2024
A brief history of metabolic gradient theory
Sozen B. A brief history of metabolic gradient theory. Nature Reviews Genetics 2024, 26: 5-5. PMID: 39414955, DOI: 10.1038/s41576-024-00790-2.Peer-Reviewed Original ResearchSplicing the Difference: Harnessing the Complexity of the Transcriptome in Hematopoiesis
Maul-Newby H, Halene S. Splicing the Difference: Harnessing the Complexity of the Transcriptome in Hematopoiesis. Experimental Hematology 2024, 140: 104655. PMID: 39393608, PMCID: PMC11732257, DOI: 10.1016/j.exphem.2024.104655.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsAlternative splicingAlternative splicing eventsStem cell maintenanceSplicing factor mutationsHematopoietic stem cell maintenanceExpression of beta-globinField of stem cell researchSplicing eventsSplicing factorsFunctional blood cellsAberrant splicingStudy of hematopoiesisComplex regulationCell maintenanceSplicingCellular differentiationBeta-globinMyelodysplastic syndromeMyeloid malignanciesHematologic malignanciesStem cell researchCell sortingMutationsTranscriptomeAberrant expressionLarge Language Models and Genomics for Summarizing the Role of microRNA in Regulating mRNA Expression
Bhasuran B, Manoharan S, Iyyappan O, Murugesan G, Prabahar A, Raja K. Large Language Models and Genomics for Summarizing the Role of microRNA in Regulating mRNA Expression. Biomedicines 2024, 12: 1535. PMID: 39062108, PMCID: PMC11274411, DOI: 10.3390/biomedicines12071535.Peer-Reviewed Original ResearchMiRNA-mRNA interactionsRegulation of gene expressionMaintenance of cellular homeostasisMicroRNA (miRNA)-messenger RNAGenomic approachesRegulate mRNA expressionCellular homeostasisCellular differentiationGene expressionBiological processesPathogenesis of numerous diseasesMiRNA-mRNAPotential therapeutic targetGenomeDisease mechanismsNumerous diseasesLLM modelTherapeutic targetMetabolic conditionsMRNA expressionExpressionMicroRNAsRNAApoptosisLlamasA Novel Variant in the Cyto-Tail of SMO Gene Underlying Isolated Postaxial Polydactyly
Khan M, Abdullah, Khan H, Zaman A, Ahmed S, Iqbal P, Bilal M, Ullah K, Hasni M, Ullah I, Mis E, Lakhani S, Ahmad W. A Novel Variant in the Cyto-Tail of SMO Gene Underlying Isolated Postaxial Polydactyly. Molecular Syndromology 2024, 15: 443-449. DOI: 10.1159/000539279.Peer-Reviewed Original ResearchHomozygous missense variantWhole-exome sequencingHereditary limb malformationsSonic hedgehog pathwayAutosomal recessive mannerSequence variantsMissense variantsProtein foldingIsolated postaxial polydactylyExome sequencingSegregation analysisNovel variantsConsanguineous familySanger sequencingSMO genesExtra digitsHomology modelingCellular differentiationHedgehog pathwayRecessive mannerEmbryonic cellsPostaxial polydactylySequencePreaxial polydactylyVariants
2023
Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation
Meyer K, Lammers N, Bugaj L, Garcia H, Weiner O. Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation. Nature Communications 2023, 14: 6929. PMID: 37903793, PMCID: PMC10616176, DOI: 10.1038/s41467-023-42643-2.Peer-Reviewed Original ResearchConceptsCell fateYAP levelsControlling gene activityCell fate analysisPluripotency regulators Oct4Stem cell fateEffector genesTranscriptional regulationGene activationControl pluripotencyYAP activityNative dynamicsCellular differentiationRegulators Oct4Developmental decision-makingControl proliferationMolecular logicCell behaviorYAPFate analysisDynamic decoderOptogenetic controlOct4 expressionCellsFateEPIREGULIN creates a developmental niche for spatially organized human intestinal enteroids
