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Velissari R, Ilieva M, Dao J, Miller HE, Madsen JH, Gorodkin J, Aikawa M, Ishii H, Uchida S. Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease. Brief Funct Genomics 2024; 23:395-405. [PMID: 37791426 PMCID: PMC11260263 DOI: 10.1093/bfgp/elad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/28/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
The cases of inflammatory bowel disease (IBD) are increasing rapidly around the world. Due to the multifactorial causes of IBD, there is an urgent need to understand the pathogenesis of IBD. As such, the usage of high-throughput techniques to profile genetic mutations, microbiome environments, transcriptome and proteome (e.g. lipidome) is increasing to understand the molecular changes associated with IBD, including two major etiologies of IBD: Crohn disease (CD) and ulcerative colitis (UC). In the case of transcriptome data, RNA sequencing (RNA-seq) technique is used frequently. However, only protein-coding genes are analyzed, leaving behind all other RNAs, including non-coding RNAs (ncRNAs) to be unexplored. Among these ncRNAs, long non-coding RNAs (lncRNAs) may hold keys to understand the pathogenesis of IBD as lncRNAs are expressed in a cell/tissue-specific manner and dysregulated in a disease, such as IBD. However, it is rare that RNA-seq data are analyzed for lncRNAs. To fill this gap in knowledge, we re-analyzed RNA-seq data of CD and UC patients compared with the healthy donors to dissect the expression profiles of lncRNA genes. As inflammation plays key roles in the pathogenesis of IBD, we conducted loss-of-function experiments to provide functional data of IBD-specific lncRNA, lung cancer associated transcript 1 (LUCAT1), in an in vitro model of macrophage polarization. To further facilitate the lncRNA research in IBD, we built a web database, IBDB (https://ibd-db.shinyapps.io/IBDB/), to provide a one-stop-shop for expression profiling of protein-coding and lncRNA genes in IBD patients compared with healthy donors.
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Affiliation(s)
- Rania Velissari
- Faculty of Biology, Medicine and Health, University of Manchester, Oxford Rd, Manchester M13 9PL, UK
- Bioinformatics Research Network, Atlanta, GA 30317, USA
| | - Mirolyuba Ilieva
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark
| | - James Dao
- Bioinformatics Research Network, Atlanta, GA 30317, USA
| | | | - Jens Hedelund Madsen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9, DK-1870 Frederiksberg C, Denmark
| | - Masanori Aikawa
- Cardiovascular Division, Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Excellence in Vascular Biology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hideshi Ishii
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, Denmark
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Xu C, Yang L, Cheng T, Wang Z, Liu C, Shao J. Sodium Houttuyfonate Ameliorates DSS-induced Colitis Aggravated by Candida albicans through Dectin-1/NF-κB/miR-32-5p/NFKBIZ Axis Based on Intestinal microRNA Profiling. Inflammation 2024:10.1007/s10753-024-02091-6. [PMID: 38963571 DOI: 10.1007/s10753-024-02091-6] [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: 05/14/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Our previous research indicated that Sodium houttuyfonate (SH) can effectively ameliorate dextran sulfate sodium (DSS)-induced colitis exacerbated by Candida albicans. However, the underlying protective mechanism of SH remains unclear. Therefore, in this study, a mice colitis model was infected with C. albicans, and the total colonic miRNAs were assessed. Furthermore, the differentially expressed miRNAs were enriched, clustered, and analyzed. Moreover, based on the dual luciferase analysis of NFKBIZ modulation by miR-32-5p, the in vitro and in vivo therapeutic effects of SH on inflammatory response, fungal burden, oxidative stress, and apoptosis were assessed at transcriptional and translational levels in the presence of agonist and antagonist. A total of 1157 miRNAs were identified, 84 of which were differentially expressed. Furthermore, qRT-PCR validated that SH treatment improved 17 differentially expressed miRNAs with > fourfold upregulation or > sixfold downregulation. Similar to most differentially altered miRNA, C. albicans significantly increased Dectin-1, NF-κB, TNF-α, IL-1β, IL-17A, and decreased miR-32-5p which negatively targeted NFKBIZ. In addition, SH treatment reduced inflammatory response and fungal burden in a colitis model with C. albicans infection. Further analyses indicated that in C. albicans infected Caco2 cells, SH inhibited fungal growth, oxidative stress, and apoptosis by increasing Dectin-1, NF-κB, NFKBIZ, TNF-α, IL-1β, IL-17A, and decreasing miR-32-5p. Therefore, SH can ameliorate the severity of colitis aggravated by C. albicans via the Dectin-1/NF-κB/miR-32-5p/NFKBIZ axis.
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Affiliation(s)
- Chen Xu
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Liu Yang
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Ting Cheng
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Zixu Wang
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Chengcheng Liu
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China
| | - Jing Shao
- Laboratory of Anti-Infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, 433 Room, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. China.
- Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei, 230012, Anhui, P. R. 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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Chen G, Deng H, Li M, Fang X, He C, Shu Y, Wang F. The role of long non-coding RNA in Crohn's disease. Heliyon 2024; 10:e32606. [PMID: 38961978 PMCID: PMC11219967 DOI: 10.1016/j.heliyon.2024.e32606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/29/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024] Open
Abstract
Emerging evidence has illuminated the pivotal role of long noncoding RNAs (lncRNAs) in orchestrating immunological functions and autoimmune responses. In the context of Crohn's disease (CD), an array of novel lncRNAs has been identified in the plasma and intestinal tissues of afflicted individuals, suggesting a dualistic influence on the disease progression, either exacerbating or mitigating its course. Current research has demonstrated the involvement of lncRNAs in competitive endogenous RNA, the inflammation process, epithelial barrier function, gut microbiota imbalance, and epigenetic regulation. This review aims to encapsulate the current knowledge on the lncRNA contribution to CD and underscore potential avenues for future research. LncRNAs are increasingly recognized as significant biomarkers and potential therapeutic targets, holding a key position in the pathogenesis of CD. Furthermore, the unique attributes of circulating lncRNAs, such as minimal side effects, combinational therapy potential, and personalized medicine, render them as promising therapeutic tools for individual health management in CD.
