MicroRNA and Cancer: Methods and Protocols

222 Pages·2018·4.267 MB·English

by  Wei Wu (eds.)

Methods in
Molecular Biology 1699
Wei Wu Editor
MicroRNA
and Cancer
Methods and Protocols
Second Edition
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
MicroRNA and Cancer
Methods and Protocols
Second Edition
Edited by
Wei Wu
Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California
in San Francisco, San Francisco, CA, USA
Editor
WeiWu
DepartmentofMedicine,HelenDillerFamilyComprehensiveCancerCenter
UniversityofCaliforniainSanFrancisco
SanFrancisco,CA,USA
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-7433-7 ISBN978-1-4939-7435-1 (eBook)
DOI10.1007/978-1-4939-7435-1
LibraryofCongressControlNumber:2017955683
©SpringerScience+BusinessMedia,LLC2011,2018
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Preface
The discovery of microRNAs (miRNAs or miRs) heralded an exciting era in biology and
started a new chapter in regulation of human genes. The miRNAs are a class of small
endogenousnoncodingRNAs(~22nt)thatfine-tunegeneexpressionattheposttranscrip-
0
tionallevel,mainlythroughbinding3-UTRofmRNAs.Theyareinvolvedinstemcellself-
renewal,cellulardevelopment,differentiation,proliferation,andapoptosis.
Small miRNAs have big impacts in cancer development. Among the many miRNAs, a
subset was identified as regulators of neoplastic transformation and tumor progression,
invasionandmetastasisaswellastumor-initiatingcells(cancerstemcells).Thewidespread
deregulationofmiRNomeshasbeenunveiledindiversecancerscomparedtonormaltissues.
The oncomirs (oncogenic miRNAs), TSmiRs (tumor-suppressive miRNAs), and Metasta-
miRs (cancer metastasis associated miRNAs) comprise an important part of the cancer
genome and, hence, they have pivotal diagnostic and prognostic significance. Moreover,
cancer-associated miRNAs are proving worthwhile as effective cancer biomarkers for indi-
vidualizedmedicineandpotentialtherapeutictargets.
Six years after publication of the first edition of our book about “microRNA and
cancer,” it has become a very popular reference in colleges, universities, and research
institutes and I was encouraged to publish a second edition. This second edition provides
thelatestinformationattheforefrontofmiRNAsbiologyasitisbeingappliedworldwideto
cancerresearch.Itisorganizedinthesamestyleasthefirsteditionwithareviewsectionand
aprotocolsection.Thereviewsectionisfocusedoncurrentcancerresearchtopicsrelatedto
microRNA functions, including the roles of microRNAs in DNA damage, cancer-immune
system interaction, cancer cell resistance, APOBEC gene expression, and gene expression
noise.TheprotocolsectionisfocusedonexperimentalapplicationsofmicroRNAsinvarious
types of cancer and the scope of research covers detection of circulating microRNA,
discovery of microRNA signatures using miRseq technology, evaluation of microRNA
deliverysystems,microRNA-basedtherapeutics,andfinally,microRNAsequencinganalysis.
MicroRNAresearchisafastgrowingfieldandmicroRNAsarepivotalelementsincancer
biology. An individual miRNA interferes with a broad range of mRNAs and, conversely, a
singlemRNAcouldbetargetedbyavarietyofmiRNAs.ThecomplexityofmiRNA::mRNA
interactions is far-reaching in our understanding to date. This book provides the basic
principles of experimental and computational methods for the study of microRNAs in
cancer research and, therefore, provides a firm grounding for those who wish to develop
furtherapplications.
IamespeciallyindebtedtoDrs.ShuZheng,SuzanneD.Conzen,andTreverBivonafor
giving me the opportunity to gain substantial experience in cancer research and I thank
Dr. Fred G. Biddle for all kinds of support. Heartfelt gratitude goes to my family, who
continue to patiently support me as I put forward my efforts related to the publication.
