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De Kumar B, Krumlauf R. HOXs and lincRNAs: Two sides of the same coin. SCIENCE ADVANCES 2016; 2:e1501402. [PMID: 27034976 PMCID: PMC4805430 DOI: 10.1126/sciadv.1501402] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/28/2015] [Indexed: 05/13/2023]
Abstract
The clustered Hox genes play fundamental roles in regulation of axial patterning and elaboration of the basic body plan in animal development. There are common features in the organization and regulatory landscape of Hox clusters associated with their highly conserved functional roles. The presence of transcribed noncoding sequences embedded within the vertebrate Hox clusters is providing insight into a new layer of regulatory information associated with Hox genes.
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Affiliation(s)
- Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
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Posttranscriptional Regulation of Splicing Factor SRSF1 and Its Role in Cancer Cell Biology. BIOMED RESEARCH INTERNATIONAL 2015; 2015:287048. [PMID: 26273603 PMCID: PMC4529898 DOI: 10.1155/2015/287048] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/16/2014] [Indexed: 01/23/2023]
Abstract
Over the past decade, alternative splicing has been progressively recognized as a major mechanism regulating gene expression patterns in different tissues and disease states through the generation of multiple mRNAs from the same gene transcript. This process requires the joining of selected exons or usage of different pairs of splice sites and is regulated by gene-specific combinations of RNA-binding proteins. One archetypical splicing regulator is SRSF1, for which we review the molecular mechanisms and posttranscriptional modifications involved in its life cycle. These include alternative splicing of SRSF1 itself, regulatory protein phosphorylation events, and the role of nuclear versus cytoplasmic SRSF1 localization. In addition, we resume current knowledge on deregulated SRSF1 expression in tumors and describe SRSF1-regulated alternative transcripts with functional consequences for cancer cell biology at different stages of tumor development.
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Warns JA, Davie JR, Dhasarathy A. Connecting the dots: chromatin and alternative splicing in EMT. Biochem Cell Biol 2015; 94:12-25. [PMID: 26291837 DOI: 10.1139/bcb-2015-0053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nature has devised sophisticated cellular machinery to process mRNA transcripts produced by RNA Polymerase II, removing intronic regions and connecting exons together, to produce mature RNAs. This process, known as splicing, is very closely linked to transcription. Alternative splicing, or the ability to produce different combinations of exons that are spliced together from the same genomic template, is a fundamental means of regulating protein complexity. Similar to transcription, both constitutive and alternative splicing can be regulated by chromatin and its associated factors in response to various signal transduction pathways activated by external stimuli. This regulation can vary between different cell types, and interference with these pathways can lead to changes in splicing, often resulting in aberrant cellular states and disease. The epithelial to mesenchymal transition (EMT), which leads to cancer metastasis, is influenced by alternative splicing events of chromatin remodelers and epigenetic factors such as DNA methylation and non-coding RNAs. In this review, we will discuss the role of epigenetic factors including chromatin, chromatin remodelers, DNA methyltransferases, and microRNAs in the context of alternative splicing, and discuss their potential involvement in alternative splicing during the EMT process.
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Affiliation(s)
- Jessica A Warns
- a Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, 501 N. Columbia Road Stop 9061, Grand Forks, ND 58202-9061, USA
| | - James R Davie
- b Children's Hospital Research Institute of Manitoba, John Buhler Research Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Archana Dhasarathy
- a Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, 501 N. Columbia Road Stop 9061, Grand Forks, ND 58202-9061, USA
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Khan FH, Pandian V, Ramraj S, Aravindan S, Herman TS, Aravindan N. Reorganization of metastamiRs in the evolution of metastatic aggressive neuroblastoma cells. BMC Genomics 2015; 16:501. [PMID: 26148557 PMCID: PMC4491873 DOI: 10.1186/s12864-015-1642-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/19/2015] [Indexed: 12/19/2022] Open
Abstract
Background MetastamiRs have momentous clinical relevance and have been correlated with disease progression in many tumors. In this study, we identified neuroblastoma metastamiRs exploiting unique mouse models of favorable and high-risk metastatic human neuroblastoma. Further, we related their deregulation to the modulation of target proteins and established their association with clinical outcomes. Results Whole genome miRNA microarray analysis identified 74 metastamiRs across the manifold of metastatic tumors. RT-qPCR on select miRNAs validated profile expression. Results from bio-informatics across the ingenuity pathway, miRCancer, and literature data-mining endorsed the expression of these miRNAs in multiple tumor systems and showed their role in metastasis, identifying them as metastamiRs. Immunoblotting and TMA-IHC analyses revealed alterations in the expression/phosphorylation of metastamiRs’ targets, including ADAMTS-1, AKT1/2/3, ASK1, AURKβ, Birc1, Birc2, Bric5, β-CATENIN, CASP8, CD54, CDK4, CREB, CTGF, CXCR4, CYCLIN-D1, EGFR, ELK1, ESR1, CFOS, FOSB, FRA, GRB10, GSK3β, IL1α, JUND, kRAS, KRTAP1, MCP1, MEGF10, MMP2, MMP3, MMP9, MMP10, MTA2, MYB, cMYC, NF2, NOS3, P21, pP38, PTPN3, CLEAVED PARP, PKC, SDF-1β, SEMA3D, SELE, STAT3, TLR3, TNFα, TNFR1, and VEGF in aggressive cells ex vivo and in a manifold of metastatic tumors in vivo. miRNA mimic (hsa-miR-125b, hsa-miR-27b, hsa-miR-93, hsa-miR-20a) and inhibitor (hsa-miR-1224-3p, hsa-miR-1260) approach for select miRNAs revealed the direct influence of the altered metastamiRs in the regulation of identified protein targets. Clinical outcome association analysis with the validated metastamiRs’ targets corresponded strongly with poor overall and relapse-free survival. Conclusions For the first time, these results identified a comprehensive list of neuroblastoma metastamiRs, related their deregulation to altered expression of protein targets, and established their association with poor clinical outcomes. The identified set of distinctive neuroblastoma metastamiRs could serve as potential candidates for diagnostic markers for the switch from favorable to high-risk metastatic disease. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1642-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Faizan H Khan
- Department of Radiation Oncology, University of Oklahoma Health Sciences Center, 940, Stanton L. Young Boulevard, BMSB 737, Oklahoma City, OK, 73104, USA.
| | - Vijayabaskar Pandian
- Department of Radiation Oncology, University of Oklahoma Health Sciences Center, 940, Stanton L. Young Boulevard, BMSB 737, Oklahoma City, OK, 73104, USA.
| | - Satishkumar Ramraj
- Department of Radiation Oncology, University of Oklahoma Health Sciences Center, 940, Stanton L. Young Boulevard, BMSB 737, Oklahoma City, OK, 73104, USA.
| | - Sheeja Aravindan
- Stephenson Cancer Center, 975 NE 10th Street, BRC 1468, Oklahoma City, OK, 73104, USA.
| | - Terence S Herman
- Department of Radiation Oncology, University of Oklahoma Health Sciences Center, 940, Stanton L. Young Boulevard, BMSB 737, Oklahoma City, OK, 73104, USA. .,Stephenson Cancer Center, 975 NE 10th Street, BRC 1468, Oklahoma City, OK, 73104, USA.
| | - Natarajan Aravindan
- Department of Radiation Oncology, University of Oklahoma Health Sciences Center, 940, Stanton L. Young Boulevard, BMSB 737, Oklahoma City, OK, 73104, USA.
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Mudduluru G, Abba M, Batliner J, Patil N, Scharp M, Lunavat TR, Leupold JH, Oleksiuk O, Juraeva D, Thiele W, Rothley M, Benner A, Ben-Neriah Y, Sleeman J, Allgayer H. A Systematic Approach to Defining the microRNA Landscape in Metastasis. Cancer Res 2015; 75:3010-9. [PMID: 26069251 DOI: 10.1158/0008-5472.can-15-0997] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 04/27/2015] [Indexed: 12/13/2022]
Abstract
The microRNA (miRNA) landscape changes during the progression of cancer. We defined a metastasis-associated miRNA landscape using a systematic approach. We profiled and validated miRNA and mRNA expression in a unique series of human colorectal metastasis tissues together with their matched primary tumors and corresponding normal tissues. We identified an exclusive miRNA signature that is differentially expressed in metastases. Three of these miRNAs were identified as key drivers of an EMT-regulating network acting though a number of novel targets. These targets include SIAH1, SETD2, ZEB2, and especially FOXN3, which we demonstrated for the first time as a direct transcriptional suppressor of N-cadherin. The modulation of N-cadherin expression had significant impact on migration, invasion, and metastasis in two different in vivo models. The significant deregulation of the miRNAs defining the network was confirmed in an independent patient set as well as in a database of diverse malignancies derived from more than 6,000 patients. Our data define a novel metastasis-orchestrating network based on systematic hypothesis generation from metastasis tissues.
