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Li Y, Han S. Metabolomic Applications in Gut Microbiota-Host Interactions in Human Diseases. Gastroenterol Clin North Am 2024; 53:383-397. [PMID: 39068001 DOI: 10.1016/j.gtc.2023.12.008] [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] [Indexed: 07/30/2024]
Abstract
The human gut microbiota, consisting of trillions of microorganisms, encodes diverse metabolic pathways that impact numerous aspects of host physiology. One key way in which gut bacteria interact with the host is through the production of small metabolites. Several of these microbiota-dependent metabolites, such as short-chain fatty acids, have been shown to modulate host diseases. In this review, we examine how disease-associated metabolic signatures are identified using metabolomic platforms, and where metabolomics is applied in gut microbiota-disease interactions. We further explore how integration of metagenomic and metabolomic data in human studies can facilitate biomarkers discoveries in precision medicine.
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Affiliation(s)
- Yuxin Li
- Biochemistry Graduate Program, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shuo Han
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA.
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2
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Onwuka S, Bravo-Merodio L, Gkoutos GV, Acharjee A. Explainable AI-prioritized plasma and fecal metabolites in inflammatory bowel disease and their dietary associations. iScience 2024; 27:110298. [PMID: 39040076 PMCID: PMC11261406 DOI: 10.1016/j.isci.2024.110298] [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: 02/12/2024] [Revised: 04/29/2024] [Accepted: 06/14/2024] [Indexed: 07/24/2024] Open
Abstract
Fecal metabolites effectively discriminate inflammatory bowel disease (IBD) and show differential associations with diet. Metabolomics and AI-based models, including explainable AI (XAI), play crucial roles in understanding IBD. Using datasets from the UK Biobank and the Human Microbiome Project Phase II IBD Multi'omics Database (HMP2 IBDMDB), this study uses multiple machine learning (ML) classifiers and Shapley additive explanations (SHAP)-based XAI to prioritize plasma and fecal metabolites and analyze their diet correlations. Key findings include the identification of discriminative metabolites like glycoprotein acetyl and albumin in plasma, as well as nicotinic acid metabolites andurobilin in feces. Fecal metabolites provided a more robust disease predictor model (AUC [95%]: 0.93 [0.87-0.99]) compared to plasma metabolites (AUC [95%]: 0.74 [0.69-0.79]), with stronger and more group-differential diet-metabolite associations in feces. The study validates known metabolite associations and highlights the impact of IBD on the interplay between gut microbial metabolites and diet.
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Affiliation(s)
- Serena Onwuka
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Laura Bravo-Merodio
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Centre for Health Data Research, University of Birmingham, Birmingham, UK
- Institute of Translational Medicine, University of Birmingham, Birmingham, UK
| | - Georgios V. Gkoutos
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Centre for Health Data Research, University of Birmingham, Birmingham, UK
- Institute of Translational Medicine, University of Birmingham, Birmingham, UK
| | - Animesh Acharjee
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Centre for Health Data Research, University of Birmingham, Birmingham, UK
- Institute of Translational Medicine, University of Birmingham, Birmingham, UK
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3
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Long X, Zhang Y, Liu M, Liu Z, Xia L, Xu X, Wu M. Causality of genetically determined blood metabolites on inflammatory bowel disease: a two-sample Mendelian randomization study. Sci Rep 2024; 14:16361. [PMID: 39014047 PMCID: PMC11252329 DOI: 10.1038/s41598-024-67376-0] [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: 01/31/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic and recurrent inflammatory disease of the gastrointestinal tract, including two subtypes: Crohn's disease (CD) and ulcerative colitis (UC). Metabolic disorders are important factors in the development of IBD. However, the evidence for the causal relationship between blood metabolites and IBD remains limited. A two-sample MR analysis was applied to evaluate relationships between 486 blood metabolites and IBD. The inverse variance weighted method was chosen as the primary MR analysis method. False discovery rate correction was used to control for false positives in multiple testing. Following complementary and sensitivity analyses were conducted using methods such as weight median, MR-egger, weighted mode, simple mode, Cochran Q test, and MR-PRESSO. Moreover, we performed replication, meta-analysis, Steiger test, and linkage disequilibrium score regression to enhance the robustness of the results. Additionally, we performed metabolic pathway analysis to identify potential metabolic pathways. As a result, we identified four significant causal associations between four blood metabolites and two IBD subtypes. Specifically, one metabolite was identified as being associated with the development of CD (mannose: odds ratio (OR) = 0.19, 95% confidence interval (CI) 0.08-0.43, P = 8.54 × 10-5). Three metabolites were identified as being associated with the development of UC (arachidonate (20:4n6): OR = 0.18, 95% CI 0.11-0.30, P = 2.09 × 10-11; 1, 5-anhydroglucitol: OR = 2.21, 95% CI 1.47-3.34, P = 1.50 × 10-4; 2-stearoylglycerophosphocholine: OR = 2.66, 95% CI 1.53-4.63, P = 5.30 × 10-4). The findings of our study suggested that the identified metabolites and metabolic pathways can be considered as useful circulating metabolic biomarkers for the screening and prevention of IBD in clinical practice, as well as candidate molecules for future mechanism exploration and drug target selection.
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Affiliation(s)
- Xiongquan Long
- Department of Gastroenterology, The First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, 410005, Hunan, China
- Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Yuyang Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, 410005, Hunan, China
- Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Mingzhu Liu
- Department of Gastroenterology, The First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, 410005, Hunan, China
- Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Zihao Liu
- Department of Endoscopic Diagnosis and Treatment Center, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410005, Hunan, China
| | - Lvzhou Xia
- Department of Gastroenterology, The First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, 410005, Hunan, China
- Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China
| | - Xiaoping Xu
- Department of Gastroenterology, The First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, 410005, Hunan, China.
- Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China.
| | - Minghao Wu
- Department of Gastroenterology, The First Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, 410005, Hunan, China.
- Central Laboratory of Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, China.
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4
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Fererberger T, Buechler C, Kandulski A, Elger T, Loibl J, Schmid S, Sommersberger S, Gunawan S, Zundler S, Huss M, Bettenworth D, Kempa S, Weidlich S, Föh B, Huang X, Grzegorzek M, Derer-Petersen S, Günther UL, Marquardt JU, Kunst C, Gülow K, Müller M, Sina C, Schmelter F, Tews HC. Distinct metabolomic and lipidomic profiles in serum samples of patients with primary sclerosing cholangitis. Front Med (Lausanne) 2024; 11:1334865. [PMID: 38895187 PMCID: PMC11184724 DOI: 10.3389/fmed.2024.1334865] [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: 11/07/2023] [Accepted: 01/22/2024] [Indexed: 06/21/2024] Open
Abstract
Intoduction Identification of specific metabolome and lipidome profile of patients with primary sclerosing cholangitis (PSC) is crucial for diagnosis, targeted personalized therapy, and more accurate risk stratification. Methods Nuclear magnetic resonance (NMR) spectroscopy revealed an altered metabolome and lipidome of 33 patients with PSC [24 patients with inflammatory bowel disease (IBD) and 9 patients without IBD] compared with 40 age-, sex-, and body mass index (BMI)-matched healthy controls (HC) as well as 64 patients with IBD and other extraintestinal manifestations (EIM) but without PSC. Results In particular, higher concentrations of pyruvic acid and several lipoprotein subfractions were measured in PSC in comparison to HC. Of clinical relevance, a specific amino acid and lipid profile was determined in PSC compared with IBD and other EIM. Discussion These results have the potential to improve diagnosis by differentiating PSC patients from HC and those with IBD and EIM.
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Affiliation(s)
- Tanja Fererberger
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
| | - Christa Buechler
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
| | - Arne Kandulski
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
| | - Tanja Elger
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
| | - Johanna Loibl
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
| | - Stephan Schmid
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
| | - Stefanie Sommersberger
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
| | - Stefan Gunawan
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
| | - Sebastian Zundler
- Department of Medicine 1, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen-Nürnberg, Germany
- Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Erlangen, Germany
| | - Muriel Huss
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
| | - Dominik Bettenworth
- Department of Medicine B - Gastroenterology and Hepatology, University Hospital Münster, Münster, Germany
- Practice for Internal Medicine, Münster, Germany
| | - Sally Kempa
- Department for Plastic, Hand, and Reconstructive Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Simon Weidlich
- Department of Internal Medicine II, School of Medicine and Health, University Hospital Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Bandik Föh
- Institute of Nutritional Medicine, University Medical Center Schleswig-Holstein, Lübeck, Germany
- Department of Medicine I, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Xinyu Huang
- Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
| | - Marcin Grzegorzek
- Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
| | - Stefanie Derer-Petersen
- Institute of Nutritional Medicine, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Ulrich L Günther
- Institute of Chemistry and Metabolomics, University of Lübeck, Lübeck, Germany
| | - Jens U Marquardt
- Department of Medicine I, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Claudia Kunst
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
| | - Karsten Gülow
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
| | - Martina Müller
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
| | - Christian Sina
- Institute of Nutritional Medicine, University Medical Center Schleswig-Holstein, Lübeck, Germany
- Department of Medicine I, University Medical Center Schleswig-Holstein, Lübeck, Germany
- Fraunhofer Research Institution for Individualized and Cell-Based Medical Engineering (IMTE), Lübeck, Germany
| | - Franziska Schmelter
- Institute of Nutritional Medicine, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Hauke C Tews
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious diseases, University Hospital Regensburg, Regensburg, Germany
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Noh JY, Farhataziz N, Kinter MT, Yan X, Sun Y. Colonic Dysregulation of Major Metabolic Pathways in Experimental Ulcerative Colitis. Metabolites 2024; 14:194. [PMID: 38668322 PMCID: PMC11052278 DOI: 10.3390/metabo14040194] [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: 12/19/2023] [Revised: 02/18/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Inflammatory bowel disease (IBD) is multifactorial chronic inflammatory disease in the gastrointestinal tract, affecting patients' quality of life profoundly. The incidence of IBD has been on the rise globally for the last two decades. Because the molecular mechanisms underlying the disease remain not well understood, therapeutic development is significantly impeded. Metabolism is a crucial cellular process to generate the energy needed for an inflammatory response and tissue repair. Comprehensive understanding of the metabolic pathways in IBD would help to unravel the disease pathogenesis/progression and facilitate therapeutic discoveries. Here, we investigated four metabolic pathways altered in experimental colitis. C57BL/6J mice were treated with dextran sulfate sodium (DSS) in drinking water for 7 days to induce experimental ulcerative colitis (UC). We conducted proteomics analysis for the colon samples using LC/MS, to profile key metabolic intermediates. Our findings revealed significant alterations in four major metabolic pathways: antioxidative defense, β-oxidation, glycolysis, and TCA cycle pathways. The energy metabolism by β-oxidation, glycolysis, and TCA cycle pathways were downregulated under UC, together with reduced antioxidative defense pathways. These results reveal metabolic re-programming in intestinal cells under UC, showing dysregulation in all four major metabolic pathways. Our study underscores the importance of metabolic drivers in the pathogenesis of IBD and suggests that the modification of metabolism may serve as a novel diagnostic/therapeutic approach for IBD.
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Affiliation(s)
- Ji Yeon Noh
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA; (J.Y.N.); (N.F.)
| | - Naser Farhataziz
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA; (J.Y.N.); (N.F.)
| | - Michael T. Kinter
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
| | - Xin Yan
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA;
| | - Yuxiang Sun
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA; (J.Y.N.); (N.F.)
