The Surfaceome: Methods and Protocols

351 Pages·2018·8.736 MB·English

by  Kenneth R. Boheler,Rebekah L. Gundry (eds.)

Methods in
Molecular Biology 1722
Kenneth R. Boheler
Rebekah L. Gundry Editors
The
Surfaceome
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
The Surfaceome
Methods and Protocols
Edited by
Kenneth R. Boheler
School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong,
SAR, China; Stem Cell & Regenerative Medicine Consortium, School of Biomedical Sciences,
LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
Rebekah L. Gundry
Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
Editors
KennethR.Boheler RebekahL.Gundry
SchoolofBiomedicalSciences DepartmentofBiochemistry
LKSFacultyofMedicine MedicalCollegeofWisconsin
TheUniversityofHongKong Milwaukee,WI,USA
HongKong,SAR,China
StemCell&RegenerativeMedicine
Consortium,SchoolofBiomedicalSciences
LKSFacultyofMedicine
TheUniversityofHongKong
HongKong,SAR,China
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-7551-8 ISBN978-1-4939-7553-2 (eBook)
https://doi.org/10.1007/978-1-4939-7553-2
LibraryofCongressControlNumber:2017960803
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Preface
The plasma membrane is the gateway through which cells sense and respond to their
microenvironment. Critical to this process are cell surface proteins that span (transmem-
brane)orareanchored/embeddedintheplasmamembrane.Cellsurfaceproteinsperform
diversefunctions,includingnutrientandiontransport,intra-andintercellularcommunica-
tion,receptorsignaling,andenzymaticreactions.Altogether,thecollectionofproteinsthat
resideatthecellsurface(i.e.,surfaceome)facilitatesinteractionswithpathogens,bindingof
chemical messengers, and transmission of signaling cascades, and it is required for cell
migration, adhesion, and survival. Surfaceome content, including protein identity and
modifications, differs among cell types and is dynamic during development and disease
states.Forthesereasons,andthefactthatcellsurfaceproteinsareaccessible,thesurfaceome
isarichsourceofdrugandimmunotherapytargetsandcontainsuniquemarkersthatcanbe
used to identify cell types, disease states, and cellular phenotypes. Despite their critical
functions in health and disease, cell surface proteins have historically been understudied in
mostcellandtissuetypes.Thisisdue,inpart,tothechallengesposedbytheirrelativelylow
abundance when compared to intracellular proteins, their hydrophobic nature, and the
difficulty in biophysically purifying plasma membrane proteins without contamination
fromintracellular membranecomponents.Moreover, high-quality antibodiesarecurrently
availableforalimitedsubsetofcellsurfaceproteins.
Consideringthesechallenges,thedevelopmentanddissemination ofmodernmethods
and technologies that enable the study of cell surface proteins will undoubtedly advance a
broadrangeofresearchefforts,includingour understandingofcellulardifferentiationand
development, host-pathogen interactions, and metastatic processes, and will lead to the
development of new treatments for disease. In this volume of Methods in Molecular
Biology: The Surfacome, we have assembled 19 chapters that cover a variety of methods
ranging from molecular and cellular biology to proteomics to bioinformatics. The overall
aim of this edition is to provide state-of-the-art techniques and tools to assess the surfa-
ceome content, modifications, and function. The volume does not include standard
approaches extensively reviewed elsewhere, nor does it include methods to analyze lipids
and glycans, which are key components of the plasma membrane and worthy of separate
volumes dedicated to their study. While most of the methods described in this volume are
generally applicable to any cell type, some chapters focus on specific cell types and/or
specific molecule classes of interest. These latter chapters are designed to illustrate the
applicationoftheseproceduresandprotocolsindefinedsystems,buttheapproachesshould
be applicable across a broad range of cells. Altogether, we hope this collection of methods
willfacilitatethestudyofcellsurfaceproteinbiologyandfunctionandleadtothediscovery
ofnewdrugandimmunotherapytargetsfor treatingdiseaseandnewimmunophenotyping
markers for studying cellular function, differentiation, and disease. The chapters are
arranged in four parts, beginning with discovery-based and then targeted strategies for
cataloging surfaceome content, moving to functional assays for specific protein and cell
types,andendingwithcomputationalapproaches.
