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Izadi M, Sadri N, Abdi A, Serajian S, Jalalei D, Tahmasebi S. Epigenetic biomarkers in aging and longevity: Current and future application. Life Sci 2024; 351:122842. [PMID: 38879158 DOI: 10.1016/j.lfs.2024.122842] [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: 12/29/2023] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
The aging process has been one of the most necessary research fields in the current century, and knowing different theories of aging and the role of different genetic, epigenetic, molecular, and environmental modulating factors in increasing the knowledge of aging mechanisms and developing appropriate diagnostic, therapeutic, and preventive ways would be helpful. One of the most conserved signs of aging is epigenetic changes, including DNA methylation, histone modifications, chromatin remodeling, noncoding RNAs, and extracellular RNAs. Numerous biological processes and hallmarks are vital in aging development, but epigenomic alterations are especially notable because of their importance in gene regulation and cellular identity. The mounting evidence points to a possible interaction between age-related epigenomic alterations and other aging hallmarks, like genome instability. To extend a healthy lifespan and possibly reverse some facets of aging and aging-related diseases, it will be crucial to comprehend global and locus-specific epigenomic modifications and recognize corresponding regulators of health and longevity. In the current study, we will aim to discuss the role of epigenomic mechanisms in aging and the most recent developments in epigenetic diagnostic biomarkers, which have the potential to focus efforts on reversing the destructive signs of aging and extending the lifespan.
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Affiliation(s)
- Mehran Izadi
- Department of Infectious and Tropical Diseases, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran
| | - Nariman Sadri
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirhossein Abdi
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Sahar Serajian
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; Royan Institute for Stem Cell Biology and Technology, Tehran, Iran
| | - Dorsa Jalalei
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Safa Tahmasebi
- Synapse Laboratory Diagnostic Technologies Accelerator, Tehran, Iran; Department of Research & Technology, Zeenome Longevity Research Institute, Tehran, Iran; Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Talepoor AG, Doroudchi M. Regulatory RNAs in immunosenescence. Immun Inflamm Dis 2024; 12:e1209. [PMID: 38456619 PMCID: PMC10921898 DOI: 10.1002/iid3.1209] [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: 10/22/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Immunosenescence is a multifactorial stress response to different intrinsic and extrinsic insults that cause immune deterioration and is accompanied by genomic or epigenomic perturbations. It is now widely recognized that genes and proteins contributing in the process of immunosenescence are regulated by various noncoding (nc) RNAs, including microRNAs (miRNAs), long ncRNAs, and circular RNAs. AIMS This review article aimed to evaluate the regulatore RNAs roles in the process of immunosenescence. METHODS We analyzed publications that were focusing on the different roles of regulatory RNAs on the several aspects of immunosenescence. RESULTS In the immunosenescence setting, ncRNAs have been found to play regulatory roles at both transcriptional and post-transcriptional levels. These factors cooperate to regulate the initiation of gene expression programs and sustaining the senescence phenotype and proinflammatory responses. CONCLUSION Immunosenescence is a complex process with pivotal alterations in immune function occurring with age. The extensive network that drive immunosenescence-related features are are mainly directed by a variety of regulatory RNAs such as miRNAs, lncRNAs, and circRNAs. Latest findings about regulation of senescence by ncRNAs in the innate and adaptive immune cells as well as their role in the immunosenescence pathways, provide a better understanding of regulatory RNAs function in the process of immunosenescence.
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Affiliation(s)
- Atefe Ghamar Talepoor
- Department of Immunology, School of MedicineShiraz University of Medical SciencesShirazIran
- Autoimmune Diseases Research CenterUniversity of Medical SciencesShirazIran
| | - Mehrnoosh Doroudchi
- Department of Immunology, School of MedicineShiraz University of Medical SciencesShirazIran
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Paniri A, Hosseini MM, Akhavan-Niaki H. Alzheimer's Disease-Related Epigenetic Changes: Novel Therapeutic Targets. Mol Neurobiol 2024; 61:1282-1317. [PMID: 37700216 DOI: 10.1007/s12035-023-03626-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Aging is a significant risk factor for Alzheimer's disease (AD), although the precise mechanism and molecular basis of AD are not yet fully understood. Epigenetic mechanisms, such as DNA methylation and hydroxymethylation, mitochondrial DNA methylation, histone modifications, and non-coding RNAs (ncRNAs), play a role in regulating gene expression related to neuron plasticity and integrity, which are closely associated with learning and memory development. This review describes the impact of dynamic and reversible epigenetic modifications and factors on memory and plasticity throughout life, emphasizing their potential as target for therapeutic intervention in AD. Additionally, we present insight from postmortem and animal studies on abnormal epigenetics regulation in AD, as well as current strategies aiming at targeting these factors in the context of AD therapy.
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Affiliation(s)
- Alireza Paniri
- Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
- Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran
| | | | - Haleh Akhavan-Niaki
- Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
- Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran.
