2025
The multilayered transcriptional architecture of glioblastoma ecosystems
Nomura M, Spitzer A, Johnson K, Garofano L, Nehar-belaid D, Galili Darnell N, Greenwald A, Bussema L, Oh Y, Varn F, D’Angelo F, Gritsch S, Anderson K, Migliozzi S, Gonzalez Castro L, ChowdhFury T, Robine N, Reeves C, Park J, Lipsa A, Hertel F, Golebiewska A, Niclou S, Nusrat L, Kellet S, Das S, Moon H, Paek S, Bielle F, Laurenge A, Di Stefano A, Mathon B, Picca A, Sanson M, Tanaka S, Saito N, Ashley D, Keir S, Ligon K, Huse J, Yung W, Lasorella A, Verhaak R, Iavarone A, Suvà M, Tirosh I. The multilayered transcriptional architecture of glioblastoma ecosystems. Nature Genetics 2025, 57: 1155-1167. PMID: 40346361, PMCID: PMC12081307, DOI: 10.1038/s41588-025-02167-5.Peer-Reviewed Original ResearchConceptsCell typesSingle-nucleus RNA sequencingDiversity of cellular statesMalignant cell statesGene expression programsTumor DNA sequencingDNA sequencesTranscriptional architectureCellular statesTranscriptional heterogeneityRNA sequencingCell statesCellular heterogeneityExpression programsGenetic aberrationsRecurrent GBM samplesPathway activationLayer of heterogeneityNeuronal-likeNonmalignant cell typesGBM samplesTherapeutic resistanceSequenceEcosystemCell-likeDeciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics
Spitzer A, Johnson K, Nomura M, Garofano L, Nehar-belaid D, Darnell N, Greenwald A, Bussema L, Oh Y, Varn F, D’Angelo F, Gritsch S, Anderson K, Migliozzi S, Gonzalez Castro L, Chowdhury T, Robine N, Reeves C, Park J, Lipsa A, Hertel F, Golebiewska A, Niclou S, Nusrat L, Kellet S, Das S, Moon H, Paek S, Bielle F, Laurenge A, Di Stefano A, Mathon B, Picca A, Sanson M, Tanaka S, Saito N, Ashley D, Keir S, Ligon K, Huse J, Yung W, Lasorella A, Iavarone A, Verhaak R, Tirosh I, Suvà M. Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics. Nature Genetics 2025, 57: 1168-1178. PMID: 40346362, PMCID: PMC12081298, DOI: 10.1038/s41588-025-02168-4.Peer-Reviewed Original ResearchConceptsSingle-cell genomicsSingle-nucleus RNA sequencingMalignant cell statesDNA sequencesNeuronal cell typesTumor microenvironmentRNA sequencingMalignant cell fractionCell statesCell typesCell fractionIsocitrate dehydrogenase (IDH)-wildtype glioblastomaStandard-of-care therapyCo-evolutionMolecular heterogeneityTumor microenvironment modifierEcosystemTumor microenvironment compositionSubsets of patientsSequenceRecurrent glioblastomaCharacterizing Rare DNA Copy-Number Variants in Pediatric Obsessive-Compulsive Disorder
Abdallah S, Olfson E, Cappi C, Greenspun S, Zai G, Rosário M, Willsey A, Shavitt R, Miguel E, Kennedy J, Richter M, Fernandez T. Characterizing Rare DNA Copy-Number Variants in Pediatric Obsessive-Compulsive Disorder. Journal Of The American Academy Of Child & Adolescent Psychiatry 2025 PMID: 40122455, DOI: 10.1016/j.jaac.2025.03.014.Peer-Reviewed Original ResearchCopy-number variantsWhole-exome DNA sequencingEXome-Hidden Markov ModelDetect copy-number variantsSingle-nucleotide variantsGenetic factorsWhole-exome sequencingExamination of genesBiological systems analysisTrio familiesDNA sequencesMicroarray dataOCD riskBurden analysisBiological processesGenesSequenceVariantsObsessive-compulsive disorderPrimary analysisXHMMPediatric obsessive-compulsive disorderCompared to controlsFamilySilicoGestational trophoblastic disease: STR genotyping for precision diagnosis
