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van der Laan L, Lauffer P, Rooney K, Silva A, Haghshenas S, Relator R, Levy MA, Trajkova S, Huisman SA, Bijlsma EK, Kleefstra T, van Bon BW, Baysal Ö, Zweier C, Palomares-Bralo M, Fischer J, Szakszon K, Faivre L, Piton A, Mesman S, Hochstenbach R, Elting MW, van Hagen JM, Plomp AS, Mannens MMAM, Alders M, van Haelst MM, Ferrero GB, Brusco A, Henneman P, Sweetser DA, Sadikovic B, Vitobello A, Menke LA. DNA methylation episignature and comparative epigenomic profiling for Pitt-Hopkins syndrome caused by TCF4 variants. HGG ADVANCES 2024; 5:100289. [PMID: 38571311 PMCID: PMC11087720 DOI: 10.1016/j.xhgg.2024.100289] [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: 11/13/2023] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder caused by pathogenic variants in TCF4, leading to intellectual disability, specific morphological features, and autonomic nervous system dysfunction. Epigenetic dysregulation has been implicated in PTHS, prompting the investigation of a DNA methylation (DNAm) "episignature" specific to PTHS for diagnostic purposes and variant reclassification and functional insights into the molecular pathophysiology of this disorder. A cohort of 67 individuals with genetically confirmed PTHS and three individuals with intellectual disability and a variant of uncertain significance (VUS) in TCF4 were studied. The DNAm episignature was developed with an Infinium Methylation EPIC BeadChip array analysis using peripheral blood cells. Support vector machine (SVM) modeling and clustering methods were employed to generate a DNAm classifier for PTHS. Validation was extended to an additional cohort of 11 individuals with PTHS. The episignature was assessed in relation to other neurodevelopmental disorders and its specificity was examined. A specific DNAm episignature for PTHS was established. The classifier exhibited high sensitivity for TCF4 haploinsufficiency and missense variants in the basic-helix-loop-helix domain. Notably, seven individuals with TCF4 variants exhibited negative episignatures, suggesting complexities related to mosaicism, genetic factors, and environmental influences. The episignature displayed degrees of overlap with other related disorders and biological pathways. This study defines a DNAm episignature for TCF4-related PTHS, enabling improved diagnostic accuracy and VUS reclassification. The finding that some cases scored negatively underscores the potential for multiple or nested episignatures and emphasizes the need for continued investigation to enhance specificity and coverage across PTHS-related variants.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Peter Lauffer
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Ananília Silva
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Sylvia A Huisman
- Amsterdam UMC location University of Amsterdam, Emma Children's Hospital, Department of Pediatrics, Amsterdam, the Netherlands; Zodiak, Prinsenstichting, Purmerend, the Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Özlem Baysal
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christiane Zweier
- Department of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Department of Human Genetics, University of Bern, Inselspital Universitätsspital Bern, Bern, Switzerland
| | - María Palomares-Bralo
- Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Madrid, Spain
| | - Jan Fischer
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Katalin Szakszon
- Institute of Paediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Laurence Faivre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD «Génétique des Anomalies du Développement», FHUTRANSLAD, Dijon, France; CHU Dijon Bourgogne, Centre de Génétique, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs», FHU-TRANSLDAD, Dijon, France
| | - Amélie Piton
- Genetic Diagnosis Laboratories, Strasbourg University Hospital, Strasbourg 67000, France
| | - Simone Mesman
- Swammerdam Institute for Life Sciences, FNWI, University of Amsterdam, Amsterdam, the Netherlands
| | - Ron Hochstenbach
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Mariet W Elting
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Johanna M van Hagen
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Astrid S Plomp
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Mieke M van Haelst
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Giovanni B Ferrero
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Peter Henneman
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - David A Sweetser
- Division of Medical Genetics and Metabolism and Center for Genomic Medicine, Massachusetts General for Children, Boston, MA, USA
| | - Bekim Sadikovic
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Leonie A Menke
- Amsterdam Reproduction & Development, Amsterdam, the Netherlands; Amsterdam UMC location University of Amsterdam, Emma Children's Hospital, Department of Pediatrics, Amsterdam, the Netherlands; Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Amsterdam, the Netherlands.
