@article {1590000,
	title = {Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion},
	journal = {Nat Genet},
	volume = {53},
	number = {3},
	year = {2021},
	month = {2021 03},
	pages = {332-341},
	abstract = {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.},
	keywords = {CD58 Antigens, Coculture Techniques, Computational Biology, CRISPR-Cas Systems, Drug Resistance, Neoplasm, Epitopes, Gene Knockout Techniques, Humans, Immune Checkpoint Inhibitors, Interferon-gamma, Lymphocytes, Tumor-Infiltrating, Melanoma, Sequence Analysis, RNA, Single-Cell Analysis, Tumor Escape},
	issn = {1546-1718},
	doi = {10.1038/s41588-021-00779-1},
	author = {Frangieh, Chris J and Melms, Johannes C and Thakore, Pratiksha I and Geiger-Schuller, Kathryn R and Ho, Patricia and Luoma, Adrienne M and Cleary, Brian and Jerby-Arnon, Livnat and Malu, Shruti and Cuoco, Michael S and Zhao, Maryann and Ager, Casey R and Rogava, Meri and Hovey, Lila and Rotem, Asaf and Bernatchez, Chantale and Wucherpfennig, Kai W and Johnson, Bruce E and Rozenblatt-Rosen, Orit and Schadendorf, Dirk and Regev, Aviv and Izar, Benjamin}
}
