# CCDC66 regulation of cytoskeleton and cilia stability is important for signaling and epithelial organization

**Authors:** Jovana Deretic, Seyma Cengiz-Emek, Ece Seyrek, Elif Nur Firat-Karalar, Ines Alvarez-Garcia, Ines Alvarez-Garcia, Ines Alvarez-Garcia, Ines Alvarez-Garcia, Ines Alvarez-Garcia

PMC · DOI: 10.1371/journal.pbio.3003313 · PLOS Biology · 2025-07-29

## TL;DR

This study shows that the protein CCDC66 helps control the structure and function of cell cilia, which are important for signaling and tissue organization.

## Contribution

The study identifies CCDC66 as a key regulator of ciliary stability and disassembly through microtubules, actin, and vesicular trafficking.

## Key findings

- CCDC66 depletion leads to unstable cilia with fluctuating lengths and increased disassembly.
- CCDC66's microtubule-stabilizing activity is essential for ciliary maintenance.
- CCDC66 also affects epithelial organization and signaling pathways like Hedgehog and Wnt.

## Abstract

The primary cilium is a conserved, microtubule-based organelle that transduces signaling pathways essential for development and homeostasis. It dynamically assembles and disassembles in response to intrinsic and extrinsic stimuli while maintaining remarkable structural stability and tightly regulated length. The mechanisms underlying this stability and length control are not well understood. Here, we characterized CCDC66, a microtubule-associated protein linked to ciliopathies, as an important regulator of cilium maintenance and disassembly in mouse epithelial cells. Live imaging revealed that cilia in CCDC66-depleted cells frequently fluctuate in length and exhibit increased cilium disassembly and ectocytosis. Phenotypic rescue experiments and in vitro assays showed that microtubule stabilization activity of CCDC66 is required for these functions. Temporal proximity mapping identified potential new regulators and molecular pathways involved in cilium disassembly. Further characterization revealed actin cytoskeleton and vesicular trafficking as additional mechanisms by which CCDC66 may mediate its ciliary functions. Finally, depletion of CCDC66 compromised Hedgehog and Wnt pathway activation and disrupted epithelial cell organization and polarity in two- and three‐dimensional cultures. Collectively, we showed that CCDC66 regulates both ciliary and non-ciliary processes through diverse mechanisms involving microtubules, actin, and vesicular trafficking, providing insights into the pathologies associated with CCDC66.

The primary cilium dynamically assembles and disassembles while maintaining structural stability and tightly regulated length, but the mechanisms that control this remain unclear. This study shows that the ciliopathy-linked protein CCDC66 regulates both cilium stability and length in epithelial cells via microtubules, actin and vesicular trafficking.

## Linked entities

- **Genes:** CCDC66 (coiled-coil domain containing 66) [NCBI Gene 285331]
- **Species:** Mus musculus (taxon 10090)

