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Suzuki E, Nakabayashi K, Aoto S, Ogata T, Kuroki Y, Miyado M, Fukami M, Matsubara K. DNA methylation changes in the genome of patients with hypogonadotropic hypogonadism. Heliyon 2024; 10:e37648. [PMID: 39309794 PMCID: PMC11416509 DOI: 10.1016/j.heliyon.2024.e37648] [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: 05/29/2024] [Revised: 08/14/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
Although some Mendelian neurodevelopmental disorders have been shown to entail specific DNA methylation changes designated as epi-signatures, it remains unknown whether epi-signatures are consistent features of other genetic disorders. Here, we analyzed DNA methylation profiles of patients with hypogonadotropic hypogonadism (HH), a rare neuroendocrine disorder typically caused by monogenic or oligogenic mutations. First, we performed microarray-based genome-wide methylation analyses of nine patients with HH due to ANOS1, SOX2, or SOX10 variants and 12 control individuals. The results showed that 1118 probes were differentially methylated in one or more patients. The differentially methylated probes were highly variable among patients. No significant methylation changes were observed in genes functionally associated with ANOS1, SOX2, or SOX10. Then, we performed pyrosequencing of six selected CpG sites in the nine patients and 35 additional HH patients. The results of the patients were compared with those of 48 fertile men. There were no common methylation changes among these patients, with the exception of hypermethylation of two CpG sites in the ZNF245 promoter of three patients. Hypermethylation of the promoter has previously been reported as a very rare epigenetic polymorphism in the general population. These results indicate that genomes of HH patients have considerable DNA methylation changes; however, these changes are more likely to be physiological epigenetic variations than disease-specific epi-signatures. Our data suggest a possible association between hypermethylation of the ZNF254 promoter and HH, which needs to be examined in future studies.
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Affiliation(s)
- Erina Suzuki
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Saki Aoto
- Medical Genome Center, National Center for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yoko Kuroki
- Department of Genome Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Mami Miyado
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
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van Karnebeek CDM, O'Donnell-Luria A, Baynam G, Baudot A, Groza T, Jans JJM, Lassmann T, Letinturier MCV, Montgomery SB, Robinson PN, Sansen S, Mehrian-Shai R, Steward C, Kosaki K, Durao P, Sadikovic B. Leaving no patient behind! Expert recommendation in the use of innovative technologies for diagnosing rare diseases. Orphanet J Rare Dis 2024; 19:357. [PMID: 39334316 DOI: 10.1186/s13023-024-03361-0] [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: 03/26/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024] Open
Abstract
Genetic diagnosis plays a crucial role in rare diseases, particularly with the increasing availability of emerging and accessible treatments. The International Rare Diseases Research Consortium (IRDiRC) has set its primary goal as: "Ensuring that all patients who present with a suspected rare disease receive a diagnosis within one year if their disorder is documented in the medical literature". Despite significant advances in genomic sequencing technologies, more than half of the patients with suspected Mendelian disorders remain undiagnosed. In response, IRDiRC proposes the establishment of "a globally coordinated diagnostic and research pipeline". To help facilitate this, IRDiRC formed the Task Force on Integrating New Technologies for Rare Disease Diagnosis. This multi-stakeholder Task Force aims to provide an overview of the current state of innovative diagnostic technologies for clinicians and researchers, focusing on the patient's diagnostic journey. Herein, we provide an overview of a broad spectrum of emerging diagnostic technologies involving genomics, epigenomics and multi-omics, functional testing and model systems, data sharing, bioinformatics, and Artificial Intelligence (AI), highlighting their advantages, limitations, and the current state of clinical adaption. We provide expert recommendations outlining the stepwise application of these innovative technologies in the diagnostic pathways while considering global differences in accessibility. The importance of FAIR (Findability, Accessibility, Interoperability, and Reusability) and CARE (Collective benefit, Authority to control, Responsibility, and Ethics) data management is emphasized, along with the need for enhanced and continuing education in medical genomics. We provide a perspective on future technological developments in genome diagnostics and their integration into clinical practice. Lastly, we summarize the challenges related to genomic diversity and accessibility, highlighting the significance of innovative diagnostic technologies, global collaboration, and equitable access to diagnosis and treatment for people living with rare disease.
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Affiliation(s)
- Clara D M van Karnebeek
- Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam Gastro-Enterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, USA
| | - Gareth Baynam
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, MMG, Marseille, France
| | - Anaïs Baudot
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, MMG, Marseille, France
| | - Tudor Groza
- Rare Care Centre, Perth Children's Hospital and Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Perth, Australia
- European Molecular Biology Laboratory (EMBL-EBI), European Bioinformatics Institute, Hinxton, UK
| | - Judith J M Jans
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | | | | | - Ruty Mehrian-Shai
- Pediatric Brain Cancer Molecular Lab, Sheba Medical Center, Ramat Gan, Israel
| | | | | | - Patricia Durao
- The Cure and Action for Tay-Sachs (CATS) Foundation, Altringham, UK
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences, London, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
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3
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LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Allan TJ, Zalusky MPG, Goffena J, Gibson SB, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel MN, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Gupta S, Jones EA, Weisz-Hubshman M, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement. Nat Commun 2024; 15:6524. [PMID: 39107278 PMCID: PMC11303402 DOI: 10.1038/s41467-024-50159-6] [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: 10/20/2023] [Accepted: 06/28/2024] [Indexed: 08/09/2024] Open
Abstract
Sequence-based genetic testing identifies causative variants in ~ 50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. We interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 582 individuals with genetically unsolved DEEs. We identify rare differentially methylated regions (DMRs) and explanatory episignatures to uncover causative and candidate genetic etiologies in 12 individuals. Using long-read sequencing, we identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and four copy number variants. We also identify pathogenic variants associated with episignatures. Finally, we refine the CHD2 episignature using an 850 K methylation array and bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate variants as 2% (12/582) for unsolved DEE cases.
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Affiliation(s)
- Christy W LaFlamme
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cassandra Rastin
- Department of Pathology & Laboratory Medicine, Western University, London, ON, N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Soham Sengupta
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Helen E Pennington
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Mathematics & Statistics, Rhodes College, Memphis, TN, 38112, USA
| | - Sophie J Russ-Hall
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Amy L Schneider
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Emily S Bonkowski
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Edith P Almanza Fuerte
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Talia J Allan
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Miranda Perez-Galey Zalusky
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Joy Goffena
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Sophia B Gibson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Denis M Nyaga
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Nico Lieffering
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Malavika Hebbar
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Emily V Walker
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Daniel Darnell
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Scott R Olsen
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Dorit Lev
- Institute of Medical Genetics, Wolfson Medical Center, Holon, 58100, Israel
| | - Tally Lerman-Sagie
- Fetal Neurology Clinic, Pediatric Neurology Unit, Wolfson Medical Center, Holon, 58100, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Kristen L Park
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Nicolas Chatron
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | - Leigh Demain
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - David Genevieve
- Montpellier University, Inserm Unit 1183, Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndrome, Clinical Genetic Department, CHU Montpellier, Montpellier, France
| | - Gaetan Lesca
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, NSW, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Damien Sanlaville
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | | | - Sachin Gupta
- TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Elizabeth A Jones
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Monika Weisz-Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Genetic Department, Houston, TX, 77030, USA
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, 77030, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC, Australia
- Florey Institute and Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Western University, London, ON, N5A 3K7, Canada.
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada.
| | - Heather C Mefford
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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Bukowska-Olech E, Majchrzak-Celińska A, Przyborska M, Jamsheer A. Chromatinopathies: insight in clinical aspects and underlying epigenetic changes. J Appl Genet 2024; 65:287-301. [PMID: 38180712 PMCID: PMC11003913 DOI: 10.1007/s13353-023-00824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Chromatinopathies (CPs), a group of rare inborn defects characterized by chromatin state imbalance, have evolved from initially resembling Cornelia de Lange syndrome to encompass a wide array of genetic diseases with diverse clinical presentations. The CPs classification now includes human developmental disorders caused by germline mutations in epigenes, genes that regulate the epigenome. Recent advances in next-generation sequencing have enabled the association of 154 epigenes with CPs, revealing distinctive DNA methylation patterns known as episignatures.It has been shown that episignatures are unique for a particular CP or share similarities among specific CP subgroup. Consequently, these episignatures have emerged as promising biomarkers for diagnosing and treating CPs, differentiating subtypes, evaluating variants of unknown significance, and facilitating targeted therapies tailored to the underlying epigenetic dysregulation.The following review was conducted to collect, summarize, and analyze data regarding CPs in such aspects as clinical evaluation encompassing long-term patient care, underlying epigenetic changes, and innovative molecular and bioinformatic methodologies that have been devised for the assessment of CPs. We have also shed light on promising novel treatment options that have surfaced in recent research and presented a synthesis of ongoing clinical trials, contributing to the current understanding of the dynamic and evolving nature of CPs investigation.
