Phosphatidylinositol 3-kinase signaling in proliferating cells maintains an anti-apoptotic transcriptional program mediated by inhibition of FOXO and non-canonical activation of NFκB transcription factors
- Jolyon Terragni†1,
- Julie R Graham†1,
- Kenneth W Adams1, 2,
- Michael E Schaffer1, 3,
- John W Tullai1 and
- Geoffrey M Cooper1Email author
© Terragni et al; licensee BioMed Central Ltd. 2008
Received: 17 August 2007
Accepted: 28 January 2008
Published: 28 January 2008
Phosphatidylinositol (PI) 3-kinase is activated by a variety of growth factor receptors and the PI 3-kinase/Akt signaling pathway is a key regulator of cell proliferation and survival. The downstream targets of PI 3-kinase/Akt signaling include direct regulators of cell cycle progression and apoptosis as well as a number of transcription factors. Growth factor stimulation of quiescent cells leads to robust activation of PI 3-kinase, induction of immediate-early genes, and re-entry into the cell cycle. A lower level of PI 3-kinase signaling is also required for the proliferation and survival of cells maintained in the presence of growth factors, but the gene expression program controlled by PI 3-kinase signaling in proliferating cells has not been elucidated.
We used microarray analyses to characterize the changes in gene expression resulting from inhibition of PI 3-kinase in proliferating cells. The genes regulated by inhibition of PI 3-kinase in proliferating cells were distinct from genes induced by growth factor stimulation of quiescent cells and highly enriched in genes that regulate programmed cell death. Computational analyses followed by chromatin immunoprecipitations demonstrated FOXO binding to both previously known and novel sites in promoter regions of approximately one-third of the up-regulated genes, consistent with activation of FOXO1 and FOXO3a in response to inhibition of PI 3-kinase. NFκB binding sites were similarly identified in promoter regions of over one-third of the down-regulated genes. RelB was constitutively bound to promoter regions in cells maintained in serum, however binding decreased following PI 3-kinase inhibition, indicating that PI 3-kinase signaling activates NFκB via the non-canonical pathway in proliferating cells. Approximately 70% of the genes targeted by FOXO and NFκB regulate cell proliferation and apoptosis, including several regulators of apoptosis that were not previously known to be targeted by these transcription factors.
PI 3-kinase signaling in proliferating cells regulates a novel transcriptional program that is highly enriched in genes that regulate apoptosis. At least one-third of these genes are regulated either by FOXO transcription factors, which are activated following PI 3-kinase inhibition, or by RelB, which is activated by PI 3-kinase via the non-canonical pathway in proliferating cells.
The PI 3-kinase/Akt signaling pathway plays a critical role in the regulation of growth factor-dependent metabolism, proliferation and survival of mammalian cells [1, 2]. The downstream targets of Akt that function to regulate cell proliferation and survival include the Bcl-2 family member Bad [3, 4] and the pro-apoptotic protein kinase GSK-3 [5, 6], both of which are inhibited by Akt phosphorylation. Targets of GSK-3 that have been implicated in cell proliferation and survival include the Bcl-2 family member Mcl-1 , cyclin D1 , and the translation initiation factor eIF2B . In addition, both Akt and GSK-3 phosphorylate a variety of transcription factors [10–13], and transcriptional regulation plays an important role in the control of cell growth and survival by PI 3-kinase/Akt/GSK-3 signaling. For example, the FOXO transcription factors are well-characterized substrates of Akt with key roles in cell proliferation and apoptosis. Phosphorylation by Akt leads to the retention of FOXOs in the cytoplasm as a result of binding to 14-3-3 proteins [14, 15]. In the absence of PI 3-kinase/Akt signaling, FOXOs translocate to the nucleus and activate transcription of their target genes, including those that encode proteins that induce cell cycle arrest (e.g., p130, p27 and cyclin G2) and apoptosis (e.g., Fas ligand, Trail, and Bim) . Additional transcription factors that are regulated either directly or indirectly by Akt and/or GSK-3 and may be involved in control of PI 3-kinase-dependent cell proliferation and survival include p53 , YAP , NFκB [19, 20], CREB [21, 22], c-Myc [23, 24], and c-Jun .