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Tan J, Ge J, Sahaer P, Li H, Sun H. Identification and functional analysis of circRIPK2 in lipopolysaccharide induced chicken macrophages. Br Poult Sci 2023; 64:678-687. [PMID: 37735991 DOI: 10.1080/00071668.2023.2261870] [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: 06/12/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023]
Abstract
1. It was hypothesised that a circular RIPK2 (circRIPK2) highly expressed in chicken macrophages plays an important role during bacterial infection.2. After PCR amplification, Sanger sequencing and RNase R exonuclease treatment of chicken macrophages, it was found that circRIPK2 was a stable circular RNA, which was formed by reverse splicing of exons 4 to 9 of the RIPK2.3. The circRIPK2 can promote the lipopolysaccharide (LPS) induced cellular injury by reducing cell viability and increasing the expression of pro-inflammatory cytokines and apoptosis genes.4. Six miRNAs were identified as interacting with circRIPK2, potentially targeting 1,817 genes, which were significantly enriched in the Wnt signalling pathway, adherens junction and NOD-like receptor signalling pathway.5. This study provides better understanding of the function of circRIPK2, which may prove a potential biomarker and indicate potential targets for the treatment of bacterial infection.
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Affiliation(s)
- J Tan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - J Ge
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - P Sahaer
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - H Li
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou, China
| | - H Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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5
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Yalamarty SSK, Filipczak N, Khan MM, Torchilin VP. Role of circular RNA and its delivery strategies to cancer - An overview. J Control Release 2023; 356:306-315. [PMID: 36878321 DOI: 10.1016/j.jconrel.2023.02.044] [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: 07/20/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023]
Abstract
With the passage of years and the progress of research on ribonucleic acids, the range of forms in which these molecules have been observed grows. One of them, discovered relatively recently, is circular RNA - covalently closed circles (circRNA). In recent years, there has been a huge increase in the interest of researchers in this group of molecules. It entailed a significant increase in the state of knowledge about them, which in turn caused a dramatic change in their perception. Rather than seeing circular RNAs as curiosities that represent a minor information noise in a cell or a result of RNA misprocessing, they came to be regarded as a common, essential, and potentially extremely useful group of molecules. Nevertheless, the current state of the art of circRNA is full of white cards. A lot of valuable information has been obtained from high-throughput methods to study whole transcriptomes, but many issues related to circular RNAs still need to be clarified. Presumably, each answer obtained will raise several new questions. However, circRNAs have a wealth of potential applications, including therapeutic applications.
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Affiliation(s)
| | - Nina Filipczak
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, Boston, MA 02115, USA
| | | | - Vladimir P Torchilin
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, Boston, MA 02115, USA; Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA.
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Shao Z, Yuan C, Hu J, Wu Y, Zeng C. Circ_0003789 Facilitates Gastric Cancer Progression by Inducing the Epithelial-Mesenchymal Transition Through the Wnt/β-Catenin Signaling Pathway. Cancer Biother Radiopharm 2023; 38:102-110. [PMID: 32865426 DOI: 10.1089/cbr.2020.4044] [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] [Indexed: 12/16/2022] Open
Abstract
Background: The role of circular RNAs in the pathogenesis of gastric cancer (GC) has been well documented by numerous studies. However, whether circ_0003789 plays a role during GC progression remains to be determined. Thus, this study investigated the biological functions of circ_0003789 during GC progression. Materials and Methods: Circ_0003789 expression was determined using quantitative real-time polymerase chain reaction in GC and matched para-carcinoma normal tissues. Functional experiments were performed to estimate changes in the proliferation, apoptosis, migration, and invasion of GC cells treated to silence circ_0003789. E-cadherin, vimentin, Wnt3a, and β-catenin expression was determined using immunofluorescence staining and Western blot assays. Xenograft tumor growth and Ki67 expression were also evaluated in vivo. Results: Circ_0003789 was upregulated in GC tissues and cells, and its upregulation positively correlated with poor tumor differentiation, distal metastasis, and advanced clinical stage. Silencing circ_0003789 inhibited GC cell proliferation, migration, invasion, and the epithelial-mesenchymal transition (EMT), both in vitro and in vivo. Mechanistically, the Wnt/β-catenin signaling pathway was repressed by circ_0003789 silencing. Conclusions: Circ_0003789 facilitates GC progression by inducing the EMT through the Wnt/β-catenin signaling pathway.
