101
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Mehandru S, Colombel JF, Juarez J, Bugni J, Lindsay JO. Understanding the molecular mechanisms of anti-trafficking therapies and their clinical relevance in inflammatory bowel disease. Mucosal Immunol 2023; 16:859-870. [PMID: 37574127 PMCID: PMC11141405 DOI: 10.1016/j.mucimm.2023.08.001] [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: 07/27/2023] [Accepted: 08/06/2023] [Indexed: 08/15/2023]
Abstract
In patients with inflammatory bowel disease (IBD), a combination of dysbiosis, increased intestinal permeability, and insufficient regulatory responses facilitate the development of chronic inflammation, which is driven by a complex interplay between the mucosal immune system and the environment and sustained by immune priming and ongoing cellular recruitment to the gut. The localization of immune cells is mediated by their expression of chemokine receptors and integrins, which bind to chemokines and adhesion molecules, respectively. In this article, we review the mechanisms of action of anti-trafficking therapies for IBD and consider clinical observations in the context of the different mechanisms of action. Furthermore, we discuss the evolution of molecular resistance to anti-cytokines, in which the composition of immune cells in the gut changes in response to treatment, and the potential implications of this for treatment sequencing. Lastly, we discuss the relevance of mechanism of action to combination therapy for IBD.
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Affiliation(s)
- Saurabh Mehandru
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Jean-Frederic Colombel
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Julius Juarez
- Takeda Pharmaceuticals U.S.A., Inc., Lexington, MA, USA
| | - James Bugni
- Takeda Pharmaceuticals U.S.A., Inc., Lexington, MA, USA
| | - James O Lindsay
- Blizard Institute, Barts and The London School of Medicine and Dentistry, London, UK; Department of Gastroenterology, Royal London Hospital, Barts Health NHS Trust, London, UK
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102
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Shao TY, Jiang TT, Stevens J, Russi AE, Troutman TD, Bernieh A, Pham G, Erickson JJ, Eshleman EM, Alenghat T, Jameson SC, Hogquist KA, Weaver CT, Haslam DB, Deshmukh H, Way SS. Kruppel-like factor 2+ CD4 T cells avert microbiota-induced intestinal inflammation. Cell Rep 2023; 42:113323. [PMID: 37889750 PMCID: PMC10822050 DOI: 10.1016/j.celrep.2023.113323] [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: 12/12/2022] [Revised: 09/05/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Intestinal colonization by antigenically foreign microbes necessitates expanded peripheral immune tolerance. Here we show commensal microbiota prime expansion of CD4 T cells unified by the Kruppel-like factor 2 (KLF2) transcriptional regulator and an essential role for KLF2+ CD4 cells in averting microbiota-driven intestinal inflammation. CD4 cells with commensal specificity in secondary lymphoid organs and intestinal tissues are enriched for KLF2 expression, and distinct from FOXP3+ regulatory T cells or other differentiation lineages. Mice with conditional KLF2 deficiency in T cells develop spontaneous rectal prolapse and intestinal inflammation, phenotypes overturned by eliminating microbiota or reconstituting with donor KLF2+ cells. Activated KLF2+ cells selectively produce IL-10, and eliminating IL-10 overrides their suppressive function in vitro and protection against intestinal inflammation in vivo. Together with reduced KLF2+ CD4 cell accumulation in Crohn's disease, a necessity for the KLF2+ subpopulation of T regulatory type 1 (Tr1) cells in sustaining commensal tolerance is demonstrated.
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Affiliation(s)
- Tzu-Yu Shao
- Division of Infectious Diseases, Center for Inflammation and Tolerance, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Tony T Jiang
- Division of Infectious Diseases, Center for Inflammation and Tolerance, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Joseph Stevens
- Division of Neonatology and Pulmonary Biology, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Abigail E Russi
- Division of Gastroenterology, Hepatology and Advanced Nutrition, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Ty D Troutman
- Division of Allergy and Immunology, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Anas Bernieh
- Division of Pathology, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Giang Pham
- Division of Infectious Diseases, Center for Inflammation and Tolerance, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - John J Erickson
- Division of Neonatology and Pulmonary Biology, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Emily M Eshleman
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Theresa Alenghat
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Stephen C Jameson
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Kristin A Hogquist
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Casey T Weaver
- Program in Immunology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35233, USA
| | - David B Haslam
- Division of Infectious Diseases, Center for Inflammation and Tolerance, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Hitesh Deshmukh
- Division of Neonatology and Pulmonary Biology, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Sing Sing Way
- Division of Infectious Diseases, Center for Inflammation and Tolerance, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA.
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103
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Handler K, Bach K, Borrelli C, Piscuoglio S, Ficht X, Acar IE, Moor AE. Fragment-sequencing unveils local tissue microenvironments at single-cell resolution. Nat Commun 2023; 14:7775. [PMID: 38012149 PMCID: PMC10681997 DOI: 10.1038/s41467-023-43005-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/27/2023] [Indexed: 11/29/2023] Open
Abstract
Cells collectively determine biological functions by communicating with each other-both through direct physical contact and secreted factors. Consequently, the local microenvironment of a cell influences its behavior, gene expression, and cellular crosstalk. Disruption of this microenvironment causes reciprocal changes in those features, which can lead to the development and progression of diseases. Hence, assessing the cellular transcriptome while simultaneously capturing the spatial relationships of cells within a tissue provides highly valuable insights into how cells communicate in health and disease. Yet, methods to probe the transcriptome often fail to preserve native spatial relationships, lack single-cell resolution, or are highly limited in throughput, i.e. lack the capacity to assess multiple environments simultaneously. Here, we introduce fragment-sequencing (fragment-seq), a method that enables the characterization of single-cell transcriptomes within multiple spatially distinct tissue microenvironments. We apply fragment-seq to a murine model of the metastatic liver to study liver zonation and the metastatic niche. This analysis reveals zonated genes and ligand-receptor interactions enriched in specific hepatic microenvironments. Finally, we apply fragment-seq to other tissues and species, demonstrating the adaptability of our method.
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Affiliation(s)
- Kristina Handler
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056, Basel, Switzerland
| | - Karsten Bach
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056, Basel, Switzerland
| | - Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056, Basel, Switzerland
| | - Salvatore Piscuoglio
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Xenia Ficht
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056, Basel, Switzerland
| | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056, Basel, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056, Basel, Switzerland.
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104
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Sun Z, Braga-Neto MB, Xiong Y, Bhagwate AV, Gibbons HR, Sagstetter MR, Hamdan FH, Baheti S, Friton J, Nair A, Ye Z, Faubion WA. Hypomethylation and Overexpression of Th17-Associated Genes is a Hallmark of Intestinal CD4+ Lymphocytes in Crohn's Disease. J Crohns Colitis 2023; 17:1847-1857. [PMID: 37280154 PMCID: PMC10673812 DOI: 10.1093/ecco-jcc/jjad093] [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: 12/15/2022] [Revised: 04/14/2023] [Accepted: 06/06/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND The development of Crohn's disease [CD] involves immune cell signalling pathways regulated by epigenetic modifications. Aberrant DNA methylation has been identified in peripheral blood and bulk intestinal tissue from CD patients. However, the DNA methylome of disease-associated intestinal CD4+ lymphocytes has not been evaluated. MATERIALS AND METHODS Genome-wide DNA methylation sequencing was performed from terminal ileum CD4+ cells from 21 CD patients and 12 age- and sex-matched controls. Data were analysed for differentially methylated CpGs [DMCs] and methylated regions [DMRs]. Integration was performed with RNA-sequencing data to evaluate the functional impact of DNA methylation changes on gene expression. DMRs were overlapped with regions of differentially open chromatin [by ATAC-seq] and CCCTC-binding factor [CTCF] binding sites [by ChIP-seq] between peripherally derived Th17 and Treg cells. RESULTS CD4+ cells in CD patients had significantly increased DNA methylation compared to those from the controls. A total of 119 051 DMCs and 8113 DMRs were detected. While hypermethylated genes were mostly related to cell metabolism and homeostasis, hypomethylated genes were significantly enriched within the Th17 signalling pathway. The differentially enriched ATAC regions in Th17 cells [compared to Tregs] were hypomethylated in CD patients, suggesting heightened Th17 activity. There was significant overlap between hypomethylated DNA regions and CTCF-associated binding sites. CONCLUSIONS The methylome of CD patients shows an overall dominant hypermethylation yet hypomethylation is more concentrated in proinflammatory pathways, including Th17 differentiation. Hypomethylation of Th17-related genes associated with areas of open chromatin and CTCF binding sites constitutes a hallmark of CD-associated intestinal CD4+ cells.
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Affiliation(s)
- Zhifu Sun
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Manuel B Braga-Neto
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuning Xiong
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Adytia V Bhagwate
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Hunter R Gibbons
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Mary R Sagstetter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Saurabh Baheti
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jessica Friton
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Asha Nair
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenqing Ye
- Greehey Children’s Cancer Research Institute, UT Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
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105
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Fan Z, Sun J, Thorpe H, Lee S, Kim S, Park HJ. Deep neural network learning biological condition information refines gene-expression-based cell subtypes. Brief Bioinform 2023; 25:bbad512. [PMID: 38233089 PMCID: PMC10794113 DOI: 10.1093/bib/bbad512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/18/2023] [Accepted: 12/05/2023] [Indexed: 01/19/2024] Open
Abstract
With the recent advent of single-cell level biological understanding, a growing interest is in identifying cell states or subtypes that are homogeneous in terms of gene expression and are also enriched in certain biological conditions, including disease samples versus normal samples (condition-specific cell subtype). Despite the importance of identifying condition-specific cell subtypes, existing methods have the following limitations: since they train models separately between gene expression and the biological condition information, (1) they do not consider potential interactions between them, and (2) the weights from both types of information are not properly controlled. Also, (3) they do not consider non-linear relationships in the gene expression and the biological condition. To address the limitations and accurately identify such condition-specific cell subtypes, we develop scDeepJointClust, the first method that jointly trains both types of information via a deep neural network. scDeepJointClust incorporates results from the power of state-of-the-art gene-expression-based clustering methods as an input, incorporating their sophistication and accuracy. We evaluated scDeepJointClust on both simulation data in diverse scenarios and biological data of different diseases (melanoma and non-small-cell lung cancer) and showed that scDeepJointClust outperforms existing methods in terms of sensitivity and specificity. scDeepJointClust exhibits significant promise in advancing our understanding of cellular states and their implications in complex biological systems.
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Affiliation(s)
- Zhenjiang Fan
- Department of Computer Science, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Jie Sun
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Henry Thorpe
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Stephen Lee
- Department of Computer Science, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Soyeon Kim
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hyun Jung Park
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
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106
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Hu Y, Hu Q, Li Y, Lu L, Xiang Z, Yin Z, Kabelitz D, Wu Y. γδ T cells: origin and fate, subsets, diseases and immunotherapy. Signal Transduct Target Ther 2023; 8:434. [PMID: 37989744 PMCID: PMC10663641 DOI: 10.1038/s41392-023-01653-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 11/23/2023] Open
Abstract
The intricacy of diseases, shaped by intrinsic processes like immune system exhaustion and hyperactivation, highlights the potential of immune renormalization as a promising strategy in disease treatment. In recent years, our primary focus has centered on γδ T cell-based immunotherapy, particularly pioneering the use of allogeneic Vδ2+ γδ T cells for treating late-stage solid tumors and tuberculosis patients. However, we recognize untapped potential and optimization opportunities to fully harness γδ T cell effector functions in immunotherapy. This review aims to thoroughly examine γδ T cell immunology and its role in diseases. Initially, we elucidate functional differences between γδ T cells and their αβ T cell counterparts. We also provide an overview of major milestones in γδ T cell research since their discovery in 1984. Furthermore, we delve into the intricate biological processes governing their origin, development, fate decisions, and T cell receptor (TCR) rearrangement within the thymus. By examining the mechanisms underlying the anti-tumor functions of distinct γδ T cell subtypes based on γδTCR structure or cytokine release, we emphasize the importance of accurate subtyping in understanding γδ T cell function. We also explore the microenvironment-dependent functions of γδ T cell subsets, particularly in infectious diseases, autoimmune conditions, hematological malignancies, and solid tumors. Finally, we propose future strategies for utilizing allogeneic γδ T cells in tumor immunotherapy. Through this comprehensive review, we aim to provide readers with a holistic understanding of the molecular fundamentals and translational research frontiers of γδ T cells, ultimately contributing to further advancements in harnessing the therapeutic potential of γδ T cells.
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Affiliation(s)
- Yi Hu
- Microbiology and Immunology Department, School of Medicine, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Qinglin Hu
- Microbiology and Immunology Department, School of Medicine, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, 510632, China
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, 519000, China
| | - Yongsheng Li
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Ligong Lu
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, 519000, China
| | - Zheng Xiang
- Microbiology and Immunology Department, School of Medicine, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Zhinan Yin
- Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong, 510632, China.
| | - Dieter Kabelitz
- Institute of Immunology, Christian-Albrechts-University Kiel, Kiel, Germany.
| | - Yangzhe Wu
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, 519000, China.
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107
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566249. [PMID: 38014022 PMCID: PMC10680570 DOI: 10.1101/2023.11.08.566249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
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. Conclusion 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
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
- Division of ENT, CLINTEC, Karolinska Institute, Stockholm, Sweden
| | - Oleg Sysoev
- Division of Statistics and Machine Learning, Department of Computer and Information Science, Linkoping University; Linköping, Sweden
| | - Yelin Zhao
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
- Division of ENT, CLINTEC, Karolinska Institute, 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, España
| | - 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, España
| | - Huan Zhang
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
| | - Xinxiu Li
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
- Division of ENT, CLINTEC, Karolinska Institute, Stockholm, Sweden
| | - Danuta Gawel
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
- Mavatar, Inc., Stockholm. Sweden
| | - Hui Wang
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
| | - Mikael Benson
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
- Division of ENT, CLINTEC, Karolinska Institute, Stockholm, Sweden
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108
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Van den Bossche J. Colonic macrophages eat and feed. Cell Metab 2023; 35:1847-1848. [PMID: 37939654 DOI: 10.1016/j.cmet.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023]
Abstract
Macrophages not only secure host defense via phagocytosis but also play a key role in tissue homeostasis. A comprehensive study by Fritsch et al. reveals a novel mechanism by which macrophages in the colon deliver polyamines to epithelial cells to support self-renewal of the epithelium during periods of high proliferation.
