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Lobo V, Nowak I, Fernandez C, Correa Muler AI, Westholm JO, Huang HC, Fabrik I, Huynh HT, Shcherbinina E, Poyraz M, Härtlova A, Benhalevy D, Angeletti D, Sarshad AA. Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference. Nucleic Acids Res 2024; 52:9917-9935. [PMID: 38994560 PMCID: PMC11381323 DOI: 10.1093/nar/gkae589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 05/31/2024] [Accepted: 06/25/2024] [Indexed: 07/13/2024] Open
Abstract
In mammals, RNA interference (RNAi) was historically studied as a cytoplasmic event; however, in the last decade, a growing number of reports convincingly show the nuclear localization of the Argonaute (AGO) proteins. Nevertheless, the extent of nuclear RNAi and its implication in biological mechanisms remain to be elucidated. We found that reduced Lamin A levels significantly induce nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cell lines, which normally have no nuclear AGO2. Lamin A KO manifested a more pronounced effect in SHSY5Y cells compared to A375 cells, evident by changes in cell morphology, increased cell proliferation, and oncogenic miRNA expression. Moreover, AGO fPAR-CLIP in Lamin A KO SHSY5Y cells revealed significantly reduced RNAi activity. Further exploration of the nuclear AGO interactome by mass spectrometry identified FAM120A, an RNA-binding protein and known interactor of AGO2. Subsequent FAM120A fPAR-CLIP, revealed that FAM120A co-binds AGO targets and that this competition reduces the RNAi activity. Therefore, loss of Lamin A triggers nuclear AGO2 translocation, FAM120A mediated RNAi impairment, and upregulation of oncogenic miRNAs, facilitating cancer cell proliferation.
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Affiliation(s)
- Vivian Lobo
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Iwona Nowak
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Carola Fernandez
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Ana Iris Correa Muler
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Jakub O Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121 Solna, Sweden
| | - Hsiang-Chi Huang
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Ivo Fabrik
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Hang T Huynh
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Evgeniia Shcherbinina
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Melis Poyraz
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Anetta Härtlova
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Daniel Benhalevy
- Lab of Cellular RNA Biology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Davide Angeletti
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- SciLifeLab, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Aishe A Sarshad
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
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2
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Zhou Y, Yao Z, Lin Y, Zhang H. From Tyrosine Kinases to Tyrosine Phosphatases: New Therapeutic Targets in Cancers and Beyond. Pharmaceutics 2024; 16:888. [PMID: 39065585 PMCID: PMC11279542 DOI: 10.3390/pharmaceutics16070888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs) regulate the level of tyrosine phosphorylation in proteins. PTKs are key enzymes that catalyze the transfer of an ATP phosphoric acid to a tyrosine residue on target protein substrates. Protein tyrosine phosphatases (PTPs) are responsible for the dephosphorylation of tyrosine residues and play a role in countering PTK overactivity. As widespread oncogenes, PTKs were once considered to be promising targets for therapy. However, tyrosine kinase inhibitors (TKIs) now face a number of challenges, including drug resistance and toxic side effects. Treatment strategies now need to be developed from a new perspective. In this review, we assess the current state of TKIs and highlight the role of PTPs in cancer and other diseases. With the advances of allosteric inhibition and the development of multiple alternative proprietary drug strategies, the reputation of PTPs as "undruggable" targets has been overturned, and they are now considered viable therapeutic targets. We also discuss the strategies and prospects of PTP-targeted therapy, as well as its future development.
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Affiliation(s)
- Yu Zhou
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Y.Z.); (Z.Y.); (Y.L.)
| | - Zhimeng Yao
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Y.Z.); (Z.Y.); (Y.L.)
- Department of Urology Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510660, China
| | - Yusheng Lin
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Y.Z.); (Z.Y.); (Y.L.)
- Department of Thoracic Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510660, China
| | - Hao Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, MOE Key Laboratory of Tumor Molecular Biology, and Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou 510632, China; (Y.Z.); (Z.Y.); (Y.L.)
- Department of Pathology, Gongli Hospital of Shanghai Pudong New Area, Shanghai 200135, China
- Zhuhai Institute of Jinan University, Zhuhai 511436, China
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3
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Yang S, Zou Q, Liang Y, Zhang D, Peng L, Li W, Li W, Liu M, Tong Y, Chen L, Xu P, Yang Z, Zhou K, Xiao J, Wang H, Yu W. miR-1246 promotes osteosarcoma cell migration via NamiRNA-enhancer network dependent on Argonaute 2. MedComm (Beijing) 2024; 5:e543. [PMID: 38585233 PMCID: PMC10999177 DOI: 10.1002/mco2.543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/09/2024] Open
Abstract
High metastatic propensity of osteosarcoma leads to its therapeutic failure and poor prognosis. Although nuclear activation miRNAs (NamiRNAs) are reported to activate gene transcription via targeting enhancer and further promote tumor metastasis, it remains uncertain whether NamiRNAs regulate osteosarcoma metastasis and their exact mechanism. Here, we found that extracellular vesicles of the malignant osteosarcoma cells (143B) remarkably increased the migratory abilities of MNNG cells representing the benign osteosarcoma cells by two folds, which attributed to their high miR-1246 levels. Specially, miR-1246 located in nucleus could activate the migration gene expression (such as MMP1) to accelerate MNNG cell migration through elevating the enhancer activities via increasing H3K27ac enrichment. Instead, MMP1 expression was dramatically inhibited after Argonaute 2 (AGO2) knockdown. Notably, in vitro assays demonstrated that AGO2 recognized the hybrids of miR-1246 and its enhancer DNA via PAZ domains to prevent their degradation from RNase H and these protective roles of AGO2 may favor the gene activation by miR-1246 in vivo. Collectively, our findings suggest that miR-1246 could facilitate osteosarcoma metastasis through interacting with enhancer to activate gene expression dependent on AGO2, highlighting the nuclear AGO2 as a guardian for NamiRNA-targeted gene activation and the potential of miR-1246 for osteosarcoma metastasis therapy.
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Affiliation(s)
- Shuai Yang
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Qingping Zou
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Ying Liang
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Dapeng Zhang
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Centre for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Lina Peng
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Wei Li
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Wenxuan Li
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Mengxing Liu
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Ying Tong
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Lu Chen
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Peng Xu
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Zhicong Yang
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Kaicheng Zhou
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Jianru Xiao
- Department of Orthopaedic OncologyChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Centre for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Wenqiang Yu
- Shanghai Public Health Clinical Centre and Department of General SurgeryHuashan HospitalCancer Metastasis Institute and Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiChina
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4
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Su JH, Hong Y, Han CC, Yu J, Guan X, Zhu YM, Wang C, Ma MM, Pang RP, Ou JS, Zhou JG, Zhang ZY, Ban T, Liang SJ. Dual action of macrophage miR-204 confines cyclosporine A-induced atherosclerosis. Br J Pharmacol 2024; 181:640-658. [PMID: 37702564 DOI: 10.1111/bph.16240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 07/15/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND AND PURPOSE Atherosclerosis induced by cyclosporine A (CsA), an inhibitor of the calcineurin/nuclear factor of activated T cells (NFAT) pathway, is a major concern after organ transplantation. However, the atherosclerotic mechanisms of CsA remain obscure. We previously demonstrated that calcineurin/NFAT signalling inhibition contributes to atherogenesis via suppressing microRNA-204 (miR-204) transcription. We therefore hypothesised that miR-204 is involved in the development of CsA-induced atherosclerosis. EXPERIMENTAL APPROACH ApoE-/- mice with macrophage-miR-204 overexpression were generated to determine the effects of miR-204 on CsA-induced atherosclerosis. Luciferase reporter assays and chromatin immunoprecipitation sequencing were performed to explore the targets mediating miR-204 effects. KEY RESULTS CsA alone did not significantly affect atherosclerotic lesions or serum lipid levels. However, it exacerbated high-fat diet-induced atherosclerosis and hyperlipidemia in C57BL/6J and ApoE-/- mice, respectively. miR-204 levels decreased in circulating monocytes and plaque lesions during CsA-induced atherosclerosis. The upregulation of miR-204 in macrophages inhibited CsA-induced atherosclerotic plaque formation but did not affect serum lipid levels. miR-204 limited the CsA-induced foam cell formation by reducing the expression of the scavenger receptors SR-BII and CD36. SR-BII was post-transcriptionally regulated by mature miR-204-5p via 3'-UTR targeting. Additionally, nuclear-localised miR-204-3p prevented the CsA-induced binding of Ago2 to the CD36 promoter, suppressing CD36 transcription. SR-BII or CD36 expression restoration dampened the beneficial effects of miR-204 on CsA-induced atherosclerosis. CONCLUSION AND IMPLICATIONS Macrophage miR-204 ameliorates CsA-induced atherosclerosis, suggesting that miR-204 may be a potential target for the prevention and treatment of CsA-related atherosclerotic side effects.
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Affiliation(s)
- Jia-Hui Su
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Yu Hong
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Department of Pharmacy, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Cong-Cong Han
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jie Yu
- Department of General Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xin Guan
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Ya-Mei Zhu
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Cheng Wang
- Program of Kidney and Cardiovascular Diseases, the Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Ming-Ming Ma
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Rui-Ping Pang
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jing-Song Ou
- Division of Cardiac Surgery, The Key Laboratory of Assisted Circulation, Ministry of Health, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jia-Guo Zhou
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Program of Kidney and Cardiovascular Diseases, the Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Zi-Yi Zhang
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Tao Ban
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Si-Jia Liang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Program of Kidney and Cardiovascular Diseases, the Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
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Sala L, Kumar M, Prajapat M, Chandrasekhar S, Cosby RL, La Rocca G, Macfarlan TS, Awasthi P, Chari R, Kruhlak M, Vidigal JA. AGO2 silences mobile transposons in the nucleus of quiescent cells. Nat Struct Mol Biol 2023; 30:1985-1995. [PMID: 37985687 DOI: 10.1038/s41594-023-01151-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/27/2023] [Indexed: 11/22/2023]
Abstract
Argonaute 2 (AGO2) is a cytoplasmic component of the miRNA pathway, with essential roles in development and disease. Yet little is known about its regulation in vivo. Here we show that in quiescent mouse splenocytes, AGO2 localizes almost exclusively to the nucleus. AGO2 subcellular localization is modulated by the Pi3K-AKT-mTOR pathway, a well-established regulator of quiescence. Signaling through this pathway in proliferating cells promotes AGO2 cytoplasmic accumulation, at least in part by stimulating the expression of TNRC6, an essential AGO2 binding partner in the miRNA pathway. In quiescent cells in which mTOR signaling is low, AGO2 accumulates in the nucleus, where it binds to young mobile transposons co-transcriptionally to repress their expression via its catalytic domain. Our data point to an essential but previously unrecognized nuclear role for AGO2 during quiescence as part of a genome-defense system against young mobile elements and provide evidence of RNA interference in the soma of mammals.
