjugated BAs in stool, whereas in plasma polyamines (N-acetylputrescine and N1-acetylspermidine) increased. Using patient samples and Veillonella parvula as a model, we uncovered nitrate- and lactate-dependent metabolic pathways, experimentally linking V. parvula expansion to immunomodulatory tryptophan metabolite production. Additionally, V. parvula metabolizes immunosuppressive thiopurine drugs through xdhA xanthine dehydrogenase, potentially impairing the therapeutic response. Our findings demonstrate that the microbiome contributes to disease-associated metabolite changes, underscoring the importance of these interactions in disease pathology and treatment.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
| | - Martin Stražar
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Eric M Brown
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Emily Temple
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Deik
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Bullock
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Jeanfavre
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kerry Pierce
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shen Jin
- Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | | | - Marie-Madlen Pust
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Zach Costliow
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R Mack
- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Anne M Griffiths
- Division of Gastroenterology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Thomas Walters
- Division of Gastroenterology, Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Brendan M Boyle
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey Hyams
- Connecticut Children's Medical Center, Division of Digestive Diseases, Hartford, CT 06106, USA
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Clary B Clish
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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6
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Peterson CR, Scott CB, Ghaffari R, Dixon G, Matz MV. Mixed Patterns of Intergenerational DNA Methylation Inheritance in Acropora. Mol Biol Evol 2024; 41:msae008. [PMID: 38243377 PMCID: PMC11079325 DOI: 10.1093/molbev/msae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/21/2024] Open
Abstract
For sessile organisms at high risk from climate change, phenotypic plasticity can be critical to rapid acclimation. Epigenetic markers like DNA methylation are hypothesized as mediators of plasticity; methylation is associated with the regulation of gene expression, can change in response to ecological cues, and is a proposed basis for the inheritance of acquired traits. Within reef-building corals, gene-body methylation (gbM) can change in response to ecological stressors. If coral DNA methylation is transmissible across generations, this could potentially facilitate rapid acclimation to environmental change. We investigated methylation heritability in Acropora, a stony reef-building coral. Two Acropora millepora and two Acropora selago adults were crossed, producing eight offspring crosses (four hybrid, two of each species). We used whole-genome bisulfite sequencing to identify methylated loci and allele-specific alignments to quantify per-locus inheritance. If methylation is heritable, differential methylation (DM) between the parents should equal DM between paired offspring alleles at a given locus. We found a mixture of heritable and nonheritable loci, with heritable portions ranging from 44% to 90% among crosses. gBM was more heritable than intergenic methylation, and most loci had a consistent degree of heritability between crosses (i.e. the deviation between parental and offspring DM were of similar magnitude and direction). Our results provide evidence that coral methylation can be inherited but that heritability is heterogenous throughout the genome. Future investigations into this heterogeneity and its phenotypic implications will be important to understanding the potential capability of intergenerational environmental acclimation in reef building corals.
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Affiliation(s)
| | - Carly B Scott
- Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Rashin Ghaffari
- Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Groves Dixon
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Mikhail V Matz
- Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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Ahn JS, Koo BC, Choi YJ, Jung WW, Kim HS, Lee SJ, Hong ST, Chung HJ. Identification of Muscle Strength-Related Gut Microbes through Human Fecal Microbiome Transplantation. Int J Mol Sci 2024; 25:662. [PMID: 38203833 PMCID: PMC10779158 DOI: 10.3390/ijms25010662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024] Open
Abstract
The gut microbiome is well known for its influence on human physiology and aging. Therefore, we speculate that the gut microbiome may affect muscle strength in the same way as the host's own genes. To demonstrate candidates for gut microbes affecting muscle strength, we remodeled the original gut microbiome of mice into human intestinal microbiome through fecal microbiome transplantation (FMT), using human feces and compared the changes in muscle strength in the same mice before and three months after FMT. After comparing before and after FMT, the mice were divided into three groups based on the observed changes in muscle strength: positive, none, and negative changes in muscle strength. As a result of analyzing the α-diversity, β-diversity, and co-occurrence network of the intestinal microbial community before and after FMT, it was observed that a more diverse intestinal microbial community was established after FMT in all groups. In particular, the group with increased muscle strength had more gut microbiome species and communities than the other groups. Fold-change comparison showed that Eisenbergiella massiliensis and Anaeroplasma abactoclasticum from the gut microbiome had positive contributions to muscle strength, while Ileibacterium valens and Ethanoligenens harbinense had negative effects. This study identifies candidates for the gut microbiome that contribute positively and those that contribute negatively to muscle strength.
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Affiliation(s)
- Ji-Seon Ahn
- Gwangju Center, Korea Basic Science Institute, Gwangju 61751, Jeolla, Republic of Korea; (J.-S.A.); (Y.-J.C.)
- Department of Biomedical Sciences and Institute for Medical Science, Jeonbuk National University Medical School, Jeonju 54907, Jeonbuk, Republic of Korea
| | - Bon-Chul Koo
- Division of Bioconvergence Analysis, Korea Basic Science Institute, Ochang 28119, Chungbuk, Republic of Korea;
- Department of Biomedical Laboratory Science, Cheongju University, Cheongju 28503, Chungbuk, Republic of Korea; (W.-W.J.); (H.-S.K.); (S.-J.L.)
| | - Yu-Jin Choi
- Gwangju Center, Korea Basic Science Institute, Gwangju 61751, Jeolla, Republic of Korea; (J.-S.A.); (Y.-J.C.)
| | - Woon-Won Jung
- Department of Biomedical Laboratory Science, Cheongju University, Cheongju 28503, Chungbuk, Republic of Korea; (W.-W.J.); (H.-S.K.); (S.-J.L.)
| | - Hyun-Sook Kim
- Department of Biomedical Laboratory Science, Cheongju University, Cheongju 28503, Chungbuk, Republic of Korea; (W.-W.J.); (H.-S.K.); (S.-J.L.)
| | - Suk-Jun Lee
- Department of Biomedical Laboratory Science, Cheongju University, Cheongju 28503, Chungbuk, Republic of Korea; (W.-W.J.); (H.-S.K.); (S.-J.L.)
| | - Seong-Tshool Hong
- Department of Biomedical Sciences and Institute for Medical Science, Jeonbuk National University Medical School, Jeonju 54907, Jeonbuk, Republic of Korea
| | - Hea-Jong Chung
- Gwangju Center, Korea Basic Science Institute, Gwangju 61751, Jeolla, Republic of Korea; (J.-S.A.); (Y.-J.C.)
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8
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Sun A, Park P, Cole L, Vaidya H, Maegawa S, Keith K, Calendo G, Madzo J, Jelinek J, Jobin C, Issa JPJ. Non-pathogenic microbiota accelerate age-related CpG Island methylation in colonic mucosa. Epigenetics 2023; 18:2160568. [PMID: 36572998 PMCID: PMC9980687 DOI: 10.1080/15592294.2022.2160568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/11/2022] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is an epigenetic process altered in cancer and ageing. Age-related methylation drift can be used to estimate lifespan and can be influenced by extrinsic factors such as diet. Here, we report that non-pathogenic microbiota accelerate age-related methylation drift in the colon when compared with germ-free mice. DNA methylation analyses showed that microbiota and IL10KO were associated with changes in 5% and 4.1% of CpG sites, while mice with both factors had 18% alterations. Microbiota, IL10KO, and their combination altered 0.4%, 0.4%, and 4% of CpG island methylation, respectively. These are comparable to what is seen in colon cancer. Ageing changes were accelerated in the IL10KO mice with microbiota, and the affected genes were more likely to be altered in colon cancer. Thus, the microbiota affect DNA methylation of the colon in patterns reminiscent of what is observed in ageing and colorectal cancer.
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Affiliation(s)
- Ang Sun
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
| | - Pyounghwa Park
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Lauren Cole
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
| | - Himani Vaidya
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Shinji Maegawa
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Research Department of Pediatrics, University of Texas, MD Anderson Cancer Center Department of Pediatrics, University of Texas, MD Anderson Cancer CenterHouston, TX, USA
| | - Kelsey Keith
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Gennaro Calendo
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Jozef Madzo
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Jaroslav Jelinek
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Christian Jobin
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Jean-Pierre J. Issa
- Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, Philadelphia, PA, United States
- Coriell Institute for Medical Research, Camden, NJ, United States
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Kolli U, Roy S. The role of the gut microbiome and microbial metabolism in mediating opioid-induced changes in the epigenome. Front Microbiol 2023; 14:1233194. [PMID: 37670983 PMCID: PMC10475585 DOI: 10.3389/fmicb.2023.1233194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/26/2023] [Indexed: 09/07/2023] Open
Abstract
The current opioid pandemic is a major public health crisis in the United States, affecting millions of people and imposing significant health and socioeconomic burdens. Preclinical and clinical research over the past few decades has delineated certain molecular mechanisms and identified various genetic, epigenetic, and environmental factors responsible for the pathophysiology and comorbidities associated with opioid use. Opioid use-induced epigenetic modifications have been identified as one of the important factors that mediate genetic changes in brain regions that control reward and drug-seeking behavior and are also implicated in the development of tolerance. Recently, it has been shown that opioid use results in microbial dysbiosis, leading to gut barrier disruption, which drives systemic inflammation, impacting the perception of pain, the development of analgesic tolerance, and behavioral outcomes. In this review, we highlight the potential role of microbiota and microbial metabolites in mediating the epigenetic modifications induced by opioid use.
