2024
Expression of Random Sequences and de novo Evolved Genes From the Mouse in Human Cells Reveals Functional Diversity and Specificity
Aldrovandi S, Castro J, Ullrich K, Karger A, Luria V, Tautz D. Expression of Random Sequences and de novo Evolved Genes From the Mouse in Human Cells Reveals Functional Diversity and Specificity. Genome Biology And Evolution 2024, 16: evae175. PMID: 39663928, PMCID: PMC11635099, DOI: 10.1093/gbe/evae175.Peer-Reviewed Original ResearchConceptsOpen reading frameGene open reading frameCellular regulatory pathwaysNoncoding DNAReading frameHuman cell linesHuman genomeAlpha-helicesGrowth experimentsCellular physiologyFunctional diversityPositive selectionBeta-sheetTranscriptomic responseRegulatory pathwaysAdaptive advantageHuman cellsGenesCell clonesCell linesSequenceClonesRandom sequencePathwayCellsWhat makes each of us unique? The nine-banded armadillo as a model to study individuality
Leao D, Duque A, Dietrich M. What makes each of us unique? The nine-banded armadillo as a model to study individuality. Frontiers In Mammal Science 2024, 3: 1450655. DOI: 10.3389/fmamm.2024.1450655.Peer-Reviewed Original ResearchScience of individualityInter-individual differencesNine-banded armadilloBrain-related traitsSources of varianceBiology of individualsBrain structuresGenetic clonesReproductive biologyArmadillosHuman brainBrainMammalian brainStochastic factorsBiological mechanismsScienceIndividualsBiologyStudy individualsComplex interplayEmotionsClonesThoughtsNeuroscienceArgumentsInferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser.
Jensen C, Sumner J, Kleinstein S, Hoehn K. Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser. The Journal Of Immunology 2024, 212: 1579-1588. PMID: 38557795, PMCID: PMC11073909, DOI: 10.4049/jimmunol.2300851.Peer-Reviewed Original ResearchConceptsPhylogenetic treeL chainsBranch lengthsBCR sequencesTree-building methodsSingle-cell sequencing dataHistory of mutationsSingle-cell sequencingPhylogenetic methodsSequence dataSequencing technologiesL chain sequencesTree accuracyEvolutionary processSingle-cellPhylogenyImmune responseSomatic hypermutationSequenceClonesMutationsB cell clonesHuman immune responseTreesBCR
2023
Epigenetic markers and therapeutic targets for metastasis
Kravitz C, Yan Q, Nguyen D. Epigenetic markers and therapeutic targets for metastasis. Cancer And Metastasis Reviews 2023, 42: 427-443. PMID: 37286865, PMCID: PMC10595046, DOI: 10.1007/s10555-023-10109-y.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsEpigenomic alterationsLineage integrityTherapeutic targetEpigenetic markersCancer cellsGenetic aberrationsCurrent knowledgeHuman tumorsMalignant cell cloneTumor progressionDNANumber of discoveriesCell clonesDisseminated diseaseCertain organsPrimary tumorTherapeutic responseMetastatic cancerEpigenomeChromatinHistonesLiquid biopsyAlterationsClonesTargetExploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires
Pelissier A, Luo S, Stratigopoulou M, Guikema J, Martínez M. Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires. Frontiers In Immunology 2023, 14: 1123968. PMID: 37138881, PMCID: PMC10150052, DOI: 10.3389/fimmu.2023.1123968.Peer-Reviewed Original ResearchConceptsClonal diversityB cell receptorB cellsB cell diversityHigh-throughput sequencing technologyAlignment-free methodsAnalysis of immune repertoiresAlignment-based methodsPatterns of variationB cell receptor sequencesSequencing technologiesClonal clustersClonal identificationB cell repertoireActivated B cellsAdaptive immune responsesDiversity indexHigh-throughput characterizationAdaptive immune systemShort sequencesClonal characterizationClonal familiesClonesRepertoire dataSomatic hypermutationClonally Selected Lines After CRISPR-Cas Editing Are Not Isogenic
Panda A, Suvakov M, Mariani J, Drucker K, Park Y, Jang Y, Kollmeyer T, Sarkar G, Bae T, Kim J, Yoon W, Jenkins R, Vaccarino F, Abyzov A. Clonally Selected Lines After CRISPR-Cas Editing Are Not Isogenic. The CRISPR Journal 2023, 6: 176-182. PMID: 37071670, PMCID: PMC10123805, DOI: 10.1089/crispr.2022.0050.Peer-Reviewed Original ResearchConceptsCopy number alterationsSeparate genomic lociSingle nucleotide mutationsApplication of CRISPRCRISPR-Cas editingOff-target editsScreening of clonesGenomic divergenceWhole-genome sequencingGenomic lociSelection of clonesGenome sequencingNucleotide mutationsTarget editsCultured cellsClonal linesNumber alterationsCell cloningClonesMutationsCloningCRISPR
2022
Is it the time to integrate novel sequencing technologies into clinical practice?
