1
|
Wang M, He X. Mendelian randomization analysis reveals causal associations of inflammatory bowel disease with Spondylarthritis. Gene 2024; 902:148170. [PMID: 38237812 DOI: 10.1016/j.gene.2024.148170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/28/2023] [Accepted: 01/15/2024] [Indexed: 01/28/2024]
Abstract
OBJECTIVE Inflammatory bowel disease (IBD) is strongly associated with Spondylarthritis (SpA), but the causal relationship remains unclear. This study explores the causal associations between IBD (Crohn's disease [CD] and ulcerative colitis [UC]) and several common subtypes of SpA (Ankylosing Spondylitis [AS], Psoriatic Arthritis [PsA], and Reactive Arthritis [ReA]), using bidirectional two-sample Mendelian randomization (TSMR). METHODS The causal effects of genetically predicted IBD on AS, PsA, and ReA were firstly investigated in this forward study. The causal effects from AS, PsA, and ReA on IBD were analyzed in the reverse MR. Inverse variance weighted, weighted median, and MR-Egger were applied in the MR analyses. The pleiotropic effects, heterogeneity, and leave-one-out sensitivity analysis were also evaluated. RESULTS The forward MR analysis demonstrated that IBD increased risk for AS (OR:1.278; P = 1.273 × 10-5), PsA (OR:1.192; P = 1.690 × 10-5), and ReA (OR:1.106; P = 1.524 × 10-3). Among them, CD increased risk of AS (OR:1.196; P = 3.424 × 10-4), PsA (OR:1.101; P = 1.537 × 10-3), ReA (OR:1.079; P = 6.321 × 10-3) whereas UC increased risk of AS (OR:1.166; P = 2.727 × 10-2), PsA (OR:1.110; P = 1.944 × 10-2), and ReA (OR:1.091; P = 1.768 × 10-2). The reverse-direction MR disclosed no notable association; neither was any evidence of pleiotropy detected. CONCLUSION Our study verifies a causal effect of IBD to AS, PsA as well as ReA, but not vice versa. This might bring new insights for the management of IBD and SpA in clinical practice.
Collapse
Affiliation(s)
- Min Wang
- The Affiliated Hospital of Nanjing University of Chinese Medicine, Department of Rheumatology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, China
| | - Xiaojin He
- The Affiliated Hospital of Nanjing University of Chinese Medicine, Department of Rheumatology, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, China.
| |
Collapse
|
2
|
Koike Y, Yin C, Sato Y, Nagano Y, Yamamoto A, Kitajima T, Shimura T, Kawamura M, Matsushita K, Okugawa Y, Amano K, Okita Y, Ohi M, Inoue M, Uchida K, Hirayama M, Toiyama Y. Promoter methylation levels of microRNA-124 in non-neoplastic rectal mucosa as a potential biomarker for ulcerative colitis-associated colorectal cancer in pediatric-onset patients. Surg Today 2024; 54:347-355. [PMID: 37610628 DOI: 10.1007/s00595-023-02738-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/25/2023] [Indexed: 08/24/2023]
Abstract
PURPOSE To determine the methylation level of the miR-124 promoter in non-neoplastic rectal mucosa of patients with pediatric-onset ulcerative colitis (UC) to predict UC-associated colorectal cancer (UC-CRC). METHODS Between 2005 and 2017, non-neoplastic rectal tissue specimens were collected from 86 patients with UC, including 13 patients with UC-CRC; cancer tissues were obtained from the latter group. The methylation status of the miR-124 promoter was quantified using bisulfite pyrosequencing and compared between pediatric- and adult-onset UC patients. RESULTS Patients with pediatric-onset UC experienced a significantly shorter disease duration than those with adult-onset UC. The levels of miR-124 promoter methylation in non-neoplastic rectal mucosa were positively correlated with the age at the diagnosis and duration of UC. The rate of increase in miR-124 methylation was accelerated in patients with pediatric-onset UC compared to those with adult-onset UC. Furthermore, the miR-124 methylation levels in non-neoplastic rectal mucosa were significantly higher in patients with UC-CRC than in those with UC alone (P = 0.02). A receiver operating characteristic analysis revealed that miR-124 methylation in non-neoplastic tissue discriminated between patients with pediatric-onset UC with or without CRC. CONCLUSION miR-124 methylation in non-neoplastic rectal mucosa may be a useful biomarker for identifying patients with pediatric-onset UC who face the highest risk of developing UC-CRC.
Collapse
Affiliation(s)
- Yuhki Koike
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan.
| | - Chengzeng Yin
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Yuki Sato
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Yuka Nagano
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Akira Yamamoto
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Takahito Kitajima
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
- Department of Genomic Medicine, Mie University Hospital, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Tadanobu Shimura
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Mikio Kawamura
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Kohei Matsushita
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Yoshinaga Okugawa
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
- Department of Genomic Medicine, Mie University Hospital, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Keishiro Amano
- Department of Pediatrics, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Yoshiki Okita
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Masaki Ohi
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Mikihiro Inoue
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Keiichi Uchida
- Department of Surgery, Mie Prefectural General Medical Center, 5450-132, Hinaga, Yokkaichi, Mie, 510-0885, Japan
| | - Masahiro Hirayama
- Department of Pediatrics, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan
| | - Yuji Toiyama
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8507, Japan.
| |
Collapse
|
3
|
Zamani M, Alizadeh-Tabari S, Murad MH, Ananthakrishnan AN, Malekzadeh R, Talley NJ. Meta-analysis: Risk of pancreatic cancer in patients with inflammatory bowel disease. Aliment Pharmacol Ther 2024; 59:918-927. [PMID: 38372406 DOI: 10.1111/apt.17919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 01/22/2024] [Accepted: 02/12/2024] [Indexed: 02/20/2024]
Abstract
BACKGROUND Studies exploring the association between inflammatory bowel disease (IBD) and pancreatic cancer have reported inconsistent results. AIMS To provide a comprehensive overview of the risk of pancreatic cancer development in patients with IBD. METHODS We searched Embase, PubMed, Scopus and ProQuest from inception to 31 October 2023. We included population-based cohort studies examining the risk of incident pancreatic cancer in adult patients with IBD compared to the non-IBD population. We also retrieved Mendelian randomisation (MR) studies investigating the relationship of IBD with pancreatic cancer risk. We conducted random-effects meta-analyses and provided pooled relative risks (RRs) with 95% confidence intervals (CIs). RESULTS We included 13 studies. Among 11 cohort studies, the risk of developing pancreatic cancer increased by 79% in patients with IBD (RR = 1.79 [95% CI: 1.16-2.75]; I2 = 95.7%). Patients either with Crohn's disease (RR = 1.42 [95% CI: 1.24-1.63]) or ulcerative colitis (RR = 1.50 [95% CI: 1.17-1.92]) had increased risk (p for interaction = 0.72). The annual incidence of pancreatic cancer potentially attributable to IBD increased by 55 cases (95% CI: 17-103) per million. Two MR studies demonstrated that genetic liability to IBD was associated with an increased risk of pancreatic cancer. CONCLUSIONS Our results suggest a moderate increase in the risk of pancreatic cancer in patients with IBD, which may be further heightened by genetic predisposition to IBD. The increased risk of pancreatic cancer is probably similar in Crohn's disease and ulcerative colitis.
Collapse
Affiliation(s)
- Mohammad Zamani
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Shaghayegh Alizadeh-Tabari
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hassan Murad
- Kern Center for the Science of Healthcare Delivery Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Nicholas J Talley
- School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| |
Collapse
|
4
|
Wang S, Su W, Wu X, Dong W. Restoring Treg/Th17 cell balance in ulcerative colitis through HRas silencing and MAPK pathway inhibition. Int Immunopharmacol 2024; 130:111608. [PMID: 38428143 DOI: 10.1016/j.intimp.2024.111608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 03/03/2024]
Abstract
This study investigates HRas-dependent mechanisms in the disruption of regulatory T (Treg) cells and T helper 17 (Th17) cells balance in ulcerative colitis (UC). Comprehensive RNA sequencing and bioinformatics analyses revealed elevated HRas and MAPK pathway-related protein expression in UC samples. Using a murine UC model induced by dextran sulfate sodium (DSS), HRas silencing was found to promote Treg cell differentiation and suppress Th17 cell production, effectively restoring balance. Inactivation of the MAPK pathway played a pivotal role in this rebalancing effect. In vivo experiments further confirmed that HRas silencing mitigated colon tissue damage in DSS-induced mice, emphasizing its potential as a therapeutic strategy for UC.
Collapse
Affiliation(s)
- Siwei Wang
- Department of Pathology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, PR China
| | - Wenhao Su
- Department of Gastroenterology, Renmin Hospital of Wuhan University,Wuhan 430060, PR China
| | - Xiaohan Wu
- Department of Gastroenterology, Renmin Hospital of Wuhan University,Wuhan 430060, PR China
| | - Weiguo Dong
- Department of Gastroenterology, Renmin Hospital of Wuhan University,Wuhan 430060, PR China.
| |
Collapse
|
5
|
Fu C, Wang Q, Chen Y, Zhang Y. Exploring the causal relationship between airborne particulate matter and ulcerative colitis: A two-sample mendelian randomization study. PLoS One 2024; 19:e0300066. [PMID: 38457365 PMCID: PMC10923436 DOI: 10.1371/journal.pone.0300066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/16/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Existing research has demonstrated links between airborne particulate matter and ulcerative colitis (UC) onset. Through Mendelian randomization, this study aims to further delineate the causal association between specific types of airborne particulates and UC. METHODS A two-sample Mendelian randomization analysis was undertaken to investigate the causality between airborne particulate matter and UC. Genetic datasets for both airborne particulates and UC were derived from accessible genome-wide association studies (GWAS). We employed a range of MR techniques, such as inverse variance weighted (IVW), weighted median, MR-Egger, and Wald Ratio, to validate the causality. In addition, sensitivity assessments were executed to ensure result reliability. RESULTS The data indicate a probable positive correlation between PM2.5 exposure and UC risk (OR: 3.6; 95% CI: [1.2-11.3]; P = 0.026). The statistical strength for causal determination via the IVW approach stood at 0.87, with a Type I error rate set at 0.025. Assessments using Cochran's Q test, MR-Egger intercept, MR-PRESSO, and leave-one-out sensitivity analyses did not identify notable heterogeneity, pleiotropy, or biases in the overall relationship between PM2.5 and UC. Furthermore, the MR-Steiger assessment indicated that PM2.5 exposure level determinants predominantly affect UC vulnerability. CONCLUSION The findings underscore the potential involvement of PM2.5 in UC pathogenesis.
Collapse
Affiliation(s)
- Chong Fu
- Department of Gastroenterology, Anqing Municipal Hospital, Anqing, PR China
| | - Qi Wang
- Department of Gastroenterology, Anqing Municipal Hospital, Anqing, PR China
| | - Yan Chen
- Department of Gastroenterology, Anqing Municipal Hospital, Anqing, PR China
| | - Yanping Zhang
- Department of Gastroenterology, Anqing Municipal Hospital, Anqing, PR China
| |
Collapse
|
6
|
Tan L, Li X, Qin H, Zhang Q, Wang J, Chen T, Zhang C, Zhang X, Tan Y. Identified S100A9 as a target for diagnosis and treatment of ulcerative colitis by bioinformatics analysis. Sci Rep 2024; 14:5517. [PMID: 38448514 PMCID: PMC10917761 DOI: 10.1038/s41598-024-55944-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/29/2024] [Indexed: 03/08/2024] Open
Abstract
Ulcerative colitis (UC) is a chronic, recurrent inflammatory bowel disease. UC confronts with severe challenges including the unclear pathogenesis and lack of specific diagnostic markers, demanding for identifying predictive biomarkers for UC diagnosis and treatment. We perform immune infiltration and weighted gene co-expression network analysis on gene expression profiles of active UC, inactive UC, and normal controls to identify UC related immune cell and hub genes. Neutrophils, M1 macrophages, activated dendritic cells, and activated mast cells are significantly enriched in active UC. MMP-9, CHI3L1, CXCL9, CXCL10, CXCR2 and S100A9 are identified as hub genes in active UC. Specifically, S100A9 is significantly overexpressed in mice with colitis. The receiver operating characteristic curve demonstrates the excellent performance of S100A9 expression in diagnosing active UC. Inhibition of S100A9 expression reduces DSS-induced colonic inflammation. These identified biomarkers associated with activity in UC patients enlighten the new insights of UC diagnosis and treatment.
Collapse
Affiliation(s)
- Lulu Tan
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Xin Li
- Wuhan Asia Heart Hospital, Wuhan, 430022, China
| | - Hong Qin
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Qingqing Zhang
- Haiyan County Hospital of Traditional Chinese Medicine, Jiaxing, 314399, China
| | - Jinfeng Wang
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Tao Chen
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Chengwu Zhang
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Xiaoying Zhang
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China.
| | - Yuyan Tan
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China.
| |
Collapse
|
7
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
8
|
Voshagh Q, Anoshiravani A, Karimpour A, Goodarzi G, Tehrani SS, Tabatabaei‐Malazy O, Panahi G. Investigating the association between the tissue expression of miRNA-101, JAK2/STAT3 with TNF-α, IL-6, IL-1β, and IL-10 cytokines in the ulcerative colitis patients. Immun Inflamm Dis 2024; 12:e1224. [PMID: 38517042 PMCID: PMC10958669 DOI: 10.1002/iid3.1224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Ulcerative colitis (UC) is a chronic inflammatory bowel disease caused by numerous factors, such as immune system dysfunction and genetic factors. MicroRNAs (miRNAs) play a crucial role in UC pathogenesis, particularly via the JAK-STAT pathway. Our aim was to investigate the association between miRNA-101 and JAK2-STAT3 signaling pathway with inflammatory cytokines in UC patients. METHODS We enrolled 35 UC patients and 35 healthy individuals as the control group, referred to Shariati Hospital, Tehran, Iran. Patients were diagnosed based on clinical, laboratory, histological, and colonoscopy criteria. RNA and protein extracted from tissue samples. Real-time PCR was used to assess the expression levels of miRNA-101, interleukin (IL)-1β, IL-6, tumor necrosis factor (TNF)-α, and IL-10 genes, while western blot was employed to measure levels of P-STAT3, total STAT3, and JAK2 proteins. RESULTS Expression of pro-inflammatory cytokines TNF-α, IL-1β, and IL-6 significantly increased, while the expression of IL-10 significantly decreased in the case group versus controls. Additionally, miRNA-101 expression was significantly higher in UC patients. A significant correlation between miRNA-101 and IL-6 expression was observed, indicating their relationship and possible impact on cell signaling pathways, JAK2-STAT3. No significant changes were observed in phosphorylated and total STAT3 and JAK2 protein expression. CONCLUSION This study provides evidence of increased miRNA-101 expression in UC tissue, suggesting a potential correlation between miRNA-101 and IL-6 expression and their involvement in the JAK2-STAT3 pathway. The study confirms alterations in UC patients' pro-inflammatory cytokines and anti-inflammatory IL-10. However, further investigations are needed to understand the exact role of miRNA-101 in UC pathogenesis fully.
