101
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Suárez-Fariñas M, Tokuyama M, Wei G, Huang R, Livanos A, Jha D, Levescot A, Irizar H, Kosoy R, Cording S, Wang W, Losic B, Ungaro RC, Di’Narzo A, Martinez-Delgado G, Suprun M, Corley MJ, Stojmirovic A, Houten SM, Peters L, Curran M, Brodmerkel C, Perrigoue J, Friedman JR, Hao K, Schadt EE, Zhu J, Ko HM, Cho J, Dubinsky MC, Sands BE, Ndhlovu L, Cerf-Bensusan N, Kasarskis A, Colombel JF, Harpaz N, Argmann C, Mehandru S. Intestinal Inflammation Modulates the Expression of ACE2 and TMPRSS2 and Potentially Overlaps With the Pathogenesis of SARS-CoV-2-related Disease. Gastroenterology 2021; 160:287-301.e20. [PMID: 32980345 PMCID: PMC7516468 DOI: 10.1053/j.gastro.2020.09.029] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS The presence of gastrointestinal symptoms and high levels of viral RNA in the stool suggest active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication within enterocytes. METHODS Here, in multiple, large cohorts of patients with inflammatory bowel disease (IBD), we have studied the intersections between Coronavirus Disease 2019 (COVID-19), intestinal inflammation, and IBD treatment. RESULTS A striking expression of ACE2 on the small bowel enterocyte brush border supports intestinal infectivity by SARS-CoV-2. Commonly used IBD medications, both biologic and nonbiologic, do not significantly impact ACE2 and TMPRSS2 receptor expression in the uninflamed intestines. In addition, we have defined molecular responses to COVID-19 infection that are also enriched in IBD, pointing to shared molecular networks between COVID-19 and IBD. CONCLUSIONS These data generate a novel appreciation of the confluence of COVID-19- and IBD-associated inflammation and provide mechanistic insights supporting further investigation of specific IBD drugs in the treatment of COVID-19. Preprint doi: https://doi.org/10.1101/2020.05.21.109124.
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Affiliation(s)
- Mayte Suárez-Fariñas
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York City, New York
| | - Minami Tokuyama
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gabrielle Wei
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruiqi Huang
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York City, New York
| | - Alexandra Livanos
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Divya Jha
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Anais Levescot
- Inserm, UMR1163, Laboratory of Intestinal Immunity and Institute Imagine, Paris, France,Université de Paris, Paris, France
| | - Haritz Irizar
- University College London, Department Mental Health Sciences Unit, London, UK
| | - Roman Kosoy
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sascha Cording
- Inserm, UMR1163, Laboratory of Intestinal Immunity and Institute Imagine, Paris, France,Université de Paris, Paris, France
| | - Wenhui Wang
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bojan Losic
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ryan C. Ungaro
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Antonio Di’Narzo
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gustavo Martinez-Delgado
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Maria Suprun
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael J. Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | | | - Sander M. Houten
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lauren Peters
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | | | | | - Ke Hao
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Eric E. Schadt
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jun Zhu
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Huaibin M. Ko
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Judy Cho
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marla C. Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bruce E. Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lishomwa Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | | | - Andrew Kasarskis
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Noam Harpaz
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Carmen Argmann
- Icahn Institute for Data Science and Genomic Technology, New York City, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Saurabh Mehandru
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York.
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102
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Carcamo-Orive I, Henrion MYR, Zhu K, Beckmann ND, Cundiff P, Moein S, Zhang Z, Alamprese M, D’Souza SL, Wabitsch M, Schadt EE, Quertermous T, Knowles JW, Chang R. Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness. PLoS Comput Biol 2020; 16:e1008491. [PMID: 33362275 PMCID: PMC7790417 DOI: 10.1371/journal.pcbi.1008491] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/07/2021] [Accepted: 11/03/2020] [Indexed: 12/16/2022] Open
Abstract
Insulin resistance (IR) precedes the development of type 2 diabetes (T2D) and increases cardiovascular disease risk. Although genome wide association studies (GWAS) have uncovered new loci associated with T2D, their contribution to explain the mechanisms leading to decreased insulin sensitivity has been very limited. Thus, new approaches are necessary to explore the genetic architecture of insulin resistance. To that end, we generated an iPSC library across the spectrum of insulin sensitivity in humans. RNA-seq based analysis of 310 induced pluripotent stem cell (iPSC) clones derived from 100 individuals allowed us to identify differentially expressed genes between insulin resistant and sensitive iPSC lines. Analysis of the co-expression architecture uncovered several insulin sensitivity-relevant gene sub-networks, and predictive network modeling identified a set of key driver genes that regulate these co-expression modules. Functional validation in human adipocytes and skeletal muscle cells (SKMCs) confirmed the relevance of the key driver candidate genes for insulin responsiveness. Insulin resistance is characterized by a defective response (“resistance”) to normal insulin concentrations to uptake the glucose present in the blood, and is the underlying condition that leads to type 2 diabetes (T2D) and increases the risk of cardiovascular disease. It is estimated that 25–33% of the US population are insulin resistant enough to be at risk of serious clinical consequences. For more than a decade, large population studies have tried to discover the genes that participate in the development of insulin resistance, but without much success. It is now increasingly clear that the complex genetic nature of insulin resistance requires novel approaches centered in patient specific cellular models. To fill this gap, we have generated an induced pluripotent stem cell (iPSC) library from individuals with accurate measurements of insulin sensitivity, and performed gene expression and key driver analyses. Our work demonstrates that iPSCs can be used as a revolutionary technology to model insulin resistance and to discover key genetic drivers. Moreover, they can develop our basic knowledge of the disease, and are ultimately expected to increase the therapeutic targets to treat insulin resistance and type 2 diabetes.
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Affiliation(s)
- Ivan Carcamo-Orive
- Stanford University School of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, and Diabetes Research Center, Stanford, California, United States of America
- * E-mail: (ICO); (JWK); (RC)
| | - Marc Y. R. Henrion
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
- Malawi—Liverpool—Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Kuixi Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, University of Arizona, Tucson, Arizona, United States of America
- The Center for Innovations in Brain Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Paige Cundiff
- Vertex Pharmaceuticals, Boston, Massachusetts, United States of America
| | - Sara Moein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, University of Arizona, Tucson, Arizona, United States of America
- The Center for Innovations in Brain Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Zenan Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Melissa Alamprese
- Department of Neurology, University of Arizona, Tucson, Arizona, United States of America
- The Center for Innovations in Brain Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Sunita L. D’Souza
- Department of Cellular, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Endocrinology, Ulm University, Ulm, Germany
| | - Eric E. Schadt
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Thomas Quertermous
- Stanford University School of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, and Diabetes Research Center, Stanford, California, United States of America
| | - Joshua W. Knowles
- Stanford University School of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, and Diabetes Research Center, Stanford, California, United States of America
- * E-mail: (ICO); (JWK); (RC)
| | - Rui Chang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, University of Arizona, Tucson, Arizona, United States of America
- The Center for Innovations in Brain Sciences, University of Arizona, Tucson, Arizona, United States of America
- INTelico Therapeutics LLC, Tucson, Arizona, United States of America
- * E-mail: (ICO); (JWK); (RC)
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103
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Gómez-Martín C, Aparicio-Puerta E, Medina JM, Barturen G, Oliver JL, Hackenberg M. geno 5mC: A Database to Explore the Association between Genetic Variation (SNPs) and CpG Methylation in the Human Genome. J Mol Biol 2020; 433:166709. [PMID: 33188782 DOI: 10.1016/j.jmb.2020.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/15/2020] [Accepted: 11/06/2020] [Indexed: 01/23/2023]
Abstract
Genetic variation, gene expression and DNA methylation influence each other in a complex way. To study the impact of sequence variation and DNA methylation on gene expression, we generated geno5mC, a database that contains statistically significant SNP-CpG associations that are biologically classified either through co-localization with known regulatory regions (promoters and enhancers), or through known correlations with the expression levels of nearby genes. The SNP rs727563 can be used to illustrate the usefulness of this approach. This SNP has been associated with inflammatory bowel disease through GWAS, but it is not located near any gene related to this phenotype. However, geno5mC reveals that rs727563 is associated with the methylation state of several CpGs located in promoter regions of genes reported to be involved in inflammatory processes. This case exemplifies how geno5mC can be used to infer relevant and previously unknown interactions between described disease-associated SNPs and their functional targets.
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Affiliation(s)
- C Gómez-Martín
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - E Aparicio-Puerta
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain; Instituto de Investigación Biosanitaria (IBS) Granada, University Hospitals of Granada-University, Granada, Spain, Conocimiento s/n, 18100 Granada, Spain; Excellence Research Unit "Modeling Nature" (MNat), University of Granada, 18071 Granada, Spain
| | - J M Medina
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - Guillermo Barturen
- Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, Genetics of Complex Diseases, 18016 Granada, Spain
| | - J L Oliver
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - M Hackenberg
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain; Instituto de Investigación Biosanitaria (IBS) Granada, University Hospitals of Granada-University, Granada, Spain, Conocimiento s/n, 18100 Granada, Spain; Excellence Research Unit "Modeling Nature" (MNat), University of Granada, 18071 Granada, Spain.
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104
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Sieberts SK, Perumal TM, Carrasquillo MM, Allen M, Reddy JS, Hoffman GE, Dang KK, Calley J, Ebert PJ, Eddy J, Wang X, Greenwood AK, Mostafavi S, Omberg L, Peters MA, Logsdon BA, De Jager PL, Ertekin-Taner N, Mangravite LM. Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions. Sci Data 2020; 7:340. [PMID: 33046718 PMCID: PMC7550587 DOI: 10.1038/s41597-020-00642-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/24/2020] [Indexed: 12/27/2022] Open
Abstract
The availability of high-quality RNA-sequencing and genotyping data of post-mortem brain collections from consortia such as CommonMind Consortium (CMC) and the Accelerating Medicines Partnership for Alzheimer's Disease (AMP-AD) Consortium enable the generation of a large-scale brain cis-eQTL meta-analysis. Here we generate cerebral cortical eQTL from 1433 samples available from four cohorts (identifying >4.1 million significant eQTL for >18,000 genes), as well as cerebellar eQTL from 261 samples (identifying 874,836 significant eQTL for >10,000 genes). We find substantially improved power in the meta-analysis over individual cohort analyses, particularly in comparison to the Genotype-Tissue Expression (GTEx) Project eQTL. Additionally, we observed differences in eQTL patterns between cerebral and cerebellar brain regions. We provide these brain eQTL as a resource for use by the research community. As a proof of principle for their utility, we apply a colocalization analysis to identify genes underlying the GWAS association peaks for schizophrenia and identify a potentially novel gene colocalization with lncRNA RP11-677M14.2 (posterior probability of colocalization 0.975).
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Affiliation(s)
| | | | | | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Joseph S Reddy
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Gabriel E Hoffman
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - John Calley
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46225, USA
| | - Philip J Ebert
- Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, 46225, USA
| | - James Eddy
- Sage Bionetworks, Seattle, WA, 98121, USA
| | - Xue Wang
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | | | - Sara Mostafavi
- Departments of Statistics and Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
- Canadian Institute for Advanced Research, CIFAR Program in Child and Brain Development, Toronto, Ontario, Canada
| | | | | | | | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
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105
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McCarter C, Howrylak J, Kim S. Learning gene networks underlying clinical phenotypes using SNP perturbation. PLoS Comput Biol 2020; 16:e1007940. [PMID: 33095769 PMCID: PMC7584257 DOI: 10.1371/journal.pcbi.1007940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 05/11/2020] [Indexed: 11/18/2022] Open
Abstract
Availability of genome sequence, molecular, and clinical phenotype data for large patient cohorts generated by recent technological advances provides an opportunity to dissect the genetic architecture of complex diseases at system level. However, previous analyses of such data have largely focused on the co-localization of SNPs associated with clinical and expression traits, each identified from genome-wide association studies and expression quantitative trait locus mapping. Thus, their description of the molecular mechanisms behind the SNPs influencing clinical phenotypes was limited to the single gene linked to the co-localized SNP. Here we introduce PerturbNet, a statistical framework for learning gene networks that modulate the influence of genetic variants on phenotypes, using genetic variants as naturally occurring perturbation of a biological system. PerturbNet uses a probabilistic graphical model to directly model the cascade of perturbation from genetic variants to the gene network to the phenotype network along with the networks at each layer of the biological system. PerturbNet learns the entire model by solving a single optimization problem with an efficient algorithm that can analyze human genome-wide data within a few hours. PerturbNet inference procedures extract a detailed description of how the gene network modulates the genetic effects on phenotypes. Using simulated and asthma data, we demonstrate that PerturbNet improves statistical power for detecting disease-linked SNPs and identifies gene networks and network modules mediating the SNP effects on traits, providing deeper insights into the underlying molecular mechanisms.
