Phage Display: Methods and Protocols

556 Pages·2018·10.75 MB·English

by  Michael Hust

Methods in
Molecular Biology 1701
Michael Hust
Theam Soon Lim Editors
Phage
Display
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
Phage Display
Methods and Protocols
Edited by
Michael Hust
€
Technische Universitat Braunschweig, Braunschweig, Germany
Theam Soon Lim
Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
Editors
MichaelHust TheamSoonLim
TechnischeUniversit€atBraunschweig InstituteforResearchinMolecularMedicine
Braunschweig,Germany UniversitiSainsMalaysia
Minden,Penang,Malaysia
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-7446-7 ISBN978-1-4939-7447-4 (eBook)
DOI10.1007/978-1-4939-7447-4
LibraryofCongressControlNumber:2017956713
©SpringerScience+BusinessMediaLLC2018
Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis
concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction
onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation,
computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped.
Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply,
evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations
andthereforefreeforgeneraluse.
Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto
betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty,
expressorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeenmade.
Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations.
Printedonacid-freepaper
ThisHumanaPressimprintispublishedbySpringerNature
TheregisteredcompanyisSpringerScience+BusinessMedia,LLC
Theregisteredcompanyaddressis:233SpringStreet,NewYork,NY10013,U.S.A.
Preface
Antibodies have emerged from humble beginnings over a century ago when Emil von
Behring and Shibasaburo Kitasato first witnessed the unique ability of antibodies in sera
(first called “Anti-toxine”) from immunized rabbits to neutralize toxins. Since then, anti-
bodieshaveemergedtobecomethemostimportantbiologicals.Inthemid-1970s,Ko¨hler
and Milstein revolutionized the application of antibodies not only in basic research and
diagnosticsbutalsointhebiomedicalfieldwiththeir workonhybridomatechnology.This
wasaturningpointformanymedicalapproachesappliedatthattime.Theinherentabilityto
produce monospecific antibodies was a game changer in the pharmaceutical industry, but
theseantibodieswerestillmainlymurineantibodieswhichcancausesideeffects.
The evolution of DNA technology coupled with a deeper understanding of molecular
biology and immunology allowed for the successive growth of antibody technology. The
groundbreakingdiscoverybySmithonM13phagedisplayallowedforthepresentationofa
specificpeptideonthesurfaceofbacteriophages.Thisworkwasthenfurtherenhancedwith
thepresentationofantibodyfragmentsonthesurfaceofbacteriophagewhichwasindepen-
dently developed around 1990 at the Deutsches Krebsforschungszentrum (DKFZ) in
Heidelberg,Germany,attheMRCLaboratoryofMolecularBiologyinCambridge,United
Kingdom, and at the Scripps Research Institute in La Jolla, USA. The advancement in
technologies allowed the selection of fully human antibodies from antibody phage display
libraries.Theplethoraofdifferenttypesofphagedisplaylibrariesandapplicationsofphage
displayhighlightstherobustnessanddurabilityofthemethodforantibodygenerationand
became a key technology for the generation of therapeutic antibodies. Antibody phage
displaywasalsothetechnologytodevelopthefirsthumanantibody,Adalimumab,andbest
soldbiological.
This book provides examples of the generation of different forms of antibody libraries
including libraries from different hosts. Many research groups share their expertise and
experienceinthisbook.Acomprehensivelistofdifferentantibodylibrariesaswellasnovel
approachesforantibodydiscoveryiscoveredinthisbook.Thechaptersinthisbookcanbe
divided into four sections: the first focuses on the construction of antibody libraries,
followed by selection strategies for antibodies, complementary approaches for antibody
selection, and finally epitope mapping and biomarker identification. This book provides a
comprehensivelistofantibodyphagedisplaytechnologiesandapplications.
Onapersonalnote,theabilitytocarryoutintercontinentalcollaborativeeffortswasthe
essence of this book. This book showcases a collection of works from researchers from
variouscountriesacrosstheglobe.Theexperienceofproducingthiseditionwhenwewere
physicallylocatedintwodifferentcontinents,inEuropeandAsia,hashelpedtostrengthen
our resolve in our quest to contribute further in science. The work on this book has also
helped strengthen the relationship and exchange between our laboratories not just on a
researchlevelbutalsomoreimportantlyonapersonallevel.Manynewfriendshipsandideas
havebeendevelopedover thecourseofthisbookthatholdswellforcross-bordercollabo-
rativeinitiatives.
