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Younesian S, Mohammadi MH, Younesian O, Momeny M, Ghaffari SH, Bashash D. DNA methylation in human diseases. Heliyon 2024; 10:e32366. [PMID: 38933971 PMCID: PMC11200359 DOI: 10.1016/j.heliyon.2024.e32366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Aberrant epigenetic modifications, particularly DNA methylation, play a critical role in the pathogenesis and progression of human diseases. The current review aims to reveal the role of aberrant DNA methylation in the pathogenesis and progression of diseases and to discuss the original data obtained from international research laboratories on this topic. In the review, we mainly summarize the studies exploring the role of aberrant DNA methylation as diagnostic and prognostic biomarkers in a broad range of human diseases, including monogenic epigenetics, autoimmunity, metabolic disorders, hematologic neoplasms, and solid tumors. The last section provides a general overview of the possibility of the DNA methylation machinery from the perspective of pharmaceutic approaches. In conclusion, the study of DNA methylation machinery is a phenomenal intersection that each of its ways can reveal the mysteries of various diseases, introduce new diagnostic and prognostic biomarkers, and propose a new patient-tailored therapeutic approach for diseases.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Ommolbanin Younesian
- School of Medicine, Tonekabon Branch, Islamic Azad University, Tonekabon, 46841-61167 Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, 1411713135 Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
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Cousu C, Mulot E, De Smet A, Formichetti S, Lecoeuche D, Ren J, Muegge K, Boulard M, Weill JC, Reynaud CA, Storck S. Germinal center output is sustained by HELLS-dependent DNA-methylation-maintenance in B cells. Nat Commun 2023; 14:5695. [PMID: 37709749 PMCID: PMC10502085 DOI: 10.1038/s41467-023-41317-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/29/2023] [Indexed: 09/16/2023] Open
Abstract
HELLS/LSH (Helicase, Lymphoid Specific) is a SNF2-like chromatin remodelling protein involved in DNA methylation. Its loss-of-function in humans causes humoral immunodeficiency, called ICF4 syndrome (Immunodeficiency, Centromeric Instability, Facial anomalies). Here we show by our newly generated B-cell-specific Hells conditional knockout mouse model that HELLS plays a pivotal role in T-dependent B-cell responses. HELLS deficiency induces accelerated decay of germinal center (GC) B cells and impairs the generation of high affinity memory B cells and circulating antibodies. Mutant GC B cells undergo dramatic DNA hypomethylation and massive de-repression of evolutionary recent retrotransposons, which surprisingly does not directly affect their survival. Instead, they prematurely upregulate either memory B cell markers or the transcription factor ATF4, which is driving an mTORC1-dependent metabolic program typical of plasma cells. Treatment of wild type mice with a DNMT1-specific inhibitor phenocopies the accelerated kinetics, thus pointing towards DNA-methylation maintenance by HELLS being a crucial mechanism to fine-tune the GC transcriptional program and enable long-lasting humoral immunity.
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Affiliation(s)
- Clara Cousu
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Eléonore Mulot
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Annie De Smet
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Sara Formichetti
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), 00015, Monterotondo, Italy
- Joint PhD degree program, European Molecular Biology Laboratory and Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Damiana Lecoeuche
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Jianke Ren
- Epigenetics Section, Frederick National Laboratory for Cancer Research in the Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
- NHC Key Lab of Reproduction Regulation,Shanghai Engineering Research Center of Reproductive Health Drug and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Kathrin Muegge
- Epigenetics Section, Frederick National Laboratory for Cancer Research in the Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
| | - Matthieu Boulard
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), 00015, Monterotondo, Italy
| | - Jean-Claude Weill
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Claude-Agnès Reynaud
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Sébastien Storck
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France.
