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

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 MM, Alders M, van Haelst MM, Ferrero GB, Brusco A, Henneman P, Sweetser DA, Sadikovic B, Vitobello A, Menke LA (2024)

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Publication Type: Journal article

Publication year: 2024

Journal

Book Volume: 5

Article Number: 100289

Journal Issue: 3

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.

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How to cite

APA:

van der Laan, L., Lauffer, P., Rooney, K., Silva, A., Haghshenas, S., Relator, R.,... Menke, L.A. (2024). DNA methylation episignature and comparative epigenomic profiling for Pitt-Hopkins syndrome caused by TCF4 variants. Human Genetics and Genomics Advances, 5(3). https://doi.org/10.1016/j.xhgg.2024.100289

MLA:

van der Laan, Liselot, et al. "DNA methylation episignature and comparative epigenomic profiling for Pitt-Hopkins syndrome caused by TCF4 variants." Human Genetics and Genomics Advances 5.3 (2024).

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