A Transcriptome Sequencing Study on Genome‐Wide Gene Expression Differences of 3D Cultured Chondrocytes in Hydrogel Scaffolds with Different Gel Density

Abstract Hydrogel is considered as a promising cell delivery vehicle in cartilage tissue engineering, whose tunable microenvironments may influence the function and fate of encapsulated chondrocytes. Here, the transcriptomes of chondrocytes that are encapsulated and cultured in hydrogel constructs respectively made of 0.8% and 4% alginate solution are investigated. Differences in chondrocyte transcriptome are detected via RNA‐sequencing from these two cultural conditions. The differentially expressed genes (DEGs) are reflected in extracellular matrix (ECM) secretion, cell cycle, proliferation, cartilage development, and so on. Significantly, the expression of DEGs associated with cartilage ECM and cell proliferation are upregulated in 0.8% constructs; whilst the expressions of DEGs involved in cell cycle and matrix degradation are upregulated in 4% constructs. Moreover, interestingly, the expressions of chondrocyte hypertrophy markers are upregulated in 0.8% constructs; while 4% constructs seemingly favor the long‐term maintenance of chondrocyte phenotype. Taken together, this study confirms on transcriptomic level that gel density affects gene expression and phenotype of the encapsulated chondrocytes; therefore, it may provide guidance for future design and fabrication of cartilage tissue engineering scaffolds.