Phosphoproteomics guides effective low-dose drug combinations against pancreatic ductal adenocarcinoma

Vallés-Martí, Andrea; Mantini, G.; Manoukian, Paul; Waasdorp, Cynthia; Sarasqueta, Arantza Fariña; Haas, Richard R. de; Henneman, Alex A.; Piersma, Sander R.; Pham, Thang V.; Knol, Jaco C.; Giovannetti, Elisa; Bijlsma, Maarten F.; Jiménez, Connie R.

doi:10.1016/j.celrep.2023.112581

Cited by 14 publications

(5 citation statements)

References 72 publications

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“…This can be abrogated by concurrent inhibition of GCN2. Hence, combining drugs is an important strategy to overcome drug resistance and inhibit processes that require significant metabolic and signaling flexibility, such as metastasis [18,50,51]. In summary, we have identified critical cellular processes, the inhibition of which causes nutrient stress and requires metabolic flexibility, which is afforded by the activation of GCN2.…”

Section: Resultsmentioning

confidence: 99%

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Inhibition of GCN2 Reveals Synergy with Cell-Cycle Regulation and Proteostasis

Gauthier-Coles,

Rahimi,

Bröer

et al. 2023

Metabolites

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The integrated stress response is a signaling network comprising four branches, each sensing different cellular stressors, converging on the phosphorylation of eIF2α to downregulate global translation and initiate recovery. One of these branches includes GCN2, which senses cellular amino acid insufficiency and participates in maintaining amino acid homeostasis. Previous studies have shown that GCN2 is a viable cancer target when amino acid stress is induced by inhibiting an additional target. In this light, we screened numerous drugs for their potential to synergize with the GCN2 inhibitor TAP20. The drug sensitivity of six cancer cell lines to a panel of 25 compounds was assessed. Each compound was then combined with TAP20 at concentrations below their IC50, and the impact on cell growth was evaluated. The strongly synergistic combinations were further characterized using synergy analyses and matrix-dependent invasion assays. Inhibitors of proteostasis and the MEK–ERK pathway, as well as the pan-CDK inhibitors, flavopiridol, and seliciclib, were potently synergistic with TAP20 in two cell lines. Among their common CDK targets was CDK7, which was more selectively targeted by THZ-1 and synergized with TAP20. Moreover, these combinations were partially synergistic when assessed using matrix-dependent invasion assays. However, TAP20 alone was sufficient to restrict invasion at concentrations well below its growth-inhibitory IC50. We conclude that GCN2 inhibition can be further explored in vivo as a cancer target.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Inhibition of GCN2 Reveals Synergy with Cell-Cycle Regulation and Proteostasis

Gauthier-Coles,

Rahimi,

Bröer

et al. 2023

Metabolites

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“…The Kinex workflow can be used jointly with other technologies, such as transcriptional profiling, including single-cell RNA-sequencing and targeted approaches such as molecular phenotyping 66,67 , epigenetic profiling, proteomics, and metabolomics to construct the causal chain of drug’s effect. Furthermore, Kinex can be used to re-purpose existing drugs and to explore tumor- or individualspecific optimal treatment regiments, as suggested by a proof-of-concept study conducted with the INKA tool 68 .…”

Section: Discussionmentioning

confidence: 99%

Kinexinfers causal kinases from phosphoproteomics data

Valeanu,

Golz,

Avila

et al. 2023

Preprint

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MotivationPhosphoproteomics data are essential for characterising signalling pathways, identifying drug targets, and evaluating efficacy and safety profiles of drug candidates. Emerging resources, including a substrate-specificity atlas and drug-induced phosphoproteomics profiles, have the potential to transform the inference of causal kinases. However, there is currently no open-source software that leverages insights derived from these resources.ResultsWe introduceKinex,a workflow implemented in the same-name Python package, which infers causal serine/threonine kinases from phosphoproteomics data. Kinex users can score kinase-substrate interactions, perform enrichment analysis, visualise candidates of causal regulators, and query similar profiles in a database of drug-induced kinase activities. Analysing seven published studies and one newly generated dataset, we demonstrate that analysis with Kinex recovers causal effects of perturbations and reveals novel biological insights. We foresee that Kinex will become an indispensable tool for basic and translational research including drug discovery.AvailabilityKinex is released with the GNU General Public License, openly accessible to all users athttps://github.com/bedapub/kinex.

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“…For each time point and cell line, we isolated the phospho-protein fraction as previously described (28). In brief, the supernatant was discarded and cells were washed with cold PBS at least three times.…”

Section: Preparation Of On-treatment Pdac Cell Line Lysatesmentioning

confidence: 99%

“…Phospho-peptide enrichment was performed by IMAC (immobilized metal ion affinity chromatography), using the BRAVO AssayMap liquid handling robot (Agilent) as previously described (28). In brief, 200 µg peptides for each sample were acidified to 0.1% TFA, and applied to a 10 mg OASIS HLB cartridge (Waters) previously activated with acetonitrile and equillibrated with 0.1% TFA.…”

Section: Sample Preparation For Phospho-proteomicsmentioning

confidence: 99%

Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent

Vallés-Martí,

Böttger,

Yau

et al. 2023

Preprint

Self Cite

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Increasing preclinical and clinical evidence has positioned high-dose vitamin C as a promising anti-cancer treatment that merits more clinical attention. Multiple cytotoxicity mechanisms have been described, including pro-oxidant effects. To contribute to the preclinical understanding of the broad pan-cancer effects of high-dose vitamin C in a global manner, we determined the IC50 of a large panel of cancer cell lines (n=51) representing 7 solid tumour types and generated proteome data. The majority of cell lines were highly sensitive (IC50 range 0.036-10mM, mean 1.7 ± 0.4 mM), well below a clinically achievable dose. The proteome data (>5000 proteins per sample), showed that high sensitivity is associated with proliferation, as indicated by functional enrichment of cell cycle, RNA splicing and chromatin organization, while lower sensitivity is linked to extracellular vesicles, glycolysis, fatty acid metabolism and mitochondria. Moreover, (phospho-)proteome analysis of on-treatment vitamin C effects on four pancreatic ductal adenocarcinoma (PDAC) cells dosed at a range of IC50 values (Hs766 T, 2 mM; Capan-2, 0.6 mM; PANC-1, 0.14 mM and Suit-2, 0.1 mM) revealed, next to cell line specific effects, down-modulation of AKT-MTOR signalling and immune suppressive signalling, while IFN-α response was enhanced upon vitamin C. Altogether, our comprehensive pharmacological and (phospho-)proteome analysis is the first to assess cancer vulnerabilities and effects of vitamin C on a large cancer cell line panel and underscores the potential of high-dose vitamin C as an anti-cancer agent.

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Phosphoproteomics guides effective low-dose drug combinations against pancreatic ductal adenocarcinoma

Cited by 14 publications

References 72 publications

Inhibition of GCN2 Reveals Synergy with Cell-Cycle Regulation and Proteostasis

Inhibition of GCN2 Reveals Synergy with Cell-Cycle Regulation and Proteostasis

Kinexinfers causal kinases from phosphoproteomics data

Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent

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