This master project is part of the Centre for Cancer Cell Reprogramming a Centre of Excellence at UiO (https://www.med.uio.no/cancell/english/). To learn more about us visit www.chromatome.no and watch our movie: https://youtu.be/6yADYLbFEo4
Background
Breast cancer is the one of the leading causes of death in females, second only to lung cancer. Gene expression and epigenetic profiling of breast cancer has shown that it is not a single disease, but rather a group of molecularly distinct neoplastic disorders [1]. There are five distinct molecular subtypes of breast cancer, which correlate with hormone responsiveness, patient prognosis, and response to therapy. Nonetheless, little is known about the initial, disease driving transcriptional and epigenetic changes, which promote the phenotypic outcomes in breast cancer.
Alternative splicing (AS) occurs in more than 90% of all human genes and increases the palette of proteins. AS of distinct isoforms is key in onset and progression of disease and a hallmark of cancer. Quaking STAR protein (QKI) is an RNA binding protein involved in RNA biogenesis such as alternative splicing, circular RNA production, protein translation and mRNA stability. QKI expression is found to be dysregulated in several cancers including colon, breast, prostate and lung cancer [2]. QKI has been shown to mediate alternative splicing of histone variant macroH2A, which regulate cancer cell proliferation [3].
Project
This master project will be a part of an ongoing project working on Quaking STAR protein in breast cancer. We aim to study the alternative splicing mediated by QKI variants in different subtypes of breast cancer. We will use lentiviral shRNAs to rapidly knock down QKI in breast cancer cell lines allowing for global RNA-seq analysis of splice variants affected. Moreover, we have setup lentiviral shRNAs for knockdown and splicing specific QKI antibodies. The master student will use various breast cancer cell lines to understand the role of this RNA binding protein QKI in epigenetic regulation of breast cancer malignancy.
Methods
The student will learn a wide range of biological/biochemical and molecular approaches used in our lab, like mammalian tissue culture, CRISPR/Cas9 technology, different knockdown methods, Cloning, Cell Transfection, Western blotting, RNA isolation, qRT-PCR, RNA-seq and bioinformatic data-analysis.
About you
We are looking for a driven, enthusiastic and hardworking student. You should be motivated to work in an interdisciplinary environment at IMB. Interests in bioinformatics and microscopy are advantageous.
References
1. Fleischer T, Tekpli X, Mathelier A, Wang S, Nebdal D, Dhakal HP, et al. DNA methylation at enhancers identifies distinct breast cancer lineages. Nat Commun. Nature Publishing Group; 2017;8: 1379. doi:10.1038/s41467-017-00510-x
2. Darbelli L, Richard S. Emerging functions of the Quaking RNA-binding proteins and link to human diseases. WIREs RNA. Wiley-Blackwell; 2016;7: 399–412. doi:10.1002/wrna.1344
3. Novikov, L. et al. QKI-mediated alternative splicing of the histone variant MacroH2A1 regulates cancer cell proliferation. MOLECULAR AND CELLULAR BIOLOGY 31, 4244–4255 (2011).