2020
A 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
Potential MMP2-mediated availability of HLA binding, mutant ECM peptides reflects better melanoma survival rates and greater T-cell infiltrates
Zaman S, Chobrutskiy BI, Patel JS, Callahan BM, Mihyu MM, Diviney A, Blanck G. Potential MMP2-mediated availability of HLA binding, mutant ECM peptides reflects better melanoma survival rates and greater T-cell infiltrates. Laboratory Investigation 2019, 99: 1287-1295. PMID: 31019293, DOI: 10.1038/s41374-019-0248-3.Peer-Reviewed Original ResearchConceptsMutant amino acidsAmino acidsStructural proteinsExtracellular matrix structural proteinsMatrix metalloproteinase-2Cancer progressionLate-stage cancer developmentMutant peptidesECM structural proteinsMatrix structural proteinsBioinformatics approachProtein mutantsProtease functionECM peptidesSuch proteasesMutantsPotential substratesCancer developmentProteaseMelanoma samplesProteinSpread of cancerTumor samplesMetalloproteinase-2Cancer microenvironment
2018
Mutant cytoskeletal and ECM peptides sensitive to the ST14 protease are associated with a worse outcome for glioblastoma multiforme
Zaman S, Chobrutskiy BI, Patel JS, Callahan BM, Tong WL, Blanck G. Mutant cytoskeletal and ECM peptides sensitive to the ST14 protease are associated with a worse outcome for glioblastoma multiforme. Biochemical And Biophysical Research Communications 2018, 503: 2218-2225. PMID: 29953855, DOI: 10.1016/j.bbrc.2018.06.141.Peer-Reviewed Original ResearchConceptsT cell receptorAa substitutionsExtracellular matrix-related proteinsMatrix-related proteinsAmino acid substitutionsTransmembrane serine proteaseBioinformatics approachECM peptidesProtease sensitivityAcid substitutionsSerine proteasesCancer developmentProteasePeptide sequencesBarcodesHigh binding affinityBinding affinitiesCancer datasetsClass IRecombinationExome filesCytoskeletalCytoskeletonSubstitutionGlioblastoma multiforme