Without their confidence and continuous support, many things would not have been
possible. Also, I thank Professor John Walker for his encouragement and all staff from
Springerfortheirhardworktoproducethebook.Finally,Iamgratefultoallthecontribut-
ingauthorsforprovidingtheirhighqualitymanuscripts.
SanFrancisco,CA,USA WeiWuM.D.,Ph.D.
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
PART I REVIEW
1 NoncodingRNAsinDNADamageResponse:Opportunities
forCancerTherapeutics ................................................. 3
WaniArjumand,AsiaAsiaf,andShiekhTanveerAhmad
2 MicroRNAsinBreastCancer:DiagnosticandTherapeuticPotential .......... 23
AsiaAsiaf,ShiekhTanveerAhmad,WaniArjumand,
andMohammadAfzalZargar
3 InvolvementofmiRNAsandPseudogenesinCancer........................ 45
Lu€tfiTutar,AykutO¨zgu€r,andYusufTutar
4 MicroRNAsReprogramTumorImmuneResponse ......................... 67
WeiCao,WenfangCheng,andWeiWu
5 ApolipoproteinBmRNAEditingEnzyme,CatalyticPolypeptide-Like
GeneExpression,RNAEditing,andMicroRNAsRegulation................. 75
WeiCaoandWeiWu
6 MicroRNAsChangetheLandscapeofCancerResistance .................... 83
JunZhu,WeiZhu,andWeiWu
7 MicroRNA,Noise,andGeneExpressionRegulation........................ 91
WeiWu
PART II PROTOCOL SECTION
8 DeepSequencingRevealsaMicroRNAExpressionSignature
inTriple-NegativeBreastCancer.......................................... 99
Yao-YinChang,Liang-ChuanLai,Mong-HsunTsai,
andEricY.Chuang
9 DetectionofPlasmaMicroRNASignatureinOsteosarcomaPatients.......... 113
WendyAllen-RhoadesandJasonT.Yustein
10 IdentificationofE6/E7-DependentMicroRNAsinHPV-Positive
CancerCells............................................................ 119
AnjaHonegger,DanielaSchilling,HolgerSu€ltmann,
KarinHoppe-Seyler,andFelixHoppe-Seyler
11 CombinationofAnti-miRNAsOligonucleotideswithLowAmounts
ofChemotherapeuticAgentsforPancreaticCancerTherapy ................. 135
MartaPassadouroandHenriqueFaneca
vii
viii Contents
12 EvaluationofMicroRNADeliveryInVivo................................. 155
RikkiA.M.Brown,KirstyL.Richardson,FelicityC.Kalinowski,
MichaelR.Epis,JessicaL.Horsham,TasnuvaD.Kabir,
MarisaH.DePinho,DianneJ.Beveridge,LisaM.Stuart,
LarissaC.Wintle,andPeterJ.Leedman
13 AngiogenesisAnalysisbyInVitroCocultureAssaysinTranswell
ChambersinOvarianCancer............................................. 179
AliFlores-Pe´rez,Dolores GallardoRinc(cid:2)on,ErikaRuiz-Garcı´a,
RaquelEchavarria,LaurenceA.Marchat,ElizbethA´lvarez-Sa´nchez,
andCe´sarL(cid:2)opez-Camarillo
14 ApplicationofIndividualqPCRPerformanceParameters
forQualityControlofCirculatingMicroRNAData......................... 187
AnnaBrunet-Vega,Marı´aElisaQuı´lez,Marı´aJose´Ramı´rez-La´zaro,
andSergioLario
