2025
Human and pathogen-encoded circular RNAs in viral infections: insights into functions and therapeutic opportunities
Mueller N, Dujsikova A, Singh A, Chen Y. Human and pathogen-encoded circular RNAs in viral infections: insights into functions and therapeutic opportunities. Human Molecular Genetics 2025, ddaf031. PMID: 40304711, DOI: 10.1093/hmg/ddaf031.Peer-Reviewed Original ResearchDNA virusesHost cellular machineryHost-virus interactionsCircular RNAsContribution to pathogenesisRNA biologyProtein translationCellular machineryProtein decoysRNA-based therapiesBiological rolePotential of circRNAsRegulatory moleculesRNAMicroRNA spongesViral systemsDNAViral replicationImmune evasionTherapeutic targetCircRNAsTherapeutic opportunitiesHostProteinViral diseasesTrogocytosis-mediated immune evasion in the tumor microenvironment
Kim J, Park S, Kim J, Kim Y, Yoon H, Rayhan B, Jeong J, Bothwell A, Shin J. Trogocytosis-mediated immune evasion in the tumor microenvironment. Experimental & Molecular Medicine 2025, 57: 1-12. PMID: 39741180, PMCID: PMC11799389, DOI: 10.1038/s12276-024-01364-2.Peer-Reviewed Original ResearchConceptsCD4 T cellsT cellsMajor histocompatibility complexTumor microenvironmentImmune evasionMechanisms of immune evasionAnti-tumor immunityImmune regulatory moleculesAntigen-presenting cellsImmune-regulatory moleculesCTLA-4Cell-to-cell interactionsDonor cellsHistocompatibility complexTrogocytosisRecipient cellsTumorMembrane lossMembrane moleculesRegulatory moleculesMicroenvironmentSurface localizationPlasma membraneCellsTrogoptosis
2023
Mitochondrial calcium signaling in cholangiocarcinoma
Loyola-Machado A, Guerra M, Nathanson M. Mitochondrial calcium signaling in cholangiocarcinoma. Hepatoma Research 2023, 9: null-null. DOI: 10.20517/2394-5079.2023.28.Peer-Reviewed Original ResearchPrimary liver cancerNew pharmacological agentsPathogenesis of cholangiocarcinomaMitochondrial Ca2Liver cancerCholangiocarcinomaPharmacological agentsIntracellular Ca2Molecular alterationsDruggable targetsER-mitochondrial contact sitesCancer cellsKey regulatory moleculesMetabolic reprogramingReceptor familyMitochondrial healthMitochondrial calciumEnergy metabolismCell deathPathways of interestLatest findingsTreatmentCa2Regulatory moleculesContact sites
2022
Immunological conversion of solid tumours using a bispecific nanobioconjugate for cancer immunotherapy
Lu Y, Huntoon K, Lee D, Wang Y, Ha J, Qie Y, Li X, Schrank B, Dong S, Gallup T, Kang M, Zhao H, An Y, Yang Z, Li J, Kim B, Jiang W. Immunological conversion of solid tumours using a bispecific nanobioconjugate for cancer immunotherapy. Nature Nanotechnology 2022, 17: 1332-1341. PMID: 36357792, PMCID: PMC10036139, DOI: 10.1038/s41565-022-01245-7.Peer-Reviewed Original ResearchConceptsInnate immune cellsSolid tumorsImmune cellsEffectiveness of immunotherapyImmune checkpoint blockadeCancer cellsImmune regulatory moleculesHigh response rateCyclic guanosine monophosphate-adenosine monophosphate synthaseBlood cancer cellsInterferon genes (STING) pathwayCheckpoint blockadeCancer immunotherapyHaematological malignanciesImmunotherapyResponse rateTumorsBiological disparitiesLimited responseMember 7Haematologic tumoursDifferential expressionCellsRegulatory moleculesGene pathways
2018
Anti‐PD‐1 Therapy‐Associated Perforating Colitis