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Affiliation(s)
- Zhongbao Shao
- Department of Electronic Information Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Chang Yuan
- Department of Electronic Information Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Junbao Hu
- Department of Electronic Information Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Yuli Wu
- Department of Electronic Information Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Chong Zeng
- Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China
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Niu R, Liu J. Circular RNA Involvement in Aging and Longevity. Curr Genomics 2022; 23:318-325. [PMID: 36778190 PMCID: PMC9878857 DOI: 10.2174/1389202923666220927110258] [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: 04/16/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/22/2022] Open
Abstract
Background Circular RNAs (circRNAs) are transcribed by RNA polymerase II and are mostly generated by the back-splicing of exons in the protein-coding gene. Massive circRNAs are reported to be differentially expressed in different species, implicating their prospects as aging biomarkers or regulators in the aging progression. Methods The possible role of circRNAs in aging and longevity was reviewed by the query of circRNAs from literature reports related to tissue, organ or cellular senescence, and individual longevity. Results A number of circRNAs have been found to positively and negatively modulate aging and longevity through canonical aging pathways in the invertebrates Caenorhabditis elegans and Drosophila. Recent studies have also shown that circRNAs regulate age-related processes and pathologies such various mammalian tissues, as the brain, serum, heart, and muscle. Besides, three identified representative circRNAs (circSfl, circGRIA1, and circNF1-419) were elucidated to correlate with aging and longevity. Conclusion This review outlined the current studies of circRNAs in aging and longevity, highlighting the role of circRNAs as a biomarker of aging and as a regulator of longevity.
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Affiliation(s)
- Ruize Niu
- Laboratory Zoology Department, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Jia Liu
- Laboratory Zoology Department, Kunming Medical University, Kunming 650500, Yunnan, China,Address correspondence to this author at the Laboratory Zoology Department, Kunming Medical University, Kunming, Yunnan, 650500, China; Tel: 15288361011; E-mail:
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Epigenetic regulation of aging: implications for interventions of aging and diseases. Signal Transduct Target Ther 2022; 7:374. [PMID: 36336680 PMCID: PMC9637765 DOI: 10.1038/s41392-022-01211-8] [Citation(s) in RCA: 110] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Aging is accompanied by the decline of organismal functions and a series of prominent hallmarks, including genetic and epigenetic alterations. These aging-associated epigenetic changes include DNA methylation, histone modification, chromatin remodeling, non-coding RNA (ncRNA) regulation, and RNA modification, all of which participate in the regulation of the aging process, and hence contribute to aging-related diseases. Therefore, understanding the epigenetic mechanisms in aging will provide new avenues to develop strategies to delay aging. Indeed, aging interventions based on manipulating epigenetic mechanisms have led to the alleviation of aging or the extension of the lifespan in animal models. Small molecule-based therapies and reprogramming strategies that enable epigenetic rejuvenation have been developed for ameliorating or reversing aging-related conditions. In addition, adopting health-promoting activities, such as caloric restriction, exercise, and calibrating circadian rhythm, has been demonstrated to delay aging. Furthermore, various clinical trials for aging intervention are ongoing, providing more evidence of the safety and efficacy of these therapies. Here, we review recent work on the epigenetic regulation of aging and outline the advances in intervention strategies for aging and age-associated diseases. A better understanding of the critical roles of epigenetics in the aging process will lead to more clinical advances in the prevention of human aging and therapy of aging-related diseases.
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Gao F, Li J, Liang S, Wei L, He X, Liu S, Cheng X, Shi K, Jiang H, Chen L. Emerging roles of circRNAs in mice kidney with aging. Microsc Res Tech 2022; 85:2984-2996. [PMID: 35656876 DOI: 10.1002/jemt.24147] [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: 02/23/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 11/06/2022]
Abstract
Circular RNA (circRNA) is a novel type of noncoding RNA expressed in different tissues and species. Up to now, little is known of the function and expression of circRNAs in kidney aging. In this research, we used RNA sequencing to identify 11,929 circRNAs in kidney from 3-, 12-, and 24-month-old mice, of which 12 circRNAs were validated by qPCR. Based on the validated circRNAs and their predicted miRNA-mRNA target pairs, a circRNA-miRNA-mRNA interactions network was conducted. Bioinformatics analysis for all the mRNAs in the ceRNA network showed that the most enriched gene ontology (GO) term and one of the most enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were associated with endoplasmic reticulum (ER). The network also identified circNpas2, which was decreased significantly in mice kidney during aging, as a hub gene. Subsequently, we found that the cell cycle was arrested in G1 phase and the expression of P53 and P16 increased significantly in the circNpas2-knockdown cells. Moreover, knockdown of circNpas2 inhibited expression of ER-related proteins, HSPA5 and ERO1L. Taken together, our findings contribute to a better understanding of the role played by circRNA during kidney aging and provide potential therapeutic targets for the prevention of kidney aging.