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Affiliation(s)
| | - Sabita Roy
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
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10
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Aurich S, Müller L, Kovacs P, Keller M. Implication of DNA methylation during lifestyle mediated weight loss. Front Endocrinol (Lausanne) 2023; 14:1181002. [PMID: 37614712 PMCID: PMC10442821 DOI: 10.3389/fendo.2023.1181002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/18/2023] [Indexed: 08/25/2023] Open
Abstract
Over the past 50 years, the number of overweight/obese people increased significantly, making obesity a global public health challenge. Apart from rare monogenic forms, obesity is a multifactorial disease, most likely resulting from a concerted interaction of genetic, epigenetic and environmental factors. Although recent studies opened new avenues in elucidating the complex genetics behind obesity, the biological mechanisms contributing to individual's risk to become obese are not yet fully understood. Non-genetic factors such as eating behaviour or physical activity are strong contributing factors for the onset of obesity. These factors may interact with genetic predispositions most likely via epigenetic mechanisms. Epigenome-wide association studies or methylome-wide association studies are measuring DNA methylation at single CpGs across thousands of genes and capture associations to obesity phenotypes such as BMI. However, they only represent a snapshot in the complex biological network and cannot distinguish between causes and consequences. Intervention studies are therefore a suitable method to control for confounding factors and to avoid possible sources of bias. In particular, intervention studies documenting changes in obesity-associated epigenetic markers during lifestyle driven weight loss, make an important contribution to a better understanding of epigenetic reprogramming in obesity. To investigate the impact of lifestyle in obesity state specific DNA methylation, especially concerning the development of new strategies for prevention and individual therapy, we reviewed 19 most recent human intervention studies. In summary, this review highlights the huge potential of targeted interventions to alter disease-associated epigenetic patterns. However, there is an urgent need for further robust and larger studies to identify the specific DNA methylation biomarkers which influence obesity.
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Affiliation(s)
- Samantha Aurich
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Luise Müller
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Deutsches Zentrum für Diabetesforschung e.V., Neuherberg, Germany
| | - Maria Keller
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
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11
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Ahn JS, Choi YJ, Kim HB, Chung HJ, Hong ST. Identification of the Intestinal Microbes Associated with Locomotion. Int J Mol Sci 2023; 24:11392. [PMID: 37511151 PMCID: PMC10380270 DOI: 10.3390/ijms241411392] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Given the impact of the gut microbiome on human physiology and aging, it is possible that the gut microbiome may affect locomotion in the same way as the host's own genes. There is not yet any direct evidence linking the gut microbiome to locomotion, though there are some potential connections, such as regular physical activity and the immune system. In this study, we demonstrate that the gut microbiome can contribute differently to locomotion. We remodeled the original gut microbiome of mice through fecal microbiota transplantation (FMT) using human feces and compared the changes in locomotion of the same mice before and three months after FMT. We found that FMT affected locomotion in three different ways: positive, none (the same), and negative. Analysis of the phylogenesis, α-diversities, and β-diversities of the gut microbiome in the three groups showed that a more diverse group of intestinal microbes was established after FMT in each of the three groups, indicating that the human gut microbiome is more diverse than that of mice. The FMT-remodeled gut microbiome in each group was also different from each other. Fold change and linear correlation analyses identified Lacrimispora indolis, Pseudoflavonifractor phocaeensis, and Alistipes senegalensis in the gut microbiome as positive contributors to locomotion, while Sphingobacterium cibi, Prevotellamassilia timonensis, Parasutterella excrementihominis, Faecalibaculum rodentium, and Muribaculum intestinale were found to have negative effects. This study not only confirms the presence of gut microbiomes that contribute differently to locomotion, but also explains the mixed results in research on the association between the gut microbiome and locomotion.
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Affiliation(s)
- Ji-Seon Ahn
- Gwangju Center, Korea Basic Science Institute, Gwangju 61751, Republic of Korea
| | - Yu-Jin Choi
- Gwangju Center, Korea Basic Science Institute, Gwangju 61751, Republic of Korea
| | - Han-Byeol Kim
- Gwangju Center, Korea Basic Science Institute, Gwangju 61751, Republic of Korea
- Department of Biomedical Sciences and Institute for Medical Science, Chonbuk National University Medical School, Jeonju 54907, Republic of Korea
| | - Hea-Jong Chung
- Gwangju Center, Korea Basic Science Institute, Gwangju 61751, Republic of Korea
| | - Seong-Tshool Hong
- Department of Biomedical Sciences and Institute for Medical Science, Chonbuk National University Medical School, Jeonju 54907, Republic of Korea
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12
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Ansari I, Solé-Boldo L, Ridnik M, Gutekunst J, Gilliam O, Korshko M, Liwinski T, Jickeli B, Weinberg-Corem N, Shoshkes-Carmel M, Pikarsky E, Elinav E, Lyko F, Bergman Y. TET2 and TET3 loss disrupts small intestine differentiation and homeostasis. Nat Commun 2023; 14:4005. [PMID: 37414790 PMCID: PMC10326054 DOI: 10.1038/s41467-023-39512-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
TET2/3 play a well-known role in epigenetic regulation and mouse development. However, their function in cellular differentiation and tissue homeostasis remains poorly understood. Here we show that ablation of TET2/3 in intestinal epithelial cells results in a murine phenotype characterized by a severe homeostasis imbalance in the small intestine. Tet2/3-deleted mice show a pronounced loss of mature Paneth cells as well as fewer Tuft and more Enteroendocrine cells. Further results show major changes in DNA methylation at putative enhancers, which are associated with cell fate-determining transcription factors and functional effector genes. Notably, pharmacological inhibition of DNA methylation partially rescues the methylation and cellular defects. TET2/3 loss also alters the microbiome, predisposing the intestine to inflammation under homeostatic conditions and acute inflammation-induced death. Together, our results uncover previously unrecognized critical roles for DNA demethylation, possibly occurring subsequently to chromatin opening during intestinal development, culminating in the establishment of normal intestinal crypts.
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Affiliation(s)
- Ihab Ansari
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Llorenç Solé-Boldo
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Meshi Ridnik
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Oliver Gilliam
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Maria Korshko
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Timur Liwinski
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
- University Psychiatric Clinics Basel, Clinic for Adults, University of Basel, Basel, Switzerland
| | - Birgit Jickeli
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Noa Weinberg-Corem
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Michal Shoshkes-Carmel
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Eli Pikarsky
- The Lautenberg Center for Immunology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Eran Elinav
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
- Division of Microbiome and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
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13
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Noble AJ, Nowak JK, Adams AT, Uhlig HH, Satsangi J. Defining Interactions Between the Genome, Epigenome, and the Environment in Inflammatory Bowel Disease: Progress and Prospects. Gastroenterology 2023; 165:44-60.e2. [PMID: 37062395 DOI: 10.1053/j.gastro.2023.03.238] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 03/08/2023] [Accepted: 03/24/2023] [Indexed: 04/18/2023]
Abstract
Recent advances in our understanding of the pathogenesis of inflammatory bowel disease (IBD) have highlighted the complex interplay between the genome, the epigenome, and the environment. Despite the exciting advances in genomics that have enabled the identification of over 200 susceptibility loci, these only account for a small proportion of the disease variance and the estimated heritability in IBD. It is likely that gene-environment (GxE) interactions contribute to "missing heritability" and these may act through epigenetic mechanisms. Several environmental factors, such as the microbiome, nutrition, and tobacco smoking, induce alterations in the epigenome of children and adults, which may impact disease susceptibility. Other mechanisms for GxE interactions are also directly pertinent in early life. We discuss a model in which environmental factors imprint disease risk in a window of susceptibility during infancy that may contribute to later disease onset, whereas other elements of the exposome act later in life and contribute directly to the pathogenesis and course of the disease. Understanding the mechanisms underlying GxE interactions may provide the basis for new therapeutic targets or preventative strategies for IBD.
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Affiliation(s)
- Alexandra J Noble
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom.
| | - Jan K Nowak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Alex T Adams
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom; Biomedical Research Center, University of Oxford, Oxford, United Kingdom
| | - Holm H Uhlig
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom; Department of Pediatrics, University of Oxford, Oxford, United Kingdom; Biomedical Research Center, University of Oxford, Oxford, United Kingdom
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom; Biomedical Research Center, University of Oxford, Oxford, United Kingdom
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14
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Yang L, Chen X, Lee C, Shi J, Lawrence EB, Zhang L, Li Y, Gao N, Jung SY, Creighton CJ, Li JJ, Cui Y, Arimura S, Lei Y, Li W, Shen L. Functional characterization of age-dependent p16 epimutation reveals biological drivers and therapeutic targets for colorectal cancer. J Exp Clin Cancer Res 2023; 42:113. [PMID: 37143122 PMCID: PMC10157929 DOI: 10.1186/s13046-023-02689-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Methylation of the p16 promoter resulting in epigenetic gene silencing-known as p16 epimutation-is frequently found in human colorectal cancer and is also common in normal-appearing colonic mucosa of aging individuals. Thus, to improve clinical care of colorectal cancer (CRC) patients, we explored the role of age-related p16 epimutation in intestinal tumorigenesis. METHODS We established a mouse model that replicates two common genetic and epigenetic events observed in human CRCs: Apc mutation and p16 epimutation. We conducted long-term survival and histological analysis of tumor development and progression. Colonic epithelial cells and tumors were collected from mice and analyzed by RNA sequencing (RNA-seq), quantitative PCR, and flow cytometry. We performed single-cell RNA sequencing (scRNA-seq) to characterize tumor-infiltrating immune cells throughout tumor progression. We tested whether anti-PD-L1 immunotherapy affects overall survival of tumor-bearing mice and whether inhibition of both epigenetic regulation and immune checkpoint is more efficacious. RESULTS Mice carrying combined Apc mutation and p16 epimutation had significantly shortened survival and increased tumor growth compared to those with Apc mutation only. Intriguingly, colon tumors with p16 epimutation exhibited an activated interferon pathway, increased expression of programmed death-ligand 1 (Pdl1), and enhanced infiltration of immune cells. scRNA-seq further revealed the presence of Foxp3+ Tregs and γδT17 cells, which contribute to an immunosuppressive tumor microenvironment (TME). Furthermore, we showed that a combined therapy using an inhibitor of DNA methylation and a PD-L1 immune checkpoint inhibitor is more effective for improving survival in tumor-bearing mice than blockade of either pathway alone. CONCLUSIONS Our study demonstrated that age-dependent p16 epimutation creates a permissive microenvironment for malignant transformation of polyps to colon cancer. Our findings provide a mechanistic rationale for future targeted therapy in patients with p16 epimutation.
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Affiliation(s)
- Li Yang
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, TX, Houston, USA
| | - Xiaomin Chen
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, TX, Houston, USA
| | - Christy Lee
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Jiejun Shi
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
- Present address: Department of General Surgery, Shanghai Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Emily B Lawrence
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, TX, Houston, USA
| | - Lanjing Zhang
- Department of Pathology, Princeton Medical Center, Plainsboro, NJ, USA
- Department of Chemical Biology, Earnest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Sung Yun Jung
- Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA
| | - Chad J Creighton
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
| | - Sumimasa Arimura
- Department of Medicine and Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA
| | - Lanlan Shen
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, TX, Houston, USA.
