Genpathway and Baylor College of Medicine Identify New Genes in Breast Cancer

Researchers at Genpathway, Inc. and Baylor College of Medicine in Houston have applied a new suite of integrated transcription-based assays to identify novel genes important in breast cancer. The newly discovered genes were identified as a result of being directly regulated by a coactivator shown previously to be a critical regulator in breast cancer.

The study, reported in Proceedings of the National Academy of Sciences, describes a collaborative effort by Genpathway and Baylor scientists to discover genes regulated by breast cancer-associated factors using Genpathway's FactorPath(TM) assay. Further analysis confirmed the involvement of both the coactivator and the transcription factor, and a second Genpathway assay, TranscriptionPath(TM), provided additional evidence that these genes are biologically relevant.

The work involved identifying genes regulated by steroid receptor coactivator-3 (SRC-3/AIB1), a protein that is overexpressed in a variety of human cancers, including breast cancer. This factor is believed to boost the cancer cells' selective growth advantage over normal cells. SRC-3 regulates genes by interacting with certain nuclear hormone receptors such as estrogen receptor (ER), a transcription factor that can turn the expression of specific genes up and down or on and off. When SRC-3 binds to ER in breast cancer cells, the combination either activates or represses transcription of the affected genes, leading to other changes important in the disease. Using Genpathway's FactorPath(TM) assay in DiscoveryMode(TM), the researchers identified binding of SRC-3 to hundreds of previously undescribed genomic sites. Further study was then done with FactorPath(TM) QueryMode(TM), Genpathway's second analysis mode. In an initial analysis of 29 of these sites, 18 were determined to be strong binding sites for SRC-3. Furthermore, QueryMode(TM) demonstrated that both SRC-3 and the transcription factor it works through, ER, exhibited increased levels of binding to many of these sites after stimulation of the cells with the hormone, estrogen. The investigators then applied a second assay, Genpathway's TranscriptionPath(TM) QueryMode(TM), to show that the genes in the vicinity of the new SRC-3/ER binding sites were indeed changed in their expression levels as a result of stimulation with estrogen.

"Because coactivators such as SRC-3 do not bind DNA directly, extensive work is usually required to distinguish which differentially expressed genes identified by other methods, such as RNA profiling, are either direct or indirect transcriptional targets," said Bert O'Malley, M.D., chairman of the Department of Molecular and Cellular Biology at Baylor College of Medicine, and a coauthor on the study. "Genpathway's new assays enabled us to rapidly identify a number of strong binding sites of SRC-3. The method was then extended to identify a subset of genes with binding by both SRC-3 and the estrogen receptor. In contrast to an RNA microarray approach that requires altered SRC-3 expression, these new methods allowed the identification of SRC- 3 target genes in cells without changing endogenous SRC-3 expression, reducing the likelihood of false positives. Further, because the putative binding sites were mapped across the entire genome as opposed to pre-selected sequences, the likelihood of discovering new sites and novel genes was higher."

"Because only a fraction of potential binding sites are actually used inside cells, the ability to zero in on the functional sites in a genome is critical," said Benjamin Monderer, Ph.D., CEO of Genpathway. "This study demonstrates the ability of FactorPath(TM) to identify the genomic regions functionally bound by a specific transcription factor or coregulating factor in living cells, and to quantify the binding levels. The results reported underscore the utility of our new methods in generating information about gene regulation to advance understanding of disease mechanisms, and in identifying new and better therapeutic and diagnostic targets and biomarkers for drug discovery."

The Genpathway-Baylor paper, published in the February 1 issue of Proceedings of the National Academy of Sciences, is entitled, "Identification of Target Genes in Breast Cancer Cells Directly Regulated by the SRC-3/AIB1 Coactivator."

The research was funded by the National Institutes of Health, the Welch Foundation, and the Susan G. Komen Breast Cancer Foundation.

Source : Genpathway, Inc.