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Affiliation(s)
- Fanfan Gao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jie Li
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shanshan Liang
- Blood Transfusion Department, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Limin Wei
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xin He
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Sixiu Liu
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xin Cheng
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Kehui Shi
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hongli Jiang
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Lei Chen
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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Chen S, Cao X, Zhang J, Wu W, Zhang B, Zhao F. circVAMP3 Drives CAPRIN1 Phase Separation and Inhibits Hepatocellular Carcinoma by Suppressing c-Myc Translation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103817. [PMID: 35072355 PMCID: PMC8922094 DOI: 10.1002/advs.202103817] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/16/2021] [Indexed: 05/04/2023]
Abstract
Previous studies have identified the regulatory roles of circular RNAs (circRNAs) in human cancers. However, the molecular mechanisms of circRNAs in hepatocellular carcinoma (HCC) remain largely unknown. This study screens the expression profile of circRNAs in HCC and identifies circVAMP3 as a significantly downregulated circRNA in HCC tissues. HCC patients with low circVAMP3 expression present poor prognosis. circVAMP3 negatively regulates the proliferation and metastasis of HCC cells in vitro and in vivo by driving phase separation of CAPRIN1 and promoting stress granule formation in cells, which can downregulate the protein level of Myc proto-oncogene protein by inhibiting c-Myc translation. Furthermore, circVAMP3 is widely expressed in many human tissues and is downregulated in related cancers. Therefore, circVAMP3 is a potential prognostic indicator for HCC and may serve as a therapeutic target for HCC treatment.
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Affiliation(s)
- Shuai Chen
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Xiaofei Cao
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- Key Laboratory of Systems BiologyHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310013China
| | - Jinyang Zhang
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
| | - Wanying Wu
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
| | - Bing Zhang
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
| | - Fangqing Zhao
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
- Key Laboratory of Systems BiologyHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310013China
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming650223China
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Wang H, Zheng G. Circ-GGA3 promotes the biological functions of human lens epithelial cells depending on the regulation of miR-497-5p/SMAD4 axis. Biochem Biophys Res Commun 2021; 598:62-68. [PMID: 35151205 DOI: 10.1016/j.bbrc.2021.09.082] [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: 08/13/2021] [Revised: 09/17/2021] [Accepted: 09/30/2021] [Indexed: 11/25/2022]
Abstract
The cause of posterior capsular opacification (PCO) is the dysfunction of lens epithelial cells (LECs). Circular RNA (circRNA) was found to regulate cell biological functions, including LECs. However, the role of circ-GGA3 in PCO formation is unclear. Quantitative real-time PCR was used to measure the expression of circ-GGA3, miR-497-5p and SMAD4. Cell proliferation, invasion and migration were determined via MTT assay, EdU staining, transwell assay and wound healing assay. The protein expression of epithelial-mesenchymal transition (EMT) markers, fibrosis markers, TGF-β/SMAD pathway markers and SMAD4 were determined by western blot assay. The interaction between miR-497-5p and circ-GGA3 or SMAD4 was confirmed using dual-luciferase reporter assay. Circ-GGA3 was highly expressed in PCO patients, and its silencing inhibited the proliferation, invasion, migration, EMT process and fibrosis of TGF-β2-induced LECs. Circ-GGA3 could sponge miR-497-5p to regulate SMAD4. Further experiments revealed that miR-497-5p inhibitor recovered the negative regulation of circ-GGA3 knockdown on the biological functions of TGF-β2-induced LECs, and SMAD4 overexpression also abolished the suppressive effect of miR-497-5p. In addition, circ-GGA3/miR-497-5p/SMAD4 axis could activate the TGF-β/SMAD pathway. Our results indicated that circ-GGA3 could enhance the biological functions of LECs, suggesting that circ-GGA3 might be a potential target for PCO therapy.
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Affiliation(s)
- Huajun Wang
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou City, Henan Province, China
| | - Guangying Zheng
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou City, Henan Province, China.
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Yang Y, Lei W, Jiang S, Ding B, Wang C, Chen Y, Shi W, Wu Z, Tian Y. CircRNAs: Decrypting the novel targets of fibrosis and aging. Ageing Res Rev 2021; 70:101390. [PMID: 34118443 DOI: 10.1016/j.arr.2021.101390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Fibrosis is a typical aging-related pathological process involving almost all organs. It is usually initiated by organic injury and leads to the gradual decline of organ function or even loss. Circular RNAs (circRNAs) are being hailed as a newly rediscovered class of covalently closed transcripts without a 5' cap or 3' tail which draw increasing attention. In particular, circRNAs have been identified to be involved in the multifaceted processes of fibrosis in various organs, including the heart, liver, lung, and kidney. As more and more circRNAs are functionally characterized, they have become novel therapies for fibrosis. In this review, we systematically summarized current studies regarding the roles of circRNAs in fibrosis and shed light on the basis of circRNAs as a potential treatment for fibrosis.
