biostudies-arrayexpressChiara LanzuoloHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14226We used a groundbreaking epigenomic profiling technique developed in our laboratory, the 4f-SAMMY-seq, along with RNA-seq on 7 healthy biopsies and 18 prostate tumor biopsies. Our study represents the first direct examination of chromatin organization in patient-derived prostate biopsies. Leveraging differences in chromatin architecture, we identified a novel Prostate Cancer transcriptional signature associated with a favorable prognosis.biostudies-arrayexpressSequencing - Libraries with distinct adapter indexes were then multiplexed and, after cluster generation on FlowCell, sequenced for 50 bases in single or paired-end reads mode on an IlluminaNovaSeq 6000 instrument at the IEO Genomic Unit in Milan.Nucleic Acid Extraction - Chromatin fractions (S2, S3 and S4) were diluted 1:2 in 1X TE buffer (10mM TrisHCl pH 8.0, 1 mM EDTA) and incubated with 3 U of RNAse cocktail (Ambion, AM2286) at 37° for 90 minutes, followed by 40μg of Proteinase K (Invitrogen, AM2548) at 55° for 150 minutes. Genomic DNA was then isolated using phenol/chloroform (Sigma-Aldrich, 77617) extraction, followed by a back extraction of phenol/chloroform with additional volume of TE1X. DNA was precipitated in 2 volumes of cold ethanol, 0.3M sodium acetate and 20ug glycogen (Ambion AM9510) for 1 hour on dry ice or overnight at -20°C. Dry pellets were resuspended in 50 ul (S2) or 15 ul (S3 and S4) of nuclease-free water and incubated at 4°C overnight. On the next day, S2 was further purified using PCR DNA Purification Kit Sample Collection - Our cohort includes chemo-naïve patients followed in the Urology Division of Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico (Milan) who underwent the transrectal ultrasound-guided systematic sampling of prostate tissue (TRUS biopsy). This diagnostic procedure was performed as part of routine clinical management following the detection of abnormal digital rectal examination or an elevated PSA blood level. According to the current standard for the detection of PCa, 14 ultrasound-guided biopsy cores (diagnostic biopsies), seven from each side of the prostate gland, were collected from each patient for the clinical diagnosis. During the same procedure, one additional biopsy core to be used for our research project (research biopsy), was taken from a site direcLibrary Construction - S2L, S3 and S4 fractions were sonicated in a Covaris M220 focused-ultrasonicator using screw cap microTUBEs (Covaris, 004078) to obtain a smear of DNA fragments peaking at 150-200 bp (waterbath 20°C, peak power 30.0, duty factor 20.0, cycles/burst 50, 150 seconds for S2L and 175 seconds for S3 and S4). Fractions were quantified using Qubit 4 fluorometer with Qubit dsDNA HS Assay Kit (Invitrogen, Q32854). Libraries were generated from each sample using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) and Unique Dual Index NEBNextMultiplex Oligos for Illumina (NEB, E6440S). Libraries were then qualitatively and quantitatively checked on and run on an Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent, 5067-4626).Sequencing - RNA-seq libraries were sequenced on the Illumina NextSeq 550 system according to the manufacturer's instructions.Library Construction - For each sample, 1 ng of total RNA was used to construct strand specific RNA-seq libraries with SMARTer Stranded Total RNA-Seq Kit - Pico Input (Takara, 634487). The yield and quality of the libraries were evaluated on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent, 5067-4626).Nucleic Acid Extraction - Ten thousand cells retrieved from the digestion step were stabilized in 200μl of 1Thioglycerol/Homogenization Solution of the Maxwell® RSC miRNA Tissue Kit (Promega, AS1460) and stored frozen at -80°C for total RNA automated purification using Maxwell® RSC 48 Instrument (Promega, AS8500). Total RNA was quantified by Qubit 4 fluorometer with Qubit RNA HS Assay Kit (Invitrogen, Q32852) and assessed by Agilent 2100 Bioanalyzer using Agilent RNA 6000 Pico Kit (Agilent, 5067-1513) to inspect RNA integrity.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMetabolomicsUnknownTranscriptomicsGenomicsProteomicsMaxwell® RSC 48 Instrument (Promega, AS8500)NextSeq 550Illumina NovaSeq 6000Transrectal ultrasound-guided systematic sampling of prostate tissue (TRUS biopsy)RNA-seq of total RNAHomo sapiensPrimary prostate cancer subtypes identified by chromatin compartments profiling at time of diagnosisValentina Rosti, Cristiano Petrini, Giovanni Lembo, Francesca Gorini, Roberto Quadri, Margherita Mutarelli, Elisa Salviato, Emanuele di Patrizio Soldateschi, Emanuele Montanari, Giancarlo Albo, Francesco Ripa, Alessandra Fasciani, Mariacristina Crosti, Valentina Vaira, Elisa De Lorenzis, Marco Maggioni, Francesco Ferrari, Chiara LanzuoloChiara LanzuoloGiovanni LemboValentina RostiFrancesco Ferrarifalse4f-SAMMY-seq (Sequential Analysis of MacroMolecules Accessibility) and total RNA-seq data from prostate biopsies of 25 chemo-naïve patients (7 healthy biopsies and 18 tumor biopsies)We used a groundbreaking epigenomic profiling technique developed in our laboratory, the 4f-SAMMY-seq, along with RNA-seq on 7 healthy biopsies and 18 prostate tumor biopsies. Our study represents the first direct examination of chromatin organization in patient-derived prostate biopsies. Leveraging differences in chromatin architecture, we identified a novel Prostate Cancer transcriptional signature associated with a favorable prognosis.2025-08-21T00:00:00Z2026-02-09T14:25:30.794Z2024-07-05T14:41:40.611ZE-MTAB-14226ERP178758EFO_0002944EFO_0004170EFO_0009653EFO_0005518EFO_0004184