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Tarasov VA, Matishov DG, Shin EF, Boyko NV, Timoshkina NN, Makhotkin MA, Lomonosov AM, Kirpiy AA, Kit OI, Maximov AY. Coordinated aberrant expression of miRNAs in colon cancer. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414080109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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52
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Conrad T, Marsico A, Gehre M, Orom UA. Microprocessor activity controls differential miRNA biogenesis In Vivo. Cell Rep 2014; 9:542-54. [PMID: 25310978 DOI: 10.1016/j.celrep.2014.09.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/02/2014] [Accepted: 09/06/2014] [Indexed: 01/10/2023] Open
Abstract
In miRNA biogenesis, pri-miRNA transcripts are converted into pre-miRNA hairpins. The in vivo properties of this process remain enigmatic. Here, we determine in vivo transcriptome-wide pri-miRNA processing using next-generation sequencing of chromatin-associated pri-miRNAs. We identify a distinctive Microprocessor signature in the transcriptome profile from which efficiency of the endogenous processing event can be accurately quantified. This analysis reveals differential susceptibility to Microprocessor cleavage as a key regulatory step in miRNA biogenesis. Processing is highly variable among pri-miRNAs and a better predictor of miRNA abundance than primary transcription itself. Processing is also largely stable across three cell lines, suggesting a major contribution of sequence determinants. On the basis of differential processing efficiencies, we define functionality for short sequence features adjacent to the pre-miRNA hairpin. In conclusion, we identify Microprocessor as the main hub for diversified miRNA output and suggest a role for uncoupling miRNA biogenesis from host gene expression.
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Affiliation(s)
- Thomas Conrad
- Otto Warburg Laboratories, Noncoding RNA Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Annalisa Marsico
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Department of Mathematics and Informatics, Free University of Berlin, 14195 Berlin, Germany
| | - Maja Gehre
- Otto Warburg Laboratories, Noncoding RNA Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Department of Biochemistry, Free University of Berlin, 14195 Berlin, Germany
| | - Ulf Andersson Orom
- Otto Warburg Laboratories, Noncoding RNA Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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53
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Kent OA, McCall MN, Cornish TC, Halushka MK. Lessons from miR-143/145: the importance of cell-type localization of miRNAs. Nucleic Acids Res 2014; 42:7528-38. [PMID: 24875473 PMCID: PMC4081080 DOI: 10.1093/nar/gku461] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
miR-143 and miR-145 are co-expressed microRNAs (miRNAs) that have been extensively studied as potential tumor suppressors. These miRNAs are highly expressed in the colon and are consistently reported as being downregulated in colorectal and other cancers. Through regulation of multiple targets, they elicit potent effects on cancer cell growth and tumorigenesis. Importantly, a recent discovery demonstrates that miR-143 and miR-145 are not expressed in colonic epithelial cells; rather, these two miRNAs are highly expressed in mesenchymal cells such as fibroblasts and smooth muscle cells. The expression patterns of miR-143 and miR-145 and other miRNAs were initially determined from tissue level data without consideration that multiple different cell types, each with their own unique miRNA expression patterns, make up each tissue. Herein, we discuss the early reports on the identification of dysregulated miR-143 and miR-145 expression in colorectal cancer and how lack of consideration of cellular composition of normal tissue led to the misconception that these miRNAs are downregulated in cancer. We evaluate mechanistic data from miR-143/145 studies in context of their cell type-restricted expression pattern and the potential of these miRNAs to be considered tumor suppressors. Further, we examine other examples of miRNAs being investigated in inappropriate cell types modulating pathways in a non-biological fashion. Our review highlights the importance of determining the cellular expression pattern of each miRNA, so that downstream studies are conducted in the appropriate cell type.
