Craniofacial Development: Methods and Protocols

319 Pages·2021·17.546 MB·English

by  Sebastian Dworkin

Methods in
Molecular Biology 2403
Sebastian Dworkin Editor
Craniofacial
Development
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
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JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire, UK
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Craniofacial Development
Methods and Protocols
Edited by
Sebastian Dworkin
La Trobe University, Bundoora, VIC, Australia
Editor
SebastianDworkin
LaTrobeUniversity
Bundoora,VIC,Australia
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-0716-1846-2 ISBN978-1-0716-1847-9 (eBook)
https://doi.org/10.1007/978-1-0716-1847-9
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Preface
Mostmulticellularorganismscompriseadefined“head”region.Theformationanddevel-
opment of this craniofacial region, comprising the face, jaws, nerves, blood vessels, and
musculature (and in vertebrates also the skull and facial bones), requires an essential,
integrated network of precisely regulated developmental cues and signals. The study of
craniofacialbiologythereforenecessitatesamultitudeofcomplementaryapproachestofully
understandhow allthemolecular and cellularcomponents acttogether to ultimatelyform
the head and face. The use of animal models as disparate as nematodes (Caenorhabditis
elegans), zebrafish (Danio rerio), and mice (Mus musculus), as well as advanced imaging of
thedevelopingskullinhumanpatients,hasprovidedanincrediblewealthofknowledgeto
allow us to understand how the human face develops and, importantly, also begin to
understand what happens when things go wrong—resulting in developmental anomalies,
termedcraniofacialdefects.
This book will explore and characterize protocols in craniofacial biology that cover
topics including anterior-posterior polarity in facial establishment (C. elegans), molecular
signalsthatunderpincraniofacialprimordiaestablishmentanddevelopment(zebrafish),and
themorecomplexmechanismsofneuraltubeclosure,palataldevelopmentandfusion,and
mammaliancraniofacial skeletonformation (mouse). This bookwill also includea number
ofchapterscoveringtechniquesemployedintheclinic,includingcomputationalanalysesof
craniosynostosis, bone microarchitecture, and X-ray micro-computed tomography (micro-
CT).Furthermore,thisbookincludeschaptersoninvestigatingcellulardynamicsofcranio-
facial cells, including osteoblasts, cells of the neural crest and salivary glands, craniofacial
primordia explant cultures, methods for bone regeneration using cryogel scaffolds, and
techniquesforinvestigatingtherelationshipbetweenepithelialandmesenchymalcellpopu-
lations. Several chapters cover histological procedures and useful staining techniques in
zebrafish and mouse models, and genomic editing is presented in two chapters outlining
the identification of genomic elements that drive gene expression and gene deletion
approaches via CRISPR/Cas9 in zebrafish and mouse. Lastly, a chapter is presented on
bioinformatic methodology currently employed to integrate genetic and molecular infor-
mationthroughsingle-cellRNAsequencing(scRNA-SEQ).
Ultimately,thisbookisintendedtoserveasa“go-to”guideforstudentsinthefieldof
craniofacial development, while also acting as an essential guide to bridge the often-large
divide between basic science researchers and doctors and surgeons in clinical practice.
Ultimately,we envisionthisbookmay alsobeofuseto more senior researcherslookingto
expandtheirexistingresearchprogramstoencompassnoveltechniques.
Bundoora,VIC,Australia SebastianDworkin
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 UsingCaenorhabditiselegansasaModelforMechanisticInsights
ofCraniofacialDevelopment ............................................. 1
MichaelGrussandAnnK.Corsi
2 WholemountIn-SituHybridization(WISH)inZebrafishEmbryos
toAnalyzeCraniofacialDevelopment...................................... 19
NishanthiMathiyalaganandSebastianDworkin
3 ElucidationofGeneExpressionPatternsintheCraniofacialTissues
ofMouseEmbryosbyWholemountInSituHybridization................... 33
JoshuaB.Studdert,HeidiBildsoe,V.PragathiMasamsetti,
andPatrickP.L.Tam
4 VisualizationoftheCartilageandBoneElementsintheCraniofacial
StructuresbyAlcianBlueandAlizarinRedStaining......................... 43
JoshuaB.Studdert,HeidiBildsoe,V.PragathiMasamsetti,
andPatrickP.L.Tam
5 MethodologyforFree-FloatingOrganCultureofMid-gestation
MaxillaryPrimordialTissue .............................................. 51
M.E.deVriesandSebastianDworkin
6 MethodsofPalateCultureinLaterPalatogenesis:Elevation,
HorizontalOutgrowth,andFusion ....................................... 63
JackD.MorganandJeremyB.A.Green
7 SingleCellRNA-Seq:CellIsolationandDataAnalysis ...................... 81
ValYianniandPaulT.Sharpe
8 GeneratingZebrafishRNA-LessMutantAllelesbyDeleting
