Vincent van Unen

Assistant Professor

Curriculum Vitae

As a PhD student in the group of prof. F. Koning at the Dept. of Immunology (then IHB) at LUMC, I was the first to apply mass cytometry to analyze the immune system in biopsy material from patients with inflammatory intestinal diseases (celiac and Crohn’s disease). I was the first adopter of mass cytometry in the Netherlands. In this work, I have connected the biomedical field with computational scientists, which has resulted in the development of Cytosplore and Hierarchical Stochastic Neighbour Embedding (HSNE). These computational tools overcome the scalability limits of t-SNE, thus enabling the analysis of millions of cells.

My studies led to the identification of tissue- and disease-associated immune subsets in inflammatory intestinal diseases. Furthermore, several significant discoveries have been made possible by the computational pipeline I have developed through collaborations with Technical University Delft, covering multiple research fields: pathogen-immune interactions, tumor immunology, autoimmunity, and pregnancy. I had the pleasure of collaborating with a diverse group of researchers. Moreover, these collaborations demonstrated that the computational immunology approach developed was versatile and readily applicable to various research topics.

To increase our understanding of inflammatory diseases affecting organs, it is crucial to gain better fundamental insight into the physiological development of the immune system. Therefore, I studied the cellular composition of the mucosal immune system in the developing human fetus with single-cell mass cytometry. We identified early-life compartmentalization of immune cells in fetal tissues, and extensive heterogeneity and multi-lineage differentiation trajectories of innate lymphoid cells in the fetal intestine. These analyses, along with single-cell RNA-seq, T cell receptor-seq and imaging-CyTOF, revealed the generation of memory CD4+ T cells in the fetal intestine, suggesting that the immune system before birth is far more mature than previously thought.

As a postdoctoral researcher at Stanford University (CA, USA), I continued my research on investigating the immune system in inflammatory intestinal diseases. In Mark Davis’s lab, I gained significant experience applying a systems immunology approach to studying human disease. I worked on analyzing multiple single-cell techniques for an in-depth analysis of T cell populations. Moreover, I was a joint postdoc in Calvin Kuo’s lab, which has developed the air-liquid interface (ALI) organoid system. I have extended this organoid technology and helped develop celiac disease and IBD organoids from human biopsies that preserve intestinal epithelium, supportive stroma, and native immune cells. When the pandemic struck, I was part of a research team where we generated human lung organoids and successfully infected them with SARS-CoV-2, identifying lung cell types amendable to infection.

My research experience has positioned me between computational sciences and immunology, which has resulted in discoveries that offer opportunities to determine cellular parameters that correlate with disease and predict response to treatment. My interests range from basic research on the immune system to direct clinical translational research of cohort studies and development of computational tools.

My key interests are

  • Investigating human immune-mediated intestinal diseases (celiac, inflammatory bowel disease).
  • Developing System Immunology approaches to study human disease.
  • Performing fundamental research on the development of the immune system in the intestine.


  • Identification of a disease-associated network of intestinal immune cells in treatment-naive inflammatory bowel disease.

    van Unen V, Ouboter L, Li N, […], Pascutti F, van der Meulen A, Koning F.

    Front. Immunol. (2022)

  • Progenitor identification and SARS-CoV-2 infection in human distal lung organoids

    Salahudeen AA, Choi SS, Rustagi A, Zhu J, van Unen V, […], Blish CA, Desai TJ, Kuo CJ.

    Nature (2020)

  • Systems analysis and controlled malaria infection in Europeans and Africans elucidate naturally acquired immunity

    de Jong SE, van Unen V, Manurung MD, […], Mordmuller B, Lell B, Yazdanbakhsh M.

    Nat Immunol. (2021)

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