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Affiliation(s)
- Oliver A Kent
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Room 8-703, Toronto Medical Discovery Tower, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Matthew N McCall
- University of Rochester, Department of Biostatistics, Rochester, NY 14642, USA
| | - Toby C Cornish
- Johns Hopkins University, Department of Pathology, Baltimore, MD 21205, USA
| | - Marc K Halushka
- Johns Hopkins University, Department of Pathology, Baltimore, MD 21205, USA
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54
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Contrant M, Fender A, Chane-Woon-Ming B, Randrianjafy R, Vivet-Boudou V, Richer D, Pfeffer S. Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs. Nucleic Acids Res 2014; 42:7981-96. [PMID: 24831544 PMCID: PMC4081064 DOI: 10.1093/nar/gku424] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Micro (mi)RNAs are small non-coding RNAs with key regulatory functions. Recent advances in the field allowed researchers to identify their targets. However, much less is known regarding the regulation of miRNAs themselves. The accumulation of these tiny regulators can be modulated at various levels during their biogenesis from the transcription of the primary transcript (pri-miRNA) to the stability of the mature miRNA. Here, we studied the importance of the pri-miRNA secondary structure for the regulation of mature miRNA accumulation. To this end, we used the Kaposi's sarcoma herpesvirus, which encodes a cluster of 12 pre-miRNAs. Using small RNA profiling and quantitative northern blot analysis, we measured the absolute amount of each mature miRNAs in different cellular context. We found that the difference in expression between the least and most expressed viral miRNAs could be as high as 60-fold. Using high-throughput selective 2′-hydroxyl acylation analyzed by primer extension, we then determined the secondary structure of the long primary transcript. We found that highly expressed miRNAs derived from optimally structured regions within the pri-miRNA. Finally, we confirmed the importance of the local structure by swapping stem-loops or by targeted mutagenesis of selected miRNAs, which resulted in a perturbed accumulation of the mature miRNA.
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Affiliation(s)
- Maud Contrant
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Aurélie Fender
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Béatrice Chane-Woon-Ming
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Ramy Randrianjafy
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Valérie Vivet-Boudou
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Delphine Richer
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
| | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN - UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France
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55
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Fuziwara CS, Kimura ET. High iodine blocks a Notch/miR-19 loop activated by the BRAF(V600E) oncoprotein and restores the response to TGFβ in thyroid follicular cells. Thyroid 2014; 24:453-62. [PMID: 23998804 PMCID: PMC3949441 DOI: 10.1089/thy.2013.0398] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Excess iodine inhibits thyroid follicular cell proliferation associated with TGFβ pathway activation, although thyroid cancers are frequently refractory to TGFβ signaling. The TGFβ pathway is predicted to be regulated by miR-17-92 cluster microRNAs. MicroRNAs are small noncoding RNAs that inhibit target mRNA translation and have emerged as potent modulators of tumorigenesis. Although the BRAF(V600E) mutation is the most prevalent alteration in thyroid cancer, the impact of iodine intake on BRAF-mediated oncogenesis remains unclear. Therefore, the aim of this study was to investigate the influence of high iodine on miR-17-92 transcriptional regulation and expression in thyroid cells expressing activated BRAF. METHODS Rat thyroid follicular cells that conditionally express BRAF(V600E) under doxycycline stimulation (PC-BRAF(V600E)-6) were derived from the PCCl3 line. These cells were treated with doxycycline for two days, in the absence or presence of 10 μM sodium iodide. The thyroid cancer cell lines BCPAP and KTC2 were also analyzed. Expression of the miR-17-92 cluster and Notch1 was analyzed by quantitative polymerase chain reaction, and expression of these genes was modulated by anti-miR or anti-Notch1 siRNAs transfection. Protein expression was assessed by Western blot. Luciferase assays were used to quantify Smad4 3'-UTR/miR-19 interaction and Notch signaling activation. TGFβ responsiveness was evaluated by cell cycle analysis of TGFβ-treated cells. RESULTS High iodine blocked BRAF(V600E)-induced upregulation of miR-17-92, including miR-19a/b. miR-17-92 promoter region analysis revealed a putative binding site for Hes1, a transcription factor responsive to Notch signaling. Notch-1 overexpression resulted in miR-19 upregulation in normal thyroid cells, while Notch-1 knockdown blocked BRAF-induced miR-19 expression. Moreover, in anaplastic thyroid cancer cells, Notch-1 knockdown reduced miR-19. Expression of BRAF(V600E) decreased Smad4 protein in normal thyroid cells. Smad4 was validated as a miR-19 target by luciferase assays, which revealed reduced luminescence associated with miR-19 interaction in Smad4 3'-UTR. Iodine treatment restored Smad4 levels in BRAF-activated cells, resulting in enhanced G1-cell cycle arrest in response to TGFβ. Moreover, this effect was mimicked in papillary thyroid cancer cells treated with anti-miR-19. CONCLUSION High iodine abrogates BRAF(V600E)-induced activation of miR-19, a newly identified Smad4 regulator, through Notch pathway inhibition and restores responsiveness to TGFβ signaling. Our results indicate that iodine exerts protective effects in thyroid cells, attenuating acute BRAF oncogene-mediated microRNA deregulation.
