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Fukuoka Y, Tashiro M, Uchiyama T. Systemes analysis of interactions between microRNAs and genes in hepatocellular carcinoma. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013; 2013:600-603. [PMID: 24109758 DOI: 10.1109/embc.2013.6609571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs and can regulate gene expression at the transcriptional and/or translational levels. There is mounting evidence that miRNAs play an important role in the control of the dynamics of localized gene expression. Expression profiling of miRNA in various cancers revealed that miRNA profiles could discriminate malignancies from their counter parts. In this study, to investigate the localized effect of miRNA in cancer, we analyzed gene and miRNA expressions in hepatocellular carcinoma (HCC) and surrounding nontumor tissues. Based on gene expression levels around miRNAs, we investigated how many miRNAs correlated positively/negatively in expression with genes in the vicinity. Next, the Pearson correlation coefficients were compared between the HCC and nontumor tissues. The results imply that the relationship between the intronic miRNAs and their host genes was altered in HCC, and that feedback loops including the host gene, intronic miRNA, target genes might be formed in HCC.
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Greliche N, Zeller T, Wild PS, Rotival M, Schillert A, Ziegler A, Deloukas P, Erdmann J, Hengstenberg C, Ouwehand WH, Samani NJ, Schunkert H, Munzel T, Lackner KJ, Cambien F, Goodall AH, Tiret L, Blankenberg S, Trégouët DA. Comprehensive exploration of the effects of miRNA SNPs on monocyte gene expression. PLoS One 2012; 7:e45863. [PMID: 23029284 PMCID: PMC3448685 DOI: 10.1371/journal.pone.0045863] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 08/22/2012] [Indexed: 11/18/2022] Open
Abstract
We aimed to assess whether pri-miRNA SNPs (miSNPs) could influence monocyte gene expression, either through marginal association or by interacting with polymorphisms located in 3'UTR regions (3utrSNPs). We then conducted a genome-wide search for marginal miSNPs effects and pairwise miSNPs × 3utrSNPs interactions in a sample of 1,467 individuals for which genome-wide monocyte expression and genotype data were available. Statistical associations that survived multiple testing correction were tested for replication in an independent sample of 758 individuals with both monocyte gene expression and genotype data. In both studies, the hsa-mir-1279 rs1463335 was found to modulate in cis the expression of LYZ and in trans the expression of CNTN6, CTRC, COPZ2, KRT9, LRRFIP1, NOD1, PCDHA6, ST5 and TRAF3IP2 genes, supporting the role of hsa-mir-1279 as a regulator of several genes in monocytes. In addition, we identified two robust miSNPs × 3utrSNPs interactions, one involving HLA-DPB1 rs1042448 and hsa-mir-219-1 rs107822, the second the H1F0 rs1894644 and hsa-mir-659 rs5750504, modulating the expression of the associated genes. As some of the aforementioned genes have previously been reported to reside at disease-associated loci, our findings provide novel arguments supporting the hypothesis that the genetic variability of miRNAs could also contribute to the susceptibility to human diseases.
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Affiliation(s)
- Nicolas Greliche
- INSERM UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- Université Paris-Sud, Paris, France
| | - Tanja Zeller
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - Philipp S. Wild
- Departments of Medicine II, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Maxime Rotival
- INSERM UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Arne Schillert
- Institut für Medizinische Biometrie und Statistik, Universität Lübeck, Lübeck, Germany
| | - Andreas Ziegler
- Institut für Medizinische Biometrie und Statistik, Universität Lübeck, Lübeck, Germany
| | - Panos Deloukas
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Christian Hengstenberg
- Klinik und Poliklinik für Innere Medizin II, Universität Regensburg, Regensburg, Germany
| | - Willem H. Ouwehand
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge and National Health Service Blood and Transplant, Cambridge, United Kingdom
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom
| | | | - Thomas Munzel
- Departments of Medicine II, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Karl J. Lackner
- Department of Clinical Chemistry, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - François Cambien
- INSERM UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Alison H. Goodall
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, United Kingdom
