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Alvarez-Martinez M, Cox LS, Pearson CF, Branchett WJ, Chakravarty P, Wu X, Slawinski H, Al-Dibouni A, Samelis VA, Gabryšová L, Priestnall SL, Suárez-Bonnet A, Mikolajczak A, Briscoe J, Powrie F, O'Garra A. Blimp-1 and c-Maf regulate immune gene networks to protect against distinct pathways of pathobiont-induced colitis. Nat Immunol 2024; 25:886-901. [PMID: 38609547 PMCID: PMC11065689 DOI: 10.1038/s41590-024-01814-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/13/2024] [Indexed: 04/14/2024]
Abstract
Intestinal immune responses to microbes are controlled by the cytokine IL-10 to avoid immune pathology. Here, we use single-cell RNA sequencing of colon lamina propria leukocytes (LPLs) along with RNA-seq and ATAC-seq of purified CD4+ T cells to show that the transcription factors Blimp-1 (encoded by Prdm1) and c-Maf co-dominantly regulate Il10 while negatively regulating proinflammatory cytokines in effector T cells. Double-deficient Prdm1fl/flMaffl/flCd4Cre mice infected with Helicobacter hepaticus developed severe colitis with an increase in TH1/NK/ILC1 effector genes in LPLs, while Prdm1fl/flCd4Cre and Maffl/flCd4Cre mice exhibited moderate pathology and a less-marked type 1 effector response. LPLs from infected Maffl/flCd4Cre mice had increased type 17 responses with increased Il17a and Il22 expression and an increase in granulocytes and myeloid cell numbers, resulting in increased T cell-myeloid-neutrophil interactions. Genes over-expressed in human inflammatory bowel disease showed differential expression in LPLs from infected mice in the absence of Prdm1 or Maf, revealing potential mechanisms of human disease.
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Affiliation(s)
| | - Luke S Cox
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Claire F Pearson
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - William J Branchett
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Probir Chakravarty
- Computational Biology Laboratory, The Francis Crick Institute, London, UK
| | - Xuemei Wu
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Hubert Slawinski
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Alaa Al-Dibouni
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Vasileios A Samelis
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Leona Gabryšová
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Simon L Priestnall
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - Alejandro Suárez-Bonnet
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - Anna Mikolajczak
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - James Briscoe
- Developmental Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Anne O'Garra
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK.
- National Heart and Lung Institute, Imperial College London, London, UK.
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Canales-Herrerias P, Uzzan M, Seki A, Czepielewski RS, Verstockt B, Livanos AE, Raso F, Dunn A, Dai D, Wang A, Al-Taie Z, Martin J, Laurent T, Ko HM, Tokuyama M, Tankelevich M, Meringer H, Cossarini F, Jha D, Krek A, Paulsen JD, Taylor MD, Nakadar MZ, Wong J, Erlich EC, Mintz RL, Onufer EJ, Helmink BA, Sharma K, Rosenstein A, Ganjian D, Chung G, Dawson T, Juarez J, Yajnik V, Cerutti A, Faith JJ, Suarez-Farinas M, Argmann C, Petralia F, Randolph GJ, Polydorides AD, Reboldi A, Colombel JF, Mehandru S. Gut-associated lymphoid tissue attrition associates with response to anti-α4β7 therapy in ulcerative colitis. Sci Immunol 2024; 9:eadg7549. [PMID: 38640252 DOI: 10.1126/sciimmunol.adg7549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/20/2024] [Indexed: 04/21/2024]
Abstract
Vedolizumab (VDZ) is a first-line treatment in ulcerative colitis (UC) that targets the α4β7- mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1) axis. To determine the mechanisms of action of VDZ, we examined five distinct cohorts of patients with UC. A decrease in naïve B and T cells in the intestines and gut-homing (β7+) plasmablasts in circulation of VDZ-treated patients suggested that VDZ targets gut-associated lymphoid tissue (GALT). Anti-α4β7 blockade in wild-type and photoconvertible (KikGR) mice confirmed a loss of GALT size and cellularity because of impaired cellular entry. In VDZ-treated patients with UC, treatment responders demonstrated reduced intestinal lymphoid aggregate size and follicle organization and a reduction of β7+IgG+ plasmablasts in circulation, as well as IgG+ plasma cells and FcγR-dependent signaling in the intestine. GALT targeting represents a previously unappreciated mechanism of action of α4β7-targeted therapies, with major implications for this therapeutic paradigm in UC.
