Quantifying protein and cell lifetimes in vivo to understand (pathological) aging

Abigail (Abby) Buchwalter, Ph.D., Assistant Professor, University of California, San Francisco

The cellular proteome undergoes constant cycles of synthesis, folding, and degradation. “Proteostasis” (protein homeostasis) is achieved by the balance of these processes. When these systems function properly, the health of the proteome is ensured by the efficient clearance of misfolded or damaged proteins and replacement with properly folded and functional copies. When these systems break down during the aging process, proteostasis defects including protein misfolding and toxic aggregation occur. Measurements of protein turnover have revealed that proteins proceed from synthesis to degradation at widely varying rates. In fact, protein lifetimes range from minutes to years! We still understand very little about the factors that control protein lifetime in healthy tissues, and it remains unclear why age-linked decreases in protein function seem to manifest only in some tissues, but not others.

Some studies have explored protein lifetimes in vivo and have observed wide variation across tissues, suggesting that contextual factors influence protein stability. It could be that variable rates of cell division underlie the observed variation in protein lifetime across tissues. Alternatively, other factors such as the activity of protein folding chaperones, the proteasome, or autophagic degradation pathways could influence protein lifetimes in tissue-specific ways. 

We set out to define the extent to which cell division versus independent factors influence protein turnover. To do this, we devised mass spectrometry-based methods to quantify both cell and protein lifetimes in mammalian tissues in parallel, using pulsed 15N stable isotope labeling in mammals (SILAM). We found that protein and organelle lifetimes vary widely across healthy tissues even after correcting for cell proliferation rates. While the origin of these differences remains unknown, this observation indicates that proteostasis is controlled in protein- and tissue-specific ways. 

To model the effects of aging on proteostasis, we applied our methods to a pathological accelerated aging disease, Hutchinson-Gilford progeria syndrome. These experiments revealed global alterations to proteostasis in this disease, and also helped us to understand how the HGPS-causative disease mutant exerts its toxic effects in specific tissues. 

Bio

Abby grew up in the Hudson Valley region of New York before attending Hope College as Chemistry major / Mathematics minor (class of ’05). During her time at Hope, she worked in Dr. Maria Burnatowska-Hledin’s lab and fell in love with cell biology. After graduating from Hope, Abby enrolled in graduate school at Washington University in St. Louis, where she obtained her Ph.D. in Biochemistry in 2011 (working in the lab of Dr. Phyllis Hanson). From there she continued her migration west and moved to San Diego to do postdoctoral work in Dr. Martin Hetzer’s lab at the Salk Institute from 2011-2018. Most recently, Abby transitioned to a tenure-track faculty position at the University of California, San Francisco, in 2018. Abby’s research has focused on understanding the dynamic regulation of cellular organization, using tools ranging from microscopy to genomics and proteomics.