CRISPR-based functional genomics in human dendritic cells

Elife. 2021 Apr 27;10:e65856. doi: 10.7554/eLife.65856.

Abstract

Dendritic cells (DCs) regulate processes ranging from antitumor and antiviral immunity to host-microbe communication at mucosal surfaces. It remains difficult, however, to genetically manipulate human DCs, limiting our ability to probe how DCs elicit specific immune responses. Here, we develop a CRISPR-Cas9 genome editing method for human monocyte-derived DCs (moDCs) that mediates knockouts with a median efficiency of >94% across >300 genes. Using this method, we perform genetic screens in moDCs, identifying mechanisms by which DCs tune responses to lipopolysaccharides from the human microbiome. In addition, we reveal donor-specific responses to lipopolysaccharides, underscoring the importance of assessing immune phenotypes in donor-derived cells, and identify candidate genes that control this specificity, highlighting the potential of our method to pinpoint determinants of inter-individual variation in immunity. Our work sets the stage for a systematic dissection of the immune signaling at the host-microbiome interface and for targeted engineering of DCs for neoantigen vaccination.

Keywords: CRISPR; bacteroides thetaiotaomicron; dendritic cells; functional genomics; human; immunology; infectious disease; inflammation; inter-individual variation; microbiology.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteroides thetaiotaomicron / immunology
  • CRISPR-Associated Protein 9 / genetics*
  • CRISPR-Associated Protein 9 / metabolism
  • CRISPR-Cas Systems*
  • Cells, Cultured
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Cytokines / genetics
  • Cytokines / metabolism
  • Dendritic Cells / drug effects
  • Dendritic Cells / immunology*
  • Dendritic Cells / metabolism
  • Gene Editing*
  • Gene Expression Regulation
  • Genomics*
  • Humans
  • Immunity, Innate / drug effects
  • Immunity, Innate / genetics*
  • Lipopolysaccharides / pharmacology
  • Phenotype
  • Signal Transduction
  • Toll-Like Receptor 4 / agonists
  • Toll-Like Receptor 4 / genetics
  • Toll-Like Receptor 4 / metabolism

Substances

  • Cytokines
  • Lipopolysaccharides
  • TLR4 protein, human
  • Toll-Like Receptor 4
  • CRISPR-Associated Protein 9

Associated data

  • GEO/GSE161401
  • GEO/GSE161466