2022
TCR gene segment usage and HLA alleles that are associated with cancer survival rates also represent racial disparities
Angelakakis G, Serraneau K, Barker V, Callahan B, Tong W, Zaman S, Huda T, Blanck G. TCR gene segment usage and HLA alleles that are associated with cancer survival rates also represent racial disparities. International Journal Of Immunogenetics 2022, 50: 41-47. PMID: 36585798, DOI: 10.1111/iji.12610.Peer-Reviewed Original ResearchConceptsTCR gene segment usageHLA allele combinationsGene segment usageCancer outcomesRacial disparitiesSegment usageHLA allelesCertain HLA allelesCancer survival ratesDistinct survival outcomesSocioeconomic factorsDisease courseSurvival outcomesInfectious disease courseSurvival rateAllele combinationsDifferent racial groupsGenetic polymorphismsPrevious pathogen exposurePathogen exposureOutcomesRacial groupsDisparitiesFactorsCancer
2021
Systemic Adaptive Immune Parameters Associated with Neuroblastoma Outcomes: the Significance of Gamma-Delta T Cells
Gozlan EC, Chobrutskiy BI, Zaman S, Yeagley M, Blanck G. Systemic Adaptive Immune Parameters Associated with Neuroblastoma Outcomes: the Significance of Gamma-Delta T Cells. Journal Of Molecular Neuroscience 2021, 71: 2393-2404. PMID: 33666857, DOI: 10.1007/s12031-021-01813-x.Peer-Reviewed Original ResearchConceptsGamma delta T cellsImmune receptor recombinationsAdaptive immune responsesT cellsImmune responseLower overall survival rateSet of neuroblastomaSystemic immune stateOverall survival rateAdaptive immune parametersImmunology parametersActive diseaseDevelopment of cancerYounger patientsImmune parametersImmune stateCancer evaluationNeuroblastoma outcomeSurvival rateImmunity developmentYounger ageTumor samplesAntigenic specificityImmune receptorsReceptor geneSpecific HLA alleles, paired with TCR V- and J-gene segment usage, link to distinct multiple myeloma survival rates
Huda TI, Mihyu M, Gozlan EC, Arndt MF, Diaz MJ, Zaman S, Chobrutskiy BI, Blanck G. Specific HLA alleles, paired with TCR V- and J-gene segment usage, link to distinct multiple myeloma survival rates. Leukemia & Lymphoma 2021, 62: 1711-1720. PMID: 33622167, DOI: 10.1080/10428194.2021.1885655.Peer-Reviewed Original ResearchConceptsHLA allele combinationsTCR VBlood samplesSurvival rateT cell receptor VOverall survival rateT cell characterizationSpecific HLA allelesLarger patient setsDistinct overall survival ratesSolid tumor typesSurvival distinctionsMM cohortHLA allelesJ-gene segment usageTumor typesPotential associationImmunogenomics studiesHLASegment usagePatient setAllele combinationsTCR recombinationImmunogenetic parametersImmunogenomic data
2020
Chemical features of blood-borne TRG CDR3s associated with an increased overall survival in breast cancer
Chobrutskiy A, Chobrutskiy BI, Zaman S, Hsiang M, Blanck G. Chemical features of blood-borne TRG CDR3s associated with an increased overall survival in breast cancer. Breast Cancer Research And Treatment 2020, 185: 591-600. PMID: 33180235, DOI: 10.1007/s10549-020-05996-6.Peer-Reviewed Original ResearchConceptsOverall survivalBreast cancerPrimary breast cancer patientsGamma delta T cellsBreast cancer tumor tissuesBreast cancer settingProgesterone receptor statusBreast cancer patientsGreater overall survivalPotential antigenic targetsCancer tumor tissuesPatient ageReceptor statusCancer patientsAntigenic targetsCancer settingT cellsSurvival correlationB cellsSurvival rateTumor tissueHigher survival rateImmunogenomic approachesConclusionsThese resultsSurvival parametersTRBV and TRBJ usage, when paired with specific HLA alleles, associates with distinct head and neck cancer survival rates
