1
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Li ZY, Sun YH, Qian-Hua, Wang HY, Wang YJ, Miao-Jiang. Single-cell analysis of Crohn's disease: Unveiling heterogeneity and evaluating ustekinumab outcomes. J Gene Med 2024; 26:e3715. [PMID: 38962887 DOI: 10.1002/jgm.3715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND The present study aimed to dissect the cellular complexity of Crohn's disease (CD) using single-cell RNA sequencing, focusing on identifying key cell populations and their transcriptional profiles in inflamed tissue. METHODS We applied scRNA-sequencing to compare the cellular composition of CD patients with healthy controls, utilizing Seurat for clustering and annotation. Differential gene expression analysis and protein-protein interaction networks were constructed to identify crucial genes and pathways. RESULTS Our study identified eight distinct cell types in CD, highlighting crucial fibroblast and T cell interactions. The analysis revealed key cellular communications and identified significant genes and pathways involved in the disease's pathology. The role of fibroblasts was underscored by elevated expression in diseased samples, offering insights into disease mechanisms and potential therapeutic targets, including responses to ustekinumab treatment, thus enriching our understanding of CD at a molecular level. CONCLUSIONS Our findings highlight the complex cellular and molecular interplay in CD, suggesting new biomarkers and therapeutic targets, offering insights into disease mechanisms and treatment implications.
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Affiliation(s)
- Zheng-Yang Li
- Department of Gastroenterology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Yong-Hong Sun
- Department of Gastroenterology, Dalian Friendship Hospital, Dalian, Liaoning, China
| | - Qian-Hua
- Department of Gastroenterology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Hai-Yan Wang
- Department of Gastroenterology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Ya-Jie Wang
- Department of Gastroenterology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Miao-Jiang
- Department of Gastroenterology, Jinshan Hospital of Fudan University, Shanghai, China
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2
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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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Ha J, Kim M, Park JS, Lee Y, Lee JY, Shin JC, Seo D, Park SS, You J, Jung SM, Kim HY, Mizuno S, Takahashi S, Kim SJ, Park SH. SERTAD1 initiates NLRP3-mediated inflammasome activation through restricting NLRP3 polyubiquitination. Cell Rep 2024; 43:113752. [PMID: 38341852 DOI: 10.1016/j.celrep.2024.113752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/03/2024] [Accepted: 01/23/2024] [Indexed: 02/13/2024] Open
Abstract
We here demonstrate that SERTAD1 is an adaptor protein responsible for the regulation of lysine 63 (K63)-linked NLRP3 polyubiquitination by the Cullin1 E3 ubiquitin ligase upon inflammasome activation. SERTAD1 specifically binds to NLRP3 but not to other inflammasome sensors. This endogenous interaction increases after inflammasome activation, interfering with the interaction between NLRP3 and Cullin1. Interleukin (IL)-1β and IL-18 secretion, as well as the cleavage of gasdermin D, are decreased in SERTAD1 knockout bone-marrow-derived macrophages, together with reduced formation of the NLRP3 inflammasome complex. Additionally, SERTAD1-deficient mice show attenuated severity of monosodium-uric-acid-induced peritonitis and experimental autoimmune encephalomyelitis. Analysis of public datasets indicates that expression of SERTAD1 mRNA is significantly increased in the patients of autoimmune diseases. Thus, our findings uncover a function of SERTAD1 that specifically reduces Cullin1-mediated NLRP3 polyubiquitination via direct binding to NLRP3, eventually acting as a crucial factor to regulate the initiation of NLRP3-mediated inflammasome activation.
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Affiliation(s)
- Jihoon Ha
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Minbeom Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jin Seok Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Yerin Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jae Young Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jin-Cheol Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Dongyeob Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seong Shil Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jiyeon You
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Su Myung Jung
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hye Young Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; SRC Center for Immune Research on Non-lymphoid Organs, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seiya Mizuno
- Laboratory Animal Resource Center, Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8578, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center, Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8578, Japan
| | - Seong-Jin Kim
- GILO Institute, GILO Foundation, Seoul 06668, Republic of Korea
| | - Seok Hee Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea; SRC Center for Immune Research on Non-lymphoid Organs, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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4
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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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5
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Zhao X, Hu C, Chen X, Ren S, Gao F. Drug Repositioning of Inflammatory Bowel Disease Based on Co-Target Gene Expression Signature of Glucocorticoid Receptor and TET2. BIOLOGY 2024; 13:82. [PMID: 38392301 PMCID: PMC10886832 DOI: 10.3390/biology13020082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/24/2024]
Abstract
The glucocorticoid receptor (GR) and ten-eleven translocation 2 (TET2), respectively, play a crucial role in regulating immunity and inflammation, and GR interacts with TET2. However, their synergetic roles in inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), remain unclear. This study aimed to investigate the co-target gene signatures of GR and TET2 in IBD and provide potential therapeutic interventions for IBD. By integrating public data, we identified 179 GR- and TET2-targeted differentially expressed genes (DEGs) in CD and 401 in UC. These genes were found to be closely associated with immunometabolism, inflammatory responses, and cell stress pathways. In vitro inflammatory cellular models were constructed using LPS-treated HT29 and HCT116 cells, respectively. Drug repositioning based on the co-target gene signatures of GR and TET2 derived from transcriptomic data of UC, CD, and the in vitro model was performed using the Connectivity Map (CMap). BMS-536924 emerged as a top therapeutic candidate, and its validation experiment within the in vitro inflammatory model confirmed its efficacy in mitigating the LPS-induced inflammatory response. This study sheds light on the pathogenesis of IBD from a new perspective and may accelerate the development of novel therapeutic agents for inflammatory diseases including IBD.
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Affiliation(s)
- Xianglin Zhao
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- School of Life Sciences, Henan University, Kaifeng 475004, China
- Shenzhen Research Institute of Henan University, Henan University, Shenzhen 518000, China
| | - Chenghao Hu
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xinyu Chen
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Shuqiang Ren
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou 310022, China
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
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6
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Vebr M, Pomahačová R, Sýkora J, Schwarz J. A Narrative Review of Cytokine Networks: Pathophysiological and Therapeutic Implications for Inflammatory Bowel Disease Pathogenesis. Biomedicines 2023; 11:3229. [PMID: 38137450 PMCID: PMC10740682 DOI: 10.3390/biomedicines11123229] [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: 08/09/2023] [Revised: 10/11/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a lifelong inflammatory immune mediated disorder, encompassing Crohn's disease (CD) and ulcerative colitis (UC); however, the cause and specific pathogenesis of IBD is yet incompletely understood. Multiple cytokines produced by different immune cell types results in complex functional networks that constitute a highly regulated messaging network of signaling pathways. Applying biological mechanisms underlying IBD at the single omic level, technologies and genetic engineering enable the quantification of the pattern of released cytokines and new insights into the cytokine landscape of IBD. We focus on the existing literature dealing with the biology of pro- or anti-inflammatory cytokines and interactions that facilitate cell-based modulation of the immune system for IBD inflammation. We summarize the main roles of substantial cytokines in IBD related to homeostatic tissue functions and the remodeling of cytokine networks in IBD, which may be specifically valuable for successful cytokine-targeted therapies via marketed products. Cytokines and their receptors are validated targets for multiple therapeutic areas, we review the current strategies for therapeutic intervention and developing cytokine-targeted therapies. New biologics have shown efficacy in the last few decades for the management of IBD; unfortunately, many patients are nonresponsive or develop therapy resistance over time, creating a need for novel therapeutics. Thus, the treatment options for IBD beyond the immune-modifying anti-TNF agents or combination therapies are expanding rapidly. Further studies are needed to fully understand the immune response, networks of cytokines, and the direct pathogenetic relevance regarding individually tailored, safe and efficient targeted-biotherapeutics.
