101
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Affiliation(s)
- Eugene Braunwald
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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102
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Ling TY, Wang XL, Chai Q, Lau TW, Koestler CM, Park SJ, Daly RC, Greason KL, Jen J, Wu LQ, Shen WF, Shen WK, Cha YM, Lee HC. Regulation of the SK3 channel by microRNA-499--potential role in atrial fibrillation. Heart Rhythm 2013; 10:1001-9. [PMID: 23499625 PMCID: PMC3710704 DOI: 10.1016/j.hrthm.2013.03.005] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Indexed: 01/27/2023]
Abstract
BACKGROUND MicroRNAs are important regulators of gene expression, including those involving electrical remodeling in atrial fibrillation (AF). Recently, KCNN3, the gene that encodes the small-conductance calcium-activated potassium channel 3 (SK3), was found to be strongly associated with AF. OBJECTIVES To evaluate the changes in atrial myocardial microRNAs in patients with permanent AF and to determine the role of microRNA on the regulation of cardiac SK3 expression. METHODS Atrial tissue obtained during cardiac surgery from patients (4 sinus rhythm and 4 permanent AF) was analyzed by using microRNA arrays. Potential targets of microRNAs were predicted by using software programs. The effects of specific microRNAs on target gene expression were evaluated in HL-1 cells from a continuously proliferating mouse hyperplastic atrial cardiomyocyte cell line. Interactions between microRNAs and targets were further evaluated by using luciferase reporter assay and by using Argonaute pull-down assay. RESULTS Twenty-one microRNAs showed significant (>2-fold) changes in AF. MicroRNA 499 (miR-499) was upregulated by 2.33-fold (P < .01) in AF atria, whereas SK3 protein expression was downregulated by 46% (P < .05). Transfection of miR-499 mimic in HL-1 cells resulted in the downregulation of SK3 protein expression, while that of miR-499 inhibitor upregulated SK3 expression. Binding of miR-499 to the 3' untranslated region of KCNN3 was confirmed by luciferase reporter assay and by the increased presence of SK3 mRNA in Argonaute pulled-down microRNA-induced silencing complexes after transfection with miR-499. CONCLUSION Atrial miR-499 is significantly upregulated in AF, leading to SK3 downregulation and possibly contributing to the electrical remodeling in AF.
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Affiliation(s)
- Tian-You Ling
- Department of Cardiology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Internal Medicine, Mayo Clinic Rochester, Minnesota
| | - Xiao-Li Wang
- Department of Internal Medicine, Mayo Clinic Rochester, Minnesota
| | - Qiang Chai
- Department of Internal Medicine, Mayo Clinic Rochester, Minnesota
- The Department of Physiology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, China
| | - Tin-Wah Lau
- Department of Internal Medicine, Mayo Clinic Rochester, Minnesota
- Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Soon J. Park
- Department of Surgery, Mayo Clinic Rochester, Minnesota
| | | | | | - Jin Jen
- Advanced Genomics Technology Center, Mayo Clinic Rochester, Minnesota
| | - Li-Qun Wu
- Department of Cardiology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei-Feng Shen
- Department of Cardiology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Win-Kuang Shen
- Department of Internal Medicine, Mayo Clinic Scottsdale, Arizona
| | - Yong-Mei Cha
- Department of Internal Medicine, Mayo Clinic Rochester, Minnesota
| | - Hon-Chi Lee
- Department of Internal Medicine, Mayo Clinic Rochester, Minnesota
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103
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Abstract
RATIONALE MicroRNAs modestly suppress their direct mRNA targets, and these direct effects are amplified by modulation of gene transcription pathways. Consequently, indirect mRNA modulatory effects of microRNAs to increase or decrease mRNAs greatly outnumber direct target suppressions. Because microRNAs are products of transcription, the potential exists for microRNAs that regulate transcription to regulate other microRNAs. OBJECTIVE Determine whether cardiac-expressed microRNAs regulate expression of other cardiac microRNAs, and measure the impact of microRNA-mediated microRNA regulation on indirect regulation of nontarget mRNAs. METHODS AND RESULTS Transgenic expression of pre-microRNAs was used to generate mouse hearts expressing 6- to 16-fold normal levels of microRNA (miR)-143, miR-378, and miR-499. Genome-wide mRNA and microRNA signatures were established using deep sequencing; expression profiles provoked by each microRNA were defined. miR-143 suppressed its direct cardiac mRNA target hexokinase 2, but exhibited little indirect target regulation and did not regulate other cardiac microRNAs. Both miR-378 and miR-499 indirectly regulated hundreds of cardiac mRNAs and 15 to 30 cardiac microRNAs. MicroRNA overexpression did not alter normal processing of either transgenic or endogenous cardiac microRNAs, and microRNA-mediated regulation of other microRNAs encoded within parent genes occurred in tandem with parent mRNAs. MicroRNA regulation by miR-378 and miR-499 was stimulus specific, and contributed to observed mRNA downregulation. CONCLUSIONS MicroRNAs that modulate cardiac transcription can indirectly regulate other microRNAs. Transcriptional modulation by microRNAs, and microRNA-mediated microRNA regulation, help explain how small direct effects of microRNAs are amplified to generate striking phenotypes.
