2851
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Nagano H, Yamagishi N, Tomida C, Yano C, Aibara K, Kohno S, Abe T, Ohno A, Hirasaka K, Okumura Y, Mills EM, Nikawa T, Teshima-Kondo S. A novel myogenic function residing in the 5' non-coding region of Insulin receptor substrate-1 (Irs-1) transcript. BMC Cell Biol 2015; 16:8. [PMID: 25887310 PMCID: PMC4373113 DOI: 10.1186/s12860-015-0054-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/16/2015] [Indexed: 11/20/2022] Open
Abstract
Background There is evidence that several messenger RNAs (mRNAs) are bifunctional RNAs, i.e. RNA transcript carrying both protein-coding capacity and activity as functional non-coding RNA via 5′ and 3′ untranslated regions (UTRs). Results In this study, we identified a novel bifunctional RNA that is transcribed from insulin receptor substrate-1 (Irs-1) gene with full-length 5′UTR sequence (FL-Irs-1 mRNA). FL-Irs-1 mRNA was highly expressed only in skeletal muscle tissue. In cultured skeletal muscle C2C12 cells, the FL-Irs-1 transcript functioned as a bifunctional mRNA. The FL-Irs-1 transcript produced IRS-1 protein during differentiation of myoblasts into myotubes; however, this transcript functioned as a regulatory RNA in proliferating myoblasts. The FL-Irs-1 5′UTR contains a partial complementary sequence to Rb mRNA, which is a critical factor for myogenic differentiation. The overexpression of the 5′UTR markedly reduced Rb mRNA expression, and this reduction was fully dependent on the complementary element and was not compensated by IRS-1 protein. Conversely, knockdown of FL-Irs-1 mRNA increased Rb mRNA expression and enhanced myoblast differentiation into myotubes. Conclusions Our findings suggest that the FL-Irs-1 transcript regulates myogenic differentiation as a regulatory RNA in myoblasts. Electronic supplementary material The online version of this article (doi:10.1186/s12860-015-0054-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hikaru Nagano
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan. .,Facalty of Nutritional Science, Sagami Women's University, Sagamihara, 252-0383, Japan.
| | - Naoko Yamagishi
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Chisato Tomida
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Chiaki Yano
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Kana Aibara
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Shohei Kohno
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Tomoki Abe
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Ayako Ohno
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Katsuya Hirasaka
- Graduate school of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki, 852-8521, Japan.
| | - Yuushi Okumura
- Facalty of Nutritional Science, Sagami Women's University, Sagamihara, 252-0383, Japan.
| | - Edward M Mills
- Division of Pharmacology/Toxicology, College of Pharmacy, University of Texas at Austin, Austin, Texas.
| | - Takeshi Nikawa
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Shigetada Teshima-Kondo
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
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2852
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Integrated genomic characterization of papillary thyroid carcinoma. Cell 2015; 159:676-90. [PMID: 25417114 DOI: 10.1016/j.cell.2014.09.050] [Citation(s) in RCA: 2020] [Impact Index Per Article: 224.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 09/16/2014] [Accepted: 09/23/2014] [Indexed: 02/07/2023]
Abstract
Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Here, we describe the genomic landscape of 496 PTCs. We observed a low frequency of somatic alterations (relative to other carcinomas) and extended the set of known PTC driver alterations to include EIF1AX, PPM1D, and CHEK2 and diverse gene fusions. These discoveries reduced the fraction of PTC cases with unknown oncogenic driver from 25% to 3.5%. Combined analyses of genomic variants, gene expression, and methylation demonstrated that different driver groups lead to different pathologies with distinct signaling and differentiation characteristics. Similarly, we identified distinct molecular subgroups of BRAF-mutant tumors, and multidimensional analyses highlighted a potential involvement of oncomiRs in less-differentiated subgroups. Our results propose a reclassification of thyroid cancers into molecular subtypes that better reflect their underlying signaling and differentiation properties, which has the potential to improve their pathological classification and better inform the management of the disease.
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Affiliation(s)
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- Cancer Genome Atlas Program Office, National Cancer Institute at NIH, 31 Center Drive, Bldg. 31, Suite 3A20, Bethesda MD 20892, USA.
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2853
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Abstract
Most RNAs transcribed in mammalian cells lack protein-coding sequences. Among them is a vast family of long (>200 nt) noncoding (lnc)RNAs. LncRNAs can modulate cellular protein expression patterns by influencing the transcription of many genes, the post-transcriptional fate of mRNAs and ncRNAs, and the turnover and localization of proteins. Given the broad impact of lncRNAs on gene regulation, there is escalating interest in elucidating the mechanisms that govern the steady-state levels of lncRNAs. In this review, we summarize our current knowledge of the factors and mechanisms that modulate mammalian lncRNA stability.
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2854
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Saitoh M. Epithelial-mesenchymal transition is regulated at post-transcriptional levels by transforming growth factor-β signaling during tumor progression. Cancer Sci 2015; 106:481-8. [PMID: 25664423 PMCID: PMC4452147 DOI: 10.1111/cas.12630] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/28/2015] [Accepted: 02/03/2015] [Indexed: 12/18/2022] Open
Abstract
Transforming growth factor (TGF)-β acts as a tumor suppressor during cancer initiation, but as a tumor promoter during tumor progression. It has become increasingly clear that TGF-β plays fundamental roles in multiple steps of tumor progression, including epithelial-mesenchymal transition (EMT). The EMT, first described by developmental biologists at the beginning of the 1980s, plays crucial roles in appropriate embryonic development, but also functions in adults during wound healing, organ fibrosis, and tumor progression. During EMT, epithelial cells lose their epithelial polarity and acquire mesenchymal phenotypes, endowing them with migratory and invasive properties. Many secreted polypeptides are implicated in this process, and act in a sequential or cooperative manner. TGF-β induces EMT by propagating intracellular signaling pathways and activating transcriptional factors. Here, I discuss new insights into the molecular mechanisms underlying induction of EMT by TGF-β in cooperation with Ras or growth factors, along with the signals that induce EMT through transcriptional and post-transcriptional regulation.
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Affiliation(s)
- Masao Saitoh
- Department of Biochemistry, Center for Medical Education and Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Japan
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2855
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Interferon-alpha competing endogenous RNA network antagonizes microRNA-1270. Cell Mol Life Sci 2015; 72:2749-61. [PMID: 25746225 PMCID: PMC4477080 DOI: 10.1007/s00018-015-1875-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 12/18/2022]
Abstract
A new form of circuitry for gene regulation has been identified in which RNAs can crosstalk by competing for shared microRNAs (miRNAs). Such competing endogenous RNAs (ceRNAs) form a network via shared miRNA response elements (MREs) to antagonize miRNA function. We previously reported natural antisense RNA (AS) as an important modulator of interferon-α1 (IFN-α1) mRNA levels by promoting IFN-α1 mRNA stability. We show that IFN-α1 AS forms a ceRNA network with specific IFN-α AS (IFN-α7/-α8/-α10/-α14) and mRNA (IFN-α8/-α10/-α14/-α17) subtypes from the IFN-α gene (IFNA) family to antagonize miRNA-1270 (miR-1270), thereby modulating IFN-α1 mRNA levels. Bioinformatic analysis demonstrated that IFN-α1 AS harbors multiple miR-1270 MREs (MRE-1270s), whose presence was substantiated by miR-1270 overexpression and transfection of antimiR-1270. The antimiR-1270, complementary to the miR-1270 seed region, revealed that IFN-α1 AS likely shares the MRE-1270 with IFN-α1 mRNA and specific IFN-α AS and mRNA subtypes. Subsequent bioinformatic analysis for MRE-1270s showed that IFN-α1 AS and other RNA subtypes shared the 6-mer MRE-1270 site. Further MRE-mapping demonstrated that the total number of MRE-1270s in IFN-α1 AS accounted for approximately 30 % of the miR-1270 population. AntimiR-1270 transfection also caused specific de-repression of five cellular mRNAs, including that of CAPRIN1. These results suggest that IFN-α1 AS, together with specific IFN-α AS and mRNA subtypes, as well as the five cellular mRNAs, participate as competing molecules in the ceRNA network against miR-1270. This coordinated regulatory architecture suggests a vital function for the innate immune system in maintaining precise physiological type I IFN levels via post-transcriptional regulatory mechanisms.
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2856
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Nyayanit D, Gadgil CJ. Mathematical modeling of combinatorial regulation suggests that apparent positive regulation of targets by miRNA could be an artifact resulting from competition for mRNA. RNA (NEW YORK, N.Y.) 2015; 21:307-319. [PMID: 25576498 PMCID: PMC4338329 DOI: 10.1261/rna.046862.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 11/10/2014] [Indexed: 06/04/2023]
Abstract
MicroRNAs bind to and regulate the abundance and activity of target messenger RNA through sequestration, enhanced degradation, and suppression of translation. Although miRNA have a predominantly negative effect on the target protein concentration, several reports have demonstrated a positive effect of miRNA, i.e., increase in target protein concentration on miRNA overexpression and decrease in target concentration on miRNA repression. miRNA-target pair-specific effects such as protection of mRNA degradation owing to miRNA binding can explain some of these effects. However, considering such pairs in isolation might be an oversimplification of the RNA biology, as it is known that one miRNA interacts with several targets, and conversely target mRNA are subject to regulation by several miRNAs. We formulate a mathematical model of this combinatorial regulation of targets by multiple miRNA. Through mathematical analysis and numerical simulations of this model, we show that miRNA that individually have a negative effect on their targets may exhibit an apparently positive net effect when the concentration of one miRNA is experimentally perturbed by repression/overexpression in such a multi-miRNA multitarget situation. We show that this apparent unexpected effect is due to competition and will not be observed when miRNA interact noncompetitively with the target mRNA. This result suggests that some of the observed unusual positive effects of miRNA may be due to the combinatorial complexity of the system rather than due to any inherently unusual positive effect of the miRNA on its target.
