Expression profiling of irradiated human lung endothelial cells using a large DNA chip

Purpose/Objective: Until recently, radiation research has mainly focused on the tumor cell compartment. However, the genetically more stable microenvironment including the endothelial cell compartment has now been widely recognized to play a key role in radiation effects in vivo. One way to better understand radiation effects is the identification of genes regulated in response to radiation, which can affect the cell cycle, DNA repair, apoptosis, metastasis and angiogenesis. DNA microarray technology is now considered as an emerging technology to potentially explore cellular pathways. In order to better understand the effects of radiation on endothelial cells, we investigate here the gene expression profile of endothelial cells in response to ionizing radiation using a DNA chip. Materials/Methods: We used a large DNA-Chip to get expression profiles from complete human Unigene II clusters which contain approximately 76,000 elements covering almost 95% of the human genome. The total RNA in human microvascular lung endothelial cells was isolated at different time points after 2 Gy radiation. RNA quality was tested using the 28S vs. 18S ratio with lab on chip technology. Hybridization was two-fold for each spot with four independent measurements. The distribution of the gene expression over the 76,000 elements was Gaussian. Appropriate hierarchies were chosen from the approximately 12,000 unambiguous characterized known genes. Results: We identified a series of genes in human microvascular lung endothelial cells whose expressions varied in response to 2 Gy radiation in vitro. Among the highly significantly up- or down-regulated genes (more than two-fold or less than 0.5 fold) were genes known to be related to apoptosis and cell cycle (31 genes), proteases (41), angiogenesis (12), tumor suppressor genes (12), cancer in a general sense (>100) and many others. DNA microarray technology allowed us to study thousands of genes at one time. Thus we were able to obtain clues to the functional role of many genes, including potentially important genes involved in different pathways like angiogenesis and apoptosis in a single experiment. Conclusions: The gene expression in human endothelial cells is dramatically changed in response to ionizing radiation at the clinically relevant dose of 2 Gy. Thus the impact of radiation on endothelial cells and therefore on (tumor-)angiogenesis is at least in part due to transcriptional changes in endothelial cells. In addition to identifying unexpected genes, DNA chip technology can facilitate the development of new hypotheses concerning how cells respond to radiation and the identification of coregulated pathways in response to radiation. Clinically, such knowledge might lead to a more individualized therapy, the definition of new molecular targets to act together with radiotherapy or the improved protection of normal tissue.