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Zhou T, Li Z, Jiang Y, Su K, Xu C, Yi H. Emerging roles of circular RNAs in regulating the hallmarks of thyroid cancer. Cancer Gene Ther 2024; 31:507-516. [PMID: 38316961 PMCID: PMC11016468 DOI: 10.1038/s41417-024-00736-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 02/07/2024]
Abstract
Thyroid cancer is a prevalent endocrine malignancy with increasing incidence in recent years. Although most thyroid cancers grow slowly, they can become refractory, leading to a high mortality rate once they exhibit recurrence, metastasis, resistance to radioiodine therapy, or a lack of differentiation. However, the mechanisms underlying these malignant characteristics remain unclear. Circular RNAs, a type of closed-loop non-coding RNAs, play multiple roles in cancer. Several studies have demonstrated that circular RNAs significantly influence the development of thyroid cancers. In this review, we summarize the circular RNAs identified in thyroid cancers over the past decade according to the hallmarks of cancer. We found that eight of the 14 hallmarks of thyroid cancers are regulated by circular RNAs, whereas the other six have not been reported to be correlated with circular RNAs. This review is expected to help us better understand the roles of circular RNAs in thyroid cancers and accelerate research on the mechanisms and cure strategies for thyroid cancers.
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Affiliation(s)
- Tianjiao Zhou
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, 200233, China
- Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai, 200233, China
| | - Zheng Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yumeng Jiang
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, 200233, China
- Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai, 200233, China
| | - Kaiming Su
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, 200233, China
- Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai, 200233, China
| | - Chuan Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Hongliang Yi
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, 200233, China.
- Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai, 200233, China.
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2
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Ali I, Zhang H, Zaidi SAA, Zhou G. Understanding the intricacies of cellular senescence in atherosclerosis: Mechanisms and therapeutic implications. Ageing Res Rev 2024; 96:102273. [PMID: 38492810 DOI: 10.1016/j.arr.2024.102273] [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: 11/14/2023] [Revised: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
Cardiovascular disease is currently the largest cause of mortality and disability globally, surpassing communicable diseases, and atherosclerosis is the main contributor to this epidemic. Aging is intimately linked to atherosclerosis development and progression, however, the mechanism of aging in atherosclerosis is not well known. To emphasize the significant research on the involvement of senescent cells in atherosclerosis, we begin by outlining compelling evidence that indicates various types of senescent cells and SASP factors linked to atherosclerotic phenotypes. We subsequently provide a comprehensive summary of the existing knowledge, shedding light on the intricate mechanisms through which cellular senescence contributes to the pathogenesis of atherosclerosis. Further, we cover that senescence can be identified by both structural changes and several senescence-associated biomarkers. Finally, we discuss that preventing accelerated cellular senescence represents an important therapeutic potential, as permanent changes may occur in advanced atherosclerosis. Together, the review summarizes the relationship between cellular senescence and atherosclerosis, and inspects the molecular knowledge, and potential clinical significance of senescent cells in developing senescent-based therapy, thus providing crucial insights into their biology and potential therapeutic exploration.
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Affiliation(s)
- Ilyas Ali
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, PR China
| | - Hongliang Zhang
- Shenzhen University General Hospital, Shenzhen University, Shenzhen 518060, PR China
| | - Syed Aqib Ali Zaidi
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China
| | - Guangqian Zhou
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, PR China.
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3
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Dhandhanya UK, Mukhopadhyay K, Kumar M. An accretive detection method for in silico identification and validation of circular RNAs in wheat (Triticum aestivum L.) using RT-qPCR. Mol Biol Rep 2024; 51:162. [PMID: 38252357 DOI: 10.1007/s11033-023-09138-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Circular RNAs (circRNAs) are novel class of non-coding RNAs, which are involved in various functions at the transcriptional and post-transcriptional level in response to a fungal pathogen (Puccinia triticina), including microRNA (miRNA) sponge, RNA binding proteins sponge, regulation of parental gene and biomarkers. Detailed analysis of wheat circRNAs is essential to accelerate the regulated expression of fungal miRNAs. Therefore, we suggest a protocol to aid circRNA identification through RNA-Seq data using various algorithms based on perl script followed by validation through divergent primer designing, standard PCR, and RT-qPCR assays. METHODS AND RESULT The divergent primer has been widely used to detect, validate, and quantify back-spliced junction (BSJ) of circRNAs. The procedure covers index file formation, circRNA identification and BSJ detections. However, the laboratory validation of circRNA includes wheat genomic DNA isolation, RNA isolation and its cDNA conversion upto validation. In this study, we identified 28 circRNAs from RNA-Seq of S0 and R0, wherein six circRNAs are commonly present and 75% of the identified circRNAs were belongs to inter-genic, 14% were exonic and intronic category were 11%. Divergent primer designing method successfully validated the two circRNAs via RT-qPCR assay, where circRNA_2 showed less relative expression pattern than circRNA_1 in contrast with housekeeping genes. CONCLUSION Thus, our results of identified and validated circRNAs showed that, this protocol is quite helpful, relatively easy, reliable, and accurate for large datasets as other algorithms need various dependencies and have complex scripts with high chances of error occurrence. Additionally, analysis time will vary depending on the expertise level and the number of RNA-Seq data. This proposed protocol can also be used for a wide range of monocotyledons belonging to the Poaceae plant family.
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Affiliation(s)
- Umang Kumar Dhandhanya
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kunal Mukhopadhyay
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Manish Kumar
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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4
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Zhao X, van den Berg A, Winkle M, Koerts J, Seitz A, de Jong D, Rutgers B, van der Sluis T, Bakker E, Kluiver J. Proliferation-promoting roles of linear and circular PVT1 are independent of their ability to bind miRNAs in B-cell lymphoma. Int J Biol Macromol 2023; 253:126744. [PMID: 37689284 DOI: 10.1016/j.ijbiomac.2023.126744] [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: 05/03/2023] [Revised: 08/01/2023] [Accepted: 08/27/2023] [Indexed: 09/11/2023]
Abstract
Plasmacytoma Variant Translocation 1 (PVT1) is a long non-coding RNA located at 8q24.21 immediately downstream of MYC. Both the linear and circular PVT1 transcripts contribute to cancer pathogenesis by binding microRNAs. However, little is known about their roles in B-cell lymphoma. Here we studied their expression patterns, role in growth, and ability to bind miRNAs in B-cell lymphoma. Linear PVT1 transcripts were downregulated in B-cell cell lymphoma lines compared to germinal center B cells, while circPVT1 levels were increased. Two Hodgkin lymphoma cell lines had a homozygous deletion including the 5' region of the PVT1 locus, resulting in a complete lack of circPVT1 and 5' linear PVT1 transcripts. Inhibition of both linear and circular PVT1 decreased growth of Burkitt lymphoma, while the effects on Hodgkin lymphoma and diffuse large B cell lymphoma were less pronounced. Overexpression of circPVT1 promoted growth of B-cell lymphoma lacking or having low endogenous circPVT1 levels. Contrary to other types of cancer, linear and circular PVT1 transcripts did not interact with miRNAs in B-cell lymphoma. Overall, we showed an opposite expression pattern of linear and circular PVT1 in B-cell lymphoma. Their effect on growth was independent of their ability to bind miRNAs.
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Affiliation(s)
- Xing Zhao
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands.
| | - Melanie Winkle
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Jasper Koerts
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Annika Seitz
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Debora de Jong
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Bea Rutgers
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Tineke van der Sluis
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Emke Bakker
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands.
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Madè A, Bibi A, Garcia-Manteiga JM, Tascini AS, Piella SN, Tikhomirov R, Voellenkle C, Gaetano C, Leszek P, Castelvecchio S, Menicanti L, Martelli F, Greco S. circRNA-miRNA-mRNA Deregulated Network in Ischemic Heart Failure Patients. Cells 2023; 12:2578. [PMID: 37947656 PMCID: PMC10648415 DOI: 10.3390/cells12212578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Noncoding RNAs (ncRNAs), which include circular RNAs (circRNAs) and microRNAs (miRNAs), regulate the development of cardiovascular diseases (CVD). Notably, circRNAs can interact with miRNAs, influencing their specific mRNA targets' levels and shaping a competing endogenous RNAs (ceRNA) network. However, these interactions and their respective functions remain largely unexplored in ischemic heart failure (IHF). This study is aimed at identifying circRNA-centered ceRNA networks in non-end-stage IHF. Approximately 662 circRNA-miRNA-mRNA interactions were identified in the heart by combining state-of-the-art bioinformatics tools with experimental data. Importantly, KEGG terms of the enriched mRNA indicated CVD-related signaling pathways. A specific network centered on circBPTF was validated experimentally. The levels of let-7a-5p, miR-18a-3p, miR-146b-5p, and miR-196b-5p were enriched in circBPTF pull-down experiments, and circBPTF silencing inhibited the expression of HDAC9 and LRRC17, which are targets of miR-196b-5p. Furthermore, as suggested by the enriched pathway terms of the circBPTF ceRNA network, circBPTF inhibition elicited endothelial cell cycle arrest. circBPTF expression increased in endothelial cells exposed to hypoxia, and its upregulation was confirmed in cardiac samples of 36 end-stage IHF patients compared to healthy controls. In conclusion, circRNAs act as miRNA sponges, regulating the functions of multiple mRNA targets, thus providing a novel vision of HF pathogenesis and laying the theoretical foundation for further experimental studies.
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Affiliation(s)
- Alisia Madè
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Alessia Bibi
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
- Department of Biosciences, University of Milan, 20122 Milan, Italy
| | - Jose Manuel Garcia-Manteiga
- Center for Omics Sciences COSR, BioInformatics Laboratory, San Raffaele Scientific Institute, 20132 Milan, Italy; (J.M.G.-M.); (A.S.T.)
| | - Anna Sofia Tascini
- Center for Omics Sciences COSR, BioInformatics Laboratory, San Raffaele Scientific Institute, 20132 Milan, Italy; (J.M.G.-M.); (A.S.T.)
- Università Vita-Salute San Raffaele, 20132 Milan, Italy
| | - Santiago Nicolas Piella
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Roman Tikhomirov
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Christine Voellenkle
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Carlo Gaetano
- Laboratory of Epigenetics, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy;
| | - Przemyslaw Leszek
- Department of Heart Failure and Transplantology, National Institute of Cardiology, 04-628 Warsaw, Poland;
| | - Serenella Castelvecchio
- Department of Adult Cardiac Surgery, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (S.C.); (L.M.)
| | - Lorenzo Menicanti
- Department of Adult Cardiac Surgery, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (S.C.); (L.M.)
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Simona Greco
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
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Derakhshan Z, Bahmanpour S, Alaee S, Fallahi J, Tabei SMB. The Role of Circular RNAs in Male Infertility and Reproductive Cancers: A Narrative Review. IRANIAN JOURNAL OF MEDICAL SCIENCES 2023; 48:527-541. [PMID: 38094281 PMCID: PMC10715113 DOI: 10.30476/ijms.2022.95302.2661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/01/2022] [Accepted: 08/28/2022] [Indexed: 12/18/2023]
Abstract
Infertility is a global health problem affecting about 15% of all couples, of which 50% are due to male infertility. Although the etiology of infertility is known in most infertile men, idiopathic male infertility remains a challenge. Therefore, there is a need for novel diagnostic methods to detect the underlying mechanisms and develop appropriate therapies. Recent studies have focused on the role of non-coding RNAs (ncRNAs) in male infertility. Circular RNAs (CircRNAs), a type of ncRNAs, are found to play a key role in the development of some pathological conditions, including cardiovascular diseases, diabetes, cancers, autoimmune diseases, etc. Several studies have reported the presence of CircRNAs and their target genes in the human reproductive system. In addition, their expression in testicular tissues, sperm cells, and seminal fluid has been identified. Abnormal expression of CircRNAs has been associated with azoospermia and asthenozoospermia in infertile men. The present narrative review provides a brief description of the role of CircRNAs in spermatogenic cells, male infertility, and reproductive cancers. In addition, some CircRNAs have been identified as potential biomarkers for disease detection and treatment.
