[en] Mutations in genes encoding components of the intraflagellar transport IFT complexes have previously been associated with a spectrum of diseases collectively termed ciliopathies. Ciliopathies relate to defects in the formation or function of the cilium, a sensory or motile organelle present on the surface of most cell types. IFT52 is a key component of the IFT-B complex and ensures the interaction of the two subcomplexes IFT-B1 and IFT-B2. Here, we report novel IFT52 biallelic mutations in cases with a short-rib thoracic dysplasia (SRTD) or a congenital anomaly of kidney and urinary tract (CAKUT). Combining in vitro and in vivo studies in zebrafish, we showed that SRTD-associated missense mutation impairs IFT-B complex assembly and IFT-B2 ciliary localization, resulting in decreased cilia length. In comparison, CAKUT-associated missense mutation has a mild pathogenicity, thus explaining the lack of skeletal defects in CAKUT case. In parallel, we demonstrated that the previously reported homozygous nonsense IFT52 mutation associated with Sensenbrenner syndrome (Girisha et al, 2016) leads to exon skipping and results in a partially functional protein. Finally, our work uncovered a novel role for IFT52 in microtubule network regulation. We showed that IFT52 interacts and partially co-localised with centrin at the distal end of centrioles, where it is involved in its recruitment and/or maintenance. Alteration of this function likely contributes to centriole splitting observed in Ift52-/- cells.
Altogether, our findings allow a better comprehensive genotype-phenotype correlation amongst IFT52-related cases and revealed a novel, extra-ciliary role for IFT52 which disruption may contribute to pathophysiological mechanisms.
Christensen, Anni; Max-Planck-Institute of Biochemistry > 6Department of Structural Cell Biology
Pouliet, Aurore; Université Paris Descartes > Structure Fédérative de Recherche Necker > Plateforme Génomique
Garfa Traoré, Meriem; Université Paris Descartes > Structure Fédérative de Recherche Necker > Plateforme Imagerie
Nitschké, Patrick; Université Paris Descartes > Institut Imagine > Plateforme bio informatique
Injeyan, Marie; Mount Sinai Hospital, University of Toronto > Department of Obstetrics and Gynecology > The Prenatal Diagnosis and Medical Genetics Program
Millar, Kathryn; Mount Sinai Hospital, University of Toronto > Department of Obstetrics and Gynecology > The Prenatal Diagnosis and Medical Genetics Program
Chitayat, David; Mount Sinai Hospital, University of Toronto > Department of Obstetrics and Gynecology > The Prenatal Diagnosis and Medical Genetics Program
Shannon, Patrick; Mount Sinai Hospital, University of Toronto > Department of Pathology and laboratory Medicine,
Girisha, Katta Mohan; Manipal Academy of Higher Education > Department of Medical Genetics, Kasturba Medical College,
Schukla, Hanju; Manipal Academy of Higher Education > Department of Medical Genetics
Mechler, Charlotte; AP HP > Hôpital Louis Mourier
Lorentzen, Esben; Max-Planck-Institute of Biochemistry > Department of Structural Cell Biology
Benmerah, Alexandre; Université Paris Descartes > Institut Imagine > Laboratoire des maladies rénales héréditaires
Cormier Daire, Valérie; Université Paris Descartes > Institut Imagine > Laboratory of Molecular and Physiopathological bases of osteochondrodysplasia
Jeanpierre, Cécile; Université Paris Descartes > Institut Imagine > Laboratoire des maladies rénales héréditaires
Saunier, Sophie; Université Paris Descartes > Institut Imagine > Laboratoire des maladies rénales héréditaires
Delous, Marion; Université Paris Descartes > Institut Imagine > Laboratoire des maladies rénales héréditaires
Cole, D.G., Diener, D.R., Himelblau, A.L., Beech, P.L., Fuster, J.C. and Rosenbaum, J.L. (1998) Chlamydomonas kinesin-II-dependent intraflagellar transport (IFT): IFT particles contain proteins required for ciliary assembly in Caenorhabditis elegans sensory neurons. J. Cell Biol., 141, 993-1008.
Lucker, B.F., Behal, R.H., Qin, H., Siron, L.C., Taggart, W.D., Rosenbaum, J.L. and Cole, D.G. (2005) Characterization of the intraflagellar transport complex B core: direct interaction of the IFT81 and IFT74/72 subunits. J. Biol. Chem., 280, 27688-27696.
Taschner, M., Kotsis, F., Braeuer, P., Kuehn, E.W. and Lorentzen, E. (2014) Crystal structures of IFT70/52 and IFT52/46 provide insight into intraflagellar transport B core complex assembly. J. Cell Biol., 207, 269-282.
