||74 (Research article)
||De Marchi, Tommaso ; Pyl, Paul; Sjöström, Martin; Klasson, Stina; Sartor, Hanna; Tran, Lena; Pekar, Gyula; Malmström, Johan; Malmström, Lars; Niméus, Emma
||Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance
||J Proteome Res (2021) 0 0
||14 citations (journal impact: 4.07)
||Proteogenomic approaches have enabled the generation of novel information levels when compared to single omics studies although burdened by extensive experimental efforts. Here we improved a data-independent acquisition mass spectrometry proteogenomic workflow to reveal distinct molecular features related to mammographic appearances in breast cancer. Our results reveal splicing processes detectable at the protein level and highlight quantitation and pathway complementarity between RNA and protein data. Furthermore we confirm previously detected enrichments of molecular pathways associated with estrogen receptor-dependent activity and provide novel evidence of epithelial-to-mesenchymal activity in mammography-detected spiculated tumors. Several transcript-protein pairs displayed radically different abundances depending on the overall clinical properties of the tumor. These results demonstrate that there are differentially regulated protein networks in clinically relevant tumor subgroups which in turn alter both cancer biology and the abundance of biomarker candidates and drug targets.