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Affiliation(s)
- Calvin McCarter
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Judie Howrylak
- Pulmonary, Allergy and Critical Care Division, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Seyoung Kim
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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106
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Patients developing inflammatory bowel disease have iron deficiency and lower plasma ferritin years before diagnosis: a nested case-control study. Eur J Gastroenterol Hepatol 2020; 32:1147-1153. [PMID: 32541236 PMCID: PMC7423531 DOI: 10.1097/meg.0000000000001816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Iron deficiency is common among inflammatory bowel disease (IBD) patients, generally reported without comparisons with controls. The aim of this study was to analyse if iron deficiency was more common among those later developing IBD compared to matched controls in a prospective setting. METHODS We included 96 healthy subjects later developing IBD and 191 matched controls from the Northern Sweden Health and Disease Study. We analysed iron, ferritin, transferrin, and calculated transferrin saturation in plasma sampled at least 1 year prior to IBD diagnosis. Iron deficiency was defined as plasma ferritin <30 µg/L if C-reactive protein (CRP) was <3 mg/L. When CRP was >3 mg/L, iron deficiency could not be excluded if ferritin was <100 µg/L. RESULTS Iron deficiency could not be excluded among more male cases vs controls (25.0% vs 2.2%; P < 0.001), whereas with no differences for women (39.6% vs 35.3%; P = 0.538). Ferritin was lower among male IBD cases (P = 0.001) and for ulcerative colitis (P = 0.016 for males and 0.017 for females), but not for Crohn's disease. Ferritin was associated with a lower risk for IBD and in the ulcerative colitis subgroup when using sex-based z-scores. Ferritin quartiles 2-4 had a 65% lower odds ratio for all IBD, ulcerative colitis, and Crohn's disease in multivariable analysis. CONCLUSIONS Lower ferritin was associated with higher risk for developing IBD in a prospective setting. Iron deficiency was more common among healthy males years later developing IBD compared to matched controls, but not among women.
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107
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Do AN, Chun Y, Grishina G, Grishin A, Rogers AJ, Raby BA, Weiss ST, Vicencio A, Schadt EE, Bunyavanich S. Network study of nasal transcriptome profiles reveals master regulator genes of asthma. J Allergy Clin Immunol 2020; 147:879-893. [PMID: 32828590 DOI: 10.1016/j.jaci.2020.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 06/19/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Nasal transcriptomics can provide an accessible window into asthma pathobiology. OBJECTIVE Our goal was to move beyond gene signatures of asthma to identify master regulator genes that causally regulate genes associated with asthma phenotypes. METHODS We recruited 156 children with severe persistent asthma and controls for nasal transcriptome profiling and applied network-based and probabilistic causal methods to identify severe asthma genes and their master regulators. We then took the same approach in an independent cohort of 190 adults with mild/moderate asthma and controls to identify mild/moderate asthma genes and their master regulators. Comparative analysis of the master regulator genes followed by validation testing in independent children with severe asthma (n = 21) and mild/moderate asthma (n = 154) was then performed. RESULTS Nasal gene signatures for severe persistent asthma and for mild/moderate persistent asthma were identified; both were found to be enriched in coexpression network modules for ciliary function and inflammatory response. By applying probabilistic causal methods to these gene signatures and validation testing in independent cohorts, we identified (1) a master regulator gene common to asthma across severity and ages (FOXJ1); (2) master regulator genes of severe persistent asthma in children (LRRC23, TMEM231, CAPS, PTPRC, and FYB); and (3) master regulator genes of mild/moderate persistent asthma in children and adults (C1orf38 and FMNL1). The identified master regulators were statistically inferred to causally regulate the expression of downstream genes that modulate ciliary function and inflammatory response to influence asthma. CONCLUSION The identified master regulator genes of asthma provide a novel path forward to further uncovering asthma mechanisms and therapy.
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Affiliation(s)
- Anh N Do
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yoojin Chun
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Galina Grishina
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Alexander Grishin
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Angela J Rogers
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Benjamin A Raby
- Division of Pulmonary Medicine, Children's Hospital Boston, Boston, Mass
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Mass
| | - Alfin Vicencio
- Division of Pulmonary Medicine, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eric E Schadt
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Supinda Bunyavanich
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
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108
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Yi Z, Keung KL, Li L, Hu M, Lu B, Nicholson L, Jimenez-Vera E, Menon MC, Wei C, Alexander S, Murphy B, O’Connell PJ, Zhang W. Key driver genes as potential therapeutic targets in renal allograft rejection. JCI Insight 2020; 5:136220. [PMID: 32634125 PMCID: PMC7455082 DOI: 10.1172/jci.insight.136220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/24/2020] [Indexed: 01/09/2023] Open
Abstract
Acute rejection (AR) in renal transplantation is an established risk factor for reduced allograft survival. Molecules with regulatory control among immune pathways of AR that are inadequately suppressed, despite standard-of-care immunosuppression, could serve as important targets for therapeutic manipulation to prevent rejection. Here, an integrative, network-based computational strategy incorporating gene expression and genotype data of human renal allograft biopsy tissue was applied, to identify the master regulators - the key driver genes (KDGs) - within dysregulated AR pathways. A 982-meta-gene signature with differential expression in AR versus non-AR was identified from a meta-analysis of microarray data from 735 human kidney allograft biopsy samples across 7 data sets. Fourteen KDGs were derived from this signature. Interrogation of 2 publicly available databases identified compounds with predicted efficacy against individual KDGs or a key driver-based gene set, respectively, which could be repurposed for AR prevention. Minocycline, a tetracycline antibiotic, was chosen for experimental validation in a murine cardiac allograft model of AR. Minocycline attenuated the inflammatory profile of AR compared with controls and when coadministered with immunosuppression prolonged graft survival. This study demonstrates that a network-based strategy, using expression and genotype data to predict KDGs, assists target prioritization for therapeutics in renal allograft rejection.
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Affiliation(s)
- Zhengzi Yi
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Karen L. Keung
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
- Department of Nephrology, Prince of Wales Hospital, Sydney, Australia
| | - Li Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, Connecticut, USA
| | - Min Hu
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Bo Lu
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Leigh Nicholson
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Elvira Jimenez-Vera
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Madhav C. Menon
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chengguo Wei
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen Alexander
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- Nephrology Department, The Children’s Hospital at Westmead, Sydney, Australia
| | - Barbara Murphy
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Philip J. O’Connell
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- Department of Nephrology, Westmead Hospital, Sydney, Australia
| | - Weijia Zhang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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109
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Brubaker DK, Kumar MP, Chiswick EL, Gregg C, Starchenko A, Vega PN, Southard-Smith AN, Simmons AJ, Scoville EA, Coburn LA, Wilson KT, Lau KS, Lauffenburger DA. An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease. Sci Signal 2020; 13:13/643/eaay3258. [PMID: 32753478 DOI: 10.1126/scisignal.aay3258] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Anti-tumor necrosis factor (anti-TNF) therapy resistance is a major clinical challenge in inflammatory bowel disease (IBD), due, in part, to insufficient understanding of disease-site, protein-level mechanisms. Although proteomics data from IBD mouse models exist, data and phenotype discrepancies contribute to confounding translation from preclinical animal models of disease to clinical cohorts. We developed an approach called translatable components regression (TransComp-R) to overcome interspecies and trans-omic discrepancies between mouse models and human subjects. TransComp-R combines mouse proteomic data with patient pretreatment transcriptomic data to identify molecular features discernable in the mouse data that are predictive of patient response to therapy. Interrogating the TransComp-R models revealed activated integrin pathway signaling in patients with anti-TNF-resistant colonic Crohn's disease (cCD) and ulcerative colitis (UC). As a step toward validation, we performed single-cell RNA sequencing (scRNA-seq) on biopsies from a patient with cCD and analyzed publicly available immune cell proteomics data to characterize the immune and intestinal cell types contributing to anti-TNF resistance. We found that ITGA1 was expressed in T cells and that interactions between these cells and intestinal cell types were associated with resistance to anti-TNF therapy. We experimentally showed that the α1 integrin subunit mediated the effectiveness of anti-TNF therapy in human immune cells. Thus, TransComp-R identified an integrin signaling mechanism with potential therapeutic implications for overcoming anti-TNF therapy resistance. We suggest that TransComp-R is a generalizable framework for addressing species, molecular, and phenotypic discrepancies between model systems and patients to translationally deliver relevant biological insights.
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Affiliation(s)
- Douglas K Brubaker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biomedical Engineering, Purdue University, West Lafayette, IN 47906, USA.,Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Manu P Kumar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Evan L Chiswick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Cecil Gregg
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alina Starchenko
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Paige N Vega
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Austin N Southard-Smith
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Alan J Simmons
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Elizabeth A Scoville
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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110
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Ho GT, Cartwright JA, Thompson EJ, Bain CC, Rossi AG. Resolution of Inflammation and Gut Repair in IBD: Translational Steps Towards Complete Mucosal Healing. Inflamm Bowel Dis 2020; 26:1131-1143. [PMID: 32232386 PMCID: PMC7365805 DOI: 10.1093/ibd/izaa045] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 02/07/2023]
Abstract
Despite significant recent therapeutic advances, complete mucosal healing remains a difficult treatment target for many patients with inflammatory bowel diseases (IBD) to achieve. Our review focuses on the translational concept of promoting resolution of inflammation and repair as a necessary adjunctive step to reach this goal. We explore the roles of inflammatory cell apoptosis and efferocytosis to promote resolution, the new knowledge of gut monocyte-macrophage populations and their secreted prorepair mediators, and the processes of gut epithelial repair and regeneration to bridge this gap. We discuss the need and rationale for this vision and the tangible steps toward integrating proresolution therapies in IBD.
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Affiliation(s)
- Gwo-tzer Ho
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queen’s Medical Research Unit, University of Edinburgh, Scotland, United Kingdom,Address correspondence to: Gwo-tzer Ho, FRCP, PhD, Edinburgh IBD Science Unit, Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, United Kingdom ()
| | - Jennifer A Cartwright
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queen’s Medical Research Unit, University of Edinburgh, Scotland, United Kingdom
| | - Emily J Thompson
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queen’s Medical Research Unit, University of Edinburgh, Scotland, United Kingdom
| | - Calum C Bain
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queen’s Medical Research Unit, University of Edinburgh, Scotland, United Kingdom
| | - Adriano G Rossi
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queen’s Medical Research Unit, University of Edinburgh, Scotland, United Kingdom
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111
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Krawiec P, Pac-Kożuchowska E. Serum interleukin 17A and interleukin 17F in children with inflammatory bowel disease. Sci Rep 2020; 10:12617. [PMID: 32724117 PMCID: PMC7387488 DOI: 10.1038/s41598-020-69567-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/14/2020] [Indexed: 12/18/2022] Open
Abstract
Interleukin 17A (IL-17A) and interleukin 17F (IL-17F) appear to play important role in pathogenesis of some autoimmune diseases. However, their role in inflammatory bowel disease (IBD) has not been yet fully elucidated. We aimed to determine serum IL-17A and IL-17F in children with IBD and to assess their association with IBD activity. Recruited children underwent blood tests including complete blood count, C-reactive protein, erythrocyte sedimentation rate, IL-17A and IL-17F and stool sampling for calprotectin. The study group comprised 68 children with IBD, including 43 with ulcerative colitis and 25 with Crohn’s disease. Control group included 20 healthy children. IL-17A was significantly increased in children with IBD (median: 10.95 pg/ml; range: 0.65–200.54 pg/ml) compared to controls (median: 4.09 pg/ml; range: 0.67–26.20 pg/ml) (p = 0.002). IL-17A was significantly increased in patients with active phase of ulcerative colitis (median: 14.58 pg/ml; range: 0.65–200.54 pg/ml) compared to those in ulcerative colitis remission (median: 8.13 pg/ml; range: 1.61–58.56 pg/ml) (p = 0.04). There were no significant differences in IL-17A among patients with active and inactive Crohn’s disease (p = 0.18). IL-17F did not differ significantly between children with IBD (median: 15.11 pg/ml; range: 0.09–189.84 pg/ml) and controls (median: 11.56 pg/ml; range: 0.19–32.49 pg/ml) (p = 0.33). Our study suggests that interleukin 17A may diverse active phase from remission only in ulcerative colitis but not in Crohn’s disease.
