ArticleGenome biology2007
An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT03515798 (A Prospective Multicenter Open-label, Randomized Phase II Study of Pembrolizumab in Combination With Neoadjuvant EC-Paclitaxel Regimen in HER2-negative Inflammatory Breast Cancer.), which is not on this map. Cited by 277 papers, 5 of them syntheses that pooled it.
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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.
A Prospective Multicenter Open-label, Randomized Phase II Study of Pembrolizumab in Combination With Neoadjuvant EC-Paclitaxel Regimen in HER2-negative Inflammatory Breast Cancer.
Who cites it
277 citing papers in PubMed, 5 syntheses or guidelines pooled it, 510 citations in OpenAlex.
- Expression and Signaling Pathways of Nerve Growth Factor (NGF) and Pro-NGF in Breast Cancer: A Systematic Review.Current oncology (Toronto, Ont.) · 2022Pooled it
- MetaDCN: meta-analysis framework for differential co-expression network detection with an application in breast cancer.Bioinformatics (Oxford, England) · 2017Pooled it
- The Role of Proliferation in Determining Response to Neoadjuvant Chemotherapy in Breast Cancer: A Gene Expression-Based Meta-Analysis.Clinical cancer research : an official journal of the American Association for Cancer Research · 2016Pooled it
- Prognostic and therapeutic significance of ribonucleotide reductase small subunit M2 in estrogen-negative breast cancers.BMC cancer · 2014Pooled it
- Systematic analysis of metastasis-associated genes identifies miR-17-5p as a metastatic suppressor of basal-like breast cancer.Breast cancer research and treatment · 2014Pooled it
- Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis.Genome biology · 2013Trial
- Advances in the Research and Development of Breast Cancer Organoids.Oncology research · 2026Review
- Immune Checkpoint Blockade and Emerging Combination Platforms in Breast Cancer: A Narrative Review.Breast cancer (Dove Medical Press) · 2026Review
- SIDISH integrates single-cell and bulk transcriptomics to identify high-risk cells and guide precision therapeutics through in silico perturbation.Nature communications · 2025Article
- Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets.Breast cancer research : BCR · 2025Article
- Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses.PLoS computational biology · 2025Article
- Tumor Immune Response as a Biomarker for Metastasis-Free Survival of Breast Cancer and Immune Checkpoint Inhibition Therapy: A Retrospective Cohort Study.Breast cancer : basic and clinical research · 2025Article
- Spatial transcriptomics reveals substantial heterogeneity in triple-negative breast cancer with potential clinical implications.Nature communications · 2024Article
- High CTLA-4 gene expression is an independent good prognosis factor in breast cancer patients, especially in the HER2-enriched subtype.Cancer cell international · 2024Article
- Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages.Nature cancer · 2024Article
- Integrated immuno-transcriptomic analysis of ovarian cancer identifies a four-chemokine-dominated subtype with antitumor immune-active phenotype and favorable prognosis.British journal of cancer · 2024Article
- Development and validation of a reliable DNA copy-number-based machine learning algorithm (CopyClust) for breast cancer integrative cluster classification.Scientific reports · 2024Article
- Breast Tumor Metastasis and Its Microenvironment: It Takes Both Seed and Soil to Grow a Tumor and Target It for Treatment.Cancers · 2024Review
- Understanding tissue-resident macrophages unlocks the potential for novel combinatorial strategies in breast cancer.Frontiers in immunology · 2024Review
- B-cells and regulatory T-cells in the microenvironment of HER2+ breast cancer are associated with decreased survival: a real-world analysis of women with HER2+ metastatic breast cancer.Breast cancer research : BCR · 2023Article
217 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEstrogen receptor (ER)-negative breast cancer specimens are predominantly of high grade, have frequent p53 mutations, and are broadly divided into HER2-positive and basal subtypes. Although ER-negative disease has overall worse prognosis than does ER-positive breast cancer, not all ER-negative breast cancer patients have poor clinical outcome. Reliable identification of ER-negative tumors that have a good prognosis is not yet possible.
resultsWe apply a recently proposed feature selection method in an integrative analysis of three major microarray expression datasets to identify molecular subclasses and prognostic markers in ER-negative breast cancer. We find a subclass of basal tumors, characterized by over-expression of immune response genes, which has a better prognosis than the rest of ER-negative breast cancers. Moreover, we show that, in contrast to ER-positive tumours, the majority of prognostic markers in ER-negative breast cancer are over-expressed in the good prognosis group and are associated with activation of complement and immune response pathways. Specifically, we identify an immune response related seven-gene module and show that downregulation of this module confers greater risk for distant metastasis (hazard ratio 2.02, 95% confidence interval 1.2-3.4; P = 0.009), independent of lymph node status and lymphocytic infiltration. Furthermore, we validate the immune response module using two additional independent datasets.
conclusionWe show that ER-negative basal breast cancer is a heterogeneous disease with at least four main subtypes. Furthermore, we show that the heterogeneity in clinical outcome of ER-negative breast cancer is related to the variability in expression levels of complement and immune response pathway genes, independent of lymphocytic infiltration.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.