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Verma A, Poondi Krishnan V, Cecere F, D’Angelo E, Lullo V, Strazzullo M, Selig S, Angelini C, Matarazzo MR, Riccio A. ICF1-Syndrome-Associated DNMT3B Mutations Prevent De Novo Methylation at a Subset of Imprinted Loci during iPSC Reprogramming. Biomolecules 2023; 13:1717. [PMID: 38136588 PMCID: PMC10741953 DOI: 10.3390/biom13121717] [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: 08/02/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Parent-of-origin-dependent gene expression of a few hundred human genes is achieved by differential DNA methylation of both parental alleles. This imprinting is required for normal development, and defects in this process lead to human disease. Induced pluripotent stem cells (iPSCs) serve as a valuable tool for in vitro disease modeling. However, a wave of de novo DNA methylation during reprogramming of iPSCs affects DNA methylation, thus limiting their use. The DNA methyltransferase 3B (DNMT3B) gene is highly expressed in human iPSCs; however, whether the hypermethylation of imprinted loci depends on DNMT3B activity has been poorly investigated. To explore the role of DNMT3B in mediating de novo DNA methylation at imprinted DMRs, we utilized iPSCs generated from patients with immunodeficiency, centromeric instability, facial anomalies type I (ICF1) syndrome that harbor biallelic hypomorphic DNMT3B mutations. Using a whole-genome array-based approach, we observed a gain of methylation at several imprinted loci in control iPSCs but not in ICF1 iPSCs compared to their parental fibroblasts. Moreover, in corrected ICF1 iPSCs, which restore DNMT3B enzymatic activity, imprinted DMRs did not acquire control DNA methylation levels, in contrast to the majority of the hypomethylated CpGs in the genome that were rescued in the corrected iPSC clones. Overall, our study indicates that DNMT3B is responsible for de novo methylation of a subset of imprinted DMRs during iPSC reprogramming and suggests that imprinting is unstable during a specific time window of this process, after which the epigenetic state at these regions becomes resistant to perturbation.
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Affiliation(s)
- Ankit Verma
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Varsha Poondi Krishnan
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
| | - Emilia D’Angelo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
| | - Vincenzo Lullo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Maria Strazzullo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Sara Selig
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel;
- Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa 31096, Israel
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo “Mauro Picone”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy;
| | - Maria R. Matarazzo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
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Fan W, Xiong R, Zhou Z, Zhang C, Han Y, Shi T, Qiu J, Zhang R. ZFP57 promotes ovarian cancer progression by transcriptionally regulating BRCA1 and managing G1 checkpoint. J Cancer 2023; 14:2039-2050. [PMID: 37497403 PMCID: PMC10367923 DOI: 10.7150/jca.84601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/12/2023] [Indexed: 07/28/2023] Open
Abstract
Ovarian cancer (OC) which is one of the frequently-occurring gynecologic malignant tumors, endangers the health of women. The zinc finger protein 57 (ZFP57) plays crucial functions during the progression of cancer and is reported as a prognostic and therapeutic candidate in a variety of cancer. However, the biological function as well as the underlying mechanism of ZFP57 during OC progression remains unknown. Here, ZFP57 expression was found prominently increased in OC tissues and correlated with the prognosis of OC patients. Knock down of ZFP57 in OC cells inhibited the cell proliferation and migration, and also arrested the cells at G1 phase as well as accelerated the apoptosis. Additionally, ZFP57 transcriptionally regulated BRCA1 expression in OC, indicating that ZFP57 may affect BRCA1 mediated G1 checkpoint to regulate the cell cycle of OC cells and further influence the progression of OC. Taken together, our present study discovered a novel function of ZFP57 in OC, suggesting that ZFP57 could be potentially treated as a prognostic biomarker and therapeutic target for OC patients.