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Affiliation(s)
| | | | | | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
- Centers for Medical Genetics GENESIS, Poznan, Poland
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Gruca-Stryjak K, Doda-Nowak E, Dzierla J, Wróbel K, Szymankiewicz-Bręborowicz M, Mazela J. Advancing the Clinical and Molecular Understanding of Cornelia de Lange Syndrome: A Multidisciplinary Pediatric Case Series and Review of the Literature. J Clin Med 2024; 13:2423. [PMID: 38673696 PMCID: PMC11050916 DOI: 10.3390/jcm13082423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/08/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a complex genetic disorder with distinct facial features, growth limitations, and limb anomalies. Its broad clinical spectrum presents significant challenges in pediatric diagnosis and management. Due to cohesin complex mutations, the disorder's variable presentation requires extensive research to refine care and improve outcomes. This article provides a case series review of pediatric CdLS patients alongside a comprehensive literature review, exploring clinical variability and the relationship between genotypic changes and phenotypic outcomes. It also discusses the evolution of diagnostic and therapeutic techniques, emphasizing innovations in genetic testing, including detecting mosaicism and novel genetic variations. The aim is to synthesize case studies with current research to advance our understanding of CdLS and the effectiveness of management strategies in pediatric healthcare. This work highlights the need for an integrated, evidence-based approach to diagnosis and treatment. It aims to fill existing research gaps and advocate for holistic care protocols and tailored treatment plans for CdLS patients, ultimately improving their quality of life.
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Affiliation(s)
- Karolina Gruca-Stryjak
- Department of Perinatology, Faculty of Medicine, University of Medical Sciences, 60-535 Poznan, Poland
- Department of Obstetrics and Gynecology, Polish Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland
- Centers for Medical Genetics Diagnostyka GENESIS, 60-406 Poznan, Poland
| | - Emilia Doda-Nowak
- Faculty of Medicine, University of Medical Sciences, 61-701 Poznan, Poland (J.D.)
| | - Julia Dzierla
- Faculty of Medicine, University of Medical Sciences, 61-701 Poznan, Poland (J.D.)
| | - Karolina Wróbel
- Department of Neonatology, Faculty of Medicine, University of Medical Sciences, 60-535 Poznan, Poland
| | | | - Jan Mazela
- Department of Neonatology, Faculty of Medicine, University of Medical Sciences, 60-535 Poznan, Poland
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6
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Harris JR, Gao CW, Britton JF, Applegate CD, Bjornsson HT, Fahrner JA. Five years of experience in the Epigenetics and Chromatin Clinic: what have we learned and where do we go from here? Hum Genet 2024; 143:607-624. [PMID: 36952035 PMCID: PMC10034257 DOI: 10.1007/s00439-023-02537-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/20/2023] [Indexed: 03/24/2023]
Abstract
The multidisciplinary Epigenetics and Chromatin Clinic at Johns Hopkins provides comprehensive medical care for individuals with rare disorders that involve disrupted epigenetics. Initially centered on classical imprinting disorders, the focus shifted to the rapidly emerging group of genetic disorders resulting from pathogenic germline variants in epigenetic machinery genes. These are collectively called the Mendelian disorders of the epigenetic machinery (MDEMs), or more broadly, Chromatinopathies. In five years, 741 clinic visits have been completed for 432 individual patients, with 153 having confirmed epigenetic diagnoses. Of these, 115 individuals have one of 26 MDEMs with every single one exhibiting global developmental delay and/or intellectual disability. This supports prior observations that intellectual disability is the most common phenotypic feature of MDEMs. Additional common phenotypes in our clinic include growth abnormalities and neurodevelopmental issues, particularly hypotonia, attention-deficit/hyperactivity disorder (ADHD), and anxiety, with seizures and autism being less common. Overall, our patient population is representative of the broader group of MDEMs and includes mostly autosomal dominant disorders impacting writers more so than erasers, readers, and remodelers of chromatin marks. There is an increased representation of dual function components with a reader and an enzymatic domain. As expected, diagnoses were made mostly by sequencing but were aided in some cases by DNA methylation profiling. Our clinic has helped to facilitate the discovery of two new disorders, and our providers are actively developing and implementing novel therapeutic strategies for MDEMs. These data and our high follow-up rate of over 60% suggest that we are achieving our mission to diagnose, learn from, and provide optimal care for our patients with disrupted epigenetics.
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Affiliation(s)
- Jacqueline R Harris
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kennedy Krieger Institute, Baltimore, MD, USA
| | - Christine W Gao
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacquelyn F Britton
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carolyn D Applegate
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Landspitali University Hospital, Reykjavik, Iceland
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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7
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Husson T, Lecoquierre F, Nicolas G, Richard AC, Afenjar A, Audebert-Bellanger S, Badens C, Bilan F, Bizaoui V, Boland A, Bonnet-Dupeyron MN, Brischoux-Boucher E, Bonnet C, Bournez M, Boute O, Brunelle P, Caumes R, Charles P, Chassaing N, Chatron N, Cogné B, Colin E, Cormier-Daire V, Dard R, Dauriat B, Delanne J, Deleuze JF, Demurger F, Denommé-Pichon AS, Depienne C, Dieux A, Dubourg C, Edery P, El Chehadeh S, Faivre L, Fergelot P, Fradin M, Garde A, Geneviève D, Gilbert-Dussardier B, Goizet C, Goldenberg A, Gouy E, Guerrot AM, Guimier A, Harzalla I, Héron D, Isidor B, Lacombe D, Le Guillou Horn X, Keren B, Kuechler A, Lacaze E, Lavillaureix A, Lehalle D, Lesca G, Lespinasse J, Levy J, Lyonnet S, Morel G, Jean-Marçais N, Marlin S, Marsili L, Mignot C, Nambot S, Nizon M, Olaso R, Pasquier L, Perrin L, Petit F, Pingault V, Piton A, Prieur F, Putoux A, Planes M, Odent S, Quélin C, Quemener-Redon S, Rama M, Rio M, Rossi M, Schaefer E, Rondeau S, Saugier-Veber P, Smol T, Sigaudy S, Touraine R, Mau-Them FT, Trimouille A, Van Gils J, Vanlerberghe C, Vantalon V, Vera G, Vincent M, Ziegler A, Guillin O, Campion D, Charbonnier C. Episignatures in practice: independent evaluation of published episignatures for the molecular diagnostics of ten neurodevelopmental disorders. Eur J Hum Genet 2024; 32:190-199. [PMID: 37872275 PMCID: PMC10853222 DOI: 10.1038/s41431-023-01474-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/29/2023] [Accepted: 09/28/2023] [Indexed: 10/25/2023] Open
Abstract
Variants of uncertain significance (VUS) are a significant issue for the molecular diagnosis of rare diseases. The publication of episignatures as effective biomarkers of certain Mendelian neurodevelopmental disorders has raised hopes to help classify VUS. However, prediction abilities of most published episignatures have not been independently investigated yet, which is a prerequisite for an informed and rigorous use in a diagnostic setting. We generated DNA methylation data from 101 carriers of (likely) pathogenic variants in ten different genes, 57 VUS carriers, and 25 healthy controls. Combining published episignature information and new validation data with a k-nearest-neighbour classifier within a leave-one-out scheme, we provide unbiased specificity and sensitivity estimates for each of the signatures. Our procedure reached 100% specificity, but the sensitivities unexpectedly spanned a very large spectrum. While ATRX, DNMT3A, KMT2D, and NSD1 signatures displayed a 100% sensitivity, CREBBP-RSTS and one of the CHD8 signatures reached <40% sensitivity on our dataset. Remaining Cornelia de Lange syndrome, KMT2A, KDM5C and CHD7 signatures reached 70-100% sensitivity at best with unstable performances, suffering from heterogeneous methylation profiles among cases and rare discordant samples. Our results call for cautiousness and demonstrate that episignatures do not perform equally well. Some signatures are ready for confident use in a diagnostic setting. Yet, it is imperative to characterise the actual validity perimeter and interpretation of each episignature with the help of larger validation sample sizes and in a broader set of episignatures.
