151
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Pfafenrot C, Schneider T, Müller C, Hung LH, Schreiner S, Ziebuhr J, Bindereif A. Inhibition of SARS-CoV-2 coronavirus proliferation by designer antisense-circRNAs. Nucleic Acids Res 2021; 49:12502-12516. [PMID: 34850109 PMCID: PMC8643703 DOI: 10.1093/nar/gkab1096] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/18/2021] [Accepted: 10/27/2021] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) are noncoding RNAs that exist in all eukaryotes investigated and are derived from back-splicing of certain pre-mRNA exons. Here, we report the application of artificial circRNAs designed to act as antisense-RNAs. We systematically tested a series of antisense-circRNAs targeted to the SARS-CoV-2 genome RNA, in particular its structurally conserved 5'-untranslated region. Functional assays with both reporter transfections as well as with SARS-CoV-2 infections revealed that specific segments of the SARS-CoV-2 5'-untranslated region can be efficiently accessed by specific antisense-circRNAs, resulting in up to 90% reduction of virus proliferation in cell culture, and with a durability of at least 48 h. Presenting the antisense sequence within a circRNA clearly proved more efficient than in the corresponding linear configuration and is superior to modified antisense oligonucleotides. The activity of the antisense-circRNA is surprisingly robust towards point mutations in the target sequence. This strategy opens up novel applications for designer circRNAs and promising therapeutic strategies in molecular medicine.
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Affiliation(s)
- Christina Pfafenrot
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - Tim Schneider
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - Christin Müller
- Institute of Medical Virology, Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - Lee-Hsueh Hung
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - Silke Schreiner
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - Albrecht Bindereif
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
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152
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Chen L, Huang C, Shan G. Circular RNAs in physiology and non-immunological diseases. Trends Biochem Sci 2021; 47:250-264. [PMID: 34865956 DOI: 10.1016/j.tibs.2021.11.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 12/27/2022]
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNAs. Four subclasses of circRNAs have been identified in animal cells, and they have unique features in their biogenesis, degradation, and transport. CircRNAs have diverse molecular functions in sponging miRNAs, regulating transcription, modulating RNA-binding proteins, and even encoding proteins. Some circRNAs are important regulators of various physiological processes to maintain homeostasis. Dysregulation of circRNAs is associated with human disorders, and individual circRNAs are crucial factors that contribute to major diseases including non-immunological diseases such as cancers, neurological disorders, cardiovascular disease, and metabolic disease. Debates on circRNAs have also been raised in recent years, and further studies would help to resolve these disputes and potentially lead to biomedical applications of circRNAs.
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Affiliation(s)
- Liang Chen
- Department of Clinical Laboratory, First Affiliated Hospital of the USTC, Hefei National Laboratory for Physical Sciences at Microscale, Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, 230027, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing 401331, China; Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing 401331, China.
| | - Ge Shan
- Department of Clinical Laboratory, First Affiliated Hospital of the USTC, Hefei National Laboratory for Physical Sciences at Microscale, Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, 230027, China; Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China.
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153
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Li L, Sheng P, Li T, Fields CJ, Hiers NM, Wang Y, Li J, Guardia CM, Licht JD, Xie M. Widespread microRNA degradation elements in target mRNAs can assist the encoded proteins. Genes Dev 2021; 35:1595-1609. [PMID: 34819352 PMCID: PMC8653786 DOI: 10.1101/gad.348874.121] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022]
Abstract
Binding of microRNAs (miRNAs) to mRNAs normally results in post-transcriptional repression of gene expression. However, extensive base-pairing between miRNAs and target RNAs can trigger miRNA degradation, a phenomenon called target RNA-directed miRNA degradation (TDMD). Here, we systematically analyzed Argonaute-CLASH (cross-linking, ligation, and sequencing of miRNA-target RNA hybrids) data and identified numerous candidate TDMD triggers, focusing on their ability to induce nontemplated nucleotide addition at the miRNA 3' end. When exogenously expressed in various cell lines, eight triggers induce degradation of corresponding miRNAs. Both the TDMD base-pairing and surrounding sequences are essential for TDMD. CRISPR knockout of endogenous trigger or ZSWIM8, a ubiquitin ligase essential for TDMD, reduced miRNA degradation. Furthermore, degradation of miR-221 and miR-222 by a trigger in BCL2L11, which encodes a proapoptotic protein, enhances apoptosis. Therefore, we uncovered widespread TDMD triggers in target RNAs and demonstrated an example that could functionally cooperate with the encoded protein.
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Affiliation(s)
- Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Christopher J Fields
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Nicholas M Hiers
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Yuzhi Wang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Jianping Li
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Division of Hematology/Oncology, University of Florida, Gainesville, Florida 32610, USA
| | - Casey M Guardia
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Jonathan D Licht
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Division of Hematology/Oncology, University of Florida, Gainesville, Florida 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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154
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Wen G, Zhou T, Gu W. The potential of using blood circular RNA as liquid biopsy biomarker for human diseases. Protein Cell 2021; 12:911-946. [PMID: 33131025 PMCID: PMC8674396 DOI: 10.1007/s13238-020-00799-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA) is a novel class of single-stranded RNAs with a closed loop structure. The majority of circRNAs are formed by a back-splicing process in pre-mRNA splicing. Their expression is dynamically regulated and shows spatiotemporal patterns among cell types, tissues and developmental stages. CircRNAs have important biological functions in many physiological processes, and their aberrant expression is implicated in many human diseases. Due to their high stability, circRNAs are becoming promising biomarkers in many human diseases, such as cardiovascular diseases, autoimmune diseases and human cancers. In this review, we focus on the translational potential of using human blood circRNAs as liquid biopsy biomarkers for human diseases. We highlight their abundant expression, essential biological functions and significant correlations to human diseases in various components of peripheral blood, including whole blood, blood cells and extracellular vesicles. In addition, we summarize the current knowledge of blood circRNA biomarkers for disease diagnosis or prognosis.
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Affiliation(s)
- Guoxia Wen
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Tong Zhou
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, 89557, USA.
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China.
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155
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van Zonneveld AJ, Kölling M, Bijkerk R, Lorenzen JM. Circular RNAs in kidney disease and cancer. Nat Rev Nephrol 2021; 17:814-826. [PMID: 34381199 DOI: 10.1038/s41581-021-00465-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are a class of endogenously expressed regulatory RNAs with a single-stranded circular structure. They are generated by back splicing and their expression can be tightly regulated by RNA binding proteins. Cytoplasmic circRNAs can function as molecular sponges that inhibit microRNA-target interactions and protein function or as templates for the efficient generation of peptides via rolling circle amplification. They can also act as molecular scaffolds that enhance the reaction kinetics of enzyme-substrate interactions. In the nucleus, circRNAs might facilitate chromatin modifications and promote gene expression. CircRNAs are resistant to degradation and can be packaged in extracellular vesicles and transported in the circulation. Initial studies suggest that circRNAs have roles in kidney disease and associated cardiovascular complications. They have been implicated in hypertensive nephropathy, diabetic kidney disease, glomerular disease, acute kidney injury and kidney allograft rejection, as well as in microvascular and macrovascular complications of chronic kidney disease, including atherosclerotic vascular disease. In addition, several circRNAs have been reported to have oncogenic or tumour suppressor roles or to regulate drug resistance in kidney cancer. The available data suggest that circRNAs could be promising diagnostic and/or prognostic biomarkers and potential therapeutic targets for kidney disease, cardiovascular disease and kidney cancer.
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Affiliation(s)
- Anton Jan van Zonneveld
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Malte Kölling
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Roel Bijkerk
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Johan M Lorenzen
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland.
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156
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Petkovic S, Graff S, Feller N, Berghaus J, Ruppert VP, Dülfer J, Sczakiel G. Circular versus linear RNA topology: different modes of RNA-RNA interactions in vitro and in human cells. RNA Biol 2021; 18:674-683. [PMID: 34839802 PMCID: PMC8782184 DOI: 10.1080/15476286.2021.1978214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Circular RNA is progressively reported to occur in various species including mammals where it is thought to be involved in the post-transcriptional regulation of gene expression, partly via interactions with microRNA. Here, we asked whether the circular topology causes functional differences to linear forms when interacting with short RNA strands in vitro and in human cells. Kinetic studies with human bladder cancer-derived synthetic circular RNA versus linear transcripts, respectively, with short oligoribonucleotides showed similar association rates for both topologies. Conversely, a substantial topology-related difference was measured for the activation entropy and the activation enthalpy of RNA–RNA annealing. This finding strongly indicates a significant difference of the mechanism of RNA–RNA interactions. To investigate whether these characteristics of circular RNA are biologically meaningful we performed transient transfection experiments with a microRNA-regulated expression system for luciferase in bladder cancer-derived cells. We co-transfected linear or circular RNA containing one microRNA binding site for the target-suppressing microRNA mlet7a. Here, the circular isoform showed a strongly increased competition with microRNA function versus linear versions. In summary, this study suggests novel topology-related characteristics of RNA–RNA interactions involving circRNA in vitro and in living cells.
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Affiliation(s)
- Sonja Petkovic
- Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Lübeck, Germany
| | - Sarah Graff
- Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Lübeck, Germany
| | - Nina Feller
- Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Lübeck, Germany
| | - Julia Berghaus
- Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Lübeck, Germany
| | | | - Jasmin Dülfer
- Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Lübeck, Germany
| | - Georg Sczakiel
- Institut für Molekulare Medizin, Universität zu Lübeck and UKSH, Campus Lübeck, Lübeck, Germany
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157
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RelA/MicroRNA-30a/NLRP3 signal axis is involved in rheumatoid arthritis via regulating NLRP3 inflammasome in macrophages. Cell Death Dis 2021; 12:1060. [PMID: 34750358 PMCID: PMC8575917 DOI: 10.1038/s41419-021-04349-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 02/07/2023]
Abstract
NLRP3 inflammasome plays an important role in the pathogenesis of rheumatoid arthritis (RA). However, the post-transcriptional regulation of NLRP3 expression by miRNA in synovial macrophages is still not well understood. The aim of the study is to elucidate the mechanisms of RA with the focus on miRNAs mediated post-transcriptional regulation of the NLRP3 inflammasome. Here, we used NLRP3-deficient mice (NLRP3KO) to cross with TNFα-transgenic mice (TNFTG) to generate NLRP3KO/TNFTG mice, and compared their joint phenotypes with those of their TNFTG and wild-type (WT) littermates at 5 months of age. In comparison to WT mice, articular bone volume and cartilage area are decreased, whereas inflammed area, eroded surface, ALP+ osteoblast number, TRAP+ osteoclast number, and the areas of RelA+F4/80+, Caspase-1+F4/80+, IL-1β+F4/80+ synoviocytes are increased in the TNFTG mice. Knockout of NLRP3 ameliorates joint inflammation and bone damage in TNFTG mice. Further, in TNFα-primed BMDMs, RelA positively regulates NLRP3 expression, but negatively regulates miR-30a. Additionally, miR-30a negatively mediates NLRP3 expression by directly binding to its 3' UTR, suggesting a miR-30a-mediated feedforward loop acting on NLRP3. Finally, intra-articular injection of AAV-miR-30a inhibits NLRP3 inflammasome activation, reduces joint inflammation, and attenuates bone damage in TNFTG mice. Thus, RelA/miR-30a/NLRP3 signal axis is involved in RA through regulating NLRP3 Inflammasome in macrophages.
