The short rib polydactyly syndromes (SRPS) are a group of recessively inherited, perinatal-lethal skeletal disorders primarily characterized by short ribs, shortened long bones, varying types of polydactyly and concomitant visceral abnormalities. Mutations in several genes affecting cilia function cause SRPS, revealing a role for cilia function in skeletal development. To identify additional SRPS genes and discover novel ciliary molecules required for normal skeletogenesis, we performed exome sequencing in a cohort of patients and identified homozygosity for a missense mutation, p.E80K, in Intestinal Cell Kinase, ICK, in one SRPS family. The p.E80K mutation abolished serine/threonine kinase activity, resulting in altered ICK subcellular and ciliary localization, increased cilia length, aberrant cartilage growth plate structure, defective Hedgehog and altered ERK signalling. These data identify ICK as an SRPS-associated gene and reveal that abnormalities in signalling pathways contribute to defective skeletogenesis.

Central European Institute of Technology Masaryk University Kamenice 753 5 62500 Brno Czech Republic

College of Pharmacy Dongguk University Seoul Goyang 410 820 Korea

Department of Biology Faculty of Medicine Masaryk University 62500 Brno Czech Republic

Department of Genome Sciences University of Washington Seattle WA 98195 USA

Department of Histology and Embryology Faculty of Medicine Masaryk University 62500 Brno Czech Republic

Department of Human Genetics

Department of Human Genetics University of California Los Angeles Los Angeles CA 90095 USA

Department of Molecular Cell and Developmental Biology University of California Los Angeles Los Angeles CA 90095 USA

Department of Obstetrics and Gynecology Orthopaedic Institute for Children University of California Los Angeles Los Angeles CA 90095 USA

Department of Orthopaedic Surgery

Division of Genetic Medicine Department of Pediatrics University of Washington Seattle WA 98195 USA

Division of Genetic Medicine Seattle Children's Hospital Seattle WA 98105 USA

Institute of Experimental Biology Masaryk University 62500 Brno Czech Republic

International Clinical Research Center St Anne's University Hospital 65691 Brno Czech Republic

International Skeletal Dysplasia Registry University of California Los Angeles Los Angeles CA 90095 USA

Virginia Commonwealth University Richmond VA 23298 USA

Zobrazit více v PubMed

Provot S., Schipani E. (2005) Molecular mechanisms of endochondral bone development. Biochem. Biophys. Res. Commun., 328, 658–865. PubMed

Bonafe L., Cormier-Daire V., Hall C., Lachman R., Mortier G., Mundlos S., Nishimura G., Sangiorgi L., Savarirayan R., Sillence D., et al. (September 23, 2015) Nosology and classification of genetic skeletal disorders: 2015 revision. Am. J. Med. Genet. A, 10.1002/ajmg.a.37365. PubMed

Huber C., Cormier-Daire V. (2012) Ciliary disorder of the skeleton. Am. J. Med. Genet. C Semin. Med. Genet., 160C, 165–174. PubMed

Beales P.L., Bland E., Tobin J.L., Bacchelli C., Tuysuz B., Hill J., Rix S., Pearson C.G., Kai M, Hartley J., et al. (2007) IFT80, which encodes a conserved intraflagellar transport protein, is mutated in Jeune asphyxiating thoracic dystrophy. Nat. Genet., 39, 727–729. PubMed

Cavalcanti D.P., Huber C., Sang K.H., Baujat G., Collins F., Delezoide A.L., Dagoneau N. L., Merrer M., Martinovic J., Mello M.F., et al. (2011) Mutation in IFT80 in a fetus with the phenotype of Verma-Naumoff provides molecular evidence for Jeune-Verma-Naumoff dysplasia spectrum. J. Med. Genet., 48, 88–92. PubMed

Bredrup C., Saunier S., Oud M.M., Fiskerstrand T., Hoischen A., Brackman D., Leh S.M., Midtbø M., Filhol E., Bole-Feysot C., et al. (2011) Ciliopathies with skeletal anomalies and renal insufficiency due to mutations in the IFT-A gene WDR19. Am. J. Hum. Genet., 89, 634–643. PubMed PMC

