Deletion of SNX9 alleviates CD8 T cell exhaustion for effective cellular cancer immunotherapy

Trefny, Marcel P.; Kirchhammer, Nicole; Maur, Priska Auf der; Natoli, Marina; Schmid, Dominic; Germann, Markus; Rodriguez, Laura Fernandez; Herzig, Petra; Lötscher, Jonas; Akrami, Maryam; Stinchcombe, Jane C.; Stanczak, Michal A.; Zingg, Andreas; Buchi, Mélanie; Roux, Julien; Marone, Romina; Don, Leyla; Lardinois, Didier; Wiese, Mark; Jeker, Lukas T.; Bentires‐Alj, Mohamed; Rossy, Jérémie; Thommen, Daniela S.; Griffiths, Gillian M.; Läubli, Heinz; Hess, Christoph; Zippelius, Alfred

doi:10.1038/s41467-022-35583-w

Cited by 39 publications

(26 citation statements)

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“…Spontaneous NFkB activation in SKM-BBz CAR-T cells (Figure 4D and Table 1) may explain NR4A upregulation, as there is a report that NR4A molecules are upregulated in macrophages in response to NFkB signaling. 30 Since SKM-BBz CAR-T cells also express other exhaustion-related genes such as SNX9 31 and DNMT3A 32 at the same level as SKM-28z CAR-T cells (Figure 5C), we speculate that SKM-BBz CAR-T cells may be in an early stage of exhaustion. In the chronic viral infection model, exhausted T cells are divided into four sequential stages; progenitor 1 (Tex prog1 ), progenitor 2 (Tex prog2 ), intermediate (Tex int ), and terminal (Tex term ).…”

Section: Discussionmentioning

confidence: 88%

Novel chimeric antigen receptor‐expressing T cells targeting the malignant mesothelioma‐specific antigen sialylated HEG1

Kouro,

Higashijima,

Horaguchi

et al. 2024

Intl Journal of Cancer

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The selection of highly specific target antigens is critical for the development of clinically efficient and safe chimeric antigen receptors (CARs). In search of diagnostic marker for malignant mesothelioma (MM), we have established SKM9‐2 monoclonal antibody (mAb) which recognizes a MM‐specific molecule, sialylated Protein HEG homolog 1 (HEG1), with high specificity and sensitivity. In this study, to develop a novel therapeutic approach against MM, we generated SKM9‐2 mAb‐derived CARs that included the CD28 (SKM‐28z) or 4‐1BB (SKM‐BBz) costimulatory domain. SKM‐28z CAR‐T cells showed continuous growth and enhanced Tim‐3, LAG‐3, and PD‐1 expression in vitro, which might be induced by tonic signaling caused by self‐activation; however, these phenotypes were not observed in SKM‐BBz CAR‐T cells. In addition, SKM‐BBz CAR‐T cells exhibited slightly stronger in vitro killing activity against MM cell lines than SKM‐28z CAR‐T cells. More importantly, only SKM‐BBz CAR‐T cells, but not SKM‐28z CAR‐T cells, significantly inhibited tumor growth in vivo in a MM cell line xenograft mouse model. Gene expression profiling and reporter assays revealed differential signaling pathway activation; in particular, SKM‐BBz CAR‐T cells exhibited enhanced NF‐kB signaling and reduced NFAT activation. In addition, SKM‐BBz CAR‐T cells showed upregulation of early memory markers, such as TCF7 and CCR7, as well as downregulation of pro‐apoptotic proteins, such as BAK1 and BID, which may be associated with phenotypical and functional differences between SKM‐BBz and SKM‐28z CAR‐T cells. In conclusion, we developed novel SKM9‐2‐derived CAR‐T cells with the 4‐1BB costimulatory domain, which could provide a promising therapeutic approach against refractory MM.

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Section: Discussionmentioning

confidence: 88%

Novel chimeric antigen receptor‐expressing T cells targeting the malignant mesothelioma‐specific antigen sialylated HEG1

Kouro,

Higashijima,

Horaguchi

et al. 2024

Intl Journal of Cancer

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“…Genes that cluster together with such may have an effect on T cell persistence and exhaustion ( Fig 5E ). For example, it was just recently shown that SNX9 deletion alleviates T cell exhaustion 75 . Detailed analysis of TFs that are strongly associated with driving exhaustion ( RUNX1 and PRMD1 ), as well as being a marker for tumor-reactive TILs ( SOX4 ) visualizes their impact on T cell differentiation towards the exhausted state ( Fig 5G ).…”

Section: Resultsmentioning

confidence: 99%

Multimodal single-cell profiling of T cell specificity and reactivity in lung cancer

