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Zhao J, Gui Y, Wu W, Li X, Wang L, Wang H, Luo Y, Zhou G, Yuan C. The function of long non-coding RNA IFNG-AS1 in autoimmune diseases. Hum Cell 2024:10.1007/s13577-024-01103-9. [PMID: 39004663 DOI: 10.1007/s13577-024-01103-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
The prevalence of autoimmune diseases ranks as the third most common disease category globally, following cancer and heart disease. Numerous studies indicate that long non-coding RNA (lncRNA) plays a pivotal role in regulating human growth, development, and the pathogenesis of various diseases. It is more than 200 nucleotides in length and is mostly involve in the regulation of gene expression. Furthermore, lncRNAs are crucial in the development and activation of immune cells, with an expanding body of research exploring their association with autoimmune disorders in humans. LncRNA Ifng antisense RNA 1 (IFNG-AS1), a key regulatory factor in the immune system, also named NeST or TMEVPG1, is proximally located to IFNG and participates in the regulation of it. The dysregulation of IFNG-AS1 is implicated in the pathogenesis of several autoimmune diseases. This study examines the role and mechanism of IFNG-AS1 in various autoimmune diseases and considers its potential as a therapeutic target.
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Affiliation(s)
- Jiale Zhao
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
| | - Yibei Gui
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, China
| | - Wei Wu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
| | - Xueqing Li
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
| | - Lijun Wang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, China
| | - Hailin Wang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
| | - Yiyang Luo
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
| | - Gang Zhou
- College of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China.
- Yichang Hospital of Traditional Chinese Medicine, Yichang, 443002, China.
| | - Chengfu Yuan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China.
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China.
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, China.
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Heydari R, Karimi P, Meyfour A. Long non-coding RNAs as pathophysiological regulators, therapeutic targets and novel extracellular vesicle biomarkers for the diagnosis of inflammatory bowel disease. Biomed Pharmacother 2024; 176:116868. [PMID: 38850647 DOI: 10.1016/j.biopha.2024.116868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing disease of the gastrointestinal (GI) system that includes two groups, Crohn's disease (CD) and ulcerative colitis (UC). To cope with these two classes of IBD, the investigation of pathogenic mechanisms and the discovery of new diagnostic and therapeutic approaches are crucial. Long non-coding RNAs (lncRNAs) which are non-coding RNAs with a length of longer than 200 nucleotides have indicated significant association with the pathology of IBD and strong potential to be used as accurate biomarkers in diagnosing and predicting responses to the IBD treatment. In the current review, we aim to investigate the role of lncRNAs in the pathology and development of IBD. We first describe recent advances in research on dysregulated lncRNAs in the pathogenesis of IBD from the perspective of epithelial barrier function, intestinal immunity, mitochondrial function, and intestinal autophagy. Then, we highlight the possible translational role of lncRNAs as therapeutic targets, diagnostic biomarkers, and predictors of therapeutic response in colon tissues and plasma samples. Finally, we discuss the potential of extracellular vesicles and their lncRNA cargo in the pathophysiology, diagnosis, and treatment of IBD.
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Affiliation(s)
- Raheleh Heydari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Padideh Karimi
- CRTD/Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Kazemifard N, Farmani M, Baradaran Ghavami S, Kazemi M, Shahrokh S, Asadzadeh Aghdaei H, Zali M. A prediction of the CRNDE role by modulating NF-κB pathway in inflammatory bowel disease (IBD). Biochem Biophys Rep 2024; 38:101731. [PMID: 38766384 PMCID: PMC11101873 DOI: 10.1016/j.bbrep.2024.101731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/28/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate multiple pathways and cellular mechanisms. Recent research has emphasized their involvement in the pathogenesis of complex diseases, such as Inflammatory Bowel Disease (IBD) which is characterized by chronic inflammation of the intestines. The two most common types of IBD are ulcerative colitis and Crohn's disease. CRNDE lncRNA was initially detected in colorectal cancer (CRC) and found to be involved in the tumorigenesis pathways. Further studies revealed the role of CRNDE in activating inflammation and promoting the release of inflammatory cytokines. This study utilizes the RNA-seq data analysis and bioinformatics tools to clarify the role of CRNDE in the IBD pathogenesis and confirms its expression in inflamed HT-29 and Caco-2 cell lines and also colonic and blood samples of UC patients and controls ex vivo. Based on our results, CRNDE was significantly upregulated in IBD samples compared to controls in RNA-seq data analysis and Real-time PCR of inflamed HT-29 cell line and colonic biopsies from UC patients. Additionally, predicted that its expression is positively correlated with the pro-inflammatory cytokines production. CRNDE interactions was investigated with several inflammation-related miRNAs and regulatory proteins computationally. Thus, CRNDE upregulation in the colon of IBD patients could be involved in IBD pathogenesis by promoting inflammatory pathways and targeting anti-inflammatory miRNAs.
