Methylation profile of neuroendocrine prostate cancer models

UID: 10627

Author(s): Puca, Loredana, Beltran, Himisha

Description: Summary from the GEO: "Our study represents a detailed molecular analysis of neuroenedocrine prostate cancer models"

Overall design from the GEO: "Understanding the global methylation profile of tumor organoids and PDOXs."

Abstract from the article on Synapse to further explain the study and the relating dataset:

"A major hurdle in the study of rare tumors is a lack of existing preclinical models. Neuroendocrine prostate cancer is an uncommon and aggressive histologic variant of prostate cancer that may arise de novo or as a mechanism of treatment resistance in patients with pre-existing castration-resistant prostate cancer. There are few available models to study neuroendocrine prostate cancer. Here, we report the generation and characterization of tumor organoids derived from needle biopsies of metastatic lesions from four patients. We demonstrate genomic, transcriptomic, and epigenomic concordance between organoids and their corresponding patient tumors. We utilize these organoids to understand the biologic role of the epigenetic modifier EZH2 in driving molecular programs associated with neuroendocrine prostate cancer progression. High-throughput organoid drug screening nominated single agents and drug combinations suggesting repurposing opportunities. This proof of principle study represents a strategy for the study of rare cancer phenotypes."

Subject of Study

Subject(s)

OncoTree Cancer Type(s)

Prostate Neuroendocrine Carcinoma
Prostate

Access via GEO
Plain Text Data of methylation profiling by high throughput sequencing
Accession #: GSE112829

Access via SRA
3 samples of Bisulfite Sequencing
Accession #: SRP137894

Access via BioProject
Additional information about overall initiative.
Accession #: PRJNA449098
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files.
Associated Publications: Puca L, Bareja R, Prandi D, et al. Patient derived organoids to model rare prostate cancer phenotypes. Nature Communications. 2018; 9:2404.
Data Type: Genomic
Equipment Used: Illumina HiSeq 2000
High throughput gene sequencing system
Software Used: SRA Toolkit
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
Dataset Format(s): Plain Text, TAR
Dataset Size: 79.6 MB

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