Journal Article

Multimodal pooled Perturb-CITE-seq screens in patient models define 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 (ICIs) is a key challenge in cancer therapy. To elucidate underlying mechanisms, we developed Perturb-CITE-sequencing (Perturb-CITE-seq), enabling pooled clustered regularly interspaced short palindromic repeat (CRISPR)–Cas9 perturbations with single-cell transcriptome and protein readouts. 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 ICI resistance (ICR). We recover known mechanisms of resistance, including defects in the interferon-γ (IFN-γ)–JAK/STAT and antigen-presentation pathways in RNA, protein and perturbation space, and new 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 protein expression was not induced by IFN-γ signaling, and CD58 loss conferred immune evasion without compromising major histocompatibility complex (MHC) expression, suggesting that it acts orthogonally to known mechanisms of ICR. This work provides a framework for the deciphering of complex mechanisms by large-scale perturbation screens with multimodal, single-cell readouts, and discovers potentially clinically relevant mechanisms of immune evasion. Pooled CRISPR perturbation screens with multimodal RNA and protein single-cell profiling readout (Perturb-CITE-seq) applied to patient-derived melanoma and tumor-infiltrating lymphocyte co-cultures identifies new tumor immune evasion mechanisms.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 45 / 45/91 / 631/114/2163 / 631/208/191 / 631/250/580 / 631/553/1833 / 692/699/67/1813/1634 / Agriculture / Animal Genetics and Genomics / Antibodies / Antigen presentation / Antigens / Biomedical and Life Sciences / Biomedicine / Cancer / Cancer Research / Care and treatment / CD58 antigen / CD58 Antigens - genetics / CD58 Antigens - immunology / CD58 Antigens - metabolism / Cell culture / Circuits / Coculture Techniques / Computational Biology - methods / CRISPR / CRISPR-Cas Systems / Drug resistance / Drug Resistance, Neoplasm - drug effects / Drug Resistance, Neoplasm - genetics / Drug Resistance, Neoplasm - immunology / Epitopes - genetics / Gene expression / Gene Function / Gene Knockout Techniques / Genetic aspects / Health aspects / Human Genetics / Humans / Immune checkpoint inhibitors / Immune Checkpoint Inhibitors - pharmacology / Immune evasion / Immune response / Interferon / Interferon-gamma - immunology / Interferon-gamma - metabolism / Libraries / Lymphocytes / Lymphocytes, Tumor-Infiltrating - pathology / Major histocompatibility complex / Melanoma / Melanoma - drug therapy / Melanoma - immunology / Melanoma - pathology / Mutation / Patients / Perturbation / Proteins / Sequence Analysis, RNA / Single-Cell Analysis - methods / Transcriptomes / Tumor Escape - genetics / Tumors / γ-Interferon