Brain Cell Type-Specific Nuclear Proteomics Is Imperative to Resolve Neurodegenerative Disease Mechanisms

Abstract

Neurodegenerative diseases (NDs) involve complex cellular mechanisms that are incompletely understood. Emerging findings have revealed that disruption of nuclear processes play key roles in ND pathogenesis. The nucleus is a nexus for gene regulation and cellular processes that together, may underlie pathomechanisms of NDs. Furthermore, many genetic risk factors for NDs encode proteins that are either present in the nucleus or are involved in nuclear processes (for example, RNA binding proteins, epigenetic regulators, or nuclear-cytoplasmic transport proteins). While recent advances in nuclear transcriptomics have been significant, studies of the nuclear proteome in brain have been relatively limited. We propose that a comprehensive analysis of nuclear proteomic alterations of various brain cell types in NDs may provide novel biological and therapeutic insights. This may be feasible because emerging technical advances allow isolation and investigation of intact nuclei from post-mortem frozen human brain tissue with cell type-specific and single-cell resolution. Accordingly, nuclei of various brain cell types harbor unique protein markers which can be used to isolate cell-type specific nuclei followed by down-stream proteomics by mass spectrometry. Here we review the literature providing a rationale for investigating proteomic changes occurring in nuclei in NDs and then highlight the potential for brain cell type-specific nuclear proteomics to enhance our understanding of distinct cellular mechanisms that drive ND pathogenesis.

In vivovalidation of late-onset Alzheimer’s disease genetic risk factors

“…Therefore, our transcriptomic comparison to post-mortem AMP-AD clinical samples, while practical, is unrealistic and we are now testing those models that best approximated human transcriptional changes at 12 months to at least 24 months of age (31, 58) (Oblak A, et al, this issue). Likewise, recent studies (as well as our pilot data) have shown that proteomics is a more reliable means to correlate models to disease than transcriptomics (59, 60) (Oblak A, et al, this issue), so we will be using proteomic analysis on prioritized models.…”

Cellular proteomic profiling using proximity labelling by TurboID-NES in microglial and neuronal cell lines

“…Mis-localization of nuclear proteins to the cytosol occur in several neurodegenerative diseases, where RNA-binding proteins such as TDP-43, Tau and FUS can aberrantly localize to the cytosol where they become more prone to aggregation. 68 Therefore, the TurboID-NES approach when employed in vivo via CIBOP, could be specifically used to interrogate mechanisms of neurodegeneration that involve dysfunction of nucleocytoplasmic transport, changes in protein trafficking, and cytosolic aggregation.…”

“…z-scores were represented in heatmaps. Mapping gene-associated risk loci with Alzheimer's disease, Parkinson's disease and Amyotrophic Lateral Sclerosis relevant terms (SF 3), MAGMA dataset sheets were directly obtained from a previous review publication from our lab 68. 6.…”

Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines

“…The resulting Z-scores underwent gene GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchical cosine–cosine clustering, and each cluster was functionally annotated and the associated Z-scores were represented in heatmaps. Mapping gene-associated risk loci with Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS) relevant terms, MAGMA dataset sheets were directly obtained from a previous review publication from our laboratory ( 36 ).…”