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Shelke V, Kale A, Sankrityayan H, Anders HJ, Gaikwad AB. Long non-coding RNAs as emerging regulators of miRNAs and epigenetics in diabetes-related chronic kidney disease. Arch Physiol Biochem 2024; 130:230-241. [PMID: 34986074 DOI: 10.1080/13813455.2021.2023580] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/22/2021] [Indexed: 01/19/2023]
Abstract
Diabetes is one of the major cause of chronic kidney disease (CKD), including "diabetic nephropathy," and is an increasingly prevalent accelerator of the progression of non-diabetic forms of CKD. The long non-coding RNAs (lncRNAs) have come into the limelight in the past few years as one of the emerging weapons against CKD in diabetes. Available data over the past few years demonstrate the interaction of lncRNAs with miRNAs and epigenetic machinery. Interestingly, the evolving data suggest that lncRNAs play a vital role in diabetes-associated CKD by regulation of epigenetic enzymes such as DNA methyltransferase, histone deacetylases, and histone methyltransferases. LncRNAs are also engaged in the regulation of several miRNAs in diabetic nephropathy. Hence this review will elaborate on the association between lncRNAs and their interaction with epigenetic regulators involved in different aspects and thus the progression of CKD in diabetes.
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Affiliation(s)
- Vishwadeep Shelke
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani, India
| | - Ajinath Kale
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani, India
| | - Himanshu Sankrityayan
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani, India
| | - Hans-Joachim Anders
- Division of Nephrology, Department of Internal Medicine IV, University Hospital of the Ludwig Maximilians University Munich, Munich, Germany
| | - Anil Bhanudas Gaikwad
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani, India
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Alharbi KS. GAS5: A pivotal lncRNA in diabetes mellitus pathogenesis and management. Pathol Res Pract 2024; 253:154955. [PMID: 38016351 DOI: 10.1016/j.prp.2023.154955] [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: 10/10/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 11/30/2023]
Abstract
The long non-coding RNA (lncRNA), GAS5, has garnered significant attention recently for its multifaceted involvement in cellular processes, particularly within the context of diabetes. This comprehensive review delves into the intricate molecular interactions associated with GAS5 and their profound implications for understanding, diagnosing, and effectively managing diabetes mellitus. The article begins by highlighting the global prevalence of diabetes and the urgent need for innovative insights into its underlying mechanisms and therapeutic approaches. It introduces GAS5 as a crucial regulator of gene expression, with emerging significance in the context of diabetes-related processes. The core of this review unravels the regulatory network of GAS5 in diabetes, elucidating its impact on various aspects of the disease. It explores how GAS5 influences insulin signaling pathways, glucose metabolism, and the function of β-cells, shedding light on its role in hyperglycemia and insulin resistance. Moreover, the article underscores the clinical relevance of GAS5's interactions by discussing their associations with different diabetes subtypes, predictive value, and potential applications as both diagnostic tools and therapeutic targets. It provides insights into ongoing research endeavours aimed at harnessing the potential of GAS5 for innovative disease management strategies, including the development of RNA-based therapeutics. Concluding with a forward-looking perspective, the abstract highlights the broader implications of GAS5 in the field of diabetes, such as its connection to diabetic complications and its potential for personalized approaches in disease management.
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Affiliation(s)
- Khalid Saad Alharbi
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia.
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Li H, Hu X, Li J, Jiang W, Wang L, Tan X. Identification of key regulatory genes and their working mechanisms in type 1 diabetes. BMC Med Genomics 2023; 16:8. [PMID: 36650594 PMCID: PMC9843847 DOI: 10.1186/s12920-023-01432-y] [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: 07/04/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) is an autoimmune disease characterized by the destruction of beta cells in pancreatic islets. Identification of the key genes involved in T1D progression and their mechanisms of action may contribute to a better understanding of T1D. METHODS The microarray profile of T1D-related gene expression was searched using the Gene Expression Omnibus (GEO) database. Then, the expression data of two messenger RNAs (mRNAs) were integrated for Weighted Gene Co-Expression Network Analysis (WGCNA) to generate candidate genes related to T1D. In parallel, T1D microRNA (miRNA) data were analyzed to screen for possible regulatory miRNAs and their target genes. An miRNA-mRNA regulatory network was then established to predict the key regulatory genes and their mechanisms. RESULTS A total of 24 modules (i.e., clusters/communities) were selected using WGCNA analysis, in which three modules were significantly associated with T1D. Further correlation analysis of the gene module revealed 926 differentially expressed genes (DEGs), of which 327 genes were correlated with T1D. Analysis of the miRNA microarray showed that 13 miRNAs had significant expression differences in T1D. An miRNA-mRNA network was established based on the prediction of miRNA target genes and the combined analysis of mRNA, in which the target genes of two miRNAs were found in T1D correlated genes. CONCLUSION An miRNA-mRNA network for T1D was established, based on which 2 miRNAs and 12 mRNAs were screened, suggesting that they may play key regulatory roles in the initiation and development of T1D.
