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Yadav P, Tamilselvan R, Mani H, Singh KK. MicroRNA-mediated regulation of nonsense-mediated mRNA decay factors: Insights into microRNA prediction tools and profiling techniques. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195022. [PMID: 38437914 DOI: 10.1016/j.bbagrm.2024.195022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) stands out as a prominent RNA surveillance mechanism within eukaryotes, meticulously overseeing both RNA abundance and integrity by eliminating aberrant transcripts. These defective transcripts are discerned through the concerted efforts of translating ribosomes, eukaryotic release factors (eRFs), and trans-acting NMD factors, with Up-Frameshift 3 (UPF3) serving as a noteworthy component. Remarkably, in humans, UPF3 exists in two paralogous forms, UPF3A (UPF3) and UPF3B (UPF3X). Beyond its role in quality control, UPF3 wields significant influence over critical cellular processes, including neural development, synaptic plasticity, and axon guidance. However, the precise regulatory mechanisms governing UPF3 remain elusive. MicroRNAs (miRNAs) emerge as pivotal post-transcriptional gene regulators, exerting substantial impact on diverse pathological and physiological pathways. This comprehensive review encapsulates our current understanding of the intricate regulatory nexus between NMD and miRNAs, with particular emphasis on the essential role played by UPF3B in neurodevelopment. Additionally, we bring out the significance of the 3'-untranslated region (3'-UTR) as the molecular bridge connecting NMD and miRNA-mediated gene regulation. Furthermore, we provide an in-depth exploration of diverse computational tools tailored for the prediction of potential miRNA targets. To complement these computational approaches, we delineate experimental techniques designed to validate predicted miRNA-mRNA interactions, empowering readers with the knowledge necessary to select the most appropriate methodology for their specific research objectives.
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Affiliation(s)
- Priyanka Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Raja Tamilselvan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Harita Mani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Kusum Kumari Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Li J, Dhilipkannah P, Holden VK, Sachdeva A, Jiang F. Red Blood Cell-Derived Exosomal Oncogenic MicroRNA Promote Cancer Development and Progression. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.10.24307177. [PMID: 38766218 PMCID: PMC11100945 DOI: 10.1101/2024.05.10.24307177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The role of red blood cells (RBCs) in tumorigenesis is poorly understood. We previously identified RBC-microRNAs with aberrations linked to lung cancer, including miR-93-5p. Here we find that miR-93-5p levels are elevated in RBC-derived exosomes among lung cancer patients and are associated with their shorter survivals. RBC-derived miR-93-5p transfers to cancer cells primarily through the exosomal pathway. The transferred RBC-miR-93-5p can target PTEN in cancer cells, and hence increase cell proliferation, invasion, and migration. RBC-derived miR-93-5p accelerates, whereas targeting miR-93-5p diminishes tumor growth in xenograft models. These findings reveal a novel biological function of RBCs in tumorigenesis, where they facilitate cancer progression by transferring the oncomiR via exosomes, thereby offering new diagnostic and treatment strategies for lung cancer.
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Antoine JC. Inflammatory sensory neuronopathies. Rev Neurol (Paris) 2024:S0035-3787(24)00455-7. [PMID: 38472032 DOI: 10.1016/j.neurol.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 03/14/2024]
Abstract
Inflammatory sensory neuronopathies are rare disorders mediated by dysimmune mechanisms targeting sensory neurons in the dorsal root ganglia. They constitute a heterogeneous group of disorders with acute, subacute, or chronic courses, and occur with cancer, systemic autoimmune diseases, notably Sjögren syndrome, and viral infections but a noticeable proportion of them remains isolated. Identifying inflammatory sensory neuronopathies is crucial because they have the potential to be stabilized or even to improve with immunomodulatory or immunosuppressant treatments provided that the treatment is applied at an early stage of the disease, before a definitive degeneration of neurons. Biomarkers, and notably antibodies, are crucial for this early identification, which is the first step to develop therapeutic trials.
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Affiliation(s)
- J-C Antoine
- Department of Neurology, University Hospital of Saint-Etienne, 42055 Saint-Étienne cedex, France.
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4
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Johnson KC, Kilikevicius A, Hofman C, Hu J, Liu Y, Aguilar S, Graswich J, Han Y, Wang T, Westcott JM, Brekken RA, Peng L, Karagkounis G, Corey DR. Nuclear localization of Argonaute 2 is affected by cell density and may relieve repression by microRNAs. Nucleic Acids Res 2024; 52:1930-1952. [PMID: 38109320 PMCID: PMC10899759 DOI: 10.1093/nar/gkad1155] [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: 07/19/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/20/2023] Open
Abstract
Argonaute protein is associated with post-transcriptional control of cytoplasmic gene expression through miRNA-induced silencing complexes (miRISC). Specific cellular and environmental conditions can trigger AGO protein to accumulate in the nucleus. Localization of AGO is central to understanding miRNA action, yet the consequences of AGO being in the nucleus are undefined. We show nuclear enrichment of AGO2 in HCT116 cells grown in two-dimensional culture to high density, HCT116 cells grown in three-dimensional tumor spheroid culture, and human colon tumors. The shift in localization of AGO2 from cytoplasm to nucleus de-represses cytoplasmic AGO2-eCLIP targets that were candidates for canonical regulation by miRISC. Constitutive nuclear localization of AGO2 using an engineered nuclear localization signal increases cell migration. Critical RNAi factors also affect the localization of AGO2. Knocking out an enzyme essential for miRNA biogenesis, DROSHA, depletes mature miRNAs and restricts AGO2 localization to the cytoplasm, while knocking out the miRISC scaffolding protein, TNRC6, results in nuclear localization of AGO2. These data suggest that AGO2 localization and miRNA activity can be regulated depending on environmental conditions, expression of mature miRNAs, and expression of miRISC cofactors. Localization and expression of core miRISC protein machinery should be considered when investigating the roles of miRNAs.
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Affiliation(s)
- Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Audrius Kilikevicius
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Cristina Hofman
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Jiaxin Hu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Yang Liu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Selina Aguilar
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Jon Graswich
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Yi Han
- UT Southwestern Medical Center, Peter O'Donnell Jr. School of Public Health, Dallas, TX 75235, USA
| | - Tao Wang
- UT Southwestern Medical Center, Peter O'Donnell Jr. School of Public Health, Dallas, TX 75235, USA
| | - Jill M Westcott
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235, USA
| | - Rolf A Brekken
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235, USA
| | - Lan Peng
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Pathology, Dallas, TX 75235, USA
| | - Georgios Karagkounis
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235, USA
- Memorial Sloan Kettering Cancer Center, New York, NY 10022, USA
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
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Proia P, Rossi C, Alioto A, Amato A, Polizzotto C, Pagliaro A, Kuliś S, Baldassano S. MiRNAs Expression Modulates Osteogenesis in Response to Exercise and Nutrition. Genes (Basel) 2023; 14:1667. [PMID: 37761807 PMCID: PMC10529960 DOI: 10.3390/genes14091667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
In recent years, many articles have been published describing the impact of physical activity and diet on bone health. This review has aimed to figure out the possible epigenetic mechanisms that influence bone metabolism. Many studies highlighted the effects of macro and micronutrients combined with exercise on the regulation of gene expression through miRs. The present review will describe how physical activity and nutrition can prevent abnormal epigenetic regulation that otherwise could lead to bone-metabolism-related diseases, the most significant of which is osteoporosis. Nowadays, it is known that this effect can be carried out not only by endogenously produced miRs, but also through those intakes through the diet. Indeed, they have also been found in the transcriptome of animals and plants, and it is possible to hypothesise an interaction between miRNAs produced by different kingdoms and epigenetic influences on human gene expression. In particular, the key to the activation pathways triggered by diet and physical activity appears to be the activation of Runt-related transcription factor 2 (RUNX2), the expression of which is regulated by several miRs. Among the main miRs involved are exercise-induced miR21 and 21-5p, and food-induced miR 221-3p and 222-3p.
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Affiliation(s)
- Patrizia Proia
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (C.R.); (A.A.); (C.P.); (A.P.)
| | - Carlo Rossi
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (C.R.); (A.A.); (C.P.); (A.P.)
- Centro Medico di Fisioterapia “Villa Sarina”, 91011 Alcamo, Italy
| | - Anna Alioto
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (C.R.); (A.A.); (C.P.); (A.P.)
| | - Alessandra Amato
- Department of Biomedical and Biotechnological Sciences, Section of Anatomy, Histology and Movement Science, School of Medicine, University of Catania, Via S. Sofia n°97, 95123 Catania, Italy;
| | - Caterina Polizzotto
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (C.R.); (A.A.); (C.P.); (A.P.)
| | - Andrea Pagliaro
- Sport and Exercise Sciences Research Unit, Department of Psychology, Educational Science and Human Movement, University of Palermo, Via Pascoli 6, 90144 Palermo, Italy; (C.R.); (A.A.); (C.P.); (A.P.)
| | - Szymon Kuliś
- Faculty of Physical Education, Józef Piłsudski University of Physical Education, 00-968 Warsaw, Poland;
| | - Sara Baldassano
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy;
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Johnson KC, Kilikevicius A, Hofman C, Hu J, Liu Y, Aguilar S, Graswich J, Han Y, Wang T, Westcott JM, Brekken RA, Peng L, Karagkounis G, Corey DR. Nuclear Localization of Argonaute is affected by Cell Density and May Relieve Repression by microRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.548119. [PMID: 37461596 PMCID: PMC10350042 DOI: 10.1101/2023.07.07.548119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Argonaute protein is associated with post-transcriptional control of cytoplasmic gene expression through miRNA-induced silencing complexes (miRISC). Specific cellular and environmental conditions can trigger AGO protein to accumulate in the nucleus. Localization of AGO is central to understanding miRNA action, yet the consequences of AGO being in the nucleus are undefined. We show nuclear enrichment of AGO2 in HCT116 cells grown in two-dimensional culture to high density, HCT116 cells grown in three-dimensional tumor spheroid culture, and human colon tumors. The shift in localization of AGO2 from cytoplasm to nucleus de-represses cytoplasmic AGO2-eCLIP targets that were candidates for canonical regulation by miRISC. Constitutive nuclear localization of AGO2 using an engineered nuclear localization signal increases cell migration. Critical RNAi factors also affect the localization of AGO2. Knocking out an enzyme essential for miRNA biogenesis, DROSHA, depletes mature miRNAs and restricts AGO2 localization to the cytoplasm, while knocking out the miRISC scaffolding protein, TNRC6, results in nuclear localization of AGO2. These data suggest that AGO2 localization and miRNA activity can be regulated depending on environmental conditions, expression of mature miRNAs, and expression of miRISC cofactors. Localization and expression of core miRISC protein machinery should be considered when investigating the roles of miRNAs.
