Context-dependent ciliary regulation of hedgehog pathway repression in tissue morphogenesis

A fundamental problem in tissue morphogenesis is identifying how subcellular signaling regulates mesoscale organization of tissues. The primary cilium is a paradigmatic organelle for compartmentalized subcellular signaling. How signaling emanating from cilia orchestrates tissue organization-especially, the role of cilia-generated effectors in mediating diverse morpho-phenotypic outcomes-is not well understood. In the hedgehog pathway, bifunctional GLI transcription factors generate both GLI-activators (GLI-A) and GLI-repressors (GLI-R). The formation of GLI-A/GLI-R requires cilia. However, how these counterregulatory effectors coordinate cilia-regulated morphogenetic pathways is unclear. Here we determined GLI-A/GLI-R requirements in phenotypes arising from lack of hedgehog pathway repression (derepression) during mouse neural tube and skeletal development. We studied hedgehog pathway repression by the GPCR GPR161, and the ankyrin repeat protein ANKMY2 that direct cAMP/protein kinase-A signaling by cilia in GLI-R generation. We performed genetic epistasis between Gpr161 or Ankmy2 mutants, and Gli2/Gli3 knockouts, Gli3R knock-in and knockout of Smoothened, the hedgehog pathway transducer. We also tested the role of cilia-generated signaling using a Gpr161 ciliary localization knock-in mutant that is cAMP signaling competent. We found that the cilia-dependent derepression phenotypes arose in three modes: lack of GLI-R only, excess GLI-A formation only, or dual regulation of either lack of GLI-R or excess GLI-A formation. These modes were mostly independent of Smoothened. The cAMP signaling-competent non-ciliary Gpr161 knock-in recapitulated Gpr161 loss-of-function tissue phenotypes solely from lack of GLI-R only. Our results show complex tissue-specific GLI-effector requirements in morphogenesis and point to tissue-specific GLI-R thresholds generated by cilia in hedgehog pathway repression. Broadly, our study sets up a conceptual framework for rationalization of different modes of signaling generated by the primary cilium in mediating morphogenesis in diverse tissues. The primary cilium is a minute cellular compartment that functions like an antenna in regulating cellular signaling. Defects in cilia and ciliary signaling disrupts tissue organization. However, how signaling generated by the cilia orchestrates tissue organization is not well understood. The hedgehog pathway is a developmental pathway that is dependent on cilia. In the hedgehog pathway, the GLI transcription factors generate mutually exclusive activators or repressors. The formation of both activators and repressors requires cilia. However, how cilia coordinate these factors in regulating tissue organization is unclear. Here, we studied defects in neural tube and skeletal development in the mouse that we described to result from lack of the ciliary repression of the hedgehog pathway. By studying whether the cilia generated activators or repressors regulated the tissue outcomes, we uncovered distinct modes by which ciliary outputs finally coordinated tissue organization. These modes showed to be from lack of the repressor only, excess activator only, or from dual regulation by lack of the repressor or activator. Lack of cilium specific trafficking also predominantly regulated tissue outcomes from lack of repressor only. Overall, our study uncovers general principles by which primary cilia organize tissue architecture.