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2
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Trajkova S, Kerkhof J, Rossi Sebastiano M, Pavinato L, Ferrero E, Giovenino C, Carli D, Di Gregorio E, Marinoni R, Mandrile G, Palermo F, Carestiato S, Cardaropoli S, Pullano V, Rinninella A, Giorgio E, Pippucci T, Dimartino P, Rzasa J, Rooney K, McConkey H, Petlichkovski A, Pasini B, Sukarova-Angelovska E, Campbell CM, Metcalfe K, Jenkinson S, Banka S, Mussa A, Ferrero GB, Sadikovic B, Brusco A. DNA methylation analysis in patients with neurodevelopmental disorders improves variant interpretation and reveals complexity. HGG ADVANCES 2024; 5:100309. [PMID: 38751117 PMCID: PMC11216013 DOI: 10.1016/j.xhgg.2024.100309] [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: 12/06/2023] [Revised: 05/09/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
Analysis of genomic DNA methylation by generating epigenetic signature profiles (episignatures) is increasingly being implemented in genetic diagnosis. Here we report our experience using episignature analysis to resolve both uncomplicated and complex cases of neurodevelopmental disorders (NDDs). We analyzed 97 NDDs divided into (1) a validation cohort of 59 patients with likely pathogenic/pathogenic variants characterized by a known episignature and (2) a test cohort of 38 patients harboring variants of unknown significance or unidentified variants. The expected episignature was obtained in most cases with likely pathogenic/pathogenic variants (53/59 [90%]), a revealing exception being the overlapping profile of two SMARCB1 pathogenic variants with ARID1A/B:c.6200, confirmed by the overlapping clinical features. In the test cohort, five cases showed the expected episignature, including (1) novel pathogenic variants in ARID1B and BRWD3; (2) a deletion in ATRX causing MRXFH1 X-linked mental retardation; and (3) confirmed the clinical diagnosis of Cornelia de Lange (CdL) syndrome in mutation-negative CdL patients. Episignatures analysis of the in BAF complex components revealed novel functional protein interactions and common episignatures affecting homologous residues in highly conserved paralogous proteins (SMARCA2 M856V and SMARCA4 M866V). Finally, we also found sex-dependent episignatures in X-linked disorders. Implementation of episignature profiling is still in its early days, but with increasing utilization comes increasing awareness of the capacity of this methodology to help resolve the complex challenges of genetic diagnoses.
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Affiliation(s)
- Slavica Trajkova
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology Center "Guido Tarone" University of Turin, 10126 Turin, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, CASSMedChem, 10126 Turin, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Enza Ferrero
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Chiara Giovenino
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Diana Carli
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Eleonora Di Gregorio
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Roberta Marinoni
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, Orbassano, TO 10049, Italy
| | - Flavia Palermo
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, Orbassano, TO 10049, Italy
| | - Silvia Carestiato
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy
| | - Simona Cardaropoli
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Verdiana Pullano
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy
| | - Antonina Rinninella
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, 94124 Catania, Italy
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; Neurogenetics Research Center, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Paola Dimartino
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| | - Jessica Rzasa
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada
| | - Aleksandar Petlichkovski
- Department of Immunology and Human Genetics, Faculty of Medicine, University "Sv. Kiril I Metodij", Skopje 1000, Republic of Macedonia
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Elena Sukarova-Angelovska
- Department of Endocrinology and Genetics, Faculty of Medicine, University "Sv. Kiril I Metodij", Skopje 1000, Republic of Macedonia
| | - Christopher M Campbell
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK; Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9WL, UK
| | - Alessandro Mussa
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; Pediatric Clinical Genetics Unit, Regina Margherita Childrens' Hospital, 10126 Turin, Italy
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada
| | - Alfredo Brusco
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy.
