Characterizing the molecular regulation of inhibitory immune checkpoints with multi-modal single-cell screens.

作者：Efthymia Papalexi, Eleni P. Mimitou, Andrew W. Butler, Samantha Foster, Bernadette Bracken, William M. Mauck, H. Wessels, Y. Hao, Bertrand Z. Yeung, Peter Smibert, R. Satija · 发表于：Nature Genetics · 年份：2021 · DOI：10.1038/s41588-021-00778-2 · 被引用次数：208 · 研究领域：Biology、Medicine

The expression of inhibitory immune checkpoint molecules, such as programmed death-ligand (PD-L)1, is frequently observed in human cancers and can lead to the suppression of T cell–mediated immune responses. Here, we apply expanded CRISPR-compatible (EC)CITE-seq, a technology that combines pooled CRISPR screens with single-cell mRNA and surface protein measurements, to explore the molecular networks that regulate PD-L1 expression. We also develop a computational framework, mixscape, that substantially improves the signal-to-noise ratio in single-cell perturbation screens by identifying and removing confounding sources of variation. Applying these tools, we identify and validate regulators of PD-L1 and leverage our multimodal data to identify both transcriptional and post-transcriptional modes of regulation. Specifically, we discover that the Kelch-like protein KEAP1 and the transcriptional activator NRF2 mediate the upregulation of PD-L1 after interferon (IFN)-γ stimulation. Our results identify a new mechanism for the regulation of immune checkpoints and present a powerful analytical framework for the analysis of multimodal single-cell perturbation screens. ECCITE-seq, which combines pooled CRISPR screens with single-cell mRNA and surface protein measurements, and the computational framework mixscape identify new regulation mechanisms of PD-L1 expression.