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Gene expression profiling upon PI3K inhibition using different inhibitors

ABSTRACT: Activation of the phosphoinositide 3-kinase (PI3K)/Akt signaling pathway is one the most frequent genetic events in human cancer. Therefore, the development of PI3K inhibitors has attracted much attention. We previously described the pyrazolopyrimidine derivative ETP-45658 as a potent inhibitor of PI3K p110α in vitro and in vivo. Here we report the gene expression signatures of MCF7 cells treated with ETP-45658 or the reference PI3K inhibitor PI-103. Both compounds potently inhibited proliferation of a wide range of human cancer cells. ETP-45658 most potently suppressed the growth of PIK3CA (E545K)-mutated MCF7 breast cancer cells. Treatment with ETP-45658 or PI-103 resulted in a time and concentration-dependent decrease in phosphorylation of AKT Ser473 in MCF7 cells. We conducted microarray analysis examining the gene expression profile in MCF7 cells at six hours post ETP-45658 or PI-103 incubation. Both compounds induced the expression of negative cell cycle regulators including Cyclin G2, p27kip1 and ING4 and decreased positive regulators such as Cyclin D1 without significantly affecting the expression of pro-apoptotic genes. We found FOXO transcription factor binding sites over-represented in both up- and down-regulated genes but not in those without significant changes. The expression of the breast cancer tumor suppressor Nischarin was found to be induced by ETP-45658 but not after PI-103 treatment while several genes differentially expressed specifically after ETP-45658 treatment are functionally associated with the focal adhesion pathway.

ORGANISM(S): Homo sapiens

PROVIDER: GSE56579 | GEO | 2014/04/08

SECONDARY ACCESSION(S): PRJNA243974

REPOSITORIES: GEO

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Gene expression profiling upon PI3K inhibition using different inhibitors

Project description:Activation of the phosphoinositide 3-kinase (PI3K)/Akt signaling pathway is one the most frequent genetic events in human cancer. Therefore, the development of PI3K inhibitors has attracted much attention. We previously described the pyrazolopyrimidine derivative ETP-45658 as a potent inhibitor of PI3K p110Œ± in vitro and in vivo. Here we report the gene expression signatures of MCF7 cells treated with ETP-45658 or the reference PI3K inhibitor PI-103. Both compounds potently inhibited proliferation of a wide range of human cancer cells. ETP-45658 most potently suppressed the growth of PIK3CA (E545K)-mutated MCF7 breast cancer cells. Treatment with ETP-45658 or PI-103 resulted in a time and concentration-dependent decrease in phosphorylation of AKT Ser473 in MCF7 cells. We conducted microarray analysis examining the gene expression profile in MCF7 cells at six hours post ETP-45658 or PI-103 incubation. Both compounds induced the expression of negative cell cycle regulators including Cyclin G2, p27kip1 and ING4 and decreased positive regulators such as Cyclin D1 without significantly affecting the expression of pro-apoptotic genes. We found FOXO transcription factor binding sites over-represented in both up- and down-regulated genes but not in those without significant changes. The expression of the breast cancer tumor suppressor Nischarin was found to be induced by ETP-45658 but not after PI-103 treatment while several genes differentially expressed specifically after ETP-45658 treatment are functionally associated with the focal adhesion pathway. Twelve samples have been analyzed in six different conditions. Two replicates have been included for each condition.

2014-04-08 | E-GEOD-56579 | biostudies-arrayexpress

FOXO3a Is A Major Target Of Inactivation By PI3K/AKT Signaling In Aggressive Neuroblastoma

