Advances in Virus Research

179 Pages·2016·21.056 MB·English

by  Kielian, Margaret, Maramorosch, Karl, Mettenleiter, Thomas

ADVISORY BOARD
DAVID BALTIMORE
SHOUWEI DING
PETER C. DOHERTY
JOHN FAZAKERLY
HANS J. GROSS
BRYAN D. HARRISON
ROGER HENDRIX
KARLA KIRKEGAARD
BERNARD MOSS
ERLING NORRBY
JULIE OVERBAUGH
PETER PALUKAITIS
FELIX REY
JUERGEN RICHT
MARILYN ROOSSINCK
JOHN J. SKEHEL
GEOFFREY SMITH
MARC H.V. VAN REGENMORTEL
VERONIKA VON MESSLING
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CONTRIBUTORS
DavidC.Bloom
DepartmentofMolecularGenetics&Microbiology,UniversityofFloridaCollegeof
Medicine,Gainesville,Florida,USA
AbrahamL.Brass
DepartmentofMicrobiologyandPhysiologicalSystems,UniversityofMassachusetts
MedicalSchool,Worcester,Massachusetts,USA
TeresaHellberg
InstituteofMolecularVirologyandCellBiology,Friedrich-Loeffler-Institut,Federal
ResearchInstituteforAnimalHealth,Greifswald-InselRiems,Germany
BarbaraG.Klupp
InstituteofMolecularVirologyandCellBiology,Friedrich-Loeffler-Institut,Federal
ResearchInstituteforAnimalHealth,Greifswald-InselRiems,Germany
PaulMeraner
DepartmentofMicrobiologyandPhysiologicalSystems,UniversityofMassachusetts
MedicalSchool,Worcester,Massachusetts,USA
ThomasC.Mettenleiter
InstituteofMolecularVirologyandCellBiology,Friedrich-Loeffler-Institut,Federal
ResearchInstituteforAnimalHealth,Greifswald-InselRiems,Germany
LarsPaßvogel
InstituteofMolecularVirologyandCellBiology,Friedrich-Loeffler-Institut,Federal
ResearchInstituteforAnimalHealth,Greifswald-InselRiems,Germany
Jean-PierrePerreault
De´partementdebiochimie,Faculte´ deme´decineetdessciencesdelasante´,Pavillonde
rechercheappliquee´ surlecancer,Universite´ deSherbrooke,Que´bec,Canada
JillM.Perreira
DepartmentofMicrobiologyandPhysiologicalSystems,UniversityofMassachusetts
MedicalSchool,Worcester,Massachusetts,USA
KatharinaS.Schulz
InstituteofMolecularVirologyandCellBiology,Friedrich-Loeffler-Institut,Federal
ResearchInstituteforAnimalHealth,Greifswald-InselRiems,Germany
GerhardSteger
Institutfu¨rPhysikalischeBiologie,Heinrich-Heine-Universita¨tDu¨sseldorf,Du¨sseldorf,
Germany
vii
CHAPTER ONE
Functional Genomic Strategies
–
for Elucidating Human Virus
Interactions: Will CRISPR Knockout
RNAi and Haploid Cells?