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158
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Vieux KF, Prothro KP, Kelley LH, Palmer C, Maine EM, Veksler-Lublinsky I, McJunkin K. Screening by deep sequencing reveals mediators of microRNA tailing in C. elegans. Nucleic Acids Res 2021; 49:11167-11180. [PMID: 34586415 DOI: 10.1093/nar/gkab840] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022] Open
Abstract
microRNAs are frequently modified by addition of untemplated nucleotides to the 3' end, but the role of this tailing is often unclear. Here we characterize the prevalence and functional consequences of microRNA tailing in vivo, using Caenorhabditis elegans. MicroRNA tailing in C. elegans consists mostly of mono-uridylation of mature microRNA species, with rarer mono-adenylation which is likely added to microRNA precursors. Through a targeted RNAi screen, we discover that the TUT4/TUT7 gene family member CID-1/CDE-1/PUP-1 is required for uridylation, whereas the GLD2 gene family member F31C3.2-here named GLD-2-related 2 (GLDR-2)-is required for adenylation. Thus, the TUT4/TUT7 and GLD2 gene families have broadly conserved roles in miRNA modification. We specifically examine the role of tailing in microRNA turnover. We determine half-lives of microRNAs after acute inactivation of microRNA biogenesis, revealing that half-lives are generally long (median = 20.7 h), as observed in other systems. Although we observe that the proportion of tailed species increases over time after biogenesis, disrupting tailing does not alter microRNA decay. Thus, tailing is not a global regulator of decay in C. elegans. Nonetheless, by identifying the responsible enzymes, this study lays the groundwork to explore whether tailing plays more specialized context- or miRNA-specific regulatory roles.
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Affiliation(s)
- Karl-Frédéric Vieux
- National Institutes of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20815, USA
| | - Katherine P Prothro
- National Institutes of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20815, USA.,Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leanne H Kelley
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - Cameron Palmer
- National Institutes of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20815, USA
| | - Eleanor M Maine
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | | | - Katherine McJunkin
- National Institutes of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20815, USA
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159
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Chen YM, Zheng YL, Su X, Wang XQ. Crosstalk Between MicroRNAs and Circular RNAs in Human Diseases: A Bibliographic Study. Front Cell Dev Biol 2021; 9:754880. [PMID: 34733854 PMCID: PMC8558455 DOI: 10.3389/fcell.2021.754880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/28/2021] [Indexed: 12/18/2022] Open
Abstract
Background: Crosstalk of circular RNAs (circRNAs) and microRNAs (miRNAs) refers to the communication and co-regulation between them. circRNAs can act as miRNAs sponges, and miRNAs can mediate circRNAs. They interact to regulate gene expression and participate in the occurrence and development of various human diseases. Methods: Publications on the crosstalk between miRNAs and circRNAs in human diseases were collected from Web of Science. The collected material was limited to English articles and reviews. CiteSpace and Microsoft Excel were used for bibliographic analysis. Results: A total of 1,013 papers satisfied the inclusion criteria. The publication outputs and types of researched diseases were analyzed, and bibliographic analysis was used to characterize the most active journals, countries, institutions, keywords, and references. The annual number of publications remarkably increased from 2011 to 2020. Neoplasm was the main research hotspot (n = 750 publications), and Biochemical and Biophysical Research Communications published the largest number of papers (n = 64) on this topic. Nanjing Medical University ranked first among institutions actively engaged in this field by publishing 72 papers, and China contributed 96.84% of the 1,013 papers (n = 981 publications) analyzed. Burst keywords in recent years included glioblastoma, miR-7, skeletal muscle, and non-coding RNA. Conclusion: Crosstalk between miRNAs and circRNAs in human diseases is a popular research topic. This study provides important clues on research trends and frontiers.
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Affiliation(s)
- Yu-Meng Chen
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai, China
| | - Yi-Li Zheng
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai, China
| | - Xuan Su
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai, China
| | - Xue-Qiang Wang
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai, China.,Shanghai Shangti Orthopaedic Hospital, Shanghai, China
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160
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Sałówka A, Martinez-Sanchez A. Molecular Mechanisms of Nutrient-Mediated Regulation of MicroRNAs in Pancreatic β-cells. Front Endocrinol (Lausanne) 2021; 12:704824. [PMID: 34803905 PMCID: PMC8600252 DOI: 10.3389/fendo.2021.704824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Pancreatic β-cells within the islets of Langerhans respond to rising blood glucose levels by secreting insulin that stimulates glucose uptake by peripheral tissues to maintain whole body energy homeostasis. To different extents, failure of β-cell function and/or β-cell loss contribute to the development of Type 1 and Type 2 diabetes. Chronically elevated glycaemia and high circulating free fatty acids, as often seen in obese diabetics, accelerate β-cell failure and the development of the disease. MiRNAs are essential for endocrine development and for mature pancreatic β-cell function and are dysregulated in diabetes. In this review, we summarize the different molecular mechanisms that control miRNA expression and function, including transcription, stability, posttranscriptional modifications, and interaction with RNA binding proteins and other non-coding RNAs. We also discuss which of these mechanisms are responsible for the nutrient-mediated regulation of the activity of β-cell miRNAs and identify some of the more important knowledge gaps in the field.
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Affiliation(s)
| | - Aida Martinez-Sanchez
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
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161
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Frédérick PM, Simard MJ. Regulation and different functions of the animal microRNA-induced silencing complex. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1701. [PMID: 34725940 DOI: 10.1002/wrna.1701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 01/03/2023]
Abstract
Among the different types of small RNAs, microRNAs (miRNAs) are key players in controlling gene expression at the mRNA level. To be active, they must associate with an Argonaute protein to form the miRNA induced silencing complex (miRISC) and binds to specific mRNA through complementarity sequences. The miRISC binding to an mRNA can lead to multiple outcomes, the most frequent being inhibition of the translation and/or deadenylation followed by decapping and mRNA decay. In the last years, several studies described different mechanisms modulating miRISC functions in animals. For instance, the regulation of the Argonaute protein through post-translational modifications can change the miRISC gene regulatory activity as well as modulate its binding to proteins, mRNA targets and miRISC stability. Furthermore, the presence of RNA binding proteins and multiple miRISCs at the targeted mRNA 3' untranslated region (3'UTR) can also affect its function through cooperation or competition mechanisms, underlying the importance of the 3'UTR environment in miRNA-mediated repression. Another way to regulate the miRISC function is by modulation of its interactors, forming different types of miRNA silencing complexes that affect gene regulation differently. It is also reported that the subcellular localization of several components of the miRNA pathway can modulate miRISC function, suggesting an important role for vesicular trafficking in the regulation of this essential silencing complex. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Pierre-Marc Frédérick
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec, QC, Canada.,Université Laval Cancer Research Centre, Québec, QC, Canada
| | - Martin J Simard
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec, QC, Canada.,Université Laval Cancer Research Centre, Québec, QC, Canada
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162
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Li S, Xiao F. The identification of crucial spreaders in complex networks by effective gravity model. Inf Sci (N Y) 2021. [DOI: 10.1016/j.ins.2021.08.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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163
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Amin ND, Senturk G, Costaguta G, Driscoll S, O'Leary B, Bonanomi D, Pfaff SL. A hidden threshold in motor neuron gene networks revealed by modulation of miR-218 dose. Neuron 2021; 109:3252-3267.e6. [PMID: 34450025 DOI: 10.1016/j.neuron.2021.07.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/01/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
Disruption of homeostatic microRNA (miRNA) expression levels is known to cause human neuropathology. However, the gene regulatory and phenotypic effects of altering a miRNA's in vivo abundance (rather than its binary gain or loss) are not well understood. By genetic combination, we generated an allelic series of mice expressing varying levels of miR-218, a motor neuron-selective gene regulator associated with motor neuron disease. Titration of miR-218 cellular dose unexpectedly revealed complex, non-ratiometric target mRNA dose responses and distinct gene network outputs. A non-linearly responsive regulon exhibited a steep miR-218 dose-dependent threshold in repression that, when crossed, resulted in severe motor neuron synaptic failure and death. This work demonstrates that a miRNA can govern distinct gene network outputs at different expression levels and that miRNA-dependent phenotypes emerge at particular dose ranges because of hidden regulatory inflection points of their underlying gene networks.
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Affiliation(s)
- Neal D Amin
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Gokhan Senturk
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Giancarlo Costaguta
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Shawn Driscoll
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Brendan O'Leary
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dario Bonanomi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Samuel L Pfaff
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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164
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Jun W, Shaobo O, Xianhua Z, Siyu Z, Mingyang C, Xin F, Ying C, Lan L. Deregulation of hsa_circ_0001971/miR-186 and hsa_circ_0001874/miR-296 signaling pathways promotes the proliferation of oral squamous carcinoma cells by synergistically activating SHP2/PLK1 signals. Sci Rep 2021; 11:20561. [PMID: 34663837 PMCID: PMC8523700 DOI: 10.1038/s41598-021-99488-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 08/31/2021] [Indexed: 12/29/2022] Open
Abstract
It has been demonstrated that circ_0001874 and circ_0001971 are potential biomarkers for the diagnosis of oral squamous carcinoma (OSCC). MiR-186 was reported to serve as a tumor suppressor in OSCC, and the down-regulation of miR-186 was reported to lead to higher expression of oncogenic factor SHP2 and the activation of growth promoting signaling. In this study, we aimed to explore the possible molecular role of circ_0001874 and circ_0001971 signaling in the pathogenesis of OSCC. RT-qPCR, Western blot, online bioinformatics tools and luciferase assay were utilized to study the molecular signaling pathways of circ_0001874 and circ_0001971. MTT assay and FCM assay were performed to investigate the synergistic effect of circ_0001971 and circ_0001874 on cell proliferation and apoptosis. By observing the effect of different miRNAs on the levels of circ_0001847 and circ_0001971, it was identified that circ_0001847 and circ_0001971 respectively sponged the expression of miR-296 and miR-186 via binding to these miRNAs. Also, SHP2 mRNA and PLK1 mRNA were respectively targeted by miR-186 and miR-296-5p. We also established two signaling pathways, i.e., circ_0001971/miR-186/SHP2 and circ_0001874/miR-296-5p/PLK1, and validated the synergistic effect of circ_0001971 and circ_0001874 via observing their positive effect on cell proliferation and negative effect on cell apoptosis. The expression of miR-186 and miR-296-5p was generally lower in saliva of OSCC patients compared with that in OLK patients, while the expression of miR-186 and miR-296-5p was specifically up-regulated in saliva of OSCC patients. In conclusion, the finding of this study demonstrated that the relative level of hsa_circ_0001971 and hsa_circ_0001874 were different in the saliva of OSCC patients and could be used as predictive biomarkers for the development of OSCC. Furthermore, oncogenic effects of hsa_circ_0001971 and hsa_circ_0001874 in the development of OSCC might be, at least partially, mediated by its downstream signaling pathways including hsa_circ_0001971/microRNA-186/SHP2 and hsa_circ_0001874/microRNA-297/PLK1.
