The prognostic value of temporal in vitro and in vivo derived hypoxia gene-expression signatures in breast cancer.

BACKGROUND AND PURPOSE: Recent data suggest that in vitro and in vivo derived hypoxia gene-expression signatures have prognostic power in breast and possibly other cancers. However, both tumour hypoxia and the biological adaptation to this stress are highly dynamic. Assessment of time-dependent gene-expression changes in response to hypoxia may thus provide additional biological insights and assist in predicting the impact of hypoxia on patient prognosis. MATERIALS AND METHODS: Transcriptome profiling was performed for three cell lines derived from diverse tumour-types after hypoxic exposure at eight time-points, which include a normoxic time-point. Time-dependent sets of co-regulated genes were identified from these data. Subsequently, gene ontology (GO) and pathway analyses were performed. The prognostic power of these novel signatures was assessed in parallel with previous in vitro and in vivo derived hypoxia signatures in a large breast cancer microarray meta-dataset (n=2312). RESULTS: We identified seven recurrent temporal and two general hypoxia signatures. GO and pathway analyses revealed regulation of both common and unique underlying biological processes within these signatures. None of the new or previously published in vitro signatures consisting of hypoxia-induced genes were prognostic in the large breast cancer dataset. In contrast, signatures of repressed genes, as well as the in vivo derived signatures of hypoxia-induced genes showed clear prognostic power. CONCLUSIONS: Only a subset of hypoxia-induced genes in vitro demonstrates prognostic value when evaluated in a large clinical dataset. Despite clear evidence of temporal patterns of gene-expression in vitro, the subset of prognostic hypoxia regulated genes cannot be identified based on temporal pattern alone. In vivo derived signatures appear to identify the prognostic hypoxia induced genes. The prognostic value of hypoxia-repressed genes is likely a surrogate for the known importance of proliferation in breast cancer outcome.

Translational control is a major contributor to hypoxia induced gene expression.

BACKGROUND AND PURPOSE: Hypoxia is a common feature of solid tumors that is associated with an aggressive phenotype, resistance to therapy and poor prognosis. Major contributors to these adverse effects are the transcriptional program activated by the HIF family of transcription factors as well as the translational response mediated by PERK-dependent phosphorylation of eIF2α and inhibition of mTORC1 activity. In this study we determined the relative contribution of both transcriptional and translational responses to changes in hypoxia induced gene expression. MATERIAL AND METHODS: Total and efficiently translated (polysomal) mRNA was isolated from DU145 prostate carcinoma cells that were exposed for up to 24 h of hypoxia (<0.02% O(2)). Changes in transcription and translation were assessed using affymetrix microarray technology. RESULTS: Our data reveal an unexpectedly large contribution of translation control on both induced and repressed gene expression at all hypoxic time points, particularly during acute hypoxia (2-4 h). Gene ontology analysis revealed that gene classes like transcription and signal transduction are stimulated by translational control whereas expression of genes involved in cell growth and protein metabolism are repressed during hypoxic conditions by translational control. CONCLUSIONS: Our data indicate that translation influences gene expression during hypoxia on a scale comparable to that of transcription.

Inhibition of 4E-BP1 sensitizes U87 glioblastoma xenograft tumors to irradiation by decreasing hypoxia tolerance.

PURPOSE: Eukaryotic initiation factor 4E (eIF4E) is an essential rate-limiting factor for cap-dependent translation in eukaryotic cells. Elevated eIF4E activity is common in many human tumors and is associated with disease progression. The growth-promoting effects of eIF4E are in turn negatively regulated by 4E-BP1. However, although 4E-BP1 harbors anti-growth activity, its expression is paradoxically elevated in some tumors. The aim of this study was to investigate the functional role of 4E-BP1 in the context of solid tumors. METHODS AND MATERIALS: In vitro and in vivo growth properties, hypoxia tolerance, and response to radiation were assessed for HeLa and U87 cells, after stable expression of shRNA specific for 4E-BP1. RESULTS: We found that loss of 4E-BP1 expression did not significantly alter in vitro growth but did accelerate the growth of U87 tumor xenografts, consistent with the growth-promoting function of deregulated eIF4E. However, cells lacking 4E-BP1 were significantly more sensitive to hypoxia-induced cell death in vitro. Furthermore, 4E-BP1 knockdown cells produced tumors more sensitive to radiation because of a reduction in the viable fraction of radioresistant hypoxic cells. Decreased hypoxia tolerance in the 4E-BP1 knockdown tumors was evident by increased cleaved caspase-3 levels and was associated with a reduction in adenosine triphosphate (ATP). CONCLUSIONS: Our results suggest that although tumors often demonstrate increases in cap-dependent translation, regulation of this activity is required to facilitate energy conservation, hypoxia tolerance, and tumor radioresistance. Furthermore, we suggest that targeting translational control may be an effective way to target hypoxic cells and radioresistance in metabolically hyperactive tumors.

