Primary cilia function as hubs for signal transduction

Abstract

Primary cilia are solitary, non-motile, microtubule-based organelles that protrude from the surface of most vertebrate cells, functioning as highly specialized sensory and signaling compartments. Architecturally, they comprise the basal body, transition zone, and 9 + 0 axoneme, which together establish a biochemically distinct and selectively permeable domain, spatially segregated from the cytoplasm. This compartmentalization enables primary cilia to integrate and modulate diverse signaling cascades, including Hedgehog, Wnt, Notch, TGF-β/BMP, Hippo, cGAS-STING, calcium, GPCR, and phosphoinositide cascades, thereby coordinating developmental programs, tissue patterning, and homeostatic regulation. Ciliogenesis proceeds through basal body docking to the plasma membrane, vesicle fusion, and axoneme elongation, a sequence precisely orchestrated by bidirectional trafficking machinery of intraflagellar transport (IFT). The dynamic equilibrium between ciliary assembly and disassembly is closely coupled to cell cycle progression and signaling flux. Within the confined ciliary compartment, molecular gating at the transition zone and the polarized trafficking of receptors and effectors confer stringent control over pathway specificity and signal fidelity. Disruption of primary cilia perturbs this spatiotemporal precision, resulting in defective signal integration and a broad spectrum of disorders collectively termed ciliopathies, which range from congenital malformations to metabolic and neoplastic diseases. This review summarizes recent advances in elucidating the structural architecture, biogenesis, and signaling functions of primary cilia, highlighting their critical roles in vertebrate biology and disease.

Introduction

The discovery of cilia probably dates back to 1676, when Antonie van Leeuwenhoek, using a simple microscope, first described tiny, rapidly moving appendages on protozoa, later identified as cilia [1, 2]. For the first time, researchers were able to visualize the intricate organization of ciliary components at nanometer resolution. In 1968, Sorokin identified primary cilia as a structurally distinct form lacking the central microtubule pair, known as the 9 + 0 configuration [3]. By the 1990s, evidence emerged that primary cilia function as crucial signaling hubs rather than merely vestigial structures [4]. The discovery that the Hedgehog (Hh) signaling pathway requires primary cilia revolutionized our understanding of ciliary function in development and disease [5]. Subsequent studies demonstrated that defects in primary cilia underlie a spectrum of genetic disorders collectively termed ciliopathies. These disorders include polycystic kidney disease (PKD), marked by cyst formation due to impaired ciliary mechanosensation; and Bardet-Biedl syndrome (BBS), which affects multiple organ systems; and primary ciliary dyskinesia (PCD), a condition that impairs motile cilia function in the respiratory and reproductive systems [6, 7]. These findings underscored the importance of primary cilia beyond development, linking their dysfunction to a variety of human diseases.

Motile cilia

Cilia are structurally classified into three types: primary cilia, nodal cilia, and motile cilia (Fig. 1A). Motile cilia are specialized microtubule-based organelles with a 9 + 2 microtubule arrangement, consisting of nine outer microtubule doublets surrounding a central microtubule pair. This structural organization enables their active movement, facilitating fluid transport in various tissues, including the respiratory tract, reproductive system, and brain ventricles. All cilia originate from the basal body, a modified centriole that anchors them at the plasma membrane, while their axonemal core is responsible for maintaining their structural integrity and function. In the respiratory epithelium, motile cilia play a crucial role in mucociliary clearance, expelling inhaled particles and pathogens to maintain airway hygiene [8]. In the female reproductive tract, motile cilia within the fallopian tubes are essential for capturing and transporting oocytes toward the uterus [9]. In the male reproductive system, motile cilia lining the efferent ductulus generate fluid turbulence that suspends spermatozoa, prevents aggregation, and facilitates their passage from the testes to the epididymis [10]. In the brain ventricles, motile cilia contribute to circulation of cerebrospinal fluid (CSF), thereby ensuring homeostasis in the central nervous system [11]. The movement of motile cilia is driven by dynein arms, ATP-dependent motor proteins that produce microtubule sliding, leading to ciliary bending and coordinated beating patterns [12]. Proper regulation of ciliary motion relies on multiple molecular mechanisms, including intracellular calcium signaling, planar cell polarity pathways, and intraflagellar transport (IFT) machinery, which ensure precise assembly and function [13].

Fig. 1.

Overview of cilia. A Schematic representation of motile cilium (9+2), nodal cilium (9+0), and primary cilium (9+0), highlighting the arrangement of microtubules and associated structures. B The primary cilium consists of the axoneme, transition zone, and basal body. Anterograde transport (IFT-B complex, kinesin) carries cargo toward the ciliary tip, while retrograde transport (IFT-A complex, dynein) returns cargo to the base. C Transmission electron microscopy of a primary cilium in mouse uterine stromal cell on day 4 of pregnancy (adapted from [26]). Scale bars, 200 nm. D Immunofluorescence of primary cilia in mouse uterine stromal cells (adapted from [27]). The ciliary membrane is labeled with Arl13b (green), basal bodies with γ-tubulin (red), and nuclei with DAPI (blue). Scale bars, 5 μm

Nodal cilia

Nodal cilia, despite possessing a 9 + 0 microtubule structure, are motile owing to the presence of dynein arms, enabling their rotational movement, which is essential for establishing left–right (L-R) asymmetry during vertebrate development [14]. This movement generates a leftward fluid flow within the embryonic node, a phenomenon known as nodal flow, which serves as a critical symmetry-breaking mechanism during early development [15]. The posterior tilt of nodal cilia, rather than a strictly vertical orientation, ensures that their clockwise rotation results in a directed leftward flow, thereby breaking embryonic symmetry [16]. The proper alignment of these cilia is regulated by planar cell polarity (PCP) signaling, which coordinates their orientation across node cells to maintain consistent fluid flow; disruption of this process can lead to defects in L-R patterning, such as situs inversus [17]. The biophysical properties of the nodal environment further contribute to this asymmetry. Theoretical models suggest that the viscosity of the surrounding fluid, in combination with the cilia-driven motion, is sufficient to establish an effective directional flow capable of influencing gene expression and organ positioning [18].

Primary cilia

Primary cilia are microtubule-based, non-motile organelles that protrude from the surface of most vertebrate cells, acting as critical sensory hubs that regulate signal transduction and intercellular communication. Unlike motile cilia, which primarily mediate fluid movement, primary cilia serve as signaling platforms that detect environmental cues and coordinate developmental and homeostatic processes [5]. The structural integrity and dynamic transport mechanisms of primary cilia are essential for proper cellular function, and defects in ciliary signaling are associated with a broad range of disorders, collectively referred to as ciliopathies [6]. Primary cilium assembly initiates at the basal body, which derives from the mother centriole and provides a foundation for axoneme extension. Encircling the base of the cilium is the transition fiber network, which anchors the basal body to the plasma membrane and acts as a gatekeeper by regulating the selective entry of ciliary proteins [19]. Adjacent to this region is the ciliary pocket, a membrane invagination that plays a pivotal role in vesicular trafficking and receptor internalization. It is increasingly recognized as an active site for signal processing, where key receptors, such as those involved in Hedgehog and G protein-coupled receptor (GPCR) pathways, are initially recruited before entering the cilium [20, 21].

