1
|
Nasimi Shad A, Akhlaghipour I, Alshakarchi HI, Saburi E, Moghbeli M. Role of microRNA-363 during tumor progression and invasion. J Physiol Biochem 2024:10.1007/s13105-024-01022-1. [PMID: 38691273 DOI: 10.1007/s13105-024-01022-1] [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: 12/21/2023] [Accepted: 04/05/2024] [Indexed: 05/03/2024]
Abstract
Recent progresses in diagnostic and therapeutic methods have significantly improved prognosis in cancer patients. However, cancer is still considered as one of the main causes of human deaths in the world. Late diagnosis in advanced tumor stages can reduce the effectiveness of treatment methods and increase mortality rate of cancer patients. Therefore, investigating the molecular mechanisms of tumor progression can help to introduce the early diagnostic markers in these patients. MicroRNA (miRNAs) has an important role in regulation of pathophysiological cellular processes. Due to their high stability in body fluids, they are always used as the non-invasive markers in cancer patients. Since, miR-363 deregulation has been reported in a wide range of cancers, we discussed the role of miR-363 during tumor progression and metastasis. It has been reported that miR-363 has mainly a tumor suppressor function through the regulation of transcription factors, apoptosis, cell cycle, and structural proteins. MiR-363 also affected the tumor progression via regulation of various signaling pathways such as WNT, MAPK, TGF-β, NOTCH, and PI3K/AKT. Therefore, miR-363 can be introduced as a probable therapeutic target as well as a non-invasive diagnostic marker in cancer patients.
Collapse
Affiliation(s)
- Arya Nasimi Shad
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Iman Akhlaghipour
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hawraa Ibrahim Alshakarchi
- Al-Zahra Center for Medical and Pharmaceutical Research Sciences (ZCMRS), Al-Zahraa University for Women, Karbala, Iraq
| | - Ehsan Saburi
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
2
|
Sartorius K, Sartorius B, Winkler C, Chuturgoon A, Shen TW, Zhao Y, An P. Serum microRNA Profiles and Pathways in Hepatitis B-Associated Hepatocellular Carcinoma: A South African Study. Int J Mol Sci 2024; 25:975. [PMID: 38256049 PMCID: PMC10815595 DOI: 10.3390/ijms25020975] [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: 11/07/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
The incidence and mortality of hepatocellular carcinoma (HCC) in Sub-Saharan Africa is projected to increase sharply by 2040 against a backdrop of limited diagnostic and therapeutic options. Two large South African-based case control studies have developed a serum-based miRNome for Hepatitis B-associated hepatocellular carcinoma (HBV-HCC), as well as identifying their gene targets and pathways. Using a combination of RNA sequencing, differential analysis and filters including a unique molecular index count (UMI) ≥ 10 and log fold change (LFC) range > 2: <-0.5 (p < 0.05), 91 dysregulated miRNAs were characterized including 30 that were upregulated and 61 were downregulated. KEGG analysis, a literature review and other bioinformatic tools identified the targeted genes and HBV-HCC pathways of the top 10 most dysregulated miRNAs. The results, which are based on differentiating miRNA expression of cases versus controls, also develop a serum-based miRNA diagnostic panel that indicates 95.9% sensitivity, 91.0% specificity and a Youden Index of 0.869. In conclusion, the results develop a comprehensive African HBV-HCC miRNome that potentially can contribute to RNA-based diagnostic and therapeutic options.