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15
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Cowardin CA, Syed S, Iqbal N, Jamil Z, Sadiq K, Iqbal J, Ali SA, Moore SR. Environmental enteric dysfunction: gut and microbiota adaptation in pregnancy and infancy. Nat Rev Gastroenterol Hepatol 2023; 20:223-237. [PMID: 36526906 PMCID: PMC10065936 DOI: 10.1038/s41575-022-00714-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 03/31/2023]
Abstract
Environmental enteric dysfunction (EED) is a subclinical syndrome of intestinal inflammation, malabsorption and barrier disruption that is highly prevalent in low- and middle-income countries in which poverty, food insecurity and frequent exposure to enteric pathogens impair growth, immunity and neurodevelopment in children. In this Review, we discuss advances in our understanding of EED, intestinal adaptation and the gut microbiome over the 'first 1,000 days' of life, spanning pregnancy and early childhood. Data on maternal EED are emerging, and they mirror earlier findings of increased risks for preterm birth and fetal growth restriction in mothers with either active inflammatory bowel disease or coeliac disease. The intense metabolic demands of pregnancy and lactation drive gut adaptation, including dramatic changes in the composition, function and mother-to-child transmission of the gut microbiota. We urgently need to elucidate the mechanisms by which EED undermines these critical processes so that we can improve global strategies to prevent and reverse intergenerational cycles of undernutrition.
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Affiliation(s)
- Carrie A Cowardin
- Division of Paediatric Gastroenterology, Hepatology and Nutrition, Department of Paediatrics, Child Health Research Center, University of Virginia, Charlottesville, VA, USA
| | - Sana Syed
- Division of Paediatric Gastroenterology, Hepatology and Nutrition, Department of Paediatrics, Child Health Research Center, University of Virginia, Charlottesville, VA, USA
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeha Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Zehra Jamil
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Kamran Sadiq
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Junaid Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Syed Asad Ali
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sean R Moore
- Division of Paediatric Gastroenterology, Hepatology and Nutrition, Department of Paediatrics, Child Health Research Center, University of Virginia, Charlottesville, VA, USA.
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16
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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17
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Gaillard V, Chastant S, England G, Forman O, German AJ, Suchodolski JS, Villaverde C, Chavatte-Palmer P, Péron F. Environmental risk factors in puppies and kittens for developing chronic disorders in adulthood: A call for research on developmental programming. Front Vet Sci 2022; 9:944821. [PMID: 36619947 PMCID: PMC9816871 DOI: 10.3389/fvets.2022.944821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Many dogs and cats are affected by chronic diseases that significantly impact their health and welfare and relationships with humans. Some of these diseases can be challenging to treat, and a better understanding of early-life risk factors for diseases occurring in adulthood is key to improving preventive veterinary care and husbandry practices. This article reviews early-life risk factors for obesity and chronic enteropathy, and for chronic behavioral problems, which can also be intractable with life-changing consequences. Aspects of early life in puppies and kittens that can impact the risk of adult disorders include maternal nutrition, establishment of the gut microbiome, maternal behavior, weaning, nutrition during growth, growth rate, socialization with conspecifics and humans, rehoming and neutering. Despite evidence in some species that the disorders reviewed here reflect the developmental origins of health and disease (DOHaD), developmental programming has rarely been studied in dogs and cats. Priorities and strategies to increase knowledge of early-life risk factors and DOHaD in dogs and cats are discussed. Critical windows of development are proposed: preconception, gestation, the suckling period, early growth pre-neutering or pre-puberty, and growth post-neutering or post-puberty to adult size, the durations of which depend upon species and breed. Challenges to DOHaD research in these species include a large number of breeds with wide genetic and phenotypic variability, and the existence of many mixed-breed individuals. Moreover, difficulties in conducting prospective lifelong cohort studies are exacerbated by discontinuity in pet husbandry between breeders and subsequent owners, and by the dispersed nature of pet ownership.
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Affiliation(s)
- Virginie Gaillard
- Research and Development Center, Royal Canin, Aimargues, France,*Correspondence: Virginie Gaillard ✉
| | - Sylvie Chastant
- NeoCare, Université de Toulouse, Ecole Nationale Vétérinaire de Toulouse (ENVT), Toulouse, France
| | - Gary England
- School of Veterinary Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Oliver Forman
- Wisdom Panel, Kinship, Waltham-on-the-Wolds, Leicestershire, United Kingdom
| | - Alexander J. German
- Institute of Life Course and Medical Sciences of Small Animal Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, United States
| | | | - Pascale Chavatte-Palmer
- Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut National de Recherche Pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Biologie de la Reproduction, Environnement, Epigénétique et Développement (BREED), Jouy-en-Josas, France,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Franck Péron
- Research and Development Center, Royal Canin, Aimargues, France
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18
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DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon. Nat Commun 2022; 13:6266. [PMID: 36271073 PMCID: PMC9587301 DOI: 10.1038/s41467-022-33844-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 10/05/2022] [Indexed: 12/25/2022] Open
Abstract
Genetic variants in the DNA methyltransferase 3 A (DNMT3A) locus have been associated with inflammatory bowel disease (IBD). DNMT3A is part of the epigenetic machinery physiologically involved in DNA methylation. We show that DNMT3A plays a critical role in maintaining intestinal homeostasis and gut barrier function. DNMT3A expression is downregulated in intestinal epithelial cells from IBD patients and upon tumor necrosis factor treatment in murine intestinal organoids. Ablation of DNMT3A in Caco-2 cells results in global DNA hypomethylation, which is linked to impaired regenerative capacity, transepithelial resistance and intercellular junction formation. Genetic deletion of Dnmt3a in intestinal epithelial cells (Dnmt3aΔIEC) in mice confirms the phenotype of an altered epithelial ultrastructure with shortened apical-junctional complexes, reduced Goblet cell numbers and increased intestinal permeability in the colon in vivo. Dnmt3aΔIEC mice suffer from increased susceptibility to experimental colitis, characterized by reduced epithelial regeneration. These data demonstrate a critical role for DNMT3A in orchestrating intestinal epithelial homeostasis and response to tissue damage and suggest an involvement of impaired epithelial DNMT3A function in the etiology of IBD.
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19
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Novel epigenetic therapeutic strategies and targets in cancer. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166552. [PMID: 36126898 DOI: 10.1016/j.bbadis.2022.166552] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/08/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022]
Abstract
The critical role of dysregulated epigenetic pathways in cancer genesis, development, and therapy has typically been established as a result of scientific and technical innovations in next generation sequencing. RNA interference, histone modification, DNA methylation and chromatin remodelling are epigenetic processes that control gene expression without causing mutations in the DNA. Although epigenetic abnormalities are thought to be a symptom of cell tumorigenesis and malignant events that impact tumor growth and drug resistance, physicians believe that related processes might be a key therapeutic target for cancer treatment and prevention due to the reversible nature of these processes. A plethora of novel strategies for addressing epigenetics in cancer therapy for immuno-oncological complications are currently available - ranging from basic treatment to epigenetic editing. - and they will be the subject of this comprehensive review. In this review, we cover most of the advancements made in the field of targeting epigenetics with special emphasis on microbiology, plasma science, biophysics, pharmacology, molecular biology, phytochemistry, and nanoscience.
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Mussard E, Lencina C, Gallo L, Barilly C, Poli M, Feve K, Albin M, Cauquil L, Knudsen C, Achard C, Devailly G, Soler L, Combes S, Beaumont M. The phenotype of the gut region is more stably retained than developmental stage in piglet intestinal organoids. Front Cell Dev Biol 2022; 10:983031. [PMID: 36105361 PMCID: PMC9465596 DOI: 10.3389/fcell.2022.983031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Intestinal organoids are innovative in vitro tools to study the digestive epithelium. The objective of this study was to generate jejunum and colon organoids from suckling and weaned piglets in order to determine the extent to which organoids retain a location-specific and a developmental stage-specific phenotype. Organoids were studied at three time points by gene expression profiling for comparison with the transcriptomic patterns observed in crypts in vivo. In addition, the gut microbiota and the metabolome were analyzed to characterize the luminal environment of epithelial cells at the origin of organoids. The location-specific expression of 60 genes differentially expressed between jejunum and colon crypts from suckling piglets was partially retained (48%) in the derived organoids at all time point. The regional expression of these genes was independent of luminal signals since the major differences in microbiota and metabolome observed in vivo between the jejunum and the colon were not reproduced in vitro. In contrast, the regional expression of other genes was erased in organoids. Moreover, the developmental stage-specific expression of 30 genes differentially expressed between the jejunum crypts of suckling and weaned piglets was not stably retained in the derived organoids. Differentiation of organoids was necessary to observe the regional expression of certain genes while it was not sufficient to reproduce developmental stage-specific expression patterns. In conclusion, piglet intestinal organoids retained a location-specific phenotype while the characteristics of developmental stage were erased in vitro. Reproducing more closely the luminal environment might help to increase the physiological relevance of intestinal organoids.
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Affiliation(s)
- Eloïse Mussard
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
- Lallemand Animal Nutrition, Blagnac Cedex, France
| | - Corinne Lencina
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Lise Gallo
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Céline Barilly
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Maryse Poli
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Katia Feve
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Mikael Albin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Laurent Cauquil
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | | | | | - Laura Soler
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Sylvie Combes
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Martin Beaumont
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
- *Correspondence: Martin Beaumont,
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21
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Parmar S, Easwaran H. Genetic and epigenetic dependencies in colorectal cancer development. Gastroenterol Rep (Oxf) 2022; 10:goac035. [PMID: 35975243 PMCID: PMC9373935 DOI: 10.1093/gastro/goac035] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/24/2022] [Accepted: 05/22/2022] [Indexed: 11/12/2022] Open
Abstract
Recent studies have mapped key genetic changes in colorectal cancer (CRC) that impact important pathways contributing to the multistep models for CRC initiation and development. In parallel with genetic changes, normal and cancer tissues harbor epigenetic alterations impacting regulation of critical genes that have been shown to play profound roles in the tumor initiation. Cumulatively, these molecular changes are only loosely associated with heterogenous transcriptional programs, reflecting the heterogeneity in the various CRC molecular subtypes and the paths to CRC development. Studies from mapping molecular alterations in early CRC lesions and use of experimental models suggest that the intricate dependencies of various genetic and epigenetic hits shape the early development of CRC via different pathways and its manifestation into various CRC subtypes. We highlight the dependency of epigenetic and genetic changes in driving CRC development and discuss factors affecting epigenetic alterations over time and, by extension, risk for cancer.
