2025
Sensitive detection of synthetic response to cancer immunotherapy driven by gene paralog pairs
Dong C, Zhang F, He E, Ren P, Verma N, Zhu X, Feng D, Cai J, Zhao H, Chen S. Sensitive detection of synthetic response to cancer immunotherapy driven by gene paralog pairs. Patterns 2025, 6: 101184. PMID: 40182179, PMCID: PMC11963098, DOI: 10.1016/j.patter.2025.101184.Peer-Reviewed Original ResearchParalogous gene pairsParalogous pairsChimeric antigen receptor T cellsResponse to cancer immunotherapyDouble knockoutCancer immunotherapy responseGene pairsCheckpoint blockadeGenome-wide screenImmunotherapy efficacyCancer immunotherapyEnhance immunotherapyImmunotherapy responseImmunotherapy effectT cellsImmunotherapyCancer treatmentIndividual genesCRISPR screensEnrichment analysisParalogsCancerTreatmentCombined targetFunctional significance
2023
Genetic associations with longevity are on average stronger in females than in males
Zeng Y, Chen H, Liu X, Song Z, Yao Y, Lei X, Lv X, Cheng L, Chen Z, Bai C, Yin Z, Lv Y, Lu J, Li J, Land K, Yashin A, O'Rand A, Sun L, Yang Z, Tao W, Gu J, Gottschalk W, Tan Q, Christensen K, Hesketh T, Tian X, Yang H, Egidi V, Caselli G, Robine J, Wang H, Shi X, Vaupel J, Lutz M, Nie C, Min J. Genetic associations with longevity are on average stronger in females than in males. Heliyon 2023, 10: e23691. PMID: 38192771, PMCID: PMC10772631, DOI: 10.1016/j.heliyon.2023.e23691.Peer-Reviewed Original ResearchGenome-wide complex trait analysisGenome-wide association study datasetGenetic associationSex-specific genetic variantsSex-specific genesGenetic variantsComplex trait analysisReplication analysisPolygenic risk score analysisIndividual genesGenetic datasetsCandidate genesBiological functionsTrait analysisRisk score analysisGenesMiddle-age controlsLongevityIndependent datasetsLongevity StudyUnderlying mechanismGWASFuture investigationsVariantsSNPsBulk and single-nucleus RNA sequencing highlight immune pathways induced in individuals during an Ixodes scapularis tick bite
Tang X, Lynn G, Cui Y, Cerny J, Arora G, Tomayko M, Craft J, Fikrig E. Bulk and single-nucleus RNA sequencing highlight immune pathways induced in individuals during an Ixodes scapularis tick bite. Infection And Immunity 2023, 91: e00282-23. PMID: 37846980, PMCID: PMC10652856, DOI: 10.1128/iai.00282-23.Peer-Reviewed Original ResearchConceptsRNA sequencingSingle-nucleus RNA sequencingBulk RNA sequencingInterleukin-17 signalingPlatelet activation pathwaysLaboratory guinea pigsSnRNA-seqHippo signalingIndividual genesPeripheral bloodTick biteAdaptive immunityAnti-tick vaccinesGuidance pathwayImmune pathwaysNew biomarkersHost responseGuinea pigsHematophagous arthropodsHost defenseCell adhesionTick attachmentNovel insightsTick feedingPhysiological consequences
2022
The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation
Miao L, Tang Y, Bonneau AR, Chan SH, Kojima ML, Pownall ME, Vejnar CE, Gao F, Krishnaswamy S, Hendry CE, Giraldez AJ. The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation. Molecular Cell 2022, 82: 986-1002.e9. PMID: 35182480, PMCID: PMC9327391, DOI: 10.1016/j.molcel.2022.01.024.Peer-Reviewed Original ResearchConceptsGenome activationChromatin openingTranscription factorsPioneer factor activityDifferent transcription factorsChromatin reprogrammingPioneer factorsNucleosome positionsActive enhancersIndividual genesCore histonesTriple mutantGene activationTF inputsDevelopmental transitionsSequence contextCell typesFactor activityHistonesPioneering activityEnhancerActivationSequence of eventsPou5f3ChromatinThe genetic basis of Gilles de la Tourette syndrome
Abdallah S, Realbuto E, Kaka M, Yang K, Topaloudi A, Paschou P, Scharf J, Fernandez T. The genetic basis of Gilles de la Tourette syndrome. International Review Of Movement Disorders 2022, 4: 3-38. DOI: 10.1016/bs.irmvd.2022.07.001.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsGenome-wide association studiesGenetic architectureCell type-specific gene expressionAssociation studiesComplex genetic architectureSingle causative geneFull genetic architectureSpecific gene expressionCandidate gene association studiesComprehensive genomic studiesCommon variant effectsPleiotropic gene effectsCommon genetic variantsGene association studiesEpigenetic marksGene regulationIndividual genesGenomic studiesLarge-scale approachGenetic basisGene expressionWhole-exome sequencing analysisBiological processesBiological pathwaysMendelian inheritance
