Single-cell derived tumor organoids display diversity in HLA class I peptide presentation

Laura C Demmers, Kai Kretzschmar, Arne Van Hoeck, Yotam E Bar-Epraïm, Henk W P van den Toorn, Mandy Koomen, Gijs van Son, Joost van Gorp, Apollo Pronk, Niels Smakman, Edwin Cuppen, Hans Clevers, Albert J R Heck, Wei Wu

Research output: Contribution to journal/periodicalArticleScientificpeer-review

39 Citations (Scopus)


Tumor heterogeneity is a major cause of therapeutic resistance. Immunotherapy may exploit alternative vulnerabilities of drug-resistant cells, where tumor-specific human leukocyte antigen (HLA) peptide ligands are promising leads to invoke targeted anti-tumor responses. Here, we investigate the variability in HLA class I peptide presentation between different clonal cells of the same colorectal cancer patient, using an organoid system. While clone-specific differences in HLA peptide presentation were observed, broad inter-clone variability was even more prevalent (15-25%). By coupling organoid proteomics and HLA peptide ligandomics, we also found that tumor-specific ligands from DNA damage control and tumor suppressor source proteins were prominently presented by tumor cells, coinciding likely with the silencing of such cytoprotective functions. Collectively, these data illustrate the heterogeneous HLA peptide presentation landscape even within one individual, and hint that a multi-peptide vaccination approach against highly conserved tumor suppressors may be a viable option in patients with low tumor-mutational burden.

Original languageEnglish
Pages (from-to)5338
JournalNature Communications
Issue number1
Publication statusPublished - 21 Oct 2020


  • Antigen Presentation
  • Cell Line, Tumor
  • Clone Cells/immunology
  • Colorectal Neoplasms/immunology
  • HLA Antigens/metabolism
  • Humans
  • Ligands
  • Models, Biological
  • Neoplasm Proteins/metabolism
  • Organoids/immunology
  • Proteome/metabolism
  • Signal Transduction
  • Single-Cell Analysis
  • TOR Serine-Threonine Kinases/metabolism


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