2025
A genetic modifier links integrin α5 to the phenotypic variation in fibronectin 1a mutant zebrafish.
Capon S, Maroufidou A, Feltes M, Xu Y, Matharoo D, Jülich D, Holley S, Farber S, Stainier D. A genetic modifier links integrin α5 to the phenotypic variation in fibronectin 1a mutant zebrafish. PLOS Genetics 2025, 21: e1011747. PMID: 40549824, PMCID: PMC12212883, DOI: 10.1371/journal.pgen.1011747.Peer-Reviewed Original ResearchConceptsMutant phenotypePhenotypic variationNonsense mutationGenetic modifiersDouble mutant analysisWhole-genome sequencingITGA5 expressionSevere phenotypeIntegrin alpha 5Mutant analysisMutant larvaeProximal promoterMutantsMutant zebrafishCardia bifidaGene expressionIntegrin A5Genetic backgroundAlpha 5PhenotypeMutationsExpression levelsFibronectinFunctional cardiovascular systemZebrafishAndrogen pathway gene expression and response to hormonal therapy in prostate cancer (SWOG S1216).
Pinski J, Ingles S, Manojlovic Z, Xiong S, Weisenberger D, Goldkorn A, McConkey D, Lara P, Hussain M, Quinn D, Thompson I, Lerner S, Dorff T, Agarwal N. Androgen pathway gene expression and response to hormonal therapy in prostate cancer (SWOG S1216). Journal Of Clinical Oncology 2025, 43 DOI: 10.1200/jco.2025.43.16_suppl.e17109.Peer-Reviewed Original ResearchMetastatic castration-sensitive prostate cancerProgression free survivalResponse to androgen deprivation therapyAndrogen metabolism genesAndrogen deprivation therapyPrimary prostate tumorsProstate cancerPSA responsePSA-CRDeprivation therapyProstate tumorsMolecular features of prostate cancerCastration-sensitive prostate cancerAnalysis of progression free survivalFeatures of prostate cancerResponse to hormonal therapyDays of follow-upAndrogen receptor inhibitorsTumor gene expression profilesUnder-expressedExpression levelsFree survivalAssociation of expression levelsHormone therapyTumor blocksBatch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns
Millard N, Chen J, Palshikar M, Pelka K, Spurrell M, Price C, He J, Hacohen N, Raychaudhuri S, Korsunsky I. Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns. Genome Biology 2025, 26: 36. PMID: 40001084, PMCID: PMC11863647, DOI: 10.1186/s13059-025-03479-9.Peer-Reviewed Original ResearchConceptsBatch effectsVisualization of gene expression patternsSpatial gene patternsGene expression analysis of cellsGene expression patternsGene expression analysisGene expression levelsGene colocalizationAnalysis of cellsGene patternsTranscriptome analysisLigand-receptor interactionsExpression patternsSpatial transcriptomicsSpatial transcriptomic analysisExpression levelsGenesMultiple samplesSpatial patternsTranscriptomeColocalizationAnatomical contextPatternsCount dataIdentification of genes associated with testicular germ cell tumor susceptibility through a transcriptome-wide association study
Ugalde-Morales E, Wilf R, Pluta J, Ploner A, Fan M, Damra M, Aben K, Anson-Cartwright L, Chen C, Cortessis V, Daneshmand S, Ferlin A, Gamulin M, Gietema J, Gonzalez-Niera A, Grotmol T, Hamilton R, Harland M, Haugen T, Hauser R, Hildebrandt M, Karlsson R, Kiemeney L, Kim J, Lessel D, Lothe R, Loveday C, Chanock S, McGlynn K, Meijer C, Nead K, Nsengimana J, Popovic M, Rafnar T, Richiardi L, Rocca M, Schwartz S, Skotheim R, Stefansson K, Stewart D, Turnbull C, Vaughn D, Winge S, Zheng T, Monteiro A, Almstrup K, Kanetsky P, Nathanson K, Wiklund F, Consortium T. Identification of genes associated with testicular germ cell tumor susceptibility through a transcriptome-wide association study. American Journal Of Human Genetics 2025, 112: 630-643. PMID: 39999848, PMCID: PMC11947167, DOI: 10.1016/j.ajhg.2025.01.022.Peer-Reviewed Original ResearchConceptsTranscriptome-wide association studyGenome-wide association studiesAssociation studiesTesticular germ cell tumorsTranscriptome-wide association study signalsGenome-wide association study lociTesticular germ cell tumour susceptibilityTesticular germ cell tumor tissuesFine-mapping analysisGene-disease linksGonadal cell typesEvidence of colocalizationProtein levels accumulationExpression levelsTesticular germ cell tumour riskPrioritized genesFalse discovery rateNeighboring genesGene-diseaseRegulatory featuresGene associationsColocalization analysisProtein patternsGenesNormal testisA comprehensive spatio-cellular map of the human hypothalamus