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Affiliation(s)
- Jan Van den Bossche
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
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109
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Fritsch SD, Sukhbaatar N, Gonzales K, Sahu A, Tran L, Vogel A, Mazic M, Wilson JL, Forisch S, Mayr H, Oberle R, Weiszmann J, Brenner M, Vanhoutte R, Hofmann M, Pirnes-Karhu S, Magnes C, Kühnast T, Weckwerth W, Bock C, Klavins K, Hengstschläger M, Moissl-Eichinger C, Schabbauer G, Egger G, Pirinen E, Verhelst SHL, Weichhart T. Metabolic support by macrophages sustains colonic epithelial homeostasis. Cell Metab 2023; 35:1931-1943.e8. [PMID: 37804836 DOI: 10.1016/j.cmet.2023.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 06/23/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023]
Abstract
The intestinal epithelium has a high turnover rate and constantly renews itself through proliferation of intestinal crypt cells, which depends on insufficiently characterized signals from the microenvironment. Here, we showed that colonic macrophages were located directly adjacent to epithelial crypt cells in mice, where they metabolically supported epithelial cell proliferation in an mTORC1-dependent manner. Specifically, deletion of tuberous sclerosis complex 2 (Tsc2) in macrophages activated mTORC1 signaling that protected against colitis-induced intestinal damage and induced the synthesis of the polyamines spermidine and spermine. Epithelial cells ingested these polyamines and rewired their cellular metabolism to optimize proliferation and defense. Notably, spermine directly stimulated proliferation of colon epithelial cells and colon organoids. Genetic interference with polyamine production in macrophages altered global polyamine levels in the colon and modified epithelial cell proliferation. Our results suggest that macrophages act as "commensals" that provide metabolic support to promote efficient self-renewal of the colon epithelium.
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Affiliation(s)
| | - Nyamdelger Sukhbaatar
- Center for Pathobiochemsitry & Genetics, Medical University of Vienna, Vienna, Austria
| | - Karine Gonzales
- Center for Pathobiochemsitry & Genetics, Medical University of Vienna, Vienna, Austria
| | - Alishan Sahu
- Center for Pathobiochemsitry & Genetics, Medical University of Vienna, Vienna, Austria
| | - Loan Tran
- Department of Pathology, Medical University of Vienna, Vienna, Austria; Ludwig Boltzmann Institute Applied Diagnostics (LBI AD), Vienna, Austria
| | - Andrea Vogel
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria; Christian Doppler Laboratory Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Mario Mazic
- Center for Pathobiochemsitry & Genetics, Medical University of Vienna, Vienna, Austria
| | - Jayne Louise Wilson
- Center for Pathobiochemsitry & Genetics, Medical University of Vienna, Vienna, Austria
| | - Stephan Forisch
- Center for Pathobiochemsitry & Genetics, Medical University of Vienna, Vienna, Austria
| | - Hannah Mayr
- Center for Pathobiochemsitry & Genetics, Medical University of Vienna, Vienna, Austria
| | - Raimund Oberle
- Center for Pathobiochemsitry & Genetics, Medical University of Vienna, Vienna, Austria
| | - Jakob Weiszmann
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Martin Brenner
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria; Department of Pharmaceutical Sciences/ Pharmacognosy, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Roeland Vanhoutte
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Melanie Hofmann
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria; Christian Doppler Laboratory Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Sini Pirnes-Karhu
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Christoph Magnes
- HEALTH-Institute for Biomedicine and Health Sciences, Joanneum Research Forschungsgesellschaft mbH, Graz, Austria
| | - Torben Kühnast
- Diagnostic and Research Department of Microbiology, Hygiene and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Kristaps Klavins
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Markus Hengstschläger
- Center for Pathobiochemsitry & Genetics, Medical University of Vienna, Vienna, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Department of Microbiology, Hygiene and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Gernot Schabbauer
- Institute for Vascular Biology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria; Christian Doppler Laboratory Arginine Metabolism in Rheumatoid Arthritis and Multiple Sclerosis, Vienna, Austria
| | - Gerda Egger
- Department of Pathology, Medical University of Vienna, Vienna, Austria; Ludwig Boltzmann Institute Applied Diagnostics (LBI AD), Vienna, Austria
| | - Eija Pirinen
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Research Unit of Biomedicine and Internal Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland; Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Steven H L Verhelst
- Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Thomas Weichhart
- Center for Pathobiochemsitry & Genetics, Medical University of Vienna, Vienna, Austria.
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Akhtar F, Ruiz JH, Liu YG, Resendez RG, Feliers D, Morales LD, Diaz-Badillo A, Lehman DM, Arya R, Lopez-Alvarenga JC, Blangero J, Duggirala R, Mummidi S. Functional characterization of the disease-associated CCL2 rs1024611G-rs13900T haplotype: The role of the RNA-binding protein HuR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564937. [PMID: 37961304 PMCID: PMC10635030 DOI: 10.1101/2023.10.31.564937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
CC-chemokine ligand 2 (CCL2) is involved in the pathogenesis of several diseases associated with monocyte/macrophage recruitment, such as HIV-associated neurocognitive disorder (HAND), tuberculosis, and atherosclerosis. The rs1024611 (alleles:A>G; G is the risk allele) polymorphism in the CCL2 cis-regulatory region is associated with increased CCL2 expression in vitro and ex vivo, leukocyte mobilization in vivo, and deleterious disease outcomes. However, the molecular basis for the rs1024611-associated differential CCL2 expression remains poorly characterized. It is conceivable that genetic variant(s) in linkage disequilibrium (LD) with rs1024611 could mediate such effects. Previously, we used rs13900 (alleles:_C>T) in the CCL2 3' untranslated region (3' UTR) that is in perfect LD with rs1024611 to demonstrate allelic expression imbalance (AEI) of CCL2 in heterozygous individuals. Here we tested the hypothesis that the rs13900 could modulate CCL2 expression by altering mRNA turnover and/or translatability. The rs13900 T allele conferred greater stability to the CCL2 transcript when compared to the rs13900 C allele. The rs13900 T allele also had increased binding to Human Antigen R (HuR), an RNA-binding protein, in vitro and ex vivo. The rs13900 alleles imparted differential activity to reporter vectors and influenced the translatability of the reporter transcript. We further demonstrated a role for HuR in mediating allele-specific effects on CCL2 expression in overexpression and silencing studies. The presence of the rs1024611G-rs13900T conferred a distinct transcriptomic signature related to inflammation and immunity. Our studies suggest that the differential interactions of HuR with rs13900 could modulate CCL2 expression and explain the interindividual differences in CCL2-mediated disease susceptibility.
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Affiliation(s)
- Feroz Akhtar
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Joselin Hernandez Ruiz
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Ya-Guang Liu
- Department of Pathology, School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Roy G. Resendez
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Denis Feliers
- Department of Medicine, School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Liza D. Morales
- South Texas Diabetes and Obesity Institute, Department of Genetics, School of Medicine, University of Texas Rio Grane Valley, Brownsville, USA
| | - Alvaro Diaz-Badillo
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Donna M. Lehman
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Rector Arya
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Juan Carlos Lopez-Alvarenga
- Department of Population Health and Biostatistics, School of Medicine, University of Texas Rio Grande Valley, Harlingen, Texas, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, Department of Genetics, School of Medicine, University of Texas Rio Grane Valley, Brownsville, USA
| | - Ravindranath Duggirala
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Srinivas Mummidi
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
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111
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Zou C, Zan X, Jia Z, Zheng L, Gu Y, Liu F, Han Y, Xu C, Wu A, Zhi Q. Crosstalk between alternative splicing and inflammatory bowel disease: Basic mechanisms, biotechnological progresses and future perspectives. Clin Transl Med 2023; 13:e1479. [PMID: 37983927 PMCID: PMC10659771 DOI: 10.1002/ctm2.1479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/07/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is an omnipresent regulatory mechanism of gene expression that enables the generation of diverse splice isoforms from a single gene. Recently, AS events have gained considerable momentum in the pathogenesis of inflammatory bowel disease (IBD). METHODS Our review has summarized the complex process of RNA splicing, and firstly highlighted the potential involved molecules that target aberrant splicing events in IBD. The quantitative transcriptome analyses such as microarrays, next-generation sequencing (NGS) for AS events in IBD have been also discussed. RESULTS Available evidence suggests that some abnormal splicing RNAs can lead to multiple intestinal disorders during the onset of IBD as well as the progression to colitis-associated cancer (CAC), including gut microbiota perturbations, intestinal barrier dysfunctions, innate/adaptive immune dysregulations, pro-fibrosis activation and some other risk factors. Moreover, current data show that the advanced technologies, including microarrays and NGS, have been pioneeringly employed to screen the AS candidates and elucidate the potential regulatory mechanisms of IBD. Besides, other biotechnological progresses such as the applications of third-generation sequencing (TGS), single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), will be desired with great expectations. CONCLUSIONS To our knowledge, the current review is the first one to evaluate the potential regulatory mechanisms of AS events in IBD. The expanding list of aberrantly spliced genes in IBD along with the developed technologies provide us new clues to how IBD develops, and how these important AS events can be explored for future treatment.
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Affiliation(s)
- Chentao Zou
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Xinquan Zan
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Zhenyu Jia
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Lu Zheng
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Yijie Gu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Fei Liu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Ye Han
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Chunfang Xu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Airong Wu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Qiaoming Zhi
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
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112
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Serrano I, Luque A, Ruiz-Cerulla A, Navas S, Blom AM, Rodríguez de Córdoba S, Fernández FJ, Cristina Vega M, Rodríguez-Moranta F, Guardiola J, Aran JM. C4BP(β-)-mediated immunomodulation attenuates inflammation in DSS-induced murine colitis and in myeloid cells from IBD patients. Pharmacol Res 2023; 197:106948. [PMID: 37806602 DOI: 10.1016/j.phrs.2023.106948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
The most recent and promising therapeutic strategies for inflammatory bowel disease (IBD) have engaged biologics targeting single effector components involved in major steps of the immune-inflammatory processes, such as tumor necrosis factor, interleukins or integrins. Nevertheless, these molecules have not yet met expectations regarding efficacy and safety, resulting in a significant percentage of refractory or relapsing patients. Thus, novel treatment options are urgently needed. The minor isoform of the complement inhibitor C4b-binding protein, C4BP(β-), has been shown to confer a robust anti-inflammatory and immunomodulatory phenotype over inflammatory myeloid cells. Here we show that C4BP(β-)-mediated immunomodulation can significantly attenuate the histopathological traits and preserve the intestinal epithelial integrity in dextran sulfate sodium (DSS)-induced murine colitis. C4BP(β-) downregulated inflammatory transcripts, notably those related to neutrophil activity, mitigated circulating inflammatory effector cytokines and chemokines such as CXCL13, key in generating ectopic lymphoid structures, and, overall, prevented inflammatory immune cell infiltration in the colon of colitic mice. PRP6-HO7, a recombinant curtailed analogue with only immunomodulatory activity, achieved a similar outcome as C4BP(β-), indicating that the therapeutic effect is not due to the complement inhibitory activity. Furthermore, both C4BP(β-) and PRP6-HO7 significantly reduced, with comparable efficacy, the intrinsic and TLR-induced inflammatory markers in myeloid cells from both ulcerative colitis and Crohn's disease patients, regardless of their medication. Thus, the pleiotropic anti-inflammatory and immunomodulatory activity of PRP6-HO7, able to "reprogram" myeloid cells from the complex inflammatory bowel environment and to restore immune homeostasis, might constitute a promising therapeutic option for IBD.
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Affiliation(s)
- Inmaculada Serrano
- Immune-inflammatory Processes and Gene Therapeutics Group, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Ana Luque
- Immune-inflammatory Processes and Gene Therapeutics Group, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Alexandra Ruiz-Cerulla
- Department of Digestive Diseases, Bellvitge University Hospital, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Sergio Navas
- Structural Biology of Host-Pathogen Interactions Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
| | - Anna M Blom
- Lund University, Department of Translational Medicine, Section of Medical Protein Chemistry, 21428 Malmö, Sweden
| | - Santiago Rodríguez de Córdoba
- Molecular Pathology/Genetics of Complement Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC) and Ciber de Enfermedades Raras (CIBERER), 28040 Madrid, Spain
| | | | - M Cristina Vega
- Structural Biology of Host-Pathogen Interactions Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
| | - Francisco Rodríguez-Moranta
- Department of Digestive Diseases, Bellvitge University Hospital, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Jordi Guardiola
- Department of Digestive Diseases, Bellvitge University Hospital, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Josep M Aran
- Immune-inflammatory Processes and Gene Therapeutics Group, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain.
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113
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O'Neil TR, Harman AN, Cunningham AL, Nasr N, Bertram KM. OMIP-096: A 24-color flow cytometry panel to identify and characterize CD4+ and CD8+ tissue-resident T cells in human skin, intestinal, and type II mucosal tissue. Cytometry A 2023; 103:851-856. [PMID: 37772977 PMCID: PMC10953338 DOI: 10.1002/cyto.a.24782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 04/06/2023] [Accepted: 07/24/2023] [Indexed: 09/30/2023]
Abstract
There is a great need to understand human immune cells within tissue, where disease manifests and infection occurs. Tissue-resident memory T cells (TRMs) were discovered over a decade ago, there is a great need to understand their role in human disease. We developed a 24-color flow cytometry panel to comprehensively interrogate CD4+ and CD8+ TRMs isolated from human tissues. When interrogating cells within human tissue, enzymatic methods used to liberate cells from within the tissue can cause cleavage of cell surface markers needed to phenotype these cells. Here we carefully select antibody clones and evaluate the effect of enzymatic digestion on the expression of markers relevant to the identification of T cell residency, as well as markers relevant to the activation and immunoregulation status of these cells. We have designed this panel to be applicable across a range of human tissues including skin, intestine, and type II mucosae such as the vagina.
