Skeletal dysplasias are a heterogeneous group of human genetic disorders that primarily affect bones and cartilage. Metaphyseal dysplasia (MD) is one of the most complex subgroups of skeletal dysplasias. The heterozygous mutations in the MMP13 gene have been identified as the cause of MMP13-related bone disorders, namely Metaphyseal anadysplasia, which includes Spondyloepimetaphyseal dysplasia, Missouri type (SEMDMO)). This study aims to identify the disease-causing variant in a pedigree with short stature using whole exome sequencing.

Trio whole-exome sequencing (Trio-WES) was performed for a Chinese female patient who presented with short stature, lacking radiographic evidence of metaphyseal, epiphyseal or vertebral abnormalities on imaging. Co-immunoprecipitation/mass spectrometry (Co-IP/MS) was performed to identify the protein with the most significant difference in expression between the wild-type and mutant groups, followed by bioinformatics analysis. We generated induced pluripotent stem cells (iPSCs) from peripheral blood mononuclear cells (PBMCs) via nucleofection with episomal plasmids. These iPSCs were further differentiated into chondrocytes via mesenchymal stem cells (MSCs).

The study identified a heterozygous frameshift MMP13 gene variant (c.1372del, p.Arg458fs) in exon 10. Heterozygous mutations in the MMP13 gene have been more commonly associated with SEMDMO. However, this family displayed solely the short stature phenotype, lacking radiographic evidence of metaphyseal, epiphyseal, or vertebral abnormalities on imaging. The proband received growth hormone therapy for more than 2 years, the patient exhibited a height increase from -1.91SD to -0.35SD with no treatment-related adverse events. We found a significant increase in HSPA5 expression in the mutant by Co-IP/MS in HEK293 cells and confirmed that the MMP13 mutant has increased interactions with HSPA5, causing the retention of HSPA5 in the endoplasmic reticulum. Bioinformatics analysis showed that the enriched proteins were associated with biological processes such as protein folding, endoplasmic reticulum protein processing, and endoplasmic reticulum stress. In the chondrocytes of patients, misfolded MMP13 protein is retained in the endoplasmic reticulum, causing endoplasmic reticulum stress and significant expansion of the endoplasmic reticulum. The expansion triggers the unfolded protein response, impairs chondrocyte differentiation, and ultimately leads to skeletal dysplasia and short stature.

Trio-WES revealed a novel MMP13 gene variant in the patient with short stature. The patient presented with isolated short stature and lacked abnormal skeletal phenotypes, and our findings expand the phenotypic spectrum of MMP13 gene variations, clarify the putative pathogenic mechanisms by which MMP13 mutations cause skeletal dysplasia and may provide novel diagnostic and treatment approaches.