OTX2 duplication is implicated in hemifacial microsomia

Abstract

Hemifacial microsomia (HFM) is the second most common facial anomaly after cleft lip and palate. The phenotype is highly variable and most cases are sporadic. We investigated the disorder in a large pedigree with five affected individuals spanning eight meioses. Whole-exome sequencing results indicated the absence of a pathogenic coding point mutation. A genome-wide survey of segmental variations identified a 1.3 Mb duplication of chromosome 14q22.3 in all affected individuals that was absent in more than 1000 chromosomes of ethnically matched controls. The duplication was absent in seven additional sporadic HFM cases, which is consistent with the known heterogeneity of the disorder. To find the critical gene in the duplicated region, we analyzed signatures of human craniofacial disease networks, mouse expression data, and predictions of dosage sensitivity. All of these approaches implicated OTX2 as the most likely causal gene. Moreover, OTX2 is a known oncogenic driver in medulloblastoma, a condition that was diagnosed in the proband during the course of the study. Our findings suggest a role for OTX2 dosage sensitivity in human craniofacial development and raise the possibility of a shared etiology between a subtype of hemifacial microsomia and medulloblastoma.

Figure 1. The five-generation pedigree.

The family consists of five affected individuals spanning eight meioses. The proband (V.3) is indicated by an arrow. We were able to obtain consent from individuals IV.3 and V.3 to publish photos.

Figure 2. The 14q22 duplicated region.

(a) Raw intensity plots of the duplicated region (contained between the dotted lines) in the four affected individuals and 4 Ashkenazi controls from . The signals represent the number of standard deviations of the probes from the mean value. The suspected copy number gain is marked by dotted vertical lines. The red line is a moving average with a window of 20 probes. (b) qPCR results of the affected family and two HapMap controls for genes in the duplicated region (OTX2OS1, EXCO5, and NAA30) and two flanking genes (KTN1 and PSMA3) are consistent with the array results.

Figure 3. Prioritization of genes in 14q22.

(a) Ranking similarity of the molecular signatures of the genes in the duplicated region to causal genes in CHARGE, VACTERL, and Townes-Brocks using Endeavour and ToppGene. The average rank of both tools is indicated in red. (b) Ranking of expression levels in pharyngeal arches (PA) compared to heart and urogenital epithelium (UG) in E10.5 and expression in the head compared to liver, heart, and lung in E13.5 for genes in the duplicated region. Comparative expression ranked OTX2 highest in the affected tissues in all conditions. (c) Ranking of dosage sensitivity predictions for 3 of the duplicated genes .