PhD Theses MedicalPancreatic ductal adenocarcinoma (PDAC) remains one of the most aggressive and lethal
malignancies. Despite significant advances in medicine and surgery, pancreatic cancer still has a dismal
5-year survival rate below 8%. Much emphasis to date has been directed into identifying somatic
mutations in the coding regions of the genome, identifying several known drivers including KRAS,
TP53, CDNK2A, AIRD1A, and SMAD4. However, the coding regions comprise only 2% of the human
genome. The other 98% comprises non-coding DNA, where somatic non-coding mutations (NCMs) are
becoming increasingly associated with pathogenic roles in cancer. To date, little is known regarding
somatic NCMs and their regulatory affects in PDAC.
We integrate publicly available ChIP-Seq data for the enrichment of active promoter and
enhancer regions, RNA-seq data for gene expression analysis and whole genome sequencing data
produced by the International Cancer Genome Consortium (659 PDAC patients). Using our analytic
pipeline of two independent approaches, we identify 14 regulatory regions harbouring putative
functional somatic mutations or recurrent variants, arising proximal to PDAC relevant genes including
an enhancer within the intron of the transcription factor FOXP1 and the promoter of the oncogenic
long non-coding RNA (lncRNA), HOTAIR. Furthermore, pathway analysis identified NCMs in close
proximity to genes involved in transcriptional regulation and biological processes such as cell
adhesion.
Using a combination of luciferase reporter and high-throughput STARR-seq assays, we assess
the regulatory activity of 587 somatic NCMs with putative transcriptional factor motif gain or loss of
function capabilities. Our results show 43 NCMs with significant gene reporter expression alterations.
Interestingly, we identify NCMs located in a 2kb region within the intron of the cancer associated
polycistronic lncRNA MIR100HG, which demonstrates an up-regulation in gene reporter activity. This
site is also located proximal to the oncogenic mir-125b-1. CRISPR-Cas9 mediated deletion of this 2kb
element demonstrated phenotypic alterations in PDAC cell lines, with a reduced capacity in cell
migration and clonogenicity. We also observe evidence of differential expression of nearby TAD
associated genes, suggesting important regulatory roles of this 2kb intronic element. This study
represents a step towards unravelling the non-coding regions of the genome and to the identification
of novel biomarkers and therapeutic targets in this deadly disease