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Future Frontier: Fighting Cancer at the Genetic Level

BY LAURA BEIL
PUBLISHED WEDNESDAY, SEPTEMBER 18, 2013
Rita Doerner was stunned earlier this year when doctors told her she had stage 2 breast cancer. The 77-year-old from St. Louis did not have any symptoms. Although her sister died from ovarian cancer, Doerner did not think she had any particular risk. She figured genetics were on her side. “When they told me I had cancer, I didn’t believe it,” she says. In addition to standard hormone therapy, Doerner has tried a new investigational drug—one that is not specifically geared to treat breast cancer. Rather, it targets cancers with a mutation in a gene called PIK3CA—which Doerner has. Because the mutation developed in her tumor and was not inherited or present in her normal cells, it created an opportunity to intervene with a treatment that is quite specific.

The human genome is the instruction manual for assembling all the molecules that keep cells alive. It’s a biochemical code, and sometimes the coding ends up with its own bad autocorrect. Often these glitches don’t matter, but sometimes, like writing “one” when you mean “none,” a slight change makes a big difference.

A malformed molecule comes off the factory line, and like paper airplanes, the proteins of life won’t work if they’re not folded just right. When a cell collects too many misshapen molecules from bad instructions, the normal checks and balances on growth can go offline. These errors manifest in two main ways. In one instance, certain genes, called oncogenes, get switched on and can lead to cancer growth. In another situation, genes, called tumor suppressor genes, are switched off. Either way, these errors can be inherited or develop in the body over time. This is why cancer is ultimately a genetic disease, and why, in Doerner’s case, genetics were not on her side.

Researchers have long searched for genetic errors responsible for corrupting a normal cell and sending it down the path to a runaway tumor. But until recently, the hunt for cancer-causing genes was a slow, tedious and expensive process. Obtaining the sequence of a gene (reading its code) had to be done by hand, sifting through DNA bit by bit. When researchers embarked on the U.S. Human Genome Project in 1990, the job of sequencing all human genes took more than a decade to complete and cost almost $3 billion. Some of the first cancer sequencing efforts cost more than $100,000 per tumor.

But just as your car now has more computing power than an Apollo spaceship, so has genetic sequencing become more compact, affordable and nimble than scientists once thought possible. The most modern method of gene sequencing—called next-generation sequencing—analyzes genes so rapidly that scientists almost have the love-struck awe of a person who’s gone from an old-style, dial-up modem to high-speed Internet overnight.

“Before, we had to search one gene at a time, going through 20,000 genes,” says Kenneth W. Kinzler about the hunt for cancer genes. “More than two decades of research can now be repeated in a week,” adds Kinzler, an oncologist who runs a lab focused on the genetics of cancer at The Johns Hopkins University School of Medicine in Baltimore. It is now possible to quickly reveal the code for every gene inside a tumor in a couple of weeks and compare that tumor’s genes to the genetic instructions of normal tissue. All for just a few thousand dollars—bargain prices, as genomes go.

Next-generation sequencing has not only transformed cancer genetics in the laboratory; it may one day directly guide the practice of oncology. The idea is that by taking a sample of a tumor and rapidly figuring out which instructions are wrong, doctors will know where the cancer drug needs to work. (If the cancer is occurring because certain genetic mutations are allowing specific proteins to take over a cell, you know specifically what task a drug needs to accomplish.) A version of this kind of tailored care is available now only for a handful of well-studied mutations, such as HER2 in breast cancer or EGFR in colon and lung cancers. Doctors envision a day when they can expose all a tumor’s genetic tricks. “I think this is going to be standard of care, and not in 10 years, but a few years,” says Michael Snyder, director of the Stanford Center for Genomics and Personalized Medicine in Stanford, Calif. In the not too distant future, he continues, “I can’t imagine getting cancer and not getting your genome sequenced.”

That said, many hurdles—some scientific, some economic—are keeping next-generation sequencing in the laboratory and out of doctors’ offices for the time being. The challenges are substantial enough that most researchers still hesitate to predict when or how rapid gene sequencing will bring dramatic improvements for patients. Think of it this way: Simply knowing all the suspects to the crime won’t necessarily tell you which ones are guilty or how to stop them. Many genetic mutations have no known drug that works against them.

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