Situated above the basal body, the transition zone is a specialized domain characterized by "Y-link" structures that create a selective barrier between the cytoplasm and the ciliary compartment. This zone ensures the proper localization of cilia-specific proteins, such as receptors and transport molecules, while restricting non-ciliary proteins from entering the cilium [19]. Extending from the transition zone, the axoneme constitutes the core structural framework of the cilium and is composed of a "9 + 0" arrangement of microtubule doublets. Within the axoneme, a highly coordinated intraflagellar transport (IFT) system mediates bidirectional protein trafficking: kinesin motors drive anterograde transport toward the ciliary tip, whereas dynein motors facilitate retrograde transport, returning cargo to the cell body [22, 23]. Signal transduction at the ciliary tip is tightly regulated, as this region serves as a key hub for the accumulation and activation of signaling molecules. Various receptors, including those involved in Hedgehog, Wnt, and GPCR signaling, localize to the ciliary membrane, where they initiate downstream cellular responses [24]. Recent studies have also identified ectosome shedding as a mechanism by which the cilium actively releases extracellular vesicles enriched in signaling components, thereby modulating intercellular communication and maintaining ciliary homeostasis [25] (Fig. 1B-D).

Structure of the primary cilium

Basal body

The basal body is the core structural element of the primary cilium, anchoring it to the plasma membrane and organizing microtubule extension during cilium assembly. Derived from the mother centriole, the basal body shifts from a centrosomal role to a ciliary assembly role during interphase, undergoing structural modifications that allow it to serve as a microtubule-organizing center (MTOC) [13]. The basal body consists of nine microtubule triplets that template for the axoneme’s nine doublets, ensuring the cilium’s structural integrity [28]. A defining feature of the basal body is the presence of distal and subdistal appendages that mediate ciliary docking and vesicular trafficking. Distal appendages (transition fibers) project from the basal body to tether the cilium to the plasma membrane, marking the onset of ciliogenesis. They also function as docking sites for vesicles carrying ciliary membrane components; regulators such as Rab8 and EH domain-containing protein 1 (EHD1) direct delivery of proteins required for axoneme elongation and membrane expansion [29]. Subdistal appendages, located near the proximal end of the basal body, anchor cytoplasmic microtubules and recruit motor proteins such as dynein, thereby promoting microtubule stability and ciliary trafficking [30]. Beyond architecture, the basal body functions as a regulatory hub for ciliogenesis and signaling. It also acts as a selective barrier, controlling protein entry into the ciliary compartment through intraflagellar transport (IFT) and transition zone gating mechanisms [19]. Additionally, the basal body is dynamically linked to the cell cycle; it must disengage from the cilium before mitotic entry, reflecting its dual role in centrosome and ciliary function [31].

Transition zone

The transition zone (TZ) is a specialized domain positioned between the basal body and the axoneme, functioning as a molecular gate that governs the selective transport of proteins and lipids between the cytoplasm and the ciliary compartment. This selective gating mechanism is critical for preserving the unique protein and lipid composition of the ciliary membrane, permitting the entry of essential signaling molecules while preventing non-ciliary proteins from accessing the cilium. The transition zone contains electron-dense Y-linkers that connect the microtubule doublets of the axoneme to the ciliary membrane, forming a diffusion barrier that is essential for ciliary compartmentalization [32]. Beyond these structural features, the transition zone is enriched with Meckel syndrome (MKS) and nephronophthisis (NPHP) protein complexes, which further refine the regulation of ciliary composition and signaling dynamics [33].

The MKS complex, comprising proteins such as MKS1, TMEM67 (also known as Meckelin or MKS3), B9D1, and CC2D2A, is indispensable for the formation and maintenance of the transition zone. These proteins help establish the molecular architecture of Y-linkers and contribute to the recruitment of additional structural and signaling components necessary for ciliary function [34]. Mutations in MKS genes are directly associated with MKS, a severe ciliopathy characterized by cystic kidney disease, polydactyly, and neural tube defects, demonstrating the critical role of the transition zone in human development [35]. Similarly, the NPHP complex, composed of proteins such as NPHP1, NPHP4, IQCB1 (NPHP5), and CEP290 (NPHP6), play a crucial role in ciliary protein trafficking and axoneme stability. Defects in this complex cause nephronophthisis (NPHP), a disorder marked by progressive kidney fibrosis and end-stage renal disease due to impaired ciliary function in renal epithelial cells [36]. The functional interplay between the MKS and NPHP complexes safeguards the fidelity of ciliary signaling, emphasizing the importance of the transition zone as a central regulatory hub.

Beyond its structural role, the transition zone is also instrumental in coordinating intraflagellar transport (IFT), a bidirectional trafficking system responsible for delivering and recycling proteins within the cilium. It also serves as a regulatory checkpoint for ciliary GPCRs, ion channels, and receptor tyrosine kinases, all of which are essential for diverse developmental and physiological processes [37]. Disruptions in this regulatory function have been implicated in a range of ciliopathies, including Joubert syndrome (JS), a disorder marked by neurological impairments arising from aberrant ciliary signaling in the cerebellum [33].

Axoneme

The axoneme forms the cytoskeletal core of the primary cilium, extending from the basal body to provide structural integrity. Unlike motile cilia, which typically exhibit a 9 + 2 microtubule arrangement, the primary ciliary axoneme adopts a 9 + 0 configuration, consisting of nine outer microtubule doublets without a central pair [4, 5]. The absence of a central microtubule pair is a defining characteristic that distinguishes primary cilia from motile cilia and aligns with their non-motile, sensory function. The axoneme is anchored to the basal body, which is derived from the mother centriole of the centrosome.

Axonemal microtubules are built from α- and β-tubulin heterodimers that undergo post-translational modifications, such as acetylation, polyglutamylation, and detyrosination, which regulate microtubule stability and motor protein interactions [38]. These modifications modulate IFT and signal transduction within the primary cilium. Axonemal assembly and maintenance depend on IFT, a conserved bidirectional transport mechanism essential for ciliary growth, maintenance, and signaling. IFT-A and IFT-B complexes coordinate the trafficking of axonemal proteins, receptors, and signaling molecules [21]. Mutations in IFT components lead to ciliary assembly defects and ciliopathies, underscoring the importance of axonemal maintenance.

Ciliary membrane

The ciliary membrane is a specialized extension of the plasma membrane that surrounds the axoneme and serves as a crucial platform for signaling pathways. Unlike the bulk plasma membrane, the ciliary membrane has a distinct lipid and protein composition that is tightly regulated to maintain the compartmentalization of signaling molecules [39]. This unique environment allows the primary cilium to act as a sensory organelle, integrating extracellular cues to regulate development, tissue homeostasis, and cellular responses [40]. A defining feature of the ciliary membrane is its enrichment in specific lipids, particularly cholesterol and sphingolipids, which promote the formation of lipid rafts that regulate protein localization and signal transduction [41]. In addition, the phosphoinositides (PIPs) composition, including PI(4)P and PI(4,5)P₂, plays a key role in regulating protein trafficking and ciliary function [42]. Perturbations in these lipids can impair receptor localization and contribute to ciliopathies, such as Bardet-Biedl syndrome [43].

