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Zakerska-Banaszak O, Zuraszek-Szymanska J, Eder P, Ladziak K, Slomski R, Skrzypczak-Zielinska M. The Role of Host Genetics and Intestinal Microbiota and Metabolome as a New Insight into IBD Pathogenesis. Int J Mol Sci 2024; 25:9589. [PMID: 39273536 DOI: 10.3390/ijms25179589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/30/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
Inflammatory bowel disease (IBD) is an incurable, chronic disorder of the gastrointestinal tract whose incidence increases every year. Scientific research constantly delivers new information about the disease and its multivariate, complex etiology. Nevertheless, full discovery and understanding of the complete mechanism of IBD pathogenesis still pose a significant challenge to today's science. Recent studies have unanimously confirmed the association of gut microbial dysbiosis with IBD and its contribution to the regulation of the inflammatory process. It transpires that the altered composition of pathogenic and commensal bacteria is not only characteristic of disturbed intestinal homeostasis in IBD, but also of viruses, parasites, and fungi, which are active in the intestine. The crucial function of the microbial metabolome in the human body is altered, which causes a wide range of effects on the host, thus providing a basis for the disease. On the other hand, human genomic and functional research has revealed more loci that play an essential role in gut homeostasis regulation, the immune response, and intestinal epithelial function. This review aims to organize and summarize the currently available knowledge concerning the role and interaction of crucial factors associated with IBD pathogenesis, notably, host genetic composition, intestinal microbiota and metabolome, and immune regulation.
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Affiliation(s)
| | | | - Piotr Eder
- Department of Gastroenterology, Dietetics and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Karolina Ladziak
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Ryszard Slomski
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
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Sæterstad S, Østvik AE, Hansen MD, Bruland T, van Beelen Granlund A. The effect of rs2910686 on ERAP2 expression in IBD and epithelial inflammatory response. J Transl Med 2024; 22:750. [PMID: 39123229 PMCID: PMC11316291 DOI: 10.1186/s12967-024-05532-w] [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: 05/03/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND ERAP2 is an aminopeptidase involved in antigen processing and presentation, and harbor genetic variants linked to several inflammatory diseases such as Inflammatory Bowel Disease (IBD). The lack of an ERAP2 gene homologue in mice has hampered functional studies, and most human studies have focused on cells of hematopoietic origin. Using an IBD biobank as vantage point, this study explores how genetic variation in ERAP2 affects gene expression in human-derived epithelial organoids upon proinflammatory stimulation. METHODS An IBD patient cohort was genotyped with regards to two single nucleotide polymorphisms (SNP) (rs2910686/rs2248374) associated with ERAP2 expression levels, and we examined the correlation between colon gene expression and genotype, specifically aiming to establish a relationship with ERAP2 expression proficiency. Human-derived colon organoids (colonoids) with known ERAP2 genotype were established and used to explore differences in whole genome gene expression between ERAP2-deficient (n = 4) and -proficient (n = 4) donors upon pro-inflammatory encounter. RESULTS When taking rs2910686 genotype into account, ERAP2 gene expression is upregulated in the inflamed colon of IBD patients. Colonoids upregulate ERAP2 upon IFNɣ stimulation, and ERAP2 expression proficiency is dependent on rs2910686 genotype. Colonoid genotyping confirms that mechanisms independent of the frequently studied SNP rs2248374 can cause ERAP2-deficiency. A total of 586 genes involved in various molecular mechanisms are differentially expressed between ERAP2 proficient- and deficient colonoids upon proinflammatory stimulation, including genes encoding proteins with the following molecular function: catalytic activity (AOC1, CPE, ANPEP and MEP1A), regulator activity (TNFSF9, MDK, GDF15, ILR6A, LGALS3 and FLNA), transmembrane transporter activity (SLC40A1 and SLC5A1), and extracellular matrix structural constituents (FGL2, HMCN2, and MUC17). CONCLUSIONS ERAP2 is upregulated in the inflamed IBD colon mucosa, and expression proficiency is highly correlated with genotype of rs2910686. While the SNP rs2248374 is commonly used to determine ERAP2 expressional proficiency, our data confirms that mechanisms independent of this SNP can lead to ERAP2 deficiency. Our data demonstrates that epithelial ERAP2 presence affects the inflammatory response in colonoids, suggesting a pleiotropic role of ERAP2 beyond MHC class I antigen processing.
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Affiliation(s)
- Siri Sæterstad
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Ann Elisabeth Østvik
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav's University Hospital, Trondheim, Norway
| | - Marianne Doré Hansen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olav's University Hospital, Trondheim, Norway
| | - Torunn Bruland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav's University Hospital, Trondheim, Norway
| | - Atle van Beelen Granlund
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
- Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav's University Hospital, Trondheim, Norway.
- Department of Pathology, St. Olav's University Hospital, Trondheim, Norway.
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
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Huang H, Yan S, Guo T, Hua Q, Wang Y, Xu S, Ji L. Bile acid metabolism modulates intestinal immunity involved in ulcerative colitis progression. Heliyon 2024; 10:e34352. [PMID: 39114032 PMCID: PMC11305184 DOI: 10.1016/j.heliyon.2024.e34352] [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: 04/02/2024] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
The bile acids (BA) in the intestine promote inflammation by interacting with immune cells, playing a crucial role in the progression of UC, but the specific mechanism between the two remains elusive. This study aims to explore the relationship between BAMand UC inflammation and determine its potential mechanisms.Firstly, we employed a hybrid approach using Lasso regression and support vector machine (SVM) feature selection in bioinformatics to identify genes linked to UC and BAM. The relationship between these genes and immune infiltration was explored, along with their correlation with immune factors in the Tumor-Immune System Interaction Database (TISIDB) database. Gene Set Enrichment Analysis (GSEA) pathway enrichment analysis was then used to predict signaling pathways associated with key genes in UC. Single-cell data from the GSE13464 dataset was also analyzed. Finally, Five differentially expressed genes (DEGs) related to BAM (APOA1, AMACR, PEX19, CH25H, and AQP9) were significantly upregulated/downregulated in UC immune cells. The expression of important genes in UC tissue was confirmed in the experimental validation section and AQP9, which showed significant differential expression, was chosen for further validation. The results showed that the AQP9 gene may regulate the IFN - γ/JAK signaling axis, thereby promoting CD8+T cell activation. This research has greatly advanced our comprehension of the pathogenesis and underlying mechanism of BAM in immune cells linked to UC.
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Affiliation(s)
- Hua Huang
- Department of Anorectal Surgery, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, Changshu, 215500, Jiangsu Province, China
| | - Shuai Yan
- Department of Anorectal Surgery, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, 215000, Jiangsu Province, China
| | - Tianwei Guo
- Department of Pathology, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, Changshu, 215500, Jiangsu Province, China
| | - Qiuwen Hua
- Department of Digestive System, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, Changshu, 215500, Jiangsu Province, China
| | - Yongtong Wang
- Department of Anorectal Surgery, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, Changshu, 215500, Jiangsu Province, China
| | - Shanshan Xu
- Department of Anorectal Surgery, Nantong Hospital of Traditional Chinese Medicine, Nantong Hospital Affiliated to Nanjing University of Chinese Medicine, Nantong, 226000, Jiangsu Province, China
| | - Lijiang Ji
- Department of Anorectal Surgery, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, Changshu, 215500, Jiangsu Province, China
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Sun S, Mao Y, Le S, Zheng M, Li M, Chen Y, Chen J, Fan Y, Lv B. Biological characteristics of molecular subtypes of ulcerative colitis characterized by ferroptosis and neutrophil infiltration. Sci Rep 2024; 14:9510. [PMID: 38664443 PMCID: PMC11045816 DOI: 10.1038/s41598-024-60137-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Clinical ulcerative colitis (UC) is a heterogeneous condition. Moreover, medical interventions are nonspecific, and thus, treatment responses are inconsistent. The aim of this study was to explore the molecular subtypes and biological characteristics of UC based on ferroptosis and neutrophil gene sets. Multiple intestinal mucosa gene expression profiles of UC patients in the Gene Expression Omnibus (GEO) database were downloaded. Unsupervised clustering methods were used to identify potential molecular subtypes based on ferroptosis and neutrophil gene sets. Multiple immune infiltration algorithms were used to evaluate the biological characteristics of the molecular subtypes. Machine learning identifies hub genes for molecular subtypes and analyses their diagnostic efficacy for UC and predictive performance for drug therapy. The relevant conclusions were verified by clinical samples and animal experiments. Four molecular subtypes were identified according to the ferroptosis and neutrophil gene sets: neutrophil, ferroptosis, mixed and quiescent. The subtypes have different biological characteristics and immune infiltration levels. Multiple machine learning methods jointly identified four hub genes (FTH1, AQP9, STEAP3 and STEAP4). Receiver operating characteristic (ROC) curve analysis revealed that the four hub genes could be used as diagnostic markers for UC. The clinical response profile data of infliximab treatment patients showed that AQP9 and STEPA4 were reliable predictors of infliximab treatment response. In human samples the AQP9 and STEAP4 protein were shown to be increased in UC intestinal samples. In animal experiments, the ferroptosis and neutrophil phenotype were confirmed. Dual analysis of ferroptosis and neutrophil gene expression revealed four subgroups of UC patients. The molecular subtype-associated hub genes can be used as diagnostic markers for UC and predict infliximab treatment response.
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Affiliation(s)
- Shaopeng Sun
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), No. 54, Youdian Road, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Yuqing Mao
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), No. 54, Youdian Road, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Sihua Le
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Mingxu Zheng
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), No. 54, Youdian Road, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Menglin Li
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), No. 54, Youdian Road, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Yifei Chen
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), No. 54, Youdian Road, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Jiajia Chen
- Department of Nursing, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
| | - Yihong Fan
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), No. 54, Youdian Road, Shangcheng District, Hangzhou, 310003, Zhejiang, China
| | - Bin Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), No. 54, Youdian Road, Shangcheng District, Hangzhou, 310003, Zhejiang, China.
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Tubau-Juni N, Hontecillas R, Leber AJ, Alva SS, Bassaganya-Riera J. Treating Autoimmune Diseases With LANCL2 Therapeutics: A Novel Immunoregulatory Mechanism for Patients With Ulcerative Colitis and Crohn's Disease. Inflamm Bowel Dis 2024; 30:671-680. [PMID: 37934790 DOI: 10.1093/ibd/izad258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Indexed: 11/09/2023]
Abstract
Lanthionine synthetase C-like 2 (LANCL2) therapeutics have gained increasing recognition as a novel treatment modality for a wide range of autoimmune diseases. Genetic ablation of LANCL2 in mice results in severe inflammatory phenotypes in inflammatory bowel disease (IBD) and lupus. Pharmacological activation of LANCL2 provides therapeutic efficacy in mouse models of intestinal inflammation, systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and psoriasis. Mechanistically, LANCL2 activation enhances regulatory CD4 + T cell (Treg) responses and downregulates effector responses in the gut. The stability and suppressive capacities of Treg cells are enhanced by LANCL2 activation through engagement of immunoregulatory mechanisms that favor mitochondrial metabolism and amplify IL-2/CD25 signaling. Omilancor, the most advanced LANCL2 immunoregulatory therapeutic in late-stage clinical development, is a phase 3 ready, first-in-class, gut-restricted, oral, once-daily, small-molecule therapeutic in clinical development for the treatment of UC and CD. In this review, we discuss this novel mechanism of mucosal immunoregulation and how LANCL2-targeting therapeutics could help address the unmet clinical needs of patients with autoimmune diseases, starting with IBD.
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Stemmer E, Zahavi T, Kellerman M, Sinberger LA, Shrem G, Salmon‐Divon M. Exploring potential biomarkers and therapeutic targets in inflammatory bowel disease: insights from a mega-analysis approach. Front Immunol 2024; 15:1353402. [PMID: 38510241 PMCID: PMC10951083 DOI: 10.3389/fimmu.2024.1353402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Background Understanding the molecular pathogenesis of inflammatory bowel disease (IBD) has led to the discovery of new therapeutic targets that are more specific and effective. Our aim was to explore the molecular pathways and genes involved in IBD pathogenesis and to identify new therapeutic targets and novel biomarkers that can aid in the diagnosis of the disease. Methods To obtain the largest possible number of samples and analyze them comprehensively, we used a mega-analysis approach. This involved reprocessing raw data from multiple studies and analyzing them using bioinformatic and machine learning techniques. Results We analyzed a total of 697 intestinal biopsies of Ulcerative Colitis (n = 386), Crohn's disease (n = 183) and non-IBD controls (n = 128). A machine learning analysis detected 34 genes whose collective expression effectively distinguishes inflamed biopsies of IBD patients from non-IBD control samples. Most of these genes were upregulated in IBD. Notably, among these genes, three novel lncRNAs have emerged as potential contributors to IBD development: ENSG00000285744, ENSG00000287626, and MIR4435-2HG. Furthermore, by examining the expression of 29 genes, among the 34, in blood samples from IBD patients, we detected a significant upregulation of 12 genes (p-value < 0.01), underscoring their potential utility as non-invasive diagnostic biomarkers. Finally, by utilizing the CMap library, we discovered potential compounds that should be explored in future studies for their therapeutic efficacy in IBD treatment. Conclusion Our findings contribute to the understanding of IBD pathogenesis, suggest novel biomarkers for IBD diagnosis and offer new prospects for therapeutic intervention.
