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Nature versus nurture: genetic background and media composition shape endothelial cell transcriptomes in vitro
Flóra Demeter1, Márta Lídia Debreczeni2,3, Zsuzsanna Németh2
1Department of Internal Medicine and Hematology, Semmelweis University, Szentkirályi u. 46, Budapest, 1088, Hungary. demeter.flora@semmelweis.hu.
Scientific Reports
|March 17, 2026
Summary
Culture media significantly impacts human umbilical vein endothelial cell (HUVEC) gene expression more than donor genetics. This finding is crucial for improving reproducibility in endothelial cell research and drug development.
Area of Science:
- Cell Biology
- Genomics
- Biotechnology
Background:
- Primary endothelial cells, such as human umbilical vein endothelial cells (HUVEC), are vital in biological research and pharmaceutical development.
- Inconsistent or irreproducible experimental outcomes are frequently reported in scientific literature concerning endothelial cell studies.
Purpose of the Study:
- To investigate the influence of distinct culture media and donor genetic variations on HUVEC gene expression.
- To identify the primary source of experimental variability in HUVEC studies.
Main Methods:
- Agilent microarray transcriptomic analysis was performed on three donor-derived HUVEC lines.
- Cells were cultured in four different media with varying compositions, serum, and growth factors.
- Genome-wide cluster analysis, correlation, and principal component analysis were employed.
Main Results:
- Transcriptomic analysis revealed that HUVEC samples clustered predominantly based on the culture medium used, not donor origin.
- Culture medium significantly impacted the expression of 1697 out of 2215 differentially expressed genes, while donor differences affected only 805 genes.
- Endothelial functions including mitosis, angiogenesis, inflammation, and adhesion were primarily influenced by media composition.
Conclusions:
- Culture media composition plays a pivotal role in shaping the HUVEC transcriptome.
- Differences in culture media are a likely cause of experimental inconsistencies observed in endothelial cell research.
- Standardizing culture media is essential for enhancing the reproducibility of HUVEC studies.
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