Huber C., Wu S., Kim A.S., Sigaudy S., Sarukhanov A., Serre V., Baujat G.L., Quan Sang K.H., Rimoin D.L., Cohn D.H., et al. (2013) WDR34 mutations that cause short-rib polydactyly syndrome type III/severe asphyxiating thoracic dysplasia reveal a role for the NF-κB pathway in cilia. Am. J. Hum. Genet., 93, 926–931. PubMed PMC

Schmidts M., Vodopiutz J., Christou-Savina S., Cortés C.R., McInerney-Leo A.M., Emes R.D., Arts H.H., Tüysüz B., D'Silva J., Leo P.J., et al. (2013) Mutations in the gene encoding IFT dynein complex component WDR34 cause Jeune asphyxiating thoracic dystrophy. Am. J. Hum. Genet., 93, 932–944. PubMed PMC

Gilissen C., Arts H.H., Hoischen A., Spruijt L., Mans D.A., Arts P., van Lier B., Steehouwer M., van Reeuwijk J., Kant S.G., et al. (2010) Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome. Am. J. Hum. Genet., 87, 418–423. PubMed PMC

Mill P., Lockhart P.J., Fitzpatrick E., Mountford H.S., Hall E.A., Reijns M.A., Keighren M., Bahlo M., Bromhead C.J., Budd P., et al. (2011) Human and mouse mutations in WDR35 cause short-rib polydactyly syndromes due to abnormal ciliogenesis. Am. J. Hum. Genet., 88, 508–515. PubMed PMC

Perrault I., Saunier S., Hanein S., Filhol E., Bizet A.A., Collins F., Salih M.A., Gerber S., Delphin N., Bigot K., et al. (2012) Mainzer-Saldino syndrome is a ciliopathy caused by IFT140 mutations. Am. J. Hum. Genet., 90, 864–870. PubMed PMC

Schmidts M., Frank V., Eisenberger T., Al Turki S., Bizet A.A., Antony D., Rix S., Decker C., Bachmann N., Bald M., et al. (2013) Combined NGS approaches identify mutations in the intraflagellar transport gene IFT140 in skeletal ciliopathies with early progressive kidney Disease. Hum. Mutat., 34, 714–724. PubMed PMC

Halbritter J., Bizet A.A., Schmidts M., Porath J.D., Braun D.A., Gee H.Y., McInerney-Leo A.M., Krug P., Filhol E., Davis E.E., et al. (2013) Defects in the IFT-B component IFT172 cause Jeune and Mainzer-Saldino syndromes in humans. Am. J. Hum. Genet., 93, 915–925. PubMed PMC

McInerney-Leo A.M., Schmidts M., Cortés C.R., Leo P.J., Gener B., Courtney A.D., Gardiner B., Harris J.A., Lu Y., Marshall M., et al. (2013) Short-rib polydactyly and Jeune syndromes are caused by mutations in WDR60. Am. J. Hum. Genet., 93, 515–523. PubMed PMC

Davis E.E., Zhang Q., Liu Q., Diplas B.H., Davey L.M., Hartley J., Stoetzel C., Szymanska K., Ramaswami G., Logan C.V., et al. (2011) TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum. Nat. Genet., 43, 189–196. PubMed PMC

Dagoneau N., Goulet M., Geneviève D., Sznajer Y., Martinovic J., Smithson S., Huber C., Baujat G., Flori E., Tecco L. et al. (2009) DYNC2H1 mutations cause asphyxiating thoracic dystrophy and short rib-polydactyly syndrome, type III. Am. J. Hum. Genet., 84, 706–711. PubMed PMC

Merrill A.E., Merriman B., Farrington-Rock C., Camacho N., Sebald E.T., Funari V.A., Schibler M.J., Firestein M.H., Cohn Z.A., Priore M.A., et al. (2009) Ciliary abnormalities due to defects in the retrograde transport protein DYNC2H1 in short-rib polydactyly syndrome. Am. J. Hum. Genet., 84, 542–549. PubMed PMC