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Affiliation(s)
- Pablo Canales-Herrerias
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mathieu Uzzan
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Paris Est Créteil University UPEC, Assistance Publique-Hôpitaux de Paris (AP-HP), Henri Mondor Hospital, Gastroenterology Department, Fédération Hospitalo-Universitaire TRUE (InnovaTive theRapy for immUne disordErs), Créteil F-94010, France
| | - Akihiro Seki
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rafael S Czepielewski
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bram Verstockt
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Translational Research in Gastrointestinal Disorders, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Alexandra E Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fiona Raso
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Alexandra Dunn
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Dai
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Wang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zainab Al-Taie
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerome Martin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nantes Université, CHU Nantes, Inserm, Centre de Recherche Translationelle en Transplantation et Immunologie, UMR 1064, Nantes, France
- CHU Nantes, Nantes Université, Laboratoire d'Immunologie, CIMNA, Nantes, France
| | - Thomas Laurent
- Nantes Université, CHU Nantes, Inserm, Centre de Recherche Translationelle en Transplantation et Immunologie, UMR 1064, Nantes, France
- CHU Nantes, Nantes Université, Laboratoire d'Immunologie, CIMNA, Nantes, France
| | - Huaibin M Ko
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minami Tokuyama
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Tankelevich
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hadar Meringer
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Cossarini
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Divya Jha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John D Paulsen
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D Taylor
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mohammad Zuber Nakadar
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua Wong
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma C Erlich
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel L Mintz
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Emily J Onufer
- Division of Pediatric Surgery, Department of Surgery, St. Louis Children's Hospital, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Beth A Helmink
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Keshav Sharma
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam Rosenstein
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danielle Ganjian
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Grace Chung
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Andrea Cerutti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Translational Clinical Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mayte Suarez-Farinas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, 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
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gwendalyn J Randolph
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexandros D Polydorides
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrea Reboldi
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jean-Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Spathakis M, Dovrolis N, Filidou E, Kandilogiannakis L, Tarapatzi G, Valatas V, Drygiannakis I, Paspaliaris V, Arvanitidis K, Manolopoulos VG, Kolios G, Vradelis S. Exploring Microbial Metabolite Receptors in Inflammatory Bowel Disease: An In Silico Analysis of Their Potential Role in Inflammation and Fibrosis. Pharmaceuticals (Basel) 2024; 17:492. [PMID: 38675452 PMCID: PMC11054721 DOI: 10.3390/ph17040492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Metabolites produced by dysbiotic intestinal microbiota can influence disease pathophysiology by participating in ligand-receptor interactions. Our aim was to investigate the differential expression of metabolite receptor (MR) genes between inflammatory bowel disease (IBD), healthy individuals (HIs), and disease controls in order to identify possible interactions with inflammatory and fibrotic pathways in the intestine. RNA-sequencing datasets containing 643 Crohn's disease (CD) patients, 467 ulcerative colitis (UC) patients and 295 HIs, and 4 Campylobacter jejuni-infected individuals were retrieved from the Sequence Read Archive, and differential expression was performed using the RaNA-seq online platform. The identified differentially expressed MR genes were used for correlation analysis with up- and downregulated genes in IBD, as well as functional enrichment analysis using a R based pipeline. Overall, 15 MR genes exhibited dysregulated expression in IBD. In inflamed CD, the hydroxycarboxylic acid receptors 2 and 3 (HCAR2, HCAR3) were upregulated and were associated with the recruitment of innate immune cells, while, in the non-inflamed CD ileum, the cannabinoid receptor 1 (CNR1) and the sphingosine-1-phospate receptor 4 (S1PR4) were downregulated and were involved in the regulation of B-cell activation. In inflamed UC, the upregulated receptors HCAR2 and HCAR3 were more closely associated with the process of TH-17 cell differentiation, while the pregnane X receptor (NR1I2) and the transient receptor potential vanilloid 1 (TRPV1) were downregulated and were involved in epithelial barrier maintenance. Our results elucidate the landscape of metabolite receptor expression in IBD, highlighting associations with disease-related functions that could guide the development of new targeted therapies.
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Affiliation(s)
- Michail Spathakis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.S.); (E.F.); (L.K.); (G.T.); (V.V.); (K.A.); (V.G.M.); (G.K.)
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), 68100 Alexandroupolis, Greece
| | - Nikolas Dovrolis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.S.); (E.F.); (L.K.); (G.T.); (V.V.); (K.A.); (V.G.M.); (G.K.)
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), 68100 Alexandroupolis, Greece
| | - Eirini Filidou
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.S.); (E.F.); (L.K.); (G.T.); (V.V.); (K.A.); (V.G.M.); (G.K.)
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), 68100 Alexandroupolis, Greece
| | - Leonidas Kandilogiannakis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.S.); (E.F.); (L.K.); (G.T.); (V.V.); (K.A.); (V.G.M.); (G.K.)
