2024
Persistent 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 analysisDeep sequencing of candidate genes identified 14 variants associated with smoking abstinence in an ethnically diverse sample
Cinciripini P, Wetter D, Wang J, Yu R, Kypriotakis G, Kumar T, Robinson J, Cui Y, Green C, Bergen A, Kosten T, Scherer S, Shete S. Deep sequencing of candidate genes identified 14 variants associated with smoking abstinence in an ethnically diverse sample. Scientific Reports 2024, 14: 6385. PMID: 38493193, PMCID: PMC10944542, DOI: 10.1038/s41598-024-56750-7.Peer-Reviewed Original ResearchConceptsIdentification of novel lociSequencing of candidate genesRare variant associationsMapped to genesReceptor Signaling PathwayNovel lociGenes associated with regulationVariant associationsCandidate genesProtective lociDeep sequencingRegulation of bodyweightGenetic studiesCanonical pathwaysSignaling pathwayRare variantsGenetic profileTarget of pharmacotherapyTumor suppressionAssociated with cancerGenesPublic health tollRandomized Controlled TrialsSubstance use disordersEthnically diverse sample
2022
A Two-tiered functional screen identifies herpesviral transcriptional modifiers and their essential domains
Morgens D, Nandakumar D, Didychuk A, Yang K, Glaunsinger B. A Two-tiered functional screen identifies herpesviral transcriptional modifiers and their essential domains. PLOS Pathogens 2022, 18: e1010236. PMID: 35041709, PMCID: PMC8797222, DOI: 10.1371/journal.ppat.1010236.Peer-Reviewed Original ResearchConceptsViral DNA replicationKaposi's sarcoma-associated herpesvirusViral genomeDsDNA virusesLate genesDNA replicationTranscriptional activityViral sequencesViral transcriptional activityCatalytic domainIndividual mutantsSgRNA librarySarcoma-associated herpesvirusTiling screensDNA bindingDeep sequencingBase pairsFunctional screeningCut sitePooled screeningTranscriptional modifiersDNA virusesGenomeEssential domainsGene expression
2020
PIWIL1 promotes gastric cancer via a piRNA-independent mechanism
Shi S, Yang ZZ, Liu S, Yang F, Lin H. PIWIL1 promotes gastric cancer via a piRNA-independent mechanism. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 22390-22401. PMID: 32848063, PMCID: PMC7486755, DOI: 10.1073/pnas.2008724117.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsPIWI proteinsGastric cancer cellsNonsense-mediated mRNA decay mechanismPiRNA-independent mechanismDomain protein familyMRNA decay mechanismMammalian somatic tissuesRNA deep sequencingGastric cancer cell line SNU-1Cancer cellsGastric cancer cell proliferationRNA pathwaysPPD proteinsProtein familyPiwil1 geneSomatic tissuesSomatic cancersCancer cell proliferationDeep sequencingRegulatory mechanismsOncogenic functionPIWIL1Gastric cancer tissuesDetectable function
2019
Rapid progression to AML in a patient with germline GATA2 mutation and acquired NRAS Q61K mutation
McReynolds L, Zhang Y, Yang Y, Tang J, Mulé M, Hsu A, Townsley D, West R, Zhu J, Hickstein D, Holland S, Calvo K, Hourigan C. Rapid progression to AML in a patient with germline GATA2 mutation and acquired NRAS Q61K mutation. Leukemia Research Reports 2019, 12: 100176. PMID: 31245276, PMCID: PMC6582196, DOI: 10.1016/j.lrr.2019.100176.Peer-Reviewed Original ResearchAcute myeloid leukemiaMyelodysplastic syndromeProgression to acute myeloid leukemiaNRAS Q61K mutationDevelopment of acute myeloid leukemiaGATA2 deficiency syndromeGermline GATA2 mutationsQ61K mutationBone marrow failureHeterozygous germline mutationsTargeted deep sequencingGATA2 mutationsAllogeneic transplantationMarrow failureMyeloid leukemiaAML developmentBone marrowDeficiency syndromeHematologic abnormalitiesGermline mutationsK mutationWhole exomePatientsDeep sequencingMutations
