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Janker L, Schuster D, Bortel P, Hagn G, Meier-Menches SM, Mohr T, Mader JC, Slany A, Bileck A, Brunmair J, Madl C, Unger L, Hennlich B, Weitmayr B, Del Favero G, Pils D, Pukrop T, Pfisterer N, Feichtenschlager T, Gerner C. Multiomics-empowered Deep Phenotyping of Ulcerative Colitis Identifies Biomarker Signatures Reporting Functional Remission States. J Crohns Colitis 2023; 17:1514-1527. [PMID: 36961872 PMCID: PMC10588787 DOI: 10.1093/ecco-jcc/jjad052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Indexed: 03/25/2023]
Abstract
INTRODUCTION Ulcerative colitis [UC] is a chronic disease with rising incidence and unclear aetiology. Deep molecular phenotyping by multiomics analyses may provide novel insights into disease processes and characteristic features of remission states. METHODS UC pathomechanisms were assessed by proteome profiling of human tissue specimens, obtained from five distinct colon locations for each of the 12 patients included in the study. Systemic disease-associated alterations were evaluated thanks to a cross-sectional setting of mass spectrometry-based multiomics analyses comprising proteins, metabolites, and eicosanoids of plasma obtained from UC patients during acute episodes and upon remission, in comparison with healthy controls. RESULTS Tissue proteome profiling indicated colitis-associated activation of neutrophils, macrophages, B and T cells, fibroblasts, endothelial cells and platelets, and hypoxic stress, and suggested a general downregulation of mitochondrial proteins accompanying the establishment of apparent wound healing-promoting activities including scar formation. Whereas pro-inflammatory proteins were apparently upregulated by immune cells, the colitis-associated epithelial cells, fibroblasts, endothelial cells, and platelets seemed to predominantly contribute anti-inflammatory and wound healing-promoting proteins. Blood plasma proteomics indicated chronic inflammation and platelet activation, whereas plasma metabolomics identified disease-associated deregulations of gut and gut microbiome-derived metabolites. Upon remission several, but not all, molecular candidate biomarker levels recovered back to normal. CONCLUSION The findings may indicate that microvascular damage and platelet deregulation hardly resolve upon remission, but apparently persist as disease-associated molecular signatures. This study presents local and systemic molecular alterations integrated in a model for UC pathomechanisms, potentially supporting the assessment of disease and remission states in UC patients.
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Affiliation(s)
- Lukas Janker
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Dina Schuster
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Patricia Bortel
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Gerhard Hagn
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Samuel M Meier-Menches
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University of Vienna, Vienna, Austria
| | - Thomas Mohr
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University of Vienna, Vienna, Austria
| | - Johanna C Mader
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Astrid Slany
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University of Vienna, Vienna, Austria
| | - Julia Brunmair
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Christian Madl
- Institute of Pathology and Microbiology, Krankenanstalt Rudolfstiftung, Vienna, Austria
| | - Lukas Unger
- Division of General Surgery, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Barbara Hennlich
- Institute of Pathology and Microbiology, Krankenanstalt Rudolfstiftung, Vienna, Austria
| | - Barbara Weitmayr
- Institute of Pathology and Microbiology, Krankenanstalt Rudolfstiftung, Vienna, Austria
| | - Giorgia Del Favero
- Core Facility Multimodal Imaging, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Dietmar Pils
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Tobias Pukrop
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - Nikolaus Pfisterer
- Institute of Pathology and Microbiology, Krankenanstalt Rudolfstiftung, Vienna, Austria
| | | | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University of Vienna, Vienna, Austria
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2
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Fiocchi C. Omics and Multi-Omics in IBD: No Integration, No Breakthroughs. Int J Mol Sci 2023; 24:14912. [PMID: 37834360 PMCID: PMC10573814 DOI: 10.3390/ijms241914912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
The recent advent of sophisticated technologies like sequencing and mass spectroscopy platforms combined with artificial intelligence-powered analytic tools has initiated a new era of "big data" research in various complex diseases of still-undetermined cause and mechanisms. The investigation of these diseases was, until recently, limited to traditional in vitro and in vivo biological experimentation, but a clear switch to in silico methodologies is now under way. This review tries to provide a comprehensive assessment of state-of-the-art knowledge on omes, omics and multi-omics in inflammatory bowel disease (IBD). The notion and importance of omes, omics and multi-omics in both health and complex diseases like IBD is introduced, followed by a discussion of the various omics believed to be relevant to IBD pathogenesis, and how multi-omics "big data" can generate new insights translatable into useful clinical tools in IBD such as biomarker identification, prediction of remission and relapse, response to therapy, and precision medicine. The pitfalls and limitations of current IBD multi-omics studies are critically analyzed, revealing that, regardless of the types of omes being analyzed, the majority of current reports are still based on simple associations of descriptive retrospective data from cross-sectional patient cohorts rather than more powerful longitudinally collected prospective datasets. Given this limitation, some suggestions are provided on how IBD multi-omics data may be optimized for greater clinical and therapeutic benefit. The review concludes by forecasting the upcoming incorporation of multi-omics analyses in the routine management of IBD.
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Affiliation(s)
- Claudio Fiocchi
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland, OH 44195, USA;
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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Bulygin I, Shatov V, Rykachevskiy A, Raiko A, Bernstein A, Burnaev E, Gelfand MS. Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods. PeerJ 2023; 11:e15838. [PMID: 37701837 PMCID: PMC10494839 DOI: 10.7717/peerj.15838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/12/2023] [Indexed: 09/14/2023] Open
Abstract
Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.
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Affiliation(s)
- Ivan Bulygin
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | | | - Arsenii Raiko
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Evgeny Burnaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Artificial Intelligence Research Institute (AIRI), Moscow, Russia
| | - Mikhail S. Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems, Moscow, Russia
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Kohli A, Moss AC. Personalizing therapy selection in inflammatory bowel disease. Expert Rev Clin Immunol 2023; 19:431-438. [PMID: 37051666 DOI: 10.1080/1744666x.2023.2185605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
INTRODUCTION Inflammatory bowel disease (IBD) is a complex disease, caused by aberrant immune responses to environmental stimuli where genetic, metabolomic, and environmental variables interact to cause mucosal inflammation. This review sheds light on the different drug and patient related factors that affect personalization of biologics in IBD treatment. AREAS COVERED We utilized the online research database PubMed to carry out literature search pertaining to therapies in IBD. We incorporated a combination of primary literature as well as review articles and meta-analyses in writing this clinical review. In this paper, we discuss the mechanisms of action for different biologics, the genotype and phenotype of patients, and pharmacokinetics/pharmacodynamics of drugs, as factors that influence response rates. We also touch upon the role of artificial intelligence in treatment personalization. EXPERT OPINION The future of IBD therapeutics is one of precision medicine, based on the identification of aberrant signaling pathways unique to individual patients as well as exploring the exposome, diet, viruses, and epithelial cell dysfunction as part of disease pathogenesis. We need global cooperation for pragmatic study designs as well as equitable access to machine learning/artificial intelligence technology to reach the unfulfilled potential of IBD care.
