1
|
Lin X, Dai Y, Gu W, Zhang Y, Zhuo F, Zhao F, Jin X, Li C, Huang D, Tong X, Zhang S. The involvement of RNA N6-methyladenosine and histone methylation modification in decidualization and endometriosis-associated infertility. Clin Transl Med 2024; 14:e1564. [PMID: 38344897 PMCID: PMC10859880 DOI: 10.1002/ctm2.1564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/18/2023] [Accepted: 01/14/2024] [Indexed: 02/15/2024] Open
Abstract
Defective decidualization of endometrial stromal cells (ESCs) in endometriosis (EM) patients leads to inadequate endometrial receptivity and EM-associated infertility. Hypoxia is an inevitable pathological process of EM and participates in deficient decidualization of the eutopic secretory endometrium. Enhancer of zeste homology 2 (EZH2) is a methyltransferase which catalyses H3K27Me3, leading to decreased expression levels of target genes. Although EZH2 expression is low under normal decidualization, it is abundantly increased in the eutopic secretory endometrium of EM and is induced by hypoxia. Chromatin immunoprecipitation-PCR results revealed that decidua marker IGFBP1 is a direct target of EZH2, partially explaining the increased levels of histone methylation modification in defected decidualization of EM. To mechanism controlling this, we examined the effects of hypoxia on EZH2 and decidualization. EZH2 mRNA showed decreased m6 A modification and increased expression levels under hypoxia and decidualization combined treatment. Increased EZH2 expression was due to the increased expression of m6 A demethylase ALKBH5 and decreased expression of the m6 A reader protein YTHDF2. YTHDF2 directly bind to the m6 A modification site of EZH2 to promote EZH2 mRNA degradation in ESCs. Moreover, selective Ezh2 depletion in mouse ESCs increased endometrial receptivity and improved mouse fertility by up-regulating decidua marker IGFBP1 expression. This is the first report showing that YTHDF2 can act as a m6 A reader to promote decidualization by decreasing the stability of EZH2 mRNA and further increasing the expression of IGFBP1 in ESCs. Taken together, our findings highlight the critical role of EZH2/H3K27Me3 in decidualization and reveal a novel epigenetic mechanism by which hypoxia can suppress EM decidualization by decreasing the m6 A modification of EZH2 mRNA.
Collapse
Affiliation(s)
- Xiang Lin
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang ProvinceHangzhouChina
| | - Yongdong Dai
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang ProvinceHangzhouChina
| | - Weijia Gu
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Yi Zhang
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Feng Zhuo
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang ProvinceHangzhouChina
| | - Fanxuan Zhao
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Xiaoying Jin
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang ProvinceHangzhouChina
| | - Chao Li
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang ProvinceHangzhouChina
| | - Dong Huang
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang ProvinceHangzhouChina
| | - Xiaomei Tong
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang ProvinceHangzhouChina
| | - Songying Zhang
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang ProvinceHangzhouChina
| |
Collapse
|
2
|
Vanhorebeek I, Coppens G, Güiza F, Derese I, Wouters PJ, Joosten KF, Verbruggen SC, Van den Berghe G. Abnormal DNA methylation within genes of the steroidogenesis pathway two years after paediatric critical illness and association with stunted growth in height further in time. Clin Epigenetics 2023; 15:116. [PMID: 37468957 PMCID: PMC10354984 DOI: 10.1186/s13148-023-01530-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Former critically ill children show an epigenetic age deceleration 2 years after paediatric intensive care unit (PICU) admission as compared with normally developing healthy children, with stunted growth in height 2 years further in time as physical correlate. This was particularly pronounced in children who were 6 years or older at the time of critical illness. As this age roughly corresponds to the onset of adrenarche and further pubertal development, a relation with altered activation of endocrine pathways is plausible. We hypothesised that children who have been admitted to the PICU, sex- and age-dependently show long-term abnormal DNA methylation within genes involved in steroid hormone synthesis or steroid sulphation/desulphation, possibly aggravated by in-PICU glucocorticoid treatment, which may contribute to stunted growth in height further in time after critical illness. RESULTS In this preplanned secondary analysis of the multicentre PEPaNIC-RCT and its follow-up, we compared the methylation status of genes involved in the biosynthesis of steroid hormones (aldosterone, cortisol and sex hormones) and steroid sulphation/desulphation in buccal mucosa DNA (Infinium HumanMethylation EPIC BeadChip) from former PICU patients at 2-year follow-up (n = 818) and healthy children with comparable sex and age (n = 392). Adjusting for technical variation and baseline risk factors and corrected for multiple testing (false discovery rate < 0.05), former PICU patients showed abnormal DNA methylation of 23 CpG sites (within CYP11A1, POR, CYB5A, HSD17B1, HSD17B2, HSD17B3, HSD17B6, HSD17B10, HSD17B12, CYP19A1, CYP21A2, and CYP11B2) and 4 DNA regions (within HSD17B2, HSD17B8, and HSD17B10) that were mostly hypomethylated. These abnormalities were partially sex- (1 CpG site) or age-dependent (7 CpG sites) and affected by glucocorticoid treatment (3 CpG sites). Finally, multivariable linear models identified robust associations of abnormal methylation of steroidogenic genes with shorter height further in time, at 4-year follow-up. CONCLUSIONS Children who have been critically ill show abnormal methylation within steroidogenic genes 2 years after PICU admission, which explained part of the stunted growth in height at 4-year follow-up. The abnormalities in DNA methylation may point to a long-term disturbance in the balance between active sex steroids and mineralocorticoids/glucocorticoids after paediatric critical illness, which requires further investigation.