Arndt MF, Koohestani DM, Chobrutskiy BI, Mihyu MM, Diaz M, Gozlan EC, Yeagley M, Zaman S, Roca AM, Blanck G. TRBV and TRBJ usage, when paired with specific HLA alleles, associates with distinct head and neck cancer survival rates. Human Immunology 2020, 81: 692-696. PMID: 32950267, DOI: 10.1016/j.humimm.2020.08.007.Peer-Reviewed Original ResearchMeSH KeywordsAllelesBiomarkers, TumorDisease-Free SurvivalExomeGenes, T-Cell Receptor betaHead and Neck NeoplasmsHistocompatibility Antigens Class IHistocompatibility Antigens Class IIHLA AntigensHumansKaplan-Meier EstimatePrognosisReceptors, Antigen, T-Cell, alpha-betaSurvival RateV(D)J RecombinationConceptsHuman papilloma virusHLA allele combinationsT cell receptorSurvival rateCervical cancerHLA allelesParticular human leukocyte antigen (HLA) allelesBetter disease-free survival rateCancer Genome Atlas (TCGA) headDisease-free survival ratesJ usageHuman leukocyte antigen (HLA) allelesFree survival rateOverall survival rateCancer survival ratesSpecific HLA allelesDistinct overall survival ratesNeck cancer datasetPapilloma virusIndependent associationAntigen presentationAntigen allelesViral infectionHLAExome filesImmunogenomics of colorectal adenocarcinoma: Survival distinctions represented by immune receptor, CDR3 chemical features and high expression of BTN gene family members
Diaz MJ, Chobrutskiy BI, Zaman S, Blanck G. Immunogenomics of colorectal adenocarcinoma: Survival distinctions represented by immune receptor, CDR3 chemical features and high expression of BTN gene family members. Cancer Treatment And Research Communications 2020, 24: 100196. PMID: 32769037, DOI: 10.1016/j.ctarc.2020.100196.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaAftercareAntineoplastic Agents, ImmunologicalBiomarkers, TumorButyrophilinsColorectal NeoplasmsComplementarity Determining RegionsComputational BiologyDisease-Free SurvivalExomeGene Expression Regulation, NeoplasticHumansKaplan-Meier EstimateReceptors, Antigen, B-CellReceptors, Antigen, T-CellRecombination, GeneticRNA-SeqSurvival RateConceptsSurvival rateLung cancerColon cancerImmune receptor recombinationsWorse survival rateCancer survival ratesCases of melanomaBetter survival rateB cell receptorFamily membersSurvival distinctionsCancer Genome AtlasImmunotherapy approachesColorectal adenocarcinomaT cellsImmunogenomics studiesCancer typesCancerConsistent associationHigh expressionGenome AtlasImmune receptorsImmunogenomic featuresMelanomaCancer exomesAntiviral T Cell Receptor Complementarity Determining Region-3 Sequences Are Associated with a Worse Cancer Outcome: A Pancancer Analysis
Zaman S, Chobrutskiy BI, Patel JS, Diviney A, Tu YN, Tong WL, Gill T, Blanck G. Antiviral T Cell Receptor Complementarity Determining Region-3 Sequences Are Associated with a Worse Cancer Outcome: A Pancancer Analysis. Viral Immunology 2020, 33: 404-412. PMID: 32315578, DOI: 10.1089/vim.2019.0156.Peer-Reviewed Original ResearchConceptsT cellsRegion 3 sequencesSurvival rateTissue-resident T cellsCancer typesImmune receptor recombinationsResident T cellsWorse survival rateHuman papilloma virusWorse cancer outcomesTCGA data setsThymus cancerCancer Genome AtlasViral etiologyCancer outcomesDistinct survival ratesNeck cancerPapilloma virusDifferent cancer typesSolid tumorsTumor samplesExome filesGenome AtlasPancancer AnalysisCancerA scoring system for the electrostatic complementarities of T‐cell receptors and cancer‐mutant amino acids: multi‐cancer analyses of associated survival rates
