2024
Cross-tissue organization of myeloid cells in scleroderma and related fibrotic diseases
Odell I. Cross-tissue organization of myeloid cells in scleroderma and related fibrotic diseases. Current Opinion In Rheumatology 2024, 36: 379-386. PMID: 39171604, PMCID: PMC11451931, DOI: 10.1097/bor.0000000000001047.Peer-Reviewed Original ResearchScRNA-seqIdiopathic pulmonary fibrosisMyeloid cell typesScRNA-seq studiesScRNA-seq analysisSingle-cell RNA sequencingCell typesDendritic cellsFc receptor genesScleroderma skinExpression of EREGLung fibrosis severityFibrotic diseasesMyeloid cell populationsRNA sequencingMultiple tissuesSignaling mechanismsReceptor geneMyeloid cellsSSc skinPulmonary fibrosisFibrosis severityLung fibrosisCardiac fibrosisSPP1CpG island turnover events predict evolutionary changes in enhancer activity
Kocher A, Dutrow E, Uebbing S, Yim K, Rosales Larios M, Baumgartner M, Nottoli T, Noonan J. CpG island turnover events predict evolutionary changes in enhancer activity. Genome Biology 2024, 25: 156. PMID: 38872220, PMCID: PMC11170920, DOI: 10.1186/s13059-024-03300-z.Peer-Reviewed Original ResearchConceptsHuman-gained enhancersCpG islandsFunction of transcriptional enhancersEvolution of biological diversityHuman CpG islandsGene regulatory changesInfluence enhancer activityCpG island contentHistone modification levelsEnhanced activitySpecies-specific activityTrait evolutionNucleotide substitutionsHistone modificationsTranscriptional enhancersMouse orthologEvolutionary changesTurnover eventsModification levelsMammalian speciesMultiple tissuesEmbryonic developmentMouse diencephalonHuman embryonic developmentSpecies
2023
More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome
Minteer C, Thrush K, Gonzalez J, Niimi P, Rozenblit M, Rozowsky J, Liu J, Frank M, McCabe T, Sehgal R, Higgins-Chen A, Hofstatter E, Pusztai L, Beckman K, Gerstein M, Levine M. More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome. Science Advances 2023, 9: eadf4163. PMID: 37467337, PMCID: PMC10355820, DOI: 10.1126/sciadv.adf4163.Peer-Reviewed Original ResearchConceptsStem cell divisionImmortalized human cellsTissue-specific cancer riskTumorigenic stateCell divisionDNA methylationEpigenetic changesAge-related accumulationHuman cellsMultiple tissuesSomatic mutationsClinical tissuesTissue differencesEpigenomeCellsTissueNormal tissuesMethylationMutationsReplicationNormal breast tissueSignaturesVitroAccumulationDivision
2022
Adipocyte plasticity in tissue regeneration, repair, and disease
Horsley V. Adipocyte plasticity in tissue regeneration, repair, and disease. Current Opinion In Genetics & Development 2022, 76: 101968. PMID: 35988318, DOI: 10.1016/j.gde.2022.101968.Peer-Reviewed Original ResearchConceptsMammalian tissue repairTissue repairEssential regulatorAdipocyte plasticityFunction of adipocytesCritical regulatorLipid-filled cellsMultiple tissuesTissue functionRegenerative medicineAdipocytesSkeletal muscleBioactive productsRegulatorMammary glandTherapeutic avenuesFibrotic lesionsEndocrine functionTissue regenerationPlasticityWound healingContractile fibroblastsTissueRepairTumorigenesisFrom COVID to fibrosis: lessons from single-cell analyses of the human lung
Justet A, Zhao AY, Kaminski N. From COVID to fibrosis: lessons from single-cell analyses of the human lung. Human Genomics 2022, 16: 20. PMID: 35698166, PMCID: PMC9189802, DOI: 10.1186/s40246-022-00393-0.Peer-Reviewed Original ResearchConceptsSingle-cell RNA-sequencing technologySingle-cell RNA sequencingRNA-sequencing technologyGene expression patternsMonocyte-derived macrophage populationSingle-cell analysisCell populationsLung diseaseCellular phenotypesRNA sequencingExpression patternsGene expressionAberrant repairMultiple tissuesPulmonary fibrosisMechanisms of diseaseFibrotic interstitial lung diseaseLife-threatening complicationsProgressive lung diseaseCOVID-19 pneumoniaInterstitial lung diseaseParenchymal lung diseaseAcute viral diseaseMacrophage populationsNovel cellTick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock
Minteer C, Morselli M, Meer M, Cao J, Higgins‐Chen A, Lang SM, Pellegrini M, Yan Q, Levine ME. Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock. Aging Cell 2022, 21: e13553. PMID: 35104377, PMCID: PMC8844113, DOI: 10.1111/acel.13553.Peer-Reviewed Original ResearchConceptsMouse embryonic fibroblastsDNA methylationEpigenetic agingImportant chromatin regulatorsPolycomb group (PcG) factorsAnti-aging interventionsChromatin regulatorsEmbryonic fibroblastsCellular senescenceTissue agingCellular agingEpigenetic clocksMultiple tissuesMouse tissuesCaloric restrictionMechanistic insightsAging changesKidney fibroblastsReduced representationTime pointsPhysiological agingMouse culturesSuch alterationsTick-TockTissue
2021
In vivo self-assembled small RNAs as a new generation of RNAi therapeutics
Fu Z, Zhang X, Zhou X, Ur-Rehman U, Yu M, Liang H, Guo H, Guo X, Kong Y, Su Y, Ye Y, Hu X, Cheng W, Wu J, Wang Y, Gu Y, Lu S, Wu D, Zen K, Li J, Yan C, Zhang C, Chen X. In vivo self-assembled small RNAs as a new generation of RNAi therapeutics. Cell Research 2021, 31: 631-648. PMID: 33782530, PMCID: PMC8169669, DOI: 10.1038/s41422-021-00491-z.Peer-Reviewed Original ResearchConceptsRNAi therapeuticsRNAi therapyVivo siRNA deliveryEGFR/KRASSiRNA deliveryVivo deliverySynthetic siRNAsLung cancerHost liverPotent target geneSecretory exosomesTherapeutic valueCircuit moduleArtificial vehiclesGenetic circuitsTherapyMultiple tissuesSiRNAsCritical targetPrinciple strategyTissueSpecific tissuesTherapeuticsDeliveryExosomesLandmarks of human embryonic development inscribed in somatic mutations
Bizzotto S, Dou Y, Ganz J, Doan R, Kwon M, Bohrson C, Kim S, Bae T, Abyzov A, Network† N, Park P, Walsh C. Landmarks of human embryonic development inscribed in somatic mutations. Science 2021, 371: 1249-1253. PMID: 33737485, PMCID: PMC8170505, DOI: 10.1126/science.abe1544.Peer-Reviewed Original ResearchConceptsSomatic single nucleotide variantsHuman embryonic developmentEmbryonic developmentEarly embryonic cell divisionsTransposase-accessible chromatin sequencingSingle cellsSingle-nucleus assayHigh-depth whole-genome sequencingSingle-nucleus RNA sequencingEmbryonic cell divisionCell lineage informationDistinct germ layersOnset of gastrulationSingle nucleotide variantsOrganismal developmentWhole-genome sequencingExtraembryonic tissuesCell divisionRNA sequencingProgenitor poolLineage informationGerm layersEarly progenitorsMultiple tissuesSequencingHOXA5 Participates in Brown Adipose Tissue and Epaxial Skeletal Muscle Patterning and in Brown Adipocyte Differentiation
Holzman MA, Ryckman A, Finkelstein TM, Landry-Truchon K, Schindler KA, Bergmann JM, Jeannotte L, Mansfield JH. HOXA5 Participates in Brown Adipose Tissue and Epaxial Skeletal Muscle Patterning and in Brown Adipocyte Differentiation. Frontiers In Cell And Developmental Biology 2021, 9: 632303. PMID: 33732701, PMCID: PMC7959767, DOI: 10.3389/fcell.2021.632303.Peer-Reviewed Original ResearchSkeletal muscle fateNull mutant embryosBAT developmentBrown adipocyte differentiationEmbryonic day 12.5Muscle fateBrown adipose tissueSkeletal muscleMutant embryosHOXA5 proteinLipid droplet morphologyForelimb levelEmbryonic developmentMolecular roleMuscle developmentLineage tracingMuscle patterningCommon progenitorDependent regulationMuscle phenotypeAdipocyte differentiationMultiple tissuesConditional deletionDay 12.5Progenitors
2020
Co-option of Neutrophil Fates by Tissue Environments
