De novo mutations in inhibitors of Wnt, BMP, and Ras/ERK signaling pathways in non-syndromic midline craniosynostosis

Abstract

Non-syndromic craniosynostosis (NSC) is a frequent congenital malformation in which one or more cranial sutures fuse prematurely. Mutations causing rare syndromic craniosynostoses in humans and engineered mouse models commonly increase signaling of the Wnt, bone morphogenetic protein (BMP), or Ras/ERK pathways, converging on shared nuclear targets that promote bone formation. In contrast, the genetics of NSC is largely unexplored. More than 95% of NSC is sporadic, suggesting a role for de novo mutations. Exome sequencing of 291 parent-offspring trios with midline NSC revealed 15 probands with heterozygous damaging de novo mutations in 12 negative regulators of Wnt, BMP, and Ras/ERK signaling (10.9-fold enrichment, P = 2.4 × 10 −11 ). SMAD6 had 4 de novo and 14 transmitted mutations; no other gene had more than 1. Four familial NSC kindreds had mutations in genes previously implicated in syndromic disease. Collectively, these mutations contribute to 10% of probands. Mutations are predominantly loss-of-function, implicating haploinsufficiency as a frequent mechanism. A common risk variant near BMP2 increased the penetrance of SMAD6 mutations and was overtransmitted to patients with de novo mutations in other genes in these pathways, supporting a frequent two-locus pathogenesis. These findings implicate new genes in NSC and demonstrate related pathophysiology of common non-syndromic and rare syndromic craniosynostoses. These findings have implications for diagnosis, risk of recurrence, and risk of adverse neurodevelopmental outcomes. Finally, the use of pathways identified in rare syndromic disease to find genes accounting for non-syndromic cases may prove broadly relevant to understanding other congenital disorders featuring high locus heterogeneity.

A Higher Proportion of Craniosynostosis Genes Are Cancer Driver Genes

“…The involvement of FGF (fibroblast growth factor), FGFR (fibroblast growth factor receptor), and MAPK/ERK signaling pathways in CRS has long been discussed in the literature (Marie et al, 2005; Shukla et al, 2007; Kim et al, 2015; Kosty and Vogel, 2015; Pfaff et al, 2016; Timberlake et al, 2017). However, our top hit gene-set is KEGG’s cancer pathway, and this link between CRS and cancer is to our knowledge rarely discussed in the literature.…”

“…These 17 new genes found through this process were added to the CRS genes list: AXIN2 (Yilmaz et al, 2018), BBS9 (Justice et al, 2012; Sewda et al, 2019), BCOR (O’Byrne et al, 2017) (for Oculo-facio-cardio-dental syndrome, or microphthalmia syndrome), BGLAP (Sowińska-Seidler et al, 2018), COLEC10 (for 3MC syndrome) (Munye et al, 2017), FGFRL1 (Rieckmann et al, 2009) (for Antley-Bixler syndrome), GCK (for Greig cephalopolysyndactyly syndrome) (Zung et al, 2011), LMNA (Sowińska-Seidler et al, 2018), PPP3CA (Mizuguchi et al, 2018), PTH2R (Kim et al, 2015), RAF1 (for Noonan syndrome with multiple lentigines, or leopard syndrome) (Rodríguez et al, 2019), SIX2 (for frontonasal dysplasia syndrome) (Hufnagel et al, 2016), SMURF1, SPRY1, SPRY4 (Timberlake et al, 2016, 2017), TCOF1 (for Treacher Collins syndrome) (Horiuchi et al, 2004), TNFRSF11B (for Juvenile Paget disease) (Saki et al, 2013).…”

“…Most of these genes are identified through a combination of family studies, candidate gene investigation, mouse model validation, etc. Recently, there are new strategies, such as GWAS (genome-wide association study) on common genetic variants (Justice et al, 2012), and exome sequencing followed by summing all rare variants (Timberlake et al, 2017). Without distinguishing different gene mapping methods, we proceed by a systematic search of all PUBMED titles/abstracts that contain the word of “craniosynostosis and “genetic, finding all gene names, then followed by a manual check of the original literature.…”

The osteogenic potential of the neural crest lineage may contribute to craniosynostosis

“…The investigation of signalling cues is very important for understanding the pathophysiology of craniosynostosis. A recent study, in fact, has identified a number of de novo mutations in negative regulators of the Wnt, BMP and Ras/ERK pathways, occurring in non-syndromic midline craniosynostosis patients 25 . These pathways, knowingly implicated in positive regulation of osteogenesis, are, among other signals previously studied 18 , good candidates for dura mater’s regulatory milieu in the context of suture patency and fusion.…”

Genetic Causes of Craniosynostosis: An Update

“…Genotyping of this SNP in the SMAD6 mutation-positive individuals provides strong evidence of epistatic interaction between SMAD6 and BMP2 . This 2-locus model is estimated to be the genetic cause in approximately 3.5% of all the craniosynostosis cases [Timberlake et al, 2016], and the results have been replicated by Timberlake et al [2017]. Activation of BMP receptors leads to phosphorylation of receptor SMADs, which can complex with SMAD4, translocate to the nucleus, and partner with RUNX2 to induce transcription of genes that promote osteoblast differentiation [Hata et al, 1998;Javed et al, 2008] as summarized by Timberlake et al [2016].…”