Impact of supervised gene signatures of early hypoxia on patient survival

doi:10.1016/j.radonc.2007.05.002

Radiotherapy and Oncology

Volume 83, Issue 3, June 2007, Pages 374-382

https://doi.org/10.1016/j.radonc.2007.05.002 Get rights and content

Abstract

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.

Section snippets

Data set

The starting material was the data set provided by the study of Chi et al., which represents, to our knowledge, the largest set of time series under hypoxia with 2.4 million of gene expression measurements. Four normal cell lines were used: human coronary artery endothelial cells (ECs), smooth muscle cells (SMCs), human mammary epithelial cells (HMECs), and renal proximal tubule epithelial cells (RPTECs 1 and 2) under two oxygen concentrations (less than 0.02% and 2%). Using cDNA microarrays of

Results

Correlating genes with a predefined pattern of interest was used to derive early hypoxia gene signatures from the HMEC cell lines under 0% and 2% oxygen. The genes reaching a correlation with the required temporal profile greater than 0.6 and a 2-fold induction or more were selected (Table 2). Results from log-rank tests on the Miller data set are reported in Table 3.

Early hypoxia

In this paper, we focus on the impact of the early response to hypoxia which with the exception of a few studies (e.g. [12]) is rarely investigated by means of microarrays. Due to potential differences arising for different oxygen concentrations, the two time series were treated independently. Both early hypoxia signatures were significant (p < 0.01 at 0%; p < 0.05 at 2%) whereas none of the late signatures were. A signature of the 15 common UniGenes (13 symbols) found in the two early signatures

Conclusions

This analysis shows that, consistent with our hypothesis, the early and late hypoxia responses are very different at the transcription level. In a relatively old cohort of patients with primary breast cancer treated by locoregional therapy and systemic adjuvant therapy, it was shown that early hypoxia signatures, but not late hypoxia responses, could correlate with survival differences. It suggests that gene signatures can provide a means to select patients for individualized therapy.

Acknowledgements

We acknowledge financial support from Siemens (to R.S. and M.H.W.S.), the Dutch Science Organization (ZonMW-NWO Top Grant 912-03-047 to B.W.), the Dutch Cancer Society (KWF Grant UM 2003-2821 to B.W.), and the EU 6th framework program (Euroxy program to B.W.).

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Clinical radiobiologyImpact of supervised gene signatures of early hypoxia on patient survival

Abstract

Background and purpose

Materials and methods

Results

Conclusions

Section snippets

Data set

Results

Early hypoxia

Conclusions

Acknowledgements

Radiother Oncol

Radiother Oncol

Biochem Pharmacol

Radiother Oncol

Radiother Oncol

Radiother Oncol

Drug Resist Updat

Linking oncogenic pathways with therapeutic opportunities

Nat Rev Cancer

Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds

PLoS Biol

Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers

PLoS Med

Molecular portraits and the family tree of cancer

Nat Genet

Clinical radiobiology
Impact of supervised gene signatures of early hypoxia on patient survival