Collapse
Affiliation(s)
- Kurt Sartorius
- Faculty of Commerce, Law and Management, University of the Witwatersrand, Johannesburg 2001, South Africa
- School of Laboratory Medicine and Molecular Sciences, University of Kwazulu-Natal, Durban 4041, South Africa;
- Africa Hepatopancreatobiliary Cancer Consortium (AHPBCC), Mayo Clinic, Jacksonville, FL 32224, USA
| | - Benn Sartorius
- School of Public Health, University of Queensland, Brisbane, QLD 4102, Australia
| | - Cheryl Winkler
- Centre for Cancer Research, Basic Research Laboratory, National Cancer Institute, Frederick Natifol Laboratory for Cancer Research, National Institute of Health, Frederick, MD 21701, USA
| | - Anil Chuturgoon
- School of Laboratory Medicine and Molecular Sciences, University of Kwazulu-Natal, Durban 4041, South Africa;
| | - Tsai-Wei Shen
- CCR-SF Bioinformatics Group, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Yongmei Zhao
- CCR-SF Bioinformatics Group, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Ping An
- Centre for Cancer Research, Basic Research Laboratory, National Cancer Institute, Frederick Natifol Laboratory for Cancer Research, National Institute of Health, Frederick, MD 21701, USA
| |
Collapse
|
3
|
Deng X, Wang Y, Guo H, Wang Q, Rao S, Wu H. Pan-Cancer Analysis and Experimental Validation of SOX4 as a Potential Diagnosis, Prognosis, and Immunotherapy Biomarker. Cancers (Basel) 2023; 15:5235. [PMID: 37958409 PMCID: PMC10649301 DOI: 10.3390/cancers15215235] [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: 09/02/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/15/2023] Open
Abstract
INTRODUCTION SOX4 plays an important role in tumorigenesis and cancer progression. The role of SOX4 in pan-cancer and its underlying molecular mechanism in liver hepatocellular carcinoma (LIHC) are not fully understood. In this study, a comprehensive analysis and experimental validation were performed to explore the function of SOX4 across tumor types. METHODS Raw data in regard to SOX4 expression in malignant tumors were downloaded from the TCGA and GTEx databases. The expression levels, prognostic values, genetic mutation, and DNA promoter methylation of SOX4 across tumor types were explored via systematic bioinformatics analysis. The ceRNA regulatory network, immune characteristics, and prognostic models were analyzed in LIHC. Finally, we conducted in vitro experiments including Western blotting, cell proliferative assay, trypan blue staining, and fluorescence microscopy to further explore the function of SOX4 in LIHC. RESULTS SOX4 expression was significantly upregulated in 24 tumor types. SOX4 expression level was strongly associated with unfavorable prognoses, genetic mutations, and DNA methylation levels across different tumor types. Especially in LIHC, LINC00152/hsa-miR-139-3p/SOX4 was identified as a crucial ceRNA network. Moreover, this study also provides insight into the roles of SOX4 expression in immune cell infiltration, macrophage polarization, immune subtype, molecular subtype, and immunomodulators, as well as the tumor immune microenvironment (TIME)-related prognosis, in LIHC. The study established six favorable prognostic models to predict LIHC prognosis based on the SOX4-associated genes. Finally, lenvatinib treatment can increase the expression of SOX4 in hepatocellular carcinoma cells and lead to drug resistance. Silencing SOX4 can effectively eliminate the drug resistance caused by lenvatinib treatment and inhibit the proliferation of cancer cells. CONCLUSIONS This study highlights that SOX4 may serve as a promising therapeutic target for tumor treatment.
Collapse
Affiliation(s)
- Xinna Deng
- Departments of Oncology, Hebei General Hospital, Shijiazhuang 050057, China; (X.D.); (H.G.); (Q.W.); (S.R.)
| | - Yashu Wang
- Department of Pathology, Hebei Medical University, Shijiazhuang 050011, China;
| | - Hao Guo
- Departments of Oncology, Hebei General Hospital, Shijiazhuang 050057, China; (X.D.); (H.G.); (Q.W.); (S.R.)
| | - Qian Wang
- Departments of Oncology, Hebei General Hospital, Shijiazhuang 050057, China; (X.D.); (H.G.); (Q.W.); (S.R.)
| | - Shuting Rao
- Departments of Oncology, Hebei General Hospital, Shijiazhuang 050057, China; (X.D.); (H.G.); (Q.W.); (S.R.)
- Department of Internal Medicine, Hebei Medical University, Shijiazhuang 050011, China
| | - Haijiang Wu
- Department of Pathology, Hebei Medical University, Shijiazhuang 050011, China;
| |
Collapse
|
4
|
Wang Y, Bai SK, Zhang T, Liao CG. MicroRNA-363-3p inhibits colorectal cancer progression by targeting interferon-induced transmembrane protein 1. World J Gastrointest Oncol 2023; 15:1556-1566. [PMID: 37746648 PMCID: PMC10514722 DOI: 10.4251/wjgo.v15.i9.1556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 08/18/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND The molecular mechanisms of colorectal cancer development and progression are far from being elucidated. AIM To investigate the role of microRNA-363-3p (miR-363-3p) in the progression of colorectal cancer. METHODS Real-time polymerase chain reaction was performed to detect miRNA expression in human colorectal cancer tissues and paired normal colorectal tissues. PITA 6 was utilized to predict the targets of miR-363-3p. Dual-luciferase reporter system was used to validate the target of miR-363-3p. Plate colony formation assay and wound-healing assay were performed to evaluate cancer cells' clonogenic survival ability and migration ability, respectively. Cell proliferation was examined by cell counting kit-8 assay. Immunohistochemical staining was used to determine the expression level of interferon-induced transmembrane protein 1 (IFITM1) in colorectal cancer tissues and adjacent tissues. The TCGA and GTEx databases were used to compare the expression levels of IFITM1 mRNA in colorectal cancer tissues and normal colorectal tissues and analyze the correlation between the expression levels of IFITM1 mRNA and overall survival and disease-free survival of patients. A colorectal cancer cell line with a deficiency of IFITM1 was constructed, and the regulation effect of IFITM1 on the clonogenic growth of colorectal cancer cells was clarified. RESULTS MiR-363-3p was decreased in colorectal cancer tissues compared to normal colorectal tissues. IFITM1 was characterized as a direct target of miR-363-3p. Overexpression of miR-363-3p led to decreased clonogenic survival, proliferation, and migration of colorectal cancer cells, which could be reversed by forced IFITM1 expression. CONCLUSION MiR-363-3p can constrain clonogenic survival, proliferation, and migration of colorectal cancer cells via targeting IFITM1.
