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  • Project No: NDORMS-2021/4
  • Intake: 2021

Project outline 

 Pancreatic cancer is one of the most lethal malignancies in human due to its highly metastatic characteristics and the poor responsiveness to current therapeutics. Pancreatic tumorigenesis involves a dedifferentiation process of cellular identity and the acquisition of a stem cell-like state of a subpopulation of cells known as cancer stem cells (CSCs). These cells resemble partly to naturally occurring stem cells and are exceptionally important because their developmental plasticity allows them to metastasize and give rise to whole tumours in the organism (1-6). Currently it remains unclear, which transcription factors and epigenetic machineries control the expression of stem cell genes and the stem cell-like identity of pancreatic CSCs. This knowledge would be valuable for developing more efficient pancreatic cancer therapeutics in the future.

The research objective of the project is to identify and characterize novel epigenetic machineries and transcriptional regulators which govern gene expression, proliferation and stem cell-like characteristics of pancreatic CSCs.

The project has three sub-aims:

  1. Performing small molecule screening experiments with compound sets targeting kinases and/or epigenetic mechanisms. The screening library will contain a unique collection of small molecule compounds with biological activity against a range of candidates including a broad range of epigenetic regulators that target distinct enzymes involved in regulating gene expression, as well as proteasome and kinase inhibitors. Our preliminary data has already uncovered interesting candidates for in-depth experiments.
  2. Studying the molecular mechanisms of selected candidates from the screen in more detail. This includes functional and mechanistic analysis of candidates by loss-of-function and gain-of-function experiments via CRISPR/Cas9; RNA-sequencing / ATAC-sequencing / ChIP-sequencing indicating the phenotype/transcriptomic effects of candidate knockdowns;
  3. Using patient samples and animal studies for candidate functional effects on tumorigenesis. We will perform CyTOF and single cell RNA-sequencing data of tumours from primary pancreatic cancer patients upon the treatment of epigenetic inhibitors; mouse tumorigenesis studies by orthotopic transplantation of pancreatic cancer cells with a knockout of candidates.

The DPhil project will apply a broad range of cutting edge research techniques covering human cell culture systems, genome-wide, proteomic, genetic and biochemical methods (3-6). These include human cancer stem cell spheres, pancreatic ductal adenocarcinoma organoids and human pluripotent stem cells, genome-wide studies (RNA-seq, ChIP-seq, ATAC-seq), proteomics (Co-IP / mass-spectrometry), functional studies (CRISPR/Cas9-mediated gene editing) and mechanistic studies (confocal microscopy, flow cytometry, cell sorting, real-time PCR, western blotting, promoter-luciferase assays).

Collectively, this research will provide key insight to the signalling pathways and molecular mechanisms essential for the formation and maintenance of pancreatic cancer stem cells, helping to better understand the tumorigenic process, and to uncover novel ways for diagnosing and treating this lethal cancer.


1.     French, R., Feng, Y., and Pauklin, S. (2020). Targeting TGFβ signalling in cancer: toward context-specific strategies. Trends in Cancer 7, 538-540.

2.     Feng, Y., and Pauklin, S. (2020). Two sides of the same coin: the roles of TGF-β in colorectal carcinogenesis. Gastroenterology 20, 30395-4.

3.     Bertero, A., Madrigal, P., Galli, A., Hubner, N.C., Moreno, I., Burks, D., Brown, S., Pedersen, R.A., Gaffney, D., Mendjan, S *., Vallier, L., * Pauklin, S * (2015). Activin/Nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark. Genes Dev 29, 702-717.

4.     Pauklin, S., and Vallier, L. (2015). Activin/Nodal signalling in stem cells. Development 142, 607-619.

5.     Pauklin, S., Madrigal, P., Bertero, A., and Vallier, L. (2016). Initiation of stem cell differentiation involves cell cycle dependent transcription of developmental genes by Cyclin D. Genes Dev 30(4), 421-33.

6.     Pauklin, S., and Vallier, L. (2013). The cell-cycle state of stem cells determines cell fate propensity. Cell 155, 135-147.


  • Pancreatic tumorigenesis
  • Cancer Stem Cells
  • Stem cell biology
  • Epigenetic mechanisms and gene expression
  • Signalling pathways regulating cellular plasticity


This multidisciplinary project is part of the research programme led by Dr Siim Pauklin, who is a Principal Investigator and a Cancer Research UK Career Development Fellow at the Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences. The DPhil project aims to identify novel molecular mechanisms that regulate the formation and maintenance of pancreatic cancer stem cells in pancreatic ductal adenocarcinomas. The student will closely interact with the research groups of Udo Oppermann and Gillian Farnie, and other colleagues at the Botnar Research Centre, while also benefitting from the collaborations with researchers at the Kennedy Institute of Rheumatology, the Target Discovery Institute, the CRUK/MRC Oxford Institute for Radiation Oncology, and the Wellcome Trust Centre for Human Genetics.

For general inquiries: Sam Burnell (, Graduate Studies Officer.

For project related inquiries: Dr Siim Pauklin (, Botnar Research Centre, University of Oxford.


The Botnar Research Centre plays host to the University of Oxford's Institute of Musculoskeletal Sciences, which enables and encourages research and education into the causes of musculoskeletal disease and their treatment. Training will be provided in techniques including state-of-the-art laboratory methods essential for cancer research and the stem cell field.

A core curriculum of lectures will be taken in the first term to provide a solid foundation in a broad range of subjects including musculoskeletal biology, inflammation, epigenetics, translational immunology, data analysis and the microbiome. Students will also be required to attend regular seminars within the Department and those relevant in the wider University.

Students will be expected to present data regularly in Departmental seminars, the Pauklin group and to attend external conferences to present their research globally, with limited financial support from the Department.

Students will also have the opportunity to work closely with the Oppermann, Farnie and Christianson groups.

Students will have access to various courses run by the Medical Sciences Division Skills Training Team and other Departments. All students are required to attend a 2-day Statistical and Experimental Design course at NDORMS and run by the IT department (information will be provided once accepted to the programme).


The Department accepts applications throughout the year but it is recommended that, in the first instance, you contact the relevant supervisor(s) or the Graduate Studies Officer, Sam Burnell (, who will be able to advise you of the essential requirements.

Interested applicants should have, or expect to obtain, a first or upper second-class BSc degree or equivalent in a relevant subject and will also need to provide evidence of English language competence (where applicable). The application guide and form is found online and the DPhil will commence in October 2021.

Applications should be made to the following programmes using the specified course code: D.Phil in Molecular and Cellular Medicine (course code: RD_MP1)

For further information, please visit