SCUBE3 loss-of-function causes a recognizable recessive developmental disorder due to defective bone morphogenetic protein signaling

Abstract

Signal peptide-CUB-EGF domain-containing protein 3 (SCUBE3) is a member of a small family of multifunctional cell surface-anchored glycoproteins functioning as co-receptors for a variety of growth factors. Here we report that biallelic inactivating variants in SCUBE3 have pleiotropic consequences on development and cause a previously unrecognized syndromic disorder. Eighteen affected individuals from nine unrelated families showed a consistent phenotype characterized by reduced growth, skeletal anomalies, distinctive craniofacial appearance, and dental anomalies. In vitro functional validation studies demonstrated a variable impact of disease-causing variants on transcript processing, protein secretion and function, and their dysregulating effect on bone morphogenetic protein (BMP) signaling. We show that SCUBE3 acts as a BMP2/BMP4 co-receptor, recruits the BMP receptor complexes into raft microdomains, and positively modulates signaling possibly by augmenting the specific interactions between BMPs and BMP type I receptors. Scube3 -/mice showed craniofacial and dental defects, reduced body size and defective endochondral bone growth due to impaired BMP-mediated chondrogenesis and osteogenesis, recapitulating the human disorder. Our findings identify a human disease caused by defective function of a member of the SCUBE family, and link SCUBE3 to processes controlling growth, morphogenesis, and bone and teeth development through modulation of BMP signaling.

Saturation mutagenesis defines novel mouse models of severe spine deformity

“…The implication of SCUBE3 as a skeletal disease-causing gene was supported by our identification of mice homozygous for the Scube3 C301Y allele developing severe skeletal defects. In the course of this study, multiple patients were reported with recessive SCUBE3 mutations presenting with skeletal and non-skeletal manifestations similar to the index patient reported here (Lin et al, 2021). Using two independent experimental assays, we show that missense variants identified in our mouse model and the undiagnosed patient reported here, as well as other missense variants recently reported (Lin et al, 2021), abrogated the interaction between SCUBE3 and SCUBE1 and reduced transactivation of Smad signaling.…”

“…(D) Schematic of the human SCUBE3 protein, including relative positions of annotated domains. Recently published variants identified in patients with skeletal disease (Lin et al, 2021) are shown in bold black. The human ortholog of the mouse ENU variant and the novel human variant reported here are shown in red.…”

“…A.U., arbitrary units. embryonic development (Fuchs et al, 2016;Lin et al, 2021;Xavier et al, 2013).…”

“…Although all three Scube genes (Scube1-3) are implicated in regulating proper skeletal development in mice (Fuchs et al, 2016;Lin et al, 2015;Tu et al, 2008), mutations in any one of three human Scube genes (SCUBE1-3) have yet to be associated with human disease. However, during the course of this study, multiple subjects with recessive SCUBE3 mutations were reported with short stature, oral-facial abnormalities, skeletal abnormalities and, although variable, spine deformity, suggesting a novel SCUBE3associated skeletal disease (Lin et al, 2021). To identify additional patients with skeletal disease potentially attributable to mutations in SCUBE3, we queried the Baylor Genetics Laboratory database, which includes nonsynonymous variants identified from clinical exome sequencing and clinician-provided clinical synopses.…”

“…We performed co-immunoprecipitation experiments to test potential deleterious effects of the novel SCUBE3 p.(Arg929Gly) variant on SCUBE1-SCUBE3 heterodimerization. Results were compared to an allelic series, including to recently reported SCUBE3 variants (Lin et al, 2021), to a common SCUBE3 p.(Thr231Ala) polymorphism (rs79753406) predicted to have normal function, and to the SCUBE3 p.(Cys301Tyr) variant orthologous to our mouse ENU allele associated with severe spine deformity (Fig. 2D).…”