MacTel patients carry rare phosphoglycerate dehydrogenase (PHGDH) variants with reduced enzymatic activity

Abstract

Purpose : Macular Telangiectasia (MacTel) is a neurodegenerative disease affecting the retina and leading to progressive vision loss. Recent genetic and metabolic studies have shown a link between the disease and serine biogenesis. Phosphoglycerate dehydrogenase (PHGDH) is the rate limiting enzyme involved in serine synthesis. Genome wide association studies (GWAS) identified the PHGDH locus as statistically significantly associated with MacTel, but a direct link between PHGDH function and MacTel has yet to be determined.

Methods : Whole exome sequencing (WES) analysis was performed in 320 MacTel patients to identify specific rare coding variants associated with the disease. To determine the effect of the identified variants on PHGDH activity, we overexpressed these variants in HEK cells and collected partially purified PHGDH by ammonium sulfate precipitation. The PHGDH activity of each lysate was indirectly determined through the reduction of a probe by the NADH produced as a byproduct of the PHGDH forward reaction. The reduced probe is stable and absorbs light at 450nm; thus, the increase in absorbance at 450nm over time was used as a readout of PHGDH activity.

Results : Analysis of WES data identified 13 rare variants (MAF<0.001) in 18 patients in the coding sequences of PHGDH, all predicted to affect the enzyme’s activity. The difference was statistically significant (p= 0.00012) when compared to matched controls from the general population. Of the 13 variants, two introduce stop codons and the rest are missense alleles predicted to have a strong functional effect. One variant was present in 7 patients, including a patient that had early onset disease. Bi-allelic mutations in PHDGH cause severe syndromic features including developmental delay and microcephaly. Heterozygous carriers of these alleles are developmentally normal and may manifest unexpected phenotypes such as MacTel. In vitro analyses showed that, compared to WT PHGDH, the variants carried by the MacTel patients lead to decreased enzymatic activity with multiple variants showing virtually no activity.

Conclusions : The PHGDH variants observed in MacTel patients are functionally compromised and may lead to decreased serine and glycine production in vivo. Our work provides the first direct link between PHGDH function, serine biosynthesis and MacTel.

This abstract was presented at the 2019 ARVO Annual Meeting, held in Vancouver, Canada, April 28 - May 2, 2019.