A Dual Molecular Analog Tuner for Dissecting Mammalian Protein Function
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE74457 | GEO | 2016/02/01
SECONDARY ACCESSION(S): PRJNA300451
REPOSITORIES: GEO
Similar Datasets
Project description:While effective anti-cancer drugs targeting the CHK1 kinase are advancing in the clinic, drug resistance is rapidly emerging. Here, we demonstrate that CRISPR-mediated knockout of the little-known gene FAM122A confers cellular resistance to CHK1 inhibitors and cross-resistance to ATR inhibitors. Knockout of FAM122A results in activation of PP2A-B55α, a phosphatase which dephosphorylates the WEE1 protein and rescues WEE1 from Ubiquitin-mediated degradation. The resulting increase in WEE1 protein expression reduces replication stress, activates the G2/M checkpoint, and confers cellular resistance to CHK1 inhibitors. Interestingly, in tumor cells with oncogene-driven replication stress, CHK1 can directly phosphorylate FAM122A, leading to activation of the PP2A-B55α phosphatase and increased WEE1 expression. A combination of a CHK1 inhibitor plus a WEE1 inhibitor can overcome CHK1 inhibitor resistance of these tumor cells, thereby enhancing anti-cancer activity. The FAM122A expression level in a tumor cell can serve as a useful biomarker for predicting CHK1 inhibitor sensitivity or resistance.
2021-01-01 | GSE158338 | GEO
Project description:The G2 DNA damage checkpoint inhibits Cdc2 and mitotic entry through the dual regulation of Wee1 and Cdc25 by the Chk1 effector kinase. Up-regulation of Chk1 by mutation or overexpression bypasses the requirement for up-stream regulators or DNA damage to promote a G2 cell cycle arrest. We screened in fission yeast for mutations that rendered cells resistant to overexpressed Chk1. We identified a mutation in tra1, which encodes one of two homologs of TRRAP, an ATM/R-related pseudokinase that scaffolds several histone acetyltransferase (HAT) complexes. Inhibition of histone deacetylases reverts the resistance to overexpressed Chk1, suggesting this phenotype is due to a HAT activity, though expression of checkpoint and cell cycle genes is not greatly affected. Cells with mutant or deleted tra1 activate Chk1 normally and are checkpoint proficient. However, these cells are semi-wee even when overexpressing Chk1, and accumulate inactive Wee1 protein. The Cdr (changed division response) kinases Cdr1 and Cdr2 are negative regulators of Wee1, and while best characterized in the cellular response to limited nutrition, we show that they are required for the Tra1-dependent alterations to Wee1 function. This identifies Tra1 as another component controlling the timing of entry into mitosis via Cdc2 activation. Two and three independent microaaray experiments were done for wild type and the mutant (tra1-1) respectively.
2010-04-11 | E-GEOD-12674 | biostudies-arrayexpress
Project description:We synthesized novel fluorescent thalidomide analogs (2,6-dialkylphenyl-4/5-amino-substituted-5,6,7-trifluorophthalimides) that localize specifically to lipid droplets. By using affinity chromatography interacting proteins were identified: Rab7, Rab10, Rab11, Sec22b, sorting nexin 2, calnexin, protein disulfide isomerase, GRP78, GRP94 among others that are involved in vesicular transport and ER stress response. Amino-trifluoro-phthalimides exerted potent anticancer activities in vitro on different cell lines including melanoma, leukemia, hepatocellular carcinoma, glioblastoma. They are non-toxic to adult animals up-to 1 g/kg but are highly teratogenic to zebrafish embryos at micromolar concentrations resulting defects in developing muscle. The analogs resulted in calcium release from the endoplasmic reticulum (ER), induction of reactive oxygen species (ROS), ER stress and finally apoptosis. Gene expression analysis confirmed the induction of ER stress-mediated apoptosis pathway components, such as growth arrest- and DNA damage-inducible gene 153 (GADD153), ATF3, Luman/CREB3 recruitment factor (LRF) and the ER-associated degradation-related gene HERPUD1. Tumor suppressors, P53, LATS2 and ING3 were also up-regulated in various cell lines after drug treatment. Exogenous docosahexaenoic acid or eicosapentaenoic acid induced calcium release and ROS and synergized with the analogs in vitro, while oleic acid had no such an effect. Different antioxidants partially, intracellular calcium chelator almost completely diminished ROS production. Amino-phthalimides down-regulated the expression of CCL2, which is implicated in tumor metastasis and angiogenesis. Because of the anticancer, anti-angiogenic action and the wide range of applicability of the immunomodulatory drugs, lipid droplet-binding members of this family could represent a new class of agents by affecting ER-membrane integrity and perturbations of ER homeostasis. 4 replica, 2 dye-swap