2019
Immune regulation by glucocorticoids can be linked to cell type–dependent transcriptional responses
Franco L, Gadkari M, Howe K, Sun J, Kardava L, Kumar P, Kumari S, Hu Z, Fraser I, Moir S, Tsang J, Germain R. Immune regulation by glucocorticoids can be linked to cell type–dependent transcriptional responses. Journal Of Experimental Medicine 2019, 216: 384-406. PMID: 30674564, PMCID: PMC6363437, DOI: 10.1084/jem.20180595.Peer-Reviewed Original ResearchConceptsCell typesHuman cell typesPrimary human cell typesCell-specific effectsTranscriptional outputTranscriptional regulationTranscriptional responseIndividual genesB cell receptorNew mechanistic understandingTranscriptional effectsImmunomodulatory cytokine IL-10Toll-like receptor 7Cytokine IL-10Immunoglobulin lociAnti-inflammatory drugsFunctional studiesMechanistic understandingBlimp-1Immunoregulatory therapyIL-10GenesCell receptorReceptor 7Glucocorticoid action
2018
Whole-Exome Sequencing of an Exceptional Longevity Cohort
Nygaard HB, Erson-Omay EZ, Wu X, Kent BA, Bernales CQ, Evans DM, Farrer MJ, Vilariño-Güell C, Strittmatter SM. Whole-Exome Sequencing of an Exceptional Longevity Cohort. The Journals Of Gerontology Series A 2018, 74: 1386-1390. PMID: 29750252, PMCID: PMC6696723, DOI: 10.1093/gerona/gly098.Peer-Reviewed Original ResearchConceptsGenetic basisRare protein-altering variantsSearch of genesGene burden analysisProtein-altering variantsIndividual genesWhole-exome sequencingAlzheimer's diseaseAging phenotypesGenesRisk variantsGenetic variantsGenetic contributionExceptional longevityExome sequencingLongevity cohortBurden analysisRare variantsNeurodegenerative disordersSequencingPhenotypeLongevityNominal statistical significanceVariantsMDN1Immune regulation by glucocorticoids can be linked to cell-lineage-specific transcriptional responses
Franco L, Gadkari M, Howe K, Sun J, Kumar P, Kardava L, Biancotto A, Hu Z, Fraser I, Moir S, Germain R, Tsang J. Immune regulation by glucocorticoids can be linked to cell-lineage-specific transcriptional responses. The Journal Of Immunology 2018, 200: 48.7-48.7. DOI: 10.4049/jimmunol.200.supp.48.7.Peer-Reviewed Original ResearchTranscriptional responseReceptor signalingSpecific transcriptional responsesGenome-wide approachesTotal RNA sequencingSmall RNA sequencingB-cell receptor signalingCell receptor signalingExpression of genesDependent transcriptional responsesPrimary cell populationsB cellsTranscriptional regulationIndividual genesRNA sequencingToll-like receptor signalingNegative regulatorKey moleculesB cell activationHuman B cellsSingle intravenous doseProtein levelsAnti-inflammatory drugsImmune pathwaysCell populations
2016
Upstream ORFs are prevalent translational repressors in vertebrates
Johnstone TG, Bazzini AA, Giraldez AJ. Upstream ORFs are prevalent translational repressors in vertebrates. The EMBO Journal 2016, 35: 706-723. PMID: 26896445, PMCID: PMC4818764, DOI: 10.15252/embj.201592759.Peer-Reviewed Original ResearchConceptsUpstream open reading framesUntranslated mRNA regionsPost-transcriptional regulationOpen reading frameMRNA leader sequenceClear repressionVertebrate transcriptomesRibosome footprintingCellular diversityTranslational repressorIndividual genesNatural selectionUpstream ORFsReading frameLeader sequenceRegulatory potentialActive translationRegulatory codeInitiation contextGene expressionMRNA regionsUnknown functionReporter experimentsVertebratesIntercistronic distanceSuper-resolution imaging reveals distinct chromatin folding for different epigenetic states
Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 2016, 529: 418-422. PMID: 26760202, PMCID: PMC4905822, DOI: 10.1038/nature16496.Peer-Reviewed Original Research
2015
Diversity in the Structure and Function of Ion Channels
Levitan I, Kaczmarek L. Diversity in the Structure and Function of Ion Channels. 2015, 127-150. DOI: 10.1093/med/9780199773893.003.0007.ChaptersIon channelsPotassium channelsFormation of heterotetramersAlternative splicingIndividual genesMultiple genesAuxiliary subunitsTwo-poreDiverse familyHuman diseasesMolecular biologyMessenger RNASubunitsDiversityGenesRectifier channelsVoltage-dependent sodiumChannel propertiesPatch-clamp techniqueSplicingDifferent mechanismsHeterotetramerClamp techniqueElectrophysiological measurementsRNA