Part I focuses on discovery-based approaches for cataloging surfaceome content and
includes methods to analyze the surfaceome of bacteria, avian embryos, and mammalian
systems.Chaptersinthispartfocusonmodernproteomicmethodsthatoffer theabilityto
v
vi Preface
specificallytargetcellsurfaceproteinswithlimitedinterferencefromintracellularmembrane
proteins. These include surface membrane protein enrichment techniques, using proteases
to “shave” proteins from the surface of bacteria to identify surface-exposed proteins, and
exploitingtheaviansystemtostudydevelopmentalchangesincellsurfaceproteins,includ-
ingbioinformatics-basedtechniquestotranslatetohumanorthologs.Subsequentchapters
describetheCellSurfaceCaptureTechnology,atargetedanalyticalapproachtospecifically
identify cell surface N-glycoproteins, the use of iron oxide nanoparticles to enrich plasma
membraneproteins,andmethodstoprofilesecretedproteinsandexosomesincellculture,a
topicthathasrecentlygainedattentionacrossavarietyofresearchdisciplines.
Part II focuses on targeted approaches to analyze the surfaceome. The chapters in this
partincludemethodstooverexpressspecifictargetsinSf9cellsandanapproachtogenerate
bispecificantibodiesthatarevaluablefortargetingcancerandsomaticcells.Alsoincludedis
a tutorial chapter on flow cytometry and its application to immunophenotyping to assist
novicesintheirpursuitofsurfaceproteins.Thelastchapterinthispartprovidesanexample
ofhowELISAandflowcytometryareappliedtodetectingtheGprotein-coupledreceptor
CXCR4,astrategyparticularlyvaluableforinvestigatorsinterestedinGproteinsandindrug
repurposing.
Part III focuses on cell-based functional analyses. This part begins with a review on
voltage-dependent sodium channels and methods for high content electrophysiological
analyses.Methodsarethendescribedfortheevaluationofvascularendothelialcellfunctions
andapproachestostudysignaltransductionofsurfacereceptortyrosinekinaseinneurons.A
comprehensive analysis of cell polarity, using retinal pigmented epithelium as a model
system, is then described, including techniques for immunostaining for apical and basolat-
eral membrane markers, polarized cytokine secretion, fluid transport, phagocytosis, and
identification of plasma membrane proteins through cell surface capturing technologies as
described in the first part. This part finishes with a description of methods that take
advantage of extracellular matrix components to capture mesenchymal stromal cells under
flow,modeldiseasestates,andultimatelyanalyzecell-matrixinteractionsthroughtheuseof
3Dmicrotissues.
PartIVfocusesoncomputationalapproachesinsurfaceomestudiesanddescribesanew
web-basedplatform,Targets-search,thatincorporatesinformationfromavarietyofsources
includingtheCellSurfaceProteinAtlasandonlinedrugdatabases,tofacilitateidentification
ofsurfaceproteinsthatareinformativeforaparticularcelltypeordiseaseandknowndrugs
thatinteractwiththeseproteins.
In closing, we would like to thank Springer for its support, dedication to this project,
andpatienceindevelopingthisbook.Wealsowishtoespeciallythankalloftheauthorsfor
their time, energy, and valuable contributions. With their efforts, we have assembled what
we hope will be a valuable resource for those research laboratories working to advance the
studyofsurfaceproteinbiology.
