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Barbagallo C, Stella M, Ferrara C, Caponnetto A, Battaglia R, Barbagallo D, Di Pietro C, Ragusa M. RNA-RNA competitive interactions: a molecular civil war ruling cell physiology and diseases. EXPLORATION OF MEDICINE 2023:504-540. [DOI: 10.37349/emed.2023.00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
The idea that proteins are the main determining factors in the functioning of cells and organisms, and their dysfunctions are the first cause of pathologies, has been predominant in biology and biomedicine until recently. This protein-centered view was too simplistic and failed to explain the physiological and pathological complexity of the cell. About 80% of the human genome is dynamically and pervasively transcribed, mostly as non-protein-coding RNAs (ncRNAs), which competitively interact with each other and with coding RNAs generating a complex RNA network regulating RNA processing, stability, and translation and, accordingly, fine-tuning the gene expression of the cells. Qualitative and quantitative dysregulations of RNA-RNA interaction networks are strongly involved in the onset and progression of many pathologies, including cancers and degenerative diseases. This review will summarize the RNA species involved in the competitive endogenous RNA network, their mechanisms of action, and involvement in pathological phenotypes. Moreover, it will give an overview of the most advanced experimental and computational methods to dissect and rebuild RNA networks.
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Affiliation(s)
- Cristina Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Michele Stella
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | | | - Angela Caponnetto
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Rosalia Battaglia
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
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Comparative Study of the Expression Profiles of miRNAs of Milk-Derived Exosomes of Yak and Jeryak. Animals (Basel) 2022; 12:ani12223189. [PMID: 36428417 PMCID: PMC9686552 DOI: 10.3390/ani12223189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
The Jeryak is the hybrid offspring of yaks and Jersey cattle and exhibit improved milk and meat yields. Biomolecules carried within milk exosomes are important for cell growth, development, immune regulation, and various pathophysiological processes. Previous studies showed that miRNAs regulate mammary gland development, lactation, and milk quality. This study explored the relationship between milk exosomes miRNAs and lactation performance. A comparison of the milk content showed that yak milk was of a better quality compared to Jeryak milk (casein, fat, TS, SNF, lactose). Milk collected in December was superior to that collected in June for both yak and Jeryak, except for lactose concentrations. Exosomes were extracted by density gradient centrifugation and miRNA expression profiles in milk exosomes from three yaks and three Jeryaks collected in June and December were detected by small RNA sequencing. In all, 22, 120, 78, and 62 differentially expressed miRNAs (DEMs) were identified in Jun_ JY vs. Jun_ Y (P1: Jeryak in June vs. Yak in June), Jun_ JY vs. Dec_ JY (P2: Jeryak in June vs. Jeryak in December), Dec_ JY vs. Dec_ Y (P3: Jeryak in December vs. Yak in December), and Jun_ Y vs. Dec_ Y (P4: Yak in June vs. Yak in December) groups. These DEMs were enriched in functions and signaling pathways related to lactation performance. In conclusion, these findings are a reference tool to study the molecular basis of lactation performance.
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Donda K, Bose T, Dame C, Maheshwari A. The Impact of MicroRNAs in Neonatal Necrotizing Enterocolitis and other Inflammatory Conditions of Intestine: A Review. Curr Pediatr Rev 2022; 19:5-14. [PMID: 35040406 DOI: 10.2174/1573396318666220117102119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/28/2021] [Accepted: 11/11/2021] [Indexed: 01/28/2023]
Abstract
The understanding of necrotizing enterocolitis (NEC) etiopathogenesis is incomplete, contributing to the lack of early biomarkers and therapeutic options. Micro RNAs (miRNAs) are a class of RNAs that can alter gene expression and modulate various physiological and pathological processes. Several studies have been performed to evaluate the role of miRNA in the pathogenesis of NEC. In this article, we review the information on miRNAs that have been specifically identified in NEC or have been noted in other inflammatory bowel disorders that share some of the histopathological abnormalities seen frequently in NEC. This review highlights miRNAs that could be useful as early biomarkers of NEC and suggests possible approaches for future translational studies focused on these analytes. It is a novel field with potential for immense translational and clinical relevance in preventing, detecting, or treating NEC in very premature infants. Impact • Current information categorizes necrotizing enterocolitis (NEC) as a multifactorial disease, but microRNAs (miRNAs) may influence the risk of occurrence of NEC. • MiRNAs may alter the severity of the intestinal injury and the clinical outcome of NEC. • The literature on intestinal diseases of adults suggests additional miRNAs that have not been studied in NEC yet but share some features and deserve further exploration in human NEC, especially if affecting gut dysbiosis, intestinal perfusion, and coagulation disorders.
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Affiliation(s)
- Keyur Donda
- Department of Pediatrics, University of South Florida Health Morsani College of Medicine, Tampa, Florida, FL, United States
| | - Tanima Bose
- Institute for Clinical Neuroimmunology, Ludwig-Maximilians- University of Munich, Munich, Germany
| | - Christof Dame
- Department of Neonatology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Akhil Maheshwari
- Department of Pediatrics, Johns Hopkins University, Baltimore, Maryland, MD, USA
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Almutairy BK, Alshetaili A, Anwer MK, Ali N. In silico identification of MicroRNAs targeting the key nucleator of stress granules, G3BP: Promising therapeutics for SARS-CoV-2 infection. Saudi J Biol Sci 2021; 28:7499-7504. [PMID: 34456603 PMCID: PMC8381622 DOI: 10.1016/j.sjbs.2021.08.056] [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: 06/24/2021] [Revised: 08/03/2021] [Accepted: 08/16/2021] [Indexed: 11/05/2022] Open
Abstract
Stress granules (SGs) are non-membrane ribonucleoprotein condensates formed in response to environmental stress conditions via liquid–liquid phase separation (LLPS). SGs are involved in the pathogenesis of aging and aging-associated diseases, cancers, viral infection, and several other diseases. GTPase-activating protein (SH3 domain)-binding protein 1 and 2 (G3BP1/2) is a key component and commonly used marker of SGs. Recent studies have shown that SARS-CoV-2 nucleocapsid protein via sequestration of G3BPs inhibits SGs formation in the host cells. In this study, we have identified putative miRNAs targeting G3BP in search of modulators of the G3BP expression. These miRNAs could be considered as new therapeutic targets against COVID-19 infection via the regulation of SG assembly and dynamics.
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Affiliation(s)
- Bjad K Almutairy
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, 11942, Saudi Arabia
| | - Abdullah Alshetaili
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, 11942, Saudi Arabia
| | - Md Khalid Anwer
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, 11942, Saudi Arabia
| | - Nemat Ali
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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Qi X, Lin Y, Chen J, Shen B. Decoding competing endogenous RNA networks for cancer biomarker discovery. Brief Bioinform 2021; 21:441-457. [PMID: 30715152 DOI: 10.1093/bib/bbz006] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/13/2018] [Accepted: 12/25/2018] [Indexed: 02/05/2023] Open
Abstract
Crosstalk between competing endogenous RNAs (ceRNAs) is mediated by shared microRNAs (miRNAs) and plays important roles both in normal physiology and tumorigenesis; thus, it is attractive for systems-level decoding of gene regulation. As ceRNA networks link the function of miRNAs with that of transcripts sharing the same miRNA response elements (MREs), e.g. pseudogenes, competing mRNAs, long non-coding RNAs, and circular RNAs, the perturbation of crucial interactions in ceRNA networks may contribute to carcinogenesis by affecting the balance of cellular regulatory system. Therefore, discovering biomarkers that indicate cancer initiation, development, and/or therapeutic responses via reconstructing and analyzing ceRNA networks is of clinical significance. In this review, the regulatory function of ceRNAs in cancer and crucial determinants of ceRNA crosstalk are firstly discussed to gain a global understanding of ceRNA-mediated carcinogenesis. Then, computational and experimental approaches for ceRNA network reconstruction and ceRNA validation, respectively, are described from a systems biology perspective. We focus on strategies for biomarker identification based on analyzing ceRNA networks and highlight the translational applications of ceRNA biomarkers for cancer management. This article will shed light on the significance of miRNA-mediated ceRNA interactions and provide important clues for discovering ceRNA network-based biomarker in cancer biology, thereby accelerating the pace of precision medicine and healthcare for cancer patients.
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Affiliation(s)
- Xin Qi
- Center for Systems Biology, Soochow University, Suzhou, China
| | - Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou, China
| | - Jiajia Chen
- School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
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Malinowska AL, Laski A, Hall J. Design and Application of Mini-libraries of miRNA Probes for an Efficient and Versatile miRNA-mRNA Cross-linking. Chemistry 2021; 27:10193-10200. [PMID: 34000095 PMCID: PMC8362200 DOI: 10.1002/chem.202101171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 01/02/2023]
Abstract
MicroRNAs constitute a class of endogenous, non-coding RNAs that influence various processes within the cell. By base-pairing to partially-complementary sites located in the 3' untranslated region of target messenger RNAs, microRNAs participate in post-transcriptional regulation of the majority of human protein-coding genes. Their dysregulation has been related to many pathological processes and diseases. Thus, an in-depth understanding of the microRNA mechanisms of action is crucial. Here, we present a new concept of probe design to achieve an efficient and sequence-independent miRNA-mRNA cross-linking. The new strategy is based on the utilization of a controlled mixture of probes for a chosen miRNA, in which a trioxsalen moiety is introduced at the N4 -position of a selected cytidine through short oligoethylene glycol-based linkers. In vitro photo-cross-linking experiments with mini-libraries of probes for microRNAs of interest showed variable cross-linking efficiencies, demonstrating a general applicability of the presented approach.
