1
|
Davydova E, Perenkov A, Vedunova M. Building Minimized Epigenetic Clock by iPlex MassARRAY Platform. Genes (Basel) 2024; 15:425. [PMID: 38674360 PMCID: PMC11049545 DOI: 10.3390/genes15040425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Epigenetic clocks are valuable tools for estimating both chronological and biological age by assessing DNA methylation levels at specific CpG dinucleotides. While conventional epigenetic clocks rely on genome-wide methylation data, targeted approaches offer a more efficient alternative. In this study, we explored the feasibility of constructing a minimized epigenetic clock utilizing data acquired through the iPlex MassARRAY technology. The study enrolled a cohort of relatively healthy individuals, and their methylation levels of eight specific CpG dinucleotides in genes SLC12A5, LDB2, FIGN, ACSS3, FHL2, and EPHX3 were evaluated using the iPlex MassARRAY system and the Illumina EPIC array. The methylation level of five studied CpG sites demonstrated significant correlations with chronological age and an acceptable convergence of data obtained by the iPlex MassARRAY and Illumina EPIC array. At the same time, the methylation level of three CpG sites showed a weak relationship with age and exhibited a low concordance between the data obtained from the two technologies. The construction of the epigenetic clock involved the utilization of different machine-learning models, including linear models, deep neural networks (DNN), and gradient-boosted decision trees (GBDT). The results obtained from these models were compared with each other and with the outcomes generated by other well-established epigenetic clocks. In our study, the TabNet architecture (deep tabular data learning architecture) exhibited the best performance (best MAE = 5.99). Although our minimized epigenetic clock yielded slightly higher age prediction errors compared to other epigenetic clocks, it still represents a viable alternative to the genome-wide epigenotyping array.
Collapse
Affiliation(s)
- Ekaterina Davydova
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Ave., Nizhny Novgorod 603022, Russia (M.V.)
| | | | | |
Collapse
|
2
|
Wang Z, Song J, Li C, Li Y, Shen L, Dong B, Zou Z, Ma J. DNA methylation of the INSR gene as a mediator of the association between prenatal exposure to famine and adulthood waist circumference. Sci Rep 2020; 10:12212. [PMID: 32699300 DOI: 10.1038/s41598-020-69120-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022] Open
Abstract
The aims of this study were to explore whether DNA methylation at INSR and IGF2 mediated the association of prenatal exposure to the Chinese great famine with adulthood waist circumference (WC) and BMI. A total of 235 subjects were selected into the present study from severely affected province and a neighbor province with less severely affected famine in China through multi-stage clustered random sampling. DNA methylation at the INSR and IGF2 gene promoter regions was detected by the Sequenom's MassARRAY system. The "mediation" package of R was used to evaluate the mediation effect of DNA methylation on the association between prenatal exposure to the famine and adult WC and BMI. The results showed that prenatal famine exposure was significantly associated with higher overall methylation level of the INSR gene (d = 3.6%; 95% CI 1.2-6.0; P = 0.027) and larger adulthood WC (d = 2.72 cm; 95% CI 0.20-5.24; P = 0.034). Furthermore, famine significantly increased methylation levels at four CpG sites. Methylation of the CpG7 site mediated 32.0% (95% CI 5.0-100.0%, P = 0.029) of the association between prenatal exposure to the Chinese great famine and adulthood WC. In conclusion, Epigenetic changes to the INSR might mediate the adverse effect of prenatal famine exposure on WC in adulthood.
Collapse
Affiliation(s)
- Zhenghe Wang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jieyun Song
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, 100191, China
| | - Changwei Li
- Department of Epidemiology and Biostatistics, University of Georgia College of Public Health, Athens, GA, USA
| | - Yanhui Li
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, 100191, China
| | - Luqi Shen
- Department of Epidemiology and Biostatistics, University of Georgia College of Public Health, Athens, GA, USA
| | - Bin Dong
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, 100191, China
| | - Zhiyong Zou
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, 100191, China. .,National Health Commission Key Laboratory of Reproductive Health, Peking University Health Science Center, Beijing, 100191, China.
| | - Jun Ma
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, 100191, China
| |
Collapse
|
3
|
Genome-Wide DNA Methylation Profiling in Early Stage I Lung Adenocarcinoma Reveals Predictive Aberrant Methylation in the Promoter Region of the Long Noncoding RNA PLUT: An Exploratory Study. J Thorac Oncol 2020; 15:1338-1350. [PMID: 32272161 DOI: 10.1016/j.jtho.2020.03.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 03/27/2020] [Accepted: 03/29/2020] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Surgical procedure is the treatment of choice in early stage I lung adenocarcinoma. However, a considerable number of patients experience recurrence within the first 2 years after complete resection. Suitable prognostic biomarkers that identify patients at high risk of recurrence (who may probably benefit from adjuvant treatment) are still not available. This study aimed at identifying methylation markers for early recurrence that may become important tools for the development of new treatment modalities. METHODS Genome-wide DNA methylation profiling was performed on 30 stage I lung adenocarcinomas, comparing 14 patients with early metastatic recurrence with 16 patients with a long-term relapse-free survival period using methylated-CpG-immunoprecipitation followed by high-throughput next-generation sequencing. The differentially methylated regions between the two subgroups were validated for their prognostic value in two independent cohorts using the MassCLEAVE assay, a high-resolution quantitative methylation analysis. RESULTS Unsupervised clustering of patients in the discovery cohort on the basis of differentially methylated regions identified patients with shorter relapse-free survival (hazard ratio: 2.23; 95% confidence interval: 0.66-7.53; p = 0.03). In two validation cohorts, promoter hypermethylation of the long noncoding RNA PLUT was significantly associated with shorter relapse-free survival (hazard ratio: 0.54; 95% confidence interval: 0.31-0.93; p < 0.026) and could be reported as an independent prognostic factor in the multivariate Cox regression analysis. CONCLUSIONS Promoter hypermethylation of the long noncoding RNA PLUT is predictive in patients with early stage I adenocarcinoma at high risk for early recurrence. Further studies are needed to validate its role in carcinogenesis and its use as a biomarker to facilitate patient selection and risk stratification.