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Affiliation(s)
- Dimpal Nyayanit
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune 411008, India Academy of Scientific and Innovative Research, New Delhi 110001, India
| | - Chetan J Gadgil
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune 411008, India Academy of Scientific and Innovative Research, New Delhi 110001, India CSIR-Institute of Genomics and Integrative Biology, New Delhi 110020, India
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2857
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Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit. Proc Natl Acad Sci U S A 2015; 112:3158-63. [PMID: 25713348 DOI: 10.1073/pnas.1413896112] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Competing endogenous RNAs (ceRNAs) cross-regulate each other at the posttranscriptional level by titrating shared microRNAs (miRNAs). Here, we established a computational model to quantitatively describe a minimum ceRNA network and experimentally validated our model predictions in cultured human cells by using synthetic gene circuits. We demonstrated that the range and strength of ceRNA regulation are largely determined by the relative abundance and the binding strength of miRNA and ceRNAs. We found that a nonreciprocal competing effect between partially and perfectly complementary targets is mainly due to different miRNA loss rates in these two types of regulations. Furthermore, we showed that miRNA-like off targets with high expression levels and strong binding sites significantly diminish the RNA interference efficiency, but the effect caused by high expression levels could be compensated by introducing more small interference RNAs (siRNAs). Thus, our results provided a quantitative understanding of ceRNA cross-regulation via shared miRNA and implied an siRNA design strategy to reduce the siRNA off-target effect in mammalian cells.
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2858
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Abstract
tRNAs are widely believed to segregate into two classes, I and II. Computational analysis of eukaryotic tRNA entries in Genomic tRNA Database, however, leads to new, albeit paradoxical, presence of more than a thousand class-I tRNAs with uncharacteristic long variable arms (V-arms), like in class-II. Out of 62,202 tRNAs from 69 eukaryotes, as many as 1431 class-I tRNAs have these novel extended V-arms, and we refer to them as paradoxical tRNAs (pxtRNAs). A great majority of these 1431 pxtRNA genes are located in intergenic regions, about 18% embedded in introns of genes or ESTs, and just one in 3'UTR. A check on the conservations of 2D and 3D base pairs for each position of these pxtRNAs reveals a few variations, but they seem to have almost all the known features (already known identity and conserved elements of tRNA). Analyses of the A-Box and B-Box of these pxtRNA genes in eukaryotes display salient deviations from the previously annotated conserved features of the standard promoters, whereas the transcription termination signals are just canonical and non-canonical runs of thymidine, similar to the ones in standard tRNA genes. There is just one such pxtRNA(ProAGG) gene in the entire human genome, and the availability of data allows epigenetic analysis of this human pxtRNA(ProAGG) in three different cell lines, H1 hESC, K562, and NHEK, to assess the level of its expression. Histone acetylation and methylation of this lone pxtRNA(ProAGG) gene in human differ from that of the nine standard human tRNA(ProAGG) genes. The V-arm nucleotide sequences and their secondary structures in pxtRNA differ from that of class-II tRNA. Considering these differences, hypotheses of alternative splicing, non-canonical intron and gene transfer are examined to partially improve the Cove scores of these pxtRNAs and to critically question their antecedence and novelty.
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Affiliation(s)
- Sanga Mitra
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Arpa Samadder
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Pijush Das
- b Cancer Biology & Inflammatory Disorder Division , Indian Institute of Chemical Biology , Kolkata , India
| | - Smarajit Das
- c Department of Medical Biochemistry and Cell Biology , Institute of Biomedicine, University of Gothenburg , Gothenburg , Sweden
| | - Jayprokas Chakrabarti
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India.,d Gyanxet, BF 286 Salt Lake, Kolkata , India
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2859
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2860
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Large noncoding RNAs are promising regulators in embryonic stem cells. J Genet Genomics 2015; 42:99-105. [PMID: 25819086 DOI: 10.1016/j.jgg.2015.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 12/31/2022]
Abstract
Embryonic stem cells (ESCs) hold great promises for treating and studying numerous devastating diseases. The molecular basis of their potential is not completely understood. Large noncoding RNAs (lncRNAs) are an important class of gene regulators that play essential roles in a variety of physiologic and pathologic processes. Dozens of lncRNAs are now identified to control ESC self-renewal and differentiation. Research on lncRNAs may provide novel insights into manipulating the cell fate or reprogramming somatic cells into induced pluripotent stem cells (iPSCs). In this review, we summarize the recent research efforts in identifying functional lncRNAs and understanding how they act in ESCs, and discuss various future directions of this field.
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2861
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Ounzain S, Micheletti R, Beckmann T, Schroen B, Alexanian M, Pezzuto I, Crippa S, Nemir M, Sarre A, Johnson R, Dauvillier J, Burdet F, Ibberson M, Guigó R, Xenarios I, Heymans S, Pedrazzini T. Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs. Eur Heart J 2015; 36:353-68a. [PMID: 24786300 PMCID: PMC4320320 DOI: 10.1093/eurheartj/ehu180] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/14/2014] [Accepted: 04/06/2014] [Indexed: 12/30/2022] Open
Abstract
AIM Heart disease is recognized as a consequence of dysregulation of cardiac gene regulatory networks. Previously, unappreciated components of such networks are the long non-coding RNAs (lncRNAs). Their roles in the heart remain to be elucidated. Thus, this study aimed to systematically characterize the cardiac long non-coding transcriptome post-myocardial infarction and to elucidate their potential roles in cardiac homoeostasis. METHODS AND RESULTS We annotated the mouse transcriptome after myocardial infarction via RNA sequencing and ab initio transcript reconstruction, and integrated genome-wide approaches to associate specific lncRNAs with developmental processes and physiological parameters. Expression of specific lncRNAs strongly correlated with defined parameters of cardiac dimensions and function. Using chromatin maps to infer lncRNA function, we identified many with potential roles in cardiogenesis and pathological remodelling. The vast majority was associated with active cardiac-specific enhancers. Importantly, oligonucleotide-mediated knockdown implicated novel lncRNAs in controlling expression of key regulatory proteins involved in cardiogenesis. Finally, we identified hundreds of human orthologues and demonstrate that particular candidates were differentially modulated in human heart disease. CONCLUSION These findings reveal hundreds of novel heart-specific lncRNAs with unique regulatory and functional characteristics relevant to maladaptive remodelling, cardiac function and possibly cardiac regeneration. This new class of molecules represents potential therapeutic targets for cardiac disease. Furthermore, their exquisite correlation with cardiac physiology renders them attractive candidate biomarkers to be used in the clinic.
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Affiliation(s)
- Samir Ounzain
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, CH-1011 Lausanne, Switzerland
| | - Rudi Micheletti
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, CH-1011 Lausanne, Switzerland
| | - Tal Beckmann
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, CH-1011 Lausanne, Switzerland
| | - Blanche Schroen
- Centre for Heart Failure Research, Cardiovascular Research Institute, Maastricht University, Maastricht, The Netherlands
| | - Michael Alexanian
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, CH-1011 Lausanne, Switzerland
| | - Iole Pezzuto
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, CH-1011 Lausanne, Switzerland
| | - Stefania Crippa
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, CH-1011 Lausanne, Switzerland
| | - Mohamed Nemir
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, CH-1011 Lausanne, Switzerland
| | - Alexandre Sarre
- Cardiovascular Assessment Facility, University of Lausanne, Lausanne, Switzerland
| | | | - Jérôme Dauvillier
- VitalIT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Frédéric Burdet
- VitalIT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Mark Ibberson
- VitalIT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Ioannis Xenarios
- VitalIT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Stephane Heymans
- Centre for Heart Failure Research, Cardiovascular Research Institute, Maastricht University, Maastricht, The Netherlands
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, CH-1011 Lausanne, Switzerland
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2862
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Wang P, Liu YH, Yao YL, Li Z, Li ZQ, Ma J, Xue YX. Long non-coding RNA CASC2 suppresses malignancy in human gliomas by miR-21. Cell Signal 2015; 27:275-82. [DOI: 10.1016/j.cellsig.2014.11.011] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/02/2014] [Accepted: 11/08/2014] [Indexed: 01/07/2023]
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2863
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Cao C, Sun J, Zhang D, Guo X, Xie L, Li X, Wu D, Liu L. The long intergenic noncoding RNA UFC1, a target of MicroRNA 34a, interacts with the mRNA stabilizing protein HuR to increase levels of β-catenin in HCC cells. Gastroenterology 2015; 148:415-26.e18. [PMID: 25449213 DOI: 10.1053/j.gastro.2014.10.012] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 09/24/2014] [Accepted: 10/16/2014] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Altered activities of long noncoding RNAs (lncRNAs) have been associated with cancer development. We investigated the mechanisms by which the long intergenic noncoding RNA UFC1 (lincRNA-UFC1) promotes progression of hepatocellular carcinoma (HCC), using human tissues and cell lines. METHODS We used microarrays to compare expression profiles of lncRNAs in HCC samples and adjacent nontumor tissues (controls) from 7 patients. HCC and nontumor tissues were collected from 2006 through 2012 from patients in Guangzhou, China. We used quantitative real-time polymerase chain reaction to measure levels of lincRNA-UFC1 in tissues from 49 patients, and in situ hybridization to measure levels in samples from 131 patients; clinical data were collected from patients for up to 5 years. The lincRNA-UFC1 was expressed transgenically, or knocked down with short hairpin RNAs, in BEL-7402, SK-Hep1, Huh7, and MHCC-97H HCC cell lines; luciferase reporter and RNA immunoprecipitation and pull-down assays were performed. We also analyzed growth of xenograft tumors from these cells in BALB/c nude mice. RESULTS Levels of the lincRNA-UFC1 were increased in HCC tissues compared with controls, and associated with tumor size, Barcelona Clinic Liver Cancer stage, and patient outcomes. Transgenic expression of the lincRNA-UFC1 in HCC cells promoted their proliferation and cell-cycle progression and inhibited apoptosis, whereas short hairpin RNA knockdown of lincRNA-UFC1 had opposite effects. Xenograft tumors grown from cells overexpressing lincRNA-UFC1 had larger mean volumes and weights, and formed more rapidly, than tumors grown from control cells. Tumors grown from lincRNA-UFC1 knockdown were smaller than controls. The lincRNA-UFC1 interacted directly with the messenger RNA (mRNA) stabilizing protein HuR (encoded by ELAVL1) to increase levels of β-catenin mRNA (encoded by CTNNB1) and protein. Levels of lincRNA-UFC1 correlated with those of β-catenin in HCC tissues. In contrast, there was a negative correlation between levels of microRNA 34a and lincRNA-UFC1 in HCC tissues; microRNA 34a reduced the stability of lincRNA-UFC1. CONCLUSIONS The lincRNA-UFC1, a target of microRNA 34a, promotes proliferation and reduces apoptosis in HCC cells to promote growth of xenograft tumors in mice. It interacts directly with the mRNA stabilizing protein HuR to regulate levels of β-catenin in HCC cells.