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Affiliation(s)
- Laura Sala
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
| | - Manish Kumar
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
| | - Mahendra Prajapat
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
| | - Srividya Chandrasekhar
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
| | - Rachel L Cosby
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA
- The National Institute for General Medical Sciences, The National Institutes of Health, Bethesda, MD, USA
| | - Gaspare La Rocca
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA
| | - Parirokh Awasthi
- Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, The National Institutes of Health, Frederick, MD, USA
| | - Raj Chari
- Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, The National Institutes of Health, Frederick, MD, USA
| | - Michael Kruhlak
- CCR Confocal Microscopy Core Facility, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
| | - Joana A Vidigal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA.
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6
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Larivera S, Neumeier J, Meister G. Post-transcriptional gene silencing in a dynamic RNP world. Biol Chem 2023; 404:1051-1067. [PMID: 37739934 DOI: 10.1515/hsz-2023-0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
MicroRNA (miRNA)-guided gene silencing is a key regulatory process in various organisms and linked to many human diseases. MiRNAs are processed from precursor molecules and associate with Argonaute proteins to repress the expression of complementary target mRNAs. Excellent work by numerous labs has contributed to a detailed understanding of the mechanisms of miRNA function. However, miRNA effects have mostly been analyzed and viewed as isolated events and their natural environment as part of complex RNA-protein particles (RNPs) is often neglected. RNA binding proteins (RBPs) regulate key enzymes of the miRNA processing machinery and furthermore RBPs or readers of RNA modifications may modulate miRNA activity on mRNAs. Such proteins may function similarly to miRNAs and add their own contributions to the overall expression level of a particular gene. Therefore, post-transcriptional gene regulation might be more the sum of individual regulatory events and should be viewed as part of a dynamic and complex RNP world.
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Affiliation(s)
- Simone Larivera
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
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7
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Luo J, Ji Y, Chen N, Song G, Zhou S, Niu X, Yu D. Nuclear miR-150 enhances hepatic lipid accumulation by targeting RNA transcripts overlapping the PLIN2 promoter. iScience 2023; 26:107837. [PMID: 37736048 PMCID: PMC10509351 DOI: 10.1016/j.isci.2023.107837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/09/2023] [Accepted: 09/02/2023] [Indexed: 09/23/2023] Open
Abstract
Alcohol-associated liver disease is a prevalent chronic liver disease caused by excessive ethanol consumption. This study aims to investigate the role of miR-150 in regulating hepatic lipid homeostasis in alcoholic fatty liver (AFL). miR-150 was mainly distributed in the nucleus of hepatocytes and correlated with the degree of liver injury. The decreased expression of miR-150 observed in AFL was a compensatory response to ethanol-induced hepatic steatosis. Overexpression of miR-150 facilitated hepatic lipid accumulation in cellulo and exacerbated ethanol-induced liver steatosis in vivo. In silico analysis identified perilipin-2 (PLIN2) as a potential target gene of miR-150. miR-150 activated PLIN2 transcription by directly binding the RNA transcripts overlapping PLIN2 promoter and facilitating the recruitment of DNA helicase DHX9 and RNA polymeraseⅡ. Overall, our study provides fresh insights into the homeostasis regulation of hepatic steatosis induced by ethanol and identifies miR-150 as a pro-steatosis effector driving transcriptional PLIN2 gene activation.
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Affiliation(s)
- Jiao Luo
- School of Public Health, Qingdao University, Qingdao, China
| | - Yanan Ji
- School of Public Health, Qingdao University, Qingdao, China
| | - Ningning Chen
- School of Public Health, Qingdao University, Qingdao, China
| | - Ge Song
- School of Public Health, Qingdao University, Qingdao, China
| | - Shuyue Zhou
- School of Public Health, Qingdao University, Qingdao, China
| | - Xuan Niu
- School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China
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8
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Johnson KC, Corey DR. RNAi in cell nuclei: potential for a new layer of biological regulation and a new strategy for therapeutic discovery. RNA (NEW YORK, N.Y.) 2023; 29:415-422. [PMID: 36657971 PMCID: PMC10019369 DOI: 10.1261/rna.079500.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
RNA interference is almost always associated with post-transcriptional silencing in the cytoplasm. MicroRNAs (miRNAs) and critical RNAi protein factors like argonaute (AGO) and trinucleotide repeat binding containing 6 protein (TNRC6), however, are also found in cell nuclei, suggesting that nuclear miRNAs may be targets for gene regulation. Designed small duplex RNAs (dsRNAs) can modulate nuclear processes such as transcription and splicing, suggesting that they can also provide leads for therapeutic discovery. The goal of this Perspective is to provide the background on nuclear RNAi necessary to guide discussions on whether nuclear RNAi can play a role in therapeutic development programs.
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Affiliation(s)
- Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, Texas 75205, USA
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9
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Dinesen S, El-Faitarouni A, Dalgaard LT. Circulating microRNAs associated with gestational diabetes mellitus: useful biomarkers? J Endocrinol 2023; 256:JOE-22-0170. [PMID: 36346274 DOI: 10.1530/joe-22-0170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/08/2022] [Indexed: 11/09/2022]
Abstract
Different types of small non-coding RNAs, especially miRNAs, may be found in the circulation, either protein-bound or enclosed in extracellular vesicles. During gestation, and particularly during gestational diabetes mellitus (GDM), the levels of several miRNAs are altered. Worldwide the incidence of GDM is increasing, in part driven by the current obesity epidemic. This is a point of public health concern because offspring of women with GDM frequently suffer from short- and long-term complications of maternal GDM. This has prompted the investigation of whether levels of specific miRNA species, detected early in gestation, may be used as diagnostic or prognostic markers for the development of GDM. Here, we summarize the mechanisms of RNA secretion and review circulating miRNAs associated with GDM. Several miRNAs are associated with GDM: miR-29a-3p and miR-29b-3p are generally upregulated in GDM pregnancies, also when measured prior to the development of GDM, while miR-16-5p is consistently upregulated in GDM pregnancies, especially in late gestation. miR-330-3p in circulation is increased in late gestation GDM women, especially in those with poor insulin secretion. miR-17-5p, miR-19a/b-3p, miR-223-3p, miR-155-5p, miR-125-a/b-5p, miR-210-3p and miR-132 are also associated with GDM, but less so and with more contradictory results reported. There could be a publication bias as miRNAs identified early are investigated the most, suggesting that it is likely that additional, more recently detected miRNAs could also be associated with GDM. Thus, circulating miRNAs show potential as biomarkers of GDM diagnosis or prognosis, especially multiple miRNAs containing prediction algorithms show promise, but further studies are needed.
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Affiliation(s)
- Sofie Dinesen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | - Alisar El-Faitarouni
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
| | - Louise T Dalgaard
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde, Denmark
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10
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Gregory GL, Copple IM. Modulating the expression of tumor suppressor genes using activating oligonucleotide technologies as a therapeutic approach in cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:211-223. [PMID: 36700046 PMCID: PMC9840112 DOI: 10.1016/j.omtn.2022.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tumor suppressor genes (TSGs) are frequently downregulated in cancer, leading to dysregulation of the pathways that they control. The continuum model of tumor suppression suggests that even subtle changes in TSG expression, for example, driven by epigenetic modifications or copy number alterations, can lead to a loss of gene function and a phenotypic effect. This approach to exploring tumor suppression provides opportunities for alternative therapies that may be able to restore TSG expression toward normal levels, such as oligonucleotide therapies. Oligonucleotide therapies involve the administration of exogenous nucleic acids to modulate the expression of specific endogenous genes. This review focuses on two types of activating oligonucleotide therapies, small-activating RNAs and synthetic mRNAs, as novel methods to increase the expression of TSGs in cancer.
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Affiliation(s)
- Georgina L. Gregory
- Department of Pharmacology & Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 3GE, UK
| | - Ian M. Copple
- Department of Pharmacology & Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 3GE, UK
- Corresponding author: Department of Pharmacology & Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 3GE, UK.
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11
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Small Interfering RNAs Targeting a Chromatin-Associated RNA Induce Its Transcriptional Silencing in Human Cells. Mol Cell Biol 2022; 42:e0027122. [PMID: 36445136 PMCID: PMC9753735 DOI: 10.1128/mcb.00271-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Transcriptional gene silencing by small interfering RNAs (siRNAs) has been widely described in various species, including plants and yeast. In mammals, its extent remains somewhat debated. Previous studies showed that siRNAs targeting gene promoters could induce the silencing of the targeted promoter, although the involvement of off-target mechanisms was also suggested. Here, by using nascent RNA capture and RNA polymerase II chromatin immunoprecipitation, we show that siRNAs targeting a chromatin-associated noncoding RNA induced its transcriptional silencing. Deletion of the sequence targeted by one of these siRNAs on the two alleles by genome editing further showed that this silencing was due to base-pairing of the siRNA to the target. Moreover, by using cells with heterozygous deletion of the target sequence, we showed that only the wild-type allele, but not the deleted allele, was silenced by the siRNA, indicating that transcriptional silencing occurred only in cis. Finally, we demonstrated that both Ago1 and Ago2 are involved in this transcriptional silencing. Altogether, our data demonstrate that siRNAs targeting a chromatin-associated RNA at a distance from its promoter induce its transcriptional silencing. Our results thus extend the possible repertoire of endogenous or exogenous interfering RNAs.