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Affiliation(s)
- Paulina Krawiec
- Department of Paediatrics and Gastroenterology, Medical University of Lublin, Al. Racławickie 1, 20-059, Lublin, Poland.
| | - Elżbieta Pac-Kożuchowska
- Department of Paediatrics and Gastroenterology, Medical University of Lublin, Al. Racławickie 1, 20-059, Lublin, Poland
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112
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Lee HS, Vancamelbeke M, Verstockt S, Wilms T, Verstockt B, Sabino J, Ferrante M, Vermeire S, Cleynen I. Molecular Changes in the Non-Inflamed Terminal Ileum of Patients with Ulcerative Colitis. Cells 2020; 9:cells9081793. [PMID: 32731480 PMCID: PMC7464680 DOI: 10.3390/cells9081793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/19/2022] Open
Abstract
Ulcerative colitis is a chronic inflammatory disease confined to the colon. Although the etiopathogenesis remains unknown, small bowel dysfunctions like histological and permeability alterations have been described in ulcerative colitis. We evaluated the molecular gene signature in the non-inflamed terminal ileum of 36 ulcerative colitis patients (7 active, with Mayo endoscopic subscore ≥2, and 29 inactive) as compared to 15 non-inflammatory bowel disease controls. Differential gene expression analysis with DESeq2 showed distinct expression patterns depending on disease activity and maximal disease extent. We found 84 dysregulated genes in patients with active extensive colitis and 20 in inactive extensive colitis, compared to controls. There was an overlap of 5 genes: REG1B, REG1A, MUC4, GRAMD2, and CASP10. In patients with left-sided colitis, ileal gene expression levels were similar to controls. Based on gene co-expression analysis, ileal changes in active ulcerative colitis patients were related to immune functions. The ileal changes in the inactive ulcerative colitis subjects converged into the maintenance of the intestinal barrier through increased mitochondrial function and dampened immune functions. In conclusion, we identified molecular changes in the non-inflamed ileum of ulcerative colitis that are dependent on colonic inflammation.
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Affiliation(s)
- Ho-Su Lee
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; (H.-S.L.); (S.V.); (T.W.)
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Maaike Vancamelbeke
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
| | - Sare Verstockt
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; (H.-S.L.); (S.V.); (T.W.)
| | - Tom Wilms
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; (H.-S.L.); (S.V.); (T.W.)
| | - Bram Verstockt
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - João Sabino
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Marc Ferrante
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Séverine Vermeire
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Isabelle Cleynen
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; (H.-S.L.); (S.V.); (T.W.)
- Correspondence: ; Tel.: +32-1637-7480
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113
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Liu AC, Patel K, Vunikili RD, Johnson KW, Abdu F, Belman SK, Glicksberg BS, Tandale P, Fontanez R, Mathew OK, Kasarskis A, Mukherjee P, Subramanian L, Dudley JT, Shameer K. Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses. Brief Bioinform 2020; 21:1182-1195. [PMID: 31190075 PMCID: PMC8179509 DOI: 10.1093/bib/bbz059] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/04/2019] [Accepted: 04/18/2019] [Indexed: 12/26/2022] Open
Abstract
Sepsis is a series of clinical syndromes caused by the immunological response to infection. The clinical evidence for sepsis could typically attribute to bacterial infection or bacterial endotoxins, but infections due to viruses, fungi or parasites could also lead to sepsis. Regardless of the etiology, rapid clinical deterioration, prolonged stay in intensive care units and high risk for mortality correlate with the incidence of sepsis. Despite its prevalence and morbidity, improvement in sepsis outcomes has remained limited. In this comprehensive review, we summarize the current landscape of risk estimation, diagnosis, treatment and prognosis strategies in the setting of sepsis and discuss future challenges. We argue that the advent of modern technologies such as in-depth molecular profiling, biomedical big data and machine intelligence methods will augment the treatment and prevention of sepsis. The volume, variety, veracity and velocity of heterogeneous data generated as part of healthcare delivery and recent advances in biotechnology-driven therapeutics and companion diagnostics may provide a new wave of approaches to identify the most at-risk sepsis patients and reduce the symptom burden in patients within shorter turnaround times. Developing novel therapies by leveraging modern drug discovery strategies including computational drug repositioning, cell and gene-therapy, clustered regularly interspaced short palindromic repeats -based genetic editing systems, immunotherapy, microbiome restoration, nanomaterial-based therapy and phage therapy may help to develop treatments to target sepsis. We also provide empirical evidence for potential new sepsis targets including FER and STARD3NL. Implementing data-driven methods that use real-time collection and analysis of clinical variables to trace, track and treat sepsis-related adverse outcomes will be key. Understanding the root and route of sepsis and its comorbid conditions that complicate treatment outcomes and lead to organ dysfunction may help to facilitate identification of most at-risk patients and prevent further deterioration. To conclude, leveraging the advances in precision medicine, biomedical data science and translational bioinformatics approaches may help to develop better strategies to diagnose and treat sepsis in the next decade.
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Affiliation(s)
- Andrew C Liu
- Department of Information Services, Northwell Health, New Hyde Park, NY, USA
- Donald and Barbara School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, USA
| | - Krishna Patel
- Department of Information Services, Northwell Health, New Hyde Park, NY, USA
- Donald and Barbara School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, USA
| | - Ramya Dhatri Vunikili
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Kipp W Johnson
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
- Institute for Next Generation Healthcare, Mount Sinai Health System, New York, NY, USA
| | - Fahad Abdu
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- Stonybrook University, 100 Nicolls Rd, Stony Brook, NY, USA
| | - Shivani Kamath Belman
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
- Institute for Next Generation Healthcare, Mount Sinai Health System, New York, NY, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Pratyush Tandale
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- School of Biotechnology and Bioinformatics, D Y Patil University, Navi Mumbai, India
| | - Roberto Fontanez
- Department of Information Services, Northwell Health, New Hyde Park, NY, USA
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
| | | | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
| | | | | | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
- Institute for Next Generation Healthcare, Mount Sinai Health System, New York, NY, USA
| | - Khader Shameer
- Department of Information Services, Northwell Health, New Hyde Park, NY, USA
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- Institute for Next Generation Healthcare, Mount Sinai Health System, New York, NY, USA
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114
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Hantisteanu S, Dicken Y, Negreanu V, Goldenberg D, Brenner O, Leshkowitz D, Lotem J, Levanon D, Groner Y. Runx3 prevents spontaneous colitis by directing the differentiation of anti-inflammatory mononuclear phagocytes. PLoS One 2020; 15:e0233044. [PMID: 32453801 PMCID: PMC7250423 DOI: 10.1371/journal.pone.0233044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/27/2020] [Indexed: 12/23/2022] Open
Abstract
Mice deficient in the transcription factor Runx3 develop a multitude of immune system defects, including early onset colitis. This paper demonstrates that Runx3 is expressed in colonic mononuclear phagocytes (MNP), including resident macrophages (RM) and dendritic cell subsets (cDC2). Runx3 deletion in MNP causes early onset colitis due to their impaired maturation. Mechanistically, the resulting MNP subset imbalance leads to up-regulation of pro-inflammatory genes as occurs in IL10R-deficient RM. In addition, RM and cDC2 display a marked decrease in expression of anti-inflammatory/TGF β-regulated genes and β-catenin signaling associated genes, respectively. MNP transcriptome and ChIP-seq data analysis suggest that a significant fraction of genes affected by Runx3 loss are direct Runx3 targets. Collectively, Runx3 imposes intestinal immune tolerance by regulating maturation of colonic anti-inflammatory MNP, befitting the identification of RUNX3 as a genome-wide associated risk gene for various immune-related diseases in humans, including gastrointestinal tract diseases such as Crohn’s disease and celiac.
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Affiliation(s)
- Shay Hantisteanu
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Yosef Dicken
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Varda Negreanu
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Dalia Goldenberg
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Ori Brenner
- Veterinary Resources, The Weizmann Institute of Science, Rehovot, Israel
| | - Dena Leshkowitz
- Bioinformatics Unit, The Weizmann Institute of Science, Rehovot, Israel
| | - Joseph Lotem
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Ditsa Levanon
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Yoram Groner
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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115
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What's new in IBD therapy: An "omics network" approach. Pharmacol Res 2020; 159:104886. [PMID: 32428668 DOI: 10.1016/j.phrs.2020.104886] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 02/07/2023]
Abstract
The industrial revolution that began in the late 1800s has resulted in dramatic changes in the environment, human lifestyle, dietary habits, social structure, and so on. Almost certainly because this rapid evolution has outpaced the ability of the body to adapt to a number of environmental and behavioral changes, there has been a parallel emergence of several chronic inflammatory diseases, among which are inflammatory bowel diseases (IBD), primarily ulcerative colitis and Crohn's disease. The ability to treat these conditions has progressively improved in the last 50 years, particularly in the last couple of decades with the introduction of biological therapy targeting primarily soluble mediators produced by inflammatory cells. A large number of biologics are now available, but all of them induce similarly unsatisfactory (<50%) rates of clinical response and remission, and most of them lose efficacy over time, requiring dose escalation or switching from one biologic to another. So, treatment of IBD still needs improvement that will occur only if different approaches are taken. A reason why even the most recent forms of IBD therapy are unsatisfactory is because they target only selected components of an exceedingly complex pathophysiological process, a reality that must be honestly considered if better IBD therapies are to be achieved. Brand new approaches must integrate all relevant factors in their totality - the "omes" - and identify the key controllers of biological responses. This can be accomplished by using systems biology-based approaches and advanced bioinformatics tools, which together represent the essence of network medicine. This review looks at the past and the present of IBD pathogenesis and therapy, and discusses how to develop new therapies based on a network medicine approach.
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116
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Potdar AA, Dube S, Naito T, Botwin G, Haritunians T, Li D, Yang S, Bilsborough J, Denson LA, Daly M, Targan SR, Fleshner P, Braun J, Kugathasan S, Stappenbeck TS, McGovern DP. Reduced expression of COVID-19 host receptor, ACE2 is associated with small bowel inflammation, more severe disease, and response to anti-TNF therapy in Crohn's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.04.19.20070995. [PMID: 32511625 PMCID: PMC7276052 DOI: 10.1101/2020.04.19.20070995] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Angiotensin-Converting Enzyme 2 ( ACE2 ) has been identified as the host receptor for SARS-coronavirus 2 (SARS-CoV-2) which has infected millions world-wide and likely caused hundreds of thousands of deaths. Utilizing transcriptomic data from four cohorts taken from Crohn's disease (CD) and non-inflammatory bowel disease (IBD) subjects, we observed evidence of increased ACE2 mRNA in ileum with demographic features that have been associated with poor outcomes in COVID-19 including age and raised BMI. ACE2 was downregulated in CD compared to controls in independent cohorts. Within CD, ACE2 expression was reduced in inflamed ileal tissue and also remarkably, from uninvolved tissue in patients with a worse prognosis in both adult and pediatric cohorts. In active CD, small bowel ACE2 expression was restored by anti-TNF therapy particularly in anti-TNF responders. Collectively our data suggest that ACE2 downregulation is associated with inflammation and worse outcomes in CD.
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Affiliation(s)
- Alka A. Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shishir Dube
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Takeo Naito
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gregory Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shaohong Yang
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Janine Bilsborough
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lee A. Denson
- Division of Pediatric Gastroenterology, Hepatology, and nutrition, Department of Pediatrics, University of Cincinnati college of Medicine and the Cincinnati children’s Hospital Medical center, Cincinnati, OH, USA
| | - Mark Daly
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Phillip Fleshner
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA; Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | | | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
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Sun H, Lin M, Zamani A, Goldsmith JR, Boggs AE, Li M, Lee CN, Chen X, Li X, Li T, Dorrity BL, Li N, Lou Y, Shi S, Wang W, Chen YH. The TIPE Molecular Pilot That Directs Lymphocyte Migration in Health and Inflammation. Sci Rep 2020; 10:6617. [PMID: 32313148 PMCID: PMC7170861 DOI: 10.1038/s41598-020-63629-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/01/2020] [Indexed: 12/12/2022] Open
Abstract
Lymphocytes are some of the most motile cells of vertebrates, constantly navigating through various organ systems. Their specific positioning in the body is delicately controlled by site-specific directional cues such as chemokines. While it has long been suspected that an intrinsic molecular pilot, akin to a ship's pilot, guides lymphocyte navigation, the nature of this pilot is unknown. Here we show that the TIPE (TNF-α-induced protein 8-like) family of proteins pilot lymphocytes by steering them toward chemokines. TIPE proteins are carriers of lipid second messengers. They mediate chemokine-induced local generation of phosphoinositide second messengers, but inhibit global activation of the small GTPase Rac. TIPE-deficient T lymphocytes are completely pilot-less: they are unable to migrate toward chemokines despite their normal ability to move randomly. As a consequence, TIPE-deficient mice have a marked defect in positioning their T lymphocytes to various tissues, both at the steady-state and during inflammation. Thus, TIPE proteins pilot lymphocytes during migration and may be targeted for the treatment of lymphocyte-related disorders.
