biostudies-arrayexpressEva FreyhultHomo sapiensGeneChip Command Console (AGCC)R version 4.6.1https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17721Background: Normal tissue in a tumor-bearing organ shows morphological and molecular differences from normal tissue in a tumor-free organ. One explanation to this is that tumors actively instruct adjacent normal tissues to support growth and invasion. The aim of this study was to examine if changes in gene-expression patterns in tumor-adjacent histologically benign prostate tissue, termed tumor instructed normal tissue (TINT), were associated with tumor proximity, grade and molecular subtype and, furthermore, whether they could indicate the presence of high-grade cancer elsewhere in the prostate. Methods: Gene-expression analysis using Clariom D microarrays was performed on matched formalin-fixed paraffin-embedded samples including tumor tissue (n=44), benign prostate tissue taken near (Tbiostudies-arrayexpressHybridization - RNA was hybridized to Clariom D Human Transcriptome Arrays (Applied Biosystems, ThermoFisher). One array experiment was conducted containing all the radical prostatectomy samples (T, TINT-N, TINT-D).Sample Collection - Samples were collected from formalin-fixed paraffin-embedded (FFPE) retrospective prostate biopsies. The biopsy group includes histologically benign initial biopsies from men later diagnosed with high-grade prostate cancer within 30 months (Bx-later-tumor; 6-8 biopsies sectioned at 10 µm, 1 section/biopsy), biopsies from men remaining cancer-free for at least 8 years (Bx-control; 6-8 biopsies sectioned at 10 µm, 1 section/biopsy), and tumor-containing biopsies (Bx-tumor; 1-4 biopsies sectioned at 10 µm, 1-4 sections/biopsy).Nucleic Acid Extraction - Total RNA was extracted using the Ionic FFPE to Pure RNA kit.Sample Collection - Samples were collected from formalin-fixed paraffin-embedded (FFPE) prostate tissue from radical prostatectomy specimens. Whole-mounted hematoxylin-eosin-stained sections were examined to define three distinct regions per patient: tumor tissue, benign tissue near the tumor on the ipsilateral side (TINT-N), and benign tissue distant from the tumor on the contralateral side (TINT-D). Guided by these sections, a biopsy punch (Ø 6 mm) was used to encircle the selected Tumor, TINT-N and TINT-D tissue areas (~5 mm in diameter) on the corresponding paraffin-embedded prostate tissue blocks. Upon sectioning (10 µm, 5 sections/patient), the encircled areas were dissected into separate tubes for RNA extraction.Scaning - Arrays were scanned using standard Affymetrix GeneChip Scanner system and raw image files (.DAT) were automatically generated by the GeneChip Command Console (AGCC) software. For feature extraction, AGCC performed grid alignment and initial feature extraction to convert raw .DAT image files into intensity .CEL files.Labeling - RNA was amplified and labeled with the GeneChipTM WT Pico Reagent Kit, according to protocol (Catalog number 902622, ThermoFisher Scientific).Hybridization - RNA was hybridized to Clariom D Human Transcriptome Arrays (Applied Biosystems, ThermoFisher). One array experiment was conducted containing all the biopsy samples (Bx-later-tumor, Bx-control, Bx-tumor).Nucleic Acid Extraction - Total RNA was extracted using the Invitrogen PureLinkTM FFPE Total RNA Isolation Kit (K156002, ThermoFisher Scientific).MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsData Transformation - Raw data was normalized, separately for biopsy and radical prostatectomy samples, using the Robust Multi-array Average (RMA) method implemented in the R package oligo.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsMicrotomeGeneChip Scanner 3000 7GThermal cycle, microcenrifuge, vortex mixer, pipettesBiopsy punch (Ø 6 mm) and microtomeIonic purification system (Bionano Genomics)Dell laptopClariom D Human Transcriptome Arrays (Applied Biosystems, ThermoFisher)transcription profiling by arrayHomo sapiensGene Expression Profiles in Benign Prostate Tissue Reflect Tumor Proximity, Grade, and Molecular subtypePernilla WikströmSofia Halin BergströmAnders BerghPernilla Wikström, Eva Freyhult, Julius Semenas, Marie Lundholm, Andreas Josefsson, Sofia Halin Bergström, and Anders BerghJulius SemenasMarie LundholmEva FreyhultAndreas JosefssonfalseData set for "Gene Expression Profiles in Benign Prostate Tissue Reflect Tumor Proximity, Grade, and Molecular subtypeBackground: Normal tissue in a tumor-bearing organ shows morphological and molecular differences from normal tissue in a tumor-free organ. One explanation to this is that tumors actively instruct adjacent normal tissues to support growth and invasion. The aim of this study was to examine if changes in gene-expression patterns in tumor-adjacent histologically benign prostate tissue, termed tumor instructed normal tissue (TINT), were associated with tumor proximity, grade and molecular subtype and, furthermore, whether they could indicate the presence of high-grade cancer elsewhere in the prostate. Methods: Gene-expression analysis using Clariom D microarrays was performed on matched formalin-fixed paraffin-embedded samples including tumor tissue (n=44), benign prostate tissue taken near (T2026-10-06T00:00:00Z2026-10-06T06:05:24.057Z2026-10-05T14:35:36.014ZE-MTAB-17721EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0005518EFO_0003816EFO_0003815