HongKong,SAR,China KennethR.Boheler
Milwaukee,WI,USA RebekahL.Gundry
Contents
Preface ..................................................................... v
Contributors................................................................. ix
PART I DISCOVERY-BASED APPROACHES TO SURFACEOME CONTENT
1 SurfaceomeAnalysisProtocolfor theIdentificationofNovel
BordetellapertussisAntigens.............................................. 3
YulandaM.Williamson,JenniferWhitmon,RolieriaWest-Deadwyler,
HerculesMoura,AdrianR.Woolfitt,JonRees,DavidM.Schieltz,
andJohnR.Barr
2 “Shaving”LiveBacterialCellswithProteasesforProteomic
AnalysisofSurfaceProteins .............................................. 21
ManuelJ.Rodrı´guez-Ortega
3 MethodsforMappingtheExtracellularandMembrane
ProteomeintheAvianEmbryo,andIdentificationofPutative
VascularTargetsorEndothelialGenes..................................... 31
WitoldW.Kilarski,JohnHerbert,andAndreasBikfalvi
4 MassSpectrometry-BasedIdentificationofExtracellularDomains
ofCellSurfaceN-Glycoproteins:DefiningtheAccessibleSurfaceome
forImmunophenotypingStemCellsandTheirDerivatives................... 57
ChelseaM.Fujinaka,MatthewWaas,andRebekahL.Gundry
5 ApplicationofHigherDensityIronOxideNanoparticlePellicles
toEnrichthePlasmaMembraneandItsProteomefromCells
inSuspension........................................................... 79
RebeccaL.Rose,WaeowaleeChoksawangkarn,andCatherineFenselau
6 ProteomicProfilingofSecretedProteins,Exosomes,
andMicrovesiclesinCellCultureConditionedMedia....................... 91
AnkitSinha,SimonaPrincipe,JavierAlfaro,AlexIgnatchenko,
VladimirIgnatchenko,andThomasKislinger
PART II TARGETED APPROACHES FOR SURFACEOME CONTENT
7 Cloning,Expression,andPurificationoftheGlycosylated
TransmembraneProtein,Cation-DependentMannose
6-PhosphateReceptor,fromSf9CellsUsingtheBaculovirusSystem.......... 105
LindaJ.OlsonandNancyM.Dahms
8 BispecificAntibodyArmedTCellstoTargetCancerCells ................... 117
ArchanaThakur,LawrenceG.Lum,andSandeepMittal
9 ImmunophenotypingofLiveHumanPluripotentStemCells
byFlowCytometry ..................................................... 127
DanielR.RiordonandKennethR.Boheler
vii
viii Contents
10 DetectingCellSurfaceExpressionoftheGProtein-Coupled
ReceptorCXCR4....................................................... 151
AmandaM.NevinsandAdrianoMarchese
PART III CELL-BASED FUNCTIONAL ANALYSES RELATED
TO SURFACEOME CONTENT
11 Na Channels:AssayingBiosynthesis,Trafficking,Function.................. 167
V
GordonF.TomaselliandFedericaFarinelli
12 High-ContentElectrophysiologicalAnalysisofHuman
PluripotentStemCell-DerivedCardiomyocytes(hPSC-CMs)................ 185
Chi-WingKong,LinGeng,andRonaldA.Li
13 MethodsforEvaluationofVascularEndothelialCellFunction
withTransientReceptorPotential(TRP)ChannelDrugs.................... 195
YungWuiTjongandXiaoqiangYao
14 MethodstoStudytheSignalTransductionoftheSurface
ReceptorTyrosineKinaseTrkBinNeurons ................................ 211
Kwok-OnLaiandNancyY.Ip
15 PolarizedHumanRetinalPigmentEpitheliumExhibits
DistinctSurfaceProteomeonApicalandBasalPlasmaMembranes ........... 223
VladimirKhristov,QinWan,RuchiSharma,MostafaLotfi,
ArvydasMaminishkis,andKapilBharti
16 ExtracellularMatrixMolecule-BasedCaptureofMesenchymal