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Affiliation(s)
- Arushi Kohli
- Division of Gastroenterology and Hepatology, Boston Medical Center, Boston, MA, USA
| | - Alan C Moss
- Division of Gastroenterology and Hepatology, Boston Medical Center, Boston, MA, USA
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5
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Kao CY, Chang CT, Kuo PY, Lin CJ, Chiu HH, Liao HW. Sequential isolation of metabolites and lipids from a single sample to achieve multiomics by using TRIzol reagent. Talanta 2023; 258:124416. [PMID: 36889188 DOI: 10.1016/j.talanta.2023.124416] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/13/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023]
Abstract
Simultaneous extraction of various types of biomolecule from a single sample can be beneficial for multiomics studies of unique specimens. An efficient and convenient sample preparation approach must be developed that can comprehensively isolate and extract biomolecules from one sample. TRIzol reagent is widely used in biological studies for DNA, RNA, and protein isolation. This study evaluated the feasibility of using TRIzol reagent for the simultaneous isolation of not only DNA, RNA, and proteins but also metabolites and lipids from a single sample. Through the comparison of known metabolites and lipids obtained using the conventional methanol (MeOH) and methyl-tert-butyl ether (MTBE) extraction methods, we determined the presence of metabolites and lipids in the supernatant during TRIzol sequential isolation. Finally, we performed untargeted metabolomics and lipidomics to examine metabolite and lipid alterations associated with the jhp0417 mutation in Helicobacter pylori by using the TRIzol sequential isolation protocol and MeOH and MTBE extraction methods. Metabolites and lipids with significant differences isolated using the TRIzol sequential isolation protocol were consistent with those obtained using the conventional MeOH and MTBE extraction methods. These results indicated that TRIzol reagent can be used to simultaneously isolate metabolites and lipids from a single sample. Thus, TRIzol reagent can be used in biological and clinical research, especially in multiomics studies.
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Affiliation(s)
- Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Chung-Te Chang
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Pei-Yun Kuo
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Chia-Jen Lin
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Huai-Hsuan Chiu
- The Metabolomics Core Laboratory, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, 10617, Taiwan; Department of Medical Research, National Taiwan University Hospital, Taipei, 10617, Taiwan
| | - Hsiao-Wei Liao
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
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MicrobiomeGWAS: A Tool for Identifying Host Genetic Variants Associated with Microbiome Composition. Genes (Basel) 2022; 13:genes13071224. [PMID: 35886007 PMCID: PMC9317577 DOI: 10.3390/genes13071224] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
The microbiome is the collection of all microbial genes and can be investigated by sequencing highly variable regions of 16S ribosomal RNA (rRNA) genes. Evidence suggests that environmental factors and host genetics may interact to impact human microbiome composition. Identifying host genetic variants associated with human microbiome composition not only provides clues for characterizing microbiome variation but also helps to elucidate biological mechanisms of genetic associations, prioritize genetic variants, and improve genetic risk prediction. Since a microbiota functions as a community, it is best characterized by β diversity; that is, a pairwise distance matrix. We develop a statistical framework and a computationally efficient software package, microbiomeGWAS, for identifying host genetic variants associated with microbiome β diversity with or without interacting with an environmental factor. We show that the score statistics have positive skewness and kurtosis due to the dependent nature of the pairwise data, which makes p-value approximations based on asymptotic distributions unacceptably liberal. By correcting for skewness and kurtosis, we develop accurate p-value approximations, whose accuracy was verified by extensive simulations. We exemplify our methods by analyzing a set of 147 genotyped subjects with 16S rRNA microbiome profiles from non-malignant lung tissues. Correcting for skewness and kurtosis eliminated the dramatic deviation in the quantile–quantile plots. We provided preliminary evidence that six established lung cancer risk SNPs were collectively associated with microbiome composition for both unweighted (p = 0.0032) and weighted (p = 0.011) UniFrac distance matrices. In summary, our methods will facilitate analyzing large-scale genome-wide association studies of the human microbiome.
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Cortes GM, Marcialis MA, Bardanzellu F, Corrias A, Fanos V, Mussap M. Inflammatory Bowel Disease and COVID-19: How Microbiomics and Metabolomics Depict Two Sides of the Same Coin. Front Microbiol 2022; 13:856165. [PMID: 35391730 PMCID: PMC8981987 DOI: 10.3389/fmicb.2022.856165] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/21/2022] [Indexed: 12/11/2022] Open
Abstract
The integrity of the gastrointestinal tract structure and function is seriously compromised by two pathological conditions sharing, at least in part, several pathogenetic mechanisms: inflammatory bowel diseases (IBD) and coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. IBD and COVID-19 are marked by gut inflammation, intestinal barrier breakdown, resulting in mucosal hyperpermeability, gut bacterial overgrowth, and dysbiosis together with perturbations in microbial and human metabolic pathways originating changes in the blood and fecal metabolome. This review compared the most relevant metabolic and microbial alterations reported from the literature in patients with IBD with those in patients with COVID-19. In both diseases, gut dysbiosis is marked by the prevalence of pro-inflammatory bacterial species and the shortfall of anti-inflammatory species; most studies reported the decrease in Firmicutes, with a specific decrease in obligately anaerobic producers short-chain fatty acids (SCFAs), such as Faecalibacterium prausnitzii. In addition, Escherichia coli overgrowth has been observed in IBD and COVID-19, while Akkermansia muciniphila is depleted in IBD and overexpressed in COVID-19. In patients with COVID-19, gut dysbiosis continues after the clearance of the viral RNA from the upper respiratory tract and the resolution of clinical symptoms. Finally, we presented and discussed the impact of gut dysbiosis, inflammation, oxidative stress, and increased energy demand on metabolic pathways involving key metabolites, such as tryptophan, phenylalanine, histidine, glutamine, succinate, citrate, and lipids.
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Affiliation(s)
- Gian Mario Cortes
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Maria Antonietta Marcialis
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Flaminia Bardanzellu
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Angelica Corrias
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Michele Mussap
- Laboratory Medicine, Department of Surgical Sciences, School of Medicine, University of Cagliari, Monserrato, Italy
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8
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Feakins R, Torres J, Borralho-Nunes P, Burisch J, Cúrdia Gonçalves T, De Ridder L, Driessen A, Lobatón T, Menchén L, Mookhoek A, Noor N, Svrcek M, Villanacci V, Zidar N, Tripathi M. ECCO Topical Review on Clinicopathological Spectrum and Differential Diagnosis of Inflammatory Bowel Disease. J Crohns Colitis 2022; 16:343-368. [PMID: 34346490 DOI: 10.1093/ecco-jcc/jjab141] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Many diseases can imitate inflammatory bowel disease [IBD] clinically and pathologically. This review outlines the differential diagnosis of IBD and discusses morphological pointers and ancillary techniques that assist with the distinction between IBD and its mimics. METHODS European Crohn's and Colitis Organisation [ECCO] Topical Reviews are the result of an expert consensus. For this review, ECCO announced an open call to its members and formed three working groups [WGs] to study clinical aspects, pathological considerations, and the value of ancillary techniques. All WGs performed a systematic literature search. RESULTS Each WG produced a draft text and drew up provisional Current Practice Position [CPP] statements that highlighted the most important conclusions. Discussions and a preliminary voting round took place, with subsequent revision of CPP statements and text and a further meeting to agree on final statements. CONCLUSIONS Clinicians and pathologists encounter a wide variety of mimics of IBD, including infection, drug-induced disease, vascular disorders, diverticular disease, diversion proctocolitis, radiation damage, and immune disorders. Reliable distinction requires a multidisciplinary approach.