Ballesteros I, Rubio-Ponce A, Genua M, Lusito E, Kwok I, Fernández-Calvo G, Khoyratty TE, van Grinsven E, González-Hernández S, Nicolás-Ávila JÁ, Vicanolo T, Maccataio A, Benguría A, Li JL, Adrover JM, Aroca-Crevillen A, Quintana JA, Martín-Salamanca S, Mayo F, Ascher S, Barbiera G, Soehnlein O, Gunzer M, Ginhoux F, Sánchez-Cabo F, Nistal-Villán E, Schulz C, Dopazo A, Reinhardt C, Udalova IA, Ng LG, Ostuni R, Hidalgo A. Co-option of Neutrophil Fates by Tissue Environments. Cell 2020, 183: 1282-1297.e18. PMID: 33098771, DOI: 10.1016/j.cell.2020.10.003.Peer-Reviewed Original ResearchConceptsNeutrophil fateDepletion of neutrophilsHematopoietic recoveryVascular repairNeutrophil statesNeutrophil propertiesViral infectionNeutrophilsTarget tissuesHealthy tissueGenotoxic injuryEarly ageMultiple tissuesTissueTissue environmentPhysiological demandsInflammationHematopoietic homeostasisCXCR4LungNon-canonical functionsInjuryCancerInfectionLeukocytesAging is associated with increased TRB3, ER stress, and hepatic glucose production in the liver of rats
Gaspar R, Muñoz V, Nakandakari S, Vieira R, da Conceição L, de Oliveira F, Crisol B, da Silva A, Cintra D, de Moura L, Ropelle E, Zaghloul I, Mekary R, Pauli J. Aging is associated with increased TRB3, ER stress, and hepatic glucose production in the liver of rats. Experimental Gerontology 2020, 139: 111021. PMID: 32659331, DOI: 10.1016/j.exger.2020.111021.Peer-Reviewed Original ResearchConceptsER stressEukaryotic translation initiation factorProtein kinase RNA-like endoplasmic reticulum kinaseRNA-like endoplasmic reticulum kinaseTranslation initiation factorPhosphorylation of inositolStress response regulationEndoplasmic reticulum kinaseEndoplasmic reticulum stress pathwayMammalian homologDrosophila tribblesEndoplasmic reticulum stressInitiation factorsProtein contentTRB3Multiple tissuesStress pathwaysImmunoglobulin proteinEnzymes of gluconeogenesisReticulum stressHepatic glucose productionEnzyme 1Response regulationMolecular changesPyruvate challengeA mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm
Garvin M, Alvarez C, Miller JI, Prates ET, Walker AM, Amos BK, Mast AE, Justice A, Aronow B, Jacobson D. A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm. ELife 2020, 9: e59177. PMID: 32633718, PMCID: PMC7410499, DOI: 10.7554/elife.59177.Peer-Reviewed Original ResearchConceptsBronchoalveolar lavage fluidCOVID-19COVID-19 patientsBradykinin stormRAS receptorsLavage fluidVasopressor systemsBradykinin levelsVascular dilationVascular permeabilityBradykinin receptorsTherapeutic interventionsTherapeutic intervention pointNovel molecular mechanismDecreased expressionACE2Atypical patternsDisease mechanismsHypotensionAngiotensinMultiple tissuesCritical imbalanceReceptorsMolecular mechanismsVirusPolycystin 2 is increased in disease to protect against stress-induced cell death
Brill AL, Fischer TT, Walters JM, Marlier A, Sewanan LR, Wilson PC, Johnson EK, Moeckel G, Cantley LG, Campbell SG, Nerbonne JM, Chung HJ, Robert ME, Ehrlich BE. Polycystin 2 is increased in disease to protect against stress-induced cell death. Scientific Reports 2020, 10: 386. PMID: 31941974, PMCID: PMC6962458, DOI: 10.1038/s41598-019-57286-x.Peer-Reviewed Original ResearchConceptsPolycystin-2General cellular homeostasisCell deathStress-induced cell deathPathological cell deathAutosomal dominant polycystic kidney diseaseEndoplasmic reticulum membraneCellular homeostasisCellular stressPrimary ciliaUbiquitous expressionExpression changesCell stressReticulum membraneTransient receptor potential cation channelHuman diseasesMultiple tissuesEndogenous roleDominant polycystic kidney diseaseTissue typesCation channelsPolycystic kidney diseaseDifferent pathological statesMultiple diseasesKidney disease
2019
Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer
Ferreira MA, Gamazon ER, Al-Ejeh F, Aittomäki K, Andrulis IL, Anton-Culver H, Arason A, Arndt V, Aronson KJ, Arun BK, Asseryanis E, Azzollini J, Balmaña J, Barnes DR, Barrowdale D, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Białkowska K, Blomqvist C, Bogdanova NV, Bojesen SE, Bolla MK, Borg A, Brauch H, Brenner H, Broeks A, Burwinkel B, Caldés T, Caligo MA, Campa D, Campbell I, Canzian F, Carter J, Carter BD, Castelao JE, Chang-Claude J, Chanock SJ, Christiansen H, Chung WK, Claes KBM, Clarke CL, Couch F, Cox A, Cross S, Czene K, Daly M, de la Hoya M, Dennis J, Devilee P, Diez O, Dörk T, Dunning A, Dwek M, Eccles D, Ejlertsen B, Ellberg C, Engel C, Eriksson M, Fasching P, Fletcher O, Flyger H, Friedman E, Frost D, Gabrielson M, Gago-Dominguez M, Ganz P, Gapstur S, Garber J, García-Closas M, García-Sáenz J, Gaudet M, Giles G, Glendon G, Godwin A, Goldberg M, Goldgar D, González-Neira A, Greene M, Gronwald J, Guénel P, Haiman C, Hall P, Hamann U, He W, Heyworth J, Hogervorst F, Hollestelle A, Hoover R, Hopper J, Hulick P, Humphreys K, Imyanitov E, Isaacs C, Jakimovska M, Jakubowska A, James P, Janavicius R, Jankowitz R, John E, Johnson N, Joseph V, Karlan B, Khusnutdinova E, Kiiski J, Ko Y, Jones M, Konstantopoulou I, Kristensen V, Laitman Y, Lambrechts D, Lazaro C, Leslie G, Lester J, Lesueur F, Lindström S, Long J, Loud J, Lubiński J, Makalic E, Mannermaa A, Manoochehri M, Margolin S, Maurer T, Mavroudis D, McGuffog L, Meindl A, Menon U, Michailidou K, Miller A, Montagna M, Moreno F, Moserle L, Mulligan A, Nathanson K, Neuhausen S, Nevanlinna H, Nevelsteen I, Nielsen F, Nikitina-Zake L, Nussbaum R, Offit K, Olah E, Olopade O, Olsson H, Osorio A, Papp J, Park-Simon T, Parsons M, Pedersen I, Peixoto A, Peterlongo P, Pharoah P, Plaseska-Karanfilska D, Poppe B, Presneau N, Radice P, Rantala J, Rennert G, Risch H, Saloustros E, Sanden K, Sawyer E, Schmidt M, Schmutzler R, Sharma P, Shu X, Simard J, Singer C, Soucy P, Southey M, Spinelli J, Spurdle A, Stone J, Swerdlow A, Tapper W, Taylor J, Teixeira M, Terry M, Teulé A, Thomassen M, Thöne K, Thull D, Tischkowitz M, Toland A, Torres D, Truong T, Tung N, Vachon C, van Asperen C, van den Ouweland A, van Rensburg E, Vega A, Viel A, Wang Q, Wappenschmidt B, Weitzel J, Wendt C, Winqvist R, Yang X, Yannoukakos D, Ziogas A, Kraft P, Antoniou A, Zheng W, Easton D, Milne R, Beesley J, Chenevix-Trench G. Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer. Nature Communications 2019, 10: 1741. PMID: 30988301, PMCID: PMC6465407, DOI: 10.1038/s41467-018-08053-5.Peer-Reviewed Original ResearchConceptsExpression quantitative trait lociGenome-wide association studiesTarget genesMultiple expression quantitative trait lociBreast cancer risk variantsPrevious genome-wide association studyQuantitative trait lociGenome-wide associationGene-based testsBreast cancerBreast cancer susceptibility lociCancer susceptibility lociRisk-associated variantsImmune cellsTrait lociTranscriptome studiesRisk lociGene expressionAssociation studiesOverall breast cancer riskSusceptibility lociMultiple tissuesBreast cancer riskNegative breast cancerRisk variants
2018
High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development
Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J. High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. Cell Reports 2018, 23: 1581-1597. PMID: 29719267, PMCID: PMC5965702, DOI: 10.1016/j.celrep.2018.03.129.Peer-Reviewed Original ResearchConceptsRegulatory sequencesEmbryonic developmentEmbryonic craniofacial developmentEmbryonic craniofacial tissueGene regulatory programsNormal facial variationHuman embryonic developmentCraniofacial abnormalitiesEpigenomic annotationsEpigenomic atlasCraniofacial developmentIntronic sequencesCraniofacial tissuesRegulatory programsCraniofacial researchersMultiple tissuesCell typesSignificant enrichmentSystematic identificationCommon variantsCausal regionOrofacial cleftingEmbryonic periodSequenceCraniofacial complex
