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Bai X, Chen S, Chi X, Xie B, Guo X, Feng H, Wei P, Zhang D, Xie S, Xie T, Chen Y, Gou M, Qiao Q, Liu X, Jin W, Xu W, Zhao Z, Xing Q, Wang X, Zhang X, Dong C. Reciprocal regulation of T follicular helper cells and dendritic cells drives colitis development. Nat Immunol 2024:10.1038/s41590-024-01882-1. [PMID: 38942990 DOI: 10.1038/s41590-024-01882-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 05/22/2024] [Indexed: 06/30/2024]
Abstract
The immunological mechanisms underlying chronic colitis are poorly understood. T follicular helper (TFH) cells are critical in helping B cells during germinal center reactions. In a T cell transfer colitis model, a lymphoid structure composed of mature dendritic cells (DCs) and TFH cells was found within T cell zones of colonic lymphoid follicles. TFH cells were required for mature DC accumulation, the formation of DC-T cell clusters and colitis development. Moreover, DCs promoted TFH cell differentiation, contributing to colitis development. A lineage-tracing analysis showed that, following migration to the lamina propria, TFH cells transdifferentiated into long-lived pathogenic TH1 cells, promoting colitis development. Our findings have therefore demonstrated the reciprocal regulation of TFH cells and DCs in colonic lymphoid follicles, which is critical in chronic colitis pathogenesis.
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Affiliation(s)
- Xue Bai
- New Cornerstone Science Laboratory, Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Sijie Chen
- Bioinformatics Division, BNRIST and Department of Automation, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Xinxin Chi
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Bowen Xie
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Xinyi Guo
- New Cornerstone Science Laboratory, Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Han Feng
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Peng Wei
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Di Zhang
- Department of Pathology, The First Hospital of China Medical University and College of Basic Medical Sciences of China Medical University, Shenyang, China
| | - Shan Xie
- Department of Gastroenterology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Tian Xie
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Yongzhen Chen
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Mengting Gou
- New Cornerstone Science Laboratory, Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China
| | - Qin Qiao
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Xinwei Liu
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Wei Jin
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Wei Xu
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Zixuan Zhao
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Qi Xing
- New Cornerstone Science Laboratory, Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Xiaohu Wang
- Institute of Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Xuegong Zhang
- Bioinformatics Division, BNRIST and Department of Automation, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
- Center for Synthetic and Systems Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China
| | - Chen Dong
- New Cornerstone Science Laboratory, Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China.
- Research Unit of Immune Regulation and Immune Diseases of Chinese Academy of Medical Sciences, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China.
- Westlake University School of Medicine, Hangzhou, China.
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2
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Hu F, Xiong L, Li Z, Li L, Wang L, Wang X, Zhou X, Zheng Y. Deciphering the shared mechanisms of Gegen Qinlian Decoction in treating type 2 diabetes and ulcerative colitis via bioinformatics and machine learning. Front Med (Lausanne) 2024; 11:1406149. [PMID: 38962743 PMCID: PMC11220276 DOI: 10.3389/fmed.2024.1406149] [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: 03/24/2024] [Accepted: 06/07/2024] [Indexed: 07/05/2024] Open
Abstract
Background Although previous clinical studies and animal experiments have demonstrated the efficacy of Gegen Qinlian Decoction (GQD) in treating Type 2 Diabetes Mellitus (T2DM) and Ulcerative Colitis (UC), the underlying mechanisms of its therapeutic effects remain elusive. Purpose This study aims to investigate the shared pathogenic mechanisms between T2DM and UC and elucidate the mechanisms through which GQD modulates these diseases using bioinformatics approaches. Methods Data for this study were sourced from the Gene Expression Omnibus (GEO) database. Targets of GQD were identified using PharmMapper and SwissTargetPrediction, while targets associated with T2DM and UC were compiled from the DrugBank, GeneCards, Therapeutic Target Database (TTD), DisGeNET databases, and differentially expressed genes (DEGs). Our analysis encompassed six approaches: weighted gene co-expression network analysis (WGCNA), immune infiltration analysis, single-cell sequencing analysis, machine learning, DEG analysis, and network pharmacology. Results Through GO and KEGG analysis of weighted gene co-expression network analysis (WGCNA) modular genes and DEGs intersection, we found that the co-morbidity between T2DM and UC is primarily associated with immune-inflammatory pathways, including IL-17, TNF, chemokine, and toll-like receptor signaling pathways. Immune infiltration analysis supported these findings. Three distinct machine learning studies identified IGFBP3 as a biomarker for GQD in treating T2DM, while BACE2, EPHB4, and EPHA2 emerged as biomarkers for GQD in UC treatment. Network pharmacology revealed that GQD treatment for T2DM and UC mainly targets immune-inflammatory pathways like Toll-like receptor, IL-17, TNF, MAPK, and PI3K-Akt signaling pathways. Conclusion This study provides insights into the shared pathogenesis of T2DM and UC and clarifies the regulatory mechanisms of GQD on these conditions. It also proposes novel targets and therapeutic strategies for individuals suffering from T2DM and UC.
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Affiliation(s)
| | | | | | | | | | | | - Xuemei Zhou
- College of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Yujiao Zheng
- College of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei, China
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3
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Dunlap G, Wagner A, Meednu N, Wang R, Zhang F, Ekabe JC, Jonsson AH, Wei K, Sakaue S, Nathan A, Bykerk VP, Donlin LT, Goodman SM, Firestein GS, Boyle DL, Holers VM, Moreland LW, Tabechian D, Pitzalis C, Filer A, Raychaudhuri S, Brenner MB, Thakar J, McDavid A, Rao DA, Anolik JH. Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nat Commun 2024; 15:4991. [PMID: 38862501 PMCID: PMC11167034 DOI: 10.1038/s41467-024-49186-0] [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: 06/04/2023] [Accepted: 05/20/2024] [Indexed: 06/13/2024] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease involving antigen-specific T and B cells. Here, we perform single-cell RNA and repertoire sequencing on paired synovial tissue and blood samples from 12 seropositive RA patients. We identify clonally expanded CD4 + T cells, including CCL5+ cells and T peripheral helper (Tph) cells, which show a prominent transcriptomic signature of recent activation and effector function. CD8 + T cells show higher oligoclonality than CD4 + T cells, with the largest synovial clones enriched in GZMK+ cells. CD8 + T cells with possibly virus-reactive TCRs are distributed across transcriptomic clusters. In the B cell compartment, NR4A1+ activated B cells, and plasma cells are enriched in the synovium and demonstrate substantial clonal expansion. We identify synovial plasma cells that share BCRs with synovial ABC, memory, and activated B cells. Receptor-ligand analysis predicted IFNG and TNFRSF members as mediators of synovial Tph-B cell interactions. Together, these results reveal clonal relationships between functionally distinct lymphocyte populations that infiltrate the synovium of patients with RA.
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Grants
- UH2 AR067685 NIAMS NIH HHS
- UM2 AR067678 NIAMS NIH HHS
- K08 AR081412 NIAMS NIH HHS
- UH2 AR067681 NIAMS NIH HHS
- UH2 AR067688 NIAMS NIH HHS
- UH2 AR067689 NIAMS NIH HHS
- UH2 AR067690 NIAMS NIH HHS
- UH2 AR067677 NIAMS NIH HHS
- UH2 AR067694 NIAMS NIH HHS
- UH2 AR067679 NIAMS NIH HHS
- UH2 AR067676 NIAMS NIH HHS
- UH2 AR067691 NIAMS NIH HHS
- Funding for AMP RA/SLE work was provided through grants from the National Institutes of Health (UH2-AR067676, UH2-AR067677, UH2-AR067679, UH2-AR067681, UH2-AR067685, UH2-AR067688, UH2-AR067689, UH2-AR067690, UH2-AR067691, UH2-AR067694, and UM2-AR067678).
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Affiliation(s)
- Garrett Dunlap
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Aaron Wagner
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Nida Meednu
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Ruoqiao Wang
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jabea Cyril Ekabe
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vivian P Bykerk
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Susan M Goodman
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego;, La Jolla, CA, USA
| | - David L Boyle
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego;, La Jolla, CA, USA
| | - V Michael Holers
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Larry W Moreland
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Darren Tabechian
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, EULAR Centre of Excellence, William Harvey Research Institute, Queen Mary University of London, London, UK
- Barts Health NHS Trust, Barts Biomedical Research Centre (BRC), National Institute for Health and Care Research (NIHR), London, UK
- Department of Biomedical Sciences, Humanitas University and Humanitas Research Hospital, Milan, Italy
| | - Andrew Filer
- Rheumatology Research Group, Institute for Inflammation and Ageing, University of Birmingham, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- Birmingham Tissue Analytics, Institute of Translational Medicine, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Juilee Thakar
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Jennifer H Anolik
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA.
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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4
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Xiao B, Liang Y, Liu G, Wang L, Zhang Z, Qiu L, Xu H, Carr S, Shi X, Reis RL, Kundu SC, Zhu Z. Gas-propelled nanomotors alleviate colitis through the regulation of intestinal immunoenvironment-hematopexis-microbiota circuits. Acta Pharm Sin B 2024; 14:2732-2747. [PMID: 38828144 PMCID: PMC11143748 DOI: 10.1016/j.apsb.2024.02.008] [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: 09/28/2023] [Revised: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 06/05/2024] Open
Abstract
The progression of ulcerative colitis (UC) is associated with immunologic derangement, intestinal hemorrhage, and microbiota imbalance. While traditional medications mainly focus on mitigating inflammation, it remains challenging to address multiple symptoms. Here, a versatile gas-propelled nanomotor was constructed by mild fusion of post-ultrasonic CaO2 nanospheres with Cu2O nanoblocks. The resulting CaO2-Cu2O possessed a desirable diameter (291.3 nm) and a uniform size distribution. It could be efficiently internalized by colonic epithelial cells and macrophages, scavenge intracellular reactive oxygen/nitrogen species, and alleviate immune reactions by pro-polarizing macrophages to the anti-inflammatory M2 phenotype. This nanomotor was found to penetrate through the mucus barrier and accumulate in the colitis mucosa due to the driving force of the generated oxygen bubbles. Rectal administration of CaO2-Cu2O could stanch the bleeding, repair the disrupted colonic epithelial layer, and reduce the inflammatory responses through its interaction with the genes relevant to blood coagulation, anti-oxidation, wound healing, and anti-inflammation. Impressively, it restored intestinal microbiota balance by elevating the proportions of beneficial bacteria (e.g., Odoribacter and Bifidobacterium) and decreasing the abundances of harmful bacteria (e.g., Prevotellaceae and Helicobacter). Our gas-driven CaO2-Cu2O offers a promising therapeutic platform for robust treatment of UC via the rectal route.
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Affiliation(s)
- Bo Xiao
- Department of Gastroenterology, the First Affiliated Hospital of Nanchang University, Nanchang 330006, China
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yuqi Liang
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Ga Liu
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Lingshuang Wang
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Zhan Zhang
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA 30322, USA
- Atlanta Veterans Affairs Medical Center, Decatur, GA 30033, USA
| | - Libin Qiu
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Haiting Xu
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Sean Carr
- Atlanta Veterans Affairs Medical Center, Decatur, GA 30033, USA
- Department of Surgery, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Xiaoxiao Shi
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Rui L. Reis
- 3Bs Research Group, I3Bs — Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Barco, Guimaraes 4805-017, Portugal
| | - Subhas C. Kundu
- 3Bs Research Group, I3Bs — Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Barco, Guimaraes 4805-017, Portugal
| | - Zhenghua Zhu
- Department of Gastroenterology, the First Affiliated Hospital of Nanchang University, Nanchang 330006, China
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5
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Qian H, Ye Z, Hu Y, Wu M, Chen L, Li L, Hu Z, Zhao Q, Zhang C, Yang M, Xudong W, Ye Q, Qin K. Molecular targets associated with ulcerative colitis and the benefits of atractylenolides-based therapy. Front Pharmacol 2024; 15:1398294. [PMID: 38860174 PMCID: PMC11163078 DOI: 10.3389/fphar.2024.1398294] [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: 03/09/2024] [Accepted: 05/08/2024] [Indexed: 06/12/2024] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory disease of the intestines that can significantly impact quality of life and lead to various complications. Currently, 5-aminosalicylic acid derivatives, corticosteroids, immunosuppressants, and biologics are the major treatment strategies for UC, but their limitations have raised concerns. Atractylenolides (ATs), sesquiterpene metabolites found in Atractylodes macrocephala Koidz., have shown promising effects in treating UC by exerting immune barrier modulation, alleviating oxidative stress, gut microbiota regulation, improving mitochondrial dysfunction and repairing the intestinal barrier. Furthermore, ATs have been shown to possess remarkable anti-fibrosis, anti-thrombus, anti-angiogenesis and anti-cancer. These findings suggest that ATs hold important potential in treating UC and its complications. Therefore, this review systematically summarizes the efficacy and potential mechanisms of ATs in treating UC and its complications, providing the latest insights for further research and clinical applications.