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Affiliation(s)
- Hui Li
- grid.508008.50000 0004 4910 8370Pediatric Department, The First Hospital of Changsha, No. 311, Yingpan Road, Kaifu District, Changsha, 410000 Hunan People’s Republic of China
| | - Xiao Hu
- grid.508008.50000 0004 4910 8370Pediatric Department, The First Hospital of Changsha, No. 311, Yingpan Road, Kaifu District, Changsha, 410000 Hunan People’s Republic of China
| | - Jieqiong Li
- grid.508008.50000 0004 4910 8370Pediatric Department, The First Hospital of Changsha, No. 311, Yingpan Road, Kaifu District, Changsha, 410000 Hunan People’s Republic of China
| | - Wen Jiang
- grid.508008.50000 0004 4910 8370Pediatric Department, The First Hospital of Changsha, No. 311, Yingpan Road, Kaifu District, Changsha, 410000 Hunan People’s Republic of China
| | - Li Wang
- grid.508008.50000 0004 4910 8370Pediatric Department, The First Hospital of Changsha, No. 311, Yingpan Road, Kaifu District, Changsha, 410000 Hunan People’s Republic of China
| | - Xin Tan
- grid.508008.50000 0004 4910 8370Pediatric Department, The First Hospital of Changsha, No. 311, Yingpan Road, Kaifu District, Changsha, 410000 Hunan People’s Republic of China
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Li G, Wang Z, Chen D, Yin J, Mo Z, Sun B, Yang T, Zhang X, Zhai Z, Li Y, Chen P, Dai Y, Wang Z, Ma J. Comprehensive analysis of a TPX2-related TRHDE-AS1/PKIA ceRNA network involving prognostic signatures in Hepatitis B virus-infected hepatocellular carcinoma. Front Cell Infect Microbiol 2022; 12:1025900. [PMID: 36204642 PMCID: PMC9530265 DOI: 10.3389/fcimb.2022.1025900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a main carcinogenic factor of hepatocellular carcinoma (HCC). TPX2 microtubule nucleation factor is recently recommended as a novel prognostic biomarker in HBV-infected HCC tissues. This study aimed to explore a TPX2-related ceRNA regulatory network in HBV-infected HCC and the potential impact on HCC prognosis. We comprehensively identified 541 differential expressed lncRNAs (DElncRNAs), 37 DEmiRNAs and 439 DEmRNAs from HBV-related TCGA-HCC cohorts in TPX2low and TPX2high groups. Based on their RNA-RNA interaction and expression analysis, four DElncRNAs (TRHDE-AS1, DLX6-AS1, SNHG14, HOXA11-AS), four DEmiRNAs (miR-23b, miR-320a, miR-589, miR-126) and five DEmRNAs (PKIA, PCDHA2, SHCBP1, PRSS16, KIF18A) in HCC tumor vs normal groups were subjected to the hub regulatory networks analysis and further prognostic value analysis. Importantly, the TRHDE-AS1/miR-23b/PKIA ceRNA network was associated with HCC prognosis. Furthermore, cellular location analysis and base-base interaction analysis indicated that the cytoplasmic lncRNA TRHDE-AS1 was regarded as a ceRNA to sponging miR-23b and then regulating PKIA. Interestingly, correlation analysis suggested the expression correlation between TRHDE-AS1 and PKIA in HCC. Finally, we further performed the methylation and immune infiltration analysis to explore the functional process of PKIA in HCC. We proposed a ceRNA regulatory network may help elucidate the mechanism by which TPX2 contributes to the prognosis of HBV-related HCC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jun Ma
- *Correspondence: Jun Ma, ;
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Brodnicki TC. A Role for lncRNAs in Regulating Inflammatory and Autoimmune Responses Underlying Type 1 Diabetes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:97-118. [DOI: 10.1007/978-3-030-92034-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Tang Y, Tang Q, Wei H, Hu P, Zou D, Liang R, Ling Y. Hub Genes Associated with the Diagnosis of Diabetic Retinopathy. Int J Gen Med 2021; 14:1739-1750. [PMID: 33986612 PMCID: PMC8110263 DOI: 10.2147/ijgm.s311683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/14/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose This study aimed to identify genes that may be effective in diagnosing or treating diabetic retinopathy (DR), the most common complication of diabetes mellitus (DM). Methods Differentially expressed genes (DEGs) were identified between DR and DM in GSE146615 dataset. DEGs that were consistently up- or down-regulated under both standard glucose and high glucose conditions were identified as common genes and used to generate a protein-protein interaction network and modules. The module genes were assessed for the area under the receiver operating characteristic curve (AUC), leading to the identification of hub genes. Differentially methylated probes in GSE76169 were also compared with common DEGs to identify specific methylation markers of DR. Enrichment analysis was used to explore the biological characteristics. The Short Time-series Expression Miner algorithm was used to identify genes that were progressively dysregulated in the sequence: healthy controls < DM < DR. Results A total of 1917 common genes were identified for seven modules. The eight genes with AUC > 0.8 under high glucose and standard glucose conditions were considered as hub genes. The module genes were significantly enriched during vascular smooth muscle cell development and regulation of oxygen metabolism, while 92 methylation markers were involved in the similar terms. Among the progressively dysregulated genes, three intersection genes under both standard glucose and high glucose conditions were found to be module genes and were considered as key genes. Conclusion We identified eight potential DR-specific diagnostic and therapeutic genes, whose abnormal expression can cause oxidative stress, thus favoring the course of the disease.
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Affiliation(s)
- Yanhui Tang
- Department of Ophthalmology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China.,Department of Ophthalmology, The First People's Hospital of Nanning, Nanning, Guangxi, 530022, People's Republic of China
| | - Qi Tang
- Department of Ophthalmology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China.,Department of Ophthalmology, The First People's Hospital of Nanning, Nanning, Guangxi, 530022, People's Republic of China
| | - Haicheng Wei
- Department of Ophthalmology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China.,Department of Ophthalmology, The First People's Hospital of Nanning, Nanning, Guangxi, 530022, People's Republic of China
| | - Pinzhang Hu
- Department of Ophthalmology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China.,Department of Ophthalmology, The First People's Hospital of Nanning, Nanning, Guangxi, 530022, People's Republic of China
| | - Donghua Zou
- Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China
| | - Rixiong Liang
- Department of Ophthalmology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China.,Department of Ophthalmology, The First People's Hospital of Nanning, Nanning, Guangxi, 530022, People's Republic of China
| | - Yu Ling
- Department of Ophthalmology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530022, People's Republic of China.,Department of Ophthalmology, The First People's Hospital of Nanning, Nanning, Guangxi, 530022, People's Republic of China
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Yi X, Cheng X. Understanding Competitive Endogenous RNA Network Mechanism in Type 1 Diabetes Mellitus Using Computational and Bioinformatics Approaches. Diabetes Metab Syndr Obes 2021; 14:3865-3945. [PMID: 34526791 PMCID: PMC8436179 DOI: 10.2147/dmso.s315488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/24/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Type 1 diabetes mellitus (T1DM), an autoimmune disease with a genetic tendency, has an increasing prevalence. Long non-coding RNA (lncRNA) and circular RNA (circRNA) are receiving increasing attention in disease pathogenesis. However, their roles in T1DM are poorly understood. The present study aimed at identifying signature lncRNAs and circRNAs and investigating their roles in T1DM using the competing endogenous RNA (ceRNA) network analysis. METHODS The T1DM expression profile was downloaded from Gene Expression Omnibus (GEO) database to identify the differentially expressed circRNAs, lncRNAs, and mRNAs. The biological functions of these differentially expressed circRNAs, lncRNAs, and mRNAs were analyzed by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Targeting relationships of circRNA-miRNA, lncRNA-miRNA, and miRNA-mRNA were predicted, and the circRNA-lncRNA-miRNA-mRNA ceRNA regulatory network was established. Finally, qRT-PCR was applied to identify the effect of hsa_circ_0002202 inhibition on the IFN-I induced macrophage inflammation. RESULTS A total of 178 circRNAs, 404 lncRNAs, and 73 mRNAs were identified to be abnormally expressed in T1DM samples. Functional enrichment analysis results indicated that the differentially expressed genes were mainly enriched in extracellular matrix components and macrophage activation. CeRNA regulatory network showed that circRNAs and lncRNAs regulate mRNAs through integrate multiple miRNAs. In addition, in vitro experiments showed that hsa_circ_0002202 inhibition suppressed the type I interferon (IFN-I)-induced macrophage inflammation. CONCLUSION In the present study, the circRNA-lncRNA-miRNA-mRNA ceRNA regulatory network in T1DM was established for the first time. We also found that hsa_circ_0002202 inhibition suppressed the IFN-I-induced macrophage inflammation. Our study may lay a foundation for future studies on the ceRNA regulatory network in T1DM.
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Affiliation(s)
- Xuanzi Yi
- Department of Medicine II, Division of Endocrinology and Diabetology, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany
- Correspondence: Xuanzi Yi Department of Medicine II, Division of Endocrinology and Diabetology, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, Freiburg, 79106, GermanyTel/Fax +49 761 270-73270 Email
| | - Xu Cheng
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany
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