## Full-text entities

- **Genes:** Arl13b (ADP-ribosylation factor-like 13B) [NCBI Gene 68146] {aka A530097K21Rik, A930014M17Rik, Arl2l1, C530009C10Rik, hnn}, Rab11a (RAB11A, member RAS oncogene family) [NCBI Gene 53869], NPHP1 (nephrocystin 1) [NCBI Gene 4867] {aka JBTS4, NPH1, SLSN1}, Myo6 (myosin VI) [NCBI Gene 17920] {aka Myo6<rsv>, Tlc, rsv, sv}, Armc9 (armadillo repeat containing 9) [NCBI Gene 78795] {aka 3830422A13Rik, 4831423D23Rik, 4930438O05Rik, 5730415N24Rik}, Shh (sonic hedgehog) [NCBI Gene 20423] {aka 9530036O11Rik, Dsh, HHG-1, Hhg1, Hx, Hxl3}, Srebf2 (sterol regulatory element binding factor 2) [NCBI Gene 20788] {aka SREBP-2, SREBP2, SREBP2gc, bHLHd2, lop13, nuc}, Hal (histidine ammonia lyase) [NCBI Gene 15109] {aka Hsd, his, histidase}, Rab7 (RAB7, member RAS oncogene family) [NCBI Gene 19349] {aka Rab7a}, Cspp1 (centrosome and spindle pole associated protein 1) [NCBI Gene 211660] {aka 2310020J12Rik, 4930413O22Rik, Cspp2, Cspp3}, Ccdc6 (coiled-coil domain containing 6) [NCBI Gene 76551] {aka 2810012H18Rik}, Invs (inversin) [NCBI Gene 16348] {aka Nphp2, inv}, Gli1 (GLI-Kruppel family member GLI1) [NCBI Gene 14632] {aka Zfp-5, Zfp5}, Actb (actin, beta) [NCBI Gene 11461] {aka Actx, E430023M04Rik, beta-actin}, Agfg1 (ArfGAP with FG repeats 1) [NCBI Gene 15463] {aka C130049H11Rik, D730048C23Rik, Hrb, RAB, Rip}, CCDC66 (coiled-coil domain containing 66) [NCBI Gene 285331], Axin2 (axin 2) [NCBI Gene 12006] {aka Axi1, Axil, Conductin}, Ift88 (intraflagellar transport 88) [NCBI Gene 305918] {aka Ttc10}, Sstr3 (somatostatin receptor 3) [NCBI Gene 20607] {aka Smstr-3, Smstr3, sst3}, Arl13b (ARF like GTPase 13B) [NCBI Gene 304037], Ccdc66 (coiled-coil domain containing 66) [NCBI Gene 306238] {aka RGD1560873}, Ptch1 (patched 1) [NCBI Gene 19206] {aka A230106A15Rik, Ptc, Ptc1, Ptch, mes, wig}, Bbs4 (Bardet-Biedl syndrome 4) [NCBI Gene 300754], Ctnnb1 (catenin beta 1) [NCBI Gene 12387] {aka Bfc, Catnb, Mesc}, WDR19 (WD repeat domain 19) [NCBI Gene 57728] {aka ATD5, CED4, CFAP66, DYF-2, FAP66, IFT144}, Tjp1 (tight junction protein 1) [NCBI Gene 21872] {aka ZO1}, Smo (smoothened, frizzled class receptor) [NCBI Gene 319757] {aka E130215L21Rik, Smoh, bnb, smoothened}, ARL13B (ARF like GTPase 13B) [NCBI Gene 200894] {aka ARL2L1, JBTS8}, Gsk3b (glycogen synthase kinase 3 beta) [NCBI Gene 56637] {aka 7330414F15Rik, 8430431H08Rik, GSK-3, GSK-3beta, GSK3}, BBS4 (Bardet-Biedl syndrome 4) [NCBI Gene 585], Tsp2 (tumor suppressor region 2) [NCBI Gene 104266] {aka MTS}, Wdr19 (WD repeat domain 19) [NCBI Gene 213081] {aka C330027H04Rik, D330023L08Rik, DYF2, Ift144, PWDMP, mKIAA1638}, Sag (S-antigen, retina and pineal gland (arrestin)) [NCBI Gene 20215] {aka A930001K18Rik, Arr1, Irbp, arrestin}, Cep104 (centrosomal protein 104) [NCBI Gene 230967] {aka A930027E11, Kiaa0562, mKIAA0562}, Nedd9 (neural precursor cell expressed, developmentally down-regulated gene 9) [NCBI Gene 18003] {aka Cas-L, CasL, HEF1, MEF1, Nedd-9, p105}, IFT88 (intraflagellar transport 88) [NCBI Gene 8100] {aka D13S1056E, DAF19, TG737, TTC10, hTg737}, Pcm1 (pericentriolar material 1) [NCBI Gene 18536] {aka 2600002H09Rik, 9430077F19Rik, C030044G17Rik}, NPHP4 (nephrocystin 4) [NCBI Gene 261734] {aka POC10, SLSN4}, Aurka (aurora kinase A) [NCBI Gene 20878] {aka AIRK1, ARK-1, Ark1, Aurora-A, Ayk1, IAK}, Cdh1 (cadherin 1) [NCBI Gene 12550] {aka ARC-1, E-cad, Ecad, L-CAM, UVO, Um}, Spag5 (sperm associated antigen 5) [NCBI Gene 54141] {aka D11Bhm180e, Deepest, MAP126, Mastrin, S17}, Mbp (myelin basic protein) [NCBI Gene 17196] {aka Hmbpr, golli-mbp, jve, mld, shi}, Ccdc66 (coiled-coil domain containing 66) [NCBI Gene 320234] {aka E230015L20Rik}, H3c7 (H3 clustered histone 7) [NCBI Gene 260423] {aka H3.2-221, H3c13, H3c14, H3c15, H3c2, H3c3}, Fn1 (fibronectin 1) [NCBI Gene 14268] {aka E330027I09, Fn, Fn-1}, Pdk1 (pyruvate dehydrogenase kinase, isoenzyme 1) [NCBI Gene 228026] {aka B830012B01, D530020C15Rik}, Hdac6 (histone deacetylase 6) [NCBI Gene 15185] {aka Hd6, Hdac5, Sfc6, mHDA2}, RPGRIP1L (RPGRIP1 like) [NCBI Gene 23322] {aka COACH3, CORS3, FTM, JBTS7, MKS5, NPHP8}, Gapdh (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 14433] {aka Gapd}