Celli R, Kluger HM, Zhang X. Anti‐PD‐1 Therapy‐Associated Perforating Colitis. Case Reports In Gastrointestinal Medicine 2018, 2018: 3406437. PMID: 29955400, PMCID: PMC6000840, DOI: 10.1155/2018/3406437.Peer-Reviewed Original ResearchAnti-PD-1/PD-L1PD-L1T-lymphocyte-associated antigen 4Immune-related adverse effectsCell death protein 1PD-1 inhibitorsDeath protein 1T-cell regulatory moleculesAdvanced malignanciesColonic perforationAntigen-4Metastatic melanomaTimely diagnosisColitisAdverse effectsProtein 1PerforationCell regulatory moleculesRegulatory moleculesPembrolizumabDiarrheaPatientsMalignancyMelanomaDiagnosis
2017
Control of Immune Cell Homeostasis and Function by lncRNAs
Mowel W, Kotzin J, McCright S, Neal V, Henao-Mejia J. Control of Immune Cell Homeostasis and Function by lncRNAs. Trends In Immunology 2017, 39: 55-69. PMID: 28919048, PMCID: PMC5748345, DOI: 10.1016/j.it.2017.08.009.Peer-Reviewed Original ResearchConceptsCell gene expression programSpecific epigenetic landscapesGene expression programsLong non-coding RNAsDiverse molecular mechanismsDiverse cell typesNon-coding RNAsKey regulatory moleculesLncRNA mechanismsEpigenetic landscapeExpression programsExtracellular cuesTranscriptional regulationTranscriptional programsTissue homeostasisTranscriptional profilesRegulatory moleculesCell homeostasisMolecular mechanismsImmune cell homeostasisCell typesLncRNAsHomeostasisImmune systemCell populations
2016
STarMir Tools for Prediction of microRNA Binding Sites
Kanoria S, Rennie W, Liu C, Carmack CS, Lu J, Ding Y. STarMir Tools for Prediction of microRNA Binding Sites. Methods In Molecular Biology 2016, 1490: 73-82. PMID: 27665594, PMCID: PMC5353976, DOI: 10.1007/978-1-4939-6433-8_6.Peer-Reviewed Original ResearchConceptsMessenger RNAEndogenous short noncoding RNAsGene expressionMammalian biological processesHigh-throughput miRNATarget messenger RNAsShort noncoding RNAsMicroRNA Binding SitesCertain human diseasesCross-species validationTranslational repressionMiRNA functionGene regulationSeedless sitesMRNA degradationNoncoding RNAsRegulatory moleculesBiological processesSequence featuresHuman diseasesImmunoprecipitation studiesMiRNAComputational predictionsBinding sitesMiRNAs
2013
The remarkable migration of the medial collateral ligament
Wang M, Nasiri A, VanHouten JN, Tommasini SM, Broadus AE. The remarkable migration of the medial collateral ligament. Journal Of Anatomy 2013, 224: 490-498. PMID: 24266550, PMCID: PMC3954274, DOI: 10.1111/joa.12145.Peer-Reviewed Original ResearchConceptsMedial collateral ligamentMigratory tractsCollateral ligamentParathyroid hormone-related proteinOsteoclastic bone resorptionHormone-related proteinCortical surfaceInsertions of tendonsInsertion siteBone resorptionLong bone growthPTHrP functionsOsteoclastic activityPeriosteal osteoclastsRegulatory moleculesOsteoblast activityGrowth spurtLong bonesOsteoclastsCortical boneLigamentRecent evidenceHistological techniquesBone surfaceTract
2012
Regulatory element copy number differences shape primate expression profiles
Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, Lee C. Regulatory element copy number differences shape primate expression profiles. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 12656-12661. PMID: 22797897, PMCID: PMC3411951, DOI: 10.1073/pnas.1205199109.Peer-Reviewed Original ResearchConceptsCopy number differencesExpression differencesExpression profilesLong intergenic noncoding RNAsCopy numberIntergenic noncoding RNAsGene expression differencesSignificant expression differencesGene expression profilesLevel of RNAUltraconserved elementsRegulatory regionsNoncoding RNAsSelective pressureDifferent genesRegulatory moleculesDevelopmental pathwaysPhenotypic differencesPrimate speciesGenesRNANumber differenceSpeciesExpressionPseudogenes