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Affiliation(s)
- Honghong Sun
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mei Lin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ali Zamani
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason R Goldsmith
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda E Boggs
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mingyue Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chin-Nien Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xu Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xinyuan Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ting Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brigid L Dorrity
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ning Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yunwei Lou
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Songlin Shi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wei Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Youhai H Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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118
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Zhang J, Xu M, Zhou W, Li D, Zhang H, Chen Y, Ning L, Zhang Y, Li S, Yu M, Chen Y, Zeng H, Cen L, Zhou T, Zhou X, Lu C, Yu C, Li Y, Sun J, Kong X, Shen Z. Deficiency in the anti-apoptotic protein DJ-1 promotes intestinal epithelial cell apoptosis and aggravates inflammatory bowel disease via p53. J Biol Chem 2020; 295:4237-4251. [PMID: 32075910 PMCID: PMC7105307 DOI: 10.1074/jbc.ra119.010143] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 02/11/2020] [Indexed: 12/31/2022] Open
Abstract
Parkinson disease autosomal recessive, early onset 7 (PARK7 or DJ-1) is involved in multiple physiological processes and exerts anti-apoptotic effects on multiple cell types. Increased intestinal epithelial cell (IEC) apoptosis and excessive activation of the p53 signaling pathway is a hallmark of inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD). However, whether DJ-1 plays a role in colitis is unclear. To determine whether DJ-1 deficiency is involved in the p53 activation that results in IEC apoptosis in colitis, here we performed immunostaining, real-time PCR, and immunoblotting analyses to assess DJ-1 expression in human UC and CD samples. In the inflamed intestines of individuals with IBD, DJ-1 expression was decreased and negatively correlated with p53 expression. DJ-1 deficiency significantly aggravated colitis, evidenced by increased intestinal inflammation and exacerbated IEC apoptosis. Moreover, DJ-1 directly interacted with p53, and reduced DJ-1 levels increased p53 levels both in vivo and in vitro and were associated with decreased p53 degradation via the lysosomal pathway. We also induced experimental colitis with dextran sulfate sodium in mice and found that compared with DJ-1-/- mice, DJ-1-/-p53-/- mice have reduced apoptosis and inflammation and increased epithelial barrier integrity. Furthermore, pharmacological inhibition of p53 relieved inflammation in the DJ-1-/- mice. In conclusion, reduced DJ-1 expression promotes inflammation and IEC apoptosis via p53 in colitis, suggesting that the modulation of DJ-1 expression may be a potential therapeutic strategy for managing colitis.
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Affiliation(s)
- Jie Zhang
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Min Xu
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Weihua Zhou
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Dejian Li
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Hong Zhang
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Yi Chen
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Longgui Ning
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Yuwei Zhang
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Sha Li
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Mengli Yu
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Yishu Chen
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Hang Zeng
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Li Cen
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Tianyu Zhou
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Xinxin Zhou
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Chao Lu
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Chaohui Yu
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Youming Li
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
| | - Jing Sun
- Department of Gastroenterology, Rui Jin Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China.
| | - Xiaoni Kong
- Institute of Clinical Immunology, Department of Liver Diseases, ShuGuang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China.
| | - Zhe Shen
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
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119
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Kaiko GE, Chen F, Lai CW, Chiang IL, Perrigoue J, Stojmirović A, Li K, Muegge BD, Jain U, VanDussen KL, Goggins BJ, Keely S, Weaver J, Foster PS, Lawrence DA, Liu TC, Stappenbeck TS. PAI-1 augments mucosal damage in colitis. Sci Transl Med 2020; 11:11/482/eaat0852. [PMID: 30842312 DOI: 10.1126/scitranslmed.aat0852] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 10/10/2018] [Accepted: 02/12/2019] [Indexed: 12/13/2022]
Abstract
There is a major unmet clinical need to identify pathways in inflammatory bowel disease (IBD) to classify patient disease activity, stratify patients that will benefit from targeted therapies such as anti-tumor necrosis factor (TNF), and identify new therapeutic targets. In this study, we conducted global transcriptome analysis to identify IBD-related pathways using colon biopsies, which highlighted the coagulation gene pathway as one of the most enriched gene sets in patients with IBD. Using this gene-network analysis across 14 independent cohorts and 1800 intestinal biopsies, we found that, among the coagulation pathway genes, plasminogen activator inhibitor-1 (PAI-1) expression was highly enriched in active disease and in patients with IBD who did not respond to anti-TNF biologic therapy and that PAI-1 is a key link between the epithelium and inflammation. Functionally, PAI-1 and its direct target, the fibrinolytic protease tissue plasminogen activator (tPA), played an important role in regulating intestinal inflammation. Intestinal epithelial cells produced tPA, which was protective against chemical and mechanical-mediated colonic injury in mice. In contrast, PAI-1 exacerbated mucosal damage by blocking tPA-mediated cleavage and activation of anti-inflammatory TGF-β, whereas the inhibition of PAI-1 reduced both mucosal damage and inflammation. This study identifies an immune-coagulation gene axis in IBD where elevated PAI-1 may contribute to more aggressive disease.
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Affiliation(s)
- Gerard E Kaiko
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Feidi Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chin-Wen Lai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - I-Ling Chiang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | | | - Katherine Li
- Janssen Research & Development LLC, Spring House, PA 19002, USA
| | - Brian D Muegge
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Bridie J Goggins
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Jessica Weaver
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Paul S Foster
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Daniel A Lawrence
- Departments of Pathology and Internal Medicine, Division of Cardiovascular Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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120
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Sayed IM, Suarez K, Lim E, Singh S, Pereira M, Ibeawuchi SR, Katkar G, Dunkel Y, Mittal Y, Chattopadhyay R, Guma M, Boland BS, Dulai PS, Sandborn WJ, Ghosh P, Das S. Host engulfment pathway controls inflammation in inflammatory bowel disease. FEBS J 2020; 287:3967-3988. [PMID: 32003126 DOI: 10.1111/febs.15236] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 12/20/2019] [Accepted: 01/29/2020] [Indexed: 12/13/2022]
Abstract
Chronic diseases, including inflammatory bowel disease (IBD) urgently need new biomarkers as a significant proportion of patients, do not respond to current medications. Inflammation is a common factor in these diseases, and microbial sensing in the intestinal tract is critical to initiate the inflammation. We have identified ELMO1 (engulfment and cell motility protein 1) as a microbial sensor in epithelial and phagocytic cells that turns on inflammatory signals. Using a stem cell-based 'gut-in-a-dish' coculture model, we studied the interactions between microbes, epithelium, and monocytes in the context of IBD. To mimic the in vivo cell physiology, enteroid-derived monolayers (EDMs) were generated from the organoids isolated from WT and ELMO1-/- mice and colonic biopsies of IBD patients. The EDMs were infected with the IBD-associated microbes to monitor the inflammatory responses. ELMO1-depleted EDMs displayed a significant reduction in bacterial internalization, a decrease in pro-inflammatory cytokine productions and monocyte recruitment. The expression of ELMO1 is elevated in the colonic epithelium and in the inflammatory infiltrates within the lamina propria of IBD patients where the higher expression is positively correlated with the elevated expression of pro-inflammatory cytokines, MCP-1 and TNF-α. MCP-1 is released from the epithelium and recruits monocytes to the site of inflammation. Once recruited, monocytes require ELMO1 to engulf the bacteria and propagate a robust TNF-α storm. These findings highlight that the dysregulated epithelial ELMO1 → MCP-1 axis can serve as an early biomarker in the diagnostics of IBD and other inflammatory disorders.
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Affiliation(s)
- Ibrahim M Sayed
- Department of Pathology, University of California, San Diego, CA, USA
| | - Katherine Suarez
- Department of Pathology, University of California, San Diego, CA, USA
| | - Eileen Lim
- Department of Pathology, University of California, San Diego, CA, USA
| | - Sujay Singh
- Department of Pathology, University of California, San Diego, CA, USA
| | - Matheus Pereira
- Department of Pathology, University of California, San Diego, CA, USA
| | | | - Gajanan Katkar
- Department of Cellular & Molecular Medicine, University of California, San Diego, CA, USA
| | - Ying Dunkel
- Department of Medicine, University of California, San Diego, CA, USA
| | - Yash Mittal
- Department of Medicine, University of California, San Diego, CA, USA
| | - Ranajoy Chattopadhyay
- Department of Cellular & Molecular Medicine, University of California, San Diego, CA, USA
| | - Monica Guma
- Department of Medicine, University of California, San Diego, CA, USA
| | - Brigid S Boland
- Department of Medicine, University of California, San Diego, CA, USA
| | - Parambir S Dulai
- Department of Medicine, University of California, San Diego, CA, USA
| | | | - Pradipta Ghosh
- Department of Medicine, University of California, San Diego, CA, USA.,Department of Cellular & Molecular Medicine, University of California, San Diego, CA, USA
| | - Soumita Das
- Department of Pathology, University of California, San Diego, CA, USA
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121
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Schleier L, Wiendl M, Heidbreder K, Binder MT, Atreya R, Rath T, Becker E, Schulz-Kuhnt A, Stahl A, Schulze LL, Ullrich K, Merz SF, Bornemann L, Gunzer M, Watson AJM, Neufert C, Atreya I, Neurath MF, Zundler S. Non-classical monocyte homing to the gut via α4β7 integrin mediates macrophage-dependent intestinal wound healing. Gut 2020; 69:252-263. [PMID: 31092589 DOI: 10.1136/gutjnl-2018-316772] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 04/12/2019] [Accepted: 04/17/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To study the role of α4β7 integrin for gut homing of monocytes and to explore the biological consequences of therapeutic α4β7 inhibition with regard to intestinal wound healing. DESIGN We studied the expression of homing markers on monocyte subsets in the peripheral blood and on macrophage subsets in the gut of patients with IBD and controls with flow cytometry and immunohistochemistry. Integrin function was addressed with dynamic adhesion assays and in vivo gut homing assays. In vivo wound healing was studied in mice deficient for or depleted of α4β7 integrin. RESULTS Classical and non-classical monocytes were clearly dichotomous regarding homing marker expression including relevant expression of α4β7 integrin on human and mouse non-classical monocytes but not on classical monocytes. Monocyte-expressed α4β7 integrin was functionally important for dynamic adhesion to mucosal vascular addressin cell adhesion molecule 1 and in vivo gut homing. Impaired α4β7-dependent gut homing was associated with reduced (effect size about 20%) and delayed wound healing and suppressed perilesional presence of wound healing macrophages. Non-classical monocytes in the peripheral blood were increased in patients with IBD under clinical treatment with vedolizumab. CONCLUSION In addition to reported effects on lymphocytes, anti-α4β7 therapy in IBD also targets non-classical monocytes. Impaired gut homing of such monocytes might lead to a reduction of wound healing macrophages and could potentially explain increased rates of postoperative complications in vedolizumab-treated patients, which have been observed in some studies.
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Affiliation(s)
- Lena Schleier
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Maximilian Wiendl
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Karin Heidbreder
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Marie-Theres Binder
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Raja Atreya
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Timo Rath
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Emily Becker
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Anja Schulz-Kuhnt
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Annette Stahl
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Lisa Lou Schulze
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Karen Ullrich
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Simon F Merz
- Institute of Experimental Immunology and Imaging, University Duisburg-Essen and University Hospital Essen, Essen, Germany
| | - Lea Bornemann
- Institute of Experimental Immunology and Imaging, University Duisburg-Essen and University Hospital Essen, Essen, Germany
| | - Matthias Gunzer
- Institute of Experimental Immunology and Imaging, University Duisburg-Essen and University Hospital Essen, Essen, Germany
| | - Alastair J M Watson
- Norwich Medical School, Norwich Research Park, University of East Anglia, Norwich, UK
| | - Clemens Neufert
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Imke Atreya
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Sebastian Zundler
- Department of Medicine 1, Kussmaul Campus for Medical Research & Translational Research Center, University of Erlangen-Nuremberg, Erlangen, Germany
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122
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Dwivedi SKD, Shameer K, Dey A, Mustafi SB, Xiong X, Bhattacharya U, Neizer-Ashun F, Rao G, Wang Y, Ivan C, Yang D, Dudley JT, Xu C, Wren JD, Mukherjee P, Bhattacharya R. KRCC1: A potential therapeutic target in ovarian cancer. FASEB J 2019; 34:2287-2300. [PMID: 31908025 DOI: 10.1096/fj.201902259r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/14/2019] [Accepted: 11/25/2019] [Indexed: 01/11/2023]
Abstract
Using a systems biology approach to prioritize potential points of intervention in ovarian cancer, we identified the lysine rich coiled-coil 1 (KRCC1), as a potential target. High-grade serous ovarian cancer patient tumors and cells express significantly higher levels of KRCC1 which correlates with poor overall survival and chemoresistance. We demonstrate that KRCC1 is predominantly present in the chromatin-bound nuclear fraction, interacts with HDAC1, HDAC2, and with the serine-threonine phosphatase PP1CC. Silencing KRCC1 inhibits cellular plasticity, invasive properties, and potentiates apoptosis resulting in reduced tumor growth. These phenotypes are associated with increased acetylation of histones and with increased phosphorylation of H2AX and CHK1, suggesting the modulation of transcription and DNA damage that may be mediated by the action of HDAC and PP1CC, respectively. Hence, we address an urgent need to develop new targets in cancer.