Although studies of individual transcription factors and their target genes have elucidated several aspects of PI 3-kinase signaling, understanding the overall program of transcriptional regulation controlled by the PI 3-kinase/Akt/GSK-3 pathway requires global expression analysis. We and others have previously used global expression profiling to identify genes whose induction is dependent on PI 3-kinase signaling following growth factor stimulation of quiescent cells [26–29]. Computational analysis to identify transcription factor binding sites that were over-represented in upstream regions of the PI 3-kinase dependent genes further implicated FOXO, NFκB and CREB as regulators of the induction of these genes in response to growth factor stimulation . Additional studies have identified a subset of these PI 3-kinase-regulated genes that are controlled by GSK-3 and have shown that inhibition of CREB by GSK-3 plays a key role in repressing PI 3-kinase-dependent gene expression in quiescent cells .
These studies of transcriptional regulation downstream of PI 3-kinase have examined gene expression in quiescent cells that have been acutely stimulated by growth factor, leading to the robust activation of PI 3-kinase signaling, the rapid induction of immediate-early genes, and the proliferation of cells arrested in G0. A lower level of PI 3-kinase signaling is also required for the survival and proliferation of cells that are normally maintained in the presence of growth factors . In the present study, we have examined the gene expression changes that result from inhibition of PI 3-kinase in cells that are actively proliferating in the presence of serum. These experiments identified a novel program of PI 3-kinase-regulated gene expression that is highly enriched in genes that function as regulators of apoptosis and distinct from the program of gene expression induced by growth factor stimulation of quiescent cells. Combined computational and experimental analyses further demonstrated that FOXO and NFκB are major regulators of genes controlled by PI 3-kinase in proliferating cells, and identified new genes with important roles in apoptosis that are targeted by these transcription factors.
Identification of Genes Regulated by PI 3-kinase Signaling in Proliferating Cells
Gene expression changes after 2 and 4 hours of PI 3-kinase inhibition
Apolipoprotein L domain containing 1
S-adenosylmethionine decarboxylase 1
F-box protein 32/Atrogin-1
Adhesion molecule with Ig-like domain 2
B-cell CLL/lymphoma 6
ATPase type 13A3
B-cell translocation gene 1
BCL2-associated athanogene 2
Chromosome 1 open reading frame 183
Brain-derived neurotrophic factor
Chromosome 1 open reading frame 63
Baculoviral IAP repeat-containing 3
Chemokine (C-C motif) ligand 2
CDC-like kinase 1
Connective tissue growth factor
Cytochrome P450 subfamily I polypeptide 1
DNA-damage-inducible transcript 3
Eukaryotic translation initiation factor 1
Deiodinase, iodothyronine, type II
Growth arrest and DNA-damage-inducible β
Hypothetical protein LOC643155
Inhibitor of DNA binding 1
Dickkopf homolog 1 (Xenopus laevis)
Striated muscle contraction regulatory prot.
Down syndrome critical region gene 1
Interferon regulatory factor 7
Kinesin family member 1B
Coagulation factor III
Kruppel-like factor 6
Fibroblast growth factor 2
Putative lymphocyte G0/G1 switch gene
Myosin regulatory light chain interacting prot.
GA binding protein transcription factor, β2
Guanylate binding protein 1
Guanylate binding protein 3
Pleckstrin homology-like domain family A
Glioma pathogenesis-related protein
Patatin-like phospholipase domain 8
G protein-coupled receptor 19
RNA, U2 small nuclear
Glutamate receptor, ionotropic, kainate 1
Serine/threonine kinase 31
Insulin-like growth factor binding protein 5
TAF9 RNA polymerase II
Interleukin 7 receptor
TGFβ inducible early growth response
Interferon stimulated exonuclease
Thioredoxin interacting protein
HRPAP20 short form
Zinc finger and BTB domain containing 1
LTV1 homolog (S. cerevisiae)
Methionine adenosyltransferase II, alpha
Matrix metalloproteinase 3
Neuron navigator 3
Nuclear receptor coactivator 7
Nucleolar protein family A, member 1
NUTF-like export factor1
PAK1 interacting protein 1
Plasminogen activator, urokinase
Peptidylprolyl isomerase F (cyclophilin F)
Peptidyl-tRNA hydrolase 2
Regulator of G-protein signalling 20
Splicing factor, arginine/serine-rich 3
Secretory granule, neuroendocrine protein 1
Tumor necrosis factor receptor 11b (OPG)
Tripartite motif-containing 16
Thymic stromal lymphopoietin
cDNA FLJ11812 fis, clone HEMBA1006364
Since LY294002 can also inhibit PI 3-kinase-related protein kinases, such as mTOR, we also tested the effect of wortmannin, a more selective PI 3-kinase inhibitor that does not inhibit mTOR at the concentration used (50 nM) . 15 of the 18 genes were similarly up or down-regulated by both wortmannin and LY294002 (Additional file 2), indicating that PI 3-kinase was responsible for the changes in expression of these genes. It is possible that the 3 genes whose expression was affected by LY294002 but not wortmannin may be regulated by other targets of LY294002. However 50 nM wortmannin was less effective than LY294002 in inhibiting PI 3-kinase, yielding approximately 90% rather than complete inhibition of Akt phosphorylation (Additional file 2), so it is also possible that the 10% of PI 3-kinase signaling remaining after wortmannin treatment was sufficient to maintain normal expression of some genes. In either case, these results support the involvement of PI 3-kinase signaling in the regulation of at least 80–90% of the genes showing altered expression in response to LY294002.
