title: A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility.
abstract: Genetic interaction (GI) maps, comprising pairwise measures of how strongly the function of one gene depends on the presence of a second, have enabled the systematic exploration of gene function in microorganisms. Here, we present a two-stage strategy to construct high-density GI maps in mammalian cells. First, we use ultracomplex pooled shRNA libraries (25 shRNAs/gene) to identify high-confidence hit genes for a given phenotype and effective shRNAs. We then construct double-shRNA libraries from these to systematically measure GIs between hits. A GI map focused on ricin susceptibility broadly recapitulates known pathways and provides many unexpected insights. These include a noncanonical role for COPI, a previously uncharacterized protein complex affecting toxin clearance, a specialized role for the ribosomal protein RPS25, and functionally distinct mammalian TRAPP complexes. The ability to rapidly generate mammalian GI maps provides a potentially transformative tool for defining gene function and designing combination therapies based on synergistic pairs.
authors: Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94122, USA. bassik@cmp.ucsf.edu
authors: Michael C
authors: MC
authors: Bassik
authors: Martin
authors: M
authors: Kampmann
authors: Robert Jan
authors: RJ
authors: Lebbink
authors: Shuyi
authors: S
authors: Wang
authors: Marco Y
authors: MY
authors: Hein
authors: Ina
authors: I
authors: Poser
authors: Jimena
authors: J
authors: Weibezahn
authors: Max A
authors: MA
authors: Horlbeck
authors: Siyuan
authors: S
authors: Chen
authors: Matthias
authors: M
authors: Mann
authors: Anthony A
authors: AA
authors: Hyman
authors: Emily M
authors: EM
authors: Leproust
authors: Michael T
authors: MT
authors: McManus
authors: Jonathan S
authors: JS
authors: Weissman
mesh_terms: D000069059:Atorvastatin; D001692:Biological Transport; D002352:Carrier Proteins / Q000378:metabolism; D045744:Cell Line, Tumor; D020755:Coat Protein Complex I / Q000378:metabolism; D004721:Endoplasmic Reticulum / Q000378:metabolism; D004843:Epistasis, Genetic; D006538:Heptanoic Acids / Q000494:pharmacology; D006801:Humans; D008565:Membrane Proteins / Q000378:metabolism; D011518:Proto-Oncogene Proteins / Q000378:metabolism; D011758:Pyrroles / Q000494:pharmacology; D034741:RNA, Small Interfering; D012269:Ribosomal Proteins / Q000378:metabolism; D012276:Ricin / Q000633:toxicity*; D033921:Vesicular Transport Proteins / Q000378:metabolism; D000092468:Bromodomain Containing Proteins
chemical_list: D000069059:Atorvastatin; D002352:Carrier Proteins; D020755:Coat Protein Complex I; D006538:Heptanoic Acids; D008565:Membrane Proteins; D011518:Proto-Oncogene Proteins; D011758:Pyrroles; D034741:RNA, Small Interfering; D012269:Ribosomal Proteins; D012276:Ricin; D033921:Vesicular Transport Proteins; C579821:C17orf75 protein, human; C489168:RPS25 protein, human; C435527:WDR11 protein, human; D000092468:Bromodomain Containing Proteins; C406327:transport protein particle, TRAPP
references: Curr Top Microbiol Immunol. 2005;300:149-68
references: 16573240
references: Cold Spring Harb Perspect Biol. 2011 Nov 01;3(11):a005231
references: 21844168
references: Science. 2012 Jul 27;337(6093):421-2
references: 22837515
references: Mol Biol Cell. 2000 Dec;11(12):4205-16
references: 11102518
references: Nature. 2002 Jan 10;415(6868):141-7
references: 11805826
references: Am J Hum Genet. 2010 Oct 8;87(4):465-79
references: 20887964