Rozenova K, Buza N, Hui P. Gestational trophoblastic disease: STR genotyping for precision diagnosis. Expert Review Of Molecular Diagnostics 2025, 25: 1-19. PMID: 39801212, DOI: 10.1080/14737159.2025.2453506.Peer-Reviewed Original ResearchConceptsShort tandem repeatsGestational trophoblastic diseaseShort tandem repeat genotypingDiagnosis of gestational trophoblastic diseaseGestational trophoblastic tumorsHydatidiform MoleSTR genotypingTrophoblastic tumorDifferential diagnosis of gestational trophoblastic diseaseRepetitive DNA sequencesManagement of gestational trophoblastic diseaseSubclassification of hydatidiform molesGestational trophoblastic neoplasmsPrognostication of patientsPaternity testingNon-neoplastic natureHuman genomeTandem repeatsDNA sequencesForensic identityTrophoblastic diseaseTrophoblastic neoplasmsGynecologic conditionsDiagnostic workupClinical outcomes
2024
Investigating Environmental Determinants of Hookworm Transmission using GPS Tracking and Metagenomics Technologies
Sumboh J, Agyenkwa-Mawuli K, Schwinger E, Donkor I, Akorli J, Dwomoh D, Ashong Y, Osabutey D, Ababio F, Nusbaum O, Humphries D, Cappello M, Koram K, Kwofie S, Wilson M. Investigating Environmental Determinants of Hookworm Transmission using GPS Tracking and Metagenomics Technologies. American Journal Of Tropical Medicine And Hygiene 2024, 112: 561-570. PMID: 39813691, PMCID: PMC11884298, DOI: 10.4269/ajtmh.24-0384.Peer-Reviewed Original ResearchConceptsEffective cation exchange capacityCation exchange capacitySandy-loam soilDominant helminth speciesSoil samplesClay contentSoil parametersExchange capacityHelminth larvaeAnalysis of DNA sequencesGPS trackingSoilParastrongyloides trichosuriAssociated with exposureLarvaeChemical propertiesPotential sourcesMovement dataSpeciesPredominant speciesHelminth speciesLarval countsMetagenomic technologiesDNA sequencesMetagenomic analysisCohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion
Yuan T, Yan H, Li K, Surovtsev I, King M, Mochrie S. Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion. Genome Biology 2024, 25: 293. PMID: 39543681, PMCID: PMC11566905, DOI: 10.1186/s13059-024-03432-2.Peer-Reviewed Original ResearchConceptsTopologically associating domainsLoop extrusionTopologically associating domains boundariesNon-vertebrate eukaryotesChIP-seq dataChromatin spatial organizationTree of lifeHi-C mapsBinds CTCFCohesin distributionTAD boundariesCTCF sitesChromatin organizationDNA sequencesCTCFCohesinYeastChromatinSpatial organizationEukaryotesGenomeResultsToVertebratesExtrusion factorsOrganizationEPCO-26. LONGITUDINAL SINGLE-CELL ANALYSES IDENTIFY DRIVERS OF GENETIC, EPIGENOMIC, AND CELLULAR EVOLUTION IN IDH-MUTANT GLIOMA
Johnson K, Spitzer A, Varn F, Nomura M, Garofano L, Chowdhury T, Anderson K, D’Angelo F, Bussema L, Gritsch S, Oh Y, Moon H, Paek S, Bielle F, Laurenge A, Di Stefano A, Mathon B, Picca A, Sanson M, Lipsa A, Hertel F, Zhao Z, Wang Q, Jiang T, Hermes B, Sanai N, Golebiewska A, Niclou S, Huse J, Yung W, Lasorella A, Suvà M, Iavarone A, Tirosh I, Verhaak R. EPCO-26. LONGITUDINAL SINGLE-CELL ANALYSES IDENTIFY DRIVERS OF GENETIC, EPIGENOMIC, AND CELLULAR EVOLUTION IN IDH-MUTANT GLIOMA. Neuro-Oncology 2024, 26: viii6-viii7. PMCID: PMC11552777, DOI: 10.1093/neuonc/noae165.0025.Peer-Reviewed Original ResearchIDH-mutant gliomasGenetic alterationsStem-like populationDifferentially accessible peaksChromatin accessibility dataCopy number alterationsCellular hierarchyCycling populationTumor microenvironment cell typesSingle nucleus RNA sequencingCell cycle alterationsMalignant cell differentiationHigh tumor gradeNucleus RNA sequencingDNA sequencesATAC sequencingGenetic analysisCellular statesAccessibility peaksMicroenvironment cell typesReduced differentiationRNA sequencingIntratumoral cellular heterogeneityCellular heterogeneityTumor gradeEPCO-34. DECIPHERING THE LONGITUDINAL TRAJECTORIES OF GLIOBLASTOMA BY INTEGRATIVE SINGLE-CELL GENOMICS
