Investigating the 3’ untranslated region of mRNA in order to understand the drivers of metastasis in primary triple negative breast tumours — ASN Events
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  2. Poster Session 2
  3. Investigating the 3’ untranslated region of mRNA in order to understand the drivers of metastasis in primary triple negative breast tumours

Investigating the 3’ untranslated region of mRNA in order to understand the drivers of metastasis in primary triple negative breast tumours (#220)

Andrew Pattison 1 , Cameron Johnstone 2 , Paul Harrison 3 , Robin Anderson 2 , David Powell 1 , Traude Beilharz 3
  1. Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
  2. Metastasis Research Laboratory, Olivia Newton-John Cancer Wellness & Research Centre, Melbourne, Victoria, Australia
  3. Monash Bioinformatics Platform, Monash University, Melbourne, VIC, Australia

While progress has been made in the detection of primary breast tumours, determining how likely a tumour will be to metastasise is still very difficult. Understanding this “metastatic potential” is most important in the so called “triple negative breast cancers” (TNBCs) which lack the classical markers that are commonly targeted in treatment. Chemotherapy is usually given for triple negative tumours, often unnecessarily. Better markers of tumour metastatic potential are clearly required.

Alternative polyadenylation (APA) is the process whereby the poly (A) tail is added to the 3’ untranslated region (3’ UTR) of mRNA at one of multiple possible sites, changing 3’ UTR length and potentially the regulatory elements that bind to it. APA has been shown to be indicative of tumour state, but is often overlooked when conducting RNA-seq analysis. We are developing a method to cheaply and effectively quantify the expression state of a primary breast tumour based off Poly (A) Test sequencing (PAT-seq) data, which sequences 3' UTRs in a genome wide fashion. PAT-Seq is also capable of measuring differential poly (A) tail length which may also play a role in metastasising tumour cells.   

We hypothesise that the metastatic potential of a primary tumour is associated with changes in RNA metabolism. We investigated changes in gene expression, APA site usage, miRNA expression and the length of the poly (A) tail. We are testing this hypothesis in an increasingly metastatic cell line model both in vitro and in vivo as well as in TCGA patient data. We have discovered some novel metastasis associated changes in RNA metabolism at the 3’ ends of mRNA transcripts as well as the differential expression of genes and miRNAs.

In order to effectively interpret and visualise PAT-seq data we make use of “Tail-tools”, a custom bioinformatics pipeline, and many additional custom bioinformatics tools and workflows. These approaches enable sophisticated data analysis, visualisation and identification of novel trends in both our TNBC model and real patient data.  

  1. Harrison, P. F., Powell, D. R., Clancy, J. L., Preiss, T., Boag, P. R., Traven, A., Seemann, T., and Beilharz, T. H. (2015) PAT-seq: a method to study the integration of 3′-UTR dynamics with gene expression in the eukaryotic transcriptome. RNA
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