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12
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Nuclear microRNAs release paused Pol II via the DDX21-CDK9 complex. Cell Rep 2022; 39:110673. [PMID: 35417682 DOI: 10.1016/j.celrep.2022.110673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/26/2021] [Accepted: 03/22/2022] [Indexed: 11/22/2022] Open
Abstract
RNA activation (RNAa) is an uncharacterized mechanism of transcriptional activation mediated by small RNAs, such as microRNAs (miRNAs). A critical issue in RNAa research is that it is difficult to distinguish between changes in gene expression caused indirectly by post-transcriptional regulation and direct induction of gene expression by RNAa. Therefore, in this study, we seek to identify a key factor involved in RNAa, using the induction of ZMYND10 by miR-34a as a system to evaluate RNAa. We identify the positive transcription elongation factors CDK9 and DDX21, which form a complex with nuclear AGO and TNRC6A, as important transcriptional activators of RNAa. In addition, we find that inhibition of DDX21 suppresses RNAa by miR-34a and other miRNAs without inhibiting post-transcriptional regulation. Our findings reveal a strong connection between RNAa and release of paused Pol II, facilitating RNAa research by making it possible to separately analyze post-transcriptional regulation and RNAa.
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13
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Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A. Innovative developments and emerging technologies in RNA therapeutics. RNA Biol 2022; 19:313-332. [PMID: 35188077 PMCID: PMC8865321 DOI: 10.1080/15476286.2022.2027150] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA-based therapeutics are emerging as a powerful platform for the treatment of multiple diseases. Currently, the two main categories of nucleic acid therapeutics, antisense oligonucleotides and small interfering RNAs (siRNAs), achieve their therapeutic effect through either gene silencing, splicing modulation or microRNA binding, giving rise to versatile options to target pathogenic gene expression patterns. Moreover, ongoing research seeks to expand the scope of RNA-based drugs to include more complex nucleic acid templates, such as messenger RNA, as exemplified by the first approved mRNA-based vaccine in 2020. The increasing number of approved sequences and ongoing clinical trials has attracted considerable interest in the chemical development of oligonucleotides and nucleic acids as drugs, especially since the FDA approval of the first siRNA drug in 2018. As a result, a variety of innovative approaches is emerging, highlighting the potential of RNA as one of the most prominent therapeutic tools in the drug design and development pipeline. This review seeks to provide a comprehensive summary of current efforts in academia and industry aimed at fully realizing the potential of RNA-based therapeutics. Towards this, we introduce established and emerging RNA-based technologies, with a focus on their potential as biosensors and therapeutics. We then describe their mechanisms of action and their application in different disease contexts, along with the strengths and limitations of each strategy. Since the nucleic acid toolbox is rapidly expanding, we also introduce RNA minimal architectures, RNA/protein cleavers and viral RNA as promising modalities for new therapeutics and discuss future directions for the field.
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Affiliation(s)
- François Halloy
- Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Annabelle Biscans
- Oligonucleotide Chemistry, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Katherine E. Bujold
- Department of Chemistry & Chemical Biology, McMaster University, (Ontario), Canada
| | | | - Alyssa C. Hill
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eth Zürich, Zürich, Switzerland
| | - Aurélie Lacroix
- Sixfold Bioscience, Translation & Innovation Hub, London, UK
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Linda Sundstrom
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (Hiri), Helmholtz Center for Infection Research (Hzi), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alice Ghidini
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
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14
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Liu H, Chen S, Sun Q, Sha Q, Tang Y, Jia W, Chen L, Zhao J, Wang T, Sun X. Let-7c increases BACE2 expression by RNAa and decreases Aβ production. Am J Transl Res 2022; 14:899-908. [PMID: 35273693 PMCID: PMC8902526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 10/30/2021] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) are highly conserved, non-coding transcripts that regulate gene expression in various ways. Evidence suggests that miRNAs may be a contributory factor in neurodegeneration, including Alzheimer's disease (AD), Parkinson's disease (PD), and triplet repeat disorders. In order to further understand the potential roles of miRNAs in the pathogenesis of AD, we analyzed Down syndrome (DS), a special model of AD, by using a TaqMan microRNA array and found that miRNA let-7c was up-regulated in both DS and AD. ELISA assay showed that let-7c reduced the expression level of Aβ significantly. Real-time quantitative-polymerase chain reaction (RT-qPCR) was conducted to reveal that the expression level of let-7c increased dramatically in DS cells, patients with DS and mice with AD compared with normal ones respectively. Additionally, western blotting illustrated that let-7c suppressed the expression of Aβ by inducing BACE2 to cut C99 and increase the content of C83/80. BACE2 expression was inhibited by let-7c and luciferase reporter gene assay revealed that let-7c increased the activity of wild-type BACE2 promoter but not 3'UTR. Furthermore, promoter analysis of BACE2 confirmed that let-7c could bind to BACE2 in the sequence between -1368 and -1347. In addition, immunoblotting assay demonstrated that let-7c induced BACE2 expression by RNAa. To the best of our knowledge, our study revealed for the first time that let-7c up-regulated BACE2 expression and decreased Aβ production.
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Affiliation(s)
- Heng Liu
- School of Medicine, Cheeloo College of Medicine, Shandong UniversityJinan 250012, Shandong, China
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
- Department of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Shuai Chen
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
- Department of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Qian Sun
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
- Department of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Qingquan Sha
- Department of Education, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Yu Tang
- Department of Neurology, Dezhou People’s HospitalDezhou 253000, Shandong, China
| | - Wenming Jia
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
- Department of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Long Chen
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
- Department of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Juan Zhao
- NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
- Department of Otorhinolaryngology, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Tan Wang
- Department of Geriatric Medicine, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
| | - Xiulian Sun
- Brain Research Institute, Qilu Hospital of Shandong UniversityJinan 250012, Shandong, China
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15
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Tan CP, Sinigaglia L, Gomez V, Nicholls J, Habib NA. RNA Activation-A Novel Approach to Therapeutically Upregulate Gene Transcription. Molecules 2021; 26:molecules26216530. [PMID: 34770939 PMCID: PMC8586927 DOI: 10.3390/molecules26216530] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/23/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
RNA activation (RNAa) is a mechanism whereby RNA oligos complementary to genomic sequences around the promoter region of genes increase the transcription output of their target gene. Small activating RNA (saRNA) mediate RNAa through interaction with protein co-factors to facilitate RNA polymerase II activity and nucleosome remodeling. As saRNA are small, versatile and safe, they represent a new class of therapeutics that can rescue the downregulation of critical genes in disease settings. This review highlights our current understanding of saRNA biology and describes various examples of how saRNA are successfully used to treat various oncological, neurological and monogenic diseases. MTL-CEBPA, a first-in-class compound that reverses CEBPA downregulation in oncogenic processes using CEBPA-51 saRNA has entered clinical trial for the treatment of hepatocellular carcinoma (HCC). Preclinical models demonstrate that MTL-CEBPA reverses the immunosuppressive effects of myeloid cells and allows for the synergistic enhancement of other anticancer drugs. Encouraging results led to the initiation of a clinical trial combining MTL-CEBPA with a PD-1 inhibitor for treatment of solid tumors.
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Affiliation(s)
- Choon Ping Tan
- MiNA Therapeutics Ltd., Translation & Innovation Hub, 84 Wood Lane, London W12 0BZ, UK; (C.P.T.); (L.S.); (V.G.); (J.N.)
| | - Laura Sinigaglia
- MiNA Therapeutics Ltd., Translation & Innovation Hub, 84 Wood Lane, London W12 0BZ, UK; (C.P.T.); (L.S.); (V.G.); (J.N.)
| | - Valentí Gomez
- MiNA Therapeutics Ltd., Translation & Innovation Hub, 84 Wood Lane, London W12 0BZ, UK; (C.P.T.); (L.S.); (V.G.); (J.N.)
| | - Joanna Nicholls
- MiNA Therapeutics Ltd., Translation & Innovation Hub, 84 Wood Lane, London W12 0BZ, UK; (C.P.T.); (L.S.); (V.G.); (J.N.)
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN, UK
| | - Nagy A. Habib
- MiNA Therapeutics Ltd., Translation & Innovation Hub, 84 Wood Lane, London W12 0BZ, UK; (C.P.T.); (L.S.); (V.G.); (J.N.)
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN, UK
- Correspondence: ; Tel.: +44-(0)20-3313-8574
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16
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Hernandez SM, Tikhonova EB, Baca KR, Zhao F, Zhu X, Karamyshev AL. Unexpected Implication of SRP and AGO2 in Parkinson's Disease: Involvement in Alpha-Synuclein Biogenesis. Cells 2021; 10:2792. [PMID: 34685771 PMCID: PMC8534902 DOI: 10.3390/cells10102792] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 01/21/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder classified by the loss of dopaminergic neurons in the substantia nigra pars compacta, the region of the brain that is responsible for motor control. Surviving neurons in this region contain aggregated protein alpha-Synuclein (αSyn) in the form of cytoplasmic inclusions, referred to as Lewy bodies. Changes in αSyn expression are also associated with PD and its progression. Previously, we demonstrated that signal recognition particle (SRP) and Argonaute 2 (AGO2) proteins are involved in protein quality control at the ribosome during translation. We also demonstrated that SRP has an mRNA protection function in addition to a protein targeting function, thus controlling mRNA and protein expression. In this study, we tested involvement of these factors in αSyn biogenesis. We hypothesize that loss of these factors may interfere with αSyn expression, and subsequently, be associated with PD. Using depletion assays in human cell culture and analysis of these proteins in the brains of deceased PD patients, we demonstrate that SRP and AGO2 are involved in the control of αSyn expression and AGO2 has reduced expression in PD. We show for the first time that SRP is involved in mRNA protection of αSyn, a protein that does not have a signal sequence or transmembrane span. Our findings suggest that SRP may interact with a hydrophobic domain in the middle of αSyn during translation. Understanding the molecular mechanisms controlling αSyn biogenesis in cells is vital to developing preventative therapies against PD.
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Affiliation(s)
- Sarah M. Hernandez
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (S.M.H.); (E.B.T.); (K.R.B.)
| | - Elena B. Tikhonova
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (S.M.H.); (E.B.T.); (K.R.B.)
| | - Kristen R. Baca
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (S.M.H.); (E.B.T.); (K.R.B.)
- Center for the Integration of STEM Education and Research (CISER), Texas Tech University, Lubbock, TX 79409, USA
| | - Fanpeng Zhao
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA; (F.Z.); (X.Z.)
| | - Xiongwei Zhu
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA; (F.Z.); (X.Z.)
| | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (S.M.H.); (E.B.T.); (K.R.B.)
