Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens

Efthymia Papalexi, Eleni P. Mimitou, Andrew W. Butler, Samantha Foster, Bernadette Bracken, William M. Mauck, Hans Hermann Wessels, Yuhan Hao, Bertrand Z. Yeung, Peter Smibert, Rahul Satija

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)322-331
Number of pages10
JournalNature Genetics
Issue number3
StatePublished - Mar 2021

ASJC Scopus subject areas

  • Genetics


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