2024
Mapping extrachromosomal DNA amplifications during cancer progression
Kim H, Kim S, Wade T, Yeo E, Lipsa A, Golebiewska A, Johnson K, An S, Ko J, Nam Y, Lee H, Kang S, Chung H, Niclou S, Moon H, Paek S, Bafna V, Luebeck J, Verhaak R. Mapping extrachromosomal DNA amplifications during cancer progression. Nature Genetics 2024, 56: 2447-2454. PMID: 39402156, PMCID: PMC11549044, DOI: 10.1038/s41588-024-01949-7.Peer-Reviewed Original ResearchConceptsPretreatment tumorsCancer progressionChemotherapy-pretreated patientsNewly diagnosed tumorsVariant allele fractionUntreated metastasesPrimary cancerUntreated cancerTreatment responseFocal amplificationTumor samplesChromosomal amplificationsDiagnosed cancerTumorExtrachromosomal DNA amplificationsAdvanced cancerCancerEcDNATime pointsMetastasisNewlyDNA amplificationProgressionExtrachromosomal DNAPatientsDefining the Role of Extrachromosomal DNA Amplifications in Medulloblastoma.
Zhao D, Verhaak R. Defining the Role of Extrachromosomal DNA Amplifications in Medulloblastoma. Cancer Research 2024, 84: 515-516. PMID: 38175761, DOI: 10.1158/0008-5472.can-23-4025.Peer-Reviewed Original ResearchConceptsCell-to-cell variabilityWhole-genome sequencingCircular extrachromosomal DNACRISPRi experimentsRewiring eventsExtrachromosomal DNAMultiomics sequencingExtrachromosomal DNA amplificationsCopy numberEcDNADNA amplificationAssociated with worse survivalOncogene amplificationSequenceAmplificationWorse survivalPatient cohortTumor heterogeneityIntratumoral heterogeneityCRISPRiMedulloblastomaPatient outcomesDNA
2023
Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels
Wong M, Wei Y, Ho Y. Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels. Current Opinion In HIV And AIDS 2023, 18: 246-256. PMID: 37535039, PMCID: PMC10442869, DOI: 10.1097/coh.0000000000000809.Peer-Reviewed Original ResearchConceptsSurface protein expressionMultiomics approachATAC-seqProtein expressionTranscription factor activityProtein levelsRNA mappingRNA-seqBioinformatics analysisHIV-1-infected cellsFalse positive discoveriesBiological insightsBulk transcriptomeFactor activityDNA amplificationExpressionCellsTranscriptomeTherapeutic strategiesEpigeneticsDiscoveryDNA PCRRNADNAHIV-1
2022
Extrachromosomal DNA amplifications in cancer
Yi E, Chamorro González R, Henssen A, Verhaak R. Extrachromosomal DNA amplifications in cancer. Nature Reviews Genetics 2022, 23: 760-771. PMID: 35953594, PMCID: PMC9671848, DOI: 10.1038/s41576-022-00521-5.Peer-Reviewed Original ResearchConceptsExtrachromosomal DNA amplificationsNew therapeutic vulnerabilitiesCopy number heterogeneityEpigenetic architectureDNA amplificationCell divisionNuclear bodiesMost cancer typesNumber heterogeneityRegulatory landscapeTherapeutic vulnerabilitiesFunctional impactCancer typesDriver alterationsCircular structureEcDNAsChromatinizationChromosomesGenesAmplificationEcDNARecent investigationsEnhancerDeregulationCancer
2020
Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers
Kim H, Nguyen N, Turner K, Wu S, Gujar A, Luebeck J, Liu J, Deshpande V, Rajkumar U, Namburi S, Amin S, Yi E, Menghi F, Schulte J, Henssen A, Chang H, Beck C, Mischel P, Bafna V, Verhaak R. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nature Genetics 2020, 52: 891-897. PMID: 32807987, PMCID: PMC7484012, DOI: 10.1038/s41588-020-0678-2.Peer-Reviewed Original ResearchConceptsOncogene amplificationPoor outcomeCancer typesEcDNA amplificationShorter survivalCancer patientsMost cancer typesExtrachromosomal DNA amplificationsClinical impactMultiple cancersPatientsNormal tissuesCancerTranscript fusionsEnhanced chromatin accessibilityIntratumoral genetic heterogeneityOncogene transcriptionChromosomal amplificationOutcomesGenetic heterogeneityHigh levelsDNA amplificationTissue typesBlood
2012
Two methods for full-length RNA sequencing for low quantities of cells and single cells
Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, Marjani SL, Euskirchen G, Ma C, LaMotte RH, Park IH, Snyder MP, Mason CE, Weissman SM. Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 110: 594-599. PMID: 23267071, PMCID: PMC3545756, DOI: 10.1073/pnas.1217322109.Peer-Reviewed Original ResearchConceptsRNA sequencingSingle cellsFull-length RNA sequencingSingle dorsal root ganglion neuronHigh-throughput sequencingGene expression patternsLower transcript levelsFull-length sequencesRandom oligonucleotide primersTranscript representationAbundant mRNAsK562 erythroleukemic cellsTranscript levelsMRNA sequencingExpression patternsBiological disciplinesErythroleukemic cellsExpression signaturesSequencingOligonucleotide primersFull lengthLow quantitiesDNA amplificationRNAPCR procedure
2010
Recruitment of DNA replication and damage response proteins to viral replication centers during infection with NS2 mutants of Minute Virus of Mice (MVM)
Ruiz Z, Mihaylov IS, Cotmore SF, Tattersall P. Recruitment of DNA replication and damage response proteins to viral replication centers during infection with NS2 mutants of Minute Virus of Mice (MVM). Virology 2010, 410: 375-384. PMID: 21193212, PMCID: PMC3072075, DOI: 10.1016/j.virol.2010.12.009.Peer-Reviewed Original ResearchConceptsViral replication centersDamage responseReplication centersDamage response proteinsMutant infectionDNA damage responsePhosphorylation of ATRNS2 mutantsProtein recruitmentViral DNA amplificationATM activationCellular proteinsDNA replicationReplication factorsResponse proteinsBody maturationA9 cellsMVM infectionMinute virusWidespread associationWestern transferDNA amplificationMechanism of actionProteinRecruitment
2005
Amplification of human DNA by primers targeted to Leishmania kinetoplast DNA and post-genome considerations in the detection of parasites by a polymerase chain reaction.
