2024
Exploring a Novel Role of Glycerol Kinase 1 in Prostate Cancer PC-3 Cells
Park B, Kim S, Yu S, Kim K, Jeon H, Ahn S. Exploring a Novel Role of Glycerol Kinase 1 in Prostate Cancer PC-3 Cells. Biomolecules 2024, 14: 997. PMID: 39199385, PMCID: PMC11352368, DOI: 10.3390/biom14080997.Peer-Reviewed Original ResearchPC-3 cellsProstate cancer PC-3 cellsGK deficiencyCell deathProstate cancerAnti-cancer agentsKinase 1Apoptotic cell deathDNA microarray analysisHuman prostate cancer PC-3 cellsCancer cell deathModulating tumor microenvironmentProstate cancer cellsBiomarkers of cell deathX chromosomeReduced cell viabilityEpigenetic regulationExpression vectorInvestigated genesSynthesis of triglyceridesMicroarray analysisGenetic alterationsTumor microenvironmentNovel roleCancer cellsPersistent Cutaneous Lesions of Darier Disease and Second-Hit Somatic Variants in ATP2A2 Gene
Atzmony L, Zagairy F, Mawassi B, Shehade M, Tatour Y, Danial-Farran N, Khayat M, Warrour N, Dodiuk-Gad R, Cohen-Barak E. Persistent Cutaneous Lesions of Darier Disease and Second-Hit Somatic Variants in ATP2A2 Gene. JAMA Dermatology 2024, 160: 518-524. PMID: 38536168, PMCID: PMC10974685, DOI: 10.1001/jamadermatol.2024.0152.Peer-Reviewed Original ResearchConceptsSomatic variantsATP2A2 geneDeep sequencingResponse to environmental factorsCopy number variantsRestriction fragment length polymorphismLoss of heterozygosityWhole-exome sequencingChromosomal microarray analysisDarier's diseaseFragment length polymorphismPaired whole exome sequencingPathogenic germline variantsHeterozygous pathogenic germline variantsDD lesionsGenomic characteristicsGenetic analysisGenetic skin disordersGermline variantsSanger sequencingLength polymorphismSkin lesionsTransient lesionsHeterozygous variantsMicroarray analysisRing Chromosome 13
Li P, Chong M. Ring Chromosome 13. 2024, 201-214. DOI: 10.1007/978-3-031-47530-6_17.Peer-Reviewed Original ResearchChromosomal microarray analysisFluorescence in situ hybridizationGenomic imbalancesMaternal germline mosaicismRing chromosome 13Termination of pregnancyMother-to-daughter transmissionGenotype-phenotype correlationConsecutive pregnanciesHearing lossGermline mosaicismCraniofacial dysmorphismClinical featuresClinical manifestationsPrenatal diagnosisAdult casesChromosome 13Skeletal anomaliesGenetic counselingDevelopmental delayMicroarray analysisDelayed speechClinical geneticistsDynamic mosaicPatientsRing Chromosome 9
Szekely A, Li P. Ring Chromosome 9. 2024, 159-169. DOI: 10.1007/978-3-031-47530-6_13.Peer-Reviewed Original ResearchRing chromosome 9Fluorescence in situ hybridizationChromosomal microarray analysisGenomic imbalancesStructural chromosomal abnormalitiesGene contentGenome sequenceChromosome 9Congenital heart defectsTermination of pregnancyOccurring de novoAdult male patientsMicroarray analysisDynamic mosaicGenetic counselingSevere growth retardationHeart defectsGenital anomaliesChromosomal abnormalitiesRespiratory complicationsMale patientsPrenatal diagnosisCardiac arrestGrowth retardationPatients
2023
Serendipitous Discovery of T Cell–Produced KLK1b22 as a Regulator of Systemic Metabolism
Arwood M, Sun I, Patel C, Sun I, Oh M, Bettencourt I, Claiborne M, Chan-Li Y, Zhao L, Waickman A, Mavrothalassitis O, Wen J, Aja S, Powell J. Serendipitous Discovery of T Cell–Produced KLK1b22 as a Regulator of Systemic Metabolism. ImmunoHorizons 2023, 7: 493-507. PMID: 37358498, PMCID: PMC10580127, DOI: 10.4049/immunohorizons.2300016.Peer-Reviewed Original ResearchConceptsGlucose toleranceT cellsSystemic metabolismGenome ProjectWild-type T cellsMicroarray analysisCell differentiationNovel roleRhebMammalian targetInsulin receptorT cell differentiationReduced glucose toleranceMarked increaseStrains of miceBeige fatExpressionInsulin sensitivityOverexpressionSystemic overexpressionMetabolismCellsMiceToleranceFurther studiesEstimation on risk of spontaneous abortions by genomic disorders from a meta‐analysis of microarray results on large case series of pregnancy losses