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Affiliation(s)
- Anna L. Malinowska
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093Zurich
| | - Artur Laski
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093Zurich
| | - Jonathan Hall
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093Zurich
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7
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Gao J, Qin Y, Luo K, Wang X, Yu C, Zhang A, Pan X. Downregulation of miR-4755-5p promotes fluoride-induced osteoblast activation via tageting Cyclin D1. J Trace Elem Med Biol 2020; 62:126626. [PMID: 32731110 DOI: 10.1016/j.jtemb.2020.126626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/01/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Endemic fluorosis remains a major public health issue in many countries. Fluoride can cause abnormalities in osteoblast proliferation and activation, leading to skeletal fluorosis. However, its detailed molecular mechanism remains unclear. Based on a previous study, the aim of this study is to explore the role of miRNA in osteoblast activation of skeletal fluorosis via targeting of Cyclin D1. METHODS A population study of coal-burning fluorosis and in vitro experiments were performed in this study. Urine fluoride (UF) concentrations of the participants were determined using a national standardized ion selective electrode approach. Based on our previous miRNA sequence results, bioinformatic analysis was used to predict miR-4755-5p targeting Cyclin D1. Quantitative real-time PCR (qRT-PCR) was used to verify the expression of miR-4755-5p. The expression of Cyclin D1 mRNA was detected by qRT-PCR. The expression of Cyclin D1 protein was detected by enzyme-linked immunosorbent assay (ELISA) and Western blotting, respectively. Cell viability was detected by CCK-8 method. The distribution of the cell cycle was analyzed by flow cytometry. The alkaline phosphatase (ALP) activity and bone Gla protein (BGP) content were detected by micronutrient enzymes standard method and ELISA. The target binding between miR-4755-5p and Cyclin D1 was verified using dual-luciferase reporter assay. RESULTS In the fluoride-exposed population, the results showed that with the increase in UF content, the expression of miR-4755-5p decreased gradually, while the mRNA transcription and protein expression of Cyclin D1 increased gradually. The relative miR-4755-5p expression showed a negative correlation with Cyclin D1 expression. Subsequently, in human osteoblasts treated with sodium fluoride (NaF), the results also showed that NaF caused low expression of miR-4755-5p and increased expression of Cyclin D1. Further, the results of miR-4755-5p mimic transfection confirmed that under the action of NaF, miR-4755-5p overexpression reduced Cyclin D1 protein expression within osteoblasts and further inhibited cell proliferation and activation. Simultaneously, luciferase reporter assays verified that Cyclin D1 was the miR-4755-5p direct target. CONCLUSION The results demonstrate that fluoride exposure induced the downregulation of miR-4755-5p and downregulated miR-4755-5p promoted fluoride-induced osteoblast activation by increasing Cyclin D1 protein expression. This study sheds new light on biomarkers and potential treatment for endemic fluorosis.
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Affiliation(s)
- Jiayu Gao
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China
| | - Yu Qin
- Guizhou Orthopedics Hospital, Guiyang, 550007, China
| | - Keke Luo
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China
| | - Xilan Wang
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China
| | - Chun Yu
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China
| | - Aihua Zhang
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China
| | - Xueli Pan
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China.
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8
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Zhan Y, Guo Z, Zheng F, Zhang Z, Li K, Wang Q, Wang L, Cai Z, Chen N, Wu S, Li H. Reactive oxygen species regulate miR-17-5p expression via DNA methylation in paraquat-induced nerve cell damage. ENVIRONMENTAL TOXICOLOGY 2020; 35:1364-1373. [PMID: 32691990 DOI: 10.1002/tox.23001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/04/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
There is emerging evidence suggesting that oxidative stress and DNA methylation can alter miRNA expression. However, little is known on the mechanism of miR-17-5p expression changes in paraquat (PQ)-induced nerve cell damage. In the present study, neuro-2a cells were pretreated with antioxidant N-acetylcysteine (NAC) or DNA methylation inhibitor decitabine (DAC), then exposed to different concentrations of PQ, while the expression levels of miR-17-5p were detected by qRT-PCR. Here, it is showed that PQ downregulated the expression of miR-17-5p dose-dependently in neuro-2a cells. The DNA methylation level was upregulated after PQ exposure, while downregulated with the pretreatment of NAC in the above content, detected by 5-mC immunofluorescence technique. The interaction effect of NAC and PQ in alternating DNA methylation level was further confirmed by flow cytometry. NAC and DAC individually had an interaction effect in PQ-induced nerve cell damage. After using NAC, PQ-induced ROS elevation and DNA methylation are reduced, thereby preventing the proapoptotic effect of miR-17-5p. Above all, PQ can induce DNA methylation variations through ROS production, leading to the downregulation of miR-17-5p expression in PQ-induced nerve cell damage.
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Affiliation(s)
- Yanting Zhan
- Department of Health Management, Fujian Health College, Fuzhou, China
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Zhenkun Guo
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
- Key Laboratory of Environment and Health, Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Fuli Zheng
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
- Key Laboratory of Environment and Health, Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Zhipeng Zhang
- Fujian Provincial Center for Adverse Drug Reaction Monitoring, Fujian Provincial Food and Drug Administration, Fuzhou, China
| | - Ke Li
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Qingqing Wang
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Lijin Wang
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Zhipeng Cai
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Nengzhou Chen
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Siying Wu
- Key Laboratory of Environment and Health, Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Fuzhou, China
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Huangyuan Li
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
- Key Laboratory of Environment and Health, Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Fuzhou, China
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9
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Berk C, Wang Y, Laski A, Tsagkris S, Hall J. Ligation of 2', 3'-cyclic phosphate RNAs for the identification of microRNA binding sites. FEBS Lett 2020; 595:230-240. [PMID: 33113149 PMCID: PMC7894349 DOI: 10.1002/1873-3468.13976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/27/2020] [Accepted: 10/08/2020] [Indexed: 11/21/2022]
Abstract
Identifying the targetome of a microRNA is key for understanding its functions. Cross‐linking and immunoprecipitation (CLIP) methods capture native miRNA‐mRNA interactions in cells. Some of these methods yield small amounts of chimeric miRNA‐mRNA sequences via ligation of 5′‐phosphorylated RNAs produced during the protocol. Here, we introduce chemically synthesized microRNAs (miRNAs) bearing 2′‐, 3′‐cyclic phosphate groups, as part of a new CLIP method that does not require 5′‐phosphorylation for ligation. We show in a system that models miRNAs bound to their targets, that addition of recombinant bacterial ligase RtcB increases ligation efficiency, and that the transformation proceeds via a 3′‐phosphate intermediate. By optimizing the chemistry underlying ligation, we provide the basis for an improved method to identify miRNA targetomes.
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Affiliation(s)
- Christian Berk
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | - Yuluan Wang
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | - Artur Laski
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | - Stylianos Tsagkris
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
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10
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Garcia A, Dunoyer-Geindre S, Fish RJ, Neerman-Arbez M, Reny JL, Fontana P. Methods to Investigate miRNA Function: Focus on Platelet Reactivity. Thromb Haemost 2020; 121:409-421. [PMID: 33124028 PMCID: PMC8263142 DOI: 10.1055/s-0040-1718730] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs modulating protein production. They are key players in regulation of cell function and are considered as biomarkers in several diseases. The identification of the proteins they regulate, and their impact on cell physiology, may delineate their role as diagnostic or prognostic markers and identify new therapeutic strategies. During the last 3 decades, development of a large panel of techniques has given rise to multiple models dedicated to the study of miRNAs. Since plasma samples are easily accessible, circulating miRNAs can be studied in clinical trials. To quantify miRNAs in numerous plasma samples, the choice of extraction and purification techniques, as well as normalization procedures, are important for comparisons of miRNA levels in populations and over time. Recent advances in bioinformatics provide tools to identify putative miRNAs targets that can then be validated with dedicated assays. In vitro and in vivo approaches aim to functionally validate candidate miRNAs from correlations and to understand their impact on cellular processes. This review describes the advantages and pitfalls of the available techniques for translational research to study miRNAs with a focus on their role in regulating platelet reactivity.