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17
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Singh N. Role of mammalian long non-coding RNAs in normal and neuro oncological disorders. Genomics 2021; 113:3250-3273. [PMID: 34302945 DOI: 10.1016/j.ygeno.2021.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 12/09/2022]
Abstract
Long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes but have a crucial role in gene regulation. LncRNA is distinct, they are being transcribed using RNA polymerase II, and their functionality depends on subcellular localization. Depending on their niche, they specifically interact with DNA, RNA, and proteins and modify chromatin function, regulate transcription at various stages, forms nuclear condensation bodies and nucleolar organization. lncRNAs may also change the stability and translation of cytoplasmic mRNAs and hamper signaling pathways. Thus, lncRNAs affect the physio-pathological states and lead to the development of various disorders, immune responses, and cancer. To date, ~40% of lncRNAs have been reported in the nervous system (NS) and are involved in the early development/differentiation of the NS to synaptogenesis. LncRNA expression patterns in the most common adult and pediatric tumor suggest them as potential biomarkers and provide a rationale for targeting them pharmaceutically. Here, we discuss the mechanisms of lncRNA synthesis, localization, and functions in transcriptional, post-transcriptional, and other forms of gene regulation, methods of lncRNA identification, and their potential therapeutic applications in neuro oncological disorders as explained by molecular mechanisms in other malignant disorders.
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Affiliation(s)
- Neetu Singh
- Molecular Biology Unit, Department of Centre for Advance Research, King George's Medical University, Lucknow, Uttar Pradesh 226 003, India.
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18
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Yokota A, Hiramoto M, Hino H, Tokuhisa M, Miyazaki M, Kazama H, Takano N, Miyazawa K. Sequestosome 1 (p62) accumulation in breast cancer cells suppresses progesterone receptor expression via argonaute 2. Biochem Biophys Res Commun 2020; 531:256-263. [PMID: 32800344 DOI: 10.1016/j.bbrc.2020.07.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/13/2020] [Indexed: 12/22/2022]
Abstract
Sequestosome 1 (p62) is a multifunctional adapter protein involved in various physiological functions, such as selective autophagy and oxidative stress response. Hence, aberrant expression and defective regulation of p62 are thought to lead to the onset of various diseases, including cancer. The expression of p62 has been shown to be increased in breast cancer tissues, and is correlated with a poor prognosis. However, the role of p62 in the breast cancer pathophysiology is still unclear. Here, we aimed to analyze the effect of changes in p62 expression on breast cancer cell lines. DNA microarray analysis revealed that the expression of progesterone receptor (PR), which is one of the indices for the classification of breast cancer subtypes, was markedly suppressed by forced expression of p62. The protein expression of PR was also decreased by forced expression of p62, but increased by knockdown of p62. Moreover, we found that p62 knockdown induced the protein expression of argonaute 2 (AGO2). Luciferase reporter assay results showed that the gene expression of PR was promoted by AGO2. Furthermore, results revealed that overexpression of AGO2 partially rescued the decrease in PR expression induced by forced expression of p62. Collectively, our findings indicated that p62 accumulation suppressed the expression of AGO2, which in turn decreased the expression of PR, suggesting that p62 may serve as a marker of aggressive breast cancer and poor prognosis. Moreover, the p62-AGO2-PR axis was identified as a crucial signaling cascade in breast cancer progression.
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Affiliation(s)
- Ayuka Yokota
- Department of Biochemistry, Tokyo Medical University, Tokyo, 160-8402, Japan
| | - Masaki Hiramoto
- Department of Biochemistry, Tokyo Medical University, Tokyo, 160-8402, Japan.
| | - Hirotsugu Hino
- Department of Biochemistry, Tokyo Medical University, Tokyo, 160-8402, Japan
| | - Mayumi Tokuhisa
- Department of Biochemistry, Tokyo Medical University, Tokyo, 160-8402, Japan
| | - Masaya Miyazaki
- Department of Biochemistry, Tokyo Medical University, Tokyo, 160-8402, Japan
| | - Hiromi Kazama
- Department of Biochemistry, Tokyo Medical University, Tokyo, 160-8402, Japan
| | - Naoharu Takano
- Department of Biochemistry, Tokyo Medical University, Tokyo, 160-8402, Japan
| | - Keisuke Miyazawa
- Department of Biochemistry, Tokyo Medical University, Tokyo, 160-8402, Japan
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19
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Developing small activating RNA as a therapeutic: current challenges and promises. Ther Deliv 2020; 10:151-164. [PMID: 30909853 DOI: 10.4155/tde-2018-0061] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA activation (RNAa) allows specific gene upregulation mediated by a small activating RNA (saRNA). Harnessing this process would help in developing novel therapeutics for undruggable diseases. Since its discovery in mid 2000s, improvements of saRNA design, synthetic chemistry and understanding of the biology have matured the way to apply RNAa. Indeed, MiNA therapeutics Ltd has conducted the first RNAa clinical trial for advanced hepatocellular carcinoma patients with promising outcomes. However, to fully realize the RNAa potential better saRNA delivery strategies are needed to target other diseases. Currently, saRNA can be delivered in vivo by lipid nanoparticles, dendrimers, lipid and polymer hybrids and aptamers. Further developing these delivery technologies and novel application of RNAa will prove to be invaluable for new treatment development.
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20
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De Hayr L, Asad S, Hussain M, Asgari S. RNA activation in insects: The targeted activation of endogenous and exogenous genes. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 119:103325. [PMID: 31978586 DOI: 10.1016/j.ibmb.2020.103325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/10/2019] [Accepted: 01/15/2020] [Indexed: 06/10/2023]
Abstract
RNA activation (RNAa) is a newly emerging area of research in which dsRNA targeting promoter regions can induce the expression of the target gene. Although still in its infancy, it is already having significant impacts in several research areas in particular as cancer therapeutics. So far, the scope of RNAa has been limited to mammals and Caenorhabditis elegans with no indication of its prevalence in insects. In this study, we aimed to demonstrate the presence of RNAa in the insect dengue vector Aedes aegypti. Furthermore, we looked to uncover some details surrounding the involvement of host factors in order to present this as a new technique for insect research. The outcomes of this study provide new opportunities to further research into arthropod-borne diseases and insect biology in the same way as RNA interference.
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Affiliation(s)
- Lachlan De Hayr
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sultan Asad
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mazhar Hussain
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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21
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Li X, Wang X, Cheng Z, Zhu Q. AGO2 and its partners: a silencing complex, a chromatin modulator, and new features. Crit Rev Biochem Mol Biol 2020; 55:33-53. [DOI: 10.1080/10409238.2020.1738331] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Xiaojing Li
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Xueying Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Zeneng Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
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22
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Abstract
The RNA interference (RNAi) pathway regulates mRNA stability and translation in nearly all human cells. Small double-stranded RNA molecules can efficiently trigger RNAi silencing of specific genes, but their therapeutic use has faced numerous challenges involving safety and potency. However, August 2018 marked a new era for the field, with the US Food and Drug Administration approving patisiran, the first RNAi-based drug. In this Review, we discuss key advances in the design and development of RNAi drugs leading up to this landmark achievement, the state of the current clinical pipeline and prospects for future advances, including novel RNAi pathway agents utilizing mechanisms beyond post-translational RNAi silencing.
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23
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Liu Z, Johnson ST, Zhang Z, Corey DR. Expression of TNRC6 (GW182) Proteins Is Not Necessary for Gene Silencing by Fully Complementary RNA Duplexes. Nucleic Acid Ther 2019; 29:323-334. [PMID: 31670606 PMCID: PMC6885777 DOI: 10.1089/nat.2019.0815] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The trinucleotide repeat containing 6 (TNRC6) family of proteins are core components of RNA interference (RNAi) and consist of three paralogs (TNRC6A, TNRC6B, and TNRC6C). The TNRC6 paralogs associate with argonaute (AGO) protein, the core RNAi factor, and bridge its interactions with other proteins. We obtained TNRC6A and TNRC6B single and double knockout cell lines to investigate how the TNRC6 paralogs contribute to RNAi. We found that TNRC6 proteins are not required for gene silencing when duplex RNAs are fully complementary. TNRC6 expression was necessary for regulation by a microRNA. TNRC6A, but not TNRC6B, expression was necessary for transcriptional activation by a duplex RNA targeting a gene promoter. By contrast, AGO2 is required for all three gene expression pathways. TNRC6A can affect the Dicer localization in cytoplasm versus the nucleus, but none of the three TNRC6 paralogs was necessary for nuclear localization of AGO2. Our data suggest that the roles of the TNRC6 paralogs differ in some details and that TNRC6 is not required for clinical therapeutic silencing mechanisms that involve fully complementary duplex RNAs.
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Affiliation(s)
- Zhongtian Liu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China.,Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center at Dallas, Dallas, Texas
| | - Samantha T Johnson
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center at Dallas, Dallas, Texas
| | - Zhiying Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - David R Corey
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center at Dallas, Dallas, Texas
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Park J, Zhu Y, Tao X, Brazill JM, Li C, Wuchty S, Zhai RG. MicroRNA miR-1002 Enhances NMNAT-Mediated Stress Response by Modulating Alternative Splicing. iScience 2019; 19:1048-1064. [PMID: 31522116 PMCID: PMC6745518 DOI: 10.1016/j.isci.2019.08.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 05/07/2019] [Accepted: 08/27/2019] [Indexed: 11/30/2022] Open
Abstract
Understanding endogenous regulation of stress resistance and homeostasis maintenance is critical to developing neuroprotective therapies. Nicotinamide mononucleotide adenylyltransferase (NMNAT) is a conserved essential enzyme that confers extraordinary protection and stress resistance in many neurodegenerative disease models. Drosophila Nmnat is alternatively spliced to two mRNA variants, RA and RB. RB translates to protein isoform PD with robust protective activity and is upregulated upon stress to confer enhanced neuroprotection. The mechanisms regulating the alternative splicing and stress response of NMNAT remain unclear. We have discovered a Drosophila microRNA, dme-miR-1002, which promotes the splicing of NMNAT pre-mRNA to RB by disrupting a pre-mRNA stem-loop structure. NMNAT pre-mRNA is preferentially spliced to RA in basal conditions, whereas miR-1002 enhances NMNAT PD-mediated stress protection by binding via RISC component Argonaute1 to the pre-mRNA, facilitating the splicing switch to RB. These results outline a new process for microRNAs in regulating alternative splicing and modulating stress resistance.