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Affiliation(s)
- Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Audrius Kilikevicius
- current address, Eli Lilly, Lilly Cambridge Innovation Center, Cambridge, MA 02142
| | - Cristina Hofman
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Jiaxin Hu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Yang Liu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Selina Aguilar
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Jon Graswich
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Yi Han
- UT Southwestern Medical Center, Quantitative Biomedical Research Center, Department of Population and Data Sciences, Dallas, TX 75235
| | - Tao Wang
- UT Southwestern Medical Center, Quantitative Biomedical Research Center, Department of Population and Data Sciences, Dallas, TX 75235
| | - Jill M Westcott
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235
| | - Rolf A Brekken
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235
| | - Lan Peng
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Pathology, Dallas, TX 75235
| | - Georgios Karagkounis
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
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Lamin V, Verry J, Dokun OS, Kronemberger A, Wong T, Lira VA, Dokun AO. microRNA-29a Regulates ADAM12 Through Direct Interaction With ADAM12 mRNA and Modulates Postischemic Perfusion Recovery. J Am Heart Assoc 2022; 11:e025727. [PMID: 35946473 PMCID: PMC9496313 DOI: 10.1161/jaha.122.025727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022]
Abstract
Background Peripheral artery disease is caused by atherosclerotic occlusion of vessels outside the heart and most commonly affects vessels of the lower extremities. Angiogenesis is a part of the postischemic adaptation involved in restoring blood flow in peripheral artery disease. Previously, in a murine hind limb ischemia model of peripheral artery disease, we identified ADAM12 (a disintegrin and metalloproteinase gene 12) as a key genetic modifier of postischemic perfusion recovery. However, less is known about ADAM12 regulation in ischemia. MicroRNAs are a class of small, noncoding, single-stranded RNAs that regulate gene expression primarily through transcriptional repression of messenger RNA (mRNA). We showed microRNA-29a (miR-29a) modulates ADAM12 expression in the setting of diabetes and ischemia. However, how miR-29a modulates ADAM12 is not known. Moreover, the physiological effects of miR-29a modulation in a nondiabetic setting is not known. Methods and Results We overexpressed or inhibited miR-29a in ischemic mouse gastrocnemius and tibialis anterior muscles, and quantified the effect on perfusion recovery, ADAM12 expression, angiogenesis, and skeletal muscle regeneration. In addition, using RNA immunoprecipitation-based anti-miR competitive assay, we investigated the interaction of miR-29a and ADAM12 mRNA in mouse microvascular endothelial cell, skeletal muscle, and human endothelial cell lysates. Ectopic expression of miR-29a in ischemic mouse hind limbs decreased ADAM12 mRNA expression, increased skeletal muscle injury, decreased skeletal muscle function, and decreased angiogenesis and perfusion recovery, with no effect on skeletal muscle regeneration and myofiber cross-sectional area following hind limb ischemia. RNA immunoprecipitation-based anti-miR competitive assay studies showed miR-29a antagomir displaced miR-29a and ADAM12 mRNA from the AGO-2 (Argonaut-2) complex in a dose dependent manner. Conclusions Taken together, the data show miR-29a suppresses ADAM12 expression by directly binding to its mRNA, resulting in impaired skeletal muscle function, angiogenesis, and poor perfusion. Hence, elevated levels of miR-29a, as seen in diabetes and aging, likely contribute to vascular pathology, and modulation of miR-29a could be a therapeutic target.
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Affiliation(s)
- Victor Lamin
- Division of Endocrinology and Metabolism, Carver College of MedicineUniversity of IowaIowa CityIA
| | - Joseph Verry
- Division of Endocrinology and Metabolism, Carver College of MedicineUniversity of IowaIowa CityIA
| | - Olumayowa S. Dokun
- Division of Endocrinology and Metabolism, Carver College of MedicineUniversity of IowaIowa CityIA
| | - Ana Kronemberger
- Fraternal Order of Eagles Diabetes Research Center, Carver College of MedicineUniversity of IowaIowa CityIA
- Department of Health and Human Physiology, College of Liberal Arts and SciencesUniversity of IowaIowa CityIA
| | - Thomas Wong
- Division of Endocrinology and Metabolism, Carver College of MedicineUniversity of IowaIowa CityIA
| | - Vitor A. Lira
- Fraternal Order of Eagles Diabetes Research Center, Carver College of MedicineUniversity of IowaIowa CityIA
- Department of Health and Human Physiology, College of Liberal Arts and SciencesUniversity of IowaIowa CityIA
| | - Ayotunde O. Dokun
- Division of Endocrinology and Metabolism, Carver College of MedicineUniversity of IowaIowa CityIA
- Fraternal Order of Eagles Diabetes Research Center, Carver College of MedicineUniversity of IowaIowa CityIA
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Jiang S, Zhang X, Li DL, Wang TT, Ma F, Zhang CY. Construction of a gold nanoparticle-based single-molecule biosensor for simple and sensitive detection of Argonaute 2 activity. J Mater Chem B 2022; 10:5594-5601. [PMID: 35796467 DOI: 10.1039/d2tb00802e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Argonaute 2 (Ago2) is an essential component of the RNA-induced silencing complex (RISC) and it participates in diverse physiological processes, while dysregulation of Ago2 activity is closely linked to a variety of human diseases including cancers. The reported Ago2 assays often suffer from laborious procedures, complicated reaction schemes, and unsatisfactory sensitivity. Herein, we develop a new gold nanoparticle (AuNP)-based single-molecule biosensor for simple and sensitive detection of Ago2 activity. The Ago2-responsive AuNP nanoprobe is constructed through the self-assembly of multiple Cy5-labeled signal probes onto the AuNP, in which the Cy5 fluorescence is efficiently quenched by the AuNP. Target Ago2 can bind with guide RNA to form an active RISC, inducing the cyclic cleavage of the signal probes and the release of Cy5 moieties from the AuNP nanoprobe. The released Cy5 molecules can be simply quantified by single-molecule counting. This single-molecule biosensor enables detection of Ago2 activity with the involvement of only a single AuNP nanoprobe, eliminating the use of any extra antibodies and protein enzymes. This single-molecule biosensor achieves good specificity and high sensitivity with a detection limit of 9.1 pM, and it can be exploited for the screening of Ago2 inhibitors, Ago2 kinetic analysis, and the imaging of intracellular Ago2 activity in live cells, holding great promise in Ago2-related biomedical research and clinical diagnosis.
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Affiliation(s)
- Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Xinyi Zhang
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan 528458, China
| | - Dong-Ling Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Ting-Ting Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
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lncRNA ADAMTS9-AS1/circFN1 Competitively Binds to miR-206 to Elevate the Expression of ACTB, Thus Inducing Hypertrophic Cardiomyopathy. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1450610. [PMID: 35401927 PMCID: PMC8989615 DOI: 10.1155/2022/1450610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/25/2021] [Accepted: 12/03/2021] [Indexed: 11/17/2022]
Abstract
Hypertrophic cardiomyopathy (HCM) is a genetic cardiac disease and can result in substantial disability. The current study explored the potentials of long noncoding RNA- (lncRNA-) circular RNA- (circRNA-) microRNA- (miRNA-) messenger RNA (mRNA) networks in HCM. Firstly, HCM-related microarray data were procured from the GEO database, with differentially expressed genes (DEGs) obtained. HCM-related target genes were retrieved in combination with GeneCards and CTD databases, and candidate target genes were subsequently obtained by intersection screening. Further, an interaction network diagram of candidate target genes was constructed using the STRING database, and the hub genes in the network were determined according to the core degree. The “ClusterProfiler” package of the R software was adopted for GO and KEGG analyses of candidate target genes, to analyze the potential molecular pathways in HCM. Next, upstream miRNA, lncRNA, and circRNA of ACTB were predicted with RNAInter, mirDIP, TargetScan, DIANA-LncBase, and StarBase databases, followed by construction of lncRNA/circRNA-miRNA-mRNA coexpression networks. ACTB, miR-206, circFN1, and ADAMTS9-AS1 expression in peripheral blood samples from HCM patients and normal healthy controls were detected using RT-qPCR. Moreover, rat cardiomyocyte cell lines H9c2 and HEK293 cells were selected for in vitro verification of competitive endogenous RNA (ceRNA) regulation mechanism. A total of 15 candidate target genes related to HCM were screened using the online databases. Further protein-protein interaction analysis identified ACTB as the hub gene for HCM. The targeted binding relationship between miR-206, miR-145-5p, miR-1-3p, and ACTB was found. Furthermore, ADAMTS9-AS1 and circFN1 were discovered as the upstream genes of miR-206. Moreover, ADAMTS9-AS1, circFN1, and ACTB were found to be poorly expressed, and miR-206 was highly expressed in HCM. In vitro experimentation further confirmed that ADAMTS9-AS1 and circFN1 could competitively bind to miR-206, thereby augmenting ACTB expression. Taken all, ADAMTS9-AS1/circFN1-miR-206-ACTB regulatory network may involve in HCM occurrence, providing a novel theoretical basis for in-depth understanding of mechanism of HCM.
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10
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Fields CJ, Li L, Hiers NM, Li T, Sheng P, Huda T, Shan J, Gay L, Gu T, Bian J, Kilberg MS, Renne R, Xie M. Sequencing of Argonaute-bound microRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a. PLoS Genet 2021; 17:e1009934. [PMID: 34914716 PMCID: PMC8675727 DOI: 10.1371/journal.pgen.1009934] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNA) are short non-coding RNAs widely implicated in gene regulation. Most metazoan miRNAs utilize the RNase III enzymes Drosha and Dicer for biogenesis. One notable exception is the RNA polymerase II transcription start sites (TSS) miRNAs whose biogenesis does not require Drosha. The functional importance of the TSS-miRNA biogenesis is uncertain. To better understand the function of TSS-miRNAs, we applied a modified Crosslinking, Ligation, and Sequencing of Hybrids on Argonaute (AGO-qCLASH) to identify the targets for TSS-miRNAs in HCT116 colorectal cancer cells with or without DROSHA knockout. We observed that miR-320a hybrids dominate in TSS-miRNA hybrids identified by AGO-qCLASH. Targets for miR-320a are enriched for the eIF2 signaling pathway, a downstream component of the unfolded protein response. Consistently, in miR-320a mimic- and antagomir- transfected cells, differentially expressed gene products are associated with eIF2 signaling. Within the AGO-qCLASH data, we identified the endoplasmic reticulum (ER) chaperone calnexin as a direct miR-320a down-regulated target, thus connecting miR-320a to the unfolded protein response. During ER stress, but not amino acid deprivation, miR-320a up-regulates ATF4, a critical transcription factor for resolving ER stress. In summary, our study investigates the targetome of the TSS-miRNAs in colorectal cancer cells and establishes miR-320a as a regulator of unfolded protein response.
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Affiliation(s)
- Christopher J. Fields
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Nicholas M. Hiers
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Taha Huda
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Jixiu Shan
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Lauren Gay
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Tongjun Gu
- Bioinformatics, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America
| | - Jiang Bian
- Department of Health Outcomes and Biomedical Informatics, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Michael S. Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Rolf Renne
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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11
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Röber N, Dellavance A, Ingénito F, Reimer ML, Carballo OG, Conrad K, Chan EKL, Andrade LEC. Strong Association of the Myriad Discrete Speckled Nuclear Pattern With Anti-SS-A/Ro60 Antibodies: Consensus Experience of Four International Expert Centers. Front Immunol 2021; 12:730102. [PMID: 34675922 PMCID: PMC8524051 DOI: 10.3389/fimmu.2021.730102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/13/2021] [Indexed: 11/26/2022] Open
Abstract
Introduction The morphological patterns in indirect immunofluorescence assay on HEp-2 cells (HEp-2 IFA) reflect the autoantibodies in the sample. The International Consensus on ANA Patterns (ICAP) classifies 30 relevant patterns (AC-0 to AC-29). AC-4 (fine speckled nuclear pattern) is associated to anti-SS-A/Ro, anti-SS-B/La, and several autoantibodies. Anti-SS-A/Ro samples may contain antibodies to Ro60 and Ro52. A variation of AC-4 (herein designated AC-4a), characterized by myriad discrete nuclear speckles, was reported to be associated with anti-SS-A/Ro. The plain fine speckled pattern (herein designated AC-4b) seldom was associated with anti-SS-A/Ro. This study reports the experience of four expert laboratories on AC-4a and AC-4b. Methods Anti-Ro60 monoclonal antibody A7 was used to investigate the HEp-2 IFA pattern. Records containing concomitant HEp-2 IFA and SS-A/Ro tests from Durand Laboratory, Argentina (n = 383) and Fleury Laboratory, Brazil (n = 144,471) were analyzed for associations between HEp-2 IFA patterns and disease-associated autoantibodies (DAA): double-stranded DNA, Scl-70, nucleosome, SS-B/La, Sm, and U1-RNP. A total of 381 samples from Dresden Technical University (TU-Dresden), Germany, were assayed for HEp-2 IFA and DAA. Results Monoclonal A7 recognized Ro60 in Western blot and immunoprecipitation, and yielded the AC-4a pattern on HEp-2 IFA. Analyses from Durand Laboratory and Fleury Laboratory yielded compatible results: AC-4a was less frequent (8.9% and 2.7%, respectively) than AC-4b (26.1% and 24.2%) in HEp-2 IFA-positive samples. Reactivity to SS-A/Ro occurred in 67.6% and 96.3% of AC-4a-pattern samples against 23% and 6.8% of AC-4b pattern samples. Reciprocally, AC-4a occurred in 24% and 47.1% of anti-SS-A/Ro-positive samples, and in 3.8% and 0.1% of anti-SS-A/Ro-negative samples. Data from TU-Dresden show that the AC-4a pattern occurred in 69% of 169 anti-SS-A/Ro-monospecific samples (62% of all anti-SS-A/Ro-positive samples) and in 4% of anti-SS-A/Ro-negative samples, whereas anti-SS-A/Ro occurred in 98.3% of AC-4a samples and in 47.9% of AC-4b samples. In all laboratories, coexistence of anti-SS-B/La, but not other DAA, in anti-SS-A/Ro-positive samples did not disturb the AC-4a pattern. AC-4a was predominantly associated with anti-Ro60 antibodies. Conclusions This study confirms the association of AC-4a pattern and anti-SS-A/Ro in opposition to the AC-4b pattern. The results of four international expert laboratories support the worldwide applicability of these AC-4 pattern variants and their incorporation into ICAP classification under codes AC-4a and AC-4b, respectively. The AC-4 pattern should be maintained as an umbrella pattern for cases in which one cannot discriminate AC-4a and AC-4b patterns. The acknowledgment of the AC-4a pattern should add value to HEp-2 IFA interpretation.