VanOudenhove J, Halene S, Mendez L. Is it the time to integrate novel sequencing technologies into clinical practice? Current Opinion In Hematology 2022, 30: 70-77. PMID: 36602939, DOI: 10.1097/moh.0000000000000754.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsNovel sequencing technologiesSequencing technologiesUnprecedented biological insightsNext-generation sequencing techniquesDNA sequencing technologiesHigh-throughput NGSRare cell populationsBiological insightsMultiomics approachSequencing techniquesGenotype-phenotype correlationClonal diversityCellular resolutionMechanistic insightsCell populationsPhenotype correlationMyeloid diseasesClonesClonal hierarchyClonal haematopoiesisResidual clonesInsightsSeqDiversityImproved captureLongitudinal single-cell analysis of a patient receiving adoptive cell therapy reveals potential mechanisms of treatment failure
Qu R, Kluger Y, Yang J, Zhao J, Hafler D, Krause D, Bersenev A, Bosenberg M, Hurwitz M, Lucca L, Kluger H. Longitudinal single-cell analysis of a patient receiving adoptive cell therapy reveals potential mechanisms of treatment failure. Molecular Cancer 2022, 21: 219. PMID: 36514045, PMCID: PMC9749221, DOI: 10.1186/s12943-022-01688-5.Peer-Reviewed Original ResearchConceptsAdoptive cell therapySingle-cell analysisDepth single-cell analysisSingle-cell RNAACT productsDisease progressionT-cell receptor sequencingCell therapyFamily genesFeatures of exhaustionMultiple tumor typesCell expansionGenesNew clonotypesTIL preparationsClonal cell expansionCytokine therapyTreatment failureSerial bloodClonesEffector functionsSerial samplesTumor typesCellular therapyTherapyClone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models
Chroni A, Miura S, Hamilton L, Vu T, Gaffney SG, Aly V, Karim S, Sanderford M, Townsend JP, Kumar S. Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models. Cancers 2022, 14: 4326. PMID: 36077861, PMCID: PMC9454754, DOI: 10.3390/cancers14174326.Peer-Reviewed Original ResearchDynamic evolutionary historyMolecular phylogenetic analysisMolecular evolutionary analysisTumor cell migrationEvolutionary historyEvolutionary analysisPhylogenetic analysisDispersal routesCell migrationTumor evolutionTumor genetic heterogeneityGenetic heterogeneityMetastatic cellsClonesTumor migrationMigration historyGeneral patternPhylogeneticsFundamental questionsEvolution of metastasesMigrationEvolutionCellsHybridsVariationAbstract A040: Intra-epithelia cell dynamics shape evolutionary dynamics and selection of therapy resistant clones in lung cancer
Fu X, Bhargava A, Bailey S, Biswas D, Ruiz C, Kumar S, French P, McGranahan N, Swanton C, Bates P, Sahai E. Abstract A040: Intra-epithelia cell dynamics shape evolutionary dynamics and selection of therapy resistant clones in lung cancer. Cancer Research 2022, 82: a040-a040. DOI: 10.1158/1538-7445.evodyn22-a040.Peer-Reviewed Original ResearchEvolutionary dynamicsResistant clonesEnhanced cell motilityCapability of cancer cellsCell-cell cohesionRNA sequencing dataCell dynamicsExpansion of clonesModel of cell proliferationLung cancer cell linesVariant allele frequencySequence dataNeutral evolutionCell motilityGenomic complexityCancer cell linesCell line modelsAllele frequenciesSelection pressureRandom motilityGrowth arrestMutational processesClonesCell migrationIntra-tumor heterogeneitySingle-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19
Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason L, Ko A, Montgomery R, Farhadian S, Iwasaki A, Shaw A, van Dijk D, Zhao H, Kleinstein S, Hafler D, Kaminski N, Dela Cruz C. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. Nature Communications 2022, 13: 440. PMID: 35064122, PMCID: PMC8782894, DOI: 10.1038/s41467-021-27716-4.Peer-Reviewed Original ResearchMeSH KeywordsAdaptive ImmunityAgedAntibodies, Monoclonal, HumanizedCD4-Positive T-LymphocytesCD8-Positive T-LymphocytesCells, CulturedCOVID-19COVID-19 Drug TreatmentFemaleGene Expression ProfilingGene Expression RegulationHumansImmunity, InnateMaleReceptors, Antigen, B-CellReceptors, Antigen, T-CellRNA-SeqSARS-CoV-2Single-Cell AnalysisConceptsProgressive COVID-19B cell clonesSingle-cell analysisT cellsImmune responseMulti-omics single-cell analysisCOVID-19Cell clonesAdaptive immune interactionsSevere COVID-19Dynamic immune responsesGene expressionSARS-CoV-2 virusAdaptive immune systemSomatic hypermutation frequenciesCellular effectsProtein markersEffector CD8Immune signaturesProgressive diseaseHypermutation frequencyProgressive courseClassical monocytesClonesImmune interactions
2021
Effects of historical co‐infection on host shift abilities of exploitative and competitive viruses
Singhal S, Turner P. Effects of historical co‐infection on host shift abilities of exploitative and competitive viruses. Evolution 2021, 75: 1878-1888. PMID: 33969482, DOI: 10.1111/evo.14263.Peer-Reviewed Original ResearchConceptsNovel hostRNA viral pathogensHost population densityViral growthPhage genotypesCo-infecting virusesHost specificityIntracellular competitionHost exploitationHost genotypeEcological historyOriginal hostInfected bacteriaRNA bacteriophagesRapid evolutionEmergence potentialHostGrowth curvesPopulation densityEquivalent growthViral pathogensClonesInfectivity differencesGenotypesCompetitive viruses
2020
LVMapper: A Large-Variance Clone Detector Using Sequencing Alignment Approach
Wu M, Wang P, Yin K, Cheng H, Xu Y, Roy C. LVMapper: A Large-Variance Clone Detector Using Sequencing Alignment Approach. IEEE Access 2020, 8: 27986-27997. DOI: 10.1109/access.2020.2971545.Peer-Reviewed Original ResearchCode clonesCode modificationsType-3 clonesSequence alignment approachEffective detection approachSequence alignmentClone detectorsBug detectionCode repositoriesCode completionSoftware applicationsDetection approachClonesAlignment approachSequenceCodeSoftware analysisProject datasetBigCloneBenchBioinformaticsType 3DeletionRepositoryDatasetBugs
2019
Second-Hit Somatic Mutations in Mevalonate Pathway Genes Underlie Porokeratosis
Atzmony L, Choate KA. Second-Hit Somatic Mutations in Mevalonate Pathway Genes Underlie Porokeratosis. Journal Of Investigative Dermatology 2019, 139: 2409-2411. PMID: 31753123, PMCID: PMC7962864, DOI: 10.1016/j.jid.2019.07.723.Peer-Reviewed Original ResearchCyclin E Overexpression in Human Mammary Epithelial Cells Promotes Epithelial Cancer-Specific Copy Number Alterations
Giraldez S, Tamayo P, Wineinger N, Kim W, Reed S. Cyclin E Overexpression in Human Mammary Epithelial Cells Promotes Epithelial Cancer-Specific Copy Number Alterations. IScience 2019, 19: 850-859. PMID: 31513970, PMCID: PMC6739637, DOI: 10.1016/j.isci.2019.08.043.Peer-Reviewed Original ResearchChromosomal copy number alterationsCopy number alterationsCyclin ECell cycle regulatory proteinsOverexpression of cyclin EChromosomal lociCyclin E overexpressionEpithelial cell clonesRegulatory proteinsReplication stressCell cycleAberrant mitosesS phaseEpithelial-like tumorsCyclinE overexpressionCell clonesClonesOncogenesisComputational approachReplicationPotential mechanismsChromosomal damageCellsLociGenerating Single Cell–Derived Knockout Clones in Mammalian Cells with CRISPR/Cas9
