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Severi G, Bernardini L, Briuglia S, Bigoni S, Buldrini B, Magini P, Dentici ML, Cordelli DM, Arrigo T, Franzoni E, Fini S, Italyankina E, Loddo I, Novelli A, Graziano C. New patients with Temple syndrome caused by 14q32 deletion: Genotype-phenotype correlations and risk of thyroid cancer. Am J Med Genet A 2015; 170A:162-9. [DOI: 10.1002/ajmg.a.37346] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 08/12/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Giulia Severi
- Medical Genetics Unit, Policlinico S. Orsola-Malpighi; University of Bologna; Bologna Italy
| | - Laura Bernardini
- IRCCS-Casa Sollievo della Sofferenza; Mendel Institute; Rome Italy
| | | | - Stefania Bigoni
- Medical Genetics Unit; Ferrara University Hospital; Ferrara Italy
| | - Barbara Buldrini
- Medical Genetics Unit; Ferrara University Hospital; Ferrara Italy
| | - Pamela Magini
- Medical Genetics Unit, Policlinico S. Orsola-Malpighi; University of Bologna; Bologna Italy
| | - Maria L. Dentici
- Medical Genetics Unit, Bambino Gesù Children's Hospital; IRCCS; Rome Italy
| | | | - Teresa Arrigo
- Department of Pediatrics; University of Messina; Messina Italy
| | | | - Sergio Fini
- Medical Genetics Unit; Ferrara University Hospital; Ferrara Italy
| | | | - Italia Loddo
- Department of Pediatrics; University of Messina; Messina Italy
| | - Antonio Novelli
- Medical Genetics Unit, Bambino Gesù Children's Hospital; IRCCS; Rome Italy
| | - Claudio Graziano
- Medical Genetics Unit, Policlinico S. Orsola-Malpighi; University of Bologna; Bologna Italy
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102
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Corsello G, Salzano E, Vecchio D, Antona V, Grasso M, Malacarne M, Carella M, Palumbo P, Piro E, Giuffrè M. Paternal uniparental disomy chromosome 14-like syndrome due a maternal de novo 160 kb deletion at the 14q32.2 region not encompassing the IG- and the MEG3-DMRs: Patient report and genotype-phenotype correlation. Am J Med Genet A 2015; 167A:3130-8. [PMID: 26333487 DOI: 10.1002/ajmg.a.37293] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 07/17/2015] [Indexed: 11/12/2022]
Abstract
The human chromosome 14q32 carries a cluster of imprinted genes which include the paternally expressed genes (PEGs) DLK1 and RTL1, as well as the maternally expressed genes (MEGs) MEG3, RTL1as, and MEG8. PEGs and MEGs expression at the 14q32.2-imprinted region are regulated by two differentially methylated regions (DMRs): the IG-DMR and the MEG3-DMR, which are respectively methylated on the paternal and unmethylated on the maternal chromosome 14 in most cells. Genetic and epigenetic abnormalities affecting these imprinted gene clusters result in two different phenotypes currently known as maternal upd(14) syndrome and paternal upd(14) syndrome. However, only few patients carrying a maternal deletion at the 14q32.2-imprinted critical region have been reported so far. Here we report on the first patient with a maternal de novo deletion of 160 kb at the 14q32.2 chromosome that does not involves the IG-DMR or the MEG3-DMR but elicits a full upd(14)pat syndrome's phenotype encompassing the three mentioned MEGs. By the analysis of this unique genotype-phenotype correlation, we further widen the spectrum of the congenital anomalies associated to this rare disorder and we propose that the paternally expressed imprinted RTL1 gene, as well as its maternally expressed RTL1as antisense transcript, may play a prominent causative role.
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Affiliation(s)
- Giovanni Corsello
- Department of Sciences for Health Promotion and Mother and Child Care, Università di Palermo, Palermo, Italy
| | - Emanuela Salzano
- Department of Sciences for Health Promotion and Mother and Child Care, Università di Palermo, Palermo, Italy
| | - Davide Vecchio
- Department of Sciences for Health Promotion and Mother and Child Care, Università di Palermo, Palermo, Italy
| | - Vincenzo Antona
- Department of Sciences for Health Promotion and Mother and Child Care, Università di Palermo, Palermo, Italy
| | - Marina Grasso
- Laboratory of Human Genetics, Galliera Hospital, Genoa, Italy
| | | | - Massimo Carella
- Medical Genetics Service, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Pietro Palumbo
- Medical Genetics Service, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Ettore Piro
- Department of Sciences for Health Promotion and Mother and Child Care, Università di Palermo, Palermo, Italy
| | - Mario Giuffrè
- Department of Sciences for Health Promotion and Mother and Child Care, Università di Palermo, Palermo, Italy
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103
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Matsubara K, Kagami M, Nakabayashi K, Hata K, Fukami M, Ogata T, Yamazawa K. Exploration of hydroxymethylation in Kagami-Ogata syndrome caused by hypermethylation of imprinting control regions. Clin Epigenetics 2015; 7:90. [PMID: 26322139 PMCID: PMC4552283 DOI: 10.1186/s13148-015-0124-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/11/2015] [Indexed: 12/14/2022] Open
Abstract
Background 5-Hydroxymethylcytosine (5hmC), converted from 5-methylcytosine (5mC) by ten-eleven translocation (Tet) enzymes, has recently drawn attention as the “sixth base” of DNA since it is considered an intermediate of the demethylation pathway. Nonetheless, it remains to be addressed how 5hmC is linked to the development of human imprinting disorders. In this regard, conventional bisulfite (BS) treatment is unable to differentiate 5hmC from 5mC. It is thus hypothesized that BS conversion-derived “hypermethylation” at imprinting control regions (ICRs), which may cause imprinting disorders, would in fact be attributable to excessively increased levels of 5hmC as well as 5mC. To test this hypothesis, we applied the newly developed oxidative BS (oxBS) treatment to detect 5hmC in blood samples from Kagami-Ogata syndrome (KOS14) patients caused by an epimutation (hypermethylation) of two differentially methylated regions (DMRs) functioning as ICRs, namely, IG-DMR and MEG3-DMR. Findings oxBS with pyrosequencing revealed that there were few amounts of 5hmC at the hypermethylated IG-DMR and MEG3-DMR in blood samples from KOS14 patients. oxBS with genome-wide methylation array demonstrated that global levels of 5hmC were very low with similar distribution patterns in blood samples from KOS14 patients and normal controls. We also confirmed the presence of large amounts of 5hmC in the brain sample from a normal control. Conclusions 5hmC is not a major component in abnormally hypermethylated ICRs or at a global level, at least in blood from KOS14 patients. As the brain sample contained large amounts of 5hmC, the neural tissues of KOS14 patients are promising candidates for analysis in elucidating the role of 5hmC in the neurodevelopmental context. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0124-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535 Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535 Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535 Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535 Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535 Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535 Japan ; Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi, Hamamatsu, Shizuoka 431-3192 Japan
| | - Kazuki Yamazawa
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535 Japan ; Department of Pediatrics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo 160-8582 Japan ; Clinical Genetics Center, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo 152-8902 Japan
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104
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Elbracht M, Buiting K, Bens S, Siebert R, Horsthemke B, Gillessen-Kaesbach G, Eggermann T. Chromosom 14-assoziierte Imprintingsyndrome – Temple- und Kagami-Ogata-Syndrome. MED GENET-BERLIN 2015. [DOI: 10.1007/s11825-015-0050-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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105
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Darcy D, Atwal PS, Angell C, Gadi I, Wallerstein R. Mosaic paternal genome-wide uniparental isodisomy with down syndrome. Am J Med Genet A 2015. [PMID: 26219535 DOI: 10.1002/ajmg.a.37187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We report on a 6-month-old girl with two apparent cell lines; one with trisomy 21, and the other with paternal genome-wide uniparental isodisomy (GWUPiD), identified using single nucleotide polymorphism (SNP) based microarray and microsatellite analysis of polymorphic loci. The patient has Beckwith-Wiedemann syndrome (BWS) due to paternal uniparental disomy (UPD) at chromosome location 11p15 (UPD 11p15), which was confirmed through methylation analysis. Hyperinsulinemic hypoglycemia is present, which is associated with paternal UPD 11p15.5; and she likely has medullary nephrocalcinosis, which is associated with paternal UPD 20, although this was not biochemically confirmed. Angelman syndrome (AS) analysis was negative but this testing is not completely informative; she has no specific features of AS. Clinical features of this patient include: dysmorphic features consistent with trisomy 21, tetralogy of Fallot, hemihypertrophy, swirled skin hyperpigmentation, hepatoblastoma, and Wilms tumor. Her karyotype is 47,XX,+21[19]/46,XX[4], and microarray results suggest that the cell line with trisomy 21 is biparentally inherited and represents 40-50% of the genomic material in the tested specimen. The difference in the level of cytogenetically detected mosaicism versus the level of mosaicism observed via microarray analysis is likely caused by differences in the test methodologies. While a handful of cases of mosaic paternal GWUPiD have been reported, this patient is the only reported case that also involves trisomy 21. Other GWUPiD patients have presented with features associated with multiple imprinted regions, as does our patient.
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Affiliation(s)
- Diana Darcy
- Silicon Valley Genetics Center, Santa Clara Valley Medical Center, San Jose, California
| | | | - Cathy Angell
- Neonatology, O'Connor Hospital, San Jose, California
| | - Inder Gadi
- Laboratory Corporation of America, Research Triangle Park, North Carolina
| | - Robert Wallerstein
- Silicon Valley Genetics Center, Santa Clara Valley Medical Center, San Jose, California
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106
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Abuhatzira L, Xu H, Tahhan G, Boulougoura A, Schäffer AA, Notkins AL. Multiple microRNAs within the 14q32 cluster target the mRNAs of major type 1 diabetes autoantigens IA-2, IA-2β, and GAD65. FASEB J 2015; 29:4374-83. [PMID: 26148972 DOI: 10.1096/fj.15-273649] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/30/2015] [Indexed: 12/25/2022]
Abstract
Islet antigen (IA)-2, IA-2β, and glutamate decarboxylase (GAD65) are major autoantigens in type 1 diabetes (T1D). Autoantibodies to these autoantigens appear years before disease onset and are widely used as predictive markers. Little is known, however, about what regulates the expression of these autoantigens. The present experiments were initiated to test the hypothesis that microRNAs (miRNAs) can target and affect the levels of these autoantigens. Bioinformatics was used to identify miRNAs predicted to target the mRNAs coding IA-2, IA-2β, and GAD65. RNA interference for the miRNA processing enzyme Dicer1 and individual miRNA mimics and inhibitors were used to confirm the effect in mouse islets and MIN6 cells. We show that the imprinted 14q32 miRNA cluster contains 56 miRNAs, 32 of which are predicted to target the mRNAs of T1D autoantigens and 12 of which are glucose-sensitive. Using miRNA mimics and inhibitors, we confirmed that at least 7 of these miRNAs modulate the mRNA levels of the T1D autoantigens. Dicer1 knockdown significantly reduced the mRNA levels of all 3 autoantigens, further confirming the importance of miRNAs in this regulation. We conclude that miRNAs are involved in regulating the expression of the major T1D autoantigens.
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Affiliation(s)
- Liron Abuhatzira
- *Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Huanyu Xu
- *Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Georges Tahhan
- *Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Afroditi Boulougoura
- *Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Alejandro A Schäffer
- *Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Abner L Notkins
- *Experimental Medicine Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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107
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Han Z, Yu C, Tian Y, Zeng T, Cui W, Mager J, Wu Q. Expression patterns of long noncoding RNAs from Dlk1-Dio3 imprinted region and the potential mechanisms of Gtl2 activation during blastocyst development. Biochem Biophys Res Commun 2015; 463:167-73. [PMID: 26005002 DOI: 10.1016/j.bbrc.2015.04.126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 04/26/2015] [Indexed: 11/26/2022]
Abstract
The function of long noncoding RNAs (lncRNAs) in cell differentiation and development have begun to be revealed in recent years. However, the expression pattern and mechanisms regulating lncRNAs are largely unknown during mammalian preimplantation development. LncRNAs expressed from Dlk1-Dio3 imprinted region have been linked to pluripotency of induced pluripotent cells (iPSCs). In this study we show that these lncRNAs (Gtl2, Rian and Mirg) are first expressed at the morula stage and gradually restricted to the inner cell mass (ICM) as the embryo differentiates into the blastocyst. Analysis of DNA methylation at IG-DMR and Gtl2-DMR showed no change during preimplantation while the presence of the activating histone modification H3K4me3 increased significantly from 8-cell to blastocyst stage, which may explain the expression activation. Additionally, knockdown of transcription factors (Oct4, Sox2 and Nanog) in blastocyst reduced the expression of Gtl2, indicating pluripotency factors regulate transcription of these lncRNAs. This study provides the spatiotemporal expression and dynamic changes of lncRNAs from Dlk1-Dio3 imprinted region in mouse preimplantation stage embryos and offers insight into the potential mechanisms responsible for Gtl2 activation.
