NOXA expression drives synthetic lethality to RUNX1 inhibition in pancreatic cancer

Abstract

Evasion from drug-induced apoptosis is a crucial mechanism of cancer treatment resistance. The pro-apoptotic protein NOXA marks an aggressive pancreatic ductal adenocarcinoma (PDAC) subtype. To identify drugs that unleash the death-inducing potential of NOXA, we performed an unbiased drug screening experiment. In NOXA-deficient isogenic cellular models we identified an inhibitor of the transcription factor heterodimer CBFβ/RUNX1. By genetic gain and loss of function experiments we validated that the mode of action depends on RUNX1 and NOXA. Of note, RUNX1 expression is significantly higher in PDACs compared to normal pancreas. We show that pharmacological RUNX1 inhibition significantly blocks tumor growth in vivo and in primary patient-derived PDAC organoids. Through genome wide analysis, we detected that RUNX1-loss reshapes the epigenetic landscape, which gains H3K27ac enrichment at the NOXA promoter. Our study demonstrates a previously unknown mechanism of NOXA-dependent cell death, which can be triggered pharmaceutically. Therefore, our data show a novel way to target a therapy resistant PDAC, an unmet clinical need.

NOXA Accentuates Apoptosis Induction by a Novel Histone Deacetylase Inhibitor

“…Moreover, HDACi-mediated upregulation of the BH3-only protein BIM is linked to the p21-regulated RB-E2F pathway [41,42]. Transcriptional activation of the pro-apoptotic sensor NOXA by HDACi occurs in pancreatic cancer and can be achieved by selective inhibition of HDAC2 [21,31]. Induction of NOXA by KH16 in PDAC cells may be due to the disruption of the RUNX1-SIN3A-HDAC corepressor complex, urging a global gain of H3K27 acetylation (which was observed in our study) at the proximal NOXA promoter [21,43].…”

“…HDAC3 is necessary to prevent DNA replication stress, thus its inhibition can accumulate lethal DNA damage in cancer cells [27,[44][45][46]. It is tempting to speculate that an accumulation of NOXA due to an inhibition of HDAC2 and a disruption of the SIN3 complex [21,31,43] combined with compromised genomic integrity due to an inhibition of HDAC3 are molecular mechanisms through which KH16 kills cancer cells.…”

“…Human pancreatic cancer cell lines (MIA PaCa-2 and MIAPaCa-2 ∆NOXA ) were recently described and created by Matthias Wirth (Berlin, Germany) [21]; the human CRC cell line HCT116 was originally from the Leibniz-Institute (DSMZ, Braunschweig, Germany), and HROC80 cells were isolated in the laboratory of Michael Linnebacher (Rostock, Germany) [22]. The human retinal pigment epithelial cell line (RPE1) was a gift from Thomas Hofmann (Mainz, Germany).…”

“…Of the tested pro-apoptotic proteins, NOXA was induced from nearly untraceable to clearly detectable levels in MIA PaCa-2 cells (Figure 3b). It has been reported that PDAC cells commonly have an altered expression of the pro-apoptotic BH3-only protein NOXA and that HDACi induce its expression [21,31]. Therefore, we integrated PDAC cells with a deletion of NOXA by CRISPR-Cas9, MIAPaCa-2 ∆NOXA cells [21], into our experiments.…”

“…It has been reported that PDAC cells commonly have an altered expression of the pro-apoptotic BH3-only protein NOXA and that HDACi induce its expression [21,31]. Therefore, we integrated PDAC cells with a deletion of NOXA by CRISPR-Cas9, MIAPaCa-2 ∆NOXA cells [21], into our experiments.…”