학술논문
Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion
Document Type
Report
Author
Frangieh, Chris J.; Melms, Johannes C.; Thakore, Pratiksha I.; Geiger-Schuller, Kathryn R.; Ho, Patricia; Luoma, Adrienne M.; Cleary, Brian; Jerby-Arnon, Livnat; Malu, Shruti; Cuoco, Michael S.; Zhao, Maryann; Ager, Casey R.; Rogava, Meri; Hovey, Lila; Rotem, Asaf; Bernatchez, Chantale; Wucherpfennig, Kai W.
Source
Nature Genetics. March 2021, Vol. 53 Issue 3, p332, 10 p.
Subject
Language
English
ISSN
1061-4036
Abstract
Author(s): Chris J. Frangieh [sup.1] [sup.2] , Johannes C. Melms [sup.3] [sup.4] , Pratiksha I. Thakore [sup.1] , Kathryn R. Geiger-Schuller [sup.1] [sup.13] , Patricia Ho [sup.3] [sup.4] , Adrienne [...]
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-[gamma] (IFN-[gamma])-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-[gamma] 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.
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-[gamma] (IFN-[gamma])-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-[gamma] 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.