TY - JOUR
T1 - Mutations in SCNM1 cause orofaciodigital syndrome due to minor intron splicing defects affecting primary cilia
AU - Iturrate, Asier
AU - Rivera-Barahona, Ana
AU - Flores, Carmen Lisset
AU - Otaify, Ghada A.
AU - Elhossini, Rasha
AU - Perez-Sanz, Marina L.
AU - Nevado, Julián
AU - Tenorio-Castano, Jair
AU - Triviño, Juan Carlos
AU - Garcia-Gonzalo, Francesc R.
AU - Piceci-Sparascio, Francesca
AU - De Luca, Alessandro
AU - Martínez, Leopoldo
AU - Kalaycı, Tugba
AU - Lapunzina, Pablo
AU - Altunoglu, Umut
AU - Aglan, Mona
AU - Abdalla, Ebtesam
AU - Ruiz-Perez, Victor L.
N1 - Publisher Copyright:
© 2022 American Society of Human Genetics
PY - 2022/10/6
Y1 - 2022/10/6
N2 - 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.
AB - 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.
KW - SCNM1
KW - U12 introns
KW - ciliopathy
KW - hedgehog signaling
KW - minor spliceosome
KW - orofaciodigital syndrome
KW - primary cilia
UR - http://www.scopus.com/inward/record.url?scp=85139276148&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85139276148&partnerID=8YFLogxK
U2 - 10.1016/j.ajhg.2022.08.009
DO - 10.1016/j.ajhg.2022.08.009
M3 - Article
C2 - 36084634
AN - SCOPUS:85139276148
SN - 0002-9297
VL - 109
SP - 1828
EP - 1849
JO - American Journal of Human Genetics
JF - American Journal of Human Genetics
IS - 10
ER -