Jill M. Perreira, Paul Meraner, Abraham L. Brass1
DepartmentofMicrobiologyandPhysiologicalSystems,UniversityofMassachusettsMedicalSchool,
Worcester,Massachusetts,USA
1Correspondingauthor:e-mailaddress:[email protected]
Contents
1. Introduction 2
2. Host–VirusGeneticScreens 2
3. RNAiGeneticScreeningTechnologiesandApproaches 3
3.1 RNAiPooledScreening 21
3.2 ArrayedRNAiScreening 23
3.3 RNAiScreeningProblemsandSomeSolutions 28
4. HaploidCellGeneticScreeningTechnologyandApproach 31
5. CRISPR/Cas9GeneticScreeningTechnologiesandApproaches 32
6. ComparisonofHRV-HFScreens:ArrayedMORRRNAiVersusPooledCRISPR/Cas9 34
7. FutureDirections 44
Acknowledgments 45
References 45
Abstract
Overthelastseveralyearsawealthoftransformativehuman–virusinteractiondiscover-
ieshavebeenproducedusingloss-of-functionfunctionalgenomics.Theseinsightshave
greatlyexpandedourunderstandingofhowhumanpathogenicvirusesexploitourcells
toreplicate.Twotechnologieshavebeenattheforefrontofthisgeneticrevolution,RNA
interference (RNAi) and random retroviral insertional mutagenesis using haploid cell
lines(haploidcellscreening),withtheformertechnologylargelypredominating.Now
the cutting edge gene editing of the CRISPR/Cas9 system has also been harnessed
for large-scale functional genomics and is poised to possibly displace these earlier
methods.Herewecompareandcontrastthesethreescreeningapproachesforelucidat-
inghost–virusinteractions,outlinetheirkeystrengthsandweaknessesincludingacom-
parisonofanarrayedmultipleorthologousRNAireagentscreentoapooledCRISPR/Cas9
humanrhinovirus14–humancellinteractionscreen,andrecountsomenotableinsights
madepossiblebyeach.Weconcludewithabriefperspectiveonwhatmightlieahead
forthefastevolvingfieldofhuman–virusfunctionalgenomics.
AdvancesinVirusResearch,Volume94 #2016ElsevierInc. 1
ISSN0065-3527 Allrightsreserved.
http://dx.doi.org/10.1016/bs.aivir.2015.11.001
2 JillM.Perreiraetal.
1. INTRODUCTION
Theburdenimposeduponthehealthoftheworld’spopulationbyjust
threeofthemajorpathogenicvirusesisstaggering,withnearly300million
peoplechronicallyinfectedbyeitherHIV-1(36million)orHBV(250mil-
lion),andanother5–6millionsevereinfections byinfluenzaAvirus(IAV)
occurring transiently each year (Ortblad, Lozano, & Murray, 2013;
Schweitzer, Horn, Mikolajczyk, Krause, & Ott, 2015) (http://www.who.
int/immunization/topics/influenza/en/). Collectively these three viruses
causethedeathsofover2.5millionpeopleannually.Theseinfectionsarise
because viruses must find and exploit the host’s cellular resources and
machinery to produce their progeny. Elucidating human pathogenic viral
dependencies has been a longstanding pursuit of health science researchers
whosegoalistousethisknowledgetotreatandcureinfections.Fordecades,
mammalian in vitro tissue culture systems have proved tremendously useful
forstudyinghost–virusinteractions.Overthissameperiod,loss-of-function
geneticscreeningproducedanimpressivenumberofdiscoveriesandillumi-
natedgeneandpathwayfunctioninmultiplemodelsystems.Whileloss-of-
function genetic screening proved extremely valuable in model systems,
such technologies did not exist for mammalian cells until the discovery
and implementation of RNA interference (RNAi) (Fire et al., 1998).
The initial technologic revolution of RNAi, and later the development
ofhaploidcellscreening,resultedinawaveofdiscoveriesthatshednewlight
onmanyvitalhumanviralrequirements(Brassetal.,2008;Haoetal.,2008;
Krishnanetal.,2008;Randalletal.,2007;Sessionsetal.,2009).Theascen-
dance of CRISPR/Cas9 technologies, which can dramatically alter gene
expression, has heralded a new era in mammalian in vitro genetic screening
(Shalem, Sanjana, & Zhang, 2015). This review will discuss the available
functional genomics strategies, highlight their strengths and weaknesses
including a comparison of matched MORR RNAi and CRISRP/Cas9
screens, and provide some future perspectives on the use of mammalian
in vitro genetics to elucidate human host–virus interactions.
