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Chen SJ, Zhang DY, Wu X, Zhang FM, Cui BT, Huang YH, Zhang ZL, Wang R, Bai FH. Washed microbiota transplantation for Crohn's disease: A metagenomic, metatranscriptomic, and metabolomic-based study. World J Gastroenterol 2024; 30:1572-1587. [PMID: 38617453 PMCID: PMC11008410 DOI: 10.3748/wjg.v30.i11.1572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/07/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) is a promising therapeutic approach for treating Crohn's disease (CD). The new method of FMT, based on the automatic washing process, was named as washed microbiota transplantation (WMT). Most existing studies have focused on observing the clinical phenomena. However, the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome, metatranscriptome, and metabolome-has not yet been reported. AIM To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT. METHODS We conducted a prospective, open-label, single-center clinical study. Eleven CD patients underwent WMT. Their clinical responses (defined as a decrease in their CD Activity Index score of > 100 points) and their microbiome (metagenome, metatranscriptome) and metabolome profiles were evaluated three months after the procedure. RESULTS Seven of the 11 patients (63.6%) showed an optimal clinical response three months post-WMT. Gut microbiome diversity significantly increased after WMT, consistent with improved clinical symptoms. Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains, such as Faecalibacterium prausnitzii, Roseburia intestinalis, and Escherichia coli. In addition, metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors. However, levels of vital amino acids that may be associated with disease progression (e.g., L-glutamic acid, gamma-glutamyl-leucine, and prolyl-glutamine) were reduced after WMT. CONCLUSION WMT demonstrated therapeutic efficacy in CD treatment, likely due to the effective reconstruction of the patient's microbiome. Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.
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Affiliation(s)
- Shi-Ju Chen
- Graduate School, Hainan Medical University, Haikou 571199, Hainan Province, China
| | - Da-Ya Zhang
- Graduate School, Hainan Medical University, Haikou 571199, Hainan Province, China
| | - Xia Wu
- Department of Microbiota Medicine & Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Fa-Ming Zhang
- Department of Microbiota Medicine & Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Bo-Ta Cui
- Department of Microbiota Medicine & Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Yi-Hao Huang
- Department of Microbiota Medicine & Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Zu-Lun Zhang
- Department of Microbiota Medicine & Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Rui Wang
- Department of Microbiota Medicine & Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China
| | - Fei-Hu Bai
- Department of Gastroenterology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570216, Hainan Province, China
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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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Paul KC, Zhang K, Walker DI, Sinsheimer J, Yu Y, Kusters C, Del Rosario I, Folle AD, Keener AM, Bronstein J, Jones DP, Ritz B. Untargeted serum metabolomics reveals novel metabolite associations and disruptions in amino acid and lipid metabolism in Parkinson's disease. Mol Neurodegener 2023; 18:100. [PMID: 38115046 PMCID: PMC10731845 DOI: 10.1186/s13024-023-00694-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Untargeted high-resolution metabolomic profiling provides simultaneous measurement of thousands of metabolites. Metabolic networks based on these data can help uncover disease-related perturbations across interconnected pathways. OBJECTIVE Identify metabolic disturbances associated with Parkinson's disease (PD) in two population-based studies using untargeted metabolomics. METHODS We performed a metabolome-wide association study (MWAS) of PD using serum-based untargeted metabolomics data derived from liquid chromatography with high-resolution mass spectrometry (LC-HRMS) using two distinct population-based case-control populations. We also combined our results with a previous publication of 34 metabolites linked to PD in a large-scale, untargeted MWAS to assess external validation. RESULTS LC-HRMS detected 4,762 metabolites for analysis (HILIC: 2716 metabolites; C18: 2046 metabolites). We identified 296 features associated with PD at FDR<0.05, 134 having a log2 fold change (FC) beyond ±0.5 (228 beyond ±0.25). Of these, 104 were independently associated with PD in both discovery and replication studies at p<0.05 (170 at p<0.10), while 27 were associated with levodopa-equivalent dose among the PD patients. Intriguingly, among the externally validated features were the microbial-related metabolites, p-cresol glucuronide (FC=2.52, 95% CI=1.67, 3.81, FDR=7.8e-04) and p-cresol sulfate. P-cresol glucuronide was also associated with motor symptoms among patients. Additional externally validated metabolites associated with PD include phenylacetyl-L-glutamine, trigonelline, kynurenine, biliverdin, and pantothenic acid. Novel associations include the anti-inflammatory metabolite itaconate (FC=0.79, 95% CI=0.73, 0.86; FDR=2.17E-06) and cysteine-S-sulfate (FC=1.56, 95% CI=1.39, 1.75; FDR=3.43E-11). Seventeen pathways were enriched, including several related to amino acid and lipid metabolism. CONCLUSIONS Our results revealed PD-associated metabolites, confirming several previous observations, including for p-cresol glucuronide, and newly implicating interesting metabolites, such as itaconate. Our data also suggests metabolic disturbances in amino acid and lipid metabolism and inflammatory processes in PD.
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Affiliation(s)
- Kimberly C Paul
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA.
| | - Keren Zhang
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Douglas I Walker
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Janet Sinsheimer
- Department of Human Genetics, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
- Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Yu Yu
- Center for Health Policy Research, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Cynthia Kusters
- Department of Human Genetics, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Irish Del Rosario
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Aline Duarte Folle
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Adrienne M Keener
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
- Parkinson's Disease Research, Education, and Clinical Center, Greater Los Angeles Veterans Affairs Medical Center, Los Angeles, CA, USA
| | - Jeff Bronstein
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Dean P Jones
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Beate Ritz
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
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Wu R, Xiong R, Li Y, Chen J, Yan R. Gut microbiome, metabolome, host immunity associated with inflammatory bowel disease and intervention of fecal microbiota transplantation. J Autoimmun 2023; 141:103062. [PMID: 37246133 DOI: 10.1016/j.jaut.2023.103062] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/30/2023]
Abstract
Gut dysbiosis has been associated with inflammatory bowel disease (IBD), one of the most common gastrointestinal diseases. The microbial communities play essential roles in host physiology, with profound effects on immune homeostasis, directly or via their metabolites and/or components. There are increasing clinical trials applying fecal microbiota transplantation (FMT) with Crohn's disease (CD) and ulcerative colitis (UC). The restoration of dysbiotic gut microbiome is considered as one of the mechanisms of FMT therapy. In this work, latest advances in the alterations in gut microbiome and metabolome features in IBD patients and experimental mechanistic understanding on their contribution to the immune dysfunction were reviewed. Then, the therapeutic outcomes of FMT on IBD were summarized based on clinical remission, endoscopic remission and histological remission of 27 clinical trials retrieved from PubMed which have been registered on ClinicalTrials.gov with the results been published in the past 10 years. Although FMT is established as an effective therapy for both subtypes of IBD, the promising outcomes are not always achieved. Among the 27 studies, only 11 studies performed gut microbiome profiling, 5 reported immune response alterations and 3 carried out metabolome analysis. Generally, FMT partially restored typical changes in IBD, resulted in increased α-diversity and species richness in responders and similar but less pronounced shifts of patient microbial and metabolomics profiles toward donor profiles. Measurements of immune responses to FMT mainly focused on T cells and revealed divergent effects on pro-/anti-inflammatory functions. The very limited information and the extremely confounding factors in the designs of the FMT trials significantly hindered a reasonable conclusion on the mechanistic involvement of gut microbiota and metabolites in clinical outcomes and an analysis of the inconsistencies.
