Behavioral-transcriptomic landscape of engineered T cells targeting human cancer organoids

Dekkers, J. F.; Alieva, M.; Cleven, A.; Keramati, F.; Brazda, P.; Rebel, H. G.; Wezenaar, A. K. L.; Puschhof, J.; Buchholz, M.-B.; Barrera Roman, M.; Johanna, I.; Meringa, A. D.; Fasci, D.; Geurts, M. H.; Ariese, H. C. R.; van Vliet, E. J.; van Ineveld, R. L.; Karaiskaki, E.; Kopper, O.; Bar-Ephraim, Y. E.; Kretzschmar, K.; Eggermont, A. M. M.; Wehrens, E. J.; Stunnenberg, H. G.; Clevers, H.; Kuball, J.; Sebestyen, Z.; Rios, A. C.

doi:10.1101/2021.05.05.442764

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bioRxiv · 10.1101/2021.05.05.442764

Behavioral-transcriptomic landscape of engineered T cells targeting human cancer organoids

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Abstract

Cellular immunotherapies are rapidly gaining clinical importance, yet predictive platforms for modeling their mode of action are lacking. Here, we developed a dynamic immuno-organoid 3D imaging-transcriptomics platform; BEHAV3D, to unravel the behavioral and underlying molecular mechanisms of solid tumor targeting. Applied to an emerging cancer metabolome-sensing immunotherapy: TEGs, we first demonstrate targeting of multiple breast cancer subtypes. Live-tracking of over 120,000 TEGs revealed a diverse behavioral landscape and identified a super engager cluster with serial killing capability. Inference of single-cell behavior with transcriptomics identified the gene signature of super engager killer TEGs, which contained 27 genes with no previously described T cell function. Furthermore, guided by a dynamic type 1 interferon (IFN-I) signaling module induced by high TEG-sensitive organoids, we show that IFN-I can prime resistant organoids for TEG-mediated killing. Thus, BEHAV3D characterizes behavioral-phenotypic heterogeneity of cellular immunotherapies and holds promise for improving solid tumor-targeting in a patient-specific manner.

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Dekkers, J. F., Alieva, M., Cleven, A., Keramati, F., Brazda, P., Rebel, H. G., Wezenaar, A. K. L., Puschhof, J., Buchholz, M.-B., Barrera Roman, M., Johanna, I., Meringa, A. D., Fasci, D., Geurts, M. H., Ariese, H. C. R., van Vliet, E. J., van Ineveld, R. L., Karaiskaki, E., Kopper, O., Bar-Ephraim, Y. E., Kretzschmar, K., Eggermont, A. M. M., Wehrens, E. J., Stunnenberg, H. G., Clevers, H., Kuball, J., Sebestyen, Z., Rios, A. C.. 2021-05-05. Behavioral-transcriptomic landscape of engineered T cells targeting human cancer organoids. https://doi.org/10.1101/2021.05.05.442764

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