| | - Laurence Tiret
- INSERM UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
| | - Stefan Blankenberg
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - David-Alexandre Trégouët
- INSERM UMR_S 937, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- ICAN Institute for Cardiometabolism And Nutrition, Pierre and Marie Curie University (UPMC, Paris 6), Paris, France
- * E-mail:
| | - Cardiogenics ConsortiumAttwoodTonyDepartment of Haematology, University of Cambridge, Long Road, Cambridge, CB2 2PT, UK and National Health Service Blood and Transplant, Cambridge Centre, Long Road, Cambridge, CB2 2PT, UKStephanieBelzMedizinische Klinik 2, Universität zu Lübeck, Lübeck GermanyBraundPeterDepartment of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UKBrochetonJessyINSERM UMRS 937, Pierre and Marie Curie University (UPMC, Paris 6) and Medical School, 91 Bd de l’Hôpital 75013, Paris, FranceCooperJasonJuvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 0XY, UKCrisp-HihnAbiDepartment of Haematology, University of Cambridge, Long Road, Cambridge, CB2 2PT, UK and National Health Service Blood and Transplant, Cambridge Centre, Long Road, Cambridge, CB2 2PT, UKDiemertPatrick (formerly Linsel-Nitschke)Medizinische Klinik 2, Universität zu Lübeck, Lübeck GermanyFoadNicolaDepartment of Haematology, University of Cambridge, Long Road, Cambridge, CB2 2PT, UK and National Health Service Blood and Transplant, Cambridge Centre, Long Road, Cambridge, CB2 2PT, UKGodefroyTiphaineINSERM UMRS 937, Pierre and Marie Curie University (UPMC, Paris 6) and Medical School, 91 Bd de l’Hôpital 75013, Paris, FranceGraceyJayDepartment of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UKGrayEmmaThe Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UKGwilliamsRhianThe Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UKHeimerlSusanneKlinik und Poliklinik für Innere Medizin II, Universität Regensburg, GermanyJolleyJenniferDepartment of Haematology, University of Cambridge, Long Road, Cambridge, CB2 2PT, UK and National Health Service Blood and Transplant, Cambridge Centre, Long Road, Cambridge, CB2 2PT, UKKrishnanUnniDepartment of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UKLloyd-JonesHeatherDepartment of Haematology, University of Cambridge, Long Road, Cambridge, CB2 2PT, UK and National Health Service Blood and Transplant, Cambridge Centre, Long Road, Cambridge, CB2 2PT, UKLiljedahlUlrikaMolecular Medicine, Department of Medical Sciences, Uppsala University, Uppsala, SwedenLugauerIngridKlinik und Poliklinik für Innere Medizin II, Universität Regensburg, GermanyLundmarkPerMolecular Medicine, Department of Medical Sciences, Uppsala University, Uppsala, SwedenMaoucheSerayaMedizinische Klinik 2, Universität zu Lübeck, Lübeck GermanyINSERM UMRS 937, Pierre and Marie Curie University (UPMC, Paris 6) and Medical School, 91 Bd de l’Hôpital 75013, Paris, FranceMooreJasbir SDepartment of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UKGillesMontalescotINSERM UMRS 937, Pierre and Marie Curie University (UPMC, Paris 6) and Medical School, 91 Bd de l’Hôpital 75013, Paris, FranceMuirDavidDepartment of Haematology, University of Cambridge, Long Road, Cambridge, CB2 2PT, UK and National Health Service Blood and Transplant, Cambridge Centre, Long Road, Cambridge, CB2 2PT, UKMurrayElizabethDepartment of Haematology, University of Cambridge, Long Road, Cambridge, CB2 2PT, UK and National Health Service Blood and Transplant, Cambridge Centre, Long Road, Cambridge, CB2 2PT, UKNelsonChris PDepartment of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UKNeudertJessicaTrium, Analysis Online GmbH, Hohenlindenerstr. 1, 81677, München, GermanyNiblettDavidThe Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UKO’LearyKarenDepartment of Haematology, University of Cambridge, Long Road, Cambridge, CB2 2PT, UK and National Health Service Blood and Transplant, Cambridge Centre, Long Road, Cambridge, CB2 2PT, UKPollardHelenDepartment of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UKProustCaroleINSERM UMRS 937, Pierre and Marie Curie University (UPMC, Paris 6) and Medical School, 91 Bd de l’Hôpital 75013, Paris, FranceRankinAngelaDepartment of Haematology, University of Cambridge, Long Road, Cambridge, CB2 2PT, UK and National Health Service Blood and Transplant, Cambridge Centre, Long Road, Cambridge, CB2 2PT, UKRendonAugustoEuropean Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UKRiceCatherine MThe Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UKSagerHendrikMedizinische Klinik 2, Universität zu Lübeck, Lübeck GermanySambrookJenniferDepartment of Haematology, University of Cambridge, Long Road, Cambridge, CB2 2PT, UK and National Health Service Blood and Transplant, Cambridge Centre, Long Road, Cambridge, CB2 2PT, UKGerdSchmitzInstitut für KlinischeChemie und Laboratoriums medizin, Universität, Regensburg, D-93053 Regensburg, GermanyScholzMichaelTrium, Analysis Online GmbH, Hohenlindenerstr. 