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BMC Genomics

Open Access

Unlocking the complexity of hypoxia non-coding transcriptome landscape of breast cancer

  • Hani Choudhry1, 4Email author,
  • Johannes Schodel2,
  • Ashwag Albukhari3,
  • Spyros Oikonomopoulos4,
  • Syed Haider5,
  • Francesca Buffa5,
  • Ioannis Ragousis6,
  • David R. Mole7 and
  • Adrian L. Harris5
BMC Genomics201415(Suppl 2):P40

https://doi.org/10.1186/1471-2164-15-S2-P40

Published: 2 April 2014

Background

Transcriptional responses to hypoxia are central to the pathogenesis of many types of cancer. Today, pan-genome analyses of hypoxia have been focused on protein-coding genes, however, the role of non-coding RNAs, in particular long non-coding RNAs (lncRNA) is not well characterized [1].

Materials and methods

We undertook an integrated pan-genomic analysis of the transcriptional responses to hypoxia in MCF7 breast cancer cells, employing total RNA-seq together with ChIP-Seq for the hypoxia-inducible transcription factor (HIF) and for epigenetic marks of transcriptional activation (RNApol2 and histone H3K4me3).

Results

Analyses revealed that all classes of RNA are significantly regulated by hypoxia. We found significant numbers of lncRNAs are up-regulated in hypoxia and these are associated with epigenetic marks of increased transcription and HIF binding. We describe a number of hypoxia regulated non-annotated RNA species, including several that are antisense to hypoxia regulated protein-coding RNAs. The most hypoxia up-regulated lncRNA was NEAT1. The role of NEAT1 in cancer has not been previously studied. We demonstrate that NEAT1 induction is common in breast cancer cell lines and xenograft models. Finally, selected hypoxia regulated lncRNAs are analysed in a large cohort of breast cancers (n=2000) and found to be associated with poor clinical outcome and clinicopathological features.

Conclusions

Our findings extend knowledge of the hypoxic transcriptional response into the spectrum of non-coding transcripts. These HIF-regulated non-coding transcripts have the potential to act as biomarkers for breast cancer as well as potential novel therapeutic targets.

Authors’ Affiliations

(1)
Biochemistry Department, King Abdulaziz University
(2)
Department of Nephrology and Hypertension, Friedrich-Alexander-University
(3)
The Weatherall Institute of Molecular Medicine, University of Oxford
(4)
The Wellcome Trust Centre for Human Genetics, University of Oxford
(5)
Department of Oncology, University of Oxford
(6)
McGill University and Genome Quebec Innovation Centre
(7)
The Henry Wellcome Building for Molecular Physiology, University of Oxford

References

  1. Choudhry H, Schodel J, Oikonomopoulos S, Camps C, Grampp S, Harris AL, Ratcliffe PJ, Ragoussis J, Mole DR: Extensive regulation of the non-coding transcriptome by hypoxia: role of HIF in releasing paused RNApol2. EMBO reports. 2014, 15 (1): 70-76.PubMed CentralView ArticlePubMedGoogle Scholar

Copyright

© Choudhry et al; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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