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Affiliation(s)
- Giridhar Mudduluru
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany. Molecular Oncology of Solid Tumors Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mohammed Abba
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany. Molecular Oncology of Solid Tumors Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany. Centre for Biomedicine and Medical Technology Mannheim, Mannheim, Germany
| | - Jasmin Batliner
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany. Molecular Oncology of Solid Tumors Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nitin Patil
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany. Molecular Oncology of Solid Tumors Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany. Centre for Biomedicine and Medical Technology Mannheim, Mannheim, Germany
| | - Maike Scharp
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany. Molecular Oncology of Solid Tumors Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Taral R Lunavat
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany. Molecular Oncology of Solid Tumors Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörg Hendrik Leupold
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany. Molecular Oncology of Solid Tumors Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany. Centre for Biomedicine and Medical Technology Mannheim, Mannheim, Germany
| | - Olga Oleksiuk
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany. Molecular Oncology of Solid Tumors Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dilafruz Juraeva
- Department of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wilko Thiele
- Centre for Biomedicine and Medical Technology Mannheim, Mannheim, Germany. Institute for Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Melanie Rothley
- Centre for Biomedicine and Medical Technology Mannheim, Mannheim, Germany. Institute for Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Axel Benner
- Department of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yinon Ben-Neriah
- Lautenberg Centre for Immunology and Cancer Research Institute for Medical Research Israel-Canada, The Hebrew University, Hadassah Medical School Jerusalem, Jerusalem, Israel
| | - Jonathan Sleeman
- Centre for Biomedicine and Medical Technology Mannheim, Mannheim, Germany. Institute for Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Heike Allgayer
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany. Centre for Biomedicine and Medical Technology Mannheim, Mannheim, Germany.
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Warth SC, Hoefig KP, Hiekel A, Schallenberg S, Jovanovic K, Klein L, Kretschmer K, Ansel KM, Heissmeyer V. Induced miR-99a expression represses Mtor cooperatively with miR-150 to promote regulatory T-cell differentiation. EMBO J 2015; 34:1195-213. [PMID: 25712478 PMCID: PMC4426480 DOI: 10.15252/embj.201489589] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 12/19/2014] [Accepted: 01/21/2015] [Indexed: 12/22/2022] Open
Abstract
Peripheral induction of regulatory T (Treg) cells provides essential protection from inappropriate immune responses. CD4(+) T cells that lack endogenous miRNAs are impaired to differentiate into Treg cells, but the relevant miRNAs are unknown. We performed an overexpression screen with T-cell-expressed miRNAs in naive mouse CD4(+) T cells undergoing Treg differentiation. Among 130 candidates, the screen identified 29 miRNAs with a negative and 10 miRNAs with a positive effect. Testing reciprocal Th17 differentiation revealed specific functions for miR-100, miR-99a and miR-10b, since all of these promoted the Treg and inhibited the Th17 program without impacting on viability, proliferation and activation. miR-99a cooperated with miR-150 to repress the expression of the Th17-promoting factor mTOR. The comparably low expression of miR-99a was strongly increased by the Treg cell inducer "retinoic acid", and the abundantly expressed miR-150 could only repress Mtor in the presence of miR-99a. Our data suggest that induction of Treg cell differentiation is regulated by a miRNA network, which involves cooperation of constitutively expressed as well as inducible miRNAs.
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Affiliation(s)
- Sebastian C Warth
- Helmholtz Zentrum München, Research Unit Molecular Immune Regulation, Institute of Molecular Immunology, Munich, Germany
| | - Kai P Hoefig
- Helmholtz Zentrum München, Research Unit Molecular Immune Regulation, Institute of Molecular Immunology, Munich, Germany
| | - Anian Hiekel
- Helmholtz Zentrum München, Research Unit Molecular Immune Regulation, Institute of Molecular Immunology, Munich, Germany
| | - Sonja Schallenberg
- Molecular and Cellular Immunology/Immune Regulation, DFG-Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | | | - Ludger Klein
- Institute for Immunology, University of Munich, Munich, Germany
| | - Karsten Kretschmer
- Molecular and Cellular Immunology/Immune Regulation, DFG-Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - K Mark Ansel
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Vigo Heissmeyer
- Helmholtz Zentrum München, Research Unit Molecular Immune Regulation, Institute of Molecular Immunology, Munich, Germany Institute for Immunology, University of Munich, Munich, Germany
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Khan S, Wall D, Curran C, Newell J, Kerin MJ, Dwyer RM. MicroRNA-10a is reduced in breast cancer and regulated in part through retinoic acid. BMC Cancer 2015; 15:345. [PMID: 25934412 PMCID: PMC4425901 DOI: 10.1186/s12885-015-1374-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/27/2015] [Indexed: 01/30/2023] Open
Abstract
Background MicroRNAs (miRNAs) are short non-coding RNA molecules that play a critical role in mRNA cleavage and translational repression, and are known to be altered in many diseases including breast cancer. MicroRNA-10a (miR-10a) has been shown to be deregulated in various cancer types. The aim of this study was to investigate miR-10a expression in breast cancer and to further delineate the role of retinoids and thyroxine in regulation of miR-10a. Methods Following informed patient consent and ethical approval, tissue samples were obtained during surgery. miR-10a was quantified in malignant (n = 103), normal (n = 30) and fibroadenoma (n = 35) tissues by RQ-PCR. Gene expression of Retinoic Acid Receptor beta (RARβ) and Thyroid Hormone receptor alpha (THRα) was also quantified in the same patient samples (n = 168). The in vitro effects of all-trans Retinoic acid (ATRA) and L-Thyroxine (T4) both individually and in combination, on miR-10a expression was investigated in breast cancer cell lines, T47D and SK-BR-3. Results The level of miR-10a expression was significantly decreased in tissues harvested from breast cancer patients (Mean (SEM) 2.1(0.07)) Log10 Relative Quantity (RQ)) compared to both normal (3.0(0.16) Log10 RQ, p < 0.001) and benign tissues (2.6(0.17) Log10 RQ, p < 0.05). The levels of both RARβ and THRα gene expression were also found to be decreased in breast cancer patients compared to controls (p < 0.001). A significant positive correlation was determined between miR-10a and RARβ (r = 0.31, p < 0.001) and also with THRα (r = 0.32, p < 0.001). In vitro stimulation assays revealed miR-10a expression was increased in both T47D and SK-BR-3 cells following addition of ATRA (2 fold (0.7)). While T4 alone did not stimulate miR-10a expression, the combination of T4 and ATRA was found to have a positive synergistic effect. Conclusion The data presented supports a potential tumour suppressor role for miR-10a in breast cancer, and highlights retinoic acid as a positive regulator of the microRNA. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1374-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sonja Khan
- Discipline of Surgery, School of Medicine, Clinical Science Institute, National University of Ireland, Galway, Galway, Ireland.
| | - Deirdre Wall
- Clinical Research Facility and School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Galway, Ireland.
| | - Catherine Curran
- Discipline of Surgery, School of Medicine, Clinical Science Institute, National University of Ireland, Galway, Galway, Ireland.
| | - John Newell
- Clinical Research Facility and School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Galway, Ireland.
| | - Michael J Kerin
- Discipline of Surgery, School of Medicine, Clinical Science Institute, National University of Ireland, Galway, Galway, Ireland.
| | - Roisin M Dwyer
- Discipline of Surgery, School of Medicine, Clinical Science Institute, National University of Ireland, Galway, Galway, Ireland.
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Pandey A, Singh P, Jauhari A, Singh T, Khan F, Pant AB, Parmar D, Yadav S. Critical role of the miR-200 family in regulating differentiation and proliferation of neurons. J Neurochem 2015; 133:640-52. [DOI: 10.1111/jnc.13089] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 02/20/2015] [Accepted: 02/20/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Ankita Pandey
- Developmental Toxicology Division; CSIR-Indian Institute of Toxicology Research; Lucknow Uttar Pradesh India
| | - Parul Singh
- Developmental Toxicology Division; CSIR-Indian Institute of Toxicology Research; Lucknow Uttar Pradesh India
| | - Abhishek Jauhari
- Developmental Toxicology Division; CSIR-Indian Institute of Toxicology Research; Lucknow Uttar Pradesh India
- Academy of Scientific and Innovative Research (AcSIR); New Delhi India
| | - Tanisha Singh
- Developmental Toxicology Division; CSIR-Indian Institute of Toxicology Research; Lucknow Uttar Pradesh India
| | - Farah Khan
- Department of Biochemistry; JamiaHamdard University; New Delhi India
| | - Aditya B. Pant
- Developmental Toxicology Division; CSIR-Indian Institute of Toxicology Research; Lucknow Uttar Pradesh India
| | - Devendra Parmar
- Developmental Toxicology Division; CSIR-Indian Institute of Toxicology Research; Lucknow Uttar Pradesh India
| | - Sanjay Yadav
- Developmental Toxicology Division; CSIR-Indian Institute of Toxicology Research; Lucknow Uttar Pradesh India
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59
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Janesick A, Wu SC, Blumberg B. Retinoic acid signaling and neuronal differentiation. Cell Mol Life Sci 2015; 72:1559-76. [PMID: 25558812 PMCID: PMC11113123 DOI: 10.1007/s00018-014-1815-9] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/15/2014] [Accepted: 12/19/2014] [Indexed: 01/13/2023]
Abstract
The identification of neurological symptoms caused by vitamin A deficiency pointed to a critical, early developmental role of vitamin A and its metabolite, retinoic acid (RA). The ability of RA to induce post-mitotic, neural phenotypes in various stem cells, in vitro, served as early evidence that RA is involved in the switch between proliferation and differentiation. In vivo studies have expanded this "opposing signal" model, and the number of primary neurons an embryo develops is now known to depend critically on the levels and spatial distribution of RA. The proneural and neurogenic transcription factors that control the exit of neural progenitors from the cell cycle and allow primary neurons to develop are partly elucidated, but the downstream effectors of RA receptor (RAR) signaling (many of which are putative cell cycle regulators) remain largely unidentified. The molecular mechanisms underlying RA-induced primary neurogenesis in anamniote embryos are starting to be revealed; however, these data have been not been extended to amniote embryos. There is growing evidence that bona fide RARs are found in some mollusks and other invertebrates, but little is known about their necessity or functions in neurogenesis. One normal function of RA is to regulate the cell cycle to halt proliferation, and loss of RA signaling is associated with dedifferentiation and the development of cancer. Identifying the genes and pathways that mediate cell cycle exit downstream of RA will be critical for our understanding of how to target tumor differentiation. Overall, elucidating the molecular details of RAR-regulated neurogenesis will be decisive for developing and understanding neural proliferation-differentiation switches throughout development.