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Affiliation(s)
- Zhengbin Han
- Harbin Institute of Technology, School of Life Science and Technology, State Key Laboratory of Urban Water Resources and Environment, Harbin 150080, China; University of Massachusetts, Veterinary and Animal Science Department, 661 North Pleasant Street, Amherst, MA 01003, USA
| | - Changwei Yu
- Harbin Institute of Technology, School of Life Science and Technology, State Key Laboratory of Urban Water Resources and Environment, Harbin 150080, China
| | - Yijun Tian
- Harbin Institute of Technology, School of Life Science and Technology, State Key Laboratory of Urban Water Resources and Environment, Harbin 150080, China
| | - Tiebo Zeng
- Harbin Institute of Technology, School of Life Science and Technology, State Key Laboratory of Urban Water Resources and Environment, Harbin 150080, China
| | - Wei Cui
- University of Massachusetts, Veterinary and Animal Science Department, 661 North Pleasant Street, Amherst, MA 01003, USA
| | - Jesse Mager
- University of Massachusetts, Veterinary and Animal Science Department, 661 North Pleasant Street, Amherst, MA 01003, USA.
| | - Qiong Wu
- Harbin Institute of Technology, School of Life Science and Technology, State Key Laboratory of Urban Water Resources and Environment, Harbin 150080, China.
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108
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Howard M, Charalambous M. Molecular basis of imprinting disorders affecting chromosome 14: lessons from murine models. Reproduction 2015; 149:R237-49. [DOI: 10.1530/rep-14-0660] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Uniparental inheritance of chromosome 14q32 causes developmental failure during gestation and early postnatal development due to mis-expression of a cluster of imprinted genes under common epigenetic control. Two syndromes associated with chromosome 14q32 abnormalities have been described, Kagami–Ogata and Temple syndromes. Both of these syndromes are characterised by specific impairments of intrauterine development, placentation and early postnatal survival. Such abnormalities arise because the processes of intrauterine growth and postnatal adaptation are critically modulated by the dosage of imprinted genes in the chromosome 14q32 cluster. Much of our understanding of how the imprinted genes in this cluster are regulated, as well as their individual functions in the molecular pathways controlling growth and postnatal adaptation, has come from murine models. Mouse chromosome 12qF1 contains an imprinted region syntenic to human chromosome 14q32, collectively referred to as the Dlk1–Dio3 cluster. In this review, we will summarise the wealth of information derived from animal models of chromosome 12 imprinted gene mis-regulation, and explore the relationship between the functions of individual genes and the phenotypic result of their mis-expression. As there is often a considerable overlap between the functions of genes in the Dlk1–Dio3 cluster, we propose that the expression dosage of these genes is controlled by common regulatory mechanisms to co-ordinate the timing of growth and postnatal adaptation. While the diseases associated with mis-regulated chromosome 14 imprinting are rare, studies carried out in mice on the functions of the affected genes as well as their normal regulatory mechanisms have revealed new mechanistic pathways for the control of growth and survival in early life.
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109
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Yu Y, Gao Q, Zhao HC, Li R, Gao JM, Ding T, Bao SY, Zhao Y, Sun XF, Fan Y, Qiao J. Ascorbic acid improves pluripotency of human parthenogenetic embryonic stem cells through modifying imprinted gene expression in the Dlk1-Dio3 region. Stem Cell Res Ther 2015; 6:69. [PMID: 25879223 PMCID: PMC4425892 DOI: 10.1186/s13287-015-0054-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 10/29/2014] [Accepted: 03/16/2015] [Indexed: 12/13/2022] Open
Abstract
Introduction Human parthenogenetic embryonic stem cells (hpESCs) are generated from artificially activated oocytes, however, the issue of whether hpESCs have equivalent differentiation ability to human fertilized embryonic stem cells remains controversial. Methods hpESCs were injected into male severe combined immunodeficiency (SCID) mice and the efficiency of teratoma formation was calculated. Then the gene expression and methylation modification were detected by real time-PCR and bisulfate methods. Results Comparison of five hpESCs with different differentiation abilities revealed that levels of paternal genes in the Dlk1-Dio3 region on chromosome 14 in the hpESCs with high differentiation potential are enhanced, but strictly methylated and silenced in the hpESCs with lower differentiation potential. Treatment with ascorbic acid, rescued their ability to support teratoma formation and altered the expression profiles of paternally expressed genes in hpESCs that could not form teratoma easily. No differences in the expression of other imprinting genes were evident between hpESCs with higher and lower differentiation potential, except for those in the Dlk1-Dio3 region. Conclusions The Dlk1-Dio3 imprinting gene cluster distinguishes the differentiation ability of hpESCs. Moreover, modification by ascorbic acid may facilitate application of hpESCs to clinical settings in the future by enhancing their pluripotency. Electronic supplementary material The online version of this article (doi:10.1186/s13287-015-0054-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Yu
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Peking University Third Hospital, No. 49 HuaYuan North Road, HaiDian District, Beijing, 100191, People's Republic of China. .,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China. .,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
| | - Qian Gao
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Peking University Third Hospital, No. 49 HuaYuan North Road, HaiDian District, Beijing, 100191, People's Republic of China.
| | - Hong-cui Zhao
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Peking University Third Hospital, No. 49 HuaYuan North Road, HaiDian District, Beijing, 100191, People's Republic of China.
| | - Rong Li
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Peking University Third Hospital, No. 49 HuaYuan North Road, HaiDian District, Beijing, 100191, People's Republic of China. .,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China. .,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
| | - Jiang-man Gao
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Peking University Third Hospital, No. 49 HuaYuan North Road, HaiDian District, Beijing, 100191, People's Republic of China.
| | - Ting Ding
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Peking University Third Hospital, No. 49 HuaYuan North Road, HaiDian District, Beijing, 100191, People's Republic of China. .,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
| | - Si-yu Bao
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Peking University Third Hospital, No. 49 HuaYuan North Road, HaiDian District, Beijing, 100191, People's Republic of China. .,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
| | - Yue Zhao
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Peking University Third Hospital, No. 49 HuaYuan North Road, HaiDian District, Beijing, 100191, People's Republic of China. .,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
| | - Xiao-fang Sun
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, the Third Affiliated Hospital of Guangzhou Medical University, No. 63, Liwan District, Guangzhou City, 510150, Guangdong Province, People's Republic of China.
| | - Yong Fan
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Peking University Third Hospital, No. 49 HuaYuan North Road, HaiDian District, Beijing, 100191, People's Republic of China. .,Key Laboratory for Major Obstetric Diseases of Guangdong Province, the Third Affiliated Hospital of Guangzhou Medical University, No. 63, Liwan District, Guangzhou City, 510150, Guangdong Province, People's Republic of China.
| | - Jie Qiao
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Peking University Third Hospital, No. 49 HuaYuan North Road, HaiDian District, Beijing, 100191, People's Republic of China. .,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China. .,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
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Cheong CY, Chng K, Ng S, Chew SB, Chan L, Ferguson-Smith AC. Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation. Genome Res 2015; 25:611-23. [PMID: 25862382 PMCID: PMC4417110 DOI: 10.1101/gr.183301.114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 03/04/2015] [Indexed: 12/22/2022]
Abstract
Genomic imprinting is an epigenetic mechanism resulting in parental allele-specific gene expression. Defects in normal imprinting are found in cancer, assisted reproductive technologies, and several human syndromes. In mouse models, germline-derived DNA methylation is shown to regulate imprinting. Though imprinting is largely conserved between mammals, species- and tissue-specific domains of imprinted expression exist. Using the cynomolgus macaque (Macaca fascicularis) to assess primate-specific imprinting, we present a comprehensive view of tissue-specific imprinted expression and DNA methylation at established imprinted gene clusters. For example, like mouse and unlike human, macaque IGF2R is consistently imprinted, and the PLAGL1, INPP5F transcript variant 2, and PEG3 imprinting control regions are not methylated in the macaque germline but acquire this post-fertilization. Methylome data from human early embryos appear to support this finding. These suggest fundamental differences in imprinting control mechanisms between primate species and rodents at some imprinted domains, with implications for our understanding of the epigenetic programming process in humans and its influence on disease.
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Affiliation(s)
- Clara Y Cheong
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Keefe Chng
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Shilen Ng
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Siew Boom Chew
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Louiza Chan
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Anne C Ferguson-Smith
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
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111
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Comprehensive clinical studies in 34 patients with molecularly defined UPD(14)pat and related conditions (Kagami-Ogata syndrome). Eur J Hum Genet 2015; 23:1488-98. [PMID: 25689926 PMCID: PMC4613461 DOI: 10.1038/ejhg.2015.13] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 01/07/2015] [Accepted: 01/14/2015] [Indexed: 11/08/2022] Open
Abstract
Paternal uniparental disomy 14 (UPD(14)pat) and epimutations and microdeletions affecting the maternally derived 14q32.2 imprinted region lead to a unique constellation of clinical features such as facial abnormalities, small bell-shaped thorax with a coat-hanger appearance of the ribs, abdominal wall defects, placentomegaly, and polyhydramnios. In this study, we performed comprehensive clinical studies in patients with UPD(14)pat (n=23), epimutations (n=5), and microdeletions (n=6), and revealed several notable findings. First, a unique facial appearance with full cheeks and a protruding philtrum and distinctive chest roentgenograms with increased coat-hanger angles to the ribs constituted the pathognomonic features from infancy through childhood. Second, birth size was well preserved, with a median birth length of ±0 SD (range, -1.7 to +3.0 SD) and a median birth weight of +2.3 SD (range, +0.1 to +8.8 SD). Third, developmental delay and/or intellectual disability was invariably present, with a median developmental/intellectual quotient of 55 (range, 29-70). Fourth, hepatoblastoma was identified in three infantile patients (8.8%), and histological examination in two patients showed a poorly differentiated embryonal hepatoblastoma with focal macrotrabecular lesions and well-differentiated hepatoblastoma, respectively. These findings suggest the necessity of an adequate support for developmental delay and periodical screening for hepatoblastoma in the affected patients, and some phenotypic overlap between UPD(14)pat and related conditions and Beckwith-Wiedemann syndrome. On the basis of our previous and present studies that have made a significant contribution to the clarification of underlying (epi)genetic factors and the definition of clinical findings, we propose the name 'Kagami-Ogata syndrome' for UPD(14)pat and related conditions.
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Watanabe T, Go H, Kagami M, Yasuda S, Nomura Y, Fujimori K. Prenatal findings and epimutations for paternal uniparental disomy for chromosome 14 syndrome. J Obstet Gynaecol Res 2015; 41:1133-6. [PMID: 25656753 DOI: 10.1111/jog.12665] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/18/2014] [Indexed: 01/01/2023]
Abstract
The phenotypes associated with paternal uniparental disomy for chromosome 14 (UPD(14)pat) are clinically distinctive and caused by genetic alterations at the 14q32.2 imprinted region. Here we describe prenatal and neonatal findings in a case of epimutation associated with UPD(14)pat-like phenotype. A 25-year-old Japanese woman was referred to hospital at 32 weeks of gestation for management of threatened premature delivery. Fetal ultrasound and magnetic resonance imaging showed a narrow thorax and polyhydramnios. At 35 weeks of gestation, emergency cesarean section was performed and placentomegaly was identified. Physical examination of the neonate indicated a small narrow thorax, diastasis recti, and dysmorphic facial features that included hirsute forehead, broad flat nasal bridge, micrognathia, small ears, and a long protruding philtrum. Genetic analysis identified epimutation at the intergenic differentially methylated region (IG-DMR) and at MEG3-DMR.
