Nanotechnology for Nucleic Acid Delivery: Methods and Protocols

404 Pages·2019·10.81 MB·English

by  Manfred Ogris

Methods in
Molecular Biology 1943
Manfred Ogris
Haider Sami Editors
Nanotechnology
for Nucleic
Acid Delivery
Methods and Protocols
Second Edition
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences,
University of Hertfordshire,Hatfield,
Hertfordshire AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Nanotechnology for Nucleic
Acid Delivery
Methods and Protocols
Second Edition
Edited by
Manfred Ogris
Laboratory of MacroMolecular Cancer Therapeutics (MMCT), Department of Pharmaceutical Chemistry,
Center of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Vienna, Austria
Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany
Haider Sami
Laboratory of MacroMolecular Cancer Therapeutics (MMCT), Department of Pharmaceutical Chemistry,
Center of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Vienna, Austria
Editors
ManfredOgris HaiderSami
LaboratoryofMacroMolecular LaboratoryofMacroMolecular
CancerTherapeutics(MMCT) CancerTherapeutics(MMCT)
DepartmentofPharmaceuticalChemistry DepartmentofPharmaceuticalChemistry
CenterofPharmaceuticalSciences CenterofPharmaceuticalSciences
FacultyofLifeSciences FacultyofLifeSciences
UniversityofVienna UniversityofVienna
Vienna,Austria Vienna,Austria
CenterforNanoScience(CeNS)
Ludwig-Maximilians-University
Munich,Germany
ISSN1064-3745 ISSN1940-6029 (electronic)
ISBN978-1-4939-9091-7 ISBN978-1-4939-9092-4 (eBook)
https://doi.org/10.1007/978-1-4939-9092-4
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Preface
Nanotechnology-enablednucleicaciddeliveryisarapidlyevolvingfieldandoffersamulti-
tude of possibilities for addressing the challenges faced by nucleic acid therapies. Since the
release of the first edition of this volume in 2013, several new technologies have emerged,
and existing protocols have further improved. Within this edition, we aim at updating the
existing chapters and at the same time adding new topics to offer an up-to-date view on
technologiesusedfor nucleicaciddelivery.
We have organized the contents of the current edition according to the sequence in
whichtechnologiesareemployedtodevelopformulationsfornucleicaciddelivery,starting
with chemical synthesis of carriers, nanoformulations, their characterization in vitro and
invivo,andtheirapplicationinpreclinicalmodels.Thefirstthreechaptersdealwithcarrier
synthesis.InChap.1,So¨renReinhardandcolleaguesprovideanewchapteronthesynthesis
of defined cationic lipid-oligomers for plasmid and siRNA transfection. David Oupicky
continueswithbiodegradableanddisulfide-crosslinkedpolymersbasedonoligo-andpoly-
cations in Chap. 2. Antoine Kichler and colleagues describe synthesis and application of
cationic,histidine-richpeptidesfornucleicaciddelivery(Chap.3).Directcovalentmodifi-
cation of oligonucleotides is described in the next two chapters. Johannes Winker and
colleagues, in Chap. 4, present a method on the generation of oligonucleotide bioconju-
0 0
gates by attaching fluorophores to the 3 or 5 end via click chemistry. Maxim Antopolski
provides detailed protocol on the covalent attachment of radionuclides for SPECT/CT
invivoimagingviaend-termattachedchelatorsinChap.5.WolfgangRo¨dletal.updatethe
synthesis protocols for peptide-polyethylenimine conjugates in Chap. 6. The new Chap. 7
byAntoineKichlerandcolleaguesdealswithamicellardeliverysystemforsiRNAdelivery,
whichcanbestabilizedbyphotopolymerization.NathalieMignetandco-workerspresenta
protocol for the synthesis of cationic and neutral lipids and their particle formation with
nucleic acids in Chap. 8. Lipidoids are a new class of transfection reagents. In Chap. 9,
KaushikThankietal.describesynthesisofalipidoid-polymer-basedformulationforsiRNA
delivery to cytosol. Coating of nanoparticles with successive layers of polymer and nucleic
acid allows formation of a well-defined, size-controlled delivery formulation. In Chap. 10,
Miriam Breunig and colleagues describe layer-by-layer technique for siRNA delivery and
also include targeting ligands. Guangzhao Mao and co-workers apply layer-by-layer tech-
nique using biodegradable polymers for coating surfaces for sequential gene delivery
(Chap. 11). Tatiana Segura and colleagues report a technology where polyplexes are
incorporated into hydrogels for surface coating, which then allows for transfection of cells
grownontopofthelayer(Chap.12).Analysisofnanoparticlesbyatomicforcemicroscopy
(AFM) gives insights not only into particle size but also surface topology. Guanzhao Mao
andcolleaguesdescribetheapplicationofAFMtechniquesforstudyingdisassemblyofDNA
nanoparticles and nanofilms in Chap. 13. For further preclinical and clinical development,
gene delivery formulations with long-term storage stability are desirable and offer ease of
usage. Wolfgang Friess and colleagues in Chap. 14 present a lyophilization protocol for
optimalfreezingwithcryoprotectantandfreeze-dryingofpolyplexes.InChap.15,ourlab
presentsarobustandcost-effectiveprotocolforthemeasurementofluciferasereportergene
expressionforinvestigatingnanoparticle-mediateddeliveryofnucleicacids.Localactivation
of nanoformulations and enhancement of nucleic acid delivery in vivo can be achieved by
v
vi Preface
several methods to achieve stimuli-based delivery. Ine Lentacker and colleagues apply
ultrasound-activated microbubbles to enhance local nucleicacid delivery (Chap.16). Olga
Mykhaylyk and colleagues describe in Chap. 17 the synthesis and in vitro evaluation of
magnetic nanoparticles and microbubbles for nucleic acid delivery, which can be targeted
withmagneticforceandactivatedbyultrasound.
