Kidney Organogenesis: Methods and Protocols

242 Pages·2019·7.381 MB·English

by  Seppo Vainio

Methods in
Molecular Biology 1926
Seppo Vainio Editor
Kidney
Organogenesis
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
Kidney Organogenesis
Methods and Protocols
Edited by
Seppo Vainio
Biocenter Oulu, Laboratory of Developmental Biology, Oulu University, Oulu, Finland;
InfoTech Oulu, Oulu University, Oulu, Finland;
Borealis Biobank of Northern Finland, Oulu University, Oulu, Finland;
Faculty of Biochemistry and Molecular Medicine, Oulu University, Oulu, Finland
Editor
SeppoVainio
BiocenterOulu,LaboratoryofDevelopmentalBiology
OuluUniversity
Oulu,Finland
InfoTechOulu
OuluUniversity
Oulu,Finland
BorealisBiobankofNorthernFinland
OuluUniversity
Oulu,Finland
FacultyofBiochemistryandMolecularMedicine
OuluUniversity
Oulu,Finland
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-9020-7 ISBN978-1-4939-9021-4 (eBook)
https://doi.org/10.1007/978-1-4939-9021-4
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CoverCaption:Opticalprojectiontomography-basedvisualizationofthenephrons(inred)andthecollectingducttree
(ingrey).AutomatedspotdetectionfunctionoftheImarisprogramwasappliedtohighlightthenephrons(inyellow).
E16.5.mousekidney.
This Humana Press imprint is published by the registered company Springer Science+Business Media, LLC, part of
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Preface
The mammalian kidney has served as a model to study the fundamental developmental
mechanismsfromthelate1950swhenCliffordGrobsteinestablishedthecapacitytoculture
the microdissected kidney rudiments. By using such microsurgery approaches and organ
culture technologies, Lauri Saxe´n’s team showed later that like in the primary embryonic
induction,the processof organogenesisinvolves signals that mediatethe secondaryinduc-
tive tissue interactions. In the context of the kidney, signaling occurs between the ureteric
budandthemetanephricmesenchyme.Thesecoordinatethestepwisekidneymorphogene-
sisandtheassociatedcelldifferentiation.
Even though the powers to use the kidney as a developmental model system were
establishedmorethan60yearsago,theclassicexvivokidneycultureapproachwastechno-
logically still very limited. Especially no ways existed to assay the roles of the molecular
players involved. Pioneers such as Peter Ekblom used initially specific antibodies and small
molecule inhibitorsto target the molecular mediators,but the actual gene functionscould
notbeapproached.
When the embryonic stem cell culture and the gene targeting technologies became a
routine, this opened the era of the renal functional genetics. By using the gene knockout
approach,manygeneswereidentifiedtobeessentialforkidneyontogenesis.Evidencecould
befinallyreachednowthatthesignalsthatmediatethekidneytubuleinductionareencoded
bytheWntgenefamily.TheWntsserveasthekeymediatorsintheclassictubuleinduction
modelsystemandinvivosignalingfromtheuretericbudtothemetanephricmesenchymeto
trigger nephrogenesis.Therenaltissue-specificgeneknockoutcapacitywasastepforward,
and to date genefunctions can be inactivated fromthe major kidney tissue compartments.
At this stage, the ex vivo kidney organ culture models provided again a valuable tool to
depicttheepistasisrelationshipsofthegenesinorganogenesis.
During the recent years, the kidney tissue engineering methods to study the mechan-
isms in tissue biogenesis have undergone a major revolution. The mammalian kidney
rudiment can be introduced to single cells. However, kidney developmental capacity can
bereconstitutedthereafter.Thekidneyprogenitorcellscanalsobefrozen,andthecellfates
canbestudiedatthesingle-celllevelaswell.
The 4D imaging technologies together with the availability of wealth of the gene-
engineered renal indicator developmental and disease models have opened a series of
experimentalstudies.Themoleculargenetictechnologieshavedevelopedtoasophistication
that theinvolvedgeneticprogramscan bestudiedalsoat thesingle-celllevel.Importantly,
functionsofspecificgenesandcandidaterenaldevelopmentalfactorscanbeapproachedin
theexvivosettingsaswell.
Majoradvancementshavetakenplacealsointherenalstemcelltechnologies.Protocols
have become available to program the pluripotent cells to the defined cell lineages such as
the ones of the kidney. Such protocols are in our toolbox for the mouse and human. The
skills to take a good use of the patient-derived cells with a kidney disease are a historical
opening in human kidney-related medical research. Such patient-derived cells can also be
storedinthebiobankstogainmorevalue.Importantlykidneyorganoidscanbegenerated
from such engineered cells, and the CRISPR gene editing can be achieved in these cells as
v
vi Preface
well. These approaches can now be combined to establish large-scale gene editing micro-
fluidicsandrobotic-automatedplatforms.
