Time Series Analysis of Benzo[A]Pyrene-Induced Transcriptome Changes Suggests That a Network of Transcription Factors Regulates the Effects on Functional Gene Sets

Abstract

Chemical carcinogens may cause a multitude of effects inside cells, thereby affecting transcript levels of genes by direct activation of transcription factors (TF) or indirectly through the formation of DNA damage. As the temporal profiles of these responses may be profoundly different, examining time-dependent changes may provide new insights in TF networks related to cellular responses to chemical carcinogens. Therefore, we investigated in human hepatoma cells gene expression changes caused by benzo[a]pyrene at 12 time points after exposure, in relation to DNA adduct and cell cycle. Temporal profiles for functional gene sets demonstrate both early and late effects in up- and downregulation of relevant gene sets involved in cell cycle, apoptosis, DNA repair, and metabolism of amino acids and lipids. Many significant transcription regulation networks appeared to be around TF that are proto-oncogenes or tumor suppressor genes. The time series analysis tool Short Time-series Expression Miner (STEM) was used to identify time-dependent correlation of pathways, gene sets, TF networks, and biological parameters. Most correlations are with DNA adduct levels, which is an early response, and less with the later responses on G1 and S phase cells. The majority of the modulated genes in the Reactome pathways can be regulated by several of these TF, e.g., 73% by nuclear factor-kappa B and 34-42% by c-MYC, SRF, AP1, and E2F1. All these TF can also regulate one or more of the others. Our data indicate that a complex network of a few TF is responsible for the majority of the transcriptional changes induced by BaP. This network hardly changes over time, despite that the transcriptional profiles clearly alter, suggesting that also other regulatory mechanisms are involved.

Impaired liver function in Xenopus tropicalis exposed to benzo[a]pyrene: transcriptomic and metabolic evidence

“…Recent in vitro studies have clearly illustrated the dynamic regulation occurring at the transcriptomic level during BaP exposure and the sequence of events leading to BaP toxicity [32]. Similarly, our results highlighted remarkable variations in hepatic gene transcription during pollutant exposure, with major changes occurring at 12 hours post-exposure.…”

“…The associated metabolic pathways are closely regulated by insulin or adipocytokines [39]. In our study, a significant enrichment of insulin signaling, adipocytokine signaling, glycolysis/gluconeogenesis, steroid (cholesterol) biosynthesis, and MAPK signaling pathways was observed; this may relate to late transcriptomic responses to BaP exposure in in vitro models [32]. To date, the in vivo kinetics of mechanisms regulated by BaP exposure have not been investigated.…”

“…The induction of BaP metabolism enzymes has been previously shown to occur rapidly after pollutant exposure. In the hepatic cellular model HepG2 for instance, a rapid increase in the expression of genes involved in “Dioxin, xenobiotic metabolism” was observed to drop over the first 9 hours after exposure to 751 μg.L -1 of BaP [32]. In fish exposed to a high concentration of BaP (5 mg.L -1 ), one of the main oxidases involved in phase I of the BaP metabolism process, encoded by the CYP1A gene, was over-transcribed immediately after BaP exposure with a high TR of ~ 46, decreasing to 10 6 hours post-exposure [38].…”

“…Today, this knowledge gap can be bridged using high throughput sequencing approaches, such as mRNA sequencing (mRNAseq), recovering information on gene expression over the whole transcriptome from a single experiment [28–31]. This technique has recently been shown to be more sensitive, reliable and informative than microarrays for the in vitro evaluation of BaP toxicity [32]. In the case of X. tropicalis , the interpretation of large numbers of sequences generated by mRNAseq takes advantage of the recently released complete genome [33], and benefits from a comprehensive repository from the standard model X. tropicalis, giving access to all levels of sequence data sets, including transcriptomic data [34].…”

Xenobiotic Metabolism Activation as a Biomarker of Cigarette Smoke Exposure Response

“…In 2010, Van Delft and colleagues generated transcription factor networks to investigate relevant transcription factors affected benzo[a]pyrene (BaP), a well-known PAH [ 30 ]. Exposure of cells to BaP (and other carcinogens) is known to alter various molecular responses, including changes in transcription factor activations.…”