Genomes offer clues to treating childhood cancers

On Tuesday, two biotech companies announced that it would soon be possible to sequence the human genome -- each individual’s complete DNA blueprint -- in about a day for around $1,000.

On Wednesday, researchers at St. Jude Children’s Hospital in Memphis, Tenn., and Washington University in St. Louis reported scientific results that hint at how this type of inexpensive genetic testing might help patients.

In one study, researchers sequenced the genomes of cancer cells from 12 St. Jude patients with early T-cell precursor acute lymphoblastic leukemia and discovered that genetically, the subtype had more in common with a different type of leukemia than with other acute lymphoblastic leukemias. This might point the way toward better treatments, St. Jude researchers said.

In the other study, investigators sequenced the tumors of four young patients with retinoblastoma, a rare cancer of the eye.

Both studies were part of the Pediatric Cancer Genome Project, a $65-million, three-year effort designed to sequence 600 pediatric cancers, along with the normal DNA of the children who have them, said St. Jude Chief Executive Dr. William Evans.


“We want to understand: What mutations cause a normal cell to turn into cancer?” Evans told Booster Shots during a recent visit to Los Angeles.

The St. Jude and Washington University researchers are targeting the cancers that they have the most difficulty treating today, he said. Overall, more than 90% of acute lymphoblastic leukemia patients at St. Jude survive long term, but only 30% to 40% of patients with the early T-cell precursor acute lymphoblastic leukemia, or ETP-ALL, subtype respond well to treatment and become long-term survivors.

Physicians do better treating retinoblastoma, but the current treatment involves loss of vision, so they’d like to find new therapies, Evans said.

Results of the genome sequencing pointed to one possible target for treating retinoblastoma: a gene known as SYK. Researchers found elevated levels of SYK protein in 82 tumor samples and none in patients’ normal tissue, suggesting that retinoblastoma patients share some kind of change in the SYK gene that promotes the growth of their cancer -- and could possibly be reversed if the gene could be turned off.

“It’s amazing that we find a drug target,” Evans said.

He said that someday, as the price of of tests continues to fall, all children coming into St. Jude for cancer treatment would have their genomes sequenced to look for clues to cure their disease.

The ETP-ALL and retinoblastoma research papers were published online in the journal Nature. More studies are on the way over the coming months, Evans said. The hospital will sequence an additional 300 cancer genomes this year and is making results available to other scientists at the Explore Web data portal.

The hope is that researchers everywhere will use the data to make inroads treating childhood cancer.

“There are only a few thousand cases of these illnesses a year, but cancer still kills more kids than any other disease,” Evans said. He said it would probably be five to 10 years before therapies derived from the research are available.