2025
Atgl-dependent adipocyte lipolysis promotes lipodystrophy and restrains fibrogenic responses during skin fibrosis
Caves E, Jussila A, Forni M, Benvie A, Lei V, King D, Edelman H, Hamdan M, Odell I, Hinchcliff M, Atit R, Horsley V. Atgl-dependent adipocyte lipolysis promotes lipodystrophy and restrains fibrogenic responses during skin fibrosis. Journal Of Investigative Dermatology 2025 PMID: 39884454, DOI: 10.1016/j.jid.2024.12.022.Peer-Reviewed Original ResearchLipid storageAdipocyte lipolysisExtracellular matrix proteinsFatty acidsTranscriptional analysisSkin fibrosisAdipocyte lipid storageTranscriptional changesSkin fibrosis developmentExtracellular matrix remodelingFibrosis developmentLipid-filled adipocytesDermal extracellular matrixHuman diseasesTreating fibrotic diseasesMouse modelMatrix proteinsDermal adipocytesFibrogenic responseGenetic modelsExtracellular matrixAdipocytesLoss of adipose tissueBleomycin-treated miceFibrotic mouse modelThe 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
Epigenetics-targeted drugs: current paradigms and future challenges
Dai W, Qiao X, Fang Y, Guo R, Bai P, Liu S, Li T, Jiang Y, Wei S, Na Z, Xiao X, Li D. Epigenetics-targeted drugs: current paradigms and future challenges. Signal Transduction And Targeted Therapy 2024, 9: 332. PMID: 39592582, PMCID: PMC11627502, DOI: 10.1038/s41392-024-02039-0.Peer-Reviewed Original ResearchConceptsNon-coding RNA regulationDNA base sequenceRNA modificationsRNA regulationChromatin remodelingHistone modificationsEnhancer of zeste homolog 2Epigenetic landscapeGenetic informationOrganismal developmentDNA methyltransferasesEpigenetic enzymesDNA modificationsBase sequenceHomolog 2Zeste homolog 2Histone deacetylasesHuman diseasesIsocitrate dehydrogenaseDNAPathological contextsRegulatory systemChromatinEnzymeHistoneAnalysis of Powassan Virus Genome Sequences from Human Cases Reveals Substantial Genetic Diversity with Implications for Molecular Assay Development
Klontz E, Chowdhury N, Holbrook N, Solomon I, Telford S, Aliota M, Vogels C, Grubaugh N, Helgager J, Hughes H, Velez J, Piantadosi A, Chiu C, Lemieux J, Branda J. Analysis of Powassan Virus Genome Sequences from Human Cases Reveals Substantial Genetic Diversity with Implications for Molecular Assay Development. Viruses 2024, 16: 1653. PMID: 39599768, PMCID: PMC11599074, DOI: 10.3390/v16111653.Peer-Reviewed Original ResearchGenome sequenceDiversity of genomic sequencesHuman infectionsPCR assay designVirus genome sequencesAssay designIn silico analysisBiology of infectionViral genomic dataGenetic diversityGenomic dataSensitivity of PCRGenomeCladePCR assayHuman diseasesVirulent strainsPCR designPowassan virusSequenceImmunocompromised patientsPCRTick-borne virusesAssay developmentClinical diagnosticsPrioritizing disease-related rare variants by integrating gene expression data
Guo H, Urban A, Wong H. Prioritizing disease-related rare variants by integrating gene expression data. PLOS Genetics 2024, 20: e1011412. PMID: 39348415, PMCID: PMC11466430, DOI: 10.1371/journal.pgen.1011412.Peer-Reviewed Original ResearchConceptsGene expression dataRare variantsExpression dataRare variant association methodsExcess of rare variantsImpact of rare variantsContext of human diseaseHuman genetic variationGenetic variationGene expressionComplex diseasesHuman diseasesGenesMolecular mechanismsFunctional consequencesRare variant typesAlzheimer's diseaseVariant typeVariantsAssociation methodStatistical frameworkSimulation studySample sizeOmicsAlzheimerEvolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals
Uebbing S, Kocher A, Baumgartner M, Ji Y, Bai S, Xing X, Nottoli T, Noonan J. Evolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals. Molecular Biology And Evolution 2024, 41: msae199. PMID: 39302728, PMCID: PMC11465374, DOI: 10.1093/molbev/msae199.Peer-Reviewed Original ResearchSequence evolutionRegulatory evolutionDevelopmental signaling genesEnhanced evolutionEvolutionary innovationMammalian phylogenyTranscriptional enhancersGenetic variationPhenotypic variationPleiotropic genesDevelopmental genesEnhancer elementsHoofed mammalsEnhancer sequencesActivation domainSignaling genesEvolutionary adaptationDiverse organismsGenesHuman diseasesRegulatory functionsDevelopmental processesDeveloping limbCell typesMammalsSensing DNA as danger: The discovery of cGAS
Flavell R, Sefik E. Sensing DNA as danger: The discovery of cGAS. Immunity 2024, 57: 2251-2254. PMID: 39303723, DOI: 10.1016/j.immuni.2024.09.009.Peer-Reviewed Original ResearchAlterations in the Skin Microbiome in Dermatologic Diseases and with External Exposures: CME Part 2
MacGibeny M, Adjei S, Pyle H, Bunick C, Ghannoum M, Grada A, Harris-Tryon T, Tyring S, Kong H. Alterations in the Skin Microbiome in Dermatologic Diseases and with External Exposures: CME Part 2. Journal Of The American Academy Of Dermatology 2024 PMID: 39173885, PMCID: PMC11839956, DOI: 10.1016/j.jaad.2024.07.1499.Peer-Reviewed Original ResearchInsights From Omics in Lyme Disease
Bockenstedt L, Belperron A. Insights From Omics in Lyme Disease. The Journal Of Infectious Diseases 2024, 230: s18-s26. PMID: 39140719, DOI: 10.1093/infdis/jiae250.Peer-Reviewed Original ResearchMaternal regulation of the vertebrate oocyte-to-embryo transition
Fuentes R, Marlow F, Abrams E, Zhang H, Kobayashi M, Gupta T, Kapp L, DiNardo Z, Heller R, Cisternas R, García-Castro P, Segovia-Miranda F, Montecinos-Franjola F, Vought W, Vejnar C, Giraldez A, Mullins M. Maternal regulation of the vertebrate oocyte-to-embryo transition. PLOS Genetics 2024, 20: e1011343. PMID: 39052672, PMCID: PMC11302925, DOI: 10.1371/journal.pgen.1011343.Peer-Reviewed Original ResearchOocyte-to-embryo transitionMutant geneZebrafish forward genetic screenEgg activationForward genetic screensGenetic entry pointsMaternal-effect mutantsBasic body planCytoplasmic segregationBody planIntracellular traffickingGenetic screeningMicrotubule nucleationProtein cleavageMaternal genesVesicle formationGenesFunctional importanceHuman diseasesMolecular mechanismsMolecular insightsCortical granulesBlack caviarMaternal regulationMolecular natureEpigenetic heterogeneity hotspots in human liver disease progression
Hlady R, Zhao X, Khoury L, Wagner R, Luna A, Pham K, Pyrosopoulos N, Jain D, Wang L, Liu C, Robertson K. Epigenetic heterogeneity hotspots in human liver disease progression. Hepatology 2024, 81: 1197-1210. PMID: 39028883, PMCID: PMC11742070, DOI: 10.1097/hep.0000000000001023.Peer-Reviewed Original ResearchEpigenetic heterogeneityGenome-wide profiling of DNA methylationProfiling of DNA methylationDNA methylation landscapeGenome-wide profilingGene expression heterogeneityCopy number variationsMethylation landscapeOnset of liver cancerDNA methylationLiver disease developmentPhenotypic effectsNumber variationsGenetic heterogeneityTranscriptional heterogeneityFunctional screeningLiver disease progressionCopy numberExpression heterogeneityGene expressionTumor suppressorHuman diseasesGenesPathological phenotypesKey pathwaysEfficient editing of the CXCR4 locus using Cas9 ribonucleoprotein complexes stabilized with polyglutamic acid
