Genomics,Multiomics

Dataset Information

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


ABSTRACT: 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. Overall design: 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.

INSTRUMENT(S): Illumina HumanWG-6 v3.0 expression beadchip (gene symbol)

ORGANISM(S): Homo sapiens  

SUBMITTER: Carter Van Waes  

PROVIDER: GSE126904 | GEO | 2019-02-22

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE126904_RAW.tar Raw
GSE126904_UMSCC46_TNF_normalized.xlsx Xlsx
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Publications

Lymphotoxin-β receptor-NIK signaling induces alternative RELB/NF-κB2 activation to promote metastatic gene expression and cell migration in head and neck cancer.

Das Rita R   Coupar Jamie J   Clavijo Paul E PE   Saleh Anthony A   Cheng Tsu-Fan TF   Yang Xinping X   Chen Jianhong J   Van Waes Carter C   Chen Zhong Z  

Molecular carcinogenesis 20181128 3


Head and neck squamous cell carcinomas (HNSCC) preferentially spread to regional cervical tissues and lymph nodes. Here, we hypothesized that lymphotoxin-β (LTβ), receptor LTβR, and NF-κB-inducing kinase (NIK), promote the aberrant activation of alternative NF-κB2/RELB pathway and genes, that enhance migration and invasion of HNSCC. Genomic and expression alterations of the alternative NF-kB pathway were examined in 279 HNSCC tumors from The Cancer Genome Atlas (TCGA) and a panel of HNSCC lines.  ...[more]