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), 68100 Alexandroupolis, Greece
| | - Gesthimani Tarapatzi
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.S.); (E.F.); (L.K.); (G.T.); (V.V.); (K.A.); (V.G.M.); (G.K.)
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), 68100 Alexandroupolis, Greece
| | - Vassilis Valatas
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.S.); (E.F.); (L.K.); (G.T.); (V.V.); (K.A.); (V.G.M.); (G.K.)
- Gastroenterology and Hepatology Research Laboratory, Medical School, University of Crete, 71003 Heraklion, Greece;
| | - Ioannis Drygiannakis
- Gastroenterology and Hepatology Research Laboratory, Medical School, University of Crete, 71003 Heraklion, Greece;
| | | | - Konstantinos Arvanitidis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.S.); (E.F.); (L.K.); (G.T.); (V.V.); (K.A.); (V.G.M.); (G.K.)
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), 68100 Alexandroupolis, Greece
| | - Vangelis G. Manolopoulos
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.S.); (E.F.); (L.K.); (G.T.); (V.V.); (K.A.); (V.G.M.); (G.K.)
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), 68100 Alexandroupolis, Greece
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.S.); (E.F.); (L.K.); (G.T.); (V.V.); (K.A.); (V.G.M.); (G.K.)
- Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), 68100 Alexandroupolis, Greece
| | - Stergios Vradelis
- Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
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Neri B, Mancone R, Fiorillo M, Schiavone SC, De Cristofaro E, Migliozzi S, Biancone L. Comprehensive overview of novel chemical drugs for ulcerative colitis: focusing on phase 3 and beyond. Expert Opin Pharmacother 2024:1-15. [PMID: 38591242 DOI: 10.1080/14656566.2024.2339926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
INTRODUCTION Despite the growing number of highly efficacious biologics and chemical drugs for ulcerative colitis (UC), steroid-free disease control is still difficult to achieve in subgroups of patients due to refractoriness, adverse events, primary or secondary failure. New treatments are therefore still required in order to optimize clinical management of patients with UC. AREAS COVERED The efficacy and safety of both currently available and newly developed small molecules have been summarized. The PubMed database and clinicaltrials.gov were considered in order to search for phase 2b and 3 trials on new chemical drugs for UC. The study drugs reviewed included Janus kinases (JAK) and sphingosine-1-phosphate receptor (S1Pr) inhibitors, α4 integrin antagonist, and micro-RNA-124 upregulators. EXPERT OPINION Rapidity of onset, low immunogenicity, and safety are the main characteristics of small molecules currently available or under evaluation for treatment patients with UC. Among the currently available chemical drugs, the selective JAK and the S1Pr inhibitors are characterized by a good safety profile combined with the ability to induce clinical remission in UC. A relatively low frequency of endoscopic improvement and healing currently appears associated with their use, being higher in UC patients treated with S1Pr inhibitor Etrasimod. Overall, additional new safe and effective drugs are still required in order to optimize disease control in a larger majority of UC patients.
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Affiliation(s)
- Benedetto Neri
- Department of Systems Medicine, Gastroenterological Unit, University "Tor Vergata" of Rome, Rome, Italy
| | - Roberto Mancone
- Department of Systems Medicine, Gastroenterological Unit, University "Tor Vergata" of Rome, Rome, Italy
| | - Mariasofia Fiorillo
- Department of Systems Medicine, Gastroenterological Unit, University "Tor Vergata" of Rome, Rome, Italy
| | - Sara Concetta Schiavone
- Department of Systems Medicine, Gastroenterological Unit, University "Tor Vergata" of Rome, Rome, Italy
| | - Elena De Cristofaro
- Department of Systems Medicine, Gastroenterological Unit, University "Tor Vergata" of Rome, Rome, Italy
| | - Stefano Migliozzi
- Department of Systems Medicine, Gastroenterological Unit, University "Tor Vergata" of Rome, Rome, Italy
| | - Livia Biancone
- Department of Systems Medicine, Gastroenterological Unit, University "Tor Vergata" of Rome, Rome, Italy
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Stemmer E, Zahavi T, Kellerman M, Sinberger LA, Shrem G, Salmon‐Divon M. Exploring potential biomarkers and therapeutic targets in inflammatory bowel disease: insights from a mega-analysis approach. Front Immunol 2024; 15:1353402. [PMID: 38510241 PMCID: PMC10951083 DOI: 10.3389/fimmu.2024.1353402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Background Understanding the molecular pathogenesis of inflammatory bowel disease (IBD) has led to the discovery of new therapeutic targets that are more specific and effective. Our aim was to explore the molecular pathways and genes involved in IBD pathogenesis and to identify new therapeutic targets and novel biomarkers that can aid in the diagnosis of the disease. Methods To obtain the largest possible number of samples and analyze them comprehensively, we used a mega-analysis approach. This involved reprocessing raw data from multiple studies and analyzing them using bioinformatic and machine learning techniques. Results We analyzed a total of 697 intestinal biopsies of Ulcerative Colitis (n = 386), Crohn's disease (n = 183) and non-IBD controls (n = 128). A machine learning analysis detected 34 genes whose collective expression effectively distinguishes inflamed biopsies of IBD patients from non-IBD control samples. Most of these genes were upregulated in IBD. Notably, among these genes, three novel lncRNAs have emerged as potential contributors to IBD development: ENSG00000285744, ENSG00000287626, and MIR4435-2HG. Furthermore, by examining the expression of 29 genes, among the 34, in blood samples from IBD patients, we detected a significant upregulation of 12 genes (p-value < 0.01), underscoring their potential utility as non-invasive diagnostic biomarkers. Finally, by utilizing the CMap library, we discovered potential compounds that should be explored in future studies for their therapeutic efficacy in IBD treatment. Conclusion Our findings contribute to the understanding of IBD pathogenesis, suggest novel biomarkers for IBD diagnosis and offer new prospects for therapeutic intervention.
