Intrinsic Diversity In Primary Cilia Revealed Through Spatial Proteomics

Abstract

Primary cilia are solitary filamentous protrusions on most human cells. Our understanding of their function is informed by the study of ciliopathies, hereditary diseases linked to cilia dysfunction. These disorders present a wide array of symptoms, highlighting the tissue-specific roles of cilia. However, cell-state and cell-type specific functions remain poorly understood due to limited tools for analyzing individual ciliary protein composition. Here, we utilize antibody-based spatial proteomics to expand the Human Protein Atlas with a dedicated section for primary cilia. We identify the subciliary locations of 654 proteins across three cell lines, analyzing 218,412 individual cilia. Our findings reveal that 67% of the ciliary proteins are cell-type specific and that 78% of ciliary proteins show heterogeneous localization patterns within cell populations, suggesting that the functional tuning of individual cilia is substantially driven by protein trafficking rather than gene expression. Our atlas portrays the cilium as a dynamic sensory organelle, suggesting that individual cells can fine-tune their ciliary structure - both in terms of receptors and signaling components - to sense and integrate diverse signals, computing a response to relay to the cell body. We identify 71 novel cilia proteins, establish CFAP300 as a specific and broad marker for cilia, and suggest multiple potential ciliopathy genes including CREB3, where we show that a coding genetic variant can be linked to blindness and skeletal abnormalities. In summary, our spatially resolved cilia atlas paves new avenues for basic and clinical research on cilia and ciliopathies.