Collapse
Affiliation(s)
- Qazaleh Voshagh
- Department of Clinical Biochemistry, School of MedicineTehran University of Medical SciencesTehranIran
| | - Amir Anoshiravani
- Digestive Disease Research Center, Digestive Disease Research InstituteTehran University of Medical SciencesTehranIran
| | - Amin Karimpour
- Department of Clinical Biochemistry, School of MedicineTehran University of Medical SciencesTehranIran
| | - Golnaz Goodarzi
- Department of Pathobiology and Laboratory Sciences, School of MedicineNorth Khorasan University of Medical SciencesBojnurdIran
| | - Sadra Samavarchi Tehrani
- Endocrine Research Center, Institute of Endocrinology and MetabolismIran University of Medical ScienceTehranIran
| | - Ozra Tabatabaei‐Malazy
- Non‐Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences InstituteTehran University of Medical SciencesTehranIran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences InstituteTehran University of Medical SciencesTehranIran
| | - Ghodratollah Panahi
- Department of Clinical Biochemistry, School of MedicineTehran University of Medical SciencesTehranIran
| |
Collapse
|
9
|
Lenfant M, Verstockt B, Sabino J, Vermeire S, Ferrante M. Letter: Should ulcerative colitis be monitored more or less invasively? Authors' reply. Aliment Pharmacol Ther 2024; 59:723-724. [PMID: 38349707 DOI: 10.1111/apt.17887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 01/14/2024] [Indexed: 02/15/2024]
Abstract
LINKED CONTENTThis article is linked to Lenfant et al papers. To view these articles, visit https://doi.org/10.1111/apt.17753 and https://doi.org/10.1111/apt.17873
Collapse
Affiliation(s)
- Matthias Lenfant
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Translational Research in Gastrointestinal Disorders, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
| | - Bram Verstockt
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Translational Research in Gastrointestinal Disorders, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
| | - João Sabino
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Translational Research in Gastrointestinal Disorders, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
| | - Séverine Vermeire
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Translational Research in Gastrointestinal Disorders, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
| | - Marc Ferrante
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Translational Research in Gastrointestinal Disorders, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
| |
Collapse
|
10
|
Wang BR, Wang J, Tian T, Zhang SX, Zhao YQ, Meng SY, Wu ZY, Huang F, Zeng J, Ni J. Genetic correlation, shared loci, but no causality between bipolar disorder and inflammatory bowel disease: A genome-wide pleiotropic analysis. J Affect Disord 2024; 348:167-174. [PMID: 38154582 DOI: 10.1016/j.jad.2023.12.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 11/21/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND AND AIMS The comorbidity between bipolar disorder (BD) and inflammatory bowel disease (IBD) has been widely reported in observational studies. However, unclear whether this comorbidity reflects a shared genetic architecture. METHODS Leveraging large-scale genome-wide association study (GWAS) summary statistics of BD, IBD and its subtypes, ulcerative colitis (UC) and Crohn's disease (CD), we performed a genome-wide pleiotropic analysis to estimate heritability and genetic correlation, identify pleiotropy loci/genes, and explore the shared biological pathway. Mendelian randomization (MR) studies were subsequently employed to infer whether the potential causal relationship is present. RESULTS We found a positive significant genetic correlation between BD and IBD (rg = 0.10, P = 7.00 × 10-4), UC (rg = 0.09, P = 2.90 × 10-3), CD (rg = 0.08, P = 6.10 × 10-3). In cross-trait meta-analysis, a total of 29, 24, and 23 independent SNPs passed the threshold for significant association between BD and IBD, UC, and CD, respectively. We identified five novel pleiotropy genes including ZDHHC2, SCRN1, INPP4B, C1orf123, and BRD3 in both BD and IBD, as well as in its subtypes UC and CD. Pathway enrichment analyses revealed that those pleiotropy genes were mainly enriched in several immune-related signal transduction pathways and cerebral disease-related pathways. MR analyses provided no evidence for a causal relationship between BD and IBD. CONCLUSION Our findings corroborated that shared genetic basis and common biological pathways may explain the comorbidity of BD and IBD. These findings further our understanding of shared genetic mechanisms underlying BD and IBD, and potentially provide points of intervention that may allow the development of new therapies for these co-occurrent disorders.
Collapse
Affiliation(s)
- Bing-Ran Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui 230032, China; Department of Clinical Medicine, the Second School of Clinical Medical, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jing Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui 230032, China
| | - Tian Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui 230032, China
| | - Shang-Xin Zhang
- Department of Gastrointestinal Surgery, Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, China
| | - Yu-Qiang Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui 230032, China
| | - Shi-Ying Meng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui 230032, China
| | - Zhuo-Yi Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui 230032, China
| | - Fen Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jing Zeng
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China.
| | - Jing Ni
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui 230032, China.
| |
Collapse
|
11
|
Ye Y, Liu L, Feng Z, Liu Y, Miao J, Wei X, Li H, Yang J, Cao X, Zhao J. The ERK-cPLA2-ACSL4 axis mediating M2 macrophages ferroptosis impedes mucosal healing in ulcerative colitis. Free Radic Biol Med 2024; 214:219-235. [PMID: 38367927 DOI: 10.1016/j.freeradbiomed.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/19/2024]
Abstract
Ulcerative colitis (UC) is a chronic gastrointestinal disease that can be managed with 5-aminosalicylic acid (5-ASA), the standard treatment for UC. However, the effectiveness of 5-ASA is not always optimal. Our study revealed that despite 5-ASA treatment, cells continued to experience excessive ferroptosis, which may hinder mucosal healing in UC and limit the success of this treatment approach in achieving disease remission. We found that combining 5-ASA with the ferroptosis inhibitor Fer-1 led to a significant inhibition of ferroptosis in macrophages present in the colon tissue, along with an increase in the proportion of M2 macrophages, suggesting that targeting ferroptosis in M2 macrophages could be a potential therapeutic strategy for alleviating UC. Our study also demonstrated that M2 macrophages are more susceptible to ferroptosis compared to M1 macrophages, and this susceptibility is associated with the activated arachidonic acid (AA) metabolism pathway mediated by ERK-cPLA2-ACSL4. Additionally, we found that the expression of cPLA2 gene pla2g4a was increased in the colon of UC patients compared to healthy controls. Furthermore, targeted metabolomics analysis revealed that the combination treatment group, as opposed to the 5-ASA treatment group, exhibited the ability to modulate AA metabolism. Overall, our findings emphasize the importance of addressing macrophage ferroptosis in order to enhance macrophage anti-inflammation, improve mucosal healing, and achieve better therapeutic outcomes for patients with UC.
Collapse
Affiliation(s)
- Yulin Ye
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China; Tianjin Institute of Digestive Diseases, Tianjin, China; Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Limin Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China; Tianjin Institute of Digestive Diseases, Tianjin, China; Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Zelin Feng
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China; Tianjin Institute of Digestive Diseases, Tianjin, China; Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yifei Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China; Tianjin Institute of Digestive Diseases, Tianjin, China; Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Junming Miao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China; Tianjin Institute of Digestive Diseases, Tianjin, China; Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xinyue Wei
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China; Tianjin Institute of Digestive Diseases, Tianjin, China; Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Huizhen Li
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China; Tianjin Institute of Digestive Diseases, Tianjin, China; Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Jie Yang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), and Key Laboratory of Cellular and Molecular Immunology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin, China; State Key Laboratory of Experimental Hematology, Tianjin, China.
| | - Xiaocang Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China; Tianjin Institute of Digestive Diseases, Tianjin, China; Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| | - Jingwen Zhao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China; Tianjin Institute of Digestive Diseases, Tianjin, China; Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| |
Collapse
|
12
|
Xu G, Xu Y, Zheng T, Liu T. Type 2 diabetes and inflammatory bowel disease: a bidirectional two-sample Mendelian randomization study. Sci Rep 2024; 14:5149. [PMID: 38429331 PMCID: PMC10907708 DOI: 10.1038/s41598-024-55869-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/28/2024] [Indexed: 03/03/2024] Open
Abstract
To investigate the association between T2DM and IBD by bidirectional two-sample Mendelian randomization (MR) to clarify the casual relationship. Independent genetic variants for T2DM and IBD were selected as instruments from published genome-wide association studies (GWAS), mainly in European ancestry. Instrumental variables (IVs) associated with T2DM and IBD were extracted separately from the largest GWAS meta-analysis. MR analyses included inverse variance weighting, weighted median estimator, MR Egger regression, and sensitivity analyses with Steiger filtering and MR PRESSO. In the data samples for Ulcerative colitis (UC) (6968 cases, 20,464 controls) and Crohn's disease (CD) (5956 cases, 14,927 controls), there was a negative causal relationship between T2DM and UC [IVW, OR/95%CI: 0.882/(0.826,0.942), p < 0.001]. However, the causal relationships between T2DM and CD, UC and T2DM, CD and T2DM were not significant, and the p value measured by the IVW method was ≥ 0.05. All SNPs showed no significant horizontal pleiotropy (p > 0.05). The results of the bidirectional MR Study suggest that T2DM has a negative causal effect on UC, which provides implications for clinical treatment decisions in IBD patients with T2DM. The findings do not support a causal relationship between T2DM and CD, UC and T2DM, or CD and T2DM, and the impact of IBD on T2DM needs further investigation.
Collapse
Affiliation(s)
- Guangyi Xu
- School of Nursing, Qingdao University, Qingdao, 266071, China
| | - Yanhong Xu
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
- Cardiovascular Surgery Intensive Care Unit, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Taohua Zheng
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Ting Liu
- School of Nursing, Qingdao University, Qingdao, 266071, China.
| |
Collapse
|
13
|
Dong H, Xu F, Linghu E. Unraveling the link between plasma caffeine concentrations and inflammatory bowel disease risk through Mendelian randomization. Am J Clin Nutr 2024; 119:711-715. [PMID: 38211690 DOI: 10.1016/j.ajcnut.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/19/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Caffeine is believed to possess anti-inflammatory properties, yet direct population-based evidence regarding its impact on inflammatory bowel disease (IBD) remains scarce. OBJECTIVES In this study, we used 2-sample Mendelian randomization (MR) study to investigate the causal relationship between long-term plasma caffeine concentrations and IBD and its subtypes, ulcerative colitis (UC) and Crohn disease (CD). METHODS We used single nucleotide polymorphisms (SNPs) associated with plasma caffeine concentrations at genome-wide significance within a ±100-kb range around the CYP1A2 or AHR genes as instrumental variables. Genome-wide association study (GWAS) data for IBD and its subtypes were obtained from FinnGen and International Inflammatory Bowel Disease Genetics Consortium. We conducted a meta-analysis of MR-related SNPs from both sources and used a multiplicative inverse variance-weighted random effects model to combine the effects of each SNP proxy on exposure to outcomes. RESULTS In our study, genetically predicted higher plasma caffeine concentrations were associated with a lower risk of IBD, with an odds ratio (OR) of 0.78 (95% confidence interval [CI]: 0.66, 0.91; PFDR = 0.004). This trend was also observed in UC and CD, with ORs of 0.79 (95% CI: 0.66, 0.94; PFDR = 0.014) and 0.78 (95% CI: 0.62, 0.98; PFDR = 0.032), respectively. CONCLUSION Our study indicates a potential causal link between genetically predicted higher plasma caffeine concentrations and a reduced risk of IBD, including its subtypes UC and CD.
Collapse
Affiliation(s)
- Hao Dong
- Department of Gastroenterology and Hepatology, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fang Xu
- Clinical Medical Laboratory Center, Taizhou People's Hospital, Taizhou, Jiangsu, China
| | - Enqiang Linghu
- Department of Gastroenterology and Hepatology, The First Medical Center of Chinese PLA General Hospital, Beijing, China.
| |
Collapse
|
14
|
James JP, Riis LB, Søkilde R, Malham M, Høgdall E, Langholz E, Nielsen BS. Short noncoding RNAs as predictive biomarkers for the development from inflammatory bowel disease unclassified to Crohn's disease or ulcerative colitis. PLoS One 2024; 19:e0297353. [PMID: 38408066 PMCID: PMC10896517 DOI: 10.1371/journal.pone.0297353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/22/2023] [Indexed: 02/28/2024] Open
Abstract
Numerous pathogenic processes are mediated by short noncoding RNAs (sncRNA). Twenty percent of inflammatory bowel disease (IBD) patients are labelled as IBD unclassified (IBDU) at disease onset. Most IBDU patients are reclassified as Crohn's disease (CD) or ulcerative colitis (UC) within few years. Since the therapeutic methods for CD and UC differ, biomarkers that can forecast the categorization of IBDU into CD or UC are highly desired. Here, we investigated whether sncRNAs can predict CD or UC among IBDU patients. 35 IBDU patients who were initially diagnosed with IBDU were included in this retrospective investigation; of them, 12, 15, and 8 were reclassified into CD (IBDU-CD), UC (IBDU-UC), or remained as IBDU (IBDU-IBDU), respectively. Eight IBD patients, were included as references. SncRNA profiling on RNA from mucosal biopsies were performed using Affymetrix miRNA 4.0 array. Selected probe sets were validated using RT-qPCR. Among all patients and only adults, 306 and 499 probe sets respectively were differentially expressed between IBDU-CD and IBDU-UC. Six of the probe sets were evaluated by RT-qPCR, of which miR-182-5p, miR-451a and ENSG00000239080 (snoU13) together with age and sex resulted in an AUC of 78.6% (95% CI: 60-97) in discriminating IBDU-CD from IBDU-UC. Based on the three sncRNAs profile it is possible to predict if IBDU patients within 3 years will be reclassified as CD or UC. We showed that the expression profile of IBDU patients differ from that of definite CD or UC, suggesting that a subgroup of IBDU patients may compose a third unique IBD subtype.