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Affiliation(s)
- Thomas Husson
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Psychiatry, F-76000, Rouen, France
- Department of Research, Centre hospitalier du Rouvray, Sotteville-Lès-Rouen, France
| | - François Lecoquierre
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Anne-Claire Richard
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Alexandra Afenjar
- APHP. Sorbonne Université, Centre de Référence Malformations et maladies congénitales du cervelet et déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, F-75012, Paris, France
| | | | - Catherine Badens
- Aix Marseille Univ, INSERM, MMG, Marseille, France; APHM, service de génétique, Marseille, France
| | - Frédéric Bilan
- CHU de Poitiers, Service de Génétique Médicale and Université de Poitiers, INSERM U1084, LNEC, F- 86000, Poitiers, France
| | - Varoona Bizaoui
- Service de génétique et neurodéveloppement, Pôle de Santé Mentale Enfant et Adolescent, Centre Hospitalier de l'Estran, Pontorson, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | | | - Elise Brischoux-Boucher
- Centre de génétique humaine, CHU Besancon, Universite de Bourgogne Franche-Comte, Besancon, France
| | - Céline Bonnet
- Laboratoire de génétique médicale, CHRU Nancy, Nancy, France
- Université de Lorraine, INSERM UMR_S1256, NGERE, F-54000, Nancy, France
| | - Marie Bournez
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Odile Boute
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
| | - Perrine Brunelle
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Institut de Génétique Médicale, F-59000, Lille, France
| | - Roseline Caumes
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
| | - Perrine Charles
- Département de génétique clinique, centre de référence des déficiences intellectuelles de causes rares, GHU Pitié Salpêtrière, Paris, France
| | | | - Nicolas Chatron
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261 -INSERM U1315, Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Benjamin Cogné
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- CHU Nantes, Service de Génétique Médicale, Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
| | - Estelle Colin
- Service de Génétique Médicale, CHU Angers, Angers, France
| | - Valérie Cormier-Daire
- Service de médecine génomique des maladies rares, hôpital Necker Enfants Malades, Paris, France
- Université Paris Cité, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Rodolphe Dard
- Génétique médicale, CHI Poissy-Saint-Germain-en-Laye, 78300, Poissy, France
| | - Benjamin Dauriat
- Service de cytogénétique et génétique médicale, Hôpital Mère Enfant, CHU Limoges, Limoges, France
| | - Julian Delanne
- Centre de Génétique et Centre de référence « Déficiences intellectuelles de causes rares », FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | | | - Anne-Sophie Denommé-Pichon
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon, Bourgogne, Dijon, France
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Anne Dieux
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique, CHU Pontchaillou, Rennes, France
- Université de Rennes, IGDR (Institut de Génétique et Développement), CNRS UMR 6290, INSERM ERL 1305, Rennes, France
| | - Patrick Edery
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, Genetics of Neurodevelopment (GENDEV) Team, 69500, Bron, France
| | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch-Graffenstaden, France
- Laboratoire de Génétique Médicale, UMRS 1112, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg et INSERM, Strasbourg, France
| | - Laurence Faivre
- Centre de Génétique et Centre de référence « Déficiences intellectuelles de causes rares », FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
| | - Patricia Fergelot
- Department of Medical Genetics, University Hospital of Bordeaux and INSERM U1211, University of Bordeaux, Bordeaux, France
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Rennes, Rennes, France
| | - Aurore Garde
- Centre de Génétique et Centre de référence « Déficiences intellectuelles de causes rares », FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
| | - David Geneviève
- Université Montpellier, Inserm U1183, Montpellier, France
- Centre de référence anomalies du développement et syndromes malformatifs, Génétique Clinique, CHU Montpellier, Montpellier, France
| | | | - Cyril Goizet
- NRGEN team, Univ. Bordeaux, CNRS, INCIA, UMR 5287, EPHE, F-33000, Bordeaux, France
- Centre de Référence Maladies Rares Neurogénétique, Service de Génétique Médicale, Bordeaux University Hospital (CHU Bordeaux), Bordeaux, France
| | - Alice Goldenberg
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Evan Gouy
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Génétique et neurobiologie de C.elegans, MéLis (CNRS UMR 5284 -INSERM U1314), Institut NeuroMyogene, Université Claude Bernard Lyon 1, Lyon, France
| | - Anne-Marie Guerrot
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Anne Guimier
- Service de médecine génomique des maladies rares - GHU Necker- Enfants malades, Paris, France
| | - Inès Harzalla
- Service de Génétique, CHU Hôpital Nord, Saint Etienne, France
| | - Delphine Héron
- APHP.Sorbonne Université, Département de Génétique, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Bertrand Isidor
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- CHU Nantes, Service de Génétique Médicale, Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
| | - Didier Lacombe
- Department of Medical Genetics, University Hospital of Bordeaux and INSERM U1211, University of Bordeaux, Bordeaux, France
| | - Xavier Le Guillou Horn
- CHU de Poitiers, Service de Génétique Médicale, F - 86000, Poitiers, France
- Université de Poitiers, CNRS 7348, LabCom I3M-Dactim mis / LMA, F-86000, Poitiers, France
| | - Boris Keren
- Département de génétique médicale, Hôpital Pitié-Salpêtrière, AP-HP.Sorbonne Université, 75013, Paris, France
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Elodie Lacaze
- Le Havre Hospital, Department of Medical Genetics, F 76600, Le Havre, France
| | - Alinoë Lavillaureix
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du développement, FHU GenOMedS, Univ Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, France
| | - Daphné Lehalle
- APHP.Sorbonne Université, Département de Génétique, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Gaëtan Lesca
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - James Lespinasse
- UF de génétique médicale, Centre Hospitalier Métropole Savoie, BP 31135, 73011, Chambéry, France
| | - Jonathan Levy
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - Stanislas Lyonnet
- Service de médecine génomique des maladies rares, Hôpital Universitaire Necker-Enfants malades, APHP, Paris, France
- Laboratoire embryologie et génétique des malformations, Institut Imagine, UMR-II63, INSERM, Université Paris Cité, GHU Necker- Enfants malades, Paris, France
| | - Godeliève Morel
- Service de Génétique Clinique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Rennes, Rennes, France
| | - Nolwenn Jean-Marçais
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du développement, FHU GenOMedS, Rennes, France
| | - Sandrine Marlin
- Service de médecine génomique des maladies rares - GHU Necker- Enfants malades, Paris, France
| | - Luisa Marsili
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
| | - Cyril Mignot
- APHP.Sorbonne Université, Département de Génétique, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Sophie Nambot
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Mathilde Nizon
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- CHU Nantes, Service de Génétique Médicale, Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Laurent Pasquier
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du développement, FHU GenOMedS, Rennes, France
| | - Laurine Perrin
- Médecine Physique et Réadaptation pédiatrique CHU Saint-Etienne, 42055, Saint-Etienne Cedex 2, France
| | - Florence Petit
- CHU Lille, Clinique de génétique Guy Fontaine, F-59000, Lille, France
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Institut de Génétique Médicale, F-59000, Lille, France
| | - Veronique Pingault
- Service de Médecine Génomique des maladies rares, AP-HP. Centre, Hôpital Necker-Enfants Malades, F-75015, Paris, France
- Université Paris Cité, Institut Imagine, Inserm U1163, F-75015, Paris, France
| | - Amélie Piton
- Laboratoire de diagnostic génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Fabienne Prieur
- Service de Génétique, CHU Hôpital Nord, Saint Etienne, France
| | - Audrey Putoux
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, Genetics of Neurodevelopment (GENDEV) Team, 69500, Bron, France
| | - Marc Planes
- Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France
| | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du développement, FHU GenOMedS, Univ Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, France
| | - Chloé Quélin
- Service de Génétique Clinique, Centre de Référence Anomalies du Développement de l'Ouest, CHU Rennes, Rennes, France
| | - Sylvia Quemener-Redon
- Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France
- Centre de Référence Déficiences Intellectuelles de causes rares, Brest, France
| | - Mélanie Rama
- CHU Lille - Institut de Génétique Médicale, F-59000, Lille, France
| | - Marlène Rio
- Service de médecine génomique des maladies rares - GHU Necker- Enfants malades, Paris, France
| | - Massimiliano Rossi
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, Genetics of Neurodevelopment (GENDEV) Team, 69500, Bron, France
| | - Elise Schaefer
- Service de Génétique Médicale -Institut de Génétique Médicale d'Alsace - CHU Strasbourg, Strasbourg, France
| | - Sophie Rondeau
- Service de médecine génomique des maladies rares - GHU Necker- Enfants malades, Paris, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Thomas Smol
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Institut de Génétique Médicale, F-59000, Lille, France
- CHU Lille - Institut de Génétique Médicale, F-59000, Lille, France
| | - Sabine Sigaudy
- Aix Marseille Univ, INSERM, MMG, CRMR syndromes malformatifs et anomalies du développement, département de génétique, APHM Hopital Timone, Marseille, France
| | - Renaud Touraine
- Service de Génétique, CHU Hôpital Nord, Saint Etienne, France
| | - Frederic Tran Mau-Them
- Équipe GAD, INSERM UMR1231, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon, Bourgogne, Dijon, France
| | - Aurélien Trimouille
- Service de Pathologie, CHU Bordeaux, Bordeaux, France
- Inserm U1211 MRGM, Université de Bordeaux, Bordeaux, France
| | - Julien Van Gils
- Department of Medical Genetics, University Hospital of Bordeaux and INSERM U1211, University of Bordeaux, Bordeaux, France
| | | | - Valérie Vantalon
- Centre d'Excellence InovAND-Service de psychiatrie de l'enfant et de l'adolescent-CHU Robert Debré, Paris, France
| | - Gabriella Vera
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, F-76000, Rouen, France
| | - Marie Vincent
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
- CHU Nantes, Service de Génétique Médicale, Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000, Nantes, France
| | - Alban Ziegler
- Service de Génétique Médicale, CHU Angers, Angers, France
| | - Olivier Guillin
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Psychiatry, F-76000, Rouen, France
| | - Dominique Campion
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Psychiatry, F-76000, Rouen, France
| | - Camille Charbonnier
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Biostatistics, F-76000, Rouen, France.
