Uncovering the mode of action of engineered T cells in patient cancer organoids

Johanna F. Dekkers; Maria Alieva; Astrid Cleven; Farid Keramati; Amber K.L. Wezenaar; Esmée J. van Vliet; Jens Puschhof; Peter Brazda; Inez Johanna; Angelo D. Meringa; Heggert G. Rebel; Maj Britt Buchholz; Mario Barrera Román; Amber L. Zeeman; Sam de Blank; Domenico Fasci; Maarten H. Geurts; Annelisa M. Cornel; Else Driehuis; Rosemary Millen; Trudy Straetemans; Mara J.T. Nicolasen; Tineke Aarts-Riemens; Hendrikus C.R. Ariese; Hannah R. Johnson; Ravian L. van Ineveld; Froso Karaiskaki; Oded Kopper; Yotam E. Bar-Ephraim; Kai Kretzschmar; Alexander M.M. Eggermont; Stefan Nierkens; Ellen J. Wehrens; Henk G. Stunnenberg; Hans Clevers; Jürgen Kuball; Zsolt Sebestyen; Anne C. Rios

doi:10.1038/s41587-022-01397-w

Uncovering the mode of action of engineered T cells in patient cancer organoids

Johanna F. Dekkers, Maria Alieva, Astrid Cleven, Farid Keramati, Amber K.L. Wezenaar, Esmée J. van Vliet, Jens Puschhof, Peter Brazda, Inez Johanna, Angelo D. Meringa, Heggert G. Rebel, Maj Britt Buchholz, Mario Barrera Román, Amber L. Zeeman, Sam de Blank, Domenico Fasci, Maarten H. Geurts, Annelisa M. Cornel, Else Driehuis, Rosemary MillenTrudy Straetemans, Mara J.T. Nicolasen, Tineke Aarts-Riemens, Hendrikus C.R. Ariese, Hannah R. Johnson, Ravian L. van Ineveld, Froso Karaiskaki, Oded Kopper, Yotam E. Bar-Ephraim, Kai Kretzschmar, Alexander M.M. Eggermont, Stefan Nierkens, Ellen J. Wehrens, Henk G. Stunnenberg, Hans Clevers, Jürgen Kuball, Zsolt Sebestyen, Anne C. Rios^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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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 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.

Original language	English
Pages (from-to)	60-69
Number of pages	10
Journal	Nature Biotechnology
Volume	41
Issue number	1
Early online date	25 Jul 2022
DOIs	https://doi.org/10.1038/s41587-022-01397-w
Publication status	Published - Jan 2023

Keywords

Humans
Immunotherapy/methods
Neoplasms/genetics
Organoids/pathology
T-Lymphocytes

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s41587-022-01397-wFinal published version, 11.2 MBLicence: CC BY

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Dekkers, J. F., Alieva, M., Cleven, A., Keramati, F., Wezenaar, A. K. L., van Vliet, E. J., Puschhof, J., Brazda, P., Johanna, I., Meringa, A. D., Rebel, H. G., Buchholz, M. B., Barrera Román, M., Zeeman, A. L., de Blank, S., Fasci, D., Geurts, M. H., Cornel, A. M., Driehuis, E., ... Rios, A. C. (2023). Uncovering the mode of action of engineered T cells in patient cancer organoids. Nature Biotechnology, 41(1), 60-69. https://doi.org/10.1038/s41587-022-01397-w

@article{be85c565cf274a899d577ca0cddc7f5f,

title = "Uncovering the mode of action of engineered T cells in patient cancer organoids",

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 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 {\textquoteleft}super engager{\textquoteright} 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.",

keywords = "Humans, Immunotherapy/methods, Neoplasms/genetics, Organoids/pathology, T-Lymphocytes",

author = "Dekkers, {Johanna F.} and Maria Alieva and Astrid Cleven and Farid Keramati and Wezenaar, {Amber K.L.} and {van Vliet}, {Esm{\'e}e J.} and Jens Puschhof and Peter Brazda and Inez Johanna and Meringa, {Angelo D.} and Rebel, {Heggert G.} and Buchholz, {Maj Britt} and {Barrera Rom{\'a}n}, Mario and Zeeman, {Amber L.} and {de Blank}, Sam and Domenico Fasci and Geurts, {Maarten H.} and Cornel, {Annelisa M.} and Else Driehuis and Rosemary Millen and Trudy Straetemans and Nicolasen, {Mara J.T.} and Tineke Aarts-Riemens and Ariese, {Hendrikus C.R.} and Johnson, {Hannah R.} and {van Ineveld}, {Ravian L.} and Froso Karaiskaki and Oded Kopper and Bar-Ephraim, {Yotam E.} and Kai Kretzschmar and Eggermont, {Alexander M.M.} and Stefan Nierkens and Wehrens, {Ellen J.} and Stunnenberg, {Henk G.} and Hans Clevers and J{\"u}rgen Kuball and Zsolt Sebestyen and Rios, {Anne C.}",