2017
Role of Dysregulated Cytokine Signaling and Bacterial Triggers in the Pathogenesis of Cutaneous T-Cell Lymphoma
Fanok MH, Sun A, Fogli LK, Narendran V, Eckstein M, Kannan K, Dolgalev I, Lazaris C, Heguy A, Laird ME, Sundrud MS, Liu C, Kutok J, Lacruz RS, Latkowski JA, Aifantis I, Ødum N, Hymes KB, Goel S, Koralov SB. Role of Dysregulated Cytokine Signaling and Bacterial Triggers in the Pathogenesis of Cutaneous T-Cell Lymphoma. Journal Of Investigative Dermatology 2017, 138: 1116-1125. PMID: 29128259, PMCID: PMC5912980, DOI: 10.1016/j.jid.2017.10.028.Peer-Reviewed Original ResearchConceptsCutaneous T-cell lymphomaT-cell lymphomaHigh-throughput transcriptional profilingJAK/STATT cell receptor engagementT cellsGenetic perturbationsTranscriptome analysisTranscriptional profilingConditional geneDeep sequencingCytokine signalingTumor genomesMalignant T cellsCellular etiologyHeterogeneous landscapesReceptor engagementSmall animal modelsCommon variantsMycosis fungoidesKey cytokineAntigenic stimulationT lymphocytesLymphoma pathogenesisMouse modelDysregulation of B Cell Repertoire Formation in Myasthenia Gravis Patients Revealed through Deep Sequencing
Vander Heiden JA, Stathopoulos P, Zhou JQ, Chen L, Gilbert TJ, Bolen CR, Barohn RJ, Dimachkie MM, Ciafaloni E, Broering TJ, Vigneault F, Nowak RJ, Kleinstein SH, O'Connor KC. Dysregulation of B Cell Repertoire Formation in Myasthenia Gravis Patients Revealed through Deep Sequencing. The Journal Of Immunology 2017, 198: 1460-1473. PMID: 28087666, PMCID: PMC5296243, DOI: 10.4049/jimmunol.1601415.Peer-Reviewed Original ResearchConceptsDeep sequencing
2016
RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq
Kelsic E, Chung H, Cohen N, Park J, Wang H, Kishony R. RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq. Cell Systems 2016, 3: 563-571.e6. PMID: 28009265, PMCID: PMC5234859, DOI: 10.1016/j.cels.2016.11.004.Peer-Reviewed Original ResearchCodon choiceMAGE-seqRNA structureEnhanced translation initiationSynonymous codon choiceRNA folding predictionsDisruption of native structureSynthetic biology applicationsRNA structure determinationAmplicon deep sequencingGenes infACodon distributionCodon preferenceOptimal codonsTranslation initiationFold predictionRNA conformationDeep sequencingCodon optimizationCodonGene expressionCodon mutantsNative structureGenesMutantsIdentifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation
Clarke D, Sethi A, Li S, Kumar S, Chang RW, Chen J, Gerstein M. Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation. Structure 2016, 24: 826-837. PMID: 27066750, PMCID: PMC4883016, DOI: 10.1016/j.str.2016.03.008.Peer-Reviewed Original ResearchConceptsAllosteric residuesIntra-species conservationEvolutionary time scalesDisease-Associated VariantsProtein conformational changesSelective constraintsAllosteric hotspotsSequencing initiativesOwn proteinsInformation-flow bottlenecksDeep sequencingConformational changesDisease locusBiophysical reasonsResiduesSurface pocketsConservationAllosteryLociSequencingProteinHotspotsPocketPDBVariantsHIV Drug Resistance Mutations (DRMs) Detected by Deep Sequencing in Virologic Failure Subjects on Therapy from Hunan Province, China