Childs C, Holloway E, Sweet C, Tsai Y, Wu A, Vallie A, Eiken M, Capeling M, Zwick R, Palikuqi B, Trentesaux C, Wu J, Pellon-Cardenas O, Zhang C, Glass I, Loebel C, Yu Q, Camp J, Sexton J, Klein O, Verzi M, Spence J. EPIREGULIN creates a developmental niche for spatially organized human intestinal enteroids. JCI Insight 2023, 8: e165566. PMID: 36821371, PMCID: PMC10070114, DOI: 10.1172/jci.insight.165566.Peer-Reviewed Original ResearchConceptsHuman intestineHuman intestinal enteroidsEGF family membersIntestinal transcription factor CDX2Chromatin landscapeHuman cryptsTranscription factor CDX2Stem cell functionIntestinal enteroidsBiological discoveryCellular differentiationStandard culture conditionsNiche cuesEpithelial developmentEnteroidsEGFCrypt domainsOrgans in vitroPersonalized medicineCentral lumenCulture conditionsCell functionNiche in vitroSpatial organizationEGF in vitro
2022
Phylogenetic analysis of migration, differentiation, and class switching in B cells
Hoehn KB, Pybus OG, Kleinstein SH. Phylogenetic analysis of migration, differentiation, and class switching in B cells. PLOS Computational Biology 2022, 18: e1009885. PMID: 35468128, PMCID: PMC9037912, DOI: 10.1371/journal.pcbi.1009885.Peer-Reviewed Original ResearchMFN2 Deficiency Impairs Mitochondrial Functions and PPAR Pathway During Spermatogenesis and Meiosis in Mice
Wang T, Xiao Y, Hu Z, Gu J, Hua R, Hai Z, Chen X, Zhang J, Yu Z, Wu T, Yeung W, Liu K, Guo C. MFN2 Deficiency Impairs Mitochondrial Functions and PPAR Pathway During Spermatogenesis and Meiosis in Mice. Frontiers In Cell And Developmental Biology 2022, 10: 862506. PMID: 35493072, PMCID: PMC9046932, DOI: 10.3389/fcell.2022.862506.Peer-Reviewed Original ResearchConditional knock-outMitochondrial functionPPAR pathwayMale germ cellsRNA-seq analysisGenes up-regulatedGenes down-regulatedPathway enrichment analysisImpaired mitochondrial functionDynamic organellesMitochondrial dynamicsRNA-seqMitochondrial fusionDisrupted spermatogenesisMfn2 deficiencyGerm cellsPachytene stageOxidative phosphorylationSpermatogenesisTranscriptome profilingEnrichment analysisMfn2Cellular differentiationMolecular mechanismsLipid droplets
2021
Pancreatoblastomas and mixed and pure acinar cell carcinomas share epigenetic signatures distinct from other neoplasms of the pancreas
Benhamida J, Vyas M, Tanaka A, Wang L, Bahrami A, Ozcan K, Basturk O, Villafania L, Mata D, El Jabbour T, Selenica P, Roehrl M, Weigelt B, Reis-Filho J, Scaltriti M, Klimstra D. Pancreatoblastomas and mixed and pure acinar cell carcinomas share epigenetic signatures distinct from other neoplasms of the pancreas. Modern Pathology 2021, 35: 956-961. PMID: 34969956, PMCID: PMC10319432, DOI: 10.1038/s41379-021-00989-2.Peer-Reviewed Original ResearchConceptsGenome-wide array platformsAcinar cell carcinomaGenomic methylation signaturesPancreatic neuroendocrine tumorsSolid pseudopapillary neoplasmCell carcinomaNeuroendocrine tumorsMethylation profilesDuctal adenocarcinomaEpigenetic relationshipsMethylation signaturesEpigenetic signaturesEpigenetic levelAcinar differentiationCellular differentiationDistinct clustersPseudopapillary neoplasmArray platformCellular lineagesPancreatic ductal adenocarcinomaPancreatic tissue samplesNeuroendocrine lineNormal pancreatic tissuesDifferentiationAdenocarcinoma clusters