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Affiliation(s)
- Sehej Parmar
- Cancer Genetics and Epigenetics, Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hariharan Easwaran
- Cancer Genetics and Epigenetics, Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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22
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Ferguson LV, Hewins B, Harding W, MacDonald E, Gibson G. Changes in the microbiome and associated host tissue structure in the blue mussel, Mytilus edulis, following exposure to polystyrene microparticles
. CAN J ZOOL 2022. [DOI: 10.1139/cjz-2021-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Marine life is increasingly exposed to microplastics, which can be ingested and disrupt the relationship between host tissues and their microbiomes. We investigated the effects of microplastics (5 µm polystyrene beads, PS) on the microbial community and host tissue structure in organs at high risk of exposure (digestive gland and gills) in blue mussels, Mytilus edulis (Linnaeus, 1758). We exposed mussels to concentrations of microplastic consistent with levels found in local coastal waters. High exposures (1000 particles m-3/mussel) decreased the alpha and beta diversity in the microbiome of the digestive gland, with an increase in relative abundance of Polaribacter and a decrease in other species in the Flavobacteriaceae. Both low (10 particles m-3/mussel) and high exposures to PS also changed tissue structure in the hosts, with an increase in immune cells (hemocytes) and reactive lysosomes in the gills, and in the digestive gland, a loss of cell specialization in digestive cells and an increase in cell break-down products. Thus, exposure to particles of polystyrene in concentrations consistent with levels detected in local coastal zones reduces microbial biodiversity of the digestive gland and disrupts host tissues, which may indicate a loss of the host-symbiont interactions that support tissue homeostasis.
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Affiliation(s)
- Laura V Ferguson
- Acadia University Faculty of Pure and Applied Sciences, 120861, Biology, 33 Westwood Avenue, NS, Wolfville, Nova Scotia, Canada, B4P 2R6
| | - Ben Hewins
- Acadia University, 8689, Biology Department, Wolfville, Canada, B4P 2R6
| | - Wesley Harding
- Acadia University, Biology, Wolfville, Nova Scotia, Canada
| | - Erin MacDonald
- Acadia University, Biology, Wolfville, Nova Scotia, Canada
| | - Glenys Gibson
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada, B0P 1X0, ,
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23
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Vieujean S, Caron B, Haghnejad V, Jouzeau JY, Netter P, Heba AC, Ndiaye NC, Moulin D, Barreto G, Danese S, Peyrin-Biroulet L. Impact of the Exposome on the Epigenome in Inflammatory Bowel Disease Patients and Animal Models. Int J Mol Sci 2022; 23:7611. [PMID: 35886959 PMCID: PMC9321337 DOI: 10.3390/ijms23147611] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic inflammatory disorders of the gastrointestinal tract that encompass two main phenotypes, namely Crohn's disease and ulcerative colitis. These conditions occur in genetically predisposed individuals in response to environmental factors. Epigenetics, acting by DNA methylation, post-translational histones modifications or by non-coding RNAs, could explain how the exposome (or all environmental influences over the life course, from conception to death) could influence the gene expression to contribute to intestinal inflammation. We performed a scoping search using Medline to identify all the elements of the exposome that may play a role in intestinal inflammation through epigenetic modifications, as well as the underlying mechanisms. The environmental factors epigenetically influencing the occurrence of intestinal inflammation are the maternal lifestyle (mainly diet, the occurrence of infection during pregnancy and smoking); breastfeeding; microbiota; diet (including a low-fiber diet, high-fat diet and deficiency in micronutrients); smoking habits, vitamin D and drugs (e.g., IBD treatments, antibiotics and probiotics). Influenced by both microbiota and diet, short-chain fatty acids are gut microbiota-derived metabolites resulting from the anaerobic fermentation of non-digestible dietary fibers, playing an epigenetically mediated role in the integrity of the epithelial barrier and in the defense against invading microorganisms. Although the impact of some environmental factors has been identified, the exposome-induced epimutations in IBD remain a largely underexplored field. How these environmental exposures induce epigenetic modifications (in terms of duration, frequency and the timing at which they occur) and how other environmental factors associated with IBD modulate epigenetics deserve to be further investigated.
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Affiliation(s)
- Sophie Vieujean
- Hepato-Gastroenterology and Digestive Oncology, University Hospital CHU of Liège, 4000 Liege, Belgium;
| | - Bénédicte Caron
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
| | - Vincent Haghnejad
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
| | - Jean-Yves Jouzeau
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Patrick Netter
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Anne-Charlotte Heba
- NGERE (Nutrition-Genetics and Exposure to Environmental Risks), National Institute of Health and Medical Research, University of Lorraine, F-54000 Nancy, France; (A.-C.H.); (N.C.N.)
| | - Ndeye Coumba Ndiaye
- NGERE (Nutrition-Genetics and Exposure to Environmental Risks), National Institute of Health and Medical Research, University of Lorraine, F-54000 Nancy, France; (A.-C.H.); (N.C.N.)
| | - David Moulin
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Guillermo Barreto
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Universidad de la Salud del Estado de Puebla, Puebla 72000, Mexico
| | - Silvio Danese
- Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele and University Vita-Salute San Raffaele, 20132 Milan, Italy;
| | - Laurent Peyrin-Biroulet
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
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Lee MH, Medina Munoz M, Rio RVM. The Tsetse Metabolic Gambit: Living on Blood by Relying on Symbionts Demands Synchronization. Front Microbiol 2022; 13:905826. [PMID: 35756042 PMCID: PMC9218860 DOI: 10.3389/fmicb.2022.905826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Tsetse flies have socioeconomic significance as the obligate vector of multiple Trypanosoma parasites, the causative agents of Human and Animal African Trypanosomiases. Like many animals subsisting on a limited diet, microbial symbiosis is key to supplementing nutrient deficiencies necessary for metabolic, reproductive, and immune functions. Extensive studies on the microbiota in parallel to tsetse biology have unraveled the many dependencies partners have for one another. But far less is known mechanistically on how products are swapped between partners and how these metabolic exchanges are regulated, especially to address changing physiological needs. More specifically, how do metabolites contributed by one partner get to the right place at the right time and in the right amounts to the other partner? Epigenetics is the study of molecules and mechanisms that regulate the inheritance, gene activity and expression of traits that are not due to DNA sequence alone. The roles that epigenetics provide as a mechanistic link between host phenotype, metabolism and microbiota (both in composition and activity) is relatively unknown and represents a frontier of exploration. Here, we take a closer look at blood feeding insects with emphasis on the tsetse fly, to specifically propose roles for microRNAs (miRNA) and DNA methylation, in maintaining insect-microbiota functional homeostasis. We provide empirical details to addressing these hypotheses and advancing these studies. Deciphering how microbiota and host activity are harmonized may foster multiple applications toward manipulating host health, including identifying novel targets for innovative vector control strategies to counter insidious pests such as tsetse.
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Affiliation(s)
- Mason H Lee
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States
| | - Miguel Medina Munoz
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States.,Department of Bacteriology, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Rita V M Rio
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States
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25
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Wang C, Sun H, Jiang X, Guan X, Gao F, Shi B. Maternal Oxidized Soybean Oil Administration in Rats during Pregnancy and Lactation Alters the Intestinal DNA Methylation in Offspring. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6224-6238. [PMID: 35549255 DOI: 10.1021/acs.jafc.2c01100] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As a food contaminant, oxidized oil or lipid oxidative products have been proven to exert toxicological effects on the growth and development of animals and humans. Research shows that maternal oxidative stress damage might transmit to another generation by epigenetic modulation. However, current evidence is still not clear on the mechanism of the effects of dietary oxidized oil during pregnancy on the two generations. This study employed a rat model fed with oxidized soybean oil (OSO) during pregnancy and lactation to explore the effects of the oxidative degree (0, 200, 400, and 800 mequiv of O2/kg) on the placental RNA methylation and DNA methylation in offspring jejunum. The results showed that following the ingestion of OSO, the placental genes of different m6A methylation were significantly enriched to nutrient metabolic processes and hormone activity. In addition, the intestine in offspring hypofunctioned observably, such as reducing the height of villi and the level of anti-inflammatory cytokine. Furthermore, maternal intake of OSO during pregnancy can damage the intestinal barrier function of offspring by inhibiting the proliferation and differentiation of intestinal epithelial cells and reducing the activity of intestinal DNA methyltransferase. In conclusion, this study reinforces the assertion that maternal OSO consumption during gestation and lactation negatively affects the placental health and intestinal development of suckling pups.
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Affiliation(s)
- Chuanqi Wang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Haoyang Sun
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Xu Jiang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Xin Guan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Feng Gao
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Baoming Shi
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
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26
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Gao S, Khan MI, Kalsoom F, Liu Z, Chen Y, Chen Z. Role of gene regulation and inter species interaction as a key factor in gut microbiota adaptation. Arch Microbiol 2022; 204:342. [PMID: 35595857 DOI: 10.1007/s00203-022-02935-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/08/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022]
Abstract
Gut microbiota is a class of microbial flora present in various eukaryotic multicellular complex animals such as human beings. Their community's growth and survival are greatly influenced by various factors such as host-pathogen, pathogen-environment and genetic regulation. Modern technologies like metagenomics have particularly extended our capacity to uncover the microbial treasures in challenging conditions like communities surviving at high altitude. Molecular characterizations by newly developed sequencing tools have shown that this complex interaction greatly influences microbial adaptation to the environment. Literature shows that gut microbiota alters the genetic expression and switches to an alternative pathway under the influence of unfavorable conditions. The remarkable adaptability of microbial genetic regulatory networks enables them to survive and expand in tough and energy-limited conditions. Variable prevalence of species in various regions has strengthened this initial evidence. In view of the interconnection of the world in the form of a global village, this phenomenon must be explored more clearly. In this regard, recently there has been significant addition of knowledge to the field of microbial adaptation. This review summarizes and shed some light on mechanisms of microbial adaptation via gene regulation and species interaction in gut microbiota.