The ciliary membrane harbors a highly selective repertoire of transmembrane proteins, including GPCRs, Hedgehog pathway components, and Wnt regulators, all of which are critical for cellular communication. Several GPCRs, such as dopamine receptor 1 (D1R), serotonin receptor 6 (5-HT6R), and somatostatin receptor 3 (SSTR3), localize specifically to the ciliary membrane, where they regulate neuronal signaling and sensory processing [24]. In the Hedgehog (Hh) signaling pathway, the ciliary membrane is the dynamic localization site where Patched1 (Ptch1) and Smoothened (Smo), facilitating signal transduction that governs cell fate determination and tissue patterning [44]. Similarly, Frizzled receptors (Fz) and Disheveled (Dvl) localize to the ciliary membrane to regulate both canonical and non-canonical Wnt signaling, thereby influencing cell polarity, proliferation, and organogenesis [5].

Ciliary tip

The ciliary tip is a specialized region at the distal end of the cilium, serving as the principal site for axonemal extension and ciliary assembly. Ciliary growth predominantly occurs at the tip, where new microtubule subunits are incorporated to achieve controlled elongation [45]. This tip functions as a molecular convergence hub where signaling molecules accumulate, interact, and undergo modifications before initiating cellular responses. Its dynamic organization is tightly regulated by IFT complexes, ensuring the proper localization, recycling, and degradation of key signaling proteins. Given its central role in cellular communication, impaired regulation of the ciliary tip is associated with developmental disorders and ciliopathies. Recent studies have revealed a network of interacting proteins at the ciliary tip that promote slow, processive microtubule elongation while preventing excessive polymerization or disassembly. Among them, CEP104, CSPP1, TOGARAM1, CCDC66, and ARMC9 are key regulators of microtubule dynamics, ciliary structural stability, and signal processing [46].

CEP104, a tubulin-binding protein containing a TOG domain, localizes to the ciliary tip and plays a fundamental role in ciliogenesis. It interacts with microtubules and acts as a positive regulator of their growth, promoting controlled extension at the ciliary tip. In contrast, CSPP1, a binding partner of CEP104, acts as a negative regulator, restricting microtubule elongation to prevent excessive elongation and premature depolymerization. This opposing regulation is essential for maintaining ciliary integrity and supporting IFT [47]. TOGARAM1 serves as a counterbalancing factor that alleviates their inhibitory effects. This TOG-domain-containing protein promotes controlled microtubule extension, ensuring that the cilium maintains its functional length while avoiding unregulated growth [46]. Dysfunction of TOGARAM1 disrupts the balance of microtubule dynamics at the ciliary tip, resulting in defects in ciliary length and ciliopathy-related disorders such as Joubert syndrome [48].

Intraflagellar transport (IFT)

The IFT system consists of two distinct protein complexes, IFT-B and IFT-A, which function with opposing motor proteins to drive bidirectional transport. IFT-B mediates anterograde transport, moving cargo from the basal body to the ciliary tip through kinesin-2 motors to deliver components required for axoneme elongation and ciliary maintenance [49]. The IFT-B complex contain multiple subunits, including IFT88, IFT81, and IFT74, that facilitate cargo loading and transport [23]. Anterograde transport relies on two types of kinesin-2 motors: the heterotrimeric kinesin-2 complex (KIF3A/KIF3B/KAP3), responsible for most cargo movement, and the homodimeric kinesin family member 17 (KIF17), which is involved in specialized transport such as receptor localization [50, 51]. Early studies on ciliary and flagellar assembly revealed that axonemal growth occurs through the addition of precursor proteins at the distal tip rather than the base, implying the existence of a specialized transport system that delivers structural and functional components from the cytoplasm to the ciliary tip [52].

Upon reaching the ciliary tip, IFT particles detach from kinesin motors, facilitating cargo unloading. These components are then reorganized into the IFT-A complex and transported back to the basal body by dynein-2, ensuring continuous renewal of ciliary proteins and removal of excess materials [53]. The IFT-A complex mediates retrograde transport, returning recycled proteins, signaling components, and excess materials from the ciliary tip to the basal body via dynein-2 motors [54]. IFT-A consists of IFT144, IFT140, IFT139, IFT122, IFT121, and IFT43, which assemble into a cargo-binding structure that interacts with dynein-2 [55]. Dynein-2, the motor driving retrograde transport, is a multi-subunit complex composed of DYNC2H1 along with associated light and intermediate chains, which propel IFT particles along the axoneme [56, 57]. Proper retrograde transport is crucial to prevent the accumulation of misfolded proteins and signaling molecules within the cilium, which would otherwise compromise its function. Defects in IFT result in a spectrum of ciliopathies, including Bardet-Biedl syndrome (BBS), Jeune syndrome, and short-rib polydactyly syndrome (SRPS). In BBS, mutations in BBS genes impair BBSome assembly, disrupting IFT-dependent GPCR trafficking. This results in defective ciliary signaling, manifesting in phenotypes such as retinal degeneration, obesity, and kidney dysfunction [43].

Biogenesis and dynamics of the primary cilium

Ciliogenesis

Ciliogenesis is a highly regulated, stepwise process that primarily occurs in quiescent cells during the G0/G1 phase of the cell cycle. It involves the conversion of the mother centriole into the basal body, followed by axoneme extension and ciliary membrane formation. Primary cilium formation proceeds via two major pathways: intracellular ciliogenesis and extracellular ciliogenesis [20, 58, 59] (Fig. 2A).

Fig. 2.

Regulation of primary cilium formation and dynamics. A Model of primary cilium biogenesis. The primary cilium formation begins with the docking of mother centrioles to the plasma membrane, facilitated by ciliary vesicle precursors. Subsequent vesicle fusion generates the ciliary vesicle, which wraps around the distal end of the mother centriole to form the ciliary sheath. As the ciliary membrane elongates, the axoneme extends, giving rise to a mature cilium. IFT mediate bidirectional trafficking within the cilium: anterograde IFT support axoneme extension, whereas retrograde IFT recycles and turns over ciliary components. B Ciliary assembly and disassembly. The dynamic balance between ciliary assembly and disassembly is regulated by coordinated signaling and structural proteins. Ciliary disassembly is initiated by Aurora A (AurA)-mediated phosphorylation, with HDAC6 promoting axonemal microtubule destabilization. Additional regulators such as Nek2, KIF2A, and PLK1 facilitate ciliary resorption in response to extracellular cues, including Wnt and calcium signaling. Conversely, ciliary assembly requires CEP164, TTBK2, and Rab GTPases, which orchestrate basal body maturation and removal of inhibitory components such as CP110. Tight regulation of these processes is essential for proper cell cycle progression and ciliary signaling

In the intracellular pathway, ciliogenesis begins with the maturation of the mother centriole, which acquires distal and sub-distal appendages, allowing its conversion into the basal body [60]. The basal body then serves as a microtubule-organizing center (MTOC) for developing cilium. Pre-ciliary vesicles, derived from the trans-Golgi network (TGN) and endocytic compartments, are recruited to the basal body [29]. These vesicles fuse to form a ciliary vesicle that encapsulates the distal end of the basal body, thereby isolating it from the cytoplasm [58]. As this vesicle enlarges, it extends to form the ciliary sheath and ciliary shaft. Ultimately, the ciliary vesicle fuses with the plasma membrane, generating a specialized ciliary pocket [61]. Once anchored at the plasma membrane, the cilium extends through coordinated IFT, which facilitates bidirectional trafficking of ciliary components. Anterograde transport, driven by kinesin motors, delivers structural and signaling proteins from the basal body to the ciliary tip, whereas retrograde transport, powered by dynein motors, recycles ciliary components and removes damaged proteins [13]. In contrast, extracellular ciliogenesis bypasses ciliary vesicle formation. Instead, the basal body directly docks to the apical plasma membrane, allowing axonemal extension without generating a ciliary pocket [20]. This mode of ciliogenesis is predominantly observed in epithelial cells. After basal body anchoring, axonemal elongation proceeds, with bidirectional IFT-mediated transport ensuring accurate assembly of ciliary components.

