Cilium proteomics reveals Numb as a positive regulator of the Hedgehog signaling pathway

Liu, X.; Pam, P.; Chen, W.-J.; Schlienger, S.; Torres Gutierrez, O.; Cai, E.; Zhang, J.; Ting, A. Y.; Branon, T. C.; Cayouette, M.; Charron, F.; Ge, X.

doi:10.1101/2022.10.10.511655

bioRxiv · 10.1101/2022.10.10.511655

Cilium proteomics reveals Numb as a positive regulator of the Hedgehog signaling pathway

Liu, X.·Pam, P.·Chen, W.-J.·Schlienger, S.·Torres Gutierrez, O.·Cai, E.·Zhang, J.·Ting, A. Y.·Branon, T. C.·Cayouette, M.·Charron, F.·Ge, X.

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Abstract

The transduction of Hedgehog (Hh) signaling relies on the primary cilium, a cell surface organelle serving as a signaling hub for the cell. Using proximity labeling and quantitative proteomics, we identified Numb as a new ciliary protein that positively regulates Hh signaling. Numb localizes to the ciliary pocket and acts as an endocytic adaptor to incorporate Ptch1 into clathrin-coated vesicles, thereby promoting Ptch1 exit from the cilium, a key step in Hh signaling activation. Numb loss hampers Sonic Hedgehog (Shh)-induced Ptch1 departure from the cilium, resulting in reduced activation of Hh signaling. Numb loss in spinal neural progenitors reduces Shh-induced differentiation into Nkx2.2-positive progenitors, a process reliant on high Hh signaling activity. Genetic ablation of Numb in the developing cerebellum impaired the proliferation of granule cell precursors, a Hh-dependent process, resulting in reduced cerebellar size. This study highlights Numb as a critical regulator of Ptch1 levels in the cilium during Hh signal activation and demonstrates the key role of ciliary pocket-mediated endocytosis in modulating the transduction of cell signaling.

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Liu, X., Pam, P., Chen, W.-J., Schlienger, S., Torres Gutierrez, O., Cai, E., Zhang, J., Ting, A. Y., Branon, T. C., Cayouette, M., Charron, F., Ge, X.. 2022-10-11. Cilium proteomics reveals Numb as a positive regulator of the Hedgehog signaling pathway. https://doi.org/10.1101/2022.10.10.511655

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