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Affiliation(s)
- Rongrong Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Rui Xiong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Yan Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Junru Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Ru Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
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Kragsnaes MS, Miguens Blanco J, Mullish BH, Serrano‐Contreras JI, Kjeldsen J, Horn HC, Pedersen JK, Munk HL, Nilsson AC, Salam A, Lewis MR, Chekmeneva E, Kristiansen K, Marchesi JR, Ellingsen T. Small Intestinal Permeability and Metabolomic Profiles in Feces and Plasma Associate With Clinical Response in Patients With Active Psoriatic Arthritis Participating in a Fecal Microbiota Transplantation Trial: Exploratory Findings From the FLORA Trial. ACR Open Rheumatol 2023; 5:583-593. [PMID: 37736702 PMCID: PMC10642255 DOI: 10.1002/acr2.11604] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023] Open
Abstract
OBJECTIVE We investigated intestinal permeability and fecal, plasma, and urine metabolomic profiles in methotrexate-treated active psoriatic arthritis (PsA) and how this related to clinical response following one sham or fecal microbiota transplantation (FMT). METHODS This exploratory study is based on the FLORA trial cohort, in which 31 patients with moderate-to-high peripheral PsA disease activity, despite at least 3 months of methotrexate-treatment, were included in a 26-week, double-blind, 1:1 randomized, sham-controlled trial. Participants were randomly allocated to receive either one healthy donor FMT (n = 15) or sham (n = 16) via gastroscopy. The primary trial end point was the proportion of treatment failures through 26 weeks. We performed a lactulose-to-mannitol ratio (LMR) test at baseline (n = 31) and at week 26 (n = 26) to assess small intestinal permeability. Metabolomic profiles in fecal, plasma, and urine samples collected at baseline, weeks 4, 12, and 26 were measured using 1 H Nuclear Magnetic Resonance. RESULTS Trial failures (n = 7) had significantly higher LMR compared with responders (n = 19) at week 26 (0.027 [0.017-0.33]) vs. 0.012 [0-0.064], P = 0.013), indicating increased intestinal permeability. Multivariate analysis revealed a significant model for responders (n = 19) versus failures (n = 12) at all time points based on their fecal (P < 0.0001) and plasma (P = 0.005) metabolomic profiles, whereas urine metabolomic profiles did not differ between groups (P = 1). Fecal N-acetyl glycoprotein GlycA correlated with Health Assessment Questionnaire Disability Index (coefficient = 0.50; P = 0.03) and fecal propionate correlated with American College of Rheumatology 20 response at week 26 (coefficient = 27, P = 0.02). CONCLUSION Intestinal permeability and fecal and plasma metabolomic profiles of patients with PsA were associated with the primary clinical trial end point, failure versus responder.
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Affiliation(s)
| | | | - Benjamin H. Mullish
- Imperial College London and St. Mary's Hospital, Imperial College Healthcare National Health Service TrustLondonUK
| | | | - Jens Kjeldsen
- Odense University Hospital and University of Southern DenmarkOdenseDenmark
| | | | | | | | | | - Ash Salam
- Imperial College London, Hammersmith Hospital CampusLondonUK
| | | | | | - Karsten Kristiansen
- University of Copenhagen, Copenhagen, Denmark, and Institute of Metagenomics, Qingdao‐Europe Advanced Institute for Life SciencesQingdaoChina
| | | | - Torkell Ellingsen
- Odense University Hospital and University of Southern DenmarkOdenseDenmark
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Ma R, Zhu Y, Li X, Hu S, Zheng D, Xiong S, Xu S, Xiang L, Zhao M, Tang C, Zeng Z, Chen M, Feng R. A Novel Serum Metabolomic Panel for the Diagnosis of Crohn's Disease. Inflamm Bowel Dis 2023; 29:1524-1535. [PMID: 37195904 DOI: 10.1093/ibd/izad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND A distinctive metabolic phenotype provides the opportunity to discover noninvasive biomarkers for the diagnosis of Crohn's disease (CD) and for differentiating it from other intestinal inflammatory diseases. The study sought to identify new biomarkers for CD diagnosis. METHODS Serum metabolites from 68 newly diagnosed and treatment-naïve patients with CD and 56 healthy control (HC) subjects were profiled using targeted liquid chromatography-mass spectrometry. Five metabolic biomarkers were identified to distinguish patients with CD from the HC subjects and validated in a separate cohort consisting of 110 patients with CD and 90 HC subjects using a combination of univariate analysis, orthogonal partial least-squares discriminant analysis, and receiver-operating characteristic curve analysis. Differences in the 5 metabolites were evaluated among patients with CD and patients with ulcerative colitis (n = 62), intestinal tuberculosis (n = 48), and Behçet's disease (n = 31). RESULTS Among the 185 quantified metabolites, a panel of 5 (pyruvate, phenylacetylglutamine, isolithocholic acid, taurodeoxycholic acid, and glycolithocholic acid) were found to distinguish patients with CD with high accuracy from HC subjects, with an area under the curve of 0.861 (P < .001). The performance of the model in assessing clinical disease activity was comparable to that of the present biomarkers: C-reactive protein and erythrocyte sedimentation rate. The 5 metabolites were significantly different among the patients and were valuable in the differentiation between CD and other chronic intestinal inflammatory diseases. CONCLUSIONS The combination of 5 serum metabolite biomarkers for the diagnosis of CD has the potential to provide an accurate, noninvasive, and inexpensive alternative to conventional tests and might be valuable for the differentiation from other diagnostically challenging intestinal inflammatory diseases.
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Affiliation(s)
- Ruiqi Ma
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yijun Zhu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaozhi Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shixian Hu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Danping Zheng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shanshan Xiong
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shu Xu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liyuan Xiang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Min Zhao
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ce Tang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhirong Zeng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rui Feng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Gastroenterology, Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning, China
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7
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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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8
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Calzadilla N, Comiskey SM, Dudeja PK, Saksena S, Gill RK, Alrefai WA. Bile acids as inflammatory mediators and modulators of intestinal permeability. Front Immunol 2022; 13:1021924. [PMID: 36569849 PMCID: PMC9768584 DOI: 10.3389/fimmu.2022.1021924] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Bile acids are critical for the digestion and absorption of lipids and fat-soluble vitamins; however, evidence continues to emerge supporting additional roles for bile acids as signaling molecules. After they are synthesized from cholesterol in the liver, primary bile acids are modified into secondary bile acids by gut flora contributing to a diverse pool and making the composition of bile acids highly sensitive to alterations in gut microbiota. Disturbances in bile acid homeostasis have been observed in patients with Inflammatory Bowel Diseases (IBD). In fact, a decrease in secondary bile acids was shown to occur because of IBD-associated dysbiosis. Further, the increase in luminal bile acids due to malabsorption in Crohn's ileitis and ileal resection has been implicated in the induction of diarrhea and the exacerbation of inflammation. A causal link between bile acid signaling and intestinal inflammation has been recently suggested. With respect to potential mechanisms related to bile acids and IBD, several studies have provided strong evidence for direct effects of bile acids on intestinal permeability in porcine and rodent models as well as in humans. Interestingly, different bile acids were shown to exert distinct effects on the inflammatory response and intestinal permeability that require careful consideration. Such findings revealed a potential effect for changes in the relative abundance of different bile acids on the induction of inflammation by bile acids and the development of IBD. This review summarizes current knowledge about the roles for bile acids as inflammatory mediators and modulators of intestinal permeability mainly in the context of inflammatory bowel diseases.