2020
Re-appraising the potential of naringin for natural, novel orthopedic biotherapies
Yu KE, Alder KD, Morris MT, Munger AM, Lee I, Cahill SV, Kwon HK, Back J, Lee FY. Re-appraising the potential of naringin for natural, novel orthopedic biotherapies. Therapeutic Advances In Musculoskeletal Disease 2020, 12: 1759720x20966135. PMID: 33343723, PMCID: PMC7727086, DOI: 10.1177/1759720x20966135.Peer-Reviewed Original ResearchBone morphogenetic proteinExtracellular signal-related kinase (ERK) pathwayRANK/RANKL interactionNumerous molecular pathwaysWnt/β-cateninBone resident cellsStem cell precursorsCellular differentiationKinase pathwayMorphogenetic proteinsPotential of naringinMolecular pathwaysΒ-cateninCellular mechanismsBone-preserving effectCommon musculoskeletal pathologiesEstrogen-sensitive tissuesOsteolytic bone diseaseCommon musculoskeletal conditionsMusculoskeletal developmentSystemic side effectsTreatment of osteoporosisDegenerative joint diseaseCell precursorsBone microenvironment
2018
Spatial distribution of marker gene activity in the mouse lung during alveolarization
Ljungberg MC, Sadi M, Wang Y, Aronow BJ, Xu Y, Kao RJ, Liu Y, Gaddis N, Ardini-Poleske ME, Umrod T, Ambalavanan N, Nicola T, Kaminski N, Ahangari F, Sontag R, Corley RA, Ansong C, Carson JP. Spatial distribution of marker gene activity in the mouse lung during alveolarization. Data In Brief 2018, 22: 365-372. PMID: 30596133, PMCID: PMC6307338, DOI: 10.1016/j.dib.2018.10.150.Peer-Reviewed Original ResearchRNA-seq expression profilesMarker gene activityGene expression patternsLung developmentLung Development ProgramGene activityRNA-seqMolecular atlasCellular differentiationDifferent genesExpression patternsExpression profilesNormal lung developmentMouse lungMRNA transcriptsMammalian lungMRNA probesProbe sequencesAbnormal lung developmentCurated CollectionGenesSpatial distributionTranscriptsE16.5E18.5
2017
A pathology atlas of the human cancer transcriptome
Uhlen M, Zhang C, Lee S, Sjöstedt E, Fagerberg L, Bidkhori G, Benfeitas R, Arif M, Liu Z, Edfors F, Sanli K, von Feilitzen K, Oksvold P, Lundberg E, Hober S, Nilsson P, Mattsson J, Schwenk J, Brunnström H, Glimelius B, Sjöblom T, Edqvist P, Djureinovic D, Micke P, Lindskog C, Mardinoglu A, Ponten F. A pathology atlas of the human cancer transcriptome. Science 2017, 357 PMID: 28818916, DOI: 10.1126/science.aan2507.Peer-Reviewed Original ResearchConceptsRegulation of genesGenome-scale metabolic modelProtein-coding genesGenome-wide transcriptomeHuman cancer transcriptomeGenome-wide explorationCellular differentiationIndividual proteinsCancer transcriptomeMolecular mechanismsMetabolic modelsCell growthGenesTranscriptomeOpen-access databaseSystem-level approachMajor cancer typesMetabolic heterogeneityPathology AtlasGeneral patternCancer typesRegulationShorter patient survivalIndividual tumorsProtein
