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

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 T cell-mediated responses. Here, we apply expanded CRISPR-compatible (EC)CITE-seq, a technology that combines pooled CRISPR screens with single-cell mRNA surface protein measurements, explore molecular networks regulate PD-L1 expression. We also develop computational framework, mixscape, substantially improves signal-to-noise ratio perturbation by identifying removing confounding sources variation. Applying these tools, identify validate regulators leverage our multimodal data both transcriptional post-transcriptional modes regulation. Specifically, discover Kelch-like KEAP1 activator NRF2 mediate upregulation after interferon (IFN)-? stimulation. Our results new mechanism for regulation checkpoints present powerful analytical framework analysis screens.