Abstract C10: Quantitative proteomics of formalin-fixed paraffin-embedded, primary triple-negative breast cancer tissues of patients who experienced distant metastasis or no recurrence
Authors: Pedersen Martin H. , Hood Brian L. , Conrads Thomas P. , Ditzel Henrik J. , Leth-Larsen Rikke 
Published: May 2016

Abstract
Triple-negative breast cancer (TNBC) represents a major subtype of breast cancer (BC) and no biomarkers or targeted treatments are available. Retrospective proteomic analysis of formalin-fixed paraffin-embedded (FFPE) BC tissue has the potential to identify novel biomarkers and pathways associated with disease recurrence in TNBC, since sample data can be coupled with clinical data, including treatment and patient outcome. Primary TNBC tissue of patients who experienced distant metastasis or no recurrence within a 10 year follow-up period was retrieved to investigate whether proteomics using liquid chromatography tandem mass spectrometry (LC-MS/MS) can identify proteins and pathways associated with their metastatic potential.
FFPE material on PEN-membrane slides were deparaffinized according to standard procedure with xylene/ethanol and stained with hematoxylin and eosin. Cancer cells were dissected by UV laser capture microdissection (LCM) and subjected to protein extraction in triethylammonium bicarbonate/acetonitrile buffer by heat-induced antigen retrieval. Extracted proteins were trypsinized and generated peptides were isobarically labelled with 6-plex tandem mass tags, combined 1:1 and subjected to hydrophilic interaction liquid chromatography LC-MS/MS.
Preliminary experiments identified &gt;500 unique proteins from BC FFPE tissue, verifying a robust setup. Cancer cells from primary TNBC FFPE tissues of 15 patients who experienced distant metastatic and 20 patients who did not have recurrence within ten years were isolated by UV-LCM and analyzed according to the above setup. The patients were stratified into four working groups based upon their menopausal status (pre or post) and their recurrence (recurrence or no-recurrence) outcome. The median aged varied from 42.2 to 63.4 years between the four groups with most tumors being diagnosed as T1 or T2 (TNM classification system). All tumors were grade 2 or higher at diagnosis, with no distant metastasis present prior to removal of the primary tumor. We identified 2564 high-confident proteins across the 35 patient samples with ≥2 unique peptides. Statistical analysis was done in RStudio and GproX and revealed distinct molecular profiles capable of separating metastatic from non-metastatic patients with a p-value ≤0.05. Furthermore three proteins were found to be differentially regulated between the two groups with a p-value &lt;0.001 making these highly interesting targets in the prevention of metastatic lesions in TNBC.
Research funded by the Danish Research Council, the A.P. Møller foundation and The Regional Strategically Research Council of Southern Denmark
Citation Format: Martin H. Pedersen, Brian L. Hood, Thomas P. Conrads, Henrik J. Ditzel, Rikke Leth-Larsen. Quantitative proteomics of formalin-fixed paraffin-embedded, primary triple-negative breast cancer tissues of patients who experienced distant metastasis or no recurrence. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C10.