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The Hedgehog signaling pathway involves three key players: the lipid-modified active Hedgehog ligand that acts as a local mediator, the Patched transmembrane protein that serves as the receptor for the Hedgehog ligand, and Cubitus Interruptus (Ci), a transcription regulator that acts as the primary effector molecule controlling gene expression.

Without Hedgehog ligand, Patched represses Smoothened protein activity, causing three kinases—PKA, GSK3, and CK1—to phosphorylate Cubitus Interruptus. This marks it for proteasomal processing into Ci75, a cleaved repressor form that translocates to the nucleus and blocks expression of Hedgehog-responsive genes.

Upon Hedgehog ligand binding to Patched and its co-receptor iHog, the Smoothened protein becomes activated and translocates from internal cell vesicles to the cell membrane. Smoothened then recruits the multiprotein complex to the membrane, interrupting the proteolysis of Cubitus Interruptus and allowing intact Ci to activate target genes.

While Drosophila has only one Hedgehog protein, mammals have three functional homologous proteins—Sonic (Shh), Desert (Dhh), and Indian Hedgehog (Ihh)—each specialized for different developmental processes. Additionally, mammalian Hedgehog signaling depends on the primary cilium, a microtubule-based organelle on vertebrate cell surfaces, unlike invertebrate signaling.

The primary cilium is a microtubule-based organelle present on most vertebrate cell surfaces that is essential for mammalian Hedgehog signaling. Unlike invertebrate Hedgehog signaling, mammalian cells rely on this ciliary structure to properly transduce the Hedgehog signal and regulate downstream gene expression.

Unrestricted or disrupted Hedgehog signaling during embryogenesis causes severe developmental abnormalities. Abnormalities in the Hedgehog signaling pathway and associated diseases include pancreatic, lung, prostate, breast, and brain cancers, as well as other developmental disorders, making the Hh pathway a valid therapeutic target.

Hedgehog signaling is essential for stem cell regeneration, which maintains and regenerates adult tissues throughout life. Beyond embryonic organ development, active Hh signaling supports the continuous renewal of tissues, making it critical for long-term tissue homeostasis and preventing degenerative conditions.