Taschner, M., Weber, K., Mourao, A., Vetter, M., Awasthi, M., Stiegler,M., Bhogaraju, S. and Lorentzen, E.(2016) Intraflagel-lar transport proteins 172, 80, 57, 54, 38, and 20 form a stable tubulin-binding IFT-B2 complex. EMBO J., 35, 773-790.
Beatson, S. and Ponting, C.P. (2004) GIFT domains: linking eukaryotic intraflagellar transport and glycosylation to bacterial gliding. Trends Biochem. Sci., 29, 396-399.
Wolf, M.T. (2015) Nephronophthisis and related syndromes. Curr. Opin. Pediatr., 27, 201-211.
Reiter, J.F. and Leroux, M.R. (2017) Genes and molecular pathways underpinning ciliopathies. Nat. Rev. Mol. Cell Biol., 18, 533-547.
Duran, I., Taylor, S.P., Zhang, W., Martin, J., Forlenza, K.N., Spiro, R.P., Nickerson, D.A., Bamshad, M., Cohn, D.H. and Krakow, D. (2016) Destabilization of the IFT-B cilia core complex due to mutations in IFT81 causes a Spectrum of short-rib polydactyly syndrome. Sci. Rep., 6, 34232.
Bizet, A.A., Becker-Heck, A., Ryan, R., Weber, K., Filhol, E., Krug, P., Halbritter, J., Delous, M., Lasbennes, M.C., Linghu, B. et al. (2015) Mutations in TRAF3IP1/IFT54 reveal a new role for IFT proteins in microtubule stabilization. Nat. Commun., 6, 8666.
Lindstrand, A., Davis, E.E., Carvalho, C.M., Pehlivan, D., Willer, J.R., Tsai, I.C., Ramanathan, S., Zuppan, C., Sabo, A., Muzny, D. et al. (2014) Recurrent CNVs and SNVs at the NPHP1 locus contribute pathogenic alleles to Bardet-Biedl syndrome. Am. J. Hum. Genet., 94, 745-754.
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.
Arts, H.H., Bongers, E.M., Mans, D.A., van, S.E., Oud, M.M., Bolat, E., Spruijt, L., Cornelissen, E.A., Schuurs-Hoeijmakers, J.H., de Leeuw, N. et al. (2011) C14ORF179 encoding IFT43 is mutated in Sensenbrenner syndrome. J. Med. Genet., 48, 390-395.
Duran, I., Taylor, S.P., Zhang, W., Martin, J., Qureshi, F., Jacques, S.M., Wallerstein, R., Lachman, R.S., Nickerson, D.A., Bamshad, M. et al. (2017) Mutations in IFT-A satellite core component genes IFT43 and IFT121 produce short rib poly-dactyly syndrome with distinctive campomelia. Cilia, 6, 7.
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.
Zhang, W., Taylor, S.P., Nevarez, L., Lachman, R.S., Nickerson, D.A., Bamshad, M., Krakow, D. and Cohn, D.H. (2016) IFT52 mutations destabilize anterograde complex assembly, disrupt ciliogenesis and result in short rib polydactyly syndrome. Hum. Mol. Genet., 25, 4012-4020.
Girisha, K.M., Shukla, A., Trujillano, D., Bhavani, G.S., Hebbar, M., Kadavigere, R. and Rolfs, A. (2016) A homozygous nonsense variant in IFT52 is associated with a human skeletal ciliopathy. Clin. Genet., 90, 536-539.
Chen, X., Wang, X., Jiang, C., Xu, M., Liu, Y., Qi, R., Qi, X., Sun, X., Xie, P., Liu, Q. et al. (2018) IFT52 as a novel candidate for ciliopathies involving retinal degeneration. Invest. Oph-thalmol. Vis. Sci., 59, 4581-4589.
Failler, M., Gee, H.Y., Krug, P., Joo, K., Halbritter, J., Belkacem, L., Filhol, E., Porath, J.D., Braun, D.A., Schueler, M. et al. (2014) Mutations of CEP83 cause infantile nephronophthisis and intellectual disability. Am. J. Hum. Genet., 94, 905-914.
Thomas, S., Legendre, M., Saunier, S., Bessieres, B., Alby, C., Bonniere, M., Toutain, A., Loeuillet, L., Szymanska, K., Jossic, F. et al. (2012) TCTN3 mutations cause Mohr-Majewski syndrome. Am. J. Hum. Genet., 91, 372-378.
Zaghloul, N.A. and Katsanis, N. (2011) Zebrafish assays of ciliopathies. Methods Cell Biol., 105, 257-272.
Pathak, N., Obara, T., Mangos, S., Liu, Y. and Drummond, I.A. (2007) The zebrafish fleer gene encodes an essential regulator of cilia tubulin polyglutamylation. Mol. Biol. Cell,18, 4353-4364.
