A Novel Truncating Mutation in HOMER2 Causes Nonsyndromic Progressive DFNA68 Hearing Loss in a Spanish Family

Abstract

Nonsyndromic hereditary hearing loss is a common sensory defect in humans that is clinically and genetically highly heterogeneous. So far, 122 genes have been associated with this disorder and 50 of them have been linked to autosomal dominant (DFNA) forms like DFNA68, a rare subtype of hearing impairment caused by disruption of a stereociliary scaffolding protein (HOMER2) that is essential for normal hearing in humans and mice. In this study, we report a novel HOMER2 variant (c.832_836delCCTCA) identified in a Spanish family by using a custom NGS targeted gene panel (OTO-NGS-v2). This frameshift mutation produces a premature stop codon that may lead in the absence of NMD to a shorter variant (p.Pro278Alafs*10) that truncates HOMER2 at the CDC42 binding domain (CBD) of the coiled-coil structure, a region that is essential for protein multimerization and HOMER2-CDC42 interaction. c.832_836delCCTCA mutation is placed close to the previously identified c.840_840dup mutation found in a Chinese family that truncates the protein (p.Met281Hisfs*9) at the CBD. Functional assessment of the Chinese mutant revealed decreased protein stability, reduced ability to multimerize, and altered distribution pattern in transfected cells when compared with wild-type HOMER2. Interestingly, the Spanish and Chinese frameshift mutations might exert a similar effect at the protein level, leading to truncated mutants with the same Ct aberrant protein tail, thus suggesting that they can share a common mechanism of pathogenesis. Indeed, age-matched patients in both families display quite similar hearing loss phenotypes consisting of early-onset, moderate-to-profound progressive hearing loss. In summary, we have identified the third variant in HOMER2, which is the first one identified in the Spanish population, thus contributing to expanding the mutational spectrum of this gene in other populations, and also to clarifying the genotype-phenotype correlations of DFNA68 hearing loss.

Keywords: CDC42; HOMER2; custom panel; hereditary hearing loss; next-generation sequencing.

Figure 1

(A) Pedigree of the S1074 family indicating the segregation of c.832_836delCCTCA mutation in HOMER2. Black symbols indicate affected patients (carrying the mutation in heterozygosis), and white symbols correspond to normal hearing individuals (wild-type for the mutation studied). The subject pointed with an arrow is the index case (studied by OTO-NGS-v2 panel), and the ones marked with an asterisk were analysed by Sanger sequencing for segregation analysis. (B) Electropherograms corresponding to the wild-type (left) and mutant (right) sequences of a normal hearing and an affected individual, respectively. (C) Audiograms of the S1074 family. The data represented correspond to the average of the audiometric thresholds in both ears. (D) Integrative Genomics Viewer (IGV) (Broad Institute) screenshot showing the genomic region corresponding to the c.832_836delCCTCA mutation of HOMER2 and the translated protein stretch corresponding to exon 8 in the reverse orientation (NP_955362.1, HOMER2 long isoform, amino acid range 292–266), as HOMER2 is transcribed by using the DNA negative strand. (E) Schematic representation of the structure of HOMER2 long isoform (NP_955362.1). The different domains [7,14,21] and the mutations identified so far associated with hearing loss (in grey) are shown. The mutation identified in this work is shown in black. EVH1 (1–111 aa): Enabled/vasodilator-stimulated phosphoprotein (Ena/VASP) homology 1; Coiled-coil domain (184–328 aa); CBD (202–294 aa): CDC42-binding domain. LZA (249–307 aa): Leucine Zipper-A; LZB (322–350 aa): Leucine Zipper-B.

Figure 2

Alignment of the wild-type protein fragment encoded by exon 8 of HOMER2 long isoform (NP_955362.1) and the truncating mutations in the CDC42-binding domain (CBD) identified in the Chinese (p.Met281Hisfs*9) and Spanish (p.Pro278Alafs*10) families. The amino acid sequence shared between both aberrant protein tails is shown in bold face.