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Taglini F, Kafetzopoulos I, Rolls W, Musialik KI, Lee HY, Zhang Y, Marenda M, Kerr L, Finan H, Rubio-Ramon C, Gautier P, Wapenaar H, Kumar D, Davidson-Smith H, Wills J, Murphy LC, Wheeler A, Wilson MD, Sproul D. DNMT3B PWWP mutations cause hypermethylation of heterochromatin. EMBO Rep 2024; 25:1130-1155. [PMID: 38291337 PMCID: PMC7615734 DOI: 10.1038/s44319-024-00061-5] [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: 04/18/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to H3K36me3 at actively transcribing gene bodies via its PWWP domain. It also functions at heterochromatin through an unknown recruitment mechanism. Here, we find that knockout of DNMT3B causes loss of methylation predominantly at H3K9me3-marked heterochromatin and that DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1α and facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest that DNMT3B is recruited to H3K9me3-marked heterochromatin in a PWWP-independent manner that is facilitated by the protein's N-terminal region through an interaction with a key heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in cancer, aging and Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.
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Affiliation(s)
- Francesca Taglini
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ioannis Kafetzopoulos
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Altos Labs, Cambridge Institute, Cambridge, UK
| | - Willow Rolls
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Kamila Irena Musialik
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, Imperial College London, London, UK
| | - Heng Yang Lee
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Endocrine Oncology Research Group, Department of Surgery, The Royal College of Surgeons RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Yujie Zhang
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Mattia Marenda
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Lyndsay Kerr
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Hannah Finan
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Swiss Federal Institute of Technology, ETH Zürich, Institute of Molecular Health Sciences, Zürich, Switzerland
| | - Cristina Rubio-Ramon
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Hannah Wapenaar
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Dhananjay Kumar
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Hazel Davidson-Smith
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jimi Wills
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ann Wheeler
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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2
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Poondi Krishnan V, Morone B, Toubiana S, Krzak M, Fioriniello S, Della Ragione F, Strazzullo M, Angelini C, Selig S, Matarazzo MR. The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory. Genome Res 2023; 33:169-183. [PMID: 36828588 PMCID: PMC10069469 DOI: 10.1101/gr.276986.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 01/12/2023] [Indexed: 02/26/2023]
Abstract
Bi-allelic hypomorphic mutations in DNMT3B disrupt DNA methyltransferase activity and lead to immunodeficiency, centromeric instability, facial anomalies syndrome, type 1 (ICF1). Although several ICF1 phenotypes have been linked to abnormally hypomethylated repetitive regions, the unique genomic regions responsible for the remaining disease phenotypes remain largely uncharacterized. Here we explored two ICF1 patient-derived induced pluripotent stem cells (iPSCs) and their CRISPR-Cas9-corrected clones to determine whether DNMT3B correction can globally overcome DNA methylation defects and related changes in the epigenome. Hypomethylated regions throughout the genome are highly comparable between ICF1 iPSCs carrying different DNMT3B variants, and significantly overlap with those in ICF1 patient peripheral blood and lymphoblastoid cell lines. These regions include large CpG island domains, as well as promoters and enhancers of several lineage-specific genes, in particular immune-related, suggesting that they are premarked during early development. CRISPR-corrected ICF1 iPSCs reveal that the majority of phenotype-related hypomethylated regions reacquire normal DNA methylation levels following editing. However, at the most severely hypomethylated regions in ICF1 iPSCs, which also display the highest increases in H3K4me3 levels and/or abnormal CTCF binding, the epigenetic memory persists, and hypomethylation remains uncorrected. Overall, we demonstrate that restoring the catalytic activity of DNMT3B can reverse the majority of the aberrant ICF1 epigenome. However, a small fraction of the genome is resilient to this rescue, highlighting the challenge of reverting disease states that are due to genome-wide epigenetic perturbations. Uncovering the basis for the persistent epigenetic memory will promote the development of strategies to overcome this obstacle.
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Affiliation(s)
- Varsha Poondi Krishnan
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy
| | - Barbara Morone
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy
| | - Shir Toubiana
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Monika Krzak
- Institute for Applied Computing (IAC) "Mauro Picone", CNR, Naples 80131 Italy
| | - Salvatore Fioriniello
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy.,IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia 86077, Italy
| | - Maria Strazzullo
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy;
| | - Claudia Angelini
- Institute for Applied Computing (IAC) "Mauro Picone", CNR, Naples 80131 Italy;
| | - 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
| | - Maria R Matarazzo
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy
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Shih HT, Chen WY, Wang HY, Chao T, Huang HD, Chou CH, Chang ZF. DNMT3b protects centromere integrity by restricting R-loop-mediated DNA damage. Cell Death Dis 2022; 13:546. [PMID: 35688824 PMCID: PMC9187704 DOI: 10.1038/s41419-022-04989-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 01/21/2023]
Abstract
This study used DNA methyltransferase 3b (DNMT3b) knockout cells and the functional loss of DNMT3b mutation in immunodeficiency-centromeric instability-facial anomalies syndrome (ICF) cells to understand how DNMT3b dysfunction causes genome instability. We demonstrated that R-loops contribute to DNA damages in DNMT3b knockout and ICF cells. More prominent DNA damage signal in DNMT3b knockout cells was due to the loss of DNMT3b expression and the acquirement of p53 mutation. Genome-wide ChIP-sequencing mapped DNA damage sites at satellite repetitive DNA sequences including (peri-)centromere regions. However, the steady-state levels of (peri-)centromeric R-loops were reduced in DNMT3b knockout and ICF cells. Our analysis indicates that XPG and XPF endonucleases-mediated cleavages remove (peri-)centromeric R-loops to generate DNA beaks, causing chromosome instability. DNMT3b dysfunctions clearly increase R-loops susceptibility to the cleavage process. Finally, we showed that DNA double-strand breaks (DSBs) in centromere are probably repaired by error-prone end-joining pathway in ICF cells. Thus, DNMT3 dysfunctions undermine the integrity of centromere by R-loop-mediated DNA damages and repair.
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Affiliation(s)
- Hsueh-Tzu Shih
- Institute of Molecular Medicine, National Taiwan University, Taipei, 10051, Taiwan
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Hsin-Yen Wang
- Institute of Molecular Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Tung Chao
- Institute of Molecular Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Hsien-Da Huang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Longgang District, 518172, Shenzhen, China
- School of Life and Health Sciences, The Chinese University of Hong Kong, Longgang District, 518172, Shenzhen, China
- School of Medicine, The Chinese University of Hong Kong, Longgang District, 518172, Shenzhen, China
| | - Chih-Hung Chou
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan
| | - Zee-Fen Chang
- Institute of Molecular Medicine, National Taiwan University, Taipei, 10051, Taiwan.
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
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4
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Janssen SM, Lorincz MC. Interplay between chromatin marks in development and disease. Nat Rev Genet 2022; 23:137-153. [PMID: 34608297 DOI: 10.1038/s41576-021-00416-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
DNA methylation (DNAme) and histone post-translational modifications (PTMs) have important roles in transcriptional regulation. Although many reports have characterized the functions of such chromatin marks in isolation, recent genome-wide studies reveal surprisingly complex interactions between them. Here, we focus on the interplay between DNAme and methylation of specific lysine residues on the histone H3 tail. We describe the impact of genetic perturbation of the relevant methyltransferases in the mouse on the landscape of chromatin marks as well as the transcriptome. In addition, we discuss the specific neurodevelopmental growth syndromes and cancers resulting from pathogenic mutations in the human orthologues of these genes. Integrating these observations underscores the fundamental importance of crosstalk between DNA and histone H3 methylation in development and disease.
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Affiliation(s)
- Sanne M Janssen
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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5
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Pappalardo XG, Barra V. Losing DNA methylation at repetitive elements and breaking bad. Epigenetics Chromatin 2021; 14:25. [PMID: 34082816 PMCID: PMC8173753 DOI: 10.1186/s13072-021-00400-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/21/2021] [Indexed: 02/08/2023] Open
Abstract
Background DNA methylation is an epigenetic chromatin mark that allows heterochromatin formation and gene silencing. It has a fundamental role in preserving genome stability (including chromosome stability) by controlling both gene expression and chromatin structure. Therefore, the onset of an incorrect pattern of DNA methylation is potentially dangerous for the cells. This is particularly important with respect to repetitive elements, which constitute the third of the human genome. Main body Repetitive sequences are involved in several cell processes, however, due to their intrinsic nature, they can be a source of genome instability. Thus, most repetitive elements are usually methylated to maintain a heterochromatic, repressed state. Notably, there is increasing evidence showing that repetitive elements (satellites, long interspersed nuclear elements (LINEs), Alus) are frequently hypomethylated in various of human pathologies, from cancer to psychiatric disorders. Repetitive sequences’ hypomethylation correlates with chromatin relaxation and unscheduled transcription. If these alterations are directly involved in human diseases aetiology and how, is still under investigation. Conclusions Hypomethylation of different families of repetitive sequences is recurrent in many different human diseases, suggesting that the methylation status of these elements can be involved in preservation of human health. This provides a promising point of view towards the research of therapeutic strategies focused on specifically tuning DNA methylation of DNA repeats.
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Affiliation(s)
- Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95125, Catania, Italy.,National Council of Research, Institute for Biomedical Research and Innovation (IRIB), Unit of Catania, 95125, Catania, Italy
| | - Viviana Barra
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128, Palermo, Italy.
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Abstract
Determining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, budding yeast, that lacks DNA methylation machinery making it a perfect model system to study the intrinsic role of DNA methylation in chromatin structure and function. We expressed the murine DNA methyltransferases in Saccharomyces cerevisiae and analyzed the correlation between DNA methylation, nucleosome positioning, gene expression and 3D genome organization. Despite lacking the machinery for positioning and reading methylation marks, induced DNA methylation follows a conserved pattern with low methylation levels at the 5’ end of the gene increasing gradually toward the 3’ end, with concentration of methylated DNA in linkers and nucleosome free regions, and with actively expressed genes showing low and high levels of methylation at transcription start and terminating sites respectively, mimicking the patterns seen in mammals. We also see that DNA methylation increases chromatin condensation in peri-centromeric regions, decreases overall DNA flexibility, and favors the heterochromatin state. Taken together, these results demonstrate that methylation intrinsically modulates chromatin structure and function even in the absence of cellular machinery evolved to recognize and process the methylation signal. Multi-layered epigenetic regulation in higher eukaryotes makes it challenging to disentangle the individual effects of modifications on chromatin structure and function. Here, the authors expressed mammalian DNA methyltransferases in yeast, which have no DNA methylation, to show that methylation has intrinsic effects on chromatin structure.