Collapse
Affiliation(s)
- Jaslin P. James
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
| | - Lene Buhl Riis
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rolf Søkilde
- Bioneer A/S, Hørsholm, Kogle Allé 2, Hørsholm, Denmark
| | - Mikkel Malham
- The Pediatric Department, Copenhagen University Hospital—Amager and Hvidovre, Hvidovre, Denmark
- Copenhagen Center for Inflammatory Bowel Disease in Children, Adolescents and Adults, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ebbe Langholz
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Gastroenheden, Herlev University Hospital, Herlev, Denmark
| | | |
Collapse
|
15
|
Chen W, Cheng B, Yu SG, Wu QF. Effects of moxibustion on visceral hypersensitivity and colonic inflammatory response in mice with chronic ulcerative colitis. Zhen Ci Yan Jiu 2024; 49:145-154. [PMID: 38413035 DOI: 10.13702/j.1000-0607.20221282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
OBJECTIVES To observe the effects of moxibustion at "Zusanli" (ST36) on the expression levels of tumor necrosis factor (TNF)-α, TNF receptor 1 (TNF-R1), p38 mitogen-activated protein kinase (P38 MAPK), and transient receptor potential vanilloid 1 (TRPV1) in the colon tissue of mice with chronic ulcerative colitis (UC), so as to explore the underlying mechanisms of moxibustion in improving visceral hypersensitivity in chronic UC. METHODS Male C57BL/6J mice were randomly divided into normal group, normal with moxibustion (NM) group, model group, and model with moxibustion (MM) group, with 10 mice in each group. The chronic UC model was established by drinking 2.5% dextran sodium sulfate for 3 cycles. Mice in the NM and MM groups received moxibustion at ST36 for 20 min, 5 days per week with a 2-day break, for a total of 4 weeks. The disease activity index (DAI) score of each group was evaluated before and after treatment. The minimum volume threshold of abdominal wall retraction reflex (AWR) was measured to observe the intestinal sensitivity of mice. The colon length was measured. The pathological changes of colon tissue were observed by HE staining. The expression of mucin in colon goblet cells was detected by periodate Scheff staining. The intestinal fibrosis was observed by Masson staining. The number of trypsin-positive cells (i.e., mast cell) and the expression level of TNF-α in colon tissue were detected by immunofluorescence staining. The expression levels of TNF-R1, P38 MAPK and TRPV1 in colon tissue were detected by immunohistochemistry. RESULTS Compared with the normal group after treatment, the model group showed increased DAI score (P<0.001), decreased AWR minimum volume threshold (P<0.01), shortened colon length (P<0.001), significant inflammatory infiltration in the colon tissue, reduced mucin secretion (P<0.01), increased collagen fiber deposition (P<0.001), and elevated expression levels of TNF-α, TNF-R1, P38 MAPK, and TRPV1 (P<0.001, P<0.01, P<0.05). Compared with the model group, the MM group showed decreased DAI score (P<0.01), increased AWR minimum volume threshold (P<0.001), elongated colon length (P<0.001), reduced inflammatory cell infiltration, improved integrity of mucosal glandular structure, enhanced mucin secretion (P<0.01), decreased collagen fiber deposition (P<0.001), decreased number of mast cells in the colon tissue (P<0.001), and decreased expression levels of TNF-α, TNF-R1, P38 MAPK, and TRPV1 (P<0.001, P<0.01, P<0.05). There were no significant differences in the above index between the NM group and the normal group. CONCLUSIONS Moxibustion can reduce visceral hypersensitivity, alleviate inflammatory infiltration and fibrotic damage in the colon tissue of mice with chronic UC. These effects may be associated with the down-regulation of TNF-α, TNF-R1, P38 MAPK, and TRPV1 expression in colon.
Collapse
Affiliation(s)
- Wei Chen
- College of Acupuncture-moxibustion and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Bin Cheng
- College of Acupuncture-moxibustion and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Shu-Guang Yu
- College of Acupuncture-moxibustion and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Qiao-Feng Wu
- College of Acupuncture-moxibustion and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
| |
Collapse
|
16
|
Inciuraite R, Steponaitiene R, Raudze O, Kulokiene U, Kiudelis V, Lukosevicius R, Ugenskiene R, Adamonis K, Kiudelis G, Jonaitis LV, Kupcinskas J, Skieceviciene J. Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level. Sci Rep 2024; 14:4456. [PMID: 38396014 PMCID: PMC10891043 DOI: 10.1038/s41598-024-55076-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 02/19/2024] [Indexed: 02/25/2024] Open
Abstract
Patient-derived human intestinal organoids are becoming an indispensable tool for the research of digestive system in health and disease. However, very little is still known about the long-term culturing effect on global genomic methylation level in colonic epithelial organoids derived from healthy individuals as well as active and quiescent ulcerative colitis (UC) patients. In this study, we aimed to evaluate the epigenetic stability of these organoids by assessing the methylation level of LINE-1 during prolonged culturing. We found that LINE-1 region of both healthy control and UC patient colon tissues as well as corresponding epithelial organoids is highly methylated (exceeding 60%). We also showed that long-term culturing of colonic epithelial organoids generated from stem cells of healthy and diseased (both active and quiescent UC) individuals results in decrease of LINE-1 (up to 8%) methylation level, when compared to tissue of origin and short-term cultures. Moreover, we revealed that LINE-1 methylation level in sub-cultured organoids decreases at different pace depending on the patient diagnosis (healthy control, active or quiescent UC). Therefore, we propose LINE-1 as a potential and convenient biomarker for reliable assessment of global methylation status of patient-derived intestinal epithelial organoids in routine testing of ex vivo cultures.
Collapse
Affiliation(s)
- Ruta Inciuraite
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Ruta Steponaitiene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Odeta Raudze
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Ugne Kulokiene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Vytautas Kiudelis
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Rokas Lukosevicius
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Rasa Ugenskiene
- Department of Genetics and Molecular Medicine, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Kestutis Adamonis
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Gediminas Kiudelis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Laimas Virginijus Jonaitis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, 44307, Kaunas, Lithuania.
| |
Collapse
|
17
|
Zou M, Liang Q, Zhang W, Liang J, Zhu Y, Xu Y. Diet-derived circulating antioxidants and risk of inflammatory bowel disease: a Mendelian randomization study and meta-analysis. Front Immunol 2024; 15:1334395. [PMID: 38449867 PMCID: PMC10915022 DOI: 10.3389/fimmu.2024.1334395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/02/2024] [Indexed: 03/08/2024] Open
Abstract
Background Previous studies have shown conflicting results regarding the impact of circulating antioxidants on the risk of inflammatory bowel disease (IBD). In this study, our intent was to investigate the causal relationship between circulating antioxidants and IBD using Mendelian randomization (MR). Methods Instrumental variables for absolute circulating antioxidants (ascorbate, retinol, lycopene, and β-carotene) and circulating antioxidant metabolites (α-tocopherol, γ-tocopherol, ascorbate, and retinol) were screened from published studies. We obtained outcome data from two genome-wide association study (GWAS) databases, including the international inflammatory bowel disease genetics consortium (IIBDGC, 14,927 controls and 5,956 cases for Crohn's disease (CD), 20,464 controls and 6,968 cases for ulcerative colitis (UC), and 21,770 controls and 12,882 cases for IBD) and the FinnGen study (375,445 controls and 1,665 cases for CD, 371,530 controls and 5,034 cases for UC, and 369,652 controls and 7,625 cases for IBD). MR analysis was performed in each of the two databases and those results were pooled using meta-analysis to assess the overall effect of exposure on each phenotype. In order to confirm the strength of the findings, we additionally conducted a replication analysis using the UK Biobank. Results In the meta-analysis of the IIBDGC and FinnGen, we found that each unit increase in absolute circulating level of retinol was associated with a 72% reduction in the risk of UC (OR: 0.28, 95% CI: 0.10 to 0.78, P=0.015). The UC GWAS data from the UK Biobank also confirmed this causal relationship (OR: 0.99, 95% CI: 0.97 to 1.00, P=0.016). In addition, there was suggestive evidence that absolute retinol level was negatively associated with IBD (OR: 0.41, 95% CI: 0.18 to 0.92, P=0.031). No other causal relationship was found. Conclusion Our results provide strong evidence that the absolute circulating level of retinol is associated with a reduction in the risk of UC. Further MR studies with more instrumental variables on circulating antioxidants, especially absolute circulating antioxidants, are needed to confirm our results.
Collapse
Affiliation(s)
- Menglong Zou
- Department of Gastroenterology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Qiaoli Liang
- Department of Oncology, Doumen Qiaoli Hospital of Traditional Chinese Medicine, Zhuhai, China
| | - Wei Zhang
- Department of Gastroenterology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Junyao Liang
- Department of Gastroenterology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Ying Zhu
- Department of Gastroenterology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Yin Xu
- Department of Gastroenterology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| |
Collapse
|
18
|
Dong X, Gong LL, Hong MZ, Pan JS. Investigating the shared genetic architecture between primary sclerosing cholangitis and inflammatory bowel diseases: a Mendelian randomization study. BMC Gastroenterol 2024; 24:77. [PMID: 38373892 PMCID: PMC10875759 DOI: 10.1186/s12876-024-03162-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Several studies have found that primary sclerosing cholangitis (PSC) and inflammatory bowel disease (IBD) are closely associated. However, the direction and causality of their interactions remain unclear. Thus, this study employs Mendelian Randomization to explore whether there are causal associations of genetically predicted PSC with IBD. METHODS Genetic variants associated with the genome-wide association study (GWAS) of PSC were used as instrumental variables. The statistics for IBD, including ulcerative colitis (UC), and Crohn's disease (CD) were derived from GWAS. Then, five methods were used to estimate the effects of genetically predicted PSC on IBD, including MR Egger, Weighted median (WM), Inverse variance weighted (IVW), Simple mode, and Weighted mode. Last, we also evaluated the pleiotropic effects, heterogeneity, and a leave-one-out sensitivity analysis that drives causal associations to confirm the validity of the analysis. RESULTS Genetically predicted PSC was significantly associated with an increased risk of UC, according to the study (odds ratio [OR] IVW= 1.0014, P<0.05). However, none of the MR methods found significant causal evidence of genetically predicted PSC in CD (All P>0.05). The sensitivity analysis results showed that the causal effect estimations of genetically predicted PSC on IBD were robust, and there was no horizontal pleiotropy or statistical heterogeneity. CONCLUSIONS Our study corroborated a causal association between genetically predicted PSC and UC but did not between genetically predicted PSC and CD. Then, we identification of shared SNPs for PSC and UC, including rs3184504, rs9858213, rs725613, rs10909839, and rs4147359. More animal experiments and clinical observational studies are required to further clarify the underlying mechanisms of PSC and IBD.
Collapse
Affiliation(s)
- Xuan Dong
- Department of Hepatology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Hepatology Research Institute, Fujian Medical University, Fuzhou, Fujian, China
- Department of Hepatology, National Regional Medical Center, Binhai Campus of the First Affiliated Hosptial, Fujian Medical University, Fuzhou, Fujian, China
- Fujian Clinical Research Center for Hepatopathy and Intestinal Diseases, Fuzhou, Fujian, China
| | - Li-Li Gong
- Department of General Practice, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
| | - Mei-Zhu Hong
- Department of Traditional Chinese Medicine, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Jin-Shui Pan
- Department of Hepatology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
- Hepatology Research Institute, Fujian Medical University, Fuzhou, Fujian, China.
- Department of Hepatology, National Regional Medical Center, Binhai Campus of the First Affiliated Hosptial, Fujian Medical University, Fuzhou, Fujian, China.
- Fujian Clinical Research Center for Hepatopathy and Intestinal Diseases, Fuzhou, Fujian, China.
| |
Collapse
|
19
|
Yang Q, Zhang P, Han L, Shi P, Zhao Z, Cui D, Hong K. Mitochondrial-related genes PDK2, CHDH, and ALDH5A1 served as a diagnostic signature and correlated with immune cell infiltration in ulcerative colitis. Aging (Albany NY) 2024; 16:3803-3822. [PMID: 38376420 DOI: 10.18632/aging.205561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/17/2024] [Indexed: 02/21/2024]
Abstract
We conducted an investigation to determine the potential of mitochondrial-related genes as diagnostic biomarkers in ulcerative colitis (UC), while also examining their association with immune cell infiltration. To achieve this, we acquired four datasets pertaining to UC, which included gene expression arrays and clinical data, from the GEO database. Subsequently, we selected three signature genes (PDK2, CHDH, and ALDH5A1) to construct a diagnostic model for UC. The nomogram and ROC curves exhibited exceptional diagnostic efficacy. Following this, quantitative real-time polymerase chain reaction and western blotting assays validated the decreased mRNA and protein expression of PDK2, CHDH, and ALDH5A1 in the model of UC cells and dextran sulfate sodium salt (DSS)-induced mice colitis tissues, aligning with the findings in the risk model. This investigation suggested a negative correlation between the expression of ALDH5A1, CHDH, and PDK2 and the infiltration of M1 macrophages. Then, immunofluorescence analysis confirmed the augmented expression of CD86 in the tissue of mice subjected to DSS, while a diminished expression of ALDH5A1, CHDH, and PDK2 was observed. Consequently, it can be inferred that targeting mitochondria-associated genes, namely PDK2, CHDH, and ALDH5A1, holds potential as a viable strategy for prognostic prediction and the implementation of immune therapy for UC.
Collapse
Affiliation(s)
- Qian Yang
- Department of Gastroenterology, Guizhou Provincial People’s Hospital, Medical College of Guizhou University, Guiyang, Guizhou, China
| | - Peng Zhang
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Lu Han
- Department of Gastroenterology, Guizhou Provincial People’s Hospital, Medical College of Guizhou University, Guiyang, Guizhou, China
| | - Pengshuang Shi
- Department of Gastroenterology, Guizhou Provincial People’s Hospital, Medical College of Guizhou University, Guiyang, Guizhou, China
| | - Zhifang Zhao
- Department of Gastroenterology, Guizhou Provincial People’s Hospital, Medical College of Guizhou University, Guiyang, Guizhou, China
| | - Dejun Cui
- Department of Gastroenterology, Guizhou Provincial People’s Hospital, Medical College of Guizhou University, Guiyang, Guizhou, China
| | - Kunqiao Hong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| |
Collapse
|
20
|
Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG. Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis. Nat Commun 2024; 15:1493. [PMID: 38374043 PMCID: PMC10876948 DOI: 10.1038/s41467-024-45665-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we perform single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.
Collapse
Affiliation(s)
- Elvira Mennillo
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Gyehyun Lee
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Iulia Rusu
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ravi K Patel
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | | | - Emily Flynn
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Stephanie Li
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jared L Bain
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christopher Andersen
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Arjun Rao
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Stanley Tamaki
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Tsui
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Alan Shen
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Madison L Lotstein
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Maha Rahim
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mohammad Naser
- Biological Imaging Development CoLab, University of California San Francisco, San Francisco, CA, USA
| | | | - Walter Eckalbar
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Soo-Jin Cho
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Kendall Beck
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Najwa El-Nachef
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sara Lewin
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Daniel R Selvig
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan P Terdiman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Uma Mahadevan
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David Y Oh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gabriela K Fragiadakis
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | | | - Alexis J Combes
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Michael G Kattah
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
21
|
Zhang S, Zhang G, Wang W, Guo SB, Zhang P, Wang F, Zhou Q, Zhou Z, Wang Y, Sun H, Cui W, Yang S, Yuan W. An assessment system for clinical and biological interpretability in ulcerative colitis. Aging (Albany NY) 2024; 16:3856-3879. [PMID: 38372705 DOI: 10.18632/aging.205564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/09/2024] [Indexed: 02/20/2024]
Abstract
Ulcerative colitis (UC) is a serious inflammatory bowel disease (IBD) with high morbidity and mortality worldwide. As the traditional diagnostic techniques have various limitations in the practice and diagnosis of early ulcerative colitis, it is necessary to develop new diagnostic models from molecular biology to supplement the existing methods. In this study, we developed a machine learning-based synthesis to construct an artificial intelligence diagnostic model for ulcerative colitis, and the correctness of the model is verified using an external independent dataset. According to the significantly expressed genes related to the occurrence of UC in the model, an unsupervised quantitative ulcerative colitis related score (UCRScore) based on principal coordinate analysis was established. The UCRScore is not only highly generalizable across UC bulk cohorts at different stages, but also highly generalizable across single-cell datasets, with the same effect in terms of cell numbers, activation pathways and mechanisms. As an important role of screening genes in disease occurrence, based on connectivity map analysis, 5 potential targeting molecular compounds were identified, which can be used as an additional supplement to the therapeutic of UC. Overall, this study provides a potential tool for differential diagnosis and assessment of bio-pathological changes in UC at the macroscopic level, providing an opportunity to optimize the diagnosis and treatment of UC.