Spitzer A, Johnson K, Nomura M, Garofano L, Nehar-belaid D, Darnell N, Greenwald A, Bussema L, Oh Y, Varn F, D’Angelo F, Gritsch S, Anderson K, Migliozzi S, Castro L, Chowdhury T, Robine N, Reeves C, Park J, Lipsa A, Hertel F, Golebiewska A, Niclou S, Nusrat L, Kellet S, Das S, Moon H, Paek S, Bielle F, Laurenge A, Di Stefano A, Mathon B, Picca A, Sanson M, Tanaka S, Saito N, Ashley D, Keir S, Huse J, Yung W, Lasorella A, Iavarone A, Verhaak R, Tirosh I, Suvà M. EPCO-34. DECIPHERING THE LONGITUDINAL TRAJECTORIES OF GLIOBLASTOMA BY INTEGRATIVE SINGLE-CELL GENOMICS. Neuro-Oncology 2024, 26: viii9-viii9. PMCID: PMC11553653, DOI: 10.1093/neuonc/noae165.0033.Peer-Reviewed Original ResearchMalignant cellsStandard-of-care therapyCell typesMalignant cell fractionIDH-wildtype glioblastomaTumor DNA sequencingRecurrent GBM specimensMesenchymal-like cellsAssociated with specific changesMGMT methylationCell statesTreatment responseSingle-cell genomicsComposition of cell typesSingle-nucleus RNA sequencingMalignant stateDistribution of cell typesRecurrent samplesGBM specimensLongitudinal cohortGlioblastomaDNA sequencesClinical annotationDeletion phenotypeCell fractionDisentangling Race from Skin Color in Modern Biology and Medicine
Horsley V, Dadzie O, Hall R, Jablonski N. Disentangling Race from Skin Color in Modern Biology and Medicine. Journal Of Investigative Dermatology 2024, 145: 240-248. PMID: 39503695, DOI: 10.1016/j.jid.2024.08.029.Peer-Reviewed Original ResearchEthnic classificationDominant cultural institutionsDiversity of peopleDisciplines of biologyModern disciplineCultural institutionsEuropean scientistsChattel slaveryModern institutionsModern biologyPolitical systemCensus classificationEconomic structureClassifying peopleHuman DNA sequencesEconomic systemSocial environmentSlaveryWorldGenomic analysisDNA sequencesModernizationPeopleRaceBiological diversityBacterial cell surface characterization by phage display coupled to high-throughput sequencing
Grun C, Jain R, Schniederberend M, Shoemaker C, Nelson B, Kazmierczak B. Bacterial cell surface characterization by phage display coupled to high-throughput sequencing. Nature Communications 2024, 15: 7502. PMID: 39209859, PMCID: PMC11362561, DOI: 10.1038/s41467-024-51912-7.Peer-Reviewed Original ResearchConceptsBacterial cell surfaceCell surfacePhage displayP. aeruginosa virulence factorsHigh-throughput DNA sequencingHigh-throughput sequencingPhage display panningCapacity of bacteriaCamelid single-domain antibodiesVirulence factorsDNA sequencesBacterial genotypesPhageSingle-domain antibodiesPseudomonas aeruginosaHost defenseBiological informationAntimicrobial resistanceLiving cellsSequenceChronic infectionCell surface characterizationAdaptive changesCellsBacteriaRare de novo damaging DNA variants are enriched in attention-deficit/hyperactivity disorder and implicate risk genes
Olfson E, Farhat L, Liu W, Vitulano L, Zai G, Lima M, Parent J, Polanczyk G, Cappi C, Kennedy J, Fernandez T. Rare de novo damaging DNA variants are enriched in attention-deficit/hyperactivity disorder and implicate risk genes. Nature Communications 2024, 15: 5870. PMID: 38997333, PMCID: PMC11245598, DOI: 10.1038/s41467-024-50247-7.Peer-Reviewed Original ResearchConceptsDNA sequencesRisk genesHigh-confidence risk genesWhole-exome DNA sequencingSequencing of familiesIdentified de novoLysine demethylase 5BDNA variantsTrio cohortBiological pathwaysGenesSequencing cohortGenetic factorsChildhood neurodevelopmental disordersAttention-deficit/hyperactivity disorderSequenceVariantsADHD riskNeurodevelopmental disordersKDM5BDNAMutationsFamilyLysineDiscovery
2023
The molecular pathology of schizophrenia: an overview of existing knowledge and new directions for future research