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Kiaee F, Zaki-Dizaji M, Hafezi N, Almasi-Hashiani A, Hamedifar H, Sabzevari A, Shirkani A, Zian Z, Jadidi-Niaragh F, Aghamahdi F, Goudarzvand M, Yazdani R, Abolhassani H, Aghamohammadi A, Azizi G. Clinical, Immunologic and Molecular Spectrum of Patients with Immunodeficiency, Centromeric Instability, and Facial Anomalies (ICF) Syndrome: A Systematic Review. Endocr Metab Immune Disord Drug Targets 2021; 21:664-672. [PMID: 32533820 DOI: 10.2174/1871530320666200613204426] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/09/2020] [Accepted: 04/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Immunodeficiency, centromeric instability and facial dysmorphism (ICF) syndrome is a rare autosomal recessive immune disorder presenting with hypogammaglobulinemia, developmental delay, and facial anomalies. The ICF type 1, type 2, type 3 and type 4 are characterized by mutations in DNMT3B, ZBTB24, CDCA7 or HELLS gene, respectively. This study aimed to present a comprehensive description of the clinical, immunologic and genetic features of patients with ICF syndrome. METHODS PubMed, Web of Science, and Scopus were searched systemically to find eligible studies. RESULTS Forty-eight studies with 118 ICF patients who met the inclusion criteria were included in our study. Among these patients, 60% reported with ICF-1, 30% with ICF-2, 4% with ICF-3, and 6% with ICF-4. The four most common symptoms reported in patients with ICF syndrome were: delay in motor development, low birth weight, chronic infections, and diarrhea. Intellectual disability and preterm birth among patients with ICF-2 and failure to thrive, sepsis and fungal infections among patients with ICF-1 were also more frequent. Moreover, the median levels of all three immunoglobulins (IgA, IgG, IgM) were markedly reduced within four types of ICF syndrome. CONCLUSION The frequency of diagnosed patients with ICF syndrome has increased. Early diagnosis of ICF is important since immunoglobulin supplementation or allogeneic stem cell transplantation can improve the disease-free survival rate.
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Affiliation(s)
- Fatemeh Kiaee
- Student Research Committee, Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Zaki-Dizaji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Nasim Hafezi
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Amir Almasi-Hashiani
- Department of Epidemiology, School of Health, Arak University of Medical Sciences, Arak, Iran
| | - Haleh Hamedifar
- CinnaGen Medical Biotechnology Research Center, Alborz University of medical sciences, Karaj, Iran
| | - Araz Sabzevari
- CinnaGen Medical Biotechnology Research Center, Alborz University of medical sciences, Karaj, Iran
| | - Afshin Shirkani
- Allergy and clinical Immunology Department, School of Medicine, Bushehr University of Medical Science, Bushehr, Iran
| | - Zeineb Zian
- Biomedical Genomics and Oncogenetics Research Laboratory, Faculty of Sciences and Techniques of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
| | | | - Fatemeh Aghamahdi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mahdi Goudarzvand
- Department of Physiology and Pharmacology, Faculty of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Reza Yazdani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Abolhassani
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholamreza Azizi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
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Camacho-Ordonez N, Ballestar E, Timmers HTM, Grimbacher B. What can clinical immunology learn from inborn errors of epigenetic regulators? J Allergy Clin Immunol 2021; 147:1602-1618. [PMID: 33609625 DOI: 10.1016/j.jaci.2021.01.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/20/2022]
Abstract
The epigenome is at the interface between environmental factors and the genome, regulating gene transcription, DNA repair, and replication. Epigenetic modifications play a crucial role in establishing and maintaining cell identity and are especially crucial for neurology, musculoskeletal integrity, and the function of the immune system. Mutations in genes encoding for the components of the epigenetic machinery lead to the development of distinct disorders, especially involving the central nervous system and host defense. In this review, we focus on the role of epigenetic modifications for the function of the immune system. By studying the immune phenotype of patients with monogenic mutations in components of the epigenetic machinery (inborn errors of epigenetic regulators), we demonstrate the importance of DNA methylation, histone modifications, chromatin remodeling, noncoding RNAs, and mRNA processing for immunity. Moreover, we give a short overview on therapeutic strategies targeting the epigenome.
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Affiliation(s)
- Nadezhda Camacho-Ordonez
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain
| | - H Th Marc Timmers
- German Cancer Consortium (DKTK), partner site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Urology, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST- Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany.
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9
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Mitochondrial DNA methylation misleads global DNA methylation detected by antibody-based methods. Anal Biochem 2020; 601:113789. [PMID: 32473121 DOI: 10.1016/j.ab.2020.113789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/12/2020] [Accepted: 05/17/2020] [Indexed: 12/27/2022]
Abstract
Cytosine methylation is the leading epigenetic modification on DNA playing a role in gene regulation. Methylation can occur in cytosines of any nucleic acids in cytosol (as mitochondrial DNA, mtDNA) and in nuclear DNA (ncDNA). mtDNA exists as multiple copies within numerous mitochondria. This suggests that the number of mitochondria and mtDNA copy number can indicate the presence of a significant amount of DNA methylation within total DNA methylation detected. However, immunofluorescence method does not have a step to discriminate the staining between ncDNA and mtDNA. Antibodies used in immunological methods are methylation-specific but not selective for DNA type and they can bind to methylated cytosines in any DNA within the specimen. Current study aimed to understand whether mtDNA methylation interferes with the detection of nuclear DNA methylation by immunofluorescence and affinity enrichment (ELISA) in different mammalian cells. Experiments were performed to distinguish methylation between mtDNA and ncDNA. Immunofluorescence showed that there was no significant difference in the detected amount of methylation between mitochondrial and nuclear DNA. But ELISA revealed that up to 25% of cellular methylation was derived from mitochondria. This suggests that significant contamination of mtDNA methylation with ncDNA methylation can result in overestimation of the quantitative level of nuclear methylation.
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10
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Chen Y, Liao LD, Wu ZY, Yang Q, Guo JC, He JZ, Wang SH, Xu XE, Wu JY, Pan F, Lin DC, Xu LY, Li EM. Identification of key genes by integrating DNA methylation and next-generation transcriptome sequencing for esophageal squamous cell carcinoma. Aging (Albany NY) 2020; 12:1332-1365. [PMID: 31962291 PMCID: PMC7053602 DOI: 10.18632/aging.102686] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 12/25/2019] [Indexed: 02/05/2023]
Abstract
Aberrant DNA methylation leads to abnormal gene expression, making it a significant regulator in the progression of cancer and leading to the requirement for integration of gene expression with DNA methylation. Here, we identified 120 genes demonstrating an inverse correlation between DNA methylation and mRNA expression in esophageal squamous cell carcinoma (ESCC). Sixteen key genes, such as SIX4, CRABP2, and EHD3, were obtained by filtering 10 datasets and verified in paired ESCC samples by qRT-PCR. 5-Aza-dC as a DNA methyltransferase (DNMT) inhibitor could recover their expression and inhibit clonal growth of cancer cells in seven ESCC cell lines. Furthermore, 11 of the 16 genes were correlated with OS (overall survival) and DFS (disease-free survival) in 125 ESCC patients. ChIP-Seq data and WGBS data showed that DNA methylation and H3K27ac histone modification of these key genes displayed inverse trends, suggesting that there was collaboration between DNA methylation and histone modification in ESCC. Our findings illustrate that the integrated multi-omics data (transcriptome and epigenomics) can accurately obtain potential prognostic biomarkers, which may provide important insight for the effective treatment of cancers.
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Affiliation(s)
- Yang Chen
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Lian-Di Liao
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Zhi-Yong Wu
- Departments of Oncology Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-Sen University, Shantou 515041, Guangdong, P.R. China
| | - Qian Yang
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Jin-Cheng Guo
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Jian-Zhong He
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Shao-Hong Wang
- Departments of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-Sen University, Shantou 515041, Guangdong, P.R. China
| | - Xiu-E Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Jian-Yi Wu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - Feng Pan
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, P.R. China
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11
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de la Calle-Fabregat C, Morante-Palacios O, Ballestar E. Understanding the Relevance of DNA Methylation Changes in Immune Differentiation and Disease. Genes (Basel) 2020; 11:E110. [PMID: 31963661 PMCID: PMC7017047 DOI: 10.3390/genes11010110] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Immune cells are one of the most complex and diverse systems in the human organism. Such diversity implies an intricate network of different cell types and interactions that are dependently interconnected. The processes by which different cell types differentiate from progenitors, mature, and finally exert their function requires an orchestrated succession of molecular processes that determine cell phenotype and function. The acquisition of these phenotypes is highly dependent on the establishment of unique epigenetic profiles that confer identity and function on the various types of effector cells. These epigenetic mechanisms integrate microenvironmental cues into the genome to establish specific transcriptional programs. Epigenetic modifications bridge environment and genome regulation and play a role in human diseases by their ability to modulate physiological programs through external stimuli. DNA methylation is one of the most ubiquitous, stable, and widely studied epigenetic modifications. Recent technological advances have facilitated the generation of a vast amount of genome-wide DNA methylation data, providing profound insights into the roles of DNA methylation in health and disease. This review considers the relevance of DNA methylation to immune system cellular development and function, as well as the participation of DNA methylation defects in immune-mediated pathologies, illustrated by selected paradigmatic diseases.
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Affiliation(s)
| | | | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain; (C.d.l.C.-F.); (O.M.-P.)
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12
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Vukic M, Daxinger L. DNA methylation in disease: Immunodeficiency, Centromeric instability, Facial anomalies syndrome. Essays Biochem 2019; 63:773-783. [PMID: 31724723 PMCID: PMC6923317 DOI: 10.1042/ebc20190035] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022]
Abstract
DNA methylation is an epigenetic modification essential for normal mammalian development. Initially associated with gene silencing, more diverse roles for DNA methylation in the regulation of gene expression patterns are increasingly being recognized. Some of these insights come from studying the function of genes that are mutated in human diseases characterized by abnormal DNA methylation landscapes. The first disorder to be associated with congenital defects in DNA methylation was Immunodeficiency, Centromeric instability, Facial anomalies syndrome (ICF). The hallmark of this syndrome is hypomethylation of pericentromeric satellite repeats, with mutations in four genes: DNMT3B, ZBTB24, CDCA7 and HELLS, being linked to the disease. Here, we discuss recent progress in understanding the molecular interactions between these genes and consider current evidence for how aberrant DNA methylation may contribute to the abnormal phenotype present in ICF syndrome patients.
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Affiliation(s)
- Maja Vukic
- Department of Human Genetics, Leiden University Medical Centre (LUMC), Leiden 2300, RC, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre (LUMC), Leiden 2300, RC, The Netherlands
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13
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Toubiana S, Gagliardi M, Papa M, Manco R, Tzukerman M, Matarazzo MR, Selig S. Persistent epigenetic memory impedes rescue of the telomeric phenotype in human ICF iPSCs following DNMT3B correction. eLife 2019; 8:e47859. [PMID: 31738163 PMCID: PMC6897513 DOI: 10.7554/elife.47859] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/17/2019] [Indexed: 12/15/2022] Open
Abstract
DNA methyltransferase 3B (DNMT3B) is the major DNMT that methylates mammalian genomes during early development. Mutations in human DNMT3B disrupt genome-wide DNA methylation patterns and result in ICF syndrome type 1 (ICF1). To study whether normal DNA methylation patterns may be restored in ICF1 cells, we corrected DNMT3B mutations in induced pluripotent stem cells from ICF1 patients. Focusing on repetitive regions, we show that in contrast to pericentromeric repeats, which reacquire normal methylation, the majority of subtelomeres acquire only partial DNA methylation and, accordingly, the ICF1 telomeric phenotype persists. Subtelomeres resistant to de novo methylation were characterized by abnormally high H3K4 trimethylation (H3K4me3), and short-term reduction of H3K4me3 by pharmacological intervention partially restored subtelomeric DNA methylation. These findings demonstrate that the abnormal epigenetic landscape established in ICF1 cells restricts the recruitment of DNMT3B, and suggest that rescue of epigenetic diseases with genome-wide disruptions will demand further manipulation beyond mutation correction.
