Proteomic Biomarker and Aging Signatures for Aggressive Human Metaplastic and other Breast Cancer Subtypes isolated from FFPE Tissues Jordan B. Burton, Philippe Gascard, Deng Pan, Joanna Bons, Joseph Caruso, Rosemary Bai, Chira Chen-Tanyolac, Christie L. Hunter, Thea D. Tlsty, Birgit Schilling
Breast cancer manifests as a disease intrinsically linked to aging and is highly heterogenous with multiple subtypes that distinctly influence patient outcomes and treatment strategies. We quantified proteins from patients with four different human breast cancer subtypes and disease-free control individuals to highlight potential therapeutic target proteins that may be involved in cancer progression. We quantified ~6,000 proteins (>2 quantifiable peptides) extracted from Formalin-Fixed Paraffin-Embedded (FFPE) tissues. We observed significant changes in over 26% of proteins comparing each cancer subtype with healthy control tissues obtained from ‘reduction mammoplasty’. Stringent statistical filters, |log2(FC)|≥0.58 and q-value≤0.001, allowed us to deeply mine conserved and unique protein changes across four different human breast cancer subtypes, including metaplastic breast cancer (MBC). We discovered 576 proteins that were significantly altered in all breast cancer subtypes investigated, and many of these were previously observed in other chronic inflammation-associated cancers. Significant changes in extracellular matrix (ECM) and senescence-associated secretory phenotype (SASP) proteins highlight potential therapeutic targets for stromal reprogramming and interventions. The majority of small leucine-rich, desmosome and basement membrane proteins that are essential for the regulation of the ECM microenvironment were significantly down-regulated, including HSPG2, desmoplakin, lumican and the majority of collagens, except for upregulated Col12A1. We discovered that over 74 quantified SASP factors, including SERPINH1 and periostin, were significantly altered in breast cancers when compared to healthy tissue, revealing early aging signatures. Our findings demonstrate evident remodeling of the ECM and changes in SASP and aging markers in all breast cancer subtypes pointing towards potential therapeutic strategies. Focus on aggressive and understudied metaplastic breast cancer (MBC) revealed changes in the immune system and neutrophil-related proteins, with specific emphasis on eosinophil peroxidase (EPX) and myeloperoxidase (MPO). In summary, deep proteomic, digitalized profiles were uncovered from bio-banked FFPE tissues for rare MBC and other major breast cancer subtypes.