2025
A Comprehensive Bioinformatics Approach to Analysis of Variants: Variant Calling, Annotation, and Prioritization
Koroglu M, Bilguvar K. A Comprehensive Bioinformatics Approach to Analysis of Variants: Variant Calling, Annotation, and Prioritization. Methods In Molecular Biology 2025, 2889: 207-233. PMID: 39745615, DOI: 10.1007/978-1-0716-4322-8_15.Peer-Reviewed Original ResearchConceptsGenomic dataHigh-throughput sequencing technologyGenomic data analysisField of genomicsNext-generation sequencingVariant callingNGS technologiesSequencing technologiesBioinformatics approachComprehensive computational approachSequenceComputational approachCancer researchGenomeTranscriptomeBioinformaticsNGSProteomicsNext-generationDNARNAEfficient sequenceAnnotationVariantsFragments
2024
Increasing the Level of Knock-In of the MT-C34-Encoding Construct into the <i>CXCR4</i> Locus by Modifying Donor DNA with Cas9 Target Sites
Shepelev M, Komkov D, Golubev D, Borovikova S, Mazurov D, Kruglova N. Increasing the Level of Knock-In of the MT-C34-Encoding Construct into the CXCR4 Locus by Modifying Donor DNA with Cas9 Target Sites. Молекулярная Биология 2024, 58 DOI: 10.31857/s0026898424040058.Peer-Reviewed Original ResearchKnock-in efficiencyDonor DNADonor plasmidGenetic constructsKnock-inApplication of genome editing technologiesCleavage in vitroDonor plasmid DNACas9 target sitesDouble-strand breaksInduction of double-strand breaksGenome editing technologyPAM sitesDonor sequenceTruncated targetsCell genomeDNA modificationsInduced cleavageIncreased knock-in efficiencyCRISPR/Cas9 systemCas9LociDNAEditing technologyPlasmid DNAEpigenetics-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 systemChromatinEnzymeHistoneHuman HDAC6 senses valine abundancy to regulate DNA damage
Jin J, Meng T, Yu Y, Wu S, Jiao C, Song S, Li Y, Zhang Y, Zhao Y, Li X, Wang Z, Liu Y, Huang R, Qin J, Chen Y, Cao H, Tan X, Ge X, Jiang C, Xue J, Yuan J, Wu D, Wu W, Jiang C, Wang P. Human HDAC6 senses valine abundancy to regulate DNA damage. Nature 2024, 637: 215-223. PMID: 39567688, DOI: 10.1038/s41586-024-08248-5.Peer-Reviewed Original ResearchConceptsHuman histone deacetylase 6Active DNA demethylationDNA demethylationValine deprivationDNA damageTen-eleven translocationRegulating DNA damageHistone deacetylase 6Repeat domainTherapeutic efficacy of PARP inhibitorsBind valineEfficacy of PARP inhibitorsCellular functionsPatient-derived xenograft modelsCytoplasmic shuttlingInduce DNA damageBranched amino acidsProtein synthesisAmino acidsIntracellular levelsPARP inhibitorsDNALevels of valineTumor growthTherapeutic efficacyEXTH-23. NEW DNA-CROSSLINKING CHEMOTHERAPY IS EFFECTIVE AGAINST POST-TEMOZOLOMIDE MISMATCH REPAIR-DEFICIENT PATIENT-DERIVED HYPERMUTANT GLIOMAS
McCord M, Wang W, An S, Sears T, Sarkaria J, James C, Ruggieri B, Bindra R, Horbinski C. EXTH-23. NEW DNA-CROSSLINKING CHEMOTHERAPY IS EFFECTIVE AGAINST POST-TEMOZOLOMIDE MISMATCH REPAIR-DEFICIENT PATIENT-DERIVED HYPERMUTANT GLIOMAS. Neuro-Oncology 2024, 26: viii241-viii241. PMCID: PMC11553709, DOI: 10.1093/neuonc/noae165.0954.Peer-Reviewed Original ResearchPatient-derived xenograftsDNA inter-strand cross-linksMismatch repairDNA mismatch repairGlioblastoma cell linesBase mismatchesShRNA knockdownGlioblastoma patient-derived xenograftsMGMT deficiencyMGMT-deficient cellsDNA damageInter-strand cross-linksDNAMMR-deficient tumor cellsCell linesPatient-derived xenograft modelsComplementary in vitro studiesAlkylating agent temozolomideMMR genesVehicle control miceDays post-engraftmentApoptosisMismatch repair mutationsDNA basesResistance to temozolomideA TRilogy of ATR’s Non-Canonical Roles Throughout the Cell Cycle and Its Relation to Cancer
