Vectorology for Optogenetics and Chemogenetics

331 Pages·2023·10.714 MB·English

by  Mark A.G. Eldridge, Adriana Galvan

Neuromethods 195
Mark A. G. Eldridge
Adriana Galvan Editors
Vectorology
for Optogenetics
and Chemo-
genetics
N
EUROMETHODS
SeriesEditor
Wolfgang Walz
University ofSaskatchewan
Saskatoon, SK,Canada
Forfurther volumes:
http://www.springer.com/series/7657
Neuromethodspublishescutting-edgemethodsandprotocolsinallareasofneuroscienceas
wellastranslationalneurologicalandmentalresearch.Eachvolumeintheseriesofferstested
laboratoryprotocols,step-by-stepmethodsforreproduciblelabexperimentsandaddresses
methodologicalcontroversiesandpitfallsinordertoaidneuroscientistsinexperimentation.
Neuromethodsfocusesontraditionalandemergingtopicswithwide-rangingimplicationsto
brain function, such as electrophysiology, neuroimaging, behavioral analysis, genomics,
neurodegeneration,translationalresearchandclinicaltrials.Neuromethodsprovidesinvesti-
gators and trainees with highly useful compendiums of key strategies and approaches for
successful research in animal and human brain function including translational “bench to
bedside”approachestomentalandneurologicaldiseases.
Vectorology for Optogenetics
and Chemogenetics
Edited by
Mark A. G. Eldridge
NIMH, National Institutes of Health, Behesda, MD, USA
Adriana Galvan
Department of Neurology, School of Medicine, and Emory National Primate Research Center,
Emory University, Atlanta, GA, USA
Editors
MarkA.G.Eldridge AdrianaGalvan
NIMH DepartmentofNeurology,SchoolofMedicine,andEmory
NationalInstitutesofHealth NationalPrimateResearchCenter
Behesda,MD,USA EmoryUniversity
Atlanta,GA,USA
ISSN0893-2336 ISSN1940-6045 (electronic)
Neuromethods
ISBN978-1-0716-2917-8 ISBN978-1-0716-2918-5 (eBook)
https://doi.org/10.1007/978-1-0716-2918-5
©ThisisaU.S.governmentworkandnotundercopyrightprotectionintheU.S.;foreigncopyrightprotectionmay
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or in any other physical way, and transmission or information storage and retrieval, electronicadaptation, computer
software,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped.
Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply,
evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations
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Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto
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Preface to the Series
Under theguidanceofitsfoundersAlanBoultonandGlenBaker,theNeuromethodsseries
byHumanaPresshasbeenverysuccessfulsincethefirstvolumeappearedin1985.Inabout
17 years, 37 volumes have been published. In 2006, Springer Science + Business Media
madearenewedcommitmenttothisseries.Thenewprogramwillfocusonmethodsthatare
either uniquetothenervoussystemandexcitablecellsor whichneedspecialconsideration
to be applied to the neurosciences. The program will strike a balance between recent and
excitingdevelopmentslikethoseconcerningnewanimalmodelsofdisease,imaging,invivo
methods, and more established techniques. These include immunocytochemistry and
electrophysiologicaltechnologies.Newtraineesinneurosciencesstillneedasoundfooting
in these older methods in order to apply a critical approach to their results. The careful
application of methods is probably the most important step in the process of scientific
inquiry. In the past, new methodologies led the way in developing new disciplines in the
biological and medical sciences. For example, Physiology emerged out of Anatomy in the
nineteenthcenturybyharnessingnewmethodsbasedonthenewlydiscoveredphenomenon
of electricity. Nowadays, therelationships between disciplines and methods are more com-
plex.Methodsarenowwidelysharedbetweendisciplinesandresearchareas.Newdevelop-
ments in electronic publishing also make it possible for scientists to download chapters or
protocolsselectivelywithinaveryshorttimeofencounteringthem.Thisnewapproachhas
beentakenintoaccountinthedesignofindividualvolumesandchaptersinthisseries.
Saskatoon,SK,Canada WolfgangWalz
v
About This Book
Thisvolumeprovidesanoverviewoftheviralvectorsandassociatedmethodsusedtoapply
chemogenetic and optogenetic tools to the study of neural circuits. The chapters in this
bookareorganizedintothreeparts.