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Sabbagh Q, Haghshenas S, Piard J, Trouvé C, Amiel J, Attié-Bitach T, Balci T, Barat-Houari M, Belonis A, Boute O, Brightman DS, Bruel AL, Caraffi SG, Chatron N, Collet C, Dufour W, Edery P, Fong CT, Fusco C, Gatinois V, Gouy E, Guerrot AM, Heide S, Joshi A, Karp N, Keren B, Lesieur-Sebellin M, Levy J, Levy MA, Lozano C, Lyonnet S, Margot H, Marzin P, McConkey H, Michaud V, Nicolas G, Nizard M, Paulet A, Peluso F, Pernin V, Perrin L, Philippe C, Prasad C, Prasad M, Relator R, Rio M, Rondeau S, Ruault V, Ruiz-Pallares N, Sanchez E, Shears D, Siu VM, Sorlin A, Tedder M, Tharreau M, Mau-Them FT, van der Laan L, Van Gils J, Verloes A, Whalen S, Willems M, Yauy K, Zuntini R, Kerkhof J, Sadikovic B, Geneviève D. Clinico-biological refinement of BCL11B-related disorder and identification of an episignature: A series of 20 unreported individuals. Genet Med 2024; 26:101007. [PMID: 37860968 DOI: 10.1016/j.gim.2023.101007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023] Open
Abstract
PURPOSE BCL11B-related disorder (BCL11B-RD) arises from rare genetic variants within the BCL11B gene, resulting in a distinctive clinical spectrum encompassing syndromic neurodevelopmental disorder, with or without intellectual disability, associated with facial features and impaired immune function. This study presents an in-depth clinico-biological analysis of 20 newly reported individuals with BCL11B-RD, coupled with a characterization of genome-wide DNA methylation patterns of this genetic condition. METHODS Through an international collaboration, clinical and molecular data from 20 individuals were systematically gathered, and a comparative analysis was conducted between this series and existing literature. We further scrutinized peripheral blood DNA methylation profile of individuals with BCL11B-RD, contrasting them with healthy controls and other neurodevelopmental disorders marked by established episignature. RESULTS Our findings unveil rarely documented clinical manifestations, notably including Rubinstein-Taybi-like facial features, craniosynostosis, and autoimmune disorders, all manifesting within the realm of BCL11B-RD. We refine the intricacies of T cell compartment alterations of BCL11B-RD, revealing decreased levels naive CD4+ T cells and recent thymic emigrants while concurrently observing an elevated proportion of effector-memory expressing CD45RA CD8+ T cells (TEMRA). Finally, a distinct DNA methylation episignature exclusive to BCL11B-RD is unveiled. CONCLUSION This study serves to enrich our comprehension of the clinico-biological landscape of BCL11B-RD, potentially furnishing a more precise framework for diagnosis and follow-up of individuals carrying pathogenic BCL11B variant. Moreover, the identification of a unique DNA methylation episignature offers a valuable diagnosis tool for BCL11B-RD, thereby facilitating routine clinical practice by empowering physicians to reevaluate variants of uncertain significance within the BCL11B gene.
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Affiliation(s)
- Quentin Sabbagh
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Juliette Piard
- University Hospital of Besançon, Department of Clinical Genetics, Besançon, France
| | - Chloé Trouvé
- University Hospital of Besançon, Department of Clinical Genetics, Besançon, France
| | - Jeanne Amiel
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Tania Attié-Bitach
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Tugce Balci
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Mouna Barat-Houari
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Alyce Belonis
- Cincinnati Children's Hospital Medical Center, Division of Human Genetics, Cincinnati, OH; University of Cincinnati College of Medicine, Department of Pediatrics, Cincinnati, OH
| | - Odile Boute
- University Hospital of Lille, Department of Clinical Genetics, Lille, France
| | - Diana S Brightman
- Cincinnati Children's Hospital Medical Center, Division of Human Genetics, Cincinnati, OH
| | - Ange-Line Bruel
- University Hospital of Dijon, Laboratory of Molecular Genetics and Cytogenetics, Inserm UMR 1231 GAD, Dijon, France
| | | | - Nicolas Chatron
- University Hospital of Lyon, Laboratory of Medical Genetics, AURAGEN Platform, Lyon, France
| | - Corinne Collet
- Robert Debré University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - William Dufour
- University Hospital of Lille, Department of Clinical Genetics, Lille, France
| | - Patrick Edery
- University Hospital of Lyon, Department of Clinical Genetics, Lyon, France
| | - Chin-To Fong
- University of Rochester, Department of Genetics, Rochester, NY
| | - Carlo Fusco
- Azienda USL-IRCCS di Reggio Emilia, Child Neurology and Psychiatry Unit, 42123 Reggio Emilia, Italy
| | - Vincent Gatinois
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Evan Gouy
- University Hospital of Lyon, Department of Clinical Genetics, Lyon, France
| | - Anne-Marie Guerrot
- Rouen-Normandie University, University Hospital of Rouen, Department of Genetics, Reference Center for Developmental Disorders, Inserm UMR1245, F-76000 Rouen, France
| | - Solveig Heide
- Pitié-Salpêtrière University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Aakash Joshi
- Churchill Hospital, Department of Clinical Genetics, ERN-ITHACA, Oxford, United Kingdom
| | - Natalya Karp
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Boris Keren
- Pitié-Salpêtrière University Hospital, Laboratory of Molecular Genetics and Cytogenetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Marion Lesieur-Sebellin
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Jonathan Levy
- Robert Debré University Hospital, Laboratory of Cytogenetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Claire Lozano
- University Hospital of Montpellier, Department of Immunology, Montpellier, France
| | - Stanislas Lyonnet
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Henri Margot
- University of Bordeaux, University Hospital of Bordeaux, Department of Medical Genetics, MRGM Inserm UMR1211, F-33000 Bordeaux, France
| | - Pauline Marzin
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Vincent Michaud
- University of Bordeaux, University Hospital of Bordeaux, Department of Medical Genetics, MRGM Inserm UMR1211, F-33000 Bordeaux, France
| | - Gaël Nicolas
- Rouen-Normandie University, University Hospital of Rouen, Department of Genetics, Reference Center for Developmental Disorders, Inserm UMR1245, F-76000 Rouen, France
| | - Mevyn Nizard
- Necker-Enfants Malades University Hospital, Department of Pediatric Endocrinology, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Alix Paulet
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Francesca Peluso
- Azienda USL-IRCCS di Reggio Emilia, Medical Genetics Unit, 42123 Reggio Emilia, Italy
| | - Vincent Pernin
- University of Montpellier, Department of Nephrology, Montpellier, France
| | - Laurence Perrin
- Robert Debré University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Christophe Philippe
- University Hospital of Dijon, Laboratory of Molecular Genetics and Cytogenetics, Inserm UMR 1231 GAD, Dijon, France; Hospital of Metz-Thionville, Mercy Hospital, Laboratory of Genetics, Metz, France
| | - Chitra Prasad
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Madhavi Prasad
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Marlène Rio
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Sophie Rondeau
- Paris Cité University, Necker-Enfants Malades University Hospital, Department of Genomic Medicine of Rare Diseases, Imagine Institute, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Valentin Ruault
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Nathalie Ruiz-Pallares
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Elodie Sanchez
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Debbie Shears
- Churchill Hospital, Department of Clinical Genetics, ERN-ITHACA, Oxford, United Kingdom
| | - Victoria Mok Siu
- University of Western Ontario, London Health Sciences Centre, Department of Pediatrics, London, Ontario, Canada
| | - Arthur Sorlin
- University Hospital of Dijon, Laboratory of Molecular Genetics and Cytogenetics, Inserm UMR 1231 GAD, Dijon, France
| | | | - Mylène Tharreau
- University Hospital of Montpellier, Department of Molecular Genetics and Cytogenomics, Montpellier, France
| | - Frédéric Tran Mau-Them
- University Hospital of Dijon, Laboratory of Molecular Genetics and Cytogenetics, Inserm UMR 1231 GAD, Dijon, France
| | - Liselot van der Laan
- University of Amsterdam, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, AUMC Department of Human Genetics, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Julien Van Gils
- University of Bordeaux, University Hospital of Bordeaux, Department of Medical Genetics, MRGM Inserm UMR1211, F-33000 Bordeaux, France
| | - Alain Verloes
- Robert Debré University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Sandra Whalen
- Pitié-Salpêtrière University Hospital, Department of Clinical Genetics, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Marjolaine Willems
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Kévin Yauy
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Roberta Zuntini
- Azienda USL-IRCCS di Reggio Emilia, Medical Genetics Unit, 42123 Reggio Emilia, Italy
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, Londo, ON N6A 5W9, Canada
| | - David Geneviève
- Montpellier University, Inserm UMR1183, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France.