Collapse
Affiliation(s)
- Shiqian Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou 450052, Henan, China
| | - Wenxiu Wang
- Department of Neonatology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Song-Bin Guo
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, Guangdong, China
| | - Pengpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Fuqi Wang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Quanbo Zhou
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Zhaokai Zhou
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Yujia Wang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
- Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou 450052, Henan, China
| | - Haifeng Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Wenming Cui
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Shuaixi Yang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| |
Collapse
|
22
|
Vineis JH, Reznikoff WS, Antonopoulos DA, Koval J, Chang E, Fallon BR, Paul BG, Morrison HG, Sogin ML. A novel conjugative transposon carrying an autonomously amplified plasmid. mBio 2024; 15:e0278723. [PMID: 38259081 PMCID: PMC10865816 DOI: 10.1128/mbio.02787-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 01/24/2024] Open
Abstract
Tetracyclines serve as broad-spectrum antibiotics to treat bacterial infections. The discovery of new tetracycline resistance genes has led to new questions about the underlying mechanisms of resistance, gene transfer, and their relevance to human health. We tracked changes in the abundance of a 55-kbp conjugative transposon (CTn214) carrying tetQ, a tetracycline resistance gene, within a Bacteroides fragilis metagenome-assembled genome derived from shotgun sequencing of microbial DNA extracted from the ileal pouch of a patient with ulcerative colitis. The mapping of metagenomic reads to CTn214 revealed the multi-copy nature of a 17,044-nt region containing tetQ in samples collected during inflammation and uninflamed visits. B. fragilis cultivars isolated from the same patient during periods of inflammation harbored CTn214 integrated into the chromosome or both a circular, multi-copy, extrachromosomal region of the CTn214 containing tetQ and the corresponding integrated form. The tetracycline-dependent mechanism for the transmission of CTn214 is nearly identical to a common conjugative transposon found in the genome of B. fragilis (CTnDOT), but the autonomously amplified nature of a circular 17,044-nt region of CTn214 that codes for tetQ and the integration of the same sequence in the linear chromosome within the same cell is a novel observation. Genome and transcriptome sequencing of B. fragilis cultivars grown under different concentrations of tetracycline and ciprofloxacin indicates that tetQ in strains containing the circular form remains actively expressed regardless of treatment, while the expression of tetQ in strains containing the linear form increases only in the presence of tetracycline.IMPORTANCEThe exchange of antibiotic production and resistance genes between microorganisms can lead to the emergence of new pathogens. In this study, short-read mapping of metagenomic samples taken over time from the illeal pouch of a patient with ulcerative colitis to a Bacteroides fragilis metagenome-assembled genome revealed two distinct genomic arrangements of a novel conjugative transposon, CTn214, that encodes tetracycline resistance. The autonomous amplification of a plasmid-like circular form from CTn214 that includes tetQ potentially provides consistent ribosome protection against tetracycline. This mode of antibiotic resistance offers a novel mechanism for understanding the emergence of pathobionts like B. fragilis and their persistence for extended periods of time in patients with inflammatory bowel disease.
Collapse
Affiliation(s)
- Joseph H. Vineis
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - William S. Reznikoff
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | | | - Jason Koval
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Eugene Chang
- Section of Gastroenterology, Department of Medicine, Knapp Center for Biomedical Discovery, The University of Chicago, Chicago, Illinois, USA
| | - Bailey R. Fallon
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Blair G. Paul
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Hilary G. Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Mitchell L. Sogin
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| |
Collapse
|
23
|
Dong X, Zhan Y, Yang M, Li S, Zheng H, Gao Y. miR-30c affects the pathogenesis of ulcerative colitis by regulating target gene VIP. Sci Rep 2024; 14:3472. [PMID: 38342939 PMCID: PMC10859366 DOI: 10.1038/s41598-024-54092-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/08/2024] [Indexed: 02/13/2024] Open
Abstract
MicroRNAs play a crucial role in regulating the epithelial barrier and immune response, which are implicated in the pathogenesis of ulcerative colitis (UC). This study aimed to investigate the role and molecular mechanism of miR-30c in the pathogenesis of UC using a dextran sulfate sodium salt (DSS)-induced colitis model, which is similar to ulcerative colitis. Wild-type (WT) and miR-30c knockout (KO) mice were assigned to either control or DSS-treated groups to evaluate the influence of aberrant miR-30c expression on UC pathogenesis. The disease activity index, inflammatory factors, and the extent of pathological and histological damage in colon tissues were analyzed. The effect of miR-30c on vasoactive intestinal peptide (VIP) gene expression was validated through luciferase reporter assay, qRT-PCR, Western blotting, and immunohistochemistry. The results showed that miR-30c KO mice with DSS-induced colitis model showed more severe phenotypes: significantly higher disease activity indices, significant body weight loss, reduced length of the colon of mice, increased number of aberrant crypt structures, reduced mucus secretion, and significant differences in inflammatory factors. These findings suggested that the absence of miR-30c might promote DSS-induced colitis, and the targe-regulatory effect of miR-30c on VIP might play an important role in the development of colitis.
Collapse
Affiliation(s)
- Xiang Dong
- School of Life Science, Laboratory Animal Center, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, China
- Bengbu Medical College Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, Bengbu Medical College, Bengbu, China
| | - Yuling Zhan
- School of Life Science, Laboratory Animal Center, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, China
- Bengbu Medical College Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, Bengbu Medical College, Bengbu, China
| | - Minghui Yang
- Bengbu Medical College Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, Bengbu Medical College, Bengbu, China
- School of Basic Courses, Bengbu Medical College, Bengbu, China
| | - Suwan Li
- School of Life Science, Laboratory Animal Center, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, China
- Bengbu Medical College Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, Bengbu Medical College, Bengbu, China
| | - Hailun Zheng
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Yu Gao
- School of Life Science, Laboratory Animal Center, Bengbu Medical College, No. 2600 Donghai Road, Bengbu, 233030, China.
- Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, Bengbu, China.
- Laboratory Animal Center, Bengbu Medical College, Bengbu, China.
| |
Collapse
|
24
|
Johnson JL, Sargsyan D, Neiman EM, Hart A, Stojmirovic A, Kosoy R, Irizar H, Suárez-Fariñas M, Song WM, Argmann C, Avey S, Shmuel-Galia L, Vierbuchen T, Bongers G, Sun Y, Edelstein L, Perrigoue J, Towne JE, Hall AO, Fitzgerald KA, Hoebe K. Gene coexpression networks reveal a broad role for lncRNAs in inflammatory bowel disease. JCI Insight 2024; 9:e168988. [PMID: 38329124 DOI: 10.1172/jci.insight.168988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 12/26/2023] [Indexed: 02/09/2024] Open
Abstract
The role of long noncoding RNAs (lncRNAs) in disease is incompletely understood, but their regulation of inflammation is increasingly appreciated. We addressed the extent of lncRNA involvement in inflammatory bowel disease (IBD) using biopsy-derived RNA-sequencing data from a large cohort of deeply phenotyped patients with IBD. Weighted gene correlation network analysis revealed gene modules of lncRNAs coexpressed with protein-coding genes enriched for biological pathways, correlated with epithelial and immune cell signatures, or correlated with distal colon expression. Correlation of modules with clinical features uncovered a module correlated with disease severity, with an enriched interferon response signature containing the hub lncRNA IRF1-AS1. Connecting genes to IBD-associated single nucleotide polymorphisms (SNPs) revealed an enrichment of SNP-adjacent lncRNAs in biologically relevant modules. Ulcerative colitis-specific SNPs were enriched in distal colon-related modules, suggesting that disease-specific mechanisms may result from altered lncRNA expression. The function of the IBD-associated SNP-adjacent lncRNA IRF1-AS1 was explored in human myeloid cells, and our results suggested IRF1-AS1 promoted optimal production of TNF-α, IL-6, and IL-23. A CRISPR/Cas9-mediated activation screen in THP-1 cells revealed several lncRNAs that modulated LPS-induced TNF-α responses. Overall, this study uncovered the expression patterns of lncRNAs in IBD that identify functional, disease-relevant lncRNAs.
Collapse
Affiliation(s)
- John L Johnson
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Davit Sargsyan
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Eric M Neiman
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Amy Hart
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | | | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, New York, USA
| | - Haritz Irizar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, New York, USA
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, New York, USA
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, New York, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, New York, USA
| | - Stefan Avey
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Liraz Shmuel-Galia
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Tim Vierbuchen
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Gerold Bongers
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Yu Sun
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Leonard Edelstein
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | | | - Jennifer E Towne
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Aisling O'Hara Hall
- Immunology Translational Early Development, Bristol Myers Squibb, Summit, New Jersey, USA
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Kasper Hoebe
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| |
Collapse
|
25
|
Yu C, Xu J, Xu S, Tang L, Han Q, Zeng X, Huang Y, Yu T, Sun Z. Exploring genetic associations of Crohn's disease and ulcerative colitis with extraintestinal cancers in European and East Asian populations. Front Immunol 2024; 15:1339207. [PMID: 38404590 PMCID: PMC10885353 DOI: 10.3389/fimmu.2024.1339207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/19/2024] [Indexed: 02/27/2024] Open
Abstract
Background Previous studies have reported associations of Crohn's disease (CD) and ulcerative colitis (UC) with the risks of extraintestinal cancers, but the causality remains unclear. Methods Using genetic variations robustly associated with CD and UC extracted from genome-wide association studies (GWAS) as instrumental variables. Nine types of extraintestinal cancers of European and Asian populations were selected as outcomes. We used the inverse variance weighted method as the primary approach for two-sample Mendelian randomization analysis. Sensitivity analyses were carried out to evaluate the reliability of our findings. Results In the European population, we found that CD showed a potential causal relationship with pancreatic cancer (OR: 1.1042; 95% CI: 1.0087-1.2088; P=0.0318). Meanwhile, both CD (outliers excluded: OR: 1.0208; 95% CI: 1.0079-1.0339; P=0.0015) and UC (outliers excluded: OR: 1.0220; 95% CI: 1.0051-1.0393; P=0.0108) were associated with a slight increase in breast cancer risk. Additionally, UC exhibited a potential causal effect on cervical cancer (outliers excluded: OR: 1.1091; 95% CI: 1.0286-1.1960; P=0.0071). In the East Asian population, CD had significant causal effects on pancreatic cancer (OR: 1.1876; 95% CI: 1.0741-1.3132; P=0.0008) and breast cancer (outliers excluded: OR: 0.9452; 95% CI: 0.9096-0.9822; P=0.0040). For UC, it exhibited significant causal associations with gastric cancer (OR: 1.1240; 95% CI: 1.0624-1.1891; P=4.7359×10-5), bile duct cancer (OR: 1.3107; 95% CI: 1.0983-1.5641; P=0.0027), hepatocellular carcinoma (OR: 1.2365; 95% CI: 1.1235-1.3608; P=1.4007×10-5) and cervical cancer (OR: 1.3941; 95% CI: 1.1708-1.6599; P=0.0002), as well as a potential causal effect on lung cancer (outliers excluded: OR: 1.1313; 95% CI: 1.0280-1.2449; P=0.0116). Conclusions Our study provided evidence that genetically predicted CD may be a risk factor for pancreatic and breast cancers in the European population, and for pancreatic cancer in the East Asian population. Regarding UC, it may be a risk factor for cervical and breast cancers in Europeans, and for gastric, bile duct, hepatocellular, lung, and cervical cancers in East Asians. Therefore, patients with CD and UC need to emphasize screening and prevention of site-specific extraintestinal cancers.
Collapse
Affiliation(s)
- Chengdong Yu
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Jiawei Xu
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Siyi Xu
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Lei Tang
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Qinyuan Han
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xiaoqiang Zeng
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yanxiao Huang
- Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Tenghua Yu
- Department of breast surgery, Jiangxi Cancer Hospital, Nanchang, China
| | - Zhengkui Sun
- Department of breast surgery, Jiangxi Cancer Hospital, Nanchang, China
| |
Collapse
|
26
|
Feng J, Chen X, Cai W, Zhou X, Zhang X. Association between inflammatory bowel disease and frailty: a two-sample Mendelian randomization study. Aging Clin Exp Res 2024; 36:21. [PMID: 38319411 PMCID: PMC10847216 DOI: 10.1007/s40520-023-02688-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND An association has been identified between inflammatory bowel disease (IBD) and frailty; however, the causal nature of this connection remains uncertain. We consequently conducted a two-sample Mendelian randomization (MR) analysis to explore this particular association. METHODS We acquired distinct datasets for inflammatory bowel disease (IBD), Crohn's disease (CD), ulcerative colitis (UC), and frailty from the published genome-wide association studies (GWAS) database, meticulously selecting instrumental variables (IVs). Subsequently, we employed a bidirection MR to examine the causal relationship between IBD (including CD and UC) and frailty. We utilized statistical methods, with a primary emphasis on inverse-variance weighted (IVW), accompanied by a series of sensitivity analyses to confirm heterogeneity and pleiotropy influenced the outcomes of the MR. RESULTS We found positive causal effects of genetically increased frailty risk on IBD (OR: 1.015, 95% CI 1.005-1.025, P = 0.004). Furthermore, when scrutinizing specific IBD subtypes, both Crohn's disease (CD) and ulcerative colitis (UC) demonstrated an increased predisposition to frailty (OR: 1.018, 95% CI 1.01-1.027, P < 0.05) and (OR = 1.016, 95% CI 1.005-1.027, P < 0.05). Nevertheless, despite the consistent trends observed in the weighted median and MR-Egger regression analyses for both conditions, statistical significance remained elusive. Notably, the results of the inverse MR analysis did not establish an association between frailty and an elevated risk of IBD development. CONCLUSIONS Our research indicates that IBD, encompassing both CD and UC, may augment the propensity for frailty. Clinical practitioners must prioritize early frailty assessment in individuals afflicted with inflammatory bowel disease, inclusive of Crohn's disease and ulcerative colitis, facilitating proactive measures and timely interventions. However, our findings do not provide evidence supporting a causal effect of frailty on IBD (including CD and UC). Consequently, further studies are essential to explore the intricate mechanisms that clarify the effect of frailty on IBD.