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Affiliation(s)
- Shir Toubiana
- Molecular Medicine LaboratoryRappaport Faculty of Medicine, TechnionHaifaIsrael
- Rambam Health Care CampusHaifaIsrael
| | | | | | - Roberta Manco
- Institute of Genetics and Biophysics, ABT CNRNaplesItaly
| | - Maty Tzukerman
- Molecular Medicine LaboratoryRappaport Faculty of Medicine, TechnionHaifaIsrael
- Rambam Health Care CampusHaifaIsrael
| | | | - Sara Selig
- Molecular Medicine LaboratoryRappaport Faculty of Medicine, TechnionHaifaIsrael
- Rambam Health Care CampusHaifaIsrael
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14
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Lim WJ, Kim KH, Kim JY, Kim HJ, Kim M, Park JL, Yoon S, Oh JH, Cho JW, Kim YS, Kim N. Investigation of Gene Expression and DNA Methylation From Seven Different Brain Regions of a Crab-Eating Monkey as Determined by RNA-Seq and Whole-Genome Bisulfite Sequencing. Front Genet 2019; 10:694. [PMID: 31428131 PMCID: PMC6690020 DOI: 10.3389/fgene.2019.00694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/02/2019] [Indexed: 01/04/2023] Open
Abstract
The crab-eating monkey is widely used in biomedical research for pharmacological experiments. Epigenetic regulation in the brain regions of primates involves complex patterns of DNA methylation. Previous studies of methylated CpG-binding domains using microarray technology or peak identification of sequence reads mostly focused on developmental stages or disease, rather than normal brains. To identify correlations between gene expression and DNA methylation levels that may be related to transcriptional regulation, we generated RNA-seq and whole-genome bisulfite sequencing data from seven different brain regions from a single crab-eating monkey. We identified 92 genes whose expression levels were significantly correlated, positively or negatively, with DNA methylation levels. Among them, 11 genes exhibited brain region-specific characteristics, and their expression patterns were strongly correlated with DNA methylation level. Nine genes (SLC2A5, MCM5, DRAM1, TTC12, DHX40, COR01A, LRAT, FLVCR2, and PTER) had effects on brain and eye function and development, and two (LHX6 and MEST) were previously identified as genes in which DNA methylation levels change significantly in the promoter region and are therefore considered brain epigenetic markers. Furthermore, we characterized DNA methylation of repetitive elements at the whole genome through repeat annotation at single-base resolution. Our results reveal the diverse roles of DNA methylation at single-base resolution throughout the genome and reflect the epigenetic variations in adult brain tissues.
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Affiliation(s)
- Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Hee-Jin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Mirang Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Jong-Lyul Park
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Seokjoo Yoon
- Predictive Toxicity Department, Korea Institute of Toxicology (KIT), Daejeon, South Korea
| | - Jung-Hwa Oh
- Predictive Toxicity Department, Korea Institute of Toxicology (KIT), Daejeon, South Korea
| | - Jae-Woo Cho
- Predictive Toxicity Department, Korea Institute of Toxicology (KIT), Daejeon, South Korea
| | - Yong Sung Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
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15
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Del Pino-Molina L, Rodríguez-Ubreva J, Torres Canizales J, Coronel-Díaz M, Kulis M, Martín-Subero JI, van der Burg M, Ballestar E, López-Granados E. Impaired CpG Demethylation in Common Variable Immunodeficiency Associates With B Cell Phenotype and Proliferation Rate. Front Immunol 2019; 10:878. [PMID: 31105700 PMCID: PMC6492528 DOI: 10.3389/fimmu.2019.00878] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/05/2019] [Indexed: 01/01/2023] Open
Abstract
Common Variable Immunodeficiency (CVID) is characterized by impaired antibody production and poor terminal differentiation of the B cell compartment, yet its pathogenesis is still poorly understood. We first reported the occurrence of epigenetic alterations in CVID by high-throughput methylation analysis in CVID-discordant monozygotic twins. Data from a recent whole DNA methylome analysis throughout different stages of normal B cell differentiation allowed us to design a new experimental approach. We selected CpG sites for analysis based on two criteria: one, CpGs with potential association with the transcriptional status of relevant genes for B cell activation and differentiation; and two, CpGs that undergo significant demethylation from naïve to memory B cells in healthy individuals. DNA methylation was analyzed by bisulfite pyrosequencing of specific CpG sites in sorted naïve and memory B cell subsets from CVID patients and healthy donors. We observed impaired demethylation in two thirds of the selected CpGs in CVID memory B cells, in genes that govern B cell-specific processes or participate in B cell signaling. The degree of demethylation impairment associated with the extent of the memory B cell reduction. The impaired demethylation in such functionally relevant genes as AICDA in switched memory B cells correlated with a lower proliferative rate. Our new results reinforce the hypothesis of altered demethylation during B cell differentiation as a contributing pathogenic mechanism to the impairment of B cell function and maturation in CVID. In particular, deregulated epigenetic control of AICDA could play a role in the defective establishment of a post-germinal center B cell compartment in CVID.
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Affiliation(s)
- Lucía Del Pino-Molina
- Lymphocyte Pathophysiology in Immunodeficiencies Group, Department of Clinical Immunology, IdiPAZ Institute for Health Research, University Hospital La Paz, Madrid, Spain
| | - Javier Rodríguez-Ubreva
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Juan Torres Canizales
- Lymphocyte Pathophysiology in Immunodeficiencies Group, Department of Clinical Immunology, IdiPAZ Institute for Health Research, University Hospital La Paz, Madrid, Spain
| | - María Coronel-Díaz
- Lymphocyte Pathophysiology in Immunodeficiencies Group, Department of Clinical Immunology, IdiPAZ Institute for Health Research, University Hospital La Paz, Madrid, Spain
| | - Marta Kulis
- Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain
| | - José I Martín-Subero
- Departamento de Fundamentos Clínicos, Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Universitat de Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Mirjam van der Burg
- Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Esteban Ballestar
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Eduardo López-Granados
- Lymphocyte Pathophysiology in Immunodeficiencies Group, Department of Clinical Immunology, IdiPAZ Institute for Health Research, University Hospital La Paz, Madrid, Spain
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16
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Velasco G, Francastel C. Genetics meets DNA methylation in rare diseases. Clin Genet 2018; 95:210-220. [DOI: 10.1111/cge.13480] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Guillaume Velasco
- Sorbonne Paris Cité, Epigenetics and Cell Fate; UMR 7216 CNRS, Université Paris Diderot; Paris France
| | - Claire Francastel
- Sorbonne Paris Cité, Epigenetics and Cell Fate; UMR 7216 CNRS, Université Paris Diderot; Paris France
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17
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Campos-Sanchez E, Martínez-Cano J, Del Pino Molina L, López-Granados E, Cobaleda C. Epigenetic Deregulation in Human Primary Immunodeficiencies. Trends Immunol 2018; 40:49-65. [PMID: 30509895 DOI: 10.1016/j.it.2018.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022]
Abstract
Primary immunodeficiencies (PIDs) are immune disorders resulting from defects in genes involved in immune regulation, and manifesting as an increased susceptibility to infections, autoimmunity, and cancer. However, the molecular basis of some prevalent entities remains poorly understood. Epigenetic control is essential for immune functions, and epigenetic alterations have been identified in different PIDs, including syndromes such as immunodeficiency-centromeric-instability-facial-anomalies, Kabuki, or Wolf-Hirschhorn, among others. Although the epigenetic changes may differ among these PIDs, the reversibility of epigenetic modifications suggests that they might become potential therapeutic targets. Here, we review recent mechanistic advances in our understanding of epigenetic alterations associated with certain PIDs, propose that a fully epigenetically driven mechanism might underlie some PIDs, and discuss the possible prophylactic and therapeutic implications.
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Affiliation(s)
- Elena Campos-Sanchez
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Jorge Martínez-Cano
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Lucía Del Pino Molina
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain.
| | - Cesar Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain.
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18
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Toubiana S, Velasco G, Chityat A, Kaindl AM, Hershtig N, Tzur-Gilat A, Francastel C, Selig S. Subtelomeric methylation distinguishes between subtypes of Immunodeficiency, Centromeric instability and Facial anomalies syndrome. Hum Mol Genet 2018; 27:3568-3581. [PMID: 30010917 DOI: 10.1093/hmg/ddy265] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 07/11/2018] [Indexed: 12/16/2022] Open
Abstract
Human telomeres and adjacent subtelomeres are packaged as heterochromatin. Subtelomeric DNA undergoes methylation during development by DNA methyltransferase 3B (DNMT3B), including the CpG-rich promoters of the long non-coding RNA (TERRA) embedded in these regions. The factors that direct DNMT3B methylation to human subtelomeres and maintain this methylation throughout lifetime are yet unknown. The importance of subtelomeric methylation is manifested through the abnormal telomeric phenotype in Immunodeficiency, Centromeric instability and Facial anomalies (ICF) syndrome type 1 patients carrying mutations in DNMT3B. Patient cells demonstrate subtelomeric hypomethylation, accompanied by elevated TERRA transcription, accelerated telomere shortening and premature senescence of fibroblasts. ICF syndrome can arise due to mutations in at least three additional genes, ZBTB24 (ICF2), CDCA7 (ICF3) and HELLS (ICF4). While pericentromeric repeat hypomethylation is evident in all ICF syndrome subtypes, the status of subtelomeric DNA methylation had not been described for patients of subtypes 2-4. Here we explored the telomeric phenotype in cells derived from ICF2-4 patients with the aim to determine whether ZBTB24, CDCA7 and HELLS also play a role in establishing and/or maintaining human subtelomeric methylation. We found normal subtelomeric methylation in ICF2-4 and accordingly low TERRA levels and unperturbed telomere length. Moreover, depleting the ICF2-4-related proteins in normal fibroblasts did not influence subtelomeric methylation. Thus, these gene products are not involved in establishing or maintaining subtelomeric methylation. Our findings indicate that human subtelomeric heterochromatin has specialized methylation regulation and highlight the telomeric phenotype as a characteristic that distinguishes ICF1 from ICF2-4.
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Affiliation(s)
- Shir Toubiana
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Guillaume Velasco
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, CNRS, Paris Cedex, France
| | - Adi Chityat
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Angela M Kaindl
- Charité - Universitätsmedizin Berlin, Department of Pediatric Neurology, Center for Chronically Sick Children, Institute of Cell Biology and Neurobiology, Augustenburger Platz 1, Berlin, Germany
| | | | - Aya Tzur-Gilat
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Claire Francastel
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, CNRS, Paris Cedex, France
| | - Sara Selig
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
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19
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Baribault C, Ehrlich KC, Ponnaluri VKC, Pradhan S, Lacey M, Ehrlich M. Developmentally linked human DNA hypermethylation is associated with down-modulation, repression, and upregulation of transcription. Epigenetics 2018; 13:275-289. [PMID: 29498561 PMCID: PMC5997157 DOI: 10.1080/15592294.2018.1445900] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA methylation can affect tissue-specific gene transcription in ways that are difficult to discern from studies focused on genome-wide analyses of differentially methylated regions (DMRs). To elucidate the variety of associations between differentiation-related DNA hypermethylation and transcription, we used available epigenomic and transcriptomic profiles from 38 human cell/tissue types to focus on such relationships in 94 genes linked to hypermethylated DMRs in myoblasts (Mb). For 19 of the genes, promoter-region hypermethylation in Mb (and often a few heterologous cell types) was associated with gene repression but, importantly, DNA hypermethylation was absent in many other repressed samples. In another 24 genes, DNA hypermethylation overlapped cryptic enhancers or super-enhancers and correlated with down-modulated, but not silenced, gene expression. However, such methylation was absent, surprisingly, in both non-expressing samples and highly expressing samples. This suggests that some genes need DMR hypermethylation to help repress cryptic enhancer chromatin only when they are actively transcribed. For another 11 genes, we found an association between intergenic hypermethylated DMRs and positive expression of the gene in Mb. DNA hypermethylation/transcription correlations similar to those of Mb were evident sometimes in diverse tissues, such as aorta and brain. Our findings have implications for the possible involvement of methylated DNA in Duchenne's muscular dystrophy, congenital heart malformations, and cancer. This epigenomic analysis suggests that DNA methylation is not simply the inevitable consequence of changes in gene expression but, instead, is often an active agent for fine-tuning transcription in association with development.
