Study of POLR3A variants in a family trio suggests mutation-specific pathogenetic mechanisms: insights from integrative OMIC approaches

Background: Hypomyelinating leukodystrophies (HLDs) are rare genetic neurodevelopmental disorders characterized by defective myelin formation. The genetic cause of these disorders has been ascribed to mutations in genes encoding myelin protein components, such as proteolipid protein 1 (PLP1) and myelin basic protein (MBP), or in genes encoding for transcription and translation-related proteins. Particularly, biallelic pathogenic variants in POLR3A, POLR3B, POLR3K, POLR3D, POLR1C lead to the insurgence of RNA Polymerase III (Pol III)-related HLDs (POLR3-HLDs). The molecular mechanisms linking Pol III dysfunction to hypomyelination remain largely elusive, though the main hypothesis is that impaired Pol III activity likely disrupts gene expression and cellular homeostasis processes critical for myelin development and lipid metabolism. Methods: In this study, we analyzed a family trio consisting of unaffected carrier parents and a proband affected by POLR3A-related HLD, carrying compound heterozygous variants (p.Phe601Tyr and p.Gly1358Arg). We investigated the structural and functional consequences of two POLR3A variants using protein modeling, functional assays and multi-omics profiling in subject-specific primary fibroblasts. Results: Structural analysis revealed alterations in DNA-binding regions and a likely impact on protein stability, whilst functional assays showed an impairment in cellular proliferation. Lipidomic and transcriptomic profiling revealed that p. Gly1358Arg mutation predominantly affects lipidomic metabolism, while p. Phe601Tyr was associated with a widespread transcriptional dysregulation. Both mutations ultimately caused a significant reduction in lipid droplets in the proband’s cells. Conclusions: These results demonstrate mutation-specific pathogenetic mechanisms in POLR3A-HLD and underline the utility of integrative multi-omics approaches in elucidating the molecular basis of rare neurodevelopmental disorders.