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Affiliation(s)
- Alix Garcia
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Richard J Fish
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Marguerite Neerman-Arbez
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,iGE3, Institute of Genetics and Genomics in Geneva, Geneva, Switzerland
| | - Jean-Luc Reny
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Division of General Internal Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Pierre Fontana
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Division of Angiology and Haemostasis, Geneva University Hospitals, Geneva, Switzerland
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11
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Lemus-Diaz N, Ferreira RR, Bohnsack KE, Gruber J, Bohnsack MT. The human box C/D snoRNA U3 is a miRNA source and miR-U3 regulates expression of sortin nexin 27. Nucleic Acids Res 2020; 48:8074-8089. [PMID: 32609813 PMCID: PMC7430653 DOI: 10.1093/nar/gkaa549] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 05/29/2020] [Accepted: 06/22/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are important regulators of eukaryotic gene expression and their dysfunction is often associated with cancer. Alongside the canonical miRNA biogenesis pathway involving stepwise processing and export of pri- and pre-miRNA transcripts by the microprocessor complex, Exportin 5 and Dicer, several alternative mechanisms of miRNA production have been described. Here, we reveal that the atypical box C/D snoRNA U3, which functions as a scaffold during early ribosome assembly, is a miRNA source. We show that a unique stem-loop structure in the 5' domain of U3 is processed to form short RNA fragments that associate with Argonaute. miR-U3 production is independent of Drosha, and an increased amount of U3 in the cytoplasm in the absence of Dicer suggests that a portion of the full length snoRNA is exported to the cytoplasm where it is efficiently processed into miRNAs. Using reporter assays, we demonstrate that miR-U3 can act as a low proficiency miRNA in vivo and our data support the 3' UTR of the sortin nexin SNX27 mRNA as an endogenous U3-derived miRNA target. We further reveal that perturbation of U3 snoRNP assembly induces miR-U3 production, highlighting potential cross-regulation of target mRNA expression and ribosome production.
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Affiliation(s)
- Nicolas Lemus-Diaz
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Junior Research Group Medical RNA Biology, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Rafael Rinaldi Ferreira
- Junior Research Group Medical RNA Biology, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Jens Gruber
- Junior Research Group Medical RNA Biology, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Justus-von-Liebig-Weg 11, 37077 Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)
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12
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Hughes CK, Maalouf SW, Liu WS, Pate JL. Molecular profiling demonstrates modulation of immune cell function and matrix remodeling during luteal rescue†. Biol Reprod 2020; 100:1581-1596. [PMID: 30915454 DOI: 10.1093/biolre/ioz037] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/15/2019] [Accepted: 03/10/2019] [Indexed: 12/22/2022] Open
Abstract
The corpus luteum (CL) is essential for maintenance of pregnancy in all mammals and luteal rescue, which occurs around day 16-19 in the cow, is necessary to maintain luteal progesterone production. Transcriptomic and proteomic profiling were performed to compare the day 17 bovine CL of the estrous cycle and pregnancy. Among mRNA and proteins measured, 140 differentially abundant mRNA and 24 differentially abundant proteins were identified. Pathway analysis was performed using four programs. Modulated pathways included T cell receptor signaling, vascular stability, cytokine signaling, and extracellular matrix remodeling. Two mRNA that were less in pregnancy were regulated by prostaglandin F2A in culture, while two mRNA that were greater in pregnancy were regulated by interferon tau. To identify mRNA that could be critical regulators of luteal fate, the mRNA that were differentially abundant during early pregnancy were compared to mRNA that were differentially abundant during luteal regression. Eight mRNA were common to both datasets, including mRNA related to regulation of steroidogenesis and gene transcription. A subset of differentially abundant mRNA and proteins, including those associated with extracellular matrix functions, were predicted targets of differentially abundant microRNA (miRNA). Integration of miRNA and protein data, using miRPath, revealed pathways such as extracellular matrix-receptor interactions, abundance of glutathione, and cellular metabolism and energy balance. Overall, this study has provided a comprehensive profile of molecular changes in the corpus luteum during maternal recognition of pregnancy and has indicated that some of these functions may be miRNA-regulated.
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Affiliation(s)
- Camilla K Hughes
- Department of Animal Science, Center for Reproductive Biology and Health, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Samar W Maalouf
- Department of Animal Science, Center for Reproductive Biology and Health, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Wan-Sheng Liu
- Department of Animal Science, Center for Reproductive Biology and Health, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Joy L Pate
- Department of Animal Science, Center for Reproductive Biology and Health, Pennsylvania State University, University Park, Pennsylvania, USA
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13
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Ma S, Tong C, Ibeagha-Awemu EM, Zhao X. Identification and characterization of differentially expressed exosomal microRNAs in bovine milk infected with Staphylococcus aureus. BMC Genomics 2019; 20:934. [PMID: 31805863 PMCID: PMC6896338 DOI: 10.1186/s12864-019-6338-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/26/2019] [Indexed: 12/26/2022] Open
Abstract
Background MicroRNAs (miRNAs) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aureus (S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-miR-378 and bta-miR-185 were also validated. Results Total RNA from milk exosomes was collected from healthy cows (n = 3, the control group) and S. aureus infected cows (n = 6, the SA group). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. Among them, 22 known and 15 novel miRNAs were differentially expressed. Target genes of DE miRNAs were significantly enriched in intracellular protein transport, endoplasmic reticulum and identical protein binding. The expression of two miRNAs (bta-miR-378 and bta-miR-185) with high read counts and log2 fold changes (> 3.5) was significantly higher in mastitic milk infected with S. aureus. One target gene (VAT1L) of bta-miR-378 and five target genes (DYRK1B, MLLT3, HP1BP3, NPR2 and PGM1) of bta-miR-185 were validated. Conclusion DE miRNAs in exosomes from normal and S. aureus infected milk were identified. The predicted targets for two DE miRNAs (bta-miR-378 and bta-miR-185) were further validated. The linkage between the validated target genes and diseases suggested that we should pay particular attention to exosome miRNAs from mastitic milk in terms of milk safety.
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Affiliation(s)
- Shaoyang Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chao Tong
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec, Canada
| | - Xin Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China. .,Department of Animal Science, McGill University, 21,111 Lakeshore, Ste-Anne-De-Bellevue, Quebec, Canada.
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14
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Plotnikova O, Baranova A, Skoblov M. Comprehensive Analysis of Human microRNA-mRNA Interactome. Front Genet 2019; 10:933. [PMID: 31649721 PMCID: PMC6792129 DOI: 10.3389/fgene.2019.00933] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/05/2019] [Indexed: 01/20/2023] Open
Abstract
MicroRNAs play a key role in the regulation of gene expression. A majority of microRNA–mRNA interactions remain unidentified. Despite extensive research, our ability to predict human microRNA-mRNA interactions using computational algorithms remains limited by a complexity of the models for non-canonical interactions, and an abundance of false-positive results. Here, we present the landscape of human microRNA–mRNA interactions derived from comprehensive analysis of HEK293 and Huh7.5 datasets, along with publicly available microRNA and mRNA expression data. We show that, while only 1–2% of human genes were the most regulated by microRNAs, few cell line–specific RNAs, including EEF1A1 and HSPA1B in HEK293 and AFP, APOB, and MALAT1 genes in Huh7.5, display substantial “sponge-like” properties. We revealed a group of microRNAs that are expressed at a very high level, while interacting with only a few mRNAs, which, indeed, serve as their specific expression regulators. In order to establish reliable microRNA-binding regions, we collected and systematically analyzed the data from 79 CLIP datasets of microRNA-binding sites. We report 46,805 experimentally confirmed mRNA–miRNA duplex regions. Resulting dataset is available at http://score.generesearch.ru/services/mirna/. Our study provides initial insight into the complexity of human microRNA–mRNA interactions.
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Affiliation(s)
- Olga Plotnikova
- Laboratory of Functional Genome Analysis, Moscow Institute of Physics and Technology, Moscow, Russia.,Laboratory of Functional Genomics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ancha Baranova
- Laboratory of Functional Genomics, Research Centre for Medical Genetics, Moscow, Russia.,School of Systems Biology, George Mason University, Fairfax, VA, United States
| | - Mikhail Skoblov
- Laboratory of Functional Genomics, Research Centre for Medical Genetics, Moscow, Russia
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15
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Lai X, Eberhardt M, Schmitz U, Vera J. Systems biology-based investigation of cooperating microRNAs as monotherapy or adjuvant therapy in cancer. Nucleic Acids Res 2019; 47:7753-7766. [PMID: 31340025 PMCID: PMC6735922 DOI: 10.1093/nar/gkz638] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/05/2019] [Accepted: 07/13/2019] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are short, noncoding RNAs that regulate gene expression by suppressing mRNA translation and reducing mRNA stability. A miRNA can potentially bind many mRNAs, thereby affecting the expression of oncogenes and tumor suppressor genes as well as the activity of whole pathways. The promise of miRNA therapeutics in cancer is to harness this evolutionarily conserved mechanism for the coordinated regulation of gene expression, and thus restoring a normal cell phenotype. However, the promiscuous binding of miRNAs can provoke unwanted off-target effects, which are usually caused by high-dose single-miRNA treatments. Thus, it is desirable to develop miRNA therapeutics with increased specificity and efficacy. To achieve that, we propose the concept of miRNA cooperativity in order to exert synergistic repression on target genes, thus lowering the required total amount of miRNAs. We first review miRNA therapies in clinical application. Next, we summarize the knowledge on the molecular mechanism and biological function of miRNA cooperativity and discuss its application in cancer therapies. We then propose and discuss a systems biology approach to investigate miRNA cooperativity for the clinical setting. Altogether, we point out the potential of miRNA cooperativity to reduce off-target effects and to complement conventional, targeted, or immune-based therapies for cancer.
