Determining the Relative Gene Expression Level of Hypoxia Related Genes in Different Cancer Cell Lines

This study aims to identify the changes in the expression of hypoxia-inducible genes in seven different cancer cell lines that vary in their oxygen levels in an attempt to identify hypoxia biomarkers that can be targeted in therapy. Profiling of hypoxia inducible-gene expression of these different cancer cell lines can be used as baseline data for further studies.

Human cancer cell lines obtained from the American Type Culture Collection were used; MCF7 breast cancer cells, PANC-1 pancreatic cancer cells, PC-3 prostate cancer cells, SHSY5Y neuroblastoma brain cancer cells, A549 lung cancer cells, and HEPG2 hepatocellular carcinoma. In addition, we used the MCF10A non-tumorigenic human breast epithelial cell line as a normal cell line. The differences in gene expression were examined using real-time PCR array (PAHS- 032Z, Human Hypoxia Signaling Pathway PCR Array) and analyzed using the ΔΔCt method.

Almost all hypoxia-inducible genes showed a PO2-dependent up- and down-regulated expression. Noticeable gene expression differences were identified. The most important changes occurred in the HIF1α and NF-KB signaling pathways targeted genes and in central carbon metabolism pathway genes such as HKs, PFKL, and solute transporters.

This study identified possible hypoxia biomarkers genes such as NF-KB, HIF1α, HK, PFKL, and PIM1 that were expressed in all hypoxic cells. Pleiotropic pathways that play a role in inducing hypoxia directly, such as HIF1 α and NF-kB pathways, were upregulated. In addition, genes expressed only in the severe hypoxic liver and pancreatic cells indicate that severe and intermediate hypoxic cancer cells vary in their gene expression. Gene expression differences between cancer and normal cells showed the shift in gene expression profile to survive and proliferate under hypoxia.