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Sun H, Sun Y, Yu X, Gao X, Wang H, Zhang L, Shi Y, He X. Analysis of Age-Related Circular RNA Expression Profiles in Mesenchymal Stem Cells of Rat Bone Marrow. Front Genet 2021; 12:600632. [PMID: 34262589 PMCID: PMC8273880 DOI: 10.3389/fgene.2021.600632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 05/21/2021] [Indexed: 01/09/2023] Open
Abstract
As multicellular organisms age, they undergo a reduction in tissue and organ function. Researchers have put forward a theory that stem cell aging is the main factor responsible for decreased tissue and organ function. The adult stem cells guarantee the maintenance and repair of adult tissues and organs. Among adult stem cells, mesenchymal stem cells (MSCs) are emerging as hopeful candidates for cell-based therapy of numerous diseases. In recent years, high-throughput sequencing technologies have evolved to identify circular RNAs (circRNAs) associated with an increasing number of diseases, such as cancer and age-related diseases. It has been reported that circRNAs can compete with microRNAs (miRNAs) to affect the stability or translation of target RNAs and further regulate gene expression at the transcriptional level. However, the role of circRNAs expressed in MSCs in aging mechanisms has not yet been deciphered. The aim of this study was to explore and analyze the expression profiles of age-related circRNAs in MSCs. In this study, bone marrow MSCs were extracted from aged and young rats and analyzed using high-throughput sequencing and bioinformatics. The reliability of high-throughput RNA sequencing was verified by quantitative real-time polymerase chain reaction. The most important circRNA functions and pathways were further selected by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomics (KEGG) analysis. Age-related circRNAs were found in the circrNA-miRNA-mRNA interaction network. The results of high-throughput sequencing showed that 4,229 circRNAs were involved in age-related senescence of MSCs. Compared with the young group, there were 29 differentially expressed circRNAs in the aged group, of which four were upregulated and 25 were downregulated. GO analysis covered three domains: biological process (BP), cellular component (CC), and molecular function (MF). The terms assigned to the BP domain were cellular metabolic processes and cellular macromolecule metabolic processes. The identified CC terms were intracellular and intracellular part, and the identified MF terms were binding and protein binding. The top five KEGG pathways were mitophagy-animal-Rattus norvegicus, prostate cancer-Rattus norvegicus, pathways in cancer-Rattus norvegicus, lysosome-Rattus norvegicus, and autophagy-animal-Rattus norvegicus. Altogether, circRNAs may play a major role in age-related MSC senescence. This study provides new mechanistic insights into MSC senescence, possibly leading to novel therapeutic strategies for age-related diseases.
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Affiliation(s)
- Hui Sun
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Yanan Sun
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xiao Yu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xingyu Gao
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Huan Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Lin Zhang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Yingai Shi
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xu He
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
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Bai XF, Niu RZ, Liu J, Pan XD, Wang F, Yang W, Wang LQ, Sun LZ. Roles of noncoding RNAs in the initiation and progression of myocardial ischemia-reperfusion injury. Epigenomics 2021; 13:715-743. [PMID: 33858189 DOI: 10.2217/epi-2020-0359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The morbidity and mortality of myocardial ischemia-reperfusion injury (MIRI) have increased in modern society. Noncoding RNAs (ncRNAs), including lncRNAs, circRNAs, piRNAs and miRNAs, have been reported in a variety of studies to be involved in pathological initiation and developments of MIRI. Hence this review focuses on the current research regarding these ncRNAs in MIRI. We comprehensively introduce the important features of lncRNAs, circRNAs, piRNA and miRNAs and then summarize the published studies of ncRNAs in MIRI. A clarification of lncRNA-miRNA-mRNA, lncRNA-transcription factor-mRNA and circRNA-miRNA-mRNA axes in MIRI follows, to further elucidate the crucial roles of ncRNAs in MIRI. Bioinformatics analysis has revealed the biological correlation of mRNAs with MIRI. We provide a comprehensive perspective for the roles of these ncRNAs and their related networks in MIRI, providing a theoretical basis for preclinical and clinical studies on ncRNA-based gene therapy for MIRI treatment.
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Affiliation(s)
- Xiang-Feng Bai
- Department of Cardiovascular Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing 100029, China.,Department of Cardiovascular Surgery, First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China
| | - Rui-Ze Niu
- Department of Animal Zoology, Kunming Medical University, Kunming 650032, Yunnan, China
| | - Jia Liu
- Department of Animal Zoology, Kunming Medical University, Kunming 650032, Yunnan, China
| | - Xu-Dong Pan
- Department of Cardiovascular Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing 100029, China
| | - Feng Wang
- Department of Animal Zoology, Kunming Medical University, Kunming 650032, Yunnan, China
| | - Wei Yang
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China
| | - Lu-Qiao Wang
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China
| | - Li-Zhong Sun
- Department of Cardiovascular Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing 100029, China
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15
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Yan C, Xu Z, Huang W. Cellular Senescence Affects Cardiac Regeneration and Repair in Ischemic Heart Disease. Aging Dis 2021; 12:552-569. [PMID: 33815882 PMCID: PMC7990367 DOI: 10.14336/ad.2020.0811] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/11/2020] [Indexed: 01/10/2023] Open
Abstract
Ischemic heart disease (IHD) is defined as a syndrome of ischemic cardiomyopathy. Myogenesis and angiogenesis in the ischemic myocardium are important for cardiomyocyte (CM) survival, improving cardiac function and decreasing the progression of heart failure after IHD. Cellular senescence is a state of permanent irreversible cell cycle arrest caused by stress that results in a decline in cellular functions, such as proliferation, migration, homing, and differentiation. In addition, senescent cells produce the senescence-associated secretory phenotype (SASP), which affects the tissue microenvironment and surrounding cells by secreting proinflammatory cytokines, chemokines, growth factors, and extracellular matrix degradation proteins. The accumulation of cardiovascular-related senescent cells, including vascular endothelial cells (VECs), vascular smooth muscle cells (VSMCs), CMs and progenitor cells, is an important risk factor of cardiovascular diseases, such as vascular aging, atherosclerotic plaque formation, myocardial infarction (MI) and ventricular remodeling. This review summarizes the processes of angiogenesis, myogenesis and cellular senescence after IHD. In addition, this review focuses on the relationship between cellular senescence and cardiovascular disease and the mechanism of cellular senescence. Finally, we discuss a potential therapeutic strategy for MI targeting senescent cells.