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Affiliation(s)
- Weirong Fan
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Rui Xiong
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Ziyang Zhou
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Cancan Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Yanli Han
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Tingyan Shi
- Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianping Qiu
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Rong Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
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Raza Z, Hussain SF, Foster VS, Wall J, Coffey PJ, Martin JF, Gomes RSM. Exposure to war and conflict: The individual and inherited epigenetic effects on health, with a focus on post-traumatic stress disorder. FRONTIERS IN EPIDEMIOLOGY 2023; 3:1066158. [PMID: 38455905 PMCID: PMC10910933 DOI: 10.3389/fepid.2023.1066158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/03/2023] [Indexed: 03/09/2024]
Abstract
War and conflict are global phenomena, identified as stress-inducing triggers for epigenetic modifications. In this state-of-the-science narrative review based on systematic principles, we summarise existing data to explore the outcomes of these exposures especially in veterans and show that they may result in an increased likelihood of developing gastrointestinal, auditory, metabolic and circadian issues, as well as post-traumatic stress disorder (PTSD). We also note that, despite a potential "healthy soldier effect", both veterans and civilians with PTSD exhibit the altered DNA methylation status in hypothalamic-pituitary-adrenal (HPA) axis regulatory genes such as NR3C1. Genes associated with sleep (PAX8; LHX1) are seen to be differentially methylated in veterans. A limited number of studies also revealed hereditary effects of war exposure across groups: decreased cortisol levels and a heightened (sex-linked) mortality risk in offspring. Future large-scale studies further identifying the heritable risks of war, as well as any potential differences between military and civilian populations, would be valuable to inform future healthcare directives.
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Affiliation(s)
- Zara Raza
- Research & Innovation, Blind Veterans UK, London, United Kingdom
- BRAVO VICTOR, Research & Innovation, London, United Kingdom
- Hull York Medical School, University of York, York, United Kingdom
| | - Syeda F Hussain
- Research & Innovation, Blind Veterans UK, London, United Kingdom
- BRAVO VICTOR, Research & Innovation, London, United Kingdom
| | - Victoria S Foster
- Research & Innovation, Blind Veterans UK, London, United Kingdom
- BRAVO VICTOR, Research & Innovation, London, United Kingdom
- St George's Hospital Medical School, London, United Kingdom
| | - Joseph Wall
- Hull York Medical School, University of York, York, United Kingdom
- Haxby Group Hull, General Practice Surgery, Hull, United Kingdom
| | - Peter J Coffey
- Development, Ageing and Disease, UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - John F Martin
- Centre for Cardiovascular Biology and Medicine, University College London, London, United Kingdom
| | - Renata S M Gomes
- Research & Innovation, Blind Veterans UK, London, United Kingdom
- BRAVO VICTOR, Research & Innovation, London, United Kingdom
- Northern Hub for Veterans and Military Families Research, Department of Nursing, Midwifery and Health, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
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Acurzio B, Cecere F, Giaccari C, Verma A, Russo R, Valletta M, Hay Mele B, Angelini C, Chambery A, Riccio A. The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex. Epigenetics Chromatin 2022; 15:27. [PMID: 35918739 PMCID: PMC9344765 DOI: 10.1186/s13072-022-00462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022] Open
Abstract
Background Imprinting Control Regions (ICRs) are CpG-rich sequences acquiring differential methylation in the female and male germline and maintaining it in a parental origin-specific manner in somatic cells. Despite their expected high mutation rate due to spontaneous deamination of methylated cytosines, ICRs show conservation of CpG-richness and CpG-containing transcription factor binding sites in mammalian species. However, little is known about the mechanisms contributing to the maintenance of a high density of methyl CpGs at these loci. Results To gain functional insights into the mechanisms for maintaining CpG methylation, we sought to identify the proteins binding the methylated allele of the ICRs by determining the interactors of ZFP57 that recognizes a methylated hexanucleotide motif of these DNA regions in mouse ESCs. By using a tagged approach coupled to LC–MS/MS analysis, we identified several proteins, including factors involved in mRNA processing/splicing, chromosome organization, transcription and DNA repair processes. The presence of the post-replicative mismatch-repair (MMR) complex components MSH2 and MSH6 among the identified ZFP57 interactors prompted us to investigate their DNA binding profile by chromatin immunoprecipitation and sequencing. We demonstrated that MSH2 was enriched at gene promoters overlapping unmethylated CpG islands and at repeats. We also found that both MSH2 and MSH6 interacted with the methylated allele of the ICRs, where their binding to DNA was mediated by the ZFP57/KAP1 complex. Conclusions Our findings show that the MMR complex is concentrated on gene promoters and repeats in mouse ESCs, suggesting that maintaining the integrity of these regions is a primary function of highly proliferating cells. Furthermore, the demonstration that MSH2/MSH6 are recruited to the methylated allele of the ICRs through interaction with ZFP57/KAP1 suggests a role of the MMR complex in the maintenance of the integrity of these regulatory regions and evolution of genomic imprinting in mammalian species. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00462-7.