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Affiliation(s)
- Huanzhu Qian
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Zhen Ye
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yu Hu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Mingquan Wu
- Department of Pharmacy, Sichuan Orthopedic Hospital, Chengdu, Sichuan, China
| | - Liulin Chen
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Linzhen Li
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Zhipeng Hu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Qian Zhao
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Chen Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Maoyi Yang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Wen Xudong
- Department of Gastroenterology, Chengdu Integrated TCM & Western Medicine Hospital, Chengdu, Sichuan, China
| | - Qiaobo Ye
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Kaihua Qin
- Health Preservation and Rehabilitation College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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6
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Ciorba MA, Konnikova L, Hirota SA, Lucchetta EM, Turner JR, Slavin A, Johnson K, Condray CD, Hong S, Cressall BK, Pizarro TT, Hurtado-Lorenzo A, Heller CA, Moss AC, Swantek JL, Garrett WS. Challenges in IBD Research 2024: Preclinical Human IBD Mechanisms. Inflamm Bowel Dis 2024; 30:S5-S18. [PMID: 38778627 DOI: 10.1093/ibd/izae081] [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: 03/15/2024] [Indexed: 05/25/2024]
Abstract
Preclinical human inflammatory bowel disease (IBD) mechanisms is one of 5 focus areas of the Challenges in IBD Research 2024 document, which also includes environmental triggers, novel technologies, precision medicine, and pragmatic clinical research. Herein, we provide a comprehensive overview of current gaps in inflammatory bowel diseases research that relate to preclinical research and deliver actionable approaches to address them with a focus on how these gaps can lead to advancements in IBD interception, remission, and restoration. The document is the result of multidisciplinary input from scientists, clinicians, patients, and funders and represents a valuable resource for patient-centric research prioritization. This preclinical human IBD mechanisms section identifies major research gaps whose investigation will elucidate pathways and mechanisms that can be targeted to address unmet medical needs in IBD. Research gaps were identified in the following areas: genetics, risk alleles, and epigenetics; the microbiome; cell states and interactions; barrier function; IBD complications (specifically fibrosis and stricturing); and extraintestinal manifestations. To address these gaps, we share specific opportunities for investigation for basic and translational scientists and identify priority actions.
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Affiliation(s)
- Matthew A Ciorba
- Inflammatory Bowel Diseases Center, Division of Gastroenterology, Washington University in St. Louis, Saint Louis, MO, USA
| | - Liza Konnikova
- Departments of Pediatrics, Immunobiology, and Obstetric, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Simon A Hirota
- Snyder Institute for Chronic Diseases, Dept. of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
| | - Elena M Lucchetta
- The Leona M. and Harry B. Helmsley Charitable Trust, New York, NY, USA
| | - Jerrold R Turner
- Departments of Pathology and Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Cass D Condray
- Patient Representative for the Crohn's & Colitis Foundation, New York, NY, USA
| | - Sungmo Hong
- Patient Representative for the Crohn's & Colitis Foundation, New York, NY, USA
| | - Brandon K Cressall
- Patient Representative for the Crohn's & Colitis Foundation, New York, NY, USA
| | - Theresa T Pizarro
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | - Caren A Heller
- Research Department, Crohn's & Colitis Foundation, New York, NY, USA
| | - Alan C Moss
- Research Department, Crohn's & Colitis Foundation, New York, NY, USA
| | | | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- The Harvard T. H. Chan Microbiome in Public Health Center, Boston, MA, USA
- Kymera Therapeutics, Watertown, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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7
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Cossarini F, Shang J, Krek A, Al-Taie Z, Hou R, Canales-Herrerias P, Tokuyama M, Tankelevich M, Tillowiz A, Jha D, Livanos AE, Leyre L, Uzzan M, Martinez-Delgado G, Tylor M, Sharma K, Bourgonje AR, Cruz M, Ioannou G, Dawson T, D'Souza D, Kim-Schulze S, Akm A, Aberg JA, Chen BK, Gnjatic S, Polydorides AD, Cerutti A, Argmann C, Vujkovic-Cvijin I, Suarez-Farinas M, Petralia F, Faith JJ, Mehandru S. HIV-1 infection is associated with depletion of germinal center B cells and a decrease in IgA + plasma cells in the GI tract. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.590425. [PMID: 38826293 PMCID: PMC11142040 DOI: 10.1101/2024.05.17.590425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Gastrointestinal (GI) B cells and plasma cells (PCs), critical to mucosal homeostasis, play an important role in the host response to HIV-1 infection. Here, high resolution mapping of human B cells and PCs from colon and ileum during both viremic and suppressed HIV-1 infection identified a significant reduction in germinal center (GC) B cells and Follicular Dendritic Cells (FDCs) during HIV-1 viremia. Further, IgA + PCs, the major cellular output of intestinal GCs were significantly reduced during viremic HIV-1 infection. PC-associated transcriptional perturbations, including type I interferon signaling persisted in antiretroviral therapy (ART) treated individuals, suggesting ongoing disruption of the intestinal immune milieu during ART. GI humoral immune perturbations associated with changes in intestinal microbiome composition and systemic inflammation. Herein, we highlight a key immune defect in the GI mucosa due to HIV-1 viremia, with major implications. One Sentence Summary Major perturbations in intestinal GC dynamics in viremic HIV-1 infection relate to reduced IgA + plasma cells, systemic inflammation and microbiota changes.
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8
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Zhang Y, Wu Z, Zhao Q, Liu Y, Huang Q, Zhang M, Li S, Wang D, Li N, Chi Y, Liu Y. Mesenteric Lymphatic B Cells Migrate to the Intestine and Aggravate DSS-Induced Colitis via the CXCR5-CXCL13 Axis. BIOLOGY 2024; 13:322. [PMID: 38785804 PMCID: PMC11117591 DOI: 10.3390/biology13050322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
The pathogenesis of inflammatory bowel disease (IBD) is still unknown. Mesenteric lymphatics (MLs), which are closely related to the intestine in both anatomy and physiology, have been suggested to be involved in IBD. In the present study, we aim to investigate the effects of ML immune cells on IBD and explore the potential associated mechanisms. Acute colitis was induced in rats using dextran sulfate sodium salt (DSS). Mesenteric lymphangiogenesis, ML stenosis, and dilation were observed, with an increased proportion of MLB cells in DSS-induced colitis rats. The adoptive transfer of B cells isolated from ML (MLB) was employed to investigate their effects on colitis. MLB cells derived from DSS-induced colitis rats exhibited a higher propensity to migrate to the intestine. The proportion of colonic T cells was altered, along with the aggravated colitis induced by the adoptive transfer of MLB cells derived from DSS-induced colitis rats. RNA sequencing revealed increased Cxcr5 expression in MLB cells from colitis rats, while real-time PCR indicated an upregulation of its ligand Cxcl13 in the colon of colitis rats. These findings suggest that MLB cells may migrate to the intestine and aggravate colitis. In summary, colonic T cells respond to MLB cells from colitis rats, and MLB cells aggravate DSS-induced colitis via the CXCR5-CXCL13 axis.
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Affiliation(s)
- Yu Zhang
- Department of Gastroenterology, Peking University People’s Hospital, Beijing 100044, China; (Y.Z.); (Z.W.); (Q.Z.)
- Clinical Center of Immune-Mediated Digestive Diseases, Peking University People’s Hospital, Beijing 100044, China
| | - Zhe Wu
- Department of Gastroenterology, Peking University People’s Hospital, Beijing 100044, China; (Y.Z.); (Z.W.); (Q.Z.)
- Clinical Center of Immune-Mediated Digestive Diseases, Peking University People’s Hospital, Beijing 100044, China
| | - Qinghe Zhao
- Department of Gastroenterology, Peking University People’s Hospital, Beijing 100044, China; (Y.Z.); (Z.W.); (Q.Z.)
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People’s Hospital, Beijing 100044, China; (D.W.); (N.L.)
| | - Yaming Liu
- Department of Gastroenterology and Hepatology, Xiamen University Zhongshan Hospital, Xiamen 361001, China;
| | - Qing Huang
- Department of Gastroenterology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China;
| | - Menglei Zhang
- Department of Animal Laboratory, Peking University People’s Hospital, Beijing 100044, China; (M.Z.); (S.L.)
| | - Shuolei Li
- Department of Animal Laboratory, Peking University People’s Hospital, Beijing 100044, China; (M.Z.); (S.L.)
| | - Di Wang
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People’s Hospital, Beijing 100044, China; (D.W.); (N.L.)
| | - Na Li
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People’s Hospital, Beijing 100044, China; (D.W.); (N.L.)
| | - Yujing Chi
- Department of Gastroenterology, Peking University People’s Hospital, Beijing 100044, China; (Y.Z.); (Z.W.); (Q.Z.)
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People’s Hospital, Beijing 100044, China; (D.W.); (N.L.)
| | - Yulan Liu
- Department of Gastroenterology, Peking University People’s Hospital, Beijing 100044, China; (Y.Z.); (Z.W.); (Q.Z.)
- Clinical Center of Immune-Mediated Digestive Diseases, Peking University People’s Hospital, Beijing 100044, China
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9
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Levitte S, Khan I, Iyahen V, Ziai J, Gubatan J, Sheng R, Glickstein SB, Sun T, Park KT, McBride J, Keir M. Differential expression of small bowel TGFβ1 and TGFβ3 characterizes intestinal strictures in patients with fibrostenotic Crohn's disease. Histochem Cell Biol 2024:10.1007/s00418-024-02290-0. [PMID: 38705911 DOI: 10.1007/s00418-024-02290-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2024] [Indexed: 05/07/2024]
Abstract
Small bowel strictures remain a debilitating consequence of Crohn's disease and contribute to poor outcomes for patients. Recently, TGFβ has been identified as an important driver of intestinal fibrosis. We studied the localization of TGFβ isoforms in ileal strictures of patients with Crohn's disease using in situ hybridization to understand TGFβ's role in stricture formation. The mucosa of strictures was characterized by higher TGFβ1 while the stricture submucosa showed higher TGFβ3 compared to normal ileum from patients without Crohn's disease (p = 0.02 and p = 0.044, respectively). We correlated these findings with single-cell transcriptomics which demonstrated that TGFβ3 transcripts overall are very rare, which may partially explain why its role in intestinal fibrosis has remained unclear to date. There were no significant differences in fibroblast or B cell TGFβ1 and/or TGFβ3 expression in inflamed vs. noninflamed ileum. We discuss the implications of these findings for therapeutic development strategies to treat patients with fibrostenotic Crohn's disease.
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Affiliation(s)
- Steven Levitte
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Stanford University, 750 Welch Rd Ste 116, Palo Alto, CA, 94304, USA.
| | - Ibaad Khan
- Morehouse School of Medicine, Atlanta, GA, USA
| | | | - James Ziai
- Genentech, Inc, South San Francisco, CA, USA
| | - John Gubatan
- Division of Gastroenterology and Hepatology, Stanford University, Palo Alto, CA, USA
| | | | | | - Tianhe Sun
- Genentech, Inc, South San Francisco, CA, USA
| | - K T Park
- Genentech, Inc, South San Francisco, CA, USA
| | | | - Mary Keir
- Genentech, Inc, South San Francisco, CA, USA
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10
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Yokode M, Shiokawa M, Kawakami H, Kuwada T, Nishikawa Y, Muramoto Y, Kitamoto H, Okabe M, Yamazaki H, Okamoto N, Morita T, Ohno K, Nakanishi R, Takimoto I, Yasuda M, Chikugo K, Matsumoto S, Yoshida H, Ota S, Nakamura T, Okada H, Hirano T, Kakiuchi N, Matsumori T, Yamamoto S, Uza N, Ooi M, Kodama Y, Chiba T, Hayashi H, Seno H. Anti-integrin αvβ6 autoantibodies are a potential biomarker for ulcerative colitis-like immune checkpoint inhibitor-induced colitis. Br J Cancer 2024; 130:1552-1560. [PMID: 38461170 PMCID: PMC11058246 DOI: 10.1038/s41416-024-02647-1] [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: 10/25/2023] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND No specific biomarker for immune checkpoint inhibitor (ICI)-induced colitis has been established. Previously, we identified anti-integrin αvβ6 autoantibodies in >90% of patients with ulcerative colitis (UC). Given that a subset of ICI-induced colitis is similar to UC, we aimed to clarify the relationship between such autoantibodies and ICI-induced colitis. METHODS Serum anti-integrin αvβ6 autoantibody levels were compared between 26 patients with ICI-induced colitis and 157 controls. Endoscopic images of ICI-induced colitis were centrally reviewed. Characteristics of anti-integrin αvβ6 autoantibodies in the ICI-induced colitis patients were compared with those of UC patients. RESULTS Anti-integrin αvβ6 autoantibodies were found in 8/26 (30.8%) patients with ICI-induced colitis and 3/157 (1.9%) controls (P < 0.001). Patients with anti-integrin αvβ6 autoantibodies had significantly more typical UC endoscopic features than those without the autoantibodies (P < 0.001). Anti-integrin αvβ6 autoantibodies in ICI-induced colitis patients were associated with grade ≥3 colitis (P = 0.001) and steroid resistance (P = 0.005). Anti-integrin αvβ6 autoantibody titers correlated with ICI-induced colitis disease activity. Anti-integrin αvβ6 autoantibodies of ICI-induced colitis exhibited similar characteristics to those of UC. CONCLUSIONS Anti-integrin αvβ6 autoantibodies may serve as potential biomarkers for the diagnosis, classification, risk management, and monitoring the disease activity, of ICI-induced colitis.