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Affiliation(s)
- Nadja Röber
- Institute of Immunology, Technical University Dresden, Dresden, Germany
| | - Alessandra Dellavance
- Division of Research and Development, Fleury Medicine and Health Laboratories, São Paulo, Brazil
| | | | | | | | - Karsten Conrad
- Institute of Immunology, Technical University Dresden, Dresden, Germany
| | - Edward K L Chan
- Department of Oral Biology, University of Florida, Gainesville, FL, United States
| | - Luis E C Andrade
- Division of Immunology, Fleury Medicine and Health Laboratories, São Paulo, Brazil.,Division of Rheumatology, Universidade Federal de São Paulo, São Paulo, Brazil
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12
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Wu H, Li Y, Wang X, Zhang Z, Huang Y. Long non-coding RNA TUG1 knockdown prevents neurons from death to alleviate acute spinal cord injury via the microRNA-338/BIK axis. Bioengineered 2021; 12:5566-5582. [PMID: 34517787 PMCID: PMC8806874 DOI: 10.1080/21655979.2021.1966258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Taurine up-regulated gene 1 (TUG1) is a cancer-associated long noncoding RNA (lncRNA) and engages in the development of spinal cord injury (SCI), a suffering neuropathological disorder. However, the regulatory role of TUG1 in acute SCI (ASCI) is still underdetermined. RT-qPCR and western blot analysis were applied to measure the expression of TUG1, microRNA-338 (miR-338), Bcl2-interacting killer (BIK), cleaved caspase 3 (c-caspase 3) and hypoxia-inducible factor-1 alpha (HIF-1α) in ASCI rats and hypoxic cells. Cell death was evaluated using flow cytometric analysis. The relationships among miR-338, TUG1 or BIK were confirmed by luciferase reporter assay, RNA immunoprecipitation and RNA pull-down. Accordingly, we monitored higher expression of TUG1 and BIK, but lower expression of miR-338 in ASCI rats and hypoxic cells. In vitro, hypoxia expedited cell death and c-caspase 3 levels. In vivo, ASCI rats were successfully developed as evidenced by diminished Basso-Beattie-Bresnahan (BBB) locomotor score and enhanced c-caspase 3 and HIF-1α expression. Nevertheless, TUG1 knockdown mitigated the cell death in ASCI rats and hypoxic cells. Mechanically, TUG1 interacted with miR-338 to regulate the BIK expression. Together, TUG1 silencing could alleviate the death in neurons and ASCI models via modulating the miR-338/BIK axis.
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Affiliation(s)
- Hongbo Wu
- Department of Orthopaedics, Huizhou City Center People's Hospital, Huizhou Guangdong, P.R. China
| | - Yi Li
- Department of Orthopaedics, Huizhou City Center People's Hospital, Huizhou Guangdong, P.R. China
| | - Xiaofeng Wang
- Department of Orthopaedics, Huizhou City Center People's Hospital, Huizhou Guangdong, P.R. China
| | - Zhiwen Zhang
- Department of Orthopaedics, Huizhou City Center People's Hospital, Huizhou Guangdong, P.R. China
| | - Yuliang Huang
- Department of Orthopaedics, Huizhou City Center People's Hospital, Huizhou Guangdong, P.R. China
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13
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Chen K, Hou Y, Liao R, Li Y, Yang H, Gong J. LncRNA SNHG6 promotes G1/S-phase transition in hepatocellular carcinoma by impairing miR-204-5p-mediated inhibition of E2F1. Oncogene 2021; 40:3217-3230. [PMID: 33824472 DOI: 10.1038/s41388-021-01671-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/17/2020] [Accepted: 01/20/2021] [Indexed: 02/06/2023]
Abstract
Emerging evidence suggests that long noncoding RNAs (lncRNAs) function as competitive endogenous RNA (ceRNA) targeting proteins and genes; however, the role of lncRNAs in hepatocellular carcinoma (HCC) is not well understood. We investigated the mechanism by which lncRNA SNHG6 promotes the development of HCC. RT-qPCR revealed upregulated lncRNA SNHG6 in the HCC setting. Elevated SNHG6 expression was indicative of poor prognosis in patients with HCC. SNHG6 overexpression resulted in increased cyclin D1, cyclin E1, and E2F1 expression both in vitro and in vivo. SNHG6 also promoted HCC cell proliferation by enhancing G1-S phase transition in vitro. Dual luciferase reporter assays, RIP, and RNA pull-down assays demonstrated SNHG6 competitively bound to miR-204-5p and inhibited its expression preventing miR-204-5p from targeting E2F1. Overexpression of miR-204-5p abolished the effect of SNHG6. Our data suggest that SNHG6 functions as a ceRNA that targets miR-204-5p resulting in an increased E2F1 expression and enhanced G1-S phase transition, thereby promoting the tumorigenesis of HCC.
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Affiliation(s)
- Kai Chen
- Organ Transplant Center, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital & Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, PR China
- The Third Ward of Hepatobiliary Pancreatic Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital & Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, PR China
| | - Yifu Hou
- Organ Transplant Center, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital & Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, PR China
- The Third Ward of Hepatobiliary Pancreatic Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital & Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, PR China
| | - Rui Liao
- Department of Hepatobiliary, School of Clinical Medicine, Southwest Medical University, Luzhou, PR China
| | - Youzan Li
- Department of Hepatobiliary, School of Clinical Medicine, Southwest Medical University, Luzhou, PR China
| | - Hongji Yang
- Organ Transplant Center, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital & Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, PR China.
- The Third Ward of Hepatobiliary Pancreatic Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital & Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, PR China.
| | - Jun Gong
- The Second Ward of Hepatobiliary Pancreatic Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital & Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, PR China.
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14
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Fernandes RC, Toubia J, Townley S, Hanson AR, Dredge BK, Pillman KA, Bert AG, Winter JM, Iggo R, Das R, Obinata D, Sandhu S, Risbridger GP, Taylor RA, Lawrence MG, Butler LM, Zoubeidi A, Gregory PA, Tilley WD, Hickey TE, Goodall GJ, Selth LA. Post-transcriptional Gene Regulation by MicroRNA-194 Promotes Neuroendocrine Transdifferentiation in Prostate Cancer. Cell Rep 2021; 34:108585. [PMID: 33406413 DOI: 10.1016/j.celrep.2020.108585] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/23/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023] Open
Abstract
Potent therapeutic inhibition of the androgen receptor (AR) in prostate adenocarcinoma can lead to the emergence of neuroendocrine prostate cancer (NEPC), a phenomenon associated with enhanced cell plasticity. Here, we show that microRNA-194 (miR-194) is a regulator of epithelial-neuroendocrine transdifferentiation. In clinical prostate cancer samples, miR-194 expression and activity were elevated in NEPC and inversely correlated with AR signaling. miR-194 facilitated the emergence of neuroendocrine features in prostate cancer cells, a process mediated by its ability to directly target a suite of genes involved in cell plasticity. One such target was FOXA1, which encodes a transcription factor with a vital role in maintaining the prostate epithelial lineage. Importantly, a miR-194 inhibitor blocked epithelial-neuroendocrine transdifferentiation and inhibited the growth of cell lines and patient-derived organoids possessing neuroendocrine features. Overall, our study reveals a post-transcriptional mechanism regulating the plasticity of prostate cancer cells and provides a rationale for targeting miR-194 in NEPC.
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Affiliation(s)
- Rayzel C Fernandes
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - John Toubia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An alliance of SA Pathology and University of South Australia, Frome Road, Adelaide, SA 5005, Australia
| | - Scott Townley
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Adrienne R Hanson
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - B Kate Dredge
- Centre for Cancer Biology, An alliance of SA Pathology and University of South Australia, Adelaide, SA 5005, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, An alliance of SA Pathology and University of South Australia, Adelaide, SA 5005, Australia
| | - Andrew G Bert
- Centre for Cancer Biology, An alliance of SA Pathology and University of South Australia, Adelaide, SA 5005, Australia
| | - Jean M Winter
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Richard Iggo
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia; Institut Bergonié Unicancer, INSERM U1218, Bordeaux, France
| | - Rajdeep Das
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia; Transplant Immunology Laboratory, Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Daisuke Obinata
- Department of Urology, Nihon University School of Medicine, Tokyo 173-8610, Japan; Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute, Prostate Cancer Research Group, Monash University, Clayton, VIC 3168, Australia
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- Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute, Prostate Cancer Research Group, Monash University, Clayton, VIC 3168, Australia; Cancer Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Shahneen Sandhu
- Cancer Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3000, Australia
| | - Gail P Risbridger
- Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute, Prostate Cancer Research Group, Monash University, Clayton, VIC 3168, Australia; Cancer Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3000, Australia
| | - Renea A Taylor
- Cancer Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC 3000, Australia; Department of Physiology, Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute, Prostate Cancer Research Group, Monash University, Clayton, VIC 3168, Australia
| | - Mitchell G Lawrence
- Department of Anatomy and Developmental Biology, Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute, Prostate Cancer Research Group, Monash University, Clayton, VIC 3168, Australia; Cancer Research Program, Cancer Research Division, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Lisa M Butler
- South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia; Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Amina Zoubeidi
- The Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Philip A Gregory
- Centre for Cancer Biology, An alliance of SA Pathology and University of South Australia, Adelaide, SA 5005, Australia; Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, An alliance of SA Pathology and University of South Australia, Adelaide, SA 5005, Australia; School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia; Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia.
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Circular RNA circ_DROSHA alleviates the neural damage in a cell model of temporal lobe epilepsy through regulating miR-106b-5p/MEF2C axis. Cell Signal 2020; 80:109901. [PMID: 33370579 DOI: 10.1016/j.cellsig.2020.109901] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 02/02/2023]
Abstract
Temporal lobe epilepsy (TLE) is the most prevalent form of acquired epilepsy. Circular RNAs (circRNAs) have recently been highlighted as important regulators in TLE. Nevertheless, the role and mechanism of circRNA Drosha ribonuclease III (circ_DROSHA) in TLE pathogenesis are still unknown. Magnesium-free extracellular solution was used to establish the TLE cell model. The levels of circ_DROSHA, myocyte-specific enhancer factor 2C (MEF2C) and miR-106b-5p were determined by qRT-PCR and western blot. Cell proliferation was detected by the Cell Counting-8 Kit (CCK-8) assay, and cell apoptosis was measured by flow cytometry. Targeted relationships among circ_DROSHA, miR-106b-5p and MEF2C were confirmed by a dual-luciferase reporter or RNA immunoprecipitation (RIP) assay. Our data showed that circ_DROSHA was down-regulated in the serum samples of TLE patients and the TLE cell model. Circ_DROSHA up-regulation alleviated the cytotoxicity of the TLE cell model by enhancing cell proliferation and repressing cell apoptosis. Circ_DROSHA directly bound to miR-106b-5p. Moreover, miR-106b-5p represented a downstream effector of circ_DROSHA function. MEF2C was a direct target of miR-106b-5p, and miR-106b-5p knockdown relieved magnesium-free treatment-induced cell injury by up-regulating MEF2C. Furthermore, circ_DROSHA regulated MEF2C expression via sponging miR-106b-5p. Our study suggested that the enforced expression of circ_DROSHA alleviated the cell damage of the TLE cell model at least in part through the regulation of the miR-106b-5p/MEF2C axis.