Collapse
Affiliation(s)
- Jingyi Feng
- School of Nursing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xi Chen
- Hospital for Skin Diseases, Institute of Dermatology Chinese Academy of Medical Sciences, Peking Union Medical College, Nanjing, China
| | - Wenjing Cai
- School of Nursing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xueying Zhou
- School of Nursing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xuefang Zhang
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210022, China.
| |
Collapse
|
27
|
Wushouer X, Aximujiang K, Kadeer N, Aihemaiti A, Zhong L, Yunusi K. Effect of huankuile on colon injury in rats with ulcerative colitis by reducing TNF-α and MMP9. Eur J Med Res 2024; 29:102. [PMID: 38321559 PMCID: PMC10845565 DOI: 10.1186/s40001-024-01695-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
OBJECTIVE To explore the mechanism of huankuile (HKL) in colon injury repair in rats with ulcerative colitis (UC). METHODS Fifty SPF Wistar male rats were divided randomly into a normal group, a negative control group, an HKL intervention group ('HKL group') and a 5-aminosalicylic acid intervention group ('5-ASA group'). After 14 days of intervention with corresponding drugs, pathological scores were obtained using the results of immunohistochemical staining; morphological changes were observed by hematoxylin-eosin staining, and the mRNA expression levels of tumour necrosis factor-α (TNF-α), matrix metalloproteinase 9 (MMP9) and interleukin-13 (IL-13) were detected by real-time quantitative PCR. RESULTS After the successful construction of the rat model, it was compared with the rats in the normal group. In the negative group, it was found that the expression of TNF-α and MMP9 was significantly increased in the colonic mucosal epithelia of the rats, the pathological score was significantly increased (P < 0.05), and the mRNA expression levels of TNF-α, MMP9 and IL-13 were increased (P < 0.05). After treatment with HKL, the colonic morphology of the rats returned to normal, the expression of TNF-α and MMP9 in the colonic mucosal epithelium of the rats returned to normal, the pathological score grade was significantly reduced (P < 0.05), and the mRNA expression levels of TNF-α, MMP9 and IL-13 were reduced; these results were largely consistent with those of the normal group, with no statistically significant difference. CONCLUSION HKL effectively improved the general symptoms and tissue injury in UC rats, and the therapeutic effect was better than that of 5-ASA group. Ulcerative colitis in rats increased the expression of TNF-α, MMP9 and IL-13. HKL repaired UC-induced colonic injury in rats by decreasing the expression of TNF-α, MMP9 and IL-13.
Collapse
Affiliation(s)
- Xilinguli Wushouer
- Department of Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, 830017, China
- Xinjiang key laboratory of Molecular Biology for endemic diseases, Urumqi , 830054, China
| | - Kasimujiang Aximujiang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, 830017, China
| | - Nafeisha Kadeer
- Department of Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, 830017, China
| | - Abulaiti Aihemaiti
- The Functional Center, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, 830017, China
| | - Li Zhong
- The Functional Center, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, 830017, China
| | - Kurexi Yunusi
- UygurMedical College, Xinjiang Medical University, Urumqi, 830017, China.
| |
Collapse
|
28
|
Wu GL, Li L, Chen XY, Zhang WF, Wu JB, Yu X, Chen HJ. Machine learning-based B cell-related diagnostic biomarker signature and molecular subtypes characteristic of ulcerative colitis. Aging (Albany NY) 2024; 16:2774-2788. [PMID: 38319729 PMCID: PMC10911385 DOI: 10.18632/aging.205510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
As an inflammatory bowel disease, ulcerative colitis (UC) does not respond well to current treatments. It is of positive clinical significance to further study the pathogenesis of UC and find new therapeutic targets. B lymphocytes play an important role in the pathogenesis of UC. The effect of anti-CD20 therapy on UC also provides new evidence for the involvement of B cells in UC process additionally, suggesting the important role and potential therapeutic value of B cells in UC. In this study, we screened the most critical immune cell-related gene modules associated with UC and found that activated B cells were closely related to the gene modules. Subsequently, key activated B cell-associated gene (BRG) signatures were obtained based on WGCNA and differential expression analysis, and three overlapping BRG-associated genes were obtained by RF and LASSO algorithms as BRG-related diagnostic biomarkers for UC. Nomogram model was further performed to evaluate the diagnostic ability of BRG-related diagnostic biomarkers, subsequently followed by UC molecular subsets identification and immunoinfiltration analysis. We also further verified the expressions of the three screened BRGs in vitro by using an LPS-induced NCM460 cell line model. Our results provide new evidence and potential intervention targets for the role of B cells in UC from a new perspective.
Collapse
Affiliation(s)
- Guo-Liang Wu
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
- Department of Anorectal Section, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, China
| | - Li Li
- Department of Endocrinology, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250014, China
| | - Xiao-Yao Chen
- Department of Anorectal Section, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, China
| | - Wei-Feng Zhang
- Department of Colorectal Surgery, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210029, China
- Department of Anorectal Section, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Jun-Bo Wu
- Department of Colorectal Surgery, Hengyang Central Hospital, Hengyang, Hunan 421001, China
| | - Xiaoning Yu
- Department of Geriatrics, Hematology and Oncology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Hong-Jin Chen
- Department of Anorectal Section, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| |
Collapse
|
29
|
Leoncini G, Cari L, Ronchetti S, Donato F, Caruso L, Calafà C, Villanacci V. Mucin Expression Profiles in Ulcerative Colitis: New Insights on the Histological Mucosal Healing. Int J Mol Sci 2024; 25:1858. [PMID: 38339134 PMCID: PMC10855303 DOI: 10.3390/ijms25031858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
A structural weakness of the mucus barrier (MB) is thought to be a cause of ulcerative colitis (UC). This study aims to investigate the mucin (MUC) composition of MB in normal mucosa and UC. Ileocolonic biopsies were taken at disease onset and after treatment in 40 patients, including 20 with relapsing and 20 with remitting UC. Ileocolonic biopsies from 10 non-IBD patients were included as controls. Gut-specific MUC1, MUC2, MUC4, MUC5B, MUC12, MUC13, MUC15, and MUC17 were evaluated immunohistochemically. The promoters of mucin genes were also examined. Normal mucosa showed MUC2, MUC5B, and MUC13 in terminal ileum and colon, MUC17 in ileum, and MUC1, MUC4, MUC12, and MUC15 in colon. Membranous, cytoplasmic and vacuolar expressions were highlighted. Overall, the mucin expression was abnormal in UC. Derangements in MUC1, MUC4, and MUC5B were detected both at onset and after treatment. MUC2 and MUC13 were unaffected. Sequence analysis revealed glucocorticoid-responsive elements in the MUC1 promoter, retinoic-acid-responsive elements in the MUC4 promoter, and butyrate-responsive elements in the MUC5B promoter. In conclusion, MUCs exhibited distinct expression patterns in the gut. Their expression was disrupted in UC, regardless of the treatment protocols. Abnormal MUC1, MUC4, and MUC5B expression marked the barrier dysfunction in UC.
Collapse
Affiliation(s)
- Giuseppe Leoncini
- First Pathology Division, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy;
| | - Luigi Cari
- Pharmacology Division, Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Simona Ronchetti
- Pharmacology Division, Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Francesco Donato
- Unit of Hygiene, Epidemiology and Public Health, University of Brescia, 25123 Brescia, Italy
| | - Laura Caruso
- Pathology Unit, Department of Pathology and Laboratory Medicine, Desenzano del Garda Hospital, ASST del Garda, 25015 Brescia, Italy
| | - Cristina Calafà
- Pathology Unit, Department of Pathology and Laboratory Medicine, Desenzano del Garda Hospital, ASST del Garda, 25015 Brescia, Italy
| | | |
Collapse
|
30
|
Wen Y, Li C, Huang P, Liu Z, He Y, Liu B. Transcriptional landscape of intestinal environment in DSS-induced ulcerative colitis mouse model. BMC Gastroenterol 2024; 24:60. [PMID: 38308210 PMCID: PMC10836045 DOI: 10.1186/s12876-024-03128-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 01/05/2024] [Indexed: 02/04/2024] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory disease that targets the colon and has seen an increasing prevalence worldwide. In our pursuit of new diagnostic and therapeutic approaches for UC, we undertook a sequencing of colons from UC mouse models. We focused on analyzing their differentially expressed genes (DEGs), enriching pathways, and constructing protein-protein interaction (PPI) and Competing Endogenous RNA (ceRNA) networks. Our analysis highlighted novel DEGs such as Tppp3, Saa3, Cemip, Pappa, and Nr1d1. These DEGs predominantly play roles in pathways like cytokine-mediated signaling, extracellular matrix organization, extracellular structure organization, and external encapsulating structure organization. This suggests that the UC pathogenesis is intricately linked to the interactions between immune and non-immune cells with the extracellular matrix (ECM). To corroborate our findings, we also verified certain DEGs through quantitative real-time PCR. Within the PPI network, nodes like Stat3, Il1b, Mmp3, and Lgals3 emerged as significant and were identified to be involved in the crucial cytokine-mediated signaling pathway, which is central to inflammation. Our ceRNA network analysis further brought to light the role of the Smad7 Long non-coding RNA (lncRNA). Key MicroRNA (miRNAs) in the ceRNA network were pinpointed as mmu-miR-17-5p, mmu-miR-93-5p, mmu-miR-20b-5p, mmu-miR-16-5p, and mmu-miR-106a-5p, while central mRNAs included Egln3, Plagl2, Sema7a, Arrdc3, and Stat3. These insights imply that ceRNA networks are influential in UC progression and could provide further clarity on its pathogenesis. In conclusion, this research deepens our understanding of UC pathogenesis and paves the way for potential new diagnostic and therapeutic methods. Nevertheless, to solidify our findings, additional experiments are essential to confirm the roles and molecular interplay of the identified DEGs in UC.
Collapse
Affiliation(s)
- Yuefei Wen
- Foshan Maternity and Child Health Care Hospital, Southern Medical University, 528000, Foshan, China
| | - Chenyang Li
- Zhujiang Hospital, Southern Medical University, 510282, Guangzhou, China
| | - Peng Huang
- Foshan Maternity and Child Health Care Hospital, Southern Medical University, 528000, Foshan, China
| | - Zhigang Liu
- Foshan Maternity and Child Health Care Hospital, Southern Medical University, 528000, Foshan, China
| | - Yanjun He
- Foshan Maternity and Child Health Care Hospital, Southern Medical University, 528000, Foshan, China.
- Zhujiang Hospital, Southern Medical University, 510282, Guangzhou, China.
| | - Bin Liu
- Zhujiang Hospital, Southern Medical University, 510282, Guangzhou, China.
| |
Collapse
|
31
|
Shi Y, Luo S, Zhai J, Chen Y. A novel causative role of imbalanced kynurenine pathway in ulcerative colitis: Upregulation of KMO and KYNU promotes intestinal inflammation. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166929. [PMID: 37918679 DOI: 10.1016/j.bbadis.2023.166929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/14/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
The kynurenine pathway (KP) is the principal metabolic route for the essential amino acid tryptophan (TRP). Recent advances have highlighted a pivotal role for several KP metabolites in inflammatory diseases, including ulcerative colitis (UC). However, the alterations of KP enzymes and their functional impact in UC remain poorly defined. Here, we focused on kynurenine 3-monooxygenase (KMO) and kynureninase (KYNU), which serve as critical branching enzymes in the KP. We observed that dextran sodium sulfate (DSS)-induced colitis mice exhibited disturbed TRP metabolism along with KMO and KYNU upregulated. In patients with active UC, both the expression of KMO and KYNU were positively correlated with inflammatory factors TNF-α and IL-1β. Pharmacological blockade of KMO or genetic silencing of KYNU suppressed IL-1β-triggered proinflammatory cytokines expression in intestinal epithelial cells. Furthermore, blockage of KMO by selective inhibitor Ro 61-8048 alleviated the symptoms of DSS-induced colitis in mice, accompanied by an expanded NAD+ pool and redox balance restoration. The protective role of Ro 61-8048 may be partly due to its effect on KP regulation, particularly in enhancing kynurenic acid production. In summary, our study provides new evidence for the proinflammatory property of KMO and KYNU in intestinal inflammation, hinting at a promising therapeutic approach in UC through targeting these enzymes.
Collapse
Affiliation(s)
- Yingying Shi
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China
| | - Shangjian Luo
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China
| | - Jinyang Zhai
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China
| | - Yingwei Chen
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
32
|
Aishwarya S, Gunasekaran K. Differential Gene Expression Profiles Involved in the Inflammations Due to COVID-19 and Inflammatory Bowel Diseases and the Investigation of Predictive Biomarkers. Biochem Genet 2024; 62:311-332. [PMID: 37335372 DOI: 10.1007/s10528-023-10414-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Gastrointestinal manifestations in COVID-19 were attributed to 74-86% of the hospitalised patients due to severe or prolonged pathogenesis. Though it is a respiratory disease, the impact it elicits on the gastrointestinal tract and brain are intense. Inflammatory bowel disease including Crohn's disease and ulcerative colitis are idiopathic inflammatory disorders of the gastrointestinal tract. The intrinsic mechanisms involved in gut inflammations due to a respiratory viral disease can be deciphered when the gene expression profiles of COVID-19 and IBD are compared. The current study utilises an integrated bioinformatics approach to unravel them. The publicly available gene expression profiles of colon transcriptomes infected with COVID-19, Crohn's disease and Ulcerative colitis were retrieved, integrated and analysed for the identification of differentially expressed genes. The inter-relational analysis along with gene annotation and pathway enrichment detailed the functional and metabolic pathways of the genes during normal and diseased conditions. The protein-protein interactions deduced from the STRING database and the identified hub genes predicted potential biomarker candidates for COVID-19, Crohn's disease and ulcerative colitis. The inflammatory response pathways were upregulated and enrichment of chemokine signalling, altered lipid metabolism, coagulation and complement cascades were seen in all three conditions along with impaired transport mechanisms. CXCL11, MMP10, and CFB are predicted to be overexpressed biomarkers, whilst GUCA2A, SLC13A2, CEACAM, and IGSF9 as downregulated novel biomarker candidates for colon inflammations. The three miRNAs hsa-miR-16-5p, hsa-miR-21-5p, and hsa-miR-27b-5p exhibited significant interactions with the upregulated hub genes and four long non-coding RNAs NEAT1, KCNQ1OT1, and LINC00852 capable of regulating miRNA were also predicted. This study offers significant information on the underlying molecular mechanisms of inflammatory bowel disease with identification of potential biomarkers.
Collapse
Affiliation(s)
- S Aishwarya
- Department of Bioinformatics, Stella Maris College (Autonomous), Chennai, India.
- CAS in Crystallography and Biophysics, University of Madras, Chennai, India.
| | - K Gunasekaran
- CAS in Crystallography and Biophysics, University of Madras, Chennai, India
| |
Collapse
|
33
|
Luo S, Chen XH. Tissue and serum miR-149-3p/5p in hospitalized patients with inflammatory bowel disease: Correlation with disease severity and inflammatory markers. Kaohsiung J Med Sci 2024; 40:131-138. [PMID: 37997516 DOI: 10.1002/kjm2.12784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/21/2023] [Accepted: 10/02/2023] [Indexed: 11/25/2023] Open
Abstract
This study aimed to investigate the expression levels of tissue and serum miR-149-3p and miR-149-5p in hospitalized patients with inflammatory bowel disease (IBD). A total of 35 ulcerative colitis (UC) patients, 12 Crohn's disease (CD) patients, and 25 healthy controls were included in the study. The miRNAs expressions were measured in tissue and serum samples using quantitative real-time polymerase chain reaction (qRT-PCR). Inflammatory biomarkers were measured, including serum albumin, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6), and fecal calprotectin. MiR-149-3p and miR-149-5p were significantly decreased in the inflamed areas of both CD and UC patients compared to tissue controls, which was consistent with decreased serum levels in IBD patients compared to healthy controls. When distinguishing UC patients from healthy controls, serum miR-149-3p showed 74% sensitivity and 96% specificity, while serum miR-149-5p exhibited 63% sensitivity and 96% specificity. In the CD versus healthy control comparison, miR-149-3p achieved 100% sensitivity and 96% specificity, while miR-149-5p demonstrated 92% sensitivity and 96% specificity. In the UC versus CD comparison, miR-149-5p showed 75% sensitivity and 77% specificity, while miR-149-3p displayed 67% sensitivity and 80% specificity. Significant correlations were identified between the tissue and serum expression of miR-149-3p/5p and disease activity scores, as well as inflammatory biomarkers in both CD and UC patients. Decreased expression of miR-149-3p and miR-149-5p is associated with disease activity in IBD patients. These miRNAs demonstrate diagnostic potential and may serve as biomarkers for monitoring disease activity in IBD.