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Affiliation(s)
- Masataka Yokode
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masahiro Shiokawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Hisato Kawakami
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan.
| | - Takeshi Kuwada
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yoshihiro Nishikawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuya Muramoto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroki Kitamoto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Makoto Okabe
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hajime Yamazaki
- Section of Clinical Epidemiology, Department of Community Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Norihiro Okamoto
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Toshihiro Morita
- Department of Gastroenterology and Hepatology, Kitano Hospital, Tazuke Kofukai Medical Research Institute, Osaka, Japan
| | - Kazuya Ohno
- Department of Gastroenterology, Shizuoka General Hospital, Shizuoka, Japan
| | - Risa Nakanishi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ikuhisa Takimoto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Muneji Yasuda
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koki Chikugo
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shimpei Matsumoto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroyuki Yoshida
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Sakiko Ota
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeharu Nakamura
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hirokazu Okada
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomonori Hirano
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomoaki Matsumori
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shuji Yamamoto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Norimitsu Uza
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Makoto Ooi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Yuzo Kodama
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Tsutomu Chiba
- Department of Gastroenterology and Hepatology, Kansai Electric Power Hospital, Osaka, Japan
| | - Hidetoshi Hayashi
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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11
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Humphreys DT, Lewis A, Pan‐Castillo B, Berti G, Mein C, Wozniak E, Gordon H, Gadhok R, Minicozzi A, ChinAleong J, Feakins R, Giannoulatou E, James LK, Stagg AJ, Lindsay JO, Silver A. Single cell sequencing data identify distinct B cell and fibroblast populations in stricturing Crohn's disease. J Cell Mol Med 2024; 28:e18344. [PMID: 38685679 PMCID: PMC11058334 DOI: 10.1111/jcmm.18344] [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: 09/27/2023] [Revised: 02/20/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Single cell RNA sequencing of human full thickness Crohn's disease (CD) small bowel resection specimens was used to identify potential therapeutic targets for stricturing (S) CD. Using an unbiased approach, 16 cell lineages were assigned within 14,539 sequenced cells from patient-matched SCD and non-stricturing (NSCD) preparations. SCD and NSCD contained identical cell types. Amongst immune cells, B cells and plasma cells were selectively increased in SCD samples. B cell subsets suggested formation of tertiary lymphoid tissue in SCD and compared with NSCD there was an increase in IgG, and a decrease in IgA plasma cells, consistent with their potential role in CD fibrosis. Two Lumican-positive fibroblast subtypes were identified and subclassified based on expression of selectively enriched genes as fibroblast clusters (C) 12 and C9. Cells within these clusters expressed the profibrotic genes Decorin (C12) and JUN (C9). C9 cells expressed ACTA2; ECM genes COL4A1, COL4A2, COL15A1, COL6A3, COL18A1 and ADAMDEC1; LAMB1 and GREM1. GO and KEGG Biological terms showed extracellular matrix and stricture organization associated with C12 and C9, and regulation of WNT pathway genes with C9. Trajectory and differential gene analysis of C12 and C9 identified four sub-clusters. Intra sub-cluster gene analysis detected 13 co-regulated gene modules that aligned along predicted pseudotime trajectories. CXCL14 and ADAMDEC1 were key markers in module 1. Our findings support further investigation of fibroblast heterogeneity and interactions with local and circulating immune cells at earlier time points in fibrosis progression. Breaking these interactions by targeting one or other population may improve therapeutic management for SCD.
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Affiliation(s)
- David T. Humphreys
- Victor Chang Cardiac Research InstituteSydneyNew South WalesAustralia
- St Vincent's Clinical SchoolUniversity of New South WalesSydneyNew South WalesAustralia
| | - Amy Lewis
- Centre for Genomics and Child Health, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUK
| | - Belen Pan‐Castillo
- Centre for Genomics and Child Health, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUK
| | - Giulio Berti
- Centre for Genomics and Child Health, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUK
| | - Charles Mein
- Genome Centre, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUK
| | - Eva Wozniak
- Genome Centre, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUK
| | - Hannah Gordon
- Centre for Immunobiology, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUK
| | - Radha Gadhok
- Centre for Immunobiology, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUK
| | - Annamaria Minicozzi
- Department of Colorectal Surgery, Division of Surgery and Perioperative CareThe Royal London HospitalLondonUK
| | | | - Roger Feakins
- Department of Cellular PathologyRoyal Free London NHS Foundation TrustLondonUK
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research InstituteSydneyNew South WalesAustralia
- St Vincent's Clinical SchoolUniversity of New South WalesSydneyNew South WalesAustralia
| | - Louisa K. James
- Centre for Immunobiology, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUK
| | - Andrew J. Stagg
- Centre for Immunobiology, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUK
| | - James Oliver Lindsay
- Centre for Immunobiology, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUK
| | - Andrew Silver
- Centre for Genomics and Child Health, Blizard InstituteBarts and The London School of Medicine and DentistryLondonUK
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12
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Canales-Herrerias P, Uzzan M, Seki A, Czepielewski RS, Verstockt B, Livanos AE, Raso F, Dunn A, Dai D, Wang A, Al-taie Z, Martin J, Laurent T, Ko HM, Tokuyama M, Tankelevich M, Meringer H, Cossarini F, Jha D, Krek A, Paulsen JD, Taylor MD, Nakadar MZ, Wong J, Erlich EC, Mintz RL, Onufer EJ, Helmink BA, Sharma K, Rosenstein A, Ganjian D, Chung G, Dawson T, Juarez J, Yajnik V, Cerutti A, Faith JJ, Suarez-Farinas M, Argmann C, Petralia F, Randolph GJ, Polydorides AD, Reboldi A, Colombel JF, Mehandru S. Gut-associated lymphoid tissue attrition associates with response to anti-α4β7 therapy in ulcerative colitis. Sci Immunol 2024; 9:eadg7549. [PMID: 38640252 PMCID: PMC11140591 DOI: 10.1126/sciimmunol.adg7549] [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: 01/18/2023] [Accepted: 03/20/2024] [Indexed: 04/21/2024]
Abstract
Vedolizumab (VDZ) is a first-line treatment in ulcerative colitis (UC) that targets the α4β7- mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1) axis. To determine the mechanisms of action of VDZ, we examined five distinct cohorts of patients with UC. A decrease in naïve B and T cells in the intestines and gut-homing (β7+) plasmablasts in circulation of VDZ-treated patients suggested that VDZ targets gut-associated lymphoid tissue (GALT). Anti-α4β7 blockade in wild-type and photoconvertible (KikGR) mice confirmed a loss of GALT size and cellularity because of impaired cellular entry. In VDZ-treated patients with UC, treatment responders demonstrated reduced intestinal lymphoid aggregate size and follicle organization and a reduction of β7+IgG+ plasmablasts in circulation, as well as IgG+ plasma cells and FcγR-dependent signaling in the intestine. GALT targeting represents a previously unappreciated mechanism of action of α4β7-targeted therapies, with major implications for this therapeutic paradigm in UC.
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Affiliation(s)
- Pablo Canales-Herrerias
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mathieu Uzzan
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Paris Est Créteil University UPEC, Assistance Publique-Hôpitaux de Paris (AP-HP), Henri Mondor Hospital, Gastroenterology Department, Fédération Hospitalo–Universitaire TRUE (InnovaTive theRapy for immUne disordErs), Créteil F-94010, France
| | - Akihiro Seki
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Bram Verstockt
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Translational Research in Gastrointestinal Disorders, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Alexandra E. Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fiona Raso
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Alexandra Dunn
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Dai
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Wang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zainab Al-taie
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerome Martin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nantes Université, CHU Nantes, Inserm, Centre de Recherche Translationelle en Transplantation et Immunologie, UMR 1064, Nantes, France
- CHU Nantes, Nantes Université, Laboratoire d’immunologie, CIMNA, Nantes, France
| | - Thomas Laurent
- Nantes Université, CHU Nantes, Inserm, Centre de Recherche Translationelle en Transplantation et Immunologie, UMR 1064, Nantes, France
- CHU Nantes, Nantes Université, Laboratoire d’immunologie, CIMNA, Nantes, France
| | - Huaibin M. Ko
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minami Tokuyama
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Tankelevich
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hadar Meringer
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Cossarini
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Divya Jha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John D. Paulsen
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D. Taylor
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mohammad Zuber Nakadar
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua Wong
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma C. Erlich
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel L. Mintz
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Emily J. Onufer
- Division of Pediatric Surgery, Department of Surgery, St. Louis Children's Hospital, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Beth A. Helmink
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Keshav Sharma
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam Rosenstein
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danielle Ganjian
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Grace Chung
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Andrea Cerutti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Translational Clinical Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jeremiah J. Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mayte Suarez-Farinas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gwendalyn J. Randolph
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexandros D. Polydorides
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrea Reboldi
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jean-Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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13
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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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14
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Liu XY, Qiao D, Zhang YL, Liu ZX, Chen YL, Que RY, Cao HY, Dai YC. Identification of marker genes associated with N6-methyladenosine and autophagy in ulcerative colitis. World J Clin Cases 2024; 12:1750-1765. [PMID: 38660076 PMCID: PMC11036473 DOI: 10.12998/wjcc.v12.i10.1750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 01/21/2024] [Accepted: 02/29/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Both N6-methyladenosine (m6A) methylation and autophagy are considered relevant to the pathogenesis of ulcerative colitis (UC). However, a systematic exploration of the role of the com-bination of m6A methylation and autophagy in UC remains to be performed. AIM To elucidate the autophagy-related genes of m6A with a diagnostic value for UC. METHODS The correlation between m6A-related genes and autophagy-related genes (ARGs) was analyzed. Finally, gene set enrichment analysis (GSEA) was performed on the characteristic genes. Additionally, the expression levels of four characteristic genes were verified in dextran sulfate sodium (DSS)-induced colitis in mice. RESULTS GSEA indicated that BAG3, P4HB and TP53INP2 were involved in the inflammatory response and TNF-α signalling via nuclear factor kappa-B. Furthermore, polymerase chain reaction results showed significantly higher mRNA levels of BAG3 and P4HB and lower mRNA levels of FMR1 and TP53INP2 in the DSS group compared to the control group. CONCLUSION This study identified four m6A-ARGs that predict the occurrence of UC, thus providing a scientific reference for further studies on the pathogenesis of UC.
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Affiliation(s)
- Xiao-Yan Liu
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Dan Qiao
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Ya-Li Zhang
- Institute of Digestive Diseases, Long Hua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Zi-Xuan Liu
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - You-Lan Chen
- Department of Gastroenterology, Shu Guang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ren-Ye Que
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Hong-Yan Cao
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Yan-Cheng Dai
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
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15
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Bai J, Wang Y, Li F, Wu Y, Chen J, Li M, Wang X, Lv B. Research advancements and perspectives of inflammatory bowel disease: A comprehensive review. Sci Prog 2024; 107:368504241253709. [PMID: 38778725 PMCID: PMC11113063 DOI: 10.1177/00368504241253709] [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] [Indexed: 05/25/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease with increasing incidence, such as Crohn's disease and ulcerative colitis. The accurate etiology and pathogenesis of IBD remain unclear, and it is generally believed that it is related to genetic susceptibility, gut microbiota, environmental factors, immunological abnormalities, and potentially other factors. Currently, the mainstream therapeutic drugs are amino salicylic acid agents, corticosteroids, immunomodulators, and biological agents, but the remission rates do not surpass 30-60% of patients in a real-life setting. As a consequence, there are many studies focusing on emerging drugs and bioactive ingredients that have higher efficacy and long-term safety for achieving complete deep healing. This article begins with a review of the latest, systematic, and credible summaries of the pathogenesis of IBD. In addition, we provide a summary of the current treatments and drugs for IBD. Finally, we focus on the therapeutic effects of emerging drugs such as microRNAs and lncRNAs, nanoparticles-mediated drugs and natural products on IBD and their mechanisms of action.
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Affiliation(s)
- Junyi Bai
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Ying Wang
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Fuhao Li
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- Key Laboratory of Digestive Pathophysiology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yueyao Wu
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- Key Laboratory of Digestive Pathophysiology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jun Chen
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Meng Li
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- Key Laboratory of Digestive Pathophysiology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xi Wang
- Key Laboratory of Digestive Pathophysiology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Chinese Medical University, Hangzhou, China
| | - Bin Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- Key Laboratory of Digestive Pathophysiology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University, Zhejiang Chinese Medical University, Hangzhou, China
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16
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Yang J, Huang MMC, Liang MMJW, Lei MMYC. The diagnostic performance of serum αvβ6 autoantibodies for ulcerative colitis: A systematic review and meta-analysis. Clin Res Hepatol Gastroenterol 2024; 48:102317. [PMID: 38499246 DOI: 10.1016/j.clinre.2024.102317] [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: 12/25/2023] [Revised: 02/20/2024] [Accepted: 03/09/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND AND OBJECTIVE Currently, there is no single golden standard for diagnosing ulcerative colitis (UC). Now serum αvβ6 autoantibodies have shown promise as a diagnostic tool for UC. Here the aim was to determine the diagnostic performance of serum αvβ6 autoantibodies for UC. METHODS PubMed, the Cochrane Library, the Embase, and the Web of Science were searched comprehensively. STATA software was utilized to analyze the relevant data. RESULTS 9 studies from 6 articles with 1827 subjects were eligible. The summary sensitivity and specificity of serum αvβ6 autoantibodies to diagnose UC were 0.82 (95 % confidence interval (CI): 0.65-0.92) and 0.94 (95 % CI: 0.90-0.97) with an area under the summary receiver operating characteristic curve of 0.96 (95 % CI: 0.94-0.97). Subgroup analysis was conducted owning to substantial heterogeneity between studies (I2 = 97 % and P < 0.001). The aggregate sensitivity and specificity to diagnose UC in adults were 0.75 (95 % CI: 0.61-0.86) and 0.95 (95 % CI: 0.90-0.97), and when using a threshold of mean control+3SD, 0.80 (95 % CI: 0.60-0.91) and 0.96 (95 % CI: 0.90-0.99), respectively. Additionally, to differentiate UC from healthy participants, non-inflammatory bowel disease, and Crohn's disease, the overall specificity was 0.96, 0.88, and 0.80, respectively. CONCLUSIONS serum αvβ6 autoantibodies, as a non-invasive tool, demonstrated good diagnostic accuracy for UC. However, their application may be limited in some immune-related disorders, and further studies are needed for validation.
