Endogenous aryl hydrocarbon receptor promotes basal and inducible expression of tumor necrosis factor target genes in MCF-7 cancer cells

Abstract

The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that upon activation by the toxicant 2,3,7,8 tetrachlorodibenzo-p-dioxin (TCDD) stimulates gene expression and toxicity. AHR is also important for normal mouse physiology and may play a role in cancer progression in the absence of environmental toxicants. The objective of this report was to identify AHR-dependent genes (ADGs) whose expression is regulated by AHR in the absence of toxicants. RNA-Seq analysis revealed that AHR regulated the expression of over 600 genes at an FDR < 10% in MCF-7 breast cancer cells upon knockdown with short interfering RNA. Pathway analysis revealed that a significant number of ADGs were components of TCDD and tumor necrosis factor (TNF) pathways. We also demonstrated that siRNA knockdown of AHR modulated TNF induction of MNSOD and cytotoxicity in MCF-7 cells. Collectively, the major new findings of this report are: 1) endogenous AHR promotes the expression of xenobiotic metabolizing enzymes even in the absence of toxicants and drugs, 2) AHR by modulating the basal expression of a large fraction of TNF target genes may prime them for TNF stimulation and 3) AHR is required for TNF induction of MNSOD and the cellular response to cytotoxicity in MCF-7 cells. This latter result provides a potentially new role for AHR in MCF-7 cancer progression as a mediator of TNF and antioxidant responses.

Empirical likelihood tests for nonparametric detection of differential expression from RNA-seq data

“…Results showing KEGG (Ogata et al, 1999;Kanehisa and Goto, 2000;Kanehisa et al, 2002) pathways that are significantly enriched in our set of DE genes are tabulated in Table 3. In agreement with Salisbury et al (2014), we find that a known 2, 3, 7, 8 tetrachlorodibenzo-p-dioxin (TCDD) pathway is enriched in the set of DE genes, namely metabolism of xenobiotics by cytochrome P450 (Dere et al, 2011;Lo and Matthews, 2012).…”

“…The 10 genes with highest likelihood ratio (after filtering of pseudogenes) are shown in Table 2, along with their likelihood ratio and corresponding (Yang et al, 2008;Salisbury et al, 2014) and HMOX1 (Lo and Matthews, 2013) are known to be regulated by AHR.…”

“…To explore the utility of our approach on an experimental data set, we consider RNA-seq experiments probing the effects of the aryl hydrocarbon receptor (AHR) transcription factor on gene expression in MCF-7 cancer cells (Salisbury et al, 2014). The data were taken from the GEO database (Edgar et al, 2002;Barrett et al, 2013), accession number GSE52036 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52036).…”

Aryl hydrocarbon receptor (AHR) regulation of L-Type Amino Acid Transporter 1 (LAT-1) expression in MCF-7 and MDA-MB-231 breast cancer cells

“…Extrinsic regulation of LAT1 by TCDD/AHR was investigated in MCF-7 cells. Intrinsic regulation of LAT1 by AHR was investigated in MCF-7 and MDA-MB-231 cells because these BCC lines have been reported to exhibit endogenous AHR activity [30-33]. Based on our findings, we report a new role for AHR as an extrinsic and intrinsic regulator of LAT1 expression in BCCs and show that AHR binds to LAT1 AHR-REs as part of a transcriptional activator complex.…”

“…RNA-Seq was performed using an Illumina HiSeq1000 in a 2 × 100 base paired end design yielding a minimum of 50 million reads per sample. Differentially expressed genes were identified at a False Discovery Rate (FDR) of 5% as detailed in our prior report [33]. Raw reads and processed data (unnormalized and normalized read counts by gene) were deposited in the Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information and are accessible via accession number GSE76608.…”