2025
Cell type and cell signalling innovations underlying mammalian pregnancy
Stadtmauer D, Basanta S, Maziarz J, Cole A, Dagdas G, Smith G, van Breukelen F, Pavličev M, Wagner G. Cell type and cell signalling innovations underlying mammalian pregnancy. Nature Ecology & Evolution 2025, 9: 1469-1486. PMID: 40596730, PMCID: PMC12328210, DOI: 10.1038/s41559-025-02748-x.Peer-Reviewed Original ResearchConceptsCell typesDecidual cellsSingle-cell transcriptomicsLigand-receptor pairsMammalian ancestorMammal diversitySignaling networksFetal-maternal interfaceMaternal decidual cellsCell signalingMaternal cell typesExclusive expressionRace dynamicsEvolutionary puzzleMammalian placentationTranscriptomic signaturesFetal trophoblastHuman deciduaMaternal stromaMammalian pregnancyInvasive trophoblastCo-evolutionHaemochorial placentationTenrecsSignal innovationTranscriptome signature in the blood of neuromyelitis optica spectrum disorder under steroid tapering
Yamamura R, Kinoshita M, Yasumizu Y, Yata T, Kihara K, Motooka D, Shiraishi N, Sugiyama Y, Beppu S, Murata H, Koizumi N, Sano I, Koda T, Okuno T, Mochizuki H. Transcriptome signature in the blood of neuromyelitis optica spectrum disorder under steroid tapering. Frontiers In Immunology 2025, 16: 1508977. PMID: 39963140, PMCID: PMC11830620, DOI: 10.3389/fimmu.2025.1508977.Peer-Reviewed Original ResearchConceptsNeuromyelitis optica spectrum disorderPeripheral blood mononuclear cellsNeuromyelitis optica spectrum disorder patientsSteroid taperIL-10Steroid dosagePeripheral blood transcriptomic signatureDecreased expressionInterferon SignalingTransform treatment strategiesIndicator of disease activityNon-relapsing patientsAnti-AQP4 antibodyDisease activity biomarkersTranscriptomic signaturesBlood mononuclear cellsAdvent of biologicsBlood transcriptomic signaturesAnti-inflammatory pathwayIL-10 signalingRelapsed patientsImmune signaturesSteroid reductionDisease activityActivation biomarkers
2024
Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells
Kim S, Seo S, Stein-O’Brien G, Jaishankar A, Ogawa K, Micali N, Luria V, Karger A, Wang Y, Kim H, Hyde T, Kleinman J, Voss T, Fertig E, Shin J, Bürli R, Cross A, Brandon N, Weinberger D, Chenoweth J, Hoeppner D, Sestan N, Colantuoni C, McKay R. Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells. Stem Cell Reports 2024, 19: 1336-1350. PMID: 39151428, PMCID: PMC11411333, DOI: 10.1016/j.stemcr.2024.07.004.Peer-Reviewed Original ResearchHuman pluripotent stem cellsEarly mammalian developmentConsequences of variationPluripotent stem cellsTranscriptomic variationMammalian developmentTranscriptomic patternsTranscriptomic traitsReplicate linesMesendodermal lineagesNeural fateAdult tissuesLineagesHindbrain fateTranscriptional signatureTranscriptomic signaturesEarly eventLineage biasHuman pluripotent stem cell linesStem cellsFateIndividual variationAnterior to posterior structuresEpigenetic originCellsLung Transcriptomics Links Emphysema to Barrier Dysfunction and Macrophage Subpopulations.