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Affiliation(s)
| | - Khader Shameer
- Institute of Next Generation Healthcare (INGH), Icahn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
| | - Anindya Dey
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | | | - Xunhao Xiong
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Udayan Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Fiifi Neizer-Ashun
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Geeta Rao
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Yue Wang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Cristina Ivan
- Department of Experimental Therapeutics & Center for RNA Interference and Non-coding RNA, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Da Yang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joel T Dudley
- Institute of Next Generation Healthcare (INGH), Icahn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
| | - Chao Xu
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jonathan D Wren
- Departments of Biochemistry & Molecular Biology and Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Priyabrata Mukherjee
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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123
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Min HK, Moon SJ, Park KS, Kim KJ. Integrated systems analysis of salivary gland transcriptomics reveals key molecular networks in Sjögren's syndrome. Arthritis Res Ther 2019; 21:294. [PMID: 31856901 PMCID: PMC6921432 DOI: 10.1186/s13075-019-2082-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/04/2019] [Indexed: 02/08/2023] Open
Abstract
Background Treatment of patients with Sjögren’s syndrome (SjS) is a clinical challenge with high unmet needs. Gene expression profiling and integrative network-based approaches to complex disease can offer an insight on molecular characteristics in the context of clinical setting. Methods An integrated dataset was created from salivary gland samples of 30 SjS patients. Pathway-driven enrichment profiles made by gene set enrichment analysis were categorized using hierarchical clustering. Differentially expressed genes (DEGs) were subjected to functional network analysis, where the elements of the core subnetwork were used for key driver analysis. Results We identified 310 upregulated DEGs, including nine known genetic risk factors and two potential biomarkers. The core subnetwork was enriched with the processes associated with B cell hyperactivity. Pathway-based subgrouping revealed two clusters with distinct molecular signatures for the relevant pathways and cell subsets. Cluster 2, with low-grade inflammation, showed a better response to rituximab therapy than cluster 1, with high-grade inflammation. Fourteen key driver genes appeared to be essential signaling mediators downstream of the B cell receptor (BCR) signaling pathway and to have a positive relationship with histopathology scores. Conclusion Integrative network-based approaches provide deep insights into the modules and pathways causally related to SjS and allow identification of key targets for disease. Intervention adjusted to the molecular traits of the disease would allow the achievement of better outcomes, and the BCR signaling pathway and its leading players are promising therapeutic targets.
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Affiliation(s)
- Hong Ki Min
- Division of Rheumatology, Department of Internal Medicine, Konkuk University Medical Center, Seoul, Republic of Korea
| | - Su-Jin Moon
- Division of Rheumatology, Department of Internal Medicine, Uijeongbu St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kyung-Su Park
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ki-Jo Kim
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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Balbas-Martinez V, Asin-Prieto E, Parra-Guillen ZP, Troconiz IF. A Quantitative Systems Pharmacology Model for the Key Interleukins Involved in Crohn's Disease. J Pharmacol Exp Ther 2019; 372:299-307. [DOI: 10.1124/jpet.119.260539] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
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125
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Fujita Y, Khateb A, Li Y, Tinoco R, Zhang T, Bar-Yoseph H, Tam MA, Chowers Y, Sabo E, Gerassy-Vainberg S, Starosvetsky E, James B, Brown K, Shen-Orr SS, Bradley LM, Tessier PA, Ronai ZA. Regulation of S100A8 Stability by RNF5 in Intestinal Epithelial Cells Determines Intestinal Inflammation and Severity of Colitis. Cell Rep 2019; 24:3296-3311.e6. [PMID: 30232010 PMCID: PMC6185744 DOI: 10.1016/j.celrep.2018.08.057] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 07/29/2018] [Accepted: 08/17/2018] [Indexed: 12/11/2022] Open
Abstract
Inflammatory bowel disease (IBD) is prevalent, but the mechanisms underlying disease development remain elusive. We identify a role for the E3 ubiquitin ligase RNF5 in IBD. Intestinal epithelial cells (IECs) express a high level of RNF5, while the colon of Rnf5−/− mice exhibits activated dendritic cells and intrinsic inflammation. Rnf5−/− mice exhibit severe acute colitis following dextran sodium sulfate (DSS) treatment. S100A8 is identified as an RNF5 substrate, resulting in S100A8 ubiquitination and proteasomal-dependent degradation that is attenuated upon inflammatory stimuli. Loss of RNF5 from IECs leads to enhanced S100A8 secretion, which induces mucosal CD4+ T cells, resulting in Th1 pro-inflammatory responses. Administration of S100A8-neutralizing antibodies to DSS-treated Rnf5−/− mice attenuates acute colitis development and increases survival. An inverse correlation between RNF5 and S100A8 protein expression in IECs of IBD patients coincides with disease severity. Collectively, RNF5-mediated regulation of S100A8 stability in IECs is required for the maintenance of intestinal homeostasis. Fujita et al. show that RNF5 regulation of S100A8 stability in intestinal epithelial cells defines the degree of pro-inflammatory response, culminating in severe intestinal inflammation following DSS treatment to Rnf5−/− mice. Neutralizing S100A8 antibodies attenuates acute colitis phenotypes, and inverse RNF5/S100A8 expression coincides with clinical severity in IBD patients.
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Affiliation(s)
- Yu Fujita
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Ali Khateb
- Technion Integrated Cancer Center, Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, 31096, Israel
| | - Yan Li
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Roberto Tinoco
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Haggai Bar-Yoseph
- Rambam Health Care Campus, Gastroenterology Institute, Haifa, 31096, Israel
| | | | - Yehuda Chowers
- Rambam Health Care Campus, Gastroenterology Institute, Haifa, 31096, Israel
| | - Edmond Sabo
- Pathology Division, Carmel Medical Center, Haifa, 34362, Israel
| | - Shiran Gerassy-Vainberg
- Technion Integrated Cancer Center, Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, 31096, Israel
| | - Elina Starosvetsky
- Technion Integrated Cancer Center, Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, 31096, Israel
| | - Brian James
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Kevin Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shai S Shen-Orr
- Technion Integrated Cancer Center, Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, 31096, Israel
| | - Linda M Bradley
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Philippe A Tessier
- Centre de Recherche du Centre Hospitalier de l'Université Laval, Sainte-Foy, Quebec, QC G1V 4G2, Canada
| | - Ze'ev A Ronai
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Technion Integrated Cancer Center, Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, 31096, Israel.
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A Comprehensive Review and Update on the Pathogenesis of Inflammatory Bowel Disease. J Immunol Res 2019; 2019:7247238. [PMID: 31886308 PMCID: PMC6914932 DOI: 10.1155/2019/7247238] [Citation(s) in RCA: 435] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic and life-threating inflammatory disease of gastroenteric tissue characterized by episodes of intestinal inflammation. The pathogenesis of IBD is complex. Recent studies have greatly improved our knowledge of the pathophysiology of IBD, leading to great advances in the treatment as well as diagnosis of IBD. In this review, we have systemically reviewed the pathogenesis of IBD and highlighted recent advances in host genetic factors, gut microbiota, and environmental factors and, especially, in abnormal innate and adaptive immune responses and their interactions, which may hold the keys to identify novel predictive or prognostic biomarkers and develop new therapies.
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127
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Rennard SI. Advancing Chronic Obstructive Pulmonary Disease Therapy: Opportunities, Challenges, and Excitement. Am J Respir Cell Mol Biol 2019; 60:1-2. [PMID: 30562048 DOI: 10.1165/rcmb.2018-0288ed] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Stephen I Rennard
- 1 IMED Biotech Unit AstraZeneca Cambridge, United Kingdom and.,2 Department of Internal Medicine University of Nebraska Medical Center Omaha, Nebraska
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Peters DE, Norris LD, Slusher BS. Spontaneous Loss-of-Function Dock2 Mutation Alters Murine Colitis Sensitivity and Is a Confounding Variable in Inflammatory Bowel Disease Research. CROHN'S & COLITIS 360 2019. [DOI: 10.1093/crocol/otz030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AbstractBackgroundDextran sodium sulfate (DSS)-induced colitis is the most commonly used mouse model of inflammatory bowel disease (IBD) due to its acute nature, reproducibility, and phenotypic overlap with human disease. Following an unexpected and sharp decline in DSS-induced colitis susceptibility in our commercially acquired C57Bl/6 wild-type mice, we discovered that a spontaneous loss-of-function mutation in dedicator of cytokinesis 2 (Dock2Hsd) was responsible. Presence of this mutation in research colonies has the capacity to broadly impact preclinical IBD studies.MethodsDSS-colitis was induced in weight-, age-, and gender-matched C57Bl/6NHsd mice. Daily treatment with vehicle or the glutamate carboxypeptidase II (GCPII) inhibitor, 2-PMPA (100 mg/kg IP), was performed and disease activity index was monitored. At termination, colon GCPII activity was measured.ResultsDSS-treated Dock2Hsd mice developed more severe colitis, had significantly increased colon GCPII activity and were more sensitive to pharmacologic inhibition of GCPII.ConclusionsThe Dock2Hsd mutation is a confounding variable of high relevance to the IBD research community. Dock2Hsd mice were distributed as wild-type C57Bl/6 for multiple years and thus it is unknown how prevalent this mutation is in investigator-maintained colonies of C57Bl/6-derived mice. In our research, presence of the Dock2Hsd mutation caused enhanced GCPII colon activity more closely resembling human disease, providing a useful platform for screening GCPII inhibitors for preclinical efficacy. However, unanticipated presence of Dock2Hsd in genetically modified mice used to study IBD pathobiology can confound conclusions. Thus, care must be taken when interpreting studies performed in mice of C57Bl/6 lineage where Dock2 status is unknown.
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Affiliation(s)
- Diane E Peters
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lauren D Norris
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Barbara S Slusher
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
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129
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Martin JC, Chang C, Boschetti G, Ungaro R, Giri M, Grout JA, Gettler K, Chuang LS, Nayar S, Greenstein AJ, Dubinsky M, Walker L, Leader A, Fine JS, Whitehurst CE, Mbow ML, Kugathasan S, Denson LA, Hyams JS, Friedman JR, Desai PT, Ko HM, Laface I, Akturk G, Schadt EE, Salmon H, Gnjatic S, Rahman AH, Merad M, Cho JH, Kenigsberg E. Single-Cell Analysis of Crohn's Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy. Cell 2019; 178:1493-1508.e20. [PMID: 31474370 PMCID: PMC7060942 DOI: 10.1016/j.cell.2019.08.008] [Citation(s) in RCA: 460] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 05/06/2019] [Accepted: 08/05/2019] [Indexed: 10/26/2022]
Abstract
Clinical benefits of cytokine blockade in ileal Crohn's disease (iCD) are limited to a subset of patients. Here, we applied single-cell technologies to iCD lesions to address whether cellular heterogeneity contributes to treatment resistance. We found that a subset of patients expressed a unique cellular module in inflamed tissues that consisted of IgG plasma cells, inflammatory mononuclear phagocytes, activated T cells, and stromal cells, which we named the GIMATS module. Analysis of ligand-receptor interaction pairs identified a distinct network connectivity that likely drives the GIMATS module. Strikingly, the GIMATS module was also present in a subset of patients in four independent iCD cohorts (n = 441), and its presence at diagnosis correlated with failure to achieve durable corticosteroid-free remission upon anti-TNF therapy. These results emphasize the limitations of current diagnostic assays and the potential for single-cell mapping tools to identify novel biomarkers of treatment response and tailored therapeutic opportunities.
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Affiliation(s)
- Jerome C Martin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christie Chang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gilles Boschetti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ryan Ungaro
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Mamta Giri
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John A Grout
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kyle Gettler
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ling-Shiang Chuang
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shikha Nayar
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander J Greenstein
- Department of Colorectal Surgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marla Dubinsky
- Department of Pediatrics, Susan and Leonard Feinstein IBD Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Walker
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew Leader
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jay S Fine
- Boehringer Ingelheim Pharmaceuticals, Immunology and Respiratory Diseases Research, Ridgefield, CT 06877, USA
| | - Charles E Whitehurst
- Boehringer Ingelheim Pharmaceuticals, Immunology and Respiratory Diseases Research, Ridgefield, CT 06877, USA
| | - M Lamine Mbow
- Boehringer Ingelheim Pharmaceuticals, Immunology and Respiratory Diseases Research, Ridgefield, CT 06877, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, CT, USA
| | | | | | - Huaibin M Ko
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ilaria Laface
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Guray Akturk
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Helene Salmon
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sacha Gnjatic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adeeb H Rahman
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Judy H Cho
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Ephraim Kenigsberg
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Estill M, Hauser R, Nassan FL, Moss A, Krawetz SA. The effects of di-butyl phthalate exposure from medications on human sperm RNA among men. Sci Rep 2019; 9:12397. [PMID: 31455814 PMCID: PMC6711971 DOI: 10.1038/s41598-019-48441-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/05/2019] [Indexed: 02/08/2023] Open
Abstract
Endocrine disruptors, such as phthalates, are suspected of affecting reproductive function. The Mesalamine and Reproductive Health Study (MARS) was designed to address the physiological effect of in vivo phthalate exposure on male reproduction in patients with Inflammatory Bowel Disease (IBD). As part of this effort, the effect on sperm RNAs to DBP exposure were longitudinally assessed using a cross-over cross-back binary design of high or background, exposures to DBP. As the DBP level was altered, numerous sperm RNA elements (REs) were differentially expressed, suggesting that exposure to or removal from high DBP produces effects that require longer than one spermatogenic cycle to resolve. In comparison, small RNAs were minimally affected by DBP exposure. While initial study medication (high or background) implicates different biological pathways, initiation on the high-DBP condition activated oxidative stress and DNA damage pathways. The negative correlation of REs with specific genomic repeats suggests a regulatory role. Using ejaculated sperm, this work provides insight into the male germline's response to phthalate exposure.