The current Springer book contains a series of protocols that allow their user to get
access both to the classic and the very modern ex vivo mammalian developmental kidney
model systems. The book contains chapters that illustrate the elegant 3D and 4D imaging
modalities, the powers of the kidney decellularizing, and how to build the kidney tissues
fromthereprogrammedcells.
Thepioneersof thefield arelikelythrilledofthe capacitiesthat thekidneycommunity
hastodayintheiruse.Attheirtimetheycouldonlydreamofthem.Viathecombinationof
the classic and the modern renal technologies, we will be now able to generate more
efficientlyvaluefor thepatientsthatlookfor newtherapiesfor theirkidneysymptoms.
Oulu,Finland SeppoVainio
Contents
Preface ..................................................................... v
Contributors................................................................. ix
PART I GENERATION OF MOSAIC EMBRYONIC KIDNEYS
AND CULTURE OF THE KIDNEY TISSUES EX VIVO
1 GeneratingGeneticMosaicMouseEmbryosorOrganoids
forStudiesofKidneyDevelopment ....................................... 3
FrankCostantini
2 MouseExVivoKidneyCultureMethods .................................. 23
AnneliisIhermann-HellaandSatuKuure
3 Serum-FreeOrganCultureoftheEmbryonicMouseUreter................. 31
FilipaM.LopesandAdrianS.Woolf
4 ExperimentalTubulogenesisInductionModelintheMouse ................. 39
AleksandraRak-Raszewska
PART II EMBRYONIC KIDNEY PROGENITOR CELL AND 3D KIDNEY
MODEL CELL LIKE BASED CULTURES
5 DissociationofTissuesforSingle-CellAnalysis ............................. 55
AndrewS.PotterandS.StevenPotter
6 Long-TermCultureofNephronProgenitorCellsExVivo................... 63
AaronC.Brown,AshwaniK.Gupta,andLeifOxburgh
7 3DCellCultureModelsofEpithelialTissues............................... 77
KaiZhangandAkiManninen
PART III PROGRAMMING THE KIDNEY CELL FATES
IN HUMAN PLURIPOTENT CELLS
8 GenerationofThree-DimensionalNephronsfromMouse
andHumanPluripotentStemCells ....................................... 87
YasuhiroYoshimura,AtsuhiroTaguchi,andRyuichiNishinakamura
9 GeneratingMultipleKidneyProgenitorsandCellTypes
fromHumanPluripotentStemCells ...................................... 103
KrithikaHariharan,PetraReinke,andAndreasKurtz
10 ProtocoltoGenerateUretericBudStructuresfromHumaniPSCells......... 117
Shin-IchiMae,MakotoRyosaka,andKenjiOsafune
vii
viii Contents
PART IV PROTOCOLS TO TARGET THE FUNCTIONAL PLAYERS
IN KIDNEY ONTOGENESIS
11 InvestigatingAspectsofRenalPhysiologyandPharmacology
inOrganandOrganoidCulture.......................................... 127
MelanieL.Lawrence,MonaElhendawi,andJamieA.Davies
12 VirusasRenalFunctionalGeneticTools................................... 143
AbhishekSharmaandSandhanakrishnanCattavarayane
13 GeneEditingin3DCulturedNephronProgenitorCellLines................ 151
ZhongweiLi,ToshikazuAraoka,andJuanCarlosIzpisuaBelmonte
PART V 4D AND 3D EX VIVO IMAGING
OF EMBRYONIC KIDNEY DECELLULARIZATION
14 Time-LapseTechnologiesand4DImagingofKidneyDevelopment .......... 163
UllaSaarelaandIlyaSkovorodkin
15 DecellularizingandRecellularizingAdultMouseKidneys.................... 169
TheresaChow,JenniferWhiteley,andIanM.Rogers
16 OpticalProjectionTomographyImagingtoStudyKidneyOrganogenesis ..... 185
