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Atreya R, Neurath MF. Biomarkers for Personalizing IBD Therapy: The Quest Continues. Clin Gastroenterol Hepatol 2024; 22:1353-1364. [PMID: 38320679 DOI: 10.1016/j.cgh.2024.01.026] [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: 08/30/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/08/2024]
Abstract
Despite recent advances in the understanding of the pathogenesis of inflammatory bowel diseases (IBD) and advent of multiple targeted therapies, approximately one-third of patients are primary non-responders to initiated treatment, and half of patients lose response over time. There is currently a lack of available biomarkers that would prognosticate therapeutic effectiveness of these advanced therapies. This is partly explained by insufficient characterization of the functional roles assumed by the chosen molecular targets during disease treatment. There is a dire need for validated objective biomarkers, which could be indicators of a biological process, that can be applied in clinical practice to assist us in assigning therapies to patients with the highest probability of response. An appropriate molecular and cellular characterization that accounts for the interindividual differences in drug efficacy and potential side effects would help to guide clinicians in the management of patients with IBD and represent a major step to tailor a more personalized approach to treatment. An appropriate combination of complementing biomarkers should ideally incorporate a multimodal analysis in which genetic, microbial, transcriptional, proteomic, metabolic, and immunologic data are combined to enable a truly personalized approach. This would classify patients into disease subgroups according to molecular characteristics, which would enable us to initiate the most appropriate therapeutic substance. Emergence of single-cell technologies to map the intestinal cellular landscape and multiomic approaches have helped to further dissect the pathogenic mechanisms of mucosal inflammation, but the clinical translation of potential biomarkers remains cumbersome, and an ongoing concerted effort by the IBD community is required.
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Affiliation(s)
- Raja Atreya
- First Department of Medicine, Erlangen University Hospital, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany.
| | - Markus F Neurath
- First Department of Medicine, Erlangen University Hospital, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
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Wang J, Yang B, Chandra J, Ivanov A, Brown JM, Florian R. Preventing fibrosis in IBD: update on immune pathways and clinical strategies. Expert Rev Clin Immunol 2024; 20:727-734. [PMID: 38475672 PMCID: PMC11180587 DOI: 10.1080/1744666x.2024.2330604] [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: 11/25/2023] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
INTRODUCTION Intestinal fibrosis is a common and serious complication of inflammatory bowel diseases (IBD) driving stricture formation in Crohn's disease patients and leading to submucosal damage in ulcerative colitis. Recent studies provided novel insights into the role of immune and nonimmune components in the pathogenesis of intestinal fibrosis. Those new findings may accelerate the development of anti-fibrotic treatment in IBD patients. AREAS COVERED This review is designed to cover the recent progress in mechanistic research and therapeutic developments on intestinal fibrosis in IBD patients, including new cell clusters, cytokines, proteins, microbiota, creeping fat, and anti-fibrotic therapies. EXPERT OPINION Due to the previously existing major obstacle of missing consensus on stricture definitions and the absence of clinical trial endpoints, testing of drugs with an anti-fibrotic mechanism is just starting in stricturing Crohn's disease (CD). A biomarker to stratify CD patients at diagnosis without any complications into at-risk populations for future strictures would be highly desirable. Further investigations are needed to identify novel mechanisms of fibrogenesis in the intestine that are targetable and ideally gut specific.
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Affiliation(s)
- Jie Wang
- Xinxiang Key Laboratory of Inflammation and Immunology, School of Medical Technology, Xinxiang Medical University, Xinxiang 453003, Henan Province, China
| | - Bo Yang
- Xinxiang Key Laboratory of Inflammation and Immunology, School of Medical Technology, Xinxiang Medical University, Xinxiang 453003, Henan Province, China
| | - Jyotsna Chandra
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Andrei Ivanov
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - J. Mark Brown
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Rieder Florian
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
- Program for Global Translational Inflammatory Bowel Diseases, Cleveland Clinic Foundation, Cleveland, Ohio, USA
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Miao J, Zhang K, Yang Y, Xu S, Du J, Wu T, Tao C, Wang Y, Yang S. Single-nucleus transcriptomics reveal cardiac cell type-specific diversification in metabolic disease transgenic pigs. iScience 2024; 27:110015. [PMID: 38868189 PMCID: PMC11166884 DOI: 10.1016/j.isci.2024.110015] [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: 12/11/2023] [Revised: 03/28/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Cardiac damage is widely present in patients with metabolic diseases, but the exact pathophysiological mechanisms involved remain unclear. The porcine heart is an ideal material for cardiovascular research due to its similarities to the human heart. This study evaluated pathological features and performed single-nucleus RNA sequencing (snRNA-seq) on myocardial samples from both wild-type and metabolic disease-susceptible transgenic pigs (previously established). We found that transgenic pigs exhibited lipid metabolism disturbances and myocardial injury after a high-fat high-sucrose diet intervention. snRNA-seq reveals the cellular landscape of healthy and metabolically disturbed pig hearts and identifies the major cardiac cell populations affected by metabolic diseases. Within metabolic disorder hearts, metabolically active cardiomyocytes exhibited impaired function and reduced abundance. Moreover, massive numbers of reparative LYVE1+ macrophages were lost. Additionally, proinflammatory endothelial cells were activated with high expression of multiple proinflammatory cytokines. Our findings provide insights into the cellular mechanisms of metabolic disease-induced myocardial injury.
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Affiliation(s)
- Jiakun Miao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Kaiyi Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yu Yang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Shuang Xu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Juan Du
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Tianwen Wu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Cong Tao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yanfang Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Shulin Yang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
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Wetwittayakhlang P, Kotrri G, Bessissow T, Lakatos PL. How close are we to a success stratification tool for improving biological therapy in ulcerative colitis? Expert Opin Biol Ther 2024. [PMID: 38903049 DOI: 10.1080/14712598.2024.2371049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024]
Abstract
INTRODUCTION Biological therapies have become the standard treatment for ulcerative colitis (UC). However, clinical remission rates post-induction therapy remain modest at 40-50%, with many initial responders losing response over time. Current treatment strategies frequently rely on a 'trial and error' approach, leading to prolonged periods of ineffective and costly therapies for patients, accompanied by associated treatment complications. AREA COVERED This review discusses current evidence on risk stratification tools for predicting therapeutic efficacy and minimizing adverse events in UC management. Recent studies have identified predictive factors for biologic therapy response. In the context of personalized medicine, the goal is to identify patients at high risk of progression and complications, as well as those likely to respond to specific therapies. Essential risk stratification tools include clinical decision-making aids, biomarkers, genomics, multi-omics factors, endoscopic, imaging, and histological assessments. EXPERT OPINION Employing risk stratification tools to predict therapeutic response and prevent treatment-related complications is essential for precision medicine in the biological management of UC. These tools are necessary to select the most suitable treatment for each individual patient, thereby enhancing efficacy and safety.
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Affiliation(s)
- Panu Wetwittayakhlang
- Gastroenterology and Hepatology Unit, Division of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Division of Gastroenterology and Hepatology, McGill University Health Center, Montreal, Quebec, Canada
| | - Gynter Kotrri
- Division of Gastroenterology and Hepatology, McGill University Health Center, Montreal, Quebec, Canada
| | - Talat Bessissow
- Division of Gastroenterology and Hepatology, McGill University Health Center, Montreal, Quebec, Canada
| | - Peter L Lakatos
- Division of Gastroenterology and Hepatology, McGill University Health Center, Montreal, Quebec, Canada
- Department of Oncology and Medicine, Semmelweis University, Budapest, Hungary
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Kenakin T. Know your molecule: pharmacological characterization of drug candidates to enhance efficacy and reduce late-stage attrition. Nat Rev Drug Discov 2024:10.1038/s41573-024-00958-9. [PMID: 38890494 DOI: 10.1038/s41573-024-00958-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 06/20/2024]
Abstract
Despite advances in chemical, computational and biological sciences, the rate of attrition of drug candidates in clinical development is still high. A key point in the small-molecule discovery process that could provide opportunities to help address this challenge is the pharmacological characterization of hit and lead compounds, culminating in the selection of a drug candidate. Deeper characterization is increasingly important, because the 'quality' of drug efficacy, at least for G protein-coupled receptors (GPCRs), is now understood to be much more than activation of commonly evaluated pathways such as cAMP signalling, with many more 'efficacies' of ligands that could be harnessed therapeutically. Such characterization is being enabled by novel assays to characterize the complex behaviour of GPCRs, such as biased signalling and allosteric modulation, as well as advances in structural biology, such as cryo-electron microscopy. This article discusses key factors in the assessments of the pharmacology of hit and lead compounds in the context of GPCRs as a target class, highlighting opportunities to identify drug candidates with the potential to address limitations of current therapies and to improve the probability of them succeeding in clinical development.
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Affiliation(s)
- Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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Matellan C, Kennedy C, Santiago-Vela MI, Hochegger J, Ní Chathail MB, Wu A, Shannon C, Roche HM, Aceves SS, Godson C, Manresa MC. The TNFSF12/TWEAK Modulates Colonic Inflammatory Fibroblast Differentiation and Promotes Fibroblast-Monocyte Interactions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1958-1970. [PMID: 38700420 PMCID: PMC11149899 DOI: 10.4049/jimmunol.2300762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/29/2024] [Indexed: 05/05/2024]
Abstract
Fibroblasts acquire a proinflammatory phenotype in inflammatory bowel disease, but the factors driving this process and how fibroblasts contribute to mucosal immune responses are incompletely understood. TNF superfamily member 12 (TNFSF12, or TNF-like weak inducer of apoptosis [TWEAK]) has gained interest as a mediator of chronic inflammation. In this study, we explore its role as a driver of inflammatory responses in fibroblasts and its contribution to fibroblast-monocyte interaction using human primary colonic fibroblasts, THP-1 and primary monocytes. Recombinant human TWEAK induced the expression of cytokines, chemokines, and immune receptors in primary colonic fibroblasts. The TWEAK upregulated transcriptome shared 29% homology with a previously published transcriptional profile of inflammatory fibroblasts from ulcerative colitis. TWEAK elevated surface expression of activated fibroblast markers and adhesion molecules (podoplanin [PDPN], ICAM-1, and VCAM-1) and secretion of IL-6, CCL2, and CXCL10. In coculture, fibroblasts induced monocyte adhesion and secretion of CXCL1 and IL-8, and they promoted a CD14high/ICAM-1high phenotype in THP-1 cells, which was enhanced when fibroblasts were prestimulated with TWEAK. Primary monocytes in coculture with TWEAK-treated fibroblasts had altered surface expression of CD16 and triggering receptor expressed on myeloid cells-1 (TREM-1) as well as increased CXCL1 and CXCL10 secretion. Conversely, inhibition of the noncanonical NF-κB pathway on colonic fibroblasts with a NF-κB-inducing kinase small molecule inhibitor impaired their ability to induce a CD14high phenotype on monocytes. Our results indicate that TWEAK promotes an inflammatory fibroblast-monocyte crosstalk that may be amenable for therapeutic intervention.
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Affiliation(s)
- Carlos Matellan
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, Conway Institute of Biomolecular and biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Ciarán Kennedy
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, Conway Institute of Biomolecular and biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- Diabetes Complications Research Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Miren Itxaso Santiago-Vela
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Johanna Hochegger
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Méabh B. Ní Chathail
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Public Health, Physiotherapy, and Sports Science, University College Dublin, Belfield, Dublin, Ireland
| | - Amanda Wu
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA
| | - Christopher Shannon
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, Conway Institute of Biomolecular and biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Helen M. Roche
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Public Health, Physiotherapy, and Sports Science, University College Dublin, Belfield, Dublin, Ireland
- Institute for Global Food Security, Queen’s University Belfast, Belfast, U.K
| | - Seema S. Aceves
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA
- Rady Children’s Hospital, San Diego, CA
| | - Catherine Godson
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, Conway Institute of Biomolecular and biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- Diabetes Complications Research Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Mario C. Manresa
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
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Verma S, Dufort MJ, Olsen TM, Kimmel S, Labuda JC, Scharffenberger S, McGuire AT, Harrison OJ. Antigen-level resolution of commensal-specific B cell responses can be enabled by phage display screening coupled with B cell tetramers. Immunity 2024; 57:1428-1441.e8. [PMID: 38723638 PMCID: PMC11168869 DOI: 10.1016/j.immuni.2024.04.014] [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: 10/12/2023] [Revised: 02/07/2024] [Accepted: 04/16/2024] [Indexed: 06/14/2024]
Abstract
Induction of commensal-specific immunity contributes to tissue homeostasis, yet the mechanisms underlying induction of commensal-specific B cells remain poorly understood in part due to a lack of tools to identify these cells. Using phage display, we identified segmented filamentous bacteria (SFB) antigens targeted by serum and intestinal antibodies and generated B cell tetramers to track SFB-specific B cells in gut-associated lymphoid tissues. We revealed a compartmentalized response in SFB-specific B cell activation, with a gradient of immunoglobulin A (IgA), IgG1, and IgG2b isotype production along Peyer's patches contrasted by selective production of IgG2b within mesenteric lymph nodes. V(D)J sequencing and monoclonal antibody generation identified somatic hypermutation driven affinity maturation to SFB antigens under homeostatic conditions. Combining phage display and B cell tetramers will enable investigation of the ontogeny and function of commensal-specific B cell responses in tissue immunity, inflammation, and repair.
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Affiliation(s)
- Sheenam Verma
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Matthew J Dufort
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Tayla M Olsen
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Samantha Kimmel
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Jasmine C Labuda
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Sam Scharffenberger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Oliver J Harrison
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Immunology, University of Washington, Seattle, WA, USA.
