A
web-based Atlas of Patient-Derived Xenografts
of cancer patients:A resource of MURAL PDX data
About the PDX-Atlas
Patient-derived xenograft (PDX) models are used to study tumour biology, identify mechanisms of drug resistance and test therapeutic targets. During the process of generating and using PDXs, a vast array of information is collected. This includes patient clinical details, the fate of tumours grafted into mice, the genomic and transcriptomic features of tumours, and the responses of PDXs to drug treatment. Lab technicians, clinicians and researchers may record these data in different formats that lack standardization and are difficult to share between researchers and laboratories
To facilitate data sharing and visualisation of genotype-phenotype connections between PDXs, we developed a user-friendly web-based compendium known as PDX-Atlas. It integrates clinical, experimental, genomic and transcriptomic data from cohorts of PDXs. PDX-Atlas was developed using the free, open-source Django web application framework using MySQL as backend data storage system. PDX-Atlas incorporates search, browse, download and visualization functions to connect and identify associations between genotype/phenotype and drug response to identify candidate targets with the click of button. The database meets the PDX-Minimal Information (PDX-MI) standards set by PDX consortium community to aid data submissions and sharing across the research laboratories.
Currently, PDX-Atlas hosts >50 PDXs collected from 30 prostate cancer patients from the Melbourne Urological Research Alliance (MURAL; https://t.co/GcC0osoUiK) as a user-friendly interface to access these data. PDX-Atlas is also a discovery tool for elucidating the molecular basis of therapy resistance in cancer, facilitating the development of novel therapeutics to improve the outcomes of cancer patients.
Acknowledgements
The Melbourne Urological Research Alliance cohort of PDXs has been supported by funding from the Movember Foundation Global Action Plan 1 PDX Project; NHMRC; Victorian Cancer Agency; Prostate Cancer Foundation of Australia; the US Department of Defense through the Prostate Cancer Research Program (W81XWH1810349; opinions, interpretations, conclusions, and recommendations are those of the authors and are not necessarily endorsed by the Department of Defense); the Rotary Club of Manningham; RULE Prostate Cancer and the EJ Whitten Foundation; the Peter and Lyndy White Foundation; and TissuPath Pathology
We acknowledge the Traditional Owners of the lands on which these studies take place and pay our respects to their Elders, past and present. We thank the patients, families, and consumers who support our research. We also thank the patient representatives, clinical co-ordinators, scientists, clinicians, pathologists and committee members who contribute to the Melbourne Urological Research Alliance (MURAL), kConFab, and CASCADE.
To request access to MURAL PDXs and/or biospecimens, researchers should contact Dr. Melissa Papargiris, MURAL Project Manager (melissa dot papargiris at monash dot edu) to initiate an expression of interest. Researchers need to provide evidence of institutional ethics approvals to experiment with human PDXs and research will be conducted under the conditions of a material/data transfer agreement.