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Bonefas KM, Iwase S. Soma-to-germline transformation in chromatin-linked neurodevelopmental disorders? FEBS J 2022; 289:2301-2317. [PMID: 34514717 PMCID: PMC8918023 DOI: 10.1111/febs.16196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/16/2021] [Accepted: 09/10/2021] [Indexed: 01/22/2023]
Abstract
Mutations in numerous chromatin regulators cause neurodevelopmental disorders (NDDs) with unknown mechanisms. Understandably, most research has focused on how chromatin regulators control gene expression that is directly relevant to brain development and function, such as synaptic genes. However, some NDD models surprisingly show ectopic expression of germline genes in the brain. These germline genes are usually expressed only in the primordial germ cells, testis, and ovaries for germ cell development and sexual reproduction. Such ectopic germline gene expression has been reported in several NDDs, including immunodeficiency, centromeric instability, facial anomalies syndrome 1; Kleefstra syndrome 1; MeCP2 duplication syndrome; and mental retardation, X-linked syndromic, Claes-Jensen type. The responsible genes, DNMT3B, G9A/GLP, MECP2, and KDM5C, all encode chromatin regulators for gene silencing. These mutations may therefore lead to germline gene derepression and, in turn, a severe identity crisis of brain cells-potentially interfering with normal brain development. Thus, the ectopic expression of germline genes is a unique hallmark defining this NDD subset and further implicates the importance of germline gene silencing during brain development. The functional impact of germline gene expression on brain development, however, remains undetermined. This perspective article explores how this apparent soma-to-germline transformation arises and how it may interfere with neurodevelopment through genomic instability and impaired sensory cilium formation. Furthermore, we also discuss how to test these hypotheses experimentally to ultimately determine the contribution of ectopic germline transcripts to chromatin-linked NDDs.
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Affiliation(s)
- Katherine M. Bonefas
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109,The University of Michigan Neuroscience Graduate Program,Corresponding authors: Please address correspondence to: , and
| | - Shigeki Iwase
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109,The University of Michigan Neuroscience Graduate Program,Corresponding authors: Please address correspondence to: , and
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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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5
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Velasco G, Ulveling D, Rondeau S, Marzin P, Unoki M, Cormier-Daire V, Francastel C. Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders. Int J Mol Sci 2021; 22:3735. [PMID: 33916664 PMCID: PMC8038329 DOI: 10.3390/ijms22073735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
DNA methylation (DNAme) profiling is used to establish specific biomarkers to improve the diagnosis of patients with inherited neurodevelopmental disorders and to guide mutation screening. In the specific case of mendelian disorders of the epigenetic machinery, it also provides the basis to infer mechanistic aspects with regard to DNAme determinants and interplay between histone and DNAme that apply to humans. Here, we present comparative methylomes from patients with mutations in the de novo DNA methyltransferases DNMT3A and DNMT3B, in their catalytic domain or their N-terminal parts involved in reading histone methylation, or in histone H3 lysine (K) methylases NSD1 or SETD2 (H3 K36) or KMT2D/MLL2 (H3 K4). We provide disease-specific DNAme signatures and document the distinct consequences of mutations in enzymes with very similar or intertwined functions, including at repeated sequences and imprinted loci. We found that KMT2D and SETD2 germline mutations have little impact on DNAme profiles. In contrast, the overlapping DNAme alterations downstream of NSD1 or DNMT3 mutations underlines functional links, more specifically between NSD1 and DNMT3B at heterochromatin regions or DNMT3A at regulatory elements. Together, these data indicate certain discrepancy with the mechanisms described in animal models or the existence of redundant or complementary functions unforeseen in humans.
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Affiliation(s)
- Guillaume Velasco
- Université de Paris, Epigenetics and Cell Fate, CNRS UMR7216, 75013 Paris, France; (G.V.); (D.U.)
| | - Damien Ulveling
- Université de Paris, Epigenetics and Cell Fate, CNRS UMR7216, 75013 Paris, France; (G.V.); (D.U.)
| | - Sophie Rondeau
- Imagine Institute, Université de Paris, Clinical Genetics, INSERM UMR 1163, Necker Enfants Malades Hospital, 75015 Paris, France; (S.R.); (P.M.); (V.C.-D.)
| | - Pauline Marzin
- Imagine Institute, Université de Paris, Clinical Genetics, INSERM UMR 1163, Necker Enfants Malades Hospital, 75015 Paris, France; (S.R.); (P.M.); (V.C.-D.)
| | - Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
| | - Valérie Cormier-Daire
- Imagine Institute, Université de Paris, Clinical Genetics, INSERM UMR 1163, Necker Enfants Malades Hospital, 75015 Paris, France; (S.R.); (P.M.); (V.C.-D.)
| | - Claire Francastel
- Université de Paris, Epigenetics and Cell Fate, CNRS UMR7216, 75013 Paris, France; (G.V.); (D.U.)
