Aberrant ClpP activation disturbs mitochondrial proteome homeostasis to suppress pancreatic ductal adenocarcinoma
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE186091 | GEO | 2021/10/21
REPOSITORIES: GEO
Similar Datasets
Project description:Aberrant ClpP activation disturbs mitochondrial proteome homeostasis to suppress pancreatic ductal adenocarcinoma
| PRJNA772584 | ENA
Project description:The peptidase ClpP is conserved from bacteria to human. In the mitochondrial matrix, it multimerizes and forms a macromolecular proteasome-like cylinder. Because of its known relevance for the mitochondrial unfolded protein response during cell stress, we characterized two ClpP knock-out mouse founder lines and documented similar phenotypes. Ubiquitously, ClpP absence led to accumulation of its interactor protein ClpX without transcript upregulation. Interestingly, most wild-type tissues with substantial ClpP amounts had no detectable ClpX. This inverse correlation suggests that ClpX levels and degradation are regulated by ClpP. The expectation of similar protein levels, in view of a reported association of heptameric ClpP rings with hexameric ClpX rings, was confirmed only in testis of wild-type animals. Germline tissue was exceptional also in its vulnerability to ClpP deletion, with both founder lines showing complete infertility for males and females. Otherwise, ubiquitous mitochondrial dysfunction was apparent from severe growth retardation and reduced spontaneous motor activity of the animals, and from a pronounced decrease in pre-/postnatal survival. Spermatogenesis was found aborted at the spermatid stage, acrosomes and axonemes were not formed. Overall, tissue-specific roles of ClpP were evident by this massive effect for germ cells, mild bioenergetic deficits in muscle and liver tissues, and excellent compensation in brain. ClpX was previously reported to chaperone unfolded proteins and also DNA condensation in mitochondria, so it is likely that this pathway is particularly susceptible in germ cells. In conclusion, our study indicates that the role of ClpP in quality control is indispensable during development for cells with rapid changes of mitochondrial numbers, and is relevant during aging for growth and survival of the organism. Factorial design comparing ClpP knock-out mice with wild type littermates in five different tissues (brain, testis, liver, skeletal and heart muscle)
2013-07-17 | E-GEOD-40207 | biostudies-arrayexpress
Project description:ClpP activators ONC201 and related small molecules (TR compounds, Madera Therapeutics), have demonstrated significant anti-cancer potential in an array of in vitro and in vivo studies, including clinical trials for refractory solid tumors. Though progress has been made in identifying specific phenotypic outcomes following ClpP activation, the exact mechanism by which ClpP activation leads to broad anti-cancer activity has yet to be fully elucidated. In this study, we utilized a multi-omics approach to identify the ClpP-dependent proteomic, transcriptomic, and metabolomic changes resulting from ONC201 or the TR compound TR-57 in triple-negative breast cancer cells. Applying mass spectrometry- based methods of proteomics and metabolomics, we identified ~8000 proteins and 588 metabolites, respectively. From proteomics data, approximately 3400 (ONC201) and 3000 (TR-57) proteins increased and ~4600 (ONC201) and ~4800 (TR-57) proteins decreased in this study. Gene ontological (GO) analysis revealed strong similarities between proteins up- or downregulated by ONC201 or TR-57 treatment. Notably, this included the downregulation of many mitochondrial processes and proteins, including mitochondrial translation and mitochondrial matrix proteins. We performed a large-scale transcriptomic analysis of WT SUM159 cells, identifying ~7700 transcripts (~3600 and 3800 increasing, ~4000 and 3900 decreasing in ONC201 and TR-57 treated cells, respectively). Less than 21% of these genes were affected by these compounds in ClpP null cells. GO analysis of these data demonstrated additional similarity of response to ONC201 and TR-57, including a decrease in transcripts related to the mitochondrial inner membrane and matrix, cell cycle, and nucleus, and increases in other nuclear transcripts and transcripts related to metal-ion binding. Comparison of response between both compounds demonstrated a highly similar response in all -omics datasets. Analysis of metabolites also revealed significant similarities between ONC201 and TR-57 with increases in α-ketoglutarate and 2-hydroxyglutaric acid and decreased ureidosuccinic acid, L-ascorbic acid, L-serine, and cytidine observed following ClpP activation in TNBC cells. Further analysis identified multiple pathways that were specifically impacted by ClpP activation, including ATF4 activation, heme biosynthesis, and the citrulline/urea cycle. In summary the results of our studies demonstrate that ONC201 and TR-57 induce highly similar and broad effects against multiple mitochondrial processes required for cell proliferation.