2014
Application of the Proximity-Dependent Assay and Fluorescence Imaging Approaches to Study Viral Entry Pathways
Lipovsky A, Zhang W, Iwasaki A, DiMaio D. Application of the Proximity-Dependent Assay and Fluorescence Imaging Approaches to Study Viral Entry Pathways. Methods In Molecular Biology 2014, 1270: 437-451. PMID: 25702134, DOI: 10.1007/978-1-4939-2309-0_30.Peer-Reviewed Original ResearchConceptsGenome-wide RNA interference screenEnriched gene categoriesConfirmation of phenotypesGenome-wide lossRNA interference screenVirus entryFunction genetic screenRNA interference studiesFluorescence imaging approachesProximity ligation assayGenetic screenGene categoriesInterference screenMembrane compartmentsIndividual genesBiochemical approachesCellular compartmentsMolecular intricaciesMicroscopy-based methodBioinformatics analysisProtein locationRNA interferenceCellular organellesViral entry pathwayCellular factorsPhylogenetic informativeness reconciles ray-finned fish molecular divergence times
Dornburg A, Townsend JP, Friedman M, Near TJ. Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. BMC Ecology And Evolution 2014, 14: 169. PMID: 25103329, PMCID: PMC4236503, DOI: 10.1186/s12862-014-0169-0.Peer-Reviewed Original ResearchConceptsMolecular age estimatesMolecular divergence timesDivergence timesSequence dataMolecular divergence time estimationMitochondrial sequence dataPhylogenetic informativeness profilesDivergence time estimationRay-finned fishesTree of lifeMolecular clock methodsSubstitution rate heterogeneityMolecular clock modelBranch length estimatesPhylogenetic informativenessNuclear sequencesRecent divergenceMolecular clockIndividual genesPhylogenetic inferenceDNA sequence alignmentRate heterogeneityFossil recordSequence alignmentClock methodIncreasing the Coding Potential of Genomes Through Alternative Splicing: The Case of PARK2 Gene
La Cognata V, Iemmolo R, D’Agata V, Scuderi S, Drago F, Zappia M, Cavallaro S. Increasing the Coding Potential of Genomes Through Alternative Splicing: The Case of PARK2 Gene. Current Genomics 2014, 15: 203-216. PMID: 24955028, PMCID: PMC4064560, DOI: 10.2174/1389202915666140426003342.Peer-Reviewed Original ResearchAlternative splicingTrans-acting mutationsE3 ubiquitin protein ligaseHuman disease genesMultiple protein isoformsUbiquitin-protein ligaseExtensive alternative splicingParkinson protein 2Alternative splice transcriptsHuman Genome ProjectTranscriptomic diversificationProtein diversityCellular lifeIndividual genesWidespread mechanismGenetic regulationProtein ligasePrimary transcriptProtein isoformsSingle geneSplicing featuresGenome ProjectCoding PotentialDisease genesSplicing
2011
An expression map for Anopheles gambiae
MacCallum R, Redmond S, Christophides G. An expression map for Anopheles gambiae. BMC Genomics 2011, 12: 620. PMID: 22185628, PMCID: PMC3341590, DOI: 10.1186/1471-2164-12-620.Peer-Reviewed Original ResearchConceptsPeptidoglycan recognition proteinsGene familyAnopheles gambiaeGene expressionA. gambiaeIndividual gene clustersMosquito Anopheles gambiaeDistinct biological contextsImmunity-related genesHouse-keeping roleSystems-level viewEvolutionary historyMolecular functionsGene clusterMost organismsTranscriptome dataIndividual genesDistinct functional groupsDNA replicationRecognition proteinsExpression mapProtein degradationPathogen recognitionBiological contextProtein productsPatterns of Histone H3 Lysine 27 Monomethylation and Erythroid Cell Type-specific Gene Expression*
Steiner LA, Schulz VP, Maksimova Y, Wong C, Gallagher PG. Patterns of Histone H3 Lysine 27 Monomethylation and Erythroid Cell Type-specific Gene Expression*. Journal Of Biological Chemistry 2011, 286: 39457-39465. PMID: 21937433, PMCID: PMC3234769, DOI: 10.1074/jbc.m111.243006.Peer-Reviewed Original ResearchConceptsTranscription start siteCell type-specific gene expressionGene expressionHistone modificationsType-specific gene expressionPost-translational histone modificationsHistone H3 lysine 27Numerous cellular processesH3 lysine 27Gene-specific patternsSpecific gene expressionContext-dependent mannerExpression array analysisChromatin signaturesGene bodiesH3K27 monomethylationActive genesActive transcriptionCellular processesChromatin immunoprecipitationIndividual genesLysine 27Start siteChip microarrayErythroid cellsGenetic Analysis of Cortical Thickness and Fractional Anisotropy of Water Diffusion in the Brain
