Journal Article

Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion

Bernatchez, Chantale, Melms, Johannes C., Luoma, Adrienne M., Geiger-Schuller, Kathryn R., Thakore, Pratiksha I., Johnson, Bruce E., Frangieh, Chris J., Ager, Casey R., Regev, Aviv, Rogava, Meri, Ho, Patricia, Rozenblatt-Rosen, Orit, Cleary, Brian, Jerby-Arnon, Livnat, Cuoco, Michael S., Hovey, Lila, Wucherpfennig, Kai W., Izar, Benjamin, Rotem, Asaf, Malu, Shruti, Schadendorf, Dirk, Zhao, Maryann

2021

Overview

Resistance to immune checkpoint inhibitors (ICR) is a key challenge in cancer therapy. To elucidate underlying mechanisms, we developed Perturb-CITE-seq, enabling pooled CRISPR-Cas9 perturbations with single-cell transcriptome and protein read-outs. In patient-derived melanoma cells and autologous tumor infiltrating lymphocyte (TIL) co-cultures, we profiled transcriptomes and 20 proteins in ~218,000 cells under ~750 perturbations associated with cancer cell-intrinsic ICR. We recover known mechanisms of resistance, including defects in the IFNγ-JAK/STAT and antigen-presentation pathways in RNA, protein and perturbation space, and novel ones, including loss/downregulation of CD58. Loss of CD58 conferred immune evasion in multiple co-culture models and was downregulated in tumors of melanoma patients with ICR. CD58 expression was not significantly regulated by IFNγ and CD58 loss conferred immune evasion without compromising MHC expression, suggesting that it acts orthogonal to known mechanisms of ICR. This work provides framework for deciphering complex mechanisms by large-scale perturbation screens with multi-modal single-cell readouts, and discovers potentially clinically relevant mechanisms of immune evasion.