2025
Age-invariant genes: multi-tissue identification and characterization of murine reference genes
González J, Thrush-Evensen K, Meer M, Levine M, Higgins-Chen A. Age-invariant genes: multi-tissue identification and characterization of murine reference genes. Aging 2025, 17: 170-202. PMID: 39873648, PMCID: PMC11810070, DOI: 10.18632/aging.206192.Peer-Reviewed Original ResearchMeSH KeywordsAgingAnimalsGene Expression ProfilingMaleMiceMice, Inbred C57BLOrgan SpecificityReference StandardsTranscriptomeConceptsRNA-seq datasetsReference genesRNA-seqHallmarks of agingPathway enrichment analysisGenes-thoseCpG islandsShorter transcriptRT-qPCRMolecular functionsExpression studiesGene normalizationTissue-specificEnrichment analysisMouse tissuesGenesMurine tissuesAged tissuesHallmarksYoung organismsLifespanTranscriptionCpGTissuePathwayThe human and non-human primate developmental GTEx projects
Bell T, Blanchard T, Hernandez R, Linn R, Taylor D, VonDran M, Ahooyi T, Beitra D, Bernieh A, Delaney M, Faith M, Fattahi E, Footer D, Gilbert M, Guambaña S, Gulino S, Hanson J, Hattrell E, Heinemann C, Kreeb J, Leino D, Mcdevitt L, Palmieri A, Pfeiffer M, Pryhuber G, Rossi C, Rasool I, Roberts R, Salehi A, Savannah E, Stachowicz K, Stokes D, Suplee L, Van Hoose P, Wilkins B, Williams-Taylor S, Zhang S, Ardlie K, Getz G, Lappalainen T, Montgomery S, Aguet F, Anderson L, Bernstein B, Choudhary A, Domenech L, Gaskell E, Johnson M, Liu Q, Marderstein A, Nedzel J, Okonda J, Padhi E, Rosano M, Russell A, Walker B, Sestan N, Gerstein M, Milosavljevic A, Borsari B, Cho H, Clarke D, Deveau A, Galeev T, Gobeske K, Hameed I, Huttner A, Jensen M, Jiang Y, Li J, Liu J, Liu Y, Ma J, Mane S, Meng R, Nadkarni A, Ni P, Park S, Petrosyan V, Pochareddy S, Salamon I, Xia Y, Yates C, Zhang M, Zhao H, Conrad D, Feng G, Brady F, Boucher M, Carbone L, Castro J, del Rosario R, Held M, Hennebold J, Lacey A, Lewis A, Lima A, Mahyari E, Moore S, Okhovat M, Roberts V, de Castro S, Wessel B, Zaniewski H, Zhang Q, Arguello A, Baroch J, Dayal J, Felsenfeld A, Ilekis J, Jose S, Lockhart N, Miller D, Minear M, Parisi M, Price A, Ramos E, Zou S. The human and non-human primate developmental GTEx projects. Nature 2025, 637: 557-564. PMID: 39815096, DOI: 10.1038/s41586-024-08244-9.Peer-Reviewed Original ResearchConceptsChromatin accessibility dataFunctional genomic studiesWhole-genome sequencingEffects of genetic variationSpatial gene expression profilesNon-human primatesGenotype-Tissue ExpressionGene expression profilesGenomic studiesGene regulationGenetic dataGenetic variationGenomic researchDonor diversityCommunity engagementHuman evolutionEarly developmental defectsGene expressionCell statesDevelopmental programmeHuman diseasesExpression profilesAdult tissuesDevelopmental defectsSingle-cell
2024
Machine-guided design of cell-type-targeting cis-regulatory elements
Gosai S, Castro R, Fuentes N, Butts J, Mouri K, Alasoadura M, Kales S, Nguyen T, Noche R, Rao A, Joy M, Sabeti P, Reilly S, Tewhey R. Machine-guided design of cell-type-targeting cis-regulatory elements. Nature 2024, 634: 1211-1220. PMID: 39443793, PMCID: PMC11525185, DOI: 10.1038/s41586-024-08070-z.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsCell typesActivation of off-target cellsGene expressionCell type-specific expressionSynthetic cis-regulatory elementsCell-type specificityHuman genomeUnique cell typeTissue identityBiotechnological applicationsTissue specificityIn vitro validationCell linesCre activitySequenceGenesNatural sequenceDevelopmental timeExpressionCellsGenomeTested in vivoMotifOff-target cells
