Dr O Heidenreich, Prof David Westhead
No more applications being accepted
Competition Funded PhD Project (European/UK Students Only)
About the Project
Alternative splicing does not only increase the complexity of the transcriptome, but, when dysregulated, is also a major driver of oncogenesis. In particular mutations of components of the SF3B splicing complex have been associated haematopoietic malignancies such as myelodysplastic syndromes and chronic lymphoblastic leukaemia. However, more “classical” genetic rearrangements such as leukaemic fusion genes have not been yet been linked to alternative splicing. The RUNX1/ETO fusion gene results from the most frequent chromosomal rearrangement found in acute myeloid leukaemia. It codes for an oncogenic transcription factor driving leukaemic propagation. Using a genome-wide next generation RNA sequencing, we have identified more than 2,500 target genes of RUNX1/ETO including genes known to be associated with self-renewal. To examine a potential involvement of RUNX1/ETO in the generation of alternative transcripts, we established a novel bioinformatics pipeline and examined not only differential exon usage, but also studied changes in existing and emergence of novel exon-exon linkages in dependence on the RUNX1/ETO status. Knockdown of RUNX1/ETO affected more than 2,000 exon-exon linkages in leukaemic cells, with 40% of these genes being direct RUNX1/ETO target genes as judged by genome-wide ChIP-seq experiments. Importantly, the majority of these alternatively spliced genes do not significantly change their overall expression and, thus, have not been identified as affected by this leukaemic fusion gene by conventional RNA-seq analysis pipelines. In conclusion, these data clearly demonstrate a strong involvement of an aberrant fusion transcription factor in the generation and maintenance of the leukaemia-associated splicing pattern.
Obviously, these findings raise a number of important questions: To what extent is the RUNX1/ETO effect on alternative splicing dependent on its binding to the gene locus? Does RUNX1/ETO regulate the splicing pattern indirectly by controlling expression levels of RNA-binding proteins? How does alternative splicing contribute to the development and maintenance of leukaemia, i.e. which alternatively spliced transcripts are essential for leukaemia?
To address these questions, you will knock down or overexpress genes and in particular alternatively spliced isoforms. You will examine the consequences of these manipulations on the molecular and cellular level in combination with bioinformatics approaches for analysis and prediction (e.g. identifying RNA binding proteins by combining motif and gene expression analyses). Candidates will then be validated in vivo in mouse experiments. These studies will be performed both in tissue culture and in immunodeficient mouse systems and will include state of the art techniques such as lentiviral transduction, application of RNAi and CRISPR technology and mouse transplantation and experimentation. In addition, you will perform bioinformatics by analysing and integrating the different data sets in order to generate models for the role of alternative splicing in the propagation of leukaemia. Wet lab experiments will be performed in the lab of Olaf Heidenreich at the Wolfson Childhood Cancer Centre at Newcastle University, while the bioinformatics will be performed with David Westhead in the Schoold of Molecular and Cellular Biology at the University of Leeds.
Funding Notes
DiMeN DTP studentships are funded for 3.5 years and include:
Tax-free maintenance grant set at the UK Research Council's national rate.
Full payment of tuition fees at the Home/EU rate.
A Research Training Support Grant to support your research studies.
Successful Home students will receive a full studentship. EU students will be considered for a full studentship/fees only support depending on the excellence of their qualifications and their employment/residency status.
Please carefully read the instructions on eligibility and how to apply at our website and use the link on the page to submit an application: http://www.dimen.org.uk/how-to-apply/application-overview
Application Website
http://www.dimen.org.uk/