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Affiliation(s)
- Carl Baribault
- a Tulane Cancer Center , Tulane University Health Sciences Center , New Orleans , LA 70112 , USA.,b Department of Mathematics , Tulane University , New Orleans , LA 70118 , USA
| | - Kenneth C Ehrlich
- c Center for Bioinformatics and Genomics , Tulane University Health Sciences Center , New Orleans , LA 70112 , USA
| | | | | | - Michelle Lacey
- b Department of Mathematics , Tulane University , New Orleans , LA 70118 , USA
| | - Melanie Ehrlich
- a Tulane Cancer Center , Tulane University Health Sciences Center , New Orleans , LA 70112 , USA.,c Center for Bioinformatics and Genomics , Tulane University Health Sciences Center , New Orleans , LA 70112 , USA.,e Hayward Genetics Center Tulane University Health Sciences Center , New Orleans , LA 70112 , USA
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20
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Snijders C, Bassil KC, de Nijs L. Methodologies of Neuroepigenetic Research: Background, Challenges and Future Perspectives. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:15-27. [DOI: 10.1016/bs.pmbts.2018.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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21
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Pei YF, Tao R, Li JF, Su LP, Yu BQ, Wu XY, Yan M, Gu QL, Zhu ZG, Liu BY. TET1 inhibits gastric cancer growth and metastasis by PTEN demethylation and re-expression. Oncotarget 2017; 7:31322-35. [PMID: 27121319 PMCID: PMC5058759 DOI: 10.18632/oncotarget.8900] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/31/2016] [Indexed: 12/29/2022] Open
Abstract
Ten-Eleven Translocation 1 (TET1) is a member of ten eleven translocation enzymes, which convert 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC). TET1 can promote CpG islands demethylation in specific genes and often absent in various cancers. Herein, we found that TET1 expression and 5-hmC content were low in gastric tumors compared to its adjacent non-tumor tissues. Cell proliferation, migration and invasion were enhanced upon TET1 knockdown in gastric cancer cells in vitro. This phenomenon was confirmed by an animal xeongraft model. We also found that TET1 directly binds to the promoter region of PTEN and activates its transcription through demethylation of CpG islands. TET1 knockdown activated AKT and FAK pathways, which were suppressed by PTEN. The activation of AKT and FAK facilitated tumor migration, invasion and accelerated cell growth. In conclusion, we found a novel mechanism that TET1 suppresses tumor cell growth, migration and invasion through demethylation of CpG island in PTEN promoter by increasing 5-hmC content. The re-expressed PTEN subsequently down regulates AKT and FAK activity.
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Affiliation(s)
- Yao-Fei Pei
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Ran Tao
- Department of Hepatobiliary-Pancreatic Surgery, Zhejiang Province People's Hospital, Hangzhou 310014, PR China
| | - Jian-Fang Li
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Li-Ping Su
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Bei-Qin Yu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Xiong-Yan Wu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Min Yan
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Qin-Long Gu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Zheng-Gang Zhu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Bing-Ya Liu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
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22
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A DNA methylation map of human cancer at single base-pair resolution. Oncogene 2017; 36:5648-5657. [PMID: 28581523 PMCID: PMC5633654 DOI: 10.1038/onc.2017.176] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/21/2017] [Accepted: 05/04/2017] [Indexed: 12/19/2022]
Abstract
Although single base-pair resolution DNA methylation landscapes for embryonic and different somatic cell types provided important insights into epigenetic dynamics and cell-type specificity, such comprehensive profiling is incomplete across human cancer types. This prompted us to perform genome-wide DNA methylation profiling of 22 samples derived from normal tissues and associated neoplasms, including primary tumors and cancer cell lines. Unlike their invariant normal counterparts, cancer samples exhibited highly variable CpG methylation levels in a large proportion of the genome, involving progressive changes during tumor evolution. The whole-genome sequencing results from selected samples were replicated in a large cohort of 1112 primary tumors of various cancer types using genome-scale DNA methylation analysis. Specifically, we determined DNA hypermethylation of promoters and enhancers regulating tumor-suppressor genes, with potential cancer-driving effects. DNA hypermethylation events showed evidence of positive selection, mutual exclusivity and tissue specificity, suggesting their active participation in neoplastic transformation. Our data highlight the extensive changes in DNA methylation that occur in cancer onset, progression and dissemination.
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23
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Gatto S, Gagliardi M, Franzese M, Leppert S, Papa M, Cammisa M, Grillo G, Velasco G, Francastel C, Toubiana S, D’Esposito M, Angelini C, Matarazzo MR. ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing. Nucleic Acids Res 2017; 45:5739-5756. [PMID: 28334849 PMCID: PMC5449610 DOI: 10.1093/nar/gkx163] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 02/07/2017] [Accepted: 02/28/2017] [Indexed: 12/11/2022] Open
Abstract
Hypomorphic mutations in DNA-methyltransferase DNMT3B cause majority of the rare disorder Immunodeficiency, Centromere instability and Facial anomalies syndrome cases (ICF1). By unspecified mechanisms, mutant-DNMT3B interferes with lymphoid-specific pathways resulting in immune response defects. Interestingly, recent findings report that DNMT3B shapes intragenic CpG-methylation of highly-transcribed genes. However, how the DNMT3B-dependent epigenetic network modulates transcription and whether ICF1-specific mutations impair this process remains unknown. We performed a transcriptomic and epigenomic study in patient-derived B-cell lines to investigate the genome-scale effects of DNMT3B dysfunction. We highlighted that altered intragenic CpG-methylation impairs multiple aspects of transcriptional regulation, like alternative TSS usage, antisense transcription and exon splicing. These defects preferentially associate with changes of intragenic H3K4me3 and at lesser extent of H3K27me3 and H3K36me3. In addition, we highlighted a novel DNMT3B activity in modulating the self-regulatory circuit of sense-antisense pairs and the exon skipping during alternative splicing, through interacting with RNA molecules. Strikingly, altered transcription affects disease relevant genes, as for instance the memory-B cell marker CD27 and PTPRC genes, providing us with biological insights into the ICF1-syndrome pathogenesis. Our genome-scale approach sheds light on the mechanisms still poorly understood of the intragenic function of DNMT3B and DNA methylation in gene expression regulation.
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Affiliation(s)
- Sole Gatto
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
- Sanford Burnham Prebys Medical Discovery Research Institute, La Jolla, CA, USA
| | - Miriam Gagliardi
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
- Institute for Applied Mathematics ‘Mauro Picone’, CNR, Naples 80131, Italy
| | - Monica Franzese
- Institute for Applied Mathematics ‘Mauro Picone’, CNR, Naples 80131, Italy
| | - Sylwia Leppert
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
| | - Mariarosaria Papa
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
| | - Marco Cammisa
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta 81100, Italy
| | - Giacomo Grillo
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, France
| | - Guillame Velasco
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, France
| | - Claire Francastel
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, France
| | - Shir Toubiana
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Maurizio D’Esposito
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Claudia Angelini
- Institute for Applied Mathematics ‘Mauro Picone’, CNR, Naples 80131, Italy
| | - Maria R. Matarazzo
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
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24
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Rechavi E, Lev A, Eyal E, Barel O, Kol N, Barhom SF, Pode-Shakked B, Anikster Y, Somech R, Simon AJ. A Novel Mutation in a Critical Region for the Methyl Donor Binding in DNMT3B Causes Immunodeficiency, Centromeric Instability, and Facial Anomalies Syndrome (ICF). J Clin Immunol 2016; 36:801-809. [PMID: 27734333 DOI: 10.1007/s10875-016-0340-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/21/2016] [Indexed: 10/20/2022]
Abstract
PURPOSE Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is an extremely rare autosomal recessive disease. The immune phenotype is characterized by hypogammaglobulinemia in the presence of B cells. T cell lymphopenia also develops in some patients. We sought to further investigate the immune defect in an ICF patient with a novel missense mutation in DNMT3B and a severe phenotype. METHODS Patient lymphocytes were examined for subset counts, immunoglobulin levels, T and B cell de novo production (via excision circles) and receptor repertoire diversity. Mutated DNMT3B protein structure was modeled to assess the effect of a mutation located outside of the catalytic region on protein function. RESULTS A novel homozygous missense mutation, Ala585Thr, was found in DNMT3B. The patient had decreased B cell counts with hypogammaglobulinemia, and normal T cell counts. CD4+ T cells decreased over time, leading to an inversion of the CD4+ to CD8+ ratio. Excision circle copy numbers were normal, signifying normal de novo lymphocyte production, but the ratio between naïve and total B cells was low, indicating decreased in vivo B cell replication. T and B cell receptor repertoires displayed normal diversity. Computerized modeling of the mutated Ala585 residue suggested reduced thermostability, possibly affecting the enzyme kinetics. CONCLUSIONS Our results highlight the existence of a T cell defect that develops over time in ICF patient, in addition to the known B cell dysfunction. With intravenous immunoglobulin (IVIG) treatment ameliorating the B cell defect, the extent of CD4+ lymphopenia may determine the severity of ICF immunodeficiency.
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Affiliation(s)
- Erez Rechavi
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Edmond and Lily Safra Children's Hospital, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Atar Lev
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Eran Eyal
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Ortal Barel
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Nitzan Kol
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Sarit Farage Barhom
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Ben Pode-Shakked
- Edmond and Lily Safra Children's Hospital, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Yair Anikster
- Edmond and Lily Safra Children's Hospital, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Metabolic Disease Unit, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Raz Somech
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Edmond and Lily Safra Children's Hospital, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
| | - Amos J Simon
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Institute of Hematology, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
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25
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Wu H, Thijssen PE, de Klerk E, Vonk KKD, Wang J, den Hamer B, Aytekin C, van der Maarel SM, Daxinger L. Converging disease genes in ICF syndrome: ZBTB24 controls expression of CDCA7 in mammals. Hum Mol Genet 2016; 25:4041-4051. [PMID: 27466202 DOI: 10.1093/hmg/ddw243] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 12/31/2022] Open
Abstract
For genetically heterogeneous diseases a better understanding of how the underlying gene defects are functionally interconnected will be important for dissecting disease etiology. The Immunodeficiency, Centromeric instability, Facial anomalies (ICF) syndrome is a chromatin disorder characterized by mutations in DNMT3B, ZBTB24, CDCA7 or HELLS Here, we generated a Zbtb24 BTB domain deletion mouse and found that loss of functional Zbtb24 leads to early embryonic lethality. Transcriptome analysis identified Cdca7 as the top down-regulated gene in Zbtb24 homozygous mutant mESCs, which can be restored by ectopic ZBTB24 expression. We further demonstrate enrichment of ZBTB24 at the CDCA7 promoter suggesting that ZBTB24 can function as a transcription factor directly controlling Cdca7 expression. Finally, we show that this regulation is conserved between species and that CDCA7 levels are reduced in patients carrying ZBTB24 nonsense mutations. Together, our findings demonstrate convergence of the two ICF genes ZBTB24 and CDCA7 at the level of transcription.