StromalCellsUnderFlow ............................................... 249
TeresaMassam-Wu,StuartA.Cain,andCayM.Kielty
17 GenerationofInducedPluripotentStemCellsfromPatients
withCOL3A1MutationsandDifferentiationtoSmooth
MuscleCellsforECM-SurfaceomeAnalyses ............................... 261
JiaoziHe,ZhihuiWeng,StanleyChunMingWu,
andKennethR.Boheler
18 FabricationandMechanicalPropertiesMeasurementsof3D
Microtissuesfor theStudyofCell–MatrixInteractions ...................... 303
PrasenjitBose,ChenYuHuang,JeroenEyckmans,
ChristopherS.Chen,andDanielH.Reich
PART IV COMPUTATIONAL APPROACHES IN SURFACEOME STUDIES
19 DiscoveryofSurfaceTargetProteinsLinkingDrugs,MolecularMarkers,
GeneRegulation,ProteinNetworks,andDiseasebyUsinga
Web-BasedPlatformTargets-search........................................ 331
BinYan,PanwenWang,JunwenWang,andKennethR.Boheler
Index ...................................................................... 345
Contributors
JAVIERALFARO (cid:1) DepartmentofMedicalBiophysics,UniversityofToronto,Toronto,ON,
Canada;PrincessMargaretCancerCentre,Toronto,ON,Canada
JOHNR.BARR (cid:1) DivisionofLaboratorySciences,NationalCenterforEnvironmentalHealth,
CentersforDiseaseControlandPrevention,Chamblee,GA,USA
KAPILBHARTI (cid:1) UnitonOcularandStemCellTranslationalResearch,NationalEye
Institute,NationalInstituteofHealth,Bethesda,MD,USA
ANDREASBIKFALVI (cid:1) AngiogenesisandTumorMicroenvironmentLaboratory,INSERM
U1029,Pessac,France;AngiogenesisandTumorMicroenvironmentLaboratory,
UniversityBordeaux,Pessac,France
KENNETHR.BOHELER (cid:1) SchoolofBiomedicalSciences,LKSFacultyofMedicine,The
UniversityofHongKong,HongKong,SAR,China;StemCell&RegenerativeMedicine
Consortium,SchoolofBiomedicalSciences,LKSFacultyofMedicine,TheUniversityof
HongKong,HongKong,SAR,China
PRASENJITBOSE (cid:1) DepartmentofPhysicsandAstronomy,JohnsHopkinsUniversity,
Baltimore,MD,USA
STUARTA.CAIN (cid:1) WellcomeTrustCentreforCell-MatrixResearch,FacultyofLifeBiology,
MedicineandHealth,UniversityofManchester,Manchester,UK
CHRISTOPHERS.CHEN (cid:1) DepartmentofBiomedicalEngineering,BiologicalDesignCenter,
BostonUniversity,Boston,MA,USA;TheWyssInstituteforBiologicallyInspired
Engineering,HarvardUniversity,Boston,MA,USA
WAEOWALEE CHOKSAWANGKARN (cid:1) DepartmentofBiochemistry,FacultyofScience,Burapha
University,Mueang,Chonburi,Thailand
NANCY M.DAHMS (cid:1) DepartmentofBiochemistry,MedicalCollegeofWisconsin,Milwaukee,
WI,USA
JEROENEYCKMANS (cid:1) DepartmentofBiomedicalEngineering,BiologicalDesignCenter,
BostonUniversity,Boston,MA,USA;TheWyssInstituteforBiologicallyInspired
Engineering,HarvardUniversity,Boston,MA,USA
FEDERICA FARINELLI (cid:1) DivisionofCardiology,DepartmentofMedicine,JohnsHopkins
University,Baltimore,MD,USA
CATHERINEFENSELAU (cid:1) DepartmentofChemistryandBiochemistry,UniversityofMaryland,
CollegePark,MD,USA
CHELSEAM.FUJINAKA (cid:1) DepartmentofBiochemistry,MedicalCollegeofWisconsin,
Milwaukee,WI,USA
LINGENG (cid:1) DepartmentofPaediatricsandAdolescentMedicine,SchoolofBiomedical
Sciences,LKSFacultyofMedicine,TheUniversityofHongKong,HongKong,SAR,China
REBEKAHL.GUNDRY (cid:1) DepartmentofBiochemistry,MedicalCollegeofWisconsin,
Milwaukee,WI,USA
JIAOZIHE (cid:1) SchoolofBiomedicalSciences,LKSFacultyofMedicine,TheUniversityofHong
