Genome-wide epigenetic signatures facilitated the variant classification of PURA gene and uncovered the pathomechanism of PURA-related neurodevelopmental disorders

Purpose Rare genetic variants in the PURA gene cause PURA-related neurodevelopmental disorder (PURA-NDD), characterized by neonatal abnormalities and developmental delay. Using genome-wide DNA methylation analysis on patients with PURA variants, we aim to establish PURA-NDD-specific methylation profile and provide further insights on the molecular basis of the PURA-NDD. Methods 23 individuals (including 12 unpublished) carrying PURA variants were enrolled. We conducted the Illumina Infinium EPIC microarray analysis in 17 PURA-NDD individuals. In vitro experiments were performed to examine how PURA variants affect Pur-α expression. Results Additional phenotypes in 12 newly identified patients were described in this study. Genome-wide DNA methylation analysis unveiled distinctive methylation profiles to PURA-NDD, and the established classifier can reclassify PURA variants of uncertain significance. Patients bearing PURA hapoloinsufficient and missense variants have comparable DNA methylation profiles, and cells expressing these PURA variants showed consistent Pur-α downregulation suggesting a haploinsufficiency mechanism. Conclusion Patients with PURA-NDD exhibit a specific epi-signature, which has potential to aid identification and diagnosis of PURA-NDD patients and offer implications for further functional investigations.