Theranostics: Methods and Protocols

294 Pages·2019·9.661 MB·English

by  Batra Jyotsna

Methods in
Molecular Biology 2054
Jyotsna Batra
Srilakshmi Srinivasan
Editors
Theranostics
Methods and Protocols
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
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step fashion, opening with an introductory overview, a list of the materials and reagents
neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported
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indexedinPubMed.
Theranostics
Methods and Protocols
Edited by
Jyotsna Batra and Srilakshmi Srinivasan
School of Biomedical Sciences, Institute of Health and Biomedical Innovation (IHBI), Translational
Research Institute, Queensland University of Technology (QUT), Brisbane, QLD, Australia
Editors
JyotsnaBatra SrilakshmiSrinivasan
SchoolofBiomedicalSciences SchoolofBiomedicalSciences
InstituteofHealthandBiomedical InstituteofHealthandBiomedical
Innovation(IHBI),Translational Innovation(IHBI),Translational
ResearchInstitute ResearchInstitute
QueenslandUniversity QueenslandUniversity
ofTechnology(QUT) ofTechnology(QUT)
Brisbane,QLD,Australia Brisbane,QLD,Australia
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-9768-8 ISBN978-1-4939-9769-5 (eBook)
https://doi.org/10.1007/978-1-4939-9769-5
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Preface
Theterm “theranostics”implies toa combinationoftherapyand diagnosticsand hasbeen
used by scientific community in a variety of contexts. Over the past decade, the field of
theranosticshasadvancedconsiderablywithrespecttoadvancesinbiomarkeridentification,
newmolecularimagingprobes,geneticsandhigh-throughputtechniques,imaging-guided
molecular therapy, and new nanotheranostics. The field is appropriate to explain the
advancementinsciencetoestablishaccurateandpersonalizedtherapiesfor variousdiseases
andtocombinediagnosticandtherapeuticapplicationsintoasingleagentfor thedevelop-
mentofapromisingparadigminvolvingdiagnosis,drugdelivery,andmonitoringofdisease
responsetotreatment.
Newclinicians,researchers,andstudentsworkinginthismultidisciplinaryfieldoftenask
howtoobtainwell-optimizedandwell-detailedprotocolstoachievetheirresearchoutcome
inthisfield.Thisbookisdesignedspecificallytomeetthatdemandandispublishedintime
to meet theneeds ofmedical researchersin acomprehensive mannerencompassingbioen-
gineering,diagnostics,invivoimaginganditsuseforimage-guidedtherapy,andavarietyof
othermiscellaneoussubjects.Toaccomplishthisdauntingtask,wehadthegoodfortuneto
recruitnearly52leadersinthefieldworldwidecontributingtothe18chapters.
Given the multidisciplinary nature of the field, the book is broken into five different
sections.
PartI(Bioengineering)consistsofthreechapters(Chapters1–3).Manytheranostic
approacheshasbeenlimitedduetothelackofrepresentativelaboratorymodelsthatmimic
thebiologicalprocessesoccurringinvivoandtherestrictiveaccessandlimitedliveimaging
capabilitiesthatinvivomodelsprovide.Syntheticscaffoldmaterialsallowtoengineerbone-
likemicroenvironmentsderivedfromprimaryhumancells,whichcanfurtherbeco-cultured
with metastatic cell lines. Chapter 1 reviews the several easy-to-follow methods for the
characterizationofcellsgrowninhydrogelsandalsodescribesanenzymaticapproachforan
improved cell recovery for subsequent analysis. Chapter 2 reviews the application of melt
electrowriting technology (MEW) to provide 3D microfiber scaffolds suitable for this
purpose. Using primary human cells, MEW scaffolds support the reproducible formation
of human bone-like 3D microenvironments. Chapter 3 describes imaging techniques to
obtain multidimensional real-time data of cancer cells in the microenvironment context.
Thisnovelpreclinicalplatformwillcontributetothebetter understandingofthenatureof
thedynamicinteractionsbetweenboneandcancer,aswellasservetomeasuretheefficiency
ofanticancerdrugs.
Part II (Molecular Diagnostics) consists of Chapters 4–9. The current diagnostic
methods,suchasbiopsysampling,tumortissuestaining,andimagingtechniques,whichare
invasive,painful,time-consuming,andexpensiverequireskilledpersonnel.Therefore,there
isanunmetclinicalneedtodevelopnoninvasive,easy-to-usetoolstoidentifypatientsbefore
clinical manifestation. Furthermore, the quality of the samples for analysis remains an
undeniable challenge which was also discussed in these chapters. Chapter 4 describes
exosome-based therapeutics that represent a most promising next-generation approach
and are considered valid diagnostic biomarkers and potential therapeutic tools. Exosomes
are widely disseminated, heterogenous entities, and the isolation of large and high-quality
exosomes is daunting. In this chapter, we reveal the protocol and key insights into the
v
vi Preface
isolation, purification,and characterization of exosomes usingultracentrifugation method.