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6
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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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7
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Lsh/HELLS is required for B lymphocyte development and immunoglobulin class switch recombination. Proc Natl Acad Sci U S A 2020; 117:20100-20108. [PMID: 32727902 PMCID: PMC7443918 DOI: 10.1073/pnas.2004112117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mutation of HELLS (Helicase, Lymphoid-Specific)/Lsh in human DNA causes a severe immunodeficiency syndrome, but the nature of the defect remains unknown. We assessed here the role of Lsh in hematopoiesis using conditional Lsh knockout mice with expression of Mx1 or Vav Cre-recombinase. Bone marrow transplantation studies revealed that Lsh depletion in hematopoietic stem cells severely reduced B cell numbers and impaired B cell development in a hematopoietic cell-autonomous manner. Lsh-deficient mice without bone marrow transplantation exhibited lower Ig levels in vivo compared to controls despite normal peripheral B cell numbers. Purified B lymphocytes proliferated normally but produced less immunoglobulins in response to in vitro stimulation, indicating a reduced capacity to undergo class switch recombination (CSR). Analysis of germline transcripts, examination of double-stranded breaks using biotin-labeling DNA break assay, and End-seq analysis indicated that the initiation of the recombination process was unscathed. In contrast, digestion-circularization PCR analysis and high-throughput sequencing analyses of CSR junctions and a chromosomal break repair assay indicated an impaired ability of the canonical end-joining pathway in Lsh-deficient B cells. Our data suggest a hematopoietic cell-intrinsic role of Lsh in B cell development and in CSR providing a potential target for immunodeficiency therapy.
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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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9
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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: 28] [Impact Index Per Article: 5.6] [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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10
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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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11
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Unoki M, Funabiki H, Velasco G, Francastel C, Sasaki H. CDCA7 and HELLS mutations undermine nonhomologous end joining in centromeric instability syndrome. J Clin Invest 2018; 129:78-92. [PMID: 30307408 DOI: 10.1172/jci99751] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023] Open
Abstract
Mutations in CDCA7 and HELLS that respectively encode a CXXC-type zinc finger protein and an SNF2 family chromatin remodeler cause immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome types 3 and 4. Here, we demonstrate that the classical nonhomologous end joining (C-NHEJ) proteins Ku80 and Ku70, as well as HELLS, coimmunoprecipitated with CDCA7. The coimmunoprecipitation of the repair proteins was sensitive to nuclease treatment and an ICF3 mutation in CDCA7 that impairs its chromatin binding. The functional importance of these interactions was strongly suggested by the compromised C-NHEJ activity and significant delay in Ku80 accumulation at DNA damage sites in CDCA7- and HELLS-deficient HEK293 cells. Consistent with the repair defect, these cells displayed increased apoptosis, abnormal chromosome segregation, aneuploidy, centrosome amplification, and significant accumulation of γH2AX signals. Although less prominent, cells with mutations in the other ICF genes DNMT3B and ZBTB24 (responsible for ICF types 1 and 2, respectively) showed similar defects. Importantly, lymphoblastoid cells from ICF patients shared the same changes detected in the mutant HEK293 cells to varying degrees. Although the C-NHEJ defect alone did not cause CG hypomethylation, CDCA7 and HELLS are involved in maintaining CG methylation at centromeric and pericentromeric repeats. The defect in C-NHEJ may account for some common features of ICF cells, including centromeric instability, abnormal chromosome segregation, and apoptosis.
