Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Patient and xenograft-derived organoids recapitulate pediatric brain tumors features and patient treatments [array]

ABSTRACT: Brain tumors are the leading cause of cancer-related death in children. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of pediatric brain cancer are limited and hard to establish. We present a protocol that enables efficient generation, expansion and biobanking of pediatric brain cancer organoids. Utilizing our protocol, we have established patient-derived organoids (PDOs) from ependymomas, medulloblastomas, low-grade glial tumors and patient-derived xenograft organoids (PDXOs) from medulloblastoma xenografts. PDOs and PDXOs recapitulate histological features, DNA methylation profiles and intratumor heterogeneity of the tumors from which they were derived. We also showed that PDOs can be xenografted. Most interestingly, when subjected to the same routinely applied therapeutic regimens, PDOs respond similarly to the patients. Taken together, our study highlights the potential of PDOs and PDXOs for research and translational applications for personalized medicine.

ORGANISM(S): Homo sapiens

PROVIDER: GSE247231 | GEO | 2023/12/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Patient and xenograft-derived organoids recapitulate pediatric brain tumors features and patient treatments [scRNA-Seq]

Project description:Brain tumors are the leading cause of cancer-related death in children. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of pediatric brain cancer are limited and hard to establish. We present a protocol that enables efficient generation, expansion and biobanking of pediatric brain cancer organoids. Utilizing our protocol, we have established patient-derived organoids (PDOs) from ependymomas, medulloblastomas, low-grade glial tumors and patient-derived xenograft organoids (PDXOs) from medulloblastoma xenografts. PDOs and PDXOs recapitulate histological features, DNA methylation profiles and intratumor heterogeneity of the tumors from which they were derived. We also showed that PDOs can be xenografted. Most interestingly, when subjected to the same routinely applied therapeutic regimens, PDOs respond similarly to the patients. Taken together, our study highlights the potential of PDOs and PDXOs for research and translational applications for personalized medicine.

2023-12-01 | GSE247380 | GEO

Single-cell landscapes of primary glioblastomas and matched organoids and cell lines reveal variable retention of inter- and intra-tumor heterogeneity [scWGS]

Project description:Glioblastomas (GBMs) are aggressive primary malignant brain tumors characterized by extensive levels of inter- and intra-tumor genetic and phenotypic heterogeneity. Patient-derived organoids (PDOs) have recently emerged as useful models to study such heterogeneity. Here, we present bulk exome as well as single-cell genome and transcriptome profiles of primary IDH wild type GBMs from ten patients, including two recurrent tumors, as well as PDOs and brain tumor-initiating cell (BTIC) lines derived from these patients. We find that PDOs are genetically similar to and variably retain gene expression characteristics of their parent tumors. At the phenotypic level, PDOs appear to exhibit similar levels of transcriptional heterogeneity as their parent tumors, whereas BTIC lines tend to be enriched for cells in a more uniform transcriptional state. The datasets introduced here will provide a valuable resource to help guide experiments using GBM-derived organoids, especially in the context of studying cellular heterogeneity.

2022-02-16 | GSE173279 | GEO

Single-cell landscapes of primary glioblastomas and matched organoids and cell lines reveal variable retention of inter- and intra-tumor heterogeneity [scRNA-seq]

2022-02-16 | GSE173278 | GEO

Single-cell landscapes of primary glioblastomas and matched organoids and cell lines reveal variable retention of inter- and intra-tumor heterogeneity [multi-generation scRNA-seq]

2022-02-16 | GSE193884 | GEO

Patient-derived Organoids Predicts the Clinical Efficiency of Colorectal Liver Metastasis

Project description:Accumulating evidence indicates that patient- derived organoids (PDOs) can predict drug responses in the clinic. Metastasis is the main cause of death in colorectal cancer patients, and the treatment of patients with liver metastasis remains poor. Tumor heterogeneity is the cause of treatment failure. In this study, we aim the investigate the consistency of drug sensitivity for the matched primary and metastatic tumor in patients with liver metastasis.

| 2400343 | ecrin-mdr-crc

Patient and xenograft-derived organoids recapitulate pediatric brain tumors features and patient treatments

Project description:Patient and xenograft-derived organoids recapitulate pediatric brain tumors features and patient treatments

| PRJNA1037468 | ENA

Mimicking tumor cell heterogeneity of colorectal cancer in a patient-derived organoid-fibroblast model

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

Patient and xenograft-derived organoids recapitulate pediatric brain tumors features and patient treatments [array]

Project description:Patient and xenograft-derived organoids recapitulate pediatric brain tumors features and patient treatments [array]

| PRJNA1036666 | ENA

Expression data from CRC patient-derived organoids

Project description:Colorectal cancer (CRC) is a commonly occurring cancer worldwide. Metastasis and recurrence are the major causes of cancer-related death. CRC progression is a multistep process, and extensive efforts have been made to identify the genomic and transcriptomic alterations that occur during this process. However, whether primary tumors and metastatic lesions possess distinct biological features remains unclear. We established 74 patient-derived organoids (PDOs) from primary tumors and patient-matched metastatic and recurrent lesions.

2021-04-01 | GSE128213 | GEO

RNA sequencing of metastatic breast patient derived organoids (PDOs) treated with control and CAF-conditioned media, in the presence and absence of Fulvestrant

Project description:To gain insight into the gene expression profile of breast patient derived organoids (PDOs) under endocrine therapy, and how cancer associated fibroblasts (CAFs) might influence gene expression and stimulate resistance, we performed RNA sequencing on three of the metastatic PDOs treated with control media and CAF-conditioned media, in the presence and absence of Fulvestrant (4-day treatment). These data revealed that Fulvestrant significantly suppressed the ER signature in the PDOs, suggesting that the ER-pathway is still active in these tumors although the patients had relapsed on ER-targeting agents (Tamoxifen, Letrozole).

2023-06-27 | GSE216540 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data