Targeted Biomarker Profiling of Matched Primary and Metastatic Estrogen Receptor Positive Breast Cancers

et al. (2014) Targeted Biomarker Profiling of Matched Primary and Metastatic Estrogen Receptor Positive Breast Cancers. PLoS ONE 9(2): e88401. doi:10.1371/journal.pone.0088401 Targeted Biomarker Profiling of Matched Primary and Metastatic Estrogen Receptor Positive Breast Cancers Erica B. Schleifman 0 Rupal Desai 0 Jill M. Spoerke 0 Yuanyuan Xiao 0 Cheryl Wong 0 Ilma Abbas 0 Carol O'Brien 0 Rajesh Patel 0 Teiko Sumiyoshi 0 Ling Fu 0 Rachel N. Tam 0 Hartmut Koeppen 0 Timothy R. Wilson 0 Rajiv Raja 0 Garret M. Hampton 0 Mark R. Lackner 0 Syed A. Aziz, Health Canada and University of Ottawa, Canada 0 1 Department of Oncology Biomarker Development, Genentech Inc. , South San Francisco , California, United States of America, 2 Department of Biostatistics, Genentech Inc. , South San Francisco , California, United States of America, 3 Department of Research Pathology, Genentech Inc. , South San Francisco, California , United States of America Patients with newly diagnosed, early stage estrogen receptor positive (ER+) breast cancer often show disease free survival in excess of five years following surgery and systemic adjuvant therapy. An important question is whether diagnostic tumor tissue from the primary lesion offers an accurate molecular portrait of the cancer post recurrence and thus may be used for predictive diagnostic purposes for patients with relapsed, metastatic disease. As the class I phosphatidylinositol 3' kinase (PI3K) pathway is frequently activated in ER+ breast cancer and has been linked to acquired resistance to hormonal therapy, we hypothesized pathway status could evolve over time and treatment. Biomarker analyses were conducted on matched, asynchronous primary and metastatic tumors from 77 patients with ER+ breast cancer. We examined whether PIK3CA and AKT1 alterations or PTEN and Ki67 levels showed differences between primary and metastatic samples. We also sought to look more broadly at gene expression markers reflective of proliferation, molecular subtype, and key receptors and signaling pathways using an mRNA analysis platform developed on the Fluidigm BioMarkTM microfluidics system to measure the relative expression of 90 breast cancer related genes in formalin-fixed paraffin-embedded (FFPE) tissue. Application of this panel of biomarker assays to matched tumor pairs showed a high concordance between primary and metastatic tissue, with generally few changes in mutation status, proliferative markers, or gene expression between matched samples. The collection of assays described here has been optimized for FFPE tissue and may have utility in exploratory analyses to identify patient subsets responsive to targeted therapies. - . These authors contributed equally to this work. Clinical management of breast cancer is currently based on diagnostic evaluation of expression of estrogen receptor (ER), progesterone receptor (PR) and HER2. Such analyses are typically conducted on primary tumor tissue collected at the time of diagnosis, although many patients will survive for years without local or distant disease recurrence. Moreover, a variety of studies have shown discordance in ER status between primary and metastatic samples ranging from 10 to 40% [1,2,3]. This has sometimes been taken to reflect a true switch in biology of the tumor in response to therapy, but has also been attributed to sampling error in focally-receptor positive disease and limited accuracy and reproducibility of the assays for receptor expression [3]. Given that novel targeted therapies are being developed in ER+ breast cancer, changes in the biology of the tumor that occur during adjuvant therapy could adversely impact predictive value of diagnostic assessments conducted on primary tumor samples but used to guide therapy in metastatic patients. In particular, the phosphatidylinositol 3 kinase (PI3K)/mTOR pathway has been linked in a variety of studies to acquired resistance to endocrine therapies both preclinically and clinically [4], and recent clinical results have validated this idea by showing that the mTOR inhibitor everolimus in combination with the aromatase inhibitor exemestane extends survival in patients with metastatic ER+ breast cancer who have progressed on prior endocrine therapy [5]. Upregulation or mutational activation of this pathway during adjuvant or front-line metastatic therapy could confound interpretation of predictive biomarkers conducted on primary tumor samples. To address the question of whether primary and metastatic ER+ breast cancer samples are generally similar in terms of biomarker prevalence, and hence whether primary tissue is an accurate indicator of biomarker status in later stage patients, we evaluated a panel of asynchronously collected matched primary and metastatic tumors with a panel of biomarkers related to proliferation, epithelial-mesenchymal biology and PI3K pathway signaling. Previous studies have found that such tissues are generally concordant for PIK3CA and PTEN sta (...truncated)