SAN ANTONIO, TX—A novel genetic driver analysis of matched breast cancer primary tumors and multiorgan metastases suggests that most genetic drivers in a single tumor are based on DNA copy number variants (CNV), are established early, and are maintained in metastases. However, drivers from somatic mutations are acquired later and most continued to acquire new genetic driving features. These findings were presented at the 2015 San Antonio Breast Cancer Symposium.
“The molecular characterization of primary breast cancers has led to signatures identifying risk of future metastasis and survival; however, the underlying biology driving metastasis development is largely unknown,” explained Marni B. Siegel, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill.
Utilizing a rapid autopsy program designed to collect tissues within 6 hours of death, the researchers collected 63 metastatic breast cancer tumors from 14 patients (9 triple-negative, 2 HER2+, 3 ER+/PR+/HER2−) including primary tumors and 3 to 6 metastases/patient. mRNA and DNA exome sequencing was performed. Next, DawnRank, a novel network-based method that integrates DNA and RNA data, was used to identify computationally determined driver genes (ie, a DNA variant that significantly alters its gene expression-network) in each individual sample. Phylogenetic tree and clonal analysis were also performed, with the computationally determined drivers mapped onto the trees.
The breast cancer primaries were molecularly subtyped as 9 basallike, 1 HER2-enriched, 1 basal, and 3 luminal A; metastases had clustered immediately adjacent to their primary tumor. Widespread DNA copy number alterations identified in the primary tumors were typically maintained throughout metastasis. “On average, 1.9 ± 1.3% of DNA copy number altered genes, and 2.4 ± 0.95% of the somatic mutations per tumor were identified as drivers by DawnRank, reported Seigel. There were an average of 199 ± 72 total drivers per tumor due to copy number alterations (amplifications or deletions) and 12 ± 23 drivers per tumor from somatic mutations,” reported Siegel.
Phylogenetic tree analysis demonstrated that most DNA copy number events occurred during early tumor development]. Founding clones, defined as genetic events present in the primary tumor, matched metastases. Chr5q13 loss and TP53 mutation were the only consistent alterations in the founding clones of all the patients. Drivers on chr5q13 identified in this cohort include CCNB1, CDK7, and TAF9, reported Seigel. DawnRank identified TP53 mutations as a driver in all patients with basallike tumors and TP53 mutations.
In the primary tumor, 39% and 20% of drivers from copy number gains and losses, respectively, were identified, while another 34% and 30%, respectively, were not seen in the primary tumor but were present in more than 1 metastasis within each patient. Metastasis-enriched copy number drivers not seen in any primary tumor included FLT1, MAP2KR, and ARNT.
“Functional drivers using the integration of DNA alterations and RNA gene expression for individual tumors provides evidence that DNA CNV accounts for the large majority of individual tumor drivers in both primaries and metastases, and most genetic drivers, whether from CNV or point mutations, are established in the primary breast cancer,” said Siegel.
1. Siegel MB, He X, Chen M, et al. Identification of early versus late drivers of breast tumors and metastasis. Oral Presentation at: San Antonio Breast Cancer Symposium; December 8-12, 2015; San Antonio, TX.