2010-02-22 | E-GEOD-14945 | biostudies-arrayexpress
Project description:Polycomb group (PcG) proteins are evolutionarily conserved repressors of developmental genes. Paradoxically, the same PcG proteins also play roles in gene activation via mechanisms that are not yet fully understood. Here, we found that S-phase kinase-associated protein 1A (SKP1A), an essential factor of SCF (SKP1A/CULLIN1/F-box) ubiquitin ligases and a subunit of the PCGF1 (Polycomb group RING finger protein 1) component of Polycomb repressive complex 1 (PCGF1-PRC1), mediates the link between PcG-dependent gene regulation and ubiquitin-dependent proteasomal degradation. By using differentiating mouse embryonic stem cells, we found that SKP1A removes EED, a core component of Polycomb repressive complex 2 (PRC2) that is bound to PcG target gene promoters, via proteasomal degradation, and it thereby sensitises these genes for subsequent activation. Furthermore, we show that SKP1A removes EED from the Meis2 promoter in the midbrain of developing mouse embryos, leading to Meis2 gene expression. In summary, we reveal here a previously unknown role of SKP1A in activating PcG-target genes via the proteasomal degradation of PRC2. This implies that SKP1A-containing PCGF1-PRC1 may confer reversibility on PcG-mediated gene silencing for robust spatiotemporal regulation of target genes.
2024-09-01 | GSE263260 | GEO
Project description:Polycomb group (PcG) proteins are evolutionarily conserved repressors of developmental genes. Paradoxically, the same PcG proteins also play roles in gene activation via mechanisms that are not yet fully understood. Here, we found that S-phase kinase-associated protein 1A (SKP1A), an essential factor of SCF (SKP1A/CULLIN1/F-box) ubiquitin ligases and a subunit of the PCGF1 (Polycomb group RING finger protein 1) component of Polycomb repressive complex 1 (PCGF1-PRC1), mediates the link between PcG-dependent gene regulation and ubiquitin-dependent proteasomal degradation. By using differentiating mouse embryonic stem cells, we found that SKP1A removes EED, a core component of Polycomb repressive complex 2 (PRC2) that is bound to PcG target gene promoters, via proteasomal degradation, and it thereby sensitises these genes for subsequent activation. Furthermore, we show that SKP1A removes EED from the Meis2 promoter in the midbrain of developing mouse embryos, leading to Meis2 gene expression. In summary, we reveal here a previously unknown role of SKP1A in activating PcG-target genes via the proteasomal degradation of PRC2. This implies that SKP1A-containing PCGF1-PRC1 may confer reversibility on PcG-mediated gene silencing for robust spatiotemporal regulation of target genes.
2024-09-01 | GSE263265 | GEO
Project description:Polycomb group (PcG) proteins are evolutionarily conserved repressors of developmental genes. Paradoxically, the same PcG proteins also play roles in gene activation via mechanisms that are not yet fully understood. Here, we found that S-phase kinase-associated protein 1A (SKP1A), an essential factor of SCF (SKP1A/CULLIN1/F-box) ubiquitin ligases and a subunit of the PCGF1 (Polycomb group RING finger protein 1) component of Polycomb repressive complex 1 (PCGF1-PRC1), mediates the link between PcG-dependent gene regulation and ubiquitin-dependent proteasomal degradation. By using differentiating mouse embryonic stem cells, we found that SKP1A removes EED, a core component of Polycomb repressive complex 2 (PRC2) that is bound to PcG target gene promoters, via proteasomal degradation, and it thereby sensitises these genes for subsequent activation. Furthermore, we show that SKP1A removes EED from the Meis2 promoter in the midbrain of developing mouse embryos, leading to Meis2 gene expression. In summary, we reveal here a previously unknown role of SKP1A in activating PcG-target genes via the proteasomal degradation of PRC2. This implies that SKP1A-containing PCGF1-PRC1 may confer reversibility on PcG-mediated gene silencing for robust spatiotemporal regulation of target genes.