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Affiliation(s)
- Jiao Yang
- Department of Gastroenterology, LiuZhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi 545000, China
| | - M M Cai Huang
- Department of Gastroenterology, LiuZhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi 545000, China
| | - M M Jing-Wen Liang
- Department of Gastroenterology, LiuZhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi 545000, China
| | - M M Yan-Chang Lei
- Department of Gastroenterology, LiuZhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi 545000, China.
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17
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He Z, Zhou Q, Du J, Huang Y, Wu B, Xu Z, Wang C, Cheng X. Integrated single-cell and bulk RNA sequencing reveals CREM is involved in the pathogenesis of ulcerative colitis. Heliyon 2024; 10:e27805. [PMID: 38496850 PMCID: PMC10944264 DOI: 10.1016/j.heliyon.2024.e27805] [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: 09/02/2023] [Revised: 02/22/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024] Open
Abstract
Background Ulcerative colitis (UC) is an inflammatory bowel disease characterized by persistent colonic inflammation. Here, we performed a systematic analysis to gain better insights into UC pathogenesis. Methods We analyzed two UC-related datasets extracted from the gene expression omnibus database using several bioinformatics tools. The primary cell types and key subgroups of primary cells associated with UC and differentially expressed genes (DEGs) between UC and control samples were identified. The molecular regulation of the key genes was also predicted. The gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses of marker genes of key cell subgroups and model genes were performed. The expression of key enriched genes was validated in 10 clinical samples using real-time quantitative polymerase chain reaction (RT-qPCR). Results Monocytes were identified as the major cell type. Ten differentially expressed marker genes were obtained by intersecting the 3121 DEGs, 38 marker genes in major cell types, and 104 marker genes in key cell subgroups. Four essential genes, associated with immune response, were obtained using support vector machine recursive feature elimination and least absolute shrinkage and selection operator analyses. The four essential genes were highly expressed in Cluster 0 during differentiation. Validation of the four key genes in colonic mucosal biopsy specimens from 10 normal and 10 UC patients revealed that CREM was highly expressed in both the lesion-free sites and lesion sites colonic mucosa of UC patients compared with normal adults. Conclusions We identified CREM involved in UC pathogenesis, which is expected to provide a new therapeutic target for UC.
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Affiliation(s)
- Zongqi He
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Qing Zhou
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210004, PR China
| | - Jun Du
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Yuyu Huang
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Bensheng Wu
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Zhizhong Xu
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Chao Wang
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
| | - Xudong Cheng
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215009, PR China
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18
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Jin XY, Li DD, Quan W, Chao Y, Zhang B. Leaky gut, circulating immune complexes, arthralgia, and arthritis in IBD: coincidence or inevitability? Front Immunol 2024; 15:1347901. [PMID: 38571963 PMCID: PMC10987687 DOI: 10.3389/fimmu.2024.1347901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
Most host-microbiota interactions occur within the intestinal barrier, which is essential for separating the intestinal epithelium from toxins, microorganisms, and antigens in the gut lumen. Gut inflammation allows pathogenic bacteria to enter the blood stream, forming immune complexes which may deposit on organs. Despite increased circulating immune complexes (CICs) in patients with inflammatory bowel disease (IBD) and discussions among IBD experts regarding their potential pathogenic role in extra-intestinal manifestations, this phenomenon is overlooked because definitive evidence demonstrating CIC-induced extra-intestinal manifestations in IBD animal models is lacking. However, clinical observations of elevated CICs in newly diagnosed, untreated patients with IBD have reignited research into their potential pathogenic implications. Musculoskeletal symptoms are the most prevalent extra-intestinal IBD manifestations. CICs are pivotal in various arthritis forms, including reactive, rheumatoid, and Lyme arthritis and systemic lupus erythematosus. Research indicates that intestinal barrier restoration during the pre-phase of arthritis could inhibit arthritis development. In the absence of animal models supporting extra-intestinal IBD manifestations, this paper aims to comprehensively explore the relationship between CICs and arthritis onset via a multifaceted analysis to offer a fresh perspective for further investigation and provide novel insights into the interplay between CICs and arthritis development in IBD.
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Affiliation(s)
- Xi-ya Jin
- Department of Gastroenterology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Dan-dan Li
- Department of Gastroenterology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Wei Quan
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yang Chao
- Department of Gastroenterology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Bin Zhang
- Department of Gastroenterology, China-Japan Union Hospital of Jilin University, Changchun, China
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19
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Pecha B, Martinez S, Milburn LJ, Rojas OL, Koch MA. Identification of Intestinal Lamina Propria Plasma Cells by Surface Transmembrane Activator and CAML Interactor Expression. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1022-1028. [PMID: 38294253 PMCID: PMC10932850 DOI: 10.4049/jimmunol.2300132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Plasma cells secrete an abundance of Abs and are a crucial component of our immune system. The intestinal lamina propria harbors the largest population of plasma cells, most of which produce IgA. These Abs can bind to beneficial gut bacteria to reinforce intestinal homeostasis and provide protection against enteric pathogens. Plasma cells downregulate many cell-surface proteins commonly used to identify B cells. In mice, expression of the surface marker CD138 has been widely used to identify plasma cells in lymph nodes, bone marrow, and spleen. Intestinal plasma cells require liberation via extensive tissue processing involving treatment with collagenase. We report that detection of CD138 surface expression is reduced following collagenase treatment. Using a mouse in which yellow fluorescent protein expression is controlled by the plasma cell requisite transcription factor Blimp-1, we show that surface detection of transmembrane activator and CAML interactor captures a significant proportion of Ab-secreting plasma cells in the intestinal lamina propria and gut-draining mesenteric lymph nodes. Additionally, we describe a flow cytometry panel based on the detection of surface markers to identify murine B cell subsets in the intestinal lamina propria and, as a proof of concept, combine it with a cutting-edge fate-tracking system to characterize the fate of germinal center B cells activated in early life. By identifying plasma cells and other key intestinal B subsets in a manner compatible with several downstream applications, including sorting and culturing and in vitro manipulations, this efficient and powerful approach can enhance studies of mucosal immunity.
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Affiliation(s)
- Bingjie Pecha
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA
- Medical Scientist Training Program, University of Washington, Seattle, WA
| | | | - Luke J Milburn
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Olga L Rojas
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Meghan A Koch
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Immunology, University of Washington, Seattle, WA
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20
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Rogalla S, Holman D, Rubin S, Ferenc M, Holman E, Koron A, Daniel R, Boland B, Nolan G, Chang J. Automated Spatial Omics Landscape Analysis Approach Reveals Novel Tissue Architectures in Ulcerative Colitis. RESEARCH SQUARE 2024:rs.3.rs-3965505. [PMID: 38559236 PMCID: PMC10980100 DOI: 10.21203/rs.3.rs-3965505/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The utility of spatial omics in leveraging cellular interactions in normal and diseased states for precision medicine is hampered by a lack of strategies for matching disease states with spatial heterogeneity-guided cellular annotations. Here we use a spatial context-dependent approach that matches spatial pattern detection to cell annotation. Using this approach in existing datasets from ulcerative colitis patient colonic biopsies, we identified architectural complexities and associated difficult-to-detect rare cell types in ulcerative colitis germinal-center B cell follicles. Our approach deepens our understanding of health and disease pathogenesis, illustrates a strategy for automating nested architecture detection for highly multiplexed spatial biology data, and informs precision diagnosis and therapeutic strategies.
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21
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Magisetty J, Gadiraju B, Kondreddy V. Genomic analysis in the colon tissues of omega-3 fatty acid-treated rats identifies novel gene signatures implicated in ulcerative colitis. Int J Biol Macromol 2024; 258:128867. [PMID: 38123036 DOI: 10.1016/j.ijbiomac.2023.128867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/11/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Several long-term intervention trials only studied the ex vivo immunological function to elucidate the beneficial mechanisms of n-3 polyunsaturated fatty acids (PUFA) in the ulcerative colitis (UC). An unbiased whole-transcriptome analysis would be more valuable to obtain a comprehensive understanding of the processes and genes regulated by n-3 PUFA in vivo. In this study, we have performed microarray analysis in the colon tissues of dextran sulfate sodium (DSS)-induced UC in rats supplemented with n-6 PUFA, n-3PUFA and long-chain n-3PUFA (LC-n3PUFA). We have identified the novel gene signatures previously not linked to colitis such as Etv3, Clec4d, CD180, CD72, Megf11, and Angptl4 which are most downregulated in both n-3PUFA and LC-n3PUFA groups compared to the n-6PUFA group. The most upregulated genes were Nr1i3, Nptx2, and Zfp810 in both n-3PUFA and LC-n3PUFA groups. The RT-PCR analysis confirmed similar results. Interestingly, LPS treatment in macrophages upregulated the Megf11, Etv3, CD180, and Angptl4, and correlated with increased secretion of cytokines. Gene silencing of Etv3, Megf11, and CD180 in rats using intravascular delivery of siRNA-lipoparticles attenuated the DSS-induced ulceration and mucosal damage. Thus, our genome-wide microarray analysis identified novel genes regulated by omega-3 PUFA and offers new drug targets that could prevent or reduce UC.
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Affiliation(s)
- Jhansi Magisetty
- Department of Biochemistry, Central Food Technological Research Institute, Mysore 570020, India
| | - Bhavani Gadiraju
- Center for Lipid Science & Technology, The Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, India
| | - Vijay Kondreddy
- Center for Lipid Science & Technology, The Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, India.
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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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23
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Rudbaek JJ, Agrawal M, Torres J, Mehandru S, Colombel JF, Jess T. Deciphering the different phases of preclinical inflammatory bowel disease. Nat Rev Gastroenterol Hepatol 2024; 21:86-100. [PMID: 37950021 PMCID: PMC11148654 DOI: 10.1038/s41575-023-00854-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/12/2023]
Abstract
Inflammatory bowel disease (IBD) is an immune-mediated inflammatory disease (IMID) of the gastrointestinal tract and includes two subtypes: Crohn's disease and ulcerative colitis. It is well-recognized that IBD is associated with a complex multifactorial aetiology that includes genetic predisposition and environmental exposures, with downstream dysregulation of systemic immune function and host-microbial interactions in the local environment in the gut. Evidence to support the notion of a multistage development of IBD is growing, as has been observed in other IMIDs such as rheumatoid arthritis and systemic lupus erythematosus. With the rising worldwide incidence of IBD, it is increasingly important to understand the complex interplay of pathological events during the different stages of disease development to enable IBD prediction and prevention strategies. In this article, we review comprehensively the current evidence pertaining to the preclinical phase of IBD, including at-risk, initiation and expansion phases. We also discuss the framework of preclinical IBD, expanding on underlying pathways in IBD development, future research directions and IBD development in the context of other IMIDs.
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Affiliation(s)
- Jonas J Rudbaek
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Section for Biomarkers, Immunology and Antibodies, Department for Congenital Disorders, Statens Serum Institut, Copenhangen, Denmark
| | - Manasi Agrawal
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joana Torres
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
- Division of Gastroenterology, Hospital da Luz, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Saurabh Mehandru
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark.
- Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark.
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24
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Yoshitomi H. Peripheral helper T cells, mavericks of peripheral immune responses. Int Immunol 2024; 36:9-16. [PMID: 37788648 PMCID: PMC10823579 DOI: 10.1093/intimm/dxad041] [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: 07/31/2023] [Accepted: 10/03/2023] [Indexed: 10/05/2023] Open
Abstract
Peripheral helper T (Tph) cells have been established, through intensive efforts to elucidate local immune responses in human rheumatoid arthritis (RA), as a CD4 subset intimately involved in acquired immunity in peripheral tissues. Initially, Tph cells were noted as a CD4 population that produces high levels of CXCL13 in RA synovial tissues, followed by a demonstration of their ability to help B cells. In contrast to follicular helper T (Tfh) cells, Tph cells do not express the transcription factor BCL6 but express molecules such as CXCL13, interleukin (IL)-21, and inducible T-cell costimulator (ICOS) to help B cells in peripheral tissues. Subsequent studies showed that Tph cells are associated with various diseases, including autoimmune diseases, infections, and malignancies, and with the development of early life immunity. This review summarizes the phenotype and function of Tph cells in RA and discusses their differentiation and diversity in various conditions.
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Affiliation(s)
- Hiroyuki Yoshitomi
- Department of Immunology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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25
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Ning K, Shi C, Chi YY, Zhou YF, Zheng W, Duan Y, Tong W, Xie Q, Xiang H. Portulaca oleracea L. polysaccharide alleviates dextran sulfate sodium-induced ulcerative colitis by regulating intestinal homeostasis. Int J Biol Macromol 2024; 256:128375. [PMID: 38000581 DOI: 10.1016/j.ijbiomac.2023.128375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/26/2023]
Abstract
Portulaca oleracea L. (purslane) is a vegetable that contains a variety of active compounds with nutritional properties and has the potential to treat ulcerative colitis (UC). However, the mechanisms underlying the effects of Portulaca oleracea L. polysaccharide (POP) in alleviating UC remain unclear. In this study, we prepared an aqueous extract of purslane and separated a fraction with molecular weight >10 kDa using membrane separation. This fraction was used to isolate POP. The effect of POP on gut microbiota and colon transcriptome in dextran sulfate sodium-induced UC model mice was evaluated. POP treatment reduced inflammation and oxidative stress imbalance in UC mice. In addition, POP improved the intestinal barrier and regulated intestinal homeostasis. Importantly, POP was found to regulate gut microbiota, maintain the levels of retinol and short-chain fatty acids in the gut, promote the proliferation and differentiation of B cells in the colon, and increase the expression of immunoglobulin A. These results provide novel insights into the role of POP in regulating intestinal homeostasis, which should guide further development of POP as a functional food.
