1
|
Kim HY, Shin CH, Lee YA, Shin CH, Kim GH, Ko JM. Deciphering Epigenetic Backgrounds in a Korean Cohort with Beckwith-Wiedemann Syndrome. Ann Lab Med 2022; 42:668-677. [PMID: 35765875 PMCID: PMC9277041 DOI: 10.3343/alm.2022.42.6.668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/07/2022] [Accepted: 06/08/2022] [Indexed: 11/22/2022] Open
Abstract
Background Beckwith–Wiedemann syndrome (BWS) is a congenital overgrowth disorder caused by genetic or epigenetic alterations at two imprinting centers (ICs) in the 11p15.5 region. Delineation of the molecular defects is important for prognosis and predicting familial recurrence. We evaluated epigenetic alterations and potential epigenotype–phenotype correlations in Korean children with BWS. Methods Forty children with BWS with proven genetic or epigenetic defects in the 11p15.5 region were included. The phenotype was scored using the BWS consensus scoring system. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), bisulfite pyrosequencing, a single-nucleotide polymorphism microarray, and CDKN1C sequencing were used for confirmative diagnosis. Results Patients met the criteria for genetic testing, with a mean clinical score of 5.4±2.0. Methylation alterations were consistent between MS-MLPA and bisulfite pyrosequencing in all patients. Twenty-six patients (65.0%) had IC2 loss of methylation (IC2-LoM), 11 (27.5%) had paternal uniparental disomy (patUPD), and one (2.5%) had IC1 gain of methylation. Macroglossia and external ear anomalies were more common in IC2-LoM than in patUPD, and lateralized overgrowth was more common in patUPD than in IC2-LoM (all P<0.05). Methylation levels at IC2 were inversely correlated with birth weight standard deviation score (r=–0.476, P=0.014) and clinical score (r=–0.520, P=0.006) in the IC2-LoM group. Conclusions Comprehensive molecular analysis of the 11p15.5 region revealed epigenotype–phenotype correlations in our BWS cohort. Bisulfite pyrosequencing can help clarify epigenotypes. Methylation levels were correlated with fetal growth and clinical severity in patients with BWS.
Collapse
Affiliation(s)
- Hwa Young Kim
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Young Ah Lee
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Ho Shin
- Department of Orthopaedic Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Gu-Hwan Kim
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Rare Disease Center, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| |
Collapse
|
2
|
Genetics of Obesity in Humans: A Clinical Review. Int J Mol Sci 2022; 23:ijms231911005. [PMID: 36232301 PMCID: PMC9569701 DOI: 10.3390/ijms231911005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/23/2022] Open
Abstract
Obesity is a complex multifactorial disorder with genetic and environmental factors. There is an increase in the worldwide prevalence of obesity in both developed and developing countries. The development of genome-wide association studies (GWAS) and next-generation sequencing (NGS) has increased the discovery of genetic associations and awareness of monogenic and polygenic causes of obesity. The genetics of obesity could be classified into syndromic and non-syndromic obesity. Prader–Willi, fragile X, Bardet–Biedl, Cohen, and Albright Hereditary Osteodystrophy (AHO) syndromes are examples of syndromic obesity, which are associated with developmental delay and early onset obesity. Non-syndromic obesity could be monogenic, polygenic, or chromosomal in origin. Monogenic obesity is caused by variants of single genes while polygenic obesity includes several genes with the involvement of members of gene families. New advances in genetic testing have led to the identification of obesity-related genes. Leptin (LEP), the leptin receptor (LEPR), proopiomelanocortin (POMC), prohormone convertase 1 (PCSK1), the melanocortin 4 receptor (MC4R), single-minded homolog 1 (SIM1), brain-derived neurotrophic factor (BDNF), and the neurotrophic tyrosine kinase receptor type 2 gene (NTRK2) have been reported as causative genes for obesity. NGS is now in use and emerging as a useful tool to search for candidate genes for obesity in clinical settings.
Collapse
|
3
|
The expression and clinical significance of the tRNA aspartic acid methyltransferase 1 protein in gastric cancer. Int J Clin Oncol 2021; 26:2229-2236. [PMID: 34689291 DOI: 10.1007/s10147-021-02019-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 07/27/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVES This study aimed to investigate the role of the tRNA aspartic acid methyltransferase 1 (TRDMT1) protein in the development and progression of gastric cancer (GC). METHODS The 90 GC tissues and 35 paracancerous tissues (gastric mucosa) were collected from patients (31 males and 59 females; average age 66), who were pathologically diagnosed as GC. The expression of TRDMT1 in three GC cell lines (MKN28, BGC823, and MGC803) and tissues from GC patients were detected by western blotting and immunological staining, respectively. The relationship between TRDMT1 expression and clinicopathological parameters in GC patients was explored. TRDMT1 was knocked down by RNAi lentivirus in GC cells. GC cell migration and invasion were analyzed using scratch and transwell assays. RESULTS TRDMT1 expression in the GC cell lines was higher than that in the normal gastric mucosal epithelial cell line (P < 0.05). Positive TRDMT1 protein expression in the GC tissue was higher than that in the adjacent tissue. The expression of TRDMT1 was positively associated with tumor size, histological grade, invasion depth, lymph node metastasis, and tumor node metastasis (TNM) stage (P < 0.05). High TRDMT1 expression predicted poor OS of GC patients. Tumor size, differentiation degree, invasion depth, lymph node metastasis, TNM stage, and TRDMT1 expression were independent predictors of the OS of GC patients. Knockdown of TRDMT1 inhibited the migration and invasion of MKN28 cells. CONCLUSION TRDMT1 was highly expressed in GC cell lines and tissues. TRDMT1 expression was independent predictor of the OS of GC patients. TRDMT1 knockdown reduced GC cell migration and invasion. All these results suggested that TRDMT1 has the potential to be used as a target for the diagnosis and treatment of GC.
Collapse
|
4
|
|
5
|
Abstract
PURPOSE OF REVIEW Mammals have two complete sets of chromosomes, one from each parent with equal autosomal gene expression. Less than one percentage of human genes are imprinted or show expression from only one parent without changing gene structure, usually by DNA methylation, but reversible in gametogenesis. Many imprinted genes affect fetal growth and development accounting for several human disorders reviewed in this report. RECENT FINDINGS Disorders include Prader-Willi and Angelman syndromes, the first examples of imprinting errors in humans, chromosome 15q11.2-q13.3 duplication, Silver-Russell syndrome, Beckwith-Weidemann syndrome, GNAS gene-related inactivation disorders (e.g. Albright hereditary osteodystrophy), uniparental chromosome 14 disomy, chromosome 6q24-related transient neonatal diabetes mellitus, parent of origin effects in 15q11.2 BP1-BP2 deletion (Burnside-Butler) syndrome and 15q11-q13 single gene imprinted disorders. SUMMARY Periconceptional and intrauterine life can be influenced by environmental factors and nutrition impacting DNA methylation. This process not only alters development of the fetus, but pregnancy complications may result from large fetal size. Epigenetic processes control imprinted gene functions and regulation with susceptibility to diseases as described. A better understanding of these processes will impact on care and treatment of affected individuals.
Collapse
Affiliation(s)
- Merlin G Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas, USA
| |
Collapse
|
6
|
Wang Y, Wu Z, Li Y, Zheng Z, Yan J, Tian S, Han L. Long Non-Coding RNA H19 Promotes Proliferation, Migration and Invasion and Inhibits Apoptosis of Breast Cancer Cells by Targeting miR-491-5p/ZNF703 Axis. Cancer Manag Res 2020; 12:9247-9258. [PMID: 33061615 PMCID: PMC7532042 DOI: 10.2147/cmar.s246009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/25/2020] [Indexed: 12/24/2022] Open
Abstract
Background Breast cancer is one of the most common cancers worldwide. Long non-coding RNAs and microRNAs act as important regulators in human cancers. This study aims to explore the molecular mechanism among H19, miR-491-5p and zinc finger 703 (ZNF703) in breast cancer. Materials and Methods Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to detect the expression of H19, miR-491-5p and ZNF703. Cell Counting Kit 8 (CCK-8) assay was performed to evaluate cell proliferation. Cell apoptosis was assessed by flow cytometry assay. The number of migrated and invaded cells was counted by transwell assay. Dual luciferase reporter assay was carried out to test luciferase activity. Protein level of ZNF703 was measured by Western blot assay. Results H19 was highly expressed in breast tissues and cells. H19 knockdown inhibited proliferation, induced apoptosis and blocked migration and invasion. Moreover, H19 bound to miR-491-5p and negatively regulated miR-491-5p expression. MiR-491-5p inhibition abrogated the activities of proliferation, apoptosis, migration and invasion affected by H19 knockdown. Furthermore, miR-491-5p directly targeted ZNF703 and inversely modulated ZNF703 expression. ZNF703 up-regulation rescued the effects of miR-491-5p overexpression on proliferation, apoptosis, migration and invasion. In addition, H19 knockdown reduced ZNF703 expression by targeting miR-491-5p/ZNF703 axis. Conclusion H19 promoted proliferation, migration and invasion and retarded apoptosis of breast cancer cells via sponging miR-491-5p to down-regulate ZNF703 expression.