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Affiliation(s)
- Guo Chen
- Department of Internal Medicine, Anhui Hospital affiliated Shanghai Shuguang Hospital, Hefei, Anhui, China
| | - Heng Deng
- Department of Anorectal Surgery, the Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Ming Li
- Department of Anorectal Surgery, the First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Xiaoli Fang
- Department of Anorectal Surgery, the First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Chunrong He
- Hefei Haiheng Health Service Center, Hefei, Anhui, China
| | - Yingzi Shu
- Department of Anorectal Surgery, the Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Feifei Wang
- Department of Anorectal Surgery, the Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
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Apte A, Bardill JR, Canchis J, Skopp SM, Fauser T, Lyttle B, Vaughn AE, Seal S, Jackson DM, Liechty KW, Zgheib C. Targeting Inflammation and Oxidative Stress to Improve Outcomes in a TNBS Murine Crohn's Colitis Model. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:894. [PMID: 38786849 PMCID: PMC11124096 DOI: 10.3390/nano14100894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Inflammation and oxidative stress are implicated in the pathogenesis of Crohn's disease. Cerium oxide nanoparticle (CNP) conjugated to microRNA 146a (miR146a) (CNP-miR146a) is a novel compound with anti-inflammatory and antioxidative properties. We hypothesized that local administration of CNP-miR146a would improve colitis in a 2,4,6-Trinitrobenzenesulfonic acid (TNBS) mouse model for Crohn's disease by decreasing colonic inflammation. Balb/c mice were instilled with TNBS enemas to induce colitis. Two days later, the mice received cellulose gel enema, cellulose gel with CNP-miR146a enema, or no treatment. Control mice received initial enemas of 50% ethanol and PBS enemas on day two. The mice were monitored daily for weight loss and clinical disease activity. The mice were euthanized on days two or five to evaluate their miR146a expression, inflammation on histology, and colonic IL-6 and TNF gene expressions and protein concentrations. CNP-miR146a enema successfully increased colonic miR146a expression at 12 h following delivery. At the end of five days from TNBS instillation, the mice treated with CNP-miR146a demonstrated reduced weight loss, improved inflammation scores on histology, and reduced gene expressions and protein concentrations of IL-6 and TNF. The local delivery of CNP-miR146a in a TNBS mouse model of acute Crohn's colitis dramatically decreased inflammatory signaling, resulting in improved clinical disease.
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Affiliation(s)
- Anisha Apte
- Laboratory for Fetal and Regenerative Biology, Department of Surgery, University of Arizona Tucson College of Medicine, Banner Children’s at Diamond Children’s Medical Center, Tucson, AZ 85721, USA (K.W.L.)
| | - James R. Bardill
- Department of Surgery, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA; (J.R.B.)
| | - Jimena Canchis
- Laboratory for Fetal and Regenerative Biology, Department of Surgery, University of Arizona Tucson College of Medicine, Banner Children’s at Diamond Children’s Medical Center, Tucson, AZ 85721, USA (K.W.L.)
| | - Stacy M. Skopp
- Laboratory for Fetal and Regenerative Biology, Department of Surgery, University of Arizona Tucson College of Medicine, Banner Children’s at Diamond Children’s Medical Center, Tucson, AZ 85721, USA (K.W.L.)
| | - Tobias Fauser
- Laboratory for Fetal and Regenerative Biology, Department of Surgery, University of Arizona Tucson College of Medicine, Banner Children’s at Diamond Children’s Medical Center, Tucson, AZ 85721, USA (K.W.L.)
| | - Bailey Lyttle
- Department of Surgery, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA; (J.R.B.)
| | - Alyssa E. Vaughn
- Department of Surgery, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA; (J.R.B.)
| | - Sudipta Seal
- Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center, University of Central Florida, Orlando, FL 32827, USA
| | | | - Kenneth W. Liechty
- Laboratory for Fetal and Regenerative Biology, Department of Surgery, University of Arizona Tucson College of Medicine, Banner Children’s at Diamond Children’s Medical Center, Tucson, AZ 85721, USA (K.W.L.)
- Ceria Therapeutics, Inc., Tucson, AZ 85721, USA
| | - Carlos Zgheib
- Laboratory for Fetal and Regenerative Biology, Department of Surgery, University of Arizona Tucson College of Medicine, Banner Children’s at Diamond Children’s Medical Center, Tucson, AZ 85721, USA (K.W.L.)
- Ceria Therapeutics, Inc., Tucson, AZ 85721, USA
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6
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Curci D, Franzin M, Zudeh G, Bramuzzo M, Lega S, Decorti G, Stocco G, Lucafò M. Expression profiles of the lncRNA antisense GAS5-AS1 in colon biopsies from pediatric inflammatory bowel disease patients and its role in regulating sense transcript GAS5. Eur J Pediatr 2024; 183:1657-1665. [PMID: 38197962 PMCID: PMC11001710 DOI: 10.1007/s00431-023-05403-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024]
Abstract
The long non-coding RNA (lncRNA) growth arrest-specific transcript 5 (GAS5) level was demonstrated as involved in pediatric inflammatory bowel disease (IBD) pathogenesis. Since its antisense transcript GAS5-AS1 has never been investigated in IBD, this study aims to detect whether GAS5-AS1 and GAS5 levels are related to IBD clinical parameters and investigate their correlation in vitro. Twenty-six IBD pediatric patients were enrolled; paired inflamed and non-inflamed intestinal biopsies were collected. We evaluated GAS5 and GAS5-AS1 levels by real-time PCR. The role of GAS5 and GAS5-AS1 was assessed in vitro by transient silencing in THP1-derived macrophages. GAS5-AS1 and GAS5 levels were associated with patients' clinical parameters; GAS5-AS1 expression was downregulated in inflamed tissues and inversely correlated with disease activity. A positive correlation between GAS5-AS1 and GAS5 levels was observed in non-inflamed biopsies. On THP1-derived macrophages, a reduced amount of both GAS5-AS1 and GAS5 was observed; accordingly, matrix metalloproteinase (MMP) 9 was increased. After GAS5-AS1 silencing, a downregulation of GAS5 was found, whereas no effect was detected on GAS5-AS1 after GAS5 silencing. Conclusion: This study provided for the first time new insights into the potential role of GAS5-AS1 in IBD. GAS5-AS1 modulates GAS5 levels in vitro and may serve as a potential IBD diagnostic biomarker. What is Known: • GAS5 is involved in regulating intestinal MMP-2 and MMP-9 in pediatric patients with IBD; • GAS5-AS1 has never been investigated in the context of IBD; • GAS5-AS1 regulates the expression of GAS5, increasing its stability in tissues and in vitro cell models of cancer. What is New: • GAS5-AS1 correlated with GAS5 and IBD clinical parameters; • GAS5-AS1 can modulate GAS5 levels in macrophages; • GAS5-AS1 may serve as potential IBD diagnostic biomarker.
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Affiliation(s)
- Debora Curci
- Department of Advanced Translational Diagnostics, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", 34137, Trieste, Italy
| | - Martina Franzin
- Department of Advanced Translational Diagnostics, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", 34137, Trieste, Italy
| | - Giulia Zudeh
- Department of Advanced Translational Diagnostics, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", 34137, Trieste, Italy
| | - Matteo Bramuzzo
- Department of Pediatric Gastroenterology, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", 34137, Trieste, Italy
| | - Sara Lega
- Department of Pediatric Gastroenterology, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", 34137, Trieste, Italy
| | - Giuliana Decorti
- Department of Medicine Surgery and Health Sciences, University of Trieste, 34149, Trieste, Italy
| | - Gabriele Stocco
- Department of Advanced Translational Diagnostics, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", 34137, Trieste, Italy.
- Department of Medicine Surgery and Health Sciences, University of Trieste, 34149, Trieste, Italy.
| | - Marianna Lucafò
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
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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] [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.
