2024
Genetic and Molecular Drivers of Scleroderma Pathogenesis
Odell I. Genetic and Molecular Drivers of Scleroderma Pathogenesis. Clinics In Dermatology 2024 PMID: 39675445, DOI: 10.1016/j.clindermatol.2024.12.007.Peer-Reviewed Original ResearchGrowth factor signalingFactor signalingScleroderma pathogenesisActivated growth factor receptorsGenetic association studiesTherapeutic approachesMolecular driversHereditary hemorrhagic telangiectasiaAssociation studiesRegulatory genesGrowth factor receptorImmune regulatory genesGenetic studiesBiological insightsVascular endothelial cellsMolecular mechanismsHemorrhagic telangiectasiaImmune dysregulationClinical findingsVascular abnormalitiesHeterogeneous diseaseClinical phenotypeFactor receptorPatient phenotypesMultiple malignanciesGranuloma Annulare Exhibits Mixed Immune and Macrophage Polarization Profiles with Spatial Transcriptomics
Mohanty C, Singh C, Daccache J, Damsky W, Kendziorski C, Yan D, Prasad A, Zhang D, Keenan T, Drolet B, Ahmad N, Shields B. Granuloma Annulare Exhibits Mixed Immune and Macrophage Polarization Profiles with Spatial Transcriptomics. Journal Of Investigative Dermatology 2024, 145: 109-121. PMID: 38844128, DOI: 10.1016/j.jid.2024.04.024.Peer-Reviewed Original ResearchGranuloma annulareGranulomatous inflammationFDA-approved therapiesInflammatory signaling cascadesImpact of GAIFN-gImmune cellsInterleukin-32Idiopathic conditionTh2 signalsAdaptive immunityInterstitial patternMacrophage activationGene expression changesMolecular driversQuality of lifeGenome-wide gene expression changesMacrophage polarizationGranulomaMacrophagesTissue remodelingInflammationTNF signalingLocal gene expression patternsSpatial transcriptomics
2023
PCSK6 and Survival in Idiopathic Pulmonary Fibrosis
Oldham J, Allen R, Lorenzo-Salazar J, Molyneaux P, Ma S, Joseph C, Kim J, Guillen-Guio B, Hernández-Beeftink T, Kropski J, Huang Y, Lee C, Adegunsoye A, Pugashetti J, Linderholm A, Vo V, Strek M, Jou J, Muñoz-Barrera A, Rubio-Rodriguez L, Hubbard R, Hirani N, Whyte M, Hart S, Nicholson A, Lancaster L, Parfrey H, Rassl D, Wallace W, Valenzi E, Zhang Y, Mychaleckyj J, Stockwell A, Kaminski N, Wolters P, Molina-Molina M, Banovich N, Fahy W, Martinez F, Hall I, Tobin M, Maher T, Blackwell T, Yaspan B, Jenkins R, Flores C, Wain L, Noth I. PCSK6 and Survival in Idiopathic Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2023, 207: 1515-1524. PMID: 36780644, PMCID: PMC10263132, DOI: 10.1164/rccm.202205-0845oc.Peer-Reviewed Original ResearchConceptsGenome-wide significanceTransplantation-free survivalIdiopathic pulmonary fibrosisStage IIPF survivalDownstream analysisPulmonary fibrosisIPF progressionWide association studyPeripheral blood gene expressionProportional hazards regressionStage II casesLimited treatment optionsStage I casesBlood gene expressionGene expressionAssociation studiesMolecular determinantsHazards regressionTreatment optionsPlasma concentrationsLung parenchymaConsistent effect directionMolecular driversProtein
2022
Biallelic inactivation of PBRM1 as a molecular driver in a rare pineoblastoma case: illustrative case
