Whole-exome Sequencing Analysis Identifies Mutations in the EYS Gene in Retinitis Pigmentosa in the Indian Population

Abstract

Retinitis pigmentosa (RP) is a rare heterogeneous genetic retinal dystrophy disease, and despite years of research, known genetic mutations can explain only approximately 60% of RP cases. We sought to identify the underlying genetic mutations in a cohort of fourteen Indian autosomal recessive retinitis pigmentosa (arRP) families and 100 Indian sporadic RP cases. Whole-exome sequencing (WES) was performed on the probands of the arRP families and sporadic RP patients, and direct Sanger sequencing was used to confirm the causal mutations identified by WES. We found that the mutations of EYS are likely pathogenic mutations in two arRP families and eight sporadic patients. Specifically, we found a novel pair of compound heterozygous mutations and a novel homozygous mutation in two separate arRP families, and found two novel heterozygous mutations in two sporadic RP patients, whereas we found six novel homozygous mutations in six sporadic RP patients. Of these, one was a frameshift mutation, two were stop-gain mutations, one was a splicing mutation, and the others were missense mutations. In conclusion, our findings expand the spectrum of EYS mutations in RP in the Indian population and provide further support for the role of EYS in the pathogenesis and clinical diagnosis of RP.

Figure 1. Fundus photographs and OCT pictures of the proband in family ARRP-49.

The fundus photographs (A) show typical changes (waxy-pale disc, arteriolar attenuation and bone-spicule pigment) of fundus in the left eye (OS LE) and right eye (OD RE); the OCT pictures of the left and right eyes (B) show atrophy of the foveal and retinal layers (macular thickness: macular cube 512 × 128).

Figure 2. Representative photographs of sporadic patients RP:S-14.

Fundus photographs (A) showed bone-spicule pigment and arteriolar attenuation; flash ERG (B) showed a-wave or b-wave with reduced or extinguished amplitude; OCT picture (C) showed thinner and atrophy retina.

Figure 3. Representative photographs of sporadic patients RP:S-48.

Fundus photographs (A) showed bone-spicule pigment and arteriolar attenuation; flash ERG (B) showed a-wave or b-wave with reduced or extinguished amplitude; OCT picture (C) showed thinner and atrophy retina.

Figure 4. Pedigree of the family ARRP-49 and mutations identified by Sanger sequencing analysis.

A shows the segregation of compound heterozygous changes c.8422G>A (MU1) and c.7868G>A (MU2). Genotypes are presented as follows: MU1/MU2 represents individuals with both mutations as compound heterozygous; MU1/+ and +/MU2 indicate heterozygous carriers; +/+ indicates individuals carrying two wild-type alleles. NA denotes DNA samples that were unavailable.

Figure 5. Pedigree of the family ARRP-206 and mutations identified by Sanger sequencing.

A shows the segregation of a homozygous mutation c.1871G>A (MU3). The proband is indicated by an arrow. MU3/MU3 represents a homozygous mutant, whereas MU3/+ indicates a heterozygous carrier. Black symbols indicate affected individuals; white symbols indicate unaffected individuals. NA denotes DNA samples that were unavailable.

Figure 6

Sanger sequencing in sporadic patients RP-S:10 and RP-S:18 (A and B) showed 2 compound heterozygous changes.

Figure 7. Sanger sequencing in sporadic patients RP-S:2, RP-S:22, RP-S:14, RP-S:34 and RP-S:48 showed homozygous mutations.

Figure 8. Distribution of EYS mutations identified in this study and sequence alignment of the affected amino acid residues.

(A) Distribution of mutations on the various domains of the EYS protein. (B) Amino acid sequence comparison of EYS among homologous genes in Euteleostomi.