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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
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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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9
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Baldan-Martin M, Rubín de Célix C, Orejudo M, Ortega Moreno L, Fernández-Tomé S, Soleto I, Ramirez C, Arroyo R, Fernández P, Santander C, Moreno-Monteagudo JA, Casanova MJ, Casals F, Casabona S, Becerro I, Lozano JJ, Aransay AM, Chaparro M, Gisbert JP. Long Non-Coding RNA Signatures in the Ileum and Colon of Crohn's Disease Patients and Effect of Anti-TNF-α Treatment on Their Modulation. Int J Mol Sci 2023; 24:15691. [PMID: 37958675 PMCID: PMC10650062 DOI: 10.3390/ijms242115691] [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: 09/01/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Biological therapies only benefit one-third of patients with Crohn's disease (CD). For this reason, a deeper understanding of the mechanisms by which biologics elicit their effect on intestinal mucosa is needed. Increasing evidence points toward the involvement of long noncoding RNAs (lncRNAs) in the pathogenesis of CD, although their role remains poorly studied. We aimed to characterize lncRNA profiles in the ileum and colon from CD patients and evaluate the effect of anti-TNF-α treatment on their transcription. Terminal ileum and left colon samples from 30 patients (active CD = 10, quiescent CD = 10, and healthy controls (HCs) = 10) were collected for RNA-seq. The patients were classified according to endoscopic activity. Furthermore, biopsies were cultured with infliximab, and their transcriptome was determined by Illumina gene expression array. A total of 678 differentially expressed lncRNAs between the terminal ileum and left colon were identified in HCs, 438 in patients with quiescent CD, and 468 in patients with active CD. Additionally, we identified three new lncRNAs in the ileum associated with CD activity. No differences were observed when comparing the effect of infliximab according to intestinal location, presence of disease (CD vs. HC), and activity (active vs. quiescent). The expression profiles of lncRNAs are associated with the location of intestinal tissue, being very different in the ileum and colon. The presence of CD and disease activity are associated with the differential expression of lncRNAs. No modulatory effect of infliximab has been observed in the lncRNA transcriptome.
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Affiliation(s)
- Montse Baldan-Martin
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Cristina Rubín de Célix
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Macarena Orejudo
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Lorena Ortega Moreno
- Área de Farmacología y Nutrición y Bromatología, Grupo de Investigación de Alto Rendimiento en Fisiopatología del Sistema Digestivo URJC: NeuGut-URJC, Departamento Ciencias Básicas de la Salud, Universidad Rey Juan Carlos, 28922 Madrid, Spain;
| | - Samuel Fernández-Tomé
- Departamento de Nutrición y Ciencia de los Alimentos, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain;
| | - Irene Soleto
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Cristina Ramirez
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Ricardo Arroyo
- Instituto de Medicina Molecular Aplicada Nemesio Díez (IMMA-ND), Facultad de Medicina, Universidad San Pablo CEU, 28668 Madrid, Spain (P.F.)
| | - Paloma Fernández
- Instituto de Medicina Molecular Aplicada Nemesio Díez (IMMA-ND), Facultad de Medicina, Universidad San Pablo CEU, 28668 Madrid, Spain (P.F.)
| | - Cecilio Santander
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - José Andrés Moreno-Monteagudo
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - María José Casanova
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Fernando Casals
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Sergio Casabona
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Irene Becerro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Juan J. Lozano
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain;
| | - Ana M. Aransay
- Genome Analysis Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Spain;
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Javier P. Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
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10
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Wang J, Yao M, Zou J, Ding W, Sun M, Zhuge Y, Gao F. pH-Sensitive Nanoparticles for Colonic Delivery Anti-miR-301a in Mouse Models of Inflammatory Bowel Diseases. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2797. [PMID: 37887947 PMCID: PMC10610125 DOI: 10.3390/nano13202797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023]
Abstract
Though the anti-miR-301a (anti-miR) is a promising treatment strategy for inflammatory bowel disease (IBD), the degradability and the poor targeting of the intestine are a familiar issue. This study aimed to develop a multifunctional oral nanoparticle delivery system loaded with anti-miR for improving the targeting ability and the therapeutic efficacy. The HA-CS/ES100/PLGA nanoparticles (HCeP NPs) were prepared using poly (lactic-co-glycolic acid) copolymer (PLGA), enteric material Eudragit®S100 (ES100), chitosan (CS), and hyaluronic acid (HA). The toxicity of nanoparticles was investigated via the Cell Counting Kit-8, and the cellular uptake and inflammatory factors of nanoparticles were further studied. Moreover, we documented the colon targeting and pharmacodynamic properties of nanoparticles. The nanoparticles with uniform particle size exhibited pH-sensitive release, favorable gene protection, and storage stability. Cytology experiments showed that anti-miR@HCeP NPs improved the cellular uptake through HA and reduced pro-inflammatory factors. Administering anti-miR@HCeP NPs orally to IBD mice markedly reduced their pro-inflammatory factors levels and disease activity indices. We also confirmed that anti-miR@HCeP NPs mostly accumulated in the colon site, and effectively repaired the intestinal barrier, as well as relieved intestinal inflammation. The above nanoparticle is a candidate of the treatment for IBD due to its anti-inflammatory properties.
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Affiliation(s)
- Junshan Wang
- Department of Gastroenterology, Chongming Branch of Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 202157, China
| | - Min Yao
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China; (M.Y.); (J.Z.); (W.D.); (M.S.)
| | - Jiafeng Zou
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China; (M.Y.); (J.Z.); (W.D.); (M.S.)
| | - Wenxing Ding
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China; (M.Y.); (J.Z.); (W.D.); (M.S.)
| | - Mingyue Sun
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China; (M.Y.); (J.Z.); (W.D.); (M.S.)
| | - Ying Zhuge
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
| | - Feng Gao
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China; (M.Y.); (J.Z.); (W.D.); (M.S.)
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, China
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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11
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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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12
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El-Boghdady NA, El-Hakk SA, Abd-Elmawla MA. The lncRNAs UCA1 and CRNDE target miR-145/TLR4/NF-қB/TNF-α axis in acetic acid-induced ulcerative colitis model: The beneficial role of 3,3-Diindolylmethane. Int Immunopharmacol 2023; 121:110541. [PMID: 37390564 DOI: 10.1016/j.intimp.2023.110541] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/07/2023] [Accepted: 06/17/2023] [Indexed: 07/02/2023]
Abstract
INTRODUCTION Ulcerative colitis (UC) is a chronic disease that alters the colonic and rectal mucosa. The high prevalence rates of UC make it a worldwide healthcare problem. However, its underlying molecular mechanisms remain vague. AIM OF THE STUDY To investigate the molecular mechanisms underlying UC and to study the cross-talk among the regulatory role of the lncRNAs UCA1, CRNDE, and miR-145 on TLR4/NF-κB/TNF-α signaling pathway. Moreover, the study was extended to examine the beneficial effects of 3,3-Diindolylmethane (DIM) on relieving UC. METHODS UC was induced in rats by injecting 2 ml of 4% acetic acid (AA) solution transrectally. After 24 h, rats were treated with either DIM (20 mg/kg) or sulphasalazine (SSZ) (500 mg/kg) orally for 7 days. RESULTS The present study revealed that the gene expression of the lncRNAs UCA1 and CRNDE were significantly upregulated in the AA-induced UC model compared with the control group, whereas miR-145 was significantly downregulated. There was a significant association between the expression of these non-coding RNAs and TLR4/ NF-κB/TNF-α axis as well as malondialdehyde and glutathione levels. Favorably, the DIM-treated group showed significant downregulation of the lncRNAs UCA1 and CRNDE along with upregulated miR-145 compared with the AA-induced UC model. Furthermore, DIM showed remarkable inhibition of the TLR4/ NF-κB /TNF-α cascade compared with non-treated UC rats. CONCLUSIONS The present study is the first to document the interrelated role of the lncRNAs UCA1 and CRNDE in UC via orchestrating miR-145/TLR4/ NF-κB /TNF-α inflammatory cascade. Furthermore, the study demonstrated a new molecular basis for the pleiotropic activities of DIM in relieving UC.