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Affiliation(s)
- Shuang Gao
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 260027, Anhui, People's Republic of China
| | - Muhammad Imran Khan
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 260027, Anhui, People's Republic of China. .,Department of Pathology, District Headquarters Hospital, Jhang, 35200, Punjab, Islamic Republic of Pakistan.
| | - Fadia Kalsoom
- Department of Microbiology, School of Medicine, Ajou University, Suwon, 16499, Republic of Korea
| | - Zhen Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Yanxin Chen
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Zhengli Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China. .,College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
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27
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Sonali S, Ray B, Ahmed Tousif H, Rathipriya AG, Sunanda T, Mahalakshmi AM, Rungratanawanich W, Essa MM, Qoronfleh MW, Chidambaram SB, Song BJ. Mechanistic Insights into the Link between Gut Dysbiosis and Major Depression: An Extensive Review. Cells 2022; 11:cells11081362. [PMID: 35456041 PMCID: PMC9030021 DOI: 10.3390/cells11081362] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Depression is a highly common mental disorder, which is often multifactorial with sex, genetic, environmental, and/or psychological causes. Recent advancements in biomedical research have demonstrated a clear correlation between gut dysbiosis (GD) or gut microbial dysbiosis and the development of anxiety or depressive behaviors. The gut microbiome communicates with the brain through the neural, immune, and metabolic pathways, either directly (via vagal nerves) or indirectly (via gut- and microbial-derived metabolites as well as gut hormones and endocrine peptides, including peptide YY, pancreatic polypeptide, neuropeptide Y, cholecystokinin, corticotropin-releasing factor, glucagon-like peptide, oxytocin, and ghrelin). Maintaining healthy gut microbiota (GM) is now being recognized as important for brain health through the use of probiotics, prebiotics, synbiotics, fecal microbial transplantation (FMT), etc. A few approaches exert antidepressant effects via restoring GM and hypothalamus–pituitary–adrenal (HPA) axis functions. In this review, we have summarized the etiopathogenic link between gut dysbiosis and depression with preclinical and clinical evidence. In addition, we have collated information on the recent therapies and supplements, such as probiotics, prebiotics, short-chain fatty acids, and vitamin B12, omega-3 fatty acids, etc., which target the gut–brain axis (GBA) for the effective management of depressive behavior and anxiety.
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Affiliation(s)
- Sharma Sonali
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India; (S.S.); (B.R.); (H.A.T.); (T.S.); (A.M.M.)
- Centre for Experimental Pharmacology and Toxicology, Central Animal Facility, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
| | - Bipul Ray
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India; (S.S.); (B.R.); (H.A.T.); (T.S.); (A.M.M.)
- Centre for Experimental Pharmacology and Toxicology, Central Animal Facility, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
| | - Hediyal Ahmed Tousif
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India; (S.S.); (B.R.); (H.A.T.); (T.S.); (A.M.M.)
- Centre for Experimental Pharmacology and Toxicology, Central Animal Facility, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
| | | | - Tuladhar Sunanda
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India; (S.S.); (B.R.); (H.A.T.); (T.S.); (A.M.M.)
- Centre for Experimental Pharmacology and Toxicology, Central Animal Facility, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
| | - Arehally M. Mahalakshmi
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India; (S.S.); (B.R.); (H.A.T.); (T.S.); (A.M.M.)
- Centre for Experimental Pharmacology and Toxicology, Central Animal Facility, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
| | - Wiramon Rungratanawanich
- Section of Molecular Pharmacology and Toxicology, Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD 20892, USA;
| | - Musthafa Mohamed Essa
- Department of Food Science and Nutrition, CAMS, Sultan Qaboos University, Muscat 123, Oman;
- Aging and Dementia Research Group, Sultan Qaboos University, Muscat 123, Oman
| | - M. Walid Qoronfleh
- Q3CG Research Institute (QRI), Research and Policy Division, 7227 Rachel Drive, Ypsilant, MI 48917, USA;
| | - Saravana Babu Chidambaram
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India; (S.S.); (B.R.); (H.A.T.); (T.S.); (A.M.M.)
- Centre for Experimental Pharmacology and Toxicology, Central Animal Facility, JSS Academy of Higher Education & Research, Mysuru 570015, Karnataka, India
- Correspondence: (S.B.C.); (B.-J.S.)
| | - Byoung-Joon Song
- Section of Molecular Pharmacology and Toxicology, Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD 20892, USA;
- Correspondence: (S.B.C.); (B.-J.S.)
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Holubekova V, Kolkova Z, Kasubova I, Samec M, Mazurakova A, Koklesova L, Kubatka P, Rokos T, Kozubik E, Biringer K, Kudela E. Interaction of cervical microbiome with epigenome of epithelial cells: Significance of inflammation to primary healthcare. Biomol Concepts 2022; 13:61-80. [PMID: 35245973 DOI: 10.1515/bmc-2022-0005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
One pillar of the predictive, preventive, and personalized medicine framework strategies is the female health. The evaluation of women's lifestyle and dietary habits in context with genetic and modifiable risk factors may reflect the prevention of cervical cancer before the occurrence of clinical symptoms and prediction of cervical lesion behavior. The main aim of this review is to analyze publications in the field of precision medicine that allow the use of research knowledge of cervical microbiome, epigenetic modifications, and inflammation in potential application in clinical practice. Personalized approach in evaluating patient's risk of future development of cervical abnormality should consider the biomarkers of the local microenvironment characterized by the microbial composition, epigenetic pattern of cervical epithelium, and presence of chronic inflammation. Novel sequencing techniques enable a more detailed characterization of actual state in cervical epithelium. Better understanding of all changes in multiomics level enables a better assessment of disease prognosis and selects the eligible targeted therapy in personalized medicine. Restoring of healthy vaginal microflora and reversing the outbreak of cervical abnormality can be also achieved by dietary habits as well as uptake of prebiotics, probiotics, synbiotics, microbial transplantation, and others.
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Affiliation(s)
- Veronika Holubekova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Zuzana Kolkova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Ivana Kasubova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Marek Samec
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Alena Mazurakova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Lenka Koklesova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, SK-03601, Slovakia
| | - Tomas Rokos
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Erik Kozubik
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Kamil Biringer
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
| | - Erik Kudela
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, SK-03601, Slovakia
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29
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Abstract
The gastrointestinal tract is continuously exposed to trillions of commensal microbes, collectively termed the microbiota, which are environmental stimuli that can direct health and disease within the host. In addition to well-established bacterial sensing pathways, microbial signals are also integrated through epigenetic modifications that calibrate the transcriptional program of host cells without altering the underlying genetic code. Microbiota-sensitive epigenetic changes include modifications to the DNA or histones, as well as regulation of non-coding RNAs. While microbiota-sensitive epigenetic mechanisms have been described in both local intestinal cells and as well in peripheral tissues, further research is required to fully decipher the complex relationship between the host and microbiota. This Review highlights current understandings of epigenetic regulation by gut microbiota and important implications of these findings in guiding therapeutic approaches to prevent or combat diseases driven by impaired microbiota-host interactions.
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Affiliation(s)
- Vivienne Woo
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Theresa Alenghat
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA,CONTACT Theresa Alenghat Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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30
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Abstract
The intestinal tract is the entry gate for nutrients and symbiotic organisms, being in constant contact with external environment. DNA methylation is one of the keys to how environmental conditions, diet and nutritional status included, shape functionality in the gut and systemically. This review aims to summarise findings on the importance of methylation to gut development, differentiation and function. Evidence to date on how external factors such as diet, dietary supplements, nutritional status and microbiota modifications modulate intestinal function through DNA methylation is also presented.
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Abstract
The interaction between the gut and its eventual trillions of microbe inhabitants during microbial colonization, represents a critical time period for establishing the overall health and wellbeing of an individual. The gut microbiome represents a diverse community of microbes that are critical for many physiological roles of the host including host metabolism. These processes are controlled by a fine-tuned chemical cross talk between the host and microbiota. Although the exact mechanisms behind this cross talk remains elusive, microbiota induced epigenetic mechanisms like DNA methylation and histone modifications may be key. This review presents our perspective on the epigenome as a mediator for host-microbiota cross talk, as well as methodology to study epigenetics, the role of dysbiosis in disease, and how the gut microbiome-host axis may be used in personal medicine.
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32
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Wu Y, Wang CZ, Wan JY, Yao H, Yuan CS. Dissecting the Interplay Mechanism between Epigenetics and Gut Microbiota: Health Maintenance and Disease Prevention. Int J Mol Sci 2021; 22:6933. [PMID: 34203243 PMCID: PMC8267743 DOI: 10.3390/ijms22136933] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/10/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota exists throughout the full life cycle of the human body, and it has been proven to have extensive impacts on health and disease. Accumulating evidence demonstrates that the interplay between gut microbiota and host epigenetics plays a multifaceted role in health maintenance and disease prevention. Intestinal microflora, along with their metabolites, could regulate multiple epigenetic pathways; e.g., DNA methylation, miRNA, or histone modification. Moreover, epigenetic factors can serve as mediators to coordinate gut microbiota within the host. Aiming to dissect this interplay mechanism, the present review summarizes the research profile of gut microbiota and epigenetics in detail, and further interprets the biofunctions of this interplay, especially the regulation of intestinal inflammation, the improvement of metabolic disturbances, and the inhibition of colitis events. This review provides new insights into the interplay of epigenetics and gut microbiota, and attempts to reveal the mysteries of health maintenance and disease prevention from this new perspective.
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Affiliation(s)
- Yuqi Wu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China;
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Chong-Zhi Wang
- Tang Center for Herbal Medicine Research, The University of Chicago, Chicago, IL 60637, USA; (C.-Z.W.); (C.-S.Y.)
- Department of Anesthesia and Critical Care, The University of Chicago, Chicago, IL 60637, USA
| | - Jin-Yi Wan
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China;
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Haiqiang Yao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China;
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Chun-Su Yuan
- Tang Center for Herbal Medicine Research, The University of Chicago, Chicago, IL 60637, USA; (C.-Z.W.); (C.-S.Y.)