Lu R, Gregory A, Suryadevara R, Xu Z, Jain D, Morrow J, Hobbs B, Yun J, Lichtblau N, Chase R, Curtis J, Sauler M, Bartholmai B, Silverman E, Hersh C, Castaldi P, Boueiz A. Lung Transcriptomics Links Emphysema to Barrier Dysfunction and Macrophage Subpopulations. American Journal Of Respiratory And Critical Care Medicine 2024, 211: 75-90. PMID: 38935868, PMCID: PMC11755365, DOI: 10.1164/rccm.202305-0793oc.Peer-Reviewed Original ResearchRNA sequencing dataAlternative splicingExpressed genesFunctional pathwaysCell typesBiological pathwaysGene expressionTranscriptomic featuresGene regulatory processesDysregulated pathwaysSingle-cell RNA sequencing dataRNA-seq analysisLung cell typesLung Tissue Research ConsortiumTranscriptome analysisGenesCell-typeDifferential expressionMultiple lung cell typesPathway activationTranscriptomic signaturesPathway dysregulationRegulatory processesSplicingPathway
2023
Clonally expanded memory CD8+ T cells accumulate in atherosclerotic plaques and are pro-atherogenic in aged mice
Tyrrell D, Wragg K, Chen J, Wang H, Song J, Blin M, Bolding C, Vardaman D, Giles K, Tidwell H, Ali M, Janappareddi A, Wood S, Goldstein D. Clonally expanded memory CD8+ T cells accumulate in atherosclerotic plaques and are pro-atherogenic in aged mice. Nature Aging 2023, 3: 1576-1590. PMID: 37996758, PMCID: PMC11924142, DOI: 10.1038/s43587-023-00515-w.Peer-Reviewed Original ResearchConceptsT cellsMemory CD8Aged miceAtherosclerotic plaquesDepletion of CD8Effector memory subsetsStrong risk factorT cell activationEnhanced atherosclerosisSplenic CD8Adoptive transferDonor miceMemory subsetsRecipient miceRisk factorsCD8Therapeutic targetCell activationAtherosclerosisSingle-cell RNA sequencingMiceTranscriptomic signaturesAtherogenesisPlaquesRNA sequencingCharacterizing the Spatiotemporal Transcriptomic Response of the Right Ventricle to Acute Pressure Overload
Kheyfets V, Kumar S, Heerdt P, Ichimura K, Brown R, Lucero M, Essafri I, Williams S, Stenmark K, Spiekerkoetter E. Characterizing the Spatiotemporal Transcriptomic Response of the Right Ventricle to Acute Pressure Overload. International Journal Of Molecular Sciences 2023, 24: 9746. PMID: 37298696, PMCID: PMC10253685, DOI: 10.3390/ijms24119746.Peer-Reviewed Original ResearchConceptsPressure overloadChronic RV pressure overloadExperimental pulmonary hypertension modelsRV pressure overloadTime pointsPulmonary hypertension modelRV outflow tractTranscriptomic signaturesAcute pressure overloadRight ventricular tissueDifferent time pointsPulmonary embolismHypertension modelSevere PEAcute increaseInitial insultOutflow tractRight ventricleRV apexVentricular tissueControl tissuesRatsSeverityWeeksTissueMulti-omics profiling of papillary thyroid microcarcinoma reveals different somatic mutations and a unique transcriptomic signature
Li Q, Feng T, Zhu T, Zhang W, Qian Y, Zhang H, Zheng X, Li D, Yun X, Zhao J, Li Y, Yu H, Gao M, Qian B. Multi-omics profiling of papillary thyroid microcarcinoma reveals different somatic mutations and a unique transcriptomic signature. Journal Of Translational Medicine 2023, 21: 206. PMID: 36941725, PMCID: PMC10026500, DOI: 10.1186/s12967-023-04045-2.Peer-Reviewed Original ResearchConceptsTCGA patientsPositive thyroglobulin antibodiesPapillary thyroid microcarcinomaNew therapeutic hypothesesUnique transcriptomic signaturesImmune-related genesWhole-exome sequencingImmune interventionPeroxidase antibodiesThyroglobulin antibodiesEtiology of cancerRET fusionsThyroid microcarcinomaTCGA cohortBRAF mutationsPatientsDifferent somatic mutationsMulti-omics profilingLarger studyConclusionsOur findingsResultsIn additionExome sequencingTherapeutic hypothesesTranscriptomic signaturesMolecular landscape
2022
Identification of monocyte-related transcriptomic signature of peripheral blood mononuclear cells in type 1 diabetes
