Genome-wide DNA methylation and gene expression patterns provide insight into polycystic ovary syndrome development

Abstract STUDY QUESTION Does imprinted DNA methylation or imprinted gene expression differ between human blastocysts from conventional ovarian stimulation (COS) and an optimized two-step IVM method (CAPA-IVM) in age-matched polycystic ovary syndrome (PCOS) patients? SUMMARY ANSWER No significant differences in imprinted DNA methylation and gene expression were detected between COS and CAPA-IVM blastocysts. WHAT IS KNOWN ALREADY Animal models have revealed alterations in DNA methylation maintenance at imprinted germline differentially methylated regions (gDMRs) after use of ARTs. This effect increases as more ART interventions are applied to oocytes or embryos. IVM is a minimal-stimulation ART with reduced hormone-related side effects and risks for patients. CAPA-IVM is an improved IVM system that includes a pre-maturation step (CAPA), followed by an IVM step, both in the presence of physiological compounds that promote oocyte developmental capacity. STUDY DESIGN, SIZE, DURATION For DNA methylation analysis 20 CAPA-IVM blastocysts were compared to 12 COS blastocysts. For RNA-Seq analysis a separate set of 15 CAPA-IVM blastocysts were compared to 5 COS blastocysts. PARTICIPANTS/MATERIALS, SETTING, METHODS COS embryos originated from 12 patients with PCOS (according to Rotterdam criteria) who underwent conventional ovarian stimulation. For CAPA-IVM 23 women were treated for 3–5 days with highly purified hMG (HP-hMG) and no hCG trigger was given before oocyte retrieval. Oocytes were first cultured in pre-maturation medium (CAPA for 24 h containing C-type natriuretic peptide), followed by an IVM step (30 h) in medium containing FSH and Amphiregulin. After ICSI, Day 5 or 6 embryos in both groups were vitrified and used for post-bisulphite adaptor tagging (PBAT) DNA methylation analysis or RNA-seq gene expression analysis of individual embryos. Data from specific genes and gDMRs were extracted from the PABT and RNA-seq datasets. MAIN RESULTS AND THE ROLE OF CHANCE CAPA-IVM blastocysts showed similar rates of methylation and gene expression at gDMRs compared to COS embryos. In addition, expression of major epigenetic regulators was similar between the groups. LIMITATIONS, REASONS FOR CAUTION The embryos from the COS group were generated in a range of culture media. The CAPA-IVM embryos were all generated using the same sperm donor. The DNA methylation level of gDMRs in purely in vivo-derived human blastocysts is not known. WIDER IMPLICATIONS OF THE FINDINGS A follow-up of children born after CAPA-IVM is important as it is for other new ARTs, which are generally introduced into clinical practice without prior epigenetic safety studies on human blastocysts. CAPA-IVM opens new perspectives for patient-friendly ART in PCOS STUDY FUNDING/COMPETING INTEREST(S) IVM research at the Vrije Universiteit Brussel has been supported by grants from the Institute for the Promotion of Innovation by Science and Technology in Flanders (Agentschap voor Innovatie door Wetenschap en Technologie-IWT, project 110680), the Fund for Research Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen-FWO-AL 679 project, project G.0343.13), the Belgian Foundation Against Cancer (HOPE project, Dossier C69Ref Nr 2016-119) and the Vrije Universiteit Brussel (IOF Project 4R-ART Nr 2042). Work in G.K.’s laboratory is supported by the UK Biotechnology and Biological Sciences Research Council and Medical Research Council. The authors have no conflicts of interest.

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Bisphenol A-associated alterations in genome-wide DNA methylation and gene expression patterns reveal sequence-dependent and non-monotonic effects in human fetal liver

Environmental Epigenetics ◽

10.1093/eep/dvv006 ◽

2015 ◽

Vol 1 (1) ◽

pp. dvv006 ◽

Cited By ~ 33

Author(s):

Christopher Faulk ◽

Jung H. Kim ◽

Tamara R. Jones ◽

Richard C. McEachin ◽

Muna S. Nahar ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Bisphenol A ◽

Fetal Liver ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Human Fetal Liver ◽

Sequence Dependent ◽

Genome Wide

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Comprehensive analysis of genome-wide DNA methylation across human polycystic ovary syndrome ovary granulosa cell

Oncotarget ◽

10.18632/oncotarget.8544 ◽

2016 ◽

Vol 7 (19) ◽

pp. 27899-27909 ◽

Cited By ~ 18

Author(s):

Jiawei Xu ◽

Xiao Bao ◽

Zhaofeng Peng ◽

Linlin Wang ◽

Linqing Du ◽

...