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Affiliation(s)
- Wang Jun
- Oral and Maxillofacial Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Ouyang Shaobo
- Department of Oral Prosthodontics, Affiliated Stomatological Hospital of Nanchang University, Jiangxi Provincial Key Laboratory of Oral Biomedicine, 49 Fuzhou Lu, Nanchang, 330006, China
| | - Zhang Xianhua
- Department of Oral Prosthodontics, Affiliated Stomatological Hospital of Nanchang University, Jiangxi Provincial Key Laboratory of Oral Biomedicine, 49 Fuzhou Lu, Nanchang, 330006, China
| | - Zhao Siyu
- Department of Oral Prosthodontics, Affiliated Stomatological Hospital of Nanchang University, Jiangxi Provincial Key Laboratory of Oral Biomedicine, 49 Fuzhou Lu, Nanchang, 330006, China
| | - Cheng Mingyang
- Department of Oral Prosthodontics, Affiliated Stomatological Hospital of Nanchang University, Jiangxi Provincial Key Laboratory of Oral Biomedicine, 49 Fuzhou Lu, Nanchang, 330006, China
| | - Fan Xin
- Department of Oral Prosthodontics, Affiliated Stomatological Hospital of Nanchang University, Jiangxi Provincial Key Laboratory of Oral Biomedicine, 49 Fuzhou Lu, Nanchang, 330006, China
| | - Cai Ying
- Department of Oral Prosthodontics, Affiliated Stomatological Hospital of Nanchang University, Jiangxi Provincial Key Laboratory of Oral Biomedicine, 49 Fuzhou Lu, Nanchang, 330006, China
| | - Liao Lan
- Department of Oral Prosthodontics, Affiliated Stomatological Hospital of Nanchang University, Jiangxi Provincial Key Laboratory of Oral Biomedicine, 49 Fuzhou Lu, Nanchang, 330006, China.
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165
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Mehta SL, Chokkalla AK, Vemuganti R. Noncoding RNA crosstalk in brain health and diseases. Neurochem Int 2021; 149:105139. [PMID: 34280469 PMCID: PMC8387393 DOI: 10.1016/j.neuint.2021.105139] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 12/27/2022]
Abstract
The mammalian brain expresses several classes of noncoding RNAs (ncRNAs), including long ncRNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs). These ncRNAs play vital roles in regulating cellular processes by RNA/protein scaffolding, sponging and epigenetic modifications during the pathophysiological conditions, thereby controlling transcription and translation. Some of these functions are the result of crosstalk between ncRNAs to form a competitive endogenous RNA network. These intricately organized networks comprise lncRNA/miRNA, circRNA/miRNA, or lncRNA/miRNA/circRNA, leading to crosstalk between coding and ncRNAs through miRNAs. The miRNA response elements predominantly mediate the ncRNA crosstalk to buffer the miRNAs and thereby fine-tune and counterbalance the genomic changes and regulate neuronal plasticity, synaptogenesis and neuronal differentiation. The perturbed levels and interactions of the ncRNAs could lead to pathologic events like apoptosis and inflammation. Although the regulatory landscape of the ncRNA crosstalk is still evolving, some well-known examples such as lncRNA Malat1 sponging miR-145, circRNA CDR1as sponging miR-7, and lncRNA Cyrano and the circRNA CDR1as regulating miR-7, has been shown to affect brain function. The ability to manipulate these networks is crucial in determining the functional outcome of central nervous system (CNS) pathologies. The focus of this review is to highlights the interactions and crosstalk of these networks in regulating pathophysiologic CNS function.
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Affiliation(s)
- Suresh L Mehta
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Anil K Chokkalla
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA; Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA; Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA; William S. Middleton Memorial Veteran Administration Hospital, Madison, WI, USA.
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166
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Wozniak M, Czyz M. The Functional Role of Long Non-Coding RNAs in Melanoma. Cancers (Basel) 2021; 13:cancers13194848. [PMID: 34638331 PMCID: PMC8508152 DOI: 10.3390/cancers13194848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/15/2022] Open
Abstract
Melanoma is the most lethal skin cancer, with increasing incidence worldwide. The molecular events that drive melanoma development and progression have been extensively studied, resulting in significant improvements in diagnostics and therapeutic approaches. However, a high drug resistance to targeted therapies and adverse effects of immunotherapies are still a major challenge in melanoma treatment. Therefore, the elucidation of molecular mechanisms of melanomagenesis and cancer response to treatment is of great importance. Recently, many studies have revealed the close association of long noncoding RNAs (lncRNAs) with the development of many cancers, including melanoma. These RNA molecules are able to regulate a plethora of crucial cellular processes including proliferation, differentiation, migration, invasion and apoptosis through diverse mechanisms, and even slight dysregulation of their expression may lead to tumorigenesis. lncRNAs are able to bind to protein complexes, DNA and RNAs, affecting their stability, activity, and localization. They can also regulate gene expression in the nucleus. Several functions of lncRNAs are context-dependent. This review summarizes current knowledge regarding the involvement of lncRNAs in melanoma. Their possible role as prognostic markers of melanoma response to treatment and in resistance to therapy is also discussed.
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167
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Wang X, Ma R, Zhang X, Cui L, Ding Y, Shi W, Guo C, Shi Y. Crosstalk between N6-methyladenosine modification and circular RNAs: current understanding and future directions. Mol Cancer 2021; 20:121. [PMID: 34560891 PMCID: PMC8461955 DOI: 10.1186/s12943-021-01415-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/31/2021] [Indexed: 02/07/2023] Open
Abstract
N6-methyladenosine (m6A) is a prevalent internal modification in eukaryotic RNAs regulated by the so-called "writers", "erasers", and "readers". m6A has been demonstrated to exert critical molecular functions in modulating RNA maturation, localization, translation and metabolism, thus playing an essential role in cellular, developmental, and disease processes. Circular RNAs (circRNAs) are a class of non-coding RNAs with covalently closed single-stranded structures generated by back-splicing. CircRNAs also participate in physiological and pathological processes through unique mechanisms. Despite their discovery several years ago, m6A and circRNAs has drawn increased research interest due to advances in molecular biology techniques these years. Recently, several scholars have investigated the crosstalk between m6A and circRNAs. In this review, we provide an overview of the current knowledge of m6A and circRNAs, as well as summarize the crosstalk between these molecules based on existing research. In addition, we present some suggestions for future research perspectives.
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Affiliation(s)
- Xin Wang
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, 1278 Baode Road, Jing'an District, Shanghai, 200443, China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China
| | - Rui Ma
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xilin Zhang
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, 1278 Baode Road, Jing'an District, Shanghai, 200443, China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China
| | - Lian Cui
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, 1278 Baode Road, Jing'an District, Shanghai, 200443, China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China
| | - Yangfeng Ding
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, 1278 Baode Road, Jing'an District, Shanghai, 200443, China.,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China
| | - Weimin Shi
- Department of Dermatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunyuan Guo
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, 1278 Baode Road, Jing'an District, Shanghai, 200443, China. .,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China.
| | - Yuling Shi
- Department of Dermatology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, 1278 Baode Road, Jing'an District, Shanghai, 200443, China. .,Institute of Psoriasis, Tongji University School of Medicine, Shanghai, China.
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168
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Babaei S, Singh MB, Bhalla PL. Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development. Int J Mol Sci 2021; 22:ijms221910297. [PMID: 34638635 PMCID: PMC8508787 DOI: 10.3390/ijms221910297] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022] Open
Abstract
Circular RNAs (circRNAs) are covalently closed RNA molecules generated by the back-splicing of exons from linear precursor mRNAs. Though various linear RNAs have been shown to play important regulatory roles in many biological and developmental processes, little is known about the role of their circular counterparts. In this study, we performed high-throughput RNA sequencing to delineate the expression profile and potential function of circRNAs during the five stages of pollen development in Brassica rapa. A total of 1180 circRNAs were detected in pollen development, of which 367 showed stage-specific expression patterns. Functional enrichment and metabolic pathway analysis showed that the parent genes of circRNAs were mainly involved in pollen-related molecular and biological processes such as mitotic and meiotic cell division, DNA processes, protein synthesis, protein modification, and polysaccharide biosynthesis. Moreover, by predicting the circRNA–miRNA network from our differentially expressed circRNAs, we found 88 circRNAs with potential miRNA binding sites, suggesting their role in post-transcriptional regulation of the genes. Finally, we confirmed the back-splicing sites of nine selected circRNAs using divergent primers and Sanger sequencing. Our study presents the systematic analysis of circular RNAs during pollen development and forms the basis of future studies for unlocking complex gene regulatory networks underpinning reproduction in flowering plants.
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169
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Butler AE, Cunningham TK, Ramachandran V, Diboun I, Halama A, Sathyapalan T, Najafi-Shoushtari SH, Atkin SL. Association of microRNAs With Embryo Development and Fertilization in Women Undergoing Subfertility Treatments: A Pilot Study. FRONTIERS IN REPRODUCTIVE HEALTH 2021; 3:719326. [PMID: 36303988 PMCID: PMC9580729 DOI: 10.3389/frph.2021.719326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: Small non-coding RNAs, known as microRNAs (miRNAs), have emerging regulatory functions within the ovary that have been related to fertility. This study was undertaken to determine if circulating miRNAs reflect the changes associated with the parameters of embryo development and fertilization.Methods: In this cross-sectional pilot study. Plasma miRNAs were collected from 48 sequentially presenting women in the follicular phase prior to commencing in vitro fertilization (IVF). Circulating miRNAs were measured using locked nucleic acid (LNA)-based quantitative PCR (qPCR), while an updated miRNA data set was used to determine their level of expression.Results: Body mass index and weight were associated with the miRNAs let7b-3p and miR-375, respectively (p < 0.05), with the same relationship being found between endometrium thickness at oocyte retrieval and miR-885-5p and miR-34a-5p (p < 0.05). In contrast, miR-1260a was found to be inversely associated with anti-Mullerian hormone (AMH; p = 0.007), while miR-365a-3p, miR122-5p, and miR-34a-5p correlated with embryo fertilization rates (p < 0.05). However, when omitting cases of male infertility (n = 15), miR122-5p remained significant (p < 0.05), while miR-365a-3p and miR-34a-5p no longer differed; interestingly, however, miR1260a and mir93.3p became significant (p = 0.0087/0.02, respectively). Furthermore, age was negatively associated with miR-335-3p, miR-28-5p, miR-155-5p, miR-501-3p, and miR-497-5p (p < 0.05). Live birth rate was negatively associated with miR-335-3p, miR-100-5p, miR-497-5p, let-7d, and miR-574-3p (p < 0.05), but these were not significant when age was accounted for.However, with the exclusion of male factor infertility, all those miRNAs were no longer significant, though miR.150.5p emerged as significant (p = 0.042). A beta-regression model identified miR-1260a, miR-486-5p, and miR-132-3p (p < 0.03, p = 0.0003, p < 0.00001, respectively) as the most predictive for fertilization rate. Notably, changes in detectable miRNAs were not linked to cleavage rate, top quality embryos (G3D3), and blastocyst or antral follicle count. An ingenuity pathway analysis showed that miRNAs associated with age were also associated with the variables found in reproductive system diseases.Conclusion: Plasma miRNAs prior to the IVF cycle were associated with differing demographic and IVF parameters, including age, and may be predictive biomarkers of fertilization rate.
