Innate antiviral immunity : methods and protocols

277 Pages·2017·5.86 MB·English

by  Mossman, Karen

Methods in
Molecular Biology 1656
Karen Mossman Editor
Innate
Antiviral
Immunity
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Innate Antiviral Immunity
Methods and Protocols
Edited by
Karen Mossman
Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
Editor
KarenMossman
BiochemistryandBiomedical
Sciences
McMasterUniversity
Hamilton,ON,Canada
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-7236-4 ISBN978-1-4939-7237-1 (eBook)
DOI10.1007/978-1-4939-7237-1
LibraryofCongressControlNumber:2017947873
©SpringerScience+BusinessMediaLLC2017
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Preface
This book on Innate Antiviral Immunity explores methods to study the complex and
evolving interplay between a virus and its host that range from model systems to the
detection of chemical molecules. The collection starts with the application of humanized
mice and zebrafish as model organisms to study virus-host interactions and induction of
innate immune responses. Subsequent chapters outline diverse methods to detect small
interferingRNAs,microRNAs,andvirus-deriveddsRNAfromavarietyofcells,tissues,and
organisms. Several chapters are dedicated to interrogating the cytosolic RNA and DNA
sensingpathways,includingusingRNAPAMPsasmolecular tools,purificationofcGAMP
fromvirusparticlesandinfectedcells,andmechanismstovisualizethesubcellularlocaliza-
tion and activation of the adaptor proteins MAVS and STING. Cutting-edge methods,
includinghigh-throughputandgenome-wideCRISPR/Cas9screens,chromosomeconfor-
mation capture, and whole-exome sequencing, are described to identify novel mediators,
pathways, and variants underlying host susceptibility. Given the importance of studying
thesepathways and players under physiologic conditions, methodsdescribing the isolation
of primary mouse sensory neurons and group 2 innate lymphoid cells are also provided.
Finally,thiscollectioncomesfullcirclebacktothewholeorganismlevelandconcludeswith
epidemiological methods to investigate virus-host interactions and the induction of innate
immunity. Thus, this collection in Methods in Molecular Biology spans a diverse array of
approachestostudyandelucidatetheintricaciesofinnateantiviralimmunity.
Hamilton,ON,Canada KarenMossman
v
Contents
Preface..................................................................... v
Contributors................................................................ ix
1 TheApplicationofHumanizedMouseModelsfor theStudy
ofHumanExclusiveViruses.............................................. 1
FatemehVahedi,ElizabethC.Giles,andAliA.Ashkar
2 ZebrafishasaModelfor theStudyofHost-VirusInteractions................ 57
PengFeiZouandPinNie
3 NorthernBlotDetectionofVirus-DerivedSmallInterfering
RNAsinCaenorhabditiselegansUsingNonradioactiveOligoProbes.......... 79
TianyunLongandRuiLu
4 ExtractionandqPCR-BasedDetectionofmiRNAsfromCultured
PBMCsofBubalineOrigin............................................... 89
ChandraS.Mukhopadhyay,RamneekVerma,andJasdeepSingh
5 VisualizingVirus-DeriveddsRNAUsingAntibody-Independent
and-DependentMethods................................................ 103
SarahJ.PoynterandStephanieJ.DeWitte-Orr
6 RNAPAMPsasMolecularToolsforEvaluatingRIG-IFunction
inInnateImmunity ..................................................... 119
ReneeC.Ireton,CourtneyWilkins,andMichaelGaleJr.
7 MethodstoVisualizeMAVSSubcellularLocalization ....................... 131
ChristineVazquez,DiaC.Beachboard,andStacyM.Horner
8 PurificationofCyclicGMP-AMPfromVirusesandMeasurement
ofItsActivityinCellCulture............................................. 143
AliceMayer,JonathanMaelfait,AnneBridgeman,andJanRehwinkel
9 cGAMPQuantificationinVirus-InfectedHumanMonocyte-Derived
CellsbyHPLC-CoupledTandemMassSpectrometry ....................... 153
JenniferPaijo,VolkhardKaever,andUlrichKalinke
10 MethodsofAssessingSTINGActivationandTrafficking .................... 167
VladislavPokatayevandNanYan
11 Genome-WideCRISPR/Cas9ScreeningforHigh-Throughput
FunctionalGenomicsinHumanCells..................................... 175
ShiyouZhu,YuexinZhou,andWenshengWei
12 High-ThroughputScreeningforIdentificationofNovelInnate
ImmuneActivators...................................................... 183
BryanJ.GallandVictorR.DeFilippis
13 ChromosomeConformationCaptureforResearchonInnate
AntiviralImmunity...................................................... 195
YoonJungKimandTaeHoonKim
vii
viii Contents
14 DiscoveryofVariantsUnderlyingHostSusceptibilitytoVirus
InfectionUsingWhole-ExomeSequencing ................................ 209
GabrielA.Leiva-Torres,NestorNebesio,andSilviaM.Vidal
15 Isolation,Purification,andCultureofPrimaryMurineSensoryNeurons ...... 229
SarahKatzenell,JorgeR.Cabrera,BrianJ.North,andDavidA.Leib
16 IsolationofGroup2InnateLymphoidCellsfromMouseLungs ............. 253
ClaudiaU.DuerrandJ¨orgH.Fritz
17 EpidemiologicalMethods................................................ 263
BiaoWangandMarkLoeb
Index ...................................................................... 273
Contributors
ALIA.ASHKAR (cid:1) DepartmentofPathologyandMolecularMedicine,McMasterImmunology
ResearchCentre,Hamilton,ON,Canada;MGDeGrooteInstituteforInfectiousDisease
Research,McMasterImmunologyResearchCentre,Hamilton,ON,Canada
DIAC.BEACHBOARD (cid:1) DepartmentofMolecularGeneticsandMicrobiology,DukeUniversity
MedicalCenter,Durham,NC,USA
ANNE BRIDGEMAN (cid:1) MedicalResearchCouncilHumanImmunologyUnit,Radcliffe
DepartmentofMedicine,MedicalResearchCouncilWeatherallInstituteofMolecular
Medicine,UniversityofOxford,JohnRadcliffeHospital,Oxford,UK
JORGER.CABRERA (cid:1) DepartmentofMicrobiologyandImmunology,GeiselSchoolofMedicine,
DartmouthUniversity,Lebanon,NH,USA
VICTOR R.DEFILIPPIS (cid:1) VaccineandGeneTherapyInstitute,OregonHealthandScience
University,Beaverton,OR,USA
STEPHANIEJ.DEWITTE-ORR (cid:1) DepartmentsofHealthSciencesandBiology,WilfridLaurier
University,Waterloo,ON,Canada
CLAUDIAU.DUERR (cid:1) DepartmentofMicrobiologyandImmunology,McGillUniversity
ResearchCentreonComplexTraits(MRCCT),McGillUniversity,Montreal,QC,
Canada
JO¨RGH.FRITZ (cid:1) DepartmentofMicrobiologyandImmunology,McGillUniversityResearch
CentreonComplexTraits(MRCCT),McGillUniversity,Montreal,QC,Canada;
DepartmentofPhysiology,McGillUniversityResearchCentreonComplexTraits
(MRCCT),McGillUniversity,Montreal,QC,Canada
MICHAELGALEJR. (cid:1) DepartmentofImmunology,Center forInnateImmunityand
ImmuneDisease,UniversityofWashingtonSchoolofMedicine,Seattle,WA,USA
BRYANJ.GALL (cid:1) VaccineandGeneTherapyInstitute,OregonHealthandScienceUniversity,
Beaverton,OR,USA
ELIZABETHC.GILES (cid:1) DepartmentofPathologyandMolecularMedicine,McMaster
ImmunologyResearchCentre,Hamilton,ON,Canada;MGDeGrooteInstitutefor
InfectiousDiseaseResearch,McMasterImmunologyResearchCentre,Hamilton,ON,
Canada
STACYM.HORNER (cid:1) DepartmentofMolecularGeneticsandMicrobiology,DukeUniversity
MedicalCenter,Durham,NC,USA;DepartmentofMedicine,DukeUniversityMedical
Center,Durham,NC,USA
RENEEC.IRETON (cid:1) DepartmentofImmunology,Center forInnateImmunityandImmune
Disease,UniversityofWashingtonSchoolofMedicine,Seattle,WA,USA
VOLKHARDKAEVER (cid:1) ResearchCoreUnitMetabolomics,HannoverMedicalSchool,
Hannover,Germany
ULRICHKALINKE (cid:1) InstituteforExperimentalInfectionResearch,TWINCORE,Centrefor
ExperimentalandClinicalInfectionResearch,HannoverMedicalSchool,Hannover,
Germany
SARAHKATZENELL (cid:1) DepartmentofMicrobiologyandImmunology,GeiselSchoolofMedicine,
DartmouthUniversity,Lebanon,NH,USA
TAEHOONKIM (cid:1) DepartmentofBiologicalScienceandCenter forSystemsBiology,The
UniversityofTexasatDallas,Richardson,TX,USA
ix
x Contributors
YOONJUNG KIM (cid:1) DepartmentofBiologicalScienceandCenter forSystemsBiology,The
UniversityofTexasatDallas,Richardson,TX,USA
DAVIDA.LEIB (cid:1) DepartmentofMicrobiologyandImmunology,GeiselSchoolofMedicine,
DartmouthUniversity,Lebanon,NH,USA
GABRIEL A.LEIVA-TORRES (cid:1) DepartmentofHumanGenetics,McGillUniversity,Montreal,
QC,Canada;McGillUniversityResearchCenteronComplexTraits,Montreal,QC,
Canada;DepartmentofMedicine,McGillUniversity,Montreal,QC,Canada
MARKLOEB (cid:1) DepartmentofMedicine,McMasterUniversity,Hamilton,ON,Canada;
DepartmentofPathologyandMolecularMedicine,McMasterUniversity,Hamilton,ON,
Canada;DepartmentofHealthResearchMethods,Evidence,andImpact,McMaster
University,Hamilton,ON,Canada
TIANYUNLONG (cid:1) DepartmentofBiologicalSciences,LouisianaStateUniversity,Baton
Rouge,LA,USA
RUILU (cid:1) DepartmentofBiologicalSciences,LouisianaStateUniversity,BatonRouge,LA,
USA
JONATHANMAELFAIT (cid:1) MedicalResearchCouncilHumanImmunologyUnit,Radcliffe
DepartmentofMedicine,MedicalResearchCouncilWeatherallInstituteofMolecular
Medicine,UniversityofOxford,JohnRadcliffeHospital,Oxford,UK;Laboratoryof
ImmunoregulationandMucosalImmunology,VIBCenter forInflammationResearch,
Ghent,Belgium;DepartmentofInternalMedicine,GhentUniversity,Ghent,Belgium
ALICEMAYER (cid:1) MedicalResearchCouncilHumanImmunologyUnit,RadcliffeDepartment
ofMedicine,MedicalResearchCouncilWeatherallInstituteofMolecularMedicine,
UniversityofOxford,JohnRadcliffeHospital,Oxford,UK
CHANDRAS.MUKHOPADHYAY (cid:1) SchoolofAnimalBiotechnology,GuruAngadDevVeterinary
andAnimalSciencesUniversity(GADVASU),Ludhiana,Punjab,India
NESTORNEBESIO (cid:1) DepartmentofHumanGenetics,McGillUniversity,Montreal,QC,
Canada;McGillUniversityResearchCenteronComplexTraits,Montreal,QC,Canada;
DepartmentofMedicine,McGillUniversity,Montreal,QC,Canada
PINNIE (cid:1) StateKeyLaboratoryofFreshwaterEcologyandBiotechnology,Instituteof
Hydrobiology,ChineseAcademyofSciences,Wuhan,HubeiProvince,China
BRIAN J.NORTH (cid:1) DepartmentofMicrobiologyandImmunology,GeiselSchoolofMedicine,
DartmouthUniversity,Lebanon,NH,USA
JENNIFERPAIJO (cid:1) InstituteforExperimentalInfectionResearch,TWINCORE,Centrefor
ExperimentalandClinicalInfectionResearch,HannoverMedicalSchool,Hannover,
Germany
VLADISLAVPOKATAYEV (cid:1) DepartmentofMicrobiology,UniversityofTexasSouthwestern
MedicalCenter,Dallas,TX,USA
SARAH J.POYNTER (cid:1) DepartmentofBiology,WilfridLaurierUniversity,Waterloo,ON,
Canada
JANREHWINKEL (cid:1) MedicalResearchCouncilHumanImmunologyUnit,Radcliffe
DepartmentofMedicine,MedicalResearchCouncilWeatherallInstituteofMolecular
Medicine,UniversityofOxford,Oxford,UK
JASDEEPSINGH (cid:1) DepartmentofExperimentalMedicineandBiotechnology,PGIMER,
Chandigarh,Punjab,India
FATEMEHVAHEDI (cid:1) DepartmentofPathologyandMolecularMedicine,McMaster
ImmunologyResearchCentre,Hamilton,ON,Canada;MGDeGrooteInstitutefor
InfectiousDiseaseResearch,McMasterImmunologyResearchCentre,Hamilton,ON,
Canada
Contributors xi
CHRISTINEVAZQUEZ (cid:1) DepartmentofMolecularGeneticsandMicrobiology,DukeUniversity
MedicalCenter,Durham,NC,USA
RAMNEEK VERMA (cid:1) SchoolofAnimalBiotechnology,GuruAngadDevVeterinaryand
AnimalSciencesUniversity(GADVASU),Ludhiana,Punjab,India
SILVIAM.VIDAL (cid:1) DepartmentofHumanGenetics,McGillUniversity,Montreal,QC,
Canada;McGillUniversityResearchCenteronComplexTraits,Montreal,QC,Canada;
DepartmentofMedicine,McGillUniversity,Montreal,QC,Canada
BIAOWANG (cid:1) DepartmentofPathologyandMolecularMedicine,McMasterUniversity,
Hamilton,ON,Canada
WENSHENGWEI (cid:1) BiodynamicOpticalImagingCenter(BIOPIC),BeijingAdvanced
InnovationCenter forGenomics,Peking-TsinghuaCenter forLifeSciences,StateKey
LaboratoryofProteinandPlantGeneResearch,SchoolofLifeSciences,PekingUniversity,
Beijing,China
COURTNEYWILKINS (cid:1) DepartmentofImmunology,Center forInnateImmunityand
ImmuneDisease,UniversityofWashingtonSchoolofMedicine,Seattle,WA,USA
NANYAN (cid:1) DepartmentofImmunologyandDepartmentofMicrobiology,UniversityofTexas
SouthwesternMedicalCenter,Dallas,TX,USA
YUEXINZHOU (cid:1) BiodynamicOpticalImagingCenter(BIOPIC),BeijingAdvanced
InnovationCenter forGenomics,Peking-TsinghuaCenter forLifeSciences,StateKey
LaboratoryofProteinandPlantGeneResearch,SchoolofLifeSciences,PekingUniversity,
Beijing,China
SHIYOU ZHU (cid:1) BiodynamicOpticalImagingCenter(BIOPIC),BeijingAdvanced
InnovationCenter forGenomics,Peking-TsinghuaNationalInstituteofBiological
Sciences,StateKeyLaboratoryofProteinandPlantGeneResearch,SchoolofLifeSciences,
PekingUniversity,Beijing,China
PENG FEIZOU (cid:1) CollegeofFisheries,JimeiUniversity,Xiamen,FujianProvince,China