A Multimodal Molecular View of Human Cartilage Development

Abstract

The skeletal system is the foundation of human mobility. Human joint development and function relies on the proper specification and differentiation of hyaline cartilage, including growth plate cartilage that forms the template for developing bones and articular cartilage that provides lubrication and resilience for joint movement. Despite their vital role, the molecular mechanisms driving these distinct cartilage types in humans remain unclear. Our lab has pioneered an in vitro model of chondrogenesis, using human pluripotent stem cells (hPSCs) to generate articular and growth plate-like chondrocytes by recapitulating developmental processes. Using this system and human donor tissue, we investigated the transcriptomic and epigenetic signatures underlying human chondrogenesis.

Articular and growth plate cartilage represent two distinct lineages of hyaline cartilage developing in the appendicular skeleton. We used bulk RNA and ATAC sequencing to build transcriptomic and epigenetic profiles of hPSC-derived articular and growth plate-like cartilage. Transcriptomic comparison to human fetal epiphyseal and growth plate cartilage tissues highlighted similarities and differences between these lineages developing in vivo and those being differentiated in vitro. Integrating the transcriptomic and epigenetic profiles of in vitro articular and growth plate cartilage uncovered lineage specific differences and revealed putative transcription factors (TFs) that drive these lineage-specific changes. We validated the function of two of these transcription factors, RELA in articular cartilage and RUNX2 in growth plate cartilage, in binding regulatory elements, predicted by integrating both motif enrichment and target gene expression, in the genome of chondrocytes. This bulk multiomic atlas of in vitro chondrogenesis therefore enabled us to identify both known and novel putative regulators of these two functionally different cartilage types in human development.

Developing human cartilage is a continuum of hyaline cartilage with multiple subtypes of chondrocytes contained within it. We therefore employed single cell multiomic sequencing to characterize the transcriptomic and epigenetic profiles of individual cells from the developing human distal femur at two developmental timepoints. Using these data, we built enhancer-based gene regulatory networks that predicted regulators of chondrogenic differentiation. In addition to identifying some of the gene regulatory networks that we discovered in our bulk sequencing approach, we also identified novel regulators of chondrogenesis and defined the specificity of each regulatory network within different computationally-defined cell types. We used our in vitro chondrogenic differentiation model to test the function of gene regulatory networks identified from in vivo human fetal chondrocyte data. One such TF, NFATC2, was predicted to be highly active in epiphyseal and superficial zone chondrocytes during fetal development. Consistent with this, we found that overexpression of NFATC2 in the in vitro chondrocytes induced articular-like epiphyseal chondrocyte gene programs, even in the presence of culture conditions that promote growth plate differentiation. In addition to uncovering this role for NFATC2, we demonstrated the utility of the in vitro hPSC-based platform to study the effect of regulators on chondrogenesis. This work therefore represents a step towards comprehensively understanding the molecular mechanisms driving human cartilage development.