Intrinsic Diversity In Primary Cilia Revealed Through Spatial Proteomics

Primary cilia are a critical organelle found on most human cells, and their dysfunction is linked to hereditary ciliopathies with diverse symptoms. Despite their significance, the specific roles of cilia in different cell types remain poorly understood due to limitations in analyzing ciliary protein composition. We employed antibody-based spatial proteomics to expand the Human Protein Atlas to primary cilia. Our analysis identified the subciliary locations of 654 proteins across three cell lines, examining 110,844 individual cilia. We found that 67% of the ciliary proteome is cell-type specific, and 78% exhibited dynamically varied localization patterns, indicating that protein trafficking is crucial for ciliary function. Our findings portray cilia as dynamic sensors tuning their proteome to effectively sense the environment and compute cellular responses. We identified 71 novel cilia proteins and linked a genetic variant in CREB3 to typical ciliopathy phenotypes. This open, spatial cilia atlas advances research on cilia and ciliopathies.