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Affiliation(s)
- Cesar Seigi Fuziwara
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo , São Paulo, Brazil
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56
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Chawla G, Sokol NS. ADAR mediates differential expression of polycistronic microRNAs. Nucleic Acids Res 2014; 42:5245-55. [PMID: 24561617 PMCID: PMC4005697 DOI: 10.1093/nar/gku145] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Adenosine deaminases acting on RNAs (ADARs) convert adenosine residues to inosines in primary microRNA (pri-miRNA) transcripts to alter the structural conformation of these precursors and the subsequent functions of the encoded microRNAs (miRNAs). Here we show that RNA editing by Drosophila ADAR modulates the expression of three co-transcribed miRNAs encoded by the evolutionarily conserved let-7-Complex (let-7-C) locus. For example, a single A-to-I change at the −6 residue of pri-miR-100, the first miRNA in this let-7-C polycistronic transcript, leads to enhanced miRNA processing by Drosha and consequently enhanced functional miR-100 both in vitro as well as in vivo. In contrast, other editing events, including one at the +43 residue of the pri-miR-125, destabilize the primary transcript and reduce the levels of all three encoded miRNAs. Consequently, loss of adar in vivo leads to reduced miR-100 but increased miR-125. In wild-type animals, the destabilizing editing events in pri-let-7-C increase during the larval-to-adult transition and are critical for the normal downregulation of all three miRNAs seen late in metamorphosis. These findings unravel a new regulatory role for ADAR and raise the possibility that ADAR mediates the differential expression characteristic of many polycistronic miRNA clusters.
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Affiliation(s)
- Geetanjali Chawla
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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57
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Chaulk SG, Xu Z, Glover MJN, Fahlman RP. MicroRNA miR-92a-1 biogenesis and mRNA targeting is modulated by a tertiary contact within the miR-17~92 microRNA cluster. Nucleic Acids Res 2014; 42:5234-44. [PMID: 24520115 PMCID: PMC4005684 DOI: 10.1093/nar/gku133] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
While functional mature microRNAs (miRNAs) are small ∼22 base oligonucleotides that target specific mRNAs, miRNAs are initially expressed as long transcripts (pri-miRNAs) that undergo sequential processing to yield the mature miRNAs. We have previously reported that the pri-miR-17∼92 cluster adopts a compact globular folded structure that internalizes a 3' core domain resulting in reduced miRNA maturation and subsequent mRNA targeting. Using a site-specific photo-cross-linker we have identified a tertiary contact within the 3' core domain of the pri-miRNA between a non-miRNA stem-loop and the pre-miR-19b hairpin. This tertiary contact is involved in the formation of the compact globular fold of the cluster while its disruption enhances miR-92a expression and mRNA targeting. We propose that this tertiary contact serves as a molecular scaffold to restrict expression of the proposed antiangiogenic miR-92a, allowing for the overall pro-angiogenic effect of miR-17∼92 expression.
