2021
Microinjection of Xenopus tropicalis Embryos.
Lane M, Mis EK, Khokha MK. Microinjection of Xenopus tropicalis Embryos. Cold Spring Harbor Protocols 2021, 2022: pdb.prot107644. PMID: 34244348, DOI: 10.1101/pdb.prot107644.Peer-Reviewed Original ResearchConceptsEmbryo sizeLarger embryo sizeTargeted gene manipulationEmbryo development timeSmall embryo sizeXenopus tropicalis embryosDevelopmental biologyEarly embryosMicroinjection protocolGene manipulationGenetic studiesFirst divisionXenopusEmbryosImportant modelDevelopment timeMicroinjectionMorpholinoCRISPRBiologySpeciesDNAMRNAOocytesFertilizationXenopus Tadpole Craniocardiac Imaging Using Optical Coherence Tomography.
Deniz E, Mis EK, Lane M, Khokha MK. Xenopus Tadpole Craniocardiac Imaging Using Optical Coherence Tomography. Cold Spring Harbor Protocols 2021, 2022: pdb.prot105676. PMID: 34031211, DOI: 10.1101/pdb.prot105676.Peer-Reviewed Original ResearchObtaining Xenopus tropicalis Eggs.
Lane M, Mis EK, Khokha MK. Obtaining Xenopus tropicalis Eggs. Cold Spring Harbor Protocols 2021, 2022: pdb.prot106344. PMID: 34031209, DOI: 10.1101/pdb.prot106344.Peer-Reviewed Original ResearchConceptsDevelopmental biologyGene manipulation toolsPowerful model systemCell biological studiesCell-free systemTetraploid genomeDiploid genomeThousands of eggsEgg extractsGenetic studiesXenopusGenomePremier systemModel systemEggsBiological studiesBiologyEmbryosFrogsManipulation toolsTiming of stepsSpeciesHormoneFemalesCellsExpansion of NEUROD2 phenotypes to include developmental delay without seizures
Mis EK, Sega AG, Signer RH, Cartwright T, Ji W, Martinez‐Agosto J, Nelson SF, Palmer CGS, Lee H, Mitzelfelt T, Konstantino M, Network U, Jeffries L, Khokha MK, Marco E, Martin MG, Lakhani SA. Expansion of NEUROD2 phenotypes to include developmental delay without seizures. American Journal Of Medical Genetics Part A 2021, 185: 1076-1080. PMID: 33438828, PMCID: PMC8212414, DOI: 10.1002/ajmg.a.62064.Peer-Reviewed Original ResearchConceptsDevelopmental delayEarly-onset seizuresDe novo heterozygous variantsNovo heterozygous variantsDifferentiation factor 2Xenopus laevis tadpolesHeterozygous variantsSeizuresNeuronal differentiationParental studiesFunctional testingMissense variantsPatient variantsFunctional evidenceFactor 2Vivo assaysLaevis tadpolesVariant pathogenicityFunction effectsAdolescentsVariants
2020
DLG5 variants are associated with multiple congenital anomalies including ciliopathy phenotypes
Marquez J, Mann N, Arana K, Deniz E, Ji W, Konstantino M, Mis EK, Deshpande C, Jeffries L, McGlynn J, Hugo H, Widmeier E, Konrad M, Tasic V, Morotti R, Baptista J, Ellard S, Lakhani SA, Hildebrandt F, Khokha MK. DLG5 variants are associated with multiple congenital anomalies including ciliopathy phenotypes. Journal Of Medical Genetics 2020, 58: 453-464. PMID: 32631816, PMCID: PMC7785698, DOI: 10.1136/jmedgenet-2019-106805.Peer-Reviewed Original ResearchConceptsLoss of ciliaPatient tissuesPatient variantsCongenital heart diseaseMultiple organ systemsMultiple congenital anomaliesDLG5 variantsVariety of pathologiesNephrotic syndromeHeart diseaseCongenital anomaliesRespiratory tractKidney tissueOrgan systemsCystic kidneysPatient phenotypesKidneyDiseaseLimb abnormalitiesUnrelated familiesRescue experimentsCraniofacial malformationsCilia dysfunctionTissue-specific manifestationsTissueNovel truncating mutations in CTNND1 cause a dominant craniofacial and cardiac syndrome