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Affiliation(s)
- Nathan Calzadilla
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, IL, United States
- Department of Bioengineering, University of Illinois, Chicago, IL, United States
| | - Shane M. Comiskey
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, IL, United States
| | - Pradeep K. Dudeja
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, IL, United States
- Research and Development, Jesse Brown VA Medical Center, Chicago, IL, United States
| | - Seema Saksena
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, IL, United States
- Research and Development, Jesse Brown VA Medical Center, Chicago, IL, United States
| | - Ravinder K. Gill
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, IL, United States
| | - Waddah A. Alrefai
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois, Chicago, IL, United States
- Research and Development, Jesse Brown VA Medical Center, Chicago, IL, United States
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9
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Zheng L. New insights into the interplay between intestinal flora and bile acids in inflammatory bowel disease. World J Clin Cases 2022; 10:10823-10839. [PMID: 36338232 PMCID: PMC9631134 DOI: 10.12998/wjcc.v10.i30.10823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/08/2022] [Accepted: 09/16/2022] [Indexed: 02/05/2023] Open
Abstract
Intestinal flora plays a key role in nutrient absorption, metabolism and immune defense, and is considered to be the cornerstone of maintaining the health of human hosts. Bile acids synthesized in the liver can not only promote the absorption of fat-soluble substances in the intestine, but also directly or indirectly affect the structure and function of intestinal flora. Under the action of intestinal flora, bile acids can be converted into secondary bile acids, which can be reabsorbed back to the liver through the enterohepatic circulation. The complex dialogue mechanism between intestinal flora and bile acids is involved in the development of intestinal inflammation such as inflammatory bowel disease (IBD). In this review, the effects of intestinal flora, bile acids and their interactions on IBD and the progress of treatment were reviewed.
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Affiliation(s)
- Lie Zheng
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Xi’an 710003, Shaanxi Province, China
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10
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Yan J, Chen Q, Tian L, Li K, Lai W, Bian L, Han J, Jia R, Liu X, Xi Z. Intestinal toxicity of micro- and nano-particles of foodborne titanium dioxide in juvenile mice: Disorders of gut microbiota-host co-metabolites and intestinal barrier damage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153279. [PMID: 35074372 DOI: 10.1016/j.scitotenv.2022.153279] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/09/2022] [Accepted: 01/16/2022] [Indexed: 05/28/2023]
Abstract
The wide use of TiO2 particles in food and the high exposure risk to children have prompted research into the health risks of TiO2. We used the microbiome and targeted metabolomics to explore the potential mechanism of intestinal toxicity of foodborne TiO2 micro-/nanoparticles after oral exposure for 28 days in juvenile mice. Results showed that the gut microbiota-including the abundance of Bacteroides, Bifidobacterium, Lactobacillus, and Prevotella-changed dynamically during exposure. The organic inflammatory response was activated, and lipopolysaccharide levels increased. Intestinal toxicity manifested as increased mucosal permeability, impaired intestinal barrier, immune damage, and pathological changes. The expression of antimicrobial peptides, occludin, and ZO-1 significantly reduced, while that of JNK2 and Src/pSrc increased. Compared with micro-TiO2 particles, the nano-TiO2 particles had strong toxicity. Fecal microbiota transplant confirmed the key role of gut microbiota in intestinal toxicity. The levels of gut microbiota-host co-metabolites, including pyroglutamic acid, L-glutamic acid, phenylacetic acid, and 3-hydroxyphenylacetic acid, changed significantly. Significant changes were observed in the glutathione and propanoate metabolic pathways. There was a significant correlation between the changes in gut microbiota, metabolites, and intestinal cytokine levels. These, together with the intestinal barrier damage signaling pathway, constitute the network mechanism of the intestinal toxicity of TiO2 particles.
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Affiliation(s)
- Jun Yan
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Qi Chen
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Lei Tian
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Kang Li
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Wenqing Lai
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Liping Bian
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Jie Han
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Rui Jia
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Xiaohua Liu
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China.
| | - Zhuge Xi
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China.
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11
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Microbial changes in stool, saliva, serum, and urine before and after anti-TNF-α therapy in patients with inflammatory bowel diseases. Sci Rep 2022; 12:6359. [PMID: 35428806 PMCID: PMC9012770 DOI: 10.1038/s41598-022-10450-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/30/2022] [Indexed: 11/08/2022] Open
Abstract
Inflammatory bowel diseases (IBD), including Crohn's disease and ulcerative colitis, are chronic immune-mediated intestinal inflammatory disorders associated with microbial dysbiosis at multiple sites, particularly the gut. Anti-tumor necrosis factor-α (TNF-α) agents are important treatments for IBD. We investigated whether microbiome changes at multiple sites can predict the effectiveness of such treatment in IBD. Stool, saliva, serum, and urine biosamples were collected from 19 IBD patients before (V1) and 3 months after (V2) anti-TNF-α treatment, and 19 healthy subjects (control). Microbiota analysis was performed using extracellular vesicles (EVs; all four sample types) and next-generation sequencing (NGS; stool and saliva). The stool, using NGS analysis, was the only sample type in which α-diversity differed significantly between the IBD and control groups at V1 and V2. Relative to non-responders, responders to anti-TNF-α treatment had significantly higher levels of Firmicutes (phylum), Clostridia (class), and Ruminococcaceae (family) in V1 stool, and Prevotella in V1 saliva. Non-responders had significantly higher V2 serum and urine levels of Lachnospiraceae than responders. Finally, Acidovorax caeni was detected in all V1 sample types in responders, but was not detected in non-responders. Microbiome changes at multiple sites may predict the effectiveness of anti-TNF-α treatment in IBD, warranting further research.
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12
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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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13
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Yu XH, Cao RR, Yang YQ, Lei SF. Identification of causal metabolites related to multiple autoimmune diseases. Hum Mol Genet 2021; 31:604-613. [PMID: 34523675 DOI: 10.1093/hmg/ddab273] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECT Observational studies provide evidence that metabolites may be involved in the development of autoimmune diseases (ADs), but whether it is causal is still unknown. METHODS Based on the large-scale GWAS summary statistics, two-sample Mendelian randomization (MR) was performed to evaluate the causal association between human serum metabolites and multiple ADs, which were inflammatory bowel disease (IBD), ulcerative Colitis (UC), crohn's disease (CD), rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), type 1 diabetes (T1D), multiple sclerosis (MS), primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC). Comprehensive sensitive analysis was used to validate the robustness of MR results and multivariable MR analysis was conducted to avoid potential pleiotropic effect of other complex traits. Finally, metabolic pathway analysis was performed based on causal metabolites for each ad, respectively. RESULTS We identified 6 causal features of metabolite after Bonferroni adjustment, i.e. glycerol 2-phosphate for T1D, hexadecanedioate, phenylacetylglutamine and laurylcarnitine for RA, glycine and arachidonate (20:4n6) for CD. Then comprehensively sensitive analysis proved the robustness of the causal associations. We also observed some overlaps of metabolites among different ADs, indicating the similar mechanisms. After controlling for several common traits, multivariable MR analysis ruled out most of potential pleiotropic effects and validated the independence of identified metabolites. Additionally, a total of 6 metabolic pathways have been identified for different ADs. CONCLUSIONS This study provided novel insights into investigating causal role of serum metabolites in development of multiple ADs through a comprehensive genetic pathway.
