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通过正交 CRISPR 筛选鉴定的人类 CD8 T 细胞功能的转录和表观遗传调控因子。

Transcriptional and epigenetic regulators of human CD8 T cell function identified through orthogonal CRISPR screens.

机构信息

Department of Biomedical Engineering, Duke University, Durham, NC, USA.

Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.

出版信息

Nat Genet. 2023 Dec;55(12):2211-2223. doi: 10.1038/s41588-023-01554-0. Epub 2023 Nov 9.


DOI:10.1038/s41588-023-01554-0
PMID:37945901
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10703699/
Abstract

Clinical response to adoptive T cell therapies is associated with the transcriptional and epigenetic state of the cell product. Thus, discovery of regulators of T cell gene networks and their corresponding phenotypes has potential to improve T cell therapies. Here we developed pooled, epigenetic CRISPR screening approaches to systematically profile the effects of activating or repressing 120 transcriptional and epigenetic regulators on human CD8 T cell state. We found that BATF3 overexpression promoted specific features of memory T cells and attenuated gene programs associated with cytotoxicity, regulatory T cell function, and exhaustion. Upon chronic antigen stimulation, BATF3 overexpression countered phenotypic and epigenetic signatures of T cell exhaustion. Moreover, BATF3 enhanced the potency of CAR T cells in both in vitro and in vivo tumor models and programmed a transcriptional profile that correlates with positive clinical response to adoptive T cell therapy. Finally, we performed CRISPR knockout screens that defined cofactors and downstream mediators of the BATF3 gene network.

摘要

过继性 T 细胞疗法的临床应答与细胞产物的转录和表观遗传状态相关。因此,发现 T 细胞基因网络的调节剂及其相应表型有可能改善 T 细胞疗法。在此,我们开发了基于 CRISPR 的混合表观遗传筛选方法,系统地分析了 120 个激活或抑制转录因子和表观遗传因子对人 CD8 T 细胞状态的影响。我们发现,BATF3 的过表达促进了记忆 T 细胞的特定特征,并减弱了与细胞毒性、调节性 T 细胞功能和耗竭相关的基因程序。在慢性抗原刺激下,BATF3 的过表达逆转了 T 细胞耗竭的表型和表观遗传特征。此外,BATF3 增强了 CAR T 细胞在体外和体内肿瘤模型中的效力,并形成了与过继性 T 细胞治疗的阳性临床应答相关的转录特征。最后,我们进行了 CRISPR 敲除筛选,确定了 BATF3 基因网络的辅助因子和下游介质。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/0d88f8a7ea00/41588_2023_1554_Fig16_ESM.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/0d88f8a7ea00/41588_2023_1554_Fig16_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/32f3c866fc88/41588_2023_1554_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/0451455f1d14/41588_2023_1554_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/99fb8c99512a/41588_2023_1554_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/ddf7d56b3cf0/41588_2023_1554_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/9be23abe4805/41588_2023_1554_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/a941fb57f9bb/41588_2023_1554_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/1798e8359294/41588_2023_1554_Fig7_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/ab6b4bd03efb/41588_2023_1554_Fig8_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/68a4333f7735/41588_2023_1554_Fig9_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/54bbbe6538ea/41588_2023_1554_Fig10_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/bbe0c5584ce4/41588_2023_1554_Fig11_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/847359e0f33e/41588_2023_1554_Fig12_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/42a4c73dd600/41588_2023_1554_Fig13_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/c9e35089b630/41588_2023_1554_Fig14_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/7b7f29956082/41588_2023_1554_Fig15_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5c68/10703699/0d88f8a7ea00/41588_2023_1554_Fig16_ESM.jpg

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Transcriptional and epigenetic regulators of human CD8 T cell function identified through orthogonal CRISPR screens.

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[2]
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[2]
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[3]
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[4]
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[5]
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[6]
Gfi1 controls the formation of effector-like CD8 T cells during chronic infection and cancer.

Nat Commun. 2025-5-15

[7]
scMINER: a mutual information-based framework for clustering and hidden driver inference from single-cell transcriptomics data.

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[8]
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[9]
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[10]
Characterization of Rationally Designed CRISPR/Cas9-Based DNA Methyltransferases with Distinct Methyltransferase and Gene Silencing Activities in Human Cell Lines and Primary Human T Cells.

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本文引用的文献

[1]
Modular pooled discovery of synthetic knockin sequences to program durable cell therapies.

Cell. 2023-9-14

[2]
Runx3-overexpression cooperates with ex vivo AKT inhibition to generate receptor-engineered T cells with better persistence, tumor-residency, and antitumor ability.

J Immunother Cancer. 2023-2

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Nature. 2023-3

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Nat Med. 2022-9

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