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Xu W, Fei X, Cui Z, Pan D, Liu Y, Liu T. DNMT1 driven by mouse amniotic fluid mesenchymal stem cell exosomes improved corneal cryoinjury via inducing microRNA-33 promoter DNA hypermethylation modification in corneal epithelium cells. Hum Cell 2024; 37:1091-1106. [PMID: 38782857 DOI: 10.1007/s13577-024-01082-x] [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: 01/12/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Severe corneal cryoinjury can cause permanent corneal swelling and bullous keratopathy, one of the main reason for loss of sight. Mouse amniotic fluid mesenchymal stem cells (mAF-MSCs) can repair corneal damage caused by freezing; however, whether the exosomes derived from mAF-MSCs have the same repair effect is unknown. In this study, the mAF-MSC-exosomes were transplanted into the eyeballs of corneal cryoinjured mice. Histopathological examination showed that the mAF-MSC-exosomes improved the corneal structure and status of corneal epithelial cells in corneal cryoinjured mice. RRBS-sequencing showed that compared with the control group, four genes (Rpl13-ps6, miR-33, Hymai, and Plagl1), underwent DNA hypermethylation modification after mAF-MSC-exosomes treatment. The result of FISH indicated that miR-33-3p hybridization signals were enhanced in corneal epithelial cells from mice treated with mAF-MSC-exosomes. Semi-quantitative PCR and western blotting indicated that mAF-MSC-exosomes contained high levels of DNMT1 mRNA and protein. Additionally, luciferase report assays indicated that miR-33-3p overexpression in NIH-3T3 mouse embryonic fibroblast cells inhibited the activity of luciferase carrying a sequence from the 3' untranslated region of Bcl6. Moreover, BCL6 mRNA and protein levels in corneal tissues from mice treated with mAF-MSC-exosomes were higher than those in the control group. Therefore, our results suggested that mAF-MSC-exosomes could repair corneal cryoinjury by releasing DNMT1, which induced hypermethylation of the miR-33 promoter in corneal epithelial cells. Consequent downregulated miR-33 transcription upregulated Bcl6 expression, ultimately achieving the repair of corneal cryoinjury in mice.
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Affiliation(s)
- Weiqi Xu
- Department of Ophthalmology, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
| | - Xinfeng Fei
- Department of Ophthalmology, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
| | - Zeyu Cui
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Building C, 365 Xiangyang Road, Shanghai, 200031, China
| | - Dikang Pan
- Department of Vascular Surgery, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Yan Liu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China.
| | - Te Liu
- Shanghai Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Building C, 365 Xiangyang Road, Shanghai, 200031, China.
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4
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Shi X, Zeng X, Jiao R, Yang Y, Du X, Qian J, Liu J, Chen G. Expression, Prognostic Value, and Biological Function of CTHRC1 in Different Types of Gliomas: A Bioinformatic Analysis and Experiment Validation. Clin Med Insights Oncol 2024; 18:11795549241260576. [PMID: 38894702 PMCID: PMC11185027 DOI: 10.1177/11795549241260576] [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: 02/06/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Background In recent years, abnormal expression of collagen triple helix repeat containing 1 (CTHRC1) has been found in some tumors, closely related to the poor prognosis of cancer patients. However, the clinical significance of CTHRC1 in gliomas is not completely understood. Methods We investigated the expression, prognostic value, and potential biological function of CTHRC1 in different types of gliomas through bioinformatics analysis and experimental verification. Results Bioinformatics analysis revealed several key findings regarding the expression and clinical significance of CTHRC1 in gliomas. First, the analysis demonstrated a positive correlation between CTHRC1 expression and the World Health Organization (WHO) grading of gliomas, a relationship that was validated through immunohistochemistry experiments. In addition, a trend was observed in which CTHRC1 expression increased with the extent of glioma invasion, as supported by Western blot experiments. Subsequent bioinformatics analysis identified the mesenchymal subtype of gliomas as having the highest levels of CTHRC1 expression, a finding reinforced by immunohistochemical staining. Moreover, high CTHRC1 expression was associated with poor prognosis in gliomas and emerged as an independent prognostic factor, with varying impacts on prognosis between low-grade gliomas (LGGs) and glioblastoma (GBM) subgroups. Notably, comparative analysis unveiled distinct patterns of immune infiltration of CTHRC1 in LGG and GBM. Furthermore, alterations in copy number variations and DNA methylation were identified as potential mechanisms underlying elevated CTHRC1 levels in gliomas. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that CTHRC1 and its associated genes mainly function in the extracellular matrix and participate in tumor-related signaling pathways. Conclusions The CTHRC1 has shown significant clinical utility as a prognostic marker and mesenchymal subtype marker of glioma.