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
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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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Kapur N, Alam MA, Hassan SA, Patel PH, Wempe LA, Bhogoju S, Goretsky T, Kim JH, Herzog J, Ge Y, Awuah SG, Byndloss M, Baumler AJ, Zadeh MM, Sartor RB, Barrett T. Enhanced mucosal mitochondrial function corrects dysbiosis and OXPHOS metabolism in IBD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.584471. [PMID: 38559035 PMCID: PMC10979996 DOI: 10.1101/2024.03.14.584471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Background Mitochondrial (Mito) dysfunction in IBD reduces mucosal O2 consumption and increases O2 delivery to the microbiome. Increased enteric O2 promotes blooms of facultative anaerobes (eg. Proteobacteria ) and restricts obligate anaerobes (eg. Firmicutes ). Dysbiotic metabolites negatively affect host metabolism and immunity. Our novel compound (AuPhos) upregulates intestinal epithelial cell (IEC) mito function, attenuates colitis and corrects dysbiosis in humanized Il10-/- mice. We posit that AuPhos corrects IBD-associated dysbiotic metabolism. Methods Primary effect of AuPhos on mucosal Mito respiration and healing process was studied in ex vivo treated human colonic biopsies and piroxicam-accelerated (Px) Il10-/- mice. Secondary effect on microbiome was tested in DSS-colitis WT B6 and germ-free 129.SvEv WT or Il10-/- mice reconstituted with human IBD stool (Hu- Il10-/- ). Mice were treated orally with AuPhos (10- or 25- mg/kg; q3d) or vehicle, stool samples collected for fecal lipocalin-2 (f-LCN2) assay and microbiome analyses using 16S rRNA sequencing. AuPhos effect on microbial metabolites was determined using untargeted global metabolomics. AuPhos-induced hypoxia in IECs was assessed by Hypoxyprobe-1 staining in sections from pimonidazole HCl-infused DSS-mice. Effect of AuPhos on enteric oxygenation was assessed by E. coli Nissle 1917 WT (aerobic respiration-proficient) and cytochrome oxidase (cydA) mutant (aerobic respiration-deficient). Results Metagenomic (16S) analysis revealed AuPhos reduced relative abundances of Proteobacteria and increased blooms of Firmicutes in uninflamed B6 WT, DSS-colitis, Hu-WT and Hu- Il10-/- mice. AuPhos also increased hypoxyprobe-1 staining in surface IECs suggesting enhanced O2 utilization. AuPhos-induced anaerobiosis was confirmed by a significant increase in cydA mutant compared to WT (O2-utlizing) E.coli . Ex vivo treatment of human biopsies with AuPhos showed significant increase in Mito mass, and complexes I and IV. Further, gene expression analysis of AuPhos-treated biopsies showed increase in stem cell markers (Lgr4, Lgr5, Lrig1), with concomitant decreases in pro-inflammatory markers (IL1β,MCP1, RankL). Histological investigation of AuPhos-fed Px- Il10-/- mice showed significantly decreased colitis score in AuPhos-treated Px- Il10-/- mice, with decrease in mRNA of pro-inflammatory cytokines and increase in Mito complexes ( ND5 , ATP6 ). AuPhos significantly altered microbial metabolites associated with SCFA synthesis, FAO, TCA cycle, tryptophan and polyamine biosynthesis pathways. AuPhos increased pyruvate, 4-hydroxybutyrate, 2-hydroxyglutarate and succinate, suggesting an upregulation of pyruvate and glutarate pathways of butyrate production. AuPhos reduced IBD-associated primary bile acids (BA) with concomitant increase in secondary BA (SBA). AuPhos treatment significantly decreased acylcarnitines and increased L-carnitine reflective of enhanced FAO. AuPhos increases TCA cycle intermediates and creatine, energy reservoir substrates indicating enhanced OxPHOS. Besides, AuPhos also upregulates tryptophan metabolism, decreases Kynurenine and its derivatives, and increases polyamine biosynthesis pathway (Putresceine and Spermine). Conclusion These findings indicate that AuPhos-enhanced IEC mitochondrial function reduces enteric O2 delivery, which corrects disease-associated metabolomics by restoring short-chain fatty acids, SBA, AA and IEC energy metabolism. Graphical abstract
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Aldars-García L, Gil-Redondo R, Embade N, Riestra S, Rivero M, Gutiérrez A, Rodríguez-Lago I, Fernández-Salazar L, Ceballos D, Manuel Benítez J, Aguas M, Baston-Rey I, Bermejo F, José Casanova M, Lorente R, Ber Y, Ginard D, Esteve M, de Francisco R, José García M, Francés R, Rodríguez Pescador A, Velayos B, Del Río EG, Marín Pedrosa S, Minguez Sabater A, Barreiro-de Acosta M, Algaba A, Verdejo Gil C, Rivas O, Royo V, Aceituno M, Garre A, Baldán-Martín M, Ramírez C, Sanz-García A, Lozano JJ, Sidorova J, Millet O, Bernardo D, Gisbert JP, Chaparro M. Serum and Urine Metabolomic Profiling of Newly Diagnosed Treatment-Naïve Inflammatory Bowel Disease Patients. Inflamm Bowel Dis 2024; 30:167-182. [PMID: 37536268 DOI: 10.1093/ibd/izad154] [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: 02/06/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND AND AIMS Inflammatory bowel disease (IBD) is a prevalent chronic noncurable disease associated with profound metabolic changes. The discovery of novel molecular indicators for unraveling IBD etiopathogenesis and the diagnosis and prognosis of IBD is therefore pivotal. We sought to determine the distinctive metabolic signatures from the different IBD subgroups before treatment initiation. METHODS Serum and urine samples from newly diagnosed treatment-naïve IBD patients and age and sex-matched healthy control (HC) individuals were investigated using proton nuclear magnetic resonance spectroscopy. Metabolic differences were identified based on univariate and multivariate statistical analyses. RESULTS A total of 137 Crohn's disease patients, 202 ulcerative colitis patients, and 338 HC individuals were included. In the IBD cohort, several distinguishable metabolites were detected within each subgroup comparison. Most of the differences revealed alterations in energy and amino acid metabolism in IBD patients, with an increased demand of the body for energy mainly through the ketone bodies. As compared with HC individuals, differences in metabolites were more marked and numerous in Crohn's disease than in ulcerative colitis patients, and in serum than in urine. In addition, clustering analysis revealed 3 distinct patient profiles with notable differences among them based on the analysis of their clinical, anthropometric, and metabolomic variables. However, relevant phenotypical differences were not found among these 3 clusters. CONCLUSIONS This study highlights the molecular alterations present within the different subgroups of newly diagnosed treatment-naïve IBD patients. The metabolomic profile of these patients may provide further understanding of pathogenic mechanisms of IBD subgroups. Serum metabotype seemed to be especially sensitive to the onset of IBD.
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Affiliation(s)
- Laila Aldars-García
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del Hospital de La Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | | | - Nieves Embade
- Precision Medicine and Metabolism Lab, CIC bioGUNE, Derio, Spain
| | - Sabino Riestra
- Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Montserrat Rivero
- Hospital Universitario Marqués de Valdecilla, Instituto de Investigación Sanitaria Marqués de Valdecilla, Santander, Spain
| | - Ana Gutiérrez
- Hospital General Universitario de Alicante, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto Investigación Sanitaria y Biomédica de Alicante, Alicante, Spain
| | - Iago Rodríguez-Lago
- Hospital Universitario de Galdakao, Biocruces Bizkaia Health Research Institute, Vizcaya, Spain
| | | | - Daniel Ceballos
- Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - José Manuel Benítez
- Hospital Universitario Reina Sofía, Instituto Maimónides de Investigación Biomédica de Córdoba, Córdoba, Spain
| | - Mariam Aguas
- Hospital Universitari i Politecnic La Fe, La Fe Health Research Institute, Valencia, Spain
| | - Iria Baston-Rey
- Complexo Hospitalario Universitario de Santiago, Santiago de Compostela, Spain
| | - Fernando Bermejo
- Hospital Universitario de Fuenlabrada, Instituto de Investigación Hospital Universitario La Paz, Madrid, Spain
| | - María José Casanova
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del Hospital de La Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Rufo Lorente
- Hospital General Universitario de Ciudad Real, Ciudad Real, Spain
| | | | - Daniel Ginard
- Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - María Esteve
- Hospital Universitari Mutua Terrassa, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Terrassa, Spain
| | - Ruth de Francisco
- Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - María José García
- Hospital Universitario Marqués de Valdecilla, Instituto de Investigación Sanitaria Marqués de Valdecilla, Santander, Spain
| | - Rubén Francés
- Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | | | - Benito Velayos
- Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Elena Guerra Del Río
- Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Sandra Marín Pedrosa
- Hospital Universitario Reina Sofía, Instituto Maimónides de Investigación Biomédica de Córdoba, Córdoba, Spain
| | | | - Manuel Barreiro-de Acosta
- Departamento Medicina Clínica, Universidad Miguel Hernández de Elche, Instituto Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Herñandez, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto Investigación Sanitaria y Biomédica de Alicante, Elche, Spain
| | - Alicia Algaba
- Hospital Universitario de Galdakao, Biocruces Bizkaia Health Research Institute, Vizcaya, Spain
| | | | | | - Vanesa Royo
- Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Montserrat Aceituno
- Hospital Universitari Mutua Terrassa, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Terrassa, Spain
| | - Ana Garre
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del Hospital de La Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Montserrat Baldán-Martín
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del Hospital de La Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Cristina Ramírez
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del Hospital de La Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Ancor Sanz-García
- Data Analysis Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa, Madrid, Spain
| | - Juan J Lozano
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
| | - Julia Sidorova
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Lab, CIC bioGUNE, Derio, Spain
| | - David Bernardo
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biología y Genética Molecular, Universidad de Valladolid, Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Madrid, Spain
| | - Javier P Gisbert
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del Hospital de La Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - María Chaparro
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del Hospital de La Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
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9
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Tews HC, Schmelter F, Kandulski A, Büchler C, Schmid S, Schlosser S, Elger T, Loibl J, Sommersberger S, Fererberger T, Gunawan S, Kunst C, Gülow K, Bettenworth D, Föh B, Maaß C, Solbach P, Günther UL, Derer S, Marquardt JU, Sina C, Müller M. Unique Metabolomic and Lipidomic Profile in Serum From Patients With Crohn's Disease and Ulcerative Colitis Compared With Healthy Control Individuals. Inflamm Bowel Dis 2023:izad298. [PMID: 38156773 DOI: 10.1093/ibd/izad298] [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: 05/17/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Accurate biomarkers for disease activity and progression in patients with inflammatory bowel disease (IBD) are a prerequisite for individual disease characterization and personalized therapy. We show that metabolic profiling of serum from IBD patients is a promising approach to establish biomarkers. The aim of this work was to characterize metabolomic and lipidomic serum profiles of IBD patients in order to identify metabolic fingerprints unique to the disease. METHODS Serum samples were obtained from 55 patients with Crohn's disease (CD), 34 patients with ulcerative colitis (UC), and 40 healthy control (HC) individuals and analyzed using proton nuclear magnetic resonance spectroscopy. Classification of patients and HC individuals was achieved by orthogonal partial least squares discriminant analysis and univariate analysis approaches. Disease activity was assessed using the Gastrointestinal Symptom Rating Scale. RESULTS Serum metabolome significantly differed between CD patients, UC patients, and HC individuals. The metabolomic differences of UC and CD patients compared with HC individuals were more pronounced than the differences between UC and CD patients. Differences in serum levels of pyruvic acid, histidine, and the branched-chain amino acids leucine and valine were detected. The size of low-density lipoprotein particles shifted from large to small dense particles in patients with CD. Of note, apolipoprotein A1 and A2 serum levels were decreased in CD and UC patients with higher fecal calprotectin levels. The Gastrointestinal Symptom Rating Scale is negatively associated with the concentration of apolipoprotein A2. CONCLUSIONS Metabolomic assessment of serum samples facilitated the differentiation of IBD patients and HC individuals. These differences were constituted by changes in amino acid and lipoprotein levels. Furthermore, disease activity in IBD patients was associated with decreased levels of the atheroprotective apolipoproteins A1 and A2.
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Affiliation(s)
- Hauke Christian Tews
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Franziska Schmelter
- Institute of Nutritional Medicine, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Arne Kandulski
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Christa Büchler
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Stephan Schmid
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Sophie Schlosser
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Tanja Elger
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Johanna Loibl
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Stefanie Sommersberger
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Tanja Fererberger
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Stefan Gunawan
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Claudia Kunst
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Karsten Gülow
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
| | - Dominik Bettenworth
- Department of Medicine B-Gastroenterology and Hepatology, University Hospital Münster, Münster, Germany
- Practice for Internal Medicine, Münster, Germany
| | - Bandik Föh
- Department of Medicine I, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Carlos Maaß
- Department of Medicine I, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Philipp Solbach
- Department of Medicine I, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Ulrich L Günther
- Institute of Chemistry and Metabolomics, University of Lübeck, Lübeck, Germany
| | - Stefanie Derer
- Institute of Nutritional Medicine, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Jens U Marquardt
- Department of Medicine I, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Christian Sina
- Institute of Nutritional Medicine, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
- Department of Medicine I, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
- Fraunhofer Research Institution for Individualized and Cell-Based Medical Engineering, Lübeck, Germany
| | - Martina Müller
- Gastroenterology, Hepatology, Endocrinology, Rheumatology and Infectious Diseases, Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany
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10
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Jia Y, Zou K, Zou L. Research progress of metabolomics in cervical cancer. Eur J Med Res 2023; 28:586. [PMID: 38093395 PMCID: PMC10717910 DOI: 10.1186/s40001-023-01490-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 10/30/2023] [Indexed: 12/17/2023] Open
Abstract
INTRODUCTION Cervical cancer threatens women's health seriously. In recent years, the incidence of cervical cancer is on the rise, and the age of onset tends to be younger. Prevention, early diagnosis and specific treatment have become the main means to change the prognosis of cervical cancer patients. Metabolomics research can directly reflect the changes of biochemical processes and microenvironment in the body, which can provide a comprehensive understanding of the changes of metabolites in the process of disease occurrence and development, and provide new ways for the prevention and diagnosis of diseases. OBJECTIVES The aim of this study is to review the metabolic changes in cervical cancer and the application of metabolomics in the diagnosis and treatment. METHODS PubMed, Web of Science, Embase and Scopus electronic databases were systematically searched for relevant studies published up to 2022. RESULTS With the emergence of metabolomics, metabolic regulation and cancer research are further becoming a focus of attention. By directly reflecting the changes in the microenvironment of the body, metabolomics research can provide a comprehensive understanding of the patterns of metabolites in the occurrence and development of diseases, thus providing new ideas for disease prevention and diagnosis. CONCLUSION With the continuous, in-depth research on metabolomics research technology, it will bring more benefits in the screening, diagnosis and treatment of cervical cancer with its advantages of holistic and dynamic nature.
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Affiliation(s)
- Yuhan Jia
- Department of Radiotherapy, The Second Hospital of Dalian Medical University, Dalian, Liaoning Province, China
| | - Kun Zou
- Department of Radiotherapy, The First Hospital of Dalian Medical University, Dalian, Liaoning Province, China.
| | - Lijuan Zou
- Department of Radiotherapy, The Second Hospital of Dalian Medical University, Dalian, Liaoning Province, China.
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11
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Kathrani A, Yen S, Hall EJ, Swann JR. The effects of a hydrolyzed protein diet on the plasma, fecal and urine metabolome in cats with chronic enteropathy. Sci Rep 2023; 13:19979. [PMID: 37968311 PMCID: PMC10652014 DOI: 10.1038/s41598-023-47334-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/12/2023] [Indexed: 11/17/2023] Open
Abstract
Hydrolyzed protein diets are extensively used to treat chronic enteropathy (CE) in cats. However, the biochemical effects of such a diet on feline CE have not been characterized. In this study an untargeted 1H nuclear magnetic resonance spectroscopy-based metabolomic approach was used to compare the urinary, plasma, and fecal metabolic phenotypes of cats with CE to control cats with no gastrointestinal signs recruited at the Royal Veterinary College (RVC). In addition, the biomolecular consequences of a hydrolyzed protein diet in cats with CE was also separately determined in cats recruited from the RVC (n = 16) and the University of Bristol (n = 24) and whether these responses differed between dietary responders and non-responders. Here, plasma metabolites related to energy and amino acid metabolism significantly varied between CE and control cats in the RVC cohort. The hydrolyzed protein diet modulated the urinary metabolome of cats with CE (p = 0.005) in both the RVC and Bristol cohort. In the RVC cohort, the urinary excretion of phenylacetylglutamine, p-cresyl-sulfate, creatinine and taurine at diagnosis was predictive of dietary response (p = 0.025) although this was not observed in the Bristol cohort. Conversely, in the Bristol cohort plasma betaine, glycerol, glutamine and alanine at diagnosis was predictive of outcome (p = 0.001), but these same results were not observed in the RVC cohort. The biochemical signature of feline CE in the RVC cohort was consistent with that identified in human and animal models of inflammatory bowel disease. The hydrolyzed protein diet had the same effect on the urinary metabolome of cats with CE at both sites. However, biomarkers that were predictive of dietary response at diagnosis differed between the 2 sites. This may be due to differences in disease severity, disease heterogeneity, factors unrelated to the disease or small sample size at both sites. As such, further studies utilizing larger number of cats are needed to corroborate these findings.