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Affiliation(s)
- Edia Stemmer
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Tamar Zahavi
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Maoz Kellerman
- Department of Molecular Biology, Ariel University, Ariel, Israel
- Kaleidoo, Bar Lev High Tech Park, Misgav, Israel
| | | | - Guy Shrem
- Obstetrics, Gynecology and Infertility (OB&GYN) Department Maccabi Healthcare Services, Tel Aviv, Israel
| | - Mali Salmon‐Divon
- Department of Molecular Biology, Ariel University, Ariel, Israel
- Adelson School of Medicine, Ariel University, Ariel, Israel
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Xu C, Shao J. High-throughput omics technologies in inflammatory bowel disease. Clin Chim Acta 2024; 555:117828. [PMID: 38355001 DOI: 10.1016/j.cca.2024.117828] [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: 07/23/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic, relapsing intestinal disease. Elucidation of the pathogenic mechanisms of IBD requires high-throughput technologies (HTTs) to effectively obtain and analyze large amounts of data. Recently, HTTs have been widely used in IBD, including genomics, transcriptomics, proteomics, microbiomics, metabolomics and single-cell sequencing. When combined with endoscopy, the application of these technologies can provide an in-depth understanding on the alterations of intestinal microbe diversity and abundance, the abnormalities of signaling pathway-mediated immune responses and functionality, and the evaluation of therapeutic effects, improving the accuracy of early diagnosis and treatment of IBD. This review comprehensively summarizes the development and advancement of HTTs, and also highlights the challenges and future directions of these technologies in IBD research. Although HTTs have made striking breakthrough in IBD, more standardized methods and large-scale dataset processing are still needed to achieve the goal of personalized medicine.
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Affiliation(s)
- Chen Xu
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China
| | - Jing Shao
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China; Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China.
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8
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Huang Y, Liu J, Liang D. Comprehensive analysis reveals key genes and environmental toxin exposures underlying treatment response in ulcerative colitis based on in-silico analysis and Mendelian randomization. Aging (Albany NY) 2023; 15:14141-14171. [PMID: 38059894 PMCID: PMC10756092 DOI: 10.18632/aging.205294] [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: 07/24/2023] [Accepted: 11/03/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND UC is increasingly prevalent worldwide and represents a significant global disease burden. Although medical therapeutics are employed, they often fall short of being optimal, leaving patients struggling with treatment non-responsiveness and many related complications. MATERIALS AND METHODS The study utilized gene microarray data and clinical information from GEO. Gene enrichment and differential expression analyses were conducted using Metascape and Limma, respectively. Lasso Regression Algorithm was constructed using glmnet and heat maps were generated using pheatmap. ROC curves were used to assess diagnostic parameter capability, while XSum was employed to screen for small-molecule drugs exacerbating UC. Molecular docking was carried out using Autodock Vina. The study also performed Mendelian randomization analysis based on TwoSampleMR and used CTD to investigate the relationship between exposure to environmental chemical toxicants and UC therapy responsiveness. RESULTS Six genes (ELL2, DAPP1, SAMD9L, CD38, IGSF6, and LYN) were found to be significantly overexpressed in UC patient samples that did not respond to multiple therapies. Lasso analysis identified ELL2 and DAPP1 as key genes influencing UC treatment response. Both genes accurately predicted intestinal inflammation in UC and impacted the immunological infiltration status. Clofibrate showed therapeutic potential for UC by binding to ELL2 and DAPP1 proteins. The study also reviews environmental toxins and drug exposures that could impact UC progression. CONCLUSIONS We used microarray technology to identify DAPP1 and ELL2 as key genes that impact UC treatment response and inflammatory progression. Clofibrate was identified as a promising UC treatment. Our review also highlights the impact of environmental toxins on UC treatment response, providing valuable insights for personalized clinical management.
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Affiliation(s)
- Yizhou Huang
- Department of Gastroenterology, The PLA Navy Anqing Hospital, Anqing 246000, Anhui Province, China
| | - Jie Liu
- Department of Gastroenterology, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, Anhui Province, China
| | - Dingbao Liang
- Department of Gastroenterology, The PLA Navy Anqing Hospital, Anqing 246000, Anhui Province, China
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Manchester AC, Chow L, Wheat W, Dow S. Modulation of In Vitro Macrophage Responses via Primary and Secondary Bile Acids in Dogs. Animals (Basel) 2023; 13:3714. [PMID: 38067065 PMCID: PMC10705343 DOI: 10.3390/ani13233714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 04/07/2024] Open
Abstract
Bile acids (BA) are important metabolites secreted into the intestinal lumen and impacted by luminal microbes and dietary intake. Prior studies in humans and rodents have shown that BAs are immunologically active and that primary and secondary BAs have distinct immune properties. Therefore, the composition of the gut BA pool may influence GI inflammatory responses. The current study investigated the relative immune modulatory properties of primary (cholic acid, CA) and secondary BAs (lithocholic acid, LCA) by assessing their effects on canine macrophage cytokine secretion and BA receptor (TGR5) expression. In addition, RNA sequencing was used to further interrogate how CA and LCA differentially modulated macrophage responses to LPS (lipopolysaccharide). We found that exposure to either CA or LCA influenced LPS-induced cytokine production via macrophages similarly, with suppression of TNF-α secretion and enhancement of IL-10 secretion. Neither BA altered the expression of the BA receptor TGR5. Transcriptomic analysis revealed that CA activated inflammatory signaling pathways in macrophages involving type II interferon signaling and the aryl hydrocarbon receptor, whereas LCA activated pathways related to nitric oxide signaling and cell cycle regulation. Thus, we concluded that both primary and secondary BAs are active modulators of macrophage responses in dogs, with differential and shared effects evident with sequencing analysis.
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Affiliation(s)
- Alison C. Manchester
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA (S.D.)
| | - Lyndah Chow
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA (S.D.)
| | - William Wheat
- Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Steven Dow
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA (S.D.)
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Lo JW, Cozzetto D, Alexander JL, Danckert NP, Madgwick M, Knox N, Sieh JYX, Olbei M, Liu Z, Ibraheim H, Blanco JM, Kudo H, Seoane RC, Possamai LA, Goldin R, Marchesi J, Korcsmaros T, Lord GM, Powell N. Immune checkpoint inhibitor-induced colitis is mediated by polyfunctional lymphocytes and is dependent on an IL23/IFNγ axis. Nat Commun 2023; 14:6719. [PMID: 37872166 PMCID: PMC10593820 DOI: 10.1038/s41467-023-41798-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/18/2023] [Indexed: 10/25/2023] Open
Abstract
Immune checkpoint inhibitors (CPIs) are a relatively newly licenced cancer treatment, which make a once previously untreatable disease now amenable to a potential cure. Combination regimens of anti-CTLA4 and anti-PD-1 show enhanced efficacy but are prone to off-target immune-mediated tissue injury, particularly at the barrier surfaces. To probe the impact of immune checkpoints on intestinal homoeostasis, mice are challenged with anti-CTLA4 and anti-PD-1 immunotherapy and manipulation of the intestinal microbiota. The immune profile of the colon of these mice with CPI-colitis is analysed using bulk RNA sequencing, single-cell RNA sequencing and flow cytometry. CPI-colitis in mice is dependent on the composition of the intestinal microbiota and by the induction of lymphocytes expressing interferon-γ (IFNγ), cytotoxicity molecules and other pro-inflammatory cytokines/chemokines. This pre-clinical model of CPI-colitis could be attenuated following blockade of the IL23/IFNγ axis. Therapeutic targeting of IFNγ-producing lymphocytes or regulatory networks, may hold the key to reversing CPI-colitis.
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Affiliation(s)
- Jonathan W Lo
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Domenico Cozzetto
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - James L Alexander
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Nathan P Danckert
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Matthew Madgwick
- Organisms and Ecosystems, Earlham Institute, NR4 7UZ, Norwich, UK
- Gut Microbes and Health Programme, Quadram Institute Bioscience, NR4 7UQ, Norwich, UK
| | - Naomi Knox
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Jillian Yong Xin Sieh
- School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
| | - Marton Olbei
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Organisms and Ecosystems, Earlham Institute, NR4 7UZ, Norwich, UK
- Gut Microbes and Health Programme, Quadram Institute Bioscience, NR4 7UQ, Norwich, UK
| | - Zhigang Liu
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Hajir Ibraheim
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Jesus Miguens Blanco
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Hiromi Kudo
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Rocio Castro Seoane
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Lucia A Possamai
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Robert Goldin
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Julian Marchesi
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Tamas Korcsmaros
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Organisms and Ecosystems, Earlham Institute, NR4 7UZ, Norwich, UK
- Gut Microbes and Health Programme, Quadram Institute Bioscience, NR4 7UQ, Norwich, UK
| | - Graham M Lord
- School of Immunology and Microbial Sciences, King's College London, London, SE1 9RT, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9NT, UK
| | - Nick Powell
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
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Fu J, Zong X, Jin M, Min J, Wang F, Wang Y. Mechanisms and regulation of defensins in host defense. Signal Transduct Target Ther 2023; 8:300. [PMID: 37574471 PMCID: PMC10423725 DOI: 10.1038/s41392-023-01553-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/11/2023] [Accepted: 06/26/2023] [Indexed: 08/15/2023] Open
Abstract
As a family of cationic host defense peptides, defensins are mainly synthesized by Paneth cells, neutrophils, and epithelial cells, contributing to host defense. Their biological functions in innate immunity, as well as their structure and activity relationships, along with their mechanisms of action and therapeutic potential, have been of great interest in recent years. To highlight the key research into the role of defensins in human and animal health, we first describe their research history, structural features, evolution, and antimicrobial mechanisms. Next, we cover the role of defensins in immune homeostasis, chemotaxis, mucosal barrier function, gut microbiota regulation, intestinal development and regulation of cell death. Further, we discuss their clinical relevance and therapeutic potential in various diseases, including infectious disease, inflammatory bowel disease, diabetes and obesity, chronic inflammatory lung disease, periodontitis and cancer. Finally, we summarize the current knowledge regarding the nutrient-dependent regulation of defensins, including fatty acids, amino acids, microelements, plant extracts, and probiotics, while considering the clinical application of such regulation. Together, the review summarizes the various biological functions, mechanism of actions and potential clinical significance of defensins, along with the challenges in developing defensins-based therapy, thus providing crucial insights into their biology and potential clinical utility.
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Affiliation(s)
- Jie Fu
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, Hangzhou, Zhejiang Province, China
| | - Xin Zong
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, Hangzhou, Zhejiang Province, China
| | - Mingliang Jin
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, Hangzhou, Zhejiang Province, China
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Fudi Wang
- The Second Affiliated Hospital, School of Public Health, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou, China.
- The First Affiliated Hospital, Basic Medical Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang, China.
| | - Yizhen Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China.
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, Hangzhou, Zhejiang Province, China.
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12
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Fenton CG, Ray MK, Meng W, Paulssen RH. Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis. Int J Mol Sci 2023; 24:10500. [PMID: 37445676 DOI: 10.3390/ijms241310500] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/26/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play a role in the pathogenesis of ulcerative colitis (UC). Although epigenetic processes such as DNA methylation and lncRNA expression are well studied in UC, the importance of the interplay between the two processes has not yet been fully explored. It is, therefore, believed that interactions between environmental factors and epigenetics contribute to disease development. Mucosal biopsies from 11 treatment-naïve UC patients and 13 normal controls were used in this study. From each individual sample, both whole-genome bisulfite sequencing data (WGBS) and lncRNA expression data were analyzed. Correlation analysis between lncRNA expression and upstream differentially methylated regions (DMRs) was used to identify lncRNAs that might be regulated by DMRs. Furthermore, proximal protein-coding genes associated with DMR-regulated lncRNAs were identified by correlating their expression. The study identified UC-associated lncRNAs such as MIR4435-2HG, ZFAS1, IL6-AS1, and Pvt1, which may be regulated by DMRs. Several genes that are involved in inflammatory immune responses were found downstream of DMR-regulated lncRNAs, including SERPINB1, CCL18, and SLC15A4. The interplay between lncRNA expression regulated by DNA methylation in UC might improve our understanding of UC pathogenesis.
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Affiliation(s)
- Christopher G Fenton
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Mithlesh Kumar Ray
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Wei Meng
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
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13
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Identification of Specific Biomarkers and Pathways in the Treatment Response of Infliximab for Inflammatory Bowel Disease: In-Silico Analysis. Life (Basel) 2023; 13:life13030680. [PMID: 36983834 PMCID: PMC10057676 DOI: 10.3390/life13030680] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Background: Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract. In biological therapy, infliximab became the first anti-tumor necrosis factor (TNF) agent approved for IBD. Despite this success, infliximab is expensive, often ineffective, and associated with adverse events. Prediction of infliximab resistance would improve overall potential outcomes. Therefore, there is a pressing need to widen the scope of investigating the role of genetics in IBD to their association with therapy response. Methods: In the current study, an in-silico analysis of publicly available IBD patient transcriptomics datasets from Gene Expression Omnibus (GEO) are used to identify subsets of differentially expressed genes (DEGs) involved in the pathogenesis of IBD and may serve as potential biomarkers for Infliximab response. Five datasets were found that met the inclusion criteria. The DEGs for datasets were identified using limma R packages through the GEOR2 tool. The probes’ annotated genes in each dataset intersected with DGEs from all other datasets. Enriched gene Ontology Clustering for the identified genes was performed using Metascape to explore the possible connections or interactions between the genes. Results: 174 DEGs between IBD and healthy controls were found from analyzing two datasets (GSE14580 and GSE73661), indicating a possible role in the pathogenesis of IBD. Of the 174 DEGs, five genes (SELE, TREM1, AQP9, FPR2, and HCAR3) were shared between all five datasets. Moreover, these five genes were identified as downregulated in the infliximab responder group compared to the non-responder group. Conclusions: We hypothesize that alteration in the expression of these genes leads to an impaired response to infliximab in IBD patients. Thus, these genes can serve as potential biomarkers for the early detection of compromised infliximab response in IBD patients.