2023
Spatial epigenome–transcriptome co-profiling of mammalian tissues
Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija G, Dwork A, Mann J, Leong K, Boldrini M, Wang L, Haeussler M, Raphael B, Kluger Y, Castelo-Branco G, Fan R. Spatial epigenome–transcriptome co-profiling of mammalian tissues. Nature 2023, 616: 113-122. PMID: 36922587, PMCID: PMC10076218, DOI: 10.1038/s41586-023-05795-1.Peer-Reviewed Original ResearchConceptsGene expressionSingle-cell resolutionChromatin accessibilityJoint profilingHistone modificationsGene regulationCellular statesEpigenetic mechanismsCentral dogmaSpatial transcriptomeTranscriptional phenotypeCell statesOmics informationSpatial transcriptomicsEpigenetic primingMammalian tissuesEpigenomeMolecular biologyTissue architectureCell dynamicsMechanistic relationshipDifferential rolesNew insightsMouse brainProfiling
2022
Cellular recovery after prolonged warm ischaemia of the whole body
Andrijevic D, Vrselja Z, Lysyy T, Zhang S, Skarica M, Spajic A, Dellal D, Thorn SL, Duckrow RB, Ma S, Duy PQ, Isiktas AU, Liang D, Li M, Kim SK, Daniele SG, Banu K, Perincheri S, Menon MC, Huttner A, Sheth KN, Gobeske KT, Tietjen GT, Zaveri HP, Latham SR, Sinusas AJ, Sestan N. Cellular recovery after prolonged warm ischaemia of the whole body. Nature 2022, 608: 405-412. PMID: 35922506, PMCID: PMC9518831, DOI: 10.1038/s41586-022-05016-1.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell DeathCell SurvivalCytoprotectionGene Expression ProfilingIschemiaOrgan SpecificityPerfusionSwineWarm IschemiaConceptsSingle-nucleus transcriptomic analysesSpecific gene expression patternsCellular recoveryGene expression patternsCellular processesMammalian cellsTranscriptomic analysisLarge mammalsExpression patternsCellular repair processesCell deathComprehensive resourceUnderappreciated potentialPhysiological challengesTissue integrityRepair processSpecific changesPorcine brainMammalsOrgansMultiple organs
2021
SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues
D’Antonio M, Nguyen J, Arthur T, Matsui H, Neale B, Daly M, Ganna A, Stevens C, Pathak G, Andrews S, Kanai M, Cordioli M, Ganna A, Karjalainen J, Pathak G, Polimanti R, Andrews S, Cordioli M, Pirinen M, Kanai M, Harerimana N, Veerapen K, Wolford B, Nguyen H, Solomonson M, Stevens C, Liao R, Chwialkowska K, Trankiem A, Balaconis M, Hayward C, Richmond A, Campbell A, Morris M, Fawns-Ritchie C, Glessner J, Shaw D, Chang X, Polikowski H, Lauren E, Chen H, Wanying Z, Hakonarson H, Porteous D, Below J, North K, McCormick J, Timmers P, Wilson J, Tenesa A, D’Mellow K, Kerr S, Niemi M, Cordioli M, Nkambul L, von Hohenstaufen K, Sobh A, Eltoukhy M, Yassen A, Hegazy M, Okasha K, Eid M, Moahmed H, Shahin D, El-Sherbiny Y, Elhadidy T, Elghafar M, El-Jawhari J, Mohamed A, Elnagdy M, Samir A, Abdel-Aziz M, Khafaga W, El-Lawaty W, Torky M, El-shanshory M, Batini C, Lee P, Shrine N, Williams A, Tobin M, Guyatt A, John C, Packer R, Ali A, Free R, Wang X, Wain L, Hollox E, Venn L, Bee C, Adams E, Niemi M, Niavarani A, Cordioli M, Nkambul L, Sharififard B, Aliannejad R, Amirsavadkouhi A, Naderpour Z, Tadi H, Aleagha A, Ahmadi S, Moghaddam S, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Chamnanphon M, Suttichet T, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Jantarabenjakul