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Rangon CM, Niezgoda A, Moyse E, Porges SW. Editorial: Vagus nerve-mediated drive in supporting homeostasis: optimizing global health through monitoring and stimulating vagal function. Front Physiol 2023; 14:1279258. [PMID: 37745246 PMCID: PMC10513081 DOI: 10.3389/fphys.2023.1279258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Affiliation(s)
- Claire Marie Rangon
- Child Neurologist and Pain Specialist, INWE’CARE Medical Center, Saint-Cloud, France
| | - Adam Niezgoda
- Department of Neurology, Heliodor Swiecicki University Hospital, University of Medical Sciences of Poznań, Poznań, Poland
| | - Emmanuel Moyse
- INRAE Centre Val-de-Loire, Physiology of Reproduction and Behavior Unit (PRC UMR-85), Nouzilly, France
| | - Stephen W. Porges
- Traumatic Stress Research Consortium, Kinsey Institute, Indiana University, Bloomington, IN, United States
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Gutierrez-Angulo M, Ayala-Madrigal MDLL, Moreno-Ortiz JM, Peregrina-Sandoval J, Garcia-Ayala FD. Microbiota composition and its impact on DNA methylation in colorectal cancer. Front Genet 2023; 14:1037406. [PMID: 37614819 PMCID: PMC10442805 DOI: 10.3389/fgene.2023.1037406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 07/20/2023] [Indexed: 08/25/2023] Open
Abstract
Colorectal cancer is a complex disease resulting from the interaction of genetics, epigenetics, and environmental factors. DNA methylation is frequently found in tumor suppressor genes to promote cancer development. Several factors are associated with changes in the DNA methylation pattern, and recently, the gastrointestinal microbiota could be associated with this epigenetic change. The predominant phyla in gut microbiota are Firmicutes and Bacteroidetes; however, an enrichment of Bacteroides fragilis, Fusobacterium nucleatum, and Streptococcus bovis, among others, has been reported in colorectal cancer, although the composition could be influenced by several factors, including diet, age, sex, and cancer stage. Fusobacterium nucleatum, a gram-negative anaerobic bacillus, is mainly associated with colorectal cancer patients positive for the CpG island methylator phenotype, although hypermethylation in genes such as MLH1, CDKN2A, MTSS1, RBM38, PKD1, PTPRT, and EYA4 has also been described. Moreover, Hungatella hathewayi, a gram-positive, rod-shaped bacterium, is related to hypermethylation in SOX11, THBD, SFRP2, GATA5, ESR1, EYA4, CDX2, and APC genes. The underlying epigenetic mechanism is unclear, although it could be implicated in the regulation of DNA methyltransferases, enzymes that catalyze the transfer of a methyl group on cytosine of CpG sites. Since DNA methylation is a reversible event, changes in gut microbiota could modulate the gene expression through DNA methylation and improve the colorectal cancer prognosis.
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Affiliation(s)
- Melva Gutierrez-Angulo
- Departamento de Ciencias de la Salud, Centro Universitario de los Altos, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
- Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Maria de la Luz Ayala-Madrigal
- Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Jose Miguel Moreno-Ortiz
- Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Jorge Peregrina-Sandoval
- Departamento de Biología Celular y Molecular, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Fernando Daniel Garcia-Ayala
- Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
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Big Data in Gastroenterology Research. Int J Mol Sci 2023; 24:ijms24032458. [PMID: 36768780 PMCID: PMC9916510 DOI: 10.3390/ijms24032458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Studying individual data types in isolation provides only limited and incomplete answers to complex biological questions and particularly falls short in revealing sufficient mechanistic and kinetic details. In contrast, multi-omics approaches to studying health and disease permit the generation and integration of multiple data types on a much larger scale, offering a comprehensive picture of biological and disease processes. Gastroenterology and hepatobiliary research are particularly well-suited to such analyses, given the unique position of the luminal gastrointestinal (GI) tract at the nexus between the gut (mucosa and luminal contents), brain, immune and endocrine systems, and GI microbiome. The generation of 'big data' from multi-omic, multi-site studies can enhance investigations into the connections between these organ systems and organisms and more broadly and accurately appraise the effects of dietary, pharmacological, and other therapeutic interventions. In this review, we describe a variety of useful omics approaches and how they can be integrated to provide a holistic depiction of the human and microbial genetic and proteomic changes underlying physiological and pathophysiological phenomena. We highlight the potential pitfalls and alternatives to help avoid the common errors in study design, execution, and analysis. We focus on the application, integration, and analysis of big data in gastroenterology and hepatobiliary research.
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Kayongo A, Robertson NM, Siddharthan T, Ntayi ML, Ndawula JC, Sande OJ, Bagaya BS, Kirenga B, Mayanja-Kizza H, Joloba ML, Forslund SK. Airway microbiome-immune crosstalk in chronic obstructive pulmonary disease. Front Immunol 2023; 13:1085551. [PMID: 36741369 PMCID: PMC9890194 DOI: 10.3389/fimmu.2022.1085551] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Chronic Obstructive Pulmonary Disease (COPD) has significantly contributed to global mortality, with three million deaths reported annually. This impact is expected to increase over the next 40 years, with approximately 5 million people predicted to succumb to COPD-related deaths annually. Immune mechanisms driving disease progression have not been fully elucidated. Airway microbiota have been implicated. However, it is still unclear how changes in the airway microbiome drive persistent immune activation and consequent lung damage. Mechanisms mediating microbiome-immune crosstalk in the airways remain unclear. In this review, we examine how dysbiosis mediates airway inflammation in COPD. We give a detailed account of how airway commensal bacteria interact with the mucosal innate and adaptive immune system to regulate immune responses in healthy or diseased airways. Immune-phenotyping airway microbiota could advance COPD immunotherapeutics and identify key open questions that future research must address to further such translation.