Golubev D, Komkov D, Shepelev M, Mazurov D, Kruglova N. Efficient editing of the CXCR4 locus using Cas9 ribonucleoprotein complexes stabilized with polyglutamic acid. Доклады Российской Академии Наук Науки О Жизни 2024, 514: 85-90. DOI: 10.31857/s2686738924010164.Peer-Reviewed Original ResearchHuman antibodies in Mexico and Brazil neutralizing tick-borne flaviviruses
Cervantes Rincón T, Kapoor T, Keeffe J, Simonelli L, Hoffmann H, Agudelo M, Jurado A, Peace A, Lee Y, Gazumyan A, Guidetti F, Cantergiani J, Cena B, Bianchini F, Tamagnini E, Moro S, Svoboda P, Costa F, Reis M, Ko A, Fallon B, Avila-Rios S, Reyes-Téran G, Rice C, Nussenzweig M, Bjorkman P, Ruzek D, Varani L, MacDonald M, Robbiani D. Human antibodies in Mexico and Brazil neutralizing tick-borne flaviviruses. Cell Reports 2024, 43: 114298. PMID: 38819991, PMCID: PMC11832053, DOI: 10.1016/j.celrep.2024.114298.Peer-Reviewed Original ResearchPowassan virusEnvelope domain IIIYellow fever virusZika virusFever virusSerological neutralizing activityTemperate regionsDengue virusTicksTropical areasInfect humansLineage IMosquito-borne flavivirusNeutralizing activityHuman antibodiesVirusNeurological illnessBrazilFlavivirusesP002P003Human diseasesLoss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder
Kohler J, Legro N, Baldridge D, Shin J, Bowman A, Ugur B, Jackstadt M, Shriver L, Patti G, Zhang B, Feng W, McAdow A, Goddard P, Ungar R, Jensen T, Smith K, Fresard L, Alvarez R, Bonner D, Reuter C, McCormack C, Kravets E, Marwaha S, Holt J, Network U, Acosta M, Adam M, Adams D, Alvarez R, Alvey J, Amendola L, Andrews A, Ashley E, Bacino C, Bademci G, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs A, Behrens E, Bejerano G, Bellen H, Bennett J, Berg-Rood B, Bernstein J, Berry G, Bican A, Bivona S, Blue E, Bohnsack J, Bonner D, Botto L, Boyd B, Briere L, Burke E, Burrage L, Butte M, Byers P, Byrd W, Carey J, Carrasquillo O, Cassini T, Chang T, Chanprasert S, Chao H, Chinn I, Clark G, Coakley T, Cobban L, Cogan J, Coggins M, Cole F, Colley H, Cope H, Corner B, Corona R, Craigen W, Crouse A, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal J, Dell’Angelica E, Dickson P, Dipple K, Doherty D, Dorrani N, Doss A, Douine E, Earl D, Eckstein D, Emrick L, Eng C, Ezell K, Falk M, Fieg E, Fisher P, Fogel B, Forghani I, Gahl W, Glass I, Gochuico B, Goddard P, Godfrey R, Golden-Grant K, Grajewski A, Hadley D, Hahn S, Halley M, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama F, Holm I, Hom J, Horike-Pyne M, Huang A, Hutchison S, Introne W, Isasi R, Izumi K, Jamal F, Jarvik G, Jarvik J, Jayadev S, Jean-Marie O, Jobanputra V, Karaviti L, Ketkar S, Kiley D, Kilich G, Kobren S, Kohane I, Kohler J, Korrick S, Kozuira M, Krakow D, Krasnewich D, Kravets E, Lalani S, Lam B, Lam C, Lanpher B, Lanza I, LeBlanc K, Lee B, Levitt R, Lewis R, Liu P, Liu X, Longo N, Loo S, Loscalzo J, Maas R, Macnamara E, MacRae C, Maduro V, Maghiro A, Mahoney R, Malicdan M, Mamounas L, Manolio T, Mao R, Maravilla K, Marom R, Marth G, Martin B, Martin M, Martínez-Agosto J, Marwaha S, McCauley