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
Soft tissue sarcomas are rare group of cancers arising from transformed cells of mesenchymal origin.
Liposarcoma accounts for ~20 % of soft tissue sarcomas and are aggressive, partly treatment resistant tumours with high mortality rate. Well-differentiated and dedifferentiated liposarcomas are the most common sub-types of liposarcoma and are characterized by the presence of giant cancer specific chromosomes, termed neochromosomes, that consists of high number of amplifications covering oncogenes such as MDM2, CDK4 and HMGA2. Gene expression levels in these amplified regions do not correlate well with the number of amplifications observed in such cancers. Moreover, where these cancer specific chromosomes are located within the nucleus and how they are regulated in the cancer cells are unknown.
Project
The main focus of this project is to characterize epigenetic deregulation in Liposarcoma. We have mapped the genome of four patient cell lines and combined this with single-cell RNA-seq and ATAC-seq and genome-wide epigenetic datasets. Collectively, these data enabled us to establish a working hypothesis of how amplified oncogenic regions found in neochromosomes are being regulated. The master student will be part of a sub team in the group that are investigating how neochromosomes are formed and maintained.
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, Molecular Cloning, Cell Transfection, Western blotting, RNA isolation, qRT-PCR, CUT&RUN, RNA-seq and Fluorescence in situ Hybridisation (FISH).
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 microscopy is essential and the student can learn bioinformatic analysis of epigenetic data.
References
Tyler et al., 2020 Cancer Treatment Reviews
https://www.sciencedirect.com/science/article/pii/S0305737220300517