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Affiliation(s)
- Roger Feakins
- Department of Cellular Pathology, Royal Free Hospital, London, and University College London, UK
| | - Joana Torres
- Department of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
| | - Paula Borralho-Nunes
- Department of Pathology, Hospital Cuf Descobertas, Lisboa and Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Johan Burisch
- Gastrounit, Medical Division, Hvidovre Hospital, University of Copenhagen, Denmark
| | - Tiago Cúrdia Gonçalves
- Department of Gastroenterology, Hospital da Senhora da Oliveira, Guimarães, Portugal.,School of Medicine, University of Minho, Braga/Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Lissy De Ridder
- Department of Paediatric Gastroenterology, Erasmus MC Sophia Children's Hospital, University Medical Center Rotterdam, The Netherlands
| | - Ann Driessen
- Department of Pathology, University Hospital Antwerp, University Antwerp, Edegem, Belgium
| | - Triana Lobatón
- Department of Gastroenterology, Ghent University Hospital, Ghent, Belgium
| | - Luis Menchén
- Department of Digestive System Medicine, Hospital General Universitario-Insitituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Department of Medicine, Universidad Complutense, Madrid, Spain.,Centro de Investigación Biomédica En Red de Enfermedades Hepáticas y Digestivas [CIBEREHD], Madrid, Spain
| | - Aart Mookhoek
- Department of Pathology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Nurulamin Noor
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Magali Svrcek
- Department of Pathology, Sorbonne Université, AP-HP, Saint-Antoine Hospital, Paris, France
| | - Vincenzo Villanacci
- Department of Histopathology, Spedali Civili and University of Brescia, Brescia, Italy
| | - Nina Zidar
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Monika Tripathi
- Department of Histopathology, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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Sudhakar P, Alsoud D, Wellens J, Verstockt S, Arnauts K, Verstockt B, Vermeire S. Tailoring Multi-omics to Inflammatory Bowel Diseases: All for One and One for All. J Crohns Colitis 2022; 16:1306-1320. [PMID: 35150242 PMCID: PMC9426669 DOI: 10.1093/ecco-jcc/jjac027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 12/13/2022]
Abstract
Inflammatory bowel disease [IBD] has a multifactorial origin and originates from a complex interplay of environmental factors with the innate immune system at the intestinal epithelial interface in a genetically susceptible individual. All these factors make its aetiology intricate and largely unknown. Multi-omic datasets obtained from IBD patients are required to gain further insights into IBD biology. We here review the landscape of multi-omic data availability in IBD and identify barriers and gaps for future research. We also outline the various technical and non-technical factors that influence the utility and interpretability of multi-omic datasets and thereby the study design of any research project generating such datasets. Coordinated generation of multi-omic datasets and their systemic integration with clinical phenotypes and environmental exposures will not only enhance understanding of the fundamental mechanisms of IBD but also improve therapeutic strategies. Finally, we provide recommendations to enable and facilitate generation of multi-omic datasets.
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Affiliation(s)
- Padhmanand Sudhakar
- Corresponding author: Padhmanand Sudhakar, Translational Research in Gastrointestinal Disorders [TARGID], ON I, Herestraat 49, box 701, 3000 Leuven, Belgium. Tel.: 0032 [0]16 19 49 40;
| | - Dahham Alsoud
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Judith Wellens
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Sare Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Kaline Arnauts
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Bram Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Severine Vermeire
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
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10
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Zhang W, Tan B, Deng J, Haitao Z. Multiomics analysis of soybean meal induced marine fish enteritis in juvenile pearl gentian grouper, Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂. Sci Rep 2021; 11:23319. [PMID: 34857775 PMCID: PMC8640039 DOI: 10.1038/s41598-021-02278-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 09/20/2021] [Indexed: 01/02/2023] Open
Abstract
As an important protein source, soybean products can cause intestinal inflammation and injury in many animals including human beings, particularly infants and juvenile individuals. Research in this field has been performed for terrestrial animals and fish, but still lacks integrity and systematicness. In this study, the main biological processes in the intestinal tract of marine fish juvenile pearl gentian grouper in the state of soybean meal-induced enteritis (SBMIE) were analyzed. A total of 720 groupers with an approximate initial weight of 12.5 g were randomly divided into three groups: the fish meal (FM) control group, the 20% SBM group (SBM20), and the SBM40 group (n = 4). Three iso-nitrogenous and iso-lipidic diets were prepared and fed to fish for 10 weeks. Each barrel contained a water volume of about 1 m3 in and was exposed to natural light and temperature. Results indicated that the growth and physiology of groupers fed with SBM were significantly negatively affected, with the gene expressions of intestinal structural protein abnormal. 16SrDNA high-throughput sequencing showed that the intestinal microflora played an important role in the pathogenesis of pearl gentian grouper SBMIE, which may activate a variety of pathogen pattern recognition receptors, such as toll-like receptors (TLRs), RIG-I-like receptors, and nod-like receptors. Transcriptome analysis revealed that changes of the SBMIE signaling pathway in pearl gentian groupers were conservative to some extent than that of terrestrial animals and freshwater fish. Moreover, the TLRs-nuclear factor kappa-B signaling pathway becomes activated, which played an important role in SBMIE. Meanwhile, the signal pathways related to nutrient absorption and metabolism were generally inhibited. Metabolomics analysis showed that isoflavones and saponins accounted for a large proportion in the potential biomarkers of pearl gentian grouper SBMIE, and most of the biomarkers had significantly positive or negative correlations with each other; 56 metabolites were exchanged between intestinal tissues and contents, which may play an important role in the development of enteritis, including unsaturated fatty acids, organic acids, amino acids, vitamins, small peptides, and nucleotides, etc. These results provide a basic theoretical reference for solving the intestinal issues of fish SBMIE and research of inflammatory bowel disease in mammals.
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Affiliation(s)
- Wei Zhang
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, Guangdong, People's Republic of China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, 524025, Guangdong, People's Republic of China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, 524025, Guangdong, People's Republic of China
| | - Beiping Tan
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, Guangdong, People's Republic of China.
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, 524025, Guangdong, People's Republic of China.
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, 524025, Guangdong, People's Republic of China.
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, People's Republic of China.
| | - Junming Deng
- Laboratory of Aquatic Animal Nutrition and Feed, College of Fisheries, Guangdong Ocean University, Zhanjiang, 524025, Guangdong, People's Republic of China
- Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, 524025, Guangdong, People's Republic of China
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, 524025, Guangdong, People's Republic of China
| | - Zhang Haitao
- Key Laboratory of Aquatic, Livestock and Poultry Feed Science and Technology in South China, Ministry of Agriculture, Zhanjiang, 524025, Guangdong, People's Republic of China
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Abstract
BACKGROUND Systems biology is a rapidly advancing field of science that allows us to look into disease mechanisms, patient diagnosis and stratification, and drug development in a completely new light. It is based on the utilization of unbiased computational systems free of the traditional experimental approaches based on personal choices of what is important and what select experiments should be performed to obtain the expected results. METHODS Systems biology can be applied to inflammatory bowel disease (IBD) by learning basic concepts of omes and omics and how omics-derived "big data" can be integrated to discover the biological networks underlying highly complex diseases like IBD. Once these biological networks (interactomes) are identified, then the molecules controlling the disease network can be singled out and specific blockers developed. RESULTS The field of systems biology in IBD is just emerging, and there is still limited information on how to best utilize its power to advance our understanding of Crohn disease and ulcerative colitis to develop novel therapeutic strategies. Few centers have embraced systems biology in IBD, but the creation of international consortia and large biobanks will make biosamples available to basic and clinical IBD investigators for further research studies. CONCLUSIONS The implementation of systems biology is indispensable and unavoidable, and the patient and medical communities will both benefit immensely from what it will offer in the near future.
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Affiliation(s)
- Claudio Fiocchi
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
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12
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Zhou M, Varol A, Efferth T. Multi-omics approaches to improve malaria therapy. Pharmacol Res 2021; 167:105570. [PMID: 33766628 DOI: 10.1016/j.phrs.2021.105570] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 01/07/2023]
Abstract
Malaria contributes to the most widespread infectious diseases worldwide. Even though current drugs are commercially available, the ever-increasing drug resistance problem by malaria parasites poses new challenges in malaria therapy. Hence, searching for efficient therapeutic strategies is of high priority in malaria control. In recent years, multi-omics technologies have been extensively applied to provide a more holistic view of functional principles and dynamics of biological mechanisms. We briefly review multi-omics technologies and focus on recent malaria progress conducted with the help of various omics methods. Then, we present up-to-date advances for multi-omics approaches in malaria. Next, we describe resistance phenomena to established antimalarial drugs and underlying mechanisms. Finally, we provide insight into novel multi-omics approaches, new drugs and vaccine developments and analyze current gaps in multi-omics research. Although multi-omics approaches have been successfully used in malaria studies, they are still limited. Many gaps need to be filled to bridge the gap between basic research and treatment of malaria patients. Multi-omics approaches will foster a better understanding of the molecular mechanisms of Plasmodium that are essential for the development of novel drugs and vaccines to fight this disastrous disease.
