2022
Identification of the extracellular metallo-endopeptidases ADAM and ADAMTS in the yellow fever mosquito Aedes aegypti
Herd C, Yu X, Cui Y, Franz A. Identification of the extracellular metallo-endopeptidases ADAM and ADAMTS in the yellow fever mosquito Aedes aegypti. Insect Biochemistry And Molecular Biology 2022, 148: 103815. PMID: 35932972, PMCID: PMC11149919, DOI: 10.1016/j.ibmb.2022.103815.Peer-Reviewed Original ResearchConceptsMosquito Aedes aegyptiVertebrate hostsSecondary tissuesYellow fever mosquito Aedes aegyptiCustom-made antibodiesProtein domain structureBloodmeal ingestionExtra-cellular matrix remodelingAedes aegyptiOvarian tissueHuman ADAM10Human orthologExpression profilingTranscriptional activityFunctional specificityTransient silencingMidgut epitheliumIngestion/digestionDependent endopeptidasesFemale reproductionBasal laminaMidgutMidgut structureMosquito tissuesSame time pointsInvestigating Sources of Zeros in 10× Single-Cell RNAseq Data
Slowik H, Zyla J, Marczyk M. Investigating Sources of Zeros in 10× Single-Cell RNAseq Data. Lecture Notes In Computer Science 2022, 13347: 71-80. DOI: 10.1007/978-3-031-07802-6_6.Peer-Reviewed Original ResearchSingle-cell levelSingle-cell RNA sequencingSingle-cell RNAseq dataNumber of transcriptsMulti-omics dataGene expression estimatesRibosomal genesRNA sequencingExpression profilingEnrichment analysisRNAseq dataBiological pathwaysSequencing platformsExpression dataGenesExpression estimatesIndividual cellsBreast cancer cell linesCancer cell linesCell linesSingle experimentLow mappabilityTranscriptsSequencingProfiling
2021
Immunoregulatory and lipid presentation pathways are upregulated in human face transplant rejection
Win T, Crisler W, Dyring-Andersen B, Lopdrup R, Teague J, Zhan Q, Barrera V, Sui S, Tasigiorgos S, Murakami N, Chandraker A, Tullius S, Pomahac B, Riella L, Clark R. Immunoregulatory and lipid presentation pathways are upregulated in human face transplant rejection. Journal Of Clinical Investigation 2021, 131 PMID: 33667197, PMCID: PMC8262560, DOI: 10.1172/jci135166.Peer-Reviewed Original ResearchConceptsVCA rejectionTransplant rejectionT cellsTissue injuryGene expression profilingAntigen-presenting cell activationT-cell receptor sequencingSolid organ transplantsCell receptor sequencingT cell activation pathwaysAntigen-specific activationProliferative T cellsCell activation pathwaysNovo Nordisk FoundationAmerican SocietyExpression profilingFace transplant patientsTransplant patientsImmunologic pathwaysImmunoregulatory networkSkin biopsiesImmunomodulatory pathwaysLimb transplantsLundbeck FoundationTransplant ResearchA venous-specific purinergic signaling cascade initiated by Pannexin 1 regulates TNFα-induced increases in endothelial permeability
Maier-Begandt D, Comstra H, Molina S, Krüger N, Ruddiman C, Chen Y, Chen X, Biwer L, Johnstone S, Lohman A, Good M, DeLalio L, Hong K, Bacon H, Yan Z, Sonkusare S, Koval M, Isakson B. A venous-specific purinergic signaling cascade initiated by Pannexin 1 regulates TNFα-induced increases in endothelial permeability. Science Signaling 2021, 14 PMID: 33653920, PMCID: PMC8011850, DOI: 10.1126/scisignal.aba2940.Peer-Reviewed Original ResearchConceptsRNA expression profilingHydrolysis of ATPPannexin-1 channelsExpression profilingArterial endothelial cellsEndothelial cellsArterial endotheliumVenous endothelial cellsBarrier functionProtein analysisLung vascular permeabilityPannexin-1Claudin compositionBarrier function impairmentProinflammatory cytokine TNFαEndothelial cell barrierTargetable pathwaysMurine veinCecal ligationCell barrierFunction impairmentInflammatory insultLife spanDeficient miceVascular leak
2020