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Affiliation(s)
- Edia Stemmer
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Tamar Zahavi
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Maoz Kellerman
- Department of Molecular Biology, Ariel University, Ariel, Israel
- Kaleidoo, Bar Lev High Tech Park, Misgav, Israel
| | | | - Guy Shrem
- Obstetrics, Gynecology and Infertility (OB&GYN) Department Maccabi Healthcare Services, Tel Aviv, Israel
| | - Mali Salmon‐Divon
- Department of Molecular Biology, Ariel University, Ariel, Israel
- Adelson School of Medicine, Ariel University, Ariel, Israel
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Ou W, Qi Z, Liu N, Zhang J, Mi X, Song Y, Fang Y, Cui B, Hou J, Yuan Z. Elucidating the role of TWIST1 in ulcerative colitis: a comprehensive bioinformatics and machine learning approach. Front Genet 2024; 15:1296570. [PMID: 38510272 PMCID: PMC10952112 DOI: 10.3389/fgene.2024.1296570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/16/2024] [Indexed: 03/22/2024] Open
Abstract
Background: Ulcerative colitis (UC) is a common and progressive inflammatory bowel disease primarily affecting the colon and rectum. Prolonged inflammation can lead to colitis-associated colorectal cancer (CAC). While the exact cause of UC remains unknown, this study aims to investigate the role of the TWIST1 gene in UC. Methods: Second-generation sequencing data from adult UC patients were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified, and characteristic genes were selected using machine learning and Lasso regression. The Receiver Operating Characteristic (ROC) curve assessed TWIST1's potential as a diagnostic factor (AUC score). Enriched pathways were analyzed, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Variation Analysis (GSVA). Functional mechanisms of marker genes were predicted, considering immune cell infiltration and the competing endogenous RNA (ceRNA) network. Results: We found 530 DEGs, with 341 upregulated and 189 downregulated genes. TWIST1 emerged as one of four potential UC biomarkers via machine learning. TWIST1 expression significantly differed in two datasets, GSE193677 and GSE83687, suggesting its diagnostic potential (AUC = 0.717 in GSE193677, AUC = 0.897 in GSE83687). Enrichment analysis indicated DEGs associated with TWIST1 were involved in processes like leukocyte migration, humoral immune response, and cell chemotaxis. Immune cell infiltration analysis revealed higher rates of M0 macrophages and resting NK cells in the high TWIST1 expression group, while TWIST1 expression correlated positively with M2 macrophages and resting NK cell infiltration. We constructed a ceRNA regulatory network involving 1 mRNA, 7 miRNAs, and 32 long non-coding RNAs (lncRNAs) to explore TWIST1's regulatory mechanism. Conclusion: TWIST1 plays a significant role in UC and has potential as a diagnostic marker. This study sheds light on UC's molecular mechanisms and underscores TWIST1's importance in its progression. Further research is needed to validate these findings in diverse populations and investigate TWIST1 as a therapeutic target in UC.