Collapse
Affiliation(s)
- Yongkun Wang
- Department of Thyroid Surgery, Liaocheng People's Hospital (Clinical Hospital of Shandong First Medical University) Liaocheng, Shandong, People's Republic of China
| | - Zhen Wu
- Department of Thyroid Surgery, Liaocheng People's Hospital (Clinical Hospital of Shandong First Medical University) Liaocheng, Shandong, People's Republic of China
| | - Yingxue Li
- Department of Pathology, Liaocheng People's Hospital (Clinical Hospital of Shandong First Medical University) Liaocheng, Shandong, People's Republic of China
| | - Zheng Zheng
- Department of Pathology, Liaocheng People's Hospital (Clinical Hospital of Shandong First Medical University) Liaocheng, Shandong, People's Republic of China
| | - Jinqiang Yan
- Department of Pathology, Liaocheng People's Hospital (Clinical Hospital of Shandong First Medical University) Liaocheng, Shandong, People's Republic of China
| | - Shuyan Tian
- Department of Pathology, Liaocheng People's Hospital (Clinical Hospital of Shandong First Medical University) Liaocheng, Shandong, People's Republic of China
| | - Lin Han
- Department of Pathology, Liaocheng People's Hospital (Clinical Hospital of Shandong First Medical University) Liaocheng, Shandong, People's Republic of China
| |
Collapse
|
7
|
Lecerf C, Le Bourhis X, Adriaenssens E. The long non-coding RNA H19: an active player with multiple facets to sustain the hallmarks of cancer. Cell Mol Life Sci 2019; 76:4673-4687. [PMID: 31338555 PMCID: PMC11105575 DOI: 10.1007/s00018-019-03240-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/09/2019] [Accepted: 07/18/2019] [Indexed: 12/24/2022]
Abstract
Cancer cells exhibit hallmarks in terms of proliferation, resistance to cell death, angiogenesis, invasion, metastasis, and genomic instability. Despite the progress in cancer research and the comprehension of tumorigenesis mechanisms, cancer remains a major issue in public health. A better understanding of the molecular factors associated with the appearance or progression of cancer may allow the development of therapeutic alternatives. Increasing data highlight the role of long non-coding RNAs in many diseases, including cancer. The long non-coding RNA H19 was the first discovered riboregulator, and it has been shown to be involved at multiple steps of tumorigenesis. Indeed, this lncRNA exert its action at various molecular scales. Understanding the role of H19 in cancer progression may allow to set up therapeutic strategies to prevent tumor expansion and metastatic dissemination. In this review, we will summarize the overexpression of the long non-coding RNA H19 in several types of cancer and the multiple implications of the long non-coding RNA H19 in the different hallmarks that define human cancer.
Collapse
Affiliation(s)
- Clément Lecerf
- INSERM, U908, 59000, Lille, France
- Univ. Lille, U908 - CPAC - Cell plasticity and Cancer, 59000, Lille, France
| | - Xuefen Le Bourhis
- INSERM, U908, 59000, Lille, France
- Univ. Lille, U908 - CPAC - Cell plasticity and Cancer, 59000, Lille, France
| | - Eric Adriaenssens
- INSERM, U908, 59000, Lille, France.
- Univ. Lille, U908 - CPAC - Cell plasticity and Cancer, 59000, Lille, France.
| |
Collapse
|
8
|
Yamaguchi Y, Tayama C, Tomikawa J, Akaishi R, Kamura H, Matsuoka K, Wake N, Minakami H, Kato K, Yamada T, Nakabayashi K, Hata K. Placenta-specific epimutation at H19-DMR among common pregnancy complications: its frequency and effect on the expression patterns of H19 and IGF2. Clin Epigenetics 2019; 11:113. [PMID: 31370882 PMCID: PMC6676526 DOI: 10.1186/s13148-019-0712-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/22/2019] [Indexed: 12/17/2022] Open
Abstract
Background H19 and IGF2 genes are imprinted and involved in regulating fetal and placental growth. The H19 differentially methylated region (DMR) is paternally methylated and maternally unmethylated and regulates the imprinted expression of H19 and IGF2. Epimutation at the H19-DMR in humans results in congenital growth disorders, Beckwith-Wiedemann and Silver-Russell syndromes, when erroneously its maternal allele becomes methylated and its paternal allele becomes unmethylated, respectively. Although H19 and IGF2 have been assessed for their involvement in pregnancy complications including fetal growth restriction (FGR) and pregnancy-induced hypertension (PIH)/hypertensive disorder of pregnancy (HDP) intensively in the last decade, it is still not established whether epimutation at the H19-DMR in the placenta results in pathogenic conditions in pregnancy. We aimed to assess the frequency of H19-DMR epimutation and its effects on the allelic expression patterns of H19 and IGF2 genes among normal and abnormal pregnancy cases. Results We enrolled two independently collected sets of placenta samples from normal pregnancies as controls and common pregnancy complications, FGR and PIH (HDP). The first set consisted of 39 controls and 140 FGR and/or PIH cases, and the second set consisted of 29 controls and 62 cases. For these samples, we initially screened for DNA methylation changes at H19-DMR and IGF2-DMRs by combined bisulfite restriction analysis, and further analyzed cases with methylation changes for their allelic methylation and expression patterns. We identified one case each of FGR and PIH showing hypomethylation of H19-DMR and IGF2-DMRs only in the placenta, but not in cord blood, from the first case/control set. For the PIH case, we were able to determine the allelic expression pattern of H19 to be biallelically expressed and the H19/IGF2 expression ratio to be highly elevated compared to controls. We also identified a PIH case with hypomethylation at H19-DMR and IGF2-DMRs in the placenta from the second case/control set. Conclusions Placental epimutation at H19-DMR was observed among common pregnancy complication cases at the frequency of 1.5% (3 out of 202 cases examined), but not in 68 normal pregnancy cases examined. Alteration of H19/IGF2 expression patterns due to hypomethylation of H19-DMR may have been involved in the pathogenesis of pregnancy complications in these cases. Electronic supplementary material The online version of this article (10.1186/s13148-019-0712-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yuko Yamaguchi
- Department of Maternal-Fetal Biology, Research Institute, National Center for Child Health and Development, Tokyo, 157-8535, Japan.,Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, Research Institute, National Center for Child Health and Development, Tokyo, 157-8535, Japan
| | - Junko Tomikawa
- Department of Maternal-Fetal Biology, Research Institute, National Center for Child Health and Development, Tokyo, 157-8535, Japan
| | - Rina Akaishi
- Center of Maternal-Fetal, Neonatal and Reproductive Medicine, National Center for Child Health and Development, Tokyo, 157-8535, Japan
| | - Hiromi Kamura
- Department of Maternal-Fetal Biology, Research Institute, National Center for Child Health and Development, Tokyo, 157-8535, Japan
| | - Kentaro Matsuoka
- Department of Pathology, National Center for Child Health and Development, Tokyo, 157-8535, Japan.,Present Address: Department of Pathology, Dokkyo Medical University, Saitama Medical Center, Koshigaya, Japan
| | - Norio Wake
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hisanori Minakami
- Department of Obstetrics and Gynecology, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
| | - Kiyoko Kato
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Takahiro Yamada
- Clinical Genetics Unit, Kyoto University Hospital, Kyoto, 606-8507, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, Research Institute, National Center for Child Health and Development, Tokyo, 157-8535, Japan.
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, Research Institute, National Center for Child Health and Development, Tokyo, 157-8535, Japan.
| |
Collapse
|
9
|
Regulation of Human Breast Cancer by the Long Non-Coding RNA H19. Int J Mol Sci 2017; 18:ijms18112319. [PMID: 29099749 PMCID: PMC5713288 DOI: 10.3390/ijms18112319] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 02/01/2023] Open
Abstract
Breast cancer is one of the most common causes of cancer related deaths in women. Despite the progress in early detection and use of new therapeutic targets associated with development of novel therapeutic options, breast cancer remains a major problem in public health. Indeed, even if the survival rate has improved for breast cancer patients, the number of recurrences within five years and the five-year relative survival rate in patients with metastasis remain dramatic. Thus, the discovery of new molecular actors involved in breast progression is essential to improve the management of this disease. Numerous data indicate that long non-coding RNA are implicated in breast cancer development. The oncofetal lncRNA H19 was the first RNA identified as a riboregulator. Studying of this lncRNA revealed its implication in both normal development and diseases. In this review, we summarize the different mechanisms of action of H19 in human breast cancer.
Collapse
|
10
|
Elliott HR, Shihab HA, Lockett GA, Holloway JW, McRae AF, Smith GD, Ring SM, Gaunt TR, Relton CL. Role of DNA Methylation in Type 2 Diabetes Etiology: Using Genotype as a Causal Anchor. Diabetes 2017; 66:1713-1722. [PMID: 28246294 PMCID: PMC5860189 DOI: 10.2337/db16-0874] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 02/21/2017] [Indexed: 12/24/2022]
Abstract
Several studies have investigated the relationship between genetic variation and DNA methylation with respect to type 2 diabetes, but it is unknown if DNA methylation is a mediator in the disease pathway or if it is altered in response to disease state. This study uses genotypic information as a causal anchor to help decipher the likely role of DNA methylation measured in peripheral blood in the etiology of type 2 diabetes. Illumina HumanMethylation450 BeadChip data were generated on 1,018 young individuals from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. In stage 1, 118 unique associations between published type 2 diabetes single nucleotide polymorphisms (SNPs) and genome-wide methylation (methylation quantitative trait loci [mQTLs]) were identified. In stage 2, a further 226 mQTLs were identified between 202 additional independent non-type 2 diabetes SNPs and CpGs identified in stage 1. Where possible, associations were replicated in independent cohorts of similar age. We discovered that around half of known type 2 diabetes SNPs are associated with variation in DNA methylation and postulated that methylation could either be on a causal pathway to future disease or could be a noncausal biomarker. For one locus (KCNQ1), we were able to provide further evidence that methylation is likely to be on the causal pathway to disease in later life.
Collapse
Affiliation(s)
- Hannah R Elliott
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, U.K.
| | - Hashem A Shihab
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - Gabrielle A Lockett
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, U.K
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, U.K
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, U.K
| | - Allan F McRae
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, Translational Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, U.K
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, U.K
| |
Collapse
|
11
|
Elhamamsy AR. Role of DNA methylation in imprinting disorders: an updated review. J Assist Reprod Genet 2017; 34:549-562. [PMID: 28281142 PMCID: PMC5427654 DOI: 10.1007/s10815-017-0895-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/23/2017] [Indexed: 12/20/2022] Open
Abstract
Genomic imprinting is a complex epigenetic process that contributes substantially to embryogenesis, reproduction, and gametogenesis. Only small fraction of genes within the whole genome undergoes imprinting. Imprinted genes are expressed in a monoallelic parent-of-origin-specific manner, which means that only one of the two inherited alleles is expressed either from the paternal or maternal side. Imprinted genes are typically arranged in clusters controlled by differentially methylated regions or imprinting control regions. Any defect or relaxation in imprinting process can cause loss of imprinting in the key imprinted loci. Loss of imprinting in most cases has a harmful effect on fetal development and can result in neurological, developmental, and metabolic disorders. Since DNA methylation and histone modifications play a key role in the process of imprinting. This review focuses on the role of DNA methylation in imprinting process and describes DNA methylation aberrations in different imprinting disorders.
Collapse
Affiliation(s)
- Amr Rafat Elhamamsy
- Department of Clinical Pharmacy, School of Pharmacy, Tanta University, Tanta, 31512, Gharbia, Egypt.
| |
Collapse
|
12
|
Dimopoulos A, Sicko RJ, Kay DM, Rigler SL, Fan R, Romitti PA, Browne ML, Druschel CM, Caggana M, Brody LC, Mills JL. Copy number variants in a population-based investigation of Klippel-Trenaunay syndrome. Am J Med Genet A 2017; 173:352-359. [PMID: 27901321 PMCID: PMC6205266 DOI: 10.1002/ajmg.a.37868] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 06/16/2016] [Indexed: 01/19/2023]
Abstract
Klippel-Trenaunay syndrome (KTS) is a rare congenital vascular disorder that is thought to occur sporadically; however, reports of familial occurrence suggest a genetic component. We examined KTS cases to identify novel, potentially causal copy number variants (CNVs). We identified 17 KTS cases from all live-births occurring in New York (1998-2010). Extracted DNA was genotyped using Illumina microarrays and CNVs were called using PennCNV software. CNVs selected for follow-up had ≥10 single nucleotide polymorphisms (SNPs) and minimal overlap with in-house controls or controls from the Database of Genomic Variants. We identified 15 candidate CNVs in seven cases; among them a deletion in two cases within transcripts of HDAC9, a histone deacetylase essential for angiogenic sprouting of endothelial cells. One of them also had a duplication upstream of SALL3, a transcription factor essential for embryonic development that inhibits DNMT3A, a DNA methyltransferase responsible for embryonic de novo DNA methylation. Another case had a duplication spanning ING5, a histone acetylation regulator active during embryogenesis. We identified rare genetic variants related to chromatin modification which may have a key role in regulating vascular development during embryogenesis. Further investigation of their implications in the pathogenesis of KTS is warranted. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Aggeliki Dimopoulos
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Robert J. Sicko
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Denise M. Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Shannon L. Rigler
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Ruzong Fan
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Paul A. Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, Iowa
| | - Marilyn L. Browne
- Congenital Malformations Registry, New York State Department of Health, Albany, New York
- Department of Epidemiology and Biostatistics, University at Albany School of Public Health, Rensselaer, New York
| | - Charlotte M. Druschel
- Congenital Malformations Registry, New York State Department of Health, Albany, New York
- Department of Epidemiology and Biostatistics, University at Albany School of Public Health, Rensselaer, New York
| | - Michele Caggana
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Lawrence C. Brody
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - James L. Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
13
|
Manzardo AM, Butler MG. Examination of Global Methylation and Targeted Imprinted Genes in Prader-Willi Syndrome. ACTA ACUST UNITED AC 2017; 2. [PMID: 28111641 DOI: 10.21767/2472-1158.100026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
CONTEXT Methylation changes observed in Prader-Willi syndrome (PWS) may impact global methylation as well as regional methylation status of imprinted genes on chromosome 15 (in cis) or other imprinted obesity-related genes on other chromosomes (in trans) leading to differential effects on gene expression impacting obesity phenotype unique to (PWS). OBJECTIVE Characterize the global methylation profiles and methylation status for select imprinted genes associated with obesity phenotype in a well-characterized imprinted, obesity-related syndrome (PWS) relative to a cohort of obese and non-obese individuals. DESIGN Global methylation was assayed using two methodologies: 1) enriched LINE-1 repeat sequences by EpigenDx and 2) ELISA-based immunoassay method sensitive to genomic 5-methylcytosine by Epigentek. Target gene methylation patterns at selected candidate obesity gene loci were determined using methylation-specific PCR. SETTING Study participants were recruited as part of an ongoing research program on obesity-related genomics and Prader-Willi syndrome. PARTICIPANTS Individuals with non-syndromic obesity (N=26), leanness (N=26) and PWS (N=39). RESULTS A detailed characterization of the imprinting status of select target genes within the critical PWS 15q11-q13 genomic region showed enhanced cis but not trans methylation of imprinted genes. No significant differences in global methylation were found between non-syndromic obese, PWS or non-obese controls. INTERVENTION None. MAIN OUTCOME MEASURES Percentage methylation and the methylation index. CONCLUSION The methylation abnormality in PWS due to errors of genomic imprinting effects both upstream and downstream effectors in the 15q11-q13 region showing enhanced cis but not trans methylation of imprinted genes. Obesity in our subject cohorts did not appear to impact global methylation levels using the described methodology.
Collapse
Affiliation(s)
- A M Manzardo
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, 3901 Rainbow Blvd, MS 4015, Kansas City, Kansas, USA
| | - M G Butler
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, 3901 Rainbow Blvd, MS 4015, Kansas City, Kansas, USA; Department of Pediatrics, University of Kansas Medical Center, Kansas City, Kansas, USA
| |
Collapse
|
14
|
Benonisdottir S, Oddsson A, Helgason A, Kristjansson RP, Sveinbjornsson G, Oskarsdottir A, Thorleifsson G, Davidsson OB, Arnadottir GA, Sulem G, Jensson BO, Holm H, Alexandersson KF, Tryggvadottir L, Walters GB, Gudjonsson SA, Ward LD, Sigurdsson JK, Iordache PD, Frigge ML, Rafnar T, Kong A, Masson G, Helgason H, Thorsteinsdottir U, Gudbjartsson DF, Sulem P, Stefansson K. Epigenetic and genetic components of height regulation. Nat Commun 2016; 7:13490. [PMID: 27848971 PMCID: PMC5116096 DOI: 10.1038/ncomms13490] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/07/2016] [Indexed: 01/12/2023] Open
Abstract
Adult height is a highly heritable trait. Here we identified 31.6 million sequence variants by whole-genome sequencing of 8,453 Icelanders and tested them for association with adult height by imputing them into 88,835 Icelanders. Here we discovered 13 novel height associations by testing four different models including parent-of-origin (|β|=0.4-10.6 cm). The minor alleles of three parent-of-origin signals associate with less height only when inherited from the father and are located within imprinted regions (IGF2-H19 and DLK1-MEG3). We also examined the association of these sequence variants in a set of 12,645 Icelanders with birth length measurements. Two of the novel variants, (IGF2-H19 and TET1), show significant association with both adult height and birth length, indicating a role in early growth regulation. Among the parent-of-origin signals, we observed opposing parental effects raising questions about underlying mechanisms. These findings demonstrate that common variations affect human growth by parental imprinting.
Collapse
Affiliation(s)
| | | | - Agnar Helgason
- deCODE Genetics/Amgen, Inc., 101 Reykjavik, Iceland.,Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland
| | | | | | | | | | | | | | - Gerald Sulem
- deCODE Genetics/Amgen, Inc., 101 Reykjavik, Iceland
| | | | - Hilma Holm
- deCODE Genetics/Amgen, Inc., 101 Reykjavik, Iceland
| | | | - Laufey Tryggvadottir
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.,Icelandic Cancer Registry, 105 Reykjavik, Iceland
| | | | | | - Lucas D Ward
- deCODE Genetics/Amgen, Inc., 101 Reykjavik, Iceland
| | | | - Paul D Iordache
- deCODE Genetics/Amgen, Inc., 101 Reykjavik, Iceland.,Reykjavik University, 101 Reykjavik, Iceland
| | | | | | - Augustine Kong
- deCODE Genetics/Amgen, Inc., 101 Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, 107 Reykjavik, Iceland
| | - Gisli Masson
- deCODE Genetics/Amgen, Inc., 101 Reykjavik, Iceland
| | - Hannes Helgason
- deCODE Genetics/Amgen, Inc., 101 Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, 107 Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Inc., 101 Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., 101 Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, 107 Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., 101 Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| |
Collapse
|
15
|
Moosavi A, Ardekani AM. Role of Epigenetics in Biology and Human Diseases. IRANIAN BIOMEDICAL JOURNAL 2016; 20:246-58. [PMID: 27377127 PMCID: PMC5075137 DOI: 10.22045/ibj.2016.01] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/22/2016] [Accepted: 03/08/2016] [Indexed: 12/11/2022]
Abstract
For a long time, scientists have tried to describe disorders just by genetic or environmental factors. However, the role of epigenetics in human diseases has been considered from a half of century ago. In the last decade, this subject has attracted many interests, especially in complicated disorders such as behavior plasticity, memory, cancer, autoimmune disease, and addiction as well as neurodegenerative and psychological disorders. This review first explains the history and classification of epigenetic modifications, and then the role of epigenetic in biology and connection between the epigenetics and environment are explained. Furthermore, the role of epigenetics in human diseases is considered by focusing on some diseases with some complicated features, and at the end, we have given the future perspective of this field. The present review article provides concepts with some examples to reveal a broad view of different aspects of epigenetics in biology and human diseases.
Collapse
Affiliation(s)
- Azam Moosavi
- Department of Biochemistry, School of Medicine, Alborz University of Medical Sciences, Alborz, Iran
| | | |
Collapse
|
16
|
Tabano S, Bonaparte E, Miozzo M. Detection of Loss of Imprinting by Pyrosequencing®. Methods Mol Biol 2016; 1315:241-58. [PMID: 26103904 DOI: 10.1007/978-1-4939-2715-9_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Genomic imprinting is an epigenetically regulated process determining allele-specific expression in a parent-of-origin dependent manner. Altered expression of imprinted genes characterizes numerous congenital diseases including Beckwith-Wiedemann, Silver-Russell, Angelman, and Prader-Willi syndromes as well as acquired disorders such as cancer. The detection of imprinting alterations has important translational implications in clinics and the application of the Pyrosequencing(®) technology offers the possibility to identify accurately also subtle modifications in allele-specific expression and in DNA methylation levels.Here, we describe two methods to investigate genomic imprinting defects (loss of imprinting, LOI) using Pyrosequencing: (1) Allele-specific expression analysis based on single nucleotide polymorphism (SNP), and (2) quantification of DNA methylation.The protocol for the quantification of the allele-specific expression is carried out by analyzing an informative SNP located within the transcribed portion of an imprinted gene. The method includes the cDNA amplification of the region containing the SNP and the Pyrosequencing-based analysis for the quantitative allelic discrimination comparing the ratio of the two alleles.The second protocol allows the accurate quantification of the DNA methylation levels at the Imprinting Control Regions (ICRs). Imprinted genes are clustered in chromosomal regions and their expression is mainly regulated by DNA methylation at CpG sites located within the ICRs. After bisulfite modification of the genomic DNA, the region of interest is amplified by PCR and analyzed by Pyrosequencing. The methylation value at each CpG site is calculated by the CpG software, which determines the ratio of the incorporation of "C" and "T" and converts the value in methylation percentage.
Collapse
Affiliation(s)
- Silvia Tabano
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Via Festa Del Perdono 7, Milan, 20122, Italy
| | | | | |
Collapse
|
17
|
Butler MG. Single Gene and Syndromic Causes of Obesity: Illustrative Examples. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 140:1-45. [PMID: 27288824 DOI: 10.1016/bs.pmbts.2015.12.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Obesity is a significant health problem in westernized societies, particularly in the United States where it has reached epidemic proportions in both adults and children. The prevalence of childhood obesity has doubled in the past 30 years. The causation is complex with multiple sources, including an obesity promoting environment with plentiful highly dense food sources and overall decreased physical activity noted for much of the general population, but genetic factors clearly play a role. Advances in genetic technology using candidate gene approaches, genome-wide association studies, structural and expression microarrays, and next generation sequencing have led to the discovery of hundreds of genes recognized as contributing to obesity. Polygenic and monogenic causes of obesity are now recognized including dozens of examples of syndromic obesity with Prader-Willi syndrome, as a classical example and recognized as the most common known cause of life-threatening obesity. Genetic factors playing a role in the causation of obesity will be discussed along with the growing evidence of single genes and the continuum between monogenic and polygenic obesity. The clinical and genetic aspects of four classical but rare obesity-related syndromes (ie, Prader-Willi, Alström, fragile X, and Albright hereditary osteodystrophy) will be described and illustrated in this review of single gene and syndromic causes of obesity.
Collapse
Affiliation(s)
- Merlin G Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS, United States of America.
| |
Collapse
|
18
|
Soellner L, Monk D, Rezwan FI, Begemann M, Mackay D, Eggermann T. Congenital imprinting disorders: Application of multilocus and high throughput methods to decipher new pathomechanisms and improve their management. Mol Cell Probes 2015; 29:282-90. [DOI: 10.1016/j.mcp.2015.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/02/2015] [Accepted: 05/05/2015] [Indexed: 12/17/2022]
|
19
|
Hoffmann A, Daniel G, Schmidt-Edelkraut U, Spengler D. Roles of imprinted genes in neural stem cells. Epigenomics 2015; 6:515-32. [PMID: 25431944 DOI: 10.2217/epi.14.42] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Imprinted genes and neural stem cells (NSC) play an important role in the developing and mature brain. A central theme of imprinted gene function in NSCs is cell survival and G1 arrest to control cell division, cell-cycle exit, migration and differentiation. Moreover, genomic imprinting can be epigenetically switched off at some genes to ensure stem cell quiescence and differentiation. At the genome scale, imprinted genes are organized in dynamic networks formed by interchromosomal interactions and transcriptional coregulation of imprinted and nonimprinted genes. Such multilayered networks may synchronize NSC activity with the demand from the niche resembling their roles in adjusting fetal size.
Collapse
Affiliation(s)
- Anke Hoffmann
- Max Planck Institute of Psychiatry, Translational Research, Kraepelinstrasse 2-10, 80804 Munich, Germany
| | | | | | | |
Collapse
|
20
|
Chromatin methylation and cardiovascular aging. J Mol Cell Cardiol 2015; 83:21-31. [DOI: 10.1016/j.yjmcc.2015.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 02/12/2015] [Indexed: 12/26/2022]
|
21
|
Eggermann T, Netchine I, Temple IK, Tümer Z, Monk D, Mackay D, Grønskov K, Riccio A, Linglart A, Maher ER. Congenital imprinting disorders: EUCID.net - a network to decipher their aetiology and to improve the diagnostic and clinical care. Clin Epigenetics 2015; 7:23. [PMID: 25784961 PMCID: PMC4362648 DOI: 10.1186/s13148-015-0050-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/26/2015] [Indexed: 12/21/2022] Open
Abstract
Imprinting disorders (IDs) are a group of eight rare but probably underdiagnosed congenital diseases affecting growth, development and metabolism. They are caused by similar molecular changes affecting regulation, dosage or the genomic sequence of imprinted genes. Each ID is characterised by specific clinical features, and, as each appeared to be associated with specific imprinting defects, they have been widely regarded as separate entities. However, they share clinical characteristics and can show overlapping molecular alterations. Nevertheless, IDs are usually studied separately despite their common underlying (epi)genetic aetiologies, and their basic pathogenesis and long-term clinical consequences remain largely unknown. Efforts to elucidate the aetiology of IDs are currently fragmented across Europe, and standardisation of diagnostic and clinical management is lacking. The new consortium EUCID.net (European network of congenital imprinting disorders) now aims to promote better clinical care and scientific investigation of imprinting disorders by establishing a concerted multidisciplinary alliance of clinicians, researchers, patients and families. By encompassing all IDs and establishing a wide ranging and collaborative network, EUCID.net brings together a wide variety of expertise and interests to engender new collaborations and initiatives.
Collapse
Affiliation(s)
- Thomas Eggermann
- Department of Human Genetics, RWTH Aachen, Aachen, 52074 Germany ; Department of Human Genetics, University Hospital, RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Irène Netchine
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris, F-75012 France ; UMR_S 938, CDR Saint-Antoine, UPMC Univ Paris 06, Sorbonne Universites, Paris, F-75012 France ; Pediatric Endocrinology, 3APHP, Armand Trousseau Hospital, Paris, 75012 France
| | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine University of Southampton, Wessex Clinical Genetics Service, Princess Anne Hospital, Coxford Road, Southampton, SO16 5YA UK
| | - Zeynep Tümer
- Clinical Genetic Clinic, Kennedy Center, Rigshospitalet, Copenhagen University Hospital, Glostrup, 2600 Denmark
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Hospital Duran i Reynals, 08907 Barcelona, Spain
| | - Deborah Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine University of Southampton, Wessex Clinical Genetics Service, Princess Anne Hospital, Coxford Road, Southampton, SO16 5YA UK
| | - Karin Grønskov
- Clinical Genetic Clinic, Kennedy Center, Rigshospitalet, Copenhagen University Hospital, Glostrup, 2600 Denmark
| | - Andrea Riccio
- DiSTABiF, Seconda Università degli Studi di Napoli, 81100 Caserta, Italy ; Institute of Genetics and Biophysics-ABT, CNR, Napoli, Italy
| | - Agnès Linglart
- Endocrinology and Diabetology for Children and Reference Center for Rare Disorders of Calcium and Phosphorus Metabolism, Bicêtre Paris Sud, APHP, Le Kremlin-Bicêtre, 94276 Paris France ; INSERM U986, INSERM, Le Kremlin-Bicêtre, 94276 Paris, France
| | - Eamonn R Maher
- Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, CB2 OXY UK
| |
Collapse
|
22
|
Eggermann T, Soellner L, Buiting K, Kotzot D. Mosaicism and uniparental disomy in prenatal diagnosis. Trends Mol Med 2015; 21:77-87. [DOI: 10.1016/j.molmed.2014.11.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/18/2014] [Accepted: 11/26/2014] [Indexed: 01/21/2023]
|
23
|
Meningocele in a congolese female with beckwith-wiedemann phenotype. Case Rep Genet 2015; 2014:989425. [PMID: 25610673 PMCID: PMC4290800 DOI: 10.1155/2014/989425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 12/03/2014] [Indexed: 11/17/2022] Open
Abstract
Beckwith-Wiedemann syndrome (BWS) is a rare congenital syndrome characterized by an overgrowth, macroglossia, exomphalos, and predisposition to embryonal tumors. Central nervous abnormalities associated with BWS are rare. We describe a one-day-old Congolese female who presented meningocele associated with BWS phenotype.
Collapse
|
24
|
Miller JL, Grant PA. The role of DNA methylation and histone modifications in transcriptional regulation in humans. Subcell Biochem 2014; 61:289-317. [PMID: 23150256 DOI: 10.1007/978-94-007-4525-4_13] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although the field of genetics has grown by leaps and bounds within the last decade due to the completion and availability of the human genome sequence, transcriptional regulation still cannot be explained solely by an individual's DNA sequence. Complex coordination and communication between a plethora of well-conserved chromatin modifying factors are essential for all organisms. Regulation of gene expression depends on histone post translational modifications (HPTMs), DNA methylation, histone variants, remodeling enzymes, and effector proteins that influence the structure and function of chromatin, which affects a broad spectrum of cellular processes such as DNA repair, DNA replication, growth, and proliferation. If mutated or deleted, many of these factors can result in human disease at the level of transcriptional regulation. The common goal of recent studies is to understand disease states at the stage of altered gene expression. Utilizing information gained from new high-throughput techniques and analyses will aid biomedical research in the development of treatments that work at one of the most basic levels of gene expression, chromatin. This chapter will discuss the effects of and mechanism by which histone modifications and DNA methylation affect transcriptional regulation.
Collapse
Affiliation(s)
- Jaime L Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | | |
Collapse
|
25
|
DNA methylation pattern as important epigenetic criterion in cancer. GENETICS RESEARCH INTERNATIONAL 2013; 2013:317569. [PMID: 24455281 PMCID: PMC3884803 DOI: 10.1155/2013/317569] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/13/2013] [Accepted: 11/02/2013] [Indexed: 11/17/2022]
Abstract
Epigenetic modifications can affect the long-term gene expression without any change in nucleotide sequence of the DNA. Epigenetic processes intervene in the cell differentiation, chromatin structure, and activity of genes since the embryonic period. However, disorders in genes' epigenetic pattern can affect the mechanisms such as cell division, apoptosis, and response to the environmental stimuli which may lead to the incidence of different diseases and cancers. Since epigenetic changes may return to their natural state, they could be used as important targets in the treatment of cancer and similar malignancies. The aim of this review is to assess the epigenetic changes in normal and cancerous cells, the causative factors, and epigenetic therapies and treatments.
Collapse
|
26
|
Baskin B, Choufani S, Chen YA, Shuman C, Parkinson N, Lemyre E, Micheil Innes A, Stavropoulos DJ, Ray PN, Weksberg R. High frequency of copy number variations (CNVs) in the chromosome 11p15 region in patients with Beckwith-Wiedemann syndrome. Hum Genet 2013; 133:321-30. [PMID: 24154661 DOI: 10.1007/s00439-013-1379-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/05/2013] [Indexed: 01/20/2023]
Abstract
Beckwith-Wiedemann syndrome (BWS), an overgrowth and tumor predisposition syndrome is clinically heterogeneous. Its variable presentation makes molecular diagnosis particularly important for appropriate counseling of patients with respect to embyronal tumor risk and recurrence risk. BWS is characterized by macrosomia, omphalocele, and macroglossia. Additional clinical features can include hemihyperplasia, embryonal tumors, umbilical hernia, and ear anomalies. BWS is etiologically heterogeneous arising from dysregulation of one or both of the chromosome 11p15.5 imprinting centers (IC) and/or imprinted growth regulatory genes on chromosome 11p15.5. Most BWS cases are sporadic and result from loss of maternal methylation at imprinting center 2 (IC2), gain of maternal methylation at imprinting center 1 (IC1) or paternal uniparental disomy (UPD). Heritable forms of BWS (15 %) have been attributed mainly to mutations in the growth suppressor gene CDKN1C, but have also infrequently been identified in patients with copy number variations (CNVs) in the chromosome 11p15.5 region. Four hundred and thirty-four unrelated BWS patients referred to the molecular diagnostic laboratory were tested by methylation-specific multiplex ligation-dependent probe amplification. Molecular alterations were detected in 167 patients, where 103 (62 %) showed loss of methylation at IC2, 23 (14 %) had gain of methylation at IC1, and 41 (25 %) showed changes at both ICs usually associated with paternal UPD. In each of the three groups, we identified patients in whom the abnormalities in the chromosome 11p15.5 region were due to CNVs. Surprisingly, 14 patients (9 %) demonstrated either deletions or duplications of the BWS critical region that were confirmed using comparative genomic hybridization array analysis. The majority of these CNVs were associated with a methylation change at IC1. Our results suggest that CNVs in the 11p15.5 region contribute significantly to the etiology of BWS. We highlight the importance of performing deletion/duplication testing in addition to methylation analysis in the molecular investigation of BWS to improve our understanding of the molecular basis of this disorder, and to provide accurate genetic counseling.
Collapse
Affiliation(s)
- Berivan Baskin
- The Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Eggermann T, Elbracht M, Schröder C, Reutter H, Soellner L, Spengler S, Begemann M. Congenital imprinting disorders: a novel mechanism linking seemingly unrelated disorders. J Pediatr 2013; 163:1202-7. [PMID: 23809048 DOI: 10.1016/j.jpeds.2013.05.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/15/2013] [Accepted: 05/13/2013] [Indexed: 01/03/2023]
Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, RWTH Technical University, Aachen, Germany.
| | | | | | | | | | | | | |
Collapse
|
28
|
Abstract
The heritability of specific phenotypical traits relevant for physical performance has been extensively investigated and discussed by experts from various research fields. By deciphering the complete human DNA sequence, the human genome project has provided impressive insights into the genomic landscape. The hope that this information would reveal the origin of phenotypical traits relevant for physical performance or disease risks has proven overly optimistic, and it is still premature to refer to a 'post-genomic' era of biological science. Linking genomic regions with functions, phenotypical traits and variation in disease risk is now a major experimental bottleneck. The recent deluge of genome-wide association studies (GWAS) generates extensive lists of sequence variants and genes potentially linked to phenotypical traits, but functional insight is at best sparse. The focus of this review is on the complex mechanisms that modulate gene expression. A large fraction of these mechanisms is integrated into the field of epigenetics, mainly DNA methylation and histone modifications, which lead to persistent effects on the availability of DNA for transcription. With the exceptions of genomic imprinting and very rare cases of epigenetic inheritance, epigenetic modifications are not inherited transgenerationally. Along with their susceptibility to external influences, epigenetic patterns are highly specific to the individual and may represent pivotal control centers predisposing towards higher or lower physical performance capacities. In that context, we specifically review how epigenetics combined with classical genetics could broaden our knowledge of genotype-phenotype interactions. We discuss some of the shortcomings of GWAS and explain how epigenetic influences can mask the outcome of quantitative genetic studies. We consider epigenetic influences, such as genomic imprinting and epigenetic inheritance, as well as the life-long variability of epigenetic modification patterns and their potential impact on phenotype with special emphasis on traits related to physical performance. We suggest that epigenetic effects may also play a considerable role in the determination of athletic potential and these effects will need to be studied using more sophisticated quantitative genetic models. In the future, epigenetic status and its potential influence on athletic performance will have to be considered, explored and validated using well controlled model systems before we can begin to extrapolate new findings to complex and heterogeneous human populations. A combination of the fields of genomics, epigenomics and transcriptomics along with improved bioinformatics tools and precise phenotyping, as well as a precise classification of the test populations is required for future research to better understand the inter-relations of exercise physiology, performance traits and also susceptibility towards diseases. Only this combined input can provide the overall outlook necessary to decode the molecular foundation of physical performance.
Collapse
Affiliation(s)
- Tobias Ehlert
- Johannes Gutenberg-Universität Mainz, Department of Sports Medicine, Disease Prevention and Rehabilitation, Mainz, Germany
| | | | | |
Collapse
|
29
|
Ito Y, Nativio R, Murrell A. Induced DNA demethylation can reshape chromatin topology at the IGF2-H19 locus. Nucleic Acids Res 2013; 41:5290-302. [PMID: 23585276 PMCID: PMC3664821 DOI: 10.1093/nar/gkt240] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 03/14/2013] [Accepted: 03/16/2013] [Indexed: 11/15/2022] Open
Abstract
Choriocarcinomas are embryonal tumours with loss of imprinting and hypermethylation at the insulin-like growth factor 2 (IGF2)-H19 locus. The DNA methyltransferase inhibitor, 5-Aza-2'deoxycytidine (5-AzaCdR) is an approved epigenetic cancer therapy. However, it is not known to what extent 5-AzaCdR influences other epigenetic marks. In this study, we set out to determine whether 5-AzaCdR treatment can reprogram the epigenomic organization of the IGF2-H19 locus in a choriocarcinoma cancer cell line (JEG3). We found that localized DNA demethylation at the H19 imprinting control region (ICR) induced by 5-AzaCdR, reduced IGF2, increased H19 expression, increased CTCF and cohesin recruitment and changed histone modifications. Furthermore chromatin accessibility was increased locus-wide and chromatin looping topography was altered such that a CTCF site downstream of the H19 enhancers switched its association with the CTCF site upstream of the IGF2 promoters to associate with the ICR. We identified a stable chromatin looping domain, which forms independently of DNA methylation. This domain contains the IGF2 gene and is marked by a histone H3 lysine 27 trimethylation block between CTCF site upstream of the IGF2 promoters and the Centrally Conserved Domain upstream of the ICR. Together, these data provide new insights into the responsiveness of chromatin topography to DNA methylation changes.
Collapse
Affiliation(s)
- Yoko Ito
- Department of Oncology, University of Cambridge, CRUK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK and Cell and Developmental Biology, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA 19104-6058, USA
| | - Raffaella Nativio
- Department of Oncology, University of Cambridge, CRUK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK and Cell and Developmental Biology, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA 19104-6058, USA
| | - Adele Murrell
- Department of Oncology, University of Cambridge, CRUK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK and Cell and Developmental Biology, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA 19104-6058, USA
| |
Collapse
|
30
|
Uddin M, Galea S, Chang SC, Koenen KC, Goldmann E, Wildman DE, Aiello AE. Epigenetic signatures may explain the relationship between socioeconomic position and risk of mental illness: preliminary findings from an urban community-based sample. BIODEMOGRAPHY AND SOCIAL BIOLOGY 2013; 59:68-84. [PMID: 23701537 PMCID: PMC3754421 DOI: 10.1080/19485565.2013.774627] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Low socioeconomic position (SEP) has previously been linked to a number of negative health indicators, including poor mental health. The biologic mechanisms linking SEP and mental health remain poorly understood. Recent work suggests that social exposures influence DNA methylation in a manner salient to mental health. We conducted a pilot investigation to assess whether SEP, measured as educational attainment, modifies the association between genomic methylation profiles and traumatic stress in a trauma-exposed sample. Results show that methylation × SEP interactions occur preferentially in genes pertaining to nervous system function, suggesting a plausible biological pathway by which SEP may enhance sensitivity to stress and, in turn, risk of posttraumatic stress disorder.[Supplementary materials are available for this article. Go to the publisher's online edition of Biodemography and Social Biology for the following free supplemental resource: Supplementary tables of full model and functional annotation clustering results.].
Collapse
Affiliation(s)
- Monica Uddin
- Department of Psychiatry and Behavioral Neurosciences , Wayne State University School of Medicine, Detroit, MI, USA.
| | | | | | | | | | | | | |
Collapse
|
31
|
Eggermann T, Spengler S, Gogiel M, Begemann M, Elbracht M. Epigenetic and genetic diagnosis of Silver-Russell syndrome. Expert Rev Mol Diagn 2012; 12:459-71. [PMID: 22702363 DOI: 10.1586/erm.12.43] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Silver-Russell syndrome (SRS) is a congenital imprinting disorder characterized by intrauterine and postnatal growth restriction and further characteristic features. SRS is genetically heterogenous: 7-10% of patients carry a maternal uniparental disomy of chromosome 7; >38% show a hypomethylation in imprinting control region 1 in 11p15; and a further class of mutations are copy number variations affecting different chromosomes, but mainly 11p15 and 7. The diagnostic work-up should thus aim to detect these three molecular subtypes. Numerous techniques are currently applied in genetic SRS testing, but none of them covers all known (epi)mutations, and they should therefore be used synergistically. However, future next-generation sequencing approaches will allow a comprehensive analysis of all types of alterations in SRS.
Collapse
Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, University Hospital Aachen, Pauwelsstr. 30, D-52074 Aachen, Germany.
| | | | | | | | | |
Collapse
|
32
|
Altered expressions and DNA methylation of imprinted genes in chromosome 7 in brain of mouse offspring conceived from in vitro maturation. Reprod Toxicol 2012; 34:420-8. [DOI: 10.1016/j.reprotox.2012.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 04/03/2012] [Accepted: 04/27/2012] [Indexed: 11/18/2022]
|
33
|
Xuan C, Wang BB, Gao G, Bai XY, Yang Q, Liu XC, Jing WB, Ma X, He GW. A novel variation of PLAGL1 in Chinese patients with isolated ventricular septal defect. Genet Test Mol Biomarkers 2012; 16:984-7. [PMID: 22784302 DOI: 10.1089/gtmb.2012.0003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
AIMS Ventricular septal defect (VSD) is the most common congenital heart disease (CHD). A number of genetic studies have linked the gene of PLAGL1 to the etiology of CHD. The present study aimed to identify potential pathogenic mutations for PLAGL1 and to provide insights into the etiology of isolated VSD. METHODS Case-control mutational analysis was performed in 300 patients with isolated VSD and 300 healthy controls. Two protein-coding extons of PLAGL1 and their partial flanking intron sequences were amplified by polymerase chain reaction and sequenced on an ABI3730 Automated Sequencer. CLC workbench software was used to compare the conservatism of PLAGL1 protein with other multiple species. RESULTS Neither missense nor frame-shift mutations were detected in two protein-coding extons of PLAGL1. But a novel synonymous variation (c.486A>G, p. E162E) was detected in protein-coding exon-2. The glutamic that translated with the mutational codon is conservative when compared with other species. CONCLUSIONS We detected a synonymous variation in the protein-coding exon-2 of PLAGL1 in isolated VSD patients. It is possible that the etiology of isolated VSD might not be directly linked with this mutation, but might be associated with other patterns of gene expression regulation in PLAGL1, such as in the methylation-dependent manner.
Collapse
Affiliation(s)
- Chao Xuan
- TEDA International Cardiovascular Hospital, Medical College, Nankai University, Tianjin, PR China
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Yang XX, He XQ, Li FX, Wu YS, Gao Y, Li M. Risk-association of DNA methyltransferases polymorphisms with gastric cancer in the Southern Chinese population. Int J Mol Sci 2012; 13:8364-8378. [PMID: 22942708 PMCID: PMC3430239 DOI: 10.3390/ijms13078364] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 06/20/2012] [Accepted: 06/27/2012] [Indexed: 01/10/2023] Open
Abstract
DNA hypomethylation and/or hypermethylation are presumed to be early events in carcinogenesis, and one or more DNA methyltransferases (DNMTs) have been suggested to play roles in carcinogenesis of gastric cancer (GC). However, there have been no systematic studies regarding the association between DNMT gene polymorphisms and GC risk. Here, we examined the associations of 16 single nucleotide polymorphisms (SNPs) from DNMT1 (rs2114724, rs2228611, rs2228612, rs8101866, rs16999593), DNMT2 (rs11695471, rs11254413), DNMT3A (rs1550117, rs11887120, rs13420827, rs13428812, rs6733301), DNMT3B (rs2424908, rs2424913, rs6087990) and DNMT3L (rs113593938) with GC in the Southern Chinese population. We assessed the associations of these 16 SNPs with GC in a case-control study that consisted of 242 GC cases and 294 controls, using the Sequenom MALDI-TOF-MS platform. Association analyses based on the χ2 test and binary logistic regression were performed to determine the odds ratio (OR) and 95% confidence interval (95%CI) for each SNP. We found that rs16999593 in DNMT1, rs11254413 in DNMT2 and rs13420827 in DNMT3A were significantly associated with GC susceptibility (OR 1.45, 0.15, 0.66, respectively; 95% CI 1.00–2.11, p = 0.047; 0.08–0.27, p < 0.01; 0.45–0.97, p = 0.034, respectively, overdominant model). These results suggested that DNMT1, DNMT2 and DNMT3A may play important roles in GC carcinogenesis. However, further studies are required to elucidate the mechanism.
Collapse
Affiliation(s)
- Xue-Xi Yang
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China; E-Mails: (X.-X.Y.); (F.-X.L.); (Y.-S.W.); (Y.G.)
| | - Xuan-Qiu He
- The First Clinical College, Southern Medical University, Guangzhou 510515, China; E-Mail:
| | - Fen-Xia Li
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China; E-Mails: (X.-X.Y.); (F.-X.L.); (Y.-S.W.); (Y.G.)
| | - Ying-Song Wu
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China; E-Mails: (X.-X.Y.); (F.-X.L.); (Y.-S.W.); (Y.G.)
| | - Yang Gao
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China; E-Mails: (X.-X.Y.); (F.-X.L.); (Y.-S.W.); (Y.G.)
| | - Ming Li
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China; E-Mails: (X.-X.Y.); (F.-X.L.); (Y.-S.W.); (Y.G.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-20-61648550; Fax: +86-20-61648554
| |
Collapse
|
35
|
Eggermann T, Leisten I, Binder G, Begemann M, Spengler S. Disturbed methylation at multiple imprinted loci: an increasing observation in imprinting disorders. Epigenomics 2012; 3:625-37. [PMID: 22126250 DOI: 10.2217/epi.11.84] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The widely accepted association between aberrant methylation at specific imprinted loci and distinct imprinting disorders has recently been brought into question by the identification of methylation defects at multiple loci (multilocus methylation defect [MLMD]). Strikingly, in different imprinting disorders, the same MLMD patterns can be observed. The cause for this ambiguous epigenotype-phenotype correlation is currently unknown. Future strategies to solve this enigma have to include all levels of imprinting regulation, ranging from DNA methylation to chromatin organization, as any disturbance of the balanced interaction between the different players in imprinting regulation might cause disturbed expression of imprinted factors. The molecular analysis of MLMD will help in discovering these interactions and contribute to the understanding of genomic imprinting and its disturbances.
Collapse
Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, D-52074 Aachen, Germany.
| | | | | | | | | |
Collapse
|
36
|
Specific changes in the expression of imprinted genes in prostate cancer--implications for cancer progression and epigenetic regulation. Asian J Androl 2012; 14:436-50. [PMID: 22367183 DOI: 10.1038/aja.2011.160] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Epigenetic dysregulation comprising DNA hypermethylation and hypomethylation, enhancer of zeste homologue 2 (EZH2) overexpression and altered patterns of histone modifications is associated with the progression of prostate cancer. DNA methylation, EZH2 and histone modifications also ensure the parental-specific monoallelic expression of at least 62 imprinted genes. Although it is therefore tempting to speculate that epigenetic dysregulation may extend to imprinted genes, expression changes in cancerous prostates are only well documented for insulin-like growth factor 2 (IGF2). A literature and database survey on imprinted genes in prostate cancer suggests that the expression of most imprinted genes remains unchanged despite global disturbances in epigenetic mechanisms. Instead, selective genetic and epigenetic changes appear to lead to the inactivation of a sub-network of imprinted genes, which might function in the prostate to limit cell growth induced via the PI3K/Akt pathway, modulate androgen responses and regulate differentiation. Whereas dysregulation of IGF2 may constitute an early change in prostate carcinogenesis, inactivation of this imprinted gene network is rather associated with cancer progression.
Collapse
|
37
|
Murphy SK, Adigun A, Huang Z, Overcash F, Wang F, Jirtle RL, Schildkraut JM, Murtha AP, Iversen ES, Hoyo C. Gender-specific methylation differences in relation to prenatal exposure to cigarette smoke. Gene 2011; 494:36-43. [PMID: 22202639 DOI: 10.1016/j.gene.2011.11.062] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/25/2011] [Accepted: 11/30/2011] [Indexed: 12/15/2022]
Abstract
Epigenetic alterations may mechanistically explain the developmental origins of adult disease, namely the hypothesis that many complex adult chronic diseases originate as a result of conditions encountered in utero. If true, epigenetically regulated imprinted genes, critical to normal growth and development, may partially mediate these outcomes. We determined the influence of in utero exposure to cigarette smoking on methylation at two differentially methylated regions (DMRs) regulating Insulin-like Growth Factor 2 (IGF2) and H19, and how this might relate to birth weight of infants born to 418 pregnant women. Smoking status was ascertained through self-report and medical records. Bisulfite pyrosequencing was used to measure methylation in umbilical cord blood DNAs. Least squares DNA methylation means at each DMR and birth weight were compared between infants of smokers and non-smokers, using generalized linear models. While there were no significant differences at the H19 DMR, infants born to smokers had higher methylation at the IGF2 DMR than those born to never smokers or those who quit during pregnancy (49.5%, SD=8.0 versus 46.6%, SD=5.6 and 45.8%, SD=6.3, respectively; p=0.0002). The smoking-related increase in methylation was most pronounced in male offspring (p for sex interaction=0.03), for whom approximately 20% of smoking-related low birth weight was mediated by DNA methylation at the IGF2 DMR. Our findings suggest that IGF2 DMR plasticity is an important mechanism by which in utero adjustments to environmental toxicants are conferred. Larger studies to replicate these findings are required.
Collapse
Affiliation(s)
- Susan K Murphy
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Duke University Medical Center, Durham, NC 27708, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Toyokawa S, Uddin M, Koenen KC, Galea S. How does the social environment 'get into the mind'? Epigenetics at the intersection of social and psychiatric epidemiology. Soc Sci Med 2011; 74:67-74. [PMID: 22119520 DOI: 10.1016/j.socscimed.2011.09.036] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 05/09/2011] [Accepted: 09/16/2011] [Indexed: 12/13/2022]
Abstract
The social environment plays a considerable role in determining major psychiatric disorders. Emerging evidence suggests that features of the social environment modify gene expression independently of the primary DNA sequence through epigenetic processes. Accordingly, dysfunction of epigenetic mechanisms offers a plausible mechanism by which an adverse social environment gets "into the mind" and results in poor mental health. The purpose of this review is to provide an overview of the studies suggesting that epigenetic changes introduced by the social environment then manifest as psychological consequences. Our goal is to build a platform to discuss the ways in which future epidemiologic studies may benefit from including epigenetic measures. We focus on schizophrenia, major depressive disorder, post-traumatic stress disorder, anorexia nervosa, and substance dependence as examples that highlight the ways in which social environmental exposures, mediated through epigenetic processes, affect mental health.
Collapse
Affiliation(s)
- Satoshi Toyokawa
- Department of Epidemiology, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | | | | | | |
Collapse
|
39
|
Robert C, Nieminen J, Dufort I, Gagné D, Grant JR, Cagnone G, Plourde D, Nivet AL, Fournier É, Paquet É, Blazejczyk M, Rigault P, Juge N, Sirard MA. Combining resources to obtain a comprehensive survey of the bovine embryo transcriptome through deep sequencing and microarrays. Mol Reprod Dev 2011; 78:651-64. [PMID: 21812063 DOI: 10.1002/mrd.21364] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 07/08/2011] [Indexed: 11/09/2022]
Abstract
While most assisted reproductive technologies (ART) are considered routine for the reproduction of species of economical importance, such as the bovine, the impact of these manipulations on the developing embryo remains largely unknown. In an effort to obtain a comprehensive survey of the bovine embryo transcriptome and how it is modified by ART, resources were combined to design an embryo-specific microarray. Close to one million high-quality reads were produced from subtracted bovine embryo libraries using Roche 454 Titanium deep sequencing technology, which enabled the creation of an augmented bovine genome catalog. This catalog was enriched with bovine embryo transcripts, and included newly discovered indel type and 3'UTR variants. Using this augmented bovine genome catalog, the EmbryoGENE Bovine Microarray was designed and is composed of a total of 42,242 probes, including 21,139 known reference genes; 9,322 probes for novel transcribed regions (NTRs); 3,677 alternatively spliced exons; 3,353 3'-tiling probes; and 3,723 controls. A suite of bioinformatics tools was also developed to facilitate microrarray data analysis and database creation; it includes a quality control module, a Laboratory Information Management System (LIMS) and microarray analysis software. Results obtained during this study have already led to the identification of differentially expressed blastocyst targets, NTRs, splice variants of the indel type, and 3'UTR variants. We were able to confirm microarray results by real-time PCR, indicating that the EmbryoGENE bovine microarray has the power to detect physiologically relevant changes in gene expression.
Collapse
Affiliation(s)
- Claude Robert
- Laboratory of Functional Genomics of Early Embryonic Development, Université Laval, Québec, Canada.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Ruden DM, Lu X. Hsp90 affecting chromatin remodeling might explain transgenerational epigenetic inheritance in Drosophila. Curr Genomics 2011; 9:500-8. [PMID: 19506739 PMCID: PMC2691676 DOI: 10.2174/138920208786241207] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 08/08/2008] [Accepted: 08/14/2008] [Indexed: 01/01/2023] Open
Abstract
Transgenerational epigenetic inheritance, while poorly understood, is of great interest because it might help explain the increase in the incidence of diseases with an environmental contribution in humans, such as cancer, diabetes, and heart disease. Here, we review five Drosophila examples of transgenerational epigenetic inheritance and propose a unified mechanism that involves Polycomb Response Element/Trithorax Response Element (PRE/TRE) occupancy by either Polycomb Group (PcG) protein complexes or Trithorax group (TrxG) complexes. Among their other activities, PcG complexes cause histone 3 lysine 27 tri-methylation associated with repressed chromatin, whereas Trithorax group (TrxG) complexes induce histone 3 lysine 4 tri-methylation associated with actively transcribed chromatin. In this model, Hsp90 is an environmentally sensitive chromatin remodeling regulator that causes a switch in the chromatin from a permissive state to a non-permissive state for transcription. Consistent with this model, Hsp90 has recently been shown to be a chaperone for Tah1p (TPR-containing protein associated with Hsp90) and Pih1p (protein interacting with Hsp90), which connect to the chromatin remodelling factor Rvb1p (RuvB-like protein 1)/Rvb2p in yeast [1]. Also, Hsp90 is required for optimal activity of the histone H3 lysine-4 methyltransferase SMYD3 in mammals [2, 3]. Since PcG and TrxG complexes are involved in the post-translational modifications of histones, and since such modifications have been shown to be required to maintain imprinted marks, this unified mechanism might also help to explain transgenerational epigenetic inheritance in humans.
Collapse
Affiliation(s)
- Douglas M Ruden
- Wayne State University, Institute for Environmental Health Sciences, 2727 2 Ave, Room 4000, Detroit, MI 48201, USA
| | | |
Collapse
|
41
|
Imumorin IG, Kim EH, Lee YM, De Koning DJ, van Arendonk JA, De Donato M, Taylor JF, Kim JJ. Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits. Front Genet 2011; 2:44. [PMID: 22303340 PMCID: PMC3268597 DOI: 10.3389/fgene.2011.00044] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/25/2011] [Indexed: 11/13/2022] Open
Abstract
Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE–QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0–9 cM; genomic region of 5.0–10.8 Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4 ∼ 5.1% of each trait’s phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits.
Collapse
|
42
|
Sandbacka M, Bruce S, Halttunen M, Puhakka M, Lahermo P, Hannula-Jouppi K, Lipsanen-Nyman M, Kere J, Aittomäki K, Laivuori H. Methylation of H19 and its imprinted control region (H19 ICR1) in Müllerian aplasia. Fertil Steril 2011; 95:2703-6. [PMID: 21458801 DOI: 10.1016/j.fertnstert.2011.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 03/04/2011] [Accepted: 03/08/2011] [Indexed: 12/16/2022]
Abstract
Severe hypomethylation of the H19 imprinted control region (ICR1) in two patients with Silver-Russell syndrome (SRS) who have genital malformations has encouraged us to study DNA methylation in a cohort of 83 patients with Müllerian aplasia (MA). Site-specific methylation analyses of H19 ICR1 by quantitative real-time polymerase chain reaction in 80 clinically well-diagnosed Finnish MA patients showed no association between hypomethylation and the MA phenotype, but studies of the H19 locus in 38 patients showed aberrant methylation in 3/16 studied sites.