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16
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miRTil: An Extensive Repository for Nile Tilapia microRNA Next Generation Sequencing Data. Cells 2020; 9:cells9081752. [PMID: 32707870 PMCID: PMC7465656 DOI: 10.3390/cells9081752] [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: 06/25/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/04/2022] Open
Abstract
Nile tilapia is the third most cultivated fish worldwide and a novel model species for evolutionary studies. Aiming to improve productivity and contribute to the selection of traits of economic impact, biotechnological approaches have been intensively applied to species enhancement. In this sense, recent studies have focused on the multiple roles played by microRNAs (miRNAs) in the post-transcriptional regulation of protein-coding genes involved in the emergence of phenotypes with relevance for aquaculture. However, there is still a growing demand for a reference resource dedicated to integrating Nile Tilapia miRNA information, obtained from both experimental and in silico approaches, and facilitating the analysis and interpretation of RNA sequencing data. Here, we present an open repository dedicated to Nile Tilapia miRNAs: the “miRTil database”. The database stores data on 734 mature miRNAs identified in 11 distinct tissues and five key developmental stages. The database provides detailed information about miRNA structure, genomic context, predicted targets, expression profiles, and relative 5p/3p arm usage. Additionally, miRTil also includes a comprehensive pre-computed miRNA-target interaction network containing 4936 targets and 19,580 interactions.
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17
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Liao X, Pan J, Zhang X, Tang Q. Sensitive Detection of Argonaute2 by Triple-Helix Molecular Switch Reaction and Pyrene Excimer Switching. Aust J Chem 2020. [DOI: 10.1071/ch19485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
RNA interference (RNAi) is a powerful tool for silencing target genes in a variety of cells and has great therapeutic potential. It is triggered by small interfering RNAs (siRNAs) and by an RNA-binding protein (argonaute, Ago). In this manuscript, we designed a simple fluorescence sensor strategy for sensitive detection of argonaute2 (Ago2) based on the base pairing principle of Watson–Crick and Hoogsteen and the pyrene excimer switch. The sensing platform has extremely high sensitivity and a detection limit of 0.1nM. It can be used to detect endogenous Ago2 in cancer cells and has great potential in clinical diagnosis and biomedical research.
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18
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Anelli V, Ordas A, Kneitz S, Sagredo LM, Gourain V, Schartl M, Meijer AH, Mione M. Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma Progression. Front Genet 2018; 9:675. [PMID: 30619488 PMCID: PMC6305343 DOI: 10.3389/fgene.2018.00675] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 12/17/2022] Open
Abstract
Ras genes are among the most commonly mutated genes in human cancer; yet our understanding of their oncogenic activity at the molecular mechanistic level is incomplete. To identify downstream events that mediate ras-induced cellular transformation in vivo, we analyzed global microRNA expression in three different models of Ras-induction and tumor formation in zebrafish. Six microRNAs were found increased in Ras-induced melanoma, glioma and in an inducible model of ubiquitous Ras expression. The upregulation of the microRNAs depended on the activation of the ERK and AKT pathways and to a lesser extent, on mTOR signaling. Two Ras-induced microRNAs (miR-146a and 193a) target Jmjd6, inducing downregulation of its mRNA and protein levels at the onset of Ras expression during melanoma development. However, at later stages of melanoma progression, jmjd6 levels were found elevated. The dynamic of Jmjd6 levels during progression of melanoma in the zebrafish model suggests that upregulation of the microRNAs targeting Jmjd6 may be part of an anti-cancer response. Indeed, triple transgenic fish engineered to express a microRNA-resistant Jmjd6 from the onset of melanoma have increased tumor burden, higher infiltration of leukocytes and shorter melanoma-free survival. Increased JMJD6 expression is found in several human cancers, including melanoma, suggesting that the up-regulation of Jmjd6 is a critical event in tumor progression. The following link has been created to allow review of record GSE37015: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=jjcrbiuicyyqgpc&acc=GSE37015.
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Affiliation(s)
| | - Anita Ordas
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - Susanne Kneitz
- Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Leonel Munoz Sagredo
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany.,Faculty of Medicine, University of Valparaiso, Valparaíso, Chile
| | - Victor Gourain
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Manfred Schartl
- Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center, University Clinic Würzburg, Würzburg, Germany.,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, United States
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19
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Xiao S, Li Y, Pan Q, Ye M, He S, Tian Q, Xue M. MiR-34c/SOX9 axis regulates the chemoresistance of ovarian cancer cell to cisplatin-based chemotherapy. J Cell Biochem 2018; 120:2940-2953. [PMID: 30537410 DOI: 10.1002/jcb.26865] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 01/13/2018] [Indexed: 01/05/2023]
Abstract
Cisplatin (DDP)-based chemotherapy is a standard strategy for ovarian cancer (OC), while chemoresistance remains a major therapeutic challenge. Transcription factor SOX9 has been reported to be associated with tumor cell proliferation, metastasis, and chemoresistance. In the current study, we observed a higher SOX9 expression in OC cell lines; SOX9 overexpression might aggravate the chemoresistance of the OC cell to DDP, whereas its knockdown enhanced the chemoresistance. We screened for candidate microRNAs (miRNAs) which might target SOX9 using online tools and further verified the effect of miR-34c, one of the candidate miRNA that significantly inhibited SOX9 expression, in the regulation of OC cell proliferation and chemoresistance to DDP. Further, we verified the interaction between SOX9 and miR-34c, as well as the involvement of β-catenin signaling in this process. Through the analysis of the correlation between miR-34c expression and the clinical features of patients with OC, we revealed that miR-34c might inhibit OC cell proliferation and chemoresistance to improve the prognosis of patients with OC. Further, the expression of SOX9, β-catenin, and c-Myc in OC tissues was upregulated and inversely correlated with miR-34c expression, indicating that rescuing miR-34c expression, thus to inhibit SOX9, β-catenin, and c-Myc expression presents a promising strategy of reducing the chemoresistance of the OC cell to DDP.
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Affiliation(s)
- Songshu Xiao
- Department of Gynecology and Obstetrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yueran Li
- Department of Gynecology and Obstetrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qiong Pan
- Department of Gynecology and Obstetrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Mingzhu Ye
- Department of Gynecology and Obstetrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Sili He
- Department of Gynecology and Obstetrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qi Tian
- Department of Gynecology and Obstetrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Min Xue
- Department of Gynecology and Obstetrics, The Third Xiangya Hospital, Central South University, Changsha, China
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20
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Bu JY, Lv WZ, Liao YF, Xiao XY, Lv BJ. Long non-coding RNA LINC00978 promotes cell proliferation and tumorigenesis via regulating microRNA-497/NTRK3 axis in gastric cancer. Int J Biol Macromol 2018; 123:1106-1114. [PMID: 30452981 DOI: 10.1016/j.ijbiomac.2018.11.162] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022]
Abstract
Gastric cancer (GC) is the most common gastrointestinal malignancy in the digestive system. Recent studies have proven that long non-coding RNAs (lncRNAs) are closely related to tumor growth and metastasis. The study aimed to explore the effect of LINC00978 on GC cells proliferation and tumorigenesis. LINC00978 was up-regulated in GC tissues and cell lines. Up-regulation of LINC00978 was positively correlated with low survival rate. LINC00978 silence inhibited proliferation, metastasis, and promoted apoptosis in BGC-823 cells. Additionally, LINC00978 functioned as competing endogenous RNA to inhibit miR-497 expression. Further, NTRK3 was confirmed as a target gene of miR-497. Up-regulation of NTRK3 was found in GC tissues, and the positive correlation was presented between LINC00978 and NTRK3. Further, LINC00978 promoted cell proliferation and tumor weight by regulation of NTRK3. These findings demonstrated that LINC00978 promoted cell proliferation and tumorigenesis by regulating miR-497/NTRK3 axis in GC.
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Affiliation(s)
- Ju-Yuan Bu
- Department of Gastrointestinal Surgery, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Wei-Ze Lv
- Department of Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Yi-Feng Liao
- Department of Tumor Chemotherapy, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Xiao-Yu Xiao
- Department of Anesthesiology, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Bao-Jun Lv
- Department of Gastrointestinal Surgery, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong 519000, China.
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21
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Sheng P, Fields C, Aadland K, Wei T, Kolaczkowski O, Gu T, Kolaczkowski B, Xie M. Dicer cleaves 5'-extended microRNA precursors originating from RNA polymerase II transcription start sites. Nucleic Acids Res 2018; 46:5737-5752. [PMID: 29746670 PMCID: PMC6009592 DOI: 10.1093/nar/gky306] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/01/2018] [Accepted: 04/11/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are approximately 22 nucleotide (nt) long and play important roles in post-transcriptional regulation in both plants and animals. In animals, precursor (pre-) miRNAs are ∼70 nt hairpins produced by Drosha cleavage of long primary (pri-) miRNAs in the nucleus. Exportin-5 (XPO5) transports pre-miRNAs into the cytoplasm for Dicer processing. Alternatively, pre-miRNAs containing a 5' 7-methylguanine (m7G-) cap can be generated independently of Drosha and XPO5. Here we identify a class of m7G-capped pre-miRNAs with 5' extensions up to 39 nt long. The 5'-extended pre-miRNAs are transported by Exportin-1 (XPO1). Unexpectedly, a long 5' extension does not block Dicer processing. Rather, Dicer directly cleaves 5'-extended pre-miRNAs by recognizing its 3' end to produce mature 3p miRNA and extended 5p miRNA both in vivo and in vitro. The recognition of 5'-extended pre-miRNAs by the Dicer Platform-PAZ-Connector (PPC) domain can be traced back to ancestral animal Dicers, suggesting that this previously unrecognized Dicer reaction mode is evolutionarily conserved. Our work reveals additional genetic sources for small regulatory RNAs and substantiates Dicer's essential role in RNAi-based gene regulation.
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Affiliation(s)
- Peike Sheng
- Department of Biochemistry and Molecular Biology
- UF Health Cancer Center
| | | | - Kelsey Aadland
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences
| | - Tianqi Wei
- Department of Biochemistry and Molecular Biology
| | - Oralia Kolaczkowski
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences
| | - Tongjun Gu
- Interdisciplinary Center for Biotechnology Research
| | - Bryan Kolaczkowski
- Department of Microbiology & Cell Science, Institute of Food and Agricultural Sciences
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology
- UF Health Cancer Center
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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22
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Hu J, Wang Z, Shan Y, Pan Y, Ma J, Jia L. Long non-coding RNA HOTAIR promotes osteoarthritis progression via miR-17-5p/FUT2/β-catenin axis. Cell Death Dis 2018; 9:711. [PMID: 29907764 PMCID: PMC6003907 DOI: 10.1038/s41419-018-0746-z] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/21/2018] [Accepted: 05/24/2018] [Indexed: 01/02/2023]
Abstract
Osteoarthritis (OA) is a chronic joint disease and hard to cure at present. Accumulating evidence suggests long noncoding RNA-HOTAIR (lncRNA-HOTAIR) plays important role in OA progression. However, the underlying molecular mechanism of HOTAIR in OA progression has not been well elucidated. In the present study, we identified that HOTAIR level was upregulated in OA cartilage tissues. High expression of HOTAIR was correlated with modified Mankin scale, extracellular matrix (ECM) degradation and chondrocytes apoptosis. The expression of miR-17-5p was down-regulated, while alpha-1, 2 fucosyltransferase 2 (FUT2) was increased in OA progression. Luciferase reporter and RNA immunoprecipitation (RIP) assays indicated that HOTAIR could directly bind to miR-17-5p and indirectly upregulate FUT2 level. Functional investigation revealed HOTAIR and FUT2 aggravated ECM degradation and chondrocytes apoptosis, and this effect could be reversed by miR-17-5p. Altered FUT2 modulated the activity of wnt/β-catenin pathway and HOTAIR/miR-17-5p also mediated wnt/β-catenin pathway through FUT2. Collectively, our findings indicated that HOTAIR/miR-17-5p/FUT2 axis contributed to OA progression via wnt/β-catenin pathway, which might provide novel insights into the function of lncRNA-driven in OA.