Project description:Neuroblastoma is a pediatric tumor of the peripheral sympathetic nervous system with a highly variable prognosis. Activation of the PI3K/AKT pathway in neuroblastoma is correlated with poor patient prognosis, but the precise downstream effectors mediating this effect have not been determined. Here, we identify the forkhead transcription factor FOXO3a as a key target of the PI3K/AKT pathway in neuroblastoma. FOXO3a expression was elevated in low stage neuroblastoma tumors and normal embryonal neuroblasts, but reduced in late stage neuroblastoma. Inactivation of FOXO3a by AKT was essential for neuroblastoma cell survival. Treatment of neuroblastoma cells with the dual PI3K/mTOR inhibitor PI-103 activated FOXO3a and triggered apoptosis. This effect was rescued by FOXO3a silencing. Conversely, apoptosis induced by PI-103 or the AKT inhibitor MK-2206 was potentiated by FOXO3a overexpression. Further, levels of total or phosphorylated FOXO3a correlated closely with apoptotic sensitivity to MK-2206. In clinical specimens, there was an inverse relationship between gene expression signatures regulated by PI3K signaling and FOXO3a transcriptional activity. Moreover, high PI3K activity and low FOXO3a activity were each associated with an extremely poor prognosis. Our work indicates that expression of FOXO3a and its targets offer useful prognostic markers as well as biomarkers for PI3K/AKT inhibitor efficacy in neuroblastoma. Affymetrix U133 Plus 2.0 profiling of SY5Y-TetR-FOXO3A cells treated with doxycycline and/or the PI3K/mTOR inhibitor PI-103. Each condition profiled in triplicate.

2013-05-01 | E-GEOD-42762 | biostudies-arrayexpress

FOXO3a Is A Major Target Of Inactivation By PI3K/AKT Signaling In Aggressive Neuroblastoma

2013-05-01 | GSE42762 | GEO

Molecular pharmacology of phosphatidylinositol 3-kinase inhibition in human glioma

Project description:Gliomas are primary brain tumors with poor prognosis that exhibit frequent abnormalities in phosphatidylinositol 3-kinase (PI3 kinase) signaling. We investigated the molecular mechanism of action of the isoform-selective class I PI3 kinase and mTOR inhibitor PI-103 in human glioma cells. The potent inhibitory effects of PI-103 on the PI3 kinase pathway were quantified. PI-103 and the mTOR inhibitor rapamycin both inhibited ribosomal protein S6 phosphorylation but there were clear differences in the response of upstream components of the PI3 kinase pathway, such as phosphorylation of Thr308-AKT, that were inhibited by PI-103 but not rapamycin. Gene expression profiling identified altered expression of genes encoding regulators of the cell cycle and cholesterol metabolism, and genes modulated by insulin or IGF1 signaling, rapamycin treatment or nutrient starvation. PI-103 decreased expression of positive regulators of G1/S phase progression and increased expression of the negative cell cycle regulator p27kip1. A reversible PI-103-mediated G1 cell cycle arrest occurred without significant apoptosis, consistent with the altered gene expression detected. PI-103 induced vacuolation and processing of LC-3i to LC-3ii, which are features of an autophagic response. In contrast to PI-103, LY294002 and PI-387 induced apoptosis, indicative of likely off-target effects. PI-103 interacted synergistically or additively with cytotoxic agents used in the treatment of glioma, namely vincristine, BCNU and temozolomide. Compared to individual treatments, the combination of PI-103 with temozolomide significantly improved the response of U87MG human glioma xenografts. Our results support the therapeutic potential for PI3 kinase inhibitors with a PI-103-like profile as therapeutic agents for the treatment of glioma. Keywords: Key words: PI-103, glioma, PI3 kinase, mTOR, cell cycle, cytostasis