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Affiliation(s)
- Noha A El-Boghdady
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | | | - Mai A Abd-Elmawla
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt.
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13
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Meng W, Johnsen KM, Fenton CG, Florholmen J, Paulssen RH. Anti-apoptotic genes and non-coding RNAs are potential outcome predictors for ulcerative colitis. Funct Integr Genomics 2023; 23:165. [PMID: 37199828 DOI: 10.1007/s10142-023-01099-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Due to the lack of clinical, immunologic, genetic, and laboratory markers to predict remission in ulcerative colitis (UC) without relapse, there is no clear recommendation regarding withdrawal of therapy. Therefore, this study was to investigate if transcriptional analysis together with Cox survival analysis might be able to reveal molecular markers that are specific for remission duration and outcome. Mucosal biopsies from patients in remission with active treatment-naïve UC and healthy control subjects underwent whole-transcriptome RNA-seq. Principal component analysis (PCA) and Cox proportional hazards regression analysis were applied to the remission data concerning duration and status of patients. A randomly chosen remission sample set was used for validation of the applied methods and results. The analyses distinguished two different UC remission patient groups with respect to remission duration and outcome (relapse). Both groups showed that altered states of UC with quiescent microscopic disease activity are still present. The patient group with the longest remission duration and no relapse revealed specific and increased expression of antiapoptotic factors belonging to the MTRNR2-like gene family and non-coding RNAs. In summary, the expression of anti-apoptotic factors and non-coding RNAs may contribute to personalized medicine approaches in UC by improving patient stratification for different treatment regimens.
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Affiliation(s)
- Wei Meng
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Kay-Martin Johnsen
- Gastroenterology and Nutrition Research Group, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
- Department of Medical Gastroenterology, University Hospital of North Norway, Tromsø, Norway
| | - Christopher G Fenton
- Genomics Support Centre Tromsø, UiT- The Arctic University of Norway, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Sykehusveien 44, N-9037, Tromsø, Norway
| | - Jon Florholmen
- Gastroenterology and Nutrition Research Group, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway.
- Genomics Support Centre Tromsø, UiT- The Arctic University of Norway, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Sykehusveien 44, N-9037, Tromsø, Norway.
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Putting the "mi" in omics: discovering miRNA biomarkers for pediatric precision care. Pediatr Res 2023; 93:316-323. [PMID: 35906312 PMCID: PMC9884316 DOI: 10.1038/s41390-022-02206-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/27/2022] [Indexed: 01/31/2023]
Abstract
In the past decade, growing interest in micro-ribonucleic acids (miRNAs) has catapulted these small, non-coding nucleic acids to the forefront of biomarker research. Advances in scientific knowledge have made it clear that miRNAs play a vital role in regulating cellular physiology throughout the human body. Perturbations in miRNA signaling have also been described in a variety of pediatric conditions-from cancer, to renal failure, to traumatic brain injury. Likewise, the number of studies across pediatric disciplines that pair patient miRNA-omics with longitudinal clinical data are growing. Analyses of these voluminous, multivariate data sets require understanding of pediatric phenotypic data, data science, and genomics. Use of machine learning techniques to aid in biomarker detection have helped decipher background noise from biologically meaningful changes in the data. Further, emerging research suggests that miRNAs may have potential as therapeutic targets for pediatric precision care. Here, we review current miRNA biomarkers of pediatric diseases and studies that have combined machine learning techniques, miRNA-omics, and patient health data to identify novel biomarkers and potential therapeutics for pediatric diseases. IMPACT: In the following review article, we summarized how recent developments in microRNA research may be coupled with machine learning techniques to advance pediatric precision care.
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15
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Feng S, Xu Z, Zhang Z, Mo Y, Deng Y, Li L, Fei S, Wu J, Wang K, Zhang Q, Song J, Zhou R. RNA-Seq approach to investigate the effects of melatonin on bone marrow-derived dendritic cells from dextran sodium sulfate-induced colitis mice. Toxicology 2022; 481:153354. [DOI: 10.1016/j.tox.2022.153354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022]
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16
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Zhao F, Li S, Liu J, Wang J, Yang B. Long non-coding RNA TRIM52-AS1 sponges microRNA-577 to facilitate diffuse large B cell lymphoma progression via increasing TRIM52 expression. Hum Cell 2022; 35:1234-1247. [PMID: 35676608 DOI: 10.1007/s13577-022-00725-1] [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: 12/07/2021] [Accepted: 05/13/2022] [Indexed: 11/04/2022]
Abstract
Diffuse large B cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma (NHL) globally, featuring heterogeneous clinical phenotypes and altered molecular manifestations. The long non-coding ribose nucleic acids (lncRNAs) play crucial roles in the diagnosis, treatment, and prognosis of DLBCL, requiring the exploration of complex functions and mechanisms. In this study, the expression of lncRNA TRIM52-AS1 in DLBCL tissues from the Cancer Genome Atlas (TCGA) database was initially analyzed and correlated to the data from collected clinical samples. Then, the significance of TRIM52-AS1 on the diagnosis and prognosis of DLBCL patients was predicted with the receiver-operating characteristic (ROC) curve and Kaplan-Meier (KM) analysis. Further, cell counting kit (CCK)-8, EdU staining, and flow cytometry analyses were performed to assess the effect of TRIM52-AS1 on DLBCL cell proliferation, apoptosis, and cell cycle. Then, the mechanism of TRIM52-AS1 sponging miR-577 to increase TRIM52 expression was explored using a starBase prediction approach, dual-luciferase reporter, RNA immunoprecipitation assay (RIPA), quantitative reverse transcription-polymerase chain reaction (RT-qPCR), and Western blot analyses. The experimental results confirmed the overexpression of TRIM52-AS1 in the DLBCL cell lines. Further, the high expression of TRIM52-AS1 predicted the poor Ann Arbor stage and were correlated with the presence of B symptoms, high international prognostic index, and poor disease prognosis. TRIM52-AS1 knockdown inhibited the DLBCL cell proliferation, and induced apoptosis and G0/G1 cycle arrest. Interestingly, the overexpression of TRIM52-AS1 increased the mRNA stability of TRIM52 through binding IGFBP3 protein and upregulated the TRIM52 protein expression by sponging miR-577. Together, the overexpressed TRIM52-AS1 could promote the DLBCL progression through IGFBP3/miR-218-5p/TRIM52 axis, highlighting the clinical significance of TRIM52-AS1 in the DLBCL diagnosis.