Collapse
|
4
|
Moret-Tatay I, Cerrillo E, Sáez-González E, Hervás D, Iborra M, Sandoval J, Busó E, Tortosa L, Nos P, Beltrán B. Identification of Epigenetic Methylation Signatures With Clinical Value in Crohn's Disease. Clin Transl Gastroenterol 2019; 10:e00083. [PMID: 31663908 PMCID: PMC6919449 DOI: 10.14309/ctg.0000000000000083] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION DNA methylation is an epigenetic mechanism that regulates gene expression and represents an important link between genotype, environment, and disease. It is a reversible and inheritable mechanism that could offer treatment targets. We aimed to assess the methylation changes on specific genes previously associated with Crohn's disease (CD) and to study their possible associations with the pathology. METHODS We included 103 participants and grouped them into 2 cohorts (a first [n = 31] and a second validation [n = 72] cohort), with active CD (aCD) and inactive CD (iCD) and healthy participants (CTR). DNA was obtained from the peripheral blood and analyzed by the Agena platform. The selected genes were catalase (CAT), α-defensin 5 (DEFA5), FasR, FasL, tumor necrosis factor (TNF), TNFRSF1A, TNFRSF1B, PPA2, ABCB1, NOD2, PPARγ, and PKCζ. We used the elastic net algorithm and R software. RESULTS We studied 240 CpGs. Sixteen CpGs showed differential methylation profiles among aCD, iCD, and CTR. We selected for validation those with the greatest differences: DEFA5 CpG_11; CpG_13; CAT CpG_31.32; TNF CpG_4, CpG_12; and ABCB1 CpG_21. Our results validated the genes DEFA5 (methylation gain) and TNF (methylation loss) with P values < 0.001. In both cases, the methylation level was maintained and did not change with CD activity (aCD vs iCD). The subanalysis comparison between aCD and iCD showed significant differential methylation profiles in other CpGs: TNF, FAS, ABCB1, CAT, and TNFRS1BF genes. DISCUSSION The methylation status of DEFA5 and TNF genes provides a signature biomarker that characterizes patients with CD and supports the possible implication of the environment and the immune system in CD pathogenesis.
Collapse
Affiliation(s)
- Inés Moret-Tatay
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Biomedical Research Centre, Hepatic and Digestive Diseases Network (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas [CIBEREHD]), Madrid, Spain
| | - Elena Cerrillo
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Department of Gastroenterology, Hospital La Fe, Valencia, Spain
| | - Esteban Sáez-González
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Department of Gastroenterology, Hospital La Fe, Valencia, Spain
| | - David Hervás
- Department of Gastroenterology, Hospital La Fe, Valencia, Spain
| | - Marisa Iborra
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Biomedical Research Centre, Hepatic and Digestive Diseases Network (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas [CIBEREHD]), Madrid, Spain
- Department of Gastroenterology, Hospital La Fe, Valencia, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
| | - Enrique Busó
- Central Unit for Research in Medicine (UCIM),University of Valencia, Valencia, Spain
| | - Luis Tortosa
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Biomedical Research Centre, Hepatic and Digestive Diseases Network (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas [CIBEREHD]), Madrid, Spain
| | - Pilar Nos
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Biomedical Research Centre, Hepatic and Digestive Diseases Network (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas [CIBEREHD]), Madrid, Spain
- Department of Gastroenterology, Hospital La Fe, Valencia, Spain
| | - Belén Beltrán
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Biomedical Research Centre, Hepatic and Digestive Diseases Network (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas [CIBEREHD]), Madrid, Spain
- Department of Gastroenterology, Hospital La Fe, Valencia, Spain
| |
Collapse
|
5
|
Wu H, Estill MS, Shershebnev A, Suvorov A, Krawetz SA, Whitcomb BW, Dinnie H, Rahil T, Sites CK, Pilsner JR. Preconception urinary phthalate concentrations and sperm DNA methylation profiles among men undergoing IVF treatment: a cross-sectional study. Hum Reprod 2018; 32:2159-2169. [PMID: 29024969 DOI: 10.1093/humrep/dex283] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 08/08/2017] [Indexed: 02/06/2023] Open
Abstract
STUDY QUESTION Are preconception phthalate and phthalate replacements associated with sperm differentially methylated regions (DMRs) among men undergoing IVF? SUMMARY ANSWER Ten phthalate metabolites were associated with 131 sperm DMRs that were enriched in genes related to growth and development, cell movement and cytoskeleton structure. WHAT IS KNOWN ALREADY Several phthalate compounds and their metabolites are known endocrine disrupting compounds and are pervasive environmental contaminants. Rodent studies report that prenatal phthalate exposures induce sperm DMRs, but the influence of preconception phthalate exposure on sperm DNA methylation in humans is unknown. STUDY DESIGN, SIZE, DURATION An exploratory cross-sectional study with 48 male participants from the Sperm Environmental Epigenetics and Development Study (SEEDS). PARTICIPANTS/MATERIALS, SETTING, METHODS The first 48 couples provided a spot urine sample on the same day as semen sample procurement. Sperm DNA methylation was assessed with the HumanMethylation 450 K array. Seventeen urinary phthalate and 1,2-Cyclohexane dicarboxylic acid diisononyl ester (DINCH) metabolite concentrations were measured from spot urine samples. The A-clust algorithm was employed to identify co-regulated regions. DMRs associated with urinary metabolite concentrations were identified via linear models, corrected for false discovery rate (FDR). MAIN RESULTS AND ROLE OF CHANCE Adjusting for age, BMI, and current smoking, 131 DMRs were associated with at least one urinary metabolite. Most sperm DMRs were associated with anti-androgenic metabolites, including mono(2-ethylhexyl) phthalate (MEHP, n = 83), mono(2-ethyl-5-oxohexyl) phthalate (MEOHP, n = 16), mono-n-butyl phthalate (MBP, n = 22) and cyclohexane-1,2-dicarboxylic acid-monocarboxy isooctyl (MCOCH, n = 7). The DMRs were enriched in lincRNAs as well as in regions near coding regions. Functional analyses of DMRs revealed enrichment of genes related to growth and development as well as cellular function and maintenance. Finally, 13% of sperm DMRs were inversely associated with high quality blastocyst-stage embryos after IVF. LIMITATIONS, REASONS FOR CAUTION Our modest sample size only included 48 males and additional larger studies are necessary to confirm our observed results. Non-differential misclassification of exposure is also a concern given the single spot urine collection. WIDER IMPLICATIONS OF THE FINDINGS To our knowledge, this is the first study to report that preconception urinary phthalate metabolite concentrations are associated with sperm DNA methylation in humans. These results suggest that paternal adult environmental conditions may influence epigenetic reprogramming during spermatogenesis, and in turn, influence early-life development. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by grant K22-ES023085 from the National Institute of Environmental Health Sciences. The authors declare no competing interests.