Telomerase Reverse Transcriptase Promoter Mutations Identify a Genomically Defined and Highly Aggressive Human Pleural Mesothelioma Subgroup
Pirker C, Bilecz A, Grusch M, Mohr T, Heidenreich B, Laszlo V, Stockhammer P, Lötsch-Gojo D, Gojo J, Gabler L, Spiegl-Kreinecker S, Dome B, Steindl A, Klikovits T, Hoda MA, Jakopovic M, Samarzija M, Mohorcic K, Kern I, Kiesel B, Brcic L, Oberndorfer F, Müllauer L, Klepetko W, Schmidt WM, Kumar R, Hegedus B, Berger W. Telomerase Reverse Transcriptase Promoter Mutations Identify a Genomically Defined and Highly Aggressive Human Pleural Mesothelioma Subgroup. Clinical Cancer Research 2020, 26: 3819-3830. PMID: 32317288, DOI: 10.1158/1078-0432.ccr-19-3573.Peer-Reviewed Original ResearchMeSH KeywordsAgedBiomarkers, TumorCell Line, TumorCell SurvivalCell Transformation, NeoplasticComparative Genomic HybridizationDisease ProgressionDNA Mutational AnalysisExome SequencingFemaleGene Expression ProfilingHumansKaplan-Meier EstimateMaleMesothelioma, MalignantMiddle AgedMutationPleuraPleural NeoplasmsPrognosisPromoter Regions, GeneticRetrospective StudiesTelomeraseConceptsHuman malignant pleural mesotheliomaMalignant pleural mesotheliomaPromoter mutationsLuciferase promoter assaysGene expression profilingImmortalized cell linesArray comparative genomic hybridizationComparative genomic hybridizationWild-type samplesGene promoterExpression profilingPromoter assaysPromoter activityTelomerase reverse transcriptase gene promoterCell immortalizationMolecular mechanismsMutations/deletionsMalignant transformation processMPM casesSpecific mutation patternsGenomic hybridizationTelomerase activityGenomic alteration patternsMutationsChromosomal alterationsCell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models
Gregory JA, Hoelzli E, Abdelaal R, Braine C, Cuevas M, Halpern M, Barretto N, Schrode N, Akbalik G, Kang K, Cheng E, Bowles K, Lotz S, Goderie S, Karch CM, Temple S, Goate A, Brennand KJ, Phatnani H. Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models. Cells 2020, 9: 1406. PMID: 32516938, PMCID: PMC7349756, DOI: 10.3390/cells9061406.Peer-Reviewed Original ResearchConceptsCell type-restricted expressionDisease-associated interactionsGene expression profilingHiPSC-derived motor neuronsHuman-induced pluripotent stem cellsPluripotent stem cellsCell-type specific perturbationsImmortalized cell linesRibosomal proteinsGenomic studiesExpression profilingMolecular mechanismsOff-target RNAMouse tissuesCell typesStem cellsPrimary mouse astrocytesExperimental replicatesCell linesMixed speciesMouse astrocytesExpressionMotor neuronsRiboTagCellsGene Expression Profiling as an Emerging Diagnostic Tool to Personalize Chemotherapy Selection for Early Stage Breast Cancer
Liedtke C, Pusztai L. Gene Expression Profiling as an Emerging Diagnostic Tool to Personalize Chemotherapy Selection for Early Stage Breast Cancer. 2020, 77-96. DOI: 10.1201/9780429137723-6.Peer-Reviewed Original ResearchBreast cancerEarly-stage breast cancerCombination chemotherapy regimensSubstantial tumor responseAdvanced breast cancerNeoadjuvant chemotherapy regimenStage breast cancerAdjuvant chemotherapyChemotherapy regimenNeoadjuvant therapyChemotherapy regimensPreoperative chemotherapyChemotherapy selectionOverall survivalInoperable cancerTumor responseStage ICancer tissuesCancerGene expression profilingChemotherapyDiagnostic toolCurrent standardSemiquantitative mannerExpression profiling
2019
Paraspinous muscle gene expression profiling following simulated staged endovascular repair of thoracoabdominal aortic aneurysm: exploring potential therapeutic pathways
