Probing the proteome-wide impact of inhibitors of Leucine-rich Repeat Kinases 1 and 2 on protein-protein interactions and phosphorylation

The Leucine-rich repeat kinases 1 and 2 (LRRK1 and 2) are large, multidomain proteins and closely related members of the Roco protein family. They share a high similarity in domain structure and are both phosphorylate members of the Rab GTPase family. However, despite these similarities, there are substantial differences between the two kinases. While mutations to LRRK1 are only implicated in rare cases of osteopetrosis, LRRK2 is associated with multiple diseases, most prominently with familial and sporadic forms of Parkinson’s disease, where pathogenic LRRK2 is associated with an increased kinase activity. While LRRK2 has received major attention from the research community, LRRK1 has been largely understudied. In this work, we employ proximity labelling mass spectrometry in combination with quantitative phosphoproteomics in a model cell line to obtain the cellular interactomes of LRRK1 and LRRK2 and corresponding phosphorylation sites. We then use this dataset to characterize the impact of small molecules targeting both LRRK1 and 2. We identify phosphorylation sites across the proteome that are impacted by these inhibitors and identify novel candidate substrates for LRRK2, including MICALL2. Taken together our data provide a powerful resource for future studies on the cellular role and function of LRRK proteins and their potential use as therapeutic targets.