Mutations in genes encoding ciliary proteins cause ciliopathies, a diverse group of disorders affecting multiple organ systems [6]. Bardet-Biedl Syndrome (BBS) is a well-characterized ciliopathy manifested obesity, polydactyly, retinal degeneration, and kidney abnormalities. Meckel-Gruber Syndrome (MKS) is a severe, often lethal condition associated with neural tube defects and renal cystic dysplasia. Polycystic Kidney Disease (PKD), caused by mutations in PKD1 or PKD2, results in kidney cyst formation and progressive renal dysfunction. Primary Ciliary Dyskinesia (PCD) affects motile cilia, leading to chronic respiratory infections and fertility impairment. The broad effects of ciliopathies highlight the essential role of cilia in human health and development.

Ciliary assembly and disassembly

The dynamic balance between ciliary assembly and disassembly is crucial for maintaining cellular homeostasis, and its disruptions is linked to ciliopathies, cancer, and developmental disorders. Understanding these mechanisms provides valuable insights into potential therapeutic strategies for diseases arising from defective ciliary dynamics [62] (Fig. 2B).

Ciliary disassembly is triggered by activation of Aurora A (AurA), a serine/threonine kinase that plays a pivotal role in promoting cilium resorption. AurA is activated by upstream regulators such as HEF1, calmodulin (CaM), calcium, Pifo, and trichoplein, which promote its phosphorylation and recruitment of histone deacetylase 6 (HDAC6) [63, 64]. HDAC6 deacetylates axonemal tubulin, causing microtubule destabilization and initiating ciliary breakdown. Additionally, Kinesin-13 family members KIF2A and KIF24, as well as Nek2 and OFD1, contribute to ciliary disassembly by severing axonemal microtubules and remodeling the basal body structure [64, 65]. Ciliary disassembly is further coupled to mitotic progression through PLK1 activity, which is regulated by Dvl2 and Wnt5a. PLK1 phosphorylates microtubule-associated proteins, facilitating axonemal disassembly and ensuring timely ciliary resorption prior to mitosis [66]. Loss of ciliary acetylation marks the completion of disassembly, allowing the transition from a ciliated, quiescent state to an actively dividing state.

Following mitosis, cilium assembly is initiated as the mother centriole transitions into the basal body, a process that requires removal of inhibitory proteins such as CEP97 and CP110 [67]. Recruitment of Tau Tubulin Kinase 2 (TTBK2) to the basal body facilitates this transition by phosphorylating substrates essential for axoneme elongation [68]. CEP164, a key distal appendages protein, anchors the basal body to the plasma membrane, thereby marking the onset of ciliogenesis [69]. Microtubule stabilization, a key step in cilium formation, is regulated by CRL3-KCTD17, which promotes tubulin acetylation and axonemal extension [70]. Rab GTPases mediate the trafficking of ciliary membrane components by directing vesicular transport to the ciliary base, ensuring proper membrane elongation [43]. Additionally, the APC-Cdc20 complex coordinates centrosome positioning and promotes the early stages of cilium assembly [71].

Signaling pathways orchestrated by primary cilia

Primary cilia are microtubule-based organelles that extend from the surface of most mammalian cells, serving as specialized hubs for cellular signaling [5]. Acting as cellular antennae, they sense and transduce extracellular signals, orchestrating key developmental, homeostatic, and pathological processes. Unlike motile cilia, which are involved in fluid movement, primary cilia are primarily dedicated to signal transduction, acting as compartmentalized domains where signaling molecules are dynamically regulated [4]. Primary cilia coordinate multiple signaling pathways, including Hedgehog, Wnt, Notch, TGF-β/BMP, Hippo, cGAS-STING, calcium, GPCR, and Phosphoinositide signaling. The ciliary membrane selectively enriches receptors and effectors for these pathways, thereby ensuring spatiotemporal control of cellular responses [72].

Hedgehog

The Hedgehog (Hh) pathway is a cilia-dependent signaling cascade crucial for embryonic development, stem cell maintenance, and tissue homeostasis [73]. In the absence of Hedgehog ligands, Patched 1 (Ptch1) is localized to the ciliary membrane, where it block Smoothened (Smo) from entering the cilium, thereby maintaining pathway inactivity [44, 74]. Concurrently, GPR161, a ciliary-localized G-protein-coupled receptor, stimulates cAMP production, which activates Protein Kinase A (PKA). Activated PKA phosphorylates full-length GLI (GLI^FL) and promotes its proteolytic processing into the repressor form (GLI^R), which translocate to the nucleus to inhibit Hedgehog target gene transcription [75, 76]. In parallel, Suppressor of Fused (Sufu) binds GLI proteins, preventing their activation and further reinforcing pathway suppression [77, 78]. Additionally, Tulp3 and the IFT-A complex, core components of the IFT machinery, facilitate the trafficking of negative regulators such as GPR161, thereby ensuring robust pathway repression [55, 76].

In mammals, the Hh family consists of three members: Sonic Hedgehog (SHH), Indian Hedgehog (IHH), and Desert Hedgehog (DHH), among which SHH is the most extensively studied [79]. Upon ligand binding, Hh proteins engage PTCH1, triggering its removal from the cilium and allowing SMO to enter. SMO then accumulates within the ciliary membrane and undergoes conformational changes that initiate downstream signal transduction [5, 44]. This event inactivates GPR161, causing reduced cAMP levels and consequent suppression of PKA activity. As a result, the proteolytic processing of GLI into its repressor form (GLI^R) is prevented, enabling the accumulation of GLI activators (GLI^A) at the ciliary tip [80]. At the ciliary tip, Kinesin Family Member 7 (Kif7) organizes the ciliary compartment and regulates GLI activation, thereby ensuring precise control of Hh signal transduction [81, 82]. Once activated, GLI^A dissociates from Sufu, exits the cilium, and translocates to the nucleus, where it binds to Hedgehog target gene promoters to drive transcriptional programs essential for developmental and tissue homeostasis [26, 73, 83]. The IFT system plays an indispensable role in the dynamic trafficking of pathway components, ensuring correct localization of Hh signaling molecules and preserving pathway fidelity. IFT-B complexes, together with kinesin-2 motors, mediate anterograde transport of activators such as SMO and GLI proteins, whereas IFT-A complexes and dynein-2 motors facilitate retrograde transport, recycling negative regulators such as GPR161 to the cytoplasm for degradation or reuse [84]. This bidirectional transport system is essential for maintaining ciliary integrity and preventing the accumulation of excess signaling components, thereby ensuring tight regulation of Hh signal transduction (Fig. 3A).