Biocompatibilityandtoxicityaredecisiveparametersfornanoformulationsandthefinal
fateofnucleicacidcargo,bothonthecellularlevelandwithinanorganism.Boththecarrier
systemandthedeliverednucleicaciditselfcantriggersideeffects,whichcanalsoinfluence
the therapeutic effect of nucleic acids. In three chapters (Chaps. 18–20), Moein Moghimi
and colleagues provide detailed protocols for a quantitative evaluation of polycation-
mediated cytotoxicity. Lactate dehydrogenase (LDH) is released after cell rupture, being
anearlyeventinnecrosisandalateeventinapoptosis.Chapter18givesaprotocolforafast
andaccurateassayforLDHrelease,whichcanbeappliedpriortomoredetailedtoxicologi-
calstudies.Trackingonsetofapoptosisgivesinsightsintothemechanismofnanoparticleor
polymer-inducedtoxicity.InChap.19,afluorimetricassayfordetectionofcaspaseactivityis
reported. For polycations, a distinct mitochondrial toxicity has been observed, which is
supposedtobeduetoperturbationofmembraneintegrity.InChap.20,ArnaldurHalland
Moein Moghimi present a protocol on measuring mitochondrial bioenergetics by high-
resolutionrespirometry.Boththeinnateandadaptiveimmunesystemcanplayaroleinthe
immunological response when an organism is exposed to exogenous nucleic acids and
carrier systems. The intrinsic effect of siRNA on cytokine induction in lung cells (after
pulmonary delivery of siRNA) is analyzed in Chap. 21 by Olivia Merkel and colleagues,
presentingaprotocolfordetectingintracellularcytokinesaftersortingofimmunecellsusing
antibody-coated magnetic beads. Although coating with polyethylene glycol (PEG) can
improve biocompatibility and blood circulation of nanoparticles, antibodies against PEG
canneutralizethiseffect.TatsuroIshidaetal.inChap.22provideaprotocolforquantifying
the anti-PEG induction in vivo to predict the blood clearance of PEGylated formulations
after repeated administration. Investigation of the biodistribution of nucleic acid after
in vivo administration is imperative for desirable therapeutic interventions. Near-infrared
imaging using fluorophores allows real-time tracking of nucleic acid delivery in vivo. Jean-
Luc Coll and colleagues describe labeling of nanoparticles with appropriate near-infrared
fluorophores and their detection in vivo (Chap. 23). The three final chapters include
protocols for tissue-directed plasmid and siRNA delivery: In Chap. 24, Olivia Merkel and
colleaguesapplysiRNAbyintratrachealinstillationintothelungandprovideaprotocolon
identification of distinct cell types in the lung that take up siRNA. In Chap. 25, Nathalie
Mignet et al. use cationic microbubbles in combination with ultrasound to allow efficient
transgeneexpression intheliver usingoptimizedsmallplasmids.In Chap.26,Mark Zabel
and colleagues describe preparation and application of lipopeptide formulation to achieve
siRNAdeliverytothecentralnervoussystem.
Taken together, the second version of Nanotechnology for Nucleic Acid Delivery deals
withnotonlyalreadyestablishedmethodsbutalsoemergingaspectsinthisfield.Abroadset
oftopicsiscoveredrangingfromchemicalsynthesisofmacromoleculesandbioconjugates;
novel and established nanoformulations; characterization of these nanoformulations for
biophysical,biological,andtoxicologicalaspects;andalsoprotocolsdealingwithapplication
andimagingofsuchcarriersystemsinvivo.
