Herpes Simplex Virus : Methods and Protocols PDF
Preview Herpes Simplex Virus : Methods and Protocols
Methods in Molecular Biology 2060 Russell J. Diefenbach Cornel Fraefel Editors Herpes Simplex Virus Methods and Protocols Second Edition M M B ETHODS IN OLECULAR IO LO GY SeriesEditor JohnM.Walker School of Lifeand MedicalSciences University ofHertfordshire Hatfield, Hertfordshire, UK Forfurther volumes: http://www.springer.com/series/7651 For over 35 years, biological scientists have come to rely on the research protocols and methodologiesinthecriticallyacclaimedMethodsinMolecularBiologyseries.Theserieswas thefirsttointroducethestep-by-stepprotocolsapproachthathasbecomethestandardinall biomedicalprotocolpublishing.Eachprotocolisprovidedinreadily-reproduciblestep-by- step fashion, opening with an introductory overview, a list of the materials and reagents neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitutethekeyingredientineachandeveryvolumeoftheMethodsinMolecularBiology series. Tested and trusted, comprehensive and reliable, all protocols from the series are indexedinPubMed. Herpes Simplex Virus Methods and Protocols Second Edition Edited by Russell J. Diefenbach Department of Biomedical Sciences, Macquarie University, Sydney, NSW, Australia Cornel Fraefel Institute of Virology, University of Zurich, Zürich, Switzerland Editors RussellJ.Diefenbach CornelFraefel DepartmentofBiomedicalSciences InstituteofVirology MacquarieUniversity UniversityofZurich Sydney,NSW,Australia Zu¨rich,Switzerland ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-4939-9813-5 ISBN978-1-4939-9814-2 (eBook) https://doi.org/10.1007/978-1-4939-9814-2 ©SpringerScience+BusinessMedia,LLC,partofSpringerNature2020 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation, computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations andthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeenmade. Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. Covercaption:HSV-1virionsintheextracellularspaceofVerocellspreparedforelectronmicroscopybyhigh-pressure freezing,freeze-substitution,embeddingineponandultrathinsectioningshowingcore,capsid,tegument,envelopeand glycoproteins.Thesizedifferenceisduetothesectionplane.Bar¼100nm.ElisabethM.Schraner,InstituteofVirology, UniversityofZurich,Zu¨rich,Switzerland. ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature. Theregisteredcompanyaddressis:233SpringStreet,NewYork,NY10013,U.S.A. Preface Herpes simplex viruses type 1 and 2 (HSV-1, HSV-2) are important human pathogens. HSV-1,forexample,hasaworldwideseroprevalenceofmorethan80%inadults.Thevirus typicallyentersorofacialmucosalepithelialcells,whereproductiveinfectiontakesplace,but itcanalsoinfectgenitalmucosaepithelialcells.Productivereplicationinepithelialcellsleads toreleaseofprogenyvirusatthesiteofhostentry,fromwheretheviruscanaccessneurons of the trigeminal ganglia to establish lifelong latency and to create a reservoir for periodic reactivation.Inimmunocompromisedpatients,HSV-1cancauseseveremeningoencephali- tis or keratoconjunctivitis that can lead to permanent neurological damage and death or blindness, respectively, if not treated. The herpes simplex viruses have been the prototype virusesoftheAlphaherpesvirinaesubfamilyandhavebeenextensivelystudiedfordecadeson allaspectsofinfection,replication,andpathogenesis.HSV-1andHSV-2havealsobecome importanttoolstostudycellbiologyandimmunology,andfor thedevelopmentofinnova- tivevaccinesandvectorsforgene-andtumor therapy. Itwouldbeimpossibletocoverallaspectsofmethodologyrelatedtotheinvestigation of herpes simplex viruses in one book. We hope in this second edition that we have again successfullyencapsulatedasignificantbreathofrelevantmethodologybutalsoincorporated new rapidly developing technologies such as next-generation sequencing, CRISPR/Cas9 engineering, and the use of BioID to identify protein–protein interactions. The chapters containedwithinwillbeofinteresttoimmunologistsaswellasmolecularandcellbiologists. It will appeal to those researchers who wish to initiate molecular- and/or cellular-based approaches to investigate HSV. Many of the techniques can be readily translated to other closelyrelatedherpesviruses. The first two chapters of this book include comprehensive reviews on HSV-1 biology and life cycle and the current state of play in antiviral and vaccine development. These are followed by a wide collection of protocols, including basic protocols on growing viruses in cell culture and manipulating viral DNA. Other chapters describe approaches to design and application of HSV-1 vectors for cancer- and gene therapy, or to study specific aspects of HSV-1 biology such as latency, intracellular transport, and protein–protein interaction using a number of cell culture and animal models. Rapidly developing areas suchasthetopicofextracellular vesicles,inthecontextofHSV-1,havealsobeenincluded. Procedures for structural analyses, microscopy, proteomics, and testing of antivirals are included as well. The methods provided are intended to aid new researchers in the field of herpes virology as well as those experienced investigators wishing to embark on new techniques. We would like to thank all who have contributed to the completion of this book, in particulartheauthorsofthechapters.WewouldalsoliketothanktheeditoroftheMethods inMolecularBiologyseries,JohnWalker,forhisconstantsupportduringthepreparationof this volume. We gladly accepted John’s invitation to co-edit a second edition of a HSV protocols book largely based on our prior experience with the first edition and how well it v vi Preface has been received. Finally, we hope that our book will help many researchers in the herpes virus field in their pursuit of understanding the complex interactions between herpes virus andhost.Still,muchremainstobediscovered! Sydney,NSW,Australia RussellJ.Diefenbach Zu¨rich,Switzerland CornelFraefel Contents Preface ..................................................................... v Contributors................................................................. xi 1 TourdeHerpes:CyclingThroughtheLifeandBiologyofHSV-1............ 