The position

Many small open reading frames (smORFs) in the genome are translated into microproteins that standard protein catalogs miss. Some of the resulting peptides are presented on HLA molecules at the cell surface, where they can act as cancer-specific antigens and potential immunotherapy targets. Yet the molecular machinery that governs which smORF-derived peptides are translated, processed, and presented remains largely uncharted, which limits their therapeutic and diagnostic use.

This project will systematically identify the regulators of smORF-derived cancer antigen presentation using a pooled CRISPR screening approach, built around a novel dual-reporter system that simultaneously monitors smORF translation and HLA surface presentation. Within ORFeus Work Package 3, which investigates the roles of the dark proteome in cancer and immunology, it provides the mechanistic understanding of antigen presentation that underpins the work package's therapeutic pipeline: screen targets are prioritized using candidates from partner projects, and top hits are validated in patient-derived cancer models to connect regulatory insights to clinically relevant settings.

Main tasks

● Develop and deploy a dual-reporter system that simultaneously monitors smORF translation and HLA surface presentation, and establish it as the readout for a pooled CRISPR screen.

● Identify key regulatory factors by screening translation and antigen-processing pathways against targets prioritized from the projects of other doctoral candidates (DCs) in the network, here DC4 on host-pathogen microproteins and DC5 on the secreted microproteome.

● Validate top candidates using immunopeptidomics and test their relevance in patient-derived cancer models together with DC15, aiming for at least one mechanistically characterized regulatory pathway with therapeutic potential.

● Collaborate across the ORFeus network, contribute reporter cell lines and a regulatory map of antigen presentation factors to the shared ORFeome platform, and produce the project's scientific report.

Methods and platforms: pooled CRISPR screening (including CRISPRa/CRISPRi libraries), dual-reporter cell-line engineering, flow cytometry and cell sorting, immunopeptidomics by mass spectrometry, HLA antigen-presentation assays, and functional validation in patient-derived cancer models, contributing data and cell lines to the ORFeome platform.

Secondment: you will spend around three months at MyNeo (Ghent, Belgium), applying the project's screening workflows to the identification of personalized cancer antigen candidates. You will also be guided by an independent academic advisor, with the possibility of a short, primarily virtual research exchange to strengthen the project.

Your profile

MSCA eligibility

You must meet all of the following on your recruitment date:

● You do not already hold a doctoral degree. If you have defended a doctoral thesis but the degree has not yet been formally awarded, you are not eligible.

● Mobility rule: you must not have lived or carried out your main activity (work, studies, and so on) in the Netherlands for more than 12 months in the 36 months immediately before your recruitment date. Compulsory national service, short stays such as holidays, and time spent in a procedure to obtain refugee status under the Geneva Convention do not count toward the 12 months.

● You hold, or will hold before the start date, a degree that formally entitles you to enroll in a doctorate, and you can enroll in the doctoral program at the Netherlands Cancer Institute / Erasmus University Rotterdam.

Candidates of any nationality may apply. There is no limit on prior research experience, as long as you do not already hold a doctorate.

Project-specific profile

● A master's degree (or equivalent) in molecular biology, cell biology, cancer biology, immunology, biochemistry, biotechnology, or a related life-science field.

● Hands-on experience with mammalian cell culture and molecular biology, and ideally with functional genomics or CRISPR screening.

● Desirable: experience with flow cytometry and cell sorting, CRISPR technologies, immunology or antigen presentation, mass-spectrometry immunopeptidomics, or the analysis of high-throughput screening data, and an interest in microproteins and the dark proteome.

● Good written and spoken English.

● Motivation for interdisciplinary, collaborative research, and willingness to travel for the secondment and network events.

What we offer

A full-time employment contract for 36 months as a salaried researcher, with full social security coverage, under the rules of the Marie Skłodowska-Curie Actions. This is a paid employment contract, not a stipend or scholarship.

We offer you a temporary, full-time PhD position for a total duration of 4 years (36 hours / 5 days a week) at the Netherlands Cancer Institute. You will also collaborate with various research groups at the NKI and abroad. Your gross monthly salary will be between €3,813 and €4,629 gross per month for a full-time working week (36 hours), in line with the OIO pay scale and depending on previous relevant experience. You also receive 8.33% holiday allowance and 8.33% end-of-year bonus. The Netherlands Cancer Institute operates according to the collective labor agreement 'CAO Ziekenhuizen'.

Beyond salary, you will receive:

● Supervision by a world-leading, interdisciplinary supervisory team.

● A secondment of around three months with an ORFeus industry partner (MyNeo).

● A structured training program: network-wide schools, transferable-skills training, workshops, and international conferences.

● Enrollment in the Oncology Graduate School at Erasmus Medical Center, leading to a PhD.

Duration and funding beyond the MSCA contract

The MSCA employment contract covers 36 months of full-time, fully funded employment. In line with the host institution's doctoral policy, the host funds completion of the doctorate beyond the 36-month MSCA contract as continued employment at the standard national doctoral salary scale where applicable; terms confirmed at offer stage.

Working at the Netherlands Cancer Institute

The Netherlands Cancer Institute (NKI-AVL) is a research-intensive comprehensive cancer center in Amsterdam, the Netherlands, combining fundamental cancer research with patient care and strong programs in cancer biology, immunology, and functional genomics. NKI-AVL offers a world-class, highly collaborative research environment where more than 750 scientists, clinicians, and support staff work side by side within an integrated comprehensive cancer center, enabling rapid translation of fundamental discoveries into innovative patient care. Researchers benefit from outstanding core facilities, including advanced genomics, proteomics, bioinformatics, imaging, flow cytometry, high-performance computing, biobanking, robotics, and expert technical support.

You will join the group of Prof. Reuven Agami, which develops pooled CRISPR screening approaches and studies how aberrant translation, including under amino acid deprivation, generates novel cancer antigens. You will work closely with the group of Prof. Michal Bassani-Sternberg at the University of Lausanne, who brings complementary expertise in immunopeptidomics and HLA antigen presentation. You will enroll as a PhD candidate at Erasmus University Rotterdam, the degree-awarding partner of the Netherlands Cancer Institute.