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Affiliation(s)
- Amanda Janesick
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, 92697-2300 USA
| | - Stephanie Cherie Wu
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, 92697-2300 USA
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, 92697-2300 USA
- Department of Pharmaceutical Sciences, University of California, Irvine, USA
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60
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Ross SA, Davis CD. The emerging role of microRNAs and nutrition in modulating health and disease. Annu Rev Nutr 2015; 34:305-36. [PMID: 25033062 DOI: 10.1146/annurev-nutr-071813-105729] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding the molecular mechanisms that inform how diet and dietary supplements influence health and disease is an active research area. One such mechanism concerns the role of diet in modulating the activity and function of microRNAs (miRNAs). miRNAs are small noncoding RNA molecules that are involved in posttranscriptional gene silencing and have been shown to control gene expression in diverse biological processes including development, differentiation, cell proliferation, metabolism, and inflammation as well as in human diseases. Recent evidence described in this review highlights how dietary factors may influence cancer, cardiovascular disease, type 2 diabetes mellitus, obesity, and nonalcoholic fatty liver disease through modulation of miRNA expression. Additionally, circulating miRNAs are emerging as putative biomarkers of disease, susceptibility, and perhaps dietary exposure. Research needs to move beyond associations in cells and animals to understanding the direct effects of diet and dietary supplements on miRNA expression and function in human health and disease.
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Affiliation(s)
- Sharon A Ross
- Nutritional Science Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland 20892;
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Hoss AG, Labadorf A, Latourelle JC, Kartha VK, Hadzi TC, Gusella JF, MacDonald ME, Chen JF, Akbarian S, Weng Z, Vonsattel JP, Myers RH. miR-10b-5p expression in Huntington's disease brain relates to age of onset and the extent of striatal involvement. BMC Med Genomics 2015; 8:10. [PMID: 25889241 PMCID: PMC4349621 DOI: 10.1186/s12920-015-0083-3] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/06/2015] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small non-coding RNAs that recognize sites of complementarity of target messenger RNAs, resulting in transcriptional regulation and translational repression of target genes. In Huntington’s disease (HD), a neurodegenerative disease caused by a trinucleotide repeat expansion, miRNA dyregulation has been reported, which may impact gene expression and modify the progression and severity of HD. Methods We performed next-generation miRNA sequence analysis in prefrontal cortex (Brodmann Area 9) from 26 HD, 2 HD gene positive, and 36 control brains. Neuropathological information was available for all HD brains, including age at disease onset, CAG-repeat size, Vonsattel grade, and Hadzi-Vonsattel striatal and cortical scores, a continuous measure of the extent of neurodegeneration. Linear models were performed to examine the relationship of miRNA expression to these clinical features, and messenger RNA targets of associated miRNAs were tested for gene ontology term enrichment. Results We identified 75 miRNAs differentially expressed in HD brain (FDR q-value <0.05). Among the HD brains, nine miRNAs were significantly associated with Vonsattel grade of neuropathological involvement and three of these, miR-10b-5p, miR-10b-3p, and miR-302a-3p, significantly related to the Hadzi-Vonsattel striatal score (a continuous measure of striatal involvement) after adjustment for CAG length. Five miRNAs (miR-10b-5p, miR-196a-5p, miR-196b-5p, miR-10b-3p, and miR-106a-5p) were identified as having a significant relationship to CAG length-adjusted age of onset including miR-10b-5p, the mostly strongly over-expressed miRNA in HD cases. Although prefrontal cortex was the source of tissue profiled in these studies, the relationship of miR-10b-5p expression to striatal involvement in the disease was independent of cortical involvement. Correlation of miRNAs to the clinical features clustered by direction of effect and the gene targets of the observed miRNAs showed association to processes relating to nervous system development and transcriptional regulation. Conclusions These results demonstrate that miRNA expression in cortical BA9 provides insight into striatal involvement and support a role for these miRNAs, particularly miR-10b-5p, in HD pathogenicity. The miRNAs identified in our studies of postmortem brain tissue may be detectable in peripheral fluids and thus warrant consideration as accessible biomarkers for disease stage, rate of progression, and other important clinical characteristics of HD. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0083-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew G Hoss
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA. .,Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, MA, USA.
| | - Adam Labadorf
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA. .,Bioinformatics Program, Boston University, Boston, MA, USA.
| | - Jeanne C Latourelle
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA.
| | - Vinay K Kartha
- Bioinformatics Program, Boston University, Boston, MA, USA.
| | - Tiffany C Hadzi
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA.
| | - James F Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Marcy E MacDonald
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Jiang-Fan Chen
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA.
| | - Schahram Akbarian
- Friedman Brain Institute, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA.
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Jean Paul Vonsattel
- Department of Pathology and Cell Biology, Columbia University Medical Center and the New York Presbyterian Hospital, New York, NY, USA.
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA. .,Genome Science Institute, Boston University School of Medicine, Boston, MA, USA.
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WANG XINGSHAN, QIAN WENWEI, WU ZHIHONG, BIAN YANYAN, WENG XISHENG. Preliminary screening of differentially expressed circulating microRNAs in patients with steroid-induced osteonecrosis of the femoral head. Mol Med Rep 2014; 10:3118-24. [DOI: 10.3892/mmr.2014.2660] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 08/07/2014] [Indexed: 11/06/2022] Open
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Characterization of paraquat-induced miRNA profiling response in hNPCs undergoing proliferation. Int J Mol Sci 2014; 15:18422-36. [PMID: 25314302 PMCID: PMC4227223 DOI: 10.3390/ijms151018422] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 01/03/2023] Open
Abstract
Aberration during the development of the central nervous system (CNS) due to environmental factors underlies a variety of adverse developmental outcomes. Paraquat (PQ) is a widely studied neurotoxicant that perturbs the normal structure/function of adult CNS. Yet, the impacts of PQ exposure on the developing CNS remain unclear. miRNAs represent a class of small non-coding RNA molecules involved in the regulation of neural development. Thus in the present study, we analyzed the impacts of PQ on the miRNome of human neural progenitor cells (hNPCs) during proliferation by using the Exiqon miRCURY™ LNA Array. A total of 66 miRNAs were identified as differentially expressed in proliferating hNPCs upon PQ treatment. miRTarBase prediction identified 1465 mRNAs, including several genes (e.g., nestin, sox1, ngn1) previously proved to be associated with the neural proliferation and differentiation, as target genes of PQ-induced differentially expressed miRNAs. The database for annotation, visualization and integrated discovery (DAVID) bioinformatics analysis showed that target genes were enriched in regulation of cell proliferation and differentiation, cell cycle and apoptosis as well as tumor protein 53 (p53), Wnt, Notch and mitogen-activated protein kinases (MAPK) signaling pathways (p < 0.001). These findings were confirmed by real-time RT-PCR. Based on our results we conclude that PQ-induced impacts on the miRNA profiling of hNPCs undergoing proliferation may underlie the developmental neurotoxicity of PQ.
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Batsché E, Ameyar-Zazoua M. The influence of Argonaute proteins on alternative RNA splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:141-56. [DOI: 10.1002/wrna.1264] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 07/28/2014] [Accepted: 07/31/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Eric Batsché
- Institut Pasteur, Dpt Biologie du Développement et Cellules Souches; Unité de Régulation Epigénétique; 75015 Paris France
- URA2578; CNRS
| | - Maya Ameyar-Zazoua
- Institut Pasteur, Dpt Biologie du Développement et Cellules Souches; Unité de Régulation Epigénétique; 75015 Paris France
- URA2578; CNRS
- Laboratoire Epigénétique et Destin Cellulaire, CNRS UMR7216; Université Paris Diderot, Cité Sorbonne Paris; Paris France
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Kasimanickam VR, Kasimanickam RK, Dernell WS. Dysregulated microRNA clusters in response to retinoic acid and CYP26B1 inhibitor induced testicular function in dogs. PLoS One 2014; 9:e99433. [PMID: 24911586 PMCID: PMC4049822 DOI: 10.1371/journal.pone.0099433] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/14/2014] [Indexed: 12/11/2022] Open
Abstract
Spermatogenesis is a multistep synchronized process. Diploid spermatogonia differentiate into haploid spermatozoa following mitosis, meiosis and spermiogenesis. Division and differentiation of male germ cells is achieved through the sequential expression of several genes. Numerous mRNAs in the differentiating germ cells undergo post-transcriptional and translational regulation. MiRNAs are powerful negative regulators of mRNA transcription, stability, and translation and recognize their mRNA targets through base-pairing. Retinoic acid (RA) signaling is essential for spermatogenesis and testicular function. Testicular RA level is critical for RA signal transduction. This study investigated the miRNAs modulation in an RA- induced testicular environment following the administration of all-trans RA (2 µM) and CYP26B1- inhibitor (1 µM) compared to control. Eighty four canine mature miRNAs were analyzed and their expression signatures were distinguished using real-time PCR based array technology. Of the miRNAs analyzed, miRNA families such as miR-200 (cfa-miR-200a, cfa-miR-200b and cfa-miR-200c), Mirlet-7 (cfa-let-7a, cfa-let-7b, cfa-let-7c, cfa-let-7g and cfa-let-7f), miR-125 (cfa-miR-125a and cfa-miR-125b), miR-146 (cfa-miR-146a and cfa-miR-146b), miR-34 (cfa-miR-34a, cfa-miR-34b and cfa-miR-34c), miR-23 (cfa-miR-23a and cfa-miR-23b), cfa-miR-184, cfa-miR-214 and cfa-miR-141 were significantly up-regulated with testicular RA intervention via administration of CYP26B1 inhibitor and all-trans-RA and species of miRNA such as cfa-miR-19a, cfa-miR-29b, cfa-miR-29c, cfa-miR-101 and cfa-miR-137 were significantly down-regulated. This study explored information regarding chromosome distribution, human orthologous sequences and the interaction of target genes of miRNA families significantly distinguished in this study using prediction algorithms. This study importantly identified dysregulated miRNA species resulting from RA-induced spermatogenesis. The present contribution serves as a useful resource for further elucidation of the regulatory role of individual miRNA in RA synchronized canine spermatogenesis.