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Affiliation(s)
- Thomas R. O'Neil
- Centre for Virus Research, The Westmead Institute for Medical ResearchWestmeadAustralia
- The Westmead Clinical School, Faculty of Medicine and HealthThe University of SydneySydneyAustralia
| | - Andrew N. Harman
- Centre for Virus Research, The Westmead Institute for Medical ResearchWestmeadAustralia
- The Westmead Clinical School, Faculty of Medicine and HealthThe University of SydneySydneyAustralia
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical ResearchWestmeadAustralia
- The Westmead Clinical School, Faculty of Medicine and HealthThe University of SydneySydneyAustralia
| | - Najla Nasr
- Centre for Virus Research, The Westmead Institute for Medical ResearchWestmeadAustralia
- The Westmead Clinical School, Faculty of Medicine and HealthThe University of SydneySydneyAustralia
| | - Kirstie M. Bertram
- Centre for Virus Research, The Westmead Institute for Medical ResearchWestmeadAustralia
- The Westmead Clinical School, Faculty of Medicine and HealthThe University of SydneySydneyAustralia
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114
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Samuels A, Whaley KG, Minar P. Precision Dosing of Anti-TNF Therapy in Pediatric Inflammatory Bowel Disease. Curr Gastroenterol Rep 2023; 25:323-332. [PMID: 37695555 PMCID: PMC10865142 DOI: 10.1007/s11894-023-00895-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 09/12/2023]
Abstract
PURPOSE OF THE REVIEW This review focuses on recent advancements in anti-TNF therapeutic drug monitoring (TDM), pharmacogenetics and personalized drug selection for children with inflammatory bowel disease (IBD). RECENT FINDINGS Several real-world studies and one clinical trial in children have demonstrated that proactive TDM, targeting higher exposure concentrations (> 5 µg/mL), can improve disease remission rates and enhance durability of the anti-TNF biologics. Recent data from both adult and pediatric IBD patients have revealed an association between a genetic polymorphism (HLA-DQA1*05) and the development of auto-drug antibodies. The impact of this association on clinical outcomes, considering more routine use proactive TDM and dose optimization in children, is still under investigation. Additionally, recent studies have identified potential inflammatory signatures and biomarkers that may serve as companion diagnostics for anti-TNF biologics. The effective management of anti-TNF therapies in children with IBD requires evidence-based precision dosing strategies, including routine TDM and proactive pharmacodynamic assessments.
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Affiliation(s)
- Abigail Samuels
- Department of Medicine, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH, 5229, USA
| | - Kaitlin G Whaley
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Phillip Minar
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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115
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Fiskin E, Eraslan G, Alora-Palli MB, Leyva-Castillo JM, Kim S, Choe H, Lareau CA, Lau H, Finan EP, Teixeira-Soldano I, LaBere B, Chu A, Woods B, Chou J, Slyper M, Waldman J, Islam S, Schneider L, Phipatanakul W, Platt C, Rozenblatt-Rosen O, Delorey TM, Deguine J, Smith GP, Geha R, Regev A, Xavier R. Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.29.563503. [PMID: 37961084 PMCID: PMC10634929 DOI: 10.1101/2023.10.29.563503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In healthy skin, a cutaneous immune system maintains the balance between tolerance towards innocuous environmental antigens and immune responses against pathological agents. In atopic dermatitis (AD), barrier and immune dysfunction result in chronic tissue inflammation. Our understanding of the skin tissue ecosystem in AD remains incomplete with regard to the hallmarks of pathological barrier formation, and cellular state and clonal composition of disease-promoting cells. Here, we generated a multi-modal cell census of 310,691 cells spanning 86 cell subsets from whole skin tissue of 19 adult individuals, including non-lesional and lesional skin from 11 AD patients, and integrated it with 396,321 cells from four studies into a comprehensive human skin cell atlas in health and disease. Reconstruction of human keratinocyte differentiation from basal to cornified layers revealed a disrupted cornification trajectory in AD. This disrupted epithelial differentiation was associated with signals from a unique immune and stromal multicellular community comprised of MMP12 + dendritic cells (DCs), mature migratory DCs, cycling ILCs, NK cells, inflammatory CCL19 + IL4I1 + fibroblasts, and clonally expanded IL13 + IL22 + IL26 + T cells with overlapping type 2 and type 17 characteristics. Cell subsets within this immune and stromal multicellular community were connected by multiple inter-cellular positive feedback loops predicted to impact community assembly and maintenance. AD GWAS gene expression was enriched both in disrupted cornified keratinocytes and in cell subsets from the lesional immune and stromal multicellular community including IL13 + IL22 + IL26 + T cells and ILCs, suggesting that epithelial or immune dysfunction in the context of the observed cellular communication network can initiate and then converge towards AD. Our work highlights specific, disease-associated cell subsets and interactions as potential targets in progression and resolution of chronic inflammation.
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116
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Lo JW, Cozzetto D, Alexander JL, Danckert NP, Madgwick M, Knox N, Sieh JYX, Olbei M, Liu Z, Ibraheim H, Blanco JM, Kudo H, Seoane RC, Possamai LA, Goldin R, Marchesi J, Korcsmaros T, Lord GM, Powell N. Immune checkpoint inhibitor-induced colitis is mediated by polyfunctional lymphocytes and is dependent on an IL23/IFNγ axis. Nat Commun 2023; 14:6719. [PMID: 37872166 PMCID: PMC10593820 DOI: 10.1038/s41467-023-41798-2] [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: 01/11/2022] [Accepted: 09/18/2023] [Indexed: 10/25/2023] Open
Abstract
Immune checkpoint inhibitors (CPIs) are a relatively newly licenced cancer treatment, which make a once previously untreatable disease now amenable to a potential cure. Combination regimens of anti-CTLA4 and anti-PD-1 show enhanced efficacy but are prone to off-target immune-mediated tissue injury, particularly at the barrier surfaces. To probe the impact of immune checkpoints on intestinal homoeostasis, mice are challenged with anti-CTLA4 and anti-PD-1 immunotherapy and manipulation of the intestinal microbiota. The immune profile of the colon of these mice with CPI-colitis is analysed using bulk RNA sequencing, single-cell RNA sequencing and flow cytometry. CPI-colitis in mice is dependent on the composition of the intestinal microbiota and by the induction of lymphocytes expressing interferon-γ (IFNγ), cytotoxicity molecules and other pro-inflammatory cytokines/chemokines. This pre-clinical model of CPI-colitis could be attenuated following blockade of the IL23/IFNγ axis. Therapeutic targeting of IFNγ-producing lymphocytes or regulatory networks, may hold the key to reversing CPI-colitis.
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Affiliation(s)
- Jonathan W Lo
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Domenico Cozzetto
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - James L Alexander
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Nathan P Danckert
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Matthew Madgwick
- Organisms and Ecosystems, Earlham Institute, NR4 7UZ, Norwich, UK
- Gut Microbes and Health Programme, Quadram Institute Bioscience, NR4 7UQ, Norwich, UK
| | - Naomi Knox
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Jillian Yong Xin Sieh
- School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
| | - Marton Olbei
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Organisms and Ecosystems, Earlham Institute, NR4 7UZ, Norwich, UK
- Gut Microbes and Health Programme, Quadram Institute Bioscience, NR4 7UQ, Norwich, UK
| | - Zhigang Liu
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Hajir Ibraheim
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Jesus Miguens Blanco
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Hiromi Kudo
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Rocio Castro Seoane
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Lucia A Possamai
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Robert Goldin
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Julian Marchesi
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Tamas Korcsmaros
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Organisms and Ecosystems, Earlham Institute, NR4 7UZ, Norwich, UK
- Gut Microbes and Health Programme, Quadram Institute Bioscience, NR4 7UQ, Norwich, UK
| | - Graham M Lord
- School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9NT, UK
| | - Nick Powell
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
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117
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Yao Y, Yang L, Zhang Z, Wang B, Feng B, Liu Z. Identification of Targets for Subsequent Treatment of Crohn's Disease Patients After Failure of Anti-TNF Therapy. J Inflamm Res 2023; 16:4617-4631. [PMID: 37868830 PMCID: PMC10590116 DOI: 10.2147/jir.s422881] [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: 05/25/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
Background Anti-TNF medications are the first-line treatment for Crohn's Disease (CD), despite the fact that a significant portion of the population continues to be ineffectively treated. This research aims to discover accurate intervention targets for the follow-up of anti-TNF non-responders using bioinformatics technology. Methods GSE16879, GSE111761, and GSE52746 retrieved from the GEO database. Unbiased differentially expressed genes (DEGs) were discovered utilizing the limma and RobustRankAggreg (RRA) tools. Then, we used weighted gene co-expression network analysis (WGCNA) to identify the module most strongly associated with non responders and subjected this module to Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis with overlapping genes of the DEGs. GSEA analysis applied to check the results of GO and KEGG. Using the Cytoscape program, the protein-protein interaction (PPI) network was constructed. The software's MCODE addon and CytoHubba addon was used to find the most important modules and the hub genes. Subsequently, we employed reverse transcription-polymerase chain reaction (RT-PCR) to confirm hub gene expression from mucosal biopsy specimens. Results There were a total of 142 genes co-upregulated and 65 genes co-downregulated. According to the WGCNA analysis, 42 genes were duplicated inside the light cyan module. GO and KEGG enrichment analyses of overlapped genes in nonresponders demonstrated an increase in the expression of genes associated with inflammation and immune response, consistent with GSEA results. The PPI network was constructed using 41 protein nodes and 177 edges. After validation, 8 of the top 10 genes were verified to be differentially expressed. Conclusion Our investigation is the first to integrate three CD databases after the anti-TNF medication treatment. We identified IL1B, CCL4, CXCL1, CXCL10, CCL3, CSF3, TREM1, and IL1RN as potential therapeutic targets for patients whose anti-TNF treatment failed.
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Affiliation(s)
- Yao Yao
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, People’s Republic of China
| | - Liu Yang
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, People’s Republic of China
| | - Zhe Zhang
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, People’s Republic of China
| | - Binbin Wang
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, People’s Republic of China
| | - Baisui Feng
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, People’s Republic of China
| | - Zhanju Liu
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, People’s Republic of China
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital of Tongji University, Shanghai, 200072, People’s Republic of China
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Raso F, Liu S, Simpson MJ, Barton GM, Mayer CT, Acharya M, Muppidi JR, Marshak-Rothstein A, Reboldi A. Antigen receptor signaling and cell death resistance controls intestinal humoral response zonation. Immunity 2023; 56:2373-2387.e8. [PMID: 37714151 PMCID: PMC10591993 DOI: 10.1016/j.immuni.2023.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/24/2023] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
Immunoglobulin A (IgA) maintains commensal communities in the intestine while preventing dysbiosis. IgA generated against intestinal microbes assures the simultaneous binding to multiple, diverse commensal-derived antigens. However, the exact mechanisms by which B cells mount broadly reactive IgA to the gut microbiome remains elusive. Here, we have shown that IgA B cell receptor (BCR) is required for B cell fitness during the germinal center (GC) reaction in Peyer's patches (PPs) and for generation of gut-homing plasma cells (PCs). We demonstrate that IgA BCR drove heightened intracellular signaling in mouse and human B cells, and as a consequence, IgA+ B cells received stronger positive selection cues. Mechanistically, IgA BCR signaling offset Fas-mediated death, possibly rescuing low-affinity B cells to promote a broad humoral response to commensals. Our findings reveal an additional mechanism linking BCR signaling, B cell fate, and antibody production location, which have implications for how intestinal antigen recognition shapes humoral immunity.
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Affiliation(s)
- Fiona Raso
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Shuozhi Liu
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Mikala J Simpson
- Experimental Immunology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Gregory M Barton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Christian T Mayer
- Experimental Immunology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Mridu Acharya
- Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Jagan R Muppidi
- Lymphoid Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Ann Marshak-Rothstein
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Andrea Reboldi
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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Chauvin C, Radulovic K, Boulard O, Delacre M, Waldschmitt N, Régnier P, Legris G, Bouchez C, Sleimi MY, Rosenstiel P, Darrasse-Jèze G, Chamaillard M, Poulin LF. Loss of NOD2 in macrophages improves colitis and tumorigenesis in a lysozyme-dependent manner. Front Immunol 2023; 14:1252979. [PMID: 37876927 PMCID: PMC10590911 DOI: 10.3389/fimmu.2023.1252979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023] Open
Abstract
Background Crohn's disease (CD) is a complex and poorly understood myeloid-mediated disorder. Genetic variants with loss of function in the NOD2 gene confer an increased susceptibility to ileal CD. While Nod2 in myeloid cells may confer protection against T-cell mediated ileopathy, it remains unclear whether it may promote resolution of the inflamed colon. In this study, we evaluated the function of Nod2 in myeloid cells in a model of acute colitis and colitis-associated colon cancer (CAC). Methods To ablate Nod2 specifically within the myeloid compartment, we generated LysMCre/+;Nod2fl/fl mice. The role of NOD2 was studied in a setting of Dextran Sodium Sulfate (DSS)-induced colitis and in azoxymethane (AOM)/DSS model. Clinical parameters were quantified by colonoscopy, histological, flow cytometry, and qRT-PCR analysis. Results Upon DSS colitis model, LysMCre/+;Nod2fl/fl mice lost less weight than control littermates and had less severe damage to the colonic epithelium. In the AOM/DSS model, endoscopic monitoring of tumor progression revealed a lowered number of adenomas within the colon of LysMCre/+;Nod2fl/fl mice, associated with less expression of Tgfb. Mechanistically, lysozyme M was required for the improved disease severity in mice with a defect of NOD2 in myeloid cells. Conclusion Our results indicate that loss of Nod2 signaling in myeloid cells aids in the tissue repair of the inflamed large intestine through lysozyme secretion by myeloid cells. These results may pave the way to design new therapeutics to limit the inflammatory and tumorigenic functions of NOD2.