Collapse
Affiliation(s)
- Haotian Wu
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, 173A Goessmann, 686 North Pleasant Street, Amherst, MA 01003, USA
| | - Molly S Estill
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 3127 Scott Hall, 540 East Canfield, Detroit, MI 48201, USA.,Department of Obstetrics and Gynecology, C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, 253 C.S. Mott 275 East. Hancock, Detroit, MI 48201, USA
| | - Alexander Shershebnev
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, 173A Goessmann, 686 North Pleasant Street, Amherst, MA 01003, USA
| | - Alexander Suvorov
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, 173A Goessmann, 686 North Pleasant Street, Amherst, MA 01003, USA
| | - Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 3127 Scott Hall, 540 East Canfield, Detroit, MI 48201, USA.,Department of Obstetrics and Gynecology, C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, 253 C.S. Mott 275 East. Hancock, Detroit, MI 48201, USA
| | - Brian W Whitcomb
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, 715 North Pleasant Street Amherst, MA 01003, USA
| | - Holly Dinnie
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Baystate Medical Center, 759 Chestnut Street, Springfield, MA 01199, USA
| | - Tayyab Rahil
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Baystate Medical Center, 759 Chestnut Street, Springfield, MA 01199, USA
| | - Cynthia K Sites
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Baystate Medical Center, 759 Chestnut Street, Springfield, MA 01199, USA
| | - J Richard Pilsner
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, 173A Goessmann, 686 North Pleasant Street, Amherst, MA 01003, USA
| |
Collapse
|
6
|
Yan P, Hao Y, Shu Z, Gu C, Zhou X, Liu X, Xiang H. Double signal enhancement strategy based on rolling circle amplification and photoinduced electron transfer for ultrasensitive fluorometric detection of methylated DNA. Mikrochim Acta 2018; 185:299. [PMID: 29754198 DOI: 10.1007/s00604-018-2839-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/06/2018] [Indexed: 12/17/2022]
Abstract
The authors describe a novel assay for the detection of methylated DNA site. Rolling circle amplification and CdSe/ZnS quantum dots with high fluorescence efficiency are applied in this method. The CdSe/ZnS quantum dots act as electron donors, and hemin and oxygen (derived from hydrogen peroxide act as acceptors in photoinduced electron transfer. The assay, best performed at excitation/emission peaks of 450/620 nm, is sensitive and specific. Fluorometric response is linear in the 1 pM to 100 nM DNA concentration range, and the lowest detectable concentration of methylated DNA is 142 fM (S/N = 3). The method is capable of recognizing 0.01% methylated DNA in a mixture of methylated/unmethylated DNA. Graphical abstract A novel method for methylated sites detection in DNA is established. Rolling circle amplification and photoinduced electron transfer. CdSe/ZnS quantum dots with high fluorescence efficiency act as the electron donor, while G-quadruplex/hemin and hydrogen peroxide derived oxygen act as electron acceptor. It presents a linear response towards 1 pM to 100 nM methylated DNA with a correlation coefficient of 0.9968, and the lowest detectable concentration of methylated DNA was 142 fM, with selectivity significantly superior to other methods.
Collapse
Affiliation(s)
- Pingdan Yan
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, People's Republic of China
| | - Yixiong Hao
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, People's Republic of China
| | - Zhaoche Shu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, People's Republic of China
| | - Chunling Gu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, People's Republic of China
| | - Xiaomei Zhou
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, People's Republic of China
| | - Xiaoyu Liu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, People's Republic of China
| | - Hua Xiang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, People's Republic of China.
| |
Collapse
|
7
|
Kunze S. Quantitative Region-Specific DNA Methylation Analysis by the EpiTYPER™ Technology. Methods Mol Biol 2018; 1708:515-535. [PMID: 29224161 DOI: 10.1007/978-1-4939-7481-8_26] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
DNA methylation plays a profound role in development and health as well as development and progression of disease. High-throughput quantitative DNA methylation analysis is therefore crucial for the study of the normal physiology of the epigenome and its dysregulation in disease. Many target areas are identified by a range of emerging genome-wide cytosine methylation techniques, but these whole genome scans usually only provide methylation data for a few individual CpG sites (CpGs) within a region. The EpiTYPER™ assay is a region-specific method for the detection and quantitative analysis of DNA methylation that allows performing a high-resolution scan of selected regions. It thus enables a more detailed analysis of single CpGs and the surrounding area and can, in addition to candidate gene methylation analysis, be used to validate CpGs detected by genome wide techniques. The EpiTYPER™ assay allows a fast and reproducible targeted quantification of individual CpGs in a high throughput manner and is based on base-specific cleavage of bisulfite-converted genomic DNA and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Up to 85% of the CpGs within a target region can be analyzed and the detection precision allows quantifying methylation differences as low as 5-7%.
Collapse
Affiliation(s)
- Sonja Kunze
- Research Unit of Molecular Epidemiology/Institute of Epidemiology II, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
| |
Collapse
|
8
|
Burdon KP, Awadalla MS, Mitchell P, Wang JJ, White A, Keane MC, Souzeau E, Graham SL, Goldberg I, Healey PR, Landers J, Mills RAD, Best S, Hewitt AW, Sharma S, Craig JE. DNA methylation at the 9p21 glaucoma susceptibility locus is associated with normal-tension glaucoma. Ophthalmic Genet 2017; 39:221-227. [PMID: 29265947 DOI: 10.1080/13816810.2017.1413659] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
PURPOSE Recent genome-wide association studies reported strong association of genetic variation at the CDKN2B/CDKN2B-AS1 locus on 9p21 with normal-tension glaucoma (NTG) in multiple populations. The mechanism by which this locus causes disease remains to be elucidated. We investigated the association of DNA methylation of CpG islands at this locus with NTG. METHODS We conducted a retrospective case-control study of 178 NTG cases and 202 unaffected controls from Australia. CDKN2B and CDKN2B-AS1 promoter methylation was measured quantitatively using the MassCleave assay, and assessed for association with the disease, and the genotype of the associated risk variants using IBM SPSS statistics 22.0 CpG sites at which methylation status was associated with NTG were validated using pyrosequencing. RESULTS We identified one CpG site (F1:13-14) in the CDKN2B promoter which showed significant association with NTG (p = 0.001). The association was highly significant in female cases (p = 0.006) but not in male cases (p = 0.054). The association was validated using an independent method confirming the likely association of DNA methylation with NTG in females (p = 0.015), but not in males (p = 0.497). In addition, methylation at CpG sites in CDKN2B was also associated with genotype at rs1063192, which is known to confer risk for NTG. CONCLUSION This study reveals an association of methylation status in the CDKN2B promoter with NTG, particularly in females. This suggests that the observed genetic association with the disease at this locus could be in part due to epigenetic mechanisms, and is likely to be independent of the association of nonsynonymous coding variation within the gene.
