DNA methylation episignature and comparative epigenomic profiling for Pitt-Hopkins syndrome caused by TCF4 variants

Liselot van der Laan; Peter Lauffer; Kathleen Rooney; Ananília Silva; Sadegheh Haghshenas; Raissa Relator; Michael A Levy; Slavica Trajkova; Sylvia A Huisman; Emilia K Bijlsma; Tjitske Kleefstra; Bregje W van Bon; Özlem Baysal; Christiane Zweier; María Palomares-Bralo; Jan Fischer; Katalin Szakszon; Laurence Faivre; Amélie Piton; Simone Mesman; Ron Hochstenbach; Mariet W Elting; Johanna M van Hagen; Astrid S Plomp; Marcel M A M Mannens; Mariëlle Alders; Mieke M van Haelst; Giovanni B Ferrero; Alfredo Brusco; Peter Henneman; David A Sweetser; Bekim Sadikovic; Antonio Vitobello; Leonie A Menke

doi:10.1016/j.xhgg.2024.100289

DNA methylation episignature and comparative epigenomic profiling for Pitt-Hopkins syndrome caused by TCF4 variants

HGG Adv. 2024 Apr 2;5(3):100289. doi: 10.1016/j.xhgg.2024.100289. Online ahead of print.

Authors

Liselot van der Laan¹, Peter Lauffer¹, Kathleen Rooney², Ananília Silva³, Sadegheh Haghshenas⁴, Raissa Relator⁴, Michael A Levy⁴, Slavica Trajkova⁵, Sylvia A Huisman⁶, Emilia K Bijlsma⁷, Tjitske Kleefstra⁸, Bregje W van Bon⁹, Özlem Baysal⁹, Christiane Zweier¹⁰, María Palomares-Bralo¹¹, Jan Fischer¹², Katalin Szakszon¹³, Laurence Faivre¹⁴, Amélie Piton¹⁵, Simone Mesman¹⁶, Ron Hochstenbach¹, Mariet W Elting¹, Johanna M van Hagen¹, Astrid S Plomp¹, Marcel M A M Mannens¹, Mariëlle Alders¹, Mieke M van Haelst¹, Giovanni B Ferrero¹⁷, Alfredo Brusco¹⁸, Peter Henneman¹, David A Sweetser¹⁹, Bekim Sadikovic²⁰, Antonio Vitobello²¹, Leonie A Menke²²

Affiliations

¹ Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands.
² Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
³ Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
⁴ Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada.
⁵ Department of Medical Sciences, University of Torino, Torino, Italy.
⁶ Amsterdam UMC location University of Amsterdam, Emma Children's Hospital, Department of Pediatrics, Amsterdam, the Netherlands; Zodiak, Prinsenstichting, Purmerend, the Netherlands.
⁷ Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands.
⁸ Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.
⁹ Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
¹⁰ Department of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Department of Human Genetics, University of Bern, Inselspital Universitätsspital Bern, Bern, Switzerland.
¹¹ Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Madrid, Spain.
¹² Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany.
¹³ Institute of Paediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
¹⁴ 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.
¹⁵ Genetic Diagnosis Laboratories, Strasbourg University Hospital, Strasbourg 67000, France.
¹⁶ Swammerdam Institute for Life Sciences, FNWI, University of Amsterdam, Amsterdam, the Netherlands.
¹⁷ Department of Public Health and Pediatrics, University of Torino, Turin, Italy.
¹⁸ Department of Medical Sciences, University of Torino, Turin, Italy.
¹⁹ Division of Medical Genetics and Metabolism and Center for Genomic Medicine, Massachusetts General for Children, Boston, MA, USA.
²⁰ 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.
²¹ Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.
²² 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. Electronic address: l.a.menke@amsterdamumc.nl.

PMID: 38571311
DOI: 10.1016/j.xhgg.2024.100289

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.

Keywords: CNV; DNA methylation; PTHS; Pitt-Hopkins syndrome; TCF4; VUS; episignature; neurodevelopmental disorder.