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Zhang X, Rao M, Gao P. 5-HT-treated mouse B cells alleviate ulcerative colitis via RIPK1: Insights from proteomic and phosphoproteomic analyses. J Proteomics 2024; 295:105085. [PMID: 38246418 DOI: 10.1016/j.jprot.2024.105085] [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: 07/17/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/23/2024]
Abstract
5-hydroxytryptamine (5-HT) exerts various physiological effects on the intestine through different signaling pathways and molecular transmission mechanisms, including pro- and anti-inflammatory effects. Adoptive transfer of regulatory B cells (Bregs) into colitis mice has exhibited significant therapeutic benefits. We aimed to elucidate the mechanism through which 5-HT-treated B cells alleviate ulcerative colitis. To this end, we analyzed the proteomic and phosphoproteomic profiles of 5-HT-stimulated B cells from naïve mice. We identified 3124 phosphorylation sites in proteins via tandem mass tagging and found 110 differential peptides after protein phosphorylation. Furthermore, we obtained three differential proteins, RIPK1, ATXN2l, and Q8C5K5 through integration of both proteomic datasets. We discovered and validated that 5-HT binds to 5-HT7R and increases the expression of RIPK1 in B cells. We propose a theoretical and experimental basis for further research on the RIPK1 signaling pathway, kinase prediction, and phosphorylation sites in ulcerative colitis. SIGNIFICANCE: Some researchers demonstrated that 5-HT can effectively suppress colitis through a variety of molecular mechanisms. Our study discovered and consistently validated the 5-HT/5-HT7R/RIPK1 pathway, further clarifying the molecular mechanism through which 5-HT stimulates B cells to alleviate intestinal inflammation.
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Affiliation(s)
- Xiuna Zhang
- Department of Gastroenterology, Lequn Branch, The First Hospital of Jilin University, Changchun 130000, China
| | - Min Rao
- Department of Gastroenterology, Lequn Branch, The First Hospital of Jilin University, Changchun 130000, China
| | - Pujun Gao
- Department of Gastroenterology, Lequn Branch, The First Hospital of Jilin University, Changchun 130000, China.
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2
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Cheng T, Xu C, Shao J. Updated immunomodulatory roles of gut flora and microRNAs in inflammatory bowel diseases. Clin Exp Med 2023; 23:1015-1031. [PMID: 36385416 PMCID: PMC9668223 DOI: 10.1007/s10238-022-00935-9] [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: 09/25/2022] [Accepted: 10/27/2022] [Indexed: 11/17/2022]
Abstract
Inflammatory bowel disease is a heterogeneous intestinal inflammatory disorder, including ulcerative colitis (UC) and Crohn's disease (CD). Existing studies have shown that the pathogenesis of IBD is closely related to the host's genetic susceptibility, intestinal flora disturbance and mucosal immune abnormalities, etc. It is generally believed that there are complicated interactions between host immunity and intestinal microflora/microRNAs during the occurrence and progression of IBD. Intestinal flora is mainly composed of bacteria, fungi, viruses and helminths. These commensals are highly implicated in the maintenance of intestinal microenvironment homeostasis alone or in combination. MiRNA is an endogenous non-coding small RNA with a length of 20 to 22 nucleotides, which can perform a variety of biological functions by silencing or activating target genes through complementary pairing bonds. A large quantity of miRNAs are involved in intestinal inflammation, mucosal barrier integrity, autophagy, vesicle transportation and other small RNA alterations in IBD circumstance. In this review, the immunomodulatory roles of gut flora and microRNAs are updated in the occurrence and progression of IBD. Meanwhile, the gut flora and microRNA targeted therapeutic strategies as well as other immunomodulatory approaches including TNF-α monoclonal antibodies are also emphasized in the treatment of IBD.
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Affiliation(s)
- Ting Cheng
- Laboratory of Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 433 Room, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, People's Republic of China
| | - Chen Xu
- Laboratory of Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 433 Room, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, People's Republic of China
| | - Jing Shao
- Laboratory of Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 433 Room, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, People's Republic of China.
- Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, People's Republic of China.