2024-09-01 | GSE263263 | GEO
Project description:The G2 DNA damage checkpoint inhibits Cdc2 and mitotic entry through the dual regulation of Wee1 and Cdc25 by the Chk1 effector kinase. Up-regulation of Chk1 by mutation or overexpression bypasses the requirement for up-stream regulators or DNA damage to promote a G2 cell cycle arrest. We screened in fission yeast for mutations that rendered cells resistant to overexpressed Chk1. We identified a mutation in tra1, which encodes one of two homologs of TRRAP, an ATM/R-related pseudokinase that scaffolds several histone acetyltransferase (HAT) complexes. Inhibition of histone deacetylases reverts the resistance to overexpressed Chk1, suggesting this phenotype is due to a HAT activity, though expression of checkpoint and cell cycle genes is not greatly affected. Cells with mutant or deleted tra1 activate Chk1 normally and are checkpoint proficient. However, these cells are semi-wee even when overexpressing Chk1, and accumulate inactive Wee1 protein. The Cdr (changed division response) kinases Cdr1 and Cdr2 are negative regulators of Wee1, and while best characterized in the cellular response to limited nutrition, we show that they are required for the Tra1-dependent alterations to Wee1 function. This identifies Tra1 as another component controlling the timing of entry into mitosis via Cdc2 activation.
2010-04-11 | GSE12674 | GEO
Project description:CSC DDR dataset contains 4 bam files of two pairs of colorectal CSCs sensitive and resistant to ATR or CHK1 inhibitor
| EGAD00001006774 | EGA
Project description:Human cytomegalovirus (HCMV) is an important pathogen with multiple immune evasion strategies, including virally facilitated degradation of host antiviral restriction factors. Here, we describe a multiplexed approach to discover proteins with innate immune function on the basis of active degradation by the proteasome or lysosome during early phase HCMV infection. Using three orthogonal proteomic/transcriptomic screens to quantify protein degradation, with high confidence we identified 35 proteins enriched in antiviral restriction factors. A final screen employed a comprehensive panel of viral mutants to predict viral genes that target >250 human proteins. This approach revealed Helicase-like Transcription Factor (HLTF), a DNA helicase important in DNA repair, potently inhibits early viral gene expression but is rapidly degraded during infection. The functionally unknown HCMV protein UL145 facilitates HLTF degradation by recruiting the Cullin4 E3 ligase complex. Our approach and data will enable further identifications of innate pathways targeted by HCMV and other viruses.
2018-08-16 | GSE111036 | GEO
Project description:Although inhibitors of the kinases CHK1, ATR and WEE1 are undergoing clinical testing, it remains unclear how these three classes of agents kill susceptible cells and whether they utilize the same cytotoxic mechanism. Here we observed that CHK1 inhibition induces apoptosis in a subset of acute leukemia cell lines, including TP53 null acute myeloid leukemia (AML) and BCR/ABL-positive acute lymphoid leukemia (ALL), in vitro and inhibits leukemic colony formation in clinical AML samples ex vivo. In further studies, CHK1 downregulation or CHK1 inhibitor treatment triggered signaling in sensitive human acute leukemia cell lines that involved CDK2 activation followed by AP1-dependent TNF transactivation, TNF production and engagement of a TNFR1- and BID-dependent apoptotic pathway. AML lines that were intrinsically CHK1 inhibitor resistant exhibited high CHK1 expression and were sensitized by CHK1 downregulation. Signaling through this same CDK2 AP1 TNF cytotoxic pathway was also initiated by ATR or WEE1 inhibitors in vitro and during CHK1 inhibitor treatment of AML xenografts in vivo. Collectively, these observations not only identify new contributors to antileukemic cell action of CHK1, ATR and WEE1 inhibitors, but also delineate a previously undescribed pathway leading from aberrant CDK2 activation to death ligand-induced killing that can potentially be exploited for acute leukemia treatment.
2020-12-28 | GSE131912 | GEO