Extracellular Matrix Origin Directs Morphogenesis and Gene Regulation in Bioengineered Human Skin

The cellular microenvironment plays a pivotal role in directing tissue development, repair, and homeostasis through a complex interplay of biochemical and mechanical cues. The extracellular matrix (ECM) serves as a key instructive component, guiding transcriptional programs that determine cell fate, function, and identity. In this study, we investigated the impact of microenvironmental context on the biofabrication of human skin equivalents, comparing constructs based on endogenous versus exogenous ECMs. Our RNA sequencing analyses reveal that ECM origin profoundly influences transcriptional trajectories, highlighting the importance of a native-like microenvironment in supporting appropriate gene expression profiles and morphogenetic processes. Notably, skin equivalents featuring endogenously produced ECMs exhibit physiologically relevant architecture, including a well-organized dermo-epidermal junction (DEJ), whereas constructs based on exogenous matrices—such as animal-derived collagen—display abnormal epithelial expansion and fail to replicate key structural features. These findings underscore the necessity of recapitulating the native ECM to achieve functional tissue constructs in vitro and raise critical considerations regarding scaffold choice in regenerative medicine and tissue engineering applications. We also discuss the implications of these findings for the development of organ-on-chip systems, where the accurate recapitulation of native tissue architecture and function is essential for modeling physiological and pathological conditions in human-relevant experimental assays. Overall design: Morphological characterization (collagen and elastin quantification) and RNA-Seq profiling (differential gene expression analysis and enrichment analysis) of endogenous and exogenous human skin equivalents to highlight the role of the ECM in guiding the correct production of relevant 3D skin model.