2010
Regulation of Hepatocyte Lipid Metabolism and Inflammatory Response by 25‐Hydroxycholesterol and 25‐Hydroxycholesterol‐3‐sulfate
Xu L, Bai Q, Rodriguez‐Agudo D, Hylemon PB, Heuman DM, Pandak WM, Ren S. Regulation of Hepatocyte Lipid Metabolism and Inflammatory Response by 25‐Hydroxycholesterol and 25‐Hydroxycholesterol‐3‐sulfate. Lipids 2010, 45: 821-832. PMID: 20700770, DOI: 10.1007/s11745-010-3451-y.Peer-Reviewed Original ResearchConceptsSREBP-1 protein levelsAcetyl-CoA carboxylase 1Fatty acid synthaseLipid metabolismPromoter-reporter geneProtein levelsImportant regulatory moleculesNFkappaB-dependent genesHepatocyte lipid metabolismLXR/SREBPTarget genesFAS mRNA levelsReporter geneRegulatory moleculesKey enzymeNFkappaB nuclear translocationAcid synthasePrimary rat hepatocytesIkappaBalpha levelsCholesterol biosynthesisNuclear translocationGenesLuciferase activityPotent regulatorNFkappaB activation
2008
25-Hydroxycholesterol-3-sulfate regulates macrophage lipid metabolism via the LXR/SREBP-1 signaling pathway
Ma Y, Xu L, Rodriguez-Agudo D, Li X, Heuman DM, Hylemon PB, Pandak WM, Ren S. 25-Hydroxycholesterol-3-sulfate regulates macrophage lipid metabolism via the LXR/SREBP-1 signaling pathway. AJP Endocrinology And Metabolism 2008, 295: e1369-e1379. PMID: 18854425, PMCID: PMC2603552, DOI: 10.1152/ajpendo.90555.2008.Peer-Reviewed Original ResearchMeSH KeywordsApoptosisCell ProliferationCells, CulturedCholesterol EstersDNA-Binding ProteinsDose-Response Relationship, DrugGene Expression RegulationHumansHydroxycholesterolsLipid MetabolismLipidsLiver X ReceptorsMacrophagesModels, BiologicalOrphan Nuclear ReceptorsReceptors, Cytoplasmic and NuclearSignal TransductionSterol Regulatory Element Binding Protein 1SulfatesConceptsLXR/SREBPFatty acid synthaseSREBP-1Lipid metabolismFatty acid synthetic pathwayKey transcriptional regulatorMacrophage lipid metabolismImportant regulatory moleculesTHP-1-derived macrophagesMature proteinTranscriptional regulatorsAcetyl-CoA carboxylase 1MRNA levelsFAS mRNA levelsKey proteinsGene expressionRegulatory moleculesHuman THP-1-derived macrophagesAcid synthaseSREBPLipid synthesisOxysterol sulfationLXR ligandsCarboxylase 1Cell proliferation
2006
Hormonal Regulation of Nuclear Permeability* ♦
O'Brien EM, Gomes DA, Sehgal S, Nathanson MH. Hormonal Regulation of Nuclear Permeability* ♦. Journal Of Biological Chemistry 2006, 282: 4210-4217. PMID: 17158097, PMCID: PMC2835336, DOI: 10.1074/jbc.m606300200.Peer-Reviewed Original ResearchConceptsProtein kinase CNuclear permeabilityGene transcriptionNuclear envelopeSecond messengerKinase CPhotoactivatable green fluorescent proteinCertain G protein-coupled receptorsG protein-coupled receptorsActivate protein kinase CCytosolic Ca2Protein-coupled receptorsGreen fluorescent proteinTargeting sequenceTranscription factorsRegulatory moleculesNuclear membraneFluorescent proteinPassage of moleculesIntranuclear eventsNovel mechanismShort-term regulationHormonal regulationTranscriptionRegulation
2005
Inducible Levels of Gelatinase B/Matrix Metalloproteinase-9 Gene Expression in Monocytes Are Associated with Marrow Cellularity in Myelodysplastic Syndrome (MDS).