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Affiliation(s)
- Min Zhou
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Ayşegül Varol
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany.
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13
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Revilla L, Mayorgas A, Corraliza AM, Masamunt MC, Metwaly A, Haller D, Tristán E, Carrasco A, Esteve M, Panés J, Ricart E, Lozano JJ, Salas A. Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis. PLoS One 2021; 16:e0246367. [PMID: 33556098 PMCID: PMC7870068 DOI: 10.1371/journal.pone.0246367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/18/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Personalized medicine requires finding relationships between variables that influence a patient's phenotype and predicting an outcome. Sparse generalized canonical correlation analysis identifies relationships between different groups of variables. This method requires establishing a model of the expected interaction between those variables. Describing these interactions is challenging when the relationship is unknown or when there is no pre-established hypothesis. Thus, our aim was to develop a method to find the relationships between microbiome and host transcriptome data and the relevant clinical variables in a complex disease, such as Crohn's disease. RESULTS We present here a method to identify interactions based on canonical correlation analysis. We show that the model is the most important factor to identify relationships between blocks using a dataset of Crohn's disease patients with longitudinal sampling. First the analysis was tested in two previously published datasets: a glioma and a Crohn's disease and ulcerative colitis dataset where we describe how to select the optimum parameters. Using such parameters, we analyzed our Crohn's disease data set. We selected the model with the highest inner average variance explained to identify relationships between transcriptome, gut microbiome and clinically relevant variables. Adding the clinically relevant variables improved the average variance explained by the model compared to multiple co-inertia analysis. CONCLUSIONS The methodology described herein provides a general framework for identifying interactions between sets of omic data and clinically relevant variables. Following this method, we found genes and microorganisms that were related to each other independently of the model, while others were specific to the model used. Thus, model selection proved crucial to finding the existing relationships in multi-omics datasets.
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Affiliation(s)
- Lluís Revilla
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Aida Mayorgas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Ana M. Corraliza
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Maria C. Masamunt
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
- ZIEL Institute for Food and Health, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Eva Tristán
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Anna Carrasco
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Maria Esteve
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Julian Panés
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Elena Ricart
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Juan J. Lozano
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
| | - Azucena Salas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
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Cammarota G, Ianiro G, Ahern A, Carbone C, Temko A, Claesson MJ, Gasbarrini A, Tortora G. Gut microbiome, big data and machine learning to promote precision medicine for cancer. Nat Rev Gastroenterol Hepatol 2020; 17:635-648. [PMID: 32647386 DOI: 10.1038/s41575-020-0327-3] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/02/2020] [Indexed: 12/13/2022]
Abstract
The gut microbiome has been implicated in cancer in several ways, as specific microbial signatures are known to promote cancer development and influence safety, tolerability and efficacy of therapies. The 'omics' technologies used for microbiome analysis continuously evolve and, although much of the research is still at an early stage, large-scale datasets of ever increasing size and complexity are being produced. However, there are varying levels of difficulty in realizing the full potential of these new tools, which limit our ability to critically analyse much of the available data. In this Perspective, we provide a brief overview on the role of gut microbiome in cancer and focus on the need, role and limitations of a machine learning-driven approach to analyse large amounts of complex health-care information in the era of big data. We also discuss the potential application of microbiome-based big data aimed at promoting precision medicine in cancer.
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Affiliation(s)
- Giovanni Cammarota
- Gastroenterology Department, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Gianluca Ianiro
- Gastroenterology Department, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Anna Ahern
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Carmine Carbone
- Oncology Department, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Andriy Temko
- School of Engineering, University College Cork, Cork, Ireland.,Qualcomm ML R&D, Cork, Ireland
| | - Marcus J Claesson
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Antonio Gasbarrini
- Gastroenterology Department, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giampaolo Tortora
- Oncology Department, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
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Bai Y, Pascal Z, Calhoun V, Wang YP. Optimized Combination of Multiple Graphs With Application to the Integration of Brain Imaging and (epi)Genomics Data. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:1801-1811. [PMID: 31825864 PMCID: PMC7394342 DOI: 10.1109/tmi.2019.2958256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
With the rapid development of high-throughput technologies, a growing amount of multi-omics data are collected, giving rise to a great demand for combining such data for biomedical discovery. Due to the cost and time to label the data manually, the number of labelled samples is limited. This motivated the need for semi-supervised learning algorithms. In this work, we applied a graph-based semi-supervised learning (GSSL) to classify a severe chronic mental disorder, schizophrenia (SZ). An advantage of GSSL is that it can simultaneously analyse more than two types of data, while many existing models focus on pairwise data analysis. In particular, we applied GSSL to the analysis of single nucleotide polymorphism (SNP), functional magnetic resonance imaging (fMRI) and DNA methylation data, which accounts for genetics, brain imaging (endophenotypes), and environmental factors (epigenomics) respectively. While parameter selection has been an open challenge for most models, another key contribution of this work is that we explored the parameter space to interpret their meaning and established practical guidelines. Based on the practical significance of each hyper-parameter, a relatively small range of candidate values can be determined in a data-driven way to both optimize and speed up the parameter tuning process. We validated the model through both synthetic data and a real SZ dataset of 184 subjects from the Mental Illness and Neuroscience Discovery (MIND) Clinical Imaging Consortium. In comparison to several existing approaches, our algorithm achieved better performance in terms of classification accuracy. We also confirmed the significance of several brain regions associated with SZ.
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16
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Dong YQ, Wang W, Li J, Ma MS, Zhong LQ, Wei QJ, Song HM. Characterization of microbiota in systemic-onset juvenile idiopathic arthritis with different disease severities. World J Clin Cases 2019; 7:2734-2745. [PMID: 31616689 PMCID: PMC6789395 DOI: 10.12998/wjcc.v7.i18.2734] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/17/2019] [Accepted: 07/27/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Systemic-onset juvenile idiopathic arthritis (SoJIA) is one of most serious subtypes of juvenile idiopathic arthritis. Although the pathogenesis of SoJIA remains unclear, several studies have suggested a correlation between gut dysbiosis and JIA. Further understanding of the intestinal microbiome may help to establish alternative ways to treat, or even prevent, the disease.
AIM To explore alterations in fecal microbiota profiles in SoJIA patients and to evaluate the correlations between microbiota and clinical parameters.
METHODS We conducted an observational single-center study at the Pediatric Department of Peking Union Medical College Hospital. Children who were diagnosed with SoJIA at our institution and followed for a minimum period of six months after diagnosis were recruited for the study. Healthy children were recruited as a control group (HS group) during the same period. Clinical data and stool samples were collected from SoJIA patients when they visited the hospital.