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Affiliation(s)
- Haoyu Wu
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands
| | - Peter E Thijssen
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands
| | - Eleonora de Klerk
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands
- Department of Microbiology and Immunology, UCSF Diabetes Center, University of California San Francisco, San Francisco, CA 94143-0534, USA
| | - Kelly K D Vonk
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands
| | - Jun Wang
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China and
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands
| | - Caner Aytekin
- Department of Pediatric Immunology, Dr Sami Ulus Maternity and Children's Research and Educational Hospital, Ankara 06080, Turkey
| | | | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2300RC, The Netherlands,
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26
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Klein C. Targeting sequence domain: a captain at the helm precisely steering DNMT1 through maintenance methylation? Epigenomics 2016; 8:737-40. [PMID: 27286477 DOI: 10.2217/epi-2016-0033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Christopher Klein
- Department of Neurology, Peripheral Nerve Division, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.,Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN 55905, USA.,Department of Medical Genetics, Mayo Clinic, Rochester, MN 55905, USA
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27
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Rodríguez-Cortez VC, Del Pino-Molina L, Rodríguez-Ubreva J, López-Granados E, Ballestar E. Dissecting Epigenetic Dysregulation of Primary Antibody Deficiencies. J Clin Immunol 2016; 36 Suppl 1:48-56. [PMID: 26984849 DOI: 10.1007/s10875-016-0267-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/07/2016] [Indexed: 01/04/2023]
Abstract
Primary antibody deficiencies (PADs), the most prevalent inherited primary immunodeficiencies (PIDs), are associated with a wide range of genetic alterations (both monogenic or polygenic) in B cell-specific genes. However, correlations between the genotype and clinical manifestations are not evident in all cases indicating that genetic interactions, environmental and epigenetic factors may have a role in PAD pathogenesis. The recent identification of key defects in DNA methylation in common variable immunodeficiency as well as the multiple evidences on the role of epigenetic control during B cell differentiation, activation and during antibody formation highlight the importance of investing research efforts in dissecting the participation of epigenetic defects in this group of diseases. This review focuses on the role of epigenetic control in B cell biology which can provide clues for the study of potential novel pathogenic defects involved in PADs.
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Affiliation(s)
- Virginia C Rodríguez-Cortez
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Lucia Del Pino-Molina
- Clinical Immunology Department, University Hospital La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
- Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Javier Rodríguez-Ubreva
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, University Hospital La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
- Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Esteban Ballestar
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain.
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28
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Moran S, Arribas C, Esteller M. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics 2015; 8:389-99. [PMID: 26673039 PMCID: PMC4864062 DOI: 10.2217/epi.15.114] [Citation(s) in RCA: 445] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: DNA methylation is the best known epigenetic mark. Cancer and other pathologies show an altered DNA methylome. However, delivering complete DNA methylation maps is compromised by the price and labor-intensive interpretation of single nucleotide methods. Material & methods: Following the success of the HumanMethylation450 BeadChip (Infinium) methylation microarray (450K), we report the technical and biological validation of the newly developed MethylationEPIC BeadChip (Infinium) microarray that covers over 850,000 CpG methylation sites (850K). The 850K microarray contains >90% of the 450K sites, but adds 333,265 CpGs located in enhancer regions identified by the ENCODE and FANTOM5 projects. Results & conclusion: The 850K array demonstrates high reproducibility at the 450K CpG sites, is consistent among technical replicates, is reliable in the matched study of fresh frozen versus formalin-fixed paraffin-embeded samples and is also useful for 5-hydroxymethylcytosine. These results highlight the value of the MethylationEPIC BeadChip as a useful tool for the analysis of the DNA methylation profile of the human genome.
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Affiliation(s)
- Sebastian Moran
- Cancer Epigenetics & Biology Program (PEBC), 08908 L'Hospitalet, Barcelona, Catalonia, Spain
| | - Carles Arribas
- Cancer Epigenetics & Biology Program (PEBC), 08908 L'Hospitalet, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics & Biology Program (PEBC), 08908 L'Hospitalet, Barcelona, Catalonia, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
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29
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Hamidi T, Singh AK, Chen T. Genetic alterations of DNA methylation machinery in human diseases. Epigenomics 2015; 7:247-65. [PMID: 25942534 DOI: 10.2217/epi.14.80] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA methylation plays a critical role in the regulation of chromatin structure and gene expression and is involved in a variety of biological processes. The levels and patterns of DNA methylation are regulated by both DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) and 'demethylating' proteins, including the ten-eleven translocation (TET) family of dioxygenases (TET1, TET2 and TET3). The effects of DNA methylation on chromatin and gene expression are largely mediated by methylated DNA 'reader' proteins, including MeCP2. Numerous mutations in DNMTs, TETs and MeCP2 have been identified in cancer and developmental disorders, highlighting the importance of the DNA methylation machinery in human development and physiology. In this review, we describe these mutations and discuss how they may lead to disease phenotypes.
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Affiliation(s)
- Tewfik Hamidi
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park - Research Division, 1808 Park Road 1C, P. O. Box 389, Smithville, TX 78957, USA
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30
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Tognini P, Napoli D, Pizzorusso T. Dynamic DNA methylation in the brain: a new epigenetic mark for experience-dependent plasticity. Front Cell Neurosci 2015; 9:331. [PMID: 26379502 PMCID: PMC4548453 DOI: 10.3389/fncel.2015.00331] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/10/2015] [Indexed: 02/04/2023] Open
Abstract
Experience-dependent plasticity is the ability of brain circuits to undergo molecular, structural and functional changes as a function of neural activity. Neural activity continuously shapes our brain during all the stages of our life, from infancy through adulthood and beyond. Epigenetic modifications of histone proteins and DNA seem to be a leading molecular mechanism to modulate the transcriptional changes underlying the fine-tuning of synaptic connections and circuitry rewiring during activity-dependent plasticity. The recent discovery that cytosine methylation is an epigenetic mark particularly dynamic in brain cells has strongly increased the interest of neuroscientists in understanding the role of covalent modifications of DNA in activity-induced remodeling of neuronal circuits. Here, we provide an overview of the role of DNA methylation and hydroxylmethylation in brain plasticity both during adulthood, with emphasis on learning and memory related processes, and during postnatal development, focusing specifically on experience-dependent plasticity in the visual cortex.
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Affiliation(s)
- Paola Tognini
- Department of Biological Chemistry, University of California, Irvine Irvine, CA, USA
| | - Debora Napoli
- BioSNS laboratory, Scuola Normale Superiore di Pisa Pisa, Italy
| | - Tommaso Pizzorusso
- Institute of Neuroscience CNR Pisa, Italy ; Department of Neuroscience, Psychology, Drug Research and Child Health Neurofarba, University of Florence Florence, Italy
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31
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Simo-Riudalbas L, Diaz-Lagares A, Gatto S, Gagliardi M, Crujeiras AB, Matarazzo MR, Esteller M, Sandoval J. Genome-Wide DNA Methylation Analysis Identifies Novel Hypomethylated Non-Pericentromeric Genes with Potential Clinical Implications in ICF Syndrome. PLoS One 2015; 10:e0132517. [PMID: 26161907 PMCID: PMC4498748 DOI: 10.1371/journal.pone.0132517] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 06/15/2015] [Indexed: 01/22/2023] Open
Abstract
INTRODUCTION AND RESULTS Immunodeficiency, centromeric instability and facial anomalies syndrome (ICF) is a rare autosomal recessive disease, characterized by severe hypomethylation in pericentromeric regions of chromosomes (1, 16 and 9), marked immunodeficiency and facial anomalies. The majority of ICF patients present mutations in the DNMT3B gene, affecting the DNA methyltransferase activity of the protein. In the present study, we have used the Infinium 450K DNA methylation array to evaluate the methylation level of 450,000 CpGs in lymphoblastoid cell lines and untrasformed fibroblasts derived from ICF patients and healthy donors. Our results demonstrate that ICF-specific DNMT3B variants A603T/STP807ins and V699G/R54X cause global DNA hypomethylation compared to wild-type protein. We identified 181 novel differentially methylated positions (DMPs) including subtelomeric and intrachromosomic regions, outside the classical ICF-related pericentromeric hypomethylated positions. Interestingly, these sites were mainly located in intergenic regions and inside the CpG islands. Among the identified hypomethylated CpG-island associated genes, we confirmed the overexpression of three selected genes, BOLL, SYCP2 and NCRNA00221, in ICF compared to healthy controls, which are supposed to be expressed in germ line and silenced in somatic tissues. CONCLUSIONS In conclusion, this study contributes in clarifying the direct relationship between DNA methylation defect and gene expression impairment in ICF syndrome, identifying novel direct target genes of DNMT3B. A high percentage of the DMPs are located in the subtelomeric regions, indicating a specific role of DNMT3B in methylating these chromosomal sites. Therefore, we provide further evidence that hypomethylation in specific non-pericentromeric regions of chromosomes might be involved in the molecular pathogenesis of ICF syndrome. The detection of DNA hypomethylation at BOLL, SYCP2 and NCRNA00221 may pave the way for the development of specific clinical biomarkers with the aim to facilitate the identification of ICF patients.
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Affiliation(s)
- L. Simo-Riudalbas
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - A. Diaz-Lagares
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - S. Gatto
- Institute of Genetics and Biophysics ABT, CNR, Naples, Italy
| | - M. Gagliardi
- Institute of Genetics and Biophysics ABT, CNR, Naples, Italy
| | - A. B. Crujeiras
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - M. R. Matarazzo
- Institute of Genetics and Biophysics ABT, CNR, Naples, Italy
| | - M. Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - J. Sandoval
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
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32
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Li Q, Suzuki M, Wendt J, Patterson N, Eichten SR, Hermanson PJ, Green D, Jeddeloh J, Richmond T, Rosenbaum H, Burgess D, Springer NM, Greally JM. Post-conversion targeted capture of modified cytosines in mammalian and plant genomes. Nucleic Acids Res 2015; 43:e81. [PMID: 25813045 PMCID: PMC4499119 DOI: 10.1093/nar/gkv244] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/10/2015] [Indexed: 11/14/2022] Open
Abstract
We present a capture-based approach for bisulfite-converted DNA that allows interrogation of pre-defined genomic locations, allowing quantitative and qualitative assessments of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) at CG dinucleotides and in non-CG contexts (CHG, CHH) in mammalian and plant genomes. We show the technique works robustly and reproducibly using as little as 500 ng of starting DNA, with results correlating well with whole genome bisulfite sequencing data, and demonstrate that human DNA can be tested in samples contaminated with microbial DNA. This targeting approach will allow cell type-specific designs to maximize the value of 5mC and 5hmC sequencing.