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Affiliation(s)
- Vanmathy R. Kasimanickam
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
| | - Ramanathan K. Kasimanickam
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, Washington, United States of America
| | - William S. Dernell
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, Washington, United States of America
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Smirnova L, Block K, Sittka A, Oelgeschläger M, Seiler AEM, Luch A. MicroRNA profiling as tool for in vitro developmental neurotoxicity testing: the case of sodium valproate. PLoS One 2014; 9:e98892. [PMID: 24896083 PMCID: PMC4045889 DOI: 10.1371/journal.pone.0098892] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/08/2014] [Indexed: 01/10/2023] Open
Abstract
Studying chemical disturbances during neural differentiation of murine embryonic stem cells (mESCs) has been established as an alternative in vitro testing approach for the identification of developmental neurotoxicants. miRNAs represent a class of small non-coding RNA molecules involved in the regulation of neural development and ESC differentiation and specification. Thus, neural differentiation of mESCs in vitro allows investigating the role of miRNAs in chemical-mediated developmental toxicity. We analyzed changes in miRNome and transcriptome during neural differentiation of mESCs exposed to the developmental neurotoxicant sodium valproate (VPA). A total of 110 miRNAs and 377 mRNAs were identified differently expressed in neurally differentiating mESCs upon VPA treatment. Based on miRNA profiling we observed that VPA shifts the lineage specification from neural to myogenic differentiation (upregulation of muscle-abundant miRNAs, mir-206, mir-133a and mir-10a, and downregulation of neural-specific mir-124a, mir-128 and mir-137). These findings were confirmed on the mRNA level and via immunochemistry. Particularly, the expression of myogenic regulatory factors (MRFs) as well as muscle-specific genes (Actc1, calponin, myosin light chain, asporin, decorin) were found elevated, while genes involved in neurogenesis (e.g. Otx1, 2, and Zic3, 4, 5) were repressed. These results were specific for valproate treatment and―based on the following two observations―most likely due to the inhibition of histone deacetylase (HDAC) activity: (i) we did not observe any induction of muscle-specific miRNAs in neurally differentiating mESCs exposed to the unrelated developmental neurotoxicant sodium arsenite; and (ii) the expression of muscle-abundant mir-206 and mir-10a was similarly increased in cells exposed to the structurally different HDAC inhibitor trichostatin A (TSA). Based on our results we conclude that miRNA expression profiling is a suitable molecular endpoint for developmental neurotoxicity. The observed lineage shift into myogenesis, where miRNAs may play an important role, could be one of the developmental neurotoxic mechanisms of VPA.
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Affiliation(s)
- Lena Smirnova
- Federal Institute for Risk Assessment (BfR), Berlin, Germany
- * E-mail:
| | - Katharina Block
- Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | | | | | | | - Andreas Luch
- Federal Institute for Risk Assessment (BfR), Berlin, Germany
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67
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Leppert U, Eisenreich A. The role of tissue factor isoforms in cancer biology. Int J Cancer 2014; 137:497-503. [PMID: 24806794 DOI: 10.1002/ijc.28959] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 05/02/2014] [Indexed: 12/17/2022]
Abstract
Tissue Factor (TF) is an evolutionary conserved glycoprotein, which is of immense importance for a variety of biologic processes. TF is expressed in two naturally occurring protein isoforms, membrane-bound "full-length" (fl)TF and soluble alternatively spliced (as)TF. The TF isoform expression is differentially modulated on post-transcriptional level via regulatory factors, such as serine/arginine-rich (SR) proteins, SR protein kinases and micro (mi)RNAs. Both isoforms mediate a variety of physiologic- and pathophysiologic-relevant functions, such as thrombogenicity, angiogenesis, cell signaling, tumor cell proliferation and metastasis. In this review, we will depict the main mechanisms regulating the TF isoform expression in cancer and under other pathophysiologic-relevant conditions. Moreover, we will summarize and discuss the latest findings regarding the role of TF and its isoforms in cancer biology.
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Affiliation(s)
- Ulrike Leppert
- Charité - Universitätsmedizin Berlin, Campus Mitte, Charite Centrum 04/13, Berlin, Germany
| | - Andreas Eisenreich
- Charité - Universitätsmedizin Berlin, Campus Mitte, Charite Centrum 04/13, Berlin, Germany
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Friedländer MR, Lizano E, Houben AJS, Bezdan D, Báñez-Coronel M, Kudla G, Mateu-Huertas E, Kagerbauer B, González J, Chen KC, LeProust EM, Martí E, Estivill X. Evidence for the biogenesis of more than 1,000 novel human microRNAs. Genome Biol 2014; 15:R57. [PMID: 24708865 PMCID: PMC4054668 DOI: 10.1186/gb-2014-15-4-r57] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 04/07/2014] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are established regulators of development, cell identity and disease. Although nearly two thousand human miRNA genes are known and new ones are continuously discovered, no attempt has been made to gauge the total miRNA content of the human genome. RESULTS Employing an innovative computational method on massively pooled small RNA sequencing data, we report 2,469 novel human miRNA candidates of which 1,098 are validated by in-house and published experiments. Almost 300 candidates are robustly expressed in a neuronal cell system and are regulated during differentiation or when biogenesis factors Dicer, Drosha, DGCR8 or Ago2 are silenced. To improve expression profiling, we devised a quantitative miRNA capture system. In a kidney cell system, 400 candidates interact with DGCR8 at transcript positions that suggest miRNA hairpin recognition, and 1,000 of the new miRNA candidates interact with Ago1 or Ago2, indicating that they are directly bound by miRNA effector proteins. From kidney cell CLASH experiments, in which miRNA-target pairs are ligated and sequenced, we observe hundreds of interactions between novel miRNAs and mRNA targets. The novel miRNA candidates are specifically but lowly expressed, raising the possibility that not all may be functional. Interestingly, the majority are evolutionarily young and overrepresented in the human brain. CONCLUSIONS In summary, we present evidence that the complement of human miRNA genes is substantially larger than anticipated, and that more are likely to be discovered in the future as more tissues and experimental conditions are sequenced to greater depth.
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Affiliation(s)
- Marc R Friedländer
- Genomics and Disease Group, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Catalonia, Spain
- Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Esther Lizano
- Genomics and Disease Group, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Catalonia, Spain
- Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Anna JS Houben
- Genomics and Disease Group, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Catalonia, Spain
- Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Daniela Bezdan
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Mónica Báñez-Coronel
- Genomics and Disease Group, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Catalonia, Spain
- Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland
| | - Elisabet Mateu-Huertas
- Genomics and Disease Group, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Catalonia, Spain
- Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Birgit Kagerbauer
- Genomics and Disease Group, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Catalonia, Spain
- Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Justo González
- Genomics and Disease Group, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Catalonia, Spain
- Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Kevin C Chen
- Department of Genetics, Rutgers, State University of New Jersey, Frelinghuysen Road 174, Piscataway, NJ 08854, USA
- BioMaPS Institute for Quantitative Biology, Rutgers, State University of New Jersey, Frelinghuysen Road 174, Piscataway, NJ 08854, USA
| | - Emily M LeProust
- Genomics Solution Unit, Agilent Technologies Inc., Santa Clara, CA 95051, USA
| | - Eulàlia Martí
- Genomics and Disease Group, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Catalonia, Spain
- Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
| | - Xavier Estivill
- Genomics and Disease Group, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Catalonia, Spain
- Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
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Martin HC, Wani S, Steptoe AL, Krishnan K, Nones K, Nourbakhsh E, Vlassov A, Grimmond SM, Cloonan N. Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs. Genome Biol 2014; 15:R51. [PMID: 24629056 PMCID: PMC4053950 DOI: 10.1186/gb-2014-15-3-r51] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 02/19/2014] [Indexed: 12/31/2022] Open
Abstract
Background MicroRNAs (miRNAs) bind to mRNAs and target them for translational inhibition or transcriptional degradation. It is thought that most miRNA-mRNA interactions involve the seed region at the 5′ end of the miRNA. The importance of seed sites is supported by experimental evidence, although there is growing interest in interactions mediated by the central region of the miRNA, termed centered sites. To investigate the prevalence of these interactions, we apply a biotin pull-down method to determine the direct targets of ten human miRNAs, including four isomiRs that share centered sites, but not seeds, with their canonical partner miRNAs. Results We confirm that miRNAs and their isomiRs can interact with hundreds of mRNAs, and that imperfect centered sites are common mediators of miRNA-mRNA interactions. We experimentally demonstrate that these sites can repress mRNA activity, typically through translational repression, and are enriched in regions of the transcriptome bound by AGO. Finally, we show that the identification of imperfect centered sites is unlikely to be an artifact of our protocol caused by the biotinylation of the miRNA. However, the fact that there was a slight bias against seed sites in our protocol may have inflated the apparent prevalence of centered site-mediated interactions. Conclusions Our results suggest that centered site-mediated interactions are much more frequent than previously thought. This may explain the evolutionary conservation of the central region of miRNAs, and has significant implications for decoding miRNA-regulated genetic networks, and for predicting the functional effect of variants that do not alter protein sequence.