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Affiliation(s)
- Xueping Shi
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, P.R. China
| | - Xi Zeng
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, P.R. China
| | - Rukai Jiao
- Department of Neurosurgery, The Jinyang Hospital Affiliated to Guizhou Medical University, Guiyang, P.R. China
| | - Yushi Yang
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, Guiyang, P.R. China
| | - Xiaolin Du
- Department of Neurosurgery, The Jinyang Hospital Affiliated to Guizhou Medical University, Guiyang, P.R. China
| | - Jiacai Qian
- Department of Neurosurgery, The Jinyang Hospital Affiliated to Guizhou Medical University, Guiyang, P.R. China
| | - Jian Liu
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang, P.R. China
| | - Guangtang Chen
- Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, P.R. China
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Caraffi SG, van der Laan L, Rooney K, Trajkova S, Zuntini R, Relator R, Haghshenas S, Levy MA, Baldo C, Mandrile G, Lauzon C, Cordelli DM, Ivanovski I, Fetta A, Sukarova E, Brusco A, Pavinato L, Pullano V, Zollino M, McConkey H, Tartaglia M, Ferrero GB, Sadikovic B, Garavelli L. Identification of the DNA methylation signature of Mowat-Wilson syndrome. Eur J Hum Genet 2024; 32:619-629. [PMID: 38351292 PMCID: PMC11153515 DOI: 10.1038/s41431-024-01548-4] [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: 10/24/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 06/07/2024] Open
Abstract
Mowat-Wilson syndrome (MOWS) is a rare congenital disease caused by haploinsufficiency of ZEB2, encoding a transcription factor required for neurodevelopment. MOWS is characterized by intellectual disability, epilepsy, typical facial phenotype and other anomalies, such as short stature, Hirschsprung disease, brain and heart defects. Despite some recognizable features, MOWS rarity and phenotypic variability may complicate its diagnosis, particularly in the neonatal period. In order to define a novel diagnostic biomarker for MOWS, we determined the genome-wide DNA methylation profile of DNA samples from 29 individuals with confirmed clinical and molecular diagnosis. Through multidimensional scaling and hierarchical clustering analysis, we identified and validated a DNA methylation signature involving 296 differentially methylated probes as part of the broader MOWS DNA methylation profile. The prevalence of hypomethylated CpG sites agrees with the main role of ZEB2 as a transcriptional repressor, while differential methylation within the ZEB2 locus supports the previously proposed autoregulation ability. Correlation studies compared the MOWS cohort with 56 previously described DNA methylation profiles of other neurodevelopmental disorders, further validating the specificity of this biomarker. In conclusion, MOWS DNA methylation signature is highly sensitive and reproducible, providing a useful tool to facilitate diagnosis.
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Grants
- MNESYS (PE0000006) Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- 20203P8C3X Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- FOE 2020 Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- RCR-2022-23682289 Ministero della Salute (Ministry of Health, Italy)
- PNRR-MR1-2022-12376811 Ministero della Salute (Ministry of Health, Italy)
- OGI-188 Ontario Genomics Institute (OGI)
- Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
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Affiliation(s)
| | - Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Torino, 10126, Torino, Italy
| | - Roberta Zuntini
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42122, Reggio Emilia, Italy
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Chiara Baldo
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, University of Torino, 10043, Orbassano (Torino), Italy
| | - Carolyn Lauzon
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Duccio Maria Cordelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Neuropsichiatria dell'Età Pediatrica, 40139, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126, Bologna, Italy
| | - Ivan Ivanovski
- Institute of Medical Genetics, University of Zürich, Zürich, Switzerland
| | - Anna Fetta
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Neuropsichiatria dell'Età Pediatrica, 40139, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126, Bologna, Italy
| | - Elena Sukarova
- Department of Endocrinology and Genetics, University Clinic for Pediatric Diseases, Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, 1000, Skopje, Republic of North Macedonia
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Torino, 10126, Torino, Italy
| | - Verdiana Pullano
- Department of Medical Sciences, University of Torino, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Torino, 10126, Torino, Italy
| | - Marcella Zollino
- Institute of Genomic Medicine, Department of Life Sciences and Public Health, 'Sacro Cuore' Catholic University of Rome, 00168, Rome, Italy
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Bekim Sadikovic
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada.
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42122, Reggio Emilia, Italy.