Lewis ER, Geisbüsch S, Chang YJ, Costa V, Husain S, Soteropoulos P, Griepp RB, Di Luozzo G. Paraspinous muscle gene expression profiling following simulated staged endovascular repair of thoracoabdominal aortic aneurysm: exploring potential therapeutic pathways. European Journal Of Cardio-Thoracic Surgery 2019, 57: 30-38. PMID: 31006003, DOI: 10.1093/ejcts/ezz113.Peer-Reviewed Original ResearchConceptsAneurysm repairGene expression profilingCollateral networkThoracoabdominal aortic aneurysm repairSpinal collateral networkSpinal segmental arteriesSuch extensive proceduresThoracoabdominal aortic aneurysmsAortic aneurysm repairSpinal cord perfusionSpinal cord injuryPotential therapeutic pathwayExpression profilingArteriolar remodellingTAAA repairCord perfusionNeurological complicationsEndovascular repairNeuroprotective effectsEndovascular techniquesCord injuryAortic aneurysmCoil embolizationEndovascular coilingEndovascular interventionGlobal gene expression of histologically normal primary skin cells from BCNS subjects reveals “single-hit” effects that are influenced by rapamycin
Phatak A, Athar M, Crowell JA, Leffel D, Herbert BS, Bale AE, Kopelovich L. Global gene expression of histologically normal primary skin cells from BCNS subjects reveals “single-hit” effects that are influenced by rapamycin. Oncotarget 2019, 10: 1360-1387. PMID: 30858923, PMCID: PMC6402716, DOI: 10.18632/oncotarget.26640.Peer-Reviewed Original ResearchGlobal gene expressionRapamycin treatmentGene expression changesGene expression profilingPresence of rapamycinBiomarkers/targetsExpression profilingGene expressionExpression changesPrimary cell culturesWnt pathwayCanonical HhGenesProbe setsMitochondrial dysfunctionStellate cell activationUnaffected skin biopsiesHeritable cancersPrimary skin cellsStem cellsRapamycinDevelopmental abnormalitiesDifferential responseGene signatureNormal fibroblastsSA72 GENE EXPRESSION IN BLOOD OF ADOLESCENTS WITH PSYCHIATRIC DISORDERS
Spindola L, Santoro M, Pan P, Talarico F, Xavier G, Carvalho C, Gadelha A, Salum G, Miguel E, Rohde L, Zanardo E, Kulikowski L, Bressan R, Ota V, Belangero S. SA72 GENE EXPRESSION IN BLOOD OF ADOLESCENTS WITH PSYCHIATRIC DISORDERS. European Neuropsychopharmacology 2019, 29: s861. DOI: 10.1016/j.euroneuro.2017.08.144.Peer-Reviewed Original ResearchHigh-risk cohortPsychiatric disordersHealthy controlsGene expression profilingChild Behavior ChecklistEarly-onset psychiatric disordersBlood of adolescentsPrevious psychiatric disorderBlood gene expression profilingCross-sectional studyOnset psychiatric disordersWell-Being AssessmentAttention deficit hyperactivity disorderMost psychiatric disordersCanonical pathwaysSchool-based studyLarge public healthExpression profilingDeficit hyperactivity disorderRisk cohortPrevalent diagnosisPD groupMajor depressionHC groupMultiple comparison correctionSU73 GENE EXPRESSION IN BLOOD OF ADOLESCENTS WITH PSYCHIATRIC DISORDERS
Spindola L, Santoro M, Pan P, Talarico F, Xavier G, Carvalho C, Gadelha A, Salum G, Miguel E, Rohde L, Zanardo E, Kulikowski L, Bressan R, Ota V, Belangero S. SU73 GENE EXPRESSION IN BLOOD OF ADOLESCENTS WITH PSYCHIATRIC DISORDERS. European Neuropsychopharmacology 2019, 29: s927-s928. DOI: 10.1016/j.euroneuro.2017.08.262.Peer-Reviewed Original ResearchHigh-risk cohortPsychiatric disordersHealthy controlsGene expression profilingChild Behavior ChecklistEarly-onset psychiatric disordersBlood of adolescentsPrevious psychiatric disorderBlood gene expression profilingCross-sectional studyOnset psychiatric disordersWell-Being AssessmentAttention deficit hyperactivity disorderMost psychiatric disordersCanonical pathwaysSchool-based studyLarge public healthExpression profilingDeficit hyperactivity disorderRisk cohortPrevalent diagnosisPD groupMajor depressionHC groupMultiple comparison correction
2018
Tissue-specific miRNA Expression Profiling in Mouse Heart Sections Using In Situ Hybridization.