Chobrutskiy BI, Yeagley M, Diviney A, Zaman S, Gozlan EC, Tipping P, Koohestani DM, Roca AM, Blanck G. A scoring system for the electrostatic complementarities of T‐cell receptors and cancer‐mutant amino acids: multi‐cancer analyses of associated survival rates. Immunology 2020, 159: 373-383. PMID: 31821535, PMCID: PMC7077996, DOI: 10.1111/imm.13165.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAmino Acid SequenceAmino AcidsAntigens, NeoplasmBinding SitesBreast NeoplasmsComplementarity Determining RegionsExomeFemaleGene ExpressionHumansLung NeoplasmsMaleMutationPrognosisProtein BindingReceptor-CD3 Complex, Antigen, T-CellResearch DesignSkin NeoplasmsStatic ElectricitySurvival RateT-LymphocytesConceptsT cell receptorImmune systemSurvival rateAnti-tumor immune responseTumor-infiltrating lymphocytesNeo-antigensPeptide vaccineImmune responseTumor antigensTumor specimensTumor specimenScoring systemStem cell proteinsHigher survival rateMutant amino acidsReceptorsAmino acidsMutant peptidesAa sequencesCell proteinsLymphocytesVaccineImmunoscoringAntigenSpecific genes
2019
Chemical complementarity between immune receptor CDR3s and IDH1 mutants correlates with increased survival for lower grade glioma
Chobrutskiy BI, Yeagley M, Tipping P, Zaman S, Diviney A, Patel DN, Falasiri S, Uversky VN, Blanck G. Chemical complementarity between immune receptor CDR3s and IDH1 mutants correlates with increased survival for lower grade glioma. Oncogene 2019, 39: 1773-1783. PMID: 31740784, DOI: 10.1038/s41388-019-1101-2.Peer-Reviewed Original ResearchConceptsLow-grade gliomasComplementarity-determining region 3T cell receptor beta chainImmune responseGrade gliomasIDH1 mutantChronic inflammationReceptor beta chainCancer immunologyLGG prognosisNRAS mutantsSurvival rateCancer developmentCDR3 domainsGliomasImmune receptorsBeta chainAnticancer processesSurvivalAn age-based, RNA expression paradigm for survival biomarker identification for pediatric neuroblastoma and acute lymphoblastic leukemia
Diviney A, Chobrutskiy BI, Zaman S, Blanck G. An age-based, RNA expression paradigm for survival biomarker identification for pediatric neuroblastoma and acute lymphoblastic leukemia. Cancer Cell International 2019, 19: 73. PMID: 30962767, PMCID: PMC6438000, DOI: 10.1186/s12935-019-0790-5.Peer-Reviewed Original ResearchAcute lymphoblastic leukemiaOlder diagnostic ageDiagnostic agePediatric neuroblastomaLymphoblastic leukemiaPrevalent pediatric cancerCancer survival ratesAge of diagnosisYounger patientsSurvival differencesPediatric cancerHigh levelsPatientsNeuroblastomaSurvival rateGene expression markersAgeExpression markersLeukemiaSurvival metricsBiomarker identificationLevelsCancerDiseaseGenes
2018
T-cell receptor-α CDR3 domain chemical features correlate with survival rates in bladder cancer
Chobrutskiy BI, Zaman S, Diviney A, Mihyu MM, Blanck G. T-cell receptor-α CDR3 domain chemical features correlate with survival rates in bladder cancer. Journal Of Cancer Research And Clinical Oncology 2018, 145: 615-623. PMID: 30539280, DOI: 10.1007/s00432-018-2815-1.Peer-Reviewed Original ResearchConceptsTumor-infiltrating lymphocytesT cell responsesBladder tumor tissuesT-cell featuresEx vivo amplificationT cell receptorBladder cancerCancer findingsFavorable outcomeCancer settingBetter outcomesSurvival rateTumor tissueCancerDriver mutationsImmunotherapyBiochemical featuresBioinformatics assessmentOutcomesAntigen bindingRegion 3TILsPatientsLymphocytesTherapyMAPT (Tau) expression is a biomarker for an increased rate of survival for low-grade glioma