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Affiliation(s)
- Aarti Kathrani
- Royal Veterinary College, Hawkshead Lane, Hertfordshire, AL9 7TA, UK.
| | - Sandi Yen
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
| | - Edward J Hall
- Bristol Veterinary School, University of Bristol, Langford, Bristol, BS40 5DU, UK
| | - Jonathan R Swann
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, SW7 2AZ, UK
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12
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Li M, Li P, Ji Y, Tian Y, Zeng H, Chen X. Precolumn derivatization LC-MS/MS method to simultaneous quantitation of 10 monosaccharides in rat plasma. J Pharm Biomed Anal 2023; 234:115537. [PMID: 37348365 DOI: 10.1016/j.jpba.2023.115537] [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: 04/25/2023] [Revised: 06/05/2023] [Accepted: 06/16/2023] [Indexed: 06/24/2023]
Abstract
Monosaccharides are essential for maintaining the normal physiological functions of living organisms. Under disease states, metabolic disorders in vivo will inevitably affect the levels of monosaccharides, which brings the possibility of monosaccharides as a biomarker of some diseases. In this study, a method was developed and validated for simultaneously determining 10 monosaccharides (glucose, galactose, mannose, rhamnose, fucose, xylose, iduronic acid, glucuronic acid, N-acetylgalactosamine and N-acetylglucosamine) in SD rat plasma using liquid chromatography-tandem mass spectrometry. The method employed 1-phenyl-3-methyl-5-pyrazolone (PMP) as a derivatization reagent, considerably improved the chromatographic retention and ionization efficiency of monosaccharides. After protein precipitation of plasma samples, monosaccharides and isotope internal standards were derivatized and liquid-liquid extraction was performed to remove excess PMP. To achieve the baseline separation of several isomers, the resulting derivatives were chromatographed on a Bridged ethyl hybrid (BEH) Phenyl column using gradient elution with a total run time of 8 min. The method was linear within the range of 0.0100-5.00 μg/mL for rhamnose, 0.0500-25.0 μg/mL for fucose, xylose, iduronic acid, glucuronic acid, N-acetylgalactosamine and N-acetylglucosamine, 1.00-500 μg/mL for galactose, 10.0-5000 μg/mL for mannose, and 50.0-25,000 μg/mL for glucose. And the accuracy and precision verification of surrogate matrix samples and plasma samples met the required criteria. The method has been used successfully to study the effect of hepatic insufficiency on monosaccharide levels in rats. It was found that the concentration of glucuronic acid in SD rat plasma was abnormally increased in rats with liver injury.
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Affiliation(s)
- Mengxue Li
- School of Pharmacy, Zunyi Medical University, No.1 Campus Road, Xinpu New District, Zunyi 563000, PR China; Zhongshan Institute for Drug Discovery, Chinese Academy of Sciences, SSIP Healthcare and Medicine Demonstration Zone, Zhongshan Tsuihang New District, Zhongshan 528437, PR China
| | - Ping Li
- Zhongshan Institute for Drug Discovery, Chinese Academy of Sciences, SSIP Healthcare and Medicine Demonstration Zone, Zhongshan Tsuihang New District, Zhongshan 528437, PR China
| | - Yuting Ji
- Zhongshan Institute for Drug Discovery, Chinese Academy of Sciences, SSIP Healthcare and Medicine Demonstration Zone, Zhongshan Tsuihang New District, Zhongshan 528437, PR China
| | - Yihua Tian
- Zhongshan Institute for Drug Discovery, Chinese Academy of Sciences, SSIP Healthcare and Medicine Demonstration Zone, Zhongshan Tsuihang New District, Zhongshan 528437, PR China
| | - Huiying Zeng
- Zhongshan Institute for Drug Discovery, Chinese Academy of Sciences, SSIP Healthcare and Medicine Demonstration Zone, Zhongshan Tsuihang New District, Zhongshan 528437, PR China
| | - Xiaoyan Chen
- Zhongshan Institute for Drug Discovery, Chinese Academy of Sciences, SSIP Healthcare and Medicine Demonstration Zone, Zhongshan Tsuihang New District, Zhongshan 528437, PR China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, PR China.
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13
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Li Q, Zhang W, Zhou E, Tao Y, Wang M, Qi S, Zhao L, Tan Y, Wu L. Integrated microbiomic and metabolomic analyses reveal the mechanisms by which bee pollen and royal jelly lipid extracts ameliorate colitis in mice. Food Res Int 2023; 171:113069. [PMID: 37330827 DOI: 10.1016/j.foodres.2023.113069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/19/2023]
Abstract
Bee pollen (BP) and royal jelly (RJ) have shown therapeutic effects against colitis, but the functional components contained therein remain elusive. Here, we used an integrated microbiomic-metabolomic strategy to clarify the mechanism by which bee pollen lipid extracts (BPL) and royal jelly lipid extracts (RJL) ameliorated dextran sulfate sodium (DSS)-induced colitis in mice. Lipidomic results showed that levels of ceramide (Cer), lysophosphatidylcholine (LPC), phosphatidylcholine (PC), and phosphatidylethanolamine (PE) were significantly higher in BPL than in RJL. The anti-inflammatory efficacy of BPL surpassed that of RJL, although both BPL and RJL could attenuate DSS-induced colitis through several mechanisms: reducing the disease activity index (DAI); decreasing histopathological damage; inhibiting the expression of genes encoding proinflammatory cytokines; improving intestinal microbial community structure, and modulating host metabolism. These findings demonstrated that BPL and RJL have great potential as functional ingredients for the production of dietary supplements to prevent early colitis.
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Affiliation(s)
- Qiangqiang Li
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Wenwen Zhang
- College of Life and Health Sciences, Anhui Science and Technology University, Bengbu 233100, China
| | - Enning Zhou
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Yuxiao Tao
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Miao Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Suzhen Qi
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Liuwei Zhao
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Yonggang Tan
- Oncology Center, Shengjing Hospital, China Medical University, Shenyang 110004, China.
| | - Liming Wu
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China.
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14
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Baldan-Martin M, Chaparro M, Gisbert JP. Systematic Review: Urine Biomarker Discovery for Inflammatory Bowel Disease Diagnosis. Int J Mol Sci 2023; 24:10159. [PMID: 37373307 DOI: 10.3390/ijms241210159] [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: 04/26/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) are chronic, heterogeneous, and inflammatory conditions mainly affecting the gastrointestinal tract. Currently, endoscopy is the gold standard test for assessing mucosal activity and healing in clinical practice; however, it is a costly, time-consuming, invasive, and uncomfortable procedure for the patients. Therefore, there is an urgent need for sensitive, specific, fast and non-invasive biomarkers for the diagnosis of IBD in medical research. Urine is an excellent biofluid for discovering biomarkers because it is non-invasive to sample. In this review, we aimed to summarize proteomics and metabolomics studies performed in both animal models of IBD and humans that identify urinary biomarkers for IBD diagnosis. Future large-scale multi-omics studies should be conducted in collaboration with clinicians, researchers, and industry to make progress toward the development of sensitive and specific diagnostic biomarkers, thereby making personalized medicine possible.
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Affiliation(s)
- Montse Baldan-Martin
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
| | - Javier P Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
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15
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Arroyo-Manzanares N, García-Nicolás M, Abellán-Alfocea F, Prieto-Baeza L, Campillo N, Del Val Oliver B, Zarauz-García J, Sáenz L, Viñas P. Application of untargeted volatile profiling in inflammatory bowel disease research. Anal Bioanal Chem 2023:10.1007/s00216-023-04748-x. [PMID: 37233766 DOI: 10.1007/s00216-023-04748-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Inflammatory bowel disease (IBD) diagnosis depends on criteria based on histological, endoscopic, radiological, and clinical results. These studies show drawbacks as being expensive, invasive, and time-consuming. In this work, an untargeted metabolomic strategy based on the monitoring of volatile compounds in serum by headspace gas chromatography-mass spectrometry is proposed as a complementary, fast, and efficient test for IBD patient diagnosis. To develop the method and build a chemometric model that allows the IBD diagnosis, serum samples including IBD patients and healthy volunteers were collected. Analyses were performed by incubating 400 µL of serum for 10 min at 90 °C. For data processing, an untargeted metabolomic strategy was used. A total of 96 features were detected, of which a total of 10 volatile compounds could be identified and confirmed by means of the analysis of real standards. The chemometric treatment consisted of a discriminant analysis of orthogonal partial least squares (OPLS-DA) obtaining a 100% of classification rate, since all the analyzed samples were correctly classified.
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Affiliation(s)
- Natalia Arroyo-Manzanares
- Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", E-30100, Murcia, Spain
| | - María García-Nicolás
- Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", E-30100, Murcia, Spain
| | - Fuensanta Abellán-Alfocea
- Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", E-30100, Murcia, Spain
| | - Laura Prieto-Baeza
- Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", E-30100, Murcia, Spain
| | - Natalia Campillo
- Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", E-30100, Murcia, Spain
| | - Blanca Del Val Oliver
- Internal Medicine Service - Gastroenterology and Hepatology Section, Hospital General Universitario Rafael Méndez, Lorca, Spain
| | - José Zarauz-García
- Laboratory Medicine Department, Hospital General Universitario Rafael Méndez, Lorca, Spain
| | - Luis Sáenz
- Laboratory Medicine Department, Hospital General Universitario Rafael Méndez, Lorca, Spain
| | - Pilar Viñas
- Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", E-30100, Murcia, Spain.
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16
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Song Z, Ohnishi Y, Osada S, Gan L, Jiang J, Hu Z, Kumeta H, Kumaki Y, Yokoi Y, Nakamura K, Ayabe T, Yamauchi K, Aizawa T. Application of Benchtop NMR for Metabolomics Study Using Feces of Mice with DSS-Induced Colitis. Metabolites 2023; 13:metabo13050611. [PMID: 37233652 DOI: 10.3390/metabo13050611] [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: 03/24/2023] [Revised: 04/22/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Nuclear magnetic resonance (NMR)-based metabolomics, which comprehensively measures metabolites in biological systems and investigates their response to various perturbations, is widely used in research to identify biomarkers and investigate the pathogenesis of underlying diseases. However, further applications of high-field superconducting NMR for medical purposes and field research are restricted by its high cost and low accessibility. In this study, we applied a low-field, benchtop NMR spectrometer (60 MHz) employing a permanent magnet to characterize the alterations in the metabolic profile of fecal extracts obtained from dextran sodium sulfate (DSS)-induced ulcerative colitis model mice and compared them with the data acquired from high-field NMR (800 MHz). Nineteen metabolites were assigned to the 60 MHz 1H NMR spectra. Non-targeted multivariate analysis successfully discriminated the DSS-induced group from the healthy control group and showed high comparability with high-field NMR. In addition, the concentration of acetate, identified as a metabolite with characteristic behavior, could be accurately quantified using a generalized Lorentzian curve fitting method based on the 60 MHz NMR spectra.
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Affiliation(s)
- Zihao Song
- Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Yuki Ohnishi
- Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | | | - Li Gan
- Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Jiaxi Jiang
- Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Zhiyan Hu
- Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Hiroyuki Kumeta
- Advanced NMR Facility, Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Yasuhiro Kumaki
- High-Resolution NMR Laboratory, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yuki Yokoi
- Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Kiminori Nakamura
- Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Tokiyoshi Ayabe
- Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Kazuo Yamauchi
- Instrumental Analysis Section, Okinawa Institute of Science and Technology, Onna 904-0495, Japan
| | - Tomoyasu Aizawa
- Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
- Advanced NMR Facility, Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0808, Japan
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Dubey R, Sinha N, Jagannathan NR. Potential of in vitro nuclear magnetic resonance of biofluids and tissues in clinical research. NMR IN BIOMEDICINE 2023; 36:e4686. [PMID: 34970810 DOI: 10.1002/nbm.4686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/18/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Body fluids, cells, and tissues contain a wide variety of metabolites that consist of a mixture of various low-molecular-weight compounds, including amino acids, peptides, lipids, nucleic acids, and organic acids, which makes comprehensive analysis more difficult. Quantitative nuclear magnetic resonance (NMR) spectroscopy is a well-established analytical technique for analyzing the metabolic profiles of body fluids, cells, and tissues. It enables fast and comprehensive detection, characterization, a high level of experimental reproducibility, minimal sample preparation, and quantification of various endogenous metabolites. In recent times, NMR-based metabolomics has been appreciably utilized in diverse branches of medicine, including microbiology, toxicology, pathophysiology, pharmacology, nutritional intervention, and disease diagnosis/prognosis. In this review, the utility of NMR-based metabolomics in clinical studies is discussed. The significance of in vitro NMR-based metabolomics as an effective tool for detecting metabolites and their variations in different diseases are discussed, together with the possibility of identifying specific biomarkers that can contribute to early detection and diagnosis of disease.
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Affiliation(s)
- Richa Dubey
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, India
| | - Neeraj Sinha
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, India
| | - Naranamangalam R Jagannathan
- Department of Radiology, Chettinad Hospital & Research Institute, Chettinad Academy of Research & Education, Kelambakkam, India
- Department of Radiology, Sri Ramachandra Institute of Higher Education & Research, Chennai, India
- Department of Electrical Engineering, Indian Institute Technology, Madras, Chennai, India
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18
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Hagenbeek FA, van Dongen J, Pool R, Roetman PJ, Harms AC, Hottenga JJ, Kluft C, Colins OF, van Beijsterveldt CEM, Fanos V, Ehli EA, Hankemeier T, Vermeiren RRJM, Bartels M, Déjean S, Boomsma DI. Integrative Multi-omics Analysis of Childhood Aggressive Behavior. Behav Genet 2023; 53:101-117. [PMID: 36344863 PMCID: PMC9922241 DOI: 10.1007/s10519-022-10126-7] [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: 09/03/2021] [Accepted: 10/25/2022] [Indexed: 11/09/2022]
Abstract
This study introduces and illustrates the potential of an integrated multi-omics approach in investigating the underlying biology of complex traits such as childhood aggressive behavior. In 645 twins (cases = 42%), we trained single- and integrative multi-omics models to identify biomarkers for subclinical aggression and investigated the connections among these biomarkers. Our data comprised transmitted and two non-transmitted polygenic scores (PGSs) for 15 traits, 78,772 CpGs, and 90 metabolites. The single-omics models selected 31 PGSs, 1614 CpGs, and 90 metabolites, and the multi-omics model comprised 44 PGSs, 746 CpGs, and 90 metabolites. The predictive accuracy for these models in the test (N = 277, cases = 42%) and independent clinical data (N = 142, cases = 45%) ranged from 43 to 57%. We observed strong connections between DNA methylation, amino acids, and parental non-transmitted PGSs for ADHD, Autism Spectrum Disorder, intelligence, smoking initiation, and self-reported health. Aggression-related omics traits link to known and novel risk factors, including inflammation, carcinogens, and smoking.