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Affiliation(s)
- Nesa Kazemifard
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Farmani
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shaghayegh Baradaran Ghavami
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Kazemi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Reproductive Sciences and Sexual Health Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shabnam Shahrokh
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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4
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Xin R. Inflammatory Gene Panel Guiding the Study of Genetics in Inflammatory Bowel Disease. Mol Diagn Ther 2024; 28:389-401. [PMID: 38635139 DOI: 10.1007/s40291-024-00709-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
Inflammatory bowel disease (IBD) is a complex disease that develops through a sequence of molecular events that are still poorly defined. This process is driven by a multitude of context-dependent genes that play different roles based on their environment. The complexity and multi-faceted nature of these genes make it difficult to study the genetic basis of IBD. The goal of this article is to review the key genes in the pathophysiology of IBD and highlight new technology that can be used in further research. This paper examines Nanostring RNA probe technology, which uses tissue analyzed without the use of enzymes, transcription, or amplification. Nanostring offers several panels of genes to test, including an inflammation panel of 234 genes. This article analyzes this panel and reviews the literature for each gene's effect in IBD for use as a framework to review the pathophysiology of the disease. The panel was narrowed to 26 genes with significant evidence of mechanistic potential in IBD, which were then categorized into specific areas of pathogenesis. These include gut barrier breakdown, inappropriate recognition of commensal bacteria, immune cell activation, proinflammatory cytokine release, and subsequent impairment of the anti-inflammatory response. The eventual goal of this paper is the creation of a customized panel of IBD genes that can be used to better understand the genetic mechanism of IBD and aid in the development of future therapies in IBD.
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Affiliation(s)
- Ryan Xin
- Columbia University Irving Medical Center, 177 Fort Washington Avenue, New York, NY, 10032, USA.
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Hu Y, Lu Y, Fang Y, Zhang Q, Zheng Z, Zheng X, Ye X, Chen Y, Ding J, Yang J. Role of long non-coding RNA in inflammatory bowel disease. Front Immunol 2024; 15:1406538. [PMID: 38895124 PMCID: PMC11183289 DOI: 10.3389/fimmu.2024.1406538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/13/2024] [Indexed: 06/21/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a group of recurrent chronic inflammatory diseases, including Crohn's disease (CD) and ulcerative colitis (UC). Although IBD has been extensively studied for decades, its cause and pathogenesis remain unclear. Existing research suggests that IBD may be the result of an interaction between genetic factors, environmental factors and the gut microbiome. IBD is closely related to non-coding RNAs (ncRNAs). NcRNAs are composed of microRNA(miRNA), long non-coding RNA(lnc RNA) and circular RNA(circ RNA). Compared with miRNA, the role of lnc RNA in IBD has been little studied. Lnc RNA is an RNA molecule that regulates gene expression and regulates a variety of molecular pathways involved in the pathbiology of IBD. Targeting IBD-associated lnc RNAs may promote personalized treatment of IBD and have therapeutic value for IBD patients. Therefore, this review summarized the effects of lnc RNA on the intestinal epithelial barrier, inflammatory response and immune homeostasis in IBD, and summarized the potential of lnc RNA as a biomarker of IBD and as a predictor of therapeutic response to IBD in the future.
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Affiliation(s)
- Yufei Hu
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Yifan Lu
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Yi Fang
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Qizhe Zhang
- Department of Geriatrics, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Zhuoqun Zheng
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Xiaojuan Zheng
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Xiaohua Ye
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Yanping Chen
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Jin Ding
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Jianfeng Yang
- Department of Gastroenterology, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
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Wang X, Zhang Q, Hou S, Qi J, Du L, Li F, Cao Q, Yang P. Association of Long Non-coding RNA C1RL-AS1 and PTPN6 Gene Polymorphisms with Ocular Behcet's Disease in Han Chinese. Ocul Immunol Inflamm 2024; 32:336-341. [PMID: 36745681 DOI: 10.1080/09273948.2023.2170887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 11/15/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023]
Abstract
PURPOSE To explore the association of the polymorphisms in PTPN6 and LncRNA C1RL-AS1 genes with ocular BD in Han Chinese patients. METHODS Correlation study was performed using the iPLEX system on a cohort of ocular BD patients andcontrols. The genotyping of 7 SNPs for LncRNA C1RL-AS1 and PTPN6 genes in ocular BD patients was performed using the iPLEX Gold genotype. RESULTS The frequencies of rs4013722 AG genotype/A allele in LncRNA C1RL-AS1 were significantly decreased in BD patients, and the frequency of GG genotype was significantly increased in BD patients. The rs4013722 was associated with ocular BD in male patients, but not in female patients. The AG and GG genotype of rs4013722 were associated with skin lesions in male patients. The gene polymorphisms of PTPN6 were not associated with BD patients. CONCLUSIONS The LncRNA C1RL-AS1/rs4013722 polymorphism conferred susceptibility to ocular BD in Han Chinese patients, which was influenced by sex.Abbreviations: LncRNA: Long Non-coding RNA; BD: Behcet's disease; SNP: single nucleotide polymorphism; PBMCs: peripheral blood mononuclear cells; PTPs: Protein tyrosine phosphatases; PTPN6: protein tyrosine phosphatase non-receptor 6; GWAS: genome-wide association study; HWE: Hardy-Weinberg equilibrium; LD: linkage disequilibrium; OR: odds ratio; CI: confidence interval; eQTL: expression quantitative trait loci; IBD: inflammatory bowel disease; RA: rheumatoid arthritis; Padj: Bonferroni corrected P value; NS: non-significant.
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Affiliation(s)
- Xiaotang Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipal Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Qi Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipal Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Shengping Hou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipal Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Jian Qi
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipal Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Liping Du
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, People's Republic of China
| | - Fuzhen Li
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, People's Republic of China
| | - Qingfeng Cao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipal Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipal Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
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Jiang F, Wu M, Li R. The significance of long non-coding RNAs in the pathogenesis, diagnosis and treatment of inflammatory bowel disease. PRECISION CLINICAL MEDICINE 2023; 6:pbad031. [PMID: 38163004 PMCID: PMC10757071 DOI: 10.1093/pcmedi/pbad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024] Open
Abstract
Inflammatory bowel diseases (IBD) are a group of chronic relapsing gastrointestinal inflammatory diseases with significant global incidence. Although the pathomechanism of IBD has been extensively investigated, several aspects of its pathogenesis remain unclear. Long non-coding RNAs (lncRNAs) are transcripts with more than 200 nucleotides in length that have potential protein-coding functions. LncRNAs play important roles in biological processes such as epigenetic modification, transcriptional regulation and post-transcriptional regulation. In this review, we summarize recent advances in research on IBD-related lncRNAs from the perspective of the overall intestinal microenvironment, as well as their potential roles as immune regulators, diagnostic biomarkers and therapeutic targets or agents for IBD.