RESULTS The SoJIA group included 17 active and 15 inactive consecutively recruited children; the control group consisted of 32 children. Firmicutes and Bacteroidetes were the two most abundant phyla among the total sample of SoJIA children and controls. There was a significant difference among the three groups in observed species, which was the highest in the Active-SoJIA group, followed by the Inactive-SoJIA group and then HS group (Active-SoJIA vs HS: P = 0.000; and Inactive-SoJIA vs HS: P = 0.005). We observed a lower Firmicutes/Bacteroidetes ratio in SoJIA patients (3.28 ± 4.47 in Active-SoJIA, 5.36 ± 8.39 in Inactive-SoJIA, and 5.67 ± 3.92 in HS). We also observed decreased abundances of Ruminococcaceae (14.9% in Active-SoJIA, 17.3% in Inactive-SoJIA, and 22.8% in HS; Active-SoJIA vs HS: P = 0.005) and Faecalibacterium (5.1% in Active-SoJIA, 9.9% in Inactive-SoJIA, and 13.0% in HS; Active-SoJIA vs HS: P = 0.000) in SoJIA compared with HS. By contrast, the abundance of Bacteroidaceae was the highest in the Active-SoJIA group, followed by the Inactive-SoJIA and HS groups (16.5% in Active-SoJIA, 12.8% in Inactive-SoJIA, and 9.7% in HS; Active-SoJIA vs HS: P = 0.03). The Spearman correlation analysis revealed a negative correlation between Proteobacteria or Enterobacteriaceae and juvenile arthritis disease activity score on 27 joints (JADAS-27).
CONCLUSION The composition of the intestinal microbiota is different in SoJIA patients compared with healthy children. The dysbiosis presents partial restoration in inactive status patients.
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Affiliation(s)
- Yan-Qing Dong
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Wei Wang
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Ji Li
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Ming-Sheng Ma
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lin-Qing Zhong
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Qi-Jiao Wei
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Hong-Mei Song
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Lai Y, Xue J, Liu CW, Gao B, Chi L, Tu P, Lu K, Ru H. Serum Metabolomics Identifies Altered Bioenergetics, Signaling Cascades in Parallel with Exposome Markers in Crohn's Disease. Molecules 2019; 24:E449. [PMID: 30691236 PMCID: PMC6385106 DOI: 10.3390/molecules24030449] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/15/2019] [Accepted: 01/22/2019] [Indexed: 02/08/2023] Open
Abstract
: Inflammatory bowel disease (IBD) has stimulated much interest due to its surging incidences and health impacts in the U.S. and worldwide. However, the exact cause of IBD remains incompletely understood, and biomarker is lacking towards early diagnostics and effective therapy assessment. To tackle these, the emerging high-resolution mass spectrometry (HRMS)-based metabolomics shows promise. Here, we conducted a pilot untargeted LC/MS metabolomic profiling in Crohn's disease, for which serum samples of both active and inactive cases were collected, extracted, and profiled by a state-of-the-art compound identification workflow. Results show a distinct metabolic profile of Crohn's from control, with most metabolites downregulated. The identified compounds are structurally diverse, pointing to important pathway perturbations ranging from energy metabolism (e.g., β-oxidation of fatty acids) to signaling cascades of lipids (e.g., DHA) and amino acid (e.g., L-tryptophan). Importantly, an integral role of gut microbiota in the pathogenesis of Crohn's disease is highlighted. Xenobiotics and their biotransformants were widely detected, calling for massive exposomic profiling for future cohort studies as such. This study endorses the analytical capacity of untargeted metabolomics for biomarker development, cohort stratification, and mechanistic interpretation; the findings might be valuable for advancing biomarker research and etiologic inquiry in IBD.
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Affiliation(s)
- Yunjia Lai
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, CB #7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Jingchuan Xue
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, CB #7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, CB #7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Bei Gao
- NIH West Coast Metabolomics Center, University of California at Davis, Davis, CA 95616, USA.
| | - Liang Chi
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, CB #7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, CB #7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Kun Lu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, CB #7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Hongyu Ru
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27695, USA.
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Wang XQ, Zhang AH, Miao JH, Sun H, Yan GL, Wu FF, Wang XJ. Gut microbiota as important modulator of metabolism in health and disease. RSC Adv 2018; 8:42380-42389. [PMID: 35558413 PMCID: PMC9092240 DOI: 10.1039/c8ra08094a] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/02/2018] [Indexed: 12/12/2022] Open
Abstract
The human gastrointestinal tract colonizes a large number of microbial microflora, forms a host-microbiota co-metabolism structure with the host to participate in various metabolic processes in the human body, and plays a major role in the host immune response. In addition, the dysbiosis of intestinal microbial homeostasis is closely related to many diseases. Thus, an in-depth understanding of the relationship between them is of importance for disease pathogenesis, prevention and treatment. The combined use of metagenomics, transcriptomics, proteomics and metabolomics techniques for the analysis of gut microbiota can reveal the relationship between microbiota and the host in many ways, which has become a hot topic of analysis in recent years. This review describes the mechanism of co-metabolites in host health, including short-chain fatty acids (SCFA) and bile acid metabolism. The metabolic role of gut microbiota in obesity, liver diseases, gastrointestinal diseases and other diseases is also summarized, and the research methods for multi-omics combined application on gut microbiota are summarized. According to the studies of the interaction mechanism between gut microbiota and the host, we have a better understanding of the use of intestinal microflora in the treatment of related diseases. It is hoped that the gut microbiota can be utilized to maintain human health, providing a reference for future research.
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Affiliation(s)
- Xiang-Qian Wang
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plant Nanning Guangxi China +86-451-82110818 +86-451-82110818
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin China
| | - Ai-Hua Zhang
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin China
| | - Jian-Hua Miao
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plant Nanning Guangxi China +86-451-82110818 +86-451-82110818
| | - Hui Sun
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin China
| | - Guang-Li Yan
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin China
| | - Fang-Fang Wu
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plant Nanning Guangxi China +86-451-82110818 +86-451-82110818
| | - Xi-Jun Wang
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plant Nanning Guangxi China +86-451-82110818 +86-451-82110818
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin China
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Ghosh D, Bernstein JA, Khurana Hershey GK, Rothenberg ME, Mersha TB. Leveraging Multilayered "Omics" Data for Atopic Dermatitis: A Road Map to Precision Medicine. Front Immunol 2018; 9:2727. [PMID: 30631320 PMCID: PMC6315155 DOI: 10.3389/fimmu.2018.02727] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/05/2018] [Indexed: 12/14/2022] Open
Abstract
Atopic dermatitis (AD) is a complex multifactorial inflammatory skin disease that affects ~280 million people worldwide. About 85% of AD cases begin in childhood, a significant portion of which can persist into adulthood. Moreover, a typical progression of children with AD to food allergy, asthma or allergic rhinitis has been reported (“allergic march” or “atopic march”). AD comprises highly heterogeneous sub-phenotypes/endotypes resulting from complex interplay between intrinsic and extrinsic factors, such as environmental stimuli, and genetic factors regulating cutaneous functions (impaired barrier function, epidermal lipid, and protease abnormalities), immune functions and the microbiome. Though the roles of high-throughput “omics” integrations in defining endotypes are recognized, current analyses are primarily based on individual omics data and using binary clinical outcomes. Although individual omics analysis, such as genome-wide association studies (GWAS), can effectively map variants correlated with AD, the majority of the heritability and the functional relevance of discovered variants are not explained or known by the identified variants. The limited success of singular approaches underscores the need for holistic and integrated approaches to investigate complex phenotypes using trans-omics data integration strategies. Integrating omics layers (e.g., genome, epigenome, transcriptome, proteome, metabolome, lipidome, exposome, microbiome), which often have complementary and synergistic effects, might provide the opportunity to capture the flow of information underlying AD disease manifestation. Overlapping genes/candidates derived from multiple omics types include FLG, SPINK5, S100A8, and SERPINB3 in AD pathogenesis. Overlapping pathways include macrophage, endothelial cell and fibroblast activation pathways, in addition to well-known Th1/Th2 and NFkB activation pathways. Interestingly, there was more multi-omics overlap at the pathway level than gene level. Further analysis of multi-omics overlap at the tissue level showed that among 30 tissue types from the GTEx database, skin and esophagus were significantly enriched, indicating the biological interconnection between AD and food allergy. The present work explores multi-omics integration and provides new biological insights to better define the biological basis of AD etiology and confirm previously reported AD genes/pathways. In this context, we also discuss opportunities and challenges introduced by “big omics data” and their integration.