Peng G, Zhou Q, Chai H, Wen J, Zhao H, Taylor H, Jiang Y, Li P. Estimation on risk of spontaneous abortions by genomic disorders from a meta‐analysis of microarray results on large case series of pregnancy losses. Molecular Genetics & Genomic Medicine 2023, 11: e2181. PMID: 37013615, PMCID: PMC10422064, DOI: 10.1002/mgg3.2181.Peer-Reviewed Original ResearchConceptsGenomic disordersChromosome microarray analysisWilliams-Beuren syndromePathogenic copy number variantsPopulation genetic studiesWolf-Hirschhorn syndromeCopy number variantsDiGeorge syndromeMicroarray analysisMicroarray resultsChromosomal abnormalitiesGenetic studiesNumber variantsGenetic counseling
2022
Functional genomics analysis identifies loss of HNF1B function as a cause of Mayer–Rokitansky–Küster–Hauser syndrome
Thomson E, Tran M, Robevska G, Ayers K, van der Bergen J, Bhaskaran PG, Haan E, Cereghini S, Vash-Margita A, Margetts M, Hensley A, Nguyen Q, Sinclair A, Koopman P, Pelosi E. Functional genomics analysis identifies loss of HNF1B function as a cause of Mayer–Rokitansky–Küster–Hauser syndrome. Human Molecular Genetics 2022, 32: 1032-1047. PMID: 36282544, PMCID: PMC9990990, DOI: 10.1093/hmg/ddac262.Peer-Reviewed Original ResearchConceptsSingle-cell RNA sequencingKüster-Hauser syndromeMRKH syndromeType II phenotypeRNA sequencingGenetic basisCandidate genesPathways downstreamMicroarray analysisMolecular mechanismsMayer-RokitanskyFirst mouse modelReproductive healthChromosomal changesCell proliferationHypoplastic developmentLhx1HNF1BWomen's reproductive healthGenetic settingExtragenital anomaliesIdentifies lossClinical genetics settingPhenotypeType II
2021
Prenatal exome sequencing and chromosomal microarray analysis in fetal structural anomalies in a highly consanguineous population reveals a propensity of ciliopathy genes causing multisystem phenotypes
Al-Hamed M, Kurdi W, Khan R, Tulbah M, AlNemer M, AlSahan N, AlMugbel M, Rafiullah R, Assoum M, Monies D, Shah Z, Rahbeeni Z, Derar N, Hakami F, Almutairi G, AlOtaibi A, Ali W, AlShammasi A, AlMubarak W, AlDawoud S, AlAmri S, Saeed B, Bukhari H, Ali M, Akili R, Alquayt L, Hagos S, Elbardisy H, Akilan A, Almuhana N, AlKhalifah A, Abouelhoda M, Ramzan K, Sayer J, Imtiaz F. Prenatal exome sequencing and chromosomal microarray analysis in fetal structural anomalies in a highly consanguineous population reveals a propensity of ciliopathy genes causing multisystem phenotypes. Human Genetics 2021, 141: 101-126. PMID: 34853893, DOI: 10.1007/s00439-021-02406-9.Peer-Reviewed Original ResearchConceptsChromosomal microarray analysisExome sequencingConsanguineous populationsFetal anomaliesMicroarray analysisHeterozygous de novo pathogenic variantLoss of function variantsFetal phenotypeParental DNA samplesFetal abnormalitiesDiagnostic yieldMolecular genetic defectMolecular genetic diagnosticsHistory of congenital anomaliesPrenatal exome sequencingVariable diagnostic yieldCiliopathy genesFetal structural anomaliesMolecular genetic abnormalitiesStructural anomaliesCiliopathy disordersCiliopathy syndromesFunctional variantsNovel variantsGenetic diagnostics
2020
An omic approach to congenital diaphragmatic hernia: a pilot study of genomic, microRNA, and metabolomic profiling
Piersigilli F, Syed M, Lam TT, Dotta A, Massoud M, Vernocchi P, Quagliariello A, Putignani L, Auriti C, Salvatori G, Bagolan P, Bhandari V. An omic approach to congenital diaphragmatic hernia: a pilot study of genomic, microRNA, and metabolomic profiling. Journal Of Perinatology 2020, 40: 952-961. PMID: 32080334, DOI: 10.1038/s41372-020-0623-3.Peer-Reviewed Original ResearchConceptsCongenital diaphragmatic herniaCDH patientsTracheal aspiratesDiaphragmatic herniaAge-matched control patientsAge-matched controlsChromosomal microarray analysisControl patientsControl neonatesBlood samplesPatientsMiR expressionIncreased expressionPilot studyMiR-19bMiR-18MiR-20aMiR-16Genetic mutationsMetabolomic profilingHerniaMiR-17NeonatesMicroarray analysisMetabolic fingerprints