Fig. 3.

Primary cilia serve as central hubs for diverse signaling pathways. A Hedgehog pathway. B WNT pathway. C Notch pathway. D TGFβ/BMP pathway. E Hippo pathway. F cGAS-STING pathway. G Calcium signaling. H GPCR signaling. I Phosphoinositide signaling

WNT

The canonical Wnt pathway is a well-established regulatory mechanism that governs gene transcription, cell fate determination, and tissue homeostasis. In the absence of Wnt ligands, cytoplasmic β-catenin is targeted for continuous degradation by a destruction complex composed of Axin, adenomatous polyposis coli (APC), casein kinase 1α (CK1α), and glycogen synthase kinase 3β (GSK3β) [85, 86]. This complex phosphorylates β-catenin, marking it for ubiquitin-mediated proteasomal degradation and thus preventing it from activating downstream target genes [87]. Upon Wnt ligand binding to Frizzled (FZD) receptors and low-density lipoprotein receptor-related proteins 5/6 (LRP5/6) co-receptors, the receptors complex undergoes a conformational change that recruit and activates Dishevelled (Dvl). Activated Dvl inhibits GSK3β, leading to the stabilization and accumulation of β-catenin in the cytoplasm [88]. β-catenin subsequently translocates into the nucleus, where it interacts with T-cell factor/lymphoid enhancer-binding factor (TCF/LEF) transcription factors to drive the transcription of Wnt target genes involved in cell proliferation, differentiation, and tumorigenesis [89, 90].

In contrast to the canonical Wnt/β-catenin pathway, the non-canonical Wnt pathway operates independently of β-catenin and predominantly regulates cytoskeletal dynamics, cell polarity, cell migration, and calcium signaling. This pathway includes two major branches: Wnt/planar cell polarity (PCP) pathway, which controls asymmetric cell division, convergent extension movements, and epithelial tissue organization [91]. Wnt/Ca^2⁺ pathway, which modulates calcium-dependent signaling processes, including neuronal differentiation and immune responses [92]. Although the non-canonical Wnt pathway is primarily associated with embryonic development, stem cell maintenance, and tumorigenesis, emerging evidence indicates a context-dependent role in ciliogenesis, by either promoting or inhibiting primary cilia formation depending on the cellular environment [93, 94].

Within primary cilia, Wnt signaling suppresses phosphatase 1 (PP1) activity by blocking GSK3-mediated phosphorylation of PPP1R2, a key regulator of PP1. This inhibition of PP1 has been shown to promote ciliogenesis in mouse embryonic neural progenitors, the kidney proximal tubules, and preadipocytes. Notably, while canonical Wnt signaling can either promote or inhibit ciliogenesis depending on cellular context, the intraciliary Wnt-PP1 axis consistently enhances ciliogenesis in a β-catenin-independent manner [5]. A critical discovery is the specific localization of LRP6 to primary cilia, where it serves as a co-receptor for intraciliary Wnt signaling. In contrast to its well-characterized role in the canonical Wnt pathway at the plasma membrane, ciliary LRP6 transduces signals within the cilium independently of nuclear β-catenin activity [95]. These findings suggest that primary cilia function as specialized organelles for Wnt signaling, providing a localized hub for Wnt-GSK3-PP1 interactions. Studies in Ccny/L1-deficient mouse models have shown that disruption of ciliary Wnt pathway leads to severe developmental abnormalities, including neural tube closure defects, kidney dysfunction, and impaired adipogenesis [95, 96]. Additionally, Wnt stimulation enhances phosphorylation of LRP6 within primary cilia, reinforcing the hypothesis that primary cilia act as specialized platforms for Wnt signaling (Fig. 3B).

Notch

The Notch pathway is an evolutionarily conserved cell–cell communication system that plays an essential role in stem cell fate determination, differentiation, and tissue homeostasis [97, 98]. Emerging evidence suggests that primary cilia act as a critical regulatory platform for Notch signaling that ensure the spatial organization and activation of Notch receptors, particularly in epithelial development, neurogenesis, and disease contexts [99, 100]. Notch receptors (Notch1–4) are membrane-bound proteins that interact with Delta-like (DLL1, DLL3, DLL4) and Jagged (JAG1, JAG2) ligands on neighboring cells, leading to receptor activation [101]. In the context of ciliary regulation, studies have shown that Notch3 localizes to the ciliary membrane, where ligand binding triggers a sequential cleavage process mediated by Presenilin-containing γ-secretase complex [99]. Upon ligand binding, Notch3 undergoes proteolytic cleavage, first by ADAM metalloproteases and subsequently by γ-secretase, resulting in the release of the Notch intracellular domain (NICD) [102]. The NICD then translocates into the nucleus, where it interacts with the Recombination Signal Binding Protein for Immunoglobulin Kappa J Region (RBPJ) transcriptional complex to drive the expression of Notch target genes, such as Hes1 and Hey1, which govern cell fate decisions [103, 104]. Notably, the ciliary localization of Notch3 and its ligands suggests that primary cilia may serve to spatially organize Notch signaling by modulating receptor-ligand interactions and processing efficiency.

Dysregulation of ciliary Notch signaling has been implicated in both developmental disorders and cancers. Mutations in ciliary genes, such as IFT components, TULP3, and ARL13B, disrupt Notch receptor trafficking, leading to aberrant signaling outputs associated with ciliopathies, neural tube defects, and polycystic kidney disease [99]. In the context of cancer, abnormal Notch activation at the cilium has been linked to tumor progression in glioblastoma and medulloblastoma. Understanding the interplay between primary cilia and Notch signaling offers new insights into developmental regulation, disease mechanisms, and potential therapeutic targets (Fig. 3C).

TGFβ/BMP

Transforming growth factor-beta (TGFβ) and bone morphogenetic proteins (BMPs) are key members of the TGFβ superfamily that play crucial roles in embryonic development, tissue homeostasis, and disease pathogenesis [105]. The TGFβ pathway is initiated upon ligand binding to the TGFβ type II receptor (TGFβRII), which then recruits and phosphorylates the TGFβ type I receptor (TGFβRI). This activation results in the phosphorylation of SMAD2/3, which subsequently forms a complex with SMAD4 and translocates into the nucleus to regulate target gene expression [106]. In contrast, the BMP signaling pathway is triggered by the binding of BMP ligands such as BMP2 to the BMP type II receptor (BMPRII), which in turn phosphorylates and activates the BMP type I receptor (BMPRI). This phosphorylation cascade results in the activation of SMAD1/5/8, which also forms a complex with SMAD4 to regulate downstream gene expression [107]. Although these pathways operate in distinct biological processes, both converge on SMAD4, highlighting a shared transcriptional regulatory mechanism.

