Harnessing the cell’s innate power for targeted protein degradation

Researchers have identified the drivers of an extracellular protein degradation pathway, which could be the key to a new generation of therapeutics.

In a recent study, chemists at Stanford University (CA, USA) have uncovered how faulty proteins are marked for destruction. Using a genetic screening approach and proteomics, the researchers identified some of the determinants of targeted protein degradation. Their findings open the door to the development of novel treatment strategies to combat diseases caused by destructive proteins.

Proteins are important to the body’s healthy function but, sometimes, they can become faulty or destructive. Most therapeutics that target faulty or destructive proteins work by blocking the protein’s function, but this is not always effective; some proteins can adapt to no longer be reactive to their normal ‘off-switch’ or are simply too difficult to block.

Targeted protein degradation (TPD) is a promising therapeutic strategy that repurposes machinery within the cell to target faulty proteins for destruction. One such technology, lysosome-targeting chimeras (LYTACs), can precisely mark destructive extracellular proteins or the cell-membrane proteins for delivery to the lysosome, the cell’s main degradation machinery. However, until now, how exactly LYTACs work has been unclear.

In the study, the team at Stanford sought to identify the determinants of protein degradation at the lysosome. Using an unbiased genetic screening approach, the team conducted a genome-wide CRISPR knockout screening combined with various proteomics techniques, including immunoprecipitation and cell surface proteomics, to identify factors that determine targeted protein degradation by LYTACs.

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From the screen, the team identified two pathways that impacted LYTAC-mediated degradation.

Firstly, they found that degradation was blocked by the post-translational modification of proteins with a sugar called mannose-6-phosphate (M6P), which acts as a marker for protein destruction. M6P-modified proteins were found to prevent LYTAC-mediated transport of faulty proteins to the degradation machinery by blocking LYTACs from binding the necessary receptor for internalization, cation-independent mannose 6–phosphate receptor (CI-M6PR). The researchers also observed that, once bound to a receptor and within the cell, LYTACs were recycled by the cell’s retromer complex, taking the LYTAC–CI-M6PR complexes back from the endosome to the cell surface, thereby counteracting their degradation activity.

Surprisingly, the team also identified a link between LYTACs and a housekeeping protein called CUL3. While the relationship between LYTACs and CUL3 is unclear, they found that a higher level of CUL3 was associated with more effective protein degradation by LYTACs. This suggests that CUL3 could be used as an indicator of whether patients are likely to respond well to LYTAC therapy.

This study represents a critical step towards a greater understanding of how targeted protein degradation can be manipulated to improve degradation activity, for example by disrupting the production of mannose-6-phosphate or the cell’s recycling machinery, and will inform the design of next-generation targeting strategies. These findings, therefore, have important implications for the development of novel therapeutics for diseases caused by proteins, such as autoimmune diseases, age-related disorders and lysosomal storage disorders.

“Understanding exactly how proteins are shuttled to lysosomes to be broken down can help us harness the innate power of a cell to get rid of proteins that cause the human body so much harm,” said Carolyn Bertozzi, senior author of the study. “The work done here is a clear look into a typically opaque intracellular process, and it’s shining a light on a new world of possible drug discovery.”