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Affiliation(s)
- Steven G Chaulk
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada and Department of Oncology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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58
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Xiong X, Kang X, Zheng Y, Yue S, Zhu S. Identification of loop nucleotide polymorphisms affecting microRNA processing and function. Mol Cells 2013; 36:518-26. [PMID: 24241682 PMCID: PMC3887969 DOI: 10.1007/s10059-013-0171-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 09/27/2013] [Accepted: 10/14/2013] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs are short 21-22 nucleotide single strand RNAs that are involved in post-transcriptional regulation of gene expression. Most microRNAs are first transcribed as long primary microRNAs and then undergo a two step-wise sequential processing to yield single-stranded mature microRNAs. It has been suggested that the loop region of primary microRNAs plays an important role in regulating microRNA biogenesis and target recognition. However, despite the fact that several single nucleotide polymorphisms have been identified in mature microRNA sequences and are related to human diseases, it remains unclear whether and how the single nucleotide polymorphisms in the loop regions of primary microRNAs would affect the biogenesis and function of microRNAs. Herein, we provide evidence that primary microRNAs loop nucleotides control the accuracy and efficiency of microRNA processing. Accordingly, we identified 32 single nucleotide polymorphisms in the loop regions of human primary microRNAs using bioinformatics, and further validated three loss-of-function and one gain-of-function single nucleotide polymorphisms using dual-luciferase assays. Thus, these results reveal a critical regulatory role encoded in the loop nucleotides of primary microRNAs for microRNA processing and function.
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Affiliation(s)
- Xiaoxing Xiong
- Department of Anesthesia, The First Affiliated Hospital, School of medicine, Zhejiang University,
China
| | - Xianhui Kang
- Department of Anesthesia, The First Affiliated Hospital, School of medicine, Zhejiang University,
China
| | - Yueying Zheng
- Department of Anesthesia, The First Affiliated Hospital, School of medicine, Zhejiang University,
China
| | - Sibiao Yue
- Department of Biology, Johns Hopkins University,
USA
| | - Shengmei Zhu
- Department of Anesthesia, The First Affiliated Hospital, School of medicine, Zhejiang University,
China
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59
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Murphy BL, Obad S, Bihannic L, Ayrault O, Zindy F, Kauppinen S, Roussel MF. Silencing of the miR-17~92 cluster family inhibits medulloblastoma progression. Cancer Res 2013; 73:7068-78. [PMID: 24145352 DOI: 10.1158/0008-5472.can-13-0927] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Medulloblastoma, originating in the cerebellum, is the most common malignant brain tumor in children. Medulloblastoma consists of four major groups where constitutive activation of the Sonic Hedgehog (SHH) signaling pathway is a hallmark of one group. Mouse and human SHH medulloblastomas exhibit increased expression of microRNAs encoded by the miR-17~92 and miR-106b~25 clusters compared with granule progenitors and postmitotic granule neurons. Here, we assessed the therapeutic potential of 8-mer seed-targeting locked nucleic acid (LNA)-modified anti-miR oligonucleotides, termed tiny LNAs, that inhibit microRNA seed families expressed by miR-17~92 and miR-106b~25 in two mouse models of SHH medulloblastomas. We found that tumor cells (medulloblastoma cells) passively took up 8-mer LNA-anti-miRs and specifically inhibited targeted microRNA seed-sharing family members. Inhibition of miR-17 and miR-19a seed families by anti-miR-17 and anti-miR-19, respectively, resulted in diminished tumor cell proliferation in vitro. Treatment of mice with systemic delivery of anti-miR-17 and anti-miR-19 reduced tumor growth in flank and brain allografts in vivo and prolonged the survival of mice with intracranial transplants, suggesting that inhibition of the miR-17~92 cluster family by 8-mer LNA-anti-miRs might be considered for the treatment of SHH medulloblastomas.
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Affiliation(s)
- Brian L Murphy
- Authors' Affiliations: Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee; Santaris Pharma, Hørsholm; and Department of Haematology, Aalborg University Hospital, Copenhagen, Denmark
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60
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Highly ordered architecture of microRNA cluster. BIOMED RESEARCH INTERNATIONAL 2013; 2013:463168. [PMID: 24195073 PMCID: PMC3806224 DOI: 10.1155/2013/463168] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/03/2013] [Indexed: 01/12/2023]
Abstract
Although it is known that the placement of genes in a cluster may be critical for proper expression patterns, it remains largely unclear whether the orders of members in an miRNA cluster have biological insights. By investigating the relationship between expression and orders for miRNAs from the oncogenic miR-17-92 cluster, we observed a highly ordered architecture in this cluster. A significant correlation between miRNA expression level and its placement was revealed. More importantly, the placement of these miRNAs is associated with their dysregulation in cancer. Here, we presented the opinion that miRNA clusters are not arranged randomly but show highly ordered architectures, which may have critical roles in physiology and pathology.