Collapse
Affiliation(s)
- Shuang Luo
- Department of Gastroenterology, Pingyang Hospital Affiliated to Wenzhou Medical University, Zhejiang, China
| | - Xi-Han Chen
- Department of Gastroenterology, Pingyang Hospital Affiliated to Wenzhou Medical University, Zhejiang, China
| |
Collapse
|
34
|
Ratajczak-Pawłowska AE, Hryhorowicz S, Szymczak-Tomczak A, Wysocka E, Michalak M, Kaczmarek-Ryś M, Lis-Tanaś E, Bielawska L, Pławski A, Słomski R, Dobrowolska A, Krela-Kaźmierczak I. Genetic variants of MTHFR gene in relation to folic acid levels and bone mineral density in Polish patients with inflammatory bowel disease. J Appl Genet 2024; 65:73-81. [PMID: 37816983 PMCID: PMC10789830 DOI: 10.1007/s13353-023-00792-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023]
Abstract
Lower bone mineral density (BMD) constitutes a common issue in inflammatory bowel disease (IBD). Studies often explore the association between BMD and folic acid level. The presented study aimed to evaluate the impact of MTHFR gene polymorphism and folic acid levels on BMD in patients with IBDs: Crohn's disease (CD) and ulcerative colitis (UC). The study group comprised IBD patients and a healthy control group. BMD, T-score, and Z-score of the lumbar spine (L1-L4) and femoral neck (FN) were assessed using dual-energy X-ray absorptiometry. Folic acid level was determined using direct chemiluminescence, and the MTHFR 677C > T (rs1801133) and 1298A > C (rs1801131) genotyping were performed by HRMA. Our study found no significant differences in the folic acid levels between the groups. Patients with CD and UC presented a lower BMD, T-score, and Z-score of the FN and L1-L4 than the CG. UC patients who were homozygotes AA in loci c.1298A>C presented lower than controls lumbar spine L1-L4 BMD and T-score values. Regarding MTHFR 677 polymorphism, we found that IBD patients carrying CC genotype demonstrated lower than controls femoral neck Z-score, lumbar spine L1-L4 BMD, T-score and Z-score. MTHFR polymorphisms were found to have no impact on folic acid concentrations. IBD patients presented a higher risk of low BMD than the healthy controls, regardless of MTHFR 677 and 1298 genotypes. However, MTHFR polymorphism may influence on bone in IBD patients. Nevertheless, it appears essential to conduct further studies.
Collapse
Affiliation(s)
- Alicja E Ratajczak-Pawłowska
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland.
- Doctoral School, Poznan University of Medical Sciences, Bukowska 70, 60-812, Poznan, Poland.
| | - Szymon Hryhorowicz
- Institute of Human Genetics, Polish Academy of Sciences Poznan, Strzeszynska 32, 60-479, Poznan, Poland
| | - Aleksandra Szymczak-Tomczak
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland
| | - Ewa Wysocka
- Department of Laboratory Diagnostics, Poznan University of Medical Sciences, Szamarzewskiego 82/84, 60-569, Poznan, Poland
| | - Michał Michalak
- Department of Computer Science and Statistics, Poznan University of Medical Sciences, Rokietnicka 7, 60-806, Poznan, Poland
| | - Marta Kaczmarek-Ryś
- Institute of Human Genetics, Polish Academy of Sciences Poznan, Strzeszynska 32, 60-479, Poznan, Poland
| | - Emilia Lis-Tanaś
- Institute of Human Genetics, Polish Academy of Sciences Poznan, Strzeszynska 32, 60-479, Poznan, Poland
| | - Lena Bielawska
- Department of Laboratory Diagnostics, Poznan University of Medical Sciences, Szamarzewskiego 82/84, 60-569, Poznan, Poland
| | - Andrzej Pławski
- Institute of Human Genetics, Polish Academy of Sciences Poznan, Strzeszynska 32, 60-479, Poznan, Poland
| | - Ryszard Słomski
- Institute of Human Genetics, Polish Academy of Sciences Poznan, Strzeszynska 32, 60-479, Poznan, Poland
| | - Agnieszka Dobrowolska
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland
| | - Iwona Krela-Kaźmierczak
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland.
| |
Collapse
|
35
|
Lafzi A, Borrelli C, Baghai Sain S, Bach K, Kretz JA, Handler K, Regan-Komito D, Ficht X, Frei A, Moor A. Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA). Mol Syst Biol 2024; 20:98-119. [PMID: 38225383 PMCID: PMC10897385 DOI: 10.1038/s44320-023-00006-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/28/2023] [Accepted: 12/08/2023] [Indexed: 01/17/2024] Open
Abstract
Sequencing-based spatial transcriptomics (ST) methods allow unbiased capturing of RNA molecules at barcoded spots, charting the distribution and localization of cell types and transcripts across a tissue. While the coarse resolution of these techniques is considered a disadvantage, we argue that the inherent proximity of transcriptomes captured on spots can be leveraged to reconstruct cellular networks. To this end, we developed ISCHIA (Identifying Spatial Co-occurrence in Healthy and InflAmed tissues), a computational framework to analyze the spatial co-occurrence of cell types and transcript species within spots. Co-occurrence analysis is complementary to differential gene expression, as it does not depend on the abundance of a given cell type or on the transcript expression levels, but rather on their spatial association in the tissue. We applied ISCHIA to analyze co-occurrence of cell types, ligands and receptors in a Visium dataset of human ulcerative colitis patients, and validated our findings at single-cell resolution on matched hybridization-based data. We uncover inflammation-induced cellular networks involving M cell and fibroblasts, as well as ligand-receptor interactions enriched in the inflamed human colon, and their associated gene signatures. Our results highlight the hypothesis-generating power and broad applicability of co-occurrence analysis on spatial transcriptomics data.
Collapse
Affiliation(s)
- Atefeh Lafzi
- Roche Pharma Research and Early Development, Immunology Infectious Diseases and Ophthalmology Discovery and Translational Area, Grenzacherstrasse 124, 4070, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Simona Baghai Sain
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Karsten Bach
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Jonas A Kretz
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Kristina Handler
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Daniel Regan-Komito
- Roche Pharma Research and Early Development, Immunology Infectious Diseases and Ophthalmology Discovery and Translational Area, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Xenia Ficht
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Andreas Frei
- Roche Pharma Research and Early Development, Immunology Infectious Diseases and Ophthalmology Discovery and Translational Area, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Andreas Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
| |
Collapse
|
36
|
Huang M, Wu Y, Li Y, Chen X, Feng J, Li Z, Li J, Chen J, Lu Y, Feng Y. Circadian clock-related genome-wide mendelian randomization identifies putatively genes for ulcerative colitis and its comorbidity. BMC Genomics 2024; 25:130. [PMID: 38302916 PMCID: PMC10832088 DOI: 10.1186/s12864-024-10003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Circadian rhythm is crucial to the function of the immune system. Disorders of the circadian rhythm can contribute to inflammatory diseases such as Ulcerative colitis (UC). This Mendelian Randomization (MR) analysis applies genetic tools to represent the aggregated statistical results of exposure to circadian rhythm disorders and UC and its comorbidities, allowing for causal inferences. METHODS Summary statistics of protein, DNA methylation and gene expression quantitative trait loci in individuals of European ancestry (pQTL, mQTL, and eQTL, respectively) were used. Genetic variants located within or near 152 circadian clock-related genes and closely related to circadian rhythm disorders were selected as instrumental variables. Causal relationships with UC and its comorbidities were then estimated through employed Summary data-based Mendelian Randomization (SMR) and Inverse-Variance-Weighted MR (IVW-MR). RESULTS Through preliminary SMR analysis, we identified a potential causal relationship between circadian clock-related genes and UC along with its comorbidities, which was further confirmed by IVW-MR analysis. Our study identified strong evidence of positive correlation involving seven overlapping genes (CSNK1E, OPRL1, PIWIL2, RORC, MAX, PPP5C, and AANAT) through MWAS and TWAS in UC, four overlapping genes (OPRL1, CHRNB2, FBXL17, and SIRT1) in UC with PSC, and three overlapping genes (ARNTL, USP7, and KRAS) in UC with arthropathy. CONCLUSIONS This SMR study demonstrates the causal effect of circadian rhythm disorders in UC and its comorbidities. Furthermore, our investigation pinpointed candidate genes that could potentially serve as drug targets.
Collapse
Affiliation(s)
- Mengfen Huang
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuan Wu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yiting Li
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xueru Chen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jieni Feng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zuming Li
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiqiang Li
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China.
| | - Jiankun Chen
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China.
| | - Yue Lu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China.
| | - Yan Feng
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China.
| |
Collapse
|
37
|
Zhang J, Feng S, Chen M, Zhang W, Zhang X, Wang S, Gan X, Zheng Y, Wang G. Identification of potential crucial genes shared in psoriasis and ulcerative colitis by machine learning and integrated bioinformatics. Skin Res Technol 2024; 30:e13574. [PMID: 38303405 PMCID: PMC10835022 DOI: 10.1111/srt.13574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024]
Abstract
BACKGROUND Mounting evidence suggest that there are an association between psoriasis and ulcerative colitis (UC), although the common pathogeneses are not fully understood. Our study aimed to find potential crucial genes in psoriasis and UC through machine learning and integrated bioinformatics. METHODS The overlapping differentially expressed genes (DEGs) of the datasets GSE13355 and GSE87466 were identified. Then the functional enrichment analysis was performed. The overlapping genes in LASSO, SVM-RFE and key module in WGCNA were considered as potential crucial genes. The receiver operator characteristic (ROC) curve was used to estimate their diagnostic confidence. The CIBERSORT was conducted to evaluate immune cell infiltration. Finally, the datasets GSE30999 and GSE107499 were retrieved to validate. RESULTS 112 overlapping DEGs were identified in psoriasis and UC and the functional enrichment analysis revealed they were closely related to the inflammatory and immune response. Eight genes, including S100A9, PI3, KYNU, WNT5A, SERPINB3, CHI3L2, ARNTL2, and SLAMF7, were ultimately identified as potential crucial genes. ROC curves showed they all had high confidence in the test and validation datasets. CIBERSORT analysis indicated there was a correlation between infiltrating immune cells and potential crucial genes. CONCLUSION In our study, we focused on the comprehensive understanding of pathogeneses in psoriasis and UC. The identification of eight potential crucial genes may contribute to not only understanding the common mechanism, but also identifying occult UC in psoriasis patients, even serving as therapeutic targets in the future.
Collapse
Affiliation(s)
- Jing Zhang
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Shuo Feng
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Minfei Chen
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Wen Zhang
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Xiu Zhang
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Shengbang Wang
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Xinyi Gan
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Yan Zheng
- Department of Dermatologythe First Affiliated HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| | - Guorong Wang
- The First Department of General Surgerythe Third Affiliated Hospital and Shaanxi Provincial People's HospitalXi'an Jiaotong UniversityXi'anShaanxi ProvinceChina
| |
Collapse
|
38
|
Huang K, Huang S, Xiong M. Correlations between genetically predicted lipid-lowering drug targets and inflammatory bowel disease. Lipids Health Dis 2024; 23:31. [PMID: 38287401 PMCID: PMC10823737 DOI: 10.1186/s12944-024-02026-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/21/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Millions of individuals globally suffer from Inflammatory bowel diseases (IBDs). There is a dearth of large population-based investigations on lipid metabolism and IBDs, and it is unclear whether lipid-lowering drugs target IBDs causally. Consequently, the aim of this study was to investigate the effects of lipid-lowering medication targets on the occurrence and progression of IBDs. METHODS Among the more than 400,000 participants in the UK Biobank cohort and the more than 170,000 participants in the Global Lipids Genetics Consortium, a total of nine genes linked to lipid-lowering drug targets were obtained (ABCG5/ABCG8, APOB, APOC3, LDLR, LPL, HMGCR, NPC1L1, PCSK9, and PPARA). IBD data were acquired from de Lange et al. (patients/sample size of IBDs: 25042/59957; ulcerative colitis (UC): 12366/45,975; Crohn's disease (CD): 12194/40,266) and the FinnGen cohort (patients/total sample size of IBDs: 4420/176,899; CD: 1520/171,906; UC: 3325/173,711). All four datasets were cross-combined for validation via Mendelian randomization analysis, and potential mediating factors were explored via mediation analysis. RESULTS Genetically proxied APOC3 inhibition was related to increased IBD risk (odds ratio (95% confidence interval): 0.87 (0.80-0.95); P < 0.01) and UC risk (0.83 (0.73-0.94); P < 0.01). IBD and CD risk were reduced by genetic mimicry of LDLR and LPL enhancements, respectively (odds ratioLDLR: 1.18 (1.03-1.36); P = 0.018; odds ratioCD: 1.26 (1.11-1.43); P = 2.60E-04). Genetically proxied HMGCR inhibition was associated with increased CD risk (0.68 (0.50-0.94); P = 0.018). These findings were confirmed through Mendelian analysis of the cross-combination of four separate datasets. APOC3-mediated triglyceride levels may contribute to IBDs partly through mediated triglycerides, Clostridium sensu stricto 1, Clostridiaceae 1, or the Lachnospiraceae FCS020 group. LDLR enhancement may contribute to IBDs partly through increasing Lactobacillaceae. CONCLUSION Vigilance is required to prevent adverse effects on IBDs (UC) for patients receiving volanesorsen (an antisense oligonucleotide targeting ApoC3 mRNA) and adverse effects on CD for statin users. LPL and LDLR show promise as candidate drug targets for CD and IBD, respectively, with mechanisms that are potentially independent of their lipid-lowering effects.
