Researchers have used mass spectrometry to conduct proteomic analyses of 77 genomically characterized breast tumors. Through this approach, they've uncovered functional consequences of somatic mutations. For instance, EGFR overexpression in basal-like breast cancer is potentially driven by the loss of two genes, SKP1 and CETN3, from the chromosome 5q deletion characteristic of this disease subtype.

By using mass spectrometry (MS) to evaluate tumors, researchers can better connect the genome to the proteome and pinpoint the phenotypic consequences of genomic alterations in cancer cells, according to a large-scale proteogenomic study of breast cancer.

MS, which quantifies the abundance of proteins and determines where they have been phosphorylated, is “the next evolution in 'omics,” says study co-author Matthew Ellis, PhD, of Baylor College of Medicine in Houston. Two years ago, Ellis and Stephen Carr, PhD, of the Broad Institute of MIT and Harvard in Cambridge, MA, were part of a group that tested the capabilities of large-scale MS by analyzing 95 colorectal tumors from The Cancer Genome Atlas (TGCA). The results revealed additional tumor subtypes and suggested that chromosome 20q amplification drives many mRNA and protein-level alterations in this cancer.

In the current study, Ellis and Carr teamed up with Philipp Mertins, PhD, of the Broad Institute, and other scientists to apply high-performance LC/MS-MS to 77 breast tumors that were already genomically characterized through TCGA. In all, they determined the relative levels of 12,553 proteins from 10,062 genes and evaluated the phosphorylation status of 33,239 sites on those proteins.

Through proteogenomics, the researchers analyzed the consequences of copy-number alterations, which occur commonly in breast cancer. About 50% of basal-like tumors are missing the long (q) arm of chromosome 5, for instance, but identifying trans effects from this loss—ramifications elsewhere in the genome—has proven difficult. When the researchers compared their MS findings with a database on the functional results of gene knockouts, they found that EGFR overexpression, which is typical in basal-like breast cancer, could result from the loss of two genes, SKP1 and CETN3, from chromosome 5q.

The team also used proteogenomics to look for candidate kinases, besides HER2, that could be drug targets. They found that amplification of chromosome 17q—which frequently occurs in the luminal B breast cancer subtype—not only resulted in HER2 overexpression, but also amplified CDK12, which is located nearby. This could also clarify why BRCA1-mutant breast tumors are usually HER2-negative, the researchers note: CDK12 stimulates DNA repair through homologous recombination, so its amplification would counteract the functional effects of BRCA1 loss. Other potentially druggable kinases the team uncovered included PAK1, TLK2, and RIPK2.

Proteogenomics could have promise for tumor profiling, says Carlos Caldas, MD, of the University of Cambridge in the United Kingdom, who wasn't connected to the study. However, he cautions that “we need a significantly larger number of samples before we know this [method] is important.”

The study “provides an incredible database,” adds Gordon Mills, MD, PhD, of The University of Texas MD Anderson Cancer Center in Houston. “But the cost [of MS] is so high as to preclude it as a broad-based approach.”

Ellis says the team plans to apply MS to more breast tumors, including tissue samples from clinical trials. Meanwhile, their study results clearly demonstrate the power of adding proteomics to tumor analysis, he says. “You are getting a much deeper and more satisfying picture of the driving biochemistry than you can get with genomics [alone].” –Mitch Leslie

©2016 American Association for Cancer Research.
2016
American Association for Cancer Research.