Gene-expression molecular subtyping of triple-negative breast cancer tumours: importance of immune response

Breast Cancer Res. 2015 Mar 20;17:43. doi: 10.1186/s13058-015-0550-y.


Introduction: Triple-negative breast cancers need to be refined in order to identify therapeutic subgroups of patients.

Methods: We conducted an unsupervised analysis of microarray gene-expression profiles of 107 triple-negative breast cancer patients and undertook robust functional annotation of the molecular entities found by means of numerous approaches including immunohistochemistry and gene-expression signatures. A triple-negative external cohort (n=87) was used for validation.

Results: Fuzzy clustering separated triple-negative tumours into three clusters: C1 (22.4%), C2 (44.9%) and C3 (32.7%). C1 patients were older (mean=64.6 years) than C2 (mean=56.8 years; P=0.03) and C3 patients (mean=51.9 years; P=0.0004). Histological grade and Nottingham prognostic index were higher in C2 and C3 than in C1 (P<0.0001 for both comparisons). Significant event-free survival (P=0.03) was found according to cluster membership: patients belonging to C3 had a better outcome than patients in C1 (P=0.01) and C2 (P=0.02). Event-free survival analysis results were confirmed when our cohort was pooled with the external cohort (n=194; P=0.01). Functional annotation showed that 22% of triple-negative patients were not basal-like (C1). C1 was enriched in luminal subtypes and positive androgen receptor (luminal androgen receptor). C2 could be considered as an almost pure basal-like cluster. C3, enriched in basal-like subtypes but to a lesser extent, included 26% of claudin-low subtypes. Dissection of immune response showed that high immune response and low M2-like macrophages were a hallmark of C3, and that these patients had a better event-free survival than C2 patients, characterized by low immune response and high M2-like macrophages: P=0.02 for our cohort, and P=0.03 for pooled cohorts.

Conclusions: We identified three subtypes of triple-negative patients: luminal androgen receptor (22%), basal-like with low immune response and high M2-like macrophages (45%), and basal-enriched with high immune response and low M2-like macrophages (33%). We noted out that macrophages and other immune effectors offer a variety of therapeutic targets in breast cancer, and particularly in triple-negative basal-like tumours. Furthermore, we showed that CK5 antibody was better suited than CK5/6 antibody to subtype triple-negative patients.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Biomarkers, Tumor
  • Cluster Analysis
  • Computational Biology
  • Female
  • Gene Expression Profiling*
  • Gene Expression Regulation, Neoplastic*
  • Humans
  • Immunity, Innate
  • Immunohistochemistry
  • Kaplan-Meier Estimate
  • Middle Aged
  • Molecular Sequence Annotation
  • Neoplasm Staging
  • Prognosis
  • Reproducibility of Results
  • Retrospective Studies
  • Transcriptome
  • Triple Negative Breast Neoplasms / diagnosis
  • Triple Negative Breast Neoplasms / genetics*
  • Triple Negative Breast Neoplasms / immunology
  • Triple Negative Breast Neoplasms / mortality
  • Triple Negative Breast Neoplasms / therapy
  • Tumor Burden


  • Biomarkers, Tumor