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Vos N, Haghshenas S, van der Laan L, Russel PKM, Rooney K, Levy MA, Relator R, Kerkhof J, McConkey H, Maas SM, Vissers LELM, de Vries BBA, Pfundt R, Elting MW, van Hagen JM, Verbeek NE, Jongmans MCJ, Lakeman P, Rumping L, Bosch DGM, Vitobello A, Thauvin-Robinet C, Faivre L, Nambot S, Garde A, Willems M, Genevieve D, Nicolas G, Busa T, Toutain A, Gérard M, Bizaoui V, Isidor B, Merla G, Accadia M, Schwartz CE, Ounap K, Hoffer MJV, Nezarati MM, van den Boogaard MJH, Tedder ML, Rogers C, Brusco A, Ferrero GB, Spodenkiewicz M, Sidlow R, Mussa A, Trajkova S, McCann E, Mroczkowski HJ, Jansen S, Donker-Kaat L, Duijkers FAM, Stuurman KE, Mannens MMAM, Alders M, Henneman P, White SM, Sadikovic B, van Haelst MM. The detection of a strong episignature for Chung-Jansen syndrome, partially overlapping with Börjeson-Forssman-Lehmann and White-Kernohan syndromes. Hum Genet 2024; 143:761-773. [PMID: 38787418 PMCID: PMC11186873 DOI: 10.1007/s00439-024-02679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Chung-Jansen syndrome is a neurodevelopmental disorder characterized by intellectual disability, behavioral problems, obesity and dysmorphic features. It is caused by pathogenic variants in the PHIP gene that encodes for the Pleckstrin homology domain-interacting protein, which is part of an epigenetic modifier protein complex. Therefore, we hypothesized that PHIP haploinsufficiency may impact genome-wide DNA methylation (DNAm). We assessed the DNAm profiles of affected individuals with pathogenic and likely pathogenic PHIP variants with Infinium Methylation EPIC arrays and report a specific and sensitive DNAm episignature biomarker for Chung-Jansen syndrome. In addition, we observed similarities between the methylation profile of Chung-Jansen syndrome and that of functionally related and clinically partially overlapping genetic disorders, White-Kernohan syndrome (caused by variants in DDB1 gene) and Börjeson-Forssman-Lehmann syndrome (caused by variants in PHF6 gene). Based on these observations we also proceeded to develop a common episignature biomarker for these disorders. These newly defined episignatures can be used as part of a multiclass episignature classifier for screening of affected individuals with rare disorders and interpretation of genetic variants of unknown clinical significance, and provide further insights into the common molecular pathophysiology of the clinically-related Chung-Jansen, Börjeson-Forssman-Lehmann and White-Kernohan syndromes.
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Affiliation(s)
- Niels Vos
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Liselot van der Laan
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Perle K M Russel
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - 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
| | - 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
- 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
| | - Saskia M Maas
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Mariet W Elting
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Johanna M van Hagen
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Nienke E Verbeek
- Department of Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Marjolijn C J Jongmans
- Department of Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Phillis Lakeman
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Lynne Rumping
- Center for Medical Genetics, Antwerp University Hospital, University of Antwerp, Drie Eikenstraat 655, 2650, Edegem, Belgium
| | - Danielle G M Bosch
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Antonio Vitobello
- Université de Bourgogne, Inserm U1231, Equipe GAD, Dijon, France
- CHU Dijon Bourgogne, FHU-TRANSLAD, Unité Fonctionnelle Innovation en Diagnostic Génomique Des Maladies Rares, 21000, Dijon, France
| | - Christel Thauvin-Robinet
- Université de Bourgogne, Inserm U1231, Equipe GAD, Dijon, France
- CHU Dijon Bourgogne, FHU-TRANSLAD, Unité Fonctionnelle Innovation en Diagnostic Génomique Des Maladies Rares, 21000, Dijon, France
- CHU Dijon Bourgogne, Centre de Génétique, Centre de Référence Maladies Rares «Déficiences Intellectuelles de Causes Rares», FHU-TRANSLAD, Dijon, France
| | - Laurence Faivre
- Université de Bourgogne, Inserm U1231, Equipe GAD, Dijon, France
- CHU Dijon Bourgogne, Centre de Génétique, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs», FHU-TRANSLAD, Dijon, France
| | - Sophie Nambot
- Université de Bourgogne, Inserm U1231, Equipe GAD, Dijon, France
- CHU Dijon Bourgogne, FHU-TRANSLAD, Unité Fonctionnelle Innovation en Diagnostic Génomique Des Maladies Rares, 21000, Dijon, France
- CHU Dijon Bourgogne, Centre de Génétique, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs», FHU-TRANSLAD, Dijon, France
| | - Aurore Garde
- Université de Bourgogne, Inserm U1231, Equipe GAD, Dijon, France
- CHU Dijon Bourgogne, Centre de Génétique, Centre de Référence Maladies Rares «Déficiences Intellectuelles de Causes Rares», FHU-TRANSLAD, Dijon, France
| | - Marjolaine Willems
- INserm U1183, Department of Clinical Genetics, Montpellier University, 34090 CHU Montpellier, Montpellier, France
| | - David Genevieve
- INserm U1183, Department of Clinical Genetics, Montpellier University, 34090 CHU Montpellier, Montpellier, France
| | - Gaël Nicolas
- Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, Univ Rouen Normandie, 76000, Rouen, France
| | - Tiffany Busa
- Department of Medical Genetics, Timone Hospital, Marseille, France
| | - Annick Toutain