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Affiliation(s)
- Alexandra E. Butler
- Research Department, Royal College of Surgeons Ireland, Adliya, Bahrain
- *Correspondence: Alexandra E. Butler ;
| | - Thomas Keith Cunningham
- Academic Diabetes, Endocrinology and Metabolism, Hull York Medical School, University of Hull, Hull, United Kingdom
- The Hull IVF Unit. Women's and Children's Hospital, Hull Royal Infirmary, Hull, United Kingdom
| | - Vimal Ramachandran
- Division of Research, MicroRNA Core Laboratory, Weill Cornell Medicine-Qatar, Qatar Foundation, Education City, Doha, Qatar
| | - Ilhame Diboun
- Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Anna Halama
- Division of Research, Weill Cornell Medicine-Qatar, Qatar Foundation, Education City, Doha, Qatar
| | - Thozhukat Sathyapalan
- Academic Diabetes, Endocrinology and Metabolism, Hull York Medical School, University of Hull, Hull, United Kingdom
| | - S. Hani Najafi-Shoushtari
- Division of Research, MicroRNA Core Laboratory, Weill Cornell Medicine-Qatar, Qatar Foundation, Education City, Doha, Qatar
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, United States
| | - Stephen L. Atkin
- Research Department, Royal College of Surgeons Ireland, Adliya, Bahrain
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170
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Frydas A, Wauters E, van der Zee J, Van Broeckhoven C. Uncovering the impact of noncoding variants in neurodegenerative brain diseases. Trends Genet 2021; 38:258-272. [PMID: 34535299 DOI: 10.1016/j.tig.2021.08.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 12/14/2022]
Abstract
Neurodegenerative brain diseases (NBDs) are characterized by cognitive decline and movement impairments caused by neuronal loss in different brain regions. A large fraction of the genetic heritability of NBDs is not explained by the current known mutations. Genome-wide association studies identified novel disease-risk loci, adding to the genetic basis of NBDs. Many of the associated variants reside in noncoding regions with distinct molecular functions. Genetic variation in these regions can alter functions and contribute to disease pathogenesis. Here, we discuss noncoding variants associated with NBDs. Methods for better functional interpretation of noncoding variation will expand our knowledge of the genetic architecture of NBDs and broaden the routes for therapeutic strategies.
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Affiliation(s)
- Alexandros Frydas
- Neurodegenerative Brain Diseases, Center for Molecular Neurology, VIB, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Eline Wauters
- Neurodegenerative Brain Diseases, Center for Molecular Neurology, VIB, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Julie van der Zee
- Neurodegenerative Brain Diseases, Center for Molecular Neurology, VIB, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases, Center for Molecular Neurology, VIB, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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171
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Learning noncoding RNA biology from viruses. Mamm Genome 2021; 33:412-420. [PMID: 34491378 DOI: 10.1007/s00335-021-09915-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
Insights into interactions between viral factors and the cellular machinery usually lead to discoveries concerning host cell biology. Thus, the gene expression field has historically relied on viral model systems to discover mechanisms underlying different cellular processes. In recent years, the functional characterization of the small nuclear noncoding RNAs expressed by the oncogenic Herpesvirus saimiri, called HSURs, resulted in the discovery of two mechanisms for the regulation of gene expression. HSUR1 and HSUR2 associate with host microRNAs, which are small noncoding RNAs that broadly regulate gene expression by binding to messenger RNAs. HSUR1 provided the first example of a process known as target-directed miRNA degradation that operates in cells to regulate miRNA populations. HSUR2 functions as a miRNA adaptor, uncovering an entirely new, indirect mechanism by which miRNAs can inhibit mRNA function. Here, I review the path that led to these discoveries and their implications and postulate new exciting questions about the functions of these fascinating viral noncoding RNAs.
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172
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Sharma AR, Bhattacharya M, Bhakta S, Saha A, Lee SS, Chakraborty C. Recent research progress on circular RNAs: Biogenesis, properties, functions, and therapeutic potential. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:355-371. [PMID: 34484862 PMCID: PMC8399087 DOI: 10.1016/j.omtn.2021.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Circular RNAs (circRNAs), an emerging family member of RNAs, have gained importance in research due to their new functional roles in cellular physiology and disease progression. circRNAs are usually available in a wide range of cells and have shown tissue-specific expression as well as developmental specific expression. circRNAs are characterized by structural stability, conservation, and high abundance in the cell. In this review, we discuss the different models of biogenesis. The properties of circRNAs such as localization, structure and conserved pattern, stability, and expression specificity are also been illustrated. Furthermore, we discuss the biological functions of circRNAs such as microRNA (miRNA) sponging, cell cycle regulation, cell-to-cell communication, transcription regulation, translational regulation, disease diagnosis, and therapeutic potential. Finally, we discuss the recent research progress and future perspective of circRNAs. This review provides an understanding of potential diagnostic markers and the therapeutic potential of circRNAs, which are emerging daily.
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Affiliation(s)
- Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Swarnav Bhakta
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Jagannathpur, Kolkata, West Bengal 700126, India
| | - Abinit Saha
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Jagannathpur, Kolkata, West Bengal 700126, India
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Jagannathpur, Kolkata, West Bengal 700126, India
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173
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Mecozzi N, Vera O, Karreth FA. Squaring the circle: circRNAs in melanoma. Oncogene 2021; 40:5559-5566. [PMID: 34331015 PMCID: PMC8521449 DOI: 10.1038/s41388-021-01977-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs are emerging as critical molecules in the genesis, progression, and therapy resistance of cutaneous melanoma. This includes circular RNAs (circRNAs), a class of non-coding RNAs with distinct characteristics that forms through non-canonical back-splicing. In this review, we summarize the features and functions of circRNAs and introduce the current knowledge of the roles of circRNAs in melanoma. We also highlight the various mechanisms of action of the well-studied circRNA CDR1as and describe how it acts as a melanoma tumor suppressor. We further discuss the utility of circRNAs as biomarkers, therapeutic targets, and therapeutic agents in melanoma and outline challenges that must be overcome to comprehensively characterize circRNA functions.
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Affiliation(s)
- Nicol Mecozzi
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Olga Vera
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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174
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Pastore B, Hertz HL, Price IF, Tang W. pre-piRNA trimming and 2'-O-methylation protect piRNAs from 3' tailing and degradation in C. elegans. Cell Rep 2021; 36:109640. [PMID: 34469728 PMCID: PMC8459939 DOI: 10.1016/j.celrep.2021.109640] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/24/2021] [Accepted: 08/10/2021] [Indexed: 11/30/2022] Open
Abstract
The Piwi-interacting RNA (piRNA) pathway suppresses transposable elements and promotes fertility in diverse organisms. Maturation of piRNAs involves pre-piRNA trimming followed by 2'-O-methylation at their 3' termini. Here, we report that the 3' termini of Caenorhabditis elegans piRNAs are subject to nontemplated nucleotide addition, and piRNAs with 3' addition exhibit extensive base-pairing interaction with their target RNAs. Animals deficient for PARN-1 (pre-piRNA trimmer) and HENN-1 (2'-O-methyltransferase) accumulate piRNAs with 3' nontemplated nucleotides. In henn-1 mutants, piRNAs are shortened prior to 3' addition, whereas long isoforms of untrimmed piRNAs are preferentially modified in parn-1 mutant animals. Loss of either PARN-1 or HENN-1 results in modest reduction in steady-state levels of piRNAs. Deletion of both enzymes leads to depletion of piRNAs, desilenced piRNA targets, and impaired fecundity. Together, our findings suggest that pre-piRNA trimming and 2'-O-methylation act collaboratively to protect piRNAs from tailing and degradation.
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Affiliation(s)
- Benjamin Pastore
- Department of Biological Chemistry and Pharmacology, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, Columbus, OH 43210, USA
| | - Hannah L Hertz
- Department of Biological Chemistry and Pharmacology, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ian F Price
- Department of Biological Chemistry and Pharmacology, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, Columbus, OH 43210, USA
| | - Wen Tang
- Department of Biological Chemistry and Pharmacology, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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175
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Tao M, Zheng M, Xu Y, Ma S, Zhang W, Ju S. CircRNAs and their regulatory roles in cancers. Mol Med 2021; 27:94. [PMID: 34445958 PMCID: PMC8393742 DOI: 10.1186/s10020-021-00359-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/18/2021] [Indexed: 01/17/2023] Open
Abstract
Circular RNAs (circRNAs), a novel type of non-coding RNAs (ncRNAs), have a covalently closed circular structure resulting from pre-mRNA back splicing via spliceosome and ribozymes. They can be classified differently in accordance with different criteria. As circRNAs are abundant, conserved, and stable, they can be used as diagnostic markers in various diseases and targets to develop new therapies. There are various functions of circRNAs, including sponge for miR/proteins, role of scaffolds, templates for translation, and regulators of mRNA translation and stability. Without m7G cap and poly-A tail, circRNAs can still be degraded in several ways, including RNase L, Ago-dependent, and Ago-independent degradation. Increasing evidence indicates that circRNAs can be modified by N-6 methylation (m6A) in many aspects such as biogenesis, nuclear export, translation, and degradation. In addition, they have been proved to play a regulatory role in the progression of various cancers. Recently, methods of detecting circRNAs with high sensitivity and specificity have also been reported. This review presents a detailed overview of circRNAs regarding biogenesis, biomarker, functions, degradation, and dynamic modification as well as their regulatory roles in various cancers. It’s particularly summarized in detail in the biogenesis of circRNAs, regulation of circRNAs by m6A modification and mechanisms by which circRNAs affect tumor progression respectively. Moreover, existing circRNA detection methods and their characteristics are also mentioned.
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Affiliation(s)
- Mei Tao
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No.20, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.,Medical School of Nantong University, Nantong University, Nantong, 226001, Jiangsu, China
| | - Ming Zheng
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No.20, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.,Medical School of Nantong University, Nantong University, Nantong, 226001, Jiangsu, China
| | - Yanhua Xu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No.20, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.,Medical School of Nantong University, Nantong University, Nantong, 226001, Jiangsu, China
| | - Shuo Ma
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No.20, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.,Medical School of Nantong University, Nantong University, Nantong, 226001, Jiangsu, China
| | - Weiwei Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No.20, Nantong, 226001, Jiangsu, China. .,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No.20, Nantong, 226001, Jiangsu, China.
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176
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Khorsandi K, Esfahani H, Abrahamse H. Characteristics of circRNA and its approach as diagnostic tool in melanoma. Expert Rev Mol Diagn 2021; 21:1079-1094. [PMID: 34380368 DOI: 10.1080/14737159.2021.1967749] [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: 12/08/2022]
Abstract
One of the most common types of cancer in the world is skin cancer, which has been divided into two groups: non-melanoma and melanoma skin cancer. Different external and internal agents are considered as risk factors for melanoma skin cancer pathogenesis but the exact mechanisms are not yet confirmed. Genetic and epigenetic changes, UV exposure, arsenic compounds, and chemical substances are contributory factors to the development of melanoma. A correlation has emerged between new therapies and the discovery of a basic molecular pattern for skin cancer patients. Circular RNAs (circRNAs) are described as a unique group of extensively expressed endogenous regulatory RNAs with closed-loop structure bonds connecting the 5' and 3' ends, which are commonly expressed in mammalian cells. In this review, we describe the biogenesis of circular RNAs and its function in cancerous conditions focusing on the crosstalk between different circRNAs and melanoma. Increasing evidence suggests that circRNAs appears to be relative to the origin and development of skin-related diseases like malignant melanoma. Different circular RNAs like hsa_circ_0025039, hsa_circRNA006612, circRNA005537, and circANRIL, by targeting different cellular and molecular targets (e.g., CDK4, DAB2IP, ZEB1, miR-889, and let-7 c-3p), can participate in melanoma cancer progression.
