Abstract 80: Programmatic re-splicing of the hypoxia transcriptome regulates the DNA damage response
Authors: Miller Crispin , Memon Danish , Dawson Keren , Smowton Christopher , Xing Wei , Dive Caroline 
Published: July 2016

Background

Hypoxia occurs within the majority of solid tumors. It has multiple impacts on tumor biology including angiogenesis, suppression of immune reactivity, enhanced receptor tyrosine kinase signaling, down regulation of DNA repair pathways, promotion of pro-survival phenotypes and increased proclivity for invasion and metastasis. Levels of hypoxia vary between and within tumors, correlate with patient outcomes, and can lead to differences in response to therapy. Despite considerable advances, our understanding of the regulatory processes that control these diverse and heterogeneous changes in cancer phenotype remain incomplete. A better understanding of how they are mediated will inform strategies for personalized medicine and promise to substantially advance our understanding of tumor heterogeneity.

Methods

Until recently, techniques for RNA-expression profiling have lacked the resolution necessary to detect genome wide changes in splicing. We exploited the increased precision offered by deep sequencing to investigate genome-wide remodelling of transcript architectures in both cell line and tumor samples. Using novel computational strategies we generated sample-specific gene models from RNA sequencing data generated over a timecourse of HCT116 colorectal carcinoma cells following a switch to 1% oxygenation and used these data to identify widespread changes in splicing. We applied similar strategies to raw RNA-sequencing data derived from TCGA.

Results

We detected the expression of thousands of novel isoforms and a systematic, pathway-dependent switch to the expression of noncoding transcripts at multiple genes, including many constituents of the Fanconi Anemia, nucleotide excision- and double strand break repair pathways. Of particular note were HDAC6 and 53BP1: critical regulators of DNA damage response. Both loci exhibited a hypoxia-dependent expression of retained-intron transcripts and a concomitant decline in protein levels, thus providing a novel and unanticipated mechanism by which hypoxia can drive genetic instability. Predictions made using our cell line model were recapitulated in a large cohort of 458 colorectal carcinomas derived from TCGA. Validation of the cell line data revealed, for the first time, a strong signature of isoform switching in which a widespread transition to noncoding expression is associated with poor patient outcome. These data were derived from independent patient biopsies sequenced by others, thus demonstrating the robustness of our findings.

Conclusions

These data therefore have clear, substantial, and immediate implications both for our understanding of the basic aetiology of solid tumors and for the development of RNA-based signatures and biomarkers in diagnostics and personalized medicine.

Citation Format: Crispin Miller, Danish Memon, Keren Dawson, Christopher Smowton, Wei Xing, Caroline Dive. Programmatic re-splicing of the hypoxia transcriptome regulates the DNA damage response. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 80.