Spatial CRISPR genomics identifies regulators of the tumor microenvironment

Dhainaut, Maxime; Rose, Samuel A.; Aktürk, Güray; Wroblewska, Aleksandra; Nielsen, Sebastian R.; Park, Eun Sook; Buckup, Mark; Roudko, Vladimir; Pia, Luisanna; Sweeney, Robert E.; Bérichel, Jessica Le; Wilk, C. Matthias; Bektesevic, Anela; Lee, Brian H; Bhardwaj, Nina; Rahman, Adeeb; Baccarini, Alessia; Gnjatic, Sacha; Pe’er, Dana; Mérad, Miriam; Brown, Brian D.

doi:10.1016/j.cell.2022.02.015

Cited by 134 publications

(103 citation statements)

References 63 publications

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“…Cancer GEMMs are a natural complement to analysis of human tumor samples because they provide a highly physiological and tractable experimental system for deep mechanistic study of the regulators of the tumor-immune microenvironment (Connolly et al, 2022; Dhainaut et al, 2022; Wroblewska et al, 2018). However, substantial method development is required to perform high-dimensional spatial characterization of the tumor-immune interactions in these models.…”

Section: Discussionmentioning

confidence: 99%

“…One challenge with this study was that the antibody panel we qualified was largely focused on phenotyping effector T-cell states, but additional antibodies will be needed to adequately characterize other important T-cell populations (i.e., resident memory, T follicular helper cells) as well as the diversity of tumor-associated myeloid cells that can be monitored using scRNA-seq methods (Leader et al, 2021). Use of emerging spatial transcriptomics methods may soon facilitate deeper phenotyping of some immune cell states and expand the range of cytokines and chemokines that can be simultaneously profiled (Dhainaut et al, 2022). Another challenge was that the MHC-peptide tetramers that are commonly used to identify antigen-specific T cells in FACS analysis are not active in FFPE tissue sections, thus, we were not able to detect and quantify the CD8 T cells that are specific for SIIN and SIY CD8 T-cell antigens.…”

Section: Limitations Of This Studymentioning

confidence: 99%

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Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma

Gaglia

Burger

Ritch

et al. 2022

Preprint

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Lymphocytes play a key role in immune surveillance of tumors, but our understanding of the spatial organization and physical interactions that facilitate lymphocyte anti-cancer functions is limited. Here, we used multiplexed imaging, quantitative spatial analysis, and machine learning to create high-definition maps of tumor-bearing lung tissues from a Kras/p53 (KP) mouse model and human resections. Networks of directly interacting lymphocytes (lymphonets) emerge as a distinctive feature of the anti-cancer immune response. Lymphonets nucleate from small T-cell clusters and incorporate B cells with increasing size. CXCR3-mediated trafficking modulates lymphonet size and number, but neoantigen expression directs intratumoral localization. Lymphonets preferentially harbor TCF1+/PD1+ progenitor CD8 T cells involved in responses to immune checkpoint blockade (ICB). Upon treatment of mice with ICB therapy or a neoantigen-targeted vaccine, lymphonets retain progenitor and gain cytotoxic CD8 T-cell populations, likely via progenitor differentiation. These data show that lymphonets create a spatial environment supportive of CD8 T-cell anti-tumor responses.

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Section: Discussionmentioning

confidence: 99%

Section: Limitations Of This Studymentioning

confidence: 99%

Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma

Gaglia

Burger

Ritch

et al. 2022

Preprint

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“…The characteristics of tumor cells with random mutations and their surrounding peritumoral stromal cells and inflammatory cells have been elucidated by applying spatial gene expression analysis technology, Visium, with CRISPR screening; however, this system screened the random mutation in the tumor cells and analyzed the expression profiles of stromal cells, i.e. not screened with random mutation in the stromal cells (Dhainaut et al, 2022). These techniques can analyze single supporting cells with randomly mutated tumors with CRISPR screening; however, it is difficult to isolate living supporting cells based on the distance and position of the tumors.…”

Section: Discussionmentioning

confidence: 99%

Indirect CRISPR screening with photoconversion revealed key factors of drug resistance with cell–cell interactions

Sugita

Onishi

Nakayama

et al. 2022

Preprint

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Comprehensive screenings to clarify indirect cell–cell interactions, such as those in the tumor microenvironment, especially comprehensive assessments of supporting cells' effects, are challenging. Therefore, in this study, indirect CRISPR screening for drug resistance with cell–cell interactions was invented. The photoconvertible fluorescent protein Dendra2 was inducted to determine the drug resistance responsible factors of supporting cells with CRISPR screenings. Random mutated supporting cells co-cultured with leukemic cells induced drug resistance with cell–cell interactions. Supporting cells responsible for drug resistance were isolated with green-to-red photoconversion, and candidate genes were identified. Knocking out C9orf89, MAGI2, MLPH, or RHBDD2 in supporting cells reduced the ratio of apoptosis of cancer cells. In addition, the low expression of RHBDD2 in supporting cells, specifically fibroblasts, of clinical pancreatic cancer showed a shortened prognosis, and a negative correlation with CXCL12 was observed. Indirect CRISPR screening was established to isolate the responsible elements of cell–cell interactions. This screening method could reveal new mechanisms in all kinds of cell–cell interactions by revealing live phenotype-inducible cells, and it could be a new platform for discovering new targets of drugs for conventional chemotherapies.

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“…Moreover, tumour microenvironment is the most important arena of oncology research. In this main, CRISPR/Cas pro-codon library aid the analysis of tumour microenvironment by silencing a series of genes in a mouse model and revealing how each gene influences tumor growth, immune composition and histopathology [ 325 ]. Its robust knockout and knock-in technology resolved the central dogma of immunosuppression and showed a relation between loss of function genes and tumour microenvironment.…”

Section: Future Perspectives and Conclusionmentioning

confidence: 99%

Nanomaterial-assisted CRISPR gene-engineering – A hallmark for triple-negative breast cancer therapeutics advancement

Farheen¹,

Hosmane²,

Zhao³

et al. 2022

Materials Today Bio

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Spatial CRISPR genomics identifies regulators of the tumor microenvironment

Cited by 134 publications

References 63 publications

Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma

Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma

Indirect CRISPR screening with photoconversion revealed key factors of drug resistance with cell–cell interactions

Nanomaterial-assisted CRISPR gene-engineering – A hallmark for triple-negative breast cancer therapeutics advancement

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