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Laudadio I, Carissimi C, Scafa N, Bastianelli A, Fulci V, Renzini A, Russo G, Oliva S, Vitali R, Palone F, Cucchiara S, Stronati L. Characterization of patient-derived intestinal organoids for modelling fibrosis in Inflammatory Bowel Disease. Inflamm Res 2024:10.1007/s00011-024-01901-9. [PMID: 38842554 DOI: 10.1007/s00011-024-01901-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND AND AIMS Intestinal fibrosis is a common complication of Inflammatory Bowel Disease (IBD), namely Crohn's disease (CD) and ulcerative colitis (UC), but the precise mechanism by which it occurs is incompletely understood hampering the development of effective therapeutic strategies. Here, we aimed at inducing and characterizing an inflammation-mediated fibrosis in patient-derived organoids (PDOs) issued from crypts isolated from colonic mucosal biopsies of IBD pediatric patients and age matched-control subjects (CTRLs). METHODS Inflammatory-driven fibrosis was induced by exposing CTRL-, CD- and UC-PDOs to the pro-inflammatory cytokine TNF-α for one day, followed by a co-treatment with TNF-α and TGF-β1 for three days. Fibrotic response was proven by analyzing inflammatory and fibrotic markers by RT-qPCR and immunofluorescence. Transcriptomic changes were assessed by RNA-sequencing. RESULTS Co-treatment with TNF-α and TGF-β1 caused in CTRL- and IBD-PDOs morphological changes towards a mesenchymal-like phenotype and up-regulation of inflammatory, mesenchymal, and fibrotic markers. Transcriptomic profiling highlighted that in all intestinal PDOs, regardless of the disease, the co-exposure to TNF-α and TGF-β1 regulated EMT genes and specifically increased genes involved in positive regulation of cell migration. Finally, we demonstrated that CD-PDOs display a specific response to fibrosis compared to both CTRL- and UC-PDOs, mainly characterized by upregulation of nuclear factors controlling transcription. CONCLUSIONS This study demonstrates that intestinal PDOs may develop an inflammatory-derived fibrosis thus representing a promising tool to study fibrogenesis in IBD. Fibrotic PDOs show increased expression of EMT genes. In particular, fibrotic CD-PDOs display a specific gene expression signature compared to UC and CTRL-PDOs.
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Affiliation(s)
- Ilaria Laudadio
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.
| | - Claudia Carissimi
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Noemi Scafa
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Alex Bastianelli
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Valerio Fulci
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Alessandra Renzini
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of Rome, Via. A. Scarpa, 16, 00161, Rome, Italy
| | - Giusy Russo
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Salvatore Oliva
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Roberta Vitali
- Laboratory of Biomedical Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123, Rome, Italy
| | - Francesca Palone
- Laboratory of Biomedical Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Via Anguillarese 301, 00123, Rome, Italy
| | - Salvatore Cucchiara
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Laura Stronati
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.
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Guillet S, Lazarov T, Jordan N, Boisson B, Tello M, Craddock B, Zhou T, Nishi C, Bareja R, Yang H, Rieux-Laucat F, Lorenzo RIF, Dyall SD, Isenberg D, D'Cruz D, Lachmann N, Elemento O, Viale A, Socci ND, Abel L, Nagata S, Huse M, Todd Miller W, Casanova JL, Geissmann F. ACK1 and BRK non-receptor tyrosine kinase deficiencies are associated with familial systemic lupus and involved in efferocytosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.15.24302255. [PMID: 38883731 PMCID: PMC11177913 DOI: 10.1101/2024.02.15.24302255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune disease, the pathophysiology and genetic basis of which are incompletely understood. Using a forward genetic screen in multiplex families with systemic lupus erythematosus (SLE) we identified an association between SLE and compound heterozygous deleterious variants in the non-receptor tyrosine kinases (NRTKs) ACK1 and BRK. Experimental blockade of ACK1 or BRK increased circulating autoantibodies in vivo in mice and exacerbated glomerular IgG deposits in an SLE mouse model. Mechanistically, non-receptor tyrosine kinases (NRTKs) regulate activation, migration, and proliferation of immune cells. We found that the patients' ACK1 and BRK variants impair efferocytosis, the MERTK-mediated anti-inflammatory response to apoptotic cells, in human induced Pluripotent Stem Cell (hiPSC)-derived macrophages, which may contribute to SLE pathogenesis. Overall, our data suggest that ACK1 and BRK deficiencies are associated with human SLE and impair efferocytosis in macrophages. One sentence summary Loss of function variants of human ACK1 and BRK kinase underlie systemic lupus erythematosus in young patients from multiplex families and disrupt the anti-inflammatory response of macrophages to apoptotic cells.
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Ando T, Takazawa I, Spencer ZT, Ito R, Tomimori Y, Mikulski Z, Matsumoto K, Ishitani T, Denson LA, Kawakami Y, Kawakami Y, Kitaura J, Ahmed Y, Kawakami T. Ileal Crohn's Disease Exhibits Reduced Activity of Phospholipase C-β3-Dependent Wnt/β-Catenin Signaling Pathway. Cells 2024; 13:986. [PMID: 38891118 PMCID: PMC11171731 DOI: 10.3390/cells13110986] [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: 05/06/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Crohn's disease is a chronic, debilitating, inflammatory bowel disease. Here, we report a critical role of phospholipase C-β3 (PLC-β3) in intestinal homeostasis. In PLC-β3-deficient mice, exposure to oral dextran sodium sulfate induced lethality and severe inflammation in the small intestine. The lethality was due to PLC-β3 deficiency in multiple non-hematopoietic cell types. PLC-β3 deficiency resulted in reduced Wnt/β-catenin signaling, which is essential for homeostasis and the regeneration of the intestinal epithelium. PLC-β3 regulated the Wnt/β-catenin pathway in small intestinal epithelial cells (IECs) at transcriptional, epigenetic, and, potentially, protein-protein interaction levels. PLC-β3-deficient IECs were unable to respond to stimulation by R-spondin 1, an enhancer of Wnt/β-catenin signaling. Reduced expression of PLC-β3 and its signature genes was found in biopsies of patients with ileal Crohn's disease. PLC-β regulation of Wnt signaling was evolutionally conserved in Drosophila. Our data indicate that a reduction in PLC-β3-mediated Wnt/β-catenin signaling contributes to the pathogenesis of ileal Crohn's disease.
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Affiliation(s)
- Tomoaki Ando
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
- Atopy Research Center, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Ikuo Takazawa
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Zachary T. Spencer
- Department of Molecular and Systems Biology and the Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA; (Z.T.S.)
| | - Ryoji Ito
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
- Central Institute for Experimental Animals, Kawasaki 210-0821, Kanagawa, Japan
| | - Yoshiaki Tomimori
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Zbigniew Mikulski
- Imaging Facility, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Tohru Ishitani
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-0044, Gunma, Japan
| | - Lee A. Denson
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yu Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Yuko Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Jiro Kitaura
- Atopy Research Center, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Yashi Ahmed
- Department of Molecular and Systems Biology and the Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA; (Z.T.S.)
| | - Toshiaki Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
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Chang H, Liu Y, Wang Y, Li L, Mu Y, Zheng M, Liu J, Zhang J, Bai R, Li Y, Zuo X. Unveiling the Links Between Microbial Alteration and Host Gene Disarray in Crohn's Disease via TAHMC. Adv Biol (Weinh) 2024:e2400064. [PMID: 38837746 DOI: 10.1002/adbi.202400064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/03/2024] [Indexed: 06/07/2024]
Abstract
A compelling correlation method linking microbial communities and host gene expression in tissues is currently absent. A novel pipeline is proposed, dubbed Transcriptome Analysis of Host-Microbiome Crosstalk (TAHMC), designed to concurrently restore both host gene expression and microbial quantification from bulk RNA-seq data. Employing this approach, it discerned associations between the tissue microbiome and host immunity in the context of Crohn's disease (CD). Further, machine learning is utilized to separately construct networks of associations among host mRNA, long non-coding RNA, and tissue microbes. Unique host genes and tissue microbes are extracted from these networks for potential utility in CD diagnosis. Experimental validation of the predicted host gene regulation by microbes from the association network is achieved through the co-culturing of Faecalibacterium prausnitzii with Caco-2 cells. Collectively, the TAHMC pipeline accurately recovers both host gene expression and microbial quantification from CD RNA-seq data, thereby illuminating potential causal links between shifts in microbial composition as well as diversity within CD mucosal tissues and aberrant host gene expression.
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Affiliation(s)
- Huijun Chang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yongshuai Liu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yue Wang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Lixiang Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, Shandong, 250012, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
- Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yijun Mu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Mengqi Zheng
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Junfei Liu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Jinghui Zhang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Runze Bai
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yanqing Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, Shandong, 250012, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
- Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Xiuli Zuo
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, 250012, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, Shandong, 250012, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
- Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
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12
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Guisado D, Talware S, Wang X, Davis A, Fozilov E, Etra A, Colombel JF, Schaniel C, Tastad C, Levine JE, Ferrara JLM, Chuang LS, Sabic K, Singh S, Marcellino BK, Hoffman R, Cho J, Cohen LJ. The reparative immunologic consequences of stem cell transplantation as a cellular therapy for refractory Crohn's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596699. [PMID: 38895305 PMCID: PMC11185544 DOI: 10.1101/2024.05.30.596699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Background Treatment strategies for Crohn's disease (CD) suppress diverse inflammatory pathways but many patients remain refractory to treatment. Autologous hematopoietic stem cell transplantation (SCT) has emerged as a therapy for medically refractory CD. SCT was developed to rescue cancer patients from myelosuppressive chemotherapy but its use for CD and other immune diseases necessitates reimagining SCT as a cellular therapy that restores appropriately responsive immune cell populations from hematopoietic progenitors in the stem cell autograft (i.e. immune "reset"). Here we present a paradigm to understand SCT as a cellular therapy for immune diseases and reveal how SCT re-establishes cellular immunity utilizing high-dimensional cellular phenotyping and functional studies of the stem cell grafts. Methods Immunophenotyping using CyTOF, single cell RNA sequencing (scRNA-seq) and T cell receptor (TCR) sequencing was performed on peripheral blood and intestinal tissue samples from refractory CD patients who underwent SCT. The stem cell graft from these patients was analyzed using flow cytometry and functionally interrogated using a murine model for engraftment. Results Our study revealed a remodeling of intestinal macrophages capable of supporting mucosal healing that was independently validated using multimodal studies of immune reconstitution events including CyTOF and scRNA-seq. Functional interrogation of hematopoietic stem cells (HSCs) using a xenograft model demonstrated that HSCs shape the timing of immune reconstitution, the selected reconstitution of specific cell lineages and potentially the clinical efficacy of SCT. Conclusions These studies indicate that SCT serves as a myeloid-directed cellular therapy re-establishing homeostatic intestinal macrophages that support intestinal healing and suggest refractory CD evolves from impairment of restorative functions in myeloid cells. Furthermore, we report heterogeneity among HSCs from CD patients which may drive SCT outcomes and suggests an unrecognized impact of CD pathophysiology on HSC in the marrow niche.
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13
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Horn V, Sonnenberg GF. Group 3 innate lymphoid cells in intestinal health and disease. Nat Rev Gastroenterol Hepatol 2024; 21:428-443. [PMID: 38467885 PMCID: PMC11144103 DOI: 10.1038/s41575-024-00906-3] [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: 02/05/2024] [Indexed: 03/13/2024]
Abstract
The gastrointestinal tract is an immunologically rich organ, containing complex cell networks and dense lymphoid structures that safeguard this large absorptive barrier from pathogens, contribute to tissue physiology and support mucosal healing. Simultaneously, the immune system must remain tolerant to innocuous dietary antigens and trillions of normally beneficial microorganisms colonizing the intestine. Indeed, a dysfunctional immune response in the intestine underlies the pathogenesis of numerous local and systemic diseases, including inflammatory bowel disease, food allergy, chronic enteric infections or cancers. Here, we discuss group 3 innate lymphoid cells (ILC3s), which have emerged as orchestrators of tissue physiology, immunity, inflammation, tolerance and malignancy in the gastrointestinal tract. ILC3s are abundant in the developing and healthy intestine but their numbers or function are altered during chronic disease and cancer. The latest studies provide new insights into the mechanisms by which ILC3s fundamentally shape intestinal homeostasis or disease pathophysiology, and often this functional dichotomy depends on context and complex interactions with other cell types or microorganisms. Finally, we consider how this knowledge could be harnessed to improve current treatments or provoke new opportunities for therapeutic intervention to promote gut health.
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Affiliation(s)
- Veronika Horn
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology & Hepatology, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology & Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gregory F Sonnenberg
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology & Hepatology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Department of Microbiology & Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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14
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Mager LF, Krause T, McCoy KD. Interaction of microbiota, mucosal malignancies, and immunotherapy-Mechanistic insights. Mucosal Immunol 2024; 17:402-415. [PMID: 38521413 DOI: 10.1016/j.mucimm.2024.03.007] [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: 12/29/2023] [Revised: 03/09/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
The microbiome has emerged as a crucial modulator of host-immune interactions and clearly impacts tumor development and therapy efficacy. The microbiome is a double-edged sword in cancer development and therapy as both pro-tumorigenic and anti-tumorigenic bacterial taxa have been identified. The staggering number of association-based studies in various tumor types has led to an enormous amount of data that makes it difficult to identify bacteria that promote tumor development or modulate therapy efficacy from bystander bacteria. Here we aim to comprehensively summarize the current knowledge of microbiome-host immunity interactions and cancer therapy in various mucosal tissues to find commonalities and thus identify potential functionally relevant bacterial taxa. Moreover, we also review recent studies identifying specific bacteria and mechanisms through which the microbiome modulates cancer development and therapy efficacy.
