ArticleNature communications2022
Proteomic analysis of archival breast cancer clinical specimens identifies biological subtypes with distinct survival outcomes.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05985577 (Mechanism of Gastric Signet Ring Cell Carcinoma Based on Microproteomics), which is not on this map. Cited by 74 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Mechanism of Gastric Signet Ring Cell Carcinoma Based on Microproteomics
Who cites it
74 citing papers in PubMed.
- Protein-protein interactions as therapeutic targets in breast cancer: integrated computational and experimental advances, mechanisms and clinical translation.Molecular biology reports · 2026Review
- Proteomic Biomarker Discovery in Breast Cancer: Advances, Challenges, and Translational Prospects.Journal of biochemical and molecular toxicology · 2026Review
- Assessing the Effects of a 3-Dimensional (3D) Pathology Tissue-Processing Workflow on Downstream Molecular Analyses.Laboratory investigation; a journal of technical methods and pathology · 2026Article
- Large-scale and high-resolution mass spectrometry-based proteomics defines molecular subtypes of nasopharyngeal carcinoma for therapeutic targeting.Signal transduction and targeted therapy · 2026Article
- T2Pdecoder enables protein-centric analyses from transcriptomic data.Nature communications · 2026Article
- Review
- A tissue-specific atlas of protein-protein associations enables prioritization of candidate disease genes.Nature biotechnology · 2026Article
- Personalized signaling pathway analysis of gastrointestinal tumors for patient stratification and drug target evaluation using clinically derived core biopsies.NPJ precision oncology · 2026Article
- The Proteome of Bilateral Macronodular Adrenocortical Disease (BMAD) Shows Different Profiles Correlating with the Genetic Causes and Reveals Specific Dysregulation of RNA Polymerase II and Cholesterol Biosynthesis Enzymes.Endocrine pathology · 2026Article
- Multiomic profiling of ER-positive HER2-negative breast cancer reveals markers associated with metastatic spread.Breast cancer research : BCR · 2026Observational
- Identification of serum peptide biomarkers for cholangiocarcinoma diagnosis and staging via MALDI-TOF MS and LC-MS/MS.British journal of cancer · 2026Article
- A comprehensive proteomic analysis uncovers novel molecular subtypes of gastric signet ring cell carcinoma: Identification of potential prognostic biomarkers and therapeutic targets.Genes & diseases · 2026Article
- Integration of ATAC-Seq, Transcriptomic, and Proteomics Reveals the Molecular Mechanism of Intramuscular Fat Deposition and Meat Tenderness Regulation in Pig Breeds.Biomolecules · 2025Article
- Tumor Imaging Heterogeneity Index-Inspired Insights into the Unveiling Tumor Microenvironment of Breast Cancer.International journal of molecular sciences · 2025Article
- Bioinformatics Strategies in Breast Cancer Research.Biomolecules · 2025Review
- Review
- Prognostic and predictive capacity of tumor infiltrating lymphocytes in the MA.20 regional node radiotherapy trial.NPJ breast cancer · 2025Article
- A Validated Proteomic Signature of Basal-like Triple-Negative Breast Cancer Subtypes Obtained from Publicly Available Data.Cancers · 2025Article
- Identification of copper related biomarkers in breast cancer using machine learning.Discover oncology · 2025Article
- Protein-Level Analysis of Differential Response to Chemotherapy in Triple-Negative Breast Cancer Identifies CYP1B1 as a Biomarker for Chemotherapy Resistance.Cancer research communications · 2025Article
14 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Despite advances in genomic classification of breast cancer, current clinical tests and treatment decisions are commonly based on protein level information. Formalin-fixed paraffin-embedded (FFPE) tissue specimens with extended clinical outcomes are widely available. Here, we perform comprehensive proteomic profiling of 300 FFPE breast cancer surgical specimens, 75 of each PAM50 subtype, from patients diagnosed in 2008-2013 (n = 178) and 1986-1992 (n = 122) with linked clinical outcomes. These two cohorts are analyzed separately, and we quantify 4214 proteins across all 300 samples. Within the aggressive PAM50-classified basal-like cases, proteomic profiling reveals two groups with one having characteristic immune hot expression features and highly favorable survival. Her2-Enriched cases separate into heterogeneous groups differing by extracellular matrix, lipid metabolism, and immune-response features. Within 88 triple-negative breast cancers, four proteomic clusters display features of basal-immune hot, basal-immune cold, mesenchymal, and luminal with disparate survival outcomes. Our proteomic analysis characterizes the heterogeneity of breast cancer in a clinically-applicable manner, identifies potential biomarkers and therapeutic targets, and provides a resource for clinical breast cancer classification.
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