Collapse
Affiliation(s)
- Kathryn P Burdon
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia.,b Menzies Institute for Medical Research , University of Tasmania , Sydney , Australia
| | - Mona S Awadalla
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| | - Paul Mitchell
- c Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research , University of Sydney , Westmead , Australia
| | - Jie Jin Wang
- c Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research , University of Sydney , Westmead , Australia
| | - Andrew White
- c Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research , University of Sydney , Westmead , Australia
| | - Miriam C Keane
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| | - Emmanuelle Souzeau
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| | - Stuart L Graham
- d Department of Clinical Medicine, Faculty of Medicine and Health Sciences , Macquarie University , Sydney , New South Wales , Australia
| | - Ivan Goldberg
- e Eye Associates, Glaucoma Unit , Sydney Eye Hospital , Australia
| | - Paul R Healey
- c Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research , University of Sydney , Westmead , Australia.,e Eye Associates, Glaucoma Unit , Sydney Eye Hospital , Australia.,f Discipline of Ophthalmology , The University of Sydney , Australia
| | - John Landers
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| | - Richard A D Mills
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| | - Stephen Best
- g Auckland Eye , Auckland , New Zealand.,h Auckland District Health Board , Greenlane Clinical Centre , Auckland , New Zealand.,i Discipline of Ophthalmology , University of Auckland , Auckland , New Zealand
| | - Alex W Hewitt
- b Menzies Institute for Medical Research , University of Tasmania , Sydney , Australia.,j Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital & Ophthalmology, Department of Surgery , The University of Melbourne , Melbourne, Australia
| | - Shiwani Sharma
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| | - Jamie E Craig
- a Department of Ophthalmology , Flinders University , Adelaide, South Australia , Australia
| |
Collapse
|
9
|
Wang S, Song J, Yang Y, Zhang Y, Wang H, Ma J. HIF3A DNA Methylation Is Associated with Childhood Obesity and ALT. PLoS One 2015; 10:e0145944. [PMID: 26717317 PMCID: PMC4696784 DOI: 10.1371/journal.pone.0145944] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/10/2015] [Indexed: 12/18/2022] Open
Abstract
Gene polymorphisms associated so far with body mass index (BMI) can explain only 1.18–1.45% of observed variation in BMI. Recent studies suggest that epigenetic modifications, especially DNA methylation, could contribute to explain part of the missing heritability, and two epigenetic genome-wide analysis studies (EWAS) have reported that Hypoxia Inducible Factor 3 Alpha Subunit (HIF3A) methylation was associated with BMI or BMI change. We therefore assessed whether the HIF3A methylation is associated with obesity and other obesity-related phenotypes in Chinese children. The subjects included 110 severe obese cases aged 7–17y and 110 normal-weight controls matched by age and gender for measurement of blood DNA methylation levels at the HIF3A gene locus using the Sequenom’s MassARRAY system. We observed significantly higher methylation levels in obese children than in controls at positions 46801642 and 46801699 in HIF3A gene (P<0.05), and found positive associations between methylation and alanine aminotransferase (ALT) levels adjusted by gender, age and BMI at the position 46801699 (r = 0.226, P = 0.007). These results suggest that HIF3A DNA methylation is associated with childhood obesity, and has a BMI-independent association with ALT. The results provide evidence for identifying epigenetic factors of elivated ALT and may be useful for risk assessment and personalized medicine of liver diseases such as non-alcoholic fatty liver disease (NAFLD).
Collapse
Affiliation(s)
- Shuo Wang
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, China
| | - Jieyun Song
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, China
| | - Yide Yang
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, China
| | - Yining Zhang
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, China
| | - Haijun Wang
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, China
| | - Jun Ma
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, China
| |
Collapse
|
10
|
Vangeel EB, Izzi B, Hompes T, Vansteelandt K, Lambrechts D, Freson K, Claes S. DNA methylation in imprinted genesIGF2andGNASXLis associated with prenatal maternal stress. GENES BRAIN AND BEHAVIOR 2015; 14:573-82. [DOI: 10.1111/gbb.12249] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/12/2015] [Accepted: 08/21/2015] [Indexed: 12/30/2022]
Affiliation(s)
- E. B. Vangeel
- Genetic Research about Stress and Psychiatry (GRASP), Department of Neurosciences; Leuven Belgium
- Center for Molecular and Vascular Biology (CMVB), Department of Cardiovascular Sciences; University of Leuven; Leuven Belgium
| | - B. Izzi
- Center for Molecular and Vascular Biology (CMVB), Department of Cardiovascular Sciences; University of Leuven; Leuven Belgium
| | - T. Hompes
- Genetic Research about Stress and Psychiatry (GRASP), Department of Neurosciences; Leuven Belgium
- University Psychiatric Center, University of Leuven; Leuven Belgium
| | - K. Vansteelandt
- University Psychiatric Center, University of Leuven; Leuven Belgium
| | - D. Lambrechts
- Laboratory of Translational Genetics, Department of Oncology; University of Leuven; Leuven Belgium
- Vesalius Research Center (VRC), VIB; Leuven Belgium
| | - K. Freson
- Center for Molecular and Vascular Biology (CMVB), Department of Cardiovascular Sciences; University of Leuven; Leuven Belgium
| | - S. Claes
- Genetic Research about Stress and Psychiatry (GRASP), Department of Neurosciences; Leuven Belgium
- University Psychiatric Center, University of Leuven; Leuven Belgium
| |
Collapse
|
11
|
Noehammer C, Pulverer W, Hassler MR, Hofner M, Wielscher M, Vierlinger K, Liloglou T, McCarthy D, Jensen TJ, Nygren A, Gohlke H, Trooskens G, Braspenning M, Van Criekinge W, Egger G, Weinhaeusel A. Strategies for validation and testing of DNA methylation biomarkers. Epigenomics 2015; 6:603-22. [PMID: 25531255 DOI: 10.2217/epi.14.43] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
DNA methylation is a stable covalent epigenetic modification of primarily CpG dinucleotides that has recently gained considerable attention for its use as a biomarker in different clinical settings, including disease diagnosis, prognosis and therapeutic response prediction. Although the advent of genome-wide DNA methylation profiling in primary disease tissue has provided a manifold resource for biomarker development, only a tiny fraction of DNA methylation-based assays have reached clinical testing. Here, we provide a critical overview of different analytical methods that are suitable for biomarker validation, including general study design considerations, which might help to streamline epigenetic marker development. Furthermore, we highlight some of the recent marker validation studies and established markers that are currently commercially available for assisting in clinical management of different cancers.