2019
Glutathione deficiency-elicited reprogramming of hepatic metabolism protects against alcohol-induced steatosis
Chen Y, Manna SK, Golla S, Krausz KW, Cai Y, Garcia-Milian R, Chakraborty T, Chakraborty J, Chatterjee R, Thompson DC, Gonzalez FJ, Vasiliou V. Glutathione deficiency-elicited reprogramming of hepatic metabolism protects against alcohol-induced steatosis. Free Radical Biology And Medicine 2019, 143: 127-139. PMID: 31351176, PMCID: PMC6848780, DOI: 10.1016/j.freeradbiomed.2019.07.025.Peer-Reviewed Original ResearchMeSH KeywordsAcetyl Coenzyme AAlcohol DrinkingAMP-Activated Protein KinasesAnimalsEthanolFatty AcidsFatty LiverGlucuronic AcidGlutamate-Cysteine LigaseGlutamatesGlutathioneHomeostasisLipogenesisLiverMaleMiceMice, Inbred C57BLMice, KnockoutOligonucleotide Array Sequence AnalysisOxidation-ReductionOxidative StressPentose Phosphate PathwayProtective AgentsTranscription, GeneticConceptsGlutamate-cysteine ligase modifier subunit geneProtein kinase pathwayAcetyl-CoA fluxMultiple cellular pathwaysAlcohol-induced steatosisCellular stressNucleotide biosynthesisLiver microarray analysisGlobal profilingSubunit geneCellular pathwaysMetabolic reprogrammingKinase pathwayMicroarray analysisMolecular mechanismsGSH poolCellular responsesMetabolic pathwaysLower GSHMolecular pathwaysMetabolic homeostasisAmino acidsDepletion of glutathioneCritical pathogenic eventGlucuronate pathway
2018
Integrated analysis of microRNA and mRNA expression profiles in splenomegaly induced by non-cirrhotic portal hypertension in rats
Saruwatari J, Dong C, Utsumi T, Tanaka M, McConnell M, Iwakiri Y. Integrated analysis of microRNA and mRNA expression profiles in splenomegaly induced by non-cirrhotic portal hypertension in rats. Scientific Reports 2018, 8: 17983. PMID: 30573742, PMCID: PMC6301948, DOI: 10.1038/s41598-018-36297-0.Peer-Reviewed Original ResearchConceptsCell proliferationWhole-genome microarray analysisInterferon-mediated antiviral activitySuppression of genesMicroRNA-mRNA networkSignificant differential expressionPotential biological functionsMRNA expression profilesTarget mRNAsBiological functionsExpression profilesMicroarray analysisDifferential expressionInnate immune responseMicroRNAsCellular mechanismsHematopoietic systemIntegrated analysisGenesNew insightsComprehensive profileMRNAProliferationTissue fibrosisImportant roleGlucocorticoid signaling regulates cell invasion and migration in the human first‐trimester trophoblast cell line Sw.71
Kisanga EP, Tang Z, Guller S, Whirledge S. Glucocorticoid signaling regulates cell invasion and migration in the human first‐trimester trophoblast cell line Sw.71. American Journal Of Reproductive Immunology 2018, 80: e12974. PMID: 29774963, DOI: 10.1111/aji.12974.Peer-Reviewed Original ResearchConceptsGene expression profilesSERPINE1 promoterPolymerase IITranscriptional regulationGlucocorticoid receptorCell movementTranscriptional profilesGlucocorticoid treatmentExpression profilesMicroarray analysisStress responseCell invasionPrimary mediatorPathogenesis of preeclampsiaCell proliferationEffects of glucocorticoidsExtravillous trophoblast functionsGlucocorticoid signalingSynthetic glucocorticoid dexamethasoneGenesTrophoblast functionsAdrenal axisInvasionTrophoblast tissueGlucocorticoid dexamethasoneCongenital second-degree heart block and total anomalous pulmonary venous return associated with microduplication of 1q32.2