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Affiliation(s)
- Marek Vebr
- Departments of Pediatrics, Faculty Hospital, Faculty of Medicine in Pilsen, Charles University of Prague, 323 00 Pilsen, Czech Republic; (R.P.); (J.S.); (J.S.)
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7
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Schulze LL, Becker E, Dedden M, Liu LJ, van Passen C, Mohamed-Abdou M, Müller TM, Wiendl M, Ullrich KAM, Atreya I, Leppkes M, Ekici AB, Kirchner P, Stürzl M, Sexton D, Palliser D, Atreya R, Siegmund B, Neurath MF, Zundler S. Differential Effects of Ontamalimab Versus Vedolizumab on Immune Cell Trafficking in Intestinal Inflammation and Inflammatory Bowel Disease. J Crohns Colitis 2023; 17:1817-1832. [PMID: 37208197 DOI: 10.1093/ecco-jcc/jjad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/16/2023] [Accepted: 05/16/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS The anti-MAdCAM-1 antibody ontamalimab demonstrated efficacy in a phase II trial in ulcerative colitis and results of early terminated phase III trials are pending, but its precise mechanisms of action are still unclear. Thus, we explored the mechanisms of action of ontamalimab and compared it to the anti-α4β7 antibody vedolizumab. METHODS We studied MAdCAM-1 expression with RNA sequencing and immunohistochemistry. The mechanisms of action of ontamalimab were assessed with fluorescence microscopy, dynamic adhesion and rolling assays. We performed in vivo cell trafficking studies in mice and compared ontamalimab and vedolizumab surrogate [-s] antibodies in experimental models of colitis and wound healing. We analysed immune cell infiltration under anti-MAdCAM-1 and anti-α4β7 treatment by single-cell transcriptomics and studied compensatory trafficking pathways. RESULTS MAdCAM-1 expression was increased in active inflammatory bowel disease. Binding of ontamalimab to MAdCAM-1 induced the internalization of the complex. Functionally, ontamalimab blocked T cell adhesion similar to vedolizumab, but also inhibited L-selectin-dependent rolling of innate and adaptive immune cells. Despite conserved mechanisms in mice, the impact of ontamalimab-s and vedolizumab-s on experimental colitis and wound healing was similar. Single-cell RNA sequencing demonstrated enrichment of ontamalimab-s-treated lamina propria cells in specific clusters, and in vitro experiments indicated that redundant adhesion pathways are active in these cells. CONCLUSIONS Ontamalimab has unique and broader mechanisms of action compared to vedolizumab. However, this seems to be compensated for by redundant cell trafficking circuits and leads to similar preclinical efficacy of anti-α4β7 and anti-MAdCAM-1 treatment. These results will be important for the interpretation of pending phase III data.
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Affiliation(s)
- Lisa Lou Schulze
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Emily Becker
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Mark Dedden
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Li-Juan Liu
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Chiara van Passen
- Department of Surgery, Division of Molecular and Experimental Surgery, University Hospital Erlangen and Friedrich-Alexander Universität Erlangen-Nürnberg, Germany
| | - Mariam Mohamed-Abdou
- Department of Surgery, Division of Molecular and Experimental Surgery, University Hospital Erlangen and Friedrich-Alexander Universität Erlangen-Nürnberg, Germany
| | - Tanja M Müller
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Germany
| | - Maximilian Wiendl
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Karen A M Ullrich
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Imke Atreya
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Germany
| | - Moritz Leppkes
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Philipp Kirchner
- Institute of Human Genetics, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Michael Stürzl
- Department of Surgery, Division of Molecular and Experimental Surgery, University Hospital Erlangen and Friedrich-Alexander Universität Erlangen-Nürnberg, Germany
| | - Dan Sexton
- Shire HGT, a Takeda company, Cambridge, MA, USA
| | | | - Raja Atreya
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Germany
| | - Britta Siegmund
- Division of Gastroenterology, Infectiology and Rheumatology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Markus F Neurath
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Germany
| | - Sebastian Zundler
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Germany
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8
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Li J, Ji Y, Chen N, Dai L, Deng H. Colitis-associated carcinogenesis: crosstalk between tumors, immune cells and gut microbiota. Cell Biosci 2023; 13:194. [PMID: 37875976 PMCID: PMC10594787 DOI: 10.1186/s13578-023-01139-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. One of the main causes of colorectal cancer is inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD). Intestinal epithelial cells (IECs), intestinal mesenchymal cells (IMCs), immune cells, and gut microbiota construct the main body of the colon and maintain colon homeostasis. In the development of colitis and colitis-associated carcinogenesis, the damage, disorder or excessive recruitment of different cells such as IECs, IMCs, immune cells and intestinal microbiota play different roles during these processes. This review aims to discuss the various roles of different cells and the crosstalk of these cells in transforming intestinal inflammation to cancer, which provides new therapeutic methods for chemotherapy, targeted therapy, immunotherapy and microbial therapy.
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Affiliation(s)
- Junshu Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Yanhong Ji
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Na Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Lei Dai
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China.
| | - Hongxin Deng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China.
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9
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Zhao XH, Zhao P, Deng Z, Yang T, Qi YX, An LY, Sun DL, He HY. Integrative analysis reveals marker genes for intestinal mucosa barrier repairing in clinical patients. iScience 2023; 26:106831. [PMID: 37250791 PMCID: PMC10212979 DOI: 10.1016/j.isci.2023.106831] [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: 11/01/2022] [Revised: 03/21/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023] Open
Abstract
This study aims to identify biomarkers of intestinal repair and provide potential therapeutic clues for improving functional recovery and prognostic performance after intestinal inflammation or injury. Here, we conducted a large-scale screening of multiple transcriptomic and scRNA-seq datasets of patients with inflammatory bowel disease (IBD), and identified 10 marker genes that potentially contribute to intestinal barrier repairing: AQP8, SULT1A1, HSD17B2, PADI2, SLC26A2, SELENBP1, FAM162A, TNNC2, ACADS, and TST. Analysis of a published scRNA-seq dataset revealed that expression of these healing markers were specific to absorptive cell types in intestinal epithelium. Furthermore, we conducted a clinical study where 11 patients underwent ileum resection demonstrating that upregulation of post-operative AQP8 and SULT1A1 expression were associated with improved recovery of bowel functions after surgery-induced intestinal injury, making them confident biomarkers of intestinal healing as well as potential prognostic markers and therapeutic targets for patients with impaired intestinal barrier functions.