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Affiliation(s)
- Takafumi Watanabe
- Department of Obstetrics and Gynecology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hayato Go
- Department of Pediatrics, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shun Yasuda
- Department of Obstetrics and Gynecology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yasuhisa Nomura
- Department of Obstetrics and Gynecology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Keiya Fujimori
- Department of Obstetrics and Gynecology, Fukushima Medical University School of Medicine, Fukushima, Japan
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Mo CF, Wu FC, Tai KY, Chang WC, Chang KW, Kuo HC, Ho HN, Chen HF, Lin SP. Loss of non-coding RNA expression from the DLK1-DIO3 imprinted locus correlates with reduced neural differentiation potential in human embryonic stem cell lines. Stem Cell Res Ther 2015; 6:1. [PMID: 25559585 PMCID: PMC4417332 DOI: 10.1186/scrt535] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION Pluripotent stem cells are increasingly used to build therapeutic models, including the transplantation of neural progenitors derived from human embryonic stem cells (hESCs). Recently, long non-coding RNAs (lncRNAs), including delta-like homolog 1 gene and the type III iodothyronine deiodinase gene (DLK1-DIO3) imprinted locus-derived maternally expressed gene 3 (MEG3), were found to be expressed during neural development. The deregulation of these lncRNAs is associated with various neurological diseases. The imprinted locus DLK1-DIO3 encodes abundant non-coding RNAs (ncRNAs) that are regulated by differential methylation of the locus. We aim to study the correlation between the DLK1-DIO3-derived ncRNAs and the capacity of hESCs to differentiate into neural lineages. METHODS We classified hESC sublines into MEG3-ON and MEG3-OFF based on the expression levels of MEG3 and its downstream microRNAs as detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). A cDNA microarray was used to analyze the gene expression profiles of hESCs. To investigate the capacity of neural differentiation in MEG3-ON and MEG3-OFF hESCs, we performed neural lineage differentiation followed by neural lineage marker expression and neurite formation analyses via qRT-PCR and immunocytochemistry, respectively. MEG3-knockdown via small interfering RNA (siRNA) and small hairpin RNA (shRNA) was used to investigate the potential causative effect of MEG3 in regulating neural lineage-related gene expression. RESULTS DLK1-DIO3-derived ncRNAs were repressed in MEG3-OFF hESCs compared with those in the MEG3-ON hESCs. The transcriptome profile indicated that many genes related to nervous system development and neural-type tumors were differentially expressed in MEG3-OFF hESCs. Three independent MEG3-knockdown assays using different siRNA and shRNA constructs consistently resulted in downregulation of some neural lineage genes. Lower expression levels of stage-specific neural lineage markers and reduced neurite formation were observed in neural lineage-like cells derived from MEG3-OFF-associated hESCs compared with those in the MEG3-ON groups at the same time points after differentiation. CONCLUSIONS Repression of ncRNAs derived from the DLK1-DIO3 imprinted locus is associated with reduced neural lineage differentiation potential in hESCs.
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Affiliation(s)
- Chu-Fan Mo
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.
| | - Fang-Chun Wu
- Department of Obstetrics & Gynecology, College of Medicine and the Hospital, National Taiwan University Hospital, Taipei, 100, Taiwan.
| | - Kang-Yu Tai
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, 100, Taiwan. .,Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan. .,Genome and Systems Biology Degree Program, Academia Sinica, Taipei, 115, Taiwan.
| | - Wei-Chun Chang
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.
| | - Kai-Wei Chang
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan. .,Genome and Systems Biology Degree Program, Academia Sinica, Taipei, 115, Taiwan.
| | - Hung-Chih Kuo
- Genomic Research Center, Academia Sinica, Taipei, 115, Taiwan. .,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan.
| | - Hong-Nerng Ho
- Department of Obstetrics & Gynecology, College of Medicine and the Hospital, National Taiwan University Hospital, Taipei, 100, Taiwan.
| | - Hsin-Fu Chen
- Department of Obstetrics & Gynecology, College of Medicine and the Hospital, National Taiwan University Hospital, Taipei, 100, Taiwan. .,Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, 100, Taiwan.
| | - Shau-Ping Lin
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan. .,Agricultural Biotechnology Research Centre, Academia Sinica, Taipei, 115, Taiwan. .,Research Centre for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 106, Taiwan. .,Centre for Systems Biology, National Taiwan University, Taipei, 106, Taiwan.
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Rosenfeld JA, Fox JE, Descartes M, Brewer F, Stroud T, Gorski JL, Upton SJ, Moeschler JB, Monteleone B, Neill NJ, Lamb AN, Ballif BC, Shaffer LG, Ravnan JB. Clinical features associated with copy number variations of the 14q32 imprinted gene cluster. Am J Med Genet A 2014; 167A:345-53. [DOI: 10.1002/ajmg.a.36866] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jill A. Rosenfeld
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
| | - Joyce E. Fox
- Division of Medical Genetics; Steven and Alexandra Cohen Children's Medical Center of New York; New York
| | - Maria Descartes
- Department of Genetics; University of Alabama at Birmingham; Alabama
| | - Fallon Brewer
- Department of Genetics; University of Alabama at Birmingham; Alabama
| | - Tracy Stroud
- Division of Developmental Pediatrics; University of Missouri; Columbia Missouri
| | - Jerome L. Gorski
- Division of Medical Genetics; University of Missouri School of Medicine; Columbia Missouri
| | - Sheila J. Upton
- Children's Hospital at Dartmouth; Dartmouth-Hitchcock Medical Center; Lebanon New Hampshire
| | - John B. Moeschler
- Children's Hospital at Dartmouth; Dartmouth-Hitchcock Medical Center; Lebanon New Hampshire
| | | | - Nicholas J. Neill
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | - Allen N. Lamb
- ARUP Laboratories; Department of Pathology; University of Utah; Salt Lake City Utah
| | - Blake C. Ballif
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
- Paw Print Genetics; Genetic Veterinary Sciences; Inc.; Spokane Washington
| | - Lisa G. Shaffer
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
- Paw Print Genetics; Genetic Veterinary Sciences; Inc.; Spokane Washington
| | - J. Britt Ravnan
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
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Greife A, Knievel J, Ribarska T, Niegisch G, Schulz WA. Concomitant downregulation of the imprinted genes DLK1 and MEG3 at 14q32.2 by epigenetic mechanisms in urothelial carcinoma. Clin Epigenetics 2014; 6:29. [PMID: 25741387 PMCID: PMC4348104 DOI: 10.1186/1868-7083-6-29] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/07/2014] [Indexed: 01/01/2023] Open
Abstract
Background The two oppositely imprinted and expressed genes, DLK1 and MEG3, are located in the same gene cluster at 14q32. Previous studies in bladder cancer have suggested that tumor suppressor genes are located in this region, but these have not been identified. Results We observed that both DLK1 and MEG3 are frequently silenced in urothelial cancer tissues and cell lines. The concomitant downregulation of the two genes is difficult to explain by known mechanisms for inactivating imprinted genes, namely deletion of active alleles or epitype switching. Indeed, quantitative PCR revealed more frequent copy number gains than losses in the gene cluster that were, moreover, consistent within each sample, excluding gene losses as the cause of downregulation. Instead, we observed distinctive epigenetic alterations at the three regions controlling DLK1 and MEG3 expression, namely the DLK1 promoter; the intergenic (IG) and MEG3 differentially methylated regions (DMRs). Bisulfite sequencing and pyrosequencing revealed novel patterns of DNA methylation in tumor cells, which were distinct from that of either paternal allele. Furthermore, chromatin immunoprecipitation demonstrated loss of active and gain of repressive histone modifications at all regulatory sequences. Conclusions Our data support the idea that the main cause of the prevalent downregulation of DLK1 and MEG3 in urothelial carcinoma is epigenetic silencing across the 14q32 imprinted gene cluster, resulting in the unusual concomitant inactivation of oppositely expressed and imprinted genes. Electronic supplementary material The online version of this article (doi:10.1186/1868-7083-6-29) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Annemarie Greife
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Judith Knievel
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Teodora Ribarska
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Günter Niegisch
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, Düsseldorf, 40225 Germany
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Kagami M, Mizuno S, Matsubara K, Nakabayashi K, Sano S, Fuke T, Fukami M, Ogata T. Epimutations of the IG-DMR and the MEG3-DMR at the 14q32.2 imprinted region in two patients with Silver-Russell Syndrome-compatible phenotype. Eur J Hum Genet 2014; 23:1062-7. [PMID: 25351781 PMCID: PMC4795120 DOI: 10.1038/ejhg.2014.234] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/16/2014] [Accepted: 09/19/2014] [Indexed: 01/05/2023] Open
Abstract
Maternal uniparental disomy 14 (UPD(14)mat) and related (epi)genetic aberrations affecting the 14q32.2 imprinted region result in a clinically recognizable condition which is recently referred to as Temple Syndrome (TS). Phenotypic features in TS include pre- and post-natal growth failure, prominent forehead, and feeding difficulties that are also found in Silver–Russell Syndrome (SRS). Thus, we examined the relevance of UPD(14)mat and related (epi)genetic aberrations to the development of SRS in 85 Japanese patients who satisfied the SRS diagnostic criteria proposed by Netchine et al and had neither epimutation of the H19-DMR nor maternal uniparental disomy 7. Pyrosequencing identified hypomethylation of the DLK1-MEG3 intergenic differentially methylated region (IG-DMR) and the MEG3-DMR in two cases. In both cases, microsatellite analysis showed biparental transmission of the homologs of chromosome 14, with no evidence for somatic mosaicism with full or segmental maternal isodisomy involving the imprinted region. FISH and array comparative genomic hybridization revealed neither deletion of the two DMRs nor discernible copy number alteration in the 14q32.2 imprinted region. Methylation patterns were apparently normal in other six disease-associated DMRs. In addition, a thorough literature review revealed a considerable degree of phenotypic overlap between SRS and TS, although body asymmetry was apparently characteristic of SRS. The results indicate the occurrence of epimutation affecting the IG-DMR and the MEG3-DMR in the two cases, and imply that UPD(14)mat and related (epi)genetic aberrations constitute a rare but important underlying factor for SRS.
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Affiliation(s)
- Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Aichi, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shinichiro Sano
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko Fuke
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- 1] Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan [2] Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
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Benetatos L, Vartholomatos G, Hatzimichael E. DLK1-DIO3 imprinted cluster in induced pluripotency: landscape in the mist. Cell Mol Life Sci 2014; 71:4421-30. [PMID: 25098353 PMCID: PMC11113449 DOI: 10.1007/s00018-014-1698-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/29/2014] [Accepted: 07/31/2014] [Indexed: 12/20/2022]
Abstract
DLK1-DIO3 represents an imprinted cluster which genes are involved in physiological cell biology as early as the stem cell level and in the pathogenesis of several diseases. Transcription factor-mediated induced pluripotent cells (iPSCs) are considered an unlimited source of patient-specific hematopoietic stem cells for clinical application in patient-tailored regenerative medicine. However, to date there is no marker established able to distinguish embryonic stem cell-equivalent iPSCs or safe human iPSCs. Recent findings suggest that the DLK1-DIO3 locus possesses the potential to represent such a marker but there are also contradictory data. This review aims to report the current data on the topic describing both sides of the coin.
