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Liu M, Guo S, Wang L. Systematic review of metabolomic alterations in ulcerative colitis: unveiling key metabolic signatures and pathways. Therap Adv Gastroenterol 2024; 17:17562848241239580. [PMID: 38560428 PMCID: PMC10981261 DOI: 10.1177/17562848241239580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
Background Despite numerous metabolomic studies on ulcerative colitis (UC), the results have been highly variable, making it challenging to identify key metabolic abnormalities in UC. Objectives This study aims to uncover key metabolites and metabolic pathways in UC by analyzing existing metabolomics data. Design A systematic review. Data sources and methods We conducted a comprehensive search in databases (PubMed, Cochrane Library, Embase, and Web of Science) and relevant study references for metabolomic research on UC up to 28 December 2022. Significant metabolite differences between UC patients and controls were identified, followed by an analysis of relevant metabolic pathways. Results This review incorporated 78 studies, identifying 2868 differentially expressed metabolites between UC patients and controls. The metabolites were predominantly from 'lipids and lipid-like molecules' and 'organic acids and derivatives' superclasses. We found 101 metabolites consistently altered in multiple datasets within the same sample type and 78 metabolites common across different sample types. Of these, 62 metabolites exhibited consistent regulatory trends across various datasets or sample types. Pathway analysis revealed 22 significantly altered metabolic pathways, with 6 pathways being recurrently enriched across different sample types. Conclusion This study elucidates key metabolic characteristics in UC, offering insights into molecular mechanisms and biomarker discovery for the disease. Future research could focus on validating these findings and exploring their clinical applications.
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Affiliation(s)
- Meiling Liu
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Siyi Guo
- Chongqing Medical University, Chongqing, China
| | - Liang Wang
- Chongqing Medical University, Chongqing, China
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2
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Questa M, Weimer BC, Fiehn O, Chow B, Hill SL, Ackermann MR, Lidbury JA, Steiner JM, Suchodolski JS, Marsilio S. Unbiased serum metabolomic analysis in cats with naturally occurring chronic enteropathies before and after medical intervention. Sci Rep 2024; 14:6939. [PMID: 38521833 PMCID: PMC10960826 DOI: 10.1038/s41598-024-57004-2] [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: 10/17/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024] Open
Abstract
Chronic enteropathies (CE) are common disorders in cats and the differentiation between the two main underlying diseases, inflammatory bowel disease (IBD) and low-grade intestinal T-cell lymphoma (LGITL), can be challenging. Characterization of the serum metabolome could provide further information on alterations of disease-associated metabolic pathways and may identify diagnostic or therapeutic targets. Unbiased metabolomics analysis of serum from 28 cats with CE (14 cats with IBD, 14 cats with LGITL) and 14 healthy controls identified 1,007 named metabolites, of which 129 were significantly different in cats with CE compared to healthy controls at baseline. Random Forest analysis revealed a predictive accuracy of 90% for differentiating controls from cats with chronic enteropathy. Metabolic pathways found to be significantly altered included phospholipids, amino acids, thiamine, and tryptophan metabolism. Several metabolites were found to be significantly different between cats with IBD versus LGITL, including several sphingolipids, phosphatidylcholine 40:7, uridine, pinitol, 3,4-dihydroxybenzoic acid, and glucuronic acid. However, random forest analysis revealed a poor group predictive accuracy of 60% for the differentiation of IBD from LGITL. Of 129 compounds found to be significantly different between healthy cats and cats with CE at baseline, 58 remained different following treatment.
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Affiliation(s)
- Maria Questa
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Bart C Weimer
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, University of California School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Betty Chow
- VCA Animal Specialty & Emergency Center, Los Angeles, CA, USA
| | - Steve L Hill
- Veterinary Specialty Hospital, San Diego, CA, USA
| | - Mark R Ackermann
- US Department of Agriculture, National Animal Disease Center, Ames, IA, USA
| | - Jonathan A Lidbury
- Gastrointestinal Laboratory, Texas A&M University, College Station, TX, USA
| | - Joerg M Steiner
- Gastrointestinal Laboratory, Texas A&M University, College Station, TX, USA
| | - Jan S Suchodolski
- Gastrointestinal Laboratory, Texas A&M University, College Station, TX, USA
| | - Sina Marsilio
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
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3
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Wu D, Li Z, Zhang Y, Zhang Y, Ren G, Zeng Y, Liu H, Guan W, Zhao X, Li P, Hu L, Hou Z, Gong J, Li J, Jin W, Hu Z, Jiang C, Li H, Zhong C. Proline uptake promotes activation of lymphoid tissue inducer cells to maintain gut homeostasis. Nat Metab 2023; 5:1953-1968. [PMID: 37857730 DOI: 10.1038/s42255-023-00908-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
Metabolic regulation is integral to the proper functioning of innate lymphoid cells, yet the underlying mechanisms remain elusive. Here, we show that disruption of exogenous proline uptake, either through dietary restriction or by deficiency of the proline transporter Slc6a7, in lymphoid tissue inducer (LTi) cells, impairs LTi activation and aggravates dextran sodium sulfate-induced colitis in mice. With an integrative transcriptomic and metabolomic analysis, we profile the metabolic characteristics of various innate lymphoid cell subsets and reveal a notable enrichment of proline metabolism in LTi cells. Mechanistically, defective proline uptake diminishes the generation of reactive oxygen species, previously known to facilitate LTi activation. Additionally, LTi cells deficient in Slc6a7 display downregulation of Cebpb and Kdm6b, resulting in compromised transcriptional and epigenetic regulation of interleukin-22. Furthermore, our study uncovers the therapeutic potential of proline supplementation in alleviating colitis. Therefore, these findings shed light on the role of proline in facilitating LTi activation and ultimately contributing to gut homeostasis.