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3
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Andersen V, Bennike TB, Bang C, Rioux JD, Hébert-Milette I, Sato T, Hansen AK, Nielsen OH. Investigating the Crime Scene-Molecular Signatures in Inflammatory Bowel Disease. Int J Mol Sci 2023; 24:11217. [PMID: 37446397 PMCID: PMC10342864 DOI: 10.3390/ijms241311217] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are without cure and troublesome to manage because of the considerable diversity between patients and the lack of reliable biomarkers. Several studies have demonstrated that diet, gut microbiota, genetics and other patient factors are essential for disease occurrence and progression. Understanding the link between these factors is crucial for identifying molecular signatures that identify biomarkers to advance the management of IBD. Recent technological breakthroughs and data integration have fuelled the intensity of this research. This research demonstrates that the effect of diet depends on patient factors and gut microbial activity. It also identifies a range of potential biomarkers for IBD management, including mucosa-derived cytokines, gasdermins and neutrophil extracellular traps, all of which need further evaluation before clinical translation. This review provides an update on cutting-edge research in IBD that aims to improve disease management and patient quality of life.
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Affiliation(s)
- Vibeke Andersen
- Molecular Diagnostic and Clinical Research Unit, University Hospital of Southern Denmark, Institute of Regional Research, University of Southern Denmark, 5000 Odense, Denmark;
- Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Tue B. Bennike
- Molecular Diagnostic and Clinical Research Unit, University Hospital of Southern Denmark, Institute of Regional Research, University of Southern Denmark, 5000 Odense, Denmark;
- Medical Microbiology and Immunology, Department of Health Science and Technology, Aalborg University, 9000 Aalborg, Denmark
| | - Corinna Bang
- Institute for Clinical Molecular Biology, Christian-Albrecht’s University, 24105 Kiel, Germany;
| | - John D. Rioux
- Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; (J.D.R.); (I.H.-M.)
- Montreal Heart Institute Research Institute, Montreal, QC H1T 1C8, Canada
| | - Isabelle Hébert-Milette
- Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; (J.D.R.); (I.H.-M.)
- Montreal Heart Institute Research Institute, Montreal, QC H1T 1C8, Canada
| | - Toshiro Sato
- Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan;
| | - Axel K. Hansen
- Experimental Animal Models, Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark;
| | - Ole H. Nielsen
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
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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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Massimino L, Barchi A, Mandarino FV, Spanò S, Lamparelli LA, Vespa E, Passaretti S, Peyrin-Biroulet L, Savarino EV, Jairath V, Ungaro F, Danese S. A multi-omic analysis reveals the esophageal dysbiosis as the predominant trait of eosinophilic esophagitis. J Transl Med 2023; 21:46. [PMID: 36698146 PMCID: PMC9875471 DOI: 10.1186/s12967-023-03898-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Eosinophilic esophagitis (EoE) is a chronic immune-mediated rare disease, characterized by esophageal dysfunctions. It is likely to be primarily activated by food antigens and is classified as a chronic disease for most patients. Therefore, a deeper understanding of the pathogenetic mechanisms underlying EoE is needed to implement and improve therapeutic lines of intervention and ameliorate overall patient wellness. METHODS RNA-seq data of 18 different studies on EoE, downloaded from NCBI GEO with faster-qdump ( https://github.com/ncbi/sra-tools ), were batch-corrected and analyzed for transcriptomics and metatranscriptomics profiling as well as biological process functional enrichment. The EoE TaMMA web app was designed with plotly and dash. Tabula Sapiens raw data were downloaded from the UCSC Cell Browser. Esophageal single-cell raw data analysis was performed within the Automated Single-cell Analysis Pipeline. Single-cell data-driven bulk RNA-seq data deconvolution was performed with MuSiC and CIBERSORTx. Multi-omics integration was performed with MOFA. RESULTS The EoE TaMMA framework pointed out disease-specific molecular signatures, confirming its reliability in reanalyzing transcriptomic data, and providing new EoE-specific molecular markers including CXCL14, distinguishing EoE from gastroesophageal reflux disorder. EoE TaMMA also revealed microbiota dysbiosis as a predominant characteristic of EoE pathogenesis. Finally, the multi-omics analysis highlighted the presence of defined classes of microbial entities in subsets of patients that may participate in inducing the antigen-mediated response typical of EoE pathogenesis. CONCLUSIONS Our study showed that the complex EoE molecular network may be unraveled through advanced bioinformatics, integrating different components of the disease process into an omics-based network approach. This may implement EoE management and treatment in the coming years.