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Affiliation(s)
- Qing Li
- Department of Plant Biology, University of Minnesota, 1445 Gortner Ave, Saint Paul, MN 55108, USA
| | - Masako Suzuki
- Center for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
| | - Jennifer Wendt
- Roche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USA
| | - Nicole Patterson
- Center for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
| | - Steven R Eichten
- Department of Plant Biology, University of Minnesota, 1445 Gortner Ave, Saint Paul, MN 55108, USA
| | - Peter J Hermanson
- Department of Plant Biology, University of Minnesota, 1445 Gortner Ave, Saint Paul, MN 55108, USA
| | - Dawn Green
- Roche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USA
| | | | - Todd Richmond
- Roche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USA
| | - Heidi Rosenbaum
- Roche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USA
| | - Daniel Burgess
- Roche-NimbleGen, 500 South Rosa Road, Madison, WI 53711, USA
| | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, 1445 Gortner Ave, Saint Paul, MN 55108, USA
| | - John M Greally
- Center for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
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33
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Scourzic L, Mouly E, Bernard OA. TET proteins and the control of cytosine demethylation in cancer. Genome Med 2015; 7:9. [PMID: 25632305 PMCID: PMC4308928 DOI: 10.1186/s13073-015-0134-6] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The discovery that ten-eleven translocation (TET) proteins are α-ketoglutarate-dependent dioxygenases involved in the conversion of 5-methylcytosines (5-mC) to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine and 5-carboxycytosine has revealed new pathways in the cytosine methylation and demethylation process. The description of inactivating mutations in TET2 suggests that cellular transformation is in part caused by the deregulation of this 5-mC conversion. The direct and indirect deregulation of methylation control through mutations in DNA methyltransferase and isocitrate dehydrogenase (IDH) genes, respectively, along with the importance of cytosine methylation in the control of normal and malignant cellular differentiation have provided a conceptual framework for understanding the early steps in cancer development. Here, we review recent advances in our understanding of the cytosine methylation cycle and its implication in cellular transformation, with an emphasis on TET enzymes and 5-hmC. Ongoing clinical trials targeting the activity of mutated IDH enzymes provide a proof of principle that DNA methylation is targetable, and will trigger further therapeutic applications aimed at controlling both early and late stages of cancer development.
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Affiliation(s)
- Laurianne Scourzic
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
| | - Enguerran Mouly
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
| | - Olivier A Bernard
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
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Jeong M, Goodell MA. New answers to old questions from genome-wide maps of DNA methylation in hematopoietic cells. Exp Hematol 2014; 42:609-17. [PMID: 24993071 PMCID: PMC4137036 DOI: 10.1016/j.exphem.2014.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/17/2014] [Accepted: 04/22/2014] [Indexed: 01/10/2023]
Abstract
DNA methylation is a well-studied epigenetic modification essential for efficient cellular differentiation. Aberrant DNA methylation patterns are a characteristic feature of cancer, including myeloid malignancies such as acute myeloid leukemia. Recurrent mutations in DNA-modifying enzymes were identified in acute myeloid leukemia and linked to distinct DNA methylation signatures. In addition, discovery of Tet enzymes provided new mechanisms for the reversal of DNA methylation. Advances in base-resolution profiling of DNA methylation have enabled a more comprehensive understanding of the methylome landscape in the genome. This review will summarize and discuss the key questions in the function of DNA methylation in the hematopoietic system, including where and how DNA methylation regulates diverse biological processes in the genome as elucidated by recent studies.
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Affiliation(s)
- Mira Jeong
- Stem Cells and Regenerative Medicine Center, Department of Pediatrics and Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Margaret A. Goodell
- Stem Cells and Regenerative Medicine Center, Department of Pediatrics and Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Sagie S, Ellran E, Katzir H, Shaked R, Yehezkel S, Laevsky I, Ghanayim A, Geiger D, Tzukerman M, Selig S. Induced pluripotent stem cells as a model for telomeric abnormalities in ICF type I syndrome. Hum Mol Genet 2014; 23:3629-40. [PMID: 24549038 DOI: 10.1093/hmg/ddu071] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Human telomeric regions are packaged as constitutive heterochromatin, characterized by extensive subtelomeric DNA methylation and specific histone modifications. ICF (immunodeficiency, centromeric instability, facial anomalies) type I patients carry mutations in DNA methyltransferase 3B (DNMT3B) that methylates de novo repetitive sequences during early embryonic development. ICF type I patient fibroblasts display hypomethylated subtelomeres, abnormally short telomeres and premature senescence. In order to study the molecular mechanism by which the failure to de novo methylate subtelomeres results in accelerated telomere shortening, we generated induced pluripotent stem cells (iPSCs) from 3 ICF type I patients. Telomeres were elongated in ICF-iPSCs during reprogramming, and the senescence phenotype was abolished despite sustained subtelomeric hypomethylation and high TERRA levels. Fibroblast-like cells (FLs) isolated from differentiated ICF-iPSCs maintained abnormally high TERRA levels, and telomeres in these cells shortened at an accelerated rate, leading to early senescence, thus recapitulating the telomeric phenotype of the parental fibroblasts. These findings demonstrate that the abnormal telomere phenotype associated with subtelomeric hypomethylation is overridden in cells expressing telomerase, therefore excluding telomerase inhibition by TERRA as a central mechanism responsible for telomere shortening in ICF syndrome. The data in the current study lend support to the use of ICF-iPSCs for modeling of phenotypic and molecular defects in ICF syndrome and for unraveling the mechanism whereby subtelomeric hypomethylation is linked to accelerated telomeric loss in this syndrome.
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Affiliation(s)
- Shira Sagie
- Laboratory of Molecular Medicine, Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Erika Ellran
- Laboratory of Molecular Medicine, Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Hagar Katzir
- Laboratory of Molecular Medicine, Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Rony Shaked
- Laboratory of Molecular Medicine, Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Shiran Yehezkel
- Laboratory of Molecular Medicine, Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Ilana Laevsky
- The Sohnis and Forman Families Stem Cell Center, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Alaa Ghanayim
- Computer Science Department, Technion, Haifa 32000, Israel
| | - Dan Geiger
- Computer Science Department, Technion, Haifa 32000, Israel
| | - Maty Tzukerman
- Laboratory of Molecular Medicine, Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Sara Selig
- Laboratory of Molecular Medicine, Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel,
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Aguiar DP, de Farias GC, de Sousa EB, de Mattos Coelho-Aguiar J, Lobo JC, Casado PL, Duarte MEL, Abreu JGR. New strategy to control cell migration and metastasis regulated by CCN2/CTGF. Cancer Cell Int 2014; 14:61. [PMID: 25120383 PMCID: PMC4130434 DOI: 10.1186/1475-2867-14-61] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/21/2014] [Indexed: 12/13/2022] Open
Abstract
Connective tissue growth factor (CTGF)/CCN family member 2 (CCN2) is a CCN family member of matricellular signaling modulators. It has been shown that CCN2/CTGF mediates cell adhesion, aggregation and migration in a large variety of cell types, including vascular endothelial cells, fibroblasts, epithelial cells, aortic smooth muscle and also pluripotent stem cells. Others matricellular proteins are capable of interacting with CCN2/CTGF to mediate its function. Cell migration is a key feature for tumor cell invasion and metastasis. CCN2/CTGF seems to be a prognostic marker for cancer. In addition, here we intend to discuss recent discoveries and a new strategy to develop therapies against CCN2/CTGF, in order to treat cancer metastasis.
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Affiliation(s)
- Diego Pinheiro Aguiar
- Research Division, National Institute of Traumatology and Orthopedics, Rio de Janeiro, RJ, Brazil
| | - Gabriel Correa de Farias
- Research Division, National Institute of Traumatology and Orthopedics, Rio de Janeiro, RJ, Brazil
| | - Eduardo Branco de Sousa
- Research Division, National Institute of Traumatology and Orthopedics, Rio de Janeiro, RJ, Brazil
| | - Juliana de Mattos Coelho-Aguiar
- Program of Cell and Developmental Biology, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Julie Calixto Lobo
- Research Division, National Institute of Traumatology and Orthopedics, Rio de Janeiro, RJ, Brazil
| | - Priscila Ladeira Casado
- Research Division, National Institute of Traumatology and Orthopedics, Rio de Janeiro, RJ, Brazil
| | | | - José Garcia Ribeiro Abreu
- Program of Cell and Developmental Biology, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Sun Z, Wu Y, Ordog T, Baheti S, Nie J, Duan X, Hojo K, Kocher JP, Dyck PJ, Klein CJ. Aberrant signature methylome by DNMT1 hot spot mutation in hereditary sensory and autonomic neuropathy 1E. Epigenetics 2014; 9:1184-93. [PMID: 25033457 DOI: 10.4161/epi.29676] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
DNA methyltransferase 1 (DNMT1) is essential for DNA methylation, gene regulation and chromatin stability. We previously discovered DNMT1 mutations cause hereditary sensory and autonomic neuropathy type 1 with dementia and hearing loss (HSAN1E; OMIM 614116). HSAN1E is the first adult-onset neurodegenerative disorder caused by a defect in a methyltransferase gene. HSAN1E patients appear clinically normal until young adulthood, then begin developing the characteristic symptoms involving central and peripheral nervous systems. Some HSAN1E patients also develop narcolepsy and it has recently been suggested that HSAN1E is allelic to autosomal dominant cerebellar ataxia, deafness, with narcolepsy (ADCA-DN; OMIM 604121), which is also caused by mutations in DNMT1. A hotspot mutation Y495C within the targeting sequence domain of DNMT1 has been identified among HSAN1E patients. The mutant DNMT1 protein shows premature degradation and reduced DNA methyltransferase activity. Herein, we investigate genome-wide DNA methylation at single-base resolution through whole-genome bisulfite sequencing of germline DNA in 3 pairs of HSAN1E patients and their gender- and age-matched siblings. Over 1 billion 75-bp single-end reads were generated for each sample. In the 3 affected siblings, overall methylation loss was consistently found in all chromosomes with X and 18 being most affected. Paired sample analysis identified 564,218 differentially methylated CpG sites (DMCs; P<0.05), of which 300 134 were intergenic and 264 084 genic CpGs. Hypomethylation was predominant in both genic and intergenic regions, including promoters, exons, most CpG islands, L1, L2, Alu, and satellite repeats and simple repeat sequences. In some CpG islands, hypermethylated CpGs outnumbered hypomethylated CpGs. In 201 imprinted genes, there were more DMCs than in non-imprinted genes and most were hypomethylated. Differentially methylated region (DMR) analysis identified 5649 hypomethylated and 1872 hypermethylated regions. Importantly, pathway analysis revealed 1693 genes associated with the identified DMRs were highly associated in diverse neurological disorders and NAD+/NADH metabolism pathways is implicated in the pathogenesis. Our results provide novel insights into the epigenetic mechanism of neurodegeneration arising from a hotspot DNMT1 mutation and reveal pathways potentially important in a broad category of neurological and psychological disorders.