Primary cilia have emerged as specialized organelles that mediate TGFβ and BMP signaling, providing a spatially confined environment that modulates receptor activation and downstream signaling dynamics [5]. Studies have demonstrated that TGFβRI and TGFβRII localize to the primary cilium, where they interact to transduce TGFβ signaling [108]. Similarly, components of the BMP pathway, including BMPRI and BMPRII, have been identified within ciliary compartments, suggesting that primary cilia contribute to the orchestration of BMP-mediated cellular responses [109].

Pulsed electromagnetic fields (PEMFs) were shown to enhance osteogenic differentiation and maturation of rat calvarial osteoblasts (ROBs) by activating BMP signaling in a primary cilium-dependent manner. BMPRII, the primary receptor for BMP ligands, was significantly upregulated following PEMF treatment and was found to be predominantly localized at the base of primary cilia [110]. Recent findings have highlighted the essential role of primary cilia in BMP-mediated skeletogenesis, particularly during heterotopic ossification (HO). Ciliary suppression by deletion of intraflagellar transport 88 (IFT88) or ADP ribosylation factor like GTPase 3 (ARL3) effectively inhibited both normal and pathological BMP signaling [111]. In addition to the role of primary cilia in BMP receptor localization and signaling, FK506-binding protein 1A (FKBP12), a negative regulator of BMP signaling, has been shown to localize at the ciliary base while also being distributed throughout the cytoplasm [111] (Fig. 3D).

Hippo

The Hippo pathway (also known as the Salvador–Warts–Hippo pathway) is essential for organ size control, cell proliferation, and tissue homeostasis, acting primarily by regulation of Yes-associated protein (YAP) and Transcriptional co-activator with PDZ-binding motif (TAZ) [112]. When the Hippo pathway is active, Mammalian STE20-like kinase 1/2 (MST1/2) phosphorylates Large tumor suppressor 1/2 (LATS1/2), which in turn phosphorylates YAP/TAZ. This phosphorylation promotes their interaction with 14–3-3 proteins, leading to cytoplasmic sequestration and preventing nuclear localization [113]. This process suppresses the transcription of Hippo target genes involved in cell proliferation and growth, such as Connective tissue growth factor (CTGF) and Cysteine-rich angiogenic inducer 61 (CYR61) [114].

Studies have uncovered an essential interplay between primary cilia and Hippo signaling, positioning cilia as a key regulatory hub that controls Hippo kinase activity and thus modulates downstream transcriptional responses [112, 115]. At the basal body of the primary cilium, core Hippo components such as MST1/2, LATS1/2, and Salvador homolog 1 (SAV1) interact with cilia-associated proteins, including NPHP4, which serve as upstream regulators of Hippo activation [116]. The NPHP complex plays a critical role in stabilizing Hippo pathway activation at the ciliary base by facilitating the assembly of MST1/2, LATS1/2, and SAV1, thereby ensuring efficient YAP/TAZ phosphorylation and maintaining their cytoplasmic sequestration. Loss of primary cilia disrupts Hippo signaling, leading to YAP/TAZ hyperactivation. Without ciliary regulation of Hippo signaling, unphosphorylated YAP/TAZ translocate into the nucleus, where they induce genes that drive cell proliferation, fibrosis, and tumorigenesis [112].

NIMA-related kinase 8 (NEK8)/NPHP9 is a ciliary kinase localized at the Inversin compartment, a specialized subdomain of the proximal axoneme located distal to the transition zone [117]. Within the primary cilium, NEK8 is targeted to the Inversin (INVS) compartment, where it promotes the recruitment of both phospho-YAP and ANKS6. However, NEK8 loss-of-function mutations disrupt its localization to the ciliary axoneme, as observed in human primary fibroblasts and mIMCD3 cells, thereby altering the composition of the INVS compartment. Specifically, ANKS6/NPHP16 fails to localize at the INVS compartment and loses its interaction with NEK8, further destabilizing the complex. Beyond its role in ciliogenesis, NEK8 is a critical modulator of Hippo signaling. NEK8 mutations impair Hippo activation, resulting in YAP/TAZ nuclear accumulation and aberrant expression of pro-proliferative genes such as CTGF and CYR61. These changes drive excessive cell proliferation, fibrosis, and cystogenesis, as observed in renal cystic dysplasia and polycystic kidney disease (PKD) [118]. In Jck mouse models carrying NEK8 mutations, increased YAP nuclear activity correlates with abnormal epithelial proliferation and cyst formation. Notably, treatment with Verteporfin, a YAP-TEAD inhibitor, partially rescues these phenotypes, confirming NEK8 as a key regulator of cilia-Hippo signaling. Furthermore, another study demonstrated that biallelic ANKS6/NPHP16 mutations disrupt the composition of the INVS compartment, leading to nuclear YAP imbalance, Hippo pathway dysregulation, and ultimately late-onset chronic kidney disease (CKD) [119] (Fig. 3E).

cGAS-STING

The cGAS-STING pathway is a fundamental mechanism for detecting cytosolic DNA and initiating innate immune response. Under normal physiological conditions, DNA is strictly confined to the nucleus and mitochondria, and its presence in the cytoplasm serves as a potent danger signal [120]. Upon detection of cytosolic DNA, cyclic GMP-AMP synthase (cGAS) binds to double-stranded DNA (dsDNA) and catalyzes the synthesis of cyclic GMP-AMP (cGAMP), which subsequently activates the stimulator of interferon genes (STING). STING then triggers a signaling cascade that leads to the production of type I and type III interferons, along with other pro-inflammatory mediators. This pathway is critical for host defense against pathogens; however, aberrant activation in response to self-DNA contributes to chronic inflammation and autoimmune diseases [121, 122].

While the cGAS-STING pathway primarily detects foreign DNA such as that derived from DNA viruses, retroviruses, dead cells and bacteria, it can also be aberrantly activated by self-DNA under conditions of genomic instability, nuclear envelope rupture, or defective DNA clearance. One of the most significant sources of cytoplasmic self-DNA is the formation of micronuclei, which arise from chromosome missegregation during mitosis. Micronuclei are small nuclear structures containing chromatin but often possess a defective nuclear envelope, thereby exposing their DNA to the cytoplasm. cGAS binds to micronuclear DNA, resulting in persistent cGAMP synthesis and chronic immune activation [123, 124]. Another major source of self-DNA is nuclear blebs, chromatin protrusions resulting from nuclear envelope instability, commonly observed in laminopathies, cellular senescence, and DNA repair deficiencies. Rupture of these blebs releases chromatin into the cytoplasm, where it is recognized by cGAS. This process has been implicated in chronic inflammation, autoimmunity, and cancer progression [120].

Primary cilia, which play a crucial role in mechanotransduction, have recently been identified as negative regulators of the cGAS-STING pathway. They maintain nuclear integrity by suppressing Ras homolog family member A (RhoA)-Myosin Light Chain 2 (MLC2)-mediated actomyosin contraction [27]. The transmembrane protein TMEM67, a critical component of the ciliary transition zone [125], is essential for both ciliogenesis and cytoskeletal homeostasis. Loss of ciliary components, such as IFT88 and TMEM67 disrupts ciliary structure and leads to aberrant activation of RhoA, a small GTPase that regulates cytoskeletal dynamics [126]. This results in increased phosphorylation of MLC2 at Ser19 (p-MLC2) and enhanced actomyosin contraction [127], generating mechanical forces that propagate to the nuclear lamina [128]. Consequently, nuclear envelope instability ensues, promoting the formation of micronuclei and nuclear blebs, which serve as major sources of self-DNA in the cytoplasm [126, 128] (Fig. 3F).