Alharatani R, Ververi A, Beleza-Meireles A, Ji W, Mis E, Patterson QT, Griffin JN, Bhujel N, Chang CA, Dixit A, Konstantino M, Healy C, Hannan S, Neo N, Cash A, Li D, Bhoj E, Zackai EH, Cleaver R, Baralle D, McEntagart M, Newbury-Ecob R, Scott R, Hurst JA, Au PYB, Hosey MT, Khokha M, Marciano DK, Lakhani SA, Liu KJ. Novel truncating mutations in CTNND1 cause a dominant craniofacial and cardiac syndrome. Human Molecular Genetics 2020, 29: 1900-1921. PMID: 32196547, PMCID: PMC7372553, DOI: 10.1093/hmg/ddaa050.Peer-Reviewed Original ResearchConceptsCell-cell junctionsNovel protein-truncating variantsP120-catenin proteinProtein-truncating variantsNext-generation sequencingTranscriptional signalingP120-cateninCRISPR/Epithelial-mesenchymal transitionSubset of phenotypesDevelopmental roleLimb dysmorphologiesAdditional phenotypesHuman diseasesCTNND1Conditional deletionDe novoTruncating mutationsBlepharocheilodontic syndromeEpithelial integrityNovel truncating mutationCraniofacial dysmorphismPhenotypeCleft palateNeurodevelopmental disordersDisrupted ER membrane protein complex-mediated topogenesis drives congenital neural crest defects
Marquez J, Criscione J, Charney RM, Prasad MS, Hwang WY, Mis EK, García-Castro MI, Khokha MK. Disrupted ER membrane protein complex-mediated topogenesis drives congenital neural crest defects. Journal Of Clinical Investigation 2020, 130: 813-826. PMID: 31904590, PMCID: PMC6994125, DOI: 10.1172/jci129308.Peer-Reviewed Original ResearchConceptsEndoplasmic reticulum (ER) membrane protein complexMultipass membrane proteinsNeural crest cellsMembrane proteinsHuman NCC developmentER membrane proteinsMembrane protein complexesCell-cell signalsMyriad of functionsNCC defectsNCC developmentProtein complexesUnbiased proteomicsXenopus modelTransmembrane proteinFunction allelesPatient phenotypesCrest cellsMolecular connectionNeural crestMolecular mechanismsBirth defectsPatient variantsEMC1Β-catenin
2018
RPSA, a candidate gene for isolated congenital asplenia, is required for pre-rRNA processing and spleen formation in Xenopus
Griffin JN, Sondalle SB, Robson A, Mis EK, Griffin G, Kulkarni SS, Deniz E, Baserga SJ, Khokha MK. RPSA, a candidate gene for isolated congenital asplenia, is required for pre-rRNA processing and spleen formation in Xenopus. Development 2018, 145: dev166181. PMID: 30337486, PMCID: PMC6215398, DOI: 10.1242/dev.166181.Peer-Reviewed Original ResearchConceptsPre-rRNA processingSmall ribosomal subunitCommon disease-associated mutationDisease-associated mutationsRpsA mRNARibosome biogenesisRibosome productionRibosome functionRibosomal subunitCandidate genesHuman mRNAsProtein componentsImpairs expressionSpleen developmentMolecular patterningRPSASpleen anlageMutationsXenopusGenesFirst animal modelUniversal requirementMRNADe novo pathogenic variants in neuronal differentiation factor 2 (NEUROD2) cause a form of early infantile epileptic encephalopathy
Sega AG, Mis EK, Lindstrom K, Mercimek-Andrews S, Ji W, Cho MT, Juusola J, Konstantino M, Jeffries L, Khokha MK, Lakhani SA. De novo pathogenic variants in neuronal differentiation factor 2 (NEUROD2) cause a form of early infantile epileptic encephalopathy. Journal Of Medical Genetics 2018, 56: 113. PMID: 30323019, DOI: 10.1136/jmedgenet-2018-105322.Peer-Reviewed Original ResearchConceptsEarly infantile epileptic encephalopathyInfantile epileptic encephalopathyEpileptic encephalopathyPatient variantsDe novo pathogenic variantsNovel de novo variantNovo pathogenic variantsEarly-onset refractory seizuresDifferentiation factor 2Whole-exome sequencingNeuronal differentiation factorRefractory seizuresSignificant developmental delaySpontaneous seizuresUnderlying etiologyEctopic neuronsDe novo variantsPatient's conditionEncephalopathyPathogenic variantsSevere disordersDevelopmental delayUnrelated childrenExome sequencingGene mutationsCRISPR/Cas9 F0 Screening of Congenital Heart Disease Genes in Xenopus tropicalis