Vienna,Austria ManfredOgris
HaiderSami
Contents
Preface ..................................................................... v
Contributors................................................................. xi
1 Sequence-DefinedCationicLipo-OligomersContainingUnsaturated
FattyAcidsforTransfection.............................................. 1
S¨orenReinhardandErnstWagner
2 SynthesisofBioreduciblePolycationswithControlledTopologies ............ 27
Ye-ZiYou,Jun-JieYan,FeiYu,Zhi-QiangYu,andDavidOupicky
3 Histidine-RichCationicCell-PenetratingPeptidesforPlasmid
DNAandsiRNADelivery................................................ 39
AntoineKichler,A.JamesMason,ArnaudMarquette,
andBurkhardBechinger
4 CovalentFluorophoreLabelingofOligonucleotidesandGeneration
ofOtherOligonucleotideBioconjugates................................... 61
CorneliaLorenzerandJohannesWinkler
5 SyntheticOligonucleotidesinSPECT/CTInVivoImaging:Chemical
Modifications,In111ComplexFormation,Incorporationinto
DrugDeliverySystems .................................................. 73
MaximAntopolsky
6 SynthesisofPolyethylenimine-BasedNanocarriersforSystemic
TumorTargetingofNucleicAcids ........................................ 83
WolfgangR¨odl,AlexanderTaschauer,DavidSchaffert,
andErnstWagner,andManfredOgris
7 CationicPhotopolymerizedPolydiacetylenic(PDA)Micellesfor
siRNADelivery......................................................... 101
ManonRipoll,PatrickNeuberg,Jean-SergeRemy,
andAntoineKichler
8 LipidsforNucleicAcidDelivery:CationicorNeutralLipoplexes,
Synthesis,andParticleFormation......................................... 123
MichelBessodes,HeleneDhotel,andNathalieMignet
9 Preparation,Characterization,andInVitroEvaluationofLipidoid–Polymer
HybridNanoparticlesforsiRNADeliverytotheCytosol .................... 141
KaushikThanki,XianghuiZeng,andCamillaFoged
10 Layer-by-LayerAssembledNanoparticlesforsiRNADelivery ................ 153
MichaelaGuterandMiriamBreunig
11 Layer-By-LayerFilmEngineeringforSequentialGeneDelivery .............. 161
LingxiaoXie,YiZou,SeanCarroll,MariaMuniz,
andGuangzhaoMao
12 Surface-andHydrogel-MediatedDeliveryofNucleic
AcidNanoparticles...................................................... 177
AngelaK.Pannier,TylerKozisek,andTatianaSegura
vii
viii Contents
13 InSituAFMAnalysisInvestigatingDisassemblyofDNA
NanoparticlesandNanofilms............................................. 199
YiZou,LeiWan,JeniferBlacklock,LingxiaoXie,SeanCarroll,
DavidOupicky,andGuangzhaoMao
14 LyophilizationofSyntheticGeneCarriers ................................. 211
JuliaChristinaKasper,SarahHedtrich,andWolfgangFriess
15 FireflyLuciferase-BasedReporterGeneAssayforInvestigating
Nanoparticle-MediatedNucleicAcidDelivery.............................. 227
KatharinaMu¨ller,ManfredOgris,andHaiderSami
16 EnhancingNucleicAcidDeliverywithUltrasound
andMicrobubbles....................................................... 241
HeleenDewitte,SilkeRoovers,StefaanC.DeSmedt,
andIneLentacker
17 MagneticandAcousticallyActiveMicrobubblesLoadedwith
NucleicAcidsforGeneDelivery.......................................... 253
DialechtiVlaskou,OlgaMykhaylyk,andChristianPlank
18 LactateDehydrogenaseAssayforAssessmentofPolycation
Cytotoxicity............................................................ 291
LadanParhamifar,HeleneAndersen,andS.MoeinMoghimi
19 CombinedFluorimetricCaspase-3/7AssayandBradfordProtein
DeterminationforAssessmentofPolycation-MediatedCytotoxicity........... 301
AnnaK.Larsen,ArnaldurHall,HenrikLundsgart,
andS.MoeinMoghimi
20 DeterminationofPolycation-MediatedPerturbationofMitochondrial
RespirationinIntactCellsbyHigh-ResolutionRespirometry
(Oxygraph-2k,OROBOROS)............................................ 313
ArnaldurHallandS.MoeinMoghimi
