Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance

Abstract

Proteogenomic approaches have enabled the generat̲ ion 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.

”Evolution of ipsilateral breast cancer decoded by proteogenomics”

“…RNAseq was performed as previously reported 21 . Briefly, the amount, concentration and quality of the extracted RNA was tested using a Bioanalyzer 2100 instrument (Agilent Technologies), a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) or Caliper HT RNA LabChip (Perkin Elmer).…”

“…Automatic gain control target was set to 1e6 for both MS and MS/MS scans, with ion accumulation time set to 100ms and 120ms for MS and MS/MS, respectively. Protein intensities were derived by employing our previously established computational workflow 21 . A total of 4,640 proteins were identified after FDR filtering (cutoff: 0.01).…”

“…RNAseq was performed as previously reported 21 . Briefly, the amount, concentration and quality of the extracted RNA was tested using a Bioanalyzer 2100 instrument (Agilent Technologies), a…”

“…Here, we have employed a previously developed proteogenomics workflow 21 to determine the evolution of IBTRs at the genomic, transcriptomic, and proteomic level from corresponding matched PTs, to investigate paths of tumor mutational evolution, identify biomarkers for therapeutic monitoring and alternative drug targets for therapy. Integrated proteogenomics analyses provide additional information regarding specific pathway activation e.g.…”

Plasma Proteome Signature to Predict the Outcome of Breast Cancer Patients Receiving Neoadjuvant Chemotherapy

“…Recent proteomic-centric multiomics studies analyzed BC clinical samples to classify BC into subtypes using protein and phosphorylated protein information, which led to the identification of novel subtypes such as basal-like and luminal B tumors by infiltration of immunological components [ 48 ]. Mass spectrometry-based proteomics that include analysis of post-translational modifications such as phosphorylation or acetylation, combined with next-generation DNA and RNA sequencing profiles, may provide a more comprehensive description of breast tumors [ 49 , 50 , 51 ]. Proteogenomic approaches highlight the potential of proteomics for clinical research in cancer through the identification of targetable signaling pathways and more precise curation of the biological signatures of tumor heterogeneity.…”