We are interested in how unwanted cellular structures are eliminated from the cell. Specifically, we are most interested in autophagy. Autophagy is an intracellular degradation and recycling pathway that removes large, potentially toxic structures - such as damaged organelles or toxic protein aggregates. Defects in autophagy allow for the accumulation of toxic structures and contribute to many human diseases including neurodegeneration, cancer, cardiovascular disease, and aging. A better understanding of autophagy mechanisms will inform our understanding of how autophagy becomes dysregulated in disease and guide therapeutic attempts to ameliorate these deficiencies.
We apply a broad variety of cellular and biochemical approaches to understand autophagy mechanisms at a molecular level.
Ongoing projects in the lab include:
A) Selective autophagy in mammalian cells
Many early studies on autophagy were conducted under the premise that autophagy is a largely nonselective process. Indeed, during periods of starvation or stress, autophagosomes nonselectively deliver bulk cytoplasm to the lysosome to regenerate biosynthetic precursors. In other conditions, however, autophagosomes can surgically target specific components – such as protein aggregates or damaged organelles – through a process known as selective autophagy. We are interested in the targets of selective autophagy, the receptors that recognize these targets, the mechanism(s) of target recognition, and ways we can exploit selective autophagy to develop better therapeutics.
B) Alternative forms of autophagy
While autophagy comes in many flavors, macroautophagy is typically afforded the most attention. Even within macroautophagy, there are alternative (non-canonical) forms that are induced under varying conditions. We are working to elucidate the substrates, mechanism(s) and physiological significance of these alternative pathways.
C) In vitro reconstitution of autophagy
The genetic requirements for canonical autophagy have been largely defined. And yet, the ability to turn this “parts list” into meaningful mechanism has been slow. Biochemical reconstitution allows us to study autophagy under defined conditions isolated from the complex environment of the cell. Reconstitution-based approaches have a notable history of providing mechanistic insight, particularly for vesicle trafficking where reconstitution has been essential for dissecting other trafficking pathways.
D) Genome-wide CRISPR screening
We use genome-wide CRISPR screens to identify novel regulators of autophagy, endolysosomal trafficking, and membrane dynamics. These unbiased genetic approaches allow us to systematically probe cellular pathways and to discover unexpected links between autophagy, lysosomal biology, and broader aspects of cell physiology. Hits from these screens form the basis for detailed mechanistic studies using biochemical, imaging, and reconstitution assays.
E) Mechanisms of endolysosomal membrane fusion
Endolysosomal trafficking culminates in membrane fusion events driven by SNARE proteins and their regulators, such as the HOPS complex. We investigate how SNARE redundancy contributes to pathway robustness, how tethering complexes coordinate fusion, and how novel regulators modulate SNARE-mediated membrane fusion. These studies aim to reveal fundamental principles of membrane dynamics and their integration with degradative and signaling pathways.