W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Hirankarn N, Nilaratanakul V, Sodsai P, Brumpton B, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold B, Abedalthagafi M, Alaamery M, Alqahtani S, Baraka D, Al Harthi F, Alsolm E, Abu Safieh L, Alowayn A, Alqubaishi F, Al Mutairi A, Mangul S, Alshareef A, Sawaji M, Almutairi M, Aljawini N, Albesher N, Arabi Y, Mahmoud E, Khattab A, Halawani R, Alahmadey Z, Albakri J, Felemban W, Suliman B, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, Alrashed M, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Massadeh S, AlMalik A, 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Band G, Earle S, Lin S, Arning N, Crook D, Wyllie D, O’Connell A, Spencer C, Koelling N, Caulfield M, Scott R, Fowler T, Moutsianas L, Kousathanas A, Pasko D, Walker S, Rendon A, Stuckey A, Odhams C, Rhodes D, Chan G, Arumugam P, Ball C, Hong E, Rand K, Girshick A, Guturu H, Baltzell A, Roberts G, Park D, Coignet M, McCurdy S, Knight S, Partha R, Rhead B, Zhang M, Berkowitz N, Gaddis M, Noto K, Ruiz L, Pavlovic M, Sloofman L, Andrews S, Charney A, Beckmann N, Schadt E, Jordan D, Thompson R, Gettler K, Abul-Husn N, Ascolillo S, Buxbaum J, Chaudhary K, Cho J, Itan Y, Kenny E, Belbin G, Sealfon S, Sebra R, Salib I, Collins B, Levy T, Britvan B, Keller K, Tang L, Peruggia M, Hiester L, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Preuss M, Loos R, Nadkarni G, Do R, Hoggart C, Choi S, Underwood S, O’Reilly P, Huckins L, Zyndorf M, D’Antonio-Chronowska A, Frazer K. SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues. Cell Reports 2021, 37: 110020. PMID: 34762851, PMCID: PMC8563343, DOI: 10.1016/j.celrep.2021.110020.Peer-Reviewed Original ResearchMeSH KeywordsChromosome MappingComputational BiologyCOVID-19Databases, GeneticEthnicityGene ExpressionGene Expression ProfilingGenetic Predisposition to DiseaseGenetic VariationGenome-Wide Association StudyHumansOrgan SpecificityPolymorphism, Single NucleotideQuantitative Trait LociSARS-CoV-2Severity of Illness IndexTranscriptomeConceptsExpression quantitative trait lociGenome-wide association study signalsTissue/cell typesQuantitative trait lociGenetic fine mappingGene expression levelsLoci colocalizeGenomic lociGWAS lociTrait lociFine mappingVariety of tissuesCausal SNPsGene expressionSNP setsStudy signalsLociCell typesSARS-CoV-2 susceptibilityGenetic variantsSuggestive associationExpression levelsTissue typesSNPsCredible setsImmunomodulatory functions of TRPM7 and its implications in autoimmune diseases
Liang H, Chen Y, Wei X, Ma G, Ding J, Lu C, Zhou R, Hu W. Immunomodulatory functions of TRPM7 and its implications in autoimmune diseases. Immunology 2021, 165: 3-21. PMID: 34558663, DOI: 10.1111/imm.13420.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAutoimmune DiseasesAutoimmunityBiomarkersDisease SusceptibilityDrug DevelopmentGene Expression RegulationHumansImmune SystemImmunomodulationIon Channel GatingOrgan SpecificityProtein Kinase InhibitorsProtein Serine-Threonine KinasesSignal TransductionStructure-Activity RelationshipTRPM Cation ChannelsConceptsAutoimmune diseasesRole of TRPM7New treatment targetsPotential therapeutic targetReceptor ion channelsImmune toleranceRheumatoid arthritisMultiple sclerosisSystemic disordersBody of evidenceImmune cellsCytokine secretionImmunoreactive substancesFunctional damageImmunomodulatory functionsTherapeutic targetTreatment targetsDiseaseEffective interventionsPharmacological propertiesOne-tissueTRPM7Physiologic conditionsInappropriate responsesCell migrationThe mutational landscape of human somatic and germline cells