Tsujikawa, M. and Malicki, J. (2004) Intraflagellar transport genes are essential for differentiation and survival of vertebrate sensory neurons. Neuron, 42, 703-716.
Krock, B.L. and Perkins, B.D. (2008) The intraflagellar transport protein IFT57 is required for cilia maintenance and regulates IFT-particle-kinesin-II dissociation in vertebrate photoreceptors. J. Cell Sci., 121, 1907-1915.
Tapadia, M.D., Cordero, D.R. and Helms, J.A. (2005) It's all in your head: new insights into craniofacial development and deformation. J. Anat., 207, 461-477.
Wada, N., Javidan, Y., Nelson, S., Carney, T.J., Kelsh, R.N. and Schilling, T.F. (2005) Hedgehog signaling is required for cranial neural crest morphogenesis and chondrogene-sis at the midline in the zebrafish skull. Development, 132, 3977-3988.
Huang, P. and Schier, A.F. (2009) Dampened hedgehog signaling but normal Wnt signaling in zebrafish without cilia. Development, 136, 3089-3098.
Liu, A., Wang, B. and Niswander, L.A. (2005) Mouse intraflag-ellar transport proteins regulate both the activator and repressor functions of Gli transcription factors. Development, 132, 3103-3111.
Salisbury, J.L., Suino, K.M., Busby, R. and Springett, M. (2002) Centrin-2 is required for centriole duplication in mammalian cells. Curr. Biol., 12, 1287-1292.
Dammermann, A. and Merdes, A. (2002) Assembly of cen-trosomal proteins and microtubule organization depends on PCM-1. J. Cell Biol., 159, 255-266.
Grigoriev, I.S., Chernobelskaya, A.A. and Vorobjev, I.A. (1999) Nocodazole, vinblastine and taxol at low concentrations affect fibroblast locomotion and saltatory movements of organelles. Membr. Cell Biol., 13, 23-48.
Jordan, M.A., Thrower, D. and Wilson, L. (1992) Effects of vinblastine, podophyllotoxin and nocodazole on mitotic spindles. Implications for the role of microtubule dynamics in mitosis. J. Cell Sci., 102, 401-416.
Mayor, T., Stierhof, Y.D., Tanaka, K., Fry, A.M. and Nigg, E.A. (2000) The centrosomal protein C-Nap1 is required for cell cycle-regulated centrosome cohesion. J. Cell Biol., 151, 837-846.
Bahe, S., Stierhof, Y.D., Wilkinson, C.J., Leiss, F. and Nigg, E.A. (2005) Rootletin forms centriole-associated filaments and functions in centrosome cohesion. J. Cell Biol., 171, 27-33.
Graser, S., Stierhof, Y.D. and Nigg, E.A. (2007) Cep68 and Cep215 (Cdk5rap2) are required for centrosome cohesion. J. Cell Sci., 120, 4321-4331.
Floriot, S., Vesque, C., Rodriguez, S., Bourgain-Guglielmetti, F., Karaiskou, A., Gautier, M., Duchesne, A., Barbey, S., Fritz, S., Vasilescu, A. et al. (2015) C-Nap1 mutation affects centriole cohesion and is associated with a Seckel-like syndrome in cattle. Nat. Commun., 6, 6894.
Euteneuer, U. and Schliwa, M. (1985) Evidence for an involvement of actin in the positioning and motility of centrosomes. J. Cell Biol., 101, 96-103.
Jean, C., Tollon, Y., Raynaud-Messina, B. and Wright, M. (1999) The mammalian interphase centrosome: two independent units maintained together by the dynamics of the micro-tubule cytoskeleton. Eur. J. Cell Biol., 78, 549-560.
Panic, M., Hata, S., Neuner, A. and Schiebel, E. (2015) The centrosomal linker and microtubules provide dual levels of spatial coordination of centrosomes. PLoS Genet., 11, e1005243.
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.
Tory, K., Lacoste, T., Burglen, L., Moriniere, V., Boddaert, N., Macher, M.A., Llanas, B., Nivet, H., Bensman, A., Niaudet, P. et al. (2007) High NPHP1 and NPHP6 mutation rate in patients with Joubert syndrome and nephronophthisis: potential epistatic effect of NPHP6 and AHI1 mutations in patients with NPHP1 mutations. J. Am. Soc. Nephrol., 18, 1566-1575.
Ryan, R., Failler, M., Reilly, M.L., Garfa-Traore, M., Delous, M., Filhol, E., Reboul, T., Bole-Feysot, C., Nitschke, P., Baudouin, V. et al. (2018) Functional characterization of tektin-1 in motile cilia and evidence for TEKT1 as a new candidate gene for motile ciliopathies. Hum. Mol. Genet., 27, 266-282.