1, 81677, München, GermanySchroederLauraMedizinische Klinik 2, Universität zu Lübeck, Lübeck GermanyStephensJonathanDepartment of Haematology, University of Cambridge, Long Road, Cambridge, CB2 2PT, UK and National Health Service Blood and Transplant, Cambridge Centre, Long Road, Cambridge, CB2 2PT, UKSyvannenAnn-ChristineMolecular Medicine, Department of Medical Sciences, Uppsala University, Uppsala, SwedenTennstedtStefanie (formerlyGulde)Medizinische Klinik 2, Universität zu Lübeck, Lübeck GermanyWallaceChrisJuvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 0XY, UK
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Inaoka H, Fukuoka Y, Kohane IS. Evidence of spatially bound gene regulation in Mus musculus: decreased gene expression proximal to microRNA genomic location. Proc Natl Acad Sci U S A 2007; 104:5020-5. [PMID: 17360362 PMCID: PMC1820821 DOI: 10.1073/pnas.0611078104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The extent, spatially and in time, of the phenomenon of localized decreased expression in the chromosomal vicinity of microRNA (miRNA) previously described in Caenorhabditis elegans is reproduced in Mus musculus across a wide range of tissues in several independent experiments. Computationally predicted miRNA targets are enriched in the vicinity of miRNAs, and transcription factors are identified as the class of genes that systematically exhibit this localized decrease. Also, those mRNA with AT-rich UTRs, particularly those that are not in the vicinity of CpG islands, most often exhibit this localized decrease. This localization broadens with the shift from developing to mature/differentiated tissues and suggests a developmentally controlled and spatially bound regulation.
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Affiliation(s)
- Hidenori Inaoka
- *School of Biomedical Science and
- Institute of Biomaterials and Biomedical Engineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan
| | | | - Isaac S. Kohane
- Informatics Program, Children's Hospital, Center for Biomedical Informatics, and Partners Center for Genetics and Genomics, Harvard Medical School, Boston, MA 02115; and
- Division of Health Sciences and Technology, Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02139
- To whom correspondence should be addressed at:
Children's Hospital Informatics Program, 300 Longwood Avenue, Boston, MA 02115. E-mail:
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Yu Z, Jian Z, Shen SH, Purisima E, Wang E. Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos. Nucleic Acids Res 2006; 35:152-64. [PMID: 17158157 PMCID: PMC1802562 DOI: 10.1093/nar/gkl1032] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding small RNAs of ∼22 nt that regulate the gene expression by base pairing with target mRNAs, leading to mRNA cleavage or translational repression. It is currently estimated that miRNAs account for ∼1% of predicted genes in higher eukaryotic genomes and that up to 30% of genes might be regulated by miRNAs. However, only very few miRNAs have been functionally characterized and the general functions of miRNAs are not globally studied. In this study, we systematically analyzed the expression patterns of miRNA targets using several public microarray profiles. We found that the expression levels of miRNA targets are lower in all mouse and Drosophila tissues than in the embryos. We also found miRNAs more preferentially target ubiquitously expressed genes than tissue-specifically expressed genes. These results support the current suggestion that miRNAs are likely to be largely involved in embryo development and maintaining of tissue identity.
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Affiliation(s)
- Zhenbao Yu
- To whom correspondence should be addressed. Tel: +514 496 6377; Fax: +514 496 6319;
| | - Zhaofeng Jian
- Computational Chemistry & Biology Group, Biotechnology Research Institute, National Research Council CanadaMontreal, Quebec, H4P 2R2, Canada
| | | | - Enrico Purisima
- Computational Chemistry & Biology Group, Biotechnology Research Institute, National Research Council CanadaMontreal, Quebec, H4P 2R2, Canada
| | - Edwin Wang
- Computational Chemistry & Biology Group, Biotechnology Research Institute, National Research Council CanadaMontreal, Quebec, H4P 2R2, Canada
- To whom correspondence should be addressed. Tel: +514 496 6377; Fax: +514 496 6319;
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