Tadross J, Steuernagel L, Dowsett G, Kentistou K, Lundh S, Porniece M, Klemm P, Rainbow K, Hvid H, Kania K, Polex-Wolf J, Knudsen L, Pyke C, Perry J, Lam B, Brüning J, Yeo G. A comprehensive spatio-cellular map of the human hypothalamus. Nature 2025, 639: 708-716. PMID: 39910307, PMCID: PMC11922758, DOI: 10.1038/s41586-024-08504-8.Peer-Reviewed Original ResearchConceptsGenome-wide association study genesRare deleterious variantsHypothalamic cell typesCell typesSingle-nucleus sequencingBody mass indexTranscription mapDeleterious variantsNeuronal cell typesG protein-coupled receptorsStudy genesBiological functions1Spatial transcriptomicsTranscriptomic identityCellular componentsExpression levelsPro-opiomelanocortin neuronsHuman hypothalamusAssociated with body mass indexPopulation levelMetabolic disordersHypothalamic cellsExpressionNeuronal clustersTranscriptomeMETTL3 modulates colonic epithelium integrity via maintaining the self-renewal and differentiation of Lgr5+ stem cell
Ding C, Yang X, Liu H, Roulis M, Chen H, Chen Y, Xu H, Gao Y, Zhong J, Li H, Ye Y, Cai W, Hu W, Wang Z. METTL3 modulates colonic epithelium integrity via maintaining the self-renewal and differentiation of Lgr5+ stem cell. Journal Of Molecular Cell Biology 2025, mjae060. PMID: 39762134, DOI: 10.1093/jmcb/mjae060.Peer-Reviewed Original ResearchSelf-RenewalStem cellsMaturation of goblet cellsDifferentiation of Lgr5Ulcerative colitisHomeostasis of intestinal epitheliumColonic stem cellsGoblet cellsSpontaneous inflammationIntestinal dysplasiaColonic mucosaUC treatmentLgr5Epithelium integrityDepletion of METTL3Intestinal epitheliumTherapeutic targetInflammationDifferentiation capacityMETTL3 expressionUC samplesMETTL3 levelsExpression levelsM6A methylationCells
2024
Lymphocyte phosphatase-associated phosphoprotein (LPAP) as CD45 protein stability regulator
Kruglova N, Mazurov D, Filatov A. Lymphocyte phosphatase-associated phosphoprotein (LPAP) as CD45 protein stability regulator. Биохимия 2024, 89: 897-907. DOI: 10.31857/s0320972524050118.Peer-Reviewed Original Research6421 Imaging Phenotype May Predict Genotype In Human Pheochromocytoma: Relationships Between Genetic Mutation Clusters, Metabolite Transporter Expression, And Radiotracer Uptake
Sakuma I, Fujimoto M, Vatner D, Yokote K, Tanaka T. 6421 Imaging Phenotype May Predict Genotype In Human Pheochromocytoma: Relationships Between Genetic Mutation Clusters, Metabolite Transporter Expression, And Radiotracer Uptake. Journal Of The Endocrine Society 2024, 8: bvae163.210. PMCID: PMC11455308, DOI: 10.1210/jendso/bvae163.210.Peer-Reviewed Original ResearchGATA binding protein 3Expression of norepinephrine transporterGlucose transporter 1Chromaffin cell differentiationNorepinephrine transporter expressionNorepinephrine transporterFDG-PETGlucocorticoid receptorCluster 1 mutationsRadiotracer uptakeLevels of norepinephrine transportersGlucose transporter 1 expressionLocalization of pheochromocytomaChromaffin cell phenotypeCluster 2 tumorsExpression of glucose transporter 1Binding protein-3Expression levelsTumor gene expressionNorepinephrine transporter geneLevels of glucose transporter 1Cell differentiationTranscription factor Phox2aPositron emission tomographyFDG avidityTuning Responses to Polatuzumab Vedotin in B-cell Lymphoma.
