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Ando T, Takazawa I, Spencer ZT, Ito R, Tomimori Y, Mikulski Z, Matsumoto K, Ishitani T, Denson LA, Kawakami Y, Kawakami Y, Kitaura J, Ahmed Y, Kawakami T. Ileal Crohn's Disease Exhibits Reduced Activity of Phospholipase C-β3-Dependent Wnt/β-Catenin Signaling Pathway. Cells 2024; 13:986. [PMID: 38891118 PMCID: PMC11171731 DOI: 10.3390/cells13110986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Crohn's disease is a chronic, debilitating, inflammatory bowel disease. Here, we report a critical role of phospholipase C-β3 (PLC-β3) in intestinal homeostasis. In PLC-β3-deficient mice, exposure to oral dextran sodium sulfate induced lethality and severe inflammation in the small intestine. The lethality was due to PLC-β3 deficiency in multiple non-hematopoietic cell types. PLC-β3 deficiency resulted in reduced Wnt/β-catenin signaling, which is essential for homeostasis and the regeneration of the intestinal epithelium. PLC-β3 regulated the Wnt/β-catenin pathway in small intestinal epithelial cells (IECs) at transcriptional, epigenetic, and, potentially, protein-protein interaction levels. PLC-β3-deficient IECs were unable to respond to stimulation by R-spondin 1, an enhancer of Wnt/β-catenin signaling. Reduced expression of PLC-β3 and its signature genes was found in biopsies of patients with ileal Crohn's disease. PLC-β regulation of Wnt signaling was evolutionally conserved in Drosophila. Our data indicate that a reduction in PLC-β3-mediated Wnt/β-catenin signaling contributes to the pathogenesis of ileal Crohn's disease.
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Affiliation(s)
- Tomoaki Ando
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
- Atopy Research Center, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Ikuo Takazawa
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Zachary T. Spencer
- Department of Molecular and Systems Biology and the Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA; (Z.T.S.)
| | - Ryoji Ito
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
- Central Institute for Experimental Animals, Kawasaki 210-0821, Kanagawa, Japan
| | - Yoshiaki Tomimori
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Zbigniew Mikulski
- Imaging Facility, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Tohru Ishitani
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-0044, Gunma, Japan
| | - Lee A. Denson
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yu Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Yuko Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
| | - Jiro Kitaura
- Atopy Research Center, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Yashi Ahmed
- Department of Molecular and Systems Biology and the Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA; (Z.T.S.)
| | - Toshiaki Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla, CA 92037, USA; (T.A.)
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Alvarez-Martinez M, Cox LS, Pearson CF, Branchett WJ, Chakravarty P, Wu X, Slawinski H, Al-Dibouni A, Samelis VA, Gabryšová L, Priestnall SL, Suárez-Bonnet A, Mikolajczak A, Briscoe J, Powrie F, O'Garra A. Blimp-1 and c-Maf regulate immune gene networks to protect against distinct pathways of pathobiont-induced colitis. Nat Immunol 2024; 25:886-901. [PMID: 38609547 PMCID: PMC11065689 DOI: 10.1038/s41590-024-01814-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/13/2024] [Indexed: 04/14/2024]
Abstract
Intestinal immune responses to microbes are controlled by the cytokine IL-10 to avoid immune pathology. Here, we use single-cell RNA sequencing of colon lamina propria leukocytes (LPLs) along with RNA-seq and ATAC-seq of purified CD4+ T cells to show that the transcription factors Blimp-1 (encoded by Prdm1) and c-Maf co-dominantly regulate Il10 while negatively regulating proinflammatory cytokines in effector T cells. Double-deficient Prdm1fl/flMaffl/flCd4Cre mice infected with Helicobacter hepaticus developed severe colitis with an increase in TH1/NK/ILC1 effector genes in LPLs, while Prdm1fl/flCd4Cre and Maffl/flCd4Cre mice exhibited moderate pathology and a less-marked type 1 effector response. LPLs from infected Maffl/flCd4Cre mice had increased type 17 responses with increased Il17a and Il22 expression and an increase in granulocytes and myeloid cell numbers, resulting in increased T cell-myeloid-neutrophil interactions. Genes over-expressed in human inflammatory bowel disease showed differential expression in LPLs from infected mice in the absence of Prdm1 or Maf, revealing potential mechanisms of human disease.
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Affiliation(s)
| | - Luke S Cox
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Claire F Pearson
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - William J Branchett
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Probir Chakravarty
- Computational Biology Laboratory, The Francis Crick Institute, London, UK
| | - Xuemei Wu
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Hubert Slawinski
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Alaa Al-Dibouni
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Vasileios A Samelis
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Leona Gabryšová
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
| | - Simon L Priestnall
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - Alejandro Suárez-Bonnet
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - Anna Mikolajczak
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - James Briscoe
- Developmental Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Anne O'Garra
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK.
- National Heart and Lung Institute, Imperial College London, London, UK.
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Galindez G, List M, Baumbach J, Völker U, Mäder U, Blumenthal DB, Kacprowski T. Inference of differential gene regulatory networks using boosted differential trees. BIOINFORMATICS ADVANCES 2024; 4:vbae034. [PMID: 38505804 PMCID: PMC10948285 DOI: 10.1093/bioadv/vbae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/24/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Summary Diseases can be caused by molecular perturbations that induce specific changes in regulatory interactions and their coordinated expression, also referred to as network rewiring. However, the detection of complex changes in regulatory connections remains a challenging task and would benefit from the development of novel nonparametric approaches. We develop a new ensemble method called BoostDiff (boosted differential regression trees) to infer a differential network discriminating between two conditions. BoostDiff builds an adaptively boosted (AdaBoost) ensemble of differential trees with respect to a target condition. To build the differential trees, we propose differential variance improvement as a novel splitting criterion. Variable importance measures derived from the resulting models are used to reflect changes in gene expression predictability and to build the output differential networks. BoostDiff outperforms existing differential network methods on simulated data evaluated in four different complexity settings. We then demonstrate the power of our approach when applied to real transcriptomics data in COVID-19, Crohn's disease, breast cancer, prostate adenocarcinoma, and stress response in Bacillus subtilis. BoostDiff identifies context-specific networks that are enriched with genes of known disease-relevant pathways and complements standard differential expression analyses. Availability and implementation BoostDiff is available at https://github.com/scibiome/boostdiff_inference.
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Affiliation(s)
- Gihanna Galindez
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig, 38106, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, 38106, Germany
| | - Markus List
- Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, 85354, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, 22607, Germany
- Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, 5230, Denmark
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
| | - Ulrike Mäder
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
| | - David B Blumenthal
- Biomedical Network Science Lab, Department of Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91052, Germany
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of Technische Universität Braunschweig and Hannover Medical School, Braunschweig, 38106, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, 38106, Germany
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Aishwarya S, Gunasekaran K. Differential Gene Expression Profiles Involved in the Inflammations Due to COVID-19 and Inflammatory Bowel Diseases and the Investigation of Predictive Biomarkers. Biochem Genet 2024; 62:311-332. [PMID: 37335372 DOI: 10.1007/s10528-023-10414-9] [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: 06/22/2022] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Gastrointestinal manifestations in COVID-19 were attributed to 74-86% of the hospitalised patients due to severe or prolonged pathogenesis. Though it is a respiratory disease, the impact it elicits on the gastrointestinal tract and brain are intense. Inflammatory bowel disease including Crohn's disease and ulcerative colitis are idiopathic inflammatory disorders of the gastrointestinal tract. The intrinsic mechanisms involved in gut inflammations due to a respiratory viral disease can be deciphered when the gene expression profiles of COVID-19 and IBD are compared. The current study utilises an integrated bioinformatics approach to unravel them. The publicly available gene expression profiles of colon transcriptomes infected with COVID-19, Crohn's disease and Ulcerative colitis were retrieved, integrated and analysed for the identification of differentially expressed genes. The inter-relational analysis along with gene annotation and pathway enrichment detailed the functional and metabolic pathways of the genes during normal and diseased conditions. The protein-protein interactions deduced from the STRING database and the identified hub genes predicted potential biomarker candidates for COVID-19, Crohn's disease and ulcerative colitis. The inflammatory response pathways were upregulated and enrichment of chemokine signalling, altered lipid metabolism, coagulation and complement cascades were seen in all three conditions along with impaired transport mechanisms. CXCL11, MMP10, and CFB are predicted to be overexpressed biomarkers, whilst GUCA2A, SLC13A2, CEACAM, and IGSF9 as downregulated novel biomarker candidates for colon inflammations. The three miRNAs hsa-miR-16-5p, hsa-miR-21-5p, and hsa-miR-27b-5p exhibited significant interactions with the upregulated hub genes and four long non-coding RNAs NEAT1, KCNQ1OT1, and LINC00852 capable of regulating miRNA were also predicted. This study offers significant information on the underlying molecular mechanisms of inflammatory bowel disease with identification of potential biomarkers.
