Determination of Stromal Gene Expression in Breast Cancer

Institution: Palo Alto Veterans Institute for Research
Investigator(s): Robert West, M.D., Ph.D. -
Award Cycle: 2007 (Cycle 13) Grant #: 13IB-0076 Award: $136,217
Award Type: IDEA
Research Priorities
Biology of the Breast Cell>Pathogenesis: understanding the disease



Initial Award Abstract (2007)
Cancer cells are surrounded by a complex mixture of blood vessels inflammatory cells and different types of connective tissue cells. These stromal cells are themselves not cancerous but have been shown to play a crucial role in cancer development and progression. The majority of breast cancer research has focused on the neoplastic cells and as a result, the therapies available to oncologists are therapeutic agents that act on these cancer cells. The cancer often develops resistance to these therapies, in large part due to their inherent genomic instability.

An alternative, emerging, avenue of therapy focuses on targeting various non-neoplastic cells that are associated with the tumor microenvironment. Since stromal cells within the tumor are thought to be “normal” and less genetically labile than the neoplastic cells, development of acquired resistance to therapy is thought to be less likely. As such, the tumor stroma may be an excellent target for directed therapy. However, they have been difficult to purify and study and there may be as yet unrecognized subtypes of these cells that are important to cancer development and progression. Soft tissue tumors are rare cancers that develop from different types of connective tissue cells and as such form practically pure populations of these different cell types. They have gene expression patterns similar to their normal counterparts and study of these tumors allows for discovery of new connective tissue markers and stromal cell types.

We will study the gene expression of soft tissue tumors to dissect and understand the gene expression of normal connective tissue cells, using the soft tissue tumors as surrogates for purified normal connective tissue cells. We will use “gene arrays” (arrays of 40,000 spots of DNA on a single glass slide) to identify genes that vary in expression between different soft tissue tumor types. We will then examine the expression levels of these genes in existing breast cancer data sets. Our initial studies show that genes that are differentially expressed in soft tissue tumors vary among groups of breast cancers and represent different stromal reaction patterns. We plan to confirm and extend our observations of these breast cancer stromal reaction patterns on “tissue microarrays” (arrays of 500 0.6 mm cores of paraffin embedded fixed tissue taken from archived tumors). Studying samples on tissue microarrays will allow us to observe what cell type expresses the genes of interest (this cannot be determined by gene arrays) and allow us to increase the number of observations.

We expect that significant, clinically relevant findings will be made by studying the genes discovered on STT in breast carcinoma. In addition to their use as prognostic markers, we believe that potential therapeutic targets may also be discovered in the group of genes.


Final Report (2009)
Note: Dr. West received two additional years of CBCRP to continue this project.

We used a novel approach to discover previously unknown types of stromal reaction patterns to invasive breast cancer (IBC) through gene expression profiling of low grade soft tissue tumors, which often recapitulate physiologic mesenchymal states. We have made progress on each of the originally stated Aims. Using soft tissue tumors as “discovery tools” for gene expression profiles specific to various stromal response types, we discovered four distinct stromal reaction patterns in IBC. For many steps, we developed new methodologies to help us improve our analyses. These studies on invasive carcinoma have led to two published reports, an invited review, and three additional reports in preparation.

Our accomplishments include:

We plan to develop clinically useful biomarkers of stromal expression patterns in invasive cancer. We will use a tissue microarray of 283 cases to screen for antibody markers for both the DTF and CSF1 stromal signatures. We will ultimately reduce each panel down to the best 2-3 markers which will serve as a clinical test for the presence of these stromal signatures in breast cancer. We will also aim to discover stromal response patterns associated with pre-invasive breast cancer. We will analyze a combination of pre-existing DCIS gene expression profiling datasets and generate our own via RNA-seq. Stromal signatures found in DCIS will be confirmed on a tissue microarray of 300 DCIS cases using biomarkers identified in the gene expression data sets.

The fibromatosis signature defines a robust stromal response in breast carcinoma
Periodical:Laboratory Investigations
Index Medicus: Lab Invest
Authors: Beck AH, Espinosa I, Gilks CB, van de Rijn M, West RB
Yr: 2008 Vol: 88 Nbr: 6 Abs: Pg:591-601

The macrophage colony-stimulating factor 1 response signature in breast carcinoma.
Periodical:Clinical Cancer Research
Index Medicus: Clin Cancer Res
Authors: Beck AH, Espinosa I, Edris B, Li R, Montgomery K, and West RB
Yr: 2009 Vol: 15 Nbr: 3 Abs: Pg:778-87