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Affiliation(s)
- Fei Jiang
- Jiangsu Province Engineering Research Center of Cardiovascular Drugs Targeting Endothelial Cells, School of Life Sciences, Jiangsu Normal University, Xuzhou 221000, China
- Department of Laboratory Medicine, the Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, China
| | - Min Wu
- Drug Discovery Section, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
- Department of Neurology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rongpeng Li
- Jiangsu Province Engineering Research Center of Cardiovascular Drugs Targeting Endothelial Cells, School of Life Sciences, Jiangsu Normal University, Xuzhou 221000, China
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Lu Q, Liang Y, Meng X, Zhao Y, Fan H, Hou S. The Role of Long Noncoding RNAs in Intestinal Health and Diseases: A Focus on the Intestinal Barrier. Biomolecules 2023; 13:1674. [PMID: 38002356 PMCID: PMC10669616 DOI: 10.3390/biom13111674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/04/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
The gut is the body's largest immune organ, and the intestinal barrier prevents harmful substances such as bacteria and toxins from passing through the gastrointestinal mucosa. Intestinal barrier dysfunction is closely associated with various diseases. However, there are currently no FDA-approved therapies targeting the intestinal epithelial barriers. Long noncoding RNAs (lncRNAs), a class of RNA transcripts with a length of more than 200 nucleotides and no coding capacity, are essential for the development and regulation of a variety of biological processes and diseases. lncRNAs are involved in the intestinal barrier function and homeostasis maintenance. This article reviews the emerging role of lncRNAs in the intestinal barrier and highlights the potential applications of lncRNAs in the treatment of various intestinal diseases by reviewing the literature on cells, animal models, and clinical patients. The aim is to explore potential lncRNAs involved in the intestinal barrier and provide new ideas for the diagnosis and treatment of intestinal barrier damage-associated diseases in the clinical setting.
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Affiliation(s)
- Qianying Lu
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Q.L.); (Y.L.); (X.M.); (S.H.)
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China
| | - Yangfan Liang
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Q.L.); (Y.L.); (X.M.); (S.H.)
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China
| | - Xiangyan Meng
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Q.L.); (Y.L.); (X.M.); (S.H.)
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China
| | - Yanmei Zhao
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Q.L.); (Y.L.); (X.M.); (S.H.)
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China
| | - Haojun Fan
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Q.L.); (Y.L.); (X.M.); (S.H.)
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China
| | - Shike Hou
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China; (Q.L.); (Y.L.); (X.M.); (S.H.)
- Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin 300072, China
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Triantaphyllopoulos KA. Long Non-Coding RNAs and Their "Discrete" Contribution to IBD and Johne's Disease-What Stands out in the Current Picture? A Comprehensive Review. Int J Mol Sci 2023; 24:13566. [PMID: 37686376 PMCID: PMC10487966 DOI: 10.3390/ijms241713566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Non-coding RNAs (ncRNA) have paved the way to new perspectives on the regulation of gene expression, not only in biology and medicine, but also in associated fields and technologies, ensuring advances in diagnostic means and therapeutic modalities. Critical in this multistep approach are the associations of long non-coding RNA (lncRNA) with diseases and their causal genes in their networks of interactions, gene enrichment and expression analysis, associated pathways, the monitoring of the involved genes and their functional roles during disease progression from one stage to another. Studies have shown that Johne's Disease (JD), caused by Mycobacterium avium subspecies partuberculosis (MAP), shares common lncRNAs, clinical findings, and other molecular entities with Crohn's Disease (CD). This has been a subject of vigorous investigation owing to the zoonotic nature of this condition, although results are still inconclusive. In this review, on one hand, the current knowledge of lncRNAs in cells is presented, focusing on the pathogenesis of gastrointestinal-related pathologies and MAP-related infections and, on the other hand, we attempt to dissect the associated genes and pathways involved. Furthermore, the recently characterized and novel lncRNAs share common pathologies with IBD and JD, including the expression, molecular networks, and dataset analysis results. These are also presented in an attempt to identify potential biomarkers pertinent to cattle and human disease phenotypes.
