Project description:OVDM1, a new ovarian cell line derived from a serous ovarian metastatic adenocarcinoma sample, was established by immortalization with SV40 large-T antigen and hTERT and then characterized Expression microarrays were used for molecular profiling of early and late passages of OVDM1 cell line, as well as the original metastatic tumor. Total RNA was extracted from early and late passages of OVDM1 and from the metastatic tumor for hybridization on Affymetrix microarrays
Project description:OVDM1, a new ovarian cell line derived from a serous ovarian metastatic adenocarcinoma sample, was established by immortalization with SV40 large-T antigen and hTERT and then characterized Expression microarrays were used for molecular profiling of early and late passages of OVDM1 cell line, as well as the original metastatic tumor.
Project description:We used bulk RNA sequencing to analyze unsupervised clustering of early and late passages of four GBM PDXs. Single cell RNAseq data was used to study transcriptional profiles of DMSO and TMZ, Primary and Recurrent as well as early and late passages of GBM PDXs.
Project description:Whole exome sequencing data to 30 PDOX models (28 early passages, 3 late passages (1 overlap)), 3 cell lines, and 20 matching human tumors
Project description:Low-coverage whole genome sequencing data for 30 PDOX models (28 early passages, 4 late passages (2 overlaps)), 3 cell lines, and 21 matching human tumors
Project description:In vitro models of pediatric brain tumors (pBT) are tools instrumental for better understanding the mechanisms contributing to oncogenesis and testing new therapies; and thus, ideally, they should recapitulate the original tumor. We applied DNA methylation (DNAm) and copy number variation (CNV) profiling to characterize 241 pBT samples, including 155 tumors and 86 pBT-derived cell cultures, and considering serum vs serum-free conditions, late vs early passages, and dimensionality (2D vs 3D cultures). We performed a t-SNE classification and identified differentially methylated regions in tumors compared to cell models. Early cell cultures recapitulate the original tumor, but serum media and 2D culturing were demonstrated to significant contribute to the divergence of DNAm profiles from the parental ones. All divergent cells clustered together acquiring a common deregulated epigenetic signature, suggesting a shared selective pressure. In conclusion, DNAm and CNV are informative tools that should be used to assess the recapitulation of pBT-cells from parental tumors.
Project description:Background: Sarcoma oncogenesis is still poorly understood and there is a pressing need to generate cell lines representative of diverse sarcoma types. Methods: We submitted to culture all sarcoma from patients receiving surgery in a large tertiary referral centre in France. Of the 32 established cell lines we report the genomic and transcriptomic study of 7 which were extensively tested for the representativeness to the original tumor and the evolution over passages. Results: Pleomorphic sarcomas are genetically heterogeneous. As a consequence, cell lines derived from that kind of tumor developed from selected clones roughly representing the initial tumor. More importantly our results show that there are no genetic imbalances and transcription modifications along passages. Conclusions: This likely means that even if pleomorphic sarcomas are genetically unstable at the cellular level, they appear to be genetically stable at the multicellular one and therefore remain representative of the initial tumor even after passages. We established a sarcoma cell line panel gathering 32 cell lines with genomic, transcriptomic and clinical data, which will be very powerful to go further in the understanding of genomic alterations, sarcoma biology and to manage preclinical studies and clinical trials.
Project description:The hypothesis was that the orthotopic xenograft model of ependymoma faithfully recapitulate the genomics signatures of the original tumor patient tissue Original tumor cells were implanted into the same location of SCID mice and check for transcriptome profiles upon subsequent passages to show that the passages preserve the overall genomics signature of the original tumor tissue.