Leveille E, Kothari S, Cosgun K, Mlynarczyk C, Müschen M. Tuning Responses to Polatuzumab Vedotin in B-cell Lymphoma. Cancer Discovery 2024, 14: 1577-1580. PMID: 39228298, DOI: 10.1158/2159-8290.cd-24-0644.Commentaries, Editorials and LettersTelomere transcripts act as tumor suppressor and are associated with favorable prognosis in colorectal cancer with low proliferating cell nuclear antigen expression
Kienzl P, Deloria A, Hunjadi M, Hadolt J, Haering M, Bothien A, Mejri D, Korkut-Demirbaş M, Sampl S, Weber G, Pirker C, Laengle S, Braunschmid T, Dragona E, Marian B, Gagos S, Lu L, Henson J, Lau L, Reddel R, Mikulits W, Stättner S, Holzmann K. Telomere transcripts act as tumor suppressor and are associated with favorable prognosis in colorectal cancer with low proliferating cell nuclear antigen expression. Cellular Oncology 2024, 48: 239-247. PMID: 39222177, PMCID: PMC11850466, DOI: 10.1007/s13402-024-00986-y.Peer-Reviewed Original ResearchSevere combined immunodeficiency diseaseTelomerase reverse transcriptaseProliferating Cell Nuclear AntigenEpithelial-mesenchymal transitionColorectal cancerTelomerase RNA componentTumor tissuesTelomerase activityTelomeric repeat-containing RNAProliferating cell nuclear antigen expressionAssociated with favorable prognosisOverall survival rateCombined immunodeficiency diseaseTelomere lengthEpithelial splicing regulatory protein 1TERRA expressionColorectal cancer tumor tissuesCell nuclear antigenNon-canonical functions of telomerase reverse transcriptaseCRC tumor growthExpression levelsFavorable prognosisNon-tumor tissuesImmunodeficiency diseaseAdjacent non-tumor tissuesSelenomethionine supplementation mitigates fluoride-induced liver apoptosis and inflammatory reactions by blocking Parkin-mediated mitophagy in mice
Wang T, Li H, Li Y, Li M, Zhao H, Zhang W, Zhao T, Wang Y, Wang J, Wang J. Selenomethionine supplementation mitigates fluoride-induced liver apoptosis and inflammatory reactions by blocking Parkin-mediated mitophagy in mice. The Science Of The Total Environment 2024, 951: 175458. PMID: 39142410, DOI: 10.1016/j.scitotenv.2024.175458.Peer-Reviewed Original ResearchParkin-mediated mitophagyCysteinyl aspartate specific proteinase 3Protein expression levelsLight chain 3Expression levelsInterleukin-6Wild-typeLiver damageContents of proinflammatory factorsTumor necrosis factor-aNuclear factor kappa BLevels of liver functionMitochondrial fusionFactor kappa BParkin-/-Inflammatory signaling pathwaysMicrotubule-associated protein light chain 3MitophagyInterferon-gMitochondrial alterationsProtein light chain 3Gene knockoutIFN-gFluorosis miceLiver functionChemical complementarity of tumor resident, T-cell receptor CDR3s and renalase-1 correlates with increased melanoma survival
Zaman S, Gorelick F, Chrobrutskiy A, Chobrutskiy B, Desir G, Blanck G. Chemical complementarity of tumor resident, T-cell receptor CDR3s and renalase-1 correlates with increased melanoma survival. Oncotarget 2024, 15: 550-561. PMID: 39102218, PMCID: PMC11299663, DOI: 10.18632/oncotarget.28633.Peer-Reviewed Original ResearchConceptsT cell receptorOverall survivalT cellsAssociated with improved overall survivalT-cell receptor CDR3sPromote T cell activationImproved overall survivalSurvival of melanomaPancreatic cancer patientsT cell activationT cell receptor recognitionTumor-residentTumor rejectionMelanoma patientsMelanoma growthMelanoma survivalImmune signature genesSurvival associationsCancer patientsMelanomaSignature genesAmino acid sequenceSurvivalPatientsExpression levelsSacituzumab Govitecan Demonstrates Efficacy across Tumor Trop-2 Expression Levels in Patients with Advanced Urothelial Cancer.
