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

Autor:	McCutcheon SR; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA., Swartz AM; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA., Brown MC; Department of Neurosurgery, Duke University School of Medicine, Durham, NC 27710, USA., Barrera A; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA.; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA., Amador CM; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA.; Department of Pharmacology and Cancer Biology, Durham, NC 27710, USA., Siklenka K; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA.; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA., Humayun L; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA., Isaacs JM; Duke Cancer Institute Center for Cancer Immunotherapy, Duke University School of Medicine, Durham, NC 27710, USA., Reddy TE; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA.; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA., Nair S; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA.; Duke Cancer Institute Center for Cancer Immunotherapy, Duke University School of Medicine, Durham, NC 27710, USA.; Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA., Antonia S; Duke Cancer Institute Center for Cancer Immunotherapy, Duke University School of Medicine, Durham, NC 27710, USA., Gersbach CA; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA.; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA.
Jazyk:	angličtina
Zdroj:	BioRxiv : the preprint server for biology [bioRxiv] 2023 May 01. Date of Electronic Publication: 2023 May 01.
DOI:	10.1101/2023.05.01.538906
Abstrakt:	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. Competing Interests: Conflict of Interest S.R.M. and C.A.G. are named inventors on patent applications related to epigenome engineering technologies in primary human T cells. S.R.M. is a consultant for Tune Therapeutics. C.A.G. is a co-founder of Tune Therapeutics and Locus Biosciences, and is an advisor to Sarepta Therapeutics.
Databáze:	MEDLINE
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