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Affiliation(s)
- Xing-Hao Yu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, P. R. China
| | - Rong-Rong Cao
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, P. R. China
| | - Yi-Qun Yang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, P. R. China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, P. R. China
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14
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Yan Y, Ren S, Duan Y, Lu C, Niu Y, Wang Z, Inglis B, Ji W, Zheng Y, Si W. Gut microbiota and metabolites of α-synuclein transgenic monkey models with early stage of Parkinson's disease. NPJ Biofilms Microbiomes 2021; 7:69. [PMID: 34475403 PMCID: PMC8413421 DOI: 10.1038/s41522-021-00242-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/02/2021] [Indexed: 02/03/2023] Open
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disease. However, it is unclear whether microbiota and metabolites have demonstrated changes at early PD due to the difficulties in diagnosis and identification of early PD in clinical practice. In a previous study, we generated A53T transgenic monkeys with early Parkinson's symptoms, including anxiety and cognitive impairment. Here we analyzed the gut microbiota by metagenomic sequencing and metabolites by targeted gas chromatography. The gut microbiota analysis showed that the A53T monkeys have higher degree of diversity in gut microbiota with significantly elevated Sybergistetes, Akkermansia, and Eggerthella lenta compared with control monkeys. Prevotella significantly decreased in A53T transgenic monkeys. Glyceric acid, L-Aspartic acid, and p-Hydroxyphenylacetic acid were significantly elevated, whereas Myristic acid and 3-Methylindole were significantly decreased in A53T monkeys. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (KO0131) and the oxidative phosphorylation reaction (KO2147) were significantly increased in metabolic pathways of A53T monkeys. Our study suggested that the transgenic A53T and α-syn aggregation may affect the intestine microbiota and metabolites of rhesus monkeys, and the identified five compositional different metabolites that are mainly associated with mitochondrial dysfunction may be related to the pathogenesis of PD.
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Affiliation(s)
- Yaping Yan
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Shuchao Ren
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Yanchao Duan
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Chenyu Lu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Zhengbo Wang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Briauna Inglis
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.
| | - Yun Zheng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.
| | - Wei Si
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.
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15
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Li N, Zhan S, Tian Z, Liu C, Xie Z, Zhang S, Chen M, Zeng Z, Zhuang X. Alterations in Bile Acid Metabolism Associated With Inflammatory Bowel Disease. Inflamm Bowel Dis 2021; 27:1525-1540. [PMID: 33399195 DOI: 10.1093/ibd/izaa342] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory disorder closely related to gut dysbiosis, which is associated with alterations in an important bacterial metabolite, bile acids (BAs). Although certain findings pertinent to BA changes in IBD vary among studies owing to the differences in sample type, quantitated BA species, study methodology, and patient characteristics, a specific trend concerning variations of BAs in IBD has been identified. In elaborating on this observation, it was noted that primary BAs and conjugated BAs are augmented in fecal samples but there is a reduction in secondary BAs in fecal samples. It is not entirely clear why patients with IBD manifest these changes and what role these changes play in the onset and development of IBD. Previous studies have shown that IBD-associated BA changes may be caused by alterations in BA absorption, synthesis, and bacterial modification. The complex relationship between bacteria and BAs may provide additional and deeper insight into host-gut microbiota interactions in the pathogenesis of IBD. The characteristic BA changes may generate profound effects in patients with IBD by shaping the gut microbiota community, affecting inflammatory processes, causing BA malabsorption associated with diarrhea, and even leading to intestinal dysplasia and cancer. Thus, therapeutic strategies correcting the alterations in the composition of BAs, including the elimination of excess BAs and the supplementation of deficient BAs, may prove promising in IBD.
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Affiliation(s)
- Na Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shukai Zhan
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhenyi Tian
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Caiguang Liu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zonglin Xie
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shenghong Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhirong Zeng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xiaojun Zhuang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
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16
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Cui X, Zhang L, Su G, Kijlstra A, Yang P. Specific sweat metabolite profile in ocular Behcet's disease. Int Immunopharmacol 2021; 97:107812. [PMID: 34091113 DOI: 10.1016/j.intimp.2021.107812] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Behcet's disease (BD) is an autoimmune disorder with the serious possibility of blindness, calling for further research on its pathogenesis. Our aim was to study the metabolite composition of sweat in BD and to identify possible biomarkers. METHODS Metabolomics analysis was performed on sweat samples from 20 BD patients and 18 normal controls by liquid chromatography tandem mass spectrometry. RESULTS A significantly different metabolic profile of sweat was observed when BD patients were compared with healthy controls. The result of the orthogonal partial least squared-discrimination analysis (OPLS-DA) showed that these two comparison groups could be separated with a relatively satisfactory fitting degree (R2Y = 0.995 and Q2 = 0.817 in positive ion mode; R2Y = 0.991 and Q2 = 0.721 in negative ion mode). Based on OPLS-DA, a panel of metabolites was selected as candidate biomarkers, including l-citrulline, l-pyroglutamic acid, urocanic acid, 2-oxoadipic acid, cholesterol 3-sulfate, and pentadecanoic acid. CONCLUSION This is the first report on the metabolite profile of sweat in BD. Our results demonstrated a significantly different metabolite composition of sweat in BD compared to that of healthy controls.
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Affiliation(s)
- Xiaoxiao Cui
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, and Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing 400016, People's Republic of China
| | - Liming Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, and Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing 400016, People's Republic of China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, and Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing 400016, People's Republic of China
| | - Aize Kijlstra
- University Eye Clinic Maastricht, Maastricht 6211, the Netherlands
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, and Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing 400016, People's Republic of China.
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17
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Zhou D, Zhu W, Sun T, Wang Y, Chi Y, Chen T, Lin J. iMAP: A Web Server for Metabolomics Data Integrative Analysis. Front Chem 2021; 9:659656. [PMID: 34026726 PMCID: PMC8133432 DOI: 10.3389/fchem.2021.659656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Metabolomics data analysis depends on the utilization of bioinformatics tools. To meet the evolving needs of metabolomics research, several integrated platforms have been developed. Our group has developed a desktop platform IP4M (integrated Platform for Metabolomics Data Analysis) which allows users to perform a nearly complete metabolomics data analysis in one-stop. With the extensive usage of IP4M, more and more demands were raised from users worldwide for a web version and a more customized workflow. Thus, iMAP (integrated Metabolomics Analysis Platform) was developed with extended functions, improved performances, and redesigned structures. Compared with existing platforms, iMAP has more methods and usage modes. A new module was developed with an automatic pipeline for train-test set separation, feature selection, and predictive model construction and validation. A new module was incorporated with sufficient editable parameters for network construction, visualization, and analysis. Moreover, plenty of plotting tools have been upgraded for highly customized publication-ready figures. Overall, iMAP is a good alternative tool with complementary functions to existing metabolomics data analysis platforms. iMAP is freely available for academic usage at https://imap.metaboprofile.cloud/ (License MPL 2.0).