Loriot Y, Balar A, Petrylak D, Kalebasty A, Grivas P, Fléchon A, Jain R, Swami U, Bupathi M, Barthélémy P, Beuzeboc P, Palmbos P, Kyriakopoulos C, Pouessel D, Sternberg C, Tonelli J, Sierecki M, Zavodovskaya M, Elboudwarej E, Diehl L, Jürgensmeier J, Tagawa S. Sacituzumab Govitecan Demonstrates Efficacy across Tumor Trop-2 Expression Levels in Patients with Advanced Urothelial Cancer. Clinical Cancer Research 2024, 30: 3179-3188. PMID: 39086310, DOI: 10.1158/1078-0432.ccr-23-3924.Peer-Reviewed Original ResearchConceptsTrop-2 expressionTrop-2Positive tumor cellsUrothelial cancerMetastatic UCSacituzumab govitecanTumor cellsTumor samplesOpen-label phase II studyTrophoblast cell surface antigen 2Human trophoblast cell-surface antigen 2Advanced urothelial cancerSN-38 payloadPhase II studyC1-3Archival tumor samplesExpression levelsCohorts 1 to 3Surface antigen 2Antibody drug conjugatesOS benefitII studyExamined tumorsH-scoreMembrane expressionComputational reassessment of RNA-seq data reveals key genes in active tuberculosis
Arya R, Shakya H, Chaurasia R, Kumar S, Vinetz J, Kim J. Computational reassessment of RNA-seq data reveals key genes in active tuberculosis. PLOS ONE 2024, 19: e0305582. PMID: 38935691, PMCID: PMC11210783, DOI: 10.1371/journal.pone.0305582.Peer-Reviewed Original ResearchConceptsMolecular Complex DetectionProtein-protein interactionsDeregulated genesGene OntologyRNA-seq dataGene Expression Omnibus (GEO) databaseIncreasing prevalence of multidrug-resistantGEO2R online toolPrevalence of multidrug resistancePathway enrichment analysisExpression levelsPatterns of variationGene expression levelsArea under curveInnate immune responseGene networksCore genesMicroarray datasetsSTRING databaseTranscript levelsEnrichment analysisGenesInterferon SignalingInterferon-gamma signalingResponse to Mtb infectionDepletion of TBC1D4 Improves the Metabolic Exercise Response by Overcoming Genetically Induced Peripheral Insulin Resistance.
Springer C, Binsch C, Weide D, Toska L, Cremer A, Backes H, Scheel A, Espelage L, Kotzka J, Sill S, Kurowski A, Kim D, Karpinski S, Schnurr T, Hansen T, Hartwig S, Lehr S, Cames S, Brüning J, Lienhard M, Herwig R, Börno S, Timmermann B, Al-Hasani H, Chadt A. Depletion of TBC1D4 Improves the Metabolic Exercise Response by Overcoming Genetically Induced Peripheral Insulin Resistance. Diabetes 2024, 73: 1058-1071. PMID: 38608276, DOI: 10.2337/db23-0463.Peer-Reviewed Original ResearchWhite adipose tissueLoss-of-function variantsAnalysis of glucose uptakeRegulation of glucose transportInterscapular brown adipose tissueHigh-fat dietEnhanced expression levelsDevelopment of insulin resistanceBrown adipose tissueMitochondrial activityTBC1D4Gene variantsInsulin resistanceAdipose tissueGlucose uptakePeripheral insulin resistanceGlucose transportExpression levelsGenesPrecision medicineInsulin toleranceGeneticsIncreased glucose clearanceExercise responseIn vivoCombined Genetic Association and Differed Expression Analysis of UBE2L3 Uncovers a Genetic Regulatory Role of (Immuno)proteasome in IgA Nephropathy
Xu L, Gan T, Li Y, Chen P, Shi S, Liu L, Lv J, Zhang H, Zhou X. Combined Genetic Association and Differed Expression Analysis of UBE2L3 Uncovers a Genetic Regulatory Role of (Immuno)proteasome in IgA Nephropathy. Kidney Diseases 2024, 10: 167-180. PMID: 38835407, PMCID: PMC11149991, DOI: 10.1159/000537987.Peer-Reviewed Original ResearchGd-IgA1IgA nephropathyHealthy controlsProteasome subunitsLevels of Gd-IgA1Genetic associationPeripheral blood mononuclear cellsExpression levelsEnd-stage renal diseaseSusceptibility to IgANBlood mononuclear cellsGd-IgA1 productionImmune cell typesBlood mRNA levelsFollow-up dataGalactose-deficient IgA1Cell typesUbiquitin-proteasome systemProcess of glycosylationPathogenesis of IgANAssociation of variantsDevelopment of IgANHigher proteinuriaLow eGFRHighest expression levelPerturbed liver gene zonation in a mouse model of non-alcoholic steatohepatitis
