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Bildstein T, Charbit-Henrion F, Azabdaftari A, Cerf-Bensussan N, Uhlig HH. Cellular and molecular basis of proximal small intestine disorders. Nat Rev Gastroenterol Hepatol 2024:10.1038/s41575-024-00962-9. [PMID: 39117867 DOI: 10.1038/s41575-024-00962-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
Abstract
The proximal part of the small intestine, including duodenum and jejunum, is not only dedicated to nutrient digestion and absorption but is also a highly regulated immune site exposed to environmental factors. Host-protective responses against pathogens and tolerance to food antigens are essential functions in the small intestine. The cellular ecology and molecular pathways to maintain those functions are complex. Maladaptation is highlighted by common immune-mediated diseases such as coeliac disease, environmental enteric dysfunction or duodenal Crohn's disease. An expanding spectrum of more than 100 rare monogenic disorders inform on causative molecular mechanisms of nutrient absorption, epithelial homeostasis and barrier function, as well as inflammatory immune responses and immune regulation. Here, after summarizing the architectural and cellular traits that underlie the functions of the proximal intestine, we discuss how the integration of tissue immunopathology and molecular mechanisms can contribute towards our understanding of disease and guide diagnosis. We propose an integrated mechanism-based taxonomy and discuss the latest experimental approaches to gain new mechanistic insight into these disorders with large disease burden worldwide as well as implications for therapeutic interventions.
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Affiliation(s)
- Tania Bildstein
- Great Ormond Street Hospital for Children, Department of Paediatric Gastroenterology, London, UK
| | - Fabienne Charbit-Henrion
- Department of Genomic Medicine for Rare Diseases, Necker-Enfants Malades Hospital, APHP, University of Paris-Cité, Paris, France
- INSERM UMR1163, Intestinal Immunity, Institut Imagine, Paris, France
| | - Aline Azabdaftari
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Oxford, UK
| | | | - Holm H Uhlig
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Oxford, UK.
- Department of Paediatrics, University of Oxford, Oxford, UK.
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK.
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Tun HM, Peng Y, Massimino L, Sin ZY, Parigi TL, Facoetti A, Rahman S, Danese S, Ungaro F. Gut virome in inflammatory bowel disease and beyond. Gut 2024; 73:350-360. [PMID: 37949638 PMCID: PMC10850733 DOI: 10.1136/gutjnl-2023-330001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023]
Abstract
OBJECTIVE The gut virome is a dense community of viruses inhabiting the gastrointestinal tract and an integral part of the microbiota. The virome coexists with the other components of the microbiota and with the host in a dynamic equilibrium, serving as a key contributor to the maintenance of intestinal homeostasis and functions. However, this equilibrium can be interrupted in certain pathological states, including inflammatory bowel disease, causing dysbiosis that may participate in disease pathogenesis. Nevertheless, whether virome dysbiosis is a causal or bystander event requires further clarification. DESIGN This review seeks to summarise the latest advancements in the study of the gut virome, highlighting its cross-talk with the mucosal microenvironment. It explores how cutting-edge technologies may build upon current knowledge to advance research in this field. An overview of virome transplantation in diseased gastrointestinal tracts is provided along with insights into the development of innovative virome-based therapeutics to improve clinical management. RESULTS Gut virome dysbiosis, primarily driven by the expansion of Caudovirales, has been shown to impact intestinal immunity and barrier functions, influencing overall intestinal homeostasis. Although emerging innovative technologies still need further implementation, they display the unprecedented potential to better characterise virome composition and delineate its role in intestinal diseases. CONCLUSIONS The field of gut virome is progressively expanding, thanks to the advancements of sequencing technologies and bioinformatic pipelines. These have contributed to a better understanding of how virome dysbiosis is linked to intestinal disease pathogenesis and how the modulation of virome composition may help the clinical intervention to ameliorate gut disease management.
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Affiliation(s)
- Hein Min Tun
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- JC School of Public Health and Primary Care, Faculty of medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ye Peng
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- JC School of Public Health and Primary Care, Faculty of medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Luca Massimino
- Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Zhen Ye Sin
- JC School of Public Health and Primary Care, Faculty of medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tommaso Lorenzo Parigi
- Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
- Università Vita-Salute San Raffaele Facoltà di Medicina e Chirurgia, Milano, Italy
| | - Amanda Facoetti
- Università Vita-Salute San Raffaele Facoltà di Medicina e Chirurgia, Milano, Italy
| | | | - Silvio Danese
- Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
- Università Vita-Salute San Raffaele Facoltà di Medicina e Chirurgia, Milano, Italy
| | - Federica Ungaro
- Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
- Università Vita-Salute San Raffaele Facoltà di Medicina e Chirurgia, Milano, Italy
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Chanpong A, Alves MM, Bonora E, De Giorgio R, Thapar N. Evaluating the molecular and genetic mechanisms underlying gut motility disorders. Expert Rev Gastroenterol Hepatol 2023; 17:1301-1312. [PMID: 38117595 DOI: 10.1080/17474124.2023.2296558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/14/2023] [Indexed: 12/22/2023]
Abstract
INTRODUCTION Gastrointestinal (GI) motility disorders comprise a wide range of different diseases affecting the structural or functional integrity of the GI neuromusculature. Their clinical presentation and burden of disease depends on the predominant location and extent of gut involvement as well as the component of the gut neuromusculature affected. AREAS COVERED A comprehensive literature review was conducted using the PubMed and Medline databases to identify articles related to GI motility and functional disorders, published between 2016 and 2023. In this article, we highlight the current knowledge of molecular and genetic mechanisms underlying GI dysmotility, including disorders of gut-brain interaction, which involve both GI motor and sensory disturbance. EXPERT OPINION Although the pathophysiology and molecular mechanisms underlying many such disorders remain unclear, recent advances in the assessment of intestinal tissue samples, genetic testing with the application of 'omics' technologies and the use of animal models will provide better insights into disease pathogenesis as well as opportunities to improve therapy.
