About the Project
Find hidden proteins in HPV-driven cancers that T cells can recognize, at the University of Dundee. Not open if you spent over 12 months in the UK in the 3 years before the start; explore the 11 other ORFeus projects!
Why it matters
When human papillomavirus (HPV) integrates into the human genome, it can create hybrid viral-human transcripts, some of which may encode uncataloged proteins. If pieces reach the cell surface, the immune system may see them as foreign, which makes them candidate immunotherapy targets in cancers such as head and neck cancer.
The project
You will map which hybrid transcripts are translated in HPV-positive and head and neck squamous cell carcinoma (HNSCC) cell lines, check whether their peptides are presented on HLA molecules, and test whether T cells respond. The result is an "HPV Immune Map" of hidden translation and antigen presentation.
What you will do
- Find hybrid viral-human transcripts with long- and short-read RNA sequencing and ribosome profiling
- Confirm which peptides are made and presented, using proteomics and immunopeptidomics, in cell lines and in primary human tumors
- Spend around three months at Immudex in Denmark, learning to detect rare T cells that recognize these peptides
About ORFeus
This PhD is one of 15 in ORFeus, a Marie Skłodowska-Curie Actions Doctoral Network funded by Horizon Europe. ORFeus brings together 15 research groups in eight European countries, with industry and research partners, to study the dark proteome: the many microproteins made from small open reading frames long dismissed as non-coding. Together, the 15 projects aim to find these proteins, understand what they do, and test their potential in diagnosis, immunotherapy and drug development, with a strong focus on cancer.
Where you will work
You will join the group of Prof. Nicola Ternette at the University of Dundee, which specializes in immunopeptidomics and tumor antigen discovery, including in HPV-driven cancers. You will work closely with the group of Dr. Sebastiaan van Heesch at the Princess Máxima Center in Utrecht, which brings expertise in microproteins and non-canonical translation.
Who should apply
We welcome applications from immunology, virology and cancer biology graduates. This is a wet-lab project with omics data analysis.
- A master's degree (or equivalent) in immunology, virology, cancer biology, molecular biology, biochemistry, or a related field
- Hands-on lab experience with cell culture and molecular biology, and with proteomics or immunology techniques
- Good written and spoken English
- Nice to have: immunopeptidomics, HLA biology or T-cell assays, ribosome profiling or RNA sequencing
Eligibility (MSCA mobility rule)
You are not eligible if you have lived, worked or studied in the UK for more than 12 months in the 36 months before your start date (around March 2027). This applies whatever your nationality, UK citizens included. For example, a one-year UK master's plus a few more months in the UK already goes over the limit. Compulsory national service, short stays such as holidays, and time spent in a refugee status procedure do not count. Studied or worked in the UK recently? You are likely eligible for our 11 ORFeus positions outside the UK.
You must not hold a doctoral degree. Any nationality may apply.
What we offer
- A 36-month, full-time employment contract with full social security, under MSCA rules
- Supervision by Prof. Nicola Ternette and Dr. Sebastiaan van Heesch, with mentoring from partners across academia and industry
- A secondment of around three months at Immudex
- Training with 14 other ORFeus PhD candidates across Europe: network schools, workshops, transferable skills and international conferences
- PhD enrollment at the University of Dundee
Practical details
Start around March 2027; the exact date depends on the host institution. Reference letters are requested only at the interview stage.
How to apply
You can only apply via https://www.orfeus-dn.eu/apply/. You can apply to up to three of the 15 ORFeus projects and rank them; every project you rank considers you. The application asks for:
- a few eligibility questions
- a short motivation per project (150 to 200 words)
- your experience with the project's key techniques
- your CV
- an overview of your bachelor's and master's grades, in one PDF
- contact details for two referees
- a short motivational video
Funding Notes
Fully funded 36-month employment contract in ORFeus, an MSCA Doctoral Network (Horizon Europe, GA [contact details available in the full listing]), with full social security. A salary, not a stipend. Salary details for this position are on the application page. Open to all nationalities. UK mobility rule: you are not eligible if you have lived, worked or studied in the UK for more than 12 months in the 36 months before your start date (around March 2027), whatever your nationality. Applicants must not hold a doctoral degree. ORFeus positions outside the UK are open to UK residents: orfeus-dn.eu/apply.
