THBS1 is a new autosomal recessive non-syndromic hearing impairment gene

Abstract

Background: Prelingual hearing impairment (HI) is genetically highly heterogenous. Early diagnosis and intervention are essential for psychosocial development. In this study we investigated a consanguineous family from Pakistan with autosomal recessive (AR) non-syndromic sensorineural HI (NSHI).

Methods: A DNA sample from an HI member of a consanguineous Pakistani family segregating ARNSHL underwent exome sequencing. Using Sanger sequencing select variants were validated and tested for segregation using DNA samples from additional family members. We further investigated RNA expression data for the candidate gene in mouse and human inner ear and human inner ear organoids using data obtained from the gene Expression Analysis Resource.

Results: We identified thrombospondin 1 (THBS1) as a new NSHI gene. A homozygous frameshift variant [c.1470del: p.(Ile491Serfs*45)] was observed in the three hearing-impaired and in the heterozygous state in three unaffected family members. Unlike for most ARNSHI, hearing-impaired individuals had audiograms with a sloping pattern, showing more pronounced HI in the mid and high frequencies (ranging from moderate to profound) compared to the low frequencies. RNA expression data indicates THBS1 is expressed during human inner ear development. Additionally, THBS1 is expressed in the cochlear epithelium and supporting cells of the mouse inner ear during embryonic and postnatal stages. Previously, THBS1 was demonstrated to affect hearing in knockout mice by influencing the formation and function of afferent synapses in the inner ear.

Conclusions: Our findings highlight THBS1 as a potential novel candidate gene for human HI characterized by a sloping high-frequency audio profile. This discovery enhances our understanding of the genetic etiology of HI and will aid in advancing molecular diagnosis.

Keywords: Autosomal recessive non-syndromic hearing impairment; Consanguinity; Exome sequencing; Inner ear; THBS1; Thrombospondin.

Fig. 1

Pedigree of family DEM4671 and audiometry. (A) Pedigree of the Pakistani family DEM4671 displaying genotypes for the variant THBS1 (NM_003246.4) [c.1470del: p.(Ile491Serfs*45)] for each family member that has an available DNA sample. A star indicates the hearing-impaired family member whose DNA sample underwent exome sequencing. Females are represented by circles and males by squares. Individuals with solid symbols have NSHI while those with clear symbols are unaffected. (B–D) Air conduction thresholds for affected members IV:2, IV3 and IV:5 respectively. IV:2 has profound hearing impairment in the high frequencies and moderate to severe in the mid to low frequencies. IV:3 and IV:5 have profound bilateral HI in both ears. The audiograms display a decrease in hearing threshold at higher frequencies. Circles with smooth connecting lines represent the right ear and crosses with dotted connecting lines, the left ear

Fig. 2

Human inner ear expression of THBS1. THBS1 is expressed in the human inner ear cells with cochlear floor cells displaying the highest expression. The dataset contains three stages of human inner ear development [18]. The left panel illustrates single-nucleus RNA sequence data from two human fetal inner ears (7.5 and 9.2 weeks) and one human adult inner ear. The X axis displays the uniform manifold approximation and projection (UMAP) 1 which is used for dimension reduction and on the Y axis UMAP 2. The scale bar displays normalized gene expression levels which range from low (yellow) to high (red) that have been adjusted for sequence depth. The right panel displays the locations of specific inner ear cell types with color codes

Fig. 3

THBS1 expression in human inner ear organoids. THBS1 is expressed in the human inner ear organoids. Chondrocytes exhibit a high expression for this gene. The dataset plotted consists of human pluripotent stem cells differentiated into complex inner ear tissue [18]. The left panel illustrates the expression of THBS1 in the single-cell and single-nucleus RNA sequence data from the differentiated inner ear organoids. The X axis displays the uniform manifold approximation and projection (UMAP) 1 which is used for dimension reduction and on the Y axis UMAP 2. The scale bar displays normalized gene expression levels which range from low (yellow) to high (red) that have been adjusted for sequence depth. The right panel displays the locations of specific inner ear cell types with color codes