- Genetics Department, University Hospital, UMR 1253, iBrain, University of Tours, Inserm, Tours, France
| | - Marion Gérard
- APHP, Department of Genetics, Robert Debré Hospital, 75019, Paris, France
| | - Varoona Bizaoui
- Clinical Genetics and Neurodevelopmental Disorders, Centre Hospitalier de L'Estran, 50170, Pontorson, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, 44000, Nantes, France
| | - 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
| | - Maria Accadia
- Servizio di Genetica Medica, Ospedale Cardinale G. Panico, Tricase, LE, Italy
| | - Charles E Schwartz
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Katrin Ounap
- Department of Clinical Genetics, Genetic and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjan M Nezarati
- Genetics Program, North York General Hospital, Toronto, ON, M2K 1E1, Canada
| | | | | | | | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
- Unit of Medical Genetics, Città Della Salute e Della Scienza Hospital, Turin, Italy
| | - Giovanni B Ferrero
- Department of Clinical and Biological Science, University of Torino, Turin, Italy
| | | | - Richard Sidlow
- Department of Medical Genetics and Metabolism, Valley Children's Hospital, Madera, CA, USA
| | - Alessandro Mussa
- Department of Public Health and Pediatric Sciences, University of Torino, Turin, Italy
- Pediatric Clinical Genetics Unit, Regina Margherita Childrens' Hospital, Turin, Italy
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
| | - Emma McCann
- Liverpool Center for Genomic Medicine, Liverpool Women's Hospital, Liverpool, UK
| | - Henry J Mroczkowski
- Department of Pediatrics, Le Bonheur Children's Hospital, Memphis, TN, USA
- Division of Genetics, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sandra Jansen
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Laura Donker-Kaat
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Floor A M Duijkers
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Kyra E Stuurman
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marcel M A M Mannens
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Mariëlle Alders
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Peter Henneman
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - 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.
| | - Mieke M van Haelst
- Amsterdam UMC, Department of Human Genetics, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands.
- Amsterdam UMC, Department of Paediatrics, Emma Children's Hospital, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Amsterdam UMC, Emma Center for Personalized Medicine, Amsterdam, The Netherlands.
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7
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van der Laan L, Karimi K, Rooney K, Lauffer P, McConkey H, Caro P, Relator R, Levy MA, Bhai P, Mignot C, Keren B, Briuglia S, Sobering AK, Li D, Vissers LELM, Dingemans AJM, Valenzuela I, Verberne EA, Misra-Isrie M, Zwijnenburg PJG, Waisfisz Q, Alders M, Sailer S, Schaaf CP, Mannens MMAM, Sadikovic B, van Haelst MM, Henneman P. DNA methylation episignature, extension of the clinical features, and comparative epigenomic profiling of Hao-Fountain syndrome caused by variants in USP7. Genet Med 2024; 26:101050. [PMID: 38126281 DOI: 10.1016/j.gim.2023.101050] [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: 07/04/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE Hao-Fountain syndrome (HAFOUS) is a neurodevelopmental disorder caused by pathogenic variants in USP7. HAFOUS is characterized by developmental delay, intellectual disability, speech delay, behavioral abnormalities, autism spectrum disorder, seizures, hypogonadism, and mild dysmorphic features. We investigated the phenotype of 18 participants with HAFOUS and performed DNA methylation (DNAm) analysis, aiming to generate a diagnostic biomarker. Furthermore, we performed comparative analysis with known episignatures to gain more insight into the molecular pathophysiology of HAFOUS. METHODS We assessed genomic DNAm profiles of 18 individuals with pathogenic variants and variants of uncertain significance (VUS) in USP7 to map and validate a specific episignature. The comparison between the USP7 cohort and 56 rare genetic disorders with earlier reported DNAm episignatures was performed with statistical and functional correlation. RESULTS We mapped a sensitive and specific DNAm episignature for pathogenic variants in USP7 and utilized this to reclassify the VUS. Comparative epigenomic analysis showed evidence of HAFOUS similarity to a number of other rare genetic episignature disorders. CONCLUSION We discovered a sensitive and specific DNAm episignature as a robust diagnostic biomarker for HAFOUS that enables VUS reclassification in USP7. We also expand the phenotypic spectrum of 9 new and 5 previously reported individuals with HAFOUS.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Karim Karimi
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Peter Lauffer
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Pilar Caro
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada
| | - Pratibha Bhai
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada
| | - Cyril Mignot
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France; Hôpital Armand Trousseau, Paris, France AND Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
| | - Boris Keren
- APHP Sorbonne Université, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Silvana Briuglia
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Andrew K Sobering