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Affiliation(s)
- Xiao-Hu Zhao
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Kunming Medical University / Second Faculty of Clinical Medicine, Kunming Medical University, Kunming 650101, China
| | - Peinan Zhao
- Department of Medicine (Alfred Hospital), Central Clinical School, Monash University, 99 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Zihao Deng
- Department of Medicine (Alfred Hospital), Central Clinical School, Monash University, 99 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Ting Yang
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Kunming Medical University / Second Faculty of Clinical Medicine, Kunming Medical University, Kunming 650101, China
| | - Yu-Xing Qi
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Kunming Medical University / Second Faculty of Clinical Medicine, Kunming Medical University, Kunming 650101, China
| | - Li-Ya An
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Kunming Medical University / Second Faculty of Clinical Medicine, Kunming Medical University, Kunming 650101, China
| | - Da-Li Sun
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Kunming Medical University / Second Faculty of Clinical Medicine, Kunming Medical University, Kunming 650101, China
| | - Hai-Yu He
- Department of Gastroenterology, Second Affiliated Hospital of Kunming Medical University / Second Faculty of Clinical Medicine, Kunming Medical University, Kunming 650101, China
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10
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Guan Y, Zhang Y, Zhu Y, Wang Y. CXCL10 as a shared specific marker in rheumatoid arthritis and inflammatory bowel disease and a clue involved in the mechanism of intestinal flora in rheumatoid arthritis. Sci Rep 2023; 13:9754. [PMID: 37328529 PMCID: PMC10276029 DOI: 10.1038/s41598-023-36833-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/10/2023] [Indexed: 06/18/2023] Open
Abstract
This study aimed to identify shared specific genes associated with rheumatoid arthritis (RA) and inflammatory bowel disease (IBD) through bioinformatic analysis and to examine the role of the gut microbiome in RA. The data were extracted from the 3 RA and 1 IBD gene expression datasets and 1 RA gut microbiome metagenomic dataset. Weighted correlation network analysis (WGCNA) and machine learnings was performed to identify candidate genes associated with RA and IBD. Differential analysis and two different machine learning algorithms were used to investigate RA's gut microbiome characteristics. Subsequently, the shared specific genes related to the gut microbiome in RA were identified, and an interaction network was constructed utilizing the gutMGene, STITCH, and STRING databases. We identified 15 candidates shared genes through a joint analysis of the WGCNA for RA and IBD. The candidate gene CXCL10 was identified as the shared hub gene by the interaction network analysis of the corresponding WGCNA module gene to each disease, and CXCL10 was further identified as the shared specific gene by two machine learning algorithms. Additionally, we identified 3 RA-associated characteristic intestinal flora (Prevotella, Ruminococcus, and Ruminococcus bromii) and built a network of interactions between the microbiomes, genes, and pathways. Finally, it was discovered that the gene CXCL10 shared between IBD and RA was associated with the three gut microbiomes mentioned above. This study demonstrates the relationship between RA and IBD and provides a reference for research into the role of the gut microbiome in RA.
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Affiliation(s)
- Yin Guan
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Yue Zhang
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Yifan Zhu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Yue Wang
- Department of Rheumatism Immunity Branch, Affiliated Hospital of Nanjing University of Chinese Medicine, No. 155 Hanzhong Road, Qinhuai, Nanjing, 210029, Jiangsu, China.
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11
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Xu S, Li X, Zhang S, Qi C, Zhang Z, Ma R, Xiang L, Chen L, Zhu Y, Tang C, Bourgonje AR, Li M, He Y, Zeng Z, Hu S, Feng R, Chen M. Oxidative stress gene expression, DNA methylation, and gut microbiota interaction trigger Crohn's disease: a multi-omics Mendelian randomization study. BMC Med 2023; 21:179. [PMID: 37170220 PMCID: PMC10173549 DOI: 10.1186/s12916-023-02878-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Oxidative stress (OS) is a key pathophysiological mechanism in Crohn's disease (CD). OS-related genes can be affected by environmental factors, intestinal inflammation, gut microbiota, and epigenetic changes. However, the role of OS as a potential CD etiological factor or triggering factor is unknown, as differentially expressed OS genes in CD can be either a cause or a subsequent change of intestinal inflammation. Herein, we used a multi-omics summary data-based Mendelian randomization (SMR) approach to identify putative causal effects and underlying mechanisms of OS genes in CD. METHODS OS-related genes were extracted from the GeneCards database. Intestinal transcriptome datasets were collected from the Gene Expression Omnibus (GEO) database and meta-analyzed to identify differentially expressed genes (DEGs) related to OS in CD. Integration analyses of the largest CD genome-wide association study (GWAS) summaries with expression quantitative trait loci (eQTLs) and DNA methylation QTLs (mQTLs) from the blood were performed using SMR methods to prioritize putative blood OS genes and their regulatory elements associated with CD risk. Up-to-date intestinal eQTLs and fecal microbial QTLs (mbQTLs) were integrated to uncover potential interactions between host OS gene expression and gut microbiota through SMR and colocalization analysis. Two additional Mendelian randomization (MR) methods were used as sensitivity analyses. Putative results were validated in an independent multi-omics cohort from the First Affiliated Hospital of Sun Yat-sen University (FAH-SYS). RESULTS A meta-analysis from six datasets identified 438 OS-related DEGs enriched in intestinal enterocytes in CD from 817 OS-related genes. Five genes from blood tissue were prioritized as candidate CD-causal genes using three-step SMR methods: BAD, SHC1, STAT3, MUC1, and GPX3. Furthermore, SMR analysis also identified five putative intestinal genes, three of which were involved in gene-microbiota interactions through colocalization analysis: MUC1, CD40, and PRKAB1. Validation results showed that 88.79% of DEGs were replicated in the FAH-SYS cohort. Associations between pairs of MUC1-Bacillus aciditolerans and PRKAB1-Escherichia coli in the FAH-SYS cohort were consistent with eQTL-mbQTL colocalization. CONCLUSIONS This multi-omics integration study highlighted that OS genes causal to CD are regulated by DNA methylation and host-microbiota interactions. This provides evidence for future targeted functional research aimed at developing suitable therapeutic interventions and disease prevention.
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Affiliation(s)
- Shu Xu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xiaozhi Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shenghong Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Cancan Qi
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhenhua Zhang
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine & TWINCORE, Joint Ventures Between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Ruiqi Ma
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Liyuan Xiang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Lianmin Chen
- Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, Jiangsu, China
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yijun Zhu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Ce Tang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Miaoxin Li
- Zhongshan School of Medicine, Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yao He
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhirong Zeng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shixian Hu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
| | - Rui Feng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
- Department of Gastroenterology, Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-Sen University, Nanning, Guangxi, China.
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
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12
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Wu Y, Gettler K, Kars ME, Giri M, Li D, Bayrak CS, Zhang P, Jain A, Maffucci P, Sabic K, Van Vleck T, Nadkarni G, Denson LA, Ostrer H, Levine AP, Schiff ER, Segal AW, Kugathasan S, Stenson PD, Cooper DN, Philip Schumm L, Snapper S, Daly MJ, Haritunians T, Duerr RH, Silverberg MS, Rioux JD, Brant SR, McGovern DPB, Cho JH, Itan Y. Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients. Nat Commun 2023; 14:2256. [PMID: 37080976 PMCID: PMC10119186 DOI: 10.1038/s41467-023-37849-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a group of chronic digestive tract inflammatory conditions whose genetic etiology is still poorly understood. The incidence of IBD is particularly high among Ashkenazi Jews. Here, we identify 8 novel and plausible IBD-causing genes from the exomes of 4453 genetically identified Ashkenazi Jewish IBD cases (1734) and controls (2719). Various biological pathway analyses are performed, along with bulk and single-cell RNA sequencing, to demonstrate the likely physiological relatedness of the novel genes to IBD. Importantly, we demonstrate that the rare and high impact genetic architecture of Ashkenazi Jewish adult IBD displays significant overlap with very early onset-IBD genetics. Moreover, by performing biobank phenome-wide analyses, we find that IBD genes have pleiotropic effects that involve other immune responses. Finally, we show that polygenic risk score analyses based on genome-wide high impact variants have high power to predict IBD susceptibility.