Comparison of the effect of PI 3-kinase inhibition on gene expression in U937 and T98G cells.
Functions of PI 3-kinase-regulated Genes
The genes that showed changes in expression after 2 and 4 hours of PI 3-kinase inhibition were largely overlapping and therefore were combined for subsequent analyses. This yielded a gene set in which altered expression was detected around the onset of apoptosis. These genes were compared to a group of 34 immediate-early genes that were induced by PI 3-kinase signaling following PDGF stimulation of quiescent T98G cells . There were only 4 genes in common between the two groups (CTGF, PLAU, CCL2 and F3), indicating that >90% of the genes regulated by continual PI 3-kinase signaling were distinct from immediate-early genes induced by PI 3-kinase in response to acute growth factor stimulation.
The genes with altered expression in response to inhibition of PI 3-kinase in T98G cells for 2 and 4 hours included well-known regulators of apoptosis and cell cycle progression. The ability of PI 3-kinase inhibition to induce apoptosis was apparent in the up-regulation of genes that can promote cell death, including DDIT3/CHOP , GADD45B , and PHLDA1 , and the down-regulation of genes that promote cell survival, including BIRC3/cIAP2  and TNFRSF11B/osteoprotegerin . Additional expression changes included the up-regulation of genes that inhibit cell cycle progression, such as CCNG2 , BTG1  and GADD45B , as well as the down-regulation of CCND1. Genes encoding several growth factors and cytokines that promote cell proliferation and survival (including FGF2, NTF3, EDN1, CCL2 and BDNF) were also down-regulated following inhibition of PI 3-kinase.
Summary of Gene Ontology (GO) term analysis.
Cellular developmental process
Negative regulation of transcription from RNA polymerase II promoter
Negative regulation of transcription, DNA-dependent
Transcription from RNA polymerase II promoter
Response to stress
Regulation of cellular process
Negative regulation of biological process
Programmed cell death
Negative regulation of cellular process
Response to external stimulus
Response to chemical stimulus
Cell surface receptor linked signal transduction
Anatomical structure morphogenesis
Prediction of Transcription Factor Binding Sites in PI 3-Kinase Regulated Genes
Co-expressed genes are often regulated by common transcription factors, therefore we analyzed the upstream regions of different sets of PI 3-kinase-regulated genes to identify over-represented transcription factor binding sites [26, 30, 44]. Predictions of functional transcription factor binding sites can be improved by incorporating phylogenetic data to identify sites that are evolutionarily conserved , so we focused on sites that were conserved in orthologous genomic regions of human and mouse. We independently analyzed the sets of genes that were either up- or down-regulated following PI 3-kinase inhibition, and also separately analyzed the genes that showed altered expression after 2 and 4 hours of PI 3-kinase inhibition and those that showed altered expression after 8 hours of PI 3-kinase inhibition. Regions 3 kb upstream of the transcription start sites in the human and corresponding mouse sequences were analyzed with the Match program using the minSUM threshold, and both the 546 vertebrate matrices in TRANSFAC Professional v8.4 and the 588 matrices in TRANSFAC Professional v11.1. Over-representation of transcription factor binding sites was assessed by comparing the frequency of predicted sites in each set of genes to the frequencies in a background set of genes that were expressed in proliferating T98G cells but not affected by PI 3-kinase inhibition (see Additional file 3 for complete results).