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Affiliation(s)
- S Aishwarya
- Department of Bioinformatics, Stella Maris College (Autonomous), Chennai, India.
- CAS in Crystallography and Biophysics, University of Madras, Chennai, India.
| | - K Gunasekaran
- CAS in Crystallography and Biophysics, University of Madras, Chennai, India
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Wacker EM, Uellendahl-Werth F, Bej S, Wolkenhauer O, Vesterhus M, Lieb W, Franke A, Karlsen TH, Folseraas T, Ellinghaus D. Whole blood RNA sequencing identifies transcriptional differences between primary sclerosing cholangitis and ulcerative colitis. JHEP Rep 2024; 6:100988. [PMID: 38304234 PMCID: PMC10832281 DOI: 10.1016/j.jhepr.2023.100988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/10/2023] [Accepted: 12/06/2023] [Indexed: 02/03/2024] Open
Abstract
Background & Aims Genetic and microbiome studies across patients with primary sclerosing cholangitis (PSC) and ulcerative colitis (UC) have indicated that UC in PSC is a separate disease entity to primary UC, but expression studies for PSC are lacking. Methods We conducted whole blood RNA sequencing experiments for 495 patients with UC, 220 patients with PSC (including 177 with UC), and 320 healthy controls from Germany and Norway. Differential expression analyses, gene ontology and coexpression analyses and random forest machine learning were performed to identify genes, ontologies and transcriptional features that discriminate diagnoses. Results The blood transcriptome in UC and PSC is dominated by neutrophil activation genes (e.g. S100A12). In UC, but not in PSC (neither PSC alone nor patients with an additional diagnosis of UC [PSC/UC]), ribosomal, mitochondrial, and energy metabolism genes are upregulated in conjunction with antibody transcript expression (MZB1, IGJ). In PSC, there is an increase in modules related to apoptosis and expression of genes of interferon-I-related ontologies. Random forest analysis could poorly discriminate PSC alone from PSC/UC (AUROC 0.56), but could discriminate PSC, UC, and controls with high accuracy (AUROC UC vs. controls 0.95, PSC vs. controls 0.88, UC vs. PSC 0.986). The main coexpression modules relevant for distinguishing PSC, UC, and controls are enriched in neutrophil degranulation and antibody production genes. Conclusions Supported by machine learning results, PSC and UC appear to be separate entities on a molecular level, while PSC/UC and PSC are indistinguishable. Impact and implications Clinical and genetic studies suggest that the colitis-like symptoms in primary sclerosing cholangitis (PSC) represent a different disease entity from primary ulcerative colitis (UC). The present study supports this assumption with transcriptomic data from whole blood and describes notable differences in gene expression between primary UC and PSC, providing insights into the still unclear pathophysiology of both diseases. These findings are of interest to scientists seeking to decipher the molecular pathophysiology of both diseases and provide evidence that a redefinition of the PSC-UC phenotype should be considered. The study practically supports future molecular research by providing a large transcriptomic whole blood reference cohort.
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Affiliation(s)
- Eike Matthias Wacker
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Saptarshi Bej
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Indian Institute of Science Education and Research, Thiruvananthapuram, India
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University Munich, Munich, Germany
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Mette Vesterhus
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
- Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tom Hemming Karlsen
- Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Trine Folseraas
- Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
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Guthrie J, Ko¨stel Bal S, Lombardo SD, Mu¨ller F, Sin C, Hu¨tter CV, Menche J, Boztug K. AutoCore: A network-based definition of the core module of human autoimmunity and autoinflammation. SCIENCE ADVANCES 2023; 9:eadg6375. [PMID: 37656781 PMCID: PMC10848965 DOI: 10.1126/sciadv.adg6375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
Although research on rare autoimmune and autoinflammatory diseases has enabled definition of nonredundant regulators of homeostasis in human immunity, because of the single gene-single disease nature of many of these diseases, contributing factors were mostly unveiled in sequential and noncoordinated individual studies. We used a network-based approach for integrating a set of 186 inborn errors of immunity with predominant autoimmunity/autoinflammation into a comprehensive map of human immune dysregulation, which we termed "AutoCore." The AutoCore is located centrally within the interactome of all protein-protein interactions, connecting and pinpointing multidisease markers for a range of common, polygenic autoimmune/autoinflammatory diseases. The AutoCore can be subdivided into 19 endotypes that correspond to molecularly and phenotypically cohesive disease subgroups, providing a molecular mechanism-based disease classification and rationale toward systematic targeting for therapeutic purposes. Our study provides a proof of concept for using network-based methods to systematically investigate the molecular relationships between individual rare diseases and address a range of conceptual, diagnostic, and therapeutic challenges.
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Affiliation(s)
- Julia Guthrie
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Zimmermannplatz 10, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
| | - Sevgi Ko¨stel Bal
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Zimmermannplatz 10, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Zimmermannplatz 10, A-1090 Vienna, Austria
| | - Salvo Danilo Lombardo
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
| | - Felix Mu¨ller
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
| | - Celine Sin
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
| | - Christiane V. R. Hu¨tter
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter, A-1030 Vienna, Austria
| | - Jo¨rg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- Max Perutz Labs, Vienna BioCenter Campus, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Department of Structural and Computational Biology, University of Vienna, Dr.-Bohr-Gasse 9, 1030, Vienna Austria
- Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, A-1090 Vienna, Austria
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Zimmermannplatz 10, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, A-1090 Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Zimmermannplatz 10, A-1090 Vienna, Austria
- St. Anna Children’s Hospital, Kinderspitalgasse 6, A-1090, Vienna, Austria
- Medical University of Vienna, Department of Pediatrics and Adolescent Medicine, Währinger Gürtel 18-20, A-1090 Vienna, Austria
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Earland N, Zhang W, Usmani A, Nene A, Bacchiocchi A, Chen DY, Sznol M, Halaban R, Chaudhuri AA, Newman AM. CD4 T cells and toxicity from immune checkpoint blockade. Immunol Rev 2023; 318:96-109. [PMID: 37491734 PMCID: PMC10838135 DOI: 10.1111/imr.13248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/27/2023] [Indexed: 07/27/2023]
Abstract
Immune-related toxicities, otherwise known as immune-related adverse events (irAEs), occur in a substantial fraction of cancer patients treated with immune checkpoint inhibitors (ICIs). Ranging from asymptomatic to life-threatening, ICI-induced irAEs can result in hospital admission, high-dose corticosteroid treatment, ICI discontinuation, and in some cases, death. A deeper understanding of the factors underpinning severe irAE development will be essential for improved irAE prediction and prevention, toward maximizing the benefits and safety profiles of ICIs. In recent work, we applied mass cytometry, single-cell RNA sequencing, single-cell V(D)J sequencing, bulk RNA sequencing, and bulk T-cell receptor (TCR) sequencing to identify pretreatment determinants of severe irAE development in patients with advanced melanoma. Across 71 patients separated into three cohorts, we found that two baseline features in circulation-elevated activated CD4 effector memory T-cell abundance and TCR diversity-are associated with severe irAE development, independent of the affected organ system within 3 months of ICI treatment initiation. Here, we provide an extended perspective on this work, synthesize and discuss related literature, and summarize practical considerations for clinical translation. Collectively, these findings lay a foundation for data-driven and mechanistic insights into irAE development, with the potential to reduce ICI morbidity and mortality in the future.
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Affiliation(s)
- Noah Earland
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Wubing Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Abul Usmani
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Antonella Bacchiocchi
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - David Y. Chen
- Division of Dermatology, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Mario Sznol
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Medicine, Division of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Ruth Halaban
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Aadel A. Chaudhuri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
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8
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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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9
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Elahimanesh M, Najafi M. Cross talk between bacterial and human gene networks enriched using ncRNAs in IBD disease. Sci Rep 2023; 13:7704. [PMID: 37169818 PMCID: PMC10175251 DOI: 10.1038/s41598-023-34780-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a long-term inflammatory immune-mediated gut illness with several extra-intestinal complications. The aims of this study were to identify a novel network-based meta-analysis approach on the basis of the combinations of the differentially expressed genes (DEGs) from microarray data, to enrich the functional modules from human protein-protein interaction (PPI) and gene ontology (GO) data, and to profile the ncRNAs on the genes involved in IBD. The gene expression profiles of GSE126124, GSE87473, GSE75214, and GSE95095 are obtained from the Gene Expression Omnibus (GEO) database based on the study criteria between 2017 and 2022. The DEGs were screened by the R software. DEGs were then used to examine gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The ncRNAs including the miRNAs and ceRNAs were predicted on the PPIs visualized using Cytoscape. Enrichment analysis of genes with differential expression (n = 342) using KEGG and GO showed that the signaling pathways related with staphylococcus aureus and pertussis bacterial infections may stimulate the immune system and exacerbate IBD via the interaction with human proteins including Fibrinogen gamma chain (FGG), Keratin 10 (KRT10), and Toll like receptor 4 (TLR4). By building a ceRNA network, lncRNA XIST and NEAT1 were determined by affecting common miRNAs, hsa-miR-6875-5p, hsa-miR-1908-5p, hsa-miR-186-5p, hsa-miR-6763-5p, hsa-miR-4436a, and hsa-miR-520a-5p. Additionally, the chromosome regions including NM_001039703 and NM_006267, which produce the most potent circRNAs play a significant role in the ceRNA network of IBD. Also, we predicted the siRNAs that would be most effective against the bacterial genes in staphylococcus aureus and pertussis infections. These findings suggested that three genes (FGG, KRT10, and TLR4), six miRNAs (hsa-miR-6875-5p, hsa-miR-1908-5p, hsa-miR-186-5p, hsa-miR-4436a, hsa-miR-520a-5p, and hsa-miR-6763-5p), two lncRNAs (XIST and NEAT1), and chromosomal regions including NM_001039703 and NM_006267 with the production of the most effective circRNAs are involved in the ncRNA-associated ceRNA network of IBD. These ncRNA profiles are related to the described gene functions and may play therapeutic targets in controlling inflammatory bowel disease.