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Affiliation(s)
- Alex Kayongo
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda,Department of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda,Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda,Department of Medicine, Center for Emerging Pathogens, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, NJ, United States
| | | | - Trishul Siddharthan
- Division of Pulmonary Medicine, School of Medicine, University of Miami, Miami, FL, United States
| | - Moses Levi Ntayi
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda,Department of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda,Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Josephine Caren Ndawula
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Obondo J. Sande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Bernard S. Bagaya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Bruce Kirenga
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Harriet Mayanja-Kizza
- Department of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses L. Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Sofia K. Forslund
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany,Experimental and Clinical Research Center, a cooperation of Charité - Universitatsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany,Charité-Universitatsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany,*Correspondence: Sofia K. Forslund,
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Fabozzi G, Rebuzzini P, Cimadomo D, Allori M, Franzago M, Stuppia L, Garagna S, Ubaldi FM, Zuccotti M, Rienzi L. Endocrine-Disrupting Chemicals, Gut Microbiota, and Human (In)Fertility-It Is Time to Consider the Triad. Cells 2022; 11:3335. [PMID: 36359730 PMCID: PMC9654651 DOI: 10.3390/cells11213335] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 07/29/2023] Open
Abstract
The gut microbiota (GM) is a complex and dynamic population of microorganisms living in the human gastrointestinal tract that play an important role in human health and diseases. Recent evidence suggests a strong direct or indirect correlation between GM and both male and female fertility: on the one hand, GM is involved in the regulation of sex hormone levels and in the preservation of the blood-testis barrier integrity; on the other hand, a dysbiotic GM is linked to the onset of pro-inflammatory conditions such as endometriosis or PCOS, which are often associated with infertility. Exposure to endocrine-disrupting chemicals (EDCs) is one of the main causes of GM dysbiosis, with important consequences to the host health and potential transgenerational effects. This perspective article aims to show that the negative effects of EDCs on reproduction are in part due to a dysbiotic GM. We will highlight (i) the link between GM and male and female fertility; (ii) the mechanisms of interaction between EDCs and GM; and (iii) the importance of the maternal-fetal GM axis for offspring growth and development.
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Affiliation(s)
- Gemma Fabozzi
- B-Woman, Via dei Monti Parioli 6, 00197 Rome, Italy
- Clinica Valle Giulia, GeneraLife IVF, Via De Notaris 2B, 00197 Rome, Italy
| | - Paola Rebuzzini
- Laboratory of Developmental Biology, Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Danilo Cimadomo
- Clinica Valle Giulia, GeneraLife IVF, Via De Notaris 2B, 00197 Rome, Italy
| | | | - Marica Franzago
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Liborio Stuppia
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Department of Psychological, Health and Territorial Sciences, School of Medicine and Health Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Silvia Garagna
- Laboratory of Developmental Biology, Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
- Centre for Health Technologies (CHT), University of Pavia, Via Ferrata 5, 27100 Pavia, Italy
| | | | - Maurizio Zuccotti
- Laboratory of Developmental Biology, Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
- Centre for Health Technologies (CHT), University of Pavia, Via Ferrata 5, 27100 Pavia, Italy
| | - Laura Rienzi
- Clinica Valle Giulia, GeneraLife IVF, Via De Notaris 2B, 00197 Rome, Italy
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Via Sant’Andrea 34, 61029 Urbino, Italy
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Functional implications of the CpG island methylation in the pathogenesis of celiac disease. Mol Biol Rep 2022; 49:10051-10064. [PMID: 35633417 DOI: 10.1007/s11033-022-07585-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/09/2022] [Indexed: 10/18/2022]
Abstract
Investigation of gene-environment cross talk through epigenetic modifications led to better understanding of the number of complex diseases. Clinical heterogeneity and differential treatment response often contributed by the epigenetic signatures which could be personal. DNA methylation at CpG islands presents a critical nuclear process as a result of gene-environment interactions. These CpG islands are frequently present near the promoter sequence of genes and get differentially methylated under specific environmental conditions. Technical advancements facilitate in high throughput screening of differentially methylated CpG islands. Recent epigenetic studies unraveled several CD susceptibility genes expressed in peripheral blood lymphocytes (PBLs), duodenal mucosa, lamina and epithelial cells that are influenced by differentially methylated CpG islands. Here we highlighted these susceptibility genes; classify these genes based on cellular functions and tissue of expression. We further discussed how these genes interacts with each other to influence critical pathways like NF-κB signaling pathway, IL-17 signaling cascade, RIG-I like receptor signaling pathway, NOD-like receptor pathways among several others. This review also shed light on how gut microbiota may lead to the differential methylation of CpG islands of CD susceptibility genes. Large scale epigenetic studies followed by estimation of heritability of these CpG methylation and polygenic risk score estimation of these genes would prioritize potentially druggable targets for better therapeutics. In vivo studies are warranted to unravel further cellular responses to CpG methylation.
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