- Department of Anesthesia and Critical Care, The University of Chicago, Chicago, IL 60637, USA
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33
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Lorzadeh A, Romero-Wolf M, Goel A, Jadhav U. Epigenetic Regulation of Intestinal Stem Cells and Disease: A Balancing Act of DNA and Histone Methylation. Gastroenterology 2021; 160:2267-2282. [PMID: 33775639 PMCID: PMC8169626 DOI: 10.1053/j.gastro.2021.03.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 02/08/2023]
Abstract
Genetic mutations or regulatory failures underlie cellular malfunction in many diseases, including colorectal cancer and inflammatory bowel diseases. However, mutational defects alone fail to explain the complexity of such disorders. Epigenetic regulation-control of gene action through chemical and structural changes of chromatin-provides a platform to integrate multiple extracellular inputs and prepares the cellular genome for appropriate gene expression responses. Coregulation by polycomb repressive complex 2-mediated trimethylation of lysine 27 on histone 3 and DNA methylation has emerged as one of the most influential epigenetic controls in colorectal cancer and many other diseases, but molecular details remain inadequate. Here we review the molecular interplay of these epigenetic features in relation to gastrointestinal development, homeostasis, and disease biology. We discuss other epigenetic mechanisms pertinent to the balance of trimethylation of lysine 27 on histone 3 and DNA methylation and their actions in gastrointestinal cancers. We also review the current molecular understanding of chromatin control in the pathogenesis of inflammatory bowel diseases.
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Affiliation(s)
- Alireza Lorzadeh
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Maile Romero-Wolf
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Unmesh Jadhav
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.
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34
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Kalbermatter C, Fernandez Trigo N, Christensen S, Ganal-Vonarburg SC. Maternal Microbiota, Early Life Colonization and Breast Milk Drive Immune Development in the Newborn. Front Immunol 2021; 12:683022. [PMID: 34054875 PMCID: PMC8158941 DOI: 10.3389/fimmu.2021.683022] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
The innate immune system is the oldest protection strategy that is conserved across all organisms. Although having an unspecific action, it is the first and fastest defense mechanism against pathogens. Development of predominantly the adaptive immune system takes place after birth. However, some key components of the innate immune system evolve during the prenatal period of life, which endows the newborn with the ability to mount an immune response against pathogenic invaders directly after birth. Undoubtedly, the crosstalk between maternal immune cells, antibodies, dietary antigens, and microbial metabolites originating from the maternal microbiota are the key players in preparing the neonate’s immunity to the outer world. Birth represents the biggest substantial environmental change in life, where the newborn leaves the protective amniotic sac and is exposed for the first time to a countless variety of microbes. Colonization of all body surfaces commences, including skin, lung, and gastrointestinal tract, leading to the establishment of the commensal microbiota and the maturation of the newborn immune system, and hence lifelong health. Pregnancy, birth, and the consumption of breast milk shape the immune development in coordination with maternal and newborn microbiota. Discrepancies in these fine-tuned microbiota interactions during each developmental stage can have long-term effects on disease susceptibility, such as metabolic syndrome, childhood asthma, or autoimmune type 1 diabetes. In this review, we will give an overview of the recent studies by discussing the multifaceted emergence of the newborn innate immune development in line with the importance of maternal and early life microbiota exposure and breast milk intake.
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Affiliation(s)
- Cristina Kalbermatter
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Nerea Fernandez Trigo
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Sandro Christensen
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Stephanie C Ganal-Vonarburg
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
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35
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Haberman Y, Iqbal NT, Ghandikota S, Mallawaarachchi I, Tzipi Braun, Dexheimer PJ, Rahman N, Hadar R, Sadiq K, Ahmad Z, Idress R, Iqbal J, Ahmed S, Hotwani A, Umrani F, Ehsan L, Medlock G, Syed S, Moskaluk C, Ma JZ, Jegga AG, Moore SR, Ali SA, Denson LA. Mucosal Genomics Implicate Lymphocyte Activation and Lipid Metabolism in Refractory Environmental Enteric Dysfunction. Gastroenterology 2021; 160:2055-2071.e0. [PMID: 33524399 PMCID: PMC8113748 DOI: 10.1053/j.gastro.2021.01.221] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Environmental enteric dysfunction (EED) limits the Sustainable Development Goals of improved childhood growth and survival. We applied mucosal genomics to advance our understanding of EED. METHODS The Study of Environmental Enteropathy and Malnutrition (SEEM) followed 416 children from birth to 24 months in a rural district in Pakistan. Biomarkers were measured at 9 months and tested for association with growth at 24 months. The duodenal methylome and transcriptome were determined in 52 undernourished SEEM participants and 42 North American controls and patients with celiac disease. RESULTS After accounting for growth at study entry, circulating insulin-like growth factor-1 (IGF-1) and ferritin predicted linear growth, whereas leptin correlated with future weight gain. The EED transcriptome exhibited suppression of antioxidant, detoxification, and lipid metabolism genes, and induction of anti-microbial response, interferon, and lymphocyte activation genes. Relative to celiac disease, suppression of antioxidant and detoxification genes and induction of antimicrobial response genes were EED-specific. At the epigenetic level, EED showed hyper-methylation of epithelial metabolism and barrier function genes, and hypo-methylation of immune response and cell proliferation genes. Duodenal coexpression modules showed association between lymphocyte proliferation and epithelial metabolic genes and histologic severity, fecal energy loss, and wasting (weight-for-length/height Z < -2.0). Leptin was associated with expression of epithelial carbohydrate metabolism and stem cell renewal genes. Immune response genes were attenuated by giardia colonization. CONCLUSIONS Children with reduced circulating IGF-1 are more likely to experience stunting. Leptin and a gene signature for lymphocyte activation and dysregulated lipid metabolism are implicated in wasting, suggesting new approaches for EED refractory to nutritional intervention. ClinicalTrials.gov, Number: NCT03588013. (https://clinicaltrials.gov/ct2/show/NCT03588013).
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Affiliation(s)
- Yael Haberman
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio,Department of Pediatrics, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Israel
| | - Najeeha T. Iqbal
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Sudhir Ghandikota
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center Cincinnati, Department of Computer Science, University of Cincinnati College of Engineering, Cincinnati, Ohio
| | | | - Tzipi Braun
- Department of Pediatrics, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Israel
| | - Phillip J. Dexheimer
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Najeeb Rahman
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Rotem Hadar
- Department of Pediatrics, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Israel
| | - Kamran Sadiq
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Zubair Ahmad
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Romana Idress
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fayyaz Umrani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Lubaina Ehsan
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia
| | - Greg Medlock
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia
| | - Sana Syed
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan,Department of Pediatrics, University of Virginia, Charlottesville, Virginia
| | - Chris Moskaluk
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia
| | - Jennie Z. Ma
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Anil G. Jegga
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center Cincinnati, Department of Computer Science, University of Cincinnati College of Engineering, Cincinnati, Ohio
| | - Sean R. Moore
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia,Sean R. Moore, MD, MS, Division of Pediatric Gastroenterology, Hepatology, & Nutrition, University of Virginia, 409 Lane Rd., Charlottesville, VA 22908.
| | - Syed Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan.
| | - Lee A. Denson
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio,Correspondence Address correspondence to: Lee A Denson, MD, Division of Pediatric Gastroenterology, Hepatology, & Nutrition, Cincinnati Children’s Hospital Medical Center, MLC 2010, 3333 Burnet Avenue, Cincinnati, Ohio 45229. fax: (513) 636-558.
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36
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Nichols RG, Davenport ER. The relationship between the gut microbiome and host gene expression: a review. Hum Genet 2021; 140:747-760. [PMID: 33221945 PMCID: PMC7680557 DOI: 10.1007/s00439-020-02237-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/06/2020] [Indexed: 12/13/2022]
Abstract
Despite the growing knowledge surrounding host-microbiome interactions, we are just beginning to understand how the gut microbiome influences-and is influenced by-host gene expression. Here, we review recent literature that intersects these two fields, summarizing themes across studies. Work in model organisms, human biopsies, and cell culture demonstrate that the gut microbiome is an important regulator of several host pathways relevant for disease, including immune development and energy metabolism, and vice versa. The gut microbiome remodels host chromatin, causes differential splicing, alters the epigenetic landscape, and directly interrupts host signaling cascades. Emerging techniques like single-cell RNA sequencing and organoid generation have the potential to refine our understanding of the relationship between the gut microbiome and host gene expression in the future. By intersecting microbiome and host gene expression, we gain a window into the physiological processes important for fostering the extensive cross-kingdom interactions and ultimately our health.
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Affiliation(s)
- Robert G. Nichols
- Department of Biology, The Pennsylvania State University, University Park, PA 16802 USA
| | - Emily R. Davenport
- Department of Biology, The Pennsylvania State University, University Park, PA 16802 USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802 USA
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37
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Ren L, Ye J, Zhao B, Sun J, Cao P, Yang Y. The Role of Intestinal Microbiota in Colorectal Cancer. Front Pharmacol 2021; 12:674807. [PMID: 33959032 PMCID: PMC8093878 DOI: 10.3389/fphar.2021.674807] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer is a multifactorial disease involving genetic, environmental, and lifestyle risk factors. Intestinal microbiota plays an important role in the occurrence and development of colorectal cancer. Studies have shown that the behavior of intestinal microbiota can lead to pathological changes in the host intestine, which can be divided into epigenetic changes and carcinogenic changes at the gene level, and ultimately promote the formation and development of colorectal cancer. Intestinal microbiota is mainly distributed in the intestinal epithelium, which is composed of a large number of microorganisms interacting with the host intestinal cells. It can affect the immune-inflammation and metabolism of the gastrointestinal tract, and may be used as a biomarker for disease diagnosis. Regulation of gut microbiota is a promising strategy for the prevention and treatment of colorectal cancer. This article reviews the role of intestinal microbiota in the development of colorectal cancer, including the related mechanisms of intestinal microbiota promoting colorectal cancer, the use of intestinal microbiota in the diagnosis of colorectal cancer, and the regulation of intestinal microbiota in the prevention or treatment of colorectal cancer.