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Affiliation(s)
- Leonidas Benetatos
- Blood Bank, Selefkeias 2, Preveza General Hospital, 48100, Preveza, Greece,
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Kamimura S, Hatanaka Y, Hirasawa R, Matsumoto K, Oikawa M, Lee J, Matoba S, Mizutani E, Ogonuki N, Inoue K, Kohda T, Ishino F, Ogura A. Establishment of Paternal Genomic Imprinting in Mouse Prospermatogonia Analyzed by Nuclear Transfer1. Biol Reprod 2014; 91:120. [DOI: 10.1095/biolreprod.114.120451] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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119
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Shiah SG, Hsiao JR, Chang WM, Chen YW, Jin YT, Wong TY, Huang JS, Tsai ST, Hsu YM, Chou ST, Yen YC, Jiang SS, Shieh YS, Chang IS, Hsiao M, Chang JY. Downregulated miR329 and miR410 promote the proliferation and invasion of oral squamous cell carcinoma by targeting Wnt-7b. Cancer Res 2014; 74:7560-72. [PMID: 25351956 DOI: 10.1158/0008-5472.can-14-0978] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
microRNA (miRNA) dysregulation contributes widely to human cancer but has not been fully assessed in oral cancers. In this study, we conducted a global microarray analysis of miRNA expression in 40 pairs of betel quid-associated oral squamous cell carcinoma (OSCC) specimens and their matched nontumorous epithelial counterparts. Eighty-four miRNAs were differentially expressed in the OSCC specimens compared with the matched tissue. Among these downregulated miRNAs, 19 miRNAs were found and mapped to the chromosome 14q32.2 miRNA cluster region, which resides within a parentally imprinted region designated as Dlk-Dio3 and known to be important in development and growth. Bioinformatic analysis predicted two miRNAs from the cluster region, miR329 and miR410, which could potentially target Wnt-7b, an activator of the Wnt-β-catenin pathway, thereby attenuating the Wnt-β-catenin signaling pathway in OSCC. Stable ectopic expression of Wnt-7b in OSCC cells overexpressing miR329 or miR410 restored proliferation and invasion capabilities abolished by these miRNA. Combining a demethylation agent and a histone deacetylase inhibitor was sufficient to reexpress miR329, miR410, and Meg3, consistent with epigenetic regulation of these miRNA in human OSCC. Specifically, arecoline, a major betel nut alkaloid, reduced miR329, miR410, and Meg3 gene expression. Overall, our results provide novel molecular insights into how betel quid contributes to oral carcinogenesis through epigenetic silencing of tumor-suppressor miRNA that targets Wnt-β-catenin signaling.
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Affiliation(s)
- Shine-Gwo Shiah
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan. Department of Oral Diagnosis and Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Jenn-Ren Hsiao
- Department of Otolaryngology, Head and Neck Collaborative Oncology Group, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Min Chang
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan. Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Ya-Wen Chen
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Ying-Tai Jin
- Department of Pathology, Taiwan Adventis Hospital, Taipei, Taiwan
| | - Tung-Yiu Wong
- Department of Stomatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jehn-Shyun Huang
- Department of Stomatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sen-Tien Tsai
- Department of Otolaryngology, Head and Neck Collaborative Oncology Group, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yuan-Ming Hsu
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Sung-Tau Chou
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Yi-Chen Yen
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Shih Sheng Jiang
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Yi-Shing Shieh
- Department of Oral Diagnosis and Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jang-Yang Chang
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan. Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Markunas CA, Xu Z, Harlid S, Wade PA, Lie RT, Taylor JA, Wilcox AJ. Identification of DNA methylation changes in newborns related to maternal smoking during pregnancy. ENVIRONMENTAL HEALTH PERSPECTIVES 2014; 122:1147-53. [PMID: 24906187 PMCID: PMC4181928 DOI: 10.1289/ehp.1307892] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 06/04/2014] [Indexed: 05/17/2023]
Abstract
BACKGROUND Maternal smoking during pregnancy is associated with significant infant morbidity and mortality, and may influence later disease risk. One mechanism by which smoking (and other environmental factors) might have long-lasting effects is through epigenetic modifications such as DNA methylation. OBJECTIVES We conducted an epigenome-wide association study (EWAS) investigating alterations in DNA methylation in infants exposed in utero to maternal tobacco smoke, using the Norway Facial Clefts Study. METHODS The Illumina HumanMethylation450 BeadChip was used to assess DNA methylation in whole blood from 889 infants shortly after delivery. Of 889 mothers, 287 reported smoking-twice as many smokers as in any previous EWAS of maternal smoking. CpG sites related to maternal smoking during the first trimester were identified using robust linear regression. RESULTS We identified 185 CpGs with altered methylation in infants of smokers at genome-wide significance (q-value < 0.05; mean Δβ = ± 2%). These correspond to 110 gene regions, of which 7 have been previously reported and 10 are newly confirmed using publicly available results. Among these 10, the most noteworthy are FRMD4A, ATP9A, GALNT2, and MEG3, implicated in processes related to nicotine dependence, smoking cessation, and placental and embryonic development. CONCLUSIONS Our study identified 10 genes with newly established links to maternal smoking. Further, we note differences between smoking-related methylation changes in newborns and adults, suggesting possible distinct effects of direct versus indirect tobacco smoke exposure as well as potential differences due to age. Further work would be needed to determine whether these small changes in DNA methylation are biologically or clinically relevant. The methylation changes identified in newborns may mediate the association between in utero maternal smoking exposure and later health outcomes.
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Welten SM, Bastiaansen AJ, de Jong RC, de Vries MR, Peters EA, Boonstra MC, Sheikh SP, La Monica N, Kandimalla ER, Quax PH, Nossent AY. Inhibition of 14q32 MicroRNAs miR-329, miR-487b, miR-494, and miR-495 Increases Neovascularization and Blood Flow Recovery After Ischemia. Circ Res 2014; 115:696-708. [DOI: 10.1161/circresaha.114.304747] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rationale:
Effective neovascularization is crucial for recovery after cardiovascular events.
Objective:
Because microRNAs regulate expression of up to several hundred target genes, we set out to identify microRNAs that target genes in all pathways of the multifactorial neovascularization process. Using
www.targetscan.org
, we performed a reverse target prediction analysis on a set of 197 genes involved in neovascularization. We found enrichment of binding sites for 27 microRNAs in a single microRNA gene cluster. Microarray analyses showed upregulation of 14q32 microRNAs during neovascularization in mice after single femoral artery ligation.
Methods and Results:
Gene silencing oligonucleotides (GSOs) were used to inhibit 4 14q32 microRNAs, miR-329, miR-487b, miR-494, and miR-495, 1 day before double femoral artery ligation. Blood flow recovery was followed by laser Doppler perfusion imaging. All 4 GSOs clearly improved blood flow recovery after ischemia. Mice treated with GSO-495 or GSO-329 showed increased perfusion already after 3 days (30% perfusion versus 15% in control), and those treated with GSO-329 showed a full recovery of perfusion after 7 days (versus 60% in control). Increased collateral artery diameters (arteriogenesis) were observed in adductor muscles of GSO-treated mice, as well as increased capillary densities (angiogenesis) in the ischemic soleus muscle. In vitro, treatment with GSOs led to increased sprout formation and increased arterial endothelial cell proliferation, as well as to increased arterial myofibroblast proliferation.
Conclusions:
The 14q32 microRNA gene cluster is highly involved in neovascularization. Inhibition of 14q32 microRNAs miR-329, miR-487b, miR-494, and miR-495 provides a promising tool for future therapeutic neovascularization.
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Affiliation(s)
- Sabine M.J. Welten
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Antonius J.N.M. Bastiaansen
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Rob C.M. de Jong
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Margreet R. de Vries
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Erna A.B. Peters
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Martin C. Boonstra
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Søren P. Sheikh
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Nicola La Monica
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Ekambar R. Kandimalla
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - Paul H.A. Quax
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
| | - A. Yaël Nossent
- From the Department of Surgery (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., M.C.B., P.H.A.Q., A.Y.N.) and Einthoven Laboratory for Experimental Vascular Medicine (S.M.J.W., A.J.N.M.B., R.C.M.d.J., M.R.d.V., E.A.B.P., P.H.A.Q., A.Y.N.), Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark (S.P.S.); and Idera Pharmaceuticals, Cambridge, MA (N.L.M., E.R.K.)
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Kota SK, Llères D, Bouschet T, Hirasawa R, Marchand A, Begon-Pescia C, Sanli I, Arnaud P, Journot L, Girardot M, Feil R. ICR noncoding RNA expression controls imprinting and DNA replication at the Dlk1-Dio3 domain. Dev Cell 2014; 31:19-33. [PMID: 25263792 DOI: 10.1016/j.devcel.2014.08.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 07/04/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
Abstract
Imprinted genes play essential roles in development, and their allelic expression is mediated by imprinting control regions (ICRs). The Dlk1-Dio3 locus is among the few imprinted domains controlled by a paternally methylated ICR. The unmethylated maternal copy activates imprinted expression early in development through an unknown mechanism. We find that in mouse embryonic stem cells (ESCs) and in blastocysts, this function is linked to maternal, bidirectional expression of noncoding RNAs (ncRNAs) from the ICR. Disruption of ICR ncRNA expression in ESCs affected gene expression in cis, led to acquisition of aberrant histone and DNA methylation, delayed replication timing along the domain on the maternal chromosome, and changed its subnuclear localization. The epigenetic alterations persisted during differentiation and affected the neurogenic potential of the stem cells. Our data indicate that monoallelic expression at an ICR of enhancer RNA-like ncRNAs controls imprinted gene expression, epigenetic maintenance processes, and DNA replication in embryonic cells.
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Affiliation(s)
- Satya K Kota
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - David Llères
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Tristan Bouschet
- Institute of Functional Genomics (IGF), CNRS and University of Montpellier, 141 rue de la Cardonille, Montpellier 34090, France
| | - Ryutaro Hirasawa
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Alice Marchand
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Christina Begon-Pescia
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Ildem Sanli
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Philippe Arnaud
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Laurent Journot
- Institute of Functional Genomics (IGF), CNRS and University of Montpellier, 141 rue de la Cardonille, Montpellier 34090, France
| | - Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France.
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Xie P, Sun Y, Ouyang Q, Hu L, Tan Y, Zhou X, Xiong B, Zhang Q, Yuan D, Pan Y, Liu T, Liang P, Lu G, Lin G. Physiological oxygen prevents frequent silencing of the DLK1-DIO3 cluster during human embryonic stem cells culture. Stem Cells 2014; 32:391-401. [PMID: 24123616 DOI: 10.1002/stem.1558] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 07/28/2013] [Accepted: 08/25/2013] [Indexed: 12/18/2022]
Abstract
Genetic and epigenetic alterations are observed in long-term culture (>30 passages) of human embryonic stem cells (hESCs); however, little information is available in early cultures. Through a large-scale gene expression analysis between initial-passage hESCs (ihESCs, <10 passages) and early-passage hESCs (ehESCs, 20-30 passages) of 12 hESC lines, we found that the DLK1-DIO3 gene cluster was normally expressed and showed normal methylation pattern in ihESC, but was frequently silenced after 20 passages. Both the DLK1-DIO3 active status in ihESCs and the inactive status in ehESCs were inheritable during differentiation. Silencing of the DLK1-DIO3 cluster did not seem to compromise the multilineage differentiation ability of hESCs, but was associated with reduced DNA damage-induced apoptosis in ehESCs and their differentiated hepatocyte-like cell derivatives, possibly through attenuation of the expression and phosphorylation of p53. Furthermore, we demonstrated that 5% oxygen, instead of the commonly used 20% oxygen, is required for preserving the expression of the DLK1-DIO3 cluster. Overall, the data suggest that active expression of the DLK1-DIO3 cluster represents a new biomarker for epigenetic stability of hESCs and indicates the importance of using a proper physiological oxygen level during the derivation and culture of hESCs.
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Affiliation(s)
- Pingyuan Xie
- Institute of Reproductive & Stem Cell Engineering, Central South University, Changsha, China; Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Changsha, China
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Lehner B, Kunz P, Saehr H, Fellenberg J. Epigenetic silencing of genes and microRNAs within the imprinted Dlk1-Dio3 region at human chromosome 14.32 in giant cell tumor of bone. BMC Cancer 2014; 14:495. [PMID: 25005035 PMCID: PMC4101709 DOI: 10.1186/1471-2407-14-495] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Growing evidence exists that the neoplastic stromal cell population (GCTSC) within giant cell tumors (GCT) originates from mesenchymal stem cells (MSC). In a previous study we identified a microRNA signature that differentiates between these cell types. Five differentially expressed microRNAs are located within the Dlk1-Dio3 region on chromosome 14. Aberrant regulation within this region is known to influence cell growth, differentiation and the development of cancer. The aim of this study was to elucidate the involvement of deregulations within the Dlk1-Dio3 region in GCT pathogenesis. METHODS Quantitative gene and microRNA expression analyses were performed on GCTSCs and MSCs with or without treatment with epigenetic modifiers. Methylation analysis of differentially methylated regions was performed by bisulfite sequencing. RESULTS In addition to microRNA silencing we detected a significant downregulation of Dlk1, Meg3 and Meg8 in GCTSCs compared to MSCs. DNA methylation analyses of the Meg3-DMR and IG-DMR revealed a frequent hypermethylation within the IG-DMR in GCTs. Epigenetic modification could restore expression of some but not all analyzed genes and microRNAs suggesting further regulatory mechanisms. CONCLUSION Epigenetic silencing of genes and microRNAs within the Dlk1-Dio3 region is a common event in GCTSCs, in part mediated by hypermethylation within the IG-DMR. The identified genes, micro RNAs and microRNA target genes might be valuable targets for the development of improved strategies for GCT diagnosis and therapy.