MicroRNAs(miRNAs)aresmallendogenousnoncodingRNAmoleculeswhicharepower-
ful regulators of the different cellular processes involved in the pathogenesis of various
diseases. The use of miRNA-based therapies has been proposed with the onset of early-
phaseclinicaltrialstoassessthetherapeuticefficacyofmiRNAs.Thestratificationofpatients
based ondifferential expression ofmiRNAs and thetherapeutictargeting ofsuchmiRNAs
wouldenablepatient-specifictailoredintervention.Chapter5describesexperimentalmeth-
odologyforthedetectionofmiRNAsinplasmasamplesbyRT-qPCR.Chapter6describesa
robust and cost-effective protocol to isolate and enrich miRNAs from saliva samples.
Similarly,circulatingtumorcells(CTCs)haveshownpromisingpotentialasliquidbiopsies
thatfacilitateearlydetection,prognosis,therapeutictargetselection,andmonitoringtreat-
ment response. Chapter 7 describes a CTC isolation and analysis method by Tianyu Guo
et al. for cancer detection and therapeutic response monitoring. Chapter 8 explains the
isolationofCTCsusingthespiralmicrofluidictechnologyfor theefficientsortingofCTCs
frompatientbloodsamplesfortargetedtherapy.BoththesetwochaptersarebasedonCTC
isolation methods using different technologies. While Chapter 7 is a marker-independent
CTCenrichmentmethodbasedonthecellsizeanddeformabilityandtheimmunofluores-
cencestainingmethodtodetectCTCs,Chapter8detailsthespiralmicrofluidictechnology
which is also a marker-independent technique but utilizes hydrodynamic forces for size-
basedefficientsortingofCTCsfrompatientbloodsamples.
Pharmacogenetics involves the search for genetic variations that lead to interindividual
differencesindrugresponse.Thisgenotypingapproachhavepavedthewaytonewoppor-
tunities to deliver a better quality of care through more precise characterization of the
individual’s genetic makeup that will, in turn, contribute to the interindividual variations
in drugresponse. Chapter 9 provides perspectives from theidentification ofsuch causative
geneticvariations—toillustratehowtoanalyzetherawdataobtainedbydifferentsequenc-
ing techniques while indicating the potential challenges that may arise at each step.
Chapter 10 explains the use of automatic Idylla™ system for the analysis of specific muta-
tionsincancerpatients.
PartIII(MolecularImaging)consistsofChapters11–13.Numerousadvanceshave
been made in recent years in exogenous probes and nanoparticles that allow precise and
specific imaging in situ as well as label-free clinical imaging approaches. Chapter 11 sum-
marizesasimplemethodofgeneratingfluorescentprobesusingbacterialartificialchromo-
somes employed in in situ genetic analysis of cells in response to treatment. Chapter 12
focusesonthelabel-freedigitallivecellimagingtechniqueandhasexpandedfromitsusein
the laboratory to the clinical setting, and currently, it is being developed for use in ther-
anostics. Chapter 13 provides a concise review and process of utilizing porous silicon
nanoparticlesforanimprovedpermeabilityintothetargettissuesandforprecisedeeptissue
imaginganddiagnostics.
PartIV(Imaging-GuidedTherapy)is composedofChapters 14–18. Thechapters
in this section reveal how advanced imaging techniques now make highly precise clinical
interventionpossible,furtherprovidingaccurateandefficientdeliveryofdrugtothetarget
deliverybycrossingthebarrierandescapeclearancethroughthereticuloendothelialsystem
to ensure sustained presence at effective concentrations. Nanoparticle-based drug delivery
systemsareemergingasapromisingdrugdeliveryplatform,duetotheirdistinctadvantages
leading to various biological actions in the body. Chapter 14 reviews generalized methods
for the use of aptamers in diagnostics using optical and electrochemical platforms of
detection and in delivering drug to the cancer cells and details a method for the in vitro
Preface vii
selection of DNA aptamers against a protein target by SELEX, a combinatorial single-
stranded oligonucleotide synthesis technique that specifically bind to a target ligand.
Chapter 15 highlights how aptamers can be utilized that has the potential to enhance the
precision of molecular medicine and targeted therapeutics. Chapter 16 reviews a simple
method of generating fluorescence in situ hybridization probes using bacterial artificial
chromosomes that have unlimited possibilities for the analysis of any genomic regions.
Chapter 17 explores the method for developing a library of nanoparticles for the efficient
delivery of therapeutic agents across the blood-brain barrier. Chapter 18 introduces the
biomimeticsyntheticstrategyandproceduresforpreparinggeneticallyengineerednanove-
siclesfordiseasecell-specifictargeting.