2. HOST–VIRUS GENETIC SCREENS
The numbers of host–virus functional genomic screens using these
technologies, particularly RNAi, have been increasing rapidly attesting to
FunctionalGenomicStrategiesforElucidatingHuman–VirusInteractions 3
theirinnovativediscoverypower,generalizabilityandremarkableeaseofuse
(Table1).DrosophilacellinvitroRNAiscreenswerethefirsttodetectnovel
hostfactorinteractionsforseveralhumanpathogenswiththepracticalfocus
being on arboviruses, although an elegant approach using a recombinant
virusalsomadeitpossibletoscreenforIAVdependencyfactorsinthissys-
tem (Arkov, Rosenbaum, Christiansen, Jonsson, & Munchow, 2008;
Cherryetal.,2005;Haoetal.,2008).RNAiscreensusinghumancellshave
now been done for the majority of major human pathogenic viruses
(Table1);theseeffortshavelargelyusedarrayedsiRNAlibrariescombined
with high-throughput imaging or plate reader-based assays as readouts for
viral replication. Collectively these works have identified multiple previ-
ouslyunappreciateddependenciesforeachvirus,aswellashostcelldefense
mechanisms.Recentpublicationscoveringvirusesthathavebeenfunction-
ally interrogated by multiple independent groups including HIV-1, IAV,
and HCV have been discussed elsewhere in detail (Bushman et al., 2009;
Hao et al., 2013; Stertz & Shaw, 2011; Zhu et al., 2014). In this work,
we focus on the functional genomic screening technologies and provide a
resource noting many of the publishedhost–virus screens along with some
of their key attributes.
3. RNAi GENETIC SCREENING TECHNOLOGIES
AND APPROACHES
NearingadecadeagotheNobelPrizewinningdiscoveryofRNAiin
C. elegans and its mercurial extension into mammalian systems provided
virologistsandgeneticistsalikewithapowerfulnewtoolfordetectingviral
dependencies (Elbashir et al., 2001; Fire et al., 1998; Grishok & Mello,
2002). Academia and industry both quickly embraced RNAi and paired
it with the contemporaneous completion of the genetic annotation of the
entire human genome to create multiple large-scale libraries for functional
genomicscreening(Paddisonetal.,2004;Root,Hacohen,Hahn,Lander,&
Sabatini, 2006; Silva et al., 2005). Because the RNA-induced silencing
complex(RISC)machinery’sexpressionisubiquitous,virtuallyallmamma-
liancelllines cancarry outRNAi,permittinghost–virusscreenstobecar-
ried out with any tropic cell line and virus pairing (Elbashir et al., 2001).
Two major types of RNAi libraries, pooled and arrayed, have been con-
structed and dictate the two methods of screening discussed below.
Table1 FunctionalGenomicScreensforElucidatingHost–ViralInteractions
Viral
Viral Viral Competitive
Viral Dependency Competitive orRestriction
Pooled/ Knockdown/ Challenge Dependency FactorSelection orRestriction factorsSelection Main StageofViral CandidateValidation
Citation Virus CellLine Arrayed Library OutTime Time Readout Factors Criteria Factors Criteria Candidates LifecycleImpacted andFollowupAssays
Haploid Caretteetal. Influenzavirus Haploid Pooled Haploidcell N/A 2–3weeksSurvival Yes Multiple No N/A CMAS; Entry RT-PCR;
cells (2009) (PR/8/34; human Insertional independent SLC35A2 immunofluorescence;
H1N1) suspension mutagenesis integrations complementationwith
cells withlentiviral cDNAs
KBM-7 exontrap