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Ng R, Harris J, Kleefstra T, Morgan AT, Simpson B. Editorial: Characterizing the neurobehavioral phenotype of mendelian disorders of epigenetic machinery. Front Genet 2023; 14:1338078. [PMID: 38116293 PMCID: PMC10728862 DOI: 10.3389/fgene.2023.1338078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Affiliation(s)
- Rowena Ng
- Department of Neuropsychology, Kennedy Krieger Institute, Baltimore, MD, United States
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jacqueline Harris
- Kennedy Krieger Institute, Baltimore, MD, United States
- Department of Genetic Medicine, Pediatrics and Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Tjitske Kleefstra
- Department of Human Genetics and Psychiatry, Radboud University Medical Center, Venray, Netherlands
- Centre of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, Netherlands
| | - Angela T. Morgan
- Speech and Language, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Department of Audiology and Speech Pathology, University of Melbourne, Parkville, VIC, Australia
- Speech Genomics Clinic, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Brittany Simpson
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, Division of Human Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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10
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LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Galey M, Goffena J, Gibson SB, Allan TJ, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel N, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Hubshman MW, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic Utility of Genome-wide DNA Methylation Analysis in Genetically Unsolved Developmental and Epileptic Encephalopathies and Refinement of a CHD2 Episignature. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.11.23296741. [PMID: 37873138 PMCID: PMC10592992 DOI: 10.1101/2023.10.11.23296741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequence-based genetic testing currently identifies causative genetic variants in ∼50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. Rare epigenetic variations ("epivariants") can drive disease by modulating gene expression at single loci, whereas genome-wide DNA methylation changes can result in distinct "episignature" biomarkers for monogenic disorders in a growing number of rare diseases. Here, we interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 516 individuals with genetically unsolved DEEs who had previously undergone extensive genetic testing. We identified rare differentially methylated regions (DMRs) and explanatory episignatures to discover causative and candidate genetic etiologies in 10 individuals. We then used long-read sequencing to identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and two copy number variants. We also identify pathogenic sequence variants associated with episignatures; some had been missed by previous exome sequencing. Although most DEE genes lack known episignatures, the increase in diagnostic yield for DNA methylation analysis in DEEs is comparable to the added yield of genome sequencing. Finally, we refine an episignature for CHD2 using an 850K methylation array which was further refined at higher CpG resolution using bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate genetic causes as ∼2% (10/516) for unsolved DEE cases.
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Haghshenas S, Foroutan A, Bhai P, Levy MA, Relator R, Kerkhof J, McConkey H, Skinner CD, Caylor RC, Tedder ML, Stevenson RE, Sadikovic B, Schwartz CE. Identification of a DNA methylation signature for Renpenning syndrome (RENS1), a spliceopathy. Eur J Hum Genet 2023; 31:879-886. [PMID: 36797465 PMCID: PMC10400603 DOI: 10.1038/s41431-023-01313-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/18/2023] Open
Abstract
The challenges and ambiguities in providing an accurate diagnosis for patients with neurodevelopmental disorders have led researchers to apply epigenetics as a technique to validate the diagnosis provided based on the clinical examination and genetic testing results. Genome-wide DNA methylation analysis has recently been adapted for clinical testing of patients with genetic neurodevelopmental disorders. In this paper, preliminary data demonstrating a DNA methylation signature for Renpenning syndrome (RENS1 - OMIM 309500), which is an X-linked recessive neurodevelopmental disorder caused by variants in polyglutamine-binding protein 1 (PQBP1) is reported. The identified episignature was then utilized to construct a highly sensitive and specific binary classification model. Besides providing evidence for the existence of a DNA methylation episignature for Renpenning syndrome, this study increases the knowledge of the molecular mechanisms related to the disease. Moreover, the availability of more subjects in future may facilitate the establishment of an episignature that can be utilized for diagnosis in a clinical setting and for reclassification of variants of unknown clinical significance.
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Affiliation(s)
- Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Pratibha Bhai
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | | | | | | | | | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada.
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.
| | - Charles E Schwartz
- Greenwood Genetic Center, Greenwood, SC, 29646, USA.
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA.
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12
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DNA methylation episignature for Witteveen-Kolk syndrome due to SIN3A haploinsufficiency. Genet Med 2023; 25:63-75. [PMID: 36399132 DOI: 10.1016/j.gim.2022.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/19/2022] Open
Abstract
PURPOSE Witteveen-Kolk syndrome (WITKOS) is a rare, autosomal dominant neurodevelopmental disorder caused by heterozygous loss-of-function alterations in the SIN3A gene. WITKOS has variable expressivity that commonly overlaps with other neurodevelopmental disorders. In this study, we characterized a distinct DNA methylation epigenetic signature (episignature) distinguishing WITKOS from unaffected individuals as well as individuals with other neurodevelopmental disorders with episignatures and described 9 previously unpublished individuals with SIN3A haploinsufficiency. METHODS We studied the phenotypic characteristics and the genome-wide DNA methylation in the peripheral blood samples of 20 individuals with heterozygous alterations in SIN3A. A total of 14 samples were used for the identification of the episignature and building of a predictive diagnostic biomarker, whereas the diagnostic model was used to investigate the methylation pattern of the remaining 6 samples. RESULTS A predominantly hypomethylated DNA methylation profile specific to WITKOS was identified, and the classifier model was able to diagnose a previously unresolved test case. The episignature was sensitive enough to detect individuals with varying degrees of phenotypic severity carrying SIN3A haploinsufficient variants. CONCLUSION We identified a novel, robust episignature in WITKOS due to SIN3A haploinsufficiency. This episignature has the potential to aid identification and diagnosis of individuals with WITKOS.
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Megagiannis P, Suresh R, Rouleau GA, Zhou Y. Reversibility and therapeutic development for neurodevelopmental disorders, insights from genetic animal models. Adv Drug Deliv Rev 2022; 191:114562. [PMID: 36183904 DOI: 10.1016/j.addr.2022.114562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/30/2022] [Accepted: 09/24/2022] [Indexed: 01/24/2023]
Abstract
Neurodevelopmental Disorders (NDDs) encompass a broad spectrum of conditions resulting from atypical brain development. Over the past decades, we have had the fortune to witness enormous progress in diagnosis, etiology discovery, modeling, and mechanistic understanding of NDDs from both fundamental and clinical research. Here, we review recent neurobiological advances from experimental models of NDDs. We introduce several examples and highlight breakthroughs in reversal studies of phenotypes using genetically engineered models of NDDs. The in-depth understanding of brain pathophysiology underlying NDDs and evaluations of reversibility in animal models paves the foundation for discovering novel treatment options. We discuss how the expanding property of cutting-edge technologies, such as gene editing and AAV-mediated gene delivery, are leveraged in animal models for the therapeutic development of NDDs. We envision opportunities and challenges toward faithful modeling and fruitful clinical translation.
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Affiliation(s)
- Platon Megagiannis
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital; Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Rahul Suresh
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital; Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Guy A Rouleau
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital; Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Yang Zhou
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital; Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec H3A 2B4, Canada.
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Genome-wide DNA methylation profiling and exome sequencing resolved a long-time misdiagnosed case. J Hum Genet 2022; 67:547-551. [PMID: 35581385 DOI: 10.1038/s10038-022-01043-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 05/05/2022] [Indexed: 11/08/2022]
Abstract
The search for aetiology of Mendelian disorders is traditionally based on the observation of clinical phenotypes and molecular screening of associated genes. However, a disease-specific diagnosis can be challenging. In this study we detail how the combinatorial genomic and epigenomic assessment allowed to find the underlying molecular event of a clinical case that remained misdiagnosed for years. The individual was referred as affected by an atypical form of Kabuki syndrome with a variant of uncertain significance in the KMT2D gene. However, significant inconsistencies with this diagnosis emerged upon familial segregation of the variant and after the clinical re-evaluation. Therefore, we applied an epigenomic strategy by studying the DNA methylation profile which resulted not consistent with the Kabuki syndrome episignature or with any other disorder-specific episignature described so far, providing strong evidence that the Kabuki syndrome diagnosis does not apply. This result led us to further investigate for epigenetic machinery diseases by using a multigene panel for chromatinopathies. Since this analysis yielded negative results, we applied a whole exome sequencing and identified a de novo pathogenic variant in the CTNNB1 gene associated to NEDSDV syndrome, a neurodevelopmental disorder characterized by intellectual disability and craniofacial anomalies. Based on molecular results and the updated clinical features, we confirmed the NEDSDV diagnosis. Our findings show that the combination of genomic and epigenomics strategies, along with a deeper analysis of clinical phenotype, may provide a significant improvement in the diagnostic protocols for rare genetic disorders and help resolve long-time misdiagnosed and unsolved case.