Calcium

Fluid flow across the apical surface is detected by the primary cilium, which functions as a mechanosensor converting extracellular mechanical stimuli into intracellular biochemical signals. This mechanotransduction is mediated in part by ciliary calcium influx through mechanosensitive channels such as Polycystin-1 (PC1), Polycystin-2 (PC2), and Transient Receptor Potential Vanilloid 4 (TRPV4) [129, 130]. Ciliary bending triggers the opening of these channels, allowing extracellular calcium to enter the cilium and generate a localized calcium transient [131]. This ciliary calcium signal can trigger immediate cytoplasmic responses but also regulates transcriptional programs via the PC1-Signal Transducer and Activator of Transcription 6 (STAT6)-P100 axis. Upon cessation of fluid flow, PC1 undergoes proteolytic cleavage, allowing the PC1 cytoplasmic tail to translocate into the nucleus, where it interacts with STAT6 and its coactivator P100 to drive STAT6-dependent transcriptional activation [132].

Primary cilia also regulate cell size and mammalian Target of Rapamycin Complex 1 (mTORC1) activity through a calcium-independent mechanism. Boehlke et al. demonstrated that mechanical bending of cilia directly activates Liver Kinase B1 (LKB1), which is localized at the basal body. Activated LKB1 phosphorylates and activates AMPK, thereby forming a cilium-specific LKB1-AMPK axis that inhibits Rheb, a critical activator of mTORC1. This results in mTORC1 suppression and reduced phosphorylation of downstream targets such as S6 kinase (S6K) and 4E-BP1, thereby constraining protein synthesis and limiting cell size [133]. This mechanism ensures that cell growth and metabolism are tightly linked to extracellular mechanical inputs, thereby directly coupling ciliary mechanosensation to metabolic homeostasis (Fig. 3G).

GPCR

Ciliary GPCRs detect a variety of extracellular cues, including neurotransmitters, hormones, and morphogens, and initiate intracellular signaling cascades that regulate cAMP production, protein kinase activation, and gene transcription [21, 24]. The highly ordered spatial organization of GPCRs, heterotrimeric G proteins (Gα, Gβ, Gγ), and adenylyl cyclases (AC3) within the ciliary membrane creates a specialized platform for compartmentalized GPCR signaling [134]. For example, ciliary GPCRs in the central nervous system (CNS) include serotonin receptor 5-HT6 [135], dopamine receptors D1R and D2R [136, 137], melanocortin receptor MC4R [138, 139], melanin-concentrating hormone receptor 1 (MCHR1) [140], and somatostatin receptor SSTR3 [141]. In the kidney, primary cilia express the vasopressin receptor V2R [142], and the receptor for EG-VEGF, PROKR1, has also been detected in primary cilia [143]. This receptor diversity allows cilia to detect and transduce a wide range of physiological signals into context-specific cellular responses. In addition, recent studies have identified several other ciliary GPCRs with tissue-specific roles. In hypothalamic neurons, NPY2R localizes to primary cilia and regulates energy homeostasis, thereby linking ciliary sensory function to feeding behavior [144, 145]. Prostaglandin E receptor 4 (PTGER4) localizes to the primary cilia of many cell types, where it mediates prostaglandin signaling [146, 147]. In cholangiocytes lining the intrahepatic bile ducts, primary cilia function as chemosensory organelles that detect biliary nucleotides through the ciliary purinergic receptor P2Y12. Upon sensing luminal ADP, ciliary P2Y12 triggers a reduction in cAMP signaling, thereby linking bile composition to epithelial secretory responses [148].

The canonical GPCR signaling cascade in primary cilia is initiated by the activation of heterotrimeric G proteins following ligand binding. Depending on the receptor subtype, this activation involves either Gαs or Gαi. Gαs-coupled receptors such as 5-HT6 and MC4R stimulate adenylyl cyclase (AC3 or AC5) to increase cAMP levels [76]. In contrast, Gαi-coupled receptors such as SSTR3 and D2R inhibit cAMP production [149]. This cilia-specific cAMP pool activates protein kinase A (PKA), which phosphorylates downstream targets, including cAMP response element-binding protein (CREB). Phosphorylated CREB translocates into the nucleus, where it binds to cAMP response elements (CRE) elements in gene promoters to initiate transcriptional responses [76]. This cilia-mediated GPCR-cAMP-PKA-CREB axis regulates processes such as neurogenesis, energy balance, and epithelial homeostasis (Fig. 3H).

Phosphoinositide

In primary cilia, the unique lipid composition maintained by tightly regulated phosphoinositide metabolism is fundamental to its sensory and signaling functions [150]. The ciliary membrane and its associated transition zone (TZ) display a specialized distribution of phosphoinositides, defining the cilium as a distinct biochemical compartment [151]. Among these lipids, PI(4)P and PI(4,5)P2 are particularly enriched at the ciliary base and transition zone, serving as gatekeepers that control receptor and effector protein entry into the ciliary compartment [42, 152]. Within the cilium, Inositol polyphosphate-5-phosphatase E (INPP5E), a cilia-localized inositol polyphosphate 5-phosphatase, converts PI(4,5)P2 into PI(4)P, thus limiting excessive accumulation of PI(4,5)P2 within the ciliary shaft.

This phosphoinositide cascade is counterbalanced by two classes of phosphatases. First, Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) dephosphorylates PI(3,4,5)P3 at the 3-position, reverting it back to PI(4,5)P2, which in turn directly opposes Phosphoinositide 3-kinase (PI3K) activity. Second, inositol polyphosphate 5-phosphatases (5-ptases), including INPP5E, Src homology 2 domain containing inositol 5-phosphatase 1 (SHIP1), Src homology 2 domain containing inositol 5-phosphatase 2 (SHIP2), and others, removes the 5-phosphate from PI(3,4,5)P3 to generate PI(3,4)P2. The intermediate lipid PI(3,4)P2 act as a signaling molecule capable of recruiting AKT and other PH domain proteins, although it elicits slightly different downstream responses compared to PI(3,4,5)P3 [153, 154]. INPP5E also converts PI(4,5)P2 into PI(4)P within the ciliary membrane, thereby maintaining low PI(4,5)P2 levels inside the cilium. The phosphoinositide network is closely integrated with ciliary receptor trafficking, particularly for PDGFRα, which resides specifically to primary cilia. Upon ligand stimulation, PDGFRα triggers both PI3K-AKT and MEK-ERK signaling cascades [155]. Notably, PDGFRα localization and activation within cilia depend on IFT20, which mediates its vesicular delivery to the cilium [156, 157]. PDGFRα turnover is further regulated by ubiquitination, mediated by the E3 ligases Cbl-b and c-Cbl, which promote its internalization and degradation. The distinct signaling roles of ciliary PDGFRα and non-ciliary PDGFRβ illustrate how ciliary phosphoinositides define compartment-specific receptor responses. While ciliary PDGFRα regulates morphogenetic and patterning signals, plasma membrane PDGFRβ governs adhesion and cytoskeletal dynamics, demonstrating the importance of subcellular lipid compartmentalization in shaping receptor outputs [155]. In addition to PDGFRα, phosphoinositides also control the activity of other ciliary receptors, such as IGF1R and insulin receptor (IR), both of which activate AKT signaling upon ligand binding [158]. The interplay between ciliary phosphoinositide turnover, receptor activation, and downstream AKT-FOXO1 signaling links extracellular growth cues to nuclear transcriptional programs, integrating environmental sensing with cell fate decisions [159, 160] (Fig. 3I).