Puvabanditsin S, Puthenpura V, Gueye-Ndiaye S, Takyi M, Madubuko A, Walzer L, Mehta R. Congenital second-degree heart block and total anomalous pulmonary venous return associated with microduplication of 1q32.2. Annals Of Pediatric Cardiology 2018, 11: 194-196. PMID: 29922018, PMCID: PMC5963235, DOI: 10.4103/apc.apc_21_17.Peer-Reviewed Original ResearchPulmonary venous returnCardiac conduction defectsVenous returnHeart blockConduction defectsTotal anomalous pulmonary venous returnAnomalous pulmonary venous returnSecond-degree heart blockCongenital heart blockTerm female infantClinical featuresFemale infantOligonucleotide microarray analysisMicroarray analysisLAMB3 geneInterstitial duplicationThe Anticancer Effects of Garlic Extracts on Bladder Cancer Compared to Cisplatin: A Common Mechanism of Action via Centromere Protein M
Kim W, Seo S, Byun Y, Kang H, Kim Y, Lee S, Jeong P, Song H, Choe S, Kim D, Kim S, Ha Y, Moon S, Lee G, Kim I, Yun S, Kim W. The Anticancer Effects of Garlic Extracts on Bladder Cancer Compared to Cisplatin: A Common Mechanism of Action via Centromere Protein M. The American Journal Of Chinese Medicine 2018, 46: 689-705. PMID: 29595070, DOI: 10.1142/s0192415x18500362.Peer-Reviewed Original ResearchConceptsCentromere protein MBladder cancerBC patientsGarlic extractBetter progression-free survivalNude mouse xenograft modelProgression-free survivalCisplatin-treated miceBALB/cTissue microarray analysisNegative control miceMouse xenograft modelBC cell linesEffect of garlicMicroarray analysisCisplatin groupControl miceTumor weightControl tumorsTumor volumeNormal controlsXenograft modelSide effectsBody weightTumor tissue
2017
De novo paternal origin duplication of chromosome 11p15.5: report of two Chinese cases with Beckwith-Wiedemann syndrome
Wang Q, Geng Q, Zhou Q, Luo F, Li P, Xie J. De novo paternal origin duplication of chromosome 11p15.5: report of two Chinese cases with Beckwith-Wiedemann syndrome. Molecular Cytogenetics 2017, 10: 46. PMID: 29270226, PMCID: PMC5738159, DOI: 10.1186/s13039-017-0347-z.Peer-Reviewed Original ResearchBeckwith-Wiedemann syndromeMethylation profilingGenome-wide copy number analysisGain of methylationAberrant methylation patternsIntegrated molecular approachSingle gene mutationsCopy number analysisSegmental uniparental disomyMethylation patternsGenetic mechanismsChromosome 11p15.5Genetic analysisTelomeric endMicroarray analysisMolecular approachesMolecular etiologyDuplicationBWS patientsNumber changesUniparental disomyGenetic defectsChromosome microarray analysisNumber analysisPaternal originIdentification of target genes downstream of semaphorin6A/PlexinA2 signaling in zebrafish
Emerson S, St. Clair R, Waldron A, Bruno S, Duong A, Driscoll H, Ballif B, McFarlane S, Ebert A. Identification of target genes downstream of semaphorin6A/PlexinA2 signaling in zebrafish. Developmental Dynamics 2017, 246: 539-549. PMID: 28440030, PMCID: PMC6322676, DOI: 10.1002/dvdy.24512.Peer-Reviewed Original ResearchConceptsSignaling pathwayTarget genesMicroarray analysisIdentification of target genesRegulate proliferationRetinal precursor cellsGuidance signaling pathwayGene expression changesTranscriptional regulationEarly eye developmentGenesDisrupted proliferationExpression changesEye developmentNeuronal developmentNeuronal positioningUp-regulatedZebrafish embryosMorphantsPLXNA2Downstream effectsRASL11BPathwayZebrafish eyeSema6AGarlic extract in bladder cancer prevention: Evidence from T24 bladder cancer cell xenograft model, tissue microarray, and gene network analysis
Kim W, Seo S, Byun Y, Kang H, Kim Y, Lee S, Jeong P, Seo Y, Choe S, Kim D, Kim S, Moon S, Choi Y, Lee G, Kim I, Yun S, Kim W. Garlic extract in bladder cancer prevention: Evidence from T24 bladder cancer cell xenograft model, tissue microarray, and gene network analysis. International Journal Of Oncology 2017, 51: 204-212. PMID: 28498422, DOI: 10.3892/ijo.2017.3993.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsApoptosisBiomarkers, TumorCell ProliferationGarlicGene Expression Regulation, NeoplasticGene Regulatory NetworksHumansMaleMiceMice, Inbred BALB CMice, NudePlant ExtractsSignal TransductionTissue Array AnalysisTumor Cells, CulturedUrinary Bladder NeoplasmsXenograft Model Antitumor AssaysConceptsCancer preventionBladder cancerGarlic extractXenograft modelNude mouse xenograft modelAcceptable safety profileBladder cancer preventionCancer prevention activitiesCell xenograft modelBALB/cTissue microarray analysisMouse xenograft modelMicroarray analysisTumor weightBC patientsSafety profileTumor volumeTissue microarrayControl groupGene network analysisControl dietPrevention activitiesPreventionExtract intakePotential mechanisms
