2023
Multimodal immunogenomic biomarker analysis of tumors from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab
Nabbi A, Danesh A, Espin-Garcia O, Pedersen S, Wellum J, Fu L, Paulson J, Geoerger B, Marshall L, Trippett T, Rossato G, Pugh T, Hutchinson K. Multimodal immunogenomic biomarker analysis of tumors from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab. Nature Cancer 2023, 4: 502-515. PMID: 37038005, PMCID: PMC10132976, DOI: 10.1038/s43018-023-00534-x.Peer-Reviewed Original ResearchConceptsPediatric patientsAssociated with progression-free survivalCD8+ T cellsT cell receptor repertoireProgression-free survivalImmune-checkpoint inhibitionB cell infiltrationTertiary lymphoid structuresBiomarker analysisAtezolizumab therapyAntitumor immunityStable diseasePD-L1Partial responseTumor neoantigensRefractory tumorsPatient tumorsLymphoid structuresT cellsB cellsReceptor repertoireClinical trialsClinical activityTumorImmune response
2022
mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis
Movassagh M, Morton S, Hehnly C, Smith J, Doan T, Irizarry R, Broach J, Schiff S, Bailey J, Paulson J. mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis. BMC Genomics 2022, 23: 439. PMID: 35698050, PMCID: PMC9191533, DOI: 10.1186/s12864-022-08558-w.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 infectionLung epithelial cellsEpithelial cellsHuman lung epithelial cellsSARS-CoV-2NK cellsStatistical PackageEBV miRNAsT cellsImmune pathwaysB cellsClinical relevanceSample cohortCD34 cellsStomach adenocarcinomaEndothelial cellsTime pointsInfectionCOVID-19CellsCD4AdenocarcinomaPatientsCD19Cytokines
2020
Abstract PR06: The immunogenomic landscape of pediatric primary solid tumors
Nabbi A, Sun P, Sumedha S, Zhu K, Yang S, Paulson J, Kool M, Rathi K, Kalletla K, Raman P, Zhu Y, Resnick A, Jones D, Jäger N, Pfister S, Pugh T. Abstract PR06: The immunogenomic landscape of pediatric primary solid tumors. Cancer Research 2020, 80: pr06-pr06. DOI: 10.1158/1538-7445.pedca19-pr06.Peer-Reviewed Original ResearchTumor mutational burdenAtypical teratoid/rhabdoid tumorPrimary solid tumorsPediatric CNS tumorsSolid tumorsCNS tumorsPediatric cancerImmune microenvironmentPediatric tumorsT cellsImmunogenomic landscapeImmune cellsLevels of CD8+ T cellsHigh T-cell infiltrationCD8+ T cellsClonal T-cell expansionAssociated with immune cell infiltrationT cell clonal expansionAnalysis of T cell repertoireLow levels of immune infiltrationImmune checkpoint inhibitionEffect of immunotherapyT cell infiltrationLevel of immune infiltrationT cell expansion