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Affiliation(s)
| | | | | | - Joerg Fellenberg
- Research Centre for Experimental Orthopedics, Department of Orthopedics, Trauma Surgery and Paraplegia, Orthopedic University Hospital Heidelberg, Schlierbacher Landstr 200a, Heidelberg 69118, Germany.
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Kameswaran V, Kaestner KH. The Missing lnc(RNA) between the pancreatic β-cell and diabetes. Front Genet 2014; 5:200. [PMID: 25071830 PMCID: PMC4077016 DOI: 10.3389/fgene.2014.00200] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 06/15/2014] [Indexed: 01/15/2023] Open
Abstract
Diabetes mellitus represents a group of complex metabolic diseases that result in impaired glucose homeostasis, which includes destruction of β-cells or the failure of these insulin-secreting cells to compensate for increased metabolic demand. Despite a strong interest in characterizing the transcriptome of the different human islet cell types to understand the molecular basis of diabetes, very little attention has been paid to the role of long non-coding RNAs (lncRNAs) and their contribution to this disease. Here we summarize the growing evidence for the potential role of these lncRNAs in β-cell function and dysregulation in diabetes, with a focus on imprinted genomic loci.
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Affiliation(s)
- Vasumathi Kameswaran
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
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Hoyo C, Daltveit AK, Iversen E, Benjamin-Neelon SE, Fuemmeler B, Schildkraut J, Murtha AP, Overcash F, Vidal AC, Wang F, Huang Z, Kurtzberg J, Seewaldt V, Forman M, Jirtle RL, Murphy SK. Erythrocyte folate concentrations, CpG methylation at genomically imprinted domains, and birth weight in a multiethnic newborn cohort. Epigenetics 2014; 9:1120-30. [PMID: 24874916 DOI: 10.4161/epi.29332] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Epigenetic mechanisms are proposed to link maternal concentrations of methyl group donor nutrients with the risk of low birth weight. However, empirical data are lacking. We have examined the association between maternal folate and birth weight and assessed the mediating role of DNA methylation at nine differentially methylated regions (DMRs) of genomically imprinted genes in these associations. Compared with newborns of women with folate levels in the lowest quartile, birth weight was higher in newborns of mothers in the second (β = 143.2, se = 63.2, P = 0.02), third (β = 117.3, se = 64.0, P = 0.07), and fourth (β = 133.9, se = 65.2, P = 0.04) quartiles, consistent with a threshold effect. This pattern of association did not vary by race/ethnicity but was more apparent in newborns of non-obese women. DNA methylation at the PLAGL1, SGCE, DLK1/MEG3 and IGF2/H19 DMRs was associated with maternal folate levels and also birth weight, suggestive of threshold effects. MEG3 DMR methylation mediated the association between maternal folate levels and birth weight (P =0.06). While the small sample size and partial scope of examined DMRs limit our conclusions, our data suggest that, with respect to birth weight, no additional benefits may be derived from increased maternal folate concentrations, especially in non-obese women. These data also support epigenetic plasticity as a key mechanistic response to folate availability during early fetal development.
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Affiliation(s)
- Cathrine Hoyo
- Department of Biological Sciences; North Carolina State University; Raleigh, NC USA; Department of Obstetrics and Gynecology; Division of Clinical Epidemiology; School of Medicine; Duke University; Durham, NC USA
| | - Anne Kjersti Daltveit
- Department of Global Public Health and Primary Care; University of Bergen; Bergen, Norway
| | - Edwin Iversen
- Department of Statistics; Duke University; Durham, NC USA
| | - Sara E Benjamin-Neelon
- Department of Community and Family Medicine; Duke University School of Medicine and Duke Global Health Institute; Durham, NC USA
| | - Bernard Fuemmeler
- Department of Community and Family Medicine; Duke University; Durham, NC USA
| | - Joellen Schildkraut
- Department of Community and Family Medicine; Duke Cancer Institute; Duke University; Durham, NC USA
| | - Amy P Murtha
- Department of Obstetrics and Gynecology; Division of Maternal-Fetal Medicine; School of Medicine; Duke University; Durham, NC USA
| | - Francine Overcash
- Department of Obstetrics and Gynecology; Division of Clinical Epidemiology; School of Medicine; Duke University; Durham, NC USA
| | - Adriana C Vidal
- Department of Obstetrics and Gynecology; Division of Clinical Epidemiology; School of Medicine; Duke University; Durham, NC USA
| | - Frances Wang
- Department of Community and Family Medicine; Duke Cancer Institute; Duke University; Durham, NC USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology; Division of Gynecologic Oncology; School of Medicine; Duke University; Durham, NC USA
| | - Joanne Kurtzberg
- Duke University Department of Pediatrics; Duke Cancer Institute; School of Medicine; Duke University; Durham, NC USA
| | - Victoria Seewaldt
- Department of Medicine; Division of Oncology; School of Medicine; Duke University; Durham, NC USA
| | - Michele Forman
- Department of Nutritional Sciences; University of Texas; Austin, TX USA
| | - Randy L Jirtle
- Department of Oncology; McArdle Laboratory for Cancer Research; University of Wisconsin-Madison; Madison, WI USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology; Division of Gynecologic Oncology; School of Medicine; Duke University; Durham, NC USA
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Gagne A, Hochman A, Qureshi M, Tong C, Arbon J, McDaniel K, Davis TL. Analysis of DNA methylation acquisition at the imprinted Dlk1 locus reveals asymmetry at CpG dyads. Epigenetics Chromatin 2014; 7:9. [PMID: 24904690 PMCID: PMC4045959 DOI: 10.1186/1756-8935-7-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/20/2014] [Indexed: 12/27/2022] Open
Abstract
Background Differential distribution of DNA methylation on the parental alleles of imprinted genes distinguishes the alleles from each other and dictates their parent of origin-specific expression patterns. While differential DNA methylation at primary imprinting control regions is inherited via the gametes, additional allele-specific DNA methylation is acquired at secondary sites during embryonic development and plays a role in the maintenance of genomic imprinting. The precise mechanisms by which this somatic DNA methylation is established at secondary sites are not well defined and may vary as methylation acquisition at these sites occurs at different times for genes in different imprinting clusters. Results In this study, we show that there is also variability in the timing of somatic DNA methylation acquisition at multiple sites within a single imprinting cluster. Paternal allele-specific DNA methylation is initially acquired at similar stages of post-implantation development at the linked Dlk1 and Gtl2 differentially methylated regions (DMRs). In contrast, unlike the Gtl2-DMR, the maternal Dlk1-DMR acquires DNA methylation in adult tissues. Conclusions These data suggest that the acquisition of DNA methylation across the Dlk1/Gtl2 imprinting cluster is variable. We further found that the Dlk1 differentially methylated region displays low DNA methylation fidelity, as evidenced by the presence of hemimethylation at approximately one-third of the methylated CpG dyads. We hypothesize that the maintenance of DNA methylation may be less efficient at secondary differentially methylated sites than at primary imprinting control regions.
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Affiliation(s)
- Alyssa Gagne
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899, USA
| | - Abigail Hochman
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899, USA
| | - Mahvish Qureshi
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899, USA
| | - Celia Tong
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899, USA
| | - Jessica Arbon
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899, USA
| | - Kayla McDaniel
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899, USA
| | - Tamara L Davis
- Department of Biology, Bryn Mawr College, 101 N. Merion Avenue, Bryn Mawr, PA 19010-2899, USA
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Sheng X, Li J, Yang L, Chen Z, Zhao Q, Tan L, Zhou Y, Li J. Promoter hypermethylation influences the suppressive role of maternally expressed 3, a long non-coding RNA, in the development of epithelial ovarian cancer. Oncol Rep 2014; 32:277-85. [PMID: 24859196 DOI: 10.3892/or.2014.3208] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 04/03/2014] [Indexed: 12/13/2022] Open
Abstract
Maternally expressed 3 (MEG3) is a long non-coding RNA that can activate p53 and inhibit tumorigenesis and progression of various types of cancers. However, the role of MEG3 in epithelial ovarian cancer (EOC) is still unknown. The aim of the present study was to confirm whether MEG3 is downregulated in human EOC, determine its possible mechanism of action and elucidate the role of MEG3 in EOC. Differences in the expression of MEG3 and in the methylation status of the MEG3 promoter between EOC and normal ovary were analyzed using RT-PCR and methylation-specific PCR (MSP), respectively. MTT and EdU assays and flow cytometric analysis were used to assess the growth of ovarian cancer cells after overexpression of MEG3. The target genes regulated by MEG3 were detected with the Dual Luciferase Reporter system. The expression levels of target genes were confirmed using RT-PCR and western blotting. In contrast to normal ovarian tissues, the expression of MEG3 was absent or decreased in most EOC tissues as well as in human EOC cell lines, and the promoter of the MEG3 gene was highly methylated in both cancer tissues and cell lines. Treatment with 5-aza-2-deoxycytidine reversed the promoter hypermethylation and increased MEG3 expression. In addition, ectopic expression of MEG3 suppressed the proliferation and growth of OVCAR3 cells and promoted apoptosis. Finally, MEG3 activated p53 in OVCAR3 cells. In conclusion, our data suggest that MEG3 is epigenetically silenced in EOC due to promoter hypermethylation, which may contribute to the development of EOC.
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Affiliation(s)
- Xiujie Sheng
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, P.R. China
| | - Jianqi Li
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, P.R. China
| | - Lei Yang
- The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 510182, P.R. China
| | - Zhiyi Chen
- Guangzhou Institute of Obstetrics and Gynecology, Guangzhou 510182, P.R. China
| | - Qin Zhao
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, P.R. China
| | - Linyu Tan
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, P.R. China
| | - Yanqing Zhou
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, P.R. China
| | - Juan Li
- Department of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, P.R. China
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Novel deletions affecting the MEG3-DMR provide further evidence for a hierarchical regulation of imprinting in 14q32. Eur J Hum Genet 2014; 23:180-8. [PMID: 24801763 DOI: 10.1038/ejhg.2014.72] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 02/18/2014] [Accepted: 02/25/2014] [Indexed: 11/08/2022] Open
Abstract
The imprinted region on chromosome 14q32 harbors several maternally or paternally expressed genes as well as two DMRs (differentially methylated regions), the IG-DMR and the MEG3-DMR, which both act as imprinting control centers. Genetic aberrations affecting the imprinted gene cluster in 14q32 result in distinct phenotypes, known as maternal or paternal uniparental disomy 14 phenotypes (upd(14)mat, upd(14)pat). In both syndromes, three types of molecular alterations have been reported: uniparental disomy 14, deletions and epimutations. In contrast to uniparental disomy and epimutations, deletions affecting regulatory elements in 14q32 are associated with a high-recurrence risk. Based on two single deletion cases a functional hierarchy of the IG-DMR as a regulator for the methylation of the MEG3-DMR has been proposed. We have identified two novel deletions of maternal origin spanning the MEG3-DMR, but not the IG-DMR in patients with upd(14)pat syndrome, one de novo deletion of 165 kb and another deletion of 5.8 kb in two siblings. The 5.8 kb deletion was inherited from the phenotypically normal mother, who carries the deletion in a mosaic state on her paternal chromosome 14. The methylation at both DMRs was investigated by quantitative next generation bisulfite sequencing and revealed normal methylation patterns at the IG-DMR in all patients with the exception of certain CpG dinucleotides. Thus, we could confirm that deletions of the MEG3-DMR does not generally influence the methylation pattern of the IG-DMR, which strengthens the hypothesis of a hierarchical structure and distinct functional properties of the two DMRs.