Although a comprehensive list of topics has been covered in this book, there are still
manymorechaptersthatcanstillbewrittenconsideringsomuchactivityinalltheantibody
laboratories in the world. As the antibody business is a multibillion dollar industry, rapid
v
vi Preface
technologicaldevelopmentsaswellastheemergenceofnewlaboratoriesareexpected.The
new kid on the block in this book is the antibody technology program at the Institute for
Research in Molecular Medicine (INFORMM), which is the brainchild of the Malaysian
MinistryofHigherEducationundertheHigherInstitutionCentreofExcellence(HICoE)
program together with Universiti Sains Malaysia (USM). It is our aim that this book can
provide technical assistance to new start-ups that are venturing into the field of antibody
phage display. We also hope this book will help spur interest and ideas in the field while
expandingourgrowingfamilyofenthusiasticantibodyresearchers.
Wewouldliketothanktheauthorswhosecontributionstothisvolumehaveallowedit
tobeacomprehensiveguidetotheprocessesinvolvedinantibodyphagedisplay.Wewould
also like to thank Prof. John M. Walker for his guidance and assistance throughout the
editorial process. Our scientific career would not be possible without our great mentors
ErhardRhiel,ThomasReinard,andStefanDu€belandZolta`nKonthurandJo¨rnGlo¨kler.On
apersonalnote, wewouldliketo thankour familiesDagmar, NoahJoris,and LenjaMarie
andPoiHong,Hayley,andHaydenfortheirpatiencewhilepreparingthisbookandallour
otherprojects.
Braunschweig,Germany MichaelHust
Penang,Malaysia TheamSoonLim
Contents
Preface ..................................................................... v
Contributors................................................................. xi
PART I CONSTRUCTION OF ANTIBODY PHAGE DISPLAY LIBRARIES
1 ConstructionofHumanImmuneandNaivescFvLibraries .................. 3
JonasKu€gler,FlorianTomszak,Andre´Frenzel,andMichaelHust
2 ConstructionofNaiveandImmuneHumanFabPhage-DisplayLibrary....... 25
NoorsharmimiOmarandTheamSoonLim
3 ConstructionofSyntheticAntibodyPhage-DisplayLibraries................. 45
JohanNilvebrantandSachdevS.Sidhu
4 ModularConstructionofLargeNon-ImmuneHuman
AntibodyPhage-DisplayLibrariesfromVariableHeavyand
LightChainGeneCassettes.............................................. 61
Nam-KyungLee,ScottBidlingmaier,YangSu,andBinLiu
5 ConstructionofMacaqueImmune-Libraries ............................... 83
ArnaudAvril,SebastianMiethe,MichaelHust,andThibautPelat
6 ConstructionofBovineImmunoglobulinLibrariesinthe
Single-ChainFragmentVariable(scFv)Format ............................. 113
UlrikeS.Diesterbeck
7 ConstructionofRabbitImmuneAntibodyLibraries ........................ 133
ThiThuHaNguyen,JongSeoLee,andHyunboShim
8 GenerationofSemi-SyntheticSharkIgNARSingle-Domain
AntibodyLibraries ...................................................... 147
JuliusGrzeschik,DoreenK¨onning,SteffenC.Hinz,SimonKrah,
ChristianSchr¨oter,MartinEmpting,HaraldKolmar,
andStefanZielonka
9 ConstructionofHigh-QualityCamelImmuneAntibodyLibraries............ 169
EmaRoma˜o,VianneyPoignavent,Ce´cileVincke,ChristopheRitzenthaler,
SergeMuyldermans,andBaptisteMonsion
10 ConstructionofChickenAntibodyLibraries ............................... 189
