biostudies-arrayexpressNicolas RosewickHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15430High levels of extracellular adenosine, highly abundant in the tumor microenvironment, promote immune suppression mainly through the A2AR expressed by tumor-infiltrating immune cells. Here we show that plasma cells are the most negatively affected by adenosine among the immune cells present in the tumor microenvironment.biostudies-arrayexpressSample Collection - Biopsies from 6 cancer patients (head and neck n=1, melanoma n=3, lung n=1, prostate n=1) enrolled in Phase I study IO-001 were processed at screening and C1D21.Nucleic Acid Extraction - Up to five FFPE sections per tissue sample were used, for HE staining and RNA extraction. For each sample a capture area of 6.5 x 6.5 mm (5.000 spots) was annotated by a pathologist. RNA extraction was performed with the High Pure FFPET RNA extraction Kit (Roche). DV200 values were evaluated using BioAnalyzer (Agilent Technologies), and only samples with DV200 values superior to 30% were included in the analysis.Library Construction - Libraries were prepared using the 10x Genomics PCR-based protocol.Sequencing - After library preparation, the generated libraries were sequenced on the Illumina NovaSeq 6000 platform.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Spatially resolved transcriptome information from 10X Genomics Visium platform was processed using Space Ranger software (v2.1.1, 10X Genomics). Raw sequencing reads were mapped to the human reference transcriptome (GRCh38; refdata-gex-GRCh38-2020-A) using 10X spaceranger count pipeline. Tumor and stroma regions were manually annotated by an experienced pathologist and used to relate gene expression patterns to tissue architecture. Downstream analysis was performed using the Seurat R package (v5.1.0). Spots were filtered to retain high-quality data based on the following criteria: total counts of detected transcripts (nCount_Spatial) > 5,000, number of detected genes (nFeature_Spatial) > 500, and percentage of mitochondrial gene expression (percent.mt) < 20%. Normalization of the data was performed using Seurat's NormalizeData() function with its default settings. Variable features were identified using FindVariableFeatures() with \"vst\" as the selection strategy and retaining the top 2,000 genes for subsequent analysis. The data were then scaled using Seurat’s ScaleData() function.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000spatial transcriptomics by high-throughput sequencingHomo sapiensNicolas RosewickPaola TieppoHussein ShehadeFrancesco StrozzifalseInhibition of A2AR relieves adenosine-mediated suppression of plasma cell differentiation​High levels of extracellular adenosine, highly abundant in the tumor microenvironment, promote immune suppression mainly through the A2AR expressed by tumor-infiltrating immune cells. Here we show that plasma cells are the most negatively affected by adenosine among the immune cells present in the tumor microenvironment.2025-12-07T00:00:00Z2025-12-07T09:36:28.7Z2025-08-05T22:41:45.688ZE-MTAB-15430ERP177860EFO_0002944EFO_0004170EFO_0030005EFO_0005518EFO_0003816EFO_0004184