Background Cytosolic deacetylase histone deacetylase 6 (HDAC6) is involved in the autophagy degradation pathway of malformed proteins, an important survival mechanism in cancer cells. We evaluated modulation of autophagy-related proteins and cell death by the HDAC6-selective inhibitor C1A. Methods Autophagy substrates (light chain-3 (LC-3) and p62 proteins) and endoplasmic reticulum (ER) stress phenotype were determined. Caspase-3/7 activation and cellular proliferation assays were used to assess consequences of autophagy modulation. Results C1A potently resolved autophagy substrates induced by 3-methyladenine and chloroquine. The mechanism of autophagy inhibition by HDAC6 genetic knockout or C1A treatment was consistent with abrogation of autophagosome–lysosome fusion, and decrease of Myc protein. C1A alone or combined with the proteasome inhibitor, bortezomib, enhanced cell death in malignant cells, demonstrating the complementary roles of the proteasome and autophagy pathways for clearing malformed proteins. Myc-positive neuroblastoma, KRAS-positive colorectal cancer and multiple myeloma cells showed marked cell growth inhibition in response to HDAC6 inhibitors. Finally, growth of neuroblastoma xenografts was arrested in vivo by single agent C1A, while combination with bortezomib slowed the growth of colorectal cancer xenografts. Conclusions C1A resolves autophagy substrates in malignant cells and induces cell death, warranting its use for in vivo pre-clinical autophagy research.
VCP/p97 regulates numerous cellular functions by mediating protein degradation through its segregase activity. Its key role in governing protein homoeostasis has made VCP/p97 an appealing anticancer drug target. Here, we provide evidence that VCP/p97 acts as a regulator of cellular metabolism. We found that VCP/p97 was tied to multiple metabolic processes on the gene expression level in a diverse range of cancer cell lines and in patient-derived multiple myeloma cells. Cellular VCP/p97 dependency to maintain proteostasis was increased under conditions of glucose and glutamine limitation in a range of cancer cell lines from different tissues. Moreover, glutamine depletion led to increased VCP/p97 expression, whereas VCP/p97 inhibition perturbed metabolic processes and intracellular amino acid turnover. GCN2, an amino acid-sensing kinase, attenuated stress signalling and cell death triggered by VCP/p97 inhibition and nutrient shortages and modulated ERK activation, autophagy, and glycolytic metabolite turnover. Together, our data point to an interconnected role of VCP/p97 and GCN2 in maintaining cancer cell metabolic and protein homoeostasis.
Cancer cells can survive chemotherapy-induced stress, but how they recover from it is not known. Using a temporal multiomics approach, we delineate the global mechanisms of proteotoxic stress resolution in multiple myeloma cells recovering from proteasome inhibition. Our observations define layered and protracted programs for stress resolution that encompass extensive changes across the transcriptome, proteome, and metabolome. Cellular recovery from proteasome inhibition involved protracted and dynamic changes of glucose and lipid metabolism and suppression of mitochondrial function. We demonstrate that recovering cells are more vulnerable to specific insults than acutely stressed cells and identify the general control nonderepressable 2 (GCN2)-driven cellular response to amino acid scarcity as a key recovery-associated vulnerability. Using a transcriptome analysis pipeline, we further show that GCN2 is also a stress-independent bona fide target in transcriptional signature-defined subsets of solid cancers that share molecular characteristics. Thus, identifying cellular trade-offs tied to the resolution of chemotherapy-induced stress in tumor cells may reveal new therapeutic targets and routes for cancer therapy optimization.