15 ConstructionofMulti-PotentMicroRNASponge
andItsFunctionalEvaluation ............................................ 201
SuhwanChang
16 MicroRNASequencingDataAnalysisToolkits ............................. 211
WeiWu
Index ...................................................................... 217
Contributors
SHIEKHTANVEERAHMAD (cid:2) ClarkeH.SmithBrainTumourCentre,ArnieCharbonneau
CancerInstitute,CummingSchoolofMedicine,2A25HRIC,UniversityofCalgary,
Calgary,AB,Canada
ELIZBETHA´LVAREZ-SA´NCHEZ (cid:2) PosgradoenCienciasGen(cid:2)omicas,UniversidadAut(cid:2)onomade
laCiudaddeMe´xico,BenitoJuarze,CDMX,Mexico
WENDYALLEN-RHOADES (cid:2) DepartmentofPediatrics,BaylorCollegeofMedicine,Houston,
TX,USA
WANIARJUMAND (cid:2) RobsonDNAScienceCentre,ArnieCharbonneauCancerInstitute,
CummingSchoolofMedicine,2A32HRIC,UniversityofCalgary,Calgary,AB,Canada
ASIAASIAF (cid:2) DepartmentofBiochemistry,FacultyofScience,UniversityofKashmir,
HazratbalSrinagar,J&K,India
DIANNEJ.BEVERIDGE (cid:2) LaboratoryforCancerMedicine,HarryPerkinsInstituteofMedical
Research,UniversityofWesternAustraliaCentreforMedicalResearch,Nedlands,WA,
Australia
RIKKIA.M.BROWN (cid:2) LaboratoryforCancerMedicine,HarryPerkinsInstituteofMedical
Research,UniversityofWesternAustraliaCentreforMedicalResearch,Nedlands,WA,
Australia
ANNABRUNET-VEGA (cid:2) OncologyService,HospitaldeSabadell,Corporaci(cid:2)o Sanit`ariaParc
Taulı´,InstitutUniversitariParcTaulı´-UAB,Sabadell,Spain;Fundaci(cid:2)o ParcTaulı´,
Corporaci(cid:2)o Sanit`ariaParcTaulı´,InstitutUniversitariParcTaulı´-UAB,Sabadell,Spain
WEICAO (cid:2) TranslationalMedicalCenter,ZhengzhouCentralHospital,Affiliatedto
ZhengzhouUniversity,Zhengzhou,People’sRepublicofChina
SUHWANCHANG (cid:2) DepartmentofBiomedicalSciences,UniversityofUlsanCollegeof
Medicine,AsanMedicalCenter,Seoul,SouthKorea
YAO-YINCHANG (cid:2) DepartmentofElectricalEngineering,GraduateInstituteofBiomedical
ElectronicsandBioinformatics, NationalTaiwanUniversity,Taipei,Taiwan;
BioinformaticsandBiostatisticsCore,NTUCenterofGenomicMedicine,Taipei,Taiwan
WENFANGCHENG (cid:2) DepartmentofGastroenterology,TheFirstAffiliatedHospitalofNanjing
MedicalUniversity,Nanjing,JiangsuProvince,China
ERICY.CHUANG (cid:2) DepartmentofElectricalEngineering,GraduateInstituteofBiomedical
ElectronicsandBioinformatics, NationalTaiwanUniversity,Taipei,Taiwan;
BioinformaticsandBiostatisticsCore,NTUCenterofGenomicMedicine,Taipei,Taiwan
MARISAH.DEPINHO (cid:2) LaboratoryforCancerMedicine,HarryPerkinsInstituteofMedical
Research,UniversityofWesternAustraliaCentreforMedicalResearch,Nedlands,WA,
Australia
RAQUEL ECHAVARRIA (cid:2) PosgradoenCienciasGen(cid:2)omicas,UniversidadAut(cid:2)onomadela
CiudaddeMe´xico,BenitoJuarze,CDMX,Mexico