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Affiliation(s)
- Mohammad Elahimanesh
- Clinical Biochemistry Department, Faculty of Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Najafi
- Clinical Biochemistry Department, Faculty of Medical Sciences, Iran University of Medical Sciences, Tehran, Iran.
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran.
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10
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Chen X, Gao Y, Xie J, Hua H, Pan C, Huang J, Jing M, Chen X, Xu C, Gao Y, Li P. Identification of FCN1 as a novel macrophage infiltration-associated biomarker for diagnosis of pediatric inflammatory bowel diseases. J Transl Med 2023; 21:203. [PMID: 36932401 PMCID: PMC10022188 DOI: 10.1186/s12967-023-04038-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/05/2023] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND The incidence of pediatric inflammatory bowel disease (PIBD) has been steadily increasing globally. Delayed diagnosis of PIBD increases the risk of complications and contributes to growth retardation. To improve long-term outcomes, there is a pressing need to identify novel markers for early diagnosis of PIBD. METHODS The candidate biomarkers for PIBD were identified from the GSE117993 dataset by two machine learning algorithms, namely LASSO and mSVM-RFE, and externally validated in the GSE126124 dataset and our PIBD cohort. The role of ficolin-1 (FCN1) in PIBD and its association with macrophage infiltration was investigated using the CIBERSORT method and enrichment analysis of the single-cell dataset GSE121380, and further validated using immunoblotting, qRT-PCR, and immunostaining in colon biopsies from PIBD patients, a juvenile murine DSS-induced colitis model, and THP-1-derived macrophages. RESULTS FCN1 showed great diagnostic performance for PIBD in an independent clinical cohort with the AUC of 0.986. FCN1 expression was upregulated in both colorectal biopsies and blood samples from PIBD patients. Functionally, FCN1 was associated with immune-related processes in the colonic mucosa of PIBD patients, and correlated with increased proinflammatory M1 macrophage infiltration. Furthermore, single-cell transcriptome analysis and immunostaining revealed that FCN1 was almost exclusively expressed in macrophages infiltrating the colonic mucosa of PIBD patients, and these FCN1+ macrophages were related to hyper-inflammation. Notably, proinflammatory M1 macrophages derived from THP-1 expressed high levels of FCN1 and IL-1β, and FCN1 overexpression in THP-1-derived macrophages strongly promoted LPS-induced activation of the proinflammatory cytokine IL-1β via the NLRP3-caspase-1 axis. CONCLUSIONS FCN1 is a novel and promising diagnostic biomarker for PIBD. FCN1+ macrophages enriched in the colonic mucosa of PIBD exhibit proinflammatory phenotypes, and FCN1 promotes IL-1β maturation in macrophages via the NLRP3-caspase-1 axis.
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Affiliation(s)
- Xixi Chen
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Ruijin Er Rd.197, Shanghai, 200025, China
| | - Yuanqi Gao
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Ruijin Er Rd.197, Shanghai, 200025, China
| | - Jinfang Xie
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Ruijin Er Rd.197, Shanghai, 200025, China
| | - Huiying Hua
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Ruijin Er Rd.197, Shanghai, 200025, China
| | - Chun Pan
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Ruijin Er Rd.197, Shanghai, 200025, China
| | - Jiebin Huang
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Ruijin Er Rd.197, Shanghai, 200025, China
| | - Mengxia Jing
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Ruijin Er Rd.197, Shanghai, 200025, China
| | - Xuehua Chen
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Ruijin Er Rd.197, Shanghai, 200025, China
| | - Chundi Xu
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Ruijin Er Rd.197, Shanghai, 200025, China.
| | - Yujing Gao
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China.
| | - Pu Li
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Ruijin Er Rd.197, Shanghai, 200025, China.
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11
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Chen ZA, Ma HH, Wang Y, Tian H, Mi JW, Yao DM, Yang CJ. Integrated multiple microarray studies by robust rank aggregation to identify immune-associated biomarkers in Crohn's disease based on three machine learning methods. Sci Rep 2023; 13:2694. [PMID: 36792688 PMCID: PMC9931764 DOI: 10.1038/s41598-022-26345-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/13/2022] [Indexed: 02/17/2023] Open
Abstract
Crohn's disease (CD) is a complex autoimmune disorder presumed to be driven by complex interactions of genetic, immune, microbial and even environmental factors. Intrinsic molecular mechanisms in CD, however, remain poorly understood. The identification of novel biomarkers in CD cases based on larger samples through machine learning approaches may inform the diagnosis and treatment of diseases. A comprehensive analysis was conducted on all CD datasets of Gene Expression Omnibus (GEO); our team then used the robust rank aggregation (RRA) method to identify differentially expressed genes (DEGs) between controls and CD patients. PPI (protein‒protein interaction) network and functional enrichment analyses were performed to investigate the potential functions of the DEGs, with molecular complex detection (MCODE) identifying some important functional modules from the PPI network. Three machine learning algorithms, support vector machine-recursive feature elimination (SVM-RFE), random forest (RF), and least absolute shrinkage and selection operator (LASSO), were applied to determine characteristic genes, which were verified by ROC curve analysis and immunohistochemistry (IHC) using clinical samples. Univariable and multivariable logistic regression were used to establish a machine learning score for diagnosis. Single-sample GSEA (ssGSEA) was performed to examine the correlation between immune infiltration and biomarkers. In total, 5 datasets met the inclusion criteria: GSE75214, GSE95095, GSE126124, GSE179285, and GSE186582. Based on RRA integrated analysis, 203 significant DEGs were identified (120 upregulated genes and 83 downregulated genes), and MCODE revealed some important functional modules in the PPI network. Machine learning identified LCN2, REG1A, AQP9, CCL2, GIP, PROK2, DEFA5, CXCL9, and NAMPT; AQP9, PROK2, LCN2, and NAMPT were further verified by ROC curves and IHC in the external cohort. The final machine learning score was defined as [Expression level of AQP9 × (2.644)] + [Expression level of LCN2 × (0.958)] + [Expression level of NAMPT × (1.115)]. ssGSEA showed markedly elevated levels of dendritic cells and innate immune cells, such as macrophages and NK cells, in CD, consistent with the gene enrichment results that the DEGs are mainly involved in the IL-17 signaling pathway and humoral immune response. The selected biomarkers analyzed by the RRA method and machine learning are highly reliable. These findings improve our understanding of the molecular mechanisms of CD pathogenesis.
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Affiliation(s)
- Zi-An Chen
- grid.452702.60000 0004 1804 3009Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000 Hebei China ,Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Disease, Shijiazhuang, 050000 Hebei China
| | - Hui-hui Ma
- grid.452702.60000 0004 1804 3009Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000 Hebei China ,Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Disease, Shijiazhuang, 050000 Hebei China
| | - Yan Wang
- grid.452702.60000 0004 1804 3009Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000 Hebei China ,Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Disease, Shijiazhuang, 050000 Hebei China
| | - Hui Tian
- grid.452702.60000 0004 1804 3009Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000 Hebei China ,Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Disease, Shijiazhuang, 050000 Hebei China
| | - Jian-wei Mi
- grid.452702.60000 0004 1804 3009Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000 Hebei China ,Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Disease, Shijiazhuang, 050000 Hebei China
| | - Dong-Mei Yao
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China. .,Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Disease, Shijiazhuang, 050000, Hebei, China.
| | - Chuan-Jie Yang
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China. .,Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Disease, Shijiazhuang, 050000, Hebei, China.