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14
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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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15
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Zhang C, Zhang J, Zhang Y, Song Z, Bian J, Yi H, Ma Z. Identifying neutrophil-associated subtypes in ulcerative colitis and confirming neutrophils promote colitis-associated colorectal cancer. Front Immunol 2023; 14:1095098. [PMID: 36845139 PMCID: PMC9950623 DOI: 10.3389/fimmu.2023.1095098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Background Ulcerative colitis (UC) is a chronic inflammatory disease of the intestinal mucosa, the incidence of which has increased worldwide. There is still a lack of clear understanding of the pathogenesis of ulcerative colitis that ultimately leads to colitis-associated colorectal cancer. Method We download UC transcriptome data from the GEO database and pass the limma package in order to identify differentially expressed genes. Gene Set Enrichment Analysis (GSEA) was used to identify potential biological pathways. We identified immune cells associated with UC by CIBERSORT and Weighted co-expression network analysis (WGCNA). We used validation cohorts and mouse models to verify the expression of the hub genes and the role of neutrophils. Result We identified 65 differentially expressed genes in UC samples and healthy controls. GSEA, KEGG, and GO analyses displayed that DEGs were enriched in immune-related pathways. CIBERSORT analysis revealed increased infiltration of neutrophils in UC tissues. The red module, obtained by WGCNA analysis, was considered to be the most relevant module for neutrophils.Based on neutrophil-associated differentially expressed genes, UC patients were classified into two subtypes of neutrophil infiltration. We discovered that the highly neutrophil-infiltrated subtype B of UC patients had a higher risk of developing CAC. Five genes were identified as biomarkers by searching for DEGs between distinct subtypes. Finally, using the mouse model, we determined the expression of these five genes in the control, DSS, and AOM/DSS groups. The degree of neutrophil infiltration in mice and the percentage of MPO and pSTAT3 expression in neutrophils were analyzed by flow cytometry. In the AOM/DSS model, MPO and pSTAT3 expressions were significantly increased. Conclusions These findings suggested neutrophils might promote the conversion of UC into CAC. These findings improve our understanding of the pathogenesis of CAC and provide new and more effective insights into the prevention and treatment of CAC.
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Affiliation(s)
- Chen Zhang
- Colorectal & Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jiantao Zhang
- Colorectal & Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Yanli Zhang
- Central Laboratory, First Hospital of Jilin University, Changchun, Jilin, China
- Echocardiography Department, First Hospital of Jilin University, Changchun, Jilin, China
| | - Zian Song
- Colorectal & Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jing Bian
- Department of Respiratory Medicine, First Affiliated Hospital of Jilin University, Changchun, Jilin, China
| | - Huanfa Yi
- Central Laboratory, First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhanchuan Ma
- Central Laboratory, First Hospital of Jilin University, Changchun, Jilin, China
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16
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Shum TF, Wang L, Chiou J. Impact of Plasticizer on the Intestinal Epithelial Integrity and Tissue-Repairing Ability within Cells in the Proximity of the Human Gut Microbiome. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2152. [PMID: 36767519 PMCID: PMC9915929 DOI: 10.3390/ijerph20032152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/22/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Toxicological research into the impact of plasticizer on different organs has been reported in the past few decades, while their effects on shifting the gut microbiota and immune cells homeostasis in zebrafish were only studied recently. However, studies on the impact of plasticizer on human gut microbiota are scarce. In this study, we co-incubated healthy human fecal microbiota with different concentrations of Di(2-ethylhexyl) phthalate (DEHP) and di-iso-nonyl phthalate (DINP), analyzed microbial composition by 16S rDNA sequencing, and compared the influence of their derived microbiomes on the human enterocyte (HT-29) and murine macrophage (RAW264.7) cell lines. Microbial diversity is reduced by DEHP treatment in a dose-dependent manner. DEHP treatment reduced the phyla Firmicutes/Bacteroidetes ratio, while DINP treatment promoted Proteobacteria. Expressions of tight/adherens junction genes in HT-29 and anti-inflammatory genes in RAW264.7 were down-regulated by plasticizer-co-incubated microbiota derived metabolites. Overall, it is observed that selected plasticizers at high dosages can induce compositional changes in human microbiota. Metabolites from such altered microbiota could affect the tight junction integrity of the intestinal epithelium and upset macrophage differentiation homeostasis in proximity. Chronic exposure to these plasticizers may promote risks of dysbiosis, leaky gut or the exacerbation of intestinal inflammation.
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Affiliation(s)
- Tim-Fat Shum
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Liwen Wang
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Jiachi Chiou
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- Research Institute for Future Food, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
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17
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Ramos L, Teo-Loy J, Barreiro-de Acosta M. Disease clearance in ulcerative colitis: Setting the therapeutic goals for future in the treatment of ulcerative colitis. Front Med (Lausanne) 2023; 9:1102420. [PMID: 36698823 PMCID: PMC9868775 DOI: 10.3389/fmed.2022.1102420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
Ulcerative colitis, one of the phenotypic patterns of inflammatory bowel disease, should be considered a progressive disease with an increased risk of complications if intestinal inflammation is not adequately controlled. The advent of new lines of treatment for this condition has changed and expanded the therapeutic goals to modify its natural history and evolution. The concept of "disease clearance" in ulcerative colitis aims to achieve clinical and biological remission as well as mucosal healing (endoscopic, histological, and in future molecular) in these patients. This review provides the available data on each of the goals of disease clearance in ulcerative colitis to be considered for application in clinical practice in the coming years.
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Affiliation(s)
- Laura Ramos
- IBD Unit, Department of Gastroenterology, Hospital Universitario de Canarias, Santa Cruz de Tenerife, Spain,Department of Internal Medicine, University of La Laguna, Santa Cruz de Tenerife, Spain,*Correspondence: Laura Ramos,
| | - Jeny Teo-Loy
- IBD Unit, Department of Gastroenterology, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Barreiro-de Acosta
- IBD Unit, Department of Gastroenterology, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain
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18
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Yarani R, Palasca O, Doncheva NT, Anthon C, Pilecki B, Svane CAS, Mirza AH, Litman T, Holmskov U, Bang-Berthelsen CH, Vilien M, Jensen LJ, Gorodkin J, Pociot F. Cross-species high-resolution transcriptome profiling suggests biomarkers and therapeutic targets for ulcerative colitis. Front Mol Biosci 2023; 9:1081176. [PMID: 36685283 PMCID: PMC9850088 DOI: 10.3389/fmolb.2022.1081176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023] Open
Abstract
Background: Ulcerative colitis (UC) is a disorder with unknown etiology, and animal models play an essential role in studying its molecular pathophysiology. Here, we aim to identify common conserved pathological UC-related gene expression signatures between humans and mice that can be used as treatment targets and/or biomarker candidates. Methods: To identify differentially regulated protein-coding genes and non-coding RNAs, we sequenced total RNA from the colon and blood of the most widely used dextran sodium sulfate Ulcerative colitis mouse. By combining this with public human Ulcerative colitis data, we investigated conserved gene expression signatures and pathways/biological processes through which these genes may contribute to disease development/progression. Results: Cross-species integration of human and mouse Ulcerative colitis data resulted in the identification of 1442 genes that were significantly differentially regulated in the same direction in the colon and 157 in blood. Of these, 51 genes showed consistent differential regulation in the colon and blood. Less known genes with importance in disease pathogenesis, including SPI1, FPR2, TYROBP, CKAP4, MCEMP1, ADGRG3, SLC11A1, and SELPLG, were identified through network centrality ranking and validated in independent human and mouse cohorts. Conclusion: The identified Ulcerative colitis conserved transcriptional signatures aid in the disease phenotyping and future treatment decisions, drug discovery, and clinical trial design.
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Affiliation(s)
- Reza Yarani
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark,*Correspondence: Reza Yarani, ; Flemming Pociot,
| | - Oana Palasca
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nadezhda T. Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bartosz Pilecki
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Cecilie A. S. Svane
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Aashiq H. Mirza
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Thomas Litman
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Uffe Holmskov
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Claus H. Bang-Berthelsen
- Research Group for Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark,Department of Gastroenterology, North Zealand Hillerød Hospital, Hillerød, Denmark
| | - Mogens Vilien
- Department of Surgery, North Zealand Hospital, Hillerød, Denmark
| | - Lars J. Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Pociot
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Copenhagen Diabetes Research Center, Department of Pediatrics, Herlev University Hospital, Herlev, Denmark,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark,*Correspondence: Reza Yarani, ; Flemming Pociot,
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19
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Matute JD, Duan J, Flak MB, Griebel P, Tascon-Arcila JA, Doms S, Hanley T, Antanaviciute A, Gundrum J, Mark Welch JL, Sit B, Abtahi S, Fuhler GM, Grootjans J, Tran F, Stengel ST, White JR, Krupka N, Haller D, Clare S, Lawley TD, Kaser A, Simmons A, Glickman JN, Bry L, Rosenstiel P, Borisy G, Waldor MK, Baines JF, Turner JR, Blumberg RS. Intelectin-1 binds and alters the localization of the mucus barrier-modifying bacterium Akkermansia muciniphila. J Exp Med 2023; 220:e20211938. [PMID: 36413219 PMCID: PMC9683900 DOI: 10.1084/jem.20211938] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 09/06/2022] [Accepted: 10/13/2022] [Indexed: 01/25/2023] Open
Abstract
Intelectin-1 (ITLN1) is a lectin secreted by intestinal epithelial cells (IECs) and upregulated in human ulcerative colitis (UC). We investigated how ITLN1 production is regulated in IECs and the biological effects of ITLN1 at the host-microbiota interface using mouse models. Our data show that ITLN1 upregulation in IECs from UC patients is a consequence of activating the unfolded protein response. Analysis of microbes coated by ITLN1 in vivo revealed a restricted subset of microorganisms, including the mucolytic bacterium Akkermansia muciniphila. Mice overexpressing intestinal ITLN1 exhibited decreased inner colonic mucus layer thickness and closer apposition of A. muciniphila to the epithelial cell surface, similar to alterations reported in UC. The changes in the inner mucus layer were microbiota and A. muciniphila dependent and associated with enhanced sensitivity to chemically induced and T cell-mediated colitis. We conclude that by determining the localization of a select group of bacteria to the mucus layer, ITLN1 modifies this critical barrier. Together, these findings may explain the impact of ITLN1 dysregulation on UC pathogenesis.
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Affiliation(s)
- Juan D. Matute
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Division of Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Jinzhi Duan
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Magdalena B. Flak
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Paul Griebel
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Jose A. Tascon-Arcila
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Shauni Doms
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Thomas Hanley
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Agne Antanaviciute
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | | | | | - Brandon Sit
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA
- Department of Microbiology, Harvard Medical School, Boston, MA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
- Howard Hughes Medical Institute, Boston, MA
| | - Shabnam Abtahi
- Laboratory of Mucosal Barrier Pathobiology, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Gwenny M. Fuhler
- Department of Gastroenterology & Hepatology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Joep Grootjans
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology and Metabolism & Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Stephanie T. Stengel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Niklas Krupka
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Dirk Haller
- Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Simon Clare
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Arthur Kaser
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, and Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Alison Simmons
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jonathan N. Glickman
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA
- Department of Microbiology, Harvard Medical School, Boston, MA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
- Howard Hughes Medical Institute, Boston, MA
| | - John F. Baines
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Jerrold R. Turner
- Laboratory of Mucosal Barrier Pathobiology, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Richard S. Blumberg
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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20
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A shared tissue transcriptome signature and pathways in psoriasis and ulcerative colitis. Sci Rep 2022; 12:19740. [PMID: 36396672 PMCID: PMC9671879 DOI: 10.1038/s41598-022-22465-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/14/2022] [Indexed: 11/18/2022] Open
Abstract
Despite multiple efficacious therapies in common between psoriasis (PS) and Ulcerative Colitis (UC), mechanisms underlying their common pathophysiology remain largely unclear. Here we sought to establish a link by evaluating expression differences and pathway alterations in diseased tissues. We identified two sets of differentially expressed genes (DEGs) between lesional and nonlesional tissues in meta-analyses of data collected from baseline samples in 3 UC and then 3 PS available clinical studies from Pfizer. A shared gene signature was defined by 190 DEGs common to both diseases. Commonly dysregulated pathways identified via enrichment analysis include interferon signaling, partly driven by genes IFI6, CXCL9, CXCL10 and CXCL11, which may attract chemotaxis of Th1 cells to inflammatory sites; IL-23 pathway (IL-23A, CCL20, PI3, CXCL1, LCN2); and Th17 pathway except IL-17A. Elevated expression of costimulatory molecules ICOS and CTLA4 suggests ongoing T-cell activation in both diseases. The clinical value of the shared signature is demonstrated by a gene set improvement score reflecting post-treatment molecular improvement for each disease. This is the first study using transcriptomic meta-analysis to define a tissue gene signature and pathways dysregulated in both PS and UC. These findings suggest immune mechanisms may initiate and sustain inflammation similarly in the two diseases.
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21
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Identification of Novel Loci Involved in Adalimumab Response in Crohn’s Disease Patients Using Integration of Genome Profiling and Isoform-Level Immune-Cell Deconvoluted Transcriptome Profiling of Colon Tissue. Pharmaceutics 2022; 14:pharmaceutics14091893. [PMID: 36145641 PMCID: PMC9500628 DOI: 10.3390/pharmaceutics14091893] [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: 08/10/2022] [Revised: 08/25/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Crohn’s disease is a consequence of dysregulated inflammatory response to the host’s microbiota. Although anti-TNF treatment improves the quality of the patient’s life, a large proportion of patients lose response to the treatment. The past decade of research has led to a continuum of studies showcasing the heterogeneity of anti-TNF response; thus, the aim of the present study was to dissect transcriptome-wide findings to transcript isoform specific levels and combine the analyses with refined information of immune cell landscapes in colon tissue, and subsequently select promising candidates using gene ontology and genomic integration. We enrolled Slovenian Crohn’s disease patients who were naïve with respect to adalimumab treatment. We performed colon tissue RNA sequencing and peripheral blood mononuclear cell DNA genotyping with a subsequent contemporary integrative approach to combine immune cell deconvoluted isoform transcript specific transcriptome analysis, gene ontology layering and genomic data. We identified nine genes (MACF1, CTSE, HDLBP, HSPA9, HLA-DMB, TAP2, LGMN, ANAPC11, ACP5) with 15 transcripts and 16 variants involved in the adalimumab response. Our study identified loci, some of which were previously shown to contribute to inflammatory bowel disease susceptibility, as novel loci involved in adalimumab response in Crohn’s disease patients.