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Affiliation(s)
- Zhifu Sun
- Division of Biomedical Statistics and Informatics; Mayo Clinic; Rochester, MN USA; Epigenomics Translational Program; Mayo Clinic Center for Individualized Medicine; Rochester, MN USA; Bioinformatics Program; Mayo Clinic Center for Individualized Medicine; Rochester, MN USA
| | - Yanhong Wu
- Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester, MN USA
| | - Tamas Ordog
- Epigenomics Translational Program; Mayo Clinic Center for Individualized Medicine; Rochester, MN USA; Department of Physiology and Biomedical Engineering; Mayo Clinic; Rochester, MN USA
| | - Saurabh Baheti
- Division of Biomedical Statistics and Informatics; Mayo Clinic; Rochester, MN USA
| | - Jinfu Nie
- Division of Biomedical Statistics and Informatics; Mayo Clinic; Rochester, MN USA
| | - Xiaohui Duan
- Department of Neurology; Mayo Clinic; Rochester, MN USA
| | - Kaori Hojo
- Harima Sanatorium; Division of Neuropsychiatry; Hyogo, Japan
| | - Jean-Pierre Kocher
- Division of Biomedical Statistics and Informatics; Mayo Clinic; Rochester, MN USA; Bioinformatics Program; Mayo Clinic Center for Individualized Medicine; Rochester, MN USA
| | - Peter J Dyck
- Department of Neurology; Mayo Clinic; Rochester, MN USA
| | - Christopher J Klein
- Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester, MN USA; Department of Neurology; Mayo Clinic; Rochester, MN USA; Department of Medical Genetics; Mayo Clinic; Rochester, MN USA
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Weissman J, Naidu S, Bjornsson HT. Abnormalities of the DNA methylation mark and its machinery: an emerging cause of neurologic dysfunction. Semin Neurol 2014; 34:249-57. [PMID: 25192503 PMCID: PMC4512289 DOI: 10.1055/s-0034-1386763] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recently, Mendelian disorders of the DNA methylation machinery have been described which demonstrate the complex roles of epigenetics in neurodevelopment and disease. For example, defects of DNMT1, the maintenance methyltransferase, lead to adult-onset progressive neurologic disorders, whereas defects of the de novo methyltransferases DNMT3A and DNMT3B lead to nonprogressive neurodevelopmental conditions. Furthermore, patients with DNMT3A deficiency demonstrate overgrowth, a feature common to disorders of histone machinery and imprinting disorders, highlighting the interconnectedness of the many epigenetic layers. Disorders of the DNA methylation machinery include both the aforementioned "writers" and also the "readers" of the methyl mark, such as MeCP2, the cause of Rett syndrome. Any dosage disruption, either haploinsufficiency or overexpression of DNA methylation machinery leads to widespread gene expression changes in trans, disrupting expression of a subset of target genes that contribute to individual disease phenotypes. In contrast, classical imprinting disorders such as Angelman syndrome have been thought generally to cause epigenetic dysregulation in cis. However, the recent description of multilocus methylation disorders challenges this generalization. Here, in addition to summarizing recent developments in identifying the pathogenesis of these diseases, we highlight clinical considerations and some unexpected therapeutic opportunities, such as topoisomerase inhibitors for classical imprinting disorders.
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Affiliation(s)
- Jacqueline Weissman
- Kennedy Krieger Institute, Baltimore, Maryland
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sakkubai Naidu
- Kennedy Krieger Institute, Baltimore, Maryland
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hans T. Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Velasco G, Walton EL, Sterlin D, Hédouin S, Nitta H, Ito Y, Fouyssac F, Mégarbané A, Sasaki H, Picard C, Francastel C. Germline genes hypomethylation and expression define a molecular signature in peripheral blood of ICF patients: implications for diagnosis and etiology. Orphanet J Rare Dis 2014; 9:56. [PMID: 24742017 PMCID: PMC4022050 DOI: 10.1186/1750-1172-9-56] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/11/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Immunodeficiency Centromeric Instability and Facial anomalies (ICF) is a rare autosomal recessive disease characterized by reduction in serum immunoglobulins with severe recurrent infections, facial dysmorphism, and more variable symptoms including mental retardation. ICF is directly related to a genomic methylation defect that mainly affects juxtacentromeric heterochromatin regions of certain chromosomes, leading to chromosomal rearrangements that constitute a hallmark of this syndrome upon cytogenetic testing. Mutations in the de novo DNA methyltransferase DNMT3B, the protein ZBTB24 of unknown function, or loci that remain to be identified, lie at its origin. Despite unifying features, common or distinguishing molecular signatures are still missing for this disease. METHOD We used the molecular signature that we identified in a mouse model for ICF1 to establish transcriptional biomarkers to facilitate diagnosis and understanding of etiology of the disease. We assayed the expression and methylation status of a set of genes whose expression is normally restricted to germ cells, directly in whole blood samples and epithelial cells of ICF patients. RESULTS We report that DNA hypomethylation and expression of MAEL and SYCE1 represent robust biomarkers, easily testable directly from uncultured cells to diagnose the most prevalent sub-type of the syndrome. In addition, we identified the first unifying molecular signatures for ICF patients. Of importance, we validated the use of our biomarkers to diagnose a baby born to a family with a sick child. Finally, our analysis revealed unsuspected complex molecular signatures in two ICF patients suggestive of a novel genetic etiology for the disease. CONCLUSIONS Early diagnosis of ICF syndrome is crucial since early immunoglobulin supplementation can improve the course of disease. However, ICF is probably underdiagnosed, especially in patients that present with incomplete phenotype or born to families with no affected relatives. The specific and robust biomarkers identified in this study could be introduced into routine clinical immunology or neurology departments to facilitate testing of patients with suspected ICF syndrome. In addition, as exemplified by two patients with a combination of molecular defects never described before, our data support the search for new types of mutations at the origin of ICF syndrome.
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Affiliation(s)
- Guillaume Velasco
- Université Paris Diderot-Paris7, CNRS UMR7216, Epigénétique et Destin Cellulaire, Case Courrier 7042; 35, rue Hélène Brion, 75205 Paris, France.
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Della Ragione F, Gagliardi M, D'Esposito M, Matarazzo MR. Non-coding RNAs in chromatin disease involving neurological defects. Front Cell Neurosci 2014; 8:54. [PMID: 24616662 PMCID: PMC3933927 DOI: 10.3389/fncel.2014.00054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/06/2014] [Indexed: 01/25/2023] Open
Abstract
Novel classes of small and long non-coding RNAs (ncRNAs) are increasingly becoming apparent, being engaged in diverse structural, functional and regulatory activities. They take part in target gene silencing, play roles in transcriptional, post-transcriptional and epigenetic processes, such as chromatin remodeling, nuclear reorganization with the formation of silent compartments and fine-tuning of gene recruitment into them. Among their functions, non-coding RNAs are thought to act either as guide or scaffold for epigenetic modifiers that write, erase, and read the epigenetic signature over the genome. Studies on human disorders caused by defects in epigenetic modifiers and involving neurological phenotypes highlight the disruption of diverse classes of non-coding RNAs. Noteworthy, these molecules mediate a wide spectrum of neuronal functions, including brain development, and synaptic plasticity. These findings imply a significant contribution of ncRNAs in pathophysiology of the aforesaid diseases and provide new concepts for potential therapeutic applications.
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Affiliation(s)
- Floriana Della Ragione
- Functional Genomics and Epigenomics Laboratory, Institute of Genetics and Biophysics "ABT," Consiglio Nazionale delle Ricerche Naples, Italy ; Laboratorio di Genomica e di Epigenomica, Istituto di Ricovero e Cura a Carattere Scientifico Neuromed Pozzilli, Italy
| | - Miriam Gagliardi
- Functional Genomics and Epigenomics Laboratory, Institute of Genetics and Biophysics "ABT," Consiglio Nazionale delle Ricerche Naples, Italy ; Laboratorio di Genomica e di Epigenomica, Istituto di Ricovero e Cura a Carattere Scientifico Neuromed Pozzilli, Italy
| | - Maurizio D'Esposito
- Functional Genomics and Epigenomics Laboratory, Institute of Genetics and Biophysics "ABT," Consiglio Nazionale delle Ricerche Naples, Italy ; Laboratorio di Genomica e di Epigenomica, Istituto di Ricovero e Cura a Carattere Scientifico Neuromed Pozzilli, Italy
| | - Maria R Matarazzo
- Functional Genomics and Epigenomics Laboratory, Institute of Genetics and Biophysics "ABT," Consiglio Nazionale delle Ricerche Naples, Italy ; Laboratorio di Genomica e di Epigenomica, Istituto di Ricovero e Cura a Carattere Scientifico Neuromed Pozzilli, Italy
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Understanding the relationship between DNA methylation and histone lysine methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1362-72. [PMID: 24560929 PMCID: PMC4316174 DOI: 10.1016/j.bbagrm.2014.02.007] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/11/2014] [Indexed: 12/19/2022]
Abstract
DNA methylation acts as an epigenetic modification in vertebrate DNA. Recently it has become clear that the DNA and histone lysine methylation systems are highly interrelated and rely mechanistically on each other for normal chromatin function in vivo. Here we examine some of the functional links between these systems, with a particular focus on several recent discoveries suggesting how lysine methylation may help to target DNA methylation during development, and vice versa. In addition, the emerging role of non-methylated DNA found in CpG islands in defining histone lysine methylation profiles at gene regulatory elements will be discussed in the context of gene regulation. This article is part of a Special Issue entitled: Methylation: A Multifaceted Modification — looking at transcription and beyond. There is an emerging realisation that DNA and histone lysine methylation in mammals are highly interrelated. Targeting of DNA methylation is mechanistically linked to H3K9 methylation. Uhrf1 acts as a link between H3K9 methylation and maintenance methylation during DNA replication. Targeting of Dnmt3a/b is influenced by H3K4 and H3K36 methylation. Non-methylated DNA at CpG islands influences histone methylation through ZF-CxxC proteins.
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Heyn H, Méndez-González J, Esteller M. Epigenetic profiling joins personalized cancer medicine. Expert Rev Mol Diagn 2014; 13:473-9. [DOI: 10.1586/erm.13.36] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Iozzo P, Holmes M, Schmidt MV, Cirulli F, Guzzardi MA, Berry A, Balsevich G, Andreassi MG, Wesselink JJ, Liistro T, Gómez-Puertas P, Eriksson JG, Seckl J. Developmental ORIgins of Healthy and Unhealthy AgeiNg: the role of maternal obesity--introduction to DORIAN. Obes Facts 2014; 7:130-51. [PMID: 24801105 PMCID: PMC5644840 DOI: 10.1159/000362656] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 02/12/2014] [Indexed: 12/31/2022] Open
Abstract
Europe has the highest proportion of elderly people in the world. Cardiovascular disease, type 2 diabetes, sarcopenia and cognitive decline frequently coexist in the same aged individual, sharing common early risk factors and being mutually reinforcing. Among conditions which may contribute to establish early risk factors, this review focuses on maternal obesity, since the epidemic of obesity involves an ever growing number of women of reproductive age and children, calling for appropriate studies to understand the consequences of maternal obesity on the offspring's health and for developing effective measures and policies to improve people's health before their conception and birth. Though the current knowledge suggests that the long-term impact of maternal obesity on the offspring's health may be substantial, the outcomes of maternal obesity over the lifespan have not been quantified, and the molecular changes induced by maternal obesity remain poorly characterized. We hypothesize that maternal insulin resistance and reduced placental glucocorticoid catabolism, leading to oxidative stress, may damage the DNA, either in its structure (telomere shortening) or in its function (via epigenetic changes), resulting in altered gene expression/repair, disease during life, and pathological ageing. This review illustrates the background to the EU-FP7-HEALTH-DORIAN project.
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Affiliation(s)
- Patricia Iozzo
- Institute of Clinical Physiology, National Research Council (CNR), Pis
- *Patricia Iozzo, MD, PhD, Institute of Clinical Physiology, National Research Council (CNR), Via Moruzzi 1, 56124 Pisa (Italy),
| | - Megan Holmes
- Endocrinology Unit, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | | | | | | | | | | | | | | | - Tiziana Liistro
- Institute of Clinical Physiology, National Research Council (CNR), Pis
| | | | - Johan G. Eriksson
- Samfundet Folkhälsan i Svenska Finland rf (Folkhälsan), Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland
| | - Jonathan Seckl
- Endocrinology Unit, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
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Sandoval J, Peiró-Chova L, Pallardó FV, García-Giménez JL. Epigenetic biomarkers in laboratory diagnostics: emerging approaches and opportunities. Expert Rev Mol Diagn 2013; 13:457-71. [PMID: 23782253 DOI: 10.1586/erm.13.37] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetics has emerged as a new and promising field in recent years. Lifestyle, stress, drugs, physiopathological situations and pharmacological interventions have a great impact on the epigenetic code of the cells by altering the methylome, miRNA expression and the covalent histone modifications. Since there exists a need to find new biomarkers and improve diagnosis for several diseases, the research on epigenetic biomarkers for molecular diagnostics encourages the translation of this field from the bench to clinical practice. In this context, deciphering intricate epigenetic modifications involved in several molecular processes is a challenge that will be solved in the near future. In this review, the authors present an overview of the high-throughput technologies and laboratory techniques available for epigenetic studies, and also discuss which of them are more reliable to be used in a clinical diagnostic laboratory. In addition, the authors describe the most promising epigenetic biomarkers in lung, colorectal and prostate cancer, in which most advances have been achieved. Finally, the authors describe epigenetic biomarkers in some rare diseases; these rare syndromes are paradigms for a specific impaired molecular pathway, thus providing valuable information on the discovery of new epigenetic biomarkers.
