Association of Rare CYP39A1 Variants With Exfoliation Syndrome Involving the Anterior Chamber of the Eye

Abstract

The Genetics of Exfoliation Syndrome Partnership IMPORTANCE Exfoliation syndrome is a systemic disorder characterized by progressive accumulation of abnormal fibrillar protein aggregates manifesting clinically in the anterior chamber of the eye. This disorder is the most commonly known cause of glaucoma and a major cause of irreversible blindness.OBJECTIVE To determine if exfoliation syndrome is associated with rare, protein-changing variants predicted to impair protein function. DESIGN, SETTING, AND PARTICIPANTSA 2-stage, case-control, whole-exome sequencing association study with a discovery cohort and 2 independently ascertained validation cohorts. Study participants from 14 countries were enrolled between February 1999 and December 2019. The date of last clinical follow-up was December 2019. Affected individuals had exfoliation material on anterior segment structures of at least 1 eye as visualized by slit lamp examination. Unaffected individuals had no signs of exfoliation syndrome.EXPOSURES Rare, coding-sequence genetic variants predicted to be damaging by bioinformatic algorithms trained to recognize alterations that impair protein function. MAIN OUTCOMES AND MEASURESThe primary outcome was the presence of exfoliation syndrome. Exome-wide significance for detected variants was defined as P < 2.5 × 10 −6 . The secondary outcomes included biochemical enzymatic assays and gene expression analyses. RESULTSThe discovery cohort included 4028 participants with exfoliation syndrome (median age, 78 years [interquartile range, 73-83 years]; 2377 [59.0%] women) and 5638 participants without exfoliation syndrome (median age, 72 years [interquartile range, 65-78 years]; 3159 [56.0%] women). In the discovery cohort, persons with exfoliation syndrome, compared with those without exfoliation syndrome, were significantly more likely to carry damaging CYP39A1 variants (1.3% vs 0.30%, respectively; odds ratio, 3.55 [95% CI, 2.07-6.10]; P = 6.1 × 10 −7 ). This outcome was validated in 2 independent cohorts. The first validation cohort included 2337 individuals with exfoliation syndrome (median age, 74 years; 1132 women; n = 1934 with demographic data) and 2813 individuals without exfoliation syndrome (median age, 72 years; 1287 women; n = 2421 with demographic data). The second validation cohort included 1663 individuals with exfoliation syndrome (median age, 75 years; 587 women; n = 1064 with demographic data) and 3962 individuals without exfoliation syndrome (median age, 74 years; 951 women; n = 1555 with demographic data). Of the individuals from both validation cohorts, 5.2% with exfoliation syndrome carried CYP39A1 damaging alleles vs 3.1% without exfoliation syndrome (odds ratio, 1.82 [95% CI, 1.47-2.26]; P < .001). Biochemical assays classified 34 of 42 damaging CYP39A1 alleles as functionally deficient (median reduction in enzymatic activity compared with wild-type CYP39A1, 94.4% [interquartile range, 78.7%-98.2%] for the 34 deficient variants). CYP39A1 transcript expression was 47% lower (95% CI, 30%-64% lower; P < ....

RNA Sequencing of Lens Capsular Epithelium Implicates Novel Pathways in Pseudoexfoliation Syndrome

“…Differentially expressed PEX GWAS loci associated genes included APOE and POMP which were upregulated, and CACNA1A , SEMA6A , and FMN1 which were downregulated. Despite previous experimental data demonstrating differential expression of LOXL1 30 , 54 and CYP39A1 20 in various ocular tissues collected from patients with PEX, neither of these genes were differentially expressed in the current study. We investigated the differential expression profiles of Mendelian glaucoma-associated genes.…”

“…Using a list of genes with single-nucleotide variants associated with PEX in GWAS, we investigated the expression profile of those genes in the lens capsular epithelium. 10 – 20 From a total of 35 investigated PEX genes, all of which were measurably expressed, 2 were upregulated and 3 downregulated in PEX samples ( Supplementary Fig. S13 ).…”

“…44 A pseudoexfoliation GWAS genes list included all genes with common variants identified by GWAS, and associated at genome-wide significance with PEX, 10 – 12 , 15 – 17 , 19 , 45 with the notable addition of CYP39A1 : rare variants of which were recently reported to be associated with PEX in an exome-wide rare variant association study. 20 A glaucoma GWAS genes list included genes collocated with 127 glaucoma single nucleotide polymorphisms previously demonstrated to be associated with POAG risk across ancestries. 46 Finally, we generated an ectopia lentis gene list from Mendelian diseases associated with ectopia lentis (a disease phenotype characterized by zonular instability) using data from the Online Mendelian Inheritance in Man (OMIM) database (see the Appendix for gene lists and accession resources).…”

“… 10 – 19 More recently, an exome-wide association study identified disease associations with rare coding variants in the cytochrome P450 gene CYP39A1 . 20 Additional attempts to understand PEX include targeted protein/proteomic analyses, which have identified more than 70 constituents of PEX material, and targeted gene expression studies, which have implicated multiple disordered biological processes in PEX. 2 , 21 – 35 Despite advances in our understanding of the genetic, structural, and functional architecture of this disease, the mechanisms by which PEX results in its various ocular disease manifestations remain unclear.…”

Analyses of pseudoexfoliation aqueous humor lipidome

“…A potential link between the abnormal cholesterol metabolism and PEX is indicated by the association of cholesterol metabolizing CYP39A1 variants with an exfoliation syndrome. 29 An intriguing aspect is that the Polymorphism Phenotyping version 2 (Polyphen-2) HumDiv software identified several damaging (for example, F175L and C31Y, D157N) and non-damaging or benign variants (H164L, N183D, E224K, This journal is © The Royal Society of Chemistry 2022 M244L, M426V, and M73V) and enzymatic activities are within similar range, which also warrants significant understanding of the lipidome in the affected individuals. 29 Lipid changes have been found in the AH as well as TM of other glaucomas.…”