Uncovering the mode of action of engineered T cells in patient cancer organoids
Dekkers, Johanna F.; Alieva, Maria; Cleven, Astrid; Keramati, Farid; Wezenaar, Amber K.L.; van Vliet, Esmée J.; Puschhof, Jens; Brazda, Peter; Johanna, Inez; Meringa, Angelo D.; Rebel, Heggert G.; Buchholz, Maj Britt; Barrera Román, Mario; Zeeman, Amber L.; de Blank, Sam; Fasci, Domenico; Geurts, Maarten H.; Cornel, Annelisa M.; Driehuis, Else; Millen, Rosemary; Straetemans, Trudy; Nicolasen, Mara J.T.; Aarts-Riemens, Tineke; Ariese, Hendrikus C.R.; Johnson, Hannah R.; van Ineveld, Ravian L.; Karaiskaki, Froso; Kopper, Oded; Bar-Ephraim, Yotam E.; Kretzschmar, Kai; Eggermont, Alexander M.M.; Nierkens, Stefan; Wehrens, Ellen J.; Stunnenberg, Henk G.; Clevers, Hans; Kuball, Jürgen; Sebestyen, Zsolt; Rios, Anne C.
(2023) Nature Biotechnology, volume 41, issue 1, pp. 60 - 69
(Article)
Abstract
Extending the success of cellular immunotherapies against blood cancers to the realm of solid tumors will require improved in vitro models that reveal therapeutic modes of action at the molecular level. Here we describe a system, called BEHAV3D, developed to study the dynamic interactions of immune cells and patient cancer
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organoids by means of imaging and transcriptomics. We apply BEHAV3D to live-track >150,000 engineered T cells cultured with patient-derived, solid-tumor organoids, identifying a ‘super engager’ behavioral cluster comprising T cells with potent serial killing capacity. Among other T cell concepts we also study cancer metabolome-sensing engineered T cells (TEGs) and detect behavior-specific gene signatures that include a group of 27 genes with no previously described T cell function that are expressed by super engager killer TEGs. We further show that type I interferon can prime resistant organoids for TEG-mediated killing. BEHAV3D is a promising tool for the characterization of behavioral-phenotypic heterogeneity of cellular immunotherapies and may support the optimization of personalized solid-tumor-targeting cell therapies.
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Keywords: Humans, Immunotherapy/methods, Neoplasms/genetics, Organoids/pathology, T-Lymphocytes, Applied Microbiology and Biotechnology, Bioengineering, Molecular Medicine, Biotechnology, Biomedical Engineering, Journal Article
ISSN: 1087-0156
Publisher: Nature Publishing Group
Note: Funding Information: We thank the Princess Máxima Center for Pediatric Oncology for technical support and the Hubrecht Institute and Zeiss for imaging support and collaboration. All imaging was performed at the Princess Máxima Imaging Center. We thank the Princess Máxima Center Organoid Facility for organoid culture support, the flow cytometry facilities at the Princess Máxima Center and Laboratory of Translational Immunology (UMCU) for cell sorting, the Princess Máxima Center Single Cell Genomics Facility for help with scRNA-seq analysis, Single Cell Discoveries (https://www.scdiscoveries.com) for library preparations and the Hartwig Medical Foundation (https://www.hartwigmedicalfoundation.nl/) for sequencing. We also thank HUB for providing PDOs, QVQ for providing NCAM1 nanobodies and D. van Vuurden (Princess Máxima Center for Pediatric Oncology) for providing DMG cultures. We thank L. Meyaard (UMCU), J. Beekman (Regenerative Medicine Center Utrecht) and the Dream3DLAB(Princess Máxima Center for Pediatric Oncology) for providing feedback on the manuscript; A. Miranda-Bedate for pilot PDO sequencing analysis; A. Alemany (Leiden University Medical Center) for insightful advice on behavioral-transcriptomics inference; S. Heijhuurs and P. Hernandez-Lopez (UMCU) for support