1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Ali MA, Shaker OG, Gomaa Ali ES, Ezzat EM, Khalifa AA, Hassan EA, Habib MA, Ahmed HM, Dawood AF, Mohamed EA. Expression profile of serum LncRNAs MALAT-1 and CCAT-1 and their correlation with Mayo severity score in ulcerative colitis patients can diagnose and predict the prognosis of the disease. Noncoding RNA Res 2024; 9:318-329. [PMID: 38505308 PMCID: PMC10945117 DOI: 10.1016/j.ncrna.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 03/21/2024] Open
Abstract
Background Ulcerative colitis (UC) has emerged as an accelerated-incidence chronic condition. UC has been identified as a precancerous lesion for colorectal cancer. Up-to-date genomic research revealed the value of many noncoding RNAs (ncRNAs) in UC pathogenesis, diagnosis, and prognosis. Aim The present study was aimed at measuring both MALAT-1 and CCAT-1 in the sera of UC patients as diagnostic and prognostic biomarkers and correlating them with the Mayo score which is a novel predictive indicator of malignant transformation as well as with clinicopathological characteristics of the disease. Patients and methods Sixty-six UC patients and 80 healthy individuals participated in this study, the serum fold changes of MALAT-1 and CCAT-1 were measured by using quantitative real-time PCR (qRT-PCR). Results The current study findings include overexpressed lncRNAs MALAT-1 and CCAT-1 in the sera of ulcerative colitis patients [(median (IQR) = 2.290 (0.16-9.36), mean ± SD = 3.37 ± 3.904 for MALAT-1, and median (IQR) = 7.305 (0.57-16.96), mean ± SD = 6.81 ± 4.002 for CCAT-1 than controls, ROC curve analysis reported that these genes could predict UC. Both genes were positively correlated with each other which enforces their synergistic effects. Both genes are diagnostic for UC patients.We related studied genes to the severity of the disease. In addition to a significant positive correlation between each gene with ESR and Mayo score, we further classified the patients according to severity (according to Mayo score to remission, mild, moderate, and severe groups) with the following results; lower levels of MALAT-1 and CCAT-1 were significantly associated with mild disease and increased gradually with more severe forms of the disease (p < 0.05). Linear regression analysis with Mayo Score as a dependent variable revealed that only the predictive power of CCAT-1 and ESR are significant. Moreover, ROC curve analysis when compared to that of the Mayo score revealed that CCAT-1 reached 99 % accuracy. In summary, both genes are prognostic factors for UC patients. Conclusion MALAT-1 and CCAT-1 are diagnostic and prognostic serum biomarkers of ulcerative colitis.
Collapse
Affiliation(s)
- Marwa A. Ali
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
- Department of Biomedical Sciences, College of Medicine, King Faisal University, Alhasa, Saudi Arabia
| | - Olfat G. Shaker
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - El Shimaa Gomaa Ali
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Eman M. Ezzat
- Department of Internal Medicine, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Abeer A. Khalifa
- Department of Physiology, Faculty of Medicine, Zagazig University, Egypt
| | - Essam A. Hassan
- Department of Tropical Medicine, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Marwa A. Habib
- Department of Physiology, Faculty of Medicine, Zagazig University, Egypt
| | - Heba Mostafa Ahmed
- Department Clinical and Chemical Pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Asmaa F.A. Dawood
- Department of Biomedical Sciences, College of Medicine, King Faisal University, Alhasa, Saudi Arabia
- Department of Histology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Esam Ali Mohamed
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| |
Collapse
|
3
|
Fenton CG, Ray MK, Paulssen RH. Challenges in Defining a Reference Set of Differentially Expressed lncRNAs in Ulcerative Colitis by Meta-Analysis. Curr Issues Mol Biol 2024; 46:3164-3174. [PMID: 38666928 PMCID: PMC11049510 DOI: 10.3390/cimb46040198] [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: 03/05/2024] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
The study aimed to identify common differentially expressed lncRNAs from manually curated ulcerative colitis (UC) gene expression omnibus (GEO) datasets. Nine UC transcriptomic datasets of clearly annotated human colonic biopsies were included in the study. The datasets were manually curated to select active UC samples and controls. R packages geneknitR, gprofiler, clusterProfiler were used for gene symbol annotation. The R EdgeR package was used to analyze differential expression. This resulted in a total of nineteen lncRNAs that were differentially expressed in at least three datasets of the nine GEO datasets. Several of the differentially expressed lncRNAs found in UC were associated with promoting colorectal cancer (CRC) through regulating gene expression, epithelial to mesenchymal transition (EMT), cell cycle progression, and by promoting tumor proliferation, invasion, and migration. The expression of several lncRNAs varied between disease states and tissue locations within the same disease state. The identified differentially expressed lncRNAs may function as general markers for active UC independent of biopsy location, age, gender, or treatment, thereby representing a comparative resource for future comparisons using available GEO UC datasets.