- **Diseases:** ciliopathies (MESH:D000072661), Joubert syndrome (MESH:C536293), epithelial tissue defects (MESH:D009375), Ciliary defects (MESH:D002925), olfactory deficits (MESH:D000857), abnormalities in kidney development (MESH:D007674), U (MESH:C536925), retinopathies (MESH:D058437), colon carcinoma (MESH:D003110), retinal degeneration (MESH:D012162), cancer (MESH:D009369), infection (MESH:D007239)
- **Chemicals:** MgCl2 (MESH:D015636), 4',6-diamidino-2-phenylindole (MESH:C007293), glycerol (MESH:D005990), glutaraldehyde (MESH:D005976), DTT (MESH:D004229), GTP (MESH:D006160), BIS (MESH:D001729), polyethylenimine (MESH:D011094), EDTA (MESH:D004492), NaCl (MESH:D012965), ATP (MESH:D000255), methanol (MESH:D000432), sodium acrylate (MESH:C036658), ammonium bicarbonate (MESH:C027043), penicillin (MESH:D010406), Tween 20 (MESH:D011136), HEPES (MESH:D006531), SA (MESH:D000077145), Nocodazole (MESH:D015739), FA (MESH:D005557), puromycin (MESH:D011691), Tubacin (MESH:C474316), Biotin (MESH:D001710), BML-284 (-), HCl (MESH:D006851), agarose (MESH:D012685), lipid (MESH:D008055), TBS (MESH:D013725), F12 (MESH:C007782), SDS (MESH:D012967), APS (MESH:C031276), Taxol (MESH:D017239), urea (MESH:D014508), paraformaldehyde (MESH:C003043), KCl (MESH:D011189), sodium deoxycholate (MESH:D003840), CaCl2 (MESH:D002122), sucrose (MESH:D013395), EGTA (MESH:D004533), Oil (MESH:D009821), PIPES (MESH:C008916), PBS (MESH:D007854), NP-40 (MESH:C010615), Na2CO3 (MESH:C005686), acrylamide (MESH:D020106), DMSO (MESH:D004121), MLN8237 (MESH:C550258), CO2 (MESH:D002245), streptomycin (MESH:D013307), Triton X-100 (MESH:D017830), CytoD (MESH:D015638), Imidazole (MESH:C029899), Alexa568 (MESH:C000607448)
- **Species:** Homo sapiens (human, species) [taxon 9606], Canis lupus familiaris (dog, subspecies) [taxon 9615], Rattus norvegicus (brown rat, species) [taxon 10116], Mycoplasma (genus) [taxon 2093], Mus musculus (house mouse, species) [taxon 10090]
- **Cell lines:** Sf9 — Spodoptera frugiperda (Fall armyworm), Spontaneously immortalized cell line (CVCL_0549), Caco-2 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0025), e3001708 — Opodiphthera eucalypti (Emperor gum moth), Spontaneously immortalized cell line (CVCL_Z109), CRL-3216 — Homo sapiens (Human), Turner syndrome, Transformed cell line (CVCL_9M67), Hi5 — Trichoplusia ni (Cabbage looper), Spontaneously immortalized cell line (CVCL_C190), HEK293T — Homo sapiens (Human), Transformed cell line (CVCL_0063), RPE1 — Homo sapiens (Human), Telomerase immortalized cell line (CVCL_4388), S2D — Mus musculus (Mouse), Hybridoma (CVCL_C5DS), MCF10A — Homo sapiens (Human), Spontaneously immortalized cell line (CVCL_0598), RPE — Homo sapiens (Human), Spontaneously immortalized cell line (CVCL_0145), IMCD3 — Mus musculus (Mouse), Transformed cell line (CVCL_0429), S2 — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z232)

## Full text

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## Figures

9 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12324684/full.md

## References

97 references — full list in the complete paper: https://tomesphere.com/paper/PMC12324684/full.md

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Source: https://tomesphere.com/paper/PMC12324684