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Affiliation(s)
- Chuanhui Cao
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China; Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jingyuan Sun
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China; Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dongyan Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuejun Guo
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Liwei Xie
- Center of Molecular Medicine, University of Georgia, Athens, Georgia; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Xin Li
- Cancer Research Institute, Southern Medical University, Guangzhou, China
| | - Dehua Wu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Li Liu
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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2864
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Sun T, Wong N. Transforming growth factor-β-induced long noncoding RNA promotes liver cancer metastasis via RNA-RNA crosstalk. Hepatology 2015; 61:722-4. [PMID: 25380484 DOI: 10.1002/hep.27599] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Tingting Sun
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong
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2865
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Mangano A, Lianos GD, Mangano A, Boni L, Dionigi G. Intratumor heterogeneity: origins, clinical significance and optimal strategies for cancer treatment. Future Oncol 2015; 11:561-4. [DOI: 10.2217/fon.14.296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Alberto Mangano
- 1st Division of General Surgery, Department of Human Morphology & Surgical Sciences, Insubria University Varese-Como, Italy
| | - Georgios D Lianos
- Department of Surgery Ioannina University Hospital, Ioannina, Greece
| | | | - Luigi Boni
- 1st Division of General Surgery, Department of Human Morphology & Surgical Sciences, Insubria University Varese-Como, Italy
| | - Gianlorenzo Dionigi
- 1st Division of General Surgery, Department of Human Morphology & Surgical Sciences, Insubria University Varese-Como, Italy
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2866
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Poliseno L, Pandolfi PP. PTEN ceRNA networks in human cancer. Methods 2015; 77-78:41-50. [PMID: 25644446 DOI: 10.1016/j.ymeth.2015.01.013] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/19/2015] [Accepted: 01/21/2015] [Indexed: 12/14/2022] Open
Abstract
In multiple human cancer types, a close link exists between the expression levels of Phosphatase and Tensin Homolog deleted on chromosome 10 (PTEN) and its oncosuppressive activities. Therefore, an in depth understanding of the molecular mechanisms by which PTEN expression is modulated is crucial in order to achieve a comprehensive knowledge of its biological roles. In recent years, the competition between PTEN mRNA and other RNAs for shared microRNA molecules has emerged as one such mechanism and has brought into focus the coding-independent activities of PTEN and other mRNAs. In this review article, we examine the competing endogenous RNA (ceRNA) partners of PTEN that have been identified so far. We also discuss how PTEN-centered ceRNA networks can contribute to a deeper understanding of PTEN function and tumorigenesis.
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Affiliation(s)
- Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori, Pisa, Italy; Institute of Clinical Physiology, CNR, Pisa, Italy.
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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2867
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Chu T, Mouillet JF, Hood BL, Conrads TP, Sadovsky Y. The assembly of miRNA-mRNA-protein regulatory networks using high-throughput expression data. ACTA ACUST UNITED AC 2015; 31:1780-7. [PMID: 25619993 DOI: 10.1093/bioinformatics/btv038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 01/18/2015] [Indexed: 11/13/2022]
Abstract
MOTIVATION Inference of gene regulatory networks from high throughput measurement of gene and protein expression is particularly attractive because it allows the simultaneous discovery of interactive molecular signals for numerous genes and proteins at a relatively low cost. RESULTS We developed two score-based local causal learning algorithms that utilized the Markov blanket search to identify direct regulators of target mRNAs and proteins. These two algorithms were specifically designed for integrated high throughput RNA and protein data. Simulation study showed that these algorithms outperformed other state-of-the-art gene regulatory network learning algorithms. We also generated integrated miRNA, mRNA, and protein expression data based on high throughput analysis of primary trophoblasts, derived from term human placenta and cultured under standard or hypoxic conditions. We applied the new algorithms to these data and identified gene regulatory networks for a set of trophoblastic proteins found to be differentially expressed under the specified culture conditions.
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Affiliation(s)
- Tianjiao Chu
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213 USA, Women's Health Integrated Research Center at Inova Health System, Annandale, VA, 22003 USA and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213 USA
| | - Jean-Francois Mouillet
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213 USA, Women's Health Integrated Research Center at Inova Health System, Annandale, VA, 22003 USA and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213 USA
| | - Brian L Hood
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213 USA, Women's Health Integrated Research Center at Inova Health System, Annandale, VA, 22003 USA and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213 USA
| | - Thomas P Conrads
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213 USA, Women's Health Integrated Research Center at Inova Health System, Annandale, VA, 22003 USA and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213 USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213 USA, Women's Health Integrated Research Center at Inova Health System, Annandale, VA, 22003 USA and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213 USA Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213 USA, Women's Health Integrated Research Center at Inova Health System, Annandale, VA, 22003 USA and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213 USA
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2868
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Zheng W, Sai W, Yao M, Gu H, Yao Y, Qian Q, Yao D. Silencing clusterin gene transcription on effects of multidrug resistance reversing of human hepatoma HepG2/ADM cells. Tumour Biol 2015. [PMID: 25600802 DOI: 10.1007/s13277-015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abnormal clusterin (CLU) expression is associated with multidrug resistance (MDR) of hepatocellular carcinoma (HCC). In the present study, the CLU expression was analyzed in human hepatoma cells and chemoresistant counterpart HepG2/ADM cells. Compared with L02 cells, the overexpression of cellular CLU was identified in HepG2, HepG2/ADM, SMMC7721, Hep3B ,and PLC cells and relatively lower expression in Bel-7404, SNU-739, and MHCC97H cells. Specific short hairpin RNAs (shRNAs) to silence CLU gene transcription were designed, and the most effective sequences were screened. After the HepG2/ADM cells transfected with shRNA-1, the inhibition of CLU expression was 73.68 % at messenger RNA (mRNA) level by real-time quantitative RT-PCR with obvious enhancement in cell chemosensitivity, increasing apoptosis induced by doxorubicin using fluorescence kit, and Rh-123 retention qualified with flow cytometry. Knockdown CLU also significantly decreased the drug efflux pump activity through the depression of MDR1/P-glycoprotein (q = 11.739, P < 0.001). Moreover, silencing CLU led to downregulation of β-catenin (q = 13.544, P = 0.001), suggesting that downregulation of CLU might be a key point to reverse multidrug resistance of HepG2/ADM cells.
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Affiliation(s)
- Wenjie Zheng
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 West Temple Road, Nantong, 226001, Jiangsu Province, China
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2869
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Hirata H, Hinoda Y, Shahryari V, Deng G, Nakajima K, Tabatabai ZL, Ishii N, Dahiya R. Long Noncoding RNA MALAT1 Promotes Aggressive Renal Cell Carcinoma through Ezh2 and Interacts with miR-205. Cancer Res 2015; 75:1322-31. [PMID: 25600645 DOI: 10.1158/0008-5472.can-14-2931] [Citation(s) in RCA: 458] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/26/2014] [Indexed: 01/17/2023]
Abstract
Recently, long noncoding RNAs (lncRNA) have emerged as new gene regulators and prognostic markers in several cancers, including renal cell carcinoma (RCC). In this study, we investigated the contributions of the lncRNA MALAT1 in RCC with a specific focus on its transcriptional regulation and its interactions with Ezh2 and miR-205. We found that MALAT1 expression was higher in human RCC tissues, where it was associated with reduced patient survival. MALAT1 silencing decreased RCC cell proliferation and invasion and increased apoptosis. Mechanistic investigations showed that MALAT1 was transcriptionally activated by c-Fos and that it interacted with Ezh2. After MALAT1 silencing, E-cadherin expression was increased, whereas β-catenin expression was decreased through Ezh2. Reciprocal interaction between MALAT1 and miR-205 was also observed. Lastly, MALAT1 bound Ezh2 and oncogenesis facilitated by MALAT1 was inhibited by Ezh2 depletion, thereby blocking epithelial-mesenchymal transition via E-cadherin recovery and β-catenin downregulation. Overall, our findings illuminate how overexpression of MALAT1 confers an oncogenic function in RCC that may offer a novel theranostic marker in this disease.
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Affiliation(s)
- Hiroshi Hirata
- Department of Urology, San Francisco Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California
| | - Yuji Hinoda
- Department of Oncology and Laboratory Medicine, Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | - Varahram Shahryari
- Department of Urology, San Francisco Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California
| | - Guoren Deng
- Department of Urology, San Francisco Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California
| | - Koichi Nakajima
- Department of Urology, Toho University Faculty of Medicine, Tokyo, Japan
| | - Z Laura Tabatabai
- Department of Pathology, San Francisco Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California
| | - Nobuhisa Ishii
- Department of Urology, Toho University Faculty of Medicine, Tokyo, Japan
| | - Rajvir Dahiya
- Department of Urology, San Francisco Veterans Affairs Medical Center and University of California at San Francisco, San Francisco, California.
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2870
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Yan B, Yao J, Liu JY, Li XM, Wang XQ, Li YJ, Tao ZF, Song YC, Chen Q, Jiang Q. lncRNA-MIAT regulates microvascular dysfunction by functioning as a competing endogenous RNA. Circ Res 2015; 116:1143-56. [PMID: 25587098 DOI: 10.1161/circresaha.116.305510] [Citation(s) in RCA: 479] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RATIONALE Pathological angiogenesis is a critical component of diseases, such as ocular disorders, cancers, and atherosclerosis. It is usually caused by the abnormal activity of biological processes, such as cell proliferation, cell motility, immune, or inflammation response. Long noncoding RNAs (lncRNAs) have emerged as critical regulators of these biological processes. However, the role of lncRNA in diabetes mellitus-induced microvascular dysfunction is largely unknown. OBJECTIVE To elucidate whether lncRNA-myocardial infarction-associated transcript (MIAT) is involved in diabetes mellitus-induced microvascular dysfunction. METHODS AND RESULTS Using quantitative polymerase chain reaction, we demonstrated increased expression of lncRNA-MIAT in diabetic retinas and endothelial cells cultured in high glucose medium. Visual electrophysiology examination, TUNEL staining, retinal trypsin digestion, vascular permeability assay, and in vitro studies revealed that MIAT knockdown obviously ameliorated diabetes mellitus-induced retinal microvascular dysfunction in vivo, and inhibited endothelial cell proliferation, migration, and tube formation in vitro. Bioinformatics analysis, luciferase assay, RNA immunoprecipitation, and in vitro studies revealed that MIAT functioned as a competing endogenous RNA, and formed a feedback loop with vascular endothelial growth factor and miR-150-5p to regulate endothelial cell function. CONCLUSIONS This study highlights the involvement of lncRNA-MIAT in pathological angiogenesis and facilitates the development of lncRNA-directed diagnostics and therapeutics against neovascular diseases.