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Affiliation(s)
- Joun Park
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Neuroscience, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yi Zhu
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xianzun Tao
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jennifer M Brazill
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Chong Li
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Human Genetics and Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Coral Gables, FL 33146, USA
| | - R Grace Zhai
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Neuroscience, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Human Genetics and Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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25
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Wang D, Sun X, Wei Y, Liang H, Yuan M, Jin F, Chen X, Liu Y, Zhang CY, Li L, Zen K. Nuclear miR-122 directly regulates the biogenesis of cell survival oncomiR miR-21 at the posttranscriptional level. Nucleic Acids Res 2019; 46:2012-2029. [PMID: 29253196 PMCID: PMC5829740 DOI: 10.1093/nar/gkx1254] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/06/2017] [Indexed: 01/04/2023] Open
Abstract
Hepatic miR-122 can serve as a pro-apoptotic factor to suppress tumorigenesis. The underlying mechanism, however, remains incompletely understood. Here we present the first evidence that miR-122 promotes hepatocellular carcinoma cell apoptosis through directly silencing the biogenesis of cell survival oncomiR miR-21 at posttranscriptional level. We find that miR-122 is strongly expressed in primary liver cell nucleus but its nuclear localization is markedly decreased in transformed cells particularly in chemoresistant tumor cells. MiRNA profiling and RT-qPCR confirm an inverse correlation between miR-122 and miR-21 in hepatocellular carcinoma tissues/cells, and increasing or decreasing nuclear level of miR-122 respectively reduces or increases miR-21 expression. Mechanistically, nuclear miR-122 suppresses miR-21 maturation via binding to a 19-nt UG-containing recognition element in the basal region of pri-miR-21 and preventing the Drosha-DGCR8 microprocessor's conversion of pri-miR-21 into pre-miR-21. Furthermore, both in vitro and in vivo studies demonstrate that nuclear miR-122 participates in the regulation of HCC cell apoptosis through modulating the miR-21-targeted programmed cell death 4 (PDCD4) signal pathway.
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Affiliation(s)
- Dong Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210093, China.,State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, Jiangsu 210009, China
| | - Xinlei Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Yao Wei
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Hongwei Liang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210093, China.,Center of Inflammation, Immunity and Infection, Center for Diagnostics and Therapeutics, Program of Cellular Biology and Immunology of Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Min Yuan
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Fangfang Jin
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Xi Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Yuan Liu
- Center of Inflammation, Immunity and Infection, Center for Diagnostics and Therapeutics, Program of Cellular Biology and Immunology of Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Chen-Yu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Limin Li
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Ke Zen
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210093, China.,Center of Inflammation, Immunity and Infection, Center for Diagnostics and Therapeutics, Program of Cellular Biology and Immunology of Department of Biology, Georgia State University, Atlanta, GA 30303, USA
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26
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Chalertpet K, Pin-On P, Aporntewan C, Patchsung M, Ingrungruanglert P, Israsena N, Mutirangura A. Argonaute 4 as an Effector Protein in RNA-Directed DNA Methylation in Human Cells. Front Genet 2019; 10:645. [PMID: 31333722 PMCID: PMC6620710 DOI: 10.3389/fgene.2019.00645] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/18/2019] [Indexed: 01/06/2023] Open
Abstract
DNA methylation of specific genome locations contributes to the distinct functions of multicellular organisms. DNA methylation can be governed by RNA-dependent DNA methylation (RdDM). RdDM is carried out by endogenous small-RNA-guided epigenomic editing complexes that add a methyl group to a precise DNA location. In plants, the Argonaute 4 (AGO4) protein is one of the main catalytic components involved in RdDM. Although small interfering RNA or short hairpin RNA has been shown to be able to guide DNA methylation in human cells, AGO protein-regulated RdDM in humans has not yet been evaluated. This study aimed to identify a key regulatory AGO protein involved in human RdDM by bioinformatics and to explore its function in RdDM by a combination of AGO4 knockdown, Alu small interfering RNA transfection, AGO4-expressing plasmid transfection, chromatin immunoprecipitation, cell-penetrating peptide-tagged AGO4 combined Alu single-guide RNA transfection, and methylation analyses. We found that first, human AGO4 showed stronger genome-wide association with DNA methylation than AGO1–AGO3. Second, endogenous AGO4 depletion demethylated DNA of known AGO4 bound loci. Finally, exogenous AGO4 de novo methylated the bound DNA sequences. Therefore, we discovered that AGO4 plays a role in human RdDM.
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Affiliation(s)
- Kanwalat Chalertpet
- Interdisciplinary Program of Biomedical Sciences, Faculty of the Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Piyapat Pin-On
- Interdisciplinary Program of Biomedical Sciences, Faculty of the Graduate School, Chulalongkorn University, Bangkok, Thailand.,Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Chatchawit Aporntewan
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Maturada Patchsung
- Interdisciplinary Program of Biomedical Sciences, Faculty of the Graduate School, Chulalongkorn University, Bangkok, Thailand.,Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Praewphan Ingrungruanglert
- Stem Cells and Cell Therapy Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nipan Israsena
- Stem Cells and Cell Therapy Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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27
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Zhang Y, Zhang H. RNAa Induced by TATA Box-Targeting MicroRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 28639194 DOI: 10.1007/978-981-10-4310-9_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent studies reveal that some nuclear microRNAs (miRNA) and synthesized siRNAs target gene promoters to activate gene transcription (RNAa). Interestingly, our group identified a novel HIV-1-encoded miRNA, miR-H3, which targets specifically the core promoter TATA box of HIV-1 and activates viral gene expression. Depletion of miR-H3 significantly impaired the replication of HIV-1. miR-H3 mimics could activate viruses from CD4+ T cells isolated from patients receiving suppressive highly active antiretroviral therapy, which is very intriguing for reducing HIV-1 latent reservoir. Further study revealed that many cellular miRNAs also function like miR-H3. For instance, let-7i targets the TATA box of the interleukin-2 (IL-2) promoter and upregulates IL-2 expression in T-lymphocytes. In RNAa induced by TATA box-targeting miRNAs, Argonaute (AGO) proteins are needed, but there is no evidence for the involvement of promoter-associated transcripts or epigenetic modifications. We propose that the binding of small RNA-AGO complex to TATA box could facilitate the assembly of RNA Polymerase II transcription preinitiation complex. In addition, synthesized small RNAs targeting TATA box can also efficiently activate transcription of interested genes, such as insulin, IL-2, and c-Myc. The discovery of RNAa induced by TATA box-targeting miRNA provides an easy-to-use tool for activating gene expression.
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Affiliation(s)
- Yijun Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
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28
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Bajczyk M, Bhat SS, Szewc L, Szweykowska-Kulinska Z, Jarmolowski A, Dolata J. Novel Nuclear Functions of Arabidopsis ARGONAUTE1: Beyond RNA Interference. PLANT PHYSIOLOGY 2019; 179:1030-1039. [PMID: 30606888 PMCID: PMC6393810 DOI: 10.1104/pp.18.01351] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/21/2018] [Indexed: 05/04/2023]
Abstract
Argonaute1 activity is not limited to the cytoplasm and has been found to be associated with the regulation of gene expression in the nucleus and to be tightly associated with chromatin and transcription.
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Affiliation(s)
- Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Susheel Sagar Bhat
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Lukasz Szewc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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29
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Lisowiec-Wąchnicka J, Bartyś N, Pasternak A. A systematic study on the influence of thermodynamic asymmetry of 5'-ends of siRNA duplexes in relation to their silencing potency. Sci Rep 2019; 9:2477. [PMID: 30792489 PMCID: PMC6385221 DOI: 10.1038/s41598-018-36620-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/23/2018] [Indexed: 01/04/2023] Open
Abstract
siRNA molecules possess high potential as molecular tools and can be used as effective therapeutics in humans. One of the key steps in the action of these molecules is the choice of antisense strand by the RNA-induced silencing complex (RISC). To explain this process, we verified the theory which states that antisense strand selection is based on the thermodynamically less stable 5′ end of siRNA. Based on the studies presented herein, we observed that for the tested siRNA duplexes, the difference in the thermodynamic stability of the terminal, penultimate and pre-penultimate pairs in the duplex siRNA is not the dominant factor in antisense strand selection. We found that both strands in each tested siRNA molecule are used as an antisense strand. The introduction of modified nucleotides, whose impact on the thermodynamic stability of siRNA duplexes was studied, results in changes in antisense strand selection by the RISC complex. The presence of a modified residue often caused predominant selection of only one antisense strand which is at variance with the theory of siRNA strand bias.
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Affiliation(s)
- Jolanta Lisowiec-Wąchnicka
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Natalia Bartyś
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Anna Pasternak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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30
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Zhang X, Shen B, Cui Y. Ago HITS-CLIP expands microRNA-mRNA interactions in nucleus and cytoplasm of gastric cancer cells. BMC Cancer 2019; 19:29. [PMID: 30621629 PMCID: PMC6325853 DOI: 10.1186/s12885-018-5246-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 12/26/2018] [Indexed: 01/22/2023] Open
Abstract
Background Intensive investigations have identified a collection of microRNAs (miRNAs) and their functional machineries in cytoplasm. However, a comprehensive view of miRNAs and mRNAs in cytoplasm and nucleus has not been explored. This study aims to reveal the mechanisms of miRNA-RNA interactions in nucleus and cytoplasm. Methods In this study, the miRNAs and their target mRNAs in the Argonaute2 (Ago2) complex of nucleus and cytoplasm of gastric cancer cells were characterized using high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP). Then, the selected miRNAs were verified by Northern blot. The target mRNAs in the Argonaute2 (Ago2) complex of nucleus and cytoplasm of gastric cancer cells were analyzed through Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analysis. Results The results revealed that there were 243 miRNAs and 265 miRNAs in the Ago2 complexes of nucleus and cytoplasm, respectively. The majority of mature miRNAs existed in cytoplasm. The analysis of miRNA targetome from the Ago2 complexes indicated that a lot of mRNAs with high expression level existed in nucleus. The target genes of miRNAs in the Ago2 complexes of nucleus and cytoplasm played important roles in cell proliferation, cell differentiation, innate immune response and tumorigenesis. Conclusions microRNA-mRNA interactions occur in nucleus and cytoplasm of gastric cancer cells. Therefore, our study demonstrated that miRNA-mRNA interactions not only took place in cytoplasm but also in nucleus.