Collapse
Affiliation(s)
- Yun Wang
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an 710038, Shaanxi Province, China
| | - Shao-Kai Bai
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an 710038, Shaanxi Province, China
| | - Tao Zhang
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an 710038, Shaanxi Province, China
| | - Cheng-Gong Liao
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi’an 710038, Shaanxi Province, China
| |
Collapse
|
5
|
Ge Y, Tang S, Xia T, Shi C. Research progress on the role of RNA N6-methyladenosine methylation in HCV infection. Virology 2023; 582:35-42. [PMID: 36996690 DOI: 10.1016/j.virol.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023]
Abstract
Hepatitis C virus (HCV) is a positive-stranded RNA virus causing chronic liver diseases. The chemical modification of RNA is a research hotspot in related fields in recent years, including the methylation and acetylation of adenine, guanine, cytosine and other bases, among which methylation is the most important modification form. m6A (N6-methyladenosine), as the most abundant RNA modification form, plays an important role in HCV virus infection by modifying viral RNA and cell transcripts. This review aims to summarize the current knowledge on the roles of m6A modification in HCV infection, and discuss the research prospect.
Collapse
|
6
|
Zhu L, Yang X, Yao Z, Wang Z, Lai Y, Xu S, Liu K, Zhao B. Bioinformatic Analysis of lncRNA Mediated CeRNA Network in Intestinal Ischemia/Reperfusion Injury. J Surg Res 2023; 284:280-289. [PMID: 36621258 DOI: 10.1016/j.jss.2022.11.063] [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: 07/26/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Recently, accumulating studies have reported the roles of competitive endogenous RNA (ceRNA) networks in ischemia/reperfusion (I/R) injury in several organs, including the liver, kidney, heart, brain, and intestine. However, the functions and mechanisms of long noncoding RNAs (lncRNAs)-which serve as ceRNA networks in intestinal I/R injury-remain elusive. METHODS RNA expression data were retrieved from the National Center for Biotechnology Information-Gene Expression Omnibus database. Differentially expressed microRNAs (miRNAs) (miDEGs) were explored between the sham and intestinal I/R injury samples. Next, targeted lncRNAs and messenger RNAs in the database were matched based on miDEGs. Hub ceRNA networks were constructed and visualized via Cytoscape. Intersection analysis was performed to screen mDEGs between two datasets. Finally, the vital nodes of the ceRNA networks were validated by quantitative PCR. RESULTS A total of 189 miDEGs were identified. Forty miRNAs were found to be associated with 240 predicted target genes from miRWalk 3.0. The ceRNA network was constructed with 10 miRNAs, including the 1700020114Rik/mmu-miR-7a-5p/Klf4 axis. Furthermore, the expression of lncRNA 1700020114Rik (P < 0.05) and messenger RNA Klf4 (P < 0.01) was markedly decreased in mouse models of intestinal I/R injury, whereas the expression level of mmu-miR-7a-5p was significantly increased (P < 0.05). CONCLUSIONS The results provide novel insights into the molecular mechanism of ceRNA networks in intestinal I/R injury and highlight the potential of the 170002700020114Rik/mmu-miR-7a-5p/Klf4 axis in the prevention and treatment of intestinal I/R injury.