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Court F, Tayama C, Romanelli V, Martin-Trujillo A, Iglesias-Platas I, Okamura K, Sugahara N, Simón C, Moore H, Harness JV, Keirstead H, Sanchez-Mut JV, Kaneki E, Lapunzina P, Soejima H, Wake N, Esteller M, Ogata T, Hata K, Nakabayashi K, Monk D. Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment. Genome Res 2014; 24:554-69. [PMID: 24402520 PMCID: PMC3975056 DOI: 10.1101/gr.164913.113] [Citation(s) in RCA: 247] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/26/2013] [Indexed: 12/16/2022]
Abstract
Differential methylation between the two alleles of a gene has been observed in imprinted regions, where the methylation of one allele occurs on a parent-of-origin basis, the inactive X-chromosome in females, and at those loci whose methylation is driven by genetic variants. We have extensively characterized imprinted methylation in a substantial range of normal human tissues, reciprocal genome-wide uniparental disomies, and hydatidiform moles, using a combination of whole-genome bisulfite sequencing and high-density methylation microarrays. This approach allowed us to define methylation profiles at known imprinted domains at base-pair resolution, as well as to identify 21 novel loci harboring parent-of-origin methylation, 15 of which are restricted to the placenta. We observe that the extent of imprinted differentially methylated regions (DMRs) is extremely similar between tissues, with the exception of the placenta. This extra-embryonic tissue often adopts a different methylation profile compared to somatic tissues. Further, we profiled all imprinted DMRs in sperm and embryonic stem cells derived from parthenogenetically activated oocytes, individual blastomeres, and blastocysts, in order to identify primary DMRs and reveal the extent of reprogramming during preimplantation development. Intriguingly, we find that in contrast to ubiquitous imprints, the majority of placenta-specific imprinted DMRs are unmethylated in sperm and all human embryonic stem cells. Therefore, placental-specific imprinting provides evidence for an inheritable epigenetic state that is independent of DNA methylation and the existence of a novel imprinting mechanism at these loci.
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Affiliation(s)
- Franck Court
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Valeria Romanelli
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
| | - Alex Martin-Trujillo
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
| | - Isabel Iglesias-Platas
- Servicio de Neonatología, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, 08950 Barcelona, Spain
| | - Kohji Okamura
- Department of Systems Biomedicine, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Naoko Sugahara
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Carlos Simón
- Fundación IVI-Instituto Universitario IVI-Universidad de Valencia, INCLIVA, 46980 Paterna, Valencia, Spain
| | - Harry Moore
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Julie V. Harness
- Reeve-Irvine Research Centre, Sue and Bill Gross Stem Cell Research Center, Department of Anatomy and Neurobiology, School of Medicine, University of California at Irvine, Irvine, California 92697, USA
| | - Hans Keirstead
- Reeve-Irvine Research Centre, Sue and Bill Gross Stem Cell Research Center, Department of Anatomy and Neurobiology, School of Medicine, University of California at Irvine, Irvine, California 92697, USA
| | - Jose Vicente Sanchez-Mut
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
| | - Eisuke Kaneki
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kyushu University, Fukuoka 812-8582, Japan
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular, CIBERER, IDIPAZ-Hospital Universitario La Paz, Universidad Autónoma de Madrid, 28046 Madrid, Spain
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Norio Wake
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kyushu University, Fukuoka 812-8582, Japan
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
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132
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Loss of imprinting at the 14q32 domain is associated with microRNA overexpression in acute promyelocytic leukemia. Blood 2014; 123:2066-74. [PMID: 24493669 DOI: 10.1182/blood-2012-12-469833] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Distinct patterns of DNA methylation characterize the epigenetic landscape of promyelocytic leukemia/retinoic acid receptor-α (PML-RARα)-associated acute promyelocytic leukemia (APL). We previously reported that the microRNAs (miRNAs) clustered on chromosome 14q32 are overexpressed only in APL. Here, using high-throughput bisulfite sequencing, we identified an APL-associated hypermethylation at the upstream differentially methylated region (DMR), which also included the site motifs for the enhancer blocking protein CCCTC-binding factor (CTCF). Comparing the profiles of diagnostic/remission paired patient samples, we show that hypermethylation was acquired in APL in a monoallelic manner. The cytosine guanine dinucleotide status of the DMR correlated with expression of the miRNAs following a characteristic position-dependent pattern. Moreover, a signature of hypermethylation was also detected in leukemic cells from an established transgenic PML-RARA APL mouse model at the orthologous region on chromosome 12, including the CTCF binding site located upstream from the mouse miRNA cluster. These results, together with the demonstration that the region does not show DNA methylation changes during myeloid differentiation, provide evidence that 14q32 hypermethylation is implicated in the pathogenesis of APL. We propose a model in which loss of imprinting at the 14q32 domain leads to overexpression of the miRNAs in APL.
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133
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Skaar DA, Li Y, Bernal AJ, Hoyo C, Murphy SK, Jirtle RL. The human imprintome: regulatory mechanisms, methods of ascertainment, and roles in disease susceptibility. ILAR J 2014; 53:341-58. [PMID: 23744971 DOI: 10.1093/ilar.53.3-4.341] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Imprinted genes form a special subset of the genome, exhibiting monoallelic expression in a parent-of-origin-dependent fashion. This monoallelic expression is controlled by parental-specific epigenetic marks, which are established in gametogenesis and early embryonic development and are persistent in all somatic cells throughout life. We define this specific set of cis-acting epigenetic regulatory elements as the imprintome, a distinct and specially tasked subset of the epigenome. Imprintome elements contain DNA methylation and histone modifications that regulate monoallelic expression by affecting promoter accessibility, chromatin structure, and chromatin configuration. Understanding their regulation is critical because a significant proportion of human imprinted genes are implicated in complex diseases. Significant species variation in the repertoire of imprinted genes and their epigenetic regulation, however, will not allow model organisms solely to be used for this crucial purpose. Ultimately, only the human will suffice to accurately define the human imprintome.
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Affiliation(s)
- David A Skaar
- Department of Oncology, Duke University Medical Center, Durham, North Carolina, USA
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134
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Kameswaran V, Bramswig NC, McKenna LB, Penn M, Schug J, Hand NJ, Chen Y, Choi I, Vourekas A, Won KJ, Liu C, Vivek K, Naji A, Friedman JR, Kaestner KH. Epigenetic regulation of the DLK1-MEG3 microRNA cluster in human type 2 diabetic islets. Cell Metab 2014; 19:135-45. [PMID: 24374217 PMCID: PMC3932527 DOI: 10.1016/j.cmet.2013.11.016] [Citation(s) in RCA: 251] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 09/25/2013] [Accepted: 11/15/2013] [Indexed: 01/09/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is a complex disease characterized by the inability of the insulin-producing β cells in the endocrine pancreas to overcome insulin resistance in peripheral tissues. To determine if microRNAs are involved in the pathogenesis of human T2DM, we sequenced the small RNAs of human islets from diabetic and nondiabetic organ donors. We identified a cluster of microRNAs in an imprinted locus on human chromosome 14q32 that is highly and specifically expressed in human β cells and dramatically downregulated in islets from T2DM organ donors. The downregulation of this locus strongly correlates with hypermethylation of its promoter. Using HITS-CLIP for the essential RISC-component Argonaute, we identified disease-relevant targets of the chromosome 14q32 microRNAs, such as IAPP and TP53INP1, that cause increased β cell apoptosis upon overexpression in human islets. Our results support a role for microRNAs and their epigenetic control by DNA methylation in the pathogenesis of T2DM.
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Affiliation(s)
- Vasumathi Kameswaran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nuria C Bramswig
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lindsay B McKenna
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melinda Penn
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan Schug
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas J Hand
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ying Chen
- Genomics and Computational Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Inchan Choi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anastassios Vourekas
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyoung-Jae Won
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chengyang Liu
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kumar Vivek
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ali Naji
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joshua R Friedman
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Klaus H Kaestner
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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135
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Sato S, Maekawa R, Yamagata Y, Asada H, Tamura I, Lee L, Okada M, Tamura H, Sugino N. Potential mechanisms of aberrant DNA hypomethylation on the x chromosome in uterine leiomyomas. J Reprod Dev 2013; 60:47-54. [PMID: 24291816 PMCID: PMC3963299 DOI: 10.1262/jrd.2013-095] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
We recently found that aberrant DNA hypomethylation is more common on the X chromosome
than on other chromosomes in uterine leiomyomas by genome-wide DNA methylation profiling.
To investigate the mechanism of aberrant hypomethylation on the X chromosome in uterine
leiomyomas, we analyzed methylome and transcriptome data from three cases of leiomyomas
and the adjacent myometrium. We found that eleven of the aberrantly hypomethylated genes
on the X chromosome were common to the three cases. None of these 11 genes were
transcriptionally upregulated in the leiomyoma. However, one of them,
TSPYL2, was hypomethylated in 68% of multiple leiomyoma specimens. The
incidence of aberrant hypomethylation of TSPYL2 was comparable to that of
the MED12 mutation (68%), which is known to be detected at a high
frequency in uterine leiomyomas. We also analyzed the aberration of the X chromosome
inactivation (XCI) mechanism in uterine leiomyomas. Hypomethylation was not enriched in
the imprinted genes, suggesting that dysfunction of polycomb repressive complexes is not
involved in the aberrant hypomethylation on the X chromosome. The expression analysis of
XCI-related genes revealed that the XIST and SATB1
expression was downregulated in 36% and 46% of 11 leiomyoma specimens, respectively, while
the HNRNPU and SMCHD1 expression was not altered. In
conclusion, the aberration of XCI-related genes such as SATB1 or
XIST may be involved in aberrant hypomethylation on the X chromosome in
a certain population of the patients with uterine leiomyomas. TSPYL2 of
the aberrantly hypomethylated genes on the X chromosome can be used as a biomarker of
uterine leiomyomas.
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Affiliation(s)
- Shun Sato
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan
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136
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Sasaki A, Sumie M, Wada S, Kosaki R, Kurosawa K, Fukami M, Sago H, Ogata T, Kagami M. Prenatal genetic testing for a microdeletion at chromosome 14q32.2 imprinted region leading to UPD(14)pat-like phenotype. Am J Med Genet A 2013; 164A:264-6. [DOI: 10.1002/ajmg.a.36185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 07/16/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Aiko Sasaki
- Department of Maternal-Fetal and Neonatal Medicine; National Center for Child Health and Development; Tokyo Japan
| | - Masahiro Sumie
- Department of Maternal-Fetal and Neonatal Medicine; National Center for Child Health and Development; Tokyo Japan
| | - Seiji Wada
- Department of Maternal-Fetal and Neonatal Medicine; National Center for Child Health and Development; Tokyo Japan
| | - Rika Kosaki
- Division of Medical Genetics; National Center for Child Health and Development; Tokyo Japan
| | - Kenji Kurosawa
- Division of Medical Genetics; Kanagawa Children's Medical Center; Yokohama Japan
| | - Maki Fukami
- Department of Molecular Endocrinology; National Research Institute for Child Health and Development; Tokyo Japan
| | - Haruhiko Sago
- Department of Maternal-Fetal and Neonatal Medicine; National Center for Child Health and Development; Tokyo Japan
| | - Tsutomu Ogata
- Department of Pediatrics; Hamamatsu University School of Medicine; Hamamatsu Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology; National Research Institute for Child Health and Development; Tokyo Japan
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137
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Lucon DR, Rocha CDS, Craveiro RB, Dilloo D, Cardinalli IA, Cavalcanti DP, Aguiar SDS, Maurer-Morelli C, Yunes JA. Downregulation of 14q32 microRNAs in Primary Human Desmoplastic Medulloblastoma. Front Oncol 2013; 3:254. [PMID: 24093088 PMCID: PMC3782711 DOI: 10.3389/fonc.2013.00254] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/10/2013] [Indexed: 11/17/2022] Open
Abstract
Medulloblastoma (MB) is one of the most common pediatric cancers, likely originating from abnormal development of cerebellar progenitor neurons. MicroRNA (miRNA) has been shown to play an important role in the development of the central nervous system. Microarray analysis was used to investigate miRNA expression in desmoplastic MB from patients diagnosed at a young age (1 or 2 years old). Normal fetal or newborn cerebellum was used as control. A total of 84 differentially expressed miRNAs (64 downregulated and 20 upregulated) were found. Most downregulated miRNAs (32/64) were found to belong to the cluster of miRNAs at the 14q32 locus, suggesting that this miRNA locus is regulated as a module in MB. Possible mechanisms of 14q32 miRNAs downregulation were investigated by the analysis of publicly available gene expression data sets. First, expression of estrogen-related receptor-γ (ESRRG), a reported positive transcriptional regulator of some 14q32 miRNAs, was found downregulated in desmoplastic MB. Second, expression of the parentally imprinted gene MEG3 was lower in MB in comparison to normal cerebellum, suggesting a possible epigenetic silencing of the 14q32 locus. miR-129-5p (11p11.2/7q32.1), miR-206 (6p12.2), and miR-323-3p (14q32.2), were chosen for functional studies in DAOY cells. Overexpression of miR-129-5p using mimics decreased DAOY proliferation. No effect was found with miR-206 or miR-323 mimics.