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Affiliation(s)
- Atchariya Chanpong
- Division of Gastroenterology and Hepatology, Department of Pediatrics, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Neurogastroenterology & Motility Unit, Gastroenterology Department, Great Ormond Street Hospital for Children, London, UK
| | - Maria M Alves
- Department of Clinical Genetics, Erasmus University Medical Center, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Elena Bonora
- Department of Medical and Surgical Sciences, DIMEC, University of Bologna, Bologna, Italy
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, AOUB, Bologna, Italy
| | - Roberto De Giorgio
- Department of Translational Sciences, University of Ferrara, Ferrara, Italy
| | - Nikhil Thapar
- Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
- Gastroenterology, Hepatology and Liver Transplant, Queensland Children's Hospital, Brisbane, Australia
- School of Medicine, University of Queensland, Brisbane, Australia
- Woolworths Centre for Child Nutrition Research, Queensland University of Technology, Brisbane, Australia
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Singh R, He X, Park AK, Hardison RC, Zhu X, Li Q. RETROFIT: Reference-free deconvolution of cell-type mixtures in spatial transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544126. [PMID: 37333291 PMCID: PMC10274808 DOI: 10.1101/2023.06.07.544126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Spatial transcriptomics (ST) profiles gene expression in intact tissues. However, ST data measured at each spatial location may represent gene expression of multiple cell types, making it difficult to identify cell-type-specific transcriptional variation across spatial contexts. Existing cell-type deconvolutions of ST data often require single-cell transcriptomic references, which can be limited by availability, completeness and platform effect of such references. We present RETROFIT, a reference-free Bayesian method that produces sparse and interpretable solutions to deconvolve cell types underlying each location independent of single-cell transcriptomic references. Results from synthetic and real ST datasets acquired by Slide-seq and Visium platforms demonstrate that RETROFIT outperforms existing reference-based and reference-free methods in estimating cell-type composition and reconstructing gene expression. Applying RETROFIT to human intestinal development ST data reveals spatiotemporal patterns of cellular composition and transcriptional specificity. RETROFIT is available at https://bioconductor.org/packages/release/bioc/html/retrofit.html.
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Affiliation(s)
- Roopali Singh
- The Pennsylvania State University, University Park, PA 16802
| | - Xi He
- The Pennsylvania State University, University Park, PA 16802
| | | | | | - Xiang Zhu
- The Pennsylvania State University, University Park, PA 16802
| | - Qunhua Li
- The Pennsylvania State University, University Park, PA 16802
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Bagyánszki M, Bódi N. Key elements determining the intestinal region-specific environment of enteric neurons in type 1 diabetes. World J Gastroenterol 2023; 29:2704-2716. [PMID: 37274063 PMCID: PMC10237112 DOI: 10.3748/wjg.v29.i18.2704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/28/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023] Open
Abstract
Diabetes, as a metabolic disorder, is accompanied with several gastrointestinal (GI) symptoms, like abdominal pain, gastroparesis, diarrhoea or constipation. Serious and complex enteric nervous system damage is confirmed in the background of these diabetic motility complaints. The anatomical length of the GI tract, as well as genetic, developmental, structural and functional differences between its segments contribute to the distinct, intestinal region-specific effects of hyperglycemia. These observations support and highlight the importance of a regional approach in diabetes-related enteric neuropathy. Intestinal large and microvessels are essential for the blood supply of enteric ganglia. Bidirectional morpho-functional linkage exists between enteric neurons and enteroglia, however, there is also a reciprocal communication between enteric neurons and immune cells on which intestinal microbial composition has crucial influence. From this point of view, it is more appropriate to say that enteric neurons partake in multidirectional communication and interact with these key players of the intestinal wall. These interplays may differ from segment to segment, thus, the microenvironment of enteric neurons could be considered strictly regional. The goal of this review is to summarize the main tissue components and molecular factors, such as enteric glia cells, interstitial cells of Cajal, gut vasculature, intestinal epithelium, gut microbiota, immune cells, enteroendocrine cells, pro-oxidants, antioxidant molecules and extracellular matrix, which create and determine a gut region-dependent neuronal environment in diabetes.
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Affiliation(s)
- Mária Bagyánszki
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Szeged H-6726, Hungary
| | - Nikolett Bódi
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Szeged H-6726, Hungary
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Perbal B. The power of combined spatial transcriptomics and genome wide association studies (GWAS) approaches to heritable prostate cancer. J Cell Commun Signal 2023; 17:5-6. [PMID: 36692634 PMCID: PMC10030723 DOI: 10.1007/s12079-023-00724-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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