Collapse
Affiliation(s)
- Christopher G. Fenton
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway; (C.G.F.); (M.K.R.)
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Mithlesh Kumar Ray
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway; (C.G.F.); (M.K.R.)
| | - Ruth H. Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway; (C.G.F.); (M.K.R.)
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Li G, Zhao C, Xu J, Huang Y, Qiao Y, Li F, Peng G, Zheng S, Zhu L, Yang L, Wang Z, Wu H. Moxibustion alleviates intestinal inflammation in ulcerative colitis rats by modulating long non-coding RNA LOC108352929 and inhibiting Phf11 expression. Heliyon 2024; 10:e26898. [PMID: 38439851 PMCID: PMC10909710 DOI: 10.1016/j.heliyon.2024.e26898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/09/2024] [Accepted: 02/21/2024] [Indexed: 03/06/2024] Open
Abstract
Long noncoding RNA (lncRNAs) are involved in the pathogenesis of ulcerative colitis (UC). Moxibustion, a traditional Chinese medicine, can improve symptoms in patients with UC and reduce intestinal inflammation in rats with UC. However, it remains unclear whether the ameliorative effect of moxibustion on intestinal mucosal inflammation in UC is related to lncRNAs. Thirty-two rats were randomly assigned to four groups: normal control, UC, moxibustion (MOX), and sulfasalazine (SASP). The UC rat model was induced by administering 4% dextran sulfate sodium (DSS) in drinking water. Rats in the moxibustion group underwent bilateral Tianshu (ST25) moxibustion using the herbs-partition moxibustion method. Rats in the sulfasalazine group received SASP solution via gavage twice daily for seven consecutive days. Our results revealed that, compared with the UC group [2.00 (1.00, 2.50)], the DAI score [0.25 (0.00, 0.50)] was significantly lower in the MOX group (P < 0.05). Compared with the UC group [13.00 (11.25, 14.00)], the histopathological score [5.50 (4.00, 7.75)] was significantly lower in the MOX group (P < 0.05). In addition, the CMDI and macroscopic scores were decreased in the MOX group (P < 0.05). Moxibustion significantly decreased the protein expression of inflammatory factors TNF-α, IFN-γ, and IL-1β in the colonic tissues of UC rats (P <0.05), thereby suppressing the inflammatory response. Moreover, moxibustion exerted a regulatory influence on colon lncRNA and mRNA expression profiles, upregulating LOC108352929 and downregulating Phf11 in rats with UC (P <0.05). Moxibustion also led to a reduction in the expression and colocalization of Phf11 and NF-κB in the colons of UC rats. Moreover, knockdown of LOC108352929 in rat enteric glial cells demonstrated a significant upregulation of TNF-α mRNA expression (P <0.05). In summary, these data illustrate that moxibustion effectively ameliorates DSS-induced colonic injury and inflammation while exerting regulatory control over the lncRNA-mRNA co-expression network in UC rats. Collectively, the in vivo and in vitro studies suggested that LOC108352929-Phf11 may serve as a potential biological marker for moxibustion in the treatment of UC.