2023-04-01 | GSE221327 | GEO
Project description:Systematic genetic interaction profiles can reveal the mechanism-of-action of bioactive compounds. The imipridone ONC201, which is currently in cancer clinical trials, has been ascribed a variety of different targets. To investigate the genetic dependencies of imipridone action, we screened a genome-wide CRISPR knockout library in the presence of either ONC201 or its more potent analog ONC212. Loss of the mitochondrial matrix protease CLPP or the mitochondrial intermediate peptidase MIPEP conferred strong resistance to both compounds. Biochemical and surrogate genetic assays showed that impridones directly activate CLPP and that MIPEP is necessary for proteolytic maturation of CLPP into a catalytically competent form. Quantitative proteomic analysis of cells treated with ONC212 revealed degradation of many mitochondrial as well as non-mitochondrial proteins. Prompted by the conservation of ClpP from bacteria to humans, we found that the imipridones also activate ClpP from Escherichia coli, B. subtilis and Staphylococcus aureus in biochemical and genetic assays. ONC212 and acyldepsipeptide (ADEP)-4, a known activator of bacterial ClpP, caused similar proteome-wide degradation profiles in S. aureus. ONC212 suppressed the proliferation of a number of Gram-positive (S. aureus, B. subtilis, Enterococcus faecium) and Gram-negative species (E. coli, Neisseria gonorrhoeae). Moreover, ONC212 enhanced the ability of rifampin to eradicate antibiotic-tolerant S. aureus persister cells. These results reveal the genetic dependencies of imipridone action in human cells and identify the imipridone scaffold as a new entry point for antibiotic development.
2020-02-23 | GSE138894 | GEO
Project description:The peptidase ClpP is conserved from bacteria to human. In the mitochondrial matrix, it multimerizes and forms a macromolecular proteasome-like cylinder. Because of its known relevance for the mitochondrial unfolded protein response during cell stress, we characterized two ClpP knock-out mouse founder lines and documented similar phenotypes. Ubiquitously, ClpP absence led to accumulation of its interactor protein ClpX without transcript upregulation. Interestingly, most wild-type tissues with substantial ClpP amounts had no detectable ClpX. This inverse correlation suggests that ClpX levels and degradation are regulated by ClpP. The expectation of similar protein levels, in view of a reported association of heptameric ClpP rings with hexameric ClpX rings, was confirmed only in testis of wild-type animals. Germline tissue was exceptional also in its vulnerability to ClpP deletion, with both founder lines showing complete infertility for males and females. Otherwise, ubiquitous mitochondrial dysfunction was apparent from severe growth retardation and reduced spontaneous motor activity of the animals, and from a pronounced decrease in pre-/postnatal survival. Spermatogenesis was found aborted at the spermatid stage, acrosomes and axonemes were not formed. Overall, tissue-specific roles of ClpP were evident by this massive effect for germ cells, mild bioenergetic deficits in muscle and liver tissues, and excellent compensation in brain. ClpX was previously reported to chaperone unfolded proteins and also DNA condensation in mitochondria, so it is likely that this pathway is particularly susceptible in germ cells. In conclusion, our study indicates that the role of ClpP in quality control is indispensable during development for cells with rapid changes of mitochondrial numbers, and is relevant during aging for growth and survival of the organism.
2013-07-17 | GSE40207 | GEO
Project description:To investigate whether ClpP/ClpX is required for maintaining mitochondrial functions in spermatocytes during meiosis and spermatogenesis. We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 different spermatocytes from control, ClpP CKO, ClpX CKO groups (3 repeats for each)
2023-09-27 | GSE220600 | GEO
Project description:The ClpP activators ONC201 and related small molecules (TR compounds, Madera Therapeutics), have demonstrated significant anti-cancer potential in an array of in vitro cell models and in vivo studies, including clinical trials for refractory solid tumors. Though progress has been made in identifying specific phenotypic outcomes following ClpP activation, the exact mechanism by which ClpP activation leads to broad anti-cancer activity has yet to be fully elucidated. In this study, we utilized a multi-omics approach to identify the ClpP-dependent proteomic, transcriptomic, and metabolomic changes resulting from ONC201 or the TR compound TR-57 in triple-negative breast cancer cells (TNBC). Applying mass spectrometry- based methods of proteomics and metabolomics, we identified ~8000 proteins and 588 metabolites, respectively. From proteomics data, approximately 3400 (ONC201) and 3000 (TR-57) proteins increased and ~4600 (ONC201) and ~4800 (TR-57) proteins decreased in this study. Additionally, gene ontological analysis revealed strong similarities between proteins up- or downregulated by ONC201 or TR-57 treatment. Notably, this included the downregulation of many mitochondrial processes and proteins, including mitochondrial translation and mitochondrial matrix proteins. We also performed a large-scale transcriptomic analysis of WT SUM159 cells, identifying ~7700 transcripts (~3600 and 3800 increasing, ~4000 and 3900 decreasing in ONC201 and TR-57 treated cells, respectively). Less than 21% of these genes were affected by these compounds in ClpP null cells. Gene ontological analysis of these data demonstrated additional similarity of response to ONC201 and TR-57. Many of the same gene ontology processes and cellular components were identified, including a decrease in transcripts related to the mitochondrial inner membrane and matrix, the cell cycle, and the nucleus, as well as increases in other nuclear transcripts and transcripts related to metal-ion binding. Comparative analysis demonstrated a highly analogous response in all -omics datasets. Analysis of metabolites also revealed significant similarities between ONC201 and TR-57 with increases in α-ketoglutarate and 2-hydroxyglutaric acid and decreased levels of ureidosuccinic acid, L-ascorbic acid, L-serine, and cytidine observed following ClpP activation in TNBC cells. Further analysis identified multiple pathways that were specifically impacted by ClpP activation, including ATF4 activation, heme biosynthesis, and the citrulline/urea cycle. In summary the results of our studies demonstrate that ONC201 and TR-57 induce highly similar and broad effects against multiple mitochondrial processes required for cell proliferation.
