Subclonal immune evasion in non-small cell lung cancer.
Dijkstra KK., Vendramin R., Karagianni D., Witsen M., Gálvez-Cancino F., Hill MS., Foster KA., Barbè V., Angelova M., Hynds RE., Pearce DR., Martínez-Ruiz C., Black JRM., Huebner A., Pich O., Rowan A., Augustine M., Puttick C., Moore DA., Liu LL., Saghafinia S., van de Haar J., Veeriah S., Naceur-Lombardelli C., Toncheva A., Bola SK., Hiley CT., Jamal-Hanjani M., McGranahan N., Litchfield K., Reading JL., Chain B., TRACERx consortium None., Quezada SA., Voest EE., Swanton C.
Cancers rarely respond completely to immunotherapy. While tumors consist of multiple genetically distinct clones, whether this affects the potential for immune escape remains unclear due to an inability to isolate and propagate individual subclones from human cancers. Here, we leverage the multi-region TRACERx lung cancer evolution study to generate a patient-derived organoid - T cell co-culture platform that allows the functional analysis of subclonal immune escape at single clone resolution. We establish organoid lines from 11 separate tumor regions from three patients, followed by isolation of 81 individual clonal sublines. Co-culture with tumor infiltrating lymphocytes (TIL) or natural killer (NK) cells reveals cancer-intrinsic and subclonal immune escape in all 3 patients. Immune evading subclones represent genetically distinct lineages with a unique evolutionary history. This indicates that immune evading and non-evading subclones can be isolated from the same tumor, suggesting that subclonal tumor evolution directly affects immune escape.