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22
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Shakerian L, Kolahdooz H, Garousi M, Keyvani V, Kamal Kheder R, Abdulsattar Faraj T, Yazdanpanah E, Esmaeili SA. IL-33/ST2 axis in autoimmune disease. Cytokine 2022; 158:156015. [PMID: 36041312 DOI: 10.1016/j.cyto.2022.156015] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 11/03/2022]
Abstract
Interleukin-33 (IL-33) is a member of the IL-1 family and plays an ambivalent role in autoimmune diseases. IL-33 signals via the ST2 receptor and drives cytokine production in mast cells, basophils, eosinophils, NK cells, and T lymphocyte cells. The vital role of IL-33 as an active component gives rise to aberrant local and systemic damage which has been demonstrated in numerous inflammatory disorders and immune-mediated pathological conditions including multiple sclerosis (MS), rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), psoriasis, Sjogren's syndrome, inflammatory bowel disease (IBD), etc. IL-33/ST2 axis can up-regulate pro-inflammatory cytokine release in autoimmune disease, however, in some metabolic diseases like diabetes mellitus type 1 IL-33 can be considered an anti-inflammatory cytokine. The purpose of this review is to discuss selected studies on IL-33/ST2 axis in autoimmune diseases and its potential role as a pathogenic or protective cytokine.
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Affiliation(s)
- Leila Shakerian
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hanieh Kolahdooz
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mitra Garousi
- Department of Internal Medicine, Faculty of Medical Sciences, Hamedan University of Medical Sciences, Hamedan, Iran
| | - Vahideh Keyvani
- Molecular Genetics, Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Ramiar Kamal Kheder
- Medical Laboratory Science Department, College of Science, University of Raparin, Rania 46012, Sulaymaniyah, Iraq; Department of Basic Sciences, College of Medicine, Hawler Medical University, Erbil, Iraq
| | - Tola Abdulsattar Faraj
- Department of Basic Sciences, College of Medicine, Hawler Medical University, Erbil, Iraq; Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Erbil, Iraq
| | - Esmaeil Yazdanpanah
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Immunology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed-Alireza Esmaeili
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Immunology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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23
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Wang M, Tang S, Yang X, Xie X, Luo Y, He S, Li X, Feng X. Identification of key genes and pathways in chronic rhinosinusitis with nasal polyps and asthma comorbidity using bioinformatics approaches. Front Immunol 2022; 13:941547. [PMID: 36059464 PMCID: PMC9428751 DOI: 10.3389/fimmu.2022.941547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/25/2022] [Indexed: 11/25/2022] Open
Abstract
Patients with chronic rhinosinusitis with nasal polyps (CRSwNP) and asthma comorbidity (ACRSwNP) present severe symptoms and are more likely to relapse. However, the pathogenesis of ACRSwNP is not fully understood. The aim of this study was to explore the underlying pathogenesis of ACRSwNP using bioinformatics approaches. ACRSwNP-related differentially expressed genes (DEGs) were identified by the analysis of the GSE23552 dataset. The clusterProfiler R package was used to carry out functional and pathway enrichment analysis. A protein–protein interaction (PPI) network was built using the STRING database to explore key genes in the pathogenesis of ACRSwNP. The bioinformatics analysis results were verified through qRT-PCR. The Connectivity Map (CMap) database was used to predict potential drugs for the treatment of ACRSwNP. A total of 36 DEGs were identified, which were mainly enriched in terms of regulation of immune response and detection sensory perception of taste. Thirteen hub genes including AZGP1, AQP9, GAPT, PIP, and PRR4 were identified as potential hub genes in ACRSwNP from the PPI network. Analysis of the GSE41861 dataset showed that upregulation of CST1 in nasal mucosa was associated with asthma. qRT-PCR detection confirmed the bioinformatics analysis results. Tacrolimus and spaglumic acid were identified as potential drugs for the treatment of ACRSwNP from the CMap database. The findings of this study provide insights into the pathogenesis of ACRSwNP and may provide a basis for the discovery of effective therapeutic modalities for ACRSwNP.
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Affiliation(s)
| | | | | | | | | | | | | | - Xin Feng
- *Correspondence: Xin Feng, ; Xuezhong Li,
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24
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Gobert AP, Latour YL, Asim M, Barry DP, Allaman MM, Finley JL, Smith TM, McNamara KM, Singh K, Sierra JC, Delgado AG, Luis PB, Schneider C, Washington MK, Piazuelo MB, Zhao S, Coburn LA, Wilson KT. Protective Role of Spermidine in Colitis and Colon Carcinogenesis. Gastroenterology 2022; 162:813-827.e8. [PMID: 34767785 PMCID: PMC8881368 DOI: 10.1053/j.gastro.2021.11.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Because inflammatory bowel disease is increasing worldwide and can lead to colitis-associated carcinoma (CAC), new interventions are needed. We have shown that spermine oxidase (SMOX), which generates spermidine (Spd), regulates colitis. Here we determined whether Spd treatment reduces colitis and carcinogenesis. METHODS SMOX was quantified in human colitis and associated dysplasia using quantitative reverse-transcription polymerase chain reaction and immunohistochemistry. We used wild-type (WT) and Smox-/- C57BL/6 mice treated with dextran sulfate sodium (DSS) or azoxymethane (AOM)-DSS as models of colitis and CAC, respectively. Mice with epithelial-specific deletion of Apc were used as a model of sporadic colon cancer. Animals were supplemented or not with Spd in the drinking water. Colonic polyamines, inflammation, tumorigenesis, transcriptomes, and microbiomes were assessed. RESULTS SMOX messenger RNA levels were decreased in human ulcerative colitis tissues and inversely correlated with disease activity, and SMOX protein was reduced in colitis-associated dysplasia. DSS colitis and AOM-DSS-induced dysplasia and tumorigenesis were worsened in Smox-/- vs WT mice and improved in both genotypes with Spd. Tumor development caused by Apc deletion was also reduced by Spd. Smox deletion and AOM-DSS treatment were both strongly associated with increased expression of α-defensins, which was reduced by Spd. A shift in the microbiome, with reduced abundance of Prevotella and increased Proteobacteria and Deferribacteres, occurred in Smox-/- mice and was reversed with Spd. CONCLUSIONS Loss of SMOX is associated with exacerbated colitis and CAC, increased α-defensin expression, and dysbiosis of the microbiome. Spd supplementation reverses these phenotypes, indicating that it has potential as an adjunctive treatment for colitis and chemopreventive for colon carcinogenesis.
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Affiliation(s)
- Alain P Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biolog Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yvonne L Latour
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Daniel P Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jordan L Finley
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Thaddeus M Smith
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kara M McNamara
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biolog Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kshipra Singh
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Johanna C Sierra
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alberto G Delgado
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Paula B Luis
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Claus Schneider
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - M Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biolog Vanderbilt University Medical Center, Nashville, Tennessee; Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biolog Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee; Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee.
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25
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Ungar B, Yavzori M, Fudim E, Picard O, Kopylov U, Eliakim R, Shouval D, Levin Y, Savidor A, Ben-Moshe S, Manco R, Dan S, Egozi A, Bahar Halpern K, Mayer C, Barshack I, Ben-Horin S, Itzkovitz S. Host transcriptome signatures in human faecal-washes predict histological remission in patients with IBD. Gut 2022; 71:gutjnl-2021-325516. [PMID: 35046090 DOI: 10.1136/gutjnl-2021-325516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/08/2021] [Indexed: 12/08/2022]
Abstract
BACKGROUND Colonoscopy is the gold standard for evaluation of inflammation in inflammatory bowel diseases (IBDs), yet entails cumbersome preparations and risks of injury. Existing non-invasive prognostic tools are limited in their diagnostic power. Moreover, transcriptomics of colonic biopsies have been inconclusive in their association with clinical features. AIMS To assess the utility of host transcriptomics of faecal wash samples of patients with IBD compared with controls. METHODS In this prospective cohort study, we obtained biopsies and faecal-wash samples from patients with IBD and controls undergoing lower endoscopy. We performed RNAseq of biopsies and matching faecal-washes, and associated them with endoscopic and histological inflammation status. We also performed faecal mass-spectrometry proteomics on a subset of samples. We inferred cell compositions using computational deconvolution and used classification algorithms to identify informative genes. RESULTS We analysed biopsies and faecal washes from 39 patients (20 IBD, 19 controls). Host faecal-transcriptome carried information that was distinct from biopsy RNAseq and faecal proteomics. Transcriptomics of faecal washes, yet not of biopsies, from patients with histological inflammation were significantly correlated to one another (p=5.3×10-12). Faecal-transcriptome had significantly higher statistical power in identifying histological inflammation compared with transctiptome of intestinal biopsies (150 genes with area under the curve >0.9 in faecal samples vs 10 genes in biopsy RNAseq). These results were replicated in a validation cohort of 22 patients (10 IBD, 12 controls). Faecal samples were enriched in inflammatory monocytes, regulatory T cells, natural killer-cells and innate lymphoid cells. CONCLUSIONS Faecal wash host transcriptome is a statistically powerful biomarker reflecting histological inflammation. Furthermore, it opens the way to identifying important correlates and therapeutic targets that may be obscured using biopsy transcriptomics.
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Affiliation(s)
- Bella Ungar
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Miri Yavzori
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Ella Fudim
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Orit Picard
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Uri Kopylov
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Rami Eliakim
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Dror Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, & Sackler School of Medicine, Tel-Aviv University, Petah Tikva, Israel
| | - Yishai Levin
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Ben-Moshe
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rita Manco
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Stav Dan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Mayer
- Department of Pathology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Shomron Ben-Horin
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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26
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Kou F, Cheng Y, Shi L, Liu J, Liu Y, Shi R, Peng G, Li J. LCN2 as a Potential Diagnostic Biomarker for Ulcerative Colitis-Associated Carcinogenesis Related to Disease Duration. Front Oncol 2022; 11:793760. [PMID: 35111677 PMCID: PMC8801604 DOI: 10.3389/fonc.2021.793760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/20/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Patients with long-duration ulcerative colitis (UC) had a higher risk of developing ulcerative colitis-associated carcinogenesis (UCAC) when compared to those with short-duration UC. This study aimed to discover the biomarker for cancer surveillance related to disease duration. METHODS The microarrays were divided into short-duration (<10 years) UC, long-duration (≥10 years) UC, UCAC, and normal groups in the Gene Expression Omnibus (GEO) datasets. Differentially expressed genes (DEGs) of GEO and the hub genes of the selected weighted gene co-expression network analysis (WGCNA) were intersected to obtain the overlapping genes. Among these genes, the key gene was identified by using the protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the cytoHubba of Cytoscape, and the expression levels. Also, immunofluorescence of human colonic mucosa and animal experiment were used to validate the expression trend of the key gene in the progress of UC developing into UCAC. RESULTS Lipocalin-2 (LCN2) was more relevant with disease duration of UC and significantly negatively correlated with the risk of UCAC. The expression level of LCN2 in short-duration UC was higher than that of long-duration UC (P < 0.01), long-duration UC was higher than that of UCAC (P = 0.001), and UC and UCAC were all higher than that of the normal (P < 0.001). We then discovered that the expression trend of LCN2 in blood and stool samples was consistent with that in colorectal mucosa. CONCLUSION The research indicates that LCN2 could be a novel biomarker to evaluate cancer surveillance related to disease duration of developing UC into UCAC. Compared with that of blood samples, stool detection of LCN2 may have more advantages for diagnosis value of early stage of UCAC as a complement to colonoscopy surveillance.
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Affiliation(s)
- Fushun Kou
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yuan Cheng
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Lei Shi
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jiajing Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Yuyue Liu
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Rui Shi
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Guiying Peng
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Junxiang Li
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
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27
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NAGATA N, OHTA H, YOKOYAMA N, TEOH YB, SASAKI N, NAKAMURA K, TAKIGUCHI M. Characterization of mucin gene expression and goblet cell proportion in inflammatory colorectal polyps in miniature dachshunds. J Vet Med Sci 2022; 84:872-876. [PMID: 35527018 PMCID: PMC9246683 DOI: 10.1292/jvms.22-0076] [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] [Indexed: 11/22/2022] Open
Abstract
Hyperplastic goblet cells and abundant mucus are significant characteristics of
inflammatory colorectal polyps (ICRPs) in miniature dachshunds. In this study, selected
mucin gene expressions and goblet cell proportions were evaluated in miniature dachshunds
with ICRPs and in healthy dogs. Mucin 2 (MUC2) gene
expression was not significantly different among the groups, whereas mucin
5AC (MUC5AC) gene expression was significantly higher in the
polypoid lesions than in healthy colonic mucosa. Although the percentage of goblet cells
in the upper crypt regions did not significantly differ between the groups, that in the
lower crypt regions was significantly decreased in polypoid lesions. In conclusion,
increased MUC5AC gene expression and goblet cell proportion changes may
be associated with the pathogenesis of ICRPs.