2016
Notch1 and Notch2 receptors regulate mouse and human gastric antral epithelial cell homoeostasis
Gifford GB, Demitrack ES, Keeley TM, Tam A, La Cunza N, Dedhia PH, Spence JR, Simeone DM, Saotome I, Louvi A, Siebel CW, Samuelson LC. Notch1 and Notch2 receptors regulate mouse and human gastric antral epithelial cell homoeostasis. Gut 2016, 66: 1001. PMID: 26933171, PMCID: PMC5009003, DOI: 10.1136/gutjnl-2015-310811.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibodies, Monoclonal, HumanizedApoptosisCell DifferentiationCell ProliferationCells, CulturedDibenzazepinesEpithelial CellsFemaleGastric MucosaGene ExpressionHomeostasisHumansMaleMiceMice, Inbred C57BLMice, TransgenicOrganoidsPyloric AntrumReceptor, Notch1Receptor, Notch2Receptors, G-Protein-CoupledSignal TransductionStem CellsConceptsEpithelial cell homeostasisCell homeostasisNotch receptorsNotch inhibitor dibenzazepineGlobal Notch inhibitionStem cellsAntral stem cellsHuman antral glandsAnalysis of miceNotch pathway receptorsLgr5 stem cellsCellular differentiationNotch signalingNotch2 receptorMolecular approachesPathway receptorsNotch pathway inhibitionHuman organoidsEpithelial cell proliferationNotch inhibitionInhibition of Notch1Notch inhibitorsOrganoid growthCell proliferationNotch2
2015
Mitochondrial ROS Signaling in Organismal Homeostasis
Shadel GS, Horvath TL. Mitochondrial ROS Signaling in Organismal Homeostasis. Cell 2015, 163: 560-569. PMID: 26496603, PMCID: PMC4634671, DOI: 10.1016/j.cell.2015.10.001.Peer-Reviewed Original ResearchConceptsReactive oxygen speciesOrganismal homeostasisMitochondrial ROS signalingMitochondrial reactive oxygen speciesAdaptive physiological responsesROS signalingCellular differentiationMitochondrial oxygen consumptionOxidative phosphorylationPhysiological responsesOxygen speciesCentral roleHomeostasisEukaryotesOrganic fuel moleculesPhosphorylationMitochondriaMoleculesSignalingSpeciesATPDifferentiationPathwayGreater understandingRoleIntegrative analysis of 111 reference human epigenomes
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller M, Amin V, Whitaker J, Schultz M, Ward L, Sarkar A, Quon G, Sandstrom R, Eaton M, Wu Y, Pfenning A, Wang X, ClaussnitzerYaping Liu M, Coarfa C, Alan Harris R, Shoresh N, Epstein C, Gjoneska E, Leung D, Xie W, David Hawkins R, Lister R, Hong C, Gascard P, Mungall A, Moore R, Chuah E, Tam A, Canfield T, Scott Hansen R, Kaul R, Sabo P, Bansal M, Carles A, Dixon J, Farh K, Feizi S, Karlic R, Kim A, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer T, Neph S, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari R, Siebenthall K, Sinnott-Armstrong N, Stevens M, Thurman R, Wu J, Zhang B, Zhou X, Abdennur N, Adli M, Akerman M, Barrera L, Antosiewicz-Bourget J, Ballinger T, Barnes M, Bates D, Bell R, Bennett D, Bianco K, Bock C, Boyle P, Brinchmann J, Caballero-Campo P, Camahort R, Carrasco-Alfonso M, Charnecki T, Chen H, Chen Z, Cheng J, Cho S, Chu A, Chung W, Cowan C, Athena Deng Q, Deshpande V, Diegel M, Ding B, Durham T, Echipare L, Edsall L, Flowers D, Genbacev-Krtolica O, Gifford C, Gillespie S, Giste E, Glass I, Gnirke A, Gormley M, Gu H, Gu J, Hafler D, Hangauer M, Hariharan M, Hatan M, Haugen E, He Y, Heimfeld S, Herlofsen