Iwata M, Pillai M, Deeg H, Opdenakker G, Torok-Storb B. Inducible Levels of Gelatinase B/Matrix Metalloproteinase-9 Gene Expression in Monocytes Are Associated with Marrow Cellularity in Myelodysplastic Syndrome (MDS). Blood 2005, 106: 1391. DOI: 10.1182/blood.v106.11.1391.1391.Peer-Reviewed Original ResearchMMP-9 gene expressionGene expressionInducible gene expressionStromal cellsMatrix metalloproteinase-9 gene expressionProtein expressionCritical regulatory moleculesMMP-9 proteinMatrix metalloproteinase-9MMP-9 protein secretionMyeloid cellsHuman matrix metalloproteinase 9Mature myeloid cellsStromal cell functionRegulatory moleculesErythroid lineageStromal signalsHematopoietic regulationProtein secretionReal-time PCRMMP-9 geneInducible levelsHS-5 stromal cellsCell functionGenesMicroRNA expression profiles classify human cancers
Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR. MicroRNA expression profiles classify human cancers. Nature 2005, 435: 834-838. PMID: 15944708, DOI: 10.1038/nature03702.Peer-Reviewed Original ResearchConceptsCluster of microRNAsHuman cancersHuman chromosome 13Non-coding RNAsImportant transcription factorMicroRNA expression profileTranscription factorsExpression profilesGlobal downregulationRegulatory moleculesDifferentiation statePotential oncogeneMiR-17C-MycChromosome 13MicroRNAsHuman B-cell lymphomasMicroRNA profilesTumor formationVivo modelRNANucleotidesOncogeneDownregulationExpressionChapter 20 New Molecular Targets for the Treatment of Neuropathic Pain
Wood J, Waxman S. Chapter 20 New Molecular Targets for the Treatment of Neuropathic Pain. 2005, 339-355. DOI: 10.1016/b978-012738903-5/50021-7.Peer-Reviewed Original ResearchNeuropathic painPeripheral nervous system degenerationGene regulation studiesMolecular targetsAnimal modelsInteresting drug targetGene expressionRegulatory moleculesNew molecular targetsMolecular mechanismsEffective drug developmentNervous system degenerationTransgenic animalsUseful animal modelRegulation studiesDrug targetsGene ablationEfficacy of drugsConsequence of diseaseHerpes zosterImmunodeficiency syndromeRecent insightsPeripheral nervesSystem degenerationPain
2004
Molecular Regulation of Müllerian Development by Hox Genes
DU H, TAYLOR HS. Molecular Regulation of Müllerian Development by Hox Genes. Annals Of The New York Academy Of Sciences 2004, 1034: 152-165. PMID: 15731308, DOI: 10.1196/annals.1335.018.Peer-Reviewed Original ResearchConceptsHox genesMolecular regulationCommon genetic systemConserved transcription factorHox gene expressionAspects of morphogenesisNormal embryonic developmentEmbryonic patterningGenetic systemTranscription factorsEmbryonic developmentDevelopmental processesGene expressionRegulatory moleculesCell differentiationGenesReproductive tract developmentAdult functionHOXA10 geneTract developmentEmbryonic periodReproductive tractRegulationMullerian tractMetazoans
1998
Stromal Cells Are Critical Targets in the Regulation of Mammary Ductal Morphogenesis by Parathyroid Hormone-Related Protein