Moore L, Cagan A, Coorens T, Neville M, Sanghvi R, Sanders M, Oliver T, Leongamornlert D, Ellis P, Noorani A, Mitchell T, Butler T, Hooks Y, Warren A, Jorgensen M, Dawson K, Menzies A, O’Neill L, Latimer C, Teng M, van Boxtel R, Iacobuzio-Donahue C, Martincorena I, Heer R, Campbell P, Fitzgerald R, Stratton M, Rahbari R. The mutational landscape of human somatic and germline cells. Nature 2021, 597: 381-386. PMID: 34433962, DOI: 10.1038/s41586-021-03822-7.Peer-Reviewed Original ResearchConceptsCell typesMutational landscapeRate of mutationLow rate of cell divisionRate of cell divisionBasal spermatogoniaGermline cellsGenetic variationCell divisionHuman cellsMutational signaturesGermlineAcquired mutationsMutationsSpermatogoniaHuman populationCellsIndividual's lifetimeSBS5/40SpermSBS18Stem cellsSBS1LandscapeTypeInfections in activated PI3K delta syndrome (APDS)
Brodsky NN, Lucas CL. Infections in activated PI3K delta syndrome (APDS). Current Opinion In Immunology 2021, 72: 146-157. PMID: 34052541, DOI: 10.1016/j.coi.2021.04.010.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsPI3K delta syndromeHematopoietic stem cell transplantAnti-microbial prophylaxisPI3K-delta syndromeStem cell transplantSenescent T cellsSpectrum of infectionsAdaptive immune functionAutosomal dominant disorderCell transplantImmune defectsImmunoglobulin replacementRecurrent infectionsImmunomodulatory agentsTherapy optionsT cellsImmune functionInfection susceptibilityInborn errorsDominant disorderInfectionLymphadenopathyPatientsFunction mutationsImmunodeficiencyIntegrated Single-Cell Atlas of Endothelial Cells of the Human Lung
Schupp JC, Adams TS, Cosme C, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP, Sauler M, DeIuliis G, Ahangari F, Neumark N, Habermann AC, Gutierrez AJ, Bui LT, Lafyatis R, Pierce RW, Meyer KB, Nawijn MC, Teichmann SA, Banovich NE, Kropski JA, Niklason LE, Pe’er D, Yan X, Homer RJ, Rosas IO, Kaminski N. Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung. Circulation 2021, 144: 286-302. PMID: 34030460, PMCID: PMC8300155, DOI: 10.1161/circulationaha.120.052318.Peer-Reviewed Original ResearchConceptsDifferential expression analysisPrimary lung endothelial cellsLung endothelial cellsCell typesMarker genesExpression analysisSingle-cell RNA sequencing dataCross-species analysisVenous endothelial cellsEndothelial marker genesSingle-cell atlasMarker gene setsRNA sequencing dataEndothelial cellsSubsequent differential expression analysisDifferent lung cell typesResident cell typesLung cell typesCellular diversityEndothelial cell typesCapillary endothelial cellsHuman lung endothelial cellsPhenotypic diversityEndothelial diversityIndistinguishable populationsImproved methods for RNAseq-based alternative splicing analysis
Halperin RF, Hegde A, Lang JD, Raupach EA, Legendre C, Liang W, LoRusso P, Sekulic A, Sosman J, Trent J, Rangasamy S, Pirrotte P, Schork N. Improved methods for RNAseq-based alternative splicing analysis. Scientific Reports 2021, 11: 10740. PMID: 34031440, PMCID: PMC8144374, DOI: 10.1038/s41598-021-89938-2.Peer-Reviewed Original ResearchConceptsProtein-level effectsSplicing analysisSplice eventsSplice isoformsRNAseq dataAlternative splicing analysisTissue-specific splice variantsDifferential splicing analysisGene expression levelsPathogenic splicing variantProtein level expressionSequence readsSplicing variantsSplice variantsOncogenic mutationsMass spectrometry dataSplice alterationsExpression levelsRNAseqIsoformsMelanoma datasetSpectrometry dataNovel statistical approachAnalysis resourcesMass spectrometryDiverse functional autoantibodies in patients with COVID-19
