A microRNA Expression Profile Consisting of 12 microRNAs Is Associated with Inflammatory Breast Cancer.

Abstract Introduction: Inflammatory breast cancer (IBC) is an aggressive form of breast cancer with a dismal clinical outcome. In the past we showed that IBC is characterized by a specific gene expression pattern. In this study, we investigate if microRNAs (miRNAs) are responsible for the specific IBC gene signature.Materials and methods: 377 miRNAs were profiled in 20 IBC tumor samples and 50 non-stage matched nIBC tumour samples using the human MicroRNA A Array Set version 2.0 (Applied Biosystems). The IBC and nIBC study populations are matched for tumor grade and ER status. All miRNAs with Ct-values less than 35 in 25% of the samples were included for analysis. Data normalization was performed relative to the median miRNA expression level per sample and expression values were log2-transformed. Principal component analysis (PCA) was performed to identify metagenes of miRNAs, associated with the IBC phenotype. Relevant metagenes were compared with prognostic/predictive gene signature-classifications (wound healing response, invasiveness gene signature, 70-gene prognostic signature, genomic grade index, recurrence score, HOXB13/IL17RB-expression ratio and the molecular breast cancer subtypes). Data were validated by analysing relevant miRNA target gene sets on an IBC/nIBC gene expression data set.Results: Using PCA, we identified a metagene associated with the IBC phenotype (Hazard Ratio: 4.500; P=0.011). This metagene was also significantly associated with the Luminal B phenotype, the IBC signature and with an elevated HOXB13/IL17RB-expresion ratio (range Rs = 0.302 – 0.366; P<0.05). MiRNAs significantly (FDR<0.1) associated with this metagene were: miR29A, miR544, miR574-3p, miR548C-3p, miR451, miR548B-5p, miR24, miR28-5p, miR137, miR302B, miR148A and miR302A (range Rs: -0.367 – 0.307). Cluster analysis using this miRNA signature identified two sample clusters, one containing 70% of the IBC samples and a second one containing 64% of the nIBC samples (Pearson X2; P=0.021). Using gene set enrichment analysis for miR24-, miR28-, miR29A-, miR137-, miR148A-, miR302A- and miR302B target gene sets, we confirmed the differential expression for the above mentioned miRNAs (P<0.01) except for miR28. Using Oncomine analyses we were able to associate the identified miRNAs with NFkB activation (miR29, miR148), steroid receptor signalling (miR302A, miR302B, and miR137), cell adhesion (miR29), stem cell signalling (miR137, miR28) and regulation of the extracellular matrix composition (miR29, miR148).Discussion: Through PCA we identified a miRNA signature associated with IBC. The miRNA signature was partly validated on the gene expression level. Interestingly, most identified miRNAs regulate biological processes previously associated with IBC through gene expression analysis, confirming our results also at the biological level. The association of the IBC-specific miRNA-metagene with the Luminal B phenotype and elevated HOXB13/IL17RB-expression ratios confirms our data that ER+ IBC samples, which constitute the majority of the present IBC study population, generally belong to the Luminal B subtype and are associated with resistance to endocrine therapy. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6119.