Collapse
Affiliation(s)
- Ilse Vanhorebeek
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, Louvain, Herestraat 49, B-3000, Leuven, Belgium
| | - Grégoire Coppens
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, Louvain, Herestraat 49, B-3000, Leuven, Belgium
| | - Fabian Güiza
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, Louvain, Herestraat 49, B-3000, Leuven, Belgium
| | - Inge Derese
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, Louvain, Herestraat 49, B-3000, Leuven, Belgium
| | - Pieter J Wouters
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, Louvain, Herestraat 49, B-3000, Leuven, Belgium
| | - Koen F Joosten
- Division of Paediatric ICU, Department of Neonatal and Paediatric ICU, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Sascha C Verbruggen
- Division of Paediatric ICU, Department of Neonatal and Paediatric ICU, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Greet Van den Berghe
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, Louvain, Herestraat 49, B-3000, Leuven, Belgium.
| |
Collapse
|
3
|
Dong X, Zhou M, Li X, Huang H, Sun Y. Gene profiling reveals the role of inflammation, abnormal uterine muscle contraction and vascularity in recurrent implantation failure. Front Genet 2023; 14:1108805. [PMID: 36911409 PMCID: PMC9998698 DOI: 10.3389/fgene.2023.1108805] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
Objective: Recurrent implantation failure (RIF) is now disturbing numerous infertile couples accepting assisted reproductive technology (ART). And the endometrial factors are crucial causes of recurrent implantation failure. However, its mechanism is still unclear. Thus, the aim of this study is to identify altered biologic processes in endometrium that may contribute to recurrent implantation failure. Methods: We recruited two microarray datasets (GSE103465, GSE111974) from Gene Expression Omnibus database (GEO), which contain endometrium from RIF and normal women during implantation period. Using the online tools GEO2R and Venny, we identified Differentially Expressed Genes (DEGs) of selected datasets, and obtained common DEGs. Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) and BioCatar pathway enrichment were conducted with Enrichr platform, "ssgsea" and "ggplot2" package of RStudio. PPI networks and hub gene related TF-gene interaction and TF-miRNA co-regulation networks were built via online tools STRING and NetworkAnalyst. Immune infiltration analysis was performed by CIBERSORT platform. Recurrent implantation failure subgroup identification was achieved through "ConsensusClusterPlus," "tsne," "ssgsea", and "ggpubr" package in RStudio. Diagnostic characteristic ROC curves were constructed via "pROC" and "ggplot2" package of RStudio. Enrichr platform was utilized to find drugs targeting hub genes. Results: 26 common DEGs were confirmed. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes/BioCarta analysis determined common DEGs were mainly enriched in inflammation associated pathways including TNF, NF-κB, IL-4, IL-10, IL-6, and TGF-β signaling pathways. Five hub genes (PTGS2, VCAM1, EDNRB, ACTA2, and LIF) and related TF-gene and TF-miRNA interactions were identified. Immune infiltration analysis indicated the importance of macrophage M2 in recurrent implantation failure patients. Importantly, subgroup identification analysis highlighted that recurrent implantation failure patients can be divided into two subgroups with different phenotypes. Moreover, the ROC curves and drugs may provide new diagnostic and therapeutic thought for recurrent implantation failure.
Collapse
Affiliation(s)
- Xinyi Dong
- Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Mi Zhou
- Department of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xinyu Li
- Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Huijing Huang
- Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yun Sun
- Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| |
Collapse
|
4
|
Lei L, Xu X, Gong C, Lin B, Li F. Integrated analysis of genome-wide gene expression and DNA methylation profiles reveals candidate genes in ovary endometriosis. Front Endocrinol (Lausanne) 2023; 14:1093683. [PMID: 37033258 PMCID: PMC10076879 DOI: 10.3389/fendo.2023.1093683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/10/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND The incidence of endometriosis (EMs), a common disease in gynecology, has increased over the years. Women suffer from the symptoms caused by EMs, such as chronic pelvic pain, dysmenorrhea, and infertility. However, the etiology and pathophysiology of EMs remain unclear. This study aimed to identify candidate genes of endometriosis through integrated analysis of genome-wide gene expression and DNA methylation profiles. RESULTS Eutopic and ectopic endometrial tissues were collected from patients who were diagnosed as ovarian EMs. Genome-wide methylation profiling identified 17551 differentially methylated loci, with 9777 hypermethylated and 7774 hypomethylated loci. Differentially methylated loci were mainly concentrated in the gene body and intergenic regions. Genome-wide gene expression profiling identified 1837 differentially expressed genes (DEGs), with 1079 genes upregulated and 758 downregulated in ectopic groups. Integrated analysis revealed that DNA methylation was negatively correlated to gene expression in most genomic regions, such as exon, 3'UTR, 5'UTR, and promoter. We also identified promoter-related (53 downregulated and 113 upregulated) and enhancer-related DMGs (212 downregulated and 232 upregulated), which were significantly correlated to the gene expression. Further validation of the top-ranked genes belonging to differentially methylated genes (DMGs) and DEGs revealed that TMEM184A, GREM2, SFN, KIR3DX1, HPGD, ESR1, BST2, PIK3CG and RNASE1 were significant candidate genes in ovarian endometriosis. CONCLUSION Our study revealed the significance of DNA methylation in the gene expression in ovary endometriosis, which provides new insights and a molecular foundation for understanding the underlying mechanisms of endometriosis.