Collapse
Affiliation(s)
- Lin Zhu
- Department of Anesthesiology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China; Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiao Yang
- Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhiwen Yao
- Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ziyi Wang
- Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yupei Lai
- Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Shiting Xu
- Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Kexuan Liu
- Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Bingcheng Zhao
- Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| |
Collapse
|
7
|
Lin J, Lin W, Bai Y, Liao Y, Lin Q, Chen L, Wu Y. Identification of exosomal hsa-miR-483-5p as a potential biomarker for hepatocellular carcinoma via microRNA expression profiling of tumor-derived exosomes. Exp Cell Res 2022; 417:113232. [PMID: 35659970 DOI: 10.1016/j.yexcr.2022.113232] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 11/04/2022]
Abstract
To date, most studies of exosomes related to hepatocellular carcinoma (HCC) have used commercial cancer cell lines or patient plasma as source material. In this study, we isolated exosomes directly from HCC tissues to investigate the potential of exosomal contents as biomarkers for HCC. Exosomes were identified and verified using transmission electron microscopy, nano-flow cytometry analysis, and western blotting. Tissue-derived exosomal miRNA expression was profiled by high-throughput sequencing, and differential expression of miRNAs was validated by quantitative real-time polymerase chain reaction analysis. The diagnostic performance of differentially expressed exosomal miRNAs for HCC was evaluated by receiver operating characteristic curve analysis. Target genes of these miRNAs were verified using luciferase reporter assays, and their functions were studied through in vitro and rescue assays. In total, 225 differentially expressed exosomal miRNAs were identified in HCC samples compared with adjacent liver tissues, and some were associated with HCC tumorigenesis and progression. Comparison of the expression profiles of tissue-derived and plasma-derived exosomal miRNAs identified hsa-miR-483-5p as the only differentially expressed miRNA detected in both HCC tissue and plasma, and this was in a validation group of HCC patients. Analysis of the diagnostic performance of plasma exosomal hsa-miR-483-5p or plasma hsa-miR-483-5p found that both could differentiate HCC and non-HCC cases. In vitro ectopic miR-483-5p expression promoted HCC cell proliferation. CDK15 was confirmed to bind with miR-483-5p directly, and thus, miR-483-5p may function by downregulating CDK15. Hsa-miR-483-5p represents a potential specific and sensitive biomarker for HCC diagnosis.
Collapse
Affiliation(s)
- Jie Lin
- Department of Pathology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, China
| | - Wansong Lin
- Laboratory of Immuno-Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, 350014, Fujian, China.
| | - Yannan Bai
- Department of Hepatobiliopancreatic Surgery, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, China
| | - Yanling Liao
- Department of Anesthesiology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, China
| | - Qiaoyan Lin
- Department of Blood Transfusion, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, 350014, Fujian, China
| | - Lingfeng Chen
- Department of Pathology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, China
| | - Yijuan Wu
- Department of Pathology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, China
| |
Collapse
|
8
|
Wang X, Zhang H, Lu X, Li S, Kong X, Liu L, Li L, Xu S, Wang T, Wang J, Wang L. LncRNA OIP5-AS1 modulates the proliferation and apoptosis of Jurkat cells by sponging miR-181c-5p to regulate IL-7 expression in myasthenia gravis. PeerJ 2022; 10:e13454. [PMID: 35602889 PMCID: PMC9121865 DOI: 10.7717/peerj.13454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/27/2022] [Indexed: 01/14/2023] Open
Abstract
Background Myasthenia gravis (MG) is an antibody-mediated autoimmune disease. In recent years, accumulating evidence has indicated that long non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs), contributing to the progression of various autoimmune diseases. Nevertheless, the regulatory roles of ceRNAs in MG pathogenesis remain unclear. In this study, we aimed to elucidate the role of lncRNA OIP5-AS1 as a ceRNA associated with MG progression. Methods Real-time PCR was used to detect OIP5-AS1 levels in peripheral blood mononuclear cells (PBMCs) from patients with MG. Luciferase reporter assays were performed to validate the relationship between OIP5-AS1 and miR-181c-5p. CCK-8 and flow cytometry were performed to test the proliferation and apoptotic abilities of OIP5-AS1 in Jurkat cells. Furthermore, real-time PCR and Western blot assays were performed to explore the interactions between OIP5-AS1, miR-181c-5p, and IL-7. Results The expression of OIP5-AS1 was up-regulated in patients with MG. Luciferase reporter assay indicated that OIP5-AS1 targeted the miR-181c-5p. Functional assays showed that OIP5-AS1 suppressed Jurkat cell apoptosis and promoted cell proliferation by sponging miR-181c-5p. Mechanistically, knockdown of OIP5-AS1 inhibited IL-7 expression at both the mRNA and protein levels in Jurkat cells, whereas the miR-181c-5p inhibitor blocked the reduction of IL-7 expression induced by OIP5-AS1 suppression. Conclusions We confirmed that OIP5-AS1 serves as an endogenous sponge for miR-181c-5p to regulate the expression of IL-7. Our findings provide novel insights into MG processes and suggests potential therapeutic targets for patients with MG.
Collapse
Affiliation(s)
- Xu Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Shuang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Li Liu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Lifang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Si Xu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Tianfeng Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| |
Collapse
|
9
|
Wang Y, Zhou G, Guan T, Wang Y, Xuan C, Ding T, Gao J. A network-based matrix factorization framework for ceRNA co-modules recognition of cancer genomic data. Brief Bioinform 2022; 23:6581436. [PMID: 35514181 DOI: 10.1093/bib/bbac154] [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: 12/14/2021] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
With the development of high-throughput technologies, the accumulation of large amounts of multidimensional genomic data provides an excellent opportunity to study the multilevel biological regulatory relationships in cancer. Based on the hypothesis of competitive endogenous ribonucleic acid (RNA) (ceRNA) network, lncRNAs can eliminate the inhibition of microRNAs (miRNAs) on their target genes by binding to intracellular miRNA sites so as to improve the expression level of these target genes. However, previous studies on cancer expression mechanism are mostly based on individual or two-dimensional data, and lack of integration and analysis of various RNA-seq data, making it difficult to verify the complex biological relationships involved. To explore RNA expression patterns and potential molecular mechanisms of cancer, a network-regularized sparse orthogonal-regularized joint non-negative matrix factorization (NSOJNMF) algorithm is proposed, which combines the interaction relations among RNA-seq data in the way of network regularization and effectively prevents multicollinearity through sparse constraints and orthogonal regularization constraints to generate good modular sparse solutions. NSOJNMF algorithm is performed on the datasets of liver cancer and colon cancer, then ceRNA co-modules of them are recognized. The enrichment analysis of these modules shows that >90% of them are closely related to the occurrence and development of cancer. In addition, the ceRNA networks constructed by the ceRNA co-modules not only accurately mine the known correlations of the three RNA molecules but also further discover their potential biological associations, which may contribute to the exploration of the competitive relationships among multiple RNAs and the molecular mechanisms affecting tumor development.
Collapse
Affiliation(s)
- Yujie Wang
- School of Science, Jiangnan University, Wuxi 214122, China
| | - Gang Zhou
- School of Science, Jiangnan University, Wuxi 214122, China
| | - Tianhao Guan
- School of Science, Jiangnan University, Wuxi 214122, China
| | - Yan Wang
- School of Science, Jiangnan University, Wuxi 214122, China
| | - Chenxu Xuan
- School of Science, Jiangnan University, Wuxi 214122, China
| | - Tao Ding
- School of Mathematics Statistics and Physics, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jie Gao
- School of Science, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
10
|
Wang LJ, Qiu BQ, Yuan MM, Zou HX, Gong CW, Huang H, Lai SQ, Liu JC. Identification and Validation of Dilated Cardiomyopathy-Related Genes via Bioinformatics Analysis. Int J Gen Med 2022; 15:3663-3676. [PMID: 35411175 PMCID: PMC8994656 DOI: 10.2147/ijgm.s350954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/24/2022] [Indexed: 12/03/2022] Open
Abstract
Purpose Dilated cardiomyopathy (DCM) is a type of cardiomyopathy that can easily cause heart failure and has a high mortality rate. Therefore, there is an urgent need to study the underlying mechanism of action of dilated cardiomyopathy. In the present study, we aimed to explore potential miRNA–mRNA pairs and drugs related to DCM. Methods The Microarray data were collected from the Gene Expression Omnibus (GEO) database. Bioinformatics analysis differentially expressed miRNAs and mRNAs in each microarray were obtained. The target genes of miRNAs were obtained from the miRWalk 2.0 database, and the intersection of these two gene sets (miRNA target genes and differentially expressed mRNAs in the microarray) was obtained. Pathway and Gene Ontology (GO) enrichment analyses were performed in the KOBAS database. Cytoscape software was used to construct the miRNA–mRNA network, and the final hub genes were obtained. Furthermore, we predicted several candidate drugs related to hub genes using DSigDB database. To confirm the abnormal expression of hub genes, qRT-PCR was performed. Results In total, eight differentially expressed miRNAs and 92 differentially expressed mRNAs were identified. In addition, 47 differentially expressed miRNA target genes were identified. According to the analysis results of the miRNA-mRNA network, we identified hsa-miR-551b-3p, hsa-miR-770-5p, hsa-miR-363-3p, PIK3R1, DDIT4, and CXCR4 as hub genes in DCM. Several candidate drugs, which are related to the hug genes, were identified. Conclusion In conclusion, in our study, we identified several hub genes that may be involved in the pathogenesis of DCM. Several drugs related to these hub genes may be used as clinical therapeutic candidates.