note = "Funding Information: We thank the Princess M{\'a}xima 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 M{\'a}xima Imaging Center. We thank the Princess M{\'a}xima Center Organoid Facility for organoid culture support, the flow cytometry facilities at the Princess M{\'a}xima Center and Laboratory of Translational Immunology (UMCU) for cell sorting, the Princess M{\'a}xima 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 M{\'a}xima Center for Pediatric Oncology) for providing DMG cultures. We thank L. Meyaard (UMCU), J. Beekman (Regenerative Medicine Center Utrecht) and the Dream3DLAB(Princess M{\'a}xima 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 M{\'a}xima 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 M{\'a}xima 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{\textquoteright}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 M{\'a}xima 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 M{\'a}xima Imaging Center. We thank the Princess M{\'a}xima Center Organoid Facility for organoid culture support, the flow cytometry facilities at the Princess M{\'a}xima Center and Laboratory of Translational Immunology (UMCU) for cell sorting, the Princess M{\'a}xima 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 M{\'a}xima Center for Pediatric Oncology) for providing DMG cultures. We thank L. Meyaard (UMCU), J. Beekman (Regenerative Medicine Center Utrecht) and the Dream3D (Princess M{\'a}xima 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 M{\'a}xima 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 M{\'a}xima 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{\textquoteright}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: {\textcopyright} 2022, The Author(s).",

year = "2023",

month = jan,

doi = "10.1038/s41587-022-01397-w",

language = "English",

volume = "41",

pages = "60--69",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

number = "1",

}

Dekkers, JF, Alieva, M, Cleven, A, Keramati, F, Wezenaar, AKL, van Vliet, EJ, Puschhof, J, Brazda, P, Johanna, I, Meringa, AD, Rebel, HG, Buchholz, MB, Barrera Román, M, Zeeman, AL, de Blank, S, Fasci, D, Geurts, MH, Cornel, AM, Driehuis, E, Millen, R, Straetemans, T, Nicolasen, MJT, Aarts-Riemens, T, Ariese, HCR, Johnson, HR, van Ineveld, RL, Karaiskaki, F, Kopper, O, Bar-Ephraim, YE, Kretzschmar, K, Eggermont, AMM, Nierkens, S, Wehrens, EJ, Stunnenberg, HG, Clevers, H, Kuball, J , Sebestyen, Z & Rios, AC 2023, 'Uncovering the mode of action of engineered T cells in patient cancer organoids', Nature Biotechnology, vol. 41, no. 1, pp. 60-69. https://doi.org/10.1038/s41587-022-01397-w

TY - JOUR

T1 - Uncovering the mode of action of engineered T cells in patient cancer organoids

AU - Dekkers, Johanna F.

AU - Alieva, Maria

AU - Cleven, Astrid

AU - Keramati, Farid

AU - Wezenaar, Amber K.L.

AU - van Vliet, Esmée J.

AU - Puschhof, Jens

AU - Brazda, Peter

AU - Johanna, Inez

AU - Meringa, Angelo D.

AU - Rebel, Heggert G.

AU - Buchholz, Maj Britt

AU - Barrera Román, Mario

AU - Zeeman, Amber L.

AU - de Blank, Sam

AU - Fasci, Domenico

AU - Geurts, Maarten H.

AU - Cornel, Annelisa M.

AU - Driehuis, Else

AU - Millen, Rosemary

AU - Straetemans, Trudy

AU - Nicolasen, Mara J.T.

AU - Aarts-Riemens, Tineke

AU - Ariese, Hendrikus C.R.

AU - Johnson, Hannah R.

AU - van Ineveld, Ravian L.

AU - Karaiskaki, Froso

AU - Kopper, Oded

AU - Bar-Ephraim, Yotam E.

AU - Kretzschmar, Kai

AU - Eggermont, Alexander M.M.

AU - Nierkens, Stefan

AU - Wehrens, Ellen J.

AU - Stunnenberg, Henk G.

AU - Clevers, Hans

AU - Kuball, Jürgen

AU - Sebestyen, Zsolt

AU - Rios, Anne C.

N1 - 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).

PY - 2023/1

Y1 - 2023/1

N2 - 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 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.

AB - 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 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.

KW - Humans

KW - Immunotherapy/methods

KW - Neoplasms/genetics

KW - Organoids/pathology

KW - T-Lymphocytes

UR - http://www.scopus.com/inward/record.url?scp=85134661174&partnerID=8YFLogxK

U2 - 10.1038/s41587-022-01397-w

DO - 10.1038/s41587-022-01397-w

M3 - Article

C2 - 35879361

AN - SCOPUS:85134661174

SN - 1087-0156

VL - 41

SP - 60

EP - 69

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 1

ER -

Uncovering the mode of action of engineered T cells in patient cancer organoids

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