Stevenson, J. | bioRxiv Science

bioRxiv2023

Transcriptomic signatures of Abeta- and tau-induced neuronal dysfunction reveal inflammatory processes at the core of Alzheimer's disease pathophysiology

Molecular mechanisms enabling pathology-induced neuronal dysfunction in Alzheimers disease (AD) remain elusive. Here, we use mechanistic computational models to infer the combined influence of PET-measured A{beta} and tau burdens on fMRI-derived neuronal activity and to subsequently identify the transcriptomic spatial correlates of AD pathophysiology. Our results reveal overrepresented genes and biological processes that participate in synaptic degeneration and interact with A{beta} and tau deposits. Furthermore, we confirmed the central role of the immune system and neuroinflammatory pathways within AD pathogenesis; microglia were significantly enriched in the gene set associated with A{beta} and tau synergistic influences on neuronal activity. Lastly, our computational approach unveiled drug candidates with the potential to halt or reduce the observed pathological effects on neuronal activity, including existing medication for cancer, immune disorders, and cardiovascular diseases, many currently under clinical evaluation in AD. Overall, these findings support the notion that the AD brain experiences functional changes intricately associated with a diverse spectrum of molecular processes.

neuroscience↗

bioRxiv2022

Parallel CRISPR-Cas9 screens reveal mechanisms of PLIN2 and lipid droplet regulation

Lipid droplets (LDs) are lipid storage organelles that consist of a central core of neutral lipids surrounded by a phospholipid monolayer decorated with a unique set of integral and peripheral proteins. Invariably, at least one member of the perilipin family of proteins (PLIN1-5) associates with LDs in all cell types. Despite key roles of PLIN2 in governing hepatic lipid metabolism, the mechanisms that regulate PLIN2 levels remain incompletely understood. Here, we develop a set of genome-edited PLIN2 reporter cell lines that facilitate the analysis of genes that regulate PLIN2 and LD abundance. Leveraging these reporter cells in a series of CRISPR-Cas9 loss-of-function screens, we generate a comprehensive inventory of genes that influence PLIN2 levels under different metabolic conditions. Moreover, we uncouple their effects on PLIN2 expression and post-translational stability. Identified genetic modifiers include canonical genes that control LD metabolism (e.g., ACSL3, DGAT2, PNPLA2, ABHD5) as well as genes with less characterized roles in PLIN2 and LD regulation such as ubiquitination machinery (e.g., MARCH6, UBE2J2), transcription regulators (e.g., HNF4A, HDAC3), mitochondrial pathways (e.g., electron transport chain and mitochondrial fatty acid synthesis), and others. These CRISPR screens, and several published screens that focus on different aspects of lipid metabolism, provide the foundation for CRISPRlipid (http://crisprlipid.org), a versatile, online data commons for lipid-related functional genomics data. Together, our study uncovers new mechanisms of PLIN2 regulation and provides an extensive, phenotype-rich resource for the exploration of LD biology and lipid metabolism.

cell biology↗