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15
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Rouxel F, Relator R, Kerkhof J, McConkey H, Levy M, Dias P, Barat-Houari M, Bednarek N, Boute O, Chatron N, Cherik F, Delahaye-Duriez A, Doco-Fenzy M, Faivre L, Gauthier LW, Heron D, Hildebrand MS, Lesca G, Lespinasse J, Mazel B, Menke LA, Morgan AT, Pinson L, Quelin C, Rossi M, Ruiz-Pallares N, Tran-Mau-Them F, Van Kessel IN, Vincent M, Weber M, Willems M, Leguyader G, Sadikovic B, Genevieve D. CDK13-related disorder: Report of a series of 18 previously unpublished individuals and description of an epigenetic signature. Genet Med 2022; 24:1096-1107. [PMID: 35063350 DOI: 10.1016/j.gim.2021.12.016] [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: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 01/02/2023] Open
Abstract
PURPOSE Rare genetic variants in CDK13 are responsible for CDK13-related disorder (CDK13-RD), with main clinical features being developmental delay or intellectual disability, facial features, behavioral problems, congenital heart defect, and seizures. In this paper, we report 18 novel individuals with CDK13-RD and provide characterization of genome-wide DNA methylation. METHODS We obtained clinical phenotype and neuropsychological data for 18 and 10 individuals, respectively, and compared this series with the literature. We also compared peripheral blood DNA methylation profiles in individuals with CDK13-RD, controls, and other neurodevelopmental disorders episignatures. Finally, we developed a support vector machine-based classifier distinguishing CDK13-RD and non-CDK13-RD samples. RESULTS We reported health and developmental parameters, clinical data, and neuropsychological profile of individuals with CDK13-RD. Genome-wide differential methylation analysis revealed a global hypomethylated profile in individuals with CDK13-RD in a highly sensitive and specific model that could aid in reclassifying variants of uncertain significance. CONCLUSION We describe the novel features such as anxiety disorder, cryptorchidism, and disrupted sleep in CDK13-RD. We define a CDK13-RD DNA methylation episignature as a diagnostic tool and a defining functional feature of the evolving clinical presentation of this disorder. We also show overlap of the CDK13 DNA methylation profile in an individual with a functionally and clinically related CCNK-related disorder.
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Affiliation(s)
- Flavien Rouxel
- Génétique clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, INSERM U1183, ERN ITHACA, Montpellier, France
| | - Raissa Relator
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer Kerkhof
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Haley McConkey
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Michael Levy
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Patricia Dias
- Genetics Department, Hospital Center of Lisbon North, ERN ITHACA, Lisbon, Portugal
| | - Mouna Barat-Houari
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique des Maladies Rares et Auto-Inflammatoires, CHU Montpellier, Université de Montpellier, Montpellier, France
| | - Nathalie Bednarek
- Genetics Department, CHU Reims, Medical school IFR53, EA3801, Reims, France
| | - Odile Boute
- Genetics Department, Guy Fontaine Medical Center, CLAD Nord de France, Jeanne de Flandre Hospital, CHRU Lille, Lille, France
| | - Nicolas Chatron
- Genetics Department, Lyon University Hospital, and Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Claude Bernard Lyon 1 University, Lyon, France
| | - Florian Cherik
- Genetics Department, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Andrée Delahaye-Duriez
- Department of Histology Embryology and Cytogenetics, Jean Verdier Hospital; Paris 13 University, Sorbonne Paris Cité, UFR SMBH Bobigny; PROTECT, INSERM, Paris Diderot University, Paris, France
| | - Martine Doco-Fenzy
- Genetics Department, CHU Reims, Medical school IFR53, EA3801, Reims, France
| | - Laurence Faivre
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, Dijon, France; Genetics of Developmental Disorders, INSERM - Bourgogne Franche-Comté University, UMR 1231 GAD Team, Dijon, France
| | - Lucas W Gauthier
- Genetics Department, Lyon University Hospital, and Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Claude Bernard Lyon 1 University, Lyon, France
| | - Delphine Heron
- Genetics Department, University Hospital Pitié-Salpétrière, Paris, France
| | - Michael S Hildebrand
- Epilepsy Research Center, Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia; Murdoch Children's Research Institute, Department of Audiology and Speech Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gaëtan Lesca
- Genetics Department, Lyon University Hospital, and Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Claude Bernard Lyon 1 University, Lyon, France
| | | | - Benoit Mazel
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, Dijon, France
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, ERN ITHACA, Amsterdam, Netherlands
| | - Angela T Morgan
- Department of Audiology and Speech Pathology, Melbourne School of Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Lucile Pinson
- Génétique clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, INSERM U1183, ERN ITHACA, Montpellier, France
| | - Chloe Quelin
- Department of Clinical Genetics, CLAD Ouest, CHU de Rennes, Hôpital Sud, Rennes, France
| | - Massimiliano Rossi
- Genetics Department, Lyon University Hospital, and Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Claude Bernard Lyon 1 University, Lyon, France; Genetics Department, Referral Centre for Developmental Abnormalities, Lyon University Hospital Lyon, France; INSERM U1028, CNRS UMR5292, Lyon Neuroscience Research Centre, GENDEV Team, Claude Bernard Lyon 1 University, Lyon, France
| | - Nathalie Ruiz-Pallares
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique des Maladies Rares et Auto-Inflammatoires, CHU Montpellier, Université de Montpellier, Montpellier, France
| | - Frederic Tran-Mau-Them
- Genetics of Developmental Disorders, INSERM - Bourgogne Franche-Comté University, UMR 1231 GAD Team, Dijon, France; Functional Unit 6254 Innovation in Genomic Diagnosis of Rare Diseases, CHU Dijon Bourgogne, Dijon, France
| | - Imke N Van Kessel
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, ERN ITHACA, Amsterdam, Netherlands
| | | | - Mathys Weber
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, CHU Dijon, Dijon, France
| | - Marjolaine Willems
- Génétique clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, INSERM U1183, ERN ITHACA, Montpellier, France
| | - Gwenael Leguyader
- Genetics Department, CHU de Poitiers, Poitiers University Hospital, Poitiers, France
| | - Bekim Sadikovic
- The Archie & Irene Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
| | - David Genevieve
- Génétique clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier University, Centre de Référence Anomalies du Développement SOOR, INSERM U1183, ERN ITHACA, Montpellier, France.
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16
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Marwaha S, Knowles JW, Ashley EA. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Med 2022; 14:23. [PMID: 35220969 PMCID: PMC8883622 DOI: 10.1186/s13073-022-01026-w] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
Rare diseases affect 30 million people in the USA and more than 300-400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25-35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.
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Affiliation(s)
- Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA.
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA.
| | - Joshua W Knowles
- Department of Medicine, Division of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Diabetes Research Center, Cardiovascular Institute and Prevention Research Center, Stanford, CA, USA
| | - Euan A Ashley
- Department of Medicine, Division of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA.
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA.
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA.
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17
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Foroutan A, Haghshenas S, Bhai P, Levy MA, Kerkhof J, McConkey H, Niceta M, Ciolfi A, Pedace L, Miele E, Genevieve D, Heide S, Alders M, Zampino G, Merla G, Fradin M, Bieth E, Bonneau D, Dieterich K, Fergelot P, Schaefer E, Faivre L, Vitobello A, Maitz S, Fischetto R, Gervasini C, Piccione M, van de Laar I, Tartaglia M, Sadikovic B, Lebre AS. Clinical Utility of a Unique Genome-Wide DNA Methylation Signature for KMT2A-Related Syndrome. Int J Mol Sci 2022; 23:ijms23031815. [PMID: 35163737 PMCID: PMC8836705 DOI: 10.3390/ijms23031815] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/28/2022] Open
Abstract
Wiedemann–Steiner syndrome (WDSTS) is a Mendelian syndromic intellectual disability (ID) condition associated with hypertrichosis cubiti, short stature, and characteristic facies caused by pathogenic variants in the KMT2A gene. Clinical features can be inconclusive in mild and unusual WDSTS presentations with variable ID (mild to severe), facies (typical or not) and other associated malformations (bone, cerebral, renal, cardiac and ophthalmological anomalies). Interpretation and classification of rare KMT2A variants can be challenging. A genome-wide DNA methylation episignature for KMT2A-related syndrome could allow functional classification of variants and provide insights into the pathophysiology of WDSTS. Therefore, we assessed genome-wide DNA methylation profiles in a cohort of 60 patients with clinical diagnosis for WDSTS or Kabuki and identified a unique highly sensitive and specific DNA methylation episignature as a molecular biomarker of WDSTS. WDSTS episignature enabled classification of variants of uncertain significance in the KMT2A gene as well as confirmation of diagnosis in patients with clinical presentation of WDSTS without known genetic variants. The changes in the methylation profile resulting from KMT2A mutations involve global reduction in methylation in various genes, including homeobox gene promoters. These findings provide novel insights into the molecular etiology of WDSTS and explain the broad phenotypic spectrum of the disease.