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Affiliation(s)
- Fiona A. Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands ,Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Peter J. Roetman
- Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center, Leiden, The Netherlands
| | - Amy C. Harms
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands ,The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands
| | | | - Olivier F. Colins
- Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center, Leiden, The Netherlands ,Department Special Needs Education, Ghent University, Ghent, Belgium
| | | | - Vassilios Fanos
- Department of Surgical Sciences, University of Cagliari and Neonatal Intensive Care Unit, Cagliari, Italy
| | - Erik A. Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota USA
| | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands ,The Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Robert R. J. M. Vermeiren
- Department of Child and Adolescent Psychiatry, LUMC-Curium, Leiden University Medical Center, Leiden, The Netherlands ,Youz, Parnassia Psychiatric Institute, The Hague, The Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Sébastien Déjean
- Toulouse Mathematics Institute, University of Toulouse, CNRS, Toulouse, France
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 7-10, 1081 BT Amsterdam, The Netherlands ,Amsterdam Public Health Research Institute, Amsterdam, The Netherlands ,Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
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19
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Chen K, Wei X, Zhang J, Kortesniemi M, Zhang Y, Yang B. Effect of Acylated and Nonacylated Anthocyanins on Urine Metabolic Profile during the Development of Type 2 Diabetes in Zucker Diabetic Fatty Rats. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15143-15156. [PMID: 36410712 PMCID: PMC9732871 DOI: 10.1021/acs.jafc.2c06802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
The effect of nonacylated and acylated anthocyanins on urinary metabolites in diabetic rats was investigated. Nonacylated anthocyanins extract from bilberries (NAAB) or acylated anthocyanins extract from purple potatoes (AAPP) was given to Zucker diabetic fatty (ZDF) rats for 8 weeks at daily doses of 25 and 50 mg/kg body weight. 1H NMR metabolomics was applied to study alterations in urinary metabolites from three time points (weeks 1, 4, and 8). Both types of anthocyanins modulated the metabolites associated with the tricarboxylic acid cycle, gut microbiota metabolism, and renal function at weeks 1 and 4, such as 2-oxoglutarate, fumarate, alanine, trigonelline, and hippurate. In addition, only a high dose of AAPP decreased monosaccharides, formate, lactate, and glucose levels at week 4, suggesting improvement in energy production in mitochondria, glucose homeostasis, and oxidative stress. This study suggested different impacts of AAPP and NAAB on the metabolic profile of urine in diabetes.
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Affiliation(s)
- Kang Chen
- Food
Sciences, Department of Life Technologies, University of Turku, FI-20014 Turu, Finland
| | - Xuetao Wei
- Beijing
Key Laboratory of Toxicological Research and Risk Assessment for Food
Safety, Department of Toxicology, School of Public Health, Peking University, Beijing 100191, China
| | - Jian Zhang
- Department
of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing 100191, China
| | - Maaria Kortesniemi
- Food
Sciences, Department of Life Technologies, University of Turku, FI-20014 Turu, Finland
| | - Yumei Zhang
- Department
of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing 100191, China
| | - Baoru Yang
- Food
Sciences, Department of Life Technologies, University of Turku, FI-20014 Turu, Finland
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20
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Bai J, Xiong T, Wang X, Cheng Y, Luo R, Yang X, Fu C. Potential mechanisms of Lian-Zhi-Fan solution for TNBS-induced ulcerative colitis in rats via a metabolomics approach. Front Pharmacol 2022; 13:1014117. [DOI: 10.3389/fphar.2022.1014117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Lian-Zhi-Fan (LZF) decoction is a hospital-prescribed traditional Chinese medicine botanical drug prepared by the fermentation of decocted Coptidis Rhizome (Huanglian), Gardeniae Fructus (Zhizi), and alum (Baifan). It has been used clinically in China for the treatment of anal fistula, perianal abscess, ulcerative colitis (UC), and other anorectal diseases for hundreds of years. However, due to the complexity of traditional Chinese medicine, the potential mechanisms of LZF in the treatment of UC have remained unknown. This study primarily investigated the remarkable pharmacological effects of LZF on TNBS-induced UC rats. To explore the complex targets and regulatory mechanisms of metabolic networks under LZF intervention, a metabolomics approach mediated by HPLC/Q-TOF-MS analysis was used to screen the different metabolites and their metabolic pathways in the serum in order to characterize the possible anti-UC mechanisms of LZF. After rectal administration of LZF for seven consecutive days, significant amelioration effects on body weight loss, DAI score, and colon inflammation were found in UC rats. Based on this, further metabolomics identified 14 potential biomarkers in the treatment of UC with LZF, of which five possessed diagnostic significance: L-alanine, taurocholic acid, niacinamide, cholic acid, and L-valine. These metabolites are mainly involved in 12 metabolic pathways, including nicotate and nicotinamide metabolism, glycospholipid metabolism, arginine and proline metabolism, primary bile acid biosynthesis, and pantothenate and CoA biosynthesis. These metabolic pathways suggest that LZF ameliorates UC by regulating amino acid metabolism, fat metabolism, and energy production. This study provides a useful approach for exploring the potential mechanisms of herbal prescription in UC treatment mediated by metabolomics.
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21
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Nyström N, Prast-Nielsen S, Correia M, Globisch D, Engstrand L, Schuppe Koistinen I, Halfvarson J. Mucosal and plasma metabolomes in new-onset paediatric inflammatory bowel disease: correlations with disease characteristics and plasma inflammation protein markers. J Crohns Colitis 2022; 17:418-432. [PMID: 36219554 PMCID: PMC10069620 DOI: 10.1093/ecco-jcc/jjac149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS To advance the understanding of inflammatory bowel disease (IBD) pathophysiology, we compared the mucosal and plasma metabolomes between new-onset paediatric IBD patients and symptomatic non-IBD controls, and correlated plasma inflammation markers and disease characteristics with the altered metabolites. METHODS Paired colonic and ileal biopsies and plasma from 67 treatment-naïve children with incident Crohn's disease (CD; n=47), ulcerative colitis (UC; n=9), and non-IBD controls (n=11) were analysed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). Inflammatory plasma proteins (n=92) were assessed. RESULTS The metabolomes in inflamed mucosal biopsies differed between IBD patients and controls. In CD, mucosal levels of several lysophospholipids (lysophosphatidylcholines, lysophosphatidyletanolamines, lysophosphatidylinositols, and lysophosphatidylserines) were decreased, correlating with various plasma metabolites, including amino acid analogues and N-acetylated compounds. In both CD and UC, mucosal sphingolipids, including ceramide (d18:2/24:1, d18:1/24:2), lactosyl-N-palmitoyl-sphingosine (d18:1/16:0), behenoyl sphingomyelin (d18:1/22:0), lignoceroyl sphingomyelin (d18:1/24:0), and/or sphingomyelin (d18:1/24:1, d18:2/24:0) were increased, correlating with sphingolipids, bile acids, and/or N-acetylated metabolites in plasma. Among proteins associated with CD, interleukin-24 correlated with plasma metabolites, including lactosyl-N-palmitoyl sphingosine (d18:1/16:0) and phosphatidyletanolamine (18:1/18:1), haemoglobin, and faecal calprotectin. In UC, interleukin-24, interleukin-17A, and C-C motif chemokine 11 correlated with several plasma metabolites, including N-acetyltryptophan, tryptophan, glycerate, and threonate, and with the paediatric ulcerative colitis activity index, C-reactive protein, and faecal-calprotectin. CONCLUSIONS Mucosal perturbations of lysophospholipids and sphingolipids characterised the metabolome in new-onset paediatric IBD and correlated with plasma metabolites. By integrating plasma metabolomics data with inflammatory proteins and clinical data, we identified clinical and inflammatory markers associated with metabolomic signatures for IBD.
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Affiliation(s)
- Niklas Nyström
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Stefanie Prast-Nielsen
- Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Mario Correia
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Daniel Globisch
- Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden.,Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Engstrand
- Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Ina Schuppe Koistinen
- Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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22
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Gur M, Zuckerman-Levin N, Masarweh K, Hanna M, Laghi L, Marazzato M, Levanon S, Hakim F, Bar-Yoseph R, Wilschanski M, Bentur L. The effect of probiotic administration on metabolomics and glucose metabolism in CF patients. Pediatr Pulmonol 2022; 57:2335-2343. [PMID: 35676769 PMCID: PMC9796051 DOI: 10.1002/ppul.26037] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND OBJECTIVES Cystic fibrosis (CF)-related diabetes (CFRD) affects 50% of CF adults. Gut microbial imbalance (dysbiosis) aggravates their inflammatory response and contributes to insulin resistance (IR). We hypothesized that probiotics may improve glucose tolerance by correcting dysbiosis. METHODS A single-center prospective pilot study assessing the effect of Vivomixx® probiotic (450 billion/sachet) on clinical status, spirometry, lung clearance index (LCI), and quality of life (QOL) questionnaires; inflammatory parameters (urine and stool metabolomics, blood cytokines); and glucose metabolism (oral glucose tolerance test [OGTT]), continuous glucose monitoring [CGM], and homeostasis model assessment of IR (HOMA-IR) in CF patients. RESULTS Twenty-three CF patients (six CFRD), mean age 17.7 ± 8.2 years. After 4 months of probiotic administration, urinary cysteine (p = 0.018), lactulose (p = 0.028), arabinose (p = 0.036), mannitol (p = 0.041), and indole 3-lactate (p = 0.046) significantly increased, while 3-methylhistidine (p = 0.046) and N-acetyl glutamine (p = 0.047) decreased. Stool 2-Hydroxyisobutyrate (p = 0.022) and 3-methyl-2-oxovalerate (p = 0.034) decreased. Principal component analysis, based on urine metabolites, found significant partitions between subjects at the end of treatment compared to baseline (p = 0.004). After 2 months of probiotics, the digestive symptoms domain of Cystic Fibrosis Questionnaire-Revised improved (p = 0.007). In the nondiabetic patients, a slight decrease in HOMA-IR, from 2.28 to 1.86, was observed. There was no significant change in spirometry results, LCI, blood cytokines and CGM. CONCLUSIONS Changes in urine and stool metabolic profiles, following the administration of probiotics, may suggest a positive effect on glucose metabolism in CF. Larger long-term studies are needed to confirm our findings. Understanding the interplay between dysbiosis, inflammation, and glucose metabolism may help preventing CFRD.
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Affiliation(s)
- Michal Gur
- Pediatric Pulmonary Institute and CF Center, Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Nehama Zuckerman-Levin
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Pediatric Diabetes Unit, Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel
| | - Kamal Masarweh
- Pediatric Pulmonary Institute and CF Center, Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel
| | - Moneera Hanna
- Pediatric Pulmonary Institute and CF Center, Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel
| | - Luca Laghi
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy.,Interdepartmental Centre for Industrial Agrofood Research, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Massimiliano Marazzato
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Shir Levanon
- Pediatric Pulmonary Institute and CF Center, Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel
| | - Fahed Hakim
- Pediatric Pulmonary Institute and CF Center, Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ronen Bar-Yoseph
- Pediatric Pulmonary Institute and CF Center, Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Michael Wilschanski
- Department of Pediatric Gastroenterology, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lea Bentur
- Pediatric Pulmonary Institute and CF Center, Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel.,Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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23
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Rojas-Tapias DF, Brown EM, Temple ER, Onyekaba MA, Mohamed AMT, Duncan K, Schirmer M, Walker RL, Mayassi T, Pierce KA, Ávila-Pacheco J, Clish CB, Vlamakis H, Xavier RJ. Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine. Nat Microbiol 2022; 7:1673-1685. [PMID: 36138166 PMCID: PMC9728153 DOI: 10.1038/s41564-022-01224-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 08/03/2022] [Indexed: 12/13/2022]
Abstract
Colonization of the intestine by oral microbes has been linked to multiple diseases such as inflammatory bowel disease and colon cancer, yet mechanisms allowing expansion in this niche remain largely unknown. Veillonella parvula, an asaccharolytic, anaerobic, oral microbe that derives energy from organic acids, increases in abundance in the intestine of patients with inflammatory bowel disease. Here we show that nitrate, a signature metabolite of inflammation, allows V. parvula to transition from fermentation to anaerobic respiration. Nitrate respiration, through the narGHJI operon, boosted Veillonella growth on organic acids and also modulated its metabolic repertoire, allowing it to use amino acids and peptides as carbon sources. This metabolic shift was accompanied by changes in carbon metabolism and ATP production pathways. Nitrate respiration was fundamental for ectopic colonization in a mouse model of colitis, because a V. parvula narG deletion mutant colonized significantly less than a wild-type strain during inflammation. These results suggest that V. parvula harness conditions present during inflammation to colonize in the intestine.
