TY - JOUR
T1 - Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion
AU - Frangieh, Chris J.
AU - Melms, Johannes C.
AU - Thakore, Pratiksha I.
AU - Geiger-Schuller, Kathryn R.
AU - Ho, Patricia
AU - Luoma, Adrienne M.
AU - Cleary, Brian
AU - Jerby-Arnon, Livnat
AU - Malu, Shruti
AU - Cuoco, Michael S.
AU - Zhao, Maryann
AU - Ager, Casey R.
AU - Rogava, Meri
AU - Hovey, Lila
AU - Rotem, Asaf
AU - Bernatchez, Chantale
AU - Wucherpfennig, Kai W.
AU - Johnson, Bruce E.
AU - Rozenblatt-Rosen, Orit
AU - Schadendorf, Dirk
AU - Regev, Aviv
AU - Izar, Benjamin
N1 - Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.
PY - 2021/3
Y1 - 2021/3
N2 - 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.
AB - 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.
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U2 - 10.1038/s41588-021-00779-1
DO - 10.1038/s41588-021-00779-1
M3 - Article
C2 - 33649592
AN - SCOPUS:85101854106
SN - 1061-4036
VL - 53
SP - 332
EP - 341
JO - Nature Genetics
JF - Nature Genetics
IS - 3
ER -