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61
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Olive V, Li Q, He L. mir-17-92: a polycistronic oncomir with pleiotropic functions. Immunol Rev 2013; 253:158-66. [PMID: 23550645 DOI: 10.1111/imr.12054] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neoplastic transformation is caused by accumulation of genetic lesions that ultimately convert normal cells into tumor cells with uncontrolled proliferation and survival, unlimited replicative potential, and invasive growth. Emerging evidence has highlighted the functional importance of non-coding RNAs, particularly microRNAs (miRNAs), in the initiation and progression of tumor development. The mir-17-92 miRNA is among the best characterized miRNA oncogenes, whose genomic amplification or aberrant elevation are frequently observed in a variety of tumor types. Unlike protein-coding oncogenes, where one transcript produces one protein, mir-17-92 encodes a polycistronic miRNA transcript that yields six individual miRNA components. This unique gene structure, shared by many important miRNA oncogenes and tumor suppressors, underlies the unique functionality of mir-17-92 in a cell type and context-dependent manner. Recent functional dissection of mir-17-92 indicates that individual mir-17-92 components perform distinct biological functions, which collectively regulate multiple related cellular processes during development and disease. The structural complexity of mir-17-92 as a polycistronic miRNA oncogene, along with the complex mode of interactions among its components, constitutes the molecular basis for its unique functional complexity during normal and tumor development.
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Affiliation(s)
- Virginie Olive
- Division of Cellular and Developmental Biology, MCB Department, University of California at Berkeley, Berkeley, CA 94705, USA
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62
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Franzosa JA, Bugel SM, Tal TL, La Du JK, Tilton SC, Waters KM, Tanguay RL. Retinoic acid-dependent regulation of miR-19 expression elicits vertebrate axis defects. FASEB J 2013; 27:4866-76. [PMID: 23975936 DOI: 10.1096/fj.12-225524] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Retinoic acid (RA) is involved in multifarious and complex functions necessary for vertebrate development. RA signaling is reliant on strict enzymatic regulation of RA synthesis and metabolism. Improper spatiotemporal expression of RA during development can result in vertebrate axis defects. microRNAs (miRNAs) are also pivotal in orchestrating developmental processes. While mechanistic links between miRNAs and axial development are established, the role of miRNAs in regulating metabolic enzymes responsible for RA abundance during axis formation has yet to be elucidated. Our results uncovered a role of miR-19 family members in controlling RA metabolism through the regulation of CYP26A1 during vertebrate axis formation. Global miRNA expression profiling showed that developmental RA exposure suppressed the expression of miR-19 family members during zebrafish somitogenesis. A reporter assay confirmed that cyp26a1 is a bona fide target of miR-19 in vivo. Transient knockdown of miR-19 phenocopied axis defects caused by RA exposure. Exogenous miR-19 rescued the axis defects induced by RA exposure. Taken together, these results indicate that the teratogenic effects of RA exposure result, in part, from repression of miR-19 expression and subsequent misregulation of cyp26a1. This highlights a previously unidentified role of miR-19 in facilitating vertebrate axis development via regulation of RA signaling.
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Affiliation(s)
- Jill A Franzosa
- 3Department of Environmental and Molecular Toxicology, Oregon State University, 28645 East HWY 34. Corvallis, OR 97333, USA.
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63
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Wang WLW, Welsh J, Tenniswood M. 1,25-Dihydroxyvitamin D3 modulates lipid metabolism in prostate cancer cells through miRNA mediated regulation of PPARA. J Steroid Biochem Mol Biol 2013; 136:247-51. [PMID: 23059473 DOI: 10.1016/j.jsbmb.2012.09.033] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 09/26/2012] [Accepted: 09/30/2012] [Indexed: 10/27/2022]
Abstract
Previous studies from our laboratory have shown that testosterone (T) and 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) co-operate to inhibit cell proliferation and induce significant changes in gene expression and differentiation in LNCaP cells. The data presented here demonstrate that the two agents alter fatty acid metabolism, and accumulation of neutral lipid. Concurrent genome wide analysis of mRNA and miRNA in LNCaP cells reveals an extensive transcription regulatory network modulated by T and 1,25(OH)2D3. This involves not only androgen receptor (AR)- and vitamin D receptor (VDR)-mediated transcription, but also transcription factors E2F1- and c-Myc-dependent transcription. Changes in the activities of these transcription factors alter the steady state levels of several miRNAs, including the miR-17/92 cluster. These changes correlate with the up-regulation of the mRNA encoding peroxisome proliferator-activated receptor alpha (PPARA) and its downstream targets, leading to increased lipogenesis. These data suggest that the coordinated effect of T and 1,25(OH)2D3 in prostate cancer cells increases lipogenesis, diverting energy away from Warburg-based tumor energy metabolism, which slows or halts cell growth and tumor progression. This article is part of a Special Issue entitled 'Vitamin D Workshop'.
