Genetic perturbations in nicotinamide adenine dinucleotide de novo (NAD) synthesis pathway predispose individuals to congenital birth defects. The NADSYN1 encodes the final enzyme in the de novo NAD synthesis pathway and, therefore, plays an important role in NAD metabolism and organ embryogenesis. Biallelic mutations in the NADSYN1 gene have been reported to be causative of congenital organ defects known as VCRL syndrome (Vertebral-Cardiac-Renal-Limb syndrome). Here, we analyzed the genetic variants in NADSYN1 in an exome-sequenced cohort consisting of patients with congenital vertebral malformations (CVMs). A total number of eight variants in NADSYN1, including two truncating variants and six missense variants, were identified in nine unrelated patients. All enrolled patients presented multiple organ defects, with the involvement of either the heart, kidney, limbs, or liver, as well as intraspinal deformities. An in vitro assay using COS-7 cells demonstrated either significantly reduced protein levels or disrupted enzymatic activity of the identified variants. Our findings demonstrated that functional variants in NADSYN1 were involved in the complex genetic etiology of CVMs and provided further evidence for the causative NADSYN1 variants in congenital NAD Deficiency Disorder.

TBX6-associated congenital scoliosis (TACS) is a genetic subtype of congenital scoliosis caused by reduced TBX6 gene dosage, most commonly through compound inheritance of a rare loss-of-function allele and a hypomorphic T-C-A haplotype. However, the mechanisms linking TBX6 dysfunction to impaired human skeletal development remain unclear. Here, we established a patient-derived induced pluripotent stem cell (iPSC) model of TACS and recapitulated key stages of axial skeletal development through stepwise differentiation into paraxial mesoderm, nascent somites, sclerotome, and subsequently osteogenic and chondrogenic lineages. TACS-derived cells showed impaired differentiation, with reduced mineralized matrix deposition and diminished cartilage matrix formation. Bulk transcriptomic profiling revealed marked alterations in both lineages. Notably, mu-cin-type O-glycan biosynthesis was consistently enriched among downregulated genes in osteogenic and chondrogenic cells and was also significantly represented among genes commonly downregulated across both lineages. qRT-PCR further confirmed reduced expression of GALNT3, GALNT5, GALNT7, GALNT10, GCNT1, and ST6GALNAC2, which participate in distinct steps of mucin-type O-glycan biosynthesis. Consistent with these transcriptional alterations, Tn-antigen staining showed reduced Tn-associated O-GalNAc signals in TACS-derived osteogenic and chondrogenic cells. In silico promoter analysis identified candidate sequences matching the TBX6-binding motif within the upstream regions of these genes, providing potential regulatory regions for future experimental investigation. Collectively, these results establish a human iPSC model for TACS and identify coordinated dysregulation of a mucin-type O-glycan biosynthesis-related transcriptional program, accompanied by reduced Tn-associated O-GalNAc signals, as molecular features associated with impaired osteochondral differentiation in this model. These findings should be interpreted within the context of a single family-based iPSC model, and validation in additional TACS lines and isogenic TBX6-corrected models will be required.