Kochunov P, Glahn DC, Nichols TE, Winkler AM, Hong EL, Holcomb HH, Stein JL, Thompson PM, Curran JE, Carless MA, Olvera RL, Johnson MP, Cole SA, Kochunov V, Kent J, Blangero J. Genetic Analysis of Cortical Thickness and Fractional Anisotropy of Water Diffusion in the Brain. Frontiers In Neuroscience 2011, 5: 120. PMID: 22028680, PMCID: PMC3199541, DOI: 10.3389/fnins.2011.00120.Peer-Reviewed Original ResearchGene expression analysisGenetic analysisQuantitative trait locus (QTL) analysisGenetic correlation analysisSignificant genetic correlationsOrphan receptor alphaSignificant QTLIndividual genesSignificant SNPsGWA findingsGene localizationChromosome 15q22Chromosomal regionsLocus analysisCommon biological mechanismsQTLSignificant logarithmIllumina BeadChipGenetic correlations
2010
Antiviral Response Dictated by Choreographed Cascade of Transcription Factors
Zaslavsky E, Hershberg U, Seto J, Pham AM, Marquez S, Duke JL, Wetmur JG, tenOever BR, Sealfon SC, Kleinstein SH. Antiviral Response Dictated by Choreographed Cascade of Transcription Factors. The Journal Of Immunology 2010, 184: 2908-2917. PMID: 20164420, PMCID: PMC2856074, DOI: 10.4049/jimmunol.0903453.Peer-Reviewed Original ResearchMeSH KeywordsConserved SequenceDendritic CellsGene Expression Regulation, ViralGenes, OverlappingHumansMonocytesMultigene FamilyNewcastle disease virusOligonucleotide Array Sequence AnalysisPredictive Value of TestsPromoter Regions, GeneticReproducibility of ResultsTranscription FactorsUp-RegulationConceptsCell state transitionsRegulatory networksTranscription factorsGenetic programMost individual genesNovel transcription factorSpecific transcription factorsSingle regulatory networkAntiviral responseGene expression changesCurrent biological knowledgeActivation of RIGChoreographed cascadePromoter analysisIndividual genesGenetic regulatory networksMaster regulatorExpression changesBiological knowledgeExpression kineticsImmune evasion genesAntiviral roleImmune antagonistsHost immune systemNewcastle disease virus
2009
How form follows functional genomics: gene expression profiling gastric epithelial cells with a particular discourse on the parietal cell
Capoccia BJ, Huh WJ, Mills JC. How form follows functional genomics: gene expression profiling gastric epithelial cells with a particular discourse on the parietal cell. Physiological Genomics 2009, 37: 67-78. PMID: 19208773, PMCID: PMC2685495, DOI: 10.1152/physiolgenomics.90408.2008.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsFunctional genomic studiesFunctional genomicsGene expressionGenomic studiesCell lineagesEntire cellular transcriptomeGene ontology analysisDifferentiated cell lineagesGene expression patternsCellular transcriptomeParietal cellsVascular endothelial growth factor BIndividual genesLineage-specific markersOntology analysisCell physiologyGene productsMolecular anatomyGastric parietal cellsExpression patternsMicroarray analysisMolecular mechanismsCell-specific markersGastric epithelial cellsGrowth factor B
2007
Comparing the DNA Hypermethylome with Gene Mutations in Human Colorectal Cancer
Schuebel KE, Chen W, Cope L, Glöckner SC, Suzuki H, Yi JM, Chan TA, Van Neste L, Van Criekinge W, van den Bosch S, van Engeland M, Ting AH, Jair K, Yu W, Toyota M, Imai K, Ahuja N, Herman JG, Baylin SB. Comparing the DNA Hypermethylome with Gene Mutations in Human Colorectal Cancer. PLOS Genetics 2007, 3: e157. PMID: 17892325, PMCID: PMC1988850, DOI: 10.1371/journal.pgen.0030157.Peer-Reviewed Original ResearchConceptsTranscriptome-wide approachCpG island DNA hypermethylationHuman colorectal cancer samplesHuman cancer genomesTumor-specific hypermethylationEpigenetic screensTranscriptional silencingIndividual genesCancer genomesEpigenetic changesDNA hypermethylationGene mutationsGenesHypermethylationCell linesIndividual tumorsHuman colorectal cancerColorectal cancer samplesCancer samplesMutationsColorectal cancerCancer biomarkersGenomeSilencingPromoter
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