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Affiliation(s)
- Kostas A Triantaphyllopoulos
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
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10
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Premadasa LS, Lee E, McDew-White M, Alvarez X, Jayakumar S, Ling B, Okeoma CM, Byrareddy SN, Kulkarni S, Mohan M. Cannabinoid enhancement of lncRNA MMP25-AS1/MMP25 interaction reduces neutrophil infiltration and intestinal epithelial injury in HIV/SIV infection. JCI Insight 2023; 8:e167903. [PMID: 37036007 PMCID: PMC10132162 DOI: 10.1172/jci.insight.167903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/16/2023] [Indexed: 04/11/2023] Open
Abstract
Intestinal epithelial barrier dysfunction, a hallmark of HIV/SIV infection, persists despite viral suppression by combination antiretroviral therapy (cART). Emerging evidence suggests a critical role for long noncoding RNAs (lncRNAs) in maintaining epithelial homeostasis. We simultaneously profiled lncRNA/mRNA expression exclusively in colonic epithelium (CE) of SIV-infected rhesus macaques (RMs) administered vehicle (VEH) or Δ-9-tetrahydrocannabinol (THC). Relative to controls, fewer lncRNAs were up- or downregulated in CE of THC/SIV compared with VEH/SIV RMs. Importantly, reciprocal expression of the natural antisense lncRNA MMP25-AS1 (up 2.3-fold) and its associated protein-coding gene MMP25 (attracts neutrophils by inactivating alpha-1 anti-trypsin/SERPINA1) (down 2.2-fold) was detected in CE of THC/SIV RMs. Computational analysis verified 2 perfectly matched complementary regions and an energetically stable (normalized binding free energy = -0.2626) MMP25-AS1/MMP25 duplex structure. MMP25-AS1 overexpression blocked IFN-γ-induced MMP25 mRNA and protein expression in vitro. Elevated MMP25 protein expression in CE of VEH/SIV but not THC/SIV RMs was associated with increased infiltration by myeloperoxidase/CD11b++ neutrophils (transendothelial migration) and epithelial CD47 (transepithelial migration) expression. Interestingly, THC administered in combination with cART increased MMP25-AS1 and reduced MMP25 mRNA/protein expression in jejunal epithelium of SIV-infected RMs. Our findings demonstrate that MMP25-AS1 is a potentially unique epigenetic regulator of MMP25 and that low-dose THC can reduce neutrophil infiltration and intestinal epithelial injury potentially by downregulating MMP25 expression through modulation of MMP25-AS1.
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Affiliation(s)
- Lakmini S. Premadasa
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Eunhee Lee
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Marina McDew-White
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Xavier Alvarez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Sahana Jayakumar
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Binhua Ling
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Chioma M. Okeoma
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, New York, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Smita Kulkarni
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Mahesh Mohan
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
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11
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Zhou J, Zhang Q, Zhao Y, Song Y, Leng Y, Chen M, Zhou S, Wang Z. The regulatory role of alternative splicing in inflammatory bowel disease. Front Immunol 2023; 14:1095267. [PMID: 37153612 PMCID: PMC10160418 DOI: 10.3389/fimmu.2023.1095267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
Inflammatory bowel disease (IBD) mainly includes Crohn's disease and ulcerative colitis. These diseases have a progressive course of chronic relapse and remission and affect a large number of children and adults worldwide. The burden of IBD is rising worldwide, with levels and trends varying greatly in countries and regions. Like most chronic diseases, the costs associated with IBD are high, including hospitalizations, outpatient and emergency visits, surgeries, and pharmacotherapies. However, there is no radical cure for it yet, and its therapeutic targets still need further study. Currently, the pathogenesis of IBD remains unclear. It is generally assumed that the occurrence and development of IBD are related to the environmental factors, gut microbiota, immune imbalance, and genetic susceptibility. Alternative splicing contributes to a various diseases, such as spinal muscular atrophy, liver diseases, and cancers. In the past, it has been reported that alternative splicing events, splicing factors, and splicing mutations were associated with IBD, but there were no reports on the practical application for clinical diagnosis and treatment of IBD using splicing-related methods. Therefore, this article reviews research progress on alternative splicing events, splicing factors, and splicing mutations associated with IBD.
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Affiliation(s)
- Jianli Zhou
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Qiao Zhang
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yuzhen Zhao
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yuchen Song
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yanan Leng
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Moxian Chen
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
| | - Shaoming Zhou
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
| | - Zhaoxia Wang
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
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12
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Genetic and Epigenetic Etiology of Inflammatory Bowel Disease: An Update. Genes (Basel) 2022; 13:genes13122388. [PMID: 36553655 PMCID: PMC9778199 DOI: 10.3390/genes13122388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease with periods of exacerbation and remission of the disease. The etiology of IBD is not fully understood. Many studies point to the presence of genetic, immunological, environmental, and microbiological factors and the interactions between them in the occurrence of IBD. The review looks at genetic factors in the context of both IBD predisposition and pharmacogenetics.
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13
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Feng F, Jiao P, Wang J, Li Y, Bao B, Luoreng Z, Wang X. Role of Long Noncoding RNAs in the Regulation of Cellular Immune Response and Inflammatory Diseases. Cells 2022; 11:cells11223642. [PMID: 36429069 PMCID: PMC9688074 DOI: 10.3390/cells11223642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are recently discovered genetic regulatory molecules that regulate immune responses and are closely associated with the occurrence and development of various diseases, including inflammation, in humans and animals. Under specific physiological conditions, lncRNA expression varies at the cell or tissue level, and lncRNAs can bind to specific miRNAs, target mRNAs, and target proteins to participate in certain processes, such as cell differentiation and inflammatory responses, via the corresponding signaling pathways. This review article summarizes the regulatory role of lncRNAs in macrophage polarization, dendritic cell differentiation, T cell differentiation, and endothelial and epithelial inflammation. In addition, it describes the molecular mechanism of lncRNAs in acute kidney injury, hepatitis, inflammatory injury of the lung, osteoarthritis, mastitis, and neuroinflammation to provide a reference for the molecular regulatory network as well as the genetic diagnosis and treatment of inflammatory diseases in humans and animals.
