Transcriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation [Exome-seq]

Abnormal promoter DNA hypermethylation arises early during tumorigenesis and yet its role in cancer initiation has remained underexplored. An important scenario for examining this is, BRAFV600E-mutant colon adenocarcinomas (COAD) which most often arise in the proximal colon and harbor extensive, abnormal gene promoter CpG-island methylation or the methylator phenotype (CIMP). How CIMP and BRAF-mutations specifically interact for COAD initiation has remained unclear. Using mouse colon-derived organoids, we show promoter hypermethylation spontaneously arises in wild type cells mimicking “aging like” phenotype. The silenced genes sufficiently activate the Wnt pathway, causing a stem–like state and profound differentiation block. This phenotype renders long-term cultured organoids to be rapidly susceptible to transformation by BRAFV600E with features of typical right-sided COAD. Our studies tightly link epigenetic abnormalities, suggested to arise with aging, to intestinal cell fate changes and define an “epi-driver” role for multiple abnormally silenced genes that predispose to BRAFV600E-driven colon tumorigenesis. Cre-activable BrafV600E and wild type proximal colon organoids were derived from mice carrying heterozygous Cre-activable BrafV600E (termed Braf+/LSL). Lentiviral delivery of Cre with the lentiviral backbone alone serving as control (EV), is used to subsequently activate BrafV600E in the organoids. Expression and methylation analyses were done in organoids 5m after induction of oncogene, and in organoids selected to grow in medium without stem-cell niche factors (Base medium). Two biological replicates of BrafEV organoids are grown for over 12-14 months which were labeled as BRAF1_EV_12m and BRAF3_EV_14m.