title: Gene-expression molecular subtyping of triple-negative breast cancer tumours: importance of immune response.
abstract: BACKGROUND
  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.
authors.affiliation: Unité 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.|Unité de Bioinfomique, Institut de Cancérologie de l'Ouest - site René Gauducheau, Bd J. Monod, 44805, Saint Herblain Cedex, France. Pascal.jezequel@ico.unicancer.fr.|Département de Biopathologie, Institut de Cancérologie de l'Ouest - site René Gauducheau, Bd J. Monod, 44805, Saint Herblain Cedex, France. Pascal.jezequel@ico.unicancer.fr.|INSERM U892, IRT-UN, 8 quai Moncousu, 44007, Nantes Cedex, France. Pascal.jezequel@ico.unicancer.fr.
authors.forename: Pascal
authors.initials: P
authors.lastname: Jézéquel
authors.affiliation: INSERM U892, IRT-UN, 8 quai Moncousu, 44007, Nantes Cedex, France. delphine.loussouarn@chu-nantes.fr.|Service d'Anatomie Pathologique B, Hôpital G&R Laënnec, Bd J. Monod, 44805, Saint Herblain, France. delphine.loussouarn@chu-nantes.fr.
authors.forename: Delphine
authors.initials: D
authors.lastname: Loussouarn
authors.affiliation: Unité Mixte de Génomique du Cancer, Institut de Cancérologie de l'Ouest - site René Gauducheau, Bd J. Monod, 44805, Saint Herblain Cedex, France. catherine.guerin@ico.unicancer.fr.|Unité de Bioinfomique, Institut de Cancérologie de l'Ouest - site René Gauducheau, Bd J. Monod, 44805, Saint Herblain Cedex, France. catherine.guerin@ico.unicancer.fr.|INSERM U892, IRT-UN, 8 quai Moncousu, 44007, Nantes Cedex, France. catherine.guerin@ico.unicancer.fr.
authors.forename: Catherine
authors.initials: C
authors.lastname: Guérin-Charbonnel
authors.affiliation: INSERM U892, IRT-UN, 8 quai Moncousu, 44007, Nantes Cedex, France. loic.campion@ico.unicancer.fr.|Unité de Biostatistique, Institut de Cancérologie de l'Ouest - site René Gauducheau, Bd J. Monod, 44805, Saint Herblain Cedex, France. loic.campion@ico.unicancer.fr.
authors.forename: Loïc
authors.initials: L
authors.lastname: Campion
authors.affiliation: Sorbonne Universités, UPMC University, Département de Biostatistique, 4 place Jussieu, 75005, Paris, France. antoine.vanier@gmail.com.|AP-HP, University Hospitals Pitié-Salpêtrière Charles-Foix, Département de Biostatistique, Santé Publique et Informatique Médicale, 47-83 Bd de l'Hôpital, 75013, Paris, France. antoine.vanier@gmail.com.
authors.forename: Antoine
authors.initials: A
authors.lastname: Vanier
authors.affiliation: Unité Mixte de Génomique du Cancer, Institut de Cancérologie de l'Ouest - site René Gauducheau, Bd J. Monod, 44805, Saint Herblain Cedex, France. wilfried.gouraud@ico.unicancer.fr.|Unité de Bioinfomique, Institut de Cancérologie de l'Ouest - site René Gauducheau, Bd J. Monod, 44805, Saint Herblain Cedex, France. wilfried.gouraud@ico.unicancer.fr.|INSERM U892, IRT-UN, 8 quai Moncousu, 44007, Nantes Cedex, France. wilfried.gouraud@ico.unicancer.fr.
authors.forename: Wilfried
authors.initials: W
authors.lastname: Gouraud
authors.affiliation: Unité de Bioinfomique, Institut de Cancérologie de l'Ouest - site René Gauducheau, Bd J. Monod, 44805, Saint Herblain Cedex, France. hamza.lasla@ico.unicancer.fr.
authors.forename: Hamza
authors.initials: H
authors.lastname: Lasla
authors.affiliation: Institut de Cancérologie de l'Ouest - site Paul Papin, 2 rue Moll, 49933, Angers Cedex 9, France. catherine.guette@ico.unicancer.fr.
authors.forename: Catherine
authors.initials: C
authors.lastname: Guette
authors.affiliation: Laboratoire d'Anatomie Pathologique, Institut de Cancérologie de l'Ouest - site Paul Papin, 2 rue Moll, 49933, Angers Cedex 9, France. isabelle.valo@ico.unicancer.fr.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Valo
authors.affiliation: Laboratoire d'Anatomie Pathologique, Institut de Cancérologie de l'Ouest - site Paul Papin, 2 rue Moll, 49933, Angers Cedex 9, France. veronique.verriele@ico.unicancer.fr.
authors.forename: Véronique
authors.initials: V
authors.lastname: Verrièle
authors.affiliation: Unité de Bioinfomique, Institut de Cancérologie de l'Ouest - site René Gauducheau, Bd J. Monod, 44805, Saint Herblain Cedex, France. mario.campone@ico.unicancer.fr.|INSERM U892, IRT-UN, 8 quai Moncousu, 44007, Nantes Cedex, France. mario.campone@ico.unicancer.fr.|Service d'Oncologie Médicale, Institut de Cancérologie de l'Ouest - site René Gauducheau, Bd J. Monod, 44805, Saint Herblain Cedex, France. mario.campone@ico.unicancer.fr.
authors.forename: Mario
authors.initials: M
authors.lastname: Campone
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor; D016000:Cluster Analysis; D019295:Computational Biology; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007113:Immunity, Innate; D007150:Immunohistochemistry; D053208:Kaplan-Meier Estimate; D008875:Middle Aged; D058977:Molecular Sequence Annotation; D009367:Neoplasm Staging; D011379:Prognosis; D015203:Reproducibility of Results; D012189:Retrospective Studies; D059467:Transcriptome; D064726:Triple Negative Breast Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000276:immunology / Q000401:mortality / Q000628:therapy; D047368:Tumor Burden
chemical_list: D014408:Biomarkers, Tumor