2022
Glioma 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 ResearchConceptsSpecific 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 growth
2021
Spatial 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 Research
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 ResearchConceptsFirst 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 ResearchConceptsGenome-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 evidenceHeterochromatinChromatinBisulfite
2016
5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients
Johnson K, Houseman E, King J, von Herrmann K, Fadul C, Christensen B. 5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients. Nature Communications 2016, 7: 13177. PMID: 27886174, PMCID: PMC5133638, DOI: 10.1038/ncomms13177.Peer-Reviewed Original ResearchMeSH Keywords5-MethylcytosineAdultAgedAged, 80 and overBrain NeoplasmsDNA MethylationDNA, NeoplasmEnhancer Elements, GeneticFemaleGene Expression Regulation, NeoplasticGene Regulatory NetworksGlioblastomaHumansIsocitrate DehydrogenaseMaleMiddle AgedPrefrontal CortexSurvival AnalysisTranscription FactorsConceptsRNA regulatory processesTissue-specific transcriptionDisease critical genesMethylation array dataGenomic distributionGenomic localizationCell maintenanceOxidative bisulfite (oxBS) treatmentTranscription factorsEnhancer elementsPrefrontal cortex tissueBisulfite treatmentCellular proliferationRegulatory processesTranscriptionArray dataMolecular alterationsCortex tissueEpigenomeGlioblastomaImmune functionGenesDNARegulationAnnotation
2013
Age-related DNA methylation in normal breast tissue and its relationship with invasive breast tumor methylation
Johnson K, Koestler D, Cheng C, Christensen B. Age-related DNA methylation in normal breast tissue and its relationship with invasive breast tumor methylation. Epigenetics 2013, 9: 268-275. PMID: 24196486, PMCID: PMC3962537, DOI: 10.4161/epi.27015.Peer-Reviewed Original Research