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bioRxiv · 10.1101/2020.06.28.175596

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

Papalexi, E.·Mimitou, E.·Butler, A. W.·Foster, S.·Bracken, B.·Mauck, W. M.·Wessels, H.-H.·Yeung, B. Z.·Smibert, P.·Satija, R.
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Abstract

The expression of inhibitory immune checkpoint molecules such as PD-L1 is frequently observed in human cancers and can lead to the suppression of T cell-mediated immune responses. Here we apply ECCITE-seq, a technology which 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 multi-modal data to identify both transcriptional and post-transcriptional modes of regulation. In particular, we discover that the kelch-like protein KEAP1 and the transcriptional activator NRF2, mediate levels of PD-L1 upregulation after IFN{gamma} stimulation. Our results identify a novel mechanism for the regulation of immune checkpoints and present a powerful analytical framework for the analysis of multi-modal single-cell perturbation screens.

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Papalexi, E., Mimitou, E., Butler, A. W., Foster, S., Bracken, B., Mauck, W. M., Wessels, H.-H., Yeung, B. Z., Smibert, P., Satija, R.. 2020-06-28. Characterizing the molecular regulation of inhibitory immune checkpoints with multi-modal single-cell screens. https://doi.org/10.1101/2020.06.28.175596

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