Oellinger, R. | Search bioRxiv

bioRxiv2020

Targeting the ubiquitin-proteasome system in a pancreatic cancer subtype with hyperactive MYC

Purpose The myelocytomatosis oncogene (MYC) is an important driver in a subtype of pancreatic ductal adenocarcinoma (PDAC). However, MYC remains a challenging therapeutic target, therefore identifying druggable synthetic lethal interactions in MYC-active PDAC may lead to novel precise therapies.Methods Cluster analysis using direct MYC target genes was used to identify PDAC with active MYC. We profiled the transcriptome of established human cell lines, murine primary PDAC cell lines and also accessed public available repositories for transcriptomic profiling. Networks active in MYC hyperactive subtypes were analyzed by gene set enrichment analysis. An unbiased pharmacological drug screen with FDA-approved anti-cancer drugs was conducted to define MYC-associated vulnerabilities, which were validated by analysis of drug response repositories and genetic gain- and loss-of-function experiments.Results In an unbiased pharmacological drug screen with FDA-approved anti-cancer drugs we detected that the proteasome inhibitor bortezomib triggers a MYC-associated vulnerability. By integrating publicly available data sets we found the unfolded protein response as a signature connected to MYC. Furthermore, the increased sensitivity of MYC hyperactive PDACs to bortezomib was validated in genetically modified PDAC cells.Conclusions In sum, we provide evidence that perturbing the ubiquitin proteasome system might be an option to target MYC hyperactive PDAC cells and our data provide the rationale to further develop precise targeting of the ubiquitin-proteasome system as a subtype-specific therapeutic approach.Competing Interest StatementThe authors have declared no competing interest.Abbrevations4-OHT4-hydoxytamoxifenATF4activating transcription factor 4BETbromodomain and extra terminal motifCNVcopy number variationCTD2cancer target discovery and development networkdepmapdependency mapDoRothEAdiscriminant regulon expression analysisGSEAgene set enrichment analysisICGCinternational cancer gene consortiumMYCmyelocytomatosis oncogenePDACpancreatic ductal adenocarcinomaPERKproteinkinase RNA-activated-like ER kinaseSUMOsmall-ubiquitin-like modifierTCGAthe cancer genome atlasUPRunfolded protein responseUPSubiquitin proteasome systemView Full Text

cancer biology↗

bioRxiv2020

A GATA6-centered gene regulatory network involving HNFs and ΔNp63 controls plasticity and immune escape in pancreatic cancer

ObjectiveMolecular taxonomy of tumors is the foundation of personalized medicine and is becoming of paramount importance for therapeutic purposes. Four transcriptomics-based classification systems of pancreatic ductal adenocarcinoma (PDAC) exist, which consistently identified a subtype of highly aggressive PDACs with basal-like features, including {Delta}Np63 expression and loss of the epithelial master regulator GATA6. We investigated the precise molecular events driving PDAC progression and the emergence of the basal program. DesignWe combined the analysis of patient-derived transcriptomics datasets and tissue samples with mechanistic experiments using a novel dual-recombinase mouse model for Gata6 deletion at late stages of KRasG12D-driven pancreatic tumorigenesis (Gata6LateKO). ResultsThis comprehensive human-to-mouse approach allowed us to show that GATA6 loss is necessary, but not sufficient, for the expression of a basal program in patients and in mice. The concomitant loss of HNF1A and HNF4A, likely through epigenetic silencing, is required for the full phenotype switch. Moreover, Gata6 deletion in mice dramatically increased the metastatic rate, with a propensity for lung metastases. Through RNA-Seq analysis of primary cells isolated from mouse tumors, we show that Gata6 inhibits tumor cell plasticity and immune evasion, suggesting that it works as a barrier for acquiring the fully developed basal and metastatic phenotype. ConclusionsOur work provides both a mechanistic molecular link between the basal phenotype and metastasis and a valuable preclinical tool to investigate the most aggressive subtype of PDAC. These data, therefore, are important for understanding the pathobiological features underlying the heterogeneity of pancreatic cancer in both mice and human. What is already known about this subject?O_LIMultiple transcriptomics-based studies have identified a basal-like subtype of pancreatic ductal adenocarcinoma (PDAC) with especially poor prognosis. C_LIO_LILoss of GATA6 in PDAC cells is associated with altered differentiation, including ectopic expression of basal markers such as KRT14. C_LIO_LIAberrant expression of the {Delta}Np63 transcription factor can drive the expression of the basal transcriptional program. C_LI What are the new findings?O_LILoss of GATA6 expression is necessary but not sufficient for the expression of {Delta}Np63 and the basal phenotype. C_LIO_LIConcomitant silencing of HNF4A and HNF1A, possibly through epigenetic mechanisms, is required for the full-blown phenotype. C_LIO_LIGata6 deletion in established murine tumors favors the basal and metastatic phenotype, with a lung tropism, in a next-generation model of KRasG12D-driven PDAC. C_LIO_LILoss of GATA6 expression is associated with features of immune escape in mouse and human PDAC cells. C_LI How might it impact on clinical practice in the foreseeable future?O_LIThe combined analysis of GATA6, HNFs, and TP63 expression in patient-derived samples will provide a more precise classification of PDAC. C_LIO_LIRestoration of the classical PDAC phenotype may not only reduce metastatic potential but also increase immune recognition of tumor cells. C_LI

cancer biology↗