Genomic analysis may lead to targeted breast cancer therapies

AACR 102nd Annual Meeting

ORLANDO, Fla. — Analysis of more than 10 trillion base pairs of DNA sequences from tumor and healthy tissue of breast cancer patients yielded new information on genetic variants of the disease, according to findings presented here at the American Association for Cancer Research 102nd Annual Meeting.

Matthew J. Ellis, MD, PhD, professor of medicine at Washington University Siteman Cancer Center in St. Louis, said the molecular basis for aggressive clinical behavior of endocrine therapy-resistant HER-2–negative luminal-type breast cancer is poorly understood.

“This approach might lead to more accurate diagnostics, which could in turn lead to better outcomes,” Ellis said. “One might imagine that we want to move into this world, where instead of doing gene sequences to find out what happened after the fact, we acquire this information at the outset and tailor the therapy accordingly.”

Although many patients have a good prognosis, a subset has very aggressive disease. “More women die from this luminal type than other subtypes combined,” he said. “The poor outcomes may be due to failure to respond to estrogen receptor-targeted approaches.”

MAP3K1 mutations

Twenty-four of the samples were resistant — which the researchers defined as surgical specimen Ki-67 >10% — and 26 were sensitive (Ki-67 ≤10%).

The mean number of single nucleotide non-silent variants and small deletions per case was 49 in the resistant group and 23 in the sensitive group (P=.02).

Results of further analysis from 121 POL/Z1031 samples indicated a 43% PIK3CA mutation rate. TP53 mutation occurred in 15.2% of these samples, and MAP3K1 occurred in 9.3%.

“The most frequently mutated genes were the well-known mutations, including PIK3CA and TP53,” Ellis said. “However, we also noted that MAP3K1, a previously undescribed gene in this patient population, also frequently occurred.”

According to Ellis, the MAP3K1 mutation accelerates cell death. “This is a knockout mutation,” he said. “It unequivocally destroys the function of the gene.”

More than 800 structural variation events that were identified in 28 patients have been validated orthogonally. Most of these events were deletions, but translocations also were present. Recurrent translocations have not been observed.

Ellis said several other mutations occurred, including ATR and MYST3, but not at higher than a 10% rate.

Single-nucleotide non-silent variant events paired with about one-quarter of the observed deletions. Ellis said this may indicate multiple novel double-hit tumor suppressor events.

Frame-shift or nonsense mutations were the most frequently occurring MAP3K1 mutations. The C-terminal kinase domain was disrupted by these mutations, which Ellis said was an expected finding in a kinase activated by caspase-7 to promote apoptosis.

Among 60 basal-like breast cancers, only one MAP3K1 mutation was observed. The frequency of luminal vs. basal MAP3K1 mutations yielded a P-value of .04, according to the results.

Massive sequencing

The researchers obtained samples from two neoadjuvant endocrine trials. They conducted parallel DNA sequencing on those samples with the aim of defining the whole genome sequence of 50 luminal-type breast cancers. About 10 trillion base pairs of sequence were analyzed 30 times each. Once the mutations were confirmed, the absence of the variant was confirmed in matched DNA from controls.

“Specimens were put into a supercomputer to align all the information to identify every type of single nucleotide non-silent variant in the tumor, including small deletions, large deletions and translocations,” Ellis said. “It was a completely unbiased analysis of the entire human genome for abnormalities associated with this disease.”

Patients in the cohort had been treated in an estrogen-lowering approach with an aromatase inhibitor.

“We could rapidly identify tumors that were responding to the estrogen lowering by virtue of the fact that tumor proliferation index lowered dramatically,” Ellis said. “The tumors that continued active proliferation despite the estrogen lowering, by definition, were resistant.”

Disclosure: Dr. Ellis reports being a speaker for Novartis, AstraZeneca and Bioclassifier LLC.

For more information:

• Ellis MJ. # LB-87. Presented at: AACR 102nd Annual Meeting; April 2-6, 2011; Orlando, Fla.

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