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Affiliation(s)
- Lukas F Mager
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada; Department of Internal Medicine I, Faculty of Medicine, University of Tübingen, Germany; M3 Research Center for Malignom, Metabolome and Microbiome, Faculty of Medicine University Tübingen, Germany
| | - Tim Krause
- Department of Internal Medicine I, Faculty of Medicine, University of Tübingen, Germany; M3 Research Center for Malignom, Metabolome and Microbiome, Faculty of Medicine University Tübingen, Germany
| | - Kathy D McCoy
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada.
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15
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Stankey CT, Bourges C, Haag LM, Turner-Stokes T, Piedade AP, Palmer-Jones C, Papa I, Silva Dos Santos M, Zhang Q, Cameron AJ, Legrini A, Zhang T, Wood CS, New FN, Randzavola LO, Speidel L, Brown AC, Hall A, Saffioti F, Parkes EC, Edwards W, Direskeneli H, Grayson PC, Jiang L, Merkel PA, Saruhan-Direskeneli G, Sawalha AH, Tombetti E, Quaglia A, Thorburn D, Knight JC, Rochford AP, Murray CD, Divakar P, Green M, Nye E, MacRae JI, Jamieson NB, Skoglund P, Cader MZ, Wallace C, Thomas DC, Lee JC. A disease-associated gene desert directs macrophage inflammation through ETS2. Nature 2024; 630:447-456. [PMID: 38839969 PMCID: PMC11168933 DOI: 10.1038/s41586-024-07501-1] [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: 04/17/2023] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
Increasing rates of autoimmune and inflammatory disease present a burgeoning threat to human health1. This is compounded by the limited efficacy of available treatments1 and high failure rates during drug development2, highlighting an urgent need to better understand disease mechanisms. Here we show how functional genomics could address this challenge. By investigating an intergenic haplotype on chr21q22-which has been independently linked to inflammatory bowel disease, ankylosing spondylitis, primary sclerosing cholangitis and Takayasu's arteritis3-6-we identify that the causal gene, ETS2, is a central regulator of human inflammatory macrophages and delineate the shared disease mechanism that amplifies ETS2 expression. Genes regulated by ETS2 were prominently expressed in diseased tissues and more enriched for inflammatory bowel disease GWAS hits than most previously described pathways. Overexpressing ETS2 in resting macrophages reproduced the inflammatory state observed in chr21q22-associated diseases, with upregulation of multiple drug targets, including TNF and IL-23. Using a database of cellular signatures7, we identified drugs that might modulate this pathway and validated the potent anti-inflammatory activity of one class of small molecules in vitro and ex vivo. Together, this illustrates the power of functional genomics, applied directly in primary human cells, to identify immune-mediated disease mechanisms and potential therapeutic opportunities.
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Affiliation(s)
- C T Stankey
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
- Department of Immunology and Inflammation, Imperial College London, London, UK
- Washington University School of Medicine, St Louis, MO, USA
| | - C Bourges
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
| | - L M Haag
- Division of Gastroenterology, Infectious Diseases and Rheumatology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - T Turner-Stokes
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - A P Piedade
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
| | - C Palmer-Jones
- Department of Gastroenterology, Royal Free Hospital, London, UK
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - I Papa
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
| | | | - Q Zhang
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Hinxton, UK
| | - A J Cameron
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - A Legrini
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - T Zhang
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - C S Wood
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - F N New
- NanoString Technologies, Seattle, WA, USA
| | - L O Randzavola
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - L Speidel
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- Genetics Institute, University College London, London, UK
| | - A C Brown
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - A Hall
- The Sheila Sherlock Liver Centre, Royal Free Hospital, London, UK
- Department of Cellular Pathology, Royal Free Hospital, London, UK
| | - F Saffioti
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
- The Sheila Sherlock Liver Centre, Royal Free Hospital, London, UK
| | - E C Parkes
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK
| | - W Edwards
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - H Direskeneli
- Department of Internal Medicine, Division of Rheumatology, Marmara University, Istanbul, Turkey
| | - P C Grayson
- Systemic Autoimmunity Branch, NIAMS, National Institutes of Health, Bethesda, MD, USA
| | - L Jiang
- Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - P A Merkel
- Division of Rheumatology, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Epidemiology, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - G Saruhan-Direskeneli
- Department of Physiology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - A H Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Lupus Center of Excellence, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - E Tombetti
- Department of Biomedical and Clinical Sciences, Milan University, Milan, Italy
- Internal Medicine and Rheumatology, ASST FBF-Sacco, Milan, Italy
| | - A Quaglia
- Department of Cellular Pathology, Royal Free Hospital, London, UK
- UCL Cancer Institute, London, UK
| | - D Thorburn
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
- The Sheila Sherlock Liver Centre, Royal Free Hospital, London, UK
| | - J C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - A P Rochford
- Department of Gastroenterology, Royal Free Hospital, London, UK
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - C D Murray
- Department of Gastroenterology, Royal Free Hospital, London, UK
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK
| | - P Divakar
- NanoString Technologies, Seattle, WA, USA
| | - M Green
- Experimental Histopathology STP, The Francis Crick Institute, London, UK
| | - E Nye
- Experimental Histopathology STP, The Francis Crick Institute, London, UK
| | - J I MacRae
- Metabolomics STP, The Francis Crick Institute, London, UK
| | - N B Jamieson
- Wolfson Wohl Cancer Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - P Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - M Z Cader
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - C Wallace
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge, UK
| | - D C Thomas
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - J C Lee
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK.
- Department of Gastroenterology, Royal Free Hospital, London, UK.
- Institute for Liver and Digestive Health, Division of Medicine, University College London, London, UK.
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16
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Herren R, Geva-Zatorsky N. Spatial features of skip lesions in Crohn's disease. Trends Immunol 2024; 45:470-481. [PMID: 38782626 DOI: 10.1016/j.it.2024.04.011] [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: 03/28/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Skip lesions are an enigmatic spatial feature characterizing Crohn's disease (CD). They comprise inflamed and adjacent non-inflamed tissue sections with a clear demarcation. Currently, spatial features of the human gastrointestinal (GI) system lack clarity regarding the organization of microbes, mucus, tissue, and host cells during inflammation. New technologies with multiplexing abilities and innovative approaches provide ways of examining the spatial organization of inflamed and non-inflamed tissues in CD, which may open new avenues for diagnosis, prognosis, and treatment. In this review, we present evidence of the relevance of spatial context in patients with CD and the methods and ideas recently published in studies of spatiality during inflammation. With this review, we aim to provide inspiration for further research to address existing gaps.
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Affiliation(s)
- Rachel Herren
- Department of Cell Biology and Cancer Science, Rappaport Technion Integrated Cancer Center (RTICC), Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, 3525422 Haifa, Israel
| | - Naama Geva-Zatorsky
- Department of Cell Biology and Cancer Science, Rappaport Technion Integrated Cancer Center (RTICC), Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, 3525422 Haifa, Israel; CIFAR, MaRS Centre, West Tower 661 University Avenue, Suite 505, Toronto, ON M5G 1M1, Canada.
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17
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Zhong T, Cheng X, Gu Q, Fu G, Wang Y, Jiang Y, Xu J, Jiang Z. Integrated analyses reveal the diagnostic and predictive values of COL5A2 and association with immune environment in Crohn's disease. Genes Immun 2024; 25:209-218. [PMID: 38789829 PMCID: PMC11178494 DOI: 10.1038/s41435-024-00276-5] [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: 09/18/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
The pathogenesis of Crohn's disease (CD) involves abnormal immune cell infiltration and dysregulated immune response. Therefore, thorough research on immune cell abnormalities in CD is crucial for improved treatment of this disease. Single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data of CD were obtained from the Gene Expression Omnibus (GEO) database. Cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT), weighted gene co-expression network analysis (WGCNA), protein-protein interaction (PPI) networks evaluated the proportion of immune infiltrating cells, constructed co-expression network and identified key genes, respectively. Based on the dataset (GSE134809), 15 cell clusters were defined and labeled as different cell types. Among the 11 modules, the yellow module had the closest relationship with plasma cells (cluster 5). Confirmed using RNA sequencing and IHC assay, the expression of COL5A2 in CD samples was higher than that in control samples. Furthermore, the COL5A2 protein expression remarkably decreased in the group of patients who responded to anti-tumor necrosis factor (TNF) treatments, compared to the non-response group. The comprehensive analyses described here provided novel insight into the landscape of CD-associated immune environment. In addition, COL5A2 were identified as potential diagnostic indicators for CD, as well as promising predictive markers for CD patients.
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Affiliation(s)
- Tingting Zhong
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqing Cheng
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianru Gu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guoxiang Fu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yihong Wang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yujie Jiang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaqi Xu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Zhinong Jiang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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18
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Borrelli C, Gurtner A, Arnold IC, Moor AE. Stress-free single-cell transcriptomic profiling and functional genomics of murine eosinophils. Nat Protoc 2024; 19:1679-1709. [PMID: 38504138 DOI: 10.1038/s41596-024-00967-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 12/20/2023] [Indexed: 03/21/2024]
Abstract
Eosinophils are a class of granulocytes with pleiotropic functions in homeostasis and various human diseases. Nevertheless, they are absent from conventional single-cell RNA sequencing atlases owing to technical difficulties preventing their transcriptomic interrogation. Consequently, eosinophil heterogeneity and the gene regulatory networks underpinning their diverse functions remain poorly understood. We have developed a stress-free protocol for single-cell RNA capture from murine tissue-resident eosinophils, which revealed distinct intestinal subsets and their roles in colitis. Here we describe in detail how to enrich eosinophils from multiple tissues of residence and how to capture high-quality single-cell transcriptomes by preventing transcript degradation. By combining magnetic eosinophil enrichment with microwell-based single-cell RNA capture (BD Rhapsody), our approach minimizes shear stress and processing time. Moreover, we report how to perform genome-wide CRISPR pooled genetic screening in ex vivo-conditioned bone marrow-derived eosinophils to functionally probe pathways required for their differentiation and intestinal maturation. These protocols can be performed by any researcher with basic skills in molecular biology and flow cytometry, and can be adapted to investigate other granulocytes, such as neutrophils and mast cells, thereby offering potential insights into their roles in both homeostasis and disease pathogenesis. Single-cell transcriptomics of eosinophils can be performed in 2-3 d, while functional genomics assays may require up to 1 month.
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Affiliation(s)
- Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Alessandra Gurtner
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Isabelle C Arnold
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland.
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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19
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Donado CA, Jonsson AH, Theisen E, Zhang F, Nathan A, Rupani KV, Jones D, Raychaudhuri S, Dwyer DF, Brenner MB. Granzyme K drives a newly-intentified pathway of complement activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595315. [PMID: 38826230 PMCID: PMC11142156 DOI: 10.1101/2024.05.22.595315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Granzymes are a family of serine proteases mainly expressed by CD8+ T cells, natural killer cells, and innate-like lymphocytes1,2. Although their major role is thought to be the induction of cell death in virally infected and tumor cells, accumulating evidence suggests some granzymes can regulate inflammation by acting on extracellular substrates2. Recently, we found that the majority of tissue CD8+ T cells in rheumatoid arthritis (RA) synovium, inflammatory bowel disease and other inflamed organs express granzyme K (GZMK)3, a tryptase-like protease with poorly defined function. Here, we show that GZMK can activate the complement cascade by cleaving C2 and C4. The nascent C4b and C2a fragments form a C3 convertase that cleaves C3, allowing further assembly of a C5 convertase that cleaves C5. The resulting convertases trigger every major event in the complement cascade, generating the anaphylatoxins C3a and C5a, the opsonins C4b and C3b, and the membrane attack complex. In RA synovium, GZMK is enriched in areas with abundant complement activation, and fibroblasts are the major producers of complement C2, C3, and C4 that serve as targets for GZMK-mediated complement activation. Our findings describe a previously unidentified pathway of complement activation that is entirely driven by lymphocyte-derived GZMK and proceeds independently of the classical, lectin, or alternative pathways. Given the widespread abundance of GZMK-expressing T cells in tissues in chronic inflammatory diseases and infection, GZMK-mediated complement activation is likely to be an important contributor to tissue inflammation in multiple disease contexts.
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Affiliation(s)
- Carlos A. Donado
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA, USA
- These authors contributed equally: Carlos A. Donado, A. Helena Jonsson
| | - A. Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA, USA
- Current affiliation: Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
- These authors contributed equally: Carlos A. Donado, A. Helena Jonsson
| | - Erin Theisen
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA, USA
- Department of Dermatology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Fan Zhang
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, 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
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA USA
- Center for Data Sciences, 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
| | - Karishma Vijay Rupani
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA, USA
| | - Dominique Jones
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA, USA
| | | | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, 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
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA USA
- Center for Data Sciences, 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
| | - Daniel F. Dwyer
- Division of Allergy and Clinical Immunology, Jeff and Penny Vinik Center for Allergic Disease Research, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA, USA
| | - Michael B. Brenner
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA, USA
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20
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Chen M, Chen Y, Fu R, Liu S, Li H, Shen T. Atox1 regulates macrophage polarization in intestinal inflammation via ROS-NLRP3 inflammasome pathway. J Transl Med 2024; 22:497. [PMID: 38796413 PMCID: PMC11128112 DOI: 10.1186/s12967-024-05314-4] [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: 11/10/2023] [Accepted: 05/20/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND Inflammation and oxidative stress play an important role in the pathophysiology of inflammatory bowel disease (IBD). This study aimed to explore the effects of copper chaperone Antioxidant-1 (Atox1) on macrophages in a mouse model of intestinal inflammation. METHODS A mouse model of TNBS-induced colitis was established and verified using the disease activity index. Atox1 conditional knockout mice were applied. The proportion of macrophages in colonic lamina propria mononuclear cells and ROS production were analyzed using flow cytometry. Inflammatory cytokines were measured using ELISA. Expression of macrophage M1/M2 polarization markers, p47phox, NLRP3, and Caspase-1 p20 was measured using quantitative RT-PCR and Western blotting. RESULTS Atox1 expression was up-regulated in colon tissues of TNBS-induced colitis mice. Macrophages isolated from TNBS-induced colitis mice showed M1 polarization and nuclear translocation of Atox1. Inhibiting copper chaperone activity decreased p47phox, ROS production, and M1 polarization induced by CuCl2 in macrophages. TNBS induced up-regulation of inflammatory cytokines, M1 polarization markers, and p47phox expression in mice, an effect which was preempted by Atox1 knockout. Inflammatory cytokines and expression of M1 polarization markers, p47phox, NLRP3, Caspase-1 p20 were also increased in macrophages isolated from TNBS-induced colitis mice. These changes were alleviated in mice with Atox1 knockout. The effects of Atox1 on macrophage polarization were mediated via the ROS-NLRP3 inflammasome pathway. CONCLUSION Atox1 plays a pro-inflammatory role, promotes M1 polarization of macrophages, and increases the concentrations of pro-inflammatory cytokines in intestinal tissue by regulating the ROS-NLRP3 inflammasome pathway. Atox1 is a potential therapeutic target in IBD.
