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Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function.

Publication ,  Journal Article
McCutcheon, SR; Swartz, AM; Brown, MC; Barrera, A; Amador, CM; Siklenka, K; Humayun, L; Isaacs, JM; Reddy, TE; Nair, S; Antonia, S; Gersbach, CA
Published in: bioRxiv
May 1, 2023

The clinical response to adoptive T cell therapies is strongly associated with transcriptional and epigenetic state. Thus, technologies to discover regulators of T cell gene networks and their corresponding phenotypes have great potential to improve the efficacy of T cell therapies. We developed pooled CRISPR screening approaches with compact epigenome editors to systematically profile the effects of activation and repression of 120 transcription factors and epigenetic modifiers on human CD8+ T cell state. These screens nominated known and novel regulators of T cell phenotypes with BATF3 emerging as a high confidence gene in both screens. We found that BATF3 overexpression promoted specific features of memory T cells such as increased IL7R expression and glycolytic capacity, while attenuating gene programs associated with cytotoxicity, regulatory T cell function, and T cell exhaustion. In the context of chronic antigen stimulation, BATF3 overexpression countered phenotypic and epigenetic signatures of T cell exhaustion. CAR T cells overexpressing BATF3 significantly outperformed control CAR T cells in both in vitro and in vivo tumor models. Moreover, we found that BATF3 programmed a transcriptional profile that correlated with positive clinical response to adoptive T cell therapy. Finally, we performed CRISPR knockout screens with and without BATF3 overexpression to define co-factors and downstream factors of BATF3, as well as other therapeutic targets. These screens pointed to a model where BATF3 interacts with JUNB and IRF4 to regulate gene expression and illuminated several other novel targets for further investigation.

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Published In

bioRxiv

DOI

Publication Date

May 1, 2023

Location

United States
 

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McCutcheon, S. R., Swartz, A. M., Brown, M. C., Barrera, A., Amador, C. M., Siklenka, K., … Gersbach, C. A. (2023). Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function. BioRxiv. https://doi.org/10.1101/2023.05.01.538906
McCutcheon, Sean R., Adam M. Swartz, Michael C. Brown, Alejandro Barrera, Christian McRoberts Amador, Keith Siklenka, Lucas Humayun, et al. “Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function.BioRxiv, May 1, 2023. https://doi.org/10.1101/2023.05.01.538906.
McCutcheon SR, Swartz AM, Brown MC, Barrera A, Amador CM, Siklenka K, et al. Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function. bioRxiv. 2023 May 1;
McCutcheon, Sean R., et al. “Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function.BioRxiv, May 2023. Pubmed, doi:10.1101/2023.05.01.538906.
McCutcheon SR, Swartz AM, Brown MC, Barrera A, Amador CM, Siklenka K, Humayun L, Isaacs JM, Reddy TE, Nair S, Antonia S, Gersbach CA. Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function. bioRxiv. 2023 May 1;

Published In

bioRxiv

DOI

Publication Date

May 1, 2023

Location

United States