MICHAELR.EPIS (cid:2) LaboratoryforCancerMedicine,HarryPerkinsInstituteofMedical
Research,UniversityofWesternAustraliaCentreforMedicalResearch,Nedlands,WA,
Australia
HENRIQUEFANECA (cid:2) Center forNeuroscienceandCellBiology,UniversityofCoimbra,
Coimbra,Portugal;DepartmentofLifeSciences,FacultyofScienceandTechnology,
UniversityofCoimbra,Coimbra,Portugal
ix
x Contributors
ALIFLORES-PE´REZ (cid:2) PosgradoenCienciasGen(cid:2)omicas,UniversidadAut(cid:2)onomadelaCiudad
deMe´xico,BenitoJuarze,CDMX,Mexico
ANJAHONEGGER (cid:2) MolecularTherapyofVirus-AssociatedCancers(F065),GermanCancer
ResearchCenter(DKFZ),Heidelberg,Germany
FELIXHOPPE-SEYLER (cid:2) MolecularTherapyofVirus-AssociatedCancers(F065),German
CancerResearchCenter(DKFZ),Heidelberg,Germany
KARINHOPPE-SEYLER (cid:2) MolecularTherapyofVirus-AssociatedCancers(F065),German
CancerResearchCenter(DKFZ),Heidelberg,Germany
JESSICAL.HORSHAM (cid:2) LaboratoryforCancerMedicine,HarryPerkinsInstituteofMedical
Research,UniversityofWesternAustraliaCentreforMedicalResearch,Nedlands,WA,
Australia
TASNUVAD.KABIR (cid:2) LaboratoryforCancerMedicine,HarryPerkinsInstituteofMedical
Research,UniversityofWesternAustraliaCentreforMedicalResearch,Nedlands,WA,
Australia
FELICITY C.KALINOWSKI (cid:2) LaboratoryforCancerMedicine,HarryPerkinsInstituteof
MedicalResearch,UniversityofWesternAustraliaCentreforMedicalResearch,Nedlands,
WA,Australia
CE´SARLO´PEZ-CAMARILLO (cid:2) PosgradoenCienciasGen(cid:2)omicas,UniversidadAut(cid:2)onomadela
CiudaddeMe´xico,BenitoJuarze,CDMX,Mexico
LIANG-CHUANLAI (cid:2) DepartmentofPhysiology,CollegeofMedicine,NationalTaiwan
University,Taipei,Taiwan
SERGIOLARIO (cid:2) DigestiveDiseasesService,HospitaldeSabadell,Corporaci(cid:2)o Sanit`ariaParc
Taulı´,InstitutUniversitariParcTaulı´-UAB,Sabadell,Spain;Fundaci(cid:2)o ParcTaulı´,
Corporaci(cid:2)oSanit`ariaParcTaulı´,InstitutUniversitariParcTaulı´-UAB,Sabadell,Spain;
CentrodeInvestigaci(cid:2)onBiome´dicaenReddeEnfermedadesHepa´ticasyDigestivas
(CIBERehd),InstitutodeSaludCarlosIII,Madrid,Spain
PETERJ.LEEDMAN (cid:2) LaboratoryforCancerMedicine,HarryPerkinsInstituteofMedical
Research,UniversityofWesternAustraliaCentreforMedicalResearch,Nedlands,WA,
Australia;SchoolofMedicineandPharmacology,TheUniversityofWesternAustralia,
Nedlands,WA,Australia
LAURENCEA.MARCHAT (cid:2) ProgramaenBiomedicinaMolecular yReddeBiotecnologı´a,
EscuelaNacionaldeMedicinayHomeopatı´a,InstitutoPolite´cnicoNacional,Ciudadde
Me´xico,CDMX,Mexico
AYKUTO¨ZGu€R (cid:2) DivisionofBiochemistry,DepartmentofBasicSciences,FacultyofPharmacy,
CumhuriyetUniversity,Sivas,Turkey
MARTAPASSADOURO (cid:2) Center forNeuroscienceandCellBiology,UniversityofCoimbra,
Coimbra,Portugal;DepartmentofLifeSciences,FacultyofScienceandTechnology,
