Research group Quantitative systems immunology

Aims

The aim of our group is to define how immune cells organize membrane receptors to guide the recognition and killing of cancer cells, and how cancer cells can hijack or block this process. There is increasing evidence that suggests that this is a highly coordinated process that operates with nanoscale precision. To decode this at the required throughput and scale, we develop and use innovative quantitative technologies. In particular proteomics, high resolution microscopy, and single cell multiomics are central. 

In short, our research focuses on:

1. Identification and interpretation of surface markers on immunce cells.
2. Define the protein composition of the immunological synapse between immune and cancer cells in various models and contexts.
3. Use high-throughput omics data for stratification of patients receiving drugs targeting the immune system.

Achievements

In particular, we have derived various proteomics technologies that in an off the shelf manner allow to derive protein colocalization in the cell membrane and intracellularly (Nature Communcations, 2021; Nature Protocols, 2023). Such technologies provide the basis for decoding the receptor interactome in the immune-cancer interaction (Trends in Immunology, 2026).

Publications

See the publication list of the research group leader on Web of Science.

• A selection of our publications

  • Decoding the immune-tumor synapse for data-driven design of next-generation immunotherapies. van Rossum ISC, van Spriel AB, van Mierlo G. Trends Immunol. 2026 Mar 17:S1471-4906(25)00317-5. doi: 10.1016/j.it.2025.12.009
  • Cell surface interactome analysis identifies TSPAN4 as a negative regulator of PD-L1 in melanoma. Franken GA, Abel Gutierrez A, van Rossum I, Spruijt CG, Vermeulen M, van Mierlo G, Scheijen B, van Spriel AB. Mol Oncol. 2026 May;20(5):1140-1160. doi: 10.1002/1878-0261.70182.
  • Off-the-shelf proximity biotinylation using ProtA-TurboID. Santos-Barriopedro I, van Mierlo G, Vermeulen M. Nat Protoc. 2023 Jan;18(1):36-57. doi: 10.1038/s41596-022-00748-w. Epub 2022 Oct 12.
  • Off-the-shelf proximity biotinylation for interaction proteomics. Santos-Barriopedro I, van Mierlo G, Vermeulen M. Nat Commun. 2021 Aug 18;12(1):5015. doi: 10.1038/s41467-021-25338-4.
  • Identification of methylation-sensitive human transcription factors using meSMiLE-seq. Gralak AJ, Faltejskova K, Yang AWH, Steiner C, Russeil J, Grenningloh N, Inukai S, Demir M, Dainese R, Owen C, Pankevich E; Codebook/GRECO-BIT Consortium; Hughes TR, Kulakovskiy IV, Kribelbauer-Swietek JF, van Mierlo G, Deplancke B. bioRxiv [Preprint]. 2024 Nov 12:2024.11.11.619598. doi: 10.1101/2024.11.11.619598.
  • Therapeutic potential of dihydronicotinamide riboside (NRH) on obesity and glucose intolerance in mice. Rumpler M, van Mierlo G, Vinten KT, Giner MP, Christen S, Hayat F, Makarov MV, Gardeux V, Russeil J, Schomakers BV, van Gijn L, Hashimi H, Steiner C, Giroud-Gerbetant J, Joffraud M, Sanchez Garcia JL, Moco S, Migaud ME, Houtkooper RH, Deplancke B, Canto C. Nat Commun. 2026 Mar 25;17(1):4386. doi: 10.1038/s41467-026-70965-4.
  • Engineering next-generation microfluidic technologies for single-cell phenomics. Lambert CLG, van Mierlo G, Bues JJ, Guillaume-Gentil OJ, Deplancke B. Nat Genet. 2025 Jun;57(6):1344-1356. doi: 10.1038/s41588-025-02198-y.
  • Context transcription factors establish cooperative environments and mediate enhancer communication. Kribelbauer-Swietek JF, Pushkarev O, Gardeux V, Faltejskova K, Russeil J, van Mierlo G, Deplancke B. Nat Genet. 2024 Oct;56(10):2199-2212. doi: 10.1038/s41588-024-01892-7.