Loss of PHF6 leads to aberrant development of human neuron-like cells

Anna Fliedner,Arif B Ekici,Christiane Zweier,Heinrich Sticht,Anne Gregor,Fulvia Ferrazzi

doi:10.1038/s41598-020-75999-2

Anna Fliedner, Arif B Ekici + Show 4 more

Open Access

https://doi.org/10.1038/s41598-020-75999-2

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Abstract

Pathogenic variants in PHD finger protein 6 (PHF6) cause Borjeson–Forssman–Lehmann syndrome (BFLS), a rare X-linked neurodevelopmental disorder, which manifests variably in both males and females. To investigate the mechanisms behind overlapping but distinct clinical aspects between genders, we assessed the consequences of individual variants with structural modelling and molecular techniques. We found evidence that de novo variants occurring in females are more severe and result in loss of PHF6, while inherited variants identified in males might be hypomorph or have weaker effects on protein stability. This might contribute to the different phenotypes in male versus female individuals with BFLS. Furthermore, we used CRISPR/Cas9 to induce knockout of PHF6 in SK-N-BE (2) cells which were then differentiated to neuron-like cells in order to model nervous system related consequences of PHF6 loss. Transcriptome analysis revealed a broad deregulation of genes involved in chromatin and transcriptional regulation as well as in axon and neuron development. Subsequently, we could demonstrate that PHF6 is indeed required for proper neuron proliferation, neurite outgrowth and migration. Impairment of these processes might therefore contribute to the neurodevelopmental and cognitive dysfunction in BFLS.

Highlights

Pathogenic variants in PHD finger protein 6 (PHF6) cause Borjeson–Forssman–Lehmann syndrome (BFLS), a rare X-linked neurodevelopmental disorder, which manifests variably in both males and females
From literature we retrieved nine missense variants in PHF6 identified in males[2,6,21,23,24] and one missense variant identified in a female with BFLS4
The only missense variant reported in females, so far, is located in the C-terminal extended atypical PHD-like zinc finger domains (ePHD) and had a very high score of 0.98, indicating a stronger destabilizing effect on the protein structure than the variants from males residing in the same ePHD (Fig. 1a,b)

Summary

Introduction

Pathogenic variants in PHD finger protein 6 (PHF6) cause Borjeson–Forssman–Lehmann syndrome (BFLS), a rare X-linked neurodevelopmental disorder, which manifests variably in both males and females. Variants in the gene encoding PHD finger protein 6 (PHF6 [MIM: 300414]) have been identified to cause Borjeson–Forssman–Lehmann syndrome (BFLS [MIM: #301900]), an X-linked syndromic neurodevelopmental disorder (NDD)[1,2], affecting both male and female individuals. De novo variants in PHF6 were identified in affected females with NDDs, partly overlapping with BFLS in males but with very distinct phenotypic aspects[4,5,6,7]. They presented with mild to severe ID, a characteristic facial gestalt, finger and toe anomalies, irregularly shaped teeth and oligodontia[4,5].

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