PhD position in pancreatic cancer bioinformatics
Department of Biology, Faculty of Science at University of Copenhagen is offering
1 PhD scholarships in Marie Skłodowska-Curie Actions Innovative Training Networks on
pH and Ion Transport in Pancreatic Cancer (pHIoniC) from October 2019
This pHIonic training network is financed by the European Commission Horizon 2020. The project is a collaboration between 10 academic and 3 industrial partners from 7 European countries. The consortium brings together highly synergistic expertise in the field of ion transport and cancer research.
Our focus is on pancreatic ductal adenocarcinoma (PDAC), which is rising in incidence and is so far incurable. The programme’s central idea is that the unique pancreatic microenvironment contributes to disease development and progression. The programme has a strong grounding in the physiology of acid/base transport in the exocrine pancreas and it develops new concepts and tools in the cancer field and beyond. Jointly, pHioniC will map pH landscape in normal and diseased pancreas, characterize the impact of the acidic microenvironment on PDAC development, and apply drug/nanocarrier/antibody designs for targeting of tumors. For further details of the network, please visit https://www.medizin.uni-muenster.de/phionic/home/.
pHioniC will provide training and collaborative network and structured PhD programme. The training will cover the fields of ion transport, oncology, imaging, bioinformatics and antibody technology, extensive transferable skills and personalized training elements.
The specific PhD project will be within Prof Sandelin’s group at the Bioinformatics Centre at University of Copenhagen. The group is a world leader in medical transcriptomics and gene regulation biology. Examples of our work include promoter-based classification of inflammatory bowel disease (Nat Commun. 2018 9(1):1661), enhancer transcription (Science 2015 347(6225):1010-4) and the creation of enhancer atlases across human cell types (Nature. 2014 507(7493):455-461)
Project description: Relation and causality between pH homeostasis and driver mutation generation in PDAC development
We hypothesize that acidic conditions synergize with PDAC mutations to drive PDAC development. An outstanding question is the causality between the two: are PDAC driver mutations more easily generated in an acidic environment, or is their ability to drive PDAC development increased due to the acidity. The experiments will be based on exposing organoid cultures that carry one, two or none of the typical PDAC driver mutations to acid conditions, and then assess changes in RNA response (RNA-seq) and generation of new mutations. This is a collaboration with another PhD in the training network, who will also assess cell phenotypes in parallel.
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