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Affiliation(s)
- Chi Yan
- 1Department of Geriatric Cardiology, The First Affiliated Hospital of Guangxi Medical University, Guangxi, China.,2Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention, Guangxi, China.,3Department of Cardiology, Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Guangxi, China
| | - Zhimeng Xu
- 4Department of Cardiology, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi, China
| | - Weiqiang Huang
- 1Department of Geriatric Cardiology, The First Affiliated Hospital of Guangxi Medical University, Guangxi, China.,2Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention, Guangxi, China.,3Department of Cardiology, Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Guangxi, China
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16
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The exosome-like vesicles derived from androgen exposed-prostate stromal cells promote epithelial cells proliferation and epithelial-mesenchymal transition. Toxicol Appl Pharmacol 2020; 411:115384. [PMID: 33359661 DOI: 10.1016/j.taap.2020.115384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/21/2020] [Indexed: 12/17/2022]
Abstract
Benign prostatic hyperplasia (BPH) is an age-related disease in men. Mesenchymal /stromal and epithelial cells interactions are essential to prostate functions. In this study, human nonmalignant prostate epithelial RWPE-1 cells were cocultured with testosterone (TE) -exposed prostate stromal fibroblasts WPMY-1 cells (TE-WPMY-1). The survival rate, epithelial-mesenchymal transition (EMT) and collagen deposition of RWPE-1 were observed. The expression profiles of circRNAs, lncRNAs and mRNAs in WPMY-1-derived exosome-like vesicles (WPMY-1-exo) were explored by high-throughput RNA sequencing. Firstly, both TE-WPMY-1 and TE-WPMY-1-exo significantly promoted RWPE-1 cells proliferation. Secondly, 41 circRNAs, 132 lncRNAs and 1057 mRNAs were differentially expressed (DE) between TE-WPMY-1-exo and the control. Functional enrichment analyses, co-expression analyses and quantitative real-time PCR verification showed that the DE RNAs played important roles in cell proliferation, structure, phenotype and fibrosis. Lastly, blocking WPMY-1-exo biogenesis/release by GW4869 can attenuate TE-WPMY-1-stimulated RWPE-1 cells EMT and collagen deposition. Taken together, our results indicated that WPMY-1-exo modulated the phenotypes changes and collagen deposition of prostate epithelial cells. It provided a novel basis for understanding the underlying mechanisms of RWPE-1 cells EMT and fibrosis induced by WPMY-1 in BPH.
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17
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Bejugam PR, Das A, Panda AC. Seeing Is Believing: Visualizing Circular RNAs. Noncoding RNA 2020; 6:E45. [PMID: 33187156 PMCID: PMC7712394 DOI: 10.3390/ncrna6040045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023] Open
Abstract
Advancement in the RNA sequencing techniques has discovered hundreds of thousands of circular RNAs (circRNAs) in humans. However, the physiological function of most of the identified circRNAs remains unexplored. Recent studies have established that spliceosomal machinery and RNA-binding proteins modulate circRNA biogenesis. Furthermore, circRNAs have been implicated in regulating crucial cellular processes by interacting with various proteins and microRNAs. However, there are several challenges in understanding the mechanism of circRNA biogenesis, transport, and their interaction with cellular factors to regulate cellular events because of their low abundance and sequence similarity with linear RNA. Addressing these challenges requires systematic studies that directly visualize the circRNAs in cells at single-molecule resolution along with the molecular regulators. In this review, we present the design, benefits, and weaknesses of RNA imaging techniques such as single-molecule RNA fluorescence in situ hybridization and BaseScope in fixed cells and fluorescent RNA aptamers in live-cell imaging of circRNAs. Furthermore, we propose the potential use of molecular beacons, multiply labeled tetravalent RNA imaging probes, and Cas-derived systems to visualize circRNAs.
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Affiliation(s)
- Pruthvi Raj Bejugam
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India; (P.R.B.); (A.D.)
| | - Aniruddha Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India; (P.R.B.); (A.D.)
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Amaresh Chandra Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India; (P.R.B.); (A.D.)