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Affiliation(s)
- Danielle Ribeiro Lucon
- Centro Infantil Boldrini , Campinas , Brazil ; Departamento de Genética Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas , Campinas , Brazil
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138
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Poole RL, Docherty LE, Al Sayegh A, Caliebe A, Turner C, Baple E, Wakeling E, Harrison L, Lehmann A, Temple IK, Mackay DJG. Targeted methylation testing of a patient cohort broadens the epigenetic and clinical description of imprinting disorders. Am J Med Genet A 2013; 161A:2174-82. [PMID: 23913548 DOI: 10.1002/ajmg.a.36049] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 03/13/2013] [Indexed: 11/11/2022]
Abstract
Imprinting disorders are associated with mutations and epimutations affecting imprinted genes, that is those whose expression is restricted by parent of origin. Their diagnosis is challenging for two reasons: firstly, their clinical features, particularly prenatal and postnatal growth disturbance, are heterogeneous and partially overlapping; secondly, their underlying molecular defects include mutation, epimutation, copy number variation, and chromosomal errors, and can be further complicated by somatic mosaicism and multi-locus methylation defects. It is currently unclear to what extent the observed phenotypic heterogeneity reflects the underlying molecular pathophysiology; in particular, the molecular and clinical diversity of multilocus methylation defects remains uncertain. To address these issues we performed comprehensive methylation analysis of imprinted genes in a research cohort of 285 patients with clinical features of imprinting disorders, with or without a positive molecular diagnosis. 20 of 91 patients (22%) with diagnosed epimutations had methylation defects of additional imprinted loci, and the frequency of developmental delay and congenital anomalies was higher among these patients than those with isolated epimutations, indicating that hypomethylation of multiple imprinted loci is associated with increased diversity of clinical presentation. Among 194 patients with clinical features of an imprinting disorder but no molecular diagnosis, we found 15 (8%) with methylation anomalies, including missed and unexpected molecular diagnoses. These observations broaden the phenotypic and epigenetic definitions of imprinting disorders, and show the importance of comprehensive molecular testing for patient diagnosis and management.
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Affiliation(s)
- Rebecca L Poole
- Faculty of Medicine, University of Southampton, Southampton, UK
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139
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Garitano-Trojaola A, Agirre X, Prósper F, Fortes P. Long non-coding RNAs in haematological malignancies. Int J Mol Sci 2013; 14:15386-422. [PMID: 23887658 PMCID: PMC3759866 DOI: 10.3390/ijms140815386] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 06/28/2013] [Accepted: 07/09/2013] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are functional RNAs longer than 200 nucleotides in length. LncRNAs are as diverse as mRNAs and they normally share the same biosynthetic machinery based on RNA polymerase II, splicing and polyadenylation. However, lncRNAs have low coding potential. Compared to mRNAs, lncRNAs are preferentially nuclear, more tissue specific and expressed at lower levels. Most of the lncRNAs described to date modulate the expression of specific genes by guiding chromatin remodelling factors; inducing chromosomal loopings; affecting transcription, splicing, translation or mRNA stability; or serving as scaffolds for the organization of cellular structures. They can function in cis, cotranscriptionally, or in trans, acting as decoys, scaffolds or guides. These functions seem essential to allow cell differentiation and growth. In fact, many lncRNAs have been shown to exert oncogenic or tumor suppressor properties in several cancers including haematological malignancies. In this review, we summarize what is known about lncRNAs, the mechanisms for their regulation in cancer and their role in leukemogenesis, lymphomagenesis and hematopoiesis. Furthermore, we discuss the potential of lncRNAs in diagnosis, prognosis and therapy in cancer, with special attention to haematological malignancies.
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Affiliation(s)
- Andoni Garitano-Trojaola
- Laboratory of Myeloproliferative Syndromes, Oncology Area, Foundation for Applied Medical Research, University of Navarra, Pamplona 31008, Spain; E-Mails: (A.G.-T.); (X.A.); (F.P.)
| | - Xabier Agirre
- Laboratory of Myeloproliferative Syndromes, Oncology Area, Foundation for Applied Medical Research, University of Navarra, Pamplona 31008, Spain; E-Mails: (A.G.-T.); (X.A.); (F.P.)
| | - Felipe Prósper
- Laboratory of Myeloproliferative Syndromes, Oncology Area, Foundation for Applied Medical Research, University of Navarra, Pamplona 31008, Spain; E-Mails: (A.G.-T.); (X.A.); (F.P.)
- Hematology Service and Area of Cell Therapy, University of Navarra Clinic, University of Navarra, Pamplona 31008, Spain
| | - Puri Fortes
- Department of Hepatology and Gene Therapy, Foundation for Applied Medical Research, University of Navarra, Pamplona 31008, Spain
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140
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Menigatti M, Staiano T, Manser CN, Bauerfeind P, Komljenovic A, Robinson M, Jiricny J, Buffoli F, Marra G. Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions. Oncogenesis 2013; 2:e56. [PMID: 23857251 PMCID: PMC3740287 DOI: 10.1038/oncsis.2013.21] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/10/2013] [Accepted: 05/15/2013] [Indexed: 12/15/2022] Open
Abstract
Epigenetic silencing of protein-encoding genes is common in early-stage colorectal tumorigenesis. Less is known about the methylation-mediated silencing of genes encoding microRNAs (miRNAs), which are also important epigenetic modulators of gene expression. Using quantitative PCR, we identified 56 miRNAs that were expressed in normal colorectal mucosa and in HT29 colorectal cancer cells treated with demethylating agents but not in untreated HT29 cells, suggesting that they probably undergo methylation-induced silencing during colorectal tumorigenesis. One of these, miR-195, had recently been reported to be underexpressed in colorectal cancers and to exert tumor-suppressor effects in colorectal cancer cells. We identified the transcription start site (TSS) for primary miRNA (pri-miR)-497/195, the primary precursor that yields miR-195 and another candidate on our list, miR-497, and a single CpG island upstream to the TSS, which controls expression of both miRNAs. Combined bisulfite restriction analysis and bisulfite genomic sequencing studies revealed monoallelic methylation of this island in normal colorectal mucosa (50/50 samples) and full methylation in most colorectal adenomas (38/50; 76%). The hypermethylated precancerous lesions displayed significantly downregulated expression of both miRNAs. Similar methylation patterns were observed at two known imprinted genes, MEG3 and GNAS-AS1, which encode several of the 56 miRNAs on our list. Imprinting at these loci was lost in over half the adenomas (62% at MEG3 and 52% at GNAS-AS1). Copy-number alterations at MEG3, GNAS-AS1 and pri-miR-497/195, which are frequent in colorectal cancers, were less common in adenomas and confined to tumors displaying differential methylation at the involved locus. Our data show that somatically acquired, epigenetic changes at monoallelically methylated regions encoding miRNAs are relatively frequent in sporadic colorectal adenomas and might contribute to the onset and progression of these tumors.
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Affiliation(s)
- M Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - T Staiano
- Gastroenterology and Endoscopy Unit, Hospital of Cremona, Cremona, Italy
| | - C N Manser
- Gastroenterology and Endoscopy Unit, University of Zurich Hospital, Zurich, Switzerland
| | - P Bauerfeind
- Gastroenterology and Endoscopy Unit, University of Zurich Hospital, Zurich, Switzerland
| | - A Komljenovic
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - M Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - J Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - F Buffoli
- Gastroenterology and Endoscopy Unit, Hospital of Cremona, Cremona, Italy
| | - G Marra
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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141
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Kelly L, Bryan K, Kim SY, Janeway KA, Killian JK, Schildhaus HU, Miettinen M, Helman L, Meltzer PS, van de Rijn M, Debiec-Rychter M, O’Sullivan M. Post-transcriptional dysregulation by miRNAs is implicated in the pathogenesis of gastrointestinal stromal tumor [GIST]. PLoS One 2013; 8:e64102. [PMID: 23717541 PMCID: PMC3663836 DOI: 10.1371/journal.pone.0064102] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 04/09/2013] [Indexed: 12/12/2022] Open
Abstract
In contrast to adult mutant gastrointestinal stromal tumors [GISTs], pediatric/wild-type GISTs remain poorly understood overall, given their lack of oncogenic activating tyrosine kinase mutations. These GISTs, with a predilection for gastric origin in female patients, show limited response to therapy with tyrosine kinase inhibitors and generally pursue a more indolent course, but still may prove fatal. Defective cellular respiration appears to underpin tumor development in these wild-type cases, which as a group lack expression of succinate dehydrogenase [SDH] B, a surrogate marker for respiratory chain metabolism. Yet, only a small subset of the wild-type tumors show mutations in the genes coding for the SDH subunits [SDHx]. To explore additional pathogenetic mechanisms in these wild-type GISTs, we elected to investigate post-transcriptional regulation of these tumors by conducting microRNA (miRNA) profiling of a mixed cohort of 73 cases including 18 gastric pediatric wild-type, 25 (20 gastric, 4 small bowel and 1 retroperitoneal) adult wild-type GISTs and 30 gastric adult mutant GISTs. By this approach we have identified distinct signatures for GIST subtypes which correlate tightly with clinico-pathological parameters. A cluster of miRNAs on 14q32 show strikingly different expression patterns amongst GISTs, a finding which appears to be explained at least in part by differential allelic methylation of this imprinted region. Small bowel and retroperitoneal wild-type GISTs segregate with adult mutant GISTs and express SDHB, while adult wild-type gastric GISTs are dispersed amongst adult mutant and pediatric wild-type cases, clustering in this situation on the basis of SDHB expression. Interestingly, global methylation analysis has recently similarly demonstrated that these wild-type, SDHB-immunonegative tumors show a distinct pattern compared with KIT and PDGFRA mutant tumors, which as a rule do express SDHB. All cases with Carney triad within our cohort cluster together tightly.
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Affiliation(s)
- Lorna Kelly
- Histopathology Department, School of Medicine, Trinity College Dublin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
| | - Kenneth Bryan
- Computational Biology, Systems Biology/Immunology, Animal and Grassland Research and Innovation Centre, Teagasc, Dunsany, County Meath, Ireland
| | - Su Young Kim
- Centre for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Katherine A. Janeway
- Department of Pediatric Hematology-Oncology, Dana Farber Cancer Institute and Children’s Hospital, Boston, Massachusetts, United States of America
| | - J. Keith Killian
- Centre for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | | | - Markku Miettinen
- Centre for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Lee Helman
- Centre for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Paul S. Meltzer
- Centre for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Matt van de Rijn
- Department of Pathology, Stanford University Medical Centre, Stanford, California, United States of America
| | - Maria Debiec-Rychter
- Department of Human Genetics, Catholic University Leuven and University Hospitals, Leuven, Belgium
| | - Maureen O’Sullivan
- Histopathology Department, School of Medicine, Trinity College Dublin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin, Ireland
- * E-mail:
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142
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Kobayashi H, Yanagisawa E, Sakashita A, Sugawara N, Kumakura S, Ogawa H, Akutsu H, Hata K, Nakabayashi K, Kono T. Epigenetic and transcriptional features of the novel human imprinted lncRNA GPR1AS suggest it is a functional ortholog to mouse Zdbf2linc. Epigenetics 2013; 8:635-45. [PMID: 23764515 PMCID: PMC3857343 DOI: 10.4161/epi.24887] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs), transcribed from the intergenic regions of animal genomes, play important roles in key biological processes. In mice, Zdbf2linc was recently identified as an lncRNA isoform of the paternally expressed imprinted Zdbf2 gene. The functional role of Zdbf2linc remains undefined, but it may control parent-of-origin-specific expression of protein-coding neighbors through epigenetic modification in cis, similar to imprinted Nespas, Kcnq1ot1 and Airn lncRNAs. Here, we identified a novel imprinted long-range non-coding RNA, termed GPR1AS, in the human GPR1-ZDBF2 intergenic region. Although GPR1AS contains no human ZDBF2 exons, this lncRNA is transcribed in the antisense orientation from the GPR1 intron to a secondary, differentially methylated region upstream of the ZDBF2 gene (ZDBF2 DMR), similar to mouse Zdbf2linc. Interestingly, GPR1AS/Zdbf2linc is exclusively expressed in human/mouse placenta with paternal-allele-specific expression and maternal-allele-specific promoter methylation (GPR1/Gpr1 DMR). The paternal-allele specific methylation of the secondary ZDBF2 DMR was established in human placentas as well as somatic lineage. Meanwhile, the ZDBF2 gene showed stochastic paternal-allele-specific expression, possibly methylation-independent, in placental tissues. Overall, we demonstrated that epigenetic regulation mechanisms in the imprinted GPR1-GPR1AS-ZDBF2 region were well-conserved between human and mouse genomes without the high sequence conservation of the intergenic lncRNAs. Our findings also suggest that lncRNAs with highly conserved epigenetic and transcriptional regulation across species arose by divergent evolution from a common ancestor, if they do not have identical exon structures.