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Affiliation(s)
- Di Wu
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Zongxian Li
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Yime Zhang
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Yinlian Zhang
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Guanqun Ren
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Yanyu Zeng
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Huiying Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Weiqiang Guan
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, China
| | - Xingyu Zhao
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Peng Li
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Luni Hu
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China
| | - Zhiyuan Hou
- Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Jingjing Gong
- Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Jun Li
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Wenfei Jin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Zeping Hu
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Houhua Li
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, China
| | - Chao Zhong
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China.
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Wang S, van Schooten FJ, Jin H, Jonkers D, Godschalk R. The Involvement of Intestinal Tryptophan Metabolism in Inflammatory Bowel Disease Identified by a Meta-Analysis of the Transcriptome and a Systematic Review of the Metabolome. Nutrients 2023; 15:2886. [PMID: 37447212 DOI: 10.3390/nu15132886] [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: 05/23/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Evidence is emerging for the role of intestinal tryptophan metabolism in the development of inflammatory bowel disease (IBD). In order to identify the role of altered intestinal tryptophan metabolism in IBD pathogenesis, a meta-analysis of the transcriptome was performed to identify differentially expressed genes involved in the tryptophan metabolism pathways in intestinal biopsies of IBD as compared to non-IBD controls. Moreover, a systematic review of the metabolome was performed to identify the concurrent changes in tryptophan metabolites. Integration of the transcriptome and metabolome identified various alterations in intestinal tryptophan metabolism during active disease in IBD patients, including decreased intestinal tryptophan absorption, enhanced kynurenine pathway, increased interstitial serotonin availability, changed indole pathway, and activated aryl hydrocarbon receptor signaling. Therefore, a network of intestinal tryptophan metabolism pathways in IBD could be established, helping to assess the potential of genes and metabolites involved in these pathways as diagnostic markers and targets for IBD management.
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Affiliation(s)
- Shan Wang
- Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Frederik-Jan van Schooten
- Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Han Jin
- Department of Pathology, School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center+ (MUMC+), 6200 MD Maastricht, The Netherlands
| | - Daisy Jonkers
- Department of Internal Medicine, Division Gastroenterology-Hepatology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Roger Godschalk
- Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands
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Colgan SP, Wang RX, Hall CH, Bhagavatula G, Lee JS. Revisiting the "starved gut" hypothesis in inflammatory bowel disease. IMMUNOMETABOLISM (COBHAM, SURREY) 2023; 5:e0016. [PMID: 36644501 PMCID: PMC9831042 DOI: 10.1097/in9.0000000000000016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/22/2022] [Indexed: 01/17/2023]
Abstract
Active episodes of inflammatory bowel disease (IBD), which include ulcerative colitis and Crohn's disease, coincide with profound shifts in the composition of the microbiota and host metabolic energy demand. Intestinal epithelial cells (IEC) that line the small intestine and colon serve as an initial point for contact for the microbiota and play a central role in innate immunity. In the 1980s, Roediger et al proposed the hypothesis that IBD represented a disease of diminished mucosal nutrition and energy deficiency ("starved gut") that strongly coincided with the degree of inflammation. These studies informed the scientific community about the important contribution of microbial-derived metabolites, particularly short-chain fatty acids (SCFA) such as butyrate, to overall energy homeostasis. Decades later, it is appreciated that disease-associated shifts in the microbiota, termed dysbiosis, places inordinate demands on energy acquisition within the mucosa, particularly during active inflammation. Here, we review the topic of tissue energetics in mucosal health and disease from the original perspective of that proposed by the starved gut hypothesis.