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Affiliation(s)
- Camille Chauvin
- Univ. Lille, Institut National de la Santé Et de la Recherche Médicale (Inserm), Centre de Recherche Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019, Lille, France
- Institut national de la santé et de la recherche médicale (INSERM) U1138, Centre de Recherche des Cordeliers, Paris, France
| | - Katarina Radulovic
- Unité de Recherche Clinique, Centre Hospitalier de Valenciennes, Valenciennes, France
| | | | - Myriam Delacre
- Univ. Lille, Institut National de la Santé Et de la Recherche Médicale (Inserm), Centre de Recherche Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019, Lille, France
| | - Nadine Waldschmitt
- Chair of Nutrition and Immunology, School of Life Sciences, Technische Universität München, Freising-Weihenstephan, Germany
| | - Paul Régnier
- Immunology-Immunopathology-Immunotherapy (i3) Laboratory, Institut national de la santé et de la recherche médicale (INSERM) UMR-S 959, Sorbonne Université, Paris, France
- Biotherapy Unit (CIC-BTi), Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | | | | | | | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Guillaume Darrasse-Jèze
- Immunology-Immunopathology-Immunotherapy (i3) Laboratory, Institut national de la santé et de la recherche médicale (INSERM) UMR-S 959, Sorbonne Université, Paris, France
- Université de Paris, Paris Descartes, Faculté de Médecine, Paris, France
- Université Paris Cité, Faculté de Médecine, Paris, France
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Fiocchi C. Omics and Multi-Omics in IBD: No Integration, No Breakthroughs. Int J Mol Sci 2023; 24:14912. [PMID: 37834360 PMCID: PMC10573814 DOI: 10.3390/ijms241914912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
The recent advent of sophisticated technologies like sequencing and mass spectroscopy platforms combined with artificial intelligence-powered analytic tools has initiated a new era of "big data" research in various complex diseases of still-undetermined cause and mechanisms. The investigation of these diseases was, until recently, limited to traditional in vitro and in vivo biological experimentation, but a clear switch to in silico methodologies is now under way. This review tries to provide a comprehensive assessment of state-of-the-art knowledge on omes, omics and multi-omics in inflammatory bowel disease (IBD). The notion and importance of omes, omics and multi-omics in both health and complex diseases like IBD is introduced, followed by a discussion of the various omics believed to be relevant to IBD pathogenesis, and how multi-omics "big data" can generate new insights translatable into useful clinical tools in IBD such as biomarker identification, prediction of remission and relapse, response to therapy, and precision medicine. The pitfalls and limitations of current IBD multi-omics studies are critically analyzed, revealing that, regardless of the types of omes being analyzed, the majority of current reports are still based on simple associations of descriptive retrospective data from cross-sectional patient cohorts rather than more powerful longitudinally collected prospective datasets. Given this limitation, some suggestions are provided on how IBD multi-omics data may be optimized for greater clinical and therapeutic benefit. The review concludes by forecasting the upcoming incorporation of multi-omics analyses in the routine management of IBD.
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Affiliation(s)
- Claudio Fiocchi
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland, OH 44195, USA;
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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Ciavattone NG, Guan J, Farfel A, Desmond T, Viglianti BL, Scott PJ, Brooks AF, Luker GD. Predicting efficacy of immunotherapy in mice with triple negative breast cancer using a cholesterol PET radiotracer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560577. [PMID: 37873149 PMCID: PMC10592945 DOI: 10.1101/2023.10.02.560577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Predicting the response to cancer immunotherapy remains an unmet challenge in triple-negative breast cancer (TNBC) and other malignancies. T cells, the major target of current checkpoint inhibitor immunotherapies, accumulate cholesterol during activation to support proliferation and signaling. The requirement of cholesterol for anti-tumor functions 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 a novel positron emission tomography (PET) radiotracer, FNP-59. FNP-59 is an analog of cholesterol that our group has validated as an imaging biomarker for cholesterol uptake in pre-clinical 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 immune checkpoint inhibitor (ICI)-responsive EO771 tumors to non-responsive AT-3 tumors, we found significantly higher uptake of a fluorescent cholesterol analog in T cells of the ICI-responsive tumors both in vitro and in vivo. Using the FNP-59 radiotracer, we discovered that accumulation of cholesterol by T cells increased further in ICI-responding tumors that received ant-PD-1 checkpoint immunotherapy. We verified these data by mining single cell sequencing data from patients with TNBC. Patients with tumors containing cycling T cells showed gene expression signatures of cholesterol uptake and trafficking. These results suggest that uptake of exogenous cholesterol analogs by tumor-infiltrating T cells predict T cell activation and success of ICI therapy.
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122
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Li J, Simmons AJ, Chiron S, Ramirez-Solano MA, Tasneem N, Kaur H, Xu Y, Revetta F, Vega PN, Bao S, Cui C, Tyree RN, Raber LW, Conner AN, Beaulieu DB, Dalal RL, Horst SN, Pabla BS, Huo Y, Landman BA, Roland JT, Scoville EA, Schwartz DA, Washington MK, Shyr Y, Wilson KT, Coburn LA, Lau KS, Liu Q. A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.560293. [PMID: 37873404 PMCID: PMC10592875 DOI: 10.1101/2023.09.30.560293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Crohn's disease (CD) is a complex chronic inflammatory disorder that may affect any part of gastrointestinal tract with extra-intestinal manifestations and associated immune dysregulation. To characterize heterogeneity in CD, we profiled single-cell transcriptomics of 170 samples from 65 CD patients and 18 non-inflammatory bowel disease (IBD) controls in both the terminal ileum (TI) and ascending colon (AC). Analysis of 202,359 cells identified a novel epithelial cell type in both TI and AC, featuring high expression of LCN2, NOS2, and DUOX2, and thus is named LND. LND cells, confirmed by high-resolution in-situ RNA imaging, were rarely found in non-IBD controls, but expanded significantly in active CD. Compared to other epithelial cells, genes defining LND cells were enriched in antimicrobial response and immunoregulation. Moreover, multiplexed protein imaging demonstrated that LND cell abundance was associated with immune infiltration. Cross-talk between LND and immune cells was explored by ligand-receptor interactions and further evidenced by their spatial colocalization. LND cells showed significant enrichment of expression specificity of IBD/CD susceptibility genes, revealing its role in immunopathogenesis of CD. Investigating lineage relationships of epithelial cells detected two LND cell subpopulations with different origins and developmental potential, early and late LND. The ratio of the late to early LND cells was related to anti-TNF response. These findings emphasize the pathogenic role of the specialized LND cell type in both Crohn's ileitis and Crohn's colitis and identify novel biomarkers associated with disease activity and treatment response.
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Affiliation(s)
- Jia Li
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Alan J. Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sophie Chiron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marisol A. Ramirez-Solano
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Naila Tasneem
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Harsimran Kaur
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yanwen Xu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Frank Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paige N. Vega
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shunxing Bao
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Can Cui
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Regina N. Tyree
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Larry W. Raber
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna N. Conner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dawn B. Beaulieu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robin L. Dalal
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara N. Horst
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Baldeep S. Pabla
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuankai Huo
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Bennett A. Landman
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Joseph T. Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville TN, USA
| | - Elizabeth A. Scoville
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - David A. Schwartz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Lori A. Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Ken S. Lau
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
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Brügger MD, Basler K. The diverse nature of intestinal fibroblasts in development, homeostasis, and disease. Trends Cell Biol 2023; 33:834-849. [PMID: 37080817 DOI: 10.1016/j.tcb.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 04/22/2023]
Abstract
Only in recent years have we begun to appreciate the involvement of fibroblasts in intestinal development, tissue homeostasis, and disease. These insights followed the advent of single-cell transcriptomics that allowed researchers to explore the heterogeneity of intestinal fibroblasts in unprecedented detail. Since researchers often defined cell types and their associated function based on the biological process they studied, there are a plethora of partially overlapping markers for different intestinal fibroblast populations. This ambiguity complicates putting different research findings into context. Here, we provide a census on the function and identity of intestinal fibroblasts in mouse and human. We propose a simplified framework consisting of three colonic and four small intestinal fibroblast populations to aid navigating the diversity of intestinal fibroblasts.
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Affiliation(s)
- Michael David Brügger
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Konrad Basler
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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124
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Cui P, Li J, Tao H, Li X, Wu L, Ma J, Wang H, Liu T, Zhang M, Hu Y. Deciphering pathogenic cellular module at single-cell resolution in checkpoint inhibitor-related pneumonitis. Oncogene 2023; 42:3098-3112. [PMID: 37653115 PMCID: PMC10575783 DOI: 10.1038/s41388-023-02805-4] [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: 01/23/2023] [Revised: 07/26/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023]
Abstract
Checkpoint inhibitor pneumonitis (CIP) is the most common fatal immune-related adverse event; however, its pathophysiology remains largely unknown. Comprehensively dissecting the key cellular players and molecular pathways associated with CIP pathobiology is critical for precision diagnosis and develop novel therapy strategy of CIP. Herein, we performed a comprehensive single-cell transcriptome analysis to dissect the complexity of the immunological response in the bronchoalveolar lavage fluid (BALF) microenvironment. CIP was characterized by a dramatic accumulation of CXCL13+ T cells and hyperinflammatory CXCL9+ monocytes. T-cell receptor (TCR) analysis revealed that CXCL13+ T cells exhibited hyperexpanded- TCR clonotypes, and pseudotime analysis revealed a potential differentiation trajectory from naïve to cytotoxic effector status. Monocyte trajectories showed that LAMP3+ DCs derived from CXCL9+ monocytes possessed the potential to migrate from tumors to the BALF, whereas the differentiation trajectory to anti-inflammatory macrophages was blocked. Intercellular crosstalk analysis revealed the signaling pathways such as CXCL9/10/11-CXCR3, FASLG-FAS, and IFNGR1/2-IFNG were activated in CIP+ samples. We also proposed a novel immune signature with high diagnostic power to distinguish CIP+ from CIP- samples (AUC = 0.755). Our data highlighted key cellular players, signatures, and interactions involved in CIP pathogenesis.
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Affiliation(s)
- Pengfei Cui
- Department of Oncology, the Second Medical Center of Chinese PLA General Hospital, 100853, Beijing, China
- Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Jinfeng Li
- Institute of oncology, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Haitao Tao
- Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Xiaoyan Li
- Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Liangliang Wu
- Institute of oncology, Senior Department of Oncology, the First Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Junxun Ma
- Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Huanhuan Wang
- Institute of oncology, Senior Department of Oncology, the First Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Tingting Liu
- Department of Pulmonary and Critical Care Medicine, the Second Medical Center of Chinese PLA General Hospital, 100853, Beijing, China
| | - Min Zhang
- State Key Laboratory of Kidney Diseases, Department of Nephrology, the First Medical Center of Chinese PLA General Hospital, 100853, Beijing, China.
| | - Yi Hu
- Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, 100853, Beijing, China.
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125
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Shi Q, Chen X, Zhang Z. Decoding Human Biology and Disease Using Single-cell Omics Technologies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:926-949. [PMID: 37739168 PMCID: PMC10928380 DOI: 10.1016/j.gpb.2023.06.003] [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: 01/19/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 09/24/2023]
Abstract
Over the past decade, advances in single-cell omics (SCO) technologies have enabled the investigation of cellular heterogeneity at an unprecedented resolution and scale, opening a new avenue for understanding human biology and disease. In this review, we summarize the developments of sequencing-based SCO technologies and computational methods, and focus on considerable insights acquired from SCO sequencing studies to understand normal and diseased properties, with a particular emphasis on cancer research. We also discuss the technological improvements of SCO and its possible contribution to fundamental research of the human, as well as its great potential in clinical diagnoses and personalized therapies of human disease.
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Affiliation(s)
- Qiang Shi
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
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126
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Hosack T, Thomas T, Ravindran R, Uhlig HH, Travis SPL, Buckley CD. Inflammation across tissues: can shared cell biology help design smarter trials? Nat Rev Rheumatol 2023; 19:666-674. [PMID: 37666996 DOI: 10.1038/s41584-023-01007-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2023] [Indexed: 09/06/2023]
Abstract
Immune-mediated inflammatory diseases (IMIDs) are responsible for substantial global disease burden and associated health-care costs. Traditional models of research and service delivery silo their management within organ-based medical disciplines. Very often patients with disease in one organ have comorbid involvement in another, suggesting shared pathogenic pathways. Moreover, different IMIDs are often treated with the same drugs (including glucocorticoids, immunoregulators and biologics). Unlocking the cellular basis of these diseases remains a major challenge, leading us to ask why, if these diseases have so much in common, they are not investigated in a common manner. A tissue-based, cellular understanding of inflammation might pave the way for cross-disease, cross-discipline basket trials (testing one drug across two or more diseases) to reduce the risk of failure of early-phase drug development in IMIDs. This new approach will enable rapid assessment of the efficacy of new therapeutic agents in cross-disease translational research in humans.
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Affiliation(s)
- Tom Hosack
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Tom Thomas
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Rahul Ravindran
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Hans Holm Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- Biomedical Research Centre, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Simon Piers Leigh Travis
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Christopher Dominic Buckley
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
- Biomedical Research Centre, University of Oxford, Oxford, UK.
- Institute for Inflammation and Aging, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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Park SK, Lee GY, Kim S, Lee CW, Choi CH, Kang SB, Kim TO, Chun J, Cha JM, Im JP, Ahn KS, Kim SY, Kim MS, Lee CK, Park DI. Enrichment of Activated Fibroblasts as a Potential Biomarker for a Non-Durable Response to Anti-Tumor Necrosis Factor Therapy in Patients with Crohn's Disease. Int J Mol Sci 2023; 24:14799. [PMID: 37834250 PMCID: PMC10573580 DOI: 10.3390/ijms241914799] [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: 08/28/2023] [Revised: 09/19/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
We investigated whether the response to anti-tumor necrosis factor (anti-TNF) treatment varied according to inflammatory tissue characteristics in Crohn's disease (CD). Bulk RNA sequencing (RNA-seq) data were obtained from inflamed and non-inflamed tissues from 170 patients with CD. The samples were clustered based on gene expression profiles using principal coordinate analysis (PCA). Cellular heterogeneity was inferred using CiberSortx, with bulk RNA-seq data. The PCA results displayed two clusters of CD-inflamed samples: one close to (Inflamed_1) and the other far away (Inflamed_2) from the non-inflamed samples. Inflamed_1 was rich in anti-TNF durable responders (DRs), and Inflamed_2 was enriched in non-durable responders (NDRs). The CiberSortx results showed that the cell fraction of activated fibroblasts was six times higher in Inflamed_2 than in Inflamed_1. Validation with public gene expression datasets (GSE16879) revealed that the activated fibroblasts were enriched in NDRs over Next, we used DRs by 1.9 times pre-treatment and 7.5 times after treatment. Fibroblast activation protein (FAP) was overexpressed in the Inflamed_2 and was also overexpressed in the NDRs in both the RISK and GSE16879 datasets. The activation of fibroblasts may play a role in resistance to anti-TNF therapy. Characterizing fibroblasts in inflamed tissues at diagnosis may help to identify patients who are likely to respond to anti-TNF therapy.