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Affiliation(s)
- Khatereh Khorsandi
- Department of Photodynamic, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran
| | - HomaSadat Esfahani
- Department of Photodynamic, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran
| | - Heidi Abrahamse
- Laser Research Centre, Nrf SARChI Chair: Laser Applications in Health, Faculty of Health Sciences, University of Johannesburg, Auckland Park, South Africa
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177
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Rahimi K, Venø MT, Dupont DM, Kjems J. Nanopore sequencing of brain-derived full-length circRNAs reveals circRNA-specific exon usage, intron retention and microexons. Nat Commun 2021; 12:4825. [PMID: 34376658 PMCID: PMC8355340 DOI: 10.1038/s41467-021-24975-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022] Open
Abstract
Circular RNA (circRNA) is a class of covalently joined non-coding RNAs with functional roles in a wide variety of cellular processes. Their composition shows extensive overlap with exons found in linear mRNAs making it difficult to delineate their composition using short-read RNA sequencing, particularly for long and multi-exonic circRNAs. Here, we use long-read nanopore sequencing of nicked circRNAs (circNick-LRS) and characterize a total of 18,266 and 39,623 circRNAs in human and mouse brain, respectively. We further develop an approach for targeted long-read sequencing of a panel of circRNAs (circPanel-LRS), eliminating the need for prior circRNA enrichment and find >30 circRNA isoforms on average per targeted locus. Our data show that circRNAs exhibit a large number of splicing events such as novel exons, intron retention and microexons that preferentially occur in circRNAs. We propose that altered exon usage in circRNAs may reflect resistance to nonsense-mediated decay in the absence of translation.
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Affiliation(s)
- Karim Rahimi
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark.
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
| | - Morten T Venø
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Omiics ApS, Aarhus, Denmark
| | - Daniel M Dupont
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark.
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
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178
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Abstract
Cardiac hypertrophy, characterized by the enlargement of cardiomyocytes, is initially an adaptive response to physiological and pathological stimuli. Decompensated cardiac hypertrophy is related to fibrosis, inflammatory cytokine, maladaptive remodeling, and heart failure. Although pathological myocardial hypertrophy is the main cause of hypertrophy-related morbidity and mortality, our understanding of its mechanism is still poor. Long noncoding RNAs (lncRNAs) are noncoding RNAs that regulate various physiological and pathological processes through multiple molecular mechanisms. Recently, accumulating evidence has indicated that lncRNA-H19 is a potent regulator of the progression of cardiac hypertrophy. For the first time, this review summarizes the current studies about the role of lncRNA-H19 in cardiac hypertrophy, including its pathophysiological processes and underlying pathological mechanism, including calcium regulation, fibrosis, apoptosis, angiogenesis, inflammation, and methylation. The context within which lncRNA-H19 might be developed as a target for cardiac hypertrophy treatment is then discussed to gain better insight into the possible biological functions of lncRNA-H19 in cardiac hypertrophy.
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179
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Cheng J, Hao J, Jiang X, Ji J, Wu T, Chen X, Zhang F. Ameliorative effects of miR-423-5p against polarization of microglial cells of the M1 phenotype by targeting a NLRP3 inflammasome signaling pathway. Int Immunopharmacol 2021; 99:108006. [PMID: 34339965 DOI: 10.1016/j.intimp.2021.108006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/15/2022]
Abstract
Spinal cord injury (SCI) causes sensation and motion dysfunction. Activation of microglial cells (MCs) in the central nervous system (CNS) is heterogeneous. Heterogeneous types of MCs can produce cytotoxic or neuroprotective effects, secrete proinflammatory or anti-inflammatory factors. The cytotoxic effect of MCs is one of the reasons for secondary damage after SCI. The NLR family pyrin domain containing 3 (NLRP3) inflammasome is a protein that can recognize pathogen-related molecular patterns or host-derived danger signal molecules, responses to microbial infection, and sterile stressors. SCI triggers activation of the NLRP3 inflammasome in the CNS. We investigated the interaction between miR-423-5p and NLRP3 in MCs polarization after SCI. A rat model of SCI was established by a modified version of Allen's method. Spinal samples were adopted for preparation and sequencing of RNA. We screenedapromising microRNA (miR-423-5p) according to the results. Then, we found that NLRP3 was one of the prediction targets of miR-423-5p. By intervening in expression of miR-423-5p and NLRP3, we observed the different polarization of MCs. We employeda dual-luciferase reporter study, proteomics, and transcriptomicsto ascertain the direct targeting relationship between miR-423-5p and NLRP3. MiR-423-5p expression was decreased significantly after SCI in vivo and in vitro. Upregulation of miR-423-5p expression could prevent MCs from lipopolysaccharide-induced M1 polarization. Knockdown of NLRP3 expression could prevent MCs from lipopolysaccharide-induced M1 polarization. MiR-423-5p inhibited MCs polarization to the M1 phenotype by targeting NLRP3.
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Affiliation(s)
- Jiaqi Cheng
- Medical School of Nantong University, Nantong, Jiangsu Province 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jie Hao
- Department of Orthopedics, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province 226001, China
| | - Xingjie Jiang
- Department of Orthopedics, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province 226001, China
| | - Jiawei Ji
- Medical School of Nantong University, Nantong, Jiangsu Province 226001, China
| | - Tong Wu
- Medical School of Nantong University, Nantong, Jiangsu Province 226001, China
| | - Xiaoqing Chen
- Department of Orthopedics, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province 226001, China.
| | - Feng Zhang
- Department of Orthopedics, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province 226001, China.
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180
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Ahmadi S, Zobeiri M, Mohammadi Talvar S, Masoudi K, Khanizad A, Fotouhi S, Bradburn S. Differential expression of H19, BC1, MIAT1, and MALAT1 long non-coding RNAs within key brain reward regions after repeated morphine treatment. Behav Brain Res 2021; 414:113478. [PMID: 34302875 DOI: 10.1016/j.bbr.2021.113478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/22/2021] [Accepted: 07/19/2021] [Indexed: 12/14/2022]
Abstract
Morphine-induced analgesic tolerance and dependence are significant limits of pain control; however, the exact molecular mechanisms underlying morphine tolerance and dependence have remained unclear. The role of long non-coding RNAs (lncRNAs) in morphine tolerance and dependence is yet to be determined. We aimed to explore the association of specific lncRNAs expression in key brain reward regions after repeated injection of morphine. Male Wistar rats received subcutaneous injections of twice-daily morphine (10 mg/kg) or saline (1 mL/kg) for eight days. On day 8 of the repeated injections, induction of morphine analgesic tolerance and dependence was confirmed through a hotplate test and a naloxone-precipitated withdrawal analysis, respectively. Expression of H19, BC1, MIAT1, and MALAT1 lncRNAs was determined from the midbrain, striatum, hypothalamus, prefrontal cortex (PFC), and hippocampus by real-time PCR on day 8 of the repeated injections. The H19 expression was significantly different between morphine-treated and control saline-treated rats in all investigated areas except for the hippocampus. The BC1 expression significantly altered in the midbrain, hypothalamus, and hippocampus, but not in the striatum and PFC after repeated morphine treatment. The MIAT1 and MALAT1 expression site-specifically altered in the midbrain, hypothalamus, and striatum; however, no significant changes were detected in their expression in the PFC and hippocampus after repeated morphine treatment. We conclude that alterations in the expression of these lncRNAs in the brain reward regions especially in the midbrain, striatum and hypothalamus may have critical roles in the development of morphine dependence and tolerance, which need to be considered in future researches.
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Affiliation(s)
- Shamseddin Ahmadi
- Department of Biological Science, Faculty of Science, University of Kurdistan, Sanandaj, Iran.
| | - Mohammad Zobeiri
- Department of Biological Science, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Shiva Mohammadi Talvar
- Department of Biological Science, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Kayvan Masoudi
- Department of Biological Science, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Amir Khanizad
- Department of Biological Science, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Shima Fotouhi
- Department of Biological Science, Faculty of Science, University of Kurdistan, Sanandaj, Iran
| | - Steven Bradburn
- Department of Life Sciences, Bioscience Research Centre, Manchester Metropolitan University, Manchester, UK
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181
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Chen D, Wu W, Yi L, Feng Y, Chang C, Chen S, Gao J, Chen G, Zhen G. A Potential circRNA-miRNA-mRNA Regulatory Network in Asthmatic Airway Epithelial Cells Identified by Integrated Analysis of Microarray Datasets. Front Mol Biosci 2021; 8:703307. [PMID: 34336929 PMCID: PMC8322703 DOI: 10.3389/fmolb.2021.703307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/30/2021] [Indexed: 01/17/2023] Open
Abstract
Background: Asthma is one of the most prevalent chronic respiratory diseases worldwide. Bronchial epithelial cells play a critical role in the pathogenesis of asthma. Circular RNAs (circRNAs) act as microRNA (miRNA) sponges to regulate downstream gene expression. However, the role of epithelial circRNAs in asthma remains to be investigated. This study aims to explore the potential circRNA-miRNA-messenger RNA (mRNA) regulatory network in asthma by integrated analysis of publicly available microarray datasets. Methods: Five mRNA microarray datasets derived from bronchial brushing samples from asthma patients and control subjects were downloaded from the Gene Expression Omnibus (GEO) database. The robust rank aggregation (RRA) method was used to identify robust differentially expressed genes (DEGs) in bronchial epithelial cells between asthma patients and controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to annotate the functions of the DEGs. Protein-protein interaction (PPI) analysis was performed to identify hub genes. Three miRNA databases (Targetscan, miRDB, and miRWalk) were used to predict the miRNAs which potentially target the hub genes. A miRNA microarray dataset derived from bronchial brushings was used to validate the miRNA-mRNA relationships. Finally, a circRNA-miRNA-mRNA network was constructed via the ENCORI database. Results: A total of 127 robust DEGs in bronchial epithelial cells between steroid-naïve asthma patients (n = 272) and healthy controls (n = 165) were identified from five mRNA microarray datasets. Enrichment analyses showed that DEGs were mainly enriched in several biological processes related to asthma, including humoral immune response, salivary secretion, and IL-17 signaling pathway. Nineteen hub genes were identified and were used to construct a potential epithelial circRNA-miRNA-mRNA network. The top 10 competing endogenous RNAs were hsa_circ_0001585, hsa_circ_0078031, hsa_circ_0000552, hsa-miR-30a-3p, hsa-miR-30d-3p, KIT, CD69, ADRA2A, BPIFA1, and GGH. Conclusion: Our study reveals a potential role for epithelial circRNA-miRNA-mRNA network in the pathogenesis of asthma.
