1. Mutations in SCNM1 cause orofaciodigital syndrome due to minor intron splicing defects affecting primary cilia
- Author
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Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), National Institutes of Health (US), Iturrate, Asier, Rivera-Barahona, Ana, Flores, Carmen-Lisset, Otaify, Ghada A., Elhossini, Rasha, Perez-Sanz, Marina L., Nevado, Julian, Tenorio, Jair, Triviño, Juan Carlos, Garcia-Gonzalo, Francesc R., Piceci-Sparascio, Francesca, Luca, Alessandro De, Martínez, Leopoldo, Kalaycı, Tugba, Lapunzina, Pablo, Altunoglu, Umut, Aglan, Mona, Abdalla, Ebtesam, Ruiz-Pérez, Victor L., Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), National Institutes of Health (US), Iturrate, Asier, Rivera-Barahona, Ana, Flores, Carmen-Lisset, Otaify, Ghada A., Elhossini, Rasha, Perez-Sanz, Marina L., Nevado, Julian, Tenorio, Jair, Triviño, Juan Carlos, Garcia-Gonzalo, Francesc R., Piceci-Sparascio, Francesca, Luca, Alessandro De, Martínez, Leopoldo, Kalaycı, Tugba, Lapunzina, Pablo, Altunoglu, Umut, Aglan, Mona, Abdalla, Ebtesam, and Ruiz-Pérez, Victor L.
- Abstract
Orofaciodigital syndrome (OFD) is a genetically heterogeneous ciliopathy characterized by anomalies of the oral cavity, face, and digits. We describe individuals with OFD from three unrelated families having bi-allelic loss-of-function variants in SCNM1 as the cause of their condition. SCNM1 encodes a protein recently shown to be a component of the human minor spliceosome. However, so far the effect of loss of SCNM1 function on human cells had not been assessed. Using a comparative transcriptome analysis between fibroblasts derived from an OFD-affected individual harboring SCNM1 mutations and control fibroblasts, we identified a set of genes with defective minor intron (U12) processing in the fibroblasts of the affected subject. These results were reproduced in SCNM1 knockout hTERT RPE-1 (RPE-1) cells engineered by CRISPR-Cas9-mediated editing and in SCNM1 siRNA-treated RPE-1 cultures. Notably, expression of TMEM107 and FAM92A encoding primary cilia and basal body proteins, respectively, and that of DERL2, ZC3H8, and C17orf75, were severely reduced in SCNM1-deficient cells. Primary fibroblasts containing SCNM1 mutations, as well as SCNM1 knockout and SCNM1 knockdown RPE-1 cells, were also found with abnormally elongated cilia. Conversely, cilia length and expression of SCNM1-regulated genes were restored in SCNM1-deficient fibroblasts following reintroduction of SCNM1 via retroviral delivery. Additionally, functional analysis in SCNM1-retrotransduced fibroblasts showed that SCNM1 is a positive mediator of Hedgehog (Hh) signaling. Our findings demonstrate that defective U12 intron splicing can lead to a typical ciliopathy such as OFD and reveal that primary cilia length and Hh signaling are regulated by the minor spliceosome through SCNM1 activity.
- Published
- 2022