The role of non-coding genome in cancer

Abstract

Tumour hypoxia is associated with poor patient outcome and resistance to therapy. It impacts upon multiple pathways and causes alterations in the levels of protein encoding transcripts throughout the cell. Next generation sequencing of human datasets have revealed widespread alternative splicing in coding genes and the presence of large numbers of non-coding loci, raising the question as to whether these additional transcripts add additional functional complexity to the genome. The goal of my PhD was to use bioinformatics approaches to identify novel transcriptional events associated with hypoxia, with a particular focus on the role of non-coding RNA expression in regulating the cell's response to changes in oxygenation. In this thesis I describe three studies. The first is a systematic analysis of changes in long non-coding RNA expression in normal (BodyMap RNA-Seq data) and cancer tissue (using data from The Cancer Genome Atlas; TCGA). This revealed a set of long non-coding RNAs that are predicted to participate in housekeeping functions, and are likely to be essential for cell survival. The second is a global transcriptomic analysis of HCT116 colorectal cancer cells following a shift to 1% oxygenation. Analysis of RNA abundance over a hypoxic timecourse identified substantial remodelling of splicing, widespread alterations in the domain structure of many critical protein-coding genes and a global shift towards non-coding isoforms. This transition from coding to non-coding isoforms was recapitulated in a large and independent cohort of colorectal samples taken from TCGA and correlated with patient tumour status at last contact. The third study focused on non-coding RNA expression in the same HCT116 dataset. Expression of one of these loci, HINCR1 (Hypoxia Induced Non Coding RNA 1), was found to be induced in many models of hypoxia, and prognostic of survival in lung cancer patients. Subsequent experimental characterization of HINCR1 revealed it to be a regulator of Egr1 activity, a transcription factor central to the gene expression programs of mitogenesis.

Date of Award	1 Aug 2016
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Crispin Miller (Supervisor) & John Brognard (Supervisor)