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Affiliation(s)
- Scot J Matkovich
- Department of Internal Medicine, Center for Pharmacogenomics, Washington University School of Medicine, St. Louis, MO 63110, USA
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104
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Aly H, Rohatgi N, Marshall CA, Grossenheider TC, Miyoshi H, Stappenbeck TS, Matkovich SJ, McDaniel ML. A novel strategy to increase the proliferative potential of adult human β-cells while maintaining their differentiated phenotype. PLoS One 2013; 8:e66131. [PMID: 23776620 PMCID: PMC3680388 DOI: 10.1371/journal.pone.0066131] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 05/01/2013] [Indexed: 12/13/2022] Open
Abstract
Our previous studies demonstrated that Wnt/GSK-3/β-catenin and mTOR signaling are necessary to stimulate proliferative processes in adult human β-cells. Direct inhibition of GSK-3, that engages Wnt signaling downstream of the Wnt receptor, increases β-catenin nuclear translocation and β-cell proliferation but results in lower insulin content. Our current goal was to engage canonical and non-canonical Wnt signaling at the receptor level to significantly increase human β-cell proliferation while maintaining a β-cell phenotype in intact islets. We adopted a system that utilized conditioned medium from L cells that expressed Wnt3a, R-spondin-3 and Noggin (L-WRN conditioned medium). In addition we used a ROCK inhibitor (Y-27632) and SB-431542 (that results in RhoA inhibition) in these cultures. Treatment of intact human islets with L-WRN conditioned medium plus inhibitors significantly increased DNA synthesis ∼6 fold in a rapamycin-sensitive manner. Moreover, this treatment strikingly increased human β-cell proliferation ∼20 fold above glucose alone. Only the combination of L-WRN conditioned medium with RhoA/ROCK inhibitors resulted in substantial proliferation. Transcriptome-wide gene expression profiling demonstrated that L-WRN medium provoked robust changes in several signaling families, including enhanced β-catenin-mediated and β-cell-specific gene expression. This treatment also increased expression of Nr4a2 and Irs2 and resulted in phosphorylation of Akt. Importantly, glucose-stimulated insulin secretion and content were not downregulated by L-WRN medium treatment. Our data demonstrate that engaging Wnt signaling at the receptor level by this method leads to necessary crosstalk between multiple signaling pathways including activation of Akt, mTOR, Wnt/β-catenin, PKA/CREB, and inhibition of RhoA/ROCK that substantially increase human β-cell proliferation while maintaining the β-cell phenotype.