No significantly over-represented binding sites were identified in the sets of genes that were either up- or down-regulated following 8 hours of PI 3-kinase inhibition, perhaps because these large sets of genes are regulated by a diverse group of transcription factors or by other mechanisms, such as mRNA degradation. However, over-represented binding site matrices were identified in the sets of genes that were either up- or down-regulated after 2 and 4 hours of PI 3-kinase inhibition.
Over-represented transcription factor binding sites in genes that were differentially expressed after PI 3-kinase inhibition.
% Genes with site
Forkhead family members
Analysis of FOXO Regulation and Target Genes
FOXO binding sites confirmed by chromatin immunoprecipitation.
Binding site position
Analysis of NFκB Regulation and Target Genes
In contrast to the forkhead family, Akt indirectly activates NFκB transcription factors, at least in part by phosphorylation of IκB kinase (IKK) [19, 20]. There are 5 different NFκB family members (p65, c-Rel, RelB, p50 and p52), which all bind to a similar consensus sequence and can be activated by several pathways that converge on IKK . Because the majority of NFκB binding sites are occupied after stimulation with cytokines , we initially performed ChIP assays following treatment of T98G cells with tumor necrosis factor α (TNFα) to determine if p65 was able to bind to the sites predicted in the genes that were down-regulated upon PI 3-kinase inhibition. In addition to the sites predicted by the matrices indicated in Table 4, we tested conserved sites predicted by 7 additional NFκB matrices to ensure that most functional binding sites were identified. When all matrices were considered, 25 NFκB sites were predicted in a total of 20 of the down-regulated genes (See Additional file 4 for all sites).
NFκB binding sites confirmed by chromatin immunoprecipitation.
Binding site position
p65 did not show increased binding to any of the predicted sites in the absence of TNFα stimulation as compared to the β-globin control (Fig. 5), which was expected due to its sequestration in the cytoplasm by IκB proteins. However, other members of the NFκB family can be found in the nucleus of proliferating cells in the absence of cytokine stimulation. p50 and p52 do not bind IκB proteins but rather enter the nucleus following their generation from cleavage of larger precursors (p105 and p100, respectively). Both p50 and p52 lack activation domains, but p52-RelB heterodimers are also able to translocate into the nucleus and activate transcription of their target genes. In the non-canonical pathway of NFκB activation, IKKα phosphorylation of p100 results in its conversion to p52, which forms a transcriptionally active complex with RelB . Since the non-canonical pathway is stimulated by Akt and can be active in the absence of cytokine stimulation , it might be responsible for NFκB activity in cells proliferating in serum growth factors.
The PI 3-kinase/Akt/GSK-3 signaling pathway plays a central role in regulation of growth factor-dependent proliferation and survival of mammalian cells, at least in part by transcriptional regulation. A number of transcription factors and target genes that are regulated by PI 3-kinase signaling have been studied on an individual basis. In addition, both we [26, 30, 44] and others [27–29] have used global expression profiling to investigate the overall program of gene regulation controlled by PI 3-kinase/Akt/GSK-3 signaling. These studies have focused on the response of quiescent cells to growth factor stimulation, which induces robust activation of PI 3-kinase, induction of immediate-early genes, and re-entry into the cell cycle. However, a lower level of continuous PI 3-kinase signaling is also required to maintain proliferation and survival of cells in the presence of serum growth factors. In the present study, we have therefore undertaken a global analysis of the transcriptional program that maintains cell survival and proliferation downstream of PI 3-kinase signaling in proliferating cells.
Inhibition of PI 3-kinase in actively proliferating T98G cells for 2 and 4 hours resulted in up-regulation of 32 genes and down-regulation of 53 genes. These gene expression changes occurred around the time at which apoptosis was first detected. Consistent with their involvement in apoptosis, the genes with altered expression following 2 and 4 hours of PI 3-kinase inhibition included growth factors and cytokines, as well as several well-known regulators of apoptosis (such as DDIT3/CHOP, GADD45B, PHLDA1, BIRC3/cIAP2 and TNFRSF11B/osteoprotegerin) and cell cycle progression (such as CCNG2 and CCND1). Functional classifications using the Gene Ontology database further indicated that these gene sets were enriched in terms related to cell stress and programmed cell death, as well as to cell signaling and transcriptional regulation. The numbers of up- and down-regulated genes both increased substantially, to a total of nearly 250 genes, after 8 hours of PI 3-kinase inhibition, probably reflecting a secondary transcriptional response. This larger set of genes was no longer significantly enriched in functional GO terms.
