PhD fellowship in spatial analysis of the tumor microenvironment

Department of Biology, Faculty of SCIENCE
University of Copenhagen



The Department of Biology invites applicants for a PhD fellowship in spatial analysis of the tumor microenvironment. The project is part of the research project “Integrating spatial transcriptomics, live tumor microenvironment imaging and focused CRISPR screens for transformative insights in cancer biology”, which is financed by a Distinguished Investigator grant from The Novo Nordisk Foundation.

Starting date is Oct. 1st 2024 or as soon as possible thereafter.

The project

The overall aim of the project is to is to establish a new way of understanding tumor biology, by integrating tumor physicochemical traits and transcriptomic landscapes. Specific aims are to develop superimposed maps of key physicochemical TME parameters and transcriptomes of the cells within them. We will then use this information in conjunction with advanced 3D spheroid CRISPR screens and functional analyses to understand how cancer cells sense and react to key aspects of their environment. Finally, we will combine these findings to identify a novel class of markers of specific physicochemical tumor traits for potential use as biomarkers and treatment targets.

The PhD student will lead the imaging of the physicochemical tumor microenvironment. The first task will be to develop bioreactor-based spheroid co-cultures of pancreatic cancer cells and stromal cells, followed by immunohistochemistry analysis of cellular organization and expression patterns of key TME-responsive proteins in the cultures. The next, and main, task will be to develop 3D live imaging of interstitial and cellular pH, lactate, and oxygen, using bespoke fluorescent reporters. The PhD student will work closely with two postdoctoral fellows and another PhD student, who together with the PI and technician will form the main project team.

Who are we looking for?

We are seeking ambitious candidates within the field(s) of biology, biochemistry and molecular biomedicine or similar. We are particularly interested in applicants with strong prior knowledge of live fluorescence imaging, and in particular fluorescent reporter proteins. Understanding of cancer biology, and in particular, the tumor microenvironment, is an advantage. Candidates must be able to perform as part of a team as well as independently, and must have good social skills and communication skills in English.

Our group and research- and what do we offer?

• A highly collaborative, friendly and enthusiastic research group with broad national and international scientific networks.
• Excellent research infrastructure and training in state-of-the-art techniques
• Highly relevant research at the crossroads between oncology, biophysics and metabolism, which will be a solid basis for your next-level career
• Beyond our own group, a strong and active PhD student organization and a great scientific and social environment

Our group is a part of the Department of Biology, Faculty of SCIENCE, University of Copenhagen. We are located in Copenhagen, Denmark.

Principal supervisor is Professor Stine Falsig Pedersen, Department of Biology, email: [email protected]; direct phone: +45 20991555.

The PhD program is a three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree. To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.

Terms of employment in the regular programme
Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.

Responsibilities and tasks in the PhD program

• Carry through an independent research project under supervision

• Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
• Participate in active research environments, including a stay at another research institution, preferably abroad
• Teaching and knowledge dissemination activities
• Write scientific papers aimed at high-impact journals
• Write and defend a PhD thesis on the basis of your project

Application and Assessment Procedure
Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.

Please include:

1. Motivated letter of application (max. one page)
2. Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
3. Contact information for 2-3 relevant reference persons (will only be contacted with your permission)
4. Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
5. Publication list (if possible)
6. Reference letters (if available)

Application deadline:

The deadline for applications is 12 August 2024, 23:59 CEST.

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/.

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.

General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/.

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.