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12
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Verstockt B, Verstockt S, Cremer J, Sabino J, Ferrante M, Vermeire S, Sudhakar P. Distinct transcriptional signatures in purified circulating immune cells drive heterogeneity in disease location in IBD. BMJ Open Gastroenterol 2023; 10:bmjgast-2022-001003. [PMID: 36746519 PMCID: PMC9906185 DOI: 10.1136/bmjgast-2022-001003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/25/2022] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE To infer potential mechanisms driving disease subtypes among patients with inflammatory bowel disease (IBD), we profiled the transcriptome of purified circulating monocytes and CD4 T-cells. DESIGN RNA extracted from purified monocytes and CD4 T-cells derived from the peripheral blood of 125 endoscopically active patients with IBD was sequenced using Illumina HiSeq 4000NGS. We used complementary supervised and unsupervised analytical methods to infer gene expression signatures associated with demographic/clinical features. Expression differences and specificity were validated by comparison with publicly available single cell datasets, tissue-specific expression and meta-analyses. Drug target information, druggability and adverse reaction records were used to prioritise disease subtype-specific therapeutic targets. RESULTS Unsupervised/supervised methods identified significant differences in the expression profiles of CD4 T-cells between patients with ileal Crohn's disease (CD) and ulcerative colitis (UC). Following a pathway-based classification (Area Under Receiver Operating Characteristic - AUROC=86%) between ileal-CD and UC patients, we identified MAPK and FOXO pathways to be downregulated in UC. Coexpression module/regulatory network analysis using systems-biology approaches revealed mediatory core transcription factors. We independently confirmed that a subset of the disease location-associated signature is characterised by T-cell-specific and location-specific expression. Integration of drug-target information resulted in the discovery of several new (BCL6, GPR183, TNFAIP3) and repurposable drug targets (TUBB2A, PRKCQ) for ileal CD as well as novel targets (NAPEPLD, SLC35A1) for UC. CONCLUSIONS Transcriptomic profiling of circulating CD4 T-cells in patients with IBD demonstrated marked molecular differences between the IBD-spectrum extremities (UC and predominantly ileal CD, sandwiching colonic CD), which could help in prioritising particular drug targets for IBD subtypes.
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Affiliation(s)
- Bram Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Sare Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium
| | - Jonathan Cremer
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium
| | - João Sabino
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Marc Ferrante
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Severine Vermeire
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Padhmanand Sudhakar
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium
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13
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Maddipatla SC, Kolachala VL, Venkateswaran S, Dodd AF, Pelia RS, Geem D, Yin H, Sun Y, Xu C, Mo A, Kosters A, Yang J, Matthews JD, Ghosn E, Kugathasan S, Qiu P. Assessing Cellular and Transcriptional Diversity of Ileal Mucosa Among Treatment-Naïve and Treated Crohn's Disease. Inflamm Bowel Dis 2023; 29:274-285. [PMID: 36206201 PMCID: PMC9890215 DOI: 10.1093/ibd/izac201] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Crohn's disease is a lifelong disease characterized by chronic inflammation of the gastrointestinal tract. Defining the cellular and transcriptional composition of the mucosa at different stages of disease progression is needed for personalized therapy in Crohn's. METHODS Ileal biopsies were obtained from (1) control subjects (n = 6), (2) treatment-naïve patients (n = 7), and (3) established (n = 14) Crohn's patients along with remission (n = 3) and refractory (n = 11) treatment groups. The biopsies processed using 10x Genomics single cell 5' yielded 139 906 cells. Gene expression count matrices of all samples were analyzed by reciprocal principal component integration, followed by clustering analysis. Manual annotations of the clusters were performed using canonical gene markers. Cell type proportions, differential expression analysis, and gene ontology enrichment were carried out for each cell type. RESULTS We identified 3 cellular compartments with 9 epithelial, 1 stromal, and 5 immune cell subtypes. We observed differences in the cellular composition between control, treatment-naïve, and established groups, with the significant changes in the epithelial subtypes of the treatment-naïve patients, including microfold, tuft, goblet, enterocyte,s and BEST4+ cells. Surprisingly, fewer changes in the composition of the immune compartment were observed; however, gene expression in the epithelial and immune compartment was different between Crohn's phenotypes, indicating changes in cellular activity. CONCLUSIONS Our study identified cellular and transcriptional signatures associated with treatment-naïve Crohn's disease that collectively point to dysfunction of the intestinal barrier with an increase in inflammatory cellular activity. Our analysis also highlights the heterogeneity among patients within the same disease phenotype, shining a new light on personalized treatment responses and strategies.
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Affiliation(s)
- Sushma Chowdary Maddipatla
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Vasantha L Kolachala
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Suresh Venkateswaran
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Anne F Dodd
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Ranjit Singh Pelia
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Duke Geem
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Hong Yin
- Department of Pathology, Children’s Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | - Yutong Sun
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Congmin Xu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Angela Mo
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Astrid Kosters
- Lowance Center for Human Immunology, Division of Immunology and Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Junkai Yang
- Lowance Center for Human Immunology, Division of Immunology and Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jason D Matthews
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Eliver Ghosn
- Emory Vaccine Center, Lowance Center for Human Immunology, Departments of Medicine and Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Department of Pediatrics and Pediatric Research Institute, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
- Genetics and Molecular Biology Program, Emory University School of Medicine, Atlanta, GA, USAand
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Peng Qiu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
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14
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Yu S, Qian H, Zhang D, Jiang Z. Ferulic acid relieved ulcerative colitis by inhibiting the TXNIP/NLRP3 pathway in rats. Cell Biol Int 2023; 47:417-427. [PMID: 36251276 DOI: 10.1002/cbin.11935] [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: 07/19/2022] [Revised: 09/26/2022] [Accepted: 10/01/2022] [Indexed: 01/17/2023]
Abstract
Ulcerative colitis (UC) is a disorder of the bowel that is characterized by a chronic inflammatory response. The traditional Chinese herbal medicine ferulic acid (FA) is known for its antioxidant, antiapoptotic, and antiinflammatory properties. However, its role in UC is still unclear. Thus, the current study was conducted to investigate the role of FA in UC. Rats were treated with 2,4,6-triabrobenzene sulfonic acid to induce UC and subjected to FA. Human intestinal microvascular endothelial cells (HIMECs) were treated with tumor necrosis factor-α (TNF-α) and pretreated with FA. Pathological changes in colonic tissues were visualized via hematoxylin-eosin staining. Enzyme linked immunosorbent assay was conducted to detect interleukin (IL)-6, IL-12, and IL-1β levels. Cell morphology was visualized by using a microscope, and viability was detected by using MTT. The percentage of apoptosis was detected via flow cytometry. Western blot analysis was performed to detect the expression of the apoptosis-related proteins thioredoxin-interacting protein (TXNIP) and NOD-like receptor pyrin domain-containing 3 (NLRP3). In vivo FA administration alleviated intestinal injury in UC rats and inhibited inflammatory factor levels (IL-6, IL-12, and IL-1β), apoptosis-related protein expression (caspase-1 and caspase-3) and the TXNIP/NLRP3 signaling pathway. In vitro, TNF-α treatment reduced HIMEC viability, increased cell apoptosis and inflammatory factor levels and activated the TXNIP/NLRP3 signaling pathway. However, FA treatment restored the viability of HIMECs, reduced TNF-α-induced cell apoptosis and inflammation and inhibited the TXNIP/NLRP3 signaling pathway. Furthermore, with increasing FA concentration, the effects were stronger. In summary, FA inhibits the inflammatory injury of endothelial cells in ulcerative colitis or alleviates TNF-α-induced HIMEC injury by inhibiting the TXNIP/NLRP3 signaling pathway.
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Affiliation(s)
- Sheng Yu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Haihua Qian
- Department of Anorectal Diseases, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu, China
| | - Dan Zhang
- Department of Anorectal Diseases, Jiangsu Provincial Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu, China
| | - Zhenzhen Jiang
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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15
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Pang X, Song H, Li X, Xu F, Lei B, Wang F, Xu J, Qi L, Wang L, Tan G. Transcriptomic analyses of treatment-naïve pediatric ulcerative colitis patients and exploration of underlying disease pathogenesis. J Transl Med 2023; 21:30. [PMID: 36647141 PMCID: PMC9843999 DOI: 10.1186/s12967-023-03881-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/08/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Ulcerative colitis (UC) is a form of chronic inflammatory bowel disease of nonspecific origin. This study used an RNA-Sequencing (RNA-Seq) approach to evaluate the transcriptomic landscape of a well-stratified treatment-naïve pediatric UC patient population by comparing them with healthy control children. The data were analyzed to evaluate the mechanisms driving UC-related intestinal inflammation and fibrosis. METHODS Intestinal mucosal samples from five pediatric UC patients and five healthy controls were analyzed by RNA-Seq, and results were verified by qPCR. A CRISPR/Cas9 approach was used to knock out the expression of HLA-DRB5, and molecular biology techniques were used for additional mechanistic studies. RESULTS In these analyses, 2290 genes were found to be differentially expressed between the UC and control samples, of which 1258 and 1032 were upregulated and downregulated, respectively. Gene Ontology analysis showed that these genes were enriched in extracellular matrix (ECM)-related processes and that 7 of 8 differentially expressed genes of interest (PIK3CD, IL1β, IL1α, TIMP1, MMP1, MMP12, COL6A3, and HLADRB5) were upregulated and involved in ECM-receptor interaction and inflammatory bowel disease-related pathways. Increased HLA-DRB5 expression driven by intestinal bacteria was found to promote IL-1α secretion, leading to intestinal inflammation and fibrosis, suggesting a possible target for the treatment of UC. CONCLUSION These data suggest that intestinal inflammation is present in pediatric UC patients for extended periods before the onset of symptoms, and intestinal fibrosis begins even during the early stages of UC. Intestinal bacteria were also found to trigger intestinal inflammation and fibrosis, with HLA-DRB5 playing a central role in this process.
