Pathogenic RAB34 variants impair primary cilium assembly and cause a novel oral-facial-digital syndrome

. 2023 Sep 05 ; 32 (18) : 2822-2831.

Jazyk angličtina Země Velká Británie, Anglie Médium print

Typ dokumentu časopisecké články, práce podpořená grantem, Research Support, N.I.H., Extramural

Perzistentní odkaz   https://www.medvik.cz/link/pmid37384395

Grantová podpora
P30 CA016359 NCI NIH HHS - United States
R35 GM137956 NIGMS NIH HHS - United States

Oral-facial-digital syndromes (OFDS) are a group of clinically and genetically heterogeneous disorders characterized by defects in the development of the face and oral cavity along with digit anomalies. Pathogenic variants in over 20 genes encoding ciliary proteins have been found to cause OFDS through deleterious structural or functional impacts on primary cilia. We identified by exome sequencing bi-allelic missense variants in a novel disease-causing ciliary gene RAB34 in four individuals from three unrelated families. Affected individuals presented a novel form of OFDS (OFDS-RAB34) accompanied by cardiac, cerebral, skeletal and anorectal defects. RAB34 encodes a member of the Rab GTPase superfamily and was recently identified as a key mediator of ciliary membrane formation. Unlike many genes required for cilium assembly, RAB34 acts selectively in cell types that use the intracellular ciliogenesis pathway, in which nascent cilia begin to form in the cytoplasm. We find that the protein products of these pathogenic variants, which are clustered near the RAB34 C-terminus, exhibit a strong loss of function. Although some variants retain the ability to be recruited to the mother centriole, cells expressing mutant RAB34 exhibit a significant defect in cilium assembly. While many Rab proteins have been previously linked to ciliogenesis, our studies establish RAB34 as the first small GTPase involved in OFDS and reveal the distinct clinical manifestations caused by impairment of intracellular ciliogenesis.

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Mill, P., Christensen, S.T. and Pedersen, L.B. (2023) Primary cilia as dynamic and diverse signalling hubs in development and disease. Nat. Rev. Genet., 24, 421–441. PubMed PMC

Anvarian, Z., Mykytyn, K., Mukhopadhyay, S., Pedersen, L.B. and Christensen, S.T. (2019) Cellular signalling by primary cilia in development, organ function and disease. Nat. Rev. Nephrol., 15, 199–219. PubMed PMC

Valente, E.M., Rosti, R.O., Gibbs, E. and Gleeson, J.G. (2014) Primary cilia in neurodevelopmental disorders. Nat. Rev. Neurol., 10, 27–36. PubMed PMC

Focşa, I.O., Budişteanu, M. and Bălgrădean, M. (2021) Clinical and genetic heterogeneity of primary ciliopathies (review). Int. J. Mol. Med., 48, 176. PubMed PMC

Bruel, A.-L., Franco, B., Duffourd, Y., Thevenon, J., Jego, L., Lopez, E., Deleuze, J.-F., Doummar, D., Giles, R.H., Johnson, C.A.  et al. (2017) Fifteen years of research on oral-facial-digital syndromes: from 1 to 16 causal genes. J. Med. Genet., 54, 371–380. PubMed PMC

Li, C., Jensen, V.L., Park, K., Kennedy, J., Garcia-Gonzalo, F.R., Romani, M., De Mori, R., Bruel, A.-L., Gaillard, D., Doray, B.  et al. (2016) MKS5 and CEP290 dependent assembly pathway of the ciliary transition zone. PLoS Biol., 14, e1002416. PubMed PMC

Lambacher, N.J., Bruel, A.-L., van  Dam, T.J.P., Szymańska, K., Slaats, G.G., Kuhns, S., McManus, G.J., Kennedy, J.E., Gaff, K., Wu, K.M.  et al. (2016) TMEM107 recruits ciliopathy proteins to subdomains of the ciliary transition zone and causes Joubert syndrome. Nat. Cell Biol., 18, 122–131. PubMed PMC

Chevrier, V., Bruel, A.-L., Van Dam, T.J.P., Franco, B., Lo Scalzo, M., Lembo, F., Audebert, S., Baudelet, E., Isnardon, D., Bole, A.  et al. (2016) OFIP/KIAA0753 forms a complex with OFD1 and FOR20 at pericentriolar satellites and centrosomes and is mutated in one individual with oral-facial-digital syndrome. Hum. Mol. Genet., 25, 497–513. PubMed

Thauvin-Robinet, C., Lee, J.S., Lopez, E., Herranz-Pérez, V., Shida, T., Franco, B., Jego, L., Ye, F., Pasquier, L., Loget, P.  et al. (2014) The oral-facial-digital syndrome gene C2CD3 encodes a positive regulator of centriole elongation. Nat. Genet., 46, 905–911. PubMed PMC