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Affiliation(s)
- Wenjie Ou
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Zhaoxue Qi
- Department of Secretory Metabolism, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Ning Liu
- General Surgery of The First Clinical Hospital of Jilin Academy of Chinese Medicine Sciences, Changchun, Jilin, China
| | - Junzi Zhang
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Xuguang Mi
- Department of Central Laboratory, Jilin Provincial People’s Hospital, Changchun, Jilin, China
| | - Yuan Song
- Department of Gastroenterology, Jilin Provincial People’s Hospital, Changchun, Jilin, China
| | - Yanqiu Fang
- Department of Central Laboratory, Jilin Provincial People’s Hospital, Changchun, Jilin, China
| | - Baiying Cui
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Junjie Hou
- Department of Comprehensive Oncology, Jilin Provincial People’s Hospital, Changchun, Jilin, China
| | - Zhixin Yuan
- Department of Emergency Surgery, Jilin Provincial People’s Hospital, Changchun, Jilin, China
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7
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Lin Z, Chen Q, Ruan HB. To die or not to die: Gasdermins in intestinal health and disease. Semin Immunol 2024; 71:101865. [PMID: 38232665 PMCID: PMC10872225 DOI: 10.1016/j.smim.2024.101865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
Intestinal homeostasis is achieved by the balance among intestinal epithelium, immune cells, and gut microbiota. Gasdermins (GSDMs), a family of membrane pore forming proteins, can trigger rapid inflammatory cell death in the gut, mainly pyroptosis and NETosis. Importantly, there is increasing literature on the non-cell lytic roles of GSDMs in intestinal homeostasis and disease. While GSDMA is low and PJVK is not expressed in the gut, high GSDMB and GSDMC expression is found almost restrictively in intestinal epithelial cells. Conversely, GSDMD and GSDME show more ubiquitous expression among various cell types in the gut. The N-terminal region of GSDMs can be liberated for pore formation by an array of proteases in response to pathogen- and danger-associated signals, but it is not fully understood what cell type-specific mechanisms activate intestinal GSDMs. The host relies on GSDMs for pathogen defense, tissue tolerance, and cancerous cell death; however, pro-inflammatory milieu caused by pyroptosis and excessive cytokine release may favor the development and progression of inflammatory bowel disease and cancer. Therefore, a thorough understanding of spatiotemporal mechanisms that control gasdermin expression, activation, and function is essential for the development of future therapeutics for intestinal disorders.
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Affiliation(s)
- Zhaoyu Lin
- MOE Key Laboratory of Model Animals for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, National Resource Center for Mutant Mice of China, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China.
| | - Qianyue Chen
- MOE Key Laboratory of Model Animals for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, National Resource Center for Mutant Mice of China, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Hai-Bin Ruan
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, USA; Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA.
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8
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Ye S, Lyu Y, Chen L, Wang Y, He Y, Li Q, Tian L, Liu F, Wang X, Ai F. Construction of a molecular inflammatory predictive model with histone modification-related genes and identification of CAMK2D as a potential response signature to infliximab in ulcerative colitis. Front Immunol 2024; 14:1282136. [PMID: 38274809 PMCID: PMC10808628 DOI: 10.3389/fimmu.2023.1282136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Background Ulcerative colitis (UC) is a lifelong inflammatory disease affecting the rectum and colon with numerous treatment options that require an individualized treatment plan. Histone modifications regulate chromosome structure and gene expression, resulting in effects on inflammatory and immune responses. However, the relationship between histone modification-related genes and UC remains unclear. Methods Transcriptomic data from GSE59071 and GSE66407 were obtained from the Gene Expression Omnibus (GEO), encompassing colonic biopsy expression profiles of UC patients in inflamed and non-inflamed status. Differentially expressed gene (DEG) analyses, functional enrichment analyses, weighted gene co-expression network analysis (WGCNA), and random forest were performed to identify histone modification-related core genes associated with UC inflammation. Features were screened through the least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE), establishing a molecular inflammatory predictive model using logistic regression. The model was validated in the GSE107499 dataset, and the performance of the features was assessed using receiver operating characteristic (ROC) and calibration curves. Immunohistochemistry (IHC) staining of colonic biopsy tissues from UC patients treated with infliximab was used to further confirm the clinical application value. Univariate logistic regression on GSE14580 highlighted features linked to infliximab response. Results A total of 253 histone modification-related DEGs were identified between inflammatory and non-inflammatory patients with UC. Seven key genes (IL-1β, MSL3, HDAC7, IRF4, CAMK2D, AUTS2, and PADI2) were selected using WGCNA and random forest. Through univariate logistic regression, three core genes (CAMK2D, AUTS2, and IL-1β) were further incorporated to construct the molecular inflammatory predictive model. The area under the curve (AUC) of the model was 0.943 in the independent validation dataset. A significant association between CAMK2D protein expression and infliximab response was observed, which was validated in another independent verification set of GSE14580 from the GEO database. Conclusion The molecular inflammatory predictive model based on CAMK2D, AUTS2, and IL-1β could reliably distinguish the mucosal inflammatory status of UC patients. We further revealed that CAMK2D was a predictive marker of infliximab response. These findings are expected to provide a new evidence base for personalized treatment and management strategies for UC patients.