Collapse
Affiliation(s)
- Li-Jun Wang
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Bai-Quan Qiu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Ming-Ming Yuan
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Hua-Xi Zou
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Cheng-Wu Gong
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Huang Huang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Song-Qing Lai
- Institute of Cardiovascular Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
- Song-Qing Lai, Institute of Cardiovascular Diseases, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China, Tel +86 13699562160, Email
| | - Ji-Chun Liu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
- Correspondence: Ji-Chun Liu, Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China, Tel +86 13907913502, Email
| |
Collapse
|
11
|
Zheng C, Chu M, Chen Q, Chen C, Wang ZW, Chen X. The role of lncRNA OIP5-AS1 in cancer development and progression. Apoptosis 2022; 27:311-321. [PMID: 35316453 DOI: 10.1007/s10495-022-01722-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2022] [Indexed: 12/23/2022]
Abstract
OIP5-AS1, a conserved lncRNA, has been reported to be involved in several biological and pathological processes, including oncogenesis. OIP5-AS1 exerts its oncogenic or antitumor functions via regulation of different miRNAs in various cancer types. In this review, we describe the dysregulation of OIP5-AS1 expression in a variety of human cancers. Moreover, we discuss the multiple functions of OIP5-AS1 in cancer, including in proliferation, apoptosis, autophagy, ferroptosis, cell cycle, migration, metastasis, invasion, epithelial to mesenchymal transition, angiogenesis, cancer stem cells and drug resistance. Furthermore, we provide a future perspective for OIP5-AS1 research. We conclude that targeting OIP5-AS1 might be a promising cancer therapy approach.
Collapse
Affiliation(s)
- Cheng Zheng
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Man Chu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Qiuli Chen
- Department of Research and Development, Zhengjiang Zhongwei Medical Research Center, Hangzhou, 310018, Zhejiang, China
- The School of Public Health, The University of Queensland, Brisbane, Australia
| | - Cheng Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Zhi-Wei Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.
| | - Xiao Chen
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
- Department of Cardiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.
| |
Collapse
|
12
|
Advance of SOX Transcription Factors in Hepatocellular Carcinoma: From Role, Tumor Immune Relevance to Targeted Therapy. Cancers (Basel) 2022; 14:cancers14051165. [PMID: 35267473 PMCID: PMC8909699 DOI: 10.3390/cancers14051165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hepatocellular carcinoma (HCC) is one of the deadliest human health burdens worldwide. However, the molecular mechanism of HCC development is still not fully understood. Sex determining region Y-related high-mobility group box (SOX) transcription factors not only play pivotal roles in cell fate decisions during development but also participate in the initiation and progression of cancer. Given the significance of SOX factors in cancer and their ‘undruggable’ properties, we summarize the role and molecular mechanism of SOX family members in HCC and the regulatory effect of SOX factors in the tumor immune microenvironment (TIME) of various cancers. For the first time, we analyze the association between the levels of SOX factors and that of immune components in HCC, providing clues to the pivotal role of SOX factors in the TIME of HCC. We also discuss the opportunities and challenges of targeting SOX factors for cancer. Abstract Sex determining region Y (SRY)-related high-mobility group (HMG) box (SOX) factors belong to an evolutionarily conserved family of transcription factors that play essential roles in cell fate decisions involving numerous developmental processes. In recent years, the significance of SOX factors in the initiation and progression of cancers has been gradually revealed, and they act as potential therapeutic targets for cancer. However, the research involving SOX factors is still preliminary, given that their effects in some leading-edge fields such as tumor immune microenvironment (TIME) remain obscure. More importantly, as a class of ‘undruggable’ molecules, targeting SOX factors still face considerable challenges in achieving clinical translation. Here, we mainly focus on the roles and regulatory mechanisms of SOX family members in hepatocellular carcinoma (HCC), one of the fatal human health burdens worldwide. We then detail the role of SOX members in remodeling TIME and analyze the association between SOX members and immune components in HCC for the first time. In addition, we emphasize several alternative strategies involved in the translational advances of SOX members in cancer. Finally, we discuss the alternative strategies of targeting SOX family for cancer and propose the opportunities and challenges they face based on the current accumulated studies and our understanding.
