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 infiltrationInfiltrates
2020
Immunogenomics 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 AnalysisCancer
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 cohort
2018
MAPT (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 associationsSurvivalTauMAPT (Tau) expression is a biomarker for an increased rate of survival in pediatric neuroblastoma
Zaman S, Chobrutskiy BI, Blanck G. MAPT (Tau) expression is a biomarker for an increased rate of survival in pediatric neuroblastoma. Cell Cycle 2018, 17: 2474-2483. PMID: 30394813, PMCID: PMC6342068, DOI: 10.1080/15384101.2018.1542898.Peer-Reviewed Original ResearchConceptsMAPT expressionGene expressionProliferation-effector genesHuman Genome OrganizationContext of tauopathyH2A histone familyCaspase-9 genesOvarian cancerPediatric neuroblastomaGenome organizationCaspase-3 geneCancer Genome AtlasHistone familyKaplan-Meier survival curvesProtein geneTransactive response DNA binding protein 43Neuronal degenerative diseasesType 1 geneDNA binding protein 43Expression of apoptosisAmyloid precursor protein geneGenesPrecursor protein geneAmyotrophic lateral sclerosisNeuronal cellsMMP7 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 decrease