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Affiliation(s)
- Biao Yan
- From the Department of Central Laboratory, Eye Hospital (B.Y., J.-Y.L., J.Y., X.-M.L., X.-Q.W., Y.-J.L., Z.-F.T., Y.-C.S., Q.J.), Department of Ophthalmology, The Fourth School of Clinical Medicine (B.Y., J.Y., Q.J.), and Department of Pathophysiology, School of Basic Medical Sciences (Q.C.), Nanjing Medical University, Nanjing, China.
| | - Jin Yao
- From the Department of Central Laboratory, Eye Hospital (B.Y., J.-Y.L., J.Y., X.-M.L., X.-Q.W., Y.-J.L., Z.-F.T., Y.-C.S., Q.J.), Department of Ophthalmology, The Fourth School of Clinical Medicine (B.Y., J.Y., Q.J.), and Department of Pathophysiology, School of Basic Medical Sciences (Q.C.), Nanjing Medical University, Nanjing, China
| | - Jing-Yu Liu
- From the Department of Central Laboratory, Eye Hospital (B.Y., J.-Y.L., J.Y., X.-M.L., X.-Q.W., Y.-J.L., Z.-F.T., Y.-C.S., Q.J.), Department of Ophthalmology, The Fourth School of Clinical Medicine (B.Y., J.Y., Q.J.), and Department of Pathophysiology, School of Basic Medical Sciences (Q.C.), Nanjing Medical University, Nanjing, China
| | - Xiu-Miao Li
- From the Department of Central Laboratory, Eye Hospital (B.Y., J.-Y.L., J.Y., X.-M.L., X.-Q.W., Y.-J.L., Z.-F.T., Y.-C.S., Q.J.), Department of Ophthalmology, The Fourth School of Clinical Medicine (B.Y., J.Y., Q.J.), and Department of Pathophysiology, School of Basic Medical Sciences (Q.C.), Nanjing Medical University, Nanjing, China
| | - Xiao-Qun Wang
- From the Department of Central Laboratory, Eye Hospital (B.Y., J.-Y.L., J.Y., X.-M.L., X.-Q.W., Y.-J.L., Z.-F.T., Y.-C.S., Q.J.), Department of Ophthalmology, The Fourth School of Clinical Medicine (B.Y., J.Y., Q.J.), and Department of Pathophysiology, School of Basic Medical Sciences (Q.C.), Nanjing Medical University, Nanjing, China
| | - Yu-Jie Li
- From the Department of Central Laboratory, Eye Hospital (B.Y., J.-Y.L., J.Y., X.-M.L., X.-Q.W., Y.-J.L., Z.-F.T., Y.-C.S., Q.J.), Department of Ophthalmology, The Fourth School of Clinical Medicine (B.Y., J.Y., Q.J.), and Department of Pathophysiology, School of Basic Medical Sciences (Q.C.), Nanjing Medical University, Nanjing, China
| | - Zhi-Fu Tao
- From the Department of Central Laboratory, Eye Hospital (B.Y., J.-Y.L., J.Y., X.-M.L., X.-Q.W., Y.-J.L., Z.-F.T., Y.-C.S., Q.J.), Department of Ophthalmology, The Fourth School of Clinical Medicine (B.Y., J.Y., Q.J.), and Department of Pathophysiology, School of Basic Medical Sciences (Q.C.), Nanjing Medical University, Nanjing, China
| | - Yu-Chen Song
- From the Department of Central Laboratory, Eye Hospital (B.Y., J.-Y.L., J.Y., X.-M.L., X.-Q.W., Y.-J.L., Z.-F.T., Y.-C.S., Q.J.), Department of Ophthalmology, The Fourth School of Clinical Medicine (B.Y., J.Y., Q.J.), and Department of Pathophysiology, School of Basic Medical Sciences (Q.C.), Nanjing Medical University, Nanjing, China
| | - Qi Chen
- From the Department of Central Laboratory, Eye Hospital (B.Y., J.-Y.L., J.Y., X.-M.L., X.-Q.W., Y.-J.L., Z.-F.T., Y.-C.S., Q.J.), Department of Ophthalmology, The Fourth School of Clinical Medicine (B.Y., J.Y., Q.J.), and Department of Pathophysiology, School of Basic Medical Sciences (Q.C.), Nanjing Medical University, Nanjing, China
| | - Qin Jiang
- From the Department of Central Laboratory, Eye Hospital (B.Y., J.-Y.L., J.Y., X.-M.L., X.-Q.W., Y.-J.L., Z.-F.T., Y.-C.S., Q.J.), Department of Ophthalmology, The Fourth School of Clinical Medicine (B.Y., J.Y., Q.J.), and Department of Pathophysiology, School of Basic Medical Sciences (Q.C.), Nanjing Medical University, Nanjing, China.
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2871
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Zhang Y, Xie S, Xu H, Qu L. CLIP: viewing the RNA world from an RNA-protein interactome perspective. SCIENCE CHINA-LIFE SCIENCES 2015; 58:75-88. [DOI: 10.1007/s11427-014-4764-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/13/2014] [Indexed: 12/20/2022]
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2872
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Mione M, Bosserhoff A. MicroRNAs in melanocyte and melanoma biology. Pigment Cell Melanoma Res 2015; 28:340-54. [PMID: 25515738 DOI: 10.1111/pcmr.12346] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/15/2014] [Indexed: 12/18/2022]
Abstract
The importance of microRNAs as key molecular components of cellular processes is now being recognized. Recent reports have shown that microRNAs regulate processes as diverse as protein expression and nuclear functions inside cells and are able to signal extracellularly, delivered via exosomes, to influence cell fate at a distance. The versatility of microRNAs as molecular tools inspires the design of novel strategies to control gene expression, protein stability, DNA repair and chromatin accessibility that may prove very useful for therapeutic approaches due to the extensive manageability of these small molecules. However, we still lack a comprehensive understanding of the microRNA network and its interactions with the other layers of regulatory elements in cellular and extracellular functions. This knowledge may be necessary before we exploit microRNA versatility in therapeutic settings. To identify rules of interactions between microRNAs and other regulatory systems, we begin by reviewing microRNA activities in a single cell type: the melanocyte, from development to disease.
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Affiliation(s)
- Marina Mione
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggestein-Leopoldshafen, Germany
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2873
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Ye LEC, Zhu DEX, Qiu JJ, Xu J, Wei Y. Involvement of long non-coding RNA in colorectal cancer: From benchtop to bedside (Review). Oncol Lett 2015; 9:1039-1045. [PMID: 25663854 PMCID: PMC4315074 DOI: 10.3892/ol.2015.2846] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 12/12/2014] [Indexed: 01/30/2023] Open
Abstract
Colorectal cancer (CRC) is one of the greatest threats to public health. Recent advances in whole-genome transcriptome analyses have enabled the identification of numerous members of a novel class of non-coding (nc)RNA, long ncRNA (lncRNA), which is broadly defined as RNA molecules that are >200 nt in length and lacking an open reading frame. In the present review, all lncRNAs associated with CRC are briefly summarized, with a particular focus on their potential roles as clinical biomarkers. CRC-associated lncRNAs involved in the underlying mechanisms of CRC progression are also initially included. This should benefit the development of novel markers and effective therapeutic targets for patients with CRC.
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Affiliation(s)
- LE-Chi Ye
- Department of Oncological Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, P.R. China
| | - DE-Xiang Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Jun-Jun Qiu
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, P.R. China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Ye Wei
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
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2874
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Zhang C, Peng G. Non-coding RNAs: An emerging player in DNA damage response. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 763:202-11. [DOI: 10.1016/j.mrrev.2014.11.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 01/02/2023]
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2875
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Noncoding RNA Expression During Viral Infection: The Long and the Short of It. MICRORNAS AND OTHER NON-CODING RNAS IN INFLAMMATION 2015. [PMCID: PMC7123390 DOI: 10.1007/978-3-319-13689-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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2876
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Nitzan M, Steiman-Shimony A, Altuvia Y, Biham O, Margalit H. Interactions between distant ceRNAs in regulatory networks. Biophys J 2014; 106:2254-66. [PMID: 24853754 PMCID: PMC4052263 DOI: 10.1016/j.bpj.2014.03.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/17/2014] [Accepted: 03/25/2014] [Indexed: 12/14/2022] Open
Abstract
Competing endogenous RNAs (ceRNAs) were recently introduced as RNA transcripts that affect each other's expression level through competition for their microRNA (miRNA) coregulators. This stems from the bidirectional effects between miRNAs and their target RNAs, where a change in the expression level of one target affects the level of the miRNA regulator, which in turn affects the level of other targets. By the same logic, miRNAs that share targets compete over binding to their common targets and therefore also exhibit ceRNA-like behavior. Taken together, perturbation effects could propagate in the posttranscriptional regulatory network through a path of coregulated targets and miRNAs that share targets, suggesting the existence of distant ceRNAs. Here we study the prevalence of distant ceRNAs and their effect in cellular networks. Analyzing the network of miRNA-target interactions deciphered experimentally in HEK293 cells, we show that it is a dense, intertwined network, suggesting that many nodes can act as distant ceRNAs of one another. Indeed, using gene expression data from a perturbation experiment, we demonstrate small, yet statistically significant, changes in gene expression caused by distant ceRNAs in that network. We further characterize the magnitude of the propagated perturbation effect and the parameters affecting it by mathematical modeling and simulations. Our results show that the magnitude of the effect depends on the generation and degradation rates of involved miRNAs and targets, their interaction rates, the distance between the ceRNAs and the topology of the network. Although demonstrated for a miRNA-mRNA regulatory network, our results offer what to our knowledge is a new view on various posttranscriptional cellular networks, expanding the concept of ceRNAs and implying possible distant cross talk within the network, with consequences for the interpretation of indirect effects of gene perturbation.