The mTOR target 4E-BP1 contributes to differential protein expression during normoxia and hypoxia through changes in mRNA translation efficiency.

Hypoxia causes a rapid and sustained inhibition in mRNA translation that is characterized by both a transient phosphorylation of eukaryotic initiation factor 2-alpha (eIF2alpha) and by inhibition of the mRNA cap binding protein eIF4E via activation of two distinct inhibitory proteins, the mammalian target of rapamycin (mTOR) target 4E-BP1 and the eIF4E transporter 4E-T. Although the importance of eIF2alpha phosphorylation during hypoxia has been clearly demonstrated, there is little information on the potential relevance of eIF4E regulation. We generated HeLa cells stably expressing a short hairpin interfering RNA (shRNA) against 4E-BP1 and found that despite efficient knockdown, no significant changes occurred in the overall inhibition of mRNA translation during hypoxia. However, using a proteomics approach we identified seven proteins that were exclusively expressed in the 4E-BP1 knockdown cells during both normoxic and hypoxic conditions. Further investigation of the transcriptional and translational regulation of these genes by quantitative RT-PCR indicated that the loss of 4E-BP1 causes a significant increase in the rate of protein synthesis of S100 calcium-binding protein A4 (S100A4) and transgelin 2. These 4E-BP1 regulated proteins have previously been associated with tumor cell motility, invasion and metastasis and may thus contribute to an adverse tumor phenotype.

Regulation of Cited2 expression provides a functional link between translational and transcriptional responses during hypoxia.

BACKGROUND AND PURPOSE: Protein synthesis rates are greatly reduced under hypoxic conditions as a consequence of an overall inhibition of mRNA translation. Certain specific mRNA species have the ability to escape this general translational repression. At the cellular level this results in differential protein expression during hypoxic conditions. The objective of this study was to characterize the translational regulation of the postulated HIF-1alpha antagonist Cited2. MATERIALS AND METHODS: DU145 prostate carcinoma cells and mouse embryonic fibroblasts with a homozygous knock-in mutation for eIF2alpha (S51A) or wild-type eIF2alpha were exposed to severe hypoxia after which both total mRNA and efficiently translated mRNA were isolated. Quantitative RT-PCR was used to measure and compare changes in transcription (total mRNA) with changes in translation (efficiently translated mRNA fraction). RESULTS: We show using HIF-1alpha null MEF cells that transcriptional induction of Cited2 during hypoxia is dependent on HIF-1alpha. Although global mRNA translation is inhibited during hypoxia Cited2 mRNA remains efficiently translated. An evolutionary conserved upstream open reading frame (uORF) in the 5'UTR of Cited2 did not stimulate translation in an eIF2alpha dependent manner during hypoxia. CONCLUSIONS: Selective translation Cited2 by an eIF2alpha independent mechanism establishes a link between translation and HIF-1 dependent transcription during hypoxia.

Phosphorylation of eIF2alpha is required for mRNA translation inhibition and survival during moderate hypoxia.

BACKGROUND AND PURPOSE: Human tumors are characterized by temporal fluctuations in oxygen tension. The biological pathways that respond to the dynamic tumor microenvironment represent potential molecular targets for cancer therapy. Anoxic conditions result in eIF2alpha dependent inhibition of overall mRNA translation, differential gene expression, hypoxia tolerance and tumor growth. The signaling pathway which governs eIF2alpha phosphorylation has therefore emerged as a potential molecular target. In this study, we investigated the role of eIF2alpha in regulating mRNA translation and hypoxia tolerance during moderate hypoxia. Since other molecular pathways that regulate protein synthesis are frequently mutated in cancer, we also assessed mRNA translation in a panel of cell lines from different origins. MATERIALS AND METHODS: Immortalized human fibroblast, transformed mouse embryo fibroblasts (MEFs) and cells from six cancer cell lines were exposed to 0.2% or 0.0% oxygen. We assayed global mRNA translation efficiency by polysome analysis, as well as proliferation and clonogenic survival. The role of eIF2alpha was assessed in MEFs harboring a homozygous inactivating mutation (S51A) as well as in U373-MG cells overexpressing GADD34 (C-term) under a tetracycline-dependent promoter. The involvement of eIF4E regulation was investigated in HeLa cells stably expressing a short hairpin RNA (shRNA) targeting 4E-BP1. RESULTS: All cells investigated inhibited mRNA translation severely in response to anoxia and modestly in response to hypoxia. Two independent genetic cell models demonstrated that inhibition of mRNA translation in response to moderate hypoxia was dependent on eIF2alpha phosphorylation. Disruption of eIF2alpha phosphorylation caused sensitivity to hypoxia and anoxia. CONCLUSIONS: Disruption of eIF2alpha phosphorylation is a potential target for hypoxia-directed molecular cancer therapy.