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Affiliation(s)
- Xiaoli Pang
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Hongxiao Song
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
| | - Xiaolu Li
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Fengchao Xu
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
| | - Bingxun Lei
- grid.430605.40000 0004 1758 4110Department of Anesthesia, The First Hospital of Jilin University, Changchun, China
| | - Fei Wang
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
| | - Jing Xu
- grid.430605.40000 0004 1758 4110Health Examination Center, The First Hospital of Jilin University, Changchun, China
| | - Lingli Qi
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Libo Wang
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Guangyun Tan
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
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16
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Zhang C, Ma Z, Nan X, Wang W, Zeng X, Chen J, Cai Z, Wang J. Comprehensive analysis to identify the influences of SARS-CoV-2 infections to inflammatory bowel disease. Front Immunol 2023; 14:1024041. [PMID: 36817436 PMCID: PMC9936160 DOI: 10.3389/fimmu.2023.1024041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) and inflammatory bowel disease (IBD) are both caused by a disordered immune response and have direct and profound impacts on health care services. In this study, we implemented transcriptomic and single-cell analysis to detect common molecular and cellular intersections between COVID-19 and IBD that help understand the linkage of COVID-19 to the IBD patients. Methods Four RNA-sequencing datasets (GSE147507, GSE126124, GSE9686 and GSE36807) from Gene Expression Omnibus (GEO) database are extracted to detect mutual differentially expressed genes (DEGs) for IBD patients with the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to find shared pathways, candidate drugs, hub genes and regulatory networks. Two single-cell RNA sequencing (scRNA-eq) datasets (GSE150728, PRJCA003980) are used to analyze the immune characteristics of hub genes and the proportion of immune cell types, so as to find common immune responses between COVID-19 and IBD. Results A total of 121 common DEGs were identified among four RNA-seq datasets, and were all involved in the functional enrichment analysis related to inflammation and immune response. Transcription factors-DEGs interactions, miRNAs-DEGs coregulatory networks, and protein-drug interactions were identified based on these datasets. Protein-protein interactions (PPIs) was built and 59 hub genes were identified. Moreover, scRNA-seq of peripheral blood monocyte cells (PBMCs) from COVID-19 patients revealed a significant increase in the proportion of CD14+ monocytes, in which 38 of 59 hub genes were highly enriched. These genes, encoding inflammatory cytokines, were also highly expressed in inflammatory macrophages (IMacrophage) of intestinal tissues of IBD patients. Conclusions We conclude that COVID-19 may promote the progression of IBD through cytokine storms. The candidate drugs and DEGs-regulated networks may suggest effective therapeutic methods for both COVID-19 and IBD.
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Affiliation(s)
- Chengyan Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Zeyu Ma
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Xi Nan
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenhui Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Xianchang Zeng
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinming Chen
- Department of Anorectal, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhijian Cai
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China.,Department of Orthopaedics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianli Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University, Hangzhou, China.,Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
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17
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A shared tissue transcriptome signature and pathways in psoriasis and ulcerative colitis. Sci Rep 2022; 12:19740. [PMID: 36396672 PMCID: PMC9671879 DOI: 10.1038/s41598-022-22465-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/14/2022] [Indexed: 11/18/2022] Open
Abstract
Despite multiple efficacious therapies in common between psoriasis (PS) and Ulcerative Colitis (UC), mechanisms underlying their common pathophysiology remain largely unclear. Here we sought to establish a link by evaluating expression differences and pathway alterations in diseased tissues. We identified two sets of differentially expressed genes (DEGs) between lesional and nonlesional tissues in meta-analyses of data collected from baseline samples in 3 UC and then 3 PS available clinical studies from Pfizer. A shared gene signature was defined by 190 DEGs common to both diseases. Commonly dysregulated pathways identified via enrichment analysis include interferon signaling, partly driven by genes IFI6, CXCL9, CXCL10 and CXCL11, which may attract chemotaxis of Th1 cells to inflammatory sites; IL-23 pathway (IL-23A, CCL20, PI3, CXCL1, LCN2); and Th17 pathway except IL-17A. Elevated expression of costimulatory molecules ICOS and CTLA4 suggests ongoing T-cell activation in both diseases. The clinical value of the shared signature is demonstrated by a gene set improvement score reflecting post-treatment molecular improvement for each disease. This is the first study using transcriptomic meta-analysis to define a tissue gene signature and pathways dysregulated in both PS and UC. These findings suggest immune mechanisms may initiate and sustain inflammation similarly in the two diseases.
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18
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Choi KD, Oh EH, Kim HS, Kim HS, Park JY, Choi SY, Choi JH. Transcriptional Down-Regulation of Major Histocompatibility Complex as a Possible Pathogenesis for Meniere's Disease. Front Neurol 2022; 13:938740. [PMID: 35923832 PMCID: PMC9339969 DOI: 10.3389/fneur.2022.938740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/20/2022] [Indexed: 12/13/2022] Open
Abstract
Objectives This study aimed to determine the underlying pathogenesis of Meniere's disease (MD) using transcriptome analysis. Methods Total RNA was extracted from the peripheral blood mononuclear cells of 39 patients with MD and 39 controls. Through microarray analysis for nine patients and controls, the differentially expressed genes (DEGs) of those two groups were screened based on cut-off criteria (|fold changes| > 2.0 and adjusted p-value < 0.05). The functional enrichment analysis of DEGs was performed using Gene Ontology (GO). Results There were 996 DEGs identified in the MD group: 415 were upregulated and 581 were downregulated. A functional enrichment analysis indicated that the downregulated DEGs were significantly enriched in terms related to immune system processes. Among them, 17 genes were enriched in terms for the major histocompatibility complex (MHC) protein complex, and the relative messenger RNA (mRNA) levels of three markedly downregulated DEGs [fold changes < −5: human leukocyte antigen (HLA)-DMA, HLA-DRB1, and HLA-DPB1] were significantly decreased in another 30 patients with MD compared with normal controls by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). However, there were no correlations between the expression levels of these three genes and clinical data, such as age, onset age, time course, or hearing threshold. Conclusions Our transcriptome analysis showed that the downregulated DEGs in MD were mainly associated with the immune system pathways including the MHC protein complex in MD. Remarkably, a breakdown in immunological tolerance mediated by MHC class II may contribute to the MD development, which has implications for targeted treatment.
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Affiliation(s)
- Kwang-Dong Choi
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, South Korea
| | - Eun Hye Oh
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Hyun Sung Kim
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Hyang-Sook Kim
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Ji-Yun Park
- Department of Neurology, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, South Korea
| | - Seo Young Choi
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, South Korea
| | - Jae-Hwan Choi
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea
- *Correspondence: Jae-Hwan Choi
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19
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Liu YW, Fu SH, Chien MW, Hsu CY, Lin MH, Dong JL, Lu RJH, Lee YJ, Chen PY, Wang CH, Sytwu HK. Blimp-1 moulds the epigenetic architecture of IL-21-mediated autoimmune diseases through an autoregulatory circuit. JCI Insight 2022; 7:151614. [PMID: 35503415 PMCID: PMC9220827 DOI: 10.1172/jci.insight.151614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 04/29/2022] [Indexed: 11/17/2022] Open
Abstract
Positive regulatory domain 1 (PRDM1) encodes B lymphocyte–induced maturation protein 1 (BLIMP1), also known as a master regulator of T cell homeostasis. We observed a negative relationship between Blimp-1 and IL-21 based on our previous data that Blimp-1 overexpression in T cells suppresses autoimmune diabetes while Blimp-1–deficient T cells contribute to colitis in NOD mice. Reanalysis of published data sets also revealed an inverse correlation between PRDM1 and IL21 in Crohn’s disease. Here, we illustrate that Blimp-1 repressed IL-21 by reducing chromatin accessibility and evicting an IL-21 activator, c-Maf, from the Il21 promoter. Moreover, Blimp-1 overexpression–mediated reduction in permissive chromatin structures at the Il21 promoter could override IL-21–accelerated autoimmune diabetogenesis in small ubiquitin-like modifier–defective c-Maf–transgenic mice. An autoregulatory feedback loop to harness IL-21 expression was unveiled by the evidence that IL-21 addition induced time-dependent Blimp-1 expression and subsequently enriched its binding to the Il21 promoter to suppress IL-21 overproduction. Furthermore, intervention of this feedback loop by IL-21 blockade, with IL-21R.Fc administration or IL-21 receptor deletion, attenuated Blimp-1 deficiency–mediated colitis and reinforced the circuit between Blimp-1 and IL-21 in the regulation of autoimmunity. We highlight the translation of Blimp-1–based epigenetic and transcriptomic profiles applicable to a personalized medicine approach in autoimmune diseases.
