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Sequencing Studies Offer Insight into Impact of Clonal Evolution on Cancer Treatment and Diagnosis


By Monica Heger

Cancer has long been known to be a heterogeneous disease, but the extent to which the genomes of cancer cells within a single tumor vary and evolve is just now beginning to be resolved by next-generation sequencing with important implications for therapeutics and diagnosis.

Clonal evolution is "important to cancer biology and important to our understanding of the way we treat cancer," Sam Aparicio of the University of British Columbia and BC Cancer Agency told Clinical Sequencing News.

Matt Walter, an assistant professor of medicine at Washington University School of Medicine, agreed. A tumor mass is "not one homogeneous population of cells," he told CSN. "You have multiple clones that are genetically distinct."

Targeting Founding Clones

Increasingly, researchers are discovering that there is often a "founding" mutation or clone that enables cancer. And, said Walter, the key to treating cancer might be in identifying these founder mutations and developing drugs that target them.

He recently led a study published in the New England Journal of Medicine that used whole-genome sequencing to study seven patients with myelodysplastic syndrome who eventually died from acute myeloid leukemia.

The team, which was led by researchers at Wash U's Genome Institute and Siteman Cancer Center, identified founding clones that were present in all seven patients with MDS and persisted as they developed AML. Additionally, said Walter, the team was able to identify multiple clones in the patients once they developed AML.

The study suggests that targeting the founding clones early could help prevent the development of secondary AML, he said. The results also suggest that therapies that hit those founding clones should still be important once a patient develops AML.

A therapy that targets a "mutation in a daughter clone … might be effective, but the founding clone would be potentially unaffected," enabling further mutations to develop, he said. It's the "paradigm of a tree with roots and branches," he explained. To ensure that a tree doesn't grow back after cutting it down, you have to cut it at its roots.

He cautioned that this theory still remains to be tested, but his work and that of others lends support to the idea.

For instance, Anna Schuh, a hematologist at the Oxford Biomedical Research Center, presented a study at last year's Biology of Genomes meeting at Cold Spring Harbor that used whole-genome sequencing to monitor B-cell chronic lymphocytic leukemia patients at five different time points throughout treatment (CSN 5/17/2011).

That work also identified founder mutations that remained present through the patients' entire course of treatment, as well as mutations that expanded, mutations that emerged, and mutations that disappeared as a result of treatment.

Targeting those founder mutations may be key to curing the disease, she said, noting that treatments that target daughter mutations may control cancer, but won't cure it. "If I had to put my money on drug development, I would look at the founders very carefully."

Additionally, she cited another recent study in the New England Journal of Medicine that found that relying on a single tumor biopsy from kidney cancer to make treatment decisions could be misleading given the heterogeneity of the tumor and the fact that around two thirds of the somatic mutations were not detectable in every region of the tumor (CSN 3/7/2012).

There can be "sets of different mutations even within the same lump of tumor," she said. And, to make treatment decisions based on the tumor's mutations, it will be important to "look for the changes that occur in all tumor cells," Schuh said.

Clonal Genotypes

Aparicio agreed. Most diagnostic tests and targeted therapies for cancer "are applied without the notion of how many cancer cells have the variation" that's being targeted by the therapy or assayed with the diagnostic, he said.

For instance, he said, when looking for KRAS mutations in colorectal cancer, researchers and physicians "don't think about what proportion of cells [in a sample] actually have that KRAS mutation."

However, rather than specifically looking for founding mutations, Aparicio's team is aiming to clonally genotype tumors. While founder mutations are important, he said, there are "other things that happen that transform the way cancers behave."

The mutations that enable or drive progression of the disease are also important, and can transform cancer cells to become more aggressive, giving them entirely different properties than the founding clones, he said.

One way Aparicio is tackling the problem is by studying cancer at the single-cell level to determine different clonal genotypes within a single tumor sample.

Clonal evolution is also important with regards to monitoring patients' response to treatment, said Schuh. For instance, whole-genome sequencing can identify what clones have essentially been eradicated and whether new clones have emerged following treatment, which allows physicians to monitor the effectiveness of a treatment and also to choose additional treatments.

"If you have clones emerging, it means you can't give the same treatment again, because the clone has emerged in that treatment environment," Schuh said.

Aparicio said that he is also looking to incorporate whole-genome sequencing into clinical trials to monitor clonal evolution throughout treatment.

This will allow the researchers to determine "which clonal genotypes are most responsive and which are least responsive," which could help in the drug development process by providing evidence for a specific drug's mechanism of action.

"The drug development process does not deal with the issue that every patient in which these drugs will be tried … in effect has multiple diseases," he said.

For instance, a drug might be effective on one clonal subtype, but still fail because other clones emerge and progress.

He thinks that eventually, cancer will be treated in the same way that HIV is treated, with a cocktail of drugs that hit multiple clones. When retrovirals for HIV were used as single agents, patients quickly developed drug resistance because the virus evolved so quickly.

Once a cocktail that hit the virus in multiple ways was developed, it was "sufficient to suppress the rate of evolution," he said, noting that while the cocktail is not a cure, it has dramatically increased life spans for people living with AIDS.

In the same way, he thinks that a cocktail of drugs targeting multiple clones that are specific to a patient's cancer will become an effective way of managing the disease.

The first step, however, is a "full appreciation of the clonal properties of cancer," he said.

Have topics you'd like to see covered by Clinical Sequencing News? Contact the editor at mheger [at] genomeweb [.] com.

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