Collapse
Affiliation(s)
- Kuiyuan Huang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Jiangxi, 330000, China
| | - Shenan Huang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Jiangxi, 330000, China
| | - Ming Xiong
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Jiangxi, 330000, China.
| |
Collapse
|
39
|
Labes S, Froy O, Tabach Y, Shamir R, Shouval DS, Weintraub Y. Mucosal Genes Encoding Clock, Inflammation and Their Mutual Regulators Are Disrupted in Pediatric Patients with Active Ulcerative Colitis. Int J Mol Sci 2024; 25:1488. [PMID: 38338765 PMCID: PMC10855499 DOI: 10.3390/ijms25031488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Patients with active ulcerative colitis (UC) display a misalignment of the circadian clock, which plays a vital role in various immune functions. Our aim was to characterize the expression of clock and inflammation genes, and their mutual regulatory genes in treatment-naïve pediatric patients with UC. Using the Inflammatory Bowel Disease Transcriptome and Metatranscriptome Meta-Analysis (IBD TaMMA) platform and R algorithms, we analyzed rectal biopsy transcriptomic data from two cohorts (206 patients with UC vs. 20 healthy controls from the GSE-109142 study, and 43 patients with UC vs. 55 healthy controls from the GSE-117993 study). We compared gene expression levels and correlation of clock genes (BMAL1, CLOCK, PER1, PER2, CRY1, CRY2), inflammatory genes (IκB, IL10, NFκB1, NFκB2, IL6, TNFα) and their mutual regulatory genes (RORα, RORγ, REV-ERBα, PGC1α, PPARα, PPARγ, AMPK, SIRT1) in patients with active UC and healthy controls. The clock genes BMAL1, CLOCK, PER1 and CRY1 and the inflammatory genes IκB, IL10, NFκB1, NFκB2, IL6 and TNFα were significantly upregulated in patients with active UC. The genes encoding the mutual regulators RORα, RORγ, PGC1α, PPARα and PPARγ were significantly downregulated in patients with UC. A uniform pattern of gene expression was found in healthy controls compared to the highly variable expression pattern in patients with UC. Among the healthy controls, inflammatory genes were positively correlated with clock genes and they all showed reduced expression. The difference in gene expression levels was associated with disease severity and endoscopic score but not with histological score. In patients with active UC, clock gene disruption is associated with abnormal mucosal immune response. Disrupted expression of genes encoding clock, inflammation and their mutual regulators together may play a role in active UC.
Collapse
Affiliation(s)
- Sapir Labes
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem 91905, Israel; (S.L.); (Y.T.)
| | - Oren Froy
- Institute of Biochemistry, Food Science and Nutrition, Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot 7610001, Israel
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem 91905, Israel; (S.L.); (Y.T.)
| | - Raanan Shamir
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children’s Medical Center of Israel, Petach Tikva 4920235, Israel; (R.S.); (D.S.S.); (Y.W.)
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dror S. Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children’s Medical Center of Israel, Petach Tikva 4920235, Israel; (R.S.); (D.S.S.); (Y.W.)
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yael Weintraub
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children’s Medical Center of Israel, Petach Tikva 4920235, Israel; (R.S.); (D.S.S.); (Y.W.)
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
40
|
Chen D, Zhou C, Luo Q, Chen C, Liu G. A Mendelian randomization study on causal effects of inflammatory bowel disease on the risk of erectile dysfunction. Sci Rep 2024; 14:2137. [PMID: 38272986 PMCID: PMC10811225 DOI: 10.1038/s41598-024-52712-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/23/2024] [Indexed: 01/27/2024] Open
Abstract
This study aimed to evaluate the causal effects of inflammatory bowel disease (IBD) and erectile dysfunction (ED) using Mendelian randomization (MR). All datasets were obtained from the public genome-wide association study database. In the exposure group, 12,882 IBD patients and 21,770 controls were included. A total of 1154 ED patients and 94,024 controls were included in the outcome group. Two-sample MR was conducted to estimate the causal effect of IBD on ED. Furthermore, Crohn's disease (CD) and ulcerative colitis (UC) were exposure factors in subgroup analyses. Weighted median, MR-egger, Inverse-variant weighted (IVW), weighted mode, and simple mode methods were used in MR analysis. Horizontal pleiotropy test, heterogeneity test, and leave-one-out method were utilized to evaluate the sensitivity and stability of results. After analysis, 62, 52, and 36 single nucleotide polymorphisms (SNPs) that IBD-ED, CD-ED, and UC-ED were included, respectively. The incidence of ED was increased by IBD (IVW: OR = 1.110, 95% CI = 1.017-1.211, P = 0.019; P-heterogeneity > 0.05) and, in addition, ED was affected by CD (IVW: OR = 1.085, 95% CI = 1.015-1.160, P = 0.016; P-heterogeneity > 0.05). However, there was no causal effect of UC on ED (IVW: OR = 1.018, 95% CI = 0.917-1.129, P = 0.743; P-heterogeneity < 0.05). All SNPs showed no significant horizontal pleiotropy (P > 0.05). These results indicate that IBD and CD can cause ED; However, UC did not cause ED. Additional research was required to determine causality and potential mechanisms further.
Collapse
Affiliation(s)
- Di Chen
- Department of Urology, The Frist Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chao Zhou
- Department of Assisted Reproduction, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Quanhai Luo
- Department of Urology, Reproductive Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Changsheng Chen
- Department of Urology, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Gang Liu
- Department of Urology, Reproductive Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
| |
Collapse
|
41
|
Zhang H, Kalla R, Chen J, Zhao J, Zhou X, Adams A, Noble A, Ventham NT, Wellens J, Ho GT, Dunlop MG, Nowak JK, Ding Y, Liu Z, Satsangi J, Theodoratou E, Li X. Altered DNA methylation within DNMT3A, AHRR, LTA/TNF loci mediates the effect of smoking on inflammatory bowel disease. Nat Commun 2024; 15:595. [PMID: 38238335 PMCID: PMC10796384 DOI: 10.1038/s41467-024-44841-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
This work aims to investigate how smoking exerts effect on the development of inflammatory bowel disease (IBD). A prospective cohort study and a Mendelian randomization study are first conducted to evaluate the association between smoking behaviors, smoking-related DNA methylation and the risks of Crohn's disease (CD) and ulcerative colitis (UC). We then perform both genome-wide methylation analysis and co-localization analysis to validate the observed associations. Compared to never smoking, current and previous smoking habits are associated with increased CD (P = 7.09 × 10-10) and UC (P < 2 × 10-16) risk, respectively. DNA methylation alteration at cg17742416 [DNMT3A] is linked to both CD (P = 7.30 × 10-8) and UC (P = 1.04 × 10-4) risk, while cg03599224 [LTA/TNF] is associated with CD risk (P = 1.91 × 10-6), and cg14647125 [AHRR] and cg23916896 [AHRR] are linked to UC risk (P = 0.001 and 0.002, respectively). Our study identifies biological mechanisms and pathways involved in the effects of smoking on the pathogenesis of IBD.
Collapse
Affiliation(s)
- Han Zhang
- Department of Big Data in Health Science School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Rahul Kalla
- Edinburgh IBD Science Unit, Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Jie Chen
- Department of Big Data in Health Science School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianhui Zhao
- Department of Big Data in Health Science School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xuan Zhou
- Department of Big Data in Health Science School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Alex Adams
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Alexandra Noble
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Nicholas T Ventham
- Academic Coloproctology, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Judith Wellens
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Department of Chronic Diseases and Metabolism, Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Gwo-Tzer Ho
- Edinburgh IBD Science Unit, Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Dunlop
- Cancer Research UK Scotland Centre and Medical Research Council Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Jan Krzysztof Nowak
- Department of Paediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Yuan Ding
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhanju Liu
- Center for IBD Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Evropi Theodoratou
- Cancer Research UK Scotland Centre and Medical Research Council Human Genetics Unit, University of Edinburgh, Edinburgh, UK.
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK.
| | - Xue Li
- Department of Big Data in Health Science School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
42
|
Kai N, Qingsong C, Kejia M, Weiwei L, Xing W, Xuejie C, Lixia C, Minzi D, Yuanyuan Y, Xiaoyan W. An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP). Database (Oxford) 2024; 2024:baad097. [PMID: 38227799 DOI: 10.1093/database/baad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/02/2023] [Accepted: 12/22/2023] [Indexed: 01/18/2024]
Abstract
IBD, including ulcerative colitis and Crohn's disease, is a chronic and debilitating gastrointestinal disorder that affects millions of people worldwide. Research on IBD has generated massive amounts of data, including literature, metagenomics, metabolomics, bioresources and databases. We aim to create an IBD Integrated Resources Portal (IBDIRP) that provides the most comprehensive resources for IBD. An integrated platform was developed that provides information on different aspects of IBD research resources, such as single-nucleotide polymorphisms (SNPs), genes, transcriptome, microbiota, metabolomics, single cells and other resources. Valuable and comprehensive IBD-related data were collected from PubMed, Google, GMrepo, gutMega, gutMDisorder, Single Cell Portal and other sources. Then, the data were systematically sorted, and these resources were manually curated. We systematically sorted and cataloged more than 320 unique risk SNPs associated with IBD in the SNP section. We presented over 289 IBD-related genes based on the database collection in the gene section. We also obtained 153 manually curated IBD transcriptomics data, including 12 388 samples, on the Gene Expression Omnibus database. The sorted IBD-related microbiota data from three primary microbiome databases (GMrepo, gutMega and gutMDisorder) were available for download. We selected 23 149 IBD-related taxonomic records from these databases. Additionally, we collected 24 IBD metabolomics studies with 2896 participants in the metabolomics section. We introduced two interactive single-cell data plug-in units that provided data visualization based on cells and genes. Finally, we listed 18 significant IBD web resources, such as the official European Crohn's and Colitis Organisation and International Organization for the Study of IBD websites, IBD scoring tools, IBD genetic and multi-omics resources, IBD biobanks and other useful research resources. The IBDIRP website is the first integrated resource for global IBD researchers. This portal will help researchers by providing comprehensive knowledge and enabling them to reinforce the multidimensional impression of IBD. The IBDIRP website is accessible via www.ibdirp.com Database URL: www.ibdirp.com.
Collapse
Affiliation(s)
- Nie Kai
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | | | - Ma Kejia
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | - Luo Weiwei
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | - Wu Xing
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | - Chen Xuejie
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | - Cai Lixia
- Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University Changsha Hunan 410000, China
| | - Deng Minzi
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | - Yang Yuanyuan
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | - Wang Xiaoyan
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
- The College of Computer Science in Sichuan University, Chengdu Sichuan 610000, China
| |
Collapse
|
43
|
Song Z, Li X, Xie J, Han F, Wang N, Hou Y, Yao J. Associations of inflammatory cytokines with inflammatory bowel disease: a Mendelian randomization study. Front Immunol 2024; 14:1327879. [PMID: 38288119 PMCID: PMC10822978 DOI: 10.3389/fimmu.2023.1327879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/27/2023] [Indexed: 01/31/2024] Open
Abstract
Objectives Previous studies have confirmed a link between specific inflammatory cytokines and inflammatory bowel disease (IBD), but the causal relationship between them is not completely clear. This Mendelian Randomization (MR) study aims to evaluate the causal relationship between 18 inflammatory cytokines and inflammatory bowel disease. Method Two-sample Mendelian randomization utilized genetic variances associated with IBD from two extensive publicly available genome-wide association studies (GWAS) (Crohn's Disease (CD): 12,194 cases and 28,072 controls; Ulcerative Colitis (UC): 12,336 cases and 33,609 controls). The data of inflammatory cytokines was acquired from a GWAS including 8,293 healthy participants. We used inverse variance weighted method, MR-Egger, weighted median, simple model and weighted model to evaluate the causal relationship between inflammatory cytokines and IBD. Sensitivity analysis includes heterogeneity and pleiotropy analysis to evaluate the robustness of the results. Results The findings indicated suggestive positive associations between Interleukin-13 (IL-13) and macrophage migration inhibitory factor (MIF) with CD (odds ratio, OR: 1.101, 95%CI: 1.021-1.188, p = 0.013; OR: 1.134, 95%CI: 1.024-1.255, p = 0.015). IL-13 also displayed a significant positive correlation with UC (OR: 1.099, 95%CI: 1.018-1.186, p = 0.016). Stem cell factor (SCF) was suggested to be associated with the development of both CD and UC (OR: 1.032, 95%CI: 0.973-1.058, p = 0.012; OR: 1.038, 95%CI: 1.005-1.072, p = 0.024). Conclusion This study proposes that IL-13 may be a factor correlated with the etiology of IBD (CD and UC), while MIF just be specifically associated with CD. Additionally, SCF appears more likely to be involved in the downstream development of IBD (CD and UC).
Collapse
Affiliation(s)
| | | | | | | | | | | | - Jianning Yao
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, ZhengZhou, China
| |
Collapse
|
44
|
Ye S, Lyu Y, Chen L, Wang Y, He Y, Li Q, Tian L, Liu F, Wang X, Ai F. Construction of a molecular inflammatory predictive model with histone modification-related genes and identification of CAMK2D as a potential response signature to infliximab in ulcerative colitis. Front Immunol 2024; 14:1282136. [PMID: 38274809 PMCID: PMC10808628 DOI: 10.3389/fimmu.2023.1282136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Background Ulcerative colitis (UC) is a lifelong inflammatory disease affecting the rectum and colon with numerous treatment options that require an individualized treatment plan. Histone modifications regulate chromosome structure and gene expression, resulting in effects on inflammatory and immune responses. However, the relationship between histone modification-related genes and UC remains unclear. Methods Transcriptomic data from GSE59071 and GSE66407 were obtained from the Gene Expression Omnibus (GEO), encompassing colonic biopsy expression profiles of UC patients in inflamed and non-inflamed status. Differentially expressed gene (DEG) analyses, functional enrichment analyses, weighted gene co-expression network analysis (WGCNA), and random forest were performed to identify histone modification-related core genes associated with UC inflammation. Features were screened through the least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE), establishing a molecular inflammatory predictive model using logistic regression. The model was validated in the GSE107499 dataset, and the performance of the features was assessed using receiver operating characteristic (ROC) and calibration curves. Immunohistochemistry (IHC) staining of colonic biopsy tissues from UC patients treated with infliximab was used to further confirm the clinical application value. Univariate logistic regression on GSE14580 highlighted features linked to infliximab response. Results A total of 253 histone modification-related DEGs were identified between inflammatory and non-inflammatory patients with UC. Seven key genes (IL-1β, MSL3, HDAC7, IRF4, CAMK2D, AUTS2, and PADI2) were selected using WGCNA and random forest. Through univariate logistic regression, three core genes (CAMK2D, AUTS2, and IL-1β) were further incorporated to construct the molecular inflammatory predictive model. The area under the curve (AUC) of the model was 0.943 in the independent validation dataset. A significant association between CAMK2D protein expression and infliximab response was observed, which was validated in another independent verification set of GSE14580 from the GEO database. Conclusion The molecular inflammatory predictive model based on CAMK2D, AUTS2, and IL-1β could reliably distinguish the mucosal inflammatory status of UC patients. We further revealed that CAMK2D was a predictive marker of infliximab response. These findings are expected to provide a new evidence base for personalized treatment and management strategies for UC patients.
