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

Abstract

SummaryCellular 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.

Advancing Tissue Decellularized Hydrogels for Engineering Human Organoids

“…Through RNA sequencing, it was also possible to correlate TEG sensitivity with organoids’ gene expression profiles, cytokine signaling, and ECM organization. [ 197 ]…”

“…Through RNA sequencing, it was also possible to correlate TEG sensitivity with organoids' gene expression profiles, cytokine signaling, and ECM organization. [197] Overall, breast cancer organoids demonstrated to be useful for evaluating the potential of immunotherapy in breast cancer treatment in a patient-specific manner. Owing to the vascularized breast tumor microenvironment, breast cancer organoids have been cultured with blood-like vessels in order to provide a more biomimetic environment and better understand such interaction.…”

Cancer-on-a-chip model shows that the adenomatous polyposis coli mutation impairs T cell engagement and killing of cancer spheroids

“…Several different MPS approaches have been developed for cancer applications, particularly for the study of cancer-immune system interactions, as reviewed in several recent articles [22][23][24][25][26]. Recent work has been focused on demonstrating the relevance of MPS models for tumor behavior in vivo [27,28], while engineering advances have involved coupling these models with imaging and image analysis methods to obtain information on the biological and biophysical processes [29][30][31]. However, none of the existing work has yet provided new mechanistic insights on CTL-cancer interactions in the context of specific diseases.…”

3D imaging for driving cancer discovery

“…This creates a critical opportunity to define immune cell functional properties based on their single‐cell dynamics captured into a behavioural landscape (Crainiciuc et al , 2022). In this light, we recently developed BEHAV3D (Table 2), a large content dynamic 3D imaging‐transcriptomic platform for the in‐depth characterization of organoid‐immunotherapy co‐cultures (preprint: Dekkers et al , 2021). When applied to various solid tumour organoid biobanks and T cell therapy products, both single and population organoid death dynamics could be extracted, as well as the behavioural and transcriptomic profile of individual therapeutic T cells.…”

“…These future directions will greatly aid in understanding the complex cellular heterogeneity of tumours and their microenvironment, as well as the heterogenous composition and mode of action of cellular cancer therapies. The latter application exemplified by the integration of dynamic 3D imaging with single‐cell transcriptomics to unveil the underlying molecular mechanisms of solid tumour targeting by cellular immunotherapy (preprint: Dekkers et al , 2021). In addition, with progress in genetic lineage tracing tools (Baron & van Oudenaarden, 2019), we can expect that in the near future a combination of 3D imaging and transcriptomics will further expand the work performed on fluorescent lineage tracing of tumour cells.…”