- AU/UGA Medical Partnership Campus of the Medical College of Georgia, Athens, Georgia; Windward Islands Research and Education Foundation, True Blue, St. George's, Grenada; St. George's University School of Medicine, Department of Biochemistry, Grenada
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, University of Pennsylvania Perelman school of Medicine, Philadelphia, PA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Irene Valenzuela
- Àrea de Genètica Clínica i Malalties Minoritàries, Hospital Vall d'Hebron, Barcelona, Spain
| | - Eline A Verberne
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mala Misra-Isrie
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Petra J G Zwijnenburg
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Quinten Waisfisz
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Sebastian Sailer
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
| | - Mieke M van Haelst
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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8
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van der Laan L, Rooney K, Haghshenas S, Silva A, McConkey H, Relator R, Levy MA, Valenzuela I, Trujillano L, Lasa-Aranzasti A, Campos B, Castells N, Verberne EA, Maas S, Alders M, Mannens MMAM, van Haelst MM, Sadikovic B, Henneman P. Functional Insight into and Refinement of the Genomic Boundaries of the JARID2-Neurodevelopmental Disorder Episignature. Int J Mol Sci 2023; 24:14240. [PMID: 37762546 PMCID: PMC10531903 DOI: 10.3390/ijms241814240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
JARID2 (Jumonji, AT-rich interactive domain 2) haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome. It is characterized by intellectual disability, developmental delay, autistic features, behavior abnormalities, cognitive impairment, hypotonia, and dysmorphic features. JARID2 acts as a transcriptional repressor protein that is involved in the regulation of histone methyltransferase complexes. JARID2 plays a role in the epigenetic machinery, and the associated syndrome has an identified DNA methylation episignature derived from sequence variants and intragenic deletions involving JARID2. For this study, our aim was to determine whether patients with larger deletions spanning beyond JARID2 present a similar DNA methylation episignature and to define the critical region involved in aberrant DNA methylation in 6p22-p24 microdeletions. We examined the DNA methylation profiles of peripheral blood from 56 control subjects, 13 patients with (likely) pathogenic JARID2 variants or patients carrying copy number variants, and three patients with JARID2 VUS variants. The analysis showed a distinct and strong differentiation between patients with (likely) pathogenic variants, both sequence and copy number, and controls. Using the identified episignature, we developed a binary model to classify patients with the JARID2-neurodevelopmental syndrome. DNA methylation analysis indicated that JARID2 is the driver gene for aberrant DNA methylation observed in 6p22-p24 microdeletions. In addition, we performed analysis of functional correlation of the JARID2 genome-wide methylation profile with the DNA methylation profiles of 56 additional neurodevelopmental disorders. To conclude, we refined the critical region for the presence of the JARID2 episignature in 6p22-p24 microdeletions and provide insight into the functional changes in the epigenome observed when regulation by JARID2 is lost.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Ananília Silva
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- 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 (R.R.)
| | - Michael A. Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Irene Valenzuela
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Laura Trujillano
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Amaia Lasa-Aranzasti
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Berta Campos
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Neus Castells
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Eline A. Verberne
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Saskia Maas
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Marcel M. A. M. Mannens
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mieke M. van Haelst
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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9
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Smirnov D, Konstantinovskiy N, Prokisch H. Integrative omics approaches to advance rare disease diagnostics. J Inherit Metab Dis 2023; 46:824-838. [PMID: 37553850 DOI: 10.1002/jimd.12663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023]
Abstract
Over the past decade high-throughput DNA sequencing approaches, namely whole exome and whole genome sequencing became a standard procedure in Mendelian disease diagnostics. Implementation of these technologies greatly facilitated diagnostics and shifted the analysis paradigm from variant identification to prioritisation and evaluation. The diagnostic rates vary widely depending on the cohort size, heterogeneity and disease and range from around 30% to 50% leaving the majority of patients undiagnosed. Advances in omics technologies and computational analysis provide an opportunity to increase these unfavourable rates by providing evidence for disease-causing variant validation and prioritisation. This review aims to provide an overview of the current application of several omics technologies including RNA-sequencing, proteomics, metabolomics and DNA-methylation profiling for diagnostics of rare genetic diseases in general and inborn errors of metabolism in particular.
