Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability

Abstract

Human ZIC1 (zinc finger protein of cerebellum 1), one of five homologs of the Drosophila pair-rule gene odd-paired, encodes a transcription factor previously implicated in vertebrate brain development. Heterozygous deletions of ZIC1 and its nearby paralog ZIC4 on chromosome 3q25.1 are associated with Dandy-Walker malformation of the cerebellum, and loss of the orthologous Zic1 gene in the mouse causes cerebellar hypoplasia and vertebral defects. We describe individuals from five families with heterozygous mutations located in the final (third) exon of ZIC1 (encoding four nonsense and one missense change) who have a distinct phenotype in which severe craniosynostosis, specifically involving the coronal sutures, and variable learning disability are the most characteristic features. The location of the nonsense mutations predicts escape of mutant ZIC1 transcripts from nonsense-mediated decay, which was confirmed in a cell line from an affected individual. Both nonsense and missense mutations are associated with altered and/or enhanced expression of a target gene, engrailed-2, in a Xenopus embryo assay. Analysis of mouse embryos revealed a localized domain of Zic1 expression at embryonic days 11.5-12.5 in a region overlapping the supraorbital regulatory center, which patterns the coronal suture. We conclude that the human mutations uncover a previously unsuspected role for Zic1 in early cranial suture development, potentially by regulating engrailed 1, which was previously shown to be critical for positioning of the murine coronal suture. The diagnosis of a ZIC1 mutation has significant implications for prognosis and we recommend genetic testing when common causes of coronal synostosis have been excluded.

Genetic advances in craniosynostosis

“…Coronal NCS (cNCS; incidence 1:10,000 live births) is thought to have a stonger genetic component compared to the other forms of NCS [Lajeunie et al, 1995; Wilkie et al, 2010] with specific monogenic mutations present in about 60% of patients with bicoronal and 30% of patients with unicoronal CS [Twigg et al, 2015c]. Indeed, diverse genes may account for the higher incidence of monogenic variants in cNCS.…”

“…A heterozygous mutation in the last exon of ZIC1 was identified by exome sequencing in a proband with severe bicoronal CS, autism and developmental delay [Twigg et al, 2015c]. In order to clarify the significance of ZIC1 in the etiology of CS, the authors screened a cohort of 307 patients with various types of syndromic and nonsyndromic CS and identified 4 additional probands with bicoronal CS who had mutations in the last exon of ZIC1 .…”

“…Because developmental disabilities and associated clinical features were present, the CS of these patients cannot be defined as nonsyndromic. Given the variable clinical severity in one multiplex family in this study, ZIC1 testing should be considered in all cCS patients in whom mutations in commonly associated genes have been excluded [Twigg et al, 2015c]. In the Xenopus embryo, Zic1 expression overlaps with that of Engrailed 1 (En1) in the supraorbital region that directs coronal suture development and patterning, which is plausibly disrupted as a consequence of ZIC1 mutations [Twigg et al, 2015c].…”

“…Given the variable clinical severity in one multiplex family in this study, ZIC1 testing should be considered in all cCS patients in whom mutations in commonly associated genes have been excluded [Twigg et al, 2015c]. In the Xenopus embryo, Zic1 expression overlaps with that of Engrailed 1 (En1) in the supraorbital region that directs coronal suture development and patterning, which is plausibly disrupted as a consequence of ZIC1 mutations [Twigg et al, 2015c]. ZIC orthologues in Drosophila and Xenopus are upstream regulators of the Wnt pathway [Merzdorf and Sive, 2006], being required for the activation of expression of the engrailed segment polarity gene [Benedyk et al, 1994; Kuo et al, 1998].…”

Understanding tissue-specificity with human tissue-specific regulatory networks

“…ZIC1 is implicated in vertebrate brain development. The heterozygous loss of ZIC1 and ZIC4 has been suspected to lead to Dandy-Walker along with mental retardation, and mutations in ZIC1 were reported to be associated with learning disability [41,42]. From the analysis, it can be observed that gene regulatory networks provide rich information about how disease genes are regulated and may help predict new disease genes.…”