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Affiliation(s)
- Xin Lai
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen, 91052 Erlangen, Germany
- Faculty of Medicine, Friedrich-Alexander University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Martin Eberhardt
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen, 91052 Erlangen, Germany
- Faculty of Medicine, Friedrich-Alexander University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Ulf Schmitz
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, 2006 Camperdown, Australia
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, 2006 Camperdown, Australia
- Sydney Medical School, The University of Sydney, 2006 Camperdown, Australia
| | - Julio Vera
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen, 91052 Erlangen, Germany
- Faculty of Medicine, Friedrich-Alexander University Erlangen-Nürnberg, 91052 Erlangen, Germany
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16
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Inwood S, Abaandou L, Betenbaugh M, Shiloach J. Improved protein expression in HEK293 cells by over-expressing miR-22 and knocking-out its target gene, HIPK1. N Biotechnol 2019; 54:28-33. [PMID: 31425885 DOI: 10.1016/j.nbt.2019.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/01/2019] [Accepted: 08/15/2019] [Indexed: 02/08/2023]
Abstract
Stable cell lines can continuously produce a recombinant protein without the need to repeatedly engineer the genome. In a previous study HIPK1, Homeodomain-interacting Protein Kinase 1, was found to be a target of the microRNA miR-22 that, when repressed, improved expression of both an intracellular and a secreted protein. In this report, HEK293 cells stably over-expressing miR-22 were compared with HEK293 with knockout of HIPK1, executed by CRISPR/Cas9, for their ability to improve recombinant protein expression. In this model case of luciferase, over-expression of miR-22 improved overall activity 2.4-fold while the HIPK1 knockout improved overall activity 4.7-fold.
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Affiliation(s)
- Sarah Inwood
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892, USA; Department of Chemical and Biomolecular Engineering Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Laura Abaandou
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892, USA.
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17
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Chan JJ, Kwok ZH, Chew XH, Zhang B, Liu C, Soong TW, Yang H, Tay Y. A FTH1 gene:pseudogene:microRNA network regulates tumorigenesis in prostate cancer. Nucleic Acids Res 2019; 46:1998-2011. [PMID: 29240947 PMCID: PMC5829750 DOI: 10.1093/nar/gkx1248] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/02/2017] [Indexed: 12/27/2022] Open
Abstract
Non-coding RNAs play a vital role in diverse cellular processes. Pseudogenes, which are non-coding homologs of protein-coding genes, were once considered non-functional evolutional relics. However, recent studies have shown that pseudogene transcripts can regulate their parental transcripts by sequestering shared microRNAs (miRNAs), thus acting as competing endogenous RNAs (ceRNAs). In this study, we utilize an unbiased screen to identify the ferritin heavy chain 1 (FTH1) transcript and multiple FTH1 pseudogenes as targets of several oncogenic miRNAs in prostate cancer (PCa). We characterize the critical role of this FTH1 gene:pseudogene:miRNA network in regulating tumorigenesis in PCa, whereby oncogenic miRNAs downregulate the expression of FTH1 and its pseudogenes to drive oncogenesis. We further show that impairing miRNA binding and subsequent ceRNA crosstalk completely rescues the slow growth phenotype in vitro and in vivo. Our results also demonstrate the reciprocal regulation between the pseudogenes and intracellular iron levels, which are crucial for multiple physiological and pathophysiological processes. In summary, we describe an extensive gene:pseudogene network comprising multiple miRNAs and multiple pseudogenes derived from a single parental gene. The network could be regulated through multiple mechanisms to modulate iron storage in various signaling pathways, the deregulation of which results in PCa development and progression.
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Affiliation(s)
- Jia Jia Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Zhi Hao Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Xiao Hong Chew
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Chao Liu
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Tuck Wah Soong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,National Neuroscience Institute, Singapore 308433, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
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18
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Paschoal AR, Lozada-Chávez I, Domingues DS, Stadler PF. ceRNAs in plants: computational approaches and associated challenges for target mimic research. Brief Bioinform 2019; 19:1273-1289. [PMID: 28575144 DOI: 10.1093/bib/bbx058] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/27/2017] [Indexed: 11/13/2022] Open
Abstract
The competing endogenous RNA hypothesis has gained increasing attention as a potential global regulatory mechanism of microRNAs (miRNAs), and as a powerful tool to predict the function of many noncoding RNAs, including miRNAs themselves. Most studies have been focused on animals, although target mimic (TMs) discovery as well as important computational and experimental advances has been developed in plants over the past decade. Thus, our contribution summarizes recent progresses in computational approaches for research of miRNA:TM interactions. We divided this article in three main contributions. First, a general overview of research on TMs in plants is presented with practical descriptions of the available literature, tools, data, databases and computational reports. Second, we describe a common protocol for the computational and experimental analyses of TM. Third, we provide a bioinformatics approach for the prediction of TM motifs potentially cross-targeting both members within the same or from different miRNA families, based on the identification of consensus miRNA-binding sites from known TMs across sequenced genomes, transcriptomes and known miRNAs. This computational approach is promising because, in contrast to animals, miRNA families in plants are large with identical or similar members, several of which are also highly conserved. From the three consensus TM motifs found with our approach: MIM166, MIM171 and MIM159/319, the last one has found strong support on the recent experimental work by Reichel and Millar [Specificity of plant microRNA TMs: cross-targeting of mir159 and mir319. J Plant Physiol 2015;180:45-8]. Finally, we stress the discussion on the major computational and associated experimental challenges that have to be faced in future ceRNA studies.
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Affiliation(s)
| | - Irma Lozada-Chávez
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany
| | - Douglas Silva Domingues
- Department of Botany, Institute of Biosciences, S~ao Paulo State University (UNESP) in Rio Claro, Brazil
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19
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Mayer O, Seidlerová J, Černá V, Kučerová A, Vaněk J, Karnosová P, Bruthans J, Wohlfahrt P, Cífková R, Pešta M, Filipovský J. The low expression of circulating microRNA-19a represents an additional mortality risk in stable patients with vascular disease. Int J Cardiol 2019; 289:101-106. [PMID: 31085080 DOI: 10.1016/j.ijcard.2019.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 03/08/2019] [Accepted: 05/02/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Secondary prevention of atherosclerotic vascular diseases represents a cascade of procedures to reduce the risk of future fatal and non-fatal cardiovascular events. We sought to determine whether the expression of selected microRNAs influenced mortality of stable chronic cardiovascular patients. METHODS The plasma concentrations of five selected microRNAs (miR-1, miR-19, miR-126, miR-133 and miR-223) were quantified in 826 patients (mean age 65.2 years) with stable vascular disease (6-36 months after acute coronary syndrome, coronary revascularization or first-ever ischemic stroke). All-cause and cardiovascular mortality rates were followed during our prospective study. RESULTS Low expression (bottom quartile) of all five miRNAs was associated with a significant increase in five-year all-cause death, even when adjusted for conventional risk factors, treatment, raised troponin I and brain natriuretic protein levels [hazard risk ratios (HRRs) were as follows: miR-1, 1.65 (95% CI: 1.16-2.35); miR-19a, 2.27 (95% CI: 1.59-3.23); miR-126, 1.64 (95% CI: 1.15-2.33); miR-133a, 1.46 (95% CI: 1.01-2.12) and miR-223, 2.05 (95% CI: 1.45-2.91)]. Nearly similar results were found if using five-year cardiovascular mortality as the outcome. However, if entering all five miRNAs (along with other covariates) into a single regression model, only low miR-19a remained a significant mortality predictor; and only in patients with coronary artery disease [3.00 (95% CI: 1.77-5.08)], but not in post-stroke patients [1.63 (95% CI: 0.94-2.86)]. CONCLUSIONS In stable chronic coronary artery disease patients, low miR-19a expression was associated with a substantial increase in mortality risk independently of other conventional cardiovascular risk factors.