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Affiliation(s)
- Ke Ning
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Chao Shi
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Yan-Yu Chi
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Yong-Fei Zhou
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Weiwei Zheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Yameng Duan
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Weiwei Tong
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Qiuhong Xie
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China; Institute of Changbai Mountain Resource and Health, Jilin University, Fusong 134504, PR China.
| | - Hongyu Xiang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China; Institute of Changbai Mountain Resource and Health, Jilin University, Fusong 134504, PR China.
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26
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Tang W, Wei Y, Ni Z, Hou K, Luo XM, Wang H. IgA-mediated control of host-microbial interaction during weaning reaction influences gut inflammation. Gut Microbes 2024; 16:2323220. [PMID: 38439579 PMCID: PMC10936605 DOI: 10.1080/19490976.2024.2323220] [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: 10/26/2023] [Accepted: 02/21/2024] [Indexed: 03/06/2024] Open
Abstract
The mechanisms of how host-microbe mutualistic relationships are established at weaning contingently upon B-cell surveillance remain inadequately elucidated. We found that CD138+ plasmacyte (PC)-mediated promotion of IgA response regulates the symbiosis between Bacteroides uniformis (B. uniformis) and the host during the weaning period. The IgA-skewed response of CD138+ PCs is essential for B. uniformis to occupy a defined gut luminal niche, thereby fostering stable colonization. Furthermore, B. uniformis within the natural gut niche was perturbed in the absence of IgA, resulting in exacerbated gut inflammation in IgA-deficient mice and weaned piglets. Thus, we propose that the priming and maintenance of intestinal IgA response from CD138+ PCs are required for host-microbial symbiosis, whereas the perturbation of which would enhance inflammation in weaning process.
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Affiliation(s)
- Wenjie Tang
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yusen Wei
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Zhixiang Ni
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Kangwei Hou
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Xin M Luo
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, USA
| | - Haifeng Wang
- College of Animal Science, Zhejiang University, Hangzhou, China
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27
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Wemlinger SM, Cambier JC. Therapeutic tactics for targeting B lymphocytes in autoimmunity and cancer. Eur J Immunol 2024; 54:e2249947. [PMID: 37816494 DOI: 10.1002/eji.202249947] [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: 01/13/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/12/2023]
Abstract
B lymphocytes have become a very popular therapeutic target in a number of autoimmune indications due to their newly appreciated roles, and approachability, in these diseases. Many of the therapies now applied in autoimmunity were initially developed to deplete malignant B cells. These strategies have also been found to benefit patients suffering from such autoimmune diseases as multiple sclerosis, type I diabetes, systemic lupus erythematosus, and rheumatoid arthritis, to name a few. These observations have supported the expansion of research addressing the mechanistic contributions of B cells in these diseases, as well as blossoming of therapeutics that target them. This review seeks to summarize cutting-edge modalities for targeting B cells, including monoclonal antibodies, bispecific antibodies, antibody-drug conjugates, chimeric antigen receptor-T cells, and small molecule inhibitors. Efforts to refine B-cell targeted therapy to eliminate only pathogenic autoreactive cells will be addressed as well as the potential for future B-cell-based cellular therapeutics. Finally, we also address approaches that seek to silence B-cell function without depletion.
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Affiliation(s)
- Scott M Wemlinger
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - John C Cambier
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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28
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Kappel-Latif S, Kotagiri P, Schlager L, Schuld G, Walterskirchen N, Schimek V, Sewell G, Binder C, Jobst J, Murthy S, Messner B, Dabsch S, Kaser A, Lyons PA, Bergmann M, Stift A, Oehler R, Unger LW. Altered B-Cell Expansion and Maturation in Draining Mesenteric Lymph Nodes of Inflamed Gut in Crohn's Disease. Cell Mol Gastroenterol Hepatol 2023; 17:662-666. [PMID: 38147955 PMCID: PMC10958343 DOI: 10.1016/j.jcmgh.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023]
Affiliation(s)
- Sonja Kappel-Latif
- Division of Visceral Surgery, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Prasanti Kotagiri
- Jeffrey Cheah Biomedical Centre, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Lukas Schlager
- Division of Visceral Surgery, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Gabor Schuld
- Division of Visceral Surgery, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Natalie Walterskirchen
- Division of Visceral Surgery, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Vanessa Schimek
- Division of Visceral Surgery, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Gavin Sewell
- Jeffrey Cheah Biomedical Centre, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Carina Binder
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Johanna Jobst
- Division of Visceral Surgery, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Supriya Murthy
- Clinical Institute of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Barbara Messner
- Cardiac Surgery Research Laboratory, Department of Cardiac Surgery, Medical University of Vienna, Vienna, Austria
| | - Stefanie Dabsch
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Arthur Kaser
- Jeffrey Cheah Biomedical Centre, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom; Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul A Lyons
- Jeffrey Cheah Biomedical Centre, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Michael Bergmann
- Division of Visceral Surgery, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Anton Stift
- Division of Visceral Surgery, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Rudolf Oehler
- Division of Visceral Surgery, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Lukas W Unger
- Division of Visceral Surgery, Department of General Surgery, Medical University of Vienna, Vienna, Austria; Jeffrey Cheah Biomedical Centre, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom.
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29
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Karmele EP, Moldoveanu AL, Kaymak I, Jugder BE, Ursin RL, Bednar KJ, Corridoni D, Ort T. Single cell RNA-sequencing profiling to improve the translation between human IBD and in vivo models. Front Immunol 2023; 14:1291990. [PMID: 38179052 PMCID: PMC10766350 DOI: 10.3389/fimmu.2023.1291990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024] Open
Abstract
Inflammatory bowel disease (IBD) is an umbrella term for two conditions (Crohn's Disease and Ulcerative Colitis) that is characterized by chronic inflammation of the gastrointestinal tract. The use of pre-clinical animal models has been invaluable for the understanding of potential disease mechanisms. However, despite promising results of numerous therapeutics in mouse colitis models, many of these therapies did not show clinical benefits in patients with IBD. Single cell RNA-sequencing (scRNA-seq) has recently revolutionized our understanding of complex interactions between the immune system, stromal cells, and epithelial cells by mapping novel cell subpopulations and their remodeling during disease. This technology has not been widely applied to pre-clinical models of IBD. ScRNA-seq profiling of murine models may provide an opportunity to increase the translatability into the clinic, and to choose the most appropriate model to test hypotheses and novel therapeutics. In this review, we have summarized some of the key findings at the single cell transcriptomic level in IBD, how specific signatures have been functionally validated in vivo, and highlighted the similarities and differences between scRNA-seq findings in human IBD and experimental mouse models. In each section of this review, we highlight the importance of utilizing this technology to find the most suitable or translational models of IBD based on the cellular therapeutic target.
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Affiliation(s)
- Erik P. Karmele
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Ana Laura Moldoveanu
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Irem Kaymak
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Bat-Erdene Jugder
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Waltham, MA, United States
| | - Rebecca L. Ursin
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Waltham, MA, United States
| | - Kyle J. Bednar
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Daniele Corridoni
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Tatiana Ort
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
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30
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Song S, Mohsin E, Zhang R, Kuznetsov A, Shen L, Grossman RL, Weber CR, Khan AA. ATAT: Automated Tissue Alignment and Traversal in Spatial Transcriptomics with Self-Supervised Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570839. [PMID: 38106010 PMCID: PMC10723486 DOI: 10.1101/2023.12.08.570839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Spatial transcriptomics (ST) has enhanced RNA analysis in tissue biopsies, but interpreting these data is challenging without expert input. We present Automated Tissue Alignment and Traversal (ATAT), a novel computational framework designed to enhance ST analysis in the context of multiple and complex tissue architectures and morphologies, such as those found in biopsies of the gastrointestinal tract. ATAT utilizes self-supervised contrastive learning on hematoxylin and eosin (H&E) stained images to automate the alignment and traversal of ST data. This approach addresses a critical gap in current ST analysis methodologies, which rely heavily on manual annotation and pathologist expertise to delineate regions of interest for accurate gene expression modeling. Our framework not only streamlines the alignment of multiple ST samples, but also demonstrates robustness in modeling gene expression transitions across specific regions. Additionally, we highlight the ability of ATAT to traverse complex tissue topologies in real-world cases from various individuals and conditions. Our method successfully elucidates differences in immune infiltration patterns across the intestinal wall, enabling the modeling of transcriptional changes across histological layers. We show that ATAT achieves comparable performance to the state-of-the-art method, while alleviating the burden of manual annotation and enabling alignment of tissue samples with complex morphologies.
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Affiliation(s)
- Steven Song
- Department of Computer Science, University of Chicago, IL 60637, USA
- Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL 60637, USA
| | - Emaan Mohsin
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Renyu Zhang
- Department of Computer Science, University of Chicago, IL 60637, USA
| | - Andrey Kuznetsov
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Le Shen
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Robert L. Grossman
- Department of Computer Science, University of Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | | | - Aly A. Khan
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
- Institute for Population and Precision Health, University of Chicago, Chicago, IL 60637, USA
- Department of Family Medicine, University of Chicago, Chicago, IL 60637, USA
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31
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Gupta A, Weinand K, Nathan A, Sakaue S, Zhang MJ, Donlin L, Wei K, Price AL, Amariuta T, Raychaudhuri S. Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability. Nat Genet 2023; 55:2200-2210. [PMID: 38036783 PMCID: PMC10787644 DOI: 10.1038/s41588-023-01577-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
In autoimmune diseases such as rheumatoid arthritis, the immune system attacks the body's own cells. Developing a precise understanding of the cell states where noncoding autoimmune risk variants impart causal mechanisms is critical to developing curative therapies. Here, to identify noncoding regions with accessible chromatin that associate with cell-state-defining gene expression patterns, we leveraged multimodal single-nucleus RNA and assay for transposase-accessible chromatin (ATAC) sequencing data across 28,674 cells from the inflamed synovial tissue of 12 donors. Specifically, we used a multivariate Poisson model to predict peak accessibility from single-nucleus RNA sequencing principal components. For 14 autoimmune diseases, we discovered that cell-state-dependent ('dynamic') chromatin accessibility peaks in immune cell types were enriched for heritability, compared with cell-state-invariant ('cs-invariant') peaks. These dynamic peaks marked regulatory elements associated with T peripheral helper, regulatory T, dendritic and STAT1+CXCL10+ myeloid cell states. We argue that dynamic regulatory elements can help identify precise cell states enriched for disease-critical genetic variation.
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Affiliation(s)
- Anika Gupta
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kathryn Weinand
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martin Jinye Zhang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Laura Donlin
- Weill Cornell Medicine, New York, NY, USA
- Hospital for Special Surgery, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alkes L Price
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tiffany Amariuta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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32
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Mo S, Shen X, Huang B, Wang Y, Lin L, Chen Q, Weng M, Sugasawa T, Gu W, Tsushima Y, Nakajima T. Single-cell dissection, hdWGCNA and deep learning reveal the role of oxidatively stressed plasma cells in ulcerative colitis. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1730-1739. [PMID: 37814814 PMCID: PMC10686794 DOI: 10.3724/abbs.2023237] [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: 02/28/2023] [Accepted: 04/19/2023] [Indexed: 10/11/2023] Open
Abstract
Ulcerative colitis (UC) develops as a result of complex interactions between various cell types in the mucosal microenvironment. In this study, we aim to elucidate the pathogenesis of ulcerative colitis at the single-cell level and unveil its clinical significance. Using single-cell RNA sequencing and high-dimensional weighted gene co-expression network analysis, we identify a subpopulation of plasma cells (PCs) with significantly increased infiltration in UC colonic mucosa, characterized by pronounced oxidative stress. Combining 10 machine learning approaches, we find that the PC oxidative stress genes accurately distinguish diseased mucosa from normal mucosa (independent external testing AUC=0.991, sensitivity=0.986, specificity=0.909). Using MCPcounter and non-negative matrix factorization, we identify the association between PC oxidative stress genes and immune cell infiltration as well as patient heterogeneity. Spatial transcriptome data is used to verify the infiltration of oxidatively stressed PCs in colitis. Finally, we develop a gene-immune convolutional neural network deep learning model to diagnose UC mucosa in different cohorts (independent external testing AUC=0.984, sensitivity=95.9%, specificity=100%). Our work sheds light on the key pathogenic cell subpopulations in UC and is essential for the development of future clinical disease diagnostic tools.