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Affiliation(s)
- Soo-Kyung Park
- Division of Gastroenterology, Department of Internal Medicine and Inflammatory Bowel Disease Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Republic of Korea;
- Medical Research Institute, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Republic of Korea;
| | - Gi-Young Lee
- Department of Bioinformatics, Soongsil University, Seoul 06978, Republic of Korea; (G.-Y.L.); (S.K.)
| | - Sangsoo Kim
- Department of Bioinformatics, Soongsil University, Seoul 06978, Republic of Korea; (G.-Y.L.); (S.K.)
| | - Chil-Woo Lee
- Medical Research Institute, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Republic of Korea;
| | - Chang-Hwan Choi
- Department of Internal Medicine, College of Medicine, Chung-Ang University, Seoul 06974, Republic of Korea;
| | - Sang-Bum Kang
- Department of Internal Medicine, Daejeon St. Mary’s Hospital, Daejeon 34943, Republic of Korea;
| | - Tae-Oh Kim
- Department of Internal Medicine, Haeundae Paik Hospital, College of Medicine, Inje University, Busan 47392, Republic of Korea;
| | - Jaeyoung Chun
- Department of Internal Medicine, Gangnam Severance Hospital, College of Medicine, Yonsei University, Seoul 03722, Republic of Korea;
| | - Jae-Myung Cha
- Department of Internal Medicine, Kyung Hee University Hospital at Gang Dong, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea;
| | - Jong-Pil Im
- Department of Internal Medicine, Liver Research Institute, College of Medicine, Seoul National University, Seoul 08826, Republic of Korea;
| | - Kwang-Sung Ahn
- Functional Genome Institute, PDXen Biosystems, Inc., Daejeon 34027, Republic of Korea;
| | - Seon-Young Kim
- Personalized Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea;
| | - Min-Suk Kim
- Department of Human Intelligence and Robot Engineering, Sangmyung University, Cheonan 31066, Republic of Korea;
| | - Chang-Kyun Lee
- Department of Gastroenterology, Center for Crohn’s and Colitis, Kyung Hee University Hospital, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea;
| | - Dong-Il Park
- Division of Gastroenterology, Department of Internal Medicine and Inflammatory Bowel Disease Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Republic of Korea;
- Medical Research Institute, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Republic of Korea;
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128
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Dong Y, Johnson BA, Ruan L, Zeineldin M, Liu AZ, Raychaudhuri S, Chiu I, Zhu J, Smith B, Zhao N, Searson P, Watanabe S, Donowitz M, Larman TC, Li R. Disruption of Epithelium Integrity by Inflammation-Associated Fibroblasts through Prostaglandin Signaling: IAFs disrupt colon epithelium via PGE2-EP4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560060. [PMID: 37808771 PMCID: PMC10557697 DOI: 10.1101/2023.09.28.560060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Inflammation-associated fibroblasts (IAFs) are associated with the progression and drug resistance of chronic inflammatory diseases such as inflammatory bowel disease (IBD), but their direct impact on epithelial function and architecture is unknown. In this study, we developed an in vitro model whereby human colon fibroblasts are induced to become IAFs by specific cytokines and recapitulate key features of IAFs in vivo. When co-cultured with patient-derived colon organoids (colonoids), IAFs induced rapid colonoid swelling and barrier disruption due to swelling and rupture of individual epithelial cells. Epithelial cells co-cultured with IAFs also exhibit increased DNA damage, mitotic errors, and proliferation arrest. These IAF-induced epithelial defects are mediated through a paracrine pathway involving prostaglandin E2 (PGE2) and the PGE2 receptor EP4, leading to PKA-dependent activation of the CFTR chloride channel. Importantly, EP4-specific chemical inhibitors effectively prevented colonoid swelling and restored normal proliferation and genome stability of IAF-exposed epithelial cells. These findings reveal a mechanism by which IAFs could promote and perpetuate IBD and suggest a potential treatment to mitigate inflammation-associated epithelial injury.
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Affiliation(s)
- Yi Dong
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Blake A. Johnson
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Linhao Ruan
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Maged Zeineldin
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Albert Z. Liu
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Ian Chiu
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Jin Zhu
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore; Singapore
| | - Barbara Smith
- Microscope Facility, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Nan Zhao
- Institute for Nanobiotechnology, Johns Hopkins University; Baltimore, Maryland, 21218, U.S.A
| | - Peter Searson
- Institute for Nanobiotechnology, Johns Hopkins University; Baltimore, Maryland, 21218, U.S.A
- Department of Materials Science and Engineering, Johns Hopkins University; Baltimore, MD, 21218, U.S.A
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Mark Donowitz
- Department of Medicine, Division of Gastroenterology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
- Department of Physiology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Tatianna C. Larman
- Department of Pathology, Division of GI/Liver Pathology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
| | - Rong Li
- Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, 21205, U.S.A
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore; Singapore
- Department of Biological Sciences, National University of Singapore; Singapore
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129
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Anderson-Crannage M, Ascensión AM, Ibanez-Solé O, Zhu H, Schaefer E, Ottomanelli D, Hochberg B, Pan J, Luo W, Tian M, Chu Y, Cairo MS, Izeta A, Liao Y. Inflammation-mediated fibroblast activation and immune dysregulation in collagen VII-deficient skin. Front Immunol 2023; 14:1211505. [PMID: 37809094 PMCID: PMC10557493 DOI: 10.3389/fimmu.2023.1211505] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/17/2023] [Indexed: 10/10/2023] Open
Abstract
Inflammation is known to play a critical role in all stages of tumorigenesis; however, less is known about how it predisposes the tissue microenvironment preceding tumor formation. Recessive dystrophic epidermolysis bullosa (RDEB), a skin-blistering disease secondary to COL7A1 mutations and associated with chronic wounding, inflammation, fibrosis, and cutaneous squamous cell carcinoma (cSCC), models this dynamic. Here, we used single-cell RNA sequencing (scRNAseq) to analyze gene expression patterns in skin cells from a mouse model of RDEB. We uncovered a complex landscape within the RDEB dermal microenvironment that exhibited altered metabolism, enhanced angiogenesis, hyperproliferative keratinocytes, infiltration and activation of immune cell populations, and inflammatory fibroblast priming. We demonstrated the presence of activated neutrophil and Langerhans cell subpopulations and elevated expression of PD-1 and PD-L1 in T cells and antigen-presenting cells, respectively. Unsupervised clustering within the fibroblast population further revealed two differentiation pathways in RDEB fibroblasts, one toward myofibroblasts and the other toward a phenotype that shares the characteristics of inflammatory fibroblast subsets in other inflammatory diseases as well as the IL-1-induced inflammatory cancer-associated fibroblasts (iCAFs) reported in various cancer types. Quantitation of inflammatory cytokines indicated dynamic waves of IL-1α, TGF-β1, TNF, IL-6, and IFN-γ concentrations, along with dermal NF-κB activation preceding JAK/STAT signaling. We further demonstrated the divergent and overlapping roles of these cytokines in inducing inflammatory phenotypes in RDEB patients as well as RDEB mouse-derived fibroblasts together with their healthy controls. In summary, our data have suggested a potential role of inflammation, driven by the chronic release of inflammatory cytokines such as IL-1, in creating an immune-suppressed dermal microenvironment that underlies RDEB disease progression.
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Affiliation(s)
- Morgan Anderson-Crannage
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, United States
| | - Alex M. Ascensión
- Biodonostia Health Research Institute, Tissue Engineering Group, San Sebastian, Spain
| | - Olga Ibanez-Solé
- Biodonostia Health Research Institute, Tissue Engineering Group, San Sebastian, Spain
| | - Hongwen Zhu
- Department of Research & Development, Guizhou Atlasus Technology Co., Ltd., Guiyang, China
| | - Edo Schaefer
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Darcy Ottomanelli
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Bruno Hochberg
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Jian Pan
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Wen Luo
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Meijuan Tian
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Yaya Chu
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Mitchell S. Cairo
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, United States
- Department of Medicine, New York Medical College, Valhalla, NY, United States
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY, United States
| | - Ander Izeta
- Biodonostia Health Research Institute, Tissue Engineering Group, San Sebastian, Spain
- Department of Biomedical Engineering and Science, School of Engineering, Tecnun University of Navarra, San Sebastian, Spain
| | - Yanling Liao
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
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130
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Zhang Y, Ma Y, Liu Q, Du Y, Peng L, Zhou J, Zhao Z, Li C, Wang S. Single-cell transcriptome sequencing reveals tumor heterogeneity in family neuroblastoma. Front Immunol 2023; 14:1197773. [PMID: 37790931 PMCID: PMC10543897 DOI: 10.3389/fimmu.2023.1197773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/01/2023] [Indexed: 10/05/2023] Open
Abstract
Neuroblastoma(NB) is the most common extracranial solid tumor in childhood, and it is now believed that some patients with NB have an underlying genetic susceptibility, which may be one of the reasons for the multiplicity of NB patients within a family line. Even within the same family, the samples show great variation and can present as ganglioneuroblastoma or even benign ganglioneuroma. The genomics of NB is still unclear and more in-depth studies are needed to reveal its key components. We first performed single-cell RNA sequencing(sc-RNAseq) analysis on clinical specimens of two family neuroblastoma(FNB) and four sporadic NB cases. A complete transcriptional profile of FNB was constructed from 18,394 cells from FNB, and we found that SDHD may be genetically associated with FNB and identified a prognostic related CAF subtype in FNB: Fib-4. Single-cell flux estimation analysis (scFEA) results showed that malignant cells were associated with arginine spermine, oxaloacetate and hypoxanthine, and that malignant cells metabolize lactate at lower levels than T cells. Our study provides new resources and ideas for the development of the genomics of family NB, and the mechanisms of cell-to-cell interactions and communication and the metabolic landscape will provide new therapeutic targets.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shan Wang
- Department of Pediatric Surgical Oncology Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
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131
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Kwak MS, Hwang CI, Cha JM, Jeon JW, Yoon JY, Park SB. Single-Cell Network-Based Drug Repositioning for Discovery of Therapies against Anti-Tumour Necrosis Factor-Resistant Crohn's Disease. Int J Mol Sci 2023; 24:14099. [PMID: 37762402 PMCID: PMC10531326 DOI: 10.3390/ijms241814099] [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: 08/25/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Primary and secondary non-response affects approximately 50% of patients with Crohn's disease treated with anti-tumour necrosis factor (TNF) monoclonal antibodies. To date, very little single cell research exists regarding drug repurposing in Crohn's disease. We aimed to elucidate the cellular phenomena underlying resistance to anti-TNF therapy in patients with Crohn's disease and to identify potential drug candidates for these patients. Single-cell transcriptome analyses were performed using data (GSE134809) from the Gene Expression Omnibus and Library of Integrated Network-Based Cellular Signatures L1000 Project. Data aligned to the Genome Reference Consortium Human Build 38 reference genome using the Cell Ranger software were processed using the Seurat package. To capture significant functional terms, gene ontology functional enrichment analysis was performed on the marker genes. For biological analysis, 93,893 cells were retained (median 20,163 genes). Through marker genes, seven major cell lineages were identified: B-cells, T-cells, natural killer cells, monocytes, endothelial cells, epithelial cells, and tissue stem cells. In the anti-TNF-resistant samples, the top 10 differentially expressed genes were HLA-DQB-1, IGHG1, RPS23, RPL7A, ARID5B, LTB, STAT1, NAMPT, COTL1, ISG20, IGHA1, IGKC, and JCHAIN, which were robustly distributed in all cell lineages, mainly in B-cells. Through molecular function analyses, we found that the biological functions of both monocyte and T-cell groups mainly involved immune-mediated functions. According to multi-cluster drug repurposing prediction, vorinostat is the top drug candidate for patients with anti-TNF-refractory Crohn's disease. Differences in cell populations and immune-related activity within tissues may influence the responsiveness of Crohn's disease to anti-TNF agents. Vorinostat may serve as a promising novel therapy for anti-TNF-resistant Crohn's disease.
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Affiliation(s)
- Min Seob Kwak
- Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul 05278, Republic of Korea
| | - Chang-Il Hwang
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California Davis, Davis, CA 95616, USA;
| | - Jae Myung Cha
- Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul 05278, Republic of Korea
| | - Jung Won Jeon
- Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul 05278, Republic of Korea
| | - Jin Young Yoon
- Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul 05278, Republic of Korea
| | - Su Bee Park
- Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul 05278, Republic of Korea
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132
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Yang Y, Zhang Y, Ren J, Feng K, Li Z, Huang T, Cai Y. Identification of Colon Immune Cell Marker Genes Using Machine Learning Methods. Life (Basel) 2023; 13:1876. [PMID: 37763280 PMCID: PMC10532943 DOI: 10.3390/life13091876] [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: 07/30/2023] [Revised: 08/24/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Immune cell infiltration that occurs at the site of colon tumors influences the course of cancer. Different immune cell compositions in the microenvironment lead to different immune responses and different therapeutic effects. This study analyzed single-cell RNA sequencing data in a normal colon with the aim of screening genetic markers of 25 candidate immune cell types and revealing quantitative differences between them. The dataset contains 25 classes of immune cells, 41,650 cells in total, and each cell is expressed by 22,164 genes at the expression level. They were fed into a machine learning-based stream. The five feature ranking algorithms (last absolute shrinkage and selection operator, light gradient boosting machine, Monte Carlo feature selection, minimum redundancy maximum relevance, and random forest) were first used to analyze the importance of gene features, yielding five feature lists. Then, incremental feature selection and two classification algorithms (decision tree and random forest) were combined to filter the most important genetic markers from each list. For different immune cell subtypes, their marker genes, such as KLRB1 in CD4 T cells, RPL30 in B cell IGA plasma cells, and JCHAIN in IgG producing B cells, were identified. They were confirmed to be differentially expressed in different immune cells and involved in immune processes. In addition, quantitative rules were summarized by using the decision tree algorithm to distinguish candidate immune cell types. These results provide a reference for exploring the cell composition of the colon cancer microenvironment and for clinical immunotherapy.