JeanniFehrsen,SusanWemmer,andWouter vanWyngaardt
®
11 ConstructionandSelectionofAffilin PhageDisplayLibraries............... 205
FlorianSettele,MadlenZwarg,SebastianFiedler,DanielKoscheinz,
andEvaBosse-Doenecke
12 ConstructionofaSyntheticAntibodyGeneLibraryfor the
SelectionofIntrabodiesandAntibodies ................................... 239
De´borahCaucheteur,GautierRobin,VincentParez,
andPierreMartineau
vii
viii Contents
13 TargetingIntracellularAntigenswithpMHC-BindingAntibodies:
APhageDisplayApproach............................................... 255
ZhihaoWu,BrianH.Santich,HongLiu,ChengLiu,
andNai-KongV.Cheung
PART II SELECTION STRATEGIES FOR ANTIBODIES
14 ParallelizedAntibodySelectioninMicrotiterPlates ......................... 273
GiulioRusso,DorisMeier,SaskiaHelmsing,EstherWenzel,
FabianOberle,Andre´Frenzel,andMichaelHust
15 MassSpectrometryImmunoAssay(MSIA™)Streptavidin
®
DisposableAutomationResearchTips(D.A.R.T’s )Antibody
PhageDisplayBiopanning ............................................... 285
ChaiFungChin,YeeSiewChoong,andTheamSoonLim
16 MagneticNanoparticle-BasedSemi-AutomatedPanningfor
High-ThroughputAntibodySelection..................................... 301
AngelaChiewWenCh’ng,NurulHamizahBintiHamidon,
Zolta´nKonthur,andTheamSoonLim
17 PhageDisplayandSelectionsonCells..................................... 321
WielandFahrandAndre´Frenzel
18 CombinePhageAntibodyDisplayLibrarySelectiononPatient
TissueSpecimenswithLaserCaptureMicrodissectiontoIdentify
NovelHumanAntibodiesTargetingClinicallyRelevantTumorAntigens...... 331
YangSu,ScottBidlingmaier,Nam-KyungLee,andBinLiu
19 AntibodyIsolationFromaHumanSyntheticCombinatorialand
OtherLibrariesofSingle-ChainAntibodies ................................ 349
AlmogBitton,LimorNahary,andItaiBenhar
20 ScreeningPhage-DisplayAntibodyLibrariesUsingProteinArrays............ 365
RicardoJara-Acevedo,PaulaDı´ez,Marı´aGonza´lez-Gonza´lez,
RosaMarı´aDe´gano,NievesIbarrola,RafaelG(cid:2)ongora,
AlbertoOrfao,andManuelFuentes
21 AntibodySelectiononFFPETissueSlides ................................. 381
AndretenHaaf,StefanGattenl¨ohner,andMehmetKemalTur
22 AntibodyAffinityandStabilityMaturationbyError-PronePCR.............. 393
TobiasUnkauf,MichaelHust,andAndre´Frenzel
PART III COMPLEMENTARYAPPROACHES FOR ANTIBODY
PHAGE DISPLAY SELECTIONS
23 UpgradingAffinityScreeningExperimentsbyAnalysisof
Next-GenerationSequencingData........................................ 411
ChristianGrohmannandMichaelBlank
24 Next-GenerationDNASequencingofV /V Repertoires:
H L
APrimerandGuidetoApplicationsinSingle-DomainAntibody
Discovery.............................................................. 425
KevinA.Henry
Contents ix
25 High-ThroughputIgGReformattingandExpression ....................... 447
Chao-GuangChen,GeorginaSansome,MichaelJ.Wilson,
andConPanousis
26 MonitoringPhageBiopanningbyNext-GenerationSequencing.............. 463
AnnaVaisman-MenteshandYarivWine
PART IV PHAGE DISPLAY FOR EPITOPE MAPPING
AND IDENTIFICATION OF BIOMARKERS
27 ORFeomePhageDisplay ................................................ 477
JonasZantow,GustavoMarc¸alSchmidtGarciaMoreira,
StefanDu€bel,andMichaelHust
28 EpitopeMappingbyPhageDisplay ....................................... 497
GustavoMarc¸alSchmidtGarciaMoreira,ViolaFu€hner,