1 ChristopherE.Denes,RogerD.Everett,andRussellJ.Diefenbach 2 VaccinesforHerpesSimplex:RecentProgressDrivenbyViral andAdjuvantImmunology............................................... 31 KerrieJ.Sandgren, NaomiR.Truong,JacintaB.Smith, KirstieBertram,andAnthonyL.Cunningham 3 HerpesSimplexVirusGrowth,Preparation,andAssay ...................... 57 SereinaO.Sutter,PeggyMarconi,andAnitaF.Meier 4 EngineeringHSV-1VectorsforGeneTherapy ............................. 73 WilliamF.Goins,ShaohuaHuang,BonnieHall,MarcoMarzulli, JustusB.Cohen,andJosephC.Glorioso 5 PreparationofHerpesSimplexVirusType1(HSV-1)-Based AmpliconVectors....................................................... 91 CornelFraefelandAlbertoL.Epstein 6 HSV-1AmpliconVectorsasGeneticVaccines .............................. 111 AnitaF.MeierandAndreaS.Laimbacher 7 oHSVGenomeEditingbyMeansofgalKRecombineering.................. 131 LauraMenotti,ValerioLeoni,ValentinaGatta,BiljanaPetrovic, AndreaVannini,SimonaPepe,TatianaGianni,andGabriella Campadelli-Fiume 8 Rescue,Purification,andCharacterizationofaRecombinant HSVExpressingaTransgenicProtein ..................................... 153 AndreaVannini,BiljanaPetrovic,ValentinaGatta, ValerioLeoni,SimonaPepe,LauraMenotti, GabriellaCampadelli-Fiume,andTatianaGianni 9 CRISPR/Cas9-BasedGenomeEditingofHSV............................. 169 ThilagaVelusamy,AnjaliGowripalan,andDavidC.Tscharke 10 Latent/QuiescentHerpesSimplexVirus1GenomeDetection byFluorescenceInSituHybridization(FISH) ............................. 185 CamilleCohen,ArmelleCorpet,MohamedAliMaroui, FrancelineJuillard,andPatrickLomonte 11 OligonucleotideEnrichmentofHSV-1GenomicDNA fromClinicalSpecimensforUseinHigh-ThroughputSequencing............ 199 MackenzieM.Shipley,MollyM.Rathbun,andMoriahL.Szpara 12 HSVMutantGenerationandDualDetectionMethods forGainingInsightintoLatent/LyticCyclesInVivo ....................... 219 NancyM.SawtellandRichardL.Thompson vii viii Contents 13 PhenotypicandGenotypicTestingofHSV-1andHSV-2 ResistancetoAntivirals .................................................. 241 AndreasSauerbreiandKathrinBohn-Wippert 14 UsingPrimarySCGNeuronCulturestoStudyMolecular DeterminantsofHSV-1LatencyandReactivation .......................... 263 Hui-LanHu,KalanghadPuthankalamSrinivas,IanMohr, TonyT.Huang,andAngusC.Wilson 15 CharacterizationofExtracellularHSV-1VirionsbyProteomics............... 279 RogerLippe´ 16 AnalysisandSortingofIndividualHSV-1ParticlesbyFlowVirometry........ 289 BitaKhadivjam,NabilElBilali,andRogerLippe´ 17 Isolation/AnalysisofExtracellularMicrovesiclesfromHSV-1-Infected Cells .................................................................. 305 RaquelBello-MoralesandJose´AntonioL(cid:1)opez-Guerrero 18 ConformationalChangeinHerpesSimplexVirusEntry GlycoproteinsDetectedbyDotBlot ...................................... 319 TriKomalaSari,KatrinaA.Gianopulos,andAnthonyV.Nicola 19 BioIDCombinedwithMassSpectrometrytoStudy HerpesvirusProtein–ProteinInteractionNetworks ......................... 327 MujeebR.CheerathodiandDavidG.MeckesJr. 20 PreparationofHerpesSimplexVirus-InfectedPrimary NeuronsforTransmissionElectronMicroscopy ............................ 343 MonicaMiranda-Saksena,RossA.Boadle, andAnthonyL.Cunningham 21 TransmissionImmunoelectronMicroscopyofHerpesSimplex Virus-1-InfectedDorsalRootGangliaNeuronsSectioned inGrowthPlane........................................................ 355 MonicaMiranda-Saksena,RossA.Boadle, andAnthonyL.Cunningham 22 MultifluorescenceLiveAnalysisofHerpesSimplexVirus Type-1Replication...................................................... 365 MichaelSeyffertandCornelFraefel 23 Expression,Purification,andCrystallizationofHSV-1 GlycoproteinsforStructureDetermination ................................ 377 EllenM.White,SamuelD.Stampfer,andEkaterinaE.Heldwein 24 Expression,Purification,andCrystallizationofFull-Length HSV-1gBforStructureDetermination.................................... 395 RebeccaS.CooperandEkaterinaE.Heldwein 25 TheUseofMicrofluidicNeuronalDevicestoStudytheAnterograde AxonalTransportofHerpesSimplexVirus-1............................... 409 KevinDanastas,AnthonyL.Cunningham, andMonicaMiranda-Saksena Contents ix 26 AModelofInVivoHSV-1DNATransportUsingMurine RetinalGanglionCells................................................... 419 JenniferH.LaVail 27 TheMurineIntravaginalHSV-2ChallengeModelforInvestigation ofDNAVaccines........................................................ 429 JoshuaO.Marshak,LichunDong,andDavidM.Koelle Index ...................................................................... 455
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