Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens

• Aleksandra Wroblewska ^[1] ; Maxime Dhainaut ^[1] ; Benjamin Ben-Zvi ^[1]
  1. [1] Icahn School of Medicine at Mount Sinai

     Icahn School of Medicine at Mount Sinai

     Estados Unidos

     
• Localización: Cell, ISSN 0092-8674, Vol. 175, Nº. 4, 2018, págs. 1141-1155
• Idioma: inglés
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• Resumen

  • CRISPR pools are being widely employed to identify gene functions. However, current technology, which utilizes DNA as barcodes, permits limited phenotyping and bulk-cell resolution. To enable novel screening capabilities, we developed a barcoding system operating at the protein level. We synthesized modules encoding triplet combinations of linear epitopes to generate >100 unique protein barcodes (Pro-Codes). Pro-Code-expressing vectors were introduced into cells and analyzed by CyTOF mass cytometry. Using just 14 antibodies, we detected 364 Pro-Code populations; establishing the largest set of protein-based reporters. By pairing each Pro-Code with a different CRISPR, we simultaneously analyzed multiple phenotypic markers, including phospho-signaling, on dozens of knockouts. Pro-Code/CRISPR screens found two interferon-stimulated genes, the immunoproteasome component Psmb8 and a chaperone Rtp4, are important for antigen-dependent immune editing of cancer cells and identified Socs1 as a negative regulator of Pd-l1. The Pro-Code technology enables simultaneous high-dimensional protein-level phenotyping of 100s of genes with single-cell resolution.