Heterozygous deletions at the ZEB1 locus verify haploinsufficiency as the mechanism of disease for posterior polymorphous corneal dystrophy type 3

Abstract

A substantial proportion of patients with posterior polymorphous corneal dystrophy (PPCD) lack a molecular diagnosis. We evaluated 14 unrelated probands who had a clinical diagnosis of PPCD who were previously determined to be negative for mutations in ZEB1 by direct sequencing. A combination of techniques was used including whole-exome sequencing (WES), single-nucleotide polymorphism (SNP) array copy number variation (CNV) analysis, quantitative real-time PCR, and long-range PCR. Segregation of potentially pathogenic changes with disease was confirmed, where possible, in family members. A putative run of homozygosity on chromosome 10 was identified by WES in a three-generation PPCD family, suggestive of a heterozygous deletion. SNP array genotyping followed by long-range PCR and direct sequencing to define the breakpoints confirmed the presence of a large deletion that encompassed multiple genes, including ZEB1. Identification of a heterozygous deletion spanning ZEB1 prompted us to further investigate potential CNVs at this locus in the remaining probands, leading to detection of two additional heterozygous ZEB1 gene deletions. This study demonstrates that ZEB1 mutations account for a larger proportion of PPCD than previously estimated, and supports the hypothesis that haploinsufficiency of ZEB1 is the underlying molecular mechanism of disease for PPCD3.

Agenesis of the corpus callosum, developmental delay, autism spectrum disorder, facial dysmorphism, and posterior polymorphous corneal dystrophy associated with ZEB1 gene deletion

“…Several studies support this association (Aldave et al, ; Krafchak et al, ; Liskova et al, ). In addition, heterozygous deletions of chromosome 10p encompassing ZEB1 gene have been recently reported in six individuals with PPCD3 (Liskova et al, ). The microdeletions found in these individuals were of different sizes, with different breakpoints.…”

“…Mutations in ZEB1 are associated with posterior polymorphous corneal dystrophy type 3 (PPCD3, OMIM 609141), which is a rare disease characterized by metaplasia and overgrowth of corneal endothelial cells, with increased risk for glaucoma (Aldave et al, ; Krafchak et al, ; Liskova et al, ). In addition, heterozygous deletions of chromosome 10p encompassing ZEB1 gene have been recently reported with PPCD3 suggesting haploinsufficiency as a mechanism (Liskova et al, ).…”

The Genetics and Pathophysiology of IC3D Category 1 Corneal Dystrophies

“…Posterior polymorphous corneal dystrophy 3 has been attributed to mutations in zinc finger E-box binding homeobox 1 (ZEB1), with more than 30 mutations identified to date. 79 Recently, analysis of copy number variants has also revealed heterozygous ZEB1 deletions in PPCD3 pedigrees. 79 Interestingly, sequence variants in both ZEB1 and COL8A2 have been associated with FECD.…”

“…79 Recently, analysis of copy number variants has also revealed heterozygous ZEB1 deletions in PPCD3 pedigrees. 79 Interestingly, sequence variants in both ZEB1 and COL8A2 have been associated with FECD.…”

Confirmation of the OVOL2 Promoter Mutation c.-307T>C in Posterior Polymorphous Corneal Dystrophy 1

“…[25] Thus, Davidson and colleagues proposed that PPCD-associated OVOL2 promoter variants cause increased OVOL2 expression and the encoded protein subsequently represses ZEB1 expression, leading to a PPCD phenotype similar to PPCD3, in which ZEB1 truncating mutations likely result in ZEB1 haploinsufficiency. [4, 12]…”