A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

Oren Parnas, Marko Jovanovic, Thomas M. Eisenhaure, Rebecca H. Herbst, Atray Dixit, Chun Jimmie Ye, Dariusz Przybylski, Randall J. Platt, Itay Tirosh, Neville E. Sanjana, Ophir Shalem, Rahul Satija, Raktima Raychowdhury, Philipp Mertins, Steven A. Carr, Feng Zhang, Nir Hacohen, Aviv Regev

Research output: Contribution to journalArticle

Abstract

Finding the components of cellular circuits and determining their functions systematically remains a major challenge in mammalian cells. Here, we introduced genome-wide pooled CRISPR-Cas9 libraries into dendritic cells (DCs) to identify genes that control the induction of tumor necrosis factor (Tnf) by bacterial lipopolysaccharide (LPS), a key process in the host response to pathogens, mediated by the Tlr4 pathway. We found many of the known regulators of Tlr4 signaling, as well as dozens of previously unknown candidates that we validated. By measuring protein markers and mRNA profiles in DCs that are deficient in known or candidate genes, we classified the genes into three functional modules with distinct effects on the canonical responses to LPS and highlighted functions for the PAF complex and oligosaccharyltransferase (OST) complex. Our findings uncover new facets of innate immune circuits in primary cells and provide a genetic approach for dissection of mammalian cell circuits.

Original languageEnglish (US)
Pages (from-to)675-686
Number of pages12
JournalCell
Volume162
Issue number3
DOIs
StatePublished - Aug 1 2015

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Clustered Regularly Interspaced Short Palindromic Repeats
Genes
Genome
Dendritic Cells
Lipopolysaccharides
Networks (circuits)
Cells
Dissection
Libraries
Pathogens
Tumor Necrosis Factor-alpha
Messenger RNA
Proteins

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Parnas, O., Jovanovic, M., Eisenhaure, T. M., Herbst, R. H., Dixit, A., Ye, C. J., ... Regev, A. (2015). A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks. Cell, 162(3), 675-686. https://doi.org/10.1016/j.cell.2015.06.059

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks. / Parnas, Oren; Jovanovic, Marko; Eisenhaure, Thomas M.; Herbst, Rebecca H.; Dixit, Atray; Ye, Chun Jimmie; Przybylski, Dariusz; Platt, Randall J.; Tirosh, Itay; Sanjana, Neville E.; Shalem, Ophir; Satija, Rahul; Raychowdhury, Raktima; Mertins, Philipp; Carr, Steven A.; Zhang, Feng; Hacohen, Nir; Regev, Aviv.

In: Cell, Vol. 162, No. 3, 01.08.2015, p. 675-686.

Research output: Contribution to journalArticle

Parnas, O, Jovanovic, M, Eisenhaure, TM, Herbst, RH, Dixit, A, Ye, CJ, Przybylski, D, Platt, RJ, Tirosh, I, Sanjana, NE, Shalem, O, Satija, R, Raychowdhury, R, Mertins, P, Carr, SA, Zhang, F, Hacohen, N & Regev, A 2015, 'A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks', Cell, vol. 162, no. 3, pp. 675-686. https://doi.org/10.1016/j.cell.2015.06.059
Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A, Ye CJ et al. A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks. Cell. 2015 Aug 1;162(3):675-686. https://doi.org/10.1016/j.cell.2015.06.059
Parnas, Oren ; Jovanovic, Marko ; Eisenhaure, Thomas M. ; Herbst, Rebecca H. ; Dixit, Atray ; Ye, Chun Jimmie ; Przybylski, Dariusz ; Platt, Randall J. ; Tirosh, Itay ; Sanjana, Neville E. ; Shalem, Ophir ; Satija, Rahul ; Raychowdhury, Raktima ; Mertins, Philipp ; Carr, Steven A. ; Zhang, Feng ; Hacohen, Nir ; Regev, Aviv. / A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks. In: Cell. 2015 ; Vol. 162, No. 3. pp. 675-686.
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