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Affiliation(s)
- Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, New York, USA
| | - Guillaume Velasco
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Claire Francastel
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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12
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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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13
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Sagie S, Edni O, Weinberg J, Toubiana S, Kozlovski T, Frostig T, Katzin N, Bar-Am I, Selig S. Non-random length distribution of individual telomeres in immunodeficiency, centromeric instability and facial anomalies syndrome, type I. Hum Mol Genet 2017; 26:4244-4256. [PMID: 28973513 DOI: 10.1093/hmg/ddx313] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/03/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations in the de novo DNA methyltransferase DNMT3B lead to Immunodeficiency, Centromeric Instability and Facial anomalies (ICF) syndrome, type I. This syndrome is characterized, among other hypomethylated genomic loci, by severe subtelomeric hypomethylation that is associated with abnormally short telomere length. While it was demonstrated that the mean telomere length is significantly shorter in ICF type I cells, it is unknown whether all telomeres are equally vulnerable to shortening. To study this question we determined by combined telomere-FISH and spectral karyotyping the relative length of each individual telomere in lymphoblastoid cell lines (LCLs) generated from multiple ICF syndrome patients and control individuals. Here we confirm the short telomere lengths, and demonstrate that telomere length variance in the ICF patient group is much larger than in the control group, suggesting that not all telomeres shorten in a uniform manner. We identified a subgroup of telomeres whose relatively short lengths can distinguish with a high degree of certainty between a control and an ICF metaphase, proposing that in ICF syndrome cells, certain individual telomeres are consistently at greater risk to shorten than others. The majority of these telomeres display high sequence identity at the distal 2 kb of their subtelomeres, suggesting that the attenuation in DNMT3B methylation capacity affects individual telomeres to different degrees based, at least in part, on the adjacent subtelomeric sequence composition.
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Affiliation(s)
- Shira Sagie
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Omer Edni
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Joseph Weinberg
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Shir Toubiana
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Tal Kozlovski
- Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 39040, Israel
| | - Tzviel Frostig
- Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 39040, Israel
| | - Nirit Katzin
- Applied Spectral Imaging Ltd., Yokneam 2069200, Israel
| | - Irit Bar-Am
- Applied Spectral Imaging Ltd., Yokneam 2069200, Israel
| | - Sara Selig
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
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14
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van den Boogaard ML, Thijssen PE, Aytekin C, Licciardi F, Kıykım AA, Spossito L, Dalm VASH, Driessen GJ, Kersseboom R, de Vries F, van Ostaijen-Ten Dam MM, Ikinciogullari A, Dogu F, Oleastro M, Bailardo E, Daxinger L, Nain E, Baris S, van Tol MJD, Weemaes C, van der Maarel SM. Expanding the mutation spectrum in ICF syndrome: Evidence for a gender bias in ICF2. Clin Genet 2017; 92:380-387. [PMID: 28128455 DOI: 10.1111/cge.12979] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/13/2017] [Accepted: 01/23/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is a rare, genetically heterogeneous, autosomal recessive disorder. Patients suffer from recurrent infections caused by reduced levels or absence of serum immunoglobulins. Genetically, 4 subtypes of ICF syndrome have been identified to date: ICF1 (DNMT3B mutations), ICF2 (ZBTB24 mutations), ICF3 (CDCA7 mutations), and ICF4 (HELLS mutations). AIM To study the mutation spectrum in ICF syndrome. MATERIALS AND METHODS Genetic studies were performed in peripheral blood lymphocyte DNA from suspected ICF patients and family members. RESULTS We describe 7 ICF1 patients and 6 novel missense mutations in DNMT3B, affecting highly conserved residues in the catalytic domain. We also describe 5 new ICF2 patients, one of them carrying a homozygous deletion of the complete ZBTB24 locus. In a meta-analysis of all published ICF cases, we observed a gender bias in ICF2 with 79% male patients. DISCUSSION The biallelic deletion of ZBTB24 provides strong support for the hypothesis that most ICF2 patients suffer from a ZBTB24 loss of function mechanism and confirms that complete absence of ZBTB24 is compatible with human life. This is in contrast to the observed early embryonic lethality in mice lacking functional Zbtb24. The observed gender bias seems to be restricted to ICF2 as it is not observed in the ICF1 cohort. CONCLUSION Our study expands the mutation spectrum in ICF syndrome and supports that DNMT3B and ZBTB24 are the most common disease genes.
