CRISPR-based functional genomics in human dendritic cells
- University of California, San Francisco, United States
- Stanford University, United States
- Chan Zuckerberg Biohub, United States
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.
Data availability
Raw data from RNA-seq of unedited and edited moDCs are available at GEO under accession codes GSE161401 and GSE161466, respectively. Raw data from amplicon sequencing for all samples are available at SRA under accession code PRJNA673198. Processed data from amplicon sequencing as well as raw and processed data from the genetic screens are provided as supplemental files (Supplementary Files 2, 3, 4).
Article and author information
Author details
Jonathan S Weissman
Funding
National Institutes of Health (K99 GM130964)
- Marco Jost
Damon Runyon Cancer Research Foundation (DRG-2262-16)
- Jeffrey A Hussmann
Howard Hughes Medical Institute (Investigator)
- Jonathan S Weissman
National Institutes of Health (U01 CA217882)
- Jonathan S Weissman
National Institutes of Health (DP1 DK113598)
- Michael A Fischbach
National Institutes of Health (R01 DK11017404)
- Michael A Fischbach
Chan-Zuckerberg Initiative
- Jonathan S Weissman
Helmsley Foundation
- Michael A Fischbach
Howard Hughes Medical Institute (Simons Faculty Scholar Award)
- Michael A Fischbach
Burroughs Wellcome Fund (Investigators in the Pathogenesis of Infectious Disease program)
- Michael A Fischbach
UCSF Program for Breakthrough Biomedical Research (Postdoctoral Independent Research Grant)
- Marco Jost
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Jost et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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CRISPR-based functional genomics in human dendritic cells
eLife 10:e65856.
https://doi.org/10.7554/eLife.65856
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