Postdoctoral and PhD Positions at the interface of Immunopeptidomics/proteomics, Tumor Immunology and Therapeutic Vaccines

As part of the national initiative ONCODE-Accelerator, the Hecklab @Utrecht University has multiple job openings related to the field of cancer vaccine development. We seek talented and motivated people for multiple research projects with a range of expertise, including LC-MS-based immunopeptidomics, proteomics, bioinformatics and tumor immunology. Within the Therapeutic Vaccines program of the ONCODE Accelerator, we primarily develop and use MS-based proteomics and immunopeptidomics workflows with the aim of identifying novel antigen targets that will be used for cancer vaccines. The target discovery platform integrates multi-omics expertise, and it is co-led by Dr. Sebastiaan van Heesch of the Princess Maxima Center for Paediatric Cancer Care (expertise in ribosome profiling and RNAseq) and Dr. Albert Heck of Utrecht University (expertise in MS-based proteomics and immunopeptidomics).

Publication date: October 2024

5 PhD/PostDoc Positions: With the framework of an ERC Advanced Grant project entitled REVAMP

In REVAMP we develop and use innovative structural mass spectrometry (MS) and proteomics techniques to generate a unique molecular understanding of the diversity and structural and functional characteristics of human antibody repertoires. These repertoires are highly personal and play a key role in our human immune response. We aim to monitor at the protein level (changes in) endogenous antibody repertoires with clonal resolution, including those induced by antigen-specific polyclonal responses in individuals. Following identification by advanced top-down and bottom up de novo sequencing these antibodies will be followed up functionally as potential therapeutic leads. The general aim of REVAMP is to overhaul the current view of the structural diversity of our human antibody repertoire and thereby elevate our understanding of how the human immune system functions.The five Interrelated projects are focused on;

1. Advance methods to extend the coverage of full antibody repertoires present in serum/plasma, enhancing fractionation methods, sample preparation methods, but also methods to extend the coverage to all (sub)classes of immunoglobulins present in our body, and measure antibody repertoires in other compartments of the body. Postdoctoral position for 3 years.
2. Enabling the sensitive, efficient, and accurate sequencing of endogenous antibodies by making use of advances in top-down and middle-down sequencing of antibodies and AI-assisted novel computational approaches to convert mass spectrometry data into sequences. Postdoctoral position for 3 years, for a MS-expert with key interests in antibody biology, MS instrumentation and data-analysis, with knowledge in programming.
3. Structural characterization of immunoglobulin modalities, IgM, IgA and IgD. Beyond IgG, the natural immunoglobulins IgA, IgD and IgM are much less well characterized structurally and functionally. Using endogenous and recombinant Ig’s we aim to elucidate new key structural features, and new interactors. Postdoctoral position for 3 years, for a MS-expert with key interests in cross-linking mass spectrometry, native mass spectrometry, electron microscopy, structural modelling, protein production and immunology. Related references
4. Finding novel antibody leads by antigen-directed antibody profiling. Using antigens mimicking either pathogens or inducing auto-antibodies as affinity baits in this project we aim to measure polyclonal responses and discover new human antibodies that bind strongly to antigens of interest, that may be further developed to neutralize the pathogens, or be developed as therapeutics. PhD position for 4 years, for a MS-expert with key interests in affinity proteomics, serum proteomics, protein production and immunology.  Related references

Elucidating longitudinal humoral immune responses is clinical cohorts of samples. Using plasma proteomics and antibody repertoire responses we will study in this project how our human body react upon viral infections, cancer, immunotherapy and stem cell transplantation. PhD position for 4 years, for a MS-expert with key interests in immunology, serum proteomics and mass spectrometry.