Chen X, Zou X, He J, Zheng J, Chiarella J, Kozal MJ. HIV Drug Resistance Mutations (DRMs) Detected by Deep Sequencing in Virologic Failure Subjects on Therapy from Hunan Province, China. PLOS ONE 2016, 11: e0149215. PMID: 26895182, PMCID: PMC4760947, DOI: 10.1371/journal.pone.0149215.Peer-Reviewed Original ResearchConceptsDrug resistance mutationsVirologic failureDetection of DRMsPrevalence of DRMsSanger sequencingHIV drug resistance mutationsResistance mutationsART-experienced patientsART-experienced subjectsTreatment-experienced subjectsMedian viral loadNNRTI resistance mutationsStandard genotypingART adherenceViral loadAE subtypeMutation prevalenceDeep sequencingFailure subjectsExperienced subjectsResistant variantsOnly variablePatientsPrevalenceSubtypesA novel KLF6-Rho GTPase axis regulates hepatocellular carcinoma cell migration and dissemination
Ahronian L, Zhu L, Chen Y, Chu H, Klimstra D, Lewis B. A novel KLF6-Rho GTPase axis regulates hepatocellular carcinoma cell migration and dissemination. Oncogene 2016, 35: 4653-4662. PMID: 26876204, PMCID: PMC4985511, DOI: 10.1038/onc.2016.2.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCarcinoma, HepatocellularCell Line, TumorCell MovementDisease Models, AnimalGene Expression Regulation, NeoplasticGene Knockdown TechniquesHumansKruppel-Like Factor 6Kruppel-Like Transcription FactorsLiver NeoplasmsMiceNeuropeptidesProto-Oncogene ProteinsProto-Oncogene Proteins c-vavrac1 GTP-Binding ProteinSignal TransductionConceptsHepatocellular carcinoma cell migrationGene expression profilesCell migrationHepatocellular carcinomaRac1 small GTPaseSingle-copy deletionCarcinoma cell migrationSmall GTPasesMurine HCC cell linesDevelopment of distant metastasesPresence of vascular invasionHCC cell migrationChromatin immunoprecipitationRac1 activationHepatocellular carcinoma mouse modelDeep sequencingHCC cell linesPotential curative optionHepatocellular carcinoma cellsTranscriptional targetsHuman hepatocellular carcinomaIncreased tumor formationPresence of invasionRac1Hepatocellular carcinoma developmentWhole exome and targeted deep sequencing identify genome-wide allelic loss and frequent SETDB1 mutations in malignant pleural mesotheliomas
Kang HC, Kim HK, Lee S, Mendez P, Kim JW, Woodard G, Yoon JH, Jen KY, Fang LT, Jones K, Jablons DM, Kim IJ. Whole exome and targeted deep sequencing identify genome-wide allelic loss and frequent SETDB1 mutations in malignant pleural mesotheliomas. Oncotarget 2016, 7: 8321-8331. PMID: 26824986, PMCID: PMC4884995, DOI: 10.18632/oncotarget.7032.Peer-Reviewed Original ResearchMeSH KeywordsBlotting, WesternExomeFemaleGenome, HumanHigh-Throughput Nucleotide SequencingHistone-Lysine N-MethyltransferaseHumansImmunoenzyme TechniquesLoss of HeterozygosityLung NeoplasmsMesotheliomaMesothelioma, MalignantMiddle AgedMutationPleural NeoplasmsPrognosisProtein MethyltransferasesReal-Time Polymerase Chain ReactionReverse Transcriptase Polymerase Chain ReactionRNA, MessengerSurvival RateConceptsMalignant pleural mesotheliomaPrimary cancerPleural mesotheliomaGenetic mechanismsDeep sequencingAdditional primary cancersMultiple primary cancersPrimary lung cancerPrimary cancer developmentAllelic lossNew genetic mechanismWhole-exome sequencingDistinct genomic alterationsMPM patientsRare malignancyPerineural invasionPoor prognosisTherapeutic optionsLung cancerLoss of heterozygosityTP53 mutationsCancer developmentPatientsExome sequencingCancerHNF1 regulates critical processes in the human epididymis epithelium
