Bidirectionally validated in silico and in vitro formation of specific depth zone-derived chondrocyte spheroids and clusters

3D multicellular self-organized cluster models, e.g., organoids are promising tools for developing new therapeutic modalities including gene and cell therapies, pharmacological mechanistic and screening assays. Various applications of these models have been used extensively for decades, however, the mechanisms of cluster formation, maintenance, and degradation of these models are not even known over in-vitro-life-time. To explore such advantageous models mimicking native tissues or organs, it is necessary to understand aforementioned mechanisms. Herein, we intend to clarify the mechanisms of the formation of cell clusters. We previously demonstrated that primary chondrocytes isolated from distinct longitudinal depth zones in articular cartilage formed zone-specific spherical multicellular clusters <i>in vitro</i>. To elucidate the mechanisms of such cluster formation, we simulated it using the computational Cellular Potts Model with parameters were translated from gene expression levels and histological characteristics corresponding to interactions between cell and extracellular matrix. This simulation <i>in silico</i> was validated morphologically with cluster formation <i>in vitro</i> and <i>vice versa</i>. Since zone specific chondrocyte cluster models <i>in silico</i> showed similarity with corresponding <i>in vitro</i> model, the <i>in silico</i> has a potential to be used for prediction of the 3D multicellular <i>in vitro</i> models used for development, disease, and therapeutic models.