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Affiliation(s)
- Otto Mayer
- 2nd Department of Internal Medicine, Medical Faculty of Charles University and University Hospital, Pilsen, Czech Republic; Biomedical Center, Medical Faculty of Charles University, Pilsen, Czech Republic.
| | - Jitka Seidlerová
- 2nd Department of Internal Medicine, Medical Faculty of Charles University and University Hospital, Pilsen, Czech Republic; Biomedical Center, Medical Faculty of Charles University, Pilsen, Czech Republic
| | - Václava Černá
- Biomedical Center, Medical Faculty of Charles University, Pilsen, Czech Republic; Department of Biology, Medical Faculty of Charles University, Pilsen, Czech Republic
| | - Alena Kučerová
- Biomedical Center, Medical Faculty of Charles University, Pilsen, Czech Republic; Department of Biology, Medical Faculty of Charles University, Pilsen, Czech Republic
| | - Jiří Vaněk
- 2nd Department of Internal Medicine, Medical Faculty of Charles University and University Hospital, Pilsen, Czech Republic
| | - Petra Karnosová
- 2nd Department of Internal Medicine, Medical Faculty of Charles University and University Hospital, Pilsen, Czech Republic; Biomedical Center, Medical Faculty of Charles University, Pilsen, Czech Republic
| | - Jan Bruthans
- 2nd Department of Internal Medicine, Medical Faculty of Charles University and University Hospital, Pilsen, Czech Republic; Centre for Cardiovascular Prevention, First Faculty of Medicine, Charles, University and Thomayer's Hospital, Prague, Czech Republic
| | - Peter Wohlfahrt
- Centre for Cardiovascular Prevention, First Faculty of Medicine, Charles, University and Thomayer's Hospital, Prague, Czech Republic
| | - Renata Cífková
- Centre for Cardiovascular Prevention, First Faculty of Medicine, Charles, University and Thomayer's Hospital, Prague, Czech Republic
| | - Martin Pešta
- Biomedical Center, Medical Faculty of Charles University, Pilsen, Czech Republic; Department of Biology, Medical Faculty of Charles University, Pilsen, Czech Republic
| | - Jan Filipovský
- 2nd Department of Internal Medicine, Medical Faculty of Charles University and University Hospital, Pilsen, Czech Republic; Biomedical Center, Medical Faculty of Charles University, Pilsen, Czech Republic
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20
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CHAUDHARY NISHANT. Evaluation of miRNAs targeted RBPs under hypoxia in cancer. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2019. [DOI: 10.56093/ijans.v89i2.87328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Micro RNAs (miRNAs) are miniature, non-coding RNA molecules which are implicated in post-transcriptional regulation of genes. RNA binding proteins (RBPs) areinvolved in a diversity of functions including posttranscriptional regulation of genes. They have also been exposed to influence the messenger RNA stability by binding to their identified sequences at the 3’ untranslated region (UTR). Specific RBPs and miRNAs uncovered to be key participant in hypoxia signaling which is present in cancer cells, have been shown to involve in the outcome of the cell and drive towards tumor aggressiveness. Since both RBPs and miRNAs have been shown to be overstated by hypoxia and additionally significant since the site of battle of both players are the same (3’UTR of mRNA), we suggests that they might have role in tandem or be occupied in each other’s regulation. Stem loop qRT-PCR was used to check the expression levels of these target miRNAs and the corresponding RBPs in cancer cell lines, namely U87MG (Glioblastoma) and MCF7 (Breast cancer) under hypoxic and normoxic conditions. Transient over expression of the aforesaid miRNAs in the two cancer cell lines was examined using qRT-PCR to see the regulatory effects of these microRNAs on the corresponding target RBPs. Taken together, our results advocate that there could possibly be communication between the miRNA-RBP pairs that we had chosen and assessing the possibility as therapeutic agents for treatment of various cancers will depend upon suitable animal model.
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21
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Navarro FJ, Baulcombe DC. miRNA-Mediated Regulation of Synthetic Gene Circuits in the Green Alga Chlamydomonas reinhardtii. ACS Synth Biol 2019; 8:358-370. [PMID: 30624905 DOI: 10.1021/acssynbio.8b00393] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs), small RNA molecules of 20-24 nts, have many features that make them useful tools for gene expression regulation-small size, flexible design, target predictability, and action at a late stage of the gene expression pipeline. In addition, their role in fine-tuning gene expression can be harnessed to increase robustness of synthetic gene networks. In this work, we apply a synthetic biology approach to characterize miRNA-mediated gene expression regulation in the unicellular green alga Chlamydomonas reinhardtii. This characterization is then used to build tools based on miRNAs, such as synthetic miRNAs, miRNA-responsive 3'UTRs, miRNA decoys, and self-regulatory loops. These tools will facilitate the engineering of gene expression for new applications and improved traits in this alga.
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Affiliation(s)
- Francisco J. Navarro
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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22
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Pockar S, Globocnik Petrovic M, Peterlin B, Vidovic Valentincic N. MiRNA as biomarker for uveitis - A systematic review of the literature. Gene 2019; 696:162-175. [PMID: 30763668 DOI: 10.1016/j.gene.2019.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/13/2019] [Accepted: 02/01/2019] [Indexed: 12/20/2022]
Abstract
AIM A systematic review of miRNA profiling studies in uveitis. METHODS Literature search strategy - Pubmed central central database, using miRNA/microRNA and intraocular inflammation/uveitis as keywords. RESULTS We found twenty publications regarding the experimental and clinical use of miRNA in uveitis, published between 2011 and 2018. CONCLUSION The publications regarding the role of miRNA in uveitis are very scarce, but provide some valuable information about the potential new mechanisms in uveitis. Some of the identified miRNAs in different uveitis entities could serve as a biomarker of intraocular inflammation. Possible candidate miRNAs could be let-7e, miRNA-1, miR-9-3, miR-20a-5p, miR-23a, mir-29a-3p, miR-140-5p, miR-143, miR-146a and miR-146a-5p, miR-155, miR-182 and miR-182-5p, miR-196a2, miR-205, miR-223-3p, miR-301a. MiR-146a, miR-146a-5p, miR-155, miR-182, miR-223-3p, have been found to be possibly associated with uveitis disease in both, human and animal species.
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Affiliation(s)
- Sasa Pockar
- Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Mojca Globocnik Petrovic
- Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia; Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Natasa Vidovic Valentincic
- Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia; Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
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23
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Ryan BC, Lowe K, Hanson L, Gil T, Braun L, Howard PL, Chow RL. Mapping the Pax6 3' untranslated region microRNA regulatory landscape. BMC Genomics 2018; 19:820. [PMID: 30442116 PMCID: PMC6238409 DOI: 10.1186/s12864-018-5212-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 10/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND PAX6 is a homeodomain transcription factor that acts in a highly dosage-sensitive manner to regulate the development and function of the eyes, nose, central nervous system, gut, and endocrine pancreas. Several individual microRNAs (miRNA) have been implicated in regulating PAX6 in different cellular contexts, but a more general view of how they contribute to the fine-tuning and homeostasis of PAX6 is poorly understood. RESULTS Here, a comprehensive analysis of the Pax6 3' untranslated region was performed to map potential miRNA recognition elements and served as a backdrop for miRNA expression profiling experiments to identify potential cell/tissue-specific miRNA codes. Pax6 3'UTR pull-down studies identified a cohort of miRNA interactors in pancreatic αTC1-6 cells that, based on the spacing of their recognition sites in the Pax6 3'UTR, revealed 3 clusters where cooperative miRNA regulation may occur. Some of these interacting miRNAs have been implicated in α cell function but have not previously been linked to Pax6 function and may therefore represent novel PAX6 regulators. CONCLUSIONS These findings reveal a regulatory landscape upon which miRNAs may participate in the developmental control, fine-tuning and/or homeostasis of PAX6 levels.
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Affiliation(s)
- Bridget C. Ryan
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
| | - Kieran Lowe
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
| | - Laura Hanson
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
| | - Talveen Gil
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
| | - Lauren Braun
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
| | - Perry L. Howard
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2 Canada
| | - Robert L. Chow
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
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24
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Borah P, Das A, Milner MJ, Ali A, Bentley AR, Pandey R. Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants. Genes (Basel) 2018; 9:E459. [PMID: 30223541 PMCID: PMC6162444 DOI: 10.3390/genes9090459] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNA (lncRNA) research in plants has recently gained momentum taking cues from studies in animals systems. The availability of next-generation sequencing has enabled genome-wide identification of lncRNA in several plant species. Some lncRNAs are inhibitors of microRNA expression and have a function known as target mimicry with the sequestered transcript known as an endogenous target mimic (eTM). The lncRNAs identified to date show diverse mechanisms of gene regulation, most of which remain poorly understood. In this review, we discuss the role of identified putative lncRNAs that may act as eTMs for nutrient-responsive microRNAs (miRNAs) in plants. If functionally validated, these putative lncRNAs would enhance current understanding of the role of lncRNAs in nutrient homeostasis in plants.
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Affiliation(s)
- Priyanka Borah
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110 012, India.
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Antara Das
- ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India.
| | - Matthew J Milner
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge CB30LE, UK.
| | - Arif Ali
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Alison R Bentley
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge CB30LE, UK.
| | - Renu Pandey
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110 012, India.
