Doctoral Researcher in Transcription biology / Cancer research
We are recruiting a
Doctoral Researcher
to the project ‘Targeting transcription elongation to modify the prostate cancer tumor immune micro-environment’ to the research group Transcriptional Rewiring in Cancer led by Harri Itkonen (University of Helsinki). The project is pursued in close collaboration with Professor Ian G Mills’ research group based in University of Oxford and it is funded by Prostate Cancer UK. The position is for 3 years, and we hope that the candidate starts in autumn 2025.
Background
The research in Itkonen laboratory is focused on how the information embedded in the genome is decoded through transcription, and how the defects in this process can be used as a basis for therapy. Currently, we are probing how the crosstalk between transcriptional kinases and other factors regulating RNA polymerase II activity function in normal and cancer cells. In particular, we are interested in the kinases that promote transcription elongation, CDK9 and CDK12, and highlight few examples that are particularly relevant for the current project. We discovered that CDK9 inhibition stimulates transcription of short mRNAs (Gondane & al. 2025, PMID: 40186208) and leads to excessive splicing defects (Hu & al., 2021, PMID: 34592899), which the cell interprets as a viral infection (Yalala & al. 2024, PMID: 38661032). In our projects, we make extensive use of comprehensive transcriptional profiling, including RNA-seq, SLAM-seq, alternative splicing analysis, combined with epigenetic profiling using ChIP-seq, FAIRE-seq and more recently also ATAC-seq (for examples, see Itkonen & al. 2020, PMID: 3261155; Gondane & al. 2022, PMID: 35164752,Gondane & al. 2023, PMID: 36975490, and Liang & al. 2024, PMID: 38775167).
For further information, please refer to our research groups’ web pages:
https://www.helsinki.fi/en/researchgroups/transcriptional-rewiring-in-cancer
https://www.nds.ox.ac.uk/team/ian-mills
Project
Prostate cancer is immunologically cold, which means that the body’s own immune system fails to detect and eradicate the cancer cells. We have discovered that the drug-induced defects in transcription elongation activate immunogenic signaling in prostate cancer cells. In particular, this can be achieved by inhibiting CDK9 using compounds already assessed in clinical trials against other cancers.
Our main aim in this project is to develop CDK9 inhibitor-based treatment against prostate cancer for durable response. To achieve this, we will model how both normal and cancer cells respond to CDK9 inhibition, and if the response can be augmented using immunomodulatory and / or other strategies.
The project is divided so that the organoid experiments and bioinformatics are performed in University of Helsinki, while the animal experimentation is performed in University of Oxford. The project utilizes a number of sequencing techniques including RNA-seq, SLAM-seq, scSLAM-seq, and ‘Breaks Labeling In Situ and Sequencing (BLISS)’.
The candidate
We are seeking a motivated Bioinformatics graduate who wants to expand their expertise to cancer research / molecular biology. The proposed project is intended for an MSc-level person who wishes to acquire PhD degree. PhD Trainees in my laboratory typically graduate within 3-4 years with competitive publication output, and we put great emphasis on planning the project with clear milestones set in the beginning. This strategy allows the Trainees and me to reflect on the progress and to make adjustments as need be. Project involves significant work together with collaborating groups based in Oxford (Mills) and Switzerland (Clémentine LeMagnen). The appointee will be based in Helsinki and the project includes research visit to Switzerland to acquire specific expertise required for the project execution.
Qualification requirements
The ideal candidate has an MSc degree from Bioinformatics, but applicable other degrees are also considered.
Essential
• Applicant must hold an MSc degree.
• Proven experience on using command line-based tools.
• Fluent oral and written communication skills in English.
In addition, the additional qualifications will be an asset
• Experience from using virtual machines.
• Experience in analyzing the data generated using the techniques mentioned in the section ‘Project’.
• Working experience (in any sector, also unrelated to the field of education).
• Demonstrable experience in presenting own work (conferences, social media etc).
• Knowledge on cancer biology.
Personal skills
• Genuine interest in science.
• Ability to work in a team and independently.
The appointee should either already have the right to pursue a doctoral degree at the University of Helsinki by the start of the appointment or apply for the right and obtain it within the probationary period of six months of their appointment. If the candidate does not already have the right to pursue a doctoral degree at the University of Helsinki, it must be applied for separately: www.helsinki.fi/en/research/doctoral-education/the-application-process-in-a-nutshell. The requirements for pursuing a doctoral degree at the University of Helsinki can be found at https://www.helsinki.fi/en/research/doctoral-education/eligibility-and-educational-documents. The appointee will be based in Helsinki.
What we offer
Project is expected to start in autumn 2025, as a fixed 3-year position. A 6-month trial period will be applied.
How to apply
Applications should be submitted through the University of Helsinki Recruitment System via the "Apply now" button. Internal applicants (i.e., current employees of the University of Helsinki) submit their applications by using the Employee Login button.
Please send your application with following enclosures:
1. CV (maximally 2 pages).
2. Cover letter (max 1-page, scientific background, motivation for the position and research interests).
3. Copies of educational certificates (academic transcripts only – please ascertain that the grading system is clearly explained, include both diploma and grades you have received from all the courses taken during BSc and MSc education).
4. 2-3 references (name, institution, e-mail, telephone number, and relation to the candidate).
The closing date for applications is July 20th 2025.
We encourage informal inquiries: harri.itkonen@helsinki.fi and ian.mills@nds.ox.ac.uk
About us
The Faculty of Medicine promotes high quality scientific research. It provides research-based undergraduate and postgraduate education in medicine, dentistry, psychology and logopedics, and an international Master's Programme in Translational Medicine. It also offers psychotherapist education. In addition to its teaching and research activities, the faculty serves as a significant expert organisation in the healthcare sector and contributes to the discourse on ethics in the field. The faculty aims to be one of the best medical research faculties in the world, while reinforcing its status as a distinguished institution of multidisciplinary education in healthcare. https://www.helsinki.fi/en/faculty-of-medicine.
The Faculty of Medicine at the University of Helsinki constitutes the academic medical centre together with HUS Helsinki University Hospital and the Helsinki Institute of Life Science (HiLIFE). This medical centre has been successful in international comparisons, ranking among the top 10 medical campuses in Europe and the top 50 globally.
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