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Affiliation(s)
- MingXian Chen
- Department of Gastroenterology, Tongde Hospital of Zhejiang Province, No. 234, Gucui road, Hangzhou, 310012, China
- Institute of Integrated Chinese and Western Medicine on Spleen-Stomach Diseases, Zhejiang Province Academy of Traditional Chinese Medicine, Hangzhou, 310012, China
| | - Yu Chen
- Laboratory Animal Center, Zhejiang Province Academy of Traditional Chinese Medicine, Hangzhou, 310012, China
| | - Rui Fu
- Department of Gastroenterology, Tongde Hospital of Zhejiang Province, No. 234, Gucui road, Hangzhou, 310012, China
| | - SaiYue Liu
- Department of Adverse Drug Reaction Monitoring, Zhejiang Province Center of Adverse Drug Reaction Monitoring, No. 39, Yile road, Hangzhou, 310012, China.
| | - HaiXia Li
- Department of Cardiology, Guanganmen Hospital of China Academy of Chinese Medical Sciences, No. 5, Beixian Ge, Xicheng District, Beijing, 100053, China.
| | - TangBiao Shen
- Department of Gastroenterology, Tongde Hospital of Zhejiang Province, No. 234, Gucui road, Hangzhou, 310012, China.
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21
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Allegretti JR, Bordeianou LG, Damas OM, Eisenstein S, Greywoode R, Minar P, Singh S, Harmon S, Lisansky E, Malone-King M, Litwin NS, Weaver A, Heller CA, Moss AC, Adler J. Challenges in IBD Research 2024: Pragmatic Clinical Research. Inflamm Bowel Dis 2024; 30:S55-S66. [PMID: 38778623 DOI: 10.1093/ibd/izae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Indexed: 05/25/2024]
Abstract
Pragmatic clinical research is 1 of the 5 focus areas of the Challenges in IBD Research 2024, a multidisciplinary effort by scientists, clinicians, patients, and funders to identify priorities for patient-centric research. This summary provides a comprehensive overview of current gaps in inflammatory bowel disease (IBD) clinical research and actionable approaches to address them. This review is focused on identifying research that is needed to achieve the best outcomes for patients in clinical practice. Research gaps include understanding the needs of understudied patient groups and addressing barriers to care so all patients receive optimal care, validating and using biomarkers to enable early diagnosis and result in better outcomes for adults and children with IBD, and determining the optimal sequencing of treatments (medical, surgical, adjunct) in children and adults. Inclusive pragmatic research is needed to address these gaps and lead to improvements in patient care and outcomes for all populations of patients with IBD.
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Affiliation(s)
- Jessica R Allegretti
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA
| | - Liliana G Bordeianou
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Oriana M Damas
- Division of Gastroenterology, Department of Medicine, University of Miami Leonard Miller School of Medicine, Miami, FL, USA
| | - Samuel Eisenstein
- Division of Colon and Rectal Surgery, Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | - Ruby Greywoode
- Division of Gastroenterology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Phillip Minar
- Division of Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic, Cleveland, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Siddharth Singh
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sabrina Harmon
- Division of Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic, Cleveland, OH, USA
| | - Eugene Lisansky
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - Myisha Malone-King
- Division of Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic, Cleveland, OH, USA
| | | | | | | | - Alan C Moss
- Crohn's & Colitis Foundation, New York, NY, USA
| | - Jeremy Adler
- Susan B. Meister Child Health Evaluation and Research Center and Division of Pediatric Gastroenterology, C.S. Mott Children's Hospital, Michigan Medicine, Ann Arbor, MI, USA
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22
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Syed S, Boland BS, Bourke LT, Chen LA, Churchill L, Dobes A, Greene A, Heller C, Jayson C, Kostiuk B, Moss A, Najdawi F, Plung L, Rioux JD, Rosen MJ, Torres J, Zulqarnain F, Satsangi J. Challenges in IBD Research 2024: Precision Medicine. Inflamm Bowel Dis 2024; 30:S39-S54. [PMID: 38778628 DOI: 10.1093/ibd/izae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Indexed: 05/25/2024]
Abstract
Precision medicine is part of 5 focus areas of the Challenges in IBD Research 2024 research document, which also includes preclinical human IBD mechanisms, environmental triggers, novel technologies, and pragmatic clinical research. Building on Challenges in IBD Research 2019, the current Challenges aims to provide a comprehensive overview of current gaps in inflammatory bowel diseases (IBDs) research and deliver actionable approaches to address them with a focus on how these gaps can lead to advancements in interception, remission, and restoration for these diseases. The document is the result of multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient-centric research prioritization. In particular, the precision medicine section is focused on the main research gaps in elucidating how to bring the best care to the individual patient in IBD. Research gaps were identified in biomarker discovery and validation for predicting disease progression and choosing the most appropriate treatment for each patient. Other gaps were identified in making the best use of existing patient biosamples and clinical data, developing new technologies to analyze large datasets, and overcoming regulatory and payer hurdles to enable clinical use of biomarkers. To address these gaps, the Workgroup suggests focusing on thoroughly validating existing candidate biomarkers, using best-in-class data generation and analysis tools, and establishing cross-disciplinary teams to tackle regulatory hurdles as early as possible. Altogether, the precision medicine group recognizes the importance of bringing basic scientific biomarker discovery and translating it into the clinic to help improve the lives of IBD patients.
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Affiliation(s)
- Sana Syed
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lauren T Bourke
- Precision Medicine Drug Development, Early Respiratory and Immunology, AstraZeneca, Boston, MA, USA
| | - Lea Ann Chen
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Laurie Churchill
- Leona M. and Harry B. Helmsley Charitable Trust, New York, NY, USA
| | | | - Adam Greene
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - Alan Moss
- Crohn's & Colitis Foundation, New York, NY, USA
| | | | - Lori Plung
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Michael J Rosen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Hospital da Luz, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Fatima Zulqarnain
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Jack Satsangi
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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23
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Chen L, Patil S, Barbon J, Waire J, Laroux S, McCarthy D, Pratibha M, Zhong S, Dong F, Orsi K, Nguyen G, Yang Y, Crosbie N, Dominguez E, Deora A, Veldman G, Westmoreland S, Jin L, Radstake T, White K, Wei HJ. Agonistic anti-DCIR antibody inhibits ITAM-mediated inflammatory signaling and promotes immune resolution. JCI Insight 2024; 9:e176064. [PMID: 38781017 DOI: 10.1172/jci.insight.176064] [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: 10/05/2023] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
DC inhibitory receptor (DCIR) is a C-type lectin receptor selectively expressed on myeloid cells, including monocytes, macrophages, DCs, and neutrophils. Its role in immune regulation has been implicated in murine models and human genome-wide association studies, suggesting defective DCIR function associates with increased susceptibility to autoimmune diseases such as rheumatoid arthritis, lupus, and Sjögren's syndrome. However, little is known about the mechanisms underlying DCIR activation to dampen inflammation. Here, we developed anti-DCIR agonistic antibodies that promote phosphorylation on DCIR's immunoreceptor tyrosine-based inhibitory motifs and recruitment of SH2 containing protein tyrosine phosphatase-2 for reducing inflammation. We also explored the inflammation resolution by depleting DCIR+ cells with antibodies. Utilizing a human DCIR-knock-in mouse model, we validated the antiinflammatory properties of the agonistic anti-DCIR antibody in experimental peritonitis and colitis. These findings provide critical evidence for targeting DCIR to develop transformative therapies for inflammatory diseases.
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Affiliation(s)
- Liang Chen
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, USA
| | - Suresh Patil
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, USA
| | - Jeffrey Barbon
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - James Waire
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Stephen Laroux
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Donna McCarthy
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Mishra Pratibha
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, USA
| | - Suju Zhong
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, USA
| | - Feng Dong
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, USA
| | - Karin Orsi
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Gunarso Nguyen
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Yingli Yang
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Nancy Crosbie
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Eric Dominguez
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Arun Deora
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, USA
| | | | | | - Liang Jin
- AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Timothy Radstake
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, USA
| | - Kevin White
- AbbVie, Cambridge Research Center, Cambridge, Massachusetts, USA
| | - Hsi-Ju Wei
- AbbVie Bay Area, South San Francisco, California, USA
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24
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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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25
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Ouboter LF, Lindelauf C, Jiang Q, Schreurs M, Abdelaal TR, Luk SJ, Barnhoorn MC, Hueting WE, Han-Geurts IJ, Peeters KCMJ, Holman FA, Koning F, van der Meulen-de Jong AE, Pascutti MF. Activated HLA-DR+CD38+ Effector Th1/17 Cells Distinguish Crohn's Disease-associated Perianal Fistulas from Cryptoglandular Fistulas. Inflamm Bowel Dis 2024:izae103. [PMID: 38776553 DOI: 10.1093/ibd/izae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Indexed: 05/25/2024]
Abstract
BACKGROUND Perianal fistulas are a debilitating complication of Crohn's disease (CD). Due to unknown reasons, CD-associated fistulas are in general more difficult to treat than cryptoglandular fistulas (non-CD-associated). Understanding the immune cell landscape is a first step towards the development of more effective therapies for CD-associated fistulas. In this work, we characterized the composition and spatial localization of disease-associated immune cells in both types of perianal fistulas by high-dimensional analyses. METHODS We applied single-cell mass cytometry (scMC), spectral flow cytometry (SFC), and imaging mass cytometry (IMC) to profile the immune compartment in CD-associated perianal fistulas and cryptoglandular fistulas. An exploratory cohort (CD fistula, n = 10; non-CD fistula, n = 5) was analyzed by scMC to unravel disease-associated immune cell types. SFC was performed on a second fistula cohort (CD, n = 10; non-CD, n = 11) to comprehensively phenotype disease-associated T helper (Th) cells. IMC was used on a third cohort (CD, n = 5) to investigate the spatial distribution/interaction of relevant immune cell subsets. RESULTS Our analyses revealed that activated HLA-DR+CD38+ effector CD4+ T cells with a Th1/17 phenotype were significantly enriched in CD-associated compared with cryptoglandular fistulas. These cells, displaying features of proliferation, regulation, and differentiation, were also present in blood, and colocalized with other CD4+ T cells, CCR6+ B cells, and macrophages in the fistula tracts. CONCLUSIONS Overall, proliferating activated HLA-DR+CD38+ effector Th1/17 cells distinguish CD-associated from cryptoglandular perianal fistulas and are a promising biomarker in blood to discriminate between these 2 fistula types. Targeting HLA-DR and CD38-expressing CD4+ T cells may offer a potential new therapeutic strategy for CD-related fistulas.
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Affiliation(s)
- Laura F Ouboter
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ciska Lindelauf
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Qinyue Jiang
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Mette Schreurs
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tamim R Abdelaal
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
- Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
- Systems and Biomedical Engineering Department, Faculty of Engineering Cairo University, Giza, Egypt
| | - Sietse J Luk
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Marieke C Barnhoorn
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Willem E Hueting
- Department of Surgery, Alrijne hospital, Leiderdorp, the Netherlands
| | | | - Koen C M J Peeters
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Fabian A Holman
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
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26
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Kodama M, Okano S, Nojri S, Abe K, Fukata M, Nagase Y, Kodama H. Longitudinal and regional association between dietary factors and prevalence of Crohn's disease in Japan. PLoS One 2024; 19:e0300580. [PMID: 38776273 PMCID: PMC11111081 DOI: 10.1371/journal.pone.0300580] [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: 08/08/2023] [Accepted: 02/29/2024] [Indexed: 05/24/2024] Open
Abstract
Although a Western diet has been identified as a risk factor for Crohn's disease (CD), there is still controversy surrounding the specific foods that may contribute to the development of the disease. In this study, we examined the association between food intake and the prevalence of CD in Japan, as Japanese patients with CD are known to have limited genetic involvement. We identified changes in food intake associated with an increase in the number of patients with CD by analyzing the per capita consumption of food types from 1981 to 2014. Additionally, we examined the association between CD prevalence and food intake in each prefecture. Finally, the relationship between food intake and estimated age at CD onset was also investigated. Between 1981 and 2014, we observed Increased consumption of meat, eggs, milk and dairy products, oil, and potatoes and decreased consumption of grains, beans, vegetables, fruit, fish, sugar, and seaweed. The annual incidence of CD increased by 1388% over the same period. We found that meat consumption was significantly associated with CD prevalence (β = 0.503, p = 0.0003), while a significant negative correlation was observed between CD prevalence and fruit and vegetable consumption (fruit, β = 0.464, p = 0.0012; vegetables, β = 0.404, p = 0.0023). Furthermore, we estimated that the peak consumption of more meat and less fruit and vegetables and the peak age of CD onset occurred within the age range of 20-24 years. Our study identified a clear correlation between the consumption of meat, fruits, and vegetables and the prevalence of CD in Japan. Additionally, we found an association between meat, fruit, and vegetable consumption and the age at CD onset.