We compared the sets of genes with altered expression following 2 and 4 hours of PI 3-kinase inhibition to those identified by previous studies of the genes induced following 0.5–4 hours of growth factor simulation of quiescent T98G cells [26, 44]. Only ~10% of the genes affected by inhibition of PI 3-kinase overlapped with either the total sets of immediate-early or delayed primary response genes, or with the subset of PI 3-kinase dependent immediate-early genes defined in these previous studies. Similar to the genes that were up-regulated following inhibition of PI 3-kinase, immediate-early genes induced in response to growth factor stimulation were enriched in GO terms related to transcriptional regulation . However, the transcription factors induced as immediate-early genes by growth factor stimulation are different from those that are up-regulated in response to PI 3-kinase inhibition. The genes regulated by continuous PI 3-kinase signaling in proliferating cells were thus clearly distinct from the primary response genes induced by growth factor stimulation of quiescent cells.
We also compared the genes affected by PI 3-kinase inhibition with the genes identified in a recent study of the effects of mitogen withdrawal on gene expression in proliferating human fibroblasts . In these experiments, primary fetal human lung fibroblasts were cultured in the presence of a low concentration of serum, IGF-1 and PDGF, and were growth-arrested by withdrawal of PDGF, which resulted in the entry of cells into G0; however, in contrast to our experiments, no significant increase in cells undergoing apoptosis was observed. This entry of cells into quiescence rather than apoptosis is consistent with the continued presence of low concentrations of serum and IGF-1 in the experiments of Coller et al , in contrast to the complete inhibition of PI 3-kinase in our studies. Comparing these two studies indicated that very little overlap exists between the genes regulated by inhibition of PI 3-kinase signaling and those regulated by 14 hours or 4 days of PDGF withdrawal. However, most of the overlapping genes, including CCNG2, PLAU, BDNF, and FGF2, and a number of non-overlapping genes regulated by mitogen withdrawal have been connected to the regulation of cell proliferation. Thus, there are functional overlaps in the genes regulated by PI 3-kinase inhibition and mitogen withdrawal, although they are clearly distinct gene sets as might be expected from the differences in treatments and their distinct effects on proliferation and apoptosis. We note that asynchronous cells were used in our study, and that similar analyses of synchronized cells might reveal PI 3-kinase regulation of distinct subsets or additional genes during specific stages of the cell cycle.
We have previously used computational analysis to identify transcription factor binding sites that are over-represented in promoter regions of immediate-early genes, including those regulated by PI 3-kinase signaling [26, 30, 44]. The transcription factors and families involved in regulation of these genes included CREB, SRF, FOXO and NFκB. We applied a similar analysis to the gene sets affected by inhibition of PI 3-kinase signaling in the present study. This revealed over-representation of phylogenetically conserved binding sites for FOXO and NFκB upstream of the genes that were up- and down-regulated, respectively, following 2 and 4 hours of PI 3-kinase inhibition. Many of the predicted FOXO and NFκB binding sites were confirmed by ChIP, indicating that the FOXO and NFκB transcription factors play major roles in the transcriptional response to PI 3-kinase inhibition. This is consistent with the established regulation of these transcription factors by PI 3-kinase/Akt signaling, which inhibits FOXO and promotes NFκB activity [16, 19, 20]. Since p53 is also a major target of PI 3-kinase/Akt signaling in control of cell proliferation and survival [12, 13], we might have expected to similarly observe an over-representation of p53 binding sites. However, p53 is inactivated by mutation in T98G cells [66, 67], accounting for its absence in the gene sets analyzed in our experiments.
In total, we identified FOXO and NFκB binding sites upstream of about one-third of the genes that were up- and down-regulated, respectively, by inhibition of PI 3-kinase. Since our computational predictions of transcription factor binding sites were limited to phylogenetically conserved sites in promoter regions, this may be an underestimate of the total fraction of PI 3-kinase regulated genes that are targeted by these transcription factors. In particular, additional genes may be regulated by FOXO or NFκB binding sites in enhancers rather than promoter sequences, or by sites that were not conserved in the mouse. Other genes may be regulated at the transcriptional level by other transcription factors (such as Myc/Max) or by non-transcriptional mechanisms, including regulation of mRNA decay .
