1
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Hasanaj E, Mathur S, Bar-Joseph Z. Integrating patients in time series clinical transcriptomics data. Bioinformatics 2024; 40:i151-i159. [PMID: 38940139 DOI: 10.1093/bioinformatics/btae241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION Analysis of time series transcriptomics data from clinical trials is challenging. Such studies usually profile very few time points from several individuals with varying response patterns and dynamics. Current methods for these datasets are mainly based on linear, global orderings using visit times which do not account for the varying response rates and subgroups within a patient cohort. RESULTS We developed a new method that utilizes multi-commodity flow algorithms for trajectory inference in large scale clinical studies. Recovered trajectories satisfy individual-based timing restrictions while integrating data from multiple patients. Testing the method on multiple drug datasets demonstrated an improved performance compared to prior approaches suggested for this task, while identifying novel disease subtypes that correspond to heterogeneous patient response patterns. AVAILABILITY AND IMPLEMENTATION The source code and instructions to download the data have been deposited on GitHub at https://github.com/euxhenh/Truffle.
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Affiliation(s)
- Euxhen Hasanaj
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Sachin Mathur
- R&D Data and Computational Sciences, Sanofi, Cambridge, MA 02141, United States
| | - Ziv Bar-Joseph
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States
- R&D Data and Computational Sciences, Sanofi, Cambridge, MA 02141, United States
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, United States
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2
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Xu B, Wen Y, Xu J, Rong Y, Wang X, Liu T. Inhibition of the STAT3-EPHX2 axis promotes regression of ulcerative colitis by treatment with novel porphyrin derivative. Bioorg Chem 2024; 150:107579. [PMID: 38908128 DOI: 10.1016/j.bioorg.2024.107579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/06/2024] [Accepted: 06/18/2024] [Indexed: 06/24/2024]
Abstract
LD4, a novel porphyrin derivative, has attracted much attention for its excellent anti-inflammatory properties. It can promote the healing of colonic mucosa, reduce inflammatory response, regulate oxidative stress, and thus improve ulcerative colitis (UC) symptoms. However, the specific signaling pathways of LD4-PDT involved in UC have not been explored. The present study aimed to elucidate the effects of LD4 on UC and to investigate the underlying mechanisms both in vivo and in vitro. We classified and screened the LD4-PDT proteomic data to obtain key targets. Proteomic data revealed that EPHX2 and STAT3 are key targets of LD4-PDT for UC. Moreover, transcription factor STAT3 positively regulates the expression of EPHX2. Inhibiting EPHX2 can prevent the activation of NF-κB signaling pathway. Next, through pharmacological inhibition experiments, we confirmed that LD4-PDT can reduce intestinal inflammation by inhibiting STAT3-EPHX2 axis. However, by treating normal intestinal epithelial cells and colon cancer cells with TPPU and Stattic, our data confirmed that the STAT3-EPHX2 axis does not exist in colon cancer. In this study, we demonstrated that the transcription factor STAT3 can positively regulate the expression of EPHX2 in normal colon. LD4 can alleviate UC by inhibiting the STAT3-EPHX2 axis, but this axis does not exist in colon cancer. LD4-PDT may become a new and effective method for treating UC.
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Affiliation(s)
- Bin Xu
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin 300192, China
| | - Ying Wen
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin 300192, China
| | - Jun Xu
- Jiangxi Synergy Pharmaceutical Co., Ltd, Yichun, Jiangxi 330700, China
| | - Yumei Rong
- The Third Central Hospital of Tianjin, 83 Jintang Road, Hedong District, Tianjin 300170, China
| | - Xueming Wang
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin 300192, China
| | - Tianjun Liu
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin 300192, China.
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3
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Kurumi H, Yokoyama Y, Hirano T, Akita K, Hayashi Y, Kazama T, Isomoto H, Nakase H. Cytokine Profile in Predicting the Effectiveness of Advanced Therapy for Ulcerative Colitis: A Narrative Review. Biomedicines 2024; 12:952. [PMID: 38790914 PMCID: PMC11117845 DOI: 10.3390/biomedicines12050952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Cytokine-targeted therapies have shown efficacy in treating patients with ulcerative colitis (UC), but responses to these advanced therapies can vary. This variability may be due to differences in cytokine profiles among patients with UC. While the etiology of UC is not fully understood, abnormalities of the cytokine profiles are deeply involved in its pathophysiology. Therefore, an approach focused on the cytokine profile of individual patients with UC is ideal. Recent studies have demonstrated that molecular analysis of cytokine profiles in UC can predict response to each advanced therapy. This narrative review summarizes the molecules involved in the efficacy of various advanced therapies for UC. Understanding these associations may be helpful in selecting optimal therapeutic agents.
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Affiliation(s)
- Hiroki Kurumi
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
- Division of Gastroenterology and Nephrology, Department of Multidisciplinary Internal Medicine, Tottori University Faculty of Medicine, 36-1, Nishi-cho, Yonago 683-8504, Tottori, Japan
| | - Yoshihiro Yokoyama
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
| | - Takehiro Hirano
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
| | - Kotaro Akita
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
| | - Yuki Hayashi
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
| | - Tomoe Kazama
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
| | - Hajime Isomoto
- Division of Gastroenterology and Nephrology, Department of Multidisciplinary Internal Medicine, Tottori University Faculty of Medicine, 36-1, Nishi-cho, Yonago 683-8504, Tottori, Japan
| | - Hiroshi Nakase
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
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4
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Cadinu P, Sivanathan KN, Misra A, Xu RJ, Mangani D, Yang E, Rone JM, Tooley K, Kye YC, Bod L, Geistlinger L, Lee T, Mertens RT, Ono N, Wang G, Sanmarco L, Quintana FJ, Anderson AC, Kuchroo VK, Moffitt JR, Nowarski R. Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling. Cell 2024; 187:2010-2028.e30. [PMID: 38569542 PMCID: PMC11017707 DOI: 10.1016/j.cell.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/20/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
Gut inflammation involves contributions from immune and non-immune cells, whose interactions are shaped by the spatial organization of the healthy gut and its remodeling during inflammation. The crosstalk between fibroblasts and immune cells is an important axis in this process, but our understanding has been challenged by incomplete cell-type definition and biogeography. To address this challenge, we used multiplexed error-robust fluorescence in situ hybridization (MERFISH) to profile the expression of 940 genes in 1.35 million cells imaged across the onset and recovery from a mouse colitis model. We identified diverse cell populations, charted their spatial organization, and revealed their polarization or recruitment in inflammation. We found a staged progression of inflammation-associated tissue neighborhoods defined, in part, by multiple inflammation-associated fibroblasts, with unique expression profiles, spatial localization, cell-cell interactions, and healthy fibroblast origins. Similar signatures in ulcerative colitis suggest conserved human processes. Broadly, we provide a framework for understanding inflammation-induced remodeling in the gut and other tissues.
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Affiliation(s)
- Paolo Cadinu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kisha N Sivanathan
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Aditya Misra
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Rosalind J Xu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Davide Mangani
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Evan Yang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph M Rone
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine Tooley
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yoon-Chul Kye
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Lloyd Bod
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ludwig Geistlinger
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, USA
| | - Tyrone Lee
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, USA
| | - Randall T Mertens
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Noriaki Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX 77030, USA
| | - Gang Wang
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Liliana Sanmarco
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Francisco J Quintana
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ana C Anderson
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Vijay K Kuchroo
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jeffrey R Moffitt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Roni Nowarski
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Mass General Hospital, and Harvard Medical School, Boston, MA 02115, USA; Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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5
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Dong Y, Johnson BA, Ruan L, Zeineldin M, Bi T, Liu AZ, Raychaudhuri S, Chiu I, Zhu J, Smith B, Zhao N, Searson P, Watanabe S, Donowitz M, Larman TC, Li R. Disruption of epithelium integrity by inflammation-associated fibroblasts through prostaglandin signaling. SCIENCE ADVANCES 2024; 10:eadj7666. [PMID: 38569041 PMCID: PMC10990275 DOI: 10.1126/sciadv.adj7666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024]
Abstract
Inflammation-associated fibroblasts (IAFs) are associated with progression and drug resistance of chronic inflammatory diseases such as inflammatory bowel disease (IBD), but their direct impact on epithelial cells is unknown. Here, we developed an in vitro model whereby human colon fibroblasts are induced by specific cytokines and recapitulate key features of IAFs in vivo. When cocultured with patient-derived colon organoids (colonoids), IAFs induced rapid colonoid expansion and barrier disruption due to swelling and rupture of individual epithelial cells. Colonoids cocultured with IAFs also show increased DNA damage, mitotic errors, and proliferation arrest. These IAF-induced epithelial defects are mediated by a paracrine pathway involving prostaglandin E2 and its receptor EP4, leading to protein kinase A -dependent activation of the cystic fibrosis transmembrane conductance regulator. EP4-specific chemical inhibitors effectively prevented IAF-induced colonoid swelling and restored normal proliferation and genome stability. These findings reveal a mechanism by which IAFs could promote and perpetuate IBD and suggest a therapeutic avenue to mitigate inflammation-associated epithelial injury.
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Affiliation(s)
- Yi Dong
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Blake A. Johnson
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Linhao Ruan
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Maged Zeineldin
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Tianhao Bi
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Albert Z. Liu
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ian Chiu
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Jin Zhu
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Barbara Smith
- Microscope Facility, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Nan Zhao
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Peter Searson
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Mark Donowitz
- Department of Medicine, Division of Gastroenterology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Tatianna C. Larman
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Rong Li
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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6
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Boles JS, Krueger ME, Jernigan JE, Cole CL, Neighbarger NK, Uriarte Huarte O, Tansey MG. A leaky gut dysregulates gene networks in the brain associated with immune activation, oxidative stress, and myelination in a mouse model of colitis. Brain Behav Immun 2024; 117:473-492. [PMID: 38341052 DOI: 10.1016/j.bbi.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/23/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024] Open
Abstract
The gut and brain are increasingly linked in human disease, with neuropsychiatric conditions classically attributed to the brain showing an involvement of the intestine and inflammatory bowel diseases (IBDs) displaying an ever-expanding list of neurological comorbidities. To identify molecular systems that underpin this gut-brain connection and thus discover therapeutic targets, experimental models of gut dysfunction must be evaluated for brain effects. In the present study, we examine disturbances along the gut-brain axis in a widely used murine model of colitis, the dextran sodium sulfate (DSS) model, using high-throughput transcriptomics and an unbiased network analysis strategy coupled with standard biochemical outcome measures to achieve a comprehensive approach to identify key disease processes in both colon and brain. We examine the reproducibility of colitis induction with this model and its resulting genetic programs during different phases of disease, finding that DSS-induced colitis is largely reproducible with a few site-specific molecular features. We focus on the circulating immune system as the intermediary between the gut and brain, which exhibits an activation of pro-inflammatory innate immunity during colitis. Our unbiased transcriptomics analysis provides supporting evidence for immune activation in the brain during colitis, suggests that myelination may be a process vulnerable to increased intestinal permeability, and identifies a possible role for oxidative stress and brain oxygenation. Overall, we provide a comprehensive evaluation of multiple systems in a prevalent experimental model of intestinal permeability, which will inform future studies using this model and others, assist in the identification of druggable targets in the gut-brain axis, and contribute to our understanding of the concomitance of intestinal and neuropsychiatric dysfunction.
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Affiliation(s)
- Jake Sondag Boles
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA; McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
| | - Maeve E Krueger
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA; McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Janna E Jernigan
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA; McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Cassandra L Cole
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA; McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Noelle K Neighbarger
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA; McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Oihane Uriarte Huarte
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA; McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Malú Gámez Tansey
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA; McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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7
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Kvedaraite E, Lourda M, Mouratidou N, Düking T, Padhi A, Moll K, Czarnewski P, Sinha I, Xagoraris I, Kokkinou E, Damdimopoulos A, Weigel W, Hartwig O, Santos TE, Soini T, Van Acker A, Rahkonen N, Flodström Tullberg M, Ringqvist E, Buggert M, Jorns C, Lindforss U, Nordenvall C, Stamper CT, Unnersjö-Jess D, Akber M, Nadisauskaite R, Jansson J, Vandamme N, Sorini C, Grundeken ME, Rolandsdotter H, Rassidakis G, Villablanca EJ, Ideström M, Eulitz S, Arnell H, Mjösberg J, Henter JI, Svensson M. Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF. Nat Commun 2024; 15:1752. [PMID: 38409190 PMCID: PMC10897309 DOI: 10.1038/s41467-024-46076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 02/09/2024] [Indexed: 02/28/2024] Open
Abstract
Stromal cells support epithelial cell and immune cell homeostasis and play an important role in inflammatory bowel disease (IBD) pathogenesis. Here, we quantify the stromal response to inflammation in pediatric IBD and reveal subset-specific inflammatory responses across colon segments and intestinal layers. Using data from a murine dynamic gut injury model and human ex vivo transcriptomic, protein and spatial analyses, we report that PDGFRA+CD142-/low fibroblasts and monocytes/macrophages co-localize in the intestine. In primary human fibroblast-monocyte co-cultures, intestinal PDGFRA+CD142-/low fibroblasts foster monocyte transition to CCR2+CD206+ macrophages through granulocyte-macrophage colony-stimulating factor (GM-CSF). Monocyte-derived CCR2+CD206+ cells from co-cultures have a phenotype similar to intestinal CCR2+CD206+ macrophages from newly diagnosed pediatric IBD patients, with high levels of PD-L1 and low levels of GM-CSF receptor. The study describes subset-specific changes in stromal responses to inflammation and suggests that the intestinal stroma guides intestinal macrophage differentiation.
