Unraveling the Molecular Landscape of Congenital Pseudoarthrosis of the Tibia: Insights from a Comprehensive Analysis of 162 Probands

Congenital pseudarthrosis of the tibia (CPT, HP:0009736), commonly known as bowing of the tibia, is a rare congenital tibia malformation characterized by spontaneous tibial fractures and the difficulty of reunion after tibial fractures during early childhood, with a very low prevalence between 1/250,000[~]1/140,000. While 80%-84% of CPT cases present with neurofibromatosis type 1, caused by the mutations in NF1, the underlying cause of CPT is still unclear. Considering the congenital nature and the low prevalence of CPT, we hypothesized that the rare genomic mutations may contribute to CPT. In this study, we conducted whole exome sequencing on 159 patients with CPT and full-length transcriptome sequencing on an additional 3 patients with CPT. The data analysis showed there were 179 significantly up-regulated genes which were enriched in 40 biological processes among which 21 biological processes hold their loss of function (LoF) excesses between 159 cases against 208 controls from 1000 Genomes Project. From those 21 biological processes with LoF excesses, there were 259 LoF-carried genes among which 40 genes with 56 LoF variations in 63 patients were enriched in osteoclast differentiation pathway (hsa04380) with its 3 directly regulated pathways including MAPK signaling pathway (hsa04010), calcium signaling pathway (hsa04020) and PI3K-Akt signaling pathway (hsa04151), as well as fluid shear stress and atherosclerosis pathway (hsa05418) while 12 patients carried 9 LoF variations in the NF1 gene. The rare LoF variations in these pathways accounted for [~]39.6% of this CPT cohort. These findings shed light on the novel genetic mutations and molecular pathways involved in CPT, providing a new framework for understanding how the genetic variations regulate the biological processes in the pathology of CPT and indicating potential next directions to further elucidate the pathogenesis of CPT.