In the current study, we report two novel mutations in CABP2 (c.490-8C > A) and OTOA (a ~ 154 kb deletion containing OTOA) genes as well as two previously reported mutations in TMPRSS3 (c.413C > A) and COL11A2 (c.966dupC) genes of four Iranian unrelated HL affected patients.
To the best of our knowledge, this is the first report of a patient with a splice site mutation c.490-8C > A in the CABP2 gene, worldwide, and the third report about a CABP2 mutation in an Iranian population. The CABP2 is a member of Ca2+-binding proteins (CABPs) subfamily with high similarity to calmodulin. This protein is expressed in the cochlea and modulates presynaptic calcium influx in inner hair cells through voltage-gated calcium channels to regulate auditory sensitivity (Sheyanth et al., 2021). The frequency and spectrum of CABP2 mutations in most ethnic populations are mainly unknown. Mutation in this gene leads to ARNSHL type DFNB93. To date, only five pathogenic variants in the CABP2 gene have been identified in Iran[20], Italy[39], Turkey[40], Danish Caucasian[38], Pakistan[41] and Israel[42] (Fig. 1a). Previous studies have shown that the protein encoded by CAPB2 is also present in the retina. Therefore, ophthalmological examinations are necessary for individuals with CABP2-related HL. However, no ocular pathology has been reported so far (Sheyanth et al., 2021). Regarding to our patient, no ophthalmologic complication has been found.
Mutations in the TMPRSS3 gene can lead to either prelingual (DFNB10) or post-lingual (DFNB8) ARNSHL. However, the occurrence of ARNSHL with post-lingual onset is rare. The phenotype of TMPRSS3 mutations depends on the type and position of mutations occurred, indicating the critical role of the TMPRSS3 gene in the auditory system (Gao et al., 2017). The c.413C > A (p.Ala138Glu) missense variant in exon 5 of the TMPRSS3 gene has been previously reported in the literature as homozygous in two siblings who were affected with ARNSHL (Hutchin et al., 2005). Furthermore, this variant has been seen in trans with a known pathogenic variant (Ala306Thr) and also co-segregated with the disorder in multiple affected family members in several families (Weegerink et al., 2011). Regarding to previous studies, mutations in SRCR and LDRRA domains of TMPRSS3 cause misfolding in these regions, which ultimately makes the target protein ENaC unable to recognize the TMPRSS3 binding site. The ENaC is a sodium channel that is expressed in many Na+ reabsorbing tissues such as the inner ear and plays a role in regulating sodium concentration in the endolymph. So, the ENaC sodium channel activation along with catalytic activity is one of the important features of TMPRSS3, which is performed by the serine protease domain (Wong et al., 2020). Although the exact function of the TMPRSS3 gene in the auditory system has not yet been fully clarified, its expression has been reported in inner hair cells, supporting cells, and stria vascularis of the cochlear canal, and especially spiral ganglion neurons (Gao et al., 2017). To date, 87 pathogenic and likely pathogenic variants have been identified, of which 80 variants are shown in Fig. 3a and other copy number variants are as follow: 8bp deletion and insertion of 18 monomeric β-satellite repeat units, deletion of E1-5 and E13, 5 exons deletion, E6-10 deletion, 4 exons duplication, duplication of E7-10, and complex genomic rearrangement. Interestingly, TMPRSS3 is known to be a tumor-associated gene, and several studies have shown its overexpression in pancreatic, ovarian, and breast tumors. In addition, by using its proteolytic activities, it also helps in the proliferation, migration and survival of malignant cells in cancer development (Akhavanfard et al., 2020).
Mutations in the OTOA gene, lead to moderate to profound ARNSHL type DFNB22 due to the disturbance in the stimulation of inner ear hair cells (Adhikary et al., 2015). Interestingly, three large segmental duplications (BP1, BP2, and BP3) are located on chromosome band 16p12.2, which provides the position for frequent recombination and chromosomal rearrangements. Moreover, these segmental repeats can act as a hotspot for copy number variants. There is a highly homologous sequence between the segmental repeats BP1 and BP2 that includes the OTOA, METTL9, and IGSF6 genes (Razmara et al., 2018). As a result, the variation of deletion size in these regions can be seen even in different ethnic groups (Table 2). Accordingly, the present study reports a novel ~ 154 kb deletion mutation and further supports the evidence of the pathogenic role of OTOA in ARNSHL.
The COL11A2 gene encodes one of the two alpha chains of type XI collagen and is expressed in the developing cochlea [18, 48]. COL11A2 variants are related to several disorders that include autosomal dominant (DFNA13) or recessive (DFNB53) NSHL, as well as Stickler syndrome, otospondylmegaepiphyseal dysplasia, fibrochondrogenesis, and Weissenbacher-Zweymuller syndrome.[18] Up to now, 61 pathogenic or likely pathogenic variants have been reported, 12 of which, including the c.966dupC mutation found in this study, lead to NSHL (http://www.hgmd.cf.ac.uk/ac/) (Table 3).
Table 3
Pathogenic and likely pathogenic mutations in COL11A2 (NM_080680) causing non-syndromic hearing loss.
cDNA /aa change | Phenotype | Origin | Exon | Ref | cDNA /aa change | Phenotype | Origin | Exon | Ref |
c.109G > T (p.A37S) | DFNB53 | Tunisia | 1 | [49] | c.2207G > T (p.G736V) | DFNA13 | NA | 29 | [19] |
c.966dupC (p.T323Hfs) | DFNB53 | Iran/ China | 8 | [18, 19] | c.2423G > A (P.G808E) | DFNA13 | NA | 28 | [50] |
c.970G > A (p.G323E) | DFNA13 | Dutch | 31 | [48] | c.2662C > A (p.P888T) | DFNB53 | Turkey | 32 | [49] |
c.1638C > T (p.R549C) | DFNA13 | America | 42 | [48] | c.3100C > T (p.R1034C) | DFNA13 | NA | 39 | [50] |
c.1861C > A (p.P621T) | DFNB53 | Iran | 17 | [50] | c.3392G > A (p.R1131Q) | DFNA13 | NA | 46 | [19] |
c.2002C > T (p.P668S) | DFNB53 | Japan | 20 | [19] | c.3743C > T (p.P1248L) | DFNA13 | NA | 51 | [19] |
NA: Not available |
The structural integrity of TM is crucial for the hearing process. Accordingly, COL11A2 pathogenic variants lead to hearing impairment due to the abnormal distribution of collagen XI in the tissue membrane and the change in the structure of the TM.[44]