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70
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Hoss AG, Kartha VK, Dong X, Latourelle JC, Dumitriu A, Hadzi TC, MacDonald ME, Gusella JF, Akbarian S, Chen JF, Weng Z, Myers RH. MicroRNAs located in the Hox gene clusters are implicated in huntington's disease pathogenesis. PLoS Genet 2014; 10:e1004188. [PMID: 24586208 PMCID: PMC3937267 DOI: 10.1371/journal.pgen.1004188] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/06/2014] [Indexed: 12/12/2022] Open
Abstract
Transcriptional dysregulation has long been recognized as central to the pathogenesis of Huntington's disease (HD). MicroRNAs (miRNAs) represent a major system of post-transcriptional regulation, by either preventing translational initiation or by targeting transcripts for storage or for degradation. Using next-generation miRNA sequencing in prefrontal cortex (Brodmann Area 9) of twelve HD and nine controls, we identified five miRNAs (miR-10b-5p, miR-196a-5p, miR-196b-5p, miR-615-3p and miR-1247-5p) up-regulated in HD at genome-wide significance (FDR q-value<0.05). Three of these, miR-196a-5p, miR-196b-5p and miR-615-3p, were expressed at near zero levels in control brains. Expression was verified for all five miRNAs using reverse transcription quantitative PCR and all but miR-1247-5p were replicated in an independent sample (8HD/8C). Ectopic miR-10b-5p expression in PC12 HTT-Q73 cells increased survival by MTT assay and cell viability staining suggesting increased expression may be a protective response. All of the miRNAs but miR-1247-5p are located in intergenic regions of Hox clusters. Total mRNA sequencing in the same samples identified fifteen of 55 genes within the Hox cluster gene regions as differentially expressed in HD, and the Hox genes immediately adjacent to the four Hox cluster miRNAs as up-regulated. Pathway analysis of mRNA targets of these miRNAs implicated functions for neuronal differentiation, neurite outgrowth, cell death and survival. In regression models among the HD brains, huntingtin CAG repeat size, onset age and age at death were independently found to be inversely related to miR-10b-5p levels. CAG repeat size and onset age were independently inversely related to miR-196a-5p, onset age was inversely related to miR-196b-5p and age at death was inversely related to miR-615-3p expression. These results suggest these Hox-related miRNAs may be involved in neuroprotective response in HD. Recently, miRNAs have shown promise as biomarkers for human diseases and given their relationship to disease expression, these miRNAs are biomarker candidates in HD.
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Affiliation(s)
- Andrew G. Hoss
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Vinay K. Kartha
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Xianjun Dong
- Program in Bioinformatics and Integrative Biology, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jeanne C. Latourelle
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Alexandra Dumitriu
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Tiffany C. Hadzi
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Marcy E. MacDonald
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - James F. Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Schahram Akbarian
- Friedman Brain Institute, Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Jiang-Fan Chen
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Richard H. Myers
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Genome Science Institute, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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Hu R, Pan W, Fedulov AV, Jester W, Jones MR, Weiss ST, Panettieri RA, Tantisira K, Lu Q. MicroRNA-10a controls airway smooth muscle cell proliferation via direct targeting of the PI3 kinase pathway. FASEB J 2014; 28:2347-57. [PMID: 24522205 DOI: 10.1096/fj.13-247247] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Airway smooth muscle (ASM) cells play important physiological roles in the lung, and abnormal proliferation of ASM directly contributes to the airway remodeling during development of lung diseases such as asthma. MicroRNAs are small yet versatile gene tuners that regulate a variety of cellular processes, including cell growth and proliferation; however, little is known about the precise role of microRNAs in the proliferation of the ASM. Here we report that a specific microRNA (miR-10a) controls ASM proliferation through directly inhibiting the phosphoinositide 3-kinase (PI3K) pathway. Next-generation sequencing identified miR-10a as the most abundant microRNA expressed in primary human airway smooth muscle (HASM) cells, accounting for > 20% of all small RNA reads. Overexpression of miR-10a reduced mitogen-induced HASM proliferation by ∼50%, whereas inhibition of miR-10a increased HASM proliferation by ∼40%. Microarray profiling of HASM cells expressing miR-10a mimics identified 52 significantly down-regulated genes as potential targets of miR-10a, including the catalytic subunit α of PI3K (PIK3CA), the central component of the PI3K pathway. MiR-10a directly suppresses PIK3CA expression by targeting the 3'-untranslated region (3'-UTR) of the gene. Inhibition of PIK3CA by miR-10a reduced V-akt murine thymoma viral oncogene homolog 1 (AKT) phosphorylation and blunted the expression of cyclins and cyclin-dependent kinases that are required for HASM proliferation. Together, our study identifies a novel microRNA-mediated regulatory mechanism for PI3K signaling and ASM proliferation and further suggests miR-10a as a potential therapeutic target for lung diseases whose etiology resides in abnormal ASM proliferation.
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Affiliation(s)
- Ruoxi Hu
- 1Program in Molecular and Integrative Physiological Sciences, Harvard School of Public Health, 665 Huntington Ave., Room I-305, Boston, MA 02115, USA.
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De Meulder B, Berger F, Bareke E, Depiereux S, Michiels C, Depiereux E. Meta-analysis and gene set analysis of archived microarrays suggest implication of the spliceosome in metastatic and hypoxic phenotypes. PLoS One 2014; 9:e86699. [PMID: 24497970 PMCID: PMC3908947 DOI: 10.1371/journal.pone.0086699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/10/2013] [Indexed: 12/17/2022] Open
Abstract
We propose to make use of the wealth of underused DNA chip data available in public repositories to study the molecular mechanisms behind the adaptation of cancer cells to hypoxic conditions leading to the metastatic phenotype. We have developed new bioinformatics tools and adapted others to identify with maximum sensitivity those genes which are expressed differentially across several experiments. The comparison of two analytical approaches, based on either Over Representation Analysis or Functional Class Scoring, by a meta-analysis-based approach, led to the retrieval of known information about the biological situation - thus validating the model - but also more importantly to the discovery of the previously unknown implication of the spliceosome, the cellular machinery responsible for mRNA splicing, in the development of metastasis.
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Affiliation(s)
- Bertrand De Meulder
- Microorganism Biology Research Unit -NARILIS, University of Namur, Namur, Belgium
| | - Fabrice Berger
- Microorganism Biology Research Unit -NARILIS, University of Namur, Namur, Belgium
| | - Eric Bareke
- Sainte Justine University Hospital Center Research Center, University of Montreal, Montreal, Canada
| | - Sophie Depiereux
- Environmental and Evolutional Research Unit, University of Namur, Namur, Belgium
| | - Carine Michiels
- Cellular Biology Research Unit - NARILIS, University of Namur, Namur, Belgium
| | - Eric Depiereux
- Microorganism Biology Research Unit -NARILIS, University of Namur, Namur, Belgium
- * E-mail:
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73
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Zhi F, Wang R, Wang Q, Xue L, Deng D, Wang S, Yang Y. MicroRNAs in neuroblastoma: small-sized players with a large impact. Neurochem Res 2014; 39:613-23. [PMID: 24477657 DOI: 10.1007/s11064-014-1247-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 12/22/2013] [Accepted: 01/21/2014] [Indexed: 12/23/2022]
Abstract
Neuroblastoma, a malignant embryonal tumor of the sympathetic nervous system, is the most common solid extracranial malignancy of childhood and accounts for 15 % of all childhood cancer deaths. The biological behavior of neuroblastoma is extensively heterogeneous, ranging from spontaneous regression to rapid progression despite multimodal aggressive therapy. Although the molecular basis of neuroblastoma has received considerable attention over the past decade, elucidating the mechanisms for the aggressive progression of neuroblastoma is needed for improving the efficacy of treatment. miRNAs (microRNAs) are small non-coding RNA molecules generally 19-22 nucleotides in length. miRNAs regulate 60 % of human gene expression at the post-transcriptional level by targeting regions of sequence complementarity on the 3'-untranslated regions (3'-UTRs) of specific mRNAs. miRNAs can either cause degradation of mRNAs or can inhibit their translation and therefore play major roles in normal growth and development. miRNA dysregulation has oncogenic or tumor-suppressive functions in virtually all forms of cancer, including neuroblastoma. The present review highlights the current insights on dysregulated miRNAs in neuroblastoma and on their roles in the diagnosis, prognosis, and treatment of this malignancy. As a rapidly evolving field of basic and biomedical sciences, miRNA research holds a great potential to impact on the management of neuroblastoma.