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Affiliation(s)
- Fen Feng
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Peng Jiao
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Jinpeng Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Yanxia Li
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Binwu Bao
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Zhuoma Luoreng
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
| | - Xingping Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
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14
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Lei N, Kong P, Chen S, Wang Q, Tang X, Liu F. Upregulated NORAD is implicated in apoptosis, inflammation, and oxidative stress in ulcerative colitis through the nuclear factor-κappaB signaling. Eur J Gastroenterol Hepatol 2022; 34:630-639. [PMID: 35412486 DOI: 10.1097/meg.0000000000002370] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
BACKGROUND Ulcerative colitis (UC) is a chronic inflammatory disease that affects the colon. It has been discovered that long non-coding RNA activated by DNA damage (NORAD) is upregulated in UC patient-derived serums, but its functional mechanism in UC has not been disclosed. METHODS Relative levels of NORAD in colonic mucosal tissues and TNF-α-stimulated human normal colonic mucosal cells (FHCs) were detected. Functional experiments were executed to evaluate the effects of NORAD silencing on TNF-α-induced FHC proliferation, apoptosis, inflammation, and oxidative stress. The molecular mechanism related to NORAD was predicted by starBase and confirmed by dual-luciferase reporter and RIP assays. RESULTS Our data exhibited higher levels of NORAD in UC patient-derived colonic mucosal tissues and TNF-α-stimulated FHCs. Functional experiments presented that NORAD inhibition impaired TNF-α-induced FHC apoptosis, inflammation, and oxidative stress. NORAD acted as a miR-552-3p sponge, and miR-552-3p silencing weakened NORAD inhibition-mediated effects on TNF-α-induced FHC apoptosis, inflammation, and oxidative stress. Myeloid differentiation primary response gene 88 (MYD88) was verified as a miR-552-3p target, and MYD88 overexpression whittled miR-552-3p mimic-mediated inhibition on TNF-α-induced FHC apoptosis, inflammation, and oxidative stress. Notably, TNF-α-induced NORAD regulated the nuclear factor-κappaB (NF-κB) signaling via the miR-552-3p/MYD88 axis. CONCLUSION NORAD participates in TNF-α-induced FHC apoptosis, inflammation, and oxidative stress via the NF-κB signaling via the miR-552-3p/MYD88 axis, offering new insights into the pathogenesis of UC.
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Affiliation(s)
- Na Lei
- Department of Basic Theory of Chinese Medicine, School of Basic Medical Sciences, Chengdu University of TCM, Chengdu
| | - Pengfei Kong
- Anorectal Department of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of North Sichuan Medical College
| | - Simin Chen
- Institute of Anorectal Diseases, North Sichuan Medical College
| | - Qiuxiao Wang
- Department of Clinical Medicine of Combination of Chinese and Western Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, China
| | - Xuegui Tang
- Anorectal Department of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of North Sichuan Medical College
| | - Fang Liu
- Anorectal Department of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of North Sichuan Medical College
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15
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Ungar B, Yavzori M, Fudim E, Picard O, Kopylov U, Eliakim R, Shouval D, Levin Y, Savidor A, Ben-Moshe S, Manco R, Dan S, Egozi A, Bahar Halpern K, Mayer C, Barshack I, Ben-Horin S, Itzkovitz S. Host transcriptome signatures in human faecal-washes predict histological remission in patients with IBD. Gut 2022; 71:gutjnl-2021-325516. [PMID: 35046090 DOI: 10.1136/gutjnl-2021-325516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/08/2021] [Indexed: 12/08/2022]
Abstract
BACKGROUND Colonoscopy is the gold standard for evaluation of inflammation in inflammatory bowel diseases (IBDs), yet entails cumbersome preparations and risks of injury. Existing non-invasive prognostic tools are limited in their diagnostic power. Moreover, transcriptomics of colonic biopsies have been inconclusive in their association with clinical features. AIMS To assess the utility of host transcriptomics of faecal wash samples of patients with IBD compared with controls. METHODS In this prospective cohort study, we obtained biopsies and faecal-wash samples from patients with IBD and controls undergoing lower endoscopy. We performed RNAseq of biopsies and matching faecal-washes, and associated them with endoscopic and histological inflammation status. We also performed faecal mass-spectrometry proteomics on a subset of samples. We inferred cell compositions using computational deconvolution and used classification algorithms to identify informative genes. RESULTS We analysed biopsies and faecal washes from 39 patients (20 IBD, 19 controls). Host faecal-transcriptome carried information that was distinct from biopsy RNAseq and faecal proteomics. Transcriptomics of faecal washes, yet not of biopsies, from patients with histological inflammation were significantly correlated to one another (p=5.3×10-12). Faecal-transcriptome had significantly higher statistical power in identifying histological inflammation compared with transctiptome of intestinal biopsies (150 genes with area under the curve >0.9 in faecal samples vs 10 genes in biopsy RNAseq). These results were replicated in a validation cohort of 22 patients (10 IBD, 12 controls). Faecal samples were enriched in inflammatory monocytes, regulatory T cells, natural killer-cells and innate lymphoid cells. CONCLUSIONS Faecal wash host transcriptome is a statistically powerful biomarker reflecting histological inflammation. Furthermore, it opens the way to identifying important correlates and therapeutic targets that may be obscured using biopsy transcriptomics.