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Affiliation(s)
- M L van den Boogaard
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - P E Thijssen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - C Aytekin
- Department of Pediatric Immunology, Dr Sami Ulus Maternity and Children's Research and Educational Hospital, Ankara, Turkey
| | - F Licciardi
- Department of Paediatrics II, Regina Margherita Hospital Città della Salute e della Scienza di Torino, Torino, Italy
| | - A A Kıykım
- Pediatric Allergy and Immunology, Marmara University Pendik Training and Research Hospital, Istanbul, Turkey
| | - L Spossito
- Department of Immunology and Rheumatology, Hospital "J.P Garrahan", Buenos Aires, Argentina
| | - V A S H Dalm
- Department of Immunology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
- Department of Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
| | - G J Driessen
- Department of Paediatric Infectious Diseases, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
- Department of Pediatrics, Juliana Children's Hospital, Haga Teaching Hospital, The Hague, The Netherlands
| | - R Kersseboom
- Department of Clinical Genetics, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
- Medical service, Stichting Zuidwester, Middelharnis, The Netherlands
| | - F de Vries
- Department of Clinical Genetics, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
| | - M M van Ostaijen-Ten Dam
- Department of Pediatrics, Laboratory Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - A Ikinciogullari
- Department of Pediatric Immunology and Allergy, Ankara University School of Medicine, Ankara, Turkey
| | - F Dogu
- Department of Pediatric Immunology and Allergy, Ankara University School of Medicine, Ankara, Turkey
| | - M Oleastro
- Department of Immunology and Rheumatology, Hospital "J.P Garrahan", Buenos Aires, Argentina
| | - E Bailardo
- Department of Genetics, Hospital "J.P. Garrahan", Buenos Aires, Argentina
| | - L Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - E Nain
- Pediatric Allergy and Immunology, Marmara University Pendik Training and Research Hospital, Istanbul, Turkey
| | - S Baris
- Pediatric Allergy and Immunology, Marmara University Pendik Training and Research Hospital, Istanbul, Turkey
| | - M J D van Tol
- Department of Pediatrics, Laboratory Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - C Weemaes
- Department of Pediatric Infectious Diseases and Immunology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - S M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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15
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Sagie S, Toubiana S, Hartono SR, Katzir H, Tzur-Gilat A, Havazelet S, Francastel C, Velasco G, Chédin F, Selig S. Telomeres in ICF syndrome cells are vulnerable to DNA damage due to elevated DNA:RNA hybrids. Nat Commun 2017; 8:14015. [PMID: 28117327 PMCID: PMC5286223 DOI: 10.1038/ncomms14015] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/21/2016] [Indexed: 12/21/2022] Open
Abstract
DNA:RNA hybrids, nucleic acid structures with diverse physiological functions, can disrupt genome integrity when dysregulated. Human telomeres were shown to form hybrids with the lncRNA TERRA, yet the formation and distribution of these hybrids among telomeres, their regulation and their cellular effects remain elusive. Here we predict and confirm in several human cell types that DNA:RNA hybrids form at many subtelomeric and telomeric regions. We demonstrate that ICF syndrome cells, which exhibit short telomeres and elevated TERRA levels, are enriched for hybrids at telomeric regions throughout the cell cycle. Telomeric hybrids are associated with high levels of DNA damage at chromosome ends in ICF cells, which are significantly reduced with overexpression of RNase H1. Our findings suggest that abnormally high TERRA levels in ICF syndrome lead to accumulation of telomeric hybrids that, in turn, can result in telomeric dysfunction. ICF syndrome cells exhibit shortened telomeres and elevated levels of the noncoding RNA TERRA. Here the authors show this is associated with high levels of DNA damage, suggesting an increase in telomere dysfunction due to the formation of DNA: RNA hybrids
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Affiliation(s)
- Shira Sagie
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Shir Toubiana
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Stella R Hartono
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Hagar Katzir
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Aya Tzur-Gilat
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Shany Havazelet
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Claire Francastel
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, CNRS UMR7216, Paris Cedex 75205, France
| | - Guillaume Velasco
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, CNRS UMR7216, Paris Cedex 75205, France
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Sara Selig
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
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16
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Kutluğ S, Ogur G, Yilmaz A, Thijssen PE, Abur U, Yildiran A. Vesicourethral reflux-induced renal failure in a patient with ICF syndrome due to a novel DNMT3B mutation. Am J Med Genet A 2016; 170:3253-3257. [PMID: 27604394 DOI: 10.1002/ajmg.a.37866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/11/2016] [Indexed: 11/07/2022]
Abstract