Collapse
Affiliation(s)
- Guona Li
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- School of Acupuncture-Moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Chen Zhao
- School of Acupuncture-Moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Jing Xu
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Yan Huang
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Yu Qiao
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Feng Li
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Guangbin Peng
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Shiyu Zheng
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Lu Zhu
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Ling Yang
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Zhaoqin Wang
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Huangan Wu
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| |
Collapse
|
6
|
Kazmi I, Altamimi ASA, Afzal M, Majami AA, Abbasi FA, Almalki WH, Alzera SI, Kukreti N, Fuloria NK, Fuloria S, Sekar M, Abida. Non-coding RNAs: Emerging biomarkers and therapeutic targets in ulcerative colitis. Pathol Res Pract 2024; 253:155037. [PMID: 38160482 DOI: 10.1016/j.prp.2023.155037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Ulcerative colitis (UC) is a persistent inflammatory condition affecting the colon's mucosal lining, leading to chronic bowel inflammation. Despite extensive research, the precise molecular mechanisms underlying UC pathogenesis remain elusive. NcRNAs form a category of functional RNA molecules devoid of protein-coding capacity. They have recently surfaced as pivotal modulators of gene expression and integral participants in various pathological processes, particularly those related to inflammatory disorders. The diverse classes of ncRNAs, encompassing miRNAs, circRNAs, and lncRNAs, have been implicated in UC. It highlights their involvement in key UC-related processes, such as immune cell activation, epithelial barrier integrity, and the production of pro-inflammatory mediators. ncRNAs have been identified as potential biomarkers for UC diagnosis and monitoring disease progression, offering promising avenues for personalized medicine. This approach may pave the way for novel, more specific treatments with reduced side effects, addressing the current limitations of conventional therapies. A comprehensive understanding of the interplay between ncRNAs and UC will advance our knowledge of the disease, potentially leading to more effective and personalized treatments for patients suffering from this debilitating condition. This review explores the pivotal role of ncRNAs in the context of UC, shedding light on their possible targets for diagnosis, prognosis, and therapeutic interventions.
Collapse
Affiliation(s)
- Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | | | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Abdullah A Majami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fahad Al Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sami I Alzera
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Al-Jouf, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | | | - Shivkanya Fuloria
- Faculty of Pharmacy, AIMST University, Bedong 08100, Kedah, Malaysia
| | - Mahendran Sekar
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia
| | - Abida
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| |
Collapse
|
7
|
Fenton CG, Ray MK, Meng W, Paulssen RH. Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis. Int J Mol Sci 2023; 24:10500. [PMID: 37445676 DOI: 10.3390/ijms241310500] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/26/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play a role in the pathogenesis of ulcerative colitis (UC). Although epigenetic processes such as DNA methylation and lncRNA expression are well studied in UC, the importance of the interplay between the two processes has not yet been fully explored. It is, therefore, believed that interactions between environmental factors and epigenetics contribute to disease development. Mucosal biopsies from 11 treatment-naïve UC patients and 13 normal controls were used in this study. From each individual sample, both whole-genome bisulfite sequencing data (WGBS) and lncRNA expression data were analyzed. Correlation analysis between lncRNA expression and upstream differentially methylated regions (DMRs) was used to identify lncRNAs that might be regulated by DMRs. Furthermore, proximal protein-coding genes associated with DMR-regulated lncRNAs were identified by correlating their expression. The study identified UC-associated lncRNAs such as MIR4435-2HG, ZFAS1, IL6-AS1, and Pvt1, which may be regulated by DMRs. Several genes that are involved in inflammatory immune responses were found downstream of DMR-regulated lncRNAs, including SERPINB1, CCL18, and SLC15A4. The interplay between lncRNA expression regulated by DNA methylation in UC might improve our understanding of UC pathogenesis.
Collapse
Affiliation(s)
- Christopher G Fenton
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Mithlesh Kumar Ray
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Wei Meng
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|