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Affiliation(s)
- Lingli Ren
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Juan Ye
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bing Zhao
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinbing Sun
- Department of General Surgery, Changshu No. 1 People's Hospital, Affiliated Changshu Hospital of Soochow University, Changshu, China
| | - Peng Cao
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yang Yang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.,Yangtze River Pharmaceutical Group, Taizhou, China
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38
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Gut Microbiota and Bipolar Disorder: An Overview on a Novel Biomarker for Diagnosis and Treatment. Int J Mol Sci 2021; 22:ijms22073723. [PMID: 33918462 PMCID: PMC8038247 DOI: 10.3390/ijms22073723] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota is the set of microorganisms that colonize the gastrointestinal tract of living creatures, establishing a bidirectional symbiotic relationship that is essential for maintaining homeostasis, for their growth and digestive processes. Growing evidence supports its involvement in the intercommunication system between the gut and the brain, so that it is called the gut-brain-microbiota axis. It is involved in the regulation of the functions of the Central Nervous System (CNS), behavior, mood and anxiety and, therefore, its implication in the pathogenesis of neuropsychiatric disorders. In this paper, we focused on the possible correlations between the gut microbiota and Bipolar Disorder (BD), in order to determine its role in the pathogenesis and in the clinical management of BD. Current literature supports a possible relationship between the compositional alterations of the intestinal microbiota and BD. Moreover, due to its impact on psychopharmacological treatment absorption, by acting on the composition of the microbiota beneficial effects can be obtained on BD symptoms. Finally, we discussed the potential of correcting gut microbiota alteration as a novel augmentation strategy in BD. Future studies are necessary to better clarify the relevance of gut microbiota alterations as state and disease biomarkers of BD.
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39
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Hageman JH, Heinz MC, Kretzschmar K, van der Vaart J, Clevers H, Snippert HJG. Intestinal Regeneration: Regulation by the Microenvironment. Dev Cell 2021; 54:435-446. [PMID: 32841594 DOI: 10.1016/j.devcel.2020.07.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Accepted: 07/13/2020] [Indexed: 01/05/2023]
Abstract
Damage to the intestinal stem cell niche can result from mechanical stress, infections, chronic inflammation or cytotoxic therapies. Progenitor cells can compensate for insults to the stem cell population through dedifferentiation. The microenvironment modulates this regenerative response by influencing the activity of signaling pathways, including Wnt, Notch, and YAP/TAZ. For instance, mesenchymal cells and immune cells become more abundant after damage and secrete signaling molecules that promote the regenerative process. Furthermore, regeneration is influenced by the nutritional state, microbiome, and extracellular matrix. Here, we review how all these components cooperate to restore epithelial homeostasis in the intestine after injury.
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Affiliation(s)
- Joris H Hageman
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Maria C Heinz
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Kai Kretzschmar
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Mildred-Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Jelte van der Vaart
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, 3521 AL Utrecht, the Netherlands; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands.
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40
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Transcriptional programmes underlying cellular identity and microbial responsiveness in the intestinal epithelium. Nat Rev Gastroenterol Hepatol 2021; 18:7-23. [PMID: 33024279 PMCID: PMC7997278 DOI: 10.1038/s41575-020-00357-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/12/2020] [Indexed: 12/19/2022]
Abstract
The intestinal epithelium serves the unique and critical function of harvesting dietary nutrients, while simultaneously acting as a cellular barrier separating tissues from the luminal environment and gut microbial ecosystem. Two salient features of the intestinal epithelium enable it to perform these complex functions. First, cells within the intestinal epithelium achieve a wide range of specialized identities, including different cell types and distinct anterior-posterior patterning along the intestine. Second, intestinal epithelial cells are sensitive and responsive to the dynamic milieu of dietary nutrients, xenobiotics and microorganisms encountered in the intestinal luminal environment. These diverse identities and responsiveness of intestinal epithelial cells are achieved in part through the differential transcription of genes encoded in their shared genome. Here, we review insights from mice and other vertebrate models into the transcriptional regulatory mechanisms underlying intestinal epithelial identity and microbial responsiveness, including DNA methylation, chromatin accessibility, histone modifications and transcription factors. These studies are revealing that most transcription factors involved in intestinal epithelial identity also respond to changes in the microbiota, raising both opportunities and challenges to discern the underlying integrative transcriptional regulatory networks.
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41
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Zhao Y, Wang C, Goel A. Role of gut microbiota in epigenetic regulation of colorectal Cancer. Biochim Biophys Acta Rev Cancer 2020; 1875:188490. [PMID: 33321173 DOI: 10.1016/j.bbcan.2020.188490] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 02/08/2023]
Abstract
Colorectal cancer (CRC) remains one of the most commonly diagnosed cancers and a leading cause of cancer-related deaths worldwide. The stepwise accumulation of epigenetic alterations in the normal colorectal epithelium has been reported to act as a driving force for the initiation and promotion of tumorigenesis in CRC. From a mechanistic standpoint, emerging evidence indicates that within the colorectal epithelium, the diverse gut microbiota can interact with host cells to regulate multiple physiological processes. In fact, recent studies have found that the gut microbiota represents a potential cause of carcinogenesis, invasion, and metastasis via DNA methylation, histone modifications, and non-coding RNAs - providing an epigenetic perspective for the connection between the gut microbiota and CRC. Herein, we comprehensively review the recent research that provides a comprehensive yet succinct evidence connecting the gut microbiota to CRC at an epigenetic level, including carcinogenic mechanisms of cancer-related microbiota, and the potential for utilizing the gut microbiota as CRC biomarkers. These scientific findings highlight a promising future for manipulating the gut microbiota to improve clinical outcomes in patients suffering from CRC.
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Affiliation(s)
- Yinghui Zhao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, China; Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, China
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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42
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Kellermayer R, Zilbauer M. The Gut Microbiome and the Triple Environmental Hit Concept of Inflammatory Bowel Disease Pathogenesis. J Pediatr Gastroenterol Nutr 2020; 71:589-595. [PMID: 33093364 DOI: 10.1097/mpg.0000000000002908] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The incidence of chronic inflammatory bowel diseases (IBDs), such as Crohn's disease (CD) and ulcerative colitis (UC) have significantly increased in recent decades implicating environmental effects. The developmental origin of disease concept provides a theoretical framework by which the complex interplay between environmental factors and host cells, particularly during vulnerable time periods, ultimately cause disease, such as IBD. Epigenetics has been proposed as the underlying mechanism within this concept, turning environmental triggers into stable changes of cellular function. Adding further to the complexity of IBD is the gut microbiome, which is equally responsive to the environment, and can impact host cell function, where recent findings underscore the stochastic and individualized nature of such effects. We review the microbiome literature through a novel triple environmental hit concept (priming, modulation, and trigger) of IBD pathogenesis. We propose that there are at least 3 distinct stages during an individual's lifespan where random/stochastic events driven by environmental influences are necessary for ultimately developing IBD. By this means, we speculate that microbiome-directed therapeutics carry potential for individualized prevention and dynamic treatment of IBD.
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Affiliation(s)
- Richard Kellermayer
- Section of Pediatric Gastroenterology, Texas Children's Hospital Baylor College of Medicine
- USDA/ARS Children's Nutrition Research Center, Houston, TX
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Epigenome-metabolome-microbiome axis in health and IBD. Curr Opin Microbiol 2020; 56:97-108. [PMID: 32920333 DOI: 10.1016/j.mib.2020.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 12/13/2022]
Abstract
Environmental triggers in the context of genetic susceptibility drive phenotypes of complex immune disorders such as Inflammatory bowel disease (IBD). One such trigger of IBD is perturbations in enteric commensal bacteria, fungi or viruses that shape both immune and neuronal state. The epigenome acts as an interface between microbiota and context-specific gene expression and is thus emerging as a third key contributor to IBD. Here we review evidence that the host epigenome plays a significant role in orchestrating the bidirectional crosstalk between mammals and their commensal microorganisms. We discuss disruption of chromatin regulatory regions and epigenetic enzyme mutants as a causative factor in IBD patients and mouse models of intestinal inflammation and consider the possible translation of this knowledge. Furthermore, we present emerging insights into the intricate connection between the microbiome and epigenetic enzyme activity via host or bacterial metabolites and how these interactions fine-tune the microorganism-host relationship.
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Beaumont M, Paës C, Mussard E, Knudsen C, Cauquil L, Aymard P, Barilly C, Gabinaud B, Zemb O, Fourre S, Gautier R, Lencina C, Eutamène H, Theodorou V, Canlet C, Combes S. Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to-weaning transition. Gut Microbes 2020; 11:1268-1286. [PMID: 32352849 PMCID: PMC7524271 DOI: 10.1080/19490976.2020.1747335] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In suckling mammals, the onset of solid food ingestion is coincident with the maturation of the gut barrier. This ontogenic process is driven by the colonization of the intestine by the microbiota. However, the mechanisms underlying the microbial regulation of the intestinal development in early life are not fully understood. Here, we studied the co-maturation of the microbiota (composition and metabolic activity) and of the gut barrier at the suckling-to-weaning transition by using a combination of experiments in vivo (suckling rabbit model), ex vivo (Ussing chambers) and in vitro (epithelial cell lines and organoids). The microbiota composition, its metabolic activity, para-cellular epithelial permeability and the gene expression of key components of the gut barrier shifted sharply at the onset of solid food ingestion in vivo, despite milk was still predominant in the diet at that time. We found that cecal content sterile supernatant (i.e. containing a mixture of metabolites) obtained after the onset of solid food ingestion accelerated the formation of the epithelial barrier in Caco-2 cells in vitro and our results suggested that these effects were driven by the bacterial metabolite butyrate. Moreover, the treatment of organoids with cecal content sterile supernatant partially replicated in vitro the effects of solid food ingestion on the epithelial barrier in vivo. Altogether, our results show that the metabolites produced by the microbiota at the onset of solid food ingestion contribute to the maturation of the gut barrier at the suckling-to-weaning transition. Targeting the gut microbiota metabolic activity during this key developmental window might therefore be a promising strategy to promote intestinal homeostasis.
