Abstract 1067: Somatic genomic mutations, RNA-Seq, and proteomic signal transduction network analysis of tumor and stroma in metastatic triple negative breast cancer
Authors: Espina Virginia A. , O'Shaughnessy Joyce A. , Levin Maren K. , Craig David W. , Carpten John D. , Hoff Daniel Von , Liotta Lance A. 
Published: May 2015

Abstract
Triple negative breast cancer (TNBC) is a heterogeneous, basal like tumor category for which there is no molecular targeted therapy that has significantly improved overall patient survival. While genomic sequencing has been conducted on primary triple negative breast cancers, these data may not correspond to metastatic TNBC because the metastatic colonies may comprise a subclone of the primary. Moreover, it has been difficult to identify the true driver mutations in the primary tumor. We have hypothesized that evaluation of the protein signal transduction pathways within the tumor-stromal microenvironment of the metastatic tumor may be vastly different than the primary tumor and can provide potential clues to the driver mutations and stromal interactions.
Somatic genomic mutations and RNA-Seq profiles were previously cataloged for a set of 14 fresh frozen metastatic TNBC samples. TP53, LRP1B, HERC1, CDH5, RB1, and NF1 were mutated in multiple tumors. FOXM1 gene overexpression was noted in tumor samples compared to non-malignant breast samples. To complement the genetic data, we evaluated more than 70 signal transduction proteins in tumor and stroma for 13 of the metastatic TNBC samples from this cohort. The samples represented lymph node (n=5) and local and distant soft tissue (n=8) metastasis. For proteomic analysis, purified populations of tumor and adjacent stromal cells were collected by Laser Capture Microdissection. Cell signaling pathway proteins were quantified by reverse phase protein microarray. Proteins from diverse pathways were included to: a) correlate our proteomic data with the previous genomic data, b) potentially identify previously unrecognized pathways involved in TNBC metastatic disease, and c) evaluate the tumor-stroma microenvironment in metastatic TNBC.
We compared the signaling network of the tumor and its matched stroma to investigate tumor-stroma crosstalk. We also compared the signal pathways to the genomic abnormalities of the matched lesion. We confirmed the down regulation of endocrine (ER, AR, ProgRec) and Her2 pathways. phosphoJAK2 and Her4 (total) were both markedly downregulated. Signal pathway data provided information about the functional importance of the genomic data.
Understanding the molecular underpinnings of metastatic TNBC may help elucidate genomic and proteomic alterations which can potentially lead to new strategies for individualizing therapy of metastasis.
Citation Format: Virginia A. Espina, Joyce A. O'Shaughnessy, Maren K. Levin, David W. Craig, John D. Carpten, Daniel Von Hoff, Lance A. Liotta. Somatic genomic mutations, RNA-Seq, and proteomic signal transduction network analysis of tumor and stroma in metastatic triple negative breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1067. doi:10.1158/1538-7445.AM2014-1067