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Affiliation(s)
- Di Zhou
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Wenjia Zhu
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Tao Sun
- Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yang Wang
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Yi Chi
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Tianlu Chen
- Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jingchao Lin
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
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18
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Beck LC, Granger CL, Masi AC, Stewart CJ. Use of omic technologies in early life gastrointestinal health and disease: from bench to bedside. Expert Rev Proteomics 2021; 18:247-259. [PMID: 33896313 DOI: 10.1080/14789450.2021.1922278] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: At birth, the gastrointestinal (GI) tract is colonized by a complex community of microorganisms, forming the basis of the gut microbiome. The gut microbiome plays a fundamental role in host health, disorders of which can lead to an array of GI diseases, both short and long term. Pediatric GI diseases are responsible for significant morbidity and mortality, but many remain poorly understood. Recent advancements in high-throughput technologies have enabled deeper profiling of GI morbidities. Technologies, such as metagenomics, transcriptomics, proteomics and metabolomics, have already been used to identify associations with specific pathologies, and highlight an exciting area of research. However, since these diseases are often complex and multifactorial by nature, reliance on a single experimental approach may not capture the true biological complexity. Therefore, multi-omics aims to integrate singular omic data to further enhance our understanding of disease.Areas covered: This review will discuss and provide an overview of the main omic technologies that are used to study complex GI pathologies in early life.Expert opinion: Multi-omic technologies can help to unravel the complexities of several diseases during early life, aiding in biomarker discovery and enabling the development of novel therapeutics and augment predictive models.
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Affiliation(s)
- Lauren C Beck
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Claire L Granger
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK.,Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Andrea C Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
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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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20
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Nong F, Luo S, Liang Y, Zhao Z, Xing S, Wen B, Zhou L. Evaluation of the effect of Dahuang-Mudan decoction on TNBS-induced colitis using UPLC-QTOF/MS-based metabolomic analysis. Biomed Chromatogr 2020; 35:e5003. [PMID: 33063880 DOI: 10.1002/bmc.5003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/28/2020] [Accepted: 10/06/2020] [Indexed: 12/19/2022]
Abstract
Dahuang-Mudan decoction (DMD) is a formula that has been widely used as a complementary treatment for inflammatory bowel disease (IBD). However, the mechanism of action of DMD in IBD has not been clearly elucidated. Therefore, we developed a metabolomics-based method to evaluate the effects and potential mechanisms of DMD in a 2,4,6-trinitobenzene sulfonic acid (TNBS)-induced colitis model. The ultra-high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC/QTOF-MS) method combined with multiple analysis approaches including principal component analysis, partial least square discriminant analysis and orthogonal partial least square discriminant analysis were used to investigate the different urinary metabolites. We identified 29 potential biomarkers of TNBS-induced colitis that returned to normal conditions after DMD administration. Pathway analysis indicated that changes in these metabolites were associated with cysteine and methionine metabolism, citric acid cycle, glycolysis and glycolic regeneration, pyruvate metabolism, biosynthesis of valine, leucine and isoleucine, biosynthesis of primary bile acids, glycine, serine and threonine metabolism, caffeine metabolism, arginine and proline metabolism and phenylalanine metabolism. It is worth noting that DMD has potential therapeutic effects on TNBS-induced colitis, which functions by restoring the balance of multiple disturbed pathways to a normal condition. This study suggests the reliability of metabolomics-based approaches to identifying biomarkers and pathways, which facilitate further investigation of the potential mechanisms of DMD.
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Affiliation(s)
- Feifei Nong
- Pi-Wei Institute, Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shuang Luo
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuqi Liang
- Pi-Wei Institute, Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhongxiang Zhao
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shangping Xing
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Bin Wen
- Pi-Wei Institute, Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lian Zhou
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
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21
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Benvenuti E, Pierini A, Gori E, Bartoli F, Erba P, Ruggiero P, Marchetti V. Serum amino acid profile in 51 dogs with immunosuppressant-responsive enteropathy (IRE): a pilot study on clinical aspects and outcomes. BMC Vet Res 2020; 16:117. [PMID: 32321505 PMCID: PMC7178940 DOI: 10.1186/s12917-020-02334-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/05/2020] [Indexed: 12/11/2022] Open
Abstract
Background Lower levels of tryptophan (TRP) have been identified in people with inflammatory bowel disease and in dogs with protein-losing enteropathy (PLE). No data on serum amino acids (AAs) but some on plasma in canine immunosuppressant-responsive enteropathy (IRE) are available. The aim of this study is to compare serum AAs between healthy and IRE dogs, considering clinicopathological variables and follow-up. Results Twenty-six healthy control dogs (CD) and 51 IRE dogs were included. IRE was diagnosed after the exclusion of extra-intestinal diseases and food and antibiotic responsive enteropathies. The canine chronic enteropathy clinical activity index (CCECAI) was assessed at presentation and during the clinical follow-up. In CD and IRE dogs, 19 different serum AAs were measured. IRE dogs were classified into responders, partial responders and non-responders, based on CCECAI after 1 month, and divided into PLE and non-PLE, based on albumin level. IRE dogs showed lower L-Tyrosine (TYR), L-Phenylalanine (PHE) and TRP (p < 0.001) and higher L-Serine (SER), L-Glutamic acid (GLU), L-Arginine (p < 0.001), L-Threonine (p = 0.013), Proline (p = 0.044), L-Cysteine (p = 0.003), L-Valine (p = 0.018), L-Lysine (p = 0.01) and L-Isoleucine (p = 0.005) than CDs. PLE dogs showed lower L-Histidine (HIS) (p = 0.008), PHE (p = 0.005) and TRP (p = 0.005) than non-PLE dogs. In IRE dogs, median GLU was significantly lower in dogs with BCS 3/9 than BCS 5/9 category (p = 0.036). Total protein was positively correlated with PHE and TRP (both p = 0.031, r = 0.30) and albumin was positively correlated with HIS (p = 0.025, r = 0.31), PHE and TRP (both p = 0.001, r = 0.46). HIS (p = 0.041), PHE (p = 0.047) and TRP (p = 0.044) concentrations were significantly lower in non-responders than in responders and partial responders. Conclusions This study may suggest further investigation on serum, HIS, PHE, TRP and TYR as markers of intestinal disease and proposed HIS, PHE and TRP as prognostic marker for response to therapy.