It is impossible to describe all the areas that encompass theranostics or will have an
impactonthescienceandpracticeofpersonalizedmedicine.Ouraimistoofferareasonable
solutiontowardsdiseasediagnosisandtherapybygivingthereadersasenseofnewmethods
andchallengesassociatedwithdevelopingtheranostics.Ithasbeenagreatpleasureworking
withtheauthorsofthisbook.Withouttheirenthusiasm,encouragement,andprofessional
deliveryoftheircontributionsinatimelymanner,itwouldnothavebeenpossibletomake
thisbookareality.Wehopethatthisbookmayformafoundationforfurtheradvancesinthe
fieldoftheranostics.
Brisbane,QLD,Australia JyotsnaBatra
Woolloongabba,QLD,Australia SrilakshmiSrinivasan
Contents
Preface ..................................................................... v
Contributors................................................................. xi
PART I BIOENGINEERING
1 CellRecoveryofHydrogel-EncapsulatedCellsforMolecularAnalysis......... 3
EleonoraPeerani,JulianaB.Candido,andDanielaLoessner
2 BioengineeredMicrotissueModelsoftheHumanBoneMetastatic
Microenvironment:ANovelInVitroTheranosticsPlatform
forCancerResearch..................................................... 23
NathalieBock
3 Real-Timeand3DQuantificationofCancerCellDynamics:
ExploitingaBioengineeredHumanBoneMetastaticMicrotissue............. 59
NathalieBockandJoanR¨ohl
PART II MOLECULAR DIAGNOSTICS
4 ExosomesExtractionandIdentification.................................... 81
XiaoxinWu,SalahAliA.Showiheen,AntoniaRujiaSun,
RossCrawford,YinXiao,XinzhanMao,andIndiraPrasadam
5 ProfilingMicroRNAMarkersinPlasma:LookingintoBetter
ApproachesandRecommendations ....................................... 93
FarhanaMatinandJyotsnaBatra
6 IsolationandQuantificationofMicroRNAsfromHumanSaliva.............. 105
SriRamArunachalam,KaiDunTang,andChamindiePunyadeera
7 TheIsolationandAnalysisofCirculatingTumorCells....................... 115
TianyuGuo,ElzbietaStankiewicz,XueyingMao,andYong-JieLu
8 TheIsolationandCharacterizationofCirculatingTumor
CellsfromHeadandNeckCancerPatientBloodSamples
UsingSpiralMicrofluidicTechnology ..................................... 129
AruthaKulasinghe,MajidEbrahimiWarkiani,
andChamindiePunyadeera
9 Pharmacogenetics:RoleofSingleNucleotidePolymorphisms................ 137
EmrahYucesanandNurOzten
10 EGFRMutationAnalysisinNon-smallCellLungCarcinoma
fromTissueSamplesUsingtheFullyAutomatedIdylla™qPCRSystem....... 147
SimonHeekeandPaulHofman
ix
x Contents
PART III MOLECULAR IMAGING
11 SubcellularLocalizationofMicroRNAsbyMicroRNAInSitu
Hybridization(miR-ISH)................................................ 159
HarleyRoseRobinson,MichelleMeiChihHill,
andAlexandreSantosCristino
12 DigitalHolographicImagingasaMethodforQuantitative,
LiveCellImagingofDrugResponsetoNovelTargetedCancerTherapies..... 171
LauraV.Croft,JaimieA.Mulders,DerekJ.Richard,
andKennethO’Byrne
13 LuminescentPorousSiliconNanoparticlesforContinuous
WaveandTime-GatedPhotoluminescenceImaging......................... 185
TusharKumeria,ZhiQu,AmiraliPopat,TariqAltalhi,
andAbelSantos
PART IV IMAGE-GUIDED THERAPY
14 NucleicAcidAptamersasEmergingToolsforDiagnostics
andTheranostics........................................................ 201
RuchiMutreja,ShahnawazAhmadBaba,andNaveenKumarNavani
15 AptamerSelectionforDetectingMolecularTargetUsing
Cell-SELEX(SystematicEvolutionofLigandsbyExponential
Enrichment)Technology ................................................ 223
KimberlyD.Stewart,WeihongTan,andJongY.Park
16 FluorescenceInSituHybridizationandRehybridization
UsingBacterialArtificialChromosomeProbes ............................. 243
ElzbietaStankiewicz,TianyuGuo,XueyingMao,andYong-JieLu
17 UpconversionNanoparticle-BasedStrategyforCrossingtheBlood-Brain
Barrier toTreattheCentralNervousSystemDisease........................ 263
LibingFu,RogerChung,andBingyangShi
18 GeneticallyEngineeredPlasmaMembraneNanovesicles
forCancer-TargetedNanotheranostics .................................... 283
PengfeiZhang,HuChen,JingyiLiu,andGangLiu
Index ...................................................................... 295