2017
Phagocytosis imprints heterogeneity in tissue-resident macrophages
A-Gonzalez N, Quintana JA, García-Silva S, Mazariegos M, de la Aleja A, Nicolás-Ávila JA, Walter W, Adrover JM, Crainiciuc G, Kuchroo VK, Rothlin CV, Peinado H, Castrillo A, Ricote M, Hidalgo A. Phagocytosis imprints heterogeneity in tissue-resident macrophages. Journal Of Experimental Medicine 2017, 214: 1281-1296. PMID: 28432199, PMCID: PMC5413334, DOI: 10.1084/jem.20161375.Peer-Reviewed Original Research
2016
Varied autopsy findings in five treated patients with Gaucher disease and parkinsonism include the absence of Gaucher cells
Monestime G, Borger DK, Kim J, Lopez G, Allgaeuer M, Jain D, Vortmeyer A, Wang HW, Sidransky E. Varied autopsy findings in five treated patients with Gaucher disease and parkinsonism include the absence of Gaucher cells. Molecular Genetics And Metabolism 2016, 118: 55-59. PMID: 26992326, DOI: 10.1016/j.ymgme.2016.02.008.Peer-Reviewed Original ResearchConceptsAutopsy findingsGaucher diseaseDose/durationEnzyme replacement therapySpleen statusPathological findingsReplacement therapyDisease burdenPathological studiesGaucher cellsPatientsHematological symptomsExtensive involvementTherapyParkinsonismDiseaseMultiple tissuesComplete absenceFindingsAutopsiesSymptomsPathologyBiomarkersCare
2014
Identification of Putative Fallopian Tube Stem Cells
Snegovskikh V, Mutlu L, Massasa E, Taylor HS. Identification of Putative Fallopian Tube Stem Cells. Reproductive Sciences 2014, 21: 1460-1464. PMID: 25305130, PMCID: PMC4231131, DOI: 10.1177/1933719114553448.Peer-Reviewed Original ResearchConceptsLabel-retaining cellsStem cellsStem/progenitor cell populationsStem cell nicheProgenitor cell populationsDAPI-stained nucleiStem cell reservePutative stem cellsCell nicheMultiple tissuesProgenitor cellsConfocal microscopyCell populationsImmunofluorescence studiesReproductive tractSection tissueCellsTissue regenerationOviductCell reserveTissueRegenerationNichePopulationNucleus
2013
The genomic landscape of cohesin-associated chromatin interactions
DeMare LE, Leng J, Cotney J, Reilly SK, Yin J, Sarro R, Noonan JP. The genomic landscape of cohesin-associated chromatin interactions. Genome Research 2013, 23: 1224-1234. PMID: 23704192, PMCID: PMC3730097, DOI: 10.1101/gr.156570.113.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesCCCTC-Binding FactorCell Cycle ProteinsChromatinChromatin ImmunoprecipitationChromosomal Proteins, Non-HistoneEnhancer Elements, GeneticGene Expression Regulation, DevelopmentalGenomeHistonesLimb BudsMiceMice, Inbred C57BLOrgan SpecificityPromoter Regions, GeneticProtein SubunitsRepressor ProteinsConceptsPaired-end tag sequencingGenome-wide scaleInsulator protein CTCFChromatin interaction analysisEnhancer-promoter interactionsEnhancer-promoter communicationEmbryonic stem cellsChromatin stateProtein CTCFChromatin interactionsTag sequencingDNA loopsRegulatory architectureMouse limbRegulatory outputMouse embryosGenomic landscapeMultiple tissuesCohesinStem cellsCTCFPromoterDemarcate regionsInteraction analysisGenomeTissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs
Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology 2013, 14: r5. PMID: 23347407, PMCID: PMC4053757, DOI: 10.1186/gb-2013-14-1-r5.Peer-Reviewed Original ResearchConceptsRb/E2FLin-35Target genesGenome-wide binding profilesGene expressionTissue-specific gene regulationLin-35 mutantsDistinct cell fatesSmall RNA pathwaysEffector target genesDirect target geneBinding profileGermline programHPL-2Chromatin associationH3K36 methylationRNA pathwaysCSR-1Germline transformationC. elegansGene regulationCell fateE2FDirect targetMultiple tissues
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