The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel.
Core Research Facility, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel.
Nat Commun. 2023 Oct 9;14(1):6295. doi: 10.1038/s41467-023-41792-8.
Genetic engineering of immune cells has opened new avenues for improving their functionality but it remains a challenge to pinpoint which genes or combination of genes are the most beneficial to target. Here, we conduct High Multiplicity of Perturbations and Cellular Indexing of Transcriptomes and Epitopes (HMPCITE-seq) to find combinations of genes whose joint targeting improves antigen-presenting cell activity and enhances their ability to activate T cells. Specifically, we perform two genome-wide CRISPR screens in bone marrow dendritic cells and identify negative regulators of CD86, that participate in the co-stimulation programs, including Chd4, Stat5b, Egr2, Med12, and positive regulators of PD-L1, that participate in the co-inhibitory programs, including Sptlc2, Nckap1l, and Pi4kb. To identify the genetic interactions between top-ranked genes and find superior combinations to target, we perform high-order Perturb-Seq experiments and we show that targeting both Cebpb and Med12 results in a better phenotype compared to the single perturbations or other combinations of perturbations.
免疫细胞的基因工程为提高其功能开辟了新途径，但确定哪些基因或基因组合最有利于靶向仍然是一个挑战。在这里，我们进行了高多重性的扰动和细胞转录组和表位的索引（HMPCITE-seq），以找到联合靶向提高抗原呈递细胞活性并增强其激活 T 细胞能力的基因组合。具体来说，我们在骨髓树突状细胞中进行了两次全基因组 CRISPR 筛选，并鉴定了 CD86 的负调控因子，这些负调控因子参与共刺激程序，包括 Chd4、Stat5b、Egr2、Med12，以及参与共抑制程序的 PD-L1 的正调控因子，包括 Sptlc2、Nckap1l 和 Pi4kb。为了鉴定排名靠前的基因之间的遗传相互作用，并找到更优的靶向组合，我们进行了高阶 Perturb-Seq 实验，结果表明，与单一扰动或其他扰动组合相比，靶向 Cebpb 和 Med12 可产生更好的表型。
