Brain Tumor Stem Cells: Methods and Protocols

257 Pages·2018·6.062 MB·English

by  Sheila K Singh, Chitra Venugopal

Methods in
Molecular Biology 1869
Sheila K. Singh
Chitra Venugopal Editors
Brain Tumor
Stem Cells
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
Brain Tumor Stem Cells
Methods and Protocols
Edited by
Sheila K. Singh
Stem Cell and Cancer Research Institute, McMaster University, Hamilton, ON, Canada
Chitra Venugopal
Stem Cell and Cancer Research Institute, McMaster University, Hamilton, ON, Canada
Editors
SheilaK.Singh ChitraVenugopal
StemCellandCancer StemCellandCancer
ResearchInstitute ResearchInstitute
McMasterUniversity McMasterUniversity
Hamilton,ON,Canada Hamilton,ON,Canada
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-8804-4 ISBN978-1-4939-8805-1 (eBook)
https://doi.org/10.1007/978-1-4939-8805-1
LibraryofCongressControlNumber:2018957127
©SpringerScience+BusinessMedia,LLC,partofSpringerNature2019
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Preface
Thestudyofhumancancerstemcell(CSC)populationsisfraughtwithtechnicalchallenges
and seemingly insurmountable experimental tribulations, including limited and highly
precious patient-derived samples, low cell numbers, optimal growth conditions, and diffi-
cultiesinsortingandpurifyingheterogeneouscellpopulationsderivedfromcancerstemcell
hierarchies. And yet the rewards of implementing the newest and most advanced technol-
ogies to obtain novel data from these CSCs far exceed any of the challenges faced by
scientists,asdiscoveriesmadeinhumanCSCpopulationsareonestepcloser totranslation
intonewtherapeuticoptionsforcancerpatients.
In this textbook, we have carefully curated and compiled the best methodologies and
experimental techniques to profile and extract maximal data from brain tumor stem cells
(BTSCs),theexperimentalparadigmforbraincancerresearchthatoffersinsightsintoCSC
populationsthatmaydrivenotonlytumorinitiationbutalsotumorrecurrenceandpatient
relapse.TheBTSCmodelrecapitulatesscientificobservationsmadeinbraincancerpatients,
and we seek to give the reader a comprehensive understanding of the skills and techniques
thatwillunlockdatafromthismostinformativesubsetofcells.
We do hope that you will enjoy reading these succinct methodological briefs on the
mostinnovativetechnologiesandapplicationstoBTSCresearch,providedbyinternational
expertsinthefield.ArmedwiththebestavailableknowledgeofBTSCtechniques,wewish
you happy data acquisitionon your journey to better understandthe complexities of brain
cancer.
Hamilton,ON,Canada SheilaK.Singh
ChitraVenugopal
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 IntroductiontoBrainTumorStemCells................................... 1
NicolasYelle,DavidBakhshinyan,ChitraVenugopal,
andSheilaK.Singh
2 IsolationandCultureofGlioblastomaBrainTumorStemCells............... 11
CharlesChesnelong,IanRestall,andSamuelWeiss
3 EstablishmentandCultureofPatient-DerivedPrimary
MedulloblastomaCellLines.............................................. 23
SaraBadodi,SilviaMarino,andLoredanaGuglielmi
4 BioinformaticStrategiesfor theGenomicandEpigenomic
CharacterizationofBrainTumors......................................... 37
VijayRamaswamyandMichaelD.Taylor
5 DetectingStemCellMarkerExpressionUsingtheNanoString
nCounterSystem ....................................................... 57
ScottRyall,AnthonyArnoldo,JavalSheth,SheilaK.Singh,
andCynthiaHawkins
6 FlowCytometricAnalysisofBrainTumorStemCells ....................... 69
MinomiK.Subapanditha,AshleyA.Adile,ChitraVenugopal,
andSheilaK.Singh
7 InVitroSelf-RenewalAssaysforBrainTumorStemCells.................... 79
