Arhinia, or absence of the nose, is a rare malformation of unknown etiology that is often accompanied by ocular and reproductive defects. Sequencing of 40 people with arhinia revealed that 84% of probands harbor a missense mutation localized to a constrained region of SMCHD1 encompassing the ATPase domain. SMCHD1 mutations cause facioscapulohumeral muscular dystrophy type 2 (FSHD2) via a trans-acting loss-of-function epigenetic mechanism. We discovered shared mutations and comparable DNA hypomethylation patterning between these distinct disorders. CRISPR/Cas9-mediated alteration of smchd1 in zebrafish yielded arhinia-relevant phenotypes. Transcriptome and protein analyses in arhinia probands and controls showed no differences in SMCHD1 mRNA or protein abundance but revealed regulatory changes in genes and pathways associated with craniofacial patterning. Mutations in SMCHD1 thus contribute to distinct phenotypic spectra, from craniofacial malformation and reproductive disorders to muscular dystrophy, which we speculate to be consistent with oligogenic mechanisms resulting in pleiotropic outcomes.
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We thank all participants, family members and clinical staff for their generous contributions of time and materials to this research. We thank T. Gillis, J. Ruliera, C. Hanscom, C. Antolik and M. Anderson for technical assistance. This project was funded by grants from the National Institutes of Health ((NIH) R00MH095867 and R01HD081256 to M.E.T.; P01GM061354 to M.E.T., J.F.G., C.C.M. and E.C.L.; T32HD007396 to H. Brand; P50HD028138 to W.F.C., S.B.S., M.E.T., N.K. and E.E.D.; R01HD043341 and MGH Robert and Laura Reynolds Research Scholar Award to S.B.S.; K23HD073304-02 and 1SI2ES025429-01 to N.D.S.; P50DK096415 to N.K. and R01AR062587 to P.L.J.); the March of Dimes (FY15-255 to M.E.T.); the Medical Research Council (MR/M02122X/1 to J.A.M.); the German Research Foundation (SFB665 to A.M.K.) and the Berlin Institute of Health (BIH-CRG1 to A.M.K.). D.R.F., R.R.M. (MC_PC_U127574433), D.S.D., H. Bengani, K.A.W., J.R., J.K.R. and J.A.M. are funded by program grants from the Medical Research Council (MRC) Human Genetics Unit award to the University of Edinburgh. M.A. is funded by the University of Edinburgh Institute of Genomics and Molecular Medicine Translational Initiative Fund. S.A.M. is supported by U54-NS053672, which funds the Iowa, Paul D. Wellstone Muscular Dystrophy Cooperative Research Center. N.K. is supported as a Distinguished Jean and George Brumley Professor at Duke University, and M.E.T. is supported as the Desmond and Ann Heathwood MGH Research Scholar.
The authors declare no competing financial interests.
Supplementary Figures 1–11 (PDF 5639 kb)
Arhina cohort-wide phenotype information. (XLSX 16 kb)
Individual level phenotype information. (XLSX 22 kb)
Ethnic specific analysis of SMCHD1 mutation frequency. (XLSX 9 kb)
DNA methylation analysis of D4Z4 repeats in arhinia cases and familial controls. (XLSX 17 kb)
Representative zebrafish morphometric data. (XLSX 21 kb)
Mouse CRISPR of SMCHD1 missense mutations. (XLSX 11 kb)
Allele-specific expression of SMCHD1 in subjects with a mutation. (XLSX 10 kb)
Differential expression analysis between arhinia cases and familial controls. (XLSX 1601 kb)
Enrichment of nominal human genes (P < 0.05) against mouse Smchd1 targets and differentially expressed genes in Smchd1-null mouse. (XLSX 10 kb)
Overlapping genes with significant dysregulation in the same direction in mouse and human. (XLSX 10 kb)
Primers used in study. (XLSX 11 kb)
About this article
26th Annual Facioscapulohumeral Dystrophy International Research Congress Marseille, France, 19–20 June 2019
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