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Affiliation(s)
- Yu-Wen Liu
- Molecular Cell Biology, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Shin-Huei Fu
- National Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Ming-Wei Chien
- National Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Chao-Yuan Hsu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Ming-Hong Lin
- Department of Microbiology and Immunology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jia-Ling Dong
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Rita Jui-Hsien Lu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Jing Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Hung Wang
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, Taipei, Taiwan
| | - Huey-Kang Sytwu
- National Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
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20
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Lozano AX, Chaudhuri AA, Nene A, Bacchiocchi A, Earland N, Vesely MD, Usmani A, Turner BE, Steen CB, Luca BA, Badri T, Gulati GS, Vahid MR, Khameneh F, Harris PK, Chen DY, Dhodapkar K, Sznol M, Halaban R, Newman AM. T cell characteristics associated with toxicity to immune checkpoint blockade in patients with melanoma. Nat Med 2022; 28:353-362. [PMID: 35027754 DOI: 10.1038/s41591-021-01623-z] [Citation(s) in RCA: 125] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 11/09/2021] [Indexed: 12/15/2022]
Abstract
Severe immune-related adverse events (irAEs) occur in up to 60% of patients with melanoma treated with immune checkpoint inhibitors (ICIs). However, it is unknown whether a common baseline immunological state precedes irAE development. Here we applied mass cytometry by time of flight, single-cell RNA sequencing, single-cell V(D)J sequencing, bulk RNA sequencing and bulk T cell receptor (TCR) sequencing to study peripheral blood samples from patients with melanoma treated with anti-PD-1 monotherapy or anti-PD-1 and anti-CTLA-4 combination ICIs. By analyzing 93 pre- and early on-ICI blood samples and 3 patient cohorts (n = 27, 26 and 18), we found that 2 pretreatment factors in circulation-activated CD4 memory T cell abundance and TCR diversity-are associated with severe irAE development regardless of organ system involvement. We also explored on-treatment changes in TCR clonality among patients receiving combination therapy and linked our findings to the severity and timing of irAE onset. These results demonstrate circulating T cell characteristics associated with ICI-induced toxicity, with implications for improved diagnostics and clinical management.
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Affiliation(s)
- Alexander X Lozano
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA.,Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Computer Science & Engineering, Washington University, St. Louis, MO, USA. .,Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Aishwarya Nene
- Yale School of Medicine, Yale University, New Haven, CT, USA
| | | | - Noah Earland
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew D Vesely
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Abul Usmani
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Brandon E Turner
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Chloé B Steen
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Bogdan A Luca
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - Ti Badri
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Milad R Vahid
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Farnaz Khameneh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Peter K Harris
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - David Y Chen
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.,Division of Dermatology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kavita Dhodapkar
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | - Mario Sznol
- Department of Medicine, Division of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA.,Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA.,Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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21
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Zhou Z, Cao J, Liu X, Li M. Evidence for the butyrate metabolism as key pathway improving ulcerative colitis in both pediatric and adult patients. Bioengineered 2021; 12:8309-8324. [PMID: 34592880 PMCID: PMC8806981 DOI: 10.1080/21655979.2021.1985815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Accumulating evidence has shown many similarities and differences of gene profiles and pathways between pediatric and adult ulcerative colitis (UC) patients. In this study, we aimed to investigate the shared genes and pathways in intestinal tissues of pediatric and adult UC. Differentially expressed genes (DEGs) between pediatric and adult UC were identified via bioinformatic analysis of Gene Expression Omnibus datasets GSE87473 and GSE126124. Gene Ontology and pathway enrichment were used to analyze overlapped and distinguished DEGs. Gene Set Variation Analysis (GSVA) was utilized for contrast consistency. Mice colitis models were induced by dextran sulfate sodium (DSS) and Citrobacter rodentium. 2616 DEGs were screened out in intestinal tissues of adult UC compared with those of adult healthy controls, and 1195 DEGs in pediatrics. Same pathways between pediatric and adult UC were enriched using overlapped DEGs, mainly related to immune responses and metabolic processes, including butyrate metabolism, which was also identified by GSVA analysis. Of note, butyrate metabolism was the exclusive down-regulated pathway enriched by these two analyses, indicating that butyrate metabolism is one of the key pathways associated with both pediatric and adult UC. In addition, butyrate suppressed DSS-induced and Citrobacter rodentium-induced intestinal inflammation in mice. Therefore, the study revealed that butyrate metabolism was critical in both pediatric and adult UC. And butyrate suppressed colitis in mice, which provided a theoretical basis for the potential treatment of butyrate for UC patients. Abbreviations: UC, Ulcerative colitis; IBD, Inflammatory bowel disease; DEGs, Differentially expressed genes; GEO, Gene Expression Omnibus; SVA, Spatial variant apodization; LIMMA, Linear models for the microarray data; FC, Fold change; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; GSVA, Gene Set Variation Analysis; MSigDB, Molecular Signatures Database; WT, Wild-type; DSS, Dextran sulfate sodium; HC, Healthy control; SD, Standard deviation; SNHG5, Small nucleolar RNA host gene 5; GLP-2, Glucagon-like peptide 2; GSE, Gene set enrichment; ECM, Extracellular matrix; TCA, Tricarboxylic acid cycle; NA, Not available.
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Affiliation(s)
- Zheng Zhou
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510515, China
| | - Jiasheng Cao
- Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310016, China
| | - Xiaoming Liu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510515, China
| | - Mingsong Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510515, China.,Department of Gastroenterology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, 510000, China
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22
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Saber S, Abd El-Fattah EE, Yahya G, Gobba NA, Maghmomeh AO, Khodir AE, Mourad AAE, Saad AS, Mohammed HG, Nouh NA, Shata A, Amin NA, Abou El-Rous M, Girgis S, El-Ahwany E, Khalaf EM, El-Kott AF, El-Baz AM. A Novel Combination Therapy Using Rosuvastatin and Lactobacillus Combats Dextran Sodium Sulfate-Induced Colitis in High-Fat Diet-Fed Rats by Targeting the TXNIP/NLRP3 Interaction and Influencing Gut Microbiome Composition. Pharmaceuticals (Basel) 2021; 14:ph14040341. [PMID: 33917884 PMCID: PMC8068273 DOI: 10.3390/ph14040341] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Inflammasome targeting and controlling dysbiosis are promising therapeutic approaches to control ulcerative colitis. This report is the first to investigate the mechanisms underlying the coloprotective effects of rosuvastatin and Lactobacillus and their combined therapy on dextran sodium sulfate (DSS)-induced colitis in high-fat diet (HFD)-fed rats. Our results demonstrate the aggravation of intestinal inflammation as a consequence of an HFD following DSS administration. An association between dyslipidemia, LDL oxidation, CD36 expression, ROS generation, thioredoxin-interacting protein (TXNIP) upregulation, and NLRP3 inflammasome activation was demonstrated by DSS exposure in HFD-fed rats. We demonstrated that rosuvastatin/Lactobacillus significantly suppressed the DSS/HFD-induced increase in colon weight/length ratio, DAI, MDI, and myeloperoxidase, as well as corrected dysbiosis and improved histological characteristics. Additionally, caspase-1 activity and IL-1β-driven pyroptotic activity was significantly reduced. Rosuvastatin/Lactobacillus showed prominent anti-inflammatory effects as revealed by the IL-10/IL-12 ratio and the levels of TNF-α and IL-6. These latter effects may be attributed to the inhibition of phosphorylation-induced activation of NF-κB and a concomitant reduction in the expression of NLRP3, pro-IL-1β, and pro-IL-18. Furthermore, rosuvastatin/Lactobacillus reduced Ox-LDL-induced TXNIP and attenuated the inflammatory response by inhibiting NLRP3 inflammasome assembly. To conclude, rosuvastatin/Lactobacillus offers a safe and effective strategy for the management of ulcerative colitis.