MathieuSeyfrid,DavidBobrowski,DavidBakhshinyan,NazaninTatari,
ChitraVenugopal,andSheilaK.Singh
8 DifferentiationofBrainTumorInitiatingCells ............................. 85
MichelleM.Kameda-Smith,MinomiK.Subapanditha,SabraK.Salim,
ChitraVenugopal,andSheilaK.Singh
9 TheStudyofBrainTumorStemCellMigration ............................ 93
MontserratLara-Velazquez,RawanAl-kharboosh,LuisPrieto,
PaulaSchiapparelli,andAlfredoQuin˜ones-Hinojosa
10 TheStudyofBrainTumorStemCellInvasion ............................. 105
RawanAl-kharboosh,MontserratLara-Velazquez,
LuisPrieto,RachelSarabia-Estrada,andAlfredoQuin˜ones-Hinojosa
11 CellCycleDynamicsinGliomaCancerStemCells.......................... 117
IngridQemoandLisaA.Porter
12 EmbryonicStemCellModelsofHumanBrainTumors ..................... 127
LudivineCoudie`reMorrison,NazaninTatari,
andTamraE.Werbowetski-Ogilvie
vii
viii Contents
13 ChromatinImmunoprecipitation(ChIP)Protocolsfor theCancer
andDevelopmentalBiologyLaboratory ................................... 143
HunterMcColl,JamieL.Zagozewski,andDavidD.Eisenstat
14 EPHProfilingofBTICPopulationsinGlioblastomaMultiforme
UsingCyTOF.......................................................... 155
AmyX.Hu,JarrettJ.Adams,ParvezVora,MaleehaQazi,SheilaK.Singh,
JasonMoffat,andSachdevS.Sidhu
15 PooledLentiviralCRISPR-Cas9ScreensforFunctionalGenomics
inMammalianCells..................................................... 169
MichaelAregger,MeghaChandrashekhar,AmyHinYanTong,
KatherineChan,andJasonMoffat
16 InVitroAssaysforScreeningSmallMolecules.............................. 189
AshleyA.Adile,DavidBakhshinyan,ChitraVenugopal,
andSheilaK.Singh
17 DrugDeliveryinanOrthotopicTumorStemCell-BasedModel
ofHumanGlioblastoma................................................. 197
ElenaBinda,AlbertoVisioli,NadiaTrivieri,andAngeloLuigiVescovi
18 EngineeringInducibleKnock-InMicetoModelOncogenicBrain
TumorMutationsfromEndogenousLoci ................................. 207
JonD.LarsonandSuzanneJ.Baker
19 InVivoMurineModelsofBrainMetastasis ................................ 231
MohiniSingh,NeilSavage,andSheilaK.Singh
20 CellularMagneticResonanceImagingforTrackingMetastatic
CancerCellsintheBrain ................................................ 239
KatieM.Parkins,AshleyV.Makela,AmandaM.Hamilton,
andPaulaJ.Foster
Index ...................................................................... 253
Contributors
JARRETTJ.ADAMS (cid:1) DepartmentofMolecularGenetics,UniversityofToronto,Toronto,ON,
Canada;DonnellyCentreforCellularandBiomolecularResearch,UniversityofToronto,
Toronto,ON,Canada
ASHLEYA.ADILE (cid:1) McMasterStemCellandCancerResearchInstitute,McMasterUniversity,
Hamilton,ON,Canada;DepartmentofBiochemistryandBiomedicalSciences,Facultyof
HealthSciences,McMasterUniversity,Hamilton,ON,Canada
RAWANAL-KHARBOOSH (cid:1) DepartmentofNeurosurgery,MayoClinicFlorida,Jacksonville,FL,
USA;MayoClinicGraduateSchool,MayoClinicCollegeofMedicine,Rochester,MN,USA
MICHAELAREGGER (cid:1) DonnellyCentreforCellularandBiomolecularResearch,Universityof
Toronto,Toronto,ON,Canada
ANTHONYARNOLDO (cid:1) DepartmentofPediatricLaboratoryMedicine,HospitalforSick
Children,Toronto,ON,Canada
SARABADODI (cid:1) BlizardInstitute,BartsandTheLondonSchoolofMedicineandDentistry,
QueenMaryUniversityofLondon,London,UK
SUZANNEJ.BAKER (cid:1) DepartmentofDevelopmentalNeurobiology,St.JudeChildren’s
ResearchHospital,Memphis,TN,USA
DAVIDBAKHSHINYAN (cid:1) McMasterStemCellandCancerResearchInstitute,McMaster
University,Hamilton,ON,Canada;DepartmentofBiochemistryandBiomedical
Sciences,McMasterUniversity,Hamilton,ON,Canada
