Improving personalized cancer immunotherapy vaccines by computationally optimizing neoantigen selection

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Trine Line Hauge Okholm


DKK 1,163,563




Internationalisation Fellowships


Our immune system protects us against diseases by recognizing and fighting pathogens. When presented with a foreign antigen, e.g. from a virus or bacteria, an immune response is elicited, leading to immune cell-mediated destruction of infected cells. Additionally, our immune system is capable of fighting cancer by recognizing tumor-specific antigens presented on cancer cells. The overall aims of my research project is to understand how the immune system responds to coronavirus infections or carcinogenesis by identifying altered immune cell populations and signaling pathways between diseased patients and healthy controls. Additionally, I will study patient immune response changes over time in the context of cancer immunotherapies with the overarching goal of identifying specific immune cells that contribute to anti-tumor immunity.


Deciphering immune responses to viral infections or cancer cell development provide important insights into human natural defence mechanisms, e.g. why some individuals are more susceptible to infection and complications than others, or why some individuals respond better to a treatment than others. Understanding how viral infection or cancer alters the composition and function of the immune system can be used to guide, optimize, and monitor treatment response, which ultimately leads to improved patient outcomes.


The project is carried out in Matthew Spitzer’s Lab at University of California San Francisco (UCSF), California, USA. The Spitzer Lab studies the coordination and regulation of immune responses across an organism in the context of virus infections, cancer immunology, and immunotherapy. I will analyze high-dimensional single-cell data, incl. mass cytometry (CyTOF), single cell RNA-Seq, and multiplexed ion beam imaging (MIBI) generated from human subjects, incl. COVID-19 patients and patients with head and neck squamous cell carcinoma. Data from multiple patient specimens, e.g. blood, tumor, and lymph nodes, longitudinal sample collection, and comprehensive clinical information allow for extensive characterization of local and systemic immune responses between distinct patient groups as well as trajectory analyses of immunological changes over time.

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