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Affiliation(s)
- Elena Benvenuti
- Department of Veterinary Science, University of Pisa, via Livornese, 56122 San Piero a Grado, Pisa, Italy
| | - Alessio Pierini
- Department of Veterinary Science, University of Pisa, via Livornese, 56122 San Piero a Grado, Pisa, Italy.
| | - Eleonora Gori
- Department of Veterinary Science, University of Pisa, via Livornese, 56122 San Piero a Grado, Pisa, Italy
| | - Francesco Bartoli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via Savi, 10, Pisa, 56126, Italy
| | - Paola Erba
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via Savi, 10, Pisa, 56126, Italy
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22
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Godin JP, Martin FP, Breton I, Schoepfer A, Nydegger A. Total and activity-induced energy expenditure measured during a year in children with inflammatory bowel disease in clinical remission remain lower than in healthy controls. Clin Nutr 2020; 39:3147-3152. [PMID: 32147199 DOI: 10.1016/j.clnu.2020.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Pediatric inflammatory bowel disease (IBD) is often associated with growth retardation due to malnutrition. However, knowledge on total energy expenditure (TEE), active-induced energy expenditure (AEE) and physical activity remains limited in children with IBD. OBJECTIVE Assessment of TEE using the doubly labelled water (DLW) method, resting energy expenditure (REE) using indirect calorimetry, and physical activity level using the actigraph GT3X+ in children with IBD (in remission) and healthy controls. METHODS TEE, REE, AEE and physical activity were measured in 21 children with IBD and 24 healthy controls at baseline. IBD children parameters were monitored further after 6 and 12 months. Predicted REE and TEE values (using Schoefield and the actigraph GT3X+, for REE and TEE respectively) were compared to measured values. RESULTS Mean ages at baseline were 14.8 ± 1.5 and 13.2 ± 2 years in children with IBD and in healthy control children, respectively. Measured TEEDLW was significantly lower (P < 0.001) in children with IBD compared to the healthy control group. REE corrected by FFM0.5, REE and AEE were also significantly lower in children with IBD. Children with IBD had AEE of 17.5% of TEE and had a significantly higher sedentary behaviour as compared to healthy children. CONCLUSIONS This study suggests that TEE and AEE are reduced in children with IBD in clinical remission which may result in a reduced moderate and vigorous physical activity level. Our result also highlights that the actigraph GT3X + might give good prediction of TEE in children with IBD at group level but it remains highly variable at individual level.
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Affiliation(s)
- Jean-Philippe Godin
- Nestlé Research, Vers-chez-les-Blanc, PO BOX 44, 1000-6, Lausanne, Switzerland.
| | | | - Isabelle Breton
- Nestlé Research, Vers-chez-les-Blanc, PO BOX 44, 1000-6, Lausanne, Switzerland
| | - Alain Schoepfer
- Gastroenterology and Hepatology Unit, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Rue du Bugnon 44, CH-1011, Lausanne, Switzerland
| | - Andreas Nydegger
- Pediatric Gastroenterology Unit, Department of Pediatrics, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Rue du Bugnon 46, CH-1011, Lausanne, Switzerland
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23
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Filimoniuk A, Daniluk U, Samczuk P, Wasilewska N, Jakimiec P, Kucharska M, Lebensztejn DM, Ciborowski M. Metabolomic profiling in children with inflammatory bowel disease. Adv Med Sci 2020; 65:65-70. [PMID: 31901795 DOI: 10.1016/j.advms.2019.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 09/25/2019] [Accepted: 12/23/2019] [Indexed: 02/06/2023]
Abstract
Ulcerative colitis (UC) and Crohn's disease (CD) represent inflammatory bowel diseases (IBD) with multifactorial pathogenesis, involving genetic, environmental and microbial factors. Interactions between gut microbiota and immune system result in changes in metabolic pathways. Metabolomics is a comprehensive and quantitative (or semi-quantitative) analysis of metabolites synthetized in human's biological system. It has been shown that metabolic profiling might be used to identify disease biomarkers. Recent findings confirmed alterations in the number of metabolites in patients with IBD. However, most of the studies included adult individuals with ongoing treatment which might have affected the metabolite profiling. Therefore, the aim of our study was to collect the knowledge about metabolomics in paediatric patients with CD or UC based on the currently published literature.
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Affiliation(s)
- Aleksandra Filimoniuk
- Department of Pediatrics, Gastroenterology, Hepatology, Nutrition and Allergology, Medical University of Bialystok, Bialystok, Poland
| | - Urszula Daniluk
- Department of Pediatrics, Gastroenterology, Hepatology, Nutrition and Allergology, Medical University of Bialystok, Bialystok, Poland.
| | - Paulina Samczuk
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Natalia Wasilewska
- Department of Pediatrics, Gastroenterology, Hepatology, Nutrition and Allergology, Medical University of Bialystok, Bialystok, Poland
| | - Piotr Jakimiec
- Department of Pediatrics, Gastroenterology, Hepatology, Nutrition and Allergology, Medical University of Bialystok, Bialystok, Poland
| | - Magdalena Kucharska
- Department of Pediatrics, Gastroenterology, Hepatology, Nutrition and Allergology, Medical University of Bialystok, Bialystok, Poland
| | - Dariusz M Lebensztejn
- Department of Pediatrics, Gastroenterology, Hepatology, Nutrition and Allergology, Medical University of Bialystok, Bialystok, Poland
| | - Michał Ciborowski
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
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24
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Synbiotic supplementation with prebiotic green banana resistant starch and probiotic Bacillus coagulans spores ameliorates gut inflammation in mouse model of inflammatory bowel diseases. Eur J Nutr 2020; 59:3669-3689. [PMID: 32067099 PMCID: PMC7669818 DOI: 10.1007/s00394-020-02200-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/06/2020] [Indexed: 02/07/2023]
Abstract
Purpose The research goal is to develop dietary strategies to help address the growing incidence of inflammatory bowel diseases (IBD). This study has investigated the effectiveness of green banana resistant starch (GBRS) and probiotic Bacillus coagulans MTCC5856 spores for the amelioration of dextran-sulfate sodium (DSS)-induced colitis in mice. Methods Eight-week-old C57BL/6 mice were fed standard rodent chow diet supplemented with either B. coagulans, GBRS or its synbiotic combination. After 7 days supplementation, colitis was induced by adding 2% DSS in drinking water for 7 days while continuing the supplemented diets. Animal health was monitored and after 14 days all animals were sacrificed to measure the biochemical and histochemical changes associated with each supplement type. Results The disease activity index and histological damage score for DSS-control mice (6.1, 17.1, respectively) were significantly higher (p < 0.0001) than the healthy mice. Synbiotic supplementation alleviated these markers (− 67%, − 94% respectively) more adequately than B. coagulans (− 52%, − 58% respectively) or GBRS (− 57%, − 26%, respectively) alone. Compared to DSS-control synbiotic supplementation significantly (p < 0.0001) maintained expressions of tight junction proteins. Moreover, synbiotic effects accounted for ~ 40% suppression of IL-1β and ~ 29% increase in IL-10 levels in serum while also reducing C-reactive protein (− 37%) compared to that of the DSS-control. While, B. coagulans alone could not induce additional levels of short-chain fatty acid (SCFA) production beyond the caecum, the synbiotic combination with GBRS resulted in substantial increased SCFA levels across the whole length of the colon. Conclusion The synbiotic supplementation with B. coagulans and GBRS ameliorated the overall inflammatory status of the experimental IBD model via synergistic functioning. This supports researching its application in mitigating inflammation in human IBD. Electronic supplementary material The online version of this article (10.1007/s00394-020-02200-9) contains supplementary material, which is available to authorized users.