Yin M, Zhang Y, Huang J, Li X, Yu H, Li X. Identification of monocyte-related transcriptomic signature of peripheral blood mononuclear cells in type 1 diabetes. Chinese Medical Journal 2022, 135: 2608-2610. PMID: 36583923, PMCID: PMC9943828, DOI: 10.1097/cm9.0000000000002142.Peer-Reviewed Original ResearchTregs in visceral adipose tissue up-regulate circadian-clock expression to promote fitness and enforce a diurnal rhythm of lipolysis
Xiao T, Langston P, Muñoz-Rojas A, Jayewickreme T, Lazar M, Benoist C, Mathis D. Tregs in visceral adipose tissue up-regulate circadian-clock expression to promote fitness and enforce a diurnal rhythm of lipolysis. Science Immunology 2022, 7: eabl7641. PMID: 36179011, PMCID: PMC9769829, DOI: 10.1126/sciimmunol.abl7641.Peer-Reviewed Original ResearchConceptsVisceral adipose tissueBmal1 deficiencyVisceral adipose tissue inflammationWeeks of high-fat diet feedingRegulatory T cellsAdipose tissueCircadian clock expressionTranscriptomic signaturesCore clock componentsLoss of fitnessHigh-fat diet feedingCore clock genesSuppression of lipolysisDiurnal rhythmNonlymphoid organsT cellsAdipose tissue lipolysisDiurnal regulationCircadian programTissue homeostasisAdipocyte lipolysisConstitutive activationDiet feedingUp-regulatedMetabolic state
2021
A Peripheral Blood Transcriptomic Signature Predicts the Progression of Chronic Kidney Damage Post Transplant
Zhang W, Yi Z, Wei C, Xi C, Huang W, Sun Z, Farouk S, Cravedi P, Menon M, Colvin R, O'Connell P, Murphy B. A Peripheral Blood Transcriptomic Signature Predicts the Progression of Chronic Kidney Damage Post Transplant. Journal Of The American Society Of Nephrology 2021, 32: 627-627. DOI: 10.1681/asn.20213210s1627a.Peer-Reviewed Original ResearchAn mRNA assay system demonstrates proteasomal-specific degradation contributes to cardiomyopathic phospholamban null mutation
Rohner E, Witman N, Sohlmer J, De Genst E, Louch W, Sahara M, Chien K. An mRNA assay system demonstrates proteasomal-specific degradation contributes to cardiomyopathic phospholamban null mutation. Molecular Medicine 2021, 27: 102. PMID: 34496741, PMCID: PMC8425124, DOI: 10.1186/s10020-021-00362-8.Peer-Reviewed Original ResearchConceptsNull mutationMolecular pathwaysProtein analysis toolsBulk RNA sequencingRNA sequencing analysisWild-type reporterDetailed molecular pathwaysDistinct transcriptomic signaturesTranscriptional profilingRNA sequencingProteasomal pathwayHuman embryonic stem cell-derived cardiomyocytesEmbryonic stem cell-derived cardiomyocytesProtein expression levelsProteasomal inhibitionChemical inhibitorsDetectable proteinTranscriptomic signaturesSequencing analysisDegradation contributesMRNA constructsStem cell-derived cardiomyocytesPLN proteinExpression levelsDegradation pathway
2020
IL-33-PU.1 Transcriptome Reprogramming Drives Functional State Transition and Clearance Activity of Microglia in Alzheimer’s Disease
Lau S, Chen C, Fu W, Qu J, Cheung T, Fu A, Ip N. IL-33-PU.1 Transcriptome Reprogramming Drives Functional State Transition and Clearance Activity of Microglia in Alzheimer’s Disease. Cell Reports 2020, 31: 107530. PMID: 32320664, DOI: 10.1016/j.celrep.2020.107530.Peer-Reviewed Original ResearchConceptsTranscriptome profilingAlzheimer's diseaseTranscription factor bindingSignature genesMicroglial state transitionChromatin accessibilityFactor bindingTranscriptome reprogrammingClearance activityBeta-amyloidTranscriptomeAD pathologyMicroglial transcriptomeTranscriptional pathwaysMajor histocompatibility complex classMicroglial subpopulationsTranscriptomic signaturesEnhanced phagocytic activityMicroglial functionHistocompatibility complex classPhagocytic activityAlzheimerInterleukin (IL)-33Activation of microgliaChromatinDissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs
Burke EE, Chenoweth JG, Shin JH, Collado-Torres L, Kim SK, Micali N, Wang Y, Colantuoni C, Straub RE, Hoeppner DJ, Chen HY, Sellers A, Shibbani K, Hamersky GR, Diaz Bustamante M, Phan BN, Ulrich WS, Valencia C, Jaishankar A, Price AJ, Rajpurohit A, Semick SA, Bürli RW, Barrow JC, Hiler DJ, Page SC, Martinowich K, Hyde TM, Kleinman JE, Berman KF, Apud JA, Cross AJ, Brandon NJ, Weinberger DR, Maher BJ, McKay RDG, Jaffe AE. Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs. Nature Communications 2020, 11: 462. PMID: 31974374, PMCID: PMC6978526, DOI: 10.1038/s41467-019-14266-z.Peer-Reviewed Original ResearchConceptsHuman induced pluripotent stem cellsNeural precursor cellsExpression dataSingle-cell expression dataNeuronal differentiationSequencing read alignmentsInduced pluripotent stem cellsEarly neuronal differentiationPluripotent stem cellsTranscriptomic resourcesIPSC donorNeuronal culturesSubclonal linesNeural differentiationTranscriptomic signaturesHuman neural precursor cellsNeuronal cellsStem cellsPrecursor cellsCell sortingGlobal patternsPowerful modelSubset of neuronsRead alignmentDifferentiation
2019
Phenotypic characterisation of regulatory T cells in dogs reveals signature transcripts conserved in humans and mice
Wu Y, Chang Y, Stell A, Priestnall S, Sharma E, Goulart M, Gribben J, Xia D, Garden O. Phenotypic characterisation of regulatory T cells in dogs reveals signature transcripts conserved in humans and mice. Scientific Reports 2019, 9: 13478. PMID: 31530890, PMCID: PMC6748983, DOI: 10.1038/s41598-019-50065-8.Peer-Reviewed Original ResearchConceptsRegulatory T cellsT cellsT cells isolated ex vivoSubsets of TregsTranscriptomic signaturesAvailability of mAbsHealthy dogsTreg functionMurine TregsVeterinary speciesTregsRegulatory phenotypeNeoplastic disordersSurface antigensImmune systemMonoclonal antibodiesDogsCross-species comparisonsMiceTranscriptomic abnormalities in peripheral blood in bipolar disorder, and discrimination of the major psychoses
Hess JL, Tylee DS, Barve R, de Jong S, Ophoff RA, Kumarasinghe N, Tooney P, Schall U, Gardiner E, Beveridge NJ, Scott RJ, Yasawardene S, Perera A, Mendis J, Carr V, Kelly B, Cairns M, Unit T, Tsuang MT, Glatt SJ. Transcriptomic abnormalities in peripheral blood in bipolar disorder, and discrimination of the major psychoses. Schizophrenia Research 2019, 217: 124-135. PMID: 31391148, PMCID: PMC6997041, DOI: 10.1016/j.schres.2019.07.036.Peer-Reviewed Original ResearchConceptsGene modulesSZ casesGene co-expression network analysisCo-expression network analysisGene expression profilesGene expression alterationsChromatin regulationChromatin remodelingNineteen genesGene networksTranscriptomic abnormalitiesDisorder-specific changesGene expressionExpression profilesBiological processesImmune signalingExpression alterationsTranscriptomic signaturesGenesReactive oxygenUnaffected comparison subjectsMajor psychosesOxidative stressBD casesApoptosisPhenotypic and transcriptomic characterization of canine myeloid-derived suppressor cells
Goulart M, Hlavaty S, Chang Y, Polton G, Stell A, Perry J, Wu Y, Sharma E, Broxholme J, Lee A, Szladovits B, Turmaine M, Gribben J, Xia D, Garden O. Phenotypic and transcriptomic characterization of canine myeloid-derived suppressor cells. Scientific Reports 2019, 9: 3574. PMID: 30837603, PMCID: PMC6400936, DOI: 10.1038/s41598-019-40285-3.Peer-Reviewed Original ResearchConceptsMyeloid-derived suppressor cellsPMN-MDSCsM-MDSCsSuppressor cellsMyeloid-derived suppressor cell subsetsMyeloid derived suppressor cell functionPeripheral blood frequenciesPolymorphonuclear (PMN)-MDSCsMonocytic (M)-MDSCsPhenotypically distinct subsetsHuman tumor developmentCanine oncology patientsTumor progressionImmune evasionTumor developmentContext of cancerOncology patientsTranscriptomic signaturesGene expression patternsPathological statesCancerExpression patternsCellsMetastasisSubsets