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Affiliation(s)
- Makoto Kodama
- Department of Pathology, Tokyo Yamate Medical Center, Tokyo, Japan
- Department of Human Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Soh Okano
- Department of Human Pathology, Juntendo University School of Medicine, Tokyo, Japan
- Center for Inflammatory Bowel Disease, Division of Gastroenterology, Department of Internal Medicine, Tokyo Yamate Medical Center, Tokyo, Japan
| | - Shuko Nojri
- Medical Technology Innovation Center, Juntendo University, Tokyo, Japan
| | - Keiko Abe
- Department of Pathology, Tokyo Yamate Medical Center, Tokyo, Japan
| | - Masayuki Fukata
- Center for Inflammatory Bowel Disease, Division of Gastroenterology, Department of Internal Medicine, Tokyo Yamate Medical Center, Tokyo, Japan
| | - Yoshihiro Nagase
- Department of Pathology, Tokyo Yamate Medical Center, Tokyo, Japan
| | - Hiroko Kodama
- Graduate School of Health Sciences, Teikyo Heisei University, Ichihara, Japan
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27
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Xu S, Jiemy WF, Brouwer E, Burgess JK, Heeringa P, van der Geest KSM, Alba-Rovira R, Corbera-Bellalta M, Boots AH, Cid MC, Sandovici M. Current evidence on the role of fibroblasts in large-vessel vasculitides: From pathogenesis to therapeutics. Autoimmun Rev 2024; 23:103574. [PMID: 38782083 DOI: 10.1016/j.autrev.2024.103574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/29/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Large-vessel vasculitides (LVV) comprise a group of chronic inflammatory diseases of the aorta and its major branches. The most common forms of LVV are giant cell arteritis (GCA) and Takayasu arteritis (TAK). Both GCA and TAK are characterized by granulomatous inflammation of the vessel wall accompanied by a maladaptive immune and vascular response that promotes vascular damage and remodeling. The inflammatory process in LVV starts in the adventitia where fibroblasts constitute the dominant cell population. Fibroblasts are traditionally recognized for synthesizing and renewing the extracellular matrix thereby being major players in maintenance of normal tissue architecture and in tissue repair. More recently, fibroblasts have emerged as a highly plastic cell population exerting various functions, including the regulation of local immune processes and organization of immune cells at the site of inflammation through production of cytokines, chemokines and growth factors as well as cell-cell interaction. In this review, we summarize and discuss the current knowledge on fibroblasts in LVV. Furthermore, we identify key questions that need to be addressed to fully understand the role of fibroblasts in the pathogenesis of LVV.
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Affiliation(s)
- Shuang Xu
- University of Groningen, University Medical Center Groningen, Department of Rheumatology and Clinical Immunology, the Netherlands
| | - William F Jiemy
- University of Groningen, University Medical Center Groningen, Department of Rheumatology and Clinical Immunology, the Netherlands
| | - Elisabeth Brouwer
- University of Groningen, University Medical Center Groningen, Department of Rheumatology and Clinical Immunology, the Netherlands
| | - Janette K Burgess
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, the Netherlands
| | - Peter Heeringa
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, the Netherlands
| | - Kornelis S M van der Geest
- University of Groningen, University Medical Center Groningen, Department of Rheumatology and Clinical Immunology, the Netherlands
| | - Roser Alba-Rovira
- Vasculitis Research Group, Department of Autoimmune Diseases, Hospital Clínic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Marc Corbera-Bellalta
- Vasculitis Research Group, Department of Autoimmune Diseases, Hospital Clínic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Annemieke H Boots
- University of Groningen, University Medical Center Groningen, Department of Rheumatology and Clinical Immunology, the Netherlands
| | - Maria C Cid
- Vasculitis Research Group, Department of Autoimmune Diseases, Hospital Clínic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Maria Sandovici
- University of Groningen, University Medical Center Groningen, Department of Rheumatology and Clinical Immunology, the Netherlands.
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28
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Tang W, Ni Z, Wei Y, Hou K, Valencak TG, Wang H. Extracellular vesicles of Bacteroides uniformis induce M1 macrophage polarization and aggravate gut inflammation during weaning. Mucosal Immunol 2024:S1933-0219(24)00045-X. [PMID: 38777177 DOI: 10.1016/j.mucimm.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/01/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
Weaning process is commonly associated with gastrointestinal inflammation and dysbiosis of the intestinal microbes. In particular, the impact of gut bacteria and of extracellular vesicles (EV) on the etiology of intestinal inflammation during weaning is not well understand. We have uncovered a potential link between gut inflammation and the corresponding variation of macrophage bacterial sensing and pro-inflammatory polarization during the weaning process of piglet through single-cell transcriptomic analyses. We conducted a comprehensive analysis of bacterial distribution across the gastrointestinal tract and pinpointed Bacteroides uniformis (B. uniformis) enriching in piglets undergoing weaning. Next, we found out that exposure to B. uniformis-derived EVs (BEVs) exacerbated gut inflammation in a murine colitis model while recruiting and polarizing intestinal macrophages towards a pro-inflammatory phenotype. BEVs modulated the function of macrophages cultured in vitro by suppressing the GM-CSF/STAT5/ARG1 pathway, thereby affecting polarization towards an M1-like state. The effects of BEVs were verified both in the macrophage-clearance murine model and by using an adoptive transfer assay. Our findings highlight the involvement of BEVs in facilitating the polarization of pro-inflammatory macrophages and promoting gut inflammation during weaning.
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Affiliation(s)
- Wenjie Tang
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, 310058, China
| | - Zhixiang Ni
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, 310058, China
| | - Yusen Wei
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, 310058, China
| | - Kangwei Hou
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, 310058, China
| | - Teresa G Valencak
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, 310058, China
| | - Haifeng Wang
- College of Animal Science, Zhejiang University, The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, 310058, China.
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29
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Lu J, Li F, Ye M. PANoptosis and Autophagy-Related Molecular Signature and Immune Landscape in Ulcerative Colitis: Integrated Analysis and Experimental Validation. J Inflamm Res 2024; 17:3225-3245. [PMID: 38800594 PMCID: PMC11122227 DOI: 10.2147/jir.s455862] [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: 12/20/2023] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
Background Ulcerative colitis (UC) is an autoimmune inflammatory disorder of the gastrointestinal tract. Programmed cell death (PCD), including PANoptosis and autophagy, plays roles in inflammation and immunity. This study aimed to investigate the molecular signature and immune landscape of the PANoptosis- and autophagy-related differentially expressed genes (DEGs) in UC. Methods Analyzing UC dataset GSE206285 yielded DEGs. Differentially expressed PANoptosis- and autophagy-related genes were identified using DEGs and relevant gene collections. Functional and pathway enrichment analyses were conducted. A protein-protein interaction (PPI) network was established to identify hub genes. TRRUST database predicted transcription factors (TFs), pivotal miRNAs, and drugs interacting with hub genes. Immune infiltration analysis, UC-associated single-cell sequencing data analysis, and construction of a competing endogenous RNA (ceRNA) network for hub genes were conducted. Machine learning identified key candidate genes, evaluated for diagnostic value via receiver operating characteristic (ROC) curves. A UC mice model verified expression of key candidate genes. Results Identifying ten PANoptosis-related hub DEGs and four autophagy-related hub DEGs associated them with cell chemotaxis, wound healing and positive MAPK cascade regulation. Immune infiltration analysis revealed increased immunocyte infiltration in UC patients, with hub genes closely linked to various immune cell infiltrations. Machine learning identified five key candidate genes, TIMP1, TIMP2, TIMP3, IL6, and CCL2, with strong diagnostic performance. At the single-cell level, these genes exhibited high expression in inflammatory fibroblasts (IAFs). They showed significant expression differences in the colon mucosa of both UC patients and UC mice model. Conclusion This study identified and validated novel molecular signatures associated with PANoptosis and autophagy in UC, potentially influencing immune dysregulation and wound healing, thus opening avenues for future research and therapeutic interventions.
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Affiliation(s)
- Jiali Lu
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, People’s Republic of China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, People’s Republic of China
| | - Fei Li
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, People’s Republic of China
| | - Mei Ye
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, People’s Republic of China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, People’s Republic of China
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30
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Gupta T, Antanaviciute A, Hyun-Jung Lee C, Ottakandathil Babu R, Aulicino A, Christoforidou Z, Siejka-Zielinska P, O'Brien-Ball C, Chen H, Fawkner-Corbett D, Geros AS, Bridges E, McGregor C, Cianci N, Fryer E, Alham NK, Jagielowicz M, Santos AM, Fellermeyer M, Davis SJ, Parikh K, Cheung V, Al-Hillawi L, Sasson S, Slevin S, Brain O, Fernandes RA, Koohy H, Simmons A. Tracking in situ checkpoint inhibitor-bound target T cells in patients with checkpoint-induced colitis. Cancer Cell 2024; 42:797-814.e15. [PMID: 38744246 DOI: 10.1016/j.ccell.2024.04.010] [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: 05/23/2023] [Revised: 02/09/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
The success of checkpoint inhibitors (CPIs) for cancer has been tempered by immune-related adverse effects including colitis. CPI-induced colitis is hallmarked by expansion of resident mucosal IFNγ cytotoxic CD8+ T cells, but how these arise is unclear. Here, we track CPI-bound T cells in intestinal tissue using multimodal single-cell and subcellular spatial transcriptomics (ST). Target occupancy was increased in inflamed tissue, with drug-bound T cells located in distinct microdomains distinguished by specific intercellular signaling and transcriptional gradients. CPI-bound cells were largely CD4+ T cells, including enrichment in CPI-bound peripheral helper, follicular helper, and regulatory T cells. IFNγ CD8+ T cells emerged from both tissue-resident memory (TRM) and peripheral populations, displayed more restricted target occupancy profiles, and co-localized with damaged epithelial microdomains lacking effective regulatory cues. Our multimodal analysis identifies causal pathways and constitutes a resource to inform novel preventive strategies.
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Affiliation(s)
- Tarun Gupta
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Agne Antanaviciute
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
| | - Chloe Hyun-Jung Lee
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Rosana Ottakandathil Babu
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Anna Aulicino
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Zoe Christoforidou
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Paulina Siejka-Zielinska
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Caitlin O'Brien-Ball
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - Hannah Chen
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - David Fawkner-Corbett
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Academic Paediatric Surgery Unit (APSU), Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK
| | - Ana Sousa Geros
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Esther Bridges
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Colleen McGregor
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Nicole Cianci
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Eve Fryer
- Pathology, Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Nasullah Khalid Alham
- Nuffield Department of Surgical Sciences and Oxford NIHR Biomedical Research Centre (BRC), University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Marta Jagielowicz
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ana Mafalda Santos
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Martin Fellermeyer
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Simon J Davis
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Kaushal Parikh
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Vincent Cheung
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Lulia Al-Hillawi
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Sarah Sasson
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Stephanie Slevin
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Oliver Brain
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ricardo A Fernandes
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - Hashem Koohy
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
| | - Alison Simmons
- Medical Research Council (MRC) Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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31
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Jiménez JM, Contreras-Riquelme JS, Vidal PM, Prado C, Bastías M, Meneses C, Martín AJM, Perez-Acle T, Pacheco R. Identification of master regulator genes controlling pathogenic CD4 + T cell fate in inflammatory bowel disease through transcriptional network analysis. Sci Rep 2024; 14:10553. [PMID: 38719901 PMCID: PMC11078927 DOI: 10.1038/s41598-024-61158-4] [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: 01/04/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
Inflammatory bowel diseases (IBD) are a group of chronic inflammatory conditions of the gastrointestinal tract associated with multiple pathogenic factors, including dysregulation of the immune response. Effector CD4+ T cells and regulatory CD4+ T cells (Treg) are central players in maintaining the balance between tolerance and inflammation. Interestingly, genetic modifications in these cells have been implicated in regulating the commitment of specific phenotypes and immune functions. However, the transcriptional program controlling the pathogenic behavior of T helper cells in IBD progression is still unknown. In this study, we aimed to find master transcription regulators controlling the pathogenic behavior of effector CD4+ T cells upon gut inflammation. To achieve this goal, we used an animal model of IBD induced by the transfer of naïve CD4+ T cells into recombination-activating gene 1 (Rag1) deficient mice, which are devoid of lymphocytes. As a control, a group of Rag1-/- mice received the transfer of the whole CD4+ T cells population, which includes both effector T cells and Treg. When gut inflammation progressed, we isolated CD4+ T cells from the colonic lamina propria and spleen tissue, and performed bulk RNA-seq. We identified differentially up- and down-regulated genes by comparing samples from both experimental groups. We found 532 differentially expressed genes (DEGs) in the colon and 30 DEGs in the spleen, mostly related to Th1 response, leukocyte migration, and response to cytokines in lamina propria T-cells. We integrated these data into Gene Regulatory Networks to identify Master Regulators, identifying four up-regulated master gene regulators (Lef1, Dnmt1, Mybl2, and Jup) and only one down-regulated master regulator (Foxo3). The altered expression of master regulators observed in the transcriptomic analysis was confirmed by qRT-PCR analysis and found an up-regulation of Lef1 and Mybl2, but without differences on Dnmt1, Jup, and Foxo3. These two master regulators have been involved in T cells function and cell cycle progression, respectively. We identified two master regulator genes associated with the pathogenic behavior of effector CD4+ T cells in an animal model of IBD. These findings provide two new potential molecular targets for treating IBD.
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Affiliation(s)
- José M Jiménez
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile
| | | | - Pía M Vidal
- Biomedical Science Research Laboratory, Neuroimmunology and Regeneration of the Central Nervous System Unit, Basic Sciences Department, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Carolina Prado
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, 7510156, Providencia, Santiago, Chile
| | - Macarena Bastías
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudio Meneses
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Facultad de Agronomía y Sistemas Naturales, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alberto J M Martín
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile
- Escuela de Ingeniería, Facultad de Ingeniería Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Tomás Perez-Acle
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile
- Escuela de Ingeniería, Facultad de Ingeniería Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Rodrigo Pacheco
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida Del Valle Norte #725, 8580702, Huechuraba, Santiago, Chile.
