2023
Specific Intratumor Bacteria Genera and TRG Recombinations Associated with Greater Survival Probability in Alimentary Tract Cancers
Zaman S, Chobrutskiy B, Quach J, Blanck G. Specific Intratumor Bacteria Genera and TRG Recombinations Associated with Greater Survival Probability in Alimentary Tract Cancers. Journal Of Gastrointestinal Cancer 2023, 54: 1300-1307. PMID: 37103748, DOI: 10.1007/s12029-023-00935-2.Peer-Reviewed Original ResearchConceptsT-cell infiltratesStomach adenocarcinomaGamma delta T cellsCox proportional hazards modelAlimentary tract cancersTumor immune milieuProportional hazards modelPrimary tumor samplesImmune milieuOS probabilityCancer Genome AtlasCell infiltrateTract cancerPatient survivalEsophageal cancerPrimary tumorCancer DatabaseT cellsHazards modelTumor samplesExome filesAlimentary tractGenome AtlasBacterial infiltrationInfiltratesBacterial Sequencing Reads in Blood Exome Files from Melanoma and Cervical Cancer Patients are Associated with Cancer Recurrence
Quach J, Diaz M, Huda T, Kinskey J, Zaman S, Desantis J, Cios K, Blanck G. Bacterial Sequencing Reads in Blood Exome Files from Melanoma and Cervical Cancer Patients are Associated with Cancer Recurrence. Molecular Biotechnology 2023, 65: 1476-1484. PMID: 36653589, DOI: 10.1007/s12033-023-00663-9.Peer-Reviewed Original ResearchConceptsCervical cancer casesCervical cancer patientsCancer patientsExome filesCancer recurrenceCancer casesDisease-free survival probabilityImmunocompromised Cancer PatientsOverall survival resultsCancer clinical outcomesBacterial blood infectionsLower DFSClinical outcomesCervical cancerPrimary tumorSurvival resultsMelanoma casesBlood infectionSolid tumorsGreater riskPatientsBacteroides fragilisBloodPresence of bacteriaBacteroides speciesChemical Complementarity of Breast Cancer Resident, T-Cell Receptor CDR3 Domains and the Cancer Antigen, ARMC3, is Associated With Higher Levels of Survival and Granzyme Expression
Pakasticali N, Chobrutskiy A, Patel D, Hsiang M, Zaman S, Cios K, Blanck G, Chobrutskiy B. Chemical Complementarity of Breast Cancer Resident, T-Cell Receptor CDR3 Domains and the Cancer Antigen, ARMC3, is Associated With Higher Levels of Survival and Granzyme Expression. Cancer Informatics 2023, 22: 11769351231177269. PMID: 37313373, PMCID: PMC10259117, DOI: 10.1177/11769351231177269.Peer-Reviewed Original ResearchCancer-testis antigensCancer antigensBreast cancer antigensT cell receptorGranzyme expressionImmune biomarkersCancer immunotherapyPatient outcomesGranzyme BCandidate antigensTestis antigensAdaptive immune receptorsAntigenCDR3 domainsImmune receptorsTumor gene expression dataReceptorsSurvivalAntigen bindingRegion 3Integration of itemsHigh levelsImmunotherapyBreast cancer datasetExpression correlation
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 groupsDisparitiesFactorsCancerChemical complementarity between tumor resident, T-cell receptor CDR3s and MAGEA3/6 correlates with increased melanoma survival: Potential relevance to MAGE vaccine auto-reactivity
Eakins R, Chobrutskiy A, Teer J, Patel D, Hsiang M, Huda T, Zaman S, Sexton W, Coppola D, Falasiri S, Blanck G, Chobrutskiy B. Chemical complementarity between tumor resident, T-cell receptor CDR3s and MAGEA3/6 correlates with increased melanoma survival: Potential relevance to MAGE vaccine auto-reactivity. Molecular Immunology 2022, 150: 58-66. PMID: 35987136, DOI: 10.1016/j.molimm.2022.08.001.Peer-Reviewed Original Research
2021
High-throughput, sliding-window algorithm for assessing chemical complementarity between immune receptor CDR3 domains and cancer mutant peptides: TRG-PIK3CA interactions and breast cancer
Chobrutskiy BI, Chobrutskiy A, Zaman S, Yeagley M, Huda TI, Blanck G. High-throughput, sliding-window algorithm for assessing chemical complementarity between immune receptor CDR3 domains and cancer mutant peptides: TRG-PIK3CA interactions and breast cancer. Molecular Immunology 2021, 135: 247-253. PMID: 33933816, DOI: 10.1016/j.molimm.2021.02.026.Peer-Reviewed Original ResearchChemical complementarity between immune receptors and cancer mutants, independent of antigen presentation protein binding, is associated with increased survival rates
Hsiang M, Chobrutskiy BI, Diaz M, Huda TI, Creadore S, Zaman S, Cios KJ, Gozlan EC, Blanck G. Chemical complementarity between immune receptors and cancer mutants, independent of antigen presentation protein binding, is associated with increased survival rates. Translational Oncology 2021, 14: 101069. PMID: 33780706, PMCID: PMC8039726, DOI: 10.1016/j.tranon.2021.101069.Peer-Reviewed Original ResearchT cell receptor alpha geneAmino acidsT cell receptorChemical complementarityV-J recombinationMutant amino acidsThe Cancer Genome Atlas (TCGA) databaseCancer Genome Atlas (TCGA) databaseCancer mutantsBioinformatics approachAlpha geneReceptor alpha geneImmune receptorsComplement genesAtlas databaseMutantsPeptide sequencesSpecific interactionsGenesII bindingLRP2Region 3 sequencesUterine cancerProtein bindingBindingSystemic 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 dataReconnaissance of tumor immune microenvironment spatial heterogeneity in metastatic renal cell carcinoma and correlation with immunotherapy response
