Comparison of genotoxic versus nongenotoxic stabilization of p53 provides insight into parallel stress-responsive transcriptional networks

Abstract

The tumor suppressor protein p53 is activated in response to diverse intrinsic and extrinsic cellular stresses and controls a broad cell-protective gene network. Whether p53:DNA binding and subsequent transcriptional activation differs downstream of these diverse intrinsic and extrinsic activators is controversial. Using primary human fibroblasts, we assessed the genome-wide profile of p53 binding, chromatin structure, and transcriptional dynamics after either genotoxic or nongenotoxic activation of p53. Activation of p53 by treatment with either etoposide or the smallmolecule MDM2 inhibitor nutlin 3A yields strikingly similar genome-wide binding of p53 and concomitant changes to local chromatin modifications and structure. DNA damage, but not p53 activation per se, leads to increased expression of genes in an inflammatory cytokine pathway. The NF-κB pathway inhibitor Bay 11-7082 abrogates etoposide-mediated activation of the inflammation gene signature but does not affect expression of canonical p53 target genes. Our data demonstrate that differential activation of p53 within the same cell type leads to highly similar genome-wide binding, chromatin dynamics, and gene expression dynamics and that DNA damage-mediated signaling through NF-κB likely controls the observed pro-inflammatory cytokine gene expression pattern.

Identification of universal and cell-type specific p53 DNA binding

“…1e, Pearson r = 0.87 or 0.88 for MCF7 and UACC257, respectively, vs r = 0.73 for the maximum line-line) and is consistent with recent work showing clustering of p53 DNA binding by cell type and not treatment [16]. Thus, IR induced and pharmacologically induced p53 do not lead to distinct p53 function as measured by acute p53 DNA binding, as is consistent with recent work [17]. Overall, our data shows that p53 DNA binding is globally conserved across cell types and treatments, however clustering of cell types by tissue or origin suggests that there may be p53 DNA binding features that are cell-type specific.…”

Helping the Released Guardian: Drug Combinations for Supporting the Anticancer Activity of HDM2 (MDM2) Antagonists

“…In such cells, the administration of HDM2 antagonists results in forced dissociation of HDM2-p53 complexes, releasing p53 from HDM2 inhibition [2]. Such a forced p53 release results in the expression of a plethora of p53-regulated genes, presenting a transcriptome landscape similar, but not identical to that of genotoxic p53 activation [3]. However, the blockade of HDM2 protein leads only to partial activation of p53, and thus the outcome of such activation differs from the full p53 activation process observed in response to genotoxic stress.…”

Transcriptomic analyses of livers from mice exposed to 1,4-dioxane for up to 90 days to assess potential mode(s) of action underlying liver tumor development

“…The few enriched gene sets related to up-regulation of DNA damage response at 6000 ppm (i.e., p53 signaling pathways) according to the more lenient GSEA enrichment analysis and BMD functional classification analysis may be related to apical endpoints reported in Lafranconi et al (2020) : up-regulation of signaling pathways for cell cycle are potentially related to the reported increased BrdU labeling, and enrichment of cell death signaling potentially related to the increase in apoptosis as evidenced by Caspase 3 staining. While p53 signaling is known to be activated by DNA damage, it also can be activated by non-genotoxicants ( Catizone et al, 2019 ). The individual genes driving the enrichment of p53-relevant pathways in the GSEA and BMDExpress analyses were regulators of apoptosis (e.g., Bax ) and cytokines, without alteration to DNA repair enzymes nor the p53 gene itself.…”