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Affiliation(s)
- Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada; (A.F.); (S.H.)
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada; (A.F.); (S.H.)
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Pratibha Bhai
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Michael A. Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (M.N.); (A.C.); (M.T.)
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (M.N.); (A.C.); (M.T.)
| | - Lucia Pedace
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (L.P.); (E.M.)
| | - Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (L.P.); (E.M.)
| | - David Genevieve
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Reference Center AD SOOR, AnDDI-RARE, Groupe DI, Inserm U1183—Institute for Regenerative Medicine and Biotherapy, Montpellier University, Centre Hospitalier Universitaire de Montpellier, 34090 Montpellier, France;
| | - Solveig Heide
- Department of Genetics, Referral Center for Intellectual Disabilities, APHP Sorbonne University, Pitié Salpêtrière Hospital, 75013 Paris, France;
| | - Mariëlle Alders
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Giuseppe Zampino
- Center for Rare Diseases and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy;
- Facoltà di Medicina e Chirurgia, Università Cattolica del S. Cuore, 20123 Roma, Italy
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, Università di Napoli “Federico II”, 80131 Naples, Italy;
- Laboratory of Regulatory and Functional Genomics, Fondazione Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Mélanie Fradin
- Service de Génétique, CHU de Rennes, 35203 Rennes, France;
| | - Eric Bieth
- Medical Genetics Department, University of Angers, CHU Angers, 49000 Angers, France;
| | - Dominique Bonneau
- Department of genetics, CHU d’Angers, 49000 Angers, France and MitoVasc, UMR CNRS 6015-INSERM 1083, University of Angers, 49055 Angers, France;
| | - Klaus Dieterich
- CHU Grenoble Alpes, Inserm, U1209, Institute of Advanced Biosciences, Université Grenoble Alpes, 38000 Grenoble, France;
| | - Patricia Fergelot
- Medical Genetics Department, Inserm U1211, Reference Center AD SOOR, AnDDI-RARE, Bordeaux University, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France;
| | - Elise Schaefer
- Service de Génétique Médicale—Institut de Génétique Médicale d’Alsace—Hôpitaux Universitaires de Strasbourg, 67091 Strasbourg, France;
| | - Laurence Faivre
- Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, 15 boulevard du Maréchal de Lattre de Tassigny, 21000 Dijon, France; (L.F.); (A.V.)
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, Department of Medical Genetics, Dijon University Hospital, 21000 Dijon, France
| | - Antonio Vitobello
- Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, 15 boulevard du Maréchal de Lattre de Tassigny, 21000 Dijon, France; (L.F.); (A.V.)
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, Department of Medical Genetics, Dijon University Hospital, 21000 Dijon, France
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, S. Gerardo Hospital, 20900 Monza, Italy;
| | - Rita Fischetto
- Clinical Genetics Unit, Department of Pediatric Medicine, Giovanni XXIII Children’s Hospital, 02115 Bari, Italy;
| | - Cristina Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy;
| | - Maria Piccione
- Department of Sciences for Health Promotion and Mother and Child Care “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy;
| | - Ingrid van de Laar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (M.N.); (A.C.); (M.T.)
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada; (A.F.); (S.H.)
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; (P.B.); (M.A.L.); (J.K.); (H.M.)
- Correspondence: (B.S.); (A.-S.L.)
| | - Anne-Sophie Lebre
- Team Physiopathologie des Maladies Psychiatriques, GDR3557-Institut de Psychiatrie, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Université de Paris, 75006 Paris, France
- Centre Hospitalier Universitaire de Reims, Pôle de Biologie Médicale et Pathologie, Service de GénéTique, 51100 Reims, France
- Correspondence: (B.S.); (A.-S.L.)
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18
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Levy MA, McConkey H, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Fletcher RS, Cherik F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Pizzi S, Plomp AS, Poulton C, Reilly J, Relator R, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, St John M, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci T, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Kerrnohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders. HGG ADVANCES 2022; 3:100075. [PMID: 35047860 PMCID: PMC8756545 DOI: 10.1016/j.xhgg.2021.100075] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, UK
| | | | - Mariet W Elting
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Florian Cherik
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, the Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Kristin D Kerrnohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Department of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
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19
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Arumugam T, Ramphal U, Adimulam T, Chinniah R, Ramsuran V. Deciphering DNA Methylation in HIV Infection. Front Immunol 2021; 12:795121. [PMID: 34925380 PMCID: PMC8674454 DOI: 10.3389/fimmu.2021.795121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
With approximately 38 million people living with HIV/AIDS globally, and a further 1.5 million new global infections per year, it is imperative that we advance our understanding of all factors contributing to HIV infection. While most studies have focused on the influence of host genetic factors on HIV pathogenesis, epigenetic factors are gaining attention. Epigenetics involves alterations in gene expression without altering the DNA sequence. DNA methylation is a critical epigenetic mechanism that influences both viral and host factors. This review has five focal points, which examines (i) fluctuations in the expression of methylation modifying factors upon HIV infection (ii) the effect of DNA methylation on HIV viral genes and (iii) host genome (iv) inferences from other infectious and non-communicable diseases, we provide a list of HIV-associated host genes that are regulated by methylation in other disease models (v) the potential of DNA methylation as an epi-therapeutic strategy and biomarker. DNA methylation has also been shown to serve as a robust therapeutic strategy and precision medicine biomarker against diseases such as cancer and autoimmune conditions. Despite new drugs being discovered for HIV, drug resistance is a problem in high disease burden settings such as Sub-Saharan Africa. Furthermore, genetic therapies that are under investigation are irreversible and may have off target effects. Alternative therapies that are nongenetic are essential. In this review, we discuss the potential role of DNA methylation as a novel therapeutic intervention against HIV.
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Affiliation(s)
- Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Theolan Adimulam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Romona Chinniah
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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20
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Kerkhof J, Squeo GM, McConkey H, Levy MA, Piemontese MR, Castori M, Accadia M, Biamino E, Della Monica M, Di Giacomo MC, Gervasini C, Maitz S, Melis D, Milani D, Piccione M, Prontera P, Selicorni A, Sadikovic B, Merla G. DNA methylation episignature testing improves molecular diagnosis of Mendelian chromatinopathies. Genet Med 2021; 24:51-60. [PMID: 34906459 DOI: 10.1016/j.gim.2021.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/06/2021] [Accepted: 08/12/2021] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Chromatinopathies include more than 50 disorders caused by disease-causing variants of various components of chromatin structure and function. Many of these disorders exhibit unique genome-wide DNA methylation profiles, known as episignatures. In this study, the methylation profile of a large cohort of individuals with chromatinopathies was analyzed for episignature detection. METHODS DNA methylation data was generated on extracted blood samples from 129 affected individuals with the Illumina Infinium EPIC arrays and analyzed using an established bioinformatic pipeline. RESULTS The DNA methylation profiles matched and confirmed the sequence findings in both the discovery and validation cohorts. Twenty-five affected individuals carrying a variant of uncertain significance, did not show a methylation profile matching any of the known episignatures. Three additional variant of uncertain significance cases with an identified KDM6A variant were re-classified as likely pathogenic (n = 2) or re-assigned as Wolf-Hirschhorn syndrome (n = 1). Thirty of the 33 Next Generation Sequencing negative cases did not match a defined episignature while three matched Kabuki syndrome, Rubinstein-Taybi syndrome and BAFopathy respectively. CONCLUSION With the expanding clinical utility of the EpiSign assay, DNA methylation analysis should be considered part of the testing cascade for individuals presenting with clinical features of Mendelian chromatinopathy disorders.
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Affiliation(s)
- Jennifer Kerkhof
- Molecular Diagnostics Program, and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Gabriella Maria Squeo
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Haley McConkey
- Molecular Diagnostics Program, and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Michael A Levy
- Molecular Diagnostics Program, and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada
| | - Maria Rosaria Piemontese
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital "Cardinale G. Panico", Tricase, Lecce, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Italy
| | - Matteo Della Monica
- Medical Genetics Unit, Cardarelli Hospital, Largo A Cardarelli, Napoli, Italy
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Daniela Melis
- Medical, Surgical, and Dental Department, Università degli Studi di Salerno, Salerno, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Sant'Anna General Hospital, Como, Italy
| | - Bekim Sadikovic
- Molecular Diagnostics Program, and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Canada.
| | - Giuseppe Merla
- Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy; Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy.
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21
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Levy MA, Beck DB, Metcalfe K, Douzgou S, Sithambaram S, Cottrell T, Ansar M, Kerkhof J, Mignot C, Nougues MC, Keren B, Moore HW, Oegema R, Giltay JC, Simon M, van Jaarsveld RH, Bos J, van Haelst M, Motazacker MM, Boon EMJ, Santen GWE, Ruivenkamp CAL, Alders M, Luperchio TR, Boukas L, Ramsey K, Narayanan V, Schaefer GB, Bonasio R, Doheny KF, Stevenson RE, Banka S, Sadikovic B, Fahrner JA. Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood. NPJ Genom Med 2021; 6:92. [PMID: 34750377 PMCID: PMC8576018 DOI: 10.1038/s41525-021-00256-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 09/23/2021] [Indexed: 11/08/2022] Open
Abstract
TET3 encodes an essential dioxygenase involved in epigenetic regulation through DNA demethylation. TET3 deficiency, or Beck-Fahrner syndrome (BEFAHRS; MIM: 618798), is a recently described neurodevelopmental disorder of the DNA demethylation machinery with a nonspecific phenotype resembling other chromatin-modifying disorders, but inconsistent variant types and inheritance patterns pose diagnostic challenges. Given TET3's direct role in regulating 5-methylcytosine and recent identification of syndrome-specific DNA methylation profiles, we analyzed genome-wide DNA methylation in whole blood of TET3-deficient individuals and identified an episignature that distinguishes affected and unaffected individuals and those with mono-allelic and bi-allelic pathogenic variants. Validation and testing of the episignature correctly categorized known TET3 variants and determined pathogenicity of variants of uncertain significance. Clinical utility was demonstrated when the episignature alone identified an affected individual from over 1000 undiagnosed cases and was confirmed upon distinguishing TET3-deficient individuals from those with 46 other disorders. The TET3-deficient signature - and the signature resulting from activating mutations in DNMT1 which normally opposes TET3 - are characterized by hypermethylation, which for BEFAHRS involves CpG sites that may be biologically relevant. This work expands the role of epi-phenotyping in molecular diagnosis and reveals genome-wide DNA methylation profiling as a quantitative, functional readout for characterization of this new biochemical category of disease.
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Affiliation(s)
- Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - David B Beck
- National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Kay Metcalfe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Sofia Douzgou
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Sivagamy Sithambaram
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Trudie Cottrell
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320, Islamabad, Pakistan
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - Cyril Mignot
- Assistance Publique-Hopitaux de Paris, Sorbonne Université, Departement de Génétique, Groupe Hospitalier Pitie-Salpetriere et Hopital Trousseau, Paris, 75651, France
| | - Marie-Christine Nougues
- Department of Neuropediatrics, Armand Trousseau Hospital, Assistance Publique-Hopitaux de Paris, Paris, 75012, France
| | - Boris Keren
- Laboratoire de génétique, Hôpital Pïtié-Salpêtrière, Assistance Publique-Hopitaux de Paris, Paris, 75013, France
| | | | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jacques C Giltay
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marleen Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Richard H van Jaarsveld
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jessica Bos
- Section Clinical Genetics, Department Human Genetics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Mieke van Haelst
- Section Clinical Genetics, Department Human Genetics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - M Mahdi Motazacker
- Department of Human Genetics, Laboratory of Genome Diagnostics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Elles M J Boon
- Department of Human Genetics, VU University Medical Center Amsterdam, Amsterdam UMC, van der Boechorststraat 7, 1081 BT, Amsterdam, The Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Teresa Romeo Luperchio
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Leandros Boukas
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Roberto Bonasio
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Kimberly F Doheny
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada.
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A5W9, Canada.
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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22
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Mossink B, Negwer M, Schubert D, Nadif Kasri N. The emerging role of chromatin remodelers in neurodevelopmental disorders: a developmental perspective. Cell Mol Life Sci 2021; 78:2517-2563. [PMID: 33263776 PMCID: PMC8004494 DOI: 10.1007/s00018-020-03714-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022]
Abstract
Neurodevelopmental disorders (NDDs), including intellectual disability (ID) and autism spectrum disorders (ASD), are a large group of disorders in which early insults during brain development result in a wide and heterogeneous spectrum of clinical diagnoses. Mutations in genes coding for chromatin remodelers are overrepresented in NDD cohorts, pointing towards epigenetics as a convergent pathogenic pathway between these disorders. In this review we detail the role of NDD-associated chromatin remodelers during the developmental continuum of progenitor expansion, differentiation, cell-type specification, migration and maturation. We discuss how defects in chromatin remodelling during these early developmental time points compound over time and result in impaired brain circuit establishment. In particular, we focus on their role in the three largest cell populations: glutamatergic neurons, GABAergic neurons, and glia cells. An in-depth understanding of the spatiotemporal role of chromatin remodelers during neurodevelopment can contribute to the identification of molecular targets for treatment strategies.
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Affiliation(s)
- Britt Mossink
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Moritz Negwer
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands.
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23
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Sadikovic B, Levy MA, Kerkhof J, Aref-Eshghi E, Schenkel L, Stuart A, McConkey H, Henneman P, Venema A, Schwartz CE, Stevenson RE, Skinner SA, DuPont BR, Fletcher RS, Balci TB, Siu VM, Granadillo JL, Masters J, Kadour M, Friez MJ, van Haelst MM, Mannens MMAM, Louie RJ, Lee JA, Tedder ML, Alders M. Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders. Genet Med 2021; 23:1065-1074. [PMID: 33547396 PMCID: PMC8187150 DOI: 10.1038/s41436-020-01096-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 01/23/2023] Open
Abstract
Purpose We describe the clinical implementation of genome-wide DNA methylation analysis in rare disorders across the EpiSign diagnostic laboratory network and the assessment of results and clinical impact in the first subjects tested. Methods We outline the logistics and data flow between an integrated network of clinical diagnostics laboratories in Europe, the United States, and Canada. We describe the clinical validation of EpiSign using 211 specimens and assess the test performance and diagnostic yield in the first 207 subjects tested involving two patient subgroups: the targeted cohort (subjects with previous ambiguous/inconclusive genetic findings including genetic variants of unknown clinical significance) and the screening cohort (subjects with clinical findings consistent with hereditary neurodevelopmental syndromes and no previous conclusive genetic findings). Results Among the 207 subjects tested, 57 (27.6%) were positive for a diagnostic episignature including 48/136 (35.3%) in the targeted cohort and 8/71 (11.3%) in the screening cohort, with 4/207 (1.9%) remaining inconclusive after EpiSign analysis. Conclusion This study describes the implementation of diagnostic clinical genomic DNA methylation testing in patients with rare disorders. It provides strong evidence of clinical utility of EpiSign analysis, including the ability to provide conclusive findings in the majority of subjects tested.
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Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Laila Schenkel
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Andrea Venema
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Victoria Mok Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Jennefer Masters
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Mike Kadour
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | | | - Mieke M van Haelst
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands.
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24
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Detection of a DNA Methylation Signature for the Intellectual Developmental Disorder, X-Linked, Syndromic, Armfield Type. Int J Mol Sci 2021; 22:ijms22031111. [PMID: 33498634 PMCID: PMC7865843 DOI: 10.3390/ijms22031111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/19/2022] Open
Abstract
A growing number of genetic neurodevelopmental disorders are known to be associated with unique genomic DNA methylation patterns, called episignatures, which are detectable in peripheral blood. The intellectual developmental disorder, X-linked, syndromic, Armfield type (MRXSA) is caused by missense variants in FAM50A. Functional studies revealed the pathogenesis to be a spliceosomopathy that is characterized by atypical mRNA processing during development. In this study, we assessed the peripheral blood specimens in a cohort of individuals with MRXSA and detected a unique and highly specific DNA methylation episignature associated with this disorder. We used this episignature to construct a support vector machine model capable of sensitive and specific identification of individuals with pathogenic variants in FAM50A. This study contributes to the expanding number of genetic neurodevelopmental disorders with defined DNA methylation episignatures, provides an additional understanding of the associated molecular mechanisms, and further enhances our ability to diagnose patients with rare disorders.
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25
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Haghshenas S, Bhai P, Aref-Eshghi E, Sadikovic B. Diagnostic Utility of Genome-Wide DNA Methylation Analysis in Mendelian Neurodevelopmental Disorders. Int J Mol Sci 2020; 21:ijms21239303. [PMID: 33291301 PMCID: PMC7730976 DOI: 10.3390/ijms21239303] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
Mendelian neurodevelopmental disorders customarily present with complex and overlapping symptoms, complicating the clinical diagnosis. Individuals with a growing number of the so-called rare disorders exhibit unique, disorder-specific DNA methylation patterns, consequent to the underlying gene defects. Besides providing insights to the pathophysiology and molecular biology of these disorders, we can use these epigenetic patterns as functional biomarkers for the screening and diagnosis of these conditions. This review summarizes our current understanding of DNA methylation episignatures in rare disorders and describes the underlying technology and analytical approaches. We discuss the computational parameters, including statistical and machine learning methods, used for the screening and classification of genetic variants of uncertain clinical significance. Describing the rationale and principles applied to the specific computational models that are used to develop and adapt the DNA methylation episignatures for the diagnosis of rare disorders, we highlight the opportunities and challenges in this emerging branch of diagnostic medicine.
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Affiliation(s)
- Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
| | - Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada;
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A 5W9, Canada;
- Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
- Correspondence:
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