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Affiliation(s)
- Jialei Hu
- College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning Province, 116044, China
| | - Zi Wang
- Department of Sports Medicine, Dalian Municipal Central Hospital, Dalian, Liaoning Province, 116033, China
| | - Yujia Shan
- College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning Province, 116044, China
| | - Yue Pan
- College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning Province, 116044, China
| | - Jia Ma
- College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning Province, 116044, China
| | - Li Jia
- College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning Province, 116044, China.
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23
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Circulating plasma microRNA profiling in patients with polymyositis/dermatomyositis before and after treatment: miRNA may be associated with polymyositis/dermatomyositis. Inflamm Regen 2018; 38:1. [PMID: 29321815 PMCID: PMC5757292 DOI: 10.1186/s41232-017-0058-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/07/2017] [Indexed: 12/25/2022] Open
Abstract
Background MicroRNAs (miRNAs) are involved in the regulation of key biological processes and have been implicated in various diseases, including autoimmune disorders. The pathogenesis of polymyositis (PM) and dermatomyositis (DM) is considered to be mediated by autoimmune reactions. To determine miRNA role in the development and progression of PM and DM, we performed plasma miRNA profiling in PM/DM patients before and after treatment. Methods Total RNA was isolated from plasma of 10 patients before and after treatment with prednisolone, or, in case of prednisolone resistance or complications, with the combination of calcineurin inhibitors (cyclosporine or tacrolims) and/or pulse intravenous cyclophosphamide. The expression of miRNAs was determined using miRNA microarray and validated by qRT-PCR. Results More differentially expressed miRNAs were found in plasma of DM patients compared to PM patients before and after treatment, and their profiles were different. Among the differentially expressed plasma miRNA identified by microarray, the levels of hsa-miR-4442 were confirmed by qRT-PCR to be significantly decreased by treatment. In addition, plasma hsa-miR-4442 content in active PM/DM significantly exceeded that in other active autoimmune diseases such as rheumatoid arthritis and systemic lupus erythematosus, as well as in healthy individuals. The level of plasma hsa-miR-4442 was positively correlated with Skeletal Disease Activity in MITAX (Myositis Intention to Treat Activity Index). Conclusion This is the first report describing plasma miRNA expression profiles in PM/DM patients. The present data suggest that plasma levels of miRNAs may be associated with polymyositis/dermatomyositis and hsa-miR-4442 could be used as a biomarker for PM/DM diagnosis and/or disease activity. Electronic supplementary material The online version of this article (10.1186/s41232-017-0058-1) contains supplementary material, which is available to authorized users.
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24
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Zhang D, Ma F, Leng J, Zhang CY. A dual signal amplification-assisted DNAzyme biosensor for ultrasensitive detection of Argonaute 2 activity. Chem Commun (Camb) 2018; 54:13678-13681. [DOI: 10.1039/c8cc08553f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We develop a new dual-signal amplification-assisted DNAzyme biosensor for sensitive detection of Argonaute 2 (Ago2) activity.
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Affiliation(s)
- Dandan Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Fei Ma
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Junhong Leng
- Jinan Maternity and Child Care Hospital
- Jinan 250000
- China
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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25
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Lei Z, Shi H, Li W, Yu D, Shen F, Yu X, Lu D, Sun C, Liao K. miR‑185 inhibits non‑small cell lung cancer cell proliferation and invasion through targeting of SOX9 and regulation of Wnt signaling. Mol Med Rep 2018; 17:1742-1752. [PMID: 29138830 PMCID: PMC5780119 DOI: 10.3892/mmr.2017.8050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 10/10/2017] [Indexed: 12/15/2022] Open
Abstract
SRY-box 9 (SOX9) is an important transcription factor required for development, which has additionally been reported to be an independent prognostic indicator for the survival of patients with non‑small cell lung cancer (NSCLC). Accumulating evidence has indicated that dysregulation of microRNAs (miRNAs/miRs) may contribute to the initiation and progression of cancer. SOX9 may be regulated by a number of miRNAs in different types of cancer, including in NSCLC. The present study sought to identify novel candidate miRNAs associated with SOX9 in NSCLC using online tools, and investigated the detailed functions of miR‑185, which suppressed SOX9 mRNA expression most strongly out of the candidate miRNAs. It was observed that ectopic miR‑185 expression significantly suppressed NSCLC cell proliferation, invasion and migration. Using luciferase reporter gene and RNA immunoprecipitation assays, SOX9 was confirmed to be a direct target of miR‑185. In addition, the downstream Wnt signaling‑associated factors β‑catenin and c‑Myc proto‑oncogene protein (Myc) were demonstrated to be inhibited by miR‑185 overexpression. SOX9, β‑catenin and c‑Myc mRNA expression was significantly upregulated in NSCLC tissues, and was inversely correlated with miR‑185 expression. The results of the present study demonstrated that rescuing miR‑185 expression in NSCLC, thereby inhibiting SOX9 expression and the downstream Wnt signaling, and leading to the suppression of NSCLC cell proliferation, invasion and migration, may be a promising strategy for the treatment of NSCLC.
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Affiliation(s)
- Zhengwen Lei
- Department of Cardiac-Vascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
- Center of Translational Medicine, Medical School of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
- Department of Cardiac-Thoracic Surgery, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu 225000, P.R. China
| | - Hongcan Shi
- Center of Translational Medicine, Medical School of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
- Department of Cardiac-Thoracic Surgery, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu 225000, P.R. China
- Correspondence to: Professor Hongcan Shi, Center of Translational Medicine, Medical School of Yangzhou University, 11 Huaihai Road, Yangzhou, Jiangsu 225000, P.R. China, E-mail:
| | - Wei Li
- Center of Translational Medicine, Medical School of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Duonan Yu
- Center of Translational Medicine, Medical School of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Feiyang Shen
- Center of Translational Medicine, Medical School of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Xi Yu
- Center of Translational Medicine, Medical School of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Dan Lu
- Department of Obstetrical, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu 225000, P.R. China
| | - Chao Sun
- Department of Cardiac-Thoracic Surgery, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu 225000, P.R. China
| | - Kai Liao
- Center of Translational Medicine, Medical School of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
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26
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Xu J, Xu Y. The lncRNA MEG3 downregulation leads to osteoarthritis progression via miR-16/SMAD7 axis. Cell Biosci 2017; 7:69. [PMID: 29255591 PMCID: PMC5727780 DOI: 10.1186/s13578-017-0195-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 12/02/2017] [Indexed: 01/02/2023] Open
Abstract
Background Osteoarthritis (OA) is a chronic joint disease and there is no a definitive cure at present. Long non-coding RNAs (lncRNAs) have been confirmed to play important roles in the development of OA. However, the underlying mechanism of lncRNA maternally expressed gene 3 (MEG3) in OA has not been well elucidated. Methods The rat OA model and interleukin-1β (IL-1β)-induced rat chondrocytes were constructed. The expression pattern of lncRNA MEG3 and miR-16 was detected by RT-qPCR assay in cartilage tissues of rat OA model. The effect of MEG3 and miR-16 on IL-1β-induced chondrocytes was evaluated on the basis of cell viability and apoptosis. Then, the interaction among MEG3, miR-16 SMAD7 was explored by dual-luciferase reporter assay and RIP assay. Results It is found that lncRNA MEG3 was down-regulated and miR-16 was up-regulated in rat OA cartilage tissues. MEG3 knockdown promoted proliferation and inhibited apoptosis, while miR-16 knockdown suppressed proliferation and promoted apoptosis in IL-1β-induced rat chondrocytes. Moreover, MEG3 was involved in miR-16 pathway and MEG3 suppressed miR-16 expression. Additionally, SMAD7 was a target gene of miR-16 and miR-16 suppressed SMAD7 expression in IL-1β-induced chondrocytes. Moreover, the expression of SMAD7 induced by MEG3 or si-MEG3 was markedly reversed by the introduction of miR-16 or anti-miR-16. Furthermore, MEG3 exerted its anti-proliferation and pro-apoptosis by regulating miR-16 and SMAD7. Conclusion MEG3 was down-regulated and miR-16 was up-regulated in cartilage tissues of rat OA model. MEG3 knockdown might lead to the progression of OA through miR-16/SMAD7 axis.
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Affiliation(s)
- Jin Xu
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, No. 899 Ping Hai Road, Gusu District, Suzhou, 215031 China.,Department of Orthopedics, Baoshan District Shanghai Integrated Traditional Chinese and Western Medicine Hospital, Shanghai, 201999 China
| | - Yaozeng Xu
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, No. 899 Ping Hai Road, Gusu District, Suzhou, 215031 China
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27
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Chen W, Zhao W, Zhang L, Wang L, Wang J, Wan Z, Hong Y, Yu L. MALAT1-miR-101-SOX9 feedback loop modulates the chemo-resistance of lung cancer cell to DDP via Wnt signaling pathway. Oncotarget 2017; 8:94317-94329. [PMID: 29212230 PMCID: PMC5706876 DOI: 10.18632/oncotarget.21693] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/04/2017] [Indexed: 01/01/2023] Open
Abstract
Cisplatin (DDP)-based chemotherapy is a standard strategy for lung cancer, while chemoresistance remains a major therapeutic challenge. Recent evidence highlights the crucial regulatory roles of long non-coding RNAs (lncRNA) in tumor biology. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has important roles in regulating the proliferation, invasion and migration of lung cancer cell. High MALAT1 expression in lung cancer was related to poorer clinicopathologic features in this study. MALAT1 knockdown alone was sufficient to amplify DDP-induced repression of cell viability. MALAT1 knockdown could also sensitized DDP-resistant lung cancer cells (A549/DDP and H1299/DDP) to DDP. Further assays indicated that MALAT1 acted as a competing endogenous RNA to upregulate SOX9 expression by sponging miR-101 in DDP-resistant cancer cells, through Wnt signaling pathway. Moreover, SOX9 could bind to the promoter of MALAT1 to activate its transcription. Taken together, MALAT1, miR-101 and SOX9 form a feedback loop to enhance the chemo-resistance of lung cancer cell to DDP; this MALAT1-miR-101-SOX9 feedback loop plays an important role in the chemo-resistance of lung cancer cell to DDP and may serve as a potential target for cancer treatment.