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Affiliation(s)
- Feng Zhi
- Modern Medical Research Center, Third Affiliated Hospital of Soochow University, 185#, Juqian Road, Changzhou, 213003, Jiangsu, China
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74
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Regulation of breast cancer and bone metastasis by microRNAs. DISEASE MARKERS 2013; 35:369-87. [PMID: 24191129 PMCID: PMC3809754 DOI: 10.1155/2013/451248] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/17/2013] [Accepted: 08/27/2013] [Indexed: 01/05/2023]
Abstract
Breast cancer progression including bone metastasis is a complex process involving numerous changes in gene expression and function. MicroRNAs (miRNAs) are small endogenous noncoding RNAs that regulate gene expression by targeting protein-coding mRNAs posttranscriptionally, often affecting a number of gene targets simultaneously. Alteration in expression of miRNAs is common in human breast cancer, possessing with either oncogenic or tumor suppressive activity. The expression and the functional role of several miRNAs (miR-206, miR-31, miR-27a/b, miR-21, miR-92a, miR-205, miR-125a/b, miR-10b, miR-155, miR-146a/b, miR-335, miR-204, miR-211, miR-7, miR-22, miR-126, and miR-17) in breast cancer has been identified. In this review we summarize the experimentally validated targets of up- and downregulated miRNAs and their regulation in breast cancer and bone metastasis for diagnostic and therapeutic purposes.
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75
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Benoit C, Ould-Hamouda H, Crepin D, Gertler A, Amar L, Taouis M. Early leptin blockade predisposes fat-fed rats to overweight and modifies hypothalamic microRNAs. J Endocrinol 2013; 218:35-47. [PMID: 23576026 DOI: 10.1530/joe-12-0561] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Perinatal leptin impairment has long-term consequences on energy homeostasis leading to body weight gain. The underlying mechanisms are still not clearly established. We aimed to analyze the long-term effects of early leptin blockade. In this study, newborn rats received daily injection of a pegylated rat leptin antagonist (pRLA) or saline from day 2 (d2) to d13 and then body weight gain, insulin/leptin sensitivity, and expression profile of microRNAs (miRNAs) at the hypothalamic level were determined at d28, d90, or d153 (following 1 month of high-fat diet (HFD) challenge). We show that pRLA treatment predisposes rats to overweight and promotes leptin/insulin resistance in both hypothalamus and liver at adulthood. pRLA treatment also modifies the hypothalamic miRNA expression profile at d28 leading to the upregulation of 34 miRNAs and the downregulation of four miRNAs. For quantitative RT-PCR confirmation, we show the upregulation of rno-miR-10a at d28 and rno-miR-200a, rno-miR-409-5p, and rno-miR-125a-3p following HFD challenge. Finally, pRLA treatment modifies the expression of genes involved in energy homeostasis control such as UCPs and AdipoRs. In pRLA rat muscle, Ucp2/3 and Adipor1/r2 are upregulated at d90. In liver, pRLA treatment upregulates Adipor1/r2 following HFD challenge. These genes are known to be involved in insulin resistance and type 2 diabetes. In conclusion, we demonstrate that the impairment of leptin action in early life promotes insulin/leptin resistance and modifies the hypothalamic miRNA expression pattern in adulthood, and finally, this study highlights the potential link between hypothalamic miRNA expression pattern and insulin/leptin responsiveness.
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Affiliation(s)
- Charlotte Benoit
- Neuroendocrinologie Moléculaire de la Prise Alimentaire, University of Paris-Sud, UMR 8195, Orsay F-91405, France
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76
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Kocamis H, Hossain M, Cinar MU, Salilew-Wondim D, Mohammadi-Sangcheshmeh A, Tesfaye D, Hölker M, Schellander K. Expression of microRNA and microRNA processing machinery genes during early quail (Coturnix japonica) embryo development. Poult Sci 2013; 92:787-97. [PMID: 23436530 DOI: 10.3382/ps.2012-02691] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
MicroRNA (miRNA) are small regulatory RNA molecules that are implicated in regulating and controlling a wide range of physiological processes including cell division, differentiation, migration, apoptosis, morphogenesis, and organogenesis. The aim of this study was to determine the expression pattern of 32 miRNA and 18 miRNA processing machinery genes during somite formation in quail embryos. The embryos were collected at stages HH (Hamburger and Hamilton) 4, 6, and 9 of embryo development (19, 24, and 30 h of incubation, respectively). Total RNA including miRNA was isolated from 4 groups of embryos (each group consisting of 6 to 8 embryos) were collected at each of the 3 stages (19, 24, and 30 h). The expression pattern of candidate miRNA and miRNA processing machinery genes was performed using quantitative real-time PCR. The results demonstrated that 7 miRNA (let-7a, mir-122, mir-125b, mir-10b, P < 0.01; let-7b, mir-26a, and mir-126, P < 0.05) were differentially expressed during early quail embryo development. In addition, the expression profile of 18 miRNA processing machinery genes was not significantly increased at 30 h of incubation compared with both 19 and 24 h. Our results suggest that machinery genes for miRNA biogenetic pathways are functional, and hence, miRNA may be involved in the regulation of early quail development. These 7 differentially expressed miRNA are suggested to play critical roles in quail embryo somite formation.
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Affiliation(s)
- H Kocamis
- Department of Histology and Embryology, Kirikkale University, Kirikkale, Turkey
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77
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Mukhopadhyay P, Das S, Ahsan MK, Otani H, Das DK. Modulation of microRNA 20b with resveratrol and longevinex is linked with their potent anti-angiogenic action in the ischaemic myocardium and synergestic effects of resveratrol and γ-tocotrienol. J Cell Mol Med 2013; 16:2504-17. [PMID: 22050707 PMCID: PMC3823443 DOI: 10.1111/j.1582-4934.2011.01480.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Resveratrol, a constituent of red wine, and γ-tocotrienol, a constituent of palm oil are important for cardioprotection. Although microRNAs are known regulators for genes involved in cardiac remodelling, the regulatory pathway involving microRNA has not been studied so far. We explored the cardioprotection by resveratrol, longevinex and γ−tocotrienol in ischaemia/reperfusion(I/R) model of rat and determined miRNA profile from isolated RNA. Systemic analyses of miRNA array and theirs targets were determined using a number of computational approaches. Resveratrol and γ-tocotrienol, either alone or in combination, modulated the expression pattern of miRNAs close to the control level based on PCA analyses. Differential expression was observed in over 75 miRNAs, some of them, such as miR-21 and miR-20b (anti-angiogenic) were previously implicated in cardiac remodelling. The target genes for the highest differentially expressed miRNA include genes of various molecular functions such as TGFβ1–Smad3 signalling pathway, inflammation and their transcription factors, which may play key role in reducing I/R injury. Administration of antagomiR-20 attenuated I/R induced vascular endothelial growth factor and HIF1α level. All the interventions treated for 3 weeks lead to significant cardioprotection against ischaemia/reperfusion injury. A unique signature of miRNA profile is observed in control heart pretreated with resveratrol or γ-tocotrienol. We have determined specific group of miRNA in heart that have altered during IR injuries. Most of those altered microRNA expressions modulated close to their basal level in resveratrol or longevinex treated I/R rat. Interestingly, resveratrol and γ-tocotrienol resulted in synergestic action.
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Affiliation(s)
- Partha Mukhopadhyay
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
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78
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Krill KT, Gurdziel K, Heaton JH, Simon DP, Hammer GD. Dicer deficiency reveals microRNAs predicted to control gene expression in the developing adrenal cortex. Mol Endocrinol 2013; 27:754-68. [PMID: 23518926 DOI: 10.1210/me.2012-1331] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
MicroRNAs (miRNAs) are small, endogenous, non-protein-coding RNAs that are an important means of posttranscriptional gene regulation. Deletion of Dicer, a key miRNA processing enzyme, is embryonic lethal in mice, and tissue-specific Dicer deletion results in developmental defects. Using a conditional knockout model, we generated mice lacking Dicer in the adrenal cortex. These Dicer-knockout (KO) mice exhibited perinatal mortality and failure of the adrenal cortex during late gestation between embryonic day 16.5 (E16.5) and E18.5. Further study of Dicer-KO adrenals demonstrated a significant loss of steroidogenic factor 1-expressing cortical cells that was histologically evident as early as E16.5 coincident with an increase in p21 and cleaved-caspase 3 staining in the cortex. However, peripheral cortical proliferation persisted in KO adrenals as assessed by staining of proliferating cell nuclear antigen. To further characterize the embryonic adrenals from Dicer-KO mice, we performed microarray analyses for both gene and miRNA expression on purified RNA isolated from control and KO adrenals of E15.5 and E16.5 embryos. Consistent with the absence of Dicer and the associated loss of miRNA-mediated mRNA degradation, we observed an up-regulation of a small subset of adrenal transcripts in Dicer-KO mice, most notably the transcripts coded by the genes Nr6a1 and Acvr1c. Indeed, several miRNAs, including let-7, miR-34c, and miR-21, that are predicted to target these genes for degradation, were also markedly down-regulated in Dicer-KO adrenals. Together these data suggest a role for miRNA-mediated regulation of a subset of genes that are essential for normal adrenal growth and homeostasis.