Nakamura T, Takata A. The molecular pathology of schizophrenia: an overview of existing knowledge and new directions for future research. Molecular Psychiatry 2023, 28: 1868-1889. PMID: 36878965, PMCID: PMC10575785, DOI: 10.1038/s41380-023-02005-2.Peer-Reviewed Original ResearchConceptsMolecular pathology of schizophreniaCopy number variantsDiscovery of copy number variantsLarge-scale exome sequencing studiesMolecular pathologyExome sequencing studiesDNA sequencesPathology of schizophreniaEpigenomic analysesSequencing studiesSingle genesGenetic variantsRare mutationsMultiple disease modelsGenesGenetic pathologyDisease modelsCurrent knowledgeSchizophrenia brainDisease riskVariantsPostmortem tissueBiological alterationsDNAEtiological validityGenome-wide analysis of aberrant position and sequence of plasma DNA fragment ends in patients with cancer
Budhraja K, McDonald B, Stephens M, Contente-Cuomo T, Markus H, Farooq M, Favaro P, Connor S, Byron S, Egan J, Ernst B, McDaniel T, Sekulic A, Tran N, Prados M, Borad M, Berens M, Pockaj B, LoRusso P, Bryce A, Trent J, Murtaza M. Genome-wide analysis of aberrant position and sequence of plasma DNA fragment ends in patients with cancer. Science Translational Medicine 2023, 15: eabm6863. PMID: 36630480, PMCID: PMC10080578, DOI: 10.1126/scitranslmed.abm6863.Peer-Reviewed Original ResearchConceptsGenome-wide analysisNucleotide frequenciesDNA fragmentsGenome-wide differencesFragment endsNovel cancer diagnosticsCopy number amplificationChromatin accessibilityGenomic regionsGenomic positionsGC contentDNA sequencesSequencing dataDifferent cancer typesNumber amplificationCell typesCellular originSomatic mutationsCancer cellsFragment lengthCell-free DNADNACancer typesFragmentsSequence
2022
Recurrent repeat expansions in human cancer genomes
Erwin G, Gürsoy G, Al-Abri R, Suriyaprakash A, Dolzhenko E, Zhu K, Hoerner C, White S, Ramirez L, Vadlakonda A, Vadlakonda A, von Kraut K, Park J, Brannon C, Sumano D, Kirtikar R, Erwin A, Metzner T, Yuen R, Fan A, Leppert J, Eberle M, Gerstein M, Snyder M. Recurrent repeat expansions in human cancer genomes. Nature 2022, 613: 96-102. PMID: 36517591, PMCID: PMC9812771, DOI: 10.1038/s41586-022-05515-1.Peer-Reviewed Original ResearchConceptsTandem repeatsCancer genomesRepeat expansionCandidate cis-regulatory elementsCis-regulatory elementsRepetitive DNA sequencesHuman cancer genomesRenal cell carcinoma samplesGene regulationLarge repeat expansionsGenetic variationRegulatory elementsDNA sequencesTR expansionsFirst intronCancer typesComprehensive catalogGenomeHuman cancersDNA sequencingShort tractsCell proliferationUnexplored sourceNeurodegenerative disordersPotential roleStructural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme
Wang J, Skeens E, Arantes PR, Maschietto F, Allen B, Kyro GW, Lisi GP, Palermo G, Batista VS. Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme. Biochemistry 2022, 61: 785-794. PMID: 35420793, PMCID: PMC9069930, DOI: 10.1021/acs.biochem.2c00127.Peer-Reviewed Original ResearchConceptsShort palindromic repeatsSubstrate specificityPalindromic repeatsAla mutantWT enzymeRNA-binding domainAssociated 9 (Cas9) systemForeign DNA sequencesDNA strandsWild-type enzymeDouble-strand breaksEnhanced substrate specificityHNH active siteDynamics of proteinsType II immunityCas9 proteinDNA substratesDNA sequencesStructural basisMutantsAla substitutionDistinct conformationsSingle LysCatalytic siteEnzymeKhorana, Har Gobind
Söll D, RajBhandary U. Khorana, Har Gobind. 2022 DOI: 10.1016/b978-0-12-822563-9.00089-5.Peer-Reviewed Original ResearchGene synthesisDNA genesChemical synthesisChemical biologyGenetic codeMembrane proteinsDNA mutagenesisDNA sequencesSynthesis of DNABacterio-opsinG proteinsSuch profound effectsProton pumpMRNA synthesisGenesDNA sequencingBiological researchSynthesisBiologyPCR amplificationDNA chipChemistryNucleic acidsDNA diagnosticsProtein
2020
Parsing the Functional Impact of Noncoding Genetic Variants in the Brain Epigenome