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Affiliation(s)
- Martin Beaumont
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France,CONTACT Martin Beaumont GenPhySE, Université De Toulouse, INRAE, ENVT, Castanet-Tolosan, ToulouseF-31326, France
| | - Charlotte Paës
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France,GEC Consortium CCPA, Evialis, Inzo, MixScience, Techna, Toulouse, France
| | - Eloïse Mussard
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Laurent Cauquil
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France
| | - Patrick Aymard
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France
| | - Céline Barilly
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Olivier Zemb
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Roselyne Gautier
- Toxalim (Research Centre in Food Toxicology), Université De Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Corinne Lencina
- Toxalim (Research Centre in Food Toxicology), Université De Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Hélène Eutamène
- Toxalim (Research Centre in Food Toxicology), Université De Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Vassilia Theodorou
- Toxalim (Research Centre in Food Toxicology), Université De Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Cécile Canlet
- Toxalim (Research Centre in Food Toxicology), Université De Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Sylvie Combes
- GenPhySE, Université De Toulouse, INRAE, ENVT, Toulouse, France
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Microbiota modification in hematology: still at the bench or ready for the bedside? Blood Adv 2020; 3:3461-3472. [PMID: 31714965 DOI: 10.1182/bloodadvances.2019000365] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022] Open
Abstract
Growing evidence suggests that human microbiota likely influence diverse processes including hematopoiesis, chemotherapy metabolism, and efficacy, as well as overall survival in patients with hematologic malignancies and other cancers. Both host genetic susceptibility and host-microbiota interactions may impact cancer risk and response to treatment; however, microbiota have the potential to be uniquely modifiable and accessible targets for treatment. Here, we focus on strategies to modify microbiota composition and function in patients with cancer. First, we evaluate the use of fecal microbiota transplant to restore microbial equilibrium following perturbation by antibiotics and chemotherapy, and as a treatment of complications of hematopoietic stem cell transplantation (HSCT), such as graft-versus-host disease and colonization with multidrug-resistant organisms. We then address the potential use of both probiotics and dietary prebiotic compounds in targeted modulation of the microbiota intended to improve outcomes in hematologic diseases. With each type of therapy, we highlight the role that abnormal, or dysbiotic, microbiota play in disease, treatment efficacy, and toxicity and evaluate their potential promise as emerging strategies for microbiota manipulation in patients with hematologic malignancies and in those undergoing HSCT.
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Rashid F, Ahmad S, Irudayaraj JMK. Effect of Perfluorooctanoic Acid on the Epigenetic and Tight Junction Genes of the Mouse Intestine. TOXICS 2020; 8:toxics8030064. [PMID: 32872178 PMCID: PMC7560341 DOI: 10.3390/toxics8030064] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022]
Abstract
Perfluorooctanoic acid (PFOA) has been implicated in various toxicities including neurotoxicity, genotoxicity, nephrotoxicity, epigenetic toxicity, immunotoxicity, reproductive toxicity, and hepatotoxicity. However, information on the accumulation of PFOA in the intestine and its toxic effects on intestinal epigenetics and tight junction (TJ) genes is sparse. CD1 mice were dosed with PFOA (1, 5, 10, or 20 mg/kg/day) for 10 days, and its accumulation and induced alterations in the expression of epigenetic and tight junction genes in the small intestine and colon were evaluated using LC-MS and qPCR techniques. PFOA reduced the expression levels of DNA methyltransferases (Dnmt1, Dnmt3a, Dnmt3b) primarily in the small intestine whereas, in the colon, a decrease was observed only at high concentrations. Moreover, ten-eleven translocation genes (Tet2 and Tet3) expression was dysregulated in the small intestine, whereas in the colon Tets remained unaffected. The tight junction genes Claudins (Cldn), Occludin (Ocln), and Tight Junction Protein (Tjp) were also heavily altered in the small intestine. TJs responded differently across the gut, in proportion to PFOA dosing. Our study reveals that PFOA triggers DNA methylation changes and alters the expression of genes essential for maintaining the physical barrier of intestine, with more profound effects in the small intestine compared to the colon.
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Affiliation(s)
- Faizan Rashid
- Biomedical Research Center in Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL 61801, USA; (F.R.); (S.A.)
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Saeed Ahmad
- Biomedical Research Center in Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL 61801, USA; (F.R.); (S.A.)
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joseph Maria Kumar Irudayaraj
- Biomedical Research Center in Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL 61801, USA; (F.R.); (S.A.)
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: ; Tel.: +1-765-404-0499
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Baulies A, Angelis N, Li VSW. Hallmarks of intestinal stem cells. Development 2020; 147:147/15/dev182675. [PMID: 32747330 DOI: 10.1242/dev.182675] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Intestinal stem cells (ISCs) are highly proliferative cells that fuel the continuous renewal of the intestinal epithelium. Understanding their regulatory mechanisms during tissue homeostasis is key to delineating their roles in development and regeneration, as well as diseases such as bowel cancer and inflammatory bowel disease. Previous studies of ISCs focused mainly on the position of these cells along the intestinal crypt and their capacity for multipotency. However, evidence increasingly suggests that ISCs also exist in distinct cellular states, which can be an acquired rather than a hardwired intrinsic property. In this Review, we summarise the recent findings into how ISC identity can be defined by proliferation state, signalling crosstalk, epigenetics and metabolism, and propose an update on the hallmarks of ISCs. We further discuss how these properties contribute to intestinal development and the dynamics of injury-induced regeneration.
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Affiliation(s)
- Anna Baulies
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nikolaos Angelis
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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48
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Verzi MP, Shivdasani RA. Epigenetic regulation of intestinal stem cell differentiation. Am J Physiol Gastrointest Liver Physiol 2020; 319:G189-G196. [PMID: 32628072 PMCID: PMC7500269 DOI: 10.1152/ajpgi.00084.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To fulfill the lifelong need to supply diverse epithelial cells, intestinal stem cells (ISCs) rely on executing accurate transcriptional programs. This review addresses the mechanisms that control those programs. Genes that define cell behaviors and identities are regulated principally through thousands of dispersed enhancers, each individually <1 kb long and positioned from a few to hundreds of kilobases away from transcription start sites, upstream or downstream from coding genes or within introns. Wnt, Notch, and other epithelial control signals feed into these cis-regulatory DNA elements, which are also common loci of polymorphisms and mutations that confer disease risk. Cell-specific gene activity requires promoters to interact with the correct combination of signal-responsive enhancers. We review the current state of knowledge in ISCs regarding active enhancers, the nucleosome modifications that may enable appropriate and hinder inappropriate enhancer-promoter contacts, and the roles of lineage-restricted transcription factors.
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Affiliation(s)
- Michael P. Verzi
- 1Department of Genetics, Rutgers, State University of New Jersey, Piscataway, New Jersey,2Cancer Institute of New Jersey and Human Genetics Institute of New Jersey, Piscataway, New Jersey
| | - Ramesh A. Shivdasani
- 3Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts,4Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts,5Harvard Stem Cell Institute, Cambridge, Massachusetts
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49
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Xia X, Wu WKK, Wong SH, Liu D, Kwong TNY, Nakatsu G, Yan PS, Chuang YM, Chan MWY, Coker OO, Chen Z, Yeoh YK, Zhao L, Wang X, Cheng WY, Chan MTV, Chan PKS, Sung JJY, Wang MH, Yu J. Bacteria pathogens drive host colonic epithelial cell promoter hypermethylation of tumor suppressor genes in colorectal cancer. MICROBIOME 2020; 8:108. [PMID: 32678024 PMCID: PMC7367367 DOI: 10.1186/s40168-020-00847-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/26/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Altered microbiome composition and aberrant promoter hypermethylation of tumor suppressor genes (TSGs) are two important hallmarks of colorectal cancer (CRC). Here we performed concurrent 16S rRNA gene sequencing and methyl-CpG binding domain-based capture sequencing in 33 tissue biopsies (5 normal colonic mucosa tissues, 4 pairs of adenoma and adenoma-adjacent tissues, and 10 pairs of CRC and CRC-adjacent tissues) to identify significant associations between TSG promoter hypermethylation and CRC-associated bacteria, followed by functional validation of the methylation-associated bacteria. RESULTS Fusobacterium nucleatum and Hungatella hathewayi were identified as the top two methylation-regulating bacteria. Targeted analysis on bona fide TSGs revealed that H. hathewayi and Streptococcus spp. significantly correlated with CDX2 and MLH1 promoter hypermethylation, respectively. Mechanistic validation with cell-line and animal models revealed that F. nucleatum and H. hathewayi upregulated DNA methyltransferase. H. hathewayi inoculation also promoted colonic epithelial cell proliferation in germ-free and conventional mice. CONCLUSION Our integrative analysis revealed previously unknown epigenetic regulation of TSGs in host cells through inducing DNA methyltransferase by F. nucleatum and H. hathewayi, and established the latter as CRC-promoting bacteria. Video abstract.
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Affiliation(s)
- Xiaoxuan Xia
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - William Ka Kei Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Sunny Hei Wong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Dabin Liu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Thomas Ngai Yeung Kwong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Geicho Nakatsu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Pearlly S Yan
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Yu-Ming Chuang
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan, Republic of China
| | - Michael Wing-Yan Chan
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan, Republic of China
| | - Olabisi Oluwabukola Coker
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Yun Kit Yeoh
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Liuyang Zhao
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Xiansong Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Wing Yin Cheng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Matthew Tak Vai Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Paul Kay Sheung Chan
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Joseph Jao Yiu Sung
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China
| | - Maggie Haitian Wang
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China.
| | - Jun Yu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China.
- State Key Laboratory of Digestive Diseases, Institute of Digestive Diseases, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China.
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Special Administrative Region of China.
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50
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Queen J, Zhang J, Sears CL. Oral antibiotic use and chronic disease: long-term health impact beyond antimicrobial resistance and Clostridioides difficile. Gut Microbes 2020; 11:1092-1103. [PMID: 32037950 PMCID: PMC7524332 DOI: 10.1080/19490976.2019.1706425] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We recently reported an increased colon cancer risk associated with oral antibiotic use in a large United Kingdom population. This association between antibiotic exposure and cancer risk adds to a growing body of evidence that antibiotic use has unintended off-target long-term health consequences. This addendum highlights major studies linking antibiotic use and chronic disease in pediatric and adult populations. Microbiota dysbiosis is the key proposed mechanism underlying antibiotic:disease associations, resulting in alterations in gene expression, epigenetic modification, colonization by pathogenic bacteria, instigation of biofilms, and immune regulation and inflammation. These adverse outcomes of antibiotic exposure underscore the need for diagnostic and antibiotic stewardship, as well as the urgency for further development of non-antibiotic therapies for bacterial infections.
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Affiliation(s)
- Jessica Queen
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA,CONTACT Cynthia Sears The Johns Hopkins University School of Medicine, 1550Orleans Street, CRB 2 Bldg., Suite 1M-05, Baltimore, MD21287, USA
| | - Jiajia Zhang
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cynthia L Sears
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA,The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA,The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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