Rxivist logo

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

By Efthymia Papalexi, Eleni Mimitou, Andrew Butler, Samantha Foster, Bernadette Bracken, William M. Mauck, Hans-Hermann Wessels, Bertrand Yeung, Peter Smibert, Rahul Satija

Posted 28 Jun 2020
bioRxiv DOI: 10.1101/2020.06.28.175596

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╬│ 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. ### Competing Interest Statement In the past three years, RS has worked as a consultant for Bristol-Myers Squibb, Regeneron, and Kallyope, and served as an SAB member for ImmunAI and Apollo Life Sciences GmbH. PS is a co-inventor of a patent related to this work. BZY is an employee at BioLegend Inc., which is the exclusive licensee of the New York Genome Center patent application related to this work.

Download data

  • Downloaded 3,388 times
  • Download rankings, all-time:
    • Site-wide: 3,464
    • In genomics: 387
  • Year to date:
    • Site-wide: 1,613
  • Since beginning of last month:
    • Site-wide: 1,492

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)