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Affiliation(s)
- Mor Nitzan
- Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, Israel; Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avital Steiman-Shimony
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ofer Biham
- Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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2877
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Zhou M, Wang X, Li J, Hao D, Wang Z, Shi H, Han L, Zhou H, Sun J. Prioritizing candidate disease-related long non-coding RNAs by walking on the heterogeneous lncRNA and disease network. MOLECULAR BIOSYSTEMS 2014; 11:760-9. [PMID: 25502053 DOI: 10.1039/c4mb00511b] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Accumulated evidence has shown that long non-coding RNAs (lncRNA) act as a widespread layer in gene regulatory networks and are involved in a wide range of biological processes. The dysregulation of lncRNA has been implicated in various complex human diseases. Although several computational methods have been developed to predict disease-related lncRNA, this still remains a considerable challenging task. In this study, we tried to construct an lncRNA-lncRNA crosstalk network by examining the significant co-occurrence of shared miRNA response elements on lncRNA transcripts from the competing endogenous RNAs viewpoint. As expected, functional analysis showed that lncRNA sharing significantly enriched interacting miRNAs tend to be involved in similar diseases and have more functionally related flanking gene sets. We further proposed a novel rank-based method, RWRHLD, to prioritize candidate lncRNA-disease associations by integrating three networks (miRNA-associated lncRNA-lncRNA crosstalk network, disease-disease similarity network and known lncRNA-disease association network) into a heterogeneous network and implementing a random walk with restart on this heterogeneous network. We used leave-one-out cross-validation to test the performance of this rank-based method in this study based on known experimentally verified lncRNA-disease associations and obtained a reliable AUC value of 0.871, which is much higher than RWR merely based on an lncRNA network, hypergeometric test and random situation. Furthermore, several novel lncRNA-disease associations predicted in case studies of ovarian cancer and prostate cancer have been confirmed in new studies by literature surveys.
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Affiliation(s)
- Meng Zhou
- School of Life Science, Jilin University, Changchun 130012, PR China.
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2878
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Åsman AKM, Vetukuri RR, Jahan SN, Fogelqvist J, Corcoran P, Avrova AO, Whisson SC, Dixelius C. Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection. BMC Microbiol 2014; 14:308. [PMID: 25492044 PMCID: PMC4272539 DOI: 10.1186/s12866-014-0308-1] [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] [Received: 09/08/2014] [Accepted: 11/24/2014] [Indexed: 12/17/2022] Open
Abstract
Background The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host. Results To identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19–40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line. Conclusions Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs with elevated levels during infection of potato by P. infestans. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0308-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna K M Åsman
- Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden.
| | - Ramesh R Vetukuri
- Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden.
| | - Sultana N Jahan
- Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden.
| | - Johan Fogelqvist
- Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden.
| | - Pádraic Corcoran
- Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. .,Current affiliation: Department of Evolutionary Biology, Uppsala University, SE-75236, Uppsala, Sweden.
| | - Anna O Avrova
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Stephen C Whisson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Christina Dixelius
- Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden.
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2879
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Competition between target sites of regulators shapes post-transcriptional gene regulation. Nat Rev Genet 2014; 16:113-26. [PMID: 25488579 DOI: 10.1038/nrg3853] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Post-transcriptional gene regulation (PTGR) of mRNA turnover, localization and translation is mediated by microRNAs (miRNAs) and RNA-binding proteins (RBPs). These regulators exert their effects by binding to specific sequences within their target mRNAs. Increasing evidence suggests that competition for binding is a fundamental principle of PTGR. Not only can miRNAs be sequestered and neutralized by the targets with which they interact through a process termed 'sponging', but competition between binding sites on different RNAs may also lead to regulatory crosstalk between transcripts. Here, we quantitatively model competition effects under physiological conditions and review the role of endogenous sponges for PTGR in light of the key features that emerge.
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2880
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Noncoding oligonucleotides: the belle of the ball in gene therapy. ADVANCES IN GENETICS 2014; 89:153-177. [PMID: 25620011 DOI: 10.1016/bs.adgen.2014.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Gene therapy carries the promise of cures for many diseases based on manipulating the expression of a person's genes toward the therapeutic goal. The relevance of noncoding oligonucleotides to human disease is attracting widespread attention. Noncoding oligonucleotides are not only involved in gene regulation, but can also be modified into therapeutic tools. There are many strategies that leverage noncoding oligonucleotides for gene therapy, including small interfering RNAs, antisense oligonucleotides, aptamers, ribozymes, decoys, and bacteriophage phi 29 RNAs. In this chapter, we will provide a broad, comprehensive overview of gene therapies that use noncoding oligonucleotides for disease treatment. The mechanism and development of each therapeutic will be described, with a particular focus on its clinical development. Finally, we will discuss the challenges associated with developing nucleic acid therapeutics and the prospects for future success.
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2881
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Welcome to the New Journal Non-Coding RNA! Noncoding RNA 2014; 1:1-3. [PMID: 33353258 PMCID: PMC5932535 DOI: 10.3390/ncrna1010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 11/13/2014] [Indexed: 11/17/2022] Open
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2882
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Rajendiran S, Parwani AV, Hare RJ, Dasgupta S, Roby RK, Vishwanatha JK. MicroRNA-940 suppresses prostate cancer migration and invasion by regulating MIEN1. Mol Cancer 2014; 13:250. [PMID: 25406943 PMCID: PMC4246551 DOI: 10.1186/1476-4598-13-250] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 10/23/2014] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) are crucial molecules that regulate gene expression and hence pathways that are key to prostate cancer progression. These non-coding RNAs are highly deregulated in prostate cancer thus facilitating progression of the disease. Among the many genes that have gained importance in this disease, Migration and invasion enhancer 1 (MIEN1), a novel gene located next to HER2/neu in the 17q12 amplicon of the human chromosome, has been shown to enhance prostate cancer cell migration and invasion, two key processes in cancer progression. MIEN1 is differentially expressed between normal and cancer cells and tissues. Understanding the regulation of MIEN1 by microRNA may enable development of better targeting strategies. Methods The miRNAs that could target MIEN1 were predicted by in silico algorithms and microarray analysis. The validation for miRNA expression was performed by qPCR and northern blotting in cells and by in situ hybridization in tissues. MIEN1 and levels of other molecules upon miRNA regulation was determined by Western blotting, qPCR, and immunofluorescence. The functional effects of miRNA on cells were determined by wound healing cell migration, Boyden chamber cell invasion, clonal and colony formation assays. For knockdown or overexpression of the miRNA or overexpression of MIEN1 3′UTR, cells were transfected with the oligomiRs and plasmids, respectively. Results A novel miRNA, hsa-miR-940 (miR-940), identified and validated to be highly expressed in immortalized normal cells compared to cancer cells, is a regulator of MIEN1. Analysis of human prostate tumors and their matched normal tissues confirmed that miR-940 is highly expressed in the normal tissues compared to its low to negligible expression in the tumors. While MIEN1 is a direct target of miR-940, miR-940 alters MIEN1 RNA, in a quantity as well as cell dependent context, along with altering its downstream effectors. The miR-940 inhibited migratory and invasive potential of cells, attenuated their anchorage-independent growth ability, and increased E-cadherin expression, implicating its role in mesenchymal-to-epithelial transition (MET). Conclusions These results, for the first time, implicate miR-940, a regulator of MIEN1, as a promising novel diagnostic and prognostic tool for prostate cancer. Electronic supplementary material The online version of this article (doi:10.1186/1476-4598-13-250) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Jamboor K Vishwanatha
- From the Department of Molecular and Medical Genetics and Institute for Cancer Research, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA.
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2883
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Nazari-Jahantigh M, Egea V, Schober A, Weber C. MicroRNA-specific regulatory mechanisms in atherosclerosis. J Mol Cell Cardiol 2014; 89:35-41. [PMID: 25450610 DOI: 10.1016/j.yjmcc.2014.10.021] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022]
Abstract
During the past decade, the crucial role of microRNAs (miRs) controlling tissue homeostasis and disease in the cardiovascular system has become widely recognized. By controlling the expression levels of their targets, several miRs have been shown to modulate the function of endothelial cells, vascular smooth muscle cells, and macrophages, thereby regulating the development and progression of atherosclerosis. For instance, miR-155 can exacerbate early stages of atherosclerosis by increasing the inflammatory activation and disturbing efficient lipid handling in macrophages. Conversely, miRs can exert atheroprotective roles, as has been established for the complementary miR-126 strand pair, which forms a dual system sustaining the endothelial proliferative reserve and promoting endothelial regeneration to counteract atherogenic effects of disturbed flow and hyperlipidemia. Under some conditions, miRs are released from cells and are transported by microvesicles, ribonucleoprotein complexes, and lipoproteins, being remarkably stable in circulation. Conferred by such delivery modules, miRs can regulate target mRNAs in recipient cells, representing a new tool for cell-cell communication in the context of atherosclerotic disease. Here, we will discuss novel aspects of miR-mediated regulatory mechanisms, namely the regulation by competing RNA targets, miRNA tandems, or complementary miR strand pairs, as well as their potential diagnostic and therapeutic value in atherosclerosis. This article is part of a Special Issue entitled 'Non-coding RNAs'.
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Affiliation(s)
| | - Virginia Egea
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Andreas Schober
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University Munich, Munich, Germany; German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention, Ludwig-Maximilians-University Munich, Munich, Germany; German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany.