Wang EY, Mao T, Klein J, Dai Y, Huck JD, Jaycox JR, Liu F, Zhou T, Israelow B, Wong P, Coppi A, Lucas C, Silva J, Oh JE, Song E, Perotti ES, Zheng NS, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE, Dela Cruz C, Farhadian S, Schulz W, Ma S, Grubaugh N, Ko A, Iwasaki A, Ring A. Diverse functional autoantibodies in patients with COVID-19. Nature 2021, 595: 283-288. PMID: 34010947, DOI: 10.1038/s41586-021-03631-y.Peer-Reviewed Original ResearchConceptsPeripheral immune cell compositionSARS-CoV-2 infectionCOVID-19Effects of autoantibodiesTissue-associated antigensSpecific clinical characteristicsInnate immune activationImmune cell compositionCOVID-19 exhibitCOVID-19 manifestsAnalysis of autoantibodiesSARS-CoV-2Functional autoantibodiesMouse surrogateClinical characteristicsVirological controlClinical outcomesImmune activationMild diseaseAsymptomatic infectionAutoantibody reactivityDisease progressionHealthcare workersHigh prevalenceAutoantibodiesComprehensive identification of somatic nucleotide variants in human brain tissue
Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino F, Moran J, Urban A, Kidd J, Mills R, Abyzov A. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biology 2021, 22: 92. PMID: 33781308, PMCID: PMC8006362, DOI: 10.1186/s13059-021-02285-3.Peer-Reviewed Original ResearchConceptsSomatic SNVsSomatic single nucleotide variantsWhole-genome sequencing dataSequencing dataBulk DNA samplesCell lineage treesSomatic mosaicismSingle nucleotide variantsLineage treesSomatic nucleotide variantsCellular processesDNA replicationHuman genomeSomatic tissuesDNA repairNucleotide variantsComprehensive identificationDNA samplesMosaic variantsNon-cancerous tissuesDNASingle individualMultiple replicatesHuman brain tissueVariantsResident memory T cells form during persistent antigen exposure leading to allograft rejection
Abou-Daya K, Tieu R, Zhao D, Rammal R, Sacirbegovic F, Williams A, Shlomchik W, Oberbarnscheidt M, Lakkis F. Resident memory T cells form during persistent antigen exposure leading to allograft rejection. Science Immunology 2021, 6 PMID: 33741656, PMCID: PMC8103522, DOI: 10.1126/sciimmunol.abc8122.Peer-Reviewed Original ResearchConceptsMemory T cellsEffector T cellsT cellsAllograft rejectionAntigen-specificTissue-resident memory T cellsFunctional memory T cellsResident memory T cellsMouse model of kidney transplantationGrafted T cellsPersistent antigen exposureModel of kidney transplantationRenal transplant outcomesRetransplantation experimentsDiscovery of therapeutic targetsExhaustion markersSurface phenotypeAntigen exposureInterferon-gTransplant outcomesKidney transplantationCognate antigenMouse modelOrgan transplantationTransplantationRegional specification and complementation with non-neuroectodermal cells in human brain organoids
