Functional proteomic characterization of early luminal breast cancers with discordant genomic and clinical risk estimates

Background Estimating the risk of relapse in early luminal breast cancers is paramount to determine the therapeutic strategy. Genomic signatures have come along clinical/pathological factors to refine this estimation. However, cases of tumors with discordant genomic and clinical risk estimates have highlighted the difficulty to delineate which risk parameter, clinical or genomic, should prevail. The aims of the study were to determine the frequency of discordant cases in a real life cohort, and provide their functional molecular characterization using mass spectrometry imaging associated to spatially-resolved tissue microproteomic. Methods Discordant cases were identified from a cohort of 222 early breast cancer patients with hormone receptor positive and HER2 negative tumors. All patients were treated at our institution and had a PAM50-based genomic assay (Prosigna®) to estimate their genomic risk of distant recurrence. The clinical estimation of the risk of relapse was based on tumor size and grade in node negative patients, and on the number of nodes involved (one versus two to three) in node positive patients. The tissue microproteomic profiling of both cancer cells and stroma was performed using a spatially resolved on-tissue shotgun mass spectrometry technology after MALDI mass spectrometry imaging. Results Nearly 30% of cases had discordant genomic and clinical risk estimates, both in node negative and node positive tumors. Proteins overexpressed in low clinical and high genomic risk tumors, compared to high clinical and high genomic risk tumors, were involved in angiogenesis, inflammatory processes, B and T cell activation, or tumor promoting signaling pathways including EGFR, PDGF, FGF, GnHR and Ras network. Proteins overexpressed in high clinical and low genomic risk tumors, compared to low clinical and low genomic risk tumors, were involved in DNA replication, inflammation or integrin signaling. Within each genomic risk group, comparison of low and high clinical risk tumors showed distinct proteomic profiles, both in tumor cells and stroma. The proteomic clusters differentially expressed between low and high clinical risk tumors varied according to the genomic risk group and nodal status. Functional analyses showed that proteins of these clusters were involved in several pathways or processes, such as nucleotides metabolism, apoptosis, tumorigenesis, integrin signaling pathways and inflammation. Conclusion Mass spectrometry microproteomics revealed distinctive tumor and microenvironment molecular profiles between low and high clinical risk tumors within homogeneous genomic risk groups. This suggests that clinical risk factors bring additional biological insight, and should be further integrated to genomic parameters. Citation Format: Nawale Hajjaji, Soulaimane Aboulouard, Yves Marie Robin, Delphine Bertin, Jacques Bonneterre, Isabelle Fournier, Michel Salzet. Functional proteomic characterization of early luminal breast cancers with discordant genomic and clinical risk estimates [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-07-08.