The gelatinases, matrix metalloproteinases 2 and 9, play individual roles in skeleton development

•The gelatinases, MMP2 and MMP9, share similarities in their structure, expression pattern and ECM substrates.•MMP2−/−/MMP9−/− double KO was characterized by analyzing the structural, histological and mechanical properties of long and flat bones.•A specific role for each gelatinase in bone development was demonstrated; MMP2 is exclusively required for intramembranous ossification while MMP9 is uniquely required for endochondral ossification.•Full transcriptome analysis of different skeletal components across the various genotypes, support their distinct and non-redundant roles via mechanistic pathways of MMP2 or MMP9 inactivation. The gelatinases, a subgroup of the matrix metalloproteinases (MMPs) superfamily are composed of two members; MMP2 and MMP9. They are known to degrade gelatin among other components of the extracellular matrix. Recently, the two gelatinases were found to be necessary for neural crest cell migration and to compensate for each other loss in these cells. To characterize their involvement in the skeletal system, and to better reveal their individual or common roles, we have generated double knockout (dKO) mice, lacking both MMP2 and MMP9. Comprehensive analysis of the skeleton morphological and mechanical parameters at postnatal day (P) 0, P21, 3 months (M) and 8M of age, revealed an unexpected distinct role for each gelatinase; MMP2 was found to be involved merely in intramembranous ossification which led to a smaller skull and inferior cortical parameters upon its loss, while MMP9 was found to affect only the endochondral ossification process, which led to shorter long-bones in its absence. Importantly, the dKO mice demonstrated a combination of both the skull and long bone phenotypes as found in the single-KOs, and not a severer additive phenotype. Transcriptome analysis on the cortical bone, the growth plate and the skull frontal bone, found many genes that were differentially expressed as a direct or indirect result of MMP-loss, and reinforced the specific and distinct role of each gelatinase in each bone type. Altogether, these results suggest that although both gelatinases share the same substrates and are highly expressed in flat and long bones, they are indispensable and control separately the development of different bones.