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Affiliation(s)
- Shuyu Ye
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yongqing Lyu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Libin Chen
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yiwei Wang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yue He
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Quansi Li
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Li Tian
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Fen Liu
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Feiyan Ai
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
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9
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Chen W, Wang D, Deng X, Zhang H, Dong D, Su T, Lu Q, Jiang C, Ni Q, Cui Y, Zhao Q, Wang X, Xiao Y, Peng Y. Bile acid profiling as an effective biomarker for staging in pediatric inflammatory bowel disease. Gut Microbes 2024; 16:2323231. [PMID: 38436673 PMCID: PMC10913721 DOI: 10.1080/19490976.2024.2323231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Rapid and accurate clinical staging of pediatric patients with inflammatory bowel disease (IBD) is crucial to determine the appropriate therapeutic approach. This study aimed to identify effective, convenient biomarkers for staging IBD in pediatric patients. We recruited cohorts of pediatric patients with varying severities of IBD to compare the features of the intestinal microbiota and metabolites between the active and remitting disease stages. Metabolites with potential for staging were targeted for further assessment in both patients and colitis model mice. The performance of these markers was determined using machine learning and was validated in a separate patient cohort. Pediatric patients with IBD exhibited distinct gut microbiota structures at different stages of disease activity. The enterotypes of patients with remitting and active disease were Bacteroides-dominant and Escherichia-Shigella-dominant, respectively. The bile secretion pathway showed the most significant differences between the two stages. Fecal and serum bile acid (BA) levels were strongly related to disease activity in both children and mice. The ratio of primary BAs to secondary BAs in serum was developed as a novel comprehensive index, showing excellent diagnostic performance in stratifying IBD activity (0.84 area under the receiver operating characteristic curve in the primary cohort; 77% accuracy in the validation cohort). In conclusion, we report profound insights into the interactions between the gut microbiota and metabolites in pediatric IBD. Serum BAs have potential as biomarkers for classifying disease activity, and may facilitate the personalization of treatment for IBD.
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Affiliation(s)
- Wei Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Daosheng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xing Deng
- Department of Gastroenterology, Xiamen Children’s Hospital, Children’s Hospital of Fudan University at Xiamen, Fujian, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Danfeng Dong
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tongxuan Su
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiuya Lu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cen Jiang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Ni
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingchao Cui
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qianli Zhao
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuan Xiao
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yibing Peng
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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10
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Wang JM, Yang J, Xia WY, Wang YM, Zhu YB, Huang Q, Feng T, Xie LS, Li SH, Liu SQ, Yu SG, Wu QF. Comprehensive Analysis of PANoptosis-Related Gene Signature of Ulcerative Colitis. Int J Mol Sci 2023; 25:348. [PMID: 38203518 PMCID: PMC10779047 DOI: 10.3390/ijms25010348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Accumulating evidence shows that the abnormal increase in the mortality of intestinal epithelial cells (IECs) caused by apoptosis, pyroptosis, and necroptosis is closely related to the function of mucous membrane immunity and barrier function in patients with ulcerative colitis (UC). As a procedural death path that integrates the above-mentioned many deaths, the role of PANoptosis in UC has not been clarified. This study aims to explore the characterization of PANoptosis patterns and determine the potential biomarkers and therapeutic targets. We constructed a PANoptosis gene set and revealed significant activation of PANoptosis in UC patients based on multiple transcriptome profiles of intestinal mucosal biopsies from the GEO database. Comprehensive bioinformatics analysis revealed five key genes (ZBP1, AIM2, CASP1/8, IRF1) of PANoptosome with good diagnostic value and were highly correlated with an increase in pro-inflammatory immune cells and factors. In addition, we established a reliable ceRNA regulatory network of PANoptosis and predicted three potential small-molecule drugs sharing calcium channel blockers that were identified, among which flunarizine exhibited the highest correlation with a high binding affinity to the targets. Finally, we used the DSS-induced colitis model to validate our findings. This study identifies key genes of PANoptosis associated with UC development and hypothesizes that IRF1 as a TF promotes PANoptosome multicomponent expression, activates PANoptosis, and then induces IECs excessive death.
