Genetic analysis of CHARGE syndrome identifies overlapping molecular biology

Abstract

Purpose: CHARGE syndrome is an autosomal-dominant, multiple congenital anomaly condition characterized by vision and hearing loss, congenital heart disease, and malformations of craniofacial and other structures. Pathogenic variants in CHD7, encoding adenosine triphosphate-dependent chromodomain helicase DNA binding protein 7, are present in the majority of affected individuals. However, no causal variant can be found in 5-30% (depending on the cohort) of individuals with a clinical diagnosis of CHARGE syndrome.

Methods: We performed whole-exome sequencing (WES) on 28 families from which at least one individual presented with features highly suggestive of CHARGE syndrome.

Results: Pathogenic variants in CHD7 were present in 15 of 28 individuals (53.6%), whereas 4 (14.3%) individuals had pathogenic variants in other genes (RERE, KMT2D, EP300, or PUF60). A variant of uncertain clinical significance in KDM6A was identified in one (3.5%) individual. The remaining eight (28.6%) individuals were not found to have pathogenic variants by WES.

Conclusion: These results demonstrate that the phenotypic features of CHARGE syndrome overlap with multiple other rare single-gene syndromes. Additionally, they implicate a shared molecular pathology that disrupts epigenetic regulation of multiple-organ development.

Keywords: CHARGE; chromatin; exome; genetics; oligogenicity.

Figure 1

Model of molecular synergy implicated by genetic determinants (asterisks) that share clinical features of CHARGE syndrome. Cis-regulatory retinoic acid response elements (red DNA; RAREs) control cell-specific transcription of retinoic acid (RA) responsive genes, like FGF8 (orange DNA). (A) In the absence of RA, Polycomb repressive complex 2 (PRC2) and KMT2D are recruited to RAREs, where they catalyze H3K27Me3 and H3K4Me1 respectively, promoting FGF8 transcriptional repression. (B) In response to RA, the RERE/NR2F2/P300 complex forms, binding nuclear heterodimers of retinoic acid receptors (RAR/RXR) at RAREs. Histone acetyltransferase P300 and KMT2D cooperate to activate enhancer and enhancer-promoter looping that requires nucleosome translocation along the DNA by CHD7. KDM6A demethylates the repressive H3K27Me3 histone modifications. Enhancer-promoter looping is stabilized by the mediator complex (grey oval). CHD7 translocates nucleosomes to permit transcription of FGF8 by RNA pol II. PUF60 helps form the transcription bubble required for RNA Pol II transcription and pre-mRNA splicing.