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Affiliation(s)
- Noriyuki NAGATA
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University
| | - Hiroshi OHTA
- Companion Animal Internal Medicine, Department of Companion Animal Clinical Sciences, School of Veterinary Medicine, Rakuno Gakuen University
| | - Nozomu YOKOYAMA
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University
| | - Yong Bin TEOH
- Laboratory of Veterinary Internal Medicine, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University
| | - Noboru SASAKI
- Laboratory of Veterinary Internal Medicine, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University
| | - Kensuke NAKAMURA
- Laboratory of Veterinary Internal Medicine, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University
| | - Mitsuyoshi TAKIGUCHI
- Laboratory of Veterinary Internal Medicine, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University
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28
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Lu J, Wang Z, Maimaiti M, Hui W, Abudourexiti A, Gao F. Identification of diagnostic signatures in ulcerative colitis patients via bioinformatic analysis integrated with machine learning. Hum Cell 2022; 35:179-188. [PMID: 34731452 DOI: 10.1007/s13577-021-00641-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023]
Abstract
Ulcerative colitis (UC) is an immune-related disorder with enhanced prevalence globally. Early diagnosis is critical for the effective treatment of UC. However, it still lacks specific diagnostic signatures. The aim of our study was to explore efficient signatures and construct the diagnostic model for UC. Microarray data of GSE87473 and GSE48634, which were obtained from tissue biopsy samples, were downloaded from the Gene Expression Omnibus (GEO), and differently expressed genes (DEGs), GO, and KEGG analyses were performed. We constructed the PPI network via STRING database. The immune infiltration of the samples was evaluated using CIBERSORT methods combined with the LM22 feature matrix. The logistic regression model was constructed, with the expression of selected genes as the predictor variable, and the UC occurrence as the responsive variable. As a result, a total of 126 DEGs between the UC patients and normal counterparts were identified. The GO and KEGG analysis revealed that multiple biological processes, such as antimicrobial humoral immune response mediated by antimicrobial peptide and IL-17 signaling pathway, were enriched. The infiltration of eight immune cell types (B cells naive, Dendritic.cells.activated, Macrophages.M0, Macrophages.M2, Mast.cells.resting, Neutrophils, Plasma.cells, and T.cells.follicular.helper) was significantly different between patients with UC and normal counterparts. The top 50 most significant DEGs were selected for the construction of the PPI network. The average AUC of the logistic regression model in the fivefold cross-validation was 0.8497 in the training set, GSE87473. The AUC of another independent verification set of GSE48634 from the GEO database was 0.7208. In conclusion, we identified potential hub genes, including REG3A, REG1A, DEFA6, REG1B, and DEFA5, which might be significantly associated with UC progression. The logistic regression model based on the five genes could reliably diagnose UC patients.
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Affiliation(s)
- Jiajie Lu
- Xinjiang Medical University, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Zhiyuan Wang
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Munila Maimaiti
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Wenjia Hui
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Adilai Abudourexiti
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Feng Gao
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China.
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Pang B, Jin H, Liao N, Li J, Jiang C, Shi J. Vitamin A supplementation ameliorates ulcerative colitis in gut microbiota-dependent manner. Food Res Int 2021; 148:110568. [PMID: 34507723 DOI: 10.1016/j.foodres.2021.110568] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 12/27/2022]
Abstract
Ulcerative colitis (UC), is a chronic relapsing inflammatory condition of the gastrointestinal track. The purpose of this study is to explore whether Vitamin A (VA) can treat UC and its mechanisms. A mouse model of UC was established using 3.0% (w/v) dextran sodium sulfate (DSS). VA was used to treat UC by intragastric administration of 5000 international unit (IU) retinyl acetate. Fecal microbiota transplantation (FMT) was also used to treat the UC model mice to verify the effect of influenced gut microbiota. The content of short-chain fatty acids (SCFAs) in cecal contents was quantitatively detected by gas chromatography and mass spectrometry. VA supplementation significantly ameliorated UC. 16S rRNA sequencing indicated that VA-treated mice exhibited much more abundant gut microbial diversity and flora composition. Targeted metabolomics analysis manifested the increased production of SCFAs in VA-treated mice. Gut microbiota depletion and FMT results confirmed the gut microbiota-dependent mechanism as that VA relieved UC via regulating gut microbiota: increase in SCFA-producing genera and decrease in UC-related genera. The restore of intestinal barrier and the inhibition of inflammation were also found to contribute to the amelioration of UC by VA. It was concluded that a VA supplement was enough to cause a significant change in gut microbiota and amelioration of UC.
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Affiliation(s)
- Bing Pang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China
| | - Han Jin
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China.
| | - Ning Liao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China
| | - Junjun Li
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China
| | - Chunmei Jiang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China.
| | - Junling Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China.
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30
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Zou J, Liu C, Jiang S, Qian D, Duan J. Cross Talk between Gut Microbiota and Intestinal Mucosal Immunity in the Development of Ulcerative Colitis. Infect Immun 2021; 89:e0001421. [PMID: 33526559 PMCID: PMC8370674 DOI: 10.1128/iai.00014-21] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ulcerative colitis (UC), a nonspecific inflammatory disease, is characterized by inflammation and mucosal damage in the colon, and its prevalence in the world is increasing. Nevertheless, the exact pathogenesis of UC is still unclear. Accumulating data have suggested that its pathogenesis is multifactorial, involving genetic predisposition, environmental factors, microbial dysbiosis, and dysregulated immune responses. Generally, UC is aroused by inappropriate immune activation based on the interaction of host and intestinal microbiota. The relationship between microbiota and host immune system in the pathogenesis of UC is complicated. However, increasing evidence indicates that the shift of microbiota composition can substantially influence intestinal immunity. In this review, we primarily focus on the delicate balance between microbiota and gut mucosal immunity during UC progression.
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Affiliation(s)
- Junfeng Zou
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Chen Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Shu Jiang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Dawei Qian
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Jinao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
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31
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Han Z, Tan X, Sun J, Wang T, Yan G, Wang C, Ma K. Systems pharmacology and transcriptomics reveal the mechanisms of Sanhuang decoction enema in the treatment of ulcerative colitis with additional Candida albicans infection. Chin Med 2021; 16:75. [PMID: 34376226 PMCID: PMC8353752 DOI: 10.1186/s13020-021-00487-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/02/2021] [Indexed: 01/16/2023] Open
Abstract
Background Ulcerative colitis (UC) is an important inflammatory phenotype in bowel disease (IBD), which is caused by multiple potential factors, including fungal dysbiosis. Candida albicans (C. albicans) was confirmed to be an important factor promoting the occurrence and development of UC. Sanhuang decoction (SHD) has been used for UC therapy in China for thousand of years, although its core active constituents and pharmacological mechanism remain undefined. Methods In this work, a murine model of UC with C. albicans colonization was established with dextran sodium sulfate (DSS) and C. albicans intragastric administration. The major bioactive constituents and potential mechanism of SHD against UC with fungal dysbiosis were comprehensively examined by combining systems pharmacology and in vivo transcriptomics. Results SHD attenuated C. albicans burden, reduced DAI, increased mucosal integrity and relived systemic inflammation in UC mice. Systems pharmacology analysis identified 9 core bioactive ingredients and 45 hub targets of SHD against UC. Transcriptomics analysis confirmed 370 differentially expressed genes (DEGs) after SHD treatment, which were mainly enriched in inflammatory and immune response related signaling pathways. Toll-like receptor and PI3K-Akt signaling pathway were screened out as the candidate targets involved in the action of SHD on fungal dysbiosis-associated UC, which were consistent with the findings in systems pharmacology. The expression of TLR4, IL-1β, NF-κB, PI3K and Akt proteins were stimulated by C. albicans, and partially reversed by SHD in UC mice. Conclusion These findings suggested SHD could be a candidate for the treatment of fungal dysbiosis-associated UC via TLR4-NF-κB and PI3K-Akt signaling pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s13020-021-00487-2.
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Affiliation(s)
- Zhijun Han
- College of Integrated Chinese and Western Medicine, College of Life Science, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Xiaofen Tan
- College of Integrated Chinese and Western Medicine, College of Life Science, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Juan Sun
- Anhui Provincial Key Laboratory of New Manufacturing Technology for Chinese Medicinal Decoction Pieces, Anhui University of Chinese Medicine, Hefei, 230012, China.,Key Laboratory of Xin'An Medicine, Ministry of Education, Anhui Academy of Chinese Medicine, Hefei, 230012, China
| | - Tianming Wang
- College of Integrated Chinese and Western Medicine, College of Life Science, Anhui University of Chinese Medicine, Hefei, 230012, China.,Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, 230012, China.,Anhui Provincial Key Laboratory of New Manufacturing Technology for Chinese Medicinal Decoction Pieces, Anhui University of Chinese Medicine, Hefei, 230012, China.,Key Laboratory of Xin'An Medicine, Ministry of Education, Anhui Academy of Chinese Medicine, Hefei, 230012, China
| | - Guiming Yan
- College of Integrated Chinese and Western Medicine, College of Life Science, Anhui University of Chinese Medicine, Hefei, 230012, China.,Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, 230012, China.,Anhui Provincial Key Laboratory of New Manufacturing Technology for Chinese Medicinal Decoction Pieces, Anhui University of Chinese Medicine, Hefei, 230012, China.,Key Laboratory of Xin'An Medicine, Ministry of Education, Anhui Academy of Chinese Medicine, Hefei, 230012, China
| | - Changzhong Wang
- College of Integrated Chinese and Western Medicine, College of Life Science, Anhui University of Chinese Medicine, Hefei, 230012, China.,Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, 230012, China.,Anhui Provincial Key Laboratory of New Manufacturing Technology for Chinese Medicinal Decoction Pieces, Anhui University of Chinese Medicine, Hefei, 230012, China.,Key Laboratory of Xin'An Medicine, Ministry of Education, Anhui Academy of Chinese Medicine, Hefei, 230012, China
| | - Kelong Ma
- College of Integrated Chinese and Western Medicine, College of Life Science, Anhui University of Chinese Medicine, Hefei, 230012, China. .,Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, 230012, China. .,Anhui Provincial Key Laboratory of New Manufacturing Technology for Chinese Medicinal Decoction Pieces, Anhui University of Chinese Medicine, Hefei, 230012, China. .,Key Laboratory of Xin'An Medicine, Ministry of Education, Anhui Academy of Chinese Medicine, Hefei, 230012, China.
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Díez-Obrero V, Moratalla-Navarro F, Ibáñez-Sanz G, Guardiola J, Rodríguez-Moranta F, Obón-Santacana M, Díez-Villanueva A, Dampier CH, Devall M, Carreras-Torres R, Casey G, Moreno V. Transcriptome-Wide Association Study for Inflammatory Bowel Disease Reveals Novel Candidate Susceptibility Genes in Specific Colon Subsites and Tissue Categories. J Crohns Colitis 2021; 16:275-285. [PMID: 34286847 PMCID: PMC8864630 DOI: 10.1093/ecco-jcc/jjab131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND AND AIMS Genome-wide association studies [GWAS] for inflammatory bowel disease [IBD] have identified 240 risk variants. However, the benefit of understanding the genetic architecture of IBD remains to be exploited. Transcriptome-wide association studies [TWAS] associate gene expression with genetic susceptibility to disease, providing functional insight into risk loci. In this study, we integrate relevant datasets for IBD and perform a TWAS to nominate novel genes implicated in IBD genetic susceptibility. METHODS We applied elastic net regression to generate gene expression prediction models for the University of Barcelona and University of Virginia RNA sequencing project [BarcUVa-Seq] and correlated expression and disease association research [CEDAR] datasets. Together with Genotype-Tissue Expression project [GTEx] data, and GWAS results from about 60 000 individuals, we employed Summary-PrediXcan and Summary-MultiXcan for single and joint analyses of TWAS results, respectively. RESULTS BarcUVa-Seq TWAS revealed 39 novel genes whose expression in the colon is associated with IBD genetic susceptibility. They included expression markers for specific colon cell types. TWAS meta-analysis including all tissues/cell types provided 186 novel candidate susceptibility genes. Additionally, we identified 78 novel susceptibility genes whose expression is associated with IBD exclusively in immune (N = 19), epithelial (N = 25), mesenchymal (N = 22) and neural (N = 12) tissue categories. Associated genes were involved in relevant molecular pathways, including pathways related to known IBD therapeutics, such as tumour necrosis factor signalling. CONCLUSION These findings provide insight into tissue-specific molecular processes underlying IBD genetic susceptibility. Associated genes could be candidate targets for new therapeutics and should be prioritized in functional studies.
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Affiliation(s)
- Virginia Díez-Obrero
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, Barcelona, Spain,ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain,Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain,Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Ferran Moratalla-Navarro
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, Barcelona, Spain,Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain,Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Gemma Ibáñez-Sanz
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, Barcelona, Spain,ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain,Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain,Gastroenterology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, Spain
| | - Jordi Guardiola
- Gastroenterology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, Spain
| | | | - Mireia Obón-Santacana
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, Barcelona, Spain,ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain,Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Anna Díez-Villanueva
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, Barcelona, Spain,ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain,Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Christopher Heaton Dampier
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Matthew Devall
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Robert Carreras-Torres
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, Barcelona, Spain,ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain,Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, Barcelona, Spain,ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain,Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain,Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain,Corresponding author: Dr Victor Moreno, Catalan Institute of Oncology, Oncology Data Analytics Program, Hospital Duran i Reynals, Gran Via de l’Hospitalet, 199–203, 08908 L’Hospitalet de Llobregat (Barcelona) Spain. Tel: +34 932 607 434;
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Wang J, Lv M, He L, Wang X, Lan Y, Chen J, Chen M, Zhang C, Tang R, Zhou D, Deng X, Li J, Guo T, Price M, Yue B, Fan Z. Transcriptomic landscape of persistent diarrhoea in rhesus macaques and comparison with humans and mouse models with inflammatory bowel disease. Gene 2021; 800:145837. [PMID: 34274469 DOI: 10.1016/j.gene.2021.145837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/26/2021] [Accepted: 07/13/2021] [Indexed: 12/19/2022]
Abstract
Diarrhoea is a widespread disease in captive rhesus macaques (Macaca mulatta) and a small proportion of individuals may experience persistent diarrhoea. Persistent diarrhoea can lead to a compromised immune system, intestinal inflammation and malnutrition. We analyzed the blood transcriptomes of 10 persistent diarrhoeal and 12 healthy rhesus macaques to investigate the gene expression differences between the two groups. We identified 330 DEGs between persistent diarrhoeal and healthy rhesus macaques. The 211 up-regulated DEGs in the diarrhoeal group were mainly enriched in immune-related and interleukin-related categories. Among them, three interleukin (IL) 18 related DEGs (IL18, IL18R1, and IL18BP) played important roles in actively regulating pro-inflammatory responses. Interestingly, the up- and down-regulated DEGs were both enriched in the same immune-related categories. Thus, we applied a new method to examine the distribution of DEGs in all child categories. We found that interleukin and T cell related categories were mainly occupied by up-regulated DEGs, while immunoglobulin production and B cell related categories were enriched by down-regulated DEGs. We also compared rhesus macaque DEGs with the DEGs of inflammatory bowel disease (IBD) humans and IBD mouse models and found that 30-40% of macaque DEGs were shared with IBD humans and mouse models. In conclusion, our results showed that there were significant immune differences between persistent diarrhoeal rhesus macaques and healthy macaques, which was similar to the expression differences in IBD patients and mouse models.