Memi F, Tirziu D, Papangeli I. Tissue-specific miRNA Expression Profiling in Mouse Heart Sections Using In Situ Hybridization. Journal Of Visualized Experiments 2018 PMID: 30272664, PMCID: PMC6235194, DOI: 10.3791/57920.Peer-Reviewed Original ResearchConceptsMouse heart sectionsMiRNA expression profilingMiRNA-182Relevant protein expressionMiRNAs of interestMiRNA transcriptsT proteinRNA transcriptsExpression profilingMicro-RNAsDetailed protocolSitu hybridization techniqueCardiac troponin T proteinsSitu hybridizationLNA probesProtein expressionTroponin T proteinsTranscriptsHybridization techniqueCardiomyocyte cellsProteinExpressionFluorescent stainingMiRNA detectionRNAsAn Integrative Analysis of Transcriptome and Epigenome Features of ASCL1–Positive Lung Adenocarcinomas
Miyashita N, Horie M, Suzuki H, Yoshihara M, Djureinovic D, Persson J, Brunnström H, Lindskog C, Elfving H, Micke P, Saito A, Nagase T. An Integrative Analysis of Transcriptome and Epigenome Features of ASCL1–Positive Lung Adenocarcinomas. Journal Of Thoracic Oncology 2018, 13: 1676-1691. PMID: 30121393, DOI: 10.1016/j.jtho.2018.07.096.Peer-Reviewed Original ResearchConceptsAchaete-scute family bHLH transcription factor 1Transcriptome profilingGenome-wide epigenetic profilingRecent transcriptome profilingGenome-wide methylation analysisFamily bHLH transcription factor 1Cell cycle controlMaster transcriptional regulatorGene expression profilingGlobal DNA hypomethylationLung adenocarcinomaEpigenome featuresTranscription factor 1Transcriptional regulatorsTranscriptional programsCancer Genome AtlasEpigenetic profilingLung adenocarcinoma cellsMolecular featuresExpression profilingCycle controlDNA hypomethylationIntegrative analysisMethylation analysisCell death ligand-1 (PD-L1) protein expressionHeterogeneity within the PF-EPN-B ependymoma subgroup
Cavalli FMG, Hübner JM, Sharma T, Luu B, Sill M, Zapotocky M, Mack SC, Witt H, Lin T, Shih DJH, Ho B, Santi M, Emery L, Hukin J, Dunham C, McLendon RE, Lipp ES, Gururangan S, Grossbach A, French P, Kros JM, van Veelen MC, Rao AAN, Giannini C, Leary S, Jung S, Faria CC, Mora J, Schüller U, Alonso MM, Chan JA, Klekner A, Chambless LB, Hwang EI, Massimino M, Eberhart CG, Karajannis MA, Lu B, Liau LM, Zollo M, Ferrucci V, Carlotti C, Tirapelli DPC, Tabori U, Bouffet E, Ryzhova M, Ellison DW, Merchant TE, Gilbert MR, Armstrong TS, Korshunov A, Pfister SM, Taylor MD, Aldape K, Pajtler KW, Kool M, Ramaswamy V. Heterogeneity within the PF-EPN-B ependymoma subgroup. Acta Neuropathologica 2018, 136: 227-237. PMID: 30019219, PMCID: PMC6373486, DOI: 10.1007/s00401-018-1888-x.Peer-Reviewed Original ResearchConceptsGenome-wide methylation dataPFA ependymomasChromosome 13q lossDNA methylation profilingGene expression profilesGene expression profilingCopy number profilingBroad copy-number aberrationsCopy number alterationsCopy number aberrationsMethylation profilingExpression profilingExpression profilesDistinct molecular variantsMethylation dataIntegrated analysisDistinct molecular subtypesMolecular variantsProfilingT-SNE analysisMolecular heterogeneityRobust markerPF-EPNNovel markerBiological heterogeneityThe genetic and molecular pathogenesis of myelodysplastic syndromes
