Exome sequencing reveals PPEF2 variant associated with high myopia.

High myopia (HM) is a serious blinding eye disease, and genetic factors play an important role in the development of HM. In this study, whole exome sequencing (WES) was used to identify a novel variant c.A875G of the PPEF2 for a large Uyghur family with nonsyndromic HM. The variant was verified to cosegregate with HM in the family using Sanger sequencing. Another novel variant c.1959C > G in PPEF2 was identified in one of 100 sporadic cases of HM by multiplex PCR targeted amplicon sequencing (MTA-seq). The Ppef2 was verified that mainly expressed in the retinal pigment epithelium (RPE), choroid and retina tissues. Immunofluorescence (IF) and immunohistochemistry (IHC) assays showed that the PPEF2 was strongly expressed in the inner segment layer formed by photoreceptor protrusions, as well as in the outer nuclear layer. Compared with the wild-type, the c.A875G resulted in reduced protein levels but had no effect on protein subcellular localization in cells. In addition, the c.A875G variant resulted in a decreased migratory and proliferative capacity but promoted apoptosis in cells. In summary, PPEF2 was identified as a novel HM-causing gene, and this variant in PPEF2 might cause HM by regulating the migration, proliferation and apoptosis of myopia-related cells.

PPEF2 Opposes PINK1-Mediated Mitochondrial Quality Control by Dephosphorylating Ubiquitin.

Dysregulation of mitophagy, whereby damaged mitochondria are labeled for degradation by the mitochondrial kinase PINK1 and E3 ubiquitin ligase Parkin with phosphorylated ubiquitin chains (p-S65 ubiquitin), may contribute to neurodegeneration in Parkinson's disease. Here, we identify a phosphatase antagonistic to PINK1, protein phosphatase with EF-hand domain 2 (PPEF2), that can dephosphorylate ubiquitin and suppress PINK1-dependent mitophagy. Knockdown of PPEF2 amplifies the accumulation of p-S65 ubiquitin in cells and enhances baseline mitophagy in dissociated cortical cultures. Overexpressing enzymatically active PPEF2 reduces the p-S65 ubiquitin signal in cells, and partially purified PPEF2 can dephosphorylate recombinant p-S65 ubiquitin chains in vitro. Using a mass spectrometry approach, we have identified several p-S65-ubiquitinated proteins following mitochondrial damage that are inversely regulated by PPEF2 and PINK1. Interestingly, many of these proteins are involved in nuclear processes such as DNA repair. Collectively, PPEF2 functions to suppress mitochondrial quality control on a cellular level through dephosphorylation of p-S65 ubiquitin.