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Affiliation(s)
- Jiao Wang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Mingyi Lv
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Lewei He
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Xinqi Wang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yue Lan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Jieyun Chen
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Minghui Chen
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Chunhui Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Ruixiang Tang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Dan Zhou
- The First People's Hospital of Neijiang, Neijiang 641000, Sichuan, China
| | - Xiaoyang Deng
- Lasa Sunshine Maternity Hospital, Lasa 850000, Xizang, China
| | - Jing Li
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Tao Guo
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Megan Price
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China.
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Pang B, Jin H, Liao N, Li J, Jiang C, Shao D, Shi J. Lactobacillus rhamnosus from human breast milk ameliorates ulcerative colitis in mice via gut microbiota modulation. Food Funct 2021; 12:5171-5186. [PMID: 33977948 DOI: 10.1039/d0fo03479g] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Gut microbiota imbalance is one of the major causes of ulcerative colitis (UC). L. rhamnosus SHA113 (LRS), a strain isolated from healthy human milk, influences the regulation of gut flora. This study aims to determine whether this strain can ameliorate UC by modulating gut microbiota. Mouse models of UC were established using C57BL/6Cnc mice with intragastric administration of 3.0% (w/v) dextran sodium sulfate (DSS). LRS was used to treat the mouse models of UC with 109 cfu mL-1 cell suspension via intragastric administration. To verify the effect of gut microbiota on UC, fecal microbiota collected from the mice after the treatment with LRS were also used to treat the UC mouse models (FMT). The severity of UC was evaluated based on body weight, colon length, disease activity index (DAI), and hematoxylin-eosin staining. The microbial composition was analyzed by 16S rRNA sequencing. The mRNA expression levels of cytokines, mucins, tight junction proteins, and antimicrobial peptides in the gastrointestinal tract were detected by quantitative real-time polymerase chain reaction. The short-chain fatty acid (SCFAs) in the cecal contents of all mice were quantitatively detected by gas chromatography and mass spectrometry. Both LRS and FMT exerted excellent therapeutic effects on UC, as evidenced by the reduction in body weight loss, colon length, and colon structural integrity, as well as the increase in the DAI (disease activity index). LRS and FMT treatments showed similar effects: (1) an increase of total SCFA production in the cecal contents and the abundance of gut microbial diversity and flora composition; (2) decreases in two genera (Parabacteroides and Escherichia/Shigella) related to the DAI and the enhancement of SCFAs and IL-10 positively related genera in the gut microbiota (Bilophila, Roseburia, Akkermansia, and Bifidobacterium); (3) downregulation of the expression of tumor necrosis factor-α, interleukin IL-6, and IL-1β, and upregulation of the expression of the anti-inflammatory cytokine IL-10; and (4) upregulation of the expression of mucins (Muc1-4) and tight junction protein ZO-1. Overall, L. rhamnosus SHA113 relieves UC via the regulation of gut microbiota: increases in SCFA-producing genera and decreases in UC-related genera. In addition, a single strain is sufficient to induce a significant change in the gut microbiota and exert therapeutic effects on UC.
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Affiliation(s)
- Bing Pang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China. NingLiao
| | - Han Jin
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China. NingLiao
| | - Ning Liao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China. NingLiao
| | - Junjun Li
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China. NingLiao
| | - Chunmei Jiang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China. NingLiao
| | - Dongyan Shao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China. NingLiao
| | - Junling Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi West Road, Xi'an, Shaanxi Province 710072, China. NingLiao
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Yu B, Yin YX, Tang YP, Wei KL, Pan ZG, Li KZ, Guo XW, Hu BL. Diagnostic and Predictive Value of Immune-Related Genes in Crohn's Disease. Front Immunol 2021; 12:643036. [PMID: 33936061 PMCID: PMC8085323 DOI: 10.3389/fimmu.2021.643036] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/30/2021] [Indexed: 12/23/2022] Open
Abstract
Abnormal immune cell infiltration is associated with the pathogenesis of Crohn’s disease (CD). This study aimed to determine the diagnostic and predictive value of immune-related genes in CD. Seven Gene Expression Omnibus datasets that analyzed the gene expression in CD tissues were downloaded. Single-sample gene set enrichment analysis (ssGSEA) was used to estimate the infiltration of the immune cells in CD tissues. Immune-related genes were screened by overlapping the immune-related genes with differentially expressed genes (DEGs). The protein-protein interaction (PPI) network was used to identify key immune-related DEGs. Diagnostic value of CD and predictive value of anti-TNFα therapy were analyzed. Immunohistochemical (IHC) assay was used to verify gene expression in CD tissues. There were significant differences among CD tissues, paired CD tissues, and normal intestinal tissues regarding the infiltration of immune cells. AQP9, CD27, and HVCN1 were identified as the key genes of the three sub-clusters in the PPI network. AQP9, CD27, and HVCN1 had mild to moderate diagnostic value in CD, and the diagnostic value of AQP9 was better than that of CD27 and HVCN1. AQP9 expression was decreased in CD after patients underwent anti-TNFα therapy, but no obvious changes were observed in non-responders. AQP9 had a moderate predictive value in patients who had undergone treatment. IHC assay confirmed that the expression of AQP9, CD27, and HVCN1 in CD tissues was higher than that in normal intestinal tissues, and AQP9, CD27 was correlated with the activity of CD. Immune-related genes, AQP9, CD27, and HVCN1 may act as auxiliary diagnostic indicators for CD, and AQP9 could serve as a promising predictive indicator in patients who underwent anti-TNF therapy.
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Affiliation(s)
- Bing Yu
- Department of Gastroenterology, Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yi-Xin Yin
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yan-Ping Tang
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Kang-Lai Wei
- Department of Gastroenterology, Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhi-Gang Pan
- Department of Gastroenterology, Third Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ke-Zhi Li
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Xian-Wen Guo
- Department of Gastroenterology, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Bang-Li Hu
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
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36
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Taman H, Fenton CG, Anderssen E, Florholmen J, Paulssen RH. DNA hypo-methylation facilitates anti-inflammatory responses in severe ulcerative colitis. PLoS One 2021; 16:e0248905. [PMID: 33793617 PMCID: PMC8016308 DOI: 10.1371/journal.pone.0248905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/06/2021] [Indexed: 12/16/2022] Open
Abstract
Severe ulcerative colitis (UC) is a potentially life-threatening disease with a potential colorectal cancer (CRC) risk. The aim of this study was to explore the relationship between transcriptomic and genome-wide DNA methylation profiles in a well-stratified, treatment-naïve severe UC patient population in order to define specific epigenetic changes that could be responsible for the grade of disease severity. Mucosal biopsies from treatment-naïve severe UC patients (n = 8), treatment-naïve mild UC (n = 8), and healthy controls (n = 8) underwent both whole transcriptome RNA-Seq and genome-wide DNA bisulfite- sequencing, and principal component analysis (PCA), cell deconvolutions and diverse statistical methods were applied to obtain a dataset of significantly differentially expressed genes (DEGs) with correlation to DNA methylation for severe UC. DNA hypo-methylation correlated with approximately 80% of all DEGs in severe UC when compared to mild UC. Enriched pathways of annotated hypo-methylated genes revealed neutrophil degranulation, and immuno-regulatory interactions of the lymphoid system. Specifically, hypo-methylated anti-inflammatory genes found for severe UC were IL10, SIGLEC5, CD86, CLMP and members of inflammasomes NLRP3 and NLRC4. Hypo-methylation of anti-inflammatory genes during severe UC implies an interplay between the epithelium and lamina propria in order to mitigate inflammation in the gut. The specifically DNA hypo-methylated genes found for severe UC can potentially be useful biomarkers for determining disease severity and in the development of new targeted treatment strategies for severe UC patients.
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Affiliation(s)
- Hagar Taman
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
- Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Christopher G. Fenton
- Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Endre Anderssen
- Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Jon Florholmen
- Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Ruth H. Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
- Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
- * E-mail:
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Lu JJ, Maimaiti M, Liu H, Liu WD, Hui WJ, Huang XL, Gao F. Potential Biomarkers Associated with Differential Manifestations of Ulcerative Colitis (UC) in Uyghur and Han Population in China. J Inflamm Res 2021; 14:7431-7441. [PMID: 35002277 PMCID: PMC8722688 DOI: 10.2147/jir.s335293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/23/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Ulcerative colitis (UC) is one of the main subtypes of inflammatory bowel disease (IBD). The incidence of UC in the Xinjiang region is relatively high in China and the manifestations of UC in Uyghur and Han patients are usually differential. This study aimed to identify potential biomarkers of UC. METHODS All miRNA and mRNA were extracted from the tissue samples obtained from participants in Xinjiang. Differential expression analysis was performed on all mRNAs and miRNAs. The target genes of miRNAs were predicted via three databases. The clusterProfiler package was used for GO and KEGG pathway enrichment analysis. RESULTS Preliminarily, four miRNAs and 15 genes were associated with the differential manifestations of UC in Uyghur and Han patients. Through the co-expression network construction and further screening in more samples, two miRNAs (hsa-miR-141-5p and hsa-miR-378a-5p) and three genes (ARNTL2, CLDN1 and SLC6A14) were found to be more crucial. These 15 genes were enriched in tight junction, NF-κB, and several other pathways. CONCLUSION Two miRNAs (hsa-miR-141-5p and hsa-miR-378a-5p) and three genes (ARNTL2, CLDN1, and SLC6A14) associated with the differential manifestations of UC in Uyghur and Han population were identified, which were potential biomarkers.
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Affiliation(s)
- Jia Jie Lu
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, People’s Republic of China
| | - Munila Maimaiti
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, People’s Republic of China
| | - Huan Liu
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, People’s Republic of China
| | - Wei Dong Liu
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, People’s Republic of China
| | - Wen Jia Hui
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, People’s Republic of China
| | - Xiao Ling Huang
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, People’s Republic of China
| | - Feng Gao
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, People’s Republic of China
- Correspondence: Feng Gao Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, No. 91 Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, People’s Republic of China Email
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Fenton CG, Taman H, Florholmen J, Sørbye SW, Paulssen RH. Transcriptional Signatures That Define Ulcerative Colitis in Remission. Inflamm Bowel Dis 2021; 27:94-105. [PMID: 32322884 PMCID: PMC7737162 DOI: 10.1093/ibd/izaa075] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND This study addresses whether existing specific transcriptional profiles can improve and support the current status of the definition of ulcerative colitis (UC) remission apart from the existing endoscopic, histologic, and laboratory scoring systems. For that purpose, a well-stratified UC patient population in remission was compared to active UC and control patients and was investigated by applying the next-generation technology RNA-Seq. METHODS Mucosal biopsies from patients in remission (n = 14), patients with active UC (n = 14), and healthy control patientss (n = 16) underwent whole-transcriptome RNA-Seq. Principal component analysis, cell deconvolution methods, gene profile enrichment, and pathway enrichment methods were applied to define a specific transcriptional signature of UC in remission. RESULTS Analyses revealed specific transcriptional signatures for UC in remission with increased expression of genes involved in O-glycosylation (MUC17, MUC3A, MUC5AC, MUC12, SPON1, B3GNT3), ephrin-mediated repulsion of cells (EFNB2E, EFNA3, EPHA10, EPHA1), GAP junction trafficking (TUBA1C, TUBA4A, TUBB4B, GJB3, CLTB), and decreased expression of several toll-like receptors (TLR1, TLR3, TLR5, TLR6). CONCLUSIONS This study reveals specific transcriptional signatures for remission. Partial restoration and improvement of homeostasis in the epithelial mucus layer and revival of immunological functions were observed. A clear role for bacterial gut flora composition can be implied. The results can be useful for the development of treatment strategies for UC in remission and may be useful targets for further investigations aiming to predict the outcome of UC in the future.