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Affiliation(s)
- Molly Estill
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Russ Hauser
- Vincent Memorial Obstetrics and Gynecology Service, Massachusetts General Hospital, Harvard Medical School, and Departments of Environmental Health and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Feiby L Nassan
- Departments of Environmental Health and Nutrition, Harvard T. H. Chan School of Public Health, MA, 02115, USA
| | - Alan Moss
- Department of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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Abstract
Inflammatory bowel disease (IBD) defines a spectrum of complex disorders. Understanding how environmental risk factors, alterations of the intestinal microbiota, and polygenetic and epigenetic susceptibility impact on immune pathways is key for developing targeted therapies. Mechanistic understanding of polygenic IBD is complemented by Mendelian disorders that present with IBD, pharmacological interventions that cause colitis, autoimmunity, and multiple animal models. Collectively, this multifactorial pathogenesis supports a concept of immune checkpoints that control microbial-host interactions in the gut by modulating innate and adaptive immunity, as well as epithelial and mesenchymal cell responses. In addition to classical immunosuppressive strategies, we discuss how resetting the microbiota and restoring innate immune responses, in particular autophagy and epithelial barrier function, might be key for maintaining remission or preventing IBD. Targeting checkpoints in genetically stratified subgroups of patients with Mendelian disorder-associated IBD increasingly directs treatment strategies as part of personalized medicine.
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Affiliation(s)
- Holm H Uhlig
- Department of Pediatrics, University of Oxford, Oxford OX3 9DU, United Kingdom; .,Translational Gastroenterology Unit, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; .,Translational Gastroenterology Unit, University of Oxford, Oxford OX3 9DU, United Kingdom
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Liu YR, Hu Y, Zeng Y, Li ZX, Zhang HB, Deng JL, Wang G. Neurexophilin and PC-esterase domain family member 4 (NXPE4) and prostate androgen-regulated mucin-like protein 1 (PARM1) as prognostic biomarkers for colorectal cancer. J Cell Biochem 2019; 120:18041-18052. [PMID: 31297877 DOI: 10.1002/jcb.29107] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/18/2019] [Indexed: 12/24/2022]
Abstract
Owing to the high morbidity and mortality, novel biomarkers in the occurrence and development of colorectal cancer (CRC) are needed nowadays. In this study, the CRC-related datasets were downloaded from the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database. After screening the differentially expressed genes (DEGs) in R software, a total of 238 upregulated and 199 downregulated DEGs were revealed simultaneously. Then the Kaplan-Meier survival analysis and Cox regression analysis were used to reveal the prognostic function of these DEGs. Neurexophilin and PC-esterase domain family member 4 (NXPE4) and prostate androgen-regulated mucin-like protein 1 (PARM1) were two outstanding independent overall survival (OS) and relapse-free survival (RFS) prognostic genes of CRC in TCGA database. We next verified the expression of NXPE4 and PARM1 messenger RNA (mRNA) levels were significantly lower in CRC tumor tissue than in the adjacent noncancerous tissue in our clinical samples, and NXPE4 mRNA expression level was related to the tumor location and tumor size, while PARM1 was related to tumor location, lymph nodes metastasis, and tumor size. This study demonstrated that NXPE4 and PARM1 might be two potential novel prognostic biomarkers for CRC.
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Affiliation(s)
- Ya-Rui Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Yang Hu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Ying Zeng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Zhi-Xing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Hai-Bo Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Jun-Li Deng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
| | - Guo Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, P. R. China
- National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, P.R. China
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Silva F, Gatica T, Pavez C. ETIOLOGÍA Y FISIOPATOLOGÍA DE LA ENFERMEDAD INFLAMATORIA INTESTINAL. REVISTA MÉDICA CLÍNICA LAS CONDES 2019. [DOI: 10.1016/j.rmclc.2019.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Ulugöl S, Hering L, Manzini R, Montalban Arques A, Gottier C, Lang S, Scharl M, Spalinger MR. Deletion of Protein Tyrosine Phosphatase Nonreceptor Type 2 in Intestinal Epithelial Cells Results in Upregulation of the Related Phosphatase Protein Tyrosine Phosphatase Nonreceptor Type 23. Inflamm Intest Dis 2019; 4:14-26. [PMID: 31172009 DOI: 10.1159/000499157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/27/2019] [Indexed: 12/17/2022] Open
Abstract
Background/Aims Knockdown of protein tyrosine phosphatase nonreceptor type 2 (PTPN2) exaggerates IFN-γ-induced intestinal barrier defects, but mice constitutively lacking PTPN2 in epithelial cells (PTPN2xVilCre mice) do not show changes in epithelial function or enhanced susceptibility to experimental colitis. Here, we investigated whether PTPN2 modulates the expression of related tyrosine phosphatases. Methods PTPN2 knockdown in HT-29 cells was induced using siRNA constructs. Acute colitis in PTPN2xVilCre mice was induced by 2% dextran sulfate sodium (DSS) in drinking water for 7 days. Colitis-associated tumors were induced by injection of azoxymethane prior to treatment with DSS for 3 consecutive cycles. Results In HT-29 cells, PTPN2 depletion resulted in enhanced mRNA expression of PTPN11 and PTPN23 and in parallel to upregulation of IL-18 mRNA upon treatment with TNF for 24 h. DSS treatment of PTPN2-deficient mice resulted in a strong induction of Ptpn23 mRNA in colon tissue in vivo. In the tumor model, Ptpn23 mRNA was again clearly upregulated in nontumor tissue from PTPN2-deficient mice; however, this was not observed in tumor tissue. Conclusions Our experiments show that PTPN23 function might, at least partially, compensate lack of PTPN2 in epithelial cells. Upregulation of PTPN23 might therefore crucially contribute to the lack of a colitis phenotype in PTPN2-VilCre mice.
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Affiliation(s)
- Sima Ulugöl
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Larissa Hering
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Roberto Manzini
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ana Montalban Arques
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Claudia Gottier
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Silvia Lang
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Scharl
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Zurich Institute for Human Physiology, University of Zurich, Zurich, Switzerland
| | - Marianne R Spalinger
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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135
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Shi W, Zou R, Yang M, Mai L, Ren J, Wen J, Liu Z, Lai R. Analysis of Genes Involved in Ulcerative Colitis Activity and Tumorigenesis Through Systematic Mining of Gene Co-expression Networks. Front Physiol 2019; 10:662. [PMID: 31214045 PMCID: PMC6554330 DOI: 10.3389/fphys.2019.00662] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 05/09/2019] [Indexed: 12/12/2022] Open
Abstract
Ulcerative colitis (UC) is an idiopathic, chronic inflammatory disorder of the colon, characterized by continuous mucosal inflammation. Recently, some studies have considered it as part of an inflammatory bowel disease-based global network. Herein, with the aim of identifying the underlying potential genetic mechanisms involved in the development of UC, multiple algorithms for weighted correlation network analysis (WGCNA), principal component analysis (PCA), and linear models for microarray data algorithm (LIMMA) were used to identify the hub genes. The map of platelet activation, ligand-receptor interaction, calcium signaling pathway, and cAMP signaling pathway showed significant links with UC development, and the hub genes CCR7, CXCL10, CXCL9, IDO1, MMP9, and VCAM1, which are associated with immune dysregulation and tumorigenesis in biological function, were found by multiple powerful bioinformatics methods. Analysis of The Cancer Genome Atlas (TCGA) also showed that the low expression of CCR7, CXCL10, CXCL9, and MMP9 may be correlated with a poor prognosis of overall survival (OS) in colorectal cancer (CRC) patients (all p < 0.05), while no significance detected in both of IDO1 and VCAM1. In addition, low expression of CCR7, CXCL10, CXCL9, MMP9, and IDO1 may be associated with a poor prognosis in recurrence free survival (RFS) time (all p < 0.05), but no significant difference was identified in VCAM1. Moreover, the NFKB1, FLI1, and STAT1 with the highest enrichment score were detected as the master regulators of hub genes. In summary, these results indicated the central role of the hub genes of CCR7, CXCL10, CXCL9, IDO1, VCAM1, and MMP9, in response to UC progression, as well as the development of UC to CRC, thus shedding light on the molecular mechanisms involved and assisting with drug target validation.
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Affiliation(s)
- Wanting Shi
- Department of Gastroenterology, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.,Digestive Endoscopy Center, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Rongjun Zou
- Department of Cardiovascular Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minglei Yang
- Department of Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Lei Mai
- Department of Gastroenterology, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Jiangnan Ren
- Digestive Endoscopy Center, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Jialing Wen
- Guangdong Institute of Gastroenterology, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhaoshi Liu
- Department of Gastroenterology, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.,Digestive Endoscopy Center, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Renxu Lai
- Department of Gastroenterology, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.,Digestive Endoscopy Center, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
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136
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Peters A, Krumbholz P, Jäger E, Heintz-Buschart A, Çakir MV, Rothemund S, Gaudl A, Ceglarek U, Schöneberg T, Stäubert C. Metabolites of lactic acid bacteria present in fermented foods are highly potent agonists of human hydroxycarboxylic acid receptor 3. PLoS Genet 2019; 15:e1008145. [PMID: 31120900 PMCID: PMC6532841 DOI: 10.1371/journal.pgen.1008145] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 04/10/2019] [Indexed: 02/02/2023] Open
Abstract
The interplay of microbiota and the human host is physiologically crucial in health and diseases. The beneficial effects of lactic acid bacteria (LAB), permanently colonizing the human intestine or transiently obtained from food, have been extensively reported. However, the molecular understanding of how LAB modulate human physiology is still limited. G protein-coupled receptors for hydroxycarboxylic acids (HCAR) are regulators of immune functions and energy homeostasis under changing metabolic and dietary conditions. Most mammals have two HCAR (HCA1, HCA2) but humans and other hominids contain a third member (HCA3) in their genomes. A plausible hypothesis why HCA3 function was advantageous in hominid evolution was lacking. Here, we used a combination of evolutionary, analytical and functional methods to unravel the role of HCA3in vitro and in vivo. The functional studies included different pharmacological assays, analyses of human monocytes and pharmacokinetic measurements in human. We report the discovery of the interaction of D-phenyllactic acid (D-PLA) and the human host through highly potent activation of HCA3. D-PLA is an anti-bacterial metabolite found in high concentrations in LAB-fermented food such as Sauerkraut. We demonstrate that D-PLA from such alimentary sources is well absorbed from the human gut leading to high plasma and urine levels and triggers pertussis toxin-sensitive migration of primary human monocytes in an HCA3-dependent manner. We provide evolutionary, analytical and functional evidence supporting the hypothesis that HCA3 was consolidated in hominids as a new signaling system for LAB-derived metabolites. Although it has been known for 15 years that HCA3 is present in humans and other hominids but absent in all other mammals, no study so far aimed to understand why HCA3 was functionally preserved during evolution. Here, we take advantage of evolutionary analyses which we combine with functional assays of hominid HCA3 orthologs. In search for a reasonable scenario explaining the accumulated amino acid changes in HCA3 of hominids we discovered D-phenyllactic acid (D-PLA), a metabolite produced by lactic acid bacteria (LAB), as the so far most potent agonist specifically activating HCA3. Further, oral ingestion of Sauerkraut, known to contain high levels of D-PLA, caused subsequent plasma concentrations sufficient to activate HCA3. Our data interpreted in an evolutionary context suggests that the availability of a new food repertoire under changed ecological conditions triggered the fixation of HCA3 which took over new functions in hominids. These findings are particularly important because they unveiled HCA3, which is not only expressed in various immune cells but also adipocytes, lung and skin, as a player that transfers signals of LAB-derived metabolites into a physiological response in humans. This opens up new directions towards the understanding of the versatile beneficial effects of LAB and their metabolites for humans.