Collapse
Affiliation(s)
- Christa Noehammer
- Health & Environment Department, Molecular Diagnostics, AIT Austrian Institute of Technology, Vienna, Austria
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Wu H, de Gannes MK, Luchetti G, Pilsner JR. Rapid method for the isolation of mammalian sperm DNA. Biotechniques 2015; 58:293-300. [PMID: 26054765 DOI: 10.2144/000114280] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/11/2015] [Indexed: 01/06/2023] Open
Abstract
The unique DNA packaging of spermatozoa renders them resistant to DNA isolation techniques used for somatic cells, requiring alternative methods that are slow and labor intensive. Here we present a rapid method for isolating high-quality sperm DNA. Isolated human sperm cells were homogenized with 0.2 mm steel beads for 5 min at room temperature in the presence of guanidine thiocyanate lysis buffer supplemented with 50 mM tris(2-carboxyethyl)phosphine (TCEP). Our method yielded >90% high-quality DNA using 3 different commercially available silica-based spin columns. DNA yields did not differ between immediate isolation (2.84 ± 0.04 pg/cell) and isolation after 2 weeks of homogenate storage at room temperature (2.91 ± 0.13 pg/cell). DNA methylation analyses revealed similar methylation levels at both time points for three imprinted loci. Our protocol has many advantages: it is conducted at room temperature; lengthy proteinase K (ProK) digestions are eliminated; the reducing agent, TCEP, is odorless and stable at room temperature; nucleic acids are stabilized, allowing storage of homogenate; and it is adaptable for other mammalian species. Taken together, the benefits of our improved method have important implications for settings where sample processing constraints exist.
Collapse
Affiliation(s)
- Haotian Wu
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, MA
| | - Matthew K de Gannes
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, MA
| | - Gianna Luchetti
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, MA
| | - J Richard Pilsner
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, MA
| |
Collapse
|
13
|
Non AL, Thayer ZM. Epigenetics for anthropologists: An introduction to methods. Am J Hum Biol 2015; 27:295-303. [DOI: 10.1002/ajhb.22679] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/22/2014] [Accepted: 12/20/2014] [Indexed: 12/17/2022] Open
Affiliation(s)
- Amy L. Non
- Department of Anthropology; Vanderbilt University; Nashville Tennessee 37235-7703
| | - Zaneta M. Thayer
- Department of Anthropology; University of Colorado Denver; Denver Colorado 80217-3364
| |
Collapse
|
14
|
Miozzo M, Vaira V, Sirchia SM. Epigenetic alterations in cancer and personalized cancer treatment. Future Oncol 2015; 11:333-48. [DOI: 10.2217/fon.14.237] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT Based on the pivotal importance of epigenetics for transcription regulation, it is not surprising that cancer is characterized by several epigenetic abnormalities. Conversely to genetic alterations, epigenetic changes are not permanent, thus represent opportunities for therapeutic strategies designed to reverse transcriptional abnormalities, and cancer is the first disease in which epigenetic therapies with chromatin remodeling agents were introduced. The role of miRNAs in gene regulation supports their potential as innovative therapeutic strategy. Recent evidences have proven that the environment can profoundly influence the epigenome: diet, smoking and alcohol consumption can negatively impact the expression profile. Given the plasticity of epigenetic marks, it is challenging the idea that the epigenetic alterations are ‘druggable’ sites using specific food components.
Collapse
Affiliation(s)
- Monica Miozzo
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Milano, Italy
| | - Valentina Vaira
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
- Istituto Nazionale di Genetica Molecolare ‘Romeo ed Enrica Invernizzi’, Integrative Biology Unit, Milano, Italy
| | | |
Collapse
|
15
|
Sensitive colorimetric biosensing for methylation analysis of p16/CDKN2 promoter with hyperbranched rolling circle amplification. Biosens Bioelectron 2014; 61:593-7. [DOI: 10.1016/j.bios.2014.06.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/16/2014] [Accepted: 06/08/2014] [Indexed: 12/18/2022]
|
16
|
von Hippel-Lindau Exonic Methylation Analysis Using MALDI-TOF Mass Spectrometry. J Urol 2014; 192:1528-33. [DOI: 10.1016/j.juro.2014.03.108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2014] [Indexed: 01/12/2023]
|
17
|
Canivell S, Ruano EG, Sisó-Almirall A, Kostov B, González-de Paz L, Fernandez-Rebollo E, Hanzu FA, Párrizas M, Novials A, Gomis R. Differential methylation of TCF7L2 promoter in peripheral blood DNA in newly diagnosed, drug-naïve patients with type 2 diabetes. PLoS One 2014; 9:e99310. [PMID: 24914535 PMCID: PMC4051650 DOI: 10.1371/journal.pone.0099310] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 05/13/2014] [Indexed: 12/15/2022] Open
Abstract
TCF7L2 is the susceptibility gene for Type 2 diabetes (T2D) with the largest effect on disease risk that has been discovered to date. However, the mechanisms by which TCF7L2 contributes to the disease remain largely elusive. In addition, epigenetic mechanisms, such as changes in DNA methylation patterns, might have a role in the pathophysiology of T2D. This study aimed to investigate the differences in terms of DNA methylation profile of TCF7L2 promoter gene between type 2 diabetic patients and age- and Body Mass Index (BMI)- matched controls. We included 93 type 2 diabetic patients that were recently diagnosed for T2D and exclusively on diet (without any pharmacological treatment). DNA was extracted from whole blood and DNA methylation was assessed using the Sequenom EpiTYPER system. Type 2 diabetic patients were more insulin resistant than their matched controls (mean HOMA IR 2.6 vs 1.8 in controls, P<0.001) and had a poorer beta-cell function (mean HOMA B 75.7 vs. 113.6 in controls, P<0.001). Results showed that 59% of the CpGs analyzed in TCF7L2 promoter had significant differences between type 2 diabetic patients and matched controls. In addition, fasting glucose, HOMA-B, HOMA-IR, total cholesterol and LDL-cholesterol correlated with methylation in specific CpG sites of TCF7L2 promoter. After adjustment by age, BMI, gender, physical inactivity, waist circumference, smoking status and diabetes status uniquely fasting glucose, total cholesterol and LDL-cholesterol remained significant. Taken together, newly diagnosed, drug-naïve type 2 diabetic patients display specific epigenetic changes at the TCF7L2 promoter as compared to age- and BMI-matched controls. Methylation in TCF7L2 promoter is further correlated with fasting glucose in peripheral blood DNA, which sheds new light on the role of epigenetic regulation of TCF7L2 in T2D.