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Affiliation(s)
- Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kyle Gettler
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Meltem Ece Kars
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dalin Li
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Cigdem Sevim Bayrak
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Aayushee Jain
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick Maffucci
- Immunology Institute, Graduate School, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Ksenija Sabic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tielman Van Vleck
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lee A Denson
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Adam P Levine
- Division of Medicine, University College London (UCL), London, UK
- Research Department of Pathology, University College London (UCL), London, UK
| | - Elena R Schiff
- Division of Medicine, University College London (UCL), London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Anthony W Segal
- Division of Medicine, University College London (UCL), London, UK
| | | | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Scott Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Oncology Boston Children's Hospital, Boston, MA, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Talin Haritunians
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Mark S Silverberg
- Inflammatory Bowel Disease Centre, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Steven R Brant
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dermot P B McGovern
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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13
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Xue C, Zhang X, Ge H, Tang Q, Jeon J, Zhao F, Wang Y, Zhu MX, Cao Z. Total flavone of flowers of Abelmoschus manihot (L.) Medic inhibits the expression of adhesion molecules in primary mesenteric arterial endothelial cells and ameliorates dextran sodium sulphate-induced ulcerative colitis in mice. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 112:154713. [PMID: 36857970 DOI: 10.1016/j.phymed.2023.154713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Flowers of Abelmoschus manihot (L.) medic (AM) is a traditional Chinese medicine used to treat chronic nephritis, nephrotic syndrome, diabetic nephropathy, and colonic inflammation. PURPOSE This study aimed to explore the influence of the total flavone of AM flowers (TFA) on acute ulcerative colitis (UC) and the potential underlying mechanism. METHODS Efficacy of TFA (30, 60, 120 mg/kg) on UC was evaluated in a dextran sodium sulphate (DSS)-induced colonic inflammatory mouse model by analyzing disease activity index (DAI), histopathological score, colon length, and cytokine expression. Expression levels of critical adhesion molecules and nuclear factor kappa B (NF-κB) were examined by qRT-PCR, Western blotting, or immunofluorescence labeling. Myeloperoxidase activity was examined using ELISA. In vitro THP-1 adhesion assay was used to evaluate monocyte adhesion. RESULTS TFA significantly reduced DAI score, prevented colon shortening, and ameliorated histological injuries of colons in DSS-treated mice. TFA inhibited the expression of cytokines (IL-1β and TNF-α) and adhesion molecules (ICAM-1, VCAM-1, and MAdCAM-1) in colon tissues of DSS mice. In vitro studies on mesenteric arterial endothelial cells (MAECs) showed that TFA attenuated TNF-α-induced upregulation of ICAM-1, VCAM-1, and MAdCAM-1, as well as THP-1 cell adhesion to MAECs. TFA also suppressed the phosphorylation and nuclear translocation of NF-κB in MAECs. CONCLUSION TFA efficaciously ameliorates UC possibly by inhibiting monocyte adhesion through blocking TNF-α-induced NF-κB activation, which in turn suppresses the upregulation of adhesive molecules in colon endothelial cells. Inhibiting the expression of adhesion molecule in MAECs may represent a useful strategy for therapeutic development to treat UC, with TFA being a safe and efficacious therapeutic agent.
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Affiliation(s)
- Chu Xue
- State Key Laboratory of Natural Medicines and Jiangsu Provincial Key Laboratory for TCM Evaluation and Translational Development, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Xian Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Provincial Key Laboratory for TCM Evaluation and Translational Development, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Haitao Ge
- Research Institute of Huanghui, Jiangsu Suzhong Pharmaceutical Group Co., Ltd., Nanjing, Jiangsu, China
| | - Qinglian Tang
- State Key Laboratory of Natural Medicines and Jiangsu Provincial Key Laboratory for TCM Evaluation and Translational Development, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Jaepyo Jeon
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Fang Zhao
- State Key Laboratory of Natural Medicines and Jiangsu Provincial Key Laboratory for TCM Evaluation and Translational Development, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Yujing Wang
- State Key Laboratory of Natural Medicines and Jiangsu Provincial Key Laboratory for TCM Evaluation and Translational Development, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Michael X Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Zhengyu Cao
- State Key Laboratory of Natural Medicines and Jiangsu Provincial Key Laboratory for TCM Evaluation and Translational Development, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, China.
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14
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Dai Z, Zhang J, Xu W, Du P, Wang Z, Liu Y. Single-Cell Sequencing-Based Validation of T Cell-Associated Diagnostic Model Genes and Drug Response in Crohn's Disease. Int J Mol Sci 2023; 24:ijms24076054. [PMID: 37047025 PMCID: PMC10093907 DOI: 10.3390/ijms24076054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Crohn's disease is a highly heterogeneous autoimmune disease with a unique inflammatory phenotype of T cells at the lesion site. We aim to further explore the diagnosis of Crohn's disease and drug prediction of T cell marker gene expression. We obtained single-cell expression profile data from 22 CDs or normal samples and performed cell annotation and cellular communication analysis. Through the intersection of T cell marker genes, differential genes, and WGCNA results, we identified T cell-specific key genes and their immune landscapes and potential pathogenesis, and validated them across multiple datasets and patient tissue samples. We also explored the differentiation characteristics of genes by pseudo-temporal analysis and assessed their diagnostic performance and drug sensitivity by molecular docking. Finally, we extended this study to the prognosis of IBD-associated colon cancer. TNF-centered 5-gene diagnostic model not only has excellent diagnostic efficacy, but is also closely associated with KRAS, P53, and IL6/JAK/STAT3 pathways and physiological processes, such as EMT, coagulation, and apoptosis. In addition, this diagnostic model may have potential synergistic immunotherapeutic effects, with positive correlations with immune checkpoints such as CTLA4, CD86, PDCD1LG2, and CD40. Molecular docking demonstrated that BIRC3 and ANXA1 have strong binding properties to Azathioprine and Glucoocorticoid. Furthermore, the 5-gene model may suggest antagonism to IFX and prognosis for colon cancer associated with inflammatory bowel disease. Single-cell sequencing targeting T cell-related features in patients with Crohn's disease may aid in new diagnostic decisions, as well as the initial exploration of high-potential therapies.