Taylor S.P., Dantas T.J., Duran I., Wu S., Lachman R.S., University of Washington Center for Mendelian Genomics Consortium. Nelson S.F., Cohn D.H., Vallee R.B., Krakow D. (2015) Mutations in DYNC2LI1 disrupt cilia function and cause short rib polydactyly syndrome. Nat. Commun., 6, 7092. PubMed PMC

Shaheen R., Schmidts M., Faqeih E., Hashem A., Lausch E., Holder I., Superti-Furga A.U.K.10K., Consortium, Mitchison H.M., Almoisheer A., et al. (2015) A founder CEP120 mutation in Jeune asphyxiating thoracic dystrophy expands the role of centriolar proteins in skeletal ciliopathies. Hum. Mol. Genet., 24, 1410–1419. PubMed PMC

Malicdan M.C., Vilboux T., Stephen J., Maglic D., Mian L., Konzman D., Guo J., Yildirimli D., Bryant J., Fischer R., et al. (September 18, 2015) Mutations in human homologue of chicken talpid3 gene (KIAA0586) cause a hybrid ciliopathy with overlapping features of Jeune and Joubert syndromes. J. Med. Genet., 10.1136/jmedgenet-2015-103316. PubMed PMC

Alby C., Piquand K., Huber C., Megarbané A., Ichkou A., Legendre M., Pelluard F., Encha-Ravazi F., Abi-Tayeh G., Bessières B., et al. (2015) Mutations in KIAA0586 Cause Lethal Ciliopathies Ranging from a Hydrolethalus Phenotype to Short-Rib Polydactyly Syndrome. Am. J. Hum. Genet., 97, 311–318. PubMed PMC

Fu Z., Kim J., Vidrich A., Sturgill T.W., Cohn S.M. (2009) Intestinal cell kinase, a MAP kinase-related kinase, regulates proliferation and G1 cell cycle progression of intestinal epithelial cells. Am. J. Physiol. Gastrointest. Liver Physiol., 297, G632–G640. PubMed PMC

Yang Y., Roine N., Mäkelä T.P. (2013) CCRK depletion inhibits glioblastoma cell proliferation in a cilium-dependent manner. EMBO Rep., 14, 741–747. PubMed PMC

Burghoorn J., Dekkers M.P., Rademakers S., de Jong T., Willemsen R., Jansen G. (2007) Mutation of the MAP kinase DYF-5 affects docking and undocking of kinesin-2 motors and reduces their speed in the cilia of Caenorhabditis elegans. Proc. Natl. Acad. Sci. U. S. A, 104, 7157–7162. PubMed PMC

Berman S.A., Wilson N.F., Haas N.A., Lefebvre P.A. (2003) A novel MAP kinase regulates flagellar length in Chlamydomonas. Curr. Biol., 13, 1145–1149. PubMed

Bengs F., Scholz A., Kuhn D., Wiese M. (2005) LmxMPK9, a mitogen-activated protein kinase homologue affects flagellar length in Leishmania mexicana. Mol. Microbiol., 55, 1606–1615. PubMed

Lahiry P., Wang J., Robinson J.F., Turowec J.P., Litchfield D.W., Lanktree M.B., Gloor G.B., Puffenberger E.G., Strauss K.A., Martens M.B., et al. (2009) A multiplex human syndrome implicates a key role for intestinal cell kinase in development of central nervous, skeletal, and endocrine systems. Am. J. Hum. Genet., 84, 134–147. PubMed PMC

Oud M.M., Bonnard C., Mans D.A., Altunoglu U., Tohari S., Ng A.Y., Eskin A., Lee H., Rupar C.A., de Wagenaar N.P., et al. (2016) A novel ICK mutation causes ciliary disruption and lethal endocrine-cerebro-osteodysplasia syndrome. Cilia, 5, doi: 10.1186/s13630-016-0029-1. PubMed PMC