Toriyama, M., Lee, C., Taylor, S.P., Duran, I., Cohn, D.H., Bruel, A.-L., Tabler, J.M., Drew, K., Kelly, M.R., Kim, S.  et al. (2016) The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery. Nat. Genet., 48, 648–656. PubMed PMC

Lopez, E., Thauvin-Robinet, C., Reversade, B., Khartoufi, N.E., Devisme, L., Holder, M., Ansart-Franquet, H., Avila, M., Lacombe, D., Kleinfinger, P.  et al. (2014) C5orf42 is the major gene responsible for OFD syndrome type VI. Hum. Genet., 133, 367–377. PubMed

Thevenon, J., Duplomb, L., Phadke, S., Eguether, T., Saunier, A., Avila, M., Carmignac, V., Bruel, A.-L., St-Onge, J., Duffourd, Y.  et al. (2016) Autosomal recessive IFT57 hypomorphic mutation cause ciliary transport defect in unclassified oral-facial-digital syndrome with short stature and brachymesophalangia. Clin. Genet., 90, 509–517. PubMed PMC

Valente, E.M., Logan, C.V., Mougou-Zerelli, S., Lee, J.H., Silhavy, J.L., Brancati, F., Iannicelli, M., Travaglini, L., Romani, S., Illi, B.  et al. (2010) Mutations in TMEM216 perturb ciliogenesis and cause Joubert, Meckel and related syndromes. Nat. Genet., 42, 619–625. PubMed PMC

Adly, N., Alhashem, A., Ammari, A. and Alkuraya, F.S. (2014) Ciliary genes TBC1D32/C6orf170 and SCLT1 are mutated in patients with OFD type IX. Hum. Mutat., 35, 36–40. PubMed

Shamseldin, H.E., Rajab, A., Alhashem, A., Shaheen, R., Al-Shidi, T., Alamro, R., Al Harassi, S. and Alkuraya, F.S. (2013) Mutations in DDX59 implicate RNA helicase in the pathogenesis of orofaciodigital syndrome. Am. J. Hum. Genet., 93, 555–560. PubMed PMC

Thomas, S., Legendre, M., Saunier, S., Bessières, B., Alby, C., Bonnière, 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. PubMed PMC

Johnston, J.J., Lee, C., Wentzensen, I.M., Parisi, M.A., Crenshaw, M.M., Sapp, J.C., Gross, J.M., Wallingford, J.B. and Biesecker, L.G. (2017) Compound heterozygous alterations in intraflagellar transport protein CLUAP1 in a child with a novel Joubert and oral-facial-digital overlap syndrome. Cold Spring Harb. Mol. Case Stud., 3, a001321. PubMed PMC

Monroe, G.R., Kappen, I.F., Stokman, M.F., Terhal, P.A., van den  Boogaard, M.-J.H., Savelberg, S.M., van der  Veken, L.T., van  Es, R.J., Lens, S.M., Hengeveld, R.C.  et al. (2016) Compound heterozygous NEK1 variants in two siblings with oral-facial-digital syndrome type II (Mohr syndrome). Eur. J. Hum. Genet., 24, 1752–1760. PubMed PMC

Strong, A., Simone, L., Krentz, A., Vaccaro, C., Watson, D., Ron, H., Kalish, J.M., Pedro, H.F., Zackai, E.H. and Hakonarson, H. (2021) Expanding the genetic landscape of oral-facial-digital syndrome with two novel genes. Am. J. Med. Genet. A, 185, 2409–2416. PubMed PMC

Shaheen, R., Jiang, N., Alzahrani, F., Ewida, N., Al-Sheddi, T., Alobeid, E., Musaev, D., Stanley, V., Hashem, M., Ibrahim, N.  et al. (2019) Bi-allelic mutations in FAM149B1 cause abnormal primary cilium and a range of ciliopathy phenotypes in humans. Am. J. Hum. Genet., 104, 731–737. PubMed PMC

Iturrate, A., Rivera-Barahona, A., Flores, C.-L., Otaify, G.A., Elhossini, R., Perez-Sanz, M.L., Nevado, J., Tenorio-Castano, J., Triviño, J.C., Garcia-Gonzalo, F.R.  et al. (2022) Mutations in SCNM1 cause orofaciodigital syndrome due to minor intron splicing defects affecting primary cilia. Am. J. Hum. Genet., 109, 1828–1849. PubMed PMC