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2884
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Carnero E, Barriocanal M, Segura V, Guruceaga E, Prior C, Börner K, Grimm D, Fortes P. Type I Interferon Regulates the Expression of Long Non-Coding RNAs. Front Immunol 2014; 5:548. [PMID: 25414701 PMCID: PMC4222131 DOI: 10.3389/fimmu.2014.00548] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/14/2014] [Indexed: 12/22/2022] Open
Abstract
Interferons (IFNs) are key players in the antiviral response. IFN sensing by the cell activates transcription of IFN-stimulated genes (ISGs) able to induce an antiviral state by affecting viral replication and release. IFN also induces the expression of ISGs that function as negative regulators to limit the strength and duration of IFN response. The ISGs identified so far belong to coding genes. However, only a small proportion of the transcriptome corresponds to coding transcripts and it has been estimated that there could be as many coding as long non-coding RNAs (lncRNAs). To address whether IFN can also regulate the expression of lncRNAs, we analyzed the transcriptome of HuH7 cells treated or not with IFNα2 by expression arrays. Analysis of the arrays showed increased levels of several well-characterized coding genes that respond to IFN both at early or late times. Furthermore, we identified several IFN-stimulated or -downregulated lncRNAs (ISRs and IDRs). Further validation showed that ISR2, 8, and 12 expression mimics that of their neighboring genes GBP1, IRF1, and IL6, respectively, all related to the IFN response. These genes are induced in response to different doses of IFNα2 in different cell lines at early (ISR2 or 8) or later (ISR12) time points. IFNβ also induced the expression of these lncRNAs. ISR2 and 8 were also induced by an influenza virus unable to block the IFN response but not by other wild-type lytic viruses tested. Surprisingly, both ISR2 and 8 were significantly upregulated in cultured cells and livers from patients infected with HCV. Increased levels of ISR2 were also detected in patients chronically infected with HIV. This is relevant as genome-wide guilt-by-association studies predict that ISR2, 8, and 12 may function in viral processes, in the IFN pathway and the antiviral response. Therefore, we propose that these lncRNAs could be induced by IFN to function as positive or negative regulators of the antiviral response.
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Affiliation(s)
- Elena Carnero
- Department of Gene therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra , Pamplona , Spain
| | - Marina Barriocanal
- Department of Gene therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra , Pamplona , Spain
| | - Victor Segura
- Bioinformatics Unit, Center for Applied Medical Research (CIMA), University of Navarra , Pamplona , Spain
| | - Elizabeth Guruceaga
- Bioinformatics Unit, Center for Applied Medical Research (CIMA), University of Navarra , Pamplona , Spain
| | - Celia Prior
- Department of Gene therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra , Pamplona , Spain
| | - Kathleen Börner
- Centre for Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks , Heidelberg , Germany ; German Center for Infection Research (DZIF) , Heidelberg , Germany
| | - Dirk Grimm
- Centre for Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks , Heidelberg , Germany
| | - Puri Fortes
- Department of Gene therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra , Pamplona , Spain
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2885
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Ibrahim SA, Hassan H, Götte M. MicroRNA regulation of proteoglycan function in cancer. FEBS J 2014; 281:5009-22. [DOI: 10.1111/febs.13026] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/08/2014] [Accepted: 08/26/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Sherif A. Ibrahim
- Department of Zoology; Faculty of Science; Cairo University; Giza Egypt
| | - Hebatallah Hassan
- Department of Zoology; Faculty of Science; Cairo University; Giza Egypt
| | - Martin Götte
- Department of Gynecology and Obstetrics; Münster University Hospital; Germany
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2886
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Bosson AD, Zamudio JR, Sharp PA. Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol Cell 2014; 56:347-359. [PMID: 25449132 PMCID: PMC5048918 DOI: 10.1016/j.molcel.2014.09.018] [Citation(s) in RCA: 309] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/09/2014] [Accepted: 09/18/2014] [Indexed: 12/14/2022]
Abstract
Target competition (ceRNA crosstalk) within miRNA-regulated gene networks has been proposed to influence biological systems. To assess target competition, we characterize and quantitate miRNA networks in two cell types. Argonaute iCLIP reveals that hierarchical binding of high- to low-affinity miRNA targets is a key characteristic of in vivo activity. Quantification of cellular miRNA and mRNA/ncRNA target pool levels indicates that miRNA:target pool ratios and an affinity partitioned target pool accurately predict in vivo Ago binding profiles and miRNA susceptibility to target competition. Using single-cell reporters, we directly test predictions and estimate that ?3,000 additional high-affinity target sites can affect active miRNA families with low endogenous miRNA:target ratios, such as miR-92/25. In contrast, the highly expressed miR-294 and let-7 families are not susceptible to increases of nearly 10,000 sites. These results show differential susceptibility based on endogenous miRNA:target pool ratios and provide a physiological context for ceRNA competition in vivo.
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Affiliation(s)
- Andrew D Bosson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jesse R Zamudio
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Phillip A Sharp
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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2887
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Chiu HS, Llobet-Navas D, Yang X, Chung WJ, Ambesi-Impiombato A, Iyer A, Kim HR, Seviour EG, Luo Z, Sehgal V, Moss T, Lu Y, Ram P, Silva J, Mills GB, Califano A, Sumazin P. Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Genome Res 2014; 25:257-67. [PMID: 25378249 PMCID: PMC4315299 DOI: 10.1101/gr.178194.114] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We introduce a method for simultaneous prediction of microRNA–target interactions and their mediated competitive endogenous RNA (ceRNA) interactions. Using high-throughput validation assays in breast cancer cell lines, we show that our integrative approach significantly improves on microRNA–target prediction accuracy as assessed by both mRNA and protein level measurements. Our biochemical assays support nearly 500 microRNA–target interactions with evidence for regulation in breast cancer tumors. Moreover, these assays constitute the most extensive validation platform for computationally inferred networks of microRNA–target interactions in breast cancer tumors, providing a useful benchmark to ascertain future improvements.
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Affiliation(s)
- Hua-Sheng Chiu
- Department of Systems Biology, Center for Computational Biology and Bioinformatics, Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA; Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - David Llobet-Navas
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei-Jen Chung
- Department of Systems Biology, Center for Computational Biology and Bioinformatics, Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA
| | - Alberto Ambesi-Impiombato
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA
| | | | - Hyunjae Ryan Kim
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, New York 10065, USA
| | - Elena G Seviour
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Zijun Luo
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Vasudha Sehgal
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Tyler Moss
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yiling Lu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
| | - Prahlad Ram
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - José Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Andrea Califano
- Department of Systems Biology, Center for Computational Biology and Bioinformatics, Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA; Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Pavel Sumazin
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
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2888
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Tan JY, Vance KW, Varela MA, Sirey T, Watson LM, Curtis HJ, Marinello M, Alves S, Steinkraus B, Cooper S, Nesterova T, Brockdorff N, Fulga T, Brice A, Sittler A, Oliver PL, Wood MJ, Ponting CP, Marques AC. Cross-talking noncoding RNAs contribute to cell-specific neurodegeneration in SCA7. Nat Struct Mol Biol 2014; 21:955-961. [PMID: 25306109 PMCID: PMC4255225 DOI: 10.1038/nsmb.2902] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 09/16/2014] [Indexed: 01/14/2023]
Abstract
What causes the tissue-specific pathology of diseases resulting from mutations in housekeeping genes? Specifically, in spinocerebellar ataxia type 7 (SCA7), a neurodegenerative disorder caused by a CAG-repeat expansion in ATXN7 (which encodes an essential component of the mammalian transcription coactivation complex, STAGA), the factors underlying the characteristic progressive cerebellar and retinal degeneration in patients were unknown. We found that STAGA is required for the transcription initiation of miR-124, which in turn mediates the post-transcriptional cross-talk between lnc-SCA7, a conserved long noncoding RNA, and ATXN7 mRNA. In SCA7, mutations in ATXN7 disrupt these regulatory interactions and result in a neuron-specific increase in ATXN7 expression. Strikingly, in mice this increase is most prominent in the SCA7 disease-relevant tissues, namely the retina and cerebellum. Our results illustrate how noncoding RNA-mediated feedback regulation of a ubiquitously expressed housekeeping gene may contribute to specific neurodegeneration.
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Affiliation(s)
- Jennifer Y Tan
- MRC Functional Genomics Unit, University of Oxford, Oxford, UK
- University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
| | - Keith W Vance
- MRC Functional Genomics Unit, University of Oxford, Oxford, UK
- University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
| | - Miguel A Varela
- University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
| | - Tamara Sirey
- MRC Functional Genomics Unit, University of Oxford, Oxford, UK
- University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
| | - Lauren M Watson
- University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
- University of Cape Town, Division of Human Genetics, Cape Town, South Africa
| | - Helen J Curtis
- University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
| | - Martina Marinello
- Centre de Recherche de l'Institut du Cerveau et de la Moëlle épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
- Université Pierre et Marie Curie-Paris 6, Paris, France
- Inserm, U 975, Paris, France
- CNRS, UMR 7225, Paris, France
- Département de Génétique et Cytogénétique, APHP, GH Pitié-Salpêtrière, Paris, France
| | - Sandro Alves
- Centre de Recherche de l'Institut du Cerveau et de la Moëlle épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
- Université Pierre et Marie Curie-Paris 6, Paris, France
- Inserm, U 975, Paris, France
- CNRS, UMR 7225, Paris, France
- Département de Génétique et Cytogénétique, APHP, GH Pitié-Salpêtrière, Paris, France
| | - Bruno Steinkraus
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sarah Cooper
- University of Oxford, Department of Biochemistry, Oxford, United Kingdom
| | - Tatyana Nesterova
- University of Oxford, Department of Biochemistry, Oxford, United Kingdom
| | - Neil Brockdorff
- University of Oxford, Department of Biochemistry, Oxford, United Kingdom
| | - Tudor Fulga
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Alexis Brice
- Centre de Recherche de l'Institut du Cerveau et de la Moëlle épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
- Université Pierre et Marie Curie-Paris 6, Paris, France
- Inserm, U 975, Paris, France
- CNRS, UMR 7225, Paris, France
- Département de Génétique et Cytogénétique, APHP, GH Pitié-Salpêtrière, Paris, France
| | - Annie Sittler
- Centre de Recherche de l'Institut du Cerveau et de la Moëlle épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
- Université Pierre et Marie Curie-Paris 6, Paris, France
- Inserm, U 975, Paris, France
- CNRS, UMR 7225, Paris, France
| | - Peter L Oliver
- MRC Functional Genomics Unit, University of Oxford, Oxford, UK
- University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
| | - Matthew J Wood
- University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
- University of Cape Town, Division of Human Genetics, Cape Town, South Africa
| | - Chris P Ponting
- MRC Functional Genomics Unit, University of Oxford, Oxford, UK
- University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
| | - Ana C Marques
- MRC Functional Genomics Unit, University of Oxford, Oxford, UK
- University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
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2889
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Li C, Yang L, Lin C. Long noncoding RNAs in prostate cancer: mechanisms and applications. Mol Cell Oncol 2014; 1:e963469. [PMID: 27308347 DOI: 10.4161/23723548.2014.963469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/04/2014] [Accepted: 08/12/2014] [Indexed: 12/26/2022]
Abstract
A large proportion of the control of gene expression in humans is mediated by noncoding elements in the genome. Long noncoding RNAs (lncRNAs) have emerged as a new class of pivotal regulatory components, orchestrating extensive cellular processes and connections. LncRNAs play various roles from chromatin modification to alternative splicing and post-transcriptional processing and are involved in almost all aspects of eukaryotic regulation. LncRNA-based mechanisms modulate cell fates during development, and their dysregulation underscores many human disorders, especially cancer, through chromosomal translocation, deletion, and nucleotide expansions. Recent studies demonstrate that multiple prostate cancer risk loci are associated with lncRNAs and that ectopic expression of these transcripts triggers a cascade of cellular events driving tumor initiation and progression. The recent increased rate of discovery of lncRNAs has been leveraged for application in clinical strategies such as novel biomarkers and therapeutic targets. Despite this potential, many issues remain to be addressed in this fast-growing field.