Collapse
|
13
|
Wooten S, Smith KN. Long non-coding RNA OIP5-AS1 (Cyrano): A context-specific regulator of normal and disease processes. Clin Transl Med 2022; 12:e706. [PMID: 35040588 PMCID: PMC8764876 DOI: 10.1002/ctm2.706] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/21/2021] [Accepted: 12/29/2021] [Indexed: 12/17/2022] Open
Abstract
Long non-coding (lnc) RNAs have been implicated in a plethora of normal biological functions, and have also emerged as key molecules in various disease processes. OIP5-AS1, also commonly known by the alias Cyrano, is a lncRNA that displays broad expression across multiple tissues, with significant enrichment in particular contexts including within the nervous system and skeletal muscle. Thus far, this multifaceted lncRNA has been found to have regulatory functions in normal cellular processes including cell proliferation and survival, as well as in the development and progression of a myriad disease states. These widespread effects on normal and disease states have been found to be mediated through context-specific intermolecular interactions with dozens of miRNAs and proteins identified to date. This review explores recent studies to highlight OIP5-AS1's contextual yet pleiotropic roles in normal homeostatic functions as well as disease oetiology and progression, which may influence its utility in the generation of future theranostics.
Collapse
Affiliation(s)
- Serena Wooten
- Department of GeneticsUniversity of North Carolina at Chapel HillNorth CarolinaUSA
| | - Keriayn N. Smith
- Department of GeneticsUniversity of North Carolina at Chapel HillNorth CarolinaUSA
| |
Collapse
|
14
|
Ghafouri-Fard S, Dashti S, Farsi M, Hussen BM, Taheri M. A review on the role of oncogenic lncRNA OIP5-AS1 in human malignancies. Biomed Pharmacother 2021; 137:111366. [PMID: 33601149 DOI: 10.1016/j.biopha.2021.111366] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
OIP5-AS1 is a long non-coding transcript with high expression in nervous system, but crucial functions in the neoplastic transformation. This lncRNA partake in the regulation of cell cycle transition at different points. Moreover, it acts a competing endogenous RNA for tens of microRNAs among them are miR-338-3p, miR-204-5p, miR-641, miR-422a, miR-367-3p, miR-153-3p, miR-186, miR-369-3p, miR-137, miR-342-3p, miR‑429, miR-3163, miR-363-3p, miR-186a-5p, hsa-miR-26a-3p, miR‑300, miR-217, miR-378a-3p and miR-448. OIP5-AS1 influence the carcinogenesis via different routes among them is modulation of epithelial-mesenchymal transition. Expression of OIP5-AS1 has been elevated in nearly all kinds of neoplastic tissues except for multiple myeloma. Moreover, in bladder, gastric cancer and lung cancers, assessment of its expression in clinical samples has led to conflicting results. In the current paper, we have provided a comprehensive collection of research papers that evaluated function of OIP5-AS1 in diverse cancer types.
Collapse
Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sepideh Dashti
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Molood Farsi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Pharmacognosy Department, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
15
|
Long Noncoding RNA OIP5-AS1 Promotes the Disease Progression in Nasopharyngeal Carcinoma by Targeting miR-203. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9850928. [PMID: 33628831 PMCID: PMC7884132 DOI: 10.1155/2021/9850928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/02/2021] [Accepted: 01/15/2021] [Indexed: 12/13/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a kind of malignancy generated from the nasopharyngeal epithelium. Recently, long noncoding RNA (lncRNA) has been shown to be involved in the regulation of many signaling pathways and is closely associated with carcinogenesis and tumor progression. However, the precise role of lncRNA Opa-interacting protein 5 antisense RNA 1 (OIP5-AS1) in NPC is not well understood. Here, we find that OIP5-AS1 is overexpressed in NPC patient specimens and NPC cell lines. Further investigations reveal that knockdown of OIP5-AS1 significantly inhibits the proliferation, migration, and invasion and accelerates the apoptosis of NPC cells in vitro. Consistent with these findings, NPC progression is significantly slowed in mice when OIP5-AS1 is knocked down. Interestingly, there is a functional link between OIP5-AS1 and microRNA-203 (miR-203), a tumor suppressor, in NPC cells. In conclusion, our data demonstrate that OIP5-AS1 plays an important role in the development and progression of NPC by targeting miR-203 and therefore provide a promising target for the treatment of NPC.