Caretteetal. rVSV-GP-Ebola Haploid Pooled Haploidcell N/A UnknownSurvival Yes Multiple No N/A NPC1, Entry,viralfusion Complementationwith
(2011) virus human Insertional independent HOPS inlysosomal cDNAs;testagainst
adherentcells mutagenesis integrations complex compartment relatedviruses;small-
(HAP1) withlentiviral moleculeU1866Aand
exontrap imipramine;
immunofluorescence/
electronmicroscopy
viralentryassays;
primarycelllines
Jaeetal. rVSV-GP-Lassa HAP1 Pooled Haploidcell Gene-Trap UnknownSurvival Yes Multiple No N/A TMEM5; Entry, NullallelesTALENs;
(2013) virus Insertional independent B3GALNT2; presentationof rescuecDNAs;analysis
mutagenesis integrations B3GNT1; laminin-binding ofknowpolymorphisms;
withlentiviral SLC35A1; carbohydrate flowcytometry;
exontrap SGK196 RT-PCR;clinical
comparison
Kleinfelter rVSV-Andes HAP1 Pooled Haploidcell N/A 8days Survival Yes Multiple No N/A S1P;S2P; Entry S1PCRISPR/Cas9
etal.(2015) virus-GP Insertional independent SREBF2; geneeditinginU2OS;
mutagenesis integrations SCAP;LSS; complementationwith
withlentiviral SQLE; cDNA;small-molecule
exontrap ACAT2 inhibitor
siRNA
Haploid Petersenetal. rVSV-Andes HAP1 Pooled Haploidcell N/A 3weeks Survival Yes Multiple No N/A SCAP;S1P; Entry Functionallydeficient
celland (2014) virus,either Insertional independent S2P;SREBF2 cellsS1P,S2P,orSCAP
siRNA recombinantor mutagenesis integrations nullCHOandSREBP2
pseudoparticles withlentiviral KDHEK293T;
expressing exontrap TALEN-mediatedgene
Renillaluciferase disruption;small-
moleculePF-429242
andmevastatin
HEK29 ArrayedAmbion 72h 24h Renillaluciferase Yes Inbothpools: SREBF2 Entry 3additionalunique
druggable expression Zscorefor siRNAsscreenedwith
genomelibrary 210dsRNAs; infection ANDVandVSV-G
(9102genes) 112genes <(cid:1)1.5 pseudoparticles;
(4siRNAs/ reconfirmed (p<0.009); validatedby1siRNA
gene) viability<(cid:1)2 repeatingfindingtwo
(2siRNAs/ times.105candidate
well) genes—33validated—9
specificforANDV
Brassetal. HIV-1-IIIB TZM-bl ArrayedDharmacon 72h 48h %Infectivity Yes Decreased No N/A RAB6A Fusion Subcellularlocalization;
(2008) siARRAY (anti-HIV-1p24) Infectivityby geneontology(GO)
siRNAlibrary (cid:3)2SDs; TNPO3 Cytosolicpost- biologicalprocesses
(21,121 viabilitynot RT–pre analysis;Expression
siRNApools) decreasedby integration GenomicInstituteofthe
>2SDs NovartisResearchFund
MED28 Transcription
(GNF);individual
shRNAs;individual
siRNAs;infectionwith
VSV-g;othercelllines
Jurkat;qPCR
Haoetal. InfluenzaAvirus DL1 ArrayedAmbion 48h 24h Renillaluciferase Yes Inhibition Yes Increase>3 COX6A1 PB2/ RT-PCR;reagent
(2008) Flu-VSV- Drosophila activity >2.4SDs; SDs;viability PB1-F2-mediated redundancy;testhuman
G-GFP RNAilibrary Viability reduction functions homologues,
(13,071genes) reduction Zscore>(cid:1)3 knockdowninHEK293
176candidate Zscore>-3 123candidate ATP6V0D1 Fusion cells;individualsiRNAs;
genes—110 genes—11 small-molecule
confirmed genes NXF1 RNAexport inhibitors;related
confirmed pathway viruses:WSN,H5N1
InfluenzaA/Indonesia/
7/05,VSV,VACV
Continued
Table1 FunctionalGenomicScreensforElucidatingHost–ViralInteractions—cont'd
Viral
Viral Viral Competitive
Viral Dependency Competitive orRestriction
Pooled/ Knockdown/ Challenge Dependency FactorSelection orRestriction factorsSelection Main StageofViral CandidateValidation