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Affiliation(s)
- Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Egypt
- Correspondence: (S.S.); or (A.M.E.-B.); Tel.: +2-01033124949 (S.S.); +2-01069096934 (A.M.E.-B.); Fax: +2-050-2770140 (S.S. & A.M.E.-B.)
| | - Eslam E. Abd El-Fattah
- Department of Biochemistry, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Egypt;
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Al Sharqia 44519, Egypt;
| | - Naglaa A. Gobba
- Department of Pharmacology and Toxicology, College of Pharmacy, Misr University for Science and Technology, Giza 12411, Egypt; or
| | - Abdalkareem Omar Maghmomeh
- Department of Biochemistry, Faculty of Pharmacy, Arab Private University for Science and Technology, Hama 1293400, Syria; or
| | - Ahmed E. Khodir
- Department of Pharmacology, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt; or
| | - Ahmed A. E. Mourad
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Port-Said University, Port-Said 42511, Egypt; (A.A.E.M.); (A.S.S.)
| | - Ahmed S. Saad
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Port-Said University, Port-Said 42511, Egypt; (A.A.E.M.); (A.S.S.)
| | | | - Nehal A. Nouh
- Department of Microbiology, Albatterjee Medical College, Jeddah 6231, Saudi Arabia;
| | - Ahmed Shata
- Department of Clinical Pharmacology, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt;
- Department of Clinical Pharmacy, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Egypt
| | - Noha A. Amin
- Department of Haematology, Theodor Bilharz Research Institute, Giza 12411, Egypt; or
| | - Magdy Abou El-Rous
- Department of Biochemistry, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt; or
| | - Samuel Girgis
- Department of Pharmaceutics, Faculty of Pharmacy, Alsalam University, Kafr El-Zayat 31612, Egypt;
| | - Eman El-Ahwany
- Department of Immunology, Theodor Bilharz Research Institute, Giza 12411, Egypt;
| | - Eman M. Khalaf
- Department of Microbiology and Immunology, Faculty of Pharmacy, Damanhour University, Damanhour 22511, Egypt;
| | - Attalla F. El-Kott
- Department of Biology, College of Science, King Khalid University, Abha 61421, Saudi Arabia;
- Department of Zoology, Faculty of Science, Damanhour University, Damanhour 22511, Egypt
| | - Ahmed M. El-Baz
- Department of Microbiology and Biotechnology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Egypt
- Correspondence: (S.S.); or (A.M.E.-B.); Tel.: +2-01033124949 (S.S.); +2-01069096934 (A.M.E.-B.); Fax: +2-050-2770140 (S.S. & A.M.E.-B.)
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23
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Wipperman MF, Bhattarai SK, Vorkas CK, Maringati VS, Taur Y, Mathurin L, McAulay K, Vilbrun SC, Francois D, Bean J, Walsh KF, Nathan C, Fitzgerald DW, Glickman MS, Bucci V. Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis. Nat Commun 2021; 12:1141. [PMID: 33602926 PMCID: PMC7892575 DOI: 10.1038/s41467-021-21475-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/21/2021] [Indexed: 12/15/2022] Open
Abstract
The composition of the gastrointestinal microbiota influences systemic immune responses, but how this affects infectious disease pathogenesis and antibiotic therapy outcome is poorly understood. This question is rarely examined in humans due to the difficulty in dissociating the immunologic effects of antibiotic-induced pathogen clearance and microbiome alteration. Here, we analyze data from two longitudinal studies of tuberculosis (TB) therapy (35 and 20 individuals) and a cross sectional study from 55 healthy controls, in which we collected fecal samples (for microbiome analysis), sputum (for determination of Mycobacterium tuberculosis (Mtb) bacterial load), and peripheral blood (for transcriptomic analysis). We decouple microbiome effects from pathogen sterilization by comparing standard TB therapy with an experimental TB treatment that did not reduce Mtb bacterial load. Random forest regression to the microbiome-transcriptome-sputum data from the two longitudinal datasets reveals that renormalization of the TB inflammatory state is associated with Mtb pathogen clearance, increased abundance of Clusters IV and XIVa Clostridia, and decreased abundance of Bacilli and Proteobacteria. We find similar associations when applying machine learning to peripheral gene expression and microbiota profiling in the independent cohort of healthy individuals. Our findings indicate that antibiotic-induced reduction in pathogen burden and changes in the microbiome are independently associated with treatment-induced changes of the inflammatory response of active TB, and the response to antibiotic therapy may be a combined effect of pathogen killing and microbiome driven immunomodulation. Antibiotic therapy can lead to pathogen clearance, but also to alterations in the gut microbiota and systemic immune responses. Here, the authors analyze data from patients with tuberculosis and healthy subjects to show that pathogen clearance and gut microbiota alterations are independently associated with antibiotic-induced changes of the inflammatory response of active tuberculosis.
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Affiliation(s)
- Matthew F Wipperman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Clinical and Translational Science Center, Weill Cornell Medicine, New York, NY, USA
| | - Shakti K Bhattarai
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Charles Kyriakos Vorkas
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Venkata Suhas Maringati
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ying Taur
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laurent Mathurin
- Haitian Study Group for Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | | | - Stalz Charles Vilbrun
- Haitian Study Group for Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - Daphie Francois
- Haitian Study Group for Kaposi's Sarcoma and Opportunistic Infections (GHESKIO), Port-au-Prince, Haiti
| | - James Bean
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathleen F Walsh
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA
| | - Carl Nathan
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, New York, NY, USA
| | | | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA. .,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School, New York, NY, USA.
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA. .,Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, USA. .,Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.
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Krawiec P, Pac-Kożuchowska E. Cathelicidin - A Novel Potential Marker of Pediatric Inflammatory Bowel Disease. J Inflamm Res 2021; 14:163-174. [PMID: 33519224 PMCID: PMC7837565 DOI: 10.2147/jir.s288742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/18/2020] [Indexed: 12/19/2022] Open
Abstract
Introduction Cathelicidin is a multifunctional host defense peptide which may also exert pro-inflammatory signals and contribute to the development of autoimmune disorders. We aimed to assess serum concentration of cathelicidin in children with inflammatory bowel disease (IBD) compared to healthy controls and to evaluate its relationship with disease activity and phenotype. Patients and Methods The study group included 68 children with IBD. The control group comprised 20 children with functional abdominal pain. All patients and controls were tested for complete blood count, C-reactive protein, erythrocyte sedimentation rate and cathelicidin. Stool samples were collected to assess calprotectin. Results Cathelicidin was significantly increased in patients with ulcerative colitis (1073.39±214.52 ng/mL) and Crohn’s disease (1057.63±176.03 ng/mL) patients compared to controls (890.56±129.37 ng/mL) (H=16.28; p=0.0003). Cathelicidin was significantly elevated in children with active IBD (1044.90±176.17 ng/mL) and IBD remission (1098.10±227.87 ng/mL) compared to controls (Z=3.21; p=0.001; Z=−4.12; p<0.0001, respectively). Negative correlation between cathelicidin and calprotectin in children with ulcerative colitis was found (R=−0.39; p=0.02). Cathelicidin exhibited AUC of 0.815 for differentiation children with ulcerative colitis from the control group. Conclusion Serum cathelicidin is increased in children with Crohn’s disease and ulcerative colitis regardless of clinical activity of the disease suggesting that it may be a potential biomarker of IBD. Inverse correlation between cathelicidin and fecal calprotectin may imply a disparate role of these molecules in the pathophysiology of pediatric ulcerative colitis.
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Affiliation(s)
- Paulina Krawiec
- Department of Pediatrics and Gastroenterology, Medical University of Lublin, Lublin, Poland
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Oh EH, Rhee JK, Shin JH, Cho JW, Kim DS, Park JY, Choi SY, Choi KD, Choi JH. Neutrophil-mediated immune response as a possible mechanism of acute unilateral vestibulopathy. J Vestib Res 2020; 30:363-374. [PMID: 33285659 DOI: 10.3233/ves-200044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE This study aimed to investigate the underlying pathogenesis of acute unilateral vestibulopathy (AUV) using gene expression profiling combined with bioinformatics analysis. METHODS Total RNA was extracted from the peripheral blood mononuclear cells of ten AUV patients in the acute phase and from ten controls. The differentially expressed genes (DEGs) between these two groups were screened using microarray analysis with the cut-off criteria (|fold changes| > 1.5 and p-value < 0.05). Functional enrichment analysis of DEGs was performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, and the protein-protein interaction (PPI) network was constructed using the STRING (Search Tool for the Retrieval of Interacting Genes) database. RESULTS There were 57 DEGs (50 up-regulated and 7 down-regulated) identified in the AUV group. Functional enrichment analysis showed that most of the up-regulated DEGs were significantly enriched in terms related to the neutrophil-mediated immune pathway. From the PPI network, the top ten hub genes were extracted by calculating four topological properties, and most of them were related to the innate immune system, inflammatory processes and vascular disorders. The complete blood count tests showed that the neutrophil-to-lymphocyte ratio was significantly higher in the 72 AUV patients than in the age-matched controls (2.93±2.25 vs 1.54±0.61, p < 0.001). CONCLUSIONS This study showed that the neutrophil-mediated immune pathway may contribute to the development of AUV by mediating inflammatory and thrombotic changes in the vestibular organ.