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Affiliation(s)
- Basilia Acurzio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Carlo Giaccari
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Ankit Verma
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Rosita Russo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Mariangela Valletta
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Bruno Hay Mele
- Department of Biology, Università Degli Studi Di Napoli "Federico II", 80126, Naples, Italy
| | - Claudia Angelini
- Istituto Per Le Applicazioni del Calcolo "Mauro Picone" (IAC), CNR, 80131, Naples, Italy
| | - Angela Chambery
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy. .,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy.
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Kojima S, Shiochi N, Sato K, Yamaura M, Ito T, Yamamura N, Goto N, Odamoto M, Kobayashi S, Kimura T, Sekita Y. Epigenome editing reveals core DNA methylation for imprinting control in the Dlk1-Dio3 imprinted domain. Nucleic Acids Res 2022; 50:5080-5094. [PMID: 35544282 PMCID: PMC9122602 DOI: 10.1093/nar/gkac344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/03/2022] [Accepted: 04/24/2022] [Indexed: 11/12/2022] Open
Abstract
The Dlk1-Dio3 imprinted domain is controlled by an imprinting control region (ICR) called IG-DMR that is hypomethylated on the maternal allele and hypermethylated on the paternal allele. Although several genetic mutation experiments have shown that IG-DMR is essential for imprinting control of the domain, how DNA methylation itself functions has not been elucidated. Here, we performed both gain and loss of DNA methylation experiments targeting IG-DMR by transiently introducing CRISPR/Cas9 based-targeted DNA methylation editing tools along with one guide RNA into mouse ES cells. Altered DNA methylation, particularly at IG-DMR-Rep, which is a tandem repeat containing ZFP57 methylated DNA-binding protein binding motifs, affected the imprinting state of the whole domain, including DNA methylation, imprinted gene expression, and histone modifications. Moreover, the altered imprinting states were persistent through neuronal differentiation. Our results suggest that the DNA methylation state at IG-DMR-Rep, but not other sites in IG-DMR, is a master element to determine whether the allele behaves as the intrinsic maternal or paternal allele. Meanwhile, this study provides a robust strategy and methodology to study core DNA methylation in cis-regulatory elements, such as ICRs and enhancers.
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Affiliation(s)
- Shin Kojima
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Naoya Shiochi
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Kazuki Sato
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Mamiko Yamaura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Toshiaki Ito
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Nodoka Yamamura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Naoki Goto
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Mika Odamoto
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Shin Kobayashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koutou-ku, Tokyo 135-0064, Japan
| | - Tohru Kimura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Yoichi Sekita
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
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Deep Learning for Human Disease Detection, Subtype Classification, and Treatment Response Prediction Using Epigenomic Data. Biomedicines 2021; 9:biomedicines9111733. [PMID: 34829962 PMCID: PMC8615388 DOI: 10.3390/biomedicines9111733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 11/17/2021] [Indexed: 12/25/2022] Open
Abstract
Deep learning (DL) is a distinct class of machine learning that has achieved first-class performance in many fields of study. For epigenomics, the application of DL to assist physicians and scientists in human disease-relevant prediction tasks has been relatively unexplored until very recently. In this article, we critically review published studies that employed DL models to predict disease detection, subtype classification, and treatment responses, using epigenomic data. A comprehensive search on PubMed, Scopus, Web of Science, Google Scholar, and arXiv.org was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Among 1140 initially identified publications, we included 22 articles in our review. DNA methylation and RNA-sequencing data are most frequently used to train the predictive models. The reviewed models achieved a high accuracy ranged from 88.3% to 100.0% for disease detection tasks, from 69.5% to 97.8% for subtype classification tasks, and from 80.0% to 93.0% for treatment response prediction tasks. We generated a workflow to develop a predictive model that encompasses all steps from first defining human disease-related tasks to finally evaluating model performance. DL holds promise for transforming epigenomic big data into valuable knowledge that will enhance the development of translational epigenomics.
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