Dunbar M, Young P, Zhang J, McCaughern-Carucci J, Lanske B, Orloff J, Karaplis A, Cunha G, Wysolmerski J. Stromal Cells Are Critical Targets in the Regulation of Mammary Ductal Morphogenesis by Parathyroid Hormone-Related Protein. Developmental Biology 1998, 203: 75-89. PMID: 9806774, DOI: 10.1006/dbio.1998.9029.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding, CompetitiveCyclic AMPEmbryonic and Fetal DevelopmentEpitheliumFemaleGene Expression Regulation, DevelopmentalIn Situ HybridizationMammary Glands, AnimalMesodermMiceMice, Inbred StrainsMorphogenesisParathyroid Hormone-Related ProteinProteinsReceptors, Parathyroid HormoneRNA, MessengerStromal CellsConceptsPTH/PTHrP receptorPTHrP receptorStromal cellsMammary epithelial cell morphogenesisMammary developmentEpithelial cell morphogenesisMammary glandAmino-terminal PTHrPEpithelial cellsHormone-related proteinMammary ductal morphogenesisMammary epithelial cellsCritical targetMammary stromal cellsDuctal branching morphogenesisDevelopmental regulatory moleculeStromal cell functionMurine mammary glandCell morphogenesisMammary morphogenesisHumoral hypercalcemiaParathyroid hormoneTumor productsRegulatory moleculesMammary mesenchymeParathyroid hormone‐related protein is a developmental regulatory molecule
Philbrick W. Parathyroid hormone‐related protein is a developmental regulatory molecule. European Journal Of Oral Sciences 1998, 106: 32-37. PMID: 9541200, DOI: 10.1111/j.1600-0722.1998.tb02150.x.Peer-Reviewed Original ResearchConceptsDevelopmental regulatory moleculeOverexpression of PTHrPHormone-related proteinHormone-related peptideSingle G protein-coupled receptorG protein-coupled receptorsProtein-coupled receptorsPTHrP overexpressionHumoral hypercalcemiaTumor productsPTHrP functionsKnockout miceMammary epithelial cellsTransgenic miceRegulatory moleculesMiceEpithelial cellsPTH geneRegulatory effectsPTHrPN-terminal productType IMultiple tissuesConvincing evidenceOverexpression
1996
Parathyroid Hormone-Related Protein: From Hypercalcemia of Malignancy to Developmental Regulatory Molecule
Dunbar M, Wysolmerski J, Broadus A. Parathyroid Hormone-Related Protein: From Hypercalcemia of Malignancy to Developmental Regulatory Molecule. The American Journal Of The Medical Sciences 1996, 312: 287-294. DOI: 10.1016/s0002-9629(15)41844-0.Peer-Reviewed Original ResearchConceptsDevelopmental regulatory moleculeCommon metabolic complicationHypercalcemia of malignancyHormone-related proteinParathyroid hormone receptorTypes of cancerMetabolic complicationsHumoral hypercalcemiaParathyroid hormoneRegulatory moleculesParacrine fashionBiochemical manifestationsMalignant cellsHypercalcemiaFetal tissuesPTHrPHormone receptorsNormal biological functionsMalignancyMolecular evolutionHHMBiological functionsMolecular mechanismsComplicationsKidneyParathyroid Hormone-Related Protein: From Hypercalcemia of Malignancy to Developmental Regulatory Molecule
Dunbar M, Wysolmerski J, Broadus A. Parathyroid Hormone-Related Protein: From Hypercalcemia of Malignancy to Developmental Regulatory Molecule. The American Journal Of The Medical Sciences 1996, 312: 287-294. PMID: 8969618, DOI: 10.1097/00000441-199612000-00007.Peer-Reviewed Original ResearchConceptsDevelopmental regulatory moleculeCommon metabolic complicationHypercalcemia of malignancyHormone-related proteinParathyroid hormone receptorTypes of cancerMetabolic complicationsHumoral hypercalcemiaParathyroid hormoneRegulatory moleculesParacrine fashionBiochemical manifestationsMalignant cellsHypercalcemiaFetal tissuesPTHrPHormone receptorsNormal biological functionsMalignancyMolecular evolutionHHMBiological functionsMolecular mechanismsComplicationsKidney
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