Antonios JP, Yalcin K, Darbinyan A, Koo A, Hong CS, DiLuna M, Erson-Omay Z. Biallelic inactivation of PBRM1 as a molecular driver in a rare pineoblastoma case: illustrative case. Journal Of Neurosurgery Case Lessons 2022, 3: case2213. PMID: 36303510, PMCID: PMC9379698, DOI: 10.3171/case2213.Peer-Reviewed Original ResearchMolecular driversPineal parenchymal tumorsRenal cell carcinomaRare tumor typeParenchymal tumorsCell carcinomaBladder carcinomaPapillary featuresPineoblastomaTumor subtypesTumor typesConsensus groupBiallelic lossGenomic profilingCancer typesMolecular level alterationsLevel alterationsGenomic driversBiallelic inactivationCarcinomaDriver eventsTumor suppressorGenetic phenotypesPathway changesMultiomics studiesIntegrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis
Farshidfar F, Rhrissorrakrai K, Levovitz C, Peng C, Knight J, Bacchiocchi A, Su J, Yin M, Sznol M, Ariyan S, Clune J, Olino K, Parida L, Nikolaus J, Zhang M, Zhao S, Wang Y, Huang G, Wan M, Li X, Cao J, Yan Q, Chen X, Newman AM, Halaban R. Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis. Nature Communications 2022, 13: 898. PMID: 35197475, PMCID: PMC8866401, DOI: 10.1038/s41467-022-28566-4.Peer-Reviewed Original ResearchConceptsAcral melanomaMelanoma subtypesClinical profilingCommon melanoma subtypeImmune checkpoint blockadeCheckpoint blockadeInferior survivalMelanoma cell linesKey molecular driversPoor prognosisTherapeutic targetAnchorage-independent growthImmunomodulatory genesNon-white individualsHotspot mutationsMolecular driversCandidate oncogeneMelanomaApoptotic cell deathLZTR1Focal amplificationTumor promoterCell linesMetastasisTumor suppressor
2021
Molecular drivers of tumor progression in microsatellite stable APC mutation-negative colorectal cancers
Grant A, Xicola RM, Nguyen V, Lim J, Thorne C, Salhia B, Llor X, Ellis N, Padi M. Molecular drivers of tumor progression in microsatellite stable APC mutation-negative colorectal cancers. Scientific Reports 2021, 11: 23507. PMID: 34873211, PMCID: PMC8648784, DOI: 10.1038/s41598-021-02806-x.Peer-Reviewed Original ResearchMeSH KeywordsAdenomatous Polyposis ColiAdenomatous Polyposis Coli ProteinColorectal NeoplasmsDisease ProgressionDNA Copy Number VariationsDNA MethylationGenes, APCHumansMicrosatellite InstabilityMicrosatellite RepeatsMutationNeoplastic ProcessesPhenotypePromoter Regions, GeneticWnt Signaling PathwayConceptsAdenomatous polyposis coliMitochondrial activationDNA methylation profilesTumor suppressor gene adenomatous polyposis coliRNA expressionExpression of Axin2Cancer Genome AtlasIntracellular WntMethylation profilesAberrant regulationGene fusionsGenetic inactivationExtracellular WntNumber variationsGenome AtlasPolyposis coliSomatic mutationsAPC mutationsMutationsMolecular driversMutations of BRAFWntRSPO3Tumor progressionExpressionIntegrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma
Bakouny Z, Braun DA, Shukla SA, Pan W, Gao X, Hou Y, Flaifel A, Tang S, Bosma-Moody A, He MX, Vokes N, Nyman J, Xie W, Nassar AH, Abou Alaiwi S, Flippot R, Bouchard G, Steinharter JA, Nuzzo PV, Ficial M, Sant’Angelo M, Forman J, Berchuck JE, Dudani S, Bi K, Park J, Camp S, Sticco-Ivins M, Hirsch L, Baca SC, Wind-Rotolo M, Ross-Macdonald P, Sun M, Lee GM, Chang SL, Wei XX, McGregor BA, Harshman LC, Genovese G, Ellis L, Pomerantz M, Hirsch MS, Freedman ML, Atkins MB, Wu CJ, Ho TH, Linehan WM, McDermott DF, Heng DYC, Viswanathan SR, Signoretti S, Van Allen EM, Choueiri TK. Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma. Nature Communications 2021, 12: 808. PMID: 33547292, PMCID: PMC7865061, DOI: 10.1038/s41467-021-21068-9.