Collapse
Affiliation(s)
- Silvia Canivell
- Department of Endocrinology and Nutrition, Hospital Clinic, Barcelona, Spain
- Les Corts Primary Health Care Centre, PHC Research Group, IDIBAPS, Barcelona, Spain
- Diabetes and Obesity Laboratory, IDIBAPS, Barcelona, Spain
| | - Elena G. Ruano
- Diabetes and Obesity Laboratory, IDIBAPS, Barcelona, Spain
- CIBERDEM, Barcelona, Spain
| | - Antoni Sisó-Almirall
- Les Corts Primary Health Care Centre, PHC Research Group, IDIBAPS, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Belchin Kostov
- Les Corts Primary Health Care Centre, PHC Research Group, IDIBAPS, Barcelona, Spain
| | - Luis González-de Paz
- Les Corts Primary Health Care Centre, PHC Research Group, IDIBAPS, Barcelona, Spain
| | | | - Felicia A. Hanzu
- Department of Endocrinology and Nutrition, Hospital Clinic, Barcelona, Spain
- Diabetes and Obesity Laboratory, IDIBAPS, Barcelona, Spain
| | | | - Anna Novials
- Department of Endocrinology and Nutrition, Hospital Clinic, Barcelona, Spain
- Diabetes and Obesity Laboratory, IDIBAPS, Barcelona, Spain
- CIBERDEM, Barcelona, Spain
| | - Ramon Gomis
- Department of Endocrinology and Nutrition, Hospital Clinic, Barcelona, Spain
- Diabetes and Obesity Laboratory, IDIBAPS, Barcelona, Spain
- CIBERDEM, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
- * E-mail:
| |
Collapse
|
18
|
Hompes T, Izzi B, Gellens E, Morreels M, Fieuws S, Pexsters A, Schops G, Dom M, Van Bree R, Freson K, Verhaeghe J, Spitz B, Demyttenaere K, Glover V, Van den Bergh B, Allegaert K, Claes S. Investigating the influence of maternal cortisol and emotional state during pregnancy on the DNA methylation status of the glucocorticoid receptor gene (NR3C1) promoter region in cord blood. J Psychiatr Res 2013; 47:880-91. [PMID: 23566423 DOI: 10.1016/j.jpsychires.2013.03.009] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 12/30/2022]
Abstract
BACKGROUND The methylation status of the human glucocorticoid receptor gene NR3C1 in newborns has been reported to be sensitive to prenatal maternal mood. This study investigates both the association between maternal cortisol and emotional state during pregnancy and the methylation state of the promoter region of NR3C1 gene. METHODS We examined 83 pregnant women. Psychological data and diurnal cortisol data were assessed to evaluate maternal stress once each trimester. DNA methylation at different loci of the NR3C1 gene, including exon 1B, 1D and 1F, was analyzed in genomic DNA from cord blood mononuclear cells. RESULTS Univariable analyses indicated pregnancy related anxiety to be the strongest psychological parameter throughout pregnancy. Most significant findings concerned 1F. Particularly the methylation state of CpG9 was significantly associated with maternal emotional wellbeing. In a multivariable model the proportion of variance in methylation state of F9 explained (PVE) by pregnancy related anxiety was 7.8% (p = 0.023) during T1. Furthermore different CpG-units located at the nerve growth factor inducible protein A (NGFI-A) binding sites of 1F were associated with maternal anxiety [(F20.21: PC PRAQ and fear of integrity in T1: respectively PVE:8.9% and PVE:9.0%; Fear of delivery T2: PVE:8.0%, Fear of integrity T2: PVE:6.0% and STAI T2: PVE:5.9%) - (F12.13: PC PRAQ T1: PVE:6.9%, fear of integrity T2: PVE:6.0% and fear of delivery T2: PVE:8.0%)] and cortisol (F38.39: PVE:8.9%) in T2. CONCLUSION These data indicate that prenatal maternal emotional state, particularly pregnancy related anxiety, are associated with the methylation state of the NR3C1 gene in the child.
Collapse
Affiliation(s)
- Titia Hompes
- Department of Psychiatry, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Riau AK, Wong TT, Finger SN, Chaurasia SS, Hou AH, Chen S, Yu SJ, Tong L. Aberrant DNA methylation of matrix remodeling and cell adhesion related genes in pterygium. PLoS One 2011; 6:e14687. [PMID: 21359202 PMCID: PMC3040179 DOI: 10.1371/journal.pone.0014687] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 01/22/2011] [Indexed: 11/18/2022] Open
Abstract
Background Pterygium is a common ocular surface disease characterized by abnormal epithelial and fibrovascular proliferation, invasion, and matrix remodeling. This lesion, which migrates from the periphery to the center of the cornea, impairs vision and causes considerable irritation. The mechanism of pterygium formation remains ambiguous, and current treatment is solely surgical excision, with a significant risk of recurrence after surgery. Here, we investigate the role of methylation in DNA sequences that regulate matrix remodeling and cell adhesion in pterygium formation. Methodology/Principal Findings Pterygium and uninvolved conjunctiva samples were obtained from the same eye of patients undergoing surgery. The EpiTYPER Sequenom technology, based on differential base cleavage and bisulfite sequencing was used to evaluate the extent of methylation of 29 matrix and adhesion related genes. In pterygium, three CpG sites at −268, −32 and −29 bp upstream of transglutaminase 2 (TGM-2) transcription initiation were significantly hypermethylated (p<0.05), whereas hypomethylation was detected at CpGs +484 and +602 bp downstream of matrix metalloproteinase 2 (MMP-2) transcription start site, and −809, −762, −631 and −629 bp upstream of the CD24 transcription start site. RT-qPCR, western blot and immunofluorescent staining showed that transcript and protein expression were reduced for TGM-2 and increased for MMP-2 and CD24. Inhibition of methylation in cultured conjunctival epithelial cells increased these transcripts. Conclusions/Significance We found regions of aberrant DNA methylation which were consistent with alteration of TGM-2, MMP-2, and CD24 transcript and protein expression, and that inhibition of methylation in cultured cells can increase the expression of these genes. Since these genes were related to cell adhesion and matrix remodeling, dysregulation may lead to fibroblastic and neovascular changes and pterygium formation. These results have implications for the prognostication of pterygium in clinical practice, for example, detection of epigenetic changes may have a role in predicting post surgical recurrence of aggressive lesions.