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Affiliation(s)
- Christopher G Fenton
- Department of Clinical Medicine,Genomics Support Centre Tromsø, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Hagar Taman
- Department of Clinical Medicine,Genomics Support Centre Tromsø, UiT-The Arctic University of Norway, Tromsø, Norway
- Department of Clinical Medicine, Gastroenterology and Nutrition Research Group, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Jon Florholmen
- Department of Clinical Medicine, Gastroenterology and Nutrition Research Group, UiT-The Arctic University of Norway, Tromsø, Norway
- Department of Medical Gastroenterology, University Hospital of North Norway, Tromsø, Norway
| | - Sveinung W Sørbye
- §Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway
| | - Ruth H Paulssen
- Department of Clinical Medicine,Genomics Support Centre Tromsø, UiT-The Arctic University of Norway, Tromsø, Norway
- Department of Clinical Medicine, Gastroenterology and Nutrition Research Group, UiT-The Arctic University of Norway, Tromsø, Norway
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Identification of Differential Intestinal Mucosa Transcriptomic Biomarkers for Ulcerative Colitis by Bioinformatics Analysis. DISEASE MARKERS 2020; 2020:8876565. [PMID: 33144895 PMCID: PMC7596466 DOI: 10.1155/2020/8876565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/05/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023]
Abstract
Background Ulcerative colitis (UC) is a complicated disease caused by the interaction between genetic and environmental factors that affect mucosal homeostasis and triggers inappropriate immune response. The purpose of the study was to identify significant biomarkers with potential therapeutic targets and the underlying mechanisms. Methods The gene expression profiles of GSE48958, GSE73661, and GSE59071 are from the GEO database. Differentially expressed genes (DEGs) were screened by the GEO2R tool. Next, the Database for Annotation, Visualization and Integrated Discovery (DAVID) was applied to analyze gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Then, protein-protein interaction (PPI) was visualized by Cytoscape with Search Tool for the Retrieval of Interacting Genes (STRING). Results There were a total of 128 common DEGs genes, including 86 upregulated genes enriched in extracellular space, regulation of inflammatory response, chemokine-mediated signaling pathway, response to lipopolysaccharide, and cell proliferation, while 42 downregulated genes enriched in the integral component of the membrane, the integral component of the plasma membrane, apical plasma membrane, symporter activity, and chloride channel activity. The KEGG pathway analysis results demonstrated that DEGs were particularly enriched in cytokine-cytokine receptor interaction, TNF signaling pathway, chemokine signaling pathway, pertussis, and rheumatoid arthritis. 18 central modules of the PPI networks were selected with Cytotype MCODE. Furthermore, 18 genes were found to significantly enrich in the extracellular space, inflammatory response, chemokine-mediated signaling pathway, TNF signaling pathway, regulation of cell proliferation, and immune response via reanalysis of DAVID. Conclusion The study identified DEGs, key target genes, functional pathways, and pathway analysis of UC, which may provide potential molecular targets and diagnostic biomarkers for UC.
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Meir M, Salm J, Fey C, Schweinlin M, Kollmann C, Kannapin F, Germer CT, Waschke J, Beck C, Burkard N, Metzger M, Schlegel N. Enteroids Generated from Patients with Severe Inflammation in Crohn's Disease Maintain Alterations of Junctional Proteins. J Crohns Colitis 2020; 14:1473-1487. [PMID: 32342109 DOI: 10.1093/ecco-jcc/jjaa085] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND The mechanisms underlying loss of intestinal epithelial barrier [IEB] function in Crohn's disease [CD] are poorly understood. We tested whether human enteroids generated from isolated intestinal crypts of CD patients serve as an appropriate in vitro model to analyse changes of IEB proteins observed in patients' specimens. METHODS Gut samples from CD patients and healthy individuals who underwent surgery were collected. Enteroids were generated from intestinal crypts and analyses of junctional proteins in comparison to full wall samples were performed. RESULTS Histopathology confirmed the presence of CD and the extent of inflammation in intestinal full wall sections. As revealed by immunostaining and Western blot analysis, profound changes in expression patterns of tight junction, adherens junction and desmosomal proteins were observed in full wall specimens when CD was present. Unexpectedly, when enteroids were generated from specimens of CD patients with severe inflammation, alterations of most tight junction proteins and the majority of changes in desmosomal proteins but not E-cadherin were maintained under culture conditions. Importantly, these changes were maintained without any additional stimulation of cytokines. Interestingly, qRT-PCR demonstrated that mRNA levels of junctional proteins were not different when enteroids from CD patients were compared to enteroids from healthy controls. CONCLUSIONS These data indicate that enteroids generated from patients with severe inflammation in CD maintain some characteristics of intestinal barrier protein changes on a post-transcriptional level. The enteroid in vitro model represents an appropriate tool to gain further cellular and molecular insights into the pathogenesis of barrier dysfunction in CD.
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Affiliation(s)
- Michael Meir
- Department of General, Visceral, Transplant, Vascular and Pediatric Surgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Jonas Salm
- Department of General, Visceral, Transplant, Vascular and Pediatric Surgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Christina Fey
- Chair for Tissue Engineering and Regenerative Medicine, Wuerzburg, Germany
| | | | - Catherine Kollmann
- Department of General, Visceral, Transplant, Vascular and Pediatric Surgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Felix Kannapin
- Department of General, Visceral, Transplant, Vascular and Pediatric Surgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Christoph-Thomas Germer
- Department of General, Visceral, Transplant, Vascular and Pediatric Surgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Jens Waschke
- Institute of Anatomy and Cell Biology, Ludwig-Maximilians-University, Munich, Germany
| | | | - Natalie Burkard
- Department of General, Visceral, Transplant, Vascular and Pediatric Surgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Marco Metzger
- Chair for Tissue Engineering and Regenerative Medicine, Wuerzburg, Germany.,Fraunhofer Institute for Silicate Research ISC, Translational Centre for Regenerative Therapies TLC-RT, Wuerzburg, Germany
| | - Nicolas Schlegel
- Department of General, Visceral, Transplant, Vascular and Pediatric Surgery, University Hospital Wuerzburg, Wuerzburg, Germany
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Florholmen JR, Johnsen KM, Meyer R, Olsen T, Moe ØK, Tandberg P, Gundersen MD, Kvamme JM, Johnsen K, Løitegård T, Raschpichler G, Vold C, Sørbye SW, Goll R. Discovery and validation of mucosal TNF expression combined with histological score - a biomarker for personalized treatment in ulcerative colitis. BMC Gastroenterol 2020; 20:321. [PMID: 33008302 PMCID: PMC7532085 DOI: 10.1186/s12876-020-01447-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022] Open
Abstract
Background There are no accurate markers that can predict clinical outcome in ulcerative colitis at time of diagnosis. The aim of this study was to explore a comprehensive data set to identify and validate predictors of clinical outcome in the first year following diagnosis. Methods Treatment naive-patients with ulcerative colitis were included at time of initial diagnosis from 2004 to 2014, followed by a validation study from 2014 to 2018. Patients were treated according to clinical guidelines following a standard step-up regime. Patients were categorized according to the treatment level necessary to achieve clinical remission: mild, moderate and severe. The biopsies were assessed by Robarts histopathology index (RHI) and TNF gene transcripts. Results We included 66 patients in the calibration cohort and 89 patients in the validation. Mucosal TNF transcripts showed high test reliability for predicting severe outcome in UC. When combined with histological activity (RHI) scores the test improved its diagnostic reliability. Based on the cut-off values of mucosal TNF and RHI scores from the calibration cohort, the combined test had still high reliability in the validation cohort (specificity 0.99, sensitivity 0.44, PPV 0.89, NPV 0.87) and a diagnostic odds-ratio (DOR) of 54. Conclusions The combined test using TNF transcript and histological score at debut of UC can predict severe outcome and the need for anti-TNF therapy with a high level of precision. These validated data may be of great clinical utility and contribute to a personalized medical approach with the possibility of top-down treatment for selected patients.
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Affiliation(s)
- Jon R Florholmen
- Research Group of Gastroenterology and Nutrition, Department of Clinical Medicine, University of Tromsø, Tromsø, Norway.,Department of Gastroenterology, Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway.,Department of Internal Medicine, Vestre Viken Hospital, Hønefoss, Norway
| | - Kay-Martin Johnsen
- Research Group of Gastroenterology and Nutrition, Department of Clinical Medicine, University of Tromsø, Tromsø, Norway. .,Department of Gastroenterology, Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway.
| | - Renate Meyer
- Research Group of Gastroenterology and Nutrition, Department of Clinical Medicine, University of Tromsø, Tromsø, Norway
| | - Trine Olsen
- Research Group of Gastroenterology and Nutrition, Department of Clinical Medicine, University of Tromsø, Tromsø, Norway.,Department of Gastroenterology, Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Øystein K Moe
- Research Group of Gastroenterology and Nutrition, Department of Clinical Medicine, University of Tromsø, Tromsø, Norway.,Department of Internal Medicine, Hammerfest Hospital, Hammerfest, Norway
| | - Petter Tandberg
- Department of Internal Medicine, Vestre Viken Hospital, Hønefoss, Norway
| | - Mona D Gundersen
- Research Group of Gastroenterology and Nutrition, Department of Clinical Medicine, University of Tromsø, Tromsø, Norway.,Department of Gastroenterology, Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Jan-Magnus Kvamme
- Research Group of Gastroenterology and Nutrition, Department of Clinical Medicine, University of Tromsø, Tromsø, Norway.,Department of Gastroenterology, Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Knut Johnsen
- Research Group of Gastroenterology and Nutrition, Department of Clinical Medicine, University of Tromsø, Tromsø, Norway.,Department of Internal Medicine, Hammerfest Hospital, Hammerfest, Norway
| | - Terje Løitegård
- Department of Gastroenterology, Vestre Viken Hospital, Drammen, Norway
| | | | - Cecilia Vold
- Department of Gastroenterology, Nordland Hospital, Bodø, Norway
| | - Sveinung W Sørbye
- Department of Pathology, University Hospital of North Norway, Tromsø, Norway
| | - Rasmus Goll
- Research Group of Gastroenterology and Nutrition, Department of Clinical Medicine, University of Tromsø, Tromsø, Norway.,Department of Gastroenterology, Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
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Eshelman MA, Harris L, Deiling S, Koltun WA, Jeganathan NA, Yochum GS. Transcriptomic analysis of ileal tissue from Crohn's disease patients identifies extracellular matrix genes that distinguish individuals by age at diagnosis. Physiol Genomics 2020; 52:478-484. [PMID: 32866088 DOI: 10.1152/physiolgenomics.00062.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Crohn's disease (CD) is a debilitating gastrointestinal (GI) disorder that can impact the entirety of the GI tract. While substantial progress has been made in the medical management of CD, it remains incurable, frequently relapses, and is a significant financial and medical burden. The pathophysiology of CD is not well understood, but it is thought to arise in genetically susceptible individuals upon an environmental insult. Further elucidation of the disease etiology promises to expose additional therapeutic avenues, with the hope of reducing the burden of CD. One approach to understanding disease pathophysiology is to identify clinically relevant molecular disease subsets by using transcriptomics. In this report, we use hierarchical clustering of the ileal transcriptomes of 34 patients and identify two CD subsets. Clinically, these clusters differed in the age of the patients at CD diagnosis, suggesting that age of onset affects disease pathophysiology. The clusters were segregated by three major gene ontology categories: developmental processes, ion homeostasis, and the immune response. Of the genes constituting the immune system category, expression of extracellular matrix-associated genes, COL4A1, S100A9, ADAMTS2, SERPINE1, and FCN1, exhibits the strongest correlation with an individual's age at CD diagnosis. Together these findings demonstrate that transcriptional profiling is a powerful approach to subclassify CD patients.
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Affiliation(s)
- Melanie A Eshelman
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Leonard Harris
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Sue Deiling
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Walter A Koltun
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - N Arjun Jeganathan
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Gregory S Yochum
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania.,Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
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Abstract
OBJECTIVES A healed intestinal mucosa is the aim of therapy in acute ulcerative colitis (UC). Disruption of mucosal wound healing may lead to severe complications including intestinal fibrosis. This study examined mucosal gene expression in the healing process of acute UC with a special focus on known mediators of fibrosis. METHODS Endoscopic biopsies from patients with acute, moderate to severe UC were analyzed with a quantitative polymerase chain reaction array for 84 genes involved in fibrosis pathways. All patients were treated with infliximab (anti- tumor necrosis factor). Biopsies were taken before therapy and when disease remission was reached, defined as a Mayo score of ≤2, with an endoscopic subscore of 0 or 1. A healthy control group was included. Immunostaining of matrix metallopeptidase 9 and smooth muscle actin was performed. RESULTS Mucosal biopsies from acute UC (n = 28), remission UC (n = 28), and healthy controls (n = 13) were analyzed. Fibrosis and extracellular matrix-associated genes were upregulated in the endoscopically healed UC mucosa vs controls, with collagen type III alpha 1 chain, actin alpha 2, lysyl oxidase, TIMP metallopeptidase inhibitor 3, and caveolin 1 uniquely showing no overlap with acute disease. Pro- and antifibrotic mediators (interleukin [IL]13 receptor subunit alpha 2, IL1B, IL10, tumor necrosis factor, snail family transcriptional repressor 1, and C-C motif chemokine ligand 2) were upregulated in both acute and healed UC compared with controls. An attenuated pattern of the canonical transforming growth factor beta (TGFB) pathway was observed in acute UC and to a lesser extent in the healed mucosa, except for TGFB2, which was enhanced. DISCUSSION The endoscopically healed mucosa of UC showed a persisting dysregulation of fibrosis-associated mediators compared with controls, including extracellular matrix remodeling, profibrotic cytokines, and TGFB signaling pathways.
