About
Titles
Research Scientist
Appointments
Education & Training
- Non Degree Program
- The Jackson Laboratory for Genomic Medicine, Postdoctoral Associate (2021)
- PhD
- Dartmouth College, Experimental and Molecular Medicine (2016)
- BS
- University of Massachusetts Amherst (2011)
Research
Overview
Dr. Kevin Johnson is a Research Scientist in Professor Roel Verhaak's laboratory with a strong background in cancer genomics, epigenetics, and glioma evolution. In the Verhaak Lab, he leads computational analyses of multi-modal bulk and single cell longitudinal genomic data to better understand glioma treatment resistance. Dr. Johnson has a proven track record of producing high-quality research including first or co-first author publications in scientific journals such as Nature, Nature Genetics, and Nature Communications. He is also an active research member in (inter)national scientific consortium such as the Glioma Longitudinal AnalySiS (GLASS) consortium that investigates brain tumor molecular evolution and the Participant Engagement and Cancer Genome Sequencing (PE-CGS) consortium that directly engages patients in cancer genomics research.
ORCID
0000-0003-0016-5158
Research at a Glance
Yale Co-Authors
Frequent collaborators of Kevin Johnson's published research.
Publications Timeline
A big-picture view of Kevin Johnson's research output by year.
Roel Verhaak, PhD
Samir Amin
16Publications
1,040Citations
Publications
2022
EPCO-13. IDENTIFYING REGULATORS OF GLIOMA CELL STATE DIVERSITY AND EVOLUTION VIA JOINT SINGLE NUCLEUS RNA AND CHROMATIN ACCESSIBILITY
Johnson K, Anderson K, Nehar-Belaid D, Varn F, Gujar A, Courtois E, Robson P, Moon H, Golebiewska A, Paek S, Niclou S, Verhaak R. EPCO-13. IDENTIFYING REGULATORS OF GLIOMA CELL STATE DIVERSITY AND EVOLUTION VIA JOINT SINGLE NUCLEUS RNA AND CHROMATIN ACCESSIBILITY. Neuro-Oncology 2022, 24: vii118-vii118. PMCID: PMC9660532, DOI: 10.1093/neuonc/noac209.448.Peer-Reviewed Original ResearchConceptsSingle-nucleus RNATranscription factorsCellular heterogeneityCell state plasticityEpigenetic gene regulationOpen chromatin stateOpen chromatin peaksWhole-genome sequencing dataDynamic epigenetic alterationsDNA methylation studiesGenome sequencing dataPatient-derived cell linesChromatin stateChromatin accessibilityEpigenetic switchChromatin changesGene regulationTranscriptional changesStem-like cellsMaster regulatorCell statesCell diversityEpigenetic alterationsEnhancer regionSequencing dataGlioma progression is shaped by genetic evolution and microenvironment interactions
Varn F, Johnson K, Martinek J, Huse J, Nasrallah M, Wesseling P, Cooper L, Malta T, Wade T, Sabedot T, Brat D, Gould P, Wöehrer A, Aldape K, Ismail A, Sivajothi S, Barthel F, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon H, Pollock S, Goldfarb C, Lee G, Garofano L, Anderson K, Nehar-Belaid D, Barnholtz-Sloan J, Bakas S, Byrne A, D’Angelo F, Gan H, Khasraw M, Migliozzi S, Ormond D, Paek S, Van Meir E, Walenkamp A, Watts C, Weiss T, Weller M, Palucka K, Stead L, Poisson L, Noushmehr H, Iavarone A, Verhaak R, Consortium T, Varn F, Johnson K, Martinek J, Huse J, Nasrallah M, Wesseling P, Cooper L, Malta T, Wade T, Sabedot T, Brat D, Gould P, Wöehrer A, Aldape K, Ismail A, Sivajothi S, Barthel F, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon H, Pollock S, Goldfarb C, Lee G, Garofano L, Anderson K, Nehar-Belaid D, Barnholtz-Sloan J, Bakas S, Byrne A, D’Angelo F, Gan H, Khasraw M, Migliozzi S, Ormond D, Paek S, Van Meir E, Walenkamp A, Watts C, Weiss T, Weller M, Alfaro K, Amin S, Ashley D, Bock C, Brodbelt A, Bulsara K, Castro A, Connelly J, Costello J, de Groot J, Finocchiaro G, French P, Golebiewska A, Hau A, Hong C, Horbinski C, Kannan K, Kouwenhoven M, Lasorella A, LaViolette P, Ligon K, Lowman A, Mehta S, Miletic H, Molinaro A, Ng H, Niclou S, Niers J, Phillips J, Rabadan R, Rao G, Reifenberger G, Sanai N, Short S, Smitt P, Sloan A, Smits M, Snyder J, Suzuki H, Tabatabai G, Tanner G, Tomaszewski W, Wells M, Westerman B, Wheeler H, Xie J, Yung W, Zadeh G, Zhao J, Palucka K, Stead L, Poisson L, Noushmehr H, Iavarone A, Verhaak R. Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell 2022, 185: 2184-2199.e16. PMID: 35649412, PMCID: PMC9189056, DOI: 10.1016/j.cell.2022.04.038.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsSpecific ligand-receptor interactionsMicroenvironment interactionsDNA sequencing dataGlioma progressionLigand-receptor interactionsNeoplastic cellsSignaling programsCell statesSequencing dataGenetic evolutionGenetic changesIDH wild-type tumorsIsocitrate dehydrogenaseMesenchymal transitionSomatic alterationsDistinct mannerActive tumor growthIDH-mutant gliomasPotential targetTherapy resistanceAdult patientsDisease progressionPossible roleCellsTumor growthLive-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer
Yi E, Gujar A, Guthrie M, Kim H, Zhao D, Johnson K, Amin S, Costa M, Yu Q, Das S, Jillette N, Clow P, Cheng A, Verhaak R. Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer. Cancer Discovery 2022, 12: 468-483. PMID: 34819316, PMCID: PMC8831456, DOI: 10.1158/2159-8290.cd-21-1376.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsExtrachromosomal DNA elementsDNA elementsUneven segregationRNA polymerase IILive-cell imagingPolymerase IIOffspring cellsGene transcriptionCell line modelsEcDNAsRandom segregationGenetic materialLiving cellsCopy numberLive cellsIndividual cellsTumor evolutionMitosisInheritance patternBreakpoint sequencesIssue featureTranscriptionFluorescent markersPatient tissuesCells
2021
Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response
Johnson K, Anderson K, Courtois E, Gujar A, Barthel F, Varn F, Luo D, Seignon M, Yi E, Kim H, Estecio M, Zhao D, Tang M, Navin N, Maurya R, Ngan C, Verburg N, de Witt Hamer P, Bulsara K, Samuels M, Das S, Robson P, Verhaak R. Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response. Nature Genetics 2021, 53: 1456-1468. PMID: 34594038, PMCID: PMC8570135, DOI: 10.1038/s41588-021-00926-8.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH KeywordsBrain NeoplasmsCell PlasticityClonal EvolutionDNA Copy Number VariationsDNA MethylationEpigenesis, GeneticGene Expression Regulation, NeoplasticGenetic HeterogeneityGenome, HumanGliomaHumansMutationPhylogenyPromoter Regions, GeneticSingle-Cell AnalysisStress, PhysiologicalTumor MicroenvironmentConceptsDNA methylation disorderEnvironmental stress responsesMethylation disordersEnvironmental stress response pathwaysStress responseStress response processesStress response pathwaysSingle-cell transcriptomesDNA methylation changesDNA methylation differencesDNA methylation dataMulti-omics profilesDNA methylomeTranscriptional disruptionEpigenetic instabilityEpigenetic heterogeneityEpigenetic regulatorsResponse pathwaysCellular plasticityMethylation changesMethylation differencesCell statesMethylation dataIrradiation stressWild-type gliomasSerum cell-free DNA epigenetic biomarkers aid glioma diagnostics and monitoring
Johnson K, Verhaak R. Serum cell-free DNA epigenetic biomarkers aid glioma diagnostics and monitoring. Neuro-Oncology 2021, 23: 1423-1424. PMID: 34139018, PMCID: PMC8408867, DOI: 10.1093/neuonc/noab146.Peer-Reviewed Original ResearchCitationsSpatial concordance of DNA methylation classification in diffuse glioma
Verburg N, Barthel F, Anderson K, Johnson K, Koopman T, Yaqub M, Hoekstra O, Lammertsma A, Barkhof F, Pouwels P, Reijneveld J, Rozemuller A, Beliën J, Boellaard R, Taylor M, Das S, Costello J, Vandertop W, Wesseling P, de Witt Hamer P, Verhaak R. Spatial concordance of DNA methylation classification in diffuse glioma. Neuro-Oncology 2021, 23: 2054-2065. PMID: 34049406, PMCID: PMC8643482, DOI: 10.1093/neuonc/noab134.Peer-Reviewed Original ResearchCitationsAltmetricRadiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer
Kocakavuk E, Anderson K, Varn F, Johnson K, Amin S, Sulman E, Lolkema M, Barthel F, Verhaak R. Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer. Nature Genetics 2021, 53: 1088-1096. PMID: 34045764, PMCID: PMC8483261, DOI: 10.1038/s41588-021-00874-3.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsWorse clinical outcomesNon-irradiated tumorsClinical outcomesRecurrent cancerPatient survivalPoor outcomeMetastatic tumorsRecurrent gliomaRadiation therapyRadiation-induced DNA damageDNA damageGlioma Longitudinal Analysis ConsortiumMutational signature analysisCancer treatmentDeletion burdenRadiotherapyMedical FoundationAPOBEC mutagenesisSignificant increaseTumorsCancerDNA damage repairDeletion signatureMutational spectrumSmall deletions
2020
Molecular and clonal evolution in recurrent metastatic gliosarcoma
Anderson K, Tan A, Parkinson J, Back M, Kastelan M, Newey A, Brewer J, Wheeler H, Hudson A, Amin S, Johnson K, Barthel F, Verhaak R, Khasraw M. Molecular and clonal evolution in recurrent metastatic gliosarcoma. Molecular Case Studies 2020, 6: a004671. PMID: 31896544, PMCID: PMC6996521, DOI: 10.1101/mcs.a004671.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsFirst recurrenceExtracranial metastasesIntracranial tumorsFrontal lobeRight iliac boneLeft frontal lobeOrigin of metastasesFrontal recurrenceMetastatic gliosarcomaConcurrent radiotherapyFurther surgeryFurther recurrenceRecurrent tumorsMetastatic tumorsIliac boneMetastasisRecurrenceTumorsMesenchymal typeSurgeryClonal relationshipRadiotherapyGliosarcomaMolecular profilePelvic bones
2019
Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue
Wilkins O, Johnson K, Houseman E, King J, Marsit C, Christensen B. Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue. Epigenetics 2019, 15: 398-418. PMID: 31842685, PMCID: PMC7153548, DOI: 10.1080/15592294.2019.1695332.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsGenome-wide characterizationGenome-wide patternsGenome-wide mapsGene regulatory programsActive chromatinGenomic lociGene regulationTranscriptional inactivityRegulatory regionsGene regionMammalian tissuesRegulatory programsCpG lociDNA treatmentImmune cell functionCell functionLociLactate oxidationNormal breast tissueIndependent data setsPre-invasive breast cancerRecent evidenceHeterochromatinChromatinBisulfiteBMP signaling mediates glioma stem cell quiescence and confers treatment resistance in glioblastoma
Sachdeva R, Wu M, Johnson K, Kim H, Celebre A, Shahzad U, Graham M, Kessler J, Chuang J, Karamchandani J, Bredel M, Verhaak R, Das S. BMP signaling mediates glioma stem cell quiescence and confers treatment resistance in glioblastoma. Scientific Reports 2019, 9: 14569. PMID: 31602000, PMCID: PMC6787003, DOI: 10.1038/s41598-019-51270-1.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH KeywordsAnimalsAntineoplastic AgentsBone Morphogenetic Protein 4Bone Morphogenetic ProteinsBrain NeoplasmsCell DivisionCell Line, TumorCell ProliferationDisease ProgressionDrug Resistance, NeoplasmGlioblastomaGliomaHomeostasisHumansMiceMice, Inbred NODNeoplasm Recurrence, LocalNeoplasm TransplantationNeoplastic Stem CellsPhenotypeRNA, Small InterferingSequence Analysis, RNASignal TransductionTemozolomideTransforming Growth Factor betaTransforming Growth Factor beta1ConceptsBMP pathway activationStem cell homeostasisStem cell systemStem cell quiescenceStem cell populationCancer stem cell populationInhibits cell proliferationStem-like cellsCancer stem cellsCell quiescenceCell homeostasisFunctional identityDismal prognosisTemozolomide chemotherapyCytotoxic therapyTumor recurrenceCellular reservoirsTreatment resistanceTherapeutic resistanceIncurable diseaseTumor progressionStem cellsCell proliferationPathway activationGlioblastoma