S, Hou Z, Humbert R, Issner R, Jackson A, Jia H, Jiang P, Johnson A, Kadlecek T, Kamoh B, Kapidzic M, Kent J, Kim A, Kleinewietfeld M, Klugman S, Krishnan J, Kuan S, Kutyavin T, Lee A, Lee K, Li J, Li N, Li Y, Ligon K, Lin S, Lin Y, Liu J, Liu Y, Luckey C, Ma Y, Maire C, Marson A, Mattick J, Mayo M, McMaster M, Metsky H, Mikkelsen T, Miller D, Miri M, Mukame E, Nagarajan R, Neri F, Nery J, Nguyen T, O’Geen H, Paithankar S, Papayannopoulou T, Pelizzola M, Plettner P, Propson N, Raghuraman S, Raney B, Raubitschek A, Reynolds A, Richards H, Riehle K, Rinaudo P, Robinson J, Rockweiler N, Rosen E, Rynes E, Schein J, Sears R, Sejnowski T, Shafer A, Shen L, Shoemaker R, Sigaroudinia M, Slukvin I, Stehling-Sun S, Stewart R, Subramanian S, Suknuntha K, Swanson S, Tian S, Tilden H, Tsai L, Urich M, Vaughn I, Vierstra J, Vong S, Wagner U, Wang H, Wang T, Wang Y, Weiss A, Whitton H, Wildberg A, Witt H, Won K, Xie M, Xing X, Xu I, Xuan Z, Ye Z, Yen C, Yu P, Zhang X, Zhang X, Zhao J, Zhou Y, Zhu J, Zhu Y, Ziegler S, Beaudet A, Boyer L, De Jager P, Farnham P, Fisher S, Haussler D, Jones S, Li W, Marra M, McManus M, Sunyaev S, Thomson J, Tlsty T, Tsai L, Wang W, Waterland R, Zhang M, Chadwick L, Bernstein B, Costello J, Ecker J, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos J, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature 2015, 518: 317-330. PMID: 25693563, PMCID: PMC4530010, DOI: 10.1038/nature14248.Peer-Reviewed Original ResearchConceptsHuman epigenomeHuman diseasesIntegrative analysisReference human genome sequenceDiverse human traitsRoadmap Epigenomics ConsortiumHuman genome sequenceHistone modification patternsRelevant cell typesEpigenomic informationEpigenomic marksDNA accessibilityRegulatory modulesGene regulationEpigenomic studiesGenome sequenceDNA methylationGenetic variationRegulatory elementsCellular differentiationMolecular basisModification patternsEpigenomeHuman traitsCell types
2013
G Protein‐Coupled Receptors and Adipogenesis: A Focus on Adenosine Receptors
Eisenstein A, Ravid K. G Protein‐Coupled Receptors and Adipogenesis: A Focus on Adenosine Receptors. Journal Of Cellular Physiology 2013, 229: 414-421. PMID: 24114647, PMCID: PMC4362544, DOI: 10.1002/jcp.24473.Peer-Reviewed Original ResearchConceptsG protein-coupled receptorsAdenosine receptorsExtracellular signalsAdenosine signalingObesity epidemicMetabolic consequencesDevelopment of therapeuticsBlood flowDownstream messengersReceptorsTranscriptional eventsAdipose tissueMature adipocytesAdipocyte differentiationCellular differentiationMetabolic homeostasisAdenosineCoupled receptorsAdipocytesPhysiological outcomesDifferentiation processExcess nutrientsRegulation functionAdipogenesisDifferentiation
2012
The Nuclear Receptor PPARs as Important Regulators of T-Cell Functions and Autoimmune Diseases
Choi JM, Bothwell AL. The Nuclear Receptor PPARs as Important Regulators of T-Cell Functions and Autoimmune Diseases. Molecules And Cells 2012, 33: 217-222. PMID: 22382683, PMCID: PMC3887706, DOI: 10.1007/s10059-012-2297-y.Peer-Reviewed Original ResearchConceptsPeroxisome proliferator-activated receptorIndependent regulatory mechanismsImportant regulatory roleNuclear receptor proteinsT helper cell differentiationTranscription factorsCellular differentiationNuclear receptor peroxisome proliferator-activated receptorGene expressionRegulatory mechanismsDiverse rolesHelper cell differentiationT cell survivalPPARβ/δCell differentiationRegulatory roleImportant regulatorReceptor proteinNuclear receptorsT cell activationProliferator-activated receptorAutoimmune diseasesLigand treatmentProteinSynthetic ligands