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic Agents, ImmunologicalB7-H1 AntigenCarcinoma, Renal CellCTLA-4 AntigenCyclin-Dependent Kinase Inhibitor p16Gene Expression ProfilingGene Expression Regulation, NeoplasticHigh-Throughput Nucleotide SequencingHumansImmune Checkpoint InhibitorsImmune Checkpoint ProteinsKidney NeoplasmsMutationProgrammed Cell Death 1 ReceptorProto-Oncogene Proteins c-mycRetrospective StudiesRhabdoid TumorSignal TransductionSurvival AnalysisTranscription, GeneticTumor Suppressor ProteinsUbiquitin ThiolesteraseConceptsRhabdoid renal cell carcinomaImmune checkpoint inhibitorsRenal cell carcinomaCell carcinomaImmune-inflamed phenotypeIntegrative molecular characterizationPD-L1 expressionReal-world cohortMultiple clinical trialsMYC transcriptional programsMolecular featuresCheckpoint inhibitorsClinical outcomesImmune activationImmunologic characteristicsAggressive tumorsImmune infiltrationClinical trialsClinical characterizationRCC tumorsBAP1 mutationsDistinctive molecular featuresTumorsCDKN2A deletionMolecular drivers
2016
Paradoxical functions of ZEB1 in EGFR -mutant lung cancer: tumor suppressor and driver of therapeutic resistance
Yochum Z, Socinski M, Burns T. Paradoxical functions of ZEB1 in EGFR -mutant lung cancer: tumor suppressor and driver of therapeutic resistance. Journal Of Thoracic Disease 2016, 8: e1528-e1531. PMID: 28066651, PMCID: PMC5179406, DOI: 10.21037/jtd.2016.11.59.Peer-Reviewed Original ResearchNon-small cell lung cancerLung cancerEGFR-mutant lung cancerCell lung cancerCancer-related deathAmplification/mutationEGFR mutationsALK translocationKRAS mutationsDistinct subtypesTherapeutic resistanceCancerMolecular driversPatientsTumor suppressorParadoxical functionsMutationsSubtypesSignificant advancesZEB1
2013
The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb
Cotney J, Leng J, Yin J, Reilly SK, DeMare LE, Emera D, Ayoub AE, Rakic P, Noonan JP. The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb. Cell 2013, 154: 185-196. PMID: 23827682, PMCID: PMC3785101, DOI: 10.1016/j.cell.2013.05.056.Peer-Reviewed Original ResearchConceptsCis-regulatory evolutionHistone modification H3K27acGenome-wide viewMouse limb developmentRegulatory activityGain of activityMost enhancersGene regulationEmbryonic limbLimb developmentHuman lineageEnhancer activityHuman embryonic tissuesGene expressionEmbryonic tissuesRegulatory functionsPromoterH3K27acMolecular driversGenetic causeHeterogeneous genetic causesEnhancerQuantitative readoutMorphological evolutionAnatomical features
2012
L4.1 Evolution of Battle Trials at Md Anderson Cancer Center
Hong W, Kim E, Herbst R, Papadimitrakopoulou V, Gold K, Wistuba I, Lee J, Lippman S. L4.1 Evolution of Battle Trials at Md Anderson Cancer Center. Annals Of Oncology 2012, 23: v7. DOI: 10.1016/s0923-7534(20)31272-2.Peer-Reviewed Original ResearchNational Lung Screening TrialLung cancerBATTLE TrialHigh riskLow-dose helical computed tomographyLung Cancer Elimination (BATTLE) trialMolecular driversMD Anderson Cancer CenterUntreated lung cancerAdvanced lung cancerFive-year survivalAdvanced cancer settingLung cancer patientsCore needle biopsyLung cancer developmentNovel trial designsAnderson Cancer CenterPatient treatment selectionFresh tumor biopsiesHelical computed tomographyEarly-stage cancerNumber one causeOptimal drug combinationsRefractory patientsPrevention setting
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