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Affiliation(s)
- Yong Yang
- Qianwei Hospital of Jilin Province, Changchun 130012, China;
| | - Yuhang Zhang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Jingxin Ren
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China;
| | - Zhandong Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun 130052, China;
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yudong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
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133
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Kamal S, Parkash N, Beattie W, Christensen B, Segal JP. Are We Ready to Reclassify Crohn's Disease Using Molecular Classification? J Clin Med 2023; 12:5786. [PMID: 37762727 PMCID: PMC10532006 DOI: 10.3390/jcm12185786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/21/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Crohn's disease (CD) is a type of inflammatory bowel disease. The number of IBD cases worldwide was estimated to be 4.9 million in 2019. CD exhibits heterogeneity in clinical presentation, anatomical involvement, disease behaviour, clinical course and response to treatment. The classical description of CD involves transmural inflammation with skip lesions anywhere along the entire gastrointestinal tract. The complexity and heterogeneity of Crohn's disease is not currently reflected in the conventional classification system. Though the knowledge of Crohn's pathophysiology remains far from understood, the established complex interplay of the omics-genomics, transcriptomics, proteomics, epigenomics, metagenomics, metabolomics, lipidomics and immunophenomics-provides numerous targets for potential molecular markers of disease. Advancing technology has enabled identification of small molecules within these omics, which can be extrapolated to differentiate types of Crohn's disease. The multi-omic future of Crohn's disease is promising, with potential for advancements in understanding of its pathogenesis and implementation of personalised medicine.
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Affiliation(s)
- Shahed Kamal
- Department of Gastroenterology, Northern Hospital, Epping, Melbourne VIC 3076, Australia
| | - Nikita Parkash
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - William Beattie
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - Britt Christensen
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
| | - Jonathan P. Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
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134
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Zilbauer M, James KR, Kaur M, Pott S, Li Z, Burger A, Thiagarajah JR, Burclaff J, Jahnsen FL, Perrone F, Ross AD, Matteoli G, Stakenborg N, Sujino T, Moor A, Bartolome-Casado R, Bækkevold ES, Zhou R, Xie B, Lau KS, Din S, Magness ST, Yao Q, Beyaz S, Arends M, Denadai-Souza A, Coburn LA, Gaublomme JT, Baldock R, Papatheodorou I, Ordovas-Montanes J, Boeckxstaens G, Hupalowska A, Teichmann SA, Regev A, Xavier RJ, Simmons A, Snyder MP, Wilson KT. A Roadmap for the Human Gut Cell Atlas. Nat Rev Gastroenterol Hepatol 2023; 20:597-614. [PMID: 37258747 PMCID: PMC10527367 DOI: 10.1038/s41575-023-00784-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2023] [Indexed: 06/02/2023]
Abstract
The number of studies investigating the human gastrointestinal tract using various single-cell profiling methods has increased substantially in the past few years. Although this increase provides a unique opportunity for the generation of the first comprehensive Human Gut Cell Atlas (HGCA), there remains a range of major challenges ahead. Above all, the ultimate success will largely depend on a structured and coordinated approach that aligns global efforts undertaken by a large number of research groups. In this Roadmap, we discuss a comprehensive forward-thinking direction for the generation of the HGCA on behalf of the Gut Biological Network of the Human Cell Atlas. Based on the consensus opinion of experts from across the globe, we outline the main requirements for the first complete HGCA by summarizing existing data sets and highlighting anatomical regions and/or tissues with limited coverage. We provide recommendations for future studies and discuss key methodologies and the importance of integrating the healthy gut atlas with related diseases and gut organoids. Importantly, we critically overview the computational tools available and provide recommendations to overcome key challenges.
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Affiliation(s)
- Matthias Zilbauer
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- University Department of Paediatrics, University of Cambridge, Cambridge, UK.
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Cambridge, UK.
| | - Kylie R James
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mandeep Kaur
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sebastian Pott
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zhixin Li
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Albert Burger
- Department of Computer Science, Heriot-watt University, Edinburgh, UK
| | - Jay R Thiagarajah
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University', Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Frode L Jahnsen
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Francesca Perrone
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- University Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Alexander D Ross
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- University Department of Paediatrics, University of Cambridge, Cambridge, UK
- University Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Gianluca Matteoli
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Nathalie Stakenborg
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Tomohisa Sujino
- Center for the Diagnostic and Therapeutic Endoscopy, School of Medicine, Keio University, Tokyo, Japan
| | - Andreas Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Raquel Bartolome-Casado
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, UK
| | - Espen S Bækkevold
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ran Zhou
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Bingqing Xie
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shahida Din
- Edinburgh IBD Unit, Western General Hospital, NHS Lothian, Edinburgh, UK
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University', Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qiuming Yao
- Department of Computer Science and Engineering, University of Nebraska Lincoln, Lincoln, NE, USA
| | - Semir Beyaz
- Cold Spring Harbour Laboratory, Cold Spring Harbour, New York, NY, USA
| | - Mark Arends
- Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, Institute of Cancer and Genetics, University of Edinburgh, Edinburgh, UK
| | - Alexandre Denadai-Souza
- Laboratory of Mucosal Biology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Lori A Coburn
- Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | | | | | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Guy Boeckxstaens
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Hinxton, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK
| | - Aviv Regev
- Genentech, San Francisco, CA, USA
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alison Simmons
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Keith T Wilson
- Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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135
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Yang X, Shi J, Wang G, Chen H, Ye Y, Zhong J, Wang Z. Novel mRNA Signature for Anti-TNF-α Therapy Primary Response in Patients With Ulcerative Colitis. Inflamm Bowel Dis 2023; 29:1458-1469. [PMID: 37080716 DOI: 10.1093/ibd/izad060] [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: 01/05/2023] [Indexed: 04/22/2023]
Abstract
BACKGROUND Ulcerative colitis (UC), an idiopathic, chronic inflammatory disorder of the colonic mucosa, is commonly treated with antitumor necrosis factor α (anti-TNF-α) agents. However, only approximately two-thirds have an initial response to these therapies. METHODS We integrated gene expression profiling from 3 independent data sets of 79 UC patients before they began anti-TNF-α therapy and calculated the differentially expressed genes between patient response and nonresponse to anti-TNF-α therapy and developed a de novo response-associated transcription signature score (logOR_Score) to demonstrate the predictive capability of anti-TNF-α therapy for therapeutic efficacy. Furthermore, we performed association analysis of the logOR_Score and clinical features, such as disease activity and immune microenvironment. RESULTS A total of 2522 responsive and 1824 nonresponsive genes were identified from the integrated data set. Responsive genes were significantly enriched in metabolism-related pathways, whereas nonresponsive ones were associated with immune response-related pathways. The logOR_Score enabled the accurate prediction of the therapeutic efficacy of anti-TNF-α in 4 independent patient cohorts and outperformed the predictions made based on 6 transcriptome-based signatures. In terms of clinical features, the logOR_Score correlated highly with the activity of UC. From an immune microenvironment perspective, logOR_Scores of CD8+IL-17+ T cells, follicular B cells, and innate lymphoid cells significantly decreased in inflamed UC tissue. CONCLUSIONS The de novo response-associated transcription signature may provide novel insights into the personalized treatment of patients with UC. Comprehensive analyses of the response-related subtypes and the association between logOR_Score and clinical features and immune microenvironment may provide insights into the underlying UC pathogenesis.
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Affiliation(s)
- Xinhui Yang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Jintong Shi
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Gaoyang Wang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Huifang Chen
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Youqiong Ye
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Jie Zhong
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Zhengting Wang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
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Spencer EA. Choosing the Right Therapy at the Right Time for Pediatric Inflammatory Bowel Disease: Does Sequence Matter. Gastroenterol Clin North Am 2023; 52:517-534. [PMID: 37543397 DOI: 10.1016/j.gtc.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2023]
Abstract
Despite the enlarging therapeutic armamentarium, IBD is still plagued by a therapeutic ceiling. Precision medicine, with the selection of the "rights," may present a solution, and this review will discuss the critical process of pairing the right patient with right therapy at the right time. Firstly, the review will discuss the shift to and evidence behind early effective therapy. Then, it delves into promising future strategies of patient profiling to identify a patients' biological pathway(s) and prognosis. Finally, the review lays out practical considerations that drive treatment selection, particularly the impact of the therapeutic sequence.
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Affiliation(s)
- Elizabeth A Spencer
- Division of Pediatric Gastroenterology & Nutrition, Department of Pediatrics, Icahn School of Medicine, Mount Sinai, 17 East 102nd Street, 5th Floor, New York, NY 10029, USA.
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137
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Wang Y, Yu Y, Li L, Zheng M, Zhou J, Gong H, Feng B, Wang X, Meng X, Cui Y, Xia Y, Chu S, Lin L, Chang H, Zhou R, Ma M, Li Z, Ji R, Lu M, Yang X, Zuo X, Li S, Li Y. Bile acid-dependent transcription factors and chromatin accessibility determine regional heterogeneity of intestinal antimicrobial peptides. Nat Commun 2023; 14:5093. [PMID: 37607912 PMCID: PMC10444805 DOI: 10.1038/s41467-023-40565-7] [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: 10/26/2022] [Accepted: 08/01/2023] [Indexed: 08/24/2023] Open
Abstract
Antimicrobial peptides (AMPs) are important mediators of intestinal immune surveillance. However, the regional heterogeneity of AMPs and its regulatory mechanisms remain obscure. Here, we clarified the regional heterogeneity of intestinal AMPs at the single-cell level, and revealed a cross-lineages AMP regulation mechanism that bile acid dependent transcription factors (BATFs), NR1H4, NR1H3 and VDR, regulate AMPs through a ligand-independent manner. Bile acids regulate AMPs by perturbing cell differentiation rather than activating BATFs signaling. Chromatin accessibility determines the potential of BATFs to regulate AMPs at the pre-transcriptional level, thus shaping the regional heterogeneity of AMPs. The BATFs-AMPs axis also participates in the establishment of intestinal antimicrobial barriers of fetuses and the defects of antibacterial ability during Crohn's disease. Overall, BATFs and chromatin accessibility play essential roles in shaping the regional heterogeneity of AMPs at pre- and postnatal stages, as well as in maintenance of antimicrobial immunity during homeostasis and disease.
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Affiliation(s)
- Yue Wang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Yanbo Yu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China
| | - Lixiang Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China
| | - Mengqi Zheng
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Jiawei Zhou
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Haifan Gong
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Bingcheng Feng
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Xiao Wang
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, China
| | - Xuanlin Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanyan Cui
- Advanced Medical Research Institute, Shandong University, Jinan, China
| | - Yanan Xia
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Shuzheng Chu
- Advanced Medical Research Institute, Shandong University, Jinan, China
| | - Lin Lin
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Huijun Chang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Ruchen Zhou
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Mingjun Ma
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Zhen Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China
| | - Rui Ji
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China
| | - Ming Lu
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Xiaoyun Yang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China
| | - Xiuli Zuo
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China.
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China.
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China.
| | - Shiyang Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China.
- Advanced Medical Research Institute, Shandong University, Jinan, China.
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, China.
| | - Yanqing Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China.
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China.
- Shandong Provincial Clinical Research Center for digestive disease, Jinan, China.
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138
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Lin S, Hannon E, Reppell M, Waring JF, Smaoui N, Pivorunas V, Guay H, Chanchlani N, Bewshea C, Bai BYH, Kennedy NA, Goodhand JR, Mill J, Ahmad T. Whole blood DNA methylation changes are associated with anti-TNF drug concentration in patients with Crohn's disease. J Crohns Colitis 2023:jjad133. [PMID: 37551994 DOI: 10.1093/ecco-jcc/jjad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND AND AIMS Anti-TNF treatment failure in patients with inflammatory bowel disease (IBD) is common and frequently related to low drug concentrations. In order to identify patients who may benefit from dose optimisation at the outset of anti-TNF therapy, we sought to define epigenetic biomarkers in whole blood at baseline associated with anti-TNF drug concentrations at week 14. METHODS DNA methylation from 1,104 whole blood samples from 385 patients in the Personalised Anti-TNF Therapy in Crohn's disease (PANTS) study were assessed using the Illumina EPIC Beadchip (v1.0) at baseline, weeks 14, 30 and 54. We compared DNA methylation profiles in anti-TNF-treated patients who experienced primary non-response at week 14 and if they were assessed at subsequent time points, were not in remission at week 30 or 54 (infliximab n = 99, adalimumab n = 94), with patients who responded at week 14 and when assessed at subsequent time points, were in remission at week 30 or 54 (infliximab n = 99, adalimumab n = 93). RESULTS Overall, between baseline and week 14, we observed 4,999 differentially methylated probes (DMPs) annotated to 2376 genes following anti-TNF treatment. Pathway analysis identified 108 significant gene ontology terms enriched in biological processes related to immune system processes and responses.Epigenome-wide association (EWAS) analysis identified 323 DMPs annotated to 210 genes at baseline associated with higher anti-TNF drug concentrations at week 14. Of these, 125 DMPs demonstrated shared associations with other common traits (proportion of shared CpGs compared to DMPs) including body mass index (23.2%), followed by CRP (11.5%), smoking (7.4%), alcohol consumption per day (7.1%) and IBD type (6.8%). EWAS of primary non-response to anti-TNF identified 20 DMPs that were associated with both anti-TNF drug concentration and primary non-response to anti-TNF with a strong correlation of the coefficients (Spearman's rho = -0.94, p < 0.001). CONCLUSION Baseline DNA methylation profiles may be used as a predictor for anti-TNF drug concentration at week 14 to identify patients who may benefit from dose optimisation at the outset of anti-TNF therapy.