with mouse experiments; M. Koomen (Hubrecht Institute) for support with head and neck cancer PDO culture; R. Collot (Princess Máxima Center for Pediatric Oncology) for experimental support with revision; and L. C. D. E. Gatti (UMCU) for FACS analysis support. This work was financially supported by the Princess Máxima Center for Pediatric Oncology (grant nos. ZonMW 43400003, VIDI ZonMW 917.11.337 and CRUK OPTIMISTICC C10674/A27140 to J.P. and H.C); by Netherlands Organ-on-Chip Initiative (no. NWO 024.003.001 to J.P. and H.C.); by KWF (grant nos. UU 2014-6790, UU 2015-7601 and UU 2019-12586 to J.K) and nos. UU 2017-11393 to Z.S and J.K). K.K. was the recipient of a VENI grant (no. NWO-ZonMW,016.166.140) from the Netherlands Organization for Scientific Research and was a long-term fellow of the Human Frontier Science Program Organization (no. LT771/2015). A.C.R is supported by an ERC-starting grant 2018 project (no. 804412) and a St. Baldrick’s Robert J. Arceci international innovation award. J.F.D was supported by a Marie Curie Global Fellowship (no. 708310) and a VENI grant (no. 91619088) from the Netherlands Organization for Scientific Research. Funding Information: We thank the Princess Máxima Center for Pediatric Oncology for technical support and the Hubrecht Institute and Zeiss for imaging support and collaboration. All imaging was performed at the Princess Máxima Imaging Center. We thank the Princess Máxima Center Organoid Facility for organoid culture support, the flow cytometry facilities at the Princess Máxima Center and Laboratory of Translational Immunology (UMCU) for cell sorting, the Princess Máxima Center Single Cell Genomics Facility for help with scRNA-seq analysis, Single Cell Discoveries ( https://www.scdiscoveries.com ) for library preparations and the Hartwig Medical Foundation ( https://www.hartwigmedicalfoundation.nl/ ) for sequencing. We also thank HUB for providing PDOs, QVQ for providing NCAM1 nanobodies and D. van Vuurden (Princess Máxima Center for Pediatric Oncology) for providing DMG cultures. We thank L. Meyaard (UMCU), J. Beekman (Regenerative Medicine Center Utrecht) and the Dream3D (Princess Máxima Center for Pediatric Oncology) for providing feedback on the manuscript; A. Miranda-Bedate for pilot PDO sequencing analysis; A. Alemany (Leiden University Medical Center) for insightful advice on behavioral-transcriptomics inference; S. Heijhuurs and P. Hernandez-Lopez (UMCU) for support with mouse experiments; M. Koomen (Hubrecht Institute) for support with head and neck cancer PDO culture; R. Collot (Princess Máxima Center for Pediatric Oncology) for experimental support with revision; and L. C. D. E. Gatti (UMCU) for FACS analysis support. This work was financially supported by the Princess Máxima Center for Pediatric Oncology (grant nos. ZonMW 43400003, VIDI ZonMW 917.11.337 and CRUK OPTIMISTICC C10674/A27140 to J.P. and H.C); by Netherlands Organ-on-Chip Initiative (no. NWO 024.003.001 to J.P. and H.C.); by KWF (grant nos. UU 2014-6790, UU 2015-7601 and UU 2019-12586 to J.K) and nos. UU 2017-11393 to Z.S and J.K). K.K. was the recipient of a VENI grant (no. NWO-ZonMW,016.166.140) from the Netherlands Organization for Scientific Research and was a long-term fellow of the Human Frontier Science Program Organization (no. LT771/2015). A.C.R is supported by an ERC-starting grant 2018 project (no. 804412) and a St. Baldrick’s Robert J. Arceci international innovation award. J.F.D was supported by a Marie Curie Global Fellowship (no. 708310) and a VENI grant (no. 91619088) from the Netherlands Organization for Scientific Research. LAB Publisher Copyright: © 2022, The Author(s).
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