Evaluation of new long-noncoding RNAs driving breast or ovarian cancer development

This project is suitable for Honours or PhD students

Background

It is now clear the majority of the human genome is transcribed from both DNA strands but only 2% encodes protein. Much of this transcription is derived from DNA sequences that do not encode functional proteins. The majority of these transcripts are long non-coding RNAs (lncRNAs) defined as being >200 bp in length. While it is generally accepted lncRNA transcription is functionally significant, the scope and function of lncRNAs in cancer is still not well understood.

Genome wide association studies (GWAS) have identified thousands of common variants associated with an increased risk of breast and ovarian cancers. Large-scale genome sequencing projects have also identified regions of the genome that are frequently mutated in breast and ovarian cancers. Importantly, the majority of these disease-associated variants and mutations lie within intergenic regions and introns of protein-coding genes, suggesting that undiscovered RNA transcripts such as lncRNAs, may play a direct role in cancer development. We have recently used different RNA sequencing and bioinformatic approaches to identify hundreds of new breast and ovarian cancer-related lncRNAs.

Aims

We have recently used RNA sequencing and bioinformatic approaches to identify hundreds of new cancer-related lncRNAs. We now want to understand how these lncRNAs modulate breast and ovarian cancer development.

Methods

Projects will use multiple in vitro approaches to determine how the variants and mutations alter lncRNA function, including CRISPR-based lncRNA editing and reporter assays. We will link lncRNAs to their target protein-coding genes using HiChIP chromatin assays and CROP-seq experiments. We expect that some of the lncRNAs will have cancer-related biological functions. We will therefore overexpress or silence lncRNAs in breast and ovarian cancer cells and examine their effects on cell growth, response to DNA damage, apoptosis, migration and tumour formation. We will also assess the function of lncRNAs in tumour formation using an explant assays in mice. The discovery of novel regulatory lncRNAs influencing cancer development may reveal entirely new avenues for breast and ovarian cancer therapeutics.

Students will have access to unique expertise and reagents, and will acquire skills in tissue culture, CRISPR-based methods, RNA and DNA manipulation, confocal microscopy, FACS analyses and other molecular biology techniques.