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25
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Mucosal Metabolomic Profiling and Pathway Analysis Reveal the Metabolic Signature of Ulcerative Colitis. Metabolites 2019; 9:metabo9120291. [PMID: 31783598 PMCID: PMC6950742 DOI: 10.3390/metabo9120291] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/21/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
The onset of ulcerative colitis (UC) is characterized by a dysregulated mucosal immune response triggered by several genetic and environmental factors in the context of host–microbe interaction. This complexity makes UC ideal for metabolomic studies to unravel the disease pathobiology and to improve the patient stratification strategies. This study aims to explore the mucosal metabolomic profile in UC patients, and to define the UC metabolic signature. Treatment- naïve UC patients (n = 18), UC patients in deep remission (n = 10), and healthy volunteers (n = 14) were recruited. Mucosa biopsies were collected during colonoscopies. Metabolomic analysis was performed by combined gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF-MS) and ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-MS). In total, 177 metabolites from 50 metabolic pathways were identified. The most prominent metabolome changes among the study groups were in lysophosphatidylcholine, acyl carnitine, and amino acid profiles. Several pathways were found perturbed according to the integrated pathway analysis. These pathways ranged from amino acid metabolism (such as tryptophan metabolism) to fatty acid metabolism, namely linoleic and butyrate. These metabolic changes during UC reflect the homeostatic disturbance in the gut, and highlight the importance of system biology approaches to identify key drivers of pathogenesis which prerequisite personalized medicine.
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26
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Profiling of Amino Acids in Urine Samples of Patients Suffering from Inflammatory Bowel Disease by Capillary Electrophoresis-Mass Spectrometry. Molecules 2019; 24:molecules24183345. [PMID: 31540027 PMCID: PMC6767150 DOI: 10.3390/molecules24183345] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/12/2022] Open
Abstract
Urine represents a convenient biofluid for metabolomic studies due to its noninvasive collection and richness in metabolites. Here, amino acids are valuable biomarkers for their ability to reflect imbalances of different biochemical pathways. An impact of amino acids on pathology, prognosis and therapy of various diseases, including inflammatory bowel disease (IBD), is therefore the subject of current clinical research. This work is aimed to develop a capillary electrophoresis-tandem mass spectrometry (CE-MS/MS) method for the quantification of the 20 proteinogenic amino acids in human urine samples obtained from patients suffering from IBD and treated with thiopurines. The optimized CE-MS/MS method, with minimum sample preparation (just “dilute and shoot”), exhibited excellent linearity for all the analytes (coefficients of determination were higher than 0.99), with inter-day and intra-day precision yielding relative standard deviations in the range of 0.91–15.12% and with accuracy yielding relative errors in the range of 85.47–112.46%. Total analysis time, an important parameter for the sample throughput demanded in routine practice, was shorter in ca. 17% when compared to established CE-MS methods. Favorable performance of the proposed CE-MS/MS method was also confirmed by the comparison with corresponding ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) method. Consistent data for the investigated amino acid metabolome were obtained using both methods. For the first time, the amino acid profiling by CE-MS approach was applied on the clinical IBD samples. Here, significant differences observed in the concentration levels of some amino acids between IBD patients undergoing thiopurine treatment and healthy volunteers could result from the simultaneous action of the disease and the corresponding therapy. These findings indicate that amino acids analysis could be a valuable tool for the study of mechanism of the IBD treatment by thiopurines.
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Shinde T, Perera AP, Vemuri R, Gondalia SV, Karpe AV, Beale DJ, Shastri S, Southam B, Eri R, Stanley R. Synbiotic Supplementation Containing Whole Plant Sugar Cane Fibre and Probiotic Spores Potentiates Protective Synergistic Effects in Mouse Model of IBD. Nutrients 2019; 11:E818. [PMID: 30979002 PMCID: PMC6521199 DOI: 10.3390/nu11040818] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/20/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are a chronic inflammatory disorders with increasing global incidence. Synbiotic, which is a two-point approach carrying probiotic and prebiotic components in mitigating inflammation in IBD, is thought to be a pragmatic approach owing to the synergistic outcomes. In this study, the impacts of dietary supplementation with probiotic Bacillus coagulans MTCC5856 spores (B. coagulans) and prebiotic whole plant sugar cane fibre (PSCF) was assessed using a murine model of IBD. Eight-week-old C57BL/6 mice were fed a normal chow diet supplemented with either B. coagulans, PSCF or its synbiotic combination. After seven days of supplementation, colitis was induced with dextran sulfate sodium (DSS) in drinking water for seven days during the continuation of the supplemented diets. Synbiotic supplementation ameliorated disease activity index and histological score (-72%, 7.38, respectively), more effectively than either B. coagulans (-47%, 10.1) and PSCF (-53%, 13.0) alone. Synbiotic supplementation also significantly (p < 0.0001) prevented the expression of tight junction proteins and modulated the altered serum IL-1β (-40%), IL-10 (+26%), and C-reactive protein (CRP) (-39%) levels. Synbiotic supplementations also raised the short-chain fatty acids (SCFA) profile more extensively compared to the unsupplemented DSS-control. The synbiotic health outcome effect of the probiotic and prebiotic combinations may be associated with a synergistic direct immune-regulating efficacy of the components, their ability to protect epithelial integrity, stimulation of probiotic spores by the prebiotic fibre, and/or with stimulation of greater levels of fermentation of fibres releasing SCFAs that mediate the reduction in colonic inflammation. Our model findings suggest synbiotic supplementation should be tested in clinical trials.
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Affiliation(s)
- Tanvi Shinde
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia.
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, TAS 7250, Australia.
| | - Agampodi Promoda Perera
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, TAS 7250, Australia.
| | - Ravichandra Vemuri
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, TAS 7250, Australia.
| | - Shakuntla V Gondalia
- Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia.
| | - Avinash V Karpe
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecosciences Precinct, Dutton Park, QLD 4102, Australia.
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecosciences Precinct, Dutton Park, QLD 4102, Australia.
| | - Sonia Shastri
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, TAS 7250, Australia.
| | - Benjamin Southam
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, TAS 7250, Australia.
| | - Rajaraman Eri
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, TAS 7250, Australia.
| | - Roger Stanley
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia.
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Sugihara K, Morhardt TL, Kamada N. The Role of Dietary Nutrients in Inflammatory Bowel Disease. Front Immunol 2019; 9:3183. [PMID: 30697218 PMCID: PMC6340967 DOI: 10.3389/fimmu.2018.03183] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/27/2018] [Indexed: 12/22/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic and relapsing inflammatory disease of the gastrointestinal tract. Although the precise etiology of IBD remains incompletely understood, accumulating evidence suggests that various environmental factors, including dietary nutrients, contribute to its pathogenesis. Dietary nutrients are known to have an impact on host physiology and diseases. The interactions between dietary nutrients and intestinal immunity are complex. Dietary nutrients directly regulate the immuno-modulatory function of gut-resident immune cells. Likewise, dietary nutrients shape the composition of the gut microbiota. Therefore, a well-balanced diet is crucial for good health. In contrast, the relationships among dietary nutrients, host immunity and/or the gut microbiota may be perturbed in the context of IBD. Genetic predispositions and gut dysbiosis may affect the utilization of dietary nutrients. Moreover, the metabolism of nutrients in host cells and the gut microbiota may be altered by intestinal inflammation, thereby increasing or decreasing the demand for certain nutrients necessary for the maintenance of immune and microbial homeostasis. Herein, we review the current knowledge of the role dietary nutrients play in the development and the treatment of IBD, focusing on the interplay among dietary nutrients, the gut microbiota and host immune cells. We also discuss alterations in the nutritional metabolism of the gut microbiota and host cells in IBD that can influence the outcome of nutritional intervention. A better understanding of the diet-host-microbiota interactions may lead to new therapeutic approaches for the treatment of IBD.