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Affiliation(s)
- Wei-Lin Winnie Wang
- Department of Biomedical Sciences, University at Albany, State University of New York, Albany, NY 12222, United States.
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64
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Yang X, Marcucci K, Anguela X, Couto LB. Preclinical evaluation of an anti-HCV miRNA cluster for treatment of HCV infection. Mol Ther 2013; 21:588-601. [PMID: 23295950 DOI: 10.1038/mt.2012.247] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We developed a strategy to treat hepatitis C virus (HCV) infection by replacing five endogenous microRNA (miRNA) sequences of a natural miRNA cluster (miR-17-92) with sequences that are complementary to the HCV genome. This miRNA cluster (HCV-miR-Cluster 5) is delivered to cells using adeno-associated virus (AAV) vectors and the miRNAs are expressed in the liver, the site of HCV replication and assembly. AAV-HCV-miR-Cluster 5 inhibited bona fide HCV replication in vitro by up to 95% within 2 days, and the spread of HCV to uninfected cells was prevented by continuous expression of the anti-HCV miRNAs. Furthermore, the number of cells harboring HCV RNA replicons decreased dramatically by sustained expression of the anti-HCV miRNAs, suggesting that the vector is capable of curing cells of HCV. Delivery of AAV-HCV-miR-Cluster 5 to mice resulted in efficient transfer of the miRNA gene cluster and expression of all five miRNAs in liver tissue, at levels up to 1,300 copies/cell. These levels achieved up to 98% gene silencing of cognate HCV sequences, and no liver toxicity was observed, supporting the safety of this approach. Therefore, AAV-HCV-miR-Cluster 5 represents a different paradigm for the treatment of HCV infection.
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Affiliation(s)
- Xiao Yang
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
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65
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O'Carroll D, Schaefer A. General principals of miRNA biogenesis and regulation in the brain. Neuropsychopharmacology 2013; 38:39-54. [PMID: 22669168 PMCID: PMC3521995 DOI: 10.1038/npp.2012.87] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/02/2012] [Accepted: 05/02/2012] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that mediate posttranscriptional gene suppression in a sequence-specific manner. The ability of a single miRNA species to target multiple messenger RNAs (mRNAs) makes miRNAs exceptionally important regulators of various cellular functions. The regulatory capacity of miRNAs is increased further by the miRNA ability to suppress gene expression using multiple mechanisms that range from translational inhibition to mRNA degradation. The high miRNA diversity multiplied by the large number of individual miRNA targets generates a vast regulatory RNA network than enables flexible control of mRNA expression. The gene-regulatory capacity and diversity of miRNAs is particularly valuable in the brain, where functional specialization of neurons and persistent flow of information requires constant neuronal adaptation to environmental cues. In this review we will summarize the current knowledge about miRNA biogenesis and miRNA expression regulation with a focus on the role of miRNAs in the mammalian nervous system.
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Affiliation(s)
- Dónal O'Carroll
- European Molecular Biology Laboratory, Mouse Biology Unit, Monterotondo Scalo, Italy
| | - Anne Schaefer
- Fishberg Department of Neuroscience and Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY, USA
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66
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Huang Y, Yang YB, Zhang XH, Yu XL, Wang ZB, Cheng XC. MicroRNA-21 gene and cancer. Med Oncol 2013; 30:376. [PMID: 23277281 DOI: 10.1007/s12032-012-0376-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 09/14/2012] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are a class of 18-27-nucleotides single-stranded RNA molecules that regulate gene expression at the post-transcriptional level. It has been demonstrated that miRNAs regulate a variety of physiological functions, including development, cell differentiation, proliferation, and apoptosis. There are growing evidence showed that miRNAs can affect the genesis and development of tumor and play a kind of tumor suppressor or oncogenic function by regulating its targetted gene-related signal pathway. miRNA-21 is one of the early discovered miRNAs in human cells, and the expression of miRNA-21 is significantly upregulated in different kinds of solid tumors. Its abnormal expression levels are closely associated with pathogenesis of cancers. This review summarizes the recent study on the field of miRNA-21 and its association with cancer.