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25
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Lemus-Diaz N, Tamon L, Gruber J. Dual Fluorescence Reporter Based Analytical Flow Cytometry for miRNA Induced Regulation in Mammalian Cells. Bio Protoc 2018; 8:e3000. [PMID: 34395794 DOI: 10.21769/bioprotoc.3000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/14/2018] [Accepted: 08/16/2018] [Indexed: 12/21/2022] Open
Abstract
MicroRNA-induced gene regulation is a growing field in basic and translational research. Examining this regulation directly in cells is necessary to validate high-throughput data originated from RNA sequencing technologies. For this several studies employ luciferase-based reporters that usually measure the whole cell population, which comes with low resolution for the complexity of the miRNA-induced regulation. Here, we provide a protocol using a dual-fluorescence reporter and flow cytometry reaching single cell resolution; the protocol contains a simplified workflow that includes: vector generation, data acquisition, processing, and analysis using the R environment. Our protocol enables high-resolution measurements of miRNA induced post-transcriptional gene regulation and combined with system biology it can be used to estimate miRNAs proficiency.
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Affiliation(s)
- Nicolas Lemus-Diaz
- Junior Research Group Medical RNA Biology, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen, Germany
| | - Liezel Tamon
- Junior Research Group Medical RNA Biology, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen, Germany
| | - Jens Gruber
- Junior Research Group Medical RNA Biology, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen, Germany
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26
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Monsanto-Hearne V, Johnson KN. miRNAs in Insects Infected by Animal and Plant Viruses. Viruses 2018; 10:E354. [PMID: 29970868 PMCID: PMC6071220 DOI: 10.3390/v10070354] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/29/2018] [Accepted: 06/29/2018] [Indexed: 12/13/2022] Open
Abstract
Viruses vectored by insects cause severe medical and agricultural burdens. The process of virus infection of insects regulates and is regulated by a complex interplay of biomolecules including the small, non-coding microRNAs (miRNAs). Considered an anomaly upon its discovery only around 25 years ago, miRNAs as a class have challenged the molecular central dogma which essentially typifies RNAs as just intermediaries in the flow of information from DNA to protein. miRNAs are now known to be common modulators or fine-tuners of gene expression. While recent years has seen an increased emphasis on understanding the role of miRNAs in host-virus associations, existing literature on the interaction between insects and their arthropod-borne viruses (arboviruses) is largely restricted to miRNA abundance profiling. Here we analyse the commonalities and contrasts between miRNA abundance profiles with different host-arbovirus combinations and outline a suggested pipeline and criteria for functional analysis of the contribution of miRNAs to the insect vector-virus interaction. Finally, we discuss the potential use of the model organism, Drosophila melanogaster, in complementing research on the role of miRNAs in insect vector-virus interaction.
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Affiliation(s)
- Verna Monsanto-Hearne
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia.
| | - Karyn N Johnson
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia.
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27
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Dash S, Balasubramaniam M, Dash C, Pandhare J. Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs. J Vis Exp 2018. [PMID: 29985341 DOI: 10.3791/57786] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that post-transcriptionally regulate cellular gene expression. MiRNAs bind to the 3' untranslated region (UTR) of target mRNA to inhibit protein translation or in some instances cause mRNA degradation. The binding of the miRNA to the 3' UTR of the target mRNA is mediated by a 2-8 nucleotide seed sequence at the 5' end of miRNA. While the role of miRNAs as cellular regulatory molecules is well established, identification of the target mRNAs with functional relevance remains a challenge. Bioinformatic tools have been employed to predict sequences within the 3' UTR of mRNAs as potential targets for miRNA binding. These tools have also been utilized to determine the evolutionary conservation of such sequences among related species in an attempt to predict functional role. However, these computational methods often generate false positive results and are limited to predicting canonical interaction between miRNA and mRNA. Therefore, experimental procedures that measure direct binding of miRNA to its mRNA target are necessary to establish functional interaction. In this report, we describe a sensitive method for validating direct interaction between the cellular miRNA miR-125b and the 3' UTR of PARP-1 mRNA. We elaborate a protocol in which synthetic biotinylated-miRNA mimics were transfected into mammalian cells and the miRNA-mRNA complex in the cellular lysate was pulled down with streptavidin-coated magnetic beads. Finally, the target mRNA in the pulled-down nucleic acid complex was quantified using a qPCR-based strategy.
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Affiliation(s)
- Sabyasachi Dash
- School of Biotechnology, Kalinga Institute of Industrial Technology University; 1. Center for AIDS Health Disparities Research Department of Biochemistry and Cancer Biology, Meharry Medical College; Kalinga Institute of Industrial Technology University
| | - Muthukumar Balasubramaniam
- 1. Center for AIDS Health Disparities Research Department of Biochemistry and Cancer Biology, Meharry Medical College
| | - Chandravanu Dash
- 1. Center for AIDS Health Disparities Research Department of Biochemistry and Cancer Biology, Meharry Medical College;
| | - Jui Pandhare
- 1. Center for AIDS Health Disparities Research Department of Biochemistry and Cancer Biology, Meharry Medical College;
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28
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Smillie CL, Sirey T, Ponting CP. Complexities of post-transcriptional regulation and the modeling of ceRNA crosstalk. Crit Rev Biochem Mol Biol 2018; 53:231-245. [PMID: 29569941 PMCID: PMC5935048 DOI: 10.1080/10409238.2018.1447542] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 01/09/2023]
Abstract
Control of gene and protein expression is required for cellular homeostasis and is disrupted in disease. Following transcription, mRNA turnover and translation is modulated, most notably by microRNAs (miRNAs). This modulation is controlled by transcriptional and post-transcriptional events that alter the availability of miRNAs for target binding. Recent studies have proposed that some transcripts - termed competitive endogenous RNAs (ceRNAs) - sequester a miRNA and diminish its repressive effects on other transcripts. Such ceRNAs thus mutually alter each other's abundance by competing for binding to a common set of miRNAs. Some question the relevance of ceRNA crosstalk, arguing that an individual transcript, when its abundance lies within a physiological range of gene expression, will fail to compete for miRNA binding due to the high abundance of other miRNA binding sites across the transcriptome. Despite this, some experimental evidence is consistent with the ceRNA hypothesis. In this review, we draw upon existing data to highlight mechanistic and theoretical aspects of ceRNA crosstalk. Our intent is to propose how understanding of ceRNA crosstalk mechanisms can be improved and what evidence is required to demonstrate a ceRNA mechanism. A greater understanding of factors affecting ceRNA crosstalk should shed light on its relevance in physiological states.
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Affiliation(s)
- Claire L. Smillie
- MRC Human Genetics Unit within the Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Tamara Sirey
- MRC Human Genetics Unit within the Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Chris P. Ponting
- MRC Human Genetics Unit within the Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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29
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Wu J, Sun C, Wang R, Li J, Zhou M, Yan M, Xue X, Wang C. Cardioprotective effect of paeonol against epirubicin-induced heart injury via regulating miR-1 and PI3K/AKT pathway. Chem Biol Interact 2018; 286:17-25. [DOI: 10.1016/j.cbi.2018.02.035] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/07/2018] [Accepted: 02/26/2018] [Indexed: 11/28/2022]
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30
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Are microRNAs Important Players in HIV-1 Infection? An Update. Viruses 2018; 10:v10030110. [PMID: 29510515 PMCID: PMC5869503 DOI: 10.3390/v10030110] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 02/21/2018] [Accepted: 02/25/2018] [Indexed: 12/15/2022] Open
Abstract
HIV-1 has already claimed over 35 million human lives globally. No curative treatments are currently available, and the only treatment option for over 36 million people currently living with HIV/AIDS are antiretroviral drugs that disrupt the function of virus-encoded proteins. However, such virus-targeted therapeutic strategies are constrained by the ability of the virus to develop drug-resistance. Despite major advances in HIV/AIDS research over the years, substantial knowledge gaps exist in many aspects of HIV-1 replication, especially its interaction with the host. Hence, understanding the mechanistic details of virus–host interactions may lead to novel therapeutic strategies for the prevention and/or management of HIV/AIDS. Notably, unprecedented progress in deciphering host gene silencing processes mediated by several classes of cellular small non-coding RNAs (sncRNA) presents a promising and timely opportunity for developing non-traditional antiviral therapeutic strategies. Cellular microRNAs (miRNA) belong to one such important class of sncRNAs that regulate protein synthesis. Evidence is mounting that cellular miRNAs play important roles in viral replication, either usurped by the virus to promote its replication or employed by the host to control viral infection by directly targeting the viral genome or by targeting cellular proteins required for productive virus replication. In this review, we summarize the findings to date on the role of miRNAs in HIV-1 biology.
