We have demonstrated that changes in the epigenome occur early in the neoplastic progression1. We have generated genome-wide DNA methylation profiles of breast tissue samples representing different stages in the progression of cancer, and validated methylation changes between normal and DCIS in an independent dataset2. DNA methylation profiles of Ductal Carcinoma In Situ (DCIS) are radically altered compared to normal breast tissue, involving more than 5,000 genes. Changes between DCIS and invasive breast carcinoma involve around 1,000 genes1,2. In tumors, DNA methylation is associated with gene expression of almost 3,000 genes, including both negative and positive correlations. A prognostic signature based on methylation level of 18 CpGs is associated with survival of breast cancer patients with invasive tumors, as well as with survival of patients with DCIS and mixed lesions of DCIS and invasive carcinoma. This is validated in 583 breast cancer samples from The Cancer Genome Atlas1
Further we have explored the alterations in gene promoter methylation as a potential cause of acquired drug resistance to doxorubicin or combined treatment with 5-fluorouracil and mitomycin C in human breast cancers3. Differentially methylated genes after treatment with doxorubicin associated to treatment response and revealed a significant association with canonical pathways enriched for immune cell response and cell-cycle regulating genes including CDKN2A, CCND2, CCNA1. Treatment with FUMI resulted in 343 differentially methylated genes representing canonical pathways such as retinoate biosynthesis, gαi signaling, and LXR/RXR activation. Despite the clearly different genes and pathways involved in the metabolism and therapeutic effect of both drugs, 46 genes were differentially methylated before and after treatment with both doxorubicin and FUMI. DNA methylation profiles in genes such as BRCA1, FOXC1, and IGFBP3, and most notably repetitive elements like ALU and LINE1, were associated with TP53 mutations status3. These studies are at present followed by randomized phase I trial with patients treated with chemotherapy alone (one arm) and combination with targeted therapy (bevasizumab).
Most recently we studied the distribution of both positive and negative expression-methylation correlation in distinct gene regions and revealed different effects on gene expression and prognosis in BC subtypes4. We identified several genes consistently associated with prognosis, whose DNA methylation could represent a promising biomarker for prognostication and clinical stratification of patients with distinct BC subtypes. These studies continue with in depth whole genome meEQTL analysis. How a change in DNA methylation in a specific locus may affect the expression of several genes distributed all over the genome is poorly understood. We adopted an original strategy which allowed us to identify statistically significant associations between the DNA methylation at specific CpGs and the expression genome wide in breast cancer tissues (n>250), which intriguingly point to the same signaling and effector pathways. Taken together these results provide evidence for the possible utilization of DNA methylation-based markers of progression in the clinic, and highlight the importance of epigenetic changes in carcinogenesis.