title: Automated genome-wide visual profiling of cellular proteins involved in HIV infection.
abstract: Recent genome-wide RNAi screens have identified >842 human genes that affect the human immunodeficiency virus (HIV) cycle. The list of genes implicated in infection differs between screens, and there is minimal overlap. A reason for this variance is the interdependence of HIV infection and host cell function, producing a multitude of indirect or pleiotropic cellular effects affecting the viral infection during RNAi screening. To overcome this, the authors devised a 15-dimensional phenotypic profile to define the viral infection block induced by CD4 silencing in HeLa cells. They demonstrate that this phenotypic profile excludes nonspecific, RNAi-based side effects and viral replication defects mediated by silencing of housekeeping genes. To achieve statistical robustness, the authors used automatically annotated RNAi arrays for seven independent genome-wide RNAi screens. This identified 56 host genes, which reliably reproduced CD4-like phenotypes upon HIV infection. The factors include 11 known HIV interactors and 45 factors previously not associated with HIV infection. As proof of concept, the authors confirmed that silencing of PAK1, Ku70, and RNAseH2A impaired HIV replication in Jurkat cells. In summary, multidimensional, visual profiling can identify genes required for HIV infection.
authors.affiliation: Institut Pasteur-Korea, Gyeonggi-do, Korea. auguste@broadinstitute.org
authors.forename: Auguste
authors.initials: A
authors.lastname: Genovesio
authors.forename: Yong-Jun
authors.initials: YJ
authors.lastname: Kwon
authors.forename: Marc P
authors.initials: MP
authors.lastname: Windisch
authors.forename: Nam Youl
authors.initials: NY
authors.lastname: Kim
authors.forename: Seo Yeon
authors.initials: SY
authors.lastname: Choi
authors.forename: Hi Chul
authors.initials: HC
authors.lastname: Kim
authors.forename: Sungyong
authors.initials: S
authors.lastname: Jung
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Mammano
authors.forename: Virginie
authors.initials: V
authors.lastname: Perrin
authors.forename: Annette S
authors.initials: AS
authors.lastname: Boese
authors.forename: Nicoletta
authors.initials: N
authors.lastname: Casartelli
authors.forename: Olivier
authors.initials: O
authors.lastname: Schwartz
authors.forename: Ulf
authors.initials: U
authors.lastname: Nehrbass
authors.forename: Neil
authors.initials: N
authors.lastname: Emans
mesh_terms: D034961:Antigens, Nuclear / Q000235:genetics / Q000378:metabolism; D057205:Automation, Laboratory; D015704:CD4 Antigens / Q000378:metabolism; D045744:Cell Line, Tumor; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D055785:Gene Knockdown Techniques; D006678:HIV / Q000502:physiology*; D006367:HeLa Cells; D006801:Humans; D019169:Jurkat Cells; D000072200:Ku Autoantigen; D046228:Microarray Analysis / Q000379:methods*; D018613:Microscopy, Confocal; D011493:Protein Kinase C / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D034622:RNA Interference; D016914:Ribonuclease H / Q000235:genetics / Q000378:metabolism; D014779:Virus Replication
chemical_list: D034961:Antigens, Nuclear; D015704:CD4 Antigens; D004268:DNA-Binding Proteins; C061570:protein kinase N; D011493:Protein Kinase C; C091139:ribonuclease HII; D016914:Ribonuclease H; C000606509:Xrcc6 protein, human; D000072200:Ku Autoantigen