Deniz E, Mis EK, Lane M, Khokha MK. CRISPR/Cas9 F0 Screening of Congenital Heart Disease Genes in Xenopus tropicalis. Methods In Molecular Biology 2018, 1865: 163-174. PMID: 30151766, DOI: 10.1007/978-1-4939-8784-9_12.Peer-Reviewed Original ResearchConceptsCardiac developmentCRISPR/Candidate genesHigh-density SNP arrayCRISPR/Cas9 systemGenome editing technologyCongenital heart disease genesNew genomic technologiesHeart disease genesCopy number variationsRapid functional assayXenopus tropicalisCas9 systemGenetic basisDevelopmental systemsEditing technologyGenomic technologiesSequence variationDisease genesDifferent genesGenetic analysisSNP arrayDevelopmental mechanismsMolecular mechanismsWhole-exome sequencing
2017
CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing
Moreno-Mateos MA, Fernandez JP, Rouet R, Vejnar CE, Lane MA, Mis E, Khokha MK, Doudna JA, Giraldez AJ. CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing. Nature Communications 2017, 8: 2024. PMID: 29222508, PMCID: PMC5722943, DOI: 10.1038/s41467-017-01836-2.Peer-Reviewed Original ResearchConceptsHomology-directed repairCpf1 activityGenome editingDifferent eukaryotic systemsGenome engineering toolsEfficient homology-directed repairPost-translational modulationEctothermic organismsEctothermic speciesEukaryotic systemsDNA endonucleaseCRISPR-Cpf1Efficient mutagenesisGenomic DNADNA integrationMolecular understandingTemporal controlZebrafishAsCpf1Cpf1LbCpf1EditingNovel classGenomeMutagenesisVisualization and quantification of injury to the ciliated epithelium using quantitative flow imaging and speckle variance optical coherence tomography
Gamm UA, Huang BK, Mis EK, Khokha MK, Choma MA. Visualization and quantification of injury to the ciliated epithelium using quantitative flow imaging and speckle variance optical coherence tomography. Scientific Reports 2017, 7: 15115. PMID: 29118359, PMCID: PMC5678121, DOI: 10.1038/s41598-017-14670-9.Peer-Reviewed Original ResearchConceptsOptical coherence tomographyCiliated epitheliumCoherence tomographyType of injuryExtent of injuryQuantification of injuryVariance optical coherence tomographyRespiratory infectionsDiffuse injuryFocal injuryImportant defense mechanismMouse tracheaInjuryMucociliary flowEpitheliumRegeneration of ciliaTomographyMultiple factorsDefense mechanismsQuantitative flowLungInfectionTracheaDisease
2015
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo
Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nature Methods 2015, 12: 982-988. PMID: 26322839, PMCID: PMC4589495, DOI: 10.1038/nmeth.3543.Peer-Reviewed Original Research
2014
Uncovering Buffered Pleiotropy: A Genome-Scale Screen for mel-28 Genetic Interactors in Caenorhabditis elegans
Fernandez A, Mis E, Lai A, Mauro M, Quental A, Bock C, Piano F. Uncovering Buffered Pleiotropy: A Genome-Scale Screen for mel-28 Genetic Interactors in Caenorhabditis elegans. G3: Genes, Genomes, Genetics 2014, 4: 185-196. PMID: 24281427, PMCID: PMC3887534, DOI: 10.1534/g3.113.008532.Peer-Reviewed Original ResearchConceptsMEL-28Caenorhabditis elegansLethal genesGenetic interaction screensGenome-scale screeningWild-type wormsNuclear envelope functionsCell-matrix attachmentWild-type larvaeDynactin functionGenetic interactorsGenome-scaleVesicle transportConserved proteinsChromosome segregationGene networksIdentified genesCellular processesPostembryonic rolesInteraction screenNuclear poresPleiotropic functionsGenesEarly embryosLarval development