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Affiliation(s)
- Zhujiang Dai
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
| | - Jie Zhang
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Weimin Xu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
| | - Peng Du
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
| | - Zhongchuan Wang
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
| | - Yun Liu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
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15
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Lilja S, Li X, Smelik M, Lee EJ, Loscalzo J, Marthanda PB, Hu L, Magnusson M, Sysoev O, Zhang H, Zhao Y, Sjöwall C, Gawel D, Wang H, Benson M. Multi-organ single-cell analysis reveals an on/off switch system with potential for personalized treatment of immunological diseases. Cell Rep Med 2023; 4:100956. [PMID: 36858042 PMCID: PMC10040389 DOI: 10.1016/j.xcrm.2023.100956] [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: 08/17/2022] [Revised: 09/30/2022] [Accepted: 02/03/2023] [Indexed: 03/03/2023]
Abstract
Prioritization of disease mechanisms, biomarkers, and drug targets in immune-mediated inflammatory diseases (IMIDs) is complicated by altered interactions between thousands of genes. Our multi-organ single-cell RNA sequencing of a mouse IMID model, namely collagen-induced arthritis, shows highly complex and heterogeneous expression changes in all analyzed organs, even though only joints showed signs of inflammation. We organized those into a multi-organ multicellular disease model, which shows predicted molecular interactions within and between organs. That model supports that inflammation is switched on or off by altered balance between pro- and anti-inflammatory upstream regulators (URs) and downstream pathways. Meta-analyses of human IMIDs show a similar, but graded, on/off switch system. This system has the potential to prioritize, diagnose, and treat optimal combinations of URs on the levels of IMIDs, subgroups, and individual patients. That potential is supported by UR analyses in more than 600 sera from patients with systemic lupus erythematosus.
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Affiliation(s)
- Sandra Lilja
- Department of Pediatrics, Biomedical and Clinical Sciences, Linköping University, 58183 Linköping, Sweden; Mavatar, Inc, Vasagatan, 11120 Stockholm, Sweden
| | - Xinxiu Li
- Department of Pediatrics, Biomedical and Clinical Sciences, Linköping University, 58183 Linköping, Sweden; Medical Digital Twin Research Group, Division of Ear, Nose and Throat Diseases, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Martin Smelik
- Department of Pediatrics, Biomedical and Clinical Sciences, Linköping University, 58183 Linköping, Sweden; Medical Digital Twin Research Group, Division of Ear, Nose and Throat Diseases, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Eun Jung Lee
- Department of Otorhinolaryngology, Yonsei University Wonju College of Medicine, Wonju, Ganwong 26460, Korea
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Pratheek Bellur Marthanda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Lang Hu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Mattias Magnusson
- The National Board of Health and Welfare, Socialstyrelsen, 11259 Stockholm, Sweden
| | - Oleg Sysoev
- Department of Computer and Information Science, Linköping University, 58183 Linköping, Sweden
| | - Huan Zhang
- Department of Pediatrics, Biomedical and Clinical Sciences, Linköping University, 58183 Linköping, Sweden
| | - Yelin Zhao
- Department of Pediatrics, Biomedical and Clinical Sciences, Linköping University, 58183 Linköping, Sweden; Medical Digital Twin Research Group, Division of Ear, Nose and Throat Diseases, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Christopher Sjöwall
- Biomedical and Clinical Sciences, Division of Inflammation and Infection/Rheumatology, Linköping University, 58183 Linköping, Sweden
| | - Danuta Gawel
- Mavatar, Inc, Vasagatan, 11120 Stockholm, Sweden
| | - Hui Wang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Mikael Benson
- Department of Pediatrics, Biomedical and Clinical Sciences, Linköping University, 58183 Linköping, Sweden; Medical Digital Twin Research Group, Division of Ear, Nose and Throat Diseases, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 17165 Stockholm, Sweden.
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16
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Haglund S, Söderman J, Almer S. Differences in Whole-Blood Transcriptional Profiles in Inflammatory Bowel Disease Patients Responding to Vedolizumab Compared with Non-Responders. Int J Mol Sci 2023; 24:ijms24065820. [PMID: 36982892 PMCID: PMC10052064 DOI: 10.3390/ijms24065820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Vedolizumab is efficacious in the treatment of Crohn's disease (CD) and ulcerative colitis (UC). However, a significant proportion of patients present with a non-response. To investigate whether differences in the clinical response to vedolizumab is reflected in changes in gene expression levels in whole blood, samples were collected at baseline before treatment, and at follow-up after 10-12 weeks. Whole genome transcriptional profiles were established by RNA sequencing. Before treatment, no differentially expressed genes were noted between responders (n = 9, UC 4, CD 5) and non-responders (n = 11, UC 3, CD 8). At follow-up, compared with baseline, responders displayed 201 differentially expressed genes, and 51 upregulated (e.g., translation initiation, mitochondrial translation, and peroxisomal membrane protein import) and 221 downregulated (e.g., Toll-like receptor activating cascades, and phagocytosis related) pathways. Twenty-two of the upregulated pathways in responders were instead downregulated in non-responders. The results correspond with a dampening of inflammatory activity in responders. Although considered a gut-specific drug, our study shows a considerable gene regulation in the blood of patients responding to vedolizumab. It also suggests that whole blood is not optimal for identifying predictive pre-treatment biomarkers based on individual genes. However, treatment outcomes may depend on several interacting genes, and our results indicate a possible potential of pathway analysis in predicting response to treatment, which merits further investigation.
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Affiliation(s)
- Sofie Haglund
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Laboratory Medicine, Region Jönköping County, 551 85 Jönköping, Sweden
| | - Jan Söderman
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Laboratory Medicine, Region Jönköping County, 551 85 Jönköping, Sweden
| | - Sven Almer
- IBD-Unit, Division of Gastroenterology, Karolinska University Hospital, 171 76 Stockholm, Sweden
- Department of Medicine, Karolinska Institutet-Solna, 171 76 Stockholm, Sweden
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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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18
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Bioinformatics Analysis of Immune Cell Infiltration and Diagnostic Biomarkers between Ankylosing Spondylitis and Inflammatory Bowel Disease. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2023; 2023:9065561. [PMID: 36643579 PMCID: PMC9836798 DOI: 10.1155/2023/9065561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/09/2022] [Accepted: 11/26/2022] [Indexed: 01/07/2023]
Abstract
Background Ankylosing spondylitis (AS) and inflammatory bowel disease (IBD) are both autoimmune diseases, and they often occur together in clinical practice, but the pathogenesis is unclear. This study is aimed at identifying the hub genes and explore the related immune molecular mechanisms between AS and IBD by bioinformatics analysis. Methods From the public Gene Expression Omnibus (GEO) database, the AS and IBD datasets (GSE73754, GSE59071, GSE25101, and GSE36807) were obtained. The immune cell infiltration in the peripheral blood tissues of GSE73754 and GSE59071 was assessed using the CIBERSORT algorithm. Then, we used the Weighted Gene Coexpression Network Analysis (WGCNA) to identify the Differentially Expressed Genes (DEGs) related to AS and IBD. Then, the immune genes from the ImmPort database intersected with the DEGs to obtain hub genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyzed the functional correlation of hub genes. Then, hub genes were verified in GSE25101 and GSE36807. The clusterProfiler software and Gene Set Enrichment Analysis (GSEA) were used to conduct functional enrichment and pathway enrichment studies. Finally, the diagnostic efficacy was assessed using Receiver Operating Characteristic (ROC) curve analysis. Results The analysis of immune characteristics showed that both AS and IBD were related to immunity, and neutrophils were positively correlated in both diseases. Nine coexpressed genes, including FCGRT, S100A11, IFNGR1, NFKBIZ, JAK2, LYN, PLAUR, ADM, and IL1RN, were linked to immune cells. The GO and KEGG analyses results showed that enrichment analysis was mainly related to cell transport and migration. Finally, the ROC curve was verified with the validation set, and it was found that PLAUR has clinical diagnostic significance and the most excellent specificity and sensitivity, respectively. Conclusions PLAUR (uPAR) is a promising biomarker and will be an underlying genetic biomarker for diagnosing AS comorbid IBD. Inflammation and immunological modulation mediated by neutrophil infiltration were important in the development of AS and IBD and may be diagnostic and therapeutic targets.