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Affiliation(s)
- Anna Peters
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Petra Krumbholz
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Elisabeth Jäger
- Department of Internal Medicine, Division of Rheumatology, Leipzig University, Leipzig, Germany
| | - Anna Heintz-Buschart
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Helmholtz-Centre for Environmental Research GmbH - UFZ, Department of Soil Ecology, Halle (Saale), Germany
| | - Mehmet Volkan Çakir
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Sven Rothemund
- Core Unit Peptide-Technologies, Leipzig University, Leipzig, Germany
| | - Alexander Gaudl
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Uta Ceglarek
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Claudia Stäubert
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany
- * E-mail:
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137
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Common functional alterations identified in blood transcriptome of autoimmune cholestatic liver and inflammatory bowel diseases. Sci Rep 2019; 9:7190. [PMID: 31076612 PMCID: PMC6510750 DOI: 10.1038/s41598-019-43699-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
Primary biliary cholangitis (PBC), primary sclerosing cholangitis (PSC), and inflammatory bowel diseases (IBDs), including Crohn’s disease (CD) and ulcerative colitis (UC), are heterogeneous chronic autoimmune diseases that may share underlying pathogenic mechanisms. Herein, we compared simultaneously analyzed blood transcriptomes from patients with PBC, PSC, and IBD. Microarray-based measurements were conducted using RNA isolated from whole blood samples from 90, 45, 95 and 93 patients with PBC, PSC, CD, and UC, respectively, and 47 healthy controls. Expression levels of selected transcripts were analyzed by quantitative reverse-transcribed PCR using an independent cohort of 292, 71 and 727 patients with PBC, PSC, and IBD, respectively. Of 4026, 2650 and 4967 probe sets differentially expressed (adjusted p-value < 0.05) in samples from patients with PBC, PSC, and IBD, respectively, compared with healthy controls, 1946 were common to all three comparisons. Functional analyses indicated that most terms enriched for genes differentially expressed in PBC, PSC, and IBD patients compared with healthy controls were related to mitochondrial function, the vesicle endomembrane system, and GTPase-mediated processes. This study indicates that microarray-based profiling of blood gene expression supports research into the molecular mechanisms underlying disease, rather than being useful for selection of diagnostic biomarkers for use in clinical practice.
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138
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Kim SS, Dai C, Hormozdiari F, van de Geijn B, Gazal S, Park Y, O'Connor L, Amariuta T, Loh PR, Finucane H, Raychaudhuri S, Price AL. Genes with High Network Connectivity Are Enriched for Disease Heritability. Am J Hum Genet 2019; 104:896-913. [PMID: 31051114 PMCID: PMC6506868 DOI: 10.1016/j.ajhg.2019.03.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/20/2019] [Indexed: 12/13/2022] Open
Abstract
Recent studies have highlighted the role of gene networks in disease biology. To formally assess this, we constructed a broad set of pathway, network, and pathway+network annotations and applied stratified LD score regression to 42 diseases and complex traits (average N = 323K) to identify enriched annotations. First, we analyzed 18,119 biological pathways. We identified 156 pathway-trait pairs whose disease enrichment was statistically significant (FDR < 5%) after conditioning on all genes and 75 known functional annotations (from the baseline-LD model), a stringent step that greatly reduced the number of pathways detected; most significant pathway-trait pairs were previously unreported. Next, for each of four published gene networks, we constructed probabilistic annotations based on network connectivity. For each gene network, the network connectivity annotation was strongly significantly enriched. Surprisingly, the enrichments were fully explained by excess overlap between network annotations and regulatory annotations from the baseline-LD model, validating the informativeness of the baseline-LD model and emphasizing the importance of accounting for regulatory annotations in gene network analyses. Finally, for each of the 156 enriched pathway-trait pairs, for each of the four gene networks, we constructed pathway+network annotations by annotating genes with high network connectivity to the input pathway. For each gene network, these pathway+network annotations were strongly significantly enriched for the corresponding traits. Once again, the enrichments were largely explained by the baseline-LD model. In conclusion, gene network connectivity is highly informative for disease architectures, but the information in gene networks may be subsumed by regulatory annotations, emphasizing the importance of accounting for known annotations.
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Affiliation(s)
- Samuel S Kim
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Chengzhen Dai
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Farhad Hormozdiari
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Bryce van de Geijn
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Steven Gazal
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Yongjin Park
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Luke O'Connor
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA 02138, USA
| | - Tiffany Amariuta
- Program in Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA 02138, USA
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hilary Finucane
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Soumya Raychaudhuri
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alkes L Price
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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139
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Meddens CA, van der List ACJ, Nieuwenhuis EES, Mokry M. Non-coding DNA in IBD: from sequence variation in DNA regulatory elements to novel therapeutic potential. Gut 2019; 68:928-941. [PMID: 30692146 DOI: 10.1136/gutjnl-2018-317516] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 12/13/2022]
Abstract
Genome-wide association studies have identified over 200 loci associated with IBD. We and others have recently shown that, in addition to variants in protein-coding genes, the majority of the associated loci are related to DNA regulatory elements (DREs). These findings add a dimension to the already complex genetic background of IBD. In this review we summarise the existing evidence on the role of DREs in IBD. We discuss how epigenetic research can be used in candidate gene approaches that take non-coding variants into account and can help to pinpoint the essential pathways and cell types in the pathogenesis of IBD. Despite the increased level of genetic complexity, these findings can contribute to novel therapeutic options that target transcription factor binding and enhancer activity. Finally, we summarise the future directions and challenges of this emerging field.
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Affiliation(s)
- Claartje Aleid Meddens
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Michal Mokry
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
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140
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Chapuy L, Bsat M, Sarkizova S, Rubio M, Therrien A, Wassef E, Bouin M, Orlicka K, Weber A, Hacohen N, Villani AC, Sarfati M. Two distinct colonic CD14 + subsets characterized by single-cell RNA profiling in Crohn's disease. Mucosal Immunol 2019; 12:703-719. [PMID: 30670762 DOI: 10.1038/s41385-018-0126-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/05/2018] [Accepted: 12/11/2018] [Indexed: 02/04/2023]
Abstract
Inflammatory bowel diseases are associated with dysregulated immune responses in the intestinal tissue. Four molecularly identified macrophage subsets control immune homeostasis in healthy gut. However, the specific roles and transcriptomic profiles of the phenotypically heterogeneous CD14+ macrophage-like population in inflamed gut remain to be investigated in Crohn's disease (CD). Here we identified two phenotypically, morphologically and functionally distinct colonic HLADR+SIRPα+CD14+ subpopulations that were further characterized using single-cell RNA-sequencing (scRNAseq) in CD. Frequencies of CD64hiCD163-/dim cells selectively augmented in inflamed colon and correlated with endoscopic score of disease severity. IL-1β and IL-23-producing CD64hiCD163-/dim cells predominated over TNF-α-producing CD64hiCD163hi cells in lesions. Purified "inflammatory monocyte-like" CD163-, but not "macrophage-like" CD163hi cells, through IL-1β, promoted Th17/Th1 but not Th1 responses in tissue memory CD4+T cells. Unsupervised scRNAseq analysis that captures the entire HLADR+SIRPα+ population revealed six clusters, two of which were enriched in either CD163- or CD163hi cells, and best defined by TREM1/FCAR/FCN1/IL1RN or CD209/MERTK/MRCI/CD163L1 genes, respectively. Selected newly identified discriminating markers were used beyond CD163 to isolate cells that shared pro-Th17/Th1 function with CD163- cells. In conclusion, a molecularly distinct pro-inflammatory CD14+ subpopulation accumulates in inflamed colon, drives intestinal inflammatory T-cell responses, and thus, might contribute to CD disease severity.
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Affiliation(s)
- Laurence Chapuy
- Immunoregulation Laboratory, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, QC, Canada
| | - Marwa Bsat
- Immunoregulation Laboratory, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, QC, Canada
| | - Siranush Sarkizova
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manuel Rubio
- Immunoregulation Laboratory, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, QC, Canada
| | - Amélie Therrien
- Immunoregulation Laboratory, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, QC, Canada.,Centre Hospitalier de l'Université de Montréal (CHUM), Université de Montréal, Montréal, QC, Canada
| | - Evelyne Wassef
- Immunoregulation Laboratory, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, QC, Canada
| | - Mickael Bouin
- Centre Hospitalier de l'Université de Montréal (CHUM), Université de Montréal, Montréal, QC, Canada
| | - Katarzina Orlicka
- Centre Hospitalier de l'Université de Montréal (CHUM), Université de Montréal, Montréal, QC, Canada
| | - Audrey Weber
- Centre Hospitalier de l'Université de Montréal (CHUM), Université de Montréal, Montréal, QC, Canada
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Marika Sarfati
- Immunoregulation Laboratory, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, QC, Canada.
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141
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Abstract
The IBDs, Crohn's disease and ulcerative colitis, are chronic inflammatory conditions of the gastrointestinal tract resulting from an aberrant immune response to enteric microbiota in genetically susceptible individuals. Disease presentation and progression within and across IBDs, especially Crohn's disease, are highly heterogeneous in location, severity of inflammation and other phenotypes. Current clinical classifications fail to accurately predict disease course and response to therapies. Genome-wide association studies have identified >240 loci that confer risk of IBD, but the clinical utility of these findings remains unclear, and mechanisms by which the genetic variants contribute to disease are largely unknown. In the past 5 years, the profiling of genome-wide gene expression, epigenomic features and gut microbiota composition in intestinal tissue and faecal samples has uncovered distinct molecular signatures that define IBD subtypes, including within Crohn's disease and ulcerative colitis. In this Review, we summarize studies in both adult and paediatric patients that have identified different IBD subtypes, which in some cases have been associated with distinct clinical phenotypes. We posit that genome-scale molecular phenotyping in large cohorts holds great promise not only to further our understanding of the diverse molecular causes of IBD but also for improving clinical trial design to develop more personalized disease management and treatment.
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142
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Dovrolis N, Filidou E, Kolios G. Systems biology in inflammatory bowel diseases: on the way to precision medicine. Ann Gastroenterol 2019; 32:233-246. [PMID: 31040620 PMCID: PMC6479645 DOI: 10.20524/aog.2019.0373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic and recurrent inflammatory disorders of the gastrointestinal tract. The elucidation of their etiopathology requires complex and multiple approaches. Systems biology has come to fulfill this need in approaching the pathogenetic mechanisms of IBD and its etiopathology, in a comprehensive way, by combining data from different scientific sources. In combination with bioinformatics and network medicine, it uses principles from computer science, mathematics, physics, chemistry, biology, medicine and computational tools to achieve its purposes. Systems biology utilizes scientific sources that provide data from omics studies (e.g., genomics, transcriptomics, etc.) and clinical observations, whose combined analysis leads to network formation and ultimately to a more integrative image of disease etiopathogenesis. In this review, we analyze the current literature on the methods and the tools utilized by systems biology in order to cover an innovative and exciting field: IBD-omics.
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Affiliation(s)
- Nikolas Dovrolis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eirini Filidou
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Correspondence to: Prof. George Kolios, MD PhD, Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Dragana, Alexandroupolis, 68100, Greece, e-mail:
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143
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Cheng B, Liang X, Wen Y, Li P, Zhang L, Ma M, Cheng S, Du Y, Liu L, Ding M, Zhao Y, Zhang F. Integrative analysis of transcriptome‐wide association study data and messenger RNA expression profiles identified candidate genes and pathways for inflammatory bowel disease. J Cell Biochem 2019; 120:14831-14837. [DOI: 10.1002/jcb.28744] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/17/2019] [Accepted: 03/22/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Xiao Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Lu Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Mei Ma
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Yanan Du
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Miao Ding
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Yan Zhao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
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144
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Di Narzo AF, Brodmerkel C, Telesco SE, Argmann C, Peters LA, Li K, Kidd B, Dudley J, Cho J, Schadt EE, Kasarskis A, Dobrin R, Hao K. High-Throughput Identification of the Plasma Proteomic Signature of Inflammatory Bowel Disease. J Crohns Colitis 2019; 13:462-471. [PMID: 30445421 PMCID: PMC6441306 DOI: 10.1093/ecco-jcc/jjy190] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND The molecular aetiology of inflammatory bowel disease [IBD] and its two subtypes, ulcerative colitis [UC] and Crohn's disease [CD], have been carefully investigated at genome and transcriptome levels. Recent advances in high-throughput proteome quantification has enabled comprehensive large-scale plasma proteomics studies of IBD. METHODS The study used two cohorts: [1] The CERTIFI-cohort: 42 samples from the CERTIFI trial of anti-TNFα-refractory CD patients; [2] the PROgECT-UNITI-HCs cohort: 46 UC samples of the PROgECT study, 84 CD samples of the UNITI I and UNITI II studies, and 72 healthy controls recruited in Mount Sinai Hospital, New York, USA. The plasma proteome for these two cohorts was quantified using high-throughput platforms. RESULTS For the PROgECT-UNITI-HCs cohort, we measured a total of 1310 proteins. Of these, 493 proteins showed different plasma levels in IBD patients to the plasma levels in controls at 10% false discovery rate [FDR], among which 11 proteins had a fold change greater than 2. The proteins upregulated in IBD were associated with immunity functionality, whereas the proteins downregulated in IBD were associated with nutrition and metabolism. The proteomic profiles were very similar between UC and CD. In the CERTIFI cohort, 1014 proteins were measured, and it was found that the plasma protein level had little correlation with the blood or intestine transcriptomes. CONCLUSIONS We report the largest proteomics study to date on IBD and controls. A large proportion of plasma proteins are altered in IBD, which provides insights into the disease aetiology and indicates a potential for biomarker discovery.
