title: A Cas9 Ribonucleoprotein Platform for Functional Genetic Studies of HIV-Host Interactions in Primary Human T Cells.
abstract: New genetic tools are needed to understand the functional interactions between HIV and human host factors in primary cells. We recently developed a method to edit the genome of primary CD4+T cells by electroporation of CRISPR/Cas9 ribonucleoproteins (RNPs). Here, we adapted this methodology to a high-throughput platform for the efficient, arrayed editing of candidate host factors. CXCR4 or CCR5 knockout cells generated with this method are resistant to HIV infection in a tropism-dependent manner, whereas knockout of LEDGF or TNPO3 results in a tropism-independent reduction in infection. CRISPR/Cas9 RNPs can furthermore edit multiple genes simultaneously, enabling studies of interactions among multiple host and viral factors. Finally, in an arrayed screen of 45 genes associated with HIV integrase, we identified several candidate dependency/restriction factors, demonstrating the power of this approach as a discovery platform. This technology should accelerate target validation for pharmaceutical and cell-based therapies to cure HIV infection.
authors: Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA.
authors: Judd F
authors: JF
authors: Hultquist
authors: Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.
authors: Kathrin
authors: K
authors: Schumann
authors: Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA.
authors: Jonathan M
authors: JM
authors: Woo
authors: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
authors: Lara
authors: L
authors: Manganaro
authors: Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA.
authors: Michael J
authors: MJ
authors: McGregor
authors: Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Lawrence Berkeley National Laboratory, Physical Biosciences Division, Berkeley, Berkeley, CA 94720, USA.
authors: Jennifer
authors: J
authors: Doudna
authors: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
authors: Viviana
authors: V
authors: Simon
authors: Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA. Electronic address: nevan.krogan@ucsf.edu.
authors: Nevan J
authors: NJ
authors: Krogan
authors: Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA; Divisions of Infectious Diseases and Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: alexander.marson@ucsf.edu.
authors: Alexander
authors: A
authors: Marson
mesh_terms: D015496:CD4-Positive T-Lymphocytes / Q000378:metabolism* / Q000821:virology*; D064113:CRISPR-Cas Systems / Q000235:genetics*; D002478:Cells, Cultured; D000072669:Gene Editing / Q000379:methods*; D055786:Gene Knockout Techniques; D015658:HIV Infections / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics; D054884:Host-Pathogen Interactions / Q000235:genetics*; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000378:metabolism; D019718:Receptors, CXCR4 / Q000378:metabolism; D054380:Receptors, CXCR5 / Q000378:metabolism; D015203:Reproducibility of Results; D012261:Ribonucleoproteins / Q000378:metabolism*; D028961:beta Karyopherins / Q000378:metabolism
chemical_list: C527276:CXCR4 protein, human; C095085:CXCR5 protein, human; D036341:Intercellular Signaling Peptides and Proteins; D019718:Receptors, CXCR4; D054380:Receptors, CXCR5; D012261:Ribonucleoproteins; C546476:TNPO3 protein, human; D028961:beta Karyopherins; C119380:lens epithelium-derived growth factor
keywords: CCR5; CRISPR/Cas9; CXCR4; HIV integrase; LEDGF; TNPO3; genome editing; host dependency factors; host-pathogen interactions; primary T cells