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Affiliation(s)
- Fang Zhao
- Department of Hematology, Cangzhou Central Hospital, 16 Middle Xinhua Road, Cangzhou, 061000, Hebei, China.
| | - Shucheng Li
- Department of Hematology, Cangzhou Central Hospital, 16 Middle Xinhua Road, Cangzhou, 061000, Hebei, China
| | - Jingjing Liu
- Department of Hematology, Cangzhou Central Hospital, 16 Middle Xinhua Road, Cangzhou, 061000, Hebei, China
| | - Juan Wang
- Department of Hematology, Cangzhou Central Hospital, 16 Middle Xinhua Road, Cangzhou, 061000, Hebei, China
| | - Bo Yang
- Department of Thoracic Surgery, Cangzhou Central Hospital, Cangzhou, Hebei, China
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Ouyang W, Wu M, Wu A, Xiao H. Circular RNA_0001187 participates in the regulation of ulcerative colitis development via upregulating myeloid differentiation factor 88. Bioengineered 2022; 13:12863-12875. [PMID: 35609334 PMCID: PMC9275921 DOI: 10.1080/21655979.2022.2077572] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Circular RNA (circRNA) had been confirmed to participate in ulcerative colitis (UC) development. Circular RNA_0001187 (Circ_0001187) had been found to be overexpressed in patients with Crohn disease. Therefore, circ_0001187 might be an important circRNA regulating intestinal inflammatory diseases. However, the role and mechanism of circ_0001187 in UC progression remains unclear. The colonic mucosal tissues were obtained from 23 UC patients and 23 healthy normal controls. Tumor necrosis factor-α (TNF-α) was used to mimic UC cell model in vitro. Cell function was assessed by cell counting kit 8 assay, EdU assay, flow cytometry, ELISA assay and oxidative stress detection. RNA interaction was confirmed by dual-luciferase reporter assay and RIP assay. Serum exosomes were isolated by ultracentrifugation and identified by transmission electron microscope. Circ_0001187 was overexpressed in UC patients. Circ_0001187 knockdown enhanced the proliferation, while suppressed apoptosis, inflammation and oxidative stress of TNF-α-induced FHC cells. Circ_0001187 acted as miR-1236-3p sponge, and the effects of circ_0001187 downregulation on TNF-α-induced FHC cell injury were overturned by miR-1236-3p inhibitor. MYD88 was targeted by miR-1236-3p, and circ_0001187 sponged miR-1236-3p to regulate MYD88. MYD88 knockdown alleviated TNF-α-induced FHC cell injury, and its upregulation revoked the inhibition effect of miR-1236-3p on TNF-α-induced FHC cell injury. High expression of circ_0001187 also was observed in the serum exosomes of UC patients. Our data confirmed that circ_0001187 facilitated UC progression through miR-1236-3p/MYD88 axis, which might be a potential treatment and diagnosis biomarker for UC.
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Affiliation(s)
- Wei Ouyang
- Department of Oncology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou City, China
| | - Min Wu
- Department of Emergency, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou City, China
| | - Anshan Wu
- Department of Oncology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou City, China
| | - Heng Xiao
- Department of Anorectal, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou City, China
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18
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Wang XJ, Li XY, Guo XC, Liu L, Jin YY, Lu YQ, Cao YJN, Long JY, Wu HG, Zhang D, Yang G, Hong J, Yang YT, Ma XP. LncRNA-miRNA-mRNA Network Analysis Reveals the Potential Biomarkers in Crohn’s Disease Rats Treated with Herb-Partitioned Moxibustion. J Inflamm Res 2022; 15:1699-1716. [PMID: 35282268 PMCID: PMC8906857 DOI: 10.2147/jir.s351672] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/19/2022] [Indexed: 12/16/2022] Open
Abstract
Background Long noncoding RNA (lncRNA) is receiving growing attention in Crohn’s disease (CD). However, the mechanism by which herb-partitioned moxibustion (HPM) regulates the expression and functions of lncRNAs in CD rats is still unclear. The aim of our study is to identify lncRNA-miRNA-mRNA network potential biological functions in CD. Methods RNA sequencing and microRNA (miRNA) sequencing were carried out to analyze lncRNA, miRNA and mRNA expression profiles among the CD rats, normal control rats, and CD rats after HPM treatment and constructed the potential related lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) networks. Then, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, protein–protein interaction (PPI) analysis and quantitative real-time polymerase chain reaction (qRT-PCR) were performed to explore potentially important genes in ceRNA networks. Results A total of 189 lncRNAs, 32 miRNAs and 463 mRNAs were determined as differentially expressed (DE) genes in CD rats compared to normal control rats, and 161 lncRNAs, 12 miRNAs and 130 mRNAs were identified as remarkably DE genes in CD rats after HPM treatment compared to CD rats. GO analysis indicated that the target genes were most enriched in cAMP and in KEGG pathway analysis the main pathways included adipocytokine, PPAR, AMPK, FoxO and PI3K-Akt signaling pathway. Finally, qRT-PCR results confirmed that lncRNA LOC102550026 sponged miRNA-34c-5p to regulate the intestinal immune inflammatory response by targeting Pck1. Conclusion By constructing a ceRNA network with lncRNA-miRNA-mRNA, PCR verification, and KEGG analysis, we revealed that LOC102550026/miRNA-34c-5p/Pck1 axis and adipocytokine, PPAR, AMPK, FoxO, and PI3K-Akt signaling pathways might regulate the intestinal immune-inflammatory response, and HPM may regulate the lncRNA LOC102550026/miR-34c-5p/Pck1 axis and adipocytokine, PPAR, AMPK, FoxO, and PI3K-Akt signaling pathways, thus improving intestinal inflammation in CD. These findings may be novel potential targets in CD.
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Affiliation(s)
- Xue-Jun Wang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Xiao-Ying Li
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Xiao-Cong Guo
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Li Liu
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - You-You Jin
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Yun-Qiong Lu
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Yao-Jia-Ni Cao
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Jun-Yi Long
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Huan-Gan Wu
- Key Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai, People’s Republic of China
| | - Dan Zhang
- Key Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai, People’s Republic of China
| | - Guang Yang
- Key Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai, People’s Republic of China
| | - Jue Hong
- Key Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai, People’s Republic of China
| | - Yan-Ting Yang
- Key Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai, People’s Republic of China
| | - Xiao-Peng Ma
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
- Key Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai, People’s Republic of China
- Correspondence: Xiao-Peng Ma; Yan-Ting Yang, Key Laboratory of Acupuncture-Moxibustion and Immunology, Shanghai Research Institute of Acupuncture and Meridian, Shanghai, People’s Republic of China, Email ;
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Zhou Z, Chen J, Huang Y, Liu D, Chen S, Qin S. Long Noncoding RNA GAS5: A New Factor Involved in Bone Diseases. Front Cell Dev Biol 2022; 9:807419. [PMID: 35155450 PMCID: PMC8826583 DOI: 10.3389/fcell.2021.807419] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), as an important type of RNA encoded in the human transcriptome, have shown to regulate different genomic processes in human cells, altering cell type and function. These factors are associated with carcinogenesis, cancer metastasis, bone diseases, and immune system diseases, among other pathologies. Although many lncRNAs are involved in various diseases, the molecular mechanisms through which lncRNAs contribute to regulation of disease are still unclear. The lncRNA growth arrest-specific 5 (GAS5) is a key player that we initially found to be associated with regulating cell growth, differentiation, and development. Further work has shown that GAS5 is involved in the occurrence and prognosis of bone diseases, such as osteoporosis, osteosarcoma, and postosteoporotic fracture. In this review, we discuss recent progress on the roles of GAS5 in bone diseases to establish novel targets for the treatment of bone diseases.