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Affiliation(s)
- Shaocong Mo
- Department of Digestive DiseasesHuashan HospitalFudan UniversityShanghai200040China
| | - Xin Shen
- Department of Digestive DiseasesHuashan HospitalFudan UniversityShanghai200040China
| | | | - Yulin Wang
- Department of NephrologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Lingxi Lin
- Department of Digestive DiseasesHuashan HospitalFudan UniversityShanghai200040China
| | - Qiuming Chen
- Department of Thoracic SurgeryThe First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310003China
| | - Meilin Weng
- Department of AnesthesiologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Takehito Sugasawa
- Laboratory of Clinical Examination and Sports MedicineDepartment of Clinical MedicineFaculty of MedicineUniversity of TsukubaIbaraki305-8577Japan
| | - Wenchao Gu
- Department of Diagnostic and Interventional RadiologyUniversity of TsukubaIbaraki305-8577Japan
- Department of Diagnostic Radiology and Nuclear MedicineGunma University Graduate School of MedicineMaebashi371-8511Japan
| | - Yoshito Tsushima
- Department of Diagnostic Radiology and Nuclear MedicineGunma University Graduate School of MedicineMaebashi371-8511Japan
| | - Takahito Nakajima
- Department of Diagnostic and Interventional RadiologyUniversity of TsukubaIbaraki305-8577Japan
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33
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Serrano I, Luque A, Ruiz-Cerulla A, Navas S, Blom AM, Rodríguez de Córdoba S, Fernández FJ, Cristina Vega M, Rodríguez-Moranta F, Guardiola J, Aran JM. C4BP(β-)-mediated immunomodulation attenuates inflammation in DSS-induced murine colitis and in myeloid cells from IBD patients. Pharmacol Res 2023; 197:106948. [PMID: 37806602 DOI: 10.1016/j.phrs.2023.106948] [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: 06/02/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
The most recent and promising therapeutic strategies for inflammatory bowel disease (IBD) have engaged biologics targeting single effector components involved in major steps of the immune-inflammatory processes, such as tumor necrosis factor, interleukins or integrins. Nevertheless, these molecules have not yet met expectations regarding efficacy and safety, resulting in a significant percentage of refractory or relapsing patients. Thus, novel treatment options are urgently needed. The minor isoform of the complement inhibitor C4b-binding protein, C4BP(β-), has been shown to confer a robust anti-inflammatory and immunomodulatory phenotype over inflammatory myeloid cells. Here we show that C4BP(β-)-mediated immunomodulation can significantly attenuate the histopathological traits and preserve the intestinal epithelial integrity in dextran sulfate sodium (DSS)-induced murine colitis. C4BP(β-) downregulated inflammatory transcripts, notably those related to neutrophil activity, mitigated circulating inflammatory effector cytokines and chemokines such as CXCL13, key in generating ectopic lymphoid structures, and, overall, prevented inflammatory immune cell infiltration in the colon of colitic mice. PRP6-HO7, a recombinant curtailed analogue with only immunomodulatory activity, achieved a similar outcome as C4BP(β-), indicating that the therapeutic effect is not due to the complement inhibitory activity. Furthermore, both C4BP(β-) and PRP6-HO7 significantly reduced, with comparable efficacy, the intrinsic and TLR-induced inflammatory markers in myeloid cells from both ulcerative colitis and Crohn's disease patients, regardless of their medication. Thus, the pleiotropic anti-inflammatory and immunomodulatory activity of PRP6-HO7, able to "reprogram" myeloid cells from the complex inflammatory bowel environment and to restore immune homeostasis, might constitute a promising therapeutic option for IBD.
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Affiliation(s)
- Inmaculada Serrano
- Immune-inflammatory Processes and Gene Therapeutics Group, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Ana Luque
- Immune-inflammatory Processes and Gene Therapeutics Group, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Alexandra Ruiz-Cerulla
- Department of Digestive Diseases, Bellvitge University Hospital, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Sergio Navas
- Structural Biology of Host-Pathogen Interactions Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
| | - Anna M Blom
- Lund University, Department of Translational Medicine, Section of Medical Protein Chemistry, 21428 Malmö, Sweden
| | - Santiago Rodríguez de Córdoba
- Molecular Pathology/Genetics of Complement Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC) and Ciber de Enfermedades Raras (CIBERER), 28040 Madrid, Spain
| | | | - M Cristina Vega
- Structural Biology of Host-Pathogen Interactions Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
| | - Francisco Rodríguez-Moranta
- Department of Digestive Diseases, Bellvitge University Hospital, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Jordi Guardiola
- Department of Digestive Diseases, Bellvitge University Hospital, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Josep M Aran
- Immune-inflammatory Processes and Gene Therapeutics Group, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain.
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34
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Planchais C, Molinos-Albert LM, Rosenbaum P, Hieu T, Kanyavuz A, Clermont D, Prazuck T, Lefrou L, Dimitrov JD, Hüe S, Hocqueloux L, Mouquet H. HIV-1 treatment timing shapes the human intestinal memory B-cell repertoire to commensal bacteria. Nat Commun 2023; 14:6326. [PMID: 37816704 PMCID: PMC10564866 DOI: 10.1038/s41467-023-42027-6] [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] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
HIV-1 infection causes severe alterations of gut mucosa, microbiota and immune system, which can be curbed by early antiretroviral therapy. Here, we investigate how treatment timing affects intestinal memory B-cell and plasmablast repertoires of HIV-1-infected humans. We show that only class-switched memory B cells markedly differ between subjects treated during the acute and chronic phases of infection. Intestinal memory B-cell monoclonal antibodies show more prevalent polyreactive and commensal bacteria-reactive clones in late- compared to early-treated individuals. Mirroring this, serum IgA polyreactivity and commensal-reactivity are strongly increased in late-treated individuals and correlate with intestinal permeability and systemic inflammatory markers. Polyreactive blood IgA memory B cells, many of which egressed from the gut, are also substantially enriched in late-treated individuals. Our data establish gut and systemic B-cell polyreactivity to commensal bacteria as hallmarks of chronic HIV-1 infection and suggest that initiating treatment early may limit intestinal B-cell abnormalities compromising HIV-1 humoral response.
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Affiliation(s)
- Cyril Planchais
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
| | - Luis M Molinos-Albert
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036, Barcelona, Spain
| | - Pierre Rosenbaum
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
| | - Thierry Hieu
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
| | - Alexia Kanyavuz
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006, Paris, France
| | - Dominique Clermont
- Collection of the Institut Pasteur, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Thierry Prazuck
- Service des Maladies Infectieuses et Tropicales, CHR d'Orléans-La Source, 45067, Orléans, France
| | - Laurent Lefrou
- Service d'Hépato-Gastro-Entérologie, CHR d'Orléans-La Source, 45067, Orléans, France
| | - Jordan D Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006, Paris, France
| | - Sophie Hüe
- INSERM U955-Équipe 16, Université Paris-Est Créteil, Faculté de Médecine, 94000, Créteil, France
| | - Laurent Hocqueloux
- Service des Maladies Infectieuses et Tropicales, CHR d'Orléans-La Source, 45067, Orléans, France
| | - Hugo Mouquet
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France.
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35
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Zogorean R, Wirtz S. The yin and yang of B cells in a constant state of battle: intestinal inflammation and inflammatory bowel disease. Front Immunol 2023; 14:1260266. [PMID: 37849749 PMCID: PMC10577428 DOI: 10.3389/fimmu.2023.1260266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract, defined by a clinical relapse-remitting course. Affecting people worldwide, the origin of IBD is still undefined, arising as a consequence of the interaction between genes, environment, and microbiota. Although the root cause is difficult to identify, data clearly indicate that dysbiosis and pathogenic microbial taxa are connected with the establishment and clinical course of IBD. The composition of the microbiota is shaped by plasma cell IgA secretion and binding, while cytokines such as IL10 or IFN-γ are important fine-tuners of the immune response in the gastrointestinal environment. B cells may also influence the course of inflammation by promoting either an anti-inflammatory or a pro-inflammatory milieu. Here, we discuss IgA-producing B regulatory cells as an anti-inflammatory factor in intestinal inflammation. Moreover, we specify the context of IgA and IgG as players that can potentially participate in mucosal inflammation. Finally, we discuss the role of B cells in mouse infection models where IL10, IgA, or IgG contribute to the outcome of the infection.
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Affiliation(s)
- Roxana Zogorean
- Medizinische Klinik 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Stefan Wirtz
- Medizinische Klinik 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Medical Immunology Campus Erlangen, FAU Erlangen-Nürnberg, Erlangen, Bavaria, Germany
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36
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Hosack T, Thomas T, Ravindran R, Uhlig HH, Travis SPL, Buckley CD. Inflammation across tissues: can shared cell biology help design smarter trials? Nat Rev Rheumatol 2023; 19:666-674. [PMID: 37666996 DOI: 10.1038/s41584-023-01007-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2023] [Indexed: 09/06/2023]
Abstract
Immune-mediated inflammatory diseases (IMIDs) are responsible for substantial global disease burden and associated health-care costs. Traditional models of research and service delivery silo their management within organ-based medical disciplines. Very often patients with disease in one organ have comorbid involvement in another, suggesting shared pathogenic pathways. Moreover, different IMIDs are often treated with the same drugs (including glucocorticoids, immunoregulators and biologics). Unlocking the cellular basis of these diseases remains a major challenge, leading us to ask why, if these diseases have so much in common, they are not investigated in a common manner. A tissue-based, cellular understanding of inflammation might pave the way for cross-disease, cross-discipline basket trials (testing one drug across two or more diseases) to reduce the risk of failure of early-phase drug development in IMIDs. This new approach will enable rapid assessment of the efficacy of new therapeutic agents in cross-disease translational research in humans.
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Affiliation(s)
- Tom Hosack
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Tom Thomas
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Rahul Ravindran
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Hans Holm Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- Biomedical Research Centre, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Simon Piers Leigh Travis
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Christopher Dominic Buckley
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
- Biomedical Research Centre, University of Oxford, Oxford, UK.
- Institute for Inflammation and Aging, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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37
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Zilbauer M, James KR, Kaur M, Pott S, Li Z, Burger A, Thiagarajah JR, Burclaff J, Jahnsen FL, Perrone F, Ross AD, Matteoli G, Stakenborg N, Sujino T, Moor A, Bartolome-Casado R, Bækkevold ES, Zhou R, Xie B, Lau KS, Din S, Magness ST, Yao Q, Beyaz S, Arends M, Denadai-Souza A, Coburn LA, Gaublomme JT, Baldock R, Papatheodorou I, Ordovas-Montanes J, Boeckxstaens G, Hupalowska A, Teichmann SA, Regev A, Xavier RJ, Simmons A, Snyder MP, Wilson KT. A Roadmap for the Human Gut Cell Atlas. Nat Rev Gastroenterol Hepatol 2023; 20:597-614. [PMID: 37258747 PMCID: PMC10527367 DOI: 10.1038/s41575-023-00784-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2023] [Indexed: 06/02/2023]
Abstract
The number of studies investigating the human gastrointestinal tract using various single-cell profiling methods has increased substantially in the past few years. Although this increase provides a unique opportunity for the generation of the first comprehensive Human Gut Cell Atlas (HGCA), there remains a range of major challenges ahead. Above all, the ultimate success will largely depend on a structured and coordinated approach that aligns global efforts undertaken by a large number of research groups. In this Roadmap, we discuss a comprehensive forward-thinking direction for the generation of the HGCA on behalf of the Gut Biological Network of the Human Cell Atlas. Based on the consensus opinion of experts from across the globe, we outline the main requirements for the first complete HGCA by summarizing existing data sets and highlighting anatomical regions and/or tissues with limited coverage. We provide recommendations for future studies and discuss key methodologies and the importance of integrating the healthy gut atlas with related diseases and gut organoids. Importantly, we critically overview the computational tools available and provide recommendations to overcome key challenges.
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Affiliation(s)
- Matthias Zilbauer
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- University Department of Paediatrics, University of Cambridge, Cambridge, UK.
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Cambridge, UK.
| | - Kylie R James
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mandeep Kaur
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sebastian Pott
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zhixin Li
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Albert Burger
- Department of Computer Science, Heriot-watt University, Edinburgh, UK
| | - Jay R Thiagarajah
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University', Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Frode L Jahnsen
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Francesca Perrone
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- University Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Alexander D Ross
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- University Department of Paediatrics, University of Cambridge, Cambridge, UK
- University Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Gianluca Matteoli
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Nathalie Stakenborg
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Tomohisa Sujino
- Center for the Diagnostic and Therapeutic Endoscopy, School of Medicine, Keio University, Tokyo, Japan
| | - Andreas Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Raquel Bartolome-Casado
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, UK
| | - Espen S Bækkevold
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ran Zhou
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Bingqing Xie
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shahida Din
- Edinburgh IBD Unit, Western General Hospital, NHS Lothian, Edinburgh, UK
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University', Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qiuming Yao
- Department of Computer Science and Engineering, University of Nebraska Lincoln, Lincoln, NE, USA
| | - Semir Beyaz
- Cold Spring Harbour Laboratory, Cold Spring Harbour, New York, NY, USA
| | - Mark Arends
- Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, Institute of Cancer and Genetics, University of Edinburgh, Edinburgh, UK
| | - Alexandre Denadai-Souza
- Laboratory of Mucosal Biology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Lori A Coburn
- Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | | | | | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Guy Boeckxstaens
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Hinxton, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK
| | - Aviv Regev
- Genentech, San Francisco, CA, USA
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alison Simmons
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Keith T Wilson
- Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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38
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Jain S, Bemark M, Spencer J. Human gut-associated lymphoid tissue: A dynamic hub propagating modulators of inflammation. Clin Transl Med 2023; 13:e1417. [PMID: 37735775 PMCID: PMC10514258 DOI: 10.1002/ctm2.1417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Affiliation(s)
- Sahil Jain
- Louise Coote Lupus UnitGuy's and St Thomas' NHS Foundation TrustLondonUK
| | - Mats Bemark
- Department of Microbiology and ImmunologyUniversity of GothenburgGothenburgSweden
| | - Jo Spencer
- School of Immunology and Microbial SciencesKing's College LondonLondonUK
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39
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Tanwar H, Gnanasekaran JM, Allison D, Chuang LS, He X, Aimetti M, Baima G, Costalonga M, Cross RK, Sears C, Mehandru S, Cho J, Colombel JF, Raufman JP, Thumbigere-Math V. Unraveling the Link between Periodontitis and Inflammatory Bowel Disease: Challenges and Outlook. ARXIV 2023:arXiv:2308.10907v1. [PMID: 37645044 PMCID: PMC10462160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Periodontitis and Inflammatory Bowel Disease (IBD) are chronic inflammatory conditions, characterized by microbial dysbiosis and hyper-immunoinflammatory responses. Growing evidence suggest an interconnection between periodontitis and IBD, implying a shift from the traditional concept of independent diseases to a complex, reciprocal cycle. This review outlines the evidence supporting an "Oral-Gut" axis, marked by a higher prevalence of periodontitis in IBD patients and vice versa. The specific mechanisms linking periodontitis and IBD remain to be fully elucidated, but emerging evidence points to the ectopic colonization of the gut by oral bacteria, which promote intestinal inflammation by activating host immune responses. This review presents an in-depth examination of the interconnection between periodontitis and IBD, highlighting the shared microbiological and immunological pathways, and proposing a "multi-hit" hypothesis in the pathogenesis of periodontitis-mediated intestinal inflammation. Furthermore, the review underscores the critical need for a collaborative approach between dentists and gastroenterologists to provide holistic oral-systemic healthcare.
