Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

TCR sequencing of peripheral blood mononuclear cells (PBMC) and prostate biopsies from prostate cancer patients undergoing cryoimmunotherapy

ABSTRACT: This dataset includes a total of 18 prostate cancer patients undergoing cryoimmunotherapy (cryoIT). The clinical trial is registered at ClinicalTrials.gov under the identifier NCT02423928. PBMC specimens obtained before and after cryoIT and prostate biopsies at the time of cryoablation are included in this dataset. The specific time points of sampling can be found in the table provided with the dataset. Both visit number and study week are provided for this purpose, with study week 0 corresponding to the time of cryoablation (cryoIT).

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Homo sapiens

SUBMITTER: Benjamin Gabriel

PROVIDER: E-MTAB-10998 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Human Natural Killer (NK) cells comprise two main subsets, CD56bright and CD56dim cells, that differ in function, phenotype and tissue localization. To further dissect the heterogeneity of CD56dim cells, we have performed transcriptome analysis and functional ex vivo characterization of human NK cell subsets according to the expression of markers related to differentiation, migration or competence. Here, we show for the first time that the ability to respond to cytokines or to activating receptors is mutually exclusive in almost all NK cells with the exception of CD56dim CD62L+ cells. Indeed, only these cells combine the ability to produce interferon (IFN)-gamma after cytokines and proliferate in vivo during viral infection with the capacity to kill and produce cytokines upon engagement of activating receptors. Therefore, CD56dim CD62L+ cells represent a unique subset of polyfunctional NK cells. Ex vivo analysis of their function, phenotype, telomere length, frequencies during ageing as well as transfer experiments of NK cell subsets into immunodeficient mice suggest that CD56dim CD62L+ cells represent an intermediate stage of NK cell maturation, which after restimulation can accomplish multiple tasks and further develop into terminally differentiated effectors. Gene expression profiles of FACSAria sorted CD3- CD56bright CD62L+, CD3- CD56dim CD62L+ and CD3- CD56dim CD62L- NK cells from human peripheral blood of three donors were compared using Affymetrix GeneChip Human Genome HG-U133_Plus_2. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 Âµg cRNA hybridized in triplicates for each of the three groups to the GeneChip arrays. Group1: CD3- CD56bright CD62L+,.Group2: CD3- CD56dim CD62L+, Group3: CD3- CD56dim CD62L-. Lists of differentially regulated genes were created using High Performance Chip Data Analysis (HPCDA) with Bioretis database (http://www.bioretis-analysis.de). Worldwide data sharing is possible via Bioretis, please ask the authors.

Dataset Information

TCR sequencing of peripheral blood mononuclear cells (PBMC) and prostate biopsies from prostate cancer patients undergoing cryoimmunotherapy

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