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Affiliation(s)
- Xinyi Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Bo Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
| | - Yalei Cui
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
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31
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Yoon S, Rossi JJ. Therapeutic Potential of Small Activating RNAs (saRNAs) in Human Cancers. Curr Pharm Biotechnol 2018; 19:604-610. [PMID: 29804529 PMCID: PMC6204660 DOI: 10.2174/1389201019666180528084059] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/09/2018] [Accepted: 05/23/2018] [Indexed: 01/24/2023]
Abstract
Background: RNA is increasingly recognized as a powerful molecule that can be used to control gene expression. Sophisticated, well-engineered RNA-based regulators are being developed as oligotherapeutics. Methods: In particular, small activating RNAs (saRNAs) are promising therapeutic options for targeting human diseases. Numerous saRNAs targeting multiple cancers have been developed in preclinical models. One saRNA targeting C/EBPα is currently undergoing clinical trials in liver cancer. Results and Conclusion: In this review, we describe the current working model of the intracellular mechanism of saRNA, discuss the recent progress of saRNA therapeutics in preclinical and clinical trials, and current advances in targeted delivery using aptamers in detail.
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Affiliation(s)
- Sorah Yoon
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California, United States
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California, United States.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, California, United States
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32
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Laham-Karam N, Laitinen P, Turunen TA, Ylä-Herttuala S. Activating the Chromatin by Noncoding RNAs. Antioxid Redox Signal 2018; 29:813-831. [PMID: 28699365 DOI: 10.1089/ars.2017.7248] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE The extent and breadth of transcription have recently been uncovered and this has revealed an extensive array of noncoding RNAs (ncRNAs). The biological role and significance of these ncRNAs have been realized and to date it appears that ncRNAs may have many important regulatory functions. ncRNAs are multifaceted and they induce a complexity of different types of transcriptional and posttranscriptional regulation, including gene activation. Recent Advances: Association of ncRNAs with gene activation is an important finding. Not only enhancer RNA (eRNA) but other types of ncRNAs, including small RNA (sRNA), long-noncoding RNA (lncRNA), microRNA (miRNA), and PIWI-associated RNA (piRNA), have also been implicated in gene activation. Interestingly, they often coincide with histone modifications that favor an open chromatin. In addition, these ncRNAs can recruit key factors important for transcription, including RNA polymerase II. They may directly bind the genomic DNA or act as scaffolds; alternatively, they may loop the chromatin to enhance transcription. CRITICAL ISSUES Although the role of small activating (sa)RNAs has been considerably studied, the roles of miRNAs and piRNAs in gene activation still need to be substantiated and issues of specificity require further studies. FUTURE DIRECTIONS The ncRNA field is coming out of its infancy and we are gaining a global picture of the importance of ncRNAs. However, detailed mechanisms of action of the different ncRNAs are still to be determined. This may reveal novel ways of transcriptional regulation, which will facilitate our ability to utilize these regulatory pathways for research and therapeutic purposes. Antioxid. Redox Signal. 29, 813-831.
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Affiliation(s)
- Nihay Laham-Karam
- 1 A.I. Virtanen Institute, University of Eastern Finland , Kuopio, Finland
| | - Pia Laitinen
- 1 A.I. Virtanen Institute, University of Eastern Finland , Kuopio, Finland
| | - Tiia A Turunen
- 1 A.I. Virtanen Institute, University of Eastern Finland , Kuopio, Finland
| | - Seppo Ylä-Herttuala
- 1 A.I. Virtanen Institute, University of Eastern Finland , Kuopio, Finland .,2 Heart Center, Kuopio University Hospital , Kuopio, Finland .,3 Gene Therapy Unit, Kuopio University Hospital , Kuopio, Finland
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33
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Yu D, Ma X, Zuo Z, Wang H, Meng Y. Classification of Transcription Boundary-Associated RNAs (TBARs) in Animals and Plants. Front Genet 2018; 9:168. [PMID: 29868116 PMCID: PMC5960741 DOI: 10.3389/fgene.2018.00168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/26/2018] [Indexed: 11/13/2022] Open
Abstract
There is increasing evidence suggesting the contribution of non-coding RNAs (ncRNAs) to the phenotypic and physiological complexity of organisms. A novel ncRNA species has been identified near the transcription boundaries of protein-coding genes in eukaryotes, bacteria, and archaea. This review provides a detailed description of these transcription boundary-associated RNAs (TBARs), including their classification. Based on their genomic distribution, TBARs are divided into two major groups: promoter-associated RNAs (PARs) and terminus-associated RNAs (TARs). Depending on the sequence length, each group is further classified into long RNA species (>200 nt) and small RNA species (<200 nt). According to these rules of TBAR classification, divergent ncRNAs with confusing nomenclatures, such as promoter upstream transcripts (PROMPTs), upstream antisense RNAs (uaRNAs), stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs), upstream non-coding transcripts (UNTs), transcription start site-associated RNAs (TSSaRNAs), transcription initiation RNAs (tiRNAs), and transcription termination site-associated RNAs (TTSaRNAs), were assigned to specific classes. Although the biogenesis pathways of PARs and TARs have not yet been clearly elucidated, previous studies indicate that some of the PARs have originated either through divergent transcription or via RNA polymerase pausing. Intriguing findings regarding the functional implications of the TBARs such as the long-range “gene looping” model, which explains their role in the transcriptional regulation of protein-coding genes, are also discussed. Altogether, this review provides a comprehensive overview of the current research status of TBARs, which will promote further investigations in this research area.
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Affiliation(s)
- Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ziwei Zuo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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34
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Hicks JA, Li L, Matsui M, Chu Y, Volkov O, Johnson KC, Corey DR. Human GW182 Paralogs Are the Central Organizers for RNA-Mediated Control of Transcription. Cell Rep 2018; 20:1543-1552. [PMID: 28813667 DOI: 10.1016/j.celrep.2017.07.058] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/10/2017] [Accepted: 07/20/2017] [Indexed: 01/21/2023] Open
Abstract
In the cytoplasm, small RNAs can control mammalian translation by regulating the stability of mRNA. In the nucleus, small RNAs can also control transcription and splicing. The mechanisms for RNA-mediated nuclear regulation are not understood and remain controversial, hindering the effective application of nuclear RNAi and investigation of its natural regulatory roles. Here, we reveal that the human GW182 paralogs TNRC6A/B/C are central organizing factors critical to RNA-mediated transcriptional activation. Mass spectrometry of purified nuclear lysates followed by experimental validation demonstrates that TNRC6A interacts with proteins involved in protein degradation, RNAi, the CCR4-NOT complex, the mediator complex, and histone-modifying complexes. Functional analysis implicates TNRC6A, NAT10, MED14, and WDR5 in RNA-mediated transcriptional activation. These findings describe protein complexes capable of bridging RNA-mediated sequence-specific recognition of noncoding RNA transcripts with the regulation of gene transcription.
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Affiliation(s)
- Jessica A Hicks
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Liande Li
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Masayuki Matsui
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Yongjun Chu
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Oleg Volkov
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Krystal C Johnson
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.
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35
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Choi S, Uehara H, Wu Y, Das S, Zhang X, Archer B, Carroll L, Ambati BK. RNA activating-double stranded RNA targeting flt-1 promoter inhibits endothelial cell proliferation through soluble FLT-1 upregulation. PLoS One 2018; 13:e0193590. [PMID: 29509796 PMCID: PMC5839558 DOI: 10.1371/journal.pone.0193590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/14/2018] [Indexed: 12/20/2022] Open
Abstract
Short-activating RNA (saRNA), which targets gene promoters, has been shown to increase the target gene expression. In this study, we describe the use of an saRNA (Flt a-1) to target the flt-1 promoter, leading to upregulation of the soluble isoform of Flt-1 and inhibition of angiogenesis. We demonstrate that Flt a-1 increased sFlt-1 mRNA and protein levels, while reducing VEGF expression. This was associated with suppression of human umbilical vascular endothelial cell (HUVEC) proliferation and cell cycle arrest at the G0/G1 phase. HUVEC migration and tube formation were also suppressed by Flt a-1. An siRNA targeting Flt-1 blocked the effects of Flt a-1. Flt a-1 effects were not mediated via argonaute proteins. However, trichostatin A and 5'-deoxy-5'-(methylthio) adenosine inhibited Flt a-1 effects, indicating that histone acetylation and methylation are mechanistically involved in RNA activation of Flt-1. In conclusion, RNA activation of sFlt-1 can be used to inhibit angiogenesis.
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Affiliation(s)
- Susie Choi
- John A Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
| | - Hironori Uehara
- John A Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
| | - Yuanyuan Wu
- John A Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
| | - Subrata Das
- Patanjali Research Institute, Haridwar, India
| | - Xiaohui Zhang
- John A Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
| | - Bonnie Archer
- John A Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
| | - Lara Carroll
- John A Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
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36
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Kang MR, Park KH, Lee CW, Lee MY, Han SB, Li LC, Kang JS. Small activating RNA induced expression of VHL gene in renal cell carcinoma. Int J Biochem Cell Biol 2018; 97:36-42. [PMID: 29425832 DOI: 10.1016/j.biocel.2018.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 12/25/2022]
Abstract
Recent studies have reported that chemically synthesized double-stranded RNAs (dsRNAs), also known as small activating RNA (saRNAs), can specifically induce gene expression by targeting promoter sequences by a mechanism termed RNA activation (RNAa). In the present study, we designed 4 candidate saRNAs targeting the Von Hippel-Lindau (VHL) gene promoter. Among these saRNAs, dsVHL-821 significantly inhibited cell growth by up-regulating VHL at both the mRNA and protein levels in renal cell carcinoma 769-P cells. Functional analysis showed that dsVHL-821 induced apoptosis by increasing p53, decreasing Bcl-xL, activating caspase 3/7 and poly-ADP-ribose polymerase in a dose-dependent manner. Chromatin immunoprecipitation analysis revealed that dsVHL-821 increased the enrichment of Ago2 and RNA polymerase II at the dsVHL-821 target site. In addition, Ago2 depletion significantly suppressed dsVHL-821-induced up-regulation of VHL gene expression and related effects. Single transfection of dsVHL-821 caused long-lasting (14 days) VHL up-regulation. Furthermore, the activation of VHL by dsVHL-821 was accompanied by an increase in dimethylation of histone 3 at lysine 4 (H3K4me2) and acetylation of histone 4 (H4ac) and a decrease in dimethylation of histone 3 at lysine 9 (H3K9me2) and lysine 27 (H3K27me2) in the dsVHL-821 target region. Taken together, these results demonstrate that dsVHL-821, a novel saRNA for VHL, induces the expression of the VHL gene by epigenetic changes, leading to inhibition of cell growth and induction of apoptosis, and suggest that targeted activation of VHL by dsVHL-821 may be explored as a novel treatment of renal cell carcinoma.