Shallis RM, Ahmad R, Zeidan AM. The genetic and molecular pathogenesis of myelodysplastic syndromes. European Journal Of Haematology 2018, 101: 260-271. PMID: 29742289, DOI: 10.1111/ejh.13092.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsMolecular pathogenesisGene expression profilingSignal transduction elementsDevelopment of MDSHigh-throughput techniquesCohesin proteinsMyelodysplastic syndromeRNA splicingDNA methylationTranscription factorsDNA repairMolecular basisExpression profilingMalignant myeloid disordersBone marrow microenvironmentGenetic materialClonal architectureSuch mutationsTransduction elementsInflammatory bone marrow microenvironmentMarrow microenvironmentImportant substrateGenetic mutationsDiverse groupPathophysiology of MDSGenome-Wide Expression Analysis Suggests Hypoxia-Triggered Hyper-Coagulation Leading to Venous Thrombosis at High Altitude
Jha PK, Sahu A, Prabhakar A, Tyagi T, Chatterjee T, Arvind P, Nair J, Gupta N, Kumari B, Nair V, Bajaj N, Shanker J, Sharma M, Kumar B, Ashraf MZ. Genome-Wide Expression Analysis Suggests Hypoxia-Triggered Hyper-Coagulation Leading to Venous Thrombosis at High Altitude. Thrombosis And Haemostasis 2018, 118: 1279-1295. PMID: 29864786, DOI: 10.1055/s-0038-1657770.Peer-Reviewed Original ResearchMeSH KeywordsAdultAltitudeBlood CoagulationBlood Coagulation DisordersCase-Control StudiesGene Expression ProfilingGene Regulatory NetworksGene-Environment InteractionGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansHypoxiaMalePhenotypeRisk AssessmentRisk FactorsTranscriptomeVenous ThrombosisConceptsDeep vein thrombosisGenome-wide expression analysisDifferential expressionVenous thromboembolismEnrichment of genesGenes/pathwaysGene expression profilesHypoxia-responsive genesGene expression profilingRisk factorsGene OntologyOnset of VTEBioinformatics analysisExpression analysisExpression profilingExpression profilesPathway analysisMolecular mechanismsAdditional risk factorsQuantitative reverse transcription polymerase chain reactionReverse transcription-polymerase chain reactionPathophysiology of DVTCommon cardiovascular diseaseRelevant pathwaysGenesNovel evidence for a PIWI-interacting RNA (piRNA) as an oncogenic mediator of disease progression, and a potential prognostic biomarker in colorectal cancer
Weng W, Liu N, Toiyama Y, Kusunoki M, Nagasaka T, Fujiwara T, Wei Q, Qin H, Lin H, Ma Y, Goel A. Novel evidence for a PIWI-interacting RNA (piRNA) as an oncogenic mediator of disease progression, and a potential prognostic biomarker in colorectal cancer. Molecular Cancer 2018, 17: 16. PMID: 29382334, PMCID: PMC5791351, DOI: 10.1186/s12943-018-0767-3.Peer-Reviewed Original ResearchMeSH KeywordsAgedAged, 80 and overApoptosisBiomarkers, TumorCell DeathCell ProliferationColorectal NeoplasmsDisease ProgressionFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansMaleMiddle AgedNeoplasm MetastasisNeoplasm StagingOncogenesPrognosisRNA InterferenceRNA, Small InterferingConceptsPIWI-interacting RNAsSmall RNA sequencingGene expression profiling resultsImportant epigenetic regulatorsDownstream target genesExpression profiling resultsCell survival pathwaysColorectal cancerPotential prognostic biomarkerTumor suppressor genePrognostic biomarkerEpigenetic regulatorsSequence complementarityNoncoding RNAsRNA sequencingTarget genesExpression profilingBiological functionsGene expressionSurvival pathwaysSuppressor geneClinical significanceDirect targetNovel oncogeneOncogenic mediators