Joo Y, Ramirez C, Kabeche L. A TRilogy of ATR’s Non-Canonical Roles Throughout the Cell Cycle and Its Relation to Cancer. Cancers 2024, 16: 3536. PMID: 39456630, PMCID: PMC11506335, DOI: 10.3390/cancers16203536.Peer-Reviewed Original ResearchDNA damage responseNon-canonical rolesCell cyclePromote faithful chromosome segregationDetect mechanical forcesDNA damage response pathwayFaithful chromosome segregationDNA damage checkpointRad3-related proteinNuclear membrane integrityCancer therapy targetATR inhibitorsChromosome segregationDamage checkpointDamage responseApical kinaseDamaged DNAMembrane integrityAtaxia telangiectasiaNon-canonicalCancer cellsDNAClinical trialsCancer therapyClinical relevanceCharacterization and functional analysis of extrachromosomal circular DNA discovered from circulating extracellular vesicles in liver failure
Qian Y, Hong X, Yu Y, Du C, Li J, Yu J, Xiao W, Chen C, Huang D, Zhong T, Li J, Xiang X, Li Z. Characterization and functional analysis of extrachromosomal circular DNA discovered from circulating extracellular vesicles in liver failure. Clinical And Translational Medicine 2024, 14: e70059. PMID: 39406484, PMCID: PMC11479749, DOI: 10.1002/ctm2.70059.Peer-Reviewed Original ResearchHBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data
Cheng Y, Cai B, Li H, Zhang X, D’Souza G, Shrestha S, Edmonds A, Meyers J, Fischl M, Kassaye S, Anastos K, Cohen M, Aouizerat B, Xu K, Zhao H. HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data. Genome Biology 2024, 25: 273. PMID: 39407252, PMCID: PMC11476968, DOI: 10.1186/s13059-024-03411-7.Peer-Reviewed Original ResearchConceptsMethylation quantitative trait lociQuantitative trait lociTrait lociMethylation dataFunctional annotation of genetic variantsAnnotation of genetic variantsGenetic variantsBisulfite sequencing dataEffects of genetic variantsBiologically relevant cell typesDNA methylation levelsCell typesFunctional annotationSequence dataComplex traitsMethylation datasetsRelevant cell typesMeQTLsMethylation levelsMethylation regulatorsReal data analysesLociVariantsMethylationDNASpatial Engineering of Heterotypic Antigens on a DNA Framework for the Preparation of Mosaic Nanoparticle Vaccines with Enhanced Immune Activation against SARS‐CoV‐2 Variants
Zhang J, Xu Y, Chen M, Wang S, Lin G, Huang Y, Yang C, Yang Y, Song Y. Spatial Engineering of Heterotypic Antigens on a DNA Framework for the Preparation of Mosaic Nanoparticle Vaccines with Enhanced Immune Activation against SARS‐CoV‐2 Variants. Angewandte Chemie International Edition 2024, 63: e202412294. PMID: 39030890, DOI: 10.1002/anie.202412294.Peer-Reviewed Original ResearchNanoparticle vaccineReceptor-binding domainHeterotypic antigensBroad-spectrum neutralizing antibodiesSARS-CoV-2 spike trimerVaccine-induced immunityNanotechnology-based strategiesEnhanced immune activationOmicron receptor-binding domainMosaic vaccinesImmune activationSystematic in vitroNeutralizing antibodiesSARS-CoV-2 variantsMosaic nanoparticlesImmunological investigationsExcessive inflammationAntigen distributionAntigenSpike trimerRBD antigenSARS-CoV-2DNAVaccineAntiviral capabilitiesSpatial Engineering of Heterotypic Antigens on a DNA Framework for the Preparation of Mosaic Nanoparticle Vaccines with Enhanced Immune Activation against SARS‐CoV‐2 Variants
Zhang J, Xu Y, Chen M, Wang S, Lin G, Huang Y, Yang C, Yang Y, Song Y. Spatial Engineering of Heterotypic Antigens on a DNA Framework for the Preparation of Mosaic Nanoparticle Vaccines with Enhanced Immune Activation against SARS‐CoV‐2 Variants. Angewandte Chemie 2024, 136 DOI: 10.1002/ange.202412294.Peer-Reviewed Original ResearchNanoparticle vaccineReceptor-binding domainHeterotypic antigensBroad-spectrum neutralizing antibodiesSARS-CoV-2 spike trimerVaccine-induced immunityNanotechnology-based strategiesEnhanced immune activationOmicron receptor-binding domainMosaic vaccinesImmune activationSystematic in vitroNeutralizing antibodiesSARS-CoV-2 variantsMosaic nanoparticlesImmunological investigationsExcessive inflammationAntigen distributionAntigenSpike trimerRBD antigenSARS-CoV-2DNAVaccineAntiviral capabilitiesDNA-Based Molecular Clamp for Probing Protein Interactions and Structure under Force