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Affiliation(s)
- Chunlai Li
- Department of Molecular and Cellular Oncology; The University of Texas MD Anderson Cancer Center ; Houston, TX, 77030, USA
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology; The University of Texas MD Anderson Cancer Center; Houston, TX, 77030, USA; Program in Cancer Biology; The University of Texas Graduate School of Biomedical Sciences at Houston; Houston, TX, 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology; The University of Texas MD Anderson Cancer Center; Houston, TX, 77030, USA; Program in Cancer Biology; The University of Texas Graduate School of Biomedical Sciences at Houston; Houston, TX, 77030, USA
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2890
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Dey BK, Mueller AC, Dutta A. Long non-coding RNAs as emerging regulators of differentiation, development, and disease. Transcription 2014; 5:e944014. [PMID: 25483404 DOI: 10.4161/21541272.2014.944014] [Citation(s) in RCA: 262] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A significant portion of the mammalian genome encodes numerous transcripts that are not translated into proteins, termed long non-coding RNAs. Initial studies identifying long non-coding RNAs inferred these RNA sequences were a consequence of transcriptional noise or promiscuous RNA polymerase II activity. However, the last decade has seen a revolution in the understanding of regulation and function of long non-coding RNAs. Now it has become apparent that long non-coding RNAs play critical roles in a wide variety of biological processes. In this review, we describe the current understanding of long non-coding RNA-mediated regulation of cellular processes: differentiation, development, and disease.
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Key Words
- Bvht, braveheart
- CDT, C-terminal domain
- DBE-T, D4Z4-binding element
- DMD, Duchenne muscular dystrophy
- ES, embryonic stem
- FSHD, facioscapulohumeral muscular dystrophy
- Fendrr, Foxf1a called fetal-lethal non-coding developmental regulatory RNA
- MEF2, myocyte enhancer factor-2
- MRFs, myogenic regulatory factors
- Malat1, metastasis associated lung adenocarcinoma transcript 1
- Mesp1, mesoderm progenitor 1
- Neat2, nuclear-enriched abundant transcript 2
- PRC2, polycomb group repressive complex 2
- RNAP II, RNA polymerase II
- SINE, short interspersed element
- SR, serine arginine
- SRA, steroid receptor activator
- SRY, sex-determining region Y
- YAM 1-4, YY1-associated muscle 1-4
- ceRNAs, competing endogenous RNAs
- ciRS-7, circular RNA sponge for miR-7
- development
- differentiation
- disease
- gene expression
- iPS, induced pluripotent stem
- lncRNAs, long non-coding RNAs
- long non-coding RNAs
- ncRNAa, non-coding RNA activating
- skeletal muscle
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Affiliation(s)
- Bijan K Dey
- a Department of Biochemistry and Molecular Genetics ; University of Virginia School of Medicine ; Charlottesville , VA USA
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2891
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19q13.33→qter trisomy in a girl with intellectual impairment and seizures. Meta Gene 2014; 2:799-806. [PMID: 25606462 PMCID: PMC4288793 DOI: 10.1016/j.mgene.2014.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/01/2014] [Accepted: 09/08/2014] [Indexed: 12/11/2022] Open
Abstract
Rearrangements in chromosome 19 are rare. Among the 35 patients with partial 19q trisomy described, only six have a breakpoint defined by array. The 19q duplication results in a variable phenotype, including dysmorphisms, intellectual disability and seizure. In a female patient, although G-banding at 550 band-resolution was normal, multiplex ligation-dependent probe amplification (MLPA) technique and genomic array showed a 10.6 Mb terminal duplication of chromosome 19q13. Fluorescent in situ hybridization (FISH) revealed that the duplicated region was attached to the short arm of chromosome 21 and silver staining showed four small acrocentrics with nucleolar organization region (NOR) activity, suggesting that the breakpoint in chromosome 21 was at p13. This is the first de novo translocation between 19q13.33 and 21p13 described in liveborn. The chromosome 19 is known to be rich in coding and non-coding regions, and chromosomal rearrangements involving this chromosome are very harmful. Furthermore, the 19q13.33→qter region is dense in pseudogenes and microRNAs, which are potent regulators of gene expression. The trisomic level of this region may contribute to deregulation of global gene expression, and consequently, may lead to abnormal development on the carriers of these rearrangements. The first patient with a de novo translocation between 19q13.33 and 21p13 reported in liveborn. The patient clinical and cytogenetic analyses are reported in details. Rearrangements in 19q13.33→qter region are correlated to intellectual disability and seizures. Chromosomal rearrangements involving rich coding and non-coding regions appear to be very harmful.
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2892
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Panuzzo C, Crivellaro S, Carrà G, Guerrasio A, Saglio G, Morotti A. BCR-ABL promotes PTEN downregulation in chronic myeloid leukemia. PLoS One 2014; 9:e110682. [PMID: 25343485 PMCID: PMC4208795 DOI: 10.1371/journal.pone.0110682] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/24/2014] [Indexed: 11/18/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative disorder characterized by the t(9;22) translocation coding for the chimeric protein p210 BCR-ABL. The tumor suppressor PTEN plays a critical role in the pathogenesis of CML chronic phase, through non genomic loss of function mechanisms, such as protein down-regulation and impaired nuclear/cytoplasmic shuttling. Here we demonstrate that BCR-ABL promotes PTEN downregulation through a MEK dependent pathway. Furthermore, we describe a novel not recurrent N212D-PTEN point mutation found in the EM2 blast crisis cell line.
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Affiliation(s)
- Cristina Panuzzo
- Department of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy
| | - Sabrina Crivellaro
- Department of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy
| | - Giovanna Carrà
- Department of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy
| | - Angelo Guerrasio
- Department of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy
| | - Alessandro Morotti
- Department of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy
- * E-mail:
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2893
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Hardeland R. Melatonin, noncoding RNAs, messenger RNA stability and epigenetics--evidence, hints, gaps and perspectives. Int J Mol Sci 2014; 15:18221-52. [PMID: 25310649 PMCID: PMC4227213 DOI: 10.3390/ijms151018221] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 09/21/2014] [Accepted: 09/24/2014] [Indexed: 02/06/2023] Open
Abstract
Melatonin is a highly pleiotropic regulator molecule, which influences numerous functions in almost every organ and, thus, up- or down-regulates many genes, frequently in a circadian manner. Our understanding of the mechanisms controlling gene expression is actually now expanding to a previously unforeseen extent. In addition to classic actions of transcription factors, gene expression is induced, suppressed or modulated by a number of RNAs and proteins, such as miRNAs, lncRNAs, piRNAs, antisense transcripts, deadenylases, DNA methyltransferases, histone methylation complexes, histone demethylases, histone acetyltransferases and histone deacetylases. Direct or indirect evidence for involvement of melatonin in this network of players has originated in different fields, including studies on central and peripheral circadian oscillators, shift work, cancer, inflammation, oxidative stress, aging, energy expenditure/obesity, diabetes type 2, neuropsychiatric disorders, and neurogenesis. Some of the novel modulators have also been shown to participate in the control of melatonin biosynthesis and melatonin receptor expression. Future work will need to augment the body of evidence on direct epigenetic actions of melatonin and to systematically investigate its role within the network of oscillating epigenetic factors. Moreover, it will be necessary to discriminate between effects observed under conditions of well-operating and deregulated circadian clocks, and to explore the possibilities of correcting epigenetic malprogramming by melatonin.
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Affiliation(s)
- Rüdiger Hardeland
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Berliner Str. 28, Göttingen D-37073, Germany.
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2894
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Kapusta A, Feschotte C. Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet 2014; 30:439-52. [PMID: 25218058 PMCID: PMC4464757 DOI: 10.1016/j.tig.2014.08.004] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/15/2014] [Accepted: 08/16/2014] [Indexed: 02/08/2023]
Abstract
Thousands of genes encoding long noncoding RNAs (lncRNAs) have been identified in all vertebrate genomes thus far examined. The list of lncRNAs partaking in arguably important biochemical, cellular, and developmental activities is steadily growing. However, it is increasingly clear that lncRNA repertoires are subject to weak functional constraint and rapid turnover during vertebrate evolution. We discuss here some of the factors that may explain this apparent paradox, including relaxed constraint on sequence to maintain lncRNA structure/function, extensive redundancy in the regulatory circuits in which lncRNAs act, as well as adaptive and non-adaptive forces such as genetic drift. We explore the molecular mechanisms promoting the birth and rapid evolution of lncRNA genes, with an emphasis on the influence of bidirectional transcription and transposable elements, two pervasive features of vertebrate genomes. Together these properties reveal a remarkably dynamic and malleable noncoding transcriptome which may represent an important source of robustness and evolvability.