Two members of the FOXO family (FOXO1 and 3a) were expressed in T98G cells and, as expected, both were activated in response to PI 3-kinase inhibition. In contrast, there are 5 members of the NFκB family (p65, c-Rel, RelB, p50 and p52), which can be activated by either the canonical or non-canonical pathways, both of which are stimulated by Akt [19, 20, 64, 68–70]). We initially demonstrated binding of p65 to predicted NFκB sites following stimulation of the canonical pathway by TNFα. In unstimulated cells growing in the presence of serum however, only binding of p50, p52 and RelB was detected by ChIP, indicating that just the non-canonical pathway was active. Of these three family members, RelB is the main effector of this pathway, as it is the only one that contains a transactivation domain. Since the binding of RelB to promoters of down-regulated genes decreased following inhibition of PI 3-kinase, it appears that PI 3-kinase signaling regulates the non-canonical pathway of NFκB activation in proliferating cells.
FOXO and NFκB regulated genes.
Growth Factor/Receptor or Cytokine
FOXO Target Genes
[49, 50, 80]
NFκB Target Genes
[57, 89, 90]
PI 3-kinase signaling in proliferating cells regulates a novel program of gene expression, which is distinct from that induced by growth factor stimulation of quiescent cells. The expression program controlled by continuous PI 3-kinase signaling in proliferating cells is enriched in genes that regulate cell survival and is mediated in large part by FOXO and RelB transcription factors.
Cell Culture and RNA Extraction
T98G human glioblastoma cells were grown in Minimal Essential Medium (Invitrogen) containing 10% fetal bovine serum (HyClone) and 100 units/ml of penicillin/streptomycin (Invitrogen). U937 cells were grown in RPMI 1640 (Cellgro) containing 10% fetal bovine serum (HyClone). For LY294002 treatments, T98G cells were plated at 2 × 106 cells per 150 mm plate or 8 × 105 cells per 100 mm plate and U937 cells at 3 × 106 cells per 25 cm flask. T98G cells were cultured for 48 hours and U937 cells for 24 hours, at which time they were actively proliferating with a doubling time of approximately 20 hours. LY294002 (Biomol) was added to a final concentration of 50 μM. Wortmannin (Biomol) was added to a final concentration of 50 nM. Culturing of cells for serum starvation and subsequent treatments with either PDGF-BB (50 ng/ml) or 20% serum were carried out as previously described .
Apoptosis was assayed by DNA fragmentation and TUNEL staining as previously described .
Enriched cytosolic and nuclear fractions were isolated from normal growing T98G cells as described elsewhere . Proteins were separated by electrophoresis in 8% or 12% SDS-polyacrylamide gels, electroblotted to polyvinylidene difluoride membranes (PerkinElmer), and immunoblotted with anti-phospho Akt (Cell Signaling 9271), pan-anti-Akt (Cell Signaling 9272), anti-FOXO3a (Upstate 07-702), anti-FOX01 (Santa Cruz sc-11350), anti-FOXO4 (Santa Cruz sc-5221), anti-PARP (poly (ADP-ribose) polymerase) (Cell Signaling 9542), and anti-14-3-3 (Upstate 06-511) as recommended by the manufacturer. The immunoblots were visualized using goat anti-rabbit or rabbit anti-goat horseradish peroxidase-linked secondary antibodies (Bio-Rad) and chemiluminescence (PerkinElmer). Densitometry was performed using IQMac v1.2 software (Molecular Dynamics, Sunnyvale, CA).
Microarray spotting, sample preparation, hybridization, image analysis and data analysis were performed as previously described . Microarrays were spotted with 21,329 70-mer oligonucleotides from Operon's Human Genome Array-Ready Oligo Set Version 2.0. RNA for microarray experiments was extracted with TRIzol reagent (Invitrogen) followed by poly(A)+ RNA isolation with an Oligotex mRNA Midi Kit (Qiagen) according to each manufacturer's protocol. Microarrays were performed with three independent biological samples. Dye-swap, background-subtracted median intensity values were used as input to the LIMMA analysis package  in Bioconductor , and average LOESS-corrected log2 ratios were used to estimate differential gene expression after LY294002 treatment. Differentially expressed genes were those with a change in expression greater than or equal to 1.87 fold (Log2 0.9) relative to untreated samples and false discovery rate (FDR)-corrected  moderated t-test p-values less than 0.01.
