Genetic and Epigenetic Characterisation of Breast Tumours

Abstract: Breast tumours harbour a large amount of genetic and epigenetic alterations, which are associated with e.g. tumour aggressiveness, prognosis, and response to therapy. The heterogeneity of breast tumours is reflected in the identification of at least five molecular subtypes named basal-like, luminal A, luminal B, HER2-enriched and normal-like, which are believed to originate from different cell types and follow different progression pathways. In the current thesis, different genetic and epigenetic alterations of breast tumours have been studied and analysed in relation to the molecular subtypes and clinicopathologic variables. In Paper I, we studied genetic alterations of PIK3CA and PTEN as well as PTEN protein expression. We found frequent alterations in the two PI3K pathway components PIK3CA (26%) and PTEN (31%). The alterations in PIK3CA were associated with oestrogen receptor (ER) positivity, whereas PTEN predominantly was lost in ER-negative tumours. In Paper II, we analysed genomic aberrations at chromosome 11q13 in CCND1 (11q13.3)-amplified breast tumours and identified cores proximal and distal of the CCND1 locus that were frequently amplified. Additionally, we found that CCND1 amplification and overexpression was most frequent in luminal B tumours. In Papers III and IV, we have focused on epigenetic studies of breast tumours. Using methylation arrays, we found specific methylation patterns and frequencies for luminal A, luminal B and basal-like tumours. Interestingly, a substantial amount of genes with subtype-specific expression appears to be regulated by DNA methylation. In addition, we found high gene expression of the Polycomb repressive complex 2 (PRC2)-member EZH2 and low methylation frequency in basal-like tumours, indicating alternative epigenetic silencing mechanism in these tumours. EZH2 is the key member of PRC2 that catalyses the histone modification trimethylation of lysine 27 on histone 3 (H3K27me3). In Paper IV, we validated our previous findings of EZH2 gene expression on protein level and found an identical pattern across the subtypes as well as identifying differential occurrence of H3K27me3 across the subtypes. Together these results add another layer to the heterogeneous nature of breast tumours.