21 EvaluatingtheRegulationofCytokineLevelsAftersiRNA
TreatmentinAntigen-SpecificTargetCellPopulationsvia
IntracellularStaining.................................................... 323
RimaKandil,DanielFeldmann,YuranXie,
andOliviaM.Merkel
22 Anti-PEGIgMProductionviaaPEGylatedNanocarrierSystem
forNucleicAcidDelivery................................................ 333
AmrS.AbuLilaandTatsuhiroIshida
23 Near-InfraredOpticalImagingofNucleicAcidNanocarriersInVivo ......... 347
ClaireRome,JulienGravier,MarieMorille,GillesDivita,
Anne-LaureBolcato-Bellemin,Ve´roniqueJosserand,
andJean-LucColl
24 FlowCytometry-BasedCellType-SpecificAssessmentofTarget
RegulationbyPulmonarysiRNADelivery ................................. 365
OliviaM.Merkel,LeighM.Marsh,HolgerGarn,
andThomasKissel
Contents ix
25 MicrobubblesforNucleicAcidDeliveryinLiverUsing
MildSonoporation...................................................... 377
NathalieMignet,CorinneMarie,AnthonyDelalande,
SimonaManta,Michel-FrancisBureau,GillesRenault,
DanielScherman,andChantalPichon
26 LipopeptideDeliveryofsiRNAtotheCentralNervousSystem............... 389
MarkD.Zabel,LukeMollnow,andHeatherBender
Index ...................................................................... 405
Contributors
AMRS.ABULILA (cid:2) DepartmentofPharmacokineticsandBiopharmaceutics, Instituteof
BiomedicalSciences,TokushimaUniversity,Tokushima,Japan;Departmentof
PharmaceuticsandIndustrialPharmacy,FacultyofPharmacy,ZagazigUniversity,
Zagazig,Egypt;DepartmentofPharmaceutics,CollegeofPharmacy,HailUniversity,
Hail,SaudiArabia
HELENEANDERSEN (cid:2) CentreforPharmaceuticalNanotechnologyandNanotoxicology,
UniversityofCopenhagen,Copenhagen,Denmark
MAXIMANTOPOLSKY (cid:2) TeachingandScientificConsulting,FGBPOU“MedicalCollege”,
Moscow,RussianFederation
BURKHARDBECHINGER (cid:2) InstitutdeChimie,CNRS,UMR7177,Universite´deStrasbourg,
Strasbourg,France
HEATHERBENDER (cid:2) DepartmentofMicrobiology,ImmunologyandPathology,PrionResearch
Center,CollegeofVeterinaryMedicineandBiomedicalSciences,ColoradoStateUniversity,
FortCollins,CO,USA
MICHELBESSODES (cid:2) Unite´deTechnologiesChimiquesetBiologiquespourlaSante´,INSERM,
U1022,Paris,France;CNRS,UMR8258,Paris,France;Faculte´dePharmacie,Sorbonne
ParisCite´,Universite´ParisDescartes,Paris,France;ChimieParisTech,PSLResearch
University,Paris,France
JENIFER BLACKLOCK (cid:2) DepartmentofBiomedicalEngineering,WayneStateUniversity,
Detroit,MI,USA
ANNE-LAUREBOLCATO-BELLEMIN (cid:2) Polyplus-Transfection,Illkirch,France
MIRIAMBREUNIG (cid:2) DepartmentofPharmaceuticalTechnology,UniversityofRegensburg,
Regensburg,Germany
MICHEL-FRANCISBUREAU (cid:2) INSERM,U1022,Paris,France;CNRS,UMR8258,Paris,
France;Faculte´dePharmacie,SorbonneParisCite´,Universite´ParisDescartes,Paris,
France;ChimieParisTech,PSLResearchUniversity,Paris,France
SEANCARROLL (cid:2) DepartmentofChemicalEngineeringandMaterialsScience,WayneState
University,Detroit,MI,USA;DepartmentofBiomedicalEngineering,WayneState
University,Detroit,MI,USA
JEAN-LUCCOLL (cid:2) INSERMU823,Equipe5,InstitutAlbertBonniot,Grenoble,France;
Universite´JosephFourier,Grenoble,France;INSERMUGAU1209,CNRS5309,
InstituteForAdvancedBiosciences,LaTronche,France
STEFAANC.DESMEDT (cid:2) GhentResearchGrouponNanomedicines,LaboratoryofGeneral
BiochemistryandPhysicalPharmacy,FacultyofPharmaceuticalSciences,Ghent
University,Ghent,Belgium
ANTHONYDELALANDE (cid:2) CentredeBiophysiqueMole´culaireandUniversite´d’Orle´ans,
CNRS-UPR4301,Orle´ans,France
HELEENDEWITTE (cid:2) GhentResearchGrouponNanomedicines,LaboratoryofGeneral
BiochemistryandPhysicalPharmacy,FacultyofPharmaceuticalSciences,Ghent
University,Ghent,Belgium
HELENEDHOTEL (cid:2) Unite´deTechnologiesChimiquesetBiologiquespourlaSante´,INSERM,
U1022,Paris,France;CNRS,UMR8258,Paris,France;Faculte´dePharmacie,Sorbonne
xi