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Affiliation(s)
- Zimo Zhou
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jiahui Chen
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ying Huang
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, China
| | - Da Liu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Da Liu,
| | - Senxiang Chen
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Sen Qin
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
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20
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Long non-coding RNA RP11-342L8.2, derived from RNA sequencing and validated via RT-qPCR, is upregulated and correlates with disease severity in psoriasis patients. Ir J Med Sci 2022; 191:2643-2649. [PMID: 35028895 DOI: 10.1007/s11845-021-02882-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/01/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVE This study aimed to explore the dysregulated long non-coding RNA (lncRNA) expression profile in psoriatic tissue vs. normal skin tissue via RNA sequencing (RNA-seq), then further sort candidate lncRNAs to be validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR), in order to investigate the comprehensive linkage of lncRNA with psoriasis. METHODS Twenty-five psoriasis patients were consecutively enrolled, with their psoriatic and surrounding normal skin tissues obtained. Ten pairs of psoriatic and normal tissues were proposed to RNA-seq. Then, top 6 differentially expressed lncRNAs (DElncRNA) were sorted as candidate lncRNAs for validation by RT-qPCR in 25 pairs of samples. RESULTS Principal component analysis (PCA) exhibited that lncRNA profile clearly distinguished psoriatic tissue from normal tissue, so did heatmap. Volcano plot disclosed 412 upregulated and 625 downregulated DElncRNAs in psoriatic tissue vs. normal tissue. Gene Ontology (GO) and Kyoko Encyclopedia of Genes and Genomes (KEGG) enrichment analyses exhibited that these DElncRNAs were mainly enriched in immune, inflammation, or proliferation-related biological processes and pathways such as neutrophil degranulation, regulation of immune response, positive regulation of cell proliferation, and MAPK signaling pathway. By RT-qPCR validation, lncRNAs RP11-22A3.2, RP11-342L8.2, and CTD-2006H14.2 were increased (all P < 0.001), while lncRNAs AP000442.4, CCDC144NL-AS1, and MIR663AHG were decreased (all P < 0.01) in psoriatic tissue vs. normal tissue. Interestingly, psoriatic lncRNA RP11-342L8.2 was also observed to positively correlated with psoriasis area and severity index (PASI) (r = 0.405, P = 0.045). CONCLUSION Our present study exhibits some evidence for the landscape of lncRNAs implicated in psoriasis.
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21
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Role of microRNAs in the Pathophysiology of Ulcerative Colitis. IMMUNO 2021. [DOI: 10.3390/immuno1040039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ulcerative colitis (UC) is an intractable disorder characterized by a chronic inflammation of the colon. Studies have identified UC as a multifactorial disorder affected by both genetic and environmental factors; however, the precise mechanism remains unclear. Recent advances in the field of microRNA (miRNA) research have identified an association between this small non-coding RNA in the pathophysiology of UC and altered miRNA expression profiles in patients with UC. Nevertheless, the roles of individual miRNAs are uncertain due to heterogeneity in both research samples and clinical backgrounds. In this review, we focus on miRNA expression in colonic mucosa where inflammation occurs in UC and discuss the potential roles of individual miRNAs in disease development, outlining the pathophysiology of UC.
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22
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Yang J, Chen W, Sun Y, Xia P, Liu J, Zhang W. The role of microRNAs in regulating cadmium-induced apoptosis by targeting Bcl-2 in IEC-6 cells. Toxicol Appl Pharmacol 2021; 432:115737. [PMID: 34662668 DOI: 10.1016/j.taap.2021.115737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/28/2021] [Accepted: 09/12/2021] [Indexed: 02/07/2023]
Abstract
Cadmium (Cd) is one of the most harmful environmental pollutants and has been found to have adverse effects on the gut. However, the toxic effects and potential mechanism of Cd on intestinal epithelial cells (IECs) are poorly understood. This study evaluated the effects of Cd exposure (0, 0.25, 0.5, 1, 2, and 4 μM) on IEC-6 cells in terms of cell viability and apoptosis, as well as apoptosis-associated gene expression. The results indicated that low doses (0.25- 1 μM) of Cd exhibited hormetic effects, while high doses of Cd (2 and 4 μM) reduced cell viability. The apoptotic effect increased in a dose-dependent pattern. Moreover, the mRNA levels of the Bcl-2, Bax and Caspase 3 genes were altered, which was in agreement with their protein expression. Based on sequencing analysis, the expression pattern of the microRNAs (miRNAs) changed significantly in the 2 μM Cd-treated group. QRT-PCR verified that 7 miRNAs, including miR-124-3p and miR-370-3p, were all upregulated with dose-effect relationship. Besides, transfection of miR-124-3p and miR-370-3p mimics /inhibitor and Bcl-2 siRNA into IEC-6 cells verified that these two miRNAs could regulate Cd-induced apoptosis by targeting Bcl-2. Finally, the direct targeting relationship between miR-370-3p and Bcl-2 gene was confirmed by luciferase reporter assay. Overall, the results demonstrated that Cd exposure could induce apoptosis in IEC-6 cells. The potential mechanism may be interference with the regulation of Bcl-2 gene expression by miR-370-3p and miR-124-3p.
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Affiliation(s)
- Jinsong Yang
- Department of Infectious Disease Prevention and Control, Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Jintai Road No.76, 350001, China.
| | - Wei Chen
- Department of Infectious Disease Prevention and Control, Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Jintai Road No.76, 350001, China
| | - Yi Sun
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environmental Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Xueyuan Road No. 1, Minhou Coudslanty, Fuzhou 350108, China
| | - Pincang Xia
- Department of Infectious Disease Prevention and Control, Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Jintai Road No.76, 350001, China
| | - Jin Liu
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environmental Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Xueyuan Road No. 1, Minhou Coudslanty, Fuzhou 350108, China
| | - Wenchang Zhang
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environmental Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Xueyuan Road No. 1, Minhou Coudslanty, Fuzhou 350108, China.
