Biology subjects

Panfilova, D.

Publications and source records attributed to Panfilova, D..

3 recordsLinked to original sources

bioRxiv2026

Endogenous lipid droplets exhibit profound proteomic and lipidomic differences across neural stem cell states

Lipid droplets (LDs) are protein-coated organelles that store neutral lipids and regulate diverse cellular processes beyond energy metabolism. In neural stem/progenitor cells (NSPCs), LD abundance and morphology vary across cellular states, yet whether LD molecular composition is similarly state-dependent remains unknown. Here, we define the first endogenous LD proteome and lipidome atlas of NSPCs and their progeny. State-resolved analyses reveal extensive differences in both LD-associated proteins and stored lipids, allowing for identification of LD signatures that distinguish quiescent and proliferative states, and uncovering selective enrichment of numerous proteins on quiescent NSPC LDs. Functional interrogation of one such protein, CIDEB, showed that its knockdown alters LD morphology and induces senescence-associated transcriptional programs, implicating CIDEB in the maintenance of NSPC quiescence. These findings establish LDs as dynamically specialized organelles in NSPCs and their progeny and provide a resource for investigating LD-mediated regulation of stem cell state and lineage progression.

cell biology↗

bioRxiv2024

An optimized method to visualize lipid droplets in brain tissue demonstrates their substantial accumulation in aged brains

Lipid droplets (LDs) are cellular stores for lipids. These organelles have recently gained interest in neuroscience because they accumulate in various cell types in neurodegenerative diseases. However, their role under physiological conditions is still not fully understood. Classical LD staining methods, which use lipophilic dyes like BODIPY 493/503 (BD493) or antibodies against LD coat proteins, show very few LDs in healthy brain tissue. Our recently developed novel endogenous LD reporter mouse challenges this view. We have been able to detect numerous LDs in healthy brain tissue from both adult and developing mice without staining. To understand why classical staining and endogenous labeling yield different results, we thoroughly investigated the effects of tissue preparation and detergent used in LD detection. We found that BD493 works poorly in brain tissue, while other lipophilic dyes visualize many LDs. We also found that antibody-based LD detection depends on tissue pretreatment and detergent concentration but can reveal a similar number of LDs as observed with the endogenous LD reporter mouse. Taken together, we here present an optimized procedure for LD detection in brain tissue using commercially available dyes and antibodies. Using these methods, we demonstrate that LDs are numerous in healthy brain tissue and substantially accumulate in aged brains in various cell types, including neurons.

neuroscience↗

bioRxiv2023

Remodeling of the protein ubiquitylation landscape in the aging vertebrate brain

Post-translational modifications (PTMs) regulate protein homeostasis and function. How aging affects the landscape of PTMs remains largely elusive. Here, we reveal changes in hundreds of protein ubiquitylation, acetylation, and phosphorylation sites in the aging brain of mice. We show that aging has a major impact on protein ubiquitylation and that 29% of the ubiquitylation sites are affected independently of protein abundance, indicating altered PTM stoichiometry. We found a subset of these sites to be also affected in the brain of the short-lived killifish Nothobranchius furzeri, highlighting a conserved aging phenotype. Furthermore, we estimated that over 35% of ubiquitylation changes observed in old mouse brains derive from partial proteasome inhibition, a well-established hallmark of brain aging. Our findings provide evidence of an evolutionarily conserved ubiquitylation signature of the aging brain and establish a causal link between proteasome inhibition and age-related remodeling of the ubiquitylome.

systems biology↗