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Affiliation(s)
- Dian Chen
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Respiratory Diseases, National Health Commission of People's Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Wenliang Wu
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Respiratory Diseases, National Health Commission of People's Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Lingling Yi
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Respiratory Diseases, National Health Commission of People's Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Yuchen Feng
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Respiratory Diseases, National Health Commission of People's Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Chenli Chang
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Respiratory Diseases, National Health Commission of People's Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Shengchong Chen
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Respiratory Diseases, National Health Commission of People's Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Jiali Gao
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Respiratory Diseases, National Health Commission of People's Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Gongqi Chen
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Respiratory Diseases, National Health Commission of People's Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Guohua Zhen
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Respiratory Diseases, National Health Commission of People's Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
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182
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[Role and mechanism of circular RNA in brain injury induced by inflammation in preterm mice: a preliminary study]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2021; 23. [PMID: 34266532 PMCID: PMC8292664 DOI: 10.7499/j.issn.1008-8830.2104067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To determine the association of circular RNA (circRNA) and circRNA-microRNA (miRNA) network regulation with brain injury induced by inflammation in preterm mice. METHODS Pregnant mice were treated with intraperitoneally injected lipopolysaccharide to establish a preterm mouse model of brain injury induced by inflammation (inflammation preterm group with 3 mice). Preterm mice born to normal pregnant mice by cesarean section were selected as controls (non-inflammation preterm group with 3 mice). The gene microarray technique was used to screen out the circRNAs associated with brain injury in preterm mice. The miRNA target prediction software was used to predict the binding sites between circRNAs and miRNAs and analyze the regulatory mechanism. RESULTS A total of 365 differentially expressed circRNAs were screened out between the inflammation preterm and non-inflammation preterm groups (fold change > 1.5, P < 0.05), among which there were 206 upregulated circRNAs and 159 downregulated circRNAs. Further analysis of the circRNAs with a fold change of > 4 showed that these circRNAs could bind to miRNAs and regulate their activity, thereby regulating the expression of the genes associated with the nervous system. CONCLUSIONS Inflammation induces a significant change in the expression profile of circRNAs in the brain tissue of mice, and the change in the expression of circRNAs plays an important role in brain injury induced by inflammation and subsequent brain development in preterm mice.
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183
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Xu Y, Qiu M, Shen M, Dong S, Ye G, Shi X, Sun M. The emerging regulatory roles of long non-coding RNAs implicated in cancer metabolism. Mol Ther 2021; 29:2209-2218. [PMID: 33775912 PMCID: PMC8261164 DOI: 10.1016/j.ymthe.2021.03.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/19/2021] [Accepted: 03/21/2021] [Indexed: 01/05/2023] Open
Abstract
Compared to normal cells, cancer cells exhibit specific metabolic characteristics that facilitate the growth and metastasis of cancer. It is now widely appreciated that long non-coding RNAs (lncRNAs) exert extensive regulatory effects on a spectrum of biological processes through diverse mechanisms. In this review, we focus on the rapidly advancing field of lncRNAs and summarize the relationship between the dysregulation of lncRNAs and cancer metabolism, with a particular emphasis on the specific roles of lncRNAs in glycolysis, mitochondrial function, glutamine, and lipid metabolism. These investigations reveal that lncRNAs are a key factor in the complexity of malignant cancer metabolism. Only through understanding the relevance between lncRNAs and cancer metabolic reprogramming can we open a new chapter in the history of carcinogenesis, one that promises to alter the methods of cancer diagnosis and treatment.
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Affiliation(s)
- Yongcan Xu
- Department of General Surgery, Huzhou Central Hospital, Affiliated Huzhou Hospital, Zhejiang University School of Medicine, Huzhou 313000, People's Republic of China
| | - Mantang Qiu
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, People's Republic of China
| | - Minmin Shen
- Drug Clinical Trial Institution Office, Huzhou Central Hospital, Affiliated Central Hospital, Huzhou University, Huzhou, People's Republic of China
| | - Shunli Dong
- Department of Central Laboratory, Huzhou Central Hospital, Affiliated Central Hospital, Huzhou University, Huzhou, People's Republic of China
| | - Guochao Ye
- Department of General Surgery, Huzhou Central Hospital, Affiliated Huzhou Hospital, Zhejiang University School of Medicine, Huzhou 313000, People's Republic of China
| | - Xuefei Shi
- Department of Respiratory Medicine, Huzhou Central Hospital, Affiliated Central Hospital, Huzhou University, Huzhou 313000, People's Republic of China.
| | - Ming Sun
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, People's Republic of China; Suzhou Cancer Center, Gusu School of Nanjing Medical University Suzhou, Jiangsu, People's Republic of China.
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184
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Deng L, Guo Y, Liu J, Wang X, Chen S, Wang Q, Rao J, Wang Y, Zuo T, Hu Q, Zhao X, Dong Z. miR-671-5p Attenuates Neuroinflammation via Suppressing NF-κB Expression in an Acute Ischemic Stroke Model. Neurochem Res 2021; 46:1801-1813. [PMID: 33871800 DOI: 10.1007/s11064-021-03321-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 12/15/2022]
Abstract
This study was designed to investigate the role of miR-671-5p in in vitro and in vivo models of ischemic stroke (IS). Middle cerebral artery occlusion and reperfusion (MCAO/R) in C57BL/6 mice as well as oxygen-glucose deprivation and reoxygenation (OGD/R) in a mouse hippocampal HT22 neuron line were used as in vivo and in vitro models of IS injury, respectively. miR-671-5p agomir, miR-671-5p antagomir, pcDNA3.1-NF-κB, and negative controls were transfected into cells using riboFECT CP reagent. miR-671-5p agomir, pcDNA3.1-NF-κB, and negative vectors were administered into MCAO/R mice via intracerebroventricular injection. The results showed that miR-671-5p was significantly downregulated and that miR-671-5p agomir alleviated injury and neuroinflammation induced by ischemic reperfusion. A dual-luciferase reporter assay confirmed that NF-κB is a direct target of miR-671-5p. Reverse experiments showed that miR-671-5p agomir reduced neuroinflammation via suppression of NF-κB expression in both in vitro and in vivo models of IS. Our data suggest that miR-671-5p may be a viable therapeutic target for diminishing neuroinflammation in patients with IS.
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Affiliation(s)
- Ling Deng
- College of Pharmacology, The Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China
- Library, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Yi Guo
- Department of Radiology, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Jingdong Liu
- College of Pharmacology, The Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China
| | - Xuan Wang
- College of Pharmacology, The Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China
| | - Sha Chen
- College of Pharmacology, The Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China
| | - Qian Wang
- College of Pharmacology, The Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China
| | - Jianyan Rao
- College of Pharmacology, The Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China
| | - Yuchun Wang
- College of Pharmacology, The Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China
| | - Tianrui Zuo
- College of Pharmacology, The Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China
| | - Qingwen Hu
- College of Pharmacology, The Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China
| | - Xiahong Zhao
- College of Pharmacology, The Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China
| | - Zhi Dong
- College of Pharmacology, The Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China.
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185
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Keihani S, Kluever V, Fornasiero EF. Brain Long Noncoding RNAs: Multitask Regulators of Neuronal Differentiation and Function. Molecules 2021; 26:molecules26133951. [PMID: 34203457 PMCID: PMC8272081 DOI: 10.3390/molecules26133951] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
The extraordinary cellular diversity and the complex connections established within different cells types render the nervous system of vertebrates one of the most sophisticated tissues found in living organisms. Such complexity is ensured by numerous regulatory mechanisms that provide tight spatiotemporal control, robustness and reliability. While the unusual abundance of long noncoding RNAs (lncRNAs) in nervous tissues was traditionally puzzling, it is becoming clear that these molecules have genuine regulatory functions in the brain and they are essential for neuronal physiology. The canonical view of RNA as predominantly a 'coding molecule' has been largely surpassed, together with the conception that lncRNAs only represent 'waste material' produced by cells as a side effect of pervasive transcription. Here we review a growing body of evidence showing that lncRNAs play key roles in several regulatory mechanisms of neurons and other brain cells. In particular, neuronal lncRNAs are crucial for orchestrating neurogenesis, for tuning neuronal differentiation and for the exact calibration of neuronal excitability. Moreover, their diversity and the association to neurodegenerative diseases render them particularly interesting as putative biomarkers for brain disease. Overall, we foresee that in the future a more systematic scrutiny of lncRNA functions will be instrumental for an exhaustive understanding of neuronal pathophysiology.
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186
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Kirschnick N, Drees D, Redder E, Erapaneedi R, Pereira da Graca A, Schäfers M, Jiang X, Kiefer F. Rapid methods for the evaluation of fluorescent reporters in tissue clearing and the segmentation of large vascular structures. iScience 2021; 24:102650. [PMID: 34151237 PMCID: PMC8192726 DOI: 10.1016/j.isci.2021.102650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/23/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
Light sheet fluorescence microscopy (LSFM) of large tissue samples does not require mechanical sectioning and allows efficient visualization of spatially complex or rare structures. Therefore, LSFM has become invaluable in developmental and biomedical research. Because sample size may limit whole-mount staining, LSFM benefits from transgenic reporter organisms expressing fluorescent proteins (FPs) and, however, requires optical clearing and computational data visualization and analysis. The former often interferes with FPs, while the latter requires massive computing resources. Here, we describe 3D-polymerized cell dispersions, a rapid and straightforward method, based on recombinant FP expression in freely selectable tester cells, to evaluate and compare fluorescence retention in different tissue-clearing protocols. For the analysis of large LSFM data, which usually requires huge computing resources, we introduce a refined, interactive, hierarchical random walker approach that is capable of efficient segmentation of the vasculature in data sets even on a consumer grade PC.
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Affiliation(s)
- Nils Kirschnick
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Dominik Drees
- Institute of Computer Science, University of Münster, Einsteinstraße 62, 48149 Münster, Germany
| | - Esther Redder
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Raghu Erapaneedi
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Abel Pereira da Graca
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Michael Schäfers
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Xiaoyi Jiang
- Institute of Computer Science, University of Münster, Einsteinstraße 62, 48149 Münster, Germany
| | - Friedemann Kiefer
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
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187
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Zeng Y, Zou Y, Gao G, Zheng S, Wu S, Xie X, Tang H. The biogenesis, function and clinical significance of circular RNAs in breast cancer. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0485. [PMID: 34110722 PMCID: PMC8763001 DOI: 10.20892/j.issn.2095-3941.2020.0485] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/13/2021] [Indexed: 11/11/2022] Open
Abstract
Circular RNAs (circRNAs) are noncoding RNAs that form covalently closed loop structures. CircRNAs are dysregulated in cancer and play key roles in tumorigenesis, diagnosis, and tumor therapy. CircRNAs function as competing endogenous RNAs or microRNA sponges that regulate transcription and splicing, binding to proteins, and translation. CircRNAs may serve as novel biomarkers for cancer diagnosis, and they show potential as therapeutic targets in cancers including breast cancer (BC). In women, BC is the most common malignant tumor worldwide and the second leading cause of cancer death. Although evidence indicates that circRNAs play a critical role in BC, the mechanisms regulating the function of circRNAs in BC remain poorly understood. Here, we provide literature review aiming to clarify the role of circRNAs in BC and summarize the latest research. We provide a systematic overview of the biogenesis and biological functions of circRNAs, elaborate on the functional roles of circRNAs in BC, and highlight the value of circRNAs as diagnostic and therapeutic targets in BC.