Keyword(s):

Dna Methylation ◽

Polycystic Ovary Syndrome ◽

Granulosa Cell ◽

Polycystic Ovary ◽

Comprehensive Analysis ◽

Ovary Syndrome ◽

Genome Wide

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Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago

PLoS Genetics ◽

10.1371/journal.pgen.1008749 ◽

2020 ◽

Vol 16 (5) ◽

pp. e1008749 ◽

Cited By ~ 3

Author(s):

Heini M. Natri ◽

Katalina S. Bobowik ◽

Pradiptajati Kusuma ◽

Chelzie Crenna Darusallam ◽

Guy S. Jacobs ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Expression Patterns ◽

Genetic Ancestry ◽

Gene Expression Patterns ◽

Indonesian Archipelago ◽

Genome Wide

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Genome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells

Oncotarget ◽

10.18632/oncotarget.4925 ◽

2015 ◽

Vol 6 (29) ◽

pp. 26729-26745 ◽

Cited By ~ 34

Author(s):

Adil El Taghdouini ◽

Anita L. Sørensen ◽

Andrew H. Reiner ◽

Mar Coll ◽

Stefaan Verhulst ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Hepatic Stellate Cells ◽

Human Liver ◽

Expression Patterns ◽

Stellate Cells ◽

Gene Expression Patterns ◽

Genome Wide Analysis ◽

Human Liver Cells ◽

Genome Wide

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Transcriptional and Epigenetic Changes Influencing Skeletal Muscle Metabolism in Women With Polycystic Ovary Syndrome

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jc.2018-00935 ◽

2018 ◽

Vol 103 (12) ◽

pp. 4465-4477 ◽

Cited By ~ 18

Author(s):

Emma Nilsson ◽

Anna Benrick ◽

Milana Kokosar ◽

Anna Krook ◽

Eva Lindgren ◽

...

Keyword(s):

Gene Expression ◽

Insulin Resistance ◽

Skeletal Muscle ◽

Dna Methylation ◽

Polycystic Ovary Syndrome ◽

Mrna Expression ◽

Polycystic Ovary ◽

Differentially Expressed ◽

Ovary Syndrome ◽

Cpg Sites

Abstract Context Insulin resistance in skeletal muscle is a major risk factor for the development of type 2 diabetes in women with polycystic ovary syndrome (PCOS). Despite this, the mechanisms underlying insulin resistance in PCOS are largely unknown. Objective To investigate the genome-wide DNA methylation and gene expression patterns in skeletal muscle from women with PCOS and controls and relate them to phenotypic variations. Design/Participants In a case-control study, skeletal muscle biopsies from women with PCOS (n = 17) and age-, weight-, and body mass index‒matched controls (n = 14) were analyzed by array-based DNA methylation and mRNA expression profiling. Results Eighty-five unique transcripts were differentially expressed in muscle from women with PCOS vs controls, including DYRK1A, SYNPO2, SCP2, and NAMPT. Furthermore, women with PCOS had reduced expression of genes involved in immune system pathways. Two CpG sites showed differential DNA methylation after correction for multiple testing. However, an mRNA expression of ∼30% of the differentially expressed genes correlated with DNA methylation levels of CpG sites in or near the gene. Functional follow-up studies demonstrated that KLF10 is under transcriptional control of insulin, where insulin promotes glycogen accumulation in myotubes of human muscle cells. Testosterone downregulates the expression levels of COL1A1 and MAP2K6. Conclusion PCOS is associated with aberrant skeletal muscle gene expression with dysregulated pathways. Furthermore, we identified specific changes in muscle DNA methylation that may affect gene expression. This study showed that women with PCOS have epigenetic and transcriptional changes in skeletal muscle that, in part, can explain the metabolic abnormalities seen in these women.