Citation Virus CellLine Arrayed Library OutTime Time Readout Factors Criteria Factors Criteria Candidates LifecycleImpacted andFollowupAssays
Krishnan WestNilevirus HeLa ArrayedDharmacon 72h 24h %Infectivity Yes Infection No NA CBLL1 Entry IndividualsiRNAs,
etal.(2008) WNVstrain siARRAY (viralE-proteins) reductionof small-molecule:
2471 siRNAlibrary >twofold MG132,cyclohexamide;
(21,121 colocalization;
Denguevirus siRNApools) 30h 283candidates MCT4 Replicationphase enrichmentanalysis
DENVNew usingPanther;gene
GuineaCstrain expression—microarray;
proteininteraction
network
Taietal. HepatitisCvirus Huh7/Rep- ArrayedDharmacon 72h N/A Viralreplication Yes Replicon Yes Increased PI1KA Replication Geneontology;
(2009) Subgenomic Feo siARRAY (luciferase) expression replicon complex clustered;literature
genotype1b human decreasesby expression formation, review;othercellline:
replicon genome >2SDs withthreshold generationof OR6repliconcellline,
siRNAlibrary ofq<0.10 HCV UHCVcon57.3;protein
(21,094genes) nonstructural expression;Western
protein-associated blot;small-molecule
membranes Wortmannin,brefeldin
A;reagentredundancy;
236pools— 13pools COPI- Early shRNAs;localization
186 Coatomer studies;virus:HCV-
replicated—96 JFH1
confirmed Hepcidin Cellulartranslation
Lietal. HepatitisCvirus Huh7.5.1 ArrayedDharmacon 72h 48h %Infectivity Yes Infectivity Yes Infectivity RAB9p40 Neededforboth IndividualsiRNAs,
(2009) JFH-1 siARRAY (HCVCore <50%plate >150%pfplate HCVandHIV enrichmentanalysesfor
siRNAlibrary; Antibody6G7) 407candidate mean;cell 114candidate mean;cell molecularfunctionand
human pools number>50% pools number>50% biologicalprocess
genome ofplatemean platemean accordingtoPanther
(19,470genes) classification;network
analysesinteractome
screens+HPRD;
RT-PCR
Sessionsetal. Denguevirus Dipterancells ArrayedGenome-wide 48h 72h Expressionof Yes Inhibited No N/A FLJ20254; RNA Geneontology;invivo
(2009) DENV-S2 RNAilibrary envelopeprotein infection TAZ; accumulation mosquitoAe.aegypti;
DRSC2.0 218candidate (cid:3)1.5-foldwith EXDL2; validationofhuman
(22,632 dsRNAs— p<0.05 CNOT2 homologuesiRNAsin
dsRNAs) rescreen179 Huh-7cells;other
dsRNA— viruses:YFV17D
identified118 vaccinestrain,Coxsackie
dsRNA¼116 B3(strain20;CB3);
genes—111 RT-qPCR
novel
Brassetal. InfluenzaAvirus U2OS ArrayedDharmacon 72h 12h %Infectivity Yes <55% Yes >200% IFITM3 Early Rescreenedcandidates;
(2009) A/PuertoRico/ siARRAY (anti-HA infectivity; infectivity; (GO)enrichment
8/34 siRNAlibrary; antibody) 312pools viability>40% 22pools viability>40% analysis;othercelllines
human primarylungfibroblasts,
genome HeLa,A549,ChEFs,
(17,877genes) MDCKs;otherviruses:
HIV,PR8,H3N2A/
Udorn/72,A/Brisbane/
59/07H1N1,A/
Uruguay/716/07
H3N2,A/Aichi/2/68
H3N2,MLV,VSV-G;
pseudoparticlesMLV
withthefollowing
envelopes:H1,H3,H5,
H7,MACH,
MLVRescueconstruct;
overexpression;Western
blot;
immunofluorescence
Shapiraetal. InfluenzaAvirus HBECs ArrayedDharmacon 72h 48h Viralparticle Yes Change Yes Change WNT/p53 NS1related Pathwayanalysis;
(2009) IAVPR8 SMARTpool production >twofoldless >twofold pathway clusteringofexpression
(reinfection); replication more data;functional
IFNproduction comparedto replication annotations;yeast2
median comparedto hybrid
median
Continued