Ferrante, M.I., Giorgio, G., Feather, S.A., Bulfone, A., Wright, V., Ghiani, M., Selicorni, A., Gammaro, L., Scolari, F., Woolf, A.S.  et al. (2001) Identification of the gene for oral-facial-digital type I syndrome. Am. J. Hum. Genet., 68, 569–576. PubMed PMC

Mascibroda, L.G., Shboul, M., Elrod, N.D., Colleaux, L., Hamamy, H., Huang, K.-L., Peart, N., Singh, M.K., Lee, H., Merriman, B.  et al. (2022) INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the integrator complex. Nat. Commun., 13, 6054. PubMed PMC

Shaheen, R., Szymanska, K., Basu, B., Patel, N., Ewida, N., Faqeih, E., Al Hashem, A., Derar, N., Alsharif, H., Aldahmesh, M.A.  et al. (2016) Characterizing the morbid genome of ciliopathies. Genome Biol., 17, 242. PubMed PMC

Wang, L. and Dynlacht, B.D. (2018) The regulation of cilium assembly and disassembly in development and disease. Development, 145, dev151407. PubMed PMC

Breslow, D.K. and Holland, A.J. (2019) Mechanism and regulation of centriole and cilium biogenesis. Annu. Rev. Biochem., 88, 691–724. PubMed PMC

Zhao, H., Khan, Z. and Westlake, C.J. (2023) Ciliogenesis membrane dynamics and organization. Semin. Cell Dev. Biol., 133, 20–31. PubMed PMC

Sorokin, S.P. (1968) Reconstructions of centriole formation and ciliogenesis in mammalian lungs. J. Cell Sci., 3, 207–230. PubMed

Sorokin, S. (1962) Centrioles and the formation of rudimentary cilia by fibroblasts and smooth muscle cells. J. Cell Biol., 15, 363–377. PubMed PMC

Molla-Herman, A., Ghossoub, R., Blisnick, T., Meunier, A., Serres, C., Silbermann, F., Emmerson, C., Romeo, K., Bourdoncle, P., Schmitt, A.  et al. (2010) The ciliary pocket: an endocytic membrane domain at the base of primary and motile cilia. J. Cell Sci., 123, 1785–1795. PubMed

Garcia, G., Raleigh, D.R. and Reiter, J.F. (2018) How the ciliary membrane is organized inside-out to communicate outside-in. Curr. Biol., 28, R421–R434. PubMed PMC

Pfeffer, S.R. (2017) Rab GTPases: master regulators that establish the secretory and endocytic pathways. Mol. Biol. Cell, 28, 712–715. PubMed PMC

Stenmark, H. (2009) Rab GTPases as coordinators of vesicle traffic. Nat. Rev. Mol. Cell Biol., 10, 513–525. PubMed

Hutagalung, A.H. and Novick, P.J. (2011) Role of Rab GTPases in membrane traffic and cell physiology. Physiol. Rev., 91, 119–149. PubMed PMC

Homma, Y., Hiragi, S. and Fukuda, M. (2021) Rab family of small GTPases: an updated view on their regulation and functions. FEBS J., 288, 36–55. PubMed PMC

Oguchi, M.E., Okuyama, K., Homma, Y. and Fukuda, M. (2020) A comprehensive analysis of Rab GTPases reveals a role for Rab34 in serum starvation-induced primary ciliogenesis. J. Biol. Chem., 295, 12674–12685. PubMed PMC

Blacque, O.E., Scheidel, N. and Kuhns, S. (2018) Rab GTPases in cilium formation and function. Small GTPases, 9, 76–94. PubMed PMC

Jewett, C.E., Soh, A.W.J., Lin, C.H., Lu, Q., Lencer, E., Westlake, C.J., Pearson, C.G. and Prekeris, R. (2021) RAB19 directs cortical remodeling and membrane growth for primary ciliogenesis. Dev. Cell, 56, 325–340.e8. PubMed PMC

Kuhns, S., Seixas, C., Pestana, S., Tavares, B., Nogueira, R., Jacinto, R., Ramalho, J.S., Simpson, J.C., Andersen, J.S., Echard, A.  et al. (2019) Rab35 controls cilium length, function and membrane composition. EMBO Rep., 20, e47625. PubMed PMC

Stuck, M.W., Chong, W.M., Liao, J.-C. and Pazour, G.J. (2021) Rab34 is necessary for early stages of intracellular ciliogenesis. Curr. Biol., 31, 2887–2894.e4. PubMed PMC

Ganga, A.K., Kennedy, M.C., Oguchi, M.E., Gray, S., Oliver, K.E., Knight, T.A., De La Cruz, E.M., Homma, Y., Fukuda, M. and Breslow, D.K. (2021) Rab34 GTPase mediates ciliary membrane formation in the intracellular ciliogenesis pathway. Curr. Biol., 31, 2895–2905.e7. PubMed PMC