J, McConkie-Rosell A, McCray A, McGee E, Mefford H, Merritt J, Might M, Mirzaa G, Morava E, Moretti P, Mulvihill J, Nakano-Okuno M, Nelson S, Neumann S, Newman J, Nicholas S, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo J, Pace L, Pak S, Pallais J, Palmer C, Papp J, Parker N, Phillips J, Posey J, Potocki L, Swerdzewski B, Quinlan A, Rao D, Raper A, Raskind W, Renteria G, Reuter C, Rives L, Robertson A, Rodan L, Rosenfeld J, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson J, Saporta M, Schaechter J, Schedl T, Schoch K, Scott D, Scott C, Seto E, Shashi V, Shin J, Silverman E, Sinsheimer J, Sisco K, Smith E, Smith K, Solnica-Krezel L, Solomon B, Spillmann R, Stoler J, Sullivan K, Sullivan J, Sun A, Sutton S, Sweetser D, Sybert V, Tabor H, Tan Q, Tan A, Tarakad A, Tekin M, Telischi F, Thorson W, Tifft C, Toro C, Tran A, Ungar R, Urv T, Vanderver A, Velinder M, Viskochil D, Vogel T, Wahl C, Walker M, Wallace S, Walley N, Wambach J, Wan J, Wangler M, Ward P, Wegner D, Hubshman M, Wener M, Wenger T, Westerfield M, Wheeler M, Whitlock J, Wolfe L, Worley K, Xiao C, Yamamoto S, Yang J, Zhang Z, Zuchner S, Worthey E, Ashley E, Montgomery S, Fisher P, Postlethwait J, De Camilli P, Solnica-Krezel L, Bernstein J, Wheeler M. Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder. Genetics In Medicine 2024, 26: 101166. PMID: 38767059, PMCID: PMC11451386, DOI: 10.1016/j.gim.2024.101166.Peer-Reviewed Original ResearchNegative regulation of cell proliferationLoss-of-function variantsPathways associated with apoptosisRegulation of cell proliferationRelationship to human diseaseHuman cell linesNeurodevelopmental disordersRNA-seqLocalized proteinsImmune-associated genesZebrafish cellsGolgi complexModel organismsGlobal developmental delayBiallelic variantsFAM177A1Negative regulatorHuman diseasesZebrafish model organismPhysiological functionsCell linesGolgiHuman fibroblastsZebrafishCell proliferationUnveiling the secrets of vimentin filament architecture relevant to human disease
Lomakin I, Ho M, Bunick C. Unveiling the secrets of vimentin filament architecture relevant to human disease. Nature Structural & Molecular Biology 2024, 31: 849-851. PMID: 38684931, DOI: 10.1038/s41594-024-01301-x.Peer-Reviewed Original ResearchThe RRE-REV module has no effect on the packaging efficiency of cas9 and Gag proteins into nanomedic virus-like particles
Kruglova N, Komkov D, Mazurov D, Shepelev M. The RRE-REV module has no effect on the packaging efficiency of cas9 and Gag proteins into nanomedic virus-like particles. Доклады Российской Академии Наук Науки О Жизни 2024, 515: 64-70. DOI: 10.31857/s2686738924020121.Peer-Reviewed Original ResearchRev expression plasmidVirus-like particlesEmpty control plasmidGene therapy of human diseasesGag proteinTherapy of human diseasesGene therapyViral Gag proteinTarget cellsControl plasmidProtein levelsCas9 nucleaseGenome editingGagEfficiency of genome editingMethods of genome editingExpression of Cas9Plasmid constructsCotransfectionHuman diseasesPlasmidCell lysatesNuclear exportParasympathetic neurons derived from human pluripotent stem cells model human diseases and development