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Affiliation(s)
- Kenneth T Krill
- Program in Cellular and Molecular Biology, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI 48109, USA
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79
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García-Segura L, Pérez-Andrade M, Miranda-Ríos J. The emerging role of MicroRNAs in the regulation of gene expression by nutrients. JOURNAL OF NUTRIGENETICS AND NUTRIGENOMICS 2013; 6:16-31. [PMID: 23445777 DOI: 10.1159/000345826] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 11/03/2012] [Indexed: 12/30/2022]
Abstract
MicroRNAs (miRNAs) are a class of evolutionarily conserved, small non-coding RNAs of 19-24 nucleotides in length that regulate gene expression mostly at the posttranscriptional level. They are known to be involved in the control of different processes such as cell cycling, programmed cell death, cell differentiation, tumor development, metastasis, and sensing of nutrient stress. This review summarizes the evidence regarding the changes in miRNA expression that are caused by diets with a deficiency or augmented intake of nutrients such as amino acids, carbohydrates, fatty acids, vitamins, and phytochemicals. As diet is known to influence the expression of miRNAs, miRNA profiling has the potential to be useful in the assessment of nutritional status in dietary intervention studies. Additionally, as it can change miRNA expression, diet may be used as a therapeutic agent to treat many different diseases. Also, we explored here some ideas on therapeutics based on the manipulation of miRNA expression levels for dietary-derived diseases as well as the putative effect of food-derived miRNAs on host gene expression.
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Affiliation(s)
- Laura García-Segura
- Unidad de Genética de la Nutrición, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas de la Universidad Nacional Autónoma de México e Instituto Nacional de Pediatría, México, México
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80
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Domingo-Fernandez R, Watters K, Piskareva O, Stallings RL, Bray I. The role of genetic and epigenetic alterations in neuroblastoma disease pathogenesis. Pediatr Surg Int 2013; 29:101-19. [PMID: 23274701 PMCID: PMC3557462 DOI: 10.1007/s00383-012-3239-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/12/2012] [Indexed: 12/11/2022]
Abstract
Neuroblastoma is a highly heterogeneous tumor accounting for 15 % of all pediatric cancer deaths. Clinical behavior ranges from the spontaneous regression of localized, asymptomatic tumors, as well as metastasized tumors in infants, to rapid progression and resistance to therapy. Genomic amplification of the MYCN oncogene has been used to predict outcome in neuroblastoma for over 30 years, however, recent methodological advances including miRNA and mRNA profiling, comparative genomic hybridization (array-CGH), and whole-genome sequencing have enabled the detailed analysis of the neuroblastoma genome, leading to the identification of new prognostic markers and better patient stratification. In this review, we will describe the main genetic factors responsible for these diverse clinical phenotypes in neuroblastoma, the chronology of their discovery, and the impact on patient prognosis.
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Affiliation(s)
- Raquel Domingo-Fernandez
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Karen Watters
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Olga Piskareva
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Raymond L. Stallings
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Isabella Bray
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland,Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
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81
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Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, Stamm S. Function of alternative splicing. Gene 2013; 514:1-30. [PMID: 22909801 PMCID: PMC5632952 DOI: 10.1016/j.gene.2012.07.083] [Citation(s) in RCA: 515] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/21/2012] [Accepted: 07/30/2012] [Indexed: 12/15/2022]
Abstract
Almost all polymerase II transcripts undergo alternative pre-mRNA splicing. Here, we review the functions of alternative splicing events that have been experimentally determined. The overall function of alternative splicing is to increase the diversity of mRNAs expressed from the genome. Alternative splicing changes proteins encoded by mRNAs, which has profound functional effects. Experimental analysis of these protein isoforms showed that alternative splicing regulates binding between proteins, between proteins and nucleic acids as well as between proteins and membranes. Alternative splicing regulates the localization of proteins, their enzymatic properties and their interaction with ligands. In most cases, changes caused by individual splicing isoforms are small. However, cells typically coordinate numerous changes in 'splicing programs', which can have strong effects on cell proliferation, cell survival and properties of the nervous system. Due to its widespread usage and molecular versatility, alternative splicing emerges as a central element in gene regulation that interferes with almost every biological function analyzed.
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Affiliation(s)
- Olga Kelemen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Paolo Convertini
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhaiyi Zhang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Yuan Wen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Manli Shen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Marina Falaleeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
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82
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Epigenetic deregulation of microRNAs in rhabdomyosarcoma and neuroblastoma and translational perspectives. Int J Mol Sci 2012; 13:16554-79. [PMID: 23443118 PMCID: PMC3546707 DOI: 10.3390/ijms131216554] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 11/21/2012] [Accepted: 11/21/2012] [Indexed: 12/21/2022] Open
Abstract
Gene expression control mediated by microRNAs and epigenetic remodeling of chromatin are interconnected processes often involved in feedback regulatory loops, which strictly guide proper tissue differentiation during embryonal development. Altered expression of microRNAs is one of the mechanisms leading to pathologic conditions, such as cancer. Several lines of evidence pointed to epigenetic alterations as responsible for aberrant microRNA expression in human cancers. Rhabdomyosarcoma and neuroblastoma are pediatric cancers derived from cells presenting features of skeletal muscle and neuronal precursors, respectively, blocked at different stages of differentiation. Consistently, tumor cells express tissue markers of origin but are unable to terminally differentiate. Several microRNAs playing a key role during tissue differentiation are often epigenetically downregulated in rhabdomyosarcoma and neuroblastoma and behave as tumor suppressors when re-expressed. Recently, inhibition of epigenetic modulators in adult tumors has provided encouraging results causing re-expression of anti-tumor master gene pathways. Thus, a similar approach could be used to correct the aberrant epigenetic regulation of microRNAs in rhabdomyosarcoma and neuroblastoma. The present review highlights the current insights on epigenetically deregulated microRNAs in rhabdomyosarcoma and neuroblastoma and their role in tumorigenesis and developmental pathways. The translational clinical implications and challenges regarding modulation of epigenetic chromatin remodeling/microRNAs interconnections are also discussed.
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83
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Izzotti A, Cartiglia C, Steele VE, De Flora S. MicroRNAs as targets for dietary and pharmacological inhibitors of mutagenesis and carcinogenesis. Mutat Res 2012; 751:287-303. [PMID: 22683846 PMCID: PMC4716614 DOI: 10.1016/j.mrrev.2012.05.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 05/28/2012] [Accepted: 05/29/2012] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) have been implicated in many biological processes, cancer, and other diseases. In addition, miRNAs are dysregulated following exposure to toxic and genotoxic agents. Here we review studies evaluating modulation of miRNAs by dietary and pharmacological agents, which could potentially be exploited for inhibition of mutagenesis and carcinogenesis. This review covers natural agents, including vitamins, oligoelements, polyphenols, isoflavones, indoles, isothiocyanates, phospholipids, saponins, anthraquinones and polyunsaturated fatty acids, and synthetic agents, including thiols, nuclear receptor agonists, histone deacetylase inhibitors, antiinflammatory drugs, and selective estrogen receptor modulators. As many as 145 miRNAs, involved in the control of a variety of carcinogenesis mechanisms, were modulated by these agents, either individually or in combination. Most studies used cancer cells in vitro with the goal of modifying their phenotype by changing miRNA expression profiles. In vivo studies evaluated regulation of miRNAs by chemopreventive agents in organs of mice and rats, either untreated or exposed to carcinogens, with the objective of evaluating their safety and efficacy. The tissue specificity of miRNAs could be exploited for the chemoprevention of site-specific cancers, and the study of polymorphic miRNAs is expected to predict the individual response to chemopreventive agents as a tool for developing new prevention strategies.
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Affiliation(s)
- Alberto Izzotti
- Department of Health Sciences, University of Genoa, Genoa, 16132, Italy
| | | | | | - Silvio De Flora
- Department of Health Sciences, University of Genoa, Genoa, 16132, Italy.
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84
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Veldhoen M, Brucklacher-Waldert V. Dietary influences on intestinal immunity. Nat Rev Immunol 2012; 12:696-708. [DOI: 10.1038/nri3299] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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85
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Risso G, Pelisch F, Quaglino A, Pozzi B, Srebrow A. Regulating the regulators: serine/arginine-rich proteins under scrutiny. IUBMB Life 2012; 64:809-16. [PMID: 22941908 DOI: 10.1002/iub.1075] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 07/04/2012] [Indexed: 01/29/2023]
Abstract
Serine/arginine-rich (SR) proteins are among the most studied splicing regulators. They constitute a family of evolutionarily conserved proteins that, apart from their initially identified and deeply studied role in splicing regulation, have been implicated in genome stability, chromatin binding, transcription elongation, mRNA stability, mRNA export and mRNA translation. Remarkably, this list of SR protein activities seems far from complete, as unexpected functions keep being unraveled. An intriguing aspect that awaits further investigation is how the multiple tasks of SR proteins are concertedly regulated within mammalian cells. In this article, we first discuss recent findings regarding the regulation of SR protein expression, activity and accessibility. We dive into recent studies describing SR protein auto-regulatory feedback loops involving different molecular mechanisms such asunproductive splicing, microRNA-mediated regulation and translational repression. In addition, we take into account another step of regulation of SR proteins, presenting new findings about a variety of post-translational modifications by proteomics approaches and how some of these modifications can regulate SR protein sub-cellular localization or stability. Towards the end, we focus in two recently revealed functions of SR proteins beyond mRNA biogenesis and metabolism, the regulation of micro-RNA processing and the regulation of small ubiquitin-like modifier (SUMO) conjugation.