- Facultad de Medicina y Ciencia, Universidad San Sebastián, 7510156, Providencia, Santiago, Chile.
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32
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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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33
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Hoffmann MH, Kirchner H, Krönke G, Riemekasten G, Bonelli M. Inflammatory tissue priming: novel insights and therapeutic opportunities for inflammatory rheumatic diseases. Ann Rheum Dis 2024:ard-2023-224092. [PMID: 38702177 DOI: 10.1136/ard-2023-224092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Due to optimised treatment strategies and the availability of new therapies during the last decades, formerly devastating chronic inflammatory diseases such as rheumatoid arthritis or systemic sclerosis (SSc) have become less menacing. However, in many patients, even state-of-the-art treatment cannot induce remission. Moreover, the risk for flares strongly increases once anti-inflammatory therapy is tapered or withdrawn, suggesting that underlying pathological processes remain active even in the absence of overt inflammation. It has become evident that tissues have the ability to remember past encounters with pathogens, wounds and other irritants, and to react more strongly and/or persistently to the next occurrence. This priming of the tissue bears a paramount role in defence from microbes, but on the other hand drives inflammatory pathologies (the Dr Jekyll and Mr Hyde aspect of tissue adaptation). Emerging evidence suggests that long-lived tissue-resident cells, such as fibroblasts, macrophages, long-lived plasma cells and tissue-resident memory T cells, determine inflammatory tissue priming in an interplay with infiltrating immune cells of lymphoid and myeloid origin, and with systemically acting factors such as cytokines, extracellular vesicles and antibodies. Here, we review the current state of science on inflammatory tissue priming, focusing on tissue-resident and tissue-occupying cells in arthritis and SSc, and reflect on the most promising treatment options targeting the maladapted tissue response during these diseases.
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Affiliation(s)
| | - Henriette Kirchner
- Institute for Human Genetics, Epigenetics and Metabolism Lab, University of Lübeck, Lübeck, Germany
| | - Gerhard Krönke
- Department of Rheumatology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Gabriela Riemekasten
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
| | - Michael Bonelli
- Division of Rheumatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Vienna, Austria
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34
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Yu M, Shi Y, Gao Y, Luo Y, Jin Y, Liang X, Tao Z, Zhu G, Lin H, Li H, Qin J, Cao Z, Zhong M. Targeting AQP9 enhanced the anti-TNF therapy response in Crohn's disease by inhibiting LPA-hippo pathway. Pharmacol Res 2024; 203:107172. [PMID: 38583685 DOI: 10.1016/j.phrs.2024.107172] [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: 12/13/2023] [Revised: 03/15/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Although anti-TNF antibodies are extensively used to treat Crohn's disease (CD), a significant proportion of patients, up to 40%, exhibit an inadequate response to this therapy. Our objective was to identify potential targets that could improve the effectiveness of anti-TNF therapy in CD. Through the integration and analysis of transcriptomic data from various CD databases, we found that the expression of AQP9 was significantly increased in anti-TNF therapy-resistant specimens. The response to anti-TNF therapy in the CD mouse model was significantly enhanced by specifically inhibiting AQP9. Further experiments found that the blockade of AQP9, which is dominantly expressed in macrophages, decreased inflamed macrophage functions and cytokine expression. Mechanistic studies revealed that AQP9 transported glycerol into macrophages, where it was metabolized to LPA, which was further metabolized to LPA, resulting in the activation of the LPAR2 receptor and downstream hippo pathway, finally promoting the expression of cytokines, especially IL23 and IL1β⊡ Taken together, the expansion of AQP9+ macrophages is associated with resistance to anti-TNF therapy in Crohn's disease. These findings indicated that AQP9 could be a potential target for enhancing anti-TNF therapy in Crohn's disease.
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Affiliation(s)
- Minhao Yu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuan Shi
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuan Gao
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yang Luo
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yihua Jin
- School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Xiaoyi Liang
- School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Zhuoran Tao
- School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Guojun Zhu
- School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Haiping Lin
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Hao Li
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jun Qin
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Zhijun Cao
- Division of Gastroenterology and Hepatology; Shanghai Institute of Digestive Disease; NHC Key Laboratory of Digestive Diseases;Renji Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Ming Zhong
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
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35
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Rodríguez-Moranta F, Argüelles-Arias F, Hinojosa Del Val J, Iborra Colomino M, Martín-Arranz MD, Menchén Viso L, Muñoz Núñez F, Ricart Gómez E, Sánchez-Hernández JG, Valdés-Delgado T, Guardiola Capón J, Barreiro-de Acosta M, Mañosa Ciria M, Zabana Abdo Y, Gutiérrez Casbas A. Therapeutic drug monitoring in inflammatory bowel diseases. Position statement of the Spanish Working Group on Crohn's Disease and Ulcerative Colitis. GASTROENTEROLOGIA Y HEPATOLOGIA 2024; 47:522-552. [PMID: 38311005 DOI: 10.1016/j.gastrohep.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/31/2023] [Accepted: 01/18/2024] [Indexed: 02/06/2024]
Abstract
The treatment of inflammatory bowel disease has undergone a significant transformation following the introduction of biologic drugs. Thanks to these drugs, treatment goals have evolved from clinical response and remission to more ambitious objectives, such as endoscopic or radiologic remission. However, even though biologics are highly effective, a significant percentage of patients will not achieve an initial response or may lose it over time. We know that there is a direct relationship between the trough concentrations of the biologic and its therapeutic efficacy, with more demanding therapeutic goals requiring higher drug levels, and inadequate exposure being common. Therapeutic drug monitoring of biologic medications, along with pharmacokinetic models, provides us with the possibility of offering a personalized approach to treatment for patients with IBD. Over the past few years, relevant information has accumulated regarding its utility during or after induction, as well as in the maintenance of biologic treatment, in reactive or proactive strategies, and prior to withdrawal or treatment de-escalation. The aim of this document is to establish recommendations regarding the utility of therapeutic drug monitoring of biologics in patients with inflammatory bowel disease, in different clinical practice scenarios, and to identify areas where its utility is evident, promising, or controversial.
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Affiliation(s)
- Francisco Rodríguez-Moranta
- Servicio de Aparato Digestivo, Hospital Universitario de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, España.
| | - Federico Argüelles-Arias
- Servicio de Aparato Digestivo, Hospital Universitario Virgen Macarena, Sevilla, España; Facultad de Medicina, Universidad de Sevilla, Sevilla, España
| | | | - Marisa Iborra Colomino
- Servicio de Aparato Digestivo, Hospital Universitario y Politécnico de La Fe, Valencia, España
| | - M Dolores Martín-Arranz
- Servicio de Aparato Digestivo, Hospital Universitario La Paz, Facultad de Medicina de la UAM, Fundación para la investigación del Hospital Universitario la Paz (IDIPAZ), Madrid, España
| | - Luis Menchén Viso
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón-IiSGM, Madrid, España; Departamento de Medicina, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, España
| | - Fernando Muñoz Núñez
- Servicio de Aparato Digestivo, Hospital Universitario de Salamanca, Salamanca, España
| | - Elena Ricart Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), H. Clínic Barcelona, Barcelona, IDIBAPS, Barcelona, España
| | | | - Teresa Valdés-Delgado
- Servicio de Aparato Digestivo, Hospital Universitario Virgen Macarena, Sevilla, España
| | - Jordi Guardiola Capón
- Servicio de Gastroenterología, Hospital Universitario de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, España
| | - Manuel Barreiro-de Acosta
- Servicio de Gastroenterología, Hospital Clínico Universitario de Santiago, A Coruña, España; Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), A Coruña, España
| | - Míriam Mañosa Ciria
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, España; Unidad de Enfermedad Inflamatoria Intestinal, Servicio de Gastroenterología, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, España
| | - Yamile Zabana Abdo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, España; Unidad de Enfermedad Inflamatoria Intestinal, Servicio de Gastroenterología, Hospital Mútua de Terrassa (HMT), Terrassa, Barcelona, España
| | - Ana Gutiérrez Casbas
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, España; Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, España
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Bamidele AO, Mishra SK, Piovezani Ramos G, Hirsova P, Klatt EE, Abdelrahman LM, Sagstetter MR, Davidson HM, Fehrenbach PJ, Valenzuela-Pérez L, Kim Lee HS, Zhang S, Aguirre Lopez A, Kurdi AT, Westphal MS, Gonzalez MM, Gaballa JM, Kosinsky RL, Lee HE, Smyrk TC, Bantug G, Gades NM, Faubion WA. Interleukin 21 Drives a Hypermetabolic State and CD4 + T-Cell-Associated Pathogenicity in Chronic Intestinal Inflammation. Gastroenterology 2024; 166:826-841.e19. [PMID: 38266738 PMCID: PMC11034723 DOI: 10.1053/j.gastro.2024.01.026] [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: 04/09/2023] [Revised: 11/23/2023] [Accepted: 01/15/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND & AIMS Incapacitated regulatory T cells (Tregs) contribute to immune-mediated diseases. Inflammatory Tregs are evident during human inflammatory bowel disease; however, mechanisms driving the development of these cells and their function are not well understood. Therefore, we investigated the role of cellular metabolism in Tregs relevant to gut homeostasis. METHODS Using human Tregs, we performed mitochondrial ultrastructural studies via electron microscopy and confocal imaging, biochemical and protein analyses using proximity ligation assay, immunoblotting, mass cytometry and fluorescence-activated cell sorting, metabolomics, gene expression analysis, and real-time metabolic profiling utilizing the Seahorse XF analyzer. We used a Crohn's disease single-cell RNA sequencing dataset to infer the therapeutic relevance of targeting metabolic pathways in inflammatory Tregs. We examined the superior functionality of genetically modified Tregs in CD4+ T-cell-induced murine colitis models. RESULTS Mitochondria-endoplasmic reticulum appositions, known to mediate pyruvate entry into mitochondria via voltage-dependent anion channel 1 (VDAC1), are abundant in Tregs. VDAC1 inhibition perturbed pyruvate metabolism, eliciting sensitization to other inflammatory signals reversible by membrane-permeable methyl pyruvate supplementation. Notably, interleukin (IL) 21 diminished mitochondria-endoplasmic reticulum appositions, resulting in enhanced enzymatic function of glycogen synthase kinase 3 β, a putative negative regulator of VDAC1, and a hypermetabolic state that amplified Treg inflammatory response. Methyl pyruvate and glycogen synthase kinase 3 β pharmacologic inhibitor (LY2090314) reversed IL21-induced metabolic rewiring and inflammatory state. Moreover, IL21-induced metabolic genes in Tregs in vitro were enriched in human Crohn's disease intestinal Tregs. Adoptively transferred Il21r-/- Tregs efficiently rescued murine colitis in contrast to wild-type Tregs. CONCLUSIONS IL21 triggers metabolic dysfunction associated with Treg inflammatory response. Inhibiting IL21-induced metabolism in Tregs may mitigate CD4+ T-cell-driven chronic intestinal inflammation.
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Affiliation(s)
- Adebowale O Bamidele
- Immunometabolism and Mucosal Immunity Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Immunology, Mayo Clinic, Rochester, Minnesota.
| | - Shravan K Mishra
- Immunometabolism and Mucosal Immunity Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Petra Hirsova
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Emily E Klatt
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - Leena M Abdelrahman
- Immunometabolism and Mucosal Immunity Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Mary R Sagstetter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Heidi M Davidson
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Patrick J Fehrenbach
- Immunometabolism and Mucosal Immunity Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Hyun Se Kim Lee
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Song Zhang
- Mayo Clinic Metabolomics Core, Mayo Clinic, Rochester, Minnesota; Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Abner Aguirre Lopez
- Immunometabolism and Mucosal Immunity Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Ahmed T Kurdi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Maria S Westphal
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Michelle M Gonzalez
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Joseph M Gaballa
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Hee Eun Lee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Thomas C Smyrk
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Glenn Bantug
- Immunobiology Laboratory, Department of Biomedicine, University Hospital of Basel, Basel, Switzerland
| | - Naomi M Gades
- Department of Comparative Medicine, Mayo Clinic, Scottsdale, Arizona
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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Karabayas M, Ibrahim HE, Roelofs AJ, Reynolds G, Kidder D, De Bari C. Vascular disease persistence in giant cell arteritis: are stromal cells neglected? Ann Rheum Dis 2024:ard-2023-225270. [PMID: 38684323 DOI: 10.1136/ard-2023-225270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 04/05/2024] [Indexed: 05/02/2024]
Abstract
Giant cell arteritis (GCA), the most common systemic vasculitis, is characterised by aberrant interactions between infiltrating and resident cells of the vessel wall. Ageing and breach of tolerance are prerequisites for GCA development, resulting in dendritic and T-cell dysfunction. Inflammatory cytokines polarise T-cells, activate resident macrophages and synergistically enhance vascular inflammation, providing a loop of autoreactivity. These events originate in the adventitia, commonly regarded as the biological epicentre of the vessel wall, with additional recruitment of cells that infiltrate and migrate towards the intima. Thus, GCA-vessels exhibit infiltrates across the vascular layers, with various cytokines and growth factors amplifying the pathogenic process. These events activate ineffective repair mechanisms, where dysfunctional vascular smooth muscle cells and fibroblasts phenotypically shift along their lineage and colonise the intima. While high-dose glucocorticoids broadly suppress these inflammatory events, they cause well known deleterious effects. Despite the emerging targeted therapeutics, disease relapse remains common, affecting >50% of patients. This may reflect a discrepancy between systemic and local mediators of inflammation. Indeed, temporal arteries and aortas of GCA-patients can show immune-mediated abnormalities, despite the treatment induced clinical remission. The mechanisms of persistence of vascular disease in GCA remain elusive. Studies in other chronic inflammatory diseases point to the fibroblasts (and their lineage cells including myofibroblasts) as possible orchestrators or even effectors of disease chronicity through interactions with immune cells. Here, we critically review the contribution of immune and stromal cells to GCA pathogenesis and analyse the molecular mechanisms by which these would underpin the persistence of vascular disease.