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Ye C, Zhu S, Gao Y, Huang Y. Landscape of sialylation patterns identify biomarkers for diagnosis and prediction of response to anti-TNF therapy in crohn's disease. Front Genet 2022; 13:1065297. [PMID: 36452157 PMCID: PMC9702336 DOI: 10.3389/fgene.2022.1065297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 10/21/2022] [Indexed: 07/22/2023] Open
Abstract
Crohn's disease (CD), a subtype of inflammatory bowel disease (IBD), causes chronic gastrointestinal tract inflammation. Thirty percent of patients do not respond to anti-tumor necrosis factor (TNF) therapy. Sialylation is involved in the pathogenesis of IBD. We aimed to identify potential biomarkers for diagnosing CD and predicting anti-TNF medication outcomes in CD. Three potential biomarkers (SERPINB2, TFPI2, and SLC9B2) were screened using bioinformatics analysis and machine learning based on sialylation-related genes. Moreover, the combined model of SERPINB2, TFPI2, and SLC9B2 showed excellent diagnostic value in both the training and validation cohorts. Importantly, a Sial-score was constructed based on the expression of SERPINB2, TFPI2, and SLC9B2. The Sial-low group showed a lower level of immune infiltration than the Sial-high group. Anti-TNF therapy was effective for 94.4% of patients in the Sial-low group but only 15.8% in the Sial-high group. The Sial-score had an outstanding ability to predict and distinguish between responders and non-responders. Our comprehensive analysis indicates that SERPINB2, TFPI2, and SLC9B2 play essential roles in pathogenesis and anti-TNF therapy resistance in CD. Furthermore, it may provide novel concepts for customizing treatment for individual patients with CD.
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Affiliation(s)
- Chenglin Ye
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Sizhe Zhu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Gao
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yabing Huang
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
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20
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Zhou Z, Plug LG, Patente TA, de Jonge-Muller ESM, Elmagd AA, van der Meulen-de Jong AE, Everts B, Barnhoorn MC, Hawinkels LJAC. Increased stromal PFKFB3-mediated glycolysis in inflammatory bowel disease contributes to intestinal inflammation. Front Immunol 2022; 13:966067. [PMID: 36405760 PMCID: PMC9670190 DOI: 10.3389/fimmu.2022.966067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/17/2022] [Indexed: 08/10/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing inflammation of the intestinal tract with currently not well-understood pathogenesis. In addition to the involvement of immune cells, increasing studies show an important role for fibroblasts in the pathogenesis of IBD. Previous work showed that glycolysis is the preferred energy source for fibroblasts in fibrotic diseases. 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase 3 (PFKFB3) is a key kinase supporting glycolysis. Increased expression of PFKFB3 in several cancers and inflammatory diseases has been previously reported, but the metabolic status of fibroblasts and the role of PFKFB3 in patients with IBD are currently unknown. Therefore, in this study, we evaluated the role of glycolysis and PFKFB3 expression in IBD. Single-sample gene set enrichment analysis (ssGSEA) revealed that glycolysis was significantly higher in IBD intestinal samples, compared to healthy controls, which was confirmed in the validation cohorts of IBD patients. Single-cell sequencing data indicated that PFKFB3 expression was higher in IBD-derived stromal cells. In vitro, PFKFB3 expression in IBD-derived fibroblasts was increased after the stimulation with pro-inflammatory cytokines. Using seahorse real-time cell metabolic analysis, inflamed fibroblasts were shown to have a higher extracellular acidification rate and a lower oxygen consumption rate, which could be reversed by inhibition of JAK/STAT pathway. Furthermore, increased expression of pro-inflammatory cytokines and chemokines in fibroblasts could be reverted by PFK15, a specific inhibitor of PFKFB3. In vivo experiments showed that PFK15 reduced the severity of dextran sulfate sodium (DSS)- and Tcell transfer induced colitis, which was accompanied by a reduction in immune cell infiltration in the intestines. These findings suggest that increased stromal PFKFB3 expression contributes to inflammation and the pathological function of fibroblasts in IBD. Inhibition of PFKFB3 suppressed their inflammatory characteristics.
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Affiliation(s)
- Zhou Zhou
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Leonie G. Plug
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Thiago A. Patente
- Department of Parasitology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Amir Abou Elmagd
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Bart Everts
- Department of Parasitology, Leiden University Medical Center, Leiden, Netherlands
| | - Marieke C. Barnhoorn
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Lukas J. A. C. Hawinkels
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
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21
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Liu T, Sun Y, Guo Z, Bai W. Knockdown of Cadherin 26 Prevents the Inflammatory Responses of Allergic Rhinitis. Laryngoscope 2022. [PMID: 36069256 DOI: 10.1002/lary.30380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 08/09/2022] [Accepted: 08/17/2022] [Indexed: 11/09/2022]
Abstract
OBJECTIVES Allergic rhinitis (AR) is an inflammatory autoimmune disease with disorder of the nasal mucosa. Cadherin 26 (CDH26), an alpha integrin-binding epithelial receptor, is regulated during allergic inflammation. This study aimed to investigate whether CDH26 contributes to the severity of AR. STUDY DESIGN In vivo and in vitro. METHODS We investigated the effects of CDH26 knockdown by lentivirus (LV)-mediated shRNA on ovalbumin (OVA)-induced AR mice and IL-13-stimulated human nasal epithelial cells (NECs). RESULTS CDH26 mRNA and protein expression was significantly increased in the nasal mucosa of AR patients and mice. Intranasal instillation of LV-shCDH26 alleviated allergic symptoms and decreased the histological changes of nasal mucosa in AR mice. Furthermore, the serum levels of OVA-specific IgE, IgG, pro-inflammatory factors IL-25, IL-33, and TSLP were decreased in AR mice with CDH26 knockdown. With regard to AR-induced Th2 inflammation, LV-shCDH26 intervention effectively decreased the distribution of CD4+ /GATA3+ Th2 cells, and the mRNA expression of IL-4, IL-5, and IL-13 in the nasal mucosa. CDH26 knockdown down-regulated the expression of β-catenin but not for E-cadherin and ZO-1 in nasal mucosa induced by AR. In vitro, CDH26 knockdown inhibited the protein expression of TSLP, GM-CSF and eotaxin in NECs, and CDH26 overexpression remarkably promoted the production of these inflammatory factors in IL-13-induced NECs. CONCLUSIONS CDH26 knockdown attenuates the AR-induced inflammatory response both in vivo and in vitro. LEVEL OF EVIDENCE NA Laryngoscope, 2022.