Real-time reverse transcription-polymerase chain reaction (RT-PCR)
Real-time RT-PCR was carried out as previously described on RNA samples isolated from either T98G cells or U937 cells treated with LY294002 for 4 hours .
Gene Ontology Analysis
Gene Ontology (GO) terms were obtained using the web-based tool GOstat . The genes that were either up- or down-regulated following 2 and 4 hours of PI 3-kinase inhibition were independently analyzed from the genes that were either up- or down-regulated following 8 hours of PI 3-kinase inhibition. Enrichment of GO categories was determined by comparing the terms associated with the differentially regulated genes to the terms associated with all genes on the array using a Fisher's exact test. Only genes annotated with at least 1 term were included in the analysis. Results were limited to the GO categories that were associated with at least 15% of the genes, with p < 0.001.
Transcription Factor Binding Site Analysis
Over-representation of transcription factor binding sites in the upstream regions of genes that were differentially expressed in response to inhibition of PI 3-kinase was determined as previously described [26, 30, 44]. The genes that were either up- or down-regulated following 2 and 4 hours of PI 3-kinase inhibition were independently analyzed from the genes that were either up- or down-regulated following 8 hours of PI 3-kinase inhibition. The regions 3 kb upstream of transcription start sites in the human and the corresponding mouse orthologous sequences were analyzed with the Match program using the MinSUM threshold , and both the 548 vertebrate position weight matrices from TRANSFAC Professional version 8.4 and the 588 matrices from TRANSFAC version 11.1 . Sequences and MULTIZ alignments were obtained from the University of California Santa Cruz Genome Browser (human version hg18, mouse version mm8) , which were available for 28 of the 32 up-regulated genes and for 48 of the 53 down-regulated genes. For each matrix, a permutation test was used to compare the frequencies of the predicted sites in the differentially expressed gene set to the frequencies of the predicted sites in a background set of 662 genes that were expressed but did not change expression upon PI 3-kinase inhibition (average log2 ratios between -0.01 and 0.01). P-values were FDR-corrected to adjust for multiple testing .
Flag-FOXO3a-AAA Chromatin Immunoprecipitations
T98G cells were plated at 4 × 105 cells per 100 mm plate in complete media 24 hours before transfection. TransIT (Mirus Bio) reagent was used to transfect 8 μg of either pcDNA3 (Invitrogen) or pcDNA3-Flag-FOXO3a-AAA [Addgene plasmid 10709, provided by Dr. William R. Sellers ], as recommended by the manufacturer. 24 hours after transfection 3 identical plates were harvested and ChIP assays were performed as previously described  except that chromatin was immunoprecipitated overnight at 4°C using 10 μg of anti-M5-Flag (Sigma F4042) antibody and Protein G agarose beads (Upstate). Protein G agarose beads were washed successively in low salt wash, high salt wash, LiCl wash and twice in 1xTE. Immunoprecipitated chromatin was quantified with real-time PCR using primers designed within 250 bp of the predicted transcription factor binding sites.
NFκB Chromatin Immunoprecipitations
For treatment with TNFα, T98G cells were plated at 8 × 105 cells per 100 mm plate in complete media 48 hours before treatment. Cells were then either left untreated, or treated with 20 μg/ml of TNFα (R & D Systems) for 0.25, 0.5 or 1 hour. For experiments using unstimulated cells, T98G cells were plated at 2 × 106 cells per 150 mm plate, and ChIP assays performed 48 hours after plating. When indicated, cells were treated with 50 μM LY294002 for 4 or 8 hours. ChIP assays were performed as previously described , except that either 5 μg of p65 antibody, c-Rel antibody, p50 antibody, RelB antibody (Santa Cruz Biotechnology, sc-372, sc-71, sc-114, sc-226), or 5 μl of p52 antibody (Upstate, 06-413) was used for the immunoprecipitations. Protein A agarose beads were washed successively in low salt wash, high salt wash, LiCl wash and twice in 1xTE. Immunoprecipitated chromatin was quantified by real-time PCR using primers that were located within 320 bp of the predicted binding site.
We are grateful to Ulla Hansen for helpful discussions and critical comments on the manuscript. This work was supported by NIH grant RO1 CA18689.
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