2011
Golgi during Development
Zhong W. Golgi during Development. Cold Spring Harbor Perspectives In Biology 2011, 3: a005363. PMID: 21768608, PMCID: PMC3181030, DOI: 10.1101/cshperspect.a005363.Peer-Reviewed Original ResearchConceptsPlasma membrane componentsSecretory traffickingSecretory pathwayProcessing proteinsCellular differentiationDevelopmental pathwaysProtein cleavageMembrane componentsGolgiAspects of developmentSpatial organizationMajor compartmentsPathwayFinal destinationInvertebratesVertebratesMorphogenesisOrganellesTraffickingGlycosylationProteinSpecific effectsDifferentiationCompartmentsCleavage
2010
3-Phosphoglycerate dehydrogenase expression is regulated by HOXA10 in murine endometrium and human endometrial cells
Du H, Vitiello D, Sarno JL, Taylor HS. 3-Phosphoglycerate dehydrogenase expression is regulated by HOXA10 in murine endometrium and human endometrial cells. Reproduction 2010, 139: 237-245. PMID: 19778996, PMCID: PMC3107855, DOI: 10.1530/rep-08-0376.Peer-Reviewed Original ResearchMeSH KeywordsAdultAnimalsCell LineCells, CulturedEndometriumEpithelial CellsFemaleGene Expression Regulation, EnzymologicHomeobox A10 ProteinsHomeodomain ProteinsHumansImmunohistochemistryMenstrual CycleMiceOligonucleotide Array Sequence AnalysisPhosphoglycerate DehydrogenasePregnancyRNA, MessengerRNA, Small InterferingStromal CellsTransfectionConceptsSerine biosynthesisRegulatory relationshipsHOXA10 regulationProtein synthesisPHGDH expressionReal-time PCR resultsStromal cellsCellular differentiationTarget genesHuman endometrial cellsPHGDHMRNA expressionHuman endometrial stromal cellsDe novoWestern blot resultsDehydrogenase expressionBiosynthesisHOXA10Epithelial cellsHOXA10 siRNARegulationExpressionEndometrial stromal cellsHOXA10 expressionBlot results
2009
Activated Wnt/ß-catenin signaling in melanoma is associated with decreased proliferation in patient tumors and a murine melanoma model
Chien AJ, Moore EC, Lonsdorf AS, Kulikauskas RM, Rothberg BG, Berger AJ, Major MB, Hwang ST, Rimm DL, Moon RT. Activated Wnt/ß-catenin signaling in melanoma is associated with decreased proliferation in patient tumors and a murine melanoma model. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 1193-1198. PMID: 19144919, PMCID: PMC2626610, DOI: 10.1073/pnas.0811902106.Peer-Reviewed Original ResearchConceptsBeta-catenin signalingNormal melanocyte developmentTranscriptional profiling revealsWnt/beta-catenin signalingMelanoma cellsUp-regulates genesWnt/ß-cateninMelanoma progressionSmall molecule activatorsRole of WntMelanocyte developmentCell fateTranscriptional changesB16 murine melanoma cellsCellular differentiationProfiling revealsMelanocyte differentiationMelanoma cell linesMurine melanoma cellsß-cateninHuman melanoma cell linesWnt3aMurine melanoma modelCell linesReduced expression
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