Vergel C, Walker J, SARAVIA NG. Amplification of human DNA by primers targeted to Leishmania kinetoplast DNA and post-genome considerations in the detection of parasites by a polymerase chain reaction. American Journal Of Tropical Medicine And Hygiene 2005, 72: 423-9. PMID: 15827280, DOI: 10.4269/ajtmh.2005.72.423.Peer-Reviewed Original ResearchConceptsMolecular amplification techniquesPerformance of primersPolymerase chain reaction productsAmplification techniquesMonocyte DNADNA probesLeishmania kinetoplast DNANew applicationsChain reaction productsDNA amplificationHuman DNA sequencesDNA sequencesDetection of parasitesPolymerase chain reaction
1991
myc family DNA amplification in 107 tumors and tumor cell lines from patients with small cell lung cancer treated with different combination chemotherapy regimens.
Brennan J, O'Connor T, Makuch R, Simmons A, Russell E, Linnoila R, Phelps R, Gazdar A, Ihde D, Johnson B. myc family DNA amplification in 107 tumors and tumor cell lines from patients with small cell lung cancer treated with different combination chemotherapy regimens. Cancer Research 1991, 51: 1708-12. PMID: 1847842.Peer-Reviewed Original ResearchConceptsMyc family DNA amplificationSmall cell lung cancerCell lung cancerLung cancerTumor cell linesExtensive-stage small-cell lung cancer patientsSmall cell lung cancer patientsCell linesPatient specimensCell lung cancer patientsDNA copy numberDifferent combination chemotherapyEtoposide/cisplatinDifferent chemotherapy regimensInitiation of therapyLung cancer patientsFrequency of amplificationChemotherapy regimensUntreated patientsCombination chemotherapyCancer patientsSame patientPatientsClinical situationsDNA amplification
1990
Susceptibility of human cells to killing by the parvoviruses H-1 and minute virus of mice correlates with viral transcription
Cornelis J, Chen Y, Spruyt N, Duponchel N, Cotmore S, Tattersall P, Rommelaere J. Susceptibility of human cells to killing by the parvoviruses H-1 and minute virus of mice correlates with viral transcription. Journal Of Virology 1990, 64: 2537-2544. PMID: 2139892, PMCID: PMC249429, DOI: 10.1128/jvi.64.6.2537-2544.1990.Peer-Reviewed Original ResearchConceptsViral mRNAsHuman cellsLevel of transcriptionMinute virusMajor viral transcriptViral DNA amplificationNonstructural polypeptidesGene productsOncogenic transformationGene expressionIntracellular localizationNonstructural proteinsViral transcriptionViral transcriptsTranscriptionViral genomeParvovirus HCell susceptibilityHuman fibroblastsVirus uptakeEpithelial cellsDNA amplificationResistant derivativesKeratinocyte lineDifferential susceptibilityHepadnavirus envelope proteins regulate covalently closed circular DNA amplification
Summers J, Smith P, Horwich A. Hepadnavirus envelope proteins regulate covalently closed circular DNA amplification. Journal Of Virology 1990, 64: 2819-2824. PMID: 2335817, PMCID: PMC249463, DOI: 10.1128/jvi.64.6.2819-2824.1990.Peer-Reviewed Original ResearchConceptsCccDNA synthesisEnvelope proteinVirus-mediated cell deathHepadnavirus envelope proteinsCircular DNA amplificationViral DNA synthesisWild-type virusWild typeViral envelope proteinsCell deathCircular DNAPrimary duck hepatocytesDNA synthesisProteinDNA amplificationPersistent infectionDuck hepatocytes
1987
myc family oncogene amplification in tumor cell lines established from small cell lung cancer patients and its relationship to clinical status and course.
Johnson B, Ihde D, Makuch R, Gazdar A, Carney D, Oie H, Russell E, Nau M, Minna J. myc family oncogene amplification in tumor cell lines established from small cell lung cancer patients and its relationship to clinical status and course. Journal Of Clinical Investigation 1987, 79: 1629-1634. PMID: 3034978, PMCID: PMC424486, DOI: 10.1172/jci112999.Peer-Reviewed Original ResearchConceptsMyc family DNA amplificationPatient tumorsTumor cell linesC-myc amplificationCell linesSmall cell lung cancer patientsCell lung cancer patientsSmall cell lung cancer cell linesCell lung cancer cell linesExtensive-stage patientsLung cancer patientsLung cancer cell linesCancer cell linesRelapsed patientsStage patientsClinical statusCancer patientsChemotherapy treatmentPatientsTumorsDNA amplificationOncogene amplification
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