{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Julia Polánsky-Biskup"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16020"],"description":["DNA methylation analysis of patient-derived lung tumoroids and matched healthy organoids demonstrates preservation of tumor-specific epigenomic identity during long-term culture. Tumoroids maintain the methylation landscape of their parental tumors, with samples from the same patient clustering together based on DNA methylation profiles regardless of culture conditions. Differential methylation analysis reveals distinct tumor-specific patterns distinguishing tumoroids from healthy organoids, confirming stable epigenomic preservation. These findings validate the tumoroid platform as a reliable model for precision CAR T-cell therapy development and personalized treatment testing in lung cancer."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - The isolated genomic DNA and cell lysates from Proteinase K digestion underwent bisulfite conversion utilizing Zymo’s EZ DNA Methylation-Gold Kit (Zymo Research) following the manufacturer’s instructions. DNA methylation levels were evaluated using the Infinium MethylationEPIC Kit (Illumina EPIC-8 BeadChip, Illumina, Inc.) according to the manufacturer’s guidelines.","Scaning - Imaging of the Illumina EPIC-8 BeadChips was performed using the iScan Microarray Scanner (Illumina).","Sample Collection - Patients undergoing surgery of a histologically proven lung tumor were included and written informed consent was obtained from all patients. Cross-sectional slices of tumor tissue were obtained by a pathologist as well as macroscopically inconspicuous healthy lung tissue as distant as possible from the tumor site.","Labeling - DNA were labelled using the Infinium MethylationEPIC Kit (Illumina EPIC-8 BeadChip, Illumina) following the manufacturer's instructions.","Growth Protocol - Tumoroids and Organoids were cultured for at least 3 month (short-term), 6 month (mid-term) and 9 month (long-term).","Nucleic Acid Extraction - DNA from fresh and frozen healthy and tumor tissue and organoid cells was extracted with Quick-DNA Miniprep Plus Kit (Zymo Research, D4068) according to the manufacturer´s instructions","Hybridization - DNA was subjected to bisulfite conversion using the EZ DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s protocol."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - The raw intensity was processed and normalized using minfi package in R."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"study_type":["methylation profiling by array"],"species":["Homo sapiens"],"pubmed_title":["Lung tumoroids as a 3D testing platform for precision CAR T-cell therapy"],"pubmed_authors":["Lukas Ehlen, Martí Farrera-Sal, Martin Szyska, Janine Arndt, Simon Schallenberg, Cedric Scholz, Mingxing Yang, Claudia Vollbrecht, Anna Loewa, Rebecca Friedrich, Marco Mai, Lena Peter, Samira Picht, Sarah Schulenberg, Daniel Geray, Gabriela Korus, Anke Sommerfeld, Denise Treue, Julia Strauchmann, Aron Elsner, Jonas Kath, Valeria Fernandez Vallone, Maria Joosten, Franka Klatte-Schulz, Ansgar Petersen, Harald Stachelscheid, Dimitrios Laurin Wagner, Claudia Spies, Jens-Carsten Rückert, Andreas Hocke, Julia Polansky, Regina Stark Oliver Klein and Michael Schmueck-Henneresse","Julia Polánsky-Biskup"],"additional_accession":[]},"is_claimable":false,"name":"Epigenomic characterization of patient-derived lung tumoroids using DNA methylation profiling","description":"DNA methylation analysis of patient-derived lung tumoroids and matched healthy organoids demonstrates preservation of tumor-specific epigenomic identity during long-term culture. Tumoroids maintain the methylation landscape of their parental tumors, with samples from the same patient clustering together based on DNA methylation profiles regardless of culture conditions. Differential methylation analysis reveals distinct tumor-specific patterns distinguishing tumoroids from healthy organoids, confirming stable epigenomic preservation. These findings validate the tumoroid platform as a reliable model for precision CAR T-cell therapy development and personalized treatment testing in lung cancer.","dates":{"release":"2025-12-29T00:00:00Z","modification":"2026-05-27T12:52:37.941Z","creation":"2025-11-13T14:40:12.964Z"},"accession":"E-MTAB-16020","cross_references":{"EFO":["EFO_0002944","EFO_0003814","EFO_0003813","EFO_0003789","EFO_0002759","EFO_0005518","EFO_0003816","EFO_0003815","EFO_0003969"],"doi":[": https://doi.org/10.21203/rs.3.rs-5418471/v1 (Preprint)"]}}