Collapse
Affiliation(s)
- Maria Sandbacka
- Folkhälsan Institute of Genetics, Biomedicum Helsinki, P.O. Box 63, FIN-00014 University of Helsinki, Helsinki, Finland.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Hori N, Nagai M, Hirayama M, Hirai T, Matsuda K, Hayashi M, Tanaka T, Ozawa T, Horike SI. Aberrant CpG methylation of the imprinting control region KvDMR1 detected in assisted reproductive technology-produced calves and pathogenesis of large offspring syndrome. Anim Reprod Sci 2010; 122:303-12. [PMID: 21035970 DOI: 10.1016/j.anireprosci.2010.09.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 09/18/2010] [Accepted: 09/24/2010] [Indexed: 12/30/2022]
Abstract
Although somatic cell nuclear transfer (NT) and in vitro fertilization (IVF) have the potential to produce genetically superior livestock, considerable numbers of abnormally large animals, including sheep and cattle affected by "large offspring syndrome" (LOS), have been produced by these assisted reproductive technologies (ART). Interestingly, these phenotypes are reminiscent of Beckwith-Wiedemann syndrome (BWS) in humans, which is an imprinting disorder characterized by pre- and/or postnatal overgrowth. The imprinting control region KvDMR1, which regulates the coordinated expression of growth control genes such as Cdkn1c, is known to be aberrantly hypomethylated in BWS. Therefore, we hypothesized that aberrant imprinting in this region could contribute to LOS. In this study, we analyzed the DNA methylation status of the Kcnq1ot1/Cdkn1c and Igf2/H19 domains on bovine chromosome 29 and examined the coordinated expression of imprinted genes surrounding them in seven calves derived by NT (which showed signs of developmental abnormality), two calves conceived by IVF (both developmentally abnormal), and three conventional calves that died of unrelated causes. Abnormal hypomethylation status at an imprinting control region of Kcnq1ot1/Cdkn1c domain was observed in two of seven NT-derived calves and one of two IVF-derived calves in almost all organs. Moreover, increased expression of Kcnq1ot1 and diminished expression of Cdkn1c were observed by RT-PCR analysis. This study is the first to describe the abnormal hypomethylation of the KvDMR1 domain and subsequent changes in the gene expression of Kcnq1ot1 and Cdkn1c in a subset of calves produced by ART. Our findings provide strong evidence for a role of altered imprinting control in the development of LOS in bovines.
Collapse
Affiliation(s)
- Noboru Hori
- Ishikawa Prefectural Livestock Research Center, Hodatsushimizu, Ishikawa 929-1325, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Pidsley R, Dempster EL, Mill J. Brain weight in males is correlated with DNA methylation at IGF2. Mol Psychiatry 2010; 15:880-1. [PMID: 20010889 DOI: 10.1038/mp.2009.138] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
45
|
Lennerz JK, Timmerman RJ, Grange DK, DeBaun MR, Feinberg AP, Zehnbauer BA. Addition of H19 'loss of methylation testing' for Beckwith-Wiedemann syndrome (BWS) increases the diagnostic yield. J Mol Diagn 2010; 12:576-88. [PMID: 20616360 DOI: 10.2353/jmoldx.2010.100005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Beckwith-Wiedemann syndrome (BWS) is a clinical diagnosis; however, molecular confirmation via abnormal methylation of DMR2(LIT1) and/or DMR1(H19) has clinical utility due to epigenotype-tumor association. Despite the strong link between H19 hypermethylation and tumor risk, several diagnostic laboratories only test for hypomethylation of LIT1. We assessed the added diagnostic value of combined LIT1 and H19 testing in a large series of referred samples from 1298 patients, including 53 well-characterized patients from the St. Louis Children's Hospital BWS-Registry (validation samples) and 1245 consecutive nationwide referrals (practice samples). Methylation-sensitive enzymatic digestion with Southern hybridization assessed loss of normal imprinting. In the validation group, abnormal LIT1 hypomethylation was detected in 60% (32/52) of patients but LIT1/H19-combined testing was abnormal in 68% (36/53); sensitivity in the practice setting demonstrated 27% (342/1245) abnormal LIT1 and 32% (404/1245) abnormal LIT1/H19-combined. In addition, H19 methylation was abnormal in 7% of LIT1-normal patients. We observed absence of uniparental disomy (UPD) in 27% of combined LIT1/H19-abnormal samples, diagnostic of multilocus methylation abnormalities; in contrast to studies implicating that combined LIT1/H19 abnormalities are diagnostic of UPD. The overall low detection rate, even in validated patient samples and despite characterization of both loci and UPD status, emphasizes the importance of clinical diagnosis in BWS.
Collapse
Affiliation(s)
- Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | | | | |
Collapse
|
46
|
Gregg C, Zhang J, Weissbourd B, Luo S, Schroth GP, Haig D, Dulac C. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 2010; 329:643-8. [PMID: 20616232 PMCID: PMC3005244 DOI: 10.1126/science.1190830] [Citation(s) in RCA: 448] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Genomic imprinting results in preferential expression of the paternal or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain. This approach uncovered parent-of-origin allelic effects of more than 1300 loci. We identified parental bias in the expression of individual genes and of specific transcript isoforms, with differences between brain regions. Many imprinted genes are expressed in neural systems associated with feeding and motivated behaviors, and parental biases preferentially target genetic pathways governing metabolism and cell adhesion. We observed a preferential maternal contribution to gene expression in the developing brain and a major paternal contribution in the adult brain. Thus, parental expression bias emerges as a major mode of epigenetic regulation in the brain.
Collapse
Affiliation(s)
- Christopher Gregg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | | | | | | | | | | | | |
Collapse
|
47
|
Abstract
The rapid increase in incidence of obesity over the past two decades cannot be explained solely by genetic and adult lifestyle factors. There is now considerable evidence that the fetal and early postnatal environments also strongly influence the risk of developing obesity in later life. Initially, human studies showed that low birth weight was associated with an increased risk of obesity but increasingly there is evidence that overnutrition in the early life can also increase susceptibility to future obesity. These findings have now been replicated in animal models, which have shown that both maternal under- and overnutrition can induce persistent changes in gene expression and metabolism. The mechanism by which the maternal nutritional environment induces such changes is beginning to be understood and involves the altered epigenetic regulation of specific genes. In this review, we discuss the recent evidence that shows that early-life environment can induce altered epigenetic regulation leading to the induction of an altered phenotype. The demonstration of a role for altered epigenetic regulation of genes in the developmental induction of obesity opens the possibility that interventions, either through nutrition or specific drugs, may modify long-term obesity risk and combat this rapid rise in obesity.
Collapse
|
48
|
Abstract
Psychiatric diseases place a tremendous burden on affected individuals, their caregivers, and the health care system. Although evidence exists for a strong inherited component to many of these conditions, dedicated efforts to identify DNA sequence-based causes have not been exceptionally productive, and very few pharmacologic treatment options are clinically available. Many features of psychiatric diseases are consistent with an epigenetic dysregulation, such as discordance of monozygotic twins, late age of onset, parent-of-origin and sex effects, and fluctuating disease course. In recent years, experimental technologies have significantly advanced, permitting indepth studies of the epigenome and its role in maintenance of normal genomic functions, as well as disease etiopathogenesis. Here, we present an epigenetic explanation for many characteristics of psychiatric disease, review the current literature on the epigenetic mechanisms involved in major psychosis, Alzheimer's disease, and autism spectrum disorders, and describe some future directions in the field of psychiatric epigenomics.
Collapse
Affiliation(s)
- Carolyn Ptak
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | | |
Collapse
|
49
|
H19 imprinting control region methylation requires an imprinted environment only in the male germ line. Mol Cell Biol 2009; 30:1108-15. [PMID: 20038532 DOI: 10.1128/mcb.00575-09] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 2.4-kb H19 imprinting control region (H19ICR) is required to establish parent-of-origin-specific epigenetic marks and expression patterns at the Igf2/H19 locus. H19ICR activity is regulated by DNA methylation. The ICR is methylated in sperm but not in oocytes, and this paternal chromosome-specific methylation is maintained throughout development. We recently showed that the H19ICR can work as an ICR even when inserted into the normally nonimprinted alpha fetoprotein locus. Paternal but not maternal copies of the ICR become methylated in somatic tissue. However, the ectopic ICR remains unmethylated in sperm. To extend these findings and investigate the mechanisms that lead to methylation of the H19ICR in the male germ line, we characterized novel mouse knock-in lines. Our data confirm that the 2.4-kb element is an autonomously acting ICR whose function is not dependent on germ line methylation. Ectopic ICRs become methylated in the male germ line, but the timing of methylation is influenced by the insertion site and by additional genetic information. Our results support the idea that DNA methylation is not the primary genomic imprint and that the H19ICR insertion is sufficient to transmit parent-of-origin-dependent DNA methylation patterns independent of its methylation status in sperm.
Collapse
|
50
|
Demars J, Shmela ME, Rossignol S, Okabe J, Netchine I, Azzi S, Cabrol S, Le Caignec C, David A, Le Bouc Y, El-Osta A, Gicquel C. Analysis of the IGF2/H19 imprinting control region uncovers new genetic defects, including mutations of OCT-binding sequences, in patients with 11p15 fetal growth disorders. Hum Mol Genet 2009; 19:803-14. [DOI: 10.1093/hmg/ddp549] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|