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Affiliation(s)
- Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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2895
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Huang CT, Oyang YJ, Huang HC, Juan HF. MicroRNA-mediated networks underlie immune response regulation in papillary thyroid carcinoma. Sci Rep 2014; 4:6495. [PMID: 25263162 PMCID: PMC4178297 DOI: 10.1038/srep06495] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/09/2014] [Indexed: 12/31/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is a common endocrine malignancy with low death rate but increased incidence and recurrence in recent years. MicroRNAs (miRNAs) are small non-coding RNAs with diverse regulatory capacities in eukaryotes and have been frequently implied in human cancer. Despite current progress, however, a panoramic overview concerning miRNA regulatory networks in PTC is still lacking. Here, we analyzed the expression datasets of PTC from The Cancer Genome Atlas (TCGA) Data Portal and demonstrate for the first time that immune responses are significantly enriched and under specific regulation in the direct miRNA--target network among distinctive PTC variants to different extents. Additionally, considering the unconventional properties of miRNAs, we explore the protein-coding competing endogenous RNA (ceRNA) and the modulatory networks in PTC and unexpectedly disclose concerted regulation of immune responses from these networks. Interestingly, miRNAs from these conventional and unconventional networks share general similarities and differences but tend to be disparate as regulatory activities increase, coordinately tuning the immune responses that in part account for PTC tumor biology. Together, our systematic results uncover the intensive regulation of immune responses underlain by miRNA-mediated networks in PTC, opening up new avenues in the management of thyroid cancer.
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Affiliation(s)
- Chen-Tsung Huang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Yen-Jen Oyang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics and Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan
| | - Hsueh-Fen Juan
- 1] Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan [2] Department of Life Science, National Taiwan University, Taipei, Taiwan [3] Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
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2896
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Yu G, Yao W, Gumireddy K, Li A, Wang J, Xiao W, Chen K, Xiao H, Li H, Tang K, Ye Z, Huang Q, Xu H. Pseudogene PTENP1 functions as a competing endogenous RNA to suppress clear-cell renal cell carcinoma progression. Mol Cancer Ther 2014; 13:3086-97. [PMID: 25249556 DOI: 10.1158/1535-7163.mct-14-0245] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PTENP1 is a pseudogene of the PTEN tumor suppression gene (TSG). The functions of PTENP1 in clear-cell renal cell carcinoma (ccRCC) have not yet been studied. We found that PTENP1 is downregulated in ccRCC tissues and cells due to methylation. PTENP1 and PTEN are direct targets of miRNA miR21 and their expression is suppressed by miR21 in ccRCC cell lines. miR21 expression promotes ccRCC cell proliferation, migration, invasion in vitro, and tumor growth and metastasis in vivo. Overexpression of PTENP1 in cells expressing miR21 reduces cell proliferation, invasion, tumor growth, and metastasis, recapitulating the phenotypes induced by PTEN expression. Overexpression of PTENP1 in ccRCC cells sensitizes these cells to cisplatin and gemcitabine treatments in vitro and in vivo. In clinical samples, the expression of PTENP1 and PTEN is correlated, and both expressions are inversely correlated with miR21 expression. Patients with ccRCC with no PTENP1 expression have a lower survival rate. These results suggest that PTENP1 functions as a competing endogenous RNA (ceRNA) in ccRCC to suppress cancer progression.
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Affiliation(s)
- Gan Yu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weimin Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | - Anping Li
- The Wistar Institute, Philadelphia, Pennsylvania
| | - Ji Wang
- Department of Urology and Helen-Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Wei Xiao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haibing Xiao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Tang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qihong Huang
- The Wistar Institute, Philadelphia, Pennsylvania.
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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2897
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Jagannathan S, Vad N, Vallabhapurapu S, Vallabhapurapu S, Anderson KC, Driscoll JJ. MiR-29b replacement inhibits proteasomes and disrupts aggresome+autophagosome formation to enhance the antimyeloma benefit of bortezomib. Leukemia 2014; 29:727-38. [PMID: 25234165 PMCID: PMC4360212 DOI: 10.1038/leu.2014.279] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/22/2014] [Accepted: 09/02/2014] [Indexed: 12/24/2022]
Abstract
Evading apoptosis is a cancer hallmark that remains a serious obstacle in current treatment approaches. Although proteasome inhibitors (PIs) have transformed management of multiple myeloma (MM), drug resistance emerges through induction of the aggresome+autophagy pathway as a compensatory protein clearance mechanism. Genome-wide profiling identified microRNAs (miRs) differentially expressed in bortezomib-resistant myeloma cells compared with drug-naive cells. The effect of individual miRs on proteasomal degradation of short-lived fluorescent reporter proteins was then determined in live cells. MiR-29b was significantly reduced in bortezomib-resistant cells as well as in cells resistant to second-generation PIs carfilzomib and ixazomib. Luciferase reporter assays demonstrated that miR-29b targeted PSME4 that encodes the proteasome activator PA200. Synthetically engineered miR-29b replacements impaired the growth of myeloma cells, patient tumor cells and xenotransplants. MiR-29b replacements also decreased PA200 association with proteasomes, reduced the proteasome's peptidase activity and inhibited ornithine decarboxylase turnover, a proteasome substrate degraded through ubiquitin-independent mechanisms. Immunofluorescence studies revealed that miR-29b replacements enhanced the bortezomib-induced accumulation of ubiquitinated proteins but did not reveal aggresome or autophagosome formation. Taken together, our study identifies miR-29b replacements as the first-in-class miR-based PIs that also disrupt the autophagy pathway and highlight their potential to synergistically enhance the antimyeloma effect of bortezomib.
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Affiliation(s)
- S Jagannathan
- 1] The Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, Cincinnati, OH, USA [2] Division of Hematology and Oncology, The Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - N Vad
- 1] The Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, Cincinnati, OH, USA [2] Division of Hematology and Oncology, The Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - S Vallabhapurapu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - S Vallabhapurapu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - K C Anderson
- Jerome Lipper Multiple Myeloma Center and LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - J J Driscoll
- 1] The Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, Cincinnati, OH, USA [2] Division of Hematology and Oncology, The Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, Cincinnati, OH, USA [3] Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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2898
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Sundermeier TR, Jin H, Kleinjan ML, Mustafi D, Licatalosi DD, Palczewski K. Argonaute high-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation reveals a snapshot of miRNA gene regulation in the mammalian retina. Biochemistry 2014; 53:5831-3. [PMID: 25204418 PMCID: PMC4172207 DOI: 10.1021/bi500966b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mounting evidence points to roles for miRNA gene regulation in promoting development, function, and cell survival in the mammalian retina. However, little is known regarding which retinal genes are targets of miRNAs. Here, we employed a systematic, nonbiased, biochemical approach to identify targets of miRNA gene regulation in the bovine retina, a common model species for vision research. Using Argonaute high-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation analysis, we identified 348 high-confidence miRNA target sites within 261 genes. This list was enriched in rod and cone photoreceptor genes and included 28 retinal disease genes, providing further evidence of a role of miRNAs in the pathology of blinding diseases.
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Affiliation(s)
- Thomas R Sundermeier
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology and ‡Center for RNA Molecular Biology, Case Western Reserve University, School of Medicine , 2109 Adelbert Road, Cleveland, Ohio 44106, United States
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2899
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The potential of microRNAs in personalized medicine against cancers. BIOMED RESEARCH INTERNATIONAL 2014; 2014:642916. [PMID: 25243170 PMCID: PMC4163464 DOI: 10.1155/2014/642916] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 08/06/2014] [Indexed: 02/06/2023]
Abstract
MicroRNAs orchestrate the expression of the genome and impact many, if not all, cellular processes. Their deregulation is thus often causative of human malignancies, including cancers. Numerous studies have implicated microRNAs in the different steps of tumorigenesis including initiation, progression, metastasis, and resistance to chemo/radiotherapies. Thus, microRNAs constitute appealing targets for novel anticancer therapeutic strategies aimed at restoring their expression or function. As microRNAs are present in a variety of human cancer types, microRNA profiles can be used as tumor-specific signatures to detect various cancers (diagnosis), to predict their outcome (prognosis), and to monitor their treatment (theranosis). In this review, we present the different aspects of microRNA biology that make them remarkable molecules in the emerging field of personalized medicine against cancers and provide several examples of their industrial exploitation.
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2900
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Wilflingseder J, Reindl-Schwaighofer R, Sunzenauer J, Kainz A, Heinzel A, Mayer B, Oberbauer R. MicroRNAs in kidney transplantation. Nephrol Dial Transplant 2014; 30:910-7. [PMID: 25170095 DOI: 10.1093/ndt/gfu280] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/27/2014] [Indexed: 12/13/2022] Open
Abstract
The discovery of novel classes of non-coding RNAs (ncRNAs) has revolutionized medicine. Long thought to be a mere cellular housekeeper, surprising functions have recently been uncovered. MicroRNAs (miRNAs), are a representative of the class of short ncRNAs, play a fundamental role in the control of DNA and protein biosynthesis and activity as well as pathology. Currently, miRNAs are being investigated as diagnostic and prognostic markers and potential therapeutic targets in kidney transplantation for such indolent processes as ischaemia-reperfusion injury, humoral rejection or viral infections. It is realistic to believe that monitoring of renal allograft recipients in the future will include genome-wide miRNA profiling of biological fluids. Based on these individual profiles, an informed decision on therapeutic consequences will be possible. A first success with a specific suppression of miRNAs by antisense oligonucleotides was achieved in experimental studies of reperfusion injury and humoral rejection. Proof of this concept in men comes from studies in such indolent viral infections as Ebola and hepatitis C, where anti-miR therapy led to sustained viral clearance. In this review, we summarize the basis of the recent ncRNA revolution and its implication for kidney transplantation.
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Affiliation(s)
- Julia Wilflingseder
- Department of Nephrology and Dialysis, Medical University Vienna, Vienna, Austria Department of Nephrology, KH Elisabethinen, Linz, Austria
| | | | | | - Alexander Kainz
- Department of Nephrology and Dialysis, Medical University Vienna, Vienna, Austria Department of Nephrology, KH Elisabethinen, Linz, Austria
| | | | - Bernd Mayer
- emergentec biodevelopment GmbH, Vienna, Austria
| | - Rainer Oberbauer
- Department of Nephrology and Dialysis, Medical University Vienna, Vienna, Austria Department of Nephrology, KH Elisabethinen, Linz, Austria
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