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Affiliation(s)
- Yan Zeng
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Yutian Zou
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Guanfeng Gao
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Shaoquan Zheng
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Song Wu
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Xiaoming Xie
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Hailin Tang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
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188
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Kingston ER, Bartel DP. Ago2 protects Drosophila siRNAs and microRNAs from target-directed degradation, even in the absence of 2'- O-methylation. RNA (NEW YORK, N.Y.) 2021; 27:710-724. [PMID: 33853897 PMCID: PMC8127995 DOI: 10.1261/rna.078746.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 04/07/2021] [Indexed: 05/07/2023]
Abstract
Target-directed microRNA (miRNA) degradation (TDMD), which is mediated by the protein ZSWIM8, plays a widespread role in shaping miRNA abundances across bilateria. Some endogenous small interfering RNAs (siRNAs) of Drosophila cells have target sites resembling those that trigger TDMD, raising the question as to whether they too might undergo such regulation by Dora, the Drosophila ZSWIM8 homolog. Here, we find that some of these siRNAs are indeed sensitive to Dora when loaded into Ago1, the Argonaute paralog that preferentially associates with miRNAs. Despite this sensitivity when loaded into Ago1, these siRNAs are not detectably regulated by target-directed degradation because most molecules are loaded into Ago2, the Argonaute paralog that preferentially associates with siRNAs, and we find that siRNAs and miRNAs loaded into Ago2 are insensitive to Dora. One explanation for the protection of these small RNAs loaded into Ago2 is that these small RNAs are 2'-O-methylated at their 3' termini. However, 2'-O-methylation does not protect these RNAs from Dora-mediated target-directed degradation, which indicates that their protection is instead conferred by features of the Ago2 protein itself. Together, these observations clarify the requirements for regulation by target-directed degradation and expand our understanding of the role of 2'-O-methylation in small-RNA biology.
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Affiliation(s)
- Elena R Kingston
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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189
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Tang M, Lv Y. The Role of N6 -Methyladenosine Modified Circular RNA in Pathophysiological Processes. Int J Biol Sci 2021; 17:2262-2277. [PMID: 34239354 PMCID: PMC8241720 DOI: 10.7150/ijbs.60131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/21/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA) is a type of covalently closed and endogenous non-coding RNA (ncRNA) with tissue- and cell-specific expression patterns generated by a non-canonical splicing event. Previous reports have indicated that circRNAs exert their functions in different ways, thereby participating in various pathophysiological processes. N6 -methyladenosine (m6A) methylation occurs in the N6-position, which is the most abundant and conserved internal transcriptional modification in eukaryotes, including mRNA and ncRNAs. Accumulating evidences confirm that m6A modification also exists in the circRNA and greatly affects the biological functions of circRNA. Their dysregulated expression can be a cause of various pathophysiological processes, such as spermatogenesis, myoblast differentiation, cancer, cardiovascular disease, mental illness and so on. Understanding the role of m6A-modified circRNAs in pathophysiological processes may contribute to better understanding the physiological mechanisms and develop new biomarkers. This review summarizes the regulatory mechanism of m6A modification on circRNA metabolism and the role of m6A-modified circRNAs in pathophysiological processes. This article may pave the way for a better understanding of the role of epigenetically modified circRNAs in pathophysiological process.
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Affiliation(s)
| | - Yonggang Lv
- Mechanobiology and Regenerative Medicine Laboratory, Bioengineering College, Chongqing University, Chongqing, 400044, China
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190
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Circular RNAs as microRNA sponges: evidence and controversies. Essays Biochem 2021; 65:685-696. [PMID: 34028529 DOI: 10.1042/ebc20200060] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/08/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022]
Abstract
Gene expression in eukaryotic cells is a complex process encompassing several layers of regulation at the transcriptional and post-transcriptional levels. At the post-transcriptional level, microRNAs (miRs) are key regulatory molecules that function by binding directly to mRNAs. This generally leads to less efficient translation of the target mRNAs. More recently, an additional layer of gene regulation has been discovered, as other molecules, including circular RNAs (circRNAs), may bind to miRs and thereby function as sponges or decoys resulting in increased expression of the corresponding miR target genes. The circRNAs constitute a large class of mainly non-coding RNAs, which have been extensively studied in recent years, in particular in the cancer research field where many circRNAs have been proposed to function as miR sponges. Here, we briefly describe miR-mediated gene regulation and the extra layer of regulation that is imposed by the circRNAs. We describe techniques and methodologies that are commonly used to investigate potential miR sponging properties of circRNAs and discuss major pitfalls and controversies within this relatively new research field.
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191
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Razavi ZS, Asgarpour K, Mahjoubin-Tehran M, Rasouli S, Khan H, Shahrzad MK, Hamblin MR, Mirzaei H. Angiogenesis-related non-coding RNAs and gastrointestinal cancer. MOLECULAR THERAPY-ONCOLYTICS 2021; 21:220-241. [PMID: 34095461 PMCID: PMC8141508 DOI: 10.1016/j.omto.2021.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gastrointestinal (GI) cancers are among the main reasons for cancer death globally. The deadliest types of GI cancer include colon, stomach, and liver cancers. Multiple lines of evidence have shown that angiogenesis has a key role in the growth and metastasis of all GI tumors. Abnormal angiogenesis also has a critical role in many non-malignant diseases. Therefore, angiogenesis is considered to be an important target for improved cancer treatment. Despite much research, the mechanisms governing angiogenesis are not completely understood. Recently, it has been shown that angiogenesis-related non-coding RNAs (ncRNAs) could affect the development of angiogenesis in cancer cells and tumors. The broad family of ncRNAs, which include long non-coding RNAs, microRNAs, and circular RNAs, are related to the development, promotion, and metastasis of GI cancers, especially in angiogenesis. This review discusses the role of ncRNAs in mediating angiogenesis in various types of GI cancers and looks forward to the introduction of mimetics and antagonists as possible therapeutic agents.
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Affiliation(s)
| | - Kasra Asgarpour
- Department of Medicine, University of Western Ontario, London, ON, Canada
| | - Maryam Mahjoubin-Tehran
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Susan Rasouli
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mohammad Karim Shahrzad
- Department of Internal Medicine and Endocrinology, Shohadae Tajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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192
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Rikhtegar R, Mosimann PJ, Rothaupt J, Mirza-Aghazadeh-Attari M, Hallaj S, Yousefi M, Amiri A, Farashi E, Kheyrollahiyan A, Dolati S. Non-coding RNAs role in intracranial aneurysm: General principles with focus on inflammation. Life Sci 2021; 278:119617. [PMID: 34004250 DOI: 10.1016/j.lfs.2021.119617] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/30/2021] [Accepted: 05/09/2021] [Indexed: 02/07/2023]
Abstract
Intracranial aneurysm (IA) is one of the most challenging vascular lesions in the brain for clinicians. It was reported that 1%-6% of the world's population is affected by IAs. Owing to serious complications arising from these lesions, much attention has been paid to better understand their pathophysiology. Non-coding RNAs including short non-coding RNAs and long non-coding RNAs, have critical roles in modulating physiologic and pathological processes. These RNAs are emerging as new fundamental regulators of gene expression, are related with the progression of IA. Non-coding RNAs act via multiple mechanisms and be involved in vascular development, growth and remodeling. Furthermore, these molecules are involved in the regulation of inflammation, a key process in the formation and rupture of IA. Studying non-coding RNAs can yield a hypothetical mechanism for better understanding IA. The present study aims to focus on the role of these non-coding RNAs in the pathogenesis of IA.
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Affiliation(s)
- Reza Rikhtegar
- Department of Intracranial Endovascular Therapy, Alfried Krupp Krankenhaus Essen, Essen, Germany
| | - Pascal J Mosimann
- Department of Intracranial Endovascular Therapy, Alfried Krupp Krankenhaus Essen, Essen, Germany
| | - Jan Rothaupt
- Department of Intracranial Endovascular Therapy, Alfried Krupp Krankenhaus Essen, Essen, Germany
| | | | - Shahin Hallaj
- Burn and Regenerative Medicine Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Mehdi Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Atefeh Amiri
- Department of Cardiology, Marien Marl Hospital, Marl, Germany
| | - Ebrahim Farashi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Sanam Dolati
- Physical Medicine and Rehabilitation Research Center, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
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193
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Zhuang A, Calkin AC, Lau S, Kiriazis H, Donner DG, Liu Y, Bond ST, Moody SC, Gould EA, Colgan TD, Carmona SR, Inouye M, de Aguiar Vallim TQ, Tarling EJ, Quaife-Ryan GA, Hudson JE, Porrello ER, Gregorevic P, Gao XM, Du XJ, McMullen JR, Drew BG. Loss of the long non-coding RNA OIP5-AS1 exacerbates heart failure in a sex-specific manner. iScience 2021; 24:102537. [PMID: 34142046 PMCID: PMC8184514 DOI: 10.1016/j.isci.2021.102537] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/28/2021] [Accepted: 05/11/2021] [Indexed: 11/30/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been demonstrated to influence numerous biological processes, being strongly implicated in the maintenance and physiological function of various tissues including the heart. The lncRNA OIP5-AS1 (1700020I14Rik/Cyrano) has been studied in several settings; however its role in cardiac pathologies remains mostly uncharacterized. Using a series of in vitro and ex vivo methods, we demonstrate that OIP5-AS1 is regulated during cardiac development in rodent and human models and in disease settings in mice. Using CRISPR, we engineered a global OIP5-AS1 knockout (KO) mouse and demonstrated that female KO mice develop exacerbated heart failure following cardiac pressure overload (transverse aortic constriction [TAC]) but male mice do not. RNA-sequencing of wild-type and KO hearts suggest that OIP5-AS1 regulates pathways that impact mitochondrial function. Thus, these findings highlight OIP5-AS1 as a gene of interest in sex-specific differences in mitochondrial function and development of heart failure. The lncRNA OIP5-AS1 is enriched in striated muscles in mice and humans. OIP5-AS1 is regulated during heart development and in models of heart disease. Global deletion of OIP5-AS1 exacerbates heart failure specifically in female mice. Transcriptomics analysis suggests that loss OIP5-AS1 alters mitochondrial function.
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Affiliation(s)
- Aowen Zhuang
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
- Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Anna C. Calkin
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
- Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Shannen Lau
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Helen Kiriazis
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Daniel G. Donner
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Yingying Liu
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Simon T. Bond
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Sarah C. Moody
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | | | | | | | - Michael Inouye
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | | | - Elizabeth J. Tarling
- Department of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | | | | | - Enzo R. Porrello
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul Gregorevic
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Xiao-Ming Gao
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Xiao-Jun Du
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Julie R. McMullen
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
- Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
- Corresponding author
| | - Brian G. Drew
- Baker Heart & Diabetes Institute, Melbourne, VIC 3004, Australia
- Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
- Corresponding author
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194
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Circular RNA Plek promotes fibrogenic activation by regulating the miR-135b-5p/TGF-βR1 axis after spinal cord injury. Aging (Albany NY) 2021; 13:13211-13224. [PMID: 33982670 PMCID: PMC8148484 DOI: 10.18632/aging.203002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/05/2021] [Indexed: 02/05/2023]
Abstract
Objectives: The spinal cord rarely repairs itself when damaged; however, methods for encouraging nerves to regrow are on the horizon. Although circular RNAs (circRNAs) contribute to various biological processes, including neuronal processes, their functions in the subacute phase of spinal cord injury (SCI) have not been elucidated. In this study, we identified a novel circRNA, named CircPlek, with increased expression in spinal tissues after SCI. Materials and Methods: We predicted a regulatory relationship between CircPlek and miR-135b-5p, which showed the most obvious decrease in post-SCI expression. We established the CircPlek/miR-135b-5p/transforming growth factor-beta receptor type I (TGF-βR1) axis using a bioinformatics approach and further evaluated the potential function of the interaction network in vitro. Results: We confirmed that in TGF-β1-induced fibroblasts, the overexpression of miR-135b-5p or/and inhibition of CircPlek inhibited fibrosis activation via the Smad pathway. Inhibitors of miR-135b-5p had antagonistic effects on CircPlek. Conclusions: the CircPlek/miR-135b-5p/TGF-βR1 axis may exert important functions in SCI and is a potential therapeutic target.