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Affiliation(s)
- Himanshi Tanwar
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
| | | | - Devon Allison
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Ling-shiang Chuang
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Mario Aimetti
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Giacomo Baima
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Massimo Costalonga
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, USA
| | - Raymond K. Cross
- Division of Gastroenterology & Hepatology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cynthia Sears
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Saurabh Mehandru
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy Cho
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Pierre Raufman
- Division of Gastroenterology & Hepatology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Vivek Thumbigere-Math
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
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40
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Le Berre C, Honap S, Peyrin-Biroulet L. Ulcerative colitis. Lancet 2023; 402:571-584. [PMID: 37573077 DOI: 10.1016/s0140-6736(23)00966-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 08/14/2023]
Abstract
Ulcerative colitis is a lifelong inflammatory disease affecting the rectum and colon to a variable extent. In 2023, the prevalence of ulcerative colitis was estimated to be 5 million cases around the world, and the incidence is increasing worldwide. Ulcerative colitis is thought to occur in people with a genetic predisposition following environmental exposures; gut epithelial barrier defects, the microbiota, and a dysregulated immune response are strongly implicated. Patients usually present with bloody diarrhoea, and the diagnosis is based on a combination of clinical, biological, endoscopic, and histological findings. The aim of medical management is, first, to induce a rapid clinical response and normalise biomarkers and, second, to maintain clinical remission and reach endoscopic normalisation to prevent long-term disability. Treatments for inducing remission include 5-aminosalicylic acid drugs and corticosteroids. Maintenance treatments include 5-aminosalicylic acid drugs, thiopurines, biologics (eg, anti-cytokines and anti-integrins), and small molecules (Janus kinase inhibitors and sphingosine-1-phosphate receptor modulators). Although the therapeutic options are expanding, 10-20% of patients still require proctocolectomy for medically refractory disease. The keys to breaking through this therapeutic ceiling might be the combination of therapeutics with precision and personalised medicine.
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Affiliation(s)
- Catherine Le Berre
- Institut des Maladies de l'Appareil Digestif, Hépato-Gastro-Entérologie et Assistance Nutritionnelle, Inserm CIC 1413, Inserm UMR 1235, Nantes Université, CHU Nantes, Nantes, France
| | - Sailish Honap
- Department of Gastroenterology, St George's University Hospitals NHS Foundation Trust, London, UK; School of Immunology and Microbial Sciences, King's College London, London UK
| | - Laurent Peyrin-Biroulet
- Department of Gastroenterology, INFINY Institute, FHU-CURE, INSERM NGERE, Nancy University Hospital, Vandœuvre-lès-Nancy, France; Division of Gastroenterology and Hepatology, McGill University Health Centre, Montreal, QC, Canada.
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Yoshida H, Shiokawa M, Kuwada T, Muramoto Y, Ota S, Nishikawa Y, Maeda H, Kakiuchi N, Okamoto K, Yamazaki H, Yokode M, Nakamura T, Matsumoto S, Hirano T, Okada H, Marui S, Sogabe Y, Matsumori T, Mima A, Uza N, Eso Y, Takai A, Takahashi K, Ueda Y, Kodama Y, Chiba T, Seno H. Anti-integrin αvβ6 autoantibodies in patients with primary sclerosing cholangitis. J Gastroenterol 2023; 58:778-789. [PMID: 37310456 PMCID: PMC10366314 DOI: 10.1007/s00535-023-02006-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND Patients with primary sclerosing cholangitis (PSC) possess autoantibodies against biliary epithelial cells. However, the target molecules remain unknown. METHODS The sera of patients with PSC and controls were subjected to enzyme-linked immunosorbent assays to detect autoantibodies using recombinant integrin proteins. Integrin αvβ6 expression in the bile duct tissues was examined using immunofluorescence. The blocking activity of the autoantibodies was examined using solid-phase binding assays. RESULTS Anti-integrin αvβ6 antibodies were detected in 49/55 (89.1%) patients with PSC and 5/150 (3.3%) controls (P < 0.001), with a sensitivity and specificity of 89.1% and 96.7%, respectively, for PSC diagnosis. When focusing on the presence or absence of IBD, the proportion of the positive antibodies in PSC with IBD was 97.2% (35/36) and that in PSC alone was 73.7% (14/19) (P = 0.008). Integrin αvβ6 was expressed in bile duct epithelial cells. Immunoglobulin (Ig)G from 15/33 patients with PSC blocked integrin αvβ6-fibronectin binding through an RGD (Arg-Gly-Asp) tripeptide motif. CONCLUSIONS Autoantibodies against integrin αvβ6 were detected in most patients with PSC; anti-integrin αvβ6 antibody may serve as a potential diagnostic biomarker for PSC.
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Affiliation(s)
- Hiroyuki Yoshida
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masahiro Shiokawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Takeshi Kuwada
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuya Muramoto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Sakiko Ota
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yoshihiro Nishikawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hirona Maeda
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Kanako Okamoto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hajime Yamazaki
- Section of Clinical Epidemiology, Department of Community Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masataka Yokode
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeharu Nakamura
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shimpei Matsumoto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomonori Hirano
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hirokazu Okada
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Saiko Marui
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuko Sogabe
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomoaki Matsumori
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Atsushi Mima
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Norimitsu Uza
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuji Eso
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Atsushi Takai
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ken Takahashi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yoshihide Ueda
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Yuzo Kodama
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Tsutomu Chiba
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Kansai Electric Power Hospital, Osaka, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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Bamias G, Kitsou K, Rivera-Nieves J. The Underappreciated Role of Secretory IgA in IBD. Inflamm Bowel Dis 2023; 29:1327-1341. [PMID: 36943800 PMCID: PMC10393212 DOI: 10.1093/ibd/izad024] [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: 09/20/2022] [Indexed: 03/23/2023]
Abstract
Eighty percent of antibody secreting cells (ASCs) are found in the intestine, where they produce grams of immunoglobulin (Ig) A daily. immunoglobulin A is actively transcytosed into the lumen, where it plays a critical role in modulating the gut microbiota. Although loss of immune tolerance to bacterial antigens is the likely trigger of the dysregulated immune response that characterizes inflammatory bowel disease (IBD), little effort has been placed on understanding the interface between B cells, IgA, and the microbiota during initiation or progression of disease. This may be in part due to the misleading fact that IgA-deficient humans are mostly asymptomatic, likely due to redundant role of secretory (S) IgM. Intestinal B cell recruitment is critically dependent on integrin α4β7-MAdCAM-1 interactions, yet antibodies that target α4β7 (ie, vedolizumab), MAdCAM-1 (ie, ontamalimab), or both β7 integrins (α4β7 and αE [CD103] β7; etrolizumab) are in clinical use or development as IBD therapeutics. The effect of such interventions on the biology of IgA is largely unknown, yet a single dose of vedolizumab lowers SIgA levels in stool and weakens the oral immunization response to cholera vaccine in healthy volunteers. Thus, it is critical to further understand the role of these integrins for the migration of ASC and other cellular subsets during homeostasis and IBD-associated inflammation and the mode of action of drugs that interfere with this traffic. We have recently identified a subset of mature ASC that employs integrin αEβ7 to dock with intestinal epithelial cells, predominantly in the pericryptal region of the terminal ileum. This role for the integrin had not been appreciated previously, nor the αEβ7-dependent mechanism of IgA transcytosis that it supports. Furthermore, we find that B cells more than T cells are critically dependent on α4β7-MAdCAM-1 interactions; thus MAdCAM-1 blockade and integrin-β7 deficiency counterintuitively hasten colitis in interleukin-10-deficient mice. In both cases, de novo recruitment of IgA ASC to the intestinal lamina propria is compromised, leading to bacterial overgrowth, dysbiosis, and lethal colitis. Thus, despite the safe and effective use of anti-integrin antibodies in patients with IBD, much remains to be learned about their various cell targets.
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Affiliation(s)
- Giorgos Bamias
- GI Unit, 3rd Academic Department of Internal Medicine, National and Kapodistrian University of Athens, Sotiria Hospital, Athens, Greece
| | - Konstantina Kitsou
- GI Unit, 3rd Academic Department of Internal Medicine, National and Kapodistrian University of Athens, Sotiria Hospital, Athens, Greece
| | - Jesús Rivera-Nieves
- Gastroenterology Section, San Diego VA Medical Center, La Jolla Village Drive, San Diego, CA, USA
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
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43
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Zheng HB. Application of single-cell omics in inflammatory bowel disease. World J Gastroenterol 2023; 29:4397-4404. [PMID: 37576705 PMCID: PMC10415967 DOI: 10.3748/wjg.v29.i28.4397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023] Open
Abstract
Over the past decade, the advent of single cell RNA-sequencing has revolutionized the approach in cellular transcriptomics research. The current technology offers an unbiased platform to understand how genotype correlates to phenotype. Single-cell omics applications in gastrointestinal (GI) research namely inflammatory bowel disease (IBD) has become popular in the last few years with multiple publications as single-cell omics techniques can be applied directly to the target organ, the GI tract at the tissue level. Through examination of mucosal tissue and peripheral blood in IBD, the recent boom in single cell research has identified a myriad of key immune players from enterocytes to tissue resident memory T cells, and explored functional heterogeneity within cellular subsets previously unreported. As we begin to unravel the complex mucosal immune system in states of health and disease like IBD, the power of exploration through single-cell omics can change our approach to translational research. As novel techniques evolve through multiplexing single-cell omics and spatial transcriptomics come to the forefront, we can begin to fully comprehend the disease IBD and better design targets of treatment. In addition, hopefully these techniques can ultimately begin to identify biomarkers of therapeutic response and answer clinically relevant questions in how to tailor individual therapy to patients through personalized medicine.
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Affiliation(s)
- Hengqi Betty Zheng
- Department of Pediatrics, Seattle Children’s Hospital, University of Washington, Seattle, WA 98105, United States
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44
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Shirai T. Common Autoantibody among Takayasu Arteritis and Ulcerative Colitis: A Possible Pathophysiology That Includes Gut-Vessel Connection in Vascular Inflammation. JMA J 2023; 6:265-273. [PMID: 37560375 PMCID: PMC10407456 DOI: 10.31662/jmaj.2023-0038] [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: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 08/11/2023] Open
Abstract
Takayasu arteritis (TAK) is a type of large-vessel vasculitis that predominantly affects young females. The precise pathomechanism of TAK is still under investigation. In TAK, the vasa vasorum is considered to be the initial inflammatory site. Disruption of the vasa vasorum induces the entry of inflammatory cells into the vascular wall of large vessels between the media and adventitia, and infiltrated cells damage the vascular components, eventually leading to stenosis or dilatation of the affected arteries. In addition, T cells are considered key players in TAK, and myeloid cells function as effector cells. Although the roles of B cells in TAK are poorly understood, recent evidence supports their contribution to the pathogenicity of TAK. Particularly, two autoantibodies have been identified in TAK through investigation of anti-endothelial cell antibodies, and they could be involved in the maintenance of vascular inflammation. Furthermore, one of the autoantibodies, anti-endothelial protein C receptor, was shown to be present in ulcerative colitis (UC), which is genetically and clinically associated with TAK. Similar autoantibodies in inflammatory diseases with different target organs indicate a common underlying pathophysiology of these diseases, which could be characterized by the aberrant activation of B cells. This review discusses recent understanding of the pathomechanisms of TAK and UC, with a focus on the involvement of B cells and autoantibodies. The close association of UC with TAK further suggests a common etiology, and the importance of the intestinal microbiota, including dysbiosis, is also becoming known in TAK. Investigation of such common factors among TAK and UC would improve understanding of the interplay between gut and vascular inflammation, which is a new concept for developing vascular inflammation through the gut-vessel connection.