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Affiliation(s)
- Bella Ungar
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Miri Yavzori
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Ella Fudim
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Orit Picard
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Uri Kopylov
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Rami Eliakim
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Dror Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, & Sackler School of Medicine, Tel-Aviv University, Petah Tikva, Israel
| | - Yishai Levin
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- The De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Ben-Moshe
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rita Manco
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Stav Dan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Mayer
- Department of Pathology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Shomron Ben-Horin
- Department of Gastroenterology, Sheba Medical Center Tel Hashomer & Sackler School of Medicine, Tel-Aviv University, Ramat Gan, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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16
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Taheri M, Barth DA, Kargl J, Rezaei O, Ghafouri-Fard S, Pichler M. Emerging Role of Non-Coding RNAs in Regulation of T-Lymphocyte Function. Front Immunol 2021; 12:756042. [PMID: 34804042 PMCID: PMC8599985 DOI: 10.3389/fimmu.2021.756042] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
T-lymphocytes (T cells) play a major role in adaptive immunity and current immune checkpoint inhibitor-based cancer treatments. The regulation of their function is complex, and in addition to cytokines, receptors and transcription factors, several non-coding RNAs (ncRNAs) have been shown to affect differentiation and function of T cells. Among these non-coding RNAs, certain small microRNAs (miRNAs) including miR-15a/16-1, miR-125b-5p, miR-99a-5p, miR-128-3p, let-7 family, miR-210, miR-182-5p, miR-181, miR-155 and miR-10a have been well recognized. Meanwhile, IFNG-AS1, lnc-ITSN1-2, lncRNA-CD160, NEAT1, MEG3, GAS5, NKILA, lnc-EGFR and PVT1 are among long non-coding RNAs (lncRNAs) that efficiently influence the function of T cells. Recent studies have underscored the effects of a number of circular RNAs, namely circ_0001806, hsa_circ_0045272, hsa_circ_0012919, hsa_circ_0005519 and circHIPK3 in the modulation of T-cell apoptosis, differentiation and secretion of cytokines. This review summarizes the latest news and regulatory roles of these ncRNAs on the function of T cells, with widespread implications on the pathophysiology of autoimmune disorders and cancer.
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Affiliation(s)
- Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Dominik A Barth
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Julia Kargl
- Otto Loewi Research Center, Division of Pharmacology, Medical University of Graz, Graz, Austria
| | - Omidvar Rezaei
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Martin Pichler
- Research Unit of Non-Coding RNAs and Genome Editing in Cancer, Division of Clinical Oncology, Department of Internal Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, Graz, Austria.,Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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17
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Schultheiß C, Paschold L, Willscher E, Simnica D, Wöstemeier A, Muscate F, Wass M, Eisenmann S, Dutzmann J, Keyßer G, Gagliani N, Binder M. Maturation trajectories and transcriptional landscape of plasmablasts and autoreactive B cells in COVID-19. iScience 2021; 24:103325. [PMID: 34723157 PMCID: PMC8536484 DOI: 10.1016/j.isci.2021.103325] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/03/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
In parasite and viral infections, aberrant B cell responses can suppress germinal center reactions thereby blunting long-lived memory and may provoke immunopathology including autoimmunity. Using COVID-19 as model, we set out to identify serological, cellular, and transcriptomic imprints of pathological responses linked to autoreactive B cells at single-cell resolution. We show that excessive plasmablast expansions are prognostically adverse and correlate with autoantibody production but do not hinder the formation of neutralizing antibodies. Although plasmablasts followed interleukin-4 (IL-4) and BAFF-driven developmental trajectories, were polyclonal, and not enriched in autoreactive B cells, we identified two memory populations (CD80+/ISG15+ and CD11c+/SOX5+/T-bet+/−) with immunogenetic and transcriptional signs of autoreactivity that may be the cellular source of autoantibodies in COVID-19 and that may persist beyond recovery. Immunomodulatory interventions discouraging such adverse responses may be useful in selected patients to shift the balance from autoreactivity toward long-term memory. Plasmablast expansions correlate with disease severity and autoantibodies in COVID-19 Patients with high plasmablast levels exhibit IGHV4-34 skewing Autoreactive BCRs are enriched in atypical memory, not plasmablast populations
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Affiliation(s)
- Christoph Schultheiß
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle (Saale), Germany
| | - Lisa Paschold
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle (Saale), Germany
| | - Edith Willscher
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle (Saale), Germany
| | - Donjete Simnica
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle (Saale), Germany
| | - Anna Wöstemeier
- I. Department of Medicine and Department for General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franziska Muscate
- I. Department of Medicine and Department for General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maxi Wass
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle (Saale), Germany
| | - Stephan Eisenmann
- Department of Internal Medicine I, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jochen Dutzmann
- Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Gernot Keyßer
- Department of Internal Medicine II, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Nicola Gagliani
- I. Department of Medicine and Department for General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle (Saale), Germany
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18
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Chen W, Liu S, Wang F. Potential impact and mechanism of Long Non-coding RNAs on cancer and associated T cells. J Cancer 2021; 12:4873-4882. [PMID: 34234857 PMCID: PMC8247393 DOI: 10.7150/jca.58859] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/30/2021] [Indexed: 01/01/2023] Open
Abstract
The discovery of many aberrant expressions of long non-coding RNAs (lncRNAs) in various cancers has focused attention on the effects of lncRNA on cancer cells themselves, including cell proliferation, growth inhibition, cell migration, cell immortality, vascular regeneration and cell viability. But with the increasing role of immunotherapy in cancer therapy, a large number of studies have revealed that the regulatory role of lncRNAs in immunity such as differentiation of immune cells can also influence the development and progression of cancer. In particular, recent publications have suggested that lncRNAs play critical roles in T-lymphocyte activation, proliferation, differentiation, function, apoptosis and metabolism. To elucidate the actual functions of lncRNAs at the molecular level of cancer pathogenesis, we summarize some of the current lncRNA regulatory mechanisms associated with T cell to discuss their effects in cancer in the hope of providing potential cancer therapeutic targets or cancer biomarkers. However, we all know that the differentiation and function of T cells is an extremely complex process that involves the expression and regulation of multiple lncRNAs. As a result, more regulatory mechanisms of lncRNAs need to be further studied.