2009-04-21 | GSE12175 | GEO

Identification of Syntaxin 7 and 12 as the first selective substrates for SGK3

Project description:Deregulation of the PI3K/Akt pathway is a common feature in many types of cancer. Recent data has demonstrated that prolonged inhibition of breast cancer cell lines with PI3K and Akt inhibitors leads to up-regulation and increased activity of the AGC kinase Serum and glucocorticoid activated kinase 3, SGK3, which in turn substitutes for Akt and leads to activation of mTORC1. SGK3 and Akt exhibit similar substrate specificity for Ser/Thr residues in the RxRxxS/T motif. However, SGK3 can be regulated by both PI3K class I and class III and possesses a unique PX domain, enabling it to bind to PI(3)P lipids in endosomes. Still, the known SGK3 substrates are either shared or have not been tested whether Akt can phosphorylate them. In the present study, we undertook genetic and pharmacologic phosphoproteomic screens to search for selective SGK3 substrates. We identified a significant number of potential in vivo SGK3 selective substrates, including the endosomal proteins STX7, STX12, RFIP4 and WDR44. In vitro phosphorylation studies demonstrated that these substrates were directly phosphorylated at the sites identified in vivo by SGK3 but, unlike all other SGK3 substrates reported, not by Akt. We provide evidence that endogenous STX7 and STX12 are physiological SGK3 substrates whose phosphorylation is potently stimulated by IGF1. Our data pinpoint that STX7 and STX12 are the first selective SGK3 substrates in vivo and this phosphorylation enhances their interaction with the respective SNARE complexes. Finally, we suggest that STX7 and STX12 phosphorylation can be utilised as in vivo biomarkers for SGK3 activity.

2020-05-26 | PXD014561 | Pride

Investigating the AZDR1208 resistance in HSB-2 cells

Project description:The study uses RNA sequencing to profile AZD1208 resistant (AZDR) vs AZD1208 sensitive HSB-2 cells. PIM inhibitor treatment decreases leukemia burden in early T-cell precursor acute lymphoblastic leukemias (ETP-ALL) both in vitro and in vivo. However, prolonged treatment of ETP-ALL with PIM kinase inhibitors results in PIM inhibitor resistance. The analysis revealed that the HOXA9, mTOR, MYC, NF-B, and PI3K-AKT pathways were activated in PIM inhibitor resistant ETP-ALL

2021-09-20 | GSE135545 | GEO

Structural analysis of the PTEN:P-Rex2 signaling node reveals how cancer-associated mutations coordinate to hyperactivate Rac1

Project description:The PTEN:P-Rex2 complex is a commonly mutated signaling nodes in metastatic cancer. The dual-specificity phosphatase PTEN canonically functions as a tumour suppressor by hydrolysing PI(3,4,5)P3 to PI(4,5)P2 to inhibit PI3K-AKT signaling. P-Rex2 is a RhoGTPase guanine nucleotide exchange factor activated by both Gβγ and PI(3,4,5)P3 downstream of G protein-coupled receptor and receptor tyrosine kinase signaling. Assembly of the PTEN:P-Rex2 complex inhibits the activity of both proteins, and its dysregulation can drive PI3K-AKT signaling and cell proliferation. However, structural insights into both PTEN:P-Rex2 complex assembly and its dysregulation by cancer-associated mutations remain limited. Here, using crosslinking mass spectrometry and functional studies, we provide mechanistic insights into PTEN:P-Rex2 complex assembly and co-inhibition. PTEN is anchored to P-Rex2 by interactions between the PTEN C-terminal tail PDZ-interacting motif and the second PDZ domain of P-Rex2. This interaction bridges PTEN across the P-Rex2 surface, occluding PI(3,4,5)P3 hydrolysis. Conversely, PTEN both allosterically promotes an autoinhibited P-Rex2 conformation and occludes Gβγ binding. These insights allow us to define a new gain-of-function class of cancer mutations within the PTEN:P-Rex2 interface that uncouples PTEN inhibition of Rac1 signaling. In addition, we observe synergy between PTEN deactivating and P-Rex2 truncation mutations that combine to drive Rac1 activation to a greater extent than either single mutation alone.

2022-08-12 | PXD021126 | Pride

Conditional loss of ErbB3 delays mammary gland hyperplasias induced by mutant PIK3CA but does not affect mammary tumor latency, gene expression or signaling

Project description:Mutations in PIK3CA, the gene encoding the p110α subunit of PI3K, induce transformation of mammary epithelial cells (MEC). Studies suggest the transforming action of mutant PIK3CA requires binding to activated receptor tyrosine kinases or adaptors. We examined in transgenic mice if ErbB3, a powerful activator of PI3K, is required for mutant PIK3CA-mediated MEC transformation. ErbB3 loss delayed PIK3CAH1047R-dependent mammary gland hyperplasia, but tumor latency, gene expression and markers of PI3K signaling were unaffected. In ErbB3-deficient tumors, mutant PI3K remained associated with other tyrosine phosphorylated adaptors, potentially explaining the dispensability of ErbB3 for tumorigenicity and PI3K activity. Combined inhibition of ErbB RTKs and PI3K with lapatinib and the p110α inhibitor BYL719, respectively, reduced PIK3CAH1047R-dependent tumor growth and PI3K signaling more potently than the p110α inhibitor alone. In human breast cancer cells harboring PIK3CAH1047R, the combination with BYL719 and an ErbB3 inhibitor synergistically inhibited tumor growth and P-Akt. These data suggest that basal tumor growth and PI3K signaling do not depend on ErbB RTKs in PIK3CAH1047R-expressing tumors. However, upon inhibition of p110α, these receptors limit the action of PI3K inhibitors potentially explaining the more potent effect of the combination against PI3K-mutant cancers. reference x sample

2013-06-20 | E-GEOD-43037 | biostudies-arrayexpress

MAGI1 prevents senescence and promotes the DNA damage response in ER+ breast cancer

Project description:MAGI1 acts as tumor suppressor in estrogen receptor positive (ER+) breast cancer (BC) and its loss correlates with a more aggressive phenotype. To identify pathways and events affected by MAGI1 loss, we deleted the MAGI1 gene in the ER+ MCF7 BC cell line and performed RNA-sequencing and functional experiments in vitro. Transcriptome analyses revealed gene sets and biological processes related to estrogen signaling, cell cycle and DNA damage response affected by MAGI1 loss. Upon exposure to TNF-alpha/IFN-gamma, MCF7 MAGI1 KO cells entered a deeper level of quiescence/senescence than MCF7 control cells and activated the AKT and MAPK signaling pathways. MCF7 MAGI1 KO cells exposed to ionizing radiations or cisplatin had reduced expression of DNA repair proteins and showed increased sensitivity towards PARP1 inhibition with olaparib. Treatment with PI3K and AKT inhibitors (alpelisib and MK-2206) restored expression of DNA repair proteins and sensitized cells to fulvestrant. Analysis of human BC patients’ transcriptomic data revealed that patients with low MAGI1 levels have a higher tumor mutational burden and homologous recombination deficiency. Also, MAGI1 expression levels correlate negatively with PI3K/AKT and MAPK signaling, confirming our in vitro observations. Pharmacological and genomic evidence indicate HDACs as regulators of MAGI1 expression. Our findings provide a new view on MAGI1 function in cancer and identify potential treatment options to improve the management of ER+ BC patients with low MAGI1 levels.

2023-07-26 | GSE237984 | GEO

PLEKHS1 drives PI3Ks and remodels pathway homeostasis in PTEN-null prostate

Project description:The PIP3/PI3K network is a central regulator of metabolism and is frequently activated in cancer, commonly by loss of the PIP3/PI(3,4)P2-phosphatase, PTEN. Despite huge investment, the drivers of the PI3K network in normal tissues and how they adapt to overactivation are unclear. We find that in healthy mouse prostate PI3K activity is driven by RTK/IRS signalling and constrained by pathway-feedback. In the absence of PTEN, the network is dramatically remodelled. A poorly understood, YXXM- and PIP3/PI(3,4)P2-binding PH domain-containing, adaptor, PLEKHS1, became the dominant activator and was required to sustain PIP3, AKT-phosphorylation and growth in PTEN-null prostate. This was because PLEKHS1 evaded pathway-feedback and experienced enhanced PI3K- and SRC-family kinase-dependent phosphorylation of Y258XXM, eliciting PI3K-activation. hPLEKHS1-mRNA and activating-Y419-phosphorylation of hSRC correlated with PI3K-pathway activity in human prostate cancers. We propose that in PTEN-null cells, receptor-independent, SRC-dependent tyrosine-phosphorylation of PLEKHS1 creates positive-feedback that escapes homeostasis, drives PIP3-signalling and supports tumour progression.

2023-08-23 | PXD043239 | Pride

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