Moon H., Song J., Shin J.O., Lee H., Kim H.K., Eggenschwiller J.T., Bok J., Ko H.W. (2014) Intestinal cell kinase, a protein associated with endocrine-cerebro-osteodysplasia syndrome, is a key regulator of cilia length and Hedgehog signaling. Proc. Natl. Acad. Sci. U. S. A., 111, 8541–8546. PubMed PMC

Chaya T., Omori Y., Kuwahara R., Furukawa T. (2014) ICK is essential for cell type-specific ciliogenesis and the regulation of ciliary transport. Embo J., 33, 1227–1242. PubMed PMC

Fu Z., Larson K.A., Chitta R.K., Parker S.A., Turk B.E., Lawrence M.W., Kaldis P., Galaktionov K., Cohn S.M., Shabanowitz J., et al. (2006) Identification of yin-yang regulators and a phosphorylation consensus for male germ cell-associated kinase (MAK)-related kinase. Mol. Cell. Biol., 26, 8639–8654. PubMed PMC

Fu Z., Schroeder M.J., Shabanowitz J., Kaldis P., Togawa K., Rustgi A.K., Hunt D.F., Sturgill T.W. (2005) Activation of a nuclear Cdc2-related kinase within a mitogen-activated protein kinase-like TDY motif by autophosphorylation and cyclin-dependent protein kinase-activating kinase. Mol. Cell. Biol., 25, 6047–6064. PubMed PMC

Wang L.Y., Kung H.J. (2012) Male germ cell-associated kinase is overexpressed in prostate cancer cells and causes mitotic defects via deregulation of APC/C-CDH1. Oncogene, 31, 2907–2918. PubMed PMC

Broekhuis J.R., Verhey K.J., Jansen G. (2014) Regulation of cilium length and intraflagellar transport by the RCK-kinases ICK and MOK in renal epithelial cells. PLoS One., 9, e108470.. PubMed PMC

Chen J.K., Taipale J., Young K.E., Maiti T., Beachy P.A. (2002) Small molecule modulation of Smoothened activity. Proc. Natl. Acad. Sci. U. S. A., 99, 14071–14076. PubMed PMC

Kronenberg H.M. (2006) PTHrP and skeletal development. Ann. N. Y. Acad. Sci., 1068, 1–13. PubMed

Krejci P., Salazar L., Goodridge H.S., Kashiwada T.A., Schibler M.J., Jelinkova P., Thompson L.M., Wilcox W.R. (2008) STAT1 and STAT3 do not participate in FGF-mediated growth arrest in chondrocytes. J. Cell Sci., 121, 272–281. PubMed

Krejci P., Prochazkova J., Smutny J., Chlebova K., Lin P., Aklian A., Bryja V., Kozubik A., Wilcox W.R. (2010) FGFR3 signaling induces a reversible senescence phenotype in chondrocytes similar to oncogene-induced premature senescence. Bone, 47, 102–110. PubMed PMC

He M., Subramanian R., Bangs F., Omelchenko T., Liem K.F., Jr., Kapoor T.M., Anderson K.V. (2014) The kinesin-4 protein Kif7 regulates mammalian Hedgehog signalling by organizing the cilium tip compartment. Nat. Cell Biol., 16, 663–672. PubMed PMC

Rosenbaum J.L., Witman G.B. (2002) Intraflagellar transport. Nat. Rev. Mol. Cell Biol., 3, 813–825. PubMed

Pazour G.J., Bloodgood R.A. (2008) Targeting proteins to ciliary membrane. Curr. Top. Dev. Biol., 85, 115–149. PubMed

Dishinger J.F., Kee H.L., Jenkins P.M., Fan S., Hurd T.W., Hammond J.W., Truong Y.N., Margolis B., Martens J.R., Verhey K.J. (2010) Ciliary entry of the kinesin-2 motor KIF17 is regulated by importin-beta2 and RanGTP. Nat. Cell. Biol., 12, 703–710. PubMed PMC