references: PLoS One. 2011;6(8):e23350
references: 21858081
references: Nat Cell Biol. 2011 Sep 25;13(11):1305-14
references: 21947079
references: Nat Methods. 2004 Nov;1(2):163-7
references: 16144086
references: Trends Cell Biol. 2011 Mar;21(3):159-67
references: 21183348
references: FEBS Lett. 2010 Jun 18;584(12):2626-34
references: 20385131
references: Nat Genet. 2005 Nov;37(11):1281-8
references: 16200065
references: J Cell Biol. 2011 Nov 28;195(5):751-64
references: 22123862
references: J Virol. 2006 Jul;80(14):6936-42
references: 16809299
references: Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12372-7
references: 21746896
references: Nat Methods. 2008 Sep;5(9):781-7
references: 19160513
references: Nat Methods. 2004 Dec;1(3):241-8
references: 15782200
references: J Cell Sci. 2007 Apr 15;120(Pt 8):1457-68
references: 17389686
references: J Biol Chem. 2003 Sep 12;278(37):35850-5
references: 12847103
references: Traffic. 2011 Jun;12(6):715-25
references: 21453443
references: Nat Protoc. 2007;2(11):2958-74
references: 18007632
references: Mol Cell. 2012 Jun 8;46(5):691-704
references: 22681890
references: Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1193-8
references: 22223662
references: Nat Genet. 2009 Aug;41(8):936-40
references: 19561605
references: J Biomol Screen. 2011 Apr;16(4):436-42
references: 21364088
references: Nature. 2010 Jul 1;466(7302):68-76
references: 20562859
references: Mol Cell. 2011 Mar 18;41(6):733-46
references: 21353615
references: Curr Top Microbiol Immunol. 2012;357:19-40
references: 21761287
references: Nature. 2007 Feb 22;445(7130):941-4
references: 17287728
references: Nat Cell Biol. 1999 Nov;1(7):423-30
references: 10559986
references: Nat Methods. 2009 Jun;6(6):443-5
references: 19448642
references: Nat Methods. 2008 Sep;5(9):789-95
references: 18677321
references: Cancer Discov. 2012 Feb;2(2):172-189
references: 22585861
references: Genes Dev. 2009 Dec 1;23(23):2753-64
references: 19952110
references: Trends Cell Biol. 2008 Jul;18(7):330-6
references: 18534853
references: RNA Biol. 2009 Jan-Mar;6(1):35-9
references: 19106622
references: Cell. 2006 Mar 24;124(6):1283-98
references: 16564017
references: Nat Biotechnol. 2011 May 29;29(6):542-6
references: 21623355
references: Biochim Biophys Acta. 2002 Apr 3;1589(2):124-39
references: 12007788
references: Cell. 2011 Apr 1;145(1):30-8
references: 21458666
references: Nat Methods. 2011 Apr;8(4):341-6
references: 21378980
references: Mol Biol Cell. 2011 Jun 15;22(12):2083-93
references: 21525244
references: Nature. 2009 Nov 5;462(7269):108-12
references: 19847166
references: Dev Cell. 2011 Aug 16;21(2):231-44
references: 21782526
references: Science. 2008 Feb 1;319(5863):617-20
references: 18239125
references: Cell. 2009 May 29;137(5):835-48
references: 19490893
references: Annu Rev Genet. 2009;43:601-25
references: 19712041
references: Mol Cell. 2001 Feb;7(2):433-42
references: 11239471
references: Cell. 2012 Jun 8;149(6):1339-52
references: 22682253
references: Science. 2009 Nov 27;326(5957):1231-5
references: 19965467
references: Cell. 2008 Dec 26;135(7):1175-87
references: 19109890
references: Mol Biol Cell. 2009 Oct;20(19):4205-15
references: 19656848
references: Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5
references: 12883005
references: Nat Methods. 2009 Oct;6(10):721-23
references: 19953683
references: Science. 2010 Dec 3;330(6009):1385-9
references: 21127252
references: Nat Rev Mol Cell Biol. 2010 Nov;11(11):759-63
references: 20966969