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Affiliation(s)
- Kohei Sugihara
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Tina L Morhardt
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States.,Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Nobuhiko Kamada
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
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29
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Godoy-Vitorino F, Ortiz-Morales G, Romaguera J, Sanchez MM, Martinez-Ferrer M, Chorna N. Discriminating high-risk cervical Human Papilloma Virus infections with urinary biomarkers via non-targeted GC-MS-based metabolomics. PLoS One 2018; 13:e0209936. [PMID: 30592768 PMCID: PMC6310238 DOI: 10.1371/journal.pone.0209936] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/13/2018] [Indexed: 02/05/2023] Open
Abstract
Genital human papillomavirus (HPV) is the world’s most commonly diagnosed sexually transmitted infection, and high-risk HPV types are strongly linked to cervical dysplasia and carcinoma. Puerto Ricans are among the US citizens with higher HPV prevalence and lower screening rates and access to treatment. This bleak statistic was as a motivation to detect biomarkers for early diagnosis of HPV in this population. We collected both urine and cervical swabs from 43 patients attending San Juan Clinics. Cervical swabs were used for genomic DNA extractions and HPV genotyping with the HPV SPF10-LiPA25 kit, and gas chromatography-mass spectrometry (GC-MS) was employed on the urine-derived products for metabolomics analyses. We aimed at discriminating between patients with different HPV categories: HPV negative (HPV-), HPV positive with simultaneous low and high-risk infections (HPV+B) and HPV positive exclusively high-risk (HPV+H). We found that the metabolome of HPV+B is closer to HPV- than to HPV+H supporting evidence that suggests HPV co-infections may be antagonistic due to viral interference leading to a lower propensity for cervical cancer development. In contrast, metabolites of patients with HPV+H were significantly different from those that were HPV-. We identified three urinary metabolites 5-Oxoprolinate, Erythronic acid and N-Acetylaspartic acid that discriminate HPV+H cases from negative controls. These metabolites are known to be involved in a variety of biochemical processes related to energy and metabolism and may likely be biomarkers for HPV high-risk cervical infection. However, further validation should follow using a larger patient cohort and diverse populations to confirm our finding.
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Affiliation(s)
- Filipa Godoy-Vitorino
- UPR School of Medicine, Department of Microbiology & Medical Zoology, San Juan, Puerto Rico
- * E-mail: (FGV); (NC)
| | | | | | - Maria M. Sanchez
- University of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico
| | - Magaly Martinez-Ferrer
- University of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico
- UPR School of Pharmacy, Department of Pharmaceutical Sciences, San Juan, Puerto Rico
| | - Natalyia Chorna
- UPR School of Medicine, Department of Biochemistry, San Juan, Puerto Rico
- * E-mail: (FGV); (NC)
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30
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Wei R, Ross AB, Su M, Wang J, Guiraud SP, Draper CF, Beaumont M, Jia W, Martin FP. Metabotypes Related to Meat and Vegetable Intake Reflect Microbial, Lipid and Amino Acid Metabolism in Healthy People. Mol Nutr Food Res 2018; 62:e1800583. [PMID: 30098305 DOI: 10.1002/mnfr.201800583] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/25/2018] [Indexed: 01/05/2023]
Abstract
SCOPE The objective of this study is to develop a new methodology to identify the relationship between dietary patterns and metabolites indicative of food intake and metabolism. METHODS AND RESULTS Plasma and urine samples from healthy Swiss subjects (n = 89) collected over two time points are analyzed for a panel of host-microbial metabolites using GC- and LC-MS. Dietary intake is evaluated using a validated food frequency questionnaire. Dietary pattern clusters and relationships with metabolites are determined using Non-Negative Matrix Factorization (NNMF) and Sparse Generalized Canonical Correlation Analysis (SGCCA). Use of NNMF allows detection of latent diet clusters in this population, which describes a high intake of meat or vegetables. SGCCA associates these clusters to i) diet-host microbial and lipid associated bile acid metabolism, and ii) essential amino acid metabolism. CONCLUSION This novel application of NNMF and SGCCA allows detection of distinct metabotypes for meat and vegetable dietary patterns in a heterogeneous population. As many of the metabolites associated with meat or vegetable intake are the result of host-microbiota interactions, the findings support a role for microbiota mediating the metabolic imprinting of different dietary choices.
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Affiliation(s)
- Runmin Wei
- University of Hawaii Cancer Center (UHCC), Honolulu, HI, 96813, USA.,Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Alastair B Ross
- Analytical Science Department, Nestlé Research Center, Lausanne, Switzerland.,Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - MingMing Su
- University of Hawaii Cancer Center (UHCC), Honolulu, HI, 96813, USA
| | - Jingye Wang
- University of Hawaii Cancer Center (UHCC), Honolulu, HI, 96813, USA
| | - Seu-Ping Guiraud
- Nutrition and Metabolic health Department, Nestle Institute of Health Sciences (NIHS), Lausanne, Switzerland
| | - Colleen Fogarty Draper
- Nutrition and Metabolic health Department, Nestle Institute of Health Sciences (NIHS), Lausanne, Switzerland
| | - Maurice Beaumont
- Clinical Development Unit, Nestlé Research Center, Lausanne, Switzerland
| | - Wei Jia
- University of Hawaii Cancer Center (UHCC), Honolulu, HI, 96813, USA
| | - Francois-Pierre Martin
- Nutrition and Metabolic health Department, Nestle Institute of Health Sciences (NIHS), Lausanne, Switzerland
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31
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Metabolic phenotyping for understanding the gut microbiome and host metabolic interplay. Emerg Top Life Sci 2017; 1:325-332. [PMID: 33525773 DOI: 10.1042/etls20170079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/08/2017] [Accepted: 11/08/2017] [Indexed: 01/08/2023]
Abstract
There is growing interest in the role of the gut microbiome in human health and disease. This unique complex ecosystem has been implicated in many health conditions, including intestinal disorders, inflammatory skin diseases and metabolic syndrome. However, there is still much to learn regarding its capacity to affect host health. Many gut microbiome research studies focus on compositional analysis to better understand the causal relationships between microbial communities and disease phenotypes. Yet, microbial diversity and complexity is such that community structure alone does not provide full understanding of microbial function. Metabolic phenotyping is an exciting field in systems biology that provides information on metabolic outputs taking place in the system at a given moment in time. These readouts provide information relating to by-products of endogenous metabolic pathways, exogenous signals arising from diet, drugs and other lifestyle and environmental stimuli, as well as products of microbe-host co-metabolism. Thus, better understanding of the gut microbiome and host metabolic interplay can be gleaned using such analytical approaches. In this review, we describe research findings focussed on gut microbiota-host interactions, for functional insights into the impact of microbiome composition on host health. We evaluate different analytical approaches for capturing metabolic activity and discuss analytical methodological advancements that have made a contribution to the field. This information will aid in developing novel approaches to improve host health in the future, and therapeutic modulation of the microbiome may soon augment conventional clinical strategies.
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