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Affiliation(s)
- Simeng Lin
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | | | | | | | | | | | - Neil Chanchlani
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Claire Bewshea
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Benjamin Y H Bai
- Genomics of Inflammation and Immunity Group, Wellcome Sanger Institute, Hinxton, UK
- Postgraduate School of Life Sciences, University of Cambridge, Cambridge, UK
| | - Nicholas A Kennedy
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - James R Goodhand
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Tariq Ahmad
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
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139
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Zhou L, Zhu L, Wu X, Hu S, Zhang S, Ning M, Yu J, Chen M. Decreased TMIGD1 aggravates colitis and intestinal barrier dysfunction via the BANF1-NF-κB pathway in Crohn's disease. BMC Med 2023; 21:287. [PMID: 37542259 PMCID: PMC10403950 DOI: 10.1186/s12916-023-02989-2] [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: 01/16/2023] [Accepted: 07/20/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND Disrupted intestinal epithelial barrier is one of the major causes of Crohn's disease (CD). Novel molecular targets for intestinal epithelial barrier are essential to treatment of CD. Transmembrane and immunoglobulin domain-containing protein 1 (TMIGD1) is an adhesion molecule that regulates cell adhesion, migration, and enterocyte differentiation. However, the function and mechanism of TMIGD1 in CD and intestinal epithelial barrier has rarely been studied. Furthermore, the association between TMIGD1 and the clinical features of CD remains unclear. METHODS Transcriptome analysis on colonic mucosa from CD patients and healthy individuals were performed to identify dysregulated genes. Multi-omics integration of the 1000IBD cohort including genomics, transcriptomics of intestinal biopsies, and serum proteomics identified the association between genes and characteristics of CD. Inflammation was assessed by cytokine production in cell lines, organoids and intestinal-specific Tmigd1 knockout (Tmigd1INT-KO) mice. Epithelial barrier integrity was evaluated by trans-epithelium electrical resistance (TEER), paracellular permeability, and apical junction complex (AJC) expression. Co-immunoprecipitation, GST pull-down assays, mass spectrometry, proteomics, and transcriptome analysis were used to explore downstream mechanisms. RESULTS Multi-omics integration suggested that TMIGD1 was negatively associated with inflammatory characteristics of CD. TMIGD1 was downregulated in inflamed intestinal mucosa of patients with CD and mice colitis models. Tmigd1INT-KO mice were more susceptible to chemically induced colitis. In epithelial cell lines and colonic organoids, TMIGD1 knockdown caused impaired intestinal barrier integrity evidenced by increased paracellular permeability and reduced TEER and AJC expression. TMIGD1 knockdown in intestinal epithelial cells also induced pro-inflammatory cytokine production. Mechanistically, TMIGD1 directly interacted with cytoplasmic BAF nuclear assembly factor 1 (BANF1) to inhibit NF-κB activation. Exogenous expression of TMIGD1 and BANF1 restored intestinal barrier function and inhibited inflammation in vitro and in vivo. TMIGD1 expression predicted response to anti-TNF treatment in patients with CD. CONCLUSIONS Our study demonstrated that TMIGD1 maintained intestinal barrier integrity and inactivated inflammation, and was therefore a potential therapeutic target for CD.
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Affiliation(s)
- Longyuan Zhou
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Liguo Zhu
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Xiaomin Wu
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Shixian Hu
- Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Shenghong Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Min Ning
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Jun Yu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China.
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140
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Medina TS, Murison A, Smith M, Kinker GS, Chakravarthy A, Vitiello GAF, Turpin W, Shen SY, Yau HL, Sarmento OF, Faubion W, Lupien M, Silverberg MS, Arrowsmith CH, De Carvalho DD. The chromatin and single-cell transcriptional landscapes of CD4 T cells in inflammatory bowel disease link risk loci with a proinflammatory Th17 cell population. Front Immunol 2023; 14:1161901. [PMID: 37600767 PMCID: PMC10436103 DOI: 10.3389/fimmu.2023.1161901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction The imbalance between Th17 and regulatory T cells in inflammatory bowel diseases (IBD) promotes intestinal epithelial cell damage. In this scenario, T helper cell lineage commitment is accompanied by dynamic changes to the chromatin that facilitate or repress gene expression. Methods Here, we characterized the chromatin landscape and heterogeneity of intestinal and peripheral CD4 T cellsfrom IBD patients using in house ATAC-Seq and single cell RNA-Seq libraries. Results We show that chromatin accessibility profiles of CD4 T cells from inflamed intestinal biopsies relate to genes associated with a network of inflammatory processes. After integrating the chromatin profiles of tissue-derived CD4 T cells and in-vitro polarized CD4 T cell subpopulations, we found that the chromatin accessibility changes of CD4 T cells were associated with a higher predominance of pathogenic Th17 cells (pTh17 cells) in inflamed biopsies. In addition, IBD risk loci in CD4 T cells were colocalized with accessible chromatin changes near pTh17-related genes, as shown in intronic STAT3 and IL23R regions enriched in areas of active intestinal inflammation. Moreover, single cell RNA-Seq analysis revealed a population of pTh17 cells that co-expresses Th1 and cytotoxic transcriptional programs associated with IBD severity. Discussion Altogether, we show that cytotoxic pTh17 cells were specifically associated with IBD genetic variants and linked to intestinal inflammation of IBD patients.
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Affiliation(s)
- Tiago S. Medina
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michelle Smith
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Gabriela S. Kinker
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Williams Turpin
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Helen L. Yau
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Olga F. Sarmento
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - William Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Mark S. Silverberg
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Cheryl H. Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Daniel D. De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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141
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Kang J, Kim M, Yoon DY, Kim WS, Choi SJ, Kwon YN, Kim WS, Park SH, Sung JJ, Park M, Lee JS, Park JE, Kim SM. AXL +SIGLEC6 + dendritic cells in cerebrospinal fluid and brain tissues of patients with autoimmune inflammatory demyelinating disease of CNS. Clin Immunol 2023; 253:109686. [PMID: 37414380 DOI: 10.1016/j.clim.2023.109686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/26/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023]
Abstract
Inflammatory demyelinating disease of the CNS (IDD) is a heterogeneous group of autoimmune diseases, and multiple sclerosis is the most common type. Dendritic cells (DCs), major antigen-presenting cells, have been proposed to play a central role in the pathogenesis of IDD. The AXL+SIGLEC6+ DC (ASDC) has been only recently identified in humans and has a high capability of T cell activation. Nevertheless, its contribution to CNS autoimmunity remains still obscure. Here, we aimed to identify the ASDC in diverse sample types from IDD patients and experimental autoimmune encephalomyelitis (EAE). A detailed analysis of DC subpopulations using single-cell transcriptomics for the paired cerebrospinal fluid (CSF) and blood samples of IDD patients (total n = 9) revealed that three subtypes of DCs (ASDCs, ACY3+ DCs, and LAMP3+ DCs) were overrepresented in CSF compared with their paired blood. Among these DCs, ASDCs were also more abundant in CSF of IDD patients than in controls, manifesting poly-adhesional and stimulatory characteristics. In the brain biopsied tissues of IDD patients, obtained at the acute attack of disease, ASDC were also frequently found in close contact with T cells. Lastly, the frequency of ASDC was found to be temporally more abundant in acute attack of disease both in CSF samples of IDD patients and in tissues of EAE, an animal model for CNS autoimmunity. Our analysis suggests that the ASDC might be involved in the pathogenesis of CNS autoimmunity.
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Affiliation(s)
- Junho Kang
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Moonhang Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Da-Young Yoon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Woo-Seok Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Seok-Jin Choi
- Department of Neurology, Seoul National University Hospital, Seoul National University of Medicine, Seoul, Republic of Korea
| | - Young-Nam Kwon
- Department of Neurology, Seoul National University Hospital, Seoul National University of Medicine, Seoul, Republic of Korea
| | - Won-Seok Kim
- Department of Neurology, Seoul National University Hospital, Seoul National University of Medicine, Seoul, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul National University of Medicine, Seoul, Republic of Korea
| | - Jung-Joon Sung
- Department of Neurology, Seoul National University Hospital, Seoul National University of Medicine, Seoul, Republic of Korea
| | - Myungsun Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jung Seok Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jong-Eun Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
| | - Sung-Min Kim
- Department of Neurology, Seoul National University Hospital, Seoul National University of Medicine, Seoul, Republic of Korea.
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142
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Zheng HB. Application of single-cell omics in inflammatory bowel disease. World J Gastroenterol 2023; 29:4397-4404. [PMID: 37576705 PMCID: PMC10415967 DOI: 10.3748/wjg.v29.i28.4397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023] Open
Abstract
Over the past decade, the advent of single cell RNA-sequencing has revolutionized the approach in cellular transcriptomics research. The current technology offers an unbiased platform to understand how genotype correlates to phenotype. Single-cell omics applications in gastrointestinal (GI) research namely inflammatory bowel disease (IBD) has become popular in the last few years with multiple publications as single-cell omics techniques can be applied directly to the target organ, the GI tract at the tissue level. Through examination of mucosal tissue and peripheral blood in IBD, the recent boom in single cell research has identified a myriad of key immune players from enterocytes to tissue resident memory T cells, and explored functional heterogeneity within cellular subsets previously unreported. As we begin to unravel the complex mucosal immune system in states of health and disease like IBD, the power of exploration through single-cell omics can change our approach to translational research. As novel techniques evolve through multiplexing single-cell omics and spatial transcriptomics come to the forefront, we can begin to fully comprehend the disease IBD and better design targets of treatment. In addition, hopefully these techniques can ultimately begin to identify biomarkers of therapeutic response and answer clinically relevant questions in how to tailor individual therapy to patients through personalized medicine.
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Affiliation(s)
- Hengqi Betty Zheng
- Department of Pediatrics, Seattle Children’s Hospital, University of Washington, Seattle, WA 98105, United States
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143
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Garrido-Trigo A, Corraliza AM, Veny M, Dotti I, Melón-Ardanaz E, Rill A, Crowell HL, Corbí Á, Gudiño V, Esteller M, Álvarez-Teubel I, Aguilar D, Masamunt MC, Killingbeck E, Kim Y, Leon M, Visvanathan S, Marchese D, Caratù G, Martin-Cardona A, Esteve M, Ordás I, Panés J, Ricart E, Mereu E, Heyn H, Salas A. Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease. Nat Commun 2023; 14:4506. [PMID: 37495570 PMCID: PMC10372067 DOI: 10.1038/s41467-023-40156-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
Ulcerative colitis and Crohn's disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in disease manifestation and response to treatment. While the molecular basis for this heterogeneity remains uncharacterized, single-cell technologies allow us to explore the transcriptional states within tissues at an unprecedented resolution which could further understanding of these complex diseases. Here, we apply single-cell RNA-sequencing to human inflamed intestine and show that the largest differences among patients are present within the myeloid compartment including macrophages and neutrophils. Using spatial transcriptomics in human tissue at single-cell resolution (CosMx Spatial Molecular Imaging) we spatially localize each of the macrophage and neutrophil subsets identified by single-cell RNA-sequencing and unravel further macrophage diversity based on their tissue localization. Finally, single-cell RNA-sequencing combined with single-cell spatial analysis reveals a strong communication network involving macrophages and inflammatory fibroblasts. Our data sheds light on the cellular complexity of these diseases and points towards the myeloid and stromal compartments as important cellular subsets for understanding patient-to-patient heterogeneity.
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Affiliation(s)
- Alba Garrido-Trigo
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Ana M Corraliza
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Marisol Veny
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Isabella Dotti
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Elisa Melón-Ardanaz
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Aina Rill
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Helena L Crowell
- Department of Molecular Life Sciences, University of Zurich, Switzerland. SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Ángel Corbí
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Victoria Gudiño
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Miriam Esteller
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Iris Álvarez-Teubel
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Daniel Aguilar
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - M Carme Masamunt
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | | | | | | | - Sudha Visvanathan
- Translational Medicine and Clinical Pharmacology, Boehringer-Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ginevra Caratù
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Albert Martin-Cardona
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Universitat de Barcelona, Terrassa, Spain
| | - Maria Esteve
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Universitat de Barcelona, Terrassa, Spain
| | - Ingrid Ordás
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Julian Panés
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Elena Ricart
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Elisabetta Mereu
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Azucena Salas
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain.
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Staufer T, Körnig C, Liu B, Liu Y, Lanzloth C, Schmutzler O, Bedke T, Machicote A, Parak WJ, Feliu N, Bosurgi L, Huber S, Grüner F. Enabling X-ray fluorescence imaging for in vivo immune cell tracking. Sci Rep 2023; 13:11505. [PMID: 37460665 DOI: 10.1038/s41598-023-38536-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
The infiltration of immune cells into sites of inflammation is one key feature of immune mediated inflammatory diseases. A detailed assessment of the in vivo dynamics of relevant cell subtypes could booster the understanding of this disease and the development of novel therapies. We show in detail how advanced X-ray fluorescence imaging enables such quantitative in vivo cell tracking, offering solutions that could pave the way beyond what other imaging modalities provide today. The key for this achievement is a detailed study of the spectral background contribution from multiple Compton scattering in a mouse-scaled object when this is scanned with a monochromatic pencil X-ray beam from a synchrotron. Under optimal conditions, the detection sensitivity is sufficient for detecting local accumulations of the labelled immune cells, hence providing experimental demonstration of in vivo immune cell tracking in mice.
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Affiliation(s)
- Theresa Staufer
- Fachbereich Physik, Universität Hamburg, 22761, Hamburg, Germany.
- Center for Free-Electron Laser Science (CFEL), 22761, Hamburg, Germany.
| | - Christian Körnig
- Fachbereich Physik, Universität Hamburg, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science (CFEL), 22761, Hamburg, Germany
| | - Beibei Liu
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Yang Liu
- Fachbereich Physik, Universität Hamburg, 22761, Hamburg, Germany
- Center for Hybrid Nanostructures (CHyN), Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Clarissa Lanzloth
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany
| | - Oliver Schmutzler
- Fachbereich Physik, Universität Hamburg, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science (CFEL), 22761, Hamburg, Germany
| | - Tanja Bedke
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Andres Machicote
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Wolfgang J Parak
- Fachbereich Physik, Universität Hamburg, 22761, Hamburg, Germany
- Center for Hybrid Nanostructures (CHyN), Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Neus Feliu
- Fraunhofer Center for Applied Nanotechnology (IAP-CAN), 20146, Hamburg, Germany
| | - Lidia Bosurgi
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany
| | - Samuel Huber
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Florian Grüner
- Fachbereich Physik, Universität Hamburg, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science (CFEL), 22761, Hamburg, Germany
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145
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Mo S, Jin B, Tseng Y, Lin L, Lin L, Shen X, Song H, Kong M, Luo Z, Chu Y, Jiang C, Cao Z, Liu J, Luo F. A precise molecular subtyping of ulcerative colitis reveals the immune heterogeneity and predicts clinical drug responses. J Transl Med 2023; 21:466. [PMID: 37443022 PMCID: PMC10347743 DOI: 10.1186/s12967-023-04326-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND AND AIMS We sought to identify novel molecular subtypes of ulcerative colitis (UC) based on large-scale cohorts and establish a clinically applicable subtyping system for the precision treatment of the disease. METHODS Eight microarray profiles containing colon samples from 357 patients were utilized. Expression heterogeneity was screened out and stable subtypes were identified among UC patients. Immune infiltration pattern and biological agent response were compared among subtypes to assess the value in guiding treatment. The relationship between PRLR and TNFSF13B genes with the highest predictive value was further validated by functional experiments. RESULTS Three stable molecular subtypes were successfully identified. Immune cell infiltration analysis defined three subtypes as innate immune activated UC (IIA), whole immune activated UC (WIA), and immune homeostasis like UC (IHL). Notably, the response rate towards biological agents (infliximab/vedolizumab) in WIA patients was the lowest (less than 10%), while the response rate in IHL patients was the highest, ranging from 42 to 60%. Among the featured genes of subtypes, the ratio of PRLR to TNFSF13B could effectively screen for IHL UC subtype suitable for biological agent therapies (Area under curve: 0.961-0.986). Furthermore, we demonstrated that PRLR expressed in epithelial cells could inhibit the expression of TNFSF13B in monocyte-derived macrophages through the CXCL1-NF-κB pathway. CONCLUSIONS We identified three stable UC subtypes with a heterogeneous immune pattern and different response rates towards biological agents for the first time. We also established a precise molecular subtyping system and classifier to predict clinical drug response and provide individualized treatment strategies for UC patients.
