2025
Tracing the evolution of single-cell 3D genomes in Kras-driven cancers
Liu M, Jin S, Agabiti S, Jensen T, Yang T, Radda J, Ruiz C, Baldissera G, Rajaei M, Li F, Townsend J, Muzumdar M, Wang S. Tracing the evolution of single-cell 3D genomes in Kras-driven cancers. Nature Genetics 2025, 1-13. PMID: 40825871, DOI: 10.1038/s41588-025-02297-w.Peer-Reviewed Original ResearchCell-to-cell heterogeneityGenome-wide chromatinGenome compactionGenome architectureGenomic structureGenome mappingGenome regulationLung adenocarcinomaDependent genesKRAS-driven cancersGenomeMouse lung adenocarcinomaCancer progressionEarly tumor progressionSingle cellsCancer stateGenesPancreatic ductal adenocarcinomaInvasive tumorsTherapeutic biomarkersDuctal adenocarcinomaTumor progressionCompartmental changesChromatinCancerPrecision projections of the delay of resistance mutations in non-small cell lung cancer via suppression of APOBEC
Nousias O, Mandell J, Anderson K, Townsend J. Precision projections of the delay of resistance mutations in non-small cell lung cancer via suppression of APOBEC. Lung Cancer 2025, 202: 108487. PMID: 40090261, DOI: 10.1016/j.lungcan.2025.108487.Peer-Reviewed Original ResearchNon-small cell lung cancer patientsNon-small cell lung cancerCell lung cancer patientsCell lung cancerLung cancer patientsEvolution of drug resistanceLung cancerDrug resistanceCancer patientsTyrosine kinase inhibitor therapyKinase inhibitor therapyTyrosine kinase inhibitorsPersonalized therapeutic strategiesTKI therapyInhibitor therapyTherapeutic failureResistance mutationsTherapeutic efficacyKinase inhibitorsAPOBEC mutationsTherapeutic strategiesTreatment efficacyCancer progressionImprove outcomesCancer
2022
Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes
Cannataro VL, Mandell JD, Townsend JP. Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes. Molecular Biology And Evolution 2022, 39: msac084. PMID: 35580068, PMCID: PMC9113445, DOI: 10.1093/molbev/msac084.Peer-Reviewed Original ResearchConceptsBurden of cancerPublic health strategiesWhole-exome sequencingTobacco exposureLung cancerProstate adenocarcinomaBreast cancerCancer effectsHealth strategiesOncogenic driversCancer originCancer typesCancer cell lineagesCancerPathogen exposureExogenous mutational processesMajority of mutationsTumorsSingle nucleotide variantsPreventable processActivity accountsSurvivalOncogenic variantsCell lineagesProliferation
2021
Identifying modules of cooperating cancer drivers
Klein MI, Cannataro VL, Townsend JP, Newman S, Stern DF, Zhao H. Identifying modules of cooperating cancer drivers. Molecular Systems Biology 2021, 17: msb20209810. PMID: 33769711, PMCID: PMC7995435, DOI: 10.15252/msb.20209810.Peer-Reviewed Original ResearchConceptsCancer typesNRAS-mutant melanomaCombination of alterationsMultiple cancer typesClinical outcomesNFE2L2 mutationsIndividual patientsDriver alterationsEffective personalized treatmentPathway inhibitionTherapeutic potentialCancer etiologyPersonalized treatmentTumor formationTCGA cancer typesAlterationsPatientsCancer driversEtiologyMelanomaCancer
2020
Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden
Qing T, Mohsen H, Marczyk M, Ye Y, O’Meara T, Zhao H, Townsend JP, Gerstein M, Hatzis C, Kluger Y, Pusztai L. Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden. Nature Communications 2020, 11: 2438. PMID: 32415133, PMCID: PMC7228928, DOI: 10.1038/s41467-020-16293-7.Peer-Reviewed Original ResearchConceptsAge groupsGermline variantsSomatic mutationsLate-onset cancerEarly-onset cancersCancer hallmark genesSomatic mutation burdenMutation burdenMalignant transformationCancer genesYounger ageGermline alterationsCancerVariant burdenBurdenAverage numberHallmark genesAgeNegative correlationStrong negative correlationMutationsPatientsGroupNon-Coding Mutations in Urothelial Bladder Cancer: Biological and Clinical Relevance and Potential Utility as Biomarkers
Yang A, Cross CN, Townsend JP. Non-Coding Mutations in Urothelial Bladder Cancer: Biological and Clinical Relevance and Potential Utility as Biomarkers. Bladder Cancer 2020, 6: 211-213. PMID: 32793790, PMCID: PMC7390591, DOI: 10.3233/blc-200278.Peer-Reviewed Original Research
2019
Molecular Biology and Evolution of Cancer: From Discovery to Action
Somarelli JA, Gardner H, Cannataro VL, Gunady EF, Boddy AM, Johnson NA, Fisk J, Gaffney SG, Chuang JH, Li S, Ciccarelli FD, Panchenko AR, Megquier K, Kumar S, Dornburg A, DeGregori J, Townsend JP. Molecular Biology and Evolution of Cancer: From Discovery to Action. Molecular Biology And Evolution 2019, 37: 320-326. PMID: 31642480, PMCID: PMC6993850, DOI: 10.1093/molbev/msz242.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsEvolutionary processesMolecular evolutionary processesEvolution of cancerCancer cell populationsEcological nichesNew therapeutic modesCancer evolutionEcological theoryMolecular biologyCancer biologyCancer progressionSuite of conceptsCell populationsBiologyNicheEvolutionCirculatory systemDeeper understandingDiscoveryCancer
2018
Neutral Theory and the Somatic Evolution of Cancer
Cannataro VL, Townsend JP. Neutral Theory and the Somatic Evolution of Cancer. Molecular Biology And Evolution 2018, 35: 1308-1315. PMID: 29684198, PMCID: PMC5967571, DOI: 10.1093/molbev/msy079.Peer-Reviewed Original Research
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