Abstract P2-04-07: Gene-expression molecular subtyping of immunohistochemistry-typed triple-negative breast cancer tumours
Authors: Campone Mario , Campion Loïc , Loussouarn Delphine , Valo Isabelle , Guérin-Charbonnel Catherine , Vanier Antoine , Gouraud Wilfried , Guette Catherine , Verrièle Véronique , Chassevent Agnès , Jézéquel Pascal 
Published: May 2015

Abstract
BACKGROUND
Recently, it has been shown that annotation of triple-negative breast tumours (TNBC) by means of immunohistochemistry (IHC) or gene-expression signatures (GES) gave different results: 20 to 30% of these tumours were not basal-like, but luminal A, B or HER2-E. In this study, we aimed at identifying gene-expression molecular subclassification of IHC-TNBC.
MATERIALS AND METHODS
Patients
Studied bi-centric cohort retrospectively included 107 randomly selected women whose primary breast tumours lacked IHC expression of estrogen receptor, progesterone receptor and HER2. Patients were diagnosed and treated primarily between 1998 and 2007 at the ICO-Gauducheau (n=65) and the ICO-Papin (n=42).
Gene expression profiling
Gene expression analysis was performed using Affymetrix Human Genome U133 Plus 2.0 Arrays that correspond to approximately 20,000 genes.
Statistical analysis
Unsupervised analysis was performed by means of fuzzy clustering. Independent IHC-TNBC cohort (GSE21653; n=87) was used for external validation.
"Fuzzy cluster" functional annotation
To annotate "fuzzy-clusters", we used clinicopathologic characteristics, gene-expression signatures (GES) (PAM50, Proliferation score, TNBCtype, Immune response, Claudin-low), Gene Ontology enrichment and IHC (CK5, CK5/6, HER1, AR, Ki-67, FOXA1).
RESULTS
Fuzzy clustering partition individualized 3 clusters in our cohort: C1, C2 and C3. "Fuzzy cluster" functional annotation results are displayed in Table 1. C1 was composed of a mixture of non-basal-like subtypes. C2 and C3 were basal-like and IHC-TNBC. Except an adenoid cystic case, C2 was exclusively composed of basal-like subtypes. C3 was essentially characterized by immune response and included 26% of claudin-low subtypes. For this reason, C3 should rather be named "immune response cluster". External validation confirmed our results.
Table1. "Fuzzy cluster" functional annotation results.N° "fuzzy cluster"C1 (n=24)C2 (n=48)C3 (n=35)P-valueClinicopathologic characteristicsAge (mean years)64.656.851.9&lt;0.05SBRLowHigh&lt;0.05NPILowHigh&lt;0.05Gene-expression signaturesPAM50Luminal B (61%), A (22%)Basal-like (98%)Basal-like (91%) Proliferation scoreLowHigh ++High +&lt;0.05TNBCtypeLuminal androgen receptorBasal-like 1, mesenchymalImmune response Immune responseSteroid hormone responseImmune responseImmune response Claudin-low0%Low frequency (2%)Higher frequency (26%) Gene Ontology enrichmentBiological processesEpithelial cell differentiation, hormone metabolic processCell adhesion, locomotion, chemotaxisImmune response ImmunohistochemistryCK5 and/or HER1 positive50%91%&lt;0.05AR positive73%5%&lt;0.05Ki-67 positive29%87%&lt;0.05FOXA1 positive83%9.6%&lt;0.05
CONCLUSION
Heterogeneity within basal-like and IHC-TNBC is still controversial and require further research to understand the complexity of the disease, and to identify molecular drivers that can be therapeutically targeted. Annotation discordances between IHC and GES clearly indicate that a robust molecular subtyping method must be found. Correct molecular assignment would permit to orientate 20 to 30% of IHC-TNBC patients towards targeted therapy (hormonotherapy or anti-HER2).
Citation Format: Mario Campone, Loïc Campion, Delphine Loussouarn, Isabelle Valo, Catherine Guérin-Charbonnel, Antoine Vanier, Wilfried Gouraud, Catherine Guette, Véronique Verrièle, Agnès Chassevent, Pascal Jézéquel. Gene-expression molecular subtyping of immunohistochemistry-typed triple-negative breast cancer tumours [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-04-07.