JUL 03, 2023 3:00 AM PDT

A New Open Resource for Pediatric Brain Cancer Research

WRITTEN BY: Katie Kokolus

All cells in the body, including tumor cells in a cancer patient, contain a complete copy of the genome.  The DNA in the genome includes instructions to the body on how to make all the proteins needed to survive, grow, and function. 

Four nucleotides, thymine (T), adenine (A), cytosine (C), and guanine (G), make up the DNA code by forming codons, a sequence of three nucleotides that correspond to genetic information.  The four nucleotides can generate 64 codons; 61, which code for an amino acid, and three, which signal the end of a protein. 

The study of the genome, known as genomics, aims to help us understand how genes interact.  Therefore, studying the cancer genome can provide valuable information on how tumor tissue forms, develops, and grows.  An in-depth analysis of the cancer genome can even inform how cancer cells die or respond to different therapeutic interventions.

One of the most notable genomic studies, the Cancer Genome Atlas (TCGA), molecularly characterized tumors from over 20,000 samples from 33 different types of cancer.  Beginning in 2006, it took twelve years to complete TCGA, which contains about 2.5 petabytes of publicly accessible data for researchers.  Indeed, genomic studies continue to advance cancer survivorship by providing new diagnostic and therapeutic approaches. 

Pediatric brain and spinal cord tumors remain the leading cause of death from disease in children creating an urgent need to improve therapeutic strategies.  A study recently published in Cell Genomics established a new resource for pediatric brain and spinal cord tumors called the Open Pediatric Brain Tumor Atlas (OpenPBTA).  The study demonstrates how genomic analysis could play a role in advancing therapeutics for pediatric cancer patients. 

The generate OpenPBTA, the researchers used data from two resources: the Children’s Brain Tumor Network (CBTN) and the Pacific Pediatric Neuro-Oncology Consortium (PNOC).  OpenPBTA includes genomic data on 1,074 pediatric brain tumors and 22 patient-derived cell lines.

In addition to generating OpenPBTA, the researchers demonstrated its utility by identifying genetic variants associated with poor prognosis.  The study revealed that certain tumors, including highly aggressive brain tumors known as ependymomas, conferred notably worse prognosis when lacking expression of a gene called TP53.  The TP53 gene instructs the body to produce a tumor suppressor protein known as p53.  The p53 protein regulates cell division, preventing cells from dividing too rapidly. 

OpenPBTA will provide a valuable resource for developing new therapeutic strategies to treat pediatric brain tumors.  Thus, it has a great potential to improve patient outcomes and survivorship quickly and efficiently. 


Sources: Neuro Oncol, Cell Genomics

About the Author
Doctorate (PhD)
I received a PhD in Tumor Immunology from SUNY Buffalo and BS and MS degrees from Duquesne University. I also completed a postdoc fellowship at the Penn State College of Medicine. I am interested in developing novel strategies to improve the efficacy of immunotherapies used to extend cancer survivorship.
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