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Affiliation(s)
- Haytham Aly
- Department of Pathology and Immunology Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Nidhi Rohatgi
- Department of Pathology and Immunology Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Connie A. Marshall
- Department of Pathology and Immunology Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Tiffani C. Grossenheider
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Hiroyuki Miyoshi
- Department of Pathology and Immunology Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Thaddeus S. Stappenbeck
- Department of Pathology and Immunology Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Scot J. Matkovich
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Michael L. McDaniel
- Department of Pathology and Immunology Washington University in St. Louis, St. Louis, Missouri, United States of America
- * E-mail:
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105
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Godnic I, Zorc M, Jevsinek Skok D, Calin GA, Horvat S, Dovc P, Kovac M, Kunej T. Genome-wide and species-wide in silico screening for intragenic MicroRNAs in human, mouse and chicken. PLoS One 2013; 8:e65165. [PMID: 23762306 PMCID: PMC3675212 DOI: 10.1371/journal.pone.0065165] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 04/22/2013] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNAs (ncRNAs) involved in regulation of gene expression. Intragenic miRNAs, especially those exhibiting a high degree of evolutionary conservation, have been shown to be coordinately regulated and/or expressed with their host genes, either with synergistic or antagonistic correlation patterns. However, the degree of cross-species conservation of miRNA/host gene co-location is not known and co-expression information is incomplete and fragmented among several studies. Using the genomic resources (miRBase and Ensembl) we performed a genome-wide in silico screening (GWISS) for miRNA/host gene pairs in three well-annotated vertebrate species: human, mouse, and chicken. Approximately half of currently annotated miRNA genes resided within host genes: 53.0% (849/1,600) in human, 48.8% (418/855) in mouse, and 42.0% (210/499) in chicken, which we present in a central publicly available Catalog of intragenic miRNAs (http://www.integratomics-time.com/miR-host/catalog). The miRNA genes resided within either protein-coding or ncRNA genes, which include long intergenic ncRNAs (lincRNAs) and small nucleolar RNAs (snoRNAs). Twenty-seven miRNA genes were found to be located within the same host genes in all three species and the data integration from literature and databases showed that most (26/27) have been found to be co-expressed. Particularly interesting are miRNA genes located within genes encoding for miRNA silencing machinery (DGCR8, DICER1, and SND1 in human and Cnot3, Gdcr8, Eif4e, Tnrc6b, and Xpo5 in mouse). We furthermore discuss a potential for phenotype misattribution of miRNA host gene polymorphism or gene modification studies due to possible collateral effects on miRNAs hosted within them. In conclusion, the catalog of intragenic miRNAs and identified 27 miRNA/host gene pairs with cross-species conserved co-location, co-expression, and potential co-regulation, provide excellent candidates for further functional annotation of intragenic miRNAs in health and disease.
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Affiliation(s)
- Irena Godnic
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Minja Zorc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Dasa Jevsinek Skok
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - George Adrian Calin
- Department of Experimental Therapeutics and The Center for RNA Interference and Non-Coding RNAs, The University of Texas, M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Peter Dovc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Milena Kovac
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
- * E-mail:
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106
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Affiliation(s)
- Paula A. Da Costa Martins
- From the Department of Cardiology (P.A.D.C.M., L.J.D.W.), CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands
| | - Leon J. De Windt
- From the Department of Cardiology (P.A.D.C.M., L.J.D.W.), CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands
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107
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Dorn GW, Matkovich SJ, Eschenbacher WH, Zhang Y. A human 3' miR-499 mutation alters cardiac mRNA targeting and function. Circ Res 2012; 110:958-67. [PMID: 22374132 DOI: 10.1161/circresaha.111.260752] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
RATIONALE MyomiRs miR-499, miR-208a and miR-208b direct cardiac myosin gene expression. Sequence complementarity between miRs and their mRNA targets determines miR effects, but the functional consequences of human myomiR sequence variants are unknown. OBJECTIVE To identify and investigate mutations in human myomiRs in order to better understand how and to what extent naturally-occurring sequence variation can impact miR-mRNA targeting and end-organ function. METHODS AND RESULTS Screening of ≈2,600 individual DNAs for myomiR sequence variants identified a rare mutation of miR-499, u17c in the 3' end, well outside the seed region thought to determine target recognition. In vitro luciferase reporter analysis showed that the 3' miR-499 mutation altered suppression of a subset of artificial and natural mRNA targets. Cardiac-specific transgenic expression was used to compare consequences of wild-type and mutant miR-499. Both wild-type and mutant miR-499 induced heart failure in mice, but miR-499 c17 misdirected recruitment of a subset of miR-499 target mRNAs to cardiomyocyte RNA-induced silencing complexes, altering steady-state cardiac mRNA and protein make-up and favorably impacting cardiac function. In vitro analysis of miR-499 target site mutations and modeling of binding energies revealed abnormal miR-mRNA duplex configurations induced by the c17 mutation. CONCLUSIONS A naturally occurring miR-499 mutation outside the critical seed sequence modifies mRNA targeting and end-organ function. This first description of in vivo effects from a natural human miR mutation outside the seed sequence supports comprehensive studies of individual phenotypes or disease-modification conferred by miR mutations.
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Affiliation(s)
- Gerald W Dorn
- Center for Pharmacogenomics, Department of Internal Medicine and Center for Pharmacogenomics, 660 S. Euclid Ave., Campus Box 8220, St. Louis, MO 63110, USA.
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