PhD Scientific Days 2025

Theoretical and Translational Medicine II.

Nature vs. nurture – Does genetic background or medium composition have a greater influence on the endothelial transcriptome?

Name of the presenter

Demeter Flóra

Institute/workplace of the presenter

Research Laboratory, Department of Internal Medicine and Hematology, Semmelweis University

Authors

Flóra Demeter¹, Márta Lídia Debreczeni¹, Erika Kajdácsi¹, Zsuzsanna Németh¹, Zoltán Doleschall¹, László Cervenak¹

1: Research Laboratory, Department of Internal Medicine and Hematology, Semmelweis University

Text of the abstract

In vitro cultured primary endothelial cells (e.g., HUVEC) are indispensable model systems in biological basic research and drug development. However, contradictory or poorly reproducible experimental results are common in the literature. Our aim was to determine, through a comprehensive transcriptomic analysis, whether these discrepancies in HUVEC cultures could be attributed to differences in the composition of cell culture media or variations in the genetic backgrounds of cell donors.
We cultured three well-characterized HUVEC lines (1302, 1309, 1314), each derived from a unique donor, in four different media (EBM, HIMV, MCDB, MCDB-S) and performed a full gene expression analysis of the 12 samples using the Agilent microarray platform. After preprocessing the raw data, 13,829 expressed genes ("full HUVEC transcriptome") were subjected to further analysis.
Hierarchical cluster analysis of the full HUVEC transcriptome revealed that the samples clustered according to the media used. A total of 1,838 genes exhibited at least a twofold, statistically significant expression difference between any two media (n=1,392) or any two cell lines (n=446). Based on correlation and PCA analyses of these 1,838 genes, the composition of the culture medium had a greater impact on gene expression profiles than the genetic differences among donors. Among the media, EBM differed the most from the other three, while MCDB and MCDB-S were the most similar. To explore the biological significance of gene expression changes, we examined nine key endothelial cell functions using g:Profiler and GSEA. The composition of the culture medium significantly influenced all nine functions, with the strongest effects observed on the mitotic cell cycle, angiogenesis, and inflammatory and cell adhesion processes. In contrast, genetic background had a considerably smaller impact on the selected endothelial cell functions.
Our results consistently indicate that, in primary endothelial cell cultures, the composition of the culture medium has a much greater effect on gene expression than donor genetic diversity. Therefore, we emphasize the fundamental importance of carefully selecting the appropriate culture medium.
Supported by Gedeon Richter Thematic Grant Proposal (2023) and Gedeon Richter Talentum Foundation in the framework of Gedeon Richter Excellence PhD Scholarship of Gedeon Richter (2024).