Chung M, Zhou K, Powell J, Lin C, Schwartz M. DNA-Based Molecular Clamp for Probing Protein Interactions and Structure under Force. ACS Nano 2024, 18: 27590-27596. PMID: 39344156, PMCID: PMC11518680, DOI: 10.1021/acsnano.4c08663.Peer-Reviewed Original ResearchConceptsTalin rod domainNegative-stain electron microscopyDouble-stranded DNADNA clampProtein functionRod domainCryptic sitesProtein interactionsMolecular clampCellular mechanotransductionStudy proteinsBiochemical studiesCell biologyAdult physiologyProtein conformationTalinProteinBiochemical scaleMultiple diseasesDNAARPC5LVinculinStructural analysisEmbryogenesisDNA-based devicesIncreased autoreactivity and maturity of EBI2+ antibody-secreting cells from nasal polyps
Bai J, Kato A, Hulse K, Wechsler J, Gujar V, Poposki J, Harmon R, Iwasaki N, Wang B, Huang J, Stevens W, Conley D, Welch K, Kern R, Peters A, Eisenbarth S, Schleimer R, Tan B. Increased autoreactivity and maturity of EBI2+ antibody-secreting cells from nasal polyps. JCI Insight 2024, 9: e177729. PMID: 39253973, PMCID: PMC11385095, DOI: 10.1172/jci.insight.177729.Peer-Reviewed Original ResearchConceptsAntibody-secreting cellsGene Ontology biological processesSingle-cell RNA-seq analysisApoptosis pathwayNumbers of antibody-secreting cellsAnti-dsDNA IgGPlasma cell differentiationBiological processesCell differentiationNasal polypsGenesMolecular characteristicsNF-kBProliferative cellsMolecular featuresCellsAnti-double-stranded DNAIgG antibody-secreting cellsEBI2B cellsXBP1Recurrent NPElevated numbersDNAIncreased autoreactivityUltra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction
Li X, Liu T, Bacchiocchi A, Li M, Cheng W, Wittkop T, Mendez F, Wang Y, Tang P, Yao Q, Bosenberg M, Sznol M, Yan Q, Faham M, Weng L, Halaban R, Jin H, Hu Z. Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction. EMBO Molecular Medicine 2024, 16: 2188-2209. PMID: 39164471, PMCID: PMC11393307, DOI: 10.1038/s44321-024-00115-0.Peer-Reviewed Original ResearchMolecular residual diseaseCirculating tumor DNAWhole-genome sequencingCell-free DNAGenome sequenceDetection of molecular residual diseaseCirculating tumor DNA detectionResidual disease detectionConsistent with clinical outcomesVariant allele frequencyResidual diseaseMelanoma patientsMonitoring immunotherapyTumor DNAEsophageal cancerClinical outcomesColorectal cancerWGS technologiesAllele frequenciesCancerDNAAnalytical sensitivitySequenceImmunotherapyRelapseHuman AKR1C3 binds agonists of GPR84 and participates in an expanded polyamine pathway
Dudkina N, Park H, Song D, Jain A, Khan S, Flavell R, Johnson C, Palm N, Crawford J. Human AKR1C3 binds agonists of GPR84 and participates in an expanded polyamine pathway. Cell Chemical Biology 2024, 32: 126-144.e18. PMID: 39163853, PMCID: PMC11748234, DOI: 10.1016/j.chembiol.2024.07.011.Peer-Reviewed Original ResearchHuman aldo-keto reductase family 1 member C3Mammalian fatty acid synthaseDNA double-strand break responseDouble-strand break responseAldo-keto reductase family 1 member C3Associated with poor prognosisPolyamine pathwayFatty acid synthesisFatty acid synthaseAcid synthaseAKR1C3 activityPoor prognosisBiochemical roleAcid synthesisClinical significanceLigand screeningFerroptosis resistanceDNA damageAKR1C3Metabolic diseasesDiverse cancersDNANADPHAgonists of GPR84GPR84DNA methylation in mammalian development and disease
