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

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

doi:10.1038/s41467-020-19142-9

Abstract

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.

Highlights

Tumor heterogeneity is a major cause of therapeutic resistance
To checkpoint blockade inhibitors, monoclonal antibodies and anti-tumor vaccines may be raised against tumor cells[9] or tumor-specific cell-surface antigens (HLA class I peptide ligands), which arise as proteasome-generated byproducts from protein homeostasis[10]
By ranking the peptide intensities and binding affinities of all ligands detected from each tumor clones, we found that clone-specific ligands were not necessarily always low abundant (Fig. 4b, Supplementary Fig. 4) or low in peptide loading affinity to the patients human leukocyte antigen (HLA) type (Fig. 4c)

Summary

Introduction

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. By coupling organoid proteomics and HLA peptide ligandomics, we 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. 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. One of the key questions that still need to be addressed, is the extent of heterogeneity in HLA class I peptide ligand presentation, between tumor cells in the same environment or individual

Methods

Results

Conclusion