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Affiliation(s)
- Moo Rim Kang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanjiro, Cheongju, 28116, Republic of Korea; Ractigen Therapeutics, Nantong, Jiangsu, 226400, China
| | - Ki Hwan Park
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanjiro, Cheongju, 28116, Republic of Korea
| | - Chang Woo Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanjiro, Cheongju, 28116, Republic of Korea
| | - Myeong Youl Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanjiro, Cheongju, 28116, Republic of Korea
| | - Sang-Bae Han
- College of Pharmacy, Chungbuk National University, 1 Chungdaero, Cheongju, 28644, Republic of Korea
| | - Long-Cheng Li
- Medical School of Nantong University, Nantong, Jiangsu, 226001, China; Ractigen Therapeutics, Nantong, Jiangsu, 226400, China
| | - Jong Soon Kang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanjiro, Cheongju, 28116, Republic of Korea.
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37
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Jiao AL, Foster DJ, Dixon J, Slack FJ. lin-4 and the NRDE pathway are required to activate a transgenic lin-4 reporter but not the endogenous lin-4 locus in C. elegans. PLoS One 2018; 13:e0190766. [PMID: 29324872 PMCID: PMC5764303 DOI: 10.1371/journal.pone.0190766] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 11/27/2017] [Indexed: 11/19/2022] Open
Abstract
As the founding member of the microRNA (miRNA) gene family, insights into lin-4 regulation and function have laid a conceptual foundation for countless miRNA-related studies that followed. We previously showed that a transcriptional lin-4 reporter in C. elegans was positively regulated by a lin-4-complementary element (LCE), and by lin-4 itself. In this study, we sought to (1) identify additional factors required for lin-4 reporter expression, and (2) validate the endogenous relevance of a potential positive autoregulatory mechanism of lin-4 expression. We report that all four core nuclear RNAi factors (nrde-1, nrde-2, nrde-3 and nrde-4), positively regulate lin-4 reporter expression. In contrast, endogenous lin-4 levels were largely unaffected in nrde-2;nrde-3 mutants. Further, an endogenous LCE deletion generated by CRISPR-Cas9 revealed that the LCE was also not necessary for the activity of the endogenous lin-4 promoter. Finally, mutations in mature lin-4 did not reduce primary lin-4 transcript levels. Taken together, these data indicate that under growth conditions that reveal effects at the transgenic locus, a direct, positive autoregulatory mechanism of lin-4 expression does not occur in the context of the endogenous lin-4 locus.
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Affiliation(s)
- Alan L. Jiao
- Institute for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States of America
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT United States of America
| | - Daniel J. Foster
- Institute for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States of America
- Department of Biological and Biomedical Sciences, Harvard University, Boston, MA, United States of America
| | - Julia Dixon
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT United States of America
| | - Frank J. Slack
- Institute for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States of America
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Setten RL, Lightfoot HL, Habib NA, Rossi JJ. Development of MTL-CEBPA: Small Activating RNA Drug for Hepatocellular Carcinoma. Curr Pharm Biotechnol 2018; 19:611-621. [PMID: 29886828 PMCID: PMC6204661 DOI: 10.2174/1389201019666180611093428] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 01/12/2023]
Abstract
BACKGROUND Oligonucleotide drug development has revolutionised the drug discovery field. Within this field, 'small' or 'short' activating RNAs (saRNA) are a more recently discovered category of short double-stranded RNA with clinical potential. saRNAs promote transcription from target loci, a phenomenon widely observed in mammals known as RNA activation (RNAa). OBJECTIVE The ability to target a particular gene is dependent on the sequence of the saRNA. Hence, the potential clinical application of saRNAs is to increase target gene expression in a sequence-specific manner. saRNA-based therapeutics present opportunities for expanding the "druggable genome" with particular areas of interest including transcription factor activation and cases of haploinsufficiency. RESULTS AND CONCLUSION In this mini-review, we describe the pre-clinical development of the first saRNA drug to enter the clinic. This saRNA, referred to as MTL-CEBPA, induces increased expression of the transcription factor CCAAT/enhancer-binding protein alpha (CEBPα), a tumour suppressor and critical regulator of hepatocyte function. MTL-CEBPA is presently in Phase I clinical trials for hepatocellular carcinoma (HCC). The clinical development of MTL-CEBPA will demonstrate "proof of concept" that saRNAs can provide the basis for drugs which enhance target gene expression and consequently improve treatment outcome in patients.
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Affiliation(s)
| | | | | | - John J. Rossi
- Address correspondence to this author at the Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA; Tel: 626-218-7390; Fax: 626-301-8371; E-mail:
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Bortezomib-induced miRNAs direct epigenetic silencing of locus genes and trigger apoptosis in leukemia. Cell Death Dis 2017; 8:e3167. [PMID: 29120412 PMCID: PMC5775404 DOI: 10.1038/cddis.2017.520] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 09/02/2017] [Accepted: 09/04/2017] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) have been suggested to repress transcription via binding the 3′-untranslated regions of mRNAs. However, the involvement and details of miRNA-mediated epigenetic regulation, particularly in targeting genomic DNA and mediating epigenetic regulation, remain largely uninvestigated. In the present study, transcription factor CCAAT/enhancer binding protein delta (CEBPD) was responsive to the anticancer drug bortezomib, a clinical and highly selective drug for leukemia treatment, and contributed to bortezomib-induced cell death. Interestingly, following the identification of CEBPD-induced miRNAs, we found that miR-744, miR-3154 and miR-3162 could target CpG islands in the 5′-flanking region of the CEBPD gene. We previously demonstrated that the Yin Yang 1 (YY1)/polycomb group (PcG) protein/DNA methyltransferase (DNMT) complex is important for CCAAT/enhancer binding protein delta (CEBPD) gene inactivation; we further found that Argonaute 2 (Ago2) interacts with YY1 and binds to the CEBPD promoter. The miRNA/Ago2/YY1/PcG group protein/DNMT complex linked the inactivation of CEBPD and genes adjacent to its 5′-flanking region, including protein kinase DNA-activated catalytic polypeptide (PRKDC), minichromosome maintenance-deficient 4 (MCM4) and ubiquitin-conjugating enzyme E2 variant 2 (UBE2V2), upon bortezomib treatment. Moreover, we revealed that miRNA binding is necessary for YY1/PcG group protein/DNMT complex-mediated epigenetic gene silencing and is associated with bortezomib-induced methylation on genomic DNA. The present study successfully characterized the interactions of the miRNA/Ago2/YY1/PcG group protein/DNMT complex and provided new insights for miRNA-mediated epigenetic regulation in bortezomib-induced leukemic cell arrest and cell death.
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40
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Herrera-Carrillo E, Berkhout B. Dicer-independent processing of small RNA duplexes: mechanistic insights and applications. Nucleic Acids Res 2017; 45:10369-10379. [PMID: 28977573 PMCID: PMC5737282 DOI: 10.1093/nar/gkx779] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) play a pivotal role in the regulation of cellular gene expression via the conserved RNA interference (RNAi) mechanism. Biogenesis of the unusual miR-451 does not require Dicer. This molecule is instead processed by the Argonaute 2 (Ago2) enzyme. Similarly, unconventional short hairpin RNA (shRNA) molecules have been designed as miR-451 mimics that rely exclusively on Ago2 for maturation. We will review recent progress made in the understanding of this alternative processing route. Next, we describe different Dicer-independent shRNA designs that have been developed and discuss their therapeutic advantages and disadvantages. As an example, we will present the route towards development of a durable gene therapy against HIV-1.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
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41
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Comprehensive Identification of Nuclear and Cytoplasmic TNRC6A-Associating Proteins. J Mol Biol 2017; 429:3319-3333. [DOI: 10.1016/j.jmb.2017.04.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 11/20/2022]
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42
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Eckenfelder A, Ségéral E, Pinzón N, Ulveling D, Amadori C, Charpentier M, Nidelet S, Concordet JP, Zagury JF, Paillart JC, Berlioz-Torrent C, Seitz H, Emiliani S, Gallois-Montbrun S. Argonaute proteins regulate HIV-1 multiply spliced RNA and viral production in a Dicer independent manner. Nucleic Acids Res 2017; 45:4158-4173. [PMID: 28003477 PMCID: PMC5397155 DOI: 10.1093/nar/gkw1289] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 12/13/2016] [Indexed: 11/30/2022] Open
Abstract
Argonaute (Ago) proteins associate with microRNAs (miRNAs) to form the core of the RNA-induced silencing complex (RISC) that mediates post-transcriptional gene silencing of target mRNAs. As key players in anti-viral defense, Ago proteins are thought to have the ability to interact with human immunodeficiency virus type 1 (HIV-1) RNA. However, the role of this interaction in regulating HIV-1 replication has been debated. Here, we used high throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) to explore the interaction between Ago2 and HIV-1 RNA in infected cells. By only considering reads of 50 nucleotides length in our analysis, we identified more than 30 distinct binding sites for Ago2 along the viral RNA genome. Using reporter assays, we found four binding sites, located near splice donor sites, capable of repressing Luciferase gene expression in an Ago-dependent manner. Furthermore, inhibition of Ago1 and Ago2 levels in cells expressing HIV-1 led to an increase of viral multiply spliced transcripts and to a strong reduction in the extracellular CAp24 level. Depletion of Dicer did not affect these activities. Our results highlight a new role of Ago proteins in the control of multiply spliced HIV-1 transcript levels and viral production, independently of the miRNA pathway.