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Affiliation(s)
- Debajyoti Ghosh
- Division of Immunology, Allergy & Rheumatology, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Jonathan A Bernstein
- Division of Immunology, Allergy & Rheumatology, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
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Palmieri O, Mazza T, Castellana S, Panza A, Latiano T, Corritore G, Andriulli A, Latiano A. Inflammatory Bowel Disease Meets Systems Biology: A Multi-Omics Challenge and Frontier. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 20:692-698. [PMID: 27930092 DOI: 10.1089/omi.2016.0147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The inflammatory bowel disease (IBD) is a systemic disease that is characterized by the inflammation of the gastrointestinal tract. It includes ulcerative colitis and the Crohn's disease. Presently, IBD is one of the most investigated common complex human disorders, although its causes remain unclear. Multi-omics mechanisms involving genomic, transcriptomic, proteomic, and epigenomic variations, not to forget the miRNome, together with environmental contributions, result in an impairment of the immune system in persons with IBD. Such interactions at multiple levels of biology and in concert with the environment constitute the actual engine of this complex disease, demanding a multifactorial and multi-omics perspective to better understand the root causes of IBD. This expert analysis reviews and examines the latest literature and underscores, from the perspective of systems biology, the value of multi-omics technologies as opportunities to unravel the "IBD integrome." We anticipate that multi-omics research will accelerate the new discoveries and insights on IBD in the near future. It shall also pave the way for early diagnosis and help clinicians and families with IBD to forecast and make informed decisions about the prognosis and, possibly, personalized therapeutics in the future.
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Affiliation(s)
- Orazio Palmieri
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- 2 Laboratory of Bioinformatics, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Stefano Castellana
- 2 Laboratory of Bioinformatics, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Anna Panza
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Tiziana Latiano
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Giuseppe Corritore
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Angelo Andriulli
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Anna Latiano
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
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21
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Recent Advances in the Etiopathogenesis of Inflammatory Bowel Disease: The Role of Omics. Mol Diagn Ther 2017; 22:11-23. [DOI: 10.1007/s40291-017-0298-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Skevaki C, Van den Berg J, Jones N, Garssen J, Vuillermin P, Levin M, Landay A, Renz H, Calder PC, Thornton CA. Immune biomarkers in the spectrum of childhood noncommunicable diseases. J Allergy Clin Immunol 2017; 137:1302-16. [PMID: 27155027 DOI: 10.1016/j.jaci.2016.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 02/07/2023]
Abstract
A biomarker is an accurately and reproducibly quantifiable biological characteristic that provides an objective measure of health status or disease. Benefits of biomarkers include identification of therapeutic targets, monitoring of clinical interventions, and development of personalized (or precision) medicine. Challenges to the use of biomarkers include optimizing sample collection, processing and storage, validation, and often the need for sophisticated laboratory and bioinformatics approaches. Biomarkers offer better understanding of disease processes and should benefit the early detection, treatment, and management of multiple noncommunicable diseases (NCDs). This review will consider the utility of biomarkers in patients with allergic and other immune-mediated diseases in childhood. Typically, biomarkers are used currently to provide mechanistic insight or an objective measure of disease severity, with their future role in risk stratification/disease prediction speculative at best. There are many lessons to be learned from the biomarker strategies used for cancer in which biomarkers are in routine clinical use and industry-wide standardized approaches have been developed. Biomarker discovery and validation in children with disease lag behind those in adults; given the early onset and therefore potential lifelong effect of many NCDs, there should be more studies incorporating cohorts of children. Many pediatric biomarkers are at the discovery stage, with a long path to evaluation and clinical implementation. The ultimate challenge will be optimization of prevention strategies that can be implemented in children identified as being at risk of an NCD through the use of biomarkers.
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Affiliation(s)
- Chrysanthi Skevaki
- International Inflammation (in-FLAME) Network of the World Universities Network; Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps University Marburg, University Hospital Giessen and Marburg GmbH Baldingerstr, Marburg, Germany
| | - Jolice Van den Berg
- International Inflammation (in-FLAME) Network of the World Universities Network; Department of Immunology/Microbiology Rush University Medical Center Chicago, Chicago, Ill
| | - Nicholas Jones
- International Inflammation (in-FLAME) Network of the World Universities Network; Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales
| | - Johan Garssen
- International Inflammation (in-FLAME) Network of the World Universities Network; Utrecht Institute for Pharmaceutical Sciences, Division of Pharmacology, Beta Faculty, Utrecht University, Utrecht, The Netherlands
| | - Peter Vuillermin
- International Inflammation (in-FLAME) Network of the World Universities Network; Child Health Research Unit, Barwon Health, School of Medicine, Deakin University, Geelong, Australia
| | - Michael Levin
- International Inflammation (in-FLAME) Network of the World Universities Network; Division of Asthma and Allergy, University of Cape Town, and the Department of Pediatrics and Child Health, Red Cross Children's Hospital, Cape Town, South Africa
| | - Alan Landay
- International Inflammation (in-FLAME) Network of the World Universities Network; Department of Immunology/Microbiology Rush University Medical Center Chicago, Chicago, Ill
| | - Harald Renz
- International Inflammation (in-FLAME) Network of the World Universities Network; Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps University Marburg, University Hospital Giessen and Marburg GmbH Baldingerstr, Marburg, Germany
| | - Philip C Calder
- International Inflammation (in-FLAME) Network of the World Universities Network; Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, and NIHR Southampton Biomedical Research Centre, Southampton University Hospital NHS Foundation Trust and University of Southampton, Southampton, United Kingdom
| | - Catherine A Thornton
- International Inflammation (in-FLAME) Network of the World Universities Network; Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, Wales.
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23
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Staley C, Weingarden AR, Khoruts A, Sadowsky MJ. Interaction of gut microbiota with bile acid metabolism and its influence on disease states. Appl Microbiol Biotechnol 2017; 101:47-64. [PMID: 27888332 PMCID: PMC5203956 DOI: 10.1007/s00253-016-8006-6] [Citation(s) in RCA: 325] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 01/18/2023]
Abstract
Primary bile acids serve important roles in cholesterol metabolism, lipid digestion, host-microbe interactions, and regulatory pathways in the human host. While most bile acids are reabsorbed and recycled via enterohepatic cycling, ∼5% serve as substrates for bacterial biotransformation in the colon. Enzymes involved in various transformations have been characterized from cultured gut bacteria and reveal taxa-specific distribution. More recently, bioinformatic approaches have revealed greater diversity in isoforms of these enzymes, and the microbial species in which they are found. Thus, the functional roles played by the bile acid-transforming gut microbiota and the distribution of resulting secondary bile acids, in the bile acid pool, may be profoundly affected by microbial community structure and function. Bile acids and the composition of the bile acid pool have historically been hypothesized to be associated with several disease states, including recurrent Clostridium difficile infection, inflammatory bowel diseases, metabolic syndrome, and several cancers. Recently, however, emphasis has been placed on how microbial communities in the dysbiotic gut may alter the bile acid pool to potentially cause or mitigate disease onset. This review highlights the current understanding of the interactions between the gut microbial community, bile acid biotransformation, and disease states, and addresses future directions to better understand these complex associations.