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Affiliation(s)
- Zahra Derakhshan
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Soghra Bahmanpour
- Department of Anatomy and Reproductive Biology, School of Medical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sanaz Alaee
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jafar Fallahi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Bagher Tabei
- Department of Medical Genetics, School of Medical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
- Maternal-Fetal Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Singh S, Sinha T, Panda AC. Regulation of microRNA by circular RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1820. [PMID: 37783567 DOI: 10.1002/wrna.1820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/04/2023]
Abstract
Circular (circ)RNAs have emerged as novel regulators of gene expression through various mechanisms. However, most publications focus on functional circRNAs regulating target gene expression by interacting with micro (mi)RNAs and acting as competing endogenous RNAs (ceRNAs). Although the theory of miRNA sponging by ceRNAs suggests the inhibition of miRNA activity, many studies are biased toward the selection of miRNAs showing a reverse expression pattern compared with circRNA expression. Although several computational tools and molecular assays have been used to predict and validate the interaction of miRNAs with circRNAs, the actual validation of functional in vivo interactions needs careful consideration of molecular experiments with specific controls. As extensive research is being performed on circRNA, many questions arise on the functional significance of circRNA-miRNA interactions. We hope the critical discussion on the criteria for selecting circRNA-miRNA pairs for functional analysis and providing standard methods for validating circRNA-miRNA interactions will advance our understanding of circRNAs as novel gene regulators. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Translation > Regulation RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Suman Singh
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Tanvi Sinha
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
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8
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Li Q, Lin M, Xie Y, Zhang J, Lai W. Research on Circular RNA Expression Profiles in the Photoaging Mouse Model. IRANIAN JOURNAL OF BIOTECHNOLOGY 2023; 21:e3445. [PMID: 38269201 PMCID: PMC10804062 DOI: 10.30498/ijb.2023.351439.3445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/12/2023] [Indexed: 01/26/2024]
Abstract
Background Nude mouse has been widely used to study photoaging induced by long-term chronic UV exposure. Circular RNAs (circRNAs) have been previously identified in several diseases. However, the roles of circRNAs in photoaging and potential regulatory mechanisms remain unclear. Objectives To identify specific circRNAs differentially expressed in photoaged skin and investigate their potential role in aging. Materials and Methods In this study, we screened out the microarray data to profile the expression of circRNAs. The circRNAs were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway. Results 36 circRNAs were identified to be differentially expressed between the UV group and control group (fold change > 1.5; P < 0.05), including 6 upregulated and 30 downregulated circRNAs. GO and KEGG biological pathway analyses indicated that the changes in circRNAs were associated with cancer, inflammation, oxidative stress, and metabolism. Conclusions This present study revealed a circRNAs expression profiling in vivo. These findings not only provide a new possibility to prevent the occurrence of photoaging but also have therapeutic values for photoaging and associated skin diseases.
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Affiliation(s)
- Qian Li
- Department of Dermatology and Venereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Mengbi Lin
- Department of Dermatology and Venereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Yalin Xie
- Department of Dermatology and Venereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Jie Zhang
- Department of Dermatology and Venereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Wei Lai
- Department of Dermatology and Venereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
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9
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Kong Y, Luo Y, Zheng S, Yang J, Zhang D, Zhao Y, Zheng H, An M, Lin Y, Ai L, Diao X, Lin Q, Chen C, Chen R. Mutant KRAS Mediates circARFGEF2 Biogenesis to Promote Lymphatic Metastasis of Pancreatic Ductal Adenocarcinoma. Cancer Res 2023; 83:3077-3094. [PMID: 37363990 PMCID: PMC10502454 DOI: 10.1158/0008-5472.can-22-3997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/05/2023] [Accepted: 06/21/2023] [Indexed: 06/28/2023]
Abstract
Circular RNAs (circRNA) contribute to cancer stemness, proliferation, and metastasis. The biogenesis of circRNAs can be impacted by the genetic landscape of tumors. Herein, we identified a novel circRNA, circARFGEF2 (hsa_circ_0060665), which was upregulated in KRASG12D pancreatic ductal adenocarcinoma (PDAC) and positively associated with KRASG12D PDAC lymph node (LN) metastasis. CircARFGEF2 overexpression significantly facilitated KRASG12D PDAC LN metastasis in vitro and in vivo. Mechanistically, circARFGEF2 biogenesis in KRASG12D PDAC was significantly activated by the alternative splicing factor QKI-5, which recruited U2AF35 to facilitate spliceosome assembly. QKI-5 bound the QKI binding motifs and neighboring reverse complement sequence in intron 3 and 6 of ARFGEF2 pre-mRNA to facilitate circARFGEF2 biogenesis. CircARFGEF2 sponged miR-1205 and promoted the activation of JAK2, which phosphorylated STAT3 to trigger KRASG12D PDAC lymphangiogenesis and LN metastasis. Importantly, circARFGEF2 silencing significantly inhibited LN metastasis in the KrasG12D/+Trp53R172H/+Pdx-1-Cre (KPC) mouse PDAC model. These findings provide insight into the mechanism and metastasis-promoting function of mutant KRAS-mediated circRNA biogenesis. SIGNIFICANCE Increased splicing-mediated biogenesis of circARFGEF2 in KRAS-mutant pancreatic ductal adenocarcinoma activates JAK2-STAT3 signaling and triggers lymph node metastasis, suggesting circARFGEF2 could be a therapeutic target to inhibit pancreatic cancer progression.
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Affiliation(s)
- Yao Kong
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, P.R. China
| | - Yuming Luo
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Shangyou Zheng
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Jiabin Yang
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, P.R. China
| | - Dingwen Zhang
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, P.R. China
| | - Yue Zhao
- Department of Tumor Intervention, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, P.R. China
| | - Hanhao Zheng
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
| | - Mingjie An
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
| | - Yan Lin
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
| | - Le Ai
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xiayao Diao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Qing Lin
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Changhao Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
| | - Rufu Chen
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, P.R. China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
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10
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Qiao LJ, Gao Z, Ji CM, Liu ZH, Zheng CH, Wang YT. Potential circRNA-Disease Association Prediction Using DeepWalk and Nonnegative Matrix Factorization. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:3154-3162. [PMID: 37018084 DOI: 10.1109/tcbb.2023.3264466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Circular RNAs (circRNAs) are a category of noncoding RNAs that exist in great numbers in eukaryotes. They have recently been discovered to be crucial in the growth of tumors. Therefore, it is important to explore the association of circRNAs with disease. This paper proposes a new method based on DeepWalk and nonnegative matrix factorization (DWNMF) to predict circRNA-disease association. Based on the known circRNA-disease association, we calculate the topological similarity of circRNA and disease via the DeepWalk-based method to learn the node features on the association network. Next, the functional similarity of the circRNAs and the semantic similarity of the diseases are fused with their respective topological similarities at different scales. Then, we use the improved weighted K-nearest neighbor (IWKNN) method to preprocess the circRNA-disease association network and correct nonnegative associations by setting different parameters K1 and K2 in the circRNA and disease matrices. Finally, the L2,1-norm, dual-graph regularization term and Frobenius norm regularization term are introduced into the nonnegative matrix factorization model to predict the circRNA-disease correlation. We perform cross-validation on circR2Disease, circRNADisease, and MNDR. The numerical results show that DWNMF is an efficient tool for forecasting potential circRNA-disease relationships, outperforming other state-of-the-art approaches in terms of predictive performance.
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11
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Barbagallo C, Stella M, Ferrara C, Caponnetto A, Battaglia R, Barbagallo D, Di Pietro C, Ragusa M. RNA-RNA competitive interactions: a molecular civil war ruling cell physiology and diseases. EXPLORATION OF MEDICINE 2023:504-540. [DOI: 10.37349/emed.2023.00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
The idea that proteins are the main determining factors in the functioning of cells and organisms, and their dysfunctions are the first cause of pathologies, has been predominant in biology and biomedicine until recently. This protein-centered view was too simplistic and failed to explain the physiological and pathological complexity of the cell. About 80% of the human genome is dynamically and pervasively transcribed, mostly as non-protein-coding RNAs (ncRNAs), which competitively interact with each other and with coding RNAs generating a complex RNA network regulating RNA processing, stability, and translation and, accordingly, fine-tuning the gene expression of the cells. Qualitative and quantitative dysregulations of RNA-RNA interaction networks are strongly involved in the onset and progression of many pathologies, including cancers and degenerative diseases. This review will summarize the RNA species involved in the competitive endogenous RNA network, their mechanisms of action, and involvement in pathological phenotypes. Moreover, it will give an overview of the most advanced experimental and computational methods to dissect and rebuild RNA networks.
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Affiliation(s)
- Cristina Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Michele Stella
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | | | - Angela Caponnetto
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Rosalia Battaglia
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
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12
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Xing J, Zhang M, Zhao S, Lu M, Lin L, Chen L, Gao W, Li W, Shang J, Zhou J, Zhu X. EIF4A3-Induced Exosomal circLRRC8A Alleviates Granulosa Cells Senescence Via the miR-125a-3p/NFE2L1 axis. Stem Cell Rev Rep 2023:10.1007/s12015-023-10564-8. [PMID: 37243831 PMCID: PMC10390409 DOI: 10.1007/s12015-023-10564-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 05/29/2023]
Abstract
Premature ovarian failure (POF) is an important cause of female infertility and seriously impacts the physical and psychological health of patients. Mesenchymal stromal cells-derived exosomes (MSCs-Exos) have an essential role in the treatment of reproductive disorders, particularly POF. However, the biological function and therapeutic mechanism of MSCs exosomal circRNAs in POF remain to be determined. Here, with bioinformatics analysis and functional assays, circLRRC8A was found to be downregulated in senescent granulosa cells (GCs) and acted as a crucial factor in MSCs-Exos for oxidative damage protection and anti-senescence of GCs in vitro and in vivo. Mechanistic investigations revealed that circLRRC8A served as an endogenous miR-125a-3p sponge to downregulate NFE2L1 expression. Moreover, eukaryotic initiation factor 4A3 (EIF4A3), acting as a pre-mRNA splicing factor, promoted circLRRC8A cyclization and expression by directly binding to the LRRC8A mRNA transcript. Notably, EIF4A3 silencing reduced circLRRC8A expression and attenuated the therapeutic effect of MSCs-Exos on oxidatively damaged GCs. This study demonstrates a new therapeutic pathway for cellular senescence protection against oxidative damage by delivering circLRRC8A-enriched exosomes through the circLRRC8A/miR-125a-3p/NFE2L1 axis and paves the way for the establishment of a cell-free therapeutic approach for POF. CircLRRC8A may be a promising circulating biomarker for diagnosis and prognosis and an exceptional candidate for further therapeutic exploration.
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Affiliation(s)
- Jie Xing
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Mengxue Zhang
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Shijie Zhao
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Mingjun Lu
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Li Lin
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lu Chen
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Wujiang Gao
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Wenxin Li
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Junyu Shang
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Jiamin Zhou
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiaolan Zhu
- Reproductive Medicine Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.
- Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China.