2018
Expression-based drug screening of neural progenitor cells from individuals with schizophrenia
Readhead B, Hartley BJ, Eastwood BJ, Collier DA, Evans D, Farias R, He C, Hoffman G, Sklar P, Dudley JT, Schadt EE, Savić R, Brennand KJ. Expression-based drug screening of neural progenitor cells from individuals with schizophrenia. Nature Communications 2018, 9: 4412. PMID: 30356048, PMCID: PMC6200740, DOI: 10.1038/s41467-018-06515-4.Peer-Reviewed Original ResearchConceptsNeural progenitor cellsHiPSC neural progenitor cellsCell typesCancer cell linesGene expression differencesProgenitor cellsDisease-associated genesPatient-specific platformPluripotent stem cellsTranscriptional responseExpression differencesTranscriptional signatureTranscriptomic signaturesStem cellsCell linesDependent mannerDrug discoveryDrug screeningCellsNeuropsychiatric disordersSchizophreniaBest treatmentDrugsDiscoveryGenesImpaired type I interferon regulation in the blood transcriptome of recurrent asthma exacerbations
Gomez JL, Diaz MP, Nino G, Britto CJ. Impaired type I interferon regulation in the blood transcriptome of recurrent asthma exacerbations. BMC Medical Genomics 2018, 11: 21. PMID: 29486764, PMCID: PMC5830339, DOI: 10.1186/s12920-018-0340-3.Peer-Reviewed Original ResearchConceptsPeripheral blood mononuclear cellsAsthma exacerbationsInterferon-stimulated genesRespiratory infectionsIL-15Vivo cohortToll-like receptor 2STAT1 responseRecurrent asthma exacerbationsAcute asthma exacerbationPro-inflammatory moleculesType I interferon regulationBlood mononuclear cellsPro-inflammatory signatureTranscriptomic signaturesType I interferonFold changeAdult asthmaAcute phaseMononuclear cellsImmunologic genesExacerbationIndependent cohortReceptor 2I interferon
2016
RNA sequencing of transformed lymphoblastoid cells from siblings discordant for autism spectrum disorders reveals transcriptomic and functional alterations: Evidence for sex‐specific effects
Tylee DS, Espinoza AJ, Hess JL, Tahir MA, McCoy SY, Rim JK, Dhimal T, Cohen OS, Glatt SJ. RNA sequencing of transformed lymphoblastoid cells from siblings discordant for autism spectrum disorders reveals transcriptomic and functional alterations: Evidence for sex‐specific effects. Autism Research 2016, 10: 439-455. PMID: 27529825, DOI: 10.1002/aur.1679.Peer-Reviewed Original ResearchConceptsTranscriptomic differencesGenome-wide expression studiesGene co-expression network analysisCo-expression network analysisTranscriptomic signaturesGene-set analysisStructural genetic variantsIdentified transcriptsGenomic studiesExpression studiesLymphoblastoid cell linesGenetic variantsCell linesExpression valuesNetwork analysisSignificant overlapGenesTranscriptsRNAASD studiesAutism spectrum disorderMale samplesLarge numberSignaturesFemalesNoninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma
Yan X, Chu JH, Gomez J, Koenigs M, Holm C, He X, Perez MF, Zhao H, Mane S, Martinez FD, Ober C, Nicolae DL, Barnes KC, London SJ, Gilliland F, Weiss ST, Raby BA, Cohn L, Chupp GL. Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma. Annals Of The American Thoracic Society 2016, 13 Suppl 1: s104-5. PMID: 27027945, PMCID: PMC5015745, DOI: 10.1513/annalsats.201510-681mg.Peer-Reviewed Original ResearchNitric oxide levelsOxide levelsHigher bronchodilator responseHistory of intubationNormal lung functionClusters of patientsCommon transcriptomic signaturesHigh ratePrebronchodilator FEV1Severe asthmaSteroid requirementsInflammatory characteristicsLung functionBronchodilator responseControl subjectsAsthmaHeterogeneous diseaseClinical phenotypeGene signaturePhysiologic characteristicsWhole bloodTranscriptomic signaturesCluster 1DiseaseHospitalization
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