Collapse
Affiliation(s)
- Lei Lei
- Department of Gynecology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xinxin Xu
- Department of Gynecology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chengchen Gong
- Department of Dermatology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bowen Lin
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Fang Li, ; Bowen Lin,
| | - Fang Li
- Department of Gynecology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Fang Li, ; Bowen Lin,
| |
Collapse
|
5
|
Li J, He Y, Liang T, Wang J, Jiang X, Zhang G. Identification of potential differentially methylated gene-related biomarkers in endometriosis. Epigenomics 2022; 14:1157-1179. [DOI: 10.2217/epi-2022-0249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To identify epigenetic alterations of differentially expressed genes and screen out targeted therapeutic drugs in endometriosis. Methods: Based on the Gene Expression Omnibus database and a series of biological information analysis tools, supplemented by validation of clinical samples, aberrant DNA methylation-driven genes and their functions were explored, as well as possible targeted drugs. Results: This study screened out a range of DNA methylation-driven genes that were associated with powerful properties and corresponding pathways. Among them, BDNF and CCL2 were key genes in the development of endometriosis. Four chemical agents have been flagged as potential treatments for endometriosis. Conclusion: These candidate genes and small-molecule agents may be further explored as potential targets and drugs for endometriosis diagnosis and therapy, respectively.
Collapse
Affiliation(s)
- Jixin Li
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 15000, China
| | - Yanan He
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 15000, China
| | - Tian Liang
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 15000, China
| | - Jing Wang
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 15000, China
| | - Xinyan Jiang
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 15000, China
| | - Guangmei Zhang
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 15000, China
| |
Collapse
|
6
|
Irimia T, Pușcașiu L, Mitranovici MI, Crișan A, Budianu MA, Bănescu C, Chiorean DM, Niculescu R, Sabău AH, Cocuz IG, Cotoi OS. Oxidative-Stress Related Gene Polymorphism in Endometriosis-Associated Infertility. Medicina (Kaunas) 2022; 58. [PMID: 36013572 DOI: 10.3390/medicina58081105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022]
Abstract
Background and Objectives: Endometriosis is a benign inflammatory disease associated with infertility and chronic pelvic pain, estimated to affect 7−10% of reproductive-age women, with the possibility of malignant transformation. Recent studies focus on oxidative stress and genetic mutations as risk factors in the pathophysiology of endometriosis-associated infertility. Materials and Methods: This case-control study is the first in Eastern European women that aimed to investigate four genes’ genetic polymorphisms that encode antioxidant enzymes involved in oxidative stress (glutathione peroxidase 1, GPX1 198Pro > Leu, catalase CAT-262C > T, glutathione S-transferase M1, and T1 null genotype) and their association with endometriosis-related infertility. We compared 103 patients with endometriosis-associated infertility with 102 post-partum women as the control group. Results: The endometriosis group had a mean age of 34.5 +/− 6.12 years, while the control group’s mean age was 35.03 +/− 5.95 years. For CAT-262C > T polymorphism, the variant genotypes were significantly more frequent in the endometriosis group. Moreover, for the GPX1 198Pro > Leu, the endometriosis group had significantly more frequent CT and TT genotypes. The null genotype of GSTM1 was detected significantly higher in the endometriosis group. No significant differences were found in the frequency of GSTT1 between the two groups. This study suggests that GPX1 198Pro > Leu, CAT-262C > T, and GSTM1 polymorphisms may be risk factors and that the association between the GSTM1-GSTT1 null genotype may play a significant role in endometriosis-associated infertility. Moreover, this study suggests that the GSTT1 null genotype does not influence the disease. Visual identification of endometriotic lesions with microscopic confirmation is the accepted gold standard for diagnosing endometriosis, but general anesthesia and laparoscopy are required. Conclusions: In this regard, a panel of genetic or laboratory markers is needed for the early diagnostics of this prevalent disease, especially in the case of young patients with future pregnancy intention.
Collapse
|