ICF syndrome is a primary immunodeficiency disease characterized by hypo- or agammaglobulinemia, centromeric instability mainly on chromosomes 1, 9, and 16 and facial anomalies. ICF syndrome presents with frequent respiratory tract infections in infancy. A 20-month-old female patient was referred to our clinic due to frequent lower respiratory tract infections. ICF syndrome was considered because of comorbidity of hypogammaglobulinemia, facial anomalies, and neuromotor growth retardation. Metaphase chromosome analysis revealed centromeric instability on chromosomes 1, 9, and 16 and through Sanger a previously unreported homozygous missense mutation (c.1805T>C; [p.V602A]) was identified in the DNMT3B, confirming ICF1. The patient was found to have a breakdown in renal function 1 year later; the urinary system was examined and bilateral vesicoureteral reflux was found, warranting the need for dialysis in time. This report expands the mutation spectrum of ICF1 and is the first to describe bilateral vesicoureteral reflux accompanying ICF syndrome. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Seyhan Kutluğ
- Division of Immunology and Allergy, Department of Pediatrics, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Gönül Ogur
- Department of Pediatric Genetics, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Aysegül Yilmaz
- Department of Pediatric Genetics, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Peter E Thijssen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Ummet Abur
- Department of Pediatric Genetics, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Alisan Yildiran
- Division of Immunology and Allergy, Department of Pediatrics, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
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17
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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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18
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Häfner SJ, Lund AH. Great expectations - Epigenetics and the meandering path from bench to bedside. Biomed J 2016; 39:166-76. [PMID: 27621117 PMCID: PMC6159761 DOI: 10.1016/j.bj.2016.01.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 01/21/2016] [Indexed: 01/12/2023] Open
Abstract
Making quick promises of major biomedical breakthroughs based on exciting discoveries at the bench is tempting. But the meandering path from fundamental science to life-saving clinical applications can be fraught with many hurdles. Epigenetics, the study of potentially heritable changes of gene function without modification of the underlying DNA sequence, has dominated the biological research field during the last decade and encountered a large public success. Driven by the unfolding of molecular biology and recent technological progress, the term has evolved significantly and shifted from a conceptual framework to a mechanistic understanding. This shift was accompanied by much hype and raised high hopes that epigenetics might hold both the key to deciphering the molecular underpinning of complex, non-Mendelian diseases and offer novel therapeutic approaches for a large panel of pathologies. However, while exciting reports of biological phenomena involving DNA methylation and histone modifications fill up the scientific literature, the realistic clinical applications of epigenetic medicines remain somewhat blurry. Here, we discuss the state of the art and speculate how epigenetics might contribute to prognostic and therapy approaches in the future.
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Affiliation(s)
- Sophia J Häfner
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
| | - Anders H Lund
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
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19
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Sterlin D, Velasco G, Moshous D, Touzot F, Mahlaoui N, Fischer A, Suarez F, Francastel C, Picard C. Genetic, Cellular and Clinical Features of ICF Syndrome: a French National Survey. J Clin Immunol 2016; 36:149-59. [PMID: 26851945 DOI: 10.1007/s10875-016-0240-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 01/31/2016] [Indexed: 12/22/2022]
Abstract
PURPOSE Autosomal recessive deficiencies of DNMT3B or ZBTB24 account for two-thirds of cases of immunodeficiency, centromeric instability and facial dysmorphism (ICF syndrome). This primary immunodeficiency (PID) is characterized mainly by an antibody deficiency, facial abnormalities and centromeric instability. We analyzed the national cohort of patients with ICF syndrome with the aim of providing a more detailed description of the phenotype and management of patients with ICF syndrome. METHODS Demographic, genetic, immunological, and clinical features were recorded for each patient. RESULTS In the French cohort, seven of the nine patients carried DNMT3B mutations, six of which had never been described before. One patient had compound heterozygous ZBTB24 mutations. All patients were found to lack CD19(+)CD27(+) memory B cells. This feature is a major diagnostic criterion for both ICF1 and ICF2. Patients suffered both bacterial and viral infections, and three patients developed bronchiectasis. Autoimmune manifestations (hepatitis, nephritis and thyroiditis) not previously reported in ICF1 patients were also detected in two of our ICF1 patients. The mode of treatment and outcome of the French patients are reported, by genetic defect, and compared with those for 68 previously reported ICF patients. Immunoglobulin (Ig) replacement treatment was administered to all nine French patients. One ICF1 patient presented severe autoimmune manifestations and pancytopenia and underwent allogeneic hematopoietic stem cell transplantation (HSCT), but she died from unknown causes 6 years post-transplant. CONCLUSION Autoimmune signs are uncommon in ICF syndrome, but, when present, they affect patient outcome and require immunosuppressive treatment. The long-term outcome of ICF patients has been improved by the combination of IgG replacement and antibiotic prophylaxis.
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Affiliation(s)
- Delphine Sterlin
- Study Center for Primary Immunodeficiencies, Necker-Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris (APHP), University Paris Descartes, 149 rue de Sevres, 75015, Paris, France
| | - Guillaume Velasco
- CNRS UMR7216, Epigenetics and Cell Fate, Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Despina Moshous
- Pediatric Immuno-Hematology Unit, Necker Children's Hospital, APHP, Université Paris Descartes, Paris, France.,INSERM UMR1163, Imagine Institute, Necker Medical School, Sorbonne Paris Cité, University Paris Descartes, Paris, France
| | - Fabien Touzot
- Pediatric Immuno-Hematology Unit, Necker Children's Hospital, APHP, Université Paris Descartes, Paris, France.,INSERM UMR1163, Imagine Institute, Necker Medical School, Sorbonne Paris Cité, University Paris Descartes, Paris, France.,Laboratory of Molecular Mechanisms of Hematologic Disorders and Therapeutic Implications, INSERM UMR1163, Imagine Institut, Necker Medical School, University Paris Descartes, Paris, France.,Biotherapy Department, Necker-Enfants Malades Hospital, APHP, University Paris Descartes, Paris, France
| | - Nizar Mahlaoui
- Pediatric Immuno-Hematology Unit, Necker Children's Hospital, APHP, Université Paris Descartes, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker - Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Alain Fischer
- Pediatric Immuno-Hematology Unit, Necker Children's Hospital, APHP, Université Paris Descartes, Paris, France.,INSERM UMR1163, Imagine Institute, Necker Medical School, Sorbonne Paris Cité, University Paris Descartes, Paris, France.,College de France, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker - Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Felipe Suarez
- Adult Hematology Unit, Necker Children's Hospital, APHP, University Paris Descartes, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker - Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris, Paris, France.,INSERM UMR1163 and CNRS ERL8254, Imagine Institute, Necker Medical School, Sorbonne Paris Cité, University Paris Descartes, Paris, France
| | - Claire Francastel
- CNRS UMR7216, Epigenetics and Cell Fate, Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Capucine Picard
- Study Center for Primary Immunodeficiencies, Necker-Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris (APHP), University Paris Descartes, 149 rue de Sevres, 75015, Paris, France. .,Pediatric Immuno-Hematology Unit, Necker Children's Hospital, APHP, Université Paris Descartes, Paris, France. .,Laboratory of the Human Genetics of Infectious Diseases, INSERM UMR1163, Imagine Institute, Necker Medical School, Sorbonne Paris Cité, University Paris Descartes, Paris, France. .,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker - Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris, Paris, France.
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Abstract
The life-threatening Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome is a genetically heterogeneous autosomal recessive disorder. Twenty percent of patients cannot be explained by mutations in the known ICF genes DNA methyltransferase 3B or zinc-finger and BTB domain containing 24. Here we report mutations in the cell division cycle associated 7 and the helicase, lymphoid-specific genes in 10 unexplained ICF cases. Our data highlight the genetic heterogeneity of ICF syndrome; however, they provide evidence that all genes act in common or converging pathways leading to the ICF phenotype.
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21
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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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Dnmt3b Prefers Germ Line Genes and Centromeric Regions: Lessons from the ICF Syndrome and Cancer and Implications for Diseases. BIOLOGY 2014; 3:578-605. [PMID: 25198254 PMCID: PMC4192629 DOI: 10.3390/biology3030578] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 07/18/2014] [Accepted: 08/21/2014] [Indexed: 01/06/2023]
Abstract
The correct establishment and maintenance of DNA methylation patterns are critical for mammalian development and the control of normal cell growth and differentiation. DNA methylation has profound effects on the mammalian genome, including transcriptional repression, modulation of chromatin structure, X chromosome inactivation, genomic imprinting, and the suppression of the detrimental effects of repetitive and parasitic DNA sequences on genome integrity. Consistent with its essential role in normal cells and predominance at repetitive genomic regions, aberrant changes of DNA methylation patterns are a common feature of diseases with chromosomal and genomic instabilities. In this context, the functions of DNA methyltransferases (DNMTs) can be affected by mutations or alterations of their expression. DNMT3B, which is involved in de novo methylation, is of particular interest not only because of its important role in development, but also because of its dysfunction in human diseases. Expression of catalytically inactive isoforms has been associated with cancer risk and germ line hypomorphic mutations with the ICF syndrome (Immunodeficiency Centromeric instability Facial anomalies). In these diseases, global genomic hypomethylation affects repeated sequences around centromeric regions, which make up large blocks of heterochromatin, and is associated with chromosome instability, impaired chromosome segregation and perturbed nuclear architecture. The review will focus on recent data about the function of DNMT3B, and the consequences of its deregulated activity on pathological DNA hypomethylation, including the illicit activation of germ line-specific genes and accumulation of transcripts originating from repeated satellite sequences, which may represent novel physiopathological biomarkers for human diseases. Notably, we focus on cancer and the ICF syndrome, pathological contexts in which hypomethylation has been extensively characterized. We also discuss the potential contribution of these deregulated protein-coding and non-coding transcription programs to the perturbation of cellular phenotypes.
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Auclair G, Guibert S, Bender A, Weber M. Ontogeny of CpG island methylation and specificity of DNMT3 methyltransferases during embryonic development in the mouse. Genome Biol 2014; 15:545. [PMID: 25476147 PMCID: PMC4295324 DOI: 10.1186/s13059-014-0545-5] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the mouse, the patterns of DNA methylation are established during early embryonic development in the epiblast. We quantified the targets and kinetics of DNA methylation acquisition in epiblast cells, and determined the contribution of the de novo methyltransferases DNMT3A and DNMT3B to this process. RESULTS We generated single-base maps of DNA methylation from the blastocyst to post-implantation stages and in embryos lacking DNMT3A or DNMT3B activity. DNA methylation is established within two days of implantation between embryonic days 4.5 and 6.5. The kinetics of de novo methylation are uniform throughout the genome, suggesting a random mechanism of deposition. In contrast, many CpG islands acquire methylation slowly in late epiblast cells. Five percent of CpG islands gain methylation and are found in the promoters of germline genes and in exons of important developmental genes. The onset of global methylation correlates with the upregulation of Dnmt3a/b genes in the early epiblast. DNMT3A and DNMT3B act redundantly to methylate the bulk genome and repetitive elements, whereas DNMT3B has a prominent role in the methylation of CpG islands on autosomes and the X chromosome. Reduced CpG island methylation in Dnmt3b-deficient embryos correlates with gene reactivation in promoters but reduced transcript abundance in gene bodies. Finally, DNMT3B establishes secondary methylation marks at imprinted loci, which distinguishes bona fide germline from somatic methylation imprints. CONCLUSIONS We reveal that the DNMT3 de novo methyltransferases play both redundant and specific functions in the establishment of DNA methylation in the mouse embryo.
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Affiliation(s)
- Ghislain Auclair
- CNRS, University of Strasbourg, UMR 7242 Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, BP 10413, 67412 Illkirch, France
| | - Sylvain Guibert
- CNRS, University of Strasbourg, UMR 7242 Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, BP 10413, 67412 Illkirch, France
| | - Ambre Bender
- CNRS, University of Strasbourg, UMR 7242 Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, BP 10413, 67412 Illkirch, France
| | - Michael Weber
- CNRS, University of Strasbourg, UMR 7242 Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, BP 10413, 67412 Illkirch, France
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