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Affiliation(s)
- Dmitrii Smirnov
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
| | - Nikita Konstantinovskiy
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
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Shalata A, Bar-Shai M, Hadid Y, Mahroum M, Mintz H, Shalata ZE, Radzishevsky E, Genizi J, Lorber A, Ben-Yosef T, Yaniv L. Danon Disease: Entire LAMP2 Gene Deletion with Unusual Clinical Presentation-Case Report and Review of the Literature. Genes (Basel) 2023; 14:1539. [PMID: 37628591 PMCID: PMC10454823 DOI: 10.3390/genes14081539] [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: 06/01/2023] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Danon disease is a rare x-linked dominant multisystemic disorder with a clinical triad of severe cardiomyopathy, skeletal myopathy, and intellectual disability. It is caused by defects in the lysosome-associated membrane protein-2 (LAMP2) gene. Numerous different mutations in the LAMP2 protein have been described. Danon disease is typically lethal by the mid-twenties in male patients due to cardiomyopathy and heart failure. Female patients usually present with milder and variable symptoms. This report describes a 42-year-old father and his 3-year-old daughter presenting with mild manifestations of the disease. The father has normal intellectual development and normal physical activity. At the age of 13, he was diagnosed with mild ventricular pre-excitation known as Wolf-Parkinson-White syndrome (WPWs), very mild and mostly asymptomatic cardiomyopathy and left ventricular hypertrophy, and at about the age of 25 presented with visual impairment due to cone-rod dystrophy. His daughter showed normal development and very mild asymptomatic electrocardiographic WPWs abnormalities with left mild ventricular hypertrophy. Genetic testing revealed an Xq24 microdeletion encompassing the entire LAMP2 gene. Relevant literature was reviewed as a reference for the etiology, diagnosis, treatment and case management.
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Affiliation(s)
- Adel Shalata
- The Simon Winter Institute for Human Genetics, Bnai Zion Medical Center, Haifa 32000, Israel; (Y.H.); (M.M.); (H.M.)
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; (E.R.); (J.G.); (A.L.); (T.B.-Y.); (L.Y.)
| | - Marina Bar-Shai
- The Institute of Medical Genetics, Carmel Medical Center, Haifa 34362, Israel;
| | - Yarin Hadid
- The Simon Winter Institute for Human Genetics, Bnai Zion Medical Center, Haifa 32000, Israel; (Y.H.); (M.M.); (H.M.)
| | - Muhammad Mahroum
- The Simon Winter Institute for Human Genetics, Bnai Zion Medical Center, Haifa 32000, Israel; (Y.H.); (M.M.); (H.M.)
| | - Hila Mintz
- The Simon Winter Institute for Human Genetics, Bnai Zion Medical Center, Haifa 32000, Israel; (Y.H.); (M.M.); (H.M.)
| | | | - Evgeny Radzishevsky
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; (E.R.); (J.G.); (A.L.); (T.B.-Y.); (L.Y.)
- Cardiology Department, Bnai Zion Medical Center, Haifa 32000, Israel
| | - Jacob Genizi
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; (E.R.); (J.G.); (A.L.); (T.B.-Y.); (L.Y.)
- Department of Pediatric, Bnai Zion Medical Center, Haifa 32000, Israel
| | - Avraham Lorber
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; (E.R.); (J.G.); (A.L.); (T.B.-Y.); (L.Y.)
- Pediatric Cardiology Unit, Rambam Medical Centre, Haifa 31096, Israel
| | - Tamar Ben-Yosef
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; (E.R.); (J.G.); (A.L.); (T.B.-Y.); (L.Y.)
| | - Liat Yaniv
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; (E.R.); (J.G.); (A.L.); (T.B.-Y.); (L.Y.)
- Department of Pediatric, Bnai Zion Medical Center, Haifa 32000, Israel
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