Genetic and Functional Dissection of Neurodegeneration: Multiomic Analysis of Genetic Risk Variants in Pontocerebellar Hypoplasia 1B and Alzheimer's Disease

Abstract

Each neurodegenerative diseases have a combination of features such as neuronal death, protein aggregation, inflammation, cytoskeletal abnormalities, altered proteostasis, synaptic defects, RNA/DNA defects, and altered energetics. While genetic variants are crucial to disease pathogenesis, the molecular mechanisms linking the genotype to these hallmarks remain unclear. We investigate two risk genes linked to different neurodegenerative diseases, pontocerebellar Hypoplasia 1B (PCH1b) and Alzheimer’s disease (AD), using a multiomic approach to uncover their genetic and functional underpinnings. PCH1b is caused by variants in an RNA exosome complex subunit EXOSC3. These variants disrupt RNA processing, leading to neuronal dysfunction and progressive neurodegeneration. By analyzing cell lines carrying a variant in between two RNA-binding domains of EXOSC3, we found significant changes in RNA abundance across multiple RNA classes and showing enrichment of transcripts containing AU-rich elements. Molecular dynamics simulations of EXOSC3 indicate that the variants produce an unstructured EXOSC3 isoform, possibly prone to degradation. Proteomics reveals altered protein abundance and thermal stability in specific RNA exosome subunits, particularly affecting the MPP6 cofactor. Apolipoprotein E (APOE) is the strongest genetic risk factor for sporadic AD though its exact molecular effects are not fully understood. Thermal proteome profiling of astrocytes from APOE knockout mice showed that APOE deficiency alters the thermal stability of mitochondrial proteins, particularly in Complex I of the electron transport chain. The functional consequences of this stability change is an increased ATP-linked respiration in APOE-deficient astrocytes, suggesting a shift in mitochondrial activity. These findings provide new insights into how APOE impacts mitochondrial function and protein stability, emphasizing thermal proteomic profiling as a powerful tool for studying neurodegenerative diseases. Multiomics analyses effectively link genotype to phenotype in neurodegenerative diseases by uncovering molecular alterations that define disease-specific hallmarks, such as RNA homeostasis changes in PCH1b and mitochondrial alteration in AD, offering valuable insights into their pathophysiology and therapeutic targets.