ELENABINDA (cid:1) CancerStemCellsUnit,InstituteforStemCellBiology,Regenerative
MedicineandInnovativeTherapies–ISBReMIT,IRCSS,S.GiovanniRotondo,FG,Italy
DAVIDBOBROWSKI (cid:1) McMasterStemCellandCancerResearchInstitute,McMaster
University,Hamilton,ON,Canada;FacultyofHealthSciences,McMasterUniversity,
Hamilton,ON,Canada
KATHERINECHAN (cid:1) DonnellyCentreforCellularandBiomolecularResearch,Universityof
Toronto,Toronto,ON,Canada
MEGHACHANDRASHEKHAR (cid:1) DonnellyCentreforCellularandBiomolecularResearch,
UniversityofToronto,Toronto,ON,Canada;DepartmentofMolecularGenetics,
UniversityofToronto,Toronto,ON,Canada
CHARLESCHESNELONG (cid:1) DepartmentofCellBiologyandAnatomy,FacultyofMedicine,
UniversityofCalgary,Calgary,AB,Canada;DepartmentofPhysiologyand
Pharmacology,FacultyofMedicine,UniversityofCalgary,Calgary,AB,Canada;
HotchkissBrainInstitute,UniversityofCalgary,Calgary,AB,Canada
DAVIDD.EISENSTAT (cid:1) DepartmentofMedicalGenetics,UniversityofAlberta,Edmonton,
AB,Canada;DepartmentofPediatrics,UniversityofAlberta,Edmonton,AB,Canada;
DepartmentofOncology,UniversityofAlberta,Edmonton,AB,Canada
PAULA J.FOSTER (cid:1) RobartsResearchInstitute,WesternUniversity,London,ON,Canada
LOREDANAGUGLIELMI (cid:1) BlizardInstitute,BartsandTheLondonSchoolofMedicineand
Dentistry,QueenMaryUniversityofLondon,London,UK
AMANDAM.HAMILTON (cid:1) RobartsResearchInstitute,WesternUniversity,London,ON,
Canada
ix
x Contributors
CYNTHIAHAWKINS (cid:1) DivisionofCellBiology,HospitalforSickChildrenResearchCenter,
Toronto,ON,Canada;DepartmentofLaboratoryMedicineandPathobiology,Facultyof
Medicine,UniversityofToronto,Toronto,ON,Canada;DepartmentofPediatric
LaboratoryMedicine,HospitalforSickChildren,Toronto,ON,Canada
AMYX.HU (cid:1) DepartmentofMolecularGenetics,UniversityofToronto,Toronto,ON,
Canada;DonnellyCentreforCellularandBiomolecularResearch,UniversityofToronto,
Toronto,ON,Canada
MICHELLEM.KAMEDA-SMITH (cid:1) McMasterStemCellandCancerResearchInstitute,
McMasterUniversity,Hamilton,ON,Canada
MONTSERRATLARA-VELAZQUEZ (cid:1) DepartmentofNeurosurgery,MayoClinicFlorida,
Jacksonville,FL,USA;PlanofCombinedStudiesinMedicine,FacultyofMedicine,
NationalAutonomousUniversityofMexico,MexicoCity,Mexico
JOND.LARSON (cid:1) DepartmentofDevelopmentalNeurobiology,St.JudeChildren’sResearch
Hospital,Memphis,TN,USA
ASHLEY V.MAKELA (cid:1) RobartsResearchInstitute,WesternUniversity,London,ON,Canada
SILVIAMARINO (cid:1) BlizardInstitute,BartsandTheLondonSchoolofMedicineandDentistry,
QueenMaryUniversityofLondon,London,UK
HUNTERMCCOLL (cid:1) DepartmentofMedicalGenetics,UniversityofAlberta,Edmonton,AB,
Canada
JASON MOFFAT (cid:1) DonnellyCentreforCellularandBiomolecularResearch,Universityof
Toronto,Toronto,ON,Canada;DepartmentofMolecularGenetics,UniversityofToronto,
Toronto,ON,Canada;CanadianInstituteforAdvancedResearch,Toronto,ON,Canada
LUDIVINECOUDIE`REMORRISON (cid:1) RegenerativeMedicineProgram,Departmentof
BiochemistryandMedicalGenetics,UniversityofManitoba,Winnipeg,MB,Canada;
RegenerativeMedicineProgram,DepartmentofPhysiologyandPathophysiology,University
ofManitoba,Winnipeg,MB,Canada
KATIEM.PARKINS (cid:1) RobartsResearchInstitute,WesternUniversity,London,ON,Canada
LISAA.PORTER (cid:1) DepartmentofBiologicalSciences,UniversityofWindsor,Windsor,ON,
Canada
LUIS PRIETO (cid:1) MayoClinicGraduateSchool,MayoClinicCollegeofMedicine,Rochester,
MN,USA
MALEEHAQAZI (cid:1) McMasterStemCellandCancerResearchInstitute,McMasterUniversity,
Hamilton,ON,Canada;DepartmentofBiochemistryandBiomedicalSciences,McMaster
University,Hamilton,ON,Canada
INGRID QEMO (cid:1) DepartmentofBiologicalSciences,UniversityofWindsor,Windsor,ON,