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Affiliation(s)
- Jun-Meng Wang
- Acupuncture and Moxibustion School, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jiao Yang
- Acupuncture and Moxibustion School, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Wan-Yu Xia
- Acupuncture and Moxibustion School, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yue-Mei Wang
- Acupuncture and Moxibustion School, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yuan-Bing Zhu
- Acupuncture and Moxibustion School, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qin Huang
- Acupuncture and Moxibustion School, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tong Feng
- Acupuncture and Moxibustion School, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lu-Shuang Xie
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Si-Hui Li
- Acupuncture and Moxibustion School, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shu-Qing Liu
- Acupuncture and Moxibustion School, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shu-Guang Yu
- Acupuncture and Moxibustion School, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qiao-Feng Wu
- Acupuncture and Moxibustion School, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Acupuncture & Chronobiology Key Laboratory of Sichuan Province, Chengdu 611137, China
- Key Laboratory of Acupuncture for Senile Disease, Chengdu University of TCM, Ministry of Education, Chengdu 611137, China
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11
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D'Adamo GL, Chonwerawong M, Gearing LJ, Marcelino VR, Gould JA, Rutten EL, Solari SM, Khoo PWR, Wilson TJ, Thomason T, Gulliver EL, Hertzog PJ, Giles EM, Forster SC. Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease. Cell Rep Med 2023; 4:101124. [PMID: 37467722 PMCID: PMC10394256 DOI: 10.1016/j.xcrm.2023.101124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/19/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023]
Abstract
Abnormal immune responses to the resident gut microbiome can drive inflammatory bowel disease (IBD). Here, we combine high-resolution, culture-based shotgun metagenomic sequencing and analysis with matched host transcriptomics across three intestinal sites (terminal ileum, cecum, rectum) from pediatric IBD (PIBD) patients (n = 58) and matched controls (n = 42) to investigate this relationship. Combining our site-specific approach with bacterial culturing, we establish a cohort-specific bacterial culture collection, comprising 6,620 isolates (170 distinct species, 32 putative novel), cultured from 286 mucosal biopsies. Phylogeny-based, clade-specific metagenomic analysis identifies key, functionally distinct Enterococcus clades associated with either IBD or health. Strain-specific in vitro validation demonstrates differences in cell cytotoxicity and inflammatory signaling in intestinal epithelial cells, consistent with the colonic mucosa-specific response measured in patients with IBD. This demonstrates the importance of strain-specific phenotypes and consideration of anatomical sites in exploring the dysregulated host-bacterial interactions in IBD.
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Affiliation(s)
- Gemma L D'Adamo
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Michelle Chonwerawong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Jodee A Gould
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Emily L Rutten
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Sean M Solari
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Patricia W R Khoo
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3800, Australia
| | - Trevor J Wilson
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia; MHTP Medical Genomics Facility, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Tamblyn Thomason
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Emily L Gulliver
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Edward M Giles
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3800, Australia.
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia.
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12
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Dan S, Ungar B, Ben-Moshe S, Halpern KB, Yavzori M, Fudim E, Picard O, Abitbol CM, Harnik S, Barshack I, Kopylov U, Ben-Horin S, Itzkovitz S. Distal Fecal Wash Host Transcriptomics Identifies Inflammation Throughout the Colon and Terminal Ileum. Cell Mol Gastroenterol Hepatol 2023; 16:1-15. [PMID: 36791991 DOI: 10.1016/j.jcmgh.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND & AIMS Noninvasive modalities for assessing active endoscopic and histologic inflammation in Crohn's disease and ulcerative colitis patients are critically needed. Fecal wash host shed-cell transcriptomics has been shown to be a robust classifier of endoscopic and histologic inflammation in inflammatory bowel disease patients with distal colitis. Whether such fecal washes can inform on inflammatory processes occurring in more proximal intestinal segments is currently unknown. METHODS Fifty-nine inflammatory bowel disease patients and 50 controls were prospectively enrolled. Biopsy specimens and fecal washes from the distal colon, proximal colon, and terminal ileum were compared. Host transcriptomics were performed on the biopsy specimens and fecal washes obtained during colonoscopy at predefined locations throughout the colon and terminal ileum and results were associated with concurrent clinical, endoscopic, and histologic parameters. RESULTS We found that host transcriptomics of distal fecal washes robustly classify histologic inflammation in ileal and proximal colonic Crohn's disease, even without distal colonic involvement (area under the receiver operating characteristic curve, 0.94 ± 0.09). We further found that fecal washes consist of modules of co-expressed genes of immune, stromal, and epithelial origin that are indicative of endoscopic disease severity. Fecal wash host transcriptomics also capture expression of gene modules previously associated with a lack of response to biological therapies. CONCLUSIONS Our study establishes the accuracy of distal colonic fecal washes for identifying and scoring inflammatory processes throughout the entire ileal-colonic axis.