Powell SK, O'Shea C, Brennand KJ, Akbarian S. Parsing the Functional Impact of Noncoding Genetic Variants in the Brain Epigenome. Biological Psychiatry 2020, 89: 65-75. PMID: 33131715, PMCID: PMC7718420, DOI: 10.1016/j.biopsych.2020.06.033.Peer-Reviewed Original ResearchConceptsGenetic variantsDisease-associated genetic variationProtein-coding lociRisk-associated genetic variantsGene regulatory lociThousands of variantsFunctional impactRare genetic variantsEpigenomic mappingRegulatory lociBrain epigenomeGenetic variationDNA sequencesNoncoding variantsGene expressionIntegrative analysisEpigenomic architectureMolecular pathwaysPsychiatric geneticsFunctional readoutRisk variantsLociVariantsHighlight findingsEpigenomeStructural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6
Schmidt JM, Bleichert F. Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6. Nature Communications 2020, 11: 4263. PMID: 32848132, PMCID: PMC7450096, DOI: 10.1038/s41467-020-18067-7.Peer-Reviewed Original ResearchMeSH KeywordsAAA DomainAdenosine TriphosphateAnimalsCell Cycle ProteinsCryoelectron MicroscopyDNADrosophila melanogasterDrosophila ProteinsHydrolysisMinichromosome Maintenance ProteinsModels, MolecularOrigin Recognition ComplexProtein BindingRecombinant ProteinsReplication OriginSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsConceptsOrigin recognition complexRecognition complexReplication originsDrosophila origin recognition complexEukaryotic DNA replication initiationMetazoan origin recognition complexCryo-electron microscopy structureMcm2-7 replicative helicaseATPase siteDNA replication initiationWalker B motifMcm2-7 loadingWinged-helix domainReplicative helicaseReplication initiationMicroscopy structureDistinct DNAB motifOrigin recognitionDNA sequencesDNA bendingDNA bindingPrimary DNADNA geometryLoop regionImproved reference genome of the arboviral vector Aedes albopictus
Palatini U, Masri RA, Cosme LV, Koren S, Thibaud-Nissen F, Biedler JK, Krsticevic F, Johnston JS, Halbach R, Crawford JE, Antoshechkin I, Failloux AB, Pischedda E, Marconcini M, Ghurye J, Rhie A, Sharma A, Karagodin DA, Jenrette J, Gamez S, Miesen P, Masterson P, Caccone A, Sharakhova MV, Tu Z, Papathanos PA, Van Rij RP, Akbari OS, Powell J, Phillippy AM, Bonizzoni M. Improved reference genome of the arboviral vector Aedes albopictus. Genome Biology 2020, 21: 215. PMID: 32847630, PMCID: PMC7448346, DOI: 10.1186/s13059-020-02141-w.Peer-Reviewed Original ResearchConceptsArboviral vector Aedes albopictusSex-determining locusFirst physical mapAsian tiger mosquito Aedes albopictusTiger mosquito Aedes albopictusMosquito Aedes albopictusAedes albopictusPiRNA clustersDiverse AeGenome assemblyInnovative control measuresReference genomeAccurate DNA sequencesNovel microRNAsImmunity genesPhysical mapDNA sequencesGenetic manipulationViral insertionVector Aedes albopictusExpression dataGenomeAlbopictus populationsSequencing methodsAdaptation potentialIdentification of a 22 bp DNA cis Element that Plays a Critical Role in Colony Stimulating Factor 1-Dependent Transcriptional Activation of the SPHK1 Gene
Yao GQ, Zhu M, Walker J, Insogna K. Identification of a 22 bp DNA cis Element that Plays a Critical Role in Colony Stimulating Factor 1-Dependent Transcriptional Activation of the SPHK1 Gene. Calcified Tissue International 2020, 107: 52-59. PMID: 32246175, PMCID: PMC7274855, DOI: 10.1007/s00223-020-00685-4.Peer-Reviewed Original ResearchConceptsColony stimulating factor 1Sphingosine kinase 1Bp fragmentSPHK1 promoterBp sequenceSphK1 geneDNA cis elementsProtein binding regionsSPHK1 gene expressionBp DNA fragmentStimulating factor 1Dual-luciferase reporterPutative DNATranscriptional activationTranscription factorsNuclear proteinsDNA sequencesCis elementsDNA bindingGene expressionPromoter activityDNA fragmentsKinase 1EMSAsProtein binding
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