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Affiliation(s)
- Daniel F Rojas-Tapias
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Agricultural Microbiology, Colombian Corporation for Agricultural Research-Agrosavia, Bogotá, Colombia
| | - Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Ahmed M T Mohamed
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Kellyanne Duncan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Melanie Schirmer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Emmy Noether Group, ZIEL-Institute for Food and Health, Technical University of Munich, Freising, Germany
| | | | - Toufic Mayassi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Kerry A Pierce
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Clary B Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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24
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Macrophage immunometabolism in inflammatory bowel diseases: From pathogenesis to therapy. Pharmacol Ther 2022; 238:108176. [DOI: 10.1016/j.pharmthera.2022.108176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/11/2022] [Accepted: 03/22/2022] [Indexed: 12/17/2022]
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25
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Çakır Gündoğdu A, Kar F, Özbayer C. Investigation of the Gastroprotective Effect of Betaine-Homocysteine Homeostasis on Oxidative Stress, Inflammation and Apoptosis in Ethanol-Induced Ulcer Model. J INVEST SURG 2022; 35:1806-1817. [PMID: 36154440 DOI: 10.1080/08941939.2022.2126566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Background: There is a growing interest in the use of natural compounds for the treatment of gastric ulcers. The multifunctional roles of betaine in various diseases make this natural substance a favorable pre-drug for ulcer treatment. This study aims to determine the competence of betaine in gastroprotection against ethanol-induced damage and to explore underlying mechanisms considering its effects on liver and kidney activity and blood parameters.Methods: Wistar albino rats were orally treated with vehicle (distilled water) or betaine (250 mg/kg) for twenty-one days and then ulcer formation was induced by ingestion of 75% ethanol. Gastric mucosal damage was evaluated by gross examination and histopathological analysis. Homocysteine levels, lipid peroxidation, total antioxidant status (TAS), total oxidant status (TAS), antioxidant enzymes and pro-inflammatory and anti-inflammatory cytokines levels were assessed by enzyme-linked immunosorbent assay (ELISA) or immunohistochemistry. Furthermore, routine biochemical tests were performed and hematological parameters were analyzed.Results: Betaine ameliorated any gastric mucosal damage and reduced homocysteine levels significantly. The TOS and malondialdehyde (MDA) levels were decreased while the TAS, glutathione (GSH) levels and catalase (CAT) activity were increased upon the betaine treatment. Betaine reduced apoptosis by regulating Bax and Bcl-2 levels, however, it did not alter inflammatory mediators. Additionally, betaine improved serum potassium (K+) and blood urea nitrogen (BUN) levels, whereas it increased alanine aminotransferase (ALT) levels and impaired hematological parameters.Conclusions: Altogether, these data illustrated that betaine exhibits a gastroprotective effect against ulcers through the homocysteine pathway by modulating oxidative stress in the gastric tissue; however, its systemic effects should not be ignored.
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Affiliation(s)
- Ayşe Çakır Gündoğdu
- Department of Histology and Embryology, Faculty of Medicine, Kütahya Health Sciences University, Kütahya, Turkey
| | - Fatih Kar
- Department of Basic Sciences, Faculty of Engineering and Natural Sciences, Kütahya Health Sciences University, Kütahya, Turkey
| | - Cansu Özbayer
- Department of Medical Biology, Faculty of Medicine, Kütahya Health Sciences University, Kütahya, Turkey
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26
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Oleic Acid and Palmitic Acid from Bacteroides thetaiotaomicron and Lactobacillus johnsonii Exhibit Anti-Inflammatory and Antifungal Properties. Microorganisms 2022; 10:microorganisms10091803. [PMID: 36144406 PMCID: PMC9504516 DOI: 10.3390/microorganisms10091803] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/21/2022] Open
Abstract
A decrease in populations of Bacteroides thetaiotaomicron and Lactobacillus johnsonii is observed during the development of colitis and fungal overgrowth, while restoration of these populations reduces inflammatory parameters and fungal overgrowth in mice. This study investigated the effect of two fatty acids from B. thetaiotaomicron and L. johnsonii on macrophages and Caco-2 cells, as well as their impact on the inflammatory immune response and on Candida glabrata overgrowth in a murine model of dextran sulfate sodium (DSS)-induced colitis. Oleic acid (OA) and palmitic acid (PA) from L. johnsonii and B. thetaiotaomicron were detected during their interaction with epithelial cells from colon samples. OA alone or OA combined with PA (FAs) reduced the expression of proinflammatory mediators in intestinal epithelial Caco-2 cells challenged with DSS. OA alone or FAs increased FFAR1, FFAR2, AMPK, and IL-10 expression in macrophages. Additionally, OA alone or FAs decreased COX-2, TNFα, IL-6, and IL-12 expression in LPS-stimulated macrophages. In the DSS murine model, oral administration of FAs reduced inflammatory parameters, decreased Escherichia coli and Enterococcus faecalis populations, and eliminated C. glabrata from the gut. Overall, these findings provide evidence that OA combined with PA exhibits anti-inflammatory and antifungal properties.
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27
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Evidence of a genetically driven metabolomic signature in actively inflamed Crohn's disease. Sci Rep 2022; 12:14101. [PMID: 35982195 PMCID: PMC9388636 DOI: 10.1038/s41598-022-18178-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/08/2022] [Indexed: 11/09/2022] Open
Abstract
Crohn's disease (CD) is characterised by chronic inflammation. We aimed to identify a relationship between plasma inflammatory metabolomic signature and genomic data in CD using blood plasma metabolic profiles. Proton NMR spectroscopy were achieved for 228 paediatric CD patients. Regression (OPLS) modelling and machine learning (ML) approaches were independently applied to establish the metabolic inflammatory signature, which was correlated against gene-level pathogenicity scores generated for all patients and functional enrichment was analysed. OPLS modelling of metabolomic spectra from unfasted patients revealed distinctive shifts in plasma metabolites corresponding to regions of the spectrum assigned to N-acetyl glycoprotein, glycerol and phenylalanine that were highly correlated (R2 = 0.62) with C-reactive protein levels. The same metabolomic signature was independently identified using ML to predict patient inflammation status. Correlation of the individual peaks comprising this metabolomic signature of inflammation with pathogenic burden across 15,854 unselected genes identified significant enrichment for genes functioning within 'intrinsic component of membrane' (p = 0.003) and 'inflammatory bowel disease (IBD)' (p = 0.003). The seven genes contributing IBD enrichment are critical regulators of pro-inflammatory signaling. Overall, a metabolomic signature of inflammation can be detected from blood plasma in CD. This signal is correlated with pathogenic mutation in pro-inflammatory immune response genes.
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28
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Walker HK, Boag AM, Ottka C, Lohi H, Handel I, Gow AG, Mellanby RJ. Serum metabolomic profiles in dogs with chronic enteropathy. J Vet Intern Med 2022; 36:1752-1759. [PMID: 35880501 PMCID: PMC9511094 DOI: 10.1111/jvim.16419] [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: 08/27/2021] [Revised: 03/20/2022] [Accepted: 03/25/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Metabolic profiles differ between healthy humans and those with inflammatory bowel disease. Few studies have examined metabolic profiles in dogs with chronic enteropathy (CE). HYPOTHESIS Serum metabolic profiles of dogs with CE are significantly different from those of healthy dogs. ANIMALS Fifty-five dogs with CE and 204 healthy controls. METHODS A cross-sectional study. The serum concentrations of 99 metabolites measured using a canine-specific proton nuclear magnetic resonance spectroscopy platform were studied. A 2-sample unpaired t-test was used to compare the 2 study samples. The threshold for significance was set at P < .05 with a Bonferroni correction for each metabolite group. RESULTS Nineteen metabolites and 18 indices of lipoprotein composition were significantly different between the CE and healthy dogs. Four metabolites were significantly higher in dogs with CE, including phenylalanine (mean and SD) (healthy: 0.0417 mmol/L; [SD] 0.0100; CE: 0.0480 mmol/L; SD: 0.0125; P value: <.001) and lactate (healthy: 1.8751 mmol/L; SD: 0.7808; CE: 2.4827 mmol/L; SD CE: 1.4166; P value: .003). Fifteen metabolites were significantly lower in dogs with CE, including total fatty acids, and glycine (healthy: 0.2273 mmol/L; SD: 0.0794; CE: 0.1828 mmol/L; SD CE: 0.0517; P value: <.001). CONCLUSIONS AND CLINICAL IMPORTANCE The metabolic profile of dogs with CE is significantly different from that of healthy dogs, this opens novel research avenues to develop better diagnostic and prognostic approaches as well as therapeutic trials.
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Affiliation(s)
- Hannah K Walker
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, Easter Bush Campus, The University of Edinburgh, Midlothian, United Kingdom
| | - Alisdair M Boag
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, Easter Bush Campus, The University of Edinburgh, Midlothian, United Kingdom
| | - Claudia Ottka
- PetBiomics Ltd, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- PetBiomics Ltd, Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Ian Handel
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, Easter Bush Campus, The University of Edinburgh, Midlothian, United Kingdom
| | - Adam G Gow
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, Easter Bush Campus, The University of Edinburgh, Midlothian, United Kingdom
| | - Richard J Mellanby
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, Easter Bush Campus, The University of Edinburgh, Midlothian, United Kingdom
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Tu P, Chi L, Bian X, Gao B, Ru H, Lu K. A Black Raspberry-Rich Diet Protects From Dextran Sulfate Sodium-Induced Intestinal Inflammation and Host Metabolic Perturbation in Association With Increased Aryl Hydrocarbon Receptor Ligands in the Gut Microbiota of Mice. Front Nutr 2022; 9:842298. [PMID: 35734371 PMCID: PMC9208328 DOI: 10.3389/fnut.2022.842298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Dietary modulation of the gut microbiota recently received considerable attention, and ligand activation of aryl hydrocarbon receptor (AHR) plays a pivotal role in intestinal immunity. Importantly, black raspberry (BRB, Rubus occidentalis) is associated with a variety of beneficial health effects. We aim to investigate effects of a BRB-rich diet on dextran sulfate sodium (DSS)-induced intestinal inflammation and to determine whether its consequent anti-inflammatory effects are relevant to modulation of the gut microbiota, especially its production of AHR ligands. A mouse model of DSS-induced intestinal inflammation was used in the present study. C57BL/6J mice were fed either AIN-76A or BRB diet. Composition and functions of the gut microbiota were assessed by 16S rRNA sequencing and comparative metagenome analysis. Metabolic profiles of host and the gut microbiome were assessed by serum and fecal metabolomic profiling and identification. BRB diet was found to ameliorate DSS-induced intestinal inflammation and host metabolic perturbation. BRB diet also protected from DSS-induced perturbation in diversity and composition in the gut microbiota. BRB diet promoted AHR ligand production by the gut microbiota, as revealed by increased levels of fecal AHR activity in addition to increased levels of two known AHR ligands, hemin and biliverdin. Accordingly, enrichment of bacterial genes and pathways responsible for production of hemin and biliverdin were found, specific gut bacteria that are highly correlated with abundances of hemin and biliverdin were also identified. BRB dietary intervention ameliorated intestinal inflammation in mice in association with promotion of AHR ligand production by the gut microbiota.
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Affiliation(s)
- Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Xiaoming Bian
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, United States
| | - Bei Gao
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, United States
| | - Hongyu Ru
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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30
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Powles STR, Gallagher KI, Chong LWL, Alexander JL, Mullish BH, Hicks LC, McDonald JAK, Marchesi JR, Williams HRT, Orchard TR. Effects of bowel preparation on intestinal bacterial associated urine and faecal metabolites and the associated faecal microbiome. BMC Gastroenterol 2022; 22:240. [PMID: 35562657 PMCID: PMC9101932 DOI: 10.1186/s12876-022-02301-1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 04/20/2022] [Indexed: 12/17/2022] Open
Abstract
Background Urinary and faecal metabolic profiling have been extensively studied in gastrointestinal diseases as potential diagnostic markers, and to enhance our understanding of the intestinal microbiome in the pathogenesis these conditions. The impact of bowel cleansing on the microbiome has been investigated in several studies, but limited to just one study on the faecal metabolome. Aim To compare the effects of bowel cleansing on the composition of the faecal microbiome, and the urine and faecal metabolome. Methods Urine and faecal samples were obtained from eleven patients undergoing colonoscopy at baseline, and then at day 3 and week 6 after colonoscopy. 16S rRNA gene sequencing was used to analyse changes in the microbiome, and metabonomic analysis was performed using proton nuclear magnetic resonance (1H NMR) spectroscopy. Results Microbiomic analysis demonstrated a reduction in alpha diversity (Shannon index) between samples taken at baseline and three days following bowel cleansing (p = 0.002), and there was no significant difference between samples at baseline and six weeks post colonoscopy. Targeted and non-targeted analysis of urinary and faecal bacterial associated metabolites showed no significant impact following bowel cleansing. Conclusions Bowel cleansing causes a temporary disturbance in bacterial alpha diversity measured in faeces, but no significant changes in the faecal and urine metabolic profiles, suggesting that overall the faecal microbiome and its associated metabolome is resistant to the effects of an induced osmotic diarrhoea. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-022-02301-1.
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Affiliation(s)
- Sam T R Powles
- Department of Metabolism, Digestion and Reproduction, Imperial College London, St. Mary's Hospital, Praed Street, London, W2 1NY, UK. .,Department of Gastroenterology, Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK.
| | - Kate I Gallagher
- Department of Metabolism, Digestion and Reproduction, Imperial College London, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Leo W L Chong
- Department of Metabolism, Digestion and Reproduction, Imperial College London, St. Mary's Hospital, Praed Street, London, W2 1NY, UK.,Department of Gastroenterology, Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - James L Alexander
- Department of Metabolism, Digestion and Reproduction, Imperial College London, St. Mary's Hospital, Praed Street, London, W2 1NY, UK.,Department of Gastroenterology, Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Benjamin H Mullish
- Department of Metabolism, Digestion and Reproduction, Imperial College London, St. Mary's Hospital, Praed Street, London, W2 1NY, UK.,Department of Gastroenterology, Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Lucy C Hicks
- Department of Metabolism, Digestion and Reproduction, Imperial College London, St. Mary's Hospital, Praed Street, London, W2 1NY, UK.,Department of Gastroenterology, Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Julie A K McDonald
- Department of Metabolism, Digestion and Reproduction, Imperial College London, St. Mary's Hospital, Praed Street, London, W2 1NY, UK.,MRC Centre for Molecular Bacteriology and Infection, Flowers Building, Imperial College London, London, SW7 2AZ, UK
| | - Julian R Marchesi
- Department of Metabolism, Digestion and Reproduction, Imperial College London, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Horace R T Williams
- Department of Metabolism, Digestion and Reproduction, Imperial College London, St. Mary's Hospital, Praed Street, London, W2 1NY, UK.,Department of Gastroenterology, Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Timothy R Orchard
- Department of Metabolism, Digestion and Reproduction, Imperial College London, St. Mary's Hospital, Praed Street, London, W2 1NY, UK.,Department of Gastroenterology, Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
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31
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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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32
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Cortes GM, Marcialis MA, Bardanzellu F, Corrias A, Fanos V, Mussap M. Inflammatory Bowel Disease and COVID-19: How Microbiomics and Metabolomics Depict Two Sides of the Same Coin. Front Microbiol 2022; 13:856165. [PMID: 35391730 PMCID: PMC8981987 DOI: 10.3389/fmicb.2022.856165] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/21/2022] [Indexed: 12/11/2022] Open
Abstract
The integrity of the gastrointestinal tract structure and function is seriously compromised by two pathological conditions sharing, at least in part, several pathogenetic mechanisms: inflammatory bowel diseases (IBD) and coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. IBD and COVID-19 are marked by gut inflammation, intestinal barrier breakdown, resulting in mucosal hyperpermeability, gut bacterial overgrowth, and dysbiosis together with perturbations in microbial and human metabolic pathways originating changes in the blood and fecal metabolome. This review compared the most relevant metabolic and microbial alterations reported from the literature in patients with IBD with those in patients with COVID-19. In both diseases, gut dysbiosis is marked by the prevalence of pro-inflammatory bacterial species and the shortfall of anti-inflammatory species; most studies reported the decrease in Firmicutes, with a specific decrease in obligately anaerobic producers short-chain fatty acids (SCFAs), such as Faecalibacterium prausnitzii. In addition, Escherichia coli overgrowth has been observed in IBD and COVID-19, while Akkermansia muciniphila is depleted in IBD and overexpressed in COVID-19. In patients with COVID-19, gut dysbiosis continues after the clearance of the viral RNA from the upper respiratory tract and the resolution of clinical symptoms. Finally, we presented and discussed the impact of gut dysbiosis, inflammation, oxidative stress, and increased energy demand on metabolic pathways involving key metabolites, such as tryptophan, phenylalanine, histidine, glutamine, succinate, citrate, and lipids.
