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California collaboration focuses on analyzing pediatric cancers

Breakthroughs in medical research can take a frustratingly long time to reach doctors and the patients they treat. But a newly funded collaboration between computational biologists at UC Santa Cruz and researchers conducting pediatric cancer clinical trials at three California institutions, including one led by Stanford's Alejandro Sweet-Cordero, MD, may set the stage to bring the power of cancer genomic research into the hands of clinicians and their patients.

The California Initiative to Advance Precision Medicine is funding the UC Santa Cruz Genomics Institute's California Kids Cancer Comparison project. The project will develop technology to use a cancer’s genetic mutations, its DNA signature, to match it to similar cancers regardless of the tissues the cancers originated from. So, if a lung cancer’s DNA signature more closely resembles a certain kind of brain cancer’s signature, then doctors may pursue treatments that have proven effective against that brain cancer. This technique is especially beneficial for pediatric cancers, which are rarer than adult cancers and less likely to have been included in clinical drug trials.

The project builds on the UC Santa Cruz Genomic Institute’s Treehouse Childhood Cancer Project, led by bioinformatics researcher and UCSC postdoctoral scholar Olena Morozova, PhD, which showed how the academic investigations could have real world consequences.

“Treehouse was started as a research project - we weren’t thinking we could go clinical with it,” Morozova told me. That changed when she and colleagues analyzed the genes of an aggressive sarcoma from an 8-year-old boy enrolled in a cancer genomic clinical trial six months ago.

The child’s cancer had originated in his brain and had gone into remission after a standard treatment of chemotherapy, radiation and a bone marrow transplant. But two years later doctors found tumor growths in his lungs.

Morozova and her colleagues found that genes turned on in the boy’s cancer cells matched those turned on in a rare neuron tumor called a neuroblastoma that is found almost exclusively in children.

Neuroblastomas happened to be the cancer Morozova researched for her PhD, and she knew of a molecular signaling pathway that could be active in the boy’s cancer. Two drugs that target this pathway had been shown to be effective in clinical trials and had received Food and Drug Administration approval for adult patients. The UCSC researcher’s passed on their data supporting that the pathway was active in the tumor to the boy’s physician, who chose to administrate the drugs.

By partnering with researchers like Sweet-Cordero, who’s conducting a trial on difficult-to-treat cancers in children and young adults, the California Kids Cancer Comparison project will be able to compare the cancer DNA sequences to a collected database of both adult and pediatric cancers. And they hope to automate parts of the analysis to make this technology accessible to doctors without degrees in bioinformatics.

“If it is successful, we hope to offer it to every child with cancer in California and elsewhere,” said Morozova.

Kim Smuga-Otto is a student in UC Santa Cruz’s science communication program and a former writing intern in the medical school’s Office of Communication and Public Affairs. 

Previously: Gene-sequencing rare tumors – and what it means for cancer research and treatment

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