2022-12-13 | ST002408 | MetabolomicsWorkbench
Project description:Ectopic activation of the conserved ClpP protease by chemical activators causes toxicity in bacteria and human cells due to unrestrained proteolysis. The imipridone ONC201 has been ascribed multiple mechanisms of action and is currently in cancer clinical trials. To systematically investigate the genetic dependencies of imipridone action, we screened a genome-wide CRISPR knockout library in the presence of ONC201 and its more potent analog ONC212. Loss of the mitochondrial matrix protease CLPP conferred strong resistance to both compounds, consistent with recent reports that ONC201 directly activates CLPP in cancer cells. Biochemical assays and surrogate genetic assays in yeast confirmed activation of CLPP in the absence of its regulatory subunits. Imipridone toxicity was bypassed by loss of only one other gene, the mitochondrial intermediate peptidase MIPEP, which we showed is necessary for proteolytic maturation of a CLPP precursor form. Quantitative proteomic analysis of cells treated with ONC212 revealed degradation of many mitochondrial proteins as well as cell cycle regulators. Prompted by the conservation of ClpP across kingdoms, we showed that the imipridones activate Escherichia coli ClpP in vitro and Staphylococcus aureus ClpP in a surrogate yeast assay. ONC212 and acyldepsipeptide (ADEP)-4, a known activator of bacterial ClpP, caused similar proteomic degradation profiles in S. aureus. ONC212 suppressed the proliferation of a number of Gram-positive (S. aureus, Bacillus subtilis, Enterococcus faecium) and Gram-negative species (E. coli, Neisseria gonorrhoeae). Moreover, a combination of ONC212 and rifampicin eradicated antibiotic-tolerant S. aureus persister cells. These results reveal the genetic dependencies of imipridone action in human cells and identify the imipridone scaffold as a new entry point for antibiotic development.
2020-03-26 | PXD016119 | Pride
Project description:To investigate whether ClpP/ClpX is required for maintaining mitochondrial functions in spermatocytes during meiosis and spermatogenesis. We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 different spermatocytes from control, ClpP CKO, ClpX CKO groups (3 repeats for each)
2023-09-27 | GSE221888 | GEO
Project description:By integration of transcriptome and metabolite analyses, we showed that pharmacological activation of the mitochondrial ClpP protease through utilization of enhanced imipridone compounds (ONC206 and ONC212) in combination with global (Panobinostat) and selective (romidepsin) HDAC – inhibitors caused synergistic reduction of viability in established and patient-derived xenograft (PDX) cultures of human GBM. This effect occurred independent of TP53 status and was partially mediated by activation of a cell death with apoptotic features accompanied by activation of initiator and effector caspases as well as cleavage of PARP. Consistently, the combination treatment altered the expression of anti-apoptotic and pro-apoptotic Bcl-2 family members, resulting in down-regulation of Bcl-xL and Mcl-1. Knockdown experiments targeting Noxa, BIM, Bcl-xL and Mcl-1 confirmed a functional implication of these proteins in the reduction of cellular viability mediated by the combination treatment. Importantly, knockdown of the ClpP protease significantly rescued the reduction of cellular viability by ClpP activators and the combination treatment, respectively, suggesting critical involvement of this protein. We used microarrays to detail the global programme of gene expression underlying cellularization and identified distinct classes of up-regulated and down-regulated genes in cells treated with ONC206 and Romidepsin.
2022-01-24 | GSE166111 | GEO