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Affiliation(s)
- Gian Mario Cortes
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Maria Antonietta Marcialis
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Flaminia Bardanzellu
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Angelica Corrias
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Michele Mussap
- Laboratory Medicine, Department of Surgical Sciences, School of Medicine, University of Cagliari, Monserrato, Italy
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33
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Piestansky J, Olesova D, Matuskova M, Cizmarova I, Chalova P, Galba J, Majerova P, Mikus P, Kovac A. Amino acids in inflammatory bowel diseases: Modern diagnostic tools and methodologies. Adv Clin Chem 2022; 107:139-213. [PMID: 35337602 DOI: 10.1016/bs.acc.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Amino acids are crucial building blocks of living organisms. Together with their derivatives, they participate in many intracellular processes to act as hormones, neuromodulators, and neurotransmitters. For several decades amino acids have been studied for their potential as markers of various diseases, including inflammatory bowel diseases. Subsequent improvements in sample pretreatment, separation, and detection methods have enabled the specific and very sensitive determination of these molecules in multicomponent matrices-biological fluids and tissues. The information obtained from targeted amino acid analysis (biomarker-based analytical strategy) can be further used for early diagnostics, to monitor the course of the disease or compliance of the patients. This review will provide an insight into current knowledge about inflammatory bowel diseases, the role of proteinogenic amino acids in intestinal inflammation and modern analytical techniques used in its diagnosis and disease activity monitoring. Current advances in the analysis of amino acids focused on sample pretreatment, separation strategy, or detection methods are highlighted, and their potential in clinical laboratories is discussed. In addition, the latest clinical data obtained from the metabolomic profiling of patients suffering from inflammatory bowel diseases are summarized with a focus on proteinogenic amino acids.
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Affiliation(s)
- Juraj Piestansky
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia; Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Dominika Olesova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Michaela Matuskova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ivana Cizmarova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Petra Chalova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jaroslav Galba
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Mikus
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia; Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.
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Zhuang Z, Li N, Wang J, Yang R, Wang W, Liu Z, Huang T. GWAS-associated bacteria and their metabolites appear to be causally related to the development of inflammatory bowel disease. Eur J Clin Nutr 2022; 76:1024-1030. [DOI: 10.1038/s41430-022-01074-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/31/2021] [Accepted: 01/10/2022] [Indexed: 12/22/2022]
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35
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Lyu S, Pan F, Ge H, Yang Q, Duan X, Feng M, Liu X, Zhang T, Liu J. Fermented egg-milk beverage alleviates dextran sulfate sodium-induced colitis in mice through the modulation of intestinal flora and short-chain fatty acids. Food Funct 2021; 13:702-715. [PMID: 34935826 DOI: 10.1039/d1fo03040j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fermented egg-milk beverage (FEMB) can alleviate the symptoms of intestinal diseases by regulating intestinal flora and supplying nutrition. This study investigated the protective effect of FEMB on dextran sulfate sodium (DSS)-induced ulcerative colitis (UC) in mice. The results showed that FEMB relieved the UC mice's pathological abnormalities and colonic inflammation, and restructured the intestinal flora composition simultaneously. After FEMB treatment for 14 days, the body weight of the mice rose and the disease activity index (DAI) value decreased. Furthermore, the length and form of colons in the UC mice were notably restored. Inflammatory cells decreased or disappeared, and goblet cells and crypt were enriched and modified. 16S rRNA gene sequencing results demonstrated that FEMB treatment could increase the abundance of beneficial bacteria in the cecum content of mice, including unclassified_f_Lachnospiraceae and Lactobacillus. Moreover, probiotics that can increase the content of short-chain fatty acids (SCFAs) may contribute to inflammation alleviation. An increase in amino acids was observed in our experiment, which may benefit nutritional supplements. In conclusion, FEMB treatment can alleviate the damage of DSS-induced colitis in Balb/c mice. This study provides a theoretical basis for both the relief of inflammation and the application of FEMB.
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Affiliation(s)
- Siwen Lyu
- Jilin Provincial Key Laboratory of Nutrition and Functional Food and College of Food Science and Engineering, Jilin University, Changchun 130062, People's Republic of China. .,College of Food Science and Engineering, Jilin University, Changchun, 130062, People's Republic of China.
| | - Fengguang Pan
- Jilin Provincial Key Laboratory of Nutrition and Functional Food and College of Food Science and Engineering, Jilin University, Changchun 130062, People's Republic of China. .,College of Food Science and Engineering, Jilin University, Changchun, 130062, People's Republic of China.
| | - Huifang Ge
- Jilin Provincial Key Laboratory of Nutrition and Functional Food and College of Food Science and Engineering, Jilin University, Changchun 130062, People's Republic of China. .,College of Food Science and Engineering, Jilin University, Changchun, 130062, People's Republic of China.
| | - Qi Yang
- Jilin Provincial Key Laboratory of Nutrition and Functional Food and College of Food Science and Engineering, Jilin University, Changchun 130062, People's Republic of China. .,College of Food Science and Engineering, Jilin University, Changchun, 130062, People's Republic of China.
| | - Xuehui Duan
- College of Food Science and Engineering, Jilin University, Changchun, 130062, People's Republic of China.
| | - Mengmeng Feng
- Jilin Provincial Key Laboratory of Nutrition and Functional Food and College of Food Science and Engineering, Jilin University, Changchun 130062, People's Republic of China. .,College of Food Science and Engineering, Jilin University, Changchun, 130062, People's Republic of China.
| | - Xuanting Liu
- Jilin Provincial Key Laboratory of Nutrition and Functional Food and College of Food Science and Engineering, Jilin University, Changchun 130062, People's Republic of China. .,College of Food Science and Engineering, Jilin University, Changchun, 130062, People's Republic of China.
| | - Ting Zhang
- Jilin Provincial Key Laboratory of Nutrition and Functional Food and College of Food Science and Engineering, Jilin University, Changchun 130062, People's Republic of China. .,College of Food Science and Engineering, Jilin University, Changchun, 130062, People's Republic of China.
| | - Jingbo Liu
- Jilin Provincial Key Laboratory of Nutrition and Functional Food and College of Food Science and Engineering, Jilin University, Changchun 130062, People's Republic of China. .,College of Food Science and Engineering, Jilin University, Changchun, 130062, People's Republic of China.
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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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The Investigation of Metabonomic Pathways of Serum of Iranian Women with Recurrent Miscarriage Using 1H NMR. BIOMED RESEARCH INTERNATIONAL 2021; 2021:3422138. [PMID: 34778450 PMCID: PMC8580660 DOI: 10.1155/2021/3422138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/28/2021] [Accepted: 10/20/2021] [Indexed: 11/23/2022]
Abstract
Purpose Recurrent miscarriage applies to pregnancy loss expulsion of the fetus within the first 24 weeks of pregnancy. This study is aimed at comparatively investigating the sera of women with RM with those who have no record of miscarriages to identify if there were any metabolite and metabolic pathway differences using 1H NMR spectroscopy. Methods Serum samples were collected from women with RM (n = 30) and those who had no records of RM (n = 30) to obtain metabolomics information. 1H NMR spectroscopy was carried out on the samples using Carr Purcell Meiboom Gill spin echo; also, Partial Least Squares Discriminant Analysis was performed in MATLAB software using the ProMetab program to obtain the classifying chemical shifts; the metabolites were identified by using the Human Metabolome Database (HMDB) in both the experimental and control groups. The pathway analysis option of the Metaboanalyst.ca website was used to identify the changed metabolic pathways. Results The results of the study revealed that 14 metabolites were different in the patients with RM. Moreover, the pathway analysis showed that taurine and hypotaurine metabolism along with phenylalanine, tyrosine, and tryptophan biosynthesis was significantly different in patients with RM. Conclusion The present study proposes that any alteration in the above metabolic pathways might lead to metabolic dysfunctions which may result in a higher probability of RM.
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Bjerrum JT, Wang YL, Seidelin JB, Nielsen OH. IBD metabonomics predicts phenotype, disease course, and treatment response. EBioMedicine 2021; 71:103551. [PMID: 34419930 PMCID: PMC8379620 DOI: 10.1016/j.ebiom.2021.103551] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/22/2021] [Accepted: 08/09/2021] [Indexed: 02/07/2023] Open
Abstract
Metabonomics in inflammatory bowel disease (IBD) characterizes the effector molecules of biological systems and thus aims to describe the molecular phenotype, generate insight into the pathology, and predict disease course and response to treatment. Nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and integrated NMR and MS platforms coupled with multivariate analyses have been applied to create such metabolic profiles. Recent advances have identified quiescent ulcerative colitis as a distinct molecular phenotype and demonstrated metabonomics as a promising clinical tool for predicting relapse and response to treatment with biologics as well as fecal microbiome transplantation, thus facilitating much needed precision medicine. However, understanding this complex research field and how it translates into clinical settings is a challenge. This review aims to describe the current workflow, analytical strategies, and associated bioinformatics, and translate current IBD metabonomic knowledge into new potential clinically applicable treatment strategies, and outline future key translational perspectives.
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Affiliation(s)
- Jacob T Bjerrum
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 1 DK-2730, Denmark.
| | - Yulan L Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Jakob B Seidelin
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 1 DK-2730, Denmark
| | - Ole H Nielsen
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of Copenhagen, Denmark
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Glinskikh A, Snytnikova O, Zelentsova E, Borisova M, Tsentalovich Y, Akulov A. The Effect of Blood Contained in the Samples on the Metabolomic Profile of Mouse Brain Tissue: A Study by NMR Spectroscopy. Molecules 2021; 26:molecules26113096. [PMID: 34067246 PMCID: PMC8196876 DOI: 10.3390/molecules26113096] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
(1) Recently, metabolic profiling of the tissue in the native state or extracts of its metabolites has become increasingly important in the field of metabolomics. An important factor, in this case, is the presence of blood in a tissue sample, which can potentially lead to a change in the concentration of tissue metabolites and, as a result, distortion of experimental data and their interpretation. (2) In this paper, the metabolomic profiling based on NMR spectroscopy was performed to determine the effect of blood contained in the studied samples of brain tissue on their metabolomic profile. We used 13 male laboratory CD-1® IGS mice for this study. The animals were divided into two groups. The first group of animals (n = 7) was subjected to the perfusion procedure, and the second group of animals (n = 6) was not perfused. The brain tissues of the animals were homogenized, and the metabolite fraction was extracted with a water/methanol/chloroform solution. Samples were studied by high-frequency 1H-NMR spectroscopy with subsequent statistical data analysis. The group comparison was performed with the use of the Student's test. We identified 36 metabolites in the brain tissue with the use of NMR spectroscopy. (3) For the major set of studied metabolites, no significant differences were found in the brain tissue metabolite concentrations in the native state and after the blood removal procedure. (4) Thus, it was shown that the presence of blood does not have a significant effect on the metabolomic profile of the brain in animals without pathologies.
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Affiliation(s)
- Anastasia Glinskikh
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Academician Lavrentiev Avenue, 10, 630090 Novosibirsk, Russia; (A.G.); (M.B.); (A.A.)
- International Tomography Center, Siberian Branch of the Russian Academy of Sciences, Institutskaya str. 3a, 630090 Novosibirsk, Russia; (E.Z.); (Y.T.)
- Faculty of Fundamental Medicine, Novosibirsk State University, Pirogova str. 2, 630090 Novosibirsk, Russia
| | - Olga Snytnikova
- International Tomography Center, Siberian Branch of the Russian Academy of Sciences, Institutskaya str. 3a, 630090 Novosibirsk, Russia; (E.Z.); (Y.T.)
- Correspondence:
| | - Ekaterina Zelentsova
- International Tomography Center, Siberian Branch of the Russian Academy of Sciences, Institutskaya str. 3a, 630090 Novosibirsk, Russia; (E.Z.); (Y.T.)
- Faculty of Fundamental Medicine, Novosibirsk State University, Pirogova str. 2, 630090 Novosibirsk, Russia
| | - Maria Borisova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Academician Lavrentiev Avenue, 10, 630090 Novosibirsk, Russia; (A.G.); (M.B.); (A.A.)
| | - Yuri Tsentalovich
- International Tomography Center, Siberian Branch of the Russian Academy of Sciences, Institutskaya str. 3a, 630090 Novosibirsk, Russia; (E.Z.); (Y.T.)
- Faculty of Fundamental Medicine, Novosibirsk State University, Pirogova str. 2, 630090 Novosibirsk, Russia
| | - Andrey Akulov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Academician Lavrentiev Avenue, 10, 630090 Novosibirsk, Russia; (A.G.); (M.B.); (A.A.)
- International Tomography Center, Siberian Branch of the Russian Academy of Sciences, Institutskaya str. 3a, 630090 Novosibirsk, Russia; (E.Z.); (Y.T.)