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Affiliation(s)
- Wei Chen
- Department of Respiratory Medicine, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
| | - Wei Zhao
- Department of Pathology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Li Zhang
- Department of Hematology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
| | - Lixin Wang
- Department of Respiratory Medicine, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
| | - Jipeng Wang
- Department of Respiratory Medicine, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
| | - Zongren Wan
- Department of Respiratory Medicine, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
| | - Yongqing Hong
- Department of Respiratory Medicine, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
| | - Liang Yu
- Department of Hematology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
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28
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Modeling miRNA-mRNA interactions that cause phenotypic abnormality in breast cancer patients. PLoS One 2017; 12:e0182666. [PMID: 28793339 PMCID: PMC5549916 DOI: 10.1371/journal.pone.0182666] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/13/2017] [Indexed: 01/04/2023] Open
Abstract
Background The dysregulation of microRNAs (miRNAs) alters expression level of pro-oncogenic or tumor suppressive mRNAs in breast cancer, and in the long run, causes multiple biological abnormalities. Identification of such interactions of miRNA-mRNA requires integrative analysis of miRNA-mRNA expression profile data. However, current approaches have limitations to consider the regulatory relationship between miRNAs and mRNAs and to implicate the relationship with phenotypic abnormality and cancer pathogenesis. Methodology/Findings We modeled causal relationships between genomic expression and clinical data using a Bayesian Network (BN), with the goal of discovering miRNA-mRNA interactions that are associated with cancer pathogenesis. The Multiple Beam Search (MBS) algorithm learned interactions from data and discovered that hsa-miR-21, hsa-miR-10b, hsa-miR-448, and hsa-miR-96 interact with oncogenes, such as, CCND2, ESR1, MET, NOTCH1, TGFBR2 and TGFB1 that promote tumor metastasis, invasion, and cell proliferation. We also calculated Bayesian network posterior probability (BNPP) for the models discovered by the MBS algorithm to validate true models with high likelihood. Conclusion/Significance The MBS algorithm successfully learned miRNA and mRNA expression profile data using a BN, and identified miRNA-mRNA interactions that probabilistically affect breast cancer pathogenesis. The MBS algorithm is a potentially useful tool for identifying interacting gene pairs implicated by the deregulation of expression.
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29
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Luo J, Chen P, Xie W, Wu F. MicroRNA-138 inhibits cell proliferation in hepatocellular carcinoma by targeting Sirt1. Oncol Rep 2017; 38:1067-1074. [PMID: 28677784 DOI: 10.3892/or.2017.5782] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 06/09/2017] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs) are a family of small, non‑coding RNA molecules that are highly conserved across species and function as regulators of gene expression. In the present study, we revealed that miR-138 expression was at a low level while sirtuin type 1 (Sirt1) mRNA expression was at high level in hepatocellular carcinoma tissues and cell lines by using real-time PCR and western blot assays, and the functions of miR-138 were achieved via targeting of Sirt1 using luciferase reporter gene vector and RNA immunoprecipitation assays. Overexpression of miR-138 attenuated Sirt1 expression and inhibited cell proliferation by using CCK-8 and BrdU assays. The inhibitory effect of miR-138 could be partially restored by forced expression of Sirt1 in cells. Our data revealed a crucial role and mechanism of miR-138 in the regulation of hepatocellular carcinoma cell growth via the miR-138/Sirt1 axis, and miR-138 could be an important potential target for the clinical management of hepatocellular carcinoma in the future.
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Affiliation(s)
- Jia Luo
- Department of Hepatobiliary Surgery, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Pan Chen
- Department of Hepatobiliary Surgery, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Wei Xie
- Department of Hepatobiliary Surgery, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Feiyue Wu
- Department of Hepatobiliary Surgery, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
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30
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Wang Q, Wang W, Zhang F, Deng Y, Long Z. NEAT1/miR-181c Regulates Osteopontin (OPN)-Mediated Synoviocyte Proliferation in Osteoarthritis. J Cell Biochem 2017; 118:3775-3784. [PMID: 28379604 DOI: 10.1002/jcb.26025] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/30/2017] [Indexed: 01/21/2023]
Abstract
Osteoarthritis (OA) is characterized by progressive destruction of articular cartilage, resulting in significant disability. Inflammatory cytokines commonly initiate the extreme changes in the synovium and cartilage microenvironment of the OA patients, subsequently resulting in cell dysfunctions, especially synoviocyte dysfunction. We revealed that the expression of osteopontin (OPN), which has been reported to regulate expression of various inflammatory factors associating with the pathogenesis of OA including matrix metalloprotease 13 (MMP13), interlukine-6 and 8 (IL-6 and IL-8), is significantly upregulated in OA tissues. In the present study, online tools were used to screen out the candidate miRNAs of OPN. Among the candidate miRNAs, miR-181c inhibited OPN mRNA expression the most strongly. Ectopic expression of miR-181c significantly repressed synoviocyte proliferation, as well as the levels of OPN, MMP13, IL-6, and IL-8. Further, the candidate lncRNAs of miR-181c were screened out by using DianaTools; among which NEAT1 showed to inversely regulate miR-181c. By performing Luciferase assays, we revealed that NEAT1 competed with OPN for miR-181c binding. After NEAT1 knockdown, MMP13, IL-6, and IL-8 expression was reduced; the synoviocyte proliferation was repressed, as well as OPN protein levels; the suppressive effect of NETA1 knockdown on synoviocyte proliferation and the indicated factors were partially reversed by miR-181c inhibition. In OA tissues, OPN mRNA, and NEAT1 expression was upregulated, whereas miR-181c expression was downregulated, indicating that targeting NEAT1 to rescue miR-181c expression so as to inhibit OPN expression and synoviocyte proliferation might be an efficient strategy for OA treatment. J. Cell. Biochem. 118: 3775-3784, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Qiyuan Wang
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Emergency Medicine and Difficult Diseases Institute, Central South University, Changsha, Hunan, China
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fan Zhang
- Department of Neonatology, The Hunan Children's Hospital, Changsha, Hunan, China
| | - Youwen Deng
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Emergency Medicine and Difficult Diseases Institute, Central South University, Changsha, Hunan, China
| | - Zeling Long
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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31
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Pawaria S, Sharma S, Baum R, Nündel K, Busto P, Gravallese EM, Fitzgerald KA, Marshak-Rothstein A. Taking the STING out of TLR-driven autoimmune diseases: good, bad, or indifferent? J Leukoc Biol 2016; 101:121-126. [PMID: 27531928 DOI: 10.1189/jlb.3mr0316-115r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/01/2016] [Accepted: 07/25/2016] [Indexed: 01/24/2023] Open
Abstract
Both endosomal and cytosolic-nucleic acid-sensing receptors can detect endogenous ligands and promote autoimmunity and autoinflammation. These responses involve a complex interplay among and between the cytosolic and endosomal sensors involving both hematopoietic and radioresistant cells. Cytosolic sensors directly promote inflammatory responses through the production of type I IFNs and proinflammatory cytokines. Inflammation-associated tissue damage can further promote autoimmune responses indirectly, as receptor-mediated internalization of the resulting cell debris can activate endosomal Toll-like receptors (TLR). Both endosomal and cytosolic receptors can also negatively regulate inflammatory responses. A better understanding of the factors and pathways that promote and constrain autoimmune diseases will have important implications for the development of agonists and antagonists that modulate these pathways.
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Affiliation(s)
- Sudesh Pawaria
- Division of Rheumatology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Shruti Sharma
- Division of Infectious Disease, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA; and.,Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Rebecca Baum
- Division of Rheumatology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kerstin Nündel
- Division of Rheumatology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Patricia Busto
- Division of Rheumatology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ellen M Gravallese
- Division of Rheumatology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Katherine A Fitzgerald
- Division of Infectious Disease, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA; and.,Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ann Marshak-Rothstein
- Division of Rheumatology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA; .,Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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32
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Kalantari R, Chiang CM, Corey DR. Regulation of mammalian transcription and splicing by Nuclear RNAi. Nucleic Acids Res 2016; 44:524-37. [PMID: 26612865 PMCID: PMC4737150 DOI: 10.1093/nar/gkv1305] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022] Open
Abstract
RNA interference (RNAi) is well known as a mechanism for controlling mammalian mRNA translation in the cytoplasm, but what would be the consequences if it also functions in cell nuclei? Although RNAi has also been found in nuclei of plants, yeast, and other organisms, there has been relatively little progress towards understanding the potential involvement of mammalian RNAi factors in nuclear processes including transcription and splicing. This review summarizes evidence for mammalian RNAi factors in cell nuclei and mechanisms that might contribute to the control of gene expression. When RNAi factors bind small RNAs, they form ribonucleoprotein complexes that can be selective for target sequences within different classes of nuclear RNA substrates. The versatility of nuclear RNAi may supply a previously underappreciated layer of regulation to transcription, splicing, and other nuclear processes.
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Affiliation(s)
- Roya Kalantari
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Cheng-Ming Chiang
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-8807, USA
| | - David R Corey
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
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33
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Lennox KA, Behlke MA. Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides. Nucleic Acids Res 2015; 44:863-77. [PMID: 26578588 PMCID: PMC4737147 DOI: 10.1093/nar/gkv1206] [Citation(s) in RCA: 329] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/26/2015] [Indexed: 12/16/2022] Open
Abstract
Thousands of long non-coding RNAs (lncRNAs) have been identified in mammalian cells. Some have important functions and their dysregulation can contribute to a variety of disease states. However, most lncRNAs have not been functionally characterized. Complicating their study, lncRNAs have widely varying subcellular distributions: some reside predominantly in the nucleus, the cytoplasm or in both compartments. One method to query function is to suppress expression and examine the resulting phenotype. Methods to suppress expression of mRNAs include antisense oligonucleotides (ASOs) and RNA interference (RNAi). Antisense and RNAi-based gene-knockdown methods vary in efficacy between different cellular compartments. It is not known if this affects their ability to suppress lncRNAs. To address whether localization of the lncRNA influences susceptibility to degradation by either ASOs or RNAi, nuclear lncRNAs (MALAT1 and NEAT1), cytoplasmic lncRNAs (DANCR and OIP5-AS1) and dual-localized lncRNAs (TUG1, CasC7 and HOTAIR) were compared for knockdown efficiency. We found that nuclear lncRNAs were more effectively suppressed using ASOs, cytoplasmic lncRNAs were more effectively suppressed using RNAi and dual-localized lncRNAs were suppressed using both methods. A mixed-modality approach combining ASOs and RNAi reagents improved knockdown efficacy, particularly for those lncRNAs that localize to both nuclear and cytoplasmic compartments.
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Affiliation(s)
- Kim A Lennox
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
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Méndez C, Ahlenstiel CL, Kelleher AD. Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus. World J Virol 2015; 4:219-244. [PMID: 26279984 PMCID: PMC4534814 DOI: 10.5501/wjv.v4.i3.219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/24/2015] [Accepted: 04/29/2015] [Indexed: 02/05/2023] Open
Abstract
While human immunodeficiency virus 1 (HIV-1) infection is controlled through continuous, life-long use of a combination of drugs targeting different steps of the virus cycle, HIV-1 is never completely eradicated from the body. Despite decades of research there is still no effective vaccine to prevent HIV-1 infection. Therefore, the possibility of an RNA interference (RNAi)-based cure has become an increasingly explored approach. Endogenous gene expression is controlled at both, transcriptional and post-transcriptional levels by non-coding RNAs, which act through diverse molecular mechanisms including RNAi. RNAi has the potential to control the turning on/off of specific genes through transcriptional gene silencing (TGS), as well as fine-tuning their expression through post-transcriptional gene silencing (PTGS). In this review we will describe in detail the canonical RNAi pathways for PTGS and TGS, the relationship of TGS with other silencing mechanisms and will discuss a variety of approaches developed to suppress HIV-1 via manipulation of RNAi. We will briefly compare RNAi strategies against other approaches developed to target the virus, highlighting their potential to overcome the major obstacle to finding a cure, which is the specific targeting of the HIV-1 reservoir within latently infected cells.