Conclusions

Primary cilia are essential organelles that coordinate a broad spectrum of signaling pathways critical for cellular function, developmental regulation, and tissue homeostasis. Their unique compartmental architecture enables spatial and temporal segregation of signaling events, allowing precise control over downstream transcriptional and metabolic responses. Instead of acting as a uniform signaling unit, primary cilia actively govern the localization, turnover, and activation of key regulatory molecules. The interplay between ciliary structure and signal dynamics is central to understanding how cells interpret external cues and make fate decisions. Disruption of ciliary assembly, maintenance, or transport machinery contributes to a wide array of disorders, from classic ciliopathies to complex diseases such as cancer, obesity, and neurodegeneration. Thus, primary cilia provide not only mechanistic insights into fundamental cell biology but also a conceptual framework for studying signal misregulation in human disease. As our understanding of ciliary signaling deepens, it becomes increasingly clear that primary cilia function as dynamic and adaptable regulators of intercellular communication. Continued investigation of their molecular logic and physiological roles will be essential for uncovering new principles of cell regulation and identifying novel targets for therapeutic intervention.

Perspectives

Despite substantial advances in ciliary biology, fundamental questions remain regarding how primary cilia decode and integrate complex extracellular signals within their highly compartmentalized structure. The mechanisms underlying the spatial organization, selective trafficking, and temporal activation of signaling components within the cilium are only partially understood. Lipid domains, post-translational modifications, and scaffolding proteins likely contribute to signal segregation, yet their interplay in ensuring pathway fidelity remains unclear. Emerging evidence indicates that primary cilia exhibit substantial context dependence, with signaling outputs shaped by cell type, developmental stage, and environmental cues. Rather than serving as a signaling hub, the cilium operates in a modular and adaptive manner. Elucidating these context-specific functions will require integrating advanced approaches such as spatially resolved omics, high-resolution imaging, and organoid-based systems that recapitulate tissue complexity. Beyond their developmental roles, primary cilia are increasingly implicated in pathological processes including tumorigenesis, metabolic imbalance, and tissue fibrosis. While ciliopathies underscore their essential functions, many common diseases also involve subtle yet consequential disruptions in ciliary signaling. This has fueled growing interest in therapeutically targeting cilia-related pathways. Realizing this potential will require bridging fundamental mechanistic insights with translational strategies tailored to specific disease contexts.

Abbreviations

5-HT6R

Serotonin receptor 6

5-ptases

Inositol polyphosphate 5-phosphatases

AC

Adenylyl cyclases

APC

Adenomatous polyposis coli

ARL3

ADP ribosylation factor like GTPase 3

AurA

Aurora A

BBS

Bardet-Biedl syndrome

BMPs

Bone morphogenetic proteins

BMPRI

BMP type I receptor

BMPRII

BMP type II receptor

CaM

Calmodulin

cGAMP

Cyclic GMP-AMP

cGAS

Cyclic GMP-AMP synthase

CK1α

Casein kinase 1α

CKD

Chronic kidney disease

CNS

Central nervous system

CRE

cAMP response elements

CREB

cAMP response element-binding protein

CSF

Cerebrospinal fluid

CTGF

Connective tissue growth factor

CYR61

Cysteine-rich angiogenic inducer 61

D1R

Dopamine receptor 1

DHH

Desert Hedgehog

Dvl

Disheveled

EHD1

EH domain-containing protein 1

dsDNA

Double-stranded DNA

FKBP12

FK506-binding protein 1A

Fz

Frizzled receptors

FZD

Frizzled

GLI^A

GLI activators

GLI^FL

GLI full-length

GLI^R

GLI repressor

GPCR

G protein-coupled receptor

GSK3β

Glycogen synthase kinase 3β

HDAC6

Histone deacetylase 6

Hh

Hedgehog

HO

Heterotopic ossification

IFT

Intraflagellar transport

IFT88

Intraflagellar transport 88

IHH

Indian Hedgehog

INPP5E

Inositol polyphosphate-5-phosphatase E

INVS

Inversin

IR

Insulin receptor

JS

Joubert syndrome

Kif7

Kinesin Family Member 7

KIF17

Kinesin family member 17

LATS1/2

Large tumor suppressor 1/2

LKB1

Liver Kinase B1

L-R

Left–right

LRP5/6

Low-density lipoprotein receptor-related proteins 5/6

MCHR1

Melanin-concentrating hormone receptor 1

MKS

Meckel syndrome

MLC2

Myosin Light Chain 2

MST1/2

Mammalian STE20-like kinase 1/2

MTOC

Microtubule-organizing center

mTORC1

mammalian Target of Rapamycin Complex 1

NEK8

NIMA-related kinase 8

NICD

Notch intracellular domain

NPHP

Nephronophthisis

PC1

Polycystin-1

PC2

Polycystin-2

PCD

Primary ciliary dyskinesia

PCP

Planar cell polarity

PEMFs

Pulsed electromagnetic fields

PI3K

Phosphoinositide 3-kinase

PIPs

Phosphoinositides

PKA

Protein kinase A

PKD

Polycystic kidney disease

PP1

Phosphatase 1

Ptch1

Patched1

PTEN

Phosphatase and tensin homolog deleted on chromosome 10

PTGER4

Prostaglandin E receptor 4

RBPJ

Recombination Signal Binding Protein for Immunoglobulin Kappa J Region

RhoA

Ras homolog family member A

ROBs

Rat calvarial osteoblasts

S6K

S6 kinase

SAV1

Salvador homolog 1

SHH

Sonic Hedgehog

SHIP1

Src homology 2 domain containing inositol 5-phosphatase 1

SHIP2

Src homology 2 domain containing inositol 5-phosphatase 2

Smo

Smoothened

SRPS

Short-rib polydactyly syndrome

SSTR3

Somatostatin receptor 3

STAT6

Signal Transducer and Activator of Transcription 6

STING

Stimulator of interferon genes

Sufu

Suppressor of Fused

TAZ

Transcriptional co-activator with PDZ-binding motif

TCF/LEF

T-cell factor/lymphoid enhancer-binding factor

TGF-β

Transforming growth factor-beta

TGFβRI

TGF-β type I receptor

TGFβRII

TGF-β type II receptor

TGN

Trans-Golgi network

TRPV4

Transient Receptor Potential Vanilloid 4

TTBK2

Tau Tubulin Kinase 2

TZ

Transition zone

YAP

Yes-associated protein

Author contributions

All authors made substantial contributions in drafting and finalizing the manuscript.

Funding

This study was supported by National Natural Science Foundation of China (32370915 and 32171114).

Data availability

Not applicable.

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

All authors consent.

Competing interests

The authors declare no competing interests in this work.