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31
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Ramanathan S, Shenoda BB, Ajit SK. Overview of microRNA Modulation in Analgesic Research. ACTA ACUST UNITED AC 2017; 79:9.25.1-9.25.10. [PMID: 29261227 DOI: 10.1002/cpph.29] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
MicroRNA(miRNA)-mediated gene regulation underlies cellular processes, playing an important role in homeostasis and diseases. The expression and function of miRNAs are altered by various pharmacological agents, with differences in the endogenous levels of miRNAs influencing drug efficacy and toxicity. Thus, miRNA levels could be a biomarker for predicting treatment response, efficacy, and safety. In addition, elucidating the mechanistic significance of miRNA alterations can aid in the identification of therapeutic targets and patient selection, and guide personalized therapy. Discussed in this overview are the properties of miRNA, their modulation, and the ways to measure them. The effects of different classes of analgesics, including opioid and non-opioid, are described as examples of drug-induced modifications of miRNA, with a discussion on how measurement of miRNA levels in patients receiving analgesic therapy can assist in maximizing effectiveness while minimizing the untoward responses to this drug class. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Sujay Ramanathan
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Botros B Shenoda
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Seena K Ajit
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania
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32
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Wu Q, Ferry QRV, Baeumler TA, Michaels YS, Vitsios DM, Habib O, Arnold R, Jiang X, Maio S, Steinkraus BR, Tapia M, Piazza P, Xu N, Holländer GA, Milne TA, Kim JS, Enright AJ, Bassett AR, Fulga TA. In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering. Nat Commun 2017; 8:2109. [PMID: 29235467 PMCID: PMC5727397 DOI: 10.1038/s41467-017-00686-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/19/2017] [Indexed: 12/21/2022] Open
Abstract
RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs. We use GenERA to survey the entire regulatory landscape of a 3′UTR, and apply it in a multiplex fashion to analyse combinatorial interactions between sets of miRNA response elements (MREs), providing strong evidence for cooperative activity. We also employ this technology to probe the functionality of an entire MRE network under cellular homeostasis, and show that high-resolution analysis of the GenERA dataset can be used to extract functional features of MREs. This study provides a genome editing-based multiplex strategy for direct functional interrogation of RNA cis-regulatory elements in a native cellular environment. RNA regulatory elements (RREs) are important post-transcriptional control features but studying them requires disrupting their activity without disturbing cellular homeostasis. Here the authors present GenERA, a CRISPR-Cas9 screening platform of in situ analysis of native RREs.
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Affiliation(s)
- Qianxin Wu
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Quentin R V Ferry
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Toni A Baeumler
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Yale S Michaels
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Dimitrios M Vitsios
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Omer Habib
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
| | - Roland Arnold
- Molecular and Population Genetics Laboratory, Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Xiaowei Jiang
- Molecular and Population Genetics Laboratory, Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Stefano Maio
- Weatherall Institute of Molecular Medicine, Developmental Immunology, University of Oxford, Oxford, OX3 9DS, UK
| | - Bruno R Steinkraus
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Marta Tapia
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Oxford, OX3 9DS, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Ni Xu
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Georg A Holländer
- Weatherall Institute of Molecular Medicine, Developmental Immunology, University of Oxford, Oxford, OX3 9DS, UK.,Department of Biomedicine, Laboratory of Paediatric Immunology, University of Basel, CH-4058, Basel, Switzerland
| | - Thomas A Milne
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Oxford, OX3 9DS, UK
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea.,Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea
| | - Anton J Enright
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Andrew R Bassett
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RF, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tudor A Fulga
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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33
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MicroRNA-based therapeutics in cardiovascular disease: screening and delivery to the target. Biochem Soc Trans 2017; 46:11-21. [PMID: 29196609 DOI: 10.1042/bst20170037] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs of ∼22 nucleotides, which have increasingly been recognized as potent post-transcriptional regulators of gene expression. MiRNA targeting is defined by the complementarities between positions 2-8 of miRNA 5'-end with generally the 3'-untranslated region of target mRNAs (messenger RNAs). The capacity of miRNAs to simultaneously inhibit many different mRNAs allows for an amplification of biological responses. Hence, miRNAs are extremely attractive targets for therapeutic regulation in several diseases, including cardiovascular. Novel approaches are emerging to identify the miRNA functions in cardiovascular biology processes and to improve miRNA delivery in the heart and vasculature. In the present study, we provide an overview of current studies of miRNA functions in cardiovascular cells by the use of high-content screening. We also discuss the challenge to achieve a safe and targeted delivery of miRNA therapeutics in cardiovascular cells.
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34
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Abstract
The discovery of the microRNAs, lin-4 and let-7 as critical mediators of normal development in Caenorhabditis elegans and their conservation throughout evolution has spearheaded research toward identifying novel roles of microRNAs in other cellular processes. To accurately elucidate these fundamental functions, especially in the context of an intact organism, various microRNA transgenic models have been generated and evaluated. Transgenic C. elegans (worms), Drosophila melanogaster (flies), Danio rerio (zebrafish), and Mus musculus (mouse) have contributed immensely toward uncovering the roles of multiple microRNAs in cellular processes such as proliferation, differentiation, and apoptosis, pathways that are severely altered in human diseases such as cancer. The simple model organisms, C. elegans, D. melanogaster, and D. rerio, do not develop cancers but have proved to be convenient systesm in microRNA research, especially in characterizing the microRNA biogenesis machinery which is often dysregulated during human tumorigenesis. The microRNA-dependent events delineated via these simple in vivo systems have been further verified in vitro, and in more complex models of cancers, such as M. musculus. The focus of this review is to provide an overview of the important contributions made in the microRNA field using model organisms. The simple model systems provided the basis for the importance of microRNAs in normal cellular physiology, while the more complex animal systems provided evidence for the role of microRNAs dysregulation in cancers. Highlights include an overview of the various strategies used to generate transgenic organisms and a review of the use of transgenic mice for evaluating preclinical efficacy of microRNA-based cancer therapeutics.
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Affiliation(s)
- Arpita S Pal
- PULSe Graduate Program, Purdue University, West Lafayette, IN, United States
| | - Andrea L Kasinski
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, United States.
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35
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Gaudet AD, Fonken LK, Watkins LR, Nelson RJ, Popovich PG. MicroRNAs: Roles in Regulating Neuroinflammation. Neuroscientist 2017; 24:221-245. [PMID: 28737113 DOI: 10.1177/1073858417721150] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that broadly affect cellular and physiological function in all multicellular organisms. Here, the role of miRNAs in neuroinflammation is considered. miRNAs are 21- to 23-oligonucleotide RNAs that regulate translation of specific RNAs by binding to complementary regulatory RNA sequences, thereby causing mRNA degradation or sequestration. More than 5000 miRNAs likely exist in humans, and each miRNA binds an average of 200 RNAs. Specific immunomodulatory miRNAs can regulate a set of RNAs in a coordinated manner, suggesting that effective miRNA-based therapeutic manipulations for neuroinflammatory conditions may be revealed. For instance, miRNAs that preferentially inhibit translation of many cellular anti-inflammatory proteins could drive a pro-inflammatory response. Key pro-inflammatory ( miR-155, miR-27b, miR-326), anti-inflammatory ( miR-124, miR-146a, miR-21, miR-223), and mixed immunomodulatory ( let-7 family) miRNAs regulate neuroinflammation in various pathologies, including spinal cord injury, multiple sclerosis, ischemic stroke, and Alzheimer's disease. miRNAs represent a newly revealed layer of physiological complexity, the therapeutic benefits of which remain to be fully explored and exploited. In this review, we discuss the role of miRNAs in neuroinflammatory regulation and discuss how controlling miRNAs could alter cellular machinery to improve neuroinflammatory dynamics.
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Affiliation(s)
- Andrew D Gaudet
- 1 Center for Neuroscience, University of Colorado Boulder, CO, USA.,2 Department of Psychology and Neuroscience, University of Colorado Boulder, CO, USA
| | - Laura K Fonken
- 1 Center for Neuroscience, University of Colorado Boulder, CO, USA.,2 Department of Psychology and Neuroscience, University of Colorado Boulder, CO, USA
| | - Linda R Watkins
- 1 Center for Neuroscience, University of Colorado Boulder, CO, USA.,2 Department of Psychology and Neuroscience, University of Colorado Boulder, CO, USA
| | - Randy J Nelson
- 3 Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, OH, USA.,4 Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Phillip G Popovich
- 3 Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, OH, USA.,4 Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH, USA.,5 Center for Brain and Spinal Cord Repair, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
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36
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Exosomal MicroRNAs in Breast Cancer towards Diagnostic and Therapeutic Applications. Cancers (Basel) 2017; 9:cancers9070071. [PMID: 28672799 PMCID: PMC5532607 DOI: 10.3390/cancers9070071] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 06/16/2017] [Accepted: 06/16/2017] [Indexed: 12/21/2022] Open
Abstract
Soon after the discovery of microRNAs over 15 years ago, a myriad of research groups around the world sought to develop clinical applications in breast cancer for these short, noncoding, regulatory RNAs. While little of this knowledge has translated into the clinic, the recent research explosion on cell-to-cell communication via exosomes and other extracellular vesicles has rekindled interest in microRNA-based clinical applications. microRNAs appear to be a preferential and important cargo of exosomes in mediating biological effects in recipient cells. This review highlights recent studies on the biology of exosomal microRNAs (exo-miRNAs) and discusses potential clinical applications. From a diagnostic perspective, circulating exo-miRNAs may represent breast cancer cell content and/or tumor microenvironmental reactions to cancer cell growth. Thus, serum or plasma analysis of exo-miRNAs could be useful for early disease detection or for monitoring treatment response and disease progression. From a therapeutic perspective, exo-miRNAs derived from different cell types have been implicated in supporting or restraining tumor growth, conferring drug resistance, and preparing the metastatic niche. Strategies to interfere with the loading or delivery of tumor-promoting exo-miRNAs or to replenish tumor-suppressive miRNAs via exosomal delivery are under investigation. These recent studies provide new hope and opportunities, but study design limitations and technical challenges will need to be overcome before seriously considering clinical application of exo-miRNAs.
