Study identifies genetic loci associated with keratoconus

This article was reviewed by Bennet J. McComish, PhD

In the largest study of its kind in keratoconus published so far, researchers conducting a genome-wide association study found a region of chromosome 11 in which multiple genetic variants were significantly more common in keratoconus patients than in unaffected individuals.

Functional annotation of the associated variants indicated that several of the genes in the identified locus are likely involved in apoptotic pathways.

The findings were published in the February issue of JAMA Ophthalmology [McComish BJ, et al. JAMA Ophthalmol. 2020;138(2):174-181.] Bennet J. McComish, PhD, research fellow, Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia, is lead author of the article. 

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“Our study, which was an international collaboration between groups in Australia, the United States, and the United Kingdom, aimed to identify genetic variants involved in the risk of developing keratoconus,” he said. “This information will allow us to better understand the biochemical pathways that are disrupted in keratoconus. It will help in the identification of potential therapeutic targets for this disease that is relatively common and can cause severe visual impairment.”

Dr. McComish said the region of chromosome 11 that researchers identified contains at least five protein-coding genes.

“The next step will be to determine which of those genes is implicated in the disease, recognizing that other genetic variations nearby can ‘hitchhike’ with the variants that cause the disease,” he said.  

Data used for the study were collected from individuals seen between January 2006 and March 2019 at eye clinics in Australia, the United States, and Northern Ireland.

First, in a discovery phase, data were analyzed from 522 Australians with keratoconus and 655 unaffected individuals representing a control group. Subjects for the control group were taken from cohorts of the Australian Blue Mountains Eye Study and a previous study of glaucoma. 

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Genotyping for 551,839 variants was done using the HumanCoreExome single-nucleotide polymorphism (SNP) array (Illumina). The SNPs with P values <1.00 x 10^-6 that were identified in the discovery cohort were assessed in three independent replication cohorts using the MassARRAY System (Agena Bioscience). 

The replication cohorts included 818 affected subjects with keratoconus and 3,858 unaffected controls. They were comprised of individuals included in a previous keratoconus GWAS data set from the United States, a cohort of subjects with keratoconus and unaffected controls from Australia and Northern Ireland, and a case-control cohort from Victoria, Australia. 

In the discovery cohort as well as in the three replication cohorts, the majority of keratoconus subjects were males (55% to 61%) and mean age for the cases in each cohort ranged from 35 to 45 years. The proportion of males among controls in the discovery cohort was greater than in the replication cohorts (47% versus ~38%). Mean age of the controls in all four cohorts was 17 to 28 years older than the mean age of their keratoconus counterparts. 

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Genome-wide association test results
The association analysis in the discovery cohort identified two novel loci with genome-wide significance. One of the novel loci was located on chromosome 11 at rs61876744 in patain-like phosphoplipase domain-containing 2 gene (PNPLA2), and it reached genome-wide significance in an analysis of all four study cohorts. The other novel loci was on chromosome 22 at rs138380, 2.2 kb upstream of casein kinase I isoform epsilon gene (CSNK1E). 

None of the SNPs in the CSNK1E locus reached significance in the replication cohorts, despite the fact that the CSNK1E locus had the strongest association in the discovery cohort. When the data from the discovery cohort and the three replication cohorts were combined, 12 SNPS at the novel PNPLA2 locus were found to be associated with keratoconus at genome-wide significance. 

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Biological significance 
Discussing their findings, the researchers noted that the function of the protein encoded by the lead SNP, which was located in an intron of PNPLA2, is to catalyze the initial step in triglyceride hydrolysis.

Stating that there is no obvious connection between this biochemical pathway and keratoconus, they observed that the closest gene to an association signal is not necessarily the causative gene. 

“Other genes in the identified region are known to be involved in regulating apoptotic cell death, a process that has been suggested previously by other authors to be part of the mechanism underlying the development of keratoconus,” Dr. McComish said. “This finding will help focus future studies on the role of these genes in keratoconus.”

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Limitations
The older mean age of the control cohorts compared to the case cohorts represents a possible study limitation. Because of the demographic difference, it will be important to assess the identified loci for age-associated effects in future studies, they wrote.

Read more by Cheryl Guttman Krader

Bennet J. McComish, PhD
E: bennet.mccomish@utas.edu.au
Dr. McComish has no relevant financial disclosures related to this topic.