PhD fellowship in cancer research

Dr. Håvard Lindholm is the principal investigator. The position will be located in the laboratory of Professor Frode Jahnsen () at the Department of Pathology Oslo University Hospital Rikshospitalet.

This is a collaborative project between the Jahnsen team the group of professor Sheraz Yaqub at Oslo University Hospital and the group of Professor Daniel De Carvalho at Princess Marget Cancer Centre in Toronto Canada. All research groups are internationally leading experts in immunology cancer and bioinformatics.

The project aims to explore how antiviral defense pathways can be harnessed to kill colorectal cancer cells. Colorectal cancer is the second most common form of cancer in Norway and novel therapies are needed to improve disease this project we will develop new method to measure double stranded RNA (dsRNA) and apply it to colorectal cancer samples. We will also explore mechanisms to induce dsRNA in cancer using intestinal organoids as a model and perform bioinformatic analysis on publicly available data. The work will be performed in a modern molecular biology lab with access to specialized equipment such as a P2 solo instrument which will be used to perform Oxford Nanopore Sequencing on site. We also have access to computational clusters which will be used for analysis.

Antiviral defense pathways can be activated if dsRNA is expressed from our own genome. Normally dsRNA is only present in a human cell infected with viruses and human cells have innate immune receptors that can recognize dsRNA. However pathways dysregulated in cancer can lead to expression of repeated elements forming dsRNA. This would lead to the activation of antiviral defenses which can kill the cancer cell. Through the analysis in this project we will hopefully understand when and where this dsRNA is expressed in cancer and how to target it for future cancer therapeutics. For more details see this review: Endogenous retroelements as alarms for disruptions to cellular homeostasis Lindholm et al (2023) Trends in cancer Please get in touch if you dont have access to the review.

• Perform Oxford Nanopore sequencing of RNA samples.
• Do wet lab experiments exploring how to induce dsRNA in intestinal organoids.
• Create scripts to analyze the output of experiments.
• Perform bioinformatic analysis of publicly available data.

Wet lab experiments are an important part of the project but they will mostly generate large datasets requiring bioinformatic analysis. Lack of experience with wet lab or bioinformatics can be accepted if the candidate has good experience in just one of the two. The principal investigator and the rest of the team have extensive experience in both molecular biology and bioinformatics and will provide necessary training.

• Applicants must hold an MsC degree in biology immunology medicine bioinformatics computational biology informatics or a related field.
• Experience in molecular biology techniques. Experience with library preparation cell culture and growing organoids is a plus.
• Experience in bioinformatics. Knowledge of Python and analysis of sequencing data is a plus.
• Fluent oral and written communication skills in English.

Personal characteristics and skills
We are looking for a highly motivated candidate who is interested in identifying and addressing important scientific problems and has a genuine passion for research. We also emphasize professional and personal qualities as well as the ability to work well with others on our team. The ideal candidate will demonstrate initiative accountability and a systematic approach to their work while also excelling in implementation and forming good collaborations with others.

• Application letter describing the applicants qualifications and motivation for the position.
• CV (summarizing education positions and academic work).
• MsC thesis.
• Copies of educational certificates and transcript of records.
• Letters of recommendation or names and contact details of 2-3 references (name relation to candidate e-mail and telephone number).

The application with attachments must be delivered in our electronic recruiting system please follow the links apply for this job. Foreign applicants should attach an explanation of their universitys grading system. Please note that all documents should be in English (or a Scandinavian language).

When assessing the applications special emphasis will be placed on the documented academic qualifications relevant to the project description excellence in relevant project tasks and the candidates motivation and personal suitability.

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