Browne JA, Yang R, Eggener SE, Leir SH, Harris A. HNF1 regulates critical processes in the human epididymis epithelium. Molecular And Cellular Endocrinology 2016, 425: 94-102. PMID: 26808453, PMCID: PMC4799753, DOI: 10.1016/j.mce.2016.01.021.Peer-Reviewed Original ResearchConceptsHepatocyte nuclear factor 1Transcription factorsHuman epididymis epithelial cellsCis-regulatory elementsChIP-seq peaksProcess enrichment analysisHNF1β transcription factorHEE cellsNuclear factor 1Luminal environmentChromatin genomeChromatin immunoprecipitationTranscriptional programsCoordinated expressionRNA-seqEpithelial transportRegulatory elementsTarget genesBioinformatics predictionCritical genesEnrichment analysisDeep sequencingEpididymis functionCritical processSperm maturation
2015
Reads meet rotamers: structural biology in the age of deep sequencing
Sethi A, Clarke D, Chen J, Kumar S, Galeev TR, Regan L, Gerstein M. Reads meet rotamers: structural biology in the age of deep sequencing. Current Opinion In Structural Biology 2015, 35: 125-134. PMID: 26658741, PMCID: PMC4751031, DOI: 10.1016/j.sbi.2015.11.003.Peer-Reviewed Original ResearchConceptsStructural biologyPersonal genome sequencesHuman populationSequence conservationCommon foldNovel foldGenome sequenceProtein interactionsDeep sequencingLarge complexesBiologySequenceStructure databaseSpeciesSequencingProteinFoldsReadsConservationPopulationGreater fractionComplexesDiscoveryVast amountStructureDeep sequencing of HIV-1 variants from paired plasma and cerebrospinal fluid during primary HIV infection
Gega A, Kozal MJ, Chiarella J, Lee E, Peterson J, Hecht FM, Liegler T, St John EP, Simen BB, Price RW, Spudich SS. Deep sequencing of HIV-1 variants from paired plasma and cerebrospinal fluid during primary HIV infection. Journal Of Virus Eradication 2015, 1: 264-268. PMID: 26855971, PMCID: PMC4743659, DOI: 10.1016/s2055-6640(20)30926-2.Peer-Reviewed Original ResearchPrimary HIV infectionHIV RNA levelsCopies/mLHIV infectionCerebrospinal fluidCSF samplesAge 32 yearsDrug resistance patternsHIV-1 variantsCSF HIVHIV plasmaHigh mutational loadMutational loadDays postDeep sequencingInfectionPilot studyLow-abundance variantsResistance variantsCells/Plasma samplesViral quasispeciesLimited dataMale participantsQuasispeciesLong Non-Coding RNAs Control Hematopoietic Stem Cell Function
Luo M, Jeong M, Sun D, Park H, Rodriguez B, Xia Z, Yang L, Zhang X, Sheng K, Darlington G, Li W, Goodell M. Long Non-Coding RNAs Control Hematopoietic Stem Cell Function. Cell Stem Cell 2015, 16: 426-438. PMID: 25772072, PMCID: PMC4388783, DOI: 10.1016/j.stem.2015.02.002.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBasic Helix-Loop-Helix Transcription FactorsBinding SitesBone Marrow CellsCell DifferentiationCell LineageCell Self RenewalCells, CulturedDNA (Cytosine-5-)-MethyltransferasesDNA MethylationDNA Methyltransferase 3AEpigenesis, GeneticGene Expression ProfilingGene Expression Regulation, DevelopmentalHematopoietic Stem CellsHigh-Throughput Nucleotide SequencingMiceMice, Inbred StrainsMice, KnockoutRNA, Long NoncodingRNA, Small InterferingConceptsHematopoietic stem cellsLong non-coding RNAsNon-coding RNAsLineage commitmentKey hematopoietic transcription factorsUnique gene expression programProtein-coding genesHematopoietic stem cell functionCell fate decisionsGene expression programsHematopoietic transcription factorsStem cell functionGenetic circuitryDifferentiated lineagesExpression programsFate decisionsLncRNA genesUnannotated lncRNAsDNA methylationEpigenetic featuresTranscription factorsHSC functionDeep sequencingGene expressionRegulated expressionCharacterization of the mammalian miRNA turnover landscape
