Leveraging Single-Cell Sequencing for Chimeric Antigen Receptor T Cell Therapies

Castellanos-Rueda, Rocío; Roberto, Raphaël B. Di; Schlatter, Fabrice S.; Reddy, Sai T.

doi:10.1016/j.tibtech.2021.03.005

Cited by 24 publications

(22 citation statements)

References 79 publications

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“…Rather, to obtain multi-dimensional and translatable CAR functional profiles, primary T cells and RNA-seq offer a powerful alternative. The use of scRNA-seq in particular is fast becoming an important tool in the characterization of CAR T cells before and during their clinical evaluation [9], and it is especially suited for the screening of a pooled library of engineered cells. Recent work by Roth et al demonstrated how scRNA-seq can be used to capture the transcriptome and the corresponding identity of a library member in engineered cells [31].…”

Section: Discussionmentioning

confidence: 99%

“…Recent advances in molecular immune profiling, such as single-cell sequencing and transcriptome analysis, are contributing important quantitative insights on CAR T cell-mediated responses and patient outcomes [9]. By going beyond methods for standard cell phenotyping (e.g., detection of surface markers by flow cytometry), transcriptional phenotyping can uncover gene expression patterns and metabolic pathways, or when used to track therapy progression and outcomes, they can help to identify predictors of therapeutic efficacy.…”

Section: Introductionmentioning

confidence: 99%

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speedingCARs: accelerating the engineering of CAR T cells by signaling domain shuffling and single-cell sequencing

Roberto

Castellanos-Rueda

Schlatter

et al. 2021

Preprint

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Chimeric antigen receptors (CARs) consist of an extracellular antigen-binding region fused to intracellular signaling domains, thus enabling customized T cell responses against target cells. Due to the low-throughput process of systematically designing and functionally testing CARs, only a small set of immune signaling domains have been thoroughly explored, despite their major role in T cell activation, effector function and persistence. Here, we present speedingCARs, an integrated method for engineering CAR T cells by signaling domain shuffling and functional screening by single-cell sequencing. Leveraging the inherent modularity of natural signaling domains, we generated a diverse library of 180 unique CAR variants, which were genomically integrated into primary human T cells by CRISPR-Cas9. Functional and pooled screening of the CAR T cell library was performed by co-culture with tumor cells, followed by single-cell RNA sequencing (scRNA-seq) and single-cell CAR sequencing (scCAR-seq), thus enabling high-throughput profiling of multi-dimensional cellular responses. This led to the discovery of several CAR variants that retained the ability to kill tumor cells, while also displaying diverse transcriptional signatures and T cell phenotypes. In summary, speedingCARs substantially expands and characterizes the signaling domain combinations suited for CAR design and supports the engineering of next-generation T cell therapies.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

speedingCARs: accelerating the engineering of CAR T cells by signaling domain shuffling and single-cell sequencing

Roberto

Castellanos-Rueda

Schlatter

et al. 2021

Preprint

Self Cite

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“…Artificial intelligence scrutiny of bulk, single-cell, and spatially resolved gene expression data of CAR-T targets [ 89 ] have provided a large-scale identification and validation of cell states and multicellular communities from multiple cancer types. By analyzing these patterns, distinct multicellular communities were discovered that showed unexpectedly strong conservation.…”

Section: Cancer-associated Immune Cell Populationsmentioning

confidence: 99%

Cancer-Homing CAR-T Cells and Endogenous Immune Population Dynamics

Guerra

Pietro

Basile

et al. 2021

IJMS

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Chimeric antigen receptor (CAR) therapy is based on patient blood-derived T cells and natural killer cells, which are engineered in vitro to recognize a target antigen in cancer cells. Most CAR-T recognize target antigens through immunoglobulin antigen-binding regions. Hence, CAR-T cells do not require the major histocompatibility complex presentation of a target peptide. CAR-T therapy has been tremendously successful in the treatment of leukemias. On the other hand, the clinical efficacy of CAR-T cells is rarely detected against solid tumors. CAR-T-cell therapy of cancer faces many hurdles, starting from the administration of engineered cells, wherein CAR-T cells must encounter the correct chemotactic signals to traffic to the tumor in sufficient numbers. Additional obstacles arise from the hostile environment that cancers provide to CAR-T cells. Intense efforts have gone into tackling these pitfalls. However, we argue that some CAR-engineering strategies may risk missing the bigger picture, i.e., that a successful CAR-T-cell therapy must efficiently intertwine with the complex and heterogeneous responses that the body has already mounted against the tumor. Recent findings lend support to this model.

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“…Auch für die Erforschung des Immunsystems, etwa im Zusammenhang mit neuartigen CAR-T-Zell-Therapien 45 gegen Krebs (siehe Fehse, Kap. 6), können Einzelzelldaten genutzt werden (Castellanos-Rueda et al, 2021).…”

Section: Einführung Und Anwendungspotenzialeunclassified

9. Genome-Editing und Einzelzellanalyse: Neue Methoden und ihre Implikationen für Forschung, Anwendung und Gesellschaft

Walter¹,

Reich²,

Marx-Stölting³

et al. 2021

Fünfter Gentechnologiebericht

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Leveraging Single-Cell Sequencing for Chimeric Antigen Receptor T Cell Therapies

Cited by 24 publications

References 79 publications

speedingCARs: accelerating the engineering of CAR T cells by signaling domain shuffling and single-cell sequencing

speedingCARs: accelerating the engineering of CAR T cells by signaling domain shuffling and single-cell sequencing

Cancer-Homing CAR-T Cells and Endogenous Immune Population Dynamics

9. Genome-Editing und Einzelzellanalyse: Neue Methoden und ihre Implikationen für Forschung, Anwendung und Gesellschaft

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