RenataPrunskaite-Hyyryla€inen
PART VI DROSOPHILA AS A MODEL TO TARGET CONSERVED
RENAL ONTOGENESIS GENES SUCH AS THE TEASHIRT
17 EpithelialFunctionintheDrosophilaMalpighianTubule:
AnInVivoRenalModel................................................. 203
Shireen-A.Davies,PabloCabrero,RichardMarley,
GuillermoMartinezCorrales,SauravGhimire,AnthonyJ.Dornan,
andJulianA.T.Dow
18 AnalysisoftheTeashirtTargetGenesinUretericBudDevelopment .......... 223
LaurentFasano,IreneSanchez-Martin,andXavierCaubit
PART VII COMPUTATIONAL APPROACHES TO KIDNEY ONTOGENESIS
19 MethodsofComputationalAnalysisinKidneyDevelopment................. 235
PauliTikkaandFranzSchaefer
Index ...................................................................... 247
Contributors
TOSHIKAZUARAOKA (cid:1) Center foriPSCellResearchandApplication(CiRA),Kyoto
University,Kyoto,Japan
JUANCARLOSIZPISUABELMONTE (cid:1) GeneExpressionLaboratory,TheSalkInstitutefor
BiologicalStudies,LaJolla,CA,USA
AARONC.BROWN (cid:1) Center forMolecularMedicine,MaineMedicalCenterResearch
Institute,Scarborough,ME,USA
PABLO CABRERO (cid:1) InstituteofMolecular,CellandSystemsBiology,CollegeofMedical,
VeterinaryandLifeSciences,UniversityofGlasgow,Glasgow,Scotland,UK
SANDHANAKRISHNANCATTAVARAYANE (cid:1) FacultyofVeterinaryMedicine,SectionofPathology,
DepartmentofVeterinaryBiosciences,UniversityofHelsinki,Helsinki,Finland
XAVIERCAUBIT (cid:1) AixMarseilleUniversity,CNRS,IBDM,Marseille,France
THERESACHOW (cid:1) Lunenfeld-TanenbaumResearchInstitute,Mt.SinaiHospital,Toronto,
ON,Canada;DepartmentofPhysiology,UniversityofToronto,Toronto,ON,Canada
GUILLERMOMARTINEZCORRALES (cid:1) InstituteofMolecular,CellandSystemsBiology,Collegeof
Medical,VeterinaryandLifeSciences,UniversityofGlasgow,Glasgow,Scotland,UK
FRANKCOSTANTINI (cid:1) DepartmentofGeneticsandDevelopment,1418HammerHealth
SciencesCenter,ColumbiaUniversity,NewYork,NY,USA
JAMIEA.DAVIES (cid:1) DeaneryofBiomedicalSciences,UniversityofEdinburgh,Edinburgh,UK
SHIREEN-A.DAVIES (cid:1) InstituteofMolecular,CellandSystemsBiology,CollegeofMedical,
VeterinaryandLifeSciences,UniversityofGlasgow,Glasgow,Scotland,UK
ANTHONYJ.DORNAN (cid:1) InstituteofMolecular,CellandSystemsBiology,CollegeofMedical,
VeterinaryandLifeSciences,UniversityofGlasgow,Glasgow,Scotland,UK
JULIAN A.T.DOW (cid:1) InstituteofMolecular,CellandSystemsBiology,CollegeofMedical,
VeterinaryandLifeSciences,UniversityofGlasgow,Glasgow,Scotland,UK
MONAELHENDAWI (cid:1) DeaneryofBiomedicalSciences,UniversityofEdinburgh,Edinburgh,
UK;FacultyofMedicine,ClinicalPathologyDepartment,MansouraUniversity,El-
Mansoura,Egypt
LAURENTFASANO (cid:1) AixMarseilleUniversity,CNRS,IBDM,Marseille,France
SAURAVGHIMIRE (cid:1) InstituteofMolecular,CellandSystemsBiology,CollegeofMedical,
VeterinaryandLifeSciences,UniversityofGlasgow,Glasgow,Scotland,UK
ASHWANIK.GUPTA (cid:1) Center forMolecularMedicine,MaineMedicalCenterResearch
Institute,Scarborough,ME,USA
KRITHIKAHARIHARAN (cid:1) Berlin–BrandenburgCenter forRegenerativeTherapies(BCRT),
Charite´-Universita€tsmedizinBerlin,Berlin,Germany
ANNELIISIHERMANN-HELLA (cid:1) GM-unitatHelsinkiInstituteofLifeScienceandMedicum,
UniversityofHelsinki,Helsinki,Finland
ANDREASKURTZ (cid:1) Berlin–BrandenburgCenterforRegenerativeTherapies(BCRT),Charite´