Wu H, Saito-Diaz K, Huang C, McAlpine J, Seo D, Magruder D, Ishan M, Bergeron H, Delaney W, Santori F, Krishnaswamy S, Hart G, Chen Y, Hogan R, Liu H, Ivanova N, Zeltner N. Parasympathetic neurons derived from human pluripotent stem cells model human diseases and development. Cell Stem Cell 2024, 31: 734-753.e8. PMID: 38608707, PMCID: PMC11069445, DOI: 10.1016/j.stem.2024.03.011.Peer-Reviewed Original ResearchConceptsAutonomic nervous systemSjogren's syndromeParasympathetic neuronsFamilial dysautonomiaWhite adipocytesAutoimmune disease Sjogren's syndromeHuman pluripotent stem cellsHuman pluripotent stem cell (hPSC)-derived neuronsHuman developmental studiesPluripotent stem cellsSARS-CoV-2 infectionSchwann cell progenitorsAutonomic neuropathyCell progenitorsStem cellsModel systemNervous systemSARS-CoV-2Human diseasesDysfunctionNeuronsDifferentiation paradigmOrgan developmentNeuropathyDrug discovery studiesTranscription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape
Boddu P, Gupta A, Roy R, De La Peña Avalos B, Olazabal-Herrero A, Neuenkirchen N, Zimmer J, Chandhok N, King D, Nannya Y, Ogawa S, Lin H, Simon M, Dray E, Kupfer G, Verma A, Neugebauer K, Pillai M. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Molecular Cell 2024, 84: 1475-1495.e18. PMID: 38521065, PMCID: PMC11061666, DOI: 10.1016/j.molcel.2024.02.032.Peer-Reviewed Original ResearchRate of RNA polymerase IIChromatin landscapeElongation defectsElongation rate of RNA polymerase IIImpaired protein-protein interactionsSplicing of pre-messenger RNATranscription elongation defectsRNA polymerase IIProtein-protein interactionsPre-messenger RNACancer-associated mutationsIsogenic cell linesSin3/HDAC complexGene bodiesPolymerase IIChromatin accessibilityH3K4me3 markChromatin changesMutant SF3B1ChromatinMutant mouse modelsEpigenetic disordersEpigenetic factorsHuman diseasesMutant stateOligodendrocyte Maturation Alters the Cell Death Mechanisms That Cause Demyelination
Chapman T, Kamen Y, Piedra E, Hill R. Oligodendrocyte Maturation Alters the Cell Death Mechanisms That Cause Demyelination. Journal Of Neuroscience 2024, 44: e1794232024. PMID: 38395617, PMCID: PMC10977033, DOI: 10.1523/jneurosci.1794-23.2024.Peer-Reviewed Original ResearchPoly-ADP-riboseCell deathSubcellular localizationCaspase-3-independent mechanismCombination of intravital imagingCaspase-3-dependent mechanismDNA damageMechanism of cell deathProgrammed cell deathPrevent cell deathCell death mechanismsExecutioner caspasesDelayed cell deathOligodendrocyte maturationCaspase-3Mature oligodendrocytesOligodendrocyte deathDeath mechanismsHuman diseasesHallmarks of diseaseMolecular mechanismsIndividual cellsMechanisms of oligodendrocyte deathIntravital imagingSingle-cell ablationThe role of mitochondrial dynamics in oocyte and early embryo development
Yildirim R, Seli E. The role of mitochondrial dynamics in oocyte and early embryo development. Seminars In Cell And Developmental Biology 2024, 159: 52-61. PMID: 38330625, DOI: 10.1016/j.semcdb.2024.01.007.Peer-Reviewed Original ResearchMitochondrial dynamicsRegulating mitochondrial dynamicsImpaired mitochondrial dynamicsMorphology of mitochondriaMitochondria importDynamic organellesMitochondrial networkDysfunctional mitochondriaEmbryo developmentCellular processesPre-implantation embryo developmentPhospholipid synthesisMitochondriaHuman diseasesMitochondrial dysfunctionInnate immunityOlder reproductive age womenCell typesReproductive processesAffecting oocyte qualityCalcium regulationSuccess of pregnancyFemale reproductive healthReproductive age womenPost-fertilization
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