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Affiliation(s)
- Sean P. Colgan
- Department of Medicine and the Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, USA
- Rocky Mountain Veterans Hospital, Aurora, CO, USA
| | - Ruth X. Wang
- Department of Medicine and the Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Caroline H.T. Hall
- Department of Medicine and the Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, USA
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital Colorado, Aurora, CO, USA
| | - Geetha Bhagavatula
- Department of Medicine and the Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, USA
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital Colorado, Aurora, CO, USA
| | - J. Scott Lee
- Department of Medicine and the Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, USA
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Sezgin E, Terlemez G, Bozkurt B, Bengi G, Akpinar H, Büyüktorun İ. Quantitative real-time PCR analysis of bacterial biomarkers enable fast and accurate monitoring in inflammatory bowel disease. PeerJ 2022; 10:e14217. [PMID: 36275453 PMCID: PMC9586115 DOI: 10.7717/peerj.14217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/20/2022] [Indexed: 01/24/2023] Open
Abstract
Inflammatory bowel diseases (IBD) affect millions of people worldwide with increasing incidence. Ulcerative colitis (UC) and Crohn's disease (CD) are the two most common IBDs. There is no definite cure for IBD, and response to treatment greatly vary among patients. Therefore, there is urgent need for biomarkers to monitor therapy efficacy, and disease prognosis. We aimed to test whether qPCR analysis of common candidate bacteria identified from a patient's individual fecal microbiome can be used as a fast and reliable personalized microbial biomarker for efficient monitoring of disease course in IBD. Next generation sequencing (NGS) of 16S rRNA gene region identified species level microbiota profiles for a subset of UC, CD, and control samples. Common high abundance bacterial species observed in all three groups, and reported to be associated with IBD are chosen as candidate marker species. These species, and total bacteria amount are quantified in all samples with qPCR. Relative abundance of anti-inflammatory, beneficial Faecalibacterium prausnitzii, Akkermansia muciniphila, and Streptococcus thermophilus was significantly lower in IBD compared to control samples. Moreover, the relative abundance of the examined common species was correlated with the severity of IBD disease. The variance in qPCR data was much lower compared to NGS data, and showed much higher statistical power for clinical utility. The qPCR analysis of target common bacterial species can be a powerful, cost and time efficient approach for monitoring disease status and identify better personalized treatment options for IBD patients.
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Affiliation(s)
- Efe Sezgin
- Izmir Institute of Technology, Izmir, Turkey
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7
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Artemisinin Alleviates Intestinal Inflammation and Metabolic Disturbance in Ulcerative Colitis Rats Induced by DSS. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:6211215. [PMID: 35497913 PMCID: PMC9042626 DOI: 10.1155/2022/6211215] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/08/2022] [Indexed: 12/11/2022]
Abstract
Objective This study is aimed to reveal the possible mechanisms of artemisinin in the treatment of ulcerative colitis (UC) through bioinformatics analysis and experimental verification in UC model rats. Methods Firstly, we searched two microarray data of the Gene Expression Omnibus (GEO) database to explore the differentially expressed genes (DEGs) between UC samples and normal samples. Then, we selected DEGs for gene ontology (GO) function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The acute UC model of rats was established by using 3.5% dextran sulfate sodium (DSS) for 10 days to verify the core pathway. Finally, we evaluated the therapeutic effect of artemisinin at the molecular level and used metabonomics to study the endogenous metabolites in the rat serum. Results We screened in the GEO database and selected two eligible microarray datasets, GSE36807 and GSE9452. We performed GO function and KEGG pathway enrichment analyses of DEGs and found that these DEGs were mainly enriched in the inflammatory response, immune response, and IL-17 and NF-κB signaling pathways. Finally, we verified the IL-17 signaling pathway and key cytokines, and ELISA and immunohistochemical results showed that artemisinin could downregulate the expression of proinflammatory cytokines such as IL-1β and IL-17 in the IL-17 signaling pathway and upregulate the expression of the anti-inflammatory cytokine PPAR-γ. Metabolomics analysis showed that 33 differential metabolites were identified in the artemisinin group (AG) compared to the model group (MG). Differential metabolites were mainly involved in alanine, aspartate, and glutamate metabolism and synthesis and degradation of ketone bodies. Conclusion In this study, we found that artemisinin can significantly inhibit the inflammatory response in UC rats and regulate metabolites and related metabolic pathways. This study provides a foundation for further research on the mechanism of artemisinin in the treatment of UC.
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Metabolomics Insights into Inflammatory Bowel Disease: A Comprehensive Review. Pharmaceuticals (Basel) 2021; 14:ph14111190. [PMID: 34832973 PMCID: PMC8625096 DOI: 10.3390/ph14111190] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic, complex relapsing disorder characterised by immune dysregulation, gut microbiota alteration, and disturbed intestinal permeability. The diagnosis and the management of IBD are challenging due to the recurrent nature and complex evolution of the disease. Furthermore, the molecular mechanism underlying the aetiology and pathogenesis of IBD is still poorly understood. There is an unmet need for novel, reliable, and noninvasive tools for diagnosing and monitoring IBD. In addition, metabolomic profiles may provide a priori determination of optimal therapeutics and reveal novel targets for therapies. This review tries to gather scientific evidence to summarise the emerging contribution of metabolomics to elucidate the mechanisms underlying IBD and changes associated with disease phenotype and therapies, as well as to identify biomarkers with metabolic imbalance in those patients. Metabolite changes during health and disease could provide insights into the disease pathogenesis and the discovery of novel indicators for the diagnosis and prognosis assessment of IBD. Metabolomic studies in IBD have shown changes in tricarboxylic acid cycle intermediates, amino-acid and fatty-acid metabolism, and oxidative pathways. Metabolomics has made progress towards identifying metabolic alterations that may provide clinically useful biomarkers and a deeper understanding of the disease. However, at present, there is insufficient evidence evaluating the predictive accuracy of these molecular signatures and their diagnostic ability, which is necessary before metabolomic data can be translated into clinical practice.
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