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23
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The Role of lncRNAs in Regulating the Intestinal Mucosal Mechanical Barrier. BIOMED RESEARCH INTERNATIONAL 2021; 2021:2294942. [PMID: 34820453 PMCID: PMC8608538 DOI: 10.1155/2021/2294942] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/29/2021] [Accepted: 10/27/2021] [Indexed: 12/18/2022]
Abstract
lncRNA is a transcript that is more than 200 bp in length. Currently, evidence has shown that lncRNA is of great significance in cell activity, involved in epigenetics, gene transcription, chromatin regulation, etc. The existence of an intestinal mucosal mechanical barrier hinders the invasion of pathogenic bacteria and toxins, maintaining the stability of the intestinal environment. Serious destruction or dysfunction of the mechanical barrier often leads to intestinal diseases. This review first summarizes the ability of lncRNAs to regulate the intestinal mucosal mechanical barrier. We then discussed how lncRNAs participate in various intestinal diseases by regulating the intestinal mucosal mechanical barrier. Finally, we envision its potential as a new marker for diagnosing and treating intestinal inflammatory diseases.
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24
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Transcriptomic Characterization of Cow, Donkey and Goat Milk Extracellular Vesicles Reveals Their Anti-Inflammatory and Immunomodulatory Potential. Int J Mol Sci 2021; 22:ijms222312759. [PMID: 34884564 PMCID: PMC8657891 DOI: 10.3390/ijms222312759] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 02/06/2023] Open
Abstract
Milk extracellular vesicles (mEVs) seem to be one of the main maternal messages delivery systems. Extracellular vesicles (EVs) are micro/nano-sized membrane-bound structures enclosing signaling molecules and thus acting as signal mediators between distant cells and/or tissues, exerting biological effects such as immune modulation and pro-regenerative activity. Milk is also a unique, scalable, and reliable source of EVs. Our aim was to characterize the RNA content of cow, donkey, and goat mEVs through transcriptomic analysis of mRNA and small RNA libraries. Over 10,000 transcripts and 2000 small RNAs were expressed in mEVs of each species. Among the most represented transcripts, 110 mRNAs were common between the species with cow acting as the most divergent. The most represented small RNA class was miRNA in all the species, with 10 shared miRNAs having high impact on the immune regulatory function. Functional analysis for the most abundant mRNAs shows epigenetic functions such as histone modification, telomere maintenance, and chromatin remodeling for cow; lipid catabolism, oxidative stress, and vitamin metabolism for donkey; and terms related to chemokine receptor interaction, leukocytes migration, and transcriptional regulation in response to stress for goat. For miRNA targets, shared terms emerged as the main functions for all the species: immunity modulation, protein synthesis, cellular cycle regulation, transmembrane exchanges, and ion channels. Moreover, donkey and goat showed additional terms related to epigenetic modification and DNA maintenance. Our results showed a potential mEVs immune regulatory purpose through their RNA cargo, although in vivo validation studies are necessary.
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25
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Allenspach K, Mochel JP. Current diagnostics for chronic enteropathies in dogs. Vet Clin Pathol 2021; 50 Suppl 1:18-28. [PMID: 34699081 DOI: 10.1111/vcp.13068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/29/2021] [Accepted: 08/16/2021] [Indexed: 12/25/2022]
Abstract
Chronic enteropathies (CEs) in dogs describe a group of idiopathic disorders characterized by chronic persistent or recurrent gastrointestinal (GI) signs. Three major subgroups of CE can be identified by their response to treatment: Food-responsive disease (FRD), antibiotic-responsive disease (ARD), and steroid-responsive disease (SRD). The clinical diagnosis of CE is made by exclusion of all other possible causes of chronic diarrhea and includes histologic assessment of intestinal biopsies. The process of diagnosing canine CE can therefore be very time-consuming and expensive, and in most cases, does not help to identify dogs that will respond to a specific treatment. The development of novel diagnostic tests for canine CE has therefore focused on the accuracy of such tests to predict treatment responses. In this article, several novel assays that have the potential to become commercially available will be discussed, such as genetic tests, perinuclear anti-neutrophil cytoplasmic antibodies (pANCA), antibodies against transglutaminase/gliadin, antibodies against E coli OmpC/flagellin, and micro RNAs.
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Affiliation(s)
- Karin Allenspach
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.,SMART Translational Medicine, Iowa State University, Ames, IA, USA
| | - Jonathan P Mochel
- SMART Translational Medicine, Iowa State University, Ames, IA, USA.,Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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26
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Skrzypczak D, Skrzypczak-Zielińska M, Ratajczak AE, Szymczak-Tomczak A, Eder P, Słomski R, Dobrowolska A, Krela-Kaźmierczak I. Myostatin and Follistatin-New Kids on the Block in the Diagnosis of Sarcopenia in IBD and Possible Therapeutic Implications. Biomedicines 2021; 9:biomedicines9101301. [PMID: 34680417 PMCID: PMC8533148 DOI: 10.3390/biomedicines9101301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/07/2021] [Accepted: 09/15/2021] [Indexed: 12/16/2022] Open
Abstract
Sarcopenia, which is a decrease in muscle strength and quality of muscle tissue, is a common disorder among patients suffering from inflammatory bowel disease. This particular group of patients often presents with malnutrition and shows low physical activity, which increases the risk of sarcopenia. Another important factor in the development of sarcopenia is an imbalanced ratio of myostatin and follistatin, which may stem from inflammation as well as genetic factors. Currently, research in this area continues, and is aimed at identifying an effective medication for the treatment of this condition. Additionally, we still have no sarcopenia markers that can be used for diagnosis. In this paper, we address the role of myostatin and follistatin as potential markers in the diagnosis of sarcopenia in patients with Crohn’s disease and ulcerative colitis, particularly in view of the genetic and biological aspects. We also present data on new perspectives in the pharmacotherapy of sarcopenia (i.e., myostatin inhibitors and gene therapy). Nevertheless, knowledge is still scarce about the roles of follistatin and myostatin in sarcopenia development among patients suffering from inflammatory bowel disease, which warrants further study.
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Affiliation(s)
- Dorota Skrzypczak
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego Street 49, 60-355 Poznan, Poland; (A.E.R.); (A.S.-T.); (P.E.); (A.D.)
- Correspondence: (D.S.); (I.K.-K.); Tel.: +48-618691343 (D.S.); +48-601-256-715 (I.K.-K.); Fax: +48-8691-314 (I.K.-K.)
| | - Marzena Skrzypczak-Zielińska
- Institute of Human Genetics, Polish Academy of Sciences Poznan, Strzeszynska Street 32, 60-479 Poznan, Poland; (M.S.-Z.); (R.S.)
| | - Alicja Ewa Ratajczak
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego Street 49, 60-355 Poznan, Poland; (A.E.R.); (A.S.-T.); (P.E.); (A.D.)
| | - Aleksandra Szymczak-Tomczak
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego Street 49, 60-355 Poznan, Poland; (A.E.R.); (A.S.-T.); (P.E.); (A.D.)
| | - Piotr Eder
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego Street 49, 60-355 Poznan, Poland; (A.E.R.); (A.S.-T.); (P.E.); (A.D.)
| | - Ryszard Słomski
- Institute of Human Genetics, Polish Academy of Sciences Poznan, Strzeszynska Street 32, 60-479 Poznan, Poland; (M.S.-Z.); (R.S.)
| | - Agnieszka Dobrowolska
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego Street 49, 60-355 Poznan, Poland; (A.E.R.); (A.S.-T.); (P.E.); (A.D.)
| | - Iwona Krela-Kaźmierczak
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Przybyszewskiego Street 49, 60-355 Poznan, Poland; (A.E.R.); (A.S.-T.); (P.E.); (A.D.)