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Affiliation(s)
- Yong Huang
- Animal Science and Technology College, He Nan University of Science and Technology, Luoyang City 471003, Henan Province, People's Republic of China.
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Santoro MM, Nicoli S. miRNAs in endothelial cell signaling: the endomiRNAs. Exp Cell Res 2012; 319:1324-30. [PMID: 23262024 DOI: 10.1016/j.yexcr.2012.12.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 12/11/2012] [Indexed: 12/30/2022]
Abstract
microRNAs (miRNAs) have a pivotal role during the formation and function of the cardiovascular system. More than 300 miRNAs have been currently found within the mammalian genome, however only few specific miRNAs, named endomiRNAs, showed conseved endothelial cell expression and function. In this review we present an overview of the currently known endomiRNAs, focusing on their genome localization, processing and target gene repression during vasculogenesis and angiogenesis.
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Affiliation(s)
- Massimo M Santoro
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Torino, Italy.
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TAF15 is important for cellular proliferation and regulates the expression of a subset of cell cycle genes through miRNAs. Oncogene 2012; 32:4646-55. [PMID: 23128393 DOI: 10.1038/onc.2012.490] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 08/31/2012] [Accepted: 09/07/2012] [Indexed: 12/16/2022]
Abstract
TAF15 (formerly TAFII68) is a member of the FET (FUS, EWS, TAF15) family of RNA- and DNA-binding proteins whose genes are frequently translocated in sarcomas. By performing global gene expression profiling, we found that TAF15 knockdown affects the expression of a large subset of genes, of which a significant percentage is involved in cell cycle and cell death. In agreement, TAF15 depletion had a growth-inhibitory effect and resulted in increased apoptosis. Among the TAF15-regulated genes, targets of microRNAs (miRNAs) generated from the onco-miR-17 locus were overrepresented, with CDKN1A/p21 being the top miRNAs-targeted gene. Interestingly, the levels of onco-miR-17 locus coded miRNAs (miR-17-5p and miR-20a) were decreased upon TAF15 depletion and shown to affect the post-transcriptional regulation of TAF15-dependent genes, such as CDKN1A/p21. Thus, our results demonstrate that TAF15 is required to regulate gene expression of cell cycle regulatory genes post-transcriptionally through a pathway involving miRNAs. The findings that high TAF15 levels are needed for rapid cellular proliferation and that endogenous TAF15 levels decrease during differentiation strongly suggest that TAF15 is a key regulator of maintaining a highly proliferative rate of cellular homeostasis.
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miR290-5p/292-5p activate the immunoglobulin kappa locus in B cell development. PLoS One 2012; 7:e43805. [PMID: 22928038 PMCID: PMC3426528 DOI: 10.1371/journal.pone.0043805] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 07/26/2012] [Indexed: 01/09/2023] Open
Abstract
Regulated expression of miRNAs influences development in a wide variety of contexts. We report here that miR290-5p (100049710) and miR292-5p (100049711) are induced at the pre-B stage of murine B cell development and that they influence assembly of the Igκ light chain gene (243469) by contributing to the activation of germline Igκ transcription (κGT). We found that upon forced over-expression of miR290-5p/292-5p in Abelson Murine Leukemia Virus (AMuLV) transformed pro-B cells, two known activators of κGT, E2A (21423) and NF-κB (19697), show increased chromosomal binding to the kappa intronic enhancer. Conversely, knockdown of miR290-5p/292-5p in AMuLV pro-B cells blunts drug-induced activation of κGT. Furthermore, miR290-5p/292-5p knockdown also diminishes κGT activation, but not Rag1/2 (19373, 19374) expression, in an IL-7 dependent primary pro-B cell culture system. In addition, we identified a deficiency in κGT induction in miR290 cluster knockout mice. We hypothesize that increased expression of miR290-5p and miR292-5p contributes to the induction of κGT at the pre-B stage of B cell development through increased binding of NF-κB and E2A to kappa locus regulatory sequences.