GenePromoterswithCRISPR/Cas9...................................... 91
PriyankaKumari,MorganSturgeon,GregoryBonde,
andRobertA.Cornell
9 CraniofacialPhenomics:Three-DimensionalAssessment
oftheSizeandShapeofCranialandDentofacialStructures.................. 107
MustafaMian,JennyTan,RobinYong,RuthWilliams,
AgathaLabrinidis,PeterJ.Anderson,andSarbinRanjitkar
10 Micro-CT–BasedBoneMicroarchitectureAnalysisoftheMurineSkull........ 129
JennyTan,AgathaLabrinidis,RuthWilliams,MustafaMian,
PeterJ.Anderson,andSarbinRanjitkar
vii
viii Contents
11 CharacterizationofMammalianInVivoEnhancersUsingMouse
TransgenesisandCRISPRGenomeEditing................................ 147
MarcoOsterwalder,StellaTran,RianaD.Hunter,EmanM.Meky,
KiannavonMaydell,AnneN.Harrington,JanethGodoy,
CatherineS.Novak,IngridPlajzer-Frick,YiwenZhu,
JenniferA.Akiyama,VeenaAfzal,EvgenyZ.Kvon,
LenA.Pennacchio,DianeE.Dickel,andAxelVisel
12 HistologicalTechniquesforSectioningBonesoftheVertebrateCraniofacial
Skeleton ............................................................... 187
DanielaM.Roth,LakshmiPuttagunta,andDanielGraf
13 EngineeringEpithelial–MesenchymalMicrotissuestoStudyCell–Cell
InteractionsinDevelopment............................................. 201
JacobI.Reynolds,RossA.Vitek,PeterG.Geiger,andBrianP.Johnson
14 ExVivoCultureofHumanCranialSutureCells............................ 215
PeterJ.Anderson
15 ScaffoldsforUseinCraniofacialBoneRegeneration ........................ 223
KatherineR.Hixon,ChristopherT.Eberlin,MeghanaPendyala,
AngelaAlarcondelaLastra,andScottA.Sell
16 MandibleExplantAssayfor theAnalysisofMeckel’sCartilage
Development........................................................... 235
SophieWiszniakandQuentenSchwarz
17 High-ResolutionHistologyforCraniofacialStudiesonZebrafish
andOtherTeleostModels ............................................... 249
A.Huysseune,M.Soenens,J.-Y.Sire,andP.E.Witten
18 LiveImagingoftheDynamicsofMammalianNeuralCrestCell
Migration.............................................................. 263
EmmaL.Moore andPaulA.Trainor
19 SalivaryGlandDevelopmentinCulture ................................... 277
MarciaGaete,TathyaneH.N.Teshima,LemoniaChatzeli,
andAbigailS.Tucker
20 AntenatalUltrasoundImagingforAnalysisofHumanCraniosynostosis....... 295
SarahConstantineandPiotrNiznik
Index ...................................................................... 311
Contributors
VEENA AFZAL • EnvironmentalGenomicsandSystemsBiologyDivision,LawrenceBerkeley
NationalLaboratory,Berkeley,CA,USA
JENNIFERA.AKIYAMA • EnvironmentalGenomicsandSystemsBiologyDivision,Lawrence
BerkeleyNationalLaboratory,Berkeley,CA,USA
ANGELAALARCON DELALASTRA • DepartmentofImmunology,WashingtonUniversity,St.
Louis,MO,USA
PETERJ.ANDERSON • AdelaideDentalSchool,TheUniversityofAdelaide,Adelaide,SA,
Australia;AustralianCraniofacialUnit,Women’sandChildren’sHospital,North
Adelaide,SA,Australia;SouthAustralianHealthandMedicalResearchInstitute
(SAHMRI),Adelaide,SA,Australia
HEIDIBILDSOE • CentreforReproductiveHealth,HudsonInstituteofMedicalResearch,
Clayton,VIC,Australia
GREGORYBONDE • DepartmentofAnatomyandCellBiology,UniversityofIowa,IowaCity,
IA,USA
LEMONIACHATZELI • WellcomeTrust/CancerResearchUKGurdonInstitute,Universityof
Cambridge,Cambridge,UK
SARAH CONSTANTINE • DepartmentofMedicalImaging,Women’sandChildren’sHospital,
NorthAdelaide,SA,Australia
ROBERTA.CORNELL • DepartmentofAnatomyandCellBiology,UniversityofIowa,Iowa
City,IA,USA
ANNK.CORSI • DepartmentofBiology,TheCatholicUniversityofAmerica,Washington,
DC,USA
M.E.DEVRIES • DepartmentofMedicine,MonashUniversityCentralClinicalSchool,
Prahran,VIC,Australia;DepartmentofPhysiology,AnatomyandMicrobiology,LaTrobe
University,Melbourne,VIC,Australia
DIANEE.DICKEL • EnvironmentalGenomicsandSystemsBiologyDivision,Lawrence
BerkeleyNationalLaboratory,Berkeley,CA,USA
SEBASTIANDWORKIN • DepartmentofPhysiology,AnatomyandMicrobiology,LaTrobe
University,Bundoora,VIC,Australia
CHRISTOPHERT.EBERLIN • UniversityofIllinoisCollegeofMedicine,Peoria,IL,USA
MARCIAGAETE • DepartmentofAnatomy,FacultyofMedicine,PontificiaUniversidad
Cat(cid:1)olicadeChile,Santiago,Chile
PETERG.GEIGER • DepartmentofBiomedicalEngineering,UniversityofWisconsin,
Madison,WI,USA
JANETHGODOY • EnvironmentalGenomicsandSystemsBiologyDivision,LawrenceBerkeley
NationalLaboratory,Berkeley,CA,USA
DANIELGRAF • SchoolofDentistry,UniversityofAlberta,Edmonton,AB,Canada;
DepartmentofMedicalGenetics,UniversityofAlberta,Edmonton,AB,Canada
JEREMYB.A.GREEN • CentreforCraniofacialandRegenerativeBiology,King’sCollege
London,London,UK
MICHAELGRUSS • DepartmentofBiology,TheCatholicUniversityofAmerica,Washington,
DC,USA
ix
x Contributors
ANNE N.HARRINGTON • EnvironmentalGenomicsandSystemsBiologyDivision,Lawrence
BerkeleyNationalLaboratory,Berkeley,CA,USA
KATHERINER.HIXON • DepartmentofOrthopaedicSurgery,WashingtonUniversity,St.
