Ph.D Student Shanghai Jiao Tong University, Shanghai, China
Abstract: Congenital limb defects are among the most prevalent categories of congenital anomalies, primarily manifesting as longitudinal deficiencies in isolated or syndromic forms. Non-syndromic limb defects often hinder effective prenatal diagnosis due to unclear pathogenic mechanisms. Most congenital limb defects are genetically driven and associated with mutations or chromosomal abnormalities. These abnormalities, including deletions, duplications, inversions, and translocations, can disrupt gene regulatory networks, thereby altering the expression of genes critical for limb development. The complexity of these anomalies poses significant challenges in generating suitable cellular and animal models. Current knockout and knock-in technologies struggle to recapitulate complex structural variants (SVs), and interspecies developmental divergence may further limit the applicability of these models. In this study, we analyzed a large family pedigree comprising individuals with bilateral ulnar longitudinal deficiency. Whole-exome sequencing (WES) failed to identify clinically significant pathogenic variants in the affected individuals. However, BioNano optical genome mapping revealed complex SVs, including duplications and inversions, within the 21q22 region of all affected individuals across the pedigree. Initial Hi-C analysis demonstrated that these SVs perturb the three-dimensional (3D) genome organization and disrupt certain topologically associating domains (TADs). Third-generation sequencing is currently being employed to investigate the transmission of variants between parents and offspring. Moreover, patient-derived and normal induced pluripotent stem cells (iPSCs) have been differentiated into induced mesenchymal stem cells (MSCs), with subsequent osteogenic and chondrogenic differentiation planned to compare phenotypic disparities across developmental stages. This investigation aims to elucidate how TAD disruption in the 21q22 region underlies non-syndromic ulnar longitudinal deficiency at the molecular level. These findings will enhance mechanistic insights into non-syndromic limb defects and provide a framework for modeling SV-associated diseases.
Funding Source: National Key Research and Development Program (2024YFC2707002), Innovation Program of Shanghai Municipal Education Commission (2023ZKZD16) and National Natural Science Foundation of China (82071262)