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40
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Heinken A, Hertel J, Thiele I. Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis. NPJ Syst Biol Appl 2021; 7:19. [PMID: 33958598 PMCID: PMC8102608 DOI: 10.1038/s41540-021-00178-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/07/2021] [Indexed: 12/26/2022] Open
Abstract
Inflammatory bowel diseases, such as Crohn's Disease, are characterised by an altered blood and faecal metabolome, and changes in gut microbiome composition. Here, we present an efficient, scalable, tractable systems biology framework to mechanistically link microbial strains and faecal metabolites. We retrieve strain-level relative abundances from metagenomics data from a cohort of paediatric Crohn's Disease patients with and without dysbiosis and healthy control children and construct and interrogate a personalised microbiome model for each sample. Predicted faecal secretion profiles and strain-level contributions to each metabolite vary broadly between healthy, dysbiotic, and non-dysbiotic microbiomes. The reduced microbial diversity in IBD results in reduced numbers of secreted metabolites, especially in sulfur metabolism. We demonstrate that increased potential to synthesise amino acids is linked to Proteobacteria contributions, in agreement with experimental observations. The established modelling framework yields testable hypotheses that may result in novel therapeutic and dietary interventions targeting the host-gut microbiome-diet axis.
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Affiliation(s)
- Almut Heinken
- School of Medicine, National University of Ireland, Galway, Ireland
- Ryan Institute, National University of Ireland, Galway, Ireland
| | - Johannes Hertel
- School of Medicine, National University of Ireland, Galway, Ireland
- Ryan Institute, National University of Ireland, Galway, Ireland
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, Ireland.
- Ryan Institute, National University of Ireland, Galway, Ireland.
- Division of Microbiology, National University of Galway, Galway, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
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41
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Gallagher K, Catesson A, Griffin JL, Holmes E, Williams HRT. Metabolomic Analysis in Inflammatory Bowel Disease: A Systematic Review. J Crohns Colitis 2021; 15:813-826. [PMID: 33175138 DOI: 10.1093/ecco-jcc/jjaa227] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS The inflammatory bowel diseases [IBD], Crohn's disease and ulcerative colitis, are chronic, idiopathic gastrointestinal diseases. Although their precise aetiology is unknown, it is thought to involve a complex interaction between genetic predisposition and an abnormal host immune response to environmental exposures, probably microbial. Microbial dysbiosis has frequently been documented in IBD. Metabolomics [the study of small molecular intermediates and end products of metabolism in biological samples] provides a unique opportunity to characterize disease-associated metabolic changes and may be of particular use in quantifying gut microbial metabolism. Numerous metabolomic studies have been undertaken in IBD populations, identifying consistent alterations in a range of molecules across several biological matrices. This systematic review aims to summarize these findings. METHODS A comprehensive, systematic search was carried out using Medline and Embase. All studies were reviewed by two authors independently using predefined exclusion criteria. Sixty-four relevant papers were assessed for quality and included in the review. RESULTS Consistent metabolic perturbations were identified, including increases in levels of branched chain amino acids and lipid classes across stool, serum, plasma and tissue biopsy samples, and reduced levels of microbially modified metabolites in both urine [such as hippurate] and stool [such as secondary bile acids] samples. CONCLUSIONS This review provides a summary of metabolomic research in IBD to date, highlighting underlying themes of perturbed gut microbial metabolism and mammalian-microbial co-metabolism associated with disease status.
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Affiliation(s)
- Kate Gallagher
- Department of Metabolism Digestion and Reproduction, Imperial College London, UK
| | - Alexandra Catesson
- Department of Metabolism Digestion and Reproduction, Imperial College London, UK
| | - Julian L Griffin
- Department of Metabolism Digestion and Reproduction, Imperial College London, UK
| | - Elaine Holmes
- Department of Metabolism Digestion and Reproduction, Imperial College London, UK.,Institute of Health Futures, Murdoch University, Perth, WA, Australia
| | - Horace R T Williams
- Department of Metabolism Digestion and Reproduction, Imperial College London, UK.,Department of Gastroenterology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
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42
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Lee JD, Kim HY, Park JJ, Oh SB, Goo H, Cho KJ, Kim S, Kim KB. Metabolomics approach to biomarkers of dry eye disease using 1H-NMR in rats. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2021; 84:313-330. [PMID: 33393448 DOI: 10.1080/15287394.2020.1867274] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Dry eye disease (DED) is a chronic and progressive lesion on the ocular surface and induces symptoms, such as burning sensation, itchy eyes, heavy eyes, tired eyes, dry feeling, facial flushing, and blurred vision. The present study was performed to develop DED biomarkers using metabolomics in a rat model. DED was induced by injecting scopolamine and exposing rats to a dry condition. Scopolamine (12 mg/kg/day for 7 days) was subcutaneously injected to male Sprague-Dawley rats. The rats were placed in dry condition with air-flow and dehumidifier. Tear volume and tear breakup time (TBUT) were measured, and eyes were examined through fluorescein staining to assess DED. Mucosal damage and immune reactions were also determined. Plasma and urinary endogenous metabolites were determined using 1H-NMR analysis. Compared with control tear and TBUT levels were significantly decreased in the DED group whereas corneal damage was significantly increased. The levels of interleukins (IL-6) and IL-1β significantly elevated in the cornea and lacrimal glands in the DED group. TNF-α was numerically increased but not significantly different between groups. Pattern recognition using principal component analysis (PCA) and orthogonal projections to latent structure-discriminant analysis (OPLS-DA) of the NMR spectra in global profiling revealed different clusters between DED and control groups. Target profiling demonstrated that PCA and OPLS-DA score plots were separated between DED and controls in plasma and urine. Subsequently, 9 plasma metabolites were selected to examine different clustering between groups, and 26 urinary metabolites were also selected. Plasma metabolites showed a non-significant rising tendency in the DED group. Urinary phenylalanine, phenylacetate, pantothenate, glycine, succinate, methanol, valine, propylene glycol, histidine, threonine, lactate, and acetate were significantly different between control and DED rats. These results may contribute to understanding the metabolic regulation that is involved in DED and might be useful for potential biomarkers related to DED in rats.
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Affiliation(s)
- Jung Dae Lee
- College of Pharmacy, Dankook University, Cheonan, Republic of Korea
- Center for Human Risk Assessment, Dankook University, Chungnam, Republic of Korea
| | - Hyang Yeon Kim
- College of Pharmacy, Dankook University, Cheonan, Republic of Korea
- Center for Human Risk Assessment, Dankook University, Chungnam, Republic of Korea
| | - Jin Ju Park
- College of Pharmacy, Dankook University, Cheonan, Republic of Korea
- Center for Human Risk Assessment, Dankook University, Chungnam, Republic of Korea
| | - Soo Bean Oh
- Department of Ophthalmology, Dankook University, Cheonan, Republic of Korea
| | - Hyeyoon Goo
- Department of Ophthalmology, Dankook University, Cheonan, Republic of Korea
| | - Kyong Jin Cho
- Department of Ophthalmology, Dankook University, Cheonan, Republic of Korea
| | - Suhkmann Kim
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, Republic of Korea
| | - Kyu-Bong Kim
- College of Pharmacy, Dankook University, Cheonan, Republic of Korea
- Center for Human Risk Assessment, Dankook University, Chungnam, Republic of Korea
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Yamamoto M, Shanmuganathan M, Hart L, Pai N, Britz-McKibbin P. Urinary Metabolites Enable Differential Diagnosis and Therapeutic Monitoring of Pediatric Inflammatory Bowel Disease. Metabolites 2021; 11:metabo11040245. [PMID: 33921143 PMCID: PMC8071482 DOI: 10.3390/metabo11040245] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/29/2021] [Accepted: 04/10/2021] [Indexed: 12/14/2022] Open
Abstract
Rates of pediatric Crohn's disease (CD) and ulcerative colitis (UC) are increasing globally. Differentiation of these inflammatory bowel disease (IBD) subtypes however can be challenging when relying on invasive endoscopic approaches. We sought to identify urinary metabolic signatures of pediatric IBD at diagnosis, and during induction treatment. Nontargeted metabolite profiling of urine samples from CD (n = 18) and UC (n = 8) in a pediatric retrospective cohort study was performed using multisegment injection-capillary electrophoresis-mass spectrometry. Over 122 urinary metabolites were reliably measured from pediatric IBD patients, and unknown metabolites were identified by tandem mass spectrometry. Dynamic changes in sum-normalized urinary metabolites were also monitored following exclusive enteral nutrition (EEN) or corticosteroid therapy (CS) in repeat urine samples collected over 8 weeks. Higher urinary excretion of indoxyl sulfate, hydroxyindoxyl sulfate, phenylacetylglutamine, and sialic acid were measured in CD as compared to UC patients, but lower threonine, serine, kynurenine, and hypoxanthine (p < 0.05). Excellent discrimination of CD from UC was achieved based on the urinary serine:indoxylsulfate ratio (AUC = 0.972; p = 3.21 × 10-5). Urinary octanoyl glucuronide, pantothenic acid, and pyridoxic acid were also identified as specific dietary biomarkers of EEN in pediatric IBD patients who achieved clinical remission. This work may complement or replace existing strategies in the diagnosis and early management of children with IBD.
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Affiliation(s)
- Mai Yamamoto
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada; (M.Y.); (M.S.)
| | - Meera Shanmuganathan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada; (M.Y.); (M.S.)
| | - Lara Hart
- Department of Pediatrics, Division of Pediatric Gastroenterology and Nutrition, McMaster University, Hamilton, ON L8S 4K1, Canada; (L.H.); (N.P.)
| | - Nikhil Pai
- Department of Pediatrics, Division of Pediatric Gastroenterology and Nutrition, McMaster University, Hamilton, ON L8S 4K1, Canada; (L.H.); (N.P.)
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada; (M.Y.); (M.S.)
- Correspondence: ; Tel.: +1-905-525-9140 (ext. 22771)
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44
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Philips AM, Khan N. Amino acid sensing pathway: A major check point in the pathogenesis of obesity and COVID-19. Obes Rev 2021; 22:e13221. [PMID: 33569904 PMCID: PMC7995014 DOI: 10.1111/obr.13221] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/13/2022]
Abstract
Obesity and obesogenic comorbidities have been associated with COVID-19 susceptibility and mortality. However, the mechanism of such correlations requires an in-depth understanding. Overnutrition/excess serum amino acid profile during obesity has been linked with inflammation and reprogramming of translational machinery through hyperactivation of amino acid sensor mammalian target of rapamycin (mTOR), which is exploited by SARS-CoV-2 for its replication. Conversely, we have shown that the activation of general control nonderepressible 2 (GCN2)-dependent amino acid starvation sensing pathway suppresses intestinal inflammation by inhibiting the production of reactive oxygen species (ROS) and interleukin-1 beta (IL-1β). While activation of GCN2 has shown to mitigate susceptibility to dengue infection, GCN2 deficiency increases viremia and inflammation-associated pathologies. These findings reveal that the amino acid sensing pathway plays a significant role in controlling inflammation and viral infections. The current fact is that obesity/excess amino acids/mTOR activation aggravates COVID-19, and it might be possible that activation of amino acid starvation sensor GCN2 has an opposite effect. This article focuses on the amino acid sensing pathways through which host cells sense the availability of amino acids and reprogram the host translation machinery to mount an effective antiviral response. Besides, how SARS-CoV-2 hijack and exploit amino acid sensing pathway for its replication and pathogenesis is also discussed.
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Affiliation(s)
- Aradhana Mariam Philips
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Nooruddin Khan
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
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45
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Bauset C, Gisbert-Ferrándiz L, Cosín-Roger J. Metabolomics as a Promising Resource Identifying Potential Biomarkers for Inflammatory Bowel Disease. J Clin Med 2021; 10:jcm10040622. [PMID: 33562024 PMCID: PMC7915257 DOI: 10.3390/jcm10040622] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a relapsing chronic disorder of the gastrointestinal tract characterized by disruption of epithelial barrier function and excessive immune response to gut microbiota. The lack of biomarkers providing early diagnosis or defining the status of the pathology difficulties an accurate assessment of the disease. Given the different metabolomic profiles observed in IBD patients, metabolomics may reveal prime candidates to be studied, which may help in understanding the pathology and identifying novel therapeutic targets. In this review, we summarize the most current advances describing the promising metabolites such as lipids or amino acids found through untargeted metabolomics from serum, faecal, urine and biopsy samples.
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Affiliation(s)
- Cristina Bauset
- Department of Pharmacology and CIBER, Faculty of Medicine, University of Valencia, 46010 Valencia, Spain; (C.B.); (L.G.-F.)
| | - Laura Gisbert-Ferrándiz
- Department of Pharmacology and CIBER, Faculty of Medicine, University of Valencia, 46010 Valencia, Spain; (C.B.); (L.G.-F.)
| | - Jesús Cosín-Roger
- Hospital Dr. Peset, Fundación para la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, FISABIO, 46017 Valencia, Spain
- Correspondence: ; Tel.: +34-963851234
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46
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Kopriva I, Jerić I, Hadžija MP, Hadžija M, Lovrenčić MV. Non-negative Least Squares Approach to Quantification of 1H Nuclear Magnetic Resonance Spectra of Human Urine. Anal Chem 2021; 93:745-751. [PMID: 33284005 DOI: 10.1021/acs.analchem.0c02837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Because of its quantitative character and capability for high-throughput screening, 1H nuclear magnetic resonance (NMR) spectroscopy is used extensively in the profiling of biofluids such as urine and blood plasma. However, the narrow frequency bandwidth of 1H NMR spectroscopy leads to a severe overlap of the spectra of components present in the complex mixtures such as biofluids. Therefore, 1H NMR-based metabolomics analysis is focused on targeted studies related to concentrations of the small number of metabolites. Here, we propose a library-based approach to quantify proportions of overlapping metabolites from 1H NMR mixture spectra. The method boils down to the linear non-negative least squares (NNLS) problem, whereas proportions of the pure components contained in the library stand for the unknowns. The method is validated on an estimation of the proportions of (i) the 78 pure spectra, presumably related to type 2 diabetes mellitus (T2DM), from their synthetic linear mixture; (ii) metabolites present in 62 1H NMR spectra of urine of subjects with T2DM and 62 1H NMR spectra of urine of control subjects. In both cases, the in-house library of 210 pure component 1H NMR spectra represented the design matrix in the related NNLS problem. The proposed method pinpoints 63 metabolites that in a statistically significant way discriminate the T2DM group from the control group and 46 metabolites discriminating control from the T2DM group. For several T2DM-discriminative metabolites, we prove their presence by independent analytical determination or by pointing out the corresponding findings in the published literature.