Louis,MO,USA;ThayerSchoolofEngineering,DartmouthCollege,Hanover,NH,USA
RIANA D.HUNTER • EnvironmentalGenomicsandSystemsBiologyDivision,Lawrence
BerkeleyNationalLaboratory,Berkeley,CA,USA
A.HUYSSEUNE • BiologyDepartment,ResearchGroupEvolutionaryDevelopmentalBiology,
GhentUniversity,Ghent,Belgium
BRIAN P.JOHNSON • DepartmentofBiomedicalEngineering,InstituteforQuantitative
HealthScienceandEngineering,MichiganStateUniversity,EastLansing,MI,USA;
DepartmentofPharmacology&Toxicology,MichiganStateUniversity,EastLansing,
MI,USA
PRIYANKAKUMARI • DepartmentofAnatomyandCellBiology,UniversityofIowa,IowaCity,
IA,USA
EVGENYZ.KVON • EnvironmentalGenomicsandSystemsBiologyDivision,Lawrence
BerkeleyNationalLaboratory,Berkeley,CA,USA;DepartmentofDevelopmentalandCell
Biology,UniversityofCalifornia,Irvine,Irvine,CA,USA
AGATHA LABRINIDIS • AdelaideMicroscopy,TheUniversityofAdelaide,Adelaide,SA,
Australia
V.PRAGATHIMASAMSETTI • EmbryologyUnit,Children’sMedicalResearchInstitute,
Westmead,NSW,Australia
NISHANTHIMATHIYALAGAN • DepartmentofPhysiology,AnatomyandMicrobiology,LaTrobe
University,Bundoora,VIC,Australia
EMANM.MEKY • EnvironmentalGenomicsandSystemsBiologyDivision,LawrenceBerkeley
NationalLaboratory,Berkeley,CA,USA
MUSTAFAMIAN • AdelaideDentalSchool,TheUniversityofAdelaide,Adelaide,
SA,Australia
EMMA L.MOORE • StowersInstituteforMedicalResearch,KansasCity,MO,USA
JACKD.MORGAN • CentreforCraniofacialandRegenerativeBiology,King’sCollege
London,London,UK
PIOTRNIZNIK • DepartmentofMedicalImaging,Women’sandChildren’sHospital,North
Adelaide,SA,Australia
CATHERINES.NOVAK • EnvironmentalGenomicsandSystemsBiologyDivision,Lawrence
BerkeleyNationalLaboratory,Berkeley,CA,USA
MARCOOSTERWALDER • EnvironmentalGenomicsandSystemsBiologyDivision,Lawrence
BerkeleyNationalLaboratory,Berkeley,CA,USA;DepartmentforBioMedicalResearch
(DBMR),UniversityofBern,Bern,Switzerland
MEGHANA PENDYALA • DepartmentofBiomedicalEngineering,RensselaerPolytechnic
Institute,Troy,NY,USA
LENA.PENNACCHIO • EnvironmentalGenomicsandSystemsBiologyDivision,Lawrence
BerkeleyNationalLaboratory,Berkeley,CA,USA;USDepartmentofEnergyJointGenome
Institute,LawrenceBerkeleyNationalLaboratory,Berkeley,CA,USA;Comparative
BiochemistryProgram,UniversityofCalifornia,Berkeley,CA,USA
INGRID PLAJZER-FRICK • EnvironmentalGenomicsandSystemsBiologyDivision,Lawrence
BerkeleyNationalLaboratory,Berkeley,CA,USA