-Universita€tsmedizinBerlin,Berlin,Germany
SATUKUURE (cid:1) GM-unitatHelsinkiInstituteofLifeScienceandMedicum,
InstituteofBiotechnology,UniversityofHelsinki,Helsinki,Finland
MELANIEL.LAWRENCE (cid:1) DeaneryofBiomedicalSciences,UniversityofEdinburgh,
Edinburgh,UK
ix
x Contributors
ZHONGWEI LI (cid:1) DivisionofNephrologyandHypertension,DepartmentofMedicineand
USC/UKROKidneyResearchCenter,KeckSchoolofMedicineoftheUniversityof
SouthernCalifornia,LosAngeles,CA,USA;DepartmentofStemCellBiologyand
RegenerativeMedicine,KeckSchoolofMedicineoftheUniversityofSouthernCalifornia,
LosAngeles,CA,USA
FILIPAM.LOPES (cid:1) FacultyofBiologyMedicineandHealth,DivisionofCellMatrixBiology
andRegenerativeMedicine,SchoolofBiologicalSciences,UniversityofManchester,
Manchester,UK
SHIN-ICHIMAE (cid:1) Center foriPSCellResearchandApplication(CiRA),KyotoUniversity,
Kyoto,Japan
AKIMANNINEN (cid:1) FacultyofBiochemistryandMolecularMedicine,BiocenterOulu,Oulu
Center forCell-MatrixResearch,UniversityofOulu,Oulu,Finland
RICHARDMARLEY (cid:1) InstituteofMolecular,CellandSystemsBiology,CollegeofMedical,
VeterinaryandLifeSciences,UniversityofGlasgow,Glasgow,Scotland,UK
RYUICHINISHINAKAMURA (cid:1) DepartmentofKidneyDevelopment,InstituteofMolecular
EmbryologyandGenetics,KumamotoUniversity,Kumamoto,Japan
KENJIOSAFUNE (cid:1) Center foriPSCellResearchandApplication(CiRA),KyotoUniversity,
Kyoto,Japan
LEIF OXBURGH (cid:1) Center forMolecularMedicine,MaineMedicalCenterResearchInstitute,
Scarborough,ME,USA
ANDREWS.POTTER (cid:1) DivisionofDevelopmentalBiology,CincinnatiChildren’sMedical
Center,Cincinnati,OH,USA
S.STEVENPOTTER (cid:1) DivisionofDevelopmentalBiology,CincinnatiChildren’sMedical
Center,Cincinnati,OH,USA
RENATAPRUNSKAITE-HYYRYLA€INEN (cid:1) FacultyofBiochemistryandMolecularMedicine,
UniversityofOulu,Oulu,Finland
ALEKSANDRARAK-RASZEWSKA (cid:1) FacultyofBiochemistryandMolecularMedicine,University
ofOulu,Oulu,Finland
PETRA REINKE (cid:1) Berlin–BrandenburgCenter forRegenerativeTherapies(BCRT),Charite´-
Universita€tsmedizinBerlin,Berlin,Germany;DepartmentofNephrologyandIntensive
Care,Charite´-UniversityMedicineBerlin,Berlin,Germany
IANM.ROGERS (cid:1) Lunenfeld-TanenbaumResearchInstitute,Mt.SinaiHospital,Toronto,
ON,Canada;DepartmentofPhysiology,UniversityofToronto,Toronto,ON,Canada;
DepartmentofObstetricsandGynecology,UniversityofToronto,Toronto,ON,Canada
MAKOTORYOSAKA (cid:1) CenterforiPSCellResearchandApplication(CiRA),KyotoUniversity,
Kyoto,Japan
ULLASAARELA (cid:1) FacultyofBiochemistryandMolecularMedicine,UniversityofOulu,Oulu,
Finland;LaboratoryofDevelopmentalBiology,BiocenterOulu,InfoTech,Oulu,Finland;
OuluCenter forCellMatrixResearch,Oulu,Finland
IRENE SANCHEZ-MARTIN (cid:1) AixMarseilleUniversity,CNRS,IBDM,Marseille,France
FRANZSCHAEFER (cid:1) DepartmentofMedicine,UniversityofHeidelberg,Heidelberg,Germany
ABHISHEKSHARMA (cid:1) FacultyofBiochemistryandMolecularMedicine,BiocenterOulu,
UniversityofOulu,Oulu,Finland
ILYASKOVORODKIN (cid:1) FacultyofBiochemistryandMolecularMedicine,UniversityofOulu,
Oulu,Finland;LaboratoryofDevelopmentalBiology,BiocenterOulu,InfoTech,Oulu,
Finland;OuluCenter forCellMatrixResearch,Oulu,Finland
ATSUHIRO TAGUCHI (cid:1) DepartmentofGenomeRegulation,MaxPlanckInstitutefor
MolecularGenetics,Berlin,Germany