Variants in SKP1, PROB1, and IL17B genes at keratoconus 5q31.1–q35.3 susceptibility locus identified by whole-exome sequencing

Abstract

Keratoconus (KTCN) is a protrusion and thinning of the cornea, resulting in impairment of visual function. The extreme genetic heterogeneity makes it difficult to discover factors unambiguously influencing the KTCN phenotype. In this study, we used whole-exome sequencing (WES) and Sanger sequencing to reduce the number of candidate genes at the 5q31.1-q35.3 locus and to prioritize other potentially relevant variants in an Ecuadorian family with KTCN. We applied WES in two affected KTCN individuals from the Ecuadorian family that showed a suggestive linkage between the KTCN phenotype and the 5q31.1-q35.3 locus. Putative variants identified by WES were further evaluated in this family using Sanger sequencing. Exome capture discovered a total of 173 rare (minor allele frequency o0.001 in control population) nonsynonymous variants in both affected individuals. Among them, 16 SNVs were selected for further evaluation. Segregation analysis revealed that variants c.475T4G in SKP1, c.671G4A in PROB1, and c.527G4A in IL17B in the 5q31.1-q35.3 linkage region, and c.850G4A in HKDC1 in the 10q22 locus completely segregated with the phenotype in the studied KTCN family. We demonstrate that a combination of various techniques significantly narrowed the studied genomic region and reduced the list of the putative exonic variants. Moreover, since this locus overlapped two other chromosomal regions previously recognized in distinct KTCN studies, our findings suggest that this 5q31.1-q35.3 locus might be linked with KTCN.

Snake-like Chromatin Cell Protein as an Indicator of Chronic Eye Rubbing in Patients with Keratoconus and Allergic Conjunctivitis

“…17 In chronic dry eye patients, SLC is attributed to the increase of mechanical friction between the eyelid and the ocular surface. 22,23 However, this has also been found with other conditions, such as eye surgery and is usually associated with chronic mechanical irritation or trauma. 17 Some hypotheses regarding the cause of keratoconus related to eye rubbing are the release of inflammatory mediators, 26 increased corneal temperature (thereby explaining corneal deformation), 29 epithelial thinning, large intraocular pressure spikes, and others.…”

“…5 Therefore, it has been postulated as a multifactorial disease. 4,5,7,22,23 Multiple studies have revealed an association with certain genes; 22,24 however, it currently cannot be diagnosed based on genetic screening. 23,24 Eye rubbing has been postulated as a significant risk factor by several authors.…”

“…33 However, it is difficult to prove that the mechanical stress induced by severe eye rubbing can cause structural changes to the cornea but not to the chromatin of conjunctival epithelial cells, which is altered by eye rubbing, contact lens use, and dry eye friction. 17,22,24 A limitation of our study was that SLC was evaluated based on epithelial conjunctival cells instead of corneal epithelial cells because SLC has been studied just in conjunctival cells. However, it is widely known that keratoconus eyes present not only alterations limited to the cornea but also tears, and that the conjunctiva expresses inflammatory alterations.…”

Peer Review #2 of "Accumulation of sequence variants in genes of Wnt signaling and focal adhesion pathways in human corneas further explains their involvement in keratoconus (v0.2)"

“…Several candidate genes for KTCN have also been identified using Sanger sequencing or next generation sequencing (NGS) including VSX1, SOD1, and DOCK9 or SKP1, MPDZ, FLG, PPIP5K2, and PCSK1, respectively. [26][27][28][29][30][31][32] However, variants detected in those genes were present in a small fraction of KTCN patients or particular populations only.…”

Peer Review #3 of "Further evaluation of differential expression of keratoconus candidate genes in human corneas (v0.2)"

“…Linkage studies also have led to the identification of a few potential KTCN candidate genes, including SPARC, IL1RN, and SKP1. These genes encode a cysteine-rich acidic matrixassociated protein, IL1 receptor antagonist, and S-phase kinase-associated protein 1 that are known to be involved in the extracellular matrix (ECM) formation, immune response, and ubiquitination, respectively (Bisceglia et al, 2009;Nowak et al, 2013;Karolak et al, 2016a).…”