Kong,HongKong,SAR,China
JOHNHERBERT (cid:1) InstituteofIntegrativeBiology,UniversityofLiverpool,Liverpool,UK
CHENYUHUANG (cid:1) DepartmentofPhysicsandAstronomy,JohnsHopkinsUniversity,
Baltimore,MD,USA
ALEXIGNATCHENKO (cid:1) PrincessMargaretCancerCentre,Toronto,ON,Canada
ix
x Contributors
VLADIMIRIGNATCHENKO (cid:1) PrincessMargaretCancerCentre,Toronto,ON,Canada
NANCY Y.IP (cid:1) DivisionofLifeScience,MolecularNeuroscienceCenterandStateKey
LaboratoryofMolecularNeuroscience,TheHongKongUniversityofScienceand
Technology,HongKong,SAR,China
VLADIMIRKHRISTOV (cid:1) SectiononEpithelialandRetinalPhysiologyandDisease,NationalEye
Institute,NationalInstitutesofHealth,Bethesda,MD,USA
CAYM.KIELTY (cid:1) WellcomeTrustCentreforCell-MatrixResearch,FacultyofLifeBiology,
MedicineandHealth,UniversityofManchester,Manchester,UK
WITOLD W.KILARSKI (cid:1) InstituteforMolecularEngineering,TheUniversityofChicago,
Chicago,IL,USA
THOMASKISLINGER (cid:1) DepartmentofMedicalBiophysics,UniversityofToronto,Toronto,ON,
Canada
CHI-WING KONG (cid:1) StemCell&RegenerativeMedicineConsortium,Departmentof
PaediatricsandAdolescentMedicine,SchoolofBiomedicalSciences,LKSFacultyof
Medicine,TheUniversityofHongKong,HongKong,SAR,China
KWOK-ONLAI (cid:1) SchoolofBiomedicalSciences,LKSFacultyofMedicine,StateKeyLaboratory
ofBrainandCognitiveSciences,TheUniversityofHongKong,HongKong,SAR,China
RONALD A.LI (cid:1) Dr.LiDak-SumResearchCentre,UniversityofHongKong,HongKong,
SAR,China;Ming-WaiLauCentreforReparativeMedicine,KarolinskaInstitutet,
Stockholm,Sweden
MOSTAFALOTFI (cid:1) SectiononEpithelialandRetinalPhysiologyandDisease,NationalEye
Institute,NationalInstitutesofHealth,Bethesda,MD,USA
LAWRENCEG.LUM (cid:1) DivisionofHematology/Oncology,DepartmentofMedicine,University
ofVirginiaCancerCenter,Charlottesville,VA,USA
ARVYDASMAMINISHKIS (cid:1) SectiononEpithelialandRetinalPhysiologyandDisease,National
EyeInstitute,NationalInstitutesofHealth,Bethesda,MD,USA
ADRIANOMARCHESE (cid:1) DepartmentofBiochemistry,MedicalCollegeofWisconsin,Milwaukee,
WI,USA
TERESAMASSAM-WU (cid:1) WellcomeTrustCentreforCell-MatrixResearch,FacultyofLife
Biology,MedicineandHealth,UniversityofManchester,Manchester,UK
SANDEEPMITTAL (cid:1) DepartmentofNeurosurgery,KarmanosCancerInstitute,WayneState
University,Detroit,MI,USA;DepartmentofOncology,KarmanosCancerInstitute,
WayneStateUniversity,Detroit,MI,USA
HERCULESMOURA (cid:1) DivisionofLaboratorySciences,NationalCenter forEnvironmental
Health,CentersforDiseaseControlandPrevention,Chamblee,GA,USA
AMANDAM.NEVINS (cid:1) DepartmentofBiochemistry,MedicalCollegeofWisconsin,Milwaukee,
WI,USA
LINDAJ.OLSON (cid:1) DepartmentofBiochemistry,MedicalCollegeofWisconsin,Milwaukee,
WI,USA
SIMONAPRINCIPE (cid:1) PrincessMargaretCancerCentre,Toronto,ON,Canada
JONREES (cid:1) DivisionofLaboratorySciences,NationalCenter forEnvironmentalHealth,
CentersforDiseaseControlandPrevention,Chamblee,GA,USA
DANIELH.REICH (cid:1) DepartmentofPhysicsandAstronomy,JohnsHopkinsUniversity,
Baltimore,MD,USA
DANIELR.RIORDON (cid:1) LaboratoryofCardiovascularSciences,NationalInstituteonAging,
NationalInstitutesofHealth,Baltimore,MD,USA
MANUELJ.RODRI´GUEZ-ORTEGA (cid:1) DepartamentodeBioquı´micayBiologı´aMolecular,
UniversidaddeC(cid:1)ordoba,C(cid:1)ordoba,Spain