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Affiliation(s)
- Maira Karabayas
- Centre for Arthritis and Musculoskeletal Health, University of Aberdeen, Aberdeen, UK
| | - Hafeez E Ibrahim
- Centre for Arthritis and Musculoskeletal Health, University of Aberdeen, Aberdeen, UK
| | - Anke J Roelofs
- Centre for Arthritis and Musculoskeletal Health, University of Aberdeen, Aberdeen, UK
| | - Gary Reynolds
- Centre for Immunology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Dana Kidder
- Centre for Arthritis and Musculoskeletal Health, University of Aberdeen, Aberdeen, UK
| | - Cosimo De Bari
- Centre for Arthritis and Musculoskeletal Health, University of Aberdeen, Aberdeen, UK
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38
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He JY, Kim YJ, Mennillo E, Rusu I, Bain J, Rao AA, Andersen C, Law K, Yang H, Tsui J, Shen A, Davidson B, Kushnoor D, Shi Y, Fan F, Cheung A, Zhang L, Fong L, Combes AJ, Pisco AO, Kattah MG, Oh DY. Dysregulation of CD4 + and CD8 + resident memory T, myeloid, and stromal cells in steroid-experienced, checkpoint inhibitor colitis. J Immunother Cancer 2024; 12:e008628. [PMID: 38642938 PMCID: PMC11033653 DOI: 10.1136/jitc-2023-008628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Colitis caused by checkpoint inhibitors (CPI) is frequent and is treated with empiric steroids, but CPI colitis mechanisms in steroid-experienced or refractory disease are unclear. METHODS Using colon biopsies and blood from predominantly steroid-experienced CPI colitis patients, we performed multiplexed single-cell transcriptomics and proteomics to nominate contributing populations. RESULTS CPI colitis biopsies showed enrichment of CD4+resident memory (RM) T cells in addition to CD8+ RM and cytotoxic CD8+ T cells. Matching T cell receptor (TCR) clonotypes suggested that both RMs are progenitors that yield cytotoxic effectors. Activated, CD38+ HLA-DR+ CD4+ RM and cytotoxic CD8+ T cells were enriched in steroid-experienced and a validation data set of steroid-naïve CPI colitis, underscoring their pathogenic potential across steroid exposure. Distinct from ulcerative colitis, CPI colitis exhibited perturbed stromal metabolism (NAD+, tryptophan) impacting epithelial survival and inflammation. Endothelial cells in CPI colitis after anti-TNF and anti-cytotoxic T-lymphocyte-associated antigen 4 (anti-CTLA-4) upregulated the integrin α4β7 ligand molecular vascular addressin cell adhesion molecule 1 (MAdCAM-1), which may preferentially respond to vedolizumab (anti-α4β7). CONCLUSIONS These findings nominate CD4+ RM and MAdCAM-1+ endothelial cells for targeting in specific subsets of CPI colitis patients.
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Affiliation(s)
- Jun Yan He
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Yang-Joon Kim
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Elvira Mennillo
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Iulia Rusu
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jared Bain
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Arjun A Rao
- CoLabs, University of California, San Francisco, San Francisco, California, USA
| | | | - Karen Law
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Hai Yang
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Jessica Tsui
- CoLabs, University of California, San Francisco, San Francisco, California, USA
| | - Alan Shen
- CoLabs, University of California, San Francisco, San Francisco, California, USA
| | - Brittany Davidson
- CoLabs, University of California, San Francisco, San Francisco, California, USA
| | - Divyashree Kushnoor
- CoLabs, University of California, San Francisco, San Francisco, California, USA
| | - Yimin Shi
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Frances Fan
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Alexander Cheung
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Li Zhang
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Lawrence Fong
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Alexis J Combes
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- CoLabs, University of California, San Francisco, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- ImmunoX Initiative, University of California, San Francisco, San Francisco, California, USA
| | | | - Michael G Kattah
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - David Y Oh
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
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Prochera A, Muppirala AN, Kuziel GA, Soualhi S, Shepherd A, Sun L, Issac B, Rosenberg HJ, Karim F, Perez K, Smith KH, Archibald TH, Rakoff-Nahoum S, Hagen SJ, Rao M. Enteric glia regulate Paneth cell secretion and intestinal microbial ecology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589545. [PMID: 38659931 PMCID: PMC11042301 DOI: 10.1101/2024.04.15.589545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Glial cells of the enteric nervous system (ENS) interact closely with the intestinal epithelium and secrete signals that influence epithelial cell proliferation and barrier formation in vitro. Whether these interactions are important in vivo, however, is unclear because previous studies reached conflicting conclusions [1]. To better define the roles of enteric glia in steady state regulation of the intestinal epithelium, we characterized the glia in closest proximity to epithelial cells and found that the majority express PLP1 in both mice and humans. To test their functions using an unbiased approach, we genetically depleted PLP1+ cells in mice and transcriptionally profiled the small and large intestines. Surprisingly, glial loss had minimal effects on transcriptional programs and the few identified changes varied along the gastrointestinal tract. In the ileum, where enteric glia had been considered most essential for epithelial integrity, glial depletion did not drastically alter epithelial gene expression but caused a modest enrichment in signatures of Paneth cells, a secretory cell type important for innate immunity. In the absence of PLP1+ glia, Paneth cell number was intact, but a subset appeared abnormal with irregular and heterogenous cytoplasmic granules, suggesting a secretory deficit. Consistent with this possibility, ileal explants from glial-depleted mice secreted less functional lysozyme than controls with corresponding effects on fecal microbial composition. Collectively, these data suggest that enteric glia do not exert broad effects on the intestinal epithelium but have an essential role in regulating Paneth cell function and gut microbial ecology.
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Affiliation(s)
- Aleksandra Prochera
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Anoohya N Muppirala
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Gavin A Kuziel
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Salima Soualhi
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Amy Shepherd
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Liang Sun
- Research Computing, Department of Information Technology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA
| | - Biju Issac
- Research Computing, Department of Information Technology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA
| | - Harry J Rosenberg
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Farah Karim
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY, USA
| | - Kristina Perez
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Kyle H Smith
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Tonora H Archibald
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Seth Rakoff-Nahoum
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Susan J Hagen
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Meenakshi Rao
- Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
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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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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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Dong Y, Johnson BA, Ruan L, Zeineldin M, Bi T, Liu AZ, Raychaudhuri S, Chiu I, Zhu J, Smith B, Zhao N, Searson P, Watanabe S, Donowitz M, Larman TC, Li R. Disruption of epithelium integrity by inflammation-associated fibroblasts through prostaglandin signaling. SCIENCE ADVANCES 2024; 10:eadj7666. [PMID: 38569041 PMCID: PMC10990275 DOI: 10.1126/sciadv.adj7666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024]
Abstract
Inflammation-associated fibroblasts (IAFs) are associated with progression and drug resistance of chronic inflammatory diseases such as inflammatory bowel disease (IBD), but their direct impact on epithelial cells is unknown. Here, we developed an in vitro model whereby human colon fibroblasts are induced by specific cytokines and recapitulate key features of IAFs in vivo. When cocultured with patient-derived colon organoids (colonoids), IAFs induced rapid colonoid expansion and barrier disruption due to swelling and rupture of individual epithelial cells. Colonoids cocultured with IAFs also show increased DNA damage, mitotic errors, and proliferation arrest. These IAF-induced epithelial defects are mediated by a paracrine pathway involving prostaglandin E2 and its receptor EP4, leading to protein kinase A -dependent activation of the cystic fibrosis transmembrane conductance regulator. EP4-specific chemical inhibitors effectively prevented IAF-induced colonoid swelling and restored normal proliferation and genome stability. These findings reveal a mechanism by which IAFs could promote and perpetuate IBD and suggest a therapeutic avenue to mitigate inflammation-associated epithelial injury.
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Affiliation(s)
- Yi Dong
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Blake A. Johnson
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Linhao Ruan
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Maged Zeineldin
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Tianhao Bi
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Albert Z. Liu
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ian Chiu
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Jin Zhu
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Barbara Smith
- Microscope Facility, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Nan Zhao
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Peter Searson
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Mark Donowitz
- Department of Medicine, Division of Gastroenterology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Tatianna C. Larman
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Rong Li
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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43
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Rieder F, Mukherjee PK, Massey WJ, Wang Y, Fiocchi C. Fibrosis in IBD: from pathogenesis to therapeutic targets. Gut 2024; 73:854-866. [PMID: 38233198 PMCID: PMC10997492 DOI: 10.1136/gutjnl-2023-329963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/29/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Intestinal fibrosis resulting in stricture formation and obstruction in Crohn's disease (CD) and increased wall stiffness leading to symptoms in ulcerative colitis (UC) is among the largest unmet needs in inflammatory bowel disease (IBD). Fibrosis is caused by a multifactorial and complex process involving immune and non-immune cells, their soluble mediators and exposure to luminal contents, such as microbiota and environmental factors. To date, no antifibrotic therapy is available. Some progress has been made in creating consensus definitions and measurements to quantify stricture morphology for clinical practice and trials, but approaches to determine the degree of fibrosis within a stricture are still lacking. OBJECTIVE We herein describe the current state of stricture pathogenesis, measuring tools and clinical trial endpoints development. DESIGN Data presented and discussed in this review derive from the past and recent literature and the authors' own research and experience. RESULTS AND CONCLUSIONS Significant progress has been made in better understanding the pathogenesis of fibrosis, but additional studies and preclinical developments are needed to define specific therapeutic targets.
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Affiliation(s)
- Florian Rieder
- Department of Inflammation and Immunity, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Pranab K Mukherjee
- Department of Inflammation and Immunity, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - William J Massey
- Department of Inflammation and Immunity, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Yan Wang
- Department of Inflammation and Immunity, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Claudio Fiocchi
- Department of Inflammation and Immunity, Cleveland Clinic Foundation, Cleveland, Ohio, USA
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44
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Kosinsky RL, Gonzalez MM, Saul D, Barros LL, Sagstetter MR, Fedyshyn Y, Nair A, Sun Z, Hamdan FH, Gibbons HR, Perez Pachon ME, Druliner BR, Johnsen SA, Faubion WA. The FOXP3 + Pro-Inflammatory T Cell: A Potential Therapeutic Target in Crohn's Disease. Gastroenterology 2024; 166:631-644.e17. [PMID: 38211712 PMCID: PMC10960691 DOI: 10.1053/j.gastro.2024.01.007] [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: 12/01/2022] [Revised: 12/27/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND & AIMS The incidence of Crohn's disease (CD) continues to increase worldwide. The contribution of CD4+ cell populations remains to be elucidated. We aimed to provide an in-depth transcriptional assessment of CD4+ T cells driving chronic inflammation in CD. METHODS We performed single-cell RNA-sequencing in CD4+ T cells isolated from ileal biopsies of patients with CD compared with healthy individuals. Cells underwent clustering analysis, followed by analysis of gene signaling networks. We overlapped our differentially expressed genes with publicly available microarray data sets and performed functional in vitro studies, including an in vitro suppression assay and organoid systems, to model gene expression changes observed in CD regulatory T (Treg) cells and to test predicted therapeutics. RESULTS We identified 5 distinct FOXP3+ regulatory Treg subpopulations. Tregs isolated from healthy controls represent the origin of pseudotemporal development into inflammation-associated subtypes. These proinflammatory Tregs displayed a unique responsiveness to tumor necrosis factor-α signaling with impaired suppressive activity in vitro and an elevated cytokine response in an organoid coculture system. As predicted in silico, the histone deacetylase inhibitor vorinostat normalized gene expression patterns, rescuing the suppressive function of FOXP3+ cells in vitro. CONCLUSIONS We identified a novel, proinflammatory FOXP3+ T cell subpopulation in patients with CD and developed a pipeline to specifically target these cells using the US Food and Drug Administration-approved drug vorinostat.
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Affiliation(s)
- Robyn Laura Kosinsky
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Robert Bosch Center for Tumor Diseases, Stuttgart, Germany
| | - Michelle M Gonzalez
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Dominik Saul
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, Minnesota; Department of Trauma and Reconstructive Surgery, Eberhard Karls University Tübingen, BG Trauma Center, Tübingen, Germany
| | - Luísa Leite Barros
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Gastroenterology, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Mary R Sagstetter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Asha Nair
- Division of Computational Biology, Mayo Clinic, Rochester, Minnesota
| | - Zhifu Sun
- Division of Computational Biology, Mayo Clinic, Rochester, Minnesota
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Hunter R Gibbons
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Brooke R Druliner
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, Arizona.