2013
Forward genetics defines Xylt1 as a key, conserved regulator of early chondrocyte maturation and skeletal length
Mis EK, Liem KF, Kong Y, Schwartz NB, Domowicz M, Weatherbee SD. Forward genetics defines Xylt1 as a key, conserved regulator of early chondrocyte maturation and skeletal length. Developmental Biology 2013, 385: 67-82. PMID: 24161523, PMCID: PMC3895954, DOI: 10.1016/j.ydbio.2013.10.014.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBone and BonesCell DifferentiationCell ProliferationChondrocytesDwarfismFibroblast Growth FactorsHedgehog ProteinsMiceMice, Inbred C57BLMice, TransgenicMutation, MissenseOsteogenesisParathyroid Hormone-Related ProteinPentosyltransferasesSequence Analysis, DNASignal TransductionConceptsChondrocyte maturationCartilage templateN-ethyl-N-nitrosourea (ENU) mutagenesis screenSkeletal precursor cellsWild-type embryosHigh-throughput sequencingHuman birth defectsProteoglycan core proteinMutagenesis screenSequence captureVertebrate bodySubcellular localizationProteoglycan functionCoordinated processMouse mutantsMutantsAbnormal bone developmentMissense mutationsCore proteinBone developmentSkeletal elementsPrecursor cellsDwarfismMaturationGAG chains
2012
High-throughput fluorescence-based isolation of live C. elegans larvae
Fernandez A, Bargmann B, Mis E, Edgley M, Birnbaum K, Piano F. High-throughput fluorescence-based isolation of live C. elegans larvae. Nature Protocols 2012, 7: 1502-1510. PMID: 22814389, PMCID: PMC5274720, DOI: 10.1038/nprot.2012.084.Peer-Reviewed Original ResearchConceptsGenetic interactionsChemical genetic screenNematode Caenorhabditis elegansFluorescence-activated cell sortingSelection of animalsTermination mutantsCaenorhabditis elegansSorting animalsGenetic screeningChemical screeningGFP expressionCell sortingLarval stageLive animalsHigh-speed sortingMutantsAnimalsFACSIsolatesGenotypesNematodesHomozygotes
2010
The Landscape of C. elegans 3′UTRs
Mangone M, Manoharan A, Thierry-Mieg D, Thierry-Mieg J, Han T, Mackowiak S, Mis E, Zegar C, Gutwein M, Khivansara V, Attie O, Chen K, Salehi-Ashtiani K, Vidal M, Harkins T, Bouffard P, Suzuki Y, Sugano S, Kohara Y, Rajewsky N, Piano F, Gunsalus K, Kim J. The Landscape of C. elegans 3′UTRs. Science 2010, 329: 432-435. PMID: 20522740, PMCID: PMC3142571, DOI: 10.1126/science.1191244.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsAnimalsBinding SitesCaenorhabditis elegansComputational BiologyConserved SequenceDisorders of Sex DevelopmentGene Expression Regulation, DevelopmentalGene LibraryGenes, HelminthHelminth ProteinsHistonesMaleMicroRNAsOperonPoly APolyadenylationRNA, HelminthRNA, MessengerTrans-SplicingConceptsMetazoan messenger RNAsPolyadenylation signalComplementary DNAProtein-coding genesAmplification of complementary DNAMicroRNA target sitesVariant polyadenylation signalHistone genesGenome-widePolyadenylation sitesAlternative isoformsTrans-splicingGene modelsRNA-seqRegulatory elementsCaenorhabditis elegansLong 3'UTRUntranslated regionIsoform specificityPolyadenylationGenesMessenger RNATarget siteIsoformsAnimal ageAutomated sorting of live C. elegans using laFACS
Fernandez A, Mis E, Bargmann B, Birnbaum K, Piano F. Automated sorting of live C. elegans using laFACS. Nature Methods 2010, 7: 417-418. PMID: 20436474, PMCID: PMC2896029, DOI: 10.1038/nmeth.f.304.Peer-Reviewed Original Research