Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA327939 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Patient derived organoids (PDOs) have been established as a 3D culture model which closely recapitulates the in vivo tumor biology. However, one limitation of this culture model is the lack of tumor microenvironment which has a significant role in tumor progression and drug response. To address this, we established and molecularly characterized a novel 3D co-culture model of colorectal cancer (CRC) based on PDOs and patient matched fibroblasts. Both normal and cancer associated fibroblasts, NFs and CAFs respectively, were able to support organoid growth without addition of niche factors to the media. Additionally, co-cultures showed closer resemblance to primary patient material than organoid mono-cultures as evaluated by histology. Finally, RNA gene expression signatures of tumor cells and fibroblasts isolated from mono- or co-cultures demonstrated that co-cultures support greater cell type heterogeneity. In this proteomics dataset we compared pairs of NFs and CAFs derived from five patients. Collectively, we present a newly established human derived organoid-fibroblast model which, closely recapitulates in vivo tumor heterogeneity and involves the tumor microenvironment.
2023-03-14 | PXD032047 | Pride
Project description:Organotypic in vitro culture is useful to model mammalian disease in numerous tissues. Normal epithelial differentiation and carcinogenesis both undergo in vivo regulation by stroma, but current culture methods exclude stroma. To mimic this in vivo environment, we developed and characterized a human 3D prostate organoid co-culture model that incorporates prostate stroma. Primary prostate stromal cells supported increased organoid formation and expressed growth factors and WNT-related genes involved in epithelial differentiation. Organoid branching occurred distal to physical contact with stromal cells, demonstrating non-random branching. Tumoroids derived from primary prostate cancer maintained differential expression of the prostate cancer marker AMACR only in the presence of stroma. Stroma-induced phenotypes were similar in all patients examined, yet maintained inter-patient heterogeneity in the degree of response. Addition of stroma to in vitro organoid culture recapitulated the in vivo microenvironment by inducing organization of benign organoids into branching structures and preserving prostate cancer phenotypes.
2018-05-30 | GSE115052 | GEO
Project description:To understand if the generation of xenograft and organoid models of breast cancer alters DNA methylation, we compared the genome-wide methylation profile of matching patient tumors, patient derived xenografts, and organoid cultures derived from xenografts.
2022-01-09 | GSE186747 | GEO
Project description:Despite the enormous replication potential of the human liver, there are currently no culture systems available that sustain hepatocyte replication and/or function in vitro. We have shown previously that single mouse Lgr5+ liver stem cells can be expanded as epithelial organoids in vitro and can be differentiated into functional hepatocytes in vitro and in vivo. We now describe conditions allowing long-term expansion of adult bile duct-derived bi-potent progenitor cells from human liver. The expanded cells are highly stable at the chromosome and structural level, while single base changes occur at very low rates. The cells can readily be converted into functional hepatocytes in vitro and upon transplantation in vivo. Organoids from α1-antitrypsin deficiency and Alagille Syndrome patients mirror the in vivo pathology. Clonal long-term expansion of primary adult liver stem cells opens up experimental avenues for disease modeling, toxicology studies, regenerative medicine and gene therapy. We generated arrays from whole human liver tissue, and human liver derived cultures maintained in our defined medium. Genes 4 fold differentially expressed were used for the clustering analsyis (see matrix 1). For the genes enriched in organoid cultures grown in ERFHNic+A compared to ERFHnic we normalized the arrays by substracting the liver tissue 1 array to the culture arrays. Then we calculated the fold difference between the ERFHNic+A and the ERFHNic samples (see matrix 2).
2015-01-15 | E-GEOD-63859 | biostudies-arrayexpress
Project description:Patient-derived breast cancer organoid study
| PRJNA786253 | ENA
Project description:Patient-derived breast cancer organoid study
| PRJNA786254 | ENA
Project description:Phosphoproteomics data of Matrigel-embedded HCT116 spheroid, and patient-derived colorecral cancer organoid
2019-02-24 | PXD009032 | JPOST Repository
Project description:The objective of this clinical trial is to demonstrate that cytoreductive surgery and patient-tailored hyperthermic intra-peritoneal chemotherapy (HIPEC) will increase efficacy in controlling peritoneal disease. Tridimensional cell cultures (organoids) derived from colorectal cancer peritoneal metastases are used to select the most active drugs in an in vitro HIPEC model on individual-patient level, based on the hypothesis that resistance to drug(s) routinely used for intraperitoneal delivery can explain peritoneal relapse after combined treatment, depending on the individual tumor biology;
| 107304 | ecrin-mdr-crc
Project description:Due to the highly heterogeneous nature of tumor, it is very challenging to study the molecular mechanisms of tumorigenesis. Recently, in vitro derived 3D organoid culture system were developed and may serves as a good model for studing the cancer molecular mechanisms in vitro, which allows long-term expansion of human colorectal colon cancer.To fully evaluate the organoid culture system, we perform a single cell RNA-seq survey of 4,792 single cells of tumor and adjacent normal tissues in vivo as well as corresponding patient-derived organoid samples from seven patients with colon cancer to investigate their gene expression signatures. We also apply whole-exon sequencing, whole genome sequencing and Sanger sequencing to characterize their genomic features accordingly. We found that tumor-derived organoid in vitro in general faithfully maintained the gene expression signatures, gene regulatory network, tumor-microenvironment cross-talk, as well as mutations such as copy number variants and point mutations of tumor cells in vivo. However adjacent normal tissue-derived organoid, despite remaining normal in genomic levels, changed their gene expression profiles drastically and acquired tumor-like gene expression signatures.
2022-05-05 | GSE121454 | GEO
Project description:Breast cancer is a heterogenous disease that is difficult to model in vitro. Frozen primary breast cancers were decellularised to generate patient-derived scaffolds which are used to model 3D growth for cancer cell lines. The cell-free cancer microenvironments in the patient-derived scaffolds influence breast cancer cell line phenotypes and enrich for cells with cancer stem cell characteristics. Growth in patient-derived scaffold cultures also influenced the expression of epithelial-to-mesenchymal transition-related genes, and several gene expression changes in the model could be associated to clinical parameters of the original tumors and corresponding patients. Previous studies also demonstrated that the relative protein composition in the cell-free cancers were related to tumor grade and proliferation in cancer cells, suggesting that the relative proteomic composition varies between individual microenvironments. Therefore, we decellularised a larger breast cancer cohort to better characterize the cell-free microenvironments and potentially link to clinical features of the tumors and patients, which could be used to identify novel processes and targets that could be used to better model the disease or targeted in drug discovery.
2024-04-18 | PXD042671 | Pride