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Affiliation(s)
- Eun Hye Oh
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Je-Keun Rhee
- School of Systems Biomedical Science, Soongsil University, Seoul, Korea
| | - Jin-Hong Shin
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Jae Wook Cho
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Dae-Seong Kim
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Ji-Yun Park
- Department of Neurology, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Korea
| | - Seo Young Choi
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, Korea
| | - Kwang-Dong Choi
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Biomedical Research Institute, Busan, Korea
| | - Jae-Hwan Choi
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
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26
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Ashton JJ, Boukas K, Davies J, Stafford IS, Vallejo AF, Haggarty R, Coelho TAF, Batra A, Afzal NA, Vadgama B, Williams AP, Beattie RM, Polak ME, Ennis S. Ileal Transcriptomic Analysis in Paediatric Crohn's Disease Reveals IL17- and NOD-signalling Expression Signatures in Treatment-naïve Patients and Identifies Epithelial Cells Driving Differentially Expressed Genes. J Crohns Colitis 2020; 15:774-786. [PMID: 33232439 PMCID: PMC8095388 DOI: 10.1093/ecco-jcc/jjaa236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Crohn's disease [CD] arises through host-environment interaction. Abnormal gene expression results from disturbed pathway activation or response to bacteria. We aimed to determine activated pathways and driving cell types in paediatric CD. METHODS We employed contemporary targeted autoimmune RNA sequencing, in parallel to single-cell sequencing, to ileal tissue derived from paediatric CD and controls. Weighted gene co-expression network analysis [WGCNA] was performed and differentially expressed genes [DEGs] were determined. We integrated clinical data to determine co-expression modules associated with outcomes. RESULTS In all, 27 treatment-naive CD [TN-CD], 26 established CD patients and 17 controls were included. WGCNA revealed a 31-gene signature characterising TN-CD patients, but not established CD, nor controls. The CSF3R gene is a hub within this module and is key in neutrophil expansion and differentiation. Antimicrobial genes, including S100A12 and the calprotectin subunit S100A9, were significantly upregulated in TN CD compared with controls [p = 2.61 x 10-15 and p = 9.13 x 10-14, respectively] and established CD [both p = 0.0055]. Gene-enrichment analysis confirmed upregulation of the IL17-, NOD- and Oncostatin-M-signalling pathways in TN-CD patients, identified in both WGCNA and DEG analyses. An upregulated gene signature was enriched for transcripts promoting Th17-cell differentiation and correlated with prolonged time to relapse [correlation-coefficient-0.36, p = 0.07]. Single-cell sequencing of TN-CD patients identified specialised epithelial cells driving differential expression of S100A9. Cell groups, determined by single-cell gene expression, demonstrated enrichment of IL17-signalling in monocytes and epithelial cells. CONCLUSIONS Ileal tissue from treatment-naïve paediatric patients is significantly upregulated for genes driving IL17-, NOD- and Oncostatin-M-signalling. This signal is driven by a distinct subset of epithelial cells expressing antimicrobial gene transcripts.
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Affiliation(s)
- James J Ashton
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK,Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Konstantinos Boukas
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK
| | - James Davies
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Imogen S Stafford
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Andres F Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Rachel Haggarty
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Tracy A F Coelho
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Akshay Batra
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Nadeem A Afzal
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Bhumita Vadgama
- Department of Paediatric Histopathology, Southampton Children’s Hospital, Southampton, UK
| | - Anthony P Williams
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - R Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Marta E Polak
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK,Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK,Corresponding author: Professor Sarah Ennis, PhD, Human Genetics and Genomic Medicine, University of Southampton, Duthie Building [Mailpoint 808], Southampton General Hospital, Southampton SO16 6YD, UK. Tel.: +44 [0]23 8079 8614;
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27
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Detecting ulcerative colitis from colon samples using efficient feature selection and machine learning. Sci Rep 2020; 10:13744. [PMID: 32792678 PMCID: PMC7426912 DOI: 10.1038/s41598-020-70583-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/30/2020] [Indexed: 02/08/2023] Open
Abstract
Ulcerative colitis (UC) is one of the most common forms of inflammatory bowel disease (IBD) characterized by inflammation of the mucosal layer of the colon. Diagnosis of UC is based on clinical symptoms, and then confirmed based on endoscopic, histologic and laboratory findings. Feature selection and machine learning have been previously used for creating models to facilitate the diagnosis of certain diseases. In this work, we used a recently developed feature selection algorithm (DRPT) combined with a support vector machine (SVM) classifier to generate a model to discriminate between healthy subjects and subjects with UC based on the expression values of 32 genes in colon samples. We validated our model with an independent gene expression dataset of colonic samples from subjects in active and inactive periods of UC. Our model perfectly detected all active cases and had an average precision of 0.62 in the inactive cases. Compared with results reported in previous studies and a model generated by a recently published software for biomarker discovery using machine learning (BioDiscML), our final model for detecting UC shows better performance in terms of average precision.
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28
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Ferosekhan S, Turkmen S, Xu H, Afonso JM, Zamorano MJ, Kaushik S, Izquierdo M. The Relationship between the Expression of Fatty Acyl Desaturase 2 ( fads2) Gene in Peripheral Blood Cells (PBCs) and Liver in Gilthead Seabream, Sparus aurata Broodstock Fed a Low n-3 LC-PUFA Diet. Life (Basel) 2020; 10:life10070117. [PMID: 32707702 PMCID: PMC7400341 DOI: 10.3390/life10070117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 12/22/2022] Open
Abstract
The principle aim of this study is to elucidate the relationship between the fatty acid desaturase 2 gene (fads2) expression pattern in peripheral blood cells (PBCs) and liver of gilthead seabream (GSB), Sparus aurata broodstock in order to determine the possible use of fads2 expression as a potential biomarker for the selection of broodstock. This selection could be utilized for breeding programs aiming to improve reproduction, health, and nutritional status. Passive Integrated Transponder (PIT)-tagged GSB broodstock (Male-1.22 ± 0.20 kg; 44.8 ± 2 cm and female-2.36 ± 0.64 kg; 55.1 cm) were fed a diet containing low levels of fish meal and fish oil (EPA 2.5; DHA 1.7 and n-3 LC-PUFA 4.6% TFA) for one month. After the feeding period, fads2 expression in PBCs and liver of both male and female broodstock were highly significantly correlated (r = 0.89; p < 0.001). Additionally, in male broodstock, liver fads2 expression was significantly correlated (p < 0.05) to liver contents in 16:0 (r = 0.95; p = 0.04) and total saturates (r = 0.97; p = 0.03) as well as to 20:3n–6/20:2n–6 (r = 0.98; p = 0.02) a Fads2 product/precursor ratio. Overall, we found a positive and significant correlation between fads2 expression levels in the PBCs and liver of GSB broodstock. PBCs fads2 expression levels indicate a strong potential for utilization as a non-invasive method to select animals having increased fatty acid bioconversion capability, better able to deal with diets free of fish meal and fish oil.
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Affiliation(s)
- Shajahan Ferosekhan
- Aquaculture Research Group (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, 35214 Telde, Spain; (S.T.); (H.X.); (J.M.A.); (M.J.Z.); (S.K.); (M.I.)
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar 751002, India
- Correspondence:
| | - Serhat Turkmen
- Aquaculture Research Group (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, 35214 Telde, Spain; (S.T.); (H.X.); (J.M.A.); (M.J.Z.); (S.K.); (M.I.)
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hanlin Xu
- Aquaculture Research Group (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, 35214 Telde, Spain; (S.T.); (H.X.); (J.M.A.); (M.J.Z.); (S.K.); (M.I.)
| | - Juan Manuel Afonso
- Aquaculture Research Group (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, 35214 Telde, Spain; (S.T.); (H.X.); (J.M.A.); (M.J.Z.); (S.K.); (M.I.)
| | - Maria Jesus Zamorano
- Aquaculture Research Group (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, 35214 Telde, Spain; (S.T.); (H.X.); (J.M.A.); (M.J.Z.); (S.K.); (M.I.)
| | - Sadasivam Kaushik
- Aquaculture Research Group (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, 35214 Telde, Spain; (S.T.); (H.X.); (J.M.A.); (M.J.Z.); (S.K.); (M.I.)
| | - Marisol Izquierdo
- Aquaculture Research Group (GIA), IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, 35214 Telde, Spain; (S.T.); (H.X.); (J.M.A.); (M.J.Z.); (S.K.); (M.I.)
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