Collapse
|
16
|
Liu X, Li X, Li J. Long Non-coding RNA FEZF1-AS1 Promotes Growth and Reduces Apoptosis Through Regulation of miR-363-3p/PAX6 Axis in Retinoblastoma. Biochem Genet 2021; 59:637-651. [PMID: 33432525 PMCID: PMC8096736 DOI: 10.1007/s10528-020-10026-7] [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: 07/09/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023]
Abstract
Retinoblastoma is the most common malignancy in children's eyes with high incidence. Long non-coding RNAs (lncRNAs) play important roles in the progression of retinoblastoma. LncRNA FEZF1 antisense RNA 1 (FEZF1-AS1) has been found to stimulate retinoblastoma. However, the mechanism of FEZF1-AS1 underlying progression of retinoblastoma is still unclear. In current study, FEZF1-AS1 was up-regulated in retinoblastoma tissues and cells. FEZF1-AS1 overexpression enhanced retinoblastoma cell viability, promoted cell cycle, and inhibited apoptosis. Conversely, FEZF1-AS1 knockdown reduced cell viability, cycle, and elevated apoptosis. The interaction between FEZF1-AS1 and microRNA-363-3p (miR-363-3p) was confirmed. FEZF1-AS1 down-regulated miR-363-3p and up-regulated PAX6. PAX6 was a target gene of miR-363-3p. EZF1-AS1 promoted retinoblastoma cell viability and suppressed apoptosis via PAX6. Further, we demonstrated that FEZF1-AS1 contribute to tumor formation in vivo. In conclusion, FEZF1-AS1 elevated growth and inhibited apoptosis by regulating miR-363-3p/PAX6 in retinoblastoma, which provide a new target for retinoblastoma treatment.
Collapse
Affiliation(s)
- Xiuming Liu
- Department of Ophthalmology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, No. 1, Huanghe Road, Huaiyin District, Huaian, 223300, Jiangsu, China.
| | - Xiaofeng Li
- Department of Ophthalmology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, No. 1, Huanghe Road, Huaiyin District, Huaian, 223300, Jiangsu, China
| | - Jianchang Li
- Department of Ophthalmology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, No. 1, Huanghe Road, Huaiyin District, Huaian, 223300, Jiangsu, China
| |
Collapse
|
17
|
Qing P, Liu Y. Inhibitory role of long non-coding RNA OIP5-AS1 in rheumatoid arthritis progression through the microRNA-448-paraoxonase 1-toll-like receptor 3-nuclear factor κB axis. Exp Physiol 2020; 105:1708-1719. [PMID: 32770578 DOI: 10.1113/ep088608] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/28/2020] [Indexed: 02/05/2023]
Abstract
NEW FINDINGS What is the central question of this study? What are the functions of long non-coding (lnc) RNA OIP5-AS1 in development of rheumatoid arthritis inflammation and what is the molecular mechanism? What is the main finding and its importance? LncRNA OIP5-AS1 mitigates rheumatoid arthritis progression through the competitive endogenous RNA network involving the miR-448-paraoxonase 1 axis and through the inactivation of the toll-like receptor 3-nuclear factor κB signalling pathway. This study may offer new ideas for molecularly based control of rheumatoid arthritis. ABSTRACT Rheumatoid arthritis (RA) is an autoimmune disorder with dysregulation of long non-coding RNAs (lncRNAs) possibly involved. This study aimed to inquire into the roles of lncRNA OIP5-AS1 in RA progression. A rat model of RA was induced. Overexpression of OIP5-AS1 was introduced in the model rats, and the changes in paw swelling, RA severity and the inflammatory factors interleukin (IL)-1β, IL-10, IL-6 and tumour necrosis factor α were measured. Fibroblast-like synoviocytes (FLSs) from RA patients were collected for in vitro experiments. A gain- and loss-of function study of OIP5-AS1, miR-448 and paraoxonase 1 (PON1) was performed to explore their roles in RA-FLS growth, apoptosis and inflammation. A toll-like receptor 3 (TLR3)-specific agonist, polyinosine-polycytidylic acid, or a nuclear factor κB (NF-κB)-specific antagonist, QNZ, was administrated in RA-FLSs. Consequently, overexpression of OIP5-AS1 reduced the symptom severity and the levels of inflammatory factors in RA rats. OIP5-AS1 could bind to miR-448 to up-regulate PON1 expression. Further overexpression of miR-448 reversed the effects of OIP5-AS1, while overexpression of PON1 inhibited RA-FLS growth and inflammation. In addition, TLR3 activation promoted RA progression. To conclude, this study evidenced that lncRNA OIP5-AS1 may mitigate RA progression through the miR-448-PON1 axis and through the inactivation of the TLR3-NF-κB signalling pathway.
Collapse
Affiliation(s)
- Pingying Qing
- Department of Rheumatology and Immunology, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Yi Liu
- Department of Rheumatology and Immunology, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| |
Collapse
|