Hajiran A, Chakiryan N, Aydin A, Zemp L, Nguyen J, Laborde J, Chahoud J, Spiess P, Zaman S, Falasiri S, Fournier M, Teer J, Dhillon J, McCarthy S, Moran-Segura C, Katende E, Sexton W, Koomen J, Mulé J, Kim Y, Manley B. Reconnaissance of tumor immune microenvironment spatial heterogeneity in metastatic renal cell carcinoma and correlation with immunotherapy response. Clinical & Experimental Immunology 2021, 204: 96-106. PMID: 33346915, PMCID: PMC7944355, DOI: 10.1111/cei.13567.Peer-Reviewed Original ResearchConceptsMetastatic clear cell renal cell carcinomaClear cell renal cell carcinomaTumor immune microenvironmentRenal cell carcinomaT-betOverall survivalCell carcinomaMetastatic renal cell carcinomaForkhead box protein 3Improved overall survivalCell renal cell carcinomaCox regression analysisImmune cell distributionT-cell markersPoor overall survivalBox protein 3Tumor-stromal interfaceMetastatic tumor samplesPrecision treatment strategiesTumor-stroma interfaceTumor coreImproved survivalImmune markersImmunotherapy responsePoor outcome
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 parametersUnproductive T cell receptor-β and T cell receptor-δ recombination recoveries in tissue and blood samples are associated with improved survival outcomes for uterine and ovarian cancers
Zaman S, Koohestani D, Diviney A, Chobrutskiy B, Arndt M. Unproductive T cell receptor-β and T cell receptor-δ recombination recoveries in tissue and blood samples are associated with improved survival outcomes for uterine and ovarian cancers. Gynecologic Oncology 2020, 159: 204. DOI: 10.1016/j.ygyno.2020.05.327.Peer-Reviewed Original ResearchTRBV 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 AnalysisCancerMP14-03 DENSITY OF T-BET POSITIVE T LYMPHOCYTES WITHIN THE TUMOR MICROENVIRONMENT IS ASSOCIATED WITH A FAVORABLE RESPONSE TO IMMUNOTHERAPY IN PATIENTS WITH METASTATIC RENAL CELL CARCINOMA
Hajiran* A, Aydin A, Kim Y, Zemp L, McCarthy S, Segura C, Nguyen J, Falasiri S, Zaman S, Spiess P, Kohli M, Mulé J, Manley B. MP14-03 DENSITY OF T-BET POSITIVE T LYMPHOCYTES WITHIN THE TUMOR MICROENVIRONMENT IS ASSOCIATED WITH A FAVORABLE RESPONSE TO IMMUNOTHERAPY IN PATIENTS WITH METASTATIC RENAL CELL CARCINOMA. Journal Of Urology 2020, 203 DOI: 10.1097/ju.0000000000000839.03.Peer-Reviewed Original ResearchPD39-06 POOR RESPONSE TO IMMUNOTHERAPY IS ASSOCIATED WITH HIGH EXPRESSION OF A NOVEL EPIDERMAL GROWTH FACTOR RECEPTOR SPLICE VARIANT IN PATIENTS WITH RENAL CELL CARCINOMA
Hajiran* A, Kim Y, Zaman S, Madanyake T, Robinson T, Falasiri S, Spiess P, Kohli M, Boyle T, Mulé J, Teer J, Manley B. PD39-06 POOR RESPONSE TO IMMUNOTHERAPY IS ASSOCIATED WITH HIGH EXPRESSION OF A NOVEL EPIDERMAL GROWTH FACTOR RECEPTOR SPLICE VARIANT IN PATIENTS WITH RENAL CELL CARCINOMA. Journal Of Urology 2020, 203 DOI: 10.1097/ju.0000000000000918.06.Peer-Reviewed Original ResearchA 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
Aberrant Epidermal Growth Factor Receptor RNA Splice Products Are Among the Most Frequent Somatic Alterations in Clear Cell Renal Cell Carcinoma and Are Associated with a Poor Response to Immunotherapy
Zaman S, Hajiran A, Coba GA, Robinson T, Madanayake TW, Segarra DT, Chobrutskiy BI, Boyle TA, Zhou JM, Kim Y, Mulé JJ, Teer JK, Manley BJ. Aberrant Epidermal Growth Factor Receptor RNA Splice Products Are Among the Most Frequent Somatic Alterations in Clear Cell Renal Cell Carcinoma and Are Associated with a Poor Response to Immunotherapy. European Urology Focus 2019, 7: 373-380. PMID: 31901438, PMCID: PMC7771328, DOI: 10.1016/j.euf.2019.12.001.Peer-Reviewed Original ResearchConceptsRenal cell carcinomaCell renal cell carcinomaClear cell renal cell carcinomaCell carcinomaPoor responseAdvanced clear cell renal cell carcinomaTumor tissueNon-RCC tumorsCohort of patientsRCC tumor tissuesReverse transcriptase-polymerase chain reactionTranscriptase-polymerase chain reactionFrequent somatic alterationsKidney cancer cell linesAdvanced ccRCCCancer cell linesCancer Genome AtlasSystemic therapyClinical outcomesInstitutional cohortPatient populationPoor prognosisHuman kidney cancer cell linesClinical significanceTCGA cohortChemical 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 processesSurvival