PartIcoverstheviralvectorsthathavebeenoptimizedforneuronalexpressionandthe
methods for their production and quality control. Note that, despite being widely used in
the field, adeno-associated viruses (AAVs) are not covered here as their capsids are being
rapidlyevolvedandrefined,andmanyarecommerciallyavailable.Henceweencouragethe
readertosearchforrecentreviewarticlesiftheyareconsideringusingAAVsintheirresearch
(e.g.,Li,C.andR.J.Samulski,NatRevGenet(2020);Wang,D.,etal.NatRevDrugDiscov
(2019)) and to purchase virus from commercial sources, such as Addgene (www.addgene.
org), the UNC vector core (www.med.unc.edu/genetherapy/vectorcore/), or the Penn
vectorcore(www.gtp.med.upenn.edu/core-laboratories-public/vector-core).
PartIIprovidesinformationonvectormodificationsandapplications.Theseincludethe
appropriateuseofcapsidselectionandenhancer/promotersequencesforcell-typeselective
expression,theuseoftranscriptomicanalysisforneuronclassification,methodsforpathway-
specifictargeting,andadescriptionofthedevelopmentofvectorsforsystemicdelivery.
PartIIIprovidespracticaladviceforthedeliveryofviralvectors,andfortheverification
ofinjectionaccuracyandmonitoringoftransgeneexpression.
Per the Neuromethods series style, all chapters include step-by-step detailed protocols
that can be easily followed, along with sections detailing tips and tricks for overcoming
commonproblems.
vii
Contents
PrefacetotheSeries ........................................................... v
AboutThisBook.............................................................. vii
Contributors................................................................. xi
PART I VECTORS USED IN SYSTEMS NEUROSCIENCE RESEARCH
1 Production,Testing,andVerificationofLentivirusforRegionalTargeting
intheOld-WorldMonkeyBrain ..... ....... ....... ........ ....... ........ 3
WalterLerchner,AlyssaLuz-Ricca,KianaDash,
VioletteDerMinassian,andBarryJ.Richmond
2 HiRet/NeuRetVectors:LentiviralSystemforHighlyEfficientGene
TransferThroughRetrogradeAxonalTransport..... ........ ....... ........ 17
KentaKobayashi,ShigekiKato,andKazutoKobayashi
3 GenerationofHigh-TiterDefectiveHSV-1AmpliconVectors........ ........ 29
RachaelNeve
4 GenerationandApplicationofEngineeredRabiesViralVectors
forNeuralCircuitResearch ......... ....... ....... ....... ....... ..... .... 51
MasahiroYamaguchi,MoeIwata,RikiKamaguchi,
andFumitakaOsakada
5 QualityControlforAdeno-AssociatedViralVectorProduction....... ........ 77
InaErsing,MeghanRego,ChenWang,YijunZhang,
KateHartenDeMaio,MichellePetrozzi,AlannaFava,
GabrielleClouse,MarcellaPatrick,Karen Guerin,
andMelinaFan
PART II VECTOR MODIFICATIONS AND APPLICATIONS
6 VectorTropism..... ....... ........ ....... ....... ........ ....... ........ 105
Shih-HengChen,BoHe,SarwynSingh,andNeginP.Martin
7 VirusesforSystemicDelivery........ ....... ....... .. ...... .... ... ........ 125
ZikaiWang,AlonGreenbaum,andJenniferB.Treweek
8 TranscriptomicDefinitionofNeuronTypes......... ........ ....... ........ 153
JingHeandWilliamR.Stauffer
9 EnhancersforSelectiveTargeting.... ....... ....... ........ ....... ........ 169
JessicaLinandJordaneDimidschstein
10 Pathway-SelectiveReversiblePerturbationsUsingaDouble-Infection
TechniqueintheMacaqueBrain..... ....... ....... ..... ... ....... ........ 185
WimVanduffelandTadashiIsa
11 Pathway-SpecificChemogeneticManipulationbyApplyingLigand
toAxonallyExpressedDREADDs .......... ....... ........ ....... ........ 207
MaricelaX.Martinez,MitchellR.Farrell,
andStephenV.Mahler
ix
x Contents
PART III VECTOR DELIVERYAND VERIFICATION OF EXPRESSION
12 ConvectionEnhancedDeliveryofViralVectors ..... ........ ....... ........ 223
DevonGriggs,TiphaineBelloir,JasmineZhou,
andAzadehYazdan-Shahmorad
13 MultichannelMicroinjectorArraysforEfficientViralVectorDelivery
intoRhesusMonkeyBrain.......... ....... ....... ........ ....... ........ 245
NanamiL.Miyazaki,BingLi,andMarkA.G.Eldridge
14 MethodstoVerifyExpressionandFunctionofDREADDsUsingPET........ 263
YujiNagaiandTakafumiMinamimoto
15 ReporterSelectionandPostmortemMethodstoVerifyTransgene
Expression ......... ....... ........ ...... .... .... ........ ....... ........ 275
KateS.Heffernan,YolandSmith,andAdrianaGalvan
16 Considerationsfor theUseofViralVectorsinNonhumanPrimates........... 293
MartinBohlenandSe´bastienTremblay
Index .......... ........ ....... ........ ....... ....... ........ ....... ........ 331
Contributors
TIPHAINEBELLOIR (cid:129) WashingtonNationalPrimateResearchCenter,Seattle,WA,USA;
DepartmentofBioengineering,UniversityofWashington,Seattle,WA,USA
MARTINBOHLEN (cid:129) DepartmentofBiomedicalEngineering,DukeUniversity,Durham,NC,
USA;DepartmentofNeurobiology,DukeUniversitySchoolofMedicine,Durham,NC,
USA
SHIH-HENG CHEN (cid:129) ViralVectorCore,NeurobiologyLaboratory,NationalInstituteof
EnvironmentalHealthSciences,NIH/DHHS,ResearchTrianglePark,NC,USA
GABRIELLECLOUSE (cid:129) Addgene,Watertown,MA,USA
KIANA DASH (cid:129) LaboratoryofNeuropsychology,NIMH,NIH,Bethesda,MD,USA
VIOLETTEDERMINASSIAN (cid:129) LaboratoryofNeuropsychology,NIMH,NIH,Bethesda,MD,
USA
JORDANEDIMIDSCHSTEIN (cid:129) BroadInstituteofMITandHarvard,Cambridge,MA,USA
MARKA.G.ELDRIDGE (cid:129) LaboratoryofNeuropsychology,NationalInstituteofMental
Health,Bethesda,MD,USA
INAERSING (cid:129) Addgene,Watertown,MA,USA
MELINAFAN (cid:129) Addgene,Watertown,MA,USA
MITCHELLR.FARRELL (cid:129) DepartmentofNeurobiology&Behavior,UniversityofCalifornia,
Irvine,CA,USA
ALANNAFAVA (cid:129) Addgene,Watertown,MA,USA
ADRIANA GALVAN (cid:129) DivisionofNeuropharmacologyandNeurologicalDisorders,Emory
NationalPrimateResearchCenter,EmoryUniversity,Atlanta,GA,USA;UdallCenter
ofExcellenceforParkinson’sDiseaseResearch,EmoryUniversity,Atlanta,GA,USA;
DepartmentofNeurology,SchoolofMedicine,EmoryUniversity,Atlanta,GA,USA
ALON GREENBAUM (cid:129) JointDepartmentofBiomedicalEngineering,NorthCarolinaState
UniversityandUniversityofNorthCarolinaatChapelHill,Raleigh,NC,USA;
ComparativeMedicineInstitute,NorthCarolinaStateUniversity,Raleigh,NC,USA
DEVON GRIGGS (cid:129) DepartmentofElectricalandComputerEngineering,Universityof
Washington,Seattle,WA,USA;WashingtonNationalPrimateResearchCenter,Seattle,
WA,USA
KARENGUERIN (cid:129) VedereBioII,Inc.,Cambridge,MA,USA
KATES.HARTENDEMAIO (cid:129) Addgene,Watertown,MA,USA
BOHE (cid:129) ViralVectorCore,NeurobiologyLaboratory,NationalInstituteofEnvironmental
HealthSciences,NIH/DHHS,ResearchTrianglePark,NC,USA
JING HE (cid:129) DepartmentofNeurobiology,UniversityofPittsburgh,Pittsburgh,PA,USA
KATES.HEFFERNAN (cid:129) DivisionofNeuropharmacologyandNeurologicalDisorders,Emory
NationalPrimateResearchCenter,EmoryUniversity,Atlanta,GA,USA;UdallCenter
ofExcellenceforParkinson’sDiseaseResearch,EmoryUniversity,Atlanta,GA,USA
TADASHIISA (cid:129) DepartmentofNeuroscience,GraduateSchoolofMedicine,KyotoUniversity,
Kyoto,Japan;Institutefor theAdvancedStudyofHumanBiology(WPI-ASHBi),Kyoto
University,Kyoto,Japan
MOEIWATA (cid:129) LaboratoryofCellularPharmacology,GraduateSchoolofPharmaceutical
Sciences,NagoyaUniversity,Nagoya,Japan
xi