Nature versus nurture: genetic background and media composition shape endothelial cell transcriptomes in vitro

Abstract Primary endothelial cells (e.g., HUVEC) are essential in basic research and drug development, yet contradictory or poorly reproducible experimental results are common in the literature. We investigated whether such discrepancies arise from differences in culture media or donor genetic backgrounds using Agilent microarray transcriptomic analysis of three donor-derived HUVEC lines cultured in four distinct media (regarding basic composition, serum- and growth factor content). Genome-wide cluster analysis of 13,823 expressed genes revealed that samples clustered primarily by medium. Of the 2215 genes showing differential expression, 1697 varied across media, while only 805 were affected by donor differences. Correlation and principal component analysis confirmed that media composition had a strong impact on gene expression. Functional analysis of nine key endothelial functions showed predominantly medium-dependent effects, particularly on mitosis, angiogenesis, inflammation, and adhesion. The pivotal role of media composition in shaping HUVEC transcriptome may underlie inconsistencies across studies.