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Affiliation(s)
- Ivica Kopriva
- Division of Electronics, Rud̵er Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Ivanka Jerić
- Division of Organic Chemistry and Biochemistry, Rud̵er Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Marijana Popović Hadžija
- Division of Molecular Medicine, Rud̵er Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Mirko Hadžija
- Division of Molecular Medicine, Rud̵er Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Marijana Vučić Lovrenčić
- Department of Medical Biochemistry and Laboratory Medicine, University Hospital Merkur, Zajčeva 19, HR-10000 Zagreb, Croatia
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47
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Holster S, Repsilber D, Geng D, Hyötyläinen T, Salonen A, Lindqvist CM, Rajan SK, de Vos WM, Brummer RJ, König J. Correlations between microbiota and metabolites after faecal microbiota transfer in irritable bowel syndrome. Benef Microbes 2020; 12:17-30. [PMID: 33350360 DOI: 10.3920/bm2020.0010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Faecal microbiota transfer (FMT) consists of the infusion of donor faecal material into the intestine of a patient with the aim to restore a disturbed gut microbiota. In this study, it was investigated whether FMT has an effect on faecal microbial composition, its functional capacity, faecal metabolite profiles and their interactions in 16 irritable bowel syndrome (IBS) patients. Faecal samples from eight different time points before and until six months after allogenic FMT (faecal material from a healthy donor) as well as autologous FMT (own faecal material) were analysed by 16S RNA gene amplicon sequencing and gas chromatography coupled to mass spectrometry (GS-MS). The results showed that the allogenic FMT resulted in alterations in the microbial composition that were detectable up to six months, whereas after autologous FMT this was not the case. Similar results were found for the functional profiles, which were predicted from the phylogenetic sequencing data. While both allogenic FMT as well as autologous FMT did not have an effect on the faecal metabolites measured in this study, correlations between the microbial composition and the metabolites showed that the microbe-metabolite interactions seemed to be disrupted after allogenic FMT compared to autologous FMT. This shows that FMT can lead to altered interactions between the gut microbiota and its metabolites in IBS patients. Further research should investigate if and how this affects efficacy of FMT treatments.
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Affiliation(s)
- S Holster
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - D Repsilber
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - D Geng
- Man-Technology-Environmental Research Centre, Faculty of Business, Science and Engineering, School of Science and Technology, Örebro University, Örebro, Sweden
| | - T Hyötyläinen
- Man-Technology-Environmental Research Centre, Faculty of Business, Science and Engineering, School of Science and Technology, Örebro University, Örebro, Sweden
| | - A Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - C M Lindqvist
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - S K Rajan
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - W M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Laboratory of Microbiology, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - R J Brummer
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - J König
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
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48
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Ruszkiewicz DM, Sanders D, O'Brien R, Hempel F, Reed MJ, Riepe AC, Bailie K, Brodrick E, Darnley K, Ellerkmann R, Mueller O, Skarysz A, Truss M, Wortelmann T, Yordanov S, Thomas CLP, Schaaf B, Eddleston M. Diagnosis of COVID-19 by analysis of breath with gas chromatography-ion mobility spectrometry - a feasibility study. EClinicalMedicine 2020; 29:100609. [PMID: 33134902 PMCID: PMC7585499 DOI: 10.1016/j.eclinm.2020.100609] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND There is an urgent need to rapidly distinguish COVID-19 from other respiratory conditions, including influenza, at first-presentation. Point-of-care tests not requiring laboratory- support will speed diagnosis and protect health-care staff. We studied the feasibility of using breath-analysis to distinguish these conditions with near-patient gas chromatography-ion mobility spectrometry (GC-IMS). METHODS Independent observational prevalence studies at Edinburgh, UK, and Dortmund, Germany, recruited adult patients with possible COVID-19 at hospital presentation. Participants gave a single breath-sample for VOC analysis by GC-IMS. COVID-19 infection was identified by transcription polymerase chain reaction (RT- qPCR) of oral/nasal swabs together with clinical-review. Following correction for environmental contaminants, potential COVID-19 breath-biomarkers were identified by multi-variate analysis and comparison to GC-IMS databases. A COVID-19 breath-score based on the relative abundance of a panel of volatile organic compounds was proposed and tested against the cohort data. FINDINGS Ninety-eight patients were recruited, of whom 21/33 (63.6%) and 10/65 (15.4%) had COVID-19 in Edinburgh and Dortmund, respectively. Other diagnoses included asthma, COPD, bacterial pneumonia, and cardiac conditions. Multivariate analysis identified aldehydes (ethanal, octanal), ketones (acetone, butanone), and methanol that discriminated COVID-19 from other conditions. An unidentified-feature with significant predictive power for severity/death was isolated in Edinburgh, while heptanal was identified in Dortmund. Differentiation of patients with definite diagnosis (25 and 65) of COVID-19 from non-COVID-19 was possible with 80% and 81.5% accuracy in Edinburgh and Dortmund respectively (sensitivity/specificity 82.4%/75%; area-under-the-receiver- operator-characteristic [AUROC] 0.87 95% CI 0.67 to 1) and Dortmund (sensitivity / specificity 90%/80%; AUROC 0.91 95% CI 0.87 to 1). INTERPRETATION These two studies independently indicate that patients with COVID-19 can be rapidly distinguished from patients with other conditions at first healthcare contact. The identity of the marker compounds is consistent with COVID-19 derangement of breath-biochemistry by ketosis, gastrointestinal effects, and inflammatory processes. Development and validation of this approach may allow rapid diagnosis of COVID-19 in the coming endemic flu seasons. FUNDING MR was supported by an NHS Research Scotland Career Researcher Clinician award. DMR was supported by the University of Edinburgh ref COV_29.
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Affiliation(s)
- Dorota M Ruszkiewicz
- Centre for Analytical Science, Chemistry, School of Science, Loughborough University, LE11 3TU, United Kingdom
| | - Daniel Sanders
- G.A.S. Gesellschaft für analytische Sensorsysteme mbH BioMedizinZentrumDortmund, Dortmund, DE, Germany
| | - Rachel O'Brien
- Emergency Medicine Research Group Edinburgh (EMERGE), Department of Emergency Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
| | - Frederik Hempel
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Matthew J Reed
- Emergency Medicine Research Group Edinburgh (EMERGE), Department of Emergency Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
- Edinburgh Acute Care, Usher Institute of Population Health Sciences and Informatics, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Ansgar C Riepe
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Kenneth Bailie
- Emergency Medicine Research Group Edinburgh (EMERGE), Department of Emergency Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
| | - Emma Brodrick
- IMSPEX Diagnostics Ltd, Ty Menter, Navigation Park, Abercynon, RCT CF45 4SN, United Kingdom
| | - Kareen Darnley
- Wellcome Clinical Research Facility, NHS Lothian, Edinburgh EH4 2XU, United Kingdom
| | | | - Oliver Mueller
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Angelika Skarysz
- Computer Science Department, School of Science, Loughborough University, United Kingdom
| | - Michael Truss
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Thomas Wortelmann
- G.A.S. Gesellschaft für analytische Sensorsysteme mbH BioMedizinZentrumDortmund, Dortmund, DE, Germany
| | - Simeon Yordanov
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - C L Paul Thomas
- Centre for Analytical Science, Chemistry, School of Science, Loughborough University, LE11 3TU, United Kingdom
| | - Bernhard Schaaf
- G.A.S. Gesellschaft für analytische Sensorsysteme mbH BioMedizinZentrumDortmund, Dortmund, DE, Germany
| | - Michael Eddleston
- Pharmacology, Toxicology & Therapeutics, Centre for Cardiovascular Science, University of Edinburgh, United Kingdom
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Ruszkiewicz DM, Sanders D, O'Brien R, Hempel F, Reed MJ, Riepe AC, Bailie K, Brodrick E, Darnley K, Ellerkmann R, Mueller O, Skarysz A, Truss M, Wortelmann T, Yordanov S, Thomas CLP, Schaaf B, Eddleston M. Diagnosis of COVID-19 by analysis of breath with gas chromatography-ion mobility spectrometry - a feasibility study. EClinicalMedicine 2020. [PMID: 33134902 DOI: 10.2139/ssrn.3675407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
BACKGROUND There is an urgent need to rapidly distinguish COVID-19 from other respiratory conditions, including influenza, at first-presentation. Point-of-care tests not requiring laboratory- support will speed diagnosis and protect health-care staff. We studied the feasibility of using breath-analysis to distinguish these conditions with near-patient gas chromatography-ion mobility spectrometry (GC-IMS). METHODS Independent observational prevalence studies at Edinburgh, UK, and Dortmund, Germany, recruited adult patients with possible COVID-19 at hospital presentation. Participants gave a single breath-sample for VOC analysis by GC-IMS. COVID-19 infection was identified by transcription polymerase chain reaction (RT- qPCR) of oral/nasal swabs together with clinical-review. Following correction for environmental contaminants, potential COVID-19 breath-biomarkers were identified by multi-variate analysis and comparison to GC-IMS databases. A COVID-19 breath-score based on the relative abundance of a panel of volatile organic compounds was proposed and tested against the cohort data. FINDINGS Ninety-eight patients were recruited, of whom 21/33 (63.6%) and 10/65 (15.4%) had COVID-19 in Edinburgh and Dortmund, respectively. Other diagnoses included asthma, COPD, bacterial pneumonia, and cardiac conditions. Multivariate analysis identified aldehydes (ethanal, octanal), ketones (acetone, butanone), and methanol that discriminated COVID-19 from other conditions. An unidentified-feature with significant predictive power for severity/death was isolated in Edinburgh, while heptanal was identified in Dortmund. Differentiation of patients with definite diagnosis (25 and 65) of COVID-19 from non-COVID-19 was possible with 80% and 81.5% accuracy in Edinburgh and Dortmund respectively (sensitivity/specificity 82.4%/75%; area-under-the-receiver- operator-characteristic [AUROC] 0.87 95% CI 0.67 to 1) and Dortmund (sensitivity / specificity 90%/80%; AUROC 0.91 95% CI 0.87 to 1). INTERPRETATION These two studies independently indicate that patients with COVID-19 can be rapidly distinguished from patients with other conditions at first healthcare contact. The identity of the marker compounds is consistent with COVID-19 derangement of breath-biochemistry by ketosis, gastrointestinal effects, and inflammatory processes. Development and validation of this approach may allow rapid diagnosis of COVID-19 in the coming endemic flu seasons. FUNDING MR was supported by an NHS Research Scotland Career Researcher Clinician award. DMR was supported by the University of Edinburgh ref COV_29.
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Affiliation(s)
- Dorota M Ruszkiewicz
- Centre for Analytical Science, Chemistry, School of Science, Loughborough University, LE11 3TU, United Kingdom
| | - Daniel Sanders
- G.A.S. Gesellschaft für analytische Sensorsysteme mbH BioMedizinZentrumDortmund, Dortmund, DE, Germany
| | - Rachel O'Brien
- Emergency Medicine Research Group Edinburgh (EMERGE), Department of Emergency Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
| | - Frederik Hempel
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Matthew J Reed
- Emergency Medicine Research Group Edinburgh (EMERGE), Department of Emergency Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
- Edinburgh Acute Care, Usher Institute of Population Health Sciences and Informatics, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Ansgar C Riepe
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Kenneth Bailie
- Emergency Medicine Research Group Edinburgh (EMERGE), Department of Emergency Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
| | - Emma Brodrick
- IMSPEX Diagnostics Ltd, Ty Menter, Navigation Park, Abercynon, RCT CF45 4SN, United Kingdom
| | - Kareen Darnley
- Wellcome Clinical Research Facility, NHS Lothian, Edinburgh EH4 2XU, United Kingdom
| | | | - Oliver Mueller
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Angelika Skarysz
- Computer Science Department, School of Science, Loughborough University, United Kingdom
| | - Michael Truss
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - Thomas Wortelmann
- G.A.S. Gesellschaft für analytische Sensorsysteme mbH BioMedizinZentrumDortmund, Dortmund, DE, Germany
| | - Simeon Yordanov
- Klinikum Dortmund, Beurhausstr. 40, 44137 Dortmund, DE, Germany
| | - C L Paul Thomas
- Centre for Analytical Science, Chemistry, School of Science, Loughborough University, LE11 3TU, United Kingdom
| | - Bernhard Schaaf
- G.A.S. Gesellschaft für analytische Sensorsysteme mbH BioMedizinZentrumDortmund, Dortmund, DE, Germany
| | - Michael Eddleston
- Pharmacology, Toxicology & Therapeutics, Centre for Cardiovascular Science, University of Edinburgh, United Kingdom
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Urinary 1H-NMR Metabolic Signature in Subjects Undergoing Colonoscopy for Colon Cancer Diagnosis. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10165401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolomics represents a promising non-invasive approach that can be applied to identify biochemical changes in colorectal cancer patients (CRC) and is potentially useful for diagnosis and follow-up. Despite the literature regarding metabolomics CRC-specific profiles, discrimination between metabolic changes specifically related to CRC and intra-individual variability is still a problem to be solved. This was a preliminary case-control study, in which 1H-NMR spectroscopy combined with multivariate statistical analysis was used to profile urine metabolites in subjects undergoing colonoscopy for colon cancer diagnosis. To reduce intra-individual variability, metabolic profiles were evaluated in participants’ urine samples, collected just before the colonoscopy and after a short-term dietary regimen required for the endoscopy procedure. Data obtained highlighted different urinary metabolic profiles between CRC and unaffected subjects (C). The metabolites altered in the CRC urine (acetoacetate, creatine, creatinine, histamine, phenylacetylglycine, and tryptophan) significantly correlated with colon cancer and discriminated with accuracy CRC patients from C patients (receiver operator characteristic (ROC) curve with an area under the curve (AUC) of 0.875; 95% CI: 0.667–1). These results confirm that urinary metabolomic analysis can be a valid tool to improve CRC diagnosis, prognosis, and response to therapy, representing a noninvasive approach that could precede more invasive tests.
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