Zaman S, Chobrutskiy BI, Sikaria D, Blanck G. MAPT (Tau) expression is a biomarker for an increased rate of survival for low-grade glioma. Oncology Reports 2018, 41: 1359-1366. PMID: 30535461, DOI: 10.3892/or.2018.6896.Peer-Reviewed Original ResearchMAPT expressionSurvival rateΑ-synuclein gene expressionDisease-free survivalCentral nervous systemLow-grade gliomasAssociation of MAPTRate of survivalCancer Genome AtlasBreast cancerNeurodegenerative roleTau expressionBrain cancerNervous systemNeurological disordersTau proteinMAPT geneHigh expressionCancerGenome AtlasPrecursor proteinExpression levelsSuch associationsSurvivalTauMMP7 sensitivity of mutant ECM proteins: An indicator of melanoma survival rates and T-cell infiltration
Zaman S, Chobrutskiy BI, Patel JS, Callahan BM, Tong WL, Mihyu MM, Blanck G. MMP7 sensitivity of mutant ECM proteins: An indicator of melanoma survival rates and T-cell infiltration. Clinical Biochemistry 2018, 63: 85-91. PMID: 30414845, DOI: 10.1016/j.clinbiochem.2018.11.004.Peer-Reviewed Original ResearchConceptsMutant amino acidsT-cell infiltratesT cell infiltrationMelanoma survival ratesDistinct survival outcomesCancer Genome AtlasSurvival outcomesWorse outcomesImmune activitySurvival rateMelanoma specimensMelanomaGenome AtlasPatientsAmino acidsOverall mutationsDetection of melanomaOutcomesOnly decreaseRecovery of T-cell receptor V(D)J recombination reads from lower grade glioma exome files correlates with reduced survival and advanced cancer grade
Chobrutskiy BI, Zaman S, Tong WL, Diviney A, Blanck G. Recovery of T-cell receptor V(D)J recombination reads from lower grade glioma exome files correlates with reduced survival and advanced cancer grade. Journal Of Neuro-Oncology 2018, 140: 697-704. PMID: 30382482, DOI: 10.1007/s11060-018-03001-1.Peer-Reviewed Original ResearchConceptsLow-grade gliomasT cell receptorCancer gradeImmune systemExome filesT-cell biomarkersDisease-free survivalT lymphocyte infiltrationPrimary tumor siteLGG survivalLymphocyte infiltrationCancer survivalPrimary tumorPancreatic cancerDisease progressionUseful biomarkerB cellsGrade gliomasSurvival rateTumor siteReduced survivalSurvivalSuch associationsBiomarkersReceptorsImmune receptor recombinations from breast cancer exome files, independently and in combination with specific HLA alleles, correlate with better survival rates
Tong WL, Callahan BM, Tu YN, Zaman S, Chobrutskiy BI, Blanck G. Immune receptor recombinations from breast cancer exome files, independently and in combination with specific HLA alleles, correlate with better survival rates. Breast Cancer Research And Treatment 2018, 173: 167-177. PMID: 30229447, DOI: 10.1007/s10549-018-4961-1.Peer-Reviewed Original ResearchConceptsImmune receptor recombinationsSpecific HLA allelesExome filesHLA typesBreast cancerHLA allelesSurvival rateImmune checkpoint inhibitor therapyImproved disease-free survivalDisease-free outcomeCheckpoint inhibitor therapyT cell receptor VUse of immunotherapyDisease-free survivalSegment usageB cell biomarkersBreast cancer subgroupsHLA allele combinationsBetter survival rateBreast cancer samplesBreast tumor samplesGene segment usageSurvival distinctionsInhibitor therapyImmune characterization