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Affiliation(s)
- Luca Massimino
- grid.18887.3e0000000417581884Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy ,grid.18887.3e0000000417581884Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Alberto Barchi
- grid.18887.3e0000000417581884Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Francesco Vito Mandarino
- grid.18887.3e0000000417581884Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Salvatore Spanò
- grid.18887.3e0000000417581884Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy ,grid.18887.3e0000000417581884Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Edoardo Vespa
- grid.18887.3e0000000417581884Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Sandro Passaretti
- grid.18887.3e0000000417581884Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Laurent Peyrin-Biroulet
- grid.29172.3f0000 0001 2194 6418Inserm NGERE, University of Lorraine, Vandoeuvre-les-Nancy, France ,grid.410527.50000 0004 1765 1301Nancy University Hospital, Vandoeuvre-les-Nancy, France
| | - Edoardo Vincenzo Savarino
- grid.5608.b0000 0004 1757 3470Department of Surgery, Oncology, and Gastroenterology, University of Padua, Padua, Italy ,grid.5608.b0000 0004 1757 3470Gastroenterology Unit, Azienda Ospedale Università di Padova, Padua, Italy
| | - Vipul Jairath
- grid.39381.300000 0004 1936 8884Department of Medicine, Division of Gastroenterology, Western University, London, ON Canada
| | - Federica Ungaro
- grid.18887.3e0000000417581884Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy ,grid.18887.3e0000000417581884Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy ,grid.15496.3f0000 0001 0439 0892Faculty of Medicine, Università Vita-Salute San Raffaele, Milan, Italy
| | - Silvio Danese
- grid.18887.3e0000000417581884Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milan, Italy ,grid.18887.3e0000000417581884Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy ,grid.15496.3f0000 0001 0439 0892Faculty of Medicine, Università Vita-Salute San Raffaele, Milan, Italy
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Sudhakar P, Wellens J, Verstockt B, Ferrante M, Sabino J, Vermeire S. Holistic healthcare in inflammatory bowel disease: time for patient-centric approaches? Gut 2023; 72:192-204. [PMID: 36171081 DOI: 10.1136/gutjnl-2022-328221] [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: 07/06/2022] [Accepted: 09/12/2022] [Indexed: 02/04/2023]
Abstract
Inflammatory bowel disease (IBD) is an emerging global disease characterised by chronic inflammation of the gastrointestinal tract. However, IBD is also manifested by several extraintestinal symptoms which, along with the intestinal symptoms, impact on the mental and emotional well-being of patients. Despite therapeutic advancements, only one-third of the diagnosed patients receiving approved medical treatments achieve short-term to medium-term remission. Consequently, patients who do not get successfully treated might resort to using complementary and alternative approaches to manage their symptoms, with or without consulting their treating clinician. Despite their possible potential, such approaches have various risks stemming from unknown adverse reactions and possible interference with medically approved therapies. In this study, we present the results of a well-performed literature review where we included randomised clinical trials which have assessed the efficacy of complementary approaches and dietary therapy on at least one of the following four outcomes: clinical remission, endoscopic remission, modulation of molecular biomarkers or quality of life metrics. By pointing out intraoutcome and interoutcome concordance, we identified possible candidates for clinical adoption and further study in larger randomised clinical trials covering the broad spectrum of IBD heterogeneity. We finally proposed a patient-centric clinical care model and a series of recommendations for stakeholders, with special attention to complementary approaches and dietary strategies, aimed at achieving holistic remission.
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Affiliation(s)
- Padhmanand Sudhakar
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders, KU Leuven, Leuven, Belgium
| | - Judith Wellens
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders, KU Leuven, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Bram Verstockt
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Marc Ferrante
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - João Sabino
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Séverine Vermeire
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
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Functional Genomics Analysis to Disentangle the Role of Genetic Variants in Major Depression. Genes (Basel) 2022; 13:genes13071259. [PMID: 35886042 PMCID: PMC9320424 DOI: 10.3390/genes13071259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 02/06/2023] Open
Abstract
Understanding the molecular basis of major depression is critical for identifying new potential biomarkers and drug targets to alleviate its burden on society. Leveraging available GWAS data and functional genomic tools to assess regulatory variation could help explain the role of major depression-associated genetic variants in disease pathogenesis. We have conducted a fine-mapping analysis of genetic variants associated with major depression and applied a pipeline focused on gene expression regulation by using two complementary approaches: cis-eQTL colocalization analysis and alteration of transcription factor binding sites. The fine-mapping process uncovered putative causally associated variants whose proximal genes were linked with major depression pathophysiology. Four colocalizing genetic variants altered the expression of five genes, highlighting the role of SLC12A5 in neuronal chlorine homeostasis and MYRF in nervous system myelination and oligodendrocyte differentiation. The transcription factor binding analysis revealed the potential role of rs62259947 in modulating P4HTM expression by altering the YY1 binding site, altogether regulating hypoxia response. Overall, our pipeline could prioritize putative causal genetic variants in major depression. More importantly, it can be applied when only index genetic variants are available. Finally, the presented approach enabled the proposal of mechanistic hypotheses of these genetic variants and their role in disease pathogenesis.
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