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Affiliation(s)
- Juan Sandoval
- Epigenetics and Cancer Biology, Institut d'Investigació Biomèdica de Bellvitge IDIBELL, Barcelona, Spain
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Fali T, Le Dantec C, Thabet Y, Jousse S, Hanrotel C, Youinou P, Brooks WH, Perl A, Renaudineau Y. DNA methylation modulates HRES1/p28 expression in B cells from patients with Lupus. Autoimmunity 2013; 47:265-71. [PMID: 24117194 DOI: 10.3109/08916934.2013.826207] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Systemic lupus erythematosus (SLE) disease is an autoimmune disease of unknown aetiology that affects predominantly women of child bearing age. Since previous studies, including ours, have demonstrated that CD4+ T cells and B cells from SLE patients are defective in their ability to methylate their DNA upon antigen stimulation, the aim of this study was to investigate whether DNA demethylation affects the transcription of HRES-1 in B cells. HRES-1 is the prototype of Human Endogenous Retrovirus (HERV) overexpressed in SLE. We have observed that SLE B cells were characterized by their incapacity to methylate the HRES-1 promoter, both in unstimulated and in anti-IgM stimulated B cells. In turn, HRES-1/p28 expression was increased in SLE B cells after B cell receptor engagement, but not in controls. In SLE B cells the Erk/DNMT1 pathway was defective. In addition, blocking the autocrine-loop of IL-6 in SLE B cells with an anti-IL-6 receptor monoclonal antibody restores DNA methylation and control of HRES-1/p28 expression became effective. As a consequence, a better understanding of HERV dysregulation in SLE reinforces our comprehension of the disease and opens new therapeutic perspectives.
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Affiliation(s)
- Tinhinane Fali
- EA2216 "Immunology, Pathology and Immunotherapy", University of Brittany, SFR ScinBios and Labex Igo "Immunotherapy Graft, Oncology" , Brest , France
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Youngson NA, Epp T, Roberts AR, Daxinger L, Ashe A, Huang E, Lester KL, Harten SK, Kay GF, Cox T, Matthews JM, Chong S, Whitelaw E. No evidence for cumulative effects in a Dnmt3b hypomorph across multiple generations. Mamm Genome 2013; 24:206-17. [PMID: 23636699 DOI: 10.1007/s00335-013-9451-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/05/2013] [Indexed: 12/31/2022]
Abstract
Observations of inherited phenotypes that cannot be explained solely through genetic inheritance are increasing. Evidence points to transmission of non-DNA molecules in the gamete as mediators of the phenotypes. However, in most cases it is unclear what the molecules are, with DNA methylation, chromatin proteins, and small RNAs being the most prominent candidates. From a screen to generate novel mouse mutants of genes involved in epigenetic reprogramming, we produced a DNA methyltransferase 3b allele that is missing exon 13. Mice that are homozygous for the mutant allele have smaller stature and reduced viability, with particularly high levels of female post-natal death. Reduced DNA methylation was also detected at telocentric repeats and the X-linked Hprt gene. However, none of the abnormal phenotypes or DNA methylation changes worsened with multiple generations of homozygous mutant inbreeding. This suggests that in our model the abnormalities are reset each generation and the processes of transgenerational epigenetic reprogramming are effective in preventing their inheritance.
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Affiliation(s)
- Neil A Youngson
- Queensland Institute of Medical Research, Herston, Brisbane, QLD 4006, Australia.
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Regionally specific and genome-wide analyses conclusively demonstrate the absence of CpG methylation in human mitochondrial DNA. Mol Cell Biol 2013; 33:2683-90. [PMID: 23671186 DOI: 10.1128/mcb.00220-13] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Although CpG methylation clearly distributes genome-wide in vertebrate nuclear DNA, the state of methylation in the vertebrate mitochondrial genome has been unclear. Several recent reports using immunoprecipitation, mass spectrometry, and enzyme-linked immunosorbent assay methods concluded that human mitochondrial DNA (mtDNA) has much more than the 2 to 5% CpG methylation previously estimated. However, these methods do not provide information as to the sites or frequency of methylation at each CpG site. Here, we have used the more definitive bisulfite genomic sequencing method to examine CpG methylation in HCT116 human cells and primary human cells to independently answer these two questions. We found no evidence of CpG methylation at a biologically significant level in these regions of the human mitochondrial genome. Furthermore, unbiased next-generation sequencing of sodium bisulfite treated total DNA from HCT116 cells and analysis of genome-wide sodium bisulfite sequencing data sets from several other DNA sources confirmed this absence of CpG methylation in mtDNA. Based on our findings using regionally specific and genome-wide approaches with multiple human cell sources, we can definitively conclude that CpG methylation is absent in mtDNA. It is highly unlikely that CpG methylation plays any role in direct control of mitochondrial function.
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Yehezkel S, Shaked R, Sagie S, Berkovitz R, Shachar-Bener H, Segev Y, Selig S. Characterization and rescue of telomeric abnormalities in ICF syndrome type I fibroblasts. Front Oncol 2013; 3:35. [PMID: 23450006 PMCID: PMC3584450 DOI: 10.3389/fonc.2013.00035] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 02/08/2013] [Indexed: 11/19/2022] Open
Abstract
Mutations in the human DNA methyltransferase 3B (DNMT3B) gene lead to ICF (immunodeficiency, centromeric region instability, and facial anomalies) syndrome type I. We have previously described a telomere-related phenotype in cells from these patients, involving severe hypomethylation of subtelomeric regions, abnormally short telomeres and high levels of telomeric-repeat-containing RNA (TERRA). Here we demonstrate that ICF-patient fibroblasts carry abnormally short telomeres at a low population doubling (PD) and enter senescence prematurely. Accordingly, we attempted to rescue the senescence phenotype by ectopic expression of human telomerase, which led to elongated telomeres with hypomethylated subtelomeres. The senescence phenotype was overcome under these conditions, thus dissociating subtelomeric-DNA hypomethylation per se from the senescence phenotype. In addition, we examined whether the subtelomeric methylation could be restored by expression of a normal copy of full length DNMT3B1 in ICF fibroblasts. Ectopic expression of DNMT3B1 failed to rescue the abnormal hypomethylation at subtelomeres. However, partial rescue of subtelomeric-hypomethylation was achieved by co-expression of DNMT3B1 together with DNA methyltransferase 3-like (DNMT3L), encoding a protein that functions as a stimulator of DNMT3A and DNMT3B. DNMT3B1 and DNMT3L are predominantly expressed during early embryonic development, suggesting that de novo subtelomeric DNA methylation during crucial stages of human embryonic development may be necessary for setting and maintaining normal telomere length.
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Affiliation(s)
- Shiran Yehezkel
- Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Molecular Medicine Laboratory, Technion-Israel Institute of Technology Haifa, Israel
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Berdasco M, Esteller M. Genetic syndromes caused by mutations in epigenetic genes. Hum Genet 2013; 132:359-83. [PMID: 23370504 DOI: 10.1007/s00439-013-1271-x] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 01/18/2013] [Indexed: 12/21/2022]
Abstract
The orchestrated organization of epigenetic factors that control chromatin dynamism, including DNA methylation, histone marks, non-coding RNAs (ncRNAs) and chromatin-remodeling proteins, is essential for the proper function of tissue homeostasis, cell identity and development. Indeed, deregulation of epigenetic profiles has been described in several human pathologies, including complex diseases (such as cancer, cardiovascular and neurological diseases), metabolic pathologies (type 2 diabetes and obesity) and imprinting disorders. Over the last decade it has become increasingly clear that mutations of genes involved in epigenetic mechanism, such as DNA methyltransferases, methyl-binding domain proteins, histone deacetylases, histone methylases and members of the SWI/SNF family of chromatin remodelers are linked to human disorders, including Immunodeficiency Centromeric instability Facial syndrome 1, Rett syndrome, Rubinstein-Taybi syndrome, Sotos syndrome or alpha-thalassemia/mental retardation X-linked syndrome, among others. As new members of the epigenetic machinery are described, the number of human syndromes associated with epigenetic alterations increases. As recent examples, mutations of histone demethylases and members of the non-coding RNA machinery have recently been associated with Kabuki syndrome, Claes-Jensen X-linked mental retardation syndrome and Goiter syndrome. In this review, we describe the variety of germline mutations of epigenetic modifiers that are known to be associated with human disorders, and discuss the therapeutic potential of epigenetic drugs as palliative care strategies in the treatment of such disorders.
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Affiliation(s)
- María Berdasco
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908 L'Hospitalet de LLobregat, Barcelona, Catalonia, Spain
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Acute hypersensitivity of pluripotent testicular cancer-derived embryonal carcinoma to low-dose 5-aza deoxycytidine is associated with global DNA Damage-associated p53 activation, anti-pluripotency and DNA demethylation. PLoS One 2012; 7:e53003. [PMID: 23300844 PMCID: PMC3531428 DOI: 10.1371/journal.pone.0053003] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 11/26/2012] [Indexed: 12/28/2022] Open
Abstract
Human embryonal carcinoma (EC) cells are the stem cells of nonseminoma testicular germ cells tumors (TGCTs) and share remarkable similarities to human embryonic stem (ES) cells. In prior work we found that EC cells are hypersensitive to low nanomolar doses of 5-aza deoxycytidine (5-aza) and that this hypersensitivity partially depended on unusually high levels of the DNA methyltransferase, DNMT3B. We show here that low-dose 5-aza treatment results in DNA damage and induction of p53 in NT2/D1 cells. In addition, low-dose 5-aza results in global and gene specific promoter DNA hypomethylation. Low-dose 5-aza induces a p53 transcriptional signature distinct from that induced with cisplatin in NT2/D1 cells and also uniquely downregulates genes associated with pluripotency including NANOG, SOX2, GDF3 and Myc target genes. Changes in the p53 and pluripotency signatures with 5-aza were to a large extent dependent on high levels of DNMT3B. In contrast to the majority of p53 target genes upregulated by 5-aza that did not show DNA hypomethylation, several other genes induced with 5-aza had corresponding decreases in promoter methylation. These genes include RIN1, SOX15, GPER, and TLR4 and are novel candidate tumors suppressors in TGCTs. Our studies suggest that the hypersensitivity of NT2/D1 cells to low-dose 5-aza is multifactorial and involves the combined activation of p53 targets, repression of pluripotency genes, and activation of genes repressed by DNA methylation. Low-dose 5-aza therapy may be a general strategy to treat those tumors that are sustained by cells with embryonic stem-like properties.GEO NUMBER FOR THE MICROARRAY DATA: GSE42647.
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