Canada
ALFREDOQUIN˜ONES-HINOJOSA (cid:1) DepartmentofNeurosurgery,MayoClinicFlorida,
Jacksonville,FL,USA
VIJAYRAMASWAMY (cid:1) DivisionofHaematology/Oncology,HospitalforSickChildren,Toronto,
ON,Canada;PrograminDevelopmentalandStemCellBiology,HospitalforSick
Children,Toronto,ON,Canada
IANRESTALL (cid:1) DepartmentofCellBiologyandAnatomy,FacultyofMedicine,Universityof
Calgary,Calgary,AB,Canada;HotchkissBrainInstitute,UniversityofCalgary,
Calgary,AB,Canada
SCOTTRYALL (cid:1) DivisionofCellBiology,HospitalforSickChildrenResearchCenter,Toronto,
ON,Canada;DepartmentofLaboratoryMedicineandPathobiology,FacultyofMedicine,
UniversityofToronto,Toronto,ON,Canada
Contributors xi
SABRAK.SALIM (cid:1) McMasterStemCellandCancerResearchInstitute,McMasterUniversity,
Hamilton,ON,Canada
RACHELSARABIA-ESTRADA (cid:1) DepartmentofNeurosurgery,MayoClinicFlorida,Jacksonville,
FL,USA
NEILSAVAGE (cid:1) StemCellandCancerResearchInstitute,McMasterUniversity,Hamilton,
ON,Canada;DepartmentofSurgery,McMasterUniversity,Hamilton,ON,Canada
PAULA SCHIAPPARELLI (cid:1) DepartmentofNeurosurgery,MayoClinicFlorida,Jacksonville,FL,
USA
MATHIEUSEYFRID (cid:1) McMasterStemCellandCancerResearchInstitute,McMaster
University,Hamilton,ON,Canada
JAVALSHETH (cid:1) DivisionofCellBiology,HospitalforSickChildrenResearchCenter,Toronto,
ON,Canada;DepartmentofPediatricLaboratoryMedicine,HospitalforSickChildren,
Toronto,ON,Canada
SACHDEVS.SIDHU (cid:1) DepartmentofMolecularGenetics,UniversityofToronto,Toronto,ON,
Canada;DonnellyCentreforCellularandBiomolecularResearch,UniversityofToronto,
Toronto,ON,Canada
MOHINISINGH (cid:1) StemCellandCancerResearchInstitute,McMasterUniversity,Hamilton,
ON,Canada;DepartmentofBiochemistryandBiomedicalSciences,McMasterUniversity,
Hamilton,ON,Canada
SHEILAK.SINGH (cid:1) StemCellandCancerResearchInstitute,McMasterUniversity,
Hamilton,ON,Canada;DepartmentofBiochemistryandBiomedicalSciences,McMaster
University,Hamilton,ON,Canada;DepartmentofSurgery,McMasterUniversity,
Hamilton,ON,Canada
MINOMI K.SUBAPANDITHA (cid:1) McMasterStemCellandCancerResearchInstitute,McMaster
University,Hamilton,ON,Canada;DepartmentofBiochemistryandBiomedical
Sciences,FacultyofHealthSciences,McMasterUniversity,Hamilton,ON,Canada
NAZANINTATARI (cid:1) RegenerativeMedicineProgram,DepartmentofBiochemistryand
MedicalGenetics,UniversityofManitoba,Winnipeg,MB,Canada;Regenerative
MedicineProgram,DepartmentofPhysiologyandPathophysiology,UniversityofManitoba,
Winnipeg,MB,Canada;McMasterStemCellandCancerResearchInstitute,McMaster
University,Hamilton,ON,Canada;DepartmentofBiochemistryandBiomedical
Sciences,McMasterUniversity,Hamilton,ON,Canada
MICHAELD.TAYLOR (cid:1) DivisionofNeurosurgery,HospitalforSickChildren,Toronto,ON,
Canada;PrograminDevelopmentalandStemCellBiology,HospitalforSickChildren,
Toronto,ON,Canada
AMYHINYANTONG (cid:1) DonnellyCentreforCellularandBiomolecularResearch,Universityof
Toronto,Toronto,ON,Canada
NADIATRIVIERI (cid:1) CancerStemCellsUnit,InstituteforStemCellBiology,Regenerative
MedicineandInnovativeTherapies–ISBReMIT,IRCSS,S.GiovanniRotondo,FG,Italy
CHITRAVENUGOPAL (cid:1) StemCellandCancerResearchInstitute,McMasterUniversity,
Hamilton,ON,Canada;DepartmentofSurgery,FacultyofHealthSciences,McMaster
University,Hamilton,ON,Canada
ANGELOLUIGI VESCOVI (cid:1) CancerStemCellsUnit,InstituteforStemCellBiology,
RegenerativeMedicineandInnovativeTherapies–ISBReMIT,IRCSS,S.Giovanni
Rotondo,FG,Italy;DepartmentofBiotechnologyandBiosciences,UniversityofMilan
Bicocca,Milan,Italy;HyperstemSA,Lugano,Switzerland
ALBERTOVISIOLI (cid:1) StemGenSpA,Milan,Italy