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Affiliation(s)
- Hisato Kobayashi
- Department of BioScience; Tokyo University of Agriculture; Tokyo, Japan
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143
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Chen CP, Chang YL, Chern SR, Wu PS, Su JW, Chen WL, Chen LF, Wang W. Prenatal diagnosis of partial trisomy 3q (3q27.3→qter) and partial monosomy 14q (14q31.3→qter) of paternal origin associated with fetal hypotonia, arthrogryposis, scoliosis and hyperextensible joints. Gene 2013; 516:132-7. [DOI: 10.1016/j.gene.2012.12.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/03/2012] [Indexed: 01/19/2023]
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144
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Benetatos L, Hatzimichael E, Londin E, Vartholomatos G, Loher P, Rigoutsos I, Briasoulis E. The microRNAs within the DLK1-DIO3 genomic region: involvement in disease pathogenesis. Cell Mol Life Sci 2013; 70:795-814. [PMID: 22825660 PMCID: PMC11114045 DOI: 10.1007/s00018-012-1080-8] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2011] [Revised: 06/26/2012] [Accepted: 06/28/2012] [Indexed: 02/07/2023]
Abstract
The mammalian genome is transcribed in a developmentally regulated manner, generating RNA strands ranging from long to short non-coding RNA (ncRNAs). NcRNAs generated by intergenic sequences and protein-coding loci, represent up to 98 % of the human transcriptome. Non-coding transcripts comprise short ncRNAs such as microRNAs, piwi-interacting RNAs, small nucleolar RNAs and long intergenic RNAs, most of which exercise a strictly controlled negative regulation of expression of protein-coding genes. In humans, the DLK1-DIO3 genomic region, located on human chromosome 14 (14q32) contains the paternally expressed imprinted genes DLK1, RTL1, and DIO3 and the maternally expressed imprinted genes MEG3 (Gtl2), MEG8 (RIAN), and antisense RTL1 (asRTL1). This region hosts, in addition to two long intergenic RNAs, the MEG3 and MEG8, one of the largest microRNA clusters in the genome, with 53 miRNAs in the forward strand and one (mir-1247) in the reverse strand. Many of these miRNAs are differentially expressed in several pathologic processes and various cancers. A better understanding of the pathophysiologic importance of the DLK1-DIO3 domain-containing microRNA cluster may contribute to innovative therapeutic strategies in a range of diseases. Here we present an in-depth review of this vital genomic region, and examine the role the microRNAs of this region may play in controlling tissue homeostasis and in the pathogenesis of some human diseases, mostly cancer, when aberrantly expressed. The potential clinical implications of this data are also discussed.
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Affiliation(s)
- Leonidas Benetatos
- Transfusion Unit, General Hospital of Preveza, Selefkias 2, 48100, Preveza, Greece.
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145
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Chen CP, Hwang KS, Su HY, Lin SP, Su YN, Chern SR, Su JW, Chen YT, Chen WL, Wang W. Prenatal diagnosis and molecular cytogenetic characterization of a de novo interstitial duplication of 14q (14q31.3→q32.12) associated with abnormal maternal serum biochemistry. Taiwan J Obstet Gynecol 2013; 52:125-8. [DOI: 10.1016/j.tjog.2012.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2012] [Indexed: 11/16/2022] Open
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146
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Court F, Martin-Trujillo A, Romanelli V, Garin I, Iglesias-Platas I, Salafsky I, Guitart M, Perez de Nanclares G, Lapunzina P, Monk D. Genome-wide allelic methylation analysis reveals disease-specific susceptibility to multiple methylation defects in imprinting syndromes. Hum Mutat 2013; 34:595-602. [PMID: 23335487 DOI: 10.1002/humu.22276] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/07/2013] [Indexed: 12/12/2022]
Abstract
Genomic imprinting is the parent-of-origin-specific allelic transcriptional silencing observed in mammals, which is governed by DNA methylation established in the gametes and maintained throughout the development. The frequency and extent of epimutations associated with the nine reported imprinting syndromes varies because it is evident that aberrant preimplantation maintenance of imprinted differentially methylated regions (DMRs) may affect multiple loci. Using a custom Illumina GoldenGate array targeting 27 imprinted DMRs, we profiled allelic methylation in 65 imprinting defect patients. We identify multilocus hypomethylation in numerous Beckwith-Wiedemann syndrome, transient neonatal diabetes mellitus (TNDM), and pseudohypoparathyroidism 1B patients, and an individual with Silver-Russell syndrome. Our data reveal a broad range of epimutations exist in certain imprinting syndromes, with the exception of Prader-Willi syndrome and Angelman syndrome patients that are associated with solitary SNRPN-DMR defects. A mutation analysis identified a 1 bp deletion in the ZFP57 gene in a TNDM patient with methylation defects at multiple maternal DMRs. In addition, we observe missense variants in ZFP57, NLRP2, and NLRP7 that are not consistent with maternal effect and aberrant establishment or methylation maintenance, and are likely benign. This work illustrates that further extensive molecular characterization of these rare patients is required to fully understand the mechanism underlying the etiology of imprint establishment and maintenance.
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Affiliation(s)
- Franck Court
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
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147
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Placentas from pregnancies conceived by IVF/ICSI have a reduced DNA methylation level at the H19 and MEST differentially methylated regions†. Hum Reprod 2013; 28:1117-26. [DOI: 10.1093/humrep/des459] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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148
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The ontogeny of cKIT+ human primordial germ cells proves to be a resource for human germ line reprogramming, imprint erasure and in vitro differentiation. Nat Cell Biol 2012; 15:113-22. [PMID: 23242216 DOI: 10.1038/ncb2638] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 11/01/2012] [Indexed: 12/13/2022]
Abstract
The generation of research-quality, clinically relevant cell types in vitro from human pluripotent stem cells requires a detailed understanding of the equivalent human cell types. Here we analysed 134 human embryonic and fetal samples from 6 to 20 developmental weeks and identified the stages at which cKIT(+) primordial germ cells (PGCs), the precursors of gametes, undergo whole-genome epigenetic reprogramming with global depletion of 5mC, H3K27me3 and H2A.Z, and the time at which imprint erasure is initiated and 5hmC is present. Using five alternative in vitro differentiation strategies combined with single-cell microfluidic analysis and a bona fide human cKIT(+) PGC signature, we show the stage of cKIT(+) PGC formation in the first 16 days of differentiation. Taken together, our study creates a resource of human germ line ontogeny that is essential for future studies aimed at in vitro differentiation and unveiling the mechanisms necessary to pass human DNA from one generation to the next.
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149
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Sittig LJ, Redei EE. Novel polymorphisms within the Dlk1-Dio3 imprinted locus in rat: a putative genetic basis for strain-specific allelic gene expression. Front Genet 2012; 3:296. [PMID: 23248649 PMCID: PMC3522107 DOI: 10.3389/fgene.2012.00296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 11/29/2012] [Indexed: 01/27/2023] Open
Abstract
The imprinted iodothyronine deiodinase-III (Dio3) thyroid hormone metabolizing gene exhibits paternal expression in most fetal tissues, yet exhibits aberrant, maternal expression in the hippocampus in F1 offspring of Sprague Dawley (SD) × Brown Norway (BN) rats. The maternal hippocampal expression is associated with lower Dio3 mRNA levels specifically in the hippocampus. Here, we tested the hypothesis that genetic polymorphisms between the SD and BN parent strains cause this aberrant allelic Dio3 expression and contribute to behavioral sequelae of higher thyroid hormone levels locally in the hippocampus, including anxiety-related behavior. We mapped and sequenced the Dio3 gene and several previously unmapped regions in the Dlk1-Dio3 locus that could regulate imprinting of the Dio3 gene. In the Dio3 promoter we identified four novel polymorphisms between the BN and SD strains. Next we took advantage of the fact that the Long Evans (LE) strain exhibits identical polymorphisms as the SD strain in the region 5' and including the Dio3 gene. By reciprocally crossing LE and BN strains we tested the relationship among Dio3 promoter region polymorphisms and Dio3 mRNA expression in the hippocampus. Aberrant strain-specific hippocampal Dio3 allelic expression replicated in the LE-BN reciprocal crosses, suggesting that hippocampal-specific imprinting of the Dio3 gene is not the result of a unique genetic or epigenetic characteristic of the SD rat strain, or a unique epistatic interaction between SD and BN. To our knowledge no other studies have reported a genetic × epigenetic interaction of genetic origin in the brain.
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Affiliation(s)
- Laura J Sittig
- Department of Psychiatry and Behavioral Sciences, The Asher Center, Feinberg School of Medicine, Northwestern University Chicago, IL, USA
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150
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Anwar SL, Krech T, Hasemeier B, Schipper E, Schweitzer N, Vogel A, Kreipe H, Lehmann U. Loss of imprinting and allelic switching at the DLK1-MEG3 locus in human hepatocellular carcinoma. PLoS One 2012; 7:e49462. [PMID: 23145177 PMCID: PMC3493531 DOI: 10.1371/journal.pone.0049462] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 10/09/2012] [Indexed: 01/09/2023] Open
Abstract
Deregulation of imprinted genes is an important molecular mechanism contributing to the development of cancer in humans. However, knowledge about imprinting defects in human hepatocellular carcinoma (HCC), the third leading cause of cancer mortality worldwide, is still limited. Therefore, a systematic meta-analysis of the expression of 223 imprinted loci in human HCC was initiated. This screen revealed that the DLK1-MEG3 locus is frequently deregulated in HCC. Deregulation of DLK1 and MEG3 expression accompanied by extensive aberrations in DNA methylation could be confirmed experimentally in an independent series of human HCC (n = 40) in more than 80% of cases. Loss of methylation at the DLK1-MEG3 locus correlates linearly with global loss of DNA methylation in HCC (r(2) = 0.63, p<0.0001). Inhibition of DNMT1 in HCC cells using siRNA led to a reduction in MEG3-DMR methylation and concomitant increase in MEG3 RNA expression. Allele-specific expression analysis identified loss of imprinting in 10 out of 31 informative samples (32%), rendering it one of the most frequent molecular defects in human HCC. In 2 cases unequivocal gain of bi-allelic expression accompanied by substantial loss of methylation at the IG-DMR could be demonstrated. In 8 cases the tumour cells displayed allelic switching by mono-allelic expression of the normally imprinted allele. Allelic switching was accompanied by gains or losses of DNA methylation primarily at IG-DMR1. Analysis of 10 hepatocellular adenomas (HCA) and 5 cases of focal nodular hyperplasia (FNH) confirmed that this epigenetic instability is specifically associated with the process of malignant transformation and not linked to increased proliferation per se. This widespread imprint instability in human HCC has to be considered in order to minimize unwanted side-effects of therapeutic approaches targeting the DNA methylation machinery. It might also serve in the future as predictive biomarker and for monitoring response to epigenetic therapy.
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Affiliation(s)
| | - Till Krech
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Britta Hasemeier
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Elisa Schipper
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Nora Schweitzer
- Department of Gastroenterology, Hepatology and Endocrinology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany
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