Smith Z, Hetzel S, Meissner A. DNA methylation in mammalian development and disease. Nature Reviews Genetics 2024, 26: 7-30. PMID: 39134824, DOI: 10.1038/s41576-024-00760-8.Peer-Reviewed Original ResearchLong-read sequencing technologiesDNA methylation fieldDNA methylation landscapeGenome functionMethylation landscapeSequencing technologiesEpigenetic codeGenomic characterizationRegulatory layerDNA methylationCell physiologyMammalian developmentMammalian lifespanGenetic featuresFunctional understandingSingle-cellDNAMechanistic discoveriesSomatic transitionsPhases of discoveryDevelopmental potentialDiscoveryPhenotypeSenescencePhysiologyDonor DNA Modification with Cas9 Targeting Sites Improves the Efficiency of MTC34 Knock-in into the CXCR4 Locus
Shepelev M, Komkov D, Golubev D, Borovikova S, Mazurov D, Kruglova N. Donor DNA Modification with Cas9 Targeting Sites Improves the Efficiency of MTC34 Knock-in into the CXCR4 Locus. Molecular Biology 2024, 58: 672-682. DOI: 10.1134/s0026893324700250.Peer-Reviewed Original ResearchCas9 target sitesDouble-strand breaksKnock-inCell genomeGenetic constructsDNA modificationsDonor DNADonor plasmid DNATarget siteKnock-in efficiencyGenome editing technologyInduce double-strand breaksProximal nucleotidesPAM sitesDonor plasmidDonor sequenceCXCR4 locusGenomeIn vitroInduced cleavageCRISPR/Cas9 systemCas9LociEditing technologyDNA13. AmpliconSuite: Analyzing focal amplifications in cancer genomes
Luebeck J, Huang E, Dameracharla B, Kim F, Liefeld T, Ahuja R, Prasad D, Prasad G, Kim S, Kim H, Bailey P, Verhaak R, Deshpande V, Reich M, Mischel P, Mesirov J, Bafna V. 13. AmpliconSuite: Analyzing focal amplifications in cancer genomes. Cancer Genetics 2024, 286: s5. DOI: 10.1016/j.cancergen.2024.08.015.Peer-Reviewed Original ResearchWhole-genome sequencingWhole-genome sequencing dataFocal amplificationCancer genomesStructural variationsAmplification of oncogenesExtrachromosomal DNACopy numberEcDNAGenomeOncogene amplificationAmpliconArchitectCancer progressionAmplificationAmplification typeTumor samplesBiocondaNextflowPCAWGGenePatternRobust identificationDNACCLESequenceOncogeneGene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging
Occean J, Yang N, Sun Y, Dawkins M, Munk R, Belair C, Dar S, Anerillas C, Wang L, Shi C, Dunn C, Bernier M, Price N, Kim J, Cui C, Fan J, Bhattacharyya M, De S, Maragkakis M, de Cabo R, Sidoli S, Sen P. Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging. Nature Communications 2024, 15: 6357. PMID: 39069555, PMCID: PMC11284234, DOI: 10.1038/s41467-024-50725-y.Peer-Reviewed Original ResearchConceptsTissue-specific functionsDNA hydroxymethylationMagnitude of transcriptional changesAlternative splicing eventsMagnitude of gene expression changesTissue-specific genesGene expression changesGene bodiesSplicing eventsDNA methylationModel organismsTranscriptional changesExpression changesGenesAge-related diseasesFunctional roleMouse liverHuman tissuesProlonged quiescenceRestriction functionSplicingDNAMiceAge-related contextSenescenceRare 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 disordersKDM5BDNAMutationsFamilyLysineDiscoveryDNA methylation profiles of cancer-related fatigue associated with markers of inflammation and immunometabolism
Xiao C, Peng G, Conneely K, Zhao H, Felger J, Wommack E, Higgins K, Shin D, Saba N, Bruner D, Miller A. DNA methylation profiles of cancer-related fatigue associated with markers of inflammation and immunometabolism. Molecular Psychiatry 2024, 30: 76-83. PMID: 38977918, DOI: 10.1038/s41380-024-02652-z.Peer-Reviewed Original ResearchGene expressionMethylation lociAssociated with gene expressionHead and neck cancerDNA methylation profilesProtein markersLipid metabolismInvolvement of genesIllumina MethylationEPICDNA methylationRelevant gene expressionEpigenetic modificationsExpression pairsInflammatory markersInflammatory responseLociHead and neck cancer patientsAssociated with inflammatory markersGenesDNAMarkers of inflammationAssociated with fatigueExpressionMethylationPost-radiotherapy
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