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Affiliation(s)
- Antonio F Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lauren A Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, a Mount Sinai venture, Stamford, CT, USA
| | | | - Brian Kidd
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joel Dudley
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, a Mount Sinai venture, Stamford, CT, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Respiratory Medicine, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
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145
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Kosinsky RL, Chua RL, Qui M, Saul D, Mehlich D, Ströbel P, Schildhaus HU, Wegwitz F, Faubion WA, Johnsen SA. Loss of RNF40 Decreases NF-κB Activity in Colorectal Cancer Cells and Reduces Colitis Burden in Mice. J Crohns Colitis 2019; 13:362-373. [PMID: 30321325 PMCID: PMC6599279 DOI: 10.1093/ecco-jcc/jjy165] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Inflammatory bowel diseases are linked to an increased risk of developing colorectal cancer [CRC]. Previous studies suggested that the H2B ubiquitin ligase RING finger protein-20 [RNF20] inhibited inflammatory signaling mediated by the nuclear factor kappa-light-chain-enhancer of activated B cells [NF-κB]. However, the role of RNF40, the obligate heterodimeric partner of RNF20, in the context of inflammation and CRC has not been addressed. Here, we examined the effect of RNF40 loss on CRC cells in vitro and on inflammation and inflammatory signaling in vitro and in vivo. METHODS We evaluated H2Bub1 levels in human and murine colorectal tumors by immunohistochemistry. Moreover, we correlated H2Bub1 and RNF40 levels in vivo and assessed the consequences of RNF40 depletion on cellular phenotype and gene expression in CRC cells in vitro. Finally, we examined the effect of a colon-specific loss of Rnf40 in a murine model of colitis, and assessed both local and systemic inflammation-associated consequences. RESULTS In vitro studies revealed that the tumorigenic phenotype of CRC cells decreased after RNF40 depletion and displayed gene expression changes related to chromosome segregation and DNA replication, as well as decreased induction of several NF-κB-associated cytokines. This effect was associated with decreased nuclear localization of NF-κB following tumor necrosis factor alpha treatment. Consistently, the colon-specific loss of Rnf40 exerted a protective local, as well as systemic, effect following acute colitis. CONCLUSIONS Our findings suggest that RNF40 plays a central role in the maintenance of tumorigenic features and inflammatory signaling by promoting nuclear NF-κB activity.
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Affiliation(s)
- Robyn Laura Kosinsky
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany
| | - Robert Lorenz Chua
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany
| | - Martin Qui
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany
| | - Dominik Saul
- Department of Trauma, Orthopedics and Reconstructive Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Dawid Mehlich
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Göttingen, Germany,Corresponding author: Prof. Steven A. Johnsen, PhD, University Medical Center Göttingen, Göttingen Center for Molecular Biosciences, Clinic for General, Visceral and Pediatric Surgery, Section of Tumor Epigenetics, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Tel.: +49 551 39-13711; fax: +49 551 39-13713; email
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146
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Pazmandi J, Kalinichenko A, Ardy RC, Boztug K. Early-onset inflammatory bowel disease as a model disease to identify key regulators of immune homeostasis mechanisms. Immunol Rev 2019; 287:162-185. [PMID: 30565237 PMCID: PMC7379380 DOI: 10.1111/imr.12726] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 09/23/2018] [Indexed: 12/11/2022]
Abstract
Rare, monogenetic diseases present unique models to dissect gene functions and biological pathways, concomitantly enhancing our understanding of the etiology of complex (and often more common) traits. Although inflammatory bowel disease (IBD) is a generally prototypic complex disease, it can also manifest in an early-onset, monogenic fashion, often following Mendelian modes of inheritance. Recent advances in genomic technologies have spurred the identification of genetic defects underlying rare, very early-onset IBD (VEO-IBD) as a disease subgroup driven by strong genetic influence, pinpointing key players in the delicate homeostasis of the immune system in the gut and illustrating the intimate relationships between bowel inflammation, systemic immune dysregulation, and primary immunodeficiency with increased susceptibility to infections. As for other human diseases, it is likely that adult-onset diseases may represent complex diseases integrating the effects of host genetic susceptibility and environmental triggers. Comparison of adult-onset IBD and VEO-IBD thus provides beautiful models to investigate the relationship between monogenic and multifactorial/polygenic diseases. This review discusses the present and novel findings regarding monogenic IBD as well as key questions and future directions of IBD research.
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Affiliation(s)
- Julia Pazmandi
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Artem Kalinichenko
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Rico Chandra Ardy
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of Pediatrics and Adolescent MedicineMedical University of ViennaViennaAustria
- Department of PediatricsSt. Anna Kinderspital and Children's Cancer Research InstituteMedical University of ViennaViennaAustria
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147
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Lin C, Zong J, Lin W, Wang M, Xu Y, Zhou R, Lin S, Guo Q, Chen H, Ye Y, Zhang B, Pan J. EBV-miR-BART8-3p induces epithelial-mesenchymal transition and promotes metastasis of nasopharyngeal carcinoma cells through activating NF-κB and Erk1/2 pathways. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:283. [PMID: 30477559 PMCID: PMC6257964 DOI: 10.1186/s13046-018-0953-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/07/2018] [Indexed: 12/22/2022]
Abstract
Background Epstein-Barr virus (EBV) is ubiquitously associated with nasopharyngeal carcinoma (NPC). EBV encodes two groups of microRNAs (miRNAs) which are divided into BamHI fragment H rightward open reading frame 1 (BHRF1) and BamHI-A rightward transcripts (BART) microRNAs. EBV miR-BART has been found to be involved in the development and progression of NPC. However, so far the role of EBV-miR-BART8-3p in NPC progression remains unknown. This study aimed to investigate the role of EBV-miR-BART8-3p in NPC and explore the underlying mechanisms. Methods miRNA expression was profiled in NPC and normal nasopharyngeal mucosal specimens using miRNA sequencing. EBV-miR-BART8-3p and RNF38 expression was quantified with qPCR assay. The migration, invasion and metastasis of NPC cells were evaluated using CCK-8, colony-forming, wound-healing, and migration and invasion assays. The expression levels of epithelial-mesenchymal transition (EMT)-related markers,metastasis-related markers and NF-κB and Erk1/2 signaling proteins were determined using Western blotting. Tumorigenic assay was performed to evaluate the pulmonary metastatic ability of NPC cells in vivo. Results EBV BART miRNAs were highly over-expressed and co-expressed in NPC and might be associated with deactivated immune response in NPC according to the sequencing analysis. EBV-miR-BART8-3p expression was significantly higher in human NPC specimens than in normal nasopharyngeal mucosal specimens. EBV-miR-BART8-3p was found to promote NPC migration, invasion and metastasis, drove an EMT process and upregulated expression of metastasis-related proteins expression in NPC cells. Our data showed EBV-miR-BART8-3p directly targeted RNF38 in NPC cells. Conclusion The present study demonstrates that EBV-miR-BART8-3p plays a significant role in inducing EMT and promoting metastasis through directly targeting RNF38 in NPC cells via the activation of NF-κB and Erk1/2 signaling pathways. Our findings suggest that EBV-miR-BART8-3p is a potential therapeutic target for NPC. Electronic supplementary material The online version of this article (10.1186/s13046-018-0953-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cheng Lin
- Fujian Medical University, Fuzhou, 350108, Fujian Province, China.,Department of Radiation Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350011, Fujian Province, China
| | - Jingfeng Zong
- Department of Radiation Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350011, Fujian Province, China
| | - Wansong Lin
- Laboratory of Immuno-Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350011, Fujian Province, China
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Yuanji Xu
- Department of Radiation Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350011, Fujian Province, China
| | - Rui Zhou
- Fujian Medical University, Fuzhou, 350108, Fujian Province, China
| | - Shaojun Lin
- Department of Radiation Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350011, Fujian Province, China
| | - Qiaojuan Guo
- Department of Radiation Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350011, Fujian Province, China
| | - Honglin Chen
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology and the Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, SAR, China
| | - Yunbin Ye
- Laboratory of Immuno-Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350011, Fujian Province, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, 350014, Fujian, China
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA.
| | - Jianji Pan
- Department of Radiation Oncology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350011, Fujian Province, China.
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148
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Wong SY, Coffre M, Ramanan D, Hines MJ, Gomez LE, Peters LA, Schadt EE, Koralov SB, Cadwell K. B Cell Defects Observed in Nod2 Knockout Mice Are a Consequence of a Dock2 Mutation Frequently Found in Inbred Strains. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2018; 201:1442-1451. [PMID: 30012848 PMCID: PMC6103850 DOI: 10.4049/jimmunol.1800014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 06/22/2018] [Indexed: 02/06/2023]
Abstract
Phenotypic differences among substrains of laboratory mice due to spontaneous mutations or pre-existing genetic variation confound the interpretation of targeted mutagenesis experiments and contribute to challenges with reproducibility across institutions. Notably, C57BL/6 Hsd mice and gene-targeted mice that have been backcrossed to this substrain have been reported to harbor a duplication in exons 28 and 29 of Dock2 In this study, we demonstrate the presence of this Dock2 variant in the widely used Nod2-/- mice. Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) is a cytosolic innate immune receptor associated with inflammatory bowel disease susceptibility. Consistent with a role of NOD2 in an immunological disorder, Nod2-/- mice bred at our institution displayed multiple B cell defects including deficiencies in recirculating B cells, marginal zone B cells, and B1a cells in vivo, as well as defects in class switch recombination in vitro. However, we found that these effects are due to the Dock2 variant and are independent of Nod2 deletion. Despite originating from the same gene-targeted founder mice, Nod2-/- mice from another source did not harbor the Dock2 variant or B cell defects. Finally, we show that Dock2-/- mice display the same B cell defects as mice harboring the Dock2 variant, confirming that the variant is a loss-of-function mutation and is sufficient to explain the alterations to the B cell compartment observed in Nod2-/- mice. Our findings highlight the effects of confounding mutations from widely used inbred strains on gene-targeted mice and reveal new functions of DOCK2 in B cells.
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Affiliation(s)
- Serre-Yu Wong
- Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
- Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Maryaline Coffre
- Department of Pathology, New York University School of Medicine, New York, NY 10016
| | - Deepshika Ramanan
- Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
| | - Marcus J Hines
- Department of Pathology, New York University School of Medicine, New York, NY 10016
| | - Luis E Gomez
- Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
| | - Lauren A Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Sema4, a Mount Sinai Venture, Stamford, CT 06902; and
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Sema4, a Mount Sinai Venture, Stamford, CT 06902; and
| | - Sergei B Koralov
- Department of Pathology, New York University School of Medicine, New York, NY 10016
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016;
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
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149
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Levine A, Sigall Boneh R, Wine E. Evolving role of diet in the pathogenesis and treatment of inflammatory bowel diseases. Gut 2018; 67:1726-1738. [PMID: 29777041 DOI: 10.1136/gutjnl-2017-315866] [Citation(s) in RCA: 219] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 12/12/2022]
Abstract
Recent advances in basic and clinical science over the last 3 years have dramatically altered our appreciation of the role of diet in inflammatory bowel diseases (IBD). The marked increase in incidence of these diseases along with the important role of non-genetic susceptibility among patients with IBD has highlighted that these diseases have a strong environmental component. Progress in the field of microbiome and IBD has demonstrated that microbiome appears to play an important role in pathogenesis, and that diet may in turn impact the composition and functionality of the microbiome. Uncontrolled clinical studies have demonstrated that various dietary therapies such as exclusive enteral nutrition and newly developed exclusion diets might be potent tools for induction of remission at disease onset, for patients failing biologic therapy, as a treatment for disease complications and in reducing the need for surgery. We review these advances from bench to bedside, along with the need for better clinical trials to support these interventions.
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Affiliation(s)
- Arie Levine
- Pediatric Gastroenterology and Nutrition Unit, Edith Wolfson Medical Center, Holon, Israel.,Tel Aviv University, Tel Aviv, Israel
| | - Rotem Sigall Boneh
- Pediatric Gastroenterology and Nutrition Unit, Edith Wolfson Medical Center, Holon, Israel.,Tel Aviv University, Tel Aviv, Israel
| | - Eytan Wine
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
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150
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Resolution of chronic inflammatory disease: universal and tissue-specific concepts. Nat Commun 2018; 9:3261. [PMID: 30111884 PMCID: PMC6093916 DOI: 10.1038/s41467-018-05800-6] [Citation(s) in RCA: 236] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/22/2018] [Indexed: 12/21/2022] Open
Abstract
Inflammation and its resolution is under-studied in medicine despite being essential for understanding the development of chronic inflammatory disease. In this review article, we discuss the resolution of inflammation in both a biological and translational context. We introduce the concept of impaired resolution leading to diseases like rheumatoid arthritis, Crohn's disease, and asthma, as well as the cellular and molecular components that contribute to resolution of joint, gut, and lung inflammation, respectively. Finally, we discuss potential intervention strategies for fostering the resolution process, and their implications for the therapy of inflammatory diseases.
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