Wong S.Y., Reiter J.F. (2008) The primary cilium at the crossroads of mammalian hedgehog signaling. Curr. Top. Dev. Biol., 85, 225–260. PubMed PMC

te Welscher P., Zuniga A., Kuijper S., Drenth T., Goedemans H.J., Meijlink F., Zeller R. (2002) Progression of vertebrate limb development through SHH-mediated counteraction of GLI3. Science, 298, 827–830. PubMed

Haycraft C.J., Zhang Q., Song B., Jackson W.S., Detloff P.J., Serra R., Yoder B.K. (2007) Intraflagellar transport is essential for endochondral bone formation. Development, 134, 307–316. PubMed

Liu A., Wang B., Niswander L.A. (2005) Mouse intraflagellar transport proteins regulate both the activator and repressor functions of Gli transcription factors. Development, 132, 3103–3111. PubMed

Jia J., Kolterud A., Zeng H., Hoover A., Teglund S., Toftgård R., Liu A. (2009) Suppressor of Fused inhibits mammalian Hedgehog signaling in the absence of cilia. Dev. Biol., 330, 452–460. PubMed PMC

Hoover A.N., Wynkoop A., Zeng H., Jia J., Niswander L.A., Liu A. (2008) C2cd3 is required for cilia formation and Hedgehog signaling in mouse. Development, 135, 4049–4058. PubMed PMC

Huangfu D., Anderson K.V. (2005) Cilia and Hedgehog responsiveness in the mouse. Proc. Natl. Acad. Sci. U. S. A., 102, 11325–11330. PubMed PMC

Heydeck W., Zeng H., Liu A. (2009) Planar cell polarity effector gene Fuzzy regulates cilia formation and Hedgehog signal transduction in mouse. Dev. Dyn., 238, 3035–3042. PubMed

Cortellino S., Wang C., Wang B., Bassi M.R., Caretti E., Champeval D., Calmont A., Jarnik M., Burch J., Zaret K.S., et al. (2009) Defective ciliogenesis, embryonic lethality and severe impairment of the Sonic Hedgehog pathway caused by inactivation of the mouse complex A intraflagellar transport gene Ift122/Wdr10, partially overlapping with the DNA repair gene Med1/Mbd4. Dev. Biol., 325, 225–237. PubMed PMC

Cheung H.O., Zhang X., Ribeiro A., Mo R., Makino S., Puviindran V., Law K.K., Briscoe J., Hui C.C. (2009) The kinesin protein Kif7 is a critical regulator of Gli transcription factors in mammalian hedgehog signaling. Sci. Signal., 2, ra29.. PubMed

Endoh-Yamagami S., Evangelista M., Wilson D., Wen X., Theunissen J.W., Phamluong K., Davis M., Scales S.J., Solloway M.J., de Sauvage F.J., et al. (2009) The mammalian Cos2 homolog Kif7 plays an essential role in modulating Hh signal transduction during development. Curr. Biol., 19, 1320–1326. PubMed

Liem K.F., Jr., He M., Ocbina P.J., Anderson K.V. (2009) Mouse Kif7/Costal2 is a cilia-associated protein that regulates Sonic hedgehog signaling. Proc. Natl. Acad. Sci. U. S. A., 106, 13377–13382. PubMed PMC

Tukachinsky H., Lopez L.V., Salic A. (2010) A mechanism for vertebrate Hedgehog signaling: recruitment to cilia and dissociation of SuFu-Gli protein complexes. J. Cell Biol., 191, 415–428. PubMed PMC

Wilcox W.R., Tavormina P.L., Krakow D., Kitoh H., Lachman R.S., Wasmuth J.J., Thompson L.M., Rimoin D.L. (1998) Molecular, radiologic, and histopathologic correlations in thanatophoric dysplasia. Am. J. Med. Genet., 78, 274–281. PubMed

Krejci P. (2014) The paradox of FGFR3 signaling in skeletal dysplasia: why chondrocytes growth arrest while other cells over proliferate. Mutat. Res. Rev. Mutat. Res., 759, 40–48. PubMed

Chen Z., Yue S.X., Zhou G., Greenfield E.M., Murakami S. (2015) ERK1 and ERK2 regulate chondrocyte terminal differentiation during endochondral bone formation. J. Bone Miner. Res., 30, 765–774. PubMed PMC

Thiel C., Kessler K., Giessl A., Dimmler A., Shalev S.A., von der Haar S., Zenker M., Zahnleiter D., Stöss H., Beinder E., et al. (2011) NEK1 mutations cause short-rib polydactyly syndrome type majewski. Am. J. Hum. Genet., 88, 106–114. PubMed PMC

White M.C., Quarmby L.M. (2008) The NIMA-family kinase, Nek1 affects the stability of centrosomes and ciliogenesis. BMC Cell Biol., 9, 29.. PubMed PMC

Letwin K., Mizzen L., Motro B., Ben-David Y., Bernstein A., Pawson T. (1992) A mammalian dual specificity protein kinase, Nek1, is related to the NIMA cell cycle regulator and highly expressed in meiotic germ cells. Embo J., 11, 3521–3531. PubMed PMC

McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M., et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome. Res., 20, 1297–1303. PubMed PMC

DePristo M.A., Banks E., Poplin R., Garimella K.V., Maguire J.R., Hartl C., Philippakis A.A., del Angel G., Rivas M.A., Hanna M., et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet., 43, 491–498. PubMed PMC

Van der Auwera G.A., Carneiro M.O., Hartl C., Poplin R., Del Angel G., Levy-Moonshine A., Jordan T., Shakir K., Roazen D., Thibault J., et al. (2013) From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinformatics, 11, 11.10.1 –11.10.33. PubMed PMC

Yourshaw M., Taylor S.P., Rao A.R., Martín M.G., Nelson S.F. (2015) Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins. Brief Bioinform., 16, 255–264. PubMed PMC

Adzhubei I.A., Schmidt S., Peshkin L., Ramensky V.E., Gerasimova A., Bork P., Kondrashov A.S., Sunyaev S.R. (2010) A method and server for predicting damaging missense mutations. Nat. Methods, 7, 248–249. PubMed PMC

Kumar P., Henikoff S., Ng P.C. (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc., 4, 1073–1081. PubMed

González-Pérez A., López-Bigas N. (2011) Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am. J. Hum. Genet., 88, 440–449. PubMed PMC

Kircher M., Witten D.M., Jain P., O'Roak B.J., Cooper G.M., Shendure J. (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet., 46, 310–315. PubMed PMC

Duran I., Marí-Beffa M., Santamaría J.A., Becerra J., Santos-Ruiz L. (2011) Freeze substitution followed by low melting point wax embedding preserves histomorphology and allows protein and mRNA localization techniques. Microsc. Res. Tech., 74, 440–448. PubMed

Kelley L.A., Sternberg M.J. (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc., 4, 363–371. PubMed

Marchler-Bauer A., Zheng C., Chitsaz F., Derbyshire M.K., Geer L.Y., Geer R.C., Gonzales N.R., Gwadz M., Hurwitz D.I., Lanczycki C.J., et al. (2013) CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res., 41, D348–D352. PubMed PMC

Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. (2004) UCSF Chimera - a visualization system for exploratory research and analysis. J. Comput. Chem., 25, 1605–1612. PubMed

Hui C.C., Joyner A.L. (1993) A mouse model of greig cephalopolysyndactyly syndrome: the extra-toesJ mutation contains an intragenic deletion of the Gli3 gene. Nat. Genet., 3, 241–246. PubMed

Milenkovic L., Goodrich L.V., Higgins K.M., Scott M.P. (1999) Mouse patched1 controls body size determination and limb patterning. Development, 126, 4431–4440. PubMed

Oncogenic FGFR Fusions Produce Centrosome and Cilia Defects by Ectopic Signaling

Mutations in GRK2 cause Jeune syndrome by impairing Hedgehog and canonical Wnt signaling

Fibroblast growth factor receptor influences primary cilium length through an interaction with intestinal cell kinase

Regulation of ciliary function by fibroblast growth factor signaling identifies FGFR3-related disorders achondroplasia and thanatophoric dysplasia as ciliopathies