Goldenberg, N.M., Grinstein, S. and Silverman, M. (2007) Golgi-bound Rab34 is a novel member of the secretory pathway. Mol. Biol. Cell, 18, 4762–4771. PubMed PMC

Kasmapour, B., Gronow, A., Bleck, C.K.E., Hong, W. and Gutierrez, M.G. (2012) Size-dependent mechanism of cargo sorting during lysosome-phagosome fusion is controlled by Rab34. Proc. Natl. Acad. Sci. U. S. A., 109, 20485–20490. PubMed PMC

Wang, T. and Hong, W. (2002) Interorganellar regulation of lysosome positioning by the Golgi apparatus through Rab34 interaction with Rab-interacting lysosomal protein. Mol. Biol. Cell, 13, 4317–4332. PubMed PMC

Xu, S., Liu, Y., Meng, Q. and Wang, B. (2018) Rab34 small GTPase is required for hedgehog signaling and an early step of ciliary vesicle formation in mouse. J. Cell Sci., 131, jcs213710. PubMed PMC

Kanie, T., Love, J.F., Fisher, S.D., Gustavsson, A.-K. and Jackson, P.K. (2023) A hierarchical pathway for assembly of the distal appendages that organize primary cilia. bioRxiv, 2023.01.06.522944. https://pubmed.ncbi.nlm.nih.gov/36711481/  https://www.biorxiv.org/content/10.1101/2023.01.06.522944v2. DOI

Pusapati, G.V., Kong, J.H., Patel, B.B., Krishnan, A., Sagner, A., Kinnebrew, M., Briscoe, J., Aravind, L. and Rohatgi, R. (2018) CRISPR screens uncover genes that regulate target cell sensitivity to the morphogen sonic hedgehog. Dev. Cell, 44, 113–129.e8. PubMed PMC

Dickinson, M.E., Flenniken, A.M., Ji, X., Teboul, L., Wong, M.D., White, J.K., Meehan, T.F., Weninger, W.J., Westerberg, H., Adissu, H.  et al. (2016) High-throughput discovery of novel developmental phenotypes. Nature, 537, 508–514. PubMed PMC

Murcia, N.S., Richards, W.G., Yoder, B.K., Mucenski, M.L., Dunlap, J.R. and Woychik, R.P. (2000) The oak ridge polycystic kidney (ORPK) disease gene is required for left-right axis determination. Development, 127, 2347–2355. PubMed

Marszalek, J.R., Ruiz-Lozano, P., Roberts, E., Chien, K.R. and Goldstein, L.S. (1999) Situs inversus and embryonic ciliary morphogenesis defects in mouse mutants lacking the KIF3A subunit of kinesin-II. Proc. Natl. Acad. Sci. U. S. A., 96, 5043–5048. PubMed PMC

Sobreira, N., Schiettecatte, F., Valle, D. and Hamosh, A. (2015) GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum. Mutat., 36, 928–930. PubMed PMC

Yakar, O. and Tatar, A. (2022) INTU-related oral-facial-digital syndrome XVII: clinical spectrum of a rare disorder. Am. J. Med. Genet. A, 188, 590–594. PubMed

Syed, S., Sawant, P.R., Spadigam, A. and Dhupar, A. (2021) Oro-facial-digital syndrome type I: a case report with novel features. Autops. Case Rep., 11, e2021315. PubMed PMC

Verma, P.K. and Bhat, N.K. (2021) Oro-facial-digital syndrome: unspecified type with the spontaneous fusion of cleft palate. Contemp. Clin. Dent., 12, 454–458. PubMed PMC

Sukarova-Angelovska, E., Angelkova, N., Palcevska-Kocevska, S. and Kocova, M. (2012) The many faces of oral-facial-digital syndrome. Balk. J. Med. Genet., 15, 37–44. PubMed PMC

Digilio, M.C., Giannotti, A., Pagnotta, G., Mingarelli, R. and Dallapiccola, B. (2008) Joint dislocation and cerebral anomalies are consistently associated with oral-facial-digital syndrome type IV. Clin. Genet., 48, 156–159. PubMed

Mahato, P.R. and Pandey, S.B. (2012) Orofaciodigital syndrome type-VI (Varadi–Papp syndrome) with several Y-shaped metacarpals. Indian J. Hum. Genet., 18, 376–378. PubMed PMC

Iaccarino, M., Lonardo, F., Giugliano, M. and Della Bruna, M.D. (1985) Prenatal diagnosis of Mohr syndrome by ultrasonography. Prenat. Diagn., 5, 415–418. PubMed