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Affiliation(s)
- Shaocong Mo
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Bryan Jin
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Yujen Tseng
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Lingxi Lin
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Lishuang Lin
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xin Shen
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Huan Song
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Mingjia Kong
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Zhongguang Luo
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China
| | - Yiwei Chu
- Biotherapy Research Center, Department of Immunology, School of Basic Medical Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Chen Jiang
- Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhiwei Cao
- School of Life Sciences, Fudan University, Shanghai, 200433, China
- School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jie Liu
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Feifei Luo
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
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146
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Chauvin C, Alvarez-Simon D, Radulovic K, Boulard O, Laine W, Delacre M, Waldschmitt N, Segura E, Kluza J, Chamaillard M, Poulin LF. NOD2 in monocytes negatively regulates macrophage development through TNFalpha. Front Immunol 2023; 14:1181823. [PMID: 37415975 PMCID: PMC10320732 DOI: 10.3389/fimmu.2023.1181823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/23/2023] [Indexed: 07/08/2023] Open
Abstract
Objective It is believed that intestinal recruitment of monocytes from Crohn's Disease (CD) patients who carry NOD2 risk alleles may repeatedly give rise to recruitment of pathogenic macrophages. We investigated an alternative possibility that NOD2 may rather inhibit their differentiation from intravasating monocytes. Design The monocyte fate decision was examined by using germ-free mice, mixed bone marrow chimeras and a culture system yielding macrophages and monocyte-derived dendritic cells (mo-DCs). Results We observed a decrease in the frequency of mo-DCs in the colon of Nod2-deficient mice, despite a similar abundance of monocytes. This decrease was independent of the changes in the gut microbiota and dysbiosis caused by Nod2 deficiency. Similarly, the pool of mo-DCs was poorly reconstituted in a Nod2-deficient mixed bone marrow (BM) chimera. The use of pharmacological inhibitors revealed that activation of NOD2 during monocyte-derived cell development, dominantly inhibits mTOR-mediated macrophage differentiation in a TNFα-dependent manner. These observations were supported by the identification of a TNFα-dependent response to muramyl dipeptide (MDP) that is specifically lost when CD14-expressing blood cells bear a frameshift mutation in NOD2. Conclusion NOD2 negatively regulates a macrophage developmental program through a feed-forward loop that could be exploited for overcoming resistance to anti-TNF therapy in CD.
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Affiliation(s)
- Camille Chauvin
- U1019, Institut Pasteur de Lille, Univ. Lille, Centre National de la Recherche Scientifique, Inserm, Centre Hospitalo- Universitaire Lille, Lille, France
- INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
| | - Daniel Alvarez-Simon
- U1019, Institut Pasteur de Lille, Univ. Lille, Centre National de la Recherche Scientifique, Inserm, Centre Hospitalo- Universitaire Lille, Lille, France
| | - Katarina Radulovic
- Unité de Recherche Clinique, Centre Hospitalier de Valenciennes, Valenciennes CEDEX, France
| | | | - William Laine
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, University Lille, Lille, France
| | - Myriam Delacre
- U1019, Institut Pasteur de Lille, Univ. Lille, Centre National de la Recherche Scientifique, Inserm, Centre Hospitalo- Universitaire Lille, Lille, France
| | - Nadine Waldschmitt
- Chair of Nutrition and Immunology, School of Life Sciences, Technische Universität München, Freising-Weihenstephan, Germany
| | - Elodie Segura
- INSERM U932, Institut Curie, Paris Sciences et Lettres Research University, Paris, France
| | - Jérome Kluza
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, University Lille, Lille, France
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147
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Campbell I, Glinka M, Shaban F, Kirkwood KJ, Nadalin F, Adams D, Papatheodorou I, Burger A, Baldock RA, Arends MJ, Din S. The Promise of Single-Cell RNA Sequencing to Redefine the Understanding of Crohn's Disease Fibrosis Mechanisms. J Clin Med 2023; 12:3884. [PMID: 37373578 PMCID: PMC10299644 DOI: 10.3390/jcm12123884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory bowel disease with a high prevalence throughout the world. The development of Crohn's-related fibrosis, which leads to strictures in the gastrointestinal tract, presents a particular challenge and is associated with significant morbidity. There are currently no specific anti-fibrotic therapies available, and so treatment is aimed at managing the stricturing complications of fibrosis once it is established. This often requires invasive and repeated endoscopic or surgical intervention. The advent of single-cell sequencing has led to significant advances in our understanding of CD at a cellular level, and this has presented opportunities to develop new therapeutic agents with the aim of preventing or reversing fibrosis. In this paper, we discuss the current understanding of CD fibrosis pathogenesis, summarise current management strategies, and present the promise of single-cell sequencing as a tool for the development of effective anti-fibrotic therapies.
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Affiliation(s)
- Iona Campbell
- Edinburgh Inflammatory Bowel Disease Unit, Western General Hospital, NHS Lothian, Edinburgh EH4 2XU, UK
| | - Michael Glinka
- Edinburgh Pathology, Centre for Comparative Pathology, Cancer Research UK Scotland Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Fadlo Shaban
- Edinburgh Colorectal Unit, Western General Hospital, NHS Lothian, Edinburgh EH4 2XU, UK
| | - Kathryn J. Kirkwood
- Department of Pathology, Western General Hospital, NHS Lothian, Edinburgh EH4 2XU, UK
| | - Francesca Nadalin
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, Cambridge CB10 1SD, UK
| | - David Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, Cambridge CB10 1SD, UK
| | - Albert Burger
- Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK;
| | - Richard A. Baldock
- Edinburgh Pathology, Centre for Comparative Pathology, Cancer Research UK Scotland Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Mark J. Arends
- Edinburgh Pathology, Centre for Comparative Pathology, Cancer Research UK Scotland Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Shahida Din
- Edinburgh Inflammatory Bowel Disease Unit, Western General Hospital, NHS Lothian, Edinburgh EH4 2XU, UK
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Bamidele AO, Mishra SK, Hirsova P, Fehrenbach PJ, Valenzuela-Pérez L, Lee HSK. Interleukin-21 Drives a Hypermetabolic State and CD4 + T Cell-associated Pathogenicity in Chronic Intestinal Inflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543518. [PMID: 37333332 PMCID: PMC10274654 DOI: 10.1101/2023.06.02.543518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
BACKGROUND & AIMS Incapacitated regulatory T cells (Tregs) contribute to immune-mediated diseases. Inflammatory Tregs are evident during human inflammatory bowel disease (IBD); 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 Seahorse XF analyzer. We utilized Crohn's disease single-cell RNA sequencing dataset to infer 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 (ER) appositions, known to mediate pyruvate entry into mitochondria via VDAC1, are abundant in Tregs. VDAC1 inhibition perturbed pyruvate metabolism, eliciting sensitization to other inflammatory signals reversible by membrane-permeable methyl pyruvate (MePyr) supplementation. Notably, IL-21 diminished mitochondria-ER appositions, resulting in enhanced enzymatic function of glycogen synthase kinase 3 β (GSK3β), a putative negative regulator of VDAC1, and a hypermetabolic state that amplified Treg inflammatory response. MePyr and GSK3β pharmacologic inhibitor (LY2090314) reversed IL-21-induced metabolic rewiring and inflammatory state. Moreover, IL-21-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 IL-21 triggers metabolic dysfunction associated with Treg inflammatory response. Inhibiting IL-21-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, 200 First Street SW, Rochester, MN 55905, USA
- Department of Immunology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Shravan K Mishra
- Immunometabolism and Mucosal Immunity Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Petra Hirsova
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Patrick J Fehrenbach
- Immunometabolism and Mucosal Immunity Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Lucia Valenzuela-Pérez
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Hyun Se Kim Lee
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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149
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Jha D, Al-Taie Z, Krek A, Eshghi ST, Fantou A, Laurent T, Tankelevich M, Cao X, Meringer H, Livanos AE, Tokuyama M, Cossarini F, Bourreille A, Josien R, Hou R, Canales-Herrerias P, Ungaro RC, Kayal M, Marion J, Polydorides AD, Ko HM, D’souza D, Merand R, Kim-Schulze S, Hackney JA, Nguyen A, McBride JM, Yuan GC, Colombel JF, Martin JC, Argmann C, Suárez-Fariñas M, Petralia F, Mehandru S. Myeloid cell influx into the colonic epithelium is associated with disease severity and non-response to anti-Tumor Necrosis Factor Therapy in patients with Ulcerative Colitis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.542863. [PMID: 37333091 PMCID: PMC10274630 DOI: 10.1101/2023.06.02.542863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Ulcerative colitis (UC) is an idiopathic chronic inflammatory disease of the colon with sharply rising global prevalence. Dysfunctional epithelial compartment (EC) dynamics are implicated in UC pathogenesis although EC-specific studies are sparse. Applying orthogonal high-dimensional EC profiling to a Primary Cohort (PC; n=222), we detail major epithelial and immune cell perturbations in active UC. Prominently, reduced frequencies of mature BEST4+OTOP2+ absorptive and BEST2+WFDC2+ secretory epithelial enterocytes were associated with the replacement of homeostatic, resident TRDC+KLRD1+HOPX+ γδ+ T cells with RORA+CCL20+S100A4+ TH17 cells and the influx of inflammatory myeloid cells. The EC transcriptome (exemplified by S100A8, HIF1A, TREM1, CXCR1) correlated with clinical, endoscopic, and histological severity of UC in an independent validation cohort (n=649). Furthermore, therapeutic relevance of the observed cellular and transcriptomic changes was investigated in 3 additional published UC cohorts (n=23, 48 and 204 respectively) to reveal that non-response to anti-Tumor Necrosis Factor (anti-TNF) therapy was associated with EC related myeloid cell perturbations. Altogether, these data provide high resolution mapping of the EC to facilitate therapeutic decision-making and personalization of therapy in patients with UC.
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Affiliation(s)
- Divya Jha
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zainab Al-Taie
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Shadi Toghi Eshghi
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Aurelie Fantou
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Thomas Laurent
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Michael Tankelevich
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuan Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Hadar Meringer
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra E Livanos
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minami Tokuyama
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Cossarini
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arnaud Bourreille
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Regis Josien
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Ruixue Hou
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Pablo Canales-Herrerias
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan C. Ungaro
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maia Kayal
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Marion
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Huaibin M. Ko
- Department of Pathology and Cell Biology, Columbia University Medical Center-New York Presbyterian Hospital, New York, New York
| | - Darwin D’souza
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raphael Merand
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason A. Hackney
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Allen Nguyen
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Jacqueline M. McBride
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Jean Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerome C. Martin
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Carmen Argmann
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Saurabh Mehandru
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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150
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Shu W, Wang Y, Li C, Zhang L, Zhuoma D, Yang P, Yan G, Chen C, Ba Y, Du P, Wang X. Single-cell Expression Atlas Reveals Cell Heterogeneity in the Creeping Fat of Crohn's Disease. Inflamm Bowel Dis 2023; 29:850-865. [PMID: 36715181 DOI: 10.1093/ibd/izac266] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND Creeping fat (CrF) has been recognized to play a positive role in Crohn's disease (CD) progression, yet the cellular compositions within mesenteric adipose tissue (MAT) and their potential mechanism in CrF formation are poorly understood. METHODS Analysis of 10X single-cell RNA sequencing was performed on 67 064 cells from 3 pairs of surgically resected samples of CrF and their uninvolved MAT. The results were validated in another cohort with 6 paired MAT samples by immunofluorescence. RESULTS All samples manifested excellent consistency and repeatability in our study, and 10 cell types from the transcriptome atlas, including 20 clusters, were identified. In CrF, a specific vascular endothelial cell subpopulation highly expressing lipoprotein lipase was first identified, with a significantly increased proportion. This vascular endothelial cell subpopulation manifested robust peroxisome proliferator-activated receptor γ (PPARγ) transcription activity and an upregulated PPAR signaling pathway and was involved in lipid metabolism and the antibacterial response. A novel fibroblast subpopulation (FC3) with remarkable GREM1 and RFLNB expression was identified and validated to predominantly accumulate in the CrF. The FC3 was annotated as inflammation-associated fibroblasts, which are characterized by inflammatory responses and the regulation of Smad phosphorylation related to intestinal fibrosis. The trajectory of fibroblasts revealed their pro-inflammatory and profibrotic conversion tendency during CrF formation with corresponding gene dynamics. Additionally, we unprecedently dissected the different origins and functions of 6 macrophage subclusters within the myeloid compartment. CONCLUSIONS Our results uncover the cellular heterogeneity in the MAT of CD and the role of these various cellular compositions in CrF development. This comprehensive understanding of CrF provides future directions for in-depth research on and potential targets for MAT-based treatment.
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Affiliation(s)
- Weigang Shu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yongheng Wang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Chuanding Li
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Lei Zhang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Deji Zhuoma
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Pengyu Yang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Guorong Yan
- Institute of Photomedicine, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai 200443, China
| | - Chunqiu Chen
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Yongbing Ba
- OE Biotech Co., Ltd., Shanghai 201114, China
| | - Peng Du
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai 200092, China
| | - Xiaolei Wang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
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