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Affiliation(s)
- Egle Kvedaraite
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden.
| | - Magda Lourda
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Natalia Mouratidou
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Tim Düking
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Avinash Padhi
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Dermatology and Venereology Section, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kirsten Moll
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Paulo Czarnewski
- Science for Life Laboratory, Department of Biochemistry and Biophysics and National Bioinformatics Infrastructure Sweden, Stockholm University, Solna, Sweden
| | - Indranil Sinha
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Ioanna Xagoraris
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Efthymia Kokkinou
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anastasios Damdimopoulos
- Bioinformatics and Expression Analysis Core Facility, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Whitney Weigel
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Olga Hartwig
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Telma E Santos
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Tea Soini
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Aline Van Acker
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Tech Watch, Flanders Institute for Biotechnology, Ghent, Belgium
| | - Nelly Rahkonen
- Integrated Cardio Metabolic Centre, Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
| | - Malin Flodström Tullberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Ringqvist
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Carl Jorns
- Department of Transplantation Surgery, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Ulrik Lindforss
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Pelvic Cancer, GI Oncology and Colorectal Surgery Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Nordenvall
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Pelvic Cancer, GI Oncology and Colorectal Surgery Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Christopher T Stamper
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - David Unnersjö-Jess
- Science for Life Laboratory, Dept. of Applied Physics, Royal Institute of Technology, Solna, Sweden
| | - Mira Akber
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ruta Nadisauskaite
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jessica Jansson
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Niels Vandamme
- VIB Single Cell Core, VIB, Ghent, Belgium
- VIB-UGent Center for Inflammation Research, 9052, Ghent, Belgium
| | - Chiara Sorini
- Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Marijke Elise Grundeken
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Helena Rolandsdotter
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children and Youth Hospital, Department of Gastroenterology, Södersjukhuset, Stockholm, Sweden
| | - George Rassidakis
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Eduardo J Villablanca
- Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Maja Ideström
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Stefan Eulitz
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Henrik Arnell
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jan-Inge Henter
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Theme of Children's Health, Karolinska University Hospital, Stockholm, Sweden
| | - Mattias Svensson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
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8
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Gadjalova I, Heinze JM, Goess MC, Hofmann J, Buck A, Weber MC, Blissenbach B, Kampick M, Krut O, Steiger K, Janssen KP, Neumann PA, Ruland J, Keppler SJ. B cell-mediated CD4 T-cell costimulation via CD86 exacerbates pro-inflammatory cytokine production during autoimmune intestinal inflammation. Mucosal Immunol 2024; 17:67-80. [PMID: 37918715 DOI: 10.1016/j.mucimm.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Dysregulated B cell responses have been described in inflammatory bowel disease (IBD) patients; however, the role of B cells in IBD pathology remained incompletely understood. We here provide evidence for the detrimental role of activated B cells during the onset of autoimmune intestinal inflammation. Using Wiskott-Aldrich Syndrome interacting protein deficient (Wipf1-/-) mice as a mouse model of chronic colitis, we identified clusters of differentiation (CD)86 expression on activated B cells as a crucial factor exacerbating pro-inflammatory cytokine production of intestinal CD4 T cells. Depleting B cells through anti-CD20 antibody treatment or blocking costimulatory signals mediated by CD86 through cytotoxic T lymphocyte antigen-4-immunoglobulin (CTLA-4-Ig) diminished intestinal inflammation in our mouse model of chronic IBD at the onset of disease. This was due to a reduction in aberrant humoral immune responses and reduced CD4 T cell pro-inflammatory cytokine production, especially interferon-g (IFN-g) and granulocyte-macrophage colony-stimulating factor (GM-CSF). Interestingly, in addition to B cells isolated from the inflamed colon of Wipf1-/- mice, we also found CD86 mRNA and protein expression upregulated on activated B cells isolated from inflamed tissue of human patients with IBD. B cell activation and CD86 expression were boosted by soluble CD40L in vitro, which we found in the serum of mice and human patients with IBD. In summary, our data provides detailed insight into the contribution of B cells to intestinal inflammation, with implications for the treatment of IBD.
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Affiliation(s)
- Iana Gadjalova
- Institute for Clinical Chemistry and Pathobiochemistry, Technical University of Munich, School of Medicine, Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University Munich, Munich, Germany
| | - Julia M Heinze
- Institute for Clinical Chemistry and Pathobiochemistry, Technical University of Munich, School of Medicine, Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University Munich, Munich, Germany
| | - Marie C Goess
- Institute for Clinical Chemistry and Pathobiochemistry, Technical University of Munich, School of Medicine, Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University Munich, Munich, Germany
| | - Julian Hofmann
- Institute for Clinical Chemistry and Pathobiochemistry, Technical University of Munich, School of Medicine, Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University Munich, Munich, Germany
| | - Annalisa Buck
- Department of Surgery, Technical University of Munich, School of Medicine, Munich, Germany
| | - Marie-Christin Weber
- Department of Surgery, Technical University of Munich, School of Medicine, Munich, Germany
| | | | - Maximilian Kampick
- Institute for Clinical Chemistry and Pathobiochemistry, Technical University of Munich, School of Medicine, Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University Munich, Munich, Germany
| | - Oleg Krut
- Paul-Ehrlich-Institut, Langen, Germany
| | - Katja Steiger
- Comparative Experimental Pathology, Institute of Pathology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Technical University of Munich, School of Medicine, Munich, Germany
| | | | - Jürgen Ruland
- Institute for Clinical Chemistry and Pathobiochemistry, Technical University of Munich, School of Medicine, Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University Munich, Munich, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; German Center for Infection Research (DZIF), Munich, Germany
| | - Selina J Keppler
- Institute for Clinical Chemistry and Pathobiochemistry, Technical University of Munich, School of Medicine, Munich, Germany; TranslaTUM, Center for Translational Cancer Research, Technical University Munich, Munich, Germany; Division of Rheumatology and Clinical Immunology, Medical University Graz, Graz, Austria.
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9
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Wacker EM, Uellendahl-Werth F, Bej S, Wolkenhauer O, Vesterhus M, Lieb W, Franke A, Karlsen TH, Folseraas T, Ellinghaus D. Whole blood RNA sequencing identifies transcriptional differences between primary sclerosing cholangitis and ulcerative colitis. JHEP Rep 2024; 6:100988. [PMID: 38304234 PMCID: PMC10832281 DOI: 10.1016/j.jhepr.2023.100988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/10/2023] [Accepted: 12/06/2023] [Indexed: 02/03/2024] Open
Abstract
Background & Aims Genetic and microbiome studies across patients with primary sclerosing cholangitis (PSC) and ulcerative colitis (UC) have indicated that UC in PSC is a separate disease entity to primary UC, but expression studies for PSC are lacking. Methods We conducted whole blood RNA sequencing experiments for 495 patients with UC, 220 patients with PSC (including 177 with UC), and 320 healthy controls from Germany and Norway. Differential expression analyses, gene ontology and coexpression analyses and random forest machine learning were performed to identify genes, ontologies and transcriptional features that discriminate diagnoses. Results The blood transcriptome in UC and PSC is dominated by neutrophil activation genes (e.g. S100A12). In UC, but not in PSC (neither PSC alone nor patients with an additional diagnosis of UC [PSC/UC]), ribosomal, mitochondrial, and energy metabolism genes are upregulated in conjunction with antibody transcript expression (MZB1, IGJ). In PSC, there is an increase in modules related to apoptosis and expression of genes of interferon-I-related ontologies. Random forest analysis could poorly discriminate PSC alone from PSC/UC (AUROC 0.56), but could discriminate PSC, UC, and controls with high accuracy (AUROC UC vs. controls 0.95, PSC vs. controls 0.88, UC vs. PSC 0.986). The main coexpression modules relevant for distinguishing PSC, UC, and controls are enriched in neutrophil degranulation and antibody production genes. Conclusions Supported by machine learning results, PSC and UC appear to be separate entities on a molecular level, while PSC/UC and PSC are indistinguishable. Impact and implications Clinical and genetic studies suggest that the colitis-like symptoms in primary sclerosing cholangitis (PSC) represent a different disease entity from primary ulcerative colitis (UC). The present study supports this assumption with transcriptomic data from whole blood and describes notable differences in gene expression between primary UC and PSC, providing insights into the still unclear pathophysiology of both diseases. These findings are of interest to scientists seeking to decipher the molecular pathophysiology of both diseases and provide evidence that a redefinition of the PSC-UC phenotype should be considered. The study practically supports future molecular research by providing a large transcriptomic whole blood reference cohort.
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Affiliation(s)
- Eike Matthias Wacker
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Saptarshi Bej
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Indian Institute of Science Education and Research, Thiruvananthapuram, India
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University Munich, Munich, Germany
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Mette Vesterhus
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
- Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tom Hemming Karlsen
- Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Trine Folseraas
- Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
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10
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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] [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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11
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Moutin EB, Bons J, Giavara G, Lourenco F, Pan D, Burton JB, Shah S, Colombé M, Gascard P, Tlsty T, Schilling B, Winton DJ. Extracellular Matrix Orchestration of Tissue Remodeling in the Chronically Inflamed Mouse Colon. Cell Mol Gastroenterol Hepatol 2024; 17:639-656. [PMID: 38199279 PMCID: PMC10905044 DOI: 10.1016/j.jcmgh.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
BACKGROUND & AIMS Chronic inflammatory illnesses are debilitating and recurrent conditions associated with significant comorbidities, including an increased risk of developing cancer. Extensive tissue remodeling is a hallmark of such illnesses, and is both a consequence and a mediator of disease progression. Despite previous characterization of epithelial and stromal remodeling during inflammatory bowel disease, a complete understanding of its impact on disease progression is lacking. METHODS A comprehensive proteomic pipeline using data-independent acquisition was applied to decellularized colon samples from the Muc2 knockout (Muc2KO) mouse model of colitis for an in-depth characterization of extracellular matrix remodeling. Unique proteomic profiles of the matrisomal landscape were extracted from prepathologic and overt colitis. Integration of proteomics and transcriptomics data sets extracted from the same murine model produced network maps describing the orchestrating role of matrisomal proteins in tissue remodeling during the progression of colitis. RESULTS The in-depth proteomic workflow used here allowed the addition of 34 proteins to the known colon matrisomal signature. Protein signatures of prepathologic and pathologic colitic states were extracted, differentiating the 2 states by expression of small leucine-rich proteoglycans. We outlined the role of this class and other matrisomal proteins in tissue remodeling during colitis, as well as the potential for coordinated regulation of cell types by matrisomal ligands. CONCLUSIONS Our work highlights a central role for matrisomal proteins in tissue remodeling during colitis and defines orchestrating nodes that can be exploited in the selection of therapeutic targets.
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Affiliation(s)
- Elisa B Moutin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, California
| | - Giada Giavara
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Filipe Lourenco
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Deng Pan
- Department of Pathology, University of California, San Francisco, California
| | | | - Samah Shah
- Buck Institute for Research on Aging, Novato, California
| | - Mathilde Colombé
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Philippe Gascard
- Department of Pathology, University of California, San Francisco, California
| | - Thea Tlsty
- Department of Pathology, University of California, San Francisco, California
| | | | - Douglas J Winton
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom.
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12
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Chiriac MT, Hracsko Z, Günther C, Gonzalez-Acera M, Atreya R, Stolzer I, Wittner L, Dressel A, Schickedanz L, Gamez-Belmonte R, Erkert L, Hundorfean G, Zundler S, Rath T, Vetrano S, Danese S, Sturm G, Trajanoski Z, Kühl AA, Siegmund B, Hartmann A, Wirtz S, Siebler J, Finotto S, Becker C, Neurath MF. IL-20 controls resolution of experimental colitis by regulating epithelial IFN/STAT2 signalling. Gut 2024; 73:282-297. [PMID: 37884352 PMCID: PMC10850655 DOI: 10.1136/gutjnl-2023-329628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 09/10/2023] [Indexed: 10/28/2023]
Abstract
OBJECTIVE We sought to investigate the role of interleukin (IL)-20 in IBD and experimental colitis. DESIGN Experimental colitis was induced in mice deficient in components of the IL-20 and signal transducer and activator of transcription (STAT)2 signalling pathways. In vivo imaging, high-resolution mini-endoscopy and histology were used to assess intestinal inflammation. We further used RNA-sequencing (RNA-Seq), RNAScope and Gene Ontology analysis, western blot analysis and co-immunoprecipitation, confocal microscopy and intestinal epithelial cell (IEC)-derived three-dimensional organoids to investigate the underlying molecular mechanisms. Results were validated using samples from patients with IBD and non-IBD control subjects by a combination of RNA-Seq, organoids and immunostainings. RESULTS In IBD, IL20 levels were induced during remission and were significantly higher in antitumour necrosis factor responders versus non-responders. IL-20RA and IL-20RB were present on IECs from patients with IBD and IL-20-induced STAT3 and suppressed interferon (IFN)-STAT2 signalling in these cells. In IBD, experimental dextran sulfate sodium (DSS)-induced colitis and mucosal healing, IECs were the main producers of IL-20. Compared with wildtype controls, Il20-/-, Il20ra-/- and Il20rb-/- mice were more susceptible to experimental DSS-induced colitis. IL-20 deficiency was associated with increased IFN/STAT2 activity in mice and IFN/STAT2-induced necroptotic cell death in IEC-derived organoids could be markedly blocked by IL-20. Moreover, newly generated Stat2ΔIEC mice, lacking STAT2 in IECs, were less susceptible to experimental colitis compared with wildtype controls and the administration of IL-20 suppressed colitis activity in wildtype animals. CONCLUSION IL-20 controls colitis and mucosal healing by interfering with the IFN/STAT2 death signalling pathway in IECs. These results indicate new directions for suppressing gut inflammation by modulating IL-20-controlled STAT2 signals.
