Mapping and Therapeutic Hijacking of Lysosomal Transport

PROJECT SUMMARY/ABSTRACT
The mammalian cell surface proteome (surfaceome) is a hub of communication that transmits information
from the extracellular space to the intracellular machinery, controlling proliferation and cell fate. A major
regulatory endpoint of the surfaceome and extracellular proteome is the lysosome. As the primary organelle for
breaking down various macromolecules, lysosomes are central to nutrient sensing, storage and distribution, as
well as modulating cell surface protein abundance. The transport of membrane and secreted proteins from the
extracellular space to lysosomes occurs through many discrete processes, including autophagy, endocytosis,
and pinocytosis. Given the critical roles of the surfaceome and lysosomes in integrating signals from the
extracellular space, the trafficking between these two compartments is highly regulated across different cell types
and in response to specific cues. Dysregulation of this trafficking is a hallmark of cancer and neurodegenerative
diseases that disrupts the homeostatic balance between cell surface protein function, recycling, and lysosomal
degradation. While an understanding of all proteins which move between the extracellular space and lysosomes
remains incomplete, this pathway has proven transformative for targeted drug delivery and new therapeutic
modalities like targeted protein degradation.
An atlas of all potential proteins which can be used as lysosome targeting moieties in specific contexts
would substantially expand therapeutic options for numerous diseases. However, a lack of methods for studying
surface-to-lysosome trafficking in organ and cell-type specific ways has limited our ability to rationally hijack this
pathway for translational applications. What is needed is a functional map across tissues, time, and disease
states for identifying potential receptors that could be used to drive targeted protein degradation, as well as more
broadly enable widespread utilization of selective trafficking pathways. In this proposal, I describe an innovative
approach which unites whole lysosome isolation from distinct mouse tissues with chemoproteomics to identify
proteins that traffic to lysosomes from the plasma membrane and extracellular space. We propose to map across
tissues and time the transport of extracellular proteins to lysosomes both in healthy tissues and in murine tumor
models. By correlating these in vivo discovery efforts with a novel high-throughput method for in vitro analysis of
lysosome translocation kinetics, we will facilitate the rational utilization of new trafficking proteins. We go on to
propose conceptual advances in designing ligands to harness lysosomal transport for targeted degradation of
disease-causing extracellular proteins using de novo protein design. Finally, we propose a new approach to
immunotherapy that directly translates our in vivo, in vitro, and ligand development efforts via lysosome targeting
chimeras (LYTACs) that selectively degrade immune checkpoint proteins from cancer cells. The outcomes of
this proposal will help revolutionize therapeutic design and drug delivery by mapping the scope and function of
extracellular-to-lysosome communication.

Grant Number: 1DP2GM154016-01
NIH Institute/Center: NIH
Principal Investigator: Steven Banik