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Affiliation(s)
- Wenxiu Chen
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China, 210029.,National Key Clinical Department of Laboratory Medicine, Nanjing, China, 210029
| | - Shuna Liu
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China, 210029.,National Key Clinical Department of Laboratory Medicine, Nanjing, China, 210029
| | - Fang Wang
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China, 210029.,National Key Clinical Department of Laboratory Medicine, Nanjing, China, 210029
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19
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Zeni PF, Mraz M. LncRNAs in adaptive immunity: role in physiological and pathological conditions. RNA Biol 2021; 18:619-632. [PMID: 33094664 PMCID: PMC8078528 DOI: 10.1080/15476286.2020.1838783] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
The adaptive immune system is responsible for generating immunological response and immunological memory. Regulation of adaptive immunity including B cell and T cell biology was mainly understood from the protein and microRNA perspective. However, long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs (ncRNAs) that influence key factors in lymphocyte biology such as NOTCH, PAX5, MYC and EZH2. LncRNAs were described to modulate lymphocyte activation by regulating pathways such as NFAT, NFκB, MYC, interferon and TCR/BCR signalling (NRON, NKILA, BCALM, GAS5, PVT1), and cell effector functions (IFNG-AS1, TH2-LCR). Here we review lncRNA involvement in adaptive immunity and the implications for autoimmune diseases (multiple sclerosis, inflammatory bowel disease, rheumatoid arthritis) and T/B cell leukaemias and lymphomas (CLL, MCL, DLBCL, T-ALL). It is becoming clear that lncRNAs are important in adaptive immune response and provide new insights into its orchestration.
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Affiliation(s)
- Pedro Faria Zeni
- Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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20
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Xie Z, Rahman I, Goniewicz ML, Li D. Perspectives on Epigenetics Alterations Associated with Smoking and Vaping. FUNCTION (OXFORD, ENGLAND) 2021; 2:zqab022. [PMID: 35330676 PMCID: PMC8788872 DOI: 10.1093/function/zqab022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/03/2021] [Accepted: 04/21/2021] [Indexed: 01/11/2023]
Abstract
Epigenetic alterations, including DNA methylation, microRNA, and long noncoding RNA, play important roles in the pathogenesis of numerous respiratory health conditions and diseases. Exposure to tobacco smoking has been found to be associated with epigenetic changes in the respiratory tract. Marketed as a less harmful alternative to combustible cigarettes, electronic cigarette (e-cigarette) has rapidly gained popularity in recent years, especially among youth and young adults. Accumulative evidence from both animal and human studies has shown that e-cigarette use (vaping) is also linked to similar respiratory health conditions as observed with cigarette smoking, including wheezing, asthma, and COPD. This review aims to provide an overview of current studies on associations of smoking and vaping with epigenetic alterations in respiratory cells and provide future research directions in epigenetic studies related to vaping.
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Affiliation(s)
- Zidian Xie
- Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Maciej L Goniewicz
- Department of Health Behavior, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, USA
| | - Dongmei Li
- Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY, USA,Address correspondence to D.L. (e-mail: )
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21
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Epigenomic and transcriptomic analysis of chronic inflammatory diseases. Genes Genomics 2021; 43:227-236. [PMID: 33638813 DOI: 10.1007/s13258-021-01045-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022]
Abstract
Chronic inflammatory diseases (CIDs) have complex pathologies that result from aberrant and persistent immune responses. However, the precise triggers and mechanisms remain elusive. An important aspect of CID research focuses on epigenetics modifications, which regulate gene expression and provide a dynamic transcriptional response to inflammation. In recent years, mounting evidence has demonstrated an association between epigenomic and transcriptomic dysregulation and the phenotypes of CIDs. In particular, epigenetic changes at cis-regulatory elements have provided new insights for immune cell-specific alterations that contribute to disease etiology. Furthermore, the advancements in single-cell genomics provide novel solutions to cell type heterogeneity, which has long posed challenges for CID diagnosis and treatment. In this review, we discuss the current state of epigenomics research of CID and the insights derived from single-cell transcriptomic and epigenomic studies.
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22
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Qu SL, Chen L, Wen XS, Zuo JP, Wang XY, Lu ZJ, Yang YF. Suppression of Th17 cell differentiation via sphingosine-1-phosphate receptor 2 by cinnamaldehyde can ameliorate ulcerative colitis. Biomed Pharmacother 2021; 134:111116. [PMID: 33341041 DOI: 10.1016/j.biopha.2020.111116] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022] Open
Abstract
Ulcerative colitis (UC) is chronic disease characterized by diffuse inflammation of the mucosa of the colon and rectum. Although the etiology is unknown, dysregulation of the intestinal mucosal immune system is closely related to UC. Cinnamaldehyde (CA) is a major active compound from cinnamon, is known as its anti-inflammatory and antibacterial. However, little research focused on its regulatory function on immune cells in UC. Therefore, we set out to explore the modulating effects of CA on immune cells in UC. We found that CA reduced the progression of colitis through controlling the production of proinflammatory cytokines and inhibiting the proportion of Th17 cells. Furthermore, the liquid chromatography-mass spectrometry (LC-MS) method was employed for analyzing and differentiating metabolites, data showed that sphingolipid pathway has a great influence on the effect of CA on UC. Meanwhile, sphingosine-1-phosphate receptor 2 (S1P2) and Rho-GTP protein levels were downregulated in colonic tissues after CA treatment. Moreover, in vitro assays showed that CA inhibited Th17 cell differentiation and downregulated of S1P2 and Rho-GTP signaling. Notably, we found that treatment with S1P2 antagonist (JTE-013) weakened the inhibitory effect of CA on Th17 cells. Furthermore, S1P2 deficiency (S1P2-/-) blocked the effect of CA on Th17 cell differentiation. In addition, CA can also improve inflammation via lncRNA H19 and MIAT. To sum up, this study provides clear evidence that CA can ameliorate ulcerative colitis through suppressing Th17 cells via S1P2 pathway and regulating lncRNA H19 and MIAT, which further supports S1P2 as a potential drug target for immunity-mediated UC.