Wentzensen, I.M., Johnston, J.J., Keppler-Noreuil, K., Acrich, K., David, K., Johnson, K.D., Graham, J.M., Sapp, J.C. and Biesecker, L.G. (2015) Exome sequencing identifies novel mutations in C5orf42 in patients with Joubert syndrome with oral–facial–digital anomalies. Hum. Genome Var., 2, 15045. PubMed PMC

Meinecke, P. and Hayek, H. (1990) Orofaciodigital syndrome type IV (Mohr-Majewski syndrome) with severe expression expanding the known spectrum of anomalies. J. Med. Genet., 27, 200–202. PubMed PMC

Simonini, C., Floeck, A., Strizek, B., Mueller, A., Gembruch, U. and Geipel, A. (2022) Fetal ciliopathies: a retrospective observational single-center study. Arch. Gynecol. Obstet., 306, 71–83. PubMed PMC

Barisic, I., Boban, L., Loane, M., Garne, E., Wellesley, D., Calzolari, E., Dolk, H., Addor, M.-C., Bergman, J.E., Braz, P.  et al. (2015) Meckel–Gruber syndrome: a population-based study on prevalence, prenatal diagnosis, clinical features, and survival in Europe. Eur. J. Hum. Genet., 23, 746–752. PubMed PMC

Roosing, S., Romani, M., Isrie, M., Rosti, R.O., Micalizzi, A., Musaev, D., Mazza, T., Al-gazali, L., Altunoglu, U., Boltshauser, E.  et al. (2016) Mutations in CEP120 cause Joubert syndrome as well as complex ciliopathy phenotypes. J. Med. Genet., 53, 608–615. PubMed PMC

Toriello, H.V., Franco, B., Bruel, A.-L. and Thauvin-Robinet, C. (2016) Oral-Facial-Digital Syndrome Type I. University of Washington, Seattle. PubMed

Hsieh, Y.C. and Hou, J.W. (1999) Oral-facial-digital syndrome with Y-shaped fourth metacarpals and endocardial cushion defect. Am. J. Med. Genet., 86, 278–281. PubMed

Kobayashi, T., Ikeda, T., Ota, R., Yasukawa, T. and Itoh, H. (2022) The atypical small GTPase RABL3 interacts with RAB11 to regulate early ciliogenesis in human cells. J. Cell Sci., 135, jcs260021. PubMed

Jenkins, D., Seelow, D., Jehee, F.S., Perlyn, C.A., Alonso, L.G., Bueno, D.F., Donnai, D., Josifova, D., Mathijssen, I.M.J., Morton, J.E.V.  et al. (2007) RAB23 mutations in carpenter syndrome imply an unexpected role for hedgehog signaling in cranial-suture development and obesity. Am. J. Hum. Genet., 80, 1162–1170. PubMed PMC

Eggenschwiler, J.T., Espinoza, E. and Anderson, K.V. (2001) Rab23 is an essential negative regulator of the mouse sonic hedgehog signalling pathway. Nature, 412, 194–198. PubMed

Fuller, K., O’Connell, J.T., Gordon, J., Mauti, O. and Eggenschwiler, J. (2014) Rab23 regulates nodal signaling in vertebrate left-right patterning independently of the hedgehog pathway. Dev. Biol., 391, 182–195. PubMed

Hor, C.H.H., Lo, J.C.W., Cham, A.L.S., Leong, W.Y. and Goh, E.L.K. (2021) Multifaceted functions of Rab23 on primary cilium-mediated and hedgehog signaling-mediated cerebellar granule cell proliferation. J. Neurosci., 41, 6850–6863. PubMed PMC

Sato, T., Iwano, T., Kunii, M., Matsuda, S., Mizuguchi, R., Jung, Y., Hagiwara, H., Yoshihara, Y., Yuzaki, M., Harada, R.  et al. (2014) Rab8a and Rab8b are essential for several apical transport pathways but insufficient for ciliogenesis. J. Cell Sci., 127, 422–431. PubMed PMC

Paila, U., Chapman, B.A., Kirchner, R. and Quinlan, A.R. (2013) GEMINI: integrative exploration of genetic variation and genome annotations. PLoS Comput. Biol., 9, e1003153. PubMed PMC

Rodrigues, C.H.M., Pires, D.E.V. and Ascher, D.B. (2021) DynaMut2: assessing changes in stability and flexibility upon single and multiple point missense mutations. Protein Sci., 30, 60–69. PubMed PMC

Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A.  et al. (2022) AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res., 50, D439–D444. PubMed PMC

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