Proteasome inhibitors (PIs) form the backbone of multiple myeloma (MM) treatment regimens used at diagnosis and relapse, but their clinical benefit is limited by varying degrees of resistance. The mechanisms that protect MM cells (MMCs) from PI-induced cell death are only partly understood, and experimental resistance studies often rely on the prolonged exposure of MMCs to relatively low levels of PIs. However, patients receive PI doses that result in high but short plasma peaks. Given that each PI dose reduces a patient's MMC load until a plateau is reached, one can assume that each PI dose kills some MMCs by triggering overwhelming stress. This proposition implies that a proportion of MMCs not only survive but also resolve PI-induced stress. We hypothesised that the mechanisms of PI-induced stress recovery require a redistribution of cellular resources, and that this process triggers specific recovery-associated and potentially druggable vulnerabilities. To test this hypothesis, we obtained a global systems-level view of the cellular response to proteasome inhibition by performing a multi-omics 10-day time-course experiment. To mimic in vivo pharmacokinetics and anti-MM effects, RPMI-8226 MMCs were treated with a 1h pulse of carfilzomib (CFZ; 750nmol/L), which reduced the number of viable MMCs to a nadir of approximately 50% on day +2, followed by a return to pretreatment baseline levels of viable cells by day +6. Levels of ubiquitinated proteins as a readout of effective proteasome inhibition peaked on day +1 and returned to baseline levels on day +6. Samples for transcriptome analysis by RNA-seq, proteome analysis by a multiplexed tandem mass tag (TMT)-based approach, and global metabolomic profiling by ultrahigh performance liquid chromatography-tandem mass spectroscopy (LC-MS) were collected 2h prior to the CFZ pulse (day 0) and on days +1, +2, +4, +6, +8, and +10. The results demonstrate extensive and kinetically complex changes of the MMC transcriptome, proteome and metabolome that did not fully return to baseline by day +10. Conventional and advanced computational analyses of RNA-seq data (including biological homogeneity score-validated graph-based clustering of temporal patterns combined with gene enrichment and KEGG/GO pathway analysis) revealed different patterns of involvement of multiple and functionally diverse pathways. Perhaps most notably, RNA-seq data revealed extensive metabolic pathway responses while cells were dying and throughout recovery. Consistently, metabolomic profiling by LC-MS showed wide-ranging metabolite changes. These included rapid intracellular depletion of glucose, which was paralleled by the accumulation of lactate and pyruvate and lasted until day +8. Consistently, the major glucose uptake regulator TXNIP stood out as upregulated during recovery, which was accompanied by the predicted downregulation of the glucose transporter GLUT1. These findings were confirmed by real-time PCR and immunoblotting in RPMI-8226 and other MMC lines. Moreover, pharmacological inhibition of glucose and lactate metabolising enzymes and transmembrane transport enhanced MMC killing by CFZ, confirming profound and druggable changes in glucose and energy metabolism during PI stress recovery. We also observed prolonged depletion of a number of amino acids, including glutamine, which was paralleled by depletion of glutamate and TCA cycle intermediates. Moreover, we found RNA-seq and real-time PCR/immunoblot-based evidence for an amino acid response (AAR) during stress recovery that was driven by the amino acid sensing kinase GCN2 (EIF2AK4). The preclinical GCN2 inhibitor GCN2iB was effective at blocking the AAR and enhanced MMC killing in a panel of CFZ-treated MMC lines. This effect was particularly pronounced during the intermediate stages of recovery, in line with the kinetics of amino acid depletion and the AAR. Thus, our observations define the complex and prolonged cellular responses that characterise the recovery of MMCs from proteasome inhibition. They reveal wide-ranging metabolic changes that persist far beyond immediate stress survival and highlight the dependence of MMCs on the GCN2-driven AAR to overcome PI stress. The findings demonstrate that the mechanisms of PI recovery trigger druggable vulnerabilities, providing the basis for ongoing investigations into sequential therapeutic interventions to enhance responses to PIs. Disclosures Caputo: GSK: Research Funding. Kaiser:Abbvie, Celgene, Takeda, Janssen, Amgen, Abbvie, Karyopharm: Consultancy; Celgene, Janssen: Research Funding; Takeda, Janssen, Celgene, Amgen: Honoraria, Other: Travel Expenses. Auner:Karyopharm: Consultancy; Takeda: Consultancy; Amgen: Other: Consultancy and Research Funding.
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