Analyzing Paediatric Brain Tumours Provide Data for Cancer Research

The first large-scale, collaborative, open analysis of genomic data provides a cloud-based resource for researchers looking for more comprehensive data on pediatric brain tumors.

A first-of-its-kind open-source, reproducible analysis platform for pediatric brain tumors is created with the help of researchers from Children’s Hospital of Philadelphia (CHOP), the Alex’s Lemonade Stand Foundation Childhood Cancer Data Lab, the Children’s Brain Tumor Network (CBTN), the Pacific Pediatric Neuro-Oncology Consortium (PNOC), and more than 20 additional institutions.

Using thousands of genomically sequenced samples, researchers have used this platform to identify initial findings about genetic variants associated with poorer outcomes that could help guide future diagnostic and therapeutic advances. The details of the platform were published in the journal Cell Genomics ().

Brain Tumor in Children - Types, Causes, Symptoms, Diagnosis & Treatment
An abnormal growth of cells in the brain is called brain tumor. Most tumors arise within the brain (primary). They can be benign or cancerous.

‘‘The Open Pediatric Brain Tumor Atlas (OpenPBTA) made it possible for experts across the globe to gain a deeper understanding of the leading cause of cancer-related death in children and young adults.#brain tumors #cancer research #pediatrics’’

Pediatric brain tumors are collectively the leading cause of cancer-related death in children in the United States. However, the severity of pediatric brain tumors varies wildly, with some having an almost universally fatal prognosis while others have relatively strong long-term survival rates, though all brain tumors negatively impact these children and their families to at least some degree.

Limited access to tissue samples and patient-derived cell lines has been a significant barrier to understanding the differences between pediatric brain tumors at a molecular level (). That long-sought-after data could lead to better diagnostic techniques and potential targeted therapies that could treat these deadly tumors.

OpenPBTA Providing More Insights into Potential Drivers of Pediatric Brain Tumors

In 2011, CBTN and PNOC began extracting and preparing what has now become nearly 6,000 tumor samples with over 68,000 sub-samples. More than 1,000 of these tumors were sequenced to form the initial release of the Pediatric Brain Tumor Atlas (PTBA) in 2018, and data were made available without embargo so that researchers could study what variants might be driving certain types of brain tumors.

With the help of Alex’s Lemonade Stand Foundation Childhood Cancer Data Lab, the team of researchers was able to build an open-source version of this atlas, the Open Pediatric Brain Tumor Atlas (OpenPBTA), to analyze these data.

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OpenPBTA is accessible to anyone conducting research who is looking for new therapeutic targets or finding new ways to translate research into clinical practice. At the time of this study, OpenPBTA contained genomic and clinical data from more than 1,000 pediatric brain tumors and 22 patient-derived cell lines from the CBTN and PNOC.

While there have been many proponents of an open-source model for scientific research, nothing like this existed for pediatric cancer. Researchers designed OpenPBTA so that anyone could access the data, contribute to its analysis, and/or use it in their research.

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OpenPBTA made it possible for experts across the globe to come together and gain a deeper understanding of the leading cause of cancer-related death in children and young adults.

In this study, researchers found that the loss of the tumor suppressor gene TP53 is a significant marker for poor overall survival in the fast-growing brain and spinal cord tumors called ependymomas and certain diffuse midline gliomas (), and dysregulation of the gene was also implicated in hypermutant high-grade gliomas.

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Solving pediatric brain tumors cannot be accomplished by any one institution. The OpenPBTA model of shared, a real-time collaboration supported by PNOC and CBTN has not only empowered discoveries but also innovative ways of performing the required science on behalf of accelerated, collaborative innovation for children affected by brain tumors.

References:

OpenPBTA: An Open Pediatric Brain Tumor Atlas - (https://www.biorxiv.org/content/10.1101/2022.09.13.507832v1)
Childhood brain tumors: current management, biological insights, and future directions - (https://thejns.org/pediatrics/view/journals/j-neurosurg-pediatr/23/3/article-p261.xml)
Targeting mutant p53 for cancer therapy: direct and indirect strategies - (https://jhoonline.biomedcentral.com/articles/10.1186/s13045-021-01169-0)

Source-Eurekalert