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Ray A, Marshall V, Uldrick T, Leighty R, Labo N, Wyvill K, Aleman K, Polizzotto MN, Little RF, Yarchoan R, Whitby D. Sequence analysis of Kaposi sarcoma-associated herpesvirus (KSHV) microRNAs in patients with multicentric Castleman disease and KSHV-associated inflammatory cytokine syndrome. J Infect Dis 2012; 205:1665-76. [PMID: 22448005 PMCID: PMC3415855 DOI: 10.1093/infdis/jis249] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 12/05/2011] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Kaposi sarcoma-associated herpesvirus (KSHV) encodes 12 pre-microRNAs that yield 25 mature microRNAs. We previously reported phylogenetic analysis of the microRNA-coding region of KSHV from Kaposi sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman disease (MCD) patients. We observed a high level of conservation for most sequences but also a divergent cluster of 5 KSHV sequences, including 2 from MCD patients. METHODS KSHV microRNA sequences from 23 MCD patients and 7 patients with a newly described KSHV-associated inflammatory cytokine syndrome (KICS) were examined by amplification, cloning, and sequencing of a 646-bp fragment of K12/T0.7 encoding microRNA-K12-10 and microRNA-K12-12 and a 2.8-kbp fragment containing the remaining 10 pre-microRNAs. RESULTS Phylogenetic analysis showed a distinct variant cluster consisting exclusively of MCD and KICS patients in all trees. Pearson χ(2) analysis revealed that 40 single-nucleotide polymorphisms (SNPs) at various loci were significantly associated with MCD and KICS risk. Cluster analysis of these SNPs generated several combinations of 3 SNPs as putative indicators of MCD and KICS risk. CONCLUSIONS These findings show that MCD and KICS patients frequently have unusual KSHV microRNA sequences and suggest an association between the observed sequence variation and risk of MCD and KICS.
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Affiliation(s)
- Alex Ray
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, National Cancer Institute (NCI)-Frederick
| | - Vickie Marshall
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, National Cancer Institute (NCI)-Frederick
| | | | | | - Nazzarena Labo
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, National Cancer Institute (NCI)-Frederick
| | | | | | | | | | | | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, National Cancer Institute (NCI)-Frederick
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Abstract
Overwhelming experimental evidence accumulated over the past decade indicates that microRNAs (miRNAs) are key regulators of gene expression in animals and plants and play important roles in development, homeostasis, and disease. The miR-17-92 family of miRNA clusters is composed of 3 related, highly conserved, polycistronic miRNA genes that collectively encode for a total of 15 miRNAs. We discuss recent studies demonstrating that these miRNAs are essential for vertebrate development and homeostasis. We also show how their mutation or deregulation contributes to the pathogenesis of a variety of human diseases, including cancer and congenital developmental defects. Finally, we discuss the current evidence suggesting how the different miRNAs encoded by these 3 clusters can functionally cooperate to fine-tune signaling and developmental pathways.
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Affiliation(s)
- Carla P. Concepcion
- Memorial Sloan Kettering Cancer Center, Cancer Biology and Genetics Program 1275 York Avenue, New York, NY, 10065
| | - Ciro Bonetti
- Memorial Sloan Kettering Cancer Center, Cancer Biology and Genetics Program 1275 York Avenue, New York, NY, 10065
| | - Andrea Ventura
- Memorial Sloan Kettering Cancer Center, Cancer Biology and Genetics Program 1275 York Avenue, New York, NY, 10065
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Amiel J, de Pontual L, Henrion-Caude A. miRNA, development and disease. ADVANCES IN GENETICS 2012; 80:1-36. [PMID: 23084872 DOI: 10.1016/b978-0-12-404742-6.00001-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Jeanne Amiel
- Unité INSERM U781, Université Paris-Sorbonne Cité, Institut IMAGINE, France.
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