Tanaka Y, Park IH. Regional specification and complementation with non-neuroectodermal cells in human brain organoids. Journal Of Molecular Medicine 2021, 99: 489-500. PMID: 33651139, PMCID: PMC8026433, DOI: 10.1007/s00109-021-02051-9.Peer-Reviewed Original ResearchAnimalsBrainCellular Reprogramming TechniquesEmbryoid BodiesEndothelial CellsFetusFibroblast Growth Factor 2Hedgehog ProteinsHuman Umbilical Vein Endothelial CellsHumansInduced Pluripotent Stem CellsIntercellular Signaling Peptides and ProteinsMicrogliaNeuronsOrgan SpecificityOrganogenesisOrganoidsRetinaSpinal CordWnt Signaling PathwaySingle-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Muus C, Luecken M, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav E, Subramanian A, Smillie C, Jagadeesh K, Duong E, Fiskin E, Torlai Triglia E, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber A, Chung H, Montoro D, Adams T, Aliee H, Allon S, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui L, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon T, Cuoco M, Cuomo A, Deprez M, Duclos G, Fine D, Fischer D, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez A, Habermann A, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos T, Kuo C, Larsson L, Leney-Greene M, Lim K, Litviňuková M, Ludwig L, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr C, Mbano I, McAdams A, Nabhan A, Nyquist S, Penland L, Poirion O, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp J, Shea C, Shi X, Sinha R, Sit R, Slowikowski K, Slyper M, Smith N, Sountoulidis A, Strunz M, Sullivan T, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini K, Tucker N, Vernon K, Wadsworth M, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler C. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature Medicine 2021, 27: 546-559. PMID: 33654293, PMCID: PMC9469728, DOI: 10.1038/s41591-020-01227-z.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAlveolar Epithelial CellsAngiotensin-Converting Enzyme 2Cathepsin LCOVID-19Datasets as TopicDemographyFemaleGene Expression ProfilingHost-Pathogen InteractionsHumansLungMaleMiddle AgedOrgan SpecificityRespiratory SystemSARS-CoV-2Sequence Analysis, RNASerine EndopeptidasesSingle-Cell AnalysisVirus InternalizationConceptsSingle-cell RNA-sequencing studiesRNA-sequencing studiesSpecific expression patternsExpression programsKey immune functionsExpression patternsSARS-CoV-2 entry genesSpecific expressionAlveolar type 2 cellsMolecular pathwaysLung parenchyma samplesCoronavirus disease 2019 (COVID-19) transmissionDifferent tissuesCellular entryGenesRespiratory epithelial cellsAirway secretory cellsSecretory cellsTumor necrosis factorEntry genesExpression levelsType 2 cellsEpithelial cellsGut tissueSpecific subsetFoxO1 suppresses Fgf21 during hepatic insulin resistance to impair peripheral glucose utilization and acute cold tolerance
Stöhr O, Tao R, Miao J, Copps K, White M. FoxO1 suppresses Fgf21 during hepatic insulin resistance to impair peripheral glucose utilization and acute cold tolerance. Cell Reports 2021, 34: 108893. PMID: 33761350, PMCID: PMC8529953, DOI: 10.1016/j.celrep.2021.108893.Peer-Reviewed Original ResearchMeSH KeywordsAdaptation, PhysiologicalAdipocytes, BrownAdipose Tissue, BrownAnimalsBlood GlucoseBody WeightCold TemperatureDiet, High-FatFibroblast Growth FactorsForkhead Box Protein O1Gene Expression RegulationGlucoseHomeostasisInsulinInsulin Receptor Substrate ProteinsInsulin ResistanceLipid MetabolismLiverMice, KnockoutOrgan SpecificityOxidation-ReductionThermogenesisConceptsHepatic insulin resistanceInsulin resistanceGlucose utilizationHigher plasma Fgf21 levelsSevere hepatic insulin resistanceFGF21 knockout micePlasma FGF21 levelsPeripheral glucose utilizationInsulin-resistant miceThermogenic gene expressionFGF21 resistancePharmacologic formsFGF21 levelsCold intoleranceFGF21 functionMetabolic healthBAT functionGlucose homeostasisKnockout miceFGF21Adenoviral infectionMiceWeight lossSkeletal muscleAcute cold toleranceTissue-specific dynamic codon redefinition in Drosophila