- Correspondence: (D.S.); (I.K.-K.); Tel.: +48-618691343 (D.S.); +48-601-256-715 (I.K.-K.); Fax: +48-8691-314 (I.K.-K.)
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27
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Lucendo AJ. Editorial: tissue findings fail to predict disease activity or prognosis in microscopic colitis: an opportunity to look at the molecular level. Aliment Pharmacol Ther 2021; 54:192-193. [PMID: 34170543 DOI: 10.1111/apt.16403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Alfredo J Lucendo
- Department of Gastroenterology, Hospital General de Tomelloso, Tomelloso, Spain.,Instituto de Investigación Sanitaria Princesa, Madrid, Spain.,Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
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28
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Rao J, Shao L, Lin M, Huang J, Fan L. LncRNA UCA1 Accelerates the Progression of Ulcerative Colitis via Mediating the miR-331-3p/BRD4 Axis. Int J Gen Med 2021; 14:2427-2435. [PMID: 34140798 PMCID: PMC8203302 DOI: 10.2147/ijgm.s304837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/06/2021] [Indexed: 12/30/2022] Open
Abstract
Background Ulcerative colitis (UC) has become one of the fastest-growing severe diseases worldwide with high morbidity. This research aimed to explore the function of lncRNA UCA1 in UC progression. Methods RT-qPCR analysis was used to examine the expression of UCA1 level in colonic mucosa tissues of UC patients. Then, fetal human cells (FHCs) were stimulated by LPS to induce inflammatory injury. CCK-8, flow cytometry and ELISA were adopted to determine the influence of UCA1 depletion on cell viability, apoptosis and pro-inflammatory factors levels in LPS-induced FHCs. The interaction between UCA1 and miR-331-3p or BRD4 was confirmed by luciferase reporter assay. The expressions of key factors involved in NF-κB pathway were assessed by Western blotting. Results LncRNA UCA1 level was elevated in colonic mucosa tissues of UC patients. LPS stimulation restrained cell viability and promoted the apoptosis and inflammatory factors levels, thus inducing FHCs inflammatory injury, while these effects were partially abolished by UCA1 knockdown. Moreover, it was found that UCA1 silence improved LPS-triggered cell injury via miR-331-3p. In addition, BRD4 was directly targeted by miR-331-3p, and BRD4 deficiency neutralized the effects of miR-331-3p repression on LPS-triggered injury in LPS-treated FHCs. Conclusion Our data determined that UCA1 knockdown attenuated UC development via targeting the miR-331-3p/BRD4/NF-κB pathway.
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Affiliation(s)
- Jun Rao
- Department of Gastroenterology, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, People's Republic of China
| | - Lihua Shao
- Department of Gastroenterology, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, People's Republic of China
| | - Min Lin
- Department of Gastroenterology, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, People's Republic of China
| | - Jin Huang
- Department of Gastroenterology, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, People's Republic of China
| | - Li Fan
- Department of Gastroenterology, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, People's Republic of China
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Zhou R, Qiu P, Wang H, Yang H, Yang X, Ye M, Wang F, Zhao Q. Identification of microRNA-16-5p and microRNA-21-5p in feces as potential noninvasive biomarkers for inflammatory bowel disease. Aging (Albany NY) 2021; 13:4634-4646. [PMID: 33535181 PMCID: PMC7906140 DOI: 10.18632/aging.202428] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic idiopathic gastrointestinal disease. Increasing evidence suggests that microRNAs (miRNAs) may participate in the pathophysiology of IBD. METHODS A miRCURY™ LNA Array and in situ hybridization were employed to screen for differentially expressed miRNAs (DEMs) in fecal specimens from 41 IBD patients (22 ulcerative colitis (UC), 19 Crohn's disease (CD)) and 23 healthy controls (HC). RT-qPCR was performed to confirm the findings. The DEMs target genes and corresponding biological functions were predicted by bioinformatics analysis. RESULTS Compared with HC, miR-16-5p in the feces was up-regulated both in UC and CD patients (p < 0.01), while miR-21-5p was up-regulated only in UC patients (p < 0.01). TargetScan 7.2, miRWalk, and miRDB were used to predict 216 public target genes of miR-16-5p and miR-21-5p, and six hub genes (PIK3R1, GRB2, SUZ12, NTRK2, Smurf2, and WWP1) were analyzed using the STRING database and Cytoscape. All the hub genes promote the occurrence and development of IBD-related colorectal cancer. CONCLUSIONS The elevated levels of miR-16-5p and miR-21-5p in feces of IBD patients have to guide significance for the noninvasive clinical diagnosis of IBD and have a warning effect on the occurrence of IBD-related colorectal cancer.
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Affiliation(s)
- Rui Zhou
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan 430071, China
| | - Peishan Qiu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan 430071, China
| | - Haizhou Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan 430071, China
| | - Huijie Yang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan 430071, China
| | - Xueying Yang
- Department of Medical Records, The Central Hospital of Enshi Autonomous Prefecture, Enshi 445000, China
| | - Mingliang Ye
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan 430071, China
| | - Fan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan 430071, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan 430071, China
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Suppression of lncRNA MALAT1 reduces pro-inflammatory cytokines production by regulating miR-150-5p/ZBTB4 axis through JAK/STAT signal pathway in systemic juvenile idiopathic arthritis. Cytokine 2020; 138:155397. [PMID: 33341002 DOI: 10.1016/j.cyto.2020.155397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022]
Abstract
Systemic juvenile idiopathic arthritis (sJIA) is a common chronic disease occurring in children. Increasing studies have demonstrated that long noncoding RNAs (lncRNAs) play important roles in the pathogenesis of diverse human diseases. This study aimed to explore the role of lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and its mechanism in sJIA. We found that the expression of MALAT1, the plasma level of pro-inflammatory cytokines (IL-6, IL-17, IL-1β, and TNF-α) as well as MMP-8 and MMP-9 production were significantly elevated in sJIA patients. Moreover, we observed that the production of these cytokines in peripheral blood mononuclear cells (PBMCs) from sJIA patients were reduced after MALAT1 knockdown. Furthermore, bioinformatics analysis predicted that MALAT1 might bind to miR-150-5p and ZBTB4 was a downstream target gene of miR-150-5p. Besides, rescue assays revealed that MALAT1 knockdown-mediated suppressive effects on cytokine production could be reversed by ZBTB4 overexpression. In addition, MALAT1 activated the JAK/STAT signaling by upregulating ZBTB4 expression. In summary, our findings demonstrated that MALAT1 promoted pro-inflammatory cytokine and MMP production by targeting the miR-150-5p/ZBTB4 axis through JAK/STAT signaling pathway in sJIA, suggesting that MALAT1 may have a potential diagnostic biomarker for the pathogenesis and therapy of sJIA.
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