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45
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Avram V, Yadav S, Sahasrabudhe P, Chang D, Wang J. IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease. Database (Oxford) 2024; 2024:baae026. [PMID: 38564306 PMCID: PMC10986744 DOI: 10.1093/database/baae026] [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: 10/04/2023] [Revised: 01/05/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
Inflammatory Bowel Disease (IBD) therapies are ineffective in at least 40% patients, and transcriptomic datasets have been widely used to reveal the pathogenesis and to identify the novel drug targets for these patients. Although public IBD transcriptomic datasets are available from many web-based tools/databases, due to the unstructured metadata and data description of these public datasets, most of these tools/databases do not allow querying datasets based on multiple keywords (e.g. colon and infliximab). Furthermore, few tools/databases can compare and integrate the datasets from the query results. To fill these gaps, we have developed IBDTransDB (https://abbviegrc.shinyapps.io/ibdtransdb/), a manually curated transcriptomic database for IBD. IBDTransDB includes a manually curated database with 34 transcriptomic datasets (2932 samples, 122 differential comparisons) and a query system supporting 35 keywords from 5 attributes (e.g. tissue and treatment). IBDTransDB also provides three modules for data analyses and integration. IBDExplore allows interactive visualization of differential gene list, pathway enrichment, gene signature and cell deconvolution analyses from a single dataset. IBDCompare supports comparisons of selected genes or pathways from multiple datasets across different conditions. IBDIntegrate performs meta-analysis to prioritize a list of genes/pathways based on user-selected datasets and conditions. Using two case studies related to infliximab treatment, we demonstrated that IBDTransDB provides a unique platform for biologists and clinicians to reveal IBD pathogenesis and identify the novel targets by integrating with other omics data. Database URL: https://abbviegrc.shinyapps.io/ibdtransdb/.
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Affiliation(s)
- Victor Avram
- Genomics Research Center, AbbVie Inc, 200 Sidney Street, Cambridge, MA 02139, USA
| | - Shweta Yadav
- Genomics Research Center, AbbVie Inc, 200 Sidney Street, Cambridge, MA 02139, USA
| | - Pranav Sahasrabudhe
- Genomics Research Center, AbbVie Inc, 200 Sidney Street, Cambridge, MA 02139, USA
| | - Dan Chang
- Genomics Research Center, AbbVie Inc, 200 Sidney Street, Cambridge, MA 02139, USA
| | - Jing Wang
- Genomics Research Center, AbbVie Inc, 200 Sidney Street, Cambridge, MA 02139, USA
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Sekiya T, Hidano S, Takaki S. Tonic TCR and IL-1β signaling mediate phenotypic alterations of naive CD4 + T cells. Cell Rep 2024; 43:113954. [PMID: 38492221 DOI: 10.1016/j.celrep.2024.113954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/06/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
Inert naive CD4+ T (TN) cells differentiate into functional T helper (Th) or regulatory T (Treg) cell subsets upon encountering antigens, mediating properly directed immune responses. Although all TN cells can differentiate into any of the Th and Treg cell subsets, heterogeneity exists among TN cells. By constructing reporter mice to detect ongoing T cell receptor (TCR) signaling, we identify that interleukin (IL)-1β signaling affects TN cell characteristics, independent of tonic TCR signaling, which also alters TN cell phenotypes. IL-1β reversibly attenuates the differentiation potential of TN cells toward Treg cells. IL-1β signaling is elevated in the splenic TN cells, consequently attenuating their differentiation potential toward Treg cells. Aberrant elevation of IL-1β signaling augments colitogenic activities of TN cells. TN cells in patients with colitis exhibited elevated IL-1β signaling. We demonstrate that phenotypic alteration in TN cells by IL-1β is an important mechanism in the regulation of immune responses.
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Affiliation(s)
- Takashi Sekiya
- Section of Immune Response Modification, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan; Department of Immune Regulation, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan.
| | - Shinya Hidano
- Department of Immune Regulation, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan
| | - Satoshi Takaki
- Department of Immune Regulation, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan
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47
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Schäfer S, Smelik M, Sysoev O, Zhao Y, Eklund D, Lilja S, Gustafsson M, Heyn H, Julia A, Kovács IA, Loscalzo J, Marsal S, Zhang H, Li X, Gawel D, Wang H, Benson M. scDrugPrio: a framework for the analysis of single-cell transcriptomics to address multiple problems in precision medicine in immune-mediated inflammatory diseases. Genome Med 2024; 16:42. [PMID: 38509600 PMCID: PMC10956347 DOI: 10.1186/s13073-024-01314-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Ineffective drug treatment is a major problem for many patients with immune-mediated inflammatory diseases (IMIDs). Important reasons are the lack of systematic solutions for drug prioritisation and repurposing based on characterisation of the complex and heterogeneous cellular and molecular changes in IMIDs. METHODS Here, we propose a computational framework, scDrugPrio, which constructs network models of inflammatory disease based on single-cell RNA sequencing (scRNA-seq) data. scDrugPrio constructs detailed network models of inflammatory diseases that integrate information on cell type-specific expression changes, altered cellular crosstalk and pharmacological properties for the selection and ranking of thousands of drugs. RESULTS scDrugPrio was developed using a mouse model of antigen-induced arthritis and validated by improved precision/recall for approved drugs, as well as extensive in vitro, in vivo, and in silico studies of drugs that were predicted, but not approved, for the studied diseases. Next, scDrugPrio was applied to multiple sclerosis, Crohn's disease, and psoriatic arthritis, further supporting scDrugPrio through prioritisation of relevant and approved drugs. However, in contrast to the mouse model of arthritis, great interindividual cellular and gene expression differences were found in patients with the same diagnosis. Such differences could explain why some patients did or did not respond to treatment. This explanation was supported by the application of scDrugPrio to scRNA-seq data from eleven individual Crohn's disease patients. The analysis showed great variations in drug predictions between patients, for example, assigning a high rank to anti-TNF treatment in a responder and a low rank in a nonresponder to that treatment. CONCLUSIONS We propose a computational framework, scDrugPrio, for drug prioritisation based on scRNA-seq of IMID disease. Application to individual patients indicates scDrugPrio's potential for personalised network-based drug screening on cellulome-, genome-, and drugome-wide scales. For this purpose, we made scDrugPrio into an easy-to-use R package ( https://github.com/SDTC-CPMed/scDrugPrio ).
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Affiliation(s)
- Samuel Schäfer
- Centre for Personalised Medicine, Linköping University, Linköping, Sweden
- Department of Gastroenterology and Hepatology, University Hospital, Linköping, Sweden
| | - Martin Smelik
- Postal Address: LIME/Medical Digital Twin Research Group, Division of ENT, CLINTEC, Karolinska Institute, Tomtebodavägen 18A. 171 65 Solna, Stockholm, Sweden
| | - Oleg Sysoev
- Division of Statistics and Machine Learning, Department of Computer and Information Science, Linkoping University, Linköping, Sweden
| | - Yelin Zhao
- Postal Address: LIME/Medical Digital Twin Research Group, Division of ENT, CLINTEC, Karolinska Institute, Tomtebodavägen 18A. 171 65 Solna, Stockholm, Sweden
| | - Desiré Eklund
- Centre for Personalised Medicine, Linköping University, Linköping, Sweden
| | - Sandra Lilja
- Centre for Personalised Medicine, Linköping University, Linköping, Sweden
- Mavatar, Inc, Stockholm, Sweden
| | - Mika Gustafsson
- Division for Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Antonio Julia
- Grup de Recerca de Reumatologia, Institut de Recerca Vall d'Hebron, Barcelona, Spain
| | - István A Kovács
- Department of Physics and Astronomy, Northwestern University, Evanston, IL, 60208, USA
- Northwestern Institute On Complex Systems, Northwestern University, Evanston, IL, 60208, USA
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Marsal
- Grup de Recerca de Reumatologia, Institut de Recerca Vall d'Hebron, Barcelona, Spain
| | - Huan Zhang
- Centre for Personalised Medicine, Linköping University, Linköping, Sweden
| | - Xinxiu Li
- Postal Address: LIME/Medical Digital Twin Research Group, Division of ENT, CLINTEC, Karolinska Institute, Tomtebodavägen 18A. 171 65 Solna, Stockholm, Sweden
| | | | - Hui Wang
- Postal Address: LIME/Medical Digital Twin Research Group, Division of ENT, CLINTEC, Karolinska Institute, Tomtebodavägen 18A. 171 65 Solna, Stockholm, Sweden
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Jiangsu, China
| | - Mikael Benson
- Postal Address: LIME/Medical Digital Twin Research Group, Division of ENT, CLINTEC, Karolinska Institute, Tomtebodavägen 18A. 171 65 Solna, Stockholm, Sweden.
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48
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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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49
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Ciavattone NG, Guan N, Farfel A, Stauff J, Desmond T, Viglianti BL, Scott PJ, Brooks AF, Luker GD. Evaluating immunotherapeutic outcomes in triple-negative breast cancer with a cholesterol radiotracer in mice. JCI Insight 2024; 9:e175320. [PMID: 38502228 PMCID: PMC11141879 DOI: 10.1172/jci.insight.175320] [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: 08/31/2023] [Accepted: 03/13/2024] [Indexed: 03/21/2024] Open
Abstract
Evaluating the response to immune checkpoint inhibitors (ICIs) remains an unmet challenge in triple-negative breast cancer (TNBC). The requirement for cholesterol in the activation and function of T cells led us to hypothesize that quantifying cellular accumulation of this molecule could distinguish successful from ineffective checkpoint immunotherapy. To analyze accumulation of cholesterol by T cells in the immune microenvironment of breast cancer, we leveraged the PET radiotracer, eFNP-59. eFNP-59 is an analog of cholesterol that our group validated as an imaging biomarker for cholesterol uptake in preclinical models and initial human studies. In immunocompetent mouse models of TNBC, we found that elevated uptake of exogenous labeled cholesterol analogs functions as a marker for T cell activation. When comparing ICI-responsive and -nonresponsive tumors directly, uptake of fluorescent cholesterol and eFNP-59 increased in T cells from ICI-responsive tumors. We discovered that accumulation of cholesterol by T cells increased in ICI-responding tumors that received anti-PD-1 checkpoint immunotherapy. In patients with TNBC, tumors containing cycling T cells had features of cholesterol uptake and trafficking within those populations. These results suggest that uptake of exogenous cholesterol analogs by tumor-infiltrating T cells allows detection of T cell activation and has potential to assess the success of ICI therapy.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Gary D Luker
- Department of Radiology, and
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
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50
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Chikkamenahalli LL, Jessen E, Bernard CE, Ip WE, Breen-Lyles M, Cipriani G, Pullapantula SR, Li Y, AlAsfoor S, Wilson L, Koch KL, Kuo B, Shulman RJ, Chumpitazi BP, McKenzie TJ, Kellogg TA, Tonascia J, Hamilton FA, Sarosiek I, McCallum R, Parkman HP, Pasricha PJ, Abell TL, Farrugia G, Dasari S, Grover M. Single cell atlas of human gastric muscle immune cells and macrophage-driven changes in idiopathic gastroparesis. iScience 2024; 27:108991. [PMID: 38384852 PMCID: PMC10879712 DOI: 10.1016/j.isci.2024.108991] [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: 05/01/2023] [Revised: 11/17/2023] [Accepted: 01/17/2024] [Indexed: 02/23/2024] Open
Abstract
Gastrointestinal immune cells, particularly muscularis macrophages (MM) interact with the enteric nervous system and influence gastrointestinal motility. Here we determine the human gastric muscle immunome and its changes in patients with idiopathic gastroparesis (IG). Single cell sequencing was performed on 26,000 CD45+ cells obtained from the gastric tissue of 20 subjects. We demonstrate 11 immune cell clusters with T cells being most abundant followed by myeloid cells. The proportions of cells belonging to the 11 clusters were similar between IG and controls. However, 9/11 clusters showed 578-11,429 differentially expressed genes. In IG, MM had decreased expression of tissue-protective and microglial genes and increased the expression of monocyte trafficking and stromal activating genes. Furthermore, in IG, IL12 mediated JAK-STAT signaling involved in the activation of tissue-resident macrophages and Eph-ephrin signaling involved in monocyte chemotaxis were upregulated. Patients with IG had a greater abundance of monocyte-like cells. These data further link immune dysregulation to the pathophysiology of gastroparesis.
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Affiliation(s)
| | - Erik Jessen
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Cheryl E. Bernard
- Division of Gastroenterology and Hepatology, Enteric Neuroscience Program, Mayo Clinic, Rochester, MN, USA
| | - W.K. Eddie Ip
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Margaret Breen-Lyles
- Division of Gastroenterology and Hepatology, Enteric Neuroscience Program, Mayo Clinic, Rochester, MN, USA
| | - Gianluca Cipriani
- Division of Gastroenterology and Hepatology, Enteric Neuroscience Program, Mayo Clinic, Rochester, MN, USA
| | - Suraj R. Pullapantula
- Division of Gastroenterology and Hepatology, Enteric Neuroscience Program, Mayo Clinic, Rochester, MN, USA
| | - Ying Li
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Shefaa AlAsfoor
- Division of Gastroenterology and Hepatology, Enteric Neuroscience Program, Mayo Clinic, Rochester, MN, USA
| | - Laura Wilson
- Johns Hopkins University Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | - Braden Kuo
- Massachusetts General Hospital, Boston, MA, USA
| | | | | | | | | | - James Tonascia
- Johns Hopkins University Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Frank A. Hamilton
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Irene Sarosiek
- Texas Tech University Health Sciences Center, El Paso, TX, USA
| | | | | | | | | | - Gianrico Farrugia
- Division of Gastroenterology and Hepatology, Enteric Neuroscience Program, Mayo Clinic, Rochester, MN, USA
| | - Surendra Dasari
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Madhusudan Grover
- Division of Gastroenterology and Hepatology, Enteric Neuroscience Program, Mayo Clinic, Rochester, MN, USA
| | - the NIDDK Gastroparesis Clinical Research Consortium (GpCRC)
- Division of Gastroenterology and Hepatology, Enteric Neuroscience Program, Mayo Clinic, Rochester, MN, USA
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
- Johns Hopkins University Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Wake Forest University, Winston-Salem, NC, USA
- Massachusetts General Hospital, Boston, MA, USA
- Baylor College of Medicine, Houston, TX, USA
- Duke University, Durham, NC, USA
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
- Texas Tech University Health Sciences Center, El Paso, TX, USA
- Temple University, Philadelphia, PA, USA
- Mayo Clinic, Scottsdale, AZ, USA
- University of Louisville, Louisville, KY, USA
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