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13
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Hosaka T, Tsuji H, Kwak S. Roles of Aging, Circular RNAs, and RNA Editing in the Pathogenesis of Amyotrophic Lateral Sclerosis: Potential Biomarkers and Therapeutic Targets. Cells 2023; 12:1443. [PMID: 37408276 DOI: 10.3390/cells12101443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 07/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable motor neuron disease caused by upper and lower motor neuron death. Despite advances in our understanding of ALS pathogenesis, effective treatment for this fatal disease remains elusive. As aging is a major risk factor for ALS, age-related molecular changes may provide clues for the development of new therapeutic strategies. Dysregulation of age-dependent RNA metabolism plays a pivotal role in the pathogenesis of ALS. In addition, failure of RNA editing at the glutamine/arginine (Q/R) site of GluA2 mRNA causes excitotoxicity due to excessive Ca2+ influx through Ca2+-permeable α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors, which is recognized as an underlying mechanism of motor neuron death in ALS. Circular RNAs (circRNAs), a circular form of cognate RNA generated by back-splicing, are abundant in the brain and accumulate with age. Hence, they are assumed to play a role in neurodegeneration. Emerging evidence has demonstrated that age-related dysregulation of RNA editing and changes in circRNA expression are involved in ALS pathogenesis. Herein, we review the potential associations between age-dependent changes in circRNAs and RNA editing, and discuss the possibility of developing new therapies and biomarkers for ALS based on age-related changes in circRNAs and dysregulation of RNA editing.
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Affiliation(s)
- Takashi Hosaka
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
- University of Tsukuba Hospital/Jichi Medical University Joint Ibaraki Western Regional Clinical Education Center, Chikusei 308-0813, Japan
- Department of Internal Medicine, Ibaraki Western Medical Center, Chikusei 308-0813, Japan
| | - Hiroshi Tsuji
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Shin Kwak
- Department of Neurology, Tokyo Medical University, Tokyo 160-0023, Japan
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Yi J, Wang L, Hu G, Zhang Y, Du J, Ding J, Ji X, Shen H, Huang H, Ye F, Liu W. CircPVT1 promotes ER-positive breast tumorigenesis and drug resistance by targeting ESR1 and MAVS. EMBO J 2023; 42:e112408. [PMID: 37009655 PMCID: PMC10183818 DOI: 10.15252/embj.2022112408] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 02/06/2023] [Accepted: 03/02/2023] [Indexed: 04/04/2023] Open
Abstract
The molecular mechanisms underlying estrogen receptor (ER)-positive breast carcinogenesis and endocrine therapy resistance remain incompletely understood. Here, we report that circPVT1, a circular RNA generated from the lncRNA PVT1, is highly expressed in ERα-positive breast cancer cell lines and tumor samples and is functionally important in promoting ERα-positive breast tumorigenesis and endocrine therapy resistance. CircPVT1 acts as a competing endogenous RNA (ceRNA) to sponge miR-181a-2-3p, promoting the expression of ESR1 and downstream ERα-target genes and breast cancer cell growth. Furthermore, circPVT1 directly interacts with MAVS protein to disrupt the RIGI-MAVS complex formation, inhibiting type I interferon (IFN) signaling pathway and anti-tumor immunity. Anti-sense oligonucleotide (ASO)-targeting circPVT1 inhibits ERα-positive breast cancer cell and tumor growth, re-sensitizing tamoxifen-resistant ERα-positive breast cancer cells to tamoxifen treatment. Taken together, our data demonstrated that circPVT1 can work through both ceRNA and protein scaffolding mechanisms to promote cancer. Thus, circPVT1 may serve as a diagnostic biomarker and therapeutic target for ERα-positive breast cancer in the clinic.
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Affiliation(s)
- Jia Yi
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation ResearchThe First Affiliated Hospital of Xiamen UniversityXiamenChina
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Lei Wang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Guo‐sheng Hu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Yue‐ying Zhang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Jiao Du
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Jian‐cheng Ding
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Xiang Ji
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Hai‐feng Shen
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Hai‐hua Huang
- Department of Pathology, The Second Affiliated HospitalShantou University Medical CollegeShantouChina
| | - Feng Ye
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation ResearchThe First Affiliated Hospital of Xiamen UniversityXiamenChina
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical SciencesXiamen UniversityXiamenChina
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15
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Tang H, Xiong Q, Yin M, Feng H, Yao F, Xiao X, Hu F, Liao Y. LncRNA PVT1 delays skin photoaging by sequestering miR-551b-3p to release AQP3 expression via ceRNA mechanism. Apoptosis 2023; 28:912-924. [PMID: 37000315 DOI: 10.1007/s10495-023-01834-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2023] [Indexed: 04/01/2023]
Abstract
Understanding human skin photoaging requires in-depth knowledge of the molecular and functional mechanisms. Human dermal fibroblasts (HDFs) gradually lose their ability to produce collagen and renew intercellular matrix with aging. Therefore, our study aims to reveal the mechanistic actions of a novel ceRNA network in the skin photoaging by regulating HDF activities. Photoaging-related genes were obtained in silico, followed by GO and KEGG enrichment analyses. Differentially expressed lncRNAs and miRNAs were screened from the GEO database to construct the ceRNA co-expression network. In skin photoaging samples, PVT1 and AQP3 were poorly expressed, while miR-551b-3p was highly expressed. The relationships among the lncRNA, miRNA and mRNA were explored through the ENCORI database and dual luciferase reporter assay. Mechanistically, PVT1 could sequester miR-551b-3p to upregulate the expression of AQP3, which further inactivated the ERK/p38 MAPK signaling pathway. HDFs were selected to construct an in vitro cell skin photoaging model, where the senescence, cell cycle distribution and viability of young and senescent HDFs were detected by SA-β-gal staining, flow cytometry and CCK-8 assay. In vitro cell experiments confirmed that overexpression of PVT1 or AQP3 enhanced viability of young and senescent HDFs and inhibited HDF senescence, while miR-551b-3p upregulation counteracted the effect of PVT1. In conclusion, PVT1-driven suppression of miR-551b-3p induces AQP3 expression to inactivate the ERK/p38 MAPK signaling pathway, thereby inhibiting HDF senescence and ultimately delaying the skin photoaging.
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Affiliation(s)
- Hua Tang
- Department of Dermatology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No. 61, Jiefang West Road, Furong District, Changsha, 410000, Hunan Province, P. R. China
| | - Qi Xiong
- Department of Dermatology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No. 61, Jiefang West Road, Furong District, Changsha, 410000, Hunan Province, P. R. China
| | - Ming Yin
- Department of Dermatology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No. 61, Jiefang West Road, Furong District, Changsha, 410000, Hunan Province, P. R. China
| | - Hao Feng
- Department of Dermatology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No. 61, Jiefang West Road, Furong District, Changsha, 410000, Hunan Province, P. R. China
| | - Fang Yao
- Department of Dermatology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No. 61, Jiefang West Road, Furong District, Changsha, 410000, Hunan Province, P. R. China
| | - Xiao Xiao
- Department of Dermatology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No. 61, Jiefang West Road, Furong District, Changsha, 410000, Hunan Province, P. R. China
| | - Feng Hu
- Department of Dermatology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No. 61, Jiefang West Road, Furong District, Changsha, 410000, Hunan Province, P. R. China
| | - Yangying Liao
- Department of Dermatology, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), No. 61, Jiefang West Road, Furong District, Changsha, 410000, Hunan Province, P. R. China.
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16
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Long Q, Lv B, Jiang S, Lin J. The Landscape of Circular RNAs in Cardiovascular Diseases. Int J Mol Sci 2023; 24:ijms24054571. [PMID: 36902000 PMCID: PMC10003248 DOI: 10.3390/ijms24054571] [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: 01/24/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023] Open
Abstract
Cardiovascular disease (CVD) remains the leading cause of mortality globally. Circular RNAs (circRNAs) have attracted extensive attention for their roles in the physiological and pathological processes of various cardiovascular diseases (CVDs). In this review, we briefly describe the current understanding of circRNA biogenesis and functions and summarize recent significant findings regarding the roles of circRNAs in CVDs. These results provide a new theoretical basis for diagnosing and treating CVDs.
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Affiliation(s)
- Qi Long
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Bingjie Lv
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shijiu Jiang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jibin Lin
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Correspondence:
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17
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Wang ZH, Ye LL, Xiang X, Wei XS, Niu YR, Peng WB, Zhang SY, Zhang P, Xue QQ, Wang HL, Du YH, Liu Y, Ai JQ, Zhou Q. Circular RNA circFBXO7 attenuates non-small cell lung cancer tumorigenesis by sponging miR-296-3p to facilitate KLF15-mediated transcriptional activation of CDKN1A. Transl Oncol 2023; 30:101635. [PMID: 36774884 PMCID: PMC9945757 DOI: 10.1016/j.tranon.2023.101635] [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: 08/13/2022] [Revised: 12/04/2022] [Accepted: 01/25/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Accumulating evidence indicates that circular RNAs (circRNAs) play important roles in various cancers. Hsa_circ_0008832 (circFBXO7) is a circRNA generated from the second exon of the human F-box only protein 7 (FBXO7). Mouse circFbxo7 is a circRNA generated from the second exon of mouse F-box only protein 7 (Fbxo7). The role of human circFBXO7 and mouse circFbxo7 in non-small cell lung cancer (NSCLC) has not been reported. METHODS The expression of circFBXO7 was measured by quantitative real-time PCR. Survival analysis was performed to explore the association between the expression of circFBXO7 and the prognosis of patients with NSCLC. Lung cancer cell lines were transfected with plasmids. Cell proliferation, cell cycle, and tumorigenesis were evaluated to assess the effects of circFBXO7. Fluorescence in situ hybridization assay was used to identify the location of circFBXO7 and circFbxo7 in human and mouse lung cancer cells. Luciferase reporter assay was conducted to confirm the relationship between circFBXO7 and microRNA. RESULTS In this study, we found that circFBXO7 was downregulated in NSCLC tissues and cell lines. NSCLC patients with high circFBXO7 expression had prolonged overall survival. Overexpression of circFBXO7 inhibited cell proliferation both in vitro and in vivo. Mechanistically, we demonstrated that circFBXO7 upregulated the expression of miR-296-3p target gene Krüppel-like factor 15 (KLF15) and KLF15 transactivated the expression of CDKN1A. CONCLUSIONS CircFBXO7 acts as a tumor suppressor by a novel circFBXO7/miR-296-3p/KLF15/CDKN1A axis, which may serve as a potential biomarker and therapeutic target for NSCLC.
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Affiliation(s)
- Zi-Hao Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin-Lin Ye
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuan Xiang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Shan Wei
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi-Ran Niu
- Department of Respiratory and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wen-Bei Peng
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Si-Yu Zhang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pei Zhang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian-Qian Xue
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao-Lei Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi-Heng Du
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia-Qi Ai
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiong Zhou
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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18
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Lv X, Luo Q, Xin S, Zheng W, Xu T, Sun Y. Circular RNA circPlce1 regulates innate immune response in miiuy croaker, Miichthys miiuy. FISH & SHELLFISH IMMUNOLOGY 2023; 133:108561. [PMID: 36690265 DOI: 10.1016/j.fsi.2023.108561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/06/2023] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
In recent years, more and more researchers have devoted to the study of circular RNAs (circRNAs) in noncoding RNAs. As an important regulator in a variety of biological processes, circRNAs are relatively abundant in the study of mammals, while research in lower vertebrates is still lacking. In this study, we found a circRNA, circPlce1, related to innate immune response in Miichthys miiuy (miiuy croaker). The experimental results confirmed that circPlce1 could promote the production of antiviral genes and inflammatory response under the stimulation of poly (I: C) and LPS. We also confirmed that circPlce1 can promote NF-κB and IRF3 pathways through luciferase reporter assay experiment. In addition, we also found that circPlce1 can promote cell proliferation and improve cell viability. In conclusion, our results showed that circPlce1 plays an active role in regulating inflammatory response, cell proliferation and cell viability, providing a foundation for the study of the biological function of circRNAs in the innate immune response in teleost fish.
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Affiliation(s)
- Xing Lv
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Qiang Luo
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Shiying Xin
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Yuena Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, China.
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Abstract
Circular RNAs (circRNAs) are closed-loop RNA transcripts formed by a noncanonical back splicing mechanism. circRNAs are expressed in various tissues and cell types in a temporospatially regulated manner and have diverse molecular functions including their ability to act as miRNA sponges, transcriptional and splicing regulators, protein traps, and even templates for polypeptide synthesis. Emerging evidence suggests that circRNAs are themselves dynamically regulated throughout development in various organisms, with a substantial accumulation during ageing. Their regulatory roles in cellular pathways associated with ageing and senescence, as well as their implications in ageing-related diseases, such as neurological disease, cancer, and cardiovascular disease, suggest that circRNAs are key molecular determinants of the ageing process. Their unique structure, expression specificity, and biological functions highlight a potential capacity for use as novel biomarkers for diagnosis, prognosis, and treatment outcomes in a variety of conditions including pathological ageing. CircRNA may also have potential as target for interventions that manipulate ageing and longevity. In this chapter, we discuss the most recent advances in circRNA changes in ageing and ageing-associated disease.
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Sun X, Wan X, Khan MA, Zhang K, Yi X, Wang Z, Chen K. Comprehensive Analysis of circRNA Expression Profiles in Human Brown Adipose Tissue. Diabetes Metab Syndr Obes 2023; 16:469-478. [PMID: 36814952 PMCID: PMC9939945 DOI: 10.2147/dmso.s398620] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
PURPOSE Brown adipose tissue (BAT) can rapidly generate heat and improve energy metabolism. Circular RNAs (circRNAs) are cellular endogenous non-coding RNAs, which can regulate the development and progress of different diseases. However, the role of circRNAs in human BAT is not fully understood. Here, we analyzed the differentially expressed circRNAs (DECs) in human BAT, as well as in white adipose tissue (WAT), and identified new biomarkers of BAT. PATIENTS AND METHODS Three human BAT and three human subcutaneous WAT samples were selected, and circRNA microarray was performed. Additionally, quantitative real-time polymerase chain reaction (qRT-PCR) was applied to determine the expression of six circRNAs. Finally, the functional analysis was performed by bioinformatics. RESULTS Compared to WAT, 152 upregulated circRNAs and 201 downregulated circRNAs were identified in BAT. The DECs were further subjected to GO and KEGG enrichment analysis. Several circRNAs, for example, hsa_circ_0006168, hsa_circ_26337 and hsa_circ_0007507 were found upregulated and hsa_circ_0030162 was found downregulated in human BAT compared to WAT. CONCLUSION This study profiles the circRNA expression in human BAT and WAT, and suggests hsa_circ_0006168, hsa_circ_26337, hsa_circ_0007507, and hsa_circ_0030162 as novel biomarkers for human BAT.
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Affiliation(s)
- Xiaoying Sun
- Department of Endocrinology, The Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Xinxing Wan
- Department of Endocrinology, The Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Md Asaduzzaman Khan
- The Research Centre for Preclinical Medicine, Southwest Medical University, Luzhou, People’s Republic of China
| | - Keke Zhang
- Department of Endocrinology, The Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Xuan Yi
- Department of Endocrinology, The Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Zhouqi Wang
- Department of Endocrinology, The Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
| | - Ke Chen
- Department of Endocrinology, The Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China
- Correspondence: Ke Chen, Department of Endocrinology, The Third Xiangya Hospital of Central South University, Changsha, People’s Republic of China, Tel +86-731-8861-8239, Email
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21
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mRNA COVID-19 Vaccines-Facts and Hypotheses on Fragmentation and Encapsulation. Vaccines (Basel) 2022; 11:vaccines11010040. [PMID: 36679885 PMCID: PMC9864138 DOI: 10.3390/vaccines11010040] [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: 11/23/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The adventure of the mRNA vaccine began thirty years ago in the context of influenza. This consisted in encapsulating the mRNA coding for a viral protein in a lipid particle. We show how the mRNA encoding S protein has been modified for that purpose in the context of the anti-SARS-CoV-2 vaccination. RESULTS by using data coming from genetic and epidemiologic databases, we show the theoretical possibility of fragmentation of this mRNA into small RNA sequences capable of inhibiting important bio-syntheses such as the production of beta-globin. DISCUSSION we discuss two aspects related to mRNA vaccine: (i) the plausibility of mRNA fragmentation, and (ii) the role of liposomal nanoparticles (LNPs) used in the vaccine and their impact on mRNA biodistribution. CONCLUSION we insist on the need to develop lipid nanoparticles allowing personalized administration of vaccines and avoiding adverse effects due to mRNA fragmentation and inefficient biodistribution. Hence, we recommend (i) adapting the mRNA of vaccines to the least mutated virus proteins and (ii) personalizing its administration to the categories of chronic patients at risk most likely to suffer from adverse effects.
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22
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Tolomeo D, Traversa D, Venuto S, Ebbesen KK, García Rodríguez JL, Tamma G, Ranieri M, Simonetti G, Ghetti M, Paganelli M, Visci G, Liso A, Kok K, Muscarella LA, Fabrizio FP, Frassanito MA, Lamanuzzi A, Saltarella I, Solimando AG, Fatica A, Ianniello Z, Marsano RM, Palazzo A, Azzariti A, Longo V, Tommasi S, Galetta D, Catino A, Zito A, Mazza T, Napoli A, Martinelli G, Kjems J, Kristensen LS, Vacca A, Storlazzi CT. circPVT1 and PVT1/AKT3 show a role in cell proliferation, apoptosis, and tumor subtype-definition in small cell lung cancer. Genes Chromosomes Cancer 2022; 62:377-391. [PMID: 36562080 DOI: 10.1002/gcc.23121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Small cell lung cancer (SCLC) is treated as a homogeneous disease, although the expression of NEUROD1, ASCL1, POU2F3, and YAP1 identifies distinct molecular subtypes. The MYC oncogene, amplified in SCLC, was recently shown to act as a lineage-specific factor to associate subtypes with histological classes. Indeed, MYC-driven SCLCs show a distinct metabolic profile and drug sensitivity. To disentangle their molecular features, we focused on the co-amplified PVT1, frequently overexpressed and originating circular (circRNA) and chimeric RNAs. We analyzed hsa_circ_0001821 (circPVT1) and PVT1/AKT3 (chimPVT1) as examples of such transcripts, respectively, to unveil their tumorigenic contribution to SCLC. In detail, circPVT1 activated a pro-proliferative and anti-apoptotic program when over-expressed in lung cells, and knockdown of chimPVT1 induced a decrease in cell growth and an increase of apoptosis in SCLC in vitro. Moreover, the investigated PVT1 transcripts underlined a functional connection between MYC and YAP1/POU2F3, suggesting that they contribute to the transcriptional landscape associated with MYC amplification. In conclusion, we have uncovered a functional role of circular and chimeric PVT1 transcripts in SCLC; these entities may prove useful as novel biomarkers in MYC-amplified tumors.
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Affiliation(s)
- Doron Tolomeo
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Debora Traversa
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Santina Venuto
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Karoline K Ebbesen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | | | - Grazia Tamma
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Marianna Ranieri
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Giorgia Simonetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Martina Ghetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Matteo Paganelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Grazia Visci
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Arcangelo Liso
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Federico Pio Fabrizio
- Laboratory of Oncology, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Maria Antonia Frassanito
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Aurelia Lamanuzzi
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Ilaria Saltarella
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Antonio Giovanni Solimando
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Zaira Ianniello
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | | | - Antonio Palazzo
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Amalia Azzariti
- Laboratory of Experimental Pharmacology, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Vito Longo
- Medical Thoracic Oncology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Stefania Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Domenico Galetta
- Medical Thoracic Oncology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Annamaria Catino
- Medical Thoracic Oncology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Alfredo Zito
- Pathology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Alessandro Napoli
- Bioinformatics Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Giovanni Martinelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola (FC), Italy
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | | | - Angelo Vacca
- Department of Precision and Regenerative Medicine and Ionian Area - (DiMePRe-J), School of Medicine, Aldo Moro University of Bari, Bari, Italy
| | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
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Chen P, Li W, Liu X, Wang Y, Mai H, Huang R. Circular RNA expression profiles of ovarian granulosa cells in advanced-age women explain new mechanisms of ovarian aging. Epigenomics 2022; 14:1029-1038. [PMID: 36154295 DOI: 10.2217/epi-2022-0211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We aimed to determine the role of granulosa cells (GCs) circular RNA (circRNA) in ovarian aging. Methods: Nine women were recruited, including three diminished ovarian reserve young women, three advanced-aged women and three normal ovarian reserve young women. The circRNA expression profiles of GCs were characterized by CLEAR software. Key circRNA were validated by quantitative reverse transcription PCR. Results: GCs in advanced-age group females exhibited active MHC class II-related biological processes. A total of 3575 circRNAs were found in the advanced age group. Hsa-circ-0031584 appears to be one of the important molecules regulating the mitotic process of GCs. Conclusion: The expression profiles of circRNAs exhibited obvious stage specificity with age which might contribute to ovarian aging progression.
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Affiliation(s)
- Peigen Chen
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510000, China
| | - Wei Li
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510000, China
| | - Xiaoping Liu
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510000, China
| | - Yanfang Wang
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510000, China
| | - Huisi Mai
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510000, China
| | - Rui Huang
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510000, China
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24
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Singh S, Shyamal S, Panda AC. Detecting RNA-RNA interactome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1715. [PMID: 35132791 DOI: 10.1002/wrna.1715] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
The last decade has seen a robust increase in various types of novel RNA molecules and their complexity in gene regulation. RNA molecules play a critical role in cellular events by interacting with other biomolecules, including protein, DNA, and RNA. It has been established that RNA-RNA interactions play a critical role in several biological processes by regulating the biogenesis and function of RNA molecules. Interestingly, RNA-RNA interactions regulate the biogenesis of diverse RNA molecules, including mRNAs, microRNAs, tRNAs, and circRNAs, through splicing or backsplicing. Structured RNAs like rRNA, tRNA, and snRNAs achieve their functional conformation by intramolecular RNA-RNA interactions. In addition, functional consequences of many intermolecular RNA-RNA interactions have been extensively studied in the regulation of gene expression. Hence, it is essential to understand the mechanism and functions of RNA-RNA interactions in eukaryotes. Conventionally, RNA-RNA interactions have been identified through diverse biochemical methods for decades. The advent of high-throughput RNA-sequencing technologies has revolutionized the identification of global RNA-RNA interactome in cells and their importance in RNA structure and function in gene expression regulation. Although these technologies revealed tens of thousands of intramolecular and intermolecular RNA-RNA interactions, we further look forward to future unbiased and quantitative high-throughput technologies for detecting transcriptome-wide RNA-RNA interactions. With the ability to detect RNA-RNA interactome, we expect that future studies will reveal the higher-order structures of RNA molecules and multi-RNA hybrids impacting human health and diseases. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Suman Singh
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
- Regional Center for Biotechnology, Faridabad, India
| | | | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
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25
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Hua T, Luo Y. Circular RNA PVT1 promotes progression of thyroid cancer by competitively binding miR‑384. Exp Ther Med 2022; 24:629. [PMID: 36185502 PMCID: PMC9520360 DOI: 10.3892/etm.2022.11566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/30/2022] [Indexed: 11/06/2022] Open
Abstract
Plasmacytoma variant translocation 1 circular RNA (circPVT1) is involved in the initiation and development of several types of cancer. However, the underlying molecular role of circPVT1 in tumorigenesis of thyroid cancer remains to be elucidated. In the present study, relative expression of circPVT1 was markedly upregulated in thyroid cancer compared with adjacent normal tissue. circPVT1 expression was associated with clinical stage and lymph node metastasis. Furthermore, Cell Counting Kit-8, colony formation and Transwell chamber assays demonstrated that knockdown of circPVT1 decreased proliferation, migration and invasion of thyroid cancer cells in vitro. Moreover, circPVT1 directly interacted with microRNA (miR)-384, as shown by bioinformatics prediction and dual luciferase and RNA pull-down assay. miR-384 inhibition partially reversed the circPVT1 knockdown-mediated inhibitory effect on proliferation, migration and invasion of thyroid cancer cells. In summary, these findings demonstrated that circPVT1 may be a potential therapeutic target for thyroid cancer.
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Affiliation(s)
- Tebo Hua
- Department of Thyroid Breast Surgery, Ningbo Medical Centre Lihuili Hospital, Ningbo, Zhejiang 315040, P.R. China
| | - Yong Luo
- Department of Thyroid Breast Surgery, Ningbo Medical Centre Lihuili Hospital, Ningbo, Zhejiang 315040, P.R. China
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26
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Role of circular RNAs in disease progression and diagnosis of cancers: An overview of recent advanced insights. Int J Biol Macromol 2022; 220:973-984. [PMID: 35977596 DOI: 10.1016/j.ijbiomac.2022.08.085] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/19/2022] [Accepted: 08/11/2022] [Indexed: 02/07/2023]
Abstract
Tumor microenvironment (TME) is a crucial regulator of tumor progression and cells in the TME release a number of molecules that are responsible for anaplasticity, invasion, metastasis of tumor, establishing stem cell niches, up-regulation and down-regulation of various pathways in cancer cells, interfering with immune surveillance and immune escape. Moreover, they can serve as diagnostic markers, and determine effective therapies. Among them, CircRNAs have gained special attention due to their involvement in mutated pathways in cancers. By functioning as a molecular sponge for miRNAs, binding with proteins, and directing selective splicing. CircRNAs modify the immunological environment of cancers to promote their growth. Besides of critical role in tumor growth, circRNAs are emerging as potential candidates as biomarkers for diagnosis cancer therapy. Also, circRNAs vaccination even offers a novel approach to tumor immunotherapy. Over the recent years, studies are advocating that circRNAs have tissue specific tumor specific expression patterns, which indicates their potential clinical utility. Especially, circRNAs have emerged as potential predictive and prognostic biomarkers. Although, there has been significant progress in deciphering the role of circRNA in cancers, literature lacks comprehensive overview on this topic. Keeping in view of these significant discoveries, this review systematically discusses circRNA and their role in the tumor in different dimensions.
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27
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Baniahmad A, Branicki W, Taheri M, Eghbali A. Emerging Role of Non-Coding RNAs in Senescence. Front Cell Dev Biol 2022; 10:869011. [PMID: 35865636 PMCID: PMC9294638 DOI: 10.3389/fcell.2022.869011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Senescence is defined as a gradual weakening of functional features of a living organism. Cellular senescence is a process that is principally aimed to remove undesirable cells by prompting tissue remodeling. This process is also regarded as a defense mechanism induced by cellular damage. In the course of oncogenesis, senescence can limit tumor progression. However, senescence participates in the pathoetiology of several disorders such as fibrotic disorders, vascular disorders, diabetes, renal disorders and sarcopenia. Recent studies have revealed contribution of different classes of non-coding RNAs in the cellular senescence. Long non-coding RNAs, microRNAs and circular RNAs are three classes of these transcripts whose contributions in this process have been more investigated. In the current review, we summarize the available literature on the impact of these transcripts in the cellular senescence.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospitals, Jena, Germany
- *Correspondence: Aria Baniahmad, ; Mohammad Taheri, ; Ahmad Eghbali,
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospitals, Jena, Germany
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Aria Baniahmad, ; Mohammad Taheri, ; Ahmad Eghbali,
| | - Ahmad Eghbali
- Anesthesiology Research Center, Mofid Children Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Aria Baniahmad, ; Mohammad Taheri, ; Ahmad Eghbali,
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28
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Wang X, Xu C, Cai Y, Zou X, Chao Y, Yan Z, Zou C, Wu X, Tang L. CircZNF652 promotes the goblet cell metaplasia by targeting the miR-452-5p/JAK2 signaling pathway in allergic airway epithelia. J Allergy Clin Immunol 2022; 150:192-203. [PMID: 35120971 DOI: 10.1016/j.jaci.2021.10.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/13/2021] [Accepted: 10/12/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Circular RNAs (circRNAs) play potentially important roles in various human diseases; however, their roles in the goblet cell metaplasia of asthma remain unknown. OBJECTIVE We sought to investigate the potential role and underlying mechanism of circZNF652 in the regulation of allergic airway epithelial remodeling. METHODS The differential expression profiles of circRNAs were analyzed by transcriptome microarray, and the effects and mechanisms underlying circZNF652-mediated goblet cell metaplasia were investigated by quantitative real-time PCR, RNA fluorescence in situ hybridization, Western blot, RNA pull-down, and RNA immunoprecipitation analyses. The roles of circZNF652 and miR-452-5p in allergic airway epithelial remodeling were explored in both the mouse model with allergic airway inflammation and children with asthma. RESULTS One hundred sixty circRNAs were differentially expressed in bronchoalveolar lavage fluid of children with asthma versus children with foreign body aspiration, and 52 and 108 of them were significantly upregulated and downregulated, respectively. Among them, circZNF652 was predominantly expressed and robustly upregulated in airway epithelia of both the children with asthma and the mouse model with allergic airway inflammation. circZNF652 promoted the goblet cell metaplasia by functioning as a sponge of miR-452-5p, which released the Janus kinase 2 (JAK2) expression and subsequently activated JAK2/signal transducer and activator of transcription 6 (STAT6) signaling in the allergic airway epithelia. In addition, epithelial splicing regulatory protein 1, a splicing factor, accelerated the biogenesis of circZNF652 by binding to its flanking intron to promote the goblet cell metaplasia in allergic airway epithelial remodeling. CONCLUSIONS Upregulation of circZNF652 expression in allergic bronchial epithelia contributed to the goblet cell metaplasia by activating the miR-452-5p/JAK2/STAT6 signaling pathway; thus, blockage of circZNF652 or agonism of miR-452-5p provided an alternative approach for the therapeutic intervention of epithelial remodeling in allergic airway inflammation.
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Affiliation(s)
- Xiangzhi Wang
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China; National Clinical Research Center for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengyun Xu
- National Clinical Research Center for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of CFDA for Respiratory Drug Research, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuqing Cai
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China; National Clinical Research Center for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyi Zou
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China; National Clinical Research Center for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China; Department of Medicine, Zhejiang University City College School of Medicine, Hangzhou, China
| | - Yunqi Chao
- National Clinical Research Center for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China; Department of Endocrinology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ziyi Yan
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China
| | - Chaochun Zou
- National Clinical Research Center for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China; Department of Endocrinology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ximei Wu
- Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of CFDA for Respiratory Drug Research, Zhejiang University School of Medicine, Hangzhou, China.
| | - Lanfang Tang
- Department of Respiratory Medicine, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China; National Clinical Research Center for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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29
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Wu F, Zhu Y, Zhou C, Gui W, Li H, Lin X. Regulation mechanism and pathogenic role of lncRNA plasmacytoma variant translocation 1 (PVT1) in human diseases. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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30
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Han X, Lei Q, Xie J, Liu H, Sun H, Jing L, Zhang X, Zhang T, Gou X. Potential regulators of the senescence-associated secretory phenotype during senescence and ageing. J Gerontol A Biol Sci Med Sci 2022; 77:2207-2218. [PMID: 35524726 DOI: 10.1093/gerona/glac097] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Indexed: 11/14/2022] Open
Abstract
Senescent cells express and secrete a variety of extracellular modulators that include cytokines, chemokines, proteases, growth factors and some enzymes associated with ECM remodeling, defined as the senescence-associated secretory phenotype (SASP). SASP reinforces senescent cell cycle arrest, stimulates and recruits immune cells for immune-mediated clearance of potentially tumorigenic cells, limits or induces fibrosis and promotes wound healing and tissue regeneration. On the other hand, SASP mediates chronic inflammation leading to destruction of tissue structure and function and stimulating the growth and survival of tumour cells. SASP is highly heterogeneous and the role of SASP depends on the context. The regulation of SASP occurs at multiple levels including chromatin remodelling, transcription, mRNA translation, intracellular trafficking and secretion. Several SASP modulators have already been identified setting the stage for future research on their clinical applications. In this review, we summarize in detail the potential signalling pathways that trigger and regulate SASP production during ageing and senescence.
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Affiliation(s)
- Xiaojuan Han
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Qing Lei
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Jiamei Xie
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Huanhuan Liu
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Haoran Sun
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Li Jing
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Xiaohua Zhang
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Tianying Zhang
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Xingchun Gou
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
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Ron M, Ulitsky I. Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs. Nat Commun 2022; 13:2481. [PMID: 35513423 PMCID: PMC9072321 DOI: 10.1038/s41467-022-30183-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 04/05/2022] [Indexed: 12/24/2022] Open
Abstract
Long RNAs vary extensively in their post-transcriptional fates, and this variation is attributed in part to short sequence elements. We used massively parallel RNA assays to study how sequences derived from noncoding RNAs influence the subcellular localization and stability of circular and linear RNAs, including spliced and unspliced forms. We find that the effects of sequence elements strongly depend on the host RNA context, with limited overlap between sequences that drive nuclear enrichment of linear and circular RNAs. Binding of specific RNA binding proteins underpins some of these differences-SRSF1 binding leads to nuclear enrichment of circular RNAs; SAFB binding is associated with nuclear enrichment of predominantly unspliced linear RNAs; and IGF2BP1 promotes export of linear spliced RNA molecules. The post-transcriptional fate of long RNAs is thus dictated by combinatorial contributions of specific sequence elements, of splicing, and of the presence of the terminal features unique to linear RNAs.
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Affiliation(s)
- Maya Ron
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, 76100, Israel.
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Jusic A, Thomas PB, Wettinger SB, Dogan S, Farrugia R, Gaetano C, Tuna BG, Pinet F, Robinson EL, Tual-Chalot S, Stellos K, Devaux Y. Noncoding RNAs in age-related cardiovascular diseases. Ageing Res Rev 2022; 77:101610. [PMID: 35338919 DOI: 10.1016/j.arr.2022.101610] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/28/2022] [Accepted: 03/15/2022] [Indexed: 11/01/2022]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality in the adult population worldwide and represent a severe economic burden and public health concern. The majority of human genes do not code for proteins. However, noncoding transcripts play important roles in ageing that significantly increases the risk for CVDs. Noncoding RNAs (ncRNAs) are critical regulators of multiple biological processes related to ageing such as oxidative stress, mitochondrial dysfunction and chronic inflammation. NcRNAs are also involved in pathophysiological developments within the cardiovascular system including arrhythmias, cardiac hypertrophy, fibrosis, myocardial infarction and heart failure. In this review article, we cover the roles of ncRNAs in cardiovascular ageing and disease as well as their potential therapeutic applications in CVDs.
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Major Role for Cellular MicroRNAs, Long Noncoding RNAs (lncRNAs), and the Epstein-Barr Virus-Encoded BART lncRNA during Tumor Growth
In Vivo. mBio 2022; 13:e0065522. [PMID: 35435703 PMCID: PMC9239068 DOI: 10.1128/mbio.00655-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study assessed the effects of Epstein-Barr virus (EBV) and one form of virally encoded BART long noncoding RNAs (lncRNAs) on cellular expression in epithelial cells grown in vitro and as tumors in vivo determined by high-throughput RNA sequencing of mRNA and small RNAs. Hierarchical clustering based on gene expression distinguished the cell lines from the tumors and distinguished the EBV-positive tumors and the BART tumors from the EBV-negative tumors. EBV and BART expression also induced specific expression changes in cellular microRNAs (miRs) and lncRNAs. Multiple known and predicted targets of the viral miRs, the induced cellular miRs, and lncRNAs were identified in the altered gene set. The changes in expression in vivo indicated that the suppression of growth pathways in vivo reflects increased expression of cellular miRs in all tumors. In the EBV and BART tumors, many of the targets of the induced miRs were not changed and the seed sequences of the nonfunctional miRs were found to have homologous regions within the BART lncRNA. The inhibition of these miR effects on known targets suggests that these induced miRs have reduced function due to sponging by the BART lncRNA. This composite analysis identified the effects of EBV on cellular miRs and lncRNAs with a functional readout through identification of the simultaneous effects on gene expression. Major shifts in gene expression in vivo are likely mediated by effects on cellular noncoding RNAs. Additionally, a predicted property of the BART lncRNA is to functionally inhibit the induced cellular miRs.
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Maimaitiyiming Y, Ye L, Yang T, Yu W, Naranmandura H. Linear and Circular Long Non-Coding RNAs in Acute Lymphoblastic Leukemia: From Pathogenesis to Classification and Treatment. Int J Mol Sci 2022; 23:ijms23084442. [PMID: 35457264 PMCID: PMC9033105 DOI: 10.3390/ijms23084442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 02/07/2023] Open
Abstract
The coding regions account for only a small part of the human genome, and the remaining vast majority of the regions generate large amounts of non-coding RNAs. Although non-coding RNAs do not code for any protein, they are suggested to work as either tumor suppressers or oncogenes through modulating the expression of genes and functions of proteins at transcriptional, posttranscriptional and post-translational levels. Acute Lymphoblastic Leukemia (ALL) originates from malignant transformed B/T-precursor-stage lymphoid progenitors in the bone marrow (BM). The pathogenesis of ALL is closely associated with aberrant genetic alterations that block lymphoid differentiation and drive abnormal cell proliferation as well as survival. While treatment of pediatric ALL represents a major success story in chemotherapy-based elimination of a malignancy, adult ALL remains a devastating disease with relatively poor prognosis. Thus, novel aspects in the pathogenesis and progression of ALL, especially in the adult population, need to be further explored. Accumulating evidence indicated that genetic changes alone are rarely sufficient for development of ALL. Recent advances in cytogenic and sequencing technologies revealed epigenetic alterations including that of non-coding RNAs as cooperating events in ALL etiology and progression. While the role of micro RNAs in ALL has been extensively reviewed, less attention, relatively, has been paid to other non-coding RNAs. Herein, we review the involvement of linear and circular long non-coding RNAs in the etiology, maintenance, and progression of ALL, highlighting the contribution of these non-coding RNAs in ALL classification and diagnosis, risk stratification as well as treatment.
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Affiliation(s)
- Yasen Maimaitiyiming
- The Affiliated Sir Run Run Shaw Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (Y.M.); (L.Y.); (T.Y.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou 310058, China
| | - Linyan Ye
- The Affiliated Sir Run Run Shaw Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (Y.M.); (L.Y.); (T.Y.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Tao Yang
- The Affiliated Sir Run Run Shaw Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (Y.M.); (L.Y.); (T.Y.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Wenjuan Yu
- Department of Hematology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Correspondence: (W.Y.); (H.N.)
| | - Hua Naranmandura
- The Affiliated Sir Run Run Shaw Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China; (Y.M.); (L.Y.); (T.Y.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- Department of Hematology, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
- Correspondence: (W.Y.); (H.N.)
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35
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D’Anca M, Buccellato FR, Fenoglio C, Galimberti D. Circular RNAs: Emblematic Players of Neurogenesis and Neurodegeneration. Int J Mol Sci 2022; 23:ijms23084134. [PMID: 35456950 PMCID: PMC9032451 DOI: 10.3390/ijms23084134] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/06/2022] [Indexed: 12/13/2022] Open
Abstract
In the fascinating landscape of non-coding RNAs (ncRNAs), circular RNAs (circRNAs) are peeping out as a new promising and appreciated class of molecules with great potential as diagnostic and prognostic biomarkers. They come from circularization of single-stranded RNA molecules covalently closed and generated through alternative mRNA splicing. Dismissed for many years, similar to aberrant splicing by-products, nowadays, their role has been regained. They are able to regulate the expression of linear mRNA transcripts at different levels acting as miRNA sponges, interacting with ribonucleoproteins or exerting a control on gene expression. On the other hand, being extremely conserved across phyla and stable, cell and tissue specific, mostly abundant than the linear RNAs, it is not surprising that they should have critical biological functions. Curiously, circRNAs are particularly expressed in brain and they build up during aging and age-related diseases. These extraordinary peculiarities make circRNAs potentially suitable as promising molecular biomarkers, especially of aging and neurodegenerative diseases. This review aims to explore new evidence on circRNAs, emphasizing their role in aging and pathogenesis of major neurodegenerative disorders, Alzheimer's disease, frontotemporal dementia, and Parkinson's diseases with a look toward their potential usefulness in biomarker searching.
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Affiliation(s)
- Marianna D’Anca
- Foundation IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.R.B.); or (C.F.); or (D.G.)
- Correspondence:
| | - Francesca R. Buccellato
- Foundation IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.R.B.); or (C.F.); or (D.G.)
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy
| | - Chiara Fenoglio
- Foundation IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.R.B.); or (C.F.); or (D.G.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Daniela Galimberti
- Foundation IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.R.B.); or (C.F.); or (D.G.)
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy
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36
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Zhang D, Li Y, Lei Y, Yang H, Huang L, Chen X, Zhou Z, Huang C, Zhou Y, Feng R, Xiong XD, Yuan Y, Cui H, Zheng HL, Sun X, Liu X, Xu S. Circular RNA circRNF169 functions as a miR-30c-5p sponge to promote cellular senescence. Biochem Biophys Res Commun 2022; 604:88-95. [PMID: 35303684 DOI: 10.1016/j.bbrc.2022.03.041] [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: 01/07/2022] [Accepted: 03/08/2022] [Indexed: 11/02/2022]
Abstract
Circular RNAs (circRNAs), characterized as single-stranded closed circular RNA molecules, have been established to exert pivotal functions in various biological or pathological processes. Nonetheless, the effects and underlying mechanisms concerning circRNAs on the aging and aging-related diseases remain elusive. We herein compared the expression patterns of circRNAs in young and senescent mouse embryonic fibroblasts (MEFs), and uncovered that circRNF169 was dramatically up-regulated in senescent MEFs compared with that in young MEFs. Therefore, we further digged into the role and potential mechanisms of circRNF169 in the senescence of MEFs. The results of senescence-associate-β-galactosidase staining and BrdU incorporation assay showed that silencing of circRNF169 significantly delayed MEFs senescence and promoted cell proliferation, while ectopic expression of circRNF169 exhibited the opposite effects. Moreover, the dual-luciferase reporter assay confirmed that circRNF169 acted as an endogenous miR-30c-5p sponge, which accelerated cellular senescence by sequestering and inhibiting miR-30c-5p activity. Taken together, our results suggested that circRNF169 exerted a crucial role in cellular senescence through sponging miR-30c-5p and represented a promising target for aging intervention.
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Affiliation(s)
- Dingyuan Zhang
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Yuting Li
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Yiting Lei
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Haiqing Yang
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Linying Huang
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Xue Chen
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Zhihao Zhou
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Cuiyi Huang
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Yantao Zhou
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Ruolan Feng
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Xing-Dong Xiong
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Yuan Yuan
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Hongjing Cui
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Hui-Ling Zheng
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Xuerong Sun
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China
| | - Xinguang Liu
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China.
| | - Shun Xu
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, PR China.
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37
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MicroRNAs, Long Non-Coding RNAs, and Circular RNAs in the Redox Control of Cell Senescence. Antioxidants (Basel) 2022; 11:antiox11030480. [PMID: 35326131 PMCID: PMC8944605 DOI: 10.3390/antiox11030480] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 12/18/2022] Open
Abstract
Cell senescence is critical in diverse aspects of organism life. It is involved in tissue development and homeostasis, as well as in tumor suppression. Consequently, it is tightly integrated with basic physiological processes during life. On the other hand, senescence is gradually being considered as a major contributor of organismal aging and age-related diseases. Increased oxidative stress is one of the main risk factors for cellular damages, and thus a driver of senescence. In fact, there is an intimate link between cell senescence and response to different types of cellular stress. Oxidative stress occurs when the production of reactive oxygen species/reactive nitrogen species (ROS/RNS) is not adequately detoxified by the antioxidant defense systems. Non-coding RNAs are endogenous transcripts that govern gene regulatory networks, thus impacting both physiological and pathological events. Among these molecules, microRNAs, long non-coding RNAs, and more recently circular RNAs are considered crucial mediators of almost all cellular processes, including those implicated in oxidative stress responses. Here, we will describe recent data on the link between ROS/RNS-induced senescence and the current knowledge on the role of non-coding RNAs in the senescence program.
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Kong P, Li CL, Dou YQ, Cao L, Zhang XY, Zhang WD, Bi ZQ, Peng ZY, Yan AQ, Han M. circ-Sirt1 Decelerates Senescence by Inhibiting p53 Activation in Vascular Smooth Muscle Cells, Ameliorating Neointima Formation. Front Cardiovasc Med 2022; 8:724592. [PMID: 34977164 PMCID: PMC8718546 DOI: 10.3389/fcvm.2021.724592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 11/29/2021] [Indexed: 01/10/2023] Open
Abstract
Vascular smooth muscle cell (VSMC) senescence is a major driver of neointimal formation. We have demonstrated that circ-Sirt1 derived from the SIRT1 gene suppressed VSMC inflammation and neointimal formation. However, the effect of circ-Sirt1 inhibiting inflammation on VSMC senescence during neointimal hyperplasia remains to be elucidated. Here, we showed that circ-Sirt1 was highly expressed in young and healthy arteries, which was decreased in aged arteries and neointima of humans and mice. Overexpression of circ-Sirt1 delayed Ang II-induced VSMC senescence in vitro and ameliorated neointimal hyperplasia in vivo. Mechanically, circ-Sirt1 inhibited p53 activity at the levels of transcription and post-translation modulation. In detail, circ-Sirt1, on the one hand, interacted with and held p53 to block its nuclear translocation, and on the other hand, promoted SIRT1-mediated p53 deacetylation and inactivation. In conclusion, our data suggest that circ-Sirt1 is a novel p53 repressor in response senescence-inducing stimuli, and targeting circ-Sirt1 may be a promising approach to ameliorating aging-related vascular disease.
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Affiliation(s)
- Peng Kong
- Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Department of Biochemistry and Molecular Biology, College of Basic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Chang-Lin Li
- Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Department of Biochemistry and Molecular Biology, College of Basic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Yong-Qing Dou
- College of Integrative Medicine, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Li Cao
- Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Department of Biochemistry and Molecular Biology, College of Basic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Xiao-Yun Zhang
- College of Integrative Medicine, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Wen-Di Zhang
- Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Department of Biochemistry and Molecular Biology, College of Basic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Ze-Qi Bi
- Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Department of Biochemistry and Molecular Biology, College of Basic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Zu-Yi Peng
- Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Department of Biochemistry and Molecular Biology, College of Basic Medicine, Hebei Medical University, Shijiazhuang, China
| | - An-Qi Yan
- Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Department of Biochemistry and Molecular Biology, College of Basic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Mei Han
- Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Department of Biochemistry and Molecular Biology, College of Basic Medicine, Hebei Medical University, Shijiazhuang, China
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Li P, Qiao G, Lu J, Ji W, Gao C, Qi F. PVT1 is a prognostic marker associated with immune invasion of bladder urothelial carcinoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:169-190. [PMID: 34902986 DOI: 10.3934/mbe.2022009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plasmacytoma variant translocation 1 (PVT1) is involved in multiple signaling pathways and plays an important regulatory role in a variety of malignant tumors. However, its role in the prognosis and immune invasion of bladder urothelial carcinoma (BLCA) remains unclear. This study investigated the expression of PVT1 in tumor tissue and its relationship with immune invasion, and determined its prognostic role in patients with BLCA. Patients were identified from the cancer genome atlas (TCGA). The enrichment pathway and function of PVT1 were explained by gene ontology (GO) term analysis, gene set enrichment analysis (GSEA) and single-sample gene set enrichment analysis (ssGSEA), and the degree of immune cell infiltration was quantified. Kaplan-Meier analysis and Cox regression were used to analyze the correlation between PVT1 and survival rate. PVT1-high BLCA patients had a lower 10-year disease-specific survival (DSS P < 0.05) and overall survival (OS P < 0.05). Multivariate Cox regression analysis showed that PVT1 (high vs. low) (P = 0.004) was an independent prognostic factor. A nomogram was used to predict the effect of PVT1 on the prognosis. PVT1 plays an important role in the progression and prognosis of BLCA and can be used as a medium biomarker to predict survival after cystectomy.
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Affiliation(s)
- Peiyuan Li
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin 300052, China
| | - Gangjie Qiao
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin 300052, China
| | - Jian Lu
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, No. 218, Jixi Road, Shushan District, Hefei 230022, China
| | - Wenbin Ji
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin 300052, China
| | - Chao Gao
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin 300052, China
| | - Feng Qi
- Department of General Surgery, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin 300052, China
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40
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Zhang Z, Guo R, Wang Y, Huang H, Liu J, Wang C, Wu H, Zou T. Diagnostic value of circRNAs as effective biomarkers in human cardiovascular disease: an updated meta-analysis. Int J Med Sci 2022; 19:446-459. [PMID: 35370465 PMCID: PMC8964318 DOI: 10.7150/ijms.67094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/07/2022] [Indexed: 11/15/2022] Open
Abstract
Background: A growing body of literature has demonstrated that circular RNAs (circRNAs) are the potential biomarkers in human cardiovascular disease (CVD). Therefore, a meta-analysis based on current studies was accomplished to appraise the role of circRNAs in the diagnostic of CVD patients. Methods: Studies before October 30, 2021, were searched using PubMed, EMBASE, the Web of Science, and Cochrane Library. The diagnostic odds ratio (DOR) with a confidence interval (CI) of 95% was used to investigate the associations between circRNAs and CVDs. Results: A total of 27 eligible articles were selected, including 47 studies, with 6833 participants meeting the criteria standard constrain. The pooled overall sensitivity and specificity for circRNAs expression profile in differentiating CVD patients from controls (non-CVDs or healthy subjects) were 0.81 (95%CI 0.78-0.83) and 0.74 (95%CI 0.68-0.78), respectively; the overall positive likelihood ratio was 3.1 (95%CI 2.5-3.7); the negative likelihood ratio was 0.26 (95%CI 0.22-0.31); the overall diagnostic odds ratio corresponding to an area under the curve of 0.85 (95%CI 0.81-0.88) was 12 (95%CI 9-16). Subgroup analysis indicated that the serum rather than blood has higher diagnostic accuracy. Likewise, meta-regression analysis demonstrated that the specimen, detection method, sample size, and publication year were the main sources of heterogeneity. Sensitivity analysis and Deeks' funnel plot revealed that our results are relatively robust. Conclusions: Our evidence-based analysis results suggested that circRNAs provide higher diagnostic accuracy in the prediction of CVDs. Thus, circRNAs might be potential biomarkers in CVDs.
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Affiliation(s)
- Zhexiao Zhang
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China.,Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Runmin Guo
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China
| | - Yuhui Wang
- Department of Surgery, the Third Affiliated Hospital of Guangdong Medical University (Longjiang Hospital of Shunde District), Foshan, China
| | - Hairong Huang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Jie Liu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Chenfei Wang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
| | - Hongfu Wu
- Key Laboratory of Stem Cell and Regenerative Tissue Engineering, Guangdong Medical University, Dongguan, China
| | - Tangbin Zou
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, China.,Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, China
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41
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KRAS-related long noncoding RNAs in human cancers. Cancer Gene Ther 2022; 29:418-427. [PMID: 34489556 PMCID: PMC9113938 DOI: 10.1038/s41417-021-00381-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/29/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
KRAS is one of the most widely prevalent proto-oncogenes in human cancers. The constitutively active KRAS oncoprotein contributes to both tumor onset and cancer development by promoting cell proliferation and anchorage-independent growth in a MAPK pathway-dependent manner. The expression of microRNAs (miRNAs) and the KRAS oncogene are known to be dysregulated in various cancers, while long noncoding RNAs (lncRNAs) can act as regulators of the miRNAs targeting KRAS oncogene in different cancers and have gradually become a focus of research in recent years. In this review article, we summarize recent advances in the research on lncRNAs that have sponging effects on KRAS-targeting miRNAs as crucial mediators of KRAS expression in different cell types and organs. A deeper understanding of lncRNA function in KRAS-driven cancers is of major fundamental importance and will provide a valuable clinical tool for the diagnosis, prognosis, and eventual treatment of cancers.
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Min X, Cai M, Shao T, Xu Z, Liao Z, Liu D, Zhou M, Wu W, Zhou Y, Mo M, Xu S, Liu X, Xiong X. A circular intronic RNA ciPVT1 delays endothelial cell senescence by regulating the miR-24-3p/CDK4/pRb axis. Aging Cell 2022; 21:e13529. [PMID: 34902213 PMCID: PMC8761008 DOI: 10.1111/acel.13529] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 11/12/2021] [Accepted: 11/28/2021] [Indexed: 11/28/2022] Open
Abstract
Circular RNAs (circRNAs) have been established to be involved in numerous processes in the human genome, but their function in vascular aging remains largely unknown. In this study, we aimed to characterize and analyze the function of a circular intronic RNA, ciPVT1, in endothelial cell senescence. We observed significant downregulation of ciPVT1 in senescent endothelial cells. In proliferating endothelial cells, ciPVT1 knockdown induced a premature senescence-like phenotype, inhibited proliferation, and led to an impairment in angiogenesis. An in vivo angiogenic plug assay revealed that ciPVT1 silencing significantly inhibited endothelial tube formation and decreased hemoglobin content. Conversely, overexpression of ciPVT1 in old endothelial cells delayed senescence, promoted proliferation, and increased angiogenic activity. Mechanistic studies revealed that ciPVT1 can sponge miR-24-3p to upregulate the expression of CDK4, resulting in enhanced Rb phosphorylation. Moreover, enforced expression of ciPVT1 reversed the senescence induction effect of miR-24-3p in endothelial cells. In summary, the present study reveals a pivotal role for ciPVT1 in regulating endothelial cell senescence and may have important implications in the search of strategies to counteract the development of age-associated vascular pathologies.
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Affiliation(s)
- Xue Min
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Institute of Biochemistry & Molecular Biology Guangdong Medical University Zhanjiang China
| | - Meng‐yun Cai
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Institute of Biochemistry & Molecular Biology Guangdong Medical University Zhanjiang China
| | - Tong Shao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Institute of Biochemistry & Molecular Biology Guangdong Medical University Zhanjiang China
| | - Zi‐yang Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Institute of Biochemistry & Molecular Biology Guangdong Medical University Zhanjiang China
| | - Zhaofu Liao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Institute of Biochemistry & Molecular Biology Guangdong Medical University Zhanjiang China
| | - Dong‐liang Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Institute of Biochemistry & Molecular Biology Guangdong Medical University Zhanjiang China
| | - Meng‐yuan Zhou
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Institute of Biochemistry & Molecular Biology Guangdong Medical University Zhanjiang China
| | - Wei‐peng Wu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Institute of Biochemistry & Molecular Biology Guangdong Medical University Zhanjiang China
| | - Yu‐lan Zhou
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Clinical Research Center Affiliated Hospital of Guangdong Medical University Zhanjiang China
| | - Miao‐hua Mo
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Institute of Biochemistry & Molecular Biology Guangdong Medical University Zhanjiang China
| | - Shun Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Institute of Biochemistry & Molecular Biology Guangdong Medical University Zhanjiang China
| | - Xinguang Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Institute of Biochemistry & Molecular Biology Guangdong Medical University Zhanjiang China
| | - Xing‐dong Xiong
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics Institute of Aging Research Guangdong Medical University Dongguan China
- Institute of Biochemistry & Molecular Biology Guangdong Medical University Zhanjiang China
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43
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Circular RNA PVT1 inhibits tendon stem/progenitor cell senescence by sponging microRNA-199a-5p. Toxicol In Vitro 2021; 79:105297. [PMID: 34896603 DOI: 10.1016/j.tiv.2021.105297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 11/23/2021] [Accepted: 12/06/2021] [Indexed: 12/16/2022]
Abstract
Tendon stem/progenitor cell (TSPC) senescence can lead to age-dependent tendon maladies and undermines both tendon repair and replacement capacity in humans. The mechanisms underlying TSPC senescence and sensitivity to adverse factors are complicated. In this study, we analyzed involvement of the circular RNA (circRNA) PVT1 (circPVT1) in TSPC senescence. circPVT1 expression was found to be significantly diminished in human TSPCs under prolonged in vitro culture. Accordingly, circPVT1 knockdown promoted senescence progression and suppressed self renewal, migration, and tenogenic differentiation of TSPCs. Furthermore, we found that circPVT1 directly targets microRNA (miR)-199a-5p thereby attenuating its negative regulation of SIRT1 expression. Either miR-199a-5p inhibition or SIRT1 overexpression attenuated the senescence-boosting effect of circPVT1 knockdown, implying that circPVT1 suppresses TSPC senescence in part by upregulating the miR-199a-5p-SIRT1 signaling axis. Our findings conclusively explain the major roles of circPVT1 in TSPC senescence regulation; circPVT1 is a novel potential therapeutic target for reducing tendon senescence.
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Wu WP, Zhou MY, Liu DL, Min X, Shao T, Xu ZY, Jing X, Cai MY, Xu S, Liang X, Mo M, Liu X, Xiong XD. circGNAQ, a circular RNA enriched in vascular endothelium, inhibits endothelial cell senescence and atherosclerosis progression. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:374-387. [PMID: 34552819 PMCID: PMC8426466 DOI: 10.1016/j.omtn.2021.07.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/30/2021] [Indexed: 11/19/2022]
Abstract
Endothelial cell senescence is one of the most important causes of vascular dysfunction and atherosclerosis. Circular RNAs (circRNAs) are endogenous RNA molecules with covalently closed-loop structures, which have been reported to be abnormally expressed in many human diseases. However, the potential role of circRNAs in endothelial cell senescence and atherosclerosis remains largely unknown. Here, we compared the expression patterns of circRNAs in young and senescent human endothelial cells with RNA sequencing. Among the differentially expressed circRNAs, circGNAQ, a circRNA enriched in vascular endothelium, was significantly downregulated in senescent endothelial cells. circGNAQ silencing triggered endothelial cell senescence, as determined by a rise in senescence-associated β-galactosidase activity, reduced cell proliferation, and suppressed angiogenesis; circGNAQ overexpression showed the opposite effects. Mechanistic studies revealed that circGNAQ acted as an endogenous miR-146a-5p sponge to increase the expression of its target gene PLK2 by decoying the miR-146a-5p, thereby delaying endothelial cell senescence. In vivo studies showed that circGNAQ overexpression in the endothelium inhibited endothelial cell senescence and atherosclerosis progression. These results suggest that circGNAQ plays critical roles in endothelial cell senescence and consequently the pathogenesis of atherosclerosis, implying that the management of circGNAQ provides a potential therapeutic approach for limiting the progression of atherosclerosis.
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Affiliation(s)
- Wei-peng Wu
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Meng-yuan Zhou
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Dong-liang Liu
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Xue Min
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Tong Shao
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Zi-yang Xu
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Xia Jing
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Meng-yun Cai
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Shun Xu
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Xin Liang
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Miaohua Mo
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
| | - Xinguang Liu
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
- Institute of Biochemistry & Molecular Biology, Guangdong Medical University, Zhanjiang 524023, P.R. China
| | - Xing-dong Xiong
- Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China
- Institute of Biochemistry & Molecular Biology, Guangdong Medical University, Zhanjiang 524023, P.R. China
- Corresponding author: Prof. Xing-dong Xiong, Institute of Aging Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, P.R. China.
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45
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Ghafouri-Fard S, Khoshbakht T, Taheri M, Jamali E. A Concise Review on the Role of CircPVT1 in Tumorigenesis, Drug Sensitivity, and Cancer Prognosis. Front Oncol 2021; 11:762960. [PMID: 34804965 PMCID: PMC8599443 DOI: 10.3389/fonc.2021.762960] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/15/2021] [Indexed: 12/16/2022] Open
Abstract
CircPVT1 (hsa_circ_0001821) is a cancer-related circular RNA (circRNA) that originated from a genomic locus on chromosome 8q24. This locus has been previously found to encode the oncogenic long non-coding RNA PVT1. Expression of this circRNA has been found to be upregulated in diverse neoplastic conditions. CircPVT1 acts as a sponge for miR-125a, miR-125b, miR-124-3p, miR-30a-5p, miR-205-5p, miR-423-5p, miR-526b, miR-137, miR-145-5p, miR-497, miR-30d/e, miR-455-5p, miR-29a-3p, miR-204-5p, miR-149, miR-106a-5p, miR-377, miR-3666, miR-203, and miR-199a-5p. Moreover, it can regulate the activities of PI3K/AKT, Wnt5a/Ror2, E2F2, and HIF-1α. Upregulation of circPVT1 has been correlated with decreased survival of patients with different cancer types. In the current review, we explain the oncogenic impact of circPVT1 in different tissues based on evidence from in vitro, in vivo, and clinical investigations.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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46
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Xu J, Hao Y, Gao X, Wu Y, Ding Y, Wang B. CircSLC7A6 promotes the progression of Wilms' tumor via microRNA-107/ ABL proto-oncogene 2 axis. Bioengineered 2021; 13:308-318. [PMID: 34787058 PMCID: PMC8805947 DOI: 10.1080/21655979.2021.2001204] [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] [Indexed: 12/14/2022] Open
Abstract
The dysregulation of circular RNAs (circRNAs) has been proved to be involved in the carcinogenesis of various cancers. Nevertheless, the biological function of circSLC7A6 remains unclear in Wilms’ tumor (WT). In our study, we found that circSLC7A6 was upregulated in cancerous WT tissues and cells. Cell apoptosis was increased while cell viability, migration, and invasion were repressed by circSLC7A6 silencing. Besides, circSLC7A6 knockdown suppressed WT tumor growth in vivo. miR-107 was identified as a direct target of circSLC7A6, and circSLC7A6 could negatively regulate miR-107 expression. In addition, circSLC7A6 knockdown inhibited WT progression, while the effect was partially abolished by the downregulation of miR-107. Additionally, ABL proto-oncogene 2 axis (ABL2) was verified as a downstream gene of miR-107, and circSLC7A6 could upregulate ABL2 expression by serving as a ceRNA of miR-107. Moreover, functional assays revealed that ABL2 overexpression reversed the impact of circSLC7A6 depletion on cell proliferation, migration, invasion, and apoptosis of WT. In conclusion, the present study demonstrated that circSLC7A6 facilitated WT progression by upregulating ABL2 through inhibiting miR-107 expression. These results suggested that circSLC7A6 might serve as a potential therapeutic target for WT.
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Affiliation(s)
- Jiaju Xu
- Department of Pediatrics, Yantai Yuhuangding Hospital, China
| | - Ying Hao
- Department of Pediatrics, Yantai Yuhuangding Hospital, China
| | - Xingjuan Gao
- Department of Pediatrics, Yantai Yuhuangding Hospital, China
| | - Yanqiu Wu
- Department of Pediatrics, Yantai Yuhuangding Hospital, China
| | - Yanjie Ding
- Department of Pediatrics, Yantai Yuhuangding Hospital, China
| | - Baohong Wang
- Department of Pediatrics, Yantai Yuhuangding Hospital, China
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47
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Traversa D, Simonetti G, Tolomeo D, Visci G, Macchia G, Ghetti M, Martinelli G, Kristensen LS, Storlazzi CT. Unravelling similarities and differences in the role of circular and linear PVT1 in cancer and human disease. Br J Cancer 2021; 126:835-850. [PMID: 34754096 PMCID: PMC8927338 DOI: 10.1038/s41416-021-01584-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/27/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
The plasmacytoma variant translocation 1 (PVT1) is a long non-coding RNA gene involved in human disease, mainly in cancer onset/progression. Although widely analysed, its biological roles need to be further clarified. Notably, functional studies on PVT1 are complicated by the occurrence of multiple transcript variants, linear and circular, which generate technical issues in the experimental procedures used to evaluate its impact on human disease. Among the many PVT1 transcripts, the linear PVT1 (lncPVT1) and the circular hsa_circ_0001821 (circPVT1) are frequently reported to perform similar pathologic and pro-tumorigenic functions when overexpressed. The stimulation of cell proliferation, invasion and drug resistance, cell metabolism regulation, and apoptosis inhibition is controlled through multiple targets, including MYC, p21, STAT3, vimentin, cadherins, the PI3K/AKT, HK2, BCL2, and CASP3. However, some of this evidence may originate from an incorrect evaluation of these transcripts as two separate molecules, as they share the lncPVT1 exon-2 sequence. We here summarise lncPVT1/circPVT1 functions by mainly focusing on shared pathways, pointing out the potential bias that may exist when the biological role of each transcript is analysed. These considerations may improve the knowledge about lncPVT1/circPVT1 and their specific targets, which deserve further studies due to their diagnostic, prognostic, and therapeutic potential.
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Affiliation(s)
- Debora Traversa
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
| | - Giorgia Simonetti
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Doron Tolomeo
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
| | - Grazia Visci
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
| | - Gemma Macchia
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
| | - Martina Ghetti
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
| | - Giovanni Martinelli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, FC, Italy
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48
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Chen CK, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK, Chang HY. Structured elements drive extensive circular RNA translation. Mol Cell 2021; 81:4300-4318.e13. [PMID: 34437836 PMCID: PMC8567535 DOI: 10.1016/j.molcel.2021.07.042] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 06/03/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022]
Abstract
The human genome encodes tens of thousands circular RNAs (circRNAs) with mostly unknown functions. Circular RNAs require internal ribosome entry sites (IRES) if they are to undergo translation without a 5' cap. Here, we develop a high-throughput screen to systematically discover RNA sequences that can direct circRNA translation in human cells. We identify more than 17,000 endogenous and synthetic sequences as candidate circRNA IRES. 18S rRNA complementarity and a structured RNA element positioned on the IRES are important for driving circRNA translation. Ribosome profiling and peptidomic analyses show extensive IRES-ribosome association, hundreds of circRNA-encoded proteins with tissue-specific distribution, and antigen presentation. We find that circFGFR1p, a protein encoded by circFGFR1 that is downregulated in cancer, functions as a negative regulator of FGFR1 oncoprotein to suppress cell growth during stress. Systematic identification of circRNA IRES elements may provide important links among circRNA regulation, biological function, and disease.
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Affiliation(s)
- Chun-Kan Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ran Cheng
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jin Chen
- Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shira Weingarten-Gabbay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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49
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Winkler L, Dimitrova N. A mechanistic view of long noncoding RNAs in cancer. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1699. [PMID: 34668345 PMCID: PMC9016092 DOI: 10.1002/wrna.1699] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/23/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as important modulators of a wide range of biological processes in normal and disease states. In particular, lncRNAs have garnered significant interest as novel players in the molecular pathology of cancer, spurring efforts to define the functions, and elucidate the mechanisms through which cancer‐associated lncRNAs operate. In this review, we discuss the prevalent mechanisms employed by lncRNAs, with a critical assessment of the methodologies used to determine each molecular function. We survey the abilities of cancer‐associated lncRNAs to enact diverse trans functions throughout the nucleus and in the cytoplasm and examine the local roles of cis‐acting lncRNAs in modulating the expression of neighboring genes. In linking lncRNA functions and mechanisms to their roles in cancer biology, we contend that a detailed molecular understanding of lncRNA functionality is key to elucidating their contributions to tumorigenesis and to unlocking their therapeutic potential. This article is categorized under:Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Lauren Winkler
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Nadya Dimitrova
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
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50
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Lin Z, Tang X, Wang L, Ling L. Prognostic and clinicopathological value of circPVT1 in human cancers: A meta-analysis. Cancer Rep (Hoboken) 2021; 4:e1385. [PMID: 33793089 PMCID: PMC8551984 DOI: 10.1002/cnr2.1385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Circular RNA PVT1 (circPVT1) is significantly upregulated in various human cancers and is related to poor clinical outcome of cancer patients. However, the prognostic and clinicopathological value of circPVT1 in diverse human cancers remains controversial and inconclusive. AIM The objective of our study is to evaluate the prognostic and clinicopathological role of circPVT1 for cancer patients. METHODS AND RESULTS PubMed, Embase, Web of Science, and Cochrane Library were searched for eligible studies by October 1, 2020. The correlation between circPVT1 expression, and overall survival (OS) and clinical parameters was assessed by pooled hazard ratios (HRs) and odds ratios (ORs) with 95% confidence intervals (CIs). Subgroup analyses, heterogeneity, and publication bias were conducted to further enhance reliability. Twelve studies (1282 patients) were selected for this meta-analysis, including 11 on prognosis and 10 on clinicopathological parameters. Elevated expression of circPVT1 was associated with a worse OS in cancer patients (HR, 2.009; 95% CI, 1.667-2.408, 1.892; P < .001). For clinicopathological value, upregulation of circPVT1 was closely related to poor clinical parameters lymph node metastasis (OR = 2.019; 95% CI, 1.026-3.976; P = .042; I2 = 77.5%; PH = 0.000), late clinical stage (OR = 3.594; 95% CI, 1.828-7.065; P < .001; I2 = 71.7%; PH = 0.001), distant metastasis (OR = 4.598; 95% CI, 1.411-14.988; P = .011; I2 = 78.1%; PH = 0.001), and chemoresistant (OR = 6.400; 95% CI, 2.107-19.441; P = .001; I2 = 49.6%; PH = 0.159). CONCLUSION High expression of circPVT1 is correlated with unfavorable prognosis of cancer patients, indicating that circPVT1 can function as a potential prognostic biomarker in human cancer.
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Affiliation(s)
- Zhengjun Lin
- Department of OrthopedicsThe Second Xiangya Hospital Central South UniversityChangshaChina
- Xiangya School of MedicineCentral South UniversityChangshaChina
| | - Xianzhe Tang
- Department of OrthopedicsChenzhou No.1 people's HospitalChenzhouChina
| | - Lu Wang
- Department of OrthopedicsThe Second Xiangya Hospital Central South UniversityChangshaChina
| | - Lin Ling
- Department of OrthopedicsThe Second Xiangya Hospital Central South UniversityChangshaChina
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