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37
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Dissecting miRNA gene repression on single cell level with an advanced fluorescent reporter system. Sci Rep 2017; 7:45197. [PMID: 28338079 PMCID: PMC5364550 DOI: 10.1038/srep45197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 02/22/2017] [Indexed: 12/16/2022] Open
Abstract
Despite major advances on miRNA profiling and target predictions, functional readouts for endogenous miRNAs are limited and frequently lead to contradicting conclusions. Numerous approaches including functional high-throughput and miRISC complex evaluations suggest that the functional miRNAome differs from the predictions based on quantitative sRNA profiling. To resolve the apparent contradiction of expression versus function, we generated and applied a fluorescence reporter gene assay enabling single cell analysis. This approach integrates and adapts a mathematical model for miRNA-driven gene repression. This model predicts three distinct miRNA-groups with unique repression activities (low, mid and high) governed not just by expression levels but also by miRNA/target-binding capability. Here, we demonstrate the feasibility of the system by applying controlled concentrations of synthetic siRNAs and in parallel, altering target-binding capability on corresponding reporter-constructs. Furthermore, we compared miRNA-profiles with the modeled predictions of 29 individual candidates. We demonstrate that expression levels only partially reflect the miRNA function, fitting to the model-projected groups of different activities. Furthermore, we demonstrate that subcellular localization of miRNAs impacts functionality. Our results imply that miRNA profiling alone cannot define their repression activity. The gene regulatory function is a dynamic and complex process beyond a minimalistic conception of "highly expressed equals high repression".
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38
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Leierer J, Mayer G, Kronbichler A. Primary focal segmental glomerulosclerosis: miRNAs and targeted therapies. Eur J Clin Invest 2016; 46:954-964. [PMID: 27651302 DOI: 10.1111/eci.12676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 09/07/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Primary focal segmental glomerulosclerosis (FSGS) is a common cause of nephrotic syndrome. AIMS The pathogenic steps leading to primary FSGS are still obscure, although evidence suggests that circulatory factor(s) are involved in the onset of disease. RESULTS Recent technical advances allow the analysis of miRNA expression in tissues and body fluids, leading to reports of miRNAs involved in the molecular mechanisms of FSGS-aetiopathogenesis. Moreover, investigations have also highlighted miRNAs that might serve as biomarkers for primary FSGS. DISCUSSION/CONCLUSIONS The aim of this review was to summarize reports showing a direct relation between miRNAs and primary FSGS. In addition, the impact of identified miRNAs on treatment response, prediction of the disease onset as well as the regulation in different disease activities is summarized.
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Affiliation(s)
- Johannes Leierer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria.
| | - Gert Mayer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Andreas Kronbichler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
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39
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Walsh CJ, Hu P, Batt J, Dos Santos CC. Discovering MicroRNA-Regulatory Modules in Multi-Dimensional Cancer Genomic Data: A Survey of Computational Methods. Cancer Inform 2016; 15:25-42. [PMID: 27721651 PMCID: PMC5051584 DOI: 10.4137/cin.s39369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/14/2016] [Accepted: 08/16/2016] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRs) are small single-stranded noncoding RNA that function in RNA silencing and post-transcriptional regulation of gene expression. An increasing number of studies have shown that miRs play an important role in tumorigenesis, and understanding the regulatory mechanism of miRs in this gene regulatory network will help elucidate the complex biological processes at play during malignancy. Despite advances, determination of miR–target interactions (MTIs) and identification of functional modules composed of miRs and their specific targets remain a challenge. A large amount of data generated by high-throughput methods from various sources are available to investigate MTIs. The development of data-driven tools to harness these multi-dimensional data has resulted in significant progress over the past decade. In parallel, large-scale cancer genomic projects are allowing new insights into the commonalities and disparities of miR–target regulation across cancers. In the first half of this review, we explore methods for identification of pairwise MTIs, and in the second half, we explore computational tools for discovery of miR-regulatory modules in a cancer-specific and pan-cancer context. We highlight strengths and limitations of each of these tools as a practical guide for the computational biologists.
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Affiliation(s)
- Christopher J Walsh
- Keenan and Li Ka Shing Knowledge Institute of Saint Michael's Hospital, Toronto, ON, Canada.; Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Jane Batt
- Keenan and Li Ka Shing Knowledge Institute of Saint Michael's Hospital, Toronto, ON, Canada.; Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Claudia C Dos Santos
- Keenan and Li Ka Shing Knowledge Institute of Saint Michael's Hospital, Toronto, ON, Canada.; Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
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Lozano E, de Lucas MP, Sáez AG. sta-1 is repressed by mir-58 family in Caenorhabditis elegans. WORM 2016; 5:e1238560. [PMID: 28090395 PMCID: PMC5190142 DOI: 10.1080/21624054.2016.1238560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 09/01/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023]
Abstract
The miR-58 family comprises 6 microRNAs with largely shared functions, and with an overall high expression, because one of its members, miR-58, is the most abundant microRNA in Caenorhabditis elegans. We recently found that 2 TGF-β signaling pathways, Sma/Mab and Dauer, responsible for body size and dauer formation respectively, among other phenotypes, are downregulated by the miR-58 family. Here, we further explore this family by showing that it also acts through the sta-1 3′UTR. sta-1 encodes a transcription factor, homologous to mammalian STATs, that inhibits dauer formation in association with the TGF-β Dauer pathway. We also observe that mutants with a constitutively active TGF-β Dauer pathway express higher levels of sta-1 mRNA. Our results reinforce the view of the miR-58 family and STA-1 as regulators of dauer formation in coordination with the TGF-β Dauer pathway.
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Affiliation(s)
- Encarnación Lozano
- Unidad Funcional de Investigación de Enfermedades Crónicas, Instituto de Salud Carlos III , Majadahonda, Madrid, Spain
| | - María Pilar de Lucas
- Unidad Funcional de Investigación de Enfermedades Crónicas, Instituto de Salud Carlos III , Majadahonda, Madrid, Spain
| | - Alberto G Sáez
- Unidad Funcional de Investigación de Enfermedades Crónicas, Instituto de Salud Carlos III , Majadahonda, Madrid, Spain
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Cretoiu D, Xu J, Xiao J, Suciu N, Cretoiu SM. Circulating MicroRNAs as Potential Molecular Biomarkers in Pathophysiological Evolution of Pregnancy. DISEASE MARKERS 2016; 2016:3851054. [PMID: 27493447 PMCID: PMC4967453 DOI: 10.1155/2016/3851054] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 06/15/2016] [Indexed: 12/17/2022]
Abstract
MicroRNAs represent nonprotein coding small RNA molecules that are very stable to degradation and responsible for gene silencing in most eukaryotic cells. Increased evidence has been accumulating over the years about their potential value as biomarkers for several diseases. MicroRNAs were predicted to be involved in nearly all biological processes from development to oncogenesis. In this review, we address the importance of circulating microRNAs in different conditions associated with pregnancy starting with the implantation period to preeclampsia and we shortly describe the correlation between placental circulating miRNAs and pregnancy status. We also discuss the importance of microRNAs in recurrent abortion and ectopic pregnancy.
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Affiliation(s)
- Dragos Cretoiu
- Division of Cellular and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Victor Babeș National Institute of Pathology, 050096 Bucharest, Romania
| | - Jiahong Xu
- Department of Cardiology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China
| | - Junjie Xiao
- Regeneration and Ageing Lab, Experimental Center of Life Sciences, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Nicolae Suciu
- Department of Obstetrics and Gynecology, Polizu Clinical Hospital, Carol Davila University of Medicine and Pharmacy, 011062 Bucharest, Romania
- Alessandrescu-Rusescu National Institute of Mother and Child Health, 020395 Bucharest, Romania
| | - Sanda Maria Cretoiu
- Division of Cellular and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Victor Babeș National Institute of Pathology, 050096 Bucharest, Romania
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Ergun S, Oztuzcu S. Sequence-based analysis of 5′UTR and coding regions of CASP3 in terms of miRSNPs and SNPs in targetting miRNAs. Comput Biol Chem 2016; 62:70-4. [DOI: 10.1016/j.compbiolchem.2016.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/06/2016] [Accepted: 04/06/2016] [Indexed: 01/18/2023]
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