UniversityofCoimbra,Coimbra,Portugal
MARI´AELISA QUI´LEZ (cid:2) OncologyService,HospitaldeSabadell,Corporaci(cid:2)o Sanit`ariaParc
Taulı´,InstitutUniversitariParcTaulı´-UAB,Sabadell,Spain;DigestiveDiseasesService,
HospitaldeSabadell,Corporaci(cid:2)o Sanit`ariaParcTaulı´,InstitutUniversitariParcTaulı´-
UAB,Sabadell,Spain;Fundaci(cid:2)o ParcTaulı´,Corporaci(cid:2)o Sanit`ariaParcTaulı´,Institut
UniversitariParcTaulı´-UAB,Sabadell,Spain
MARI´AJOSE´ RAMI´REZ-LA´ZARO (cid:2) DigestiveDiseasesService,HospitaldeSabadell,Corporaci(cid:2)o
Sanit`ariaParcTaulı´,InstitutUniversitariParcTaulı´-UAB,Sabadell,Spain;Centrode
Investigaci(cid:2)onBiome´dicaenReddeEnfermedadesHepa´ticasyDigestivas(CIBERehd),
InstitutodeSaludCarlosIII,Madrid,Spain
Contributors xi
KIRSTYL.RICHARDSON (cid:2) LaboratoryforCancerMedicine,HarryPerkinsInstituteofMedical
Research,UniversityofWesternAustraliaCentreforMedicalResearch,Nedlands,WA,
Australia
DOLORESGALLARDORINCO´N (cid:2) LaboratoriodeMedicinaTranslacional,InstitutoNacional
deCancerologı´a,Tlalpan,CDMX,Mexico
ERIKARUIZ-GARCI´A (cid:2) LaboratoriodeMedicinaTranslacional,InstitutoNacionalde
Cancerologı´a,Tlalpan,CDMX,Mexico
HOLGERSu€LTMANN (cid:2) CancerGenomeResearch(B063),GermanCancerResearchCenter
(DKFZ)andGermanCancerConsortium(DKTK),Heidelberg,Germany
DANIELA SCHILLING (cid:2) CancerGenomeResearch(B063),GermanCancerResearchCenter
(DKFZ)andGermanCancerConsortium(DKTK),Heidelberg,Germany
LISAM.STUART (cid:2) LaboratoryforCancerMedicine,HarryPerkinsInstituteofMedical
Research,UniversityofWesternAustraliaCentreforMedicalResearch,Nedlands,WA,
Australia
MONG-HSUNTSAI (cid:2) InstituteofBiotechnology,CollegeofBio-resourcesandAgriculture,
NationalTaiwanUniversity,Taipei,Taiwan
Lu€TFITUTAR (cid:2) DepartmentofMolecularBiologyandGenetics,FacultyofArtsandSciences,
AhiEvranUniversity,Kır¸sehir,Turkey
YUSUFTUTAR (cid:2) DivisionofBiochemistry,DepartmentofBasicSciences,FacultyofPharmacy,
CumhuriyetUniversity,Sivas,Turkey;DepartmentofNutritionandDietetics,Health
SciencesFaculty,UniversityofHealthSciences,U€sku€dar,Istanbul,Turkey
LARISSAC.WINTLE (cid:2) LaboratoryforCancerMedicine,HarryPerkinsInstituteofMedical
Research,UniversityofWesternAustraliaCentreforMedicalResearch,Nedlands,WA,
Australia
WEIWU (cid:2) DepartmentofMedicine,HelenDillerFamilyComprehensiveCancerCenter,
UniversityofCaliforniainSanFrancisco,SanFrancisco,CA,USA
JASONT.YUSTEIN (cid:2) DepartmentofPediatrics,BaylorCollegeofMedicine,Houston,TX,USA
MOHAMMADAFZALZARGAR (cid:2) DepartmentofBiochemistry,FacultyofScience,Universityof
Kashmir,HazratbalSrinagar,J&K,India
JUNZHU (cid:2) JiangsuCancerHospital,Nanjing,Jiangsu,China
WEIZHU (cid:2) DepartmentofOncology,FirstAffiliatedHospitalofNanjingMedical
University,Nanjing,PRChina