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Complementary omics strategies to dissect p53 signaling networks under nutrient stress

ABSTRACT: Signaling trough cytoplasmic or nuclear action of p53 is a major response mechanism to cellular stresses. While p53 protein levels have been shown to increase upon nutrient stresses such as starvation, the exact signaling cascade in this context remains elusive. Here, we show in a human hepatoma cell line that nutrient withdrawal leads to robust nuclear p53 stabilization and utilize various complementary omics approaches to dissect upstream and downstream networks in the response to starvation. Using the affinity purification mass spectrometry (MS) method BioID, we determine the cytoplasmic p53 interaction network within the immediate-early starvation response and show that p53 is dissociated from several metabolic enzymes and the kinase PAK2. Direct binding of p53 DNA-binding domain and N-terminal PAK2 was confirmed with nuclear magnetic resonance (NMR) interaction studies. Furthermore, rapid immunoprecipitation MS of endogenous proteins (RIME) uncovered the nuclear interactome under prolonged starvation, where we confirmed the novel p53 interactors SORBS1, involved in insulin signaling, and UGP2, a key enzyme of glycogen synthesis. Finally, transcriptomics after p53 re-expression on a CRISPR/Cas9 knock out background revealed a distinct starvation-specific transcriptome response and suggested novel nutrient-dependent p53 target genes. Together, our complementary approaches delineate several nodes of the p53 signaling cascade in response to starvation, shedding new light on the mechanisms of p53 as a nutrient stress sensor and regulator of specific transcriptional output. Given the central role of p53 in cancer biology and the beneficial effects of fasting in cancer treatment, the identified interaction partners and networks could pinpoint novel pharmacologic targets to fine-tune p53 activity.

INSTRUMENT(S): maXis

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Barbara Darnhofer

LAB HEAD: Ruth Birner-Gruenberger

PROVIDER: PXD028341 | Pride | 2022-06-09

REPOSITORIES: Pride

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Publications

Complementary omics strategies to dissect p53 signaling networks under nutrient stress.

Galhuber Markus M Michenthaler Helene H Heininger Christoph C Reinisch Isabel I Nössing Christoph C Krstic Jelena J Kupper Nadja N Moyschewitz Elisabeth E Auer Martina M Heitzer Ellen E Ulz Peter P Birner-Gruenberger Ruth R Liesinger Laura L Lenihan-Geels Georgia Ngawai GN Oster Moritz M Spreitzer Emil E Zenezini Chiozzi Riccardo R Schulz Tim J TJ Schupp Michael M Madl Tobias T Heck Albert J R AJR Prokesch Andreas A

Cellular and molecular life sciences : CMLS 20220530 6

Signaling trough p53is a major cellular stress response mechanism and increases upon nutrient stresses such as starvation. Here, we show in a human hepatoma cell line that starvation leads to robust nuclear p53 stabilization. Using BioID, we determine the cytoplasmic p53 interaction network within the immediate-early starvation response and show that p53 is dissociated from several metabolic enzymes and the kinase PAK2 for which direct binding with the p53 DNA-binding domain was confirmed with N ...[more]

PMID: 35635656

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Project description:Macrophages play critical roles in immune function and are implicated as etiological agents in disease states such as cardiovascular disease and cancer. However, there is limited understanding of macrophage fitness molecular regulators, including survival, proliferation, and adhesion. This work identifies positive and negative regulators of macrophage fitness by harnessing the power of CRISPR/Cas9 whole genome screening technology. Here, we identified loss-of-function gene disruptions that caused mutant bone marrow-derived macrophages (BMDM) to decrease in culture abundance as supporters of macrophage fitness. Similarly, we identified genes that limit or suppress macrophage fitness by identifying those gene disruptions that caused BMDM to increase in abundance in cell culture. To do this, we analyzed the difference in frequency of sgRNA between the purified plasmid library used for lentiviral transfection versus the amplified sgRNA inserts from the DNA of BMDM following a 14-day post-viral transduction culture. With this approach, we identified gene disruptions to canonical essential genes, including previously described macrophage-specific essential genes such as Csf1r, as well as novel genes required for macrophage growth and survival. In addition, we also identified gene disruptions that increased macrophage abundance in culture, including canonical tumor suppressors such as p53 (Trp53) and cell cycle regulators (Cdkn1a/2a). Interestingly, targeting p21-activated kinase-2 (Pak2) led to those mutants becoming more productive, suggesting a novel role for Pak2 in suppressing macrophage fitness. Using targeted knockouts of PAK2, we show that PAK2 protein depletion affects NF2/Merlin-mediated downregulation of cyclin-d1. Further, this work indicates that PAK2 suppresses macropinocytic uptake in macrophages by modulating actin dynamics impacting pro-mitogenic signaling pathways downstream of macropinocytosis. Overall, this work shows how multiple pathways impact macrophage fitness and highlights the central role of PAK2 in macrophage fitness and macropinocytosis.

Dataset Information

Complementary omics strategies to dissect p53 signaling networks under nutrient stress

Publications

Complementary omics strategies to dissect p53 signaling networks under nutrient stress.

Similar Datasets

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