An integrated 'omics approach highlights the role of epigenetic events to explain and predict response to neoadjuvant chemotherapy and bevacizumab

Here we present an integrated omics approach for DNA methylation profiling using copy number alteration, gene expression and proteomic data to predict response to therapy and to pinpoint response-related epigenetic events. Fresh frozen tumor biopsies taken before, during and after treatment from patients receiving neoadjuvant chemotherapy with or without the anti-angiogenic drug bevacizumab were subjected to molecular profiling. Our previous studies have shown that administration of bevacizumab in addition to chemotherapy (combination treatment) may confer improved response for patients; here we report that DNA methylation at enhancer CpGs related to cell cycle regulation can predict response to chemotherapy and bevacizumab for ER positive patients with high fidelity (AUC=0.874), and we validate this observation in an independent patient cohort with similar treatment regimen (AUC=0.762). When combining the DNA methylation score with a previously reported proteomic score (ViRP), the prediction accuracy further improved in the validation cohort (AUC=0.784). We also show that tumors receiving the combination treatment underwent more extensive epigenetic alterations than tumors receiving only chemotherapy. Finally, we performed an integrative emQTL analysis on alterations in DNA methylation and gene expression levels, showing that the epigenetic alterations that occur during treatment are different between responders and non-responders and that these differences may be explained by the proliferation-EMT axis through the activity of the transcription factor GRHL2. Taken together, these results illustrate the clinical benefit of the addition of bevacizumab to chemotherapy if administered to the correct patients.