Collapse
Affiliation(s)
- Shuyu Ye
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yongqing Lyu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Libin Chen
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yiwei Wang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yue He
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Quansi Li
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Li Tian
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Fen Liu
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Feiyan Ai
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| |
Collapse
|
45
|
Miao Z, Gu M, Raza F, Zafar H, Huang J, Yang Y, Sulaiman M, Yan J, Xu Y. Isoliquiritin Ameliorates Ulcerative Colitis in Rats through Caspase 3/HMGB1/TLR4 Dependent Signaling Pathway. Curr Gene Ther 2024; 24:73-92. [PMID: 37526181 DOI: 10.2174/1566523223666230731115236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND Isoliquiritin belongs to flavanol glycosides and has a strong antiinflammatory activity. This study sought to investigate the anti-inflammatory effect of isoliquiritin and its underlying mechanism. METHODS The inflammatory (trinitro-benzene-sulfonic acid-TNBS-induced ulcerative colitis (UC)) model was established to ascertain the effect of isoliquiritin on the caspase-3/HMGB1/TLR4 pathway in rats. We also explored its protective effect on intestinal inflammation and its underlying mechanism using the LPS-induced inflammation model of Caco-2 cells. Besides, Deseq2 was used to analyze UCassociated protein levels. RESULTS Isoliquiritin treatment significantly attenuated shortened colon length (induced by TNBS), disease activity index (DAI) score, and body weight loss in rats. A decrease in the levels of inflammatory mediators (IL-1β, I IL-4, L-6, IL-10, PGE2, and TNF-α), coupled with malondialdehyde (MDA) and superoxide dismutase (SOD), was observed in colon tissue and serum of rats after they have received isoliquiritin. Results of techniques (like western blotting, real-time PCR, immunohistochemistry, and immunofluorescence-IF) demonstrated the potential of isoliquiritin to decrease expressions of key genes in the TLR4 downstream pathways, viz., MyD88, IRAK1, TRAF6, NF-κB, p38, and JNK at mRNA and protein levels as well as inhibit HMGB1 expression, which is the upstream ligand of TLR4. Bioinformational analysis showed enteritis to be associated with a high expression of HMGB1, TLR4, and caspase-3. CONCLUSION Isoliquiritin could reduce intestinal inflammation and mucosal damage of TNBS-induced colitis in rats with a certain anti-UC effect. Meanwhile, isoliquiritin treatment also inhibited the expression of HMGB1, TLR4, and MyD88 in LPS-induced Caco-2 cells. These results indicated that isoliquiritin could ameliorate UC through the caspase-3/HMGB1/TLR4-dependent signaling pathway.
Collapse
Affiliation(s)
- Zhiwei Miao
- Department of Gastroenterology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, 215600, China
| | - Mingjia Gu
- Department of Nephrology, Changshu Hospital Affiliated to Nanjing University of Chinese medicine, Changshu, 215500, China
| | - Faisal Raza
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hajra Zafar
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianyi Huang
- Taizhou Hospital of Traditional Chinese Medicine, Taizhou, 318000, China
| | - Yuhang Yang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, China
| | | | - Jing Yan
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210000, China
| | - Yi Xu
- Department of Gastroenterology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210000, China
| |
Collapse
|
46
|
Morrill V, Benke K, Brinton J, Soke GN, Schieve LA, Fields V, Farzadegan H, Holingue C, Newschaffer CJ, Reynolds AM, Daniele Fallin M, Ladd-Acosta C. Genetic liability for gastrointestinal inflammation disorders and association with gastrointestinal symptoms in children with and without autism. Am J Med Genet B Neuropsychiatr Genet 2024; 195:e32952. [PMID: 37455590 PMCID: PMC10792104 DOI: 10.1002/ajmg.b.32952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/12/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
Children with autism spectrum disorder (ASD) have a greater prevalence of gastrointestinal (GI) symptoms than children without ASD. We tested whether polygenic scores for each of three GI disorders (ulcerative colitis, inflammatory bowel disease, and Crohn's disease) were related to GI symptoms in children with and without ASD. Using genotyping data (564 ASD cases and 715 controls) and external genome-wide association study summary statistics, we computed GI polygenic scores for ulcerative colitis (UC-PGS), inflammatory bowel disease (IDB-PGS), and Crohn's disease (CD-PGS). Multivariable logistic regression models, adjusted for genetic ancestry, were used to estimate associations between each GI-PGS and (1) ASD case-control status, and (2) specific GI symptoms in neurotypical children and separately in ASD children. In children without ASD, polygenic scores for ulcerative colitis were significantly associated with experiencing any GI symptom (adjusted odds ratio (aOR) = 1.36, 95% confidence interval (CI) = 1.03-1.81, p = 0.03) and diarrhea specifically (aOR = 5.35, 95% CI = 1.77-26.20, p = 0.01). Among children without ASD, IBD-PGS, and Crohn's PGS were significantly associated with diarrhea (aOR = 3.55, 95% CI = 1.25-12.34, p = 0.02) and loose stools alternating with constipation (aOR = 2.57, 95% CI = 1.13-6.55, p = 0.03), respectively. However, the three PGS were not associated with GI symptoms in the ASD case group. Furthermore, polygenic scores for ulcerative colitis significantly interacted with ASD status on presentation of any GI symptom within a European ancestry subset (aOR = 0.42, 95% CI = 0.19-0.88, p = 0.02). Genetic risk factors for some GI symptoms differ between children with and without ASD. Furthermore, our finding that increased genetic risks for GI inflammatory disorders are associated with GI symptoms in children without ASD informs future work on the early detection of GI disorders.
Collapse
Affiliation(s)
- Valerie Morrill
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Kelly Benke
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - John Brinton
- Department of Pediatrics, School of Medicine, University of Colorado and Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Gnakub N. Soke
- Centers for Disease Control and Prevention, Division of Scientific Education and Professional Development, Epidemic Intelligence Service, Atlanta, Georgia, USA
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Laura A. Schieve
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Victoria Fields
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Homayoon Farzadegan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Calliope Holingue
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Craig J. Newschaffer
- AJ Drexel Autism Institute, Drexel University, Philadelphia, Pennsylvania, USA
- College of Health and Human Development, Pennsylvania State University, Pennsylvania, USA
| | - Ann M. Reynolds
- Department of Pediatrics, School of Medicine, University of Colorado and Children’s Hospital Colorado, Aurora, Colorado, USA
| | - M. Daniele Fallin
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| |
Collapse
|
47
|
El Hadad J, Schreiner P, Vavricka SR, Greuter T. The Genetics of Inflammatory Bowel Disease. Mol Diagn Ther 2024; 28:27-35. [PMID: 37847439 PMCID: PMC10787003 DOI: 10.1007/s40291-023-00678-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 10/18/2023]
Abstract
The genetic background of inflammatory bowel disease, both Crohn's disease and ulcerative colitis, has been known for more than 2 decades. In the last 20 years, genome-wide association studies have dramatically increased our knowledge on the genetics of inflammatory bowel disease with more than 200 risk genes having been identified. Paralleling this increasing knowledge, the armamentarium of inflammatory bowel disease medications has been growing constantly. With more available therapeutic options, treatment decisions become more complex, with still many patients experiencing a debilitating disease course and a loss of response to treatment over time. With a better understanding of the disease, more effective personalized treatment strategies are looming on the horizon. Genotyping has long been considered a strategy for treatment decisions, such as the detection of thiopurine S-methyltransferase and nudix hydrolase 15 polymorphisms before the initiation of azathioprine. However, although many risk genes have been identified in inflammatory bowel disease, a substantial impact of genetic risk assessment on therapeutic strategies and disease outcome is still missing. In this review, we discuss the genetic background of inflammatory bowel disease, with a particular focus on the latest advances in the field and their potential impact on management decisions.
Collapse
Affiliation(s)
- Jasmina El Hadad
- Department of Internal Medicine, Triemli Hospital, Zurich, Switzerland
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Philipp Schreiner
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Stephan R Vavricka
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
- Center for Gastroenterology and Hepatology, Zurich, Switzerland
| | - Thomas Greuter
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland.
- Division of Gastroenterology and Hepatology, University Hospital Lausanne-CHUV, Lausanne, Switzerland.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, GZO Zurich Regional Health Center, Spitalstrasse 66, 8620, Wetzikon, Switzerland.
| |
Collapse
|
48
|
Li H, Xin Q, Hong L, Hu Y, Lin L, Guo M, Jiang H, He C, Wang S, Li M. Mendelian randomization analysis reveals causality of inflammatory bowel disease on risks of Henoch-Schönlein purpura and immune thrombocytopenia. Dig Liver Dis 2024; 56:92-97. [PMID: 37659917 DOI: 10.1016/j.dld.2023.08.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 09/04/2023]
Abstract
BACKGROUND Emerging clinical evidence has been discovered associating Inflammatory bowel disease (IBD) with Henoch-Schönlein purpura (HSP) and immune thrombocytopenia (ITP). However, it is unclear whether a cause-effect relationship exists between them. We aimed to examine the casual effect of IBD on the risk of HSP and ITP. METHODS Based on summary statistics from International IBD Genetics (IIBDG) Consortium and FinnGen study, a two-sample Mendelian randomization study was carried out to determine whether IBD including ulcerative colitis (UC) and Crohn's disease (CD) is causally related to HSP, ITP or secondary thrombocytopenia. To support the results, a variety of sensitivity analyses were performed. RESULTS Significant causal relationships between IBD and HSP (odds ratios = 1.20, 95% confidence interval: 1.07-1.36, adjusted P = 0.006) and ITP (odds ratios =1.22, 95% confidence interval: 1.08-1.38, adjusted P = 0.006) were found. Both genetically predicted UC and CD were positively related with ITP, while CD alone may be responsible for the higher risk of HSP. Besides, no significant association was observed between IBD and secondary thrombocytopenia. CONCLUSIONS The results of this Mendelian randomization study supported the causal association of IBD with HSP and ITP. Taken together, our findings may present implications for management of IBD.
Collapse
Affiliation(s)
- Haojia Li
- Inflammatory Bowel Diseases Research Center, Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Qing Xin
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Liping Hong
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Yuqi Hu
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Liangcai Lin
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Mingkai Guo
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Huixin Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Chengcheng He
- Inflammatory Bowel Diseases Research Center, Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shanping Wang
- Inflammatory Bowel Diseases Research Center, Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Mingsong Li
- Inflammatory Bowel Diseases Research Center, Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| |
Collapse
|
49
|
Chen J, Ruan X, Sun Y, Lu S, Hu S, Yuan S, Li X. Multi-omic insight into the molecular networks of mitochondrial dysfunction in the pathogenesis of inflammatory bowel disease. EBioMedicine 2024; 99:104934. [PMID: 38103512 PMCID: PMC10765009 DOI: 10.1016/j.ebiom.2023.104934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Mitochondrial dysfunction has been linked to the development of inflammatory bowel disease (IBD), but the genetic pathophysiology was not fully elucidated. We employed Mendelian randomization and colocalization analyses to investigate the associations between mitochondrial-related genes and IBD via integrating multi-omics. METHODS Summary-level data of mitochondrial gene methylation, expression and protein abundance levels were obtained from corresponding methylation, expression and protein quantitative trait loci studies, respectively. We obtained genetic associations with IBD and its two subtypes from the Inflammatory Bowel Disease Genetics Consortium (discovery), the UK Biobank (replication), and the FinnGen study (replication). We performed summary-data-based Mendelian randomization analysis to assess the associations of mitochondrial gene-related molecular features with IBD. Colocalization analysis was further conducted to assess whether the identified signal pairs shared a causal genetic variant. FINDINGS After integrating the multi-omics data between mQTL-eQTL and eQTL-pQTL, we identified two mitochondrial genes, i.e., PARK7 and ACADM, with tier 1 evidence for their associations with IBD and ulcerative colitis (UC). PDK1 and FISI genes were associated with UC risk with tier 2 and tier 3 evidence, respectively. The methylation of cg05467918 in ACADM was associated with lower expression of ACADM, which fits with the positive effect of cg05467918 methylation on UC risk. Consistently, the inverse associations between gene methylation and gene expression were also observed in PARK7 (cg10385390) and PDK1 (cg17679246), which were corroborated with the protective role in UC. At circulating protein level, genetically predicted higher levels of PARK7 (OR 0.36, 95% CI 0.25-0.52) and HINT1 (OR 0.47, 95% CI 0.30-0.74) were inversely associated with IBD risk; genetically predicted higher level of HINT1 was associated with a decreased risk of Crohn's disease (CD) (OR 0.26, 95% CI 0.14-0.49) and a higher level of ACADM (OR 0.67, 95% CI 0.55-0.83), PDK1 (OR 0.63, 95% CI 0.49-0.81), FIS1 (OR 0.63, 95% CI 0.47-0.83) was associated with a decreased risk of UC. INTERPRETATION We found that the mitochondrial PARK7 gene was putatively associated with IBD risk, and mitochondrial FIS1, PDK1, and ACADM genes were associated with UC risk with evidence from multi-omics levels. This study identified mitochondrial genes in relation to IBD, which may enhance the understanding of the pathogenic mechanisms of IBD development. FUNDING XL is supported by the Natural Science Fund for Distinguished Young Scholars of Zhejiang Province (LR22H260001) and Healthy Zhejiang One Million People Cohort (K-20230085).
Collapse
Affiliation(s)
- Jie Chen
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xixian Ruan
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yuhao Sun
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Shiyuan Lu
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Shixian Hu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
| | - Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Xue Li
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| |
Collapse
|
50
|
Kazmi I, Altamimi ASA, Afzal M, Majami AA, Abbasi FA, Almalki WH, Alzera SI, Kukreti N, Fuloria NK, Fuloria S, Sekar M, Abida. Non-coding RNAs: Emerging biomarkers and therapeutic targets in ulcerative colitis. Pathol Res Pract 2024; 253:155037. [PMID: 38160482 DOI: 10.1016/j.prp.2023.155037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Ulcerative colitis (UC) is a persistent inflammatory condition affecting the colon's mucosal lining, leading to chronic bowel inflammation. Despite extensive research, the precise molecular mechanisms underlying UC pathogenesis remain elusive. NcRNAs form a category of functional RNA molecules devoid of protein-coding capacity. They have recently surfaced as pivotal modulators of gene expression and integral participants in various pathological processes, particularly those related to inflammatory disorders. The diverse classes of ncRNAs, encompassing miRNAs, circRNAs, and lncRNAs, have been implicated in UC. It highlights their involvement in key UC-related processes, such as immune cell activation, epithelial barrier integrity, and the production of pro-inflammatory mediators. ncRNAs have been identified as potential biomarkers for UC diagnosis and monitoring disease progression, offering promising avenues for personalized medicine. This approach may pave the way for novel, more specific treatments with reduced side effects, addressing the current limitations of conventional therapies. A comprehensive understanding of the interplay between ncRNAs and UC will advance our knowledge of the disease, potentially leading to more effective and personalized treatments for patients suffering from this debilitating condition. This review explores the pivotal role of ncRNAs in the context of UC, shedding light on their possible targets for diagnosis, prognosis, and therapeutic interventions.
Collapse
Affiliation(s)
- Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | | | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Abdullah A Majami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fahad Al Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sami I Alzera
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Al-Jouf, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | | | - Shivkanya Fuloria
- Faculty of Pharmacy, AIMST University, Bedong 08100, Kedah, Malaysia
| | - Mahendran Sekar
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia
| | - Abida
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| |
Collapse
|