Loss of Apc impairs Lgr5+ intestinal stem cell fate programs [RRBS]

Loss of APC is the main driving alteration associated with colorectal cancer (CRC) development. We investigate the immediate outcome of this genetic event on the transcriptomic and DNA methylation profiles of Lgr5+ intestinal stem cells (ISCs), considered as the cell-of-origin of CRC. RNA-seq analyses show that the sequential deletion of Apc alleles has a rapid impact on the transcriptional profiles of ISCs. Indeed, Apc loss-of-function dictates an altered cell fate program at transcriptional level, resuting in an impaired commitment of those cells to differentiation. Reduced-representation bisufite sequencing (RRBS) on the genomic DNA (gDNA) also shows that focal alterations occur in the DNA methylations profiles of ISCs at this stage, and functionally contribute to altered cell fate in those cells. This study sheds light on the earliest events in CRC development, proving evidences on the role exerted by DNA methylation changes associated with Apc inactivation in the homeostatic rupture at CRC initation. Lgr5+-GFP+ Intestinal stem cells were FACS-sorted from 4 Apc+/+ : , 4 ApcFlox/+, : and 4 ApcFlox/Flox : Lgr5-CreERT2-ires-eGFP mice 15 days after the activation of the Cre recombinase by tamoxifen administration to study the impact of the mutation on gene expression and DNA methylation profiles.