andMichaelHust
29 MetasecretomePhageDisplay............................................ 519
MilicaCiric,FilomenaNg,JasnaRakonjac,andDraganaGagic
30 Phagekines:ScreeningBindingPropertiesandBiological
ActivityofFunctionalCytokinesDisplayedonPhages....................... 535
GertrudisRojasandTaniaCarmenate
Index ...................................................................... 561
Contributors
ARNAUDAVRIL (cid:1) De´partementdesMaladiesInfectieuses,unite´biothe´rapiesanti-infectieuses
etimmunite´,InstitutdeRechercheBiome´dicaledesArme´es,Bre´tigny-sur-Orge,France
ITAIBENHAR (cid:1) DepartmentofMolecularMicrobiologyandBiotechnology,TheGeorgeS.Wise
FacultyofLifeSciences,Tel-AvivUniversity,Tel-Aviv,Israel
SCOTTBIDLINGMAIER (cid:1) DepartmentofAnesthesia,UCSFHelenDillerFamilyComprehensive
CancerCenter,UniversityofCaliforniaatSanFrancisco,SanFrancisco,CA,USA
ALMOGBITTON (cid:1) DepartmentofMolecularMicrobiologyandBiotechnology,TheGeorge
S.WiseFacultyofLifeSciences,Tel-AvivUniversity,Tel-Aviv,Israel
MICHAELBLANK (cid:1) AptaITGmbH,Planegg-Martinsried,Germany
EVABOSSE-DOENECKE (cid:1) NavigoProteinsGmbH,Halle(Saale),Germany
TANIACARMENATE (cid:1) CenterofMolecularImmunology,Atabey,Playa,LaHabana,Cuba
DE´BORAHCAUCHETEUR (cid:1) IRCM,InstitutdeRechercheenCance´rologiedeMontpellier,
Montpellier,France;INSERM,U1194,Montpellier,France;Universite´deMontpellier,
Montpellier,France;Institutre´gionalduCancerdeMontpellier,Montpellier,France
ANGELACHIEWWENCH’NG (cid:1) AnalyticalBiochemistryResearchCentre,Institutefor
ResearchinMolecularMedicine,UniversitiSainsMalaysia,Penang,Malaysia
CHAO-GUANGCHEN (cid:1) ResearchandDevelopment,CSLLimited,Parkville,VIC,Australia
NAI-KONGV.CHEUNG (cid:1) DepartmentofPediatrics,MemorialSloanKetteringCancer
Center,NewYork,NY,USA;GerstnerSloanKetteringGraduateSchoolofBiomedical
Sciences,MemorialSloanKetteringCancerCenter,NewYork,NY,USA
CHAIFUNGCHIN (cid:1) InstituteforResearchinMolecularMedicine,UniversitiSainsMalaysia,
Penang,Malaysia
YEESIEWCHOONG (cid:1) InstituteforResearchinMolecularMedicine,UniversitiSains
Malaysia,Penang,Malaysia
MILICA CIRIC (cid:1) InstituteofFundamentalSciences,MasseyUniversity,PalmerstonNorth,
NewZealand
ROSAMARI´ADE´GANO (cid:1) ProteomicsUnit,CancerResearchCenter(CSIC/USAL/IBSAL),
Salamanca,Spain
PAULA DI´EZ (cid:1) DepartmentofMedicineandGeneralCytometryService-Nucleus,Cancer
ResearchCenter(CSIC/USAL/IBSAL),Salamanca,Spain;ProteomicsUnit,Cancer
ResearchCenter(CSIC/USAL/IBSAL),Salamanca,Spain
STEFANDu€BEL (cid:1) Institutfu€rBiochemie,BiotechnologieundBioinformatik, Abteilung
Biotechnologie,TechnischeUniversita€tBraunschweig,Braunschweig,Germany
ULRIKES.DIESTERBECK (cid:1) LaboratoryofViralDiseases,NationalInstituteofAllergy
andInfectiousDiseases,NationalInstitutesofHealth,Bethesda,MD,USA
MARTINEMPTING (cid:1) DepartmentDrugDesignandOptimization,Helmholtz-Institute
forPharmaceuticalResearchSaarland(HIPS),SaarlandUniversity,Saarbru€cken,
Germany
VIOLAFu€HNER (cid:1) AbteilungBiotechnologie,Institutfu€rBiochemie,Biotechnologie
undBioinformatik, TechnischeUniversita€tBraunschweig,Braunschweig,Germany
WIELANDFAHR (cid:1) AbteilungBiotechnologie,Institutfu€rBiochemie,Biotechnologie
undBioinformatik, TechnischeUniversita€tBraunschweig,Braunschweig,Germany
xi