Leitch, C.C., Zaghloul, N.A., Davis, E.E., Stoetzel, C., Diaz-Font, A., Rix, S., Alfadhel, M., Lewis, R.A., Eyaid, W., Banin, E. et al. (2008) Hypomorphic mutations in syndromic encephalocele genes are associated with Bardet-Biedl syndrome. Nat. Genet., 40, 443-448.
Wilson, F.H., Disse-Nicodeme, S., Choate, K.A., Ishikawa, K., Nelson-Williams, C., Desitter, I., Gunel, M., Milford, D.V., Lipkin, G.W., Achard, J.M. et al. (2001) Human hypertension caused by mutations in WNK kinases. Science, 293, 1107-1112.
Townsley, F.M., Aristarkhov, A., Beck, S., Hershko, A. and Ruderman, J.V. (1997) Dominant-negative cyclin-selective ubiquitin carrier protein E2-C/UbcH10 blocks cells in metaphase. Proc. Natl. Acad. Sci. U. S. A., 94, 2362-2367.
Lindstrom, N.O., De, G., Tran, T., Ransick, A., Suh, G., Guo, J., Kim, A.D., Parvez, R.K., Ruffins, S.W., Rutledge, E.A. et al. (2018) Progressive recruitment of mesenchymal progenitors reveals a time-dependent process of cell fate acquisition in mouse and human nephrogenesis. Dev. Cell, 45, 651.e4-660.e4.
Rachel, R.A., May-Simera, H.L., Veleri, S., Gotoh, N., Choi, B.Y., Murga-Zamalloa, C., McIntyre, J.C., Marek, J., Lopez, I., Hack-ett, A.N. et al. (2012) Combining Cep290 and Mkks ciliopathy alleles in mice rescues sensory defects and restores ciliogen-esis. J. Clin. Invest., 122, 1233-1245.
Delaval, B., Bright, A., Lawson, N.D. and Doxsey, S. (2011) The cilia protein IFT88 is required for spindle orientation in mitosis. Nat. Cell Biol., 13, 461-468.
Fischer, E., Legue, E., Doyen, A., Nato, F., Nicolas, J.F., Torres, V., Yaniv, M. and Pontoglio, M. (2006) Defective planar cell polarity in polycystic kidney disease. Nat. Genet., 38, 21-23.
Pradeep, J., Sambashivaiah, S., Thomas, T., Radhakrishnan, R., Vaz, M. and Srinivasan, K. (2012) Heart rate variability responses to standing are attenuated in drug naive depressed patients. Indian J. Physiol. Pharmacol., 56, 213-221.
Taschner, M., Bhogaraju, S., Vetter, M., Morawetz, M. and Lorentzen, E. (2011) Biochemical mapping of interactions within the intraflagellar transport (IFT) B core complex: IFT52 binds directly to four other IFT-B subunits. J. Biol. Chem., 286, 26344-26352.
Haeussler, M., Schonig, K., Eckert, H., Eschstruth, A., Mianne, J., Renaud, J.B., Schneider-Maunoury, S., Shkumatava, A., Teboul, L., Kent, J. et al. (2016) Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol., 17, 148.
Ran, F.A., Hsu, P.D., Wright, J., Agarwala, V., Scott, D.A. and Zhang, F. (2013) Genome engineering using the CRISPR-Cas9 system. Nat. Protoc., 8, 2281-2308.
Kishore, S., Khanna, A. and Stamm, S. (2008) Rapid generation of splicing reporters with pSpliceExpress. Gene, 427, 104-110.
Cox, J. and Mann, M. (2008) MaxQuant enables high pep-tide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol., 26, 1367-1372.
Luber, C.A., Cox, J., Lauterbach, H., Fancke, B., Selbach, M., Tschopp, J., Akira, S., Wiegand, M., Hochrein, H., O'Keeffe, M. et al. (2010) Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity, 32, 279-289.
Perner, B., Englert, C. and Bollig, F. (2007) The Wilms tumor genes wt1a and wt1b control different steps during formation of the zebrafish pronephros. Dev. Biol., 309, 87-96.
Haas, P. and Gilmour, D. (2006) Chemokine signaling mediates self-organizing tissue migration in the zebrafish lateral line. Dev. Cell, 10, 673-680.
Hammond, C.L. and Schulte-Merker, S. (2009) Two populations of endochondral osteoblasts with differential sensitivity to hedgehog signalling. Development, 136, 3991-4000.
Hwang, W.Y., Fu, Y., Reyon, D., Maeder, M.L., Tsai, S.Q., Sander, J.D., Peterson, R.T., Yeh, J.R. and Joung, J.K. (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat. Biotechnol., 31, 227-229.
Jao, L.E., Wente, S.R. and Chen, W. (2013) Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc. Natl. Acad. Sci. U. S. A., 110, 13904-13909.