2017
Glutaminase 2 expression is associated with regional heterogeneity of 5-aminolevulinic acid fluorescence in glioblastoma
Kim S, Kim J, Kim Y, Hwang T, Kim S, Xu W, Shin J, Kim J, Choi H, Kim H, Cho H, Choi A, Chowdhury T, Seo Y, Dho Y, Kim J, Kim D, Park S, Kim H, Choi S, Park S, Lee S, Park C. Glutaminase 2 expression is associated with regional heterogeneity of 5-aminolevulinic acid fluorescence in glioblastoma. Scientific Reports 2017, 7: 12221. PMID: 28939850, PMCID: PMC5610329, DOI: 10.1038/s41598-017-12557-3.Peer-Reviewed Original ResearchConceptsGlutaminase 2Subsequent metabolite profilingInsufficient NADPHKey genesRNA sequencingExpression profilingGene expressionFunctional analysisGenesExpression levelsMetabolite profilingGBM tissuesFluorescence heterogeneityMetabolic mechanismsNADPH production capacityFluorescence intensityAcid fluorescenceProfilingExpressionGlioblastoma treatmentProtoporphyrin IXFluorescenceIntratumoral heterogeneityFluorescence-guided surgeryTissue
2016
Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions
Silva JC, Cornillot E, McCracken C, Usmani-Brown S, Dwivedi A, Ifeonu OO, Crabtree J, Gotia HT, Virji AZ, Reynes C, Colinge J, Kumar V, Lawres L, Pazzi JE, Pablo JV, Hung C, Brancato J, Kumari P, Orvis J, Tretina K, Chibucos M, Ott S, Sadzewicz L, Sengamalay N, Shetty AC, Su Q, Tallon L, Fraser CM, Frutos R, Molina DM, Krause PJ, Ben Mamoun C. Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions. Scientific Reports 2016, 6: 35284. PMID: 27752055, PMCID: PMC5082761, DOI: 10.1038/srep35284.Peer-Reviewed Original ResearchConceptsGene expression profilingExpression profilingGenome-wide diversityHost-parasite interactionsHost-pathogen interactionsParasite secretomeParasite evolutionIntraerythrocytic protozoan parasiteGenome compositionGenetic diversityImmuno-proteomic approachSurface proteomeGenetic variationMammalian hostsSmall mammalsSelective pressurePolymorphic genesGenesFirst insightProtozoan parasiteBabesia microtiSecretomeProteome arrayStrong host immune responseHost immune responseBCOR regulates myeloid cell proliferation and differentiation
Cao Q, Gearhart M, Gery S, Shojaee S, Yang H, Sun H, Lin D, Bai J, Mead M, Zhao Z, Chen Q, Chien W, Alkan S, Alpermann T, Haferlach T, Müschen M, Bardwell V, Koeffler H. BCOR regulates myeloid cell proliferation and differentiation. Leukemia 2016, 30: 1155-1165. PMID: 26847029, PMCID: PMC5131645, DOI: 10.1038/leu.2016.2.Peer-Reviewed Original ResearchConceptsMyeloid cell proliferationHox genesCell proliferationFunction mutationsUbiquitin ligase subunitRNA expression profilingPolycomb groupEnhanced cell proliferationOverexpression allelesHOXA genesExpression profilingGene expressionConditional lossMyeloid differentiationMurine cellsFamily complexesNormal hematopoiesisGenesBone marrow cellsBCOR expressionProtein levelsMechanistic explanationDifferentiation rateAML patient samplesMutations
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