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195
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Yang Q, Li F, He AT, Yang BB. Circular RNAs: Expression, localization, and therapeutic potentials. Mol Ther 2021; 29:1683-1702. [PMID: 33484969 PMCID: PMC8116570 DOI: 10.1016/j.ymthe.2021.01.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are RNAs with a unique circular structure that is generated from back-splicing processes. These circular molecules were discovered more than 40 years ago but failed to raise scientific interest until lately. Increasing studies have found that these circular RNAs might not just be byproducts of the splicing process but possess important regulatory functions through different cellular events. Most circular RNAs are currently being studied in the field of cancer, and many of them have been confirmed to be involved in the process of tumorigenesis. However, many circular RNAs are implicated in the developmental stages of diseases other than cancer. In this review, we focus on discussing the role of circular RNAs in non-cancer diseases, especially in cardiovascular diseases. Following the summary of the life cycle of circRNAs, we provide input on studying circRNA-protein interactions based on our experience, which modulate protein translocation. Furthermore, we outline the potential of circRNAs to be potent biomarkers, effective therapeutic targets, and potential treatments in cardiovascular diseases as well as other non-cancer fields.
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Affiliation(s)
- Qiwei Yang
- Sunnybrook Research Institute, Toronto, ON, Canada; Medical Research Center, Second Hospital of Jilin University, Changchun, China; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Feiya Li
- Sunnybrook Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Alina T He
- Sunnybrook Research Institute, Toronto, ON, Canada
| | - Burton B Yang
- Sunnybrook Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada.
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196
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Jiang Y, Liu H, Yu H, Zhou Y, Zhang J, Xin W, Li Y, He S, Ma C, Zheng X, Zhang L, Zhao X, Wu B, Jiang C, Zhu D. Circular RNA Calm4 Regulates Hypoxia-Induced Pulmonary Arterial Smooth Muscle Cells Pyroptosis via the Circ-Calm4/miR-124-3p/PDCD6 Axis. Arterioscler Thromb Vasc Biol 2021; 41:1675-1693. [PMID: 33657879 PMCID: PMC8057524 DOI: 10.1161/atvbaha.120.315525] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 02/10/2021] [Indexed: 12/30/2022]
Abstract
[Figure: see text].
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MESH Headings
- Animals
- Apoptosis Regulatory Proteins/genetics
- Apoptosis Regulatory Proteins/metabolism
- Calcium-Binding Proteins/genetics
- Calcium-Binding Proteins/metabolism
- Cells, Cultured
- Disease Models, Animal
- Hypertension, Pulmonary/genetics
- Hypertension, Pulmonary/metabolism
- Hypertension, Pulmonary/pathology
- Hypertension, Pulmonary/physiopathology
- Male
- Mice, Inbred C57BL
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/physiopathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Pulmonary Artery/metabolism
- Pulmonary Artery/pathology
- Pulmonary Artery/physiopathology
- Pyroptosis
- RNA, Circular/genetics
- RNA, Circular/metabolism
- Signal Transduction
- Mice
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Affiliation(s)
- Yuan Jiang
- Central Laboratory of Harbin Medical University, Daqing, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.X., X. Zhao, D.Z.)
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
| | - Huiyu Liu
- Central Laboratory of Harbin Medical University, Daqing, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.X., X. Zhao, D.Z.)
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
| | - Hang Yu
- Central Laboratory of Harbin Medical University, Daqing, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.X., X. Zhao, D.Z.)
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
| | - Yang Zhou
- Department of Medical Oncology, The Third Affiliated Hospital of Harbin Medical University, China (Y.Z.)
| | - Junting Zhang
- Central Laboratory of Harbin Medical University, Daqing, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.X., X. Zhao, D.Z.)
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
| | - Wei Xin
- Central Laboratory of Harbin Medical University, Daqing, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.X., X. Zhao, D.Z.)
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
| | - Yiying Li
- Central Laboratory of Harbin Medical University, Daqing, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.X., X. Zhao, D.Z.)
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
| | - Siyu He
- Central Laboratory of Harbin Medical University, Daqing, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.X., X. Zhao, D.Z.)
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
| | - Cui Ma
- Central Laboratory of Harbin Medical University, Daqing, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.X., X. Zhao, D.Z.)
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
| | - Xiaodong Zheng
- Central Laboratory of Harbin Medical University, Daqing, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.X., X. Zhao, D.Z.)
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
| | - Lixin Zhang
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
| | - Xijuan Zhao
- Central Laboratory of Harbin Medical University, Daqing, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.X., X. Zhao, D.Z.)
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
| | - Bingxiang Wu
- Central Laboratory of Harbin Medical University, Daqing, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.X., X. Zhao, D.Z.)
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
- Department of Medical Oncology, The Third Affiliated Hospital of Harbin Medical University, China (Y.Z.)
- The Second Affiliated Hospital of Harbin Medical University, Heilongjiang Province, China (B.X.)
- Department of Biology, Georgia State University, Atlanta, GA (C.J.)
- State Province Key Laboratories of Biomedicine-Pharmaceutics of China, Daqing (D.Z.)
- Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, China (D.Z.)
| | - Chun Jiang
- Department of Biology, Georgia State University, Atlanta, GA (C.J.)
| | - Daling Zhu
- Central Laboratory of Harbin Medical University, Daqing, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.X., X. Zhao, D.Z.)
- Department of Pharmacology, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, College of Pharmacy, Harbin Medical University, China (Y.J., H.L., H.Y., J.Z., W.X., Y.L., S.H., C.M., X. Zheng, L.Z., X. Zhao, D.Z.)
- State Province Key Laboratories of Biomedicine-Pharmaceutics of China, Daqing (D.Z.)
- Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, China (D.Z.)
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197
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He L, Zhang F, Zhu Y, Lu M. Noncoding RNAs: Novel Insights into Postoperative Neurocognitive Disorders. ACS Chem Neurosci 2021; 12:1480-1486. [PMID: 33899470 DOI: 10.1021/acschemneuro.1c00148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Postoperative recovery for patients (particularly elderly) will be commonly encountered for postoperative neurocognitive disorders. Although effort has been undertaken to better understand and prevent these disorders, little improvement has been observed, due to largely unknown mechanisms. Emerging evidence indicates that noncoding RNAs including microRNA(s), long noncoding RNA(s), and circular RNA(s) are promising biomarkers for diagnosis, prognosis, and novel pathways to reveal mechanisms of postoperative neurocognitive disorders. However, there has been little crosstalk between noncoding RNA biology and development of postoperative neurocognitive disorders. We discuss the major noncoding RNAs in mechanisms, diagnosis, risk-stratification, prognosis, and treatment in postoperative neurocognitive disorders in a novel approach.
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Affiliation(s)
- Liang He
- Department of Anesthesiology, Yan’an Hospital of Kunming City, Kunming 650051, China
| | - Furong Zhang
- Department of Anesthesiology, Yan’an Hospital of Kunming City, Kunming 650051, China
| | - Yuling Zhu
- Department of Anesthesiology, Yan’an Hospital of Kunming City, Kunming 650051, China
| | - Meilin Lu
- Department of Anesthesiology, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
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198
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Abstract
Hundreds of microRNAs (miRNAs) are expressed in distinct spatial and temporal patterns during embryonic and postnatal mouse development. The loss of all miRNAs through the deletion of critical miRNA biogenesis factors results in early lethality. The function of each miRNA stems from their cumulative negative regulation of multiple mRNA targets expressed in a particular cell type. During development, miRNAs often coordinate the timing and direction of cell fate transitions. In adults, miRNAs frequently contribute to organismal fitness through homeostatic roles in physiology. Here, we review how the recent dissection of miRNA-knockout phenotypes in mice as well as advances related to their targets, dosage, and interactions have collectively informed our understanding of the roles of miRNAs in mammalian development and adaptive responses.
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199
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Xu K, Zhang Y, Li J. Expression and function of circular RNAs in the mammalian brain. Cell Mol Life Sci 2021; 78:4189-4200. [PMID: 33558994 PMCID: PMC11071837 DOI: 10.1007/s00018-021-03780-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/07/2021] [Accepted: 01/27/2021] [Indexed: 01/19/2023]
Abstract
Mammalian brain presents extraordinary complexity reflected in the structure, function, and dynamic changes in the biological and physiological processes of development, maturity, and aging. Recent transcriptomic profiles from the brain tissues of distinct species have described a novel class of transcripts with a covalently closed-loop structure, called circular RNAs (circRNAs), which are produced by alternative back-splicing and derived from genes associated with synaptogenesis and neural activities. Brain is a tightly regulated and largely unexplored organ where circRNAs are highly enriched and expressed in the cell type-, spatiotemporal-specific, sex-biased, and age-related manner. Although the biological functions of most of the circRNAs in the brain remain elusive, increased evidence suggests that dynamic changes in circRNA expression are critical for brain function and the maintenance of physiological homeostasis in the brain. Here, we review the latest immense progresses in the understanding of circRNA expression and function in the mammalian brain. We also discuss possibly biological functions of circRNAs in the brain, which may provide new sights of understanding brain development and aging, as well as the pathogenesis of mental diseases.
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Affiliation(s)
- Kaiyu Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ying Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jiali Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
- National Institute on Drug Dependence, Peking University, Beijing, China.
- PKU/McGovern Institute for Brain Research, Peking University, Beijing, China.
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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200
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Danac JMC, Garcia RL. CircPVT1 attenuates negative regulation of NRAS by let-7 and drives cancer cells towards oncogenicity. Sci Rep 2021; 11:9021. [PMID: 33907219 PMCID: PMC8079436 DOI: 10.1038/s41598-021-88539-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/14/2021] [Indexed: 12/30/2022] Open
Abstract
Circular RNAs have emerged as functional regulatory molecules whose aberrant expression has been linked to diverse pathophysiological processes. Here, we report that circPVT1 interferes with let-7 binding to NRAS, confirming this axis as one route by which circPVT1 can instigate an oncogenic program in A549 lung cancer cells and HCT116 colorectal cancer cells. CircPVT1 knockdown significantly reduced NRAS levels and attenuated cancer hallmark phenotypes such as proliferation, migration, resistance to apoptosis, cytoskeletal disorganization, and epithelial-mesenchymal transition. The effects of circPVT1 knockdown were at least partially rescued by blocking binding of let-7 to NRAS 3′UTR with a target protector, suggesting that a circPVT1/let-7/NRAS axis exists and acts in cells to reverse NRAS downregulation and favor oncogenicity. While the phenotypic effects of circPVT1 knockdown may be attributable to the global action of circPVT1, the target protection assays resolved the relative contribution of the circPVT1/let-7/NRAS axis specifically.
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Affiliation(s)
- Joshua Miguel C Danac
- Disease Molecular Biology and Epigenetics Laboratory, National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, 1101, Quezon City, Philippines
| | - Reynaldo L Garcia
- Disease Molecular Biology and Epigenetics Laboratory, National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, 1101, Quezon City, Philippines.
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