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Updated: Apr 14, 2026
Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
Published on: August 1, 2018
Gene-expression molecular subtyping of triple-negative breast cancer tumours: importance of immune response
Pascal Jézéquel1,2,3,4, Delphine Loussouarn5,6, Catherine Guérin-Charbonnel7,8,9
1Unité Mixte de Génomique du Cancer, Institut de Cancérologie de l'Ouest - site René Gauducheau, Bd J. Monod, 44805, Saint Herblain Cedex, France. Pascal.jezequel@ico.unicancer.fr.
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.
Insights
Triple-negative breast cancer (TNBC) can be classified into three distinct subtypes based on gene expression. These subtypes, characterized by immune response and macrophage profiles, offer potential therapeutic targets for TNBC patients.
Area of Science:
- Oncology
- Genomics
- Immunology
Background:
- Triple-negative breast cancer (TNBC) lacks targeted therapies, necessitating refined classification for therapeutic subgroup identification.
- Understanding molecular heterogeneity within TNBC is crucial for developing effective treatment strategies.
Purpose of the Study:
- To classify triple-negative breast cancer (TNBC) patients into distinct molecular subtypes using unsupervised analysis.
- To identify potential therapeutic targets by characterizing the functional and immune profiles of identified TNBC subtypes.
Main Methods:
- Unsupervised analysis of gene-expression profiles from 107 TNBC patients.
- Functional annotation using immunohistochemistry and gene-expression signatures.
- Validation using an external TNBC cohort (n=87).
Main Results:
- Fuzzy clustering identified three TNBC subtypes (C1: 22.4%, C2: 44.9%, C3: 32.7%) with significant differences in age, histological grade, and Nottingham prognostic index.
- Cluster C3 demonstrated significantly better event-free survival compared to C1 and C2, a finding validated in a pooled cohort (n=194).
- Subtypes were functionally annotated as luminal androgen receptor (C1), basal-like with low immune response (C2), and basal-enriched with high immune response (C3), with C3 showing better survival.
Conclusions:
- Identified three TNBC subtypes: luminal androgen receptor (22%), basal-like with low immune response/high M2 macrophages (45%), and basal-enriched with high immune response/low M2 macrophages (33%).
- Macrophages and immune effectors represent potential therapeutic targets, particularly in basal-like TNBC.
- CK5 antibody is more suitable than CK5/6 for subtyping TNBC patients.
