Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens

Aleksandra Wroblewska, Maxime Dhainaut, Benjamin Ben-Zvi, Samuel A. Rose, Eun Sook Park, El Ad David Amir, Anela Bektesevic, Alessia Baccarini, Miriam Merad, Adeeb H. Rahman, Brian D. Brown

Research output: Contribution to journalArticlepeer-review

53 Scopus citations

Abstract

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. Protein-level genetic barcodes enable single-cell high-dimensional phenotyping by mass cytometry in CRISPR screens.

Original languageEnglish
Pages (from-to)1141-1155.e16
JournalCell
Volume175
Issue number4
DOIs
StatePublished - 1 Nov 2018

Keywords

  • CRISPR
  • T cells
  • cancer
  • functional genomics
  • interferon gamma pathway
  • mass cytometry
  • pooled screen
  • protein barcodes
  • single cell analysis
  • tumor immunology

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