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Affiliation(s)
- Tiancong Liu
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yang Sun
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhaohui Guo
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Weiliang Bai
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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22
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Sun Y, Cai D, Hu W, Fang T. Identifying hub genes and miRNAs in Crohn’s disease by bioinformatics analysis. Front Genet 2022; 13:950136. [PMID: 36118873 PMCID: PMC9471261 DOI: 10.3389/fgene.2022.950136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
Introduction: Crohn’s disease (CD) is a disease that manifests mainly as chronic inflammation of the gastrointestinal tract, which is still not well understood in terms of its pathogenesis. The aim of this study was to use bioinformatics analysis to identify differentially expressed genes (DEGs) and miRNAs with diagnostic and therapeutic potential in CD. Materials and methods: Three CD datasets (GSE179285, GSE102133, GSE75214) were downloaded from the Gene Expression Omnibus (GEO) database. DEGs between normal and CD tissues were identified using the GEO2R online tool. The Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the DEGs were conducted using the clusterProfiler function in the R package. Protein-protein interaction network (PPI) analysis and visualization were performed with STRING and Cytoscape. Ten hub genes were identified using cytoHubba’s MCC algorithm and validated with datasets GSE6731 and GSE52746. Finally, the miRNA gene regulatory network was constructed by Cytoscape and NetworkAnalyst to predict potential microRNAs (miRNAs) associated with DEGs. Results: A total of 97 DEGs were identified, consisting of 88 downregulated genes and 9 upregulated genes. The enriched functions and pathways of the DEGs include immune system process, response to stress, response to cytokine and extracellular region. KEGG pathway analysis indicates that the genes were significantly enriched in Cytokine-cytokine receptor interaction, IL-17 signaling pathway, Rheumatoid arthritis and TNF signaling pathway. In combination with the results of the protein-protein interaction (PPI) network and CytoHubba, 10 hub genes including IL1B, CXCL8, CXCL10, CXCL1, CXCL2, CXCL5, ICAM1, IL1RN, TIMP1 and MMP3 were selected. Based on the DEG-miRNAs network construction, 5 miRNAs including hsa-mir-21-5p, hsa-mir-93-5p, hsa-mir-98-5p, hsa-mir-1-3p and hsa-mir-335-5p were identified as potential critical miRNAs. Conclusion: In conclusion, a total of 97 DEGs, 10 hub genes and 5 miRNAs that may be involved in the progression or occurrence of CD were identified in this study, which could be regarded as biomarkers of CD.
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Affiliation(s)
- Yuxin Sun
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Daxing Cai
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Weitao Hu
- Department of Rheumatology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Taiyong Fang
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
- *Correspondence: Taiyong Fang,
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23
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Differential Effects of Anti-TNFα and Anti-α4β7 Drugs on Circulating Dendritic Cells Migratory Capacity in Inflammatory Bowel Disease. Biomedicines 2022; 10:biomedicines10081885. [PMID: 36009431 PMCID: PMC9405461 DOI: 10.3390/biomedicines10081885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/16/2022] Open
Abstract
Inflammatory bowel disease (IBD) is an idiopathic and chronic disorder that includes ulcerative colitis (UC) and Crohn’s disease (CD). Both diseases show an uncontrolled intestinal immune response that generates tissue inflammation. Dendritic cells (DCs) are antigen-presenting cells that play a key role in tolerance maintenance in the gastrointestinal mucosa. Although it has been reported that DC recruitment by the intestinal mucosa is more prominent in IBD patients, the specific mechanisms governing this migration are currently unknown. In this study, the expression of several homing markers and the migratory profile of circulating DC subsets towards intestinal chemo-attractants were evaluated and the effect of biological drugs with different mechanisms of action, such as anti-TNFα or anti-integrin α4β7 (vedolizumab), on this mechanism in healthy controls (HCs) and IBD patients was also assessed. Our results revealed that type 2 conventional DCs (cDC2) express differential homing marker profiles in UC and CD patients compared to HCs. Indeed, integrin β7 was differentially modulated by vedolizumab in CD and UC. Additionally, although CCL2 displayed a chemo-attractant effect over cDC2, while biological therapies did not modulate the expression of the homing markers, we paradoxically found that anti-TNF-treated cDC2 increased their migratory capacity towards CCL2 in HCs and IBD. Our results therefore suggest a key role for cDC2 migration towards the intestinal mucosa in IBD, something that could be explored in order to develop novel diagnostic biomarkers or to unravel new immunomodulatory targets in IBD.
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Fajardo P, Taskova M, Martín-Serrano MA, Hansen J, Slott S, Jakobsen AK, Wibom ML, Salegi B, Muñoz A, Barbachano A, Sharma A, Gubatan JM, Habtezion A, Sanz-Ezquerro JJ, Astakhova K, Cuenda A. p38γ and p38δ as biomarkers in the interplay of colon cancer and inflammatory bowel diseases. CANCER COMMUNICATIONS (LONDON, ENGLAND) 2022; 42:897-901. [PMID: 35796643 PMCID: PMC9456697 DOI: 10.1002/cac2.12331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/07/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Pilar Fajardo
- Department of Immunology and Oncology, National Centre of Biotechnology/Consejo Superior de Investigaciones Científicas, Darwin 3, Madrid, 28049, Spain.,PhD Programme in Molecular Bioscience, Doctoral School, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Maria Taskova
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.,Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Miguel A Martín-Serrano
- Department of Immunology and Oncology, National Centre of Biotechnology/Consejo Superior de Investigaciones Científicas, Darwin 3, Madrid, 28049, Spain
| | - Jonas Hansen
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.,Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Sofie Slott
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Anna K Jakobsen
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Marie-Louise Wibom
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Beñat Salegi
- Department of Immunology and Oncology, National Centre of Biotechnology/Consejo Superior de Investigaciones Científicas, Darwin 3, Madrid, 28049, Spain
| | - Alberto Muñoz
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, 28029, Spain.,Centro de Investigación Biomédica en Red-Cáncer, Instituto de Salud Carlos III, Madrid, 28029, Spain.,Instituto de Investigación Sanitaria del Hospital Universitario La Paz, Madrid, 28029, Spain
| | - Antonio Barbachano
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, 28029, Spain.,Centro de Investigación Biomédica en Red-Cáncer, Instituto de Salud Carlos III, Madrid, 28029, Spain.,Instituto de Investigación Sanitaria del Hospital Universitario La Paz, Madrid, 28029, Spain
| | - Arpita Sharma
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - John Mark Gubatan
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Aida Habtezion
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Juan J Sanz-Ezquerro
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología/ Consejo Superior de Investigaciones Científicas, Darwin 3, Madrid, 28049, Spain
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Ana Cuenda
- Department of Immunology and Oncology, National Centre of Biotechnology/Consejo Superior de Investigaciones Científicas, Darwin 3, Madrid, 28049, Spain
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25
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Hu W, Fang T, Chen X. Identification of Differentially Expressed Genes and miRNAs for Ulcerative Colitis Using Bioinformatics Analysis. Front Genet 2022; 13:914384. [PMID: 35719390 PMCID: PMC9201719 DOI: 10.3389/fgene.2022.914384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction: Ulcerative colitis (UC) is a chronic inflammatory disease of the intestine whose cause and underlying mechanisms are not fully understood. The aim of this study was to use bioinformatics analysis to identify differentially expressed genes (DEGs) with diagnostic and therapeutic potential in UC.Materials and methods: Three UC datasets (GSE179285, GSE75214, GSE48958) were downloaded from the Gene Expression Omnibus (GEO) database. DEGs between normal and UC tissues were identified using the GEO2R online tool. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the DEGs were performed using Metascape. Protein-protein interaction network (PPI) analysis and visualization using STRING and Cytoscape. Finally, the miRNA gene regulatory network was constructed by Cytoscape to predict potential microRNAs (miRNAs) associated with DEGs.Results: A total of 446 DEGs were identified, consisting of 309 upregulated genes and 137 downregulated genes. The enriched functions and pathways of the DEGs include extracellular matrix, regulation of cell adhesion, inflammatory response, response to cytokine, monocarboxylic acid metabolic process, response to toxic substance. The analysis of KEGG pathway indicates that the DEGs were significantly enriched in Complement and coagulation cascades, Amoebiasis, TNF signaling pathway, bile secretion, and Mineral absorption. Combining the results of the PPI network and CytoHubba, 9 hub genes including CXCL8, ICAM1, CXCR4, CD44, IL1B, MMP9, SPP1, TIMP1, and HIF1A were selected. Based on the DEG-miRNAs network construction, 7 miRNAs including miR-335-5p, mir-204-5p, miR-93-5p, miR106a-5p, miR-21-5p, miR-146a-5p, and miR-155-5p were identified as potential critical miRNAs.Conclusion: In summary, we identified DEGs that may be involved in the progression or occurrence of UC. A total of 446 DEGs,9 hub genes and 7 miRNAs were identified, which may be considered as biomarkers of UC. Further studies, however, are needed to elucidate the biological functions of these genes in UC.