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Affiliation(s)
- Mircea Teodor Chiriac
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
| | - Zsuzsanna Hracsko
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Claudia Günther
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
| | - Miguel Gonzalez-Acera
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Raja Atreya
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, and the Ludwig Demling Endoscopy Center of Excellence, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Iris Stolzer
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Leonie Wittner
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Anja Dressel
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Laura Schickedanz
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Reyes Gamez-Belmonte
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Lena Erkert
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Gheorghe Hundorfean
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, and the Ludwig Demling Endoscopy Center of Excellence, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Sebastian Zundler
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
| | - Timo Rath
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, and the Ludwig Demling Endoscopy Center of Excellence, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Stefania Vetrano
- IBD Center, Department of Gastroenterology, IRCCS Humanitas Research Hospital, Rozzano, Italy
- Pieve Emanuele, Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Silvio Danese
- Department of Gastroenterology and Digestive Endoscopy & Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milano, Italy
- Faculty of Medicine, Universita Vita Salute San Raffaele, Milano, Italy
| | - Gregor Sturm
- Medical University of Innsbruck, Biocenter, Institute of Bioinformatics, Innsbruck, Austria
| | - Zlatko Trajanoski
- Medical University of Innsbruck, Biocenter, Institute of Bioinformatics, Innsbruck, Austria
| | - Anja A Kühl
- iPATH.Berlin, Core Unit of Charité, Campus Benjamin Franklin, Charite Universitatsmedizin Berlin, Berlin, Germany
| | - Britta Siegmund
- Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Medical Department, Division of Gastroenterology, Infectious Diseases and Rheumatology, Campus Benjamin Franklin, Charite Universitatsmedizin Berlin, Berlin, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Stefan Wirtz
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
| | - Jürgen Siebler
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, and the Ludwig Demling Endoscopy Center of Excellence, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Susetta Finotto
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
- Department of Molecular Pneumology, University Hospital Erlangen, Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany
| | - Christoph Becker
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
| | - Markus F Neurath
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Erlangen, Germany
- Department of Medicine 1, Gastroenterology, Endocrinology and Pneumology, and the Ludwig Demling Endoscopy Center of Excellence, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
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13
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Ahmad R, Kumar B, Thapa I, Tamang RL, Yadav SK, Washington MK, Talmon GA, Yu AS, Bastola DK, Dhawan P, Singh AB. Claudin-2 protects against colitis-associated cancer by promoting colitis-associated mucosal healing. J Clin Invest 2023; 133:e170771. [PMID: 37815870 PMCID: PMC10688979 DOI: 10.1172/jci170771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023] Open
Abstract
Patients with inflammatory bowel disease (IBD) are susceptible to colitis-associated cancer (CAC). Chronic inflammation promotes the risk for CAC. In contrast, mucosal healing predicts improved prognosis in IBD and reduced risk of CAC. However, the molecular integration among colitis, mucosal healing, and CAC remains poorly understood. Claudin-2 (CLDN2) expression is upregulated in IBD; however, its role in CAC is not known. The current study was undertaken to examine the role for CLDN2 in CAC. The AOM/DSS-induced CAC model was used with WT and CLDN2-modified mice. High-throughput expression analyses, murine models of colitis/recovery, chronic colitis, ex vivo crypt culture, and pharmacological manipulations were employed in order to increase our mechanistic understanding. The Cldn2KO mice showed significant inhibition of CAC despite severe colitis compared with WT littermates. Cldn2 loss also resulted in impaired recovery from colitis and increased injury when mice were subjected to intestinal injury by other methods. Mechanistic studies demonstrated a possibly novel role of CLDN2 in promotion of mucosal healing downstream of EGFR signaling and by regulation of Survivin expression. An upregulated CLDN2 expression protected from CAC and associated positively with crypt regeneration and Survivin expression in patients with IBD. We demonstrate a potentially novel role of CLDN2 in promotion of mucosal healing in patients with IBD and thus regulation of vulnerability to colitis severity and CAC, which can be exploited for improved clinical management.
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Affiliation(s)
- Rizwan Ahmad
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Balawant Kumar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Ishwor Thapa
- School of Interdisciplinary Informatics, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Raju Lama Tamang
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Santosh K. Yadav
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Mary K. Washington
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Geoffrey A. Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Alan S. Yu
- Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Dhundy K. Bastola
- School of Interdisciplinary Informatics, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Punita Dhawan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
- VA Nebraska-Western Iowa Health Care System, Omaha, Nebraska, USA
| | - Amar B. Singh
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
- VA Nebraska-Western Iowa Health Care System, Omaha, Nebraska, USA
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14
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Peña-Cearra A, Castelo J, Lavín JL, Gonzalez-Lopez M, Pascual-Itoiz MA, Fuertes M, Gutiérrez de Juan V, Bárcena L, Martín-Ruiz I, Pellón A, Seoane I, Barriales D, Palacios A, Fullaondo A, Rodríguez-Lago I, Martinez-Chantar ML, Aransay AM, Rodriguez H, Anguita J, Abecia L. Mitochondrial dysfunction-associated microbiota establishes a transmissible refractory response to anti-TNF therapy during ulcerative colitis. Gut Microbes 2023; 15:2266626. [PMID: 37842919 PMCID: PMC10586225 DOI: 10.1080/19490976.2023.2266626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023] Open
Abstract
Anti-TNF therapy can induce and maintain a remission status during intestinal bowel disease. However, up to 30% of patients do not respond to this therapy by mechanisms that are unknown. Here, we show that the absence of MCJ, a natural inhibitor of the respiratory chain Complex I, induces gut microbiota changes that are critical determinants of the lack of response in a murine model of DSS-induced inflammation. First, we found that MCJ expression is restricted to macrophages in human colonic tissue. Therefore, we demonstrate by transcriptomic analysis of colon macrophages from DSS-induced mice that MCJ-deficiency is linked to the expression of genes belonging to the FcγR signaling pathway and contains an anti-TNF refractory gene signature identified in ulcerative colitis patients. The gut microbial composition changes observed upon DSS treatment in the MCJ-deficient mice revealed the increased presence of specific colitogenic members, including Ruminococcus gnavus and Oscillospira, which could be associated with the non-response to TNF inhibitors. Further, we show that the presence of a microbiota associated resistance to treatment is dominant and transmissible to responsive individuals. Collectively, our findings underscore the critical role played by macrophage mitochondrial function in the gut ecological niche that can substantially affect not only the severity of inflammation but also the ability to successfully respond to current therapies.
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Affiliation(s)
- Ainize Peña-Cearra
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
- Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Janire Castelo
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Jose Luis Lavín
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
- Applied Mathematics Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | | | | | - Miguel Fuertes
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | | | - Laura Bárcena
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Itziar Martín-Ruiz
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Aize Pellón
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Iratxe Seoane
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Diego Barriales
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Ainhoa Palacios
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Asier Fullaondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | | | - María L. Martinez-Chantar
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
- CIBERehd, ISCIII, Madrid, Spain
| | - Ana Mª Aransay
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
- CIBERehd, ISCIII, Madrid, Spain
| | - Hector Rodriguez
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Juan Anguita
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Leticia Abecia
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
- Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Bilbao, Spain
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15
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Salvatori S, Neri B, Marafini I, Brigida M, Monteleone G. Emerging oral drug options for ulcerative colitis. Expert Opin Emerg Drugs 2023; 28:191-201. [PMID: 37668153 DOI: 10.1080/14728214.2023.2254686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/22/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
INTRODUCTION Despite the availability of a variety of therapeutic compounds and improved management strategies, one-third of UC patients with moderate-to-severe disease do not benefit from the existing treatments or experience drug-related side effects. This has boosted intensive research focusing on the development of new drugs for UC therapy. This article aims to summarize the available evidence on oral drugs, which are now being explored in clinical trials or are ready to enter the clinics. AREAS COVERED From May 15 to June 11, we searched on PubMed using the keywords 'oral drugs ulcerative colitis,' 'ulcerative colitis clinical trials,' 'UC phase 2 and 3 trials' excluding case reports, case series, phase 1 and 4 studies, and studies about approved therapies. EXPERT OPINION The findings discussed in this article suggest that the future treatment of UC patients will be probably characterized by the possibility of using various small-molecule drugs. All these new compounds, even those belonging to the same class, differ in terms of efficacy and safety. Identification of predictors of response could help optimize the efficacy and safety of these treatments, thus improving resource allocation through a pretreatment stratification of patients.
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Affiliation(s)
- Silvia Salvatori
- Gastroenterology Unit, Policlinico Universitario Tor Vergata, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Benedetto Neri
- Gastroenterology Unit, Policlinico Universitario Tor Vergata, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Irene Marafini
- Gastroenterology Unit, Policlinico Universitario Tor Vergata, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Mattia Brigida
- Gastroenterology Unit, Policlinico Universitario Tor Vergata, Rome, Italy
| | - Giovanni Monteleone
- Gastroenterology Unit, Policlinico Universitario Tor Vergata, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
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16
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Bahar Halpern K, Korem Kohanim Y, Biram A, Harnik Y, Egozi A, Yakubovsky O, Shulman Z, Itzkovitz S. The cellular states and fates of shed intestinal cells. Nat Metab 2023; 5:1858-1869. [PMID: 37857731 DOI: 10.1038/s42255-023-00905-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 09/11/2023] [Indexed: 10/21/2023]
Abstract
The intestinal epithelium is replaced every few days1. Enterocytes are shed into the gut lumen predominantly from the tips of villi2,3 and have been believed to rapidly die upon their dissociation from the tissue4,5. However, technical limitations prohibited studying the cellular states and fates of shed intestinal cells. Here we show that shed epithelial cells remain viable and upregulate distinct anti-microbial programmes upon shedding, using bulk and single-cell RNA sequencing of male mouse intestinal faecal washes. We further identify abundant shedding of immune cells, which is elevated in mice with dextran sulfate sodium-induced colitis. We find that faecal host transcriptomics reflect changes in the intestinal tissue following perturbations. Our study suggests potential functions of shed cells in the intestinal lumen and demonstrates that host cell transcriptomes in intestinal washes can be used to probe tissue states.
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Affiliation(s)
- Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Yael Korem Kohanim
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Adi Biram
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yotam Harnik
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Oran Yakubovsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of General Surgery and Transplantation, Sheba Medical Center, Tel-Hashomer, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ziv Shulman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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17
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Kovatcheva M, Melendez E, Chondronasiou D, Pietrocola F, Bernad R, Caballe A, Junza A, Capellades J, Holguín-Horcajo A, Prats N, Durand S, Rovira M, Yanes O, Stephan-Otto Attolini C, Kroemer G, Serrano M. Vitamin B 12 is a limiting factor for induced cellular plasticity and tissue repair. Nat Metab 2023; 5:1911-1930. [PMID: 37973897 PMCID: PMC10663163 DOI: 10.1038/s42255-023-00916-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 09/27/2023] [Indexed: 11/19/2023]
Abstract
Transient reprogramming by the expression of OCT4, SOX2, KLF4 and MYC (OSKM) is a therapeutic strategy for tissue regeneration and rejuvenation, but little is known about its metabolic requirements. Here we show that OSKM reprogramming in mice causes a global depletion of vitamin B12 and molecular hallmarks of methionine starvation. Supplementation with vitamin B12 increases the efficiency of reprogramming both in mice and in cultured cells, the latter indicating a cell-intrinsic effect. We show that the epigenetic mark H3K36me3, which prevents illegitimate initiation of transcription outside promoters (cryptic transcription), is sensitive to vitamin B12 levels, providing evidence for a link between B12 levels, H3K36 methylation, transcriptional fidelity and efficient reprogramming. Vitamin B12 supplementation also accelerates tissue repair in a model of ulcerative colitis. We conclude that vitamin B12, through its key role in one-carbon metabolism and epigenetic dynamics, improves the efficiency of in vivo reprogramming and tissue repair.
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Affiliation(s)
- Marta Kovatcheva
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Elena Melendez
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Dafni Chondronasiou
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Federico Pietrocola
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Raquel Bernad
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Adrià Caballe
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Alexandra Junza
- Universitat Rovira i Virgili, Department of Electronic Engineering, IISPV, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Capellades
- Universitat Rovira i Virgili, Department of Electronic Engineering, IISPV, Tarragona, Spain
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Metabolomics Platform, Reus, Spain
| | - Adrián Holguín-Horcajo
- Department of Physiological Science, School of Medicine, Universitat de Barcelona (UB), L'Hospitalet de Llobregat, Spain
- Pancreas Regeneration: Pancreatic Progenitors and Their Niche Group, Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
| | - Neus Prats
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sylvere Durand
- Metabolomics and Cell Biology Platforms UMS AMMICa/UMR 1138, Institut Gustave Roussy, Villejuif, France
- Equipe labellisée par la Ligue contre le cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université de Paris, Sorbonne Université, Institut Universitaire de France, Paris, France
| | - Meritxell Rovira
- Department of Physiological Science, School of Medicine, Universitat de Barcelona (UB), L'Hospitalet de Llobregat, Spain
- Pancreas Regeneration: Pancreatic Progenitors and Their Niche Group, Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
| | - Oscar Yanes
- Universitat Rovira i Virgili, Department of Electronic Engineering, IISPV, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms UMS AMMICa/UMR 1138, Institut Gustave Roussy, Villejuif, France
- Equipe labellisée par la Ligue contre le cancer, Centre de Recherche des Cordeliers, Inserm U1138, Université de Paris, Sorbonne Université, Institut Universitaire de France, Paris, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
- Altos Labs, Cambridge Institute of Science, Cambridge, UK.
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18
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Laudisi F, Stolfi C, Monteleone I, Monteleone G. TGF-β1 signaling and Smad7 control T-cell responses in health and immune-mediated disorders. Eur J Immunol 2023; 53:e2350460. [PMID: 37611637 DOI: 10.1002/eji.202350460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/14/2023] [Accepted: 08/22/2023] [Indexed: 08/25/2023]
Abstract
Transforming growth factor (TGF)-β1, a member of the TGF-β superfamily, is produced by many immune and nonimmune cells and has pleiotropic effects on both innate and adaptive immunity, especially in the control of T-cell differentiation and function. Consistently, loss of TGF-β1 function is associated with exacerbated T-cell-dependent inflammatory responses that culminate in pathological processes in allergic and immune-mediated diseases. In this review, we highlight the roles of TGF-β1 in immunity, focusing mainly on its ability to promote differentiation of regulatory T cells, T helper (Th)-17, and Th9 cells, thus contributing to amplifying or restricting T-cell responses in health and human diseases (e.g., inflammatory bowel diseases, type 1 diabetes, asthma, and MS). In addition, we discuss the involvement of Smad7, an inhibitor of TGF-β1 signaling, in immune-mediated disorders (e.g., psoriasis, rheumatoid arthritis, MS, and inflammatory bowel diseases), as well as the discordant results of clinical trials with mongersen, an oral pharmaceutical compound containing a Smad7 antisense oligonucleotide, in patients with Crohn's disease. Further work is needed to ascertain the reasons for such a discrepancy as well as to identify better candidates for treatment with Smad7 inhibitors.
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Affiliation(s)
- Federica Laudisi
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Carmine Stolfi
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Ivan Monteleone
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Giovanni Monteleone
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
- Gastroenterology Unit, Azienda Ospedaliera Policlinico Tor Vergata, Rome, Italy
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19
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Castrillón-Betancur JC, López-Agudelo VA, Sommer N, Cleeves S, Bernardes JP, Weber-Stiehl S, Rosenstiel P, Sommer F. Epithelial Dual Oxidase 2 Shapes the Mucosal Microbiome and Contributes to Inflammatory Susceptibility. Antioxidants (Basel) 2023; 12:1889. [PMID: 37891968 PMCID: PMC10603924 DOI: 10.3390/antiox12101889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/03/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Reactive oxygen species (ROS) are highly reactive molecules formed from diatomic oxygen. They act as cellular signals, exert antibiotic activity towards invading microorganisms, but can also damage host cells. Dual oxidase 2 (DUOX2) is the main ROS-producing enzyme in the intestine, regulated by cues of the commensal microbiota and functions in pathogen defense. DUOX2 plays multiple roles in different organs and cell types, complicating the functional analysis using systemic deletion models. Here, we interrogate the precise role of epithelial DUOX2 for intestinal homeostasis and host-microbiome interactions. Conditional Duox2∆IEC mice lacking DUOX2, specifically in intestinal epithelial cells, were generated, and their intestinal mucosal immune phenotype and microbiome were analyzed. Inflammatory susceptibility was evaluated by challenging Duox2∆IEC mice in the dextran sodium sulfate (DSS) colitis model. DUOX2-microbiome interactions in humans were investigated by paired analyses of mucosal DUOX2 expression and fecal microbiome data in patients with intestinal inflammation. Under unchallenged conditions, we did not observe any obvious phenotype of Duox2∆IEC mice, although intestinal epithelial ROS production was drastically decreased, and the mucosal microbiome composition was altered. When challenged with DSS, Duox2∆IEC mice were protected from colitis, possibly by inhibiting ROS-mediated damage and fostering epithelial regenerative responses. Finally, in patients with intestinal inflammation, DUOX2 expression was increased in inflamed tissue, and high DUOX2 levels were linked to a dysbiotic microbiome. Our findings demonstrate that bidirectional DUOX2-microbiome interactions contribute to mucosal homeostasis, and their dysregulation may drive disease development, thus highlighting this axis as a therapeutic target to treat intestinal inflammation.
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Affiliation(s)
| | - Víctor Alonso López-Agudelo
- Institute of Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Nina Sommer
- Institute of Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Sven Cleeves
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs-Straße 1, 30625 Hannover, Germany
| | - Joana Pimenta Bernardes
- Institute of Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Saskia Weber-Stiehl
- Institute of Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Felix Sommer
- Institute of Clinical Molecular Biology, University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
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20
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Li X, Morel JD, Benegiamo G, Poisson J, Bachmann A, Rapin A, Sulc J, Williams E, Perino A, Schoonjans K, Bou Sleiman M, Auwerx J. Genetic and dietary modulators of the inflammatory response in the gastrointestinal tract of the BXD mouse genetic reference population. eLife 2023; 12:RP87569. [PMID: 37855835 PMCID: PMC10586803 DOI: 10.7554/elife.87569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023] Open
Abstract
Inflammatory gut disorders, including inflammatory bowel disease (IBD), can be impacted by dietary, environmental, and genetic factors. While the incidence of IBD is increasing worldwide, we still lack a complete understanding of the gene-by-environment interactions underlying inflammation and IBD. Here, we profiled the colon transcriptome of 52 BXD mouse strains fed with a chow or high-fat diet (HFD) and identified a subset of BXD strains that exhibit an IBD-like transcriptome signature on HFD, indicating that an interplay of genetics and diet can significantly affect intestinal inflammation. Using gene co-expression analyses, we identified modules that are enriched for IBD-dysregulated genes and found that these IBD-related modules share cis-regulatory elements that are responsive to the STAT2, SMAD3, and REL transcription factors. We used module quantitative trait locus analyses to identify genetic loci associated with the expression of these modules. Through a prioritization scheme involving systems genetics in the mouse and integration with external human datasets, we identified Muc4 and Epha6 as the top candidates mediating differences in HFD-driven intestinal inflammation. This work provides insights into the contribution of genetics and diet to IBD risk and identifies two candidate genes, MUC4 and EPHA6, that may mediate IBD susceptibility in humans.
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Affiliation(s)
- Xiaoxu Li
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Jean-David Morel
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Giorgia Benegiamo
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Johanne Poisson
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Alexis Bachmann
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Alexis Rapin
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Jonathan Sulc
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Evan Williams
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-AlzetteLuxembourg
| | - Alessia Perino
- Laboratory of Metabolic Signaling, Institute of Bioengineering, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Kristina Schoonjans
- Laboratory of Metabolic Signaling, Institute of Bioengineering, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de LausanneLausanneSwitzerland
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21
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Monteleone G, Moscardelli A, Colella A, Marafini I, Salvatori S. Immune-mediated inflammatory diseases: Common and different pathogenic and clinical features. Autoimmun Rev 2023; 22:103410. [PMID: 37597601 DOI: 10.1016/j.autrev.2023.103410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
The term "immune-mediated inflammatory diseases (IMIDs)" refers to several inflammatory pathologies of multifactorial etiology and involving either simultaneously or sequentially more organs. IMIDs share some common pathogenic mechanisms, which account for some similarities in the clinical course and the impact that these diseases may have on other organs and systems of the body. However, there are some differences in the IMID-associated pathological process, including the synthesis and function of multiple inflammatory cytokines, which are supposed to perpetuate the tissue-damaging inflammation. This justifies the different indications and responsiveness to corticosteroids, immunosuppressors, small molecules, and biologics. Many individuals with IMIDs are, however, intolerant, or unresponsive to the current drugs, thus suggesting the necessity of novel therapeutic approaches, such as the combination of compounds that either inhibit more immuno-inflammatory networks selectively or simultaneously suppress inflammatory signals and activate counter-regulatory pathways. In this article, we highlight the most relevant features of IMIDs and discuss how clinicians can combat the detrimental immune response in such disorders.
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Affiliation(s)
- Giovanni Monteleone
- Gastroenterology Unit, Azienda Ospedaliera Policlinico Tor Vergata, Rome, Italy; Department of Systems Medicine, University of "Tor Vergata", Rome, Italy.
| | | | - Alice Colella
- Gastroenterology Unit, Azienda Ospedaliera Policlinico Tor Vergata, Rome, Italy
| | - Irene Marafini
- Gastroenterology Unit, Azienda Ospedaliera Policlinico Tor Vergata, Rome, Italy
| | - Silvia Salvatori
- Gastroenterology Unit, Azienda Ospedaliera Policlinico Tor Vergata, Rome, Italy; Department of Systems Medicine, University of "Tor Vergata", Rome, Italy
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22
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Dong Y, Johnson BA, Ruan L, Zeineldin M, Liu AZ, Raychaudhuri S, Chiu I, Zhu J, Smith B, Zhao N, Searson P, Watanabe S, Donowitz M, Larman TC, Li R. Disruption of Epithelium Integrity by Inflammation-Associated Fibroblasts through Prostaglandin Signaling: IAFs disrupt colon epithelium via PGE2-EP4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560060. [PMID: 37808771 PMCID: PMC10557697 DOI: 10.1101/2023.09.28.560060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Inflammation-associated fibroblasts (IAFs) are associated with the progression and drug resistance of chronic inflammatory diseases such as inflammatory bowel disease (IBD), but their direct impact on epithelial function and architecture is unknown. In this study, we developed an in vitro model whereby human colon fibroblasts are induced to become IAFs by specific cytokines and recapitulate key features of IAFs in vivo. When co-cultured with patient-derived colon organoids (colonoids), IAFs induced rapid colonoid swelling and barrier disruption due to swelling and rupture of individual epithelial cells. Epithelial cells co-cultured with IAFs also exhibit increased DNA damage, mitotic errors, and proliferation arrest. These IAF-induced epithelial defects are mediated through a paracrine pathway involving prostaglandin E2 (PGE2) and the PGE2 receptor EP4, leading to PKA-dependent activation of the CFTR chloride channel. Importantly, EP4-specific chemical inhibitors effectively prevented colonoid swelling and restored normal proliferation and genome stability of IAF-exposed epithelial cells. These findings reveal a mechanism by which IAFs could promote and perpetuate IBD and suggest a potential treatment to mitigate inflammation-associated epithelial injury.
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Affiliation(s)
- Yi Dong
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Blake A. Johnson
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Linhao Ruan
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Maged Zeineldin
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Albert Z. Liu
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Ian Chiu
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Jin Zhu
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore; Singapore
| | - Barbara Smith
- Microscope Facility, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Nan Zhao
- Institute for Nanobiotechnology, Johns Hopkins University; Baltimore, Maryland, 21218, U.S.A
| | - Peter Searson
- Institute for Nanobiotechnology, Johns Hopkins University; Baltimore, Maryland, 21218, U.S.A
- Department of Materials Science and Engineering, Johns Hopkins University; Baltimore, MD, 21218, U.S.A
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Mark Donowitz
- Department of Medicine, Division of Gastroenterology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
- Department of Physiology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Tatianna C. Larman
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Rong Li
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore; Singapore
- Department of Biological Sciences, National University of Singapore; Singapore
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23
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Petsakou A, Liu Y, Liu Y, Comjean A, Hu Y, Perrimon N. Epithelial Ca 2+ waves triggered by enteric neurons heal the gut. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553227. [PMID: 37645990 PMCID: PMC10461974 DOI: 10.1101/2023.08.14.553227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
A fundamental and unresolved question in regenerative biology is how tissues return to homeostasis after injury. Answering this question is essential for understanding the etiology of chronic disorders such as inflammatory bowel diseases and cancer. We used the Drosophila midgut to investigate this question and discovered that during regeneration a subpopulation of cholinergic enteric neurons triggers Ca2+ currents among enterocytes to promote return of the epithelium to homeostasis. Specifically, we found that down-regulation of the cholinergic enzyme Acetylcholinesterase in the epithelium enables acetylcholine from defined enteric neurons, referred as ARCENs, to activate nicotinic receptors in enterocytes found near ARCEN-innervations. This activation triggers high Ca2+ influx that spreads in the epithelium through Inx2/Inx7 gap junctions promoting enterocyte maturation followed by reduction of proliferation and inflammation. Disrupting this process causes chronic injury consisting of ion imbalance, Yki activation and increase of inflammatory cytokines together with hyperplasia, reminiscent of inflammatory bowel diseases. Altogether, we found that during gut regeneration the conserved cholinergic pathway facilitates epithelial Ca2+ waves that heal the intestinal epithelium. Our findings demonstrate nerve- and bioelectric-dependent intestinal regeneration which advance the current understanding of how a tissue returns to its homeostatic state after injury and could ultimately help existing therapeutics.
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Affiliation(s)
| | - Yifang Liu
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Ying Liu
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Aram Comjean
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, USA
- Howard Hughes Medical Institute, Boston, USA
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24
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Boles JS, Krueger ME, Jernigan JE, Cole CL, Neighbarger NK, Huarte OU, Tansey MG. A leaky gut dysregulates gene networks in the brain associated with immune activation, oxidative stress, and myelination in a mouse model of colitis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552488. [PMID: 37609290 PMCID: PMC10441416 DOI: 10.1101/2023.08.10.552488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The gut and brain are increasingly linked in human disease, with neuropsychiatric conditions classically attributed to the brain showing an involvement of the intestine and inflammatory bowel diseases (IBDs) displaying an ever-expanding list of neurological comorbidities. To identify molecular systems that underpin this gut-brain connection and thus discover therapeutic targets, experimental models of gut dysfunction must be evaluated for brain effects. In the present study, we examine disturbances along the gut-brain axis in a widely used murine model of colitis, the dextran sodium sulfate (DSS) model, using high-throughput transcriptomics and an unbiased network analysis strategy coupled with standard biochemical outcome measures to achieve a comprehensive approach to identify key disease processes in both colon and brain. We examine the reproducibility of colitis induction with this model and its resulting genetic programs during different phases of disease, finding that DSS-induced colitis is largely reproducible with a few site-specific molecular features. We focus on the circulating immune system as the intermediary between the gut and brain, which exhibits an activation of pro-inflammatory innate immunity during colitis. Our unbiased transcriptomics analysis provides supporting evidence for immune activation in the brain during colitis, suggests that myelination may be a process vulnerable to increased intestinal permeability, and identifies a possible role for oxidative stress and brain oxygenation. Overall, we provide a comprehensive evaluation of multiple systems in a prevalent experimental model of intestinal permeability, which will inform future studies using this model and others, assist in the identification of druggable targets in the gut-brain axis, and contribute to our understanding of the concomitance of intestinal and neuropsychiatric dysfunction.
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Affiliation(s)
- Jake Sondag Boles
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Maeve E. Krueger
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Janna E. Jernigan
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Cassandra L. Cole
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Noelle K. Neighbarger
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Oihane Uriarte Huarte
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Malú Gámez Tansey
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
- Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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25
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Cadinu P, Sivanathan KN, Misra A, Xu RJ, Mangani D, Yang E, Rone JM, Tooley K, Kye YC, Bod L, Geistlinger L, Lee T, Ono N, Wang G, Sanmarco L, Quintana FJ, Anderson AC, Kuchroo VK, Moffitt JR, Nowarski R. Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539701. [PMID: 37214800 PMCID: PMC10197602 DOI: 10.1101/2023.05.08.539701] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Gut inflammation involves contributions from immune and non-immune cells, whose interactions are shaped by the spatial organization of the healthy gut and its remodeling during inflammation. The crosstalk between fibroblasts and immune cells is an important axis in this process, but our understanding has been challenged by incomplete cell-type definition and biogeography. To address this challenge, we used MERFISH to profile the expression of 940 genes in 1.35 million cells imaged across the onset and recovery from a mouse colitis model. We identified diverse cell populations; charted their spatial organization; and revealed their polarization or recruitment in inflammation. We found a staged progression of inflammation-associated tissue neighborhoods defined, in part, by multiple inflammation-associated fibroblasts, with unique expression profiles, spatial localization, cell-cell interactions, and healthy fibroblast origins. Similar signatures in ulcerative colitis suggest conserved human processes. Broadly, we provide a framework for understanding inflammation-induced remodeling in the gut and other tissues.
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Affiliation(s)
- Paolo Cadinu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- These authors contributed equally
| | - Kisha N Sivanathan
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- These authors contributed equally
| | - Aditya Misra
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Rosalind J Xu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138 USA
| | - Davide Mangani
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Evan Yang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Joseph M Rone
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Katherine Tooley
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yoon-Chul Kye
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Lloyd Bod
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ludwig Geistlinger
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, USA
| | - Tyrone Lee
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA 02115, USA
| | - Noriaki Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX 77030 USA
| | - Gang Wang
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Liliana Sanmarco
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Francisco J Quintana
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Jeffrey R Moffitt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115 USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Roni Nowarski
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
- Lead contact
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26
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Shin AE, Tesfagiorgis Y, Larsen F, Derouet M, Zeng PYF, Good HJ, Zhang L, Rubinstein MR, Han YW, Kerfoot SM, Nichols AC, Hayakawa Y, Howlett CJ, Wang TC, Asfaha S. F4/80 +Ly6C high Macrophages Lead to Cell Plasticity and Cancer Initiation in Colitis. Gastroenterology 2023; 164:593-609.e13. [PMID: 36634827 PMCID: PMC10038892 DOI: 10.1053/j.gastro.2023.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 12/15/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023]
Abstract
BACKGROUND & AIMS Colorectal cancer is a leading cause of cancer death, and a major risk factor is chronic inflammation. Despite the link between colitis and cancer, the mechanism by which inflammation leads to colorectal cancer is not well understood. METHODS To investigate whether different forms of inflammation pose the same risk of cancer, we compared several murine models of colitis (dextran sodium sulfate [DSS], 2,4,6-trinitrobenzene sulfonic acid, 4-ethoxylmethylene-2-phenyloxazol-5-one, Citrobacter rodentium, Fusobacterium nucleatum, and doxorubicin) with respect to their ability to lead to colonic tumorigenesis. We attempted to correlate the severity of colitis and inflammatory profile with the risk of tumorigenesis in both azoxymethane-dependent and Dclk1/APCfl/fl murine models of colitis-associated cancer. RESULTS DSS colitis reproducibly led to colonic tumors in both mouse models of colitis-associated cancer. In contrast, all other forms of colitis did not lead to cancer. When compared with the colitis not associated with tumorigenesis, DSS colitis was characterized by significantly increased CD11b+F4/80+Ly6Chigh macrophages and CD11b+Ly6G+ neutrophils. Interestingly, depletion of the CD11b+F4/80+Ly6Chigh macrophages inhibited tumorigenesis, whereas depletion of CD11b+Ly6G+ neutrophils had no effect on tumorigenesis. Furthermore, the macrophage-derived cytokines interleukin-1β, tumor necrosis factor-α, and interleukin-6 were significantly increased in DSS colitis and promoted stemness of Dclk1+ tuft cells that serve as the cellular origin of cancer. CONCLUSIONS We have identified CD11b+F4/80+Ly6Chigh macrophages as key mediators of cancer initiation in colitis-associated cancer. Development of new therapies that target these cells may provide an effective preventative strategy for colitis-associated cancer.
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Affiliation(s)
- Alice E Shin
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Medicine, Western University, London, Ontario, Canada
| | - Yodit Tesfagiorgis
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
| | - Frederikke Larsen
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Medicine, Western University, London, Ontario, Canada
| | - Mathieu Derouet
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Medicine, Western University, London, Ontario, Canada
| | - Peter Y F Zeng
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Otolaryngology and Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Hayley J Good
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Medicine, Western University, London, Ontario, Canada
| | - Liyue Zhang
- Department of Medicine, Western University, London, Ontario, Canada
| | - Mara R Rubinstein
- Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University Irving Medical Center, New York, New York
| | - Yiping W Han
- Section of Oral, Diagnostic and Rehabilitation Sciences, College of Dental Medicine, Columbia University Irving Medical Center, New York, New York; Departments of Microbiology & Immunology and Medicine (Medical Sciences), Columbia University Irving Medical Center, New York, New York
| | - Steven M Kerfoot
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
| | - Anthony C Nichols
- Department of Otolaryngology and Head and Neck Surgery, Western University, London, Ontario, Canada
| | - Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Christopher J Howlett
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Timothy C Wang
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Samuel Asfaha
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Medicine, Western University, London, Ontario, Canada.
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27
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Chang Y, Wu X, Lu S, Du J, Long Y, Zhu Y, Qin H. Engineered procyanidin-Fe nanoparticle alleviates intestinal inflammation through scavenging ROS and altering gut microbiome in colitis mice. Front Chem 2023; 11:1089775. [PMID: 37065822 PMCID: PMC10090317 DOI: 10.3389/fchem.2023.1089775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
Inflammatory bowel disease (IBD) is an idiopathic chronic inflammatory bowel disease characterized by inflammation, intestinal barrier injury, and imbalance of gut microbiota. Excess accumulation of reactive oxygen species (ROS) is closely correlated with the development and reoccurrence of IBD. Previous researches demonstrate that procyanidin, as a natural antioxidant, exhibits strong ability of eliminating ROS, thus showing good therapeutic effects in the inflammation-related diseases. Non-etheless, its poor stability and solubility always limits the therapeutic outcomes. Here, we typically designed an antioxidant coordination polymer nanoparticle using the engineering of procyanidin (Pc) and free iron (Fe), named Pc-Fe nanozyme, for effectively scavenging ROS and further inhibiting inflammation while altering the gut microbiome for the treatment of colitis. Furthermore, in vitro experiments uncover that Pc-Fe nanoparticles exert strong multi biomimic activities, including peroxidase, and glutathione peroxidase, for the scavenging of ROS and protecting cells from oxidative injury. In addition, the colon accumulation of Pc-Fe nanozyme effectively protects the intestinal mucosa from oxidative damage while significantly downregulates pro-inflammatory factors, repairs the intestinal barriers and alternates gut microbiome after orally administrated in sodium dextran sulfate (DSS) induced colitis mice. The results collectively illustrate that the multienzyme mimicking Pc-Fe nanozyme owns high potential for treating IBD through scavenging ROS, inhibiting inflammation, repairing gut barriers and alternating gut microbiome, which further promising its clinical translation on IBD treatment and other ROS induced intestinal diseases.
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Affiliation(s)
- Yongliang Chang
- Shanghai Clinical College, Anhui Medical University, Shanghai, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei, China
- Department of General Surgery, School of Medicine, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Xiawei Wu
- Shanghai Clinical College, Anhui Medical University, Shanghai, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei, China
- Department of General Surgery, School of Medicine, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Shengwei Lu
- Shanghai Clinical College, Anhui Medical University, Shanghai, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei, China
- Department of General Surgery, School of Medicine, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Jiahao Du
- Medical School of Nantong University, Nantong, China
| | - Yixiu Long
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- *Correspondence: Yixiu Long, ; Yefei Zhu, ; Huanlong Qin,
| | - Yefei Zhu
- Department of General Surgery, School of Medicine, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
- *Correspondence: Yixiu Long, ; Yefei Zhu, ; Huanlong Qin,
| | - Huanlong Qin
- Shanghai Clinical College, Anhui Medical University, Shanghai, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei, China
- Department of General Surgery, School of Medicine, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
- Medical School of Nantong University, Nantong, China
- *Correspondence: Yixiu Long, ; Yefei Zhu, ; Huanlong Qin,
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28
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Morino K, Kunimura K, Sugiura Y, Izumi Y, Matsubara K, Akiyoshi S, Maeda R, Hirotani K, Sakata D, Mizuno S, Takahashi S, Bamba T, Uruno T, Fukui Y. Cholesterol sulfate limits neutrophil recruitment and gut inflammation during mucosal injury. Front Immunol 2023; 14:1131146. [PMID: 37006281 PMCID: PMC10063914 DOI: 10.3389/fimmu.2023.1131146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 03/09/2023] [Indexed: 03/19/2023] Open
Abstract
During mucosal injury, intestinal immune cells play a crucial role in eliminating invading bacteria. However, as the excessive accumulation of immune cells promotes inflammation and delays tissue repair, it is essential to identify the mechanism that limits the infiltration of immune cells to the mucosal-luminal interface. Cholesterol sulfate (CS) is the lipid product of the sulfotransferase SULT2B1 and suppresses immune reactions by inhibiting DOCK2-mediated Rac activation. In this study, we aimed to elucidate the physiological role of CS in the intestinal tract. We found that, in the small intestine and colon, CS is predominantly produced in the epithelial cells close to the lumen. While dextran sodium sulfate (DSS)-induced colitis was exacerbated in Sult2b1-deficient mice with increased prevalence of neutrophils, the elimination of either neutrophils or intestinal bacteria in Sult2b1-deficient mice attenuated disease development. Similar results were obtained when the Dock2 was genetically deleted in Sult2b1-deficient mice. In addition, we also show that indomethacin-induced ulcer formation in the small intestine was exacerbated in Sult2b1-deficient mice and was ameliorated by CS administration. Thus, our results uncover that CS acts on inflammatory neutrophils, and prevents excessive gut inflammation by inhibiting the Rac activator DOCK2. The administration of CS may be a novel therapeutic strategy for inflammatory bowel disease and non-steroidal anti-inflammatory drug-induced ulcers.
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Affiliation(s)
- Kenji Morino
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kazufumi Kunimura
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- *Correspondence: Kazufumi Kunimura, ; Yoshinori Fukui,
| | - Yuki Sugiura
- Multiomics Platform, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keisuke Matsubara
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Sayaka Akiyoshi
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Rae Maeda
- Multiomics Platform, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichiro Hirotani
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Daiji Sakata
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center in Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center in Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takeshi Bamba
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takehito Uruno
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshinori Fukui
- Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- *Correspondence: Kazufumi Kunimura, ; Yoshinori Fukui,
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29
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Friedrich M, Travis S. Shining a Light on Barrier Function. Gastroenterology 2023; 164:184-186. [PMID: 36410444 DOI: 10.1053/j.gastro.2022.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Affiliation(s)
- Matthias Friedrich
- Translational Gastroenterology Unit, Nuffield Department of Medicine and, Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences and, Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Simon Travis
- Translational Gastroenterology Unit, Nuffield Department of Medicine and, Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences and, Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.
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30
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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] [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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31
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Liu XY, Tang H, Zhou QY, Zeng YL, Chen D, Xu H, Li Y, Tan B, Qian JM. Advancing the precision management of inflammatory bowel disease in the era of omics approaches and new technology. World J Gastroenterol 2023; 29:272-285. [PMID: 36687128 PMCID: PMC9846940 DOI: 10.3748/wjg.v29.i2.272] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
There is great heterogeneity among inflammatory bowel disease (IBD) patients in terms of pathogenesis, clinical manifestation, response to treatment, and prognosis, which requires the individualized and precision management of patients. Many studies have focused on prediction biomarkers and models for assessing IBD disease type, activity, severity, and prognosis. During the era of biologics, how to predict the response and side effects of patients to different treatments and how to quickly recognize the loss of response have also become important topics. Multiomics is a promising area for investigating the complex network of IBD pathogenesis. Integrating numerous amounts of data requires the use of artificial intelligence.
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Affiliation(s)
- Xin-Yu Liu
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
- Eight-year Medical Doctor Program, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Hao Tang
- Department of Internal Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Qing-Yang Zhou
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Yan-Lin Zeng
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dan Chen
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing 100730, China
| | - Hui Xu
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Yue Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Bei Tan
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Jia-Ming Qian
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
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32
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Yarani R, Palasca O, Doncheva NT, Anthon C, Pilecki B, Svane CAS, Mirza AH, Litman T, Holmskov U, Bang-Berthelsen CH, Vilien M, Jensen LJ, Gorodkin J, Pociot F. Cross-species high-resolution transcriptome profiling suggests biomarkers and therapeutic targets for ulcerative colitis. Front Mol Biosci 2023; 9:1081176. [PMID: 36685283 PMCID: PMC9850088 DOI: 10.3389/fmolb.2022.1081176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023] Open
Abstract
Background: Ulcerative colitis (UC) is a disorder with unknown etiology, and animal models play an essential role in studying its molecular pathophysiology. Here, we aim to identify common conserved pathological UC-related gene expression signatures between humans and mice that can be used as treatment targets and/or biomarker candidates. Methods: To identify differentially regulated protein-coding genes and non-coding RNAs, we sequenced total RNA from the colon and blood of the most widely used dextran sodium sulfate Ulcerative colitis mouse. By combining this with public human Ulcerative colitis data, we investigated conserved gene expression signatures and pathways/biological processes through which these genes may contribute to disease development/progression. Results: Cross-species integration of human and mouse Ulcerative colitis data resulted in the identification of 1442 genes that were significantly differentially regulated in the same direction in the colon and 157 in blood. Of these, 51 genes showed consistent differential regulation in the colon and blood. Less known genes with importance in disease pathogenesis, including SPI1, FPR2, TYROBP, CKAP4, MCEMP1, ADGRG3, SLC11A1, and SELPLG, were identified through network centrality ranking and validated in independent human and mouse cohorts. Conclusion: The identified Ulcerative colitis conserved transcriptional signatures aid in the disease phenotyping and future treatment decisions, drug discovery, and clinical trial design.
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Affiliation(s)
- Reza Yarani
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark,*Correspondence: Reza Yarani, ; Flemming Pociot,
| | - Oana Palasca
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nadezhda T. Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bartosz Pilecki
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Cecilie A. S. Svane
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Aashiq H. Mirza
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Thomas Litman
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Uffe Holmskov
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Claus H. Bang-Berthelsen
- Research Group for Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark,Department of Gastroenterology, North Zealand Hillerød Hospital, Hillerød, Denmark
| | - Mogens Vilien
- Department of Surgery, North Zealand Hospital, Hillerød, Denmark
| | - Lars J. Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Pociot
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Copenhagen Diabetes Research Center, Department of Pediatrics, Herlev University Hospital, Herlev, Denmark,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark,*Correspondence: Reza Yarani, ; Flemming Pociot,
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33
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Ghrelin Alleviates Experimental Ulcerative Colitis in Old Mice and Modulates Colonocyte Metabolism via PPARγ Pathway. Int J Mol Sci 2022; 24:ijms24010565. [PMID: 36614012 PMCID: PMC9820475 DOI: 10.3390/ijms24010565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/24/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022] Open
Abstract
There is a growing prevalence of inflammatory bowel disease (IBD), a chronic inflammatory condition of the gastrointestinal tract, among the aging population. Ghrelin is a gut hormone that, in addition to controlling feeding and energy metabolism, has been shown to exert anti-inflammatory effects; however, the effect of ghrelin in protecting against colitis in old mice has not been assessed. Here, we subjected old female C57BL/6J mice to dextran sulfate sodium (DSS) in drinking water for six days, then switched back to normal drinking water, administered acyl-ghrelin or vehicle control from day 3 to 13, and monitored disease activities throughout the disease course. Our results showed that treatment of old mice with acyl-ghrelin attenuated DSS-induced colitis. Compared to the DSS group, ghrelin treatment decreased levels of the inflammation marker S100A9 in the colons collected on day 14 but not on day 8, suggesting that the anti-inflammatory effect was more prominent in the recovery phase. Ghrelin treatment also significantly reduced F4/80 and interleukin-17A on day 14. Moreover, acyl-ghrelin increased mitochondrial respiration and activated transcriptional activity of the peroxisome proliferator-activated receptor gamma (PPARγ) in Caco-2 cells. Together, our data show that ghrelin alleviated DSS-induced colitis, suggesting that ghrelin may promote tissue repair in part through regulating epithelial metabolism via PPARγ mediated signaling.
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34
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Frede A, Czarnewski P, Monasterio G, Tripathi KP, Bejarano DA, Ramirez Flores RO, Sorini C, Larsson L, Luo X, Geerlings L, Novella-Rausell C, Zagami C, Kuiper R, Morales RA, Castillo F, Hunt M, Mariano LL, Hu YOO, Engblom C, Lennon-Duménil AM, Mittenzwei R, Westendorf AM, Hövelmeyer N, Lundeberg J, Saez-Rodriguez J, Schlitzer A, Das S, Villablanca EJ. B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing. Immunity 2022; 55:2336-2351.e12. [PMID: 36462502 DOI: 10.1016/j.immuni.2022.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 07/14/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022]
Abstract
Therapeutic promotion of intestinal regeneration holds great promise, but defining the cellular mechanisms that influence tissue regeneration remains an unmet challenge. To gain insight into the process of mucosal healing, we longitudinally examined the immune cell composition during intestinal damage and regeneration. B cells were the dominant cell type in the healing colon, and single-cell RNA sequencing (scRNA-seq) revealed expansion of an IFN-induced B cell subset during experimental mucosal healing that predominantly located in damaged areas and associated with colitis severity. B cell depletion accelerated recovery upon injury, decreased epithelial ulceration, and enhanced gene expression programs associated with tissue remodeling. scRNA-seq from the epithelial and stromal compartments combined with spatial transcriptomics and multiplex immunostaining showed that B cells decreased interactions between stromal and epithelial cells during mucosal healing. Activated B cells disrupted the epithelial-stromal cross talk required for organoid survival. Thus, B cell expansion during injury impairs epithelial-stromal cell interactions required for mucosal healing, with implications for the treatment of IBD.
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Affiliation(s)
- Annika Frede
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paulo Czarnewski
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Gustavo Monasterio
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kumar P Tripathi
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David A Bejarano
- Quantitative Systems Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | | | - Chiara Sorini
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ludvig Larsson
- KTH Royal Institute of Technology Stockholm, Science for Life Laboratory, Stockholm, Sweden
| | - Xinxin Luo
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Laura Geerlings
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Claudio Novella-Rausell
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Chiara Zagami
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Raoul Kuiper
- Norwegian Veterinary Institute, Section for Aquatic Biosecurity Research, Elisabeth Stephansens vei 1, 1433 Ås, Norway; Core Facility for Morphologic Phenotype Analysis, Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rodrigo A Morales
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Francisca Castillo
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Matthew Hunt
- Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | | | - Yue O O Hu
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Camilla Engblom
- Department of Cell and Molecular Biology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | | | - Romy Mittenzwei
- Institute for Molecular Medicine and Research Center for Immunotherapy (FZI), University Medical Center Mainz, Johannes Gutenberg University of Mainz, 55131 Mainz, Germany
| | - Astrid M Westendorf
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Nadine Hövelmeyer
- Institute for Molecular Medicine and Research Center for Immunotherapy (FZI), University Medical Center Mainz, Johannes Gutenberg University of Mainz, 55131 Mainz, Germany
| | - Joakim Lundeberg
- KTH Royal Institute of Technology Stockholm, Science for Life Laboratory, Stockholm, Sweden
| | - Julio Saez-Rodriguez
- Institute of Computational Biomedicine, University of Heidelberg, Heidelberg, Germany
| | - Andreas Schlitzer
- Quantitative Systems Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Srustidhar Das
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
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35
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Pavlidis P, Tsakmaki A, Pantazi E, Li K, Cozzetto D, Digby-Bell J, Yang F, Lo JW, Alberts E, Sa ACC, Niazi U, Friedman J, Long AK, Ding Y, Carey CD, Lamb C, Saqi M, Madgwick M, Gul L, Treveil A, Korcsmaros T, Macdonald TT, Lord GM, Bewick G, Powell N. Interleukin-22 regulates neutrophil recruitment in ulcerative colitis and is associated with resistance to ustekinumab therapy. Nat Commun 2022; 13:5820. [PMID: 36192482 PMCID: PMC9530232 DOI: 10.1038/s41467-022-33331-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 09/14/2022] [Indexed: 11/28/2022] Open
Abstract
The function of interleukin-22 (IL-22) in intestinal barrier homeostasis remains controversial. Here, we map the transcriptional landscape regulated by IL-22 in human colonic epithelial organoids and evaluate the biological, functional and clinical significance of the IL-22 mediated pathways in ulcerative colitis (UC). We show that IL-22 regulated pro-inflammatory pathways are involved in microbial recognition, cancer and immune cell chemotaxis; most prominently those involving CXCR2+ neutrophils. IL-22-mediated transcriptional regulation of CXC-family neutrophil-active chemokine expression is highly conserved across species, is dependent on STAT3 signaling, and is functionally and pathologically important in the recruitment of CXCR2+ neutrophils into colonic tissue. In UC patients, the magnitude of enrichment of the IL-22 regulated transcripts in colonic biopsies correlates with colonic neutrophil infiltration and is enriched in non-responders to ustekinumab therapy. Our data provide further insights into the biology of IL-22 in human disease and highlight its function in the regulation of pathogenic immune pathways, including neutrophil chemotaxis. The transcriptional networks regulated by IL-22 are functionally and clinically important in UC, impacting patient trajectories and responsiveness to biological intervention. Mechanisms of non-response to ustekinumab, a biologic targeting IL-23, are currently unclear. Here, the authors show that the transcriptional program regulated by IL-22, an IL-23 responsive cytokine, is enriched in patients with ulcerative colitis unresponsive to ustekinumab and associated with higher colon neutrophil recruitment and activation of upstream IL-22 regulators.
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Affiliation(s)
| | - Anastasia Tsakmaki
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Eirini Pantazi
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Katherine Li
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Domenico Cozzetto
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Jonathan Digby-Bell
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Feifei Yang
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Jonathan W Lo
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Elena Alberts
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Umar Niazi
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Joshua Friedman
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Anna K Long
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Yuchun Ding
- Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Christopher D Carey
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Christopher Lamb
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Mansoor Saqi
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Matthew Madgwick
- Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Leila Gul
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK.,Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Agatha Treveil
- Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Tamas Korcsmaros
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK.,Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Thomas T Macdonald
- Centre for Immunobiology, Barts and the London School of Medicine and Dentistry, QMUL, London, UK
| | - Graham M Lord
- School of Immunology and Microbial Sciences, King's College London, London, UK.,Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gavin Bewick
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Nick Powell
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK.
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36
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Tuchaai E, Endres V, Jones B, Shankar S, Klemashevich C, Sun Y, Wu CS. Deletion of ghrelin alters tryptophan metabolism and exacerbates experimental ulcerative colitis in aged mice. Exp Biol Med (Maywood) 2022; 247:1558-1569. [PMID: 35833540 PMCID: PMC9554169 DOI: 10.1177/15353702221110647] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A major component of aging is chronic, low-grade inflammation, attributable in part by impaired gut barrier function. We previously reported that deletion of ghrelin, a peptidergic hormone released mainly from the gut, exacerbates experimental muscle atrophy in aged mice. In addition, ghrelin has been shown to ameliorate colitis in experimental models of inflammatory bowel disease (IBD), although the role of endogenous ghrelin in host-microbe interactions is less clear. Here, we showed that 22-month-old global ghrelin knockout (Ghrl-/-) mice exhibited significantly increased depressive-like behaviors, while anxiety levels and working memory were similar to littermate wild-type (WT) mice. Furthermore, old Ghrl-/- mice showed significantly increased intestinal permeability to fluorescein isothiocyanate (FITC)-dextran, significantly higher colonic interleukin (IL-1β) levels, and trends for higher colonic IL-6 and tumor necrosis factor-α (TNF-α) compared to WT mice. Interestingly, young Ghrl-/- and WT mice showed comparable depressive-like behavior and gut permeability, suggesting age-dependent exacerbation in gut barrier dysfunction in Ghrl-/- mice. While fecal short-chain fatty acids levels were comparable between old Ghrl-/- and WT mice, serum metabolome revealed alterations in metabolic cascades including tryptophan metabolism. Specifically, tryptophan and its microbial derivatives indole-3-acetic acid and indole-3-lactic acid were significantly reduced in old Ghrl-/-mice. Furthermore, in an experimental model of dextran sulfate sodium (DSS)-induced colitis, Ghrl-/- mice showed exacerbated disease symptoms, and higher levels of chemoattractant and pro-inflammatory cytokines in the colon. Overall, these data demonstrated that ghrelin deficiency is associated with gut barrier dysfunction, alterations in microbially derived tryptophan metabolites, and increased susceptibility to colitis. These data suggested that endogenous ghrelin contributes to maintaining a healthy host-microbe environment, ultimately impacting on brain function.
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Affiliation(s)
- Ellie Tuchaai
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA
| | - Valerie Endres
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA
| | - Brock Jones
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA
| | - Smriti Shankar
- Integrated Metabolomics Analysis Core, Texas A&M University, College Station, TX 77843, USA
| | - Cory Klemashevich
- Integrated Metabolomics Analysis Core, Texas A&M University, College Station, TX 77843, USA
| | - Yuxiang Sun
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA
| | - Chia-Shan Wu
- Department of Nutrition, Texas A&M University, College Station, TX 77843, USA,Chia-Shan Wu.
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37
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Nowak JK, Adams AT, Kalla R, Lindstrøm JC, Vatn S, Bergemalm D, Keita ÅV, Gomollón F, Jahnsen J, Vatn MH, Ricanek P, Ostrowski J, Walkowiak J, Halfvarson J, Satsangi J. Characterisation of the Circulating Transcriptomic Landscape in Inflammatory Bowel Disease Provides Evidence for Dysregulation of Multiple Transcription Factors Including NFE2, SPI1, CEBPB, and IRF2. J Crohns Colitis 2022; 16:1255-1268. [PMID: 35212366 PMCID: PMC9426667 DOI: 10.1093/ecco-jcc/jjac033] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/11/2022] [Accepted: 02/23/2022] [Indexed: 01/11/2023]
Abstract
AIM To assess the pathobiological and translational importance of whole-blood transcriptomic analysis in inflammatory bowel disease [IBD]. METHODS We analysed whole-blood expression profiles from paired-end sequencing in a discovery cohort of 590 Europeans recruited across six countries in the IBD Character initiative (newly diagnosed patients with Crohn's disease [CD; n = 156], ulcerative colitis [UC; n = 167], and controls [n = 267]), exploring differential expression [DESeq2], co-expression networks [WGCNA], and transcription factor involvement [EPEE, ChEA, DoRothEA]. Findings were validated by analysis of an independent replication cohort [99 CD, 100 UC, 95 controls]. In the discovery cohort, we also defined baseline expression correlates of future treatment escalation using cross-validated elastic-net and random forest modelling, along with a pragmatic ratio detection procedure. RESULTS Disease-specific transcriptomes were defined in IBD [8697 transcripts], CD [7152], and UC [8521], with the most highly significant changes in single genes, including CD177 (log2-fold change [LFC] = 4.63, p = 4.05 × 10-118), MCEMP1 [LFC = 2.45, p = 7.37 × 10-109], and S100A12 [LFC = 2.31, p = 2.15 × 10-93]. Significantly over-represented pathways included IL-1 [p = 1.58 × 10-11], IL-4, and IL-13 [p = 8.96 × 10-9]. Highly concordant results were obtained using multiple regulatory activity inference tools applied to the discovery and replication cohorts. These analyses demonstrated central roles in IBD for the transcription factors NFE2, SPI1 [PU.1], CEBPB, and IRF2, all regulators of cytokine signalling, based on a consistent signal across cohorts and transcription factor ranking methods. A number of simple transcriptome-based models were associated with the need for treatment escalation, including the binary CLEC5A/CDH2 expression ratio in UC (hazard ratio = 23.4, 95% confidence interval [CI] 5.3-102.0). CONCLUSIONS Transcriptomic analysis has allowed for a detailed characterisation of IBD pathobiology, with important potential translational implications.
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Affiliation(s)
- Jan K Nowak
- Corresponding authors: Dr Jan K. Nowak, Translational Gastroenterology Unit, Experimental Medicine Division, John Radcliffe Hospital, Headley Way, Headington, Oxford OX3 9DU, UK.
| | | | - Rahul Kalla
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Jonas C Lindstrøm
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Simen Vatn
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Daniel Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Åsa V Keita
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | | | - Jørgen Jahnsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Morten H Vatn
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- EpiGen Institute, Akershus University Hospital, University of Oslo, Oslo, Norway
| | - Petr Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Jerzy Ostrowski
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Jaroslaw Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Jack Satsangi
- Jack Satsangi, Translational Gastroenterology Unit, Experimental Medicine Division, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK.
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Prior episode of colitis impairs contextual fear memory. Mol Brain 2022; 15:74. [PMID: 36038926 PMCID: PMC9426209 DOI: 10.1186/s13041-022-00961-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/21/2022] [Indexed: 12/03/2022] Open
Abstract
Accumulating evidence has shown that intestinal inflammations in inflammatory bowel disease (IBD) also drive pathological responses in organs outside the intestine, including the brain. Previous studies using the dextran sodium sulfate (DSS)-induced colitis model have shown that colonic inflammation contributes to the development of anxiety- and depression-related behaviors; however, little is known about whether memory function is affected. Here, we subjected male and female C57BL/6J mice to DSS-induced colitis for 6 days, followed by Pavlovian conditioned fear (CF) tests 15 days after the start of inflammation, when local colonic inflammation has receded. The contextual and cued CF tests were used to assess associative fear memory. We found that DSS-induced colitis led to significant impairment in contextual fear memory in both male and female mice; on the other hand, auditory cued fear memories were comparable between control and DSS-treated mice. There were marked signs of astrogliosis in the hippocampal regions 17 days (D17) after colitis induction. Furthermore, molecular characterization of hippocampi showed marked but transient increases in the expression of inflammatory genes Nfkb, Trem2 (microglial marker), GFAP (astrocyte marker), Il1b, and S100a8 in DSS-treated mice. While the expression of Nfkb, Trem2, and GFAP showed a peak on day 10, the S100a8 expression was high on days 10 and 17 and subsided on day 42. Interestingly, expression of Bdnf remained elevated in the times assessed (D10, 17, 42). Together, these results demonstrated that DSS-induced colitis could induce prolonged neuroinflammation and impaired contextual fear memory.
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Lin MK, Yang YT, Lin LJ, Yu WH, Chen HY. Pulsatilla decoction suppresses matrix metalloproteinase-7-mediated leukocyte recruitment in dextran sulfate sodium-induced colitis mouse model. BMC Complement Med Ther 2022; 22:211. [PMID: 35933374 PMCID: PMC9356479 DOI: 10.1186/s12906-022-03696-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
Background Intestinal inflammation is considered to be an important characteristic of ulcerative colitis (UC) and the current medical treatments for UC are usually proposed to suppress abnormal intestinal immune responses. Pulsatilla decoction (PD), a traditional Chinese medicine, is frequently used in UC treatments in Asian countries; however, the mechanism of the action of PD remains unclear. In the present study, the mechanism of the action of PD was elucidated in the dextran sulfate sodium (DSS)-induced colitis mouse model, a model to mimic UC. Methods Murine colitis was evaluated by comparing the disease activity index score. The intestinal inflammation was examined by histology analyses. The leukocyte infiltration in the colonic tissues was examined by immunohistochemistry analyses. The cytokines level in colonic tissues was examined by Multi-Plex immunoassay. The epithelial proliferation was evaluated by histological analyses. Immunofluorescence double staining was used to examine the expression of MMP-7 in the immune cells. Results In the DSS-induced colitis mouse model, administration of PD attenuated the intestinal inflammation, with a marked decrease in colonic infiltration of innate immune cells. Immunohistochemical analyses further showed that matrix metalloproteinase-7 (MMP-7) expressed by the infiltrating leukocytes, including neutrophils and macrophages was inhibited by PD treatment. PD increases the cytokine level of IL-6 in colonic tissues. Conclusion PD suppresses intestinal inflammation, with a marked decrease in colonic infiltration of innate immune cells, through decreasing MMP-7 expression. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-022-03696-w.
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Sun H, Tang C, Chung SH, Ye XQ, Makusheva Y, Han W, Kubo M, Shichino S, Ueha S, Matsushima K, Ikeo K, Asano M, Iwakura Y. Blocking DCIR mitigates colitis and prevents colorectal tumors by enhancing the GM-CSF-STAT5 pathway. Cell Rep 2022; 40:111158. [PMID: 35926458 DOI: 10.1016/j.celrep.2022.111158] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/26/2022] [Accepted: 07/13/2022] [Indexed: 11/28/2022] Open
Abstract
Dendritic cell immunoreceptor (DCIR; Clec4a2), a member of the C-type lectin receptor family, plays important roles in homeostasis of the immune and bone systems. However, the intestinal role of this molecule is unclear. Here, we show that dextran sodium sulfate (DSS)-induced colitis and azoxymethane-DSS-induced intestinal tumors are reduced in Clec4a2-/- mice independently of intestinal microbiota. STAT5 phosphorylation and expression of Csf2 and tight junction genes are enhanced, while Il17a and Cxcl2 are suppressed in the Clec4a2-/- mouse colon, which exhibits reduced infiltration of neutrophils and myeloid-derived suppressor cells. Granulocyte-macrophage colony-stimulating factor (GM-CSF) administration ameliorates DSS colitis associated with reduced Il17a and enhanced tight junction gene expression, whereas anti-GM-CSF exacerbates symptoms. Furthermore, anti-NA2, a ligand for DCIR, ameliorates colitis and prevents colorectal tumors. These observations indicate that blocking DCIR signaling ameliorates colitis and suppresses colonic tumors, suggesting DCIR as a possible target for the treatment of these diseases.
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Affiliation(s)
- Haiyang Sun
- Center for Animal Disease Models, Research Institute for Biomedical Sciences, Tokyo University of Science, Yamazaki 2669, Noda, Chiba 278-0022, Japan
| | - Ce Tang
- Center for Animal Disease Models, Research Institute for Biomedical Sciences, Tokyo University of Science, Yamazaki 2669, Noda, Chiba 278-0022, Japan; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58, Zhong Shan Er Lu, Guangzhou, Guangdong Province 510080, China
| | - Soo-Hyun Chung
- Center for Animal Disease Models, Research Institute for Biomedical Sciences, Tokyo University of Science, Yamazaki 2669, Noda, Chiba 278-0022, Japan
| | - Xiao-Qi Ye
- Center for Animal Disease Models, Research Institute for Biomedical Sciences, Tokyo University of Science, Yamazaki 2669, Noda, Chiba 278-0022, Japan
| | - Yulia Makusheva
- Center for Animal Disease Models, Research Institute for Biomedical Sciences, Tokyo University of Science, Yamazaki 2669, Noda, Chiba 278-0022, Japan
| | - Wei Han
- Center for Animal Disease Models, Research Institute for Biomedical Sciences, Tokyo University of Science, Yamazaki 2669, Noda, Chiba 278-0022, Japan
| | - Masato Kubo
- Division of Molecular Pathology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Satoshi Ueha
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Koji Matsushima
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Kazuho Ikeo
- DNA Data Analysis Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masahide Asano
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoichiro Iwakura
- Center for Animal Disease Models, Research Institute for Biomedical Sciences, Tokyo University of Science, Yamazaki 2669, Noda, Chiba 278-0022, Japan.
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Villablanca EJ, Selin K, Hedin CRH. Mechanisms of mucosal healing: treating inflammatory bowel disease without immunosuppression? NATURE REVIEWS. GASTROENTEROLOGY & HEPATOLOGY 2022. [PMID: 35440774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Almost all currently available treatments for inflammatory bowel disease (IBD) act by inhibiting inflammation, often blocking specific inflammatory molecules. However, given the infectious and neoplastic disease burden associated with chronic immunosuppressive therapy, the goal of attaining mucosal healing without immunosuppression is attractive. The absence of treatments that directly promote mucosal healing and regeneration in IBD could be linked to the lack of understanding of the underlying pathways. The range of potential strategies to achieve mucosal healing is diverse. However, the targeting of regenerative mechanisms has not yet been achieved for IBD. Stem cells provide hope as a regenerative treatment and are used in limited clinical situations. Growth factors are available for the treatment of short bowel syndrome but have not yet been applied in IBD. The therapeutic application of organoid culture and stem cell therapy to generate new intestinal tissue could provide a novel mechanism to restore barrier function in IBD. Furthermore, blocking key effectors of barrier dysfunction (such as MLCK or damage-associated molecular pattern molecules) has shown promise in experimental IBD. Here, we review the diversity of molecular targets available to directly promote mucosal healing, experimental models to identify new potential pathways and some of the anticipated potential therapies for IBD.
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Affiliation(s)
- Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden.
| | - Katja Selin
- Gastroenterology unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte R H Hedin
- Gastroenterology unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden. .,Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.
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Villablanca EJ, Selin K, Hedin CRH. Mechanisms of mucosal healing: treating inflammatory bowel disease without immunosuppression? Nat Rev Gastroenterol Hepatol 2022; 19:493-507. [PMID: 35440774 DOI: 10.1038/s41575-022-00604-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/08/2022] [Indexed: 12/12/2022]
Abstract
Almost all currently available treatments for inflammatory bowel disease (IBD) act by inhibiting inflammation, often blocking specific inflammatory molecules. However, given the infectious and neoplastic disease burden associated with chronic immunosuppressive therapy, the goal of attaining mucosal healing without immunosuppression is attractive. The absence of treatments that directly promote mucosal healing and regeneration in IBD could be linked to the lack of understanding of the underlying pathways. The range of potential strategies to achieve mucosal healing is diverse. However, the targeting of regenerative mechanisms has not yet been achieved for IBD. Stem cells provide hope as a regenerative treatment and are used in limited clinical situations. Growth factors are available for the treatment of short bowel syndrome but have not yet been applied in IBD. The therapeutic application of organoid culture and stem cell therapy to generate new intestinal tissue could provide a novel mechanism to restore barrier function in IBD. Furthermore, blocking key effectors of barrier dysfunction (such as MLCK or damage-associated molecular pattern molecules) has shown promise in experimental IBD. Here, we review the diversity of molecular targets available to directly promote mucosal healing, experimental models to identify new potential pathways and some of the anticipated potential therapies for IBD.
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Affiliation(s)
- Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden.
| | - Katja Selin
- Gastroenterology unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte R H Hedin
- Gastroenterology unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden. .,Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.
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Korsunsky I, Wei K, Pohin M, Kim EY, Barone F, Major T, Taylor E, Ravindran R, Kemble S, Watts GFM, Jonsson AH, Jeong Y, Athar H, Windell D, Kang JB, Friedrich M, Turner J, Nayar S, Fisher BA, Raza K, Marshall JL, Croft AP, Tamura T, Sholl LM, Vivero M, Rosas IO, Bowman SJ, Coles M, Frei AP, Lassen K, Filer A, Powrie F, Buckley CD, Brenner MB, Raychaudhuri S. Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases. MED 2022; 3:481-518.e14. [PMID: 35649411 PMCID: PMC9271637 DOI: 10.1016/j.medj.2022.05.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 02/02/2023]
Abstract
BACKGROUND Pro-inflammatory fibroblasts are critical for pathogenesis in rheumatoid arthritis, inflammatory bowel disease, interstitial lung disease, and Sjögren's syndrome and represent a novel therapeutic target for chronic inflammatory disease. However, the heterogeneity of fibroblast phenotypes, exacerbated by the lack of a common cross-tissue taxonomy, has limited our understanding of which pathways are shared by multiple diseases. METHODS We profiled fibroblasts derived from inflamed and non-inflamed synovium, intestine, lungs, and salivary glands from affected individuals with single-cell RNA sequencing. We integrated all fibroblasts into a multi-tissue atlas to characterize shared and tissue-specific phenotypes. FINDINGS Two shared clusters, CXCL10+CCL19+ immune-interacting and SPARC+COL3A1+ vascular-interacting fibroblasts, were expanded in all inflamed tissues and mapped to dermal analogs in a public atopic dermatitis atlas. We confirmed these human pro-inflammatory fibroblasts in animal models of lung, joint, and intestinal inflammation. CONCLUSIONS This work represents a thorough investigation into fibroblasts across organ systems, individual donors, and disease states that reveals shared pathogenic activation states across four chronic inflammatory diseases. FUNDING Grant from F. Hoffmann-La Roche (Roche) AG.
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Affiliation(s)
- Ilya Korsunsky
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Mathilde Pohin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK
| | - Edy Y Kim
- Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Francesca Barone
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK
| | - Triin Major
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; Birmingham Tissue Analytics, Institute for Inflammation and Ageing, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK
| | - Emily Taylor
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; Birmingham Tissue Analytics, Institute for Inflammation and Ageing, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK
| | - Rahul Ravindran
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK
| | - Samuel Kemble
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - A Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yunju Jeong
- Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Humra Athar
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dylan Windell
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK
| | - Joyce B Kang
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Matthias Friedrich
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK
| | - Jason Turner
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; Birmingham Tissue Analytics, Institute for Inflammation and Ageing, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK
| | - Saba Nayar
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; Birmingham Tissue Analytics, Institute for Inflammation and Ageing, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK
| | - Benjamin A Fisher
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK
| | - Karim Raza
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK
| | - Jennifer L Marshall
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK
| | - Adam P Croft
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK
| | - Tomoyoshi Tamura
- Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Marina Vivero
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ivan O Rosas
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Dallas, TX 75246, USA
| | - Simon J Bowman
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK
| | - Mark Coles
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK
| | - Andreas P Frei
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, Basel 4070, Switzerland
| | - Kara Lassen
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, Basel 4070, Switzerland
| | - Andrew Filer
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; Birmingham Tissue Analytics, Institute for Inflammation and Ageing, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK.
| | - Christopher D Buckley
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK; Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK.
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester M14 9PR UK.
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Söderman J, Berglind L, Almer S. Inverse and Concordant Mucosal Pathway Gene Expressions in Inflamed and Non-Inflamed Ulcerative Colitis Patients: Potential Relevance to Aetiology and Pathogenesis. Int J Mol Sci 2022; 23:ijms23136944. [PMID: 35805947 PMCID: PMC9266769 DOI: 10.3390/ijms23136944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 02/05/2023] Open
Abstract
Ulcerative colitis (UC) arises from a complex interplay between host and environmental factors, but with a largely unsolved pathophysiology. The pathophysiology was outlined by RNA-sequencing of mucosal biopsies from non-inflamed and inflamed colon of UC patients (14 and 17, respectively), and from 27 patients without intestinal inflammation. Genes differentially expressed (DE), or present in enriched gene sets, were investigated using statistical text analysis of functional protein information. Compared with controls, inflamed and non-inflamed UC mucosa displayed 9360 and 52 DE genes, respectively. Seventy-three non-pseudogenes were DE relative to both gender and inflammation. Mitochondrial processes were downregulated in inflamed and upregulated in non-inflamed UC mucosa, whereas angiogenesis and endoplasmic reticulum (ER) stress were upregulated in both tissue states. Immune responses were upregulated in inflamed mucosa, whereas the non-inflamed UC mucosa presented both up- and downregulated gene sets. DE and enriched genes overlapped with genes present in inflammatory bowel disease genome-wide associated loci (p = 1.43 × 10−18), especially regarding immune responses, respiratory chain, angiogenesis, ER stress, and steroid hormone metabolism. Apart from confirming established pathophysiological mechanisms of immune cells, our study provides evidence for involvement of less described pathways (e.g., respiratory chain, ER stress, fatty-acid oxidation, steroid hormone metabolism and angiogenesis).
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Affiliation(s)
- Jan Söderman
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Laboratory Medicine, Region Jönköping County, 551 85 Jönköping, Sweden;
- Correspondence:
| | - Linda Berglind
- Laboratory Medicine, Region Jönköping County, 551 85 Jönköping, Sweden;
| | - Sven Almer
- Department of Medicine, Solna, Karolinska Institutet, 171 77 Stockholm, Sweden;
- IBD Unit, Division of Gastroenterology, Karolinska University Hospital, 171 76 Stockholm, Sweden
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45
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Regulation of the Intestinal Extra-Adrenal Steroidogenic Pathway Component LRH-1 by Glucocorticoids in Ulcerative Colitis. Cells 2022; 11:cells11121905. [PMID: 35741034 PMCID: PMC9221003 DOI: 10.3390/cells11121905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/27/2022] [Accepted: 06/08/2022] [Indexed: 02/01/2023] Open
Abstract
Ulcerative colitis (UC) is an inflammatory bowel disease (IBD) and can be treated with glucocorticoids (GC), although some patients are unresponsive to this therapy. The transcription factor LRH-1/NR5A2 is critical to intestinal cortisol production (intestinal steroidogenesis), being reduced in UC patients. However, the relationship between LRH-1 expression and distribution with altered corticosteroid responses is unknown. To address this, we categorized UC patients by their steroid response. Here, we found that steroid-dependent and refractory patients presented reduced glucocorticoid receptor (GR)-mediated intestinal steroidogenesis compared to healthy individuals and responder patients, possibly related to increased colonic mucosa GR isoform beta (GRβ) content and cytoplasmic LRH-1 levels in epithelial and lamina propria cells. Interestingly, an intestinal epithelium-specific GR-induced knockout (GRiKO) dextran sodium sulfate (DSS)-colitis mice model presented decreased epithelial LRH-1 expression, whilst it increased in the lamina propria compared to DSS-treated control mice. Mechanistically, GR directly induced NR5A2 gene expression in CCD841CoN cells and human colonic organoids. Furthermore, GR bound to two glucocorticoid-response elements within the NR5A2 promoter in dexamethasone-stimulated CCD841CoN cells. We conclude that GR contributes to intestinal steroidogenesis by inducing LRH-1 in epithelial cells, suggesting LRH-1 as a potential marker for glucocorticoid-impaired response in UC. However, further studies with a larger patient cohort will be necessary to confirm role of LRH-1 as a therapeutic biomarker.
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46
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Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps. NPJ Syst Biol Appl 2022; 8:13. [PMID: 35473910 PMCID: PMC9042890 DOI: 10.1038/s41540-022-00222-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/22/2022] [Indexed: 01/09/2023] Open
Abstract
Complex diseases are inherently multifaceted, and the associated data are often heterogeneous, making linking interactions across genes, metabolites, RNA, proteins, cellular functions, and clinically relevant phenotypes a high-priority challenge. Disease maps have emerged as knowledge bases that capture molecular interactions, disease-related processes, and disease phenotypes with standardized representations in large-scale molecular interaction maps. Various tools are available for disease map analysis, but an intuitive solution to perform in silico experiments on the maps in a wide range of contexts and analyze high-dimensional data is currently missing. To this end, we introduce a two-dimensional enrichment analysis (2DEA) approach to infer downstream and upstream elements through the statistical association of network topology parameters and fold changes from molecular perturbations. We implemented our approach in a plugin suite for the MINERVA platform, providing an environment where experimental data can be mapped onto a disease map and predict potential regulatory interactions through an intuitive graphical user interface. We show several workflows using this approach and analyze two RNA-seq datasets in the Atlas of Inflammation Resolution (AIR) to identify enriched downstream processes and upstream transcription factors. Our work improves the usability of disease maps and increases their functionality by facilitating multi-omics data integration and exploration.
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47
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Kuttke M, Hromadová D, Yildirim C, Brunner JS, Vogel A, Paar H, Peters S, Weber M, Hofmann M, Kerndl M, Kieler M, Datler H, Musiejovsky L, Salzmann M, Lang M, Soukup K, Halfmann A, Sharif O, Schabbauer G. PI3K Signaling in Dendritic Cells Aggravates DSS-Induced Colitis. Front Immunol 2022; 13:695576. [PMID: 35514976 PMCID: PMC9063450 DOI: 10.3389/fimmu.2022.695576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Aberrant innate immune responses to the gut microbiota are causally involved in the pathogenesis of inflammatory bowel diseases (IBD). The exact triggers and main signaling pathways activating innate immune cells and how they modulate adaptive immunity in IBD is still not completely understood. Here, we report that the PI3K/PTEN signaling pathway in dendritic cells enhances IL-6 production in a model of DSS-induced colitis. This results in exacerbated Th1 cell responses and increased mortality in DC-specific PTEN knockout (PTENΔDC) animals. Depletion of the gut microbiota using antibiotics as well as blocking IL-6R signaling rescued mortality in PTENΔDC mice, whereas adoptive transfer of Flt3L-derived PTEN-/- DCs into WT recipients exacerbated DSS-induced colitis and increased mortality. Taken together, we show that the PI3K signaling pathway in dendritic cells contributes to disease pathology by promoting IL-6 mediated Th1 responses.
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Affiliation(s)
- Mario Kuttke
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Dominika Hromadová
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Ceren Yildirim
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Julia S. Brunner
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Andrea Vogel
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Hannah Paar
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Sophie Peters
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Maria Weber
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Melanie Hofmann
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Martina Kerndl
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Markus Kieler
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Hannes Datler
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Laszlo Musiejovsky
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Manuel Salzmann
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Michaela Lang
- Department of Gastroenterology and Hepatology, Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Klara Soukup
- St. Anna Children’s Cancer Research Institute, Vienna, Austria
| | - Angela Halfmann
- St. Anna Children’s Cancer Research Institute, Vienna, Austria
| | - Omar Sharif
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Gernot Schabbauer
- Institute for Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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48
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Yang J, Germano PM, Oh S, Wang S, Wang J, Lee R, Paige H, Yang S, Henning SM, Zhong J, Jacobs JP, Li Z. Pomegranate Extract Improves Colitis in IL-10 Knockout Mice Fed a High Fat High Sucrose Diet. Mol Nutr Food Res 2022; 66:e2100730. [PMID: 34932869 DOI: 10.1002/mnfr.202100730] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/19/2021] [Indexed: 11/10/2022]
Abstract
SCOPE The study tests the hypothesis that dietary pomegranate extract (PomX) supplementation attenuates colitis in a Western diet feed IL-10 deficient (IL-10-/-) murine model. METHODS AND RESULTS Four-week-old male IL-10-/- mice are randomly assigned to a high fat high sucrose (HFHS) diet or a HFHS diet supplement with 0.25% PomX for 8 weeks. PomX supplementation lead to significantly lower histological score for colitis (2.6 ± 0.5 vs 3.9 ± 1.0), lower spleen weight (0.11 ± 0.01 vs 0.15 ± 0.02), and lower circulating Interleukin 6(IL-6) levels (15.8±2.2 vs 29.5±5.5) compared with HFHS fed controls. RNAseq analysis of colonic tissues showed 483 downregulated and 263 upregulated genes with PomX supplementation, which are mainly associated with inflammatory responses, defenses, and neutrophil degranulation. In addition, PomX treatment affects the cecal microbiome with increased alpha diversity, altered microbial composition, and increased levels of the tryptophan-related microbial metabolite indole propionate. CONCLUSION The data demonstrate that dietary PomX supplementation ameliorated colitis and lowered inflammatory markers in HFHS fed IL-10-/- mice. These data support the anti-inflammatory effects of dietary PomX supplementation for IBD and a potential mediating role of gut microbiome, suggesting the need for future clinical studies to explore the use of PomX dietary supplementation in IBD patients.
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Affiliation(s)
- Jieping Yang
- Center for Human Nutrition, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Patrizia Maria Germano
- Department of Medicine at the David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Research Service Department, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, 90095, USA
| | - Suwan Oh
- Research Service Department, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, 90095, USA
| | - Sijia Wang
- Center for Human Nutrition, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Jing Wang
- Center for Human Nutrition, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Rupo Lee
- Center for Human Nutrition, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Hayden Paige
- Center for Human Nutrition, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Scarlet Yang
- Center for Human Nutrition, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Susanne M Henning
- Center for Human Nutrition, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Jin Zhong
- Department of Pathology and Laboratory Medicine, VA Greater Los Angeles Health Care System, Los Angeles, CA, 90095, USA
| | - Jonathan P Jacobs
- Department of Medicine at the David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Medicine, VA Greater Los Angeles Health Care System, Los Angeles, CA, 90095, USA
| | - Zhaoping Li
- Center for Human Nutrition, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
- Department of Medicine at the David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Medicine, VA Greater Los Angeles Health Care System, Los Angeles, CA, 90095, USA
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49
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Parigi SM, Larsson L, Das S, Ramirez Flores RO, Frede A, Tripathi KP, Diaz OE, Selin K, Morales RA, Luo X, Monasterio G, Engblom C, Gagliani N, Saez-Rodriguez J, Lundeberg J, Villablanca EJ. The spatial transcriptomic landscape of the healing mouse intestine following damage. Nat Commun 2022; 13:828. [PMID: 35149721 PMCID: PMC8837647 DOI: 10.1038/s41467-022-28497-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions, we demonstrate a previously unappreciated molecular regionalization of the colon, which dramatically changes during mucosal healing. Here, we identified spatially-organized transcriptional programs defining compartmentalized mucosal healing, and regions with dominant wired pathways. Furthermore, we showed that decreased p53 activation defined areas with increased presence of proliferating epithelial stem cells. Finally, we mapped transcriptomics modules associated with human diseases demonstrating the translational potential of our dataset. Overall, we provide a publicly available resource defining principles of transcriptomic regionalization of the colon during mucosal healing and a framework to develop and progress further hypotheses.
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Affiliation(s)
- Sara M Parigi
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Srustidhar Das
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Ricardo O Ramirez Flores
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Annika Frede
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Kumar P Tripathi
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Oscar E Diaz
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Katja Selin
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Rodrigo A Morales
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Xinxin Luo
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Gustavo Monasterio
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Camilla Engblom
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Nicola Gagliani
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
- I. Department of Medicine and Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden.
- Center of Molecular Medicine, Stockholm, Sweden.
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50
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Suarez-Lopez L, Shui B, Brubaker DK, Hill M, Bergendorf A, Changelian PS, Laguna A, Starchenko A, Lauffenburger DA, Haigis KM. Cross-species transcriptomic signatures predict response to MK2 inhibition in mouse models of chronic inflammation. iScience 2021; 24:103406. [PMID: 34849469 PMCID: PMC8609096 DOI: 10.1016/j.isci.2021.103406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/28/2021] [Accepted: 11/03/2021] [Indexed: 11/30/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are genetically complex and exhibit significant inter-patient heterogeneity in disease presentation and therapeutic response. Here, we show that mouse models of IBD exhibit variable responses to inhibition of MK2, a pro-inflammatory serine/threonine kinase, and that MK2 inhibition suppresses inflammation by targeting inflammatory monocytes and neutrophils in murine models. Using a computational approach (TransComp-R) that allows for cross-species comparison of transcriptomic features, we identified an IBD patient subgroup that is predicted to respond to MK2 inhibition, and an independent preclinical model of chronic intestinal inflammation predicted to be non-responsive, which we validated experimentally. Thus, cross-species mouse-human translation approaches can help to identify patient subpopulations in which to deploy new therapies. MK2 kinase inhibition shows variable efficacy in different IBD mouse models TCT and TNFΔARE mice express distinct inflammatory and MK2-responsive genes “Response to MK2i” signature is enriched in monocytes and neutrophils Cross-species modeling identifies patient groups potentially responsive to MK2i
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Affiliation(s)
- Lucia Suarez-Lopez
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Bing Shui
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Douglas K. Brubaker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47906, USA
- Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Marza Hill
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexander Bergendorf
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Paul S. Changelian
- Aclaris Therapeutics, Inc., 4320 Forest Park Avenue, St. Louis, MO 63108, USA
| | - Aisha Laguna
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Alina Starchenko
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin M. Haigis
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Corresponding author
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