Advanced proteomics and microscopy to investigate protein trafficking in the endolysosomal system and its links with neurodegeneration

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Defects in the endolysosomal system are strongly linked to neurodegeneration and correct trafficking of proteins between endocytic organelles is essential for healthy ageing. The adaptor protein complex family of vesicle adaptors (AP-1 to AP-5) act as central trafficking controllers, by selecting cargo and coordinating machinery to build vesicles. AP-5, the most recently discovered AP complex, is implicated in protein recycling at late endosomes/lysosomes and its recruitment is enhanced under starvation conditions (Hirst et al., 2021). Furthermore, AP-5-deficient cells have lysosomal and autophagy defects, and loss of AP-5 in humans leads to neurodegeneration, suggesting that AP-5 may play a role in protecting neurons from stress- or age-induced damage (Khundadze et al., 2019). Despite its importance for neuronal health, the cargo proteins of the AP-5 vesicle pathway are poorly defined, particularly under stress conditions.The goal of this project is to identify and characterise AP-5 vesicle cargo proteins under basal and starvation conditions and to investigate the role of AP-5 cargo missorting in lysosomal and autophagic dysfunction. Ultimately, this will further our understanding of how protein trafficking in the endolysosomal system maintains a healthy cell and how defects in this pathway lead to neurodegeneration.You will be trained in cutting-edge proteomics and cell biology approaches, including mass spectrometry-based spatial proteomics (Davies et al., 2018), proximity labelling (Kubitz et al., 2022), CRISPR/Cas9-mediated gene editing, functional cell biology assays, and advanced quantitative microscopy (Han et al., 2020). You will use these methods to identify AP-5 cargo proteins, visualise AP-5 vesicle trafficking in cells and test whether specific AP-5 cargo proteins are required for normal lysosomal function and autophagy.