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Affiliation(s)
- Weitao Hu
- Department of Rheumatology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Taiyong Fang
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Xiaoqing Chen
- Department of Rheumatology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- *Correspondence: Xiaoqing Chen,
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26
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Shi H, Sun S, Zhou X, He Y, Peng Q. GBP4 is an immune-related biomarker for patients with ileocolonic Crohn’s disease by comprehensive analysis. EUR J INFLAMM 2022. [DOI: 10.1177/1721727x221116743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Extensive evidence has shown that immune cell infiltration is associated with the pathogenesis of Crohn’s disease (CD). Methods: Differentially expressed genes (DEGs) from the GSE179285 dataset in the intestinal mucosa of CD patients and healthy individuals were then identified. The infiltration pattern of 22 immune cell types was assessed using the CIBERSORT algorithm. The DEGs and 22 immune cell types were combined to find the key gene network using weighted gene co-expression network analysis (WGCNA). A linear regression model for the relationship between the expression of the hub genes in CD patients and infiltration of immune cells was also developed. The utility and accuracy of the hub genes for CD diagnosis were assessed using receiver operating characteristic (ROC) analysis. The accuracy of the model was validated using the GSE20881 dataset. Results: There were 1135 DEGs between the intestinal mucosal tissue of CD patients and healthy individuals. Of these DEGs, 711 genes were upregulated, whereas 424 of them were downregulated. There was also a significant difference in the infiltration of immune cells to the intestinal mucosal between the CD patients and healthy individuals. WGCNA revealed that the turquoise module genes were strongly correlated with the infiltration of M1 macrophages (cor =0.68, p = 10−16). Finally, the expression of GBP4, the identified hub gene, strongly correlated with the infiltration of M1 macrophages (adjusted r-squared =0.661, p < 2×10−16), and is a relatively good marker for CD diagnostic prediction (AUC =0.736). The relationship between GBP4 expression and infiltration of M1 macrophages (adjusted r-squared =0.435, p < 2×10−16) and diagnostic value of the gene (AUC =0.702) were verified using the GSE20881 validation dataset. Conclusion: The expression of GBP4 is associated with the infiltration of M1 macrophages to the intestinal mucosa of CD patients.
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Affiliation(s)
- Heng Shi
- Department of Gastroenterology, The Central Hospital of Shaoyang, University of South China, Shaoyang, Hunan Province, China
- Department of Traditional Chinese Medicine, the First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong Province, China
| | - Shengyun Sun
- Department of Traditional Chinese Medicine, the First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong Province, China
| | - Xianling Zhou
- Department of Traditional Chinese Medicine, the First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong Province, China
| | - Yushan He
- Department of Gastroenterology, The Central Hospital of Shaoyang, University of South China, Shaoyang, Hunan Province, China
| | - Qin Peng
- Department of Gastroenterology, The Central Hospital of Shaoyang, University of South China, Shaoyang, Hunan Province, China
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Singh A, Fenton CG, Anderssen E, Paulssen RH. Identifying predictive signalling networks for Vedolizumab response in ulcerative colitis. Int J Colorectal Dis 2022; 37:1321-1333. [PMID: 35543875 PMCID: PMC9167201 DOI: 10.1007/s00384-022-04176-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND In ulcerative colitis (UC), the molecular mechanisms that drive disease development and patient response to therapy are not well understood. A significant proportion of patients with UC fail to respond adequately to biologic therapy. Therefore, there is an unmet need for biomarkers that can predict patients' responsiveness to the available UC therapies as well as ascertain the most effective individualised therapy. Our study focused on identifying predictive signalling pathways that predict anti-integrin therapy response in patients with UC. METHODS We retrieved and pre-processed two publicly accessible gene expression datasets (GSE73661 and GSE72819) of UC patients treated with anti-integrin therapies: (1) 12 non-IBD controls and 41 UC patients treated with Vedolizumab therapy, and (2) 70 samples with 58 non-responder and 12 responder UC patient samples treated with Etrolizumab therapy without non-IBD controls. We used a diffusion-based signalling model which is mainly focused on the T-cell receptor signalling network. The diffusion model uses network connectivity between receptors and transcription factors. RESULTS The network diffusion scores were able to separate VDZ responder and non-responder patients before treatment better than the original gene expression. On both anti-integrin treatment datasets, the diffusion model demonstrated high predictive performance for discriminating responders from non-responders in comparison with 'nnet'. We have found 48 receptor-TF pairs identified as the best predictors for VDZ therapy response with AUC ≥ 0.76. Among these receptor-TF predictors pairs, FFAR2-NRF1, FFAR2-RELB, FFAR2-EGR1, and FFAR2-NFKB1 are the top best predictors. For Etrolizumab, we have identified 40 best receptor-TF pairs and CD40-NFKB2 as the best predictor receptor-TF pair (AUC = 0.72). We also identified subnetworks that highlight the network interactions, connecting receptors and transcription factors involved in cytokine and fatty acid signalling. The findings suggest that anti-integrin therapy responses in cytokine and fatty acid signalling can stratify UC patient subgroups. CONCLUSIONS We identified signalling pathways that may predict the efficacy of anti-integrin therapy in UC patients and personalised therapy alternatives. Our results may lead to the advancement of a promising clinical decision-making tool for the stratification of UC patients.
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Affiliation(s)
- Amrinder Singh
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Christopher G. Fenton
- Genomics Support Centre Tromso, UiT- The Arctic University of Norway, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromso, Norway
| | - Endre Anderssen
- Genomics Support Centre Tromso, UiT- The Arctic University of Norway, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromso, Norway
| | - Ruth H. Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway ,Genomics Support Centre Tromso, UiT- The Arctic University of Norway, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromso, Norway
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