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Affiliation(s)
- Guillermo Risso
- Instituto de Fisiología, Biología Molecular y Neurociencias - Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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86
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Takahashi H, Kanno T, Nakayamada S, Hirahara K, Sciumè G, Muljo SA, Kuchen S, Casellas R, Wei L, Kanno Y, O'Shea JJ. TGF-β and retinoic acid induce the microRNA miR-10a, which targets Bcl-6 and constrains the plasticity of helper T cells. Nat Immunol 2012; 13:587-95. [PMID: 22544395 DOI: 10.1038/ni.2286] [Citation(s) in RCA: 231] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 03/12/2012] [Indexed: 12/12/2022]
Abstract
Distinct CD4(+) T cell subsets are critical for host defense and immunoregulation. Although these subsets can act as terminally differentiated lineages, they have been increasingly noted to demonstrated plasticity. MicroRNAs are factors that control T cell stability and plasticity. Here we report that naturally occurring regulatory T cells (T(reg) cells) had high expression of the microRNA miR-10a and that miR-10a was induced by retinoic acid and transforming growth factor-β (TGF-β) in inducible T(reg) cells. By simultaneously targeting the transcriptional repressor Bcl-6 and the corepressor Ncor2, miR-10a attenuated the phenotypic conversion of inducible T(reg) cells into follicular helper T cells. We also found that miR-10a limited differentiation into the T(H)17 subset of helper T cells and therefore represents a factor that can fine-tune the plasticity and fate of helper T cells.
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Affiliation(s)
- Hayato Takahashi
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
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87
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Zhang L, Zhou Y, Zhu J, Xu Q. An updated view on stem cell differentiation into smooth muscle cells. Vascul Pharmacol 2012; 56:280-7. [PMID: 22421140 DOI: 10.1016/j.vph.2012.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 02/17/2012] [Accepted: 02/28/2012] [Indexed: 12/16/2022]
Abstract
Stem cells possess the ability of self-renewal and give rise to specific cell types. The differentiation of stem cells involves environmental factors, transduction of extra and intra-cellular signals, regulation of gene expression by transcriptional factors, microRNAs and chromosome structural modifiers. Vascular SMCs play a profound role in blood vessel physiology and participate in a number of cardiovascular diseases such as atherosclerosis, hypertension and restenosis. In addition, SMCs could be a crucial cell component for vascular tissue engineering. In this review, we aim to update the recent progress on the mechanisms of SMC differentiation from stem cells, which involve reactive oxygen species, epigenetic modifiers, transcription factors and microRNAs coordinately regulated during stem cell differentiation. We will also discuss the potential application of stem cell therapy for patients with cardiovascular diseases.
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Affiliation(s)
- Li Zhang
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University, School of Medicine, Hangzhou 310003, PR China
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88
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Lim QE, Zhou L, Ho YK, Wan G, Too HP. snoU6 and 5S RNAs are not reliable miRNA reference genes in neuronal differentiation. Neuroscience 2011; 199:32-43. [PMID: 22051575 DOI: 10.1016/j.neuroscience.2011.10.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/08/2011] [Accepted: 10/14/2011] [Indexed: 12/20/2022]
Abstract
Accurate profiling of microRNAs (miRNAs) is an essential step for understanding the functional significance of these small RNAs in both physiological and pathological processes. Quantitative real-time PCR (qPCR) has gained acceptance as a robust and reliable transcriptomic method to profile subtle changes in miRNA levels and requires reference genes for accurate normalization of gene expression. 5S and snoU6 RNAs are commonly used as reference genes in microRNA quantification. It is currently unknown if these small RNAs are stably expressed during neuronal differentiation. Panels of miRNAs have been suggested as alternative reference genes to 5S and snoU6 in various physiological contexts. To test the hypothesis that miRNAs may serve as stable references during neuronal differentiation, the expressions of eight miRNAs, 5S and snoU6 RNAs in five differentiating neuronal cell types were analyzed using qPCR. The stabilities of the expressions were evaluated using two complementary statistical approaches (geNorm and Normfinder). Expressions of 5S and snoU6 RNAs were stable under some but not all conditions of neuronal differentiation and thus are not suitable reference genes. In contrast, a combination of three miRNAs (miR-103, miR-106b and miR-26b) allowed accurate expression normalization across different models of neuronal differentiation.
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Affiliation(s)
- Q E Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore
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89
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Skalsky RL, Cullen BR. Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene. PLoS One 2011; 6:e24248. [PMID: 21912681 PMCID: PMC3166303 DOI: 10.1371/journal.pone.0024248] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 08/05/2011] [Indexed: 01/11/2023] Open
Abstract
Glioblastoma is a highly aggressive malignant tumor involving glial cells in the human brain. We used high-throughput sequencing to comprehensively profile the small RNAs expressed in glioblastoma and non-tumor brain tissues. MicroRNAs (miRNAs) made up the large majority of small RNAs, and we identified over 400 different cellular pre-miRNAs. No known viral miRNAs were detected in any of the samples analyzed. Cluster analysis revealed several miRNAs that were significantly down-regulated in glioblastomas, including miR-128, miR-124, miR-7, miR-139, miR-95, and miR-873. Post-transcriptional editing was observed for several miRNAs, including the miR-376 family, miR-411, miR-381, and miR-379. Using the deep sequencing information, we designed a lentiviral vector expressing a cell suicide gene, the herpes simplex virus thymidine kinase (HSV-TK) gene, under the regulation of a miRNA, miR-128, that was found to be enriched in non-tumor brain tissue yet down-regulated in glioblastomas, Glioblastoma cells transduced with this vector were selectively killed when cultured in the presence of ganciclovir. Using an in vitro model to recapitulate expression of brain-enriched miRNAs, we demonstrated that neuronally differentiated SH-SY5Y cells transduced with the miRNA-regulated HSV-TK vector are protected from killing by expression of endogenous miR-128. Together, these results provide an in-depth analysis of miRNA dysregulation in glioblastoma and demonstrate the potential utility of these data in the design of miRNA-regulated therapies for the treatment of brain cancers.
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Affiliation(s)
- Rebecca L. Skalsky
- Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bryan R. Cullen
- Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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90
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Abstract
The miR-10 microRNA precursor family encodes a group of short non-coding RNAs involved in gene regulation. The miR-10 family is highly conserved and has sparked the interest of many research groups because of the genomic localization in the vicinity of, coexpression with and regulation of the Hox gene developmental regulators. Here, we review the current knowledge of the evolution, physiological function and involvement in cancer of this family of microRNAs.
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Affiliation(s)
- Disa Tehler
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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91
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Abstract
Serine-arginine (SR) proteins commonly designate a family of eukaryotic RNA binding proteins containing a protein domain composed of several repeats of the arginine-serine dipeptide, termed the arginine-serine (RS) domain. This protein family is involved in essential nuclear processes such as constitutive and alternative splicing of mRNA precursors. Besides participating in crucial activities in the nuclear compartment, several SR proteins are able to shuttle between the nucleus and the cytoplasm and to exert regulatory functions in the latter compartment. This review aims at discussing the properties of shuttling SR proteins with particular emphasis on their nucleo-cytoplasmic traffic and their cytoplasmic functions. Indeed, recent findings have unravelled the complex regulation of SR protein nucleo-cytoplasmic distribution and the diversity of cytoplasmic mechanisms in which these proteins are involved.
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Affiliation(s)
- Laure Twyffels
- Laboratoire de Biologie Moléculaire du Gène, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium
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92
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MicroRNA and DNA methylation alterations mediating retinoic acid induced neuroblastoma cell differentiation. Semin Cancer Biol 2011; 21:283-90. [PMID: 21771658 DOI: 10.1016/j.semcancer.2011.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 07/04/2011] [Indexed: 01/14/2023]
Abstract
Many neuroblastoma cell lines can be induced to differentiate into a mature neuronal cell type with retinoic acid and other compounds, providing an important model system for elucidating signalling pathways involved in this highly complex process. Recently, it has become apparent that miRNAs, which act as regulators of gene expression at a post-transcriptional level, are differentially expressed in differentiating cells and play important roles governing many aspects of this process. This includes the down-regulation of DNA methyltransferases that cause the de-methylation and transcriptional activation of numerous protein coding gene sequences. The purpose of this article is to review involvement of miRNAs and DNA methylation alterations in the process of neuroblastoma cell differentiation. A thorough understanding of miRNA and genetic pathways regulating neuroblastoma cell differentiation potentially could lead to targeted therapies for this disease.
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93
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Zhang J, Alston MA, Huang H, Rabin RL. Human T cell cytokine responses are dependent on multidrug resistance protein-1. Int Immunol 2006; 18:485-93. [PMID: 16481346 DOI: 10.1093/intimm/dxh389] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Multidrug resistance protein-1 (MRP1) belongs to subfamily C of the ATP-binding cassette transporters, and exports leukotriene C(4) and organic anions including the fluorescent calcium indicator indo-1. The observation that leukocytes from patients with an autoimmune disease exported indo-1 at a higher rate than controls prompted the hypothesis that MRP1 contributes to the function of activated cells. To test this, we defined the expression of MRP1 on resting and activated human T cells, and determined whether T cell activation is dependent upon MRP1 function. MRP1 is expressed on resting memory but not on naive CD4 and CD8 T cells. After activation through the TCR, cord blood CD4 T cells express high levels of MRP1. Blockade of MRP1 with the specific inhibitor MK-571 abrogated superantigen-induced expression of IFN-gamma, tumor necrosis factor-alpha, IL-10, IL-2, IL-4 and CD69 by T cells without affecting their viability, and was reversible upon removal of MK-571 from the culture media. Electrophoretic mobility shift assays demonstrate that MRP1 blockade with MK-571 induces activation of the transcriptional repressor peroxisome proliferator-activated receptor-gamma in CD4 T cells, thus providing insight into the potential mechanism by which their responses are abrogated.
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Affiliation(s)
- Jinsong Zhang
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20892-4555, USA
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