Hudson AM, Szabo NL, Loughran G, Wills NM, Atkins JF, Cooley L. Tissue-specific dynamic codon redefinition in Drosophila. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2012793118. PMID: 33500350, PMCID: PMC7865143, DOI: 10.1073/pnas.2012793118.Peer-Reviewed Original ResearchConceptsStop codonTranslational stop codon readthroughReadthrough efficiencyHuman tissue culture cellsStop codon readthroughTissue-specific regulationAdult central nervous system (CNS) tissueTissue culture cellsReadthrough productKelch proteinUbiquitin ligaseSingle geneAdult brainIndividual proteinsCodon readthroughReadthroughViral mRNAsC-terminalMalpighian tubulesCodonNeuronal proteinsCell typesAmino acidsCulture cellsDrosophila
2020
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue
Liu Y, Yang M, Deng Y, Su G, Enninful A, Guo CC, Tebaldi T, Zhang D, Kim D, Bai Z, Norris E, Pan A, Li J, Xiao Y, Halene S, Fan R. High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. Cell 2020, 183: 1665-1681.e18. PMID: 33188776, PMCID: PMC7736559, DOI: 10.1016/j.cell.2020.10.026.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAutomationBrainCluster AnalysisDNA Barcoding, TaxonomicDNA, ComplementaryEmbryo, MammalianEyeFemaleGene Expression Regulation, DevelopmentalGenomicsHuman Umbilical Vein Endothelial CellsHumansMice, Inbred C57BLMicrofluidicsOrgan SpecificityReproducibility of ResultsRNA, MessengerSingle-Cell AnalysisTranscriptomeConceptsDeterministic barcodingNext-generation sequencingSingle-cell transcriptomesGene expression profilesMajor tissue typesDBiT-seqDNA barcodesDevelopmental biologyExpression profilesEarly organogenesisCancer biologyCell typesBarcodingTissue typesSequencingBarcodesBiologyRapid identificationSets of barcodesTranscriptomeParallel microfluidic channelsOrganogenesisEmbryosProteinTissue pixelsThe Transcription Factor Foxp3 Shapes Regulatory T Cell Identity by Tuning the Activity of trans-Acting Intermediaries
van der Veeken J, Glasner A, Zhong Y, Hu W, Wang Z, Bou-Puerto R, Charbonnier L, Chatila T, Leslie C, Rudensky A. The Transcription Factor Foxp3 Shapes Regulatory T Cell Identity by Tuning the Activity of trans-Acting Intermediaries. Immunity 2020, 53: 971-984.e5. PMID: 33176163, PMCID: PMC8363055, DOI: 10.1016/j.immuni.2020.10.010.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAutoimmune DiseasesAutoimmunityBinding SitesChromatin Assembly and DisassemblyDisease Models, AnimalEpigenesis, GeneticFemaleForkhead Transcription FactorsGene Expression RegulationImmunohistochemistryMaleMiceNucleotide MotifsOrgan SpecificityProtein BindingT-Lymphocytes, RegulatoryTrans-ActivatorsConceptsRegulatory T Cell IdentityChromatin accessibilityCell identityT cell identityDNA sequence motifsGene expression patternsMajor chromatinChromatin regionsTF bindingSequence motifsTCF7 geneEpigenetic featuresGenetic variationNegative regulationNull allelesExpression patternsPresence of DNATreg cell identityFOXP3 functionTCF1MotifIndirect mannerCellsTranscription factor Foxp3Chromatin
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