Collapse
Affiliation(s)
- Andri K. Riau
- Ocular Wound Healing and Therapeutics Laboratory, Singapore Eye Research Institute, Singapore, Singapore
| | - Tina T. Wong
- Ocular Wound Healing and Therapeutics Laboratory, Singapore Eye Research Institute, Singapore, Singapore
- Singapore National Eye Center, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sharon N. Finger
- Ocular Wound Healing and Therapeutics Laboratory, Singapore Eye Research Institute, Singapore, Singapore
| | - Shyam S. Chaurasia
- Ocular Wound Healing and Therapeutics Laboratory, Singapore Eye Research Institute, Singapore, Singapore
| | - Ai Hua Hou
- Ocular Wound Healing and Therapeutics Laboratory, Singapore Eye Research Institute, Singapore, Singapore
| | - Silin Chen
- Ocular Wound Healing and Therapeutics Laboratory, Singapore Eye Research Institute, Singapore, Singapore
| | - Shang Juan Yu
- Ocular Wound Healing and Therapeutics Laboratory, Singapore Eye Research Institute, Singapore, Singapore
| | - Louis Tong
- Ocular Wound Healing and Therapeutics Laboratory, Singapore Eye Research Institute, Singapore, Singapore
- Singapore National Eye Center, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
- * E-mail:
| |
Collapse
|
20
|
Izzi B, Decallonne B, Devriendt K, Bouillon R, Vanderschueren D, Levtchenko E, de Zegher F, Van den Bruel A, Lambrechts D, Van Geet C, Freson K. A new approach to imprinting mutation detection in GNAS by Sequenom EpiTYPER system. Clin Chim Acta 2010; 411:2033-9. [PMID: 20807523 DOI: 10.1016/j.cca.2010.08.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 08/19/2010] [Accepted: 08/24/2010] [Indexed: 11/28/2022]
Abstract
BACKGROUND Pseudohypoparathyroidism type Ib (PHPIb) results from abnormal imprinting of GNAS. Familial and sporadic forms of PHPIb have distinct GNAS imprinting patterns: familial PHPIb patients have an exon A/B-only imprinting defect and an intragenic STX16 deletion, whereas sporadic PHPIb cases have abnormal imprinting of the three differentially methylated regions (DMRs) in GNAS without the STX16 deletion. Overall GNAS methylation defects have recently been detected in some PHPIa patients. METHODS This study describes the first quantitative methylation analysis of multiple CpG sites for three different GNAS DMRs using the Sequenom EpiTYPER in 35 controls, 12 PHPIb patients, 2 PHPIa patients and 2 patients without parathormone (PTH) resistance but having only hypocalcemia and hyperphosphatemia. RESULTS All patients have GNAS methylation defects typically with NESP hypermethylation versus XL and exon A/B hypomethylation while the imprinting of SNURF/SNRPN was normal. PHPIa patients showed an abnormal methylation in the three DMRs of GNAS. For the first time, a marked abnormal GNAS methylation was also found in 2 patients without PTH resistance but having hypocalcemia and hyperphosphatemia. CONCLUSIONS The Sequenom EpiTYPER proves to be very sensitive in detecting DNA methylation changes. Our analysis also suggests that GNAS imprinting defects might be more frequent and diverse than previously thought.
Collapse
Affiliation(s)
- Benedetta Izzi
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, 3000, Belgium
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Specificity of methylation assays in cancer research: a guideline for designing primers and probes. Obstet Gynecol Int 2010; 2010. [PMID: 20798774 PMCID: PMC2926695 DOI: 10.1155/2010/870865] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Accepted: 06/21/2010] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is an epigenetic regulation mechanism of genomic function, and aberrant methylation pattern has been found to be a common event in many diseases and human cancers. A large number of cancer studies have been focused on identification of methylation changes as biomarkers (i.e., breast cancer). However, still clinical use of them is very limited because of lack of specificity and sensitivity for diagnostic test. This highlights the critical need for specific primer and probe design to avoid false-positive detection of methylation profiling. The guideline and online web tools that are introduced in this paper might help to perform a successful experiment and to develop specific diagnosis biomarkers by designing right primer pair and probe prior to experimental step.
Collapse
|
22
|
von Kanel T, Gerber D, Schaller A, Baumer A, Wey E, Jackson CB, Gisler FM, Heinimann K, Gallati S. Quantitative 1-Step DNA Methylation Analysis with Native Genomic DNA as Template. Clin Chem 2010; 56:1098-106. [PMID: 20472822 DOI: 10.1373/clinchem.2009.142828] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: DNA methylation analysis currently requires complex multistep procedures based on bisulfite conversion of unmethylated cytosines or on methylation-sensitive endonucleases. To facilitate DNA methylation analysis, we have developed a quantitative 1-step assay for DNA methylation analysis.
Methods: The assay is based on combining methylation-sensitive FastDigest® endonuclease digestion and quantitative real-time PCR (qPCR) in a single reaction. The first step consists of DNA digestion, followed by endonuclease inactivation and qPCR. The degree of DNA methylation is evaluated by comparing the quantification cycles of a reaction containing a methylation-sensitive endonuclease with the reaction of a sham mixture containing no endonuclease. Control reactions interrogating an unmethylated locus allow the detection and correction of artifacts caused by endonuclease inhibitors, while simultaneously permitting copy number assessment of the locus of interest.
Results: With our novel approach, we correctly diagnosed the imprinting disorders Prader–Willi syndrome and Angelman syndrome in 35 individuals by measuring methylation levels and copy numbers for the SNRPN (small nuclear ribonucleoprotein polypeptide N) promoter. We also demonstrated that the proposed correction model significantly (P < 0.05) increases the assay’s accuracy with low-quality DNA, allowing analysis of DNA samples with decreased digestibility, as is often the case in retrospective studies.
Conclusions: Our novel DNA methylation assay reduces both the hands-on time and errors caused by handling and pipetting and allows methylation analyses to be completed within 90 min after DNA extraction. Combined with its precision and reliability, these features make the assay well suited for diagnostic procedures as well as high-throughput analyses.
Collapse
Affiliation(s)
- Thomas von Kanel
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Dominik Gerber
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - André Schaller
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Alessandra Baumer
- Institute for Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Eva Wey
- Institute for Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Christopher B Jackson
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Franziska M Gisler
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Karl Heinimann
- Division of Medical Genetics, University Children’s Hospital and Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sabina Gallati
- Division of Human Genetics, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| |
Collapse
|
23
|
Couldrey C, Lee RS. DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming. BMC DEVELOPMENTAL BIOLOGY 2010; 10:27. [PMID: 20205951 PMCID: PMC2848150 DOI: 10.1186/1471-213x-10-27] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 03/07/2010] [Indexed: 01/03/2023]
Abstract
BACKGROUND Cloning of cattle by somatic cell nuclear transfer (SCNT) is associated with a high incidence of pregnancy failure characterized by abnormal placental and foetal development. These abnormalities are thought to be due, in part, to incomplete re-setting of the epigenetic state of DNA in the donor somatic cell nucleus to a state that is capable of driving embryonic and foetal development to completion. Here, we tested the hypothesis that DNA methylation patterns were not appropriately established during nuclear reprogramming following SCNT. A panel of imprinted, non-imprinted genes and satellite repeat sequences was examined in tissues collected from viable and failing mid-gestation SCNT foetuses and compared with similar tissues from gestation-matched normal foetuses generated by artificial insemination (AI). RESULTS Most of the genomic regions examined in tissues from viable and failing SCNT foetuses had DNA methylation patterns similar to those in comparable tissues from AI controls. However, statistically significant differences were found between SCNT and AI at specific CpG sites in some regions of the genome, particularly those associated with SNRPN and KCNQ1OT1, which tended to be hypomethylated in SCNT tissues. There was a high degree of variation between individuals in methylation levels at almost every CpG site in these two regions, even in AI controls. In other genomic regions, methylation levels at specific CpG sites were tightly controlled with little variation between individuals. Only one site (HAND1) showed a tissue-specific pattern of DNA methylation. Overall, DNA methylation patterns in tissues of failing foetuses were similar to apparently viable SCNT foetuses, although there were individuals showing extreme deviant patterns. CONCLUSION These results show that SCNT foetuses that had developed to mid-gestation had largely undergone nuclear reprogramming and that the epigenetic signature at this stage was not a good predictor of whether the foetus would develop to term or not.