Giuliano CJ, Lin A, Girish V, Sheltzer JM. Generating Single Cell–Derived Knockout Clones in Mammalian Cells with CRISPR/Cas9. Current Protocols In Molecular Biology 2019, 128: e100. PMID: 31503414, PMCID: PMC6741428, DOI: 10.1002/cpmb.100.Peer-Reviewed Original ResearchConceptsKnockout clonesMammalian cellsCell linesCRISPR/Cas9 technologyGuide RNA designMammalian cell linesGene lossClonal cell linesGene functionProtein functionGene targetingNew cell lineCas9 technologyTargeted geneFunction mutationsInterclonal heterogeneityRNA designSingle cellsSuccessful derivationClonesCRISPRCRISPR deliveryBiological reagentsRapid generationMutationsComparative analysis of CEACAM1 expression in thin melanomas with and without regression
Nichita L, Zurac S, Bastian A, Stinga P, Nedelcu R, Brinzea A, Turcu G, Ion D, Jilaveanu L, Sticlaru L, Popp C, Cioplea M. Comparative analysis of CEACAM1 expression in thin melanomas with and without regression. Oncology Letters 2019, 17: 4149-4154. PMID: 30944609, PMCID: PMC6444332, DOI: 10.3892/ol.2019.10067.Peer-Reviewed Original ResearchCarcinoembryonic antigen-related cell adhesion molecule 1CEACAM1 expressionThin melanomasMelanoma cell invasionTumor cellsHomophilic interactionsAA-1Extracellular domainStructural roleNatural killer cell activityCell invasionCell adhesion molecule-1Key moleculesKiller cell activityNatural killer cellsDeep invasive frontAdhesion molecule-1Full lengthValuable modelCEACAM1 overexpressionDifferent clonesExpressionKiller cellsTumor immunityClones
2018
Keeping Tumors Out of the MAPK Fitness Zone
Stern DF. Keeping Tumors Out of the MAPK Fitness Zone. Cancer Discovery 2018, 8: 20-23. PMID: 29311225, DOI: 10.1158/2159-8290.cd-17-1243.Peer-Reviewed Original ResearchConceptsMAPK-targeted therapiesGreater fitnessMAPK signalingTumor cell subclonesMAPK pathwayCell deathERK inhibitorDNA damageTumor cell deathFitness barriersCell subclonesNew therapeutic approachesInhibitor withdrawalResistant clonesTherapeutic approachesTriple combinationMEKSignalingClonesSubclonesFitnessPathwayPatients
2017
Identification of the gene that codes for the σ2 receptor
Alon A, Schmidt H, Wood M, Sahn J, Martin S, Kruse A. Identification of the gene that codes for the σ2 receptor. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: 7160-7165. PMID: 28559337, PMCID: PMC5502638, DOI: 10.1073/pnas.1705154114.Peer-Reviewed Original ResearchMeSH KeywordsAlzheimer DiseaseAnimalsAspartic AcidCarrier ProteinsCattleCholesterolEndoplasmic ReticulumGene Expression RegulationHumansInsectaIntracellular Signaling Peptides and ProteinsLigandsLiverMCF-7 CellsMembrane GlycoproteinsMembrane ProteinsNiemann-Pick C1 ProteinPC12 CellsProtein BindingRatsReceptors, sigmaRecombinant ProteinsRNA, Small InterferingSchizophreniaConceptsEndoplasmic reticulum-resident transmembrane proteinChemical biology approachPotential drug targetsTransmembrane proteinsMolecular cloningBiology approachLigand recognitionDrug targetsGenesBiological methodsTMEM97Therapeutic targetProteinMedical interestReceptorsAsp56NPC1ClonesS2 receptorsMolecular propertiesNeurological disordersSterolsTarget
2015
Decoding astrocyte heterogeneity: New tools for clonal analysis
Bribián A, Figueres-Oñate M, Martín-López E, López-Mascaraque L. Decoding astrocyte heterogeneity: New tools for clonal analysis. Neuroscience 2015, 323: 10-19. PMID: 25917835, DOI: 10.1016/j.neuroscience.2015.04.036.Peer-Reviewed Original ResearchConceptsEmbryonic developmentAstrocyte lineagePowerful genetic toolsBiology of astrocytesGenetic toolsCell heterogeneityLineagesOntogenetic originAstrocyte heterogeneityClonal analysisPhysiological featuresSpecific labelingAstrocyte progenitorsClonesAdult brainCell clonesAstrocyte clonesFinal fateExciting areaNew toolProgenyBiologyProgenitors
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