Bieberich,

Vazquez-Lombardi,

Jin

et al. 2023

Preprint

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SUMMARYAdoptive transfer of autologous tumor-infiltrating lymphocyte T cells (TILs) offers one of the most promising approaches for cancer immunotherapy. However, high variability in patient responses highlight the need for an enhanced understanding of the transcriptional phenotypes of TILs and reactivity of their T cell receptors (TCR). Here, we employ single-cell multiomics approaches and TCR functional screening to investigate TILs from treatment-naive non-small cell lung cancer patients. This comprehensive analysis integrates scRNA-seq, scTCR-seq, and scATAC-seq, enabling a high-resolution examination of TILs within lung cancer tissue, as well as the adjacent non-tumor tissue. We apply a cellular functional screening platform to identify reactive TCRs that represent >1,000 TILs and have specificity towards a multitude of targets, including primary tumor cells, neoantigens, tumor-associated antigens, and viral antigens. Tumor-reactive TILs were primarily associated with dysfunctional phenotypes, whereas viral antigen-reactive TCRs were found in effector phenotype clusters. Key marker genes were identified and used to construct a tumor or viral reactivity score. Comparing clones shared in tumor and non-tumor tissue, a higher fraction of exhausted cells was observed in the tumor tissue, whereas non-tumor adjacent tissue possessed more effector cells, thus providing insight into potential sources for therapeutic T cells. Elucidating the specific T cell populations within TILs and their associated TCRs may support strategies to enhance the efficacy of TIL-based therapies.Graphical AbstractMultimodal single cell profiling and reactivity testing of TILs(A) CD8+T cells of treatment naive non-small cell lung cancer patients and adjacent lung tissue were isolated by fluorescence-activated cell sorting (FACS) and were then subjected to scRNA-seq + scTCR-seq or scATAC-seq. (B) TCRs were functionally screened using a cellular platform (TnT cells) and target cells (tumor cells, antigen-pulsed antigen-presenting cells, PBMCs) by flow cytometry and deep sequencing. (C) scRNA-seq + scATAC-seq allowed trajectory inference of transcription factors and genes along pseudotime. (D) Gene scores for tumor- and virus-reactivity were developed by combining functional reactivity and transcriptomic profiling for each CD8+T cell. (E) TIL scRNA-seq pre and post IL-2 treatment in tumor suspension displayed as alluvial plot shows change of clonal cell state composition.

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“…While some statistical analysis issues can be addressed by increasing the selective pressure or increasing the number of cells and replicates, these solutions can be challenging or infeasible for in vivo screens. For this reason, it is very common to see high‐profile studies opt to use a simple fold change to determine hits rather than use any of the CRISPR analysis strategies available 17,37,126,127 . Unfortunately, this simple method will fall short when analyzing any screen design more complicated than screen‐vs‐control.…”

Section: Conclusion and Future Directionmentioning

confidence: 99%

“…For this reason, it is very common to see high-profile studies opt to use a simple fold change to determine hits rather than use any of the CRISPR analysis strategies available. 17,37,126,127 Unfortunately, this simple method will fall short when analyzing any screen design more complicated than screen-vs-control. Another major bottleneck with screens in cancer immunology is the high clone dropout of in vivo CRISPR screens.…”

Section: Representative Challenges In Crispr Screening For Future Opt...mentioning

confidence: 99%

Applications of CRISPR technology in cellular immunotherapy

Zhou

Renauer

Zhou

et al. 2023

Immunological Reviews

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SummaryCRISPR technology has transformed multiple fields, including cancer and immunology. CRISPR‐based gene editing and screening empowers direct genomic manipulation of immune cells, opening doors to unbiased functional genetic screens. These screens aid in the discovery of novel factors that regulate and reprogram immune responses, offering novel drug targets. The engineering of immune cells using CRISPR has sparked a transformation in the cellular immunotherapy field, resulting in a multitude of ongoing clinical trials. In this review, we discuss the development and applications of CRISPR and related gene editing technologies in immune cells, focusing on functional genomics screening, gene editing‐based cell therapies, as well as future directions in this rapidly advancing field.

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Deletion of SNX9 alleviates CD8 T cell exhaustion for effective cellular cancer immunotherapy

Cited by 39 publications

References 100 publications

Novel chimeric antigen receptor‐expressing T cells targeting the malignant mesothelioma‐specific antigen sialylated HEG1

Novel chimeric antigen receptor‐expressing T cells targeting the malignant mesothelioma‐specific antigen sialylated HEG1

Multimodal single-cell profiling of T cell specificity and reactivity in lung cancer

Applications of CRISPR technology in cellular immunotherapy

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