Identification of therapeutic targets in colon cancer through epigenetic edition

In recent years, the analysis of genome-wide DNA methylation patterns has made it possible to identify new biomarkers in colorectal cancer (CRC). Even though many of these alterations can be useful in the diagnosis, prognosis or even evaluation of response to treatment, their value as possible therapeutic targets has proven to be much more limited, mainly because their true role as causal or passenger perturbations in the tumoral process has not been determined. In order to identify aberrant DNA methylation patterns that can constitute possible biological
targets in CRC, we propose a novel experimental design based in a progressive screening of candidate genes and regions. Firstly, we will integrate epigenomic and transcriptomic data of ~30 normal and ~250 tumor tissue samples obtained from colon adenocarcinoma. Secondly, to determine true functional associations between changes in DNA methylation and gene expression, we will ectopically modify the levels of methylation by using CRISPR technology (fusion proteins of deactivated Cas9 with the catalytic domains of TET1, DEMETER and DNMT3) in tumoral cell lines, organoids, and animal models. Finally, to determine the clinical implications of the functional methylation alterations, we will analyze the methylation state and expression of candidate genes in 150
samples obtained from patients with colorectal tumors for which there is ample clinical information the disease progression and other factors. The obtained results may be used to the development of biomarkers based on functional aspects, and, more importantly, they will enable the identification of new therapeutic targets in colorectal cancer.