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Affiliation(s)
- Christopher Staley
- BioTechnology Institute, Center for Immunology University of Minnesota, Minneapolis, MN
| | - Alexa R Weingarden
- BioTechnology Institute, Center for Immunology University of Minnesota, Minneapolis, MN
| | - Alexander Khoruts
- BioTechnology Institute, Center for Immunology University of Minnesota, Minneapolis, MN
- Division of Gastroenterology, Department of Medicine, Center for Immunology University of Minnesota, Minneapolis, MN
| | - Michael J Sadowsky
- BioTechnology Institute, Center for Immunology University of Minnesota, Minneapolis, MN
- Department of Soil, Water and Climate, University of Minnesota, St. Paul, MN
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24
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Patlevič P, Vašková J, Švorc P, Vaško L, Švorc P. Reactive oxygen species and antioxidant defense in human gastrointestinal diseases. Integr Med Res 2016; 5:250-258. [PMID: 28462126 PMCID: PMC5390420 DOI: 10.1016/j.imr.2016.07.004] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/11/2016] [Accepted: 07/25/2016] [Indexed: 02/07/2023] Open
Abstract
Crohn's disease and ulcerative colitis, known together as inflammatory bowel diseases (IBDs), and celiac disease are the most common disorders affecting not only adults but also children. Both IBDs and celiac disease are associated with oxidative stress, which may play a significant role in their etiologies. Reactive oxygen species (ROS) such as superoxide radicals (O2•-), hydroxyl radicals (•OH), hydrogen peroxide (H2O2), and singlet oxygen (1O2) are responsible for cell death via oxidation of DNA, proteins, lipids, and almost any other cellular constituent. To protect biological systems from free radical toxicity, several cellular antioxidant defense mechanisms exist to regulate the production of ROS, including enzymatic and nonenzymatic pathways. Superoxide dismutase catalyzes the dismutation of O2•- to H2O2 and oxygen. The glutathione redox cycle involves two enzymes: glutathione peroxidase, which uses glutathione to reduce organic peroxides and H2O2; and glutathione reductase, which reduces the oxidized form of glutathione with concomitant oxidation of nicotinamide adenine dinucleotide phosphate. In addition to this cycle, GSH can react directly with free radicals. Studies into the effects of free radicals and antioxidant status in patients with IBDs and celiac disease are scarce, especially in pediatric patients. It is therefore very necessary to conduct additional research studies to confirm previous data about ROS status and antioxidant activities in patients with IBDs and celiac disease, especially in children.
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Affiliation(s)
- Peter Patlevič
- Department of Ecology, Faculty of Humanities and Natural Sciences, Prešov University in Prešov, Prešov, Slovak Republic
| | - Janka Vašková
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovak Republic
| | - Pavol Švorc
- Department of Physiology and Pathophysiology, Faculty of Medicine, University of Ostrava, Ostrava-Zábřeh, Czech Republic
| | - Ladislav Vaško
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovak Republic
| | - Pavol Švorc
- Department of Medical Physiology, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovak Republic
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25
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Alonso A, Julià A, Vinaixa M, Domènech E, Fernández-Nebro A, Cañete JD, Ferrándiz C, Tornero J, Gisbert JP, Nos P, Casbas AG, Puig L, González-Álvaro I, Pinto-Tasende JA, Blanco R, Rodríguez MA, Beltran A, Correig X, Marsal S. Urine metabolome profiling of immune-mediated inflammatory diseases. BMC Med 2016; 14:133. [PMID: 27609333 PMCID: PMC5016926 DOI: 10.1186/s12916-016-0681-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/25/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Immune-mediated inflammatory diseases (IMIDs) are a group of complex and prevalent diseases where disease diagnostic and activity monitoring is highly challenging. The determination of the metabolite profiles of biological samples is becoming a powerful approach to identify new biomarkers of clinical utility. In order to identify new metabolite biomarkers of diagnosis and disease activity, we have performed the first large-scale profiling of the urine metabolome of the six most prevalent IMIDs: rheumatoid arthritis, psoriatic arthritis, psoriasis, systemic lupus erythematosus, Crohn's disease, and ulcerative colitis. METHODS Using nuclear magnetic resonance, we analyzed the urine metabolome in a discovery cohort of 1210 patients and 100 controls. Within each IMID, two patient subgroups were recruited representing extreme disease activity (very high vs. very low). Metabolite association analysis with disease diagnosis and disease activity was performed using multivariate linear regression in order to control for the effects of clinical, epidemiological, or technical variability. After multiple test correction, the most significant metabolite biomarkers were validated in an independent cohort of 1200 patients and 200 controls. RESULTS In the discovery cohort, we identified 28 significant associations between urine metabolite levels and disease diagnosis and three significant metabolite associations with disease activity (P FDR < 0.05). Using the validation cohort, we validated 26 of the diagnostic associations and all three metabolite associations with disease activity (P FDR < 0.05). Combining all diagnostic biomarkers using multivariate classifiers we obtained a good disease prediction accuracy in all IMIDs and particularly high in inflammatory bowel diseases. Several of the associated metabolites were found to be commonly altered in multiple IMIDs, some of which can be considered as hub biomarkers. The analysis of the metabolic reactions connecting the IMID-associated metabolites showed an over-representation of citric acid cycle, phenylalanine, and glycine-serine metabolism pathways. CONCLUSIONS This study shows that urine is a source of biomarkers of clinical utility in IMIDs. We have found that IMIDs show similar metabolic changes, particularly between clinically similar diseases and we have found, for the first time, the presence of hub metabolites. These findings represent an important step in the development of more efficient and less invasive diagnostic and disease monitoring methods in IMIDs.
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Affiliation(s)
- Arnald Alonso
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain.
| | - Maria Vinaixa
- Centre for Omic Sciences, COS-DEEEA-URV-IISPV, Reus, Spain.,Metabolomics Platform, CIBERDEM, Reus, Spain
| | - Eugeni Domènech
- Hospital Universitari Germans Trias i Pujol, Badalona, Spain.,CIBERehd, Madrid, Spain
| | - Antonio Fernández-Nebro
- UGC Reumatología, Instituto de Investigación Biomédica (IBIMA), Hospital Regional Universitario de Málaga, Universidad de Málaga, Málaga, Spain
| | - Juan D Cañete
- Hospital Clínic de Barcelona and IDIBAPS, Barcelona, Spain
| | | | - Jesús Tornero
- Hospital Universitario Guadalajara, Guadalajara, Spain
| | - Javier P Gisbert
- CIBERehd, Madrid, Spain.,Hospital Universitario de la Princesa and IIS-IP, Madrid, Spain
| | - Pilar Nos
- CIBERehd, Madrid, Spain.,Hospital la Fe, Valencia, Spain
| | | | - Lluís Puig
- Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | | | | | - Ricardo Blanco
- Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Miguel A Rodríguez
- Centre for Omic Sciences, COS-DEEEA-URV-IISPV, Reus, Spain.,Metabolomics Platform, CIBERDEM, Reus, Spain
| | - Antoni Beltran
- Centre for Omic Sciences, COS-DEEEA-URV-IISPV, Reus, Spain.,Metabolomics Platform, CIBERDEM, Reus, Spain
| | - Xavier Correig
- Centre for Omic Sciences, COS-DEEEA-URV-IISPV, Reus, Spain.,Metabolomics Platform, CIBERDEM, Reus, Spain
| | - Sara Marsal
- Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain.
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26
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Danese S, Fiocchi C, Panés J. Drug development in IBD: from novel target identification to early clinical trials. Gut 2016; 65:1233-9. [PMID: 27196598 DOI: 10.1136/gutjnl-2016-311717] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/19/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Silvio Danese
- IBD Center, Department of Gastroenterology, Humanitas Research Hospital, Humanitas University, Milan, Italy
| | - Claudio Fiocchi
- Department of Gastroenterology and Hepatology, Digestive Disease Institute, Cleveland, Ohio, USA Department of Pathobiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Julián Panés
- Gastroenterology Department, Hospital Clínic Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
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27
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Moller FT, Knudsen L, Harbord M, Satsangi J, Gordon H, Christiansen L, Christensen K, Jess T, Andersen V. Danish cohort of monozygotic inflammatory bowel disease twins: Clinical characteristics and inflammatory activity. World J Gastroenterol 2016; 22:5050-5059. [PMID: 27275097 PMCID: PMC4886380 DOI: 10.3748/wjg.v22.i21.5050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/21/2016] [Accepted: 05/04/2016] [Indexed: 02/06/2023] Open
Abstract
AIM: To describe the establishment of a Danish inflammatory bowel diseases (IBD) twin cohort with focus on concordance of treatment and inflammatory markers.