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18
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Jin M, Shi C, Hua Q, Li T, Yang C, Wu Y, Zhao L, Yang H, Zhang J, Hu C, Huang G. High circ-SEC31A expression predicts unfavorable prognoses in non-small cell lung cancer by regulating the miR-520a-5p/GOT-2 axis. Aging (Albany NY) 2020; 12:10381-10397. [PMID: 32499446 PMCID: PMC7346017 DOI: 10.18632/aging.103264] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
Dysregulation of circular RNAs (circRNAs) has recently been shown to play important regulatory roles in cancer development and progression, including non-small cell lung cancer (NSCLC). However, the roles of most circRNAs in NSCLC are still unknown. In this study, we found that hsa_circ_0001421 (circ-SEC31A) was upregulated in NSCLC tissues and cell lines. Increased circ-SEC31A expression in NSCLC was significantly correlated with malignant characteristics and served as an independent risk factor for the post-surgical overall survival of NSCLC patients. Reduced circ-SEC31A expression in NSCLC decreased tumor cell proliferation, migration, invasion, and malate-aspartate metabolism. Mechanistically, we demonstrated that silencing circ-SEC31A downregulated GOT-2 expression by relieving the sponging effect of miR-520a-5p, which resulted in significantly reduced malate-aspartate metabolism in NSCLC cells. Taken together, these results revealed the important role of circ-SEC31A in the proliferation, migration, invasion, and metabolic regulation of NSCLC cells, providing a new perspective on circRNAs in NSCLC progression.
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Affiliation(s)
- Mingming Jin
- Shanghai University of Traditional Chinese Medicine, Shanghai University of Medicine and Health Sciences, Shanghai 201203, P.R. China.,Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, P.R. China
| | - Chunzi Shi
- Shanghai University of Traditional Chinese Medicine, Shanghai University of Medicine and Health Sciences, Shanghai 201203, P.R. China.,Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, P.R. China
| | - Qian Hua
- Department of Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200127, China
| | - Tian Li
- Shanghai University of Traditional Chinese Medicine, Shanghai University of Medicine and Health Sciences, Shanghai 201203, P.R. China.,Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, P.R. China
| | - Chen Yang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Yue Wu
- Shanghai University of Traditional Chinese Medicine, Shanghai University of Medicine and Health Sciences, Shanghai 201203, P.R. China.,Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, P.R. China
| | - Licong Zhao
- China Medical University, Shenyang 110011, Liaoning, China
| | - Hao Yang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, P.R. China
| | - Jiaqi Zhang
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Cheng Hu
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Gang Huang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, P.R. China.,Department of Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200127, China
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19
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Pandey PR, Yang JH, Tsitsipatis D, Panda AC, Noh JH, Kim KM, Munk R, Nicholson T, Hanniford D, Argibay D, Yang X, Martindale JL, Chang MW, Jones SW, Hernando E, Sen P, De S, Abdelmohsen K, Gorospe M. circSamd4 represses myogenic transcriptional activity of PUR proteins. Nucleic Acids Res 2020; 48:3789-3805. [PMID: 31980816 PMCID: PMC7144931 DOI: 10.1093/nar/gkaa035] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 02/02/2023] Open
Abstract
By interacting with proteins and nucleic acids, the vast family of mammalian circRNAs is proposed to influence many biological processes. Here, RNA sequencing analysis of circRNAs differentially expressed during myogenesis revealed that circSamd4 expression increased robustly in mouse C2C12 myoblasts differentiating into myotubes. Moreover, silencing circSamd4, which is conserved between human and mouse, delayed myogenesis and lowered the expression of myogenic markers in cultured myoblasts from both species. Affinity pulldown followed by mass spectrometry revealed that circSamd4 associated with PURA and PURB, two repressors of myogenesis that inhibit transcription of the myosin heavy chain (MHC) protein family. Supporting the hypothesis that circSamd4 might complex with PUR proteins and thereby prevent their interaction with DNA, silencing circSamd4 enhanced the association of PUR proteins with the Mhc promoter, while overexpressing circSamd4 interfered with the binding of PUR proteins to the Mhc promoter. These effects were abrogated when using a mutant circSamd4 lacking the PUR binding site. Our results indicate that the association of PUR proteins with circSamd4 enhances myogenesis by contributing to the derepression of MHC transcription.