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Affiliation(s)
- Shu-Lan Qu
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Long Chen
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xue-Shan Wen
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jian-Ping Zuo
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Laboratory of Anti-inflammation and Immunopharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiao-Yu Wang
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Laboratory of Anti-inflammation and Immunopharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Zhi-Jie Lu
- Department of Anesthesiology and Intensive Care Unit, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, China.
| | - Yi-Fu Yang
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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23
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Liu H, Li T, Zhong S, Yu M, Huang W. Intestinal epithelial cells related lncRNA and mRNA expression profiles in dextran sulphate sodium-induced colitis. J Cell Mol Med 2021; 25:1060-1073. [PMID: 33300279 PMCID: PMC7812259 DOI: 10.1111/jcmm.16174] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/10/2020] [Accepted: 11/22/2020] [Indexed: 12/15/2022] Open
Abstract
Intestinal epithelial barrier damage caused by intestinal epithelial cells (IECs) dysfunction plays a crucial role in the pathogenesis and development of inflammatory bowel disease (IBD). Recently, some studies have suggested the emerging role of long non-coding RNAs (lncRNAs) in IBD. The aim of this study was to reveal lncRNAs and mRNA expression profiles in IECs from a mouse model of colitis and to expand our understanding in the intestinal epithelial barrier regulation. IECs from the colons of wild-type mice and dextran sulphate sodium (DSS)-induced mice were isolated for high-throughput RNA-sequencing. A total of 254 up-regulated and 1013 down-regulated mRNAs and 542 up-regulated and 766 down-regulated lncRNAs were detected in the DSS group compared with the Control group. Four mRNAs and six lncRNAs were validated by real-time quantitative PCR. Function analysis showed that dysregulated mRNAs participated in TLR7 signalling pathway, IL-1 receptor activity, BMP receptor binding and IL-17 signalling pathway. Furthermore, the possibility of indirect interactions between differentially expressed mRNAs and lncRNAs was illustrated by the competing endogenous RNA (ceRNA) network. LncRNA ENSMUST00000128026 was predicted to bind to mmu-miR-6899-3p, regulating Dnmbp expression. LncRNA NONMMUT143162.1 was predicted to competitively bind to mmu-miR-6899-3p, regulating Tnip3 expression. Finally, the protein-protein interaction (PPI) network analysis was constructed with 311 nodes and 563 edges. And the highest connectivity degrees were Mmp9, Fpr2 and Ccl3. These results provide novel insights into the functions of lncRNAs and mRNAs involved in the regulation of the intestinal epithelial barrier.
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Affiliation(s)
- Huan Liu
- The Precision Medicine InstituteThe Third Affiliated HospitalSouthern Medical UniversityGuangzhouChina
- Affiliated Traditional Chinese Medicine HospitalSouthwest Medical UniversityLuzhouChina
| | - Teming Li
- Department of General SurgeryXinqiao HospitalArmy Medical UniversityChongqingChina
| | - Shizhen Zhong
- Guangdong Engineering Research Center for Translation of Medical 3D Printing ApplicationGuangdong Provincial Key Laboratory of Medical BiomechanicsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
| | - Min Yu
- Department of General SurgeryXinqiao HospitalArmy Medical UniversityChongqingChina
| | - Wenhua Huang
- The Precision Medicine InstituteThe Third Affiliated HospitalSouthern Medical UniversityGuangzhouChina
- Guangdong Engineering Research Center for Translation of Medical 3D Printing ApplicationGuangdong Provincial Key Laboratory of Medical BiomechanicsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
- Pathological Diagnosis and Research CenterAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
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24
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Which long noncoding RNAs and circular RNAs contribute to inflammatory bowel disease? Cell Death Dis 2020; 11:456. [PMID: 32541691 PMCID: PMC7295799 DOI: 10.1038/s41419-020-2657-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease (IBD), a chronic relapsing gastrointestinal inflammatory disease, mainly comprises ulcerative colitis (UC) and Crohn’s disease (CD). Although the mechanisms and pathways of IBD have been widely examined in recent decades, its exact pathogenesis remains unclear. Studies have focused on the discovery of new therapeutic targets and application of precision medicine. Recently, a strong connection between IBD and noncoding RNAs (ncRNAs) has been reported. ncRNAs include microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). The contributions of lncRNAs and circRNAs in IBD are less well-studied compared with those of miRNAs. However, lncRNAs and circRNAs are likely to drive personalized therapy for IBD. They will enable accurate diagnosis, prognosis, and prediction of therapeutic responses and promote IBD therapy. Herein, we briefly describe the molecular functions of lncRNAs and circRNAs and provide an overview of the current knowledge of the altered expression profiles of lncRNAs and circRNAs in patients with IBD. Further, we discuss how these RNAs are involved in the nosogenesis of IBD and are emerging as biomarkers.
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