Significance: Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal cancers to treat. Existing drugs rarely work as a single agent. Therefore, identifying novel drug combinations that will synergistically and selectively kill PDAC cells is a significant unmet need. Here, we used CRISPR gene knockout s creening to identify combinatorial targets of gemcitabine (Gem) in PDAC. We discovered that PRMT5 depletion makes PDAC cells significantly sensitive to Gem. Our mechanistic findings show that PRMT5 inhibition impairs DNA repair mechanism. Hence the combination results in synergistic accumulation of Gem-induced DNA damage. We show that the combination leads to synergistic cell death in PDAC cells in vitro and in vivo.

The tumor microenvironment in pancreatic ductal adenocarcinoma (PDAC) plays a key role in tumor progression and response to therapy. The dense PDAC stroma causes hypovascularity, which leads to hypoxia. Here, we showed that hypoxia drives long-lasting epithelial–mesenchymal transition (EMT) in PDAC primarily through a positive-feedback histone methylation–MAPK signaling axis. Transformed cells preferentially underwent EMT in hypoxic tumor regions in multiple model systems. Hypoxia drove a cell autonomous EMT in PDAC cells, which, unlike EMT in response to growth factors, could last for weeks. Furthermore, hypoxia reduced histone demethylase KDM2A activity, suppressed PP2 family phosphatase expression, and activated MAPKs to post-translationally stabilize histone methyltransferase NSD2, leading to an H3K36me2-dependent EMT in which hypoxia-inducible factors played only a supporting role. Hypoxia-driven EMT could be antagonized in vivo by combinations of MAPK inhibitors. Collectively, these results suggest that hypoxia promotes durable EMT in PDAC by inducing a histone methylation–MAPK axis that can be effectively targeted with multidrug therapies, providing a potential strategy for overcoming chemoresistance. Significance: Integrated regulation of histone methylation and MAPK signaling by the low-oxygen environment of pancreatic cancer drives long-lasting EMT that promotes chemoresistance and shortens patient survival and that can be pharmacologically inhibited. See related commentary by Wirth and Schneider, p. 1739

Due to low numbers of circulating tumor cells (CTCs) in liquid biopsies, there is much interest in enrichment of alternative circulating-like mesenchymal cancer cell subpopulations from in vitro tumor cultures for utilization within molecular profiling and drug screening. Viable cancer cells that are released into the media of drug-treated adherent cancer cell cultures exhibit anoikis resistance or anchorage-independent survival away from their extracellular matrix with nutrient sources and waste sinks, which serves as a pre-requisite for metastasis. The enrichment of these cell subpopulations from tumor cultures can potentially serve as an in vitro source of circulating-like cancer cells with greater potential for scale-up in comparison with CTCs. However, these live circulating-like cancer cell subpopulations exhibit size overlaps with necrotic and apoptotic cells in the culture media, which makes it challenging to selectively enrich them, while maintaining them in their suspended state. We present optimization of a flowthrough high frequency (1 MHz) positive dielectrophoresis (pDEP) device with sequential 3D field non-uniformities that enables enrichment of the live chemo-resistant circulating cancer cell subpopulation from an in vitro culture of metastatic patient-derived pancreatic tumor cells. Central to this strategy is the utilization of single-cell impedance cytometry with gates set by supervised machine learning, to optimize the frequency for pDEP, so that live circulating cells are selected based on multiple biophysical metrics, including membrane physiology, cytoplasmic conductivity and cell size, which is not possible using deterministic lateral displacement that is solely based on cell size. Using typical drug-treated samples with low levels of live circulating cells (90% of dead cells. This strategy of utilizing single-cell impedance cytometry to guide the optimization of dielectrophoresis has implications for other complex biological samples.

Cellular biophysical metrics exhibit systematic alterations during processes, such as metastasis and immune cell activation, which can be used to identify and separate live cell subpopulations for targeting drug screening. Image‐based biophysical cytometry under extensional flows can accurately quantify cell deformability based on cell shape alterations but needs extensive image reconstruction, which limits its inline utilization to activate cell sorting. Impedance cytometry can measure these cell shape alterations based on electric field screening, while its frequency response offers functional information on cell viability and interior structure, which are difficult to discern by imaging. Furthermore, 1‐D temporal impedance signal trains exhibit characteristic shapes that can be rapidly templated in near real‐time to extract single‐cell biophysical metrics to activate sorting. We present a multilayer perceptron neural network signal templating approach that utilizes raw impedance signals from cells under extensional flow, alongside its training with image metrics from corresponding cells to derive net electrical anisotropy metrics that quantify cell deformability over wide anisotropy ranges and with minimal errors from cell size distributions. Deformability and electrical physiology metrics are applied in conjunction on the same cell for multiparametric classification of live pancreatic cancer cells versus cancer associated fibroblasts using the support vector machine model.

Pancreatic ductal adenocarcinoma (PDAC) is defined by the near universal occurrence of KRAS mutations. The KRASG12R mutation is detected in approximately 15% to 20% of patients with PDAC and rare in other KRAS-mutant cancers. KRASG12R is unable to activate the lipid kinase PIK3CA, suggesting that alternative mechanisms might be employed to activate KRASG12R-independent PI3K signaling in PDAC. In this study, we detected elevated expression of all four PI3K isoforms in PDAC cell lines, with the PIK3CG isoform showing higher overall expression in KRASG12R-mutant PDAC. All four PI3K isoforms contributed to global PI3K signaling, and inhibition of any single isoform was insufficient to limit PDAC proliferation. The combined inhibition of all PI3K isoforms was required to limit proliferation, providing a potential explanation for the limited efficacy of PI3K inhibitors in the clinic. Additionally, PTEN, a negative regulator of PI3K signaling, was inactivated in PDAC by the formation of an intramolecular disulfide, which elevated overall PI3K signaling and reduced the dependency of PI3K signaling on KRAS. Oxidation of PTEN was independent of KRAS mutation status. Finally, nutrient-limiting conditions mimicking the PDAC tumor microenvironment further elevated PTEN oxidation and significantly increased macropinocytosis. Thus, this study uncovered a mechanism that supports elevated PI3K signaling in PDAC, thereby reducing the need for KRAS to directly activate the PI3K pathway. Significance: PTEN inactivation by intramolecular disulfide bond formation and elevated expression of PI3K isoforms in pancreatic cancer leads to unchecked KRAS-independent PI3K signaling, highlighting the need for therapeutic approaches targeting constitutive PI3K signaling. See related commentary by Tiriac and Engle, p. 1817 See related article by Burge et al., p. 1868 See related article by Kamgar et al., p. 2042