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Affiliation(s)
- Agathe Eckenfelder
- INSERM, U1016, Institut Cochin, Paris 75014, France.,CNRS, UMR8104, Paris 75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris 75006, France
| | - Emmanuel Ségéral
- INSERM, U1016, Institut Cochin, Paris 75014, France.,CNRS, UMR8104, Paris 75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris 75006, France
| | - Natalia Pinzón
- CNRS, UPR 1142, Institut de Génétique Humaine, Montpellier 34396, France
| | - Damien Ulveling
- CNAM, Laboratoire Génomique, Bioinformatique et Applications (EA 4627), Paris 75003, France
| | - Céline Amadori
- INSERM, U1016, Institut Cochin, Paris 75014, France.,CNRS, UMR8104, Paris 75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris 75006, France
| | - Marine Charpentier
- INSERM, U1154, CNRS, UMR7196, Museum National d'Histoire Naturelle, Paris 75231, France
| | - Sabine Nidelet
- Plateforme MGX, Institut de Génomique Fonctionnelle, CNRS, UMR5203, INSERM, U661, Montpellier 34094, France
| | - Jean-Paul Concordet
- INSERM, U1154, CNRS, UMR7196, Museum National d'Histoire Naturelle, Paris 75231, France
| | - Jean-François Zagury
- CNAM, Laboratoire Génomique, Bioinformatique et Applications (EA 4627), Paris 75003, France
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg 67084, France
| | - Clarisse Berlioz-Torrent
- INSERM, U1016, Institut Cochin, Paris 75014, France.,CNRS, UMR8104, Paris 75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris 75006, France
| | - Hervé Seitz
- CNRS, UPR 1142, Institut de Génétique Humaine, Montpellier 34396, France
| | - Stéphane Emiliani
- INSERM, U1016, Institut Cochin, Paris 75014, France.,CNRS, UMR8104, Paris 75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris 75006, France
| | - Sarah Gallois-Montbrun
- INSERM, U1016, Institut Cochin, Paris 75014, France.,CNRS, UMR8104, Paris 75014, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris 75006, France
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43
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Reactivity of human AGO2 monoclonal antibody 11A9 with the SWI/SNF complex: A case study for rigorously defining antibody selectivity. Sci Rep 2017; 7:7278. [PMID: 28779093 PMCID: PMC5544689 DOI: 10.1038/s41598-017-07539-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022] Open
Abstract
In this study, we originally aimed to characterize the potential role of Argonaute 2 (AGO2) in the nucleus, a key protein of the miRNA machinery. We combined Chromatin Immunoprecipitation (ChIP) with high throughput sequencing (ChIP-seq) and quantitative mass spectrometry (ChIP-MS) using the broadly used AGO2 11A9 antibody to determine interactions with chromatin and nuclear proteins. We found a previously described interaction between AGO2 and SWI/SNF on chromatin with ChIP-MS and observed enrichment at enhancers and transcription start sites using ChIP-seq. However, antibody specificity issues can produce misleading results for ChIP, RNA-seq and Mass spectrometry. Therefore, we developed a CRISPR/Cas9 engineered AGO2−/− HEK293T cell line to validate our findings. ChIP-qPCR and immunoprecipitation combined with MS (IP-MS) showed that the 11A9 antibody associates with chromatin and SWI/SNF in the absence of AGO2. Furthermore, stoichiometry, IP-MS and co-IP analysis suggests a direct interaction of this antibody with SMARCC1, a component of the SWI/SNF complex. For this reason, particular care should be taken in performing and interpreting experiments in which the 11A9 antibody is used to study a nuclear role of AGO2.
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44
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Voutila J, Reebye V, Roberts TC, Protopapa P, Andrikakou P, Blakey DC, Habib R, Huber H, Saetrom P, Rossi JJ, Habib NA. Development and Mechanism of Small Activating RNA Targeting CEBPA, a Novel Therapeutic in Clinical Trials for Liver Cancer. Mol Ther 2017; 25:2705-2714. [PMID: 28882451 PMCID: PMC5768526 DOI: 10.1016/j.ymthe.2017.07.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/31/2017] [Accepted: 07/31/2017] [Indexed: 01/05/2023] Open
Abstract
Small activating RNAs (saRNAs) are short double-stranded oligonucleotides that selectively increase gene transcription. Here, we describe the development of an saRNA that upregulates the transcription factor CCATT/enhancer binding protein alpha (CEBPA), investigate its mode of action, and describe its development into a clinical candidate. A bioinformatically directed nucleotide walk around the CEBPA gene identified an saRNA sequence that upregulates CEBPA mRNA 2.5-fold in human hepatocellular carcinoma cells. A nuclear run-on assay confirmed that this upregulation is a transcriptionally driven process. Mechanistic experiments demonstrate that Argonaute-2 (Ago2) is required for saRNA activity, with the guide strand of the saRNA shown to be associated with Ago2 and localized at the CEBPA genomic locus using RNA chromatin immunoprecipitation (ChIP) assays. The data support a sequence-specific on-target saRNA activity that leads to enhanced CEBPA mRNA transcription. Chemical modifications were introduced in the saRNA duplex to prevent activation of the innate immunity. This modified saRNA retains activation of CEBPA mRNA and downstream targets and inhibits growth of liver cancer cell lines in vitro. This novel drug has been encapsulated in a liposomal formulation for liver delivery, is currently in a phase I clinical trial for patients with liver cancer, and represents the first human study of an saRNA therapeutic.
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Affiliation(s)
| | - Vikash Reebye
- Department of Surgery and Cancer, Imperial College London, London, UK
| | | | | | | | | | | | - Hans Huber
- BioTD Strategies, LLC, Philadelphia, PA, USA
| | - Pal Saetrom
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Nagy A Habib
- Department of Surgery and Cancer, Imperial College London, London, UK.
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45
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Li LC. Small RNA-Guided Transcriptional Gene Activation (RNAa) in Mammalian Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [DOI: 10.1007/978-981-10-4310-9_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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46
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Li C, Ge Q, Liu J, Zhang Q, Wang C, Cui K, Chen Z. Effects of miR-1236-3p and miR-370-5p on activation of p21 in various tumors and its inhibition on the growth of lung cancer cells. Tumour Biol 2017. [PMID: 28631573 DOI: 10.1177/1010428317710824] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Chuanchang Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiangqiang Ge
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Urology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Jiaxuan Liu
- Department of Pathology, Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Qingsong Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chenghe Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Urology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Kai Cui
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhong Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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47
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Long-term regulation of gene expression in muscle cells by systemically delivered siRNA. J Control Release 2017; 256:101-113. [DOI: 10.1016/j.jconrel.2017.04.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/20/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022]
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48
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Oligonucleotide therapies for disorders of the nervous system. Nat Biotechnol 2017; 35:249-263. [PMID: 28244991 DOI: 10.1038/nbt.3784] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/09/2017] [Indexed: 12/14/2022]
Abstract
Oligonucleotide therapies are currently experiencing a resurgence driven by advances in backbone chemistry and discoveries of novel therapeutic pathways that can be uniquely and efficiently modulated by the oligonucleotide drugs. A quarter of a century has passed since oligonucleotides were first applied in living mammalian brain to modulate gene expression. Despite challenges in delivery to the brain, multiple oligonucleotide-based compounds are now being developed for treatment of human brain disorders by direct delivery inside the blood brain barrier (BBB). Notably, the first new central nervous system (CNS)-targeted oligonucleotide-based drug (nusinersen/Spinraza) was approved by US Food and Drug Administration (FDA) in late 2016 and several other compounds are in advanced clinical trials. Human testing of brain-targeted oligonucleotides has highlighted unusual pharmacokinetic and pharmacodynamic properties of these compounds, including complex active uptake mechanisms, low systemic exposure, extremely long half-lives, accumulation and gradual release from subcellular depots. Further work on oligonucleotide uptake, development of formulations for delivery across the BBB and relevant disease biology studies are required for further optimization of the oligonucleotide drug development process for brain applications.
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49
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Abd Rahman N, Ibrahim F, Yafouz B. Dielectrophoresis for Biomedical Sciences Applications: A Review. SENSORS 2017; 17:s17030449. [PMID: 28245552 PMCID: PMC5375735 DOI: 10.3390/s17030449] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/10/2016] [Accepted: 12/20/2016] [Indexed: 12/18/2022]
Abstract
Dielectrophoresis (DEP) is a label-free, accurate, fast, low-cost diagnostic technique that uses the principles of polarization and the motion of bioparticles in applied electric fields. This technique has been proven to be beneficial in various fields, including environmental research, polymer research, biosensors, microfluidics, medicine and diagnostics. Biomedical science research is one of the major research areas that could potentially benefit from DEP technology for diverse applications. Nevertheless, many medical science research investigations have yet to benefit from the possibilities offered by DEP. This paper critically reviews the fundamentals, recent progress, current challenges, future directions and potential applications of research investigations in the medical sciences utilizing DEP technique. This review will also act as a guide and reference for medical researchers and scientists to explore and utilize the DEP technique in their research fields.
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Affiliation(s)
- Nurhaslina Abd Rahman
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
- Centre for Innovation in Medical Engineering (CIME), Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Fatimah Ibrahim
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
- Centre for Innovation in Medical Engineering (CIME), Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Bashar Yafouz
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
- Centre for Innovation in Medical Engineering (CIME), Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
- Faculty of Engineering and Information Technology, Taiz University, 6803 Taiz, Yemen.
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Rajpathak SN, Deobagkar DD. Micro RNAs and DNA methylation are regulatory players in human cells with altered X chromosome to autosome balance. Sci Rep 2017; 7:43235. [PMID: 28233878 PMCID: PMC5324395 DOI: 10.1038/srep43235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/20/2017] [Indexed: 01/04/2023] Open
Abstract
The gene balance hypothesis predicts that an imbalance in the dosage sensitive genes affects the cascade of gene networks that may influence the fitness of individuals. The phenotypes associated with chromosomal aneuploidies demonstrate the importance of gene dosage balance. We have employed untransformed human fibroblast cells with different number of X chromosomes to assess the expression of miRNAs and autosomal genes in addition to the DNA methylation status. High throughput NGS analysis using illumina Next seq500 has detected several autosomal as well as X linked miRNAs as differentially expressed in X monosomy and trisomy cells. Two of these miRNAs (hsa-miR-125a-5p and 335-5p) are likely to be involved in regulation of the autosomal gene expression. Additionally, our data demonstrates altered expression and DNA methylation signatures of autosomal genes in X monosomy and trisomy cells. In addition to miRNAs, expression of DNMT1 which is an important epigenetic player involved in many processes including cancer, is seen to be altered. Overall, present study provides a proof for regulatory roles of micro RNAs and DNA methylation in human X aneuploidy cells opening up possible new ways for designing therapeutic strategies.
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Affiliation(s)
- Shriram N Rajpathak
- Centre for Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
| | - Deepti D Deobagkar
- Centre for Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune 411007, India.,Bioinformatics Center, Savitribai Phule Pune University, Pune 411007, India
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