METHODS: We identified MZ twins, likely to be discordant or concordant for IBD, by merging information from the Danish Twin Register and the National Patient Register. The twins were asked to provide biological samples, questionnaires, and data access to patient files and public registries. Biological samples were collected via a mobile laboratory, which allowed for immediate centrifugation, fractionation, and storage of samples. The mean time from collection of samples to storage in the -80 °C mobile freezer was less than one hour. The diagnoses where validated using the Copenhagen diagnostic criteria.
RESULTS: We identified 159 MZ IBD twin pairs, in a total of 62 (39%) pairs both twins agreed to participate. Of the supposed 62 IBD pairs, the IBD diagnosis could be confirmed in 54 pairs. The cohort included 10 concordant pairs, whereof some were discordant for either treatment or surgery. The 10 concordant pairs, where both pairs suffered from IBD, included eight CD/CD pairs, one UC/UC pair and one UC/IBDU pair. The discordant pairs comprised 31 UC, 5 IBDU (IBD unclassified), and 8 CD discordant pairs. In the co-twins not affected by IBD, calprotectin was above 100 μg/g in 2 participants, and above 50 μg/g in a further 5 participants.
CONCLUSION: The presented IBD twin cohorts are an excellent resource for bioinformatics studies with proper adjustment for disease-associated exposures including medication and inflammatory activity in the co-twins.
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Kaunitz J, Nayyar P. Bugs, genes, fatty acids, and serotonin: Unraveling inflammatory bowel disease? F1000Res 2015; 4:F1000 Faculty Rev-1146. [PMID: 27508055 PMCID: PMC4963018 DOI: 10.12688/f1000research.6456.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/30/2015] [Indexed: 12/13/2022] Open
Abstract
The annual incidence of the inflammatory bowel diseases (IBDs) ulcerative colitis and Crohn's disease has increased at an alarming rate. Although the specific pathophysiology underlying IBD continues to be elusive, it is hypothesized that IBD results from an aberrant and persistent immune response directed against microbes or their products in the gut, facilitated by the genetic susceptibility of the host and intrinsic alterations in mucosal barrier function. In this review, we will describe advances in the understanding of how the interaction of host genetics and the intestinal microbiome contribute to the pathogenesis of IBD, with a focus on bacterial metabolites such as short chain fatty acids (SCFAs) as possible key signaling molecules. In particular, we will describe alterations of the intestinal microbiota in IBD, focusing on how genetic loci affect the gut microbial phylogenetic distribution and the production of their major microbial metabolic product, SCFAs. We then describe how enteroendocrine cells and myenteric nerves express SCFA receptors that integrate networks such as the cholinergic and serotonergic neural systems and the glucagon-like peptide hormonal pathway, to modulate gut inflammation, permeability, and growth as part of an integrated model of IBD pathogenesis. Through this integrative approach, we hope that novel hypotheses will emerge that will be tested in reductionist, hypothesis-driven studies in order to examine the interrelationship of these systems in the hope of better understanding IBD pathogenesis and to inform novel therapies.
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Affiliation(s)
- Jonathan Kaunitz
- Medical Service, West Los Angeles VAMC, Los Angeles, CA, 90073, USA
- Department of Medicine, David Geffen School of Medicine, Los Angeles, CA, 90095, USA
- Department of Surgery, David Geffen School of Medicine, Los Angeles, CA, 90095, USA
| | - Piyush Nayyar
- Medical Service, West Los Angeles VAMC, Los Angeles, CA, 90073, USA
- Department of Medicine, David Geffen School of Medicine, Los Angeles, CA, 90095, USA
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29
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Plé C, Richoux R, Jardin J, Nurdin M, Briard-Bion V, Parayre S, Ferreira S, Pot B, Bouguen G, Deutsch SM, Falentin H, Foligné B, Jan G. Single-strain starter experimental cheese reveals anti-inflammatory effect of Propionibacterium freudenreichii CIRM BIA 129 in TNBS-colitis model. J Funct Foods 2015. [DOI: 10.1016/j.jff.2015.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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30
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Ferguson LR. Nutritional Modulation of Gene Expression: Might This be of Benefit to Individuals with Crohn's Disease? Front Immunol 2015; 6:467. [PMID: 26441972 PMCID: PMC4566049 DOI: 10.3389/fimmu.2015.00467] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/27/2015] [Indexed: 12/18/2022] Open
Abstract
The incidence of inflammatory bowel diseases (IBD), including Crohn's disease (CD), is increasing worldwide, especially in young children and adolescents. Although hospitalized patients are usually provided with enteral or parenteral support, continuing care typically requires a trial-and-error approach to suppressing symptoms and maintaining disease remission. Current nutritional advice does not differ from general population guidelines. International collaborative studies have revealed 163 distinct genetic loci affecting susceptibility to IBD, in some of which host-microbe interactions can be seen to play an important role. The nature of these loci enables a rationale for predicting nutritional requirements that may not be evident through standard therapeutic approaches. Certain recognized nutrients, such as vitamin D and long-chain omega-3 polyunsaturated fatty acids, may be required at higher than anticipated levels. Various phytochemicals, not usually considered in the same class as classic nutrients, could play an important role. Prebiotics and probiotics may also be beneficial. Genomic approaches enable proof of principle of nutrient optimization rather than waiting for disease symptoms to appear and/or progress. We suggest a paradigm shift in diagnostic tools and nutritional therapy for CD, involving a systems biology approach for implementation.
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Affiliation(s)
- Lynnette R Ferguson
- Discipline of Nutrition and Dietetics, Faculty of Medical and Health Sciences, The University of Auckland , Auckland , New Zealand ; Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland , Auckland , New Zealand
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31
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Can inflammatory bowel disease really be solved by the multiple -omics and meta-omics analyses? Immunol Lett 2015; 165:107-8. [PMID: 25827759 DOI: 10.1016/j.imlet.2015.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 03/20/2015] [Indexed: 12/19/2022]
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32
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Wang RS, Maron BA, Loscalzo J. Systems medicine: evolution of systems biology from bench to bedside. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:141-61. [PMID: 25891169 DOI: 10.1002/wsbm.1297] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 12/11/2022]
Abstract
High-throughput experimental techniques for generating genomes, transcriptomes, proteomes, metabolomes, and interactomes have provided unprecedented opportunities to interrogate biological systems and human diseases on a global level. Systems biology integrates the mass of heterogeneous high-throughput data and predictive computational modeling to understand biological functions as system-level properties. Most human diseases are biological states caused by multiple components of perturbed pathways and regulatory networks rather than individual failing components. Systems biology not only facilitates basic biological research but also provides new avenues through which to understand human diseases, identify diagnostic biomarkers, and develop disease treatments. At the same time, systems biology seeks to assist in drug discovery, drug optimization, drug combinations, and drug repositioning by investigating the molecular mechanisms of action of drugs at a system's level. Indeed, systems biology is evolving to systems medicine as a new discipline that aims to offer new approaches for addressing the diagnosis and treatment of major human diseases uniquely, effectively, and with personalized precision.
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Affiliation(s)
- Rui-Sheng Wang
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Bradley A Maron
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Cardiology, Veterans Affairs Boston Healthcare System, West Roxbury, MA, USA
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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