ArticleJournal of proteome research2021
Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance.
Article in Journal of proteome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- ESR1 mutations are associated with enhanced MTORC1 signaling in a context-dependent manner.Communications biology · 2026Article
- Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments.BMC bioinformatics · 2026Article
- Considerations and Software for Successful Immune Cell Deconvolution Using Proteomics Data.Journal of proteome research · 2025Article
- MammOnc-DB, an integrative breast cancer data analysis platform for target discovery.NPJ breast cancer · 2025Article
- Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets.Journal of proteome research · 2025Article
- Epidemiology of Breast Cancer Mortality in Kazakhstan, trends and Geographic Distribution.Asian Pacific journal of cancer prevention : APJCP · 2023Article
- Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis.Nature communications · 2023Article
- Generalized precursor prediction boosts identification rates and accuracy in mass spectrometry based proteomics.Communications biology · 2023Article
- Article
- Identification of Novel Genes and Proteoforms inPathogens (Basel, Switzerland) · 2022Article
- Plasma Proteome Signature to Predict the Outcome of Breast Cancer Patients Receiving Neoadjuvant Chemotherapy.Cancers · 2021Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteogenomic approaches have enabled the generat̲ion 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.
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