Zhou Y, Zhao Y, Carbonaro M, Chen H, Germino M, Adler C, Ni M, Zhu Y, Kim S, Altarejos J, Li Z, Burczynski M, Glass D, Sleeman M, Lee A, Halasz G, Cheng X. Perturbed liver gene zonation in a mouse model of non-alcoholic steatohepatitis. Metabolism 2024, 154: 155830. PMID: 38428673, DOI: 10.1016/j.metabol.2024.155830.Peer-Reviewed Original ResearchWnt target genesWnt signalingGene expressionActivate gene expressionLiver zonationAlteration of Wnt signalingMouse NASH modelNon-alcoholic steatohepatitisSuppress gene expressionGene expression levelsNon-alcoholic steatohepatitis liversWnt regulationMetabolic pathwaysMetabolic zonationGenesRSPO3 expressionSpatial transcriptomicsIn situ hybridizationSpatial expressionExpression levelsRSPO3Perivenous hepatocytesMouse model of non-alcoholic steatohepatitisZonationModel of non-alcoholic steatohepatitisSkeletal muscle TET3 promotes insulin resistance through destabilisation of PGC-1α
Liu B, Xie D, Huang X, Jin S, Dai Y, Sun X, Li D, Bennett A, Diano S, Huang Y. Skeletal muscle TET3 promotes insulin resistance through destabilisation of PGC-1α. Diabetologia 2024, 67: 724-737. PMID: 38216792, PMCID: PMC10904493, DOI: 10.1007/s00125-023-06073-5.Peer-Reviewed Original ResearchConceptsTen-eleven translocationMuscle insulin sensitivityRNA-seqPGC-1aRegulation of muscle insulin sensitivityType 2 diabetesAnalysis of RNA-seqResponse to environmental cuesGenome-wide expression profilingWild-typeHFD-fedHFD-induced insulin resistanceHigh-fat diet (HFD)-inducedExpression levelsMaintenance of glucoseSkeletal muscle insulin sensitivityAccession numbersSkeletal muscleEnhanced glucose toleranceFamily dioxygenasesMitochondrial respirationSkeletal muscle of humansEnvironmental cuesMitochondrial functionBiological processesPotential role of RhoA GTPase regulation in type interferon signaling in systemic lupus erythematosus
Fan W, Wei B, Chen X, Zhang Y, Xiao P, Li K, Zhang Y, Huang J, Leng L, Bucala R. Potential role of RhoA GTPase regulation in type interferon signaling in systemic lupus erythematosus. Arthritis Research & Therapy 2024, 26: 31. PMID: 38243295, PMCID: PMC10799493, DOI: 10.1186/s13075-024-03263-3.Peer-Reviewed Original ResearchConceptsPeripheral blood mononuclear cellsRhoA GTPaseExpression levelsTreatment of SLEFunctions of RhoA.Knockdown of RhoAI IFN-stimulated genesSiRNA-mediated knockdownI interferonEnzyme-linked immunoassayIFN-stimulated genesGTPase signalingExpression levels of RhoASLE patientsLevels of RhoALupus erythematosusSLE peripheral blood mononuclear cellsGTPase regulatorHealthy controlsExpression of RhoAResponse pathwaysReporter gene assayRhoAType I IFN signalingSignal transducer
2023
PET Imaging of Rho‐Associated Protein Kinase 2 in A Mouse Model of Alzheimer’s Disease
Zheng C, Nicholson L, Chen B, Toyonaga T, Liu M, Strittmatter S, Carson R, Huang Y, Cai Z. PET Imaging of Rho‐Associated Protein Kinase 2 in A Mouse Model of Alzheimer’s Disease. Alzheimer's & Dementia 2023, 19 DOI: 10.1002/alz.081695.Peer-Reviewed Original ResearchAPP/PS1 micePS1 miceWT miceCentral nervous systemTime-activity curvesAlzheimer's diseaseAPP/PS1 transgenic miceAPP/PS1 transgenic AD miceMouse brainAge-matched WT controlsPS1 transgenic miceAPP/PS1Transgenic AD miceDynamic PET imaging dataROCK2 protein expressionAD drug discoveryHigh tracer uptakeMin post injectionPET imaging resultsExpression levelsReference tissue model 2PET imaging dataProtein expression levelsAD miceRegional time-activity curves
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