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Affiliation(s)
- Tsuyoshi Shirai
- Department of Rheumatology, Tohoku University Hospital, Sendai, Japan
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45
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Mo S, Jin B, Tseng Y, Lin L, Lin L, Shen X, Song H, Kong M, Luo Z, Chu Y, Jiang C, Cao Z, Liu J, Luo F. A precise molecular subtyping of ulcerative colitis reveals the immune heterogeneity and predicts clinical drug responses. J Transl Med 2023; 21:466. [PMID: 37443022 PMCID: PMC10347743 DOI: 10.1186/s12967-023-04326-w] [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: 03/22/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND AND AIMS We sought to identify novel molecular subtypes of ulcerative colitis (UC) based on large-scale cohorts and establish a clinically applicable subtyping system for the precision treatment of the disease. METHODS Eight microarray profiles containing colon samples from 357 patients were utilized. Expression heterogeneity was screened out and stable subtypes were identified among UC patients. Immune infiltration pattern and biological agent response were compared among subtypes to assess the value in guiding treatment. The relationship between PRLR and TNFSF13B genes with the highest predictive value was further validated by functional experiments. RESULTS Three stable molecular subtypes were successfully identified. Immune cell infiltration analysis defined three subtypes as innate immune activated UC (IIA), whole immune activated UC (WIA), and immune homeostasis like UC (IHL). Notably, the response rate towards biological agents (infliximab/vedolizumab) in WIA patients was the lowest (less than 10%), while the response rate in IHL patients was the highest, ranging from 42 to 60%. Among the featured genes of subtypes, the ratio of PRLR to TNFSF13B could effectively screen for IHL UC subtype suitable for biological agent therapies (Area under curve: 0.961-0.986). Furthermore, we demonstrated that PRLR expressed in epithelial cells could inhibit the expression of TNFSF13B in monocyte-derived macrophages through the CXCL1-NF-κB pathway. CONCLUSIONS We identified three stable UC subtypes with a heterogeneous immune pattern and different response rates towards biological agents for the first time. We also established a precise molecular subtyping system and classifier to predict clinical drug response and provide individualized treatment strategies for UC patients.
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Affiliation(s)
- Shaocong Mo
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Bryan Jin
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Yujen Tseng
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Lingxi Lin
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Lishuang Lin
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xin Shen
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Huan Song
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Mingjia Kong
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Zhongguang Luo
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Yiwei Chu
- Biotherapy Research Center, Department of Immunology, School of Basic Medical Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Chen Jiang
- Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhiwei Cao
- School of Life Sciences, Fudan University, Shanghai, 200433, China
- School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jie Liu
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Feifei Luo
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
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46
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Kim H, Kim HK, Hong D, Kim M, Jang S, Yang CS, Yoon S. Identification of ulcerative colitis-specific immune cell signatures from public single-cell RNA-seq data. Genes Genomics 2023; 45:957-967. [PMID: 37133723 DOI: 10.1007/s13258-023-01390-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/13/2023] [Indexed: 05/04/2023]
Abstract
BACKGROUND Single-cell RNA-seq enabled microscopic studies on tissue microenvironment of many diseases. Inflammatory bowel disease, an autoimmune disease, is involved with various dysfunction of immune cells, for which single-cell RNA-seq may provide us a deeper insight into the causes and mechanism of this complex disease. OBJECTIVE In this work, we used public single-cell RNA-seq data to study tissue microenvironment around ulcerative colitis, an inflammatory bowel disease causing chronic inflammation and ulcers in large intestine. METHODS Since not all the datasets provide cell-type annotations, we first identified cell identities to select cell populations of our interest. Differentially expressed genes and gene set enrichment analysis was then performed to infer the polarization/activation state of macrophages and T cells. Cell-to-cell interaction analysis was also performed to discover distinct interactions in ulcerative colitis. RESULTS Differentially expressed genes analysis of the two datasets confirmed the regulation of CTLA4, IL2RA, and CCL5 genes in the T cell subset and regulation of S100A8/A9, CLEC10A genes in macrophages. Cell-to-cell interaction analysis showed CD4+ T cells and macrophages interact actively to each other. We also identified IL-18 pathway activation in inflammatory macrophages, evidence that CD4+ T cells induce Th1 and Th2 differentiation, and also found that macrophages regulate T cell activation through different ligand-receptor pairs, viz. CD86-CTL4, LGALS9-CD47, SIRPA-CD47, and GRN-TNFRSF1B. CONCLUSION Analysis of these immune cell subsets may suggest novel strategies for the treatment of inflammatory bowel disease.
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Affiliation(s)
- Hanbyeol Kim
- Dept of Computer Science, College of SW Convergence, Dankook Univ, Yongin-si, 16890, Korea
| | - Hyo Keun Kim
- Dept of Molecular and Life Science and Center for Bionano Intelligence Education and Research, Hanyang University, Ansan-si, 15588, Korea
| | - Dawon Hong
- Dept of Molecular Biology, Graduate Department of Bioconvergence Engineering, Dankook University, Yongin-si, 16890, Korea
| | - Minsu Kim
- Dept of Computer Science, College of SW Convergence, Dankook Univ, Yongin-si, 16890, Korea
| | - Sein Jang
- Dept of Molecular and Life Science and Center for Bionano Intelligence Education and Research, Hanyang University, Ansan-si, 15588, Korea
| | - Chul-Su Yang
- Dept of Medicinal/Molecular and Life Science and Center for Bionano Intelligence Education and Research, Hanyang University, Ansan-si, 15588, Korea
| | - Seokhyun Yoon
- Dept of Electronics & Electrical Eng, College of Engineering, Dankook Univ, Yongin-si, 16890, Korea.
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Borbet TC, Pawline MB, Li J, Ho ML, Yin YS, Zhang X, Novikova E, Jackson K, Mullins BJ, Ruiz VE, Hines MJ, Zhang XS, Müller A, Koralov SB, Blaser MJ. Disruption of the early-life microbiota alters Peyer's patch development and germinal center formation in gastrointestinal-associated lymphoid tissue. iScience 2023; 26:106810. [PMID: 37235047 PMCID: PMC10206152 DOI: 10.1016/j.isci.2023.106810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/17/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023] Open
Abstract
During postnatal development, both the maturing microbiome and the host immune system are susceptible to environmental perturbations such as antibiotic use. The impact of timing in which antibiotic exposure occurs was investigated by treating mice from days 5-9 with amoxicillin or azithromycin, two of the most commonly prescribed medications in children. Both early-life antibiotic regimens disrupted Peyer's patch development and immune cell abundance, with a sustained decrease in germinal center formation and diminished intestinal immunoglobulin A (IgA) production. These effects were less pronounced in adult mice. Through comparative analysis of microbial taxa, Bifidobacterium longum abundance was found to be associated with germinal center frequency. When re-introduced to antibiotic-exposed mice, B. longum partially rescued the immunological deficits. These findings suggest that early-life antibiotic use affects the development of intestinal IgA-producing B cell functions and that probiotic strains could be used to restore normal development after antibiotic exposure.
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Affiliation(s)
- Timothy C. Borbet
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Miranda B. Pawline
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Jackie Li
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Melody L. Ho
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Yue Sandra Yin
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ 08854, USA
| | - Xiaozhou Zhang
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Ekaterina Novikova
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Katelyn Jackson
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Briana J. Mullins
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Victoria E. Ruiz
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Marcus J. Hines
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Xue-Song Zhang
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ 08854, USA
| | - Anne Müller
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Sergei B. Koralov
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Martin J. Blaser
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ 08854, USA
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Canales-Herrerias P, Garcia-Carmona Y, Shang J, Meringer H, Yee DS, Radigan L, Buta S, Martinez-Delgado G, Tankelevich M, Helmus D, Dubinsky M, Everts-van der Mind A, Dervieux T, Bogunovic D, Colombel JF, Brenchley JM, Faith J, Cunningham-Rundles C, Cerutti A, Mehandru S. Selective IgA2 deficiency in a patient with small intestinal Crohn's disease. J Clin Invest 2023; 133:e167742. [PMID: 37129981 PMCID: PMC10266768 DOI: 10.1172/jci167742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Affiliation(s)
- Pablo Canales-Herrerias
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yolanda Garcia-Carmona
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joan Shang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hadar Meringer
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Debra S. Yee
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Lin Radigan
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sofija Buta
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gustavo Martinez-Delgado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael Tankelevich
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Drew Helmus
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Marla Dubinsky
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | - Dusan Bogunovic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jean-Frederic Colombel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Jeremiah Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Andrea Cerutti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Translational Clinical Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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49
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Choi EL, Taheri N, Chandra A, Hayashi Y. Cellular Senescence, Inflammation, and Cancer in the Gastrointestinal Tract. Int J Mol Sci 2023; 24:9810. [PMID: 37372958 DOI: 10.3390/ijms24129810] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Due to modern medical advancements, greater proportions of the population will continue to age with longer life spans. Increased life span, however, does not always correlate with improved health span, and may result in an increase in aging-related diseases and disorders. These diseases are often attributed to cellular senescence, in which cells become disengaged from the cell cycle and inert to cell death. These cells are characterized by a proinflammatory secretome. The proinflammatory senescence-associated secretory phenotype, although part of a natural function intended to prevent further DNA damage, creates a microenvironment suited to tumor progression. This microenvironment is most evident in the gastrointestinal tract (GI), where a combination of bacterial infections, senescent cells, and inflammatory proteins can lead to oncogenesis. Thus, it is important to find potential senescence biomarkers as targets of novel therapies for GI diseases and disorders including cancers. However, finding therapeutic targets in the GI microenvironment to reduce the risk of GI tumor onset may also be of value. This review summarizes the effects of cellular senescence on GI aging, inflammation, and cancers, and aims to improve our understanding of these processes with a goal of enhancing future therapy.
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Affiliation(s)
- Egan L Choi
- Graduate Research Education Program (Choi), Mayo Clinic, Rochester, MN 55905, USA
| | - Negar Taheri
- Department of Physiology and Biomedical Engineering (Taheri, Chandra and Hayashi), Mayo Clinic, Rochester, MN 55905, USA
- Division of Gastroenterology and Hepatology (Taheri and Hayashi), Mayo Clinic, Rochester, MN 55905, USA
| | - Abhishek Chandra
- Department of Physiology and Biomedical Engineering (Taheri, Chandra and Hayashi), Mayo Clinic, Rochester, MN 55905, USA
- Robert and Arlene Kogod Center on Aging (Chandra), Mayo Clinic, Rochester, MN 55905, USA
| | - Yujiro Hayashi
- Department of Physiology and Biomedical Engineering (Taheri, Chandra and Hayashi), Mayo Clinic, Rochester, MN 55905, USA
- Division of Gastroenterology and Hepatology (Taheri and Hayashi), Mayo Clinic, Rochester, MN 55905, USA
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50
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Jha D, Al-Taie Z, Krek A, Eshghi ST, Fantou A, Laurent T, Tankelevich M, Cao X, Meringer H, Livanos AE, Tokuyama M, Cossarini F, Bourreille A, Josien R, Hou R, Canales-Herrerias P, Ungaro RC, Kayal M, Marion J, Polydorides AD, Ko HM, D’souza D, Merand R, Kim-Schulze S, Hackney JA, Nguyen A, McBride JM, Yuan GC, Colombel JF, Martin JC, Argmann C, Suárez-Fariñas M, Petralia F, Mehandru S. Myeloid cell influx into the colonic epithelium is associated with disease severity and non-response to anti-Tumor Necrosis Factor Therapy in patients with Ulcerative Colitis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.542863. [PMID: 37333091 PMCID: PMC10274630 DOI: 10.1101/2023.06.02.542863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Ulcerative colitis (UC) is an idiopathic chronic inflammatory disease of the colon with sharply rising global prevalence. Dysfunctional epithelial compartment (EC) dynamics are implicated in UC pathogenesis although EC-specific studies are sparse. Applying orthogonal high-dimensional EC profiling to a Primary Cohort (PC; n=222), we detail major epithelial and immune cell perturbations in active UC. Prominently, reduced frequencies of mature BEST4+OTOP2+ absorptive and BEST2+WFDC2+ secretory epithelial enterocytes were associated with the replacement of homeostatic, resident TRDC+KLRD1+HOPX+ γδ+ T cells with RORA+CCL20+S100A4+ TH17 cells and the influx of inflammatory myeloid cells. The EC transcriptome (exemplified by S100A8, HIF1A, TREM1, CXCR1) correlated with clinical, endoscopic, and histological severity of UC in an independent validation cohort (n=649). Furthermore, therapeutic relevance of the observed cellular and transcriptomic changes was investigated in 3 additional published UC cohorts (n=23, 48 and 204 respectively) to reveal that non-response to anti-Tumor Necrosis Factor (anti-TNF) therapy was associated with EC related myeloid cell perturbations. Altogether, these data provide high resolution mapping of the EC to facilitate therapeutic decision-making and personalization of therapy in patients with UC.
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Affiliation(s)
- Divya Jha
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zainab Al-Taie
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Shadi Toghi Eshghi
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Aurelie Fantou
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Thomas Laurent
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Michael Tankelevich
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuan Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Hadar Meringer
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra E Livanos
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minami Tokuyama
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Cossarini
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arnaud Bourreille
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Regis Josien
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Ruixue Hou
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Pablo Canales-Herrerias
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan C. Ungaro
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maia Kayal
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Marion
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Huaibin M. Ko
- Department of Pathology and Cell Biology, Columbia University Medical Center-New York Presbyterian Hospital, New York, New York
| | - Darwin D’souza
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raphael Merand
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason A. Hackney
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Allen Nguyen
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Jacqueline M. McBride
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Jean Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerome C. Martin
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Carmen Argmann
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Saurabh Mehandru
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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