TNFα and LTβ stimulated UM-SCC 46 gene expression [TNF]

To investigate the regulatory mechanisms and targets of the activation of NF-kB and inflammatory pathways, we treated HPV(-) head and neck cancer line UM-SCC 46 cells with TNFα and LTβ at different time points, and compared the gene expression by microarray. TNFα uniquely induced 172 genes, LTβ specifically induced 202 genes, while 155 genes were induced by both ligands. Total RNA samples were isolated from UM-SCC 46 cells after TNFα or LTβ treatment at different time points, and the gene expression were compared with untreated cell controls. UM-SCC 46 cells were treated with TNFα (20ng/ml) or LTβ (100ng/ml) for 1, 3, 6, 12, and 24 hours. RNA was isolated and global gene expression was examined by beads based array using Illumina HumanWG-6-v3-BeadChip (Illumina, CA). Raw data were imported to the GenomeStudio software, and normalized data were imported to Parte to detect differentially expressed genes by using an ANOVA test. Hierarchical clustering of altered gene expression when treated with LTβ was compared to untreated cells using MeV software. The heat map represents two-fold increased gene expression when compared to untreated samples.