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35
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Nahid MA, Satoh M, Chan EKL. Interleukin 1β-Responsive MicroRNA-146a Is Critical for the Cytokine-Induced Tolerance and Cross-Tolerance to Toll-Like Receptor Ligands. J Innate Immun 2015; 7:428-40. [PMID: 25896300 DOI: 10.1159/000371517] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 12/12/2014] [Indexed: 01/07/2023] Open
Abstract
Unwarranted overproduction of cytokines, such as interleukin (IL)-1β, can cause moderate to severe pathological complications, and thus elaborate mechanisms are needed to regulate its onset and termination. One such, well-known, mechanism is endotoxin tolerance, generally described as controlling lipopolysaccharide Toll-like receptor 4 (LPS-TLR4) signaling. Similarly, cytokine-induced tolerance plays an important role in regulating an overactive cytokine response. In this report, the capability of IL-1β to induce tolerance and cross-tolerance to various inflammatory ligands was investigated. IL-1β-stimulated THP-1 monocytes showed a gradual increase of microRNA (miR)-146a, reaching 15-fold expression by 24 h. miR-146a upregulation induced tolerance toward subsequent challenges of IL-1β, LPS, peptidoglycan, Pam and flagellin in THP-1 cells. The induction of tolerance was dependent on the IL-1β priming dose and associated increase of miR-146a expression. Moreover, IL-1β-treated THP-1 cells showed sustained miR-146a upregulation that repressed IRAK1 and TRAF6 adaptor molecules. Transfection of miR-146a alone mimicked IL-1β-induced tolerance in monocytes, while cells transfected with miR-146a inhibitor increased chemokine production. A comparable cytokine response regulated by miR-146a was also detected in lung epithelial A549 cells, purified human monocytes and mouse peritoneal macrophages. Thus, our studies showed that miR-146a was crucial for monocytic cell-based IL-1β tolerance and cross-tolerance, and thus opens the way for future research in the development of therapeutics for inflammatory diseases.
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Affiliation(s)
- Md A Nahid
- Department of Oral Biology, University of Florida, Gainesville, Fla., USA
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36
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Batsché E, Ameyar-Zazoua M. The influence of Argonaute proteins on alternative RNA splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:141-56. [DOI: 10.1002/wrna.1264] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 07/28/2014] [Accepted: 07/31/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Eric Batsché
- Institut Pasteur, Dpt Biologie du Développement et Cellules Souches; Unité de Régulation Epigénétique; 75015 Paris France
- URA2578; CNRS
| | - Maya Ameyar-Zazoua
- Institut Pasteur, Dpt Biologie du Développement et Cellules Souches; Unité de Régulation Epigénétique; 75015 Paris France
- URA2578; CNRS
- Laboratoire Epigénétique et Destin Cellulaire, CNRS UMR7216; Université Paris Diderot, Cité Sorbonne Paris; Paris France
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37
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Gagnon KT, Li L, Janowski BA, Corey DR. Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nat Protoc 2014; 9:2045-60. [PMID: 25079428 PMCID: PMC4251768 DOI: 10.1038/nprot.2014.135] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
RNAi is well known for its ability to regulate gene expression in the cytoplasm of mammalian cells. In mammalian cell nuclei, however, the impact of RNAi has remained more controversial. A key technical hurdle has been a lack of optimized protocols for the isolation and analysis of cell nuclei. Here we describe a simplified protocol for nuclei isolation from cultured cells that incorporates a method for obtaining nucleoplasmic and chromatin fractions and removing cytoplasmic contamination. Cell fractions can then be used to detect the presence and activity of RNAi factors in the nucleus. We include a method for investigating an early step in RNAi, Argonaute protein loading with small RNAs, which is enabled by our improved extract preparations. This protocol facilitates the characterization of nuclear RNAi, and it can be applied to the analysis of other nuclear proteins and pathways. From cellular fractionation to analysis of Argonaute loading results, this protocol takes 4-6 d to complete.
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Affiliation(s)
- Keith T Gagnon
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Liande Li
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Bethany A Janowski
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - David R Corey
- 1] Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA. [2] Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
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38
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Hogan DJ, Vincent TM, Fish S, Marcusson EG, Bhat B, Chau BN, Zisoulis DG. Anti-miRs competitively inhibit microRNAs in Argonaute complexes. PLoS One 2014; 9:e100951. [PMID: 24992387 PMCID: PMC4084633 DOI: 10.1371/journal.pone.0100951] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/02/2014] [Indexed: 11/23/2022] Open
Abstract
MicroRNAs (miRNAs), small RNA molecules that post-transcriptionally regulate mRNA expression, are crucial in diverse developmental and physiological programs and their misregulation can lead to disease. Chemically modified oligonucleotides have been developed to modulate miRNA activity for therapeutic intervention in disease settings, but their mechanism of action has not been fully elucidated. Here we show that the miRNA inhibitors (anti-miRs) physically associate with Argonaute proteins in the context of the cognate target miRNA in vitro and in vivo. The association is mediated by the seed region of the miRNA and is sensitive to the placement of chemical modifications. Furthermore, the targeted miRNAs are stable and continue to be associated with Argonaute. Our results suggest that anti-miRs specifically associate with Argonaute-bound miRNAs, preventing association with target mRNAs, which leads to subsequent stabilization and thus increased expression of the targeted mRNAs.
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Affiliation(s)
- Daniel J. Hogan
- Regulus Therapeutics, San Diego, California, United States of America
| | - Thomas M. Vincent
- Regulus Therapeutics, San Diego, California, United States of America
| | - Sarah Fish
- Regulus Therapeutics, San Diego, California, United States of America
| | - Eric G. Marcusson
- Regulus Therapeutics, San Diego, California, United States of America
| | - Balkrishen Bhat
- Regulus Therapeutics, San Diego, California, United States of America
| | - B. Nelson Chau
- Regulus Therapeutics, San Diego, California, United States of America
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39
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Androsavich JR, Chau BN. Non-inhibited miRNAs shape the cellular response to anti-miR. Nucleic Acids Res 2014; 42:6945-55. [PMID: 24810853 PMCID: PMC4066772 DOI: 10.1093/nar/gku344] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Identification of primary microRNA (miRNA) gene targets is critical for developing miRNA-based therapeutics and understanding their mechanisms of action. However, disentangling primary target derepression induced by miRNA inhibition from secondary effects on the transcriptome remains a technical challenge. Here, we utilized RNA immunoprecipitation (RIP) combined with competitive binding assays to identify novel primary targets of miR-122. These transcripts physically dissociate from AGO2-miRNA complexes when anti-miR is spiked into liver lysates. mRNA target displacement strongly correlated with expression changes in these genes following in vivo anti-miR dosing, suggesting that derepression of these targets directly reflects changes in AGO2 target occupancy. Importantly, using a metric based on weighted miRNA expression, we found that the most responsive mRNA target candidates in both RIP competition assays and expression profiling experiments were those with fewer alternative seed sites for highly expressed non-inhibited miRNAs. These data strongly suggest that miRNA co-regulation modulates the transcriptomic response to anti-miR. We demonstrate the practical utility of this ‘miR-target impact’ model, and encourage its incorporation, together with the RIP competition assay, into existing target prediction and validation pipelines.
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Affiliation(s)
- John R Androsavich
- Regulus Therapeutics Inc., 3545 John Hopkins Ct, San Diego, CA 92121, USA
| | - B Nelson Chau
- Regulus Therapeutics Inc., 3545 John Hopkins Ct, San Diego, CA 92121, USA
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40
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Gagnon KT, Li L, Chu Y, Janowski BA, Corey DR. RNAi factors are present and active in human cell nuclei. Cell Rep 2014; 6:211-21. [PMID: 24388755 PMCID: PMC3916906 DOI: 10.1016/j.celrep.2013.12.013] [Citation(s) in RCA: 279] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/12/2013] [Accepted: 12/06/2013] [Indexed: 12/21/2022] Open
Abstract
RNAi is widely appreciated as a powerful regulator of mRNA translation in the cytoplasm of mammalian cells. However, the presence and activity of RNAi factors in the mammalian nucleus has been the subject of considerable debate. Here, we show that Argonaute-2 (Ago2) and RNAi factors Dicer, TRBP, and TRNC6A/GW182 are in the human nucleus and associate together in multiprotein complexes. Small RNAs can silence nuclear RNA and guide site-specific cleavage of the targeted RNA, demonstrating that RNAi can function in the human nucleus. Nuclear Dicer is active and miRNAs are bound to nuclear Ago2, consistent with the existence of nuclear miRNA pathways. Notably, we do not detect loading of duplex small RNAs in nuclear extracts and known loading factors are absent. These results extend RNAi into the mammalian nucleus and suggest that regulation of RNAi via small RNA loading of Ago2 differs between the cytoplasm and the nucleus.
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Affiliation(s)
- Keith T Gagnon
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA
| | - Liande Li
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA
| | - Yongjun Chu
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA
| | - Bethany A Janowski
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA
| | - David R Corey
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041, USA.
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41
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Human RNAi pathway: crosstalk with organelles and cells. Funct Integr Genomics 2013; 14:31-46. [PMID: 24197738 DOI: 10.1007/s10142-013-0344-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 12/12/2022]
Abstract
Understanding gene regulation mechanisms has been a serious challenge in biology. As a novel mechanism, small non-coding RNAs are an alternative means of gene regulation in a specific and efficient manner. There are growing reports on regulatory roles of these RNAs including transcriptional gene silencing/activation and post-transcriptional gene silencing events. Also, there are several known small non-coding RNAs which all work through RNA interference pathway. Interestingly, these small RNAs are secreted from cells toward targeted cells presenting new communication approach in cell-cell or cell-organ signal transduction. In fact, understanding cellular and molecular basis of these pathways will strongly improve developing targeted therapies and potent and specific regulatory tools. This study will review some of the most recent findings in this subject and will introduce a super-pathway RNA interference-based small RNA silencing network.
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42
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Salim H, Arvanitis A, de Petris L, Kanter L, Hååg P, Zovko A, Özata DM, Lui WO, Lundholm L, Zhivotovsky B, Lewensohn R, Viktorsson K. miRNA-214 is related to invasiveness of human non-small cell lung cancer and directly regulates alpha protein kinase 2 expression. Genes Chromosomes Cancer 2013; 52:895-911. [DOI: 10.1002/gcc.22085] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 05/21/2013] [Accepted: 05/30/2013] [Indexed: 01/20/2023] Open
Affiliation(s)
- Hogir Salim
- Department of Oncology-Pathology; Karolinska Biomics Center, Karolinska Institutet; SE-171 76; Stockholm; Sweden
| | - Alexandros Arvanitis
- Department of Oncology-Pathology; Karolinska Biomics Center, Karolinska Institutet; SE-171 76; Stockholm; Sweden
| | - Luigi de Petris
- Department of Oncology-Pathology; Karolinska Biomics Center, Karolinska Institutet; SE-171 76; Stockholm; Sweden
| | - Lena Kanter
- Department of Oncology-Pathology; Karolinska Biomics Center, Karolinska Institutet; SE-171 76; Stockholm; Sweden
| | - Petra Hååg
- Department of Oncology-Pathology; Karolinska Biomics Center, Karolinska Institutet; SE-171 76; Stockholm; Sweden
| | - Ana Zovko
- Department of Oncology-Pathology; Karolinska Biomics Center, Karolinska Institutet; SE-171 76; Stockholm; Sweden
| | - Deniz Mahmut Özata
- Departmenzt of Oncology-Pathology; Cancer Center Karolinska, Karolinska Institutet; SE- 171 76; Stockholm; Sweden
| | - Weng-Onn Lui
- Departmenzt of Oncology-Pathology; Cancer Center Karolinska, Karolinska Institutet; SE- 171 76; Stockholm; Sweden
| | - Lovisa Lundholm
- Department of Oncology-Pathology; Karolinska Biomics Center, Karolinska Institutet; SE-171 76; Stockholm; Sweden
| | - Boris Zhivotovsky
- Division of Toxicology; Institute of Environmental Medicine, Karolinska Institutet; Box 210; SE-171 77; Stockholm; Sweden
| | - Rolf Lewensohn
- Department of Oncology-Pathology; Karolinska Biomics Center, Karolinska Institutet; SE-171 76; Stockholm; Sweden
| | - Kristina Viktorsson
- Department of Oncology-Pathology; Karolinska Biomics Center, Karolinska Institutet; SE-171 76; Stockholm; Sweden
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43
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Flores-Jasso CF, Salomon WE, Zamore PD. Rapid and specific purification of Argonaute-small RNA complexes from crude cell lysates. RNA (NEW YORK, N.Y.) 2013; 19:271-9. [PMID: 23249751 PMCID: PMC3543083 DOI: 10.1261/rna.036921.112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/16/2012] [Indexed: 06/01/2023]
Abstract
Small interfering RNAs (siRNAs) direct Argonaute proteins, the core components of the RNA-induced silencing complex (RISC), to cleave complementary target RNAs. Here, we describe a method to purify active RISC containing a single, unique small RNA guide sequence. We begin by capturing RISC using a complementary 2'-O-methyl oligonucleotide tethered to beads. Unlike other methods that capture RISC but do not allow its recovery, our strategy purifies active, soluble RISC in good yield. The method takes advantage of the finding that RISC partially paired to a target through its siRNA guide dissociates more than 300 times faster than a fully paired siRNA in RISC. We use this strategy to purify fly Ago1- and Ago2-RISC, as well as mouse AGO2-RISC. The method can discriminate among RISCs programmed with different guide strands, making it possible to deplete and recover specific RISC populations. Endogenous microRNA:Argonaute complexes can also be purified from cell lysates. Our method scales readily and takes less than a day to complete.