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Genome-wide screen of ovary-specific DNA methylation in polycystic ovary syndrome

Fertility and Sterility ◽

10.1016/j.fertnstert.2015.04.005 ◽

2015 ◽

Vol 104 (1) ◽

pp. 145-153.e6 ◽

Cited By ~ 33

Author(s):

Ying-Ying Yu ◽

Cui-Xiang Sun ◽

Yin-Kun Liu ◽

Yan Li ◽

Li Wang ◽

...

Keyword(s):

Dna Methylation ◽

Polycystic Ovary Syndrome ◽

Polycystic Ovary ◽

Ovary Syndrome ◽

Genome Wide

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Faculty Opinions recommendation of Genome-wide excision repair in Arabidopsis is coupled to transcription and reflects circadian gene expression patterns.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.733074375.793569726 ◽

2020 ◽

Author(s):

Alex Webb

Keyword(s):

Gene Expression ◽

Excision Repair ◽

Expression Patterns ◽

Wide Excision ◽

Gene Expression Patterns ◽

Circadian Gene ◽

Genome Wide

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Sterol regulatory element binding protein-1 (SREBP1) gene expression is similarly increased in polycystic ovary syndrome and endometrial cancer

Acta Obstetricia Et Gynecologica Scandinavica ◽

10.1111/aogs.13106 ◽

2017 ◽

Vol 96 (5) ◽

pp. 556-562 ◽

Cited By ~ 7

Author(s):

Mohamad N. Shafiee ◽

Nigel Mongan ◽

Claire Seedhouse ◽

Caroline Chapman ◽

Suha Deen ◽

...

Keyword(s):

Gene Expression ◽

Endometrial Cancer ◽

Polycystic Ovary Syndrome ◽

Polycystic Ovary ◽

Binding Protein ◽

Regulatory Element ◽

Ovary Syndrome ◽

Element Binding Protein ◽

Sterol Regulatory Element

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Gene expression profiling of epigenetic chromatin modification enzymes and histone marks by cigarette smoke: implications for COPD and lung cancer

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.00253.2016 ◽

2016 ◽

Vol 311 (6) ◽

pp. L1245-L1258 ◽

Cited By ~ 19

Author(s):

Isaac K. Sundar ◽

Irfan Rahman

Keyword(s):

Gene Expression ◽

Lung Cancer ◽

Dna Methylation ◽

Cigarette Smoke ◽

Histone Modifications ◽

Expression Patterns ◽

Chromatin Modification ◽

Gene Expression Patterns ◽

Validation Data ◽

Histone Marks

Chromatin-modifying enzymes mediate DNA methylation and histone modifications on recruitment to specific target gene loci in response to various stimuli. The key enzymes that regulate chromatin accessibility for maintenance of modifications in DNA and histones, and for modulation of gene expression patterns in response to cigarette smoke (CS), are not known. We hypothesize that CS exposure alters the gene expression patterns of chromatin-modifying enzymes, which then affects multiple downstream pathways involved in the response to CS. We have, therefore, analyzed chromatin-modifying enzyme profiles and validated by quantitative real-time PCR (qPCR). We also performed immunoblot analysis of targeted histone marks in C57BL/6J mice exposed to acute and subchronic CS, and of lungs from nonsmokers, smokers, and patients with chronic obstructive pulmonary disease (COPD). We found a significant increase in expression of several chromatin modification enzymes, including DNA methyltransferases, histone acetyltransferases, histone methyltransferases, and SET domain proteins, histone kinases, and ubiquitinases. Our qPCR validation data revealed a significant downregulation of Dnmt1, Dnmt3a, Dnmt3b, Hdac2, Hdac4, Hat1, Prmt1, and Aurkb. We identified targeted chromatin histone marks (H3K56ac and H4K12ac), which are induced by CS. Thus CS-induced genotoxic stress differentially affects the expression of epigenetic modulators that regulate transcription of target genes via DNA methylation and site-specific histone modifications. This may have implications in devising epigenetic-based therapies for COPD and lung cancer.

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