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Affiliation(s)
- Poonam R Pandey
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jen-Hao Yang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Ji Heon Noh
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, Republic of Korea
| | - Kyoung Mi Kim
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Thomas Nicholson
- Institute of Inflammation and Ageing, MRC-ARUK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, UK
| | - Douglas Hanniford
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Diana Argibay
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Xiaoling Yang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ming-Wen Chang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Simon W Jones
- Institute of Inflammation and Ageing, MRC-ARUK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, UK
| | - Eva Hernando
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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20
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Identification and characterization of circular RNAs in atrial appendage of patients with atrial fibrillation. Exp Cell Res 2020; 389:111821. [PMID: 31923425 DOI: 10.1016/j.yexcr.2020.111821] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/28/2019] [Accepted: 01/06/2020] [Indexed: 02/06/2023]
Abstract
Circular RNAs (circRNAs) have emerged as a novel type of non-coding RNA (ncRNA) of interest in gene regulation, especially for its vital function underlying many diseases. Atrial fibrillation is the most common sustained arrythmia. However, the expression spectrum and function of circRNAs in atrial appendage of patients with atrial fibrillation (AF) has seldomly been investigated. Human atrial appendage tissues were acquired during cardiac surgery, which were divided into the AF group and the Sinus rhythm (SR) group. The expression characterization of circRNAs of two groups was revealed by high-throughput sequencing. The dysregulated circRNAs were identified and analyzed by bioinformatics methods, and further validated by realtime PCR. A total 18109 circRNAs in human atrial appendage tissues were targeted. Among them, 147 differentially expressed circRNAs (102 up-regulated and 45 down-regulated) were found between AF group and SR group. Gene ontology (GO) and KEGG pathway analysis indicated that many mRNAs transcribed from the host genes of altered circRNAs were implicated in regulation of sequence-specific DNA binding transcription factor activity, as well as nicotinate and nicotinamide metabolism pathways. Analysis of the association between differently expressed circRNA and miRNA were explored, which revealed an ample interaction. Our study firstly revealed the expression spectrum of circRNAs in both left and right atrial appendage of patients with or without AF. Differentially expressed circRNAs in the atrial appendage were also identified, analyzed and validated. The results of this study may provide novel biomarkers and potential therapeutic targets for AF.
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21
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The Epigenetics of Aging in Invertebrates. Int J Mol Sci 2019; 20:ijms20184535. [PMID: 31540238 PMCID: PMC6769462 DOI: 10.3390/ijms20184535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/03/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022] Open
Abstract
Aging is an unstoppable process coupled to the loss of physiological function and increased susceptibility to diseases. Epigenetic alteration is one of the hallmarks of aging, which involves changes in DNA methylation patterns, post-translational modification of histones, chromatin remodeling and non-coding RNA interference. Invertebrate model organisms, such as Drosophila melanogaster and Caenorhabditis elegans, have been used to investigate the biological mechanisms of aging because they show, evolutionarily, the conservation of many aspects of aging. In this review, we focus on recent advances in the epigenetic changes of aging with invertebrate models, providing insight into the relationship between epigenetic dynamics and aging.
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22
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Pandey PR, Munk R, Kundu G, De S, Abdelmohsen K, Gorospe M. Methods for analysis of circular RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1566. [PMID: 31489773 DOI: 10.1002/wrna.1566] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/11/2019] [Accepted: 08/13/2019] [Indexed: 12/26/2022]
Abstract
Eukaryotic cells express a myriad of circular RNAs (circRNAs), many of them displaying tissue-specific expression patterns. They arise from linear precursor RNAs in which 5' and 3' ends become covalently ligated. Given these features, biochemical and computational approaches traditionally used to study linear RNA must be adapted for analysis of circular RNAs. Such circRNA-specific methodologies are allowing the systematic identification of circRNAs and the analysis of their biological functions. Here, we review the resources and molecular methods currently utilized to quantify circRNAs, visualize their distribution, identify interacting partners, and elucidate their function. We discuss the challenges of analyzing circRNAs and propose alternative approaches for studying this unique class of transcripts. This article is characterized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Methods > RNA Analyses in vitro and In Silico RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Poonam R Pandey
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Gautam Kundu
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
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23
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Kim SS, Lee SJV. Non-Coding RNAs in Caenorhabditis elegans Aging. Mol Cells 2019; 42:379-385. [PMID: 31094164 PMCID: PMC6537654 DOI: 10.14348/molcells.2019.0077] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 04/29/2019] [Indexed: 01/04/2023] Open
Abstract
Non-coding RNAs (ncRNAs) comprise various RNA species, including small ncRNAs and long ncRNAs (lncRNAs). ncRNAs regulate various cellular processes, including transcription and translation of target messenger RNAs. Recent studies also indicate that ncRNAs affect organismal aging and conversely aging influences ncRNA levels. In this review, we discuss our current understanding of the roles of ncRNAs in aging and longevity, focusing on recent advances using the roundworm Caenorhabditis elegans. Expression of various ncRNAs, including microRNA (miRNA), tRNA-derived small RNA (tsRNA), ribosomal RNA (rRNA), PIWI-interacting RNA (piRNA), circular RNA (circRNA), and lncRNA, is altered during aging in C. elegans. Genetic modulation of specific ncRNAs affects longevity and aging rates by modulating established aging-regulating protein factors. Because many aging-regulating mechanisms in C. elegans are evolutionarily conserved, these studies will provide key information regarding how ncRNAs modulate aging and lifespan in complex organisms, including mammals.
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Affiliation(s)
- Sieun S. Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Seung-Jae V. Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141,
Korea
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24
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Prenatal hypoxia affected endothelium-dependent vasodilation in mesenteric arteries of aged offspring via increased oxidative stress. Hypertens Res 2019; 42:863-875. [DOI: 10.1038/s41440-018-0181-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 12/27/2022]
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