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Affiliation(s)
- Stav Dan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bella Ungar
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Shani Ben-Moshe
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Miri Yavzori
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Ella Fudim
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Orit Picard
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Chaya Mushka Abitbol
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Sivan Harnik
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Uri Kopylov
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Shomron Ben-Horin
- Gastroenterology Institute, Sheba Medical Center Tel Hashomer, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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13
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Peters LA, Friedman JR, Stojmirovic A, Hagen J, Houten S, Dodatko T, Amaro MP, Restrepo P, Chai Z, Rodrigo Mora J, Raymond HA, Curran M, Dobrin R, Das A, Xiong H, Schadt EE, Argmann C, Losic B. A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients. Commun Biol 2023; 6:95. [PMID: 36694043 PMCID: PMC9873918 DOI: 10.1038/s42003-023-04469-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
Previous studies have conducted time course characterization of murine colitis models through transcriptional profiling of differential expression. We characterize the transcriptional landscape of acute and chronic models of dextran sodium sulfate (DSS) and adoptive transfer (AT) colitis to derive temporal gene expression and splicing signatures in blood and colonic tissue in order to capture dynamics of colitis remission and relapse. We identify sub networks of patient-derived causal networks that are enriched in these temporal signatures to distinguish acute and chronic disease components within the broader molecular landscape of IBD. The interaction between the DSS phenotype and chronological time-point naturally defines parsimonious temporal gene expression and splicing signatures associated with acute and chronic phases disease (as opposed to ordinary time-specific differential expression/splicing). We show these expression and splicing signatures are largely orthogonal, i.e. affect different genetic bodies, and that using machine learning, signatures are predictive of histopathological measures from both blood and intestinal data in murine colitis models as well as an independent cohort of IBD patients. Through access to longitudinal multi-scale profiling from disease tissue in IBD patient cohorts, we can apply this machine learning pipeline to generation of direct patient temporal multimodal regulatory signatures for prediction of histopathological outcomes.
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Affiliation(s)
- Lauren A. Peters
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Joshua R. Friedman
- grid.476706.40000 0004 7647 0615Spark Therapeutics, Philadelphia, PA USA ,grid.497530.c0000 0004 0389 4927Janssen Research & Development, LLC, Spring House, Philadelphia, PA USA
| | - Aleksandar Stojmirovic
- grid.497530.c0000 0004 0389 4927Janssen Research & Development, LLC, Spring House, Philadelphia, PA USA
| | - Jacob Hagen
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Sander Houten
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Tetyana Dodatko
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Mariana P. Amaro
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Paula Restrepo
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Zhi Chai
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - J. Rodrigo Mora
- grid.497530.c0000 0004 0389 4927Janssen Research & Development, LLC, Spring House, Philadelphia, PA USA ,grid.479574.c0000 0004 1791 3172Moderna, Cambridge, MA USA
| | - Holly A. Raymond
- grid.497530.c0000 0004 0389 4927Janssen Research & Development, LLC, Spring House, Philadelphia, PA USA
| | - Mark Curran
- grid.497530.c0000 0004 0389 4927Janssen Research & Development, LLC, Spring House, Philadelphia, PA USA
| | - Radu Dobrin
- grid.497530.c0000 0004 0389 4927Janssen Research & Development, LLC, Spring House, Philadelphia, PA USA ,Pathos AI, Berwyn, PA USA
| | - Anuk Das
- grid.497530.c0000 0004 0389 4927Janssen Research & Development, LLC, Spring House, Philadelphia, PA USA
| | - Huabao Xiong
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Eric E. Schadt
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Carmen Argmann
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Bojan Losic
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.511203.4Present Address: Guardant Health, Redwood City, CA USA
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14
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Lee JC. Going deeper: molecular inflammatory scores in IBD. Gut 2022:gutjnl-2022-328539. [PMID: 36307179 DOI: 10.1136/gutjnl-2022-328539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/14/2022] [Indexed: 12/08/2022]
Affiliation(s)
- James C Lee
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK .,Institute of Liver and Digestive Health, Royal Free Hospital, University College London, London, UK
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15
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Dong Y, Yang Q, Niu R, Zhang Z, Huang Y, Bi Y, Liu G. Modulation of tumor‐associated macrophages in colitis‐associated colorectal cancer. J Cell Physiol 2022; 237:4443-4459. [DOI: 10.1002/jcp.30906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Yingjie Dong
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences Beijing Normal University Beijing China
| | - Qiuli Yang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences Beijing Normal University Beijing China
| | - Ruiying Niu
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences Beijing Normal University Beijing China
| | - Zhiyuan Zhang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences Beijing Normal University Beijing China
| | - Yijin Huang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences Beijing Normal University Beijing China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and Epidemiology Beijing China
| | - Guangwei Liu
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences Beijing Normal University Beijing China
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