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Olli KE, Rapp C, O’Connell L, Collins CB, McNamee EN, Jensen O, Jedlicka P, Allison KC, Goldberg MS, Gerich ME, Frank DN, Ir D, Robertson CE, Evans CM, Aherne CM. Muc5ac Expression Protects the Colonic Barrier in Experimental Colitis. Inflamm Bowel Dis 2020; 26:1353-1367. [PMID: 32385500 PMCID: PMC7441107 DOI: 10.1093/ibd/izaa064] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The mucus gel layer (MGL) lining the colon is integral to exclusion of bacteria and maintaining intestinal homeostasis in health and disease. Some MGL defects allowing bacteria to directly contact the colonic surface are commonly observed in ulcerative colitis (UC). The major macromolecular component of the colonic MGL is the secreted gel-forming mucin MUC2, whose expression is essential for homeostasis in health. In UC, another gel-forming mucin, MUC5AC, is induced. In mice, Muc5ac is protective during intestinal helminth infection. Here we tested the expression and functional role of MUC5AC/Muc5ac in UC biopsies and murine colitis. METHODS We measured MUC5AC/Muc5ac expression in UC biopsies and in dextran sulfate sodium (DSS) colitis. We performed DSS colitis in mice deficient in Muc5ac (Muc5ac-/-) to model the potential functional role of Muc5ac in colitis. To assess MGL integrity, we quantified bacterial-epithelial interaction and translocation to mesenteric lymph nodes. Antibiotic treatment and 16S rRNA gene sequencing were performed to directly investigate the role of bacteria in murine colitis. RESULTS Colonic MUC5AC/Muc5ac mRNA expression increased significantly in active UC and murine colitis. Muc5ac-/- mice experienced worsened injury and inflammation in DSS colitis compared with control mice. This result was associated with increased bacterial-epithelial contact and translocation to the mesenteric lymph nodes. However, no change in microbial abundance or community composition was noted. Antibiotic treatment normalized colitis severity in Muc5ac-/- mice to that of antibiotic-treated control mice. CONCLUSIONS MUC5AC/Muc5ac induction in the acutely inflamed colon controls injury by reducing bacterial breach of the MGL.
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Affiliation(s)
- Kristine E Olli
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Caroline Rapp
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Lauren O’Connell
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Colm B Collins
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Digestive Health Institute, Children’s Hospital Colorado, Aurora, Colorado, USA
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Eoin N McNamee
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
- Kathleen Lonsdale Institute for Human Health Research, Department of Biology, Maynooth University, County Kildare, Ireland
| | - Owen Jensen
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Paul Jedlicka
- Department of Pathology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kristen C Allison
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Matthew S Goldberg
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Mark E Gerich
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Daniel N Frank
- Department of Medicine, Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Diana Ir
- Department of Medicine, Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Charles E Robertson
- Department of Medicine, Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Christopher M Evans
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Carol M Aherne
- Department of Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, Colorado, USA
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
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Lee HS, Vancamelbeke M, Verstockt S, Wilms T, Verstockt B, Sabino J, Ferrante M, Vermeire S, Cleynen I. Molecular Changes in the Non-Inflamed Terminal Ileum of Patients with Ulcerative Colitis. Cells 2020; 9:cells9081793. [PMID: 32731480 PMCID: PMC7464680 DOI: 10.3390/cells9081793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/19/2022] Open
Abstract
Ulcerative colitis is a chronic inflammatory disease confined to the colon. Although the etiopathogenesis remains unknown, small bowel dysfunctions like histological and permeability alterations have been described in ulcerative colitis. We evaluated the molecular gene signature in the non-inflamed terminal ileum of 36 ulcerative colitis patients (7 active, with Mayo endoscopic subscore ≥2, and 29 inactive) as compared to 15 non-inflammatory bowel disease controls. Differential gene expression analysis with DESeq2 showed distinct expression patterns depending on disease activity and maximal disease extent. We found 84 dysregulated genes in patients with active extensive colitis and 20 in inactive extensive colitis, compared to controls. There was an overlap of 5 genes: REG1B, REG1A, MUC4, GRAMD2, and CASP10. In patients with left-sided colitis, ileal gene expression levels were similar to controls. Based on gene co-expression analysis, ileal changes in active ulcerative colitis patients were related to immune functions. The ileal changes in the inactive ulcerative colitis subjects converged into the maintenance of the intestinal barrier through increased mitochondrial function and dampened immune functions. In conclusion, we identified molecular changes in the non-inflamed ileum of ulcerative colitis that are dependent on colonic inflammation.
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Affiliation(s)
- Ho-Su Lee
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; (H.-S.L.); (S.V.); (T.W.)
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Maaike Vancamelbeke
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
| | - Sare Verstockt
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; (H.-S.L.); (S.V.); (T.W.)
| | - Tom Wilms
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; (H.-S.L.); (S.V.); (T.W.)
| | - Bram Verstockt
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - João Sabino
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Marc Ferrante
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Séverine Vermeire
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Isabelle Cleynen
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; (H.-S.L.); (S.V.); (T.W.)
- Correspondence: ; Tel.: +32-1637-7480
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Escudero-Hernández C, Münch A, Østvik AE, Granlund AVB, Koch S. The Water Channel Aquaporin 8 is a Critical Regulator of Intestinal Fluid Homeostasis in Collagenous Colitis. J Crohns Colitis 2020; 14:962-973. [PMID: 32016376 PMCID: PMC7393183 DOI: 10.1093/ecco-jcc/jjaa020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIMS Diarrhoea is a common, debilitating symptom of gastrointestinal disorders. Pathomechanisms probably involve defects in trans-epithelial water transport, but the role of aquaporin [AQP] family water channels in diarrhoea-predominant diseases is unknown. We investigated the involvement of AQPs in the pathobiology of collagenous colitis [CC], which features chronic, watery diarrhoea despite overtly normal intestinal epithelial cells [IECs]. METHODS We assessed the expression of all AQP family members in mucosal samples of CC patients before and during treatment with the corticosteroid drug budesonide, steroid-refractory CC patients and healthy controls. Samples were analysed by genome-wide mRNA sequencing [RNA-seq] and quantitative real-time PCR [qPCR]. In some patients, we performed tissue microdissection followed by RNA-seq to explore the IEC-specific CC transcriptome. We determined changes in the protein levels of the lead candidates in IEC by confocal microscopy. Finally, we investigated the regulation of AQP expression by corticosteroids in model cell lines. RESULTS Using qPCR and RNA-seq, we identified loss of AQP8 expression as a hallmark of active CC, which was reverted by budesonide treatment in steroid-responsive but not refractory patients. Consistently, decreased AQP8 mRNA and protein levels were observed in IECs of patients with active CC, and steroid drugs increased AQP8 expression in model IECs. Moreover, low APQ8 expression was strongly associated with higher stool frequency in CC patients. CONCLUSION Down-regulation of epithelial AQP8 may impair water resorption in active CC, resulting in watery diarrhoea. Our results suggest that AQP8 is a potential drug target for the treatment of diarrhoeal disorders.
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Affiliation(s)
| | - Andreas Münch
- Department of Biomedical and Clinical Sciences [BKV), Linköping University, Linköping, Sweden,Division of Gastroenterology and Hepatology, Department of Biomedical and Clinical Sciences [BKV), Faculty of Health Science, Linköpings University, Linköping, Sweden,Corresponding authors: Andreas Münch, MD PhD, Division of Gastroenterology and Hepatology, Department of Biomedical and Clinical Sciences [BKV), Faculty of Health Sciences, Linköping University, Linköping, 58185, Sweden. Tel: +46 100130000; ; Stefan Koch, PhD, BKV/MII—Plan 13, s-581 83 Linköping, Sweden. Tel: +46 13 282969;
| | - Ann-Elisabet Østvik
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway,Department of Gastroenterology and Hepatology, St Olav’s University Hospital, Trondheim, Norway,Clinic of Medicine, St Olav’s University Hospital, Trondheim, Norway
| | - Atle van Beelen Granlund
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway,Clinic of Medicine, St Olav’s University Hospital, Trondheim, Norway,Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Stefan Koch
- Department of Biomedical and Clinical Sciences [BKV), Linköping University, Linköping, Sweden,Wallenberg Centre for Molecular Medicine (WCMM), Linköping University, Linköping, Sweden,Corresponding authors: Andreas Münch, MD PhD, Division of Gastroenterology and Hepatology, Department of Biomedical and Clinical Sciences [BKV), Faculty of Health Sciences, Linköping University, Linköping, 58185, Sweden. Tel: +46 100130000; ; Stefan Koch, PhD, BKV/MII—Plan 13, s-581 83 Linköping, Sweden. Tel: +46 13 282969;
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47
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Remote ischemic conditioning in active ulcerative colitis: An explorative randomized clinical trial. Sci Rep 2020; 10:9537. [PMID: 32533085 PMCID: PMC7293253 DOI: 10.1038/s41598-020-65692-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023] Open
Abstract
Remote ischemic conditioning (RIC) by repetitive brief periods of limb ischemia and reperfusion renders organs more resistant to ischemic injury. The protection is partly through down-regulation of the inflammatory response. Our aim was to investigate the clinical and anti-inflammatory effects of RIC in patients with active ulcerative colitis (UC). We included 22 patients with active UC in this explorative, randomized, sham-controlled clinical trial. The patients were randomly assigned 1:1 to RIC (induced in the arm through four cycles of 5-min inflation and 5-min deflation of a blood-pressure cuff) or sham (incomplete inflation of the blood-pressure cuff) once daily for 10 days. Outcome variables were measured at baseline and on day 11. When compared with sham, RIC did not affect inflammation in the UC patients measured by fecal calprotectin, plasma C-reactive protein, Mayo Score, Mayo Endoscopic Subscore, Nancy Histological Index or inflammatory cytokines involved in UC and RIC. The mRNA and miRNA expression profiles in the UC patients were measured by RNA sequencing and multiplexed hybridization, respectively, but were not significantly affected by RIC. We used the Langendorff heart model to assess activation of the organ protective mechanism induced by RIC, but could not confirm activation of the organ protective mechanism in the UC patients.
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48
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Cormican S, Griffin MD. Human Monocyte Subset Distinctions and Function: Insights From Gene Expression Analysis. Front Immunol 2020; 11:1070. [PMID: 32582174 PMCID: PMC7287163 DOI: 10.3389/fimmu.2020.01070] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/04/2020] [Indexed: 12/30/2022] Open
Abstract
Monocytes are a highly plastic innate immune cell population that displays significant heterogeneity within the circulation. Distinct patterns of surface marker expression have become accepted as a basis for distinguishing three monocyte subsets in humans. These phenotypic subsets, termed classical, intermediate and nonclassical, have also been demonstrated to differ in regard to their functional properties and disease associations when studied in vitro and in vivo. Nonetheless, for the intermediate monocyte subset in particular, functional experiments have yielded conflicting results and some studies point to further levels of heterogeneity. Developments in genetic sequencing technology have provided opportunities to more comprehensively explore the phenotypic and functional differences among conventionally-recognized immune cell subtypes as well as the potential to identify novel subpopulations. In this review, we summarize the transcriptomic evidence in support of the existence of three separate monocyte subsets. We also critically evaluate the insights into subset functional distinctions that have been garnered from monocyte gene expression analysis and the potential utility of such studies to unravel subset-specific functional changes which arise in disease states.
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Affiliation(s)
- Sarah Cormican
- Regenerative Medical Institute (REMEDI) at CÚRAM Centre for Research in Medical Devices, School of Medicine, College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway, Ireland.,Nephrology Services, Galway University Hospitals, Saolta University Health Group, Galway, Ireland
| | - Matthew D Griffin
- Regenerative Medical Institute (REMEDI) at CÚRAM Centre for Research in Medical Devices, School of Medicine, College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway, Ireland.,Nephrology Services, Galway University Hospitals, Saolta University Health Group, Galway, Ireland
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49
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Estill M, Hauser R, Nassan FL, Moss A, Krawetz SA. The effects of di-butyl phthalate exposure from medications on human sperm RNA among men. Sci Rep 2019; 9:12397. [PMID: 31455814 PMCID: PMC6711971 DOI: 10.1038/s41598-019-48441-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/05/2019] [Indexed: 02/08/2023] Open
Abstract
Endocrine disruptors, such as phthalates, are suspected of affecting reproductive function. The Mesalamine and Reproductive Health Study (MARS) was designed to address the physiological effect of in vivo phthalate exposure on male reproduction in patients with Inflammatory Bowel Disease (IBD). As part of this effort, the effect on sperm RNAs to DBP exposure were longitudinally assessed using a cross-over cross-back binary design of high or background, exposures to DBP. As the DBP level was altered, numerous sperm RNA elements (REs) were differentially expressed, suggesting that exposure to or removal from high DBP produces effects that require longer than one spermatogenic cycle to resolve. In comparison, small RNAs were minimally affected by DBP exposure. While initial study medication (high or background) implicates different biological pathways, initiation on the high-DBP condition activated oxidative stress and DNA damage pathways. The negative correlation of REs with specific genomic repeats suggests a regulatory role. Using ejaculated sperm, this work provides insight into the male germline's response to phthalate exposure.
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Affiliation(s)
- Molly Estill
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Russ Hauser
- Vincent Memorial Obstetrics and Gynecology Service, Massachusetts General Hospital, Harvard Medical School, and Departments of Environmental Health and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Feiby L Nassan
- Departments of Environmental Health and Nutrition, Harvard T. H. Chan School of Public Health, MA, 02115, USA
| | - Alan Moss
- Department of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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50
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Conserved transcriptomic profile between mouse and human colitis allows unsupervised patient stratification. Nat Commun 2019; 10:2892. [PMID: 31253778 PMCID: PMC6598981 DOI: 10.1038/s41467-019-10769-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023] Open
Abstract
Clinical manifestations and response to therapies in ulcerative colitis (UC) are heterogeneous, yet patient classification criteria for tailored therapies are currently lacking. Here, we present an unsupervised molecular classification of UC patients, concordant with response to therapy in independent retrospective cohorts. We show that classical clustering of UC patient tissue transcriptomic data sets does not identify clinically relevant profiles, likely due to associated covariates. To overcome this, we compare cross-sectional human data sets with a newly generated longitudinal transcriptome profile of murine DSS-induced colitis. We show that the majority of colitis risk-associated gene expression peaks during the inflammatory rather than the recovery phase. Moreover, we achieve UC patient clustering into two distinct transcriptomic profiles, differing in neutrophil-related gene activation. Notably, 87% of patients in UC1 cluster are unresponsive to two most widely used biological therapies. These results demonstrate that cross-species comparison enables stratification of patients undistinguishable by other molecular approaches.
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