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Affiliation(s)
| | | | - Phillip D. Zamore
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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44
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Li J, Hobman TC, Simmonds AJ. Gawky (GW) is the Drosophila melanogaster GW182 homologue. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 768:127-45. [PMID: 23224968 DOI: 10.1007/978-1-4614-5107-5_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jing Li
- Department of Cell Biology, University of Alberta, Edmonton, Canada.
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45
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He M, Liu Y, Wang X, Zhang MQ, Hannon GJ, Huang ZJ. Cell-type-based analysis of microRNA profiles in the mouse brain. Neuron 2012; 73:35-48. [PMID: 22243745 DOI: 10.1016/j.neuron.2011.11.010] [Citation(s) in RCA: 222] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2011] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNA) are implicated in brain development and function but the underlying mechanisms have been difficult to study in part due to the cellular heterogeneity in neural circuits. To systematically analyze miRNA expression in neurons, we have established a miRNA tagging and affinity-purification (miRAP) method that is targeted to cell types through the Cre-loxP binary system in mice. Our studies of the neocortex and cerebellum reveal the expression of a large fraction of known miRNAs with distinct profiles in glutamatergic and GABAergic neurons and subtypes of GABAergic neurons. We further detected putative novel miRNAs, tissue or cell type-specific strand selection of miRNAs, and miRNA editing. Our method thus will facilitate a systematic analysis of miRNA expression and regulation in specific neuron types in the context of neuronal development, physiology, plasticity, pathology, and disease models, and is generally applicable to other cell types and tissues.
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Affiliation(s)
- Miao He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Genetics Program, State University of New York, Stony Brook, NY 11790, USA
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46
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Long JM, Lahiri DK. Advances in microRNA experimental approaches to study physiological regulation of gene products implicated in CNS disorders. Exp Neurol 2012; 235:402-18. [PMID: 22245616 DOI: 10.1016/j.expneurol.2011.12.043] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/13/2011] [Accepted: 12/25/2011] [Indexed: 11/28/2022]
Abstract
The central nervous system (CNS) is a remarkably complex organ system, requiring an equally complex network of molecular pathways controlling the multitude of diverse, cellular activities. Gene expression is a critical node at which regulatory control of molecular networks is implemented. As such, elucidating the various mechanisms employed in the physiological regulation of gene expression in the CNS is important both for establishing a reference for comparison to the diseased state and for expanding the set of validated drug targets available for disease intervention. MicroRNAs (miRNAs) are an abundant class of small RNA that mediates potent inhibitory effects on global gene expression. Recent advances have been made in methods employed to study the contribution of these miRNAs to gene expression. Here we review these latest advances and present a methodological workflow from the perspective of an investigator studying the physiological regulation of a gene of interest. We discuss methods for identifying putative miRNA target sites in a transcript of interest, strategies for validating predicted target sites, assays for detecting miRNA expression, and approaches for disrupting endogenous miRNA function. We consider both advantages and limitations, highlighting certain caveats that inform the suitability of a given method for a specific application. Through careful implementation of the appropriate methodologies discussed herein, we are optimistic that important discoveries related to miRNA participation in CNS physiology and dysfunction are on the horizon.
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Affiliation(s)
- Justin M Long
- Department of Psychiatry, Institute of Psychiatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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47
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Berezhna SY, Supekova L, Sever MJ, Schultz PG, Deniz AA. Dual regulation of hepatitis C viral RNA by cellular RNAi requires partitioning of Ago2 to lipid droplets and P-bodies. RNA (NEW YORK, N.Y.) 2011; 17:1831-45. [PMID: 21868483 PMCID: PMC3185916 DOI: 10.1261/rna.2523911] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The antiviral role of RNA interference (RNAi) in humans remains to be better understood. In RNAi, Ago2 proteins and microRNAs (miRNAs) or small interfering RNAs (siRNAs) form endonucleolytically active complexes which down-regulate expression of target mRNAs. P-bodies, cytoplasmic centers of mRNA decay, are involved in these pathways. Evidence exists that hepatitis C virus (HCV) utilizes host cellular RNAi machinery, including miRNA-122, Ago1-4, and Dicer proteins for replication and viral genome translation in Huh7 cells by, so far, nebulous mechanisms. Conversely, synthetic siRNAs have been used to suppress HCV replication. Here, using a combination of biochemical, transfection, confocal imaging, and digital image analysis approaches, we reveal that replication of HCV RNA depends on recruitment of Ago2 and miRNA-122 to lipid droplets, while suppression of HCV RNA by siRNA and Ago2 involves interaction with P-bodies. Such partitioning of Ago2 proteins into different complexes and separate subcellular domains likely results in modulation of their activity by different reaction partners. We propose a model in which partitioning of host RNAi and viral factors into physically and functionally distinct subcellular compartments emerges as a mechanism regulating the dual interaction of cellular RNAi with HCV RNA.
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Affiliation(s)
- Svitlana Yu. Berezhna
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Lubica Supekova
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Mary J. Sever
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Ashok A. Deniz
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Corresponding author.E-mail .
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48
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Moser JJ, Fritzler MJ, Rattner JB. Repression of GW/P body components and the RNAi microprocessor impacts primary ciliogenesis in human astrocytes. BMC Cell Biol 2011; 12:37. [PMID: 21880135 PMCID: PMC3179929 DOI: 10.1186/1471-2121-12-37] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Accepted: 08/31/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In most cells, the centriolar component of the centrosome can function as a basal body supporting the formation of a primary cilium, a non-motile sensory organelle that monitors information from the extracellular matrix and relays stimuli into the cell via associated signaling pathways. Defects in the formation and function of primary cilia underlie multiple human diseases and are hallmarks of malignancy. The RNA silencing pathway is involved in the post-transcriptional silencing of > 50% of mRNA that occurs within GW/P bodies. GW/P bodies are found throughout the cytoplasm and previously published live cell imaging data suggested that in a malignant cell type (U2OS), two GW/P bodies reside at the centrosome during interphase. This led us to investigate if a similar relationship exists in primary cells and if the inhibition of the miRNA pathway impairs primary cilium formation. RESULTS Two GW/P bodies as marked by GW182 and hAgo2 colocalized to the basal body of primary human astrocytes as well as human synoviocytes during interphase and specifically with the distal end of the basal body in the pericentriolar region. Since it is technically challenging to examine the two centrosomal GW/P bodies in isolation, we investigated the potential relationship between the global population of GW/P bodies and primary ciliogenesis. Astrocytes were transfected with siRNA directed to GW182 and hAgo2 and unlike control astrocytes, a primary cilium was no longer associated with the centrosome as detected in indirect immunofluorescence assays. Ultrastructural analysis of siRNA transfected astrocytes revealed that knock down of GW182, hAgo2, Drosha and DGCR8 mRNA did not affect the appearance of the earliest stage of ciliogenesis but did prevent the formation and elongation of the ciliary axoneme. CONCLUSIONS This study confirms and extends a previously published report that GW/P bodies reside at the centrosome in U2OS cells and documents that GW/P bodies are resident at the centrosome in diverse non-malignant cells. Further, our study demonstrates that repression of key effector proteins in the post-transcriptional miRNA pathway impairs primary cilium formation.
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Affiliation(s)
- Joanna J Moser
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Alberta, Canada
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Macfarlane LA, Murphy PR. MicroRNA: Biogenesis, Function and Role in Cancer. Curr Genomics 2011; 11:537-61. [PMID: 21532838 PMCID: PMC3048316 DOI: 10.2174/138920210793175895] [Citation(s) in RCA: 1216] [Impact Index Per Article: 93.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 08/23/2010] [Accepted: 09/06/2010] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs are small, highly conserved non-coding RNA molecules involved in the regulation of gene expression. MicroRNAs are transcribed by RNA polymerases II and III, generating precursors that undergo a series of cleavage events to form mature microRNA. The conventional biogenesis pathway consists of two cleavage events, one nuclear and one cytoplasmic. However, alternative biogenesis pathways exist that differ in the number of cleavage events and enzymes responsible. How microRNA precursors are sorted to the different pathways is unclear but appears to be determined by the site of origin of the microRNA, its sequence and thermodynamic stability. The regulatory functions of microRNAs are accomplished through the RNA-induced silencing complex (RISC). MicroRNA assembles into RISC, activating the complex to target messenger RNA (mRNA) specified by the microRNA. Various RISC assembly models have been proposed and research continues to explore the mechanism(s) of RISC loading and activation. The degree and nature of the complementarity between the microRNA and target determine the gene silencing mechanism, slicer-dependent mRNA degradation or slicer-independent translation inhibition. Recent evidence indicates that P-bodies are essential for microRNA-mediated gene silencing and that RISC assembly and silencing occurs primarily within P-bodies. The P-body model outlines microRNA sorting and shuttling between specialized P-body compartments that house enzymes required for slicer –dependent and –independent silencing, addressing the reversibility of these silencing mechanisms. Detailed knowledge of the microRNA pathways is essential for understanding their physiological role and the implications associated with dysfunction and dysregulation.
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Affiliation(s)
- Leigh-Ann Macfarlane
- Department of Physiology & Biophysics, Faculty of Medicine, Dalhousie University, 5850 College Street, Sir Charles Tupper Medical Building, Halifax, Nova Scotia, B3H 1X5, Canada
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Wu D, Raafat M, Pak E, Hammond S, Murashov AK. MicroRNA machinery responds to peripheral nerve lesion in an injury-regulated pattern. Neuroscience 2011; 190:386-97. [PMID: 21689732 DOI: 10.1016/j.neuroscience.2011.06.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 06/02/2011] [Indexed: 12/20/2022]
Abstract
Recently, functional and potent RNA interference (RNAi) has been reported in peripheral nerve axons transfected with short-interfering RNA (siRNA). In addition, components of RNA-induced silencing complex (RISC) have been identified in axotomized sciatic nerve fibers as well as in regenerating dorsal root ganglia (DRG) neurons in vitro. Based on these observations, and on the fact that siRNA and microRNA (miRNA) share the same effector enzymes, we hypothesized that the endogenous miRNA biosynthetic pathway would respond to peripheral nerve injury. To answer this question, we investigated changes in the expression of miRNA biosynthetic enzymes following peripheral nerve crush injury in mice. Here, we show that several pivotal miRNA biosynthetic enzymes are expressed in an injury-regulated pattern in sciatic nerve in vivo, and in DRG axons in vitro. Moreover, the sciatic nerve lesion induced expression of mRNA-processing bodies (P-bodies), which are the local foci of mRNA degradation in DRG axons. In addition, a group of injury-regulated miRNAs was identified by miRNA microarray and validated by real-time quantitative PCR (qPCR) and in situ hybridization analyses. Taken together, our data support the hypothesis that the peripheral nerve regeneration processes may be regulated by miRNA pathway.
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Affiliation(s)
- D Wu
- Department of Physiology, East Carolina University, Greenville, NC 27834, USA
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