Proteomic analysis of gene expression following hypoxia and reoxygenation reveals proteins involved in the recovery from endoplasmic reticulum and oxidative stress.

BACKGROUND AND PURPOSE: Human tumors are characterized by large variations in oxygen concentration and hypoxic tumors are associated with poor prognosis. In addition, tumors are subjected to periodic changes in oxygenation characterized by hypoxia followed by reoxygenation. Cellular adaptation to hypoxia is well documented, nevertheless little is known about adaptive mechanisms to reoxygenation. Here, we investigate the changes in protein expression during reoxygenation using proteomics. MATERIALS AND METHODS: HeLa cervix carcinoma cells were exposed to 4h of hypoxia (<0.01% O(2)) followed by 1h of reoxygenation. The cellular proteome was examined using 2D gel electrophoresis coupled with mass spectrometry. Validation and investigation of the underlying basis for induced protein expression was investigated using Western blot analysis and quantitative RT-PCR. RESULTS: We identified proteins involved in several cellular processes that are responsible for regulating RNA metabolism, protein synthesis and degradation, including ribosomal protein P0, VCP/p97 and FUSE binding protein 2. CONCLUSIONS: Our results suggest that these newly identified proteins function in pathways that may assist in the recovery of ER stress and protein synthesis during reoxygenation. These proteins may thus be important determinants of the behaviour and survival of tumor cells to transient hypoxic exposures.

Impact of supervised gene signatures of early hypoxia on patient survival.

BACKGROUND AND PURPOSE: Hypoxia is a common feature of solid tumors associated with therapy resistance, increased malignancy and poor prognosis. Several approaches have been developed with the hope of identifying patients harboring hypoxic tumors including the use of microarray based gene signatures. However, studies to date have largely ignored the strong time dependency of hypoxia-regulated gene expression. We hypothesized that use of time-dependent patterns of gene expression during hypoxia would enable development of superior prognostic expression signatures. MATERIALS AND METHODS: Using published data from the microarray study of Chi et al., we extracted gene signatures correlating with induction during either early or late hypoxic exposure. Gene signatures were derived from in vitro exposed human mammary epithelial cell line (HMEC) under 0% or 2% oxygen. Gene signatures correlating with early and late up-regulation were tested by means of Kaplan-Meier survival, univariate, and multivariate analysis on a patient data set with primary breast cancer treated conventionally (surgery plus on indication radiotherapy and systemic therapy). RESULTS: We found that the two early hypoxia gene signatures extracted from 0% and 2% hypoxia showed significant prognostic power (log-rank test: p=0.004 at 0%, p=0.034 at 2%) in contrast to the late hypoxia signatures. Both early gene signatures were linked to the insulin pathway. From the multivariate Cox-regression analysis, the early hypoxia signature (p=0.254) was found to be the 4th best prognostic factor after lymph node status (p=0.002), tumor size (p=0.016) and Elston grade (p=0.111). On this data set it indeed provided more information than ER status or p53 status. CONCLUSIONS: The hypoxic stress elicits a wide panel of temporal responses corresponding to different biological pathways. Early hypoxia signatures were shown to have a significant prognostic power. These data suggest that gene signatures identified from in vitro experiments could contribute to individualized medicine.

Patterns of tumor oxygenation and their influence on the cellular hypoxic response and hypoxia-directed therapies.

Deficiencies in the oxygenation of solid tumors are associated with poor patient prognosis due to changes in cell metabolism, angiogenesis, invasiveness and resistance to therapy. Work over the past 10 years has defined several distinct oxygen sensing pathways that together determine the cellular response to hypoxia. These include both a transcriptional response initiated by oxygen-dependent stabilisation of the HIF-1 transcription factor and an mRNA translational response characterized by activation of the unfolded protein response (UPR) and inhibition of mTOR signalling. Laboratory experiments have established the importance of these hypoxic response pathways for tumor growth and resistance to treatment. This has led to the development of agents aimed at targeting hypoxic response pathways in tumors, several of which are in clinical trials. However, several important features of the tumor microenvironment that may affect the success of these new therapies have not been thoroughly evaluated. Oxygenation patterns in human tumors have proven to be highly complex, leading to a large degree of heterogeneity with respect to the severity and duration of hypoxic exposure. Because both of these properties strongly influence the known cellular responses to hypoxia, this heterogeneity is expected to be a strong determinant of the fate of hypoxic cells and the success of new hypoxia-directed therapies. Here we summarize the important oxygen response pathways that currently serve as targets for therapy and their dependence on the specific oxygenation patterns that are expected in human tumors.