Guo Y, Liu J, Elfenbein SJ, Ma Y, Zhong M, Qiu C, Ding Y, Lu J. Characterization of the mammalian miRNA turnover landscape. Nucleic Acids Research 2015, 43: 2326-2341. PMID: 25653157, PMCID: PMC4344502, DOI: 10.1093/nar/gkv057.Peer-Reviewed Original ResearchConceptsMiRNA turnoverStable small RNAsMammalian cell typesCultured mammalian cellsSubset of miRNAsTurnover kineticsMiRNA biogenesisMost miRNAsMiR-222-5pNucleotide biasSmall RNAsMiRNA maturationMammalian cellsSame miRNAMiRNA poolExpression profilingHsp90 associationSequence determinantsDeep sequencingHsp90 inhibitionTurnover rateMiRNA isoformsDifferent turnover ratesSequence featuresCell types
2014
Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains
Bai G, Cheung I, Shulha H, Coelho J, Li P, Dong X, Jakovcevski M, Wang Y, Grigorenko A, Jiang Y, Hoss A, Patel K, Zheng M, Rogaev E, Myers R, Weng Z, Akbarian S, Chen J. Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains. Human Molecular Genetics 2014, 24: 1441-1456. PMID: 25480889, PMCID: PMC4321450, DOI: 10.1093/hmg/ddu561.Peer-Reviewed Original ResearchMeSH KeywordsAdultAutopsyBasic Helix-Loop-Helix Transcription FactorsCase-Control StudiesCell Line, TumorChromatin ImmunoprecipitationDNA MethylationEpigenesis, GeneticFemaleGenetic LociGenetic MarkersGenome-Wide Association StudyHigh-Throughput Nucleotide SequencingHomeodomain ProteinsHumansHuntington DiseaseMaleNeostriatumNeuronsPhylogenyPromoter Regions, GeneticRNA, MessengerRNA, Small InterferingTranscription Factor HES-1ConceptsHuntington's diseaseGenome-wide distribution of H3K4me3Reduced binding of nuclear proteinsLoss of H3K4me3Genome-wide distributionEpigenetic dysregulationGenome-wide mappingCpG-rich sequencesDistribution of H3K4me3Binding of nuclear proteinsExcessive DNA methylationNotch signaling genesP21 mRNA expressionHuman neuroblastoma cellsPromoter sequencesNeuronal epigenomeTranscriptional marksChromatin immunoprecipitationMethylation regionsDNA methylationNuclear proteinsDeep sequencingEpigenetic contributionsHD brainSignaling GenesLow-Frequency NNRTI-Resistant HIV-1 Variants and Relationship to Mutational Load in Antiretroviral-Naïve Subjects
Gupta S, Lataillade M, Kyriakides TC, Chiarella J, St. John EP, Webb S, Moreno EA, Simen BB, Kozal MJ. Low-Frequency NNRTI-Resistant HIV-1 Variants and Relationship to Mutational Load in Antiretroviral-Naïve Subjects. Viruses 2014, 6: 3428-3437. PMID: 25256391, PMCID: PMC4189030, DOI: 10.3390/v6093428.Peer-Reviewed Original ResearchConceptsNNRTI resistance mutationsMajor NNRTI-resistance mutationsResistance mutationsAntiretroviral-naïve subjectsARV-naïve HIVMajor NNRTI mutationsNNRTI-resistant variantsTreatment-naïve HIVHIV-1 variantsNon-nucleoside reverseMutational loadNaïve HIVNNRTI mutationsNNRTI resistanceVariant frequencyTrue burdenTherapeutic failureTreatment outcomesTreatment responseAa positionsHIVViral variantsFurther evaluationResistant variantsDeep sequencingAnalysis of Multiple Tsetse Fly Populations in Uganda Reveals Limited Diversity and Species-Specific Gut Microbiota
Aksoy E, Telleria EL, Echodu R, Wu Y, Okedi LM, Weiss BL, Aksoy S, Caccone A. Analysis of Multiple Tsetse Fly Populations in Uganda Reveals Limited Diversity and Species-Specific Gut Microbiota. Applied And Environmental Microbiology 2014, 80: 4301-4312. PMID: 24814785, PMCID: PMC4068677, DOI: 10.1128/aem.00079-14.Peer-Reviewed Original ResearchConceptsDifferent tsetse speciesRRNA gene clone librariesDifferent sympatric speciesGene clone librariesTsetse speciesLimited diversityQuantitative PCRV4 hypervariable regionGut microbiotaGut microbial abundanceSympatric speciesGut microbial diversityClone librariesMicrobial diversityMicrobial abundanceField fliesRRNA geneHost physiologyTsetse fly populationsDeep sequencingReduced diversityDifferent speciesFly populationsSpeciesWigglesworthia
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply