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Bure IV, Nemtsova MV. Mutual Regulation of ncRNAs and Chromatin Remodeling Complexes in Normal and Pathological Conditions. Int J Mol Sci 2023; 24:ijms24097848. [PMID: 37175555 PMCID: PMC10178202 DOI: 10.3390/ijms24097848] [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: 03/23/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Chromatin remodeling is the one of the main epigenetic mechanisms of gene expression regulation both in normal cells and in pathological conditions. In recent years, a growing number of investigations have confirmed that epigenetic regulators are tightly connected and form a comprehensive network of regulatory pathways and feedback loops. Genes encoding protein subunits of chromatin remodeling complexes are often mutated and change their expression in diseases, as well as non-coding RNAs (ncRNAs). Moreover, different mechanisms of their mutual regulation have already been described. Further understanding of these processes may help apply their clinical potential for establishment of the diagnosis, prognosis, and treatment of the diseases. The therapeutic targeting of the chromatin structure has many limitations because of the complexity of its regulation, with the involvement of a large number of genes, proteins, non-coding transcripts, and other intermediary molecules. However, several successful strategies have been proposed to target subunits of chromatin remodeling complexes and genes encoding them, as well as the ncRNAs that regulate the operation of these complexes and direct them to the target gene regions. In our review, we focus on chromatin remodeling complexes and ncRNAs, their mutual regulation, role in cellular processes and potential clinical application.
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Affiliation(s)
- Irina V Bure
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Marina V Nemtsova
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
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Dawoud A, Ihab Zakaria Z, Hisham Rashwan H, Braoudaki M, Youness RA. Circular RNAs: New layer of complexity evading breast cancer heterogeneity. Noncoding RNA Res 2023; 8:60-74. [PMID: 36380816 PMCID: PMC9637558 DOI: 10.1016/j.ncrna.2022.09.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/04/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
Advances in high-throughput sequencing techniques and bioinformatic analysis have refuted the "junk" RNA hypothesis that was claimed against non-coding RNAs (ncRNAs). Circular RNAs (circRNAs); a class of single-stranded covalently closed loop RNA molecules have recently emerged as stable epigenetic regulators. Although the exact regulatory role of circRNAs is still to be clarified, it has been proven that circRNAs could exert their functions by interacting with other ncRNAs or proteins in their own physiologically authentic environment, regulating multiple cellular signaling pathways and other classes of ncRNAs. CircRNAs have also been reported to exhibit a tissue-specific expression and have been associated with the malignant transformation process of several hematological and solid malignancies. Along this line of reasoning, this review aims to highlight the importance of circRNAs in Breast Cancer (BC), which is ranked as the most prevalent malignancy among females. Notwithstanding the substantial efforts to develop a suitable anticancer therapeutic regimen against the heterogenous BC, inter- and intra-tumoral heterogeneity have resulted in an arduous challenge for drug development research, which in turn necessitates the investigation of other markers to be therapeutically targeted. Herein, the potential of circRNAs as possible diagnostic and prognostic biomarkers have been highlighted together with their possible application as novel therapeutic targets.
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Affiliation(s)
- Alyaa Dawoud
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, 11835, Cairo, Egypt
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, 11835, Cairo, Egypt
| | - Zeina Ihab Zakaria
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, 11835, Cairo, Egypt
| | - Hannah Hisham Rashwan
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, 11835, Cairo, Egypt
| | - Maria Braoudaki
- Clinical, Pharmaceutical, and Biological Science Department, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Rana A. Youness
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, 11835, Cairo, Egypt
- Clinical, Pharmaceutical, and Biological Science Department, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
- Biology and Biochemistry Department, School of Life and Medical Sciences, University of Hertfordshire hosted By Global Academic Foundation, New Administrative Capital, 11586, Cairo, Egypt
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Saberiyan M, Karimi E, Safi A, Movahhed P, Dehdehi L, Haririan N, Mirfakhraie R. Circular RNAs: Novel Biomarkers in Spermatogenesis Defects and Male Infertility. Reprod Sci 2023; 30:62-71. [PMID: 35178677 DOI: 10.1007/s43032-022-00885-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/09/2022] [Indexed: 01/06/2023]
Abstract
Circular RNAs (circRNAs) are a new class of endogenous non-coding RNAs involved in several cellular and biological processes, including gene expression regulation, microRNA function, transcription regulation, and translation modification. Therefore, these non-coding RNAs have important roles in the pathogenesis of various diseases. Male infertility is mainly due to abnormal sperm parameters such as motility, morphology, and concentration. Recent studies have confirmed the role of circRNAs in spermatogenesis, and the expression of several circRNAs is confirmed in seminal plasma, spermatozoa, and testicular tissue. It is suggested that deregulation of circRNAs is involved in different types of male infertility, including azoospermia, oligozoospermia, and asthenozoospermia. In the present review, we aimed to discuss the potential roles of circRNAs in spermatogenesis failure, sperm defects, and male infertility. Due to their conserved and special structure and tissue-specific expression pattern, circRNAs can be applied as reliable noninvasive molecular biomarkers, therapeutic and pharmaceutical targets in male infertility.
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Affiliation(s)
- Mohammadreza Saberiyan
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Elham Karimi
- Department of Medical Genetics, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Amir Safi
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
- Young Researchers and Elite Club, Islamic Azad University, Najafabad Branch, , Najafabad, Iran
| | - Parvaneh Movahhed
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Dehdehi
- Clinical Research Developmental Unit, Hajar Hospital, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Nazanin Haririan
- Biology Department, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Koodakyar St, Velenjak Ave, Chamran highway, 19395-4719, Tehran, Iran.
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In silico analysis revealed the potential circRNA-miRNA-mRNA regulative network of non-small cell lung cancer (NSCLC). Comput Biol Med 2023; 152:106315. [PMID: 36495751 DOI: 10.1016/j.compbiomed.2022.106315] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 10/31/2022] [Accepted: 11/13/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND The primary source of death in the world is non-small cell lung cancer (NSCLC). However, NSCLCs pathophysiology is still not completely understood. The current work sought to study the differential expression of mRNAs involved in NSCLC and their interactions with miRNAs and circRNAs. METHODS We utilized three microarray datasets (GSE21933, GSE27262, and GSE33532) from the GEO NCBI database to identify the differentially expressed genes (DEGs) in NSCLC. We employed DAVID Functional annotation tool to investigate the underlying GO biological process, molecular functions, and KEGG pathways involved in NSCLC. We performed the Protein-protein interaction (PPI) network, MCODE, and CytoHubba analysis from Cytoscape software to identify the significant DEGs in NSCLC. We utilized miRnet to anticipate and build interaction between miRNAs and mRNAs in NSCLC and ENCORI to predict the miRNA-circRNA relationships and build the ceRNA regulatory network. Finally, we executed the gene expression and Kaplan-Meier survival analysis to validate the significant DEGs in the ceRNA network utilizing TCGA NSCLC and GEPIA data. RESULTS We revealed a total of 156 overlapped DEGs (47 upregulated and 109 downregulated genes) in NSCLC. The PPI network, MCODE, and CytoHubba analysis revealed 12 hub genes (cdkn3, rrm2, ccnb1, aurka, nuf2, tyms, kif11, hmmr, ccnb2, nek2, anln, and birc5) that are associated with NSCLC. We identified that these 12 genes encode 12 mRNAs that are strongly linked with 8 miRNAs, and further, we revealed that 1 circRNA was associated with this 5 miRNA. We constructed the ceRNAs network that contained 1circRNA-5miRNAs-7mRNAs. The expression of these seven significant genes in LUAD & LUSC (NSCLC) was considerably higher in the TCGA database than in normal tissues. Kaplan-Meier survival plot reveals that increased expression of these hub genes was related to a poor survival rate in LUAD. CONCLUSION Overall, we developed a circRNA-miRNA-mRNA regulation network to study the probable mechanism of NSCLC.
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Lin L, Xiao L, Jin C, Qin Y, Deng H, Li M, Lin H, Gong X. Circ_0058058 Drives the Malignant Phenotypes and Immune Evasion of Pancreatic Cancer by the MicroRNA-557-Dependent Regulation of PDL1. Pancreas 2022; 51:1444-1454. [PMID: 37099790 DOI: 10.1097/mpa.0000000000002205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
OBJECTIVES Pancreatic cancer (PC) is one of the most deadly malignancies in the world. Recently, circular RNAs play crucial roles in PC progression. However, the functions of circ_0058058 in PC are barely known. METHODS The expression of circ_0058058, microRNA-557-5p (miR-557), and programmed cell death receptor ligand 1 (PDL1) was detected by quantitative real-time polymerase chain reaction. Functional experiments were implemented to disclose the effect of circ_0058058 deficiency on PC cell proliferation, apoptosis, invasion, angiogenesis, and immune escape. The binding relationship between miR-557 and circ_0058058 or PDL1 was identified by dual-luciferase reporter assay and RNA immunoprecipitation assay. In vivo assay was used to disclose the impact of circ_0058058 silencing on tumor formation in vivo. RESULTS Circ_0058058 was highly expressed in PC tissues and cell lines. Knockdown of circ_0058058 repressed cell proliferation, invasion, angiogenesis, and immune escape while contributed to apoptosis in PC cells. Mechanically, circ_0058058 worked as a molecular sponge of miR-557 to regulate PDL1 expression. Moreover, circ_0058058 showed a promotional effect on tumor growth in vivo. CONCLUSIONS Our findings suggested that circ_0058058 served as miR-557 sponge to upregulate PDL1, thereby triggering PC proliferation, invasion, angiogenesis, and immune escape.
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Affiliation(s)
- Lin Lin
- From the Department of Surgery and Oncology, Shenzhen Second People's Hospital/First Affiliated Hospital to Shenzhen University
| | - Liang Xiao
- From the Department of Surgery and Oncology, Shenzhen Second People's Hospital/First Affiliated Hospital to Shenzhen University
| | - Chang'e Jin
- Department of Respiratory and Critical Care Medicine, Shenzhen People's Hospital/The Second Clinical Medical College, Jinan University/The First Affiliated Hospital, Southern University of Science and Technology
| | - Ying Qin
- Department of Gastrointestinal Surgery
| | | | - Meixiang Li
- From the Department of Surgery and Oncology, Shenzhen Second People's Hospital/First Affiliated Hospital to Shenzhen University
| | | | - Xuehao Gong
- Department of Ultrasound, Shenzhen Second People's Hospital/First Affiliated Hospital to Shenzhen University, Shenzhen, China
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Xu Z, Zhong K, Guo G, Xu C, Song Z, Wang D, Pan J. circ_TGFBR2 Inhibits Vascular Smooth Muscle Cells Phenotypic Switch and Suppresses Aortic Dissection Progression by Sponging miR-29a. J Inflamm Res 2021; 14:5877-5890. [PMID: 34795497 PMCID: PMC8593842 DOI: 10.2147/jir.s336094] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/22/2021] [Indexed: 12/20/2022] Open
Abstract
Background Aortic dissection (AD) is a threatening and catastrophic vascular disease with high mortality rate and limited therapeutic strategies. There is emerging evidence showing that circular RNAs play crucial role in regulating various cardiovascular diseases. However, the biological functions and molecular mechanisms of circRNAs in AD still remains elusive. The purpose of this study was to illustrate the potential functional roles and mechanisms of hsa_circ_TGFBR2 in vitro and in vivo. Methods The vascular smooth muscle cells (VSMCs) and AD-VSMCs were isolated from normal aorta and AD tissues. The expression of circ_TGFBR2, miR-29a and KLF4 were detected by realtime polymerase chain reaction (RT-PCR) and fluorescence in situ hybridization (FISH). Cell proliferation was assessed by CCK-8 assay, colony formation and EDU assay. Cell migration was evaluated through transwell assay. Dual-luciferase reporter assay and RNA pulldown were performed to identify the interaction between circ_TGFBR2 and miR-29a or between miR-29a and KLF4. The wild-type sequence of circ_TGFBR2 or KLF4 were cloned into the luciferase reporter plasmid, and the activity was measured using dual-luciferase reporter assay system. And for RNA pulldown, the relative RNA enrichment of circ_TGFBR2 and miR-29a were confirmed using RT-PCR. Western Blot measured the expression of phenotype switch-related proteins. AD rat model induced by β-aminopropionitrile monofumarate (BAPN) was used to verify the role and mechanism of circ_TGFBR2. Results Circ_TGFBR2 inhibited cell proliferation and migration of AD-VSMCs cells. Overexpression of circ_TGFBR2 promoted the expression of contractile markers (α-SMA, SM22α) and inhibited the expression of synthetic markers (MGP, OPN) in AD-VSMCs cells. Circ_TGFBR2 served as a sponge for miR-29a targeting KLF4. MiR-29a mimics rescued biological roles induced by circ_TGFBR2 overexpression. The in vivo experiments revealed that overexpression of TGFBR2 suppressed the progression of AD and increased the expression of contractile markers while inhibited the expression of synthetic markers. Conclusion Our study revealed that circ_TGFBR2 regulated VSMCs phenotype switch and suppressed the progression of AD.
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Affiliation(s)
- Zhenjun Xu
- Department of Thoracic and Cardiovascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, People's Republic of China
| | - Kai Zhong
- Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210008, People's Republic of China
| | - Guanjun Guo
- Department of Thoracic and Cardiovascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, People's Republic of China
| | - Can Xu
- Department of Thoracic and Cardiovascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, People's Republic of China
| | - Zhizhao Song
- Department of Thoracic and Cardiovascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, People's Republic of China
| | - Dongjin Wang
- Department of Thoracic and Cardiovascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, People's Republic of China
| | - Jun Pan
- Department of Thoracic and Cardiovascular Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, People's Republic of China
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