Collapse
Affiliation(s)
- Christine Couldrey
- AgResearch, Reproductive Technologies Group, Ruakura Research Centre, East Street, Private Bag 3123, Hamilton, New Zealand
| | | |
Collapse
|
24
|
Oberacher H. Frontiers of mass spectrometry in nucleic acids analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:351-365. [PMID: 20530841 DOI: 10.1255/ejms.1045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Nucleic acids research is a highly competitive field of research. A number of well established methods are available. The current output of high throughput ("next generation") sequencing technologies is impressive, and still technologies are continuing to make progress regarding read lengths, bp per second, accuracy and costs. Although in the 1990s MS was considered as an analytical platform for sequencing, it was soon realized that MS will never be competitive. Thus, the focus shifted from de novo sequencing towards other areas of application where MS has proven to be a powerful analytical tool. Potential niches for the application of MS in nucleic acids research include genotyping of genetic markers (single nucleotide polymorphisms, short tandem repeats, and combinations thereof), quality control of synthetic oligonucleotides, metabolic profiling of therapeutics, characterization of modified nucleobases in DNA and RNA molecules, and the study of non covalent interactions among nucleic acids as well as interactions of nucleic acids with drugs and proteins. The diversity of possible applications for MS highlights its significance for nucleic acid research.
Collapse
Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
| |
Collapse
|
25
|
Dehan P, Kustermans G, Guenin S, Horion J, Boniver J, Delvenne P. DNA methylation and cancer diagnosis: new methods and applications. Expert Rev Mol Diagn 2009; 9:651-7. [PMID: 19817550 DOI: 10.1586/erm.09.53] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Methylation of cytosines in cytosine-guanine (CpG) dinucleotides is one of the most important epigenetic alterations in animals. The presence of methylcytosine in the promoter of specific genes has profound consequences on local chromatin structure and on the regulation of gene expression. Changes in DNA methylation play a central role in carcinogenesis. Hypermethylation and consecutive transcriptional silencing of tumor-suppressor genes has been documented in numerous cancers. The identification of target genes silenced by this modification has a great impact on diagnosis, classification, definition of risk groups and prognosis of cancer patients. Here we outline genome-wide techniques aiming at the identification of relevant methylated promoters. Methods and applications allowing clinicians to monitor the methylation of target genes will be also reviewed.
Collapse
Affiliation(s)
- Pierre Dehan
- Experimental Pathology, University of Liege, CHU Sart-Tilman, Boulevard de l'Hopital, 4000 Liege, Belgium.
| | | | | | | | | | | |
Collapse
|
26
|
Affiliation(s)
- Tomasz K Wojdacz
- Human Genetics Institute, University of Aarhus, Wilhelm Meyers Alle 240, DK-8000 Aarhus C, Denmark
| |
Collapse
|
27
|
Kristensen LS, Hansen LL. PCR-based methods for detecting single-locus DNA methylation biomarkers in cancer diagnostics, prognostics, and response to treatment. Clin Chem 2009; 55:1471-83. [PMID: 19520761 DOI: 10.1373/clinchem.2008.121962] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND DNA methylation is a highly characterized epigenetic modification of the human genome that is implicated in cancer. The altered DNA methylation patterns found in cancer cells include not only global hypomethylation but also discrete hypermethylation of specific genes. In particular, numerous tumor suppressor genes undergo epigenetic silencing because of hypermethylated promoter regions. Some of these genes are considered promising DNA methylation biomarkers for early cancer diagnostics, and some have been shown to be valuable for predicting prognosis or the response to therapy. CONTENT PCR-based methods that use sodium bisulfite-treated DNA as a template are generally accepted as the most analytically sensitive and specific techniques for analyzing DNA methylation at single loci. A number of new methods, such as methylation-specific fluorescent amplicon generation (MS-FLAG), methylation-sensitive high-resolution melting (MS-HRM), and sensitive melting analysis after real-time methylation-specific PCR (SMART-MSP), now complement the traditional PCR-based methods and promise to be valuable diagnostic tools. In particular, the HRM technique shows great potential as a diagnostic tool because of its closed-tube format and cost-effectiveness. SUMMARY Numerous traditional and new PCR-based methods have been developed for detecting DNA methylation at single loci. All have characteristic advantages and disadvantages, particularly with regard to use in clinical settings.
Collapse
|
28
|
Oeth P, del Mistro G, Marnellos G, Shi T, van den Boom D. Qualitative and quantitative genotyping using single base primer extension coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MassARRAY). Methods Mol Biol 2009; 578:307-43. [PMID: 19768603 DOI: 10.1007/978-1-60327-411-1_20] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has developed over the past decade into a versatile tool for the analysis of nucleic acids and especially as a reliable genotyping platform. This chapter summarizes its use in the context of the most widely used MALDI-TOF MS genomics platform, the Sequenom MassARRAY system. MassARRAY genotyping is based upon region-specific PCR followed by allele-specific single base primer extension reactions which are then desalted, dispensed onto a silica array preloaded with matrix, and the genotyping products are resolved on the basis of mass using MALDI-TOF MS. The platform is versatile in that it can resolve multiplexed reactions (40+ separate loci per reaction), acquires and interprets data quickly, gives a quantitative output which reflects the amount of product generated for each allele within an assay for multiplexed reactions, and is highly sensitive. These characteristics coupled with integrated software for sequence annotation, assay design, data interpretation, and data storage have lead to its wide adoption and use for multiple nucleic acid analysis applications in both the realm of genomics research and molecular diagnostics.
Collapse
Affiliation(s)
- Paul Oeth
- Research and Development, Sequenom, Inc, San Diego, CA, USA
| | | | | | | | | |
Collapse
|