RNA Sequencing Shows Epigenetics Behind Pediatric Cancer

Using RNA sequencing for individual pediatric cancer cases could more effectively target gene expression in tumors, according to a new study published in JAMA Network Open.

The data, pulled from 4 precision medicine clinical trial databases, showed RNA targets could be more informative than DNA sequences, the study authors wrote.

“Herein, we described a framework for including RNA-Sequenced-derived gene expression information into precision medicine studies,” they concluded. “Most notably, we show for the first time to date that such a framework can be used consistently across separate precision medicine clinical trials.”

The study was conducted as a consortium between University of California Santa Cruz’s Treehouse Childhood Cancer Initiative. It focused on gene expression in 144 tumor samples taken from 128 patients between January 2016 and March 2017 at 4 clinical sites: the British Columbia Children’s Hospital in Vancouver (n = 31), the Lucile Packard Children’s Hospital at Stanford University (n = 80), the CHOC Children’s Hospital and Hyundai Cancer Institute in California (n = 46), and the Pacific Pediatric Neuro-Oncology Consortium in San Francisco (n = 24).

Median age at diagnosis was 9 years (range, 0 to 26).

The Treehouse Childhood Cancer Initiative did secondary analysis of each site’s tumor RNA-Sequence data, by either downloading the data in the cloud or by providing a Docker pipeline composed of gene-level expression calculation, which was run at the partner institution. Gene expression outlier analysis and identification of potential drug-targetable genes and pathways was conducted at UCSC, according to the study.

The Drug-Gene International Database was also instructed to query for drug-gene interactions among the 4 curated cancer databases (CIViC, Cancer Commons, My Cancer Genome, and My Cancer Genome Clinical Trial).

The RNA of each of the patients was compared against 11,340 uniformly analyzed adult, pediatric, and young adult tumor profiles in a compendium made up of public data.

The RNA, when compared to DNA, showed more efficacious routes for treatment, according to the paper. Among the 144 tumor samples, 99 comparative RNA sequencing analyses (68%) were feasible and potentially useful. The DBNA mutation information was potentially useful for only 34 of 74 samples (46%).

For 36% of tumor samples, druggable and overexpressed genes and/or pathways were identified based on RNA analysis alone, and were not found by assessing the tumor DNA.

Overall, the overexpression of 92 genes was considered directly or indirectly actionable. 

“The most common gene expression outlier was FLT3 (OMIM 136351), overexpressed in 16 samples, all from hematopoietic tumors. This was followed by BTK (OMIM 300300) and CDK6 (OMIM 603368), overexpressed in 14 samples each,” the researchers wrote. “While BTK was overexpressed in 14 hematopoietic tumors, CDK6 was expressed in both hematopoietic and nonhematopoietic tumors, including neuroblastomas and gliomas.

“The most common gene expression outlier in nonhematopoietic tumors was PTCH1 (OMIM 601309), overexpressed in 11 samples from craniopharyngioma, neurofibroma, sarcoma, glioma, medulloblastoma, and osteosarcoma,” they added. “The most common overrepresented gene set was receptor tyrosine kinases, overexpressed in 55 samples from all diagnostic categories.”

The authors said in a UC Santa Cruz statement that they designed the research as a feasibility study to show they can get data for prospective patients and analyze it quickly enough to benefit individuals.

“In pediatric cancer, it often isn’t a DNA mutation driving the cancer but an error in development caused by a change in how gene expression is regulated,” said Olena Vaske, the corresponding author, the Colligan Presidential Chair in Pediatric Genomics at the University of California Santa Cruz. “We showed for the first time that this framework can be used consistently across separate precision medicine clinical trials.”

REFERENCES:

Vaske O, Bjork I, Salama S, et al. Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer. JAMA Network Open. 2019;2(10):e1913968. doi:10.1001/jamanetworkopen.2019.13968.