2016
A novel de novo mutation in ATP1A3 and childhood-onset schizophrenia
Smedemark-Margulies N, Brownstein CA, Vargas S, Tembulkar SK, Towne MC, Shi J, Gonzalez-Cuevas E, Liu KX, Bilguvar K, Kleiman RJ, Han MJ, Torres A, Berry GT, Yu TW, Beggs AH, Agrawal PB, Gonzalez-Heydrich J. A novel de novo mutation in ATP1A3 and childhood-onset schizophrenia. Molecular Case Studies 2016, 2: a001008. PMID: 27626066, PMCID: PMC5002930, DOI: 10.1101/mcs.a001008.Peer-Reviewed Original ResearchRapid-onset dystonia-parkinsonismCommand auditory hallucinationsNovel clinical presentationHemiplegia of childhoodChildhood-onset schizophreniaNovel de novo mutationYr of ageMild motor delayWhole-exome sequencingChromosomal microarray analysisNeuron-specific isoformSodium-potassium pumpClinical presentationDystonia-parkinsonismBehavioral regressionAuditory hallucinationsMotor delayNeuronal functionDe novo mutationsHeterozygous mutationsMutation c.ATP1A3Novo mutationsMicroarray analysisPast functional studiesA novel mosquito ubiquitin targets viral envelope protein for degradation and reduces virion production during dengue virus infection
Troupin A, Londono-Renteria B, Conway MJ, Cloherty E, Jameson S, Higgs S, Vanlandingham DL, Fikrig E, Colpitts TM. A novel mosquito ubiquitin targets viral envelope protein for degradation and reduces virion production during dengue virus infection. Biochimica Et Biophysica Acta 2016, 1860: 1898-1909. PMID: 27241849, PMCID: PMC4949077, DOI: 10.1016/j.bbagen.2016.05.033.Peer-Reviewed Original ResearchConceptsProtein degradationUbiquitin proteinGene expressionProtein expression constructsSite-directed mutagenesisViral protein degradationInnate immune signalingDengue virusProteasomal degradationProtein interactionsExpression constructsMosquito cellsSignificant human diseaseMicroarray analysisImmune signalingViral envelope proteinsVirus infectionHuman diseasesBlood feedingAmino acidsProteinMultiple functionsQRT-PCRVirion productionAntiviral functionChromosomal microarray analysis in clinical evaluation of neurodevelopmental disorders-reporting a novel deletion of SETDB1 and illustration of counseling challenge
Xu Q, Goldstein J, Wang P, Gadi IK, Labreche H, Rehder C, Wang WP, McConkie A, Xu X, Jiang YH. Chromosomal microarray analysis in clinical evaluation of neurodevelopmental disorders-reporting a novel deletion of SETDB1 and illustration of counseling challenge. Pediatric Research 2016, 80: 371-381. PMID: 27119313, PMCID: PMC5382808, DOI: 10.1038/pr.2016.101.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAlgorithmsAutistic DisorderChildChild, PreschoolChromatinComparative Genomic HybridizationCounselingDevelopmental DisabilitiesDNA Copy Number VariationsFemaleGene DeletionGene RearrangementHistone-Lysine N-MethyltransferaseHumansInfantIntellectual DisabilityMaleMicroarray AnalysisNeurodevelopmental DisordersPedigreeProtein MethyltransferasesConceptsNeurodevelopmental disordersAutism spectrum disorderIntellectual disabilityDevelopmental disabilitiesCopy number variationsChromosomal microarray analysisEtiological evaluationClinical evaluationClinical significanceUnknown significanceCNV analysisGenetics clinicEtiology of ASDCounseling familiesDisordersVariable penetranceClinicMicroarray analysisNovel deletionSpectrum disorderDisabilityCounseling challengesFurther supportEtiologyCohort
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