Gene expression during acute and prolonged hypoxia is regulated by distinct mechanisms of translational control.

Hypoxia has recently been shown to activate the endoplasmic reticulum kinase PERK, leading to phosphorylation of eIF2alpha and inhibition of mRNA translation initiation. Using a quantitative assay, we show that this inhibition exhibits a biphasic response mediated through two distinct pathways. The first occurs rapidly, reaching a maximum at 1-2 h and is due to phosphorylation of eIF2alpha. Continued hypoxic exposure activates a second, eIF2alpha-independent pathway that maintains repression of translation. This phase is characterized by disruption of eIF4F and sequestration of eIF4E by its inhibitor 4E-BP1 and transporter 4E-T. Quantitative RT-PCR analysis of polysomal RNA indicates that the translation efficiency of individual genes varies widely during hypoxia. Furthermore, the translation efficiency of individual genes is dynamic, changing dramatically during hypoxic exposure due to the initial phosphorylation and subsequent dephosphorylation of eIF2alpha. Together, our data indicate that acute and prolonged hypoxia regulates mRNA translation through distinct mechanisms, each with important contributions to hypoxic gene expression.

The hypoxic proteome is influenced by gene-specific changes in mRNA translation.

BACKGROUND AND PURPOSE: Hypoxia causes a rapid reduction in mRNA translation efficiency. This inhibition does not affect all mRNA species to the same extent and can therefore contribute significantly to hypoxia-induced differential protein expression. Our aim in this study was to characterize changes in gene expression during acute hypoxia and evaluate the contribution of regulation via mRNA translation on these changes. For each gene, the contribution of changes in mRNA abundance versus mRNA translation was determined. MATERIALS AND METHODS: DU145 prostate carcinoma cells were exposed to 4h of hypoxia (<0.02% O2). Efficiently translated mRNAs were isolated by sedimentation through a sucrose gradient. Affymetrix microarray technology was used to evaluate both the transcriptional and translational contribution to gene expression. Results were validated by quantitative PCR. RESULTS: One hundred and twenty genes were more than 4-fold upregulated by hypoxia in the efficiently translated fraction of mRNA, in comparison to only 76 genes at the level of transcription. Of the 50 genes demonstrating the largest changes in translation, 11 were found to be more than 2-fold over represented in the translated fraction in comparison to their overall transcriptional level. The gene with the highest translational contribution to its induction was CITED-2, which is a negative regulator of HIF-1 transcriptional activity. CONCLUSIONS: Gene-specific regulation of mRNA translation contributes significantly to differential gene expression during hypoxia.

Control of the hypoxic response through regulation of mRNA translation.

Hypoxia is a common feature of most solid tumors which negatively impacts their treatment response. This is due in part to the biological changes that result from a coordinated cellular response to hypoxia. A large part of this response is driven by a transcriptional program initiated via stabilization of HIF, promoting both angiogenesis and cell survival. However, hypoxia also results in a rapid inhibition of protein synthesis which occurs through the repression of the initiation step of mRNA translation. This inhibition is fully reversible and occurs in all cell lines tested to date. Inhibition of translation is mediated by two distinct mechanisms during hypoxia. The first is through phosphorylation and inhibition of an essential eukaryotic initiation factor, eIF2alpha. Phosphorylation of this factor occurs through activation of the PERK kinase as part of a coordinated ER stress response program known as the UPR. Activation of this program promotes cell survival during hypoxia and facilitates tumor growth. Translation during hypoxia can also be inhibited through the inactivation of a second eukaryotic initiation complex, eIF4F. At least part of this inhibition is mediated through a REDD1 and TSC1/TSC2 dependent inhibition of the mTOR kinase. Inhibition of mRNA translation is hypothesized to affect the cellular tolerance to hypoxia in part by promoting energy homeostasis. However, regulation of translation also results in a specific increase in the synthesis of a subset of hypoxia induced proteins. Consequently, both arms of translational control during hypoxia influence hypoxia induced gene expression and the hypoxic phenotype.

Targeting hypoxia tolerance in cancer.

Regulation of tissue oxygen homeostasis is critical for cell function, proliferation and survival. Evidence for this continues to accumulate along with our understanding of the complex oxygen-sensing pathways present within cells. Several pathophysiological disorders are associated with a loss in oxygen homeostasis, including heart disease, stroke, and cancer. The microenvironment of tumors